diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 56fcf548e6..f2a73c3cf2 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -22,42 +22,42 @@ src/MESSAGE/* @sjplimp src/MLIAP/* @athomps src/SNAP/* @athomps src/SPIN/* @julient31 -src/USER-BROWNIAN/* @samueljmcameron -src/USER-CGDNA/* @ohenrich -src/USER-CGSDK/* @akohlmey -src/USER-COLVARS/* @giacomofiorin -src/USER-DIELECTRIC/* @ndtrung81 -src/USER-FEP/* @agiliopadua -src/USER-HDNNP/* @singraber -src/USER-INTEL/* @wmbrownintel -src/USER-MANIFOLD/* @Pakketeretet2 -src/USER-MDI/* @taylor-a-barnes -src/USER-MEAMC/* @martok -src/USER-MESONT/* @iafoss -src/USER-MOFFF/* @hheenen -src/USER-MOLFILE/* @akohlmey -src/USER-NETCDF/* @pastewka -src/USER-PACE/* @yury-lysogorskiy -src/USER-PLUMED/* @gtribello -src/USER-PHONON/* @lingtikong -src/USER-PTM/* @pmla -src/USER-OMP/* @akohlmey -src/USER-QMMM/* @akohlmey -src/USER-REAXC/* @hasanmetin -src/USER-REACTION/* @jrgissing -src/USER-SCAFACOS/* @rhalver -src/USER-TALLY/* @akohlmey -src/USER-UEF/* @danicholson -src/USER-VTK/* @rbberger - +src/BROWNIAN/* @samueljmcameron +src/CG-DNA/* @ohenrich +src/CG-SDK/* @akohlmey +src/COLVARS/* @giacomofiorin +src/DIELECTRIC/* @ndtrung81 +src/FEP/* @agiliopadua +src/ML-HDNNP/* @singraber +src/INTEL/* @wmbrownintel +src/MANIFOLD/* @Pakketeretet2 +src/MDI/* @taylor-a-barnes +src/MEAM/* @martok +src/MESONT/* @iafoss +src/MOFFF/* @hheenen +src/MOLFILE/* @akohlmey +src/NETCDF/* @pastewka +src/ML-PACE/* @yury-lysogorskiy +src/PLUMED/* @gtribello +src/PHONON/* @lingtikong +src/PTM/* @pmla +src/OPENMP/* @akohlmey +src/QMMM/* @akohlmey +src/REAXFF/* @hasanmetin @stanmoore1 +src/REACTION/* @jrgissing +src/SCAFACOS/* @rhalver +src/TALLY/* @akohlmey +src/UEF/* @danicholson +src/VTK/* @rbberger # individual files in packages src/GPU/pair_vashishta_gpu.* @andeplane src/KOKKOS/pair_vashishta_kokkos.* @andeplane src/MANYBODY/pair_vashishta_table.* @andeplane src/MANYBODY/pair_atm.* @sergeylishchuk -src/USER-MISC/*_grem.* @dstelter92 -src/USER-MISC/compute_stress_mop*.* @RomainVermorel +src/REPLICA/*_grem.* @dstelter92 +src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel +src/MISC/*_tracker.* @jtclemm # core LAMMPS classes src/lammps.* @sjplimp @@ -81,6 +81,7 @@ src/kspace.* @sjplimp src/lmptyp.h @sjplimp src/library.* @sjplimp src/main.cpp @sjplimp +src/min_*.* @sjplimp src/memory.* @sjplimp src/modify.* @sjplimp src/molecule.* @sjplimp @@ -109,7 +110,6 @@ src/thermo.* @sjplimp src/universe.* @sjplimp src/update.* @sjplimp src/variable.* @sjplimp -src/verlet.* @sjplimp src/velocity.* @sjplimp src/write_data.* @sjplimp src/write_restart.* @sjplimp @@ -122,6 +122,7 @@ src/info.* @akohlmey @rbberger src/timer.* @akohlmey src/min* @sjplimp @stanmoore1 src/utils.* @akohlmey @rbberger +src/verlet.* @sjplimp @stanmoore1 src/math_eigen_impl.h @jewettaij # tools @@ -138,7 +139,7 @@ unittest/* @akohlmey @rbberger # cmake cmake/* @junghans @rbberger -cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin +cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167 cmake/presets/*.cmake @akohlmey diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 31b9becc0c..54cb975723 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -74,13 +74,13 @@ Here is a checklist of steps you need to follow to submit a single file or user * For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included ( instead of , or instead of ). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. * Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'. * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `.cpp` and `.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. -* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. +* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this FOO directory. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. -* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. -* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind +* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. +* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind * For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree. * When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.). -* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the .cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. +* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the .cpp source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature. diff --git a/.gitignore b/.gitignore index 0f1b01775d..ae708ff184 100644 --- a/.gitignore +++ b/.gitignore @@ -12,6 +12,7 @@ *.sif *.dll *.pyc +a.out __pycache__ Obj_* @@ -43,6 +44,8 @@ Thumbs.db /build* /CMakeCache.txt /CMakeFiles/ +/Testing /Makefile +/Testing /cmake_install.cmake /lmp diff --git a/bench/POTENTIALS/in.meamc b/bench/POTENTIALS/in.meam similarity index 94% rename from bench/POTENTIALS/in.meamc rename to bench/POTENTIALS/in.meam index 0739b49411..9c6e06cd4d 100644 --- a/bench/POTENTIALS/in.meamc +++ b/bench/POTENTIALS/in.meam @@ -8,7 +8,7 @@ region box block 0 20 0 20 0 20 create_box 1 box create_atoms 1 box -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 velocity all create 1600.0 376847 loop geom diff --git a/bench/POTENTIALS/log.9Oct20.meamc.1 b/bench/POTENTIALS/log.9Oct20.meam.1 similarity index 96% rename from bench/POTENTIALS/log.9Oct20.meamc.1 rename to bench/POTENTIALS/log.9Oct20.meam.1 index d6bebcd664..03e027674f 100644 --- a/bench/POTENTIALS/log.9Oct20.meamc.1 +++ b/bench/POTENTIALS/log.9Oct20.meam.1 @@ -15,7 +15,7 @@ create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.002 seconds -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -38,12 +38,12 @@ Neighbor list info ... ghost atom cutoff = 5 binsize = 2.5, bins = 29 29 29 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/bench/POTENTIALS/log.9Oct20.meamc.4 b/bench/POTENTIALS/log.9Oct20.meam.4 similarity index 96% rename from bench/POTENTIALS/log.9Oct20.meamc.4 rename to bench/POTENTIALS/log.9Oct20.meam.4 index 4ccae5ddce..fa343e33b5 100644 --- a/bench/POTENTIALS/log.9Oct20.meamc.4 +++ b/bench/POTENTIALS/log.9Oct20.meam.4 @@ -15,7 +15,7 @@ create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.001 seconds -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -38,12 +38,12 @@ Neighbor list info ... ghost atom cutoff = 5 binsize = 2.5, bins = 29 29 29 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/bench/POTENTIALS/log.9Oct20.reaxc.1 b/bench/POTENTIALS/log.9Oct20.reaxc.1 index fc89a32c85..86e35aa664 100644 --- a/bench/POTENTIALS/log.9Oct20.reaxc.1 +++ b/bench/POTENTIALS/log.9Oct20.reaxc.1 @@ -24,7 +24,7 @@ velocity all create 300.0 9999 pair_style reax/c NULL pair_coeff * * ffield.reax C H O N -WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315) +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315) timestep 0.1 fix 1 all nve diff --git a/bench/POTENTIALS/log.9Oct20.reaxc.4 b/bench/POTENTIALS/log.9Oct20.reaxc.4 index c72cc9185d..f83ad2a05a 100644 --- a/bench/POTENTIALS/log.9Oct20.reaxc.4 +++ b/bench/POTENTIALS/log.9Oct20.reaxc.4 @@ -24,7 +24,7 @@ velocity all create 300.0 9999 pair_style reax/c NULL pair_coeff * * ffield.reax C H O N -WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315) +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315) timestep 0.1 fix 1 all nve diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index ab1fd6bba6..a778c89d42 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -77,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR}) include(CheckIncludeFileCXX) # set required compiler flags and compiler/CPU arch specific optimizations -if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") +if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512") @@ -138,17 +138,92 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR}) option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE - GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS - PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT - USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB - USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN) +set(STANDARD_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR + FEP + GRANULAR + H5MD + INTERLAYER + KIM + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + ORIENT + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + VORONOI + VTK + YAFF) -set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) +set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) @@ -159,7 +234,7 @@ endforeach() ###################################################### target_include_directories(lammps PUBLIC $) -if(PKG_USER-ADIOS) +if(PKG_ADIOS) # The search for ADIOS2 must come before MPI because # it includes its own MPI search with the latest FindMPI.cmake # script that defines the MPI::MPI_C target @@ -169,15 +244,16 @@ if(PKG_USER-ADIOS) endif() if(NOT CMAKE_CROSSCOMPILING) - set(MPI_CXX_SKIP_MPICXX TRUE) find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) else() - set(MPI_CXX_SKIP_MPICXX TRUE) option(BUILD_MPI "Build MPI version" OFF) endif() if(BUILD_MPI) + # do not include the (obsolete) MPI C++ bindings which makes + # for leaner object files and avoids namespace conflicts + set(MPI_CXX_SKIP_MPICXX TRUE) # We use a non-standard procedure to cross-compile with MPI on Windows if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) include(MPI4WIN) @@ -229,13 +305,16 @@ endif() # "hard" dependencies between packages resulting # in an error instead of skipping over files -pkg_depends(MLIAP SNAP) +pkg_depends(ML-IAP ML-SNAP) pkg_depends(MPIIO MPI) -pkg_depends(USER-ATC MANYBODY) -pkg_depends(USER-LB MPI) -pkg_depends(USER-PHONON KSPACE) -pkg_depends(USER-SCAFACOS MPI) -pkg_depends(USER-DIELECTRIC KSPACE) +pkg_depends(ATC MANYBODY) +pkg_depends(LATBOLTZ MPI) +pkg_depends(PHONON KSPACE) +pkg_depends(SCAFACOS MPI) +pkg_depends(DIELECTRIC KSPACE) +pkg_depends(DIELECTRIC EXTRA-PAIR) +pkg_depends(CG-DNA MOLECULE) +pkg_depends(CG-DNA ASPHERE) # detect if we may enable OpenMP support by default set(BUILD_OMP_DEFAULT OFF) @@ -271,7 +350,7 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() -if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) +if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE) enable_language(C) find_package(LAPACK) find_package(BLAS) @@ -291,6 +370,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) endif() endif() +# tweak jpeg library names to avoid linker errors with MinGW cross-compilation +set(JPEG_NAMES libjpeg libjpeg-62) find_package(JPEG QUIET) option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) if(WITH_JPEG) @@ -350,8 +431,8 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF - USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) +foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF + PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() @@ -444,9 +525,8 @@ endforeach() ############################################## # add lib sources of (simple) enabled packages ############################################ -foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) - if(PKG_${SIMPLE_LIB}) - string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") +foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT) + if(PKG_${PKG_LIB}) string(TOLOWER "${PKG_LIB}" PKG_LIB) if(PKG_LIB STREQUAL "mesont") enable_language(Fortran) @@ -470,13 +550,13 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) endif() endforeach() -if(PKG_USER-AWPMD) +if(PKG_AWPMD) target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES}) endif() -if(PKG_USER-ATC) +if(PKG_ATC) if(LAMMPS_SIZES STREQUAL "BIGBIG") - message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") + message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG") endif() target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES}) if(BUILD_MPI) @@ -488,15 +568,15 @@ if(PKG_USER-ATC) target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES}) endif() -if(PKG_USER-H5MD) - include(Packages/USER-H5MD) +if(PKG_H5MD) + include(Packages/H5MD) endif() ###################################################################### # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### -foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU) +foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index 8a97b7dd81..597e3e4609 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -22,7 +22,7 @@ find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib") # # target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS) # -# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake. +# to "lib/lammps-extra.cmake" which is then included by ML-HDNNP.cmake. find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib") find_package_handle_standard_args(N2P2 DEFAULT_MSG diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 6cb23db12a..74102ab244 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -67,7 +67,7 @@ endfunction() macro(pkg_depends PKG1 PKG2) if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2})) - message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}") + message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package") endif() endmacro() diff --git a/cmake/Modules/OpenCLLoader.cmake b/cmake/Modules/OpenCLLoader.cmake index ea83f8e447..239fba5ba9 100644 --- a/cmake/Modules/OpenCLLoader.cmake +++ b/cmake/Modules/OpenCLLoader.cmake @@ -1,6 +1,6 @@ message(STATUS "Downloading and building OpenCL loader library") -set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball") -set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball") +set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball") +set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball") mark_as_advanced(OPENCL_LOADER_URL) mark_as_advanced(OPENCL_LOADER_MD5) diff --git a/cmake/Modules/Packages/USER-COLVARS.cmake b/cmake/Modules/Packages/COLVARS.cmake similarity index 100% rename from cmake/Modules/Packages/USER-COLVARS.cmake rename to cmake/Modules/Packages/COLVARS.cmake diff --git a/cmake/Modules/Packages/USER-SDPD.cmake b/cmake/Modules/Packages/DPD-SMOOTH.cmake similarity index 50% rename from cmake/Modules/Packages/USER-SDPD.cmake rename to cmake/Modules/Packages/DPD-SMOOTH.cmake index c9f419d918..c5271d9091 100644 --- a/cmake/Modules/Packages/USER-SDPD.cmake +++ b/cmake/Modules/Packages/DPD-SMOOTH.cmake @@ -1,13 +1,13 @@ # Fix rigid/meso requires RIGID to be installed -set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD) +set(DPD-SMOOTH_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/DPD-SMOOTH) get_property(hlist GLOBAL PROPERTY FIX) if(NOT PKG_RIGID) - list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h) + list(REMOVE_ITEM hlist ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.h) get_target_property(LAMMPS_SOURCES lammps SOURCES) - list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp) + list(REMOVE_ITEM LAMMPS_SOURCES ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.cpp) set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES}) endif() set_property(GLOBAL PROPERTY FIX "${hlist}") -target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR}) +target_include_directories(lammps PRIVATE ${DPD-SMOOTH_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-H5MD.cmake b/cmake/Modules/Packages/H5MD.cmake similarity index 100% rename from cmake/Modules/Packages/USER-H5MD.cmake rename to cmake/Modules/Packages/H5MD.cmake diff --git a/cmake/Modules/Packages/USER-INTEL.cmake b/cmake/Modules/Packages/INTEL.cmake similarity index 66% rename from cmake/Modules/Packages/USER-INTEL.cmake rename to cmake/Modules/Packages/INTEL.cmake index ecad135b70..af08249090 100644 --- a/cmake/Modules/Packages/USER-INTEL.cmake +++ b/cmake/Modules/Packages/INTEL.cmake @@ -3,9 +3,9 @@ if(NOT FOUND_IMMINTRIN) message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it") endif() -target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL) +target_compile_definitions(lammps PRIVATE -DLMP_INTEL) -set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") +set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by INTEL (cpu or knl)") set(INTEL_ARCH_VALUES cpu knl) set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) validate_option(INTEL_ARCH INTEL_ARCH_VALUES) @@ -40,10 +40,10 @@ endif() if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) - message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") endif() else() - message(WARNING "USER-INTEL gives best performance with Intel compilers") + message(WARNING "INTEL gives best performance with Intel compilers") endif() find_package(TBB_MALLOC QUIET) @@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND) else() target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB) if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries") + message(WARNING "INTEL with Intel compilers should use TBB malloc libraries") endif() endif() @@ -65,12 +65,12 @@ else() endif() if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256")) - message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform") + message(FATAL_ERROR "INTEL only supports memory alignment of 64, 128 or 256 on this platform") endif() if(INTEL_ARCH STREQUAL "KNL") if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture") + message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture") endif() set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") @@ -91,26 +91,26 @@ else() endif() # collect sources -set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) -set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp - ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp - ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp - ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp - ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp) +set(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL) +set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp + ${INTEL_SOURCES_DIR}/fix_nh_intel.cpp + ${INTEL_SOURCES_DIR}/intel_buffers.cpp + ${INTEL_SOURCES_DIR}/nbin_intel.cpp + ${INTEL_SOURCES_DIR}/npair_intel.cpp) -set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") +set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${INTEL_SOURCES}") -# detect styles which have a USER-INTEL version -RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES) -RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h) -RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h) -RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h) +# detect styles which have a INTEL version +RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES) +RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h) +RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h) +RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h) -get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) +get_property(INTEL_SOURCES GLOBAL PROPERTY INTEL_SOURCES) if(PKG_KSPACE) - list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) - RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h) + list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) + RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h) endif() -target_sources(lammps PRIVATE ${USER-INTEL_SOURCES}) -target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR}) +target_sources(lammps PRIVATE ${INTEL_SOURCES}) +target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 234c1f140d..aea766b79c 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -79,6 +79,7 @@ target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS) set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS) set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/atom_map_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp @@ -116,7 +117,7 @@ RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h) -if(PKG_USER-DPD) +if(PKG_DPD-REACT) get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h) diff --git a/cmake/Modules/Packages/USER-SMD.cmake b/cmake/Modules/Packages/MACHDYN.cmake similarity index 77% rename from cmake/Modules/Packages/USER-SMD.cmake rename to cmake/Modules/Packages/MACHDYN.cmake index 6d941f9798..fab532541e 100644 --- a/cmake/Modules/Packages/USER-SMD.cmake +++ b/cmake/Modules/Packages/MACHDYN.cmake @@ -7,8 +7,8 @@ endif() option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT}) if(DOWNLOAD_EIGEN3) message(STATUS "Eigen3 download requested - we will build our own") - set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball") - set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball") + set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball") + set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball") mark_as_advanced(EIGEN3_URL) mark_as_advanced(EIGEN3_MD5) include(ExternalProject) @@ -30,3 +30,8 @@ else() endif() target_link_libraries(lammps PRIVATE Eigen3::Eigen) endif() + +# PGI/Nvidia compiler internals collide with vector intrinsics support in Eigen3 +if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC")) + target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE) +endif() diff --git a/cmake/Modules/Packages/USER-MDI.cmake b/cmake/Modules/Packages/MDI.cmake similarity index 97% rename from cmake/Modules/Packages/USER-MDI.cmake rename to cmake/Modules/Packages/MDI.cmake index a75160a6d6..047c30c603 100644 --- a/cmake/Modules/Packages/USER-MDI.cmake +++ b/cmake/Modules/Packages/MDI.cmake @@ -114,5 +114,5 @@ else() target_link_libraries(lmp PRIVATE ${mdi_LIBRARY}) endif() -target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI) -target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI) +target_compile_definitions(lammps PRIVATE -DLMP_MDI) +target_compile_definitions(lmp PRIVATE -DLMP_MDI) diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/ML-HDNNP.cmake similarity index 100% rename from cmake/Modules/Packages/USER-HDNNP.cmake rename to cmake/Modules/Packages/ML-HDNNP.cmake diff --git a/cmake/Modules/Packages/MLIAP.cmake b/cmake/Modules/Packages/ML-IAP.cmake similarity index 78% rename from cmake/Modules/Packages/MLIAP.cmake rename to cmake/Modules/Packages/ML-IAP.cmake index 81bb10cb8f..63f91ba8d3 100644 --- a/cmake/Modules/Packages/MLIAP.cmake +++ b/cmake/Modules/Packages/ML-IAP.cmake @@ -1,4 +1,4 @@ -# if PYTHON package is included we may also include Python support in MLIAP +# if PYTHON package is included we may also include Python support in ML-IAP set(MLIAP_ENABLE_PYTHON_DEFAULT OFF) if(PKG_PYTHON) find_package(Cythonize QUIET) @@ -7,25 +7,25 @@ if(PKG_PYTHON) endif() endif() -option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT}) +option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT}) if(MLIAP_ENABLE_PYTHON) find_package(Cythonize REQUIRED) if(NOT PKG_PYTHON) - message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP") + message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP") endif() if(CMAKE_VERSION VERSION_LESS 3.12) if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6) - message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later") + message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later") endif() else() if(Python_VERSION VERSION_LESS 3.6) - message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later") + message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later") endif() endif() set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython) - set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx) + set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx) get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE) file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR}) add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/ML-PACE.cmake similarity index 100% rename from cmake/Modules/Packages/USER-PACE.cmake rename to cmake/Modules/Packages/ML-PACE.cmake diff --git a/cmake/Modules/Packages/ML-QUIP.cmake b/cmake/Modules/Packages/ML-QUIP.cmake new file mode 100644 index 0000000000..ff9c7b3a7c --- /dev/null +++ b/cmake/Modules/Packages/ML-QUIP.cmake @@ -0,0 +1,70 @@ +enable_language(Fortran) +find_package(QUIP QUIET) + +if(QUIP_FOUND) + set(DOWNLOAD_QUIP_DEFAULT OFF) +else() + set(DOWNLOAD_QUIP_DEFAULT ON) +endif() +option(DOWNLOAD_QUIP "Download the QUIP library instead of using an already installed one" ${DOWNLOAD_QUIP_DEFAULT}) +if(DOWNLOAD_QUIP) + string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) + set(temp "F77 = ${CMAKE_Fortran_COMPILER}\nF90 = ${CMAKE_Fortran_COMPILER}\nF95 = ${CMAKE_Fortran_COMPILER}\n") + set(temp "${temp}CC=${CMAKE_C_COMPILER}\nCPLUSPLUS=${CMAKE_CXX_COMPILER}\nLINKER=${CMAKE_Fortran_COMPILER}\n") + if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel) + set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n") + set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n") + set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n") + set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n") + elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU) + set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n") + set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n") + set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n") + set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n") + else() + message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP") + endif() + set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n") + set(temp "${temp}MATH_LINKOPTS=") + foreach(flag ${BLAS_LIBRARIES}) + set(temp "${temp} ${flag}") + endforeach() + foreach(flag ${LAPACK_LIBRARIES}) + set(temp "${temp} ${flag}") + endforeach() + set(temp "${temp}\n") + set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n") + set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n") + set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n") + set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n") + set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n") + set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n") + file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}") + + message(STATUS "QUIP download via git requested - we will build our own") + # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch + # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime. + include(ExternalProject) + ExternalProject_Add(quip_build + GIT_REPOSITORY "https://github.com/libAtoms/QUIP/" + GIT_TAG origin/public + GIT_SHALLOW YES + GIT_PROGRESS YES + PATCH_COMMAND cp ${CMAKE_BINARY_DIR}/quip.config /arch/Makefile.lammps + CONFIGURE_COMMAND env QUIP_ARCH=lammps make config + BUILD_COMMAND env QUIP_ARCH=lammps make libquip + INSTALL_COMMAND "" + BUILD_IN_SOURCE YES + BUILD_BYPRODUCTS /build/lammps/libquip.a + ) + ExternalProject_get_property(quip_build SOURCE_DIR) + add_library(LAMMPS::QUIP UNKNOWN IMPORTED) + set_target_properties(LAMMPS::QUIP PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a" + INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}") + target_link_libraries(lammps PRIVATE LAMMPS::QUIP) + add_dependencies(LAMMPS::QUIP quip_build) +else() + find_package(QUIP REQUIRED) + target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES}) +endif() diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/MOLFILE.cmake similarity index 100% rename from cmake/Modules/Packages/USER-MOLFILE.cmake rename to cmake/Modules/Packages/MOLFILE.cmake diff --git a/cmake/Modules/Packages/USER-NETCDF.cmake b/cmake/Modules/Packages/NETCDF.cmake similarity index 89% rename from cmake/Modules/Packages/USER-NETCDF.cmake rename to cmake/Modules/Packages/NETCDF.cmake index d63e9773c3..2e521b81b0 100644 --- a/cmake/Modules/Packages/USER-NETCDF.cmake +++ b/cmake/Modules/Packages/NETCDF.cmake @@ -1,4 +1,4 @@ -# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary. +# NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary. # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio" # may use NetCDF or PNetCDF with MPI, but must have NetCDF without diff --git a/cmake/Modules/Packages/OPENMP.cmake b/cmake/Modules/Packages/OPENMP.cmake new file mode 100644 index 0000000000..a69a81acec --- /dev/null +++ b/cmake/Modules/Packages/OPENMP.cmake @@ -0,0 +1,40 @@ + set(OPENMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPENMP) + set(OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/thr_data.cpp + ${OPENMP_SOURCES_DIR}/thr_omp.cpp + ${OPENMP_SOURCES_DIR}/fix_omp.cpp + ${OPENMP_SOURCES_DIR}/fix_nh_omp.cpp + ${OPENMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp + ${OPENMP_SOURCES_DIR}/domain_omp.cpp) + target_compile_definitions(lammps PRIVATE -DLMP_OPENMP) + set_property(GLOBAL PROPERTY "OMP_SOURCES" "${OPENMP_SOURCES}") + + # detects styles which have OPENMP version + RegisterStylesExt(${OPENMP_SOURCES_DIR} omp OMP_SOURCES) + RegisterFixStyle(${OPENMP_SOURCES_DIR}/fix_omp.h) + + get_property(OPENMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) + + # manually add package dependent source files from OPENMP that do not provide styles + + if(PKG_ASPHERE) + list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp) + endif() + + if(PKG_RIGID) + list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) + endif() + + if(PKG_REAXFF) + list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp) + endif() + + target_sources(lammps PRIVATE ${OPENMP_SOURCES}) + target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/PLUMED.cmake similarity index 95% rename from cmake/Modules/Packages/USER-PLUMED.cmake rename to cmake/Modules/Packages/PLUMED.cmake index e9eba779f5..0f063f3e14 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/PLUMED.cmake @@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED) set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumedWrapper.a") endif() - set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball") - set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball") + set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball") + set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball") mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) @@ -72,7 +72,6 @@ if(DOWNLOAD_PLUMED) ${PLUMED_CONFIG_OMP} CXX=${PLUMED_CONFIG_CXX} CC=${PLUMED_CONFIG_CC} - PATCH_COMMAND sed -i "/^#include /a #include " /src/lepton/Operation.h BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS} ) ExternalProject_get_property(plumed_build INSTALL_DIR) diff --git a/cmake/Modules/Packages/USER-QMMM.cmake b/cmake/Modules/Packages/QMMM.cmake similarity index 100% rename from cmake/Modules/Packages/USER-QMMM.cmake rename to cmake/Modules/Packages/QMMM.cmake diff --git a/cmake/Modules/Packages/USER-SCAFACOS.cmake b/cmake/Modules/Packages/SCAFACOS.cmake similarity index 100% rename from cmake/Modules/Packages/USER-SCAFACOS.cmake rename to cmake/Modules/Packages/SCAFACOS.cmake diff --git a/cmake/Modules/Packages/USER-OMP.cmake b/cmake/Modules/Packages/USER-OMP.cmake deleted file mode 100644 index a1053ad355..0000000000 --- a/cmake/Modules/Packages/USER-OMP.cmake +++ /dev/null @@ -1,40 +0,0 @@ - set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP) - set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp - ${USER-OMP_SOURCES_DIR}/thr_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp - ${USER-OMP_SOURCES_DIR}/domain_omp.cpp) - target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP) - set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}") - - # detects styles which have USER-OMP version - RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) - RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h) - - get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) - - # manually add package dependent source files from USER-OMP that do not provide styles - - if(PKG_ASPHERE) - list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp) - endif() - - if(PKG_RIGID) - list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) - endif() - - if(PKG_USER-REAXC) - list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp) - endif() - - target_sources(lammps PRIVATE ${USER-OMP_SOURCES}) - target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-QUIP.cmake b/cmake/Modules/Packages/USER-QUIP.cmake deleted file mode 100644 index 790f27def7..0000000000 --- a/cmake/Modules/Packages/USER-QUIP.cmake +++ /dev/null @@ -1,3 +0,0 @@ -enable_language(Fortran) -find_package(QUIP REQUIRED) -target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES}) diff --git a/cmake/Modules/Packages/USER-VTK.cmake b/cmake/Modules/Packages/VTK.cmake similarity index 100% rename from cmake/Modules/Packages/USER-VTK.cmake rename to cmake/Modules/Packages/VTK.cmake diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 457750c690..2893bbab6b 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -1,17 +1,96 @@ -# preset that turns on all existing packages off. can be used to reset +# Preset that turns on all existing packages off. Can be used to reset # an existing package selection without losing any other settings -set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE - MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN - SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) +set(ALL_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR + FEP + GPU + GRANULAR + H5MD + INTEL + INTERLAYER + KIM + KOKKOS + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + OPENMP + OPT + ORIENT + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + VORONOI + VTK + YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index ae40bb0809..9f38f1e1e4 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -1,19 +1,98 @@ -# preset that turns on all existing packages. using the combination -# this preset followed by the nolib.cmake preset should configure a -# LAMMPS binary, with as many packages included, that can be compiled +# Preset that turns on all existing packages. Using the combination +# of this preset followed by the nolib.cmake preset should configure +# a LAMMPS binary, with as many packages included, that can be compiled # with just a working C++ compiler and an MPI library. -set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE - MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN - SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) +set(ALL_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR + FEP + GPU + GRANULAR + H5MD + INTEL + INTERLAYER + KIM + KOKKOS + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + OPENMP + OPT + ORIENT + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + VORONOI + VTK + YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/minimal.cmake b/cmake/presets/basic.cmake similarity index 100% rename from cmake/presets/minimal.cmake rename to cmake/presets/basic.cmake diff --git a/cmake/presets/download.cmake b/cmake/presets/download.cmake index ebab6ab658..2030a97dbb 100644 --- a/cmake/presets/download.cmake +++ b/cmake/presets/download.cmake @@ -1,7 +1,7 @@ # Preset that turns on packages with automatic downloads of sources or potentials. # Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time. -set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE) +set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index e1a6c5cf79..fe828a6d9a 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -1,13 +1,76 @@ -set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT - PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI - USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD - USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP - USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC - USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF - USER-YAFF USER-DIELECTRIC) +set(WIN_PACKAGES + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR + FEP + GPU + GRANULAR + INTEL + INTERLAYER + KSPACE + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MGPT + MISC + ML-HDNNP + ML-IAP + ML-SNAP + ML-RANN + MOFFF + MOLECULE + MOLFILE + OPENMP + OPT + ORIENT + PERI + PHONON + POEMS + PTM + QEQ + QTB + REACTION + REAXFF + REPLICA + RIGID + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + VORONOI + YAFF) foreach(PKG ${WIN_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) @@ -16,7 +79,7 @@ endforeach() # these two packages require a full MPI implementation if(BUILD_MPI) set(PKG_MPIIO ON CACHE BOOL "" FORCE) - set(PKG_USER-LB ON CACHE BOOL "" FORCE) + set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE) endif() set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index e124b25d2b..9546f1f9a3 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -2,13 +2,65 @@ # external libraries. Compared to all_on.cmake some more unusual packages # are removed. The resulting binary should be able to run most inputs. -set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE - GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI - PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI - USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC - USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION - USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF USER-DIELECTRIC) +set(ALL_PACKAGES + ASPHERE + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + EXTRA-COMPUTE + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR + FEP + GRANULAR + INTERLAYER + KSPACE + MACHDYN + MANYBODY + MC + MEAM + MISC + ML-IAP + ML-SNAP + MOFFF + MOLECULE + OPENMP + OPT + ORIENT + PERI + PHONON + PLUGIN + POEMS + PYTHON + QEQ + REACTION + REAXFF + REPLICA + RIGID + SHOCK + SPH + SPIN + SRD + TALLY + UEF + VORONOI + YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 08a3a531a1..fd9c2ed1ac 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -1,11 +1,34 @@ # preset that turns off all packages that require some form of external # library or special compiler (fortran or cuda) or equivalent. -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG - PYTHON VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE - USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP - USER-SCAFACOS USER-SMD USER-VTK) +set(PACKAGES_WITH_LIB + ADIOS + ATC + AWPMD + COMPRESS + GPU + H5MD + KIM + KOKKOS + LATBOLTZ + LATTE + MACHDYN + MDI + MESONT + MESSAGE + ML-HDNNP + ML-PACE + ML-QUIP + MOLFILE + MPIIO + MSCG + NETCDF + PLUMED + PYTHON + QMMM + SCAFACOS + VORONOI + VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 87b9eba8df..454964f0a9 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -122,7 +122,7 @@ recorded compilation commands information when typing `make iwyu`. A lot of code predates the application of the rules in this document and the rules themselves are a moving target. So there are going to be significant chunks of code that do not fully comply. This applies -for example to the USER-REAXC, or the USER-ATC package. The LAMMPS +for example to the REAXFF, or the ATC package. The LAMMPS developers are dedicated to make an effort to improve the compliance and welcome volunteers wanting to help with the process. diff --git a/doc/lammps.1 b/doc/lammps.1 index f18a9a118d..a111f7e092 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "27 May 2021" "2021-05-27" +.TH LAMMPS "30 July 2021" "2021-07-30" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. @@ -135,7 +135,7 @@ For example "-pk gpu 2" is the same as "package gpu 2" in the input script. The possible styles and options are discussed in the .B LAMMPS manual for the "package" command. This switch can be used multiple -times, e.g. to set options for the USER-INTEL and USER-OMP packages +times, e.g. to set options for the INTEL and OPENMP packages when used together. Along with the "-sf" or "-suffix" switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index a4a1076831..0256552332 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -191,7 +191,7 @@ Bibliography A.\ Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996). **(Campana)** - C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ + C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) `_ **(Cao1)** J.\ Cao and B. Berne, J Chem Phys, 99, 2902 (1993). @@ -767,7 +767,7 @@ Bibliography Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997). **(Moustafa)** - Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) `_ + Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) `_ **(Muller-Plathe1)** Muller-Plathe, J Chem Phys, 106, 6082 (1997). diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 30e668a283..9ef209b3b3 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below. directory, or ``make`` from the ``src/STUBS`` dir. If the build fails, you may need to edit the ``STUBS/Makefile`` for your platform. The stubs library does not provide MPI/IO functions - required by some LAMMPS packages, e.g. ``MPIIO`` or ``USER-LB``, + required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``, and thus is not compatible with those packages. .. note:: @@ -120,19 +120,19 @@ self-installed MPICH or OpenMPI, so you should study the provided documentation to find out how to build and link with it. The majority of OpenMP (threading) support in LAMMPS is provided by the -``USER-OMP`` package; see the :doc:`Speed_omp` -page for details. The ``USER-INTEL`` package also includes OpenMP -threading (it is compatible with ``USER-OMP`` and will usually fall -back on styles from that package, if a ``USER-INTEL`` does not exist) +``OPENMP`` package; see the :doc:`Speed_omp` +page for details. The ``INTEL`` package also includes OpenMP +threading (it is compatible with ``OPENMP`` and will usually fall +back on styles from that package, if a ``INTEL`` does not exist) and adds vectorization support when compiled with compatible compilers, in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` package can be compiled to include OpenMP threading. In addition, there are a few commands in LAMMPS that have native OpenMP support included as well. These are commands in the ``MPIIO``, -``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages. In addition +``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. In addition some packages support OpenMP threading indirectly through the libraries -they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``. +they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``. See the :doc:`Packages details ` page for more info on these packages and the pages for their respective commands for OpenMP threading info. @@ -176,7 +176,7 @@ performance. Vendor provided compilers for a specific hardware can produce faster code than open-source compilers like the GNU compilers. On the most common x86 hardware most popular C++ compilers are quite similar in performance of C/C++ code at high optimization levels. When -using the ``USER-INTEL`` package, there is a distinct advantage in using +using the ``INTEL`` package, there is a distinct advantage in using the `Intel C++ compiler `_ due to much improved vectorization through SSE and AVX instructions on compatible hardware as the source code includes changes and Intel compiler specific directives to enable @@ -325,9 +325,9 @@ LAMMPS. .. code-block:: bash Makefile.opt # OPT package - Makefile.omp # USER-OMP package - Makefile.intel_cpu # USER-INTEL package for CPUs - Makefile.intel_coprocessor # USER-INTEL package for KNLs + Makefile.omp # OPENMP package + Makefile.intel_cpu # INTEL package for CPUs + Makefile.intel_coprocessor # INTEL package for KNLs Makefile.gpu # GPU package Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP) diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 73268af0ce..2a64bc3240 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -140,7 +140,7 @@ can be used several times in one command. For your convenience we provide :ref:`CMake presets ` that combine multiple settings to enable optional LAMMPS packages or use a different compiler tool chain. Those are loaded with the *-C* flag -(``-C ../cmake/presets/minimal.cmake``). This step would only be needed +(``-C ../cmake/presets/basic.cmake``). This step would only be needed once, as the settings from the preset files are stored in the ``CMakeCache.txt`` file. It is also possible to customize the build by adding one or more *-D* flags to the CMake command line. diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index ea5c969056..a15d91c629 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -310,7 +310,7 @@ and working. parameter needs to be adjusted. Typically a value around 1.0e-13 can be used, but it may need to be as large as 1.0e-8 in some cases. - - The tests for pair styles from OPT, USER-OMP and USER-INTEL are + - The tests for pair styles from OPT, OPENMP and INTEL are performed with automatically rescaled epsilon to account for additional loss of precision from code optimizations and different summation orders. @@ -345,7 +345,7 @@ and compared. If the fix is a thermostat and thus the internal property ``t_target`` can be extracted, then this is compared to the reference data. The tests are repeated with the respa run style. -If the fix has a multi-threaded version in the USER-OMP package, then +If the fix has a multi-threaded version in the OPENMP package, then the entire set of tests is repeated for that version as well. For this to work, some additional conditions have to be met by the diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 423897fd7a..2157fe86c8 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -31,37 +31,37 @@ This is the list of packages that may require additional steps. .. table_from_list:: :columns: 6 + * :ref:`ADIOS ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`COLVARS ` * :ref:`COMPRESS ` * :ref:`GPU ` + * :ref:`H5MD ` + * :ref:`INTEL ` * :ref:`KIM ` * :ref:`KOKKOS ` * :ref:`LATTE ` + * :ref:`MACHDYN ` + * :ref:`MDI ` + * :ref:`MESONT ` * :ref:`MESSAGE ` - * :ref:`MLIAP ` + * :ref:`ML-HDNNP ` + * :ref:`ML-IAP ` + * :ref:`ML-PACE ` + * :ref:`ML-QUIP ` + * :ref:`MOLFILE ` * :ref:`MSCG ` + * :ref:`NETCDF ` + * :ref:`OPENMP ` * :ref:`OPT ` + * :ref:`PLUMED ` * :ref:`POEMS ` * :ref:`PYTHON ` + * :ref:`QMMM ` + * :ref:`SCAFACOS ` * :ref:`VORONOI ` - * :ref:`USER-ADIOS ` - * :ref:`USER-ATC ` - * :ref:`USER-AWPMD ` - * :ref:`USER-COLVARS ` - * :ref:`USER-H5MD ` - * :ref:`USER-HDNNP ` - * :ref:`USER-INTEL ` - * :ref:`USER-MDI ` - * :ref:`USER-MESONT ` - * :ref:`USER-MOLFILE ` - * :ref:`USER-NETCDF ` - * :ref:`USER-PACE ` - * :ref:`USER-PLUMED ` - * :ref:`USER-OMP ` - * :ref:`USER-QMMM ` - * :ref:`USER-QUIP ` - * :ref:`USER-SCAFACOS ` - * :ref:`USER-SMD ` - * :ref:`USER-VTK ` + * :ref:`VTK ` ---------- @@ -74,7 +74,8 @@ To build with this package you must have the `zlib compression library `_ available on your system to build dump styles with a '/gz' suffix. There are also styles using the `Zstandard `_ library which have a -'/zstd' suffix. +'/zstd' suffix. The zstd library version must be at least 1.4. Older +versions use an incompatible API and thus LAMMPS will fail to compile. .. tabs:: @@ -622,7 +623,7 @@ This list was last updated for version 3.4.1 of the Kokkos library. mkdir build-kokkos-cuda cd build-kokkos-cuda - cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake + cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake cmake --build . .. tab:: Basic traditional make settings: @@ -811,16 +812,17 @@ be installed on your system. .. _mliap: -MLIAP package +ML-IAP package --------------------------- -Building the MLIAP package requires including the :ref:`SNAP ` -package. There will be an error message if this requirement is not satisfied. -Using the *mliappy* model also requires enabling Python support, which -in turn requires the :ref:`PYTHON ` -package **and** requires you have the `cython `_ software -installed and with it a working ``cythonize`` command. This feature requires -compiling LAMMPS with Python version 3.6 or later. +Building the ML-IAP package requires including the :ref:`ML-SNAP +` package. There will be an error message if this requirement +is not satisfied. Using the *mliappy* model also requires enabling +Python support, which in turn requires to include the :ref:`PYTHON +` package **and** requires to have the `cython +`_ software installed and with it a working +``cythonize`` command. This feature requires compiling LAMMPS with +Python version 3.6 or later. .. tabs:: @@ -834,9 +836,9 @@ compiling LAMMPS with Python version 3.6 or later. suitable Python version and the ``cythonize`` command and choose the default accordingly. During the build procedure the provided .pyx file(s) will be automatically translated to C++ code and compiled. - Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder, + Please do **not** run ``cythonize`` manually in the ``src/ML-IAP`` folder, as that can lead to compilation errors if Python support is not enabled. - If you did by accident, please remove the generated .cpp and .h files. + If you did it by accident, please remove the generated .cpp and .h files. .. tab:: Traditional make @@ -845,15 +847,16 @@ compiling LAMMPS with Python version 3.6 or later. the ``cythonize`` command in case the corresponding .pyx file(s) were modified. You may need to modify ``lib/python/Makefile.lammps`` if the LAMMPS build fails. - To manually enforce building MLIAP with Python support enabled, - you can add - ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile. - You may have to manually run the ``cythonize`` command on .pyx file(s) - in the ``src`` folder, if this is not automatically done during - installing the MLIAP package. Please do **not** run ``cythonize`` - in the ``src/MLIAP`` folder, as that can lead to compilation errors - if Python support is not enabled. - If you did by accident, please remove the generated .cpp and .h files. + + To enable building the ML-IAP package with Python support enabled, + you need to add ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in + your machine makefile. You may have to manually run the + ``cythonize`` command on .pyx file(s) in the ``src`` folder, if + this is not automatically done during installing the ML-IAP + package. Please do **not** run ``cythonize`` in the ``src/ML-IAP`` + folder, as that can lead to compilation errors if Python support + is not enabled. If you did this by accident, please remove the + generated .cpp and .h files. ---------- @@ -1054,12 +1057,12 @@ binary package provided by your operating system. ---------- -.. _user-adios: +.. _adios: -USER-ADIOS package +ADIOS package ----------------------------------- -The USER-ADIOS package requires the `ADIOS I/O library +The ADIOS package requires the `ADIOS I/O library `_, version 2.3.1 or newer. Make sure that you have ADIOS built either with or without MPI to match if you build LAMMPS with or without MPI. ADIOS compilation settings for @@ -1075,38 +1078,38 @@ systems. .. code-block:: bash -D ADIOS2_DIR=path # path is where ADIOS 2.x is installed - -D PKG_USER-ADIOS=yes + -D PKG_ADIOS=yes .. tab:: Traditional make - Turn on the USER-ADIOS package before building LAMMPS. If the + Turn on the ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do: .. code-block:: bash - $ make yes-user-adios + $ make yes-adios otherwise, set ADIOS2_DIR environment variable when turning on the package: .. code-block:: bash - $ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed + $ ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed ---------- -.. _user-atc: +.. _atc: -USER-ATC package +ATC package ------------------------------- -The USER-ATC package requires the MANYBODY package also be installed. +The ATC package requires the MANYBODY package also be installed. .. tabs:: .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-ATC=yes`` + No additional settings are needed besides ``-D PKG_ATC=yes`` and ``-D PKG_MANYBODY=yes``. .. tab:: Traditional make @@ -1149,16 +1152,16 @@ The USER-ATC package requires the MANYBODY package also be installed. ---------- -.. _user-awpmd: +.. _awpmd: -USER-AWPMD package +AWPMD package ------------------ .. tabs:: .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``. + No additional settings are needed besides ``-D PKG_AQPMD=yes``. .. tab:: Traditional make @@ -1200,9 +1203,9 @@ USER-AWPMD package ---------- -.. _user-colvars: +.. _colvars: -USER-COLVARS package +COLVARS package --------------------------------------- This package includes the `Colvars library @@ -1216,7 +1219,7 @@ be built for the most part with all major versions of the C++ language. This is the recommended build procedure for using Colvars in LAMMPS. No additional settings are normally needed besides - ``-D PKG_USER-COLVARS=yes``. + ``-D PKG_COLVARS=yes``. .. tab:: Traditional make @@ -1259,9 +1262,9 @@ be built for the most part with all major versions of the C++ language. ---------- -.. _user-pace: +.. _ml-pace: -USER-PACE package +ML-PACE package ----------------------------- This package requires a library that can be downloaded and built @@ -1274,8 +1277,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ `_. -The USER-PLUMED package has been tested to work with Plumed versions +The PLUMED package has been tested to work with Plumed versions 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations with a different version of the Plumed kernel. @@ -1345,7 +1348,7 @@ LAMMPS build. .. tab:: CMake build - When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake + When the ``-D PKG_PLUMED=yes`` flag is included in the cmake command you must ensure that GSL is installed in locations that are specified in your environment. There are then two additional variables that control the manner in which PLUMED is obtained and @@ -1378,7 +1381,7 @@ LAMMPS build. .. tab:: Traditional make - PLUMED needs to be installed before the USER-PLUMED package is + PLUMED needs to be installed before the PLUMED package is installed so that LAMMPS can find the right settings when compiling and linking the LAMMPS executable. You can either download and build PLUMED inside the LAMMPS plumed library folder @@ -1403,12 +1406,12 @@ LAMMPS build. build to use. A new file ``lib/plumed/Makefile.lammps`` is also created with settings suitable for LAMMPS to compile and link PLUMED using the desired linkage mode. After this step is - completed, you can install the USER-PLUMED package and compile + completed, you can install the PLUMED package and compile LAMMPS in the usual manner: .. code-block:: bash - $ make yes-user-plumed + $ make yes-plumed $ make machine Once this compilation completes you should be able to run LAMMPS @@ -1423,15 +1426,15 @@ LAMMPS build. If you want to change the linkage mode, you have to re-run "make lib-plumed" with the desired settings **and** do a re-install if - the USER-PLUMED package with "make yes-user-plumed" to update the + the PLUMED package with "make yes-plumed" to update the required makefile settings with the changes in the lib/plumed folder. ---------- -.. _user-h5md: +.. _h5md: -USER-H5MD package +H5MD package --------------------------------- To build with this package you must have the HDF5 software package @@ -1442,7 +1445,7 @@ the HDF5 library. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-H5MD=yes``. + No additional settings are needed besides ``-D PKG_H5MD=yes``. This should auto-detect the H5MD library on your system. Several advanced CMake H5MD options exist if you need to specify where it @@ -1474,13 +1477,13 @@ the HDF5 library. ---------- -.. _user-hdnnp: +.. _ml-hdnnp: -USER-HDNNP package ---------------------------------- +ML-HDNNP package +---------------- -To build with the USER-HDNNP package it is required to download and build the -external `n2p2 `__ library ``v2.1.4`` +To build with the ML-HDNNP package it is required to download and build the +external `n2p2 `_ library ``v2.1.4`` (or higher). The LAMMPS build process offers an automatic download and compilation of *n2p2* or allows you to choose the installation directory of *n2p2* manually. Please see the boxes below for the CMake and traditional build @@ -1490,7 +1493,7 @@ In case of a manual installation of *n2p2* you only need to build the *n2p2* cor library ``libnnp`` and interface library ``libnnpif``. When using GCC it should suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more details please see ``lib/hdnnp/README`` and the `n2p2 build documentation -`__. +`_. .. tabs:: @@ -1528,24 +1531,24 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation ---------- -.. _user-intel: +.. _intel: -USER-INTEL package +INTEL package ----------------------------------- To build with this package, you must choose which hardware you want to build for, either x86 CPUs or Intel KNLs in offload mode. You should -also typically :ref:`install the USER-OMP package `, as it can be -used in tandem with the USER-INTEL package to good effect, as explained +also typically :ref:`install the OPENMP package `, as it can be +used in tandem with the INTEL package to good effect, as explained on the :doc:`Speed_intel` page. When using Intel compilers version 16.0 or later is required. You can also use the GNU or Clang compilers and they will provide performance -improvements over regular styles and USER-OMP styles, but less so than +improvements over regular styles and OPENMP styles, but less so than with the Intel compilers. Please also note, that some compilers have been found to apply memory alignment constraints incompletely or incorrectly and thus can cause segmentation faults in otherwise correct -code when using features from the USER-INTEL package. +code when using features from the INTEL package. .. tabs:: @@ -1562,7 +1565,7 @@ code when using features from the USER-INTEL package. Choose which hardware to compile for in Makefile.machine via the following settings. See ``src/MAKE/OPTIONS/Makefile.intel_cpu*`` and ``Makefile.knl`` files for examples. and - ``src/USER-INTEL/README`` for additional information. + ``src/INTEL/README`` for additional information. For CPUs: @@ -1598,9 +1601,9 @@ TBB and MKL. ---------- -.. _user-mdi: +.. _mdi: -USER-MDI package +MDI package ----------------------------- .. tabs:: @@ -1627,9 +1630,9 @@ USER-MDI package ---------- -.. _user-mesont: +.. _mesont: -USER-MESONT package +MESONT package ------------------------- This package includes a library written in Fortran 90 in the @@ -1642,7 +1645,7 @@ they will be downloaded the first time this package is installed. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-MESONT=yes`` + No additional settings are needed besides ``-D PKG_MESONT=yes`` .. tab:: Traditional make @@ -1669,9 +1672,9 @@ they will be downloaded the first time this package is installed. ---------- -.. _user-molfile: +.. _molfile: -USER-MOLFILE package +MOLFILE package --------------------------------------- .. tabs:: @@ -1681,9 +1684,9 @@ USER-MOLFILE package .. code-block:: bash -D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed - -D PKG_USER-MOLFILE=yes + -D PKG_MOLFILE=yes - Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting + Using ``-D PKG_MOLFILE=yes`` enables the package, and setting ``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for the molfile plugin header files. These should match the ABI of the plugin files used, and thus one typically sets them to include @@ -1707,9 +1710,9 @@ USER-MOLFILE package ---------- -.. _user-netcdf: +.. _netcdf: -USER-NETCDF package +NETCDF package ------------------------------------- To build with this package you must have the NetCDF library installed @@ -1719,7 +1722,7 @@ on your system. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``. + No additional settings are needed besides ``-D PKG_NETCDF=yes``. This should auto-detect the NETCDF library if it is installed on your system at standard locations. Several advanced CMake NETCDF @@ -1738,9 +1741,9 @@ on your system. ---------- -.. _user-omp: +.. _openmp: -USER-OMP package +OPENMP package ------------------------------- .. tabs:: @@ -1748,13 +1751,13 @@ USER-OMP package .. tab:: CMake build No additional settings are required besides ``-D - PKG_USER-OMP=yes``. If CMake detects OpenMP compiler support, the - USER-OMP code will be compiled with multi-threading support + PKG_OPENMP=yes``. If CMake detects OpenMP compiler support, the + OPENMP code will be compiled with multi-threading support enabled, otherwise as optimized serial code. .. tab:: Traditional make - To enable multi-threading support in the USER-OMP package (and + To enable multi-threading support in the OPENMP package (and other styles supporting OpenMP) the following compile and link flags must be added to your Makefile.machine file. See ``src/MAKE/OPTIONS/Makefile.omp`` for an example. @@ -1771,12 +1774,12 @@ USER-OMP package ---------- -.. _user-qmmm: +.. _qmmm: -USER-QMMM package +QMMM package --------------------------------- -For using LAMMPS to do QM/MM simulations via the USER-QMMM package you +For using LAMMPS to do QM/MM simulations via the QMMM package you need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix qmmm ` included can be built, but will not be able to do a QM/MM simulation on as such. You must also build a QM code - currently @@ -1799,11 +1802,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to libqmmm.a) are not included in the static LAMMPS library and (currently) not installed, while their code is included in the shared LAMMPS library. Thus a typical command line to configure - building LAMMPS for USER-QMMM would be: + building LAMMPS for QMMM would be: .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \ + cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \ -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake After completing the LAMMPS build and also configuring and @@ -1846,16 +1849,16 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to ---------- -.. _user-quip: +.. _ml-quip: -USER-QUIP package +ML-QUIP package --------------------------------- To build with this package, you must download and build the QUIP library. It can be obtained from GitHub. For support of GAP potentials, additional files with specific licensing conditions need -to be downloaded and configured. See step 1 and step 1.1 in the -``lib/quip/README`` file for details on how to do this. +to be downloaded and configured. The automatic download will from +within CMake will download the non-commercial use version. .. tabs:: @@ -1863,11 +1866,14 @@ to be downloaded and configured. See step 1 and step 1.1 in the .. code-block:: bash + -D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) - CMake will **not** download and build the QUIP library. But once you have - done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should - work. Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library. + CMake will try to download and build the QUIP library from GitHub, if it is not + found on the local machine. This requires to have git installed. It will use the same compilers + and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the + Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled + and installed QUIP library and CMake cannot find it. .. tab:: Traditional make @@ -1881,9 +1887,9 @@ to be downloaded and configured. See step 1 and step 1.1 in the ---------- -.. _user-scafacos: +.. _scafacos: -USER-SCAFACOS package +SCAFACOS package ----------------------------------------- To build with this package, you must download and build the @@ -1928,9 +1934,9 @@ To build with this package, you must download and build the ---------- -.. _user-smd: +.. _machdyn: -USER-SMD package +MACHDYN package ------------------------------- To build with this package, you must download the Eigen3 library. @@ -1972,9 +1978,9 @@ Eigen3 is a template library, so you do not need to build it. ---------- -.. _user-vtk: +.. _vtk: -USER-VTK package +VTK package ------------------------------- To build with this package you must have the VTK library installed on @@ -1984,7 +1990,7 @@ your system. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-VTK=yes``. + No additional settings are needed besides ``-D PKG_VTK=yes``. This should auto-detect the VTK library if it is installed on your system at standard locations. Several advanced VTK options exist diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index 06f87fe904..c7b063e8a9 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -117,10 +117,10 @@ settings may become outdated: make mac # build serial LAMMPS on a Mac make mac_mpi # build parallel LAMMPS on a Mac - make intel_cpu # build with the USER-INTEL package optimized for CPUs - make knl # build with the USER-INTEL package optimized for KNLs + make intel_cpu # build with the INTEL package optimized for CPUs + make knl # build with the INTEL package optimized for KNLs make opt # build with the OPT package optimized for CPUs - make omp # build with the USER-OMP package optimized for OpenMP + make omp # build with the OPENMP package optimized for OpenMP make kokkos_omp # build with the KOKKOS package for OpenMP make kokkos_cuda_mpi # build with the KOKKOS package for GPUs make kokkos_phi # build with the KOKKOS package for KNLs diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index e379153e6f..bd96a8dafb 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -204,9 +204,9 @@ be multiple tests run automatically: .. parsed-literal:: - Found 33 standard and 41 user packages - Standard package NEWPACKAGE missing in Packages_standard.rst - Standard package NEWPACKAGE missing in Packages_details.rst + Found 88 packages + Package NEWPACKAGE missing in Packages_list.rst + Package NEWPACKAGE missing in Packages_details.rst - A test that only standard, printable ASCII text characters are used. This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 2b2993de50..a7dda52b41 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,37 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-HDNNP ` | :ref:`USER-INTEL ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +.. table_from_list:: + :columns: 6 + + * :ref:`ADIOS ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`COLVARS ` + * :ref:`COMPRESS ` + * :ref:`GPU ` + * :ref:`H5MD ` + * :ref:`INTEL ` + * :ref:`KIM ` + * :ref:`KOKKOS ` + * :ref:`LATTE ` + * :ref:`MACHDYN ` + * :ref:`MESSAGE ` + * :ref:`ML-HDNNP ` + * :ref:`ML-PACE ` + * :ref:`ML-QUIP ` + * :ref:`MOLFILE ` + * :ref:`MSCG ` + * :ref:`NETCDF ` + * :ref:`OPENMP ` + * :ref:`OPT ` + * :ref:`PLUMED ` + * :ref:`POEMS ` + * :ref:`PYTHON ` + * :ref:`QMMM ` + * :ref:`SCAFACOS ` + * :ref:`VORONOI ` + * :ref:`VTK ` The mechanism for including packages is simple but different for CMake versus make. @@ -58,14 +78,10 @@ versus make. .. code-block:: csh -D PKG_MANYBODY=yes - -D PKG_USER-INTEL=yes + -D PKG_INTEL=yes - All standard and user packages are included the same way. Note - that USER packages have a hyphen between USER and the rest of the - package name, not an underscore. - - See the shortcut section below for how to install many packages at - once with CMake. + All packages are included the same way. See the shortcut section + below for how to install many packages at once with CMake. .. note:: @@ -89,12 +105,10 @@ versus make. .. code-block:: bash make no-rigid - make yes-user-intel + make yes-intel - All standard and user packages are included the same way. - - See the shortcut section below for how to install many packages at - once with make. + All packages are included the same way. See the shortcut section + below for how to install many packages at once with make. .. note:: @@ -126,7 +140,7 @@ other files dependent on that package are also excluded. .. note:: - By default no package is installed. Prior to August 2018, however, + By default no packages are installed. Prior to August 2018, however, if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE) were pre-installed via the traditional make procedure in the ``src`` directory. That is no longer the case, so that CMake will build @@ -153,7 +167,7 @@ one of them as a starting point and customize it to your needs. .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages + cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools @@ -208,10 +222,10 @@ These commands install/un-install sets of packages: make yes-all # install all packages make no-all # uninstall all packages - make yes-standard or make yes-std # install standard packages - make no-standard or make no-std # uninstall standard packages - make yes-user # install user packages - make no-user # uninstall user packages + make yes-basic # install a few commonly used packages' + make no-basic # remove a few commonly used packages' + make yes-most # install most packages w/o libs' + make no-most # remove most packages w/o libs' make yes-lib # install packages that require extra libraries make no-lib # uninstall packages that require extra libraries make yes-ext # install packages that require external libraries @@ -225,15 +239,14 @@ package`` will list all the these commands. Installing or un-installing a package for the make based build process works by simply copying files back and forth between the main source directory src and the sub-directories with the package name (e.g. - src/KSPACE, src/USER-ATC), so that the files are included or excluded + src/KSPACE, src/ATC), so that the files are included or excluded when LAMMPS is built. Only source files in the src folder will be compiled. The following make commands help manage files that exist in both the src directory and in package sub-directories. You do not normally need to use these commands unless you are editing LAMMPS files or are -:doc:`installing a patch ` downloaded from the LAMMPS web -site. +updating LAMMPS via git. Type ``make package-status`` or ``make ps`` to show which packages are currently installed. For those that are installed, it will list any @@ -245,10 +258,10 @@ currently installed, without listing the status of packages that are not installed. Type ``make package-update`` or ``make pu`` to overwrite src files with -files from the package sub-directories if the package is installed. -It should be used after a :doc:`patch has been applied `, -since patches only update the files in the package sub-directory, but -not the src files. +files from the package sub-directories if the package is installed. It +should be used after the checkout has been :doc:`updated or changed +withy git `, this will only update the files in the package +sub-directories, but not the copies in the src folder. Type ``make package-overwrite`` to overwrite files in the package sub-directories with src files. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index caa6042a51..074a6349e6 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -64,7 +64,7 @@ LAMMPS can use them if they are available on your system. selected, then CMake will try to detect, if threaded FFTW libraries are available and enable them by default. This setting is independent of whether OpenMP threads are enabled and a - packages like KOKKOS or USER-OMP is used. If CMake cannot detect + packages like KOKKOS or OPENMP is used. If CMake cannot detect the FFT library, you can set these variables to assist: .. code-block:: bash @@ -242,8 +242,8 @@ does not support 64-bit integers or incurs performance penalties when using them. These are limits for the core of the LAMMPS code, specific features or -some styles may impose additional limits. The :ref:`USER-ATC -` package cannot be compiled with the "bigbig" setting. +some styles may impose additional limits. The :ref:`ATC +` package cannot be compiled with the "bigbig" setting. Also, there are limitations when using the library interface where some functions with known issues have been replaced by dummy calls printing a corresponding error message rather than crashing randomly or corrupting diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 70a021849d..1a0876e88f 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -18,7 +18,7 @@ Bond_style potentials All LAMMPS :doc:`bond_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -57,7 +57,7 @@ Angle_style potentials All LAMMPS :doc:`angle_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -99,7 +99,7 @@ Dihedral_style potentials All LAMMPS :doc:`dihedral_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -135,7 +135,7 @@ Improper_style potentials All LAMMPS :doc:`improper_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst index da40ada999..4a08d040b7 100644 --- a/doc/src/Commands_category.rst +++ b/doc/src/Commands_category.rst @@ -2,7 +2,7 @@ Commands by category ==================== This page lists most of the LAMMPS commands, grouped by category. The -:doc:`General commands ` doc page lists all general commands +:doc:`General commands ` page lists all general commands alphabetically. Style options for entries like fix, compute, pair etc. have their own pages where they are listed alphabetically. diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 72cc305bb3..9dfb28fa8b 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -16,8 +16,8 @@ Compute commands An alphabetic list of all LAMMPS :doc:`compute ` commands. Some styles have accelerated versions. This is indicated by -additional letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. +additional letters in parenthesis: g = GPU, i = INTEL, k = +KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: :columns: 5 @@ -60,6 +60,7 @@ KOKKOS, o = USER-OMP, t = OPT. * :doc:`erotate/sphere ` * :doc:`erotate/sphere/atom ` * :doc:`event/displace ` + * :doc:`fabric ` * :doc:`fep ` * :doc:`force/tally ` * :doc:`fragment/atom ` @@ -71,6 +72,7 @@ KOKKOS, o = USER-OMP, t = OPT. * :doc:`gyration/shape/chunk ` * :doc:`heat/flux ` * :doc:`heat/flux/tally ` + * :doc:`heat/flux/virial/tally ` * :doc:`hexorder/atom ` * :doc:`hma ` * :doc:`improper ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index c9c55277b2..45a75ff394 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -16,7 +16,7 @@ Fix commands An alphabetic list of all LAMMPS :doc:`fix ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -157,6 +157,7 @@ OPT. * :doc:`orient/fcc ` * :doc:`orient/eco ` * :doc:`pafi ` + * :doc:`pair/tracker ` * :doc:`phonon ` * :doc:`pimd ` * :doc:`planeforce ` @@ -178,14 +179,14 @@ OPT. * :doc:`qeq/dynamic ` * :doc:`qeq/fire ` * :doc:`qeq/point ` - * :doc:`qeq/reax (ko) ` + * :doc:`qeq/reaxff (ko) ` * :doc:`qeq/shielded ` * :doc:`qeq/slater ` * :doc:`qmmm ` * :doc:`qtb ` * :doc:`rattle ` - * :doc:`reax/c/bonds (k) ` - * :doc:`reax/c/species (k) ` + * :doc:`reaxff/bonds (k) ` + * :doc:`reaxff/species (k) ` * :doc:`recenter ` * :doc:`restrain ` * :doc:`rhok ` diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index 8fc658a215..3313474686 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -50,6 +50,6 @@ values are not desired, the :doc:`processors ` and tell LAMMPS how to map processors to the simulation box. Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. The :doc:`Errors ` doc page gives +WARNING message is printed. The :doc:`Errors ` page gives more information on what errors mean. The documentation for each command lists restrictions on how the command can be used. diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index 2f7cd35f15..553bfc845f 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -16,7 +16,7 @@ KSpace solvers All LAMMPS :doc:`kspace_style ` solvers. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -33,8 +33,10 @@ OPT. * :doc:`pppm/cg (o) ` * :doc:`pppm/dipole ` * :doc:`pppm/dipole/spin ` + * :doc:`pppm/dielectric ` * :doc:`pppm/disp (io) ` * :doc:`pppm/disp/tip4p (o) ` + * :doc:`pppm/disp/dielectric ` * :doc:`pppm/stagger ` * :doc:`pppm/tip4p (o) ` * :doc:`pppm/dielectric ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 192c40b27a..184fb25300 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -16,7 +16,7 @@ Pair_style potentials All LAMMPS :doc:`pair_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -29,7 +29,7 @@ OPT. * :doc:`hybrid/scaled ` * :doc:`kim ` * :doc:`list ` - * + * :doc:`tracker ` * * * @@ -190,7 +190,7 @@ OPT. * :doc:`lubricateU/poly ` * :doc:`mdpd ` * :doc:`mdpd/rhosum ` - * :doc:`meam/c ` + * :doc:`meam ` * :doc:`meam/spline (o) ` * :doc:`meam/sw/spline ` * :doc:`mesocnt ` @@ -235,7 +235,7 @@ OPT. * :doc:`python ` * :doc:`quip ` * :doc:`rann ` - * :doc:`reax/c (ko) ` + * :doc:`reaxff (ko) ` * :doc:`rebo (io) ` * :doc:`resquared (go) ` * :doc:`sdpd/taitwater/isothermal ` diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index 563b18a4c2..efc3c5030d 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -47,7 +47,7 @@ LAMMPS: named "x" followed by an "x" character. How the variable is converted to a text string depends on what style - of variable it is; see the :doc:`variable ` doc page for + of variable it is; see the :doc:`variable ` page for details. It can be a variable that stores multiple text strings, and return one of them. The returned text string can be multiple "words" (space separated) which will then be interpreted as multiple diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 1f6da57945..1000d11e29 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -25,23 +25,20 @@ The reset_ids command has been renamed to :doc:`reset_atom_ids ` MEAM package ------------ -The MEAM package has been removed since it was superseded by the -:ref:`USER-MEAMC package `. The code in -the USER-MEAMC package is a translation of the Fortran code of MEAM into C++, -which removes several restrictions (e.g. there can be multiple instances -in hybrid pair styles) and allows for some optimizations leading -to better performance. The new pair style :doc:`meam/c ` has -the exact same syntax as the old "meam" pair style and thus pair style -meam is an alias to the new style and backward -compatibility of old inputs is preserved. +The MEAM package in Fortran has been replaced by a C++ implementation. +The code in the :ref:`MEAM package ` is a translation of the +Fortran code of MEAM into C++, which removes several restrictions +(e.g. there can be multiple instances in hybrid pair styles) and allows +for some optimizations leading to better performance. The pair style +:doc:`meam ` has the exact same syntax. REAX package ------------ The REAX package has been removed since it was superseded by the -:ref:`USER-REAXC package `. The USER-REAXC +:ref:`REAXFF package `. The REAXFF package has been tested to yield equivalent results to the REAX package, -offers better performance, supports OpenMP multi-threading via USER-OMP, +offers better performance, supports OpenMP multi-threading via OPENMP, and GPU and threading parallelization through KOKKOS. The new pair styles are not syntax compatible with the removed reax pair style, so input files will have to be adapted. diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst index 133d567cb3..b5acdf5631 100644 --- a/doc/src/Developer_org.rst +++ b/doc/src/Developer_org.rst @@ -17,7 +17,7 @@ currently supports building with :doc:`conventional makefiles differ in how packages are enabled or disabled for inclusion into a LAMMPS binary so they cannot be mixed. The source files for each package are in all-uppercase sub-directories of the ``src`` folder, for -example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS`` +example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``. The ``src/STUBS`` sub-directory is not a package but contains a dummy MPI library, that is used when building a serial version of the code. The ``src/MAKE`` directory and its sub-directories contain makefiles with settings and diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 52753ee1b4..820e911a8f 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -404,8 +404,8 @@ noise). Then it will restart from the previously generated restart and compare with the reference and also start from the data file. A final check will use multi-cutoff r-RESPA (if supported by the pair style) at a 1:1 split and compare to the Verlet results. These sets of tests are -run with multiple test fixtures for accelerated styles (OPT, USER-OMP, -USER-INTEL) and for the latter two with 4 OpenMP threads enabled. For +run with multiple test fixtures for accelerated styles (OPT, OPENMP, +INTEL) and for the latter two with 4 OpenMP threads enabled. For these tests the relative error (epsilon) is lowered by a common factor due to the additional numerical noise, but the tests are still comparing to the same reference data. diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 44210218c0..60eded42e0 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -334,10 +334,11 @@ arguments of commands in LAMMPS are parsed and to make abstractions of repetitive tasks. The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction -for parsing references to compute or fix styles or variables. These -would start with a "c\_", "f\_", "v\_" followed by the ID or name of -than instance and may be postfixed with one or two array indices -"[]" with numbers > 0. +for parsing references to compute or fix styles, variables or custom +integer or double properties handled by :doc:`fix property/atom `. +These would start with a "c\_", "f\_", "v\_", "d\_", "d2\_", "i\_", or "i2_" +followed by the ID or name of than instance and may be postfixed with +one or two array indices "[]" with numbers > 0. A typical code segment would look like this: diff --git a/doc/src/Errors.rst b/doc/src/Errors.rst index 48db5f6472..5975c22c41 100644 --- a/doc/src/Errors.rst +++ b/doc/src/Errors.rst @@ -1,11 +1,11 @@ Errors ****** -These doc pages describe the errors you can encounter when using -LAMMPS. The common problems include conceptual issues. The messages -and warnings doc pages give complete lists of all the messages the -code may generate (except those generated by USER packages), with -additional details for many of them. +These doc pages describe many of the error and warning message you can +encounter when using LAMMPS. The common problems include conceptual +issues. The messages and warnings doc pages give complete lists of all +the messages the code may generate, with additional details for many of +them. .. toctree:: :maxdepth: 1 diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index 1ea368a5a3..dbec1ef895 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -17,8 +17,9 @@ the steps outlined below: if your issue has already been reported and if it is still open. * Check the `GitHub Pull Requests page `_ to see if there is already a fix for your bug pending. - * Check the `mailing list archives `_ - to see if the issue has been discussed before. + * Check the `mailing list archives `_ or + the `LAMMPS forum `_ to see if the + issue has been discussed before. If none of these steps yields any useful information, please file a new bug report on the `GitHub Issue page `_. diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index d532ce7a31..a26857ebf5 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -14,10 +14,6 @@ For example, a message like this: means that line #78 in the file src/velocity.cpp generated the error. Looking in the source code may help you figure out what went wrong. -Note that error messages from :doc:`user-contributed packages ` are not listed here. If such an error -occurs and is not self-explanatory, you will need to look in the source -code or contact the author of the package. - Doc page with :doc:`WARNING messages ` ---------- @@ -574,10 +570,10 @@ Doc page with :doc:`WARNING messages ` See the region prism command for details. *Can only use -plog with multiple partitions* - Self-explanatory. See doc page discussion of command-line switches. + Self-explanatory. See page discussion of command-line switches. *Can only use -pscreen with multiple partitions* - Self-explanatory. See doc page discussion of command-line switches. + Self-explanatory. See page discussion of command-line switches. *Can only use Kokkos supported regions with Kokkos package* Self-explanatory. @@ -1158,7 +1154,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Cannot use -reorder after -partition* - Self-explanatory. See doc page discussion of command-line switches. + Self-explanatory. See page discussion of command-line switches. *Cannot use Ewald with 2d simulation* The kspace style ewald cannot be used in 2d simulations. You can use @@ -2351,14 +2347,14 @@ Doc page with :doc:`WARNING messages ` *Compute used in variable between runs is not current* Computes cannot be invoked by a variable in between runs. Thus they must have been evaluated on the last timestep of the previous run in - order for their value(s) to be accessed. See the doc page for the + order for their value(s) to be accessed. See the page for the variable command for more info. *Compute used in variable thermo keyword between runs is not current* Some thermo keywords rely on a compute to calculate their value(s). Computes cannot be invoked by a variable in between runs. Thus they must have been evaluated on the last timestep of the previous run in - order for their value(s) to be accessed. See the doc page for the + order for their value(s) to be accessed. See the page for the variable command for more info. *Compute vcm/chunk does not use chunk/atom compute* @@ -3130,7 +3126,7 @@ Doc page with :doc:`WARNING messages ` *Energy was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied energy, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Epsilon or sigma reference not set by pair style in PPPMDisp* Self-explanatory. @@ -4539,10 +4535,10 @@ Doc page with :doc:`WARNING messages ` particles. *Incorrect # of floating-point values in Bodies section of data file* - See doc page for body style. + See page for body style. *Incorrect # of integer values in Bodies section of data file* - See doc page for body style. + See page for body style. *Incorrect %s format in data file* A section of the data file being read by fix property/atom does @@ -4577,7 +4573,7 @@ Doc page with :doc:`WARNING messages ` The number of fields per line is not what expected. *Incorrect bonus data format in data file* - See the read_data doc page for a description of how various kinds of + See the read_data page for a description of how various kinds of bonus data must be formatted for certain atom styles. *Incorrect boundaries with slab Ewald* @@ -4645,7 +4641,7 @@ Doc page with :doc:`WARNING messages ` Incorrect number of words per line in the potential file. *Incorrect integer value in Bodies section of data file* - See doc page for body style. + See page for body style. *Incorrect multiplicity arg for dihedral coefficients* Self-explanatory. Check the input script or data file. @@ -5899,7 +5895,7 @@ Doc page with :doc:`WARNING messages ` other. *Must set number of threads via package omp command* - Because you are using the USER-OMP package, set the number of threads + Because you are using the OPENMP package, set the number of threads via its settings, not by the pair_style snap nthreads setting. *Must shrink-wrap piston boundary* @@ -6000,7 +5996,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Needed bonus data not in data file* - Some atom styles require bonus data. See the read_data doc page for + Some atom styles require bonus data. See the read_data page for details. *Needed molecular topology not in data file* @@ -6202,7 +6198,7 @@ keyword to allow for additional bonds to be formed *One or more atom IDs is too big* The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL - setting in your LAMMPS build. See the :doc:`Build settings ` doc page for more info. + setting in your LAMMPS build. See the :doc:`Build settings ` page for more info. *One or more atom IDs is zero* Either all atoms IDs must be zero or none of them. @@ -6344,16 +6340,16 @@ keyword to allow for additional bonds to be formed The GPU package must be installed via "make yes-gpu" before LAMMPS is built. -*Package intel command without USER-INTEL package installed* - The USER-INTEL package must be installed via "make yes-user-intel" +*Package intel command without INTEL package installed* + The INTEL package must be installed via "make yes-intel" before LAMMPS is built. *Package kokkos command without KOKKOS package enabled* The KOKKOS package must be installed via "make yes-kokkos" before LAMMPS is built, and the "-k on" must be used to enable the package. -*Package omp command without USER-OMP package installed* - The USER-OMP package must be installed via "make yes-user-omp" before +*Package omp command without OPENMP package installed* + The OPENMP package must be installed via "make yes-openmp" before LAMMPS is built. *Pair body requires atom style body* @@ -6597,7 +6593,7 @@ keyword to allow for additional bonds to be formed *Pair style bop requires comm ghost cutoff at least 3x larger than %g* Use the communicate ghost command to set this. See the pair bop - doc page for more details. + page for more details. *Pair style born/coul/long requires atom attribute q* An atom style that defines this attribute must be used. @@ -6917,7 +6913,7 @@ keyword to allow for additional bonds to be formed *Per-atom energy was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied energy, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Per-atom fix in equal-style variable formula* Equal-style variables cannot use per-atom quantities. @@ -6925,7 +6921,7 @@ keyword to allow for additional bonds to be formed *Per-atom virial was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied the virial, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Per-processor system is too big* The number of owned atoms plus ghost atoms on a single @@ -8064,13 +8060,13 @@ keyword to allow for additional bonds to be formed *Using suffix gpu without GPU package installed* Self-explanatory. -*Using suffix intel without USER-INTEL package installed* +*Using suffix intel without INTEL package installed* Self-explanatory. *Using suffix kk without KOKKOS package enabled* Self-explanatory. -*Using suffix omp without USER-OMP package installed* +*Using suffix omp without OPENMP package installed* Self-explanatory. *Using update dipole flag requires atom attribute mu* @@ -8412,7 +8408,7 @@ keyword to allow for additional bonds to be formed *Virial was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied the virial, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Voro++ error: narea and neigh have a different size* This error is returned by the Voro++ library. diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 4f29fad9dd..d7a97c1507 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -14,10 +14,6 @@ generated. For example, a message like this: means that line #187 in the file src/domain.cpp generated the error. Looking in the source code may help you figure out what went wrong. -Note that warning messages from :doc:`user-contributed packages ` are not listed here. If such a warning -occurs and is not self-explanatory, you will need to look in the source -code or contact the author of the package. - Doc page with :doc:`ERROR messages ` ---------- @@ -217,7 +213,7 @@ Doc page with :doc:`ERROR messages ` in unexpected behavior. *Fix bond/swap will ignore defined angles* - See the doc page for fix bond/swap for more info on this + See the page for fix bond/swap for more info on this restriction. *Fix deposit near setting < possible overlap separation %g* @@ -518,7 +514,7 @@ This will most likely cause errors in kinetic fluctuations. will integrate the body motion, but it would be more efficient to use fix rigid. -*Not using real units with pair reax* +*Not using real units with pair reaxff* This is most likely an error, unless you have created your own ReaxFF parameter file in a different set of units. @@ -529,7 +525,7 @@ This will most likely cause errors in kinetic fluctuations. *OMP_NUM_THREADS environment is not set.* This environment variable must be set appropriately to use the - USER-OMP package. + OPENMP package. *One or more atoms are time integrated more than once* This is probably an error since you typically do not want to @@ -809,5 +805,3 @@ This will most likely cause errors in kinetic fluctuations. *Using pair tail corrections with pair_modify compute no* The tail corrections will thus not be computed. -*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c* - Self-explanatory. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 3eb25d5b30..649be52ab7 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -150,6 +150,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | threebody | regression test input for a variety of manybody potentials | +-------------+------------------------------------------------------------------+ +| tracker | track interactions in LJ melt | ++-------------+------------------------------------------------------------------+ | vashishta | use of the Vashishta potential | +-------------+------------------------------------------------------------------+ | voronoi | Voronoi tesselation via compute voronoi/atom command | @@ -172,10 +174,10 @@ web site. If you uncomment the :doc:`dump image ` line(s) in the input script a series of JPG images will be produced by the run (assuming you built LAMMPS with JPG support; see the -:doc:`Build_settings ` doc page for details). These can +:doc:`Build_settings ` page for details). These can be viewed individually or turned into a movie or animated by tools like ImageMagick or QuickTime or various Windows-based tools. See the -:doc:`dump image ` doc page for more details. E.g. this +:doc:`dump image ` page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser. @@ -205,23 +207,23 @@ Uppercase directories +------------+--------------------------------------------------------------------------------------------------+ | MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system | +------------+--------------------------------------------------------------------------------------------------+ +| PACKAGES | examples for specific packages and contributed commands | ++------------+--------------------------------------------------------------------------------------------------+ | SPIN | examples for features of the SPIN package | +------------+--------------------------------------------------------------------------------------------------+ | UNITS | examples that run the same simulation in lj, real, metal units | +------------+--------------------------------------------------------------------------------------------------+ -| USER | examples for USER packages and USER-contributed commands | -+------------+--------------------------------------------------------------------------------------------------+ | VISCOSITY | compute viscosity via several methods | +------------+--------------------------------------------------------------------------------------------------+ Nearly all of these directories have README files which give more details on how to understand and use their contents. -The USER directory has a large number of sub-directories which -correspond by name to a USER package. They contain scripts that -illustrate how to use the command(s) provided in that package. Many +The PACKAGES directory has a large number of sub-directories which +correspond by name to specific packages. They contain scripts that +illustrate how to use the command(s) provided in those packages. Many of the sub-directories have their own README files which give further instructions. See the :doc:`Packages_details ` doc -page for more info on specific USER packages. +page for more info on specific packages. .. _openkim: https://openkim.org diff --git a/doc/src/Howto_barostat.rst b/doc/src/Howto_barostat.rst index 87dab8dd95..0c25e2c53c 100644 --- a/doc/src/Howto_barostat.rst +++ b/doc/src/Howto_barostat.rst @@ -50,7 +50,7 @@ a temperature or pressure compute to a barostatting fix. Thermodynamic output, which can be setup via the :doc:`thermo_style ` command, often includes pressure -values. As explained on the doc page for the +values. As explained on the page for the :doc:`thermo_style ` command, the default pressure is setup by the thermo command itself. It is NOT the pressure associated with any barostatting fix you have defined or with any compute you diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 9bffe5d4c9..172ba3da3a 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -49,7 +49,7 @@ command's documentation for the formula it computes. COMPASS is a general force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers which was developed using ab initio and empirical parameterization techniques. -See the :doc:`Tools ` doc page for the msi2lmp tool for creating +See the :doc:`Tools ` page for the msi2lmp tool for creating LAMMPS template input and data files from BIOVIA's Materials Studio files. Please note that the msi2lmp tool is very old and largely unmaintained, so it does not support all features of Materials Studio diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 0c0a930221..cc02e3d52f 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -10,7 +10,7 @@ deformable objects, etc. Note that other kinds of finite-size spherical and aspherical particles are also supported by LAMMPS, such as spheres, ellipsoids, line segments, and triangles, but they are simpler entities than body particles. See the :doc:`Howto spherical -` doc page for a general overview of all these +` page for a general overview of all these particle types. Body particles are used via the :doc:`atom_style body ` @@ -170,14 +170,14 @@ with this body style to compute body/body and body/non-body interactions. The *rounded/polygon* body style represents body particles as a 2d polygon with a variable number of N vertices. This style can only be used for 2d models; see the :doc:`boundary ` command. See the -"pair_style body/rounded/polygon" doc page for a diagram of two +"pair_style body/rounded/polygon" page for a diagram of two squares with rounded circles at the vertices. Special cases for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified. One use of this body style is for 2d discrete element models, as described in :ref:`Fraige `. -Similar to body style *nparticle*\ , the atom_style body command for +Similar to body style *nparticle*, the atom_style body command for this body style takes two additional arguments: .. parsed-literal:: @@ -284,7 +284,7 @@ The *rounded/polyhedron* body style represents body particles as a 3d polyhedron with a variable number of N vertices, E edges and F faces. This style can only be used for 3d models; see the :doc:`boundary ` command. See the "pair_style -body/rounded/polygon" doc page for a diagram of a two 2d squares with +body/rounded/polygon" page for a diagram of a two 2d squares with rounded circles at the vertices. A 3d cube with rounded spheres at the 8 vertices and 12 rounded edges would be similar. Special cases for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be @@ -293,7 +293,7 @@ specified. This body style is for 3d discrete element models, as described in :ref:`Wang `. -Similar to body style *rounded/polygon*\ , the atom_style body command +Similar to body style *rounded/polygon*, the atom_style body command for this body style takes two additional arguments: .. parsed-literal:: diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index c0a7792448..858e8241d1 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -51,7 +51,7 @@ scales the floating point value to spread it across multiple integers. Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = pencils, 3d bins = boxes, spherical bins, cylindrical bins. -This compute also calculates the number of chunks *Nchunk*\ , which is +This compute also calculates the number of chunks *Nchunk*, which is used by other commands to tally per-chunk data. *Nchunk* can be a static value or change over time (e.g. the number of clusters). The chunk ID for an individual atom can also be static (e.g. a molecule diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst index c22e1ca3ab..7e21b78dfd 100644 --- a/doc/src/Howto_client_server.rst +++ b/doc/src/Howto_client_server.rst @@ -119,7 +119,7 @@ server code. Another code could be substituted for either. The examples below show launching both codes from the same window (or batch script), using the "&" character to launch the first code in the -background. For all modes except *mpi/one*\ , you could also launch the +background. For all modes except *mpi/one*, you could also launch the codes in separate windows on your desktop machine. It does not matter whether you launch the client or server first. @@ -132,7 +132,7 @@ mpirun, even if one or both of them runs on a single processor. This is so that MPI can figure out how to connect both MPI processes together to exchange MPI messages between them. -For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes: +For message exchange in *file*, *zmq*, or *mpi/two* modes: .. code-block:: bash diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst index 655c90bfd9..832a8b8770 100644 --- a/doc/src/Howto_cmake.rst +++ b/doc/src/Howto_cmake.rst @@ -362,7 +362,7 @@ have to be enabled to be included into a LAMMPS executable. Packages are enabled through setting variables of the kind ``PKG_`` to ``on`` and disabled by setting them to ``off`` (or using ``yes``, ``no``, ``1``, ``0`` correspondingly). ```` has to be replaced by -the name of the package, e.g. ``MOLECULE`` or ``USER-MISC``. +the name of the package, e.g. ``MOLECULE`` or ``EXTRA-PAIR``. Using presets @@ -382,9 +382,9 @@ change some variables later with additional *-D* flags. A few examples: .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake + cmake -C ../cmake/presets/basic.cmake -D PKG_MISC=on ../cmake cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake - cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake + cmake -C ../cmake/presets/basic.cmake -D BUILD_MPI=off ../cmake The first command will install the packages ``KSPACE``, ``MANYBODY``, ``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset @@ -400,7 +400,7 @@ It is also possible to do this incrementally. .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake ../cmake + cmake -C ../cmake/presets/basic.cmake ../cmake cmake -D PKG_MISC=on . will achieve the same final configuration as in the first example above. diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst index 0c1fc924ac..bffee0ca01 100644 --- a/doc/src/Howto_coreshell.rst +++ b/doc/src/Howto_coreshell.rst @@ -5,7 +5,7 @@ The adiabatic core-shell model by :ref:`Mitchell and Fincham ` to a system. In order to mimic the electron shell of an ion, a satellite particle is attached to it. This way the ions are split into a core and a shell where the latter is meant to react to the -electrostatic environment inducing polarizability. See the :doc:`Howto polarizable ` doc page for a discussion of all +electrostatic environment inducing polarizability. See the :doc:`Howto polarizable ` page for a discussion of all the polarizable models available in LAMMPS. Technically, shells are attached to the cores by a spring force f = @@ -78,7 +78,7 @@ satellite particle if desired. Since the core/shell model permits distances of r = 0.0 between the core and shell, a pair style with a "cs" suffix needs to be used to implement a valid long-range Coulombic correction. Several such pair -styles are provided in the CORESHELL package. See :doc:`this doc page ` for details. All of the core/shell enabled pair +styles are provided in the CORESHELL package. See :doc:`this page ` for details. All of the core/shell enabled pair styles require the use of a long-range Coulombic solver, as specified by the :doc:`kspace_style ` command. Either the PPPM or Ewald solvers can be used. diff --git a/doc/src/Howto_couple.rst b/doc/src/Howto_couple.rst index 36ba2a526e..31cafd1f94 100644 --- a/doc/src/Howto_couple.rst +++ b/doc/src/Howto_couple.rst @@ -42,7 +42,7 @@ context of your application. stand-alone code could communicate with LAMMPS through files that the command writes and reads. - See the :doc:`Modify command ` doc page for info on how + See the :doc:`Modify command ` page for info on how to add a new command to LAMMPS. .. spacer diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 24c21f27b1..589e9d7b9a 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -2,14 +2,14 @@ Tutorial for Thermalized Drude oscillators in LAMMPS ==================================================== This tutorial explains how to use Drude oscillators in LAMMPS to -simulate polarizable systems using the USER-DRUDE package. As an +simulate polarizable systems using the DRUDE package. As an illustration, the input files for a simulation of 250 phenol molecules are documented. First of all, LAMMPS has to be compiled with the -USER-DRUDE package activated. Then, the data file and input scripts +DRUDE package activated. Then, the data file and input scripts have to be modified to include the Drude dipoles and how to handle them. -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude ---------- @@ -82,7 +82,7 @@ The data file is similar to a standard LAMMPS data file for to their DC should appear in the data file as normal atoms and bonds. You can use the *polarizer* tool (Python script distributed with the -USER-DRUDE package) to convert a non-polarizable data file (here +DRUDE package) to convert a non-polarizable data file (here *data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ ) .. code-block:: bash @@ -91,7 +91,7 @@ USER-DRUDE package) to convert a non-polarizable data file (here This will automatically insert the new atoms and bonds. The masses and charges of DCs and DPs are computed -from *phenol.dff*\ , as well as the DC-DP bond constants. The file +from *phenol.dff*, as well as the DC-DP bond constants. The file *phenol.dff* contains the polarizabilities of the atom types and the mass of the Drude particles, for instance: @@ -106,7 +106,7 @@ and the mass of the Drude particles, for instance: The hydrogen atoms are absent from this file, so they will be treated as non-polarizable atoms. In the non-polarizable data file -*data.102494.lmp*\ , atom names corresponding to the atom type numbers +*data.102494.lmp*, atom names corresponding to the atom type numbers have to be specified as comments at the end of lines of the *Masses* section. You probably need to edit it to add these names. It should look like @@ -125,7 +125,7 @@ look like **Basic input file** -The atom style should be set to (or derive from) *full*\ , so that you +The atom style should be set to (or derive from) *full*, so that you can define atomic charges and molecular bonds, angles, dihedrals... The *polarizer* tool also outputs certain lines related to the input @@ -143,7 +143,7 @@ and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and the atom types 6 to 8 are the newly created DPs. -By recognizing the fix *drude*\ , LAMMPS will find and store matching +By recognizing the fix *drude*, LAMMPS will find and store matching DC-DP pairs and will treat DP as equivalent to their DC in the *special bonds* relations. It may be necessary to extend the space for storing such special relations. In this case extra space should @@ -340,11 +340,11 @@ For the *thole* pair style the coefficients are The special neighbors have charge-charge and charge-dipole interactions screened by the *coul* factors of the *special_bonds* command (0.0, 0.0, and 0.5 in the example above). Without using the -pair_style *thole*\ , dipole-dipole interactions are screened by the -same factor. By using the pair_style *thole*\ , dipole-dipole +pair_style *thole*, dipole-dipole interactions are screened by the +same factor. By using the pair_style *thole*, dipole-dipole interactions are screened by Thole's function, whatever their special relationship (except within each DC-DP pair of course). Consider for -example 1-2 neighbors: using the pair_style *thole*\ , their dipoles +example 1-2 neighbors: using the pair_style *thole*, their dipoles will see each other (despite the *coul* factor being 0.) and the interactions between these dipoles will be damped by Thole's function. @@ -384,7 +384,7 @@ For our phenol example, the groups would be defined as group CORES type 1 2 3 # DCs group DRUDES type 6 7 8 # DPs -Note that with the fixes *drude/transform*\ , it is not required to +Note that with the fixes *drude/transform*, it is not required to specify *comm_modify vel yes* because the fixes do it anyway (several times and for the forces also). diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 311d716f18..0bb931fccd 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -140,8 +140,8 @@ After everything is done, add the files to the branch and commit them: flag) will automatically include **all** modified **and** new files and that is rarely the behavior you want. It can easily lead to accidentally adding unrelated and unwanted changes into the - repository. Instead it is preferable to explicitly use *git add*\ , - *git rm*\ , *git mv* for adding, removing, renaming individual files, + repository. Instead it is preferable to explicitly use *git add*, + *git rm*, *git mv* for adding, removing, renaming individual files, respectively, and then *git commit* to finalize the commit. Carefully check all pending changes with *git status* before committing them. If you find doing this on the command line too diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index 70c2b2fbb7..9492e5755e 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -17,6 +17,11 @@ This compute * :doc:`compute erotate/sphere ` calculates rotational kinetic energy which can be :doc:`output with thermodynamic info `. +The compute + +* :doc:`compute fabric ` + +calculates various versions of the fabric tensor for granular and non-granular pair styles. Use one of these 4 pair potentials, which compute forces and torques between interacting pairs of particles: diff --git a/doc/src/Howto_kappa.rst b/doc/src/Howto_kappa.rst index 08697ecc84..ca9a418d5e 100644 --- a/doc/src/Howto_kappa.rst +++ b/doc/src/Howto_kappa.rst @@ -4,7 +4,7 @@ Calculate thermal conductivity The thermal conductivity kappa of a material can be measured in at least 4 ways using various options in LAMMPS. See the examples/KAPPA directory for scripts that implement the 4 methods discussed here for -a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity ` doc page for an analogous discussion +a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity ` page for an analogous discussion for viscosity. The thermal conductivity tensor kappa is a measure of the propensity @@ -58,7 +58,7 @@ between hot and cold regions of the simulation box. The :doc:`compute heat/flux ` command can calculate the needed heat flux and describes how to implement the Green_Kubo formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate ` command to calculate the needed -auto-correlation. See the doc page for the :doc:`compute heat/flux ` command for an example input script +auto-correlation. See the page for the :doc:`compute heat/flux ` command for an example input script that calculates the thermal conductivity of solid Ar via the GK formalism. diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index 41e1fb6a4c..8c2cbadc42 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -3,13 +3,13 @@ Manifolds (surfaces) **Overview:** -This doc page is not about a LAMMPS input script command, but about +This page is not about a LAMMPS input script command, but about manifolds, which are generalized surfaces, as defined and used by the -USER-MANIFOLD package, to track particle motion on the manifolds. See -the src/USER-MANIFOLD/README file for more details about the package +MANIFOLD package, to track particle motion on the manifolds. See +the src/MANIFOLD/README file for more details about the package and its commands. -Below is a list of currently supported manifolds by the USER-MANIFOLD +Below is a list of currently supported manifolds by the MANIFOLD package, their parameters and a short description of them. The parameters listed here are in the same order as they should be passed to the relevant fixes. diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst index 7cfcd01a50..12c4cfa527 100644 --- a/doc/src/Howto_mdi.rst +++ b/doc/src/Howto_mdi.rst @@ -3,7 +3,7 @@ Using LAMMPS with the MDI library for code coupling .. note:: - This Howto doc page will eventually replace the + This Howto page will eventually replace the :doc:`Howto client/server ` doc page. Client/server coupling of two codes is where one code is the "client" @@ -120,7 +120,7 @@ input script will continue. After finishing execution of the input script, the instance of LAMMPS will be destroyed. LAMMPS supports the full set of MD-appropriate engine commands defined -by the MDI library. See the :doc:`mdi/engine ` doc page for +by the MDI library. See the :doc:`mdi/engine ` page for a list of these. If those commands are not sufficient for a user-developed driver to use diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 61afce17ae..d17b865bbd 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -268,7 +268,7 @@ Computes that generate values to output Every :doc:`compute ` in LAMMPS produces either global or per-atom or local values. The values can be scalars or vectors or arrays of data. These values can be output using the other commands -described in this section. The doc page for each compute command +described in this section. The page for each compute command describes what it produces. Computes that produce per-atom or local values have the word "atom" or "local" in their style name. Computes without the word "atom" or "local" produce global values. @@ -281,7 +281,7 @@ Fixes that generate values to output Some :doc:`fixes ` in LAMMPS produces either global or per-atom or local values which can be accessed by other commands. The values can be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The doc page for +using the other commands described in this section. The page for each fix command tells whether it produces any output quantities and describes them. diff --git a/doc/src/Howto_polarizable.rst b/doc/src/Howto_polarizable.rst index c1c6e1fc76..6361f8ad88 100644 --- a/doc/src/Howto_polarizable.rst +++ b/doc/src/Howto_polarizable.rst @@ -10,7 +10,7 @@ systems can be simulated in LAMMPS using three methods: * the adiabatic core-shell method, implemented in the :doc:`CORESHELL ` package, * the thermalized Drude dipole method, implemented in the - :doc:`USER-DRUDE ` package. + :doc:`DRUDE ` package. The fluctuating charge method calculates instantaneous charges on interacting atoms based on the electronegativity equalization diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst index e9fba37dcd..d286762e01 100644 --- a/doc/src/Howto_replica.rst +++ b/doc/src/Howto_replica.rst @@ -8,34 +8,33 @@ periodically. These are the relevant commands: -* :doc:`neb ` for nudged elastic band calculations +* :doc:`hyper ` for bond boost hyperdynamics (HD) +* :doc:`neb ` for nudged elastic band calculations (NEB) * :doc:`neb_spin ` for magnetic nudged elastic band calculations -* :doc:`prd ` for parallel replica dynamics -* :doc:`tad ` for temperature accelerated dynamics -* :doc:`temper ` for parallel tempering +* :doc:`prd ` for parallel replica dynamics (PRD) +* :doc:`tad ` for temperature accelerated dynamics (TAD) +* :doc:`temper ` for parallel tempering with fixed volume +* :doc:`temper/npt ` for parallel tempering extended for NPT +* :doc:`temper/grem ` for parallel tempering with generalized replica exchange (gREM) * :doc:`fix pimd ` for path-integral molecular dynamics (PIMD) -NEB is a method for finding transition states and barrier energies. -PRD and TAD are methods for performing accelerated dynamics to find -and perform infrequent events. Parallel tempering or replica exchange -runs different replicas at a series of temperature to facilitate -rare-event sampling. +NEB is a method for finding transition states and barrier potential energies. +HD, PRD, and TAD are methods for performing accelerated dynamics to find and +perform infrequent events. Parallel tempering or replica exchange runs +different replicas at a series of temperature to facilitate rare-event +sampling. PIMD runs different replicas whose individual particles in different +replicas are coupled together by springs to model a system of ring-polymers which +can represent the quantum nature of atom cores. These commands can only be used if LAMMPS was built with the REPLICA -package. See the :doc:`Build package ` doc page for more -info. - -PIMD runs different replicas whose individual particles are coupled -together by springs to model a system or ring-polymers. - -This commands can only be used if LAMMPS was built with the USER-MISC -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. In all these cases, you must run with one or more processors per replica. The processors assigned to each replica are determined at -run-time by using the :doc:`-partition command-line switch ` to launch LAMMPS on multiple partitions, -which in this context are the same as replicas. E.g. these commands: +run-time by using the :doc:`-partition command-line switch +` to launch LAMMPS on multiple partitions, which in this +context are the same as replicas. E.g. these commands: .. code-block:: bash @@ -46,9 +45,11 @@ would each run 8 replicas, on either 16 or 8 processors. Note the use of the :doc:`-in command-line switch ` to specify the input script which is required when running in multi-replica mode. -Also note that with MPI installed on a machine (e.g. your desktop), -you can run on more (virtual) processors than you have physical -processors. Thus the above commands could be run on a -single-processor (or few-processor) desktop so that you can run -a multi-replica simulation on more replicas than you have -physical processors. +Also note that with MPI installed on a machine (e.g. your desktop), you +can run on more (virtual) processors than you have physical processors. +Thus the above commands could be run on a single-processor (or +few-processor) desktop so that you can run a multi-replica simulation on +more replicas than you have physical processors. This is useful for +testing and debugging, since with most modern processors and MPI +libraries the efficiency of a calculation can severely diminish when +oversubscribing processors. diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 7bddb1c89d..fbeb1f7785 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -28,7 +28,7 @@ can be invoked via the *dpd/tstat* pair style: :doc:`Fix nvt ` only thermostats the translational velocity of particles. :doc:`Fix nvt/sllod ` also does this, except that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the :doc:`Howto nemd ` doc page for further details. :doc:`Fix nvt/sphere ` and :doc:`fix nvt/asphere ` thermostat not only translation +integrates the SLLOD equations of motion. See the :doc:`Howto nemd ` page for further details. :doc:`Fix nvt/sphere ` and :doc:`fix nvt/asphere ` thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. @@ -88,7 +88,7 @@ Below is a list of some custom temperature computes that can be used like that: Thermodynamic output, which can be setup via the :doc:`thermo_style ` command, often includes temperature -values. As explained on the doc page for the +values. As explained on the page for the :doc:`thermo_style ` command, the default temperature is setup by the thermo command itself. It is NOT the temperature associated with any thermostatting fix you have defined or with any diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 13383f44df..5e952709c9 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -23,21 +23,21 @@ origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** = and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors **a**\ , **b**\ , and **c** cannot be arbitrary +simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary vectors. As indicated, **a** must lie on the positive x axis. **b** must lie in the xy plane, with strictly positive y component. **c** may have any orientation with strictly positive z component. The requirement -that **a**\ , **b**\ , and **c** have strictly positive x, y, and z components, -respectively, ensures that **a**\ , **b**\ , and **c** form a complete +that **a**, **b**, and **c** have strictly positive x, y, and z components, +respectively, ensures that **a**, **b**, and **c** form a complete right-handed basis. These restrictions impose no loss of generality, since it is possible to rotate/invert any set of 3 crystal basis vectors so that they conform to the restrictions. -For example, assume that the 3 vectors **A**\ ,\ **B**\ ,\ **C** are the edge +For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge vectors of a general parallelepiped, where there is no restriction on -**A**\ ,\ **B**\ ,\ **C** other than they form a complete right-handed basis i.e. -**A** x **B** . **C** > 0. The equivalent LAMMPS **a**\ ,\ **b**\ ,\ **c** are a linear -rotation of **A**\ , **B**\ , and **C** and can be computed as follows: +**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e. +**A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear +rotation of **A**, **B**, and **C** and can be computed as follows: .. math:: @@ -57,9 +57,9 @@ rotation of **A**\ , **B**\ , and **C** and can be computed as follows: where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^) indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles between the vectors described below. Note that by construction, -**a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively. +**a**, **b**, and **c** have strictly positive x, y, and z components, respectively. If it should happen that -**A**\ , **B**\ , and **C** form a left-handed basis, then the above equations +**A**, **B**, and **C** form a left-handed basis, then the above equations are not valid for **c**\ . In this case, it is necessary to first apply an inversion. This can be achieved by interchanging two basis vectors or by changing the sign of one of them. @@ -95,7 +95,7 @@ for details. The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the time the simulation box is created. This happens in one of 3 ways. If the :doc:`create_box ` command is used with a region of -style *prism*\ , then a triclinic box is setup. See the +style *prism*, then a triclinic box is setup. See the :doc:`region ` command for details. If the :doc:`read_data ` command is used to define the simulation box, and the header of the data file contains a line with the "xy xz @@ -135,7 +135,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all equivalent. If the box tilt exceeds this limit during a dynamics run (e.g. via the :doc:`fix deform ` command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the :doc:`fix deform ` doc page for further details. +factor within the bounds, so the run can continue. See the :doc:`fix deform ` page for further details. One exception to this rule is if the first dimension in the tilt factor (x for xy) is non-periodic. In that case, the limits on the @@ -160,10 +160,10 @@ For extreme values of tilt, LAMMPS may also lose atoms and generate an error. Triclinic crystal structures are often defined using three lattice -constants *a*\ , *b*\ , and *c*\ , and three angles :math:`\alpha`, +constants *a*, *b*, and *c*, and three angles :math:`\alpha`, :math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the a, b, and c lattice constants are the scalar lengths of the edge -vectors **a**\ , **b**\ , and **c** defined above. The relationship +vectors **a**, **b**, and **c** defined above. The relationship between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`, :math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: @@ -188,10 +188,10 @@ The inverse relationship can be written as follows: {\rm yz} = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\ {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\ -The values of *a*\ , *b*\ , *c* , :math:`\alpha` , :math:`\beta`, and +The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and :math:`\gamma` can be printed out or accessed by computes using the :doc:`thermo_style custom ` keywords -*cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ , +*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively. As discussed on the :doc:`dump ` command doc page, when the BOX diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index cfe9497665..5cabf63de3 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -42,7 +42,7 @@ command, which determines grad(Vstream) in the equation above. E.g. the derivative in the y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of the pressure or stress tensor, as calculated by the :doc:`compute pressure ` command, can also be monitored, which -is the J term in the equation above. See the :doc:`Howto nemd ` doc page for details on NEMD simulations. +is the J term in the equation above. See the :doc:`Howto nemd ` page for details on NEMD simulations. The third method is to perform a reverse non-equilibrium MD simulation using the :doc:`fix viscosity ` command which implements diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index 2eb009c185..7c74aab8bf 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -13,7 +13,7 @@ by several popular visualization tools. The :doc:`dump image ` and : output internally rendered images and convert a sequence of them to a movie during the MD run. Several programs included with LAMMPS as auxiliary tools can convert between LAMMPS format files and other -formats. See the :doc:`Tools ` doc page for details. +formats. See the :doc:`Tools ` page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of @@ -25,7 +25,7 @@ RasMol visualization programs. Pizza.py has tools that do interactive 3d OpenGL visualization and one that creates SVG images of dump file snapshots. -.. _pizza: https://pizza.sandia.gov +.. _pizza: https://lammps.github.io/pizza .. _ensight: https://www.ansys.com/products/fluids/ansys-ensight diff --git a/doc/src/Howto_walls.rst b/doc/src/Howto_walls.rst index 6e3e22a3f0..a77f116fd4 100644 --- a/doc/src/Howto_walls.rst +++ b/doc/src/Howto_walls.rst @@ -53,7 +53,7 @@ granular particles; all the other commands create smooth walls. * :doc:`fix wall/region ` - use region surface as wall * :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair_style granular ` potential -The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all +The *lj93*, *lj126*, *colloid*, *harmonic*, and *morse* styles all allow the flat walls to move with a constant velocity, or oscillate in time. The :doc:`fix wall/region ` command offers the most generality, since the region surface is treated as a wall, and diff --git a/doc/src/Howto_wsl.rst b/doc/src/Howto_wsl.rst index 28251ba5ee..df5644451f 100644 --- a/doc/src/Howto_wsl.rst +++ b/doc/src/Howto_wsl.rst @@ -208,7 +208,7 @@ Presets are a way to specify a collection of CMake options using a file. .. code-block:: bash - cmake ../cmake/presets/minimal.cmake ../cmake + cmake ../cmake/presets/basic.cmake ../cmake This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command. diff --git a/doc/src/Install.rst b/doc/src/Install.rst index e0204c0bbd..157bd32208 100644 --- a/doc/src/Install.rst +++ b/doc/src/Install.rst @@ -18,7 +18,6 @@ need the source code. Install_tarball Install_git - Install_patch These are the files and sub-directories in the LAMMPS distribution: @@ -27,6 +26,8 @@ These are the files and sub-directories in the LAMMPS distribution: +------------+-------------------------------------------+ | LICENSE | GNU General Public License (GPL) | +------------+-------------------------------------------+ +| SECURITY.md| Security Policy for the LAMMPS package | ++------------+-------------------------------------------+ | bench | benchmark problems | +------------+-------------------------------------------+ | cmake | CMake build files | diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 1a07b7f917..f62bad6847 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -120,8 +120,11 @@ changed. How to do this depends on the build system you are using. $ make package-update # sync package files with src files $ make foo # re-build for your machine (mpi, serial, etc) - Just as described on the :doc:`Apply patch ` page, - after a patch has been installed. + to enforce consistency of the source between the src folder + and package directories. This is OK to do even if you don't + use any packages. The "make purge" command removes any deprecated + src files if they were removed by the patch from a package + sub-directory. .. warning:: diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst deleted file mode 100644 index f1f37f86c2..0000000000 --- a/doc/src/Install_patch.rst +++ /dev/null @@ -1,96 +0,0 @@ -Applying patches ----------------- - -It is easy to stay current with the most recent LAMMPS patch releases -if you use git to track the LAMMPS development. Instructions for -how to stay current are on the -:doc:`Download the LAMMPS source with git ` page. - -If you prefer to download a tarball, as described on the -:doc:`tarball download ` page, you can stay current by -downloading "patch files" when new patch releases are made. A link to -a patch file is posted on the -`bug fixes and new feature page `_ -of the LAMMPS website, along -with a list of changed files and details about what is in the new patch -release. This page explains how to apply the patch file to your local -LAMMPS directory. - -.. note:: - - You should not apply patch files to a local git checkout of - LAMMPS, only to an unpacked tarball. Use git commands to - update such a version of the LAMMPS source code. - -Here are the steps to apply a patch file. Note that if your version -of LAMMPS is several patch releases behind, you need to apply all the -intervening patch files in succession to bring your version of LAMMPS -up to date. - -* Download the patch file. You may have to shift-click in your browser - to download the file instead of display it. Patch files have names - like patch.12Dec16. -* Put the patch file in your top-level LAMMPS directory, where the - LICENSE and README files are. -* Apply the patch by typing the following command from your top-level - LAMMPS directory, where the redirected file is the name of the patch - file. - - .. code-block:: bash - - $ patch -bp1 < patch.12Dec16 - -* A list of updated files print out to the screen. The -b switch - creates backup files of your originals (e.g. src/force.cpp.orig), so - you can manually undo the patch if something goes wrong. - -* Once you have updated your local files you need to re-build LAMMPS. - If you are applying several patches successively, you only need to - do the rebuild once at the end. How to do it depends on the build - system you are using. - - .. tabs:: - - .. tab:: CMake build - - Change to your build folder and type: - - .. code-block:: bash - - cmake . --build - - CMake should auto-detect whether it needs to re-run the CMake - configuration step and otherwise redo the build for all files - that have been changed or files that depend on changed files. - In case some build options have been changed or renamed, you - may have to update those by running: - - .. code-block:: bash - - cmake . - - and then rebuild. - - .. tab:: Traditional make - - Switch to the src directory and type: - - .. code-block:: bash - - $ make purge # remove any deprecated src files - $ make package-update # sync package files with src files - $ make foo # re-build for your machine (mpi, serial, etc) - - to enforce consistency of the source between the src folder - and package directories. This is OK to do even if you don't - use any packages. The "make purge" command removes any deprecated - src files if they were removed by the patch from a package - sub-directory. - - .. warning:: - - If you wish to edit/change a src file that is from a package, - you should edit the version of the file inside the package - sub-directory with src, then re-install the package. The - version in the source directory is merely a copy and will be - wiped out if you type "make package-update". diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index 921ce8785a..caa8f700a9 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -47,15 +47,3 @@ release. .. _git: https://github.com/lammps/lammps/releases ----------- - -If you download a current LAMMPS tarball, one way to stay current as -new patch tarballs are released, is to download a patch file which you -can apply to your local directory to update it for each new patch -release. (Or of course you could just download the newest tarball -periodically.) - -The patch files are posted on the `bug and feature page `_ of the -website, along with a list of changed files and details about what is -in the new patch release. Instructions for applying a patch file are -on the :doc:`Install patch ` page. diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 1df7ae7f3f..1e5c9684ac 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -18,9 +18,9 @@ needed to run in parallel with MPI. The LAMMPS binaries contain *all* :doc:`optional packages ` included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON, -USER-ADIOS, USER-H5MD, USER-NETCDF, USER-QMMM, USER-QUIP, and USER-VTK. +ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK. The serial version also does not include the MPIIO and -USER-LB packages. The GPU package is compiled for OpenCL with +LATBOLTZ packages. The GPU package is compiled for OpenCL with mixed precision kernels. The LAMMPS library is compiled as a shared library and the diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index 6af3996d1e..720221d4b7 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -29,19 +29,19 @@ The following folks deserve special recognition. Many of the packages they have written are unique for an MD code and LAMMPS would not be as general-purpose as it is without their expertise and efforts. -* Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF -* Mike Brown (Intel), GPU and USER-INTEL packages -* Colin Denniston (U Western Ontario), USER-LB package -* Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages -* Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field -* Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling +* Metin Aktulga (MSU), REAXFF package for C version of ReaxFF +* Mike Brown (Intel), GPU and INTEL packages +* Colin Denniston (U Western Ontario), LATBOLTZ package +* Georg Ganzenmuller (EMI), MACHDYN and SPH packages +* Andres Jaramillo-Botero (Caltech), EFF package for electron force field +* Reese Jones (Sandia) and colleagues, ATC package for atom/continuum coupling * Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS * Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion * Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages * Mike Parks (Sandia), PERI package for Peridynamics * Roy Pollock (LLNL), Ewald and PPPM solvers -* Christian Trott (Sandia), USER-CUDA and KOKKOS packages -* Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD +* Christian Trott (Sandia), CUDA and KOKKOS packages +* Ilya Valuev (JIHT), AWPMD package for wave packet MD * Greg Wagner (Northwestern U), MEAM package for MEAM potential ---------- diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 648c427b11..f1c04bdb23 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -24,11 +24,15 @@ General features ^^^^^^^^^^^^^^^^ * runs on a single processor or in parallel -* distributed-memory message-passing parallelism (MPI) -* spatial-decomposition of simulation domain for parallelism -* open-source distribution -* highly portable C++ -* optional libraries used: MPI and single-processor FFT +* distributed memory message-passing parallelism (MPI) +* shared memory multi-threading parallelism (OpenMP) +* spatial decomposition of simulation domain for MPI parallelism +* particle decomposition inside of spatial decomposition for OpenMP parallelism +* GPLv2 licensed open-source distribution +* highly portable C++-11 +* modular code with most functionality in optional packages +* only depends on MPI library for basic parallel functionality +* other libraries are optional and only required for specific packages * GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features * easy to extend with new features and functionality * runs from an input script @@ -68,9 +72,9 @@ Interatomic potentials (force fields) :doc:`improper style `, :doc:`kspace style ` commands) -* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated +* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated * charged pairwise potentials: Coulombic, point-dipole -* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic +* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic * long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald) * polarization models: :doc:`QEq `, :doc:`core/shell model `, :doc:`Drude dipole model ` * charge equilibration (QEq via dynamic, point, shielded, Slater methods) @@ -170,9 +174,12 @@ Multi-replica models ^^^^^^^^^^^^^^^^^^^^ * :doc:`nudged elastic band ` +* :doc:`hyperdynamics ` * :doc:`parallel replica dynamics ` * :doc:`temperature accelerated dynamics ` * :doc:`parallel tempering ` +* :doc:`path-integral MD ` +* multi-walker collective variables with :doc:`Colvars ` and :doc:`Plumed ` .. _prepost: @@ -187,7 +194,7 @@ Pre- and post-processing plotting, and visualization for LAMMPS simulations. Pizza.py is written in `Python `_ and is available for download from `the Pizza.py WWW site `_. -.. _pizza: https://pizza.sandia.gov +.. _pizza: https://lammps.github.io/pizza .. _python: http://www.python.org diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index d034ccb443..d9a977196f 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -32,7 +32,7 @@ Here are suggestions on how to perform these tasks: are simple programs that will build simple molecular systems, such as linear bead-spring polymer chains. The moltemplate program is a true molecular builder that will generate complex molecular models. See - the :doc:`Tools ` doc page for details on tools packaged with + the :doc:`Tools ` page for details on tools packaged with LAMMPS. The `Pre/post processing page `_ of the LAMMPS website describes a variety of third party tools for this task. Furthermore, some LAMMPS internal commands allow to reconstruct, or selectively add @@ -49,7 +49,7 @@ Here are suggestions on how to perform these tasks: * **Simulation analysis:** If you want to perform analysis on-the-fly as your simulation runs, see the :doc:`compute ` and :doc:`fix ` doc pages, which list commands that can be used in a - LAMMPS input script. Also see the :doc:`Modify ` doc page for + LAMMPS input script. Also see the :doc:`Modify ` page for info on how to add your own analysis code or algorithms to LAMMPS. For post-processing, LAMMPS output such as :doc:`dump file snapshots ` can be converted into formats used by other MD or post-processing codes. To some degree, that conversion can be done @@ -61,7 +61,7 @@ Here are suggestions on how to perform these tasks: LAMMPS will do these conversions. Scripts provided in the tools/python directory can extract and massage data in dump files to make it easier to import into other programs. See the - :doc:`Tools ` doc page for details on these various options. + :doc:`Tools ` page for details on these various options. * **Visualization:** LAMMPS can produce NETPBM, JPG or PNG snapshot images on-the-fly via its :doc:`dump image ` command and pass them to an external program, `FFmpeg `_ to generate @@ -71,13 +71,13 @@ Here are suggestions on how to perform these tasks: LAMMPS website for visualization packages that can process LAMMPS output data. * **Plotting:** See the next bullet about Pizza.py as well as the - :doc:`Python ` doc page for examples of plotting LAMMPS + :doc:`Python ` page for examples of plotting LAMMPS output. Scripts provided with the *python* tool in the tools directory will extract and massage data in log and dump files to make it easier to analyze and plot. See the :doc:`Tools ` doc page for more discussion of the various tools. * **Pizza.py:** Our group has also written a separate toolkit called - `Pizza.py `_ which can do certain kinds of + `Pizza.py `_ which can do certain kinds of setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS simulations. It thus provides some functionality for several of the above bullets. Pizza.py is written in `Python `_ diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 8ab85a0d99..a25f91bc48 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -18,14 +18,15 @@ supercomputers. .. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface .. _lws: https://www.lammps.org -LAMMPS is written in C++. Earlier versions were written in F77 and -F90. See the `History page `_ of -the website for details. All versions can be downloaded from the -`LAMMPS website `_. +LAMMPS is written in C++ and requires a compiler that is at least +compatible with the C++-11 standard. +Earlier versions were written in F77 and F90. See the `History page +`_ of the website for details. All +versions can be downloaded from the `LAMMPS website `_. LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See the :doc:`Modify ` doc page for +conditions, or diagnostics. See the :doc:`Modify ` page for more details. In the most general sense, LAMMPS integrates Newton's equations of @@ -41,8 +42,9 @@ short distances, so that the local density of particles never becomes too large. This is in contrast to methods used for modeling plasma or gravitational bodies (e.g. galaxy formation). -On parallel machines, LAMMPS uses spatial-decomposition techniques to -partition the simulation domain into small sub-domains of equal -computational cost, one of which is assigned to each processor. -Processors communicate and store "ghost" atom information for atoms -that border their sub-domain. +On parallel machines, LAMMPS uses spatial-decomposition techniques with +MPI parallelization to partition the simulation domain into small +sub-domains of equal computational cost, one of which is assigned to +each processor. Processors communicate and store "ghost" atom +information for atoms that border their sub-domain. Multi-threading +parallelization with with particle-decomposition can be used in addition. diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index 3fccaf4dca..2ea1969f2a 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -20,7 +20,8 @@ available online are listed below. * `Glossary of terms relevant to LAMMPS `_ * `LAMMPS highlights with images `_ * `LAMMPS highlights with movies `_ -* `Mail list `_ +* `Mailing list `_ +* `LAMMPS forum `_ * `Workshops `_ * `Tutorials `_ diff --git a/doc/src/Library.rst b/doc/src/Library.rst index 0eddc5afb3..05b652f7a7 100644 --- a/doc/src/Library.rst +++ b/doc/src/Library.rst @@ -31,7 +31,7 @@ that are not possible with existing input script commands. applies to the core LAMMPS code and less so on add-on packages, especially when those packages require additional code in the *lib* folder, interface LAMMPS to Fortran libraries, or the code uses - static variables (like the USER-COLVARS package). + static variables (like the COLVARS package). Another major issue to deal with is to correctly handle MPI. Creating a LAMMPS instance requires passing an MPI communicator, or diff --git a/doc/src/Library_create.rst b/doc/src/Library_create.rst index 350569e54e..b3fea4b89e 100644 --- a/doc/src/Library_create.rst +++ b/doc/src/Library_create.rst @@ -9,6 +9,7 @@ This section documents the following functions: - :cpp:func:`lammps_close` - :cpp:func:`lammps_mpi_init` - :cpp:func:`lammps_mpi_finalize` +- :cpp:func:`lammps_kokkos_finalize` -------------------- diff --git a/doc/src/Library_scatter.rst b/doc/src/Library_scatter.rst index b45f45f6fb..8380ef91bd 100644 --- a/doc/src/Library_scatter.rst +++ b/doc/src/Library_scatter.rst @@ -17,6 +17,7 @@ It documents the following functions: - :cpp:func:`lammps_gather_atoms_subset` - :cpp:func:`lammps_scatter_atoms` - :cpp:func:`lammps_scatter_atoms_subset` +- :cpp:func:`lammps_gather_bonds` - :cpp:func:`lammps_gather` - :cpp:func:`lammps_gather_concat` - :cpp:func:`lammps_gather_subset` @@ -51,6 +52,11 @@ It documents the following functions: ----------------------- +.. doxygenfunction:: lammps_gather_bonds + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_gather :project: progguide diff --git a/doc/src/Library_utility.rst b/doc/src/Library_utility.rst index b2f3666f88..32fac6bcc8 100644 --- a/doc/src/Library_utility.rst +++ b/doc/src/Library_utility.rst @@ -8,7 +8,11 @@ functions. They do not directly call the LAMMPS library. - :cpp:func:`lammps_decode_image_flags` - :cpp:func:`lammps_set_fix_external_callback` - :cpp:func:`lammps_fix_external_set_energy_global` +- :cpp:func:`lammps_fix_external_set_energy_peratom` - :cpp:func:`lammps_fix_external_set_virial_global` +- :cpp:func:`lammps_fix_external_set_virial_peratom` +- :cpp:func:`lammps_fix_external_set_vector_length` +- :cpp:func:`lammps_fix_external_set_vector` - :cpp:func:`lammps_free` - :cpp:func:`lammps_is_running` - :cpp:func:`lammps_force_timeout` @@ -33,7 +37,7 @@ where such memory buffers were allocated that require the use of ----------------------- -.. doxygenfunction:: lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*) +.. doxygenfunction:: lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void*) :project: progguide ----------------------- @@ -43,11 +47,31 @@ where such memory buffers were allocated that require the use of ----------------------- +.. doxygenfunction:: lammps_fix_external_set_energy_peratom + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_fix_external_set_virial_global :project: progguide ----------------------- +.. doxygenfunction:: lammps_fix_external_set_virial_peratom + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_fix_external_set_vector_length + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_fix_external_set_vector + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_free :project: progguide diff --git a/doc/src/Modify_body.rst b/doc/src/Modify_body.rst index b923416bdc..3435b673e3 100644 --- a/doc/src/Modify_body.rst +++ b/doc/src/Modify_body.rst @@ -6,7 +6,7 @@ Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -See the :doc:`Howto body ` doc page for an overview of using +See the :doc:`Howto body ` page for an overview of using body particles and the various body styles LAMMPS supports. New styles can be created to add new kinds of body particles to LAMMPS. diff --git a/doc/src/Modify_compute.rst b/doc/src/Modify_compute.rst index e910d6f8e2..bf580a6561 100644 --- a/doc/src/Modify_compute.rst +++ b/doc/src/Modify_compute.rst @@ -53,5 +53,5 @@ in two stages: the callback function is registered with the pair style and then called from the Pair::ev_tally() function, which is called for each pair after force and energy has been computed for this pair. Then the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The :doc:`compute styles in the USER-TALLY package ` +compute_vector or compute_peratom methods. The :doc:`compute styles in the TALLY package ` provide *examples* for utilizing this mechanism. diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 4382753c42..ff39773764 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -25,13 +25,16 @@ the work of others (and possibly get scooped by them) or have your work duplicated by others. For informal communication with (some of) the LAMMPS developers you may -ask to join the `LAMMPS developers on Slack `_. -This slack work space is by invitation only. Thus for access, please -send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS -you are working on. Only discussions related to LAMMPS development are -tolerated, so this is **NOT** for people that look for help with compiling, -installing, or using LAMMPS. Please contact the `lammps-users mailing -list `_ for those purposes instead. +ask to join the `LAMMPS developers on Slack +`_. This slack work space is by invitation +only. Thus for access, please send an e-mail to ``slack@lammps.org`` +explaining what part of LAMMPS you are working on. Only discussions +related to LAMMPS development are tolerated, so this is **NOT** for +people that look for help with compiling, installing, or using +LAMMPS. Please contact the +`lammps-users mailing list `_ or the +`LAMMPS forum `_ for those purposes +instead. How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how many and what @@ -49,13 +52,9 @@ with gzip. Please only use gzip compression, as this works well and is available on all platforms. If the new features/files are broadly useful we may add them as core -files to LAMMPS or as part of a :doc:`standard package `. Else we will add them as a -user-contributed file or :doc:`user package `. Examples -of user packages are in src sub-directories that start with USER. The -USER-MISC package is simply a collection of (mostly) unrelated single -files, which is the simplest way to have your contribution quickly -added to the LAMMPS distribution. All the standard and user packages -are listed and described on the :doc:`Packages details ` doc page. +files to LAMMPS or as part of a :doc:`package `. All +packages are listed and described on the :doc:`Packages details +` doc page. Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL @@ -63,33 +62,25 @@ them open-source, i.e. we can release them under the terms of the GPL a LGPL (version 2.1) distribution that we make available to developers on request only and with files that are authorized for that kind of distribution removed (e.g. interface to FFTW). See the -:doc:`LAMMPS license ` doc page for details. - -With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the `Authors page `_ -of the `LAMMPS WWW site `_), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). +:doc:`LAMMPS license ` page for details. .. note:: - If you prefer to actively develop and support your add-on - feature yourself, then you may wish to make it available for download - from your own website, as a user package that LAMMPS users can add to - their copy of LAMMPS. See the `Offsite LAMMPS packages and tools `_ page of the LAMMPS web - site for examples of groups that do this. We are happy to advertise - your package and web site from that page. Simply email the - `developers `_ with info about - your package and we will post it there. + If you prefer to actively develop and support your add-on feature + yourself, then you may wish to make it available for download from + your own website, as a user package that LAMMPS users can add to + their copy of LAMMPS. See the `Offsite LAMMPS packages and tools + `_ page of the LAMMPS web site + for examples of groups that do this. We are happy to advertise your + package and web site from that page. Simply email the `developers + `_ with info about your package + and we will post it there. We recommend to name external packages + USER-\ so they can be easily distinguished from bundled packages + that do not have the USER- prefix. .. _lws: https://www.lammps.org -The previous sections of this doc page describe how to add new "style" +The previous sections of this page describe how to add new "style" files of various kinds to LAMMPS. Packages are simply collections of one or more new class files which are invoked as a new style within a LAMMPS input script. If designed correctly, these additions typically @@ -102,7 +93,7 @@ trivial change is making a parent-class method "virtual" when you derive a new child class from it. Here is a checklist of steps you need to follow to submit a single file -or user package for our consideration. Following these steps will save +or package for our consideration. Following these steps will save both you and us time. Please have a look at the existing files in packages in the src directory for examples. If you are uncertain, please ask. @@ -116,7 +107,7 @@ packages in the src directory for examples. If you are uncertain, please ask. your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per - level, **no tabs**\ , no lines over 100 characters. I/O is done via + level, **no tabs**, no lines over 100 characters. I/O is done via the C-style stdio library (mixing of stdio and iostreams is generally discouraged), class header files should not import any system headers outside of , STL containers should be avoided in headers, @@ -160,73 +151,79 @@ packages in the src directory for examples. If you are uncertain, please ask. You may also use ``// clang-format on/off`` throughout your file to protect sections of the file from being reformatted. -* If you want your contribution to be added as a user-contributed - feature, and it's a single file (actually a \*.cpp and \*.h file) it can - rapidly be added to the USER-MISC directory. Send us the one-line - entry to add to the USER-MISC/README file in that dir, along with the - 2 source files. You can do this multiple times if you wish to - contribute several individual features. +* Please review the list of :doc:`available Packages ` + to see if your contribution could be added to be added to one of them. + It should fit into the general purposed of that package. If it does not + fit well, it can be added to one of the EXTRA- packages or the MISC package. -* If you want your contribution to be added as a user-contribution and - it is several related features, it is probably best to make it a user - package directory with a name like USER-FOO. In addition to your new - files, the directory should contain a README text file. The README - should contain your name and contact information and a brief - description of what your new package does. If your files depend on - other LAMMPS style files also being installed (e.g. because your file - is a derived class from the other LAMMPS class), then an Install.sh - file is also needed to check for those dependencies. See other README - and Install.sh files in other USER directories as examples. Send us a - tarball of this USER-FOO directory. +* If your contribution has several related features that are not covered + by one of the existing packages or is dependent on a library (bundled + or external), it is best to make it a package directory with a name + like FOO. In addition to your new files, the directory should contain + a README text file. The README should contain your name and contact + information and a brief description of what your new package does. If + your files depend on other LAMMPS style files also being installed + (e.g. because your file is a derived class from the other LAMMPS + class), then an Install.sh file is also needed to check for those + dependencies and modifications to src/Depend.sh to trigger the checks. + See other README and Install.sh files in other directories as examples. + Similarly for CMake support changes need to be made to cmake/CMakeLists.txt, + the files in cmake/presets, and possibly a file to cmake/Modules/Packages/ + added. Please check out how this is handled for existing packages and + ask the LAMMPS developers if you need assistance. Please submit a pull + request on GitHub or send us a tarball of this FOO directory and all + modified files. Pull requests are strongly encouraged since they greatly + reduce the effort required to integrate a contribution and simplify the + process of adjusting the contributed code to cleanly fit into the + LAMMPS distribution. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class - that is inside the LAMMPS namespace. If the file is for one of the - USER packages, including USER-MISC, then we are not as picky about the - coding style (see above). I.e. the files do not need to be in the - same stylistic format and syntax as other LAMMPS files, though that - would be nice for developers as well as users who try to read your - code. + that is inside the LAMMPS namespace. To simplify maintenance, we + may ask to adjust the programming style and formatting style to closer + match the rest of LAMMPS. We bundle a clang-format configuration file + that can help with adjusting the formatting, although this is not a + strict requirement. * You **must** also create a **documentation** file for each new command - or style you are adding to LAMMPS. For simplicity and convenience, the - documentation of groups of closely related commands or styles may be - combined into a single file. This will be one file for a single-file - feature. For a package, it might be several files. These are text - files with a .rst extension using the `reStructuredText `_ - markup language, that are then converted to HTML and PDF using the - `Sphinx `_ documentation generator tool. Running Sphinx with - the included configuration requires Python 3.x. Configuration - settings and custom extensions for this conversion are included in the - source distribution, and missing python packages will be transparently - downloaded into a virtual environment via pip. Thus, if your local - system is missing required packages, you need access to the - internet. The translation can be as simple as doing "make html pdf" in - the doc folder. As appropriate, the text files can include inline - mathematical expression or figures (see doc/JPG for examples). + or style you are adding to LAMMPS. For simplicity and convenience, + the documentation of groups of closely related commands or styles may + be combined into a single file. This will be one file for a + single-file feature. For a package, it might be several files. These + are text files with a .rst extension using the `reStructuredText + `_ markup language, that are then converted to HTML and PDF + using the `Sphinx `_ documentation generator tool. Running + Sphinx with the included configuration requires Python 3.x. + Configuration settings and custom extensions for this conversion are + included in the source distribution, and missing python packages will + be transparently downloaded into a virtual environment via pip. Thus, + if your local system is missing required packages, you need access to + the internet. The translation can be as simple as doing "make html + pdf" in the doc folder. As appropriate, the text files can include + inline mathematical expression or figures (see doc/JPG for examples). Additional PDF files with further details (see doc/PDF for examples) - may also be included. The doc page should also include literature + may also be included. The page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. Citation labels must be unique across all .rst files. - The "Restrictions" section of the doc page should indicate if your + The "Restrictions" section of the page should indicate if your command is only available if LAMMPS is built with the appropriate - USER-MISC or USER-FOO package. See other user package doc files for - examples of how to do this. Please run at least "make html" and "make - spelling" and carefully inspect and proofread the resulting HTML - format doc page before submitting your code. Upon submission of a - pull request, checks for error free completion of the HTML and PDF - build will be performed and also a spell check, a check for correct - anchors and labels, and a check for completeness of references all - styles in their corresponding tables and lists is run. In case the - spell check reports false positives they can be added to the file + FOO package. See other package doc files for examples of + how to do this. Please run at least "make html" and "make spelling" + and carefully inspect and proofread the resulting HTML format doc page + before submitting your code. Upon submission of a pull request, + checks for error free completion of the HTML and PDF build will be + performed and also a spell check, a check for correct anchors and + labels, and a check for completeness of references all styles in their + corresponding tables and lists is run. In case the spell check + reports false positives they can be added to the file doc/utils/sphinx-config/false_positives.txt * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require - large data files as input. See directories under examples/USER for + large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind @@ -234,7 +231,7 @@ packages in the src directory for examples. If you are uncertain, please ask. * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the \*.cpp - source file. See src/USER-EFF/atom_vec_electron.cpp for an example. + source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code registering this variable is added to the constructor of the class. If there is additional functionality (which diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index 556c858735..f065664c6a 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -129,7 +129,7 @@ derived class. See fix.h for details. Typically, only a small fraction of these methods are defined for a particular fix. Setmask is mandatory, as it determines when the fix will be invoked during the timestep. Fixes that perform time -integration (\ *nve*\ , *nvt*\ , *npt*\ ) implement initial_integrate() and +integration (\ *nve*, *nvt*, *npt*\ ) implement initial_integrate() and final_integrate() to perform velocity Verlet updates. Fixes that constrain forces implement post_force(). diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/CG-DNA.pdf similarity index 97% rename from doc/src/PDF/USER-CGDNA.pdf rename to doc/src/PDF/CG-DNA.pdf index 2577875f68..632df1fdff 100644 Binary files a/doc/src/PDF/USER-CGDNA.pdf and b/doc/src/PDF/CG-DNA.pdf differ diff --git a/doc/src/PDF/SMD_LAMMPS_userguide.pdf b/doc/src/PDF/MACHDYN_LAMMPS_userguide.pdf similarity index 100% rename from doc/src/PDF/SMD_LAMMPS_userguide.pdf rename to doc/src/PDF/MACHDYN_LAMMPS_userguide.pdf diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 8fcc37c26e..8b6e5bffdc 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index 042485eb4b..933294a9f7 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -7,13 +7,12 @@ specific set of features. For example, force fields for molecular systems or rigid-body constraints are in packages. You can see the list of all packages and "make" commands to manage them by typing "make package" from within the src directory of the LAMMPS -distribution. The :doc:`Build package ` doc page gives +distribution. The :doc:`Build package ` page gives general info on how to install and un-install packages as part of the LAMMPS build process. .. toctree:: :maxdepth: 1 - Packages_standard - Packages_user + Packages_list Packages_details diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 478bc2c282..b4e50fad75 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1,13 +1,12 @@ Package details =============== -Here is a brief description of all the standard and user packages in -LAMMPS. It lists authors (if applicable) and summarizes the package -contents. It has specific instructions on how to install the package, -including, if necessary, info on how to download or build any extra -library it requires. It also gives links to documentation, example -scripts, and pictures/movies (if available) that illustrate use of the -package. +Here is a brief description of all packages in LAMMPS. It lists authors +(if applicable) and summarizes the package contents. It has specific +instructions on how to install the package, including, if necessary, +info on how to download or build any extra library it requires. It also +gives links to documentation, example scripts, and pictures/movies (if +available) that illustrate use of the package. The majority of packages can be included in a LAMMPS build with a single setting (``-D PGK_=on`` for CMake) or command @@ -27,92 +26,125 @@ page gives those details. .. table_from_list:: :columns: 6 + * :ref:`ADIOS ` * :ref:`ASPHERE ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`BOCS ` * :ref:`BODY ` + * :ref:`BROWNIAN ` + * :ref:`CG-DNA ` + * :ref:`CG-SDK ` * :ref:`CLASS2 ` * :ref:`COLLOID ` + * :ref:`COLVARS ` * :ref:`COMPRESS ` * :ref:`CORESHELL ` + * :ref:`DIELECTRIC ` + * :ref:`DIFFRACTION ` * :ref:`DIPOLE ` + * :ref:`DPD-BASIC ` + * :ref:`DPD-MESO ` + * :ref:`DPD-REACT ` + * :ref:`DPD-SMOOTH ` + * :ref:`DRUDE ` + * :ref:`EFF ` + * :ref:`EXTRA-COMPUTE ` + * :ref:`EXTRA-DUMP ` + * :ref:`EXTRA-FIX ` + * :ref:`EXTRA-MOLECULE ` + * :ref:`EXTRA-PAIR ` + * :ref:`FEP ` * :ref:`GPU ` * :ref:`GRANULAR ` + * :ref:`H5MD ` + * :ref:`INTEL ` + * :ref:`INTERLAYER ` * :ref:`KIM ` * :ref:`KOKKOS ` * :ref:`KSPACE ` + * :ref:`LATBOLTZ ` * :ref:`LATTE ` + * :ref:`MACHDYN ` + * :ref:`MANIFOLD ` * :ref:`MANYBODY ` * :ref:`MC ` + * :ref:`MDI ` + * :ref:`MEAM ` + * :ref:`MESONT ` * :ref:`MESSAGE ` + * :ref:`MGPT ` * :ref:`MISC ` - * :ref:`MLIAP ` + * :ref:`ML-HDNNP ` + * :ref:`ML-IAP ` + * :ref:`ML-PACE ` + * :ref:`ML-QUIP ` + * :ref:`ML-RANN ` + * :ref:`ML-SNAP ` + * :ref:`MOFFF ` * :ref:`MOLECULE ` + * :ref:`MOLFILE ` * :ref:`MPIIO ` * :ref:`MSCG ` + * :ref:`NETCDF ` + * :ref:`OPENMP ` * :ref:`OPT ` + * :ref:`ORIENT ` * :ref:`PERI ` + * :ref:`PHONON ` * :ref:`PLUGIN ` + * :ref:`PLUMED ` * :ref:`POEMS ` + * :ref:`PTM ` * :ref:`PYTHON ` * :ref:`QEQ ` + * :ref:`QMMM ` + * :ref:`QTB ` + * :ref:`REACTION ` + * :ref:`REAXFF ` * :ref:`REPLICA ` * :ref:`RIGID ` + * :ref:`SCAFACOS ` * :ref:`SHOCK ` - * :ref:`SNAP ` + * :ref:`SMTBQ ` + * :ref:`SPH ` * :ref:`SPIN ` * :ref:`SRD ` + * :ref:`TALLY ` + * :ref:`UEF ` * :ref:`VORONOI ` + * :ref:`VTK ` + * :ref:`YAFF ` -.. table_from_list:: - :columns: 6 +---------- - * :ref:`USER-ADIOS ` - * :ref:`USER-ATC ` - * :ref:`USER-AWPMD ` - * :ref:`USER-BOCS ` - * :ref:`USER-BROWNIAN ` - * :ref:`USER-CGDNA ` - * :ref:`USER-CGSDK ` - * :ref:`USER-COLVARS ` - * :ref:`USER-DIELECTRIC ` - * :ref:`USER-DIFFRACTION ` - * :ref:`USER-DPD ` - * :ref:`USER-DRUDE ` - * :ref:`USER-EFF ` - * :ref:`USER-FEP ` - * :ref:`USER-H5MD ` - * :ref:`USER-HDNNP ` - * :ref:`USER-INTEL ` - * :ref:`USER-LB ` - * :ref:`USER-MANIFOLD ` - * :ref:`USER-MDI ` - * :ref:`USER-MEAMC ` - * :ref:`USER-MESODPD ` - * :ref:`USER-MESONT ` - * :ref:`USER-MGPT ` - * :ref:`USER-MISC ` - * :ref:`USER-MOFFF ` - * :ref:`USER-MOLFILE ` - * :ref:`USER-NETCDF ` - * :ref:`USER-OMP ` - * :ref:`USER-PACE ` - * :ref:`USER-PHONON ` - * :ref:`USER-PLUMED ` - * :ref:`USER-PTM ` - * :ref:`USER-QMMM ` - * :ref:`USER-QTB ` - * :ref:`USER-QUIP ` - * :ref:`USER-RANN ` - * :ref:`USER-REACTION ` - * :ref:`USER-REAXC ` - * :ref:`USER-SCAFACOS ` - * :ref:`USER-SDPD ` - * :ref:`USER-SMD ` - * :ref:`USER-SMTBQ ` - * :ref:`USER-SPH ` - * :ref:`USER-TALLY ` - * :ref:`USER-UEF ` - * :ref:`USER-VTK ` - * :ref:`USER-YAFF ` +.. _PKG-ADIOS: + +ADIOS package +------------------ + +**Contents:** + +ADIOS is a high-performance I/O library. This package implements the +:doc:`dump atom/adios `, :doc:`dump custom/adios ` and +:doc:`read_dump ... format adios ` +commands to write and read data using the ADIOS library. + +**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/ADIOS: filenames -> commands +* src/ADIOS/README +* examples/PACKAGES/adios +* https://github.com/ornladios/ADIOS2 +* :doc:`dump atom/adios ` +* :doc:`dump custom/adios ` +* :doc:`read_dump ` ---------- @@ -141,6 +173,94 @@ particle models including ellipsoids, 2d lines, and 3d triangles. ---------- +.. _PKG-ATC: + +ATC package +---------------- + +**Contents:** + +ATC stands for atoms-to-continuum. This package implements a :doc:`fix atc ` command to either couple molecular dynamics with +continuum finite element equations or perform on-the-fly conversion of +atomic information to continuum fields. + +**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. +The ATC package requires that also the `MANYBODY `_ package is installed. + +**Supporting info:** + +* src/ATC: filenames -> commands +* src/ATC/README +* :doc:`fix atc ` +* examples/PACKAGES/atc +* https://www.lammps.org/pictures.html#atc + +---------- + +.. _PKG-AWPMD: + +AWPMD package +------------------ + +**Contents:** + +AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This +package implements an atom, pair, and fix style which allows electrons +to be treated as explicit particles in a classical molecular dynamics +model. + +**Author:** Ilya Valuev (JIHT, Russia). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/AWPMD: filenames -> commands +* src/AWPMD/README +* :doc:`pair_style awpmd/cut ` +* examples/PACKAGES/awpmd + +---------- + +.. _PKG-BOCS: + +BOCS package +----------------- + +**Contents:** + +This package provides :doc:`fix bocs `, a modified version +of :doc:`fix npt ` which includes the pressure correction to +the barostat as outlined in: + +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +accurately describe the structure, pressure, and compressibility of +molecular liquids," J. Chem. Phys. 143, 243148 (2015). + +**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The +Pennsylvania State University) + +**Supporting info:** + +The BOCS package for LAMMPS is part of the BOCS software package: +`https://github.com/noid-group/BOCS `_ + +See the following reference for information about the entire package: + +Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. +"BOCS: Bottom-Up Open-Source Coarse-Graining Software." +J. Phys. Chem. B. 122, 13, 3363-3377 (2018). + +Example inputs are in the examples/PACKAGES/bocs folder. + +---------- + .. _PKG-BODY: BODY package @@ -164,6 +284,84 @@ overview. ---------- +.. _PKG-BROWNIAN: + +BROWNIAN package +--------------------- + +**Contents:** + +This package provides :doc:`fix brownian, fix brownian/sphere, and +fix brownian/asphere ` as well as +:doc:`fix propel/self ` which allow to do Brownian +Dynamics time integration of point, spherical and aspherical particles +and also support self-propelled particles. + +**Authors:** Sam Cameron (University of Bristol), +Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) + +Example inputs are in the examples/PACKAGES/brownian folder. + +---------- + +.. _PKG-CG-DNA: + +CG-DNA package +------------------ + +**Contents:** + +Several pair styles, bond styles, and integration fixes for coarse-grained +modelling of single- and double-stranded DNA and RNA based on the oxDNA and +oxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-type +rigid-body integrators with improved stability. + +**Author:** Oliver Henrich (University of Strathclyde, Glasgow). + +**Install:** + +The CG-DNA package requires that also the `MOLECULE `_ and +`ASPHERE `_ packages are installed. + +**Supporting info:** + +* src/CG-DNA: filenames -> commands +* /src/CG-DNA/README +* :doc:`pair_style oxdna/\* ` +* :doc:`pair_style oxdna2/\* ` +* :doc:`pair_style oxrna2/\* ` +* :doc:`bond_style oxdna/\* ` +* :doc:`bond_style oxdna2/\* ` +* :doc:`bond_style oxrna2/\* ` +* :doc:`fix nve/dotc/langevin ` + +---------- + +.. _PKG-CG-SDK: + +CG-SDK package +------------------ + +**Contents:** + +Several pair styles and an angle style which implement the +coarse-grained SDK model of Shinoda, DeVane, and Klein which enables +simulation of ionic liquids, electrolytes, lipids and charged amino +acids. + +**Author:** Axel Kohlmeyer (Temple U). + +**Supporting info:** + +* src/CG-SDK: filenames -> commands +* src/CG-SDK/README +* :doc:`pair_style lj/sdk/\* ` +* :doc:`angle_style sdk ` +* examples/PACKAGES/cgsdk +* https://www.lammps.org/pictures.html#cg + +---------- + .. _PKG-CLASS2: CLASS2 package @@ -215,6 +413,41 @@ Higdon's group at UIUC. ---------- +.. _PKG-COLVARS: + +COLVARS package +-------------------- + +**Contents:** + +COLVARS stands for collective variables, which can be used to +implement various enhanced sampling methods, including Adaptive +Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and +Restraints. A :doc:`fix colvars ` command is implemented +which wraps a COLVARS library, which implements these methods. +simulations. + +**Authors:** The COLVARS library is written and maintained by +Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) +and Jerome Henin (LISM, CNRS, Marseille, France), originally for +the NAMD MD code, but with portability in mind. Axel Kohlmeyer +(Temple U) provided the interface to LAMMPS. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/COLVARS: filenames -> commands +* `doc/PDF/colvars-refman-lammps.pdf `_ +* src/COLVARS/README +* lib/colvars/README +* :doc:`fix colvars ` +* examples/PACKAGES/colvars + +---------- + .. _PKG-COMPRESS: COMPRESS package @@ -274,6 +507,56 @@ this package. ---------- +.. _PKG-DIELECTRIC: + +DIELECTRIC package +------------------------ + +**Contents:** + +An atom style, multiple pair styles, several fixes, Kspace styles and a +compute for simulating systems using boundary element solvers for +computing the induced charges at the interface between two media with +different dielectric constants. + +**Install:** + +To use this package, also the :ref:`KSPACE ` and +:ref:`EXTRA-PAIR ` packages need to be installed. + +**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) + +**Supporting info:** + +* src/DIELECTRIC: filenames -> commands +* :doc:`compute efield/atom ` +* TODO: add all styles +* examples/PACKAGES/dielectric + +---------- + +.. _PKG-DIFFRACTION: + +DIFFRACTION package +------------------------ + +**Contents:** + +Two computes and a fix for calculating x-ray and electron diffraction +intensities based on kinematic diffraction theory. + +**Author:** Shawn Coleman while at the U Arkansas. + +**Supporting info:** + +* src/DIFFRACTION: filenames -> commands +* :doc:`compute saed ` +* :doc:`compute xrd ` +* :doc:`fix saed/vtk ` +* examples/PACKAGES/diffraction + +---------- + .. _PKG-DIPOLE: DIPOLE package @@ -291,10 +574,309 @@ short-range or long-range interactions. * :doc:`pair_style lj/cut/dipole/cut ` * :doc:`pair_style lj/cut/dipole/long ` * :doc:`pair_style lj/long/dipole/long ` +* :doc: `angle_style dipole ` * examples/dipole ---------- +.. _PKG-DPD-BASIC: + +DPD-BASIC package +-------------------- + +**Contents:** + +Pair styles for the basic dissipative particle dynamics (DPD) method +and DPD thermostatting. + +**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP) + +**Supporting info:** + +* src/DPD-BASIC: filenames -> commands +* :doc:`pair_style dpd ` +* :doc:`pair_style dpd/tstat ` +* :doc:`pair_style dpd/ext ` +* :doc:`pair_style dpd/ext/tstat ` +* examples/PACKAGES/dpd-basic + +---------- + +.. _PKG-DPD-MESO: + +DPD-MESO package +-------------------- + +**Contents:** + +Several extensions of the dissipative particle dynamics (DPD) +method. Specifically, energy-conserving DPD (eDPD) that can model +non-isothermal processes, many-body DPD (mDPD) for simulating +vapor-liquid coexistence, and transport DPD (tDPD) for modeling +advection-diffusion-reaction systems. The equations of motion of these +DPD extensions are integrated through a modified velocity-Verlet (MVV) +algorithm. + +**Author:** Zhen Li (Division of Applied Mathematics, Brown University) + +**Supporting info:** + +* src/DPD-MESO: filenames -> commands +* src/DPD-MESO/README +* :doc:`atom_style edpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` +* :doc:`fix mvv/dpd ` +* examples/PACKAGES/mesodpd +* https://www.lammps.org/movies.html#mesodpd + +---------- + +.. _PKG-DPD-REACT: + +DPD-REACT package +----------------- + +**Contents:** + +DPD stands for dissipative particle dynamics. This package implements +coarse-grained DPD-based models for energetic, reactive molecular +crystalline materials. It includes many pair styles specific to these +systems, including for reactive DPD, where each particle has internal +state for multiple species and a coupled set of chemical reaction ODEs +are integrated each timestep. Highly accurate time integrators for +isothermal, isoenergetic, isobaric and isenthalpic conditions are +included. These enable long timesteps via the Shardlow splitting +algorithm. + +**Authors:** Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John +Brennan (ARL). + +**Supporting info:** + +* src/DPD-REACT: filenames -> commands +* /src/DPD-REACT/README +* :doc:`compute dpd ` +* :doc:`compute dpd/atom ` +* :doc:`fix eos/cv ` +* :doc:`fix eos/table ` +* :doc:`fix eos/table/rx ` +* :doc:`fix shardlow ` +* :doc:`fix rx ` +* :doc:`pair_style table/rx ` +* :doc:`pair_style dpd/fdt ` +* :doc:`pair_style dpd/fdt/energy ` +* :doc:`pair_style exp6/rx ` +* :doc:`pair_style multi/lucy ` +* :doc:`pair_style multi/lucy/rx ` +* examples/PACKAGES/dpd-react + +---------- + +.. _PKG-DPD-SMOOTH: + +DPD-SMOOTH package +------------------ + +**Contents:** + +A pair style for smoothed dissipative particle dynamics (SDPD), which +is an extension of smoothed particle hydrodynamics (SPH) to mesoscale +where thermal fluctuations are important (see the +:ref:`SPH package `). +Also two fixes for moving and rigid body integration of SPH/SDPD particles +(particles of atom_style meso). + +**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic +Sciences, Iran). + +**Supporting info:** + +* src/DPD-SMOOTH: filenames -> commands +* src/DPD-SMOOTH/README +* :doc:`pair_style sdpd/taitwater/isothermal ` +* :doc:`fix meso/move ` +* :doc:`fix rigid/meso ` +* examples/PACKAGES/dpd-smooth + +---------- + +.. _PKG-DRUDE: + +DRUDE package +------------------ + +**Contents:** + +Fixes, pair styles, and a compute to simulate thermalized Drude +oscillators as a model of polarization. See the :doc:`Howto drude ` and :doc:`Howto drude2 ` pages +for an overview of how to use the package. There are auxiliary tools +for using this package in tools/drude. + +**Authors:** Alain Dequidt (U Clermont Auvergne), Julien +Devemy (CNRS), and Agilio Padua (ENS de Lyon). + +**Supporting info:** + +* src/DRUDE: filenames -> commands +* :doc:`Howto drude ` +* :doc:`Howto drude2 ` +* :doc:`Howto polarizable ` +* src/DRUDE/README +* :doc:`fix drude ` +* :doc:`fix drude/transform/\* ` +* :doc:`compute temp/drude ` +* :doc:`pair_style thole ` +* :doc:`pair_style lj/cut/thole/long ` +* examples/PACKAGES/drude +* tools/drude + +---------- + +.. _PKG-EFF: + +EFF package +---------------- + +**Contents:** + +EFF stands for electron force field which allows a classical MD code +to model electrons as particles of variable radius. This package +contains atom, pair, fix and compute styles which implement the eFF as +described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, +JCC, 2010. The eFF potential was first introduced by Su and Goddard, +in 2007. There are auxiliary tools for using this package in +tools/eff; see its README file. + +**Author:** Andres Jaramillo-Botero (CalTech). + +**Supporting info:** + +* src/EFF: filenames -> commands +* src/EFF/README +* :doc:`atom_style electron ` +* :doc:`fix nve/eff ` +* :doc:`fix nvt/eff ` +* :doc:`fix npt/eff ` +* :doc:`fix langevin/eff ` +* :doc:`compute temp/eff ` +* :doc:`pair_style eff/cut ` +* :doc:`pair_style eff/inline ` +* examples/PACKAGES/eff +* tools/eff/README +* tools/eff +* https://www.lammps.org/movies.html#eff + +------------------- + +.. _PKG-EXTRA-COMPUTE: + +EXTRA-COMPUTE package +--------------------- + +**Contents:** + +Additional compute styles that are less commonly used. + +**Supporting info:** + +* src/EXTRA-COMPUTE: filenames -> commands +* :doc:`compute ` + +---------- + +.. _PKG-EXTRA-DUMP: + +EXTRA-DUMP package +------------------ + +**Contents:** + +Additional dump styles that are less commonly used. + +**Supporting info:** + +* src/EXTRA-DUMP: filenames -> commands +* :doc:`dump ` + +---------- + +.. _PKG-EXTRA-FIX: + +EXTRA-FIX package +----------------- + +**Contents:** + +Additional fix styles that are less commonly used. + +**Supporting info:** + +* src/EXTRA-FIX: filenames -> commands +* :doc:`fix ` + +---------- + +.. _PKG-EXTRA-MOLECULE: + +EXTRA-MOLECULE package +---------------------- + +**Contents:** + +Additional bond, angle, dihedral, and improper styles that are less commonly used. + +**Supporting info:** + +* src/EXTRA-MOLECULE: filenames -> commands +* :doc:`molecular styles ` + +---------- + +.. _PKG-EXTRA-PAIR: + +EXTRA-PAIR package +------------------ + +**Contents:** + +Additional pair styles that are less commonly used. + +**Supporting info:** + +* src/EXTRA-PAIR: filenames -> commands +* :doc:`pair_style ` + +---------- + +.. _PKG-FEP: + +FEP package +---------------- + +**Contents:** + +FEP stands for free energy perturbation. This package provides +methods for performing FEP simulations by using a :doc:`fix adapt/fep ` command with soft-core pair potentials, +which have a "soft" in their style name. There are auxiliary tools +for using this package in tools/fep; see its README file. + +**Author:** Agilio Padua (ENS de Lyon) + +**Supporting info:** + +* src/FEP: filenames -> commands +* src/FEP/README +* :doc:`fix adapt/fep ` +* :doc:`compute fep ` +* :doc:`pair_style \*/soft ` +* examples/PACKAGES/fep +* tools/fep/README +* tools/fep + +---------- + .. _PKG-GPU: GPU package @@ -367,6 +949,106 @@ potentials. ---------- +.. _PKG-H5MD: + +H5MD package +----------------- + +**Contents:** + +H5MD stands for HDF5 for MD. `HDF5 `_ is a portable, binary, +self-describing file format, used by many scientific simulations. +H5MD is a format for molecular simulations, built on top of HDF5. +This package implements a :doc:`dump h5md ` command to output +LAMMPS snapshots in this format. + +.. _HDF5: http://www.hdfgroup.org/HDF5 + +To use this package you must have the HDF5 library available on your +system. + +**Author:** Pierre de Buyl (KU Leuven) created both the package and the +H5MD format. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/H5MD: filenames -> commands +* src/H5MD/README +* lib/h5md/README +* :doc:`dump h5md ` + +---------- + +.. _PKG-INTEL: + +INTEL package +------------------ + +**Contents:** + +Dozens of pair, fix, bond, angle, dihedral, improper, and kspace +styles which are optimized for Intel CPUs and KNLs (Knights Landing). +All of them have an "intel" in their style name. The +:doc:`INTEL package ` page gives details of what hardware and +compilers are required on your system, and how to build and use this +package. Its styles can be invoked at run time via the "-sf intel" or +"-suffix intel" :doc:`command-line switches `. Also see +the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`OPENMP ` packages, +which have styles optimized for CPUs and KNLs. + +You need to have an Intel compiler, version 14 or higher to take full +advantage of this package. While compilation with GNU compilers is +supported, performance will be sub-optimal. + +.. note:: + + the INTEL package contains styles that require using the + -restrict flag, when compiling with Intel compilers. + +**Author:** Mike Brown (Intel). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/INTEL: filenames -> commands +* src/INTEL/README +* :doc:`Accelerator packages ` +* :doc:`INTEL package ` +* :doc:`Section 2.6 -sf intel ` +* :doc:`Section 2.6 -pk intel ` +* :doc:`package intel ` +* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, + :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) +* src/INTEL/TEST +* `Benchmarks page `_ of web site + +---------- + +.. _PKG-INTERLAYER: + +INTERLAYER package +------------------ + +**Contents:** + +A collection of pair styles specifically to be used for modeling layered +materials, most commonly graphene sheets (or equivalents). + +**Supporting info:** + +* src/INTERLAYER: filenames -> commands +* :doc:`Pair style ` page +* examples/PACKAGES/interlayer + +---------- + .. _PKG-KIM: KIM package @@ -447,7 +1129,7 @@ style name. The :doc:`KOKKOS package ` page gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf kk" or "-suffix kk" :doc:`command-line switches `. Also see the :ref:`GPU `, :ref:`OPT `, -:ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which +:ref:`INTEL `, and :ref:`OPENMP ` packages, which have styles optimized for CPUs, KNLs, and GPUs. You must have a C++14 compatible compiler to use this package. @@ -521,6 +1203,34 @@ different FFT options for your LAMPMS build. ---------- +.. _PKG-LATBOLTZ: + +LATBOLTZ package +---------------- + +**Contents:** + +Fixes which implement a background Lattice-Boltzmann (LB) fluid, which +can be used to model MD particles influenced by hydrodynamic forces. + +**Authors:** Frances Mackay and Colin Denniston (University of Western +Ontario). + +**Install:** + +The LATBOLTZ package requires that LAMMPS is build in :ref:`MPI parallel mode `. + +**Supporting info:** + +* src/LATBOLTZ: filenames -> commands +* src/LATBOLTZ/README +* :doc:`fix lb/fluid ` +* :doc:`fix lb/momentum ` +* :doc:`fix lb/viscous ` +* examples/PACKAGES/latboltz + +---------- + .. _PKG-LATTE: LATTE package @@ -557,6 +1267,75 @@ This package has :ref:`specific installation instructions ` on the :doc:` ---------- +.. _PKG-MACHDYN: + +MACHDYN package +---------------- + +**Contents:** + +An atom style, fixes, computes, and several pair styles which +implements smoothed Mach dynamics (SMD) for solids, which is a model +related to smoothed particle hydrodynamics (SPH) for liquids (see the +:ref:`SPH package `). + +This package solves solids mechanics problems via a state of the art +stabilized meshless method with hourglass control. It can specify +hydrostatic interactions independently from material strength models, +i.e. pressure and deviatoric stresses are separated. It provides many +material models (Johnson-Cook, plasticity with hardening, +Mie-Grueneisen, Polynomial EOS) and allows new material models to be +added. It implements rigid boundary conditions (walls) which can be +specified as surface geometries from \*.STL files. + +**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed +Dynamics, Ernst Mach Institute, Germany). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/MACHDYN: filenames -> commands +* src/MACHDYN/README +* doc/PDF/MACHDYN_LAMMPS_userguide.pdf +* examples/PACKAGES/machdyn +* https://www.lammps.org/movies.html#smd + +---------- + +.. _PKG-MANIFOLD: + +MANIFOLD package +--------------------- + +**Contents:** + +Several fixes and a "manifold" class which enable simulations of +particles constrained to a manifold (a 2D surface within the 3D +simulation box). This is done by applying the RATTLE constraint +algorithm to formulate single-particle constraint functions +g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) +n = grad(g). + +**Author:** Stefan Paquay (until 2017: Eindhoven University of +Technology (TU/e), The Netherlands; since 2017: Brandeis University, +Waltham, MA, USA) + +**Supporting info:** + +* src/MANIFOLD: filenames -> commands +* src/MANIFOLD/README +* :doc:`Howto manifold ` +* :doc:`fix manifoldforce ` +* :doc:`fix nve/manifold/rattle ` +* :doc:`fix nvt/manifold/rattle ` +* examples/PACKAGES/manifold +* https://www.lammps.org/movies.html#manifold + +---------- + .. _PKG-MANYBODY: MANYBODY package @@ -610,6 +1389,100 @@ bonds, for performing atomic swaps, and performing grand-canonical MC ---------- +.. _PKG-MDI: + +MDI package +---------------- + +**Contents:** + +A LAMMPS command and fix to allow client-server coupling of LAMMPS to +other atomic or molecular simulation codes via the `MolSSI Driver Interface +(MDI) library `_. + +**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com + +**Supporting info:** + +* src/MDI/README +* :doc:`mdi/engine ` +* :doc:`fix mdi/engine ` +* examples/PACKAGES/mdi + +---------- + +.. _PKG-MEAM: + +MEAM package +------------------ + +**Contents:** + +A pair style for the modified embedded atom (MEAM) potential +translated from the Fortran version in the (obsolete) MEAM package +to plain C++. The MEAM fully replaces the MEAM package, which +has been removed from LAMMPS after the 12 December 2018 version. + +**Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg) +based on the Fortran version of Greg Wagner (Northwestern U) while at +Sandia. + +**Supporting info:** + +* src/MEAM: filenames -> commands +* src/MEAM/README +* :doc:`pair_style meam ` +* examples/meam + +---------- + +.. _PKG-MESONT: + +MESONT package +------------------- + +**Contents:** + +MESONT is a LAMMPS package for simulation of nanomechanics of +nanotubes (NTs). The model is based on a coarse-grained representation +of NTs as "flexible cylinders" consisting of a variable number of +segments. Internal interactions within a NT and the van der Waals +interaction between the tubes are described by a mesoscopic force field +designed and parameterized based on the results of atomic-level +molecular dynamics simulations. The description of the force field is +provided in the papers listed below. This package contains two +independent implementations of this model: :doc:`pair_style mesocnt +` is a (minimal) C++ implementation, and :doc:`pair_style +mesont/tpm ` is a more general and feature rich +implementation based on a Fortran library in the ``lib/mesont`` folder. + +**Download of potential files:** + +The potential files for these pair styles are *very* large and thus +are not included in the regular downloaded packages of LAMMPS or the +git repositories. Instead, they will be automatically downloaded +from a web server when the package is installed for the first time. + +**Authors of the *mesont* styles:** + +Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia) + +**Author of the *mesocnt* pair style:** +Philipp Kloza (U Cambridge) + +**Supporting info:** + +* src/MESONT: filenames -> commands +* src/MESONT/README +* :doc:`atom_style mesont ` +* :doc:`pair_style mesont/tpm ` +* :doc:`compute mesont ` +* :doc:`pair_style mesocnt ` +* examples/PACKAGES/mesont +* tools/mesont + +---------- + .. _PKG-MESSAGE: MESSAGE package @@ -636,6 +1509,33 @@ This package has :ref:`specific installation instructions ` on the :doc ---------- +.. _PKG-MGPT: + +MGPT package +----------------- + +**Contents:** + +A pair style which provides a fast implementation of the quantum-based +MGPT multi-ion potentials. The MGPT or model GPT method derives from +first-principles DFT-based generalized pseudopotential theory (GPT) +through a series of systematic approximations valid for mid-period +transition metals with nearly half-filled d bands. The MGPT method +was originally developed by John Moriarty at LLNL. The pair style in +this package calculates forces and energies using an optimized +matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. + +**Authors:** Tomas Oppelstrup and John Moriarty (LLNL). + +**Supporting info:** + +* src/MGPT: filenames -> commands +* src/MGPT/README +* :doc:`pair_style mgpt ` +* examples/PACKAGES/mgpt + +---------- + .. _PKG-MISC: MISC package @@ -643,7 +1543,7 @@ MISC package **Contents:** -A variety of compute, fix, pair, dump styles with specialized +A variety of compute, fix, pair, bond styles with specialized capabilities that don't align with other packages. Do a directory listing, "ls src/MISC", to see the list of commands. @@ -655,23 +1555,57 @@ listing, "ls src/MISC", to see the list of commands. **Supporting info:** * src/MISC: filenames -> commands -* :doc:`compute ti ` -* :doc:`fix evaporate ` -* :doc:`fix orient/fcc ` -* :doc:`fix ttm ` -* :doc:`fix thermal/conductivity ` -* :doc:`fix viscosity ` -* examples/KAPPA -* examples/VISCOSITY -* https://www.lammps.org/pictures.html#ttm -* https://www.lammps.org/movies.html#evaporation +* :doc:`bond_style special ` +* :doc:`compute viscosity/cos ` +* :doc:`fix accelerate/cos ` +* :doc:`fix imd ` +* :doc:`fix ipi ` +* :doc:`pair_style agni ` +* :doc:`pair_style list ` +* :doc:`pair_style srp ` +* :doc:`pair_style tracker ` +* :doc:`fix pair/tracker ` ---------- -.. _PKG-MLIAP: +.. _PKG-ML-HDNNP: -MLIAP package -------------- +ML-HDNNP package +------------------ + +**Contents:** + +A :doc:`pair_style hdnnp ` command which allows to use +high-dimensional neural network potentials (HDNNPs), a form of machine learning +potentials. HDNNPs must be carefully trained prior to their application in a +molecular dynamics simulation. + +.. _n2p2: https://github.com/CompPhysVienna/n2p2 + +To use this package you must have the `n2p2 `_ library installed and +compiled on your system. + +**Author:** Andreas Singraber + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-HDNNP: filenames -> commands +* src/ML-HDNNP/README +* lib/hdnnp/README +* :doc:`pair_style hdnnp ` +* examples/PACKAGES/hdnnp + +---------- + +.. _PKG-ML-IAP: + +ML-IAP package +-------------- **Contents:** @@ -679,9 +1613,9 @@ A general interface for machine-learning interatomic potentials, including PyTor **Install:** -To use this package, also the :ref:`SNAP package ` package needs +To use this package, also the :ref:`ML-SNAP ` package needs to be installed. To make the *mliappy* model available, also the -:ref:`PYTHON package ` package needs to be installed, the version +:ref:`PYTHON ` package needs to be installed, the version of Python must be 3.6 or later, and the `cython `_ software must be installed. @@ -689,8 +1623,8 @@ must be installed. **Supporting info:** -* src/MLIAP: filenames -> commands -* src/MLIAP/README +* src/ML-IAP: filenames -> commands +* src/ML-IAP/README.md * :doc:`pair_style mliap ` * :doc:`compute_style mliap ` * examples/mliap (see README) @@ -703,6 +1637,163 @@ therefore also needs to be installed to run those examples. ---------- +.. _PKG-ML-PACE: + +ML-PACE package +------------------- + +**Contents:** + +A pair style for the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. The ML-PACE +package provides an efficient implementation for running simulations +with ACE potentials. + +**Authors:** + +This package was written by Yury Lysogorskiy^1, +Cas van der Oord^2, Anton Bochkarev^1, +Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, +Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. + + ^1: Ruhr-University Bochum, Bochum, Germany + + ^2: University of Cambridge, Cambridge, United Kingdom + + ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + + ^4: University of British Columbia, Vancouver, BC, Canada + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-PACE: filenames -> commands +* :doc:`pair_style pace ` +* examples/PACKAGES/pace + +---------- + +.. _PKG-ML-QUIP: + +ML-QUIP package +----------------- + +**Contents:** + +A :doc:`pair_style quip ` command which wraps the `QUIP +libAtoms library `_, which includes a variety of interatomic +potentials, including Gaussian Approximation Potential (GAP) models +developed by the Cambridge University group. + +.. _quip: https://github.com/libAtoms/QUIP + +To use this package you must have the QUIP libAtoms library available +on your system. + +**Author:** Albert Bartok (Cambridge University) + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-QUIP: filenames -> commands +* src/ML-QUIP/README +* :doc:`pair_style quip ` +* examples/PACKAGES/quip + +---------- + +.. _PKG-ML-RANN: + +ML-RANN package +----------------- + +**Contents:** + +A pair style for using rapid atomistic neural network (RANN) potentials. +These neural network potentials work by first generating a series of symmetry +functions from the neighbor list and then using these values as the input layer +of a neural network. + +**Authors:** + +This package was written by Christopher Barrett +with contributions by Doyl Dickel, Mississippi State University. + +**Supporting info:** + +* src/ML-RANN: filenames -> commands +* :doc:`pair_style rann ` +* examples/PACKAGES/rann + +---------- + +.. _PKG-ML-SNAP: + +ML-SNAP package +--------------- + +**Contents:** + +A pair style for the spectral neighbor analysis potential (SNAP). +SNAP is methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. Also several +computes which analyze attributes of the potential. + +**Author:** Aidan Thompson (Sandia). + +**Supporting info:** + +* src/ML-SNAP: filenames -> commands +* :doc:`pair_style snap ` +* :doc:`compute sna/atom ` +* :doc:`compute snad/atom ` +* :doc:`compute snav/atom ` +* examples/snap + +---------- + +.. _PKG-MOFFF: + +MOFFF package +------------------ + +**Contents:** + +Pair, angle and improper styles needed to employ the MOF-FF +force field by Schmid and coworkers with LAMMPS. +MOF-FF is a first principles derived force field with the primary aim +to simulate MOFs and related porous framework materials, using spherical +Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B +2013, 250, 1128-1141. +For the usage of MOF-FF see the example in the example directory as +well as the `MOF+ `_ website. + +.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF + +**Author:** Hendrik Heenen (Technical U of Munich), +Rochus Schmid (Ruhr-University Bochum). + +**Supporting info:** + +* src/MOFFF: filenames -> commands +* src/MOFFF/README +* :doc:`pair_style buck6d/coul/gauss ` +* :doc:`angle_style class2 ` +* :doc:`angle_style cosine/buck6d ` +* :doc:`improper_style inversion/harmonic ` +* examples/PACKAGES/mofff + +---------- + .. _PKG-MOLECULE: MOLECULE package @@ -735,6 +1826,48 @@ force fields, and a TIP4P water model. ---------- +.. _PKG-MOLFILE: + +MOLFILE package +-------------------- + +**Contents:** + +A :doc:`dump molfile ` command which uses molfile plugins +that are bundled with the `VMD `_ +molecular visualization and analysis program, to enable LAMMPS to dump +snapshots in formats compatible with various molecular simulation +tools. + +To use this package you must have the desired VMD plugins available on +your system. + +Note that this package only provides the interface code, not the +plugins themselves, which will be accessed when requesting a specific +plugin via the :doc:`dump molfile ` command. Plugins can +be obtained from a VMD installation which has to match the platform +that you are using to compile LAMMPS for. By adding plugins to VMD, +support for new file formats can be added to LAMMPS (or VMD or other +programs that use them) without having to re-compile the application +itself. More information about the VMD molfile plugins can be found +at +`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile `_. + +**Author:** Axel Kohlmeyer (Temple U). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/MOLFILE: filenames -> commands +* src/MOLFILE/README +* lib/molfile/README +* :doc:`dump molfile ` + +---------- + .. _PKG-MPIIO: MPIIO package @@ -747,6 +1880,10 @@ MPIIO library. It adds :doc:`dump styles ` with a "mpiio" in their style name. Restart files with an ".mpiio" suffix are also written and read in parallel. +**Install:** + +The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode `. + **Supporting info:** * src/MPIIO: filenames -> commands @@ -757,7 +1894,7 @@ written and read in parallel. ---------- -.. _PKG-mscg: +.. _PKG-MSCG: MSCG package ------------ @@ -789,6 +1926,101 @@ This package has :ref:`specific installation instructions ` on the :doc:`B ---------- +.. _PKG-NETCDF: + +NETCDF package +------------------- + +**Contents:** + +Dump styles for writing NetCDF formatted dump files. NetCDF is a +portable, binary, self-describing file format developed on top of +HDF5. The file contents follow the AMBER NetCDF trajectory conventions +(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. + +To use this package you must have the NetCDF library available on your +system. + +Note that NetCDF files can be directly visualized with the following +tools: + +* `Ovito `_ (Ovito supports the AMBER convention and the extensions mentioned above) +* `VMD `_ + +.. _ovito: http://www.ovito.org + +.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ + +**Author:** Lars Pastewka (Karlsruhe Institute of Technology). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/NETCDF: filenames -> commands +* src/NETCDF/README +* lib/netcdf/README +* :doc:`dump netcdf ` + +---------- + +.. _PKG-OPENMP: + +OPENMP package +---------------- + +**Contents:** + +Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and +kspace styles which are altered to enable threading on many-core CPUs +via OpenMP directives. All of them have an "omp" in their style name. +The :doc:`OPENMP package ` page gives details of what hardware +and compilers are required on your system, and how to build and use +this package. Its styles can be invoked at run time via the "-sf omp" +or "-suffix omp" :doc:`command-line switches `. Also see +the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`INTEL ` +packages, which have styles optimized for CPUs. + +**Author:** Axel Kohlmeyer (Temple U). + +.. note:: + + To enable multi-threading support the compile flag "-fopenmp" + and the link flag "-fopenmp" (for GNU compilers, you have to look up + the equivalent flags for other compilers) must be used to build LAMMPS. + When using Intel compilers, also the "-restrict" flag is required. + The OPENMP package can be compiled without enabling OpenMP; then + all code will be compiled as serial and the only improvement over the + regular styles are some data access optimization. These flags should + be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. + See src/MAKE/OPTIONS/Makefile.omp for an example. + +Once you have an appropriate Makefile.machine, you can +install/un-install the package and build LAMMPS in the usual manner: + +**Install:** + +This package has :ref:`specific installation instructions ` on +the :doc:`Build extras ` page. + +**Supporting info:** + +* src/OPENMP: filenames -> commands +* src/OPENMP/README +* :doc:`Accelerator packages ` +* :doc:`OPENMP package ` +* :doc:`Command line option -suffix/-sf omp ` +* :doc:`Command line option -package/-pk omp ` +* :doc:`package omp ` +* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, + :doc:`pair `, :doc:`bond, angle, dihedral, improper `, + :doc:`kspace `) for styles followed by (o) +* `Benchmarks page `_ of web site + +---------- + .. _PKG-OPT: OPT package @@ -802,7 +2034,7 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in their style name. The :doc:`OPT package ` page gives details of how to build and use this package. Its styles can be invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches `. See also the :ref:`KOKKOS `, -:ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which +:ref:`INTEL `, and :ref:`OPENMP ` packages, which have styles optimized for CPU performance. **Authors:** James Fischer (High Performance Technologies), David Richie, @@ -821,6 +2053,23 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * Search the :doc:`pair style ` page for styles followed by (t) * `Benchmarks page `_ of web site +.. _PKG-ORIENT: + +ORIENT package +-------------- + +**Contents:** + +A few fixes that apply orientation dependent forces for studying +grain boundary migration. + +**Supporting info:** + +* src/ORIENT: filenames -> commands +* :doc:`fix orient/bcc ` +* :doc:`fix orient/fcc ` +* :doc:`fix orient/eco ` + ---------- .. _PKG-PERI: @@ -854,6 +2103,40 @@ Foster (UTSA). ---------- +.. _PKG-PHONON: + +PHONON package +------------------- + +**Contents:** + +A :doc:`fix phonon ` command that calculates dynamical +matrices, which can then be used to compute phonon dispersion +relations, directly from molecular dynamics simulations. +And a :doc:`dynamical_matrix ` as well as a +:doc:`third_order ` command to compute the dynamical matrix +and third order tensor from finite differences. + +**Install:** + +The PHONON package requires that also the `KSPACE `_ +package is installed. + + +**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" +and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" + +**Supporting info:** + +* src/PHONON: filenames -> commands +* src/PHONON/README +* :doc:`fix phonon ` +* :doc:`dynamical_matrix ` +* :doc:`third_order ` +* examples/PACKAGES/phonon + +---------- + .. _PKG-PLUGIN: PLUGIN package @@ -876,6 +2159,35 @@ having to recompile and relink LAMMPS. ---------- +.. _PKG-PLUMED: + +PLUMED package +------------------- + +**Contents:** + +The fix plumed command allows you to use the PLUMED free energy plugin +for molecular dynamics to analyze and bias your LAMMPS trajectory on +the fly. The PLUMED library is called from within the LAMMPS input +script by using the :doc:`fix plumed ` command. + +**Authors:** The `PLUMED library `_ is written +and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni, +and Gareth Tribello. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/PLUMED/README +* lib/plumed/README +* :doc:`fix plumed ` +* examples/PACKAGES/plumed + +---------- + .. _PKG-POEMS: POEMS package @@ -905,6 +2217,28 @@ This package has :ref:`specific installation instructions ` on the :doc:` ---------- +.. _PKG-PTM: + +PTM package +---------------- + +**Contents:** + +A :doc:`compute ptm/atom ` command that calculates +local structure characterization using the Polyhedral Template +Matching methodology. + +**Author:** Peter Mahler Larsen (MIT). + +**Supporting info:** + +* src/PTM: filenames not starting with ptm\_ -> commands +* src/PTM: filenames starting with ptm\_ -> supporting code +* src/PTM/LICENSE +* :doc:`compute ptm/atom ` + +---------- + .. _PKG-PYTHON: PYTHON package @@ -958,6 +2292,135 @@ part of their formulation. ---------- +.. _PKG-QMMM: + +QMMM package +----------------- + +**Contents:** + +A :doc:`fix qmmm ` command which allows LAMMPS to be used as +the MM code in a QM/MM simulation. This is currently only available +in combination with the `Quantum ESPRESSO `_ package. + +.. _espresso: http://www.quantum-espresso.org + +To use this package you must have Quantum ESPRESSO (QE) available on +your system and include its coupling library in the compilation and +then compile LAMMPS as a library. For QM/MM calculations you then +build a custom binary with MPI support, that sets up 3 partitions with +MPI sub-communicators (for inter- and intra-partition communication) +and then calls the corresponding library interfaces on each partition +(2x LAMMPS and 1x QE). + +The current implementation supports an ONIOM style mechanical coupling +and a multi-pole based electrostatic coupling to the Quantum ESPRESSO +plane wave DFT package. The QM/MM interface has been written in a +manner that coupling to other QM codes should be possible without +changes to LAMMPS itself. + +**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy) + +**Install:** + +This package has :ref:`specific installation instructions ` +on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/QMMM: filenames -> commands +* src/QMMM/README +* lib/qmmm/README +* :doc:`fix phonon ` +* lib/qmmm/example-ec/README +* lib/qmmm/example-mc/README + +---------- + +.. _PKG-QTB: + +QTB package +---------------- + +**Contents:** + +Two fixes which provide a self-consistent quantum treatment of +vibrational modes in a classical molecular dynamics simulation. By +coupling the MD simulation to a colored thermostat, it introduces zero +point energy into the system, altering the energy power spectrum and +the heat capacity to account for their quantum nature. This is useful +when modeling systems at temperatures lower than their classical +limits or when temperatures ramp across the classical limits in a +simulation. + +**Author:** Yuan Shen (Stanford U). + +**Supporting info:** + +* src/QTB: filenames -> commands +* src/QTB/README +* :doc:`fix qtb ` +* :doc:`fix qbmsst ` +* examples/PACKAGES/qtb + +---------- + +.. _PKG-REACTION: + +REACTION package +--------------------- + +**Contents:** + +This package allows for complex bond topology changes (reactions) +during a running MD simulation, when using classical force fields. +Topology changes are defined in pre- and post-reaction molecule +templates and can include creation and deletion of bonds, angles, +dihedrals, impropers, atom types, bond types, angle types, dihedral +types, improper types, and/or atomic charges. Other options currently +available include reaction constraints (e.g. angle and Arrhenius +constraints), deletion of reaction byproducts or other small +molecules, and chiral-sensitive reactions. + +**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. + +**Supporting info:** + +* src/REACTION: filenames -> commands +* src/REACTION/README +* :doc:`fix bond/react ` +* examples/PACKAGES/reaction +* `2017 LAMMPS Workshop `_ +* `2019 LAMMPS Workshop `_ +* reacter.org + +---------- + +.. _PKG-REAXFF: + +REAXFF package +------------------ + +**Contents:** + +A pair style which implements the ReaxFF potential in C/C++. ReaxFF +is a universal reactive force field. See the src/REAXFF/README file +for more info on differences between the two packages. Also two fixes +for monitoring molecules as bonds are created and destroyed. + +**Author:** Hasan Metin Aktulga (MSU) while at Purdue University. + +**Supporting info:** + +* src/REAXFF: filenames -> commands +* src/REAXFF/README +* :doc:`pair_style reaxff ` +* :doc:`fix reaxff/bonds ` +* :doc:`fix reaxff/species ` +* examples/reaxff + +---------- + .. _PKG-REPLICA: REPLICA package @@ -982,10 +2445,13 @@ another set. * :doc:`prd ` * :doc:`tad ` * :doc:`temper `, +* :doc:`temper/npt `, +* :doc:`temper/grem `, * :doc:`run_style verlet/split ` * examples/neb * examples/prd * examples/tad +* examples/PACKAGES/grem ---------- @@ -1016,6 +2482,42 @@ Also several computes which calculate properties of rigid bodies. ---------- +.. _PKG-SCAFACOS: + +SCAFACOS package +--------------------- + +**Contents:** + +A KSpace style which wraps the `ScaFaCoS Coulomb solver library `_ to compute long-range Coulombic +interactions. + +To use this package you must have the ScaFaCoS library available on +your system. + +**Author:** Rene Halver (JSC) wrote the scafacos LAMMPS command. + +ScaFaCoS itself was developed by a consortium of German research +facilities with a BMBF (German Ministry of Science and Education) +funded project in 2009-2012. Participants of the consortium were the +Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as +the Forschungszentrum Juelich. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. +The SCAFACOS package requires that LAMMPS is build in :ref:`MPI parallel mode `. + +**Supporting info:** + +* src/SCAFACOS: filenames -> commands +* src/SCAFACOS/README +* :doc:`kspace_style scafacos ` +* :doc:`kspace_modify ` +* examples/PACKAGES/scafacos + +---------- + .. _PKG-SHOCK: SHOCK package @@ -1038,28 +2540,60 @@ a material. ---------- -.. _PKG-SNAP: +.. _PKG-SMTBQ: -SNAP package ------------- +SMTBQ package +------------------ **Contents:** -A pair style for the spectral neighbor analysis potential (SNAP). -SNAP is methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. Also several -computes which analyze attributes of the potential. +A pair style which implements a Second Moment Tight Binding model with +QEq charge equilibration (SMTBQ) potential for the description of +ionocovalent bonds in oxides. -**Author:** Aidan Thompson (Sandia). +**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert +Tetot (LAAS-CNRS, France). **Supporting info:** -* src/SNAP: filenames -> commands -* :doc:`pair_style snap ` -* :doc:`compute sna/atom ` -* :doc:`compute snad/atom ` -* :doc:`compute snav/atom ` -* examples/snap +* src/SMTBQ: filenames -> commands +* src/SMTBQ/README +* :doc:`pair_style smtbq ` +* examples/PACKAGES/smtbq + +---------- + +.. _PKG-SPH: + +SPH package +---------------- + +**Contents:** + +An atom style, fixes, computes, and several pair styles which +implements smoothed particle hydrodynamics (SPH) for liquids. See the +related :ref:`MACHDYN package ` package for smooth Mach dynamics +(SMD) for solids. + +This package contains ideal gas, Lennard-Jones equation of states, +Tait, and full support for complete (i.e. internal-energy dependent) +equations of state. It allows for plain or Monaghans XSPH integration +of the equations of motion. It has options for density continuity or +density summation to propagate the density field. It has +:doc:`set ` command options to set the internal energy and density +of particles from the input script and allows the same quantities to +be output with thermodynamic output or to dump files via the :doc:`compute property/atom ` command. + +**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed +Dynamics, Ernst Mach Institute, Germany). + +**Supporting info:** + +* src/SPH: filenames -> commands +* src/SPH/README +* doc/PDF/SPH_LAMMPS_userguide.pdf +* examples/PACKAGES/sph +* https://www.lammps.org/movies.html#sph ---------- @@ -1119,6 +2653,54 @@ colloidal particles. ---------- +.. _PKG-TALLY: + +TALLY package +------------------ + +**Contents:** + +Several compute styles that can be called when pairwise interactions +are calculated to tally information (forces, heat flux, energy, +stress, etc) about individual interactions. + +**Author:** Axel Kohlmeyer (Temple U). + +**Supporting info:** + +* src/TALLY: filenames -> commands +* src/TALLY/README +* :doc:`compute \*/tally ` +* examples/PACKAGES/tally + +---------- + +.. _PKG-UEF: + +UEF package +---------------- + +**Contents:** + +A fix style for the integration of the equations of motion under +extensional flow with proper boundary conditions, as well as several +supporting compute styles and an output option. + +**Author:** David Nicholson (MIT). + +**Supporting info:** + +* src/UEF: filenames -> commands +* src/UEF/README +* :doc:`fix nvt/uef ` +* :doc:`fix npt/uef ` +* :doc:`compute pressure/uef ` +* :doc:`compute temp/uef ` +* :doc:`dump cfg/uef ` +* examples/uef + +---------- + .. _PKG-VORONOI: VORONOI package @@ -1154,1439 +2736,9 @@ This package has :ref:`specific installation instructions ` on the :doc ---------- -.. _PKG-USER-ADIOS: +.. _PKG-VTK: -USER-ADIOS package ------------------- - -**Contents:** - -ADIOS is a high-performance I/O library. This package implements the -:doc:`dump atom/adios `, :doc:`dump custom/adios ` and -:doc:`read_dump ... format adios ` -commands to write and read data using the ADIOS library. - -**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-ADIOS: filenames -> commands -* src/USER-ADIOS/README -* examples/USER/adios -* https://github.com/ornladios/ADIOS2 -* :doc:`dump atom/adios ` -* :doc:`dump custom/adios ` -* :doc:`read_dump ` - ----------- - -.. _PKG-USER-ATC: - -USER-ATC package ----------------- - -**Contents:** - -ATC stands for atoms-to-continuum. This package implements a :doc:`fix atc ` command to either couple molecular dynamics with -continuum finite element equations or perform on-the-fly conversion of -atomic information to continuum fields. - -**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-ATC: filenames -> commands -* src/USER-ATC/README -* :doc:`fix atc ` -* examples/USER/atc -* https://www.lammps.org/pictures.html#atc - ----------- - -.. _PKG-USER-AWPMD: - -USER-AWPMD package ------------------- - -**Contents:** - -AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This -package implements an atom, pair, and fix style which allows electrons -to be treated as explicit particles in a classical molecular dynamics -model. - -**Author:** Ilya Valuev (JIHT, Russia). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-AWPMD: filenames -> commands -* src/USER-AWPMD/README -* :doc:`pair_style awpmd/cut ` -* examples/USER/awpmd - ----------- - -.. _PKG-USER-BOCS: - -USER-BOCS package ------------------ - -**Contents:** - -This package provides :doc:`fix bocs `, a modified version -of :doc:`fix npt ` which includes the pressure correction to -the barostat as outlined in: - -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that -accurately describe the structure, pressure, and compressibility of -molecular liquids," J. Chem. Phys. 143, 243148 (2015). - -**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The -Pennsylvania State University) - -**Supporting info:** - -The USER-BOCS user package for LAMMPS is part of the BOCS software package: -`https://github.com/noid-group/BOCS `_ - -See the following reference for information about the entire package: - -Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. -"BOCS: Bottom-Up Open-Source Coarse-Graining Software." -J. Phys. Chem. B. 122, 13, 3363-3377 (2018). - -Example inputs are in the examples/USER/bocs folder. - ----------- - -.. _PKG-USER-BROWNIAN: - -USER-BROWNIAN package ---------------------- - -**Contents:** - -This package provides :doc:`fix brownian, fix brownian/sphere, and -fix brownian/asphere ` as well as -:doc:`fix propel/self ` which allow to do Brownian -Dynamics time integration of point, spherical and aspherical particles -and also support self-propelled particles. - -**Authors:** Sam Cameron (University of Bristol), -Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) - -Example inputs are in the examples/USER/brownian folder. - ----------- - -.. _PKG-USER-CGDNA: - -USER-CGDNA package ------------------- - -**Contents:** - -Several pair styles, bond styles, and integration fixes for coarse-grained -modelling of single- and double-stranded DNA and RNA based on the oxDNA and -oxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-type -rigid-body integrators with improved stability. - -**Author:** Oliver Henrich (University of Strathclyde, Glasgow). - -**Supporting info:** - -* src/USER-CGDNA: filenames -> commands -* /src/USER-CGDNA/README -* :doc:`pair_style oxdna/\* ` -* :doc:`pair_style oxdna2/\* ` -* :doc:`pair_style oxrna2/\* ` -* :doc:`bond_style oxdna/\* ` -* :doc:`bond_style oxdna2/\* ` -* :doc:`bond_style oxrna2/\* ` -* :doc:`fix nve/dotc/langevin ` - ----------- - -.. _PKG-USER-CGSDK: - -USER-CGSDK package ------------------- - -**Contents:** - -Several pair styles and an angle style which implement the -coarse-grained SDK model of Shinoda, DeVane, and Klein which enables -simulation of ionic liquids, electrolytes, lipids and charged amino -acids. - -**Author:** Axel Kohlmeyer (Temple U). - -**Supporting info:** - -* src/USER-CGSDK: filenames -> commands -* src/USER-CGSDK/README -* :doc:`pair_style lj/sdk/\* ` -* :doc:`angle_style sdk ` -* examples/USER/cgsdk -* https://www.lammps.org/pictures.html#cg - ----------- - -.. _PKG-USER-COLVARS: - -USER-COLVARS package --------------------- - -**Contents:** - -COLVARS stands for collective variables, which can be used to -implement various enhanced sampling methods, including Adaptive -Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and -Restraints. A :doc:`fix colvars ` command is implemented -which wraps a COLVARS library, which implements these methods. -simulations. - -**Authors:** The COLVARS library is written and maintained by -Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) -and Jerome Henin (LISM, CNRS, Marseille, France), originally for -the NAMD MD code, but with portability in mind. Axel Kohlmeyer -(Temple U) provided the interface to LAMMPS. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-COLVARS: filenames -> commands -* `doc/PDF/colvars-refman-lammps.pdf `_ -* src/USER-COLVARS/README -* lib/colvars/README -* :doc:`fix colvars ` -* examples/USER/colvars - ----------- - -.. _PKG-USER-DIELECTRIC: - -USER-DIELECTRIC package ------------------------- - -**Contents:** - -An atom style, multiple pair styles, several fixes, Kspace styles and a -compute for simulating systems using boundary element solvers for -computing the induced charges at the interface between two media with -different dielectric constants. - -**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) - -**Supporting info:** - -* src/USER-DIELECTRIC: filenames -> commands -* :doc:`compute efield/atom ` -* TODO: add all styles -* examples/USER/dielectric - ----------- - -.. _PKG-USER-DIFFRACTION: - -USER-DIFFRACTION package ------------------------- - -**Contents:** - -Two computes and a fix for calculating x-ray and electron diffraction -intensities based on kinematic diffraction theory. - -**Author:** Shawn Coleman while at the U Arkansas. - -**Supporting info:** - -* src/USER-DIFFRACTION: filenames -> commands -* :doc:`compute saed ` -* :doc:`compute xrd ` -* :doc:`fix saed/vtk ` -* examples/USER/diffraction - ----------- - -.. _PKG-USER-DPD: - -USER-DPD package ----------------- - -**Contents:** - -DPD stands for dissipative particle dynamics. This package implements -coarse-grained DPD-based models for energetic, reactive molecular -crystalline materials. It includes many pair styles specific to these -systems, including for reactive DPD, where each particle has internal -state for multiple species and a coupled set of chemical reaction ODEs -are integrated each timestep. Highly accurate time integrators for -isothermal, isoenergetic, isobaric and isenthalpic conditions are -included. These enable long timesteps via the Shardlow splitting -algorithm. - -**Authors:** Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John -Brennan (ARL). - -**Supporting info:** - -* src/USER-DPD: filenames -> commands -* /src/USER-DPD/README -* :doc:`compute dpd ` -* :doc:`compute dpd/atom ` -* :doc:`fix eos/cv ` -* :doc:`fix eos/table ` -* :doc:`fix eos/table/rx ` -* :doc:`fix shardlow ` -* :doc:`fix rx ` -* :doc:`pair_style table/rx ` -* :doc:`pair_style dpd/fdt ` -* :doc:`pair_style dpd/fdt/energy ` -* :doc:`pair_style exp6/rx ` -* :doc:`pair_style multi/lucy ` -* :doc:`pair_style multi/lucy/rx ` -* examples/USER/dpd - ----------- - -.. _PKG-USER-DRUDE: - -USER-DRUDE package ------------------- - -**Contents:** - -Fixes, pair styles, and a compute to simulate thermalized Drude -oscillators as a model of polarization. See the :doc:`Howto drude ` and :doc:`Howto drude2 ` pages -for an overview of how to use the package. There are auxiliary tools -for using this package in tools/drude. - -**Authors:** Alain Dequidt (U Clermont Auvergne), Julien -Devemy (CNRS), and Agilio Padua (ENS de Lyon). - -**Supporting info:** - -* src/USER-DRUDE: filenames -> commands -* :doc:`Howto drude ` -* :doc:`Howto drude2 ` -* :doc:`Howto polarizable ` -* src/USER-DRUDE/README -* :doc:`fix drude ` -* :doc:`fix drude/transform/\* ` -* :doc:`compute temp/drude ` -* :doc:`pair_style thole ` -* :doc:`pair_style lj/cut/thole/long ` -* examples/USER/drude -* tools/drude - ----------- - -.. _PKG-USER-EFF: - -USER-EFF package ----------------- - -**Contents:** - -EFF stands for electron force field which allows a classical MD code -to model electrons as particles of variable radius. This package -contains atom, pair, fix and compute styles which implement the eFF as -described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, -JCC, 2010. The eFF potential was first introduced by Su and Goddard, -in 2007. There are auxiliary tools for using this package in -tools/eff; see its README file. - -**Author:** Andres Jaramillo-Botero (CalTech). - -**Supporting info:** - -* src/USER-EFF: filenames -> commands -* src/USER-EFF/README -* :doc:`atom_style electron ` -* :doc:`fix nve/eff ` -* :doc:`fix nvt/eff ` -* :doc:`fix npt/eff ` -* :doc:`fix langevin/eff ` -* :doc:`compute temp/eff ` -* :doc:`pair_style eff/cut ` -* :doc:`pair_style eff/inline ` -* examples/USER/eff -* tools/eff/README -* tools/eff -* https://www.lammps.org/movies.html#eff - ----------- - -.. _PKG-USER-FEP: - -USER-FEP package ----------------- - -**Contents:** - -FEP stands for free energy perturbation. This package provides -methods for performing FEP simulations by using a :doc:`fix adapt/fep ` command with soft-core pair potentials, -which have a "soft" in their style name. There are auxiliary tools -for using this package in tools/fep; see its README file. - -**Author:** Agilio Padua (ENS de Lyon) - -**Supporting info:** - -* src/USER-FEP: filenames -> commands -* src/USER-FEP/README -* :doc:`fix adapt/fep ` -* :doc:`compute fep ` -* :doc:`pair_style \*/soft ` -* examples/USER/fep -* tools/fep/README -* tools/fep - ----------- - -.. _PKG-USER-H5MD: - -USER-H5MD package ------------------ - -**Contents:** - -H5MD stands for HDF5 for MD. `HDF5 `_ is a portable, binary, -self-describing file format, used by many scientific simulations. -H5MD is a format for molecular simulations, built on top of HDF5. -This package implements a :doc:`dump h5md ` command to output -LAMMPS snapshots in this format. - -.. _HDF5: http://www.hdfgroup.org/HDF5 - -To use this package you must have the HDF5 library available on your -system. - -**Author:** Pierre de Buyl (KU Leuven) created both the package and the -H5MD format. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-H5MD: filenames -> commands -* src/USER-H5MD/README -* lib/h5md/README -* :doc:`dump h5md ` - ----------- - -.. _PKG-USER-HDNNP: - -USER-HDNNP package ------------------- - -**Contents:** - -A :doc:`pair_style hdnnp ` command which allows to use -high-dimensional neural network potentials (HDNNPs), a form of machine learning -potentials. HDNNPs must be carefully trained prior to their application in a -molecular dynamics simulation. - -.. _n2p2: https://github.com/CompPhysVienna/n2p2 - -To use this package you must have the `n2p2 `_ library installed and -compiled on your system. - -**Author:** Andreas Singraber - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-HDNNP: filenames -> commands -* src/USER-HDNNP/README -* lib/hdnnp/README -* :doc:`pair_style hdnnp ` -* examples/USER/hdnnp - ----------- - -.. _PKG-USER-INTEL: - -USER-INTEL package ------------------- - -**Contents:** - -Dozens of pair, fix, bond, angle, dihedral, improper, and kspace -styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. The -:doc:`USER-INTEL package ` page gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf intel" or -"-suffix intel" :doc:`command-line switches `. Also see -the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`USER-OMP ` packages, -which have styles optimized for CPUs and KNLs. - -You need to have an Intel compiler, version 14 or higher to take full -advantage of this package. While compilation with GNU compilers is -supported, performance will be sub-optimal. - -.. note:: - - the USER-INTEL package contains styles that require using the - -restrict flag, when compiling with Intel compilers. - -**Author:** Mike Brown (Intel). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-INTEL: filenames -> commands -* src/USER-INTEL/README -* :doc:`Accelerator packages ` -* :doc:`USER-INTEL package ` -* :doc:`Section 2.6 -sf intel ` -* :doc:`Section 2.6 -pk intel ` -* :doc:`package intel ` -* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, - :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) -* src/USER-INTEL/TEST -* `Benchmarks page `_ of web site - ----------- - -.. _PKG-USER-LB: - -USER-LB package ---------------- - -**Contents:** - -Fixes which implement a background Lattice-Boltzmann (LB) fluid, which -can be used to model MD particles influenced by hydrodynamic forces. - -**Authors:** Frances Mackay and Colin Denniston (University of Western -Ontario). - -**Supporting info:** - -* src/USER-LB: filenames -> commands -* src/USER-LB/README -* :doc:`fix lb/fluid ` -* :doc:`fix lb/momentum ` -* :doc:`fix lb/viscous ` -* examples/USER/lb - ----------- - -.. _PKG-USER-MGPT: - -USER-MGPT package ------------------ - -**Contents:** - -A pair style which provides a fast implementation of the quantum-based -MGPT multi-ion potentials. The MGPT or model GPT method derives from -first-principles DFT-based generalized pseudopotential theory (GPT) -through a series of systematic approximations valid for mid-period -transition metals with nearly half-filled d bands. The MGPT method -was originally developed by John Moriarty at LLNL. The pair style in -this package calculates forces and energies using an optimized -matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. - -**Authors:** Tomas Oppelstrup and John Moriarty (LLNL). - -**Supporting info:** - -* src/USER-MGPT: filenames -> commands -* src/USER-MGPT/README -* :doc:`pair_style mgpt ` -* examples/USER/mgpt - ----------- - -.. _PKG-USER-MISC: - -USER-MISC package ------------------ - -**Contents:** - -A potpourri of (mostly) unrelated features contributed to LAMMPS by -users. Each feature is a single fix, compute, pair, bond, angle, -dihedral, improper, or command style. - -**Authors:** The author for each style in the package is listed in the -src/USER-MISC/README file. - -**Supporting info:** - -* src/USER-MISC: filenames -> commands -* src/USER-MISC/README -* one page per individual command listed in src/USER-MISC/README -* examples/USER/misc - ----------- - -.. _PKG-USER-MANIFOLD: - -USER-MANIFOLD package ---------------------- - -**Contents:** - -Several fixes and a "manifold" class which enable simulations of -particles constrained to a manifold (a 2D surface within the 3D -simulation box). This is done by applying the RATTLE constraint -algorithm to formulate single-particle constraint functions -g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) -n = grad(g). - -**Author:** Stefan Paquay (until 2017: Eindhoven University of -Technology (TU/e), The Netherlands; since 2017: Brandeis University, -Waltham, MA, USA) - -**Supporting info:** - -* src/USER-MANIFOLD: filenames -> commands -* src/USER-MANIFOLD/README -* :doc:`Howto manifold ` -* :doc:`fix manifoldforce ` -* :doc:`fix nve/manifold/rattle ` -* :doc:`fix nvt/manifold/rattle ` -* examples/USER/manifold -* https://www.lammps.org/movies.html#manifold - ----------- - -.. _PKG-USER-MDI: - -USER-MDI package ----------------- - -**Contents:** - -A LAMMPS command and fix to allow client-server coupling of LAMMPS to -other atomic or molecular simulation codes via the `MolSSI Driver Interface -(MDI) library `_. - -**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com - -**Supporting info:** - -* src/USER-MDI/README -* :doc:`mdi/engine ` -* :doc:`fix mdi/engine ` -* examples/USER/mdi - ----------- - -.. _PKG-USER-MEAMC: - -USER-MEAMC package ------------------- - -**Contents:** - -A pair style for the modified embedded atom (MEAM) potential -translated from the Fortran version in the (obsolete) MEAM package -to plain C++. The USER-MEAMC fully replaces the MEAM package, which -has been removed from LAMMPS after the 12 December 2018 version. - -**Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg) -based on the Fortran version of Greg Wagner (Northwestern U) while at -Sandia. - -**Supporting info:** - -* src/USER-MEAMC: filenames -> commands -* src/USER-MEAMC/README -* :doc:`pair_style meam/c ` -* examples/meamc - ----------- - -.. _PKG-USER-MESODPD: - -USER-MESODPD package --------------------- - -**Contents:** - -Several extensions of the dissipative particle dynamics (DPD) -method. Specifically, energy-conserving DPD (eDPD) that can model -non-isothermal processes, many-body DPD (mDPD) for simulating -vapor-liquid coexistence, and transport DPD (tDPD) for modeling -advection-diffusion-reaction systems. The equations of motion of these -DPD extensions are integrated through a modified velocity-Verlet (MVV) -algorithm. - -**Author:** Zhen Li (Division of Applied Mathematics, Brown University) - -**Supporting info:** - -* src/USER-MESODPD: filenames -> commands -* src/USER-MESODPD/README -* :doc:`atom_style edpd ` -* :doc:`pair_style edpd ` -* :doc:`pair_style mdpd ` -* :doc:`pair_style tdpd ` -* :doc:`fix mvv/dpd ` -* examples/USER/mesodpd -* https://www.lammps.org/movies.html#mesodpd - ----------- - -.. _PKG-USER-MESONT: - -USER-MESONT package -------------------- - -**Contents:** - -USER-MESONT is a LAMMPS package for simulation of nanomechanics of -nanotubes (NTs). The model is based on a coarse-grained representation -of NTs as "flexible cylinders" consisting of a variable number of -segments. Internal interactions within a NT and the van der Waals -interaction between the tubes are described by a mesoscopic force field -designed and parameterized based on the results of atomic-level -molecular dynamics simulations. The description of the force field is -provided in the papers listed below. This package contains two -independent implementations of this model: :doc:`pair_style mesocnt -` is a (minimal) C++ implementation, and :doc:`pair_style -mesont/tpm ` is a more general and feature rich -implementation based on a Fortran library in the ``lib/mesont`` folder. - -**Download of potential files:** - -The potential files for these pair styles are *very* large and thus -are not included in the regular downloaded packages of LAMMPS or the -git repositories. Instead, they will be automatically downloaded -from a web server when the package is installed for the first time. - -**Authors of the *mesont* styles:** - -Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia) - -**Author of the *mesocnt* pair style:** -Philipp Kloza (U Cambridge) - -**Supporting info:** - -* src/USER-MESONT: filenames -> commands -* src/USER-MESONT/README -* :doc:`atom_style mesont ` -* :doc:`pair_style mesont/tpm ` -* :doc:`compute mesont ` -* :doc:`pair_style mesocnt ` -* examples/USER/mesont -* tools/mesont - ----------- - -.. _PKG-USER-MOFFF: - -USER-MOFFF package ------------------- - -**Contents:** - -Pair, angle and improper styles needed to employ the MOF-FF -force field by Schmid and coworkers with LAMMPS. -MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical -Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B -2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as -well as the `MOF+ `_ website. - -.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF - -**Author:** Hendrik Heenen (Technical U of Munich), -Rochus Schmid (Ruhr-University Bochum). - -**Supporting info:** - -* src/USER-MOFFF: filenames -> commands -* src/USER-MOFFF/README -* :doc:`pair_style buck6d/coul/gauss ` -* :doc:`angle_style class2 ` -* :doc:`angle_style cosine/buck6d ` -* :doc:`improper_style inversion/harmonic ` -* examples/USER/mofff - ----------- - -.. _PKG-USER-MOLFILE: - -USER-MOLFILE package --------------------- - -**Contents:** - -A :doc:`dump molfile ` command which uses molfile plugins -that are bundled with the `VMD `_ -molecular visualization and analysis program, to enable LAMMPS to dump -snapshots in formats compatible with various molecular simulation -tools. - -To use this package you must have the desired VMD plugins available on -your system. - -Note that this package only provides the interface code, not the -plugins themselves, which will be accessed when requesting a specific -plugin via the :doc:`dump molfile ` command. Plugins can -be obtained from a VMD installation which has to match the platform -that you are using to compile LAMMPS for. By adding plugins to VMD, -support for new file formats can be added to LAMMPS (or VMD or other -programs that use them) without having to re-compile the application -itself. More information about the VMD molfile plugins can be found -at -`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile `_. - -**Author:** Axel Kohlmeyer (Temple U). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-MOLFILE: filenames -> commands -* src/USER-MOLFILE/README -* lib/molfile/README -* :doc:`dump molfile ` - ----------- - -.. _PKG-USER-NETCDF: - -USER-NETCDF package -------------------- - -**Contents:** - -Dump styles for writing NetCDF formatted dump files. NetCDF is a -portable, binary, self-describing file format developed on top of -HDF5. The file contents follow the AMBER NetCDF trajectory conventions -(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. - -To use this package you must have the NetCDF library available on your -system. - -Note that NetCDF files can be directly visualized with the following -tools: - -* `Ovito `_ (Ovito supports the AMBER convention and the extensions mentioned above) -* `VMD `_ - -.. _ovito: http://www.ovito.org - -.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ - -**Author:** Lars Pastewka (Karlsruhe Institute of Technology). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-NETCDF: filenames -> commands -* src/USER-NETCDF/README -* lib/netcdf/README -* :doc:`dump netcdf ` - ----------- - -.. _PKG-USER-OMP: - -USER-OMP package ----------------- - -**Contents:** - -Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and -kspace styles which are altered to enable threading on many-core CPUs -via OpenMP directives. All of them have an "omp" in their style name. -The :doc:`USER-OMP package ` page gives details of what hardware -and compilers are required on your system, and how to build and use -this package. Its styles can be invoked at run time via the "-sf omp" -or "-suffix omp" :doc:`command-line switches `. Also see -the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`USER-INTEL ` -packages, which have styles optimized for CPUs. - -**Author:** Axel Kohlmeyer (Temple U). - -.. note:: - - To enable multi-threading support the compile flag "-fopenmp" - and the link flag "-fopenmp" (for GNU compilers, you have to look up - the equivalent flags for other compilers) must be used to build LAMMPS. - When using Intel compilers, also the "-restrict" flag is required. - The USER-OMP package can be compiled without enabling OpenMP; then - all code will be compiled as serial and the only improvement over the - regular styles are some data access optimization. These flags should - be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. - See src/MAKE/OPTIONS/Makefile.omp for an example. - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner: - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-OMP: filenames -> commands -* src/USER-OMP/README -* :doc:`Accelerator packages ` -* :doc:`USER-OMP package ` -* :doc:`Section 2.6 -sf omp ` -* :doc:`Section 2.6 -pk omp ` -* :doc:`package omp ` -* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, - :doc:`pair `, :doc:`bond, angle, dihedral, improper `, - :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of web site - ----------- - -.. _PKG-USER-PACE: - -USER-PACE package -------------------- - -**Contents:** - -A pair style for the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. The USER-PACE -package provides an efficient implementation for running simulations -with ACE potentials. - -**Authors:** - -This package was written by Yury Lysogorskiy^1, -Cas van der Oord^2, Anton Bochkarev^1, -Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, -Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. - - ^1: Ruhr-University Bochum, Bochum, Germany - - ^2: University of Cambridge, Cambridge, United Kingdom - - ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - - ^4: University of British Columbia, Vancouver, BC, Canada - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-PACE: filenames -> commands -* :doc:`pair_style pace ` -* examples/USER/pace - ----------- - -.. _PKG-USER-PHONON: - -USER-PHONON package -------------------- - -**Contents:** - -A :doc:`fix phonon ` command that calculates dynamical -matrices, which can then be used to compute phonon dispersion -relations, directly from molecular dynamics simulations. -And a :doc:`dynamical_matrix ` as well as a -:doc:`third_order ` command to compute the dynamical matrix -and third order tensor from finite differences. - -**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" -and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" - -**Supporting info:** - -* src/USER-PHONON: filenames -> commands -* src/USER-PHONON/README -* :doc:`fix phonon ` -* :doc:`dynamical_matrix ` -* :doc:`third_order ` -* examples/USER/phonon - ----------- - -.. _PKG-USER-PLUMED: - -USER-PLUMED package -------------------- - -**Contents:** - -The fix plumed command allows you to use the PLUMED free energy plugin -for molecular dynamics to analyze and bias your LAMMPS trajectory on -the fly. The PLUMED library is called from within the LAMMPS input -script by using the :doc:`fix plumed ` command. - -**Authors:** The `PLUMED library `_ is written -and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni, -and Gareth Tribello. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-PLUMED/README -* lib/plumed/README -* :doc:`fix plumed ` -* examples/USER/plumed - ----------- - -.. _PKG-USER-PTM: - -USER-PTM package ----------------- - -**Contents:** - -A :doc:`compute ptm/atom ` command that calculates -local structure characterization using the Polyhedral Template -Matching methodology. - -**Author:** Peter Mahler Larsen (MIT). - -**Supporting info:** - -* src/USER-PTM: filenames not starting with ptm\_ -> commands -* src/USER-PTM: filenames starting with ptm\_ -> supporting code -* src/USER-PTM/LICENSE -* :doc:`compute ptm/atom ` - ----------- - -.. _PKG-USER-QMMM: - -USER-QMMM package ------------------ - -**Contents:** - -A :doc:`fix qmmm ` command which allows LAMMPS to be used as -the MM code in a QM/MM simulation. This is currently only available -in combination with the `Quantum ESPRESSO `_ package. - -.. _espresso: http://www.quantum-espresso.org - -To use this package you must have Quantum ESPRESSO (QE) available on -your system and include its coupling library in the compilation and -then compile LAMMPS as a library. For QM/MM calculations you then -build a custom binary with MPI support, that sets up 3 partitions with -MPI sub-communicators (for inter- and intra-partition communication) -and then calls the corresponding library interfaces on each partition -(2x LAMMPS and 1x QE). - -The current implementation supports an ONIOM style mechanical coupling -and a multi-pole based electrostatic coupling to the Quantum ESPRESSO -plane wave DFT package. The QM/MM interface has been written in a -manner that coupling to other QM codes should be possible without -changes to LAMMPS itself. - -**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy) - -**Install:** - -This package has :ref:`specific installation instructions ` -on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-QMMM: filenames -> commands -* src/USER-QMMM/README -* lib/qmmm/README -* :doc:`fix phonon ` -* lib/qmmm/example-ec/README -* lib/qmmm/example-mc/README - ----------- - -.. _PKG-USER-QTB: - -USER-QTB package ----------------- - -**Contents:** - -Two fixes which provide a self-consistent quantum treatment of -vibrational modes in a classical molecular dynamics simulation. By -coupling the MD simulation to a colored thermostat, it introduces zero -point energy into the system, altering the energy power spectrum and -the heat capacity to account for their quantum nature. This is useful -when modeling systems at temperatures lower than their classical -limits or when temperatures ramp across the classical limits in a -simulation. - -**Author:** Yuan Shen (Stanford U). - -**Supporting info:** - -* src/USER-QTB: filenames -> commands -* src/USER-QTB/README -* :doc:`fix qtb ` -* :doc:`fix qbmsst ` -* examples/USER/qtb - ----------- - -.. _PKG-USER-QUIP: - -USER-QUIP package ------------------ - -**Contents:** - -A :doc:`pair_style quip ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic -potentials, including Gaussian Approximation Potential (GAP) models -developed by the Cambridge University group. - -.. _quip: https://github.com/libAtoms/QUIP - -To use this package you must have the QUIP libAtoms library available -on your system. - -**Author:** Albert Bartok (Cambridge University) - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-QUIP: filenames -> commands -* src/USER-QUIP/README -* :doc:`pair_style quip ` -* examples/USER/quip - ----------- - -.. _PKG-USER-RANN: - -USER-RANN package ------------------ - -**Contents:** - -A pair style for using rapid atomistic neural network (RANN) potentials. -These neural network potentials work by first generating a series of symmetry -functions from the neighbor list and then using these values as the input layer -of a neural network. - -**Authors:** - -This package was written by Christopher Barrett -with contributions by Doyl Dickel, Mississippi State University. - -**Supporting info:** - -* src/USER-RANN: filenames -> commands -* :doc:`pair_style rann ` -* examples/USER/rann - ----------- - -.. _PKG-USER-REACTION: - -USER-REACTION package ---------------------- - -**Contents:** - -This package allows for complex bond topology changes (reactions) -during a running MD simulation, when using classical force fields. -Topology changes are defined in pre- and post-reaction molecule -templates and can include creation and deletion of bonds, angles, -dihedrals, impropers, atom types, bond types, angle types, dihedral -types, improper types, and/or atomic charges. Other options currently -available include reaction constraints (e.g. angle and Arrhenius -constraints), deletion of reaction byproducts or other small -molecules, and chiral-sensitive reactions. - -**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. - -**Supporting info:** - -* src/USER-REACTION: filenames -> commands -* src/USER-REACTION/README -* :doc:`fix bond/react ` -* examples/USER/reaction -* `2017 LAMMPS Workshop `_ -* `2019 LAMMPS Workshop `_ -* reacter.org - ----------- - -.. _PKG-USER-REAXC: - -USER-REAXC package ------------------- - -**Contents:** - -A pair style which implements the ReaxFF potential in C/C++. ReaxFF -is a universal reactive force field. See the src/USER-REAXC/README file -for more info on differences between the two packages. Also two fixes -for monitoring molecules as bonds are created and destroyed. - -**Author:** Hasan Metin Aktulga (MSU) while at Purdue University. - -**Supporting info:** - -* src/USER-REAXC: filenames -> commands -* src/USER-REAXC/README -* :doc:`pair_style reax/c ` -* :doc:`fix reax/c/bonds ` -* :doc:`fix reax/c/species ` -* examples/reax - ----------- - -.. _PKG-USER-SCAFACOS: - -USER-SCAFACOS package ---------------------- - -**Contents:** - -A KSpace style which wraps the `ScaFaCoS Coulomb solver library `_ to compute long-range Coulombic -interactions. - -To use this package you must have the ScaFaCoS library available on -your system. - -**Author:** Rene Halver (JSC) wrote the scafacos LAMMPS command. - -ScaFaCoS itself was developed by a consortium of German research -facilities with a BMBF (German Ministry of Science and Education) -funded project in 2009-2012. Participants of the consortium were the -Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as -the Forschungszentrum Juelich. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-SCAFACOS: filenames -> commands -* src/USER-SCAFACOS/README -* :doc:`kspace_style scafacos ` -* :doc:`kspace_modify ` -* examples/USER/scafacos - ----------- - -.. _PKG-USER-SDPD: - -USER-SDPD package ------------------ - -**Contents:** - -A pair style for smoothed dissipative particle dynamics (SDPD), which -is an extension of smoothed particle hydrodynamics (SPH) to mesoscale -where thermal fluctuations are important (see the -:ref:`USER-SPH package `). -Also two fixes for moving and rigid body integration of SPH/SDPD particles -(particles of atom_style meso). - -**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic -Sciences, Iran). - -**Supporting info:** - -* src/USER-SDPD: filenames -> commands -* src/USER-SDPD/README -* :doc:`pair_style sdpd/taitwater/isothermal ` -* :doc:`fix meso/move ` -* :doc:`fix rigid/meso ` -* examples/USER/sdpd - ----------- - -.. _PKG-USER-SMD: - -USER-SMD package ----------------- - -**Contents:** - -An atom style, fixes, computes, and several pair styles which -implements smoothed Mach dynamics (SMD) for solids, which is a model -related to smoothed particle hydrodynamics (SPH) for liquids (see the -:ref:`USER-SPH package `). - -This package solves solids mechanics problems via a state of the art -stabilized meshless method with hourglass control. It can specify -hydrostatic interactions independently from material strength models, -i.e. pressure and deviatoric stresses are separated. It provides many -material models (Johnson-Cook, plasticity with hardening, -Mie-Grueneisen, Polynomial EOS) and allows new material models to be -added. It implements rigid boundary conditions (walls) which can be -specified as surface geometries from \*.STL files. - -**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-SMD: filenames -> commands -* src/USER-SMD/README -* doc/PDF/SMD_LAMMPS_userguide.pdf -* examples/USER/smd -* https://www.lammps.org/movies.html#smd - ----------- - -.. _PKG-USER-SMTBQ: - -USER-SMTBQ package ------------------- - -**Contents:** - -A pair style which implements a Second Moment Tight Binding model with -QEq charge equilibration (SMTBQ) potential for the description of -ionocovalent bonds in oxides. - -**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert -Tetot (LAAS-CNRS, France). - -**Supporting info:** - -* src/USER-SMTBQ: filenames -> commands -* src/USER-SMTBQ/README -* :doc:`pair_style smtbq ` -* examples/USER/smtbq - ----------- - -.. _PKG-USER-SPH: - -USER-SPH package ----------------- - -**Contents:** - -An atom style, fixes, computes, and several pair styles which -implements smoothed particle hydrodynamics (SPH) for liquids. See the -related :ref:`USER-SMD package ` package for smooth Mach dynamics -(SMD) for solids. - -This package contains ideal gas, Lennard-Jones equation of states, -Tait, and full support for complete (i.e. internal-energy dependent) -equations of state. It allows for plain or Monaghans XSPH integration -of the equations of motion. It has options for density continuity or -density summation to propagate the density field. It has -:doc:`set ` command options to set the internal energy and density -of particles from the input script and allows the same quantities to -be output with thermodynamic output or to dump files via the :doc:`compute property/atom ` command. - -**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -**Supporting info:** - -* src/USER-SPH: filenames -> commands -* src/USER-SPH/README -* doc/PDF/SPH_LAMMPS_userguide.pdf -* examples/USER/sph -* https://www.lammps.org/movies.html#sph - ----------- - -.. _PKG-USER-TALLY: - -USER-TALLY package ------------------- - -**Contents:** - -Several compute styles that can be called when pairwise interactions -are calculated to tally information (forces, heat flux, energy, -stress, etc) about individual interactions. - -**Author:** Axel Kohlmeyer (Temple U). - -**Supporting info:** - -* src/USER-TALLY: filenames -> commands -* src/USER-TALLY/README -* :doc:`compute \*/tally ` -* examples/USER/tally - ----------- - -.. _PKG-USER-UEF: - -USER-UEF package ----------------- - -**Contents:** - -A fix style for the integration of the equations of motion under -extensional flow with proper boundary conditions, as well as several -supporting compute styles and an output option. - -**Author:** David Nicholson (MIT). - -**Supporting info:** - -* src/USER-UEF: filenames -> commands -* src/USER-UEF/README -* :doc:`fix nvt/uef ` -* :doc:`fix npt/uef ` -* :doc:`compute pressure/uef ` -* :doc:`compute temp/uef ` -* :doc:`dump cfg/uef ` -* examples/uef - ----------- - -.. _PKG-USER-VTK: - -USER-VTK package +VTK package ---------------- **Contents:** @@ -2606,20 +2758,20 @@ system. **Install:** -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. **Supporting info:** -* src/USER-VTK: filenames -> commands -* src/USER-VTK/README +* src/VTK: filenames -> commands +* src/VTK/README * lib/vtk/README * :doc:`dump vtk ` ---------- -.. _PKG-USER-YAFF: +.. _PKG-YAFF: -USER-YAFF package +YAFF package ----------------- **Contents:** @@ -2641,7 +2793,7 @@ which discuss the `QuickFF `_ methodology. **Supporting info:** -* src/USER-YAFF/README +* src/YAFF/README * :doc:`angle_style cross ` * :doc:`angle_style mm3 ` * :doc:`bond_style mm3 ` @@ -2649,4 +2801,4 @@ which discuss the `QuickFF `_ methodology. * :doc:`improper_style sqdistharm ` * :doc:`pair_style mm3/switch3/coulgauss/long ` * :doc:`pair_style lj/switch3/coulgauss/long ` -* examples/USER/yaff +* examples/PACKAGES/yaff diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst new file mode 100644 index 0000000000..22dfa2c69e --- /dev/null +++ b/doc/src/Packages_list.rst @@ -0,0 +1,479 @@ +Available Packages +================== + +This is the list of packages included in LAMMPS. The link for each +package name gives more details. + +Packages are supported by either the LAMMPS developers or the +contributing authors and written in a syntax and style consistent with +the rest of LAMMPS. + +The "Example" column is a sub-directory in the examples directory of the +distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; PACKAGES/atc refers +to the examples/PACKAGES/atc directory. The "Library" column indicates +whether an extra library is needed to build and use the package: + +* no = no library +* sys = system library: you likely have it on your machine +* int = internal library: provided with LAMMPS, but you may need to build it +* ext = external library: you will need to download and install it on your machine + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Package + - Description + - Doc page + - Example + - Library + * - :ref:`ADIOS ` + - dump output via ADIOS + - :doc:`dump adios ` + - PACKAGES/adios + - ext + * - :ref:`ASPHERE ` + - aspherical particle models + - :doc:`Howto spherical ` + - ellipse + - no + * - :ref:`ATC ` + - Atom-to-Continuum coupling + - :doc:`fix atc ` + - PACKAGES/atc + - int + * - :ref:`AWPMD ` + - wave packet MD + - :doc:`pair_style awpmd/cut ` + - PACKAGES/awpmd + - int + * - :ref:`BOCS ` + - BOCS bottom up coarse graining + - :doc:`fix bocs ` + - PACKAGES/bocs + - no + * - :ref:`BODY ` + - body-style particles + - :doc:`Howto body ` + - body + - no + * - :ref:`BROWNIAN ` + - Brownian dynamics, self-propelled particles + - :doc:`fix brownian `, :doc:`fix propel/self ` + - PACKAGES/brownian + - no + * - :ref:`CG-DNA ` + - coarse-grained DNA force fields + - src/CG-DNA/README + - PACKAGES/cgdna + - no + * - :ref:`CG-SDK ` + - SDK coarse-graining model + - :doc:`pair_style lj/sdk ` + - PACKAGES/cgsdk + - no + * - :ref:`CLASS2 ` + - class 2 force fields + - :doc:`pair_style lj/class2 ` + - n/a + - no + * - :ref:`COLLOID ` + - colloidal particles + - :doc:`atom_style colloid ` + - colloid + - no + * - :ref:`COLVARS ` + - collective variables library + - :doc:`fix colvars ` + - PACKAGES/colvars + - int + * - :ref:`COMPRESS ` + - I/O compression + - :doc:`dump \*/gz ` + - n/a + - sys + * - :ref:`CORESHELL ` + - adiabatic core/shell model + - :doc:`Howto coreshell ` + - coreshell + - no + * - :ref:`DIELECTRIC ` + - dielectric boundary solvers and force styles + - :doc:`compute efield/atom ` + - PACKAGES/dielectric + - no + * - :ref:`DIFFRACTION ` + - virtual x-ray and electron diffraction + - :doc:`compute xrd ` + - PACKAGES/diffraction + - no + * - :ref:`DIPOLE ` + - point dipole particles + - :doc:`pair_style lj/.../dipole ` + - dipole + - no + * - :ref:`DPD-BASIC ` + - basic DPD models + - :doc:`pair_styles dpd dpd/tstat ` :doc:`dpd/ext dpd/ext/tstat ` + - PACKAGES/dpd-basic + - no + * - :ref:`DPD-MESO ` + - mesoscale DPD models + - :doc:`pair_style edpd ` + - PACKAGES/dpd-meso + - no + * - :ref:`DPD-REACT ` + - reactive dissipative particle dynamics + - src/DPD-REACT/README + - PACKAGES/dpd-react + - no + * - :ref:`DPD-SMOOTH ` + - smoothed dissipative particle dynamics + - src/DPD-SMOOTH/README + - PACKAGES/dpd-smooth + - no + * - :ref:`DRUDE ` + - Drude oscillators + - :doc:`Howto drude ` + - PACKAGES/drude + - no + * - :ref:`EFF ` + - electron force field + - :doc:`pair_style eff/cut ` + - PACKAGES/eff + - no + * - :ref:`EXTRA-COMPUTE ` + - additional compute styles + - :doc:`compute ` + - n/a + - no + * - :ref:`EXTRA-DUMP ` + - additional dump styles + - :doc:`dump ` + - n/a + - no + * - :ref:`EXTRA-FIX ` + - additional fix styles + - :doc:`fix ` + - n/a + - no + * - :ref:`EXTRA-MOLECULE ` + - additional molecular styles + - :doc:`molecular styles ` + - n/a + - no + * - :ref:`EXTRA-PAIR ` + - additional pair styles + - :doc:`pair_style ` + - n/a + - no + * - :ref:`FEP ` + - free energy perturbation + - :doc:`compute fep ` + - PACKAGES/fep + - no + * - :ref:`GPU ` + - GPU-enabled styles + - :doc:`Section gpu ` + - `Benchmarks `_ + - int + * - :ref:`GRANULAR ` + - granular systems + - :doc:`Howto granular ` + - pour + - no + * - :ref:`H5MD ` + - dump output via HDF5 + - :doc:`dump h5md ` + - n/a + - ext + * - :ref:`INTEL ` + - optimized Intel CPU and KNL styles + - :doc:`Speed intel ` + - `Benchmarks `_ + - no + * - :ref:`INTERLAYER ` + - Inter-layer pair potentials + - :doc:`several pair styles ` + - PACKAGES/interlayer + - no + * - :ref:`KIM ` + - OpenKIM wrapper + - :doc:`pair_style kim ` + - kim + - ext + * - :ref:`KOKKOS ` + - Kokkos-enabled styles + - :doc:`Speed kokkos ` + - `Benchmarks `_ + - no + * - :ref:`KSPACE ` + - long-range Coulombic solvers + - :doc:`kspace_style ` + - peptide + - no + * - :ref:`LATBOLTZ ` + - Lattice Boltzmann fluid + - :doc:`fix lb/fluid ` + - PACKAGES/latboltz + - no + * - :ref:`LATTE ` + - quantum DFTB forces via LATTE + - :doc:`fix latte ` + - latte + - ext + * - :ref:`MACHDYN ` + - smoothed Mach dynamics + - `SMD User Guide `_ + - PACKAGES/machdyn + - ext + * - :ref:`MANIFOLD ` + - motion on 2d surfaces + - :doc:`fix manifoldforce ` + - PACKAGES/manifold + - no + * - :ref:`MANYBODY ` + - many-body potentials + - :doc:`pair_style tersoff ` + - shear + - no + * - :ref:`MC ` + - Monte Carlo options + - :doc:`fix gcmc ` + - n/a + - no + * - :ref:`MDI ` + - client-server coupling + - :doc:`MDI Howto ` + - PACKAGES/mdi + - ext + * - :ref:`MEAM ` + - modified EAM potential (C++) + - :doc:`pair_style meam ` + - meam + - no + * - :ref:`MESONT ` + - mesoscopic tubular potential model + - pair styles :doc:`mesont/tpm `, :doc:`mesocnt ` + - PACKAGES/mesont + - int + * - :ref:`MESSAGE ` + - client/server messaging + - :doc:`message ` + - message + - int + * - :ref:`MGPT ` + - fast MGPT multi-ion potentials + - :doc:`pair_style mgpt ` + - PACKAGES/mgpt + - no + * - :ref:`MISC ` + - miscellaneous single-file commands + - n/a + - no + - no + * - :ref:`ML-HDNNP ` + - High-dimensional neural network potentials + - :doc:`pair_style hdnnp ` + - PACKAGES/hdnnp + - ext + * - :ref:`ML-IAP ` + - multiple machine learning potentials + - :doc:`pair_style mliap ` + - mliap + - no + * - :ref:`ML-PACE ` + - Atomic Cluster Expansion potential + - :doc:`pair pace ` + - PACKAGES/pace + - ext + * - :ref:`ML-QUIP ` + - QUIP/libatoms interface + - :doc:`pair_style quip ` + - PACKAGES/quip + - ext + * - :ref:`ML-RANN ` + - Pair style for RANN potentials + - :doc:`pair rann ` + - PACKAGES/rann + - no + * - :ref:`ML-SNAP ` + - quantum-fitted potential + - :doc:`pair_style snap ` + - snap + - no + * - :ref:`MOFFF ` + - styles for `MOF-FF `_ force field + - :doc:`pair_style buck6d/coul/gauss ` + - PACKAGES/mofff + - no + * - :ref:`MOLECULE ` + - molecular system force fields + - :doc:`Howto bioFF ` + - peptide + - no + * - :ref:`MOLFILE ` + - `VMD `_ molfile plug-ins + - :doc:`dump molfile ` + - n/a + - ext + * - :ref:`MPIIO ` + - MPI parallel I/O dump and restart + - :doc:`dump ` + - n/a + - no + * - :ref:`MSCG ` + - multi-scale coarse-graining wrapper + - :doc:`fix mscg ` + - mscg + - ext + * - :ref:`NETCDF ` + - dump output via NetCDF + - :doc:`dump netcdf ` + - n/a + - ext + * - :ref:`OPENMP ` + - OpenMP-enabled styles + - :doc:`Speed omp ` + - `Benchmarks `_ + - no + * - :ref:`OPT ` + - optimized pair styles + - :doc:`Speed opt ` + - `Benchmarks `_ + - no + * - :ref:`ORIENT ` + - fixes for orientation depended forces + - :doc:`fix orient/* ` + - PACKAGES/orient_eco + - no + * - :ref:`PERI ` + - Peridynamics models + - :doc:`pair_style peri ` + - peri + - no + * - :ref:`PHONON ` + - phonon dynamical matrix + - :doc:`fix phonon ` + - PACKAGES/phonon + - no + * - :ref:`PLUGIN ` + - Plugin loader command + - :doc:`plugin ` + - plugins + - no + * - :ref:`PLUMED ` + - :ref:`PLUMED ` free energy library + - :doc:`fix plumed ` + - PACKAGES/plumed + - ext + * - :ref:`POEMS ` + - coupled rigid body motion + - :doc:`fix poems ` + - rigid + - int + * - :ref:`PTM ` + - Polyhedral Template Matching + - :doc:`compute ptm/atom ` + - n/a + - no + * - :ref:`PYTHON ` + - embed Python code in an input script + - :doc:`python ` + - python + - sys + * - :ref:`QEQ ` + - QEq charge equilibration + - :doc:`fix qeq ` + - qeq + - no + * - :ref:`QMMM ` + - QM/MM coupling + - :doc:`fix qmmm ` + - PACKAGES/qmmm + - ext + * - :ref:`QTB ` + - quantum nuclear effects + - :doc:`fix qtb ` :doc:`fix qbmsst ` + - qtb + - no + * - :ref:`REACTION ` + - chemical reactions in classical MD + - :doc:`fix bond/react ` + - PACKAGES/reaction + - no + * - :ref:`REAXFF ` + - ReaxFF potential (C/C++) + - :doc:`pair_style reaxff ` + - reax + - no + * - :ref:`REPLICA ` + - multi-replica methods + - :doc:`Howto replica ` + - tad + - no + * - :ref:`RIGID ` + - rigid bodies and constraints + - :doc:`fix rigid ` + - rigid + - no + * - :ref:`SCAFACOS ` + - wrapper for ScaFaCoS Kspace solver + - :doc:`kspace_style scafacos ` + - PACKAGES/scafacos + - ext + * - :ref:`SHOCK ` + - shock loading methods + - :doc:`fix msst ` + - n/a + - no + * - :ref:`SMTBQ ` + - second moment tight binding potential + - :doc:`pair_style smtbq ` + - PACKAGES/smtbq + - no + * - :ref:`SPH ` + - smoothed particle hydrodynamics + - `SPH User Guide `_ + - PACKAGES/sph + - no + * - :ref:`SPIN ` + - magnetic atomic spin dynamics + - :doc:`Howto spins ` + - SPIN + - no + * - :ref:`SRD ` + - stochastic rotation dynamics + - :doc:`fix srd ` + - srd + - no + * - :ref:`TALLY ` + - pairwise tally computes + - :doc:`compute XXX/tally ` + - PACKAGES/tally + - no + * - :ref:`UEF ` + - extensional flow + - :doc:`fix nvt/uef ` + - PACKAGES/uef + - no + * - :ref:`VORONOI ` + - Voronoi tesselation + - :doc:`compute voronoi/atom ` + - n/a + - ext + * - :ref:`VTK ` + - dump output via VTK + - :doc:`compute vtk ` + - n/a + - ext + * - :ref:`YAFF ` + - additional styles implemented in YAFF + - :doc:`angle_style cross ` + - PACKAGES/yaff + - no + +.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF +.. _PLUMED: https://www.plumed.org +.. _VMD: https://www.ks.uiuc.edu/Research/vmd/ diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst deleted file mode 100644 index 8fc1e7df7a..0000000000 --- a/doc/src/Packages_standard.rst +++ /dev/null @@ -1,95 +0,0 @@ -Standard packages -================= - -This is the list of standard packages in LAMMPS. The link for each -package name gives more details. - -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means the developers will answer questions about them, debug and -fix them if necessary, and keep them compatible with future changes to -LAMMPS. - -The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory; USER/atc -refers to the examples/USER/atc directory. The "Library" column -indicates whether an extra library is needed to build and use the -package: - -* no = no library -* sys = system library: you likely have it on your machine -* int = internal library: provided with LAMMPS, but you may need to build it -* ext = external library: you will need to download and install it on your machine - -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| Package | Description | Doc page | Example | Library | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`ASPHERE ` | aspherical particle models | :doc:`Howto spherical ` | ellipse | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`BODY ` | body-style particles | :doc:`Howto body ` | body | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair_style lj/class2 ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`COLLOID ` | colloidal particles | :doc:`atom_style colloid ` | colloid | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`COMPRESS ` | I/O compression | :doc:`dump \*/gz ` | n/a | sys | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style lj/.../dipole ` | dipole | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`LATTE ` | quantum DFTB forces via LATTE | :doc:`fix latte ` | latte | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MANYBODY ` | many-body potentials | :doc:`pair_style tersoff ` | shear | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MC ` | Monte Carlo options | :doc:`fix gcmc ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MESSAGE ` | client/server messaging | :doc:`message ` | message | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MISC ` | miscellaneous single-file commands | n/a | no | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MLIAP ` | multiple machine learning potentials | :doc:`pair_style mliap ` | mliap | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MOLECULE ` | molecular system force fields | :doc:`Howto bioFF ` | peptide | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MPIIO ` | MPI parallel I/O dump and restart | :doc:`dump ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MSCG ` | multi-scale coarse-graining wrapper | :doc:`fix mscg ` | mscg | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`PLUGIN ` | Plugin loader command | :doc:`plugin ` | plugins | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`PYTHON ` | embed Python code in an input script | :doc:`python ` | python | sys | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`QEQ ` | QEq charge equilibration | :doc:`fix qeq ` | qeq | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`REPLICA ` | multi-replica methods | :doc:`Howto replica ` | tad | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`RIGID ` | rigid bodies and constraints | :doc:`fix rigid ` | rigid | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SHOCK ` | shock loading methods | :doc:`fix msst ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair_style snap ` | snap | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SPIN ` | magnetic atomic spin dynamics | :doc:`Howto spins ` | SPIN | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SRD ` | stochastic rotation dynamics | :doc:`fix srd ` | srd | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`VORONOI ` | Voronoi tesselation | :doc:`compute voronoi/atom ` | n/a | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst deleted file mode 100644 index 89d740939e..0000000000 --- a/doc/src/Packages_user.rst +++ /dev/null @@ -1,132 +0,0 @@ -User packages -============= - -This is a list of user packages in LAMMPS. The link for each package -name gives more details. - -User packages have been contributed by users, and begin with the -"user" prefix. If a contribution is a single command (single file), -it is typically in the USER-MISC package. User packages don't -necessarily meet the requirements of the :doc:`standard packages `. This means the developers will try -to keep things working and usually can answer technical questions -about compiling the package. If you have problems using a specific -feature provided in a user package, you may need to contact the -contributor directly to get help. Information on how to submit -additions you make to LAMMPS as single files or as a standard or user -package is explained on the :doc:`Modify contribute ` -doc page. - -The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory; USER/atc -refers to the examples/USER/atc directory. The "Library" column -indicates whether an extra library is needed to build and use the -package: - -* no = no library -* sys = system library: you likely have it on your machine -* int = internal library: provided with LAMMPS, but you may need to build it -* ext = external library: you will need to download and install it on your machine - -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| Package | Description | Doc page | Example | Library | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-ADIOS ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-BROWNIAN ` | Brownian dynamics and self-propelled particles | :doc:`fix brownian `, :doc:`fix propel/self ` | USER/brownian | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DIELECTRIC ` | dielectric boundary solvers and force styles | :doc:`compute efield/atom ` | USER/dielectric | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-HDNNP ` | High-dimensional neural network potentials | :doc:`pair_style hdnnp ` | USER/hdnnp | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MDI ` | client-server coupling | :doc:`MDI Howto ` | USER/mdi | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MESONT ` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm `, :doc:`mesocnt ` | USER/mesont | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-RANN ` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann ` | USER/rann | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ - -.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF -.. _PLUMED: https://www.plumed.org diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 3a09678539..796adfe1c0 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -43,7 +43,7 @@ complex loop with branching logic, than can be created using the simple looping and branching logic enabled by the :doc:`next ` and :doc:`if ` commands. -See the :doc:`python ` doc page and the :doc:`variable ` +See the :doc:`python ` page and the :doc:`variable ` doc page for its python-style variables for more info, including examples of Python code you can write for both pure Python operations and callbacks to LAMMPS. diff --git a/doc/src/Python_create.rst b/doc/src/Python_create.rst index 00b1c08814..ec4241f36a 100644 --- a/doc/src/Python_create.rst +++ b/doc/src/Python_create.rst @@ -134,7 +134,10 @@ compiled with. The :py:func:`lmp.close() ` call is optional since the LAMMPS class instance will also be deleted automatically during the :py:class:`lammps ` class -destructor. +destructor. Instead of :py:func:`lmp.close() ` +it is also possible to call :py:func:`lmp.finalize() `; +this will destruct the LAMMPS instance, but also finalized and release +the MPI and/or Kokkos environment if enabled and active. Note that you can create multiple LAMMPS objects in your Python script, and coordinate and run multiple simulations, e.g. diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index 7466b52ba9..fe5fe812c5 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -35,9 +35,9 @@ visualization package you have installed. Note that for GL, you need to be able to run the Pizza.py GL tool, which is included in the pizza sub-directory. See the Pizza.py doc pages for more info: -* `https://pizza.sandia.gov `_ +* `https://lammps.github.io/pizza `_ -.. _pizza: https://pizza.sandia.gov +.. _pizza: https://lammps.github.io/pizza Note that for AtomEye, you need version 3, and there is a line in the scripts that specifies the path and name of the executable. See the diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 6b224bbf40..abf96accbf 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -69,7 +69,7 @@ this. cd build # configure LAMMPS compilation - cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \ + cmake -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on \ -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake # compile LAMMPS diff --git a/doc/src/Python_objects.rst b/doc/src/Python_objects.rst index 4c8161b8bd..4a1496632e 100644 --- a/doc/src/Python_objects.rst +++ b/doc/src/Python_objects.rst @@ -20,7 +20,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. global vector or array, a single double value from the vector or array is returned, indexed by I (vector) or I and J (array). I,J are zero-based indices. - See the :doc:`Howto output ` doc page for a discussion of + See the :doc:`Howto output ` page for a discussion of global, per-atom, and local data, and of scalar, vector, and array data types. See the doc pages for individual :doc:`computes ` and :doc:`fixes ` for a description of what they calculate and diff --git a/doc/src/Python_trouble.rst b/doc/src/Python_trouble.rst index b94a043a6a..aae96d6701 100644 --- a/doc/src/Python_trouble.rst +++ b/doc/src/Python_trouble.rst @@ -41,4 +41,4 @@ first importing from the ``lammps`` module: >>> CDLL("liblammps.so") If an error occurs, carefully go through the steps in :ref:`python_install_guides` and on the -:doc:`Build_basics ` doc page about building a shared library. +:doc:`Build_basics ` page about building a shared library. diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 35d5f829a0..3d57633df2 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -42,7 +42,7 @@ single processor. In theory you should get identical answers on any number of processors and on any machine. In practice, numerical round-off due to using floating-point math can cause slight differences and an eventual divergence of molecular dynamics trajectories. See the -:doc:`Errors common ` doc page for discussion of this. +:doc:`Errors common ` page for discussion of this. LAMMPS can run as large a problem as will fit in the physical memory of one or more processors. If you run out of memory, you must run on more diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index d8adfcc5be..c4004c87e0 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -10,7 +10,7 @@ letter abbreviation can be used: * :ref:`-i or -in ` * :ref:`-k or -kokkos ` * :ref:`-l or -log ` -* :ref:`-mdi ` +* :ref:`-mdi ` * :ref:`-m or -mpicolor ` * :ref:`-c or -cite ` * :ref:`-nc or -nocite ` @@ -89,7 +89,7 @@ in the :doc:`the KOKKOS package page `, this switch must be set to running with KOKKOS-enabled styles the package provides. If the switch is not set (the default), LAMMPS will operate as if the KOKKOS package were not installed; i.e. you can run standard LAMMPS or with -the GPU or USER-OMP packages, for testing or benchmarking purposes. +the GPU or OPENMP packages, for testing or benchmarking purposes. Additional optional keyword/value pairs can be specified which determine how Kokkos will use the underlying hardware on your @@ -197,12 +197,12 @@ Option -plog will override the name of the partition log files file.N. ---------- -.. _mdi: +.. _mdi_flags: **-mdi 'multiple flags'** This flag is only recognized and used when LAMMPS has support for the MolSSI -Driver Interface (MDI) included as part of the :ref:`USER-MDI ` +Driver Interface (MDI) included as part of the :ref:`MDI ` package. This flag is specific to the MDI library and controls how LAMMPS interacts with MDI. There are usually multiple flags that have to follow it and those have to be placed in quotation marks. For more information about @@ -274,7 +274,7 @@ script. For example "-package gpu 2" or "-pk gpu 2" is the same as :doc:`package gpu 2 ` in the input script. The possible styles and args are documented on the :doc:`package ` doc page. This switch can be used multiple times, e.g. to set options for the -USER-INTEL and USER-OMP packages which can be used together. +INTEL and OPENMP packages which can be used together. Along with the "-suffix" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without @@ -365,7 +365,7 @@ to insure that a specific Kspace processor (in the second partition) is matched up with a specific set of processors in the first partition. See the :doc:`General tips ` page for more details. -If the keyword *nth* is used with a setting *N*\ , then it means every +If the keyword *nth* is used with a setting *N*, then it means every Nth processor will be moved to the end of the ranking. This is useful when using the :doc:`run_style verlet/split ` command with 2 partitions via the -partition command-line switch. The first set of @@ -397,7 +397,7 @@ so that the processors in each partition will be See the "processors" command for how to insure processors from each partition could then be grouped optimally for quad-core nodes. -If the keyword is *custom*\ , then a file that specifies a permutation +If the keyword is *custom*, then a file that specifies a permutation of the processor ranks is also specified. The format of the reorder file is as follows. Any number of initial blank or comment lines (starting with a "#" character) can be present. These should be @@ -464,7 +464,7 @@ The syntax following restartfile (or remap), namely datafile keyword value ... is identical to the arguments of the :doc:`write_data ` -command. See its doc page for details. This includes its +command. See its page for details. This includes its optional keyword/value settings. ---------- @@ -505,11 +505,11 @@ The syntax following restartfile (or remap), namely group-ID dumpstyle dumpfile arg1 arg2 ... is identical to the arguments of the :doc:`write_dump ` -command. See its doc page for details. This includes what per-atom +command. See its page for details. This includes what per-atom fields are written to the dump file and optional dump_modify settings, including ones that affect how parallel dump files are written, e.g. the *nfile* and *fileper* keywords. See the -:doc:`dump_modify ` doc page for details. +:doc:`dump_modify ` page for details. ---------- @@ -537,19 +537,19 @@ partition screen files file.N. **-suffix style args** Use variants of various styles if they exist. The specified style can -be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ . These +be *gpu*, *intel*, *kk*, *omp*, *opt*, or *hybrid*\ . These refer to optional packages that LAMMPS can be built with, as described in :doc:`Accelerate performance `. The "gpu" style corresponds to the -GPU package, the "intel" style to the USER-INTEL package, the "kk" +GPU package, the "intel" style to the INTEL package, the "kk" style to the KOKKOS package, the "opt" style to the OPT package, and -the "omp" style to the USER-OMP package. The hybrid style is the only +the "omp" style to the OPENMP package. The hybrid style is the only style that accepts arguments. It allows for two packages to be specified. The first package specified is the default and will be used if it is available. If no style is available for the first package, the style for the second package will be used if available. For example, "-suffix hybrid intel omp" will use styles from the -USER-INTEL package if they are installed and available, but styles for -the USER-OMP package otherwise. +INTEL package if they are installed and available, but styles for +the OPENMP package otherwise. Along with the "-package" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without @@ -570,15 +570,15 @@ default GPU settings, as if the command "package gpu 1" were used at the top of your input script. These settings can be changed by using the "-package gpu" command-line switch or the :doc:`package gpu ` command in your script. -For the USER-INTEL package, using this command-line switch also -invokes the default USER-INTEL settings, as if the command "package +For the INTEL package, using this command-line switch also +invokes the default INTEL settings, as if the command "package intel 1" were used at the top of your input script. These settings can be changed by using the "-package intel" command-line switch or the :doc:`package intel ` command in your script. If the -USER-OMP package is also installed, the hybrid style with "intel omp" +OPENMP package is also installed, the hybrid style with "intel omp" arguments can be used to make the omp suffix a second choice, if a -requested style is not available in the USER-INTEL package. It will -also invoke the default USER-OMP settings, as if the command "package +requested style is not available in the INTEL package. It will +also invoke the default OPENMP settings, as if the command "package omp 0" were used at the top of your input script. These settings can be changed by using the "-package omp" command-line switch or the :doc:`package omp ` command in your script. diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index d7d92dc5ee..8adfd4b293 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -152,7 +152,7 @@ information is provided about the line search and statistics on how many iterations and force-evaluations the minimizer required. Multiple force evaluations are typically done at each iteration to perform a 1d line minimization in the search direction. See the -:doc:`minimize ` doc page for more details. +:doc:`minimize ` page for more details. ---------- diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index 8813d6d59e..f29155a839 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -11,7 +11,7 @@ To run a serial (non-MPI) executable, follow these steps: in.file is the name of your LAMMPS input script. Note that the serial executable includes support for multi-threading -parallelization from the styles in the USER-OMP packages. To run with +parallelization from the styles in the OPENMP packages. To run with 4 threads, you can type this: .. code-block:: bash diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index 4ab616a5da..7821214c83 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -67,12 +67,12 @@ section below for examples where this has been done. pair style - on the CPU. This can often be easily achieved with placing a *suffix off* command before and a *suffix on* command after the *kspace_style pppm* command. -* The KOKKOS/OpenMP and USER-OMP package have different thread management - strategies, which should result in USER-OMP being more efficient for a +* The KOKKOS/OpenMP and OPENMP package have different thread management + strategies, which should result in OPENMP being more efficient for a small number of threads with increasing overhead as the number of threads per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that case, but have lower performance with few threads. -* The USER-INTEL package contains many options and settings for achieving +* The INTEL package contains many options and settings for achieving additional performance on Intel hardware (CPU and accelerator cards), but to unlock this potential, an Intel compiler is required. The package code will compile with GNU gcc, but it will not be as efficient. @@ -90,5 +90,5 @@ section below for examples where this has been done. both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically resulting in equal or better performance over OpenCL. * OpenCL in the GPU package does theoretically also support Intel CPUs or - Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL) + Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL) is superior. diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 2cb8c08fd5..656ce08bbc 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -71,7 +71,7 @@ by AMD. **Building LAMMPS with the GPU package:** -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` page for instructions. **Run with the GPU package from the command line:** @@ -118,7 +118,7 @@ automatic selection of the number of GPUs to use. Using the "-pk" switch explicitly allows for setting of the number of GPUs/node to use and additional options. Its syntax is the same as the "package gpu" command. See the :doc:`package ` -command doc page for details, including the default values used for +command page for details, including the default values used for all its options if it is not specified. Note that the default for the :doc:`package gpu ` command is to @@ -150,7 +150,7 @@ hardware, which pair style is used, the number of atoms/GPU, and the precision used on the GPU (double, single, mixed). Using the GPU package in OpenCL mode on CPUs (which uses vectorization and multithreading) is usually resulting in inferior performance compared to using LAMMPS' native -threading and vectorization support in the USER-OMP and USER-INTEL packages. +threading and vectorization support in the OPENMP and INTEL packages. See the `Benchmark page `_ of the LAMMPS web site for performance of the GPU package on various @@ -182,7 +182,7 @@ deterministic results. calculations can be dynamically balanced across the CPU cores and GPUs. GPU-specific settings can be made which can be optimized for different hardware. See the :doc:`package ` command - doc page for details. + page for details. * As described by the :doc:`package gpu ` command, GPU accelerated pair styles can perform computations asynchronously with CPU computations. The "Pair" time reported by LAMMPS will be the diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 0d0551c008..6526f836b2 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -1,7 +1,7 @@ -USER-INTEL package +INTEL package ================== -The USER-INTEL package is maintained by Mike Brown at Intel +The INTEL package is maintained by Mike Brown at Intel Corporation. It provides two methods for accelerating simulations, depending on the hardware you have. The first is acceleration on Intel CPUs by running in single, mixed, or double precision with @@ -12,7 +12,7 @@ When offloading to a co-processor from a CPU, the same routine is run twice, once on the CPU and once with an offload flag. This allows LAMMPS to run on the CPU cores and co-processor cores simultaneously. -Currently Available USER-INTEL Styles +Currently Available INTEL Styles """"""""""""""""""""""""""""""""""""" * Angle Styles: charmm, harmonic @@ -28,7 +28,7 @@ Currently Available USER-INTEL Styles .. warning:: - None of the styles in the USER-INTEL package currently + None of the styles in the INTEL package currently support computing per-atom stress. If any compute or fix in your input requires it, LAMMPS will abort with an error message. @@ -41,7 +41,7 @@ precision mode. Performance improvements are shown compared to LAMMPS *without using other acceleration packages* as these are under active development (and subject to performance changes). The measurements were performed using the input files available in -the src/USER-INTEL/TEST directory with the provided run script. +the src/INTEL/TEST directory with the provided run script. These are scalable in size; the results given are with 512K particles (524K for Liquid Crystal). Most of the simulations are standard LAMMPS benchmarks (indicated by the filename extension in @@ -56,7 +56,7 @@ Results are speedups obtained on Intel Xeon E5-2697v4 processors Knights Landing), and Intel Xeon Gold 6148 processors (code-named Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio 2017 update 2. Results are with 1 MPI task per physical core. See -*src/USER-INTEL/TEST/README* for the raw simulation rates and +*src/INTEL/TEST/README* for the raw simulation rates and instructions to reproduce. ---------- @@ -67,11 +67,11 @@ Accuracy and order of operations In most molecular dynamics software, parallelization parameters (# of MPI, OpenMP, and vectorization) can change the results due to changing the order of operations with finite-precision -calculations. The USER-INTEL package is deterministic. This means +calculations. The INTEL package is deterministic. This means that the results should be reproducible from run to run with the *same* parallel configurations and when using deterministic libraries or library settings (MPI, OpenMP, FFT). However, there -are differences in the USER-INTEL package that can change the +are differences in the INTEL package that can change the order of operations compared to LAMMPS without acceleration: * Neighbor lists can be created in a different order @@ -88,7 +88,7 @@ order of operations compared to LAMMPS without acceleration: Twister generator included in the Intel MKL library (that should be more robust than the default Masaglia random number generator) -The precision mode (described below) used with the USER-INTEL +The precision mode (described below) used with the INTEL package can change the *accuracy* of the calculations. For the default *mixed* precision option, calculations between pairs or triplets of atoms are performed in single precision, intended to @@ -102,8 +102,8 @@ mode should not be used without appropriate validation. Quick Start for Experienced Users """"""""""""""""""""""""""""""""" -LAMMPS should be built with the USER-INTEL package installed. -Simulations should be run with 1 MPI task per physical *core*\ , +LAMMPS should be built with the INTEL package installed. +Simulations should be run with 1 MPI task per physical *core*, not *hardware thread*\ . * Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. @@ -148,7 +148,7 @@ When using Intel compilers version 16.0 or later is required. In order to use offload to co-processors, an Intel Xeon Phi co-processor and an Intel compiler are required. -Although any compiler can be used with the USER-INTEL package, +Although any compiler can be used with the INTEL package, currently, vectorization directives are disabled by default when not using Intel compilers due to lack of standard support and observations of decreased performance. The OpenMP standard now @@ -185,7 +185,7 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, :doc:`USER-OMP package `, or +INTEL package, :doc:`OPENMP package `, or :doc:`KOKKOS package `. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% @@ -202,10 +202,10 @@ this information can normally be obtained with: cat /proc/cpuinfo -Building LAMMPS with the USER-INTEL package +Building LAMMPS with the INTEL package """"""""""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` page for instructions. Some additional details are covered here. For building with make, several example Makefiles for building with @@ -228,7 +228,7 @@ simple as: .. code-block:: bash - make yes-user-intel + make yes-intel source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi @@ -238,7 +238,7 @@ binary can be used on nodes with or without co-processors installed. However, if you do not have co-processors on your system, building without offload support will produce a smaller binary. -The general requirements for Makefiles with the USER-INTEL package +The general requirements for Makefiles with the INTEL package are as follows. When using Intel compilers, "-restrict" is required and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads @@ -253,7 +253,7 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias .. note:: - See the src/USER-INTEL/README file for additional flags that + See the src/INTEL/README file for additional flags that might be needed for best performance on Intel server processors code-named "Skylake". @@ -270,14 +270,14 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias in most of the example Makefiles is to use "-xHost", however this should not be used when cross-compiling. -Running LAMMPS with the USER-INTEL package +Running LAMMPS with the INTEL package """""""""""""""""""""""""""""""""""""""""" -Running LAMMPS with the USER-INTEL package is similar to normal use +Running LAMMPS with the INTEL package is similar to normal use with the exceptions that one should 1) specify that LAMMPS should use -the USER-INTEL package, 2) specify the number of OpenMP threads, and +the INTEL package, 2) specify the number of OpenMP threads, and 3) optionally specify the specific LAMMPS styles that should use the -USER-INTEL package. 1) and 2) can be performed from the command-line +INTEL package. 1) and 2) can be performed from the command-line or by editing the input script. 3) requires editing the input script. Advanced performance tuning options are also described below to get the best performance. @@ -312,27 +312,27 @@ almost all cases. recommended, especially when running on a machine with Intel Hyper-Threading technology disabled. -Run with the USER-INTEL package from the command line +Run with the INTEL package from the command line """"""""""""""""""""""""""""""""""""""""""""""""""""" -To enable USER-INTEL optimizations for all available styles used in +To enable INTEL optimizations for all available styles used in the input script, the "-sf intel" :doc:`command-line switch ` can be used without any requirement for editing the input script. This switch will automatically append "intel" to styles that support it. It also invokes a default command: :doc:`package intel 1 `. This package command is used to set -options for the USER-INTEL package. The default package command will -specify that USER-INTEL calculations are performed in mixed precision, +options for the INTEL package. The default package command will +specify that INTEL calculations are performed in mixed precision, that the number of OpenMP threads is specified by the OMP_NUM_THREADS environment variable, and that if co-processors are present and the binary was built with offload support, that 1 co-processor per node will be used with automatic balancing of work between the CPU and the co-processor. -You can specify different options for the USER-INTEL package by using +You can specify different options for the INTEL package by using the "-pk intel Nphi" :doc:`command-line switch ` with keyword/value pairs as specified in the documentation. Here, Nphi = # of Xeon Phi co-processors/node (ignored without offload -support). Common options to the USER-INTEL package include *omp* to +support). Common options to the INTEL package include *omp* to override any OMP_NUM_THREADS setting and specify the number of OpenMP threads, *mode* to set the floating-point precision mode, and *lrt* to enable Long-Range Thread mode as described below. See the :doc:`package intel ` command for details, including the default values @@ -348,11 +348,11 @@ launching MPI applications): mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision -Or run with the USER-INTEL package by editing an input script +Or run with the INTEL package by editing an input script """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As an alternative to adding command-line arguments, the input script -can be edited to enable the USER-INTEL package. This requires adding +can be edited to enable the INTEL package. This requires adding the :doc:`package intel ` command to the top of the input script. For the second example above, this would be: @@ -360,7 +360,7 @@ script. For the second example above, this would be: package intel 0 omp 2 mode double -To enable the USER-INTEL package only for individual styles, you can +To enable the INTEL package only for individual styles, you can add an "intel" suffix to the individual style, e.g.: .. code-block:: LAMMPS @@ -368,7 +368,7 @@ add an "intel" suffix to the individual style, e.g.: pair_style lj/cut/intel 2.5 Alternatively, the :doc:`suffix intel ` command can be added to -the input script to enable USER-INTEL styles for the commands that +the input script to enable INTEL styles for the commands that follow in the input script. Tuning for Performance @@ -376,7 +376,7 @@ Tuning for Performance .. note:: - The USER-INTEL package will perform better with modifications + The INTEL package will perform better with modifications to the input script when :doc:`PPPM ` is used: :doc:`kspace_modify diff ad ` should be added to the input script. @@ -388,7 +388,7 @@ is dedicated to performing some of the PPPM calculations and MPI communications. This feature requires setting the pre-processor flag -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset in the default makefiles (\ *Makefile.mpi* and *Makefile.serial*\ ) but -it is set in all makefiles tuned for the USER-INTEL package. On Intel +it is set in all makefiles tuned for the INTEL package. On Intel Xeon Phi x200 series CPUs, the LRT feature will likely improve performance, even on a single node. On Intel Xeon processors, using this mode might result in better performance when using multiple nodes, @@ -407,9 +407,9 @@ when using offload. performance and/or scalability for simple 2-body potentials such as lj/cut or when using LRT mode on processors supporting AVX-512. -Not all styles are supported in the USER-INTEL package. You can mix -the USER-INTEL package with styles from the :doc:`OPT ` -package or the :doc:`USER-OMP package `. Of course, this +Not all styles are supported in the INTEL package. You can mix +the INTEL package with styles from the :doc:`OPT ` +package or the :doc:`OPENMP package `. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" and "omp" @@ -420,7 +420,7 @@ where Nt is the number of OpenMP threads. The number of OpenMP threads should not be set differently for the different packages. Note that the :doc:`suffix hybrid intel omp ` command can also be used within the input script to automatically append the "omp" suffix to -styles when USER-INTEL styles are not available. +styles when INTEL styles are not available. .. note:: @@ -492,7 +492,7 @@ tuning of the number of threads to use per MPI task or the number of threads to use per core can be accomplished with keyword settings of the :doc:`package intel ` command. -The USER-INTEL package has two modes for deciding which atoms will be +The INTEL package has two modes for deciding which atoms will be handled by the co-processor. This choice is controlled with the *ghost* keyword of the :doc:`package intel ` command. When set to 0, ghost atoms (atoms at the borders between MPI tasks) are not offloaded @@ -528,7 +528,7 @@ accelerated style may be used with hybrid styles when offloading. :doc:`Special_bonds ` exclusion lists are not currently supported with offload, however, the same effect can often be accomplished by setting cutoffs for excluded atom types to 0. None of -the pair styles in the USER-INTEL package currently support the +the pair styles in the INTEL package currently support the "inner", "middle", "outer" options for rRESPA integration via the :doc:`run_style respa ` command; only the "pair" option is supported. diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index c3f8945c62..400db9585c 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -67,7 +67,7 @@ produce an executable compatible with a specific hardware. Building LAMMPS with the KOKKOS package """"""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for instructions. +See the :ref:`Build extras ` page for instructions. Running LAMMPS with the KOKKOS package """""""""""""""""""""""""""""""""""""" @@ -217,7 +217,7 @@ threads/task as Nt. The product of these two values should be N, i.e. be best for many-body potentials. For simpler pair-wise potentials, it may be faster to use a "full" neighbor list with Newton flag to "off". Use the "-pk kokkos" :doc:`command-line switch ` to change - the default :doc:`package kokkos ` options. See its doc page for + the default :doc:`package kokkos ` options. See its page for details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: @@ -235,7 +235,7 @@ threads/task as Nt. The product of these two values should be N, i.e. To build with Kokkos support for Intel Xeon Phi co-processors such as Knight's Corner (KNC), your system must be configured to use - them in "native" mode, not "offload" mode like the USER-INTEL package + them in "native" mode, not "offload" mode like the INTEL package supports. Running on GPUs @@ -279,7 +279,7 @@ one or more nodes, each with two GPUs: setting the neighbor binsize equal to twice the CPU default value will give speedup, which is the default when running on GPUs. Use the "-pk kokkos" :doc:`command-line switch ` to change the default - :doc:`package kokkos ` options. See its doc page for details and + :doc:`package kokkos ` options. See its page for details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: @@ -390,10 +390,10 @@ Generally speaking, the following rules of thumb apply: * When running on CPUs only, with a single thread per MPI task, performance of a KOKKOS style is somewhere between the standard (un-accelerated) styles (MPI-only mode), and those provided by the - USER-OMP package. However the difference between all 3 is small (less + OPENMP package. However the difference between all 3 is small (less than 20%). * When running on CPUs only, with multiple threads per MPI task, - performance of a KOKKOS style is a bit slower than the USER-OMP + performance of a KOKKOS style is a bit slower than the OPENMP package. * When running large number of atoms per GPU, KOKKOS is typically faster than the GPU package when compiled for double precision. The benefit @@ -401,8 +401,8 @@ Generally speaking, the following rules of thumb apply: significantly on the hardware in use and the simulated system and pair style. * When running on Intel hardware, KOKKOS is not as fast as - the USER-INTEL package, which is optimized for x86 hardware (not just - from Intel) and compilation with the Intel compilers. The USER-INTEL + the INTEL package, which is optimized for x86 hardware (not just + from Intel) and compilation with the Intel compilers. The INTEL package also can increase the vector length of vector instructions by switching to single or mixed precision mode. diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index f29e3743b4..3d9cbe19e0 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -1,7 +1,7 @@ -USER-OMP package +OPENMP package ================ -The USER-OMP package was developed by Axel Kohlmeyer at Temple +The OPENMP package was developed by Axel Kohlmeyer at Temple University. It provides optimized and multi-threaded versions of many pair styles, nearly all bonded styles (bond, angle, dihedral, improper), several Kspace styles, and a few fix styles. It uses @@ -15,13 +15,13 @@ To enable multi-threading, your compiler must support the OpenMP interface. You should have one or more multi-core CPUs, as multiple threads can only be launched by each MPI task on the local node (using shared memory). -Building LAMMPS with the USER-OMP package +Building LAMMPS with the OPENMP package """"""""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` page for instructions. -Run with the USER-OMP package from the command line +Run with the OPENMP package from the command line """"""""""""""""""""""""""""""""""""""""""""""""""" These examples assume one or more 16-core nodes. @@ -39,7 +39,7 @@ tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. You need to choose how many OpenMP threads per MPI task will be used -by the USER-OMP package. Note that the product of MPI tasks \* +by the OPENMP package. Note that the product of MPI tasks \* threads/task should not exceed the physical number of cores (on a node), otherwise performance will suffer. @@ -50,12 +50,12 @@ threads per MPI task via the OMP_NUM_THREADS environment variable. You can also use the "-pk omp Nt" :doc:`command-line switch `, to explicitly set Nt = # of OpenMP threads per MPI task to use, as well as additional options. Its syntax is the -same as the :doc:`package omp ` command whose doc page gives +same as the :doc:`package omp ` command whose page gives details, including the default values used if it is not specified. It also gives more details on how to set the number of threads via the OMP_NUM_THREADS environment variable. -Or run with the USER-OMP package by editing an input script +Or run with the OPENMP package by editing an input script """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" The discussion above for the mpirun/mpiexec command, MPI tasks/node, @@ -69,8 +69,8 @@ Use the :doc:`suffix omp ` command, or you can explicitly add an pair_style lj/cut/omp 2.5 You must also use the :doc:`package omp ` command to enable the -USER-OMP package. When you do this you also specify how many threads -per MPI task to use. The command doc page explains other options and +OPENMP package. When you do this you also specify how many threads +per MPI task to use. The command page explains other options and how to set the number of threads via the OMP_NUM_THREADS environment variable. @@ -82,10 +82,10 @@ reduction in the "Pair time", "Bond time", "KSpace time", and "Loop time" values printed at the end of a run. You may see a small performance advantage (5 to 20%) when running a -USER-OMP style (in serial or parallel) with a single thread per MPI +OPENMP style (in serial or parallel) with a single thread per MPI task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This -is because many of the USER-OMP styles contain similar optimizations +is because many of the OPENMP styles contain similar optimizations to those used in the OPT package, described in :doc:`the OPT package ` doc page. @@ -95,19 +95,19 @@ tested via benchmark runs for a specific simulation running on a specific machine, paying attention to guidelines discussed in the next sub-section. -A description of the multi-threading strategy used in the USER-OMP +A description of the multi-threading strategy used in the OPENMP package and some performance examples are `presented here `_. Guidelines for best performance """"""""""""""""""""""""""""""" -For many problems on current generation CPUs, running the USER-OMP +For many problems on current generation CPUs, running the OPENMP package with a single thread/task is faster than running with multiple threads/task. This is because the MPI parallelization in LAMMPS is often more efficient than multi-threading as implemented in the -USER-OMP package. The parallel efficiency (in a threaded sense) also -varies for different USER-OMP styles. +OPENMP package. The parallel efficiency (in a threaded sense) also +varies for different OPENMP styles. Using multiple threads/task can be more effective under the following circumstances: @@ -143,7 +143,7 @@ circumstances: sometimes be achieved by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the :doc:`run_style verlet/split ` command, which is compatible - with the USER-OMP package, is an alternative way to reduce the number + with the OPENMP package, is an alternative way to reduce the number of MPI tasks assigned to the KSpace calculation. Additional performance tips are as follows: diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst index 338c4f2030..e115393017 100644 --- a/doc/src/Speed_opt.rst +++ b/doc/src/Speed_opt.rst @@ -15,7 +15,7 @@ Any hardware. Any compiler. Building LAMMPS with the OPT package """""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for instructions. +See the :ref:`Build extras ` page for instructions. Run with the OPT package from the command line """""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index f5da991f0b..be3f205f4b 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -12,17 +12,16 @@ All of these commands are in packages provided with LAMMPS. An overview of packages is give on the :doc:`Packages ` doc pages. -These are the accelerator packages currently in LAMMPS, either as -standard or user packages: +These are the accelerator packages currently in LAMMPS: +-----------------------------------------+-------------------------------------------------------+ | :doc:`GPU Package ` | for GPUs via CUDA, OpenCL, or ROCm HIP | +-----------------------------------------+-------------------------------------------------------+ -| :doc:`USER-INTEL Package ` | for Intel CPUs and Intel Xeon Phi | +| :doc:`INTEL Package ` | for Intel CPUs and Intel Xeon Phi | +-----------------------------------------+-------------------------------------------------------+ | :doc:`KOKKOS Package ` | for NVIDIA GPUs, Intel Xeon Phi, and OpenMP threading | +-----------------------------------------+-------------------------------------------------------+ -| :doc:`USER-OMP Package ` | for OpenMP threading and generic CPU optimizations | +| :doc:`OPENMP Package ` | for OpenMP threading and generic CPU optimizations | +-----------------------------------------+-------------------------------------------------------+ | :doc:`OPT Package ` | generic CPU optimizations | +-----------------------------------------+-------------------------------------------------------+ @@ -41,11 +40,11 @@ Inverting this list, LAMMPS currently has acceleration support for three kinds of hardware, via the listed packages: +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ -| Many-core CPUs | :doc:`USER-INTEL `, :doc:`KOKKOS `, :doc:`USER-OMP `, :doc:`OPT ` packages | +| Many-core CPUs | :doc:`INTEL `, :doc:`KOKKOS `, :doc:`OPENMP `, :doc:`OPT ` packages | +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ | GPUs | :doc:`GPU `, :doc:`KOKKOS ` packages | +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ -| Intel Phi/AVX | :doc:`USER-INTEL `, :doc:`KOKKOS ` packages | +| Intel Phi/AVX | :doc:`INTEL `, :doc:`KOKKOS ` packages | +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ Which package is fastest for your hardware may depend on the size @@ -84,9 +83,9 @@ listed above: +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | build the accelerator library | only for GPU package | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ -| install the accelerator package | make yes-opt, make yes-user-intel, etc | +| install the accelerator package | make yes-opt, make yes-intel, etc | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ -| add compile/link flags to Makefile.machine in src/MAKE | only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | +| add compile/link flags to Makefile.machine in src/MAKE | only for INTEL, KOKKOS, OPENMP, OPT packages | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | re-build LAMMPS | make machine | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ @@ -116,15 +115,15 @@ script. With a few exceptions, you can build a single LAMMPS executable with all its accelerator packages installed. Note however that the - USER-INTEL and KOKKOS packages require you to choose one of their + INTEL and KOKKOS packages require you to choose one of their hardware options when building for a specific platform. I.e. CPU or - Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi + Phi option for the INTEL package. Or the OpenMP, Cuda, or Phi option for the KOKKOS package. These are the exceptions. You cannot build a single executable with: -* both the USER-INTEL Phi and KOKKOS Phi options -* the USER-INTEL Phi or Kokkos Phi option, and the GPU package +* both the INTEL Phi and KOKKOS Phi options +* the INTEL Phi or Kokkos Phi option, and the GPU package See the examples/accelerate/README and make.list files for sample Make.py commands that build LAMMPS with any or all of the accelerator @@ -156,7 +155,7 @@ are in the individual accelerator sections. * Styles with a "gpu" suffix are part of the GPU package and can be run on Intel, NVIDIA, or AMD GPUs. The speed-up on a GPU depends on a variety of factors, discussed in the accelerator sections. -* Styles with an "intel" suffix are part of the USER-INTEL +* Styles with an "intel" suffix are part of the INTEL package. These styles support vectorized single and mixed precision calculations, in addition to full double precision. In extreme cases, this can provide speedups over 3.5x on CPUs. The package also @@ -167,7 +166,7 @@ are in the individual accelerator sections. run using OpenMP on multicore CPUs, on an NVIDIA or AMD GPU, or on an Intel Xeon Phi in "native" mode. The speed-up depends on a variety of factors, as discussed on the KOKKOS accelerator page. -* Styles with an "omp" suffix are part of the USER-OMP package and allow +* Styles with an "omp" suffix are part of the OPENMP package and allow a pair-style to be run in multi-threaded mode using OpenMP. This can be useful on nodes with high-core counts when using less MPI processes than cores is advantageous, e.g. when running with PPPM so that FFTs diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 4d46d32037..72cfc7db9e 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -15,7 +15,7 @@ Sandia which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. .. _lws: https://www.lammps.org -.. _pizza: https://pizza.sandia.gov +.. _pizza: https://lammps.github.io/pizza .. _python: https://www.python.org Additional tools included in the LAMMPS distribution are described on @@ -67,7 +67,7 @@ Post-processing tools * :ref:`amber2lmp ` * :ref:`binary2txt ` * :ref:`ch2lmp ` - * :ref:`colvars ` + * :ref:`colvars ` * :ref:`eff ` * :ref:`fep ` * :ref:`lmp2arc ` @@ -76,7 +76,6 @@ Post-processing tools * :ref:`phonon ` * :ref:`pymol_asphere ` * :ref:`python ` - * :ref:`reax ` * :ref:`replica ` * :ref:`smd ` * :ref:`spin ` @@ -214,7 +213,7 @@ tool and the specific name of the program used (e.g. ``ninja-v1.10`` or ---------- -.. _colvars: +.. _colvars_tools: colvars tools --------------------------- @@ -341,7 +340,7 @@ fep tool The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation -simulations using the USER-FEP package. +simulations using the FEP package. The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr. @@ -364,7 +363,7 @@ michele.ceriotti at gmail.com, to interface to a variety of molecular dynamics codes. See the tools/i-pi/manual.pdf file for an overview of i-PI, and the -:doc:`fix ipi ` doc page for further details on running PIMD +:doc:`fix ipi ` page for further details on running PIMD calculations with LAMMPS. ---------- @@ -861,10 +860,10 @@ phonon tool The phonon sub-directory contains a post-processing tool useful for analyzing the output of the :doc:`fix phonon ` command in -the USER-PHONON package. +the PHONON package. See the README file for instruction on building the tool and what -library it needs. And see the examples/USER/phonon directory +library it needs. And see the examples/PACKAGES/phonon directory for example problems that can be post-processed with this tool. This tool was written by Ling-Ti Kong at Shanghai Jiao Tong @@ -947,20 +946,6 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) ---------- -.. _reax_tool: - -reax tool --------------------------- - -The reax sub-directory contains stand-alone codes that can -post-process the output of the :doc:`fix reax/c/bonds ` -command from a LAMMPS simulation using :doc:`ReaxFF `. See -the README.txt file for more info. - -These tools were written by Aidan Thompson at Sandia. - ----------- - .. _smd: smd tool @@ -968,13 +953,13 @@ smd tool The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output -files created by the Smooth-Mach Dynamics (USER-SMD) package into a +files created by the Smooth-Mach Dynamics (MACHDYN) package into a VTK-compatible unstructured grid file. It could then be read in and visualized by VTK. See the header of dump2vtk.cpp for more details. -This tool was written by the USER-SMD package author, Georg +This tool was written by the MACHDYN package author, Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). diff --git a/doc/src/accel_styles.rst b/doc/src/accel_styles.rst index b5ef400f12..27a798d731 100644 --- a/doc/src/accel_styles.rst +++ b/doc/src/accel_styles.rst @@ -1,17 +1,17 @@ -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index e557648d9f..0da31e54e7 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -56,22 +56,22 @@ radian\^2. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See :doc:`Speed packages ` doc page for more +See :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index bf0305055a..f257d96dc3 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -126,7 +126,7 @@ Restrictions This angle style can only be used if LAMMPS was built with the CLASS2 package. For the *class2/p6* style LAMMPS needs to be built with the -USER-MOFFF package. See the :doc:`Build package ` doc +MOFFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 4b8497d743..5061bc7b87 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -60,7 +60,7 @@ Restrictions :doc:`special_bonds ` 0.0 weighting of 1-3 interactions. This angle style can only be used if LAMMPS was built with the -USER-MOFFF package. See the :doc:`Build package ` doc +MOFFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 280e6ea2c4..b417b7a4a2 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc page +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 4983745618..1eb5240011 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc page +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index 71bda194c7..a22f93b1d0 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -53,7 +53,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER-MISC package. +MOLECULE package. Related commands """""""""""""""" diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index 4ae4928751..72962abc1c 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 3cd1884be0..318bce9513 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_YAFF package. See the :doc:`Build package ` doc +YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 4dd8aadfb8..8aaed55132 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -88,7 +88,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +DIPOLE package. See the :doc:`Build package ` doc page for more info. .. note:: @@ -106,7 +106,9 @@ page for more info. The :doc:`newton ` command for intramolecular interactions must be "on" (which is the default except when using some accelerator packages). -This angle style should not be used with SHAKE. +.. note:: + + This angle style should **NOT** be used with fix shake. Related commands """""""""""""""" diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index 231f45e808..780ecd510c 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -50,7 +50,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index 14b4bbcfe9..29a493a442 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -49,7 +49,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_gaussian.rst b/doc/src/angle_gaussian.rst index 1caae3b20c..9f2964f5f7 100644 --- a/doc/src/angle_gaussian.rst +++ b/doc/src/angle_gaussian.rst @@ -49,7 +49,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index 1a562b0118..cf8ea1a3fb 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -58,7 +58,7 @@ specifying additional BondBond (and BondAngle) coefficients either via the input script or in the data file. I.e. *class2* must be added to each line after the angle type. For lines in the BondBond (or BondAngle) section of the data file for angle types that are not -*class2*\ , you must use an angle style of *skip* as a placeholder, e.g. +*class2*, you must use an angle style of *skip* as a placeholder, e.g. .. parsed-literal:: diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 0905ff6e4c..c1011da47e 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -49,7 +49,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_YAFF package. See the :doc:`Build package ` doc +YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 7dfb4b2896..e153faee73 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -57,7 +57,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 340a3e4de7..50f4a5b360 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -37,7 +37,7 @@ where :math:`\theta_0` is the equilibrium value of the angle and *lj/sdk* pair style between the atoms 1 and 3. This angle potential is intended for coarse grained MD simulations with the CMM parameterization using the :doc:`pair_style lj/sdk `. Relative to the -pair_style *lj/sdk*\ , however, the energy is shifted by +pair_style *lj/sdk*, however, the energy is shifted by :math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor is included in :math:`K`. @@ -64,7 +64,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER-CGSDK package. See the :doc:`Build package ` doc +CG-SDK package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 540d15fee2..0715625d45 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -66,7 +66,7 @@ specified by the associated :doc:`angle_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :ref:`Commands angle ` doc page are followed by one or more +The individual style names on the :ref:`Commands angle ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off angle interactions @@ -103,7 +103,7 @@ Angle styles can only be set for atom_styles that allow angles to be defined. Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual bond potentials tell if it is part of a package. Related commands diff --git a/doc/src/atc_control_thermal.rst b/doc/src/atc_control_thermal.rst index d6d6c25405..7a17701c5c 100644 --- a/doc/src/atc_control_thermal.rst +++ b/doc/src/atc_control_thermal.rst @@ -66,7 +66,7 @@ Restrictions Only for be used with the specific controllers *thermal* or *momentum*. They are ignored if a lumped solution is requested. -*control thermal* is only for be used with specific transfers: thermal (*rescale*\ , *hoover*\ , *flux*\ ), *two_temperature* (*flux*\ ). +*control thermal* is only for be used with specific transfers: thermal (*rescale*, *hoover*, *flux*\ ), *two_temperature* (*flux*\ ). *rescale* not valid with time filtering activated *correction_max_iterations* is only for use with *thermal* physics using diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index c142fb6519..2f01877ac7 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -40,7 +40,7 @@ command. The *id* and *map* keywords must be specified before a simulation box is defined; other keywords can be specified any time. The *id* keyword determines whether non-zero atom IDs can be assigned -to each atom. If the value is *yes*\ , which is the default, IDs are +to each atom. If the value is *yes*, which is the default, IDs are assigned, whether you use the :doc:`create atoms ` or :doc:`read_data ` or :doc:`read_restart ` commands to initialize atoms. If the value is *no* the IDs for all diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 1b5aaccb9a..bade8c2f79 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -10,7 +10,7 @@ Syntax atom_style style args -* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid* +* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid* .. parsed-literal:: @@ -61,7 +61,7 @@ command. Restrictions section. Once a style is assigned, it cannot be changed, so use a style general -enough to encompass all attributes. E.g. with style *bond*\ , angular +enough to encompass all attributes. E.g. with style *bond*, angular terms cannot be used or added later to the model. It is OK to use a style more general than needed, though it may be slightly inefficient. @@ -110,6 +110,8 @@ quantities. +--------------+-----------------------------------------------------+--------------------------------------+ | *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules | +--------------+-----------------------------------------------------+--------------------------------------+ +| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models | ++--------------+-----------------------------------------------------+--------------------------------------+ | *peri* | mass, volume | mesoscopic Peridynamic models | +--------------+-----------------------------------------------------+--------------------------------------+ | *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | @@ -134,13 +136,13 @@ quantities. It is possible to add some attributes, such as a molecule ID, to atom styles that do not have them via the :doc:`fix property/atom ` command. This command also allows new custom attributes consisting of extra integer or - floating-point values to be added to atoms. See the :doc:`fix property/atom ` doc page for examples of cases + floating-point values to be added to atoms. See the :doc:`fix property/atom ` page for examples of cases where this is useful and details on how to initialize, access, and output the custom values. -All of the above styles define point particles, except the *sphere*\ , -*ellipsoid*\ , *electron*\ , *peri*\ , *wavepacket*\ , *line*\ , *tri*\ , and -*body* styles, which define finite-size particles. See the :doc:`Howto spherical ` doc page for an overview of using +All of the above styles define point particles, except the *sphere*, +*ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, *tri*, and +*body* styles, which define finite-size particles. See the :doc:`Howto spherical ` page for an overview of using finite-size particle models with LAMMPS. All of the point-particle styles assign mass to particles on a @@ -193,8 +195,14 @@ position, which is represented by the eradius = electron size. For the *peri* style, the particles are spherical and each stores a per-particle mass and volume. +The *oxdna* style is for coarse-grained nucleotides and stores the +3'-to-5' polarity of the nucleotide strand, which is set through +the bond topology in the data file. The first (second) atom in a +bond definition is understood to point towards the 3'-end (5'-end) +of the strand. Note that this style is part of the CG-DNA package. + The *dpd* style is for dissipative particle dynamics (DPD) particles. -Note that it is part of the USER-DPD package, and is not for use with +Note that it is part of the DPD-REACT package, and is not for use with the :doc:`pair_style dpd or dpd/stat ` commands, which can simply use atom_style atomic. Atom_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive @@ -228,7 +236,7 @@ individual physical bodies from penetrating each other. For the *spin* style, a magnetic spin is associated to each atom. Those spins have a norm (their magnetic moment) and a direction. -The *wavepacket* style is similar to *electron*\ , but the electrons may +The *wavepacket* style is similar to *electron*, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate particle in LAMMPS, wave packets belonging to the same electron must @@ -248,7 +256,7 @@ command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms only store a template index and template atom to identify which molecule and which atom-within-the-molecule they represent. Using the -*template* style instead of the *bond*\ , *angle*\ , *molecular* styles +*template* style instead of the *bond*, *angle*, *molecular* styles can save memory for systems comprised of a large number of small molecules, all of a single type (or small number of types). See the paper by Grime and Voth, in :ref:`(Grime) `, for examples of how this @@ -275,7 +283,7 @@ the *bstyle* argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The :doc:`Howto body ` doc page describes the body styles +The :doc:`Howto body ` page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent. For all styles, each body particle stores moments of inertia and a quaternion 4-vector, so that its @@ -319,17 +327,19 @@ styles take the same arguments and should produce the same results, except for round-off and precision issues. Note that other acceleration packages in LAMMPS, specifically the GPU, -USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom +INTEL, OPENMP, and OPT packages do not use accelerated atom styles. The accelerated styles are part of the KOKKOS package. They are only -enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with those packages. See the :doc:`Build +package ` page for more info. You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the +by including their suffix, or you can use the :doc:`-suffix command-line +switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. Restrictions @@ -339,9 +349,10 @@ This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. Many of the styles listed above are only enabled if LAMMPS was built -with a specific package, as listed below. See the :doc:`Build package ` doc page for more info. +with a specific package, as listed below. See the :doc:`Build package +` page for more info. -The *angle*\ , *bond*\ , *full*\ , *molecular*\ , and *template* styles are +The *angle*, *bond*, *full*, *molecular*, and *template* styles are part of the MOLECULE package. The *line* and *tri* styles are part of the ASPHERE package. @@ -352,24 +363,26 @@ The *dipole* style is part of the DIPOLE package. The *peri* style is part of the PERI package for Peridynamics. -The *electron* style is part of the USER-EFF package for :doc:`electronic force fields `. +The *oxdna* style is part of the CG-DNA package for coarse-grained simulation of DNA and RNA. -The *dpd* style is part of the USER-DPD package for dissipative +The *electron* style is part of the EFF package for :doc:`electronic force fields `. + +The *dpd* style is part of the DPD-REACT package for dissipative particle dynamics (DPD). -The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESODPD package +The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. -The *sph* style is part of the USER-SPH package for smoothed particle -hydrodynamics (SPH). See `this PDF guide `_ to using SPH in LAMMPS. +The *sph* style is part of the SPH package for smoothed particle +hydrodynamics (SPH). See `this PDF guide `_ to using SPH in LAMMPS. -The *mesont* style is part of the USER-MESONT package. +The *mesont* style is part of the MESONT package. The *spin* style is part of the SPIN package. -The *wavepacket* style is part of the USER-AWPMD package for the +The *wavepacket* style is part of the AWPMD package for the :doc:`antisymmetrized wave packet MD method `. Related commands diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 5d42fabb21..94ea27f49e 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -11,7 +11,7 @@ Syntax balance thresh style args ... keyword args ... * thresh = imbalance threshold that must be exceeded to perform a re-balance -* one style/arg pair can be used (or multiple for *x*\ ,\ *y*\ ,\ *z*\ ) +* one style/arg pair can be used (or multiple for *x*,\ *y*,\ *z*\ ) * style = *x* or *y* or *z* or *shift* or *rcb* .. parsed-literal:: @@ -170,10 +170,10 @@ fractions of the box length) are also printed. ---------- The method used to perform a load balance is specified by one of the -listed styles (or more in the case of *x*\ ,\ *y*\ ,\ *z*\ ), which are +listed styles (or more in the case of *x*,\ *y*,\ *z*\ ), which are described in detail below. There are 2 kinds of styles. -The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which +The *x*, *y*, *z*, and *shift* styles are "grid" methods which produce a logical 3d grid of processors. They operate by changing the cutting planes (or lines) between processors in 3d (or 2d), to adjust the volume (area in 2d) assigned to each processor, as in the @@ -222,7 +222,7 @@ from scratch. ---------- -The *x*\ , *y*\ , and *z* styles invoke a "grid" method for balancing, as +The *x*, *y*, and *z* styles invoke a "grid" method for balancing, as described above. Note that any or all of these 3 styles can be specified together, one after the other, but they cannot be used with any other style. This style adjusts the position of cutting planes @@ -263,7 +263,7 @@ once. You should normally only list dimensions where you expect there to be a density variation in the particles. Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in *dimstr*\ , one dimension at a time. For a single +dimensions listed in *dimstr*, one dimension at a time. For a single dimension, the balancing operation (described below) is iterated on up to *Niter* times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the *stopthresh* @@ -428,8 +428,8 @@ weights. It assigns the same weight to each particle owned by a processor based on the total computational time spent by that processor. See details below on what time window is used. It uses the same timing information as is used for the :doc:`MPI task timing -breakdown `, namely, for sections *Pair*\ , *Bond*\ , -*Kspace*\ , and *Neigh*\ . The time spent in those portions of the +breakdown `, namely, for sections *Pair*, *Bond*, +*Kspace*, and *Neigh*\ . The time spent in those portions of the timestep are measured for each MPI rank, summed, then divided by the number of particles owned by that processor. I.e. the weight is an effective CPU time/particle averaged over the particles on that @@ -455,7 +455,7 @@ are for the entire previous run. For the *fix balance* command the timing data is for only the timesteps since the last balancing operation was performed. If timing information for the required sections is not available, e.g. at the beginning of a run, or when the -:doc:`timer ` command is set to either *loop* or *off*\ , a warning +:doc:`timer ` command is set to either *loop* or *off*, a warning is issued. In this case no weights are computed. .. note:: @@ -558,7 +558,7 @@ Related commands :doc:`group `, :doc:`processors `, :doc:`fix balance `, :doc:`comm_style ` -.. _pizza: https://pizza.sandia.gov +.. _pizza: https://lammps.github.io/pizza Default """"""" diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index aea503738f..559e031229 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -55,7 +55,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the CLASS2 -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index 0c6a37ca62..108f538628 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. You typically should specify :doc:`special_bonds fene ` diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 1be06561e9..8e04da6146 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -60,7 +60,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. You typically should specify :doc:`special_bonds fene ` diff --git a/doc/src/bond_gaussian.rst b/doc/src/bond_gaussian.rst index dc9bea1cce..369b9eac26 100644 --- a/doc/src/bond_gaussian.rst +++ b/doc/src/bond_gaussian.rst @@ -50,7 +50,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index d4eb958ebe..16b5cb0f36 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -51,7 +51,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index e3320f2e19..a76cc54746 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -53,7 +53,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index 469c370969..24bbc98b83 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -56,7 +56,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index d0f44740b3..05fb245727 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 0da93ccade..1ffd4a1c98 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Unlike other bond styles, the hybrid bond style does not store bond diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index 2a255e7590..aa219f0cc7 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -47,7 +47,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER_YAFF package. See the :doc:`Build package ` doc +YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index f096624ba0..4aa76a6712 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -52,7 +52,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 77271502ea..91bd03421a 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -51,8 +51,8 @@ or :doc:`read_restart ` commands: Restrictions """""""""""" -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +This bond style can only be used if LAMMPS was built with the EXTRA-MOLECULE +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 3f52424d49..f863c0e98f 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -39,7 +39,7 @@ Examples Description """"""""""" -The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential +The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential .. math:: @@ -76,17 +76,33 @@ commands: The coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. +.. note:: + + This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna* + (see documentation of :doc:`atom_style `). The *atom_style oxdna* + stores the 3'-to-5' polarity of the nucleotide strand, which is set through + the bond topology in the data file. The first (second) atom in a bond definition + is understood to point towards the 3'-end (5'-end) of the strand. + +.. warning:: + + If data files are produced with :doc:`write_data `, then the + :doc:`newton ` command should be set to *newton on* or *newton off on*. + Otherwise the data files will not have the same 3'-to-5' polarity as the + initial data file. This limitation does not apply to binary restart files + produced with :doc:`write_restart `. + Example input and data files for DNA and RNA duplexes can be found in -examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python +examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA duplexes can be found in -examples/USER/cgdna/util/. +examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxDNA/oxRNA publications. These are :ref:`(Ouldridge) ` and :ref:`(Ouldridge-DPhil) ` for oxDNA, @@ -101,14 +117,14 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +CG-DNA package and the MOLECULE and ASPHERE package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" :doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv `, :doc:`pair_style oxrna2/excv `, -:doc:`bond_coeff `, :doc:`fix nve/dotc/langevin ` +:doc:`bond_coeff `, :doc:`atom_style oxdna `, :doc:`fix nve/dotc/langevin ` Default """"""" diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 8c5b363e54..89c33607ac 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -96,7 +96,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. The *quartic* style requires that :doc:`special_bonds ` diff --git a/doc/src/bond_special.rst b/doc/src/bond_special.rst index d2423c9e23..cc11c41f11 100644 --- a/doc/src/bond_special.rst +++ b/doc/src/bond_special.rst @@ -86,7 +86,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MISC package. See the :doc:`Build package ` doc page for more info. This bond style requires the use of a :doc:`pair_style ` which diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index e302ea792d..177dc8cc05 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -111,7 +111,7 @@ Bond styles can only be set for atom styles that allow bonds to be defined. Most bond styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual bond potentials tell if it is part of a package. Related commands diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index fedb50355d..898503b951 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -143,7 +143,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index aa68357e1d..d6458e7c39 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -10,7 +10,7 @@ Syntax boundary x y z -* x,y,z = *p* or *s* or *f* or *m*\ , one or two letters +* x,y,z = *p* or *s* or *f* or *m*, one or two letters .. parsed-literal:: @@ -45,17 +45,17 @@ the other end. A periodic dimension can change in size due to constant pressure boundary conditions or box deformation (see the :doc:`fix npt ` and :doc:`fix deform ` commands). The *p* style must be applied to both faces of a dimension. -The styles *f*\ , *s*\ , and *m* mean the box is non-periodic, so that +The styles *f*, *s*, and *m* mean the box is non-periodic, so that particles do not interact across the boundary and do not move from one side of the box to the other. -For style *f*\ , the position of the face is fixed. If an atom moves +For style *f*, the position of the face is fixed. If an atom moves outside the face it will be deleted on the next timestep that reneighboring occurs. This will typically generate an error unless you have set the :doc:`thermo_modify lost ` option to allow for lost atoms. -For style *s*\ , the position of the face is set so as to encompass the +For style *s*, the position of the face is set so as to encompass the atoms in that dimension (shrink-wrapping), no matter how far they move. Note that when the difference between the current box dimensions and the shrink-wrap box dimensions is large, this can lead to lost @@ -67,7 +67,7 @@ This is best addressed by setting initial box dimensions to match the shrink-wrapped dimensions more closely, by using *m* style boundaries (see below). -For style *m*\ , shrink-wrapping occurs, but is bounded by the value +For style *m*, shrink-wrapping occurs, but is bounded by the value specified in the data or restart file or set by the :doc:`create_box ` command. For example, if the upper z face has a value of 50.0 in the data file, the face will always be @@ -85,7 +85,7 @@ and xhi faces of the box are planes tilting in the +y direction as y increases. These tilted planes are shrink-wrapped around the atoms to determine the x extent of the box. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. diff --git a/doc/src/box.rst b/doc/src/box.rst index c5937df75c..b9c586b6f7 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -34,15 +34,15 @@ For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword allows simulation domains to be created with arbitrary tilt factors, e.g. via the :doc:`create_box ` or :doc:`read_data ` commands. Tilt factors determine how -skewed the triclinic box is; see the :doc:`Howto triclinic ` doc page for a discussion of triclinic +skewed the triclinic box is; see the :doc:`Howto triclinic ` page for a discussion of triclinic boxes in LAMMPS. LAMMPS normally requires that no tilt factor can skew the box more than half the distance of the parallel box length, which is the first dimension in the tilt factor (x for xz). If *tilt* is set to -*small*\ , which is the default, then an error will be +*small*, which is the default, then an error will be generated if a box is created which exceeds this limit. If *tilt* -is set to *large*\ , then no limit is enforced. You can create +is set to *large*, then no limit is enforced. You can create a box with any tilt factors you wish. Note that if a simulation box has a large tilt factor, LAMMPS will run diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index 328326a83a..f63949bcd8 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -16,7 +16,7 @@ Syntax .. parsed-literal:: parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap* - *x*\ , *y*\ , *z* args = style value(s) + *x*, *y*, *z* args = style value(s) style = *final* or *delta* or *scale* or *volume* *final* values = lo hi lo hi = box boundaries after displacement (distance units) @@ -25,14 +25,14 @@ Syntax *scale* values = factor factor = multiplicative factor for change in box length after displacement *volume* value = none = adjust this dim to preserve volume of system - *xy*\ , *xz*\ , *yz* args = style value + *xy*, *xz*, *yz* args = style value style = *final* or *delta* *final* value = tilt tilt = tilt factor after displacement (distance units) *delta* value = dtilt dtilt = change in tilt factor after displacement (distance units) *boundary* args = x y z - x,y,z = *p* or *s* or *f* or *m*\ , one or two letters + x,y,z = *p* or *s* or *f* or *m*, one or two letters *p* is periodic *f* is non-periodic and fixed *s* is non-periodic and shrink-wrapped @@ -82,7 +82,7 @@ The :doc:`create_box `, :doc:`read data `, and simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. @@ -179,18 +179,18 @@ new owning processors. ---------- -For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their +For the *x*, *y*, and *z* parameters, this is the meaning of their styles and values. -For style *final*\ , the final lo and hi box boundaries of a dimension +For style *final*, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , plus or minus changes in the lo/hi box boundaries +For style *delta*, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *scale*\ , a multiplicative factor to apply to the box length +For style *scale*, a multiplicative factor to apply to the box length of a dimension is specified. For example, if the initial box length is 10, and the factor is 1.1, then the final box length will be 11. A factor less than 1.0 means compression. @@ -199,7 +199,7 @@ The *volume* style changes the specified dimension in such a way that the overall box volume remains constant with respect to the operation performed by the preceding keyword. The *volume* style can only be used following a keyword that changed the volume, which is any of the -*x*\ , *y*\ , *z* keywords. If the preceding keyword "key" had a *volume* +*x*, *y*, *z* keywords. If the preceding keyword "key" had a *volume* style, then both it and the current keyword apply to the keyword preceding "key". I.e. this sequence of keywords is allowed: @@ -249,15 +249,15 @@ compressed around its mid point. ---------- -For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their +For the *xy*, *xz*, and *yz* parameters, this is the meaning of their styles and values. Note that changing the tilt factors of a triclinic box does not change its volume. -For style *final*\ , the final tilt factor is specified. The value +For style *final*, the final tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , a plus or minus change in the tilt factor is +For style *delta*, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. @@ -281,10 +281,10 @@ and upper face of the box. Two letters assigns the first style to the lower face and the second style to the upper face. The style *p* means the box is periodic; the other styles mean -non-periodic. For style *f*\ , the position of the face is fixed. For -style *s*\ , the position of the face is set so as to encompass the +non-periodic. For style *f*, the position of the face is fixed. For +style *s*, the position of the face is set so as to encompass the atoms in that dimension (shrink-wrapping), no matter how far they -move. For style *m*\ , shrink-wrapping occurs, but is bounded by the +move. For style *m*, shrink-wrapping occurs, but is bounded by the current box edge in that dimension, so that the box will become no smaller. See the :doc:`boundary ` command for more explanation of these style options. diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 27b370c941..914509b14d 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -80,7 +80,7 @@ with the *multi* neighbor style. The *multi/old* communication mode is comparabl with both the *multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance -for communication mode *single*\ , which is the distance from the borders +for communication mode *single*, which is the distance from the borders of a processor's sub-domain at which ghost atoms are acquired from other processors. By default the ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See the :doc:`neighbor ` command @@ -96,7 +96,7 @@ style present and no *comm_modify cutoff* command used. Otherwise a warning is printed, if this bond based estimate is larger than the communication cutoff used. -The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to +The *cutoff/multi* option is equivalent to *cutoff*, but applies to communication mode *multi* instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of @@ -132,9 +132,9 @@ different processors, or when the interaction straddles a periodic boundary. The appropriate ghost cutoff depends on the :doc:`newton bond ` -setting. For newton bond *off*\ , the distance needs to be the furthest +setting. For newton bond *off*, the distance needs to be the furthest distance between any two atoms in the bond, angle, etc. E.g. the -distance between 1-4 atoms in a dihedral. For newton bond *on*\ , the +distance between 1-4 atoms in a dihedral. For newton bond *on*, the distance between the central atom in the bond, angle, etc and any other atom is sufficient. E.g. the distance between 2-4 atoms in a dihedral. @@ -173,7 +173,7 @@ The *vel* keyword enables velocity information to be communicated with ghost particles. Depending on the :doc:`atom_style `, velocity info includes the translational velocity, angular velocity, and angular momentum of a particle. If the *vel* option is set to -*yes*\ , then ghost atoms store these quantities; if *no* then they do +*yes*, then ghost atoms store these quantities; if *no* then they do not. The *yes* setting is needed by some pair styles which require the velocity state of both the I and J particles to compute a pairwise I,J interaction, as well as by some compute and fix commands. diff --git a/doc/src/compute.rst b/doc/src/compute.rst index afe54a69be..71d3bada76 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -35,7 +35,7 @@ information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. -See the :doc:`Howto output ` doc page for a summary of +See the :doc:`Howto output ` page for a summary of various LAMMPS output options, many of which involve computes. The ID of a compute can only contain alphanumeric characters and @@ -59,7 +59,7 @@ style produce global quantities. Note that a single compute can produce either global or per-atom or local quantities, but not both global and per-atom. It can produce local quantities in tandem with global or per-atom quantities. The -compute doc page will explain. +compute page will explain. Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The @@ -119,7 +119,7 @@ values by the number of atoms in the system, depending on the "thermo_modify norm" setting. It will not normalize intensive values. If a compute value is accessed in another way, e.g. by a :doc:`variable `, you may want to know whether it is an -intensive or extensive value. See the doc page for individual +intensive or extensive value. See the page for individual computes for further info. ---------- @@ -153,19 +153,19 @@ via the :doc:`compute_modify ` command. Computes can be deleted with the :doc:`uncompute ` command. Code for new computes can be added to LAMMPS; see the -:doc:`Modify ` doc page for details. The results of their +:doc:`Modify ` page for details. The results of their calculations accessed in the various ways described above. ---------- -Each compute style has its own doc page which describes its arguments +Each compute style has its own page which describes its arguments and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also listed in more compact form on the :doc:`Commands compute ` doc page. There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :doc:`Commands compute ` doc page are followed by one or more of +The individual style names on the :doc:`Commands compute ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`ackland/atom ` - determines the local lattice structure based on the Ackland formulation @@ -206,8 +206,9 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`erotate/sphere ` - rotational energy of spherical particles * :doc:`erotate/sphere/atom ` - rotational energy for each spherical particle * :doc:`event/displace ` - detect event on atom displacement +* :doc:`fabric ` - calculates fabric tensors from pair interactions * :doc:`fep ` - -* :doc:`force/tally ` - +* :doc:`force/tally ` - force between two groups of atoms via the tally callback mechanism * :doc:`fragment/atom ` - fragment ID for each atom * :doc:`global/atom ` - * :doc:`group/group ` - energy/force between two groups of atoms @@ -216,7 +217,8 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`gyration/shape ` - shape parameters from gyration tensor * :doc:`gyration/shape/chunk ` - shape parameters from gyration tensor for each chunk * :doc:`heat/flux ` - heat flux through a group of atoms -* :doc:`heat/flux/tally ` - +* :doc:`heat/flux/tally ` - heat flux through a group of atoms via the tally callback mechanism +* :doc:`heat/flux/virial/tally ` - virial heat flux between two groups via the tally callback mechanism * :doc:`hexorder/atom ` - bond orientational order parameter q6 * :doc:`hma ` - harmonically mapped averaging for atomic crystals * :doc:`improper ` - energy of each improper sub-style @@ -239,8 +241,8 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`pe ` - potential energy * :doc:`pe/atom ` - potential energy for each atom * :doc:`mesont ` - Nanotube bending,stretching, and intertube energies -* :doc:`pe/mol/tally ` - -* :doc:`pe/tally ` - +* :doc:`pe/mol/tally ` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism +* :doc:`pe/tally ` - potential energy between two groups of atoms via the tally callback mechanism * :doc:`plasticity/atom ` - Peridynamic plasticity for each atom * :doc:`pressure ` - total pressure and pressure tensor * :doc:`pressure/cylinder ` - pressure tensor in cylindrical coordinates @@ -288,7 +290,7 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`stress/atom ` - stress tensor for each atom * :doc:`stress/mop ` - normal components of the local stress tensor using the method of planes * :doc:`stress/mop/profile ` - profile of the normal components of the local stress tensor using the method of planes -* :doc:`stress/tally ` - +* :doc:`stress/tally ` - stress between two groups of atoms via the tally callback mechanism * :doc:`tdpd/cc/atom ` - per-atom chemical concentration of a specified species for each tDPD particle * :doc:`temp ` - temperature of group of atoms * :doc:`temp/asphere ` - temperature of aspherical particles diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst index 74922ba17b..0dc6630980 100644 --- a/doc/src/compute_ackland_atom.rst +++ b/doc/src/compute_ackland_atom.rst @@ -63,14 +63,14 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The per-atom vector values will be unitless since they are the integers defined above. diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index 6ec5c5bc10..31351a547c 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -62,7 +62,7 @@ neighbor atom in each requested ADF. command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses a neighbor list, it also means those pairs will not be included in the ADF. This does not apply when - using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , + using long-range coulomb interactions (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and @@ -81,7 +81,7 @@ neighbor atom in each requested ADF. cannot be performed, and LAMMPS will give an error message. The *skin* value is what is specified with the :doc:`neighbor ` command. -The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two +The *itypeN*,\ *jtypeN*,\ *ktypeN* settings can be specified in one of two ways. An explicit numeric value can be used, as in the first example above. Or a wild-card asterisk can be used to specify a range of atom types as in the second example above. @@ -92,10 +92,10 @@ all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A middle asterisk means all types from m to n (inclusive). -If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the first example +If *itypeN*, *jtypeN*, and *ktypeN* are single values, as in the first example above, this means that the ADF is computed where atoms of type *itypeN* are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN* -are forming the angle. If any of *itypeN*\ , *jtypeN*\ , or *ktypeN* +are forming the angle. If any of *itypeN*, *jtypeN*, or *ktypeN* represent a range of values via the wild-card asterisk, as in the second example above, this means that the ADF is computed where atoms of any of the range of types represented @@ -103,7 +103,7 @@ by *itypeN* are the central atom, and the angle is formed by two neighbors, one neighbor in the range of types represented by *jtypeN* and another neighbor in the range of types represented by *ktypeN*\ . -If no *itypeN*\ , *jtypeN*\ , *ktypeN* settings are specified, then +If no *itypeN*, *jtypeN*, *ktypeN* settings are specified, then LAMMPS will generate a single ADF for all atoms in the group. The inner cutoff is set to zero and the outer cutoff is set to the force cutoff. If no pair_style is specified, there is no @@ -135,7 +135,7 @@ Each unique angle satisfying the above criteria is counted only once, regardless of whether either or both of the neighbor atoms making up the angle appear in both the J and K lists. It is OK if a particular angle is included in more than -one individual histogram, due to the way the *itypeN*\ , *jtypeN*\ , *ktypeN* +one individual histogram, due to the way the *itypeN*, *jtypeN*, *ktypeN* arguments are specified. The first ADF value for a bin is calculated from the histogram count by @@ -177,13 +177,13 @@ Output info """"""""""" This compute calculates a global array with the number of rows = -*Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the +*Nbins*, and the number of columns = 1 + 2\*Ntriples, where Ntriples is the number of I,J,K triples specified. The first column has the bin coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has -the two ADF values for a specific set of (\ *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN*\ ) +the two ADF values for a specific set of (\ *itypeN*,\ *jtypeN*,\ *ktypeN*\ ) interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". @@ -191,7 +191,7 @@ The array values calculated by this compute are all "intensive". The first column of array values is the angle-related ordinate, either the angle in degrees or radians, or the cosine of the angle. Each subsequent pair of columns gives the first and second kinds of ADF -for a specific set of (\ *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN*\ ). The values +for a specific set of (\ *itypeN*,\ *jtypeN*,\ *ktypeN*\ ). The values in the first ADF column are normalized numbers >= 0.0, whose integral w.r.t. the ordinate is 1, i.e. the first ADF is a normalized probability distribution. @@ -204,6 +204,9 @@ angles per atom satisfying the ADF criteria. Restrictions """""""""""" +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. + The ADF is not computed for neighbors outside the force cutoff, since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an ADF for larger diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index f3e5ee93c0..93677b4953 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -38,7 +38,7 @@ Output info This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 169ef4f238..688bfbeecb 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -128,7 +128,7 @@ array is the number of angles. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses -local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *theta* will be in degrees. The output for *eng* will diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index da27cb3d19..10678c4e47 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -75,7 +75,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 3 for the 3 xyz components of the angular momentum for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index a5558e6232..3a74379acb 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -42,7 +42,7 @@ too frequently or to have multiple compute/dump commands, each of which computes this quantity. An example input script that uses this compute is provided -in examples/USER/misc/basal. +in examples/PACKAGES/basal. Output info """"""""""" @@ -58,8 +58,8 @@ components of a unit vector. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The output of this compute will be meaningless unless the atoms are on (or near) hcp lattice sites, since the calculation assumes a diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index e0369049cb..662838b08f 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -36,7 +36,7 @@ Define a computation that calculates properties of individual body sub-particles. The number of datums generated, aggregated across all processors, equals the number of body sub-particles plus the number of non-body particles in the system, modified by the group parameter as -explained below. See the :doc:`Howto body ` doc page for +explained below. See the :doc:`Howto body ` page for more details on using body particles. The local data stored by this command is generated by looping over all @@ -52,7 +52,7 @@ For both body particles and non-body particles, the *type* keyword will store the type of the particle. The *integer* keywords mean different things for body and non-body -particles. If the atom is not a body particle, only its *x*\ , *y*\ , *z* +particles. If the atom is not a body particle, only its *x*, *y*, *z* coordinates can be referenced, using the *integer* keywords 1,2,3. Note that this means that if you want to access more fields than this for body particles, then you cannot include non-body particles in the @@ -84,7 +84,7 @@ is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The :doc:`units ` for output values depend on the body style. diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 00b99d1f9f..ddca97420d 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -38,7 +38,7 @@ Output info This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`bond_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 5264a86634..8bdde70dd9 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -21,7 +21,7 @@ Syntax *engpot* = bond potential energy *force* = bond force - *fx*\ ,\ *fy*\ ,\ *fz* = components of bond force + *fx*,\ *fy*,\ *fz* = components of bond force *engvib* = bond kinetic energy of vibration *engrot* = bond kinetic energy of rotation *engtrans* = bond kinetic energy of translation @@ -70,7 +70,7 @@ based on the current separation of the pair of atoms in the bond. The value *force* is the magnitude of the force acting between the pair of atoms in the bond. -The values *fx*\ , *fy*\ , and *fz* are the xyz components of +The values *fx*, *fy*, and *fz* are the xyz components of *force* between the pair of atoms in the bond. The remaining properties are all computed for motion of the two atoms @@ -178,13 +178,13 @@ array is the number of bonds. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses local -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *dist* will be in distance :doc:`units `. The output for *velvib* will be in velocity :doc:`units `. The output for *omega* will be in velocity/distance :doc:`units `. The -output for *engtrans*\ , *engvib*\ , *engrot*\ , and *engpot* will be in +output for *engtrans*, *engvib*, *engrot*, and *engpot* will be in energy :doc:`units `. The output for *force* will be in force :doc:`units `. diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst index b250634b5c..3d32b75459 100644 --- a/doc/src/compute_centro_atom.rst +++ b/doc/src/compute_centro_atom.rst @@ -76,7 +76,7 @@ positive parameter. If the atom does not have :math:`N` neighbors (within the potential cutoff), then its centro-symmetry parameter is set to 0.0. -If the keyword *axes* has the setting *yes*\ , then this compute also +If the keyword *axes* has the setting *yes*, then this compute also estimates three symmetry axes for each atom's local neighborhood. The first two of these are the vectors joining the two pairs of neighbor atoms with smallest contributions to the centrosymmetry parameter, @@ -106,10 +106,10 @@ Output info By default, this compute calculates the centrosymmetry value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -If the *axes* keyword setting is *yes*\ , then a per-atom array is +If the *axes* keyword setting is *yes*, then a per-atom array is calculated. The first column is the centrosymmetry parameter. The next three columns are the x, y, and z components of the first symmetry axis, followed by the second, and third symmetry axes in diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index a650c8fb0a..42a5ca9301 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -108,7 +108,7 @@ can simply be accessed by any command that uses per-atom values from a compute as input, as discussed on the :doc:`Howto output ` doc page. -See the :doc:`Howto chunk ` doc page for an overview of how +See the :doc:`Howto chunk ` page for an overview of how this compute can be used with a variety of other commands to tabulate properties of a simulation. The page gives several examples of input script commands that can be used to calculate interesting properties. @@ -130,7 +130,7 @@ those chunks, or not assigned to any chunk. There are many options for specifying for how and when *Nchunk* is calculated, and how and when chunk IDs are assigned to atoms. The -details depend on the chunk *style* and its *args*\ , as well as +details depend on the chunk *style* and its *args*, as well as optional keyword settings. They can also depend on whether a :doc:`fix ave/chunk ` command is using this compute, since that command requires *Nchunk* to remain static across windows of timesteps it specifies, while it accumulates per-chunk averages. @@ -153,13 +153,13 @@ size changes. This also depends on the setting of the *units* keyword; e.g. for *reduced* units the number of chunks may not change even if the box size does. -The *bin/1d*\ , *bin/2d*\ , and *bin/3d* styles define bins as 1d layers -(slabs), 2d pencils, or 3d boxes. The *dim*\ , *origin*\ , and *delta* +The *bin/1d*, *bin/2d*, and *bin/3d* styles define bins as 1d layers +(slabs), 2d pencils, or 3d boxes. The *dim*, *origin*, and *delta* settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is no restriction on specifying dim = x before dim = y or z, or dim = y before dim = z. Bins in a particular *dim* have a bin size in that dimension given by *delta*\ . In each dimension, bins are defined -relative to a specified *origin*\ , which may be the lower/upper edge of +relative to a specified *origin*, which may be the lower/upper edge of the simulation box (in that dimension), or its center point, or a specified coordinate value. Starting at the origin, sufficient bins are created in both directions to completely span the simulation box @@ -168,7 +168,7 @@ or the bounds specified by the optional *bounds* keyword. For orthogonal simulation boxes, the bins are layers, pencils, or boxes aligned with the xyz coordinate axes. For triclinic (non-orthogonal) simulation boxes, the bin faces are parallel to the -tilted faces of the simulation box. See the :doc:`Howto triclinic ` doc page for a discussion of the +tilted faces of the simulation box. See the :doc:`Howto triclinic ` page for a discussion of the geometry of triclinic boxes in LAMMPS. As described there, a tilted simulation box has edge vectors a,b,c. In that nomenclature, bins in the x dimension have faces with normals in the "b" cross "c" @@ -188,7 +188,7 @@ means there will be 10 layers from 0.0 to 1.0, regardless of the current size or shape of the simulation box. The *bin/sphere* style defines a set of spherical shell bins around -the origin (\ *xorig*\ ,\ *yorig*\ ,\ *zorig*\ ), using *nsbin* bins with radii +the origin (\ *xorig*,\ *yorig*,\ *zorig*\ ), using *nsbin* bins with radii equally spaced between *srmin* and *srmax*\ . This is effectively a 1d vector of bins. For example, if *srmin* = 1.0 and *srmax* = 10.0 and *nsbin* = 9, then the first bin spans 1.0 < r < 2.0, and the last bin @@ -199,12 +199,12 @@ transform them into ellipsoidal shells. The *bin/cylinder* style defines bins for a cylinder oriented along the axis *dim* with the axis coordinates in the other two radial -dimensions at (\ *c1*\ ,\ *c2*\ ). For dim = x, c1/c2 = y/z; for dim = y, +dimensions at (\ *c1*,\ *c2*\ ). For dim = x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array of bins. The first dimension is along the cylinder axis, the second dimension is radially outward from the cylinder axis. The bin size and positions along the cylinder axis are specified by the *origin* -and *delta* values, the same as for the *bin/1d*\ , *bin/2d*\ , and +and *delta* values, the same as for the *bin/1d*, *bin/2d*, and *bin/3d* styles. There are *ncbin* concentric circle bins in the radial direction from the cylinder axis with radii equally spaced between *crmin* and *crmax*\ . For example, if *crmin* = 1.0 and @@ -216,12 +216,12 @@ scaled differently in the two different dimensions to transform them into ellipses. The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*\ , the +from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*, the numbering varies most rapidly in the first dimension (which could be x, y, or z), next rapidly in the second dimension, and most slowly in the -third dimension. For *bin/sphere*\ , the bin with smallest radii is chunk +third dimension. For *bin/sphere*, the bin with smallest radii is chunk 1 and the bni with largest radii is chunk Nchunk = *ncbin*\ . For -*bin/cylinder*\ , the numbering varies most rapidly in the dimension +*bin/cylinder*, the numbering varies most rapidly in the dimension along the cylinder axis and most slowly in the radial direction. Each time this compute is invoked, each atom is mapped to a bin based @@ -254,7 +254,7 @@ only the first time that *Nchunk* is calculated. Note that atoms with a molecule ID = 0, which may be non-molecular solvent atoms, have an out-of-range chunk ID. These atoms are -discarded (not assigned to any chunk) or assigned to *Nchunk*\ , +discarded (not assigned to any chunk) or assigned to *Nchunk*, depending on the value of the *discard* keyword. ---------- @@ -304,14 +304,14 @@ explained below, the *nchunk* keyword can be set to *once* which means If a :doc:`fix ave/chunk ` command uses this compute, it can also turn off the re-calculation of *Nchunk* for one or more windows of timesteps. The extent of the windows, during which Nchunk -is held constant, are determined by the *Nevery*\ , *Nrepeat*\ , *Nfreq* +is held constant, are determined by the *Nevery*, *Nrepeat*, *Nfreq* values and the *ave* keyword setting that are used by the :doc:`fix ave/chunk ` command. -Specifically, if *ave* = *one*\ , then for each span of *Nfreq* +Specifically, if *ave* = *one*, then for each span of *Nfreq* timesteps, *Nchunk* is held constant between the first timestep when averaging is done (within the Nfreq-length window), and the last timestep when averaging is done (multiple of Nfreq). If *ave* = -*running* or *window*\ , then *Nchunk* is held constant forever, +*running* or *window*, then *Nchunk* is held constant forever, starting on the first timestep when the :doc:`fix ave/chunk ` command invokes this compute. Note that multiple :doc:`fix ave/chunk ` commands can use @@ -336,9 +336,9 @@ The *nchunk* keyword applies to all chunk styles. It specifies how often *Nchunk* is recalculated, which in turn can affect the chunk IDs assigned to individual atoms. -If *nchunk* is set to *once*\ , then *Nchunk* is only calculated once, +If *nchunk* is set to *once*, then *Nchunk* is only calculated once, the first time this compute is invoked. If *nchunk* is set to -*every*\ , then *Nchunk* is re-calculated every time the compute is +*every*, then *Nchunk* is re-calculated every time the compute is invoked. Note that, as described above, the use of this compute by the :doc:`fix ave/chunk ` command can override the *every* setting. @@ -358,12 +358,12 @@ any atom. The *limit* keyword is used by all chunk styles except the can be tailored using the *bound* keyword (described below) which effectively limits the size of *Nchunk*\ . -If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*\ , -though the *compress* keyword can still be used to reduce *Nchunk*\ , as +If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*, +though the *compress* keyword can still be used to reduce *Nchunk*, as described below. If *Nc* > 0, then the effect of the *limit* keyword depends on whether -the *compress* keyword is also used with a setting of *yes*\ , and +the *compress* keyword is also used with a setting of *yes*, and whether the *compress* keyword is specified before the *limit* keyword or after. @@ -371,11 +371,11 @@ In all cases, *Nchunk* is first calculated in the usual way for each chunk style, as described above. First, here is what occurs if *compress yes* is not set. If *limit* -is set to *Nc max*\ , then *Nchunk* is reset to the smaller of *Nchunk* -and *Nc*\ . If *limit* is set to *Nc exact*\ , then *Nchunk* is reset to -*Nc*\ , whether the original *Nchunk* was larger or smaller than *Nc*\ . +is set to *Nc max*, then *Nchunk* is reset to the smaller of *Nchunk* +and *Nc*\ . If *limit* is set to *Nc exact*, then *Nchunk* is reset to +*Nc*, whether the original *Nchunk* was larger or smaller than *Nc*\ . If *Nchunk* shrank due to the *limit* setting, then atom chunk IDs > -*Nchunk* will be reset to 0 or *Nchunk*\ , depending on the setting of +*Nchunk* will be reset to 0 or *Nchunk*, depending on the setting of the *discard* keyword. If *Nchunk* grew, there will simply be some chunks with no atoms assigned to them. @@ -384,21 +384,21 @@ If *compress yes* is set, and the *compress* keyword comes before the described below, which resets *Nchunk*\ . The *limit* keyword is then applied to the new *Nchunk* value, exactly as described in the preceding paragraph. Note that in this case, all atoms will end up -with chunk IDs <= *Nc*\ , but their original values (e.g. molecule ID or -compute/fix/variable) may have been > *Nc*\ , because of the compression +with chunk IDs <= *Nc*, but their original values (e.g. molecule ID or +compute/fix/variable) may have been > *Nc*, because of the compression operation. If *compress yes* is set, and the *compress* keyword comes after the *limit* keyword, then the *limit* value of *Nc* is applied first to -the uncompressed value of *Nchunk*\ , but only if *Nc* < *Nchunk* +the uncompressed value of *Nchunk*, but only if *Nc* < *Nchunk* (whether *Nc max* or *Nc exact* is used). This effectively means all -atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*\ , +atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*, depending on the setting of the *discard* keyword. The compression operation is then performed, which may shrink *Nchunk* further. If the new *Nchunk* < *Nc* and *limit* = *Nc exact* is specified, then -*Nchunk* is reset to *Nc*\ , which results in extra chunks with no atoms +*Nchunk* is reset to *Nc*, which results in extra chunks with no atoms assigned to them. Note that in this case, all atoms will end up with -chunk IDs <= *Nc*\ , and their original values (e.g. molecule ID or +chunk IDs <= *Nc*, and their original values (e.g. molecule ID or compute/fix/variable value) will also have been <= *Nc*\ . ---------- @@ -413,7 +413,7 @@ time windows (discussed above), the chunk ID's assigned to atoms on the first step of the time window will persist until the end of the time window. -If the setting is *every*\ , which is the default, then chunk IDs are +If the setting is *every*, which is the default, then chunk IDs are re-calculated on any timestep this compute is invoked. .. note:: @@ -435,18 +435,18 @@ set of IDs, where every chunk has one or more atoms assigned to it. Two possible use cases are as follows. If a large simulation box is mostly empty space, then the *binning* style may produce many bins -with no atoms. If *compress* is set to *yes*\ , only bins with atoms +with no atoms. If *compress* is set to *yes*, only bins with atoms will be contribute to *Nchunk*\ . Likewise, the *molecule* or *compute/fix/variable* styles may produce large *Nchunk* values. For example, the :doc:`compute cluster/atom ` command assigns every atom an atom ID for one of the atoms it is clustered with. For a million-atom system with 5 clusters, there would only be 5 unique chunk IDs, but the largest chunk ID might be 1 million, -resulting in *Nchunk* = 1 million. If *compress* is set to *yes*\ , +resulting in *Nchunk* = 1 million. If *compress* is set to *yes*, *Nchunk* will be reset to 5. -If *compress* is set to *no*\ , which is the default, no compression is -done. If it is set to *yes*\ , all chunk IDs with no atoms are removed +If *compress* is set to *no*, which is the default, no compression is +done. If it is set to *yes*, all chunk IDs with no atoms are removed from the list of chunk IDs, and the list is sorted. The remaining chunk IDs are renumbered from 1 to *Nchunk* where *Nchunk* is the new length of the list. The chunk IDs assigned to each atom reflect @@ -498,23 +498,23 @@ return chunk IDs that are invalid for the previously calculated *Nchunk*\ . All the chunk styles except the *binning* styles, must use *discard* -set to either *yes* or *no*\ . If *discard* is set to *yes*\ , which is +set to either *yes* or *no*\ . If *discard* is set to *yes*, which is the default, then every "discard" atom has its chunk ID set to 0. If -*discard* is set to *no*\ , every "discard" atom has its chunk ID set to +*discard* is set to *no*, every "discard" atom has its chunk ID set to *Nchunk*\ . I.e. it becomes part of the last chunk. The *binning* styles use the *discard* keyword to decide whether to discard atoms outside the spatial domain covered by bins, or to assign them to the bin they are nearest to. -For the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles the details are as -follows. If *discard* is set to *yes*\ , an out-of-domain atom will -have its chunk ID set to 0. If *discard* is set to *no*\ , the atom +For the *bin/1d*, *bin/2d*, *bin/3d* styles the details are as +follows. If *discard* is set to *yes*, an out-of-domain atom will +have its chunk ID set to 0. If *discard* is set to *no*, the atom will have its chunk ID set to the first or last bin in that dimension. -If *discard* is set to *mixed*\ , which is the default, it will only +If *discard* is set to *mixed*, which is the default, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in that dimension. This is the case if the -*bound* keyword settings are *lower* and *upper*\ , which is the +*bound* keyword settings are *lower* and *upper*, which is the default. If the *bound* keyword settings are numeric values, then the atom will have its chunk ID set to 0 if it is outside the bounds of any bin. Note that in this case, it is possible that the first or @@ -524,24 +524,24 @@ is only set to 0 if it is outside the first or last bin, not if it is simply outside the numeric *bounds* setting. For the *bin/sphere* style the details are as follows. If *discard* -is set to *yes*\ , an out-of-domain atom will have its chunk ID set to -0. If *discard* is set to *no* or *mixed*\ , the atom will have its +is set to *yes*, an out-of-domain atom will have its chunk ID set to +0. If *discard* is set to *no* or *mixed*, the atom will have its chunk ID set to the first or last bin, i.e. the innermost or outermost spherical shell. If the distance of the atom from the origin is less -than *rmin*\ , it will be assigned to the first bin. If the distance of -the atom from the origin is greater than *rmax*\ , it will be assigned +than *rmin*, it will be assigned to the first bin. If the distance of +the atom from the origin is greater than *rmax*, it will be assigned to the last bin. For the *bin/cylinder* style the details are as follows. If *discard* -is set to *yes*\ , an out-of-domain atom will have its chunk ID set to -0. If *discard* is set to *no*\ , the atom will have its chunk ID set +is set to *yes*, an out-of-domain atom will have its chunk ID set to +0. If *discard* is set to *no*, the atom will have its chunk ID set to the first or last bin in both the radial and axis dimensions. If -*discard* is set to *mixed*\ , which is the default, the radial +*discard* is set to *mixed*, which is the default, the radial dimension is treated the same as for *discard* = no. But for the axis dimension, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in the axis dimension. This is the case if the *bound* keyword settings are -*lower* and *upper*\ , which is the default. If the *bound* keyword +*lower* and *upper*, which is the default. If the *bound* keyword settings are numeric values, then the atom will have its chunk ID set to 0 if it is outside the bounds of any bin. Note that in this case, it is possible that the first or last bin extends beyond the numeric @@ -550,22 +550,22 @@ the case, the chunk ID of the atom is only set to 0 if it is outside the first or last bin, not if it is simply outside the numeric *bounds* setting. -If *discard* is set to *no* or *mixed*\ , the atom will have its +If *discard* is set to *no* or *mixed*, the atom will have its chunk ID set to the first or last bin, i.e. the innermost or outermost spherical shell. If the distance of the atom from the origin is less -than *rmin*\ , it will be assigned to the first bin. If the distance of -the atom from the origin is greater than *rmax*\ , it will be assigned +than *rmin*, it will be assigned to the first bin. If the distance of +the atom from the origin is greater than *rmax*, it will be assigned to the last bin. ---------- -The *bound* keyword only applies to the *bin/1d*\ , *bin/2d*\ , *bin/3d* +The *bound* keyword only applies to the *bin/1d*, *bin/2d*, *bin/3d* styles and to the axis dimension of the *bin/cylinder* style; otherwise it is ignored. It can be used one or more times to limit the extent of bin coverage in a specified dimension, i.e. to only bin a portion of the box. If the *lo* setting is *lower* or the *hi* -setting is *upper*\ , the bin extent in that direction extends to the -box boundary. If a numeric value is used for *lo* and/or *hi*\ , then +setting is *upper*, the bin extent in that direction extends to the +box boundary. If a numeric value is used for *lo* and/or *hi*, then the bin extent in the *lo* or *hi* direction extends only to that value, which is assumed to be inside (or at least near) the simulation box boundaries, though LAMMPS does not check for this. Note that @@ -573,7 +573,7 @@ using the *bound* keyword typically reduces the total number of bins and thus the number of chunks *Nchunk*\ . The *pbc* keyword only applies to the *bin/sphere* and *bin/cylinder* -styles. If set to *yes*\ , the distance an atom is from the sphere +styles. If set to *yes*, the distance an atom is from the sphere origin or cylinder axis is calculated in a minimum image sense with respect to periodic dimensions, when determining which bin the atom is in. I.e. if x is a periodic dimension and the distance between the @@ -582,18 +582,18 @@ simulation box length in x, then a box length is subtracted to give a distance < 0.5 \* simulation box length. This allosws the sphere or cylinder center to be near a box edge, and atoms on the other side of the periodic box will still be close to the center point/axis. Note -that with a setting of *yes*\ , the outer sphere or cylinder radius must +that with a setting of *yes*, the outer sphere or cylinder radius must also be <= 0.5 \* simulation box length in any periodic dimension except for the cylinder axis dimension, or an error is generated. The *units* keyword only applies to the *binning* styles; otherwise it -is ignored. For the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles, it +is ignored. For the *bin/1d*, *bin/2d*, *bin/3d* styles, it determines the meaning of the distance units used for the bin sizes *delta* and for *origin* and *bounds* values if they are coordinate values. For the *bin/sphere* style it determines the meaning of the -distance units used for *xorig*\ ,\ *yorig*\ ,\ *zorig* and the radii *srmin* +distance units used for *xorig*,\ *yorig*,\ *zorig* and the radii *srmin* and *srmax*\ . For the *bin/cylinder* style it determines the meaning -of the distance units used for *delta*\ ,\ *c1*\ ,\ *c2* and the radii *crmin* +of the distance units used for *delta*,\ *c1*,\ *c2* and the radii *crmin* and *crmax*\ . For orthogonal simulation boxes, any of the 3 options may @@ -627,7 +627,7 @@ This compute calculates a per-atom vector (the chunk ID), which can be accessed by any command that uses per-atom values from a compute as input. It also calculates a global scalar (the number of chunks), which can be similarly accessed everywhere outside of a per-atom context. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless chunk IDs, ranging from 1 to @@ -637,7 +637,7 @@ belonging to a chunk. The scalar contains the value of *Nchunk*. Restrictions """""""""""" -Even if the *nchunk* keyword is set to *once*\ , the chunk IDs assigned +Even if the *nchunk* keyword is set to *once*, the chunk IDs assigned to each atom are not stored in a restart files. This means you cannot expect those assignments to persist in a restarted simulation. Instead you must re-specify this command and assign atoms to chunks when diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index 9e6489f828..1fd260ab2c 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -193,7 +193,7 @@ Output info This compute calculates a per-atom vector or array, which can be accessed by any command that uses per-atom values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output is a per-atom vector if a single input value is specified, diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index ab47aed9b3..32954480cc 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -89,7 +89,7 @@ style computes. command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included when computing the clusters. This - does not apply when using long-range coulomb (\ *coul/long*\ , *coul/msm*\ , + does not apply when using long-range coulomb (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and @@ -111,14 +111,15 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be an ID > 0, as explained above. Restrictions """""""""""" - none + +none Related commands """""""""""""""" @@ -128,6 +129,5 @@ Related commands Default """"""" - The default for fragment/atom is single no. diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 41d7113b60..756a9d932c 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -84,7 +84,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be a number from 0 to 5, as explained diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index 1a1b509162..59c45107b3 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -40,10 +40,10 @@ This parameter is computed using the following formula from .. math:: - Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2 + Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} \left | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} \right | ^{2} where the index *j* goes over the :math:`n_i` nearest neighbors of atom -*i*\ , and the index *k* goes over the :math:`n_{ij}` common nearest neighbors +*i*, and the index *k* goes over the :math:`n_{ij}` common nearest neighbors between atom *i* and atom *j*\ . :math:`\vec{R}_{ik}` and :math:`\vec{R}_{jk}` are the vectors connecting atom *k* to atoms *i* and *j*\ . The quantity in the double sum is computed @@ -91,7 +91,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be real positive numbers. Some typical CNP @@ -110,8 +110,8 @@ values: Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index f22a78c63c..20dcbfae29 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -39,7 +39,7 @@ Output info This compute calculates a per-atom vector, whose values can be accessed by any command that uses per-atom values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained @@ -48,6 +48,10 @@ above. Restrictions """""""""""" +This compute is part of the GRANULAR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. + This compute requires that atoms store a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index f3c6f818af..bff2a8a8af 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -73,7 +73,7 @@ from 1 to N. A leading asterisk means all types from 1 to n (inclusive). The *orientorder* cstyle calculates the number of "connected" neighbor -atoms J around each central atom I. For this *cstyle*\ , connected is +atoms J around each central atom I. For this *cstyle*, connected is defined by the orientational order parameter calculated by the :doc:`compute orientorder/atom ` command. This *cstyle* thus allows one to apply the ten Wolde's criterion to @@ -85,7 +85,7 @@ calculate components of the *Ybar_lm* vector for each atoms, as described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the scalar product (*Ybar_lm(i)*,*Ybar_lm(j)*), calculated by the -orientorder/atom compute is larger than the specified *threshold*\ , +orientorder/atom compute is larger than the specified *threshold*, then I and J are connected, and the coordination value of I is incremented by one. diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index 2439bd5a1b..3847a4de66 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -45,7 +45,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (damage) >= 0.0. @@ -54,7 +54,7 @@ Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index 0bbcb370b5..d4198dde3c 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -37,7 +37,7 @@ Output info This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 75c0e69790..82d3c3ab72 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -122,7 +122,7 @@ array is the number of dihedrals. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses -local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *phi* will be in degrees. diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index 85b5770c64..0e3159ffe7 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -48,7 +48,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (theta) >= 0.0. @@ -57,7 +57,7 @@ Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_dipole.rst b/doc/src/compute_dipole.rst index c0e17f27d3..243efc0576 100644 --- a/doc/src/compute_dipole.rst +++ b/doc/src/compute_dipole.rst @@ -12,7 +12,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * dipole = style name of this compute command -* charge-correction = *mass* or *geometry*\ , use COM or geometric center for charged chunk correction (optional) +* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional) Examples """""""" @@ -51,7 +51,7 @@ Output info This compute calculations a global scalar containing the magnitude of the computed dipole moment and a global vector of length 3 with the -dipole vector. See the :doc:`Howto output ` doc page for +dipole vector. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The computed values are "intensive". The array values will be in diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 4207d3d180..fc1e8d7709 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * dipole/chunk = style name of this compute command * chunkID = ID of :doc:`compute chunk/atom ` command -* charge-correction = *mass* or *geometry*\ , use COM or geometric center for charged chunk correction (optional) +* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional) Examples """""""" @@ -84,7 +84,7 @@ chunk/atom ` command. The number of columns = 4 for the x,y,z dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output -` doc page for an overview of LAMMPS output options. +` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in dipole units, i.e. charge units times distance :doc:`units `. diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index a3b68451db..bc6e1d2321 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -52,7 +52,7 @@ Output info This compute calculates a global vector of length 5 (:math:`U^{cond}`, :math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`), which can be accessed by indices 1-5. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values will be in energy and temperature :doc:`units `. @@ -60,8 +60,8 @@ The vector values will be in energy and temperature :doc:`units `. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 85dc977c52..6104c4a273 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -40,7 +40,7 @@ This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`, :math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle array values will be in energy (:math:`u^{cond}`, @@ -50,8 +50,8 @@ and temperature (:math:`theta`) :doc:`units `. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index e31974f98a..3568a6364f 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -36,7 +36,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in temperature :doc:`units `. @@ -44,8 +44,8 @@ The per-atom vector values will be in temperature :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-MESODPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the DPD-MESO package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_efield_atom.rst b/doc/src/compute_efield_atom.rst index 1e87ad2556..a3d2cb888d 100644 --- a/doc/src/compute_efield_atom.rst +++ b/doc/src/compute_efield_atom.rst @@ -21,12 +21,19 @@ Examples compute 1 all efield/atom compute 1 all efield/atom pair yes kspace no +Used in input scripts: + + .. parsed-literal:: + + examples/PACKAGES/dielectric/in.confined + examples/PACKAGES/dielectric/in.nopbc + Description """"""""""" Define a computation that calculates the electric field at each atom in a group. The compute should only enabled with pair and kspace styles that are provided -by the USER-DIELECTRIC package because only these styles compute the per-atom +by the DIELECTRIC package because only these styles compute the per-atom electric field at every time step. The electric field is a 3-component vector. The value of the electric field @@ -45,14 +52,14 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in electric field :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-DIELECTRIC package. It is only enabled if +This compute is part of the DIELECTRIC package. It is only enabled if LAMMPS was built with that package. Related commands diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index 59b0059376..e3d585dfde 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -67,7 +67,7 @@ is a parameter to control the smoothing. The input parameters are *sigma* the smoothing parameter :math:`\sigma`, and the *cutoff* for the calculation of g(r). -If the keyword *avg* has the setting *yes*\ , then this compute also +If the keyword *avg* has the setting *yes*, then this compute also averages the parameter over the neighbors of atom i according to: .. math:: @@ -114,7 +114,7 @@ Output info By default, this compute calculates the pair entropy value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The pair entropy values have units of the Boltzmann constant. They are @@ -124,8 +124,8 @@ ordered environments. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 0210279560..2b4edc8017 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -45,7 +45,7 @@ Output info This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index b5b594f781..acbcf5cb0c 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -43,7 +43,7 @@ Output info This compute calculates a global scalar (the summed rotational energy of all the rigid bodies). This value can be used by any command that -uses a global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -53,7 +53,7 @@ Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index c10d13c318..6890f18212 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -40,7 +40,7 @@ Output info This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index b12669ed0c..76025b36f7 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -44,7 +44,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index a147ca0d7d..6cf04e83ba 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -48,7 +48,7 @@ Output info This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_fabric.rst b/doc/src/compute_fabric.rst new file mode 100644 index 0000000000..3ded3d7adc --- /dev/null +++ b/doc/src/compute_fabric.rst @@ -0,0 +1,185 @@ +.. index:: compute fabric + +compute fabric command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID fabric cutoff attribute1 attribute2 ... keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* fabric = style name of this compute command +* cutoff = *type* or *radius* + + .. parsed-literal:: + + *type* = cutoffs determined based on atom types + *radius* = cutoffs determined based on atom diameters (atom style sphere) + +* one or more attributes may be appended + + .. parsed-literal:: + + *contact* = contact tensor + *branch* = branch tensor + *force/normal* = normal force tensor + *force/tangential* = tangential force tensor + +* zero or more keyword/value pairs may be appended +* keyword = *type/include* + + .. parsed-literal:: + + *type/include* value = arg1 arg2 + arg = separate lists of types (see below) + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute 1 all fabric type contact force/normal type/include 1,2 3*4 + compute 1 all fabric radius force/normal force/tangential + +Description +""""""""""" + +Define a compute that calculates various fabric tensors for pairwise +interaction :ref:`(Ouadfel) `. Fabric tensors are commonly used +to quantify the anisotropy or orientation of granular contacts but can also +be used to characterize the direction of pairwise interactions in general +systems. The *type* and *radius* settings are used to select whether interactions +cutoffs are determined by atom types or by the sum of atomic radii (atom +style sphere), respectively. Calling this compute is roughly the cost of a +pair style invocation as it involves a loop over the neighbor list. If the +normal or tangential force tensors are requested, it will be more expensive +than a pair style invocation as it will also recalculate all pair forces. + +Four fabric tensors are available: the contact, branch, normal force, or +tangential force tensor. The contact tensor is calculated as + +.. math:: + + C_{ab} = \frac{15}{2} (\phi_{ab} - \mathrm{tr}(\phi) \delta_{ab}) + +where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z` +directions, :math:`\delta_{ab}` is the Kronecker delta function, and +the tensor :math:`\phi` is defined as + +.. math:: + + \phi_{ab} = \sum_{n = 1}^{N_p} \frac{r_{a} r_{b}}{r^2} + +where :math:`n` loops over the :math:`N_p` pair interactions in the simulation, +:math:`r_{a}` is the :math:`a` component of the radial vector between the +two pairwise interacting particles, and :math:`r` is the magnitude of the radial vector. + +The branch tensor is calculated as + +.. math:: + + B_{ab} = \frac{15}{6 \mathrm{tr}(D)} (D_{ab} - \mathrm{tr}(D) \delta_{ab}) + +where the tensor :math:`D` is defined as + +.. math:: + + D_{ab} = \sum_{n = 1}^{N_p} + \frac{1}{N_c (r^2 + C_{cd} r_c r_d)} + \frac{r_{a} r_{b}}{r} + +where :math:`N_c` is the total number of contacts in the system and the subscripts +:math:`c` and :math:`d` indices are summed according to Einstein notation. + +The normal force fabric tensor is calculated as + +.. math:: + + F^n_{ab} = \frac{15}{6 \mathrm{tr}(N)} (N_{ab} - \mathrm{tr}(N) \delta_{ab}) + +where the tensor :math:`N` is defined as + +.. math:: + + N_{ab} = \sum_{n = 1}^{N_p} + \frac{1}{N_c (r^2 + C_{cd} r_c r_d)} + \frac{r_{a} r_{b}}{r^2} f_n + +and :math:`f_n` is the magnitude of the normal, central-body force between the two atoms. + +Finally, the tangential force fabric tensor is only defined for pair styles that +apply tangential forces to particles, namely granular pair styles. It is calculated +as + +.. math:: + + F^t_{ab} = \frac{15}{9 \mathrm{tr}(N)} (T_{ab} - \mathrm{tr}(T) \delta_{ab}) + +where the tensor :math:`T` is defined as + +.. math:: + + T_{ab} = \sum_{n = 1}^{N_p} + \frac{1}{N_c (r^2 + C_{cd} r_c r_d)} + \frac{r_{a} r_{b}}{r^2} f_t + +and :math:`f_t` is the magnitude of the tangential force between the two atoms. + +The *type/include* keyword filters interactions based on the types of the two atoms. +Interactions between two atoms are only included in calculations if the atom types +are in the two lists. Each list consists of a series of type +ranges separated by commas. The range can be specified as a +single numeric value, or a wildcard asterisk can be used to specify a range +of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For +example, if M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M +(inclusive). A middle asterisk means all types from m to n (inclusive). +Multiple *type/include* keywords may be added. + +Output info +""""""""""" + +This compute calculates a local vector of doubles and a scalar. The vector stores the +unique components of the first requested tensor in the order xx, yy, zz, xy, xz, yz +followed by the same components for all subsequent tensors. The length of the vector +is therefore six times the number of requested tensors. The scalar output is the +number of pairwise interactions included in the calculation of the fabric tensor. + +Restrictions +"""""""""""" + +This fix is part of the GRANULAR package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` +doc page for more info. + +Currently, compute *fabric* does not support pair styles +with many-body interactions. It also does not +support models with long-range Coulombic or dispersion forces, +i.e. the kspace_style command in LAMMPS. It also does not support the +following fixes which add rigid-body constraints: :doc:`fix shake +`, :doc:`fix rattle `, :doc:`fix rigid +`, :doc:`fix rigid/small `. It does not support +granular pair styles that extend beyond the contact of atomic radii +(e.g. JKR and DMT). + +Related commands +"""""""""""""""" + +none + +Default +""""""" + +none + +---------- + +.. _Ouadfel: + +**(Ouadfel)** Ouadfel and Rothenburg +"Stress-force-fabric relationship for assemblies of ellipsoids", +Mechanics of Materials (2001). (`link to paper `_) diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index ef908acfc0..5275716c45 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -48,7 +48,7 @@ Examples compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes compute 1 all fep 300 atom charge 2 v_delta -Example input scripts available: examples/USER/fep +Example input scripts available: examples/PACKAGES/fep Description """"""""""" @@ -269,7 +269,7 @@ activated via the :doc:`pair_modify ` command. If the perturbation is small, the tail contribution to the energy difference between the reference and perturbed systems should be negligible. -If the keyword *volume* = *yes*\ , then the Boltzmann term is multiplied +If the keyword *volume* = *yes*, then the Boltzmann term is multiplied by the volume so that correct ensemble averaging can be performed over trajectories during which the volume fluctuates or changes :ref:`(Allen and Tildesley) `: @@ -295,7 +295,7 @@ unperturbed parameters. The energies include kspace terms if these are used in the simulation. These output results can be used by any command that uses a global -scalar or vector from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +scalar or vector from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. For example, the computed values can be averaged using :doc:`fix ave/time `. The values calculated by this compute are "extensive". @@ -303,8 +303,8 @@ The values calculated by this compute are "extensive". Restrictions """""""""""" -This compute is distributed as the USER-FEP package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is distributed as the FEP package. It is only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" @@ -315,7 +315,7 @@ Related commands Default """"""" -The option defaults are *tail* = *no*\ , *volume* = *no*\ . +The option defaults are *tail* = *no*, *volume* = *no*\ . ---------- diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index 1c8ff6c85e..1ee4abdde0 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -146,7 +146,7 @@ to effectively specify multiple values. If *index* begins with "f\_", a fix ID must follow which has been previously defined in the input script. The Fix must generate -per-atom quantities. See the individual :doc:`fix ` doc page for +per-atom quantities. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute global/atom references the values, else an error results. If no bracketed integer @@ -213,7 +213,7 @@ vector. If multiple inputs are specified, this compute produces a per-atom array values, where the number of columns is equal to the number of inputs specified. These values can be used by any command that uses per-atom vector or array values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector or array values will be in whatever units the diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index b22689d4b3..d361bc806d 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -39,7 +39,7 @@ Define a computation that calculates the total energy and force interaction between two groups of atoms: the compute group and the specified group2. The two groups can be the same. -If the *pair* keyword is set to *yes*\ , which is the default, then the +If the *pair* keyword is set to *yes*, which is the default, then the the interaction energy will include a pair component which is defined as the pairwise energy between all pairs of atoms where one atom in the pair is in the first group and the other is in the second group. @@ -60,7 +60,7 @@ force. For the *inter* setting, the two atoms must be in different molecules. For the *intra* setting, the two atoms must be in the same molecule. -If the *kspace* keyword is set to *yes*\ , which is not the default, and +If the *kspace* keyword is set to *yes*, which is not the default, and if a :doc:`kspace_style ` is defined, then the interaction energy will include a Kspace component which is the long-range Coulombic energy between all the atoms in the first group and all the @@ -73,7 +73,7 @@ charge of the unit cell is zero. However, one can assume the net charge of the system is neutralized by a uniform background plasma, and a correction to the system energy can be applied to reduce artifacts. For more information see :ref:`(Bogusz) `. If the -*boundary* keyword is set to *yes*\ , which is the default, and *kspace* +*boundary* keyword is set to *yes*, which is the default, and *kspace* contributions are included, then this energy correction term will be added to the total group-group energy. This correction term does not affect the force calculation and will be zero if one or both of the @@ -108,7 +108,7 @@ frequently. neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. This does not apply when using long-range coulomb interactions - (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar. One way to get + (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to @@ -134,7 +134,7 @@ Output info This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. Both the scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index da0b14abe8..18c46f4772 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -62,7 +62,7 @@ Output info This compute calculates a global scalar (:math:`R_g`) and a global vector of length 6 (:math:`{R_g}^2` tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index eaa048c111..0255d4f95a 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -101,7 +101,7 @@ number of rows in the array = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. If the *tensor* keyword is specified, the global array has 6 columns. The vector or array can be accessed by any command that uses global values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. All the vector or array values calculated by this compute are diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index fced528015..8eee14e787 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -70,7 +70,7 @@ This compute calculates a global vector of length 6, which can be accessed by indices 1-6. The first three values are the eigenvalues of the gyration tensor followed by the asphericity, the acylindricity and the relative shape anisotropy. The computed values can be used by any command -that uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses global vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values calculated by this compute are @@ -80,8 +80,8 @@ distance\^2 :doc:`units ` while the sixth one is dimensionless. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 375dc85134..f9d9df8db0 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -71,7 +71,7 @@ This compute calculates a global array with six columns, which can be accessed by indices 1-6. The first three columns are the eigenvalues of the gyration tensor followed by the asphericity, the acylindricity and the relative shape anisotropy. The computed values can be used by any command -that uses global array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array calculated by this compute is @@ -81,8 +81,8 @@ distance\^2 :doc:`units ` while the sixth one is dimensionless. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 3e8469617f..94d6f09700 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -41,7 +41,7 @@ which can add or subtract heat from groups of atoms. The compute takes three arguments which are IDs of other :doc:`computes `. One calculates per-atom kinetic energy -(\ *ke-ID*\ ), one calculates per-atom potential energy (\ *pe-ID)*\ , and the +(\ *ke-ID*\ ), one calculates per-atom potential energy (\ *pe-ID)*, and the third calculates per-atom stress (\ *stress-ID*\ ). .. note:: @@ -131,7 +131,7 @@ of just the convective portion of the flux, i.e. the first term in the equation for :math:`\mathbf{J}`. Each component can be accessed by indices 1-6. These values can be used by any command that -uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses global vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive", meaning diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index a8e70245df..8b8bc3f4d0 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -48,7 +48,7 @@ is formed by the bond vector :math:`r_{ij}` and the *x* axis. :math:`\theta` is calculated only using the *x* and *y* components, whereas the distance from the central atom is calculated using all three -*x*\ , *y*\ , and *z* components of the bond vector. +*x*, *y*, and *z* components of the bond vector. Neighbor atoms not in the group are included in the order parameter of atoms in the group. @@ -110,7 +110,9 @@ page for an overview of LAMMPS output options. Restrictions """""""""""" - none + +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 5efb133bea..e9c3133ebb 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -152,7 +152,7 @@ The following example illustrates the placement of this command in the input scr The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. An example input script that uses this compute is included in -examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA +examples/PACKAGES/hma/ along with corresponding LAMMPS output showing that the HMA properties fluctuate less than the corresponding conventional properties. Output info @@ -161,7 +161,7 @@ Output info This compute calculates a global vector that includes the n properties requested as arguments to the command (the potential energy, pressure and/or heat capacity). The elements of the vector can be accessed by indices 1-n by any -command that uses global vector values as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. +command that uses global vector values as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive". The scalar value will be in energy :doc:`units `. @@ -169,8 +169,8 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is enabled only -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is enabled only +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Usage restricted to canonical (NVT) ensemble simulation only. @@ -192,5 +192,5 @@ none .. _hma-Moustafa: -**(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , +**(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) `_ diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 3eb008c3b2..2d6684b240 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -37,7 +37,7 @@ Output info This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`improper_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 4c4af36149..3a849bf20c 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -69,7 +69,7 @@ array is the number of impropers. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *chi* will be in degrees. diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 638a0baec8..42f5725d92 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -74,7 +74,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index 8828ee4e3f..277b6ea6d6 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -37,7 +37,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index 3ff9ce0c1f..4587632818 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -65,7 +65,7 @@ Output info This compute calculates a scalar quantity for each atom, which can be accessed by any command that uses per-atom computes as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. @@ -73,8 +73,8 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index 874ae8d629..233352ba7a 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -69,7 +69,7 @@ Output info This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -78,8 +78,8 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index c8bd663da7..680b1a60fc 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -42,7 +42,7 @@ Output info This compute calculates a global scalar (the summed KE of all the rigid bodies). This value can be used by any command that uses a -global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -52,7 +52,7 @@ Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index 44d6054e22..c396a33dbc 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -36,14 +36,14 @@ Output info These computes calculate per-node (per-atom) vectors, which can be accessed by any command that uses per-atom values from a compute as input, and global -scalars. See the :doc:`Howto output ` doc page for an overview of +scalars. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The computed values are provided in energy :doc:`units `. Restrictions """""""""""" -These computes are part of the USER-MESONT package. They are only enabled if +These computes are part of the MESONT package. They are only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. In addition, :doc:`mesont pair_style ` must be used. diff --git a/doc/src/compute_mliap.rst b/doc/src/compute_mliap.rst index 579086ad4a..350f4c800c 100644 --- a/doc/src/compute_mliap.rst +++ b/doc/src/compute_mliap.rst @@ -56,21 +56,22 @@ and it is also straightforward to add new descriptor styles. The compute *mliap* command must be followed by two keywords *model* and *descriptor* in either order. -The *model* keyword is followed by the model style (*linear*, *quadratic* or *mliappy*). -The *mliappy* model is only available -if lammps is built with MLIAPPY package. +The *model* keyword is followed by the model style (*linear*, +*quadratic* or *mliappy*). The *mliappy* model is only available if +LAMMPS is built with the *mliappy* python module. There are +:ref:`specific installation instructions ` for that. -The *descriptor* keyword is followed by a descriptor style, and additional arguments. -The compute currently supports just one descriptor style, but it is -is straightforward to add new descriptor styles. -The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap `, -including the linear, quadratic, and chem variants. -A single additional argument specifies the descriptor filename -containing the parameters and setting used by the SNAP descriptor. -The descriptor filename usually ends in the *.mliap.descriptor* extension. -The format of this file is identical to the descriptor file in the -:doc:`pair_style mliap `, and is described in detail -there. +The *descriptor* keyword is followed by a descriptor style, and +additional arguments. The compute currently supports two descriptor +styles *sna* and *so3*, but it is is straightforward to add additional +descriptor styles. The SNAP descriptor style *sna* is the same as that +used by :doc:`pair_style snap `, including the linear, +quadratic, and chem variants. A single additional argument specifies +the descriptor filename containing the parameters and setting used by +the SNAP descriptor. The descriptor filename usually ends in the +*.mliap.descriptor* extension. The format of this file is identical to +the descriptor file in the :doc:`pair_style mliap `, and is +described in detail there. .. note:: @@ -164,11 +165,12 @@ potentials, see the examples in `FitSNAP `_. Restrictions """""""""""" -This compute is part of the MLIAP package. It is only enabled if LAMMPS -was built with that package. In addition, building LAMMPS with the MLIAP package -requires building LAMMPS with the SNAP package. -The *mliappy* model requires building LAMMPS with the PYTHON package. -See the :doc:`Build package ` doc page for more info. +This compute is part of the ML-IAP package. It is only enabled if +LAMMPS was built with that package. In addition, building LAMMPS with +the ML-IAP package requires building LAMMPS with the ML-SNAP package. +The *mliappy* model also requires building LAMMPS with the PYTHON +package. See the :doc:`Build package ` page for more +info. Related commands """""""""""""""" diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index 3b8f613744..a68f3c14e1 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -18,10 +18,10 @@ Syntax *extra/dof* value = N N = # of extra degrees of freedom to subtract - *extra* syntax is identical to *extra/dof*\ , will be disabled at some point + *extra* syntax is identical to *extra/dof*, will be disabled at some point *dynamic/dof* value = *yes* or *no* yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature - *dynamic* syntax is identical to *dynamic/dof*\ , will be disabled at some point + *dynamic* syntax is identical to *dynamic/dof*, will be disabled at some point Examples """""""" diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index bcc5f3d421..c86901933b 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -34,7 +34,7 @@ Output info This compute calculates a global vector (the summed momentum) of length 3. This value can be used by any command that uses a global -vector value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector value calculated by this compute is "extensive". The vector @@ -43,8 +43,8 @@ value will be in mass\*velocity :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index ee2c4612d7..ed13a32b7c 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -112,7 +112,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute -as input. See the :doc:`Howto output ` doc page for an +as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 63d8deb2cd..70f4505d7f 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -56,7 +56,7 @@ If the *com* option is set to *yes* then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacement of each atom is calculated. -See the :doc:`compute msd ` doc page for further important +See the :doc:`compute msd ` page for further important NOTEs, which also apply to this compute. Output info @@ -74,8 +74,8 @@ the third is dimensionless. Restrictions """""""""""" -This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index d0af88b1a4..90baf9e2b3 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -75,7 +75,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 3 for the 3 xyz components of the angular velocity for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index af4e6a21e8..bc608e21d7 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -181,7 +181,8 @@ page for an overview of LAMMPS output options. Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 1b074203aa..b43c4bd6d7 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -24,7 +24,7 @@ Examples compute 1 all pair gauss compute 1 all pair lj/cut/coul/cut ecoul compute 1 all pair tersoff 2 epair - compute 1 all pair reax/c + compute 1 all pair reaxff Description """"""""""" @@ -50,11 +50,11 @@ two parts: *evdwl* and *ecoul* such that *epair* = *evdwl* + *ecoul*\ . If the pair style calculates Coulombic interactions, their energy will be tallied in *ecoul*\ . Everything else (whether it is a Lennard-Jones style van der Waals interaction or not) is tallied in *evdwl*\ . If -*evalue* is blank or specified as *epair*\ , then *epair* is stored +*evalue* is blank or specified as *epair*, then *epair* is stored as a global scalar by this compute. This is useful when using :doc:`pair_style hybrid ` if you want to know the portion of the total energy contributed by one sub-style. If *evalue* is -specified as *evdwl* or *ecoul*\ , then just that portion of the energy +specified as *evdwl* or *ecoul*, then just that portion of the energy is stored as a global scalar. .. note:: @@ -64,8 +64,9 @@ is stored as a global scalar. :doc:`pair_modify ` command. Some pair styles tally additional quantities, e.g. a breakdown of -potential energy into 14 components is tallied by the :doc:`pair_style reax/c ` command. These values (1 or more) -are stored as a global vector by this compute. See the doc page for +potential energy into 14 components is tallied by the +:doc:`pair_style reaxff ` command. These values (1 or more) +are stored as a global vector by this compute. See the page for :doc:`individual pair styles ` for info on these values. Output info @@ -83,7 +84,7 @@ The scalar and vector values calculated by this compute are The scalar value will be in energy :doc:`units `. The vector values will typically also be in energy :doc:`units `, but see -the doc page for the pair style for details. +the page for the pair style for details. Restrictions """""""""""" @@ -97,4 +98,4 @@ Related commands Default """"""" -The keyword defaults are *evalue* = *epair*\ , nsub = 0. +The keyword defaults are *evalue* = *epair*, nsub = 0. diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index e269aaadfe..f464c7cec6 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -20,7 +20,7 @@ Syntax *dist* = pairwise distance *eng* = pairwise energy *force* = pairwise force - *fx*\ ,\ *fy*\ ,\ *fz* = components of pairwise force + *fx*,\ *fy*,\ *fz* = components of pairwise force *pN* = pair style specific quantities for allowed N values * zero or more keyword/arg pairs may be appended @@ -61,20 +61,20 @@ The value *eng* is the interaction energy for the pair of atoms. The value *force* is the force acting between the pair of atoms, which is positive for a repulsive force and negative for an attractive -force. The values *fx*\ , *fy*\ , and *fz* are the xyz components of +force. The values *fx*, *fy*, and *fz* are the xyz components of *force* on atom I. A pair style may define additional pairwise quantities which can be -accessed as *p1* to *pN*\ , where N is defined by the pair style. Most +accessed as *p1* to *pN*, where N is defined by the pair style. Most pair styles do not define any additional quantities, so N = 0. An example of ones that do are the :doc:`granular pair styles ` which calculate the tangential force between two particles and return its components and magnitude acting on atom I for N = 1,2,3,4. See individual pair styles for details. -When using *pN* with pair style *hybrid*\ , the output will be the Nth +When using *pN* with pair style *hybrid*, the output will be the Nth quantity from the sub-style that computes the pairwise interaction -(based on atom types). If that sub-style does not define a *pN*\ , +(based on atom types). If that sub-style does not define a *pN*, the output will be 0.0. The maximum allowed N is the maximum number of quantities provided by any sub-style. @@ -90,12 +90,12 @@ is not computed for the specific pairwise interaction (based on atom types), then the output will be 0.0. The value *dist* will be in distance :doc:`units `. The value -*eng* will be in energy :doc:`units `. The values *force*\ , *fx*\ , -*fy*\ , and *fz* will be in force :doc:`units `. The values *pN* +*eng* will be in energy :doc:`units `. The values *force*, *fx*, +*fy*, and *fz* will be in force :doc:`units `. The values *pN* will be in whatever units the pair style defines. The optional *cutoff* keyword determines how the force cutoff distance -for an interaction is determined. For the default setting of *type*\ , +for an interaction is determined. For the default setting of *type*, the pairwise cutoff defined by the :doc:`pair_style ` command for the types of the two atoms is used. For the *radius* setting, the sum of the radii of the two particles is used as a @@ -147,12 +147,12 @@ array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *dist* will be in distance :doc:`units `. The output for *eng* will be in energy :doc:`units `. The output for -*force*\ , *fx*\ , *fy*\ , and *fz* will be in force :doc:`units `. +*force*, *fx*, *fy*, and *fz* will be in force :doc:`units `. The output for *pN* will be in whatever units the pair style defines. Restrictions diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index 91aaaf867c..ab6db9c786 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -89,7 +89,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index b78f706afd..6861dd7cfc 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -43,7 +43,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (lambda) >= 0.0. @@ -52,7 +52,7 @@ Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 3c98208261..6d76713b41 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -124,7 +124,7 @@ This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output -` doc page for an overview of LAMMPS output options. +` page for an overview of LAMMPS output options. The ordering of values in the symmetric pressure tensor is as follows: pxx, pyy, pzz, pxy, pxz, pyz. diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index d1102cd9bc..a008254540 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -67,8 +67,8 @@ calculations are also excluded. Note that this pressure compute outputs the configurational terms only; the kinetic contribution is not included and may be calculated from the number density output by P_kin=density\*k\*T. -This compute is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index bdd212cf5c..2e53961d00 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -41,8 +41,8 @@ The keywords and output information are documented in Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the UEF package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. This command can only be used when :doc:`fix nvt/uef ` or :doc:`fix npt/uef ` is active. diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index ec9322bb7b..333f31d013 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -74,7 +74,7 @@ Syntax .. parsed-literal:: - USER-EFF and USER-AWPMD package per-atom properties: + EFF and AWPMD package per-atom properties: spin = electron spin eradius = electron radius ervel = electron radial velocity @@ -82,7 +82,7 @@ Syntax .. parsed-literal:: - USER-SPH package per-atom properties: + SPH package per-atom properties: rho = density of SPH particles drho = change in density e = energy @@ -130,25 +130,25 @@ quantities that are not defined for a particular particle in the group The additional quantities only accessible via this command, and not directly via the :doc:`dump custom ` command, are as follows. -*Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles +*Shapex*, *shapey*, and *shapez* are defined for ellipsoidal particles and define the 3d shape of each particle. -*Quatw*\ , *quati*\ , *quatj*\ , and *quatk* are defined for ellipsoidal +*Quatw*, *quati*, *quatj*, and *quatk* are defined for ellipsoidal particles and body particles and store the 4-vector quaternion representing the orientation of each particle. See the :doc:`set ` command for an explanation of the quaternion vector. -*End1x*\ , *end1y*\ , *end1z*\ , *end2x*\ , *end2y*\ , *end2z*\ , are +*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are defined for line segment particles and define the end points of each line segment. -*Corner1x*\ , *corner1y*\ , *corner1z*\ , *corner2x*\ , *corner2y*\ , -*corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for +*Corner1x*, *corner1y*, *corner1z*, *corner2x*, *corner2y*, +*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for triangular particles and define the corner points of each triangle. *Nbonds* is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the -:doc:`newton bond ` command is set to *on*\ , which is the +:doc:`newton bond ` command is set to *on*, which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off ` is @@ -169,7 +169,7 @@ per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses per-atom values from a compute as input. See the :doc:`Howto output -` doc page for an overview of LAMMPS output options. +` page for an overview of LAMMPS output options. The vector or array values will be in whatever :doc:`units ` the corresponding attribute is in, e.g. velocity units for vx, charge diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 246ab09120..48b3641e84 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -67,14 +67,14 @@ then be 415 for the third chunk. The *coordN* attributes can only be used if a *binning* style was used in the :doc:`compute chunk/atom ` command referenced -by chunkID. For *bin/1d*\ , *bin/2d*\ , and *bin/3d* styles the attribute +by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles the attribute is the center point of the bin in the corresponding dimension. Style *bin/1d* only defines a *coord1* attribute. Style *bin/2d* adds a *coord2* attribute. Style *bin/3d* adds a *coord3* attribute. -Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*\ , the +Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the *coordN* attributes will be in distance :doc:`units `. If the -value of the *units* keyword is *reduced*\ , the *coordN* attributes +value of the *units* keyword is *reduced*, the *coordN* attributes will be in unitless reduced units (0-1). The simplest way to output the results of the compute property/chunk @@ -102,7 +102,7 @@ single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values are "intensive". The values will be diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index dd92334266..357f46b70d 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -72,17 +72,17 @@ property/local command. If the inputs are pair attributes, the local data is generated by looping over the pairwise neighbor list. Info about an individual pairwise interaction will only be included if both atoms in the pair -are in the specified compute group. For *natom1* and *natom2*\ , all +are in the specified compute group. For *natom1* and *natom2*, all atom pairs in the neighbor list are considered (out to the neighbor cutoff = force cutoff + :doc:`neighbor skin `). For *patom1* -and *patom2*\ , the distance between the atoms must be less than the +and *patom2*, the distance between the atoms must be less than the force cutoff distance for that pair to be included, as defined by the :doc:`pair_style ` and :doc:`pair_coeff ` commands. The optional *cutoff* keyword determines how the force cutoff distance for an interaction is determined for the *patom1* and *patom2* -attributes. For the default setting of *type*\ , the pairwise cutoff +attributes. For the default setting of *type*, the pairwise cutoff defined by the :doc:`pair_style ` command for the types of the two atoms is used. For the *radius* setting, the sum of the radii of the two particles is used as a cutoff. For example, this is @@ -113,10 +113,10 @@ same for local vectors or arrays generated by other compute commands. For example, output from the :doc:`compute bond/local ` command can be combined with bond atom indices from this command and output by the :doc:`dump local ` command in a consistent way. -The *natom1* and *natom2*\ , or *patom1* and *patom2* attributes refer +The *natom1* and *natom2*, or *patom1* and *patom2* attributes refer to the atom IDs of the 2 atoms in each pairwise interaction computed by the :doc:`pair_style ` command. The *ntype1* and -*ntype2*\ , or *ptype1* and *ptype2* attributes refer to the atom types +*ntype2*, or *ptype1* and *ptype2* attributes refer to the atom types of the 2 atoms in each pairwise interaction. .. note:: @@ -149,7 +149,7 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index fb590f6e4c..3e209d1dc5 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -89,7 +89,7 @@ Output info This compute calculates a per-atom array, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. Results are stored in the per-atom array in the following order: @@ -112,8 +112,8 @@ For atoms that are not within the compute group-ID, all values are set to zero. Restrictions """""""""""" -This fix is part of the USER-PTM package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the PTM package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index a9e6674816..85366eab2a 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -55,7 +55,7 @@ shell of distances in 3d and a thin ring of distances in 2d. command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses a neighbor list, it also means those pairs will not be included in the RDF. This does not apply when - using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , + using long-range coulomb interactions (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and @@ -94,7 +94,7 @@ The *itypeN* and *jtypeN* arguments are optional. These arguments must come in pairs. If no pairs are listed, then a single histogram is computed for g(r) between all atom types. If one or more pairs are listed, then a separate histogram is generated for each -*itype*\ ,\ *jtype* pair. +*itype*,\ *jtype* pair. The *itypeN* and *jtypeN* settings can be specified in one of two ways. An explicit numeric value can be used, as in the fourth example @@ -156,13 +156,13 @@ Output info """"""""""" This compute calculates a global array with the number of rows = -*Nbins*\ , and the number of columns = 1 + 2\*Npairs, where Npairs is the +*Nbins*, and the number of columns = 1 + 2\*Npairs, where Npairs is the number of I,J pairings specified. The first column has the bin coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of *itypeN* versus *jtypeN* interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". @@ -186,7 +186,7 @@ your model. The definition of g(r) used by LAMMPS is only appropriate for characterizing atoms that are uniformly distributed throughout the simulation cell. In such cases, the coordination number is still correct and meaningful. As an example, if a large simulation cell -contains only one atom of type *itypeN* and one of *jtypeN*\ , then g(r) +contains only one atom of type *itypeN* and one of *jtypeN*, then g(r) will register an arbitrarily large spike at whatever distance they happen to be at, and zero everywhere else. Coord(r) will show a step change from zero to one at the location of the spike in g(r). diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 660ef87042..1793830e0a 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -74,7 +74,7 @@ or *max* options find the minimum or maximum value across all vector values. The *ave* setting adds the vector values into a global total, then divides by the number of values in the vector. The *sumsq* option sums the square of the values in the vector into a global -total. The *avesq* setting does the same as *sumsq*\ , then divides the +total. The *avesq* setting does the same as *sumsq*, then divides the sum of squares by the number of values. The last two options can be useful for calculating the variance of some quantity, e.g. variance = sumsq - ave\^2. @@ -126,7 +126,7 @@ an input value from that compute. If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual -:doc:`compute ` doc page for details. If no bracketed integer +:doc:`compute ` page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own @@ -136,7 +136,7 @@ to effectively specify multiple values. If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom -or local quantities. See the individual :doc:`fix ` doc page for +or local quantities. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 342c6ceb05..256ff15920 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -169,7 +169,7 @@ in the array is the number of inputs provided. The length of the vector or the number of vector elements or array rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The vector or array can be accessed by any command that uses global values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom values for the vector or each column of the array will be diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index f7bb6d6166..574f3343be 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -61,7 +61,7 @@ command and its variants. The ID of the :doc:`fix rigid/small ` comm be specified as *rigidID*\ . The :doc:`fix rigid ` command is typically used to define a handful of (potentially very large) rigid bodies. It outputs similar per-body information as this command -directly from the fix as global data; see the :doc:`fix rigid ` doc page for details +directly from the fix as global data; see the :doc:`fix rigid ` page for details The local data stored by this command is generated by looping over all the atoms owned on a processor. If the atom is not in the specified @@ -107,43 +107,43 @@ rigid bodies. The *mass* attribute is the total mass of the rigid body. There are two options for outputting the coordinates of the center of -mass (COM) of the body. The *x*\ , *y*\ , *z* attributes write the COM +mass (COM) of the body. The *x*, *y*, *z* attributes write the COM "unscaled", in the appropriate distance :doc:`units ` (Angstroms, -sigma, etc). Use *xu*\ , *yu*\ , *zu* if you want the COM "unwrapped" by +sigma, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by the image flags for each body. Unwrapped means that if the body COM has passed through a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box. -The image flags for the body can be generated directly using the *ix*\ , -*iy*\ , *iz* attributes. For periodic dimensions, they specify which +The image flags for the body can be generated directly using the *ix*, +*iy*, *iz* attributes. For periodic dimensions, they specify which image of the simulation box the COM is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid body COMs cross periodic boundaries during the simulation. -The *vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz* attributes are components of +The *vx*, *vy*, *vz*, *fx*, *fy*, *fz* attributes are components of the COM velocity and force on the COM of the body. -The *omegax*\ , *omegay*\ , and *omegaz* attributes are the angular +The *omegax*, *omegay*, and *omegaz* attributes are the angular velocity components of the body around its COM. -The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular +The *angmomx*, *angmomy*, and *angmomz* attributes are the angular momentum components of the body around its COM. -The *quatw*\ , *quati*\ , *quatj*\ , and *quatk* attributes are the +The *quatw*, *quati*, *quatj*, and *quatk* attributes are the components of the 4-vector quaternion representing the orientation of the rigid body. See the :doc:`set ` command for an explanation of the quaternion vector. -The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular +The *angmomx*, *angmomy*, and *angmomz* attributes are the angular momentum components of the body around its COM. -The *tqx*\ , *tqy*\ , *tqz* attributes are components of the torque acting +The *tqx*, *tqy*, *tqz* attributes are components of the torque acting on the body around its COM. -The *inertiax*\ , *inertiay*\ , *inertiaz* attributes are components of +The *inertiax*, *inertiay*, *inertiaz* attributes are components of diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS. @@ -160,7 +160,7 @@ specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values will be in whatever :doc:`units ` the @@ -181,7 +181,7 @@ Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 1057208900..37ee302f8f 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -90,7 +90,7 @@ unless small spacing parameters <0.05 Angstrom\^(-1) are implemented. Meshes with manual spacing do not require a periodic boundary. The limits of the reciprocal lattice mesh are determined by the use of -the *Kmax*\ , *Zone*\ , and *dR_Ewald* parameters. The rectilinear mesh +the *Kmax*, *Zone*, and *dR_Ewald* parameters. The rectilinear mesh created about the origin of reciprocal space is terminated at the boundary of a sphere of radius *Kmax* centered at the origin. If *Zone* parameters z1=z2=z3=0 are used, diffraction intensities are @@ -245,8 +245,8 @@ All array values calculated by this compute are "intensive". Restrictions """""""""""" -This compute is part of the USER-DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The compute_saed command does not work for triclinic cells. diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 2d558b871f..9b4e7df626 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -44,9 +44,9 @@ quantities; they cannot be per-atom or local quantities. group specified with this command is ignored. The values extracted from the input vector(s) are determined by the -*Nstart*\ , *Nstop*\ , and *Nskip* parameters. The elements of an input +*Nstart*, *Nstop*, and *Nskip* parameters. The elements of an input vector of length N are indexed from 1 to N. Starting at element -*Nstart*\ , every Mth element is extracted, where M = *Nskip*\ , until +*Nstart*, every Mth element is extracted, where M = *Nskip*, until element *Nstop* is reached. The extracted quantities are stored as a vector, which is typically shorter than the input vector. @@ -65,7 +65,7 @@ used. Users can also write code for their own compute styles and :doc:`add them If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script and which generates a global -vector or array. See the individual :doc:`fix ` doc page for +vector or array. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute slice references the values, else an error results. If no bracketed integer is @@ -97,7 +97,7 @@ specified or a global array with N columns where N is the number of inputs. The length of the vector or the number of rows in the array is equal to the number of values extracted from each input vector. These values can be used by any command that uses global vector or -array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values calculated by this compute are simply diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index 71630b827d..25f346625c 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -40,7 +40,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will be in distance :doc:`units `. @@ -48,8 +48,8 @@ The per-particle vector values will be in distance :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index ee3671e20c..10070eaf0e 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -32,7 +32,7 @@ See `this PDF guide `_ to use Smooth Mach Dynamics This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values are dimensionless an in the range of zero to one. @@ -40,7 +40,7 @@ The per-particle values are dimensionless an in the range of zero to one. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the "Build Related commands diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index 980d31454e..aee87592aa 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -41,7 +41,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will are dimensionless. See @@ -50,8 +50,8 @@ The per-particle vector values will are dimensionless. See Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with tlsph pair style. diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index c4df459d5f..535384e38b 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -34,7 +34,7 @@ Output Info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will be given in :doc:`units ` of energy. @@ -42,8 +42,8 @@ The per-particle vector values will be given in :doc:`units ` of energy. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index 81bacdc4bb..17614df548 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -34,7 +34,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given dimensionless. See :doc:`units `. @@ -42,8 +42,8 @@ The per-particle values will be given dimensionless. See :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index cdcd377b41..dc78b627ef 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -34,7 +34,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given in :doc:`units ` of one over time. @@ -42,8 +42,8 @@ The per-particle values will be given in :doc:`units ` of one over time. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index e7cdb8a9d3..0adbc9db34 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -36,7 +36,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be in :doc:`units ` of mass over volume. @@ -44,8 +44,8 @@ The per-particle values will be in :doc:`units ` of mass over volume. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index d74b684c5d..813bd32507 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -47,8 +47,8 @@ entry is the determinant of the deformation gradient. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. TThis compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. TThis compute can only be used for particles which interact via the total Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 888140c534..44b2311898 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -40,7 +40,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given in :doc:`units ` of time. @@ -48,8 +48,8 @@ The per-particle values will be given in :doc:`units ` of time. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index 5d34f1acef..bc76ec260f 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -35,7 +35,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values are dimensionless. See :doc:`units `. @@ -43,8 +43,8 @@ The per-particle values are dimensionless. See :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian pair style. diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index d9ce1e3d9a..aefedb64eb 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -36,7 +36,7 @@ Output info This compute calculates a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute -as input. See the :doc:`Howto output ` doc page for an +as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector has 7 entries. The first three entries @@ -50,8 +50,8 @@ particle relative to its initial state. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index b89311eb4b..3ecb509e9f 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -46,8 +46,8 @@ zz, xy, xz, yz components of the symmetric strain tensor. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index d1fc399b42..41251d7095 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -45,8 +45,8 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index d3711954c5..11cec3bda8 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -47,8 +47,8 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index d797891618..9f478b7262 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -34,7 +34,7 @@ Output info This compute returns a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute -as input. See the :doc:`Howto output ` doc page for an +as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and @@ -53,8 +53,8 @@ The values will be given in :doc:`units ` of distance. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index ff12f9cdac..4b4959fbe1 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -34,7 +34,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector contains the current effective per atom shear @@ -44,8 +44,8 @@ style. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index 3579a88079..c446c477c0 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -35,7 +35,7 @@ Output info This compute returns a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given dimensionless, see :doc:`units `. @@ -43,8 +43,8 @@ The per-particle values will be given dimensionless, see :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index 09f06b084b..31defe4b32 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -34,7 +34,7 @@ Output info This compute calculates a per-particle tensor, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector has 6 entries, corresponding to the xx, yy, @@ -46,8 +46,8 @@ The per-particle tensor values will be given dimensionless, see Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index 391367321a..0a2ca91081 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -46,8 +46,8 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index e1db7640a6..a993a08c06 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -46,8 +46,8 @@ stress tensor, i.e., the von Mises equivalent stress. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index 4f9314ac32..f09c48e0ed 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -34,7 +34,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will be given in :doc:`units ` of @@ -46,8 +46,8 @@ per-particle volumes of the group for which the fix is defined. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 08b06a32ec..f156133521 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -72,64 +72,66 @@ Description """"""""""" Define a computation that calculates a set of quantities related to the -bispectrum components of the atoms in a group. These computes are -used primarily for calculating the dependence of energy, force, and -stress components on the linear coefficients in the -:doc:`snap pair_style `, which is useful when training a -SNAP potential to match target data. +bispectrum components of the atoms in a group. These computes are used +primarily for calculating the dependence of energy, force, and stress +components on the linear coefficients in the :doc:`snap pair_style +`, which is useful when training a SNAP potential to match +target data. -Bispectrum components of an atom are order parameters characterizing -the radial and angular distribution of neighbor atoms. The detailed +Bispectrum components of an atom are order parameters characterizing the +radial and angular distribution of neighbor atoms. The detailed mathematical definition is given in the paper by Thompson et al. :ref:`(Thompson) ` -The position of a neighbor atom *i'* relative to a central atom *i* is -a point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* :math:`(R_i + R_i')` +The position of a neighbor atom *i'* relative to a central atom *i* is a +point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* +:math:`(R_i + R_i')` -Bartok et al. :ref:`(Bartok) `, proposed mapping this 3D ball -onto the 3-sphere, the surface of the unit ball in a four-dimensional -space. The radial distance *r* within *R_ii'* is mapped on to a third -polar angle :math:`\theta_0` defined by, +Bartok et al. :ref:`(Bartok) `, proposed mapping this 3D +ball onto the 3-sphere, the surface of the unit ball in a +four-dimensional space. The radial distance *r* within *R_ii'* is +mapped on to a third polar angle :math:`\theta_0` defined by, .. math:: \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi In this way, all possible neighbor positions are mapped on to a subset -of the 3-sphere. Points south of the latitude :math:`\theta_0` = *rfac0* :math:`\pi` -are excluded. +of the 3-sphere. Points south of the latitude :math:`\theta_0` = +*rfac0* :math:`\pi` are excluded. The natural basis for functions on the 3-sphere is formed by the -representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, \theta_0)`. -These functions are better known as :math:`D^j_{m,m'}`, the elements of the Wigner -*D*\ -matrices :ref:`(Meremianin `, -:ref:`Varshalovich `, :ref:`Mason) ` -The density of neighbors on the 3-sphere can be written as a sum of -Dirac-delta functions, one for each neighbor, weighted by species and -radial distance. Expanding this density function as a generalized -Fourier series in the basis functions, we can write each Fourier -coefficient as +representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, +\theta_0)`. These functions are better known as :math:`D^j_{m,m'}`, the +elements of the Wigner *D*\ -matrices :ref:`(Meremianin +`, :ref:`Varshalovich `, :ref:`Mason) +` The density of neighbors on the 3-sphere can be written as +a sum of Dirac-delta functions, one for each neighbor, weighted by +species and radial distance. Expanding this density function as a +generalized Fourier series in the basis functions, we can write each +Fourier coefficient as .. math:: u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{\mu_{i'}} U^j_{m,m'}(\theta_0,\theta,\phi)} -The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that depend on -:math:`\mu_{i'}`, the SNAP element of atom *i'*, while the central atom is -arbitrarily assigned a unit weight. The function :math:`f_c(r)` ensures that -the contribution of each neighbor atom goes smoothly to zero at -:math:`R_{ii'}`: +The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that +depend on :math:`\mu_{i'}`, the SNAP element of atom *i'*, while the +central atom is arbitrarily assigned a unit weight. The function +:math:`f_c(r)` ensures that the contribution of each neighbor atom goes +smoothly to zero at :math:`R_{ii'}`: .. math:: f_c(r) = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\ = & 0, r > R_{ii'} -The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and they are -not directly useful as descriptors, because they are not invariant -under rotation of the polar coordinate frame. However, the following -scalar triple products of expansion coefficients can be shown to be -real-valued and invariant under rotation :ref:`(Bartok) `. +The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and +they are not directly useful as descriptors, because they are not +invariant under rotation of the polar coordinate frame. However, the +following scalar triple products of expansion coefficients can be shown +to be real-valued and invariant under rotation :ref:`(Bartok) +`. .. math:: @@ -140,27 +142,26 @@ real-valued and invariant under rotation :ref:`(Bartok) `. {j_2} {m_2} {m'_2} \end{array}} u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2} -The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}` -are coupling coefficients, -analogous to Clebsch-Gordan coefficients for rotations on the -2-sphere. These invariants are the components of the bispectrum and -these are the quantities calculated by the compute *sna/atom*\ . They -characterize the strength of density correlations at three points on -the 3-sphere. The j2=0 subset form the power spectrum, which -characterizes the correlations of two points. The lowest-order -components describe the coarsest features of the density function, -while higher-order components reflect finer detail. Each bispectrum -component contains terms that depend on the positions of up to 4 -atoms (3 neighbors and the central atom). +The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}` are +coupling coefficients, analogous to Clebsch-Gordan coefficients for +rotations on the 2-sphere. These invariants are the components of the +bispectrum and these are the quantities calculated by the compute +*sna/atom*\ . They characterize the strength of density correlations at +three points on the 3-sphere. The j2=0 subset form the power spectrum, +which characterizes the correlations of two points. The lowest-order +components describe the coarsest features of the density function, while +higher-order components reflect finer detail. Each bispectrum component +contains terms that depend on the positions of up to 4 atoms (3 +neighbors and the central atom). -Compute *snad/atom* calculates the derivative of the bispectrum components -summed separately for each LAMMPS atom type: +Compute *snad/atom* calculates the derivative of the bispectrum +components summed separately for each LAMMPS atom type: .. math:: -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i} -The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*\ , +The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*, this compute evaluates the above expression for each direction, each atom type, and each bispectrum component. See section below on output for a detailed explanation. @@ -173,23 +174,23 @@ derivatives: -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i} Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom -*i*\ , this compute evaluates the above expression for each of the six +*i*, this compute evaluates the above expression for each of the six virial components, each atom type, and each bispectrum component. See section below on output for a detailed explanation. Compute *snap* calculates a global array containing information related -to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ , +to all three of the above per-atom computes *sna/atom*, *snad/atom*, and *snav/atom*\ . The first row of the array contains the summation of -*sna/atom* over all atoms, but broken out by type. The last six rows -of the array contain the summation of *snav/atom* over all atoms, broken -out by type. In between these are 3\*\ *N* rows containing the same values -computed by *snad/atom* (these are already summed over all atoms and -broken out by type). The element in the last column of each row contains -the potential energy, force, or stress, according to the row. +*sna/atom* over all atoms, but broken out by type. The last six rows of +the array contain the summation of *snav/atom* over all atoms, broken +out by type. In between these are 3\*\ *N* rows containing the same +values computed by *snad/atom* (these are already summed over all atoms +and broken out by type). The element in the last column of each row +contains the potential energy, force, or stress, according to the row. These quantities correspond to the user-specified reference potential -that must be subtracted from the target data when fitting SNAP. -The potential energy calculation uses the built in compute *thermo_pe*. -The stress calculation uses a compute called *snap_press* that is +that must be subtracted from the target data when fitting SNAP. The +potential energy calculation uses the built in compute *thermo_pe*. The +stress calculation uses a compute called *snap_press* that is automatically created behind the scenes, according to the following command: @@ -224,37 +225,33 @@ ordered in which they are listed. The keyword *switchflag* can be used to turn off the switching function :math:`f_c(r)`. -The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum -components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword -normally only affects compute *sna/atom*\ . However, when -*quadraticflag* is on, it also affects *snad/atom* and *snav/atom*\ . +The keyword *bzeroflag* determines whether or not *B0*, the bispectrum +components of an atom with no neighbors, are subtracted from the +calculated bispectrum components. This optional keyword normally only +affects compute *sna/atom*\ . However, when *quadraticflag* is on, it +also affects *snad/atom* and *snav/atom*\ . -The keyword *quadraticflag* determines whether or not the -quadratic combinations of bispectrum quantities are generated. -These are formed by taking the outer product of the vector -of bispectrum components with itself. -See section below on output for a -detailed explanation of the number of quadratic terms and the -ordered in which they are listed. +The keyword *quadraticflag* determines whether or not the quadratic +combinations of bispectrum quantities are generated. These are formed +by taking the outer product of the vector of bispectrum components with +itself. See section below on output for a detailed explanation of the +number of quadratic terms and the ordered in which they are listed. -The keyword *chem* activates the explicit multi-element variant -of the SNAP bispectrum components. The argument *nelements* -specifies the number of SNAP elements that will be handled. -This is followed by *elementlist*, a list of integers of -length *ntypes*, with values in the range [0, *nelements* ), -which maps each LAMMPS type to one of the SNAP elements. -Note that multiple LAMMPS types can be mapped to the same element, -and some elements may be mapped by no LAMMPS type. However, in typical -use cases (training SNAP potentials) the mapping from LAMMPS types -to elements is one-to-one. +The keyword *chem* activates the explicit multi-element variant of the +SNAP bispectrum components. The argument *nelements* specifies the +number of SNAP elements that will be handled. This is followed by +*elementlist*, a list of integers of length *ntypes*, with values in the +range [0, *nelements* ), which maps each LAMMPS type to one of the SNAP +elements. Note that multiple LAMMPS types can be mapped to the same +element, and some elements may be mapped by no LAMMPS type. However, in +typical use cases (training SNAP potentials) the mapping from LAMMPS +types to elements is one-to-one. The explicit multi-element variant invoked by the *chem* keyword -partitions the density of neighbors into partial densities -for each chemical element. This is described in detail in the -paper by :ref:`Cusentino et al. ` -The bispectrum components are indexed on -ordered triplets of elements: +partitions the density of neighbors into partial densities for each +chemical element. This is described in detail in the paper by +:ref:`Cusentino et al. ` The bispectrum components are +indexed on ordered triplets of elements: .. math:: @@ -272,17 +269,19 @@ of element :math:`\mu` u^{\mu}_{j,m,m'} = w^{self}_{\mu_{i}\mu} U^{j,m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{\delta_{\mu\mu_{i'}}f_c(r_{ii'}) w_{\mu_{i'}} U^{j,m,m'}(\theta_0,\theta,\phi)} -where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is either 1 or 0 -(see keyword *wselfallflag* below), :math:`\delta_{\mu\mu_{i'}}` indicates -that the sum is only over neighbor atoms of element :math:`\mu`, -and all other quantities are the same as those appearing in the -original equation for :math:`u^j_{m,m'}` given above. +where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is +either 1 or 0 (see keyword *wselfallflag* below), +:math:`\delta_{\mu\mu_{i'}}` indicates that the sum is only over +neighbor atoms of element :math:`\mu`, and all other quantities are the +same as those appearing in the original equation for :math:`u^j_{m,m'}` +given above. -The keyword *wselfallflag* defines the rule used for the self-contribution. -If *wselfallflag* is on, then :math:`w^{self}_{\mu_{i}\mu}` = 1. If it is -off then :math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case -of :math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1. -When the *chem* keyword is not used, this keyword has no effect. +The keyword *wselfallflag* defines the rule used for the +self-contribution. If *wselfallflag* is on, then +:math:`w^{self}_{\mu_{i}\mu}` = 1. If it is off then +:math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case of +:math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1. When the +*chem* keyword is not used, this keyword has no effect. The keyword *bnormflag* determines whether or not the bispectrum component :math:`B_{j_1,j_2,j}` is divided by a factor of :math:`2j+1`. @@ -299,16 +298,16 @@ are not both set or not both unset. .. note:: - If you have a bonded system, then the settings of - :doc:`special_bonds ` command can remove pairwise - interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special_bonds ` - command, and means those pairwise interactions do not appear in the - neighbor list. Because this fix uses the neighbor list, it also means - those pairs will not be included in the calculation. One way to get - around this, is to write a dump file, and use the :doc:`rerun ` - command to compute the bispectrum components for snapshots in the dump - file. The rerun script can use a :doc:`special_bonds ` + If you have a bonded system, then the settings of :doc:`special_bonds + ` command can remove pairwise interactions between + atoms in the same bond, angle, or dihedral. This is the default + setting for the :doc:`special_bonds ` command, and + means those pairwise interactions do not appear in the neighbor list. + Because this fix uses the neighbor list, it also means those pairs + will not be included in the calculation. One way to get around this, + is to write a dump file, and use the :doc:`rerun ` command to + compute the bispectrum components for snapshots in the dump file. + The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. ---------- @@ -317,10 +316,10 @@ Output info """"""""""" Compute *sna/atom* calculates a per-atom array, each column -corresponding to a particular bispectrum component. The total number -of columns and the identity of the bispectrum component contained in -each column depend of the value of *twojmax*\ , as -described by the following piece of python code: +corresponding to a particular bispectrum component. The total number of +columns and the identity of the bispectrum component contained in each +column depend of the value of *twojmax*, as described by the following +piece of python code: .. parsed-literal:: @@ -338,73 +337,72 @@ For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramida since all potentials use the value of 3, corresponding to the above set of bispectrum components. -Compute *snad/atom* evaluates a per-atom array. The columns are -arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each -block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z* +Compute *snad/atom* evaluates a per-atom array. The columns are arranged +into *ntypes* blocks, listed in order of atom type *I*\ . Each block +contains three sub-blocks corresponding to the *x*, *y*, and *z* components of the atom position. Each of these sub-blocks contains *K* -columns for the *K* bispectrum components, the same as for compute *sna/atom* +columns for the *K* bispectrum components, the same as for compute +*sna/atom* -Compute *snav/atom* evaluates a per-atom array. The columns are -arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each -block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ , -*yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt -notation. Each of these sub-blocks contains *K* -columns for the *K* bispectrum components, the same as for compute *sna/atom* +Compute *snav/atom* evaluates a per-atom array. The columns are arranged +into *ntypes* blocks, listed in order of atom type *I*\ . Each block +contains six sub-blocks corresponding to the *xx*, *yy*, *zz*, +*yz*, *xz*, and *xy* components of the virial tensor in Voigt +notation. Each of these sub-blocks contains *K* columns for the *K* +bispectrum components, the same as for compute *sna/atom* -Compute *snap* evaluates a global array. -The columns are arranged into -*ntypes* blocks, listed in order of atom type *I*\ . Each block -contains one column for each bispectrum component, the same as for compute -*sna/atom*\ . A final column contains the corresponding energy, force component -on an atom, or virial stress component. The rows of the array appear -in the following order: +Compute *snap* evaluates a global array. The columns are arranged into +*ntypes* blocks, listed in order of atom type *I*\ . Each block contains +one column for each bispectrum component, the same as for compute +*sna/atom*\ . A final column contains the corresponding energy, force +component on an atom, or virial stress component. The rows of the array +appear in the following order: * 1 row: *sna/atom* quantities summed for all atoms of type *I* * 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID. * 6 rows: *snav/atom* quantities summed for all atoms of type *I* -For example, if *K* =30 and ntypes=1, the number of columns in the per-atom -arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom* -are 30, 90, and 180, respectively. With *quadratic* value=1, -the numbers of columns are 930, 2790, and 5580, respectively. -The number of columns in the global array generated by *snap* -are 31, and 931, respectively, while the number of rows is -1+3\*\ *N*\ +6, where *N* is the total number of atoms. +For example, if *K* =30 and ntypes=1, the number of columns in the +per-atom arrays generated by *sna/atom*, *snad/atom*, and +*snav/atom* are 30, 90, and 180, respectively. With *quadratic* value=1, +the numbers of columns are 930, 2790, and 5580, respectively. The +number of columns in the global array generated by *snap* are 31, and +931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N* +is the total number of atoms. -If the *quadratic* keyword value is set to 1, then additional -columns are generated, corresponding to -the products of all distinct pairs of bispectrum components. If the -number of bispectrum components is *K*\ , then the number of distinct pairs -is *K*\ (\ *K*\ +1)/2. -For compute *sna/atom* these columns are appended to existing *K* columns. -The ordering of quadratic terms is upper-triangular, -(1,1),(1,2)...(1,\ *K*\ ),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ). +If the *quadratic* keyword value is set to 1, then additional columns +are generated, corresponding to the products of all distinct pairs of +bispectrum components. If the number of bispectrum components is *K*, +then the number of distinct pairs is *K*\ (\ *K*\ +1)/2. For compute +*sna/atom* these columns are appended to existing *K* columns. The +ordering of quadratic terms is upper-triangular, (1,1),(1,2)...(1,\ *K*\ +),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*,\ *K*\ ). For computes *snad/atom* and *snav/atom* each set of *K*\ (\ *K*\ +1)/2 -additional columns is inserted directly after each of sub-block -of linear terms i.e. linear and quadratic terms are contiguous. -So the nesting order from inside to outside is bispectrum component, -linear then quadratic, vector/tensor component, type. +additional columns is inserted directly after each of sub-block of +linear terms i.e. linear and quadratic terms are contiguous. So the +nesting order from inside to outside is bispectrum component, linear +then quadratic, vector/tensor component, type. -If the *chem* keyword is used, then the data is arranged into :math:`N_{elem}^3` -sub-blocks, each sub-block corresponding to a particular chemical labeling -:math:`\kappa\lambda\mu` with the last label changing fastest. -Each sub-block contains *K* bispectrum components. For the purposes -of handling contributions to force, virial, and quadratic combinations, -these :math:`N_{elem}^3` sub-blocks are treated as a single block -of :math:`K N_{elem}^3` columns. +If the *chem* keyword is used, then the data is arranged into +:math:`N_{elem}^3` sub-blocks, each sub-block corresponding to a +particular chemical labeling :math:`\kappa\lambda\mu` with the last +label changing fastest. Each sub-block contains *K* bispectrum +components. For the purposes of handling contributions to force, virial, +and quadratic combinations, these :math:`N_{elem}^3` sub-blocks are +treated as a single block of :math:`K N_{elem}^3` columns. These values can be accessed by any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. To see how this command -can be used within a Python workflow to train SNAP potentials, -see the examples in `FitSNAP `_. +can be used within a Python workflow to train SNAP potentials, see the +examples in `FitSNAP `_. Restrictions """""""""""" -These computes are part of the SNAP package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` -doc page for more info. +These computes are part of the ML-SNAP package. They are only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index 17591257f2..5e6706fa27 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -30,7 +30,7 @@ The internal energy is the energy associated with the internal degrees of freedom of an SPH particle, i.e. a Smooth-Particle Hydrodynamics particle. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The value of the internal energy will be 0.0 for atoms not in the @@ -41,7 +41,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. @@ -49,8 +49,8 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the SPH package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index c422a5ecbb..7fcec0c9da 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -29,7 +29,7 @@ atom in a group, i.e. a Smooth-Particle Hydrodynamics density. The SPH density is the mass density of an SPH particle, calculated by kernel function interpolation using "pair style sph/rhosum". -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The value of the SPH density will be 0.0 for atoms not in the @@ -40,7 +40,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in mass/volume :doc:`units `. @@ -48,8 +48,8 @@ The per-atom vector values will be in mass/volume :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the SPH package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index 922adfff58..702d81027d 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -34,7 +34,7 @@ particles, i.e. a Smooth-Particle Hydrodynamics particle. T_{int} = E_{int} / C_{V,int} -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The value of the internal energy will be 0.0 for atoms not in the @@ -45,7 +45,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in temperature :doc:`units `. @@ -53,8 +53,8 @@ The per-atom vector values will be in temperature :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the SPH package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst index aaf9d8cc74..6694da000b 100644 --- a/doc/src/compute_spin.rst +++ b/doc/src/compute_spin.rst @@ -65,7 +65,7 @@ Restrictions """""""""""" The *spin* compute is part of the SPIN package. This compute is only -enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. The atom_style +enabled if LAMMPS was built with this package. See the :doc:`Build package ` page for more info. The atom_style has to be "spin" for this compute to be valid. **Related commands:** diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 393d3b2ffb..cdb464a9d0 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -213,7 +213,7 @@ which can be accessed by indices 1-6 by any command that uses per-atom values from a compute as input. Compute *centroid/stress/atom* produces a per-atom array with 9 columns, but otherwise can be used in an identical manner to compute *stress/atom*. See the :doc:`Howto -output ` doc page for an overview of LAMMPS output +output ` page for an overview of LAMMPS output options. The ordering of the 6 columns for *stress/atom* is as follows: xx, yy, @@ -233,7 +233,7 @@ since its computations are performed pairwise), nor granular pair styles with pairwise forces which are not aligned with the vector between the pair of particles. All bond styles are supported. All angle, dihedral, improper styles are supported with the exception of -USER-INTEL and KOKKOS variants of specific styles. It also does not +INTEL and KOKKOS variants of specific styles. It also does not support models with long-range Coulombic or dispersion forces, i.e. the kspace_style command in LAMMPS. It also does not support the following fixes which add rigid-body constraints: :doc:`fix shake diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index d68bafa48b..bcc1a87e5f 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -45,8 +45,8 @@ Description Compute *stress/mop* and compute *stress/mop/profile* define computations that calculate components of the local stress tensor using the method of planes :ref:`(Todd) `. Specifically in compute *stress/mop* calculates 3 -components are computed in directions *dir*\ ,\ *x*\ ; *dir*\ ,\ *y*\ ; and -*dir*\ ,\ *z*\ ; where *dir* is the direction normal to the plane, while +components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and +*dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while in compute *stress/mop/profile* the profile of the stress is computed. Contrary to methods based on histograms of atomic stress (i.e. using @@ -87,12 +87,12 @@ and stress_dir,z. The values are in pressure :doc:`units `. -The values produced by this compute can be accessed by various :doc:`output commands `. For instance, the results can be written to a file using the :doc:`fix ave/time ` command. Please see the example in the examples/USER/mop folder. +The values produced by this compute can be accessed by various :doc:`output commands `. For instance, the results can be written to a file using the :doc:`fix ave/time ` command. Please see the example in the examples/PACKAGES/mop folder. Restrictions """""""""""" -These styles are part of the USER-MISC package. They are only enabled if +These styles are part of the EXTRA-COMPUTE package. They are only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page on for more info. diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 0e2856ea5e..313b54645c 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -1,5 +1,6 @@ .. index:: compute force/tally .. index:: compute heat/flux/tally +.. index:: compute heat/flux/virial/tally .. index:: compute pe/tally .. index:: compute pe/mol/tally .. index:: compute stress/tally @@ -10,6 +11,9 @@ compute force/tally command compute heat/flux/tally command =============================== +compute heat/flux/virial/tally command +====================================== + compute pe/tally command ======================== @@ -27,7 +31,7 @@ Syntax compute ID group-ID style group2-ID * ID, group-ID are documented in :doc:`compute ` command -* style = *force/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally* +* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally* * group2-ID = group ID of second (or same) group Examples @@ -38,15 +42,19 @@ Examples compute 1 lower force/tally upper compute 1 left pe/tally right compute 1 lower stress/tally lower + compute 1 subregion heat/flux/tally all + compute 1 liquid heat/flux/virial/tally solid Description """"""""""" Define a computation that calculates properties between two groups of -atoms by accumulating them from pairwise non-bonded computations. The -two groups can be the same. This is similar to :doc:`compute group/group ` only that the data is +atoms by accumulating them from pairwise non-bonded computations. +Except for *heat/flux/virial/tally*, the two groups can be the same. +This is similar to :doc:`compute group/group ` +only that the data is accumulated directly during the non-bonded force computation. The -computes *force/tally*\ , *pe/tally*\ , *stress/tally*\ , and +computes *force/tally*, *pe/tally*, *stress/tally*, and *heat/flux/tally* are primarily provided as example how to program additional, more sophisticated computes using the tally callback mechanism. Compute *pe/mol/tally* is one such style, that can @@ -57,6 +65,76 @@ the based classes of LAMMPS. ---------- +Compute *heat/flux/tally* obtains the heat flux +(strictly speaking, heat flow) inside the first group, +which is the sum of the convective contribution +due to atoms in the first group and the virial contribution +due to interaction between the first and second groups: + +.. math:: + + \mathbf{Q}= \sum_{i \in \text{group 1}} e_i \mathbf{v}_i + \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{\substack{j \in \text{group 2} \\ j \neq i } } \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij} + +When the second group in *heat/flux/tally* is set to "all", +the resulting values will be identical +to that obtained by :doc:`compute heat/flux `, +provided only pairwise interactions exist. + +Compute *heat/flux/virial/tally* obtains the total virial heat flux +(strictly speaking, heat flow) into the first group due to interaction +with the second group, and is defined as: + +.. math:: + + Q = \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{j \in \text{group 2}} \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right) + +Although, the *heat/flux/virial/tally* compute +does not include the convective term, +it can be used to obtain the total heat flux over control surfaces, +when there are no particles crossing over, +such as is often in solid-solid and solid-liquid interfaces. +This would be identical to the method of planes method. +Note that the *heat/flux/virial/tally* compute is distinctly different +from the *heat/flux* and *heat/flux/tally* computes, +that are essentially volume averaging methods. +The following example demonstrates the difference: + +.. code-block:: LAMMPS + + # System with only pairwise interactions. + # Non-periodic boundaries in the x direction. + # Has LeftLiquid and RightWall groups along x direction. + + # Heat flux over the solid-liquid interface + compute hflow_hfvt RightWall heat/flux/virial/tally LeftLiquid + variable hflux_hfvt equal c_hflow_hfvt/(ly*lz) + + # x component of approximate heat flux vector inside the liquid region, + # two approaches. + # + compute myKE all ke/atom + compute myPE all pe/atom + compute myStress all stress/atom NULL virial + compute hflow_hf LeftLiquid heat/flux myKE myPE myStress + variable hflux_hf equal c_hflow_hf[1]/${volLiq} + # + compute hflow_hft LeftLiquid heat/flux/tally all + variable hflux_hft equal c_hflow_hft[1]/${volLiq} + + # Pressure over the solid-liquid interface, three approaches. + # + compute force_gg RightWall group/group LeftLiquid + variable press_gg equal c_force_gg[1]/(ly*lz) + # + compute force_ft RightWall force/tally LeftLiquid + compute rforce_ft RightWall reduce sum c_force_ft[1] + variable press_ft equal c_rforce_ft/(ly*lz) + # + compute rforce_hfvt all reduce sum c_hflow_hfvt[1] + variable press_hfvt equal c_rforce_hfvt/(ly*lz) + +---------- + The pairwise contributions are computing via a callback that the compute registers with the non-bonded pairwise force computation. This limits the use to systems that have no bonds, no Kspace, and no @@ -83,7 +161,17 @@ magnitude) and a per atom 3-element vector (force contribution from each atom). Compute *stress/tally* calculates a global scalar (average of the diagonal elements of the stress tensor) and a per atom vector (the 6 elements of stress tensor contributions from the -individual atom). +individual atom). As in :doc:`compute heat/flux `, +compute *heat/flux/tally* calculates a global vector of length 6, +where the first 3 components are the :math:`x`, :math:`y`, :math:`z` +components of the full heat flow vector, +and the next 3 components are the corresponding components +of just the convective portion of the flow, i.e. the +first term in the equation for :math:`\mathbf{Q}`. +Compute *heat/flux/virial/tally* calculates a global scalar (heat flow) +and a per atom 3-element vector +(contribution to the force acting over atoms in the first group +from individual atoms in both groups). Both the scalar and vector values calculated by this compute are "extensive". @@ -91,8 +179,8 @@ Both the scalar and vector values calculated by this compute are Restrictions """""""""""" -This compute is part of the USER-TALLY package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the TALLY package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index dc18145e72..d12cca7591 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -37,7 +37,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in the units of chemical species @@ -46,8 +46,8 @@ per unit mass. Restrictions """""""""""" -This compute is part of the USER-MESODPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the DPD-MESO package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index a82046367e..3163de2272 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -63,7 +63,7 @@ LAMMPS starts up, as if this command were in the input script: See the "thermo_style" command for more details. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -79,7 +79,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index ef04cad327..815a42f76c 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -99,7 +99,7 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -129,7 +129,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -142,7 +142,7 @@ Restrictions """""""""""" This compute is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute requires that atoms store angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index f334c1e11b..72d74d0c4a 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -79,7 +79,7 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -109,7 +109,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -122,7 +122,7 @@ Restrictions """""""""""" This compute is part of the BODY package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute requires that atoms store angular momentum and a quaternion as defined by the :doc:`atom_style body ` diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index f1c34b42fa..1bd5ecbb40 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -172,7 +172,7 @@ allows calculation of the global or per-chunk temperature using only the thermal temperature of atoms in each chunk after the translational kinetic energy components have been altered in a prescribed way, e.g. to remove a velocity profile. It also applies to the calculation -of the other per-chunk values, such as *kecom* or *internal*\ , which +of the other per-chunk values, such as *kecom* or *internal*, which involve the center-of-mass velocity of each chunk, which is calculated after the velocity bias is removed from each atom. Note that the temperature compute will apply its bias globally to the entire system, @@ -207,7 +207,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. This compute also optionally calculates a global array, if one or more diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index 07ae9ad648..d233029ea0 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -63,7 +63,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -73,7 +73,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 6b9f0a7e83..8a7fd0a3a5 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -30,7 +30,7 @@ Define a computation that calculates the temperature of a system based on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of :ref:`(Mitchell and Finchham) `. See -the :doc:`Howto coreshell ` doc page for an overview of +the :doc:`Howto coreshell ` page for an overview of the model as implemented in LAMMPS. Specifically, this compute enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of @@ -81,7 +81,7 @@ Thermostatting fixes that work in this way include :doc:`fix nvt `, :doc The internal energy of core/shell pairs can be calculated by the :doc:`compute temp/chunk ` command, if chunks are -defined as core/shell pairs. See the :doc:`Howto coreshell ` doc page doc page for more discussion +defined as core/shell pairs. See the :doc:`Howto coreshell ` page doc page for more discussion on how to do this. Output info diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index 026064000c..bc4d1ae3f3 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -104,7 +104,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -114,7 +114,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 03be4a89fd..b03aa00702 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -49,7 +49,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -61,8 +61,8 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 7e0f5f6555..c2a0479cae 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -20,7 +20,7 @@ Examples compute TDRUDE all temp/drude -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -60,7 +60,7 @@ are 6. kinetic energy of the dipoles (energy units) These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. Both the scalar value and the first two values of the vector diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index 6bbad345e2..ba139dd547 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -74,7 +74,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -89,8 +89,8 @@ the simulation. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index fc3bfc5c88..471f3bcfd4 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -63,7 +63,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -79,7 +79,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 0fa8ce5807..b70206781f 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -54,14 +54,14 @@ flow, e.g. via a profile-unbiased thermostat (PUT) as described in that computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. -The *xflag*\ , *yflag*\ , *zflag* settings determine which components of +The *xflag*, *yflag*, *zflag* settings determine which components of average velocity are subtracted out. -The *binstyle* setting and its *Nx*\ , *Ny*\ , *Nz* arguments determine +The *binstyle* setting and its *Nx*, *Ny*, *Nz* arguments determine how bins are setup to perform spatial averaging. "Bins" can be 1d slabs, 2d pencils, or 3d bricks depending on which *binstyle* is used. The simulation box is partitioned conceptually into *Nx* by *Ny* by -*Nz* bins. Depending on the *binstyle*\ , you may only specify one or +*Nz* bins. Depending on the *binstyle*, you may only specify one or two of these values; the others are effectively set to 1 (no binning in that dimension). For non-orthogonal (triclinic) simulation boxes, the bins are "tilted" slabs or pencils or bricks that are parallel to @@ -122,13 +122,13 @@ needed, the subtracted degrees-of-freedom can be altered using the .. note:: - When using the *out* keyword with a value of *bin*\ , the + When using the *out* keyword with a value of *bin*, the calculated temperature for each bin does not include the degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the *extra* option, which is applied to each bin. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a @@ -139,7 +139,7 @@ Output info This compute calculates a global scalar (the temperature). Depending on the setting of the *out* keyword, it also calculates a global -vector or array. For *out* = *tensor*\ , it calculates a vector of +vector or array. For *out* = *tensor*, it calculates a vector of length 6 (KE tensor), which can be accessed by indices 1-6. For *out* = *bin* it calculates a global array which has 2 columns and N rows, where N is the number of bins. The first column contains the number @@ -152,7 +152,7 @@ indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)\*10\*10 + (iy-1)\*10 indices are numbered from 1 to 10 in each dimension. These values can be used by any command that uses global scalar or -vector or array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector or array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 078ac66002..9cda8bef30 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -84,7 +84,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -94,7 +94,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 5bf80c8f09..86ae03be9b 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -77,7 +77,7 @@ If needed the number of subtracted degrees-of-freedom can be set explicitly using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -87,7 +87,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 622b3eb203..d6623ec02d 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -41,7 +41,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -53,8 +53,8 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index e489136d2b..a0e2cb14ac 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -62,7 +62,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -72,7 +72,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -84,8 +84,8 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index b39bad80c0..b752719741 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -86,7 +86,7 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -116,7 +116,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index 11bfca48e9..782b5b9acb 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -38,8 +38,8 @@ documentation for :doc:`compute temp `. Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the UEF package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. This command can only be used when :doc:`fix nvt/uef ` or :doc:`fix npt/uef ` is active. diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 4a2f9cca21..e377042dcf 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -42,7 +42,7 @@ Description """"""""""" Define a computation that calculates the derivative of the interaction -potential with respect to *lambda*\ , the coupling parameter used in a +potential with respect to *lambda*, the coupling parameter used in a thermodynamic integration. This derivative can be used to infer a free energy difference resulting from an alchemical simulation, as described in :ref:`Eike `. @@ -128,8 +128,8 @@ The scalar value will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index fd874998ab..190947b087 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -64,7 +64,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 862f65a482..d08217a590 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -108,7 +108,7 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -124,7 +124,7 @@ and the 7-th is the cosine-shaped velocity amplitude :math:`V`, which can be used to calculate the reciprocal viscosity, as shown in the example. These values can be used by any command that uses global scalar or vector values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The first 6 elements of vector values are "extensive", @@ -137,7 +137,7 @@ The 7-th element of vector value will be in velocity :doc:`units `. Restrictions """""""""""" -This command is only available when LAMMPS was built with the USER-MISC package. +This command is only available when LAMMPS was built with the MISC package. Since this compute depends on :doc:`fix accelerate/cos ` which can only work for 3d systems, it cannot be used for 2d systems. diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 8998115841..a84590ff02 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -134,7 +134,7 @@ Voronoi cell. The 3 columns are the atom ID of the atom that owns the cell, the atom ID of the atom in the neighboring cell (or zero if the face is external), and the area of the face. The array can be accessed by any command that uses local values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. More specifically, the array can be accessed by a :doc:`dump local ` command to write a file containing all the Voronoi neighbors in a system: @@ -196,7 +196,7 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the *occupation* keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. If the *peratom* keyword is set to "no", the per-atom array is still created, but it is not accessible. @@ -216,7 +216,7 @@ Voronoi cell. quantity. This effect can be eliminated by using the *peratom* keyword to turn off the production of the per-atom quantities. For the default value *yes* both quantities are produced. For the value - *no*\ , only the local array is produced. + *no*, only the local array is produced. The Voronoi cell volume will be in distance :doc:`units ` cubed. The Voronoi face area will be in distance :doc:`units ` squared. @@ -225,7 +225,7 @@ Restrictions """""""""""" This compute is part of the VORONOI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. It also requires you have a copy of the Voro++ library built and installed on your system. See instructions on obtaining and diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index d927b6599f..480bee6150 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -223,8 +223,8 @@ All array values calculated by this compute are "intensive". Restrictions """""""""""" -This compute is part of the USER-DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The compute_xrd command does not work for triclinic cells. diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 26da54573a..d10498baf2 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -80,7 +80,7 @@ with units = box or the *random* style. For the remainder of this doc page, a created atom or molecule is referred to as a "particle". If created particles are individual atoms, they are assigned the -specified atom *type*\ , though this can be altered via the *basis* +specified atom *type*, though this can be altered via the *basis* keyword as discussed below. If molecules are being created, the type of each atom in the created molecule is specified in the file read by the :doc:`molecule ` command, and those values are added to @@ -116,7 +116,7 @@ positions. For the *random* style, N particles are added to the system at randomly generated coordinates, which can be useful for generating an amorphous system. The particles are created one by one using the -specified random number *seed*\ , resulting in the same set of particles +specified random number *seed*, resulting in the same set of particles coordinates, independent of how many processors are being used in the simulation. If the *region-ID* argument is specified as NULL, then the created particles will be anywhere in the simulation box. If a @@ -159,7 +159,7 @@ used to remove overlapping atoms or molecules. However, you can first use the :doc:`change_box ` command to temporarily expand the box, then add atoms via create_atoms, then finally use change_box command again if needed to re-shrink-wrap the - new atoms. See the :doc:`change_box ` doc page for an + new atoms. See the :doc:`change_box ` page for an example of how to do this, using the create_atoms *single* style to insert a new atom outside the current simulation box. @@ -227,9 +227,9 @@ fashion. Which lattice sites are selected will change with the number of processors used. The *remap* keyword only applies to the *single* style. If it is set -to *yes*\ , then if the specified position is outside the simulation +to *yes*, then if the specified position is outside the simulation box, it will mapped back into the box, assuming the relevant -dimensions are periodic. If it is set to *no*\ , no remapping is done +dimensions are periodic. If it is set to *no*, no remapping is done and no particle is created if its position is outside the box. The *var* and *set* keywords can be used together to provide a @@ -288,7 +288,7 @@ determined by the rotation vector (Rx,Ry,Rz) that goes through the insertion point. The specified *theta* determines the angle of rotation around that axis. Note that the direction of rotation for the atoms around the rotation axis is consistent with the right-hand -rule: if your right-hand's thumb points along *R*\ , then your fingers +rule: if your right-hand's thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. The *units* keyword determines the meaning of the distance units used diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 056b60c7aa..664d870cb0 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -105,7 +105,7 @@ data file for a complex system of molecules. The *many* style will create bonds between pairs of atoms I,J where I is in one of the two specified groups, and J is in the other. The two groups can be the same, e.g. group "all". The created bonds will be -of bond type *btype*\ , where *btype* must be a value between 1 and the +of bond type *btype*, where *btype* must be a value between 1 and the number of bond types defined. For a bond to be created, an I,J pair of atoms must be a distance D @@ -156,7 +156,7 @@ two atoms with IDs *batom1* and *batom2*\ . *Btype* must be a value between 1 and the number of bond types defined. The *single/angle* style creates a single angle of type *atype* -between three atoms with IDs *aatom1*\ , *aatom2*\ , and *aatom3*\ . The +between three atoms with IDs *aatom1*, *aatom2*, and *aatom3*\ . The ordering of the atoms is the same as in the *Angles* section of a data file read by the :doc:`read_data ` command. I.e. the 3 atoms are ordered linearly within the angle; the central atom is *aatom2*\ . @@ -164,14 +164,14 @@ ordered linearly within the angle; the central atom is *aatom2*\ . defined. The *single/dihedral* style creates a single dihedral of type *dtype* -between four atoms with IDs *datom1*\ , *datom2*\ , *datom3*\ , and *datom4*\ . The +between four atoms with IDs *datom1*, *datom2*, *datom3*, and *datom4*\ . The ordering of the atoms is the same as in the *Dihedrals* section of a data file read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the dihedral. *dtype* must be a value between 1 and the number of dihedral types defined. The *single/improper* style creates a single improper of type *itype* -between four atoms with IDs *iatom1*\ , *iatom2*\ , *iatom3*\ , and *iatom4*\ . The +between four atoms with IDs *iatom1*, *iatom2*, *iatom3*, and *iatom4*\ . The ordering of the atoms is the same as in the *Impropers* section of a data file read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the improper. *itype* must be a value between 1 and diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 9b7b5a1a65..aa01be43cd 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -49,11 +49,11 @@ changed by the :doc:`balance ` or :doc:`fix balance ` comm The argument N is the number of atom types that will be used in the simulation. -If the region is not of style *prism*\ , then LAMMPS encloses the region +If the region is not of style *prism*, then LAMMPS encloses the region (block, sphere, etc) with an axis-aligned orthogonal bounding box which becomes the simulation domain. -If the region is of style *prism*\ , LAMMPS creates a non-orthogonal +If the region is of style *prism*, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. As defined by the :doc:`region prism ` command, the parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 @@ -76,7 +76,7 @@ factors that exceed these limits, you can use the :doc:`box tilt ` command, with a setting of *large*\ ; a setting of *small* is the default. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 127518535f..d47743071b 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -52,9 +52,9 @@ Delete the specified atoms. This command can be used to carve out voids from a block of material or to delete created atoms that are too close to each other (e.g. at a grain boundary). -For style *group*\ , all atoms belonging to the group are deleted. +For style *group*, all atoms belonging to the group are deleted. -For style *region*\ , all atoms in the region volume are deleted. +For style *region*, all atoms in the region volume are deleted. Additional atoms can be deleted if they are in a molecule for which one or more atoms were deleted within the region; see the *mol* keyword discussion below. @@ -83,7 +83,7 @@ randomly. There is no guarantee that the exact fraction of atoms will be deleted, or that the same atoms will be deleted when running on different numbers of processors. -If the *compress* keyword is set to *yes*\ , then after atoms are +If the *compress* keyword is set to *yes*, then after atoms are deleted, then atom IDs are re-assigned so that they run from 1 to the number of atoms in the system. Note that this is not done for molecular systems (see the :doc:`atom_style ` command), @@ -117,7 +117,7 @@ atoms. Note that simply deleting interactions due to dangling bonds (e.g. at a surface) may result in a inaccurate or invalid model for the remaining atoms. -It the *mol* keyword is set to *yes*\ , then for every atom that is +It the *mol* keyword is set to *yes*, then for every atom that is deleted, all other atoms in the same molecule (with the same molecule ID) will also be deleted. This is not done for atoms with molecule ID = 0, since such an ID is assumed to flag isolated atoms that are not diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index ffb06e55b2..5603214b2f 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -52,7 +52,7 @@ For all styles, by default, an interaction is only turned off (or on) if all the atoms involved are in the specified group. See the *any* keyword to change the behavior. -Several of the styles (\ *atom*\ , *bond*\ , *angle*\ , *dihedral*\ , +Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ ) take a *type* as an argument. The specified *type* should be an integer from 0 to N, where N is the number of relevant types (atom types, bond types, etc). A value of 0 is only relevant for @@ -73,11 +73,11 @@ Style *atom* is the same as style *multi* except that in addition, one or more of the atoms involved in the bond, angle, dihedral, or improper interaction must also be of the specified atom type. -For style *bond*\ , only bonds are candidates for turn-off, and the bond -must also be of the specified type. Styles *angle*\ , *dihedral*\ , and +For style *bond*, only bonds are candidates for turn-off, and the bond +must also be of the specified type. Styles *angle*, *dihedral*, and *improper* are treated similarly. -For style *bond*\ , you can set the type to 0 to delete bonds that have +For style *bond*, you can set the type to 0 to delete bonds that have been previously broken by a bond-breaking potential (which sets the bond type to 0 when a bond is broken); e.g. see the :doc:`bond_style quartic ` command. @@ -108,7 +108,7 @@ keyword is used). The *undo* keyword inverts the delete_bonds command so that the specified bonds, angles, etc are turned on if they are currently turned off. This means a negative value is toggled to positive. For -example, for style *angle*\ , if *type* is specified as 2, then all +example, for style *angle*, if *type* is specified as 2, then all angles with current type = -2, are reset to type = 2. Note that the :doc:`fix shake ` command also sets bond and angle types negative, so this option should not be used on those interactions. diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index 9588cf8272..cc792693a2 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -107,7 +107,7 @@ i.e. within the outer cutoff specified for the pair style. The :doc:`pair_style lj/charmmfsw/coul/long ` commands. Use the *charmm* style with the older :doc:`pair_style ` commands that have just "charmm" in their style name. See the -discussion on the :doc:`CHARMM pair_style ` doc page for +discussion on the :doc:`CHARMM pair_style ` page for details. Note that for AMBER force fields, which use pair styles with "lj/cut", diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 1f0195df83..0bd0a8fa2f 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index f55011c902..7889b3c58f 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -55,7 +55,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 89258cff35..cd5bed7cd2 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -59,7 +59,7 @@ Restrictions """""""""""" This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc page +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index c0a803755d..998a752275 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -57,8 +57,8 @@ If *class2* is one of the dihedral hybrid styles, the same rule holds for specifying additional AngleTorsion (and EndBondTorsion, etc) coefficients either via the input script or in the data file. I.e. *class2* must be added to each line after the dihedral type. For -lines in the AngleTorsion (or EndBondTorsion, etc) section of the data -file for dihedral types that are not *class2*\ , you must use an +lines in the AngleTorsion (or EndBondTorsion, etc) Coeffs section of the data +file for dihedral types that are not *class2*, you must use an dihedral style of *skip* as a placeholder, e.g. .. parsed-literal:: diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index 2411903126..06ae8be8a0 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -51,7 +51,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index dbe680fc82..a776c953c1 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -56,7 +56,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index be672a3699..9704bff1a8 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -89,7 +89,7 @@ Restrictions """""""""""" This dihedral style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 4301824b40..f037d95226 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -93,7 +93,7 @@ command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :ref:`Commands dihedral ` doc page are followed by one or +The individual style names on the :ref:`Commands dihedral ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off dihedral interactions @@ -124,7 +124,7 @@ Dihedral styles can only be set for atom styles that allow dihedrals to be defined. Most dihedral styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual dihedral potentials tell if it is part of a package. Related commands diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index a456fecebd..7c08241458 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -245,7 +245,7 @@ Restrictions """""""""""" These dihedral styles can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index be711815a6..d22d3f19fa 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -28,7 +28,7 @@ prior to setting up a simulation box via the :doc:`create_box ` or :doc:`read_data ` commands. Restart files also store this setting. -See the discussion on the :doc:`Howto 2d ` doc page for +See the discussion on the :doc:`Howto 2d ` page for additional instructions on how to run 2d simulations. .. note:: diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index efc6f9230b..9916126dad 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -93,7 +93,7 @@ The *rotate* style rotates each atom in the group by the angle *theta* around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your -right-hand thumb points along *R*\ , then your fingers wrap around the +right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of positive theta. If the defined :doc:`atom_style ` assigns an orientation to diff --git a/doc/src/dump.rst b/doc/src/dump.rst index a5f11a792a..1917d2db95 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -52,7 +52,7 @@ Syntax *cfg/gz* args = same as *custom* args, see below *cfg/zstd* args = same as *custom* args, see below *cfg/mpiio* args = same as *custom* args, see below - *custom*\ , *custom/gz*\ , *custom/zstd* , *custom/mpiio* args = see below + *custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below *custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios ` doc page *dcd* args = none *h5md* args = discussed on :doc:`dump h5md ` doc page @@ -185,12 +185,12 @@ or multiple smaller files). parallel, because data for a single snapshot is collected from multiple processors, each of which owns a subset of the atoms. -For the *atom*\ , *custom*\ , *cfg*\ , and *local* styles, sorting is off by -default. For the *dcd*\ , *xtc*\ , *xyz*\ , and *molfile* styles, sorting by +For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by +default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by atom ID is on by default. See the :doc:`dump_modify ` doc page for details. -The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , *local/gz*, and *xyz/gz* styles are identical +The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical in command syntax to the corresponding styles without "gz", however, they generate compressed files using the zlib library. Thus the filename suffix ".gz" is mandatory. This is an alternative approach to writing @@ -201,13 +201,13 @@ For the remainder of this doc page, you should thus consider the *atom* and *atom/gz* styles (etc) to be inter-changeable, with the exception of the required filename suffix. -Similarly, the *atom/zstd*\ , *cfg/zstd*\ , *custom/zstd*\ , *local/zstd*, +Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and *xyz/zstd* styles are identical to the gz styles, but use the Zstd compression library instead and require the ".zst" suffix. See the -:doc:`dump_modify ` doc page for details on how to control +:doc:`dump_modify ` page for details on how to control the compression level in both variants. -As explained below, the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and +As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles are identical in command syntax and in the format of the dump files they create, to the corresponding styles without "mpiio", except the single dump file they produce is written in @@ -227,13 +227,13 @@ file and in what format. Settings made via the :doc:`dump_modify ` command can also alter the format of individual values and the file itself. -The *atom*\ , *local*\ , and *custom* styles create files in a simple text +The *atom*, *local*, and *custom* styles create files in a simple text format that is self-explanatory when viewing a dump file. Some of the LAMMPS post-processing tools described on the :doc:`Tools ` doc -page, including `Pizza.py `_, +page, including `Pizza.py `_, work with this format, as does the :doc:`rerun ` command. -For post-processing purposes the *atom*\ , *local*\ , and *custom* text +For post-processing purposes the *atom*, *local*, and *custom* text files are self-describing in the following sense. The dimensions of the simulation box are included in each snapshot. @@ -272,7 +272,7 @@ This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic ` doc page for a geometric description +of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the triclinic parameters, and how to transform those parameters to and @@ -283,7 +283,7 @@ the per-atom lines that follow. For example, the descriptors would be "id type xs ys zs" for the default *atom* style, and would be the atom attributes you specify in the dump command for the *custom* style. -For style *atom*\ , atom coordinates are written to the file, along with +For style *atom*, atom coordinates are written to the file, along with the atom ID and atom type. By default, atom coords are written in a scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom is at a location 1/4 of the distance from xlo to xhi of the box @@ -295,13 +295,13 @@ Style *custom* allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. You cannot specify a quantity that is not defined for a particular simulation - -such as *q* for atom style *bond*\ , since that atom style does not +such as *q* for atom style *bond*, since that atom style does not assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the possible dump custom attributes is given below. -For style *local*\ , local output generated by :doc:`computes ` +For style *local*, local output generated by :doc:`computes ` and :doc:`fixes ` is used to generate lines of output that is written to the dump file. This local data is typically calculated by each processor based on the atoms it owns, but there may be zero or @@ -326,7 +326,7 @@ explicitly in the file). Any remaining attributes will be stored as want to use the :doc:`dump_modify element ` command with CFG-formatted files, to associate element names with atom types, so that AtomEye can render atoms appropriately. When unwrapped -coordinates *xsu*\ , *ysu*\ , and *zsu* are requested, the nominal AtomEye +coordinates *xsu*, *ysu*, and *zsu* are requested, the nominal AtomEye periodic cell dimensions are expanded by a large factor UNWRAPEXPAND = 10.0, which ensures atoms that are displayed correctly for up to UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond @@ -374,7 +374,7 @@ from using the (numerical) atom type to an element name (or some other label). This will help many visualization programs to guess bonds and colors. -Note that *atom*\ , *custom*\ , *dcd*\ , *xtc*\ , and *xyz* style dump files +Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files can be read directly by `VMD `_, a popular molecular viewing program. @@ -417,7 +417,7 @@ with the processor ID from 0 to P-1. For example, tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller files and can be a fast mode of output on parallel machines that support parallel I/O for output. This option is not available for the -*dcd*\ , *xtc*\ , and *xyz* styles. +*dcd*, *xtc*, and *xyz* styles. By default, P = the number of processors meaning one file per processor, but P can be set to a smaller value via the *nfile* or @@ -428,7 +428,7 @@ when running on large numbers of processors. Note that using the "\*" and "%" characters together can produce a large number of small dump files! -For the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and *xyz/mpiio* +For the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles, a single dump file is written in parallel via the MPI-IO library, which is part of the MPI standard for versions 2.0 and above. Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO @@ -474,7 +474,7 @@ styles. ---------- Note that in the discussion which follows, for styles which can -reference values from a compute or fix, like the *custom*\ , *cfg*\ , or +reference values from a compute or fix, like the *custom*, *cfg*, or *local* styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the @@ -557,8 +557,8 @@ the distance and energy of each bond: This section explains the atom attributes that can be specified as part of the *custom* and *cfg* styles. -The *id*\ , *mol*\ , *proc*\ , *procp1*\ , *type*\ , *element*\ , *mass*\ , *vx*\ , -*vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , *q* attributes are self-explanatory. +The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*, +*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory. *Id* is the atom ID. *Mol* is the molecule ID, included in the data file for molecular systems. *Proc* is the ID of the processor (0 to @@ -568,31 +568,31 @@ for coloring atoms in a visualization program. *Type* is the atom type (1 to Ntypes). *Element* is typically the chemical name of an element, which you must assign to each type via the :doc:`dump_modify element ` command. More generally, it can be any string you wish to associated with an atom type. *Mass* is the atom -mass. *Vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , and *q* are components of +mass. *Vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components of atom velocity and force and atomic charge. -There are several options for outputting atom coordinates. The *x*\ , -*y*\ , *z* attributes write atom coordinates "unscaled", in the +There are several options for outputting atom coordinates. The *x*, +*y*, *z* attributes write atom coordinates "unscaled", in the appropriate distance :doc:`units ` (Angstroms, sigma, etc). Use -*xs*\ , *ys*\ , *zs* if you want the coordinates "scaled" to the box size, +*xs*, *ys*, *zs* if you want the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are the non-orthogonal vectors of the simulation box edges, as discussed on the :doc:`Howto triclinic ` doc page. -Use *xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the +Use *xu*, *yu*, *zu* if you want the coordinates "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped -back into the periodic box. Note that using *xu*\ , *yu*\ , *zu* means +back into the periodic box. Note that using *xu*, *yu*, *zu* means that the coordinate values may be far outside the box bounds printed -with the snapshot. Using *xsu*\ , *ysu*\ , *zsu* is similar to using -*xu*\ , *yu*\ , *zu*\ , except that the unwrapped coordinates are scaled by +with the snapshot. Using *xsu*, *ysu*, *zsu* is similar to using +*xu*, *yu*, *zu*, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will have the corresponding coordinate increased or decreased by 1.0. -The image flags can be printed directly using the *ix*\ , *iy*\ , *iz* +The image flags can be printed directly using the *ix*, *iy*, *iz* attributes. For periodic dimensions, they specify which image of the simulation box the atom is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths @@ -600,7 +600,7 @@ to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as atoms cross periodic boundaries during the simulation. -The *mux*\ , *muy*\ , *muz* attributes are specific to dipolar systems +The *mux*, *muy*, *muz* attributes are specific to dipolar systems defined with an atom style of *dipole*\ . They give the orientation of the atom's point dipole moment. The *mu* attribute gives the magnitude of the atom's dipole moment. @@ -609,15 +609,15 @@ The *radius* and *diameter* attributes are specific to spherical particles that have a finite size, such as those defined with an atom style of *sphere*\ . -The *omegax*\ , *omegay*\ , and *omegaz* attributes are specific to +The *omegax*, *omegay*, and *omegaz* attributes are specific to finite-size spherical particles that have an angular velocity. Only certain atom styles, such as *sphere* define this quantity. -The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are specific to +The *angmomx*, *angmomy*, and *angmomz* attributes are specific to finite-size aspherical particles that have an angular momentum. Only the *ellipsoid* atom style defines this quantity. -The *tqx*\ , *tqy*\ , *tqz* attributes are for finite-size particles that +The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles. @@ -673,7 +673,7 @@ The *d_name* and *i_name* attributes allow to output custom per atom floating point or integer properties that are managed by :doc:`fix property/atom `. -See the :doc:`Modify ` doc page for information on how to add +See the :doc:`Modify ` page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. @@ -684,20 +684,20 @@ Restrictions To write gzipped dump files, you must either compile LAMMPS with the -DLAMMPS_GZIP option or use the styles from the COMPRESS package. -See the :doc:`Build settings ` doc page for details. +See the :doc:`Build settings ` page for details. -The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are part of +The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of the COMPRESS package. They are only enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +that package. See the :doc:`Build package ` page for more info. -The *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and *xyz/mpiio* styles +The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles are part of the MPIIO package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The *xtc* style is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index e1b0fe000a..71ab6a07d9 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -64,9 +64,9 @@ When using the ADIOS tool 'bpls' to list the content of a .bp file, bpls will print *__* for the size of the output table indicating that its size is changing every step. -The *atom/adios* and *custom/adios* dump styles are part of the USER-ADIOS +The *atom/adios* and *custom/adios* dump styles are part of the ADIOS package. They are only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. ---------- diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index ee027e9347..7e95d8f30d 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -42,8 +42,8 @@ reference frame as the atomic positions. Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the UEF package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. This command can only be used when :doc:`fix nvt/uef ` or :doc:`fix npt/uef ` is active. diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index de44572307..202d5fb89d 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -32,7 +32,7 @@ Syntax Note that at least one element must be specified and image may only be present if position is specified first. -For the elements *position*\ , *velocity*\ , *force* and *species*\ , a +For the elements *position*, *velocity*, *force* and *species*, a sub-interval may be specified to write the data only every N_element iterations of the dump (i.e. every N\*N_element time steps). This is specified by this option directly following the element declaration: @@ -66,7 +66,7 @@ another particle group must specify *create_group yes*. .. _h5md: http://nongnu.org/h5md/ -Each data element is written every N\*N_element steps. For *image*\ , no +Each data element is written every N\*N_element steps. For *image*, no sub-interval is needed as it must be present at the same interval as *position*\ . *image* must be given after *position* in any case. The box information (edges in each dimension) is stored at the same @@ -106,9 +106,9 @@ The position data is stored wrapped (box boundaries not enforced, see note above). Only orthogonal domains are currently supported. This is a limitation of the present dump h5md command and not of H5MD itself. -The *h5md* dump style is part of the USER-H5MD package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. It also requires -(i) building the ch5md library provided with LAMMPS (See the :doc:`Build package ` doc page for more info.) and (ii) having +The *h5md* dump style is part of the H5MD package. It is only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. It also requires +(i) building the ch5md library provided with LAMMPS (See the :doc:`Build package ` page for more info.) and (ii) having the `HDF5 `_ library installed (C bindings are sufficient) on your system. The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 3923d5c2dc..be14a237e5 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -153,7 +153,7 @@ framerate can be set using the :doc:`dump_modify ` command. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG -flag. See the :doc:`Build settings ` doc page for +flag. See the :doc:`Build settings ` page for details. .. note:: @@ -261,7 +261,7 @@ The *atom* keyword allow you to turn off the drawing of all atoms, if the specified value is *no*\ . Note that this will not turn off the drawing of particles that are represented as lines, triangles, or bodies, as discussed below. These particles can be drawn separately -if the *line*\ , *tri*\ , or *body* keywords are used. +if the *line*, *tri*, or *body* keywords are used. The *adiam* keyword allows you to override the *diameter* setting to set a single numeric *size*\ . All atoms will be drawn with that @@ -318,7 +318,7 @@ The *line* keyword can be used when :doc:`atom_style line ` is used to define particles as line segments, and will draw them as lines. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. The only setting -currently allowed for the *color* value is *type*\ , which will color +currently allowed for the *color* value is *type*, which will color the lines according to the atom type of the particle. By default the mapping of types to colors is as follows: @@ -345,7 +345,7 @@ or edges (3 lines) or both, depending on the setting for *tflag*\ . If edges are drawn, the *width* setting determines the diameters of the line segments. If this keyword is not used, triangle particles will be drawn as spheres, the same as if they were regular atoms. The only -setting currently allowed for the *color* value is *type*\ , which will +setting currently allowed for the *color* value is *type*, which will color the triangles according to the atom type of the particle. By default the mapping of types to colors is as follows: @@ -367,7 +367,7 @@ is used to define body particles with internal state body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The :doc:`Howto body ` doc page describes the body styles +The :doc:`Howto body ` page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent and how they are drawn by this dump image command. For all the body styles, individual atoms can be @@ -375,10 +375,10 @@ either a body particle or a usual point (non-body) particle. Non-body particles will be drawn the same way they would be as a regular atom. The *bflag1* and *bflag2* settings are numerical values which are passed to the body style to affect how the drawing of a body particle -is done. See the :doc:`Howto body ` doc page for a +is done. See the :doc:`Howto body ` page for a description of what these parameters mean for each body style. -The only setting currently allowed for the *color* value is *type*\ , +The only setting currently allowed for the *color* value is *type*, which will color the body particles according to the atom type of the particle. By default the mapping of types to colors is as follows: @@ -399,10 +399,10 @@ objects to be drawn. The *fflag1* and *fflag2* settings are numerical values which are passed to the fix to affect how the drawing of its objects is done. -See the individual fix doc page for a description of what these +See the individual fix page for a description of what these parameters mean for a particular fix. -The only setting currently allowed for the *color* value is *type*\ , +The only setting currently allowed for the *color* value is *type*, which will color the fix objects according to their type. By default the mapping of types to colors is as follows: @@ -423,11 +423,11 @@ i.e. the number of pixels in each direction. ---------- -The *view*\ , *center*\ , *up*\ , and *zoom* values determine how +The *view*, *center*, *up*, and *zoom* values determine how 3d simulation space is mapped to the 2d plane of the image. Basically they control how the simulation box appears in the image. -All of the *view*\ , *center*\ , *up*\ , and *zoom* values can be +All of the *view*, *center*, *up*, and *zoom* values can be specified as numeric quantities, whose meaning is explained below. Any of them can also be specified as an :doc:`equal-style variable `, by using v_name as the value, where "name" is @@ -447,13 +447,13 @@ specified via variables, then the variable values should be in degrees. The *center* keyword determines the point in simulation space that -will be at the center of the image. *Cx*\ , *Cy*\ , and *Cz* are +will be at the center of the image. *Cx*, *Cy*, and *Cz* are specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is the center of the simulation box. These values do not have to be between 0.0 and 1.0, if you want the simulation box to be offset from the center of the image. Note, however, that if you choose strange -values for *Cx*\ , *Cy*\ , or *Cz* you may get a blank image. Internally, -*Cx*\ , *Cy*\ , and *Cz* are converted into a point in simulation space. +values for *Cx*, *Cy*, or *Cz* you may get a blank image. Internally, +*Cx*, *Cy*, and *Cz* are converted into a point in simulation space. If *flag* is set to "s" for static, then this conversion is done once, at the time the dump command is issued. If *flag* is set to "d" for dynamic then the conversion is performed every time a new image is @@ -590,8 +590,8 @@ Play the movie: % mplayer foo.mpg % ffplay bar.avi -* c) Use the `Pizza.py `_ - `animate tool `_, +* c) Use the `Pizza.py `_ + `animate tool `_, which works directly on a series of image files. .. code-block:: python @@ -607,7 +607,7 @@ Play the movie: ---------- -See the :doc:`Modify ` doc page for information on how to add +See the :doc:`Modify ` page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. @@ -626,7 +626,7 @@ building LAMMPS and have the FFmpeg executable available on the machine where LAMMPS is being run. Typically it's name is lowercase, i.e. ffmpeg. -See the :doc:`Build settings ` doc page for details. +See the :doc:`Build settings ` page for details. Note that since FFmpeg is run as an external program via a pipe, LAMMPS has limited control over its execution and no knowledge about diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 07f00c4030..5fea976e70 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -66,7 +66,7 @@ Syntax *unwrap* arg = *yes* or *no* * these keywords apply only to the *image* and *movie* :doc:`styles ` -* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* +* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header* .. parsed-literal:: @@ -113,6 +113,9 @@ Syntax rate = target bitrate for movie in kbps *framerate* arg = fps fps = frames per second for movie + *header* arg = *yes* or *no* + *yes* to write the header + *no* to not write the header * these keywords apply only to the */gz* and */zstd* dump styles * keyword = *compression_level* @@ -149,8 +152,8 @@ Description Modify the parameters of a previously defined dump command. Not all parameters are relevant to all dump styles. -As explained on the :doc:`dump ` doc page, the *atom/mpiio*\ , -*custom/mpiio*\ , and *xyz/mpiio* dump styles are identical in command +As explained on the :doc:`dump ` doc page, the *atom/mpiio*, +*custom/mpiio*, and *xyz/mpiio* dump styles are identical in command syntax and in the format of the dump files they create, to the corresponding styles without "mpiio", except the single dump file they produce is written in parallel via the MPI-IO library. Thus if a @@ -167,9 +170,9 @@ description gives details. The *append* keyword applies to all dump styles except *cfg* and *xtc* and *dcd*\ . It also applies only to text output files, not to binary -or gzipped or image/movie files. If specified as *yes*\ , then dump +or gzipped or image/movie files. If specified as *yes*, then dump snapshots are appended to the end of an existing dump file. If -specified as *no*\ , then a new dump file will be created which will +specified as *no*, then a new dump file will be created which will overwrite an existing file with the same name. ---------- @@ -177,7 +180,7 @@ overwrite an existing file with the same name. The *at* keyword only applies to the *netcdf* dump style. It can only be used if the *append yes* keyword is also used. The *N* argument is the index of which frame to append to. A negative value can be -specified for *N*\ , which means a frame counted from the end of the +specified for *N*, which means a frame counted from the end of the file. The *at* keyword can only be used if the dump_modify command is before the first command that causes dump snapshots to be output, e.g. a :doc:`run ` or :doc:`minimize ` command. Once the @@ -185,13 +188,13 @@ dump file has been opened, this keyword has no further effect. ---------- -The *buffer* keyword applies only to dump styles *atom*\ , *cfg*\ , -*custom*\ , *local*\ , and *xyz*\ . It also applies only to text output -files, not to binary or gzipped files. If specified as *yes*\ , which +The *buffer* keyword applies only to dump styles *atom*, *cfg*, +*custom*, *local*, and *xyz*\ . It also applies only to text output +files, not to binary or gzipped files. If specified as *yes*, which is the default, then each processor writes its output into an internal text buffer, which is then sent to the processor(s) which perform file writes, and written by those processors(s) as one large chunk of text. -If specified as *no*\ , each processor sends its per-atom data in binary +If specified as *no*, each processor sends its per-atom data in binary format to the processor(s) which perform file wirtes, and those processor(s) format and write it line by line into the output file. @@ -210,16 +213,16 @@ during an equilibration phase. ---------- -The *element* keyword applies only to the dump *cfg*\ , *xyz*\ , and +The *element* keyword applies only to the dump *cfg*, *xyz*, and *image* styles. It associates element names (e.g. H, C, Fe) with LAMMPS atom types. See the list of element names at the bottom of this page. -In the case of dump *cfg*\ , this allows the `AtomEye `_ +In the case of dump *cfg*, this allows the `AtomEye `_ visualization package to read the dump file and render atoms with the appropriate size and color. -In the case of dump *image*\ , the output images will follow the same +In the case of dump *image*, the output images will follow the same `AtomEye `_ convention. An element name is specified for each atom type (1 to Ntype) in the simulation. The same element name can be given to multiple atom types. @@ -295,7 +298,7 @@ the very first timestep after the dump command is invoked. This will always occur if the current timestep is a multiple of N, the frequency specified in the :doc:`dump ` command, including timestep 0. But if this is not the case, a dump snapshot will only be written if the -setting of this keyword is *yes*\ . If it is *no*\ , which is the +setting of this keyword is *yes*\ . If it is *no*, which is the default, then it will not be written. ---------- @@ -309,7 +312,7 @@ performed with dump style *xtc*\ . ---------- The *format* keyword can be used to change the default numeric format output -by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and +by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and *xyz* styles, and their MPIIO variants. Only the *line* or *none* options can be used with the *atom* and *xyz* styles. @@ -378,7 +381,7 @@ The *fileper* keyword is documented below with the *nfile* keyword. ---------- The *image* keyword applies only to the dump *atom* style. If the -image value is *yes*\ , 3 flags are appended to each atom's coords which +image value is *yes*, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means the atom is in the center of the box, but has passed through the box @@ -420,7 +423,7 @@ files produced, even if you run for 1000s of steps. The *nfile* or *fileper* keywords can be used in conjunction with the "%" wildcard character in the specified dump file name, for all dump -styles except the *dcd*\ , *image*\ , *movie*\ , *xtc*\ , and *xyz* styles +styles except the *dcd*, *image*, *movie*, *xtc*, and *xyz* styles (for which "%" is not allowed). As explained on the :doc:`dump ` command doc page, the "%" character causes the dump file to be written in pieces, one piece for each of P processors. By default P = the @@ -458,7 +461,7 @@ slightly outside the simulation box. This is because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, which will not typically coincide with the timesteps dump snapshots are written. If the setting of this keyword is set to -*yes*\ , then all atoms will be remapped to the periodic box before the +*yes*, then all atoms will be remapped to the periodic box before the snapshot is written, then restored to their original position. If it is set to *no* they will not be. The *no* setting is the default because it requires no extra computation. @@ -472,8 +475,8 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to ---------- -The *refresh* keyword only applies to the dump *custom*\ , *cfg*\ , -*image*\ , and *movie* styles. It allows an "incremental" dump file to +The *refresh* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. It allows an "incremental" dump file to be written, by refreshing a compute that is used as a threshold for determining which atoms are included in a dump snapshot. The specified *c_ID* gives the ID of the compute. It is prefixed by "c\_" @@ -541,8 +544,8 @@ simply do nothing. ---------- -The *region* keyword only applies to the dump *custom*\ , *cfg*\ , -*image*\ , and *movie* styles. If specified, only atoms in the region +The *region* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only one region can be applied as a filter (the last one specified). See the :doc:`region ` command for more details. Note that a region @@ -587,7 +590,7 @@ order. The dump *local* style cannot be sorted by atom ID, since there are typically multiple lines of output per atom. Some dump styles, such -as *dcd* and *xtc*\ , require sorting by atom ID to format the output +as *dcd* and *xtc*, require sorting by atom ID to format the output file correctly. If multiple processors are writing the dump file, via the "%" wildcard in the dump filename, then sorting cannot be performed. @@ -607,8 +610,8 @@ identical to the values specified by :doc:`thermo_style `. ---------- -The *thresh* keyword only applies to the dump *custom*\ , *cfg*\ , -*image*\ , and *movie* styles. Multiple thresholds can be specified. +The *thresh* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. Multiple thresholds can be specified. Specifying *none* turns off all threshold criteria. If thresholds are specified, only atoms whose attributes meet all the threshold criteria are written to the dump file or included in the image. The possible @@ -623,7 +626,7 @@ produce continuous numeric values or effective Boolean 0/1 values which may be useful for the comparison operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). -See the :doc:`variable ` command doc page for details. +See the :doc:`variable ` command page for details. The specified value must be a simple numeric value or the word LAST. If LAST is used, it refers to the value of the attribute the last time @@ -667,9 +670,9 @@ threshold criterion is met. Otherwise it is not met. ---------- -The *time* keyword only applies to the dump *atom*\ , *custom*\ , and -*local* styles (and their COMPRESS package versions *atom/gz*\ , -*custom/gz* and *local/gz*\ ). If set to *yes*\ , each frame will will +The *time* keyword only applies to the dump *atom*, *custom*, and +*local* styles (and their COMPRESS package versions *atom/gz*, +*custom/gz* and *local/gz*\ ). If set to *yes*, each frame will will contain two extra lines before the "ITEM: TIMESTEP" entry: .. parsed-literal:: @@ -685,9 +688,9 @@ The default setting is *no*\ . ---------- -The *units* keyword only applies to the dump *atom*\ , *custom*\ , and -*local* styles (and their COMPRESS package versions *atom/gz*\ , -*custom/gz* and *local/gz*\ ). If set to *yes*\ , each individual dump +The *units* keyword only applies to the dump *atom*, *custom*, and +*local* styles (and their COMPRESS package versions *atom/gz*, +*custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump file will contain two extra lines at the very beginning with: .. parsed-literal:: @@ -703,7 +706,7 @@ The default setting is *no*\ . ---------- The *unwrap* keyword only applies to the dump *dcd* and *xtc* styles. -If set to *yes*\ , coordinates will be written "unwrapped" by the image +If set to *yes*, coordinates will be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the @@ -720,7 +723,7 @@ images. Some of the keywords only affect the :doc:`dump movie ` sty ---------- The *acolor* keyword can be used with the :doc:`dump image ` -command, when its atom color setting is *type*\ , to set the color that +command, when its atom color setting is *type*, to set the color that atoms of each type will be drawn in the image. The specified *type* should be an integer from 1 to Ntypes = the @@ -744,7 +747,7 @@ of the specified atom types. ---------- The *adiam* keyword can be used with the :doc:`dump image ` -command, when its atom diameter setting is *type*\ , to set the size +command, when its atom diameter setting is *type*, to set the size that atoms of each type will be drawn in the image. The specified *type* should be an integer from 1 to Ntypes. As with the *acolor* keyword, a wildcard asterisk can be used as part of the *type* @@ -773,7 +776,7 @@ There are many possible options for the color map, enabled by the *amap* keyword. Here are the details. The *lo* and *hi* settings determine the range of values allowed for -the atom attribute. If numeric values are used for *lo* and/or *hi*\ , +the atom attribute. If numeric values are used for *lo* and/or *hi*, then values that are lower/higher than that value are set to the value. I.e. the range is static. If *lo* is specified as *min* or *hi* as *max* then the range is dynamic, and the lower and/or @@ -844,7 +847,7 @@ for the color map. Here is how the entries are used to determine the color of an individual atom, given the value X of its atom attribute. The entries are scanned from first to last. The first time that *lo* <= X <= -*hi*\ , X is assigned the color associated with that entry. You can +*hi*, X is assigned the color associated with that entry. You can think of the last entry as assigning a default color (since it will always be matched by X), and the earlier entries as colors that override the default. Also note that no interpolation of a color RGB @@ -891,7 +894,7 @@ name defined by the dump_modify color option. ---------- The *bcolor* keyword can be used with the :doc:`dump image ` -command, with its *bond* keyword, when its color setting is *type*\ , to +command, with its *bond* keyword, when its color setting is *type*, to set the color that bonds of each type will be drawn in the image. The specified *type* should be an integer from 1 to Nbondtypes = the @@ -915,7 +918,7 @@ of the specified bond types. ---------- The *bdiam* keyword can be used with the :doc:`dump image ` -command, with its *bond* keyword, when its diam setting is *type*\ , to +command, with its *bond* keyword, when its diam setting is *type*, to set the diameter that bonds of each type will be drawn in the image. The specified *type* should be an integer from 1 to Nbondtypes. As with the *bcolor* keyword, a wildcard asterisk can be used as part of @@ -977,6 +980,13 @@ images less frequently. ---------- +The *header* keyword toggles whether the dump file will include a header. +Excluding a header will reduce the size of the dump file for fixes such as +:doc:`fix pair/tracker ` which do not require the information +typically written to the header. + +---------- + The COMPRESS package offers both GZ and Zstd compression variants of styles atom, custom, local, cfg, and xyz. When using these styles the compression level can be controlled by the :code:`compression_level` parameter. File names @@ -1014,7 +1024,7 @@ Default The option defaults are * append = no -* buffer = yes for dump styles *atom*\ , *custom*\ , *loca*\ , and *xyz* +* buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz* * element = "C" for every atom type * every = whatever it was set to via the :doc:`dump ` command * fileper = # of processors @@ -1030,8 +1040,8 @@ The option defaults are * precision = 1000 * region = none * scale = yes -* sort = off for dump styles *atom*\ , *custom*\ , *cfg*\ , and *local* -* sort = id for dump styles *dcd*\ , *xtc*\ , and *xyz* +* sort = off for dump styles *atom*, *custom*, *cfg*, and *local* +* sort = id for dump styles *dcd*, *xtc*, and *xyz* * thresh = none * units = no * unwrap = no diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index 69bd8aa8c2..c1f0b48fe6 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -92,12 +92,12 @@ determine the sequence of timesteps on which dump files are written. Restrictions """""""""""" -The *molfile* dump style is part of the USER-MOLFILE package. It is -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +The *molfile* dump style is part of the MOLFILE package. It is +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Molfile plugins provide a consistent programming interface to read and write file formats commonly used in molecular simulations. The -USER-MOLFILE package only provides the interface code, not the plugins. +MOLFILE package only provides the interface code, not the plugins. These can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index 5627060452..d53a0a3b12 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -69,10 +69,13 @@ Restrictions """""""""""" The *netcdf* and *netcdf/mpiio* dump styles are part of the -USER-NETCDF package. They are only enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +NETCDF package. They are only enabled if LAMMPS was built with +that package. See the :doc:`Build package ` page for more info. +The *netcdf* and *netcdf/mpiio* dump styles currently cannot dump +string properties or properties from variables. + ---------- Related commands diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 4f607c4fdd..8eec479292 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -70,7 +70,7 @@ determine the kind of output. of which owns a subset of the atoms. For the *vtk* style, sorting is off by default. See the -:doc:`dump_modify ` doc page for details. +:doc:`dump_modify ` page for details. ---------- @@ -88,7 +88,7 @@ hexahedrons in either legacy .vtk or .vtu XML format. Style *vtk* allows you to specify a list of atom attributes to be written to the dump file for each atom. The list of possible attributes is the same as for the :doc:`dump_style custom ` command; see -its doc page for a listing and an explanation of each attribute. +its page for a listing and an explanation of each attribute. .. note:: @@ -162,8 +162,8 @@ Restrictions The *vtk* style does not support writing of gzipped dump files. -The *vtk* dump style is part of the USER-VTK package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +The *vtk* dump style is part of the VTK package. It is only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. To use this dump style, you also must link to the VTK library. See the info in lib/vtk/README and insure the Makefile.lammps file in that diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index 9c4530eade..37b9e5b4a5 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -63,9 +63,9 @@ The command collects an array of nine times the number of atoms in a group on every single MPI rank, so the memory requirements can be very significant for large systems. -This command is part of the USER-PHONON package. It is only enabled if +This command is part of the PHONON package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix.rst b/doc/src/fix.rst index b4ac1e5e45..81c0c87320 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -34,7 +34,7 @@ positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary conditions, computing diagnostics, etc. There are hundreds of fixes defined in LAMMPS and new ones can be added; see the -:doc:`Modify ` doc page for details. +:doc:`Modify ` page for details. Fixes perform their operations at different stages of the timestep. If 2 or more fixes operate at the same stage of the timestep, they are @@ -65,7 +65,7 @@ was. Note that this operation also wipes out any additional changes made to the old fix via the :doc:`fix_modify ` command. The :doc:`fix modify ` command allows settings for some -fixes to be reset. See the doc page for individual fixes for details. +fixes to be reset. See the page for individual fixes for details. Some fixes store an internal "state" which is written to binary restart files via the :doc:`restart ` or @@ -90,7 +90,7 @@ more per atoms. Note that a single fix can produce either global or per-atom or local quantities (or none at all), but not both global and per-atom. It can produce local quantities in tandem with global or per-atom quantities. -The fix doc page will explain. +The fix page will explain. Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The @@ -136,7 +136,7 @@ In LAMMPS, the values generated by a fix can be used in several ways: command. Or the per-atom values can be referenced in an :doc:`atom-style variable `. * Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command. -See the :doc:`Howto output ` doc page for a summary of +See the :doc:`Howto output ` page for a summary of various LAMMPS output options, many of which involve fixes. The results of fixes that calculate global quantities can be either @@ -149,12 +149,12 @@ values by the number of atoms in the system, depending on the "thermo_modify norm" setting. It will not normalize intensive values. If a fix value is accessed in another way, e.g. by a :doc:`variable `, you may want to know whether it is an -intensive or extensive value. See the doc page for individual fixes +intensive or extensive value. See the page for individual fixes for further info. ---------- -Each fix style has its own doc page which describes its arguments and +Each fix style has its own page which describes its arguments and what it does, as listed below. Here is an alphabetic list of fix styles available in LAMMPS. They are also listed in more compact form on the :doc:`Commands fix ` doc page. @@ -300,6 +300,7 @@ accelerated styles exist. * :doc:`orient/fcc ` - add grain boundary migration force for FCC * :doc:`orient/eco ` - add generalized grain boundary migration force * :doc:`pafi ` - constrained force averages on hyper-planes to compute free energies (PAFI) +* :doc:`pair/tracker ` - track properties of pairwise interactions * :doc:`phonon ` - calculate dynamical matrix from MD simulations * :doc:`pimd ` - Feynman path integral molecular dynamics * :doc:`planeforce ` - constrain atoms to move in a plane @@ -321,14 +322,14 @@ accelerated styles exist. * :doc:`qeq/dynamic ` - charge equilibration via dynamic method * :doc:`qeq/fire ` - charge equilibration via FIRE minimizer * :doc:`qeq/point ` - charge equilibration via point method -* :doc:`qeq/reax ` - charge equilibration for ReaxFF potential +* :doc:`qeq/reaxff ` - charge equilibration for ReaxFF potential * :doc:`qeq/shielded ` - charge equilibration via shielded method * :doc:`qeq/slater ` - charge equilibration via Slater method * :doc:`qmmm ` - functionality to enable a quantum mechanics/molecular mechanics coupling * :doc:`qtb ` - implement quantum thermal bath scheme * :doc:`rattle ` - RATTLE constraints on bonds and/or angles -* :doc:`reax/c/bonds ` - write out ReaxFF bond information -* :doc:`reax/c/species ` - write out ReaxFF molecule information +* :doc:`reaxff/bonds ` - write out ReaxFF bond information +* :doc:`reaxff/species ` - write out ReaxFF molecule information * :doc:`recenter ` - constrain the center-of-mass position of a group of atoms * :doc:`restrain ` - constrain a bond, angle, dihedral * :doc:`rhok ` - add bias potential for long-range ordered systems @@ -406,7 +407,7 @@ Restrictions """""""""""" Some fix styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual fixes tell if it is part of a package. Related commands diff --git a/doc/src/fix_accelerate_cos.rst b/doc/src/fix_accelerate_cos.rst index 7fad6be913..46e08e68b4 100644 --- a/doc/src/fix_accelerate_cos.rst +++ b/doc/src/fix_accelerate_cos.rst @@ -86,7 +86,7 @@ This fix is not invoked during energy minimization. Restrictions """""""""""" -This command is only available when LAMMPS was built with the USER-MISC package. +This command is only available when LAMMPS was built with the MISC package. Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations. Related commands diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index aa34516d52..b7151334db 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -85,19 +85,19 @@ variable that is time-dependent. Depending on the value of the *reset* keyword, attributes changed by this fix will or will not be reset back to their original values at -the end of a simulation. Even if *reset* is specified as *yes*\ , a +the end of a simulation. Even if *reset* is specified as *yes*, a restart file written during a simulation will contain the modified settings. -If the *scale* keyword is set to *no*\ , which is the default, then +If the *scale* keyword is set to *no*, which is the default, then the value of the altered parameter will be whatever the variable -generates. If the *scale* keyword is set to *yes*\ , then the value +generates. If the *scale* keyword is set to *yes*, then the value of the altered parameter will be the initial value of that parameter multiplied by whatever the variable generates. I.e. the variable is now a "scale factor" applied in (presumably) a time-varying fashion to the parameter. -Note that whether scale is *no* or *yes*\ , internally, the parameters +Note that whether scale is *no* or *yes*, internally, the parameters themselves are actually altered by this fix. Make sure you use the *reset yes* option if you want the parameters to be restored to their initial values after the run. @@ -186,7 +186,9 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | E0,R0,m,n,coulombic_cutoff | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`reax/c ` | chi, eta, gamma | type global | +| :doc:`reaxff ` | chi, eta, gamma | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`snap ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`spin/dmi ` | coulombic_cutoff | type global | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 81a34ab75e..affb893117 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -57,7 +57,7 @@ Examples fix 1 all adapt/fep 10 atom diameter 1 v_size -Example input scripts available: examples/USER/fep +Example input scripts available: examples/PACKAGES/fep Description """"""""""" @@ -84,13 +84,13 @@ variable that is time-dependent. Depending on the value of the *reset* keyword, attributes changed by this fix will or will not be reset back to their original values at -the end of a simulation. Even if *reset* is specified as *yes*\ , a +the end of a simulation. Even if *reset* is specified as *yes*, a restart file written during a simulation will contain the modified settings. -If the *scale* keyword is set to *no*\ , then the value the parameter is +If the *scale* keyword is set to *no*, then the value the parameter is set to will be whatever the variable generates. If the *scale* -keyword is set to *yes*\ , then the value of the altered parameter will +keyword is set to *yes*, then the value of the altered parameter will be the initial value of that parameter multiplied by whatever the variable generates. I.e. the variable is now a "scale factor" applied in (presumably) a time-varying fashion to the parameter. Internally, @@ -98,7 +98,7 @@ the parameters themselves are actually altered; make sure you use the *reset yes* option if you want the parameters to be restored to their initial values after the run. -If the *after* keyword is set to *yes*\ , then the parameters are +If the *after* keyword is set to *yes*, then the parameters are changed one timestep after the multiple of N. In this manner, if a fix such as "fix ave/time" is used to calculate averages at every N timesteps, all the contributions to the average will be obtained with @@ -173,10 +173,12 @@ styles and their energy formulas for the meaning of these parameters: +------------------------------------------------------------------------------+-------------------------+------------+ | :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | e0,r0,nn,mm | type pairs | +------------------------------------------------------------------------------+-------------------------+------------+ -| :doc:`ufm ` | epsilon,sigma,scale | type pairs | +| :doc:`snap ` | scale | type pairs | +------------------------------------------------------------------------------+-------------------------+------------+ | :doc:`soft ` | a | type pairs | +------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`ufm ` | epsilon,sigma,scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ .. note:: diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 0137066ff7..15f433f520 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -48,8 +48,8 @@ atoms in a simulation, such as for a simulation of Poiseuille flow in a channel. Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style :doc:`variable `, namely *fx*\ , -*fy*\ , *fz*\ . If the value is a variable, it should be specified as +as an equal-style or atom-style :doc:`variable `, namely *fx*, +*fy*, *fz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value(s) used to determine the force component. @@ -98,7 +98,7 @@ one or more variables, and you are performing energy minimization via the "minimize" command. The keyword specifies the name of an atom-style :doc:`variable ` which is used to compute the energy of each atom as function of its position. Like variables used -for *fx*\ , *fy*\ , *fz*\ , the energy variable is specified as v_name, +for *fx*, *fy*, *fz*, the energy variable is specified as v_name, where name is the variable name. Note that when the *energy* keyword is used during an energy diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index fbb957e547..4e1ca12228 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -37,8 +37,8 @@ the group such that: This command can be used to drive a group of atoms into rotation. Any of the 3 quantities defining the torque components can be specified -as an equal-style :doc:`variable `, namely *Tx*\ , -*Ty*\ , *Tz*\ . If the value is a variable, it should be specified as +as an equal-style :doc:`variable `, namely *Tx*, +*Ty*, *Tz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the torque component. @@ -99,9 +99,9 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 754183b55b..c175fa429f 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -31,7 +31,7 @@ Syntax seed = random number seed for langevin kicks extent = extent of thermostatted region (distance units) *random* args = xmax ymax zmax seed - *xmax*\ , *ymax*\ , *zmax* = maximum displacement in particular direction (distance units) + *xmax*, *ymax*, *zmax* = maximum displacement in particular direction (distance units) *seed* = random number seed for random displacement *units* value = *lattice* or *box* *lattice* = the wall position is defined in lattice units @@ -99,7 +99,7 @@ Restrictions """""""""""" This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The boundary on which atoms are added with append/atoms must be shrink/minimum. The opposite boundary may be any boundary type other diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 25f85f6f6c..06bdc9a69e 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -253,7 +253,7 @@ miscellaneous *fix_modify* commands: * :doc:`fix_modify AtC remove_molecule ` Note: a set of example input files with the attendant material files -are included in the ``examples/USER/atc`` folders. +are included in the ``examples/PACKAGES/atc`` folders. Default """"""" diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index a2d365dbe2..eb56572db7 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -66,7 +66,7 @@ The *types* keyword is required. At least two atom types must be specified. The *ke* keyword can be set to *no* to turn off kinetic energy -conservation for swaps. The default is *yes*\ , which means that swapped +conservation for swaps. The default is *yes*, which means that swapped atoms have their velocities scaled by the ratio of the masses of the swapped atom types. This ensures that the kinetic energy of each atom is the same after the swap as it was before the swap, even though the @@ -75,12 +75,12 @@ atom masses have changed. The *semi-grand* keyword can be set to *yes* to switch to the semi-grand canonical ensemble as discussed in :ref:`(Sadigh) `. This means that the total number of each particle type does not need to be -conserved. The default is *no*\ , which means that the only kind of swap +conserved. The default is *no*, which means that the only kind of swap allowed exchanges an atom of one type with an atom of a different given type. In other words, the relative mole fractions of the swapped atoms remains constant. Whereas in the semi-grand canonical ensemble, the composition of the system can change. Note that when using -*semi-grand*\ , atoms in the fix group whose type is not listed +*semi-grand*, atoms in the fix group whose type is not listed in the *types* keyword are ineligible for attempted conversion. An attempt is made to switch the selected atom (if eligible) to one of the other listed types @@ -111,7 +111,7 @@ If not using *semi-grand* this fix checks to ensure all atoms of the given types have the same atomic charge. LAMMPS does not enforce this in general, but it is needed for this fix to simplify the swapping procedure. Successful swaps will swap the atom type and charge -of the swapped atoms. Conversely, when using *semi-grand*\ , it is assumed that all the atom +of the swapped atoms. Conversely, when using *semi-grand*, it is assumed that all the atom types involved in switches have the same charge. Otherwise, charge would not be conserved. As a consequence, no checks on atomic charges are performed, and successful switches update the atom type but not the diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index e506b62cfa..7719dfa7e1 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -89,7 +89,7 @@ command creates a per-atom array with 6 columns: ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps that are a multiple of *Nfreq*\ . The average is over *Nrepeat* @@ -136,7 +136,7 @@ appended, the per-atom vector calculated by the fix is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be -compatible with *Nevery*\ , else an error will result. Users can also +compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index ce7fcd1fca..6d5e0b0380 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -102,7 +102,7 @@ a file. In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and the :doc:`Howto chunk ` doc page for details of how chunks can be +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` page and the :doc:`Howto chunk ` page for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -168,7 +168,7 @@ case, a per-atom array with 3 columns: ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be accessed and contribute to the average. The final averaged quantities are generated on timesteps that are a multiples of *Nfreq*\ . The average is over *Nrepeat* @@ -199,14 +199,14 @@ discussed below. remain constant for the duration of the simulation. This fix forces the chunk/atom compute specified by chunkID to hold *Nchunk* constant for the appropriate time windows, by not allowing it to re-calculate - *Nchunk*\ , which can also affect how it assigns chunk IDs to atoms. + *Nchunk*, which can also affect how it assigns chunk IDs to atoms. This is particularly important to understand if the chunks defined by the :doc:`compute chunk/atom ` command are spatial - bins. If its *units* keyword is set to *box* or *lattice*\ , then the + bins. If its *units* keyword is set to *box* or *lattice*, then the number of bins *Nchunk* and size of each bin will be fixed over the *Nfreq* time window, which can affect which atoms are discarded if the simulation box size changes. If its *units* keyword is set to - *reduced*\ , then the number of bins *Nchunk* will still be fixed, but + *reduced*, then the number of bins *Nchunk* will still be fixed, but the size of each bin can vary at each timestep if the simulation box size changes, e.g. for an NPT simulation. @@ -221,7 +221,7 @@ The *density/number* value means the number density is computed for each chunk, i.e. number/volume. The *density/mass* value means the mass density is computed for each chunk, i.e. total-mass/volume. The output values are in units of 1/volume or density (mass/volume). See -the :doc:`units ` command doc page for the definition of density +the :doc:`units ` command page for the definition of density for each choice of units, e.g. gram/cm\^3. If the chunks defined by the :doc:`compute chunk/atom ` command are spatial bins, the volume is the bin volume. Otherwise it is the volume of the @@ -280,7 +280,7 @@ appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with -*Nevery*\ , else an error results. Users can also write code for their +*Nevery*, else an error results. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -300,7 +300,7 @@ and its outputs. The *norm* keyword affects how averaging is done for the per-chunk values that are output every *Nfreq* timesteps. -It the *norm* setting is *all*\ , which is the default, a chunk value is +It the *norm* setting is *all*, which is the default, a chunk value is summed over all atoms in all *Nrepeat* samples, as is the count of atoms in the chunk. The averaged output value for the chunk on the *Nfreq* timesteps is Total-sum / Total-count. In other words it is an @@ -311,7 +311,7 @@ the final *Nfreq* timestep. For the *temp* values, degrees of freedom and kinetic energy are summed separately across the entire *Nfreq* timescale, and the output value is calculated by dividing those two sums. -If the *norm* setting is *sample*\ , the chunk value is summed over +If the *norm* setting is *sample*, the chunk value is summed over atoms for each sample, as is the count, and an "average sample value" is computed for each sample, i.e. Sample-sum / Sample-count. The output value for the chunk on the *Nfreq* timesteps is the average of @@ -322,7 +322,7 @@ values, the volume (bin volume or system volume) used in the per-sample normalization will be the current volume at each sampling step. -If the *norm* setting is *none*\ , a similar computation as for the +If the *norm* setting is *none*, a similar computation as for the *sample* setting is done, except the individual "average sample values" are "summed sample values". A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by @@ -335,15 +335,15 @@ normalization will be the current volume at each sampling step. The *ave* keyword determines how the per-chunk values produced every *Nfreq* steps are averaged with values produced on previous steps that -were multiples of *Nfreq*\ , before they are accessed by another output +were multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , which is the default, then the chunk +If the *ave* setting is *one*, which is the default, then the chunk values produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the chunk values produced on +If the *ave* setting is *running*, then the chunk values produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each output chunk value is thus the average of the chunk value produced on that timestep with all @@ -352,7 +352,7 @@ the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the chunk values produced on +If the *ave* setting is *window*, then the chunk values produced on timesteps that are multiples of *Nfreq* are summed and averaged within a moving "window" of time, so that the last M values for the same chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000, @@ -440,18 +440,18 @@ chunk ID of 3 may correspond to an original chunk ID or molecule ID of 415. The OrigID column will list 415 for the third chunk. The CoordN columns only appear if a *binning* style was used in the -:doc:`compute chunk/atom ` command. For *bin/1d*\ , -*bin/2d*\ , and *bin/3d* styles the column values are the center point +:doc:`compute chunk/atom ` command. For *bin/1d*, +*bin/2d*, and *bin/3d* styles the column values are the center point of the bin in the corresponding dimension. Just Coord1 is used for -*bin/1d*\ , Coord2 is added for *bin/2d*\ , Coord3 is added for *bin/3d*\ . -For *bin/sphere*\ , just Coord1 is used, and it is the radial -coordinate. For *bin/cylinder*\ , Coord1 and Coord2 are used. Coord1 +*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\ . +For *bin/sphere*, just Coord1 is used, and it is the radial +coordinate. For *bin/cylinder*, Coord1 and Coord2 are used. Coord1 is the radial coordinate (away from the cylinder axis), and coord2 is the coordinate along the cylinder axis. -Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*\ , the +Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the coordinate values will be in distance :doc:`units `. If the -value of the *units* keyword is *reduced*\ , the coordinate values will +value of the *units* keyword is *reduced*, the coordinate values will be in unitless reduced units (0-1). This is not true for the Coord1 value of style *bin/sphere* or *bin/cylinder* which both represent radial dimensions. Those values are always in distance :doc:`units `. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 58aff114af..23086d465f 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -130,7 +130,7 @@ values. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used to calculate correlation data. The input values are sampled every *Nevery* timesteps. The correlation data for the preceding samples is computed on timesteps @@ -194,7 +194,7 @@ be specified with a wildcard asterisk to effectively specify multiple values. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -237,14 +237,14 @@ pair Vi(t)\*Vj(t+delta) is always the one sampled at the later time. The *ave* keyword determines what happens to the accumulation of correlation samples every *Nfreq* timesteps. If the *ave* setting is -*one*\ , then the accumulation is restarted or zeroed every *Nfreq* +*one*, then the accumulation is restarted or zeroed every *Nfreq* timesteps. Thus the outputs on successive *Nfreq* timesteps are essentially independent of each other. The exception is that the Cij(0) = Vi(T)\*Vj(T) value at a timestep T, where T is a multiple of -*Nfreq*\ , contributes to the correlation output both at time T and at +*Nfreq*, contributes to the correlation output both at time T and at time T+Nfreq. -If the *ave* setting is *running*\ , then the accumulation is never +If the *ave* setting is *running*, then the accumulation is never zeroed. Thus the output of correlation data at any timestep is the average over samples accumulated every *Nevery* steps since the fix was defined. it can only be restarted by deleting the fix via the @@ -263,7 +263,7 @@ the size of the time window or other unit conversions. The *file* keyword allows a filename to be specified. Every *Nfreq* steps, an array of correlation data is written to the file. The -number of rows is *Nrepeat*\ , as described above. The number of +number of rows is *Nrepeat*, as described above. The number of columns is the Npair+2, also as described above. Thus the file ends up to be a series of these array sections. @@ -327,19 +327,19 @@ samples contributing to the correlation average, as described above. The remaining Npair columns are for I,J pairs of the N input values, as determined by the *type* keyword, as described above. -* For *type* = *auto*\ , the Npair = N columns are ordered: C11, C22, ..., +* For *type* = *auto*, the Npair = N columns are ordered: C11, C22, ..., CNN. -* For *type* = *upper*\ , the Npair = N\*(N-1)/2 columns are ordered: C12, +* For *type* = *upper*, the Npair = N\*(N-1)/2 columns are ordered: C12, C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. -* For *type* = *lower*\ , the Npair = N\*(N-1)/2 columns are ordered: C21, +* For *type* = *lower*, the Npair = N\*(N-1)/2 columns are ordered: C21, C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. -* For *type* = *auto/upper*\ , the Npair = N\*(N+1)/2 columns are ordered: +* For *type* = *auto/upper*, the Npair = N\*(N+1)/2 columns are ordered: C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N, CNN. -* For *type* = *auto/lower*\ , the Npair = N\*(N+1)/2 columns are ordered: +* For *type* = *auto/lower*, the Npair = N\*(N+1)/2 columns are ordered: C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1, CNN. -* For *type* = *full*\ , the Npair = N\^2 columns are ordered: C11, C12, +* For *type* = *full*, the Npair = N\^2 columns are ordered: C11, C12, ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, CNN. diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index c740099aae..a69d8f5695 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -78,18 +78,18 @@ specified values may represent calculations performed by computes and fixes which store their own "group" definitions. Each listed value can be the result of a compute or fix or the -evaluation of an equal-style variable. See the :doc:`fix ave/correlate ` doc page for details. +evaluation of an equal-style variable. See the :doc:`fix ave/correlate ` page for details. The *Nevery* and *Nfreq* arguments specify on what timesteps the input values will be used to calculate correlation data, and the frequency with which the time correlation functions will be output to a file. Note that there is no *Nrepeat* argument, unlike the :doc:`fix ave/correlate ` command. -The optional keywords *ncorr*\ , *nlen*\ , and *ncount* are unique to this +The optional keywords *ncorr*, *nlen*, and *ncount* are unique to this command and determine the number of correlation points calculated and the memory and CPU overhead used by this calculation. *Nlen* and *ncount* determine the amount of averaging done at longer correlation -times. The default values *nlen=16*\ , *ncount=2* ensure that the +times. The default values *nlen=16*, *ncount=2* ensure that the systematic error of the multiple-tau correlator is always below the level of the statistical error of a typical simulation (which depends on the ensemble size and the simulation length). @@ -127,8 +127,8 @@ the run command. This fix is not invoked during energy minimization. Restrictions """""""""""" -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 3a2857f383..05c63a6faf 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -100,7 +100,7 @@ component) or can be the result of a :doc:`compute ` or atom-style :doc:`variable `. The set of input values can be either all global, all per-atom, or all local quantities. Inputs of different kinds (e.g. global and per-atom) cannot be mixed. Atom -attributes are per-atom vector values. See the doc page for +attributes are per-atom vector values. See the page for individual "compute" and "fix" commands to see what kinds of quantities they generate. See the optional *kind* keyword below for how to force the fix ave/histo command to disambiguate if necessary. @@ -153,7 +153,7 @@ the first vector. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the histogram. The final histogram is generated on timesteps that are multiple of *Nfreq*\ . It is averaged over *Nrepeat* histograms, @@ -210,7 +210,7 @@ be specified with a wildcard asterisk to effectively specify multiple values. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -223,7 +223,7 @@ atom-style variables can be used, which produce a global or per-atom vector respectively. The vector-style variable must be used without a bracketed term. See the :doc:`variable ` command for details. -Note that variables of style *equal*\ , *vector*\ , and *atom* define a +Note that variables of style *equal*, *vector*, and *atom* define a formula which can reference individual atom properties or thermodynamic keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of @@ -233,9 +233,9 @@ specifying quantities to histogram. Additional optional keywords also affect the operation of this fix. -If the *mode* keyword is set to *scalar*\ , then all input values must +If the *mode* keyword is set to *scalar*, then all input values must be global scalars, or elements of global vectors. If the *mode* -keyword is set to *vector*\ , then all input values must be global or +keyword is set to *vector*, then all input values must be global or per-atom or local vectors, or columns of global or per-atom or local arrays. @@ -263,14 +263,14 @@ values > *hi* are counted in the last bin (Nbins+2). Values between The *ave* keyword determines how the histogram produced every *Nfreq* steps are averaged with histograms produced on previous steps that -were multiples of *Nfreq*\ , before they are accessed by another output +were multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , then the histograms produced on +If the *ave* setting is *one*, then the histograms produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the histograms produced on +If the *ave* setting is *running*, then the histograms produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each bin value in the histogram is thus the average of the bin value produced on that timestep with @@ -279,7 +279,7 @@ when the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or by re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the histograms produced on +If the *ave* setting is *window*, then the histograms produced on timesteps that are multiples of *Nfreq* are summed within a moving "window" of time, so that the last M histograms are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then the output on step diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index ad1aca233c..dfa385ea46 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -136,7 +136,7 @@ with 3 columns, each of length 50: ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps that are a multiple of *Nfreq*\ . The average is over *Nrepeat* @@ -185,7 +185,7 @@ for how I can be specified with a wildcard asterisk to effectively specify multiple values. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -207,23 +207,23 @@ quantities to time average. Additional optional keywords also affect the operation of this fix. -If the *mode* keyword is set to *scalar*\ , then all input values must +If the *mode* keyword is set to *scalar*, then all input values must be global scalars, or elements of global vectors. If the *mode* -keyword is set to *vector*\ , then all input values must be global +keyword is set to *vector*, then all input values must be global vectors, or columns of global arrays. They can also be global arrays, which are converted into a series of global vectors (one per column), as explained above. The *ave* keyword determines how the values produced every *Nfreq* steps are averaged with values produced on previous steps that were -multiples of *Nfreq*\ , before they are accessed by another output +multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , then the values produced on timesteps +If the *ave* setting is *one*, then the values produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the values produced on +If the *ave* setting is *running*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding @@ -231,7 +231,7 @@ values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or by re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the values produced on +If the *ave* setting is *window*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged within a moving "window" of time, so that the last M values are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then the output @@ -332,7 +332,7 @@ element are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either "intensive" or "extensive". If a compute or fix provides the value being time averaged, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for +intensive or extensive; see the page for that compute or fix for further info. Values produced by a variable are treated as intensive. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index 36e1e28ea6..414fa497ed 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -54,7 +54,7 @@ same as specifying a 0.0 value, since that sets all forces to the same average value without adding in any additional force. Any of the 3 quantities defining the force components can be specified -as an equal-style :doc:`variable `, namely *fx*\ , *fy*\ , *fz*\ . +as an equal-style :doc:`variable `, namely *fx*, *fy*, *fz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the average diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 8bab8ebefc..66457cb61a 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -222,7 +222,7 @@ once. You should normally only list dimensions where you expect there to be a density variation in the particles. Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in *dimstr*\ , one dimension at a time. For a single +dimensions listed in *dimstr*, one dimension at a time. For a single dimension, the balancing operation (described below) is iterated on up to *Niter* times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the *stopthresh* @@ -403,7 +403,7 @@ Related commands :doc:`group `, :doc:`processors `, :doc:`balance `, :doc:`comm_style ` -.. _pizza: https://pizza.sandia.gov +.. _pizza: https://lammps.github.io/pizza Default """"""" diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index f4b3080cc0..566bf8e68d 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -41,10 +41,10 @@ The first half of the command mimics a standard fix npt command: fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp -The two differences are replacing *npt* with *bocs*\ , and replacing +The two differences are replacing *npt* with *bocs*, and replacing *iso*\ /\ *aniso*\ /\ *etc* with *cgiso*\ . The rest of the command details what form you would like to use for -the pressure correction equation. The choices are: *analytic*\ , *linear_spline*, +the pressure correction equation. The choices are: *analytic*, *linear_spline*, or *cubic_spline*. With either spline method, the only argument that needs to follow it @@ -58,7 +58,7 @@ as a function of volume. The file must be formatted so each line has: Note both the COMMA and the SPACE separating the volume's value and its corresponding pressure correction. The volumes in the file must be uniformly spaced. Both the volumes and the pressure corrections -should be provided in the proper units, e.g. if you are using *units real*\ , +should be provided in the proper units, e.g. if you are using *units real*, the volumes should all be in cubic angstroms, and the pressure corrections should all be in atmospheres. Furthermore, the table should start/end at a volume considerably smaller/larger than you expect your system to sample @@ -72,7 +72,7 @@ With the *analytic* option, the arguments are as follows: ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you -are using *units real*\ , *V_avg* should be in cubic angstroms, and the +are using *units real*, *V_avg* should be in cubic angstroms, and the coefficients should all be in atmospheres \* cubic angstroms. ---------- @@ -124,8 +124,8 @@ the examples. For the last argument in the command, you should put XXXX_press, where XXXX is the ID given to the fix bocs command (in the example, the ID of the fix bocs command is 1 ). -This fix is part of the USER-BOCS package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the BOCS package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Further information """"""""""""""""""" diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index 4f2e2840ab..9538fa8ef3 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -51,7 +51,7 @@ interactions from timestep to timestep as atoms move. A check for possible bond breakage is performed every *Nevery* timesteps. If two bonded atoms I,J are further than a distance *Rmax* -of each other, if the bond is of type *bondtype*\ , and if both I and J +of each other, if the bond is of type *bondtype*, and if both I and J are in the specified fix group, then I,J is labeled as a "possible" bond to break. diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 34f0d19f8d..c286482f81 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -64,7 +64,7 @@ context, a bond means an interaction between a pair of atoms computed by the :doc:`bond_style ` command. Once the bond is created it will be permanently in place. Optionally, the creation of a bond can also create angle, dihedral, and improper interactions that bond -is part of. See the discussion of the *atype*\ , *dtype*\ , and *itype* +is part of. See the discussion of the *atype*, *dtype*, and *itype* keywords below. This is different than a :doc:`pairwise ` bond-order @@ -75,7 +75,7 @@ interactions from timestep to timestep as atoms move. A check for possible new bonds is performed every *Nevery* timesteps. If two atoms I,J are within a distance *Rmin* of each other, if I is -of atom type *itype*\ , if J is of atom type *jtype*\ , if both I and J +of atom type *itype*, if J is of atom type *jtype*, if both I and J are in the specified fix group, if a bond does not already exist between I and J, and if both I and J meet their respective *maxbond* requirement (explained below), then I,J is labeled as a "possible" @@ -133,7 +133,7 @@ When a bond is created, data structures within LAMMPS that store bond topology are updated to reflect the creation. If the bond is part of new 3-body (angle) or 4-body (dihedral, improper) interactions, you can choose to create new angles, dihedrals, impropers as well, using -the *atype*\ , *dtype*\ , and *itype* keywords. All of these changes +the *atype*, *dtype*, and *itype* keywords. All of these changes typically affect pairwise interactions between atoms that are now part of new bonds, angles, etc. @@ -147,7 +147,7 @@ of new bonds, angles, etc. If the *atype* keyword is used and if an angle potential is defined via the :doc:`angle_style ` command, then any new 3-body interactions inferred by the creation of a bond will create new angles -of type *angletype*\ , with parameters assigned by the corresponding +of type *angletype*, with parameters assigned by the corresponding :doc:`angle_coeff ` command. Likewise, the *dtype* and *itype* keywords will create new dihedrals and impropers of type *dihedraltype* and *impropertype*\ . @@ -183,7 +183,7 @@ of type *angletype*\ , with parameters assigned by the corresponding .. note:: - Even if you do not use the *atype*\ , *dtype*\ , or *itype* + Even if you do not use the *atype*, *dtype*, or *itype* keywords, the list of topological neighbors is updated for atoms affected by the new bond. This in turn affects which neighbors are considered for pairwise interactions, using the weighting rules set by diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index c421185d87..a48675dcf2 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -69,7 +69,7 @@ Syntax Examples """""""" -For unabridged example scripts and files, see examples/USER/reaction. +For unabridged example scripts and files, see examples/PACKAGES/reaction. .. code-block:: LAMMPS @@ -159,7 +159,7 @@ constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example -above (full examples can be found at examples/USER/reaction). The time +above (full examples can be found at examples/PACKAGES/reaction). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. @@ -424,7 +424,7 @@ The constraint of type 'angle' has the following syntax: angle *ID1* *ID2* *ID3* *amin* *amax* -where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are +where 'angle' is the required keyword, *ID1*, *ID2* and *ID3* are pre-reaction atom IDs (or molecule-fragment IDs, see below), and these three atoms must form an angle between *amin* and *amax* for the reaction to occur (where *ID2* is the central atom). Angles must be @@ -437,7 +437,7 @@ The constraint of type 'dihedral' has the following syntax: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* -where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* +where 'dihedral' is the required keyword, and *ID1*, *ID2*, *ID3* and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see below). Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style ` documentation for @@ -667,9 +667,9 @@ all other fixes that use any group created by fix bond/react. Restrictions """""""""""" -This fix is part of the USER-REACTION package. It is only enabled if +This fix is part of the REACTION package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index e3b756476d..da000c98b2 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -27,21 +27,26 @@ Examples Description """"""""""" -In a simulation of polymer chains, this command attempts to swap bonds -between two different chains, effectively grafting the end of one -chain onto another chain and vice versa. This is done via Monte Carlo -rules using the Boltzmann acceptance criterion. The purpose is to -equilibrate the polymer chain conformations more rapidly than dynamics -alone would do it, by enabling instantaneous large conformational -changes in a dense polymer melt. The polymer chains should thus more -rapidly converge to the proper end-to-end distances and radii of -gyration. It is designed for use with systems of -:doc:`FENE ` or :doc:`harmonic ` bead-spring -polymer chains where each polymer is a linear chain of monomers, but -LAMMPS does not enforce this requirement, i.e. any -:doc:`bond_style ` can be used. +In a simulation of polymer chains, this command attempts to swap a +pair of bonds, as illustrated below. This is done via Monte Carlo +rules using the Boltzmann acceptance criterion, typically with the +goal of equilibrating the polymer system more quickly. This fix is +designed for use with idealized bead-spring polymer chains where each +polymer is a linear chain of monomers, but LAMMPS does not check that +is the case for your system. -A schematic of the kinds of bond swaps that can occur is shown here: +Here are two use cases where this fix can be used effectively. + +The first use case is for swapping bonds on two different chains, +effectively grafting the end of one chain onto the other chain and +vice versa. The purpose is to equilibrate the polymer chain +conformations more rapidly than dynamics alone would do it, by +enabling instantaneous large conformational changes in a dense polymer +melt. The polymer chains should thus more rapidly converge to the +proper end-to-end distances and radii of gyration. + +A schematic of the kinds of bond swaps that can occur in this use case +is shown here: .. image:: JPG/bondswap.jpg :align: center @@ -53,38 +58,55 @@ attempt to delete the A1-A2 and B1-B2 bonds and replace them with A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the two chains on the right are the result and each polymer chain has undergone a dramatic conformational change. This reference, -:ref:`(Sides) ` provides more details on how the algorithm works and -its application: +:ref:`(Sides) ` provides more details on the algorithm's +effectiveness for this use case. + +The second use case is a collection of polymer chains with some +fraction of their sites identified as "sticker" sites. + The bond swapping operation is invoked every *Nevery* timesteps. If -any bond is swapped, a re-build of the neighbor lists is triggered, -since a swap alters the list of which neighbors are considered for -pairwise interaction. At each invocation, each processor considers a -random specified *fraction* of its atoms as potential swapping -monomers for this timestep. Choosing a small *fraction* value can -reduce the likelihood of a reverse swap occurring soon after an -initial swap. +any bond in the entire system is swapped, a re-build of the neighbor +lists is triggered, since a swap alters the list of which neighbors +are considered for pairwise interaction. At each invocation, each +processor considers a random specified *fraction* of its atoms as +potential swapping monomers for this timestep. Choosing a small +*fraction* value can reduce the likelihood of a reverse swap occurring +soon after an initial swap. -NOTE: is cutoff applied to all new bonds? +For each monomer A1, its neighbors are looped over as B1 monomers. An +additional double loop of bond partners A2 of A1, and bond partners B2 +of B1 a is performed. For each pair of A1-A2 and B1-B2 bonds to be +eligible for swapping, the following 4 criteria must be met: -For each monomer A1, its neighbors are looped over as B1 monomers. -All bond partners of both A1 and B1 are also looped over. For a pair -of A1-A2 and B1-B2 bonds to be eligible for swapping, these criteria -must be met. All 4 monomers must be in the fix group. The separation -between A1 and B1 must be less than the specified *cutoff*\ . And the -molecule IDs of A1 and B1 must be the same (see below). If an -eligible B1 partner is found, the energy change due to swapping the 2 -bonds is computed. This includes changes in pairwise, bond, and angle -energies due to the altered connectivity of the 2 chains. Dihedral -and improper interactions are not allowed to be defined when this fix -is used. +(1) All 4 monomers must be in the fix group. + +(2) All 4 monomers must be owned by the processor (not ghost atoms). +This insures that another processor does not attempt to swap bonds +involving the same atoms on the same timestep. Note that this also +means that bond pairs which straddle processor boundaries are not +eligible for swapping on this step. + +(3) The distances between 4 pairs of atoms -- (A1,A2), (B1,B2), +(A1,B2), (B1,A2) -- must all be less thann the specified *cutoff*\ . + +(4) The molecule IDs of A1 and B1 must be the same (see below). + +If an eligible B1 partner is found, the energy change due to swapping +the 2 bonds is computed. This includes changes in pairwise, bond, and +angle energies due to the altered connectivity of the 2 chains. +Dihedral and improper interactions are not allowed to be defined when +this fix is used. If the energy decreases due to the swap operation, the bond swap is accepted. If the energy increases it is accepted with probability exp(-delta/kT) where delta is the increase in energy, k is the Boltzmann constant, and T is the current temperature of the system. -Whether the swap is accepted or rejected, no other swaps are attempted -by this processor on this timestep. + +IMPORTANT: Whether the swap is accepted or rejected, no other swaps +are attempted by this processor on this timestep. + +---------- The criterion for matching molecule IDs is how bond swaps performed by this fix conserve chain length. To use this features you must setup @@ -122,7 +144,7 @@ ends of a chain swap with each other. This fix computes a temperature each time it is invoked for use by the Boltzmann criterion. To do this, the fix creates its own compute of -style *temp*\ , as if this command had been issued: +style *temp*, as if this command had been issued: .. code-block:: LAMMPS @@ -134,27 +156,28 @@ appended and the group for the new compute is "all", so that the temperature of the entire system is used. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo_temp*. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -:doc:`compute_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo_temp* will have no -effect on this fix. +the :doc:`thermo_style ` command) with ID = +*thermo_temp*. This means you can change the attributes of this fix's +temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify +` command or print this temperature during +thermodynamic output via the :doc:`thermo_style custom ` +command using the appropriate compute-ID. It also means that changing +attributes of *thermo_temp* will have no effect on this fix. ---------- Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. Also note that -each processor generates possible swaps independently of other -processors. Thus if you repeat the same simulation on a different number -of processors, the specific swaps performed will be different. +No information about this fix is written to :doc:`binary restart files +`. Because the state of the random number generator is not +saved in restart files, this means you cannot do "exact" restarts with +this fix, where the simulation continues on the same as if no restart +had taken place. However, in a statistical sense, a restarted +simulation should produce the same behavior. Also note that each +processor generates possible swaps independently of other processors. +Thus if you repeat the same simulation on a different number of +processors, the specific swaps performed will be different. The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have @@ -162,16 +185,18 @@ defined to this fix which will be used to compute the temperature for the Boltzmann criterion. This fix computes two statistical quantities as a global 2-vector of -output, which can be accessed by various :doc:`output commands `. The first component of the vector is the -cumulative number of swaps performed by all processors. The second -component of the vector is the cumulative number of swaps attempted -(whether accepted or rejected). Note that a swap "attempt" only -occurs when swap partners meeting the criteria described above are -found on a particular timestep. The vector values calculated by this -fix are "intensive". +output, which can be accessed by various :doc:`output commands +`. The first component of the vector is the cumulative +number of swaps performed by all processors. The second component of +the vector is the cumulative number of swaps attempted (whether +accepted or rejected). Note that a swap "attempt" only occurs when +swap partners meeting the criteria described above are found on a +particular timestep. The vector values calculated by this fix are +"intensive". No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. Restrictions """""""""""" diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 7a9abdfe26..5827fe3732 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -53,7 +53,7 @@ pressure typically allows the box to expand. ---------- The external pressure tensor is specified using one or more of the -*iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* +*iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, *xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are @@ -66,25 +66,25 @@ specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The target pressures *Ptarget* for each of the 6 components of the -stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ , -*xy*\ , *xz*\ , *yz* keywords, which correspond to the 6 simulation box +stress tensor can be specified independently via the *x*, *y*, *z*, +*xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box dimensions. For example, if the *y* keyword is used, the y-box length will change during the minimization. If the *xy* keyword is used, the xy tilt factor will change. A box dimension will not change if that component is not specified. -Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the +Note that in order to use the *xy*, *xz*, or *yz* keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.0. When the size of the simulation box changes, all atoms are re-scaled to new positions, unless the keyword *dilate* is specified with a -value of *partial*\ , in which case only the atoms in the fix group are +value of *partial*, in which case only the atoms in the fix group are re-scaled. This can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid. -The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when relaxing triclinic periodic cells. The default values *yes* will turn on scaling, which corresponds to adjusting the @@ -99,7 +99,7 @@ The *fixedpoint* keyword specifies the fixed point for cell relaxation. By default, it is the center of the box. Whatever point is chosen will not move during the simulation. For example, if the lower periodic boundaries pass through (0,0,0), and this point is provided -to *fixedpoint*\ , then the lower periodic boundaries will remain at +to *fixedpoint*, then the lower periodic boundaries will remain at (0,0,0), while the upper periodic boundaries will move twice as far. In all cases, the particle positions at each iteration are unaffected by the chosen value, except that all particles are @@ -107,7 +107,7 @@ displaced by the same amount, different on each iteration. .. note:: - Applying an external pressure to tilt dimensions *xy*\ , *xz*\ , *yz* + Applying an external pressure to tilt dimensions *xy*, *xz*, *yz* can sometimes result in arbitrarily large values of the tilt factors, i.e. a dramatically deformed simulation box. This typically indicates that there is something badly wrong with how the simulation was @@ -149,7 +149,7 @@ simply ignored. ---------- -The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. The keyword *iso* means couple all 3 diagonal components together when @@ -164,8 +164,8 @@ these 4 keywords: z Ptarget couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Ptarget" is the same as specifying these 4 keywords: @@ -177,7 +177,7 @@ keywords: z Ptarget couple none -The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions are controlled independently using their individual stress components as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Ptarget" is the same as specifying @@ -246,7 +246,7 @@ minimization steps, the reference dimensions are set to those of the current simulation domain. Note that resetting the reference dimensions changes the objective function and gradients, which sometimes causes the minimization to fail. This can be resolved by -changing the value of *nreset*\ , or simply continuing the minimization +changing the value of *nreset*, or simply continuing the minimization from a restart file. .. note:: @@ -362,8 +362,8 @@ Restrictions """""""""""" Only dimensions that are available can be adjusted by this fix. -Non-periodic dimensions are not available. *z*\ , *xz*\ , and *yz*\ , are -not available for 2D simulations. *xy*\ , *xz*\ , and *yz* are only +Non-periodic dimensions are not available. *z*, *xz*, and *yz*, are +not available for 2D simulations. *xy*, *xz*, and *yz* are only available if the simulation domain is non-orthogonal. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the @@ -371,10 +371,10 @@ simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used -for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . Related commands """""""""""""""" diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst index d032346617..c274c394f3 100644 --- a/doc/src/fix_brownian.rst +++ b/doc/src/fix_brownian.rst @@ -185,7 +185,7 @@ as defined by the :doc:`atom_style ellipsoid ` command. If the *dipole* keyword is used, they must also store a dipole moment as defined by the :doc:`atom_style dipole ` command. -This fix is part of the USER-BROWNIAN package. It is only enabled if +This fix is part of the BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index 06c1d92b79..9ff28b6ac3 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -227,7 +227,7 @@ Restrictions This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index 3bcc6bdaa5..a688d38e25 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -27,7 +27,7 @@ This fix style enables LAMMPS to run as a "client" code and communicate each timestep with a separate "server" code to perform an MD simulation together. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -101,7 +101,7 @@ Restrictions This fix is part of the MESSAGE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. A script that uses this command must also use the :doc:`message ` command to setup and shut down the messaging diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index e6e8d0c627..6475e538a2 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -73,7 +73,7 @@ remaining 5 columns are the atom IDs of the atoms in the two 4-atom dihedrals that overlap to create the CMAP 5-body interaction. Note that the "crossterm" and "CMAP" keywords for the header and body sections match those specified in the read_data command following the -data file name; see the :doc:`read_data ` doc page for +data file name; see the :doc:`read_data ` page for more details. A data file containing CMAP cross-terms can be generated from a PDB @@ -147,7 +147,7 @@ To function as expected this fix command must be issued *before* a :doc:`read_restart ` command. This fix can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 3f503410d3..21b235cb6b 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -50,7 +50,7 @@ The Colvars library is developed at `https://github.com/colvars/colvars `. There are some example scripts for using this package with LAMMPS in the -examples/USER/colvars directory. +examples/PACKAGES/colvars directory. ---------- @@ -80,7 +80,7 @@ that will be used in the colvars module. The *unwrap* keyword controls whether wrapped or unwrapped coordinates are passed to the colvars library for calculation of the collective -variables and the resulting forces. The default is *yes*\ , i.e. to use +variables and the resulting forces. The default is *yes*, i.e. to use the image flags to reconstruct the absolute atom positions. Setting this to *no* will use the current local coordinates that are wrapped back into the simulation cell at each re-neighboring instead. @@ -122,9 +122,9 @@ energy mentioned above. The scalar value calculated by this fix is Restrictions """""""""""" -This fix is part of the USER-COLVARS package. It is only enabled if +This fix is part of the COLVARS package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. There can only be one colvars fix active at a time. Since the interface communicates only the minimum amount of information and colvars module diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 0b7332cdd7..0ff38ae010 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -127,17 +127,17 @@ When choosing the values of the four constants, it is best to first pick a value and sign for :math:`\alpha` that is consistent with the magnitudes and signs of *pvar* and *cvar*\ . The magnitude of :math:`K_p` should then be tested over a large positive range keeping :math:`K_i = K_d =0`. -A good value for :math:`K_p` will produce a fast response in *pvar*\ , +A good value for :math:`K_p` will produce a fast response in *pvar*, without overshooting the *setpoint*\ . For many applications, proportional feedback is sufficient, and so :math:`K_i` = K_d =0` can be used. In cases where there is a substantial lag time in the response of *pvar* to a change -in *cvar*\ , this can be counteracted by increasing :math:`K_d`. In situations -where *pvar* plateaus without reaching *setpoint*\ , this can be +in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations +where *pvar* plateaus without reaching *setpoint*, this can be counteracted by increasing :math:`K_i`. In the language of Charles Dickens, :math:`K_p` represents the error of the present, :math:`K_i` the error of the past, and :math:`K_d` the error yet to come. -Because this fix updates *cvar*\ , but does not initialize its value, +Because this fix updates *cvar*, but does not initialize its value, the initial value is that assigned by the user in the input script via the :doc:`internal-style variable ` command. This value is used (by the other LAMMPS command that used the variable) until this @@ -162,7 +162,7 @@ used. Users can also write code for their own compute styles and :doc:`add them If *pvar* begins with "f\_", a fix ID must follow which has been previously defined in the input script and which generates a global -scalar or vector. See the individual :doc:`fix ` doc page for +scalar or vector. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when fix controller references the values, or else an error results. If no bracketed integer @@ -215,7 +215,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 999a88c4e7..a21a3a6044 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -21,7 +21,7 @@ Syntax .. parsed-literal:: parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* - *x*\ , *y*\ , *z* args = style value(s) + *x*, *y*, *z* args = style value(s) style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* *final* values = lo hi lo hi = box boundaries at end of run (distance units) @@ -43,7 +43,7 @@ Syntax *variable* values = v_name1 v_name2 v_name1 = variable with name1 for box length change as function of time v_name2 = variable with name2 for change rate as function of time - *xy*\ , *xz*\ , *yz* args = style value + *xy*, *xz*, *yz* args = style value style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* *final* value = tilt tilt = tilt factor at end of run (distance units) @@ -100,10 +100,10 @@ adjusted independently and simultaneously by this command. This fix can be used to perform non-equilibrium MD (NEMD) simulations of a continuously strained system. See the :doc:`fix nvt/sllod ` and :doc:`compute temp/deform ` commands for more details. Note that simulation of a continuously extended system (extensional flow) -can be modeled using the :ref:`USER-UEF package ` and its :doc:`fix commands `. +can be modeled using the :ref:`UEF package ` and its :doc:`fix commands `. -For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be -shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated +For the *x*, *y*, *z* parameters, the associated dimension cannot be +shrink-wrapped. For the *xy*, *yz*, *xz* parameters, the associated second dimension cannot be shrink-wrapped. Dimensions not varied by this command can be periodic or non-periodic. Dimensions corresponding to unspecified parameters can also be controlled by a :doc:`fix npt ` or :doc:`fix nph ` command. @@ -127,29 +127,29 @@ and final values. ---------- -For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their +For the *x*, *y*, and *z* parameters, this is the meaning of their styles and values. -The *final*\ , *delta*\ , *scale*\ , *vel*\ , and *erate* styles all change +The *final*, *delta*, *scale*, *vel*, and *erate* styles all change the specified dimension of the box via "constant displacement" which is effectively a "constant engineering strain rate". This means the box dimension changes linearly with time from its initial to final value. -For style *final*\ , the final lo and hi box boundaries of a dimension +For style *final*, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , plus or minus changes in the lo/hi box boundaries +For style *delta*, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *scale*\ , a multiplicative factor to apply to the box length +For style *scale*, a multiplicative factor to apply to the box length of a dimension is specified. For example, if the initial box length is 10, and the factor is 1.1, then the final box length will be 11. A factor less than 1.0 means compression. -For style *vel*\ , a velocity at which the box length changes is +For style *vel*, a velocity at which the box length changes is specified in units of distance/time. This is effectively a "constant engineering strain rate", where rate = V/L0 and L0 is the initial box length. The distance can be in lattice or box distance units. See @@ -207,7 +207,7 @@ triple every picosecond. R = ln(0.99) means the box length will shrink by 1% of its current length every picosecond. Note that for a "true" rate the change is continuous and based on the current length, so running with R = ln(2) for 10 picoseconds does not expand the box -length by a factor of 11 as it would with *erate*\ , but by a factor of +length by a factor of 11 as it would with *erate*, but by a factor of 1024 since the box length will double every picosecond. Note that to change the volume (or cross-sectional area) of the @@ -288,30 +288,30 @@ assume that the current timestep = 0. variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" fix 2 all deform 1 x variable v_displace v_rate remap v -For the *scale*\ , *vel*\ , *erate*\ , *trate*\ , *volume*\ , *wiggle*\ , and +For the *scale*, *vel*, *erate*, *trate*, *volume*, *wiggle*, and *variable* styles, the box length is expanded or compressed around its mid point. ---------- -For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their +For the *xy*, *xz*, and *yz* parameters, this is the meaning of their styles and values. Note that changing the tilt factors of a triclinic box does not change its volume. -The *final*\ , *delta*\ , *vel*\ , and *erate* styles all change the shear +The *final*, *delta*, *vel*, and *erate* styles all change the shear strain at a "constant engineering shear strain rate". This means the tilt factor changes linearly with time from its initial to final value. -For style *final*\ , the final tilt factor is specified. The value +For style *final*, the final tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , a plus or minus change in the tilt factor is +For style *delta*, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. -For style *vel*\ , a velocity at which the tilt factor changes is +For style *vel*, a velocity at which the tilt factor changes is specified in units of distance/time. This is effectively an "engineering shear strain rate", where rate = V/L0 and L0 is the initial box length perpendicular to the direction of shear. The @@ -449,7 +449,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent. To obey this constraint and allow for large shear deformations to be -applied via the *xy*\ , *xz*\ , or *yz* parameters, the following +applied via the *xy*, *xz*, or *yz* parameters, the following algorithm is used. If *prd* is the associated parallel box length (10 in the example above), then if the tilt factor exceeds the accepted range of -5 to 5 during the simulation, then the box is flipped to the @@ -476,13 +476,13 @@ Each time the box size or shape is changed, the *remap* keyword determines whether atom positions are remapped to the new box. If *remap* is set to *x* (the default), atoms in the fix group are remapped; otherwise they are not. Note that their velocities are not -changed, just their positions are altered. If *remap* is set to *v*\ , +changed, just their positions are altered. If *remap* is set to *v*, then any atom in the fix group that crosses a periodic boundary will have a delta added to its velocity equal to the difference in velocities between the lo and hi boundaries. Note that this velocity difference can include tilt components, e.g. a delta in the x velocity when an atom crosses the y periodic boundary. If *remap* is set to -*none*\ , then neither of these remappings take place. +*none*, then neither of these remappings take place. Conceptually, setting *remap* to *x* forces the atoms to deform via an affine transformation that exactly matches the box deformation. This @@ -529,20 +529,20 @@ box without explicit remapping of their coordinates. .. note:: If a :doc:`fix rigid ` is defined for rigid bodies, and - *remap* is set to *x*\ , then the center-of-mass coordinates of rigid + *remap* is set to *x*, then the center-of-mass coordinates of rigid bodies will be remapped to the changing simulation box. This will be done regardless of whether atoms in the rigid bodies are in the fix deform group or not. The velocity of the centers of mass are not - remapped even if *remap* is set to *v*\ , since :doc:`fix nvt/sllod ` does not currently do anything special + remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod ` does not currently do anything special for rigid particles. If you wish to perform a NEMD simulation of rigid particles, you can either thermostat them independently or include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod `. The *flip* keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed -above. If the *flip* value is set to *yes*\ , the bound is enforced by +above. If the *flip* value is set to *yes*, the bound is enforced by flipping the box when it is exceeded. If the *flip* value is set to -*no*\ , the tilt will continue to change without flipping. Note that if +*no*, the tilt will continue to change without flipping. Note that if you apply large deformations, this means the box shape can tilt dramatically LAMMPS will run less efficiently, due to the large volume of communication needed to acquire ghost atoms around a processor's @@ -557,8 +557,8 @@ in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacing. Note that the units choice also affects the *vel* style parameters since it is defined in terms of distance/time. Also note that the units keyword -does not affect the *variable* style. You should use the *xlat*\ , -*ylat*\ , *zlat* keywords of the :doc:`thermo_style ` +does not affect the *variable* style. You should use the *xlat*, +*ylat*, *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. ---------- diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 42975eb0b2..ad3c37b24c 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -220,7 +220,7 @@ ignored if the *global* or *local* keywords are used, since those options choose a z-coordinate for insertion independently. The vx, vy, and vz components of velocity for the inserted particle -are set using the values specified for the *vx*\ , *vy*\ , and *vz* +are set using the values specified for the *vx*, *vy*, and *vz* keywords. Note that normally, new particles should be a assigned a negative vertical velocity so that they move towards the surface. For molecules, the same velocity is given to every particle (no rotation @@ -296,9 +296,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. - The specified insertion region cannot be a "dynamic" region, as defined by the :doc:`region ` command. diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 732f99b516..d6e8dd7230 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -32,7 +32,7 @@ the group at each timestep. It must be used in conjunction with a deterministic integrator (e.g. :doc:`fix nve `) that updates the particle positions and velocities. -For fix *dpd/energy*\ , the particle internal temperature is related to +For fix *dpd/energy*, the particle internal temperature is related to the particle internal energy through a mesoparticle equation of state. An additional fix must be specified that defines the equation of state for each particle, e.g. :doc:`fix eos/cv `. @@ -41,11 +41,11 @@ This fix must be used with the :doc:`pair_style dpd/fdt/energy ` com Note that numerous variants of DPD can be specified by choosing an appropriate combination of the integrator and :doc:`pair_style dpd/fdt/energy ` command. DPD under isoenergetic conditions -can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style +can be specified by using fix *dpd/energy*, fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isoenthalpic conditions can -be specified by using fix *dpd/energy*\ , fix *nph* and pair_style +be specified by using fix *dpd/energy*, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the -examples/USER/dpd directory. +examples/PACKAGES/dpd-react directory. ---------- @@ -56,8 +56,8 @@ examples/USER/dpd directory. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix must be used with an additional fix that specifies time integration, e.g. :doc:`fix nve `. diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 29bbc92f78..ef1a70c3d4 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -77,8 +77,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MESODPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the DPD-MESO package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the :doc:`pair_style tdpd ` command. diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 6bf9b909c6..3bfc5420de 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -57,7 +57,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index a879f1594b..5300d1f490 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -22,7 +22,7 @@ Examples fix 1 all drude 1 1 0 1 0 2 2 2 fix 1 all drude C C N C N D D D -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 28d57306ea..bd63a411be 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -25,7 +25,7 @@ Examples fix 3 all drude/transform/direct fix 1 all drude/transform/inverse -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -152,7 +152,7 @@ temperatures of cores and Drude particles, in center-of-mass and relative coordinates, are calculated using :doc:`compute temp/drude ` In addition, if you want to use a barostat to simulate a system at -constant pressure, only one of the Nose-Hoover fixes must be *npt*\ , +constant pressure, only one of the Nose-Hoover fixes must be *npt*, the other one should be *nvt*\ . You must add a *compute temp/com* and a *fix_modify* command so that the temperature of the *npt* fix be just that of its group (the Drude cores) but the pressure be the overall diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index a413f8f60d..c3aa431e18 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -59,7 +59,7 @@ displace *Xmax* on the next integration step, as a function of its current velocity and force. Since performing this calculation exactly would require the solution to a quartic equation, a cheaper estimate is generated. The estimate is conservative in that the atom's -displacement is guaranteed not to exceed *Xmax*\ , though it may be +displacement is guaranteed not to exceed *Xmax*, though it may be smaller. In addition if the *emax* keyword is used, the specified *Emax* value @@ -72,7 +72,7 @@ across all atoms is computed. Then the *Tmin* and *Tmax* bounds are applied, if specified. If one (or both) is specified as NULL, it is not applied. -When the :doc:`run style ` is *respa*\ , this fix resets the +When the :doc:`run style ` is *respa*, this fix resets the outer loop (largest) timestep, which is the same timestep that the :doc:`timestep ` command sets. diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index 86dcda9bc5..7d958e0afe 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -42,7 +42,7 @@ external electric field. For charges, any of the 3 quantities defining the E-field components can be specified as an equal-style or atom-style -:doc:`variable `, namely *ex*\ , *ey*\ , *ez*\ . If the value is a +:doc:`variable `, namely *ex*, *ey*, *ez*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the E-field component. @@ -100,8 +100,8 @@ minimize the orientation of dipoles in an applied electric field. The *energy* keyword specifies the name of an atom-style :doc:`variable ` which is used to compute the energy of each -atom as function of its position. Like variables used for *ex*\ , -*ey*\ , *ez*\ , the energy variable is specified as v_name, where name +atom as function of its position. Like variables used for *ex*, +*ey*, *ez*, the energy variable is specified as v_name, where name is the variable name. Note that when the *energy* keyword is used during an energy @@ -169,8 +169,7 @@ the iteration count during the minimization. Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +None Related commands """""""""""""""" diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 2065ec5033..186ed7065e 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -92,7 +92,7 @@ The thermostatting force is given by where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle position to the respective reservoir. The quantity :math:`F_{\Gamma_{k(\mathbf r_i)}}` corresponds to the input parameter -*F*\ , which is the energy flux into the reservoir. Furthermore, +*F*, which is the energy flux into the reservoir. Furthermore, :math:`K_{\Gamma_{k(\mathbf r_i)}}` and :math:`v_{\Gamma_{k(\mathbf r_i)}}` denote the non-translational kinetic energy and the center of mass velocity of that reservoir. The thermostatting force does not affect @@ -176,7 +176,7 @@ Restrictions """""""""""" This fix is part of the RIGID package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 4533e0bbe9..fa0fc763f5 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -92,7 +92,7 @@ its velocity and :math:`S_e` is the stopping power of the ion. atomic subsystems with the two-temperature model (:doc:`fix_ttm `). At low velocities the electronic stopping is negligible. The electronic -friction is not applied to atoms whose kinetic energy is smaller than *Ecut*\ , +friction is not applied to atoms whose kinetic energy is smaller than *Ecut*, or smaller than the lowest energy value given in the table in *file*\ . Electronic stopping should be applied only when a projectile reaches bulk material. This fix scans neighbor list and excludes atoms with fewer than @@ -133,7 +133,7 @@ For example: 750 100 150 If an atom which would have electronic stopping applied to it has a -kinetic energy higher than the largest energy given in *file*\ , LAMMPS +kinetic energy higher than the largest energy given in *file*, LAMMPS will exit with an error message. The stopping power depends on the energy of the ion and the target @@ -153,7 +153,7 @@ atoms moving above some minimum cutoff velocity (i.e., kinetic energy). These coefficients can be determined by fitting a quadratic polynomial to electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple 'Ecut c1 c2' values can be provided for multi-species simulations in the order -of the atom types. There is an examples/USER/misc/electron_stopping/ directory, +of the atom types. There is an examples/PACKAGES/electron_stopping/ directory, which illustrates uses of this command. Details of this implementation are further described in :ref:`Stewart2018 ` and :ref:`Lee2020 `. @@ -175,7 +175,7 @@ on this fix. Restrictions """""""""""" -This pair style is part of the USER-MISC package. It is only enabled if +This pair style is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 5cbe0053ff..c43b5461b1 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -43,8 +43,8 @@ equation of state are possible. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index ad734c391a..bfb8ec2c3c 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -102,8 +102,8 @@ one that matches the specified keyword. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 56bde44d98..2e91b7dd88 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -48,9 +48,9 @@ computed according to the following relation: U_{i} = \displaystyle\sum_{j=1}^{m} c_{i,j}(u_{j} + \Delta H_{f,j}) + \frac{3k_{b}T}{2} + Nk_{b}T \\ where *m* is the number of species, :math:`c_{i,j}` is the -concentration of species *j* in particle *i*\ , :math:`u_j` is the +concentration of species *j* in particle *i*, :math:`u_j` is the internal energy of species j, :math:`\Delta H_{f,j} is the heat of -formation of species *j*\ , N is the number of molecules represented +formation of species *j*, N is the number of molecules represented by the coarse-grained particle, :math:`k_b` is the Boltzmann constant, and *T* is the temperature of the system. Additionally, it is possible to modify the concentration-dependent particle internal @@ -177,8 +177,8 @@ coefficient. In this case, the format of the file is as follows: Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index 5eae16b196..4fa888273c 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -41,14 +41,14 @@ fix group and within the specified region are counted. M of these are chosen at random and deleted. If there are less than M eligible particles, then all of them are deleted. -If the setting for the *molecule* keyword is *no*\ , then only single +If the setting for the *molecule* keyword is *no*, then only single atoms are deleted. In this case, you should insure you do not delete only a portion of a molecule (only some of its atoms), or LAMMPS will soon generate an error when it tries to find those atoms. LAMMPS will warn you if any of the atoms eligible for deletion have a non-zero molecule ID, but does not check for this at the time of deletion. -If the setting for the *molecule* keyword is *yes*\ , then when an atom +If the setting for the *molecule* keyword is *yes*, then when an atom is chosen for deletion, the entire molecule it is part of is deleted. The count of deleted atoms is incremented by the number of atoms in the molecule, which may make it exceed *M*\ . If the molecule ID of the @@ -89,8 +89,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +None Related commands """""""""""""""" diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index 938b798ddf..d251eb65e9 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -46,7 +46,7 @@ If mode is *pf/callback* then the fix will make a callback every The external program computes forces on atoms by setting values in an array owned by the fix. The fix then adds these forces to each atom in the group, once every *Napply* steps, similar to the way the :doc:`fix addforce ` command works. Note that if *Ncall* > -*Napply*\ , the force values produced by one callback will persist, and +*Napply*, the force values produced by one callback will persist, and be used multiple times to update atom forces. The callback function "foo" is invoked by the fix as: diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index 0bfdaf87c9..6058b0ed3e 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -110,8 +110,8 @@ In order to perform constant-pressure simulations please use :doc:`fix npt `, to avoid duplicate integration of the equations of motion. -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index e33fc0ac4a..c0a2216be3 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -72,8 +72,8 @@ fixes are not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Currently, it does not support :doc:`molecule templates `. diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 67a0218c9b..3697142a37 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -73,7 +73,7 @@ pressure correction is discussed and described in :ref:`(Strong) `. For a complete example including the considerations discussed -above, see the examples/USER/flow_gauss directory. +above, see the examples/PACKAGES/flow_gauss directory. .. note:: @@ -81,7 +81,7 @@ above, see the examples/USER/flow_gauss directory. velocities of the group-ID atoms are coupled to the velocities of other atoms in the simulation, the flux will not be conserved. For example, in a simulation with fluid atoms and harmonically constrained - wall atoms, if a single thermostat is applied to group *all*\ , the + wall atoms, if a single thermostat is applied to group *all*, the fluid atom velocities will be coupled to the wall atom velocities, and the flux will not be conserved. This issue can be avoided by thermostatting the fluid and wall groups separately. @@ -158,9 +158,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index a7370c7f44..ce79ce3caf 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -59,7 +59,7 @@ Restrictions """""""""""" This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. There can only be a single freeze fix defined. This is because other the :doc:`granular pair styles ` treat frozen particles diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 894e4ec4b1..9955390454 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -24,7 +24,7 @@ Syntax .. parsed-literal:: - keyword = *mol*\ , *region*\ , *maxangle*\ , *pressure*\ , *fugacity_coeff*, *full_energy*, *charge*\ , *group*\ , *grouptype*\ , *intra_energy*, *tfac_insert*, or *overlap_cutoff* + keyword = *mol*, *region*, *maxangle*, *pressure*, *fugacity_coeff*, *full_energy*, *charge*, *group*, *grouptype*, *intra_energy*, *tfac_insert*, or *overlap_cutoff* *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *mcmoves* values = Patomtrans Pmoltrans Pmolrotate @@ -208,8 +208,8 @@ their bonds or angles constrained via SHAKE, use the *shake* keyword, specifying as its value the ID of a separate :doc:`fix shake ` command which also appears in your input script. Optionally, users may specify the relative amounts of different MC -moves using the *mcmoves* keyword. The values *Patomtrans*\ , -*Pmoltrans*\ , *Pmolrotate* specify the average proportion of +moves using the *mcmoves* keyword. The values *Patomtrans*, +*Pmoltrans*, *Pmolrotate* specify the average proportion of atom translations, molecule translations, and molecule rotations, respectively. The values must be non-negative integers or real numbers, with at least one non-zero value. For example, (10,30,0) @@ -272,7 +272,7 @@ styles except *lj* it is defined as the thermal de Broglie wavelength \Lambda = \sqrt{ \frac{h^2}{2 \pi m k T}} where *h* is Planck's constant, and *m* is the mass of the exchanged atom -or molecule. For unit style *lj*\ , :math:`\Lambda` is simply set to +or molecule. For unit style *lj*, :math:`\Lambda` is simply set to unity. Note that prior to March 2017, :math:`\Lambda` for unit style *lj* was calculated using the above formula with *h* set to the rather specific value of 0.18292026. Chemical potential under the old definition can @@ -374,7 +374,7 @@ in the context of NVT dynamics. has been reached. With some pair_styles, such as :doc:`Buckingham `, -:doc:`Born-Mayer-Huggins ` and :doc:`ReaxFF `, two +:doc:`Born-Mayer-Huggins ` and :doc:`ReaxFF `, two atoms placed close to each other may have an arbitrary large, negative potential energy due to the functional form of the potential. While these unphysical configurations are inaccessible to typical dynamical @@ -451,6 +451,11 @@ When using fix gcmc in combination with fix shake or fix rigid, only GCMC exchange moves are supported, so the argument *M* must be zero. +When using fix gcmc in combination with fix rigid, deletion +of the last remaining molecule is not allowed for technical reasons, +and so the molecule count will never drop below 1, regardless of the +specified chemical potential. + Note that very lengthy simulations involving insertions/deletions of billions of gas molecules may run out of atom or molecule IDs and trigger an error, so it is better to run multiple shorter-duration diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index c47e30a880..d0fd6a4c9e 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -81,7 +81,7 @@ correlated random forces as specified in the third term of the force. Presently, the Prony series coefficients are limited to being greater than or equal to zero, and the time constants are limited to being greater than zero. To this end, the value of series MUST be set to -*pprony*\ , for now. Future updates will allow for negative coefficients +*pprony*, for now. Future updates will allow for negative coefficients and other representations of the memory kernel. It is with these updates in mind that the series option was included. @@ -107,7 +107,7 @@ The keyword/value option pairs are used in the following ways. The keyword *frozen* can be used to specify how the extended variables associated with the GLD memory kernel are initialized. Specifying no (the default), the initial values are drawn at random from an -equilibrium distribution at *Tstart*\ , consistent with the +equilibrium distribution at *Tstart*, consistent with the Fluctuation-Dissipation Theorem. Specifying yes, initializes the extended variables to zero. @@ -116,7 +116,7 @@ thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix applies a small random force to the entire system, and the center-of-mass of the system undergoes a slow random walk. If the -keyword *zero* is set to *yes*\ , the total random force is set exactly +keyword *zero* is set to *yes*, the total random force is set exactly to zero by subtracting off an equal part of it from each atom in the group. As a result, the center-of-mass of a system with zero initial momentum will not drift over time. @@ -146,8 +146,8 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index a341e0fa08..a42fddf7f5 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -63,7 +63,7 @@ un-correlated Gaussian random forces. The A matrix couples the physical and makes it possible to obtain effectively a history-dependent noise and friction kernel. -The drift matrix should be given as an external file *Afile*\ , +The drift matrix should be given as an external file *Afile*, as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are optimal for a given application and the system of choice can be obtained from :ref:`(GLE4MD) `. @@ -142,8 +142,8 @@ In order to perform constant-pressure simulations please use :doc:`fix npt `, to avoid duplicate integration of the equations of motion. -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index bd585b1312..7b0f7669ed 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -77,7 +77,7 @@ Style *vector* imposes an acceleration in the vector direction given by (x,y,z). Only the direction of the vector is important; it's length is ignored. For 2d systems, the *z* component is ignored. -Any of the quantities *magnitude*\ , *angle*\ , *phi*\ , *theta*\ , *x*\ , *y*\ , +Any of the quantities *magnitude*, *angle*, *phi*, *theta*, *x*, *y*, *z* which define the gravitational magnitude and direction, can be specified as an equal-style :doc:`variable `. If the value is a variable, it should be specified as v_name, where name is the diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 85702b909f..3e3ec02994 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -66,7 +66,7 @@ processors be on the order of the number of desired replicas. A 100-replica simulation would require at least 100 processors (1 per world at minimum). If many replicas are needed on a small number of processors, multi-replica runs can be run outside of LAMMPS. An -example of this can be found in examples/USER/misc/grem and has no +example of this can be found in examples/PACKAGES/grem and has no limit on the number of replicas per processor. However, this is very inefficient and error prone and should be avoided if possible. @@ -100,8 +100,8 @@ fix is "intensive". Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the REPLICA package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 06f068bb7d..d7f7f75515 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -54,7 +54,7 @@ dynamics or minimization iterations, as specified by the :doc:`run The specified group-ID is ignored by this fix. The specified *attribute* can be one of the options listed above, namely -*bondmax*, *tlimit*\ , *diskfree*\ , or an :doc:`equal-style variable +*bondmax*, *tlimit*, *diskfree*, or an :doc:`equal-style variable ` referenced as *v_name*, where "name" is the name of a variable that has been defined previously in the input script. @@ -138,16 +138,16 @@ The specified *avalue* must be a numeric value. ---------- The optional *error* keyword determines how the current run is halted. -If its value is *hard*\ , then LAMMPS will stop with an error message. +If its value is *hard*, then LAMMPS will stop with an error message. -If its value is *soft*\ , LAMMPS will exit the current run, but continue +If its value is *soft*, LAMMPS will exit the current run, but continue to execute subsequent commands in the input script. However, additional :doc:`run ` or :doc:`minimize ` commands will be skipped. For example, this allows a script to output the current state of the system, e.g. via a :doc:`write_dump ` or :doc:`write_restart ` command. -If its value is *continue*\ , the behavior is the same as for *soft*\ , +If its value is *continue*, the behavior is the same as for *soft*, except subsequent :doc:`run ` or :doc:`minimize ` commands are executed. This allows your script to remedy the condition that triggered the halt, if necessary. Note that you may wish use the diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 0b46616c5e..c8643b3b86 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -46,7 +46,7 @@ This can lead to a dramatic speed-up in the rate at which events occurs, without altering their relative frequencies, thus leading to an overall increase in the elapsed real time of the simulation as compared to running for the same number of timesteps with normal MD. -See the :doc:`hyper ` doc page for a more general discussion of +See the :doc:`hyper ` page for a more general discussion of hyperdynamics and citations that explain both GHD and LHD. The equations and logic used by this fix and described here to perform @@ -56,8 +56,8 @@ Fichthorn as described in :ref:`(Miron) `. In LAMMPS we use a simplified version of bond-boost GHD where a single bond in the system is biased at any one timestep. -Bonds are defined between each pair of atoms *ij*\ , whose :math:`R^0_{ij}` -distance is less than *cutbond*\ , when the system is in a quenched state +Bonds are defined between each pair of atoms *ij*, whose :math:`R^0_{ij}` +distance is less than *cutbond*, when the system is in a quenched state (minimum) energy. Note that these are not "bonds" in a covalent sense. A bond is simply any pair of atoms that meet the distance criterion. *Cutbond* is an argument to this fix; it is discussed @@ -70,7 +70,7 @@ The current strain of bond *ij* (when running dynamics) is defined as E_{ij} = \frac{R_{ij} - R^0_{ij}}{R^0_{ij}} -where :math:`R_{ij}` is the current distance between atoms *i* and *j*\ , +where :math:`R_{ij}` is the current distance between atoms *i* and *j*, and :math:`R^0_{ij}` is the equilibrium distance in the quenched state. The bias energy :math:`V_{ij}` of any bond between atoms *i* and *j* @@ -136,7 +136,7 @@ Note that in GHD, the boost factor varies from timestep to timestep. Likewise, which bond has :math:`E^{max}` strain and thus which pair of atoms the bias potential is added to, will also vary from timestep to timestep. This is in contrast to local hyperdynamics (LHD) where the boost -factor is an input parameter; see the :doc:`fix hyper/local ` doc page for details. +factor is an input parameter; see the :doc:`fix hyper/local ` page for details. ---------- @@ -192,7 +192,7 @@ beta term in the exponential factor that determines how much boost is achieved as a function of the bias potential. In general, the lower the value of *Tequil* and the higher the value -of *Vmax*\ , the more time boost will be achievable by the GHD +of *Vmax*, the more time boost will be achievable by the GHD algorithm. ---------- @@ -264,7 +264,7 @@ Restrictions """""""""""" This command can only be used if LAMMPS was built with the REPLICA -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 90238e0b4a..22de3bc3ca 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -61,7 +61,7 @@ This can lead to a dramatic speed-up in the rate at which events occurs, without altering their relative frequencies, thus leading to an overall increase in the elapsed real time of the simulation as compared to running for the same number of timesteps with normal MD. -See the :doc:`hyper ` doc page for a more general discussion of +See the :doc:`hyper ` page for a more general discussion of hyperdynamics and citations that explain both GHD and LHD. The equations and logic used by this fix and described here to perform @@ -139,7 +139,7 @@ to this fix. running constant-temperature (NVT) dynamics. LAMMPS does not check that this is done. -Note that if *ij*\ == *kl*\ , then bond *ij* is a biased bond on that +Note that if *ij*\ == *kl*, then bond *ij* is a biased bond on that timestep, otherwise it is not. But regardless, the boost factor :math:`B_{ij}` can be thought of an estimate of time boost currently being applied within a local region centered on bond *ij*. For LHD, @@ -162,15 +162,15 @@ Note that in LHD, the boost factor :math:`B_{target}` is specified by the user. This is in contrast to global hyperdynamics (GHD) where the boost factor varies each timestep and is computed as a function of :math:`V_{max}`, :math:`E_{max}`, and :math:`T_{equil}`; see the -:doc:`fix hyper/global ` doc page for details. +:doc:`fix hyper/global ` page for details. ---------- Here is additional information on the input parameters for LHD. -Note that the *cutbond*\ , *qfactor*\ , and *Tequil* arguments have the +Note that the *cutbond*, *qfactor*, and *Tequil* arguments have the same meaning as for GHD. The *Vmax* argument is slightly different. -The *Dcut*\ , *alpha*\ , and *Btarget* parameters are unique to LHD. +The *Dcut*, *alpha*, and *Btarget* parameters are unique to LHD. The *cutbond* argument is the cutoff distance for defining bonds between pairs of nearby atoms. A pair of I,J atoms in their @@ -310,7 +310,7 @@ Here is additional information on the optional keywords for this fix. The *bound* keyword turns on min/max bounds for bias coefficients :math:`C_{ij}` for all bonds. :math:`C_{ij}` is a prefactor for each bond on the bias potential of maximum strength :math:`V^{max}`. Depending on the -choice of *alpha* and *Btarget* and *Vmax*\ , the boostostatting can cause +choice of *alpha* and *Btarget* and *Vmax*, the boostostatting can cause individual :math:`C_{ij}` values to fluctuate. If the fluctuations are too large :math:`C_{ij} \cdot V^{max}` can exceed low barrier heights and induce bad event dynamics. Bounding the :math:`C_{ij}` values is a way to prevent @@ -326,7 +326,7 @@ The *reset* keyword allow *Vmax* to be adjusted dynamically depending on the average value of all :math:`C_{ij}` prefactors. This can be useful if you are unsure what value of *Vmax* will match the *Btarget* boost for the system. The :math:`C_{ij}` values will then adjust in aggregate (up or down) -so that :math:`C_{ij} \cdot V^{max}` produces a boost of *Btarget*\ , but this +so that :math:`C_{ij} \cdot V^{max}` produces a boost of *Btarget*, but this may conflict with the *bound* keyword settings. By using *bound* and *reset* together, :math:`V^{max}` itself can be reset, and desired bounds still applied to the :math:`C_{ij}` values. @@ -354,7 +354,7 @@ The *check/bias* keyword turns on extra computation and communication to check if any biased bonds are closer than *Dcut* to each other, which should not be the case if LHD is operating correctly. Thus it is a debugging check. The *Nevery* setting determines how often the -check is made. The *error*\ , *warn*\ , or *ignore* setting determines +check is made. The *error*, *warn*, or *ignore* setting determines what is done if the count of too-close bonds is not zero. Either the code will exit, or issue a warning, or silently tally the count. The count can be output as vector value 17, as described below. If this @@ -447,13 +447,13 @@ next event occurs they may move further than *Dcut* away from the sub-box boundary. Value 19 is the furthest (from the sub-box) any ghost atom in the neighbor list with maxstrain < *qfactor* was accessed during the run. Value 20 is the same except that the ghost -atom's maxstrain may be >= *qfactor*\ , which may mean it is about to +atom's maxstrain may be >= *qfactor*, which may mean it is about to participate in an event. Value 21 is a count of how many ghost atoms could not be found on reneighbor steps, presumably because they moved too far away due to their participation in an event (which will likely be detected at the next quench). -Typical values for 19 and 20 should be slightly larger than *Dcut*\ , +Typical values for 19 and 20 should be slightly larger than *Dcut*, which accounts for ghost atoms initially at a *Dcut* distance moving thermally before the next event takes place. diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 3b84ec6f72..004bc0b614 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -52,7 +52,7 @@ latencies for slow communication links. This feature has only been tested under linux. There are example scripts for using this package with LAMMPS in -examples/USER/imd. Additional examples and a driver for use with the +examples/PACKAGES/imd. Additional examples and a driver for use with the Novint Falcon game controller as haptic device can be found at: http://sites.google.com/site/akohlmey/software/vrpn-icms. @@ -78,7 +78,7 @@ fixes would be active at the same time, each needs to use a different port number. The *nowait* keyword controls the behavior of the fix when no IMD -client is connected. With the default setting of *off*\ , LAMMPS will +client is connected. With the default setting of *off*, LAMMPS will wait until a connection is made before continuing with the execution. Setting *nowait* to *on* will have the LAMMPS code be ready to connect to a client, but continue with the simulation. This can for @@ -149,8 +149,8 @@ fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MISC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index e9dab5141f..bb4b450c94 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -96,9 +96,9 @@ the plane's current position will feel no force. Vice versa if *side* is specified as *hi*\ . Any of the 4 quantities defining a spherical indenter's geometry can -be specified as an equal-style :doc:`variable `, namely *x*\ , -*y*\ , *z*\ , or *R*\ . Similarly, for a cylindrical indenter, any of *c1*\ , -*c2*\ , or *R*\ , can be a variable. For a planar indenter, *pos* can be +be specified as an equal-style :doc:`variable `, namely *x*, +*y*, *z*, or *R*\ . Similarly, for a cylindrical indenter, any of *c1*, +*c2*, or *R*, can be a variable. For a planar indenter, *pos* can be a variable. If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to define the @@ -139,10 +139,10 @@ rate. variable rate equal 1.0 variable r equal "v_r0 + step*dt*v_rate" -If the *side* keyword is specified as *out*\ , which is the default, +If the *side* keyword is specified as *out*, which is the default, then particles outside the indenter are pushed away from its outer surface, as described above. This only applies to spherical or -cylindrical indenters. If the *side* keyword is specified as *in*\ , +cylindrical indenters. If the *side* keyword is specified as *in*, the action of the indenter is reversed. Particles inside the indenter are pushed away from its inner surface. In other words, the indenter is now a containing wall that traps the particles inside it. If the @@ -160,7 +160,7 @@ cylindrical indenter is scaled by the x lattice spacing. Note that the units keyword only affects indenter geometry parameters specified directly with numbers, not those specified as variables. In -the latter case, you should use the *xlat*\ , *ylat*\ , *zlat* keywords of +the latter case, you should use the *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. @@ -168,7 +168,7 @@ The force constant *K* is not affected by the *units* keyword. It is always in force/distance\^2 units where force and distance are defined by the :doc:`units ` command. If you wish K to be scaled by the lattice spacing, you can define K with a variable whose formula -contains *xlat*\ , *ylat*\ , *zlat* keywords of the +contains *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style ` command, e.g. .. code-block:: LAMMPS diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 1d1ed795cd..bd4b4d84e8 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -14,8 +14,8 @@ Syntax * ipi = style name of this fix command * address = internet address (FQDN or IP), or UNIX socket name * port = port number (ignored for UNIX sockets) -* optional keyword = *unix*\ , if present uses a unix socket -* optional keyword = *reset*\ , if present reset electrostatics at each call +* optional keyword = *unix*, if present uses a unix socket +* optional keyword = *reset*, if present reset electrostatics at each call Examples """""""" @@ -36,7 +36,7 @@ following publication :ref:`(IPI-CPC) `. A version of the i-PI package, containing only files needed for use with LAMMPS, is provided in the tools/i-pi directory. See the tools/i-pi/manual.pdf for an introduction to i-PI. The -examples/USER/i-pi directory contains example scripts for using i-PI +examples/PACKAGES/i-pi directory contains example scripts for using i-PI with LAMMPS. In brief, the path integral molecular dynamics is performed by the @@ -84,10 +84,11 @@ coordinates are transferred. However, one could use this strategy to define an external potential acting on the atoms that are moved by i-PI. -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Because of the -use of UNIX domain sockets, this fix will only work in a UNIX -environment. +This fix is part of the MISC package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. +Because of the use of UNIX domain sockets, this fix will only +work in a UNIX environment. Related commands """""""""""""""" diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 918573fc6b..c8be9afc31 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -112,7 +112,7 @@ thermostatting takes place; see the description below. fix - e.g. by :doc:`fix nvt ` or :doc:`fix temp/rescale ` commands. -See the :doc:`Howto thermostat ` doc page for +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -239,7 +239,7 @@ thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix applies a small random force to the entire system, and the center-of-mass of the system undergoes a slow random walk. If the -keyword *zero* is set to *yes*\ , the total random force is set exactly +keyword *zero* is set to *yes*, the total random force is set exactly to zero by subtracting off an equal part of it from each atom in the group. As a result, the center-of-mass of a system with zero initial momentum will not drift over time. @@ -252,7 +252,7 @@ limit of the integrator), while still producing the correct Boltzmann distribution of atom positions. The current implementation provides the user with the option to output -the velocity in one of two forms: *vfull* or *vhalf*\ , which replaces +the velocity in one of two forms: *vfull* or *vhalf*, which replaces the outdated option *yes*\ . The *gjf* option *vfull* outputs the on-site velocity given in :ref:`Gronbech-Jensen/Farago `; this velocity is shown to be systematically lower @@ -291,8 +291,8 @@ this fix and by the compute should be the same. The cumulative energy change in the system imposed by this fix is included in the :doc:`thermodynamic output ` keywords -*ecouple* and *econserve*\ , but only if the *tally* keyword to set to -*yes*\ . See the :doc:`thermo_style ` doc page for +*ecouple* and *econserve*, but only if the *tally* keyword to set to +*yes*\ . See the :doc:`thermo_style ` page for details. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index c075a56549..3486723a67 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -35,7 +35,7 @@ Examples fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -100,7 +100,7 @@ transform: f = \frac m {M'}\, F' + f' This fix also thermostats non-polarizable atoms in the group at -temperature *Tcom*\ , as if they had a massless Drude partner. The +temperature *Tcom*, as if they had a massless Drude partner. The Drude particles themselves need not be in the group. The center of mass and the dipole are thermostatted iff the core atom is in the group. @@ -122,7 +122,7 @@ from them before thermostatting takes place; see the description below. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix temp/rescale ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -207,7 +207,7 @@ thermostat on centers of mass. Because the random forces on different centers of mass are independent, they do not sum exactly to zero. As a result, this fix applies a small random force to the entire system, and the momentum of the total center of mass of the system undergoes a -slow random walk. If the keyword *zero* is set to *yes*\ , the total +slow random walk. If the keyword *zero* is set to *yes*, the total random force on the centers of mass is set exactly to zero by subtracting off an equal part of it from each center of mass in the group. As a result, the total center of mass of a system with zero @@ -239,7 +239,7 @@ Comments: * *zero yes* avoids a drift of the center of mass of the system, but is a bit slower. * Use two different random seeds to avoid unphysical correlations. -* Temperature is controlled by the fix *langevin/drude*\ , so the +* Temperature is controlled by the fix *langevin/drude*, so the time-integration fixes do not thermostat. Don't forget to time-integrate both cores and Drude particles. * Pressure is time-integrated only once by using *nve* for Drude @@ -251,7 +251,7 @@ Comments: fix *npt* and :doc:`fix drude/transform `, the *fix_modify* command is not required here, because the fix *nph* computes the global pressure even if its group is *ATOMS*\ . This is - what we want. If we thermostatted *ATOMS* using *npt*\ , the pressure + what we want. If we thermostatted *ATOMS* using *npt*, the pressure should be the global one, but the temperature should be only that of the cores. That's why the command *fix_modify* should be called in that case. diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index c6fd1b0b40..506b5052d5 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -83,8 +83,8 @@ this fix and by the compute should be the same. The cumulative energy change in the system imposed by this fix is included in the :doc:`thermodynamic output ` keywords -*ecouple* and *econserve*\ , but only if the *tally* keyword to set to -*yes*\ . See the :doc:`thermo_style ` doc page for +*ecouple* and *econserve*, but only if the *tally* keyword to set to +*yes*\ . See the :doc:`thermo_style ` page for details. This fix computes a global scalar which can be accessed by various @@ -104,8 +104,8 @@ Restrictions """""""""""" none -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst index c73968df48..0926881eef 100644 --- a/doc/src/fix_langevin_spin.rst +++ b/doc/src/fix_langevin_spin.rst @@ -85,7 +85,7 @@ Restrictions """""""""""" The *langevin/spin* fix is part of the SPIN package. This style is -only enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with this package. See the :doc:`Build package ` page for more info. The numerical integration has to be performed with *fix nve/spin* when *fix langevin/spin* is enabled. diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index 58a8ddbe20..f75d44e3a4 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -153,7 +153,7 @@ Restrictions This fix is part of the LATTE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. You must use metal units, as set by the :doc:`units ` command to use this fix. @@ -171,7 +171,7 @@ doing 99% or more of the work to compute quantum-accurate forces. NEB calculations can be done using this fix using multiple replicas and running LAMMPS in parallel. However, each replica must be run on a single MPI task. For details, see the :doc:`neb ` - command doc page and the :doc:`-partition command-line switch ` + command page and the :doc:`-partition command-line switch ` Related commands """""""""""""""" diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index b2b85b8f5f..21d5d0cb84 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -210,7 +210,7 @@ By default, :math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1. However, the user has the option of specifying their own values for :math:`dm_{LB}`, and :math:`dx_{LB}`, by using -the optional keywords *dm*\ , and *dx* respectively. +the optional keywords *dm*, and *dx* respectively. .. note:: @@ -224,7 +224,7 @@ the optional keywords *dm*\ , and *dx* respectively. :math:`dx_{LB}` is used, this will automatically be satisfied. Physical parameters describing the fluid are specified through -*viscosity*\ , *density*\ , and *a0*\ . If the force coupling constant is +*viscosity*, *density*, and *a0*\ . If the force coupling constant is set the default way, the surface area associated with the MD particles is specified using the *setArea* keyword. If the user chooses to specify a value for the force coupling constant, this is set using the @@ -341,8 +341,8 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. This fix can only be used with an orthogonal simulation domain. diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 479f480e50..f967c1300a 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -46,7 +46,7 @@ and the fluid velocities at each lattice site. This fix only considers the linear momentum of the system. By default, the subtraction is performed for each dimension. This can -be changed by specifying the keyword *linear*\ , along with a set of +be changed by specifying the keyword *linear*, along with a set of three flags set to 0/1 in order to exclude/ include the corresponding dimension. @@ -66,8 +66,8 @@ Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this command. -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index c6f5048126..6ba3e72482 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -24,7 +24,7 @@ Description """"""""""" Update the positions and velocities of the individual particles -described by *group-ID*\ , experiencing velocity-dependent hydrodynamic +described by *group-ID*, experiencing velocity-dependent hydrodynamic forces, using the integration algorithm described in :ref:`Mackay et al. `. This integration algorithm should only be used if a user-specified value for the force-coupling constant used in :doc:`fix lb/fluid ` has been set; do not use this integration algorithm if the force coupling constant has been set by default. @@ -41,8 +41,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index b6a19c98d5..16e00ba12f 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -139,9 +139,9 @@ of the :doc:`run ` command. These fixes are not invoked during Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index da8922c92f..cd3712aac4 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -71,8 +71,8 @@ for details." Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 6d13fab7b8..2d72743707 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -48,8 +48,8 @@ the :doc:`run ` command. This fix is invoked during :doc:`energy minimizat Restrictions """""""""""" -This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MANIFOLD package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Only use this with *min_style hftn* or *min_style quickmin*. If not, the constraints will not be satisfied very well at all. A warning is diff --git a/doc/src/fix_mdi_engine.rst b/doc/src/fix_mdi_engine.rst index 76506f3e19..51a4545fd8 100644 --- a/doc/src/fix_mdi_engine.rst +++ b/doc/src/fix_mdi_engine.rst @@ -44,9 +44,9 @@ For more information about running LAMMPS as an MDI engine, see the Restrictions """""""""""" -This command is part of the USER-MDI package. It is only enabled if +This command is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index 06b0d16686..7b3609a8c7 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -125,7 +125,7 @@ notation as where *X0* = (x0,y0,z0) is their position at the time the fix is specified, *A* is the specified amplitude vector with components -(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time +(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. This style also sets the velocity of each particle to the time derivative of this expression. If any of the amplitude components is specified as NULL, then the @@ -150,7 +150,7 @@ The *rotate* style rotates particles around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The *period* of the rotation is also specified. The direction of rotation for the particles around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along *R*\ , then your fingers wrap +rule: if your right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. This style also sets the velocity of each particle to (omega cross @@ -238,9 +238,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-SDPD package. It is only enabled if +This fix is part of the DPD-SMOOTH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This fix requires that atoms store density and internal energy as defined by the :doc:`atom_style sph ` command. diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index a6bac6ac44..47080fcd58 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -85,7 +85,7 @@ appropriate fix. For most fixes that support the *energy* keyword, the default setting is *no*. For a few it is *yes*, when a user would expect - that to be the case. The doc page of each fix gives the default. + that to be the case. The page of each fix gives the default. The *virial* keyword can be used with fixes that support it, which is explained at the bottom of their doc page. *Virial yes* will add a @@ -110,7 +110,7 @@ option to include or exclude the contribution from fixes. For most fixes that support the *virial* keyword, the default setting is *no*. For a few it is *yes*, when a user would expect - that to be the case. The doc page of each fix gives the default. + that to be the case. The page of each fix gives the default. For fixes that set or modify forces, it may be possible to select at which :doc:`r-RESPA ` level the fix operates via the *respa* diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index 393a6a16cd..7d00a4c67b 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -97,9 +97,9 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" -Fix momentum/chunk is part of the USER-MISC package. It is only enabled +Fix momentum/chunk is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 7ede1f3050..5d3a9de47f 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -118,7 +118,7 @@ notation as where *X0* = (x0,y0,z0) is their position at the time the fix is specified, *A* is the specified amplitude vector with components -(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time +(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. This style also sets the velocity of each atom to the time derivative of this expression. If any of the amplitude components is specified as NULL, then the @@ -143,7 +143,7 @@ The *rotate* style rotates atoms around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The *period* of the rotation is also specified. The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: -if your right-hand thumb points along *R*\ , then your fingers wrap +if your right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. This style also sets the velocity of each atom to (omega cross Rperp) diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index fe32acdbd5..5e9bc520b5 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -93,8 +93,8 @@ for more info. ---------- The *range* keyword specifies which MS-CG library functionality should -be invoked. If *on*\ , the step 4 range finder functionality is invoked. -*off*\ , the step 5 force matching functionality is invoked. +be invoked. If *on*, the step 4 range finder functionality is invoked. +*off*, the step 5 force matching functionality is invoked. If the *name* keyword is used, string names are defined to associate with the integer atom types in LAMMPS. *Ntype* names must be diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index e3996776a1..9502fe21b8 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -71,7 +71,7 @@ kinetic energy at the start of the simulation. Setting this parameter to a non-zero value may assist in compression at the start of simulations where it is slow to occur. -If keywords *e0*\ , *p0*\ ,or *v0* are not supplied, these quantities will +If keywords *e0*, *p0*,or *v0* are not supplied, these quantities will be calculated on the first step, after the energy specified by *tscale* is removed. The value of *e0* is not used in the dynamical equations, but is used in calculating the deviation from the Hugoniot. @@ -112,7 +112,7 @@ new computes are the fix-ID + "_MSST_temp" or "MSST_press" or The *dftb* keyword is to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the -keyword *dftb* is used with a value of *yes*\ , then the MSST equations +keyword *dftb* is used with a value of *yes*, then the MSST equations are altered to account for the electron entropy contribution to the Hugonio relations and total energy. See :ref:`(Reed2) ` and :ref:`(Goldman) ` for details on this contribution. In this case, @@ -152,7 +152,7 @@ integration of the dynamic equations. The global vector contains four values in the following order. The vector values output by this fix are "intensive". -[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, +[\ *dhugoniot*, *drayleigh*, *lagrangian_speed*, *lagrangian_position*] 1. *dhugoniot* is the departure from the Hugoniot (temperature units). @@ -177,7 +177,7 @@ Restrictions This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The MSST fix has been tested only for the group-ID diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index d0df1bd0f9..efabab2183 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -90,8 +90,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MESODPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the DPD-MESO package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 848369d3ea..f319269220 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -89,14 +89,14 @@ first stage) is changed to: .. parsed-literal:: - Fi = -Grad(V) + 2 (Grad(V) dot T') T' + Fi = -Grad(V) + 2 (Grad(V) dot T') T' + Fnudge_perp and the relaxation procedure is continued to a new converged MEP. ---------- The keyword *parallel* specifies how the parallel nudging force is -computed. With a value of *neigh*\ , the parallel nudging force is +computed. With a value of *neigh*, the parallel nudging force is computed as in :ref:`(Henkelman1) ` by connecting each intermediate replica with the previous and the next image: @@ -107,7 +107,7 @@ intermediate replica with the previous and the next image: Note that in this case the specified *Kspring* is in force/distance units. -With a value of *ideal*\ , the spring force is computed as suggested in +With a value of *ideal*, the spring force is computed as suggested in ref`(WeinanE) ` .. parsed-literal:: @@ -151,7 +151,7 @@ force is added. By default, no additional forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their -respective local minima. By using the key word *end*\ , additional +respective local minima. By using the key word *end*, additional forces can be applied to the first and/or last replicas, to enable them to relax toward a MEP while constraining their energy E to the target energy ETarget. @@ -166,8 +166,8 @@ If ETarget>E, the interatomic force Fi for the specified replica becomes: The "spring" constant on the difference in energies is the specified *Kspring3* value. -When *estyle* is specified as *first*\ , the force is applied to the -first replica. When *estyle* is specified as *last*\ , the force is +When *estyle* is specified as *first*, the force is applied to the +first replica. When *estyle* is specified as *last*, the force is applied to the last replica. Note that the *end* keyword can be used twice to add forces to both the first and last replicas. @@ -175,13 +175,13 @@ For both these *estyle* settings, the target energy *ETarget* is set to the initial energy of the replica (at the start of the NEB calculation). -If the *estyle* is specified as *last/efirst* or *last/efirst/middle*\ , +If the *estyle* is specified as *last/efirst* or *last/efirst/middle*, force is applied to the last replica, but the target energy *ETarget* is continuously set to the energy of the first replica, as it evolves during the NEB relaxation. The difference between these two *estyle* options is as follows. When -*estyle* is specified as *last/efirst*\ , no change is made to the +*estyle* is specified as *last/efirst*, no change is made to the inter-replica force applied to the intermediate replicas (neither first or last). If the initial path is too far from the MEP, an intermediate replica may relax "faster" and reach a lower energy than @@ -195,7 +195,7 @@ than the first replica. This should effectively prevent the intermediate replicas from over-relaxing. After converging a NEB calculation using an *estyle* of -*last/efirst/middle*\ , you should check that all intermediate replicas +*last/efirst/middle*, you should check that all intermediate replicas have a larger energy than the first replica. If this is not the case, the path is probably not a MEP. diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index f40ce0c463..46b343fdce 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -104,7 +104,7 @@ addition to basic thermostatting and barostatting, these fixes can also create a chain of thermostats coupled to the particle thermostat, and another chain of thermostats coupled to the barostat variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the *xy*\ , *xz* and *yz* tilt +to individual dimensions, including the *xy*, *xz* and *yz* tilt dimensions. The external pressure of the barostat can be specified as either a scalar pressure (isobaric ensemble) or as components of a symmetric stress tensor (constant stress ensemble). When used @@ -124,7 +124,7 @@ integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. The thermostat parameters for fix styles *nvt* and *npt* are specified using the *temp* keyword. Other thermostat-related keywords are -*tchain*\ , *tloop* and *drag*\ , which are discussed below. +*tchain*, *tloop* and *drag*, which are discussed below. The thermostat is applied to only the translational degrees of freedom for the particles. The translational degrees of freedom can also have @@ -156,15 +156,15 @@ by the velocity/position update portion of the integration. ---------- The barostat parameters for fix styles *npt* and *nph* is specified -using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , -*xz*\ , *yz*\ , and *couple* keywords. These keywords give you the +using one or more of the *iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, +*xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure simulation. -Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , -*nreset*\ , *drag*\ , and *dilate*\ , which are discussed below. +Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *drag*, and *dilate*, which are discussed below. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable @@ -173,7 +173,7 @@ specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The target pressures for each of the 6 components of the stress tensor -can be specified independently via the *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz* +can be specified independently via the *x*, *y*, *z*, *xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . @@ -184,7 +184,7 @@ the *xy* keyword is used, the xy tilt factor will change. A box dimension will not change if that component is not specified, although you have the option to change that dimension via the :doc:`fix deform ` command. -Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the +Note that in order to use the *xy*, *xz*, or *yz* keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.0. @@ -253,13 +253,13 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. ---------- -The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. The keyword *iso* means couple all 3 diagonal components together when @@ -274,8 +274,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: @@ -287,7 +287,7 @@ these 4 keywords: z Pstart Pstop Pdamp couple none -The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions are controlled independently using their individual stress components as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Pstart Pstop Pdamp" is the same as @@ -352,7 +352,7 @@ specified values of the external stress tensor. A value of *nstep* means that every *nstep* timesteps, the reference dimensions are set to those of the current simulation domain. -The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when barostatting triclinic periodic cells. The default values *yes* will turn on scaling, which corresponds to adjusting the @@ -365,9 +365,9 @@ scale keywords to *no*\ . The *flip* keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed -below. If the *flip* value is set to *yes*\ , the bound is enforced by +below. If the *flip* value is set to *yes*, the bound is enforced by flipping the box when it is exceeded. If the *flip* value is set to -*no*\ , the tilt will continue to change without flipping. Note that if +*no*, the tilt will continue to change without flipping. Note that if applied stress induces large deformations (e.g. in a liquid), this means the box shape can tilt dramatically and LAMMPS will run less efficiently, due to the large volume of communication needed to @@ -379,7 +379,7 @@ The *fixedpoint* keyword specifies the fixed point for barostat volume changes. By default, it is the center of the box. Whatever point is chosen will not move during the simulation. For example, if the lower periodic boundaries pass through (0,0,0), and this point is provided -to *fixedpoint*\ , then the lower periodic boundaries will remain at +to *fixedpoint*, then the lower periodic boundaries will remain at (0,0,0), while the upper periodic boundaries will move twice as far. In all cases, the particle trajectories are unaffected by the chosen value, except for a time-dependent constant translation of @@ -402,7 +402,7 @@ at only a small additional computational cost. .. note:: - Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can + Using a barostat coupled to tilt dimensions *xy*, *xz*, *yz* can sometimes result in arbitrarily large values of the tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS allows the tilt factors to grow a small amount beyond the normal limit of half the box @@ -410,7 +410,7 @@ at only a small additional computational cost. an equivalent periodic cell. See the discussion of the *flip* keyword above, to allow this bound to be exceeded, if desired. -The flip operation is described in more detail in the doc page for +The flip operation is described in more detail in the page for :doc:`fix deform `. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on @@ -504,7 +504,7 @@ thermal degrees of freedom, and the bias is added back in. These fixes can be used with either the *verlet* or *respa* :doc:`integrators `. When using one of the barostat fixes -with *respa*\ , LAMMPS uses an integrator constructed +with *respa*, LAMMPS uses an integrator constructed according to the following factorization of the Liouville propagator (for two rRESPA levels): @@ -557,7 +557,7 @@ of the underlying non-Hamiltonian equations of motion. The fix npt and fix nph commands can be used with rigid bodies or mixtures of rigid bodies and non-rigid particles (e.g. solvent). But there are also :doc:`fix rigid/npt ` and :doc:`fix rigid/nph ` commands, which are typically a more natural -choice. See the doc page for those commands for more discussion of +choice. See the page for those commands for more discussion of the various ways to do this. ---------- @@ -599,7 +599,7 @@ compute temperature on a subset of atoms. The cumulative energy change in the system imposed by these fixes, via either thermostatting and/or barostatting, is included in the :doc:`thermodynamic output ` keywords *ecouple* and -*econserve*. See the :doc:`thermo_style ` doc page for +*econserve*. See the :doc:`thermo_style ` page for details. These fixes compute a global scalar which can be accessed by various @@ -613,7 +613,7 @@ vector values are "intensive". The vector stores internal Nose/Hoover thermostat and barostat variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords *tchain* and *pchain*\ , +which fix is used and the settings for keywords *tchain* and *pchain*, which specify the number of Nose/Hoover chains for the thermostat and barostat. If no thermostatting is done, then *tchain* is 0. If no barostatting is done, then *pchain* is 0. In the following list, @@ -653,10 +653,10 @@ These fixes are not invoked during :doc:`energy minimization `. Restrictions """""""""""" -*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not -periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the simulation domain is triclinic and the second dimension in the keyword -(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be +(\ *y* dimension in *xy*\ ) is periodic. *Z*, *xz*, and *yz*, cannot be barostatted for 2D simulations. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or @@ -668,10 +668,10 @@ make the external T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used -for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . These fixes can be used with dynamic groups as defined by the :doc:`group ` command. Likewise they can be used with groups to diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 3e54ed9765..11990d365b 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -68,7 +68,7 @@ domain dimensions (barostatting). In addition to basic thermostatting and barostatting, these fixes can also create a chain of thermostats coupled to the particle thermostat, and another chain of thermostats coupled to the barostat variables. The barostat can be coupled to the -overall box volume, or to individual dimensions, including the *xy*\ , +overall box volume, or to individual dimensions, including the *xy*, *xz* and *yz* tilt dimensions. The external pressure of the barostat can be specified as either a scalar pressure (isobaric ensemble) or as components of a symmetric stress tensor (constant stress ensemble). @@ -110,16 +110,16 @@ to the temperature or kinetic energy from the electron radial velocity. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -See the doc page for the :doc:`fix nvt, npt, and nph ` commands +See the page for the :doc:`fix nvt, npt, and nph ` commands for details. Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph ` commands also apply. +Other restriction discussed on the page for the :doc:`fix nvt, npt, and nph ` commands also apply. .. note:: diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 74e61472c6..b51e232a3c 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -16,7 +16,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style_name = *nvt/uef* or *npt/uef* -* *Tstart*\ , *Tstop*\ , and *Tdamp* are documented in the :doc:`fix npt ` command +* *Tstart*, *Tstop*, and *Tdamp* are documented in the :doc:`fix npt ` command * *edot_x* and *edot_y* are the strain rates in the x and y directions (1/(time units)) * one or more keyword/value pairs may be appended @@ -27,7 +27,7 @@ Syntax sets the external dimensions used to calculate the scalar pressure *strain* values = e_x e_y = initial strain usually not needed, but may be needed to resume a run with a data file. - *iso*\ , *x*\ , *y*\ , *z*\ , *tchain*\ , *pchain*\ , *tloop*\ , *ploop*\ , *mtk* keywords + *iso*, *x*, *y*, *z*, *tchain*, *pchain*, *tloop*, *ploop*, *mtk* keywords documented by the :doc:`fix npt ` command Examples @@ -111,7 +111,7 @@ pressure using this fix. The first method involves using the *ext* keyword along with the *iso* pressure style. With this method, the pressure is controlled by scaling the simulation box isotropically to achieve the average pressure only in the directions specified by -*ext*\ . For example, if the *ext* value is set to *xy*\ , the average +*ext*\ . For example, if the *ext* value is set to *xy*, the average pressure (Pxx+Pyy)/2 will be controlled. This example command will control the total hydrostatic pressure under @@ -130,7 +130,7 @@ drawing with uniaxial tension: fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy The second method for pressure control involves setting the normal -stresses using the *x*\ , *y* , and/or *z* keywords. When using this +stresses using the *x*, *y*, and/or *z* keywords. When using this method, the same pressure must be specified via *Pstart* and *Pstop* for all dimensions controlled. Any choice of pressure conditions that would cause LAMMPS to compute a deviatoric stress are not permissible @@ -199,8 +199,8 @@ The fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the UEF package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Due to requirements of the boundary conditions, when the *strain* keyword is set to zero (or unset), the initial simulation box must be diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 011630a534..a1028efacc 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -41,7 +41,7 @@ point particles and only updates their position and velocity. Additional parameters affecting the barostat are specified by keywords and values documented with the :doc:`fix nph ` command. See, -for example, discussion of the *aniso*\ , and *dilate* keywords. +for example, discussion of the *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -50,7 +50,7 @@ NPH integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -120,7 +120,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index 4c91d28588..1b740a5ae2 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -38,7 +38,7 @@ point particles and only updates their position and velocity. Additional parameters affecting the barostat are specified by keywords and values documented with the :doc:`fix nph ` command. See, -for example, discussion of the *aniso*\ , and *dilate* keywords. +for example, discussion of the *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -47,7 +47,7 @@ NPH integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -117,7 +117,7 @@ Restrictions """""""""""" This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style body ` diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index 6062faa50e..2ef85953e5 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -54,7 +54,7 @@ moment of inertia, as used in the time integration. Additional parameters affecting the barostat are specified by keywords and values documented with the :doc:`fix nph ` command. See, -for example, discussion of the *aniso*\ , and *dilate* keywords. +for example, discussion of the *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -63,7 +63,7 @@ NPH integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index 776b3e4849..b45cfe964f 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -63,8 +63,8 @@ jump conditions for steady shocks. The compression can be performed either -hydrostatically (using keyword *iso*\ , *aniso*\ , or *tri*\ ) or uniaxially -(using keywords *x*\ , *y*\ , or *z*\ ). In the hydrostatic case, +hydrostatically (using keyword *iso*, *aniso*, or *tri*\ ) or uniaxially +(using keywords *x*, *y*, or *z*\ ). In the hydrostatic case, the cell dimensions change dynamically so that the average axial stress in all three directions converges towards the specified target value. In the uniaxial case, the chosen cell dimension changes dynamically @@ -74,10 +74,10 @@ other two cell dimensions are kept fixed (zero lateral strain). This leads to the following additional restrictions on the keywords: -* One and only one of the following keywords should be used: *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z* +* One and only one of the following keywords should be used: *iso*, *aniso*, *tri*, *x*, *y*, *z* * The specified initial and final target pressures must be the same. -* The keywords *xy*\ , *xz*\ , *yz* may not be used. -* The only admissible value for the couple keyword is *xyz*\ , which has the same effect as keyword *iso* +* The keywords *xy*, *xz*, *yz* may not be used. +* The only admissible value for the couple keyword is *xyz*, which has the same effect as keyword *iso* * The *temp* keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored. Essentially, a Hugoniostat simulation is an NPT simulation in which the @@ -100,8 +100,8 @@ When the system reaches a stable equilibrium, the value of :math:`\Delta` should fluctuate about zero. The values of :math:`E_0`, :math:`V_0`, and :math:`P_0` are the instantaneous values at the start of -the simulation. These can be overridden using the fix_modify keywords *e0*\ , -*v0*\ , and *p0* described below. +the simulation. These can be overridden using the fix_modify keywords *e0*, +*v0*, and *p0* described below. ---------- @@ -159,7 +159,7 @@ as well as the state of all the thermostat and barostat variables to script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix_modify ` *e0*\ , *v0* and *p0* keywords can be +The :doc:`fix_modify ` *e0*, *v0* and *p0* keywords can be used to define the values of :math:`E_0`, :math:`V_0`, and :math:`P_0`. Note the the values for *e0* and *v0* are extensive, and so must correspond to the total energy and volume of the entire system, not @@ -205,7 +205,7 @@ Restrictions This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. All the usual restrictions for :doc:`fix npt ` apply, plus the additional ones mentioned above. diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index f65ecd8d19..28edb59f8d 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -48,8 +48,8 @@ can also have a bias velocity removed from them before thermostatting takes place; see the description below. Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*\ , -*iso*\ , *aniso*\ , and *dilate* keywords. +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -58,7 +58,7 @@ NPT integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -143,7 +143,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index af0a0fb252..d44870a4fb 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -46,8 +46,8 @@ takes place; see the description below. Additional parameters affecting the thermostat and barostat are specified by keywords and values documented with the :doc:`fix npt -` command. See, for example, discussion of the *temp*\ , -*iso*\ , *aniso*\ , and *dilate* keywords. +` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -56,7 +56,7 @@ NPT integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -141,7 +141,7 @@ Restrictions """""""""""" This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style body ` diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 8ef74b25c9..13b5b7bf70 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -73,7 +73,7 @@ addition to basic thermostatting and barostatting, this fix can also create a chain of thermostats coupled to the particle thermostat, and another chain of thermostats coupled to the barostat variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the *xy*\ , *xz* and *yz* tilt +to individual dimensions, including the *xy*, *xz* and *yz* tilt dimensions. The external pressure of the barostat can be specified as either a scalar pressure (isobaric ensemble) or as components of a symmetric stress tensor (constant stress ensemble). When used @@ -92,7 +92,7 @@ integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. ---------- The thermostat parameters are specified using the *temp* keyword. -Other thermostat-related keywords are *tchain*\ , *tloop* and *drag*\ , +Other thermostat-related keywords are *tchain*, *tloop* and *drag*, which are discussed below. The thermostat is applied to only the translational degrees of freedom @@ -118,15 +118,15 @@ by the velocity/position update portion of the integration. ---------- -The barostat parameters are specified using one or more of the *iso*\ , -*aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* keywords. +The barostat parameters are specified using one or more of the *iso*, +*aniso*, *tri*, *x*, *y*, *z*, *xy*, *xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure simulation. -Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , -*nreset*\ , *drag*\ , and *dilate*\ , which are discussed below. +Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *drag*, and *dilate*, which are discussed below. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable @@ -135,7 +135,7 @@ specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The target pressures for each of the 6 components of the stress tensor -can be specified independently via the *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz* +can be specified independently via the *x*, *y*, *z*, *xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . @@ -146,7 +146,7 @@ the *xy* keyword is used, the xy tilt factor will change. A box dimension will not change if that component is not specified, although you have the option to change that dimension via the :doc:`fix deform ` command. -Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the +Note that in order to use the *xy*, *xz*, or *yz* keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.0. @@ -193,13 +193,13 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. ---------- -The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. The keyword *iso* means couple all 3 diagonal components together when @@ -214,8 +214,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: @@ -227,7 +227,7 @@ these 4 keywords: z Pstart Pstop Pdamp couple none -The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions are controlled independently using their individual stress components as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Pstart Pstop Pdamp" is the same as @@ -292,7 +292,7 @@ specified values of the external stress tensor. A value of *nstep* means that every *nstep* timesteps, the reference dimensions are set to those of the current simulation domain. -The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when barostatting triclinic periodic cells. The default values *yes* will turn on scaling, which corresponds to adjusting the @@ -305,9 +305,9 @@ scale keywords to *no*\ . The *flip* keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed -below. If the *flip* value is set to *yes*\ , the bound is enforced by +below. If the *flip* value is set to *yes*, the bound is enforced by flipping the box when it is exceeded. If the *flip* value is set to -*no*\ , the tilt will continue to change without flipping. Note that if +*no*, the tilt will continue to change without flipping. Note that if applied stress induces large deformations (e.g. in a liquid), this means the box shape can tilt dramatically and LAMMPS will run less efficiently, due to the large volume of communication needed to @@ -319,7 +319,7 @@ The *fixedpoint* keyword specifies the fixed point for barostat volume changes. By default, it is the center of the box. Whatever point is chosen will not move during the simulation. For example, if the lower periodic boundaries pass through (0,0,0), and this point is provided -to *fixedpoint*\ , then the lower periodic boundaries will remain at +to *fixedpoint*, then the lower periodic boundaries will remain at (0,0,0), while the upper periodic boundaries will move twice as far. In all cases, the particle trajectories are unaffected by the chosen value, except for a time-dependent constant translation of @@ -329,7 +329,7 @@ positions. .. note:: - Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can + Using a barostat coupled to tilt dimensions *xy*, *xz*, *yz* can sometimes result in arbitrarily large values of the tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS allows the tilt factors to grow a small amount beyond the normal limit of half the box @@ -337,7 +337,7 @@ positions. an equivalent periodic cell. See the discussion of the *flip* keyword above, to allow this bound to be exceeded, if desired. -The flip operation is described in more detail in the doc page for +The flip operation is described in more detail in the page for :doc:`fix deform `. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on @@ -418,7 +418,7 @@ thermal degrees of freedom, and the bias is added back in. This fix can be used with either the *verlet* or *respa* :doc:`integrators `. When using this fix -with *respa*\ , LAMMPS uses an integrator constructed +with *respa*, LAMMPS uses an integrator constructed according to the following factorization of the Liouville propagator (for two rRESPA levels): @@ -500,7 +500,7 @@ compute temperature on a subset of atoms. The cumulative energy change in the system imposed by this fix, due to thermostatting and/or barostatting, is included in the :doc:`thermodynamic output ` keywords *ecouple* and -*econserve*. See the :doc:`thermo_style ` doc page for +*econserve*. See the :doc:`thermo_style ` page for details. This fix computes a global scalar which can be accessed by various @@ -514,7 +514,7 @@ values are "intensive". The vector stores internal Nose/Hoover thermostat and barostat variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords *tchain* and *pchain*\ , +which fix is used and the settings for keywords *tchain* and *pchain*, which specify the number of Nose/Hoover chains for the thermostat and barostat. If no thermostatting is done, then *tchain* is 0. If no barostatting is done, then *pchain* is 0. In the following list, @@ -554,13 +554,13 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not -periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the simulation domain is triclinic and the second dimension in the keyword -(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be +(\ *y* dimension in *xy*\ ) is periodic. *Z*, *xz*, and *yz*, cannot be barostatted for 2D simulations. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or @@ -572,10 +572,10 @@ make the external T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used -for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . The *alpha* keyword modifies the barostat as per Miller et al. (Miller)_"#nc-Miller" so that the Cauchy stress is controlled. diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index dd78cebbf1..75e4c9a4ec 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -61,8 +61,8 @@ The only difference between discs and spheres in this context is their moment of inertia, as used in the time integration. Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*\ , -*iso*\ , *aniso*\ , and *dilate* keywords. +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -71,7 +71,7 @@ NPT integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst index 22c1c59748..b0686f471f 100644 --- a/doc/src/fix_numdiff.rst +++ b/doc/src/fix_numdiff.rst @@ -101,7 +101,9 @@ minimization `. Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index ae472b1a38..da2184c99f 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -29,10 +29,11 @@ Examples Description """"""""""" -Perform constant NVE integration to update position and velocity for -atoms in the group each timestep. V is volume; E is energy. This -creates a system trajectory consistent with the microcanonical -ensemble. +Perform plain time integration to update position and velocity for +atoms in the group each timestep. This creates a system trajectory +consistent with the microcanonical ensemble (NVE) provided there +are (full) periodic boundary conditions and no other "manipulations" +of the system (e.g. fixes that modify forces or velocities). ---------- diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index c49de34d0b..fbba2bc8dd 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index 6bc4b98c7f..7d904bef1c 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -48,7 +48,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index b112aacd60..c716a94a84 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -45,8 +45,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-AWPMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the AWPMD package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index 7a763e7d42..45beee0659 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -26,7 +26,7 @@ Description Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See the :doc:`Howto body ` doc page for more details on using body +consistent with the microcanonical ensemble. See the :doc:`Howto body ` page for more details on using body particles. This fix differs from the :doc:`fix nve ` command, which @@ -45,7 +45,7 @@ Restrictions """""""""""" This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style body ` diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index ac60b40f47..0a99e11452 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -36,9 +36,9 @@ in a NVE ensemble prior to using the Langevin-type DOTC-integrator The command is equivalent to the :doc:`fix nve `. The particles are always considered to have a finite size. -An example input file can be found in /examples/USER/cgdna/examples/duplex1/. +An example input file can be found in /examples/PACKAGES/cgdna/examples/duplex1/. Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) `. -The preprint version of the article can be found `here `_. +The preprint version of the article can be found `here `_. ---------- @@ -46,8 +46,8 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -:ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. -See the :doc:`Build package ` doc page for more info. +:ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 4ffead3f25..c2835aaccd 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -120,9 +120,9 @@ freedom in addition to the usual translational degrees of freedom. The scale factor after the *angmom* keyword gives the ratio of the rotational to the translational friction coefficient. -An example input file can be found in examples/USER/cgdna/examples/duplex2/. +An example input file can be found in examples/PACKAGES/cgdna/examples/duplex2/. Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) `. -The preprint version of the article can be found `here `_. +The preprint version of the article can be found `here `_. ---------- @@ -130,8 +130,8 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -:ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. -See the :doc:`Build package ` doc page for more info. +:ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index 2c14bb07a9..60bece43d0 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -42,8 +42,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index b65c543529..5bb6fd4213 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -26,7 +26,7 @@ Description Perform constant NVE integration to update position, velocity, orientation, and angular velocity for line segment particles in the group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See :doc:`Howto spherical ` doc page for an overview of using line +trajectory consistent with the microcanonical ensemble. See :doc:`Howto spherical ` page for an overview of using line segment particles. This fix differs from the :doc:`fix nve ` command, which @@ -45,7 +45,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that particles be line segments as defined by the :doc:`atom_style line ` command. diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index b24277a8c7..a9bf07de60 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -83,8 +83,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MANIFOLD package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index 167da24475..ed13123403 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -48,7 +48,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index 143ddb2426..e35647aef4 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This fix style can only be used if LAMMPS was built with the SPIN -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. To use the spin algorithm, it is necessary to define a map with diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index ad4376e8ec..b511d9b318 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -27,7 +27,7 @@ Perform constant NVE integration to update position, velocity, orientation, and angular momentum for triangular particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. See the -:doc:`Howto spherical ` doc page for an overview of +:doc:`Howto spherical ` page for an overview of using triangular particles. This fix differs from the :doc:`fix nve ` command, which @@ -46,7 +46,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that particles be triangles as defined by the :doc:`atom_style tri ` command. diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index 6226635010..0d83a4b1be 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -56,8 +56,9 @@ the simulation box. Therefore, the group must be set to all. This fix has not yet been implemented to work with the RESPA integrator. -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 98e8a5b495..00f4588f7f 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -121,7 +121,7 @@ Restrictions """""""""""" This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index 02b7d0c66c..28ad3e7857 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -118,7 +118,7 @@ Restrictions """""""""""" This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the :doc:`atom_style body ` diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index f822df5b8d..fe889bda79 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -63,8 +63,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MANIFOLD package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index e07e990d4b..7500735054 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -69,8 +69,8 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix works best without Nose-Hoover chain thermostats, i.e. using tchain = 1. Setting tchain to larger values can result in poor diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 180a394ba0..f54cc42ed0 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -50,7 +50,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 3397261552..68522209b7 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -177,11 +177,11 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS +These fixes are part of the ORIENT package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. -This fix should only be used with fcc or bcc lattices. +These fixes should only be used with fcc or bcc lattices. Related commands """""""""""""""" diff --git a/doc/src/fix_orient_eco.rst b/doc/src/fix_orient_eco.rst index 1db83338d4..b2fc71f1f7 100644 --- a/doc/src/fix_orient_eco.rst +++ b/doc/src/fix_orient_eco.rst @@ -122,9 +122,9 @@ the run command. This fix is not invoked during energy minimization. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the ORIENT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands diff --git a/doc/src/fix_pafi.rst b/doc/src/fix_pafi.rst index 8f1d02ac49..c8830316a2 100644 --- a/doc/src/fix_pafi.rst +++ b/doc/src/fix_pafi.rst @@ -45,7 +45,7 @@ projection is also calculated, whose time integral can be shown to be equal to the true free energy gradient along the minimum free energy path local to the reference pathway. A detailed discussion of the projection technique can be found in :ref:`(Swinburne) `. -This fix can be used with LAMMPS as demonstrated in examples/USER/misc/pafi, +This fix can be used with LAMMPS as demonstrated in examples/PACKAGES/pafi, though it is primarily intended to be coupled with the PAFI C++ code, developed at `https://github.com/tomswinburne/pafi `_, which distributes multiple LAMMPS workers in parallel to compute and collate @@ -84,8 +84,8 @@ This fix produces a global vector each timestep which can be accessed by various Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Default diff --git a/doc/src/fix_pair_tracker.rst b/doc/src/fix_pair_tracker.rst new file mode 100644 index 0000000000..5c2ecf5774 --- /dev/null +++ b/doc/src/fix_pair_tracker.rst @@ -0,0 +1,124 @@ +.. index:: fix pair/tracker + +fix pair/tracker command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID pair/tracker N attribute1 attribute2 ... keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* pair/tracker = style name of this fix command +* N = prepare data for output every this many timesteps +* one or more attributes may be appended + + .. parsed-literal:: + + possible attributes = id1 id2 time/created time/broken time/total + rmin rave x y z + + .. parsed-literal:: + + id1, id2 = IDs of the 2 atoms in each pair interaction + time/created = the time that the 2 atoms began interacting + time/broken = the time that the 2 atoms stopped interacting + time/total = the total time the 2 atoms interacted + r/min = the minimum radial distance between the 2 atoms during the interaction + r/ave = the average radial distance between the 2 atoms during the interaction + x, y, z = the center of mass position of the 2 atoms when they stopped interacting + +* zero or more keyword/value pairs may be appended +* keyword = *time/min* or *type/include* + + .. parsed-literal:: + + *time/min* value = T + T = minimum interaction time + *type/include* value = arg1 arg2 + arg = separate lists of types (see below) + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all pair/tracker 1000 id1 id2 time/min 100 + fix 1 all pair/tracker 1000 time/created time/broken type/include 1 * type/include 2 3,4 + +Description +""""""""""" + +Tracks properties of pairwise interactions between two atoms and records data +whenever the atoms move beyond the interaction cutoff. +Must be used in conjunction with :doc:`pair tracker `. +Data is accumulated over a span of *N* timesteps before being deleted. +The number of datums generated, aggregated across all processors, equals +the number of broken interactions. Interactions are only included if both +atoms are included in the specified fix group. Additional filters can be +applied using the *time/min* or *type/include* keywords described below. + +.. note:: + + For extremely long-lived interactions, the calculation of *r/ave* may not be + correct due to double overflow. + +The *time/min* keyword sets a minimum amount of time that an interaction must +persist to be included. This setting can be used to censor short-lived interactions. +The *type/include* keyword filters interactions based on the types of the two atoms. +Data is only saved for interactions between atoms with types in the two lists. +Each list consists of a series of type +ranges separated by commas. The range can be specified as a +single numeric value, or a wildcard asterisk can be used to specify a range +of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For +example, if M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M +(inclusive). A middle asterisk means all types from m to n (inclusive). +Multiple *type/include* keywords may be added. + +---------- + +Restart, fix_modify, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. +None of the :doc:`fix_modify ` options are +relevant to this fix. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +Output info +""""""""""" + +This compute calculates a local vector or local array depending on the +number of input values. The length of the vector or number of rows in +the array is the number of recorded, lost interactions. If a single input is +specified, a local vector is produced. If two or more inputs are +specified, a local array is produced where the number of columns = the +number of inputs. The vector or array can be accessed by any command +that uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output +options. + +The vector or array values will be doubles that correspond to the +specified attribute. + +Restrictions +"""""""""""" + +Must be used in conjunction with :doc:`pair style tracker `. + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`pair tracker ` + +Default +""""""" + +none diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index b30037ade7..d1b19173ce 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -138,7 +138,7 @@ code, `latgen `_, can be employed to generate the compatible map file for various crystals. In case one simulates a non-periodic system, where the whole simulation -box is treated as a unit cell, one can set *map_file* as *GAMMA*\ , so +box is treated as a unit cell, one can set *map_file* as *GAMMA*, so that the mapping info will be generated internally and a file is not needed. In this case, the dynamical matrix at only the gamma-point will/can be evaluated. Please keep in mind that fix-phonon is designed @@ -181,10 +181,10 @@ This fix assumes a crystalline system with periodical lattice. The temperature of the system should not exceed the melting temperature to keep the system in its solid state. -This fix is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the PHONON package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings ` doc page for details. +This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings ` page for details. Related commands """""""""""""""" @@ -204,19 +204,19 @@ the :doc:`dimension ` command, and nasr = 20. **(Campana)** C. Campana and M. H. Muser, *Practical Green's function approach to the -simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ +simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) `_ .. _Kong: **(Kong)** L.T. Kong, G. Bartels, C. Campana, C. Denniston, and Martin H. Muser, *Implementation of Green's -function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). `_ +function molecular dynamics: An extension to LAMMPS*, `Computer Physics Communications [180](6):1004-1010 (2009). `_ L.T. Kong, C. Denniston, and Martin H. Muser, *An improved version of the Green's function molecular dynamics -method*\ , `Computer Physics Communications [182](2):540-541 (2011). `_ +method*, `Computer Physics Communications [182](2):540-541 (2011). `_ .. _Kong2011: **(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from -molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). `_ +molecular dynamics simulations*, `Computer Physics Communications [182](10):2201-2207, (2011). `_ diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 5bc7b75c90..9735284280 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -152,8 +152,9 @@ related tasks for each of the partitions, e.g. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the REPLICA package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. A PIMD simulation can be initialized with a single data file read via the :doc:`read_data ` command. However, this means all diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index bd2c05adfe..c562ecc81d 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -41,10 +41,10 @@ and when PLUMED is used as a stand alone code for analysis. The full `documentation for PLUMED `_ is available online and included in the PLUMED source code. The PLUMED library development is hosted at `https://github.com/plumed/plumed2 `_ -A detailed discussion of the code can be found in :ref:`(PLUMED) `. +A detailed discussion of the code can be found in :ref:`(Tribello) `. There is an example input for using this package with LAMMPS in the -examples/USER/plumed directory. +examples/PACKAGES/plumed directory. ---------- @@ -113,9 +113,9 @@ are native to PLUMED. Restrictions """""""""""" -This fix is part of the USER-PLUMED package. It is only enabled if +This fix is part of the PLUMED package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. There can only be one fix plumed command active at a time. @@ -132,9 +132,9 @@ The default options are plumedfile = NULL and outfile = NULL ---------- -.. _PLUMED: +.. _Tribello: -**(PLUMED)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) +**(Tribello)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) .. _plumeddocs: https://www.plumed.org/doc.html diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index b782b7809e..7ecb4eef7d 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -57,14 +57,14 @@ Each body must have a non-degenerate inertia tensor, which means if must contain at least 3 non-collinear atoms. Which atoms are in which bodies can be defined via several options. -For option *group*\ , each of the listed groups is treated as a rigid +For option *group*, each of the listed groups is treated as a rigid body. Note that only atoms that are also in the fix group are included in each rigid body. -For option *molecule*\ , each set of atoms in the group with a different +For option *molecule*, each set of atoms in the group with a different molecule ID is treated as a rigid body. -For option *file*\ , sets of atoms are read from the specified file and +For option *file*, sets of atoms are read from the specified file and each set is treated as a rigid body. Each line of the file specifies a rigid body in the following format: @@ -136,7 +136,7 @@ Restrictions This fix is part of the :ref:`POEMS ` package. It is only enabled if LAMMPS was built with that package, which also requires the POEMS library be built and linked with LAMMPS. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst index 2c499fce3c..e130d3010d 100644 --- a/doc/src/fix_polarize.rst +++ b/doc/src/fix_polarize.rst @@ -29,9 +29,17 @@ Examples .. code-block:: LAMMPS - fix 2 all polarize/bem/gmres 5 0.0001 + fix 2 interface polarize/bem/gmres 5 0.0001 fix 1 interface polarize/bem/icc 1 0.0001 - fix 3 all polarize/functional 1 0.001 + fix 3 interface polarize/functional 1 0.001 + + +Used in input scripts: + + .. parsed-literal:: + + examples/PACKAGES/dielectric/in.confined + examples/PACKAGES/dielectric/in.nopbc Description """"""""""" @@ -40,7 +48,7 @@ These fixes compute induced charges at the interface between two impermeable media with different dielectric constants. There are some example scripts for using this fix -with LAMMPS in the examples/USER/dielectric directory. +with LAMMPS in the examples/PACKAGES/dielectric directory. ---------- @@ -77,10 +85,10 @@ Restart, fix_modify, output, run start/stop, minimize info Restrictions """""""""""" -These fixes are part of the USER-DIELECTRIC package. It is only enabled +These fixes are part of the DIELECTRIC package. It is only enabled if LAMMPS was built with that package, which requires that also the KSPACE package is installed. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 7757191482..742648ac76 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -158,10 +158,10 @@ many timesteps until the desired # of particles has been inserted. All other keywords are optional with defaults as shown below. The *diam* option is only used when inserting atoms and specifies the -diameters of inserted particles. There are 3 styles: *one*\ , *range*\ , -or *poly*\ . For *one*\ , all particles will have diameter *D*\ . For -*range*\ , the diameter of each particle will be chosen randomly and -uniformly between the specified *Dlo* and *Dhi* bounds. For *poly*\ , a +diameters of inserted particles. There are 3 styles: *one*, *range*, +or *poly*\ . For *one*, all particles will have diameter *D*\ . For +*range*, the diameter of each particle will be chosen randomly and +uniformly between the specified *Dlo* and *Dhi* bounds. For *poly*, a series of *Npoly* diameters is specified. For each diameter a percentage value from 0.0 to 1.0 is also specified. The *Npoly* percentages must sum to 1.0. For the example shown above with "diam 2 @@ -252,7 +252,7 @@ Restrictions """""""""""" This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. For 3d simulations, a gravity fix in the -z direction must be defined for use in conjunction with this fix. For 2d simulations, gravity diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 6a563bc32f..36a10c8ce6 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -175,7 +175,7 @@ Restrictions The *precession/spin* style is part of the SPIN package. This style is only enabled if LAMMPS was built with this package, and if the atom_style "spin" was declared. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index eb7adafc57..6d92a00178 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -46,7 +46,7 @@ timestep. Regardless of what atoms are in the fix group, a global pressure is computed for all atoms. Similarly, when the size of the simulation box is changed, all atoms are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the atoms in the fix group are re-scaled. The latter can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -61,13 +61,13 @@ unchanged and controlling the pressure of a surrounding fluid. atoms. This fix can be used in conjunction with thermostatting fixes to control the temperature, such as :doc:`fix nvt ` or :doc:`fix langevin ` or :doc:`fix temp/berendsen `. -See the :doc:`Howto baroostat ` doc page for a +See the :doc:`Howto baroostat ` page for a discussion of different ways to perform barostatting. ---------- -The barostat is specified using one or more of the *iso*\ , *aniso*\ , -*x*\ , *y*\ , *z*\ , and *couple* keywords. These keywords give you the +The barostat is specified using one or more of the *iso*, *aniso*, +*x*, *y*, *z*, and *couple* keywords. These keywords give you the ability to specify the 3 diagonal components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a @@ -77,7 +77,7 @@ constant-pressure simulation. Unlike the :doc:`fix npt ` and general pressure tensor. The target pressures for each of the 3 diagonal components of the -stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ , +stress tensor can be specified independently via the *x*, *y*, *z*, keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . @@ -131,7 +131,7 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. @@ -152,8 +152,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index ddc96817f9..863d43b6f2 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -146,9 +146,9 @@ Restrictions """""""""""" With keyword *dipole*, this fix only works when the DIPOLE package is enabled. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. -This fix is part of the USER-BROWNIAN package. It is only enabled if +This fix is part of the BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 0768c59ac8..8ac19af25d 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -56,7 +56,7 @@ is read. This fix will augment the set of properties with new custom ones. This can be useful in several scenarios. If the atom style does not define molecule IDs, per-atom charge, -or per-atom mass, they can be added using the *mol*\ , *q* or *rmass* +or per-atom mass, they can be added using the *mol*, *q* or *rmass* keywords. This can be useful, e.g, to define "molecules" to use as rigid bodies with the :doc:`fix rigid ` command, or just to carry around an extra flag with the atoms (stored as a molecule ID) @@ -80,7 +80,7 @@ and second, it may define additional properties that are not needed such as bond lists, which has some overhead when there are no bonds. In the future, we may add additional per-atom properties similar to -*mol*\ , *q* or *rmass*\ , which "turn-on" specific properties defined +*mol*, *q* or *rmass*, which "turn-on" specific properties defined by some atom styles, so they can be used by atom styles that do not define them. @@ -108,7 +108,7 @@ new properties are also defined for the ghost atoms. .. admonition:: Properties on ghost atoms :class: note - If you use this command with the *mol*\ , *q* or *rmass* vectors, + If you use this command with the *mol*, *q* or *rmass* vectors, then you most likely want to set *ghost* yes, since these properties are stored with ghost atoms if you use an :doc:`atom_style ` that defines them, and many LAMMPS operations that use molecule IDs or diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 94bad11f00..c82fb91a27 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -70,7 +70,7 @@ Restrictions """""""""""" This fix is part of the PYTHON package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Building LAMMPS with the PYTHON package will link LAMMPS with the Python library on your system. Settings to enable this are in the diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index 15014ef4fe..b338dcbfac 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -95,7 +95,7 @@ Restrictions """""""""""" This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index ef820a68d6..5428eeb637 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -100,10 +100,10 @@ command :doc:`fix qtb ` at constant temperature *T_init* could be used before applying this command to introduce self-consistent quantum nuclear effects into the initial state. -The parameters *q*\ , *mu*\ , *e0*\ , *p0*\ , *v0* and *tscale* are described -in the command :doc:`fix msst `. The values of *e0*\ , *p0*\ , or +The parameters *q*, *mu*, *e0*, *p0*, *v0* and *tscale* are described +in the command :doc:`fix msst `. The values of *e0*, *p0*, or *v0* will be calculated on the first step if not specified. The -parameter of *damp*\ , *f_max*, and *N_f* are described in the command +parameter of *damp*, *f_max*, and *N_f* are described in the command :doc:`fix qtb `. The *fix qbmsst* command couples the shock system to a quantum thermal @@ -152,8 +152,8 @@ Because the state of the random number generator is not written to "exactly" in an uninterrupted fashion. However, in a statistical sense, a restarted simulation should produce similar behaviors of the system as if it is not interrupted. To achieve such a restart, one -should write explicitly the same value for *q*\ , *mu*\ , *damp*\ , -*f_max*, *N_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system +should write explicitly the same value for *q*, *mu*, *damp*, +*f_max*, *N_f*, *eta*, and *beta* and set *tscale* = 0 if the system is compressed during the first run. The cumulative energy change in the system imposed by this fix is @@ -177,7 +177,7 @@ integration of the dynamic equations. The global vector contains five values in the following order. The vector values output by this fix are "intensive". -[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*, +[\ *dhugoniot*, *drayleigh*, *lagrangian_speed*, *lagrangian_position*, *quantum_temperature*] 1. *dhugoniot* is the departure from the Hugoniot (temperature units). @@ -208,9 +208,9 @@ It is worth noting that the temp keyword for the :doc:`thermo_style Restrictions """""""""""" -This fix style is part of the USER-QTB package. It is only enabled if +This fix style is part of the QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The QBMSST fix has been tested only for the group-ID diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index c655076ce8..eab35391b5 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -32,15 +32,16 @@ Syntax * cutoff = global cutoff for charge-charge interactions (distance unit) * tolerance = precision to which charges will be equilibrated * maxiter = maximum iterations to perform charge equilibration -* qfile = a filename with QEq parameters or *coul/streitz* or *reax/c* +* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff* * zero or more keyword/value pairs may be appended -* keyword = *alpha* or *qdamp* or *qstep* +* keyword = *alpha* or *qdamp* or *qstep* or *warn* .. parsed-literal:: *alpha* value = Slater type orbital exponent (qeq/slater only) *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only) *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only) + *warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached Examples """""""" @@ -90,19 +91,19 @@ on the current atom configuration), then remove the fix via the The :doc:`fix qeq/comb ` command must still be used to perform charge equilibration with the :doc:`COMB potential - `. The :doc:`fix qeq/reax ` command can be + `. The :doc:`fix qeq/reaxff ` command can be used to perform charge equilibration with the :doc:`ReaxFF force - field `, although fix qeq/shielded yields the same - results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* - are the same. Eventually the fix qeq/reax command will be + field `, although fix qeq/shielded yields the same + results as fix qeq/reaxff if *Nevery*, *cutoff*, and *tolerance* + are the same. Eventually the fix qeq/reaxff command will be deprecated. The QEq method minimizes the electrostatic energy of the system (or equalizes the derivative of energy with respect to charge of all the atoms) by adjusting the partial charge on individual atoms based on interactions with their neighbors within *cutoff*\ . It requires a few -parameters, in *metal* units, for each atom type which provided in a -file specified by *qfile*\ . The file has the following format +parameters in the appropriate units for each atom type which are read +from a file specified by *qfile*\ . The file has the following format .. parsed-literal:: @@ -112,7 +113,7 @@ file specified by *qfile*\ . The file has the following format Ntype chi eta gamma zeta qcore There have to be parameters given for every atom type. Wildcard entries -are possible using the same syntax as elsewhere in LAMMPS +are possible using the same type range syntax as for "coeff" commands (i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones. Empty lines or any text following the pound sign (#) are ignored. Each line starts with the atom type followed by five parameters. @@ -126,6 +127,14 @@ entries per line are required. * *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire ` potential in reverse distance units * *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential ` potential in charge units +The fix qeq styles will print a warning if the charges are not +equilibrated within *tolerance* by *maxiter* steps, unless the +*warn* keyword is used with "no" as argument. This latter option +may be useful for testing and benchmarking purposes, as it allows +to use a fixed number of QEq iterations when *tolerance* is set +to a small enough value to always reach the *maxiter* limit. Turning +off warnings will avoid the excessive output in that case. + The *qeq/point* style describes partial charges on atoms as point charges. Interaction between a pair of charged particles is 1/r, which is the simplest description of the interaction between charges. @@ -141,11 +150,11 @@ interaction between a pair of charged particles. Interaction through the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same -as :doc:`fix qeq/reax `, and can be used with -:doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and +as :doc:`fix qeq/reaxff `, and can be used with +:doc:`pair_style reaxff `. Only the *chi*, *eta*, and *gamma* parameters from the *qfile* file are used. When using the string -*reax/c* as filename, these parameters are extracted directly from an -active *reax/c* pair style. This style solves partial charges on atoms +*reaxff* as filename, these parameters are extracted directly from an +active *reaxff* pair style. This style solves partial charges on atoms via the matrix inversion method. A tolerance of 1.0e-6 is usually a good number. @@ -154,7 +163,7 @@ charge densities centered around atoms via the Slater 1\ *s* orbital, so that the interaction between a pair of charged particles is the product of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s* orbital is given under equation (6) of the :ref:`Streitz-Mintmire -` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore* +` paper. Only the *chi*, *eta*, *zeta*, and *qcore* parameters from the *qfile* file are used. When using the string *coul/streitz* as filename, these parameters are extracted directly from an active *coul/streitz* pair style. This style solves partial charges @@ -177,16 +186,16 @@ minimization algorithm to solve for equilibrium charges. Keyword *qdamp* can be used to change the damping factor, while keyword *qstep* can be used to change the time step size. -Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe +Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe different charge models, whereas the matrix inversion method and the extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are different solvers. -Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all +Note that *qeq/point*, *qeq/dynamic* and *qeq/fire* styles all describe charges as point charges that interact through 1/r relationship, but solve partial charges on atoms using different solvers. These three styles should yield comparable results if the QEq -parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same. +parameters and *Nevery*, *cutoff*, and *tolerance* are the same. Style *qeq/point* is typically faster, *qeq/dynamic* scales better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . @@ -219,17 +228,19 @@ Restrictions These fixes are part of the QEQ package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. + +The qeq fixes are not compatible with the GPU and USER-INTEL packages. Related commands """""""""""""""" -:doc:`fix qeq/reax `, :doc:`fix qeq/comb ` +:doc:`fix qeq/reaxff `, :doc:`fix qeq/comb ` Default """"""" -none +warn yes ---------- diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index 74a97720dc..8eeea6c5b4 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -41,7 +41,7 @@ Perform charge equilibration (QeQ) in conjunction with the COMB equilibration portion of the calculation using the so-called QEq method, whereby the charge on each atom is adjusted to minimize the energy of the system. This fix can only be used with the COMB -potential; see the :doc:`fix qeq/reax ` command for a QeQ +potential; see the :doc:`fix qeq/reaxff ` command for a QeQ calculation that can be used with any potential. Only charges on the atoms in the specified group are equilibrated. diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst deleted file mode 100644 index 8752888c4c..0000000000 --- a/doc/src/fix_qeq_reax.rst +++ /dev/null @@ -1,131 +0,0 @@ -.. index:: fix qeq/reax -.. index:: fix qeq/reax/kk -.. index:: fix qeq/reax/omp - -fix qeq/reax command -==================== - -Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp* - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args - -* ID, group-ID are documented in :doc:`fix ` command -* qeq/reax = style name of this fix command -* Nevery = perform QEq every this many steps -* cutlo,cuthi = lo and hi cutoff for Taper radius -* tolerance = precision to which charges will be equilibrated -* params = reax/c or a filename -* one or more keywords or keyword/value pairs may be appended - - .. parsed-literal:: - - keyword = *dual* or *maxiter* - *dual* = process S and T matrix in parallel (only for qeq/reax/omp) - *maxiter* N = limit the number of iterations to *N* - - -Examples -"""""""" - -.. code-block:: LAMMPS - - fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c - fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq maxiter 500 - -Description -""""""""""" - -Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) `. It is -typically used in conjunction with the ReaxFF force field model as -implemented in the :doc:`pair_style reax/c ` command, but -it can be used with any potential in LAMMPS, so long as it defines and -uses charges on each atom. The :doc:`fix qeq/comb ` -command should be used to perform charge equilibration with the :doc:`COMB potential `. For more technical details about the -charge equilibration performed by fix qeq/reax, see the -:ref:`(Aktulga) ` paper. - -The QEq method minimizes the electrostatic energy of the system by -adjusting the partial charge on individual atoms based on interactions -with their neighbors. It requires some parameters for each atom type. -If the *params* setting above is the word "reax/c", then these are -extracted from the :doc:`pair_style reax/c ` command and -the ReaxFF force field file it reads in. If a file name is specified -for *params*\ , then the parameters are taken from the specified file -and the file must contain one line for each atom type. The latter -form must be used when performing QeQ with a non-ReaxFF potential. -Each line should be formatted as follows: - -.. parsed-literal:: - - itype chi eta gamma - -where *itype* is the atom type from 1 to Ntypes, *chi* denotes the -electronegativity in eV, *eta* denotes the self-Coulomb -potential in eV, and *gamma* denotes the valence orbital -exponent. Note that these 3 quantities are also in the ReaxFF -potential file, except that eta is defined here as twice the eta value -in the ReaxFF file. Note that unlike the rest of LAMMPS, the units -of this fix are hard-coded to be A, eV, and electronic charge. - -The optional *dual* keyword allows to perform the optimization -of the S and T matrices in parallel. This is only supported for -the *qeq/reax/omp* style. Otherwise they are processed separately. - -The optional *maxiter* keyword allows changing the max number -of iterations in the linear solver. The default value is 200. - -Restart, fix_modify, output, run start/stop, minimize info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -No information about this fix is written to :doc:`binary restart files `. No global scalar or vector or per-atom -quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used -with the *start/stop* keywords of the :doc:`run ` command. - -This fix is invoked during :doc:`energy minimization `. - ----------- - -.. include:: accel_styles.rst - ----------- - -Restrictions -"""""""""""" - -This fix is part of the USER-REAXC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - -This fix does not correctly handle interactions -involving multiple periodic images of the same atom. Hence, it should not -be used for periodic cell dimensions less than 10 angstroms. - -Related commands -"""""""""""""""" - -:doc:`pair_style reax/c ` - -Default -""""""" - -maxiter 200 - ----------- - -.. _Rappe2: - -**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95, -3358-3363 (1991). - -.. _Nakano2: - -**(Nakano)** Nakano, Computer Physics Communications, 104, 59-69 (1997). - -.. _qeq-Aktulga: - -**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, -245-259 (2012). diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst new file mode 100644 index 0000000000..ada9e22ed7 --- /dev/null +++ b/doc/src/fix_qeq_reaxff.rst @@ -0,0 +1,143 @@ +.. index:: fix qeq/reaxff +.. index:: fix qeq/reaxff/kk +.. index:: fix qeq/reaxff/omp + +fix qeq/reaxff command +====================== + +Accelerator Variants: *qeq/reaxff/kk*, *qeq/reaxff/omp* + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID qeq/reaxff Nevery cutlo cuthi tolerance params args + +* ID, group-ID are documented in :doc:`fix ` command +* qeq/reaxff = style name of this fix command +* Nevery = perform QEq every this many steps +* cutlo,cuthi = lo and hi cutoff for Taper radius +* tolerance = precision to which charges will be equilibrated +* params = reaxff or a filename +* one or more keywords or keyword/value pairs may be appended + + .. parsed-literal:: + + keyword = *dual* or *maxiter* or *nowarn* + *dual* = process S and T matrix in parallel (only for qeq/reaxff/omp) + *maxiter* N = limit the number of iterations to *N* + *nowarn* = do not print a warning message if the maximum number of iterations was reached + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff + fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq maxiter 500 + +Description +""""""""""" + +Perform the charge equilibration (QEq) method as described in +:ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) +`. It is typically used in conjunction with the ReaxFF force +field model as implemented in the :doc:`pair_style reaxff ` +command, but it can be used with any potential in LAMMPS, so long as it +defines and uses charges on each atom. The :doc:`fix qeq/comb +` command should be used to perform charge equilibration +with the :doc:`COMB potential `. For more technical details +about the charge equilibration performed by fix qeq/reaxff, see the +:ref:`(Aktulga) ` paper. + +The QEq method minimizes the electrostatic energy of the system by +adjusting the partial charge on individual atoms based on interactions +with their neighbors. It requires some parameters for each atom type. +If the *params* setting above is the word "reaxff", then these are +extracted from the :doc:`pair_style reaxff ` command and +the ReaxFF force field file it reads in. If a file name is specified +for *params*, then the parameters are taken from the specified file +and the file must contain one line for each atom type. The latter +form must be used when performing QeQ with a non-ReaxFF potential. +Each line should be formatted as follows: + +.. parsed-literal:: + + itype chi eta gamma + +where *itype* is the atom type from 1 to Ntypes, *chi* denotes the +electronegativity in eV, *eta* denotes the self-Coulomb +potential in eV, and *gamma* denotes the valence orbital +exponent. Note that these 3 quantities are also in the ReaxFF +potential file, except that eta is defined here as twice the eta value +in the ReaxFF file. Note that unlike the rest of LAMMPS, the units +of this fix are hard-coded to be A, eV, and electronic charge. + +The optional *dual* keyword allows to perform the optimization +of the S and T matrices in parallel. This is only supported for +the *qeq/reaxff/omp* style. Otherwise they are processed separately. + +The optional *maxiter* keyword allows changing the max number +of iterations in the linear solver. The default value is 200. + +The optional *nowarn* keyword silences the warning message printed +when the maximum number of iterations was reached. This can be +useful for comparing serial and parallel results where having the +same fixed number of QEq iterations is desired, which can be achieved +by using a very small tolerance and setting *maxiter* to the desired +number of iterations. + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files +`. This fix computes a global scalar (the number of +iterations) for access by various :doc:`output commands `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +This fix is invoked during :doc:`energy minimization `. + +---------- + +.. include:: accel_styles.rst + +---------- + +Restrictions +"""""""""""" + +This fix is part of the REAXFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +This fix does not correctly handle interactions involving multiple +periodic images of the same atom. Hence, it should not be used for +periodic cell dimensions less than 10 angstroms. + +Related commands +"""""""""""""""" + +:doc:`pair_style reaxff `, :doc:`fix qeq/shielded ` + +Default +""""""" + +maxiter 200 + +---------- + +.. _Rappe2: + +**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95, +3358-3363 (1991). + +.. _Nakano2: + +**(Nakano)** Nakano, Computer Physics Communications, 104, 59-69 (1997). + +.. _qeq-Aktulga: + +**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, +245-259 (2012). diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index 81bb315e23..a62bd5ab1e 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -54,9 +54,9 @@ fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-QMMM package. It is only enabled if +This fix is part of the QMMM package. It is only enabled if LAMMPS was built with that package. It also requires building a -library provided with LAMMPS. See the :doc:`Build package ` doc page for more info. +library provided with LAMMPS. See the :doc:`Build package ` page for more info. The fix is only functional when LAMMPS is built as a library and linked with a compatible QM program and a QM/MM front end into a QM/MM diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 594b8b78a7..e6975748c4 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -161,9 +161,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix style is part of the USER-QTB package. It is only enabled if +This fix style is part of the QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. ---------- diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxff_bonds.rst similarity index 74% rename from doc/src/fix_reaxc_bonds.rst rename to doc/src/fix_reaxff_bonds.rst index 2d0d2d18db..15b2eb6da9 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxff_bonds.rst @@ -1,17 +1,17 @@ -.. index:: fix reax/c/bonds -.. index:: fix reax/c/bonds/kk +.. index:: fix reaxff/bonds +.. index:: fix reaxff/bonds/kk -fix reax/c/bonds command +fix reaxff/bonds command ======================== -Accelerator Variants: *reax/c/bonds/kk* +Accelerator Variants: *reaxff/bonds/kk* Syntax """""" .. parsed-literal:: - fix ID group-ID reaxc/bonds Nevery filename + fix ID group-ID reaxff/bonds Nevery filename * ID, group-ID are documented in :doc:`fix ` command * reax/bonds = style name of this fix command @@ -23,17 +23,17 @@ Examples .. code-block:: LAMMPS - fix 1 all reax/c/bonds 100 bonds.reaxc + fix 1 all reaxff/bonds 100 bonds.reaxff Description """"""""""" Write out the bond information computed by the ReaxFF potential specified -by :doc:`pair_style reax/c ` in the exact same format as the +by :doc:`pair_style reaxff ` in the exact same format as the original stand-alone ReaxFF code of Adri van Duin. The bond information -is written to *filename* on timesteps that are multiples of *Nevery*\ , +is written to *filename* on timesteps that are multiples of *Nevery*, including timestep 0. For time-averaged chemical species analysis, -please see the :doc:`fix reaxc/c/species ` command. +please see the :doc:`fix reaxff/species ` command. The specified group-ID is ignored by this fix. @@ -76,9 +76,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -The fix reax/c/bonds command requires that the :doc:`pair_style reax/c ` is invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more +The fix reaxff/bonds command requires that the :doc:`pair_style reaxff ` is invoked. This fix is part of the +REAXFF package. It is only enabled if LAMMPS was built with that +package. See the :doc:`Build package ` page for more info. To write gzipped bond files, you must compile LAMMPS with the @@ -87,7 +87,7 @@ To write gzipped bond files, you must compile LAMMPS with the Related commands """""""""""""""" -:doc:`pair_style reax/c `, :doc:`fix reax/c/species ` +:doc:`pair_style reaxff `, :doc:`fix reaxff/species ` Default """"""" diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxff_species.rst similarity index 73% rename from doc/src/fix_reaxc_species.rst rename to doc/src/fix_reaxff_species.rst index 9935ecaa3a..434e18d8a5 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxff_species.rst @@ -1,20 +1,20 @@ -.. index:: fix reax/c/species -.. index:: fix reax/c/species/kk +.. index:: fix reaxff/species +.. index:: fix reaxff/species/kk -fix reax/c/species command +fix reaxff/species command ========================== -Accelerator Variants: *reax/c/species/kk* +Accelerator Variants: *reaxff/species/kk* Syntax """""" .. parsed-literal:: - fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... + fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* reax/c/species = style name of this command +* reaxff/species = style name of this command * Nevery = sample bond-order every this many timesteps * Nrepeat = # of bond-order samples used for calculating averages * Nfreq = calculate average bond-order every this many timesteps @@ -37,15 +37,15 @@ Examples .. code-block:: LAMMPS - fix 1 all reax/c/species 10 10 100 species.out - fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55 - fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos + fix 1 all reaxff/species 10 10 100 species.out + fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55 + fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos Description """"""""""" Write out the chemical species information computed by the ReaxFF -potential specified by :doc:`pair_style reax/c `. +potential specified by :doc:`pair_style reaxff `. Bond-order values (either averaged or instantaneous, depending on value of *Nrepeat*\ ) are used to determine chemical bonds. Every *Nfreq* timesteps, chemical species information is written to @@ -73,7 +73,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these symbols should be chosen to match the chemical identity of each LAMMPS atom type, as -specified using the :doc:`reax/c pair_coeff ` command and +specified using the :doc:`reaxff pair_coeff ` command and the ReaxFF force field file. The optional keyword *position* writes center-of-mass positions of @@ -87,15 +87,15 @@ chemical formula, total charge, and center-of-mass xyz positions of this molecule. The xyz positions are in fractional coordinates relative to the box dimensions. -For the keyword *position*\ , the *filepos* is the name of the output +For the keyword *position*, the *filepos* is the name of the output file. It can contain the wildcard character "\*". If the "\*" -character appears in *filepos*\ , then one file per snapshot is written +character appears in *filepos*, then one file per snapshot is written at *posfreq* and the "\*" character is replaced with the timestep value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the bond-order values are sampled to get the average bond order. The species analysis is performed using the average bond-order on timesteps that are a multiple of *Nfreq*\ . The average is over @@ -115,12 +115,12 @@ average bond-order for the species analysis output on timestep 100. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. +No information about this fix is written to :doc:`binary restart files `. +None of the :doc:`fix_modify ` options are relevant to this fix. -This fix computes both a global vector of length 2 and a per-atom -vector, either of which can be accessed by various :doc:`output commands `. The values in the global vector are -"intensive". +This fix computes both a global vector of length 2 and a per-atom vector, +either of which can be accessed by various :doc:`output commands `. +The values in the global vector are "intensive". The 2 values in the global vector are as follows: @@ -134,7 +134,8 @@ will be the same and will be equal to the smallest atom ID of any atom in the molecule. No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. ---------- @@ -145,26 +146,20 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -The "fix reax/c/species" currently only works with :doc:`pair_style reax/c ` and it requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more -info. +The "fix reaxff/species" requires that :doc:`pair_style reaxff ` is used. +This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that +package. See the :doc:`Build package ` page for more info. -To write gzipped species files, you must compile LAMMPS with the --DLAMMPS_GZIP option. - -It should be possible to extend it to other reactive pair_styles (such as -:doc:`rebo `, :doc:`airebo `, -:doc:`comb `, and :doc:`bop `), but this has not yet been done. +To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option. Related commands """""""""""""""" -:doc:`pair_style reax/c `, :doc:`fix reax/c/bonds ` +:doc:`pair_style reaxff `, :doc:`fix reaxff/bonds ` Default """"""" -The default values for bond-order cutoffs are 0.3 for all I-J pairs. The -default element symbols are C, H, O, N. Position files are not written -by default. +The default values for bond-order cutoffs are 0.3 for all I-J pairs. +The default element symbols are C, H, O, N. +Position files are not written by default. diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 583b4d46c5..a6243e693f 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -58,7 +58,7 @@ example, the COM could be computed on a protein to keep it in the center of the simulation box. But the entire system (protein + water) could be shifted. -If the *units* keyword is set to *box*\ , then the distance units of +If the *units* keyword is set to *box*, then the distance units of x,y,z are defined by the :doc:`units ` command - e.g. Angstroms for *real* units. A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index cffba5bafa..9d6114328f 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -43,7 +43,7 @@ used to study crystal-liquid interfaces and determine melting temperatures :ref:`(Pedersen) `. An example of using the interface pinning method is located in the -*examples/USER/misc/rhok* directory. +*examples/PACKAGES/rhok* directory. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -70,9 +70,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 43750d59a1..5b367a48a4 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -253,7 +253,7 @@ differences may accumulate to produce divergent trajectories. they effect any computation of per-atom forces or torques. If the keyword *reinit* is set to *yes* (the default), the rigid body data structures will be recreated at the beginning of each *run* command; - if the keyword *reinit* is set to *no*\ , the rigid body data structures + if the keyword *reinit* is set to *no*, the rigid body data structures will be built only at the very first *run* command and maintained for as long as the rigid fix is defined. For example, you might think you could displace the atoms in a body or add a large velocity to each atom @@ -275,7 +275,7 @@ via several options. .. note:: With the *rigid/small* styles, which require that *bodystyle* be - specified as *molecule* or *custom*\ , you can define a system that has + specified as *molecule* or *custom*, you can define a system that has no rigid bodies initially. This is useful when you are using the *mol* keyword in conjunction with another fix that is adding rigid bodies on-the-fly as molecules, such as :doc:`fix deposit ` @@ -284,7 +284,7 @@ via several options. For bodystyle *single* the entire fix group of atoms is treated as one rigid body. This option is only allowed for the *rigid* styles. -For bodystyle *molecule*\ , atoms are grouped into rigid bodies by their +For bodystyle *molecule*, atoms are grouped into rigid bodies by their respective molecule IDs: each set of atoms in the fix group with the same molecule ID is treated as a different rigid body. This option is allowed for both the *rigid* and *rigid/small* styles. Note that @@ -300,7 +300,7 @@ of atoms that form rigid bodies. An integer vector defined by the :doc:`fix property/atom ` command can be used. Or an :doc:`atom-style or atomfile-style variable ` can be used; the floating-point value produced by the variable is rounded to an -integer. As with bodystyle *molecule*\ , each set of atoms in the fix +integer. As with bodystyle *molecule*, each set of atoms in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all atoms, you should be careful to use a fix group @@ -388,7 +388,7 @@ body. ---------- -The *rigid*\ , *rigid/nve*\ , *rigid/small*\ , and *rigid/small/nve* styles +The *rigid*, *rigid/nve*, *rigid/small*, and *rigid/small/nve* styles perform constant NVE time integration. They are referred to below as the 4 NVE rigid styles. The only difference is that the *rigid* and *rigid/small* styles use an integration technique based on Richardson @@ -404,14 +404,14 @@ of the rigid bodies. They are referred to below as the 2 NVT rigid styles. The rigid-body algorithm used by *rigid/nvt* is described in the paper by :ref:`Kamberaj `. -The *rigid/npt*\ , *rigid/nph*\ , *rigid/npt/small*\ , and *rigid/nph/small* +The *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small* styles perform constant NPT or NPH integration using a Nose/Hoover barostat with chains. They are referred to below as the 4 NPT and NPH rigid styles. For the NPT case, the same Nose/Hoover thermostat is also used as with *rigid/nvt* and *rigid/nvt/small*\ . -The barostat parameters are specified using one or more of the *iso*\ , -*aniso*\ , *x*\ , *y*\ , *z* and *couple* keywords. These keywords give you +The barostat parameters are specified using one or more of the *iso*, +*aniso*, *x*, *y*, *z* and *couple* keywords. These keywords give you the ability to specify 3 diagonal components of the external stress tensor, and to couple these components together so that the dimensions they represent are varied together during a constant-pressure @@ -420,12 +420,12 @@ defined in :doc:`fix npt/nph ` .. note:: - Currently the *rigid/npt*\ , *rigid/nph*\ , *rigid/npt/small*\ , and + Currently the *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small* styles do not support triclinic (non-orthogonal) boxes. The target pressures for each of the 6 components of the stress tensor -can be specified independently via the *x*\ , *y*\ , *z* keywords, which +can be specified independently via the *x*, *y*, *z* keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . If a target pressure is @@ -465,7 +465,7 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. @@ -484,8 +484,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: @@ -517,8 +517,8 @@ discussed below. The *langevin* keyword applies a Langevin thermostat to the constant NVE time integration performed by any of the 4 NVE rigid styles: -*rigid*\ , *rigid/nve*\ , *rigid/small*\ , *rigid/small/nve*\ . It cannot be -used with the 2 NVT rigid styles: *rigid/nvt*\ , *rigid/small/nvt*\ . The +*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot be +used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . The desired temperature at each timestep is a ramped value during the run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in time units and determines how rapidly the temperature is relaxed. For @@ -531,7 +531,7 @@ The way that Langevin thermostatting operates is explained on the :doc:`fix lang damp the rotational motion without thermostatting, you can set *Tstart* and *Tstop* to 0.0, which means only the viscous drag term in the Langevin thermostat will be applied. See the discussion on the -:doc:`fix viscous ` doc page for details. +:doc:`fix viscous ` page for details. .. note:: @@ -851,7 +851,7 @@ Restrictions """""""""""" These fixes are all part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Assigning a temperature via the :doc:`velocity create ` command to a system with :doc:`rigid bodies ` may not have diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index dea2354bad..0883897aae 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -104,7 +104,7 @@ internal energy and extrapolated velocity are also updated. they effect any computation of per-particle forces or torques. If the keyword *reinit* is set to *yes* (the default), the rigid body data structures will be recreated at the beginning of each *run* command; - if the keyword *reinit* is set to *no*\ , the rigid body data structures + if the keyword *reinit* is set to *no*, the rigid body data structures will be built only at the very first *run* command and maintained for as long as the rigid fix is defined. For example, you might think you could displace the particles in a body or add a large velocity to each particle @@ -126,7 +126,7 @@ defined via several options. For bodystyle *single* the entire fix group of particles is treated as one rigid body. -For bodystyle *molecule*\ , particles are grouped into rigid bodies by their +For bodystyle *molecule*, particles are grouped into rigid bodies by their respective molecule IDs: each set of particles in the fix group with the same molecule ID is treated as a different rigid body. Note that particles with a molecule ID = 0 will be treated as a single rigid body. For a @@ -141,13 +141,13 @@ of particles that form rigid bodies. An integer vector defined by the :doc:`fix property/atom ` command can be used. Or an :doc:`atom-style or atomfile-style variable ` can be used; the floating-point value produced by the variable is rounded to an -integer. As with bodystyle *molecule*\ , each set of particles in the fix +integer. As with bodystyle *molecule*, each set of particles in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all particles, you should be careful to use a fix group that only includes particles you want to be part of rigid bodies. -For bodystyle *group*\ , each of the listed groups is treated as a +For bodystyle *group*, each of the listed groups is treated as a separate rigid body. Only particles that are also in the fix group are included in each rigid body. @@ -344,9 +344,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-SDPD package and also depends on the RIGID +This fix is part of the DPD-SMOOTH package and also depends on the RIGID package. It is only enabled if LAMMPS was built with both packages. See -the :doc:`Build package ` doc page for more info. +the :doc:`Build package ` page for more info. This fix requires that atoms store density and internal energy as defined by the :doc:`atom_style sph ` command. diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 9eab06ffad..4028a4e7e1 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -62,7 +62,7 @@ in concentration of a given species as a function of time are then constructed based on the *n* reaction rate equations. The ODE systems are solved over the full DPD timestep *dt* using either a fourth -order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified +order Runge-Kutta *rk4* method with a fixed step-size *h*, specified by the *lammps_rk4* keyword, or a fourth order Runge-Kutta-Fehlberg (rkf45) method with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep for the rk4 method is optionally specified immediately after the rk4 @@ -182,8 +182,8 @@ through its stoichiometric coefficient and a species tag. Reactant species are specified on the left-hand side of the equation and product species are specified on the right-hand side of the equation. After specifying the reactant and product species, the final three -arguments of each line represent the Arrhenius parameter *A*\ , the -temperature exponent *n*\ , and the activation energy *Ea*\ . +arguments of each line represent the Arrhenius parameter *A*, the +temperature exponent *n*, and the activation energy *Ea*\ . Note that the species tags that are defined in the reaction equations are used by the :doc:`fix eos/table/rx ` command to @@ -206,8 +206,8 @@ read_data data.dpd fix foo_SPECIES NULL Species Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index 9dd8fb8641..a9e8f154e6 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -72,7 +72,7 @@ values, e.g. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps that are a multiple of *Nfreq*\ . The average is over *Nrepeat* @@ -126,14 +126,14 @@ Additional optional keywords also affect the operation of this fix. The *ave* keyword determines how the values produced every *Nfreq* steps are averaged with values produced on previous steps that were -multiples of *Nfreq*\ , before they are accessed by another output +multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , then the values produced on timesteps +If the *ave* setting is *one*, then the values produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the values produced on +If the *ave* setting is *running*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding @@ -141,7 +141,7 @@ values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or by re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the values produced on +If the *ave* setting is *window*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged within a moving "window" of time, so that the last M values are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then the output diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 406826e5b9..fd1eb70c4a 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -54,8 +54,8 @@ Any of the fx,fy,fz values can be specified as NULL which means do not alter the force component in that dimension. Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style :doc:`variable `, namely *fx*\ , -*fy*\ , *fz*\ . If the value is a variable, it should be specified as +as an equal-style or atom-style :doc:`variable `, namely *fx*, +*fy*, *fz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the force component. @@ -89,7 +89,7 @@ precession vectors instead of the forces. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -101,13 +101,13 @@ region must be used. See the region :doc:`region ` command for more information. These accelerated styles are part of the r Kokkos package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 8e8f3e0988..f0c847cb5e 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -71,8 +71,8 @@ required in order to eliminate velocity components along the bonds In order to formulate individual constraints for SHAKE and RATTLE, focus on a single molecule whose bonds are constrained. Let Ri and Vi -be the position and velocity of atom *i* at time *n*\ , for -*i* =1,...,\ *N*\ , where *N* is the number of sites of our reference +be the position and velocity of atom *i* at time *n*, for +*i* =1,...,\ *N*, where *N* is the number of sites of our reference molecule. The distance vector between sites *i* and *j* is given by .. math:: @@ -213,7 +213,7 @@ Restrictions These fixes are part of the RIGID package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. For computational efficiency, there can only be one shake or rattle fix defined in a simulation. diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index f928044db7..94e4b557f5 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -42,14 +42,14 @@ necessary). Note that numerous variants of DPD can be specified by choosing an appropriate combination of the integrator and :doc:`pair_style dpd/fdt ` command. DPD under isothermal conditions can -be specified by using fix *shardlow*\ , fix *nve* and pair_style +be specified by using fix *shardlow*, fix *nve* and pair_style *dpd/fdt*\ . DPD under isoenergetic conditions can be specified by -using fix *shardlow*\ , fix *nve* and pair_style *dpd/fdt/energy*\ . DPD +using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isobaric conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the -examples/USER/dpd directory. +examples/PACKAGES/dpd-react directory. ---------- @@ -60,8 +60,8 @@ examples/USER/dpd directory. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix is currently limited to orthogonal simulation cell geometries. diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 8bf7c25478..93554a4510 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -144,8 +144,8 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MISC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index fb19c07b15..0f1be7ed24 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -49,13 +49,13 @@ Dynamics in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor minimization. +Currently, no part of MACHDYN supports restarting nor minimization. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index 867141bd6f..c4f5e61c7e 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -44,14 +44,14 @@ velocity limit. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index 5b4c117452..8f2e0b2b88 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -52,14 +52,14 @@ the velocity vector to max_vel in case it exceeds this velocity limit. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 293f5401a2..76f7240007 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -66,14 +66,14 @@ Dynamics in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index 53aa5f649c..9dcc3c636c 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -42,8 +42,8 @@ alter the velocity component in that dimension. This fix is indented to be used together with a time integration fix. Any of the 3 quantities defining the velocity components can be specified -as an equal-style or atom-style :doc:`variable `, namely *vx*\ , -*vy*\ , *vz*\ . If the value is a variable, it should be specified as +as an equal-style or atom-style :doc:`variable `, namely *vx*, +*vy*, *vz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the force component. @@ -66,7 +66,7 @@ specified geometric :doc:`region ` in order to have its velocity set by Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor minimization +Currently, no part of MACHDYN supports restarting nor minimization None of the :doc:`fix_modify ` options are relevant to this fix. @@ -81,8 +81,8 @@ the :doc:`run ` command. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 38efee0977..192ab7a518 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -44,7 +44,7 @@ is possible to move the triangulated surface via the Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles -in the system. See the "funnel_flow" example in the USER-SMD examples +in the system. See the "funnel_flow" example in the MACHDYN examples directory. See `this PDF guide `_ to use Smooth Mach @@ -53,14 +53,14 @@ Dynamics in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535. diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 5ba752debb..1133142f05 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -29,7 +29,7 @@ needed to time-integrate SPH systems where particles carry internal variables such as internal energy. SPH stands for Smoothed Particle Hydrodynamics. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info @@ -44,8 +44,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the SPH package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index c86a30b542..4496a10eca 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -29,7 +29,7 @@ This fix is needed for SPH simulations to correctly time-integrate fixed boundary particles which constrain a fluid to a given region in space. SPH stands for Smoothed Particle Hydrodynamics. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info @@ -44,8 +44,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the SPH package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index 21035f9def..aba35c8134 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -83,7 +83,9 @@ integrator the fix is adding its forces. Default is the outermost level. Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 4ff260f575..872bee181c 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -185,7 +185,7 @@ needed. The *radius* keyword scales the effective size of big particles. If big particles will overlap as they undergo dynamics, then this keyword can be used to scale down their effective collision radius by an -amount *rfactor*\ , so that SRD particle will only collide with one big +amount *rfactor*, so that SRD particle will only collide with one big particle at a time. For example, in a Lennard-Jones system at a temperature of 1.0 (in reduced LJ units), the minimum separation between two big particles is as small as about 0.88 sigma. Thus an @@ -267,15 +267,15 @@ vector. The specified random number *shiftseed* is used to generate these vectors. This operation sufficiently randomizes which SRD particles are in the same bin, even if :math:`lambda` is small. -If the *shift* flag is set to *no*\ , then no shifting is performed, but +If the *shift* flag is set to *no*, then no shifting is performed, but bin data will be communicated if bins overlap processor boundaries. An error will be generated if :math:`\lambda < 0.6` of the SRD bin size. -If the *shift* flag is set to *possible*\ , then shifting is performed +If the *shift* flag is set to *possible*, then shifting is performed only if :math:`\lambda < 0.6` of the SRD bin size. A warning is generated to let you know this is occurring. If the *shift* flag is set to *yes* then shifting is performed regardless of the magnitude of :math:`\lambda`. Note that the *shiftseed* is not used if the *shift* -flag is set to *no*\ , but must still be specified. +flag is set to *no*, but must still be specified. Note that shifting of SRD coordinates requires extra communication, hence it should not normally be enabled unless required. diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 3841ef6359..829a25b517 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -94,7 +94,7 @@ steps. The list of possible attributes is the same as that used by the :doc:`dump custom ` command, which describes their meaning. -If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu* +If the *com* keyword is set to *yes* then the *xu*, *yu*, and *zu* inputs store the position of each atom relative to the center-of-mass of the group of atoms, instead of storing the absolute position. diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 59f4de64a9..89fc2392f4 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -76,7 +76,7 @@ time. Thus it is easy to specify a time-dependent temperature. be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 3652635340..81379f346b 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -85,7 +85,7 @@ time. Thus it is easy to specify a time-dependent temperature. normally be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -178,6 +178,9 @@ Restrictions Fix *temp/csld* is not compatible with :doc:`fix shake `. +These fixes are part of the EXTRA-FIX package. They are only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. + These fixes can be used with dynamic groups as defined by the :doc:`group ` command. Likewise it can be used with groups to which atoms are added or deleted over time, e.g. a deposition diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 125f74306e..a61773d2a2 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -83,7 +83,7 @@ value. be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index 01017c0267..ea3996e9b6 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -66,8 +66,8 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EFF package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index ae8420089a..7eb4d24935 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -84,7 +84,7 @@ and the :doc:`simulated time ` as calculated by LAMMPS is meaningless. The critical parameter determining the success of a tfMC simulation is -*Delta*\ , the maximal displacement length of the lightest element in +*Delta*, the maximal displacement length of the lightest element in the system: the larger it is, the longer the effective time scale of the simulation will be (there is an approximately quadratic dependence). However, *Delta* must also be chosen sufficiently small @@ -92,7 +92,7 @@ in order to comply with detailed balance; in general values between 5 and 10 % of the nearest neighbor distance are found to be a good choice. For a more extensive discussion with specific examples, please refer to :ref:`(Bal) `, which also describes how the code calculates -element-specific maximal displacements from *Delta*\ , based on the +element-specific maximal displacements from *Delta*, based on the fourth root of their mass. Because of the uncorrelated movements of the atoms, the center-of-mass diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst index a6e9832833..7088692353 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -62,7 +62,7 @@ Examples fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0 fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -139,7 +139,7 @@ The parameter *Tdrude* is the desired temperature for Drude motion at each times Similar to *Tdamp*, the *Tdamp_drude* parameter determines the relaxation speed for Drude motion. Fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the integration. -Other thermostat-related keywords are *tchain*\ and *tloop*\ , +Other thermostat-related keywords are *tchain*\ and *tloop*, which are detailed in :doc:`fix nvt `. .. note:: @@ -158,13 +158,13 @@ which are detailed in :doc:`fix nvt `. ---------- The barostat parameters for fix style *tgnpt/drude* is specified -using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , -*xz*\ , *yz*\ , and *couple* keywords. These keywords give you the +using one or more of the *iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, +*xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure -simulation. Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , -*nreset*\ , *scalexy*\ , *scaleyz*\ , *scalexz*\ , *flip*\ and *fixedpoint*. +simulation. Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *scalexy*, *scaleyz*, *scalexz*, *flip*\ and *fixedpoint*. The meaning of barostat parameters are detailed in :doc:`fix npt `. Regardless of what atoms are in the fix group (the only atoms which @@ -244,7 +244,7 @@ compute temperature on a subset of atoms. The cumulative energy change in the system imposed by these fixes, due to thermostatting and/or barostatting, are included in the :doc:`thermodynamic output ` keywords *ecouple* and -*econserve*. See the :doc:`thermo_style ` doc page for +*econserve*. See the :doc:`thermo_style ` page for details. These fixes compute a global scalar which can be accessed by various @@ -271,12 +271,12 @@ Restrictions """""""""""" These fixes are only available when LAMMPS was built with the -USER-DRUDE package. These fixes cannot be used with dynamic groups as +DRUDE package. These fixes cannot be used with dynamic groups as defined by the :doc:`group ` command. These fixes cannot be used in 2D simulations. -*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not -periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the simulation domain is triclinic and the second dimension in the keyword (\ *y* dimension in *xy*\ ) is periodic. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` @@ -288,10 +288,10 @@ For the *temp* keyword, the final *Tstop* cannot be 0.0 since it would make the external T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. -The *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +The *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . Related commands """""""""""""""" diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 96dbc43540..0652810267 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -129,9 +129,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. - Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to thermostat the system. If you do use a thermostat, you may want to diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 7003100631..d519f36157 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -170,8 +170,9 @@ Related commands Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Default """"""" diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 9c9d77820d..b4595d24cd 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -105,6 +105,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. + All TMD fixes must be listed in the input script after all integrator fixes (nve, nvt, npt) are applied. This ensures that atoms are moved before their positions are corrected to comply with the constraint. diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 24bc6f297f..ee416304c4 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -322,10 +322,9 @@ of the :doc:`run ` command. The fixes are not invoked during Restrictions """""""""""" -Fix *ttm* is part of the MISC package. It is only enabled if LAMMPS -was built with that package. Fix *ttm/mod* is part of the USER-MISC -package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +Fix *ttm* and *ttm/mod* are part of the EXTRA-FIX package. They are +only enabled if LAMMPS was built with that package. +See the :doc:`Build package ` page for more info. These fixes can only be used for 3d simulations and orthogonal simulation boxes. You must also use periodic diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 744db9dcf3..6a3cba16e4 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -81,7 +81,7 @@ Restrictions """""""""""" This fix is part of the KSPACE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index b2c05b1af7..f4eee41269 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -75,7 +75,7 @@ be used, since they produce per-atom values. The *Nevery* argument specifies on what timesteps the input values will be used in order to be stored. Only timesteps that are a -multiple of *Nevery*\ , including timestep 0, will contribute values. +multiple of *Nevery*, including timestep 0, will contribute values. Note that if you perform multiple runs, using the "pre no" option of the :doc:`run ` command to avoid initialization on subsequent runs, @@ -107,7 +107,7 @@ bracketed term is appended, the Ith element of the global vector calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -144,7 +144,7 @@ the vector are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either "intensive" or "extensive". If a compute or fix provides the value stored, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for +intensive or extensive; see the page for that compute or fix for further info. Values produced by a variable are treated as intensive. This fix can allocate storage for stored values accumulated over diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index d238c099b5..e077af19f4 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -134,8 +134,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 2a2aba777d..bcbead8824 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -103,7 +103,7 @@ wall that interacts with the atoms in the group by generating a force on the atom in a direction perpendicular to the wall. The energy of wall-particle interactions depends on the style. -For style *wall/lj93*\ , the energy E is given by the 9/3 potential: +For style *wall/lj93*, the energy E is given by the 9/3 potential: .. math:: @@ -111,7 +111,7 @@ For style *wall/lj93*\ , the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c -For style *wall/lj126*\ , the energy E is given by the 12/6 potential: +For style *wall/lj126*, the energy E is given by the 12/6 potential: .. math:: @@ -119,7 +119,7 @@ For style *wall/lj126*\ , the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: +For style *wall/lj1043*, the energy E is given by the 10/4/3 potential: .. math:: @@ -128,7 +128,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c -For style *wall/colloid*\ , the energy E is given by an integrated form +For style *wall/colloid*, the energy E is given by an integrated form of the :doc:`pair_style colloid ` potential: .. math:: @@ -138,14 +138,14 @@ of the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c -For style *wall/harmonic*\ , the energy E is given by a harmonic spring +For style *wall/harmonic*, the energy E is given by a harmonic spring potential: .. math:: E = \epsilon \quad (r - r_c)^2 \qquad r < r_c -For style *wall/morse*\ , the energy E is given by a Morse potential: +For style *wall/morse*, the energy E is given by a Morse potential: .. math:: @@ -153,13 +153,13 @@ For style *wall/morse*\ , the energy E is given by a Morse potential: \qquad r < r_c In all cases, *r* is the distance from the particle to the wall at -position *coord*\ , and :math:`r_c` is the *cutoff* distance at which the +position *coord*, and :math:`r_c` is the *cutoff* distance at which the particle and wall no longer interact. The energy of the wall potential is shifted so that the wall-particle interaction energy is 0.0 at the cutoff distance. -Up to 6 walls or faces can be specified in a single command: *xlo*\ , -*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ . A *lo* face interacts with +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*\ . A *lo* face interacts with particles near the lower side of the simulation box in that dimension. A *hi* face interacts with particles near the upper side of the simulation box in that dimension. @@ -267,13 +267,13 @@ The *fld* keyword can be used with a *yes* setting to invoke the wall constraint before pairwise interactions are computed. This allows an implicit FLD model using :doc:`pair_style lubricateU ` to include the wall force in its calculations. If the setting is -*no*\ , wall forces are imposed after pairwise interactions, in the +*no*, wall forces are imposed after pairwise interactions, in the usual manner. The *pbc* keyword can be used with a *yes* setting to allow walls to be specified in a periodic dimension. See the :doc:`boundary ` command for options on simulation box -boundaries. The default for *pbc* is *no*\ , which means the system +boundaries. The default for *pbc* is *no*, which means the system must be non-periodic when using a wall. But you may wish to use a periodic box. E.g. to allow some particles to interact with the wall via the fix group-ID, and others to pass through it and wrap around a @@ -306,7 +306,7 @@ sigma) could be varied with additional variable definitions. The *ramp(lo,hi)* function adjusts the wall position linearly from *lo* to *hi* over the course of a run. The *vdisplace(c0,velocity)* function does -something similar using the equation *position = c0 + velocity\*delta*\ , +something similar using the equation *position = c0 + velocity\*delta*, where *delta* is the elapsed time. The *swiggle(c0,A,period)* function causes the wall position to diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 079bd633ea..ac0a58f55c 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -51,7 +51,7 @@ particles in the group interact with the wall when they are close enough to touch it. The nature of the interaction between the wall and the polygon particles is the same as that between the polygon particles themselves, which is similar to a Hookean potential. See -the :doc:`Howto body ` doc page for more details on using +the :doc:`Howto body ` page for more details on using body particles. The parameters *k_n*, *c_n*, *c_t* have the same meaning and units as @@ -83,7 +83,7 @@ is set according to this equation: position = coord + A - A cos (omega \* delta) where *coord* is the specified initial position of the wall, *A* is -the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. @@ -100,7 +100,7 @@ Restrictions """""""""""" This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Any dimension (xy) that has a wall must be non-periodic. diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index ad6540de1d..9930c10f74 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -50,7 +50,7 @@ All particles in the group interact with the wall when they are close enough to touch it. The nature of the interaction between the wall and the polygon particles is the same as that between the polygon particles themselves, which is similar to a Hookean potential. See -the :doc:`Howto body ` doc page for more details on using +the :doc:`Howto body ` page for more details on using body particles. The parameters *k_n*, *c_n*, *c_t* have the same meaning and units as @@ -79,7 +79,7 @@ is set according to this equation: position = coord + A - A cos (omega \* delta) where *coord* is the specified initial position of the wall, *A* is -the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. @@ -96,7 +96,7 @@ Restrictions """""""""""" This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Any dimension (xyz) that has a wall must be non-periodic. diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index cf689f3a77..13a7935d0d 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -73,7 +73,7 @@ energy of wall-particle interactions E is given by: Introduced by Babadi and Ejtehadi in :ref:`(Babadi) `. Here, *r* is the distance from the particle to the -wall at position *coord*\ , and Rc is the *cutoff* distance at which +wall at position *coord*, and Rc is the *cutoff* distance at which the particle and wall no longer interact. Also, :math:`\sigma_n` is the distance between center of ellipsoid and the nearest point of its surface to the wall as shown below. @@ -117,7 +117,7 @@ ellipsoidal particles according to the EES potential introduced above. Other details of this command are the same as for the :doc:`fix wall/region ` command. One may also find an example -of using this fix in the examples/USER/misc/ees/ directory. +of using this fix in the examples/PACKAGES/ees/ directory. ---------- @@ -160,9 +160,9 @@ minimization, invoked by the :doc:`minimize ` command. Restrictions """""""""""" -These fixes are part of the USER-MISC package. They are only enabled +These fixes are part of the EXTRA-FIX package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. These fixes requires that atoms be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 57bec679e4..cf8b659df0 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -22,7 +22,7 @@ Syntax .. parsed-literal:: - For *hooke*\ , *hooke/history*\ , and *hertz/history*\ , *fstyle_params* are: + For *hooke*, *hooke/history*, and *hertz/history*, *fstyle_params* are: Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) @@ -33,7 +33,7 @@ Syntax .. parsed-literal:: - For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` + For *granular*, *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` * wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* * args = list of arguments for a particular style @@ -85,7 +85,7 @@ The nature of the wall/particle interactions are determined by the *fstyle* setting. It can be any of the styles defined by the :doc:`pair_style gran/\* ` or the more general :doc:`pair_style granular ` commands. Currently the -options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the +options are *hooke*, *hooke/history*, or *hertz/history* for the former, and *granular* with all the possible options of the associated *pair_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the @@ -96,12 +96,12 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is set to the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +The parameters *Kn*, *Kt*, *gamma_n*, *gamma_t*, *xmu*, *dampflag*, and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a -NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 +NULL is used for *Kt*, then a default value is used where *Kt* = 2/7 *Kn*\ . If a NULL is used for *gamma_t*, then a default value is used where *gamma_t* = 1/2 *gamma_n*. @@ -117,7 +117,7 @@ material. .. note:: - As discussed on the doc page for :doc:`pair_style gran/\* `, + As discussed on the page for :doc:`pair_style gran/\* `, versions of LAMMPS before 9Jan09 used a different equation for Hertzian interactions. This means Hertizian wall/particle interactions have also changed. They now include a @@ -131,7 +131,7 @@ material. Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were previously. -The effective mass *m_eff* in the formulas listed on the :doc:`pair_style granular ` doc page is the mass of the particle for +The effective mass *m_eff* in the formulas listed on the :doc:`pair_style granular ` page is the mass of the particle for particle/wall interactions (mass of wall is infinite). If the particle is part of a rigid body, its mass is replaced by the mass of the rigid body in those formulas. This is determined by searching for @@ -163,13 +163,13 @@ is set according to this equation: position = coord + A - A cos (omega \* delta) where *coord* is the specified initial position of the wall, *A* is -the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. For the *shear* keyword, the wall moves continuously in the specified dimension with velocity *vshear*\ . The dimension must be tangential to -walls with a planar *wallstyle*\ , e.g. in the *y* or *z* directions for +walls with a planar *wallstyle*, e.g. in the *y* or *z* directions for an *xplane* wall. For *zcylinder* walls, a dimension of *z* means the cylinder is moving in the z-direction along it's axis. A dimension of *x* or *y* means the cylinder is spinning around the z-axis, either in @@ -225,7 +225,7 @@ Restrictions """""""""""" This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Any dimension (xyz) that has a granular wall must be non-periodic. diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 35995fedf0..95634238aa 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -22,7 +22,7 @@ Syntax .. parsed-literal:: - For *hooke*\ , *hooke/history*\ , and *hertz/history*\ , *fstyle_params* are: + For *hooke*, *hooke/history*, and *hertz/history*, *fstyle_params* are: Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) @@ -32,7 +32,7 @@ Syntax .. parsed-literal:: - For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` + For *granular*, *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` * wallstyle = region (see :doc:`fix wall/gran ` for options for other kinds of walls) * region-ID = region whose boundary will act as wall @@ -106,7 +106,7 @@ or combinations of primitive shapes specified via the *union* or construct particle containers with complex shapes. Regions can also move dynamically via the :doc:`region ` command -keywords (move) and *rotate*\ , or change their shape by use of variables +keywords (move) and *rotate*, or change their shape by use of variables as inputs to the :doc:`region ` command. If such a region is used with this fix, then the region surface will move in time in the corresponding manner. @@ -163,7 +163,7 @@ The nature of the wall/particle interactions are determined by the *fstyle* setting. It can be any of the styles defined by the :doc:`pair_style gran/\* ` or the more general :doc:`pair_style granular ` commands. Currently the -options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the +options are *hooke*, *hooke/history*, or *hertz/history* for the former, and *granular* with all the possible options of the associated *pair_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the @@ -181,12 +181,12 @@ radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact is just the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +The parameters *Kn*, *Kt*, *gamma_n*, *gamma_t*, *xmu*, *dampflag*, and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a -NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 +NULL is used for *Kt*, then a default value is used where *Kt* = 2/7 *Kn*\ . If a NULL is used for *gamma_t*, then a default value is used where *gamma_t* = 1/2 *gamma_n*. @@ -265,7 +265,7 @@ Restrictions """""""""""" This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index 00cad094eb..af3dece2f5 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -103,7 +103,7 @@ Restrictions """""""""""" This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The face that has the wall/piston must be boundary type 's' (shrink-wrapped). The opposing face can be diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 4f014cc628..8bb895280c 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -62,8 +62,8 @@ divides the corresponding timestep asymmetrically, energy conservation is only satisfied to O(dt), rather than to O(dt\^2) as it would be for velocity-Verlet integration without reflective walls. -Up to 6 walls or faces can be specified in a single command: *xlo*\ , -*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ . A *lo* face reflects particles +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*\ . A *lo* face reflects particles that move to a coordinate less than the wall position, back in the *hi* direction. A *hi* face reflects particles that move to a coordinate higher than the wall position, back in the *lo* direction. @@ -117,7 +117,7 @@ in a time-dependent fashion using equal-style The *ramp(lo,hi)* function adjusts the wall position linearly from *lo* to *hi* over the course of a run. The *vdisplace(c0,velocity)* function does -something similar using the equation *position = c0 + velocity\*delta*\ , +something similar using the equation *position = c0 + velocity\*delta*, where *delta* is the elapsed time. The *swiggle(c0,A,period)* function causes the wall position to diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst index ddeebfbe38..64e3d759c1 100644 --- a/doc/src/fix_wall_reflect_stochastic.rst +++ b/doc/src/fix_wall_reflect_stochastic.rst @@ -66,25 +66,25 @@ particle is treated stochastically. The randomness can come from many sources: thermal motion of the wall atoms, surface roughness, etc. Three stochastic reflection models are currently implemented. -For rstyle *diffusive*\ , particles are reflected diffusively. Their +For rstyle *diffusive*, particles are reflected diffusively. Their velocity distribution corresponds to an equilibrium distribution of particles at the wall temperature. No accommodation coefficients are specified. -For rstyle *maxwell*\ , particle reflection is Maxwellian which means +For rstyle *maxwell*, particle reflection is Maxwellian which means partially diffusive and partially specular (:ref:`Maxwell `). A single accommodation coeff is specified which must be between 0.0 and 1.0 inclusive. It determines the fraction of the collision which is diffusive versus specular. An accommodation coefficient of 1.0 is fully diffusive; a coefficient of 0.0 is fully specular. -For rstyle *cll*\ , particle collisions are computed by the +For rstyle *cll*, particle collisions are computed by the Cercignani/Lampis model. See :ref:`CL ` and :ref:`To ` for details. Three accommodations coefficient are specified. Each must be between 0.0 and 1.0 inclusive. Two are velocity accommodation coefficients; one is a normal kinetic energy accommodation. The normal coeff is the one corresponding to the normal of the wall itself. For example if -the wall is *ylo* or *yhi*\ , *accomx* and *accomz* are the tangential +the wall is *ylo* or *yhi*, *accomx* and *accomz* are the tangential velocity accommodation coefficients, and *accomy* is the normal kinetic energy accommodation coefficient. @@ -106,8 +106,8 @@ bodies such as those defined by the :doc:`fix rigid ` command. The wall velocity must lie on the same plane as the wall itself. -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the EXTRA-FIX package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 3803d4b74b..f79a9d6da0 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -127,7 +127,7 @@ region surface will move over time in the corresponding manner. The energy of wall-particle interactions depends on the specified style. -For style *lj93*\ , the energy E is given by the 9/3 potential: +For style *lj93*, the energy E is given by the 9/3 potential: .. math:: @@ -135,7 +135,7 @@ For style *lj93*\ , the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c -For style *lj126*\ , the energy E is given by the 12/6 potential: +For style *lj126*, the energy E is given by the 12/6 potential: .. math:: @@ -143,7 +143,7 @@ For style *lj126*\ , the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: +For style *wall/lj1043*, the energy E is given by the 10/4/3 potential: .. math:: @@ -152,7 +152,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c -For style *colloid*\ , the energy E is given by an integrated form of +For style *colloid*, the energy E is given by an integrated form of the :doc:`pair_style colloid ` potential: .. math:: @@ -162,14 +162,14 @@ the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c -For style *wall/harmonic*\ , the energy E is given by a harmonic spring +For style *wall/harmonic*, the energy E is given by a harmonic spring potential (the distance parameter is ignored): .. math:: E = \epsilon \quad (r - r_c)^2 \qquad r < r_c -For style *wall/morse*\ , the energy E is given by the Morse potential: +For style *wall/morse*, the energy E is given by the Morse potential: .. math:: diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index 72e7c771b7..6363995988 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -17,11 +17,11 @@ Syntax .. parsed-literal:: - *xlo*\ ,\ *ylo*\ ,\ *zlo* arg = EDGE or constant or variable + *xlo*,\ *ylo*,\ *zlo* arg = EDGE or constant or variable EDGE = current lo edge of simulation box constant = number like 0.0 or -30.0 (distance units) variable = :doc:`equal-style variable ` like v_x or v_wiggle - *xhi*\ ,\ *yhi*\ ,\ *zhi* arg = EDGE or constant or variable + *xhi*,\ *yhi*,\ *zhi* arg = EDGE or constant or variable EDGE = current hi edge of simulation box constant = number like 50.0 or 100.3 (distance units) variable = :doc:`equal-style variable ` like v_x or v_wiggle @@ -72,8 +72,8 @@ tangential direction for the SRD velocity is chosen randomly. This collision style imparts both a normal and tangential force to the wall. -Up to 6 walls or faces can be specified in a single command: *xlo*\ , -*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ . A *lo* face reflects particles +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*\ . A *lo* face reflects particles that move to a coordinate less than the wall position, back in the *hi* direction. A *hi* face reflects particles that move to a coordinate higher than the wall position, back in the *lo* direction. diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst index 8ec5a1308d..34b9ae44f6 100644 --- a/doc/src/fix_widom.rst +++ b/doc/src/fix_widom.rst @@ -21,7 +21,7 @@ Syntax .. parsed-literal:: - keyword = *mol*\ , *region*\ , *full_energy*, *charge*\ , *intra_energy* + keyword = *mol*, *region*, *full_energy*, *charge*, *intra_energy* *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *region* value = region-ID diff --git a/doc/src/group.rst b/doc/src/group.rst index 3ce885bdc5..aedf1d39bc 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -113,7 +113,7 @@ Note that this is a static one-time assignment. The atoms remain assigned (or not assigned) to the group even in they later move out of the region volume. -The *type*\ , *id*\ , and *molecule* styles put all atoms with the +The *type*, *id*, and *molecule* styles put all atoms with the specified atom types, atom IDs, or molecule IDs into the group. These 3 styles can use arguments specified in one of two formats. @@ -181,7 +181,7 @@ pe/atom compute was actually invoked during the run. Printing the thermodynamic info for compute 2 insures that this is the case, since it sums the pe/atom compute values (in the reduce compute) to output them to the screen. See the "Variable Accuracy" section of the -:doc:`variable ` doc page for more details on insuring that +:doc:`variable ` page for more details on insuring that variables are current when they are evaluated between runs. The *include* style with its arg *molecule* adds atoms to a group that @@ -236,7 +236,7 @@ per-atom property. The per-atom property is evaluated and atoms whose values are 0.0 are removed from the dynamic group. The assignment of atoms to a dynamic group is done at the beginning of -each run and on every timestep that is a multiple of *N*\ , which is the +each run and on every timestep that is a multiple of *N*, which is the argument for the *every* keyword (N = 1 is the default). For an energy minimization, via the :doc:`minimize ` command, an assignment is made at the beginning of the minimization, but not diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 8c265db197..7d66db367b 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -57,8 +57,8 @@ Restrictions This command requires that atoms have atom IDs, since this is the information that is written to the index file. -These commands are part of the USER-COLVARS package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These commands are part of the COLVARS package. They are only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index 5b2c931b1f..9266a95523 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -72,7 +72,7 @@ the system and runs dynamics on each independently with a normal unbiased potential until an event occurs in one of the replicas. The time between events is reduced by a factor of Nr replicas. For both methods, per CPU second, more physical time elapses and more events -occur. See the :doc:`prd ` doc page for more info about PRD. +occur. See the :doc:`prd ` page for more info about PRD. An HD run has several stages, which are repeated each time an event occurs, as explained below. The logic for an HD run is as follows: @@ -148,7 +148,7 @@ the specified *dump-ID* to output a snapshot each time an event is detected. It can be specified multiple times with different *dump-ID* values, as in the example above. These snapshots will be for the quenched state of the system on a timestep that is a multiple of -*Nevent*\ , i.e. a timestep after the event has occurred. Note that any +*Nevent*, i.e. a timestep after the event has occurred. Note that any dump command in the input script will also output snapshots at whatever timestep interval it defines via its *N* argument; see the :doc:`dump ` command for details. This means if you only want a diff --git a/doc/src/if.rst b/doc/src/if.rst index e779ec5a04..08ec6f2c3e 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -68,7 +68,7 @@ above. If a command itself requires a quoted argument (e.g. a :doc:`print ` command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. - The :doc:`Commands parse ` doc page has more details on + The :doc:`Commands parse ` page has more details on using quotes in arguments. Only one of level of nesting is allowed, but that should be sufficient for most use cases. diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index a6281bc260..27cb6e5538 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index 1486550c9f..545222e0a3 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index e29ae95ac5..0399a5c6e2 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -48,7 +48,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-YAFF package. See the :doc:`Build package ` doc +YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 84ea97509d..5852a57038 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -60,7 +60,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 4f21e48fa9..42cd3b75c5 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -64,24 +64,24 @@ radian\^2. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package -` doc page for more info. +` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index cc26e14ce5..7c070d2e9c 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -40,13 +40,38 @@ potential with coefficients 120.0, 30 for :math:`K`, :math:`\chi_0`. Improper type 2 would be computed with a *cvff* potential with coefficients 20.0, -1, 2 for K, d, and n, respectively. -If the improper *class2* potential is one of the hybrid styles, it -requires additional AngleAngle coefficients be specified in the data -file. These lines must also have an additional "class2" argument -added after the improper type. For improper types which are assigned -to other hybrid styles, use the style name (e.g. "harmonic") -appropriate to that style. The AngleAngle coeffs for that improper -type will then be ignored. +If improper coefficients are specified in the data file read via the +:doc:`read_data ` command, then the same rule applies. +E.g. "harmonic" or "cvff", must be added after the improper type, for +each line in the "Improper Coeffs" section, e.g. + +.. parsed-literal:: + + Improper Coeffs + + 1 harmonic 120.0 30 + 2 cvff 20.0 -1 2 + ... + +If *class2* is one of the improper hybrid styles, the same rule holds +for specifying additional AngleAngle coefficients either via the input +script or in the data file. I.e. *class2* must be added to each line +after the improper type. For +lines in the AngleAngle Coeffs section of the data +file for dihedral types that are not *class2*, you must use an +improper style of *skip* as a placeholder, e.g. + +.. parsed-literal:: + + AngleAngle Coeffs + + 1 skip + 2 class2 0.0 0.0 0.0 115.06 130.01 115.06 + ... + +Note that it is not necessary to use the improper style *skip* in the +input script, since AngleAngle coefficients +need not be specified at all for improper types that are not *class2*. An improper style of *none* can be specified as the second argument to the improper_coeff command, if you desire to turn off certain improper diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 1c57b5daf1..9826ab6218 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-MOFFF package. See the :doc:`Build package ` doc +MOFFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index d67c999714..99eed00b90 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -72,7 +72,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index 09a661700f..43f824733e 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -49,7 +49,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index 0667b8f5b9..ca7c31a923 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -70,7 +70,7 @@ command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :ref:`Commands improper ` doc page are followed by one or +The individual style names on the :ref:`Commands improper ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off improper interactions @@ -99,7 +99,7 @@ Improper styles can only be set for atom_style choices that allow impropers to be defined. Most improper styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual improper potentials tell if it is part of a package. Related commands diff --git a/doc/src/info.rst b/doc/src/info.rst index 395bc2c1f4..853e5020fc 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -10,9 +10,9 @@ Syntax info args -* args = one or more of the following keywords: *out*\ , *all*\ , *system*\ , *memory*\ , *communication*\ , *computes*\ , *dumps*\ , *fixes*\ , *groups*\ , *regions*\ , *variables*\ , *coeffs*\ , *styles*\ , *time*\ , *accelerator*\ , or *configuration* -* *out* values = *screen*\ , *log*\ , *append* filename, *overwrite* filename -* *styles* values = *all*\ , *angle*\ , *atom*\ , *bond*\ , *compute*\ , *command*\ , *dump*\ , *dihedral*\ , *fix*\ , *improper*\ , *integrate*\ , *kspace*\ , *minimize*\ , *pair*\ , *region* +* args = one or more of the following keywords: *out*, *all*, *system*, *memory*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *coeffs*, *styles*, *time*, *accelerator*, or *configuration* +* *out* values = *screen*, *log*, *append* filename, *overwrite* filename +* *styles* values = *all*, *angle*, *atom*, *bond*, *compute*, *command*, *dump*, *dihedral*, *fix*, *improper*, *integrate*, *kspace*, *minimize*, *pair*, *region* Examples """""""" @@ -89,8 +89,8 @@ corresponding coefficients have been set. This can be very helpful to debug error messages like "All pair coeffs are not set". The *accelerator* category prints out information about compile time -settings of included accelerator support for the GPU, KOKKOS, USER-INTEL, -and USER-OMP packages. +settings of included accelerator support for the GPU, KOKKOS, INTEL, +and OPENMP packages. The *styles* category prints the list of styles available in the current LAMMPS binary. It supports one of the following options diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index f116a70922..1be907888c 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -372,9 +372,9 @@ the *kim interactions* command executes the following LAMMPS input commands: .. code-block:: LAMMPS - pair_style reax/c lmp_control safezone 2.0 mincap 100 + pair_style reaxff lmp_control safezone 2.0 mincap 100 pair_coeff * * ffield.reax.rdx C H N O - fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq + fix reaxqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq .. note:: @@ -476,7 +476,7 @@ performed. The second required argument *query_function* is the name of the query function to be called (e.g. *get_lattice_constant_cubic*\ ). All following :doc:`arguments ` are parameters handed over to the web query in -the format *keyword=value*\ , where *value* is always an array of one or more +the format *keyword=value*, where *value* is always an array of one or more comma-separated items in brackets. The list of supported keywords and the type and format of their values depend on the query function used. The current list of query functions is available on the OpenKIM webpage at diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index afe3a8c381..5d603782c0 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -75,7 +75,7 @@ relevant to all kspace styles. The *collective* keyword applies only to PPPM. It is set to *no* by default, except on IBM BlueGene machines. If this option is set to -*yes*\ , LAMMPS will use MPI collective operations to remap data for +*yes*, LAMMPS will use MPI collective operations to remap data for 3d-FFT operations instead of the default point-to-point communication. This is faster on IBM BlueGene machines, and may also be faster on other machines if they have an efficient implementation of MPI @@ -131,11 +131,11 @@ always used for MSM. ---------- The *disp/auto* option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to *no*\ , parameters have -to be specified using the *gewald/disp*\ , *mesh/disp*\ , +generate PPPM parameters automatically. If set to *no*, parameters have +to be specified using the *gewald/disp*, *mesh/disp*, *force/disp/real* or *force/disp/kspace* keywords, or the code will stop with an error message. When this option is set to -*yes*\ , the error message will not appear and the simulation will start. +*yes*, the error message will not appear and the simulation will start. For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good @@ -165,8 +165,8 @@ calculated by the long-range solver and is thus specified in force units. A negative value for the accuracy setting means to use the relative accuracy parameter. The accuracy setting is used in conjunction with the pairwise cutoff to determine the number of -K-space vectors for style *ewald*\ , the FFT grid size for style -*pppm*\ , or the real space grid size for style *msm*\ . +K-space vectors for style *ewald*, the FFT grid size for style +*pppm*, or the real space grid size for style *msm*\ . ---------- @@ -223,7 +223,7 @@ The *minorder* keyword allows LAMMPS to reduce the *order* setting if necessary to keep the communication of ghost grid point limited to exchanges between nearest-neighbor processors. See the discussion of the *overlap* keyword for details. If the *overlap* keyword is set to -*yes*\ , which is the default, this is never needed. If it set to *no* +*yes*, which is the default, this is never needed. If it set to *no* and overlap occurs, then LAMMPS will reduce the order setting, one step at a time, until the ghost grid overlap only extends to nearest neighbor processors. The *minorder* keyword limits how small the @@ -237,13 +237,13 @@ MSM. ---------- The *mix/disp* keyword selects the mixing rule for the dispersion -coefficients. With *pair*\ , the dispersion coefficients of unlike +coefficients. With *pair*, the dispersion coefficients of unlike types are computed as indicated with :doc:`pair_modify `. -With *geom*\ , geometric mixing is enforced on the dispersion +With *geom*, geometric mixing is enforced on the dispersion coefficients in the kspace coefficients. When using the arithmetic mixing rule, this will speed-up the simulations but introduces some error in the force computations, as shown in :ref:`(Wennberg) `. -With *none*\ , it is assumed that no mixing rule is +With *none*, it is assumed that no mixing rule is applicable. Splitting of the dispersion coefficients will be performed as described in :ref:`(Isele-Holder) `. @@ -398,8 +398,8 @@ boundaries can be set using :doc:`boundary ` (the slab approximation in not needed). The *slab* keyword is not currently supported by Ewald or PPPM when using a triclinic simulation cell. The slab correction has also been extended to point dipole interactions -:ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*\ , -*ewald/dipole*\ , and *pppm/dipole*\ . +:ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*, +*ewald/dipole*, and *pppm/dipole*\ . .. note:: @@ -419,10 +419,10 @@ optimal performance and accuracy in the results is obtained when these values are different. The *disp/auto* option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to *no*\ , parameters -have to be specified using the *gewald/disp*\ , *mesh/disp*\ , +generate PPPM parameters automatically. If set to *no*, parameters +have to be specified using the *gewald/disp*, *mesh/disp*, *force/disp/real* or *force/disp/kspace* keywords, or the code will -stop with an error message. When this option is set to *yes*\ , the +stop with an error message. When this option is set to *yes*, the error message will not appear and the simulation will start. For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 01ad15a08e..055f0b02b2 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -9,6 +9,7 @@ .. index:: kspace_style pppm/gpu .. index:: kspace_style pppm/intel .. index:: kspace_style pppm/cg +.. index:: kspace_style pppm/dielectric .. index:: kspace_style pppm/dipole .. index:: kspace_style pppm/dipole/spin .. index:: kspace_style pppm/disp @@ -16,7 +17,7 @@ .. index:: kspace_style pppm/disp/tip4p .. index:: kspace_style pppm/disp/tip4p/omp .. index:: kspace_style pppm/disp/intel -.. index:: kspace_style pppm/dielectric +.. index:: kspace_style pppm/disp/dielectric .. index:: kspace_style pppm/cg/omp .. index:: kspace_style pppm/stagger .. index:: kspace_style pppm/tip4p @@ -38,7 +39,7 @@ Syntax kspace_style style value -* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos* +* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos* .. parsed-literal:: @@ -91,6 +92,8 @@ Syntax accuracy = desired relative error in forces *pppm/dielectric* value = accuracy accuracy = desired relative error in forces + *pppm/disp/dielectric* value = accuracy + accuracy = desired relative error in forces *msm* value = accuracy accuracy = desired relative error in forces *msm/cg* value = accuracy (smallq) @@ -118,6 +121,12 @@ Examples kspace style scafacos fmm 1.0e-4 kspace_style none +Used in input scripts: + + .. parsed-literal:: + + examples/peptide/in.peptide + Description """"""""""" @@ -298,9 +307,9 @@ be cloned from the git-repository "git://github.com/scafacos/scafacos.git". In order to use this KSpace style, you must download and build the -ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package +ScaFaCoS library, then build LAMMPS with the SCAFACOS package installed package which links LAMMPS to the ScaFaCoS library. -See details on :ref:`this page `. +See details on :ref:`this page `. .. note:: @@ -399,7 +408,7 @@ relative RMS error. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -420,11 +429,11 @@ The *pppm/kk* style performs charge assignment and force interpolation calculations, along with the FFTs themselves, on the GPU or (optionally) threaded on the CPU when using OpenMP and FFTW3. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP, and OPT packages respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP, and OPT packages respectively. They are only enabled if +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -436,19 +445,19 @@ Note that the long-range electrostatic solvers in LAMMPS assume conducting metal (tinfoil) boundary conditions for both charge and dipole interactions. Vacuum boundary conditions are not currently supported. -The *ewald/disp*\ , *ewald*\ , *pppm*\ , and *msm* styles support +The *ewald/disp*, *ewald*, *pppm*, and *msm* styles support non-orthogonal (triclinic symmetry) simulation boxes. However, triclinic simulation cells may not yet be supported by all suffix versions of these styles. Most of the base kspace styles are part of the KSPACE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. The *msm/dielectric* and *pppm/dielectric* kspace styles are part of the -USER-DIELECTRIC package. They are only enabled if LAMMPS was built with +DIELECTRIC package. They are only enabled if LAMMPS was built with that package **and** the KSPACE package. See the :doc:`Build package -` doc page for more info. +` page for more info. For MSM, a simulation must be 3d and one can use any combination of periodic, non-periodic, or shrink-wrapped boundaries (specified using @@ -460,7 +469,7 @@ dimensions. The only exception is if the slab option is set with must be periodic and the z dimension must be non-periodic. The scafacos KSpace style will only be enabled if LAMMPS is built with -the USER-SCAFACOS package. See the :doc:`Build package ` +the SCAFACOS package. See the :doc:`Build package ` doc page for more info. The use of ScaFaCos in LAMMPS does not yet support molecular charged diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index b87ddaaf70..a03036de1c 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -30,7 +30,7 @@ Syntax i,j,k = integer lattice directions *spacing* values = dx dy dz dx,dy,dz = lattice spacings in the x,y,z box directions - *a1*\ ,\ *a2*\ ,\ *a3* values = x y z + *a1*,\ *a2*,\ *a3* values = x y z x,y,z = primitive vector components that define unit cell *basis* values = x y z x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) @@ -102,7 +102,7 @@ default, a "lattice none 1.0" is defined, which means the lattice spacing is the same as one distance unit, as defined by the :doc:`units ` command. -Lattices of style *sc*\ , *fcc*\ , *bcc*\ , and *diamond* are 3d lattices +Lattices of style *sc*, *fcc*, *bcc*, and *diamond* are 3d lattices that define a cubic unit cell with edge length = 1.0. This means a1 = 1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style *hcp* has a1 = 1 0 0, a2 = 0 sqrt(3) 0, and a3 = 0 0 sqrt(8/3). The placement of the basis atoms @@ -147,14 +147,14 @@ lattice of the desired size and distance units in the simulation box. The meaning of the *scale* argument depends on the :doc:`units ` being used in your simulation. -For all unit styles except *lj*\ , the scale argument is specified in +For all unit styles except *lj*, the scale argument is specified in the distance units defined by the unit style. For example, in *real* or *metal* units, if the unit cell is a unit cube with edge length 1.0, specifying scale = 3.52 would create a cubic lattice with a spacing of 3.52 Angstroms. In *cgs* units, the spacing would be 3.52 cm. -For unit style *lj*\ , the scale argument is the Lennard-Jones reduced +For unit style *lj*, the scale argument is the Lennard-Jones reduced density, typically written as rho\*. LAMMPS converts this value into the multiplicative factor via the formula "factor\^dim = rho/rho\*", where rho = N/V with V = the volume of the lattice unit cell and N = diff --git a/doc/src/log.rst b/doc/src/log.rst index 2632f34b68..5d4036dc06 100644 --- a/doc/src/log.rst +++ b/doc/src/log.rst @@ -26,7 +26,7 @@ Description This command closes the current LAMMPS log file, opens a new file with the specified name, and begins logging information to it. If the -specified file name is *none*\ , then no new log file is opened. If the +specified file name is *none*, then no new log file is opened. If the optional keyword *append* is specified, then output will be appended to an existing log file, instead of overwriting it. diff --git a/doc/src/mdi_engine.rst b/doc/src/mdi_engine.rst index b39999606d..e06f571922 100644 --- a/doc/src/mdi_engine.rst +++ b/doc/src/mdi_engine.rst @@ -21,7 +21,7 @@ More specifically, this command causes LAMMPS to begin using the `MDI Library `_ to run as an MDI engine (server), responding to commands made by an external MDI driver code (client). See the :doc:`Howto mdi -` doc page for more information about how LAMMPS can work +` page for more information about how LAMMPS can work as both an MDI driver or engine. General information about launching codes that communicate using the @@ -67,15 +67,15 @@ about these commands in the `MDI library documentation If these commands are not sufficient to support what a driver which you write needs, additional commands can be defined by simply using a new command name not in this list. Code to support the new command -needs to be added to the USER-MDI package within LAMMPS; see its -src/USER-MDI/mdi_engine.cpp and fix_mdi_engine.cpp files. +needs to be added to the MDI package within LAMMPS; see its +src/MDI/mdi_engine.cpp and fix_mdi_engine.cpp files. Restrictions """""""""""" -This command is part of the USER-MDI package. It is only enabled if +This command is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/message.rst b/doc/src/message.rst index 718a68f994..83ce965e91 100644 --- a/doc/src/message.rst +++ b/doc/src/message.rst @@ -50,7 +50,7 @@ Description Establish a messaging protocol between LAMMPS and another code for the purpose of client/server coupling. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -73,10 +73,10 @@ are: * md = run dynamics with another code * mc = perform Monte Carlo moves with another code -For protocol *md*\ , LAMMPS can be either a client or server. See the -:doc:`server md ` doc page for details on the protocol. +For protocol *md*, LAMMPS can be either a client or server. See the +:doc:`server md ` page for details on the protocol. -For protocol *mc*\ , LAMMPS can be the server. See the :doc:`server mc ` doc page for details on the protocol. +For protocol *mc*, LAMMPS can be the server. See the :doc:`server mc ` page for details on the protocol. ---------- @@ -84,13 +84,13 @@ The *mode* argument specifies how messages are exchanged between the client and server codes. Both codes must use the same mode and use consistent parameters. -For mode *file*\ , the 2 codes communicate via binary files. They must +For mode *file*, the 2 codes communicate via binary files. They must use the same filename, which is actually a file prefix. Several files with that prefix will be created and deleted as a simulation runs. The filename can include a path. Both codes must be able to access the path/file in a common filesystem. -For mode *zmq*\ , the 2 codes communicate via a socket on the server +For mode *zmq*, the 2 codes communicate via a socket on the server code's machine. Support for socket messaging is provided by the open-source `ZeroMQ library `_, which must be installed on your system. The client specifies an IP address (IPv4 @@ -130,7 +130,7 @@ what the client specifies. Additional explanation is needed here about how to use the *zmq* mode on a parallel machine, e.g. a cluster with many nodes. -For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched +For mode *mpi/one*, the 2 codes communicate via MPI and are launched by the same mpirun command, e.g. with this syntax for OpenMPI: .. code-block:: bash @@ -139,10 +139,10 @@ by the same mpirun command, e.g. with this syntax for OpenMPI: mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server Note the use of the "-mpicolor color" command-line argument with -LAMMPS. See the :doc:`command-line args ` doc page for +LAMMPS. See the :doc:`command-line args ` page for further explanation. -For mode *mpi/two*\ , the 2 codes communicate via MPI, but are launched +For mode *mpi/two*, the 2 codes communicate via MPI, but are launched be 2 separate mpirun commands. The specified *filename* argument is a file the 2 MPI processes will use to exchange info so that an MPI inter-communicator can be established to enable the 2 codes to send @@ -191,7 +191,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 731d2ace62..6b416a9b6a 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -81,8 +81,8 @@ energy after) and that difference may be smaller than machine epsilon even if atoms could move in the gradient direction to reduce forces further. -The choice of a norm can be modified for the min styles *cg*\ , *sd*\ -, *quickmin*\ , *fire*\ , *fire/old*\ , *spin*\ , *spin/cg* and +The choice of a norm can be modified for the min styles *cg*, *sd*\ +, *quickmin*, *fire*, *fire/old*, *spin*, *spin/cg* and *spin/lbfgs* using the *norm* keyword. The default *two* norm computes the 2-norm (Euclidean length) of the global force vector: @@ -104,7 +104,7 @@ all atoms in the system: || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) -For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force +For the min styles *spin*, *spin/cg* and *spin/lbfgs*, the force norm is replaced by the spin-torque norm. Keywords *alpha_damp* and *discrete_factor* only make sense when @@ -138,8 +138,8 @@ minimization is 4fs. Note that parameter defaults has been chosen to be reliable in most cases, but one should consider adjusting :doc:`timestep ` and *tmax* to optimize the minimization for large or complex systems. Other -parameters of the *fire* minimization can be tuned (\ *tmin*\ , -*delaystep*\ , *dtgrow*\ , *dtshrink*\ , *alpha0*\ , and +parameters of the *fire* minimization can be tuned (\ *tmin*, +*delaystep*, *dtgrow*, *dtshrink*, *alpha0*, and *alphashrink*\ ). Please refer to the references describing the :doc:`min_style ` *fire*. An additional stopping criteria *vdfmax* is used by *fire* in order to avoid @@ -176,7 +176,7 @@ Default The option defaults are dmax = 0.1, line = quadratic and norm = two. -For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the option +For the *spin*, *spin/cg* and *spin/lbfgs* styles, the option defaults are alpha_damp = 1.0, discrete_factor = 10.0, line = spin_none, and norm = euclidean. diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 46fd08b838..4aef3e0fe2 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -81,7 +81,7 @@ The :doc:`min_modify ` command can be used to activate the line search procedure, and to modify the discretization factor *discrete_factor*. -For more information about styles *spin/cg* and *spin/lbfgs*\ , +For more information about styles *spin/cg* and *spin/lbfgs*, see their implementation reported in :ref:`(Ivanov) `. .. note:: diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index caf2ebd7b2..03a6073994 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -42,7 +42,7 @@ of the energy is not formed directly, but approximated in each conjugate search direction by a finite difference directional derivative. When close to an energy minimum, the algorithm behaves like a Newton method and exhibits a quadratic convergence rate to high -accuracy. In most cases the behavior of *hftn* is similar to *cg*\ , +accuracy. In most cases the behavior of *hftn* is similar to *cg*, but it offers an alternative if *cg* seems to perform poorly. This style is not affected by the :doc:`min_modify ` command. @@ -88,14 +88,14 @@ Style *spin/lbfgs* uses an orthogonal spin optimization (OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) approach to minimize spin configurations. -See the :doc:`min/spin ` doc page for more information about -the *spin*\ , *spin/cg* and *spin/lbfgs* styles. +See the :doc:`min/spin ` page for more information about +the *spin*, *spin/cg* and *spin/lbfgs* styles. -Either the *quickmin*\ , *fire* and *fire/old* styles are useful in the +Either the *quickmin*, *fire* and *fire/old* styles are useful in the context of nudged elastic band (NEB) calculations via the :doc:`neb ` command. -Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful in +Either the *spin*, *spin/cg* and *spin/lbfgs* styles are useful in the context of magnetic geodesic nudged elastic band (GNEB) calculations via the :doc:`neb/spin ` command. @@ -110,7 +110,7 @@ calculations via the :doc:`neb/spin ` command. .. note:: - The *quickmin*\ , *fire*\ , *fire/old*\ , *hftn*\ , and *cg/kk* styles do not yet + The *quickmin*, *fire*, *fire/old*, *hftn*, and *cg/kk* styles do not yet support the use of the :doc:`fix box/relax ` command or minimizations involving the electron radius in :doc:`eFF ` models. diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index a9f60fe8f6..14bc4d0d21 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -57,7 +57,7 @@ coordinates of other atoms fixed by applying :doc:`fix setforce ` to the other atoms. See a fuller discussion of using fixes while minimizing below. -The :doc:`minimization styles ` *cg*\ , *sd*\ , and *hftn* +The :doc:`minimization styles ` *cg*, *sd*, and *hftn* involves an outer iteration loop which sets the search direction along which atom coordinates are changed. An inner iteration is then performed using a line search algorithm. The line search typically @@ -68,7 +68,7 @@ be more robust than previous line searches we have tried. The backtracking method is described in Nocedal and Wright's Numerical Optimization (Procedure 3.1 on p 41). -The :doc:`minimization styles ` *quickmin*\ , *fire* and +The :doc:`minimization styles ` *quickmin*, *fire* and *fire/old* perform damped dynamics using an Euler integration step. Thus they require a :doc:`timestep ` be defined. @@ -118,12 +118,12 @@ The minimization procedure stops if any of several criteria are met: .. note:: - the :doc:`minimization style ` *spin*\ , - *spin/cg*\ , and *spin/lbfgs* replace + the :doc:`minimization style ` *spin*, + *spin/cg*, and *spin/lbfgs* replace the force tolerance *ftol* by a torque tolerance. The minimization procedure stops if the 2-norm (length) of the torque vector on atom (defined as the cross product between the - atomic spin and its precession vectors omega) is less than *ftol*\ , + atomic spin and its precession vectors omega) is less than *ftol*, or if any of the other criteria are met. Torque have the same units as the energy. .. note:: diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index b86983766d..f380d82c7d 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -79,7 +79,7 @@ make it easy to use the same molecule file in different molecule templates or in different simulations. You can specify the same file multiple times with different optional keywords. -The *offset*\ , *toff*\ , *boff*\ , *aoff*\ , *doff*\ , *ioff* keywords +The *offset*, *toff*, *boff*, *aoff*, *doff*, *ioff* keywords add the specified offset values to the atom types, bond types, angle types, dihedral types, and/or improper types as they are read from the molecule file. E.g. if *toff* = 2, and the file uses atom types @@ -150,7 +150,7 @@ appear if the value(s) are different than the default. * Xc Yc Zc *com* = coordinates of center-of-mass of molecule * Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule -For *mass*\ , *com*\ , and *inertia*\ , the default is for LAMMPS to +For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate this quantity itself if needed, assuming the molecules consists of a set of point particles or finite-size particles (with a non-zero diameter) that do not overlap. If finite-size particles in @@ -349,7 +349,7 @@ the doc pages for individual styles for details. N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of this atom within the topology of the molecule. See the -:doc:`special_bonds ` doc page for more discussion of +:doc:`special_bonds ` page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds section must also appear. @@ -390,7 +390,7 @@ This section is only needed when molecules created using the template will be constrained by SHAKE via the "fix shake" command. The other two Shake sections must also appear in the file, following this one. -The meaning of the flag for each atom is as follows. See the :doc:`fix shake ` doc page for a further description of SHAKE +The meaning of the flag for each atom is as follows. See the :doc:`fix shake ` page for a further description of SHAKE clusters. * 0 = not part of a SHAKE cluster @@ -432,7 +432,7 @@ and b,c = IDs of other two atoms bonded to the central atom. If flag = 4, a,b,c,d are listed, where a = ID of central atom, and b,c,d = IDs of other three atoms bonded to the central atom. -See the :doc:`fix shake ` doc page for a further description +See the :doc:`fix shake ` page for a further description of SHAKE clusters. ---------- @@ -477,7 +477,7 @@ the second non-central atom (value c in the Shake Atoms section), and c = bondtype of the bond between the central atom and the third non-central atom (value d in the Shake Atoms section). -See the :doc:`fix shake ` doc page for a further description +See the :doc:`fix shake ` page for a further description of SHAKE clusters. ---------- diff --git a/doc/src/neb.rst b/doc/src/neb.rst index fdccdf3d9f..69a0877f3a 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -114,7 +114,7 @@ closer to the MEP and read them in. ---------- -For a *file-style* setting of *final*\ , a filename is specified which +For a *file-style* setting of *final*, a filename is specified which contains atomic coordinates for zero or more atoms, in the format described below. For each atom that appears in the file, the new coordinates are assigned to that atom in the final replica. Each @@ -143,7 +143,7 @@ case. interpolation is outside the periodic box, the atom will be wrapped back into the box when the NEB calculation begins. -For a *file-style* setting of *each*\ , a filename is specified which is +For a *file-style* setting of *each*, a filename is specified which is assumed to be unique to each replica. This can be done by using a variable in the filename, e.g. @@ -162,7 +162,7 @@ as described below, and for any atom that appears in the file, assign the specified coordinates to its atom. The various files do not need to contain the same set of atoms. -For a *file-style* setting of *none*\ , no filename is specified. Each +For a *file-style* setting of *none*, no filename is specified. Each replica is assumed to already be in its initial configuration at the time the neb command is issued. This allows each replica to define its own configuration by reading a replica-specific data or restart or @@ -185,13 +185,13 @@ that a long calculation can be restarted if needed. A NEB calculation proceeds in two stages, each of which is a minimization procedure, performed via damped dynamics. To enable this, you must first define a damped dynamics -:doc:`min_style `, such as *quickmin* or *fire*\ . The *cg*\ , -*sd*\ , and *hftn* styles cannot be used, since they perform iterative +:doc:`min_style `, such as *quickmin* or *fire*\ . The *cg*, +*sd*, and *hftn* styles cannot be used, since they perform iterative line searches in their inner loop, which cannot be easily synchronized across multiple replicas. The minimizer tolerances for energy and force are set by *etol* and -*ftol*\ , the same as for the :doc:`minimize ` command. +*ftol*, the same as for the :doc:`minimize ` command. A non-zero *etol* means that the NEB calculation will terminate if the energy criterion is met by every replica. The energies being compared diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 10b08f674b..9f714096dc 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -114,7 +114,7 @@ closer to the MEP and read them in. ---------- -For a *file-style* setting of *final*\ , a filename is specified which +For a *file-style* setting of *final*, a filename is specified which contains atomic and spin coordinates for zero or more atoms, in the format described below. For each atom that appears in the file, the new coordinates are @@ -168,12 +168,12 @@ opposite directions, an arbitrary rotation vector belonging to the plane perpendicular to initial and final spins is chosen. In this case, a warning message is displayed. -For a *file-style* setting of *each*\ , a filename is specified which is +For a *file-style* setting of *each*, a filename is specified which is assumed to be unique to each replica. See the :doc:`neb ` documentation page for more information about this option. -For a *file-style* setting of *none*\ , no filename is specified. Each +For a *file-style* setting of *none*, no filename is specified. Each replica is assumed to already be in its initial configuration at the time the neb command is issued. This allows each replica to define its own configuration by reading a replica-specific data or restart or @@ -196,14 +196,14 @@ that a long calculation can be restarted if needed. A NEB calculation proceeds in two stages, each of which is a minimization procedure. To enable this, you must first define a -:doc:`min_style `, using either the *spin*\ , -*spin/cg*\ , or *spin/lbfgs* style (see +:doc:`min_style `, using either the *spin*, +*spin/cg*, or *spin/lbfgs* style (see :doc:`min_spin ` for more information). The other styles cannot be used, since they relax the lattice degrees of freedom instead of the spins. The minimizer tolerances for energy and force are set by *etol* and -*ttol*\ , the same as for the :doc:`minimize ` command. +*ttol*, the same as for the :doc:`minimize ` command. A non-zero *etol* means that the GNEB calculation will terminate if the energy criterion is met by every replica. The energies being compared diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 25c2c2ac77..d6fa12f713 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -75,13 +75,13 @@ pairwise neighbor lists. Depending on what pair interactions and other commands are defined, a simulation may require one or more neighbor lists. -The *every*\ , *delay*\ , *check*\ , and *once* options affect how often +The *every*, *delay*, *check*, and *once* options affect how often lists are built as a simulation runs. The *delay* setting means never build new lists until at least N steps after the previous build. The *every* setting means build lists every M steps (after the delay has -passed). If the *check* setting is *no*\ , the lists are built on the +passed). If the *check* setting is *no*, the lists are built on the first step that satisfies the *delay* and *every* settings. If the -*check* setting is *yes*\ , then the *every* and *delay* settings +*check* setting is *yes*, then the *every* and *delay* settings determine when a build may possibly be performed, but an actual build only occurs if some atom has moved more than half the skin distance (specified in the :doc:`neighbor ` command) since the last @@ -112,7 +112,7 @@ pairwise cutoff is so short that atoms that are part of the same interaction are not communicated as ghost atoms. This is an unusual model (e.g. no pair interactions at all) and the problem can be fixed by use of the :doc:`comm_modify cutoff ` command. Note -that to save time, the default *cluster* setting is *no*\ , so that this +that to save time, the default *cluster* setting is *no*, so that this check is not performed. The *include* option limits the building of pairwise neighbor lists to diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 1b10ec8998..0cfedfc090 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -87,7 +87,7 @@ stored in the list. When a run is finished, counts of the number of neighbors stored in the pairwise list and the number of times neighbor lists were built -are printed to the screen and log file. See the :doc:`Run output ` doc page for details. +are printed to the screen and log file. See the :doc:`Run output ` page for details. Restrictions """""""""""" diff --git a/doc/src/next.rst b/doc/src/next.rst index 2b578a43f5..46d39660eb 100644 --- a/doc/src/next.rst +++ b/doc/src/next.rst @@ -37,8 +37,8 @@ be used in an input script command as $a or $z. If it is multiple letters, it can be used as ${myTemp}. If multiple variables are used as arguments to the *next* command, -then all must be of the same variable style: *index*\ , *loop*\ , *file*\ , -*universe*\ , or *uloop*\ . An exception is that *universe*\ - and +then all must be of the same variable style: *index*, *loop*, *file*, +*universe*, or *uloop*\ . An exception is that *universe*\ - and *uloop*\ -style variables can be mixed in the same *next* command. All the variables specified with the next command are incremented by @@ -93,7 +93,7 @@ directories run1 through run8. next d jump in.polymer -If the variable "d" were of style *universe*\ , and the same in.polymer +If the variable "d" were of style *universe*, and the same in.polymer input script were run on 3 partitions of processors, then the first 3 simulations would begin, one on each set of processors. Whichever partition finished first, it would assign variable "d" the fourth value diff --git a/doc/src/package.rst b/doc/src/package.rst index 1613ff2fae..cbff28cee3 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -130,8 +130,8 @@ Description This command invokes package-specific settings for the various accelerator packages available in LAMMPS. Currently the following -packages use settings from this command: GPU, USER-INTEL, KOKKOS, and -USER-OMP. +packages use settings from this command: GPU, INTEL, KOKKOS, and +OPENMP. If this command is specified in an input script, it must be near the top of the script, before the simulation box has been defined. This @@ -152,7 +152,7 @@ accelerator settings. The KOKKOS package requires a "-k on" :doc:`command-line switch ` respectively, which invokes a "package kokkos" command with default settings. -For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf +For the GPU, INTEL, and OPENMP packages, if a "-sf gpu" or "-sf intel" or "-sf omp" :doc:`command-line switch ` is used to auto-append accelerator suffixes to various styles in the input script, then those switches also invoke a "package gpu", "package @@ -166,7 +166,7 @@ intel", or "package omp" command with default settings. set, either to default values or to specified settings. I.e. settings from previous invocations do not persist across multiple invocations. -See the :doc:`Speed packages ` doc page for more details +See the :doc:`Speed packages ` page for more details about using the various accelerator packages for speeding up LAMMPS simulations. @@ -192,8 +192,8 @@ Optional keyword/value pairs can also be specified. Each has a default value as listed below. The *neigh* keyword specifies where neighbor lists for pair style -computation will be built. If *neigh* is *yes*\ , which is the default, -neighbor list building is performed on the GPU. If *neigh* is *no*\ , +computation will be built. If *neigh* is *yes*, which is the default, +neighbor list building is performed on the GPU. If *neigh* is *no*, neighbor list building is performed on the CPU. GPU neighbor list building currently cannot be used with a triclinic box. GPU neighbor lists are not compatible with commands that are not GPU-enabled. When @@ -202,7 +202,7 @@ built on the CPU. In these cases, it will typically be more efficient to only use CPU neighbor list builds. The *newton* keyword sets the Newton flags for pairwise (not bonded) -interactions to *off* or *on*\ , the same as the :doc:`newton ` +interactions to *off* or *on*, the same as the :doc:`newton ` command allows. Currently, only an *off* value is allowed, since all the GPU package pair styles require this setting. This means more computation is done, but less communication. In the future a value of @@ -288,8 +288,8 @@ The *Nthreads* value for the *omp* keyword sets the number of OpenMP threads allocated for each MPI task. This setting controls OpenMP parallelism only for routines run on the CPUs. For more details on setting the number of OpenMP threads, see the discussion of the -*Nthreads* setting on this doc page for the "package omp" command. -The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL, +*Nthreads* setting on this page for the "package omp" command. +The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. The *platform* keyword is only used with OpenCL to specify the ID for @@ -333,7 +333,7 @@ specify additional flags for the runtime build. ---------- The *intel* style invokes settings associated with the use of the -USER-INTEL package. All of its settings, except the *omp* and *mode* +INTEL package. All of its settings, except the *omp* and *mode* keywords, are ignored if LAMMPS was not built with Xeon Phi co-processor support. All of its settings, including the *omp* and *mode* keyword are applicable if LAMMPS was built with co-processor @@ -350,14 +350,14 @@ The *Nthreads* value for the *omp* keyword sets the number of OpenMP threads allocated for each MPI task. This setting controls OpenMP parallelism only for routines run on the CPUs. For more details on setting the number of OpenMP threads, see the discussion of the -*Nthreads* setting on this doc page for the "package omp" command. -The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL, +*Nthreads* setting on this page for the "package omp" command. +The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. The *mode* keyword determines the precision mode to use for computing pair style forces, either on the CPU or on the co-processor, -when using a USER-INTEL supported :doc:`pair style `. It -can take a value of *single*\ , *mixed* which is the default, or +when using a INTEL supported :doc:`pair style `. It +can take a value of *single*, *mixed* which is the default, or *double*\ . *Single* means single precision is used for the entire force calculation. *Mixed* means forces between a pair of atoms are computed in single precision, but accumulated and stored in double @@ -376,7 +376,7 @@ Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel processors. In this mode, one additional thread is generated per MPI process. LAMMPS will generate a warning in the case that more threads are used than available in SMT hardware on a node. If the PPPM solver -from the USER-INTEL package is not used, then the LRT setting is +from the INTEL package is not used, then the LRT setting is ignored and no extra threads are generated. Enabling LRT will replace the :doc:`run_style ` with the *verlet/lrt/intel* style that is identical to the default *verlet* style aside from supporting the @@ -448,13 +448,14 @@ does not require atomic operations in the calculation of pair forces. For that reason, *full* is the default setting for GPUs. However, when running on CPUs, a *half* neighbor list is the default because it are often faster, just as it is for non-accelerated pair styles. Similarly, -the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk `. +the *neigh/qeq* keyword determines how neighbor lists are built for +:doc:`fix qeq/reaxff/kk `. -If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package +If the *neigh/thread* keyword is set to *off*, then the KOKKOS package threads only over atoms. However, for small systems, this may not expose -enough parallelism to keep a GPU busy. When this keyword is set to *on*\ , +enough parallelism to keep a GPU busy. When this keyword is set to *on*, the KOKKOS package threads over both atoms and neighbors of atoms. When -using *neigh/thread* *on*\ , a full neighbor list must also be used. Using +using *neigh/thread* *on*, a full neighbor list must also be used. Using *neigh/thread* *on* may be slower for large systems, so this this option is turned on by default only when there are 16K atoms or less owned by an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled @@ -463,7 +464,7 @@ simple pair-wise potentials such as Lennard-Jones do support threading over both atoms and neighbors. The *newton* keyword sets the Newton flags for pairwise and bonded -interactions to *off* or *on*\ , the same as the :doc:`newton ` +interactions to *off* or *on*, the same as the :doc:`newton ` command allows. The default for GPUs is *off* because this will almost always give better performance for the KOKKOS package. This means more computation is done, but less communication. However, when running on @@ -530,7 +531,7 @@ performing the exchange pack/unpack on the host CPU can give speedup since it reduces the number of CUDA kernel launches. The *gpu/aware* keyword chooses whether GPU-aware MPI will be used. When -this keyword is set to *on*\ , buffers in GPU memory are passed directly +this keyword is set to *on*, buffers in GPU memory are passed directly through MPI send/receive calls. This reduces overhead of first copying the data to the host CPU. However GPU-aware MPI is not supported on all systems, which can lead to segmentation faults and would require using a @@ -538,7 +539,7 @@ value of *off*\ . If LAMMPS can safely detect that GPU-aware MPI is not available (currently only possible with OpenMPI v2.0.0 or later), then the *gpu/aware* keyword is automatically set to *off* by default. When the *gpu/aware* keyword is set to *off* while any of the *comm* -keywords are set to *device*\ , the value for these *comm* keywords will +keywords are set to *device*, the value for these *comm* keywords will be automatically changed to *no*\ . This setting has no effect if not running on GPUs or if using only one MPI rank. GPU-aware MPI is available for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the @@ -556,7 +557,7 @@ result in better performance for certain configurations and system sizes. ---------- The *omp* style invokes settings associated with the use of the -USER-OMP package. +OPENMP package. The *Nthreads* argument sets the number of OpenMP threads allocated for each MPI task. For example, if your system has nodes with dual @@ -595,12 +596,12 @@ for OpenMPI. Check your MPI documentation for additional details. What combination of threads and MPI tasks gives the best performance is difficult to predict and can depend on many components of your input. Not all features of LAMMPS support OpenMP threading via the -USER-OMP package and the parallel efficiency can be very different, +OPENMP package and the parallel efficiency can be very different, too. .. note:: - If you build LAMMPS with the GPU, USER-INTEL, and / or USER-OMP + If you build LAMMPS with the GPU, INTEL, and / or OPENMP packages, be aware these packages all allow setting of the *Nthreads* value via their package commands, but there is only a single global *Nthreads* value used by OpenMP. Thus if multiple package commands are @@ -642,14 +643,14 @@ with the GPU package. See the :doc:`Build package ` doc page for more info. The intel style of this command can only be invoked if LAMMPS was -built with the USER-INTEL package. See the :doc:`Build package ` doc page for more info. +built with the INTEL package. See the :doc:`Build package ` page for more info. The kk style of this command can only be invoked if LAMMPS was built with the KOKKOS package. See the :doc:`Build package ` doc page for more info. The omp style of this command can only be invoked if LAMMPS was built -with the USER-OMP package. See the :doc:`Build package ` +with the OPENMP package. See the :doc:`Build package ` doc page for more info. Related commands @@ -667,7 +668,7 @@ automatically if the "-sf gpu" :doc:`command-line switch ` is used. If it is not used, you must invoke the package gpu command in your input script or via the "-pk gpu" :doc:`command-line switch `. -For the USER-INTEL package, the default is Nphi = 1 and the option +For the INTEL package, the default is Nphi = 1 and the option defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240. The default ghost option is determined by the pair style being used. This value is output to the screen in the offload diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index abc8cb3c4c..87493724b0 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -72,7 +72,7 @@ where :math:`N` is the number of LAMMPS atom types: * filename * :math:`N` element names = mapping of extended *setfl* elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways to +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the @@ -156,7 +156,7 @@ an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 087c39e8f9..8e91e57b72 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -57,13 +57,13 @@ pair_coeff command, where :math:`N` is the number of LAMMPS atom types: * filename * :math:`N` element names = mapping of AGNI elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the parameters of the force field, i.e., the reference training environments used to construct the machine learning force field. Example force field -and input files are provided in the examples/USER/misc/agni directory. +and input files are provided in the examples/PACKAGES/agni directory. ---------- @@ -73,14 +73,14 @@ depending on your available hardware, as discussed on the :doc:`Speed packages < the same arguments and should produce the same results, except for round-off and precision issues. -The accelerated style is part of the USER-OMP. They are only enabled -if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +The accelerated style is part of the OPENMP. They are only enabled +if LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated style explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -97,7 +97,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -112,8 +112,8 @@ It should work with damped dynamics based minimizers like *fire* or *quickmin*\ . However, one can access the energy via thermodynamic integration of the forces as discussed in :ref:`(Botu3) `. This pair style is part of the -USER-MISC package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more +MISC package. It is only enabled if LAMMPS was built with that +package. See the :doc:`Build package ` page for more info. The AGNI force field files provided with LAMMPS (see the diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index d631d0a3d0..28d7811f06 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -122,7 +122,7 @@ would be 10.2 Angstroms. By default, the longer-ranged interaction is smoothly switched off between 2.16 and 3.0 :math:`\sigma`. By specifying *cutoff_min* in addition -to *cutoff*\ , the switching can be configured to take place between +to *cutoff*, the switching can be configured to take place between *cutoff_min* and *cutoff*\ . *cutoff_min* can only be specified if all optional arguments are given. @@ -131,7 +131,7 @@ various dihedral angle preferences in hydrocarbon configurations. ---------- -Only a single pair_coeff command is used with the *airebo*\ , *airebo* +Only a single pair_coeff command is used with the *airebo*, *airebo* or *rebo* style which specifies an AIREBO, REBO, or AIREBO-M potential file with parameters for C and H. Note that as of LAMMPS version 15 May 2019 the *rebo* style in LAMMPS uses its own potential @@ -142,7 +142,7 @@ where N is the number of LAMMPS atom types: * filename * :math:`N` element names = mapping of AIREBO elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want @@ -211,13 +211,13 @@ script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner* , *middle*, *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair potentials require the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index 0bdfecd517..18c66961fb 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -155,7 +155,7 @@ re-specified in the restart input script. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner* , *middle* , *outer* keywords. +*inner*, *middle*, and *outer* keywords. ---------- @@ -163,7 +163,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 919656a8f5..604baceb8a 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -52,7 +52,7 @@ Rc is the cutoff. The pair_style command allows for several optional keywords to be specified. -The *hartree*\ , *dproduct*\ , and *uhf* keywords specify the form of the +The *hartree*, *dproduct*, and *uhf* keywords specify the form of the initial trial wave function for the system. If the *hartree* keyword is used, then a Hartree multielectron trial wave function is used. If the *dproduct* keyword is used, then a trial function which is a @@ -60,7 +60,7 @@ product of two determinants for each spin type is used. If the *uhf* keyword is used, then an unrestricted Hartree-Fock trial wave function is used. -The *free*\ , *pbc*\ , and *fix* keywords specify a width constraint on +The *free*, *pbc*, and *fix* keywords specify a width constraint on the electron wave packets. If the *free* keyword is specified, then there is no constraint. If the *pbc* keyword is used and *Plen* is specified as -1, then the maximum width is half the shortest box length. If *Plen* @@ -91,7 +91,7 @@ commands, or by mixing as described below: * cutoff (distance units) -For *awpmd/cut*\ , the cutoff coefficient is optional. If it is not +For *awpmd/cut*, the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. @@ -108,7 +108,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 44bc317138..2bf027515c 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -78,13 +78,16 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst index 963f9f4b50..24d5beeb3d 100644 --- a/doc/src/pair_body_nparticle.rst +++ b/doc/src/pair_body_nparticle.rst @@ -31,7 +31,7 @@ for more details on using body particles. This pair style is designed for use with the "nparticle" body style, which is specified as an argument to the "atom-style body" command. -See the :doc:`Howto body ` doc page for more details about +See the :doc:`Howto body ` page for more details about the body styles LAMMPS supports. The "nparticle" style treats a body particle as a rigid body composed of N sub-particles. @@ -74,7 +74,7 @@ interaction, using the standard formula where :math:`R_c` is the cutoff. As explained above, an interaction involving one or two body sub-particles may be computed even for :math:`r > R_c`. -For style *body*\ , the following coefficients must be defined for each +For style *body*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` @@ -104,7 +104,7 @@ This pair style does not write its information to :doc:`binary restart files ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -112,7 +112,7 @@ Restrictions """""""""""" This style is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Defining particles to be bodies so they participate in body/body or body/particle interactions requires the use of the :doc:`atom_style body ` command. diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 6301bf23b1..6757d9d60e 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -34,7 +34,7 @@ Style *body/rounded/polygon* is for use with 2d models of body particles of style *rounded/polygon*\ . It calculates pairwise body/body interactions which can include body particles modeled as 1-vertex circular disks with a specified diameter. See the -:doc:`Howto body ` doc page for more details on using body +:doc:`Howto body ` page for more details on using body rounded/polygon particles. This pairwise interaction between rounded polygons is described in @@ -127,13 +127,13 @@ pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These pair styles are part of the BODY package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 3ef4fb7ca2..f2f7c1676a 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -34,7 +34,7 @@ Style *body/rounded/polygon* is for use with 3d models of body particles of style *rounded/polyhedron*\ . It calculates pairwise body/body interactions which can include body particles modeled as 1-vertex spheres with a specified diameter. See the -:doc:`Howto body ` doc page for more details on using body +:doc:`Howto body ` page for more details on using body rounded/polyhedron particles. This pairwise interaction between the rounded polyhedra is described @@ -122,13 +122,13 @@ commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These pair styles are part of the BODY package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index f566d41e2c..42b9c54406 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -372,7 +372,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -380,7 +380,7 @@ Restrictions """""""""""" These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair potentials require the :doc:`newtion ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 65be948f82..555e78eecd 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -147,7 +147,7 @@ The second coefficient, rho, must be greater than zero. The last coefficient is optional. If not specified, the global A,C,D cutoff specified in the pair_style command is used. -For *born/coul/long*\ , *born/coul/wolf* and *born/coul/dsf* no +For *born/coul/long*, *born/coul/wolf* and *born/coul/dsf* no Coulombic cutoff can be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. @@ -179,8 +179,8 @@ Thess styles writes thei information to binary :doc:`restart ` files, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , -*middle*\ , *outer* keywords. +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*, +*middle*, *outer* keywords. ---------- @@ -188,7 +188,13 @@ Restrictions """""""""""" The *born/coul/long* style is part of the KSPACE package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. + +The *born/coul/dsf* and *born/coul/wolf* pair styles are part of the +EXTRA-PAIR package. They are only enabled if LAMMPS was built with +that package. See the :doc:`Build package ` page +for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index 43c17c9087..780a181a69 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -50,7 +50,7 @@ spherical particles. These pair styles are designed to be used with either the :doc:`pair_style lubricate ` or :doc:`pair_style lubricateU ` commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters -*mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , and *cutoff* should be +*mu*, *flaglog*, *flagfld*, *cutinner*, and *cutoff* should be specified consistent with the settings in the lubrication pair styles. For details, refer to either of the lubrication pair styles. @@ -104,7 +104,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -112,7 +112,7 @@ Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Only spherical monodisperse particles are allowed for pair_style brownian. diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 5f255ece39..eb88d09fd0 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -100,7 +100,7 @@ where :math:`\rho` is an ionic-pair dependent length parameter, and The styles with *coul/cut* or *coul/long* or *coul/msm* add a Coulombic term as described for the :doc:`lj/cut ` pair styles. -For *buck/coul/long* and *buc/coul/msm*\ , an additional damping factor +For *buck/coul/long* and *buc/coul/msm*, an additional damping factor is applied to the Coulombic term so it can be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. The Coulombic cutoff specified for this style means @@ -145,7 +145,7 @@ A,C and Coulombic cutoffs are used. If only one cutoff is specified, it is used as the cutoff for both A,C and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the A,C and Coulombic cutoffs for this type pair. You cannot specify -2 cutoffs for style *buck*\ , since it has no Coulombic terms. +2 cutoffs for style *buck*, since it has no Coulombic terms. For *buck/coul/long* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the @@ -177,14 +177,14 @@ pair interaction. These styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , -*middle*\ , *outer* keywords. +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" The *buck/coul/long* style is part of the KSPACE package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 5f96a93fee..be23f11416 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -135,8 +135,8 @@ to be specified in an input script that reads a restart file. Restrictions """""""""""" -These styles are part of the USER-MOFFF package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These styles are part of the MOFFF package. They are only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 0e19873500..82dd41ff6f 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -64,22 +64,22 @@ settings. The :ref:`Ismail ` paper has more details on when it is appropriate to include long-range 1/r\^6 interactions, using this potential. -If *flag_buck* is set to *long*\ , no cutoff is used on the Buckingham +If *flag_buck* is set to *long*, no cutoff is used on the Buckingham 1/r\^6 dispersion term. The long-range portion can be calculated by using the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified Buckingham cutoff then determines which portion of the Buckingham interactions are computed directly by the pair potential versus which part is computed in reciprocal space via -the Kspace style. If *flag_buck* is set to *cut*\ , the Buckingham +the Kspace style. If *flag_buck* is set to *cut*, the Buckingham interactions are simply cutoff, as with :doc:`pair_style buck `. -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic +If *flag_coul* is set to *long*, no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of several :doc:`kspace_style ` command options such as *pppm* or *ewald*\ . Note that if *flag_buck* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the Buckingham and -Coulombic interactions. If *flag_coul* is set to *off*\ , Coulombic +Coulombic interactions. If *flag_coul* is set to *off*, Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms @@ -102,9 +102,9 @@ are used. If only one cutoff is specified, it is used as the cutoff for both Buckingham and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the Buckingham and Coulombic cutoffs for this type pair. Note that if you are using -*flag_buck* set to *long*\ , you cannot specify a Buckingham cutoff for +*flag_buck* set to *long*, you cannot specify a Buckingham cutoff for an atom type pair, since only one global Buckingham cutoff is allowed. -Similarly, if you are using *flag_coul* set to *long*\ , you cannot +Similarly, if you are using *flag_coul* set to *long*, you cannot specify a Coulombic cutoff for an atom type pair, since only one global Coulombic cutoff is allowed. @@ -135,7 +135,7 @@ the long-range Coulombic and dispersion interactions. This pair style write its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -This pair style supports the use of the *inner*\ , *middle*\ , and *outer* +This pair style supports the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for @@ -147,7 +147,7 @@ Restrictions """""""""""" This style is part of the KSPACE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index b3d2a2b878..d45ef58060 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -169,7 +169,7 @@ where S(r) is the energy switching function mentioned above for the functional forms of the force switching and force shifting functions used in the *charmmfsw* and *charmmfsh* styles. -When using the *lj/charmm/coul/charmm styles*\ , both the LJ and +When using the *lj/charmm/coul/charmm styles*, both the LJ and Coulombic terms require an inner and outer cutoff. They can be the same for both formulas or different depending on whether 2 or 4 arguments are used in the pair_style command. For the @@ -193,7 +193,7 @@ biomolecule (no explicit water molecules). Styles *lj/charmm/coul/long* and *lj/charmm/coul/msm* compute the same formulas as style *lj/charmm/coul/charmm* and style *lj/charmmfsw/coul/long* computes the same formulas as style -*lj/charmmfsw/coul/charmmfsh*\ , except that an additional damping +*lj/charmmfsw/coul/charmmfsh*, except that an additional damping factor is applied to the Coulombic term, so it can be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. Only one Coulombic cutoff is @@ -260,7 +260,7 @@ pair_coeff commands do not need to be specified in an input script that reads a restart file. The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* pair styles -support the use of the *inner*\ , *middle*\ , and *outer* keywords of the +support the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index cfa085cc28..8c6f90efa8 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -100,7 +100,7 @@ class 2 and Coulombic cutoffs are used. If only one cutoff is specified, it is used as the cutoff for both class 2 and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the class 2 and Coulombic cutoffs for this type pair. -You cannot specify 2 cutoffs for style *lj/class2*\ , since it has no +You cannot specify 2 cutoffs for style *lj/class2*, since it has no Coulombic terms. For *lj/class2/coul/long* only the class 2 cutoff can be specified @@ -120,10 +120,10 @@ for mixing the cutoff distance. ---------- -A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with +A version of these styles with a soft core, *lj/cut/soft*, suitable for use in +free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is -only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only available if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- @@ -158,7 +158,7 @@ All of the lj/class2 pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. Only the *lj/class2* and *lj/class2/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be +*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. @@ -167,7 +167,7 @@ Restrictions """""""""""" These styles are part of the CLASS2 package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index ea62d839ab..147b9177ec 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -78,7 +78,7 @@ not set explicitly by a pair_coeff command, the values are inferred from the I,I and J,J settings by mixing rules; see the :doc:`pair_modify ` command for a discussion. Details on this option as it pertains to individual potentials are described on -the doc page for the potential. +the page for the potential. Many pair styles, typically for many-body potentials, use tabulated potential files as input, when specifying the pair_coeff command. diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 040bea2487..9e68e65778 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -187,7 +187,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -195,7 +195,7 @@ Restrictions """""""""""" This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Normally, this pair style should be used with finite-size particles which have a diameter, e.g. see the :doc:`atom_style sphere ` command. However, this is not a requirement, diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 2e164d46fc..aff28cd892 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -52,7 +52,7 @@ total energy :math:`E_T` of a system of atoms is given by where :math:`E_i^{self}` is the self-energy of atom *i* (including atomic ionization energies and electron affinities), :math:`E_{ij}^{short}` is the bond-order potential between atoms *i* and -*j*\ , :math:`E_{ij}^{Coul}` is the Coulomb interactions, +*j*, :math:`E_{ij}^{Coul}` is the Coulomb interactions, :math:`E^{polar}` is the polarization term for organic systems (style *comb3* only), :math:`E^{vdW}` is the van der Waals energy (style *comb3* only), :math:`E^{barr}` is a charge barrier function, and @@ -93,10 +93,10 @@ This can be used when a *comb* potential is used as part of the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with other potentials. -For style *comb*\ , the provided potential file *ffield.comb* contains +For style *comb*, the provided potential file *ffield.comb* contains all currently-available second generation COMB parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style -*comb3*\ , the potential file *ffield.comb3* contains all +*comb3*, the potential file *ffield.comb3* contains all currently-available third generation COMB parameterizations: O, Cu, N, C, H, Ti, Zn and Zr. The status of the optimization of the compounds, for example Cu2O, TiN and hydrocarbons, are given in the @@ -126,8 +126,8 @@ following table: * M = Only optimized for dimer molecule * P = in progress, but have it from mixing rule -For style *comb3*\ , in addition to ffield.comb3, a special parameter -file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be +For style *comb3*, in addition to ffield.comb3, a special parameter +file, *lib.comb3*, that is exclusively used for C/O/H systems, will be automatically loaded if carbon atom is detected in LAMMPS input structure. This file must be in your working directory or in the directories listed in the environment variable ``LAMMPS_POTENTIALS``, as @@ -139,7 +139,7 @@ has not yet been implemented, it can only set polar_off at present. .. note:: - You can not use potential file *ffield.comb* with style *comb3*\ , + You can not use potential file *ffield.comb* with style *comb3*, nor file *ffield.comb3* with style *comb*\ . ---------- @@ -164,7 +164,7 @@ restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -172,7 +172,7 @@ Restrictions """""""""""" These pair styles are part of the MANYBODY package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index faa45c9286..f68df419a4 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -93,22 +93,22 @@ Mixing, shift, table, tail correction, restart, rRESPA info Mixing is not supported for this style. -The *shift*\ , *table* and *tail* options are not relevant for this style. +The *shift*, *table* and *tail* options are not relevant for this style. This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -The *cosine/squared* style is part of the USER-MISC package. It is only -enabled if LAMMPS is build with that package. See the :doc:`Build package ` doc page for more info. +The *cosine/squared* style is part of the EXTRA-PAIR package. It is only +enabled if LAMMPS is build with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index b8303622aa..990458887d 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -283,7 +283,7 @@ Coulombic solver (Ewald or PPPM). atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the :doc:`Howto tip4p ` doc page for more information +See the :doc:`Howto tip4p ` page for more information on how to use the TIP4P pair styles and lists of parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2\*qdist when using the TIP4P pair @@ -311,14 +311,14 @@ commands, or by mixing as described below: * cutoff (distance units) -For *coul/cut* and *coul/debye*\ , the cutoff coefficient is optional. +For *coul/cut* and *coul/debye* the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. -For *coul/long* and *coul/msm* no cutoff can be specified for an -individual I,J type pair via the pair_coeff command. All type pairs -use the same global Coulomb cutoff specified in the pair_style -command. +For *coul/cut/global*, *coul/long* and *coul/msm* no cutoff can be +specified for an individual I,J type pair via the pair_coeff command. +All type pairs use the same global Coulomb cutoff specified in the +pair_style command. ---------- @@ -349,17 +349,17 @@ to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -The *coul/long*\ , *coul/msm* and *tip4p/long* styles are part of the -KSPACE package. They are only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more -info. +The *coul/cut/global*, *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles +are part of the KSPACE package. They are only enabled if LAMMPS was built +with that package. See the :doc:`Build package ` doc page +for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index bcf0c48e4d..7dc245f449 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -90,13 +90,13 @@ pressure. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -This style is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index 31e1bcc176..a7f99500f5 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -77,13 +77,14 @@ pressure. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -This style is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the INTERLAYER package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_slater.rst b/doc/src/pair_coul_slater.rst index a4d8b253b1..443de4262b 100644 --- a/doc/src/pair_coul_slater.rst +++ b/doc/src/pair_coul_slater.rst @@ -93,15 +93,15 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" The *coul/slater/long* style requires the long-range solvers included in the KSPACE package. -These styles are part of the USER-MISC package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These styles are part of the EXTRA-PAIR package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_tt.rst b/doc/src/pair_coul_tt.rst index b01d46d7ae..f6c3a1f6f2 100644 --- a/doc/src/pair_coul_tt.rst +++ b/doc/src/pair_coul_tt.rst @@ -29,7 +29,7 @@ Examples pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0 pair_coeff 1 3* coul/tt 4.5 1.0 4 -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -70,7 +70,7 @@ interactions between the (non-polarizable part of the) charge of a core, The :math:`b_{ij}` and :math:`c_{ij}` are equal to :math:`b_{ji}` and :math:`c_{ji}` in the case of core-core interactions. -For pair_style *coul/tt*\ , the following coefficients must be defined for +For pair_style *coul/tt*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. @@ -95,9 +95,9 @@ for all I,J pairs must be specified explicitly. Restrictions """""""""""" -These pair styles are part of the USER-DRUDE package. They are only +These pair styles are part of the DRUDE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index f41d840216..ef40eb310f 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -115,7 +115,7 @@ Description These pair styles are designed to be used with the adiabatic core/shell model of :ref:`(Mitchell and Finchham) `. See -the :doc:`Howto coreshell ` doc page for an overview of +the :doc:`Howto coreshell ` page for an overview of the model as implemented in LAMMPS. All the styles are identical to the corresponding pair style without @@ -181,7 +181,7 @@ Restrictions """""""""""" These pair styles are part of the CORESHELL package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_dielectric.rst b/doc/src/pair_dielectric.rst index f98cfce976..c1f28c2089 100644 --- a/doc/src/pair_dielectric.rst +++ b/doc/src/pair_dielectric.rst @@ -36,263 +36,53 @@ pair_style lj/long/coul/long/dielectric command Syntax """""" -TODO FIX the rest of the file - .. code-block:: LAMMPS - pair_style lj/cut/dipole/cut cutoff (cutoff2) - pair_style lj/sf/dipole/sf cutoff (cutoff2) - pair_style lj/cut/dipole/long cutoff (cutoff2) - pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) + pair_style style args -* cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) -* cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) -* flag_lj = *long* or *cut* or *off* - - .. parsed-literal:: - - *long* = use long-range damping on dispersion 1/r\^6 term - *cut* = use a cutoff on dispersion 1/r\^6 term - *off* = omit disperion 1/r\^6 term entirely - -* flag_coul = *long* or *off* - - .. parsed-literal:: - - *long* = use long-range damping on Coulombic 1/r and point-dipole terms - *off* = omit Coulombic and point-dipole terms entirely +* style = *lj/cut/coul/cut/dielectric* or *lj/cut/coul/long/dielectric* or *lj/cut/coul/msm/dielectric* or *lj/long/coul/msm/dielectric* +* args = list of arguments for a particular style Examples """""""" .. code-block:: LAMMPS - pair_style lj/cut/dipole/cut 10.0 - pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_style coul/cut/dielectric 10.0 + pair_coeff * * + pair_coeff 1 1 9.0 - pair_style lj/sf/dipole/sf 9.0 - pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_style lj/cut/coul/cut/dielectric 10.0 + pair_style lj/cut/coul/cut/dielectric 10.0 8.0 + pair_coeff * * 100.0 3.0 + pair_coeff 1 1 100.0 3.5 9.0 - pair_style lj/cut/dipole/long 10.0 - pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_style lj/cut/coul/long/dielectric 10.0 + pair_style lj/cut/coul/long/dielectric 10.0 8.0 + pair_coeff * * 100.0 3.0 + pair_coeff 1 1 100.0 3.5 9.0 - pair_style lj/long/dipole/long long long 3.5 10.0 - pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 +Used in input scripts: + + .. parsed-literal:: + + examples/PACKAGES/dielectric/in.confined + examples/PACKAGES/dielectric/in.nopbc Description """"""""""" -Style *lj/cut/dipole/cut* computes interactions between pairs of particles -that each have a charge and/or a point dipole moment. In addition to -the usual Lennard-Jones interaction between the particles (Elj) the -charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp) -interactions are computed by these formulas for the energy (E), force -(F), and torque (T) between particles I and J. +All these pair styles are derived from the corresponding pair styles +without the *dielectric*\ suffix. In addition to computing atom forces +and energies, these pair styles compute the electrical field vector +at each atom, which are to be used in the :doc:`fix polarize ` commands. -.. math:: +These pair styles should be used with :doc:`atom_style dielectric `, +which uses atom charges rescaled by their local dielectric constant. - E_{LJ} = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] \\ - E_{qq} = & \frac{q_i q_j}{r} \\ - E_{qp} = & \frac{q}{r^3} (p \bullet \vec{r}) \\ - E_{pp} = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) - - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r}) \\ - & \\ - F_{qq} = & \frac{q_i q_j}{r^3} \vec{r} \\ - F_{qp} = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5} - (\vec{p} \bullet \vec{r}) \vec{r} \\ - F_{pp} = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} - - \frac{15}{r^7} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \bullet \vec{r}) \vec{r} + - \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + - (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right] \\ - & \\ - T_{pq} = T_{ij} = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\ - T_{qp} = T_{ji} = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\ - T_{pp} = T_{ij} = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) + - \frac{3}{r^5} (\vec{p_j} \bullet \vec{r}) - (\vec{p_i} \times \vec{r}) \\ - T_{pp} = T_{ji} = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) + - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \times \vec{r}) - -where :math:`q_i` and :math:`q_j` are the charges on the two particles, -:math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole moment vectors of -the two particles, r is their separation distance, and the vector r = -Ri - Rj is the separation vector between the two particles. Note that -Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as -symmetric forces, and Tij != -Tji since the torques do not act -symmetrically. These formulas are discussed in :ref:`(Allen) ` -and in :ref:`(Toukmaji) `. - -Also note, that in the code, all of these terms (except Elj) have a -:math:`C/\epsilon` prefactor, the same as the Coulombic term in the LJ + -Coulombic pair styles discussed :doc:`here `. C is an -energy-conversion constant and epsilon is the dielectric constant -which can be set by the :doc:`dielectric ` command. The -same is true of the equations that follow for other dipole pair -styles. - -Style *lj/sf/dipole/sf* computes "shifted-force" interactions between -pairs of particles that each have a charge and/or a point dipole -moment. In general, a shifted-force potential is a (slightly) modified -potential containing extra terms that make both the energy and its -derivative go to zero at the cutoff distance; this removes -(cutoff-related) problems in energy conservation and any numerical -instability in the equations of motion :ref:`(Allen) `. Shifted-force -interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq), -charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp) -potentials are computed by these formulas for the energy (E), force -(F), and torque (T) between particles I and J: - -.. math:: - - E_{LJ} = & 4\epsilon \left\{ \left[ \left( \frac{\sigma}{r} \right)^{\!12} - - \left( \frac{\sigma}{r} \right)^{\!6} \right] + - \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} - - 3\left(\frac{\sigma}{r_c}\right)^{\!6}\right]\left(\frac{r}{r_c}\right)^{\!2} - - 7\left( \frac{\sigma}{r_c} \right)^{\!12} + - 4\left( \frac{\sigma}{r_c} \right)^{\!6}\right\} \\ - E_{qq} = & \frac{q_i q_j}{r}\left(1-\frac{r}{r_c}\right)^{\!2} \\ - E_{pq} = & E_{ji} = -\frac{q}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ - E_{qp} = & E_{ij} = \frac{q}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ - E_{pp} = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3} - (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5} - (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\ - & \\ - - F_{LJ} = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} - - 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} - - \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon - \left(\frac{\sigma}{r_c}\right)^{\!6} \right]\frac{1}{r_c^2}\right\}\vec{r}\\ - F_{qq} = & \frac{q_i q_j}{r}\left(\frac{1}{r^2} - - \frac{1}{r_c^2}\right)\vec{r} \\ - F_{pq} = & F_{ij } = -\frac{3q}{r^5} \left[ 1 - - \left(\frac{r}{r_c}\right)^{\!2}\right](\vec{p}\bullet\vec{r})\vec{r} + - \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ - F_{qp} = & F_{ij} = \frac{3q}{r^5} \left[ 1 - - \left(\frac{r}{r_c}\right)^{\!2}\right] (\vec{p}\bullet\vec{r})\vec{r} - - \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ - F_{pp} = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right] - \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r}) - (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\ - & \left[1 - - 4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right] - \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r}) - \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\} - -.. math:: - - T_{pq} = T_{ij} = & \frac{q_j}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\ - T_{qp} = T_{ji} = & - \frac{q_i}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p_j}\times\vec{r}) \\ - T_{pp} = T_{ij} = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \times \vec{p_j}) + \\ - & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_j}\bullet\vec{r}) - (\vec{p_i} \times \vec{r}) \\ - T_{pp} = T_{ji} = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\ - & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \times \vec{r}) - -where :math:`\epsilon` and :math:`\sigma` are the standard LJ -parameters, :math:`r_c` is the cutoff, :math:`q_i` and :math:`q_j` are -the charges on the two particles, :math:`\vec{p_i}` and -:math:`\vec{p_j}` are the dipole moment vectors of the two particles, r -is their separation distance, and the vector r = Ri - Rj is the -separation vector between the two particles. Note that Eqq and Fqq are -simply Coulombic energy and force, Fij = -Fji as symmetric forces, and -Tij != -Tji since the torques do not act symmetrically. The -shifted-force formula for the Lennard-Jones potential is reported in -:ref:`(Stoddard) `. The original (non-shifted) formulas for -the electrostatic potentials, forces and torques can be found in -:ref:`(Price) `. The shifted-force electrostatic potentials have -been obtained by applying equation 5.13 of :ref:`(Allen) `. The -formulas for the corresponding forces and torques have been obtained by -applying the 'chain rule' as in appendix C.3 of :ref:`(Allen) `. - -If one cutoff is specified in the pair_style command, it is used for -both the LJ and Coulombic (q,p) terms. If two cutoffs are specified, -they are used as cutoffs for the LJ and Coulombic (q,p) terms -respectively. This pair style also supports an optional *scale* keyword -as part of a pair_coeff statement, where the interactions can be -scaled according to this factor. This scale factor is also made available -for use with fix adapt. - -Style *lj/cut/dipole/long* computes long-range point-dipole -interactions as discussed in :ref:`(Toukmaji) `. Dipole-dipole, -dipole-charge, and charge-charge interactions are all supported, along -with the standard 12/6 Lennard-Jones interactions, which are computed -with a cutoff. A :doc:`kspace_style ` must be defined to -use this pair style. Currently, only :doc:`kspace_style ewald/disp ` support long-range point-dipole -interactions. - -Style *lj/long/dipole/long* also computes point-dipole interactions as -discussed in :ref:`(Toukmaji) `. Long-range dipole-dipole, -dipole-charge, and charge-charge interactions are all supported, along -with the standard 12/6 Lennard-Jones interactions. LJ interactions -can be cutoff or long-ranged. - -For style *lj/long/dipole/long*\ , if *flag_lj* is set to *long*\ , no -cutoff is used on the LJ 1/r\^6 dispersion term. The long-range -portion is calculated by using the :doc:`kspace_style ewald_disp ` command. The specified LJ cutoff then -determines which portion of the LJ interactions are computed directly -by the pair potential versus which part is computed in reciprocal -space via the Kspace style. If *flag_lj* is set to *cut*\ , the LJ -interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag_lj* is set to *off*\ , LJ interactions -are not computed at all. - -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic or -dipole interactions. The long-range portion is calculated by using -*ewald_disp* of the :doc:`kspace_style ` command. If -*flag_coul* is set to *off*\ , Coulombic and dipole interactions are not -computed at all. - -Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole ` or the :doc:`fix nvt/sphere update dipole ` command to rotate the -dipole moments. The *omega* option on the :doc:`fix langevin ` command can be used to thermostat the -rotational motion. The :doc:`compute temp/sphere ` -command can be used to monitor the temperature, since it includes -rotational degrees of freedom. The :doc:`atom_style hybrid dipole sphere ` command should be used since -it defines the point dipoles and their rotational state. -The magnitude and orientation of the dipole moment for each particle -can be defined by the :doc:`set ` command or in the "Atoms" section -of the data file read in by the :doc:`read_data ` command. - -The following coefficients must be defined for each pair of atoms -types via the :doc:`pair_coeff ` command as in the examples -above, or in the data file or restart files read by the -:doc:`read_data ` or :doc:`read_restart ` -commands, or by mixing as described below: - -* :math:`\epsilon` (energy units) -* :math:`\sigma` (distance units) -* cutoff1 (distance units) -* cutoff2 (distance units) - -The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. +The styles lj/cut/coul/long/dielectric, lj/cut/coul/msm/dielectric, and +lj/long/coul/long/dielectric should be used with their kspace style counterparts, +namely, pppm/dielectric, pppm/disp/dielectric, and msm/dielectric, respectively. ---------- @@ -307,48 +97,26 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair_modify" command for details. -For atom type pairs I,J and I != J, the A, sigma, d1, and d2 -coefficients and cutoff distance for this pair style can be mixed. A -is an energy value mixed like a LJ epsilon. D1 and d2 are distance -values and are mixed like sigma. The default mix value is -*geometric*\ . See the "pair_modify" command for details. - -This pair style does not support the :doc:`pair_modify ` -shift option for the energy of the Lennard-Jones portion of the pair -interaction; such energy goes to zero at the cutoff by construction. - The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair_modify ` -tail option for adding long-range tail corrections to energy and -pressure. - This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -The *lj/cut/dipole/cut*\ , *lj/cut/dipole/long*\ , and -*lj/long/dipole/long* styles are part of the DIPOLE package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - -The *lj/sf/dipole/sf* style is part of the USER-MISC package. It is -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - -Using dipole pair styles with *electron* :doc:`units ` is not -currently supported. +These styles are part of the DIELECTRIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`set `, :doc:`read_data `, -:doc:`fix nve/sphere `, :doc:`fix nvt/sphere ` +:doc:`pair_coeff `, :doc:`fix polarize `, :doc:`read_data ` Default """"""" diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 602c374d9f..372ea26794 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -242,19 +242,19 @@ dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions. LJ interactions can be cutoff or long-ranged. -For style *lj/long/dipole/long*\ , if *flag_lj* is set to *long*\ , no +For style *lj/long/dipole/long*, if *flag_lj* is set to *long*, no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range portion is calculated by using the :doc:`kspace_style ewald_disp ` command. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal -space via the Kspace style. If *flag_lj* is set to *cut*\ , the LJ -interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag_lj* is set to *off*\ , LJ interactions +space via the Kspace style. If *flag_lj* is set to *cut*, the LJ +interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag_lj* is set to *off*, LJ interactions are not computed at all. -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic or +If *flag_coul* is set to *long*, no cutoff is used on the Coulombic or dipole interactions. The long-range portion is calculated by using *ewald_disp* of the :doc:`kspace_style ` command. If -*flag_coul* is set to *off*\ , Coulombic and dipole interactions are not +*flag_coul* is set to *off*, Coulombic and dipole interactions are not computed at all. Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole ` or the :doc:`fix nvt/sphere update dipole ` command to rotate the @@ -320,20 +320,17 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -The *lj/cut/dipole/cut*\ , *lj/cut/dipole/long*\ , and -*lj/long/dipole/long* styles are part of the DIPOLE package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +The *lj/cut/dipole/cut*, *lj/cut/dipole/long*, *lj/long/dipole/long*, +and lj/sf/dipole/sf* styles are part of the DIPOLE package. They are only +enabled if LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. -The *lj/sf/dipole/sf* style is part of the USER-MISC package. It is -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - -Using dipole pair styles with *electron* :doc:`units ` is not -currently supported. +Using dipole pair styles with *electron* :doc:`units ` is not currently supported. Related commands """""""""""""""" diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 62cf94786d..8a8b35e50a 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -57,7 +57,7 @@ Nose Hoover as implemented by :doc:`fix nvt `. To use *dpd/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. -For style *dpd*\ , the force on atom I due to atom J is given as a sum +For style *dpd*, the force on atom I due to atom J is given as a sum of 3 terms .. math:: @@ -79,18 +79,18 @@ is set equal to :math:`\sqrt{2 k_B T \gamma}`, where :math:`k_B` is the Boltzmann constant and T is the temperature parameter in the pair_style command. -For style *dpd/tstat*\ , the force on atom I due to atom J is the same +For style *dpd/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative Fc term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For style *dpd*\ , the pairwise energy associated with style *dpd* is +For style *dpd*, the pairwise energy associated with style *dpd* is only due to the conservative force term Fc, and is shifted to be zero at the cutoff distance Rc. The pairwise virial is calculated using all 3 terms. For style *dpd/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. -For style *dpd*\ , the following coefficients must be defined for each +For style *dpd*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` @@ -105,7 +105,7 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), where T is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. -For style *dpd/tstat*\ , the coefficients defined for each pair of +For style *dpd/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. @@ -154,18 +154,18 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles writes their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. +These pair styles write their information to :doc:`binary restart files +`, so pair_style and pair_coeff commands do not need to be +specified in an input script that reads a restart file. Note that the +user-specified random number seed is stored in the restart file, so when +a simulation is restarted, each processor will re-initialize its random +number generator the same way it did initially. This means the random +forces will be random, but will not be the same as they would have been +if the original simulation had continued past the restart time. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The *dpd/tstat* style can ramp its target temperature over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` @@ -177,22 +177,26 @@ this. Restrictions """""""""""" +These styles are part of the DPD-BASIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too -infrequent for style *dpd* simulations since particles move rapidly -and can overlap by large amounts. If this setting yields a non-zero -number of "dangerous" reneighborings (printed at the end of a -simulation), you should experiment with forcing reneighboring more -often and see if system energies/trajectories change. +infrequent for style *dpd* simulations since particles move rapidly and +can overlap by large amounts. If this setting yields a non-zero number +of "dangerous" reneighborings (printed at the end of a simulation), you +should experiment with forcing reneighboring more often and see if +system energies/trajectories change. -These pair styles requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost -atoms. +These pair styles requires you to use the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -:doc:`read_restart ` command for more details. +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. Related commands """""""""""""""" diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index cfc72fe84c..7512f8e688 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -38,12 +38,19 @@ Examples Description """"""""""" -The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. +The style *dpd/ext* computes an extended force field for dissipative +particle dynamics (DPD) following the exposition in :ref:`(Groot) +`, :ref:`(Junghans) `. -Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. +Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise +interactions, equivalent to the non-conservative portion of the extended +DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair +style, use the :doc:`pair_style hybrid/overlay ` command to +compute both the desired pair interaction and the thermostat for each +pair of particles. -For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum -of 3 terms +For the style *dpd/ext*, the force on atom I due to atom J is given as +a sum of 3 terms .. math:: @@ -53,17 +60,51 @@ of 3 terms f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ w(r) = & 1 - r/r_c \\ -where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` +is a dissipative force, and :math:`\mathbf{f}^R` is a random +force. :math:`A_{ij}` is the maximum repulsion between the two atoms, +:math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction +:math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = +\mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of +the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian +random numbers with zero mean and unit variance, :math:`\Delta t` is the +timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the +conservative interactions that varies between 0 and 1, :math:`r_c` is +the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c +)^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight +functions with coefficients :math:`s_\alpha` that vary between 0 and 1, +:math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the +unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, +where :math:`k` is the Boltzmann constant and :math:`T` is the +temperature in the pair\_style command. -For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*, the force on atom I due to atom J is +the same as the above equation, except that the conservative +:math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set +each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. +For the style *dpd/ext*, the pairwise energy associated with style +*dpd/ext* is only due to the conservative force term +:math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance +:math:`r_c`. The pairwise virial is calculated using all three +terms. There is no pairwise energy for style *dpd/ext/tstat*, but the +last two terms of the formula contribute the virial. -For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the +same as the above equation, except that the conservative +:math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set +each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. +For the style *dpd/ext*, the pairwise energy associated with style +*dpd/ext* is only due to the conservative force term +:math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance +:math:`r_c`. The pairwise virial is calculated using all three +terms. There is no pairwise energy for style *dpd/ext/tstat*, but the +last two terms of the formula contribute the virial. -For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: +For the style *dpd/ext*, the following coefficients must be defined for +each pair of atoms types via the :doc:`pair_coeff ` command +as in the examples above: * A (force units) * :math:`\gamma_{\perp}` (force/velocity units) @@ -72,35 +113,55 @@ For the style *dpd/ext*, the following coefficients must be defined for each pai * :math:`s_{\parallel}` (unitless) * :math:`r_c` (distance units) -The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. +The last coefficient is optional. If not specified, the global DPD +cutoff is used. Note that :math:`\sigma`'s are set equal to +:math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by +the :doc:`pair_style ` command so it does not need to be +specified. - -For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. +For the style *dpd/ext/tstat*, the coefficients defined for each pair of +atoms types via the :doc:`pair_coeff ` command is the same, +except that A is not included. .. note:: - If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. + If you are modeling DPD polymer chains, you may want to use the + :doc:`pair_style srp ` command in conjunction with these pair + styles. It is a soft segmental repulsive potential (SRP) that can + prevent DPD polymer chains from crossing each other. .. note:: - The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force. + The virial calculation for pressure when using this pair style includes + all the components of force listed above, including the random force. ---------- **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. +The style *dpd/ext* does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. -The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. +The pair styles do not support the :doc:`pair_modify ` +shift option for the energy of the pair interaction. Note that as +discussed above, the energy due to the conservative :math:`\mathbf{f}^C` +term is already shifted to be zero at the cutoff distance :math:`r_c`. -The :doc:`pair_modify ` table option is not relevant for the style *dpd/ext*. +The :doc:`pair_modify ` table option is not relevant for +the style *dpd/ext*. -The style *dpd/ext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. +The style *dpd/ext* does not support the :doc:`pair_modify +` tail option for adding long-range tail corrections to +energy and pressure. -The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. +The pair styles can only be used via the pair keyword of the +:doc:`run_style respa ` command. They do not support the +*inner*, *middle*, and *outer*\ keywords. -The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. +The style *dpd/ext/tstat* can ramp its target temperature over multiple +runs, using the start and stop keywords of the :doc:`run ` +command. See the :doc:`run ` command for details of how to do this. ---------- @@ -108,31 +169,42 @@ The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, us Restrictions """""""""""" -The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. +These styles are part of the DPD-BASIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. -The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. +The default frequency for rebuilding neighbor lists is every 10 steps +(see the :doc:`neigh_modify ` command). This may be too +infrequent for style *dpd/ext* simulations since particles move rapidly +and can overlap by large amounts. If this setting yields a non-zero +number of \say{dangerous} reneighborings (printed at the end of a +simulation), you should experiment with forcing reneighboring more often +and see if system energies/trajectories change. -The pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart ` command for more details. +The pair styles require to use the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. + +The pair styles will not restart exactly when using the +:doc:`read_restart ` command, though they should provide +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. Related commands """""""""""""""" -:doc:`pair_style dpd `, :doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` +:doc:`pair_style dpd `, :doc:`pair_coeff `, +:doc:`fix nvt `, :doc:`fix langevin `, +:doc:`pair_style srp ` **Default:** none - ---------- - .. _Groot: - - **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). .. _Junghans: - - **(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008). diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index bb810b0fe6..25fe2581db 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -77,7 +77,7 @@ following functional form: Note that alternative definitions of the weighting function exist, but would have to be implemented as a separate pair style command. -For style *dpd/fdt*\ , the fluctuation-dissipation theorem defines :math:`\gamma` +For style *dpd/fdt*, the fluctuation-dissipation theorem defines :math:`\gamma` to be set equal to :math:`\sigma^2/(2 T)`, where T is the set point temperature specified as a pair style parameter in the above examples. The following coefficients must be defined for each pair of atoms types @@ -162,8 +162,8 @@ significantly larger timesteps to be taken. Restrictions """""""""""" -These commands are part of the USER-DPD package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These commands are part of the DPD-REACT package. They are only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the :doc:`comm_modify vel yes ` option so that velocities are diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index e3b986615e..f7b01eee25 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -117,18 +117,18 @@ pair_coeff commands in an input script that reads a restart file. Restrictions """""""""""" -This pair style is part of the USER-MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc -page for more info. +This pair style is part of the INTERLAYER package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. -This pair potential requires the :doc:`newton ` setting to be "on" for +This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. The *C.drip* parameter file provided with LAMMPS (see the "potentials" -directory) is parameterized for metal :doc:`units `. You can use the DRIP -potential with any LAMMPS units, but you would need to create your own custom -parameter file with coefficients listed in the appropriate units, if your -simulation does not use "metal" units. +directory) is parameterized for metal :doc:`units `. You can use +the DRIP potential with any LAMMPS units, but you would need to create +your own custom parameter file with coefficients listed in the +appropriate units, if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index d7542ea801..b0a508b054 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -131,7 +131,7 @@ continued past the restart time. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -139,7 +139,7 @@ Restrictions """""""""""" This style is part of the MC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index f031bf193d..b75fb8450c 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -98,7 +98,7 @@ The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model ` command as a vector of values of length 4. The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term. -See the examples/USER/misc/e3b directory for a complete example script. +See the examples/PACKAGES/e3b directory for a complete example script. ---------- @@ -132,8 +132,8 @@ This pair style is incompatible with :doc:`respa `. Restrictions """""""""""" -This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the EXTRA-PAIR package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index a8b67e7f41..fd05d7189e 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -145,7 +145,7 @@ provides EAM potentials that can be used directly in LAMMPS with the ---------- -For style *eam*\ , potential values are read from a file that is in the +For style *eam*, potential values are read from a file that is in the DYNAMO single-element *funcfl* format. If the DYNAMO file was created by a Fortran program, it cannot have "D" values in it for exponents. C only recognizes "e" or "E" for scientific notation. @@ -225,7 +225,7 @@ above, *setfl* files contain explicit tabulated values for alloy interactions. Thus they allow more generality than *funcfl* files for modeling alloys. -For style *eam/alloy*\ , potential values are read from a file that is +For style *eam/alloy*, potential values are read from a file that is in the DYNAMO multi-element *setfl* format, except that element names (Ni, Cu, etc) are added to one of the lines in the file. If the DYNAMO file was created by a Fortran program, it cannot have "D" @@ -372,7 +372,7 @@ require that; the user can tabulate any functional form desired in the FS potential files. For style *eam/fs* and *eam/he* the form of the pair_coeff command is exactly -the same as for style *eam/alloy*\ , e.g. +the same as for style *eam/alloy*, e.g. .. code-block:: LAMMPS @@ -383,13 +383,13 @@ the number of LAMMPS atom types. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. The N values determine the mapping of LAMMPS atom types to EAM elements in the file, as described above for style *eam/alloy*\ . As -with *eam/alloy*\ , if a mapping value is NULL, the mapping is not +with *eam/alloy*, if a mapping value is NULL, the mapping is not performed. This can be used when an *eam/fs* or *eam/he* potential is used as part of a *hybrid* pair style. The NULL values are used as placeholders for atom types that will be used with other potentials. FS EAM and HE EAM files include more information than the DYNAMO *setfl* -format files read by *eam/alloy*\ , in that i,j density functionals for +format files read by *eam/alloy*, in that i,j density functionals for all pairs of elements are included as needed by the Finnis/Sinclair formulation of the EAM. @@ -465,7 +465,7 @@ an input script that reads a restart file. The eam pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -473,7 +473,7 @@ Restrictions """""""""""" All of these styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index 8f8d70f2f6..6b6bfbb11b 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -69,7 +69,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of EDIP elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine a file Si.edip has EDIP values for Si. @@ -142,7 +142,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -150,7 +150,7 @@ Restrictions """""""""""" This pair style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +MANYBODY package. See the :doc:`Build package ` doc page for more info. This pair style requires the :doc:`newton ` setting to be "on" diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index b5462aab01..b104b01b40 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -141,7 +141,7 @@ commands, or by mixing as described below: * cutoff (distance units) -For *eff/cut*\ , the cutoff coefficient is optional. If it is not used +For *eff/cut*, the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. @@ -232,7 +232,7 @@ complexity in higher Z elements (up to Z<18). A fixed-core should be defined with a mass that includes the corresponding nuclear mass plus the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a radius equivalent to that of minimized 1s electrons (see examples -under /examples/USER/eff/fixed-core). An pseudo-core should be +under /examples/PACKAGES/eff/fixed-core). An pseudo-core should be described with a mass that includes the corresponding nuclear mass, plus all the core electrons (i.e no outer shell electrons), and a radius equivalent to that of a corresponding minimized full-electron @@ -283,7 +283,7 @@ to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -291,8 +291,8 @@ Restrictions """""""""""" These pair styles will only be enabled if LAMMPS is built with the -USER-EFF package. It will only be enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +EFF package. It will only be enabled if LAMMPS was built with +that package. See the :doc:`Build package ` page for more info. These pair styles require that particles store electron attributes diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 8360dbab64..c84bce9d53 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -105,7 +105,7 @@ command, where N is the number of LAMMPS atom types: * EIM potential file * N element names = mapping of EIM elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example like one of those above, suppose you want to model a diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index 49a4c5436f..55395bcd0d 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -71,7 +71,7 @@ to be the internal chemical energy (uChem). The fourth argument specifies the type of scaling that will be used to scale the EXP-6 parameters as reactions occur. Currently, there -are three scaling options: *exponent*\ , *polynomial* and *none*\ . +are three scaling options: *exponent*, *polynomial* and *none*\ . Exponent scaling requires two additional arguments for scaling the :math:`R_m` and :math:`\epsilon` parameters, respectively. The scaling factor @@ -178,8 +178,8 @@ pair interaction. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index ce8227abeb..400ad0cc4a 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -182,7 +182,7 @@ Examples pair_coeff * * 100.0 2.0 1.5 1.0 pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 -Example input scripts available: examples/USER/fep +Example input scripts available: examples/PACKAGES/fep Description """"""""""" @@ -259,7 +259,7 @@ LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style *lj/cut/soft*\ , +type pair. You cannot specify 2 cutoffs for style *lj/cut/soft*, since it has no Coulombic terms. For the *coul/cut/soft* and *coul/long/soft* only lambda and the optional cutoff2 are to be specified. @@ -290,7 +290,7 @@ activation parameter lambda is introduced as an argument of the the :doc:`pair_coeff ` command, after :math:`\epsilon` and :math:`\sigma` and before the optional cutoffs. -The *coul/cut/soft*\ , *coul/long/soft* and *tip4p/long/soft* sub-styles are +The *coul/cut/soft*, *coul/long/soft* and *tip4p/long/soft* sub-styles are designed to be combined with other pair potentials via the :doc:`pair_style hybrid/overlay ` command. This is because they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two @@ -304,7 +304,7 @@ the second coefficient. .. note:: When using the soft-core Coulomb potentials with long-range solvers (\ - *coul/long/soft*\ , *lj/cut/coul/long/soft*\ , etc.) in a free energy + *coul/long/soft*, *lj/cut/coul/long/soft*, etc.) in a free energy calculation in which sites holding electrostatic charges are being created or annihilated (using :doc:`fix adapt/fep ` and :doc:`compute fep `) it is important to adapt both the :math:`\lambda` activation @@ -313,7 +313,7 @@ the second coefficient. electrostatic terms (kspace) are correct. It is not necessary to use soft-core Coulomb potentials if the van der Waals site is present during the free-energy route, thus avoiding overlap of the charges. Examples are - provided in the LAMMPS source directory tree, under examples/USER/fep. + provided in the LAMMPS source directory tree, under examples/PACKAGES/fep. .. note:: @@ -414,10 +414,10 @@ Restrictions """""""""""" The pair styles with soft core are only enabled if LAMMPS was built with the -USER-FEP package. The *long* versions also require the KSPACE package to be +FEP package. The *long* versions also require the KSPACE package to be installed. The soft *tip4p* versions also require the MOLECULE package to be installed. These styles are only enabled if LAMMPS was built with those -packages. See the :doc:`Build package ` doc page for more +packages. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 9b516cce7b..4eb45a416b 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -143,7 +143,7 @@ to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well sites have an atom within the distance at which the force is a maximum @@ -163,9 +163,9 @@ heading) the following commands could be included in an input script: Restrictions """""""""""" -The *gauss/cut* style is part of the USER-MISC package. It is only -enabled if LAMMPS is build with that package. See the :doc:`Build -package ` doc page for more info. +The *gauss* and *gauss/cut* styles are part of the EXTRA-PAIR package. +They are only enabled if LAMMPS is build with that package. See the +:doc:`Build package ` page for more info. The *gauss* style does not apply :doc:`special_bonds ` factors. When using this pair style on a system that has bonds, the diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 448f3a26de..09bc3706c2 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -178,7 +178,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -186,7 +186,7 @@ Restrictions """""""""""" The *gayberne* style is part of the ASPHERE package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles require that atoms store torque and a quaternion to represent their orientation, as defined by the diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index fbcacb5c76..c4024a391a 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -101,7 +101,7 @@ damping force. The tangential force also has 2 terms: a shear force and a damping force. The shear force is a "history" effect that accounts for the tangential displacement between the particles for the duration of the time they are in contact. This term is included in -pair styles *hooke/history* and *hertz/history*\ , but is not included +pair styles *hooke/history* and *hertz/history*, but is not included in pair style *hooke*\ . The tangential damping force term is included in all three pair styles if *dampflag* is set to 1; it is not included if *dampflag* is set to 0. @@ -240,7 +240,7 @@ specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these @@ -254,7 +254,7 @@ normal direction (along the line joining the 2 sphere centers). The last 3 (8-10) the components of the relative velocity in the tangential direction. -These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*\ , *p2*\ , ..., +These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*, *p2*, ..., *p10*\ . ---------- @@ -263,7 +263,7 @@ Restrictions """""""""""" All the granular pair styles are part of the GRANULAR package. It is -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles require that atoms store torque and angular velocity (omega) as defined by the :doc:`atom_style `. They also diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 432fd29584..b7f9da9f8b 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -99,8 +99,8 @@ Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two particle centers (note the i-j ordering so that :math:`F_{ne}` is positive for repulsion), and :math:`\mathbf{n} = \frac{\mathbf{r}_{ij}}{\|\mathbf{r}_{ij}\|}`. Therefore, -for *hooke*\ , the units of the spring constant :math:`k_n` are -*force*\ /\ *distance*\ , or equivalently *mass*\ /*time\^2*. +for *hooke*, the units of the spring constant :math:`k_n` are +*force*\ /\ *distance*, or equivalently *mass*\ /*time\^2*. For the *hertz* model, the normal component of force is given by: @@ -109,7 +109,7 @@ For the *hertz* model, the normal component of force is given by: \mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective -radius, denoted for simplicity as *R* from here on. For *hertz*\ , the +radius, denoted for simplicity as *R* from here on. For *hertz*, the units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or equivalently *pressure*\ . @@ -188,7 +188,7 @@ for the damping model currently supported are: If the *damping* keyword is not specified, the *viscoelastic* model is used by default. -For *damping velocity*\ , the normal damping is simply equal to the +For *damping velocity*, the normal damping is simply equal to the user-specified damping coefficient in the *normal* model: .. math:: @@ -219,8 +219,8 @@ damping is given by: \eta_n = \eta_{n0}\ a m_{eff} Here, *a* is the contact radius, given by :math:`a =\sqrt{R\delta}` -for all models except *jkr*\ , for which it is given implicitly according -to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*\ , +for all models except *jkr*, for which it is given implicitly according +to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*, :math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ). The *tsuji* model is based on the work of :ref:`(Tsuji et al) `. Here, the damping coefficient specified as part of @@ -302,14 +302,14 @@ The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\ The normal force value :math:`F_{n0}` used to compute the critical force depends on the form of the contact model. For non-cohesive models -(\ *hertz*\ , *hertz/material*\ , *hooke*\ ), it is given by the magnitude of +(\ *hertz*, *hertz/material*, *hooke*\ ), it is given by the magnitude of the normal force: .. math:: F_{n0} = \|\mathbf{F}_n\| -For cohesive models such as *jkr* and *dmt*\ , the critical force is +For cohesive models such as *jkr* and *dmt*, the critical force is adjusted so that the critical tangential force approaches :math:`\mu_t F_{pulloff}`, see :ref:`Marshall `, equation 43, and :ref:`Thornton `. For both models, :math:`F_{n0}` takes the form: @@ -318,7 +318,7 @@ form: F_{n0} = \|\mathbf{F}_{ne} + 2 F_{pulloff}\| -Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*\ , and +Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*, and :math:`F_{pulloff} = 4\pi \gamma R` for *dmt*\ . The remaining tangential options all use accumulated tangential @@ -392,7 +392,7 @@ overlap region) to induce a torque on each particle according to: \mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t -For *tangential mindlin*\ , the :ref:`Mindlin ` no-slip solution +For *tangential mindlin*, the :ref:`Mindlin ` no-slip solution is used which differs from the *linear_history* option by an additional factor of :math:`a`, the radius of the contact region. The tangential force is given by: @@ -402,7 +402,7 @@ of :math:`a`, the radius of the contact region. The tangential force is given by Here, :math:`a` is the radius of the contact region, given by :math:`a =\sqrt{R\delta}` -for all normal contact models, except for *jkr*\ , where it is given +for all normal contact models, except for *jkr*, where it is given implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see discussion above. To match the Mindlin solution, one should set :math:`k_t = 8G_{eff}`, where :math:`G_{eff}` is the effective shear modulus given by: @@ -415,7 +415,7 @@ where :math:`G` is the shear modulus, related to Young's modulus :math:`E` and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be achieved by specifying *NULL* for :math:`k_t`, in which case a normal contact model that specifies material parameters :math:`E` and -:math:`\nu` is required (e.g. *hertz/material*\ , *dmt* or *jkr*\ ). In this +:math:`\nu` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this case, mixing of the shear modulus for different particle types *i* and *j* is done according to the formula above. @@ -455,7 +455,7 @@ the critical force: The same rules as those described for *mindlin* apply regarding the tangential stiffness and mixing of the shear modulus for different particle types. -The *mindlin_rescale* option uses the same form as *mindlin*\ , but the +The *mindlin_rescale* option uses the same form as *mindlin*, but the magnitude of the tangential displacement is re-scaled as the contact unloads, i.e. if :math:`a < a_{t_{n-1}}`: @@ -504,7 +504,7 @@ pure rolling motion of particles. The options currently supported are: If the *rolling* keyword is not specified, the model defaults to *none*\ . -For *rolling sds*\ , rolling friction is computed via a +For *rolling sds*, rolling friction is computed via a spring-dashpot-slider, using a 'pseudo-force' formulation, as detailed by :ref:`Luding `. Unlike the formulation in :ref:`Marshall `, this allows for the required adjustment of @@ -564,7 +564,7 @@ supported are: If the *twisting* keyword is not specified, the model defaults to *none*\ . -For both *twisting sds* and *twisting marshall*\ , a history-dependent +For both *twisting sds* and *twisting marshall*, a history-dependent spring-dashpot-slider is used to compute the twisting torque. Because twisting displacement is a scalar, there is no need to adjust for changes in the frame of reference due to rotations of the particle @@ -591,7 +591,7 @@ if the twisting torque exceeds this critical value: \xi_{twist} = \frac{1}{k_{twist}} (\mu_{twist} F_{n,0}sgn(\Omega_{twist}) - \gamma_{twist}\Omega_{twist}) -For *twisting sds*\ , the coefficients :math:`k_{twist}, \gamma_{twist}` +For *twisting sds*, the coefficients :math:`k_{twist}, \gamma_{twist}` and :math:`\mu_{twist}` are simply the user input parameters that follow the *twisting sds* keywords in the *pair_coeff* command. @@ -665,12 +665,6 @@ then LAMMPS will use that cutoff for the specified atom type combination, and automatically set pairwise cutoffs for the remaining atom types. -If two particles are moving away from each other while in contact, there -is a possibility that the particles could experience an effective attractive -force due to damping. If the *limit_damping* keyword is used, this option -will zero out the normal component of the force if there is an effective -attractive force. This keyword cannot be used with the JKR or DMT models. - ---------- .. include:: accel_styles.rst @@ -690,7 +684,7 @@ interactions is set to :math:`\mu_1`, and friction coefficient for type for type1-type2 interactions is computed as :math:`\sqrt{\mu_1\mu_2}` (unless explicitly specified to a different value by a *pair_coeff 1 2 ...* command). The exception to this is elastic modulus, only -applicable to *hertz/material*\ , *dmt* and *jkr* normal contact +applicable to *hertz/material*, *dmt* and *jkr* normal contact models. In that case, the effective elastic modulus is computed as: .. math:: @@ -715,7 +709,7 @@ specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these @@ -731,7 +725,7 @@ about the vector connecting the two particle centers. The last 3 (10-12) are the components of the vector connecting the centers of the two particles (x_I - x_J). -These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*\ , *p2*\ , ..., +These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*, *p2*, ..., *p12*\ . ---------- @@ -740,7 +734,7 @@ Restrictions """""""""""" All the granular pair styles are part of the GRANULAR package. It is -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles require that atoms store torque and angular velocity (omega) as defined by the :doc:`atom_style `. They also @@ -765,7 +759,7 @@ Related commands Default """"""" -For the *pair_coeff* settings: *damping viscoelastic*\ , *rolling none*\ , +For the *pair_coeff* settings: *damping viscoelastic*, *rolling none*, *twisting none*\ . References diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 88cb4ce880..ed24b481f9 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -140,13 +140,16 @@ not need to be specified in an input script that reads a restart file. All of the GROMACS pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not -support the *inner*\ , *middle*\ , *outer* keywords. +support the *inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" - none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index d0a7e69b00..6945356ecd 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -51,7 +51,7 @@ command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of GW elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. @@ -96,7 +96,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -104,7 +104,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 5e7183a348..f9b2a010fd 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -88,7 +88,7 @@ potential for the Donor-Acceptor interactions. :ref:`(Liu) ` showed that the Morse form gives improved results for Dendrimer simulations, when n = 2. -See the :doc:`Howto bioFF ` doc page for more information +See the :doc:`Howto bioFF ` page for more information on the DREIDING force field. .. note:: @@ -170,11 +170,11 @@ A single hydrogen atom type K can be specified, or a wild-card asterisk can be used in place of or in conjunction with the K arguments to select multiple types as hydrogen atoms. This takes the form "\*" or "\*n" or "n\*" or "m\*n". See the :doc:`pair_coeff ` -command doc page for details. +command page for details. -If the donor flag is *i*\ , then the atom of type I in the pair_coeff +If the donor flag is *i*, then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor. If the donor -flag is *j*\ , then the atom of type J in the pair_coeff command is +flag is *j*, then the atom of type J in the pair_coeff command is treated as the donor and I is the donor. This option is required because the :doc:`pair_coeff ` command requires that I <= J. @@ -219,7 +219,7 @@ re-specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. These pair styles tally a count of how many hydrogen bonding interactions they calculate each timestep and the hbond energy. These diff --git a/doc/src/pair_hdnnp.rst b/doc/src/pair_hdnnp.rst index 77a87642c4..1bd3030bf5 100644 --- a/doc/src/pair_hdnnp.rst +++ b/doc/src/pair_hdnnp.rst @@ -182,13 +182,13 @@ Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa -` command. It does not support the *inner*\ , *middle*\ , *outer* +` command. It does not support the *inner*, *middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-HDNNP package. It is only enabled if LAMMPS +This pair style is part of the ML-HDNNP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index f7de713c94..972c30c36f 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -83,7 +83,7 @@ general any combination of pair potentials can be used together in to produce an interaction that is not encoded in any single pair_style file, e.g. adding Coulombic forces between granular particles. -If the *hybrid/scaled* style is used instead of *hybrid/overlay*\ , +If the *hybrid/scaled* style is used instead of *hybrid/overlay*, contributions from sub-styles are weighted by their scale factors, which may be fractional or even negative. Furthermore the scale factors may be variables that may change during a simulation. This enables @@ -288,7 +288,7 @@ command can be used to selectively turn off processing of the compute tally styles, for example, if those pair styles (e.g. many-body styles) do not support this feature. -See the :doc:`pair_modify ` doc page for details on +See the :doc:`pair_modify ` page for details on the specific syntax, requirements and restrictions. ---------- @@ -375,7 +375,7 @@ coefficients to 0.0. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -389,15 +389,15 @@ corresponding suffix to all sub-styles, if those versions exist. Otherwise the non-accelerated version will be used. The individual accelerated sub-styles are part of the GPU, KOKKOS, -USER-INTEL, USER-OMP, and OPT packages, respectively. They are only +INTEL, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -422,7 +422,7 @@ generated, even if the sub-styles support mixing, and I,J pair coefficients must be explicitly defined. See the :doc:`pair_modify ` command for -details of mixing rules. See the See the doc page for the sub-style to +details of mixing rules. See the See the page for the sub-style to see if allows for mixing. The hybrid pair styles supports the :doc:`pair_modify ` @@ -439,7 +439,7 @@ style *hybrid/scaled* also the names of any variables used as scale factors are restored, but not the variables themselves, so those may need to be redefined when continuing from a restart. -These pair styles support the use of the *inner*\ , *middle*\ , and +These pair styles support the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, if their sub-styles do. diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index bc460c58a2..c188b4011e 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -77,7 +77,7 @@ calculating the normals. The parameter file (e.g. BNCH.ILP), is intended for use with *metal* :doc:`units `, with energies in meV. Two additional parameters, -*S*\ , and *rcut* are included in the parameter file. *S* is designed to +*S*, and *rcut* are included in the parameter file. *S* is designed to facilitate scaling of energies. *rcut* is designed to build the neighbor list for calculating the normals for each atom pair. @@ -139,10 +139,11 @@ that reads a restart file. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the INTERLAYER package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. -This pair potential requires the newton setting to be *on* for pair +This pair style requires the newton setting to be *on* for pair interactions. The BNCH.ILP potential file provided with LAMMPS (see the potentials diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 551a0bc46e..fcc86e0d77 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -99,7 +99,7 @@ an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 858b0eb984..1a33a3f4bb 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -64,7 +64,7 @@ can be found in pair style :doc:`ilp/graphene/hbn `. thus a data file with the "full" atom style is required to use this potential. The parameter file (e.g. CH.KC), is intended for use with *metal* -:doc:`units `, with energies in meV. Two additional parameters, *S*\ , +:doc:`units `, with energies in meV. Two additional parameters, *S*, and *rcut* are included in the parameter file. *S* is designed to facilitate scaling of energies. *rcut* is designed to build the neighbor list for calculating the normals for each atom pair. @@ -119,14 +119,15 @@ that reads a restart file. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the INTERLAYER package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. -This pair potential requires the newton setting to be *on* for pair +This pair style requires the newton setting to be *on* for pair interactions. The CH.KC potential file provided with LAMMPS (see the potentials -folder) are parameterized for metal units. You can use this potential +folder) is parameterized for metal units. You can use this pair style with any LAMMPS units, but you would need to create your own custom CC.KC potential file with all coefficients converted to the appropriate units. diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index bd02221074..937d868b55 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -48,7 +48,7 @@ each layer should have a separate atom type and interactions should only be computed between atom types of neighboring layers. The parameter file (e.g. CC.KC), is intended for use with metal -:doc:`units `, with energies in meV. An additional parameter, *S*\ , +:doc:`units `, with energies in meV. An additional parameter, *S*, is available to facilitate scaling of energies in accordance with :ref:`(vanWijk) `. @@ -58,8 +58,9 @@ Other interactions can be set to zero using pair_style *none*\ . Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the INTERLAYER package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index c44ad1f8a4..e8a6ccd7a4 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -34,7 +34,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of LCBOP elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want @@ -70,14 +70,14 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index 22b3114bf6..5afd0da92c 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -44,7 +44,7 @@ that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fas This shift is achieved by the last term in the equation for :math:`V_{ij}` above. The parameter file (e.g. CC.Lebedeva), is intended for use with metal -:doc:`units `, with energies in meV. An additional parameter, *S*\ , +:doc:`units `, with energies in meV. An additional parameter, *S*, is available to facilitate scaling of energies. This potential must be used in combination with hybrid/overlay. @@ -53,8 +53,9 @@ Other interactions can be set to zero using pair_style *none*\ . Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the INTERLAYER package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index c803d327e2..bfea7d172a 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -32,7 +32,7 @@ spherical particles, are calculated as the pairwise sum of N1\*N2 Lennard-Jones interactions. Interactions between a line segment with N spherical particles and a point particle are treated as the pairwise sum of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut -` doc page for the definition of Lennard-Jones interactions. +` page for the definition of Lennard-Jones interactions. The set of non-overlapping spherical sub-particles that represent a line segment are generated in the following manner. Their size is a @@ -76,7 +76,7 @@ the pair of particles to be included in the neighbor list. setting that is consistent with the length of the line segments you are using and the sub-particle cutoff settings. -For style *line/lj*\ , the following coefficients must be defined for +For style *line/lj*, the following coefficients must be defined for each pair of atom types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` @@ -126,7 +126,7 @@ This pair style does not write its information to :doc:`binary restart files ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -134,7 +134,7 @@ Restrictions """""""""""" This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Defining particles to be line segments so they participate in line/line or line/particle interactions requires the use the diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index caa1506994..321bf61be9 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -125,7 +125,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -142,8 +142,8 @@ styles in LAMMPS, an atom I will not interact with multiple images of atom J (assuming the images are within the cutoff distance), but only with the nearest image. -This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the :doc:`Build package ` doc page on for more info. +This style is part of the MISC package. It is only enabled if +LAMMPS is build with that package. See the :doc:`Build package ` page on for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 22f0d0dd37..939756e550 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -72,8 +72,8 @@ LJ cutoff specified in the pair_style command are used. ---------- -A version of these styles with a soft core, *lj/cut/soft*\ , suitable -for use in free energy calculations, is part of the USER-FEP package and +A version of these styles with a soft core, *lj/cut/soft*, suitable +for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. @@ -104,7 +104,7 @@ All of the *lj/cut* pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. The *lj/cut* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be +*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 3f1172618b..47000fe70a 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -79,7 +79,7 @@ pressure of the pair interaction. This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -This pair style supports the use of the *inner*\ , *middle*\ , and *outer* +This pair style supports the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for @@ -89,7 +89,10 @@ details. Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index e220e6e67c..d6470b26be 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -98,13 +98,16 @@ not need to be specified in an input script that reads a restart file. The lj/cubic pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not -support the *inner*\ , *middle*\ , *outer* keywords. +support the *inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" - none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index f729c2016e..e04da852dd 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -244,8 +244,8 @@ the pair_style command. ---------- A version of these styles with a soft core, *lj/cut/coul/soft*\ and -*lj/cut/coul/long/soft*\ , suitable for use in free energy calculations, is -part of the USER-FEP package and is documented with the :doc:`pair_style */soft ` styles. +*lj/cut/coul/long/soft*, suitable for use in free energy calculations, is +part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. ---------- @@ -278,7 +278,7 @@ All of the *lj/cut* pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. The *lj/cut/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be +*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. @@ -288,9 +288,13 @@ See the :doc:`run_style ` command for details. Restrictions """""""""""" -The *lj/cut/coul/long* styles are part of the KSPACE package. -These styles are only enabled if LAMMPS was built with those -packages. See the :doc:`Build package ` doc page for +The *lj/cut/coul/long* and *lj/cut/coul/msm* styles are part of the KSPACE package. + +The *lj/cut/coul/debye*, *lj/cut/coul/dsf*, and *lj/cut/coul/wolf* styles are part +of the EXTRA-PAIR package. + +These styles are only enabled if LAMMPS was built with those respective +packages. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 5f3b4e48e7..7198b60159 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -109,7 +109,7 @@ long-range Coulombic solver (Ewald or PPPM). atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the :doc:`Howto tip4p ` doc page for more information +See the :doc:`Howto tip4p ` page for more information on how to use the TIP4P pair styles and lists of parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2\*qdist when using the TIP4P pair @@ -163,8 +163,8 @@ the pair_style command. ---------- -A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable -for use in free energy calculations, is part of the USER-FEP package and +A version of these styles with a soft core, *lj/cut/tip4p/long/soft*, suitable +for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. @@ -199,7 +199,7 @@ All of the *lj/cut* pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be +*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. @@ -212,7 +212,7 @@ Restrictions The *lj/cut/tip4p/long* styles are part of the KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE package. These styles are only enabled if LAMMPS was built with those -packages. See the :doc:`Build package ` doc page for +packages. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 4d619a67e2..dca7a2dd2f 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -108,7 +108,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index 3609d093d9..f7bdf49189 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -113,7 +113,7 @@ massless charge site are specified as pair_style arguments. atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the :doc:`Howto tip4p ` doc page for more +See the :doc:`Howto tip4p ` page for more information on how to use the TIP4P pair style. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2\*qdist when using the TIP4P pair style, to account for @@ -123,22 +123,22 @@ LJ cutoff >= Coulombic cutoff + 2\*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. -If *flag_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 +If *flag_lj* is set to *long*, no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range portion can be calculated by using the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If -*flag_lj* is set to *cut*\ , the LJ interactions are simply cutoff, as +*flag_lj* is set to *cut*, the LJ interactions are simply cutoff, as with :doc:`pair_style lj/cut `. -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic +If *flag_coul* is set to *long*, no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of several :doc:`kspace_style ` command options such as *pppm* or *ewald*\ . Note that if *flag_lj* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the LJ and Coulombic -interactions. If *flag_coul* is set to *off*\ , Coulombic interactions +interactions. If *flag_coul* is set to *off*, Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms @@ -163,10 +163,10 @@ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. -Note that if you are using *flag_lj* set to *long*\ , you +Note that if you are using *flag_lj* set to *long*, you cannot specify a LJ cutoff for an atom type pair, since only one global LJ cutoff is allowed. Similarly, if you are using *flag_coul* -set to *long*\ , you cannot specify a Coulombic cutoff for an atom type +set to *long*, you cannot specify a Coulombic cutoff for an atom type pair, since only one global Coulombic cutoff is allowed. For *lj/long/tip4p/long* only the LJ cutoff can be specified @@ -176,10 +176,10 @@ specified in the pair_style command. ---------- -A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with +A version of these styles with a soft core, *lj/cut/soft*, suitable for use in +free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is -only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only available if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- @@ -210,8 +210,8 @@ Lennard-Jones portion of the energy and pressure. These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -The pair lj/long/coul/long styles support the use of the *inner*\ , -*middle*\ , and *outer* keywords of the :doc:`run_style respa ` +The pair lj/long/coul/long styles support the use of the *inner*, +*middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -222,7 +222,7 @@ Restrictions """""""""""" These styles are part of the KSPACE package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_relres.rst b/doc/src/pair_lj_relres.rst index 20a705d876..df5227ebbb 100644 --- a/doc/src/pair_lj_relres.rst +++ b/doc/src/pair_lj_relres.rst @@ -235,7 +235,7 @@ For atom type pairs :math:`I,\:J` with :math:`I\;!=J`, the :math:`\sigma^{CG}`, :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, and :math:`r_{co}` parameters for this pair style can be mixed, if not defined explicitly. All parameters are mixed according to the -pair_modify mix option. The default mix value is *geometric*\ , +pair_modify mix option. The default mix value is *geometric*, and it is recommended to use with this *lj/relres* style. See the "pair_modify" command for details. @@ -259,13 +259,16 @@ specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index a77eefd023..4799ca3277 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -102,13 +102,16 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index b105fc4911..7a3ba7a3d5 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -82,13 +82,16 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" - none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 6b918c1071..19ca8df973 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -130,14 +130,14 @@ to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -These styles are part of the USER-YAFF package. They are only enabled +These styles are part of the YAFF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index 8fab58ef12..f7e26389c3 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -114,8 +114,8 @@ with the LD expressed as \rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij}) -where :math:`\alpha` gives the type of atom *i*\ , :math:`\beta` the -type of atom *j*\ , and the coefficients *a* and *b* filter for atom +where :math:`\alpha` gives the type of atom *i*, :math:`\beta` the +type of atom *j*, and the coefficients *a* and *b* filter for atom types as specified by the user. *a* is called the central atom filter as it determines to which atoms the potential applies; :math:`a_{\alpha} = 1` if the LD potential applies to atom type :math:`\alpha` else zero. On the @@ -220,8 +220,9 @@ an input script that reads a restart file. Restrictions """""""""""" -The local/density pair style is a part of the USER-MISC package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +The local/density pair style is a part of the MANYBODY package. It is +only enabled if LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index e83a16c80b..49872c31f2 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -139,8 +139,8 @@ Since lubrication forces are dissipative, it is usually desirable to thermostat the system at a constant temperature. If Brownian motion (at a constant temperature) is desired, it can be set using the :doc:`pair_style brownian ` command. These pair styles -and the brownian style should use consistent parameters for *mu*\ , -*flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . +and the brownian style should use consistent parameters for *mu*, +*flaglog*, *flagfld*, *cutinner*, *cutoff*, *flagHI* and *flagVF*\ . ---------- @@ -185,7 +185,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -193,7 +193,7 @@ Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Only spherical monodisperse particles are allowed for pair_style lubricate. diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index a9382556c5..2706291da1 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -137,15 +137,15 @@ for with the following types of walls: :doc:`wall/lj93 `, volume fraction will be used when walls do not coincide with the box boundary, as well as when walls move and thereby cause a change in the volume fraction. To use these wall styles with pair_style *lubricateU* -or *lubricateU/poly*\ , the *fld yes* option must be specified in the +or *lubricateU/poly*, the *fld yes* option must be specified in the fix wall command. Since lubrication forces are dissipative, it is usually desirable to thermostat the system at a constant temperature. If Brownian motion (at a constant temperature) is desired, it can be set using the :doc:`pair_style brownian ` command. These pair styles -and the brownian style should use consistent parameters for *mu*\ , -*flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . +and the brownian style should use consistent parameters for *mu*, +*flaglog*, *flagfld*, *cutinner*, *cutoff*, *flagHI* and *flagVF*\ . ---------- @@ -186,7 +186,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -194,7 +194,7 @@ Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Currently, these pair styles assume that all other types of forces/torques on the particles have been already been computed when diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 84d312e47c..dc2667dba7 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -53,7 +53,7 @@ Examples Description """"""""""" -The *lj/mdf*\ , *buck/mdf* and *lennard/mdf* compute the standard 12-6 +The *lj/mdf*, *buck/mdf* and *lennard/mdf* compute the standard 12-6 Lennard-Jones and Buckingham potential with the addition of a taper function that ramps the energy and force smoothly to zero between an inner and outer cutoff. @@ -62,7 +62,7 @@ inner and outer cutoff. E_{smooth}(r) = E(r)*f(r) -The tapering, *f(r)*\ , is done by using the Mei, Davenport, Fernando +The tapering, *f(r)*, is done by using the Mei, Davenport, Fernando function :ref:`(Mei) `. .. math:: @@ -82,7 +82,7 @@ outer cutoff radius. ---------- -For the *lj/mdf* pair_style, the potential energy, *E(r)*\ , is the +For the *lj/mdf* pair_style, the potential energy, *E(r)*, is the standard 12-6 Lennard-Jones written in the epsilon/sigma form: .. math:: @@ -104,7 +104,7 @@ described below: ---------- -For the *buck/mdf* pair_style, the potential energy, *E(r)*\ , is the +For the *buck/mdf* pair_style, the potential energy, *E(r)*, is the standard Buckingham potential with three required coefficients. The two cutoffs can be omitted and default to the corresponding global values: @@ -121,7 +121,7 @@ global values: ---------- -For the *lennard/mdf* pair_style, the potential energy, *E(r)*\ , is the +For the *lennard/mdf* pair_style, the potential energy, *E(r)*, is the standard 12-6 Lennard-Jones written in the A/B form: .. math:: @@ -158,8 +158,8 @@ tail corrections to pressure and energy. These styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , -*middle*\ , *outer* keywords. +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*, +*middle*, *outer* keywords. ---------- @@ -167,7 +167,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +EXTRA-PAIR package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meam.rst similarity index 97% rename from doc/src/pair_meamc.rst rename to doc/src/pair_meam.rst index 757c4c6712..d091496325 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meam.rst @@ -1,6 +1,6 @@ -.. index:: pair_style meam/c +.. index:: pair_style meam -pair_style meam/c command +pair_style meam command ========================= Syntax @@ -8,14 +8,14 @@ Syntax .. code-block:: LAMMPS - pair_style meam/c + pair_style meam Examples """""""" .. code-block:: LAMMPS - pair_style meam/c + pair_style meam pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni @@ -28,13 +28,13 @@ Description as of November 2010; see description below of the mixture_ref_t parameter -Style *meam/c* computes pairwise interactions for a variety of materials +Style *meam* computes pairwise interactions for a variety of materials using modified embedded-atom method (MEAM) potentials :ref:`(Baskes) `. Conceptually, it is an extension to the original :doc:`EAM potentials ` which adds angular forces. It is thus suitable for modeling metals and alloys with fcc, bcc, hcp and diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. Style *meam/c* is a translation of the (now obsolete) +silicon and carbon. Style *meam* is a translation of the (now obsolete) *meam* code from Fortran to C++. It is functionally equivalent to *meam* but more efficient, and thus *meam* has been removed from LAMMPS after the 12 December 2018 release. @@ -79,7 +79,7 @@ command, where N is the number of LAMMPS atom types: * MEAM parameter file * N element names = mapping of MEAM elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential files. As an example, the potentials/library.meam file has generic MEAM @@ -376,22 +376,22 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -The *meam/c* style is provided in the USER-MEAMC package. It is +The *meam* style is provided in the MEAM package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. The maximum number of elements, that can be read from the MEAM library file, is determined at compile time. The default is 5. If you need support for more elements, you have to change the define for the constant 'maxelt' at the beginning of the file -src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no +src/MEAM/meam.h and update/recompile LAMMPS. There is no limit on the number of atoms types. Related commands diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 6bedb9b4fb..9f231cb78c 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -50,7 +50,7 @@ the total energy E is given by where the five functions :math:`\phi, U, \rho, f,` and *g* depend on the chemistry of the atoms in the interaction. In particular, if there are -N different chemistries, there are N different *U*\ , :math:`\rho`, and +N different chemistries, there are N different *U*, :math:`\rho`, and *f* functions, while there are N(N+1)/2 different :math:`\phi` and *g* functions. The new style multicomponent MEAM potential files are indicated by the second line in the file starts with "meam/spline" @@ -81,7 +81,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of spline-based MEAM elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine the Ti.meam.spline file has values for Ti (old style). @@ -132,7 +132,7 @@ and pair_coeff commands in an input script that reads a restart file. The *meam/spline* pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -144,14 +144,14 @@ for pair interactions. This pair style does not support mapping multiple atom types to the same element. -This pair style is only enabled if LAMMPS was built with the USER-MISC -package. See the :doc:`Build package ` doc page for more +This pair style is only enabled if LAMMPS was built with the MANYBODY +package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style meam/c ` +:doc:`pair_coeff `, :doc:`pair_style meam ` Default """"""" diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 70567d9ffa..686081e854 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -67,7 +67,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of spline-based MEAM+SW elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine the Ti.meam.sw.spline file has values for Ti. @@ -94,7 +94,7 @@ potentials. systems in the future. Example input scripts that use this pair style are provided -in the examples/USER/misc/meam_sw_spline directory. +in the examples/PACKAGES/meam_sw_spline directory. ---------- @@ -114,7 +114,7 @@ and pair_coeff commands in an input script that reads a restart file. The *meam/sw/spline* pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not -support the *inner*\ , *middle*\ , *outer* keywords. +support the *inner*, *middle*, *outer* keywords. ---------- @@ -124,14 +124,14 @@ Restrictions This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. -This pair style is only enabled if LAMMPS was built with the USER-MISC -package. See the :doc:`Build package ` doc page for more +This pair style is only enabled if LAMMPS was built with the MANYBODY +package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style meam/c `, +:doc:`pair_coeff `, :doc:`pair_style meam `, :doc:`pair_style meam/spline ` Default diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 90b6644fd9..78a6680b6b 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -115,15 +115,15 @@ an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This style is part of the USER-MESONT package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This style is part of the MESONT package. It is only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 6bb259a10d..e5cd2643dd 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -238,7 +238,7 @@ Example scripts """"""""""""""" There are example scripts for using all these pair styles in -examples/USER/mesodpd. The example for an eDPD simulation models heat +examples/PACKAGES/mesodpd. The example for an eDPD simulation models heat conduction with source terms analog of periodic Poiseuille flow problem. The setup follows Fig.12 in :ref:`(Li2014_JCP) `. The output of the short eDPD simulation (about 2 minutes on a single core) @@ -284,13 +284,13 @@ concentration profiles of the two chemical species as Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support +The styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support +The styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* do not support the :doc:`pair_modify ` shift, table, and tail options. -The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not write +The styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* do not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. @@ -298,9 +298,9 @@ that reads a restart file. Restrictions """""""""""" -The pair styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* are part of -the USER-MESODPD package. It is only enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +The pair styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* are part of +the DPD-MESO package. It is only enabled if LAMMPS was built with +that package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_mesont_tpm.rst b/doc/src/pair_mesont_tpm.rst index d698dddd92..efdb70baf0 100644 --- a/doc/src/pair_mesont_tpm.rst +++ b/doc/src/pair_mesont_tpm.rst @@ -132,7 +132,7 @@ Restrictions """""""""""" -This pair style is a part of the USER-MSEONT package, and it is only enabled if +This pair style is a part of the MSEONT package, and it is only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more information. diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 673c5f5160..6ef9f52fac 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -132,7 +132,7 @@ range for each potential and give appropriate references for the potentials. It is expected that MGPT potentials for additional materials will be added over time. -Useful example MGPT scripts are given in the examples/USER/mgpt +Useful example MGPT scripts are given in the examples/PACKAGES/mgpt directory. These scripts show the necessary steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples @@ -161,15 +161,15 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This pair style is part of the USER-MGPT package and is only enabled -if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the MGPT package and is only enabled +if LAMMPS is built with that package. See the :doc:`Build package ` page for more info. The MGPT potentials require the :doc:`newtion ` setting to be "on" for pair style interactions. diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index e1a34893c9..089f8d3d29 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -82,7 +82,7 @@ pressure of the pair interaction. This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -This pair style supports the use of the *inner*\ , *middle*\ , and *outer* +This pair style supports the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for @@ -92,7 +92,10 @@ details. Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index 73ebe48856..900a2c2e6a 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -156,7 +156,7 @@ contains a few more arguments (e.g., *nmax* and *alpha*). The preparation of SO3 descriptor and model files can be done with the `Pyxtal_FF `_ package. -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for these *model* and *descriptor* files. .. note:: @@ -185,18 +185,18 @@ that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This pair style is part of the MLIAP package. It is only enabled if +This pair style is part of the ML-IAP package. It is only enabled if LAMMPS was built with that package. In addition, building LAMMPS with -the MLIAP package requires building LAMMPS with the SNAP package. The -*mliappy* model requires building LAMMPS with the PYTHON package. See -the :doc:`Build package ` doc page for more info. +the ML-IAP package requires building LAMMPS with the ML-SNAP package. +The *mliappy* model requires building LAMMPS with the PYTHON package. +See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index b8969c0131..1a62a4c1a0 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -82,7 +82,7 @@ as sigma. Note that not all pair styles support mixing and some mix options are not available for certain pair styles. Also, there are additional restrictions when using :doc:`pair style hybrid or hybrid/overlay `. -See the doc page for individual pair styles for those restrictions. Note also that the +See the page for individual pair styles for those restrictions. Note also that the :doc:`pair_coeff ` command also can be used to directly set coefficients for a specific I != J pairing, in which case no mixing is performed. @@ -117,7 +117,7 @@ option. The *table* and *table/disp* keywords apply to pair styles with a long-range Coulombic term or long-range dispersion term respectively; -see the doc page for individual styles to see which potentials support +see the page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2\^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a @@ -149,11 +149,11 @@ pairwise interactions are computed via table lookup for simulations with "real" units, but some close pairs may be computed directly (non-table) for simulations with "lj" units. -When the *tail* keyword is set to *yes*\ , certain pair styles will +When the *tail* keyword is set to *yes*, certain pair styles will add a long-range VanderWaals tail "correction" to the energy and pressure. These corrections are bookkeeping terms which do not affect dynamics, unless a constant-pressure simulation is being performed. -See the doc page for individual styles to see which support this +See the page for individual styles to see which support this option. These corrections are included in the calculation and printing of thermodynamic quantities (see the :doc:`thermo_style ` command). Their effect will also be included in @@ -256,7 +256,7 @@ and *coul* settings to different values. .. note:: The *special* keyword is not compatible with pair styles from the - GPU or the USER-INTEL package and attempting to use it will cause + GPU or the INTEL package and attempting to use it will cause an error. .. note:: @@ -289,7 +289,7 @@ Restrictions You cannot use *shift* yes with *tail* yes, since those are conflicting options. You cannot use *tail* yes with 2d simulations. You cannot use *special* with pair styles from the GPU or -USER-INTEL package. +INTEL package. Related commands """""""""""""""" diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index b1d43252fd..982ef86603 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -55,9 +55,9 @@ read by the :doc:`read_data ` as described below: Restrictions """""""""""" -This style is part of the USER-MISC package. It is only enabled if +This style is part of the EXTRA-PAIR package. It is only enabled if LAMMPS is built with that package. See the :doc:`Build package -` doc page on for more info. +` page on for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 5ede37a916..686dd6e511 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -85,12 +85,12 @@ the *morse* and *morse/smooth/linear* styles. ---------- -A version of the *morse* style with a soft core, *morse/soft*\ , -suitable for use in free energy calculations, is part of the USER-FEP +A version of the *morse* style with a soft core, *morse/soft*, +suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. ---------- @@ -119,7 +119,7 @@ to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -127,7 +127,8 @@ Restrictions """""""""""" The *morse/smooth/linear* pair style is only enabled if LAMMPS was -built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. +built with the EXTRA-PAIR package. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 111660c2bb..c8c8551df5 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -11,7 +11,7 @@ Syntax pair_style multi/lucy style N keyword ... * style = *lookup* or *linear* = method of interpolation -* N = use N values in *lookup*\ , *linear* tables +* N = use N values in *lookup*, *linear* tables Examples """""""" @@ -186,15 +186,15 @@ commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index f6e6652271..6cb56360ba 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -14,7 +14,7 @@ Syntax pair_style multi/lucy/rx style N keyword ... * style = *lookup* or *linear* = method of interpolation -* N = use N values in *lookup*\ , *linear* tables +* N = use N values in *lookup*, *linear* tables * weighting = fractional or molecular (optional) Examples @@ -214,7 +214,7 @@ commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -225,8 +225,8 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index 853da9d821..203c707ec0 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -30,7 +30,7 @@ energy E of a system of atoms as where :math:`\theta_0` is the equilibrium value of the angle and *K* is a prefactor. Note that the usual 1/2 factor is included in *K*\ . The form -of the potential is identical to that used in angle_style *harmonic*\ , +of the potential is identical to that used in angle_style *harmonic*, but in this case, the atoms do not need to be explicitly bonded. Only a single pair_coeff command is used with this style which @@ -42,7 +42,7 @@ number of LAMMPS atom types: * filename * N element names = mapping of elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.nb3b.harmonic has potential values @@ -100,7 +100,7 @@ Restrictions """""""""""" This pair style can only be used if LAMMPS was built with the MANYBODY -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index d38e21fd15..2c356bb4ca 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -114,7 +114,7 @@ N-M and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both N-M and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the N-M and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style *nm*\ , since it +type pair. You cannot specify 2 cutoffs for style *nm*, since it has no Coulombic terms. For *nm/cut/coul/long* only the N-M cutoff can be specified since a @@ -147,7 +147,7 @@ to be specified in an input script that reads a restart file. All of the *nm* pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -156,8 +156,9 @@ the :doc:`run_style respa ` command. They do not support the Restrictions """""""""""" -These pair styles are part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These pair styles are part of the EXTRA-PAIR package. They are only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index b2f27c355e..3dc87a7815 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -30,7 +30,7 @@ skin distance is large enough to acquire atoms needed for computing bonds, angles, etc. A pair style of *none* will also prevent pairwise neighbor lists from -being built. However if the :doc:`neighbor ` style is *bin*\ , +being built. However if the :doc:`neighbor ` style is *bin*, data structures for binning are still allocated. If the neighbor skin distance is small, then these data structures can consume a large amount of memory. So you should either set the neighbor style to diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 4cc57868b4..fcc7dc2e49 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -63,7 +63,7 @@ Description The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxdna/excv*\ , the stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* +excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*, cross-stacking *oxdna/xstk* and coaxial stacking interaction *oxdna/coaxstk* as well as the hydrogen-bonding interaction *oxdna/hbond* between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths @@ -91,15 +91,23 @@ for a detailed description of the oxDNA force field. or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +.. note:: + + These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* + (see documentation of :doc:`atom_style `). The *atom_style oxdna* + stores the 3'-to-5' polarity of the nucleotide strand, which is set through + the bond topology in the data file. The first (second) atom in a bond definition + is understood to point towards the 3'-end (5'-end) of the strand. + +Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxDNA publications :ref:`(Ouldridge) `, :ref:`(Ouldridge-DPhil) ` @@ -111,8 +119,8 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +CG-DNA package and the MOLECULE and ASPHERE package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" @@ -120,7 +128,7 @@ Related commands :doc:`bond_style oxdna/fene `, :doc:`pair_coeff `, :doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, :doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, -:doc:`fix nve/dotc/langevin ` +:doc:`atom_style oxdna `, :doc:`fix nve/dotc/langevin ` Default """"""" diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index ee01f2f488..f253c4ae10 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -72,8 +72,8 @@ Description The *oxdna2* pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxdna2/excv*\ , the stacking *oxdna2/stk*\ , cross-stacking *oxdna2/xstk* -and coaxial stacking interaction *oxdna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxdna2/dh* +excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*, cross-stacking *oxdna2/xstk* +and coaxial stacking interaction *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* as well as the hydrogen-bonding interaction *oxdna2/hbond* between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using @@ -100,15 +100,23 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 fo e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +.. note:: + + These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* + (see documentation of :doc:`atom_style `). The *atom_style oxdna* + stores the 3'-to-5' polarity of the nucleotide strand, which is set through + the bond topology in the data file. The first (second) atom in a bond definition + is understood to point towards the 3'-end (5'-end) of the strand. + +Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxDNA2 publications :ref:`(Snodin) ` and :ref:`(Sulc) `. @@ -118,8 +126,8 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +CG-DNA package and the MOLECULE and ASPHERE package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" @@ -127,7 +135,7 @@ Related commands :doc:`bond_style oxdna2/fene `, :doc:`pair_coeff `, :doc:`bond_style oxdna/fene `, :doc:`pair_style oxdna/excv `, :doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, -:doc:`fix nve/dotc/langevin ` +:doc:`atom_style oxdna `, :doc:`fix nve/dotc/langevin ` Default """"""" diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 831e4d9c4e..7b8220740c 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -73,8 +73,8 @@ Description The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk* -and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh* +excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk* +and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths are supported :ref:`(Sulc2) `. Quasi-unique base-pairing between nucleotides can be achieved by using @@ -101,15 +101,23 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxRNA2 fo e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +.. note:: + + These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* + (see documentation of :doc:`atom_style `). The *atom_style oxdna* + stores the 3'-to-5' polarity of the nucleotide strand, which is set through + the bond topology in the data file. The first (second) atom in a bond definition + is understood to point towards the 3'-end (5'-end) of the strand. + +Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxRNA2 publications :ref:`(Sulc1) ` and :ref:`(Sulc2) `. @@ -119,8 +127,8 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +CG-DNA package and the MOLECULE and ASPHERE package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" @@ -128,7 +136,7 @@ Related commands :doc:`bond_style oxrna2/fene `, :doc:`pair_coeff `, :doc:`bond_style oxdna/fene `, :doc:`pair_style oxdna/excv `, :doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, -:doc:`fix nve/dotc/langevin ` +:doc:`atom_style oxdna `, :doc:`fix nve/dotc/langevin ` Default """"""" diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 56ae0f32dc..ad66febdf5 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -64,7 +64,7 @@ The pair_style *pace* command may be followed by an optional keyword is used for the calculation of basis functions and derivatives. The default is *recursive*. -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the ACE coefficient file. Mixing, shift, table, tail correction, restart, rRESPA info @@ -84,16 +84,16 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This pair style is part of the USER-PACE package. It is only enabled if LAMMPS +This pair style is part of the ML-PACE package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 2a1c7f6aa5..45b406dd61 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -170,7 +170,7 @@ to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -178,7 +178,7 @@ Restrictions """""""""""" All of these styles are part of the PERI package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 3df70a017c..8968c9d7d2 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -195,7 +195,7 @@ atom types: * filename * N element names = mapping of polymorphic potential elements to atom types -See the pair_coeff doc page for alternate ways to specify the path for +See the pair_coeff page for alternate ways to specify the path for the potential file. Several files for polymorphic potentials are included in the potentials directory of the LAMMPS distribution. They have a "poly" suffix. @@ -317,7 +317,7 @@ atomic structure data file. This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 99b8ebd766..3d087565be 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -184,7 +184,7 @@ always **append** to a table file, while pair style table will use the class, the table pair style will still read the old variant unless the table file is first deleted. -After switching the pair style to *table*\ , the potential tables need +After switching the pair style to *table*, the potential tables need to be assigned to the LAMMPS atom types like this: .. code-block:: LAMMPS @@ -215,7 +215,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -223,7 +223,7 @@ Restrictions """""""""""" This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 43aa2eef62..c150561cb1 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -42,7 +42,7 @@ number of LAMMPS atom types: * QUIP initialization string * N atomic numbers = mapping of QUIP elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the @@ -55,7 +55,7 @@ appropriate initialization strings are also advised. The list of atomic numbers must be matched to the LAMMPS atom types specified in the LAMMPS data file or elsewhere. -Two examples input scripts are provided in the examples/USER/quip +Two examples input scripts are provided in the examples/PACKAGES/quip directory. Mixing, shift, table, tail correction, restart, rRESPA info @@ -70,13 +70,13 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-QUIP package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the ML-QUIP package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. QUIP potentials are parameterized in electron-volts and Angstroms and therefore should be used with LAMMPS metal :doc:`units `. diff --git a/doc/src/pair_rann.rst b/doc/src/pair_rann.rst index 4177bae0c7..a9ad5d9236 100644 --- a/doc/src/pair_rann.rst +++ b/doc/src/pair_rann.rst @@ -378,10 +378,12 @@ The activation functions are computed as follows: Restrictions """""""""""" -Pair style *rann* is part of the USER-RANN package. It is only enabled if LAMMPS was built with that +Pair style *rann* is part of the ML-RANN package. It is only enabled if LAMMPS was built with that package. Additionally, if any spin fingerprint styles are used LAMMPS must be built with the SPIN package as well. +Pair style *rann* does not support computing per-atom stress or using :doc:`pair_modify nofdotr `. + Defaults """""""""""" diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxff.rst similarity index 75% rename from doc/src/pair_reaxc.rst rename to doc/src/pair_reaxff.rst index b28b387e0b..a3a9c81cb8 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxff.rst @@ -1,18 +1,18 @@ -.. index:: pair_style reax/c -.. index:: pair_style reax/c/kk -.. index:: pair_style reax/c/omp +.. index:: pair_style reaxff +.. index:: pair_style reaxff/kk +.. index:: pair_style reaxff/omp -pair_style reax/c command +pair_style reaxff command ========================= -Accelerator Variants: *reax/c/kk*, *reax/c/omp* +Accelerator Variants: *reaxff/kk*, *reaxff/omp* Syntax """""" .. code-block:: LAMMPS - pair_style reax/c cfile keyword value + pair_style reaxff cfile keyword value * cfile = NULL or name of a control file * zero or more keyword/value pairs may be appended @@ -20,7 +20,7 @@ Syntax .. parsed-literal:: keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds* - *checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix + *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff fix *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction *safezone* = factor used for array allocation @@ -32,37 +32,38 @@ Examples .. code-block:: LAMMPS - pair_style reax/c NULL - pair_style reax/c controlfile checkqeq no - pair_style reax/c NULL lgvdw yes - pair_style reax/c NULL safezone 1.6 mincap 100 + pair_style reaxff NULL + pair_style reaxff controlfile checkqeq no + pair_style reaxff NULL lgvdw yes + pair_style reaxff NULL safezone 1.6 mincap 100 pair_coeff * * ffield.reax C H O N Description """"""""""" -Style *reax/c* computes the ReaxFF potential of van Duin, Goddard and +Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and co-workers. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. There is more than one version of ReaxFF. The version implemented in LAMMPS uses the functional forms documented in the -supplemental information of the following paper: :ref:`(Chenoweth et al., 2008) `. The version integrated into LAMMPS matches -the most up-to-date version of ReaxFF as of summer 2010. For more -technical details about the pair reax/c implementation of ReaxFF, see -the :ref:`(Aktulga) ` paper. The *reax/c* style was initially -implemented as a stand-alone C code and is now integrated into LAMMPS -as a package. +supplemental information of the following paper: +:ref:`(Chenoweth et al., 2008) `. The version integrated +into LAMMPS matches the version of ReaxFF From Summer 2010. For more +technical details about the pair reaxff implementation of ReaxFF, see +the :ref:`(Aktulga) ` paper. The *reaxff* style was initially +implemented as a stand-alone C code and is now converted to C++ and +integrated into LAMMPS as a package. -The *reax/c/kk* style is a Kokkos version of the ReaxFF potential that -is derived from the *reax/c* style. The Kokkos version can run on GPUs +The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that +is derived from the *reaxff* style. The Kokkos version can run on GPUs and can also use OpenMP multithreading. For more information about the Kokkos package, see :doc:`Packages details ` and :doc:`Speed kokkos ` doc pages. One important -consideration when using the *reax/c/kk* style is the choice of either +consideration when using the *reaxff/kk* style is the choice of either half or full neighbor lists. This setting can be changed using the Kokkos :doc:`package ` command. -The *reax/c* style differs from the (obsolete) "pair_style reax" +The *reaxff* style differs from the (obsolete) "pair_style reax" command in the implementation details. The *reax* style was a Fortran library, linked to LAMMPS. The *reax* style has been removed from LAMMPS after the 12 December 2018 version. @@ -73,7 +74,7 @@ documented in potentials/README.reax. The default ffield.reax contains parameterizations for the following elements: C, H, O, N. The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of *pair_style reax/c* potential +Duin. We have tested the accuracy of *pair_style reaxff* potential against the original ReaxFF code for the systems mentioned above. You can use other ffield files for specific chemical systems that may be available elsewhere (but note that their accuracy may not have been @@ -102,10 +103,11 @@ control variable. The format of the control file is described below. The LAMMPS default values for the ReaxFF global parameters correspond to those used by Adri van Duin's stand-alone serial - code. If these are changed by setting control variables in the control - file, the results from LAMMPS and the serial code will not agree. + code. If these are changed by setting control variables in the + control file, the results from LAMMPS and the serial code will + not agree. -Examples using *pair_style reax/c* are provided in the examples/reax +Examples using *pair_style reaxff* are provided in the examples/reax sub-directory. Use of this pair style requires that a charge be defined for every @@ -115,27 +117,30 @@ charges. The ReaxFF parameter files provided were created using a charge equilibration (QEq) model for handling the electrostatic interactions. -Therefore, by default, LAMMPS requires that the :doc:`fix qeq/reax ` command be used with *pair_style reax/c* -when simulating a ReaxFF model, to equilibrate charge each timestep. -Using the keyword *checkqeq* with the value *no* -turns off the check for *fix qeq/reax*\ , -allowing a simulation to be run without charge equilibration. -In this case, the static charges you -assign to each atom will be used for computing the electrostatic -interactions in the system. -See the :doc:`fix qeq/reax ` command for details. +Therefore, by default, LAMMPS requires that either the +:doc:`fix qeq/reaxff ` or the +:doc:`fix qeq/shielded ` command be used with +*pair_style reaxff* when simulating a ReaxFF model, to equilibrate +the charges each timestep. + +Using the keyword *checkqeq* with the value *no* turns off the check +for the QEq fixes, allowing a simulation to be run without charge +equilibration. In this case, the static charges you assign to each +atom will be used for computing the electrostatic interactions in +the system. See the :doc:`fix qeq/reaxff ` or +:doc:`fix qeq/shielded ` command documentation for more details. Using the optional keyword *lgvdw* with the value *yes* turns on the -low-gradient correction of the ReaxFF/C for long-range London -Dispersion, as described in the :ref:`(Liu) ` paper. Force field -file *ffield.reax.lg* is designed for this correction, and is trained -for several energetic materials (see "Liu"). When using lg-correction, -recommended value for parameter *thb* is 0.01, which can be set in the +low-gradient correction of ReaxFF for long-range London Dispersion, +as described in the :ref:`(Liu) ` paper. The bundled force +field file *ffield.reax.lg* is designed for this correction, and is +trained for several energetic materials (see "Liu"). When using *lgvdw yes*, +the recommended value for parameter *thb* is 0.01, which can be set in the control file. Note: Force field files are different for the original -or lg corrected pair styles, using wrong ffield file generates an -error message. +or lg corrected pair styles, using the wrong ffield file generates an +error. -Using the optional keyword *enobonds* with the value *yes*\ , the energy +Using the optional keyword *enobonds* with the value *yes*, the energy of atoms with no bonds (i.e. isolated atoms) is included in the total potential energy and the per-atom energy of that atom. If the value *no* is specified then the energy of atoms with no bonds is set to @@ -143,8 +148,8 @@ zero. The latter behavior is usual not desired, as it causes discontinuities in the potential energy when the bonding of an atom drops to zero. -Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used -for allocating reax/c arrays. Increasing these values can avoid memory +Optional keywords *safezone*, *mincap*, and *minhbonds* are used +for allocating reaxff arrays. Increasing these values can avoid memory problems, such as segmentation faults and bondchk failed errors, that could occur under certain conditions. These keywords are not used by the Kokkos version, which instead uses a more robust memory allocation @@ -158,7 +163,8 @@ equilibration contributions which are stored in the thermo variable :doc:`thermo ` command. This pair style tallies a breakdown of the total ReaxFF potential -energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 14. +energy into sub-categories, which can be accessed via the +:doc:`compute pair ` command as a vector of values of length 14. The 14 values correspond to the following sub-categories (the variable names in italics match those used in the original FORTRAN ReaxFF code): @@ -183,14 +189,14 @@ headings) the following commands could be included in an input script: .. code-block:: LAMMPS - compute reax all pair reax/c + compute reax all pair reaxff variable eb equal c_reax[1] variable ea equal c_reax[2] [...] variable eqeq equal c_reax[14] thermo_style custom step temp epair v_eb v_ea [...] v_eqeq -Only a single pair_coeff command is used with the *reax/c* style which +Only a single pair_coeff command is used with the *reaxff* style which specifies a ReaxFF potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N additional arguments after the filename in the pair_coeff command, @@ -209,7 +215,7 @@ to M. Each of the N indices you specify for the N atom types of LAMMPS atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will be mapped to whatever element you specify as the first index value, etc. If a mapping value is specified as NULL, the mapping is not -performed. This can be used when the *reax/c* style is used as part +performed. This can be used when the *reaxff* style is used as part of the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with other potentials. @@ -241,7 +247,7 @@ brief description of their use and default values. *simulation_name* - Output files produced by *pair_style reax/c* carry + Output files produced by *pair_style reaxff* carry this name + extensions specific to their contents. Partial energies are reported with a ".pot" extension, while the trajectory file has ".trj" extension. @@ -286,8 +292,7 @@ brief description of their use and default values. to be considered in three body interactions. (default value = 0.00001) *write_freq* - Frequency of writes into the trajectory file. (default - value = 0) + Frequency of writes into the trajectory file. (default value = 0) *traj_title* Title of the trajectory - not the name of the trajectory file. @@ -315,13 +320,14 @@ Mixing, shift, table, tail correction, restart, rRESPA info This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you +This pair style does not write its information to :doc:`binary restart files `, +since it is stored in potential files. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -332,19 +338,21 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-REAXC package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the REAXFF package. It is only enabled +if LAMMPS was built with that package. +See the :doc:`Build package ` page for more info. The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real :doc:`units `. You can use -the ReaxFF potential with any LAMMPS units, but you would need to +directory are parameterized for *real* :doc:`units `. You can use +the ReaxFF pair style with any LAMMPS units, but you would need to create your own potential file with coefficients listed in the appropriate units if your simulation does not use "real" units. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`fix qeq/reax `, :doc:`fix reax/c/bonds `, :doc:`fix reax/c/species ` +:doc:`pair_coeff `, :doc:`fix qeq/reaxff `, +:doc:`fix reaxff/bonds `, :doc:`fix reaxff/species ` Default """"""" diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 0932730469..8d7b5eca5b 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -191,7 +191,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords of the :doc:`run_style command `. +*inner*, *middle*, *outer* keywords of the :doc:`run_style command `. ---------- @@ -199,7 +199,7 @@ Restrictions """""""""""" This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires that atoms be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 541c53d37e..f389079e15 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -141,14 +141,14 @@ All of the lj/sdk pair styles write their information to :doc:`binary restart fi not need to be specified in an input script that reads a restart file. The lj/sdk and lj/cut/coul/long pair styles do not support -the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command. +the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command. ---------- Restrictions """""""""""" -All of the lj/sdk pair styles are part of the USER-CGSDK package. The +All of the lj/sdk pair styles are part of the CG-SDK package. The *lj/sdk/coul/long* style also requires the KSPACE package to be built (which is enabled by default). They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index b45ac31f63..7eaab203c9 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -91,14 +91,14 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-SDPD package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the DPD-SMOOTH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index c15a8d26dc..deb3f69ec5 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -41,7 +41,7 @@ approach each other. Usually, *scale_factor* =1.0. Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No mixing is performed automatically. Currently, no part of USER-SMD +No mixing is performed automatically. Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. @@ -50,8 +50,8 @@ pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index bd46209cdc..3884b0fec3 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -56,7 +56,7 @@ complete listing of the possible keywords and material models. Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No mixing is performed automatically. Currently, no part of USER-SMD +No mixing is performed automatically. Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. @@ -65,8 +65,8 @@ pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 1e33254865..76385ae7fb 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -43,7 +43,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. +Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. ---------- @@ -51,8 +51,8 @@ rRESPA does not apply to this pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 33946d4649..fd63908e3d 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -67,7 +67,7 @@ complete listing of the possible keywords and material models. Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No mixing is performed automatically. Currently, no part of USER-SMD +No mixing is performed automatically. Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. @@ -76,8 +76,8 @@ pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This fix is part of the MACHDYN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index 0f309869f0..50b4afaf2d 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -94,8 +94,8 @@ ffield.SMTBQ.Syst. The energy band term is given by: \delta Q_i \bigl( 2\frac{n_0}{\eta_i} - \delta Q_i \bigr) \biggr\}^{1/2} \\ \delta Q_i & = | Q_i^{F} | - | Q_i | -where :math:`\eta_i` is the stoichiometry of atom *i*\ , -:math:`\delta Q_i` is the charge delocalization of atom *i*\ , +where :math:`\eta_i` is the stoichiometry of atom *i*, +:math:`\delta Q_i` is the charge delocalization of atom *i*, compared to its formal charge :math:`Q^F_i`. :math:`n_0`, the number of hybridized orbitals, is calculated with to the atomic orbitals shared @@ -161,7 +161,7 @@ For the anion (oxygen) * Name of element (char) and stoichiometry in oxide * Formal charge and mass of element * Principal quantum number of outer orbital n), electronegativity (:math:`\chi^0_i`) and hardness (:math:`J^0_i`) -* Ionic radius parameters : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*\ , surface coordination number *(coordS)* and *rBB, rB and rS* the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**) +* Ionic radius parameters : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*, surface coordination number *(coordS)* and *rBB, rB and rS* the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**) * Number of orbital shared by the element in the oxide (:math:`d_i`) * Divider line @@ -169,7 +169,7 @@ For each cations (metal): * Name of element (char) and stoichiometry in oxide * Formal charge and mass of element -* Number of electron in outer orbital *(ne)*\ , electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation. +* Number of electron in outer orbital *(ne)*, electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation. * Number of orbitals shared by the elements in the oxide (:math:`d_i`) * Divider line @@ -244,7 +244,7 @@ For each cations (metal): :math:`N_{Energy}` time steps. If the value is 'false' then :math:`N_{Energy} = 0`. The file takes into account the possibility to have several QEq groups *g* then it writes: time step, number of atoms - in group *g*\ , electrostatic part of energy, :math:`E_{ES}`, the + in group *g*, electrostatic part of energy, :math:`E_{ES}`, the interaction between oxygen, :math:`E_{OO}`, and short range metal-oxygen interaction, :math:`E_{MO}`. * If you want to print to the file 'Electroneg_component.txt' the @@ -252,9 +252,9 @@ For each cations (metal): Q_i}`) or not: 'true' or 'false' and :math:`N_{Electroneg}`. This option writes to the file every :math:`N_{Electroneg}` time steps. If the value is 'false' then :math:`N_{Electroneg} = 0`. The file - consist of atom number *i*\ , atom type (1 for oxygen and # higher - than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge - of atom *i*\ , electrostatic part of atom *i* electronegativity, + consist of atom number *i*, atom type (1 for oxygen and # higher + than 1 for metal), atom position: *x*, *y* and *z*, atomic charge + of atom *i*, electrostatic part of atom *i* electronegativity, covalent part of atom *i* electronegativity, the hopping integral of atom *i* :math:`(Z\beta^2)_i` and box electronegativity. @@ -277,15 +277,15 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This pair style is part of the USER-SMTBQ package and is only enabled -if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SMTBQ package and is only enabled +if LAMMPS is built with that package. See the :doc:`Build package ` page for more info. This potential requires using atom type 1 for oxygen and atom type higher than 1 for metal atoms. diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 2de1b59dd4..381250f57b 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -24,32 +24,28 @@ Examples Description """"""""""" -Pair style *snap* defines the spectral -neighbor analysis potential (SNAP), a machine-learning -interatomic potential :ref:`(Thompson) `. -Like the GAP framework of Bartok et al. :ref:`(Bartok2010) `, -SNAP uses bispectrum components -to characterize the local neighborhood of each atom -in a very general way. The mathematical definition of the -bispectrum calculation and its derivatives w.r.t. atom positions -is identical to that used by :doc:`compute snap `, -which is used to fit SNAP potentials to *ab initio* energy, force, -and stress data. -In SNAP, the total energy is decomposed into a sum over -atom energies. The energy of atom *i* is -expressed as a weighted sum over bispectrum components. +Pair style *snap* defines the spectral neighbor analysis potential +(SNAP), a machine-learning interatomic potential :ref:`(Thompson) +`. Like the GAP framework of Bartok et +al. :ref:`(Bartok2010) `, SNAP uses bispectrum components +to characterize the local neighborhood of each atom in a very general +way. The mathematical definition of the bispectrum calculation and its +derivatives w.r.t. atom positions is identical to that used by +:doc:`compute snap `, which is used to fit SNAP +potentials to *ab initio* energy, force, and stress data. In SNAP, the +total energy is decomposed into a sum over atom energies. The energy of +atom *i* is expressed as a weighted sum over bispectrum components. .. math:: E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i -where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ , -and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient -that depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The -number of bispectrum components used and their definitions -depend on the value of *twojmax* and other parameters -defined in the SNAP parameter file described below. -The bispectrum calculation is described in more detail +where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*, +and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient that +depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The number of +bispectrum components used and their definitions depend on the value of +*twojmax* and other parameters defined in the SNAP parameter file +described below. The bispectrum calculation is described in more detail in :doc:`compute sna/atom `. Note that unlike for other potentials, cutoffs for SNAP potentials are @@ -80,32 +76,28 @@ The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types 3 and 4 to the SNAP 'P' element. -If a SNAP mapping value is -specified as NULL, the mapping is not performed. -This can be used when a *snap* potential is used as part of the -*hybrid* pair style. The NULL values are placeholders for atom types -that will be used with other potentials. +If a SNAP mapping value is specified as NULL, the mapping is not +performed. This can be used when a *snap* potential is used as part of +the *hybrid* pair style. The NULL values are placeholders for atom +types that will be used with other potentials. -The name of the SNAP coefficient file usually ends in the -".snapcoeff" extension. It may contain coefficients -for many SNAP elements. The only requirement is that -each of the unique element names appearing in the -LAMMPS pair_coeff command appear exactly once in -the SNAP coefficient file. It is okay if the SNAP coefficient file -contains additional elements not in the pair_coeff command, -except when using *chemflag* (see below). -The name of the SNAP parameter file usually ends in the ".snapparam" -extension. It contains a small number -of parameters that define the overall form of the SNAP potential. -See the :doc:`pair_coeff ` doc page for alternate ways -to specify the path for these files. +The name of the SNAP coefficient file usually ends in the ".snapcoeff" +extension. It may contain coefficients for many SNAP elements. The only +requirement is that each of the unique element names appearing in the +LAMMPS pair_coeff command appear exactly once in the SNAP coefficient +file. It is okay if the SNAP coefficient file contains additional +elements not in the pair_coeff command, except when using *chemflag* +(see below). The name of the SNAP parameter file usually ends in the +".snapparam" extension. It contains a small number of parameters that +define the overall form of the SNAP potential. See the :doc:`pair_coeff +` page for alternate ways to specify the path for these +files. -Quite commonly, -SNAP potentials are combined with one or more other LAMMPS pair styles -using the *hybrid/overlay* pair style. As an example, the SNAP -tantalum potential provided in the LAMMPS potentials directory -combines the *snap* and *zbl* pair styles. It is invoked -by the following commands: +SNAP potentials are quite commonly combined with one or more other +LAMMPS pair styles using the *hybrid/overlay* pair style. As an +example, the SNAP tantalum potential provided in the LAMMPS potentials +directory combines the *snap* and *zbl* pair styles. It is invoked by +the following commands: .. code-block:: LAMMPS @@ -118,13 +110,13 @@ by the following commands: pair_coeff 1 1 zbl ${zblz} pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta -It is convenient to keep these commands in a separate file that can -be inserted in any LAMMPS input script using the :doc:`include ` +It is convenient to keep these commands in a separate file that can be +inserted in any LAMMPS input script using the :doc:`include ` command. -The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict -format after that. The first non-blank non-comment -line must contain two integers: +The top of the SNAP coefficient file can contain any number of blank and +comment lines (start with #), but follows a strict format after +that. The first non-blank non-comment line must contain two integers: * nelem = Number of elements * ncoeff = Number of coefficients @@ -141,9 +133,9 @@ This line is followed by *ncoeff* coefficients, one per line. The SNAP parameter file can contain blank and comment lines (start with #) anywhere. Each non-blank non-comment line must contain one keyword/value pair. The required keywords are *rcutfac* and -*twojmax*\ . Optional keywords are *rfac0*\ , *rmin0*\ , -*switchflag*\ , *bzeroflag*\ , *quadraticflag*\ , *chemflag*\ , -*bnormflag*\ , *wselfallflag*\ , and *chunksize*\ . +*twojmax*\ . Optional keywords are *rfac0*, *rmin0*, +*switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*, +*bnormflag*, *wselfallflag*, and *chunksize*\ . The default values for these keywords are @@ -157,39 +149,44 @@ The default values for these keywords are * *wselfallflag* = 0 * *chunksize* = 4096 -If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms -that have been shown to increase the overall accuracy of the potential without much increase -in computational cost :ref:`(Wood) `. +If *quadraticflag* is set to 1, then the SNAP energy expression includes +additional quadratic terms that have been shown to increase the overall +accuracy of the potential without much increase in computational cost +:ref:`(Wood) `. .. math:: E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \boldsymbol{\beta}^{\mu_i} \cdot \mathbf{B}_i + \frac{1}{2}\mathbf{B}^t_i \cdot \boldsymbol{\alpha}^{\mu_i} \cdot \mathbf{B}_i where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components, -:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients -for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}` -is the symmetric *K* by *K* matrix of quadratic coefficients. -The SNAP coefficient file should contain *K*\ (\ *K*\ +1)/2 additional coefficients -in each element block, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`. +:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear +coefficients for element :math:`\mu_i`, and +:math:`\boldsymbol{\alpha}^{\mu_i}` is the symmetric *K* by *K* matrix +of quadratic coefficients. The SNAP coefficient file should contain +*K*\ (\ *K*\ +1)/2 additional coefficients in each element block, the +upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`. -If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum -components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP -potential to capture energy differences in chemically complex systems, -at the expense of a significant increase in computational cost :ref:`(Cusentino) `. +If *chemflag* is set to 1, then the energy expression is written in +terms of explicit multi-element bispectrum components indexed on ordered +triplets of elements, which has been shown to increase the ability of +the SNAP potential to capture energy differences in chemically complex +systems, at the expense of a significant increase in computational cost +:ref:`(Cusentino) `. .. math:: E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i -where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components -for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and -:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector -of linear coefficients for element :math:`\mu_i`. The SNAP coefficient file should contain -a total of :math:`K N_{elem}^3` coefficients in each element block, -where :math:`N_{elem}` is the number of elements in the SNAP coefficient file, -which must equal the number of unique elements appearing in the -LAMMPS pair_coeff command, to avoid ambiguity in the -number of coefficients. +where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of +bispectrum components for neighbors of elements :math:`\kappa`, +:math:`\lambda`, and :math:`\mu` and +:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the +corresponding *K*-vector of linear coefficients for element +:math:`\mu_i`. The SNAP coefficient file should contain a total of +:math:`K N_{elem}^3` coefficients in each element block, where +:math:`N_{elem}` is the number of elements in the SNAP coefficient file, +which must equal the number of unique elements appearing in the LAMMPS +pair_coeff command, to avoid ambiguity in the number of coefficients. The keyword *chunksize* is only applicable when using the pair style *snap* with the KOKKOS package and is ignored otherwise. @@ -221,13 +218,14 @@ specify a pair_coeff command with I != J arguments for this style. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -238,8 +236,9 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This style is part of the SNAP package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This style is part of the ML-SNAP package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index cc024cb6dd..7986b1286e 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -113,7 +113,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index 404a99e785..4716ed54fb 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -24,7 +24,7 @@ Description The sph/heatconduction style computes heat transport between SPH particles. The transport model is the diffusion equation for the internal energy. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms @@ -48,14 +48,14 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SPH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 74bc2d4f7e..02949849c4 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -33,7 +33,7 @@ the local density, and e is the internal energy per unit mass. This pair style also computes Monaghan's artificial viscosity to prevent particles from interpenetrating :ref:`(Monaghan) `. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms @@ -57,14 +57,14 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SPH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index b678f3c149..b5c02c41ff 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -28,7 +28,7 @@ epsilon and sigma are set to unity. This pair style also computes Monaghan's artificial viscosity to prevent particles from interpenetrating :ref:`(Monaghan) `. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms @@ -52,8 +52,8 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" @@ -61,8 +61,8 @@ Restrictions As noted above, the Lennard-Jones parameters epsilon and sigma are set to unity. -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SPH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 6d0cbeb133..ecbff98486 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -26,7 +26,7 @@ Description The sph/rhosum style computes the local particle mass density rho for SPH particles by kernel function interpolation, every Nstep timesteps. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms @@ -49,14 +49,14 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SPH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index b06d15579a..34eb65f005 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -35,7 +35,7 @@ speed of sound. This pair style also computes Monaghan's artificial viscosity to prevent particles from interpenetrating :ref:`(Monaghan) `. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms @@ -61,14 +61,14 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SPH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index f26a5db356..cd8346364b 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -34,7 +34,7 @@ speed of sound. This pair style also computes laminar viscosity :ref:`(Morris) `. -See `this PDF guide `_ to using SPH in +See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms @@ -60,14 +60,14 @@ shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, +*middle*, *outer* keywords. Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the SPH package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index d1bbf3b699..c38bba03ae 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -97,7 +97,7 @@ Restrictions The *spin/dipole/cut* and *spin/dipole/long* styles are part of the SPIN package. They are only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Using dipole/spin pair styles with *electron* :doc:`units ` is not diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index eb945acc04..3d1498b769 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -81,7 +81,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 630ec6608e..553af72983 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -196,7 +196,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the atom_style "spin" was declared. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 1860ed4677..b422b6a070 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -60,7 +60,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst index c0df74187d..e5d655f196 100644 --- a/doc/src/pair_spin_neel.rst +++ b/doc/src/pair_spin_neel.rst @@ -80,7 +80,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 59df8be1e2..ea094aa720 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -49,7 +49,7 @@ acts between pairs of bonds. This potential is useful for preventing bonds from passing through one another when a soft non-bonded potential acts between beads in, for example, DPD polymer chains. An example input script that uses this command is provided in -examples/USER/srp. +examples/PACKAGES/srp. Bonds of specified type *btype* interact with one another through a bond-pairwise potential, such that the force on bond *i* due to bond @@ -91,7 +91,7 @@ is used. .. note:: Pair style srp considers each bond of type *btype* to be a - fictitious "particle" of type *bptype*\ , where *bptype* is either the + fictitious "particle" of type *bptype*, where *bptype* is either the largest atom type in the system, or the type set by the *bptype* flag. Any actual existing particles with this atom type will be deleted at the beginning of a run. This means you must specify the number of @@ -108,7 +108,7 @@ is used. The optional *exclude* keyword determines if forces are computed between first neighbor (directly connected) bonds. For a setting of -*no*\ , first neighbor forces are computed; for *yes* they are not +*no*, first neighbor forces are computed; for *yes* they are not computed. A setting of *no* cannot be used with the *min* option for distance calculation because the minimum distance between directly connected bonds is zero. @@ -143,14 +143,14 @@ specified in the input script when reading a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -This pair style is part of the USER-MISC package. It is only enabled +This pair style is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1f023a7312..7677cd9535 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -255,7 +255,7 @@ accelerated styles exist. * :doc:`lubricateU/poly ` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity * :doc:`mdpd ` - mDPD particle interactions * :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density -* :doc:`meam/c ` - modified embedded atom method (MEAM) in C +* :doc:`meam ` - modified embedded atom method (MEAM) in C * :doc:`meam/spline ` - splined version of MEAM * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term * :doc:`mesocnt ` - mesoscale model for (carbon) nanotubes @@ -299,7 +299,7 @@ accelerated styles exist. * :doc:`python ` - * :doc:`quip ` - * :doc:`rann ` - -* :doc:`reax/c ` - ReaxFF potential in C +* :doc:`reaxff ` - ReaxFF potential * :doc:`rebo ` - second generation REBO potential of Brenner * :doc:`resquared ` - Everaers RE-Squared ellipsoidal potential * :doc:`sdpd/taitwater/isothermal ` - smoothed dissipative particle dynamics for water at isothermal conditions @@ -338,6 +338,7 @@ accelerated styles exist. * :doc:`tip4p/cut ` - Coulomb for TIP4P water w/out LJ * :doc:`tip4p/long ` - long-range Coulomb for TIP4P water w/out LJ * :doc:`tip4p/long/soft ` - +* :doc:`tracker ` - monitor information about pairwise interactions * :doc:`tri/lj ` - LJ potential between triangles * :doc:`ufm ` - * :doc:`vashishta ` - Vashishta 2-body and 3-body potential @@ -357,7 +358,7 @@ This command must be used before any coefficients are set by the :doc:`read_restart ` commands. Some pair styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual pair potentials tell if it is part of a package. Related commands diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index bea417ed3d..f207b25863 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -57,7 +57,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of SW elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.sw has Stillinger-Weber values for @@ -155,31 +155,31 @@ parameters used only for two-body interactions (A, B, p, and q) in entries whose second and third element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired. This is also true for the parameters in :math:`\phi_3` that are -taken from the ij and ik pairs (:math:`\sigma`, *a*\ , :math:`\gamma`) +taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -When using the USER-INTEL package with this style, there is an +When using the INTEL package with this style, there is an additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -200,7 +200,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -208,7 +208,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 39ed690551..79eb8f5b42 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -16,7 +16,7 @@ Syntax pair_style table style N keyword ... * style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation -* N = use N values in *lookup*\ , *linear*\ , *spline* tables +* N = use N values in *lookup*, *linear*, *spline* tables * N = use 2\^N values in *bitmap* tables * zero or more keywords may be appended * keyword = *ewald* or *pppm* or *msm* or *dispersion* or *tip4p* @@ -47,7 +47,7 @@ cubic splines to the file values and interpolating energy and force values at each of *N* distances. During a simulation, the tables are used to interpolate energy and force values as needed for each pair of particles separated by a distance *R*\ . The interpolation is done in -one of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ . +one of 4 styles: *lookup*, *linear*, *spline*, or *bitmap*\ . For the *lookup* style, the distance *R* is used to find the nearest table entry, which is the energy or force. @@ -240,7 +240,7 @@ commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 9d23a479a3..094107d9ef 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -14,7 +14,7 @@ Syntax pair_style table style N ... * style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation -* N = use N values in *lookup*\ , *linear*\ , *spline* tables +* N = use N values in *lookup*, *linear*, *spline* tables * weighting = fractional or molecular (optional) Examples @@ -47,7 +47,7 @@ The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of *N* distances. During a simulation, these tables are used to interpolate energy and force values as needed. The interpolation is done in one -of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ . +of 4 styles: *lookup*, *linear*, *spline*, or *bitmap*\ . For the *lookup* style, the distance between 2 atoms is used to find the nearest table entry, which is the energy or force. @@ -221,7 +221,7 @@ commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -232,8 +232,8 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the DPD-REACT package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 0f0750e9df..ab88806ca6 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -16,9 +16,6 @@ pair_style tersoff/table command Accelerator Variants: *tersoff/table/omp* -pair_style tersoff/shift command -================================ - Syntax """""" @@ -93,7 +90,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine the SiC.tersoff file has Tersoff values for Si @@ -291,7 +288,7 @@ that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -300,7 +297,7 @@ Restrictions This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. @@ -309,6 +306,9 @@ The *shift* keyword is not supported by the *tersoff/gpu*, *tersoff/intel*, *tersoff/kk*, *tersoff/table* or *tersoff/table/omp* variants. +The *tersoff/intel* pair style is only available when compiling LAMMPS +with the Intel compilers. + The Tersoff potential files provided with LAMMPS (see the potentials directory) are parameterized for :doc:`"metal" units `. In addition the pair style supports converting potential parameters on-the-fly between diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index e59005c2b0..8c9605d62c 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -189,7 +189,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -197,7 +197,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index 345ebf3e03..276905163f 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -101,7 +101,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff/ZBL elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values @@ -270,7 +270,7 @@ that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -279,7 +279,7 @@ Restrictions This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 183bab48c9..5a1e72f569 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -42,7 +42,7 @@ Examples pair_style lj/cut/thole/long 2.6 12.0 -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -107,7 +107,7 @@ non-polarizable atoms are also subject to these weighting factors. The Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from their respective cores. -For pair_style *thole*\ , the following coefficients must be defined for +For pair_style *thole*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. @@ -120,7 +120,7 @@ Thole damping parameter or global cutoff specified in the pair_style command are used. In order to specify a cutoff (third argument) a damp parameter (second argument) must also be specified. -For pair style *lj/cut/thole/long*\ , the following coefficients must be +For pair style *lj/cut/thole/long*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command. @@ -155,8 +155,8 @@ are defined using Restrictions """""""""""" -These pair styles are part of the USER-DRUDE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These pair styles are part of the DRUDE package. They are only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting factors. This is because the *thole* pair style does not know which diff --git a/doc/src/pair_tracker.rst b/doc/src/pair_tracker.rst new file mode 100644 index 0000000000..d2cee1d879 --- /dev/null +++ b/doc/src/pair_tracker.rst @@ -0,0 +1,97 @@ +.. index:: pair_style tracker + +pair_style tracker command +========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style tracker keyword + +* zero or more keyword/arg pairs may be appended +* keyword = *finite* + + .. parsed-literal:: + + *finite* value = none + pair style uses atomic diameters to identify contacts + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style hybrid/overlay tracker ... + pair_coeff 1 1 tracker 2.0 + + pair_style hybrid/overlay tracker finite ... + pair_coeff * * tracker + + fix 1 all pair/tracker 1000 time/created time/broken + dump 1 all local 1000 dump.local f_1[1] f_1[2] + dump_modify 1 write_header no + +Description +""""""""""" + +Style *tracker* monitors information about pairwise interactions. +It does not calculate any forces on atoms. +:doc:`Pair hybrid/overlay ` can be used to combine this pair +style with another pair style. Style *tracker* must be used in conjunction +with about :doc:`fix pair_tracker ` which contains +information on what data can be output. + +If the *finite* keyword is not defined, the following coefficients must be +defined for each pair of atom types via the :doc:`pair_coeff ` +command as in the examples above, or in the data file or restart files +read by the :doc:`read_data ` or :doc:`read_restart ` +commands, or by mixing as described below: + +* cutoff (distance units) + +If the *finite* keyword is defined, no coefficients may be defined. +Interaction cutoffs are alternatively calculated based on the +diameter of finite particles. + + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, the cutoff coefficient and cutoff +distance for this pair style can be mixed. The cutoff is always mixed via a +*geometric* rule. The cutoff is mixed according to the pair_modify +mix value. The default mix value is *geometric*\ . See the +"pair_modify" command for details. + +This pair style writes its information to :doc:`binary restart files `, so +pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +The :doc:`pair_modify ` shift, table, and tail options +are not relevant for this pair style. + +---------- + +Restrictions +"""""""""""" + +A corresponding :doc:`fix pair_tracker ` must be defined +to use this pair style. + +This pair style is currently incompatible with granular pair styles that extend +beyond the contact (e.g. JKR and DMT). + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix pair_tracker ` + +Default +""""""" + +none diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 5516f60408..d72a061bf3 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -66,7 +66,7 @@ using only sigma_II values, specific to the triangles's type, this means that any specified sigma_IJ values (for I != J) are effectively ignored. -For style *tri/lj*\ , the following coefficients must be defined for +For style *tri/lj*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` @@ -96,7 +96,7 @@ This pair style does not write its information to :doc:`binary restart files ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -104,7 +104,7 @@ Restrictions """""""""""" This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Defining particles to be triangles so they participate in tri/tri or tri/particle interactions requires the use the :doc:`atom_style tri ` command. diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index 140bb75ee7..22438d559b 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -107,13 +107,16 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 9edb77ecbe..d38ac02a96 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -93,7 +93,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Vashishta elements to atom types -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.vashishta has parameters for @@ -156,13 +156,13 @@ unambiguous, general, and simple to code, LAMMPS uses a slightly confusing method for specifying parameters. All parameters are divided into two classes: two-body and three-body. Two-body and three-body parameters are handled differently, as described below. -The two-body parameters are *H*\ , :math:`\eta`, :math:`\lambda_1`, -*D*\ , :math:`\lambda_4`, *W*, :math:`r_c`, :math:`\gamma`, +The two-body parameters are *H*, :math:`\eta`, :math:`\lambda_1`, +*D*, :math:`\lambda_4`, *W*, :math:`r_c`, :math:`\gamma`, and :math:`r_0`. They appear in the above formulae with two subscripts. The parameters :math:`Z_i` and :math:`Z_j` are also classified as two-body parameters, even -though they only have 1 subscript. The three-body parameters are *B*\ , -*C*\ , :math:`\cos\theta_0`. They appear in the above formulae with +though they only have 1 subscript. The three-body parameters are *B*, +*C*, :math:`\cos\theta_0`. They appear in the above formulae with three subscripts. Two-body and three-body parameters are handled differently, as described below. @@ -210,7 +210,7 @@ script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -218,7 +218,7 @@ Restrictions """""""""""" These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_wf_cut.rst b/doc/src/pair_wf_cut.rst index e69b982d8a..8f6e352665 100644 --- a/doc/src/pair_wf_cut.rst +++ b/doc/src/pair_wf_cut.rst @@ -91,7 +91,7 @@ This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -This pair style does not support the use of the *inner*\ , *middle*\ , +This pair style does not support the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command. ---------- @@ -99,7 +99,7 @@ and *outer* keywords of the :doc:`run_style respa ` command. Restrictions """""""""""" This pair style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc +EXTRA-PAIR package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 340c151226..1d88137255 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -44,13 +44,13 @@ will refuse to add a table if the units are not the same. The energy and force values are computed at distances from inner to outer for 2 interacting atoms of type itype and jtype, using the appropriate :doc:`pair_coeff ` coefficients. If the style -is *r*\ , then N distances are used, evenly spaced in r; if the style is -*rsq*\ , N distances are used, evenly spaced in r\^2. +is *r*, then N distances are used, evenly spaced in r; if the style is +*rsq*, N distances are used, evenly spaced in r\^2. -For example, for N = 7, style = *r*\ , inner = 1.0, and outer = 4.0, +For example, for N = 7, style = *r*, inner = 1.0, and outer = 4.0, values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. -If the style is *bitmap*\ , then 2\^N values are written to the file in a +If the style is *bitmap*, then 2\^N values are written to the file in a format and order consistent with how they are read in by the :doc:`pair_coeff ` command for pair style *table*\ . For reasonable accuracy in a bitmapped table, choose N >= 12, an *inner* diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 057adbd60f..2b832f187a 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -79,7 +79,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 4d21d8e8c3..6611ea04e4 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -112,7 +112,7 @@ to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -120,7 +120,7 @@ Restrictions """""""""""" This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires that atoms be finite-size spheres with a diameter, as defined by the :doc:`atom_style sphere ` diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index e01cbf45f2..bbf9f6bc29 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -117,7 +117,7 @@ specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 416958de1b..062b5204f8 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -72,7 +72,7 @@ shift, table, and tail options. This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -This pair style supports the use of the *inner*\ , *middle*\ , +This pair style supports the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command. ---------- diff --git a/doc/src/partition.rst b/doc/src/partition.rst index e63a4941bb..f05c3fa446 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -42,7 +42,7 @@ script operate differently on different partitions. It is basically a prefix on any LAMMPS command. The command will only be invoked on the partition(s) specified by the *style* and *N* arguments. -If the *style* is *yes*\ , the command will be invoked on any partition +If the *style* is *yes*, the command will be invoked on any partition which matches the *N* argument. If the *style* is *no* the command will be invoked on all the partitions which do not match the Np argument. diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index 02228636bc..7995ddc369 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -62,7 +62,7 @@ Restrictions The *plugin* command is part of the PLUGIN package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for +See the :doc:`Build package ` page for more info. Plugins are not available on Windows. For the loading of plugins to work the LAMMPS library must be diff --git a/doc/src/prd.rst b/doc/src/prd.rst index d1acaf645e..758aa4f570 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -30,8 +30,8 @@ Syntax *temp* value = Tdephase Tdephase = target temperature for velocity randomization, used in dephasing *vel* values = loop dist - loop = *all* or *local* or *geom*\ , used in dephasing - dist = *uniform* or *gaussian*\ , used in dephasing + loop = *all* or *local* or *geom*, used in dephasing + dist = *uniform* or *gaussian*, used in dephasing *time* value = *steps* or *clock* *steps* = simulation runs for N timesteps on each replica (default) *clock* = simulation runs for N timesteps across all replicas @@ -72,7 +72,7 @@ reduced by a factor of Nr replicas. HD uses a single replica of the system and accelerates time by biasing the interaction potential in a manner such that each timestep is effectively longer. For both methods, per CPU second, more physical time elapses and more events -occur. See the :doc:`hyper ` doc page for more info about HD. +occur. See the :doc:`hyper ` page for more info about HD. In PRD, each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the :doc:`-partition command-line switch `. Note that if you have MPI @@ -171,8 +171,8 @@ dynamics have been performed. Note that *N* only includes the dynamics of stages 2 and 3, not the steps taken during dephasing or the minimization iterations of quenching. The specified *N* is interpreted in one of two ways, depending on the *time* keyword. If -the *time* value is *steps*\ , which is the default, then each replica -runs for *N* timesteps. If the *time* value is *clock*\ , then the +the *time* value is *steps*, which is the default, then each replica +runs for *N* timesteps. If the *time* value is *clock*, then the simulation runs until *N* aggregate timesteps across all replicas have elapsed. This aggregate time is the "clock" time defined below, which typically advances nearly M times faster than the timestepping on a diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 899c87f4b0..d717fa9b73 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -85,7 +85,7 @@ communication costs due to the high surface area of each processor's sub-domain. Also note that if multiple partitions are being used then P is the -number of processors in this partition; see the :doc:`-partition command-line switch ` doc page for details. Also note +number of processors in this partition; see the :doc:`-partition command-line switch ` page for details. Also note that you can prefix the processors command with the :doc:`partition ` command to easily specify different Px,Py,Pz values for different partitions. @@ -140,7 +140,7 @@ For example if *Nc* is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of the 3d grid will correspond to the cores of each node. This affects both the factorization and mapping steps. -The *Cx*\ , *Cy*\ , *Cz* settings are similar to the *Px*\ , *Py*\ , *Pz* +The *Cx*, *Cy*, *Cz* settings are similar to the *Px*, *Py*, *Pz* settings, only their product should equal *Nc*\ . Any of the 3 parameters can be specified with an asterisk "\*", which means LAMMPS will choose the number of cores in that dimension of the node's @@ -222,7 +222,7 @@ The *cart/reorder* style does the same thing as the *cart* style except it sets the reorder flag to 1, so that MPI can reorder processors if it desires. -The *xyz*\ , *xzy*\ , *yxz*\ , *yzx*\ , *zxy*\ , and *zyx* styles are all +The *xyz*, *xzy*, *yxz*, *yzx*, *zxy*, and *zyx* styles are all similar. If the style is IJK, then it maps the P processors to the grid so that the processor ID in the I direction varies fastest, the processor ID in the J direction varies next fastest, and the processor @@ -275,7 +275,7 @@ regular 3d grid and will use the sender's Px,Py,Pz values as a constraint. The nature of the constraint is determined by the *cstyle* argument. -For a *cstyle* of *multiple*\ , each dimension of the sender's processor +For a *cstyle* of *multiple*, each dimension of the sender's processor grid is required to be an integer multiple of the corresponding dimension in the receiver's processor grid. This is a requirement of the :doc:`run_style verlet/split ` command. diff --git a/doc/src/python.rst b/doc/src/python.rst index a4c3d7097c..aad2f636d3 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -185,12 +185,12 @@ output as a string, then the default maximum length of that string is a longer string, the *length* keyword can be specified with its *Nlen* value set to a larger number (the code allocates space for Nlen+1 to include the string terminator). If the Python function generates a -string longer than the default 63 or the specified *Nlen*\ , it will be +string longer than the default 63 or the specified *Nlen*, it will be truncated. ---------- -Either the *file*\ , *here*\ , or *exists* keyword must be used, but only +Either the *file*, *here*, or *exists* keyword must be used, but only one of them. These keywords specify what Python code to load into the Python interpreter. The *file* keyword gives the name of a file, which should end with a ".py" suffix, which contains Python code. The @@ -340,7 +340,7 @@ to the screen and log file. Note that since the LAMMPS print command itself takes a string in quotes as its argument, the Python string must be delimited with a different style of quotes. -The :doc:`Python_head` doc page describes the syntax +The :doc:`Python_head` page describes the syntax for how Python wraps the various functions included in the LAMMPS library interface. @@ -495,7 +495,7 @@ Restrictions """""""""""" This command is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Building LAMMPS with the PYTHON package will link LAMMPS with the Python library on your system. Settings to enable this are in the diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index bd7c480af2..e0cd38416e 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -70,7 +70,7 @@ Also see the explanation of the :doc:`-restart command-line switch file. This command can be used multiple times to add new atoms and their -properties to an existing system by using the *add*\ , *offset*\ , and +properties to an existing system by using the *add*, *offset*, and *shift* keywords. See more details below, which includes the use case for the *extra* keywords. @@ -105,7 +105,7 @@ other side of the fluid. The third set of atoms could be rotated to an opposing direction using the :doc:`displace_atoms ` command, after the third read_data command is used. -The *add*\ , *offset*\ , *shift*\ , *extra*\ , and *group* keywords are +The *add*, *offset*, *shift*, *extra*, and *group* keywords are useful in this context. If a simulation box does not yet exist, the *add* keyword cannot be @@ -249,7 +249,7 @@ a fix that will be used to process a specific portion of the data file. Any header line containing *header-string* and any section with a name containing *section-string* will be passed to the specified fix. See the :doc:`fix property/atom ` command for -an example of a fix that operates in this manner. The doc page for +an example of a fix that operates in this manner. The page for the fix defines the syntax of the header line(s) and section(s) that it reads from the data file. Note that the *header-string* can be specified as NULL, in which case no header lines are passed to the @@ -332,7 +332,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, with tilt factors that exceed these limits, you can use the :doc:`box tilt ` command, with a setting of *large*\ ; a setting of *small* is the default. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. @@ -460,9 +460,9 @@ are point particles. See the discussion of ellipsoidflag and the For :doc:`atom_style template `, the molecular topology (bonds,angles,etc) is contained in the molecule templates read-in by the :doc:`molecule ` command. This means you - cannot set the *bonds*\ , *angles*\ , etc header keywords in the data - file, nor can you define *Bonds*\ , *Angles*\ , etc sections as discussed - below. You can set the *bond types*\ , *angle types*\ , etc header + cannot set the *bonds*, *angles*, etc header keywords in the data + file, nor can you define *Bonds*, *Angles*, etc sections as discussed + below. You can set the *bond types*, *angle types*, etc header keywords, though it is not necessary. If specified, they must match the maximum values defined in any of the template molecules. @@ -491,7 +491,7 @@ For example, these lines: Pair Coeffs # lj/cut will check if the currently-defined :doc:`atom_style ` is -*sphere*\ , and the current :doc:`pair_style ` is *lj/cut*\ . +*sphere*, and the current :doc:`pair_style ` is *lj/cut*\ . If not, LAMMPS will issue a warning to indicate that the data file section likely does not contain the correct number or type of parameters expected for the currently-defined style. @@ -722,8 +722,8 @@ The ellipsoidflag, lineflag, triangleflag, and bodyflag determine whether the particle is a finite-size ellipsoid or line or triangle or body of finite size, or whether the particle is a point particle. Additional attributes must be defined for each ellipsoid, line, -triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ , -*Triangles*\ , or *Bodies* section. +triangle, or body in the corresponding *Ellipsoids*, *Lines*, +*Triangles*, or *Bodies* section. The *template-index* and *template-atom* are only defined used by :doc:`atom_style template `. In this case the @@ -1051,7 +1051,7 @@ The 3 shape values specify the 3 diameters or aspect ratios of a finite-size ellipsoidal particle, when it is oriented along the 3 coordinate axes. They must all be non-zero values. -The values *quatw*\ , *quati*\ , *quatj*\ , and *quatk* set the orientation +The values *quatw*, *quati*, *quatj*, and *quatk* set the orientation of the atom as a quaternion (4-vector). Note that the shape attributes specify the aspect ratios of an ellipsoidal particle, which is oriented by default with its x-axis along the simulation box's diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index f9a8c87c86..c873156a38 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -17,11 +17,11 @@ Syntax .. parsed-literal:: field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz* - *x*\ ,\ *y*\ ,\ *z* = atom coordinates - *vx*\ ,\ *vy*\ ,\ *vz* = velocity components + *x*,\ *y*,\ *z* = atom coordinates + *vx*,\ *vy*,\ *vz* = velocity components *q* = charge - *ix*\ ,\ *iy*\ ,\ *iz* = image flags in each dimension - *fx*\ ,\ *fy*\ ,\ *fz* = force components + *ix*,\ *iy*,\ *iz* = image flags in each dimension + *fx*,\ *fy*,\ *fz* = force components * zero or more keyword/value pairs may be appended * keyword = *nfile* or *box* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format* @@ -121,7 +121,7 @@ formatted dump files. These formats take no additional values. The *molfile* format supports reading data through using the `VMD `_ molfile plugin interface. This dump reader format is only available, -if the USER-MOLFILE package has been installed when compiling +if the MOLFILE package has been installed when compiling LAMMPS. The *molfile* format takes one or two additional values. The *style* @@ -188,7 +188,7 @@ you must set the *box* flag to *no*\ . See details below. For the *molfile* format, reading simulation box information is typically supported, but the location of the simulation box origin is lost and no explicit information about periodicity or -orthogonal/triclinic box shape is available. The USER-MOLFILE package +orthogonal/triclinic box shape is available. The MOLFILE package makes a best effort to guess based on heuristics, but this may not always work perfectly. @@ -197,11 +197,11 @@ always work perfectly. Per-atom information from the dump file snapshot is then read from the dump file snapshot. This corresponds to the specified *fields* listed in the read_dump command. It is an error to specify a z-dimension -field, namely *z*\ , *vz*\ , or *iz*\ , for a 2d simulation. +field, namely *z*, *vz*, or *iz*, for a 2d simulation. For dump files in *native* format, each column of per-atom data has a text label listed in the file. A matching label for each field must -appear, e.g. the label "vy" for the field *vy*\ . For the *x*\ , *y*\ , *z* +appear, e.g. the label "vy" for the field *vy*\ . For the *x*, *y*, *z* fields any of the following labels are considered a match: .. parsed-literal:: @@ -217,7 +217,7 @@ file, in order, until a match is found. The dump file must also contain atom IDs, with a column label of "id". -If the *add* keyword is specified with a value of *yes* or *keep*\ , as +If the *add* keyword is specified with a value of *yes* or *keep*, as discussed below, the dump file must contain atom types, with a column label of "type". @@ -230,7 +230,7 @@ will then have a label corresponding to the fix-ID rather than "x" or "xs". The *label* keyword can also be used to specify new column labels for fields *id* and *type*\ . -For dump files in *xyz* format, only the *x*\ , *y*\ , and *z* fields are +For dump files in *xyz* format, only the *x*, *y*, and *z* fields are supported. The dump file does not store atom IDs, so these are assigned consecutively to the atoms as they appear in the dump file, starting from 1. Thus you should insure that order of atoms is @@ -238,7 +238,7 @@ consistent from snapshot to snapshot in the XYZ dump file. See the :doc:`dump_modify sort ` command if the XYZ dump file was written by LAMMPS. -For dump files in *molfile* format, the *x*\ , *y*\ , *z*\ , *vx*\ , *vy*\ , and +For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and *vz* fields can be specified. However, not all molfile formats store velocities, or their respective plugins may not support reading of velocities. The molfile dump files do not store atom IDs, so these @@ -277,7 +277,7 @@ current simulation box is unchanged. If the *purge* keyword is specified with a *yes* value, then all current atoms in the system are deleted before any of the operations -invoked by the *replace*\ , *trim*\ , or *add* keywords take place. +invoked by the *replace*, *trim*, or *add* keywords take place. If the *replace* keyword is specified with a *yes* value, then atoms with IDs that are in both the current system and the dump snapshot @@ -330,7 +330,7 @@ atom will be lost if it is outside the simulation box. For *native* format dump files, the 3 xyz image flags for an atom in the dump file are set to the corresponding values appearing in the -dump file if the *ix*\ , *iy*\ , *iz* fields are specified. If not +dump file if the *ix*, *iy*, *iz* fields are specified. If not specified, the image flags for replaced atoms are not changed and image flags for new atoms are set to default values. If coordinates read from the dump file are in unwrapped format (e.g. *xu*\ ) then the @@ -343,13 +343,13 @@ conditions are applied to remap an atom back into the simulation box. If you get a warning about inconsistent image flags after reading in a dump snapshot, it means one or more pairs of bonded atoms - now have inconsistent image flags. As discussed on the :doc:`Errors common ` doc page this may or may not cause problems + now have inconsistent image flags. As discussed on the :doc:`Errors common ` page this may or may not cause problems for subsequent simulations. One way this can happen is if you read image flag fields from the dump file but do not also use the dump file box parameters. LAMMPS knows how to compute unscaled and remapped coordinates for the -snapshot column labels discussed above, e.g. *x*\ , *xs*\ , *xu*\ , *xsu*\ . +snapshot column labels discussed above, e.g. *x*, *xs*, *xu*, *xsu*\ . If another column label is assigned to the *x* or *y* or *z* field via the *label* keyword, e.g. for coordinates output by the :doc:`fix ave/atom ` command, then LAMMPS needs to know whether the coordinate information in the dump file is scaled and/or wrapped. @@ -359,10 +359,10 @@ the value of the *scaled* and *wrapped* keywords is ignored for fields column label to that field. The scaled/unscaled and wrapped/unwrapped setting must be identical -for any of the *x*\ , *y*\ , *z* fields that are specified. Thus you +for any of the *x*, *y*, *z* fields that are specified. Thus you cannot read *xs* and *yu* from the dump file. Also, if the dump file coordinates are scaled and the simulation box is triclinic, then all 3 -of the *x*\ , *y*\ , *z* fields must be specified, since they are all +of the *x*, *y*, *z* fields must be specified, since they are all needed to generate absolute, unscaled coordinates. ---------- @@ -376,12 +376,12 @@ To read gzipped dump files, you must compile LAMMPS with the -DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. -The *molfile* dump file formats are part of the USER-MOLFILE package. +The *molfile* dump file formats are part of the MOLFILE package. They are only enabled if LAMMPS was built with that packages. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. To write and read adios .bp files, you must compile LAMMPS with the -:ref:`USER-ADIOS ` package. +:ref:`ADIOS ` package. Related commands """""""""""""""" diff --git a/doc/src/region.rst b/doc/src/region.rst index 9f2d996b20..d891a69410 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -147,24 +147,24 @@ non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi. define the region so that its intersection with the 2d x-y plane of the simulation has the 2d geometric extent you want. -For style *cone*\ , an axis-aligned cone is defined which is like a +For style *cone*, an axis-aligned cone is defined which is like a *cylinder* except that two different radii (one at each end) can be defined. Either of the radii (but not both) can be 0.0. -For style *cone* and *cylinder*\ , the c1,c2 params are coordinates in +For style *cone* and *cylinder*, the c1,c2 params are coordinates in the 2 other dimensions besides the cylinder axis dimension. For dim = x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. Thus the third example above specifies a cylinder with its axis in the y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and extending in the y-direction from -5.0 to the upper box boundary. -For style *plane*\ , a plane is defined which contain the point +For style *plane*, a plane is defined which contain the point (px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does not have to be of unit length. The "inside" of the plane is the half-space in the direction of the normal vector; see the discussion of the *side* option below. -For style *prism*\ , a parallelepiped is defined (it's too hard to spell +For style *prism*, a parallelepiped is defined (it's too hard to spell parallelepiped in an input script!). The parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = @@ -200,7 +200,7 @@ keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent radius or have a time dependent position of the sphere or cylinder region. -See the :doc:`Howto tricilinc ` doc page for a +See the :doc:`Howto tricilinc ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. @@ -239,25 +239,25 @@ A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings which are used as follows: -* For style *block*\ , the lattice spacing in dimension x is applied to +* For style *block*, the lattice spacing in dimension x is applied to xlo and xhi, similarly the spacings in dimensions y,z are applied to ylo/yhi and zlo/zhi. -* For style *cone*\ , the lattice spacing in argument *dim* is applied to +* For style *cone*, the lattice spacing in argument *dim* is applied to lo and hi. The spacings in the two radial dimensions are applied to c1 and c2. The two cone radii are scaled by the lattice spacing in the dimension corresponding to c1. -* For style *cylinder*\ , the lattice spacing in argument *dim* is applied +* For style *cylinder*, the lattice spacing in argument *dim* is applied to lo and hi. The spacings in the two radial dimensions are applied to c1 and c2. The cylinder radius is scaled by the lattice spacing in the dimension corresponding to c1. -* For style *plane*\ , the lattice spacing in dimension x is applied to +* For style *plane*, the lattice spacing in dimension x is applied to px and nx, similarly the spacings in dimensions y,z are applied to py/ny and pz/nz. -* For style *prism*\ , the lattice spacing in dimension x is applied to +* For style *prism*, the lattice spacing in dimension x is applied to xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing in dimension x is applied to xy and xz, and the spacing in dimension y to yz. -* For style *sphere*\ , the lattice spacing in dimensions x,y,z are +* For style *sphere*, the lattice spacing in dimensions x,y,z are applied to the sphere center x,y,z. The spacing in dimension x is applied to the sphere radius. @@ -311,7 +311,7 @@ angle is calculated, presumably as a function of time, by a variable specified as v_theta, where theta is the variable name. The variable should generate its result in radians. The direction of rotation for the region around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along *R*\ , then your fingers +rule: if your right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. The *move* and *rotate* keywords can be used together. In this case, @@ -341,25 +341,25 @@ sub-regions that use them. The indices specified as part of the *open* keyword have the following meanings: -For style *block*\ , indices 1-6 correspond to the xlo, xhi, ylo, yhi, +For style *block*, indices 1-6 correspond to the xlo, xhi, ylo, yhi, zlo, zhi surfaces of the block. I.e. 1 is the yz plane at x = xlo, 2 is the yz-plane at x = xhi, 3 is the xz plane at y = ylo, 4 is the xz plane at y = yhi, 5 is the xy plane at z = zlo, 6 is the xy plane at z = zhi). In the second-to-last example above, the region is a box open at both xy planes. -For style *prism*\ , values 1-6 have the same mapping as for style -*block*\ . I.e. in an untilted *prism*\ , *open* indices correspond to +For style *prism*, values 1-6 have the same mapping as for style +*block*\ . I.e. in an untilted *prism*, *open* indices correspond to the xlo, xhi, ylo, yhi, zlo, zhi surfaces. -For style *cylinder*\ , index 1 corresponds to the flat end cap at the +For style *cylinder*, index 1 corresponds to the flat end cap at the low coordinate along the cylinder axis, index 2 corresponds to the high-coordinate flat end cap along the cylinder axis, and index 3 is the curved cylinder surface. For example, a *cylinder* region with *open 1 open 2* keywords will be open at both ends (e.g. a section of pipe), regardless of the cylinder orientation. -For style *cone*\ , the mapping is the same as for style *cylinder*\ . +For style *cone*, the mapping is the same as for style *cylinder*\ . Index 1 is the low-coordinate flat end cap, index 2 is the high-coordinate flat end cap, and index 3 is the curved cone surface. In the last example above, a *cone* region is defined along the z-axis @@ -371,7 +371,7 @@ sub-regions can be defined with the *open* keyword. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -383,13 +383,13 @@ by Kokkos or no acceleration will occur. Currently, only *block* style regions are supported by Kokkos. These accelerated styles are part of the Kokkos package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index e9e23afba8..21c6f68643 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -114,11 +114,11 @@ Note that the dump files specified as part of the *dump* keyword can be parallel files, i.e. written as multiple files either per processor and/or per snapshot. If that is the case they will also be read in parallel which can make the rerun command operate dramatically faster -for large systems. See the doc page for the :doc:`read_dump +for large systems. See the page for the :doc:`read_dump ` and :doc:`dump ` commands which describe how to read and write parallel dump files. -The *first*\ , *last*\ , *every*\ , *skip* keywords determine which +The *first*, *last*, *every*, *skip* keywords determine which snapshots are read from the dump file(s). Snapshots are skipped until they have a timestep >= *Nfirst*\ . When a snapshot with a timestep > *Nlast* is encountered, the rerun command finishes. Note that @@ -145,7 +145,7 @@ do for the :doc:`run ` command. They only need to be defined if (a) you are using a :doc:`fix ` command that changes some value over time, and (b) you want the reference point for elapsed time (from start to stop) to be different than the *first* and *last* settings. -See the doc page for individual fixes to see which ones can be used +See the page for individual fixes to see which ones can be used with the *start/stop* keywords. Note that if you define neither of the *start*\ /\ *stop* or *first*\ /\ *last* keywords, then LAMMPS treats the pseudo run as going from 0 to a huge value (effectively infinity). @@ -163,7 +163,7 @@ The *dump* keyword is required and must be the last keyword specified. Its arguments are passed internally to the :doc:`read_dump ` command. The first argument following the *dump* keyword should be the *field1* argument of the :doc:`read_dump ` command. See -the :doc:`read_dump ` doc page for details on the various +the :doc:`read_dump ` page for details on the various options it allows for extracting information from the dump file snapshots, and for using that information to alter the LAMMPS simulation. @@ -192,14 +192,14 @@ angle evaluations, if no pair style is being used. Every time a snapshot is read, the timestep for the simulation is reset, as if the :doc:`reset_timestep ` command were used. This command has some restrictions as to what fixes can be -defined. See its doc page for details. For example, the :doc:`fix deposit ` and :doc:`fix dt/reset ` fixes +defined. See its page for details. For example, the :doc:`fix deposit ` and :doc:`fix dt/reset ` fixes are in this category. They also make no sense to use with a rerun command. If time-averaging fixes like :doc:`fix ave/time ` are used, they are invoked on timesteps that are a function of their -*Nevery*\ , *Nrepeat*\ , and *Nfreq* settings. As an example, see the -:doc:`fix ave/time ` doc page for details. You must +*Nevery*, *Nrepeat*, and *Nfreq* settings. As an example, see the +:doc:`fix ave/time ` page for details. You must insure those settings are consistent with the snapshot timestamps that are read from the dump file(s). If an averaging fix is not invoked on a timestep it expects to be, LAMMPS will flag an error. diff --git a/doc/src/run.rst b/doc/src/run.rst index 6c47721e91..75c3bc93f0 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -45,7 +45,7 @@ Description Run or continue dynamics for a specified number of timesteps. -When the :doc:`run style ` is *respa*\ , N refers to outer +When the :doc:`run style ` is *respa*, N refers to outer loop (largest) timesteps. A value of N = 0 is acceptable; only the thermodynamics of the system @@ -64,7 +64,7 @@ completes. The *start* or *stop* keywords can be used if multiple runs are being performed and you want a :doc:`fix ` command that changes some value over time (e.g. temperature) to make the change across the -entire set of runs and not just a single run. See the doc page for +entire set of runs and not just a single run. See the page for individual fixes to see which ones can be used with the *start/stop* keywords. @@ -136,7 +136,7 @@ be useful for invoking a command you have added to LAMMPS that wraps some other code (e.g. as a library) to perform a computation periodically during a long LAMMPS run. See the :doc:`Modify ` doc page for info about how to add new commands to LAMMPS. See the -:doc:`Howto couple ` doc page for ideas about how to +:doc:`Howto couple ` page for ideas about how to couple LAMMPS to other codes. With the *every* option, N total steps are simulated, in shorter runs @@ -203,7 +203,7 @@ Restrictions When not using the *upto* keyword, the number of specified timesteps N must fit in a signed 32-bit integer, so you are limited to slightly -more than 2 billion steps (2\^31) in a single run. When using *upto*\ , +more than 2 billion steps (2\^31) in a single run. When using *upto*, N can be larger than a signed 32-bit integer, however the difference between N and the current timestep must still be no larger than 2\^31 steps. diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 713fedae70..bcfa3d7b54 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -125,7 +125,7 @@ screen.0 by default; see the :doc:`-plog and -pscreen command-line switches ` doc page for performance +See the :doc:`Speed packages ` page for performance details of the speed-up offered by the *verlet/split* style. One important performance consideration is the assignment of logical processors in the 2 partitions to the physical cores of a parallel @@ -298,7 +298,7 @@ can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -308,7 +308,7 @@ Restrictions The *verlet/split* style can only be used if LAMMPS was built with the REPLICA package. Correspondingly the *respa/omp* style is available -only if the USER-OMP package was included. See the :doc:`Build package ` doc page for more info. +only if the OPENMP package was included. See the :doc:`Build package ` page for more info. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are diff --git a/doc/src/server.rst b/doc/src/server.rst index f305f314c1..7423653c14 100644 --- a/doc/src/server.rst +++ b/doc/src/server.rst @@ -28,7 +28,7 @@ message back to the client. The specified *protocol* determines the format and content of messages LAMMPS expects to receive and how it responds. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -47,9 +47,9 @@ are: * :doc:`md ` = run dynamics with another code * :doc:`mc ` = perform Monte Carlo moves with another code -For protocol *md*\ , LAMMPS can be either a client (via the :doc:`fix client/md ` command) or server. See the :doc:`server md ` doc page for details on the protocol. +For protocol *md*, LAMMPS can be either a client (via the :doc:`fix client/md ` command) or server. See the :doc:`server md ` page for details on the protocol. -For protocol *mc*\ , LAMMPS can be the server. See the :doc:`server mc ` doc page for details on the protocol. +For protocol *mc*, LAMMPS can be the server. See the :doc:`server mc ` page for details on the protocol. ---------- @@ -57,7 +57,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. A script that uses this command must also use the :doc:`message ` command to setup the messaging protocol with diff --git a/doc/src/server_mc.rst b/doc/src/server_mc.rst index eae3ead5b4..f5ddf2f468 100644 --- a/doc/src/server_mc.rst +++ b/doc/src/server_mc.rst @@ -27,7 +27,7 @@ expect messages from a separate "client" code that match the *mc* protocol for format and content explained below. For each message LAMMPS receives it will send a message back to the client. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -39,7 +39,7 @@ signals when it is done sending messages to LAMMPS, at which point the loop will exit, and the remainder of the LAMMPS script will be processed. -The :doc:`server ` doc page gives other options for using LAMMPS +The :doc:`server ` page gives other options for using LAMMPS See an example of how this command is used in examples/COUPLE/lammps_mc/in.server. @@ -109,7 +109,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. A script that uses this command must also use the :doc:`message ` command to setup the messaging protocol with diff --git a/doc/src/server_md.rst b/doc/src/server_md.rst index 86a8225e7a..f9a25a4718 100644 --- a/doc/src/server_md.rst +++ b/doc/src/server_md.rst @@ -27,7 +27,7 @@ expect messages from a separate "client" code that match the *md* protocol for format and content explained below. For each message LAMMPS receives it will send a message back to the client. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -39,7 +39,7 @@ signals when it is done sending messages to LAMMPS, at which point the loop will exit, and the remainder of the LAMMPS script will be processed. -The :doc:`server ` doc page gives other options for using LAMMPS +The :doc:`server ` page gives other options for using LAMMPS in server mode. See an example of how this command is used in examples/message/in.message.server. @@ -148,7 +148,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/set.rst b/doc/src/set.rst index 420190f0fd..e61c288a74 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -42,9 +42,9 @@ Syntax seed = random # seed (positive integer) *mol* value = molecule ID value can be an atom-style variable (see below) - *x*\ ,\ *y*\ ,\ *z* value = atom coordinate (distance units) + *x*,\ *y*,\ *z* value = atom coordinate (distance units) value can be an atom-style variable (see below) - *vx*\ ,\ *vy*\ ,\ *vz* value = atom velocity (velocity units) + *vx*,\ *vy*,\ *vz* value = atom velocity (velocity units) value can be an atom-style variable (see below) *charge* value = atomic charge (charge units) value can be an atom-style variable (see below) @@ -175,12 +175,12 @@ style *type* selects all the atoms in a range of types. The style In each of the range cases, the range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For -example, for the style *type*\ , if N = the number of atom types, then +example, for the style *type*, if N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). For all the styles except -*mol*\ , the lowest value for the wildcard is 1; for *mol* it is 0. +*mol*, the lowest value for the wildcard is 1; for *mol* it is 0. The style *group* selects all the atoms in the specified group. The style *region* selects all the atoms in the specified geometric @@ -250,10 +250,10 @@ Keyword *mol* sets the molecule ID for all selected atoms. The :doc:`atom style ` being used must support the use of molecule IDs. -Keywords *x*\ , *y*\ , *z*\ , and *charge* set the coordinates or -charge of all selected atoms. For *charge*\ , the :doc:`atom style +Keywords *x*, *y*, *z*, and *charge* set the coordinates or +charge of all selected atoms. For *charge*, the :doc:`atom style ` being used must support the use of atomic -charge. Keywords *vx*\ , *vy*\ , and *vz* set the velocities of all +charge. Keywords *vx*, *vy*, and *vz* set the velocities of all selected atoms. Keyword *dipole* uses the specified x,y,z values as components of a @@ -303,7 +303,7 @@ the :doc:`atom_style ` command. Random numbers are used in such a way that the orientation of a particular atom is the same, regardless of how many processors are being used. For 2d systems, only orientations in the xy plane are generated. As with keyword -*quat*\ , for ellipsoidal particles, the 3 shape values must be non-zero +*quat*, for ellipsoidal particles, the 3 shape values must be non-zero for each particle set by this command. This keyword does not allow use of an atom-style variable. @@ -316,7 +316,7 @@ a density, e.g. via the :doc:`read_data ` command. Keyword *shape* sets the size and shape of the selected atoms. The particles must be ellipsoids as defined by the :doc:`atom_style -ellipsoid ` command. The *Sx*\ , *Sy*\ , *Sz* settings +ellipsoid ` command. The *Sx*, *Sy*, *Sz* settings are the 3 diameters of the ellipsoid in each direction. All 3 can be set to the same value, which means the ellipsoid is effectively a sphere. They can also all be set to 0.0 which means the particle will @@ -430,28 +430,28 @@ up analysis of the trajectories if a LAMMPS diagnostic or your own analysis relies on the image flags to unwrap a molecule which straddles the periodic box. -Keywords *bond*\ , *angle*\ , *dihedral*\ , and *improper*\ , set the bond +Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type (angle type, etc) of all bonds (angles, etc) of selected atoms to the specified value from 1 to nbondtypes (nangletypes, etc). All atoms in a particular bond (angle, etc) must be selected atoms in order for the change to be made. The value of nbondtype (nangletypes, -etc) was set by the *bond types* (\ *angle types*\ , etc) field in the +etc) was set by the *bond types* (\ *angle types*, etc) field in the header of the data file read by the :doc:`read_data ` command. These keywords do not allow use of an atom-style variable. -Keywords *sph/e*\ , *sph/cv*\ , and *sph/rho* set the energy, heat +Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity, and density of smoothed particle hydrodynamics (SPH) -particles. See `this PDF guide `_ +particles. See `this PDF guide `_ to using SPH in LAMMPS. Keyword *smd/mass/density* sets the mass of all selected particles, but it is only applicable to the Smooth Mach Dynamics package -USER-SMD. It assumes that the particle volume has already been +MACHDYN. It assumes that the particle volume has already been correctly set and calculates particle mass from the provided mass density value. Keyword *smd/contact/radius* only applies to simulations with the -Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius +Smooth Mach Dynamics package MACHDYN. Itsets an interaction radius for computing short-range interactions, e.g. repulsive forces to prevent different individual physical bodies from penetrating each other. Note that the SPH smoothing kernel diameter used for computing @@ -459,7 +459,7 @@ long range, nonlocal interactions, is set using the *diameter* keyword. Keyword *dpd/theta* sets the internal temperature of a DPD particle as -defined by the USER-DPD package. If the specified value is a number +defined by the DPD-REACT package. If the specified value is a number it must be >= 0.0. If the specified value is NULL, then the kinetic temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal @@ -470,13 +470,13 @@ value >= 0.0, the internal temperature is set to that value. If it is temperature is set to that value. Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric -heat capacity of an eDPD particle as defined by the USER-MESODPD package. +heat capacity of an eDPD particle as defined by the DPD-MESO package. Currently, only :doc:`atom_style edpd ` defines particles with these attributes. The values for the temperature and heat capacity must be positive. Keyword *cc* sets the chemical concentration of a tDPD particle for a -specified species as defined by the USER-MESODPD package. Currently, only +specified species as defined by the DPD-MESO package. Currently, only :doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom_style command. The value diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 95f72a27ba..af5c110fee 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -58,7 +58,7 @@ of the input script. Or you can run a program that pre-processes data for input into LAMMPS. Or you can run a program that post-processes LAMMPS output data. -With the exception of *cd*\ , all commands, including ones invoked via a +With the exception of *cd*, all commands, including ones invoked via a system() call, are executed by only a single processor, so that files/directories are not being manipulated by multiple processors. diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 779056f87a..4b197fbf3a 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -148,7 +148,7 @@ LJ and Coulombic interactions, which is consistent with a coarse-grained polymer model with :doc:`FENE bonds `. See :ref:`(Kremer) ` for a description of FENE bonds. -The *lj/coul*\ , *lj*\ , and *coul* keywords allow the 3 coefficients to +The *lj/coul*, *lj*, and *coul* keywords allow the 3 coefficients to be set explicitly. The *lj/coul* keyword sets both the LJ and Coulombic coefficients to the same 3 values. The *lj* and *coul* keywords only set either the LJ or Coulombic coefficients. Use both @@ -165,7 +165,7 @@ as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a dihedral, then the pairwise interaction between atoms 1 and 3 will always be weighted by 0.5, but different force fields use different rules for weighting the pairwise interaction between atoms 2 and 4. -If the *angle* keyword is specified as *yes*\ , then the pairwise +If the *angle* keyword is specified as *yes*, then the pairwise interaction between atoms 2 and 4 will be unaffected (full weighting of 1.0). If the *angle* keyword is specified as *no* which is the default, then the 2,4 interaction will also be weighted by 0.5. @@ -179,7 +179,7 @@ defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a dihedral, then the pairwise interaction between atoms 1 and 4 will always be weighted by 0.5, but different force fields use different rules for weighting the pairwise interaction between atoms 2 and 5. -If the *dihedral* keyword is specified as *yes*\ , then the pairwise +If the *dihedral* keyword is specified as *yes*, then the pairwise interaction between atoms 2 and 5 will be unaffected (full weighting of 1.0). If the *dihedral* keyword is specified as *no* which is the default, then the 2,5 interaction will also be weighted by 0.5. diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 9df3ce1658..4789229800 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -32,25 +32,25 @@ This command allows you to use variants of various styles if they exist. In that respect it operates the same as the :doc:`-suffix command-line switch `. It also has options to turn off or back on any suffix setting made via the command line. -The specified style can be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt* or +The specified style can be *gpu*, *intel*, *kk*, *omp*, *opt* or *hybrid*\ . These refer to optional packages that LAMMPS can be built with, as described on the :doc:`Build package ` doc page. The "gpu" style corresponds to the GPU package, the "intel" style to -the USER-INTEL package, the "kk" style to the KOKKOS package, the -"omp" style to the USER-OMP package, and the "opt" style to the OPT +the INTEL package, the "kk" style to the KOKKOS package, the +"omp" style to the OPENMP package, and the "opt" style to the OPT package. These are the variants these packages provide: * GPU = a handful of pair styles and the PPPM kspace_style, optimized to run on one or more GPUs or multicore CPU/GPU nodes -* USER-INTEL = a collection of pair styles and neighbor routines +* INTEL = a collection of pair styles and neighbor routines optimized to run in single, mixed, or double precision on CPUs and Intel(R) Xeon Phi(TM) co-processors. * KOKKOS = a collection of atom, pair, and fix styles optimized to run using the Kokkos library on various kinds of hardware, including GPUs via CUDA and many-core chips via OpenMP or threading. -* USER-OMP = a collection of pair, bond, angle, dihedral, improper, +* OPENMP = a collection of pair, bond, angle, dihedral, improper, kspace, compute, and fix styles with support for OpenMP multi-threading * OPT = a handful of pair styles, cache-optimized for faster CPU @@ -74,13 +74,13 @@ created. For "hybrid", two packages are specified. The first is used whenever available. If a style with the first suffix is not available, the style with the suffix for the second package will be used if available. For -example, "hybrid intel omp" will use styles from the USER-INTEL package -as a first choice and styles from the USER-OMP package as a second choice -if no USER-INTEL variant is available. +example, "hybrid intel omp" will use styles from the INTEL package +as a first choice and styles from the OPENMP package as a second choice +if no INTEL variant is available. -If the specified style is *off*\ , then any previously specified suffix +If the specified style is *off*, then any previously specified suffix is temporarily disabled, whether it was specified by a command-line -switch or a previous suffix command. If the specified style is *on*\ , +switch or a previous suffix command. If the specified style is *on*, a disabled suffix is turned back on. The use of these 2 commands lets your input script use a standard LAMMPS style (i.e. a non-accelerated variant), which can be useful for testing or benchmarking purposes. diff --git a/doc/src/tad.rst b/doc/src/tad.rst index c3cd3b825b..b36ad2e431 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -160,7 +160,7 @@ events must be generated before one is finally executed. Conversely, if this criterion is too aggressive, high-entropy high-barrier events will be over-sampled, while low-entropy low-barrier events will be under-sampled. If the lowest pre-exponential factor is known fairly -accurately, then it can be used to estimate *tmax*\ , and the value of +accurately, then it can be used to estimate *tmax*, and the value of *delta* can be set to the desired confidence level e.g. *delta* = 0.05 corresponds to 95% confidence. However, for systems where the dynamics are not well characterized (the most common case), it will be @@ -181,7 +181,7 @@ files, and restart files. Event statistics are printed to the screen and master log.lammps file each time an event is executed. The quantities are the timestep, CPU -time, global event number *N*\ , local event number *M*\ , event status, +time, global event number *N*, local event number *M*, event status, energy barrier, time margin, *t_lo* and *delt_lo*. The timestep is the usual LAMMPS timestep, which corresponds to the high-temperature time at which the event was detected, in units of timestep. The CPU @@ -204,7 +204,7 @@ high-temperature time since entering the current basin, scaled by an exponential factor that depends on the hi/lo temperature ratio and the energy barrier for that event. -On lines for executed events, with status *E*\ , the global event number +On lines for executed events, with status *E*, the global event number is incremented by one, the local event number and time margin are reset to zero, while the global event number, energy barrier, and @@ -304,7 +304,7 @@ Default """"""" The option defaults are *min* = 0.1 0.1 40 50, *neb* = 0.01 100 100 -10, *neb_style* = *quickmin*\ , *neb_step* = the same timestep set by +10, *neb_style* = *quickmin*, *neb_step* = the same timestep set by the :doc:`timestep ` command, and *neb_log* = "none". ---------- diff --git a/doc/src/temper.rst b/doc/src/temper.rst index bdc0e426ec..363e0102fc 100644 --- a/doc/src/temper.rst +++ b/doc/src/temper.rst @@ -45,7 +45,7 @@ Each replica's temperature is controlled at a different value by a fix with *fix-ID* that controls temperature. Most thermostat fix styles (with and without included time integration) are supported. The command will print an error message and abort, if the chosen fix is unsupported. -The desired temperature is specified by *temp*\ , which is typically a +The desired temperature is specified by *temp*, which is typically a variable previously set in the input script, so that each partition is assigned a different temperature. See the :doc:`variable ` command for more details. For example: diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst index c270c1a450..312df21254 100644 --- a/doc/src/temper_grem.rst +++ b/doc/src/temper_grem.rst @@ -48,7 +48,7 @@ discussed there in greater detail. Instead of temperature, this command performs replica exchanges in lambda as per the generalized ensemble enforced by :doc:`fix grem -`. The desired lambda is specified by *lambda*\ , which is +`. The desired lambda is specified by *lambda*, which is typically a variable previously set in the input script, so that each partition is assigned a different temperature. See the :doc:`variable ` command for more details. For example: @@ -101,7 +101,7 @@ identical to :doc:`temper `. Restrictions """""""""""" -This command can only be used if LAMMPS was built with the USER-MISC +This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst index 8eaea05701..a8f5999dbe 100644 --- a/doc/src/temper_npt.rst +++ b/doc/src/temper_npt.rst @@ -51,8 +51,8 @@ on how the parallel tempering is handled in general. Restrictions """""""""""" -This command can only be used if LAMMPS was built with the USER-MISC -package. See the :doc:`Build package ` doc page for more +This command can only be used if LAMMPS was built with the REPLICA +package. See the :doc:`Build package ` page for more info. This command should be used with a fix that maintains the diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 1815a7cb76..31de925492 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -59,8 +59,8 @@ simulation box :doc:`boundary ` or if it moves more than a box length outside the simulation domain (or more than a processor sub-domain length) before reneighboring occurs. The latter case is typically due to bad dynamics, e.g. too large a timestep or huge -forces and velocities. If the value is *ignore*\ , LAMMPS does not -check for lost atoms. If the value is *error* or *warn*\ , LAMMPS +forces and velocities. If the value is *ignore*, LAMMPS does not +check for lost atoms. If the value is *error* or *warn*, LAMMPS checks and either issues an error or warning. The code will exit with an error and continue with a warning. A warning will only be issued once, the first time an atom is lost. This can be a useful debugging @@ -117,15 +117,15 @@ The *norm* keyword determines whether various thermodynamic output values are normalized by the number of atoms or not, depending on whether it is set to *yes* or *no*\ . Different unit styles have different defaults for this setting (see below). Even if *norm* is -set to *yes*\ , a value is only normalized if it is an "extensive" +set to *yes*, a value is only normalized if it is an "extensive" quantity, meaning that it scales with the number of atoms in the -system. For the thermo keywords described by the doc page for the +system. For the thermo keywords described by the page for the :doc:`thermo_style ` command, all energy-related keywords are extensive, such as *pe* or *ebond* or *enthalpy*\ . Other keywords such as *temp* or *press* are "intensive" meaning their value is independent (in a statistical sense) of the number of atoms in the system and thus are never normalized. For thermodynamic output values -extracted from fixes and computes in a :doc:`thermo_style custom ` command, the doc page for the individual +extracted from fixes and computes in a :doc:`thermo_style custom ` command, the page for the individual :doc:`fix ` or :doc:`compute ` lists whether the value is "extensive" or "intensive" and thus whether it is normalized. Thermodynamic output values calculated by a variable formula are @@ -174,7 +174,7 @@ settings, reverting all values to their default format. a "%d"-style format identifier in the format string and LAMMPS will convert this to the corresponding 8-byte form when it is applied to those keywords. However, when specifying the *line* option or *format - M string* option for *step* and *natoms*\ , you should specify a format + M string* option for *step* and *natoms*, you should specify a format string appropriate for an 8-byte signed integer, e.g. one with "%ld". The *temp* keyword is used to determine how thermodynamic temperature @@ -222,7 +222,7 @@ Default """"""" The option defaults are lost = error, warn = 100, norm = yes for unit -style of *lj*\ , norm = no for unit style of *real* and *metal*\ , +style of *lj*, norm = no for unit style of *real* and *metal*, flush = no, and temp/press = compute IDs defined by thermo_style. The defaults for the line and format options depend on the thermo diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 8ea487fd0a..a04504b1a6 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -117,7 +117,7 @@ thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to :doc:`computes `, :doc:`fixes `, and equal-style :doc:`variables ` that have been defined elsewhere in the input script or can even be new styles which users have added -to LAMMPS. See the :doc:`Modify ` doc page for details on the +to LAMMPS. See the :doc:`Modify ` page for details on the latter. Thus the *custom* style provides a flexible means of outputting essentially any desired quantity as a simulation proceeds. @@ -218,16 +218,16 @@ to see which ones contribute and whether their default A long-range tail correction *etail* for the van der Waals pairwise energy will be non-zero only if the :doc:`pair_modify tail ` option is turned on. The *etail* contribution is -included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the +included in *evdwl*, *epair*, *pe*, and *etotal*, and the corresponding tail correction to the pressure is included in *press* -and *pxx*\ , *pyy*\ , etc. +and *pxx*, *pyy*, etc. ---------- Here is more information on other keywords whose meaning may not be clear: -The *step*\ , *elapsed*\ , and *elaplong* keywords refer to timestep +The *step*, *elapsed*, and *elaplong* keywords refer to timestep count. *Step* is the current timestep, or iteration count when a :doc:`minimization ` is being performed. *Elapsed* is the number of timesteps elapsed since the beginning of this run. @@ -318,13 +318,13 @@ to reduce the delay factor to insure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place. -The keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , -*cellbeta*\ , *cellgamma*\ , correspond to the usual crystallographic +The keywords *cella*, *cellb*, *cellc*, *cellalpha*, +*cellbeta*, *cellgamma*, correspond to the usual crystallographic quantities that define the periodic unit cell of a crystal. See the -:doc:`Howto triclinic ` doc page for a geometric +:doc:`Howto triclinic ` page for a geometric description of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell -dimensions *lx*\ , *ly*\ , *lz*\ , *yz*\ , *xz*\ , *xy*\ . +dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ . ---------- diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 2a6de933e0..f020511aad 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -55,8 +55,8 @@ Restrictions The command collects a 9 times the number of atoms in the group on every single MPI rank, so the memory requirements can be very significant for large systems. -This command is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This command is part of the PHONON package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/timer.rst b/doc/src/timer.rst index eac86656af..a604cc2212 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -81,7 +81,7 @@ which can be set with the *every* keyword. Default is checking every 10 steps. After the timer timeout has expired all subsequent run or minimize commands in the input script will be skipped. The remaining time or timer status can be accessed with the -:doc:`thermo ` variable *timeremain*\ , which will be +:doc:`thermo ` variable *timeremain*, which will be zero, if the timeout is inactive (default setting), it will be negative, if the timeout time is expired and positive if there is time remaining and in this case the value of the variable are diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index e512eed1b2..3142509611 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -30,7 +30,7 @@ each choice of units that LAMMPS supports. The default value for the timestep size also depends on the choice of units for the simulation; see the default values below. -When the :doc:`run style ` is *respa*\ , dt is the timestep for +When the :doc:`run style ` is *respa*, dt is the timestep for the outer loop (largest) timestep. Restrictions diff --git a/doc/src/units.rst b/doc/src/units.rst index 3c0f4a220a..da81c17078 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -29,7 +29,7 @@ and data file, as well as quantities output to the screen, log file, and dump files. Typically, this command is used at the very beginning of an input script. -For all units except *lj*\ , LAMMPS uses physical constants from +For all units except *lj*, LAMMPS uses physical constants from www.physics.nist.gov. For the definition of Kcal in real units, LAMMPS uses the thermochemical calorie = 4.184 J. @@ -60,7 +60,7 @@ automatic conversion has happened is printed to the screen. ---------- -For style *lj*\ , all quantities are unitless. Without loss of +For style *lj*, all quantities are unitless. Without loss of generality, LAMMPS sets the fundamental quantities mass, :math:`\sigma`, :math:`\epsilon`, and the Boltzmann constant :math:`k_B = 1`. The masses, distances, energies you specify are multiples of these @@ -97,7 +97,7 @@ energy/atom. Temperature is intensive since it is already normalized by the number of atoms, so it is output as-is. This behavior can be changed via the :doc:`thermo_modify norm ` command. -For style *real*\ , these are the units: +For style *real*, these are the units: * mass = grams/mole * distance = Angstroms @@ -114,7 +114,7 @@ For style *real*\ , these are the units: * electric field = volts/Angstrom * density = gram/cm\^dim -For style *metal*\ , these are the units: +For style *metal*, these are the units: * mass = grams/mole * distance = Angstroms @@ -131,7 +131,7 @@ For style *metal*\ , these are the units: * electric field = volts/Angstrom * density = gram/cm\^dim -For style *si*\ , these are the units: +For style *si*, these are the units: * mass = kilograms * distance = meters @@ -148,7 +148,7 @@ For style *si*\ , these are the units: * electric field = volts/meter * density = kilograms/meter\^dim -For style *cgs*\ , these are the units: +For style *cgs*, these are the units: * mass = grams * distance = centimeters @@ -165,7 +165,7 @@ For style *cgs*\ , these are the units: * electric field = statvolt/cm or dyne/esu * density = grams/cm\^dim -For style *electron*\ , these are the units: +For style *electron*, these are the units: * mass = atomic mass units * distance = Bohr @@ -179,7 +179,7 @@ For style *electron*\ , these are the units: * dipole moment = Debye * electric field = volts/cm -For style *micro*\ , these are the units: +For style *micro*, these are the units: * mass = picograms * distance = micrometers @@ -196,7 +196,7 @@ For style *micro*\ , these are the units: * electric field = volt/micrometer * density = picograms/micrometer\^dim -For style *nano*\ , these are the units: +For style *nano*, these are the units: * mass = attograms * distance = nanometers diff --git a/doc/src/variable.rst b/doc/src/variable.rst index ef876847d6..25861ae17b 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -189,7 +189,7 @@ executed. override a corresponding index variable setting in the input script. There are two exceptions to this rule. First, variables of style -*string*\ , *getenv*\ , *internal*\ , *equal*\ , *vector*\ , *atom*\ , and +*string*, *getenv*, *internal*, *equal*, *vector*, *atom*, and *python* ARE redefined each time the command is encountered. This allows these style of variables to be redefined multiple times in an input script. In a loop, this means the formula associated with an @@ -204,14 +204,14 @@ the same thing. ---------- -The :doc:`Commands parse ` doc page explains how +The :doc:`Commands parse ` page explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as ${LoopVar} if the name "LoopVar" is one or more characters. -As described below, for variable styles *index*\ , *loop*\ , *file*\ , -*universe*\ , and *uloop*\ , which string is assigned to a variable can be +As described below, for variable styles *index*, *loop*, *file*, +*universe*, and *uloop*, which string is assigned to a variable can be incremented via the :doc:`next ` command. When there are no more strings to assign, the variable is exhausted and a flag is set that causes the next :doc:`jump ` command encountered in the input @@ -439,7 +439,7 @@ compute, fix, or other vector-style variable. For *atom*\ -style variables the formula computes one quantity for each atom whenever it is evaluated. -Note that *equal*\ , *vector*\ , and *atom* variables can produce +Note that *equal*, *vector*, and *atom* variables can produce different values at different stages of the input script or at different times during a run. For example, if an *equal* variable is used in a :doc:`fix print ` command, different values could @@ -451,7 +451,7 @@ of Variables". The next command cannot be used with *equal* or *vector* or *atom* style variables, since there is only one string. -The formula for an *equal*\ , *vector*\ , or *atom* variable can contain a +The formula for an *equal*, *vector*, or *atom* variable can contain a variety of quantities. The syntax for each kind of quantity is simple, but multiple quantities can be nested and combined in various ways to build up formulas of arbitrary complexity. For example, this @@ -527,8 +527,8 @@ Numbers can contain digits, scientific notation (3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs. Constants are set at compile time and cannot be changed. *PI* will -return the number 3.14159265358979323846; *on*\ , *true* or *yes* will -return 1.0; *off*\ , *false* or *no* will return 0.0; *version* will +return the number 3.14159265358979323846; *on*, *true* or *yes* will +return 1.0; *off*, *false* or *no* will return 0.0; *version* will return a numeric version code of the current LAMMPS version (e.g. version 2 Sep 2015 will return the number 20150902). The corresponding value for newer versions of LAMMPS will be larger, for older versions @@ -788,7 +788,7 @@ Group and Region Functions Group functions are specified as keywords followed by one or two parenthesized arguments. The first argument *ID* is the group-ID. The *dim* argument, if it exists, is *x* or *y* or *z*\ . The *dir* -argument, if it exists, is *xmin*\ , *xmax*\ , *ymin*\ , *ymax*\ , *zmin*\ , or +argument, if it exists, is *xmin*, *xmax*, *ymin*, *ymax*, *zmin*, or *zmax*\ . The *dimdim* argument, if it exists, is *xx* or *yy* or *zz* or *xy* or *yz* or *xz*\ . @@ -943,7 +943,7 @@ features or LAMMPS, *respa* allows to check whether the inner/middle/outer mode of r-RESPA is supported. In the various style categories, the checking is also done using suffix flags, if available and enabled. -Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP). +Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with OPENMP). .. code-block:: LAMMPS @@ -958,21 +958,21 @@ Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, othe timestep $(2.0*(1.0+2.0*is_active(pair,respa)) if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3" -The *is_defined()* function allows to query categories like *compute*\ , -*dump*\ , *fix*\ , *group*\ , *region*\ , and *variable* whether an entry +The *is_defined()* function allows to query categories like *compute*, +*dump*, *fix*, *group*, *region*, and *variable* whether an entry with the provided name or id is defined. The *is_available(category,name)* function allows to query whether a specific optional feature is available, i.e. compiled in. -This currently works for the following categories: *command*\ , -*compute*\ , *fix*\ , *pair_style* and *feature*\ . For all categories +This currently works for the following categories: *command*, +*compute*, *fix*, *pair_style* and *feature*\ . For all categories except *command* and *feature* also appending active suffixes is tried before reporting failure. The *feature* category is used to check the availability of compiled in features such as GZIP support, PNG support, JPEG support, FFMPEG support, and C++ exceptions for error handling. Corresponding values for name are -*gzip*\ , *png*\ , *jpeg*\ , *ffmpeg* and *exceptions*\ . +*gzip*, *png*, *jpeg*, *ffmpeg* and *exceptions*\ . This enables writing input scripts which only dump using a given format if the compiled binary supports it. @@ -1025,7 +1025,7 @@ Compute References Compute references access quantities calculated by a :doc:`compute `. The ID in the reference should be replaced by the ID of a compute defined elsewhere in the input script. As -discussed in the doc page for the :doc:`compute ` command, +discussed in the page for the :doc:`compute ` command, computes can produce global, per-atom, or local values. Only global and per-atom values can be used in a variable. Computes can also produce a scalar, vector, or array. @@ -1086,7 +1086,7 @@ Fix References Fix references access quantities calculated by a :doc:`fix `. The ID in the reference should be replaced by the ID of a fix defined -elsewhere in the input script. As discussed in the doc page for the +elsewhere in the input script. As discussed in the page for the :doc:`fix ` command, fixes can produce global, per-atom, or local values. Only global and per-atom values can be used in a variable. Fixes can also produce a scalar, vector, or array. An equal-style @@ -1198,7 +1198,7 @@ Immediate Evaluation of Variables If you want an equal-style variable to be evaluated immediately, it may be the case that you do not need to define a variable at all. See -the :doc:`Commands parse ` doc page for info on how to +the :doc:`Commands parse ` page for info on how to use "immediate" variables in an input script, specified as $(formula) with parenthesis, where the formula has the same syntax as equal-style variables described on this page. This effectively evaluates a diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index d8823d6b7e..0c8de5b854 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -115,7 +115,7 @@ body. All temperatures specified in the velocity command are in temperature units; see the :doc:`units ` command. The units of velocities and coordinates depend on whether the *units* keyword is set to *box* or -*lattice*\ , as discussed below. +*lattice*, as discussed below. For all styles, no atoms are assigned z-component velocities if the simulation is 2d; see the :doc:`dimension ` command. @@ -161,12 +161,12 @@ appropriate fix command must be specified before the velocity command is issued. The *bias* keyword with a *yes* setting is used by *create* and -*scale*\ , but only if the *temp* keyword is also used to specify a +*scale*, but only if the *temp* keyword is also used to specify a :doc:`compute ` that calculates temperature in a desired way. If the temperature compute also calculates a velocity bias, the bias is subtracted from atom velocities before the *create* and *scale* operations are performed. After the operations, the bias is -added back to the atom velocities. See the :doc:`Howto thermostat ` doc page for more discussion of +added back to the atom velocities. See the :doc:`Howto thermostat ` page for more discussion of temperature computes with biases. Note that the velocity bias is only applied to atoms in the temperature compute specified with the *temp* keyword. diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 0aa26f8bbf..e14d1b7f4c 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -107,7 +107,7 @@ from :doc:`fix property/atom `. The *pair* keyword lets you specify in what format the pair coefficient information is written into the data file. If the value -is specified as *ii*\ , then one line per atom type is written, to +is specified as *ii*, then one line per atom type is written, to specify the coefficients for each of the I=J interactions. This means that no cross-interactions for I != J will be specified in the data file and the pair style will apply its mixing rule, as documented on @@ -116,7 +116,7 @@ behavior can be overridden in the input script after reading the data file, by specifying additional :doc:`pair_coeff ` commands for any desired I,J pairs. -If the value is specified as *ij*\ , then one line of coefficients is +If the value is specified as *ij*, then one line of coefficients is written for all I,J pairs where I <= J. These coefficients will include any specific settings made in the input script up to that point. The presence of these I != J coefficients in the data file diff --git a/doc/utils/check-packages.py b/doc/utils/check-packages.py index 339d584c59..cb64259f15 100755 --- a/doc/utils/check-packages.py +++ b/doc/utils/check-packages.py @@ -41,12 +41,10 @@ if not os.path.isdir(doc_dir): pkgdirs = glob(os.path.join(src_dir, '[A-Z][A-Z]*')) dirs = re.compile(".*/([0-9A-Z-]+)$") -user = re.compile("USER-.*") -stdpkg = [] -usrpkg = [] +pkgs = [] -# find package names and add to standard and user package lists. +# find package names and add package list. # anything starting with at least two upper case characters, is a # folder, and is not called 'MAKE' is a package @@ -54,47 +52,29 @@ for d in pkgdirs: pkg = dirs.match(d).group(1) if not os.path.isdir(os.path.join(src_dir, pkg)): continue if pkg in ['DEPEND','MAKE','STUBS']: continue - if user.match(pkg): - usrpkg.append(pkg) - else: - stdpkg.append(pkg) + pkgs.append(pkg) -print(f"Found {len(stdpkg)} standard and {len(usrpkg)} user packages") +print(f"Found {len(pkgs)} packages") counter = 0 -with open(os.path.join(doc_dir, 'Packages_standard.rst')) as fp: +with open(os.path.join(doc_dir, 'Packages_list.rst')) as fp: text = fp.read() matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE)) -for p in stdpkg: +for p in pkgs: if not p in matches: counter += 1 - print(f"Standard package {p} missing in Packages_standard.rst") - -with open(os.path.join(doc_dir, 'Packages_user.rst')) as fp: - text = fp.read() - -matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE)) -for p in usrpkg: - if not p in matches: - counter += 1 - print(f"User package {p} missing in Packages_user.rst") + print(f"Package {p} missing in Packages_list.rst") with open(os.path.join(doc_dir, 'Packages_details.rst')) as fp: text = fp.read() -matches = set(re.findall(':ref:`([A-Z0-9]+) `', text, re.MULTILINE)) -for p in stdpkg: +matches = set(re.findall(':ref:`([A-Z0-9-]+) `', text, re.MULTILINE)) +for p in pkgs: if not p in matches: counter += 1 - print(f"Standard package {p} missing in Packages_details.rst") - -matches = set(re.findall(':ref:`(USER-[A-Z0-9]+) `', text, re.MULTILINE)) -for p in usrpkg: - if not p in matches: - counter +=1 - print(f"User package {p} missing in Packages_details.rst") + print(f"Package {p} missing in Packages_details.rst") if counter: print(f"Found {counter} issue(s) with package lists") diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index f9a7d3e39a..6c1fd6dd35 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -254,40 +254,27 @@ for command_type, entries in index.items(): print("Total number of style index entries:", total_index) +skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species') +skip_pair = ('meam/c','lj/sf','reax/c') + counter = 0 -counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`", - command,'Command',suffix=False) -counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) `", - compute,'Compute',suffix=True) -counter += check_style('compute.rst', doc_dir, ":doc:`(.+) ` -", - compute,'Compute',suffix=False) -counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) `", - fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=True) -counter += check_style('fix.rst', doc_dir, ":doc:`(.+) ` -", - fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False) -counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) `", - pair,'Pair',skip=('meam','lj/sf'),suffix=True) -counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) ` -", - pair,'Pair',skip=('meam','lj/sf'),suffix=False) -counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `", - bond,'Bond',suffix=True) -counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) ` -", - bond,'Bond',suffix=False) -counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `", - angle,'Angle',suffix=True) -counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) ` -", - angle,'Angle',suffix=False) -counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `", - dihedral,'Dihedral',suffix=True) -counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) ` -", - dihedral,'Dihedral',suffix=False) -counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `", - improper,'Improper',suffix=True) -counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) ` -", - improper,'Improper',suffix=False) -counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) `", - kspace,'KSpace',suffix=True) +counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=False) +counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) `",compute,'Compute',suffix=True) +counter += check_style('compute.rst', doc_dir, ":doc:`(.+) ` -",compute,'Compute',suffix=False) +counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) `",fix,'Fix',skip=skip_fix,suffix=True) +counter += check_style('fix.rst', doc_dir, ":doc:`(.+) ` -",fix,'Fix',skip=skip_fix,suffix=False) +counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) `",pair,'Pair',skip=skip_pair,suffix=True) +counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) ` -",pair,'Pair',skip=skip_pair,suffix=False) +counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",bond,'Bond',suffix=True) +counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) ` -",bond,'Bond',suffix=False) +counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",angle,'Angle',suffix=True) +counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) ` -",angle,'Angle',suffix=False) +counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",dihedral,'Dihedral',suffix=True) +counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) ` -",dihedral,'Dihedral',suffix=False) +counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",improper,'Improper',suffix=True) +counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) ` -",improper,'Improper',suffix=False) +counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) `",kspace,'KSpace',suffix=True) if counter: print(f"Found {counter} issue(s) with style lists") @@ -295,13 +282,13 @@ if counter: counter = 0 counter += check_style_index("compute", compute, index["compute"]) -counter += check_style_index("fix", fix, index["fix"], skip=['python']) +counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species']) counter += check_style_index("angle_style", angle, index["angle_style"]) counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) -counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam', 'lj/sf']) +counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c']) if counter: print(f"Found {counter} issue(s) with style index") diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index 9b8e106875..7e4563a1ec 100644 --- a/doc/utils/requirements.txt +++ b/doc/utils/requirements.txt @@ -1,4 +1,4 @@ -Sphinx +Sphinx==4.0.3 sphinxcontrib-spelling git+git://github.com/akohlmey/sphinx-fortran@parallel-read sphinx_tabs diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 5d9b3eb8c1..c866a9409b 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -448,6 +448,7 @@ clo Clovertown cmake CMake +CMakeLists cmap Cmax cmd @@ -1132,6 +1133,7 @@ Germano gerolf Gerolf Gershgorin +getter gettimeofday gewald Gezelter @@ -1325,6 +1327,7 @@ hyperradius hyperspherical hysteretic hz +IAP Ibanez iatom ibar @@ -1647,6 +1650,8 @@ larentzos Larentzos Laroche lars +LATBOLTZ +latboltz latencies Latour latourr @@ -1797,6 +1802,8 @@ Lysogorskiy Lyulin lz Maaravi +MACHDYN +machdyn Mackay Mackrodt Macromolecules @@ -1891,8 +1898,7 @@ mdi mdpd mDPD meam -meamc -MEAMC +MEAM meamf meanDist mech @@ -2319,6 +2325,7 @@ Ntriples Ntype ntypes Ntypes +nucleotide nucleotides nullptr num @@ -2403,6 +2410,7 @@ orthorhombic Ortner oso Otype +Ouadfel Ouldridge outfile outmost @@ -2735,8 +2743,9 @@ README realtime reamin reax -REAXC +REAXFF ReaxFF +reaxff rebo recursing Ree @@ -2857,6 +2866,7 @@ Rossky rosybrown rotationally Rotenberg +Rothenburg Rovigatti royalblue rozero @@ -3149,6 +3159,7 @@ Suter Sutmann Suzen svn +Svoboda sw Swegat swiggle diff --git a/examples/USER/misc/addtorque/in.addtorque b/examples/PACKAGES/addtorque/in.addtorque similarity index 100% rename from examples/USER/misc/addtorque/in.addtorque rename to examples/PACKAGES/addtorque/in.addtorque diff --git a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1 b/examples/PACKAGES/addtorque/log.9Nov16.addtorque.g++.1 similarity index 100% rename from examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1 rename to examples/PACKAGES/addtorque/log.9Nov16.addtorque.g++.1 diff --git a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4 b/examples/PACKAGES/addtorque/log.9Nov16.addtorque.g++.4 similarity index 100% rename from examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4 rename to examples/PACKAGES/addtorque/log.9Nov16.addtorque.g++.4 diff --git a/examples/USER/adios/balance/adios2_config.xml b/examples/PACKAGES/adios/balance/adios2_config.xml similarity index 100% rename from examples/USER/adios/balance/adios2_config.xml rename to examples/PACKAGES/adios/balance/adios2_config.xml diff --git a/examples/USER/adios/balance/in.adios_balance b/examples/PACKAGES/adios/balance/in.adios_balance similarity index 100% rename from examples/USER/adios/balance/in.adios_balance rename to examples/PACKAGES/adios/balance/in.adios_balance diff --git a/examples/USER/adios/balance/in.adios_balance2 b/examples/PACKAGES/adios/balance/in.adios_balance2 similarity index 100% rename from examples/USER/adios/balance/in.adios_balance2 rename to examples/PACKAGES/adios/balance/in.adios_balance2 diff --git a/examples/USER/adios/balance/log.balance b/examples/PACKAGES/adios/balance/log.balance similarity index 100% rename from examples/USER/adios/balance/log.balance rename to examples/PACKAGES/adios/balance/log.balance diff --git a/examples/USER/adios/rerun/README b/examples/PACKAGES/adios/rerun/README similarity index 100% rename from examples/USER/adios/rerun/README rename to examples/PACKAGES/adios/rerun/README diff --git a/examples/USER/adios/rerun/adios2_config.xml b/examples/PACKAGES/adios/rerun/adios2_config.xml similarity index 100% rename from examples/USER/adios/rerun/adios2_config.xml rename to examples/PACKAGES/adios/rerun/adios2_config.xml diff --git a/examples/USER/adios/rerun/in.first b/examples/PACKAGES/adios/rerun/in.first similarity index 100% rename from examples/USER/adios/rerun/in.first rename to examples/PACKAGES/adios/rerun/in.first diff --git a/examples/USER/adios/rerun/in.read_dump b/examples/PACKAGES/adios/rerun/in.read_dump similarity index 100% rename from examples/USER/adios/rerun/in.read_dump rename to examples/PACKAGES/adios/rerun/in.read_dump diff --git a/examples/USER/adios/rerun/in.rerun b/examples/PACKAGES/adios/rerun/in.rerun similarity index 100% rename from examples/USER/adios/rerun/in.rerun rename to examples/PACKAGES/adios/rerun/in.rerun diff --git a/examples/USER/adios/rerun/log.20Jan20.first.g++.7.4 b/examples/PACKAGES/adios/rerun/log.20Jan20.first.g++.7.4 similarity index 100% rename from examples/USER/adios/rerun/log.20Jan20.first.g++.7.4 rename to examples/PACKAGES/adios/rerun/log.20Jan20.first.g++.7.4 diff --git a/examples/USER/adios/rerun/log.20Jan20.read_dump.g++.7.4 b/examples/PACKAGES/adios/rerun/log.20Jan20.read_dump.g++.7.4 similarity index 100% rename from examples/USER/adios/rerun/log.20Jan20.read_dump.g++.7.4 rename to examples/PACKAGES/adios/rerun/log.20Jan20.read_dump.g++.7.4 diff --git a/examples/USER/adios/rerun/log.20Jan20.rerun.g++.7.4 b/examples/PACKAGES/adios/rerun/log.20Jan20.rerun.g++.7.4 similarity index 100% rename from examples/USER/adios/rerun/log.20Jan20.rerun.g++.7.4 rename to examples/PACKAGES/adios/rerun/log.20Jan20.rerun.g++.7.4 diff --git a/examples/USER/misc/agni/Al_jpc.agni b/examples/PACKAGES/agni/Al_jpc.agni similarity index 100% rename from examples/USER/misc/agni/Al_jpc.agni rename to examples/PACKAGES/agni/Al_jpc.agni diff --git a/examples/USER/misc/agni/adatom.data b/examples/PACKAGES/agni/adatom.data similarity index 100% rename from examples/USER/misc/agni/adatom.data rename to examples/PACKAGES/agni/adatom.data diff --git a/examples/USER/misc/agni/in.adatom b/examples/PACKAGES/agni/in.adatom similarity index 100% rename from examples/USER/misc/agni/in.adatom rename to examples/PACKAGES/agni/in.adatom diff --git a/examples/USER/misc/agni/in.vacancy b/examples/PACKAGES/agni/in.vacancy similarity index 100% rename from examples/USER/misc/agni/in.vacancy rename to examples/PACKAGES/agni/in.vacancy diff --git a/examples/USER/misc/agni/log.20Jan21.adatom.g++.1 b/examples/PACKAGES/agni/log.20Jan21.adatom.g++.1 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.adatom.g++.1 rename to examples/PACKAGES/agni/log.20Jan21.adatom.g++.1 diff --git a/examples/USER/misc/agni/log.20Jan21.adatom.g++.4 b/examples/PACKAGES/agni/log.20Jan21.adatom.g++.4 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.adatom.g++.4 rename to examples/PACKAGES/agni/log.20Jan21.adatom.g++.4 diff --git a/examples/USER/misc/agni/log.20Jan21.vacancy.g++.1 b/examples/PACKAGES/agni/log.20Jan21.vacancy.g++.1 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.vacancy.g++.1 rename to examples/PACKAGES/agni/log.20Jan21.vacancy.g++.1 diff --git a/examples/USER/misc/agni/log.20Jan21.vacancy.g++.4 b/examples/PACKAGES/agni/log.20Jan21.vacancy.g++.4 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.vacancy.g++.4 rename to examples/PACKAGES/agni/log.20Jan21.vacancy.g++.4 diff --git a/examples/USER/misc/agni/vacancy.data b/examples/PACKAGES/agni/vacancy.data similarity index 100% rename from examples/USER/misc/agni/vacancy.data rename to examples/PACKAGES/agni/vacancy.data diff --git a/examples/USER/atc/README b/examples/PACKAGES/atc/README similarity index 100% rename from examples/USER/atc/README rename to examples/PACKAGES/atc/README diff --git a/examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat b/examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat rename to examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn.mat diff --git a/examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat b/examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn_linear.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat rename to examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn_linear.mat diff --git a/examples/USER/atc/cauchy_born/Au_CauchyBorn.mat b/examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_CauchyBorn.mat rename to examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn.mat diff --git a/examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat b/examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn_linear.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat rename to examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn_linear.mat diff --git a/examples/USER/atc/cauchy_born/Au_eam.mat b/examples/PACKAGES/atc/cauchy_born/Au_eam.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_eam.mat rename to examples/PACKAGES/atc/cauchy_born/Au_eam.mat diff --git a/examples/USER/atc/cauchy_born/Au_eam_linear.mat b/examples/PACKAGES/atc/cauchy_born/Au_eam_linear.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_eam_linear.mat rename to examples/PACKAGES/atc/cauchy_born/Au_eam_linear.mat diff --git a/examples/USER/atc/cauchy_born/Au_u3.eam b/examples/PACKAGES/atc/cauchy_born/Au_u3.eam similarity index 100% rename from examples/USER/atc/cauchy_born/Au_u3.eam rename to examples/PACKAGES/atc/cauchy_born/Au_u3.eam diff --git a/examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat b/examples/PACKAGES/atc/cauchy_born/Cu_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat rename to examples/PACKAGES/atc/cauchy_born/Cu_CauchyBorn.mat diff --git a/examples/USER/atc/cauchy_born/cb_biaxial.screen b/examples/PACKAGES/atc/cauchy_born/cb_biaxial.screen similarity index 100% rename from examples/USER/atc/cauchy_born/cb_biaxial.screen rename to examples/PACKAGES/atc/cauchy_born/cb_biaxial.screen diff --git a/examples/USER/atc/cauchy_born/cb_shear.screen b/examples/PACKAGES/atc/cauchy_born/cb_shear.screen similarity index 100% rename from examples/USER/atc/cauchy_born/cb_shear.screen rename to examples/PACKAGES/atc/cauchy_born/cb_shear.screen diff --git a/examples/USER/atc/cauchy_born/cb_unistrain.screen b/examples/PACKAGES/atc/cauchy_born/cb_unistrain.screen similarity index 100% rename from examples/USER/atc/cauchy_born/cb_unistrain.screen rename to examples/PACKAGES/atc/cauchy_born/cb_unistrain.screen diff --git a/examples/USER/atc/cauchy_born/cb_unistrain_eam.screen b/examples/PACKAGES/atc/cauchy_born/cb_unistrain_eam.screen similarity index 100% rename from examples/USER/atc/cauchy_born/cb_unistrain_eam.screen rename to examples/PACKAGES/atc/cauchy_born/cb_unistrain_eam.screen diff --git a/examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen 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examples/USER/atc/elastic/in.bar1d_frac_step rename to examples/PACKAGES/atc/elastic/in.bar1d_frac_step diff --git a/examples/USER/atc/elastic/in.bar1d_ghost_flux b/examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux similarity index 100% rename from examples/USER/atc/elastic/in.bar1d_ghost_flux rename to examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux diff --git a/examples/USER/atc/elastic/in.bar1d_thermo_elastic b/examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic similarity index 100% rename from examples/USER/atc/elastic/in.bar1d_thermo_elastic rename to examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic diff --git a/examples/USER/atc/elastic/in.eam_energy b/examples/PACKAGES/atc/elastic/in.eam_energy similarity index 100% rename from examples/USER/atc/elastic/in.eam_energy rename to examples/PACKAGES/atc/elastic/in.eam_energy diff --git a/examples/USER/atc/elastic/in.electron_density b/examples/PACKAGES/atc/elastic/in.electron_density similarity index 100% rename from examples/USER/atc/elastic/in.electron_density rename to examples/PACKAGES/atc/elastic/in.electron_density diff --git a/examples/USER/atc/elastic/in.no_atoms b/examples/PACKAGES/atc/elastic/in.no_atoms similarity index 100% rename from examples/USER/atc/elastic/in.no_atoms rename to examples/PACKAGES/atc/elastic/in.no_atoms diff --git a/examples/USER/atc/elastic/in.no_atoms_cb b/examples/PACKAGES/atc/elastic/in.no_atoms_cb similarity index 100% rename from examples/USER/atc/elastic/in.no_atoms_cb rename to examples/PACKAGES/atc/elastic/in.no_atoms_cb diff --git a/examples/USER/atc/elastic/in.no_atoms_cb_linear b/examples/PACKAGES/atc/elastic/in.no_atoms_cb_linear similarity index 100% rename from examples/USER/atc/elastic/in.no_atoms_cb_linear rename to examples/PACKAGES/atc/elastic/in.no_atoms_cb_linear diff --git a/examples/USER/atc/elastic/no_atoms.screen b/examples/PACKAGES/atc/elastic/no_atoms.screen similarity index 100% rename from examples/USER/atc/elastic/no_atoms.screen rename to examples/PACKAGES/atc/elastic/no_atoms.screen diff --git a/examples/USER/atc/elastic/no_atoms_cb.screen b/examples/PACKAGES/atc/elastic/no_atoms_cb.screen similarity index 100% rename from examples/USER/atc/elastic/no_atoms_cb.screen rename to examples/PACKAGES/atc/elastic/no_atoms_cb.screen diff --git a/examples/USER/atc/elastic/no_atoms_cb_linear.screen b/examples/PACKAGES/atc/elastic/no_atoms_cb_linear.screen similarity index 100% rename from examples/USER/atc/elastic/no_atoms_cb_linear.screen rename to examples/PACKAGES/atc/elastic/no_atoms_cb_linear.screen diff --git a/examples/USER/atc/elastic/temp.init b/examples/PACKAGES/atc/elastic/temp.init similarity index 100% rename from examples/USER/atc/elastic/temp.init rename to examples/PACKAGES/atc/elastic/temp.init diff --git a/examples/USER/atc/fluids/Ar_elastic.mat b/examples/PACKAGES/atc/fluids/Ar_elastic.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_elastic.mat rename to examples/PACKAGES/atc/fluids/Ar_elastic.mat diff --git a/examples/USER/atc/fluids/Ar_electrostatic.mat b/examples/PACKAGES/atc/fluids/Ar_electrostatic.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_electrostatic.mat rename to examples/PACKAGES/atc/fluids/Ar_electrostatic.mat diff --git a/examples/USER/atc/fluids/Ar_liquid.mat b/examples/PACKAGES/atc/fluids/Ar_liquid.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_liquid.mat rename to examples/PACKAGES/atc/fluids/Ar_liquid.mat diff --git a/examples/USER/atc/fluids/Ar_species.mat b/examples/PACKAGES/atc/fluids/Ar_species.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_species.mat rename to examples/PACKAGES/atc/fluids/Ar_species.mat diff --git a/examples/USER/atc/fluids/Ar_species_dl.mat b/examples/PACKAGES/atc/fluids/Ar_species_dl.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_species_dl.mat rename to examples/PACKAGES/atc/fluids/Ar_species_dl.mat diff --git a/examples/USER/atc/fluids/Ar_thermal.mat b/examples/PACKAGES/atc/fluids/Ar_thermal.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_thermal.mat rename to examples/PACKAGES/atc/fluids/Ar_thermal.mat diff --git a/examples/USER/atc/fluids/Ar_visc_no_atoms.mat b/examples/PACKAGES/atc/fluids/Ar_visc_no_atoms.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_visc_no_atoms.mat rename to examples/PACKAGES/atc/fluids/Ar_visc_no_atoms.mat diff --git a/examples/USER/atc/fluids/Ar_viscosity.mat b/examples/PACKAGES/atc/fluids/Ar_viscosity.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_viscosity.mat rename to examples/PACKAGES/atc/fluids/Ar_viscosity.mat diff --git a/examples/USER/atc/fluids/bar1d_fluids.screen b/examples/PACKAGES/atc/fluids/bar1d_fluids.screen similarity index 100% rename from examples/USER/atc/fluids/bar1d_fluids.screen rename to examples/PACKAGES/atc/fluids/bar1d_fluids.screen diff --git a/examples/USER/atc/fluids/concentration.screen b/examples/PACKAGES/atc/fluids/concentration.screen similarity index 100% rename from examples/USER/atc/fluids/concentration.screen rename to examples/PACKAGES/atc/fluids/concentration.screen diff --git a/examples/USER/atc/fluids/concentration_init.data b/examples/PACKAGES/atc/fluids/concentration_init.data similarity index 100% rename from examples/USER/atc/fluids/concentration_init.data rename to examples/PACKAGES/atc/fluids/concentration_init.data diff --git a/examples/USER/atc/fluids/conducting_interface.screen b/examples/PACKAGES/atc/fluids/conducting_interface.screen similarity index 100% rename from examples/USER/atc/fluids/conducting_interface.screen rename to examples/PACKAGES/atc/fluids/conducting_interface.screen diff --git a/examples/USER/atc/fluids/dielectric.mat b/examples/PACKAGES/atc/fluids/dielectric.mat similarity index 100% rename from examples/USER/atc/fluids/dielectric.mat rename to 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examples/PACKAGES/atc/fluids/in.concentration diff --git a/examples/USER/atc/fluids/in.conducting_interface b/examples/PACKAGES/atc/fluids/in.conducting_interface similarity index 100% rename from examples/USER/atc/fluids/in.conducting_interface rename to examples/PACKAGES/atc/fluids/in.conducting_interface diff --git a/examples/USER/atc/fluids/in.dielectric_interface b/examples/PACKAGES/atc/fluids/in.dielectric_interface similarity index 100% rename from examples/USER/atc/fluids/in.dielectric_interface rename to examples/PACKAGES/atc/fluids/in.dielectric_interface diff --git a/examples/USER/atc/fluids/in.double_layer b/examples/PACKAGES/atc/fluids/in.double_layer similarity index 100% rename from examples/USER/atc/fluids/in.double_layer rename to examples/PACKAGES/atc/fluids/in.double_layer diff --git a/examples/USER/atc/fluids/in.liquid_electrostatic b/examples/PACKAGES/atc/fluids/in.liquid_electrostatic similarity index 100% rename from examples/USER/atc/fluids/in.liquid_electrostatic rename to examples/PACKAGES/atc/fluids/in.liquid_electrostatic diff --git a/examples/USER/atc/fluids/in.opp_force b/examples/PACKAGES/atc/fluids/in.opp_force similarity index 100% rename from examples/USER/atc/fluids/in.opp_force rename to examples/PACKAGES/atc/fluids/in.opp_force diff --git a/examples/USER/atc/fluids/in.poisson b/examples/PACKAGES/atc/fluids/in.poisson similarity index 100% rename from examples/USER/atc/fluids/in.poisson rename to examples/PACKAGES/atc/fluids/in.poisson diff --git a/examples/USER/atc/fluids/in.shear_flow b/examples/PACKAGES/atc/fluids/in.shear_flow similarity index 100% rename from examples/USER/atc/fluids/in.shear_flow rename to examples/PACKAGES/atc/fluids/in.shear_flow diff --git a/examples/USER/atc/fluids/in.shear_no_atoms b/examples/PACKAGES/atc/fluids/in.shear_no_atoms similarity index 100% rename from examples/USER/atc/fluids/in.shear_no_atoms rename to examples/PACKAGES/atc/fluids/in.shear_no_atoms diff --git a/examples/USER/atc/fluids/interface_init.data b/examples/PACKAGES/atc/fluids/interface_init.data similarity index 100% rename from examples/USER/atc/fluids/interface_init.data rename to examples/PACKAGES/atc/fluids/interface_init.data diff --git a/examples/USER/atc/fluids/liquid_electrostatic.screen b/examples/PACKAGES/atc/fluids/liquid_electrostatic.screen similarity index 100% rename from examples/USER/atc/fluids/liquid_electrostatic.screen rename to examples/PACKAGES/atc/fluids/liquid_electrostatic.screen diff --git a/examples/USER/atc/fluids/opp_force.screen b/examples/PACKAGES/atc/fluids/opp_force.screen similarity index 100% rename from examples/USER/atc/fluids/opp_force.screen rename to examples/PACKAGES/atc/fluids/opp_force.screen diff --git a/examples/USER/atc/fluids/poisson.screen b/examples/PACKAGES/atc/fluids/poisson.screen similarity index 100% rename from examples/USER/atc/fluids/poisson.screen rename to examples/PACKAGES/atc/fluids/poisson.screen diff --git a/examples/USER/atc/fluids/post_eq.init b/examples/PACKAGES/atc/fluids/post_eq.init similarity index 100% rename from examples/USER/atc/fluids/post_eq.init rename to examples/PACKAGES/atc/fluids/post_eq.init diff --git a/examples/USER/atc/fluids/shear_flow.screen b/examples/PACKAGES/atc/fluids/shear_flow.screen similarity index 100% rename from examples/USER/atc/fluids/shear_flow.screen rename to examples/PACKAGES/atc/fluids/shear_flow.screen diff --git a/examples/USER/atc/fluids/shear_no_atoms.screen b/examples/PACKAGES/atc/fluids/shear_no_atoms.screen similarity index 100% rename from examples/USER/atc/fluids/shear_no_atoms.screen rename to examples/PACKAGES/atc/fluids/shear_no_atoms.screen diff --git a/examples/USER/atc/fluids/temp.init b/examples/PACKAGES/atc/fluids/temp.init similarity index 100% rename from examples/USER/atc/fluids/temp.init rename to examples/PACKAGES/atc/fluids/temp.init diff --git a/examples/USER/atc/fluids/velocities.init b/examples/PACKAGES/atc/fluids/velocities.init similarity index 100% rename from examples/USER/atc/fluids/velocities.init rename to examples/PACKAGES/atc/fluids/velocities.init diff --git a/examples/USER/atc/fluids/waternve.atm b/examples/PACKAGES/atc/fluids/waternve.atm similarity index 100% rename from examples/USER/atc/fluids/waternve.atm rename to examples/PACKAGES/atc/fluids/waternve.atm diff --git a/examples/USER/atc/hardy/consistency.screen b/examples/PACKAGES/atc/hardy/consistency.screen similarity index 100% rename from examples/USER/atc/hardy/consistency.screen rename to examples/PACKAGES/atc/hardy/consistency.screen diff --git a/examples/USER/atc/hardy/eam_kernel_convergence.screen b/examples/PACKAGES/atc/hardy/eam_kernel_convergence.screen similarity index 100% rename from examples/USER/atc/hardy/eam_kernel_convergence.screen rename to examples/PACKAGES/atc/hardy/eam_kernel_convergence.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_cell.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_cell.screen similarity index 100% rename from examples/USER/atc/hardy/eam_unistrain_cell.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_cell.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_mesh.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_mesh.screen similarity index 100% rename from examples/USER/atc/hardy/eam_unistrain_mesh.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_mesh.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_qcylinder.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_qcylinder.screen similarity index 100% rename from examples/USER/atc/hardy/eam_unistrain_qcylinder.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_qcylinder.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_qsphere.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_qsphere.screen similarity index 100% rename from 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a/examples/USER/atc/hardy/in.eam_unistrain_qcylinder b/examples/PACKAGES/atc/hardy/in.eam_unistrain_qcylinder similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_qcylinder rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_qcylinder diff --git a/examples/USER/atc/hardy/in.eam_unistrain_qsphere b/examples/PACKAGES/atc/hardy/in.eam_unistrain_qsphere similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_qsphere rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_qsphere diff --git a/examples/USER/atc/hardy/in.eam_unistrain_step b/examples/PACKAGES/atc/hardy/in.eam_unistrain_step similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_step rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_step diff --git a/examples/USER/atc/hardy/in.eam_volume_stretch b/examples/PACKAGES/atc/hardy/in.eam_volume_stretch similarity index 100% rename from examples/USER/atc/hardy/in.eam_volume_stretch rename to examples/PACKAGES/atc/hardy/in.eam_volume_stretch diff --git a/examples/USER/atc/hardy/in.eshelby_static b/examples/PACKAGES/atc/hardy/in.eshelby_static similarity index 100% rename from examples/USER/atc/hardy/in.eshelby_static rename to examples/PACKAGES/atc/hardy/in.eshelby_static diff --git a/examples/USER/atc/hardy/in.nvt b/examples/PACKAGES/atc/hardy/in.nvt similarity index 100% rename from examples/USER/atc/hardy/in.nvt rename to examples/PACKAGES/atc/hardy/in.nvt diff --git a/examples/USER/atc/hardy/nvt.data b/examples/PACKAGES/atc/hardy/nvt.data similarity index 100% rename from examples/USER/atc/hardy/nvt.data rename to examples/PACKAGES/atc/hardy/nvt.data diff --git a/examples/USER/atc/hardy/nvt.init b/examples/PACKAGES/atc/hardy/nvt.init similarity index 100% rename from examples/USER/atc/hardy/nvt.init rename to examples/PACKAGES/atc/hardy/nvt.init diff --git a/examples/USER/atc/hardy/nvt.screen b/examples/PACKAGES/atc/hardy/nvt.screen similarity index 100% rename from examples/USER/atc/hardy/nvt.screen rename to examples/PACKAGES/atc/hardy/nvt.screen diff --git a/examples/USER/atc/mesh/Ar_ttm.mat b/examples/PACKAGES/atc/mesh/Ar_ttm.mat similarity index 100% rename from examples/USER/atc/mesh/Ar_ttm.mat rename to examples/PACKAGES/atc/mesh/Ar_ttm.mat diff --git a/examples/USER/atc/mesh/Si.mat b/examples/PACKAGES/atc/mesh/Si.mat similarity index 100% rename from examples/USER/atc/mesh/Si.mat rename to examples/PACKAGES/atc/mesh/Si.mat diff --git a/examples/USER/atc/mesh/circle_temp.init b/examples/PACKAGES/atc/mesh/circle_temp.init similarity index 100% rename from examples/USER/atc/mesh/circle_temp.init rename to examples/PACKAGES/atc/mesh/circle_temp.init diff --git a/examples/USER/atc/mesh/gaussianIC1d_hex.screen b/examples/PACKAGES/atc/mesh/gaussianIC1d_hex.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC1d_hex.screen rename to examples/PACKAGES/atc/mesh/gaussianIC1d_hex.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex20_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex20_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex27_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex27_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_tet.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_tet.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_tet.screen diff --git a/examples/USER/atc/mesh/in.gaussianIC1d_hex b/examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC1d_hex rename to examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform similarity index 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similarity index 100% rename from examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.1 rename to examples/PACKAGES/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.1 diff --git a/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 b/examples/PACKAGES/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 similarity index 100% rename from examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 rename to examples/PACKAGES/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 diff --git a/examples/USER/brownian/asphere/in2d.ellipsoid b/examples/PACKAGES/brownian/asphere/in2d.ellipsoid similarity index 100% rename from examples/USER/brownian/asphere/in2d.ellipsoid rename to examples/PACKAGES/brownian/asphere/in2d.ellipsoid diff --git a/examples/USER/brownian/asphere/in3d.ellipsoid b/examples/PACKAGES/brownian/asphere/in3d.ellipsoid similarity index 100% rename from examples/USER/brownian/asphere/in3d.ellipsoid rename to examples/PACKAGES/brownian/asphere/in3d.ellipsoid diff --git a/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 b/examples/PACKAGES/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 similarity index 100% rename from examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 rename to examples/PACKAGES/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 diff --git a/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 b/examples/PACKAGES/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 similarity index 100% rename from examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 rename to examples/PACKAGES/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 diff --git a/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 b/examples/PACKAGES/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 similarity index 100% rename from examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 rename to examples/PACKAGES/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 diff --git a/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 b/examples/PACKAGES/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 similarity index 100% rename from examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 rename to examples/PACKAGES/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 diff --git a/examples/USER/brownian/point/in2d.point b/examples/PACKAGES/brownian/point/in2d.point similarity index 100% rename from examples/USER/brownian/point/in2d.point rename to examples/PACKAGES/brownian/point/in2d.point diff --git a/examples/USER/brownian/point/in3d.point b/examples/PACKAGES/brownian/point/in3d.point similarity index 100% rename from examples/USER/brownian/point/in3d.point rename to examples/PACKAGES/brownian/point/in3d.point diff --git a/examples/USER/brownian/point/log.11May2021.in2d.point.g++.1 b/examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.1 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in2d.point.g++.1 rename to examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.1 diff --git a/examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 b/examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.4 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 rename to examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.4 diff --git a/examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 b/examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.1 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 rename to examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.1 diff --git a/examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 b/examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.4 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 rename to examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.4 diff --git a/examples/USER/brownian/sphere/in2d.sphere b/examples/PACKAGES/brownian/sphere/in2d.sphere similarity index 100% rename from examples/USER/brownian/sphere/in2d.sphere rename to examples/PACKAGES/brownian/sphere/in2d.sphere diff --git a/examples/USER/brownian/sphere/in3d.sphere b/examples/PACKAGES/brownian/sphere/in3d.sphere similarity index 100% rename from examples/USER/brownian/sphere/in3d.sphere rename to examples/PACKAGES/brownian/sphere/in3d.sphere diff --git a/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 b/examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.1 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.1 diff --git a/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 b/examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.4 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.4 diff --git a/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 b/examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.1 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.1 diff --git a/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 b/examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.4 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.4 diff --git a/examples/USER/brownian/spherical_ABP/in2d.abp b/examples/PACKAGES/brownian/spherical_ABP/in2d.abp similarity index 100% rename from examples/USER/brownian/spherical_ABP/in2d.abp rename to examples/PACKAGES/brownian/spherical_ABP/in2d.abp diff --git a/examples/USER/brownian/spherical_ABP/in3d.ideal_abp b/examples/PACKAGES/brownian/spherical_ABP/in3d.ideal_abp similarity index 100% rename from examples/USER/brownian/spherical_ABP/in3d.ideal_abp rename to examples/PACKAGES/brownian/spherical_ABP/in3d.ideal_abp diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 diff --git a/examples/PACKAGES/cauchy/NiAlH_jea.eam.alloy b/examples/PACKAGES/cauchy/NiAlH_jea.eam.alloy new file mode 120000 index 0000000000..da57022dd3 --- /dev/null +++ b/examples/PACKAGES/cauchy/NiAlH_jea.eam.alloy @@ -0,0 +1 @@ +../../../potentials/NiAlH_jea.eam.alloy \ No newline at end of file diff --git a/examples/USER/misc/cauchy/README b/examples/PACKAGES/cauchy/README similarity index 100% rename from examples/USER/misc/cauchy/README rename to examples/PACKAGES/cauchy/README diff --git a/examples/USER/misc/cauchy/in.cauchystat b/examples/PACKAGES/cauchy/in.cauchystat similarity index 100% rename from examples/USER/misc/cauchy/in.cauchystat rename to examples/PACKAGES/cauchy/in.cauchystat diff --git a/examples/USER/misc/cauchy/log.2Jun2020.cauchystat.g++.1 b/examples/PACKAGES/cauchy/log.2Jun2020.cauchystat.g++.1 similarity index 100% rename from examples/USER/misc/cauchy/log.2Jun2020.cauchystat.g++.1 rename to examples/PACKAGES/cauchy/log.2Jun2020.cauchystat.g++.1 diff --git a/examples/USER/cgdna/README b/examples/PACKAGES/cgdna/README similarity index 91% rename from examples/USER/cgdna/README rename to examples/PACKAGES/cgdna/README index a403ce0321..949dda91af 100644 --- a/examples/USER/cgdna/README +++ b/examples/PACKAGES/cgdna/README @@ -72,7 +72,15 @@ between two individual nucleotides can be established. /******************************************************************************/ -/examples/oxRNA2/duplex4 +/examples/oxDNA2/dsring: + +This example uses a dsDNA ring of 74 base pairs. The bonds which close the ring +are (in 3' to 5' direction) between nucleotide 74 and 1 and between nucleotide +148 and 75, respectively. + +/******************************************************************************/ + +/examples/oxRNA2/duplex2 This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/data.duplex1 new file mode 100644 index 0000000000..54eb2beaf5 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file via write_data, version 27 May 2021 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0 +2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0 +3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0 +4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0 +5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0 +6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0 +7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0 +8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0 +9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0 +10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397 +2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385 +3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783 +4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775 +5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883 +6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354 +7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567 +8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627 +9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048 +10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1 similarity index 65% rename from examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 rename to examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1 index 04ff545704..f0ca98c59f 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1 @@ -7,15 +7,15 @@ units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 1 delay 0 check yes read_data data.duplex1 @@ -40,27 +40,16 @@ pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 # NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" +compute quat all property/atom quatw quati quatj quatk compute erot all erotate/asphere compute ekin all ke @@ -71,10 +60,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" run 1000000 -#write_restart config.${number}.* +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 new file mode 100644 index 0000000000..f1b7eb56eb --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 @@ -0,0 +1,1171 @@ +LAMMPS (2 Jul 2021) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +set atom * mass 3.1575 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.9560004 + ghost atom cutoff = 3.8 + binsize = 1.4780002, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -13.0576219534369 | etot = -9.13334913094246 +Per MPI rank memory allocation (min/avg/max) = 8.949 | 8.949 | 8.949 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3488546 0.043092397 -1.1949086 -4.6816211e-05 64000 +1000 ekin = 1.08024346604046 | erot = 2.90873406534668 | epot = -13.1223266626202 | etot = -9.13334913123308 +2000 ekin = 1.05028450914437 | erot = 2.98006324808558 | epot = -13.1636968886591 | etot = -9.13334913142915 +3000 ekin = 1.01964458529397 | erot = 3.02592193798632 | epot = -13.1789156547658 | etot = -9.13334913148547 +4000 ekin = 0.989515033089539 | erot = 3.04428486059471 | epot = -13.1671490250724 | etot = -9.13334913138813 +5000 ekin = 0.961283929687833 | erot = 3.03510855539557 | epot = -13.1297416162282 | etot = -9.13334913114481 +6000 ekin = 0.936412193404256 | erot = 3.00022299571975 | epot = -13.0699843199583 | etot = -9.13334913083425 +7000 ekin = 0.916233699107968 | erot = 2.9427713444016 | epot = -12.9923541739966 | etot = -9.13334913048708 +8000 ekin = 0.901760662506268 | erot = 2.86671228744165 | epot = -12.9018220800865 | etot = -9.13334913013859 +9000 ekin = 0.893571390067879 | erot = 2.77649686780605 | epot = -12.8034173876806 | etot = -9.13334912980667 +10000 ekin = 0.891805685056847 | erot = 2.67686855006734 | epot = -12.7020233645916 | etot = -9.13334912946739 +11000 ekin = 0.896243557993589 | erot = 2.57266042063119 | epot = -12.6022531078194 | etot = -9.13334912919467 +12000 ekin = 0.906416039154817 | erot = 2.46827537271556 | epot = -12.5080405408347 | etot = -9.13334912896436 +13000 ekin = 0.921704091778492 | erot = 2.36760645470833 | epot = -12.4226596752787 | etot = -9.1333491287919 +14000 ekin = 0.941405275130078 | erot = 2.27374941641176 | epot = -12.3485038202328 | etot = -9.13334912869101 +15000 ekin = 0.964770892951776 | erot = 2.18876720165113 | epot = -12.2868872232635 | etot = -9.13334912866063 +16000 ekin = 0.991029016801088 | erot = 2.11380018376645 | epot = -12.2381783292305 | etot = -9.13334912866292 +17000 ekin = 1.01940907375712 | erot = 2.04893605182118 | epot = -12.2016942543555 | etot = -9.13334912877719 +18000 ekin = 1.04917923728265 | erot = 1.993350175781 | epot = -12.1758785419805 | etot = -9.13334912891683 +19000 ekin = 1.07969247848165 | erot = 1.94569933362969 | epot = -12.1587409411761 | etot = -9.13334912906478 +20000 ekin = 1.11043268152286 | erot = 1.90411175657082 | epot = -12.1478935672813 | etot = -9.13334912918758 +21000 ekin = 1.14104909735583 | erot = 1.86695882979249 | epot = -12.1413570564147 | etot = -9.13334912926637 +22000 ekin = 1.17136821848099 | erot = 1.83313674901903 | epot = -12.1378540967921 | etot = -9.13334912929204 +23000 ekin = 1.20137634097693 | erot = 1.80222523558983 | epot = -12.1369507058332 | etot = -9.13334912926643 +24000 ekin = 1.231172496229 | erot = 1.77451266102193 | epot = -12.1390342864516 | etot = -9.13334912920062 +25000 ekin = 1.26089526640645 | erot = 1.75088411697597 | epot = -12.1451285124969 | etot = -9.13334912911452 +26000 ekin = 1.29063712254632 | erot = 1.73259428379508 | epot = -12.1565805353676 | etot = -9.1333491290262 +27000 ekin = 1.32035987087029 | erot = 1.72114061671176 | epot = -12.1748496165411 | etot = -9.133349128959 +28000 ekin = 1.34980460658797 | erot = 1.71795709927856 | epot = -12.2011108348018 | etot = -9.1333491289353 +29000 ekin = 1.37841624051162 | erot = 1.7241401378574 | epot = -12.2359055073442 | etot = -9.13334912897517 +30000 ekin = 1.40529015727354 | erot = 1.74019656639668 | epot = -12.2788358527639 | etot = -9.13334912909368 +31000 ekin = 1.42915801743398 | erot = 1.76583252336949 | epot = -12.3283396701001 | etot = -9.13334912929662 +32000 ekin = 1.44843712560543 | erot = 1.7998218174534 | epot = -12.381608072634 | etot = -9.13334912957516 +33000 ekin = 1.46136904668682 | erot = 1.84000474140072 | epot = -12.4347229179884 | etot = -9.13334912990089 +34000 ekin = 1.46625940785516 | erot = 1.88346459856615 | epot = -12.4830731366474 | etot = -9.13334913022613 +35000 ekin = 1.46179739484308 | erot = 1.92688889524936 | epot = -12.5220354205852 | etot = -9.13334913049271 +36000 ekin = 1.44738855724077 | erot = 1.96705754746493 | epot = -12.5477952353503 | etot = -9.13334913064463 +37000 ekin = 1.4234005446855 | erot = 2.00129614949924 | epot = -12.5580458249024 | etot = -9.13334913071767 +38000 ekin = 1.39122781542981 | erot = 2.02761655303763 | epot = -12.5521934990546 | etot = -9.13334913058721 +39000 ekin = 1.35313842096817 | erot = 2.04547852103601 | epot = -12.5319660723436 | etot = -9.13334913033938 +40000 ekin = 1.31193587699363 | erot = 2.05554364627558 | epot = -12.5008286533155 | etot = -9.13334913004627 +41000 ekin = 1.27054093924544 | erot = 2.05894429581371 | epot = -12.4628343648332 | etot = -9.13334912977403 +42000 ekin = 1.23161000992328 | erot = 2.05694893255707 | epot = -12.4219080720069 | etot = -9.1333491295265 +43000 ekin = 1.19723969759494 | erot = 2.05085758075658 | epot = -12.3814464076995 | etot = -9.13334912934802 +44000 ekin = 1.16880185863999 | erot = 2.04172238360627 | epot = -12.3438733714904 | etot = -9.13334912924412 +45000 ekin = 1.1469078717572 | erot = 2.03029950061773 | epot = -12.3105565015799 | etot = -9.13334912920493 +46000 ekin = 1.13147919636052 | erot = 2.01712256175374 | epot = -12.2819508873243 | etot = -9.13334912921 +47000 ekin = 1.12189300492722 | erot = 2.00264798837256 | epot = -12.2578901225351 | etot = -9.13334912923528 +48000 ekin = 1.11716788112728 | erot = 1.98739120721192 | epot = -12.2379082176346 | etot = -9.13334912929539 +49000 ekin = 1.1161579479525 | erot = 1.97187368108372 | epot = -12.2213807583349 | etot = -9.13334912929866 +50000 ekin = 1.11772326336401 | erot = 1.95708534394624 | epot = -12.2081577365825 | etot = -9.13334912927229 +51000 ekin = 1.12084924497878 | erot = 1.94437394210215 | epot = -12.1985723162997 | etot = -9.13334912921873 +52000 ekin = 1.12470549785255 | erot = 1.93529800314867 | epot = -12.1933526301509 | etot = -9.13334912914966 +53000 ekin = 1.12864556674979 | erot = 1.93145365271657 | epot = -12.1934483485496 | etot = -9.13334912908328 +54000 ekin = 1.1321611352309 | erot = 1.93430274875498 | epot = -12.199813013012 | etot = -9.13334912902616 +55000 ekin = 1.13481106600236 | erot = 1.94490436967234 | epot = -12.2130645647021 | etot = -9.13334912902736 +56000 ekin = 1.13614343535817 | erot = 1.96361884590778 | epot = -12.233111410353 | etot = -9.13334912908703 +57000 ekin = 1.13563178311283 | erot = 1.99002978527236 | epot = -12.2590106975984 | etot = -9.13334912921322 +58000 ekin = 1.13263976908247 | erot = 2.02286978616487 | epot = -12.2888586846524 | etot = -9.1333491294051 +59000 ekin = 1.12642426113435 | erot = 2.06004413441698 | epot = -12.3198175252027 | etot = -9.13334912965138 +60000 ekin = 1.11618536041537 | erot = 2.09876774945535 | epot = -12.3483022398003 | etot = -9.13334912992962 +61000 ekin = 1.10116810417871 | erot = 2.13581434618259 | epot = -12.3703315805682 | etot = -9.1333491302069 +62000 ekin = 1.08081637521808 | erot = 2.16786879318293 | epot = -12.3820342988431 | etot = -9.13334913044213 +63000 ekin = 1.05497014428156 | erot = 2.19194503254429 | epot = -12.3802643074575 | etot = -9.13334913063163 +64000 ekin = 1.02408601603164 | erot = 2.20562384873125 | epot = -12.3630589954179 | etot = -9.13334913065498 +65000 ekin = 0.98943441580777 | erot = 2.20769180278656 | epot = -12.330475349125 | etot = -9.13334913053072 +66000 ekin = 0.953195593563924 | erot = 2.19842250482629 | epot = -12.2849672286538 | etot = -9.13334913026361 +67000 ekin = 0.918366365968288 | erot = 2.17942400884185 | epot = -12.2311395047048 | etot = -9.13334912989465 +68000 ekin = 0.888467814666294 | erot = 2.15321364358206 | epot = -12.1750305877201 | etot = -9.13334912947173 +69000 ekin = 0.867150037001647 | erot = 2.1228863370438 | epot = -12.1233855031208 | etot = -9.13334912907536 +70000 ekin = 0.857579951604761 | erot = 2.09151913845159 | epot = -12.0824482188431 | etot = -9.13334912878671 +71000 ekin = 0.861815425267466 | erot = 2.06157004239568 | epot = -12.0567345963619 | etot = -9.13334912869875 +72000 ekin = 0.88019181568545 | erot = 2.03435275439371 | epot = -12.0478936988732 | etot = -9.13334912879399 +73000 ekin = 0.911201453876652 | erot = 2.00982694750408 | epot = -12.0543775304379 | etot = -9.13334912905718 +74000 ekin = 0.951849895585105 | erot = 1.98685418272633 | epot = -12.0720532077345 | etot = -9.1333491294231 +75000 ekin = 0.998151008641228 | erot = 1.96362530027612 | epot = -12.0951254387264 | etot = -9.13334912980904 +76000 ekin = 1.04581734271593 | erot = 1.93821700241365 | epot = -12.117383475267 | etot = -9.13334913013739 +77000 ekin = 1.09091996835707 | erot = 1.90910715282296 | epot = -12.1333762515352 | etot = -9.13334913035515 +78000 ekin = 1.13037631927924 | erot = 1.87551578135396 | epot = -12.139241231075 | etot = -9.13334913044181 +79000 ekin = 1.16219588597792 | erot = 1.83750580183272 | epot = -12.1330508182183 | etot = -9.13334913040767 +80000 ekin = 1.1854897263224 | erot = 1.79585942670001 | epot = -12.1146982833062 | etot = -9.13334913028383 +81000 ekin = 1.20030605718963 | erot = 1.75181365939761 | epot = -12.0854688466956 | etot = -9.13334913010839 +82000 ekin = 1.20737786492204 | erot = 1.70676694760234 | epot = -12.047493942439 | etot = -9.13334912991461 +83000 ekin = 1.2078605140208 | erot = 1.66205278152646 | epot = -12.0032624252717 | etot = -9.13334912972448 +84000 ekin = 1.20310991572484 | erot = 1.61882913247335 | epot = -11.9552881777461 | etot = -9.13334912954791 +85000 ekin = 1.19452073297172 | erot = 1.57808043002433 | epot = -11.9059502923819 | etot = -9.13334912938589 +86000 ekin = 1.18342100682564 | erot = 1.5406926889625 | epot = -11.8574628250235 | etot = -9.13334912923537 +87000 ekin = 1.1710085895735 | erot = 1.50755090689531 | epot = -11.8119086255617 | etot = -9.13334912909291 +88000 ekin = 1.15831377551687 | erot = 1.47961680456731 | epot = -11.7712797090417 | etot = -9.13334912895749 +89000 ekin = 1.14617682817404 | erot = 1.45796378128901 | epot = -11.7374897382937 | etot = -9.13334912883065 +90000 ekin = 1.13523447969425 | erot = 1.44376438030032 | epot = -11.7123479887108 | etot = -9.13334912871622 +91000 ekin = 1.12591345720554 | erot = 1.43823772500951 | epot = -11.6975003108346 | etot = -9.13334912861951 +92000 ekin = 1.1184309948929 | erot = 1.44256930748519 | epot = -11.6943494309244 | etot = -9.13334912854634 +93000 ekin = 1.1128032963482 | erot = 1.45781524814484 | epot = -11.7039676729951 | etot = -9.13334912850205 +94000 ekin = 1.10886209127345 | erot = 1.48480045701872 | epot = -11.7270116767841 | etot = -9.13334912849191 +95000 ekin = 1.10627886010346 | erot = 1.52396220647538 | epot = -11.7635901951104 | etot = -9.13334912853156 +96000 ekin = 1.10459509814429 | erot = 1.57519859223418 | epot = -11.8131428189842 | etot = -9.13334912860576 +97000 ekin = 1.10325943769911 | erot = 1.63800664193794 | epot = -11.8746152083615 | etot = -9.13334912872444 +98000 ekin = 1.10166959581651 | erot = 1.71130689804963 | epot = -11.9463256227536 | etot = -9.13334912888747 +99000 ekin = 1.09921849385167 | erot = 1.79339905630353 | epot = -12.0259666792468 | etot = -9.13334912909161 +100000 ekin = 1.0953459688011 | erot = 1.88196872528563 | epot = -12.1106638234158 | etot = -9.1333491293291 +101000 ekin = 1.08959720755121 | erot = 1.97415616931445 | epot = -12.1971025064517 | etot = -9.13334912958605 +102000 ekin = 1.08168751154818 | erot = 2.0667028218517 | epot = -12.2817394632422 | etot = -9.13334912984234 +103000 ekin = 1.07156932342316 | erot = 2.15618192508056 | epot = -12.3611003785769 | etot = -9.13334913007318 +104000 ekin = 1.05949237996073 | erot = 2.23930158373562 | epot = -12.4321430939482 | etot = -9.13334913025183 +105000 ekin = 1.04604342224878 | erot = 2.31323902285843 | epot = -12.4926315754928 | etot = -9.13334913038555 +106000 ekin = 1.0322431631856 | erot = 2.37579242095981 | epot = -12.541384714564 | etot = -9.13334913041858 +107000 ekin = 1.01951120148932 | erot = 2.42585603740565 | epot = -12.57871636928 | etot = -9.133349130385 +108000 ekin = 1.00875017477207 | erot = 2.46348952984492 | epot = -12.6055888348732 | etot = -9.13334913025623 +109000 ekin = 1.00109573552394 | erot = 2.48980806114969 | epot = -12.6242529267276 | etot = -9.13334913005395 +110000 ekin = 0.997931591358091 | erot = 2.50673918610801 | epot = -12.6380199072772 | etot = -9.13334912981112 +111000 ekin = 1.00076792351317 | erot = 2.51665915373046 | epot = -12.6507762068073 | etot = -9.13334912956366 +112000 ekin = 1.01109610479922 | erot = 2.5220070159966 | epot = -12.6664522501388 | etot = -9.13334912934299 +113000 ekin = 1.03019016817879 | erot = 2.52496101252896 | epot = -12.688500309986 | etot = -9.13334912927824 +114000 ekin = 1.05821017520623 | erot = 2.52722573627529 | epot = -12.7187850407015 | etot = -9.13334912921997 +115000 ekin = 1.0947253040014 | erot = 2.53003930448843 | epot = -12.7581137377192 | etot = -9.13334912922939 +116000 ekin = 1.13884650903332 | erot = 2.53414832430464 | epot = -12.8063439626439 | etot = -9.1333491293059 +117000 ekin = 1.18909444999485 | erot = 2.5398083927715 | epot = -12.862251972215 | etot = -9.13334912944861 +118000 ekin = 1.24341490970477 | erot = 2.54678348242654 | epot = -12.9235475217869 | etot = -9.13334912965561 +119000 ekin = 1.29923662064195 | erot = 2.55432909401028 | epot = -12.9869148445731 | etot = -9.13334912992089 +120000 ekin = 1.35358959215651 | erot = 2.56118615921813 | epot = -13.0481248816038 | etot = -9.13334913022921 +121000 ekin = 1.40329803815456 | erot = 2.56563135861672 | epot = -13.1022785273256 | etot = -9.13334913055428 +122000 ekin = 1.44524692196618 | erot = 2.56562448409235 | epot = -13.1442205369174 | etot = -9.13334913085884 +123000 ekin = 1.47669540804833 | erot = 2.55906317998209 | epot = -13.169107719131 | etot = -9.1333491311006 +124000 ekin = 1.49558302658162 | erot = 2.54411105943722 | epot = -13.1730432172611 | etot = -9.13334913124229 +125000 ekin = 1.50076122489739 | erot = 2.51952798471306 | epot = -13.1536383408712 | etot = -9.13334913126069 +126000 ekin = 1.49214728684713 | erot = 2.48515933103515 | epot = -13.1106557490372 | etot = -9.13334913115489 +127000 ekin = 1.47053410713955 | erot = 2.44174480075122 | epot = -13.0456280388473 | etot = -9.13334913095656 +128000 ekin = 1.43743445323503 | erot = 2.39059049317544 | epot = -12.9613740770757 | etot = -9.1333491306652 +129000 ekin = 1.39501109707052 | erot = 2.33380120125816 | epot = -12.8621614286433 | etot = -9.13334913031463 +130000 ekin = 1.34584042016751 | erot = 2.27401545397174 | epot = -12.7532050040791 | etot = -9.13334912993981 +131000 ekin = 1.2926893078659 | erot = 2.21410134111222 | epot = -12.6401397785506 | etot = -9.13334912957246 +132000 ekin = 1.23832315616825 | erot = 2.15686384200884 | epot = -12.5285361274152 | etot = -9.13334912923814 +133000 ekin = 1.18535267681203 | erot = 2.10479906741759 | epot = -12.4235008731851 | etot = -9.13334912895549 +134000 ekin = 1.13612155562822 | erot = 2.05991346428629 | epot = -12.3293841486504 | etot = -9.13334912873585 +135000 ekin = 1.09263262326065 | erot = 2.02360952444368 | epot = -12.2495912762904 | etot = -9.13334912858607 +136000 ekin = 1.05650575788363 | erot = 1.99662030668686 | epot = -12.186475193078 | etot = -9.13334912850755 +137000 ekin = 1.02895878679475 | erot = 1.9789921283489 | epot = -12.1413000436433 | etot = -9.13334912849969 +138000 ekin = 1.01080388995867 | erot = 1.97013512172238 | epot = -12.1142881402333 | etot = -9.13334912855223 +139000 ekin = 1.00245459395367 | erot = 1.96888144460881 | epot = -12.1046851672403 | etot = -9.13334912867788 +140000 ekin = 1.0039378074064 | erot = 1.97333010973459 | epot = -12.1106170460028 | etot = -9.13334912886182 +141000 ekin = 1.01490973367055 | erot = 1.98104530944802 | epot = -12.1293041722137 | etot = -9.13334912909515 +142000 ekin = 1.03468044934439 | erot = 1.98917872502442 | epot = -12.1572083037337 | etot = -9.13334912936491 +143000 ekin = 1.06225104646196 | erot = 1.99463134790795 | epot = -12.1902315240232 | etot = -9.13334912965333 +144000 ekin = 1.09636709127271 | erot = 1.99441220318412 | epot = -12.2241284243805 | etot = -9.13334912992366 +145000 ekin = 1.13559045362142 | erot = 1.98572590466024 | epot = -12.2546654884644 | etot = -9.13334913018269 +146000 ekin = 1.17838854122111 | erot = 1.96612892354277 | epot = -12.2778665951536 | etot = -9.13334913038972 +147000 ekin = 1.22300699749199 | erot = 1.93405129395 | epot = -12.290407421963 | etot = -9.13334913052099 +148000 ekin = 1.26785677863037 | erot = 1.88891621350868 | epot = -12.2901221226998 | etot = -9.13334913056074 +149000 ekin = 1.31170551487317 | erot = 1.83123494690896 | epot = -12.2762895922885 | etot = -9.13334913050637 +150000 ekin = 1.35361858091215 | erot = 1.76263607509638 | epot = -12.2496037863728 | etot = -9.13334913036431 +151000 ekin = 1.39299848911443 | erot = 1.68572491420634 | epot = -12.2120725334744 | etot = -9.13334913015361 +152000 ekin = 1.42958376961924 | erot = 1.6038154911236 | epot = -12.1667483906421 | etot = -9.13334912989928 +153000 ekin = 1.46340801747604 | erot = 1.52060159601932 | epot = -12.1173587431247 | etot = -9.1333491296293 +154000 ekin = 1.4947265022457 | erot = 1.43981503875287 | epot = -12.0678906703689 | etot = -9.13334912937036 +155000 ekin = 1.52392161825086 | erot = 1.36491657683224 | epot = -12.0221873242285 | etot = -9.13334912914535 +156000 ekin = 1.55140022159559 | erot = 1.29884972381829 | epot = -11.9835990743856 | etot = -9.13334912897169 +157000 ekin = 1.57749707056588 | erot = 1.24387068637228 | epot = -11.9547168857973 | etot = -9.13334912885916 +158000 ekin = 1.60239506185781 | erot = 1.20145363967816 | epot = -11.9371978303524 | etot = -9.13334912881648 +159000 ekin = 1.62604462003781 | erot = 1.17226436760497 | epot = -11.9316581164848 | etot = -9.13334912884202 +160000 ekin = 1.64813303486538 | erot = 1.15619534708312 | epot = -11.9376775108798 | etot = -9.13334912893126 +161000 ekin = 1.66807327612968 | erot = 1.15245312716186 | epot = -11.9538755323659 | etot = -9.13334912907436 +162000 ekin = 1.68501875283042 | erot = 1.15969471512798 | epot = -11.9780625972157 | etot = -9.13334912925727 +163000 ekin = 1.69790620824657 | erot = 1.17620989126095 | epot = -12.0074652289689 | etot = -9.13334912946134 +164000 ekin = 1.70552711798374 | erot = 1.20014309389817 | epot = -12.0390193415462 | etot = -9.13334912966433 +165000 ekin = 1.70662691809323 | erot = 1.22974121417707 | epot = -12.0697172621122 | etot = -9.13334912984189 +166000 ekin = 1.7000290802682 | erot = 1.26360423252395 | epot = -12.0969824427627 | etot = -9.13334912997052 +167000 ekin = 1.68477683955852 | erot = 1.30090518403747 | epot = -12.1190311536261 | etot = -9.13334913003012 +168000 ekin = 1.66027923283154 | erot = 1.34154370359055 | epot = -12.1351720664303 | etot = -9.1333491300082 +169000 ekin = 1.62644124957696 | erot = 1.38619810991375 | epot = -12.1459884893935 | etot = -9.13334912990279 +170000 ekin = 1.58375251890744 | erot = 1.43625221626168 | epot = -12.1533538648942 | etot = -9.1333491297251 +171000 ekin = 1.53331003043897 | erot = 1.49359459893384 | epot = -12.1602537588716 | etot = -9.13334912949884 +172000 ekin = 1.47676106161375 | erot = 1.56031583407018 | epot = -12.1704260249395 | etot = -9.13334912925553 +173000 ekin = 1.41695754705502 | erot = 1.63848249765388 | epot = -12.188789173044 | etot = -9.13334912833507 +174000 ekin = 1.3593768430446 | erot = 1.72968793645215 | epot = -12.2224139078247 | etot = -9.13334912832798 +175000 ekin = 1.30537540818791 | erot = 1.83369980102237 | epot = -12.2724243375748 | etot = -9.13334912836452 +176000 ekin = 1.25571357800286 | erot = 1.94952726339924 | epot = -12.3385899698484 | etot = -9.1333491284463 +177000 ekin = 1.21104692225297 | erot = 2.07558802224364 | epot = -12.4199840730635 | etot = -9.13334912856687 +178000 ekin = 1.17189512057024 | erot = 2.20976079574621 | epot = -12.5150050450635 | etot = -9.13334912874708 +179000 ekin = 1.13864315857362 | erot = 2.34949890132868 | epot = -12.621491188811 | etot = -9.13334912890871 +180000 ekin = 1.11156621835588 | erot = 2.49234008539985 | epot = -12.7372554328242 | etot = -9.13334912906844 +181000 ekin = 1.09087167613582 | erot = 2.6356735753612 | epot = -12.8598943807494 | etot = -9.13334912925239 +182000 ekin = 1.07675226579839 | erot = 2.77693577183312 | epot = -12.9870371670189 | etot = -9.13334912938736 +183000 ekin = 1.06942294234152 | erot = 2.91405263083421 | epot = -13.1168247026758 | etot = -9.13334912950012 +184000 ekin = 1.0691348870584 | erot = 3.04520163111638 | epot = -13.2476856477697 | etot = -9.13334912959496 +185000 ekin = 1.07614345922793 | erot = 3.16875772929902 | epot = -13.3782503182121 | etot = -9.13334912968517 +186000 ekin = 1.09060563376754 | erot = 3.28317984154833 | epot = -13.5071346051098 | etot = -9.13334912979394 +187000 ekin = 1.11239929858154 | erot = 3.38683780589066 | epot = -13.632586234424 | etot = -9.13334912995184 +188000 ekin = 1.14088837562648 | erot = 3.47780595660491 | epot = -13.7520434624193 | etot = -9.1333491301879 +189000 ekin = 1.17469755695855 | erot = 3.55369218298227 | epot = -13.8617388704565 | etot = -9.13334913051572 +190000 ekin = 1.21158961983346 | erot = 3.61161008256054 | epot = -13.9565488333127 | etot = -9.13334913091872 +191000 ekin = 1.24837558083735 | erot = 3.6478034512754 | epot = -14.0295281634881 | etot = -9.13334913137538 +192000 ekin = 1.2810231168297 | erot = 3.65810395428983 | epot = -14.0724762027871 | etot = -9.13334913166757 +193000 ekin = 1.30598320816993 | erot = 3.64139295006491 | epot = -14.0807252900249 | etot = -9.13334913179008 +194000 ekin = 1.32049648836639 | erot = 3.59844552363037 | epot = -14.0522911436922 | etot = -9.13334913169541 +195000 ekin = 1.32298604774295 | erot = 3.53212928134953 | epot = -13.9884644604292 | etot = -9.13334913133677 +196000 ekin = 1.31323645162593 | erot = 3.44751612705315 | epot = -13.8941017095234 | etot = -9.13334913084434 +197000 ekin = 1.2922893469817 | erot = 3.35072340322508 | epot = -13.776361880499 | etot = -9.13334913029222 +198000 ekin = 1.26212633786657 | erot = 3.24789114382005 | epot = -13.6433666114232 | etot = -9.13334912973654 +199000 ekin = 1.22527047461741 | erot = 3.14483705467218 | epot = -13.5034566585632 | etot = -9.13334912927362 +200000 ekin = 1.1844179920726 | erot = 3.04594245963003 | epot = -13.3637095806218 | etot = -9.13334912891917 +201000 ekin = 1.14216630511967 | erot = 2.95390025492359 | epot = -13.2294156887272 | etot = -9.13334912868389 +202000 ekin = 1.10084220211764 | erot = 2.86987712396347 | epot = -13.1040684546434 | etot = -9.13334912856225 +203000 ekin = 1.06240856569029 | erot = 2.7936606722683 | epot = -12.9894183664997 | etot = -9.13334912854108 +204000 ekin = 1.02841768821234 | erot = 2.72389144275509 | epot = -12.8856582595718 | etot = -9.13334912860439 +205000 ekin = 0.999988405220884 | erot = 2.65832732458315 | epot = -12.7916648585388 | etot = -9.13334912873479 +206000 ekin = 0.977799621225236 | erot = 2.59412391514193 | epot = -12.7052726652797 | etot = -9.13334912891252 +207000 ekin = 0.962105653965488 | erot = 2.52813792126126 | epot = -12.6235927043397 | etot = -9.13334912911293 +208000 ekin = 0.952783648018927 | erot = 2.45726642892325 | epot = -12.5433992062486 | etot = -9.13334912930642 +209000 ekin = 0.949416945748607 | erot = 2.37882137049742 | epot = -12.4615874457066 | etot = -9.1333491294606 +210000 ekin = 0.95140226321529 | erot = 2.29090939419253 | epot = -12.3756607869544 | etot = -9.13334912954655 +211000 ekin = 0.958051952077684 | erot = 2.19275562021927 | epot = -12.2841567018439 | etot = -9.13334912954696 +212000 ekin = 0.968659667700569 | erot = 2.08489619855882 | epot = -12.18690499572 | etot = -9.1333491294606 +213000 ekin = 0.982515908120069 | erot = 1.96918422281071 | epot = -12.0850492602328 | etot = -9.133349129302 +214000 ekin = 0.998888701919883 | erot = 1.84860041862004 | epot = -11.9808382496359 | etot = -9.13334912909602 +215000 ekin = 1.01700134912583 | erot = 1.72690897492257 | epot = -11.8772594529197 | etot = -9.13334912887129 +216000 ekin = 1.03603050122469 | erot = 1.60822693577908 | epot = -11.777606565659 | etot = -9.13334912865519 +217000 ekin = 1.05512477228488 | erot = 1.49657917533874 | epot = -11.6850530760954 | etot = -9.1333491284718 +218000 ekin = 1.07342860744204 | erot = 1.3955009267025 | epot = -11.602278662484 | etot = -9.13334912833946 +219000 ekin = 1.09009860355596 | erot = 1.30773521951615 | epot = -11.5311829513412 | etot = -9.1333491282691 +220000 ekin = 1.10431207607371 | erot = 1.23505496062935 | epot = -11.472716164966 | etot = -9.13334912826293 +221000 ekin = 1.11527717993067 | erot = 1.17821867809287 | epot = -11.426844986338 | etot = -9.13334912831448 +222000 ekin = 1.12225437592992 | erot = 1.1370482394417 | epot = -11.3926517437816 | etot = -9.13334912841001 +223000 ekin = 1.12459297621428 | erot = 1.11060060825122 | epot = -11.3685427129972 | etot = -9.13334912853172 +224000 ekin = 1.12177911879631 | erot = 1.09739625543932 | epot = -11.3525245028961 | etot = -9.13334912866044 +225000 ekin = 1.11348637905767 | erot = 1.09566402531935 | epot = -11.3424995331558 | etot = -9.13334912877875 +226000 ekin = 1.09961800000716 | erot = 1.10360909760944 | epot = -11.336576226485 | etot = -9.13334912886841 +227000 ekin = 1.08033165066228 | erot = 1.11952730043406 | epot = -11.3332080800317 | etot = -9.13334912893538 +228000 ekin = 1.0560460287279 | erot = 1.1418786542186 | epot = -11.3312738119169 | etot = -9.13334912897037 +229000 ekin = 1.02742418663516 | erot = 1.16938489301675 | epot = -11.3301582086283 | etot = -9.1333491289764 +230000 ekin = 0.995339184991672 | erot = 1.20102048198615 | epot = -11.3297087959367 | etot = -9.13334912895884 +231000 ekin = 0.960829492708774 | erot = 1.23597735762306 | epot = -11.3301559792542 | etot = -9.13334912892236 +232000 ekin = 0.925050432735309 | erot = 1.27360958612391 | epot = -11.3320091477352 | etot = -9.133349128876 +233000 ekin = 0.889225435959791 | erot = 1.3133791021064 | epot = -11.3359536668891 | etot = -9.13334912882295 +234000 ekin = 0.854600006628736 | erot = 1.35483402381932 | epot = -11.3427831592147 | etot = -9.1333491287666 +235000 ekin = 0.822390924845177 | erot = 1.3975743001585 | epot = -11.3533143537192 | etot = -9.13334912871557 +236000 ekin = 0.79373284871178 | erot = 1.44121433399083 | epot = -11.3682963113762 | etot = -9.13334912867361 +237000 ekin = 0.769632191219341 | erot = 1.48535644446082 | epot = -11.3883377643263 | etot = -9.13334912864614 +238000 ekin = 0.750918993365902 | erot = 1.52956143549227 | epot = -11.4138295574956 | etot = -9.1333491286374 +239000 ekin = 0.738206267497023 | erot = 1.57333361162164 | epot = -11.4448890077676 | etot = -9.13334912864891 +240000 ekin = 0.731862193743802 | erot = 1.61613149974237 | epot = -11.4813428221653 | etot = -9.13334912867911 +241000 ekin = 0.731999328001815 | erot = 1.65741090456868 | epot = -11.5227593612932 | etot = -9.1333491287227 +242000 ekin = 0.738482620157072 | erot = 1.69669130986314 | epot = -11.5685230587939 | etot = -9.13334912877369 +243000 ekin = 0.75095504232512 | erot = 1.73364929482327 | epot = -11.617953465968 | etot = -9.1333491288196 +244000 ekin = 0.768877080466331 | erot = 1.76822360275621 | epot = -11.6704498120767 | etot = -9.13334912885412 +245000 ekin = 0.791573929294351 | erot = 1.80068045121317 | epot = -11.7256035093789 | etot = -9.13334912887142 +246000 ekin = 0.818282914271264 | erot = 1.83164107445174 | epot = -11.7832731175936 | etot = -9.13334912887061 +247000 ekin = 0.848193621601397 | erot = 1.86205096555236 | epot = -11.8435937160096 | etot = -9.13334912885583 +248000 ekin = 0.880474358635198 | erot = 1.89308546777783 | epot = -11.9069089552495 | etot = -9.13334912883646 +249000 ekin = 0.914280881218976 | erot = 1.92599713223874 | epot = -11.9736271422836 | etot = -9.13334912882589 +250000 ekin = 0.948746730716201 | erot = 1.96192054843714 | epot = -12.0440164079935 | etot = -9.13334912884016 +251000 ekin = 0.982959063854084 | erot = 2.00165977259887 | epot = -12.1179679653479 | etot = -9.13334912889495 +252000 ekin = 1.01592948249831 | erot = 2.0454925239635 | epot = -12.1947711354629 | etot = -9.13334912900106 +253000 ekin = 1.04657777483961 | erot = 2.09303441305945 | epot = -12.2729613170589 | etot = -9.13334912915988 +254000 ekin = 1.07373541755056 | erot = 2.14319803018433 | epot = -12.350282577098 | etot = -9.13334912936307 +255000 ekin = 1.0962016316301 | erot = 2.19430966720531 | epot = -12.4238604284171 | etot = -9.13334912958168 +256000 ekin = 1.11287206428135 | erot = 2.24438579427423 | epot = -12.4906069883384 | etot = -9.13334912978286 +257000 ekin = 1.12287782510614 | erot = 2.29146665865398 | epot = -12.5476936136917 | etot = -9.13334912993153 +258000 ekin = 1.12572293500256 | erot = 2.33396623628263 | epot = -12.5930383012893 | etot = -9.13334913000415 +259000 ekin = 1.12139026023636 | erot = 2.37095948468546 | epot = -12.6256988749107 | etot = -9.1333491299889 +260000 ekin = 1.11036122819321 | erot = 2.40229658115387 | epot = -12.6460069392473 | etot = -9.13334912990019 +261000 ekin = 1.09354805445073 | erot = 2.42847877902924 | epot = -12.6553759632423 | etot = -9.13334912976234 +262000 ekin = 1.07216031825785 | erot = 2.45046938603033 | epot = -12.6559788338922 | etot = -9.13334912960407 +263000 ekin = 1.04754368718294 | erot = 2.46943297797202 | epot = -12.6503257946118 | etot = -9.13334912945686 +264000 ekin = 1.02102495133829 | erot = 2.48647844637155 | epot = -12.6408525270502 | etot = -9.13334912934033 +265000 ekin = 0.993788783443617 | erot = 2.50247063136407 | epot = -12.6296085440767 | etot = -9.13334912926897 +266000 ekin = 0.966800247929904 | erot = 2.51790683905028 | epot = -12.6180562162301 | etot = -9.1333491292499 +267000 ekin = 0.940784249459205 | erot = 2.53283827184828 | epot = -12.6069716505894 | etot = -9.13334912928191 +268000 ekin = 0.916272152394379 | erot = 2.54684612152521 | epot = -12.5964674032729 | etot = -9.13334912935328 +269000 ekin = 0.893722172477211 | erot = 2.55907244306967 | epot = -12.5861437450344 | etot = -9.13334912948749 +270000 ekin = 0.873709285128844 | erot = 2.56799722891236 | epot = -12.5750556436016 | etot = -9.13334912956044 +271000 ekin = 0.857156433251437 | erot = 2.57226369508371 | epot = -12.5627692579078 | etot = -9.13334912957266 +272000 ekin = 0.845541083723894 | erot = 2.57096110909472 | epot = -12.5498513223268 | etot = -9.13334912950816 +273000 ekin = 0.840983736969615 | erot = 2.56364270819397 | epot = -12.5379755745176 | etot = -9.13334912935404 +274000 ekin = 0.846103061110367 | erot = 2.5505449718361 | epot = -12.5299971620896 | etot = -9.13334912914317 +275000 ekin = 0.863570741244853 | erot = 2.53260377851069 | epot = -12.5295236486814 | etot = -9.13334912892586 +276000 ekin = 0.895419299415193 | erot = 2.51114645014795 | epot = -12.5399148783707 | etot = -9.13334912880754 +277000 ekin = 0.942302359418757 | erot = 2.48734970425704 | epot = -12.5630011925124 | etot = -9.13334912883659 +278000 ekin = 1.00299069941587 | erot = 2.46199112036433 | epot = -12.59833094881 | etot = -9.13334912902983 +279000 ekin = 1.0743456158926 | erot = 2.43529774590789 | epot = -12.64299249114 | etot = -9.13334912933949 +280000 ekin = 1.15182340984036 | erot = 2.40711596365541 | epot = -12.6922885031804 | etot = -9.1333491296846 +281000 ekin = 1.23030856581827 | erot = 2.37726964751254 | epot = -12.7409273433239 | etot = -9.13334912999313 +282000 ekin = 1.30483974879784 | erot = 2.34551973870787 | epot = -12.7837086176988 | etot = -9.13334913019314 +283000 ekin = 1.37151257999461 | erot = 2.3123145281989 | epot = -12.8171762384382 | etot = -9.13334913024467 +284000 ekin = 1.42789685319406 | erot = 2.27901843146204 | epot = -12.8402644148116 | etot = -9.13334913015548 +285000 ekin = 1.47299679574489 | erot = 2.24762833985815 | epot = -12.8539742655639 | etot = -9.13334912996081 +286000 ekin = 1.50701906587725 | erot = 2.22050056283323 | epot = -12.8608687584215 | etot = -9.13334912971103 +287000 ekin = 1.53099472144792 | erot = 2.19999584806494 | epot = -12.8643396989721 | etot = -9.13334912945926 +288000 ekin = 1.54636449768904 | erot = 2.18811490987488 | epot = -12.8678285368149 | etot = -9.13334912925098 +289000 ekin = 1.55461163491235 | erot = 2.18618804174345 | epot = -12.8741488057735 | etot = -9.1333491291177 +290000 ekin = 1.55699428674705 | erot = 2.19466879450583 | epot = -12.8850122103268 | etot = -9.1333491290739 +291000 ekin = 1.55439775255683 | erot = 2.21306131817971 | epot = -12.9008081998535 | etot = -9.13334912911697 +292000 ekin = 1.54729960240299 | erot = 2.23998314421967 | epot = -12.920631875854 | etot = -9.13334912923138 +293000 ekin = 1.53582108608446 | erot = 2.27333490842355 | epot = -12.9425051239026 | etot = -9.13334912939456 +294000 ekin = 1.51982864506222 | erot = 2.31049721096849 | epot = -12.9636749856262 | etot = -9.13334912959544 +295000 ekin = 1.4990515421338 | erot = 2.34851873983922 | epot = -12.9809194117666 | etot = -9.13334912979358 +296000 ekin = 1.47319364802853 | erot = 2.38443281021056 | epot = -12.990975588222 | etot = -9.13334912998291 +297000 ekin = 1.44203124546029 | erot = 2.4153685458993 | epot = -12.9907489215098 | etot = -9.13334913015026 +298000 ekin = 1.40549976702145 | erot = 2.43867409046083 | epot = -12.9775229877652 | etot = -9.1333491302829 +299000 ekin = 1.36377241662857 | erot = 2.45204871800437 | epot = -12.9491702650002 | etot = -9.13334913036728 +300000 ekin = 1.31732711912207 | erot = 2.45368408092568 | epot = -12.9043603304389 | etot = -9.13334913039114 +301000 ekin = 1.26699022414763 | erot = 2.44240353914598 | epot = -12.84274289364 | etot = -9.13334913034639 +302000 ekin = 1.21394210637195 | erot = 2.41777278592971 | epot = -12.7650640225334 | etot = -9.13334913023172 +303000 ekin = 1.15967414429362 | erot = 2.38015189683675 | epot = -12.6731751711848 | etot = -9.13334913005445 +304000 ekin = 1.10589726251318 | erot = 2.33066939618194 | epot = -12.5699157885246 | etot = -9.13334912982947 +305000 ekin = 1.05441504199278 | erot = 2.27111808933748 | epot = -12.4588822609066 | etot = -9.13334912957634 +306000 ekin = 1.00698421397165 | erot = 2.20379218514104 | epot = -12.3441255284279 | etot = -9.13334912931524 +307000 ekin = 0.965188337627694 | erot = 2.1312976438547 | epot = -12.2298351105458 | etot = -9.13334912906342 +308000 ekin = 0.930345631944623 | erot = 2.05636814615639 | epot = -12.120062906934 | etot = -9.13334912883299 +309000 ekin = 0.903461768093111 | erot = 1.98167791132949 | epot = -12.0184888080552 | etot = -9.13334912863261 +310000 ekin = 0.885228515008148 | erot = 1.90967870211655 | epot = -11.9282563455897 | etot = -9.13334912846497 +311000 ekin = 0.876047647700613 | erot = 1.84263812610127 | epot = -11.8520349021344 | etot = -9.1333491283325 +312000 ekin = 0.876068182199134 | erot = 1.78248869456961 | epot = -11.7919060050075 | etot = -9.13334912823871 +313000 ekin = 0.885223985970026 | erot = 1.73072892882286 | epot = -11.7493020429823 | etot = -9.1333491281894 +314000 ekin = 0.90325834251522 | erot = 1.6883206698841 | epot = -11.7249281405912 | etot = -9.13334912819187 +315000 ekin = 0.929731391718518 | erot = 1.65558558099762 | epot = -11.7186661009695 | etot = -9.13334912825333 +316000 ekin = 0.964013828970734 | erot = 1.63211973509068 | epot = -11.72948269244 | etot = -9.13334912837856 +317000 ekin = 1.0052762921168 | erot = 1.61675326466496 | epot = -11.7553786853484 | etot = -9.13334912856667 +318000 ekin = 1.05248736450138 | erot = 1.60758570940588 | epot = -11.7934222027157 | etot = -9.13334912880845 +319000 ekin = 1.10443332868138 | erot = 1.60212494474532 | epot = -11.8399074025111 | etot = -9.13334912908443 +320000 ekin = 1.15976924920831 | erot = 1.59754526105424 | epot = -11.8906636396273 | etot = -9.13334912936474 +321000 ekin = 1.21710352305675 | erot = 1.59105554518188 | epot = -11.9415081978521 | etot = -9.1333491296135 +322000 ekin = 1.2751075118947 | erot = 1.58033324923108 | epot = -11.9887898909202 | etot = -9.13334912979443 +323000 ekin = 1.33263084645705 | erot = 1.56394390937361 | epot = -12.0299238857106 | etot = -9.13334912987991 +324000 ekin = 1.38879590712203 | erot = 1.54164678485257 | epot = -12.0637918218337 | etot = -9.1333491298591 +325000 ekin = 1.44304623679693 | erot = 1.51450056885279 | epot = -12.0908959353908 | etot = -9.13334912974113 +326000 ekin = 1.49513435445661 | erot = 1.4847307306606 | epot = -12.1132142146703 | etot = -9.13334912955313 +327000 ekin = 1.5450506593832 | erot = 1.4553840086035 | epot = -12.1337837973211 | etot = -9.13334912933442 +328000 ekin = 1.59290981434222 | erot = 1.42984788209345 | epot = -12.1561068255634 | etot = -9.13334912912769 +329000 ekin = 1.6388186097559 | erot = 1.41133335467792 | epot = -12.1835010934059 | etot = -9.13334912897204 +330000 ekin = 1.68274896183058 | erot = 1.40240729591338 | epot = -12.2185053866415 | etot = -9.1333491288975 +331000 ekin = 1.72443467169528 | erot = 1.40463116342013 | epot = -12.2624149640389 | etot = -9.13334912892348 +332000 ekin = 1.76330533674292 | erot = 1.41833479327437 | epot = -12.3149892590739 | etot = -9.13334912905662 +333000 ekin = 1.79846823309258 | erot = 1.44253834966203 | epot = -12.3743557120439 | etot = -9.13334912928929 +334000 ekin = 1.82874900591076 | erot = 1.47503277033831 | epot = -12.4371309058471 | etot = -9.13334912959799 +335000 ekin = 1.85279616115802 | erot = 1.5126357019748 | epot = -12.4987809930758 | etot = -9.133349129943 +336000 ekin = 1.8692763055876 | erot = 1.55160162438138 | epot = -12.5542270602382 | etot = -9.13334913026923 +337000 ekin = 1.87711735413924 | erot = 1.58820049773308 | epot = -12.5986669823874 | etot = -9.13334913051506 +338000 ekin = 1.87574840923161 | erot = 1.61938868722915 | epot = -12.6284862270849 | etot = -9.13334913062411 +339000 ekin = 1.8653486636272 | erot = 1.64338736517843 | epot = -12.6420851593666 | etot = -9.13334913056097 +340000 ekin = 1.84695798886999 | erot = 1.66009075059765 | epot = -12.6403978697903 | etot = -9.13334913032267 +341000 ekin = 1.8224396907666 | erot = 1.67114820362601 | epot = -12.6269370243337 | etot = -9.13334912994108 +342000 ekin = 1.79428655955893 | erot = 1.67969211618916 | epot = -12.6073278052237 | etot = -9.13334912947557 +343000 ekin = 1.76531632972558 | erot = 1.68978090506883 | epot = -12.5884463637907 | etot = -9.13334912899625 +344000 ekin = 1.73833039739302 | erot = 1.70570000747012 | epot = -12.577379533433 | etot = -9.1333491285699 +345000 ekin = 1.71580589060289 | erot = 1.73127559556322 | epot = -12.5804306144148 | etot = -9.13334912824874 +346000 ekin = 1.6996635309761 | erot = 1.76931234934734 | epot = -12.6023250083906 | etot = -9.13334912806714 +347000 ekin = 1.69112042623298 | erot = 1.82120184302248 | epot = -12.6456713972995 | etot = -9.13334912804407 +348000 ekin = 1.69061396982769 | erot = 1.88669704033581 | epot = -12.71066013835 | etot = -9.13334912818651 +349000 ekin = 1.6977768178821 | erot = 1.96382926866158 | epot = -12.7949552150345 | etot = -9.13334912849085 +350000 ekin = 1.71145115010259 | erot = 2.04895591402506 | epot = -12.8937561930702 | etot = -9.13334912894252 +351000 ekin = 1.72974629646179 | erot = 2.13695636910459 | epot = -13.0000517950764 | etot = -9.13334912951007 +352000 ekin = 1.75015893903938 | erot = 2.22162008456559 | epot = -13.105128153745 | etot = -9.13334913014002 +353000 ekin = 1.76978034905558 | erot = 2.2962702964592 | epot = -13.1993997762713 | etot = -9.13334913075652 +354000 ekin = 1.78560210911966 | erot = 2.35462017023351 | epot = -13.27357141062 | etot = -9.13334913126686 +355000 ekin = 1.79489785472858 | erot = 2.39176336004096 | epot = -13.3200103463511 | etot = -9.13334913158154 +356000 ekin = 1.79561393246616 | erot = 2.40509186859444 | epot = -13.3340549326997 | etot = -9.13334913163909 +357000 ekin = 1.78667091072668 | erot = 2.39487614134844 | epot = -13.3148961835033 | etot = -9.13334913142816 +358000 ekin = 1.76810167230557 | erot = 2.36429897994081 | epot = -13.2657497831712 | etot = -9.13334913092478 +359000 ekin = 1.7417056904474 | erot = 2.31907684809561 | epot = -13.1941316689282 | etot = -9.13334913038514 +360000 ekin = 1.70943632676234 | erot = 2.26611368397217 | epot = -13.1088991405414 | etot = -9.13334912980693 +361000 ekin = 1.67315005965486 | erot = 2.21234166615777 | epot = -13.0188408550991 | etot = -9.13334912928651 +362000 ekin = 1.63480994001601 | erot = 2.16376887379877 | epot = -12.9319279427067 | etot = -9.13334912889189 +363000 ekin = 1.59622606057561 | erot = 2.12469986683801 | epot = -12.8542750560709 | etot = -9.13334912865731 +364000 ekin = 1.55890205833797 | erot = 2.09734631559815 | epot = -12.7895975025219 | etot = -9.13334912858577 +365000 ekin = 1.52397421076781 | erot = 2.08181308416714 | epot = -12.7391364235917 | etot = -9.13334912865673 +366000 ekin = 1.49221260734017 | erot = 2.07639009796196 | epot = -12.7019518341355 | etot = -9.13334912883336 +367000 ekin = 1.46405952364962 | erot = 2.07805510122151 | epot = -12.6754637539438 | etot = -9.13334912907266 +368000 ekin = 1.43967726932399 | erot = 2.08307216057582 | epot = -12.6560985592337 | etot = -9.13334912933388 +369000 ekin = 1.41899010811501 | erot = 2.08756917147262 | epot = -12.639908409173 | etot = -9.13334912958535 +370000 ekin = 1.4017155735679 | erot = 2.08800173652872 | epot = -12.6230664399024 | etot = -9.13334912980582 +371000 ekin = 1.38739280854902 | erot = 2.08146226240632 | epot = -12.6022042009375 | etot = -9.1333491299822 +372000 ekin = 1.37542340308629 | erot = 2.06585193702345 | epot = -12.5746244702142 | etot = -9.1333491301045 +373000 ekin = 1.36513752357954 | erot = 2.03996886737167 | epot = -12.5384555211136 | etot = -9.13334913016239 +374000 ekin = 1.35583949105216 | erot = 2.0035197577249 | epot = -12.4927083789469 | etot = -9.13334913016985 +375000 ekin = 1.34694157711492 | erot = 1.95716038268595 | epot = -12.4374510898692 | etot = -9.13334913006829 +376000 ekin = 1.33814968105299 | erot = 1.90258032253382 | epot = -12.3740791334842 | etot = -9.13334912989743 +377000 ekin = 1.3293626112084 | erot = 1.84227265725276 | epot = -12.3049843981381 | etot = -9.13334912967697 +378000 ekin = 1.32063159991378 | erot = 1.77926043319083 | epot = -12.2332411625438 | etot = -9.13334912943922 +379000 ekin = 1.31208340368883 | erot = 1.71672941783678 | epot = -12.1621619507418 | etot = -9.13334912921615 +380000 ekin = 1.30384179784231 | erot = 1.65764204155824 | epot = -12.0948329684342 | etot = -9.13334912903366 +381000 ekin = 1.29657917475847 | erot = 1.60487100826719 | epot = -12.0347993118457 | etot = -9.13334912882004 +382000 ekin = 1.29092190134704 | erot = 1.5606106770711 | epot = -11.9848817072436 | etot = -9.13334912882546 +383000 ekin = 1.28620909068432 | erot = 1.52536833770028 | epot = -11.9449265572235 | etot = -9.13334912883891 +384000 ekin = 1.28205683099636 | erot = 1.49922806168843 | epot = -11.9146340215165 | etot = -9.1333491288317 +385000 ekin = 1.27850478017873 | erot = 1.48216189144837 | epot = -11.8940158004146 | etot = -9.1333491287875 +386000 ekin = 1.27603762173997 | erot = 1.47423730493026 | epot = -11.8836240553805 | etot = -9.13334912871028 +387000 ekin = 1.27548287271909 | erot = 1.47565716104746 | epot = -11.8844891623904 | etot = -9.13334912862385 +388000 ekin = 1.27780044585781 | erot = 1.48660964097428 | epot = -11.8977592153986 | etot = -9.13334912856648 +389000 ekin = 1.28381262703568 | erot = 1.50697425852404 | epot = -11.9241360141384 | etot = -9.13334912857867 +390000 ekin = 1.29393930260845 | erot = 1.53598035068237 | epot = -11.9632687819857 | etot = -9.13334912869492 +391000 ekin = 1.30800074456098 | erot = 1.5719098492443 | epot = -12.0132597227343 | etot = -9.13334912892906 +392000 ekin = 1.32513099179446 | erot = 1.61197584867681 | epot = -12.0704559697433 | etot = -9.13334912927198 +393000 ekin = 1.34382543000145 | erot = 1.6524144888335 | epot = -12.1295890485248 | etot = -9.13334912968983 +394000 ekin = 1.36212102398639 | erot = 1.68881012624701 | epot = -12.1842802803622 | etot = -9.13334913012882 +395000 ekin = 1.37788072140316 | erot = 1.71661593053998 | epot = -12.2278457824672 | etot = -9.13334913052405 +396000 ekin = 1.38913154512402 | erot = 1.731811126183 | epot = -12.2542918021043 | etot = -9.13334913079732 +397000 ekin = 1.39439357479737 | erot = 1.73153617599033 | epot = -12.2592788817201 | etot = -9.13334913093241 +398000 ekin = 1.39293904659182 | erot = 1.71441550438733 | epot = -12.240703681855 | etot = -9.13334913087585 +399000 ekin = 1.3849317477743 | erot = 1.68094766350868 | epot = -12.1992285419448 | etot = -9.13334913066178 +400000 ekin = 1.37142116074087 | erot = 1.6333076419787 | epot = -12.138077933025 | etot = -9.13334913030545 +401000 ekin = 1.35412991252433 | erot = 1.57501044311684 | epot = -12.0624894855334 | etot = -9.13334912989227 +402000 ekin = 1.33517991856889 | erot = 1.51048364980015 | epot = -11.9790126977735 | etot = -9.13334912940443 +403000 ekin = 1.31709653187258 | erot = 1.44458891478878 | epot = -11.8950345755997 | etot = -9.13334912893839 +404000 ekin = 1.30234590493863 | erot = 1.38198365576701 | epot = -11.8176786892407 | etot = -9.13334912853503 +405000 ekin = 1.29301391716261 | erot = 1.32673455588803 | epot = -11.7530976012884 | etot = -9.13334912823777 +406000 ekin = 1.2906546746278 | erot = 1.28204116436322 | epot = -11.7060449670165 | etot = -9.13334912802551 +407000 ekin = 1.29643237294787 | erot = 1.25006436588367 | epot = -11.6798458667504 | etot = -9.13334912791888 +408000 ekin = 1.31094700615241 | erot = 1.23190986721484 | epot = -11.6762060012831 | etot = -9.13334912791581 +409000 ekin = 1.33422438303354 | erot = 1.22763489752227 | epot = -11.6952084085704 | etot = -9.13334912801461 +410000 ekin = 1.36572014154941 | erot = 1.23628017302481 | epot = -11.7353494427861 | etot = -9.1333491282119 +411000 ekin = 1.40432668760742 | erot = 1.25592548503564 | epot = -11.793601301144 | etot = -9.13334912850095 +412000 ekin = 1.44839088645837 | erot = 1.28379672627856 | epot = -11.8655367416044 | etot = -9.13334912886744 +413000 ekin = 1.4957679524182 | erot = 1.31646032748941 | epot = -11.9455774091906 | etot = -9.13334912928304 +414000 ekin = 1.54394920889428 | erot = 1.35014055217881 | epot = -12.0274388907764 | etot = -9.13334912970329 +415000 ekin = 1.59029421705125 | erot = 1.38116660571204 | epot = -12.1048099528333 | etot = -9.13334913007006 +416000 ekin = 1.63235973909076 | erot = 1.40649922749326 | epot = -12.1722080969088 | etot = -9.13334913032477 +417000 ekin = 1.66825800489191 | erot = 1.42422016761206 | epot = -12.2258273029356 | etot = -9.13334913043163 +418000 ekin = 1.69693219837215 | erot = 1.43381449957517 | epot = -12.2640958283214 | etot = -9.13334913037409 +419000 ekin = 1.71824951894772 | erot = 1.43620625779659 | epot = -12.287804906928 | etot = -9.13334913018368 +420000 ekin = 1.73288337430554 | erot = 1.43350825350812 | epot = -12.2997407577243 | etot = -9.13334912991064 +421000 ekin = 1.74204129532368 | erot = 1.42856028674974 | epot = -12.3039507116831 | etot = -9.1333491296097 +422000 ekin = 1.74713701807706 | erot = 1.42445618730841 | epot = -12.3049423347125 | etot = -9.13334912932706 +423000 ekin = 1.74949063384707 | erot = 1.42413436044398 | epot = -12.3069741233949 | etot = -9.13334912910383 +424000 ekin = 1.75009754643003 | erot = 1.4300564192515 | epot = -12.3135030946278 | etot = -9.1333491289463 +425000 ekin = 1.74947257256719 | erot = 1.44412400802322 | epot = -12.3269457094739 | etot = -9.13334912888348 +426000 ekin = 1.69664946387423 | erot = 1.40011304962606 | epot = -12.2301116345993 | etot = -9.13334912109897 +427000 ekin = 1.76448154345998 | erot = 1.46695774970195 | epot = -12.3647884699807 | etot = -9.1333491768188 +428000 ekin = 1.7786404038274 | erot = 1.51204937412237 | epot = -12.4240389057573 | etot = -9.13334912780751 +429000 ekin = 1.7774425409066 | erot = 1.55645173379887 | epot = -12.4672434028096 | etot = -9.13334912810414 +430000 ekin = 1.76864481713924 | erot = 1.60567169371185 | epot = -12.5076656392886 | etot = -9.13334912843749 +431000 ekin = 1.7504144399306 | erot = 1.65655638514155 | epot = -12.5403199538335 | etot = -9.13334912876136 +432000 ekin = 1.72143753020936 | erot = 1.70559294341342 | epot = -12.5603796026441 | etot = -9.13334912902131 +433000 ekin = 1.68129756274209 | erot = 1.74934007551142 | epot = -12.5639867674184 | etot = -9.13334912916485 +434000 ekin = 1.6307765097996 | erot = 1.78490039303309 | epot = -12.5490260319873 | etot = -9.13334912915464 +435000 ekin = 1.5719888208448 | erot = 1.81033246556215 | epot = -12.5156704153874 | etot = -9.13334912898044 +436000 ekin = 1.50828072851463 | erot = 1.82489908961126 | epot = -12.4665289467908 | etot = -9.13334912866491 +437000 ekin = 1.44388315301219 | erot = 1.82908776308031 | epot = -12.4063200443508 | etot = -9.13334912825832 +438000 ekin = 1.38337900429708 | erot = 1.82441107452572 | epot = -12.3411392066477 | etot = -9.13334912782489 +439000 ekin = 1.33110407576217 | erot = 1.81306694504129 | epot = -12.277520148228 | etot = -9.13334912742457 +440000 ekin = 1.29061754888996 | erot = 1.79757475508412 | epot = -12.2215414310741 | etot = -9.13334912710001 +441000 ekin = 1.26434687832154 | erot = 1.78048600607446 | epot = -12.178182011266 | etot = -9.13334912687002 +442000 ekin = 1.25344985037922 | erot = 1.76421040799477 | epot = -12.1510093851077 | etot = -9.13334912673374 +443000 ekin = 1.25787308938405 | erot = 1.75093400476739 | epot = -12.1421562208303 | etot = -9.13334912667884 +444000 ekin = 1.27654491138795 | erot = 1.7425672785205 | epot = -12.1524613166016 | etot = -9.13334912669317 +445000 ekin = 1.30762960642471 | erot = 1.74066161517058 | epot = -12.1816403483643 | etot = -9.13334912676902 +446000 ekin = 1.34878485335224 | erot = 1.74626611357115 | epot = -12.2284000938275 | etot = -9.13334912690411 +447000 ekin = 1.39739993763739 | erot = 1.75974793458101 | epot = -12.2904969993182 | etot = -9.13334912709981 +448000 ekin = 1.4507664919091 | erot = 1.78060717934162 | epot = -12.3647227986027 | etot = -9.13334912735198 +449000 ekin = 1.50623999605369 | erot = 1.80738848344727 | epot = -12.4469776071503 | etot = -9.13334912764936 +450000 ekin = 1.56138908054611 | erot = 1.83773497344371 | epot = -12.5324731819606 | etot = -9.13334912797076 +451000 ekin = 1.61412412964536 | erot = 1.86859865234449 | epot = -12.6160719102764 | etot = -9.13334912828658 +452000 ekin = 1.66280931630125 | erot = 1.89658548036403 | epot = -12.692743925228 | etot = -9.13334912856274 +453000 ekin = 1.70634971637102 | erot = 1.91837476586826 | epot = -12.7580736110106 | etot = -9.1333491287713 +454000 ekin = 1.74423056750382 | erot = 1.93111374790662 | epot = -12.8086934443055 | etot = -9.13334912889508 +455000 ekin = 1.77648988409904 | erot = 1.93270291378203 | epot = -12.8425419268135 | etot = -9.13334912893246 +456000 ekin = 1.80361911556763 | erot = 1.92192628287829 | epot = -12.858894527342 | etot = -9.13334912889608 +457000 ekin = 1.82640016706247 | erot = 1.89842961389972 | epot = -12.8581789097703 | etot = -9.13334912880812 +458000 ekin = 1.84570455025974 | erot = 1.86259298695773 | epot = -12.8416466659124 | etot = -9.13334912869491 +459000 ekin = 1.86229070170989 | erot = 1.81535342315173 | epot = -12.8109932534393 | etot = -9.13334912857765 +460000 ekin = 1.87663848085908 | erot = 1.75803306182813 | epot = -12.7680206711607 | etot = -9.1333491284735 +461000 ekin = 1.88883864523231 | erot = 1.69219746384324 | epot = -12.7143852374646 | etot = -9.13334912838905 +462000 ekin = 1.89856203652343 | erot = 1.61956678027461 | epot = -12.6514779451225 | etot = -9.1333491283245 +463000 ekin = 1.90510221764518 | erot = 1.54196437877865 | epot = -12.5804157247 | etot = -9.13334912827615 +464000 ekin = 1.90747686786698 | erot = 1.46127993198498 | epot = -12.5021059280868 | etot = -9.1333491282348 +465000 ekin = 1.90457977356204 | erot = 1.37946070091751 | epot = -12.4173896026653 | etot = -9.13334912818579 +466000 ekin = 1.89536572152371 | erot = 1.29851485172167 | epot = -12.3272297013669 | etot = -9.13334912812149 +467000 ekin = 1.87901831710021 | erot = 1.22048659414392 | epot = -12.23285403928 | etot = -9.13334912803591 +468000 ekin = 1.85509917792101 | erot = 1.1473912628405 | epot = -12.1358395686897 | etot = -9.13334912792815 +469000 ekin = 1.82366605107361 | erot = 1.08110787535082 | epot = -12.0381230542268 | etot = -9.13334912780238 +470000 ekin = 1.7853521607565 | erot = 1.02324127043668 | epot = -11.9419425588574 | etot = -9.13334912766426 +471000 ekin = 1.74141051513418 | erot = 0.974982090043544 | epot = -11.8497417326969 | etot = -9.13334912751917 +472000 ekin = 1.69372019705967 | erot = 0.937000644454867 | epot = -11.7640699688862 | etot = -9.13334912737167 +473000 ekin = 1.64473632771003 | erot = 0.909402534931779 | epot = -11.687487989869 | etot = -9.1333491272272 +474000 ekin = 1.59734995177387 | erot = 0.891755018431486 | epot = -11.6224540973009 | etot = -9.13334912709558 +475000 ekin = 1.55462885495273 | erot = 0.883174765260199 | epot = -11.5711527472045 | etot = -9.13334912699156 +476000 ekin = 1.51944866261178 | erot = 0.882459888569591 | epot = -11.5352576781131 | etot = -9.13334912693173 +477000 ekin = 1.49408243529042 | erot = 0.888250161716877 | epot = -11.5156817239351 | etot = -9.13334912692782 +478000 ekin = 1.47985622585632 | erot = 0.899197335532762 | epot = -11.5124026883711 | etot = -9.13334912698202 +479000 ekin = 1.47695373952845 | erot = 0.914115348457381 | epot = -11.5244182150797 | etot = -9.13334912709389 +480000 ekin = 1.48439477575444 | erot = 0.93207251662073 | epot = -11.5498164196176 | etot = -9.13334912724239 +481000 ekin = 1.50022741217502 | erot = 0.952423999183962 | epot = -11.5860005387814 | etot = -9.13334912742239 +482000 ekin = 1.52172985963414 | erot = 0.9747542118462 | epot = -11.6298331991069 | etot = -9.13334912762657 +483000 ekin = 1.54567018241497 | erot = 0.998770450814422 | epot = -11.6777897610753 | etot = -9.13334912784592 +484000 ekin = 1.56858614723089 | erot = 1.02419763510822 | epot = -11.7261329104079 | etot = -9.13334912806883 +485000 ekin = 1.58707346955084 | erot = 1.05070585623108 | epot = -11.7711284540615 | etot = -9.13334912827962 +486000 ekin = 1.59807103603109 | erot = 1.07788995424654 | epot = -11.8093101187376 | etot = -9.13334912845999 +487000 ekin = 1.59911980804461 | erot = 1.10529931942145 | epot = -11.837768256059 | etot = -9.13334912859298 +488000 ekin = 1.58856342116693 | erot = 1.13249736396193 | epot = -11.854409913796 | etot = -9.13334912866709 +489000 ekin = 1.5656614290475 | erot = 1.15911683125774 | epot = -11.858127388984 | etot = -9.13334912867874 +490000 ekin = 1.53060268554712 | erot = 1.1848850242731 | epot = -11.8488368384537 | etot = -9.13334912863345 +491000 ekin = 1.48443427069534 | erot = 1.20959914015965 | epot = -11.8273825393275 | etot = -9.13334912847252 +492000 ekin = 1.42930345354516 | erot = 1.2329182959332 | epot = -11.7955708778624 | etot = -9.13334912838407 +493000 ekin = 1.36749564145212 | erot = 1.25438544605068 | epot = -11.7552302157785 | etot = -9.13334912827565 +494000 ekin = 1.3013726298813 | erot = 1.27348228002522 | epot = -11.7082040380617 | etot = -9.13334912815521 +495000 ekin = 1.23360970817059 | erot = 1.28954660636125 | epot = -11.6565054425593 | etot = -9.1333491280275 +496000 ekin = 1.16375548641053 | erot = 1.30023195608647 | epot = -11.5973366205417 | etot = -9.1333491780447 +497000 ekin = 1.02574644939826 | erot = 1.24927230426371 | epot = -11.4083678755036 | etot = -9.13334912184166 +498000 ekin = 1.13339044616106 | erot = 1.24939677704367 | epot = -11.516136389112 | etot = -9.13334916590723 +499000 ekin = 1.1643476239324 | erot = 1.25864673154955 | epot = -11.5563434800377 | etot = -9.13334912455579 +500000 ekin = 1.16768486506763 | erot = 1.25769344443904 | epot = -11.5587274345812 | etot = -9.13334912507452 +501000 ekin = 1.17559895497533 | erot = 1.25038915442595 | epot = -11.5593372343039 | etot = -9.13334912490261 +502000 ekin = 1.18926606273922 | erot = 1.23784323633033 | epot = -11.5604584237502 | etot = -9.13334912468066 +503000 ekin = 1.20982408114937 | erot = 1.22204157664317 | epot = -11.565214782232 | etot = -9.13334912443942 +504000 ekin = 1.23811782737044 | erot = 1.2057286537842 | epot = -11.5771956053585 | etot = -9.13334912420385 +505000 ekin = 1.2746096622879 | erot = 1.19199209322121 | epot = -11.5999508795099 | etot = -9.13334912400081 +506000 ekin = 1.31928047819602 | erot = 1.18393687677856 | epot = -11.6365664788293 | etot = -9.13334912385472 +507000 ekin = 1.3715770090051 | erot = 1.1843511838655 | epot = -11.6892773166535 | etot = -9.13334912378287 +508000 ekin = 1.43042502721544 | erot = 1.19541187481536 | epot = -11.7591860258238 | etot = -9.13334912379299 +509000 ekin = 1.49431413372851 | erot = 1.21846596295601 | epot = -11.8461292205675 | etot = -9.13334912388301 +510000 ekin = 1.56143815899976 | erot = 1.25390781315331 | epot = -11.9486950961964 | etot = -9.13334912404328 +511000 ekin = 1.62985405359518 | erot = 1.30115550673923 | epot = -12.0643586845951 | etot = -9.13334912426069 +512000 ekin = 1.69760948238416 | erot = 1.35871536004227 | epot = -12.18967396695 | etot = -9.13334912452357 +513000 ekin = 1.76279412854755 | erot = 1.42431355746689 | epot = -12.3204568108389 | etot = -9.13334912482451 +514000 ekin = 1.82349978434179 | erot = 1.49507387317699 | epot = -12.4519227826769 | etot = -9.13334912515816 +515000 ekin = 1.87772649131692 | erot = 1.56773414236046 | epot = -12.5788097591909 | etot = -9.13334912551357 +516000 ekin = 1.92332299298487 | erot = 1.63891274675816 | epot = -12.6955848656085 | etot = -9.13334912586549 +517000 ekin = 1.9580568110205 | erot = 1.70543998933956 | epot = -12.796845926533 | etot = -9.13334912617288 +518000 ekin = 1.97984991947 | erot = 1.76473849815176 | epot = -12.8779375440093 | etot = -9.13334912638759 +519000 ekin = 1.98711819296686 | erot = 1.81518192784827 | epot = -12.9356492472857 | etot = -9.1333491264706 +520000 ekin = 1.979089110772 | erot = 1.85632478175013 | epot = -12.9687630189341 | etot = -9.13334912641202 +521000 ekin = 1.95594858056397 | erot = 1.88892760796643 | epot = -12.9782253147566 | etot = -9.13334912622617 +522000 ekin = 1.91881161738192 | erot = 1.91475582237447 | epot = -12.9669165657073 | etot = -9.13334912595088 +523000 ekin = 1.8695404534331 | erot = 1.93620351350285 | epot = -12.9390930925716 | etot = -9.1333491256356 +524000 ekin = 1.81047332181729 | erot = 1.95582271022136 | epot = -12.8996451573702 | etot = -9.13334912533158 +525000 ekin = 1.74413482435741 | erot = 1.97582576721596 | epot = -12.8533097166598 | etot = -9.13334912508643 +526000 ekin = 1.67297434024971 | erot = 1.99761678040444 | epot = -12.8039402455921 | etot = -9.13334912493798 +527000 ekin = 1.59916865616246 | erot = 2.02141684187606 | epot = -12.753934622945 | etot = -9.1333491249065 +528000 ekin = 1.52452149634699 | erot = 2.04605877912568 | epot = -12.7039294004611 | etot = -9.13334912498842 +529000 ekin = 1.45048141638071 | erot = 2.06903286947777 | epot = -12.6528634110106 | etot = -9.13334912515212 +530000 ekin = 1.37827485203383 | erot = 2.08683821123052 | epot = -12.5984621886053 | etot = -9.133349125341 +531000 ekin = 1.30911544825177 | erot = 2.09562136598152 | epot = -12.5380859397197 | etot = -9.13334912548638 +532000 ekin = 1.24441932206891 | erot = 2.09198653946257 | epot = -12.4697549870577 | etot = -9.13334912552618 +533000 ekin = 1.18594679653149 | erot = 2.07377924595455 | epot = -12.3930751679099 | etot = -9.13334912542387 +534000 ekin = 1.13581312461362 | erot = 2.0406294196016 | epot = -12.3097916693935 | etot = -9.13334912517829 +535000 ekin = 1.09635528031391 | erot = 1.99411201499553 | epot = -12.2238164201321 | etot = -9.13334912482269 +536000 ekin = 1.06988655695557 | erot = 1.93750945181437 | epot = -12.1407451331833 | etot = -9.1333491244134 +537000 ekin = 1.05839509271197 | erot = 1.87547351818625 | epot = -12.0672177348914 | etot = -9.13334912399314 +538000 ekin = 1.06323891385436 | erot = 1.81331424698503 | epot = -12.0099022845181 | etot = -9.13334912367869 +539000 ekin = 1.08487929969881 | erot = 1.7556239231471 | epot = -11.9738523463394 | etot = -9.13334912349346 +540000 ekin = 1.12268189022869 | erot = 1.70611667318478 | epot = -11.9621476868877 | etot = -9.13334912347426 +541000 ekin = 1.17481105395755 | erot = 1.6671748123082 | epot = -11.9753349899041 | etot = -9.13334912363839 +542000 ekin = 1.23824417790831 | erot = 1.63956314455178 | epot = -12.0111564464395 | etot = -9.13334912397937 +543000 ekin = 1.30892832431953 | erot = 1.62236761446633 | epot = -12.0646450632485 | etot = -9.13334912446267 +544000 ekin = 1.38208514507435 | erot = 1.61318872881536 | epot = -12.1286229989201 | etot = -9.13334912503035 +545000 ekin = 1.45263801176001 | erot = 1.60857948401617 | epot = -12.1945666213826 | etot = -9.13334912560646 +546000 ekin = 1.51570974605509 | erot = 1.6046737747277 | epot = -12.2537326468934 | etot = -9.13334912611061 +547000 ekin = 1.56711452712088 | erot = 1.59788800381636 | epot = -12.2983516574118 | etot = -9.13334912647456 +548000 ekin = 1.60376221827898 | erot = 1.58554162816685 | epot = -12.3226529731016 | etot = -9.13334912665578 +549000 ekin = 1.6239104162611 | erot = 1.566256264213 | epot = -12.3235158071199 | etot = -9.13334912664576 +550000 ekin = 1.62723358008893 | erot = 1.54012357328677 | epot = -12.3007062798211 | etot = -9.13334912644538 +551000 ekin = 1.61471889891605 | erot = 1.50851459570777 | epot = -12.2565826207683 | etot = -9.13334912614448 +552000 ekin = 1.58843016682361 | erot = 1.47348936384284 | epot = -12.1952686564364 | etot = -9.13334912576998 +553000 ekin = 1.55120098109954 | erot = 1.43753302719075 | epot = -12.1220831336597 | etot = -9.13334912536936 +554000 ekin = 1.50631636213207 | erot = 1.40318755323182 | epot = -12.042853040342 | etot = -9.13334912497809 +555000 ekin = 1.45722878986545 | erot = 1.37279698199939 | epot = -11.9633748964846 | etot = -9.13334912461971 +556000 ekin = 1.40732293285206 | erot = 1.3483759063901 | epot = -11.8890479635485 | etot = -9.13334912430635 +557000 ekin = 1.35973750772892 | erot = 1.33157707038875 | epot = -11.8246637021606 | etot = -9.13334912404289 +558000 ekin = 1.31723590732968 | erot = 1.32371628032645 | epot = -11.7743013114878 | etot = -9.1333491238317 +559000 ekin = 1.28211028309144 | erot = 1.32580526483645 | epot = -11.7412646716043 | etot = -9.13334912367643 +560000 ekin = 1.2561059040487 | erot = 1.33855626265777 | epot = -11.7280112902897 | etot = -9.13334912358324 +561000 ekin = 1.24035844263301 | erot = 1.36234138770193 | epot = -11.7360489538955 | etot = -9.13334912356059 +562000 ekin = 1.23534624012637 | erot = 1.39711468447301 | epot = -11.7658100482156 | etot = -9.13334912361619 +563000 ekin = 1.24087113988421 | erot = 1.4423315029815 | epot = -11.8165517666166 | etot = -9.13334912375085 +564000 ekin = 1.25609129143038 | erot = 1.49691875867427 | epot = -11.8863591740582 | etot = -9.13334912395359 +565000 ekin = 1.27963015842595 | erot = 1.55937933470899 | epot = -11.9723586173234 | etot = -9.13334912418842 +566000 ekin = 1.30976945418457 | erot = 1.6279566472584 | epot = -12.0710752258912 | etot = -9.13334912444824 +567000 ekin = 1.34469873511337 | erot = 1.70073738336711 | epot = -12.1787852431714 | etot = -9.13334912469093 +568000 ekin = 1.38275779930792 | erot = 1.77591787229856 | epot = -12.2920247965114 | etot = -9.13334912490494 +569000 ekin = 1.42260294142322 | erot = 1.8518312790153 | epot = -12.4077833455332 | etot = -9.13334912509465 +570000 ekin = 1.4631143309606 | erot = 1.92670412004171 | epot = -12.5231675763701 | etot = -9.13334912536776 +571000 ekin = 1.50327753328919 | erot = 1.99853100879909 | epot = -12.6351576677695 | etot = -9.13334912568126 +572000 ekin = 1.54192966726675 | erot = 2.06497613729181 | epot = -12.7402549304336 | etot = -9.133349125875 +573000 ekin = 1.57823855406974 | erot = 2.12427016695888 | epot = -12.8358578469861 | etot = -9.13334912595745 +574000 ekin = 1.61207502224264 | erot = 2.17570201380341 | epot = -12.9211261619163 | etot = -9.1333491258703 +575000 ekin = 1.64402582173703 | erot = 2.22028441013991 | epot = -12.9976593575026 | etot = -9.13334912562569 +576000 ekin = 1.67538587678288 | erot = 2.26042238856323 | epot = -13.0691573906371 | etot = -9.13334912529099 +577000 ekin = 1.7078920937888 | erot = 2.29915883242413 | epot = -13.1404000511807 | etot = -9.13334912496776 +578000 ekin = 1.74326819508329 | erot = 2.33909725076283 | epot = -13.2157145705948 | etot = -9.13334912474865 +579000 ekin = 1.78272231838223 | erot = 2.38182643842076 | epot = -13.2978978814978 | etot = -9.13334912469481 +580000 ekin = 1.82652189372901 | erot = 2.42751679139609 | epot = -13.3873878099583 | etot = -9.13334912483316 +581000 ekin = 1.87370675175335 | erot = 2.47480205693756 | epot = -13.4818579338651 | etot = -9.13334912517415 +582000 ekin = 1.92197052578458 | erot = 2.52092715153073 | epot = -13.5762468029754 | etot = -9.13334912566012 +583000 ekin = 1.96774925896891 | erot = 2.56227660801421 | epot = -13.6633749932237 | etot = -9.13334912624054 +584000 ekin = 2.00657374540248 | erot = 2.59498886542586 | epot = -13.7349117376487 | etot = -9.13334912682033 +585000 ekin = 2.03371871575753 | erot = 2.6156627420009 | epot = -13.7827305850408 | etot = -9.13334912728238 +586000 ekin = 2.04507827703364 | erot = 2.62214006251189 | epot = -13.8005674670621 | etot = -9.13334912751658 +587000 ekin = 2.03806243485761 | erot = 2.6141199488879 | epot = -13.7855315112053 | etot = -9.13334912745983 +588000 ekin = 2.0122311518449 | erot = 2.5933503011183 | epot = -13.7389305800887 | etot = -9.13334912712549 +589000 ekin = 1.96942837554717 | erot = 2.56324673362595 | epot = -13.6660242357775 | etot = -9.13334912660437 +590000 ekin = 1.91334419959158 | erot = 2.52801524733165 | epot = -13.5747085729552 | etot = -9.13334912603198 +591000 ekin = 1.84865383330942 | erot = 2.49158313368603 | epot = -13.4735860925311 | etot = -9.13334912553562 +592000 ekin = 1.78006004419971 | erot = 2.45674050608129 | epot = -13.3701496754662 | etot = -9.1333491251852 +593000 ekin = 1.71159279762554 | erot = 2.42478693108865 | epot = -13.269728853693 | etot = -9.13334912497882 +594000 ekin = 1.64634946405776 | erot = 2.39569805900991 | epot = -13.1753966479387 | etot = -9.13334912487102 +595000 ekin = 1.58659479949359 | erot = 2.36854432556902 | epot = -13.0884882498818 | etot = -9.13334912481919 +596000 ekin = 1.53398103551836 | erot = 2.34182175785199 | epot = -13.0091519181808 | etot = -9.13334912481048 +597000 ekin = 1.48969441622996 | erot = 2.31355286210448 | epot = -12.9365964031859 | etot = -9.13334912485146 +598000 ekin = 1.45449014890807 | erot = 2.28129539495794 | epot = -12.8691346688086 | etot = -9.1333491249426 +599000 ekin = 1.42868283606302 | erot = 2.24230571379656 | epot = -12.8043376749205 | etot = -9.13334912506095 +600000 ekin = 1.41215819513097 | erot = 2.19421771509131 | epot = -12.7397250351199 | etot = -9.13334912489764 +601000 ekin = 1.40437980063911 | erot = 2.13675092848281 | epot = -12.6744798541827 | etot = -9.13334912506081 +602000 ekin = 1.40442466853377 | erot = 2.06863595764429 | epot = -12.6064097512965 | etot = -9.13334912511842 +603000 ekin = 1.4111230244965 | erot = 1.98998056957671 | epot = -12.5344527191447 | etot = -9.13334912507154 +604000 ekin = 1.42310135152174 | erot = 1.9027452432298 | epot = -12.4591957196962 | etot = -9.13334912494464 +605000 ekin = 1.43883447822476 | erot = 1.81030632011248 | epot = -12.382489923109 | etot = -9.13334912477176 +606000 ekin = 1.45673760095162 | erot = 1.71684240505004 | epot = -12.3069291305857 | etot = -9.13334912458401 +607000 ekin = 1.47529863713107 | erot = 1.6267229875319 | epot = -12.235370749066 | etot = -9.13334912440305 +608000 ekin = 1.49323166610301 | erot = 1.54399943869226 | epot = -12.1705802290357 | etot = -9.13334912424047 +609000 ekin = 1.50961256615701 | erot = 1.47208306434056 | epot = -12.1150447546074 | etot = -9.13334912410979 +610000 ekin = 1.52396039431294 | erot = 1.41350705715211 | epot = -12.07081657546 | etot = -9.13334912399491 +611000 ekin = 1.53622860047066 | erot = 1.36992443741294 | epot = -12.0395021618076 | etot = -9.13334912392405 +612000 ekin = 1.5466853662619 | erot = 1.34205362873082 | epot = -12.0220881189033 | etot = -9.13334912391059 +613000 ekin = 1.5557130969566 | erot = 1.32960894336052 | epot = -12.0186711642886 | etot = -9.13334912397147 +614000 ekin = 1.56356369221714 | erot = 1.33131277562629 | epot = -12.0282255919643 | etot = -9.13334912412092 +615000 ekin = 1.57013881826686 | erot = 1.3449453976181 | epot = -12.0484333402226 | etot = -9.13334912433764 +616000 ekin = 1.57485681903945 | erot = 1.36757312206294 | epot = -12.0757790657607 | etot = -9.13334912465831 +617000 ekin = 1.57672646781253 | erot = 1.39546251366803 | epot = -12.1055381065034 | etot = -9.13334912502289 +618000 ekin = 1.57456346737848 | erot = 1.42448013453603 | epot = -12.1323927272926 | etot = -9.13334912537807 +619000 ekin = 1.56732946470158 | erot = 1.45059208152816 | epot = -12.1512706718922 | etot = -9.13334912566249 +620000 ekin = 1.55451321753919 | erot = 1.47039334455609 | epot = -12.1582556879152 | etot = -9.13334912581989 +621000 ekin = 1.53644782338414 | erot = 1.48161304590982 | epot = -12.1514099951073 | etot = -9.13334912581332 +622000 ekin = 1.51447783518378 | erot = 1.48347710481945 | epot = -12.1313040656382 | etot = -9.13334912563501 +623000 ekin = 1.49092960733049 | erot = 1.47683215248909 | epot = -12.1011108851285 | etot = -9.13334912530896 +624000 ekin = 1.46886130170039 | erot = 1.4642219859157 | epot = -12.0664324125271 | etot = -9.13334912491099 +625000 ekin = 1.45155188812642 | erot = 1.44918251594291 | epot = -12.0340835285536 | etot = -9.13334912448426 +626000 ekin = 1.44224748157898 | erot = 1.4353339959176 | epot = -12.0109306015698 | etot = -9.13334912407321 +627000 ekin = 1.44381530879958 | erot = 1.42638005354778 | epot = -12.0035444860837 | etot = -9.13334912373637 +628000 ekin = 1.45833081620082 | erot = 1.42560824875229 | epot = -12.0172881884915 | etot = -9.13334912353836 +629000 ekin = 1.4867698553702 | erot = 1.43535417577129 | epot = -12.0554731546303 | etot = -9.13334912348884 +630000 ekin = 1.52866417049099 | erot = 1.45689184513512 | epot = -12.1189051392527 | etot = -9.1333491236266 +631000 ekin = 1.58193413338882 | erot = 1.49015054897646 | epot = -12.2054338063841 | etot = -9.13334912401885 +632000 ekin = 1.64234851055621 | erot = 1.53357750659019 | epot = -12.3092751416898 | etot = -9.13334912454337 +633000 ekin = 1.70466841197014 | erot = 1.58426390210209 | epot = -12.4222814392228 | etot = -9.13334912515061 +634000 ekin = 1.7631835469935 | erot = 1.63860587790712 | epot = -12.5351385506359 | etot = -9.13334912573525 +635000 ekin = 1.8124262503478 | erot = 1.69306627320784 | epot = -12.6388416497418 | etot = -9.13334912618614 +636000 ekin = 1.84805557838125 | erot = 1.74492785470201 | epot = -12.7263325594989 | etot = -9.13334912641569 +637000 ekin = 1.86755595284743 | erot = 1.79286465559366 | epot = -12.7937697348525 | etot = -9.13334912641142 +638000 ekin = 1.87047357468798 | erot = 1.83697965057525 | epot = -12.8408023514712 | etot = -9.13334912620798 +639000 ekin = 1.85817220593296 | erot = 1.87849437006716 | epot = -12.8700157018825 | etot = -9.13334912588239 +640000 ekin = 1.83325502874934 | erot = 1.91930247136692 | epot = -12.8859066256304 | etot = -9.13334912551417 +641000 ekin = 1.79889805051557 | erot = 1.96149522932338 | epot = -12.893742404998 | etot = -9.13334912515906 +642000 ekin = 1.75833330344904 | erot = 2.00701454517244 | epot = -12.8986969734775 | etot = -9.133349124856 +643000 ekin = 1.71452400738663 | erot = 2.05742054585165 | epot = -12.9052936778351 | etot = -9.13334912459681 +644000 ekin = 1.67006045206701 | erot = 2.11379950766718 | epot = -12.9172090841657 | etot = -9.1333491244315 +645000 ekin = 1.62710169193798 | erot = 2.17652829047829 | epot = -12.936979106775 | etot = -9.13334912435878 +646000 ekin = 1.58731920571204 | erot = 2.24499987972367 | epot = -12.9656682098073 | etot = -9.13334912437156 +647000 ekin = 1.5519287985014 | erot = 2.31774723145759 | epot = -13.0030251544529 | etot = -9.13334912449392 +648000 ekin = 1.52155547404613 | erot = 2.39216849405126 | epot = -13.0470730928269 | etot = -9.13334912472954 +649000 ekin = 1.49615701172709 | erot = 2.46459269466492 | epot = -13.0940988314686 | etot = -9.13334912507659 +650000 ekin = 1.474958204083 | erot = 2.53042613107551 | epot = -13.1387334606789 | etot = -9.13334912552037 +651000 ekin = 1.45644758276087 | erot = 2.58442104122293 | epot = -13.1742177500129 | etot = -9.1333491260291 +652000 ekin = 1.43848054670287 | erot = 2.62109720355956 | epot = -13.1929268768105 | etot = -9.13334912654803 +653000 ekin = 1.41853538646939 | erot = 2.63533318879064 | epot = -13.1872177022588 | etot = -9.13334912699876 +654000 ekin = 1.39414099594885 | erot = 2.62311445987543 | epot = -13.1506045831169 | etot = -9.13334912729267 +655000 ekin = 1.36342278664737 | erot = 2.58232798191585 | epot = -13.0790998958952 | etot = -9.13334912733202 +656000 ekin = 1.32754554560149 | erot = 2.51343997306709 | epot = -12.974334644813 | etot = -9.1333491261444 +657000 ekin = 1.0773875979315 | erot = 2.44669612963509 | epot = -12.6574327808011 | etot = -9.13334905323452 +658000 ekin = 1.0065201423019 | erot = 2.49084781647133 | epot = -12.6307170433323 | etot = -9.13334908455911 +659000 ekin = 1.07240085017882 | erot = 2.42929901831716 | epot = -12.6350489837836 | etot = -9.13334911528764 +660000 ekin = 1.09381648980894 | erot = 2.30102308261805 | epot = -12.5281886879237 | etot = -9.13334911549675 +661000 ekin = 1.11701334338068 | erot = 2.16959631554352 | epot = -12.4199587738197 | etot = -9.13334911489549 +662000 ekin = 1.14263894058022 | erot = 2.04231481245904 | epot = -12.3183028674896 | etot = -9.1333491144503 +663000 ekin = 1.17093665277086 | erot = 1.92510458369842 | epot = -12.2293903506468 | etot = -9.13334911417751 +664000 ekin = 1.20146324496785 | erot = 1.82207009510998 | epot = -12.1568824541679 | etot = -9.13334911409009 +665000 ekin = 1.23289032447881 | erot = 1.73564836427755 | epot = -12.1018878027987 | etot = -9.13334911404235 +666000 ekin = 1.26340464455085 | erot = 1.66702592668226 | epot = -12.063779685498 | etot = -9.13334911426491 +667000 ekin = 1.2910257481443 | erot = 1.61488086820513 | epot = -12.0392557309138 | etot = -9.13334911456438 +668000 ekin = 1.31376054134743 | erot = 1.57649712773723 | epot = -12.0236067839922 | etot = -9.13334911490756 +669000 ekin = 1.32989404565269 | erot = 1.54828621181597 | epot = -12.0115293726986 | etot = -9.1333491152299 +670000 ekin = 1.33826340890556 | erot = 1.5264084479746 | epot = -11.9980209723666 | etot = -9.13334911548643 +671000 ekin = 1.33847461323153 | erot = 1.50724764864793 | epot = -11.9790713775219 | etot = -9.1333491156424 +672000 ekin = 1.33101969554493 | erot = 1.48781306139196 | epot = -11.9521818726168 | etot = -9.13334911567988 +673000 ekin = 1.31737035051004 | erot = 1.46610228053022 | epot = -11.9168217466032 | etot = -9.13334911556297 +674000 ekin = 1.29992521798033 | erot = 1.44131241760729 | epot = -11.8745867509649 | etot = -9.13334911537732 +675000 ekin = 1.28129254582364 | erot = 1.41347048294498 | epot = -11.8281121439057 | etot = -9.13334911513707 +676000 ekin = 1.26413925333592 | erot = 1.38336835396545 | epot = -11.7808567221882 | etot = -9.13334911488686 +677000 ekin = 1.25080949629856 | erot = 1.35227525692428 | epot = -11.7364338679149 | etot = -9.1333491146921 +678000 ekin = 1.24240325883756 | erot = 1.32122246363638 | epot = -11.6969748370326 | etot = -9.13334911455865 +679000 ekin = 1.23935164124627 | erot = 1.29124446461099 | epot = -11.663945220357 | etot = -9.1333491144997 +680000 ekin = 1.24151057851555 | erot = 1.26358348831348 | epot = -11.6384431811757 | etot = -9.13334911434665 +681000 ekin = 1.24810791985181 | erot = 1.2399896630051 | epot = -11.6214466973234 | etot = -9.1333491144665 +682000 ekin = 1.2573808847233 | erot = 1.22073219170823 | epot = -11.6114621910621 | etot = -9.13334911463059 +683000 ekin = 1.2671525486385 | erot = 1.20554909695207 | epot = -11.6060507604014 | etot = -9.13334911481088 +684000 ekin = 1.27521936884053 | erot = 1.19392995256927 | epot = -11.6024984363892 | etot = -9.13334911497939 +685000 ekin = 1.27965818657722 | erot = 1.18525667281445 | epot = -11.5982639744963 | etot = -9.13334911510462 +686000 ekin = 1.27906445706303 | erot = 1.17887846191199 | epot = -11.5912920341667 | etot = -9.13334911519169 +687000 ekin = 1.2726826175371 | erot = 1.17407129022534 | epot = -11.5801030230234 | etot = -9.13334911526098 +688000 ekin = 1.26041914406367 | erot = 1.17007604783822 | epot = -11.5638443071308 | etot = -9.13334911522896 +689000 ekin = 1.24287938495264 | erot = 1.16656725574657 | epot = -11.5427957558574 | etot = -9.1333491151582 +690000 ekin = 1.22118240404667 | erot = 1.16336387131456 | epot = -11.5178953904217 | etot = -9.13334911506044 +691000 ekin = 1.1967986722508 | erot = 1.16037339233334 | epot = -11.4905211795314 | etot = -9.1333491149473 +692000 ekin = 1.17139142555375 | erot = 1.15758648593269 | epot = -11.4623270263152 | etot = -9.13334911482871 +693000 ekin = 1.14685376597224 | erot = 1.15519232867544 | epot = -11.4353952091894 | etot = -9.13334911454167 +694000 ekin = 1.12537035278714 | erot = 1.15368599836412 | epot = -11.4124054656051 | etot = -9.13334911445381 +695000 ekin = 1.10824764597523 | erot = 1.15324052660646 | epot = -11.394837286965 | etot = -9.13334911438336 +696000 ekin = 1.09641524899192 | erot = 1.15407441364768 | epot = -11.3838387769754 | etot = -9.13334911433576 +697000 ekin = 1.09040706959839 | erot = 1.15645735234543 | epot = -11.3802135362623 | etot = -9.13334911431848 +698000 ekin = 1.09030542376286 | erot = 1.16063392710773 | epot = -11.3842884652002 | etot = -9.1333491143296 +699000 ekin = 1.09552536142002 | erot = 1.1666963994192 | epot = -11.3955708752025 | etot = -9.13334911436329 +700000 ekin = 1.1052737980322 | erot = 1.17478862116005 | epot = -11.4134115336292 | etot = -9.13334911443695 +701000 ekin = 1.11851271408142 | erot = 1.1849247094831 | epot = -11.4367865380899 | etot = -9.13334911452537 +702000 ekin = 1.13395549372733 | erot = 1.1969466725183 | epot = -11.4642512808767 | etot = -9.13334911463104 +703000 ekin = 1.15018285433259 | erot = 1.21057055971515 | epot = -11.4941025287932 | etot = -9.1333491147455 +704000 ekin = 1.16576673457825 | erot = 1.22535908060284 | epot = -11.5244749300396 | etot = -9.13334911485848 +705000 ekin = 1.17938915503441 | erot = 1.24076765314222 | epot = -11.5535059231357 | etot = -9.13334911495904 +706000 ekin = 1.18994261306284 | erot = 1.25622348494784 | epot = -11.5795152130472 | etot = -9.13334911503652 +707000 ekin = 1.19660107195477 | erot = 1.271227802675 | epot = -11.601177989712 | etot = -9.13334911508227 +708000 ekin = 1.19885615186669 | erot = 1.28546332267847 | epot = -11.617668589636 | etot = -9.13334911509088 +709000 ekin = 1.19651981509465 | erot = 1.29888532038639 | epot = -11.628754250542 | etot = -9.13334911506097 +710000 ekin = 1.1896995749713 | erot = 1.31177606554571 | epot = -11.6348247555125 | etot = -9.13334911499551 +711000 ekin = 1.1787538760285 | erot = 1.32474791483293 | epot = -11.6368509057635 | etot = -9.13334911490209 +712000 ekin = 1.16423391783903 | erot = 1.3386894522939 | epot = -11.6362724849244 | etot = -9.13334911479145 +713000 ekin = 1.14681758773111 | erot = 1.35466305350948 | epot = -11.6348297559194 | etot = -9.13334911467886 +714000 ekin = 1.1272417359068 | erot = 1.37373509014029 | epot = -11.6343259406256 | etot = -9.13334911457847 +715000 ekin = 1.10624050749987 | erot = 1.39681075797674 | epot = -11.6364003799808 | etot = -9.13334911450423 +716000 ekin = 1.08449847088991 | erot = 1.42446438144424 | epot = -11.6423119668015 | etot = -9.13334911446732 +717000 ekin = 1.06262586730289 | erot = 1.45678801962933 | epot = -11.6527630014069 | etot = -9.13334911447464 +718000 ekin = 1.04116056517779 | erot = 1.49328580498838 | epot = -11.6677954846927 | etot = -9.13334911452649 +719000 ekin = 1.02059756446672 | erot = 1.53283565406445 | epot = -11.6867823331474 | etot = -9.13334911461623 +720000 ekin = 1.00144276091342 | erot = 1.57373478107647 | epot = -11.7085266567203 | etot = -9.13334911473045 +721000 ekin = 0.984282698239534 | erot = 1.61383653730909 | epot = -11.7314683503984 | etot = -9.13334911484977 +722000 ekin = 0.969856334573777 | erot = 1.65076935458572 | epot = -11.7539748041154 | etot = -9.1333491149559 +723000 ekin = 0.959109074095258 | erot = 1.6821909054059 | epot = -11.774649094524 | etot = -9.13334911502286 +724000 ekin = 0.953206498551327 | erot = 1.70610525280051 | epot = -11.7926608663905 | etot = -9.13334911503871 +725000 ekin = 0.953487871457424 | erot = 1.72112406445021 | epot = -11.8079610509069 | etot = -9.13334911499926 +726000 ekin = 0.961348420447325 | erot = 1.72664218756103 | epot = -11.8213397229212 | etot = -9.13334911491282 +727000 ekin = 0.978055186997788 | erot = 1.7229032003249 | epot = -11.8343075021199 | etot = -9.13334911479722 +728000 ekin = 1.00452582497494 | erot = 1.71095374106883 | epot = -11.8488286807179 | etot = -9.13334911467413 +729000 ekin = 1.04110137579694 | erot = 1.69252215340574 | epot = -11.8669726437725 | etot = -9.13334911456981 +730000 ekin = 1.08735958690082 | erot = 1.66981008957716 | epot = -11.8905187909853 | etot = -9.13334911450737 +731000 ekin = 1.14200418374795 | erot = 1.64524141705747 | epot = -11.92059471531 | etot = -9.13334911450463 +732000 ekin = 1.20285318013947 | erot = 1.6211909571287 | epot = -11.9573932518406 | etot = -9.13334911457241 +733000 ekin = 1.26692596391162 | erot = 1.5997652890967 | epot = -12.0000403677124 | etot = -9.13334911470405 +734000 ekin = 1.33064406417666 | erot = 1.58254289880322 | epot = -12.0465360778896 | etot = -9.13334911490977 +735000 ekin = 1.39013484388142 | erot = 1.57032898633065 | epot = -12.0938129453729 | etot = -9.13334911516086 +736000 ekin = 1.4415750913924 | erot = 1.56317476788441 | epot = -12.1380989747062 | etot = -9.13334911542938 +737000 ekin = 1.4815784558939 | erot = 1.56044545881345 | epot = -12.1753730303861 | etot = -9.13334911567875 +738000 ekin = 1.50757504377756 | erot = 1.56100911666917 | epot = -12.2019332763167 | etot = -9.13334911586997 +739000 ekin = 1.51813561812094 | erot = 1.56352092529369 | epot = -12.2150056593822 | etot = -9.13334911596754 +740000 ekin = 1.51318914849053 | erot = 1.56675183784939 | epot = -12.213290102287 | etot = -9.13334911594711 +741000 ekin = 1.49408865829905 | erot = 1.56989906103909 | epot = -12.1973368351391 | etot = -9.13334911580091 +742000 ekin = 1.46350061535481 | erot = 1.57280025700558 | epot = -12.1696499879032 | etot = -9.13334911554281 +743000 ekin = 1.42512524133773 | erot = 1.57593310600599 | epot = -12.1344074625124 | etot = -9.13334911516871 +744000 ekin = 1.38338487585256 | erot = 1.58054361278157 | epot = -12.0972776034327 | etot = -9.13334911479862 +745000 ekin = 1.34281951274 | erot = 1.58823582840464 | epot = -12.0644044556012 | etot = -9.13334911445656 +746000 ekin = 1.30747334765452 | erot = 1.60047096980675 | epot = -12.0412934316601 | etot = -9.13334911419886 +747000 ekin = 1.28046646005585 | erot = 1.61821768665649 | epot = -12.0320332608062 | etot = -9.1333491140939 +748000 ekin = 1.26367955923824 | erot = 1.64132893143325 | epot = -12.0383576048425 | etot = -9.13334911417101 +749000 ekin = 1.25742934420247 | erot = 1.66831440024385 | epot = -12.0590928588851 | etot = -9.1333491144388 +750000 ekin = 1.26047795508088 | erot = 1.69628448614714 | epot = -12.0901115560798 | etot = -9.1333491148518 +751000 ekin = 1.27026186447405 | erot = 1.72133386885978 | epot = -12.1249448486747 | etot = -9.13334911534087 +752000 ekin = 1.28339547086619 | erot = 1.73919075505813 | epot = -12.1559353417341 | etot = -9.13334911580981 +753000 ekin = 1.29635957466858 | erot = 1.74596876191937 | epot = -12.1756774528081 | etot = -9.13334911622012 +754000 ekin = 1.305991587411 | erot = 1.73885024063304 | epot = -12.1781909444331 | etot = -9.13334911638902 +755000 ekin = 1.31024888116247 | erot = 1.71683511468109 | epot = -12.1604331121857 | etot = -9.13334911634218 +756000 ekin = 1.30846938321578 | erot = 1.68097972249515 | epot = -12.1227982218035 | etot = -9.13334911609258 +757000 ekin = 1.30124985041401 | erot = 1.63419006476408 | epot = -12.0687890308681 | etot = -9.13334911569 +758000 ekin = 1.29019641090511 | erot = 1.58073563388873 | epot = -12.004281159999 | etot = -9.13334911520514 +759000 ekin = 1.27761222227597 | erot = 1.52554636406335 | epot = -11.9365077010389 | etot = -9.13334911469955 +760000 ekin = 1.26609069506725 | erot = 1.47348693038405 | epot = -11.872926739711 | etot = -9.13334911425972 +761000 ekin = 1.25808964011594 | erot = 1.42869550462338 | epot = -11.8201342586639 | etot = -9.13334911392455 +762000 ekin = 1.25572222200511 | erot = 1.39407442311129 | epot = -11.783145758866 | etot = -9.13334911374965 +763000 ekin = 1.26054534569688 | erot = 1.37090045943945 | epot = -11.7647949188328 | etot = -9.1333491136965 +764000 ekin = 1.27353435439888 | erot = 1.35887199086076 | epot = -11.7657554590522 | etot = -9.13334911379256 +765000 ekin = 1.29496682599825 | erot = 1.35616457697877 | epot = -11.7844805169708 | etot = -9.13334911399382 +766000 ekin = 1.32454629042115 | erot = 1.35977679502513 | epot = -11.8176721997104 | etot = -9.13334911426407 +767000 ekin = 1.36163954271771 | erot = 1.36618632223442 | epot = -11.861174979508 | etot = -9.13334911455588 +768000 ekin = 1.40531019892517 | erot = 1.37181010082903 | epot = -11.9104694145842 | etot = -9.13334911482995 +769000 ekin = 1.4544651286899 | erot = 1.37353498050634 | epot = -11.9613492242376 | etot = -9.1333491150414 +770000 ekin = 1.50793050152265 | erot = 1.36921125649153 | epot = -12.0104908732514 | etot = -9.1333491152372 +771000 ekin = 1.56389616693309 | erot = 1.35775090660432 | epot = -12.0549961887964 | etot = -9.13334911525901 +772000 ekin = 1.62113703504511 | erot = 1.3397032350436 | epot = -12.0941893852785 | etot = -9.13334911518981 +773000 ekin = 1.67872851569553 | erot = 1.31702982988342 | epot = -12.1291074606422 | etot = -9.13334911506325 +774000 ekin = 1.7356925710885 | erot = 1.29264163249809 | epot = -12.1616833185099 | etot = -9.13334911492332 +775000 ekin = 1.79085656133578 | erot = 1.26988000051448 | epot = -12.1940856766627 | etot = -9.13334911481246 +776000 ekin = 1.84276100468205 | erot = 1.25197534037568 | epot = -12.2280854598173 | etot = -9.13334911475961 +777000 ekin = 1.88967118603722 | erot = 1.24159765891101 | epot = -12.2646179597212 | etot = -9.13334911477299 +778000 ekin = 1.92971622260643 | erot = 1.24057583214232 | epot = -12.3036411695905 | etot = -9.1333491148417 +779000 ekin = 1.96113164254841 | erot = 1.24980912493202 | epot = -12.3442898824219 | etot = -9.13334911494147 +780000 ekin = 1.98254203386216 | erot = 1.26932045666817 | epot = -12.385211605575 | etot = -9.13334911504462 +781000 ekin = 1.99321406405672 | erot = 1.29840823518498 | epot = -12.4249714143722 | etot = -9.13334911513049 +782000 ekin = 1.99321095940753 | erot = 1.33580885492049 | epot = -12.4623689295169 | etot = -9.13334911518889 +783000 ekin = 1.98342491293452 | erot = 1.37983642298362 | epot = -12.4966104511367 | etot = -9.13334911521853 +784000 ekin = 1.96551238429987 | erot = 1.42849371621254 | epot = -12.5273552156832 | etot = -9.1333491151708 +785000 ekin = 1.94195910112018 | erot = 1.47961348821827 | epot = -12.5549217045005 | etot = -9.1333491151621 +786000 ekin = 1.91549982326101 | erot = 1.53087711626749 | epot = -12.5797260546654 | etot = -9.13334911513693 +787000 ekin = 1.88902915933146 | erot = 1.57997565975786 | epot = -12.6023539341832 | etot = -9.13334911509392 +788000 ekin = 1.86553746554079 | erot = 1.62478646025308 | epot = -12.6236730408322 | etot = -9.13334911503829 +789000 ekin = 1.84793067284234 | erot = 1.66350572426619 | epot = -12.6447855120735 | etot = -9.13334911496502 +790000 ekin = 1.83884831412187 | erot = 1.69477325871876 | epot = -12.6669706877359 | etot = -9.13334911489531 +791000 ekin = 1.84038435201513 | erot = 1.71768127848726 | epot = -12.6914147453586 | etot = -9.13334911485621 +792000 ekin = 1.85374621231265 | erot = 1.73169683790606 | epot = -12.7187921650974 | etot = -9.13334911487869 +793000 ekin = 1.87892178729741 | erot = 1.73653576924417 | epot = -12.7488066715284 | etot = -9.13334911498679 +794000 ekin = 1.91440510045496 | erot = 1.73204169928189 | epot = -12.7797959149166 | etot = -9.13334911517973 +795000 ekin = 1.95726697872503 | erot = 1.71818976217653 | epot = -12.8088058563231 | etot = -9.13334911542157 +796000 ekin = 2.0036085177973 | erot = 1.6952533545941 | epot = -12.8322109880401 | etot = -9.13334911564871 +797000 ekin = 2.04914358120449 | erot = 1.66405946742086 | epot = -12.8465521644162 | etot = -9.13334911579087 +798000 ekin = 2.08995546227467 | erot = 1.62623745952773 | epot = -12.849542037606 | etot = -9.13334911580362 +799000 ekin = 2.12309292251187 | erot = 1.58427028116486 | epot = -12.8407123193644 | etot = -9.13334911568768 +800000 ekin = 2.14682990847441 | erot = 1.5412613855955 | epot = -12.8214404095528 | etot = -9.13334911548289 +801000 ekin = 2.16058282772631 | erot = 1.50048202047263 | epot = -12.7944139634459 | etot = -9.13334911524694 +802000 ekin = 2.16461511109248 | erot = 1.46486615503018 | epot = -12.7628303811541 | etot = -9.13334911503146 +803000 ekin = 2.15969104316299 | erot = 1.436613354422 | epot = -12.7296535124545 | etot = -9.13334911486954 +804000 ekin = 2.14679128687703 | erot = 1.41698988508254 | epot = -12.6971302867198 | etot = -9.1333491147602 +805000 ekin = 2.12692065943749 | erot = 1.40638520514779 | epot = -12.6666549793107 | etot = -9.1333491147254 +806000 ekin = 2.10099028263278 | erot = 1.40422932574972 | epot = -12.6385687231443 | etot = -9.1333491147618 +807000 ekin = 2.06982763841615 | erot = 1.40909451158558 | epot = -12.612271264841 | etot = -9.13334911483923 +808000 ekin = 2.03419092297578 | erot = 1.41919422166642 | epot = -12.5867342595721 | etot = -9.13334911492987 +809000 ekin = 1.99478586655788 | erot = 1.43238858340864 | epot = -12.5605235650204 | etot = -9.13334911505391 +810000 ekin = 1.95230744546468 | erot = 1.44625258192789 | epot = -12.531909142569 | etot = -9.13334911517639 +811000 ekin = 1.90747094188594 | erot = 1.45847148723389 | epot = -12.4992915444039 | etot = -9.13334911528412 +812000 ekin = 1.86102893102468 | erot = 1.46703963548491 | epot = -12.461417681874 | etot = -9.13334911536441 +813000 ekin = 1.81416432243396 | erot = 1.47049868907499 | epot = -12.4180121266462 | etot = -9.13334911513727 +814000 ekin = 1.76902926167497 | erot = 1.46826739311181 | epot = -12.3706457700733 | etot = -9.13334911528648 +815000 ekin = 1.71533069952261 | erot = 1.45797598424312 | epot = -12.3066557947912 | etot = -9.13334911102542 +816000 ekin = 1.68468183703031 | erot = 1.4393594201938 | epot = -12.2573903676328 | etot = -9.13334911040871 +817000 ekin = 1.67569540451555 | erot = 1.4202275919316 | epot = -12.2292721045969 | etot = -9.1333491081497 +818000 ekin = 1.65431804078353 | erot = 1.40071144600215 | epot = -12.1883785945476 | etot = -9.13334910776196 +819000 ekin = 1.63740188371294 | erot = 1.38256931717014 | epot = -12.1533203082699 | etot = -9.13334910738683 +820000 ekin = 1.62512170450313 | erot = 1.36928168853244 | epot = -12.1277525000606 | etot = -9.13334910702506 +821000 ekin = 1.61915909097285 | erot = 1.36404110716291 | epot = -12.1165493048444 | etot = -9.13334910670864 +822000 ekin = 1.6217234397592 | erot = 1.36925913748176 | epot = -12.1243316837597 | etot = -9.13334910651875 +823000 ekin = 1.63427494812447 | erot = 1.38616632191162 | epot = -12.1537903765462 | etot = -9.13334910651009 +824000 ekin = 1.6569838261775 | erot = 1.41459711185629 | epot = -12.2049300447278 | etot = -9.13334910669403 +825000 ekin = 1.68854753273286 | erot = 1.45301631841967 | epot = -12.274912958192 | etot = -9.13334910703944 +826000 ekin = 1.72638863495672 | erot = 1.49875661579725 | epot = -12.3584943582431 | etot = -9.13334910748916 +827000 ekin = 1.76710423380397 | erot = 1.54839439234335 | epot = -12.4488477341246 | etot = -9.13334910797724 +828000 ekin = 1.80698482333775 | erot = 1.59818184901415 | epot = -12.5385157807975 | etot = -9.13334910844559 +829000 ekin = 1.84246939970021 | erot = 1.64447465718115 | epot = -12.6202931657278 | etot = -9.13334910884642 +830000 ekin = 1.87048980343534 | erot = 1.6841293343913 | epot = -12.6879682469682 | etot = -9.1333491091416 +831000 ekin = 1.88871335828166 | erot = 1.71486645418171 | epot = -12.7369289217645 | etot = -9.13334910930117 +832000 ekin = 1.89569916792162 | erot = 1.73558694752007 | epot = -12.7646352247477 | etot = -9.13334910930601 +833000 ekin = 1.89096344935954 | erot = 1.74659447552026 | epot = -12.7709070340352 | etot = -9.13334910915537 +834000 ekin = 1.87493429545157 | erot = 1.74964392180517 | epot = -12.7579273261474 | etot = -9.13334910889062 +835000 ekin = 1.84878280514366 | erot = 1.74762027308112 | epot = -12.7297521867504 | etot = -9.13334910852562 +836000 ekin = 1.81414476909689 | erot = 1.74421722088709 | epot = -12.6917110981255 | etot = -9.13334910814155 +837000 ekin = 1.77277875467446 | erot = 1.74335285139409 | epot = -12.6494807138737 | etot = -9.13334910780514 +838000 ekin = 1.72624445531579 | erot = 1.74841404792436 | epot = -12.608007610808 | etot = -9.13334910756784 +839000 ekin = 1.67568816110983 | erot = 1.76165550554219 | epot = -12.5706927741085 | etot = -9.13334910745645 +840000 ekin = 1.62179135099634 | erot = 1.78387657045585 | epot = -12.5390170289096 | etot = -9.13334910745744 +841000 ekin = 1.56488441151472 | erot = 1.81456573942431 | epot = -12.5127992584783 | etot = -9.13334910753923 +842000 ekin = 1.50517399563221 | erot = 1.8520564586452 | epot = -12.490579561976 | etot = -9.13334910769857 +843000 ekin = 1.44300548284182 | erot = 1.89358112521869 | epot = -12.4699357158682 | etot = -9.1333491078077 +844000 ekin = 1.37906620631093 | erot = 1.93639685185858 | epot = -12.4488121660417 | etot = -9.13334910787217 +845000 ekin = 1.31446352833354 | erot = 1.97812996435952 | epot = -12.4259426005654 | etot = -9.13334910787236 +846000 ekin = 1.25068692329396 | erot = 2.01700234953182 | epot = -12.4010383806301 | etot = -9.13334910780431 +847000 ekin = 1.18947724707884 | erot = 2.05204320491269 | epot = -12.374869559668 | etot = -9.13334910767643 +848000 ekin = 1.13265732504607 | erot = 2.0831473327768 | epot = -12.3491537653283 | etot = -9.13334910750544 +849000 ekin = 1.0819765776984 | erot = 2.11099249694196 | epot = -12.326318181951 | etot = -9.13334910731063 +850000 ekin = 1.03899924537856 | erot = 2.13684654284089 | epot = -12.3091948953332 | etot = -9.13334910711374 +851000 ekin = 1.00503792489494 | erot = 2.16230618698725 | epot = -12.3006932188177 | etot = -9.13334910693551 +852000 ekin = 0.981116857869898 | erot = 2.18901371772944 | epot = -12.303479682393 | etot = -9.13334910679369 +853000 ekin = 0.967947652221222 | erot = 2.21839549971848 | epot = -12.3196922586439 | etot = -9.13334910670417 +854000 ekin = 0.965908910686802 | erot = 2.25145766400248 | epot = -12.3507156813638 | etot = -9.13334910667455 +855000 ekin = 0.975031148290994 | erot = 2.28866143867577 | epot = -12.3970416936738 | etot = -9.13334910670709 +856000 ekin = 0.994993726116945 | erot = 2.32988587265759 | epot = -12.4582287055722 | etot = -9.13334910679762 +857000 ekin = 1.02514000045915 | erot = 2.37447147763714 | epot = -12.5329605850328 | etot = -9.13334910693653 +858000 ekin = 1.06451194043047 | erot = 2.42132581263365 | epot = -12.6191868601752 | etot = -9.13334910711109 +859000 ekin = 1.11189872921075 | erot = 2.46906217646551 | epot = -12.714310012985 | etot = -9.1333491073087 +860000 ekin = 1.16588800432665 | erot = 2.51613734357055 | epot = -12.8153744554171 | etot = -9.13334910751989 +861000 ekin = 1.22490604809667 | erot = 2.56095681693176 | epot = -12.9192119727686 | etot = -9.13334910774017 +862000 ekin = 1.28723632580447 | erot = 2.60192847236029 | epot = -13.022513906136 | etot = -9.13334910797121 +863000 ekin = 1.35101431938041 | erot = 2.63746581474908 | epot = -13.1218292423466 | etot = -9.13334910821708 +864000 ekin = 1.41420820518429 | erot = 2.66596355874352 | epot = -13.2135208724088 | etot = -9.13334910848103 +865000 ekin = 1.47460562928546 | erot = 2.68578195464374 | epot = -13.2937366926903 | etot = -9.13334910876114 +866000 ekin = 1.5298330372055 | erot = 2.69527584727798 | epot = -13.3584579935299 | etot = -9.13334910904638 +867000 ekin = 1.57743376516636 | erot = 2.69288933097043 | epot = -13.4036722054528 | etot = -9.13334910931604 +868000 ekin = 1.61502389037206 | erot = 2.67731200501669 | epot = -13.4256850049295 | etot = -9.13334910954074 +869000 ekin = 1.64053051308178 | erot = 2.64766625528912 | epot = -13.421545878058 | etot = -9.13334910968713 +870000 ekin = 1.65249590025136 | erot = 2.60367561917437 | epot = -13.38952062915 | etot = -9.13334910972428 +871000 ekin = 1.65040511754078 | erot = 2.54576053415582 | epot = -13.329514761328 | etot = -9.1333491096314 +872000 ekin = 1.63497077371293 | erot = 2.47502461264468 | epot = -13.2433444957612 | etot = -9.13334910940362 +873000 ekin = 1.6082955108688 | erot = 2.39312864672026 | epot = -13.1347732666444 | etot = -9.13334910905533 +874000 ekin = 1.57383856498408 | erot = 2.30208675137097 | epot = -13.0092744249747 | etot = -9.13334910861963 +875000 ekin = 1.53613967513203 | erot = 2.20404109165622 | epot = -12.8735298749335 | etot = -9.13334910814528 +876000 ekin = 1.50030007472214 | erot = 2.10106901469196 | epot = -12.7347181971036 | etot = -9.13334910768948 +877000 ekin = 1.47128183650777 | erot = 1.99505592487523 | epot = -12.5996868686917 | etot = -9.13334910730873 +878000 ekin = 1.45315269235532 | erot = 1.88764504254126 | epot = -12.4741468419429 | etot = -9.13334910704632 +879000 ekin = 1.44845009593015 | erot = 1.78026193725074 | epot = -12.3620611401013 | etot = -9.13334910692044 +880000 ekin = 1.4578339719455 | erot = 1.67420503622086 | epot = -12.2653881150852 | etot = -9.13334910691887 +881000 ekin = 1.48012455416734 | erot = 1.57078382964406 | epot = -12.184257490814 | etot = -9.13334910700256 +882000 ekin = 1.51270015736882 | erot = 1.47147015192399 | epot = -12.1175194164123 | etot = -9.13334910711945 +883000 ekin = 1.5521156829147 | erot = 1.37801244882999 | epot = -12.0634772389667 | etot = -9.13334910722205 +884000 ekin = 1.59475301549298 | erot = 1.29246300162939 | epot = -12.0205651244028 | etot = -9.13334910728044 +885000 ekin = 1.63734681491783 | erot = 1.21709221485172 | epot = -11.9877881370549 | etot = -9.13334910728538 +886000 ekin = 1.67731211299644 | erot = 1.15420415260496 | epot = -11.9648653728463 | etot = -9.13334910724494 +887000 ekin = 1.71288068345002 | erot = 1.10590165063891 | epot = -11.9521314412646 | etot = -9.13334910717564 +888000 ekin = 1.74309500656368 | erot = 1.07385834531183 | epot = -11.9503024589727 | etot = -9.13334910709715 +889000 ekin = 1.76770969090686 | erot = 1.05913784424623 | epot = -11.9601966421816 | etot = -9.13334910702852 +890000 ekin = 1.7870324099566 | erot = 1.06207375035493 | epot = -11.9824552673 | etot = -9.13334910698845 +891000 ekin = 1.80172329224281 | erot = 1.08220747466598 | epot = -12.0172798739023 | etot = -9.13334910699346 +892000 ekin = 1.81257293682221 | erot = 1.1182805801851 | epot = -12.064202624064 | etot = -9.13334910705668 +893000 ekin = 1.82028982711125 | erot = 1.1682876962526 | epot = -12.1219266305453 | etot = -9.13334910718146 +894000 ekin = 1.82533649727985 | erot = 1.22960280171713 | epot = -12.1882884063585 | etot = -9.13334910736153 +895000 ekin = 1.82785071659378 | erot = 1.29918775471206 | epot = -12.2603875788826 | etot = -9.13334910757676 +896000 ekin = 1.82766966747854 | erot = 1.37387583336296 | epot = -12.334894608639 | etot = -9.13334910779752 +897000 ekin = 1.82444603808238 | erot = 1.45069893543995 | epot = -12.4084940815129 | etot = -9.13334910799056 +898000 ekin = 1.81781661005979 | erot = 1.52720356356028 | epot = -12.4783692817479 | etot = -9.1333491081278 +899000 ekin = 1.80756915109739 | erot = 1.60168843028089 | epot = -12.5426066895719 | etot = -9.1333491081936 +900000 ekin = 1.79375843956086 | erot = 1.67330364930568 | epot = -12.6004111970559 | etot = -9.13334910818937 +901000 ekin = 1.77674318476137 | erot = 1.74197941464808 | epot = -12.652071707542 | etot = -9.13334910813253 +902000 ekin = 1.75714245728773 | erot = 1.80819394407498 | epot = -12.6986855094148 | etot = -9.13334910805206 +903000 ekin = 1.73573344441431 | erot = 1.87263325990667 | epot = -12.741715812301 | etot = -9.13334910798001 +904000 ekin = 1.7133262590842 | erot = 1.93582474192346 | epot = -12.7825001089509 | etot = -9.13334910794324 +905000 ekin = 1.69065428570201 | erot = 1.9978324843968 | epot = -12.8218358780553 | etot = -9.13334910795651 +906000 ekin = 1.66831072855916 | erot = 2.05808381417767 | epot = -12.8597436507574 | etot = -9.13334910802061 +907000 ekin = 1.64674588303716 | erot = 2.11535919821792 | epot = -12.8954541893759 | etot = -9.13334910812081 +908000 ekin = 1.62631907113886 | erot = 2.16793324010528 | epot = -12.9276014194796 | etot = -9.13334910823546 +909000 ekin = 1.60738004100335 | erot = 2.2138158198134 | epot = -12.9545449691584 | etot = -9.13334910834161 +910000 ekin = 1.5903440249144 | erot = 2.25102295599297 | epot = -12.9747160893297 | etot = -9.13334910842234 +911000 ekin = 1.57572782711049 | erot = 2.27781488081455 | epot = -12.9868918163941 | etot = -9.13334910846902 +912000 ekin = 1.56413054683393 | erot = 2.29287003003197 | epot = -12.990349685346 | etot = -9.13334910848011 +913000 ekin = 1.55616398737689 | erot = 2.2953998333346 | epot = -12.9849129291698 | etot = -9.13334910845829 +914000 ekin = 1.55235379274254 | erot = 2.28522760386261 | epot = -12.970930505012 | etot = -9.13334910840683 +915000 ekin = 1.5530363607569 | erot = 2.2628450869647 | epot = -12.9492305560514 | etot = -9.13334910832976 +916000 ekin = 1.55827003373003 | erot = 2.22943339360228 | epot = -12.9210525355656 | etot = -9.13334910823328 +917000 ekin = 1.56776924055464 | erot = 2.18681551598354 | epot = -12.8879338646662 | etot = -9.13334910812807 +918000 ekin = 1.58086450735197 | erot = 2.13731406706442 | epot = -12.851527682446 | etot = -9.13334910802957 +919000 ekin = 1.59649190921053 | erot = 2.0835190789399 | epot = -12.8133600961043 | etot = -9.13334910795384 +920000 ekin = 1.61321892883084 | erot = 2.02800735916847 | epot = -12.7745753959125 | etot = -9.1333491079132 +921000 ekin = 1.62931395437238 | erot = 1.97307497751136 | epot = -12.7357380397975 | etot = -9.13334910791373 +922000 ekin = 1.6428610474625 | erot = 1.92053870341511 | epot = -12.6967488588289 | etot = -9.1333491079513 +923000 ekin = 1.65191234390675 | erot = 1.87163759208757 | epot = -12.6568990440089 | etot = -9.13334910801458 +924000 ekin = 1.65466206201082 | erot = 1.82703710614041 | epot = -12.6150482762383 | etot = -9.1333491080871 +925000 ekin = 1.64962158355934 | erot = 1.78691680129246 | epot = -12.5698874930024 | etot = -9.13334910815058 +926000 ekin = 1.63577435705778 | erot = 1.75111283231488 | epot = -12.5202362975603 | etot = -9.13334910818759 +927000 ekin = 1.61269412580857 | erot = 1.71928618608573 | epot = -12.4653294200782 | etot = -9.13334910818394 +928000 ekin = 1.58061327338292 | erot = 1.69109387513529 | epot = -12.4050562566482 | etot = -9.13334910813002 +929000 ekin = 1.54043465718479 | erot = 1.66634444994143 | epot = -12.3401282151476 | etot = -9.13334910802139 +930000 ekin = 1.49368612296849 | erot = 1.64511875929677 | epot = -12.2721539901256 | etot = -9.13334910786036 +931000 ekin = 1.44242020035617 | erot = 1.62783092394369 | epot = -12.2036002319582 | etot = -9.13334910765832 +932000 ekin = 1.38906420477875 | erot = 1.61520048768176 | epot = -12.1376137998968 | etot = -9.13334910743626 +933000 ekin = 1.33622958396202 | erot = 1.60811568410273 | epot = -12.0776943752882 | etot = -9.1333491072235 +934000 ekin = 1.28649486983171 | erot = 1.60739378972841 | epot = -12.0272377666154 | etot = -9.13334910705533 +935000 ekin = 1.24218246525754 | erot = 1.61347919083366 | epot = -11.9890107630562 | etot = -9.13334910696505 +936000 ekin = 1.20515312898325 | erot = 1.62614770365923 | epot = -11.9646499396204 | etot = -9.1333491069779 +937000 ekin = 1.17664231217296 | erot = 1.64429583354639 | epot = -11.9542872528248 | etot = -9.13334910710542 +938000 ekin = 1.15716006421498 | erot = 1.66588444175068 | epot = -11.956393613306 | etot = -9.13334910734034 +939000 ekin = 1.14647171712104 | erot = 1.68810326831473 | epot = -11.9679240930833 | etot = -9.13334910764757 +940000 ekin = 1.14367004082417 | erot = 1.70771457433394 | epot = -11.984733723155 | etot = -9.13334910799694 +941000 ekin = 1.14733884564608 | erot = 1.72149292699552 | epot = -12.0021808809642 | etot = -9.13334910832257 +942000 ekin = 1.15580134681802 | erot = 1.72687300439696 | epot = -12.016023459778 | etot = -9.133349108563 +943000 ekin = 1.16743729514705 | erot = 1.7224993662481 | epot = -12.0232857700608 | etot = -9.13334910866566 +944000 ekin = 1.18103106475781 | erot = 1.70858712463103 | epot = -12.0229672979907 | etot = -9.13334910860188 +945000 ekin = 1.19606804454874 | erot = 1.68696892705953 | epot = -12.0163860799918 | etot = -9.13334910838354 +946000 ekin = 1.21284058110413 | erot = 1.66075870248247 | epot = -12.0069483916594 | etot = -9.13334910807277 +947000 ekin = 1.23222210573009 | erot = 1.63367011138546 | epot = -11.9992413248872 | etot = -9.13334910777163 +948000 ekin = 1.25509690715666 | erot = 1.60916358071022 | epot = -11.9976095954539 | etot = -9.13334910758698 +949000 ekin = 1.28167104220759 | erot = 1.58969080393156 | epot = -12.0047109537196 | etot = -9.13334910758041 +950000 ekin = 1.31105510037976 | erot = 1.57628415674081 | epot = -12.0206883648589 | etot = -9.13334910773835 +951000 ekin = 1.34140314928361 | erot = 1.56859135849568 | epot = -12.0433436157626 | etot = -9.13334910798332 +952000 ekin = 1.37054117668508 | erot = 1.56526000759192 | epot = -12.069150292499 | etot = -9.13334910822196 +953000 ekin = 1.39670348101218 | erot = 1.56444621742546 | epot = -12.0944988068303 | etot = -9.1333491083927 +954000 ekin = 1.41897529237445 | erot = 1.56423287015234 | epot = -12.1165572710095 | etot = -9.13334910848276 +955000 ekin = 1.43729048069951 | erot = 1.56287479953571 | epot = -12.1335143887474 | etot = -9.13334910851214 +956000 ekin = 1.45211066332091 | erot = 1.55892938548475 | epot = -12.1443891573122 | etot = -9.13334910850651 +957000 ekin = 1.4640219062269 | erot = 1.55132217597068 | epot = -12.1486931906817 | etot = -9.13334910848408 +958000 ekin = 1.47342593725198 | erot = 1.53954965712689 | epot = -12.1463247028157 | etot = -9.13334910843678 +959000 ekin = 1.48038578494589 | erot = 1.52394133602205 | epot = -12.1376762293279 | etot = -9.13334910835997 +960000 ekin = 1.48460604033859 | erot = 1.50575363437883 | epot = -12.1237087829637 | etot = -9.13334910824631 +961000 ekin = 1.4854997593599 | erot = 1.48721075412849 | epot = -12.1060596215818 | etot = -9.13334910809345 +962000 ekin = 1.48229853496357 | erot = 1.47141202583616 | epot = -12.0870596687072 | etot = -9.13334910790745 +963000 ekin = 1.47417603272179 | erot = 1.46210240867471 | epot = -12.0696275490992 | etot = -9.13334910770273 +964000 ekin = 1.46036644525135 | erot = 1.46332191688904 | epot = -12.057037469638 | etot = -9.13334910749761 +965000 ekin = 1.4402666218216 | erot = 1.47896324786175 | epot = -12.0525789770021 | etot = -9.13334910731876 +966000 ekin = 1.41351583400846 | erot = 1.51227943251394 | epot = -12.0591443737143 | etot = -9.13334910719188 +967000 ekin = 1.38005134112547 | erot = 1.56539665062183 | epot = -12.0787970988885 | etot = -9.13334910714117 +968000 ekin = 1.34025482725015 | erot = 1.63885686276797 | epot = -12.1124607971955 | etot = -9.13334910717734 +969000 ekin = 1.29476921982091 | erot = 1.73132793710158 | epot = -12.1594462642466 | etot = -9.13334910732407 +970000 ekin = 1.24442005393454 | erot = 1.8397252071199 | epot = -12.2174943685955 | etot = -9.13334910754106 +971000 ekin = 1.19046696427949 | erot = 1.9594309140889 | epot = -12.2832469861657 | etot = -9.13334910779734 +972000 ekin = 1.13463097114298 | erot = 2.08475088502088 | epot = -12.3527309642144 | etot = -9.13334910805052 +973000 ekin = 1.07911059568441 | erot = 2.20953944501593 | epot = -12.4219991489594 | etot = -9.13334910825907 +974000 ekin = 1.02657367042055 | erot = 2.32774347839927 | epot = -12.4876662572453 | etot = -9.13334910842543 +975000 ekin = 0.979977932772385 | erot = 2.43392801404127 | epot = -12.5472550553015 | etot = -9.13334910848787 +976000 ekin = 0.942304887104193 | erot = 2.52399013955623 | epot = -12.5996441351349 | etot = -9.13334910847449 +977000 ekin = 0.916335295710406 | erot = 2.59517570124227 | epot = -12.6448601053644 | etot = -9.13334910841174 +978000 ekin = 0.90431642289583 | erot = 2.64601698757986 | epot = -12.6836825188087 | etot = -9.13334910833299 +979000 ekin = 0.907654941512796 | erot = 2.67612704046034 | epot = -12.7171310902433 | etot = -9.13334910827012 +980000 ekin = 0.926700183439719 | erot = 2.68592744664337 | epot = -12.7459767383288 | etot = -9.1333491082457 +981000 ekin = 0.960659745242588 | erot = 2.67638285527906 | epot = -12.7703917087896 | etot = -9.13334910826798 +982000 ekin = 1.00766017971421 | erot = 2.64879736701492 | epot = -12.7898066550609 | etot = -9.13334910833177 +983000 ekin = 1.06493892794264 | erot = 2.60470505316782 | epot = -12.802993089529 | etot = -9.13334910841856 +984000 ekin = 1.12913508942066 | erot = 2.54586103456236 | epot = -12.8083452324842 | etot = -9.13334910850118 +985000 ekin = 1.19663599745497 | erot = 2.47431116852831 | epot = -12.8042962745336 | etot = -9.13334910855034 +986000 ekin = 1.26393164267455 | erot = 2.39249159639475 | epot = -12.7897723476103 | etot = -9.13334910854103 +987000 ekin = 1.32792910235941 | erot = 2.30329384118403 | epot = -12.7645720520038 | etot = -9.13334910846032 +988000 ekin = 1.38618594051163 | erot = 2.21003704542525 | epot = -12.7295720942475 | etot = -9.13334910831058 +989000 ekin = 1.43703663164537 | erot = 2.11631776637245 | epot = -12.6867035061266 | etot = -9.13334910810878 +990000 ekin = 1.47960743025451 | erot = 2.02574976477645 | epot = -12.6387063029132 | etot = -9.1333491078822 +991000 ekin = 1.51373724651808 | erot = 1.94164272478242 | epot = -12.5887290789621 | etot = -9.13334910766159 +992000 ekin = 1.53983818591944 | erot = 1.86668512517351 | epot = -12.5398724185674 | etot = -9.13334910747449 +993000 ekin = 1.5587349067319 | erot = 1.80268982006318 | epot = -12.4947738341354 | etot = -9.13334910734036 +994000 ekin = 1.5715165151441 | erot = 1.75043914207065 | epot = -12.4553047644837 | etot = -9.13334910726898 +995000 ekin = 1.5794217343562 | erot = 1.7096407947002 | epot = -12.4224116363175 | etot = -9.13334910726107 +996000 ekin = 1.58376261672286 | erot = 1.67898574513777 | epot = -12.3960974691702 | etot = -9.13334910730955 +997000 ekin = 1.58587878575187 | erot = 1.65629050261344 | epot = -12.375518395768 | etot = -9.13334910740269 +998000 ekin = 1.58710748471221 | erot = 1.63870906511927 | epot = -12.3591656573558 | etot = -9.13334910752431 +999000 ekin = 1.58875603199319 | erot = 1.62299637539262 | epot = -12.3451015150442 | etot = -9.13334910765843 +1000000 ekin = 1.59207001214972 | erot = 1.60581739808396 | epot = -12.3312365180166 | etot = -9.13334910778296 + 1000000 0.11793111 -1.2674127 0.034288999 -1.0739167 -1.3883882e-05 64000 +Loop time of 15.7069 on 1 procs for 1000000 steps with 10 atoms + +Performance: 55007.553 tau/day, 63666.149 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.948 | 12.948 | 12.948 | 0.0 | 82.43 +Bond | 0.58409 | 0.58409 | 0.58409 | 0.0 | 3.72 +Neigh | 0.016199 | 0.016199 | 0.016199 | 0.0 | 0.10 +Comm | 0.32752 | 0.32752 | 0.32752 | 0.0 | 2.09 +Output | 0.096494 | 0.096494 | 0.096494 | 0.0 | 0.61 +Modify | 1.4762 | 1.4762 | 1.4762 | 0.0 | 9.40 +Other | | 0.2584 | | | 1.65 + +Nlocal: 10.0000 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37.0000 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7000000 +Ave special neighs/atom = 3.6000000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:15 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 new file mode 100644 index 0000000000..3a44cb7943 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 @@ -0,0 +1,1171 @@ +LAMMPS (2 Jul 2021) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +set atom * mass 3.1575 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.9560004 + ghost atom cutoff = 3.8 + binsize = 1.4780002, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -13.057621953437 | etot = -9.13334913094248 +Per MPI rank memory allocation (min/avg/max) = 8.855 | 8.861 | 8.867 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3488546 0.043092397 -1.1949086 -4.6816211e-05 64000 +1000 ekin = 1.08024346604046 | erot = 2.90873406534668 | epot = -13.1223266626202 | etot = -9.13334913123309 +2000 ekin = 1.05028450914436 | erot = 2.98006324808558 | epot = -13.1636968886591 | etot = -9.13334913142917 +3000 ekin = 1.01964458529397 | erot = 3.02592193798631 | epot = -13.1789156547658 | etot = -9.13334913148549 +4000 ekin = 0.989515033089522 | erot = 3.04428486059471 | epot = -13.1671490250723 | etot = -9.13334913138808 +5000 ekin = 0.961283929687805 | erot = 3.03510855539557 | epot = -13.1297416162282 | etot = -9.13334913114478 +6000 ekin = 0.936412193404224 | erot = 3.00022299571977 | epot = -13.0699843199583 | etot = -9.13334913083427 +7000 ekin = 0.916233699107934 | erot = 2.94277134440163 | epot = -12.9923541739966 | etot = -9.13334913048703 +8000 ekin = 0.901760662506231 | erot = 2.86671228744168 | epot = -12.9018220800865 | etot = -9.13334913013854 +9000 ekin = 0.893571390067841 | erot = 2.77649686780611 | epot = -12.8034173876806 | etot = -9.13334912980665 +10000 ekin = 0.89180568505681 | erot = 2.6768685500674 | epot = -12.7020233645916 | etot = -9.13334912946735 +11000 ekin = 0.896243557993558 | erot = 2.57266042063126 | epot = -12.6022531078195 | etot = -9.13334912919466 +12000 ekin = 0.906416039154792 | erot = 2.46827537271563 | epot = -12.5080405408348 | etot = -9.13334912896439 +13000 ekin = 0.921704091778471 | erot = 2.3676064547084 | epot = -12.4226596752788 | etot = -9.13334912879193 +14000 ekin = 0.941405275130066 | erot = 2.27374941641182 | epot = -12.3485038202329 | etot = -9.13334912869102 +15000 ekin = 0.964770892951772 | erot = 2.18876720165118 | epot = -12.2868872232636 | etot = -9.13334912866064 +16000 ekin = 0.991029016801091 | erot = 2.11380018376647 | epot = -12.2381783292305 | etot = -9.13334912866296 +17000 ekin = 1.01940907375713 | erot = 2.04893605182118 | epot = -12.2016942543555 | etot = -9.13334912877723 +18000 ekin = 1.04917923728266 | erot = 1.99335017578097 | epot = -12.1758785419805 | etot = -9.13334912891687 +19000 ekin = 1.07969247848164 | erot = 1.94569933362964 | epot = -12.1587409411761 | etot = -9.13334912906482 +20000 ekin = 1.11043268152285 | erot = 1.90411175657075 | epot = -12.1478935672812 | etot = -9.13334912918763 +21000 ekin = 1.14104909735581 | erot = 1.8669588297924 | epot = -12.1413570564147 | etot = -9.13334912926644 +22000 ekin = 1.17136821848097 | erot = 1.83313674901893 | epot = -12.137854096792 | etot = -9.13334912929212 +23000 ekin = 1.2013763409769 | erot = 1.80222523558974 | epot = -12.1369507058332 | etot = -9.13334912926651 +24000 ekin = 1.23117249622896 | erot = 1.77451266102185 | epot = -12.1390342864516 | etot = -9.13334912920075 +25000 ekin = 1.2608952664064 | erot = 1.75088411697588 | epot = -12.1451285124969 | etot = -9.13334912911462 +26000 ekin = 1.29063712254627 | erot = 1.732594283795 | epot = -12.1565805353676 | etot = -9.13334912902628 +27000 ekin = 1.32035987087023 | erot = 1.7211406167117 | epot = -12.174849616541 | etot = -9.13334912895908 +28000 ekin = 1.34980460658792 | erot = 1.71795709927852 | epot = -12.2011108348018 | etot = -9.13334912893532 +29000 ekin = 1.37841624051157 | erot = 1.72414013785738 | epot = -12.2359055073442 | etot = -9.13334912897525 +30000 ekin = 1.40529015727349 | erot = 1.74019656639667 | epot = -12.2788358527639 | etot = -9.13334912909375 +31000 ekin = 1.42915801743393 | erot = 1.7658325233695 | epot = -12.3283396701001 | etot = -9.1333491292967 +32000 ekin = 1.44843712560538 | erot = 1.79982181745342 | epot = -12.3816080726341 | etot = -9.13334912957529 +33000 ekin = 1.46136904668678 | erot = 1.84000474140074 | epot = -12.4347229179886 | etot = -9.13334912990108 +34000 ekin = 1.46625940785512 | erot = 1.88346459856618 | epot = -12.4830731366476 | etot = -9.1333491302263 +35000 ekin = 1.46179739484304 | erot = 1.92688889524938 | epot = -12.5220354205853 | etot = -9.1333491304929 +36000 ekin = 1.44738855724073 | erot = 1.96705754746494 | epot = -12.5477952353505 | etot = -9.13334913064482 +37000 ekin = 1.42340054468545 | erot = 2.00129614949923 | epot = -12.5580458249025 | etot = -9.13334913071784 +38000 ekin = 1.39122781542975 | erot = 2.02761655303761 | epot = -12.5521934990548 | etot = -9.13334913058741 +39000 ekin = 1.35313842096811 | erot = 2.04547852103599 | epot = -12.5319660723437 | etot = -9.1333491303396 +40000 ekin = 1.31193587699355 | erot = 2.05554364627555 | epot = -12.5008286533156 | etot = -9.13334913004651 +41000 ekin = 1.27054093924535 | erot = 2.05894429581367 | epot = -12.4628343648332 | etot = -9.13334912977421 +42000 ekin = 1.23161000992317 | erot = 2.05694893255704 | epot = -12.4219080720069 | etot = -9.13334912952669 +43000 ekin = 1.19723969759481 | erot = 2.05085758075655 | epot = -12.3814464076996 | etot = -9.13334912934824 +44000 ekin = 1.16880185863983 | erot = 2.04172238360625 | epot = -12.3438733714904 | etot = -9.13334912924435 +45000 ekin = 1.14690787175701 | erot = 2.03029950061771 | epot = -12.3105565015799 | etot = -9.13334912920518 +46000 ekin = 1.13147919636031 | erot = 2.01712256175374 | epot = -12.2819508873243 | etot = -9.13334912921025 +47000 ekin = 1.12189300492699 | erot = 2.00264798837259 | epot = -12.2578901225351 | etot = -9.13334912923553 +48000 ekin = 1.11716788112702 | erot = 1.98739120721197 | epot = -12.2379082176347 | etot = -9.13334912929566 +49000 ekin = 1.11615794795222 | erot = 1.9718736810838 | epot = -12.221380758335 | etot = -9.13334912929896 +50000 ekin = 1.11772326336371 | erot = 1.95708534394635 | epot = -12.2081577365827 | etot = -9.13334912927264 +51000 ekin = 1.12084924497847 | erot = 1.94437394210229 | epot = -12.1985723162998 | etot = -9.13334912921909 +52000 ekin = 1.12470549785224 | erot = 1.93529800314884 | epot = -12.1933526301511 | etot = -9.13334912915001 +53000 ekin = 1.12864556674948 | erot = 1.93145365271676 | epot = -12.1934483485499 | etot = -9.13334912908363 +54000 ekin = 1.1321611352306 | erot = 1.93430274875519 | epot = -12.1998130130122 | etot = -9.13334912902645 +55000 ekin = 1.13481106600207 | erot = 1.94490436967255 | epot = -12.2130645647024 | etot = -9.13334912902774 +56000 ekin = 1.1361434353579 | erot = 1.963618845908 | epot = -12.2331114103533 | etot = -9.13334912908738 +57000 ekin = 1.13563178311257 | erot = 1.99002978527258 | epot = -12.2590106975988 | etot = -9.13334912921363 +58000 ekin = 1.13263976908222 | erot = 2.02286978616508 | epot = -12.2888586846529 | etot = -9.13334912940556 +59000 ekin = 1.12642426113412 | erot = 2.06004413441716 | epot = -12.3198175252031 | etot = -9.13334912965185 +60000 ekin = 1.11618536041516 | erot = 2.09876774945551 | epot = -12.3483022398007 | etot = -9.13334912993006 +61000 ekin = 1.10116810417853 | erot = 2.13581434618271 | epot = -12.3703315805686 | etot = -9.13334913020733 +62000 ekin = 1.08081637521793 | erot = 2.16786879318301 | epot = -12.3820342988436 | etot = -9.13334913044262 +63000 ekin = 1.05497014428143 | erot = 2.19194503254432 | epot = -12.3802643074578 | etot = -9.13334913063208 +64000 ekin = 1.02408601603155 | erot = 2.20562384873124 | epot = -12.3630589954182 | etot = -9.13334913065538 +65000 ekin = 0.989434415807706 | erot = 2.20769180278651 | epot = -12.3304753491253 | etot = -9.13334913053111 +66000 ekin = 0.95319559356389 | erot = 2.19842250482622 | epot = -12.2849672286541 | etot = -9.13334913026396 +67000 ekin = 0.918366365968281 | erot = 2.17942400884176 | epot = -12.2311395047051 | etot = -9.13334912989503 +68000 ekin = 0.888467814666307 | erot = 2.15321364358195 | epot = -12.1750305877204 | etot = -9.13334912947213 +69000 ekin = 0.867150037001672 | erot = 2.12288633704368 | epot = -12.1233855031211 | etot = -9.13334912907575 +70000 ekin = 0.857579951604792 | erot = 2.09151913845146 | epot = -12.0824482188433 | etot = -9.13334912878707 +71000 ekin = 0.861815425267495 | erot = 2.06157004239555 | epot = -12.0567345963621 | etot = -9.13334912869911 +72000 ekin = 0.880191815685466 | erot = 2.03435275439356 | epot = -12.0478936988734 | etot = -9.13334912879439 +73000 ekin = 0.911201453876645 | erot = 2.00982694750392 | epot = -12.0543775304381 | etot = -9.13334912905759 +74000 ekin = 0.951849895585073 | erot = 1.98685418272615 | epot = -12.0720532077348 | etot = -9.13334912942353 +75000 ekin = 0.998151008641159 | erot = 1.96362530027592 | epot = -12.0951254387265 | etot = -9.13334912980946 +76000 ekin = 1.04581734271582 | erot = 1.93821700241342 | epot = -12.1173834752671 | etot = -9.13334913013786 +77000 ekin = 1.09091996835692 | erot = 1.90910715282271 | epot = -12.1333762515352 | etot = -9.1333491303556 +78000 ekin = 1.13037631927904 | erot = 1.87551578135369 | epot = -12.139241231075 | etot = -9.1333491304423 +79000 ekin = 1.16219588597769 | erot = 1.83750580183243 | epot = -12.1330508182182 | etot = -9.1333491304081 +80000 ekin = 1.18548972632214 | erot = 1.79585942669971 | epot = -12.1146982833061 | etot = -9.13334913028424 +81000 ekin = 1.20030605718935 | erot = 1.7518136593973 | epot = -12.0854688466955 | etot = -9.13334913010885 +82000 ekin = 1.20737786492175 | erot = 1.70676694760203 | epot = -12.0474939424388 | etot = -9.13334912991501 +83000 ekin = 1.2078605140205 | erot = 1.66205278152614 | epot = -12.0032624252715 | etot = -9.13334912972487 +84000 ekin = 1.20310991572453 | erot = 1.61882913247303 | epot = -11.9552881777459 | etot = -9.13334912954831 +85000 ekin = 1.19452073297141 | erot = 1.57808043002402 | epot = -11.9059502923817 | etot = -9.13334912938628 +86000 ekin = 1.18342100682534 | erot = 1.54069268896221 | epot = -11.8574628250233 | etot = -9.13334912923578 +87000 ekin = 1.17100858957321 | erot = 1.50755090689503 | epot = -11.8119086255615 | etot = -9.13334912909331 +88000 ekin = 1.1583137755166 | erot = 1.47961680456705 | epot = -11.7712797090415 | etot = -9.13334912895786 +89000 ekin = 1.1461768281738 | erot = 1.45796378128877 | epot = -11.7374897382936 | etot = -9.13334912883104 +90000 ekin = 1.13523447969403 | erot = 1.44376438030011 | epot = -11.7123479887108 | etot = -9.13334912871663 +91000 ekin = 1.12591345720535 | erot = 1.43823772500934 | epot = -11.6975003108346 | etot = -9.13334912861991 +92000 ekin = 1.11843099489273 | erot = 1.44256930748506 | epot = -11.6943494309245 | etot = -9.1333491285467 +93000 ekin = 1.11280329634805 | erot = 1.45781524814475 | epot = -11.7039676729953 | etot = -9.13334912850246 +94000 ekin = 1.10886209127331 | erot = 1.48480045701869 | epot = -11.7270116767843 | etot = -9.13334912849234 +95000 ekin = 1.10627886010333 | erot = 1.5239622064754 | epot = -11.7635901951108 | etot = -9.13334912853206 +96000 ekin = 1.10459509814417 | erot = 1.57519859223426 | epot = -11.8131428189846 | etot = -9.13334912860619 +97000 ekin = 1.10325943769899 | erot = 1.63800664193805 | epot = -11.8746152083619 | etot = -9.13334912872485 +98000 ekin = 1.1016695958164 | erot = 1.71130689804978 | epot = -11.9463256227541 | etot = -9.13334912888788 +99000 ekin = 1.09921849385157 | erot = 1.79339905630371 | epot = -12.0259666792473 | etot = -9.13334912909204 +100000 ekin = 1.09534596880101 | erot = 1.88196872528582 | epot = -12.1106638234163 | etot = -9.13334912932951 +101000 ekin = 1.08959720755113 | erot = 1.97415616931464 | epot = -12.1971025064522 | etot = -9.13334912958639 +102000 ekin = 1.08168751154811 | erot = 2.06670282185186 | epot = -12.2817394632427 | etot = -9.13334912984268 +103000 ekin = 1.0715693234231 | erot = 2.1561819250807 | epot = -12.3611003785773 | etot = -9.13334913007349 +104000 ekin = 1.0594923799607 | erot = 2.23930158373573 | epot = -12.4321430939486 | etot = -9.13334913025215 +105000 ekin = 1.04604342224877 | erot = 2.3132390228585 | epot = -12.4926315754931 | etot = -9.13334913038584 +106000 ekin = 1.03224316318561 | erot = 2.37579242095983 | epot = -12.5413847145642 | etot = -9.1333491304188 +107000 ekin = 1.01951120148936 | erot = 2.42585603740561 | epot = -12.5787163692802 | etot = -9.13334913038522 +108000 ekin = 1.00875017477215 | erot = 2.46348952984483 | epot = -12.6055888348734 | etot = -9.13334913025643 +109000 ekin = 1.00109573552405 | erot = 2.48980806114955 | epot = -12.6242529267278 | etot = -9.13334913005421 +110000 ekin = 0.997931591358236 | erot = 2.50673918610783 | epot = -12.6380199072775 | etot = -9.13334912981144 +111000 ekin = 1.00076792351335 | erot = 2.51665915373024 | epot = -12.6507762068076 | etot = -9.13334912956397 +112000 ekin = 1.01109610479944 | erot = 2.52200701599634 | epot = -12.6664522501391 | etot = -9.13334912934334 +113000 ekin = 1.03019016817903 | erot = 2.52496101252866 | epot = -12.6885003099863 | etot = -9.13334912927859 +114000 ekin = 1.05821017520648 | erot = 2.52722573627497 | epot = -12.7187850407017 | etot = -9.13334912922025 +115000 ekin = 1.09472530400165 | erot = 2.53003930448809 | epot = -12.7581137377194 | etot = -9.13334912922962 +116000 ekin = 1.13884650903356 | erot = 2.5341483243043 | epot = -12.8063439626439 | etot = -9.13334912930608 +117000 ekin = 1.18909444999508 | erot = 2.53980839277117 | epot = -12.8622519722151 | etot = -9.13334912944883 +118000 ekin = 1.24341490970497 | erot = 2.54678348242622 | epot = -12.9235475217871 | etot = -9.13334912965586 +119000 ekin = 1.29923662064213 | erot = 2.55432909400999 | epot = -12.9869148445733 | etot = -9.13334912992119 +120000 ekin = 1.35358959215664 | erot = 2.56118615921788 | epot = -13.048124881604 | etot = -9.13334913022946 +121000 ekin = 1.40329803815465 | erot = 2.56563135861651 | epot = -13.1022785273257 | etot = -9.13334913055449 +122000 ekin = 1.44524692196623 | erot = 2.5656244840922 | epot = -13.1442205369175 | etot = -9.13334913085908 +123000 ekin = 1.47669540804833 | erot = 2.559063179982 | epot = -13.1691077191312 | etot = -9.13334913110085 +124000 ekin = 1.49558302658158 | erot = 2.54411105943717 | epot = -13.1730432172613 | etot = -9.13334913124258 +125000 ekin = 1.5007612248973 | erot = 2.51952798471307 | epot = -13.1536383408714 | etot = -9.13334913126099 +126000 ekin = 1.49214728684699 | erot = 2.48515933103519 | epot = -13.1106557490374 | etot = -9.1333491311552 +127000 ekin = 1.47053410713936 | erot = 2.4417448007513 | epot = -13.0456280388476 | etot = -9.13334913095689 +128000 ekin = 1.43743445323482 | erot = 2.39059049317554 | epot = -12.9613740770759 | etot = -9.13334913066556 +129000 ekin = 1.39501109707029 | erot = 2.33380120125828 | epot = -12.8621614286436 | etot = -9.13334913031504 +130000 ekin = 1.34584042016727 | erot = 2.27401545397185 | epot = -12.7532050040794 | etot = -9.13334912994024 +131000 ekin = 1.29268930786566 | erot = 2.21410134111234 | epot = -12.6401397785509 | etot = -9.13334912957287 +132000 ekin = 1.23832315616802 | erot = 2.15686384200895 | epot = -12.5285361274155 | etot = -9.13334912923854 +133000 ekin = 1.1853526768118 | erot = 2.10479906741768 | epot = -12.4235008731854 | etot = -9.13334912895591 +134000 ekin = 1.136121555628 | erot = 2.05991346428637 | epot = -12.3293841486506 | etot = -9.13334912873626 +135000 ekin = 1.09263262326044 | erot = 2.02360952444374 | epot = -12.2495912762907 | etot = -9.13334912858652 +136000 ekin = 1.05650575788342 | erot = 1.9966203066869 | epot = -12.1864751930783 | etot = -9.13334912850799 +137000 ekin = 1.02895878679454 | erot = 1.97899212834894 | epot = -12.1413000436437 | etot = -9.13334912850018 +138000 ekin = 1.01080388995847 | erot = 1.97013512172241 | epot = -12.1142881402336 | etot = -9.13334912855268 +139000 ekin = 1.00245459395346 | erot = 1.96888144460882 | epot = -12.1046851672406 | etot = -9.13334912867834 +140000 ekin = 1.00393780740619 | erot = 1.97333010973458 | epot = -12.1106170460031 | etot = -9.13334912886233 +141000 ekin = 1.01490973367033 | erot = 1.98104530944798 | epot = -12.129304172214 | etot = -9.13334912909566 +142000 ekin = 1.03468044934417 | erot = 1.98917872502435 | epot = -12.1572083037339 | etot = -9.13334912936537 +143000 ekin = 1.06225104646174 | erot = 1.99463134790784 | epot = -12.1902315240234 | etot = -9.13334912965385 +144000 ekin = 1.09636709127249 | erot = 1.99441220318397 | epot = -12.2241284243807 | etot = -9.13334912992419 +145000 ekin = 1.13559045362119 | erot = 1.98572590466005 | epot = -12.2546654884645 | etot = -9.13334913018322 +146000 ekin = 1.17838854122087 | erot = 1.96612892354251 | epot = -12.2778665951536 | etot = -9.13334913039023 +147000 ekin = 1.22300699749175 | erot = 1.93405129394969 | epot = -12.290407421963 | etot = -9.13334913052156 +148000 ekin = 1.26785677863012 | erot = 1.88891621350833 | epot = -12.2901221226998 | etot = -9.13334913056131 +149000 ekin = 1.31170551487292 | erot = 1.83123494690858 | epot = -12.2762895922885 | etot = -9.13334913050698 +150000 ekin = 1.3536185809119 | erot = 1.762636075096 | epot = -12.2496037863728 | etot = -9.13334913036486 +151000 ekin = 1.39299848911419 | erot = 1.68572491420596 | epot = -12.2120725334743 | etot = -9.13334913015418 +152000 ekin = 1.42958376961901 | erot = 1.60381549112324 | epot = -12.1667483906421 | etot = -9.13334912989989 +153000 ekin = 1.46340801747584 | erot = 1.52060159601899 | epot = -12.1173587431247 | etot = -9.1333491296299 +154000 ekin = 1.49472650224552 | erot = 1.43981503875257 | epot = -12.067890670369 | etot = -9.13334912937093 +155000 ekin = 1.52392161825071 | erot = 1.364916576832 | epot = -12.0221873242286 | etot = -9.13334912914587 +156000 ekin = 1.55140022159549 | erot = 1.2988497238181 | epot = -11.9835990743858 | etot = -9.13334912897225 +157000 ekin = 1.57749707056582 | erot = 1.24387068637214 | epot = -11.9547168857976 | etot = -9.13334912885968 +158000 ekin = 1.60239506185778 | erot = 1.20145363967807 | epot = -11.9371978303529 | etot = -9.13334912881703 +159000 ekin = 1.62604462003782 | erot = 1.17226436760493 | epot = -11.9316581164853 | etot = -9.13334912884255 +160000 ekin = 1.64813303486544 | erot = 1.15619534708312 | epot = -11.9376775108803 | etot = -9.13334912893177 +161000 ekin = 1.66807327612978 | erot = 1.15245312716188 | epot = -11.9538755323666 | etot = -9.13334912907489 +162000 ekin = 1.68501875283056 | erot = 1.15969471512802 | epot = -11.9780625972164 | etot = -9.13334912925781 +163000 ekin = 1.69790620824675 | erot = 1.176209891261 | epot = -12.0074652289697 | etot = -9.13334912946192 +164000 ekin = 1.70552711798396 | erot = 1.20014309389824 | epot = -12.0390193415471 | etot = -9.13334912966488 +165000 ekin = 1.70662691809348 | erot = 1.22974121417714 | epot = -12.069717262113 | etot = -9.1333491298424 +166000 ekin = 1.70002908026848 | erot = 1.26360423252402 | epot = -12.0969824427635 | etot = -9.13334912997104 +167000 ekin = 1.68477683955882 | erot = 1.30090518403754 | epot = -12.119031153627 | etot = -9.13334913003062 +168000 ekin = 1.66027923283184 | erot = 1.34154370359062 | epot = -12.1351720664311 | etot = -9.13334913000864 +169000 ekin = 1.62644124957725 | erot = 1.38619810991383 | epot = -12.1459884893943 | etot = -9.13334912990326 +170000 ekin = 1.58375251890772 | erot = 1.43625221626178 | epot = -12.153353864895 | etot = -9.13334912972554 +171000 ekin = 1.53331003043924 | erot = 1.49359459893396 | epot = -12.1602537588724 | etot = -9.13334912949918 +172000 ekin = 1.476761061614 | erot = 1.56031583407033 | epot = -12.1704260249402 | etot = -9.13334912925584 +173000 ekin = 1.41695754705525 | erot = 1.63848249765407 | epot = -12.1887891730447 | etot = -9.13334912833541 +174000 ekin = 1.35937684304481 | erot = 1.72968793645238 | epot = -12.2224139078255 | etot = -9.13334912832827 +175000 ekin = 1.3053754081881 | erot = 1.83369980102265 | epot = -12.2724243375756 | etot = -9.13334912836484 +176000 ekin = 1.25571357800303 | erot = 1.94952726339955 | epot = -12.3385899698493 | etot = -9.13334912844669 +177000 ekin = 1.21104692225311 | erot = 2.07558802224398 | epot = -12.4199840730644 | etot = -9.13334912856735 +178000 ekin = 1.17189512057037 | erot = 2.20976079574657 | epot = -12.5150050450644 | etot = -9.13334912874749 +179000 ekin = 1.13864315857372 | erot = 2.34949890132906 | epot = -12.6214911888119 | etot = -9.13334912890909 +180000 ekin = 1.11156621835596 | erot = 2.49234008540024 | epot = -12.737255432825 | etot = -9.1333491290688 +181000 ekin = 1.09087167613587 | erot = 2.63567357536161 | epot = -12.8598943807503 | etot = -9.13334912925281 +182000 ekin = 1.07675226579842 | erot = 2.77693577183354 | epot = -12.9870371670197 | etot = -9.13334912938778 +183000 ekin = 1.06942294234152 | erot = 2.91405263083466 | epot = -13.1168247026767 | etot = -9.13334912950054 +184000 ekin = 1.06913488705838 | erot = 3.04520163111684 | epot = -13.2476856477707 | etot = -9.13334912959545 +185000 ekin = 1.07614345922789 | erot = 3.16875772929948 | epot = -13.378250318213 | etot = -9.13334912968562 +186000 ekin = 1.09060563376747 | erot = 3.28317984154881 | epot = -13.5071346051107 | etot = -9.13334912979441 +187000 ekin = 1.11239929858146 | erot = 3.38683780589114 | epot = -13.6325862344249 | etot = -9.13334912995233 +188000 ekin = 1.14088837562638 | erot = 3.47780595660538 | epot = -13.7520434624201 | etot = -9.13334913018836 +189000 ekin = 1.17469755695842 | erot = 3.55369218298273 | epot = -13.8617388704573 | etot = -9.13334913051617 +190000 ekin = 1.2115896198333 | erot = 3.61161008256096 | epot = -13.9565488333134 | etot = -9.13334913091917 +191000 ekin = 1.24837558083714 | erot = 3.64780345127574 | epot = -14.0295281634887 | etot = -9.13334913137586 +192000 ekin = 1.28102311682943 | erot = 3.65810395429009 | epot = -14.0724762027876 | etot = -9.13334913166806 +193000 ekin = 1.30598320816959 | erot = 3.64139295006505 | epot = -14.0807252900252 | etot = -9.13334913179052 +194000 ekin = 1.32049648836597 | erot = 3.59844552363042 | epot = -14.0522911436923 | etot = -9.13334913169586 +195000 ekin = 1.32298604774247 | erot = 3.5321292813495 | epot = -13.9884644604292 | etot = -9.1333491313372 +196000 ekin = 1.31323645162539 | erot = 3.44751612705309 | epot = -13.8941017095232 | etot = -9.13334913084476 +197000 ekin = 1.29228934698113 | erot = 3.350723403225 | epot = -13.7763618804987 | etot = -9.13334913029261 +198000 ekin = 1.26212633786599 | erot = 3.24789114381998 | epot = -13.643366611423 | etot = -9.13334912973699 +199000 ekin = 1.22527047461683 | erot = 3.14483705467214 | epot = -13.5034566585631 | etot = -9.13334912927412 +200000 ekin = 1.18441799207204 | erot = 3.04594245963003 | epot = -13.3637095806218 | etot = -9.13334912891969 +201000 ekin = 1.14216630511914 | erot = 2.95390025492363 | epot = -13.2294156887272 | etot = -9.1333491286844 +202000 ekin = 1.10084220211718 | erot = 2.86987712396353 | epot = -13.1040684546434 | etot = -9.13334912856272 +203000 ekin = 1.06240856568988 | erot = 2.79366067226835 | epot = -12.9894183664997 | etot = -9.13334912854149 +204000 ekin = 1.02841768821199 | erot = 2.72389144275511 | epot = -12.885658259572 | etot = -9.13334912860488 +205000 ekin = 0.999988405220592 | erot = 2.65832732458309 | epot = -12.7916648585389 | etot = -9.13334912873525 +206000 ekin = 0.977799621225001 | erot = 2.59412391514179 | epot = -12.7052726652798 | etot = -9.13334912891299 +207000 ekin = 0.962105653965304 | erot = 2.528137921261 | epot = -12.6235927043398 | etot = -9.1333491291135 +208000 ekin = 0.952783648018777 | erot = 2.45726642892286 | epot = -12.5433992062486 | etot = -9.133349129307 +209000 ekin = 0.949416945748481 | erot = 2.37882137049687 | epot = -12.4615874457066 | etot = -9.13334912946124 +210000 ekin = 0.951402263215182 | erot = 2.29090939419182 | epot = -12.3756607869542 | etot = -9.13334912954718 +211000 ekin = 0.958051952077585 | erot = 2.19275562021841 | epot = -12.2841567018437 | etot = -9.13334912954766 +212000 ekin = 0.968659667700472 | erot = 2.08489619855782 | epot = -12.1869049957197 | etot = -9.13334912946136 +213000 ekin = 0.982515908119962 | erot = 1.9691842228096 | epot = -12.0850492602323 | etot = -9.13334912930278 +214000 ekin = 0.998888701919759 | erot = 1.84860041861888 | epot = -11.9808382496354 | etot = -9.13334912909675 +215000 ekin = 1.01700134912568 | erot = 1.72690897492139 | epot = -11.877259452919 | etot = -9.13334912887197 +216000 ekin = 1.03603050122452 | erot = 1.60822693577792 | epot = -11.7776065656583 | etot = -9.13334912865589 +217000 ekin = 1.05512477228468 | erot = 1.49657917533765 | epot = -11.6850530760948 | etot = -9.13334912847249 +218000 ekin = 1.07342860744181 | erot = 1.39550092670151 | epot = -11.6022786624835 | etot = -9.13334912834018 +219000 ekin = 1.09009860355571 | erot = 1.30773521951529 | epot = -11.5311829513408 | etot = -9.13334912826979 +220000 ekin = 1.10431207607343 | erot = 1.23505496062862 | epot = -11.4727161649657 | etot = -9.13334912826362 +221000 ekin = 1.11527717993037 | erot = 1.17821867809227 | epot = -11.4268449863377 | etot = -9.13334912831507 +222000 ekin = 1.12225437592962 | erot = 1.13704823944124 | epot = -11.3926517437815 | etot = -9.1333491284106 +223000 ekin = 1.12459297621399 | erot = 1.11060060825087 | epot = -11.3685427129972 | etot = -9.13334912853233 +224000 ekin = 1.12177911879604 | erot = 1.09739625543906 | epot = -11.3525245028961 | etot = -9.133349128661 +225000 ekin = 1.11348637905741 | erot = 1.09566402531915 | epot = -11.3424995331559 | etot = -9.13334912877937 +226000 ekin = 1.09961800000693 | erot = 1.10360909760929 | epot = -11.3365762264852 | etot = -9.13334912886903 +227000 ekin = 1.08033165066208 | erot = 1.11952730043394 | epot = -11.333208080032 | etot = -9.13334912893602 +228000 ekin = 1.05604602872772 | erot = 1.14187865421848 | epot = -11.3312738119171 | etot = -9.13334912897095 +229000 ekin = 1.027424186635 | erot = 1.16938489301662 | epot = -11.3301582086286 | etot = -9.13334912897701 +230000 ekin = 0.995339184991533 | erot = 1.201020481986 | epot = -11.3297087959369 | etot = -9.13334912895939 +231000 ekin = 0.960829492708657 | erot = 1.23597735762286 | epot = -11.3301559792544 | etot = -9.13334912892285 +232000 ekin = 0.92505043273521 | erot = 1.27360958612367 | epot = -11.3320091477353 | etot = -9.13334912887644 +233000 ekin = 0.889225435959709 | erot = 1.31337910210612 | epot = -11.3359536668892 | etot = -9.13334912882337 +234000 ekin = 0.854600006628674 | erot = 1.35483402381901 | epot = -11.3427831592147 | etot = -9.133349128767 +235000 ekin = 0.822390924845149 | erot = 1.39757430015815 | epot = -11.3533143537193 | etot = -9.13334912871597 +236000 ekin = 0.793732848711787 | erot = 1.44121433399046 | epot = -11.3682963113762 | etot = -9.13334912867398 +237000 ekin = 0.769632191219387 | erot = 1.48535644446045 | epot = -11.3883377643264 | etot = -9.13334912864658 +238000 ekin = 0.750918993365987 | erot = 1.52956143549191 | epot = -11.4138295574957 | etot = -9.13334912863784 +239000 ekin = 0.738206267497149 | erot = 1.5733336116213 | epot = -11.4448890077678 | etot = -9.13334912864934 +240000 ekin = 0.731862193743969 | erot = 1.61613149974206 | epot = -11.4813428221655 | etot = -9.13334912867947 +241000 ekin = 0.73199932800202 | erot = 1.65741090456841 | epot = -11.5227593612935 | etot = -9.13334912872305 +242000 ekin = 0.738482620157313 | erot = 1.69669130986291 | epot = -11.5685230587942 | etot = -9.13334912877397 +243000 ekin = 0.750955042325396 | erot = 1.7336492948231 | epot = -11.6179534659684 | etot = -9.13334912881989 +244000 ekin = 0.768877080466636 | erot = 1.7682236027561 | epot = -11.6704498120772 | etot = -9.13334912885446 +245000 ekin = 0.791573929294678 | erot = 1.80068045121315 | epot = -11.7256035093796 | etot = -9.13334912887177 +246000 ekin = 0.81828291427161 | erot = 1.8316410744518 | epot = -11.7832731175944 | etot = -9.13334912887095 +247000 ekin = 0.848193621601761 | erot = 1.8620509655525 | epot = -11.8435937160104 | etot = -9.13334912885613 +248000 ekin = 0.880474358635575 | erot = 1.89308546777806 | epot = -11.9069089552504 | etot = -9.13334912883675 +249000 ekin = 0.914280881219353 | erot = 1.92599713223906 | epot = -11.9736271422846 | etot = -9.13334912882621 +250000 ekin = 0.948746730716563 | erot = 1.96192054843754 | epot = -12.0440164079946 | etot = -9.13334912884045 +251000 ekin = 0.982959063854421 | erot = 2.00165977259934 | epot = -12.117967965349 | etot = -9.13334912889524 +252000 ekin = 1.01592948249861 | erot = 2.04549252396402 | epot = -12.1947711354641 | etot = -9.13334912900142 +253000 ekin = 1.04657777483986 | erot = 2.09303441305998 | epot = -12.2729613170601 | etot = -9.13334912916028 +254000 ekin = 1.07373541755075 | erot = 2.14319803018483 | epot = -12.350282577099 | etot = -9.1333491293634 +255000 ekin = 1.09620163163022 | erot = 2.19430966720576 | epot = -12.423860428418 | etot = -9.13334912958205 +256000 ekin = 1.1128720642814 | erot = 2.24438579427459 | epot = -12.4906069883393 | etot = -9.13334912978327 +257000 ekin = 1.12287782510611 | erot = 2.29146665865421 | epot = -12.5476936136922 | etot = -9.13334912993191 +258000 ekin = 1.12572293500246 | erot = 2.33396623628273 | epot = -12.5930383012897 | etot = -9.13334913000448 +259000 ekin = 1.12139026023621 | erot = 2.37095948468543 | epot = -12.6256988749109 | etot = -9.13334912998925 +260000 ekin = 1.11036122819302 | erot = 2.40229658115372 | epot = -12.6460069392473 | etot = -9.13334912990051 +261000 ekin = 1.09354805445053 | erot = 2.42847877902901 | epot = -12.6553759632422 | etot = -9.13334912976261 +262000 ekin = 1.07216031825766 | erot = 2.45046938603004 | epot = -12.655978833892 | etot = -9.13334912960435 +263000 ekin = 1.04754368718277 | erot = 2.46943297797168 | epot = -12.6503257946116 | etot = -9.13334912945713 +264000 ekin = 1.02102495133818 | erot = 2.4864784463712 | epot = -12.64085252705 | etot = -9.1333491293406 +265000 ekin = 0.99378878344356 | erot = 2.5024706313637 | epot = -12.6296085440765 | etot = -9.13334912926926 +266000 ekin = 0.966800247929908 | erot = 2.51790683904988 | epot = -12.61805621623 | etot = -9.13334912925017 +267000 ekin = 0.940784249459268 | erot = 2.53283827184786 | epot = -12.6069716505894 | etot = -9.13334912928228 +268000 ekin = 0.916272152394494 | erot = 2.54684612152474 | epot = -12.5964674032729 | etot = -9.13334912935369 +269000 ekin = 0.89372217247737 | erot = 2.55907244306913 | epot = -12.5861437450345 | etot = -9.13334912948799 +270000 ekin = 0.87370928512903 | erot = 2.56799722891172 | epot = -12.5750556436016 | etot = -9.13334912956089 +271000 ekin = 0.857156433251639 | erot = 2.57226369508294 | epot = -12.5627692579077 | etot = -9.13334912957308 +272000 ekin = 0.845541083724111 | erot = 2.5709611090938 | epot = -12.5498513223264 | etot = -9.13334912950853 +273000 ekin = 0.840983736969857 | erot = 2.56364270819288 | epot = -12.5379755745172 | etot = -9.13334912935446 +274000 ekin = 0.846103061110646 | erot = 2.55054497183486 | epot = -12.5299971620892 | etot = -9.13334912914368 +275000 ekin = 0.863570741245198 | erot = 2.53260377850931 | epot = -12.5295236486809 | etot = -9.13334912892642 +276000 ekin = 0.895419299415623 | erot = 2.51114645014646 | epot = -12.5399148783702 | etot = -9.13334912880815 +277000 ekin = 0.942302359419293 | erot = 2.48734970425548 | epot = -12.563001192512 | etot = -9.13334912883719 +278000 ekin = 1.00299069941652 | erot = 2.46199112036275 | epot = -12.5983309488097 | etot = -9.13334912903046 +279000 ekin = 1.07434561589334 | erot = 2.43529774590631 | epot = -12.6429924911399 | etot = -9.13334912934022 +280000 ekin = 1.15182340984115 | erot = 2.40711596365384 | epot = -12.6922885031804 | etot = -9.13334912968536 +281000 ekin = 1.23030856581906 | erot = 2.37726964751099 | epot = -12.7409273433239 | etot = -9.13334912999385 +282000 ekin = 1.30483974879861 | erot = 2.34551973870636 | epot = -12.7837086176988 | etot = -9.13334913019381 +283000 ekin = 1.37151257999533 | erot = 2.31231452819746 | epot = -12.8171762384381 | etot = -9.13334913024529 +284000 ekin = 1.42789685319471 | erot = 2.27901843146069 | epot = -12.8402644148115 | etot = -9.13334913015614 +285000 ekin = 1.47299679574546 | erot = 2.24762833985691 | epot = -12.8539742655639 | etot = -9.13334912996152 +286000 ekin = 1.50701906587772 | erot = 2.22050056283213 | epot = -12.8608687584216 | etot = -9.13334912971172 +287000 ekin = 1.53099472144828 | erot = 2.19999584806399 | epot = -12.8643396989721 | etot = -9.13334912945983 +288000 ekin = 1.54636449768928 | erot = 2.18811490987408 | epot = -12.867828536815 | etot = -9.13334912925162 +289000 ekin = 1.55461163491245 | erot = 2.18618804174281 | epot = -12.8741488057737 | etot = -9.13334912911842 +290000 ekin = 1.55699428674702 | erot = 2.19466879450533 | epot = -12.885012210327 | etot = -9.13334912907464 +291000 ekin = 1.55439775255665 | erot = 2.21306131817934 | epot = -12.9008081998537 | etot = -9.13334912911775 +292000 ekin = 1.54729960240266 | erot = 2.2399831442194 | epot = -12.9206318758542 | etot = -9.13334912923217 +293000 ekin = 1.53582108608398 | erot = 2.27333490842332 | epot = -12.9425051239027 | etot = -9.13334912939539 +294000 ekin = 1.51982864506158 | erot = 2.31049721096826 | epot = -12.9636749856261 | etot = -9.1333491295963 +295000 ekin = 1.49905154213301 | erot = 2.34851873983899 | epot = -12.9809194117664 | etot = -9.13334912979436 +296000 ekin = 1.47319364802762 | erot = 2.38443281021029 | epot = -12.9909755882216 | etot = -9.1333491299837 +297000 ekin = 1.44203124545927 | erot = 2.41536854589898 | epot = -12.9907489215093 | etot = -9.13334913015106 +298000 ekin = 1.40549976702035 | erot = 2.43867409046045 | epot = -12.9775229877645 | etot = -9.1333491302837 +299000 ekin = 1.36377241662742 | erot = 2.45204871800392 | epot = -12.9491702649994 | etot = -9.13334913036807 +300000 ekin = 1.3173271191209 | erot = 2.45368408092518 | epot = -12.904360330438 | etot = -9.13334913039193 +301000 ekin = 1.26699022414646 | erot = 2.44240353914543 | epot = -12.8427428936391 | etot = -9.13334913034725 +302000 ekin = 1.21394210637081 | erot = 2.41777278592915 | epot = -12.7650640225325 | etot = -9.13334913023257 +303000 ekin = 1.15967414429252 | erot = 2.38015189683622 | epot = -12.673175171184 | etot = -9.13334913005528 +304000 ekin = 1.10589726251214 | erot = 2.33066939618148 | epot = -12.5699157885239 | etot = -9.13334912983026 +305000 ekin = 1.05441504199182 | erot = 2.27111808933713 | epot = -12.4588822609061 | etot = -9.13334912957715 +306000 ekin = 1.00698421397077 | erot = 2.20379218514084 | epot = -12.3441255284277 | etot = -9.13334912931605 +307000 ekin = 0.965188337626888 | erot = 2.13129764385469 | epot = -12.2298351105458 | etot = -9.1333491290642 +308000 ekin = 0.930345631943897 | erot = 2.05636814615661 | epot = -12.1200629069343 | etot = -9.13334912883379 +309000 ekin = 0.903461768092468 | erot = 1.98167791132994 | epot = -12.0184888080557 | etot = -9.13334912863331 +310000 ekin = 0.885228515007583 | erot = 1.90967870211724 | epot = -11.9282563455905 | etot = -9.13334912846572 +311000 ekin = 0.876047647700123 | erot = 1.84263812610218 | epot = -11.8520349021355 | etot = -9.1333491283332 +312000 ekin = 0.876068182198715 | erot = 1.78248869457073 | epot = -11.7919060050089 | etot = -9.1333491282394 +313000 ekin = 0.885223985969676 | erot = 1.73072892882416 | epot = -11.749302042984 | etot = -9.13334912819014 +314000 ekin = 0.903258342514934 | erot = 1.68832066988553 | epot = -11.724928140593 | etot = -9.13334912819258 +315000 ekin = 0.929731391718292 | erot = 1.65558558099914 | epot = -11.7186661009715 | etot = -9.13334912825407 +316000 ekin = 0.964013828970557 | erot = 1.63211973509223 | epot = -11.7294826924421 | etot = -9.13334912837931 +317000 ekin = 1.00527629211667 | erot = 1.61675326466648 | epot = -11.7553786853505 | etot = -9.13334912856736 +318000 ekin = 1.05248736450128 | erot = 1.6075857094073 | epot = -11.7934222027177 | etot = -9.13334912880913 +319000 ekin = 1.10443332868131 | erot = 1.60212494474658 | epot = -11.8399074025131 | etot = -9.13334912908516 +320000 ekin = 1.15976924920824 | erot = 1.59754526105528 | epot = -11.8906636396291 | etot = -9.13334912936554 +321000 ekin = 1.21710352305667 | erot = 1.59105554518265 | epot = -11.9415081978536 | etot = -9.1333491296143 +322000 ekin = 1.2751075118946 | erot = 1.58033324923157 | epot = -11.9887898909214 | etot = -9.13334912979523 +323000 ekin = 1.33263084645693 | erot = 1.56394390937382 | epot = -12.0299238857114 | etot = -9.13334912988067 +324000 ekin = 1.3887959071219 | erot = 1.54164678485252 | epot = -12.0637918218343 | etot = -9.13334912985991 +325000 ekin = 1.4430462367968 | erot = 1.51450056885254 | epot = -12.0908959353913 | etot = -9.13334912974193 +326000 ekin = 1.49513435445647 | erot = 1.48473073066021 | epot = -12.1132142146706 | etot = -9.13334912955392 +327000 ekin = 1.54505065938307 | erot = 1.45538400860302 | epot = -12.1337837973213 | etot = -9.13334912933518 +328000 ekin = 1.59290981434211 | erot = 1.42984788209296 | epot = -12.1561068255636 | etot = -9.13334912912848 +329000 ekin = 1.6388186097558 | erot = 1.41133335467746 | epot = -12.1835010934061 | etot = -9.1333491289728 +330000 ekin = 1.6827489618305 | erot = 1.40240729591298 | epot = -12.2185053866417 | etot = -9.13334912889822 +331000 ekin = 1.72443467169521 | erot = 1.40463116341981 | epot = -12.2624149640393 | etot = -9.13334912892428 +332000 ekin = 1.76330533674286 | erot = 1.41833479327414 | epot = -12.3149892590744 | etot = -9.13334912905745 +333000 ekin = 1.79846823309252 | erot = 1.44253834966185 | epot = -12.3743557120445 | etot = -9.13334912929011 +334000 ekin = 1.8287490059107 | erot = 1.47503277033816 | epot = -12.4371309058477 | etot = -9.13334912959887 +335000 ekin = 1.85279616115795 | erot = 1.51263570197463 | epot = -12.4987809930765 | etot = -9.13334912994388 +336000 ekin = 1.8692763055875 | erot = 1.55160162438115 | epot = -12.5542270602387 | etot = -9.13334913027 +337000 ekin = 1.87711735413911 | erot = 1.58820049773275 | epot = -12.5986669823878 | etot = -9.1333491305159 +338000 ekin = 1.87574840923148 | erot = 1.61938868722871 | epot = -12.6284862270852 | etot = -9.13334913062505 +339000 ekin = 1.86534866362706 | erot = 1.64338736517787 | epot = -12.6420851593668 | etot = -9.13334913056187 +340000 ekin = 1.84695798886985 | erot = 1.66009075059703 | epot = -12.6403978697904 | etot = -9.13334913032354 +341000 ekin = 1.82243969076648 | erot = 1.67114820362537 | epot = -12.6269370243338 | etot = -9.13334912994199 +342000 ekin = 1.79428655955884 | erot = 1.67969211618856 | epot = -12.6073278052239 | etot = -9.13334912947647 +343000 ekin = 1.76531632972554 | erot = 1.68978090506835 | epot = -12.588446363791 | etot = -9.13334912899712 +344000 ekin = 1.73833039739303 | erot = 1.70570000746982 | epot = -12.5773795334337 | etot = -9.13334912857081 +345000 ekin = 1.71580589060296 | erot = 1.73127559556315 | epot = -12.5804306144157 | etot = -9.13334912824961 +346000 ekin = 1.69966353097621 | erot = 1.76931234934753 | epot = -12.6023250083918 | etot = -9.13334912806805 +347000 ekin = 1.69112042623312 | erot = 1.82120184302293 | epot = -12.6456713973011 | etot = -9.13334912804505 +348000 ekin = 1.69061396982785 | erot = 1.88669704033651 | epot = -12.7106601383518 | etot = -9.13334912818742 +349000 ekin = 1.69777681788225 | erot = 1.9638292686625 | epot = -12.7949552150365 | etot = -9.13334912849176 +350000 ekin = 1.7114511501027 | erot = 2.04895591402613 | epot = -12.8937561930722 | etot = -9.1333491289434 +351000 ekin = 1.72974629646184 | erot = 2.13695636910572 | epot = -13.0000517950785 | etot = -9.13334912951095 +352000 ekin = 1.75015893903934 | erot = 2.2216200845667 | epot = -13.1051281537469 | etot = -9.13334913014089 +353000 ekin = 1.7697803490554 | erot = 2.29627029646019 | epot = -13.199399776273 | etot = -9.1333491307574 +354000 ekin = 1.78560210911933 | erot = 2.35462017023432 | epot = -13.2735714106214 | etot = -9.13334913126776 +355000 ekin = 1.79489785472807 | erot = 2.39176336004151 | epot = -13.320010346352 | etot = -9.13334913158243 +356000 ekin = 1.79561393246548 | erot = 2.40509186859473 | epot = -13.3340549327002 | etot = -9.13334913163996 +357000 ekin = 1.78667091072583 | erot = 2.3948761413485 | epot = -13.3148961835033 | etot = -9.13334913142896 +358000 ekin = 1.76810167230458 | erot = 2.36429897994071 | epot = -13.2657497831709 | etot = -9.13334913092556 +359000 ekin = 1.74170569044632 | erot = 2.31907684809542 | epot = -13.1941316689276 | etot = -9.13334913038585 +360000 ekin = 1.70943632676121 | erot = 2.26611368397199 | epot = -13.1088991405408 | etot = -9.13334912980763 +361000 ekin = 1.67315005965374 | erot = 2.21234166615766 | epot = -13.0188408550985 | etot = -9.13334912928712 +362000 ekin = 1.63480994001495 | erot = 2.1637688737988 | epot = -12.9319279427063 | etot = -9.13334912889251 +363000 ekin = 1.59622606057464 | erot = 2.12469986683822 | epot = -12.8542750560708 | etot = -9.13334912865792 +364000 ekin = 1.55890205833711 | erot = 2.09734631559854 | epot = -12.789597502522 | etot = -9.13334912858635 +365000 ekin = 1.52397421076708 | erot = 2.08181308416768 | epot = -12.7391364235921 | etot = -9.13334912865734 +366000 ekin = 1.49221260733957 | erot = 2.07639009796262 | epot = -12.7019518341362 | etot = -9.13334912883398 +367000 ekin = 1.46405952364913 | erot = 2.07805510122222 | epot = -12.6754637539446 | etot = -9.13334912907327 +368000 ekin = 1.4396772693236 | erot = 2.08307216057651 | epot = -12.6560985592346 | etot = -9.13334912933452 +369000 ekin = 1.4189901081147 | erot = 2.08756917147321 | epot = -12.6399084091739 | etot = -9.13334912958597 +370000 ekin = 1.40171557356763 | erot = 2.08800173652916 | epot = -12.6230664399032 | etot = -9.1333491298064 +371000 ekin = 1.38739280854876 | erot = 2.08146226240655 | epot = -12.6022042009382 | etot = -9.13334912998285 +372000 ekin = 1.37542340308599 | erot = 2.06585193702345 | epot = -12.5746244702146 | etot = -9.13334913010515 +373000 ekin = 1.36513752357922 | erot = 2.03996886737141 | epot = -12.5384555211136 | etot = -9.13334913016301 +374000 ekin = 1.35583949105178 | erot = 2.00351975772439 | epot = -12.4927083789467 | etot = -9.1333491301705 +375000 ekin = 1.34694157711448 | erot = 1.95716038268523 | epot = -12.4374510898687 | etot = -9.133349130069 +376000 ekin = 1.33814968105251 | erot = 1.90258032253295 | epot = -12.3740791334836 | etot = -9.13334912989819 +377000 ekin = 1.32936261120791 | erot = 1.8422726572518 | epot = -12.3049843981374 | etot = -9.13334912967769 +378000 ekin = 1.3206315999133 | erot = 1.77926043318984 | epot = -12.2332411625432 | etot = -9.13334912944002 +379000 ekin = 1.31208340368839 | erot = 1.71672941783581 | epot = -12.1621619507412 | etot = -9.13334912921698 +380000 ekin = 1.30384179784195 | erot = 1.65764204155733 | epot = -12.0948329684337 | etot = -9.13334912903439 +381000 ekin = 1.2965791747582 | erot = 1.60487100826636 | epot = -12.0347993118453 | etot = -9.13334912882077 +382000 ekin = 1.29092190134689 | erot = 1.56061067707034 | epot = -11.9848817072435 | etot = -9.1333491288263 +383000 ekin = 1.28620909068431 | erot = 1.52536833769959 | epot = -11.9449265572238 | etot = -9.13334912883987 +384000 ekin = 1.28205683099651 | erot = 1.4992280616878 | epot = -11.914634021517 | etot = -9.13334912883267 +385000 ekin = 1.27850478017905 | erot = 1.4821618914478 | epot = -11.8940158004154 | etot = -9.13334912878854 +386000 ekin = 1.27603762174048 | erot = 1.47423730492973 | epot = -11.8836240553815 | etot = -9.13334912871131 +387000 ekin = 1.27548287271979 | erot = 1.47565716104701 | epot = -11.8844891623916 | etot = -9.13334912862484 +388000 ekin = 1.2778004458587 | erot = 1.4866096409739 | epot = -11.8977592154001 | etot = -9.1333491285675 +389000 ekin = 1.28381262703675 | erot = 1.50697425852375 | epot = -11.9241360141402 | etot = -9.13334912857974 +390000 ekin = 1.29393930260966 | erot = 1.53598035068215 | epot = -11.9632687819878 | etot = -9.13334912869599 +391000 ekin = 1.3080007445623 | erot = 1.57190984924413 | epot = -12.0132597227366 | etot = -9.13334912893016 +392000 ekin = 1.32513099179581 | erot = 1.61197584867668 | epot = -12.0704559697456 | etot = -9.13334912927313 +393000 ekin = 1.3438254300028 | erot = 1.65241448883335 | epot = -12.1295890485272 | etot = -9.13334912969108 +394000 ekin = 1.36212102398765 | erot = 1.68881012624681 | epot = -12.1842802803645 | etot = -9.13334913013003 +395000 ekin = 1.37788072140428 | erot = 1.71661593053968 | epot = -12.2278457824692 | etot = -9.13334913052525 +396000 ekin = 1.38913154512495 | erot = 1.73181112618257 | epot = -12.2542918021061 | etot = -9.1333491307986 +397000 ekin = 1.39439357479808 | erot = 1.73153617598979 | epot = -12.2592788817216 | etot = -9.13334913093374 +398000 ekin = 1.39293904659231 | erot = 1.71441550438671 | epot = -12.2407036818562 | etot = -9.13334913087719 +399000 ekin = 1.38493174777457 | erot = 1.680947663508 | epot = -12.1992285419457 | etot = -9.1333491306631 +400000 ekin = 1.37142116074094 | erot = 1.63330764197803 | epot = -12.1380779330257 | etot = -9.13334913030669 +401000 ekin = 1.35412991252425 | erot = 1.57501044311623 | epot = -12.062489485534 | etot = -9.13334912989352 +402000 ekin = 1.3351799185687 | erot = 1.51048364979967 | epot = -11.979012697774 | etot = -9.13334912940564 +403000 ekin = 1.31709653187235 | erot = 1.44458891478846 | epot = -11.8950345756004 | etot = -9.13334912893958 +404000 ekin = 1.30234590493842 | erot = 1.38198365576689 | epot = -11.8176786892416 | etot = -9.13334912853627 +405000 ekin = 1.29301391716245 | erot = 1.32673455588811 | epot = -11.7530976012896 | etot = -9.13334912823905 +406000 ekin = 1.29065467462772 | erot = 1.2820411643635 | epot = -11.7060449670181 | etot = -9.13334912802684 +407000 ekin = 1.2964323729479 | erot = 1.25006436588412 | epot = -11.6798458667523 | etot = -9.13334912792027 +408000 ekin = 1.31094700615256 | erot = 1.2319098672154 | epot = -11.6762060012851 | etot = -9.13334912791717 +409000 ekin = 1.33422438303383 | erot = 1.22763489752287 | epot = -11.6952084085727 | etot = -9.13334912801602 +410000 ekin = 1.36572014154981 | erot = 1.23628017302536 | epot = -11.7353494427884 | etot = -9.13334912821327 +411000 ekin = 1.40432668760791 | erot = 1.25592548503606 | epot = -11.7936013011463 | etot = -9.13334912850236 +412000 ekin = 1.44839088645893 | erot = 1.28379672627876 | epot = -11.8655367416066 | etot = -9.13334912886888 +413000 ekin = 1.49576795241879 | erot = 1.3164603274893 | epot = -11.9455774091926 | etot = -9.13334912928451 +414000 ekin = 1.54394920889486 | erot = 1.35014055217834 | epot = -12.027438890778 | etot = -9.13334912970475 +415000 ekin = 1.59029421705179 | erot = 1.38116660571118 | epot = -12.1048099528345 | etot = -9.13334913007151 +416000 ekin = 1.63235973909122 | erot = 1.40649922749203 | epot = -12.1722080969095 | etot = -9.13334913032622 +417000 ekin = 1.66825800489225 | erot = 1.42422016761049 | epot = -12.2258273029358 | etot = -9.13334913043303 +418000 ekin = 1.69693219837238 | erot = 1.43381449957335 | epot = -12.2640958283212 | etot = -9.13334913037547 +419000 ekin = 1.71824951894782 | erot = 1.43620625779461 | epot = -12.2878049069275 | etot = -9.13334913018508 +420000 ekin = 1.73288337430553 | erot = 1.4335082535061 | epot = -12.2997407577237 | etot = -9.13334912991204 +421000 ekin = 1.74204129532355 | erot = 1.42856028674781 | epot = -12.3039507116824 | etot = -9.13334912961099 +422000 ekin = 1.74713701807683 | erot = 1.42445618730668 | epot = -12.3049423347118 | etot = -9.13334912932833 +423000 ekin = 1.74949063384674 | erot = 1.42413436044253 | epot = -12.3069741233944 | etot = -9.13334912910517 +424000 ekin = 1.7500975464296 | erot = 1.43005641925039 | epot = -12.3135030946277 | etot = -9.13334912894769 +425000 ekin = 1.74947257256668 | erot = 1.44412400802246 | epot = -12.3269457094741 | etot = -9.13334912888491 +426000 ekin = 1.69664946387263 | erot = 1.40011304962393 | epot = -12.230111634597 | etot = -9.13334912110046 +427000 ekin = 1.76448154346123 | erot = 1.46695774970364 | epot = -12.3647884699851 | etot = -9.13334917682027 +428000 ekin = 1.77864040382666 | erot = 1.51204937412276 | epot = -12.4240389057584 | etot = -9.13334912780898 +429000 ekin = 1.77744254090577 | erot = 1.55645173379945 | epot = -12.4672434028109 | etot = -9.13334912810564 +430000 ekin = 1.76864481713832 | erot = 1.60567169371254 | epot = -12.5076656392898 | etot = -9.13334912843893 +431000 ekin = 1.7504144399296 | erot = 1.65655638514225 | epot = -12.5403199538346 | etot = -9.13334912876274 +432000 ekin = 1.72143753020831 | erot = 1.70559294341405 | epot = -12.5603796026451 | etot = -9.13334912902271 +433000 ekin = 1.68129756274101 | erot = 1.74934007551191 | epot = -12.5639867674192 | etot = -9.13334912916631 +434000 ekin = 1.63077650979853 | erot = 1.78490039303337 | epot = -12.549026031988 | etot = -9.13334912915609 +435000 ekin = 1.57198882084381 | erot = 1.81033246556218 | epot = -12.5156704153879 | etot = -9.13334912898188 +436000 ekin = 1.50828072851379 | erot = 1.82489908961103 | epot = -12.4665289467912 | etot = -9.13334912866637 +437000 ekin = 1.44388315301155 | erot = 1.82908776307981 | epot = -12.4063200443511 | etot = -9.13334912825977 +438000 ekin = 1.38337900429669 | erot = 1.82441107452496 | epot = -12.341139206648 | etot = -9.13334912782634 +439000 ekin = 1.33110407576205 | erot = 1.8130669450403 | epot = -12.2775201482284 | etot = -9.13334912742604 +440000 ekin = 1.29061754889013 | erot = 1.79757475508295 | epot = -12.2215414310745 | etot = -9.13334912710145 +441000 ekin = 1.26434687832198 | erot = 1.78048600607314 | epot = -12.1781820112667 | etot = -9.13334912687157 +442000 ekin = 1.2534498503799 | erot = 1.76421040799336 | epot = -12.1510093851086 | etot = -9.13334912673532 +443000 ekin = 1.25787308938493 | erot = 1.75093400476591 | epot = -12.1421562208312 | etot = -9.13334912668041 +444000 ekin = 1.27654491138898 | erot = 1.74256727851903 | epot = -12.1524613166026 | etot = -9.13334912669464 +445000 ekin = 1.30762960642584 | erot = 1.74066161516913 | epot = -12.1816403483655 | etot = -9.1333491267705 +446000 ekin = 1.34878485335343 | erot = 1.74626611356976 | epot = -12.2284000938288 | etot = -9.13334912690563 +447000 ekin = 1.39739993763858 | erot = 1.7597479345797 | epot = -12.2904969993197 | etot = -9.13334912710141 +448000 ekin = 1.45076649191025 | erot = 1.78060717934041 | epot = -12.3647227986042 | etot = -9.13334912735352 +449000 ekin = 1.50623999605478 | erot = 1.80738848344613 | epot = -12.4469776071518 | etot = -9.13334912765089 +450000 ekin = 1.56138908054711 | erot = 1.83773497344263 | epot = -12.532473181962 | etot = -9.13334912797229 +451000 ekin = 1.61412412964626 | erot = 1.86859865234344 | epot = -12.6160719102778 | etot = -9.13334912828812 +452000 ekin = 1.66280931630206 | erot = 1.89658548036298 | epot = -12.6927439252293 | etot = -9.13334912856426 +453000 ekin = 1.70634971637175 | erot = 1.91837476586721 | epot = -12.7580736110117 | etot = -9.13334912877277 +454000 ekin = 1.74423056750446 | erot = 1.93111374790554 | epot = -12.8086934443065 | etot = -9.13334912889654 +455000 ekin = 1.77648988409962 | erot = 1.93270291378094 | epot = -12.8425419268145 | etot = -9.13334912893392 +456000 ekin = 1.80361911556815 | erot = 1.92192628287717 | epot = -12.8588945273429 | etot = -9.13334912889758 +457000 ekin = 1.82640016706293 | erot = 1.89842961389858 | epot = -12.8581789097711 | etot = -9.13334912880958 +458000 ekin = 1.84570455026014 | erot = 1.86259298695662 | epot = -12.8416466659131 | etot = -9.13334912869634 +459000 ekin = 1.86229070171023 | erot = 1.81535342315067 | epot = -12.81099325344 | etot = -9.13334912857905 +460000 ekin = 1.87663848085934 | erot = 1.75803306182718 | epot = -12.7680206711614 | etot = -9.1333491284749 +461000 ekin = 1.88883864523247 | erot = 1.69219746384243 | epot = -12.7143852374653 | etot = -9.13334912839042 +462000 ekin = 1.89856203652347 | erot = 1.61956678027398 | epot = -12.6514779451233 | etot = -9.13334912832583 +463000 ekin = 1.90510221764509 | erot = 1.54196437877821 | epot = -12.5804157247008 | etot = -9.13334912827746 +464000 ekin = 1.90747686786675 | erot = 1.46127993198476 | epot = -12.5021059280876 | etot = -9.13334912823606 +465000 ekin = 1.90457977356165 | erot = 1.3794607009175 | epot = -12.4173896026663 | etot = -9.13334912818713 +466000 ekin = 1.89536572152317 | erot = 1.29851485172186 | epot = -12.3272297013678 | etot = -9.13334912812279 +467000 ekin = 1.8790183170995 | erot = 1.22048659414428 | epot = -12.232854039281 | etot = -9.13334912803722 +468000 ekin = 1.85509917792015 | erot = 1.147391262841 | epot = -12.1358395686905 | etot = -9.1333491279294 +469000 ekin = 1.82366605107261 | erot = 1.08110787535143 | epot = -12.0381230542277 | etot = -9.13334912780364 +470000 ekin = 1.78535216075537 | erot = 1.02324127043735 | epot = -11.9419425588581 | etot = -9.13334912766542 +471000 ekin = 1.74141051513297 | erot = 0.974982090044234 | epot = -11.8497417326976 | etot = -9.13334912752035 +472000 ekin = 1.69372019705842 | erot = 0.937000644455532 | epot = -11.7640699688868 | etot = -9.13334912737288 +473000 ekin = 1.6447363277088 | erot = 0.909402534932388 | epot = -11.6874879898697 | etot = -9.13334912722851 +474000 ekin = 1.59734995177274 | erot = 0.89175501843202 | epot = -11.6224540973017 | etot = -9.13334912709692 +475000 ekin = 1.55462885495176 | erot = 0.883174765260651 | epot = -11.5711527472053 | etot = -9.13334912699285 +476000 ekin = 1.51944866261102 | erot = 0.88245988856996 | epot = -11.5352576781141 | etot = -9.13334912693313 +477000 ekin = 1.4940824352899 | erot = 0.888250161717166 | epot = -11.5156817239363 | etot = -9.13334912692924 +478000 ekin = 1.47985622585605 | erot = 0.899197335532983 | epot = -11.5124026883723 | etot = -9.13334912698329 +479000 ekin = 1.4769537395284 | erot = 0.914115348457546 | epot = -11.5244182150811 | etot = -9.13334912709511 +480000 ekin = 1.48439477575458 | erot = 0.932072516620843 | epot = -11.5498164196191 | etot = -9.13334912724368 +481000 ekin = 1.50022741217527 | erot = 0.952423999184045 | epot = -11.586000538783 | etot = -9.13334912742371 +482000 ekin = 1.52172985963443 | erot = 0.974754211846249 | epot = -11.6298331991085 | etot = -9.13334912762786 +483000 ekin = 1.54567018241522 | erot = 0.998770450814447 | epot = -11.6777897610768 | etot = -9.13334912784716 +484000 ekin = 1.56858614723106 | erot = 1.02419763510823 | epot = -11.7261329104093 | etot = -9.13334912807003 +485000 ekin = 1.58707346955088 | erot = 1.05070585623107 | epot = -11.7711284540628 | etot = -9.1333491282808 +486000 ekin = 1.598071036031 | erot = 1.07788995424652 | epot = -11.8093101187388 | etot = -9.13334912846124 +487000 ekin = 1.59911980804437 | erot = 1.10529931942143 | epot = -11.83776825606 | etot = -9.13334912859421 +488000 ekin = 1.58856342116656 | erot = 1.13249736396192 | epot = -11.8544099137967 | etot = -9.13334912866827 +489000 ekin = 1.56566142904702 | erot = 1.15911683125775 | epot = -11.8581273889848 | etot = -9.13334912867998 +490000 ekin = 1.53060268554657 | erot = 1.18488502427314 | epot = -11.8488368384544 | etot = -9.13334912863472 +491000 ekin = 1.48443427069478 | erot = 1.20959914015972 | epot = -11.8273825393283 | etot = -9.13334912847376 +492000 ekin = 1.4293034535446 | erot = 1.23291829593332 | epot = -11.7955708778633 | etot = -9.13334912838534 +493000 ekin = 1.36749564145159 | erot = 1.25438544605084 | epot = -11.7552302157792 | etot = -9.1333491282768 +494000 ekin = 1.30137262988081 | erot = 1.27348228002541 | epot = -11.7082040380626 | etot = -9.13334912815639 +495000 ekin = 1.23360970817014 | erot = 1.28954660636146 | epot = -11.6565054425603 | etot = -9.13334912802866 +496000 ekin = 1.1637554864094 | erot = 1.3002319560863 | epot = -11.5973366205416 | etot = -9.13334917804587 +497000 ekin = 1.02574644939812 | erot = 1.24927230426314 | epot = -11.4083678755048 | etot = -9.13334912184354 +498000 ekin = 1.13339044616265 | erot = 1.24939677704399 | epot = -11.5161363891156 | etot = -9.13334916590892 +499000 ekin = 1.16434762393176 | erot = 1.25864673154956 | epot = -11.5563434800389 | etot = -9.13334912455754 +500000 ekin = 1.16768486506669 | erot = 1.25769344443893 | epot = -11.5587274345819 | etot = -9.13334912507627 +501000 ekin = 1.1755989549741 | erot = 1.25038915442576 | epot = -11.5593372343042 | etot = -9.13334912490429 +502000 ekin = 1.18926606273772 | erot = 1.23784323633009 | epot = -11.5604584237502 | etot = -9.13334912468237 +503000 ekin = 1.20982408114765 | erot = 1.22204157664294 | epot = -11.5652147822317 | etot = -9.1333491244411 +504000 ekin = 1.23811782736855 | erot = 1.20572865378404 | epot = -11.5771956053581 | etot = -9.1333491242055 +505000 ekin = 1.27460966228592 | erot = 1.19199209322116 | epot = -11.5999508795095 | etot = -9.13334912400242 +506000 ekin = 1.319280478194 | erot = 1.18393687677866 | epot = -11.636566478829 | etot = -9.13334912385632 +507000 ekin = 1.37157700900311 | erot = 1.18435118386577 | epot = -11.6892773166534 | etot = -9.13334912378454 +508000 ekin = 1.43042502721353 | erot = 1.19541187481578 | epot = -11.7591860258239 | etot = -9.13334912379463 +509000 ekin = 1.49431413372674 | erot = 1.21846596295653 | epot = -11.846129220568 | etot = -9.13334912388472 +510000 ekin = 1.56143815899816 | erot = 1.25390781315388 | epot = -11.948695096197 | etot = -9.133349124045 +511000 ekin = 1.6298540535938 | erot = 1.30115550673976 | epot = -12.064358684596 | etot = -9.13334912426245 +512000 ekin = 1.69760948238301 | erot = 1.35871536004267 | epot = -12.189673966951 | etot = -9.13334912452536 +513000 ekin = 1.76279412854663 | erot = 1.42431355746706 | epot = -12.32045681084 | etot = -9.13334912482629 +514000 ekin = 1.8234997843411 | erot = 1.49507387317685 | epot = -12.4519227826779 | etot = -9.13334912515993 +515000 ekin = 1.87772649131639 | erot = 1.56773414235994 | epot = -12.5788097591916 | etot = -9.13334912551528 +516000 ekin = 1.92332299298445 | erot = 1.63891274675724 | epot = -12.6955848656088 | etot = -9.13334912586715 +517000 ekin = 1.95805681102012 | erot = 1.70543998933825 | epot = -12.7968459265329 | etot = -9.13334912617454 +518000 ekin = 1.9798499194696 | erot = 1.76473849815008 | epot = -12.877937544009 | etot = -9.13334912638928 +519000 ekin = 1.98711819296642 | erot = 1.81518192784633 | epot = -12.935649247285 | etot = -9.13334912647229 +520000 ekin = 1.97908911077148 | erot = 1.85632478174803 | epot = -12.9687630189332 | etot = -9.13334912641371 +521000 ekin = 1.95594858056338 | erot = 1.88892760796433 | epot = -12.9782253147555 | etot = -9.13334912622781 +522000 ekin = 1.91881161738128 | erot = 1.91475582237251 | epot = -12.9669165657063 | etot = -9.13334912595252 +523000 ekin = 1.86954045343242 | erot = 1.93620351350113 | epot = -12.9390930925708 | etot = -9.13334912563722 +524000 ekin = 1.81047332181658 | erot = 1.95582271021995 | epot = -12.8996451573697 | etot = -9.13334912533321 +525000 ekin = 1.74413482435669 | erot = 1.97582576721489 | epot = -12.8533097166597 | etot = -9.1333491250881 +526000 ekin = 1.67297434024897 | erot = 1.99761678040369 | epot = -12.8039402455923 | etot = -9.13334912493961 +527000 ekin = 1.59916865616169 | erot = 2.02141684187556 | epot = -12.7539346229454 | etot = -9.13334912490811 +528000 ekin = 1.52452149634617 | erot = 2.04605877912529 | epot = -12.7039294004615 | etot = -9.13334912499007 +529000 ekin = 1.45048141637983 | erot = 2.06903286947734 | epot = -12.6528634110109 | etot = -9.13334912515376 +530000 ekin = 1.37827485203287 | erot = 2.08683821122988 | epot = -12.5984621886054 | etot = -9.13334912534265 +531000 ekin = 1.30911544825075 | erot = 2.09562136598055 | epot = -12.5380859397193 | etot = -9.13334912548803 +532000 ekin = 1.24441932206786 | erot = 2.09198653946119 | epot = -12.4697549870569 | etot = -9.13334912552781 +533000 ekin = 1.18594679653044 | erot = 2.07377924595274 | epot = -12.3930751679086 | etot = -9.13334912542548 +534000 ekin = 1.13581312461263 | erot = 2.0406294195994 | epot = -12.3097916693919 | etot = -9.1333491251799 +535000 ekin = 1.09635528031307 | erot = 1.99411201499304 | epot = -12.2238164201304 | etot = -9.13334912482426 +536000 ekin = 1.06988655695491 | erot = 1.93750945181173 | epot = -12.1407451331816 | etot = -9.13334912441493 +537000 ekin = 1.05839509271157 | erot = 1.87547351818365 | epot = -12.0672177348899 | etot = -9.13334912399464 +538000 ekin = 1.06323891385424 | erot = 1.81331424698259 | epot = -12.0099022845169 | etot = -9.13334912368006 +539000 ekin = 1.08487929969898 | erot = 1.75562392314494 | epot = -11.9738523463387 | etot = -9.13334912349475 +540000 ekin = 1.12268189022913 | erot = 1.70611667318299 | epot = -11.9621476868877 | etot = -9.13334912347558 +541000 ekin = 1.17481105395823 | erot = 1.66717481230683 | epot = -11.9753349899048 | etot = -9.13334912363973 +542000 ekin = 1.23824417790918 | erot = 1.63956314455086 | epot = -12.0111564464407 | etot = -9.13334912398066 +543000 ekin = 1.30892832432052 | erot = 1.62236761446585 | epot = -12.0646450632503 | etot = -9.13334912446392 +544000 ekin = 1.3820851450754 | erot = 1.61318872881531 | epot = -12.1286229989223 | etot = -9.13334912503159 +545000 ekin = 1.45263801176102 | erot = 1.60857948401649 | epot = -12.1945666213852 | etot = -9.13334912560772 +546000 ekin = 1.51570974605596 | erot = 1.60467377472834 | epot = -12.2537326468962 | etot = -9.13334912611191 +547000 ekin = 1.56711452712151 | erot = 1.59788800381725 | epot = -12.2983516574146 | etot = -9.13334912647585 +548000 ekin = 1.6037622182793 | erot = 1.58554162816792 | epot = -12.3226529731044 | etot = -9.13334912665713 +549000 ekin = 1.62391041626105 | erot = 1.56625626421421 | epot = -12.3235158071224 | etot = -9.13334912664713 +550000 ekin = 1.62723358008848 | erot = 1.54012357328806 | epot = -12.3007062798233 | etot = -9.13334912644672 +551000 ekin = 1.61471889891519 | erot = 1.50851459570911 | epot = -12.2565826207701 | etot = -9.13334912614583 +552000 ekin = 1.58843016682235 | erot = 1.47348936384422 | epot = -12.1952686564379 | etot = -9.1333491257713 +553000 ekin = 1.55120098109793 | erot = 1.43753302719219 | epot = -12.1220831336608 | etot = -9.13334912537071 +554000 ekin = 1.50631636213018 | erot = 1.40318755323333 | epot = -12.0428530403429 | etot = -9.13334912497942 +555000 ekin = 1.45722878986335 | erot = 1.37279698200099 | epot = -11.9633748964853 | etot = -9.133349124621 +556000 ekin = 1.40732293284981 | erot = 1.34837590639181 | epot = -11.8890479635491 | etot = -9.13334912430749 +557000 ekin = 1.35973750772659 | erot = 1.33157707039056 | epot = -11.8246637021612 | etot = -9.13334912404406 +558000 ekin = 1.31723590732733 | erot = 1.32371628032833 | epot = -11.7743013114885 | etot = -9.13334912383284 +559000 ekin = 1.28211028308911 | erot = 1.32580526483835 | epot = -11.7412646716049 | etot = -9.13334912367748 +560000 ekin = 1.25610590404642 | erot = 1.3385562626596 | epot = -11.7280112902903 | etot = -9.13334912358425 +561000 ekin = 1.2403584426308 | erot = 1.36234138770357 | epot = -11.7360489538959 | etot = -9.13334912356153 +562000 ekin = 1.23534624012421 | erot = 1.39711468447432 | epot = -11.7658100482156 | etot = -9.1333491236171 +563000 ekin = 1.24087113988208 | erot = 1.44233150298232 | epot = -11.8165517666162 | etot = -9.13334912375181 +564000 ekin = 1.25609129142822 | erot = 1.49691875867446 | epot = -11.8863591740572 | etot = -9.13334912395452 +565000 ekin = 1.27963015842373 | erot = 1.55937933470843 | epot = -11.9723586173214 | etot = -9.13334912418923 +566000 ekin = 1.30976945418227 | erot = 1.62795664725703 | epot = -12.0710752258883 | etot = -9.13334912444901 +567000 ekin = 1.34469873511096 | erot = 1.70073738336496 | epot = -12.1787852431675 | etot = -9.13334912469163 +568000 ekin = 1.38275779930543 | erot = 1.77591787229575 | epot = -12.2920247965067 | etot = -9.13334912490556 +569000 ekin = 1.42260294142073 | erot = 1.85183127901208 | epot = -12.407783345528 | etot = -9.13334912509522 +570000 ekin = 1.46311433095821 | erot = 1.92670412003837 | epot = -12.5231675763648 | etot = -9.13334912536826 +571000 ekin = 1.503277533287 | erot = 1.998531008796 | epot = -12.6351576677647 | etot = -9.13334912568171 +572000 ekin = 1.54192966726487 | erot = 2.06497613728929 | epot = -12.7402549304297 | etot = -9.1333491258755 +573000 ekin = 1.57823855406826 | erot = 2.12427016695721 | epot = -12.8358578469833 | etot = -9.13334912595785 +574000 ekin = 1.61207502224162 | erot = 2.1757020138028 | epot = -12.9211261619152 | etot = -9.13334912587075 +575000 ekin = 1.6440258217365 | erot = 2.22028441014041 | epot = -12.9976593575031 | etot = -9.13334912562622 +576000 ekin = 1.67538587678283 | erot = 2.26042238856481 | epot = -13.0691573906392 | etot = -9.13334912529152 +577000 ekin = 1.70789209378918 | erot = 2.29915883242667 | epot = -13.1404000511839 | etot = -9.13334912496807 +578000 ekin = 1.74326819508402 | erot = 2.33909725076618 | epot = -13.2157145705993 | etot = -9.13334912474906 +579000 ekin = 1.78272231838322 | erot = 2.38182643842473 | epot = -13.2978978815032 | etot = -9.13334912469522 +580000 ekin = 1.82652189373014 | erot = 2.42751679140051 | epot = -13.3873878099642 | etot = -9.13334912483355 +581000 ekin = 1.8737067517545 | erot = 2.47480205694227 | epot = -13.4818579338712 | etot = -9.13334912517445 +582000 ekin = 1.9219705257856 | erot = 2.52092715153558 | epot = -13.5762468029815 | etot = -9.13334912566034 +583000 ekin = 1.96774925896963 | erot = 2.56227660801906 | epot = -13.6633749932294 | etot = -9.13334912624074 +584000 ekin = 2.00657374540273 | erot = 2.59498886543059 | epot = -13.7349117376539 | etot = -9.13334912682061 +585000 ekin = 2.03371871575717 | erot = 2.61566274200543 | epot = -13.7827305850452 | etot = -9.13334912728264 +586000 ekin = 2.04507827703258 | erot = 2.62214006251621 | epot = -13.8005674670656 | etot = -9.13334912751683 +587000 ekin = 2.03806243485583 | erot = 2.61411994889205 | epot = -13.7855315112079 | etot = -9.13334912746004 +588000 ekin = 2.01223115184246 | erot = 2.59335030112239 | epot = -13.7389305800906 | etot = -9.13334912712576 +589000 ekin = 1.96942837554415 | erot = 2.56324673363008 | epot = -13.6660242357789 | etot = -9.13334912660463 +590000 ekin = 1.91334419958811 | erot = 2.52801524733592 | epot = -13.5747085729562 | etot = -9.13334912603221 +591000 ekin = 1.84865383330561 | erot = 2.49158313369046 | epot = -13.4735860925319 | etot = -9.13334912553585 +592000 ekin = 1.78006004419564 | erot = 2.45674050608586 | epot = -13.3701496754669 | etot = -9.13334912518538 +593000 ekin = 1.7115927976213 | erot = 2.42478693109326 | epot = -13.2697288536935 | etot = -9.13334912497898 +594000 ekin = 1.64634946405339 | erot = 2.39569805901444 | epot = -13.175396647939 | etot = -9.13334912487118 +595000 ekin = 1.58659479948916 | erot = 2.36854432557332 | epot = -13.0884882498818 | etot = -9.13334912481927 +596000 ekin = 1.53398103551393 | erot = 2.34182175785591 | epot = -13.0091519181804 | etot = -9.13334912481053 +597000 ekin = 1.4896944162256 | erot = 2.31355286210786 | epot = -12.9365964031849 | etot = -9.13334912485144 +598000 ekin = 1.45449014890386 | erot = 2.28129539496066 | epot = -12.869134668807 | etot = -9.13334912494252 +599000 ekin = 1.42868283605903 | erot = 2.24230571379847 | epot = -12.8043376749183 | etot = -9.13334912506079 +600000 ekin = 1.41215819512729 | erot = 2.19421771509236 | epot = -12.7397250351172 | etot = -9.13334912489753 +601000 ekin = 1.40437980063583 | erot = 2.136750928483 | epot = -12.6744798541796 | etot = -9.13334912506074 +602000 ekin = 1.40442466853094 | erot = 2.06863595764367 | epot = -12.6064097512931 | etot = -9.13334912511845 +603000 ekin = 1.41112302449417 | erot = 1.98998056957542 | epot = -12.5344527191411 | etot = -9.13334912507147 +604000 ekin = 1.42310135151995 | erot = 1.902745243228 | epot = -12.4591957196925 | etot = -9.13334912494458 +605000 ekin = 1.43883447822351 | erot = 1.81030632011036 | epot = -12.3824899231056 | etot = -9.13334912477171 +606000 ekin = 1.45673760095088 | erot = 1.71684240504777 | epot = -12.3069291305825 | etot = -9.13334912458388 +607000 ekin = 1.4752986371308 | erot = 1.62672298752963 | epot = -12.2353707490633 | etot = -9.13334912440289 +608000 ekin = 1.49323166610316 | erot = 1.54399943869013 | epot = -12.1705802290336 | etot = -9.13334912424029 +609000 ekin = 1.5096125661575 | erot = 1.47208306433867 | epot = -12.1150447546059 | etot = -9.13334912410968 +610000 ekin = 1.52396039431372 | erot = 1.41350705715054 | epot = -12.0708165754589 | etot = -9.13334912399469 +611000 ekin = 1.53622860047165 | erot = 1.36992443741171 | epot = -12.0395021618072 | etot = -9.13334912392386 +612000 ekin = 1.54668536626305 | erot = 1.34205362872995 | epot = -12.0220881189034 | etot = -9.13334912391043 +613000 ekin = 1.55571309695784 | erot = 1.32960894336 | epot = -12.0186711642891 | etot = -9.13334912397129 +614000 ekin = 1.5635636922184 | erot = 1.33131277562608 | epot = -12.0282255919652 | etot = -9.13334912412073 +615000 ekin = 1.57013881826808 | erot = 1.34494539761815 | epot = -12.0484333402237 | etot = -9.13334912433747 +616000 ekin = 1.5748568190406 | erot = 1.36757312206317 | epot = -12.0757790657619 | etot = -9.13334912465813 +617000 ekin = 1.57672646781355 | erot = 1.39546251366834 | epot = -12.1055381065046 | etot = -9.13334912502268 +618000 ekin = 1.57456346737936 | erot = 1.42448013453632 | epot = -12.1323927272935 | etot = -9.13334912537785 +619000 ekin = 1.56732946470231 | erot = 1.45059208152833 | epot = -12.1512706718929 | etot = -9.13334912566224 +620000 ekin = 1.55451321753977 | erot = 1.4703933445561 | epot = -12.1582556879156 | etot = -9.13334912581974 +621000 ekin = 1.5364478233846 | erot = 1.48161304590965 | epot = -12.1514099951074 | etot = -9.13334912581318 +622000 ekin = 1.51447783518414 | erot = 1.48347710481912 | epot = -12.1313040656381 | etot = -9.13334912563484 +623000 ekin = 1.49092960733081 | erot = 1.47683215248869 | epot = -12.1011108851283 | etot = -9.13334912530885 +624000 ekin = 1.46886130170072 | erot = 1.46422198591534 | epot = -12.0664324125269 | etot = -9.13334912491083 +625000 ekin = 1.45155188812679 | erot = 1.44918251594271 | epot = -12.0340835285536 | etot = -9.13334912448408 +626000 ekin = 1.44224748157941 | erot = 1.43533399591765 | epot = -12.0109306015701 | etot = -9.13334912407301 +627000 ekin = 1.44381530880005 | erot = 1.4263800535482 | epot = -12.0035444860843 | etot = -9.1333491237361 +628000 ekin = 1.4583308162013 | erot = 1.42560824875312 | epot = -12.0172881884924 | etot = -9.13334912353797 +629000 ekin = 1.48676985537066 | erot = 1.43535417577253 | epot = -12.0554731546316 | etot = -9.13334912348845 +630000 ekin = 1.52866417049136 | erot = 1.45689184513674 | epot = -12.1189051392542 | etot = -9.13334912362608 +631000 ekin = 1.58193413338903 | erot = 1.49015054897836 | epot = -12.2054338063858 | etot = -9.13334912401841 +632000 ekin = 1.64234851055617 | erot = 1.53357750659224 | epot = -12.3092751416912 | etot = -9.13334912454282 +633000 ekin = 1.70466841196976 | erot = 1.58426390210415 | epot = -12.422281439224 | etot = -9.13334912515012 +634000 ekin = 1.76318354699271 | erot = 1.63860587790906 | epot = -12.5351385506365 | etot = -9.13334912573474 +635000 ekin = 1.81242625034656 | erot = 1.69306627320957 | epot = -12.6388416497418 | etot = -9.13334912618564 +636000 ekin = 1.84805557837959 | erot = 1.74492785470348 | epot = -12.7263325594984 | etot = -9.1333491264153 +637000 ekin = 1.86755595284548 | erot = 1.79286465559487 | epot = -12.7937697348514 | etot = -9.13334912641102 +638000 ekin = 1.87047357468591 | erot = 1.83697965057624 | epot = -12.8408023514698 | etot = -9.13334912620763 +639000 ekin = 1.85817220593092 | erot = 1.87849437006802 | epot = -12.870015701881 | etot = -9.13334912588202 +640000 ekin = 1.83325502874749 | erot = 1.9193024713677 | epot = -12.8859066256289 | etot = -9.13334912551372 +641000 ekin = 1.79889805051405 | erot = 1.96149522932417 | epot = -12.8937424049968 | etot = -9.13334912515859 +642000 ekin = 1.75833330344794 | erot = 2.00701454517332 | epot = -12.8986969734767 | etot = -9.1333491248554 +643000 ekin = 1.71452400738602 | erot = 2.05742054585266 | epot = -12.905293677835 | etot = -9.13334912459635 +644000 ekin = 1.67006045206695 | erot = 2.11379950766835 | epot = -12.9172090841664 | etot = -9.13334912443105 +645000 ekin = 1.62710169193844 | erot = 2.17652829047967 | epot = -12.9369791067766 | etot = -9.13334912435848 +646000 ekin = 1.58731920571299 | erot = 2.24499987972527 | epot = -12.9656682098095 | etot = -9.13334912437126 +647000 ekin = 1.55192879850279 | erot = 2.31774723145938 | epot = -13.0030251544558 | etot = -9.13334912449359 +648000 ekin = 1.52155547404789 | erot = 2.39216849405319 | epot = -13.0470730928303 | etot = -9.13334912472921 +649000 ekin = 1.4961570117291 | erot = 2.46459269466688 | epot = -13.0940988314722 | etot = -9.13334912507625 +650000 ekin = 1.47495820408513 | erot = 2.53042613107739 | epot = -13.1387334606825 | etot = -9.13334912552003 +651000 ekin = 1.45644758276295 | erot = 2.58442104122457 | epot = -13.1742177500163 | etot = -9.13334912602877 +652000 ekin = 1.43848054670472 | erot = 2.62109720356082 | epot = -13.1929268768132 | etot = -9.13334912654768 +653000 ekin = 1.41853538647083 | erot = 2.63533318879135 | epot = -13.1872177022606 | etot = -9.13334912699846 +654000 ekin = 1.39414099594975 | erot = 2.62311445987549 | epot = -13.1506045831176 | etot = -9.13334912729239 +655000 ekin = 1.36342278664765 | erot = 2.58232798191524 | epot = -13.0790998958947 | etot = -9.1333491273318 +656000 ekin = 1.32754554560135 | erot = 2.5134399730659 | epot = -12.9743346448114 | etot = -9.13334912614414 +657000 ekin = 1.07738759792173 | erot = 2.44669612963653 | epot = -12.6574327807928 | etot = -9.13334905323454 +658000 ekin = 1.00652014230627 | erot = 2.49084781647582 | epot = -12.6307170433399 | etot = -9.13334908455785 +659000 ekin = 1.0724008501796 | erot = 2.42929901831606 | epot = -12.6350489837819 | etot = -9.13334911528626 +660000 ekin = 1.09381648980953 | erot = 2.30102308261687 | epot = -12.5281886879217 | etot = -9.1333491154953 +661000 ekin = 1.11701334338117 | erot = 2.16959631554243 | epot = -12.4199587738177 | etot = -9.1333491148941 +662000 ekin = 1.14263894058074 | erot = 2.04231481245821 | epot = -12.3183028674878 | etot = -9.13334911444888 +663000 ekin = 1.17093665277153 | erot = 1.92510458369797 | epot = -12.2293903506455 | etot = -9.13334911417605 +664000 ekin = 1.20146324496873 | erot = 1.82207009510993 | epot = -12.1568824541672 | etot = -9.13334911408858 +665000 ekin = 1.23289032447991 | erot = 1.73564836427791 | epot = -12.1018878027987 | etot = -9.13334911404089 +666000 ekin = 1.26340464455219 | erot = 1.66702592668296 | epot = -12.0637796854985 | etot = -9.13334911426337 +667000 ekin = 1.29102574814588 | erot = 1.61488086820599 | epot = -12.0392557309147 | etot = -9.13334911456284 +668000 ekin = 1.31376054134924 | erot = 1.57649712773806 | epot = -12.0236067839933 | etot = -9.13334911490603 +669000 ekin = 1.32989404565469 | erot = 1.54828621181657 | epot = -12.0115293726996 | etot = -9.13334911522832 +670000 ekin = 1.33826340890773 | erot = 1.52640844797481 | epot = -11.9980209723674 | etot = -9.13334911548489 +671000 ekin = 1.33847461323381 | erot = 1.50724764864764 | epot = -11.9790713775224 | etot = -9.13334911564091 +672000 ekin = 1.33101969554729 | erot = 1.48781306139111 | epot = -11.9521818726168 | etot = -9.13334911567844 +673000 ekin = 1.31737035051244 | erot = 1.46610228052886 | epot = -11.9168217466028 | etot = -9.13334911556153 +674000 ekin = 1.29992521798278 | erot = 1.44131241760553 | epot = -11.8745867509642 | etot = -9.13334911537591 +675000 ekin = 1.28129254582611 | erot = 1.41347048294297 | epot = -11.8281121439047 | etot = -9.13334911513566 +676000 ekin = 1.26413925333842 | erot = 1.38336835396336 | epot = -11.7808567221873 | etot = -9.13334911488549 +677000 ekin = 1.25080949630108 | erot = 1.35227525692229 | epot = -11.7364338679141 | etot = -9.13334911469074 +678000 ekin = 1.24240325884008 | erot = 1.32122246363462 | epot = -11.696974837032 | etot = -9.1333491145573 +679000 ekin = 1.23935164124878 | erot = 1.29124446460954 | epot = -11.6639452203567 | etot = -9.1333491144984 +680000 ekin = 1.24151057851806 | erot = 1.26358348831243 | epot = -11.6384431811759 | etot = -9.13334911434536 +681000 ekin = 1.24810791985433 | erot = 1.23998966300449 | epot = -11.621446697324 | etot = -9.13334911446517 +682000 ekin = 1.25738088472581 | erot = 1.22073219170803 | epot = -11.6114621910631 | etot = -9.13334911462927 +683000 ekin = 1.26715254864098 | erot = 1.20554909695223 | epot = -11.6060507604029 | etot = -9.13334911480967 +684000 ekin = 1.27521936884296 | erot = 1.19392995256969 | epot = -11.6024984363908 | etot = -9.13334911497818 +685000 ekin = 1.27965818657957 | erot = 1.18525667281503 | epot = -11.598263974498 | etot = -9.13334911510344 +686000 ekin = 1.27906445706524 | erot = 1.17887846191262 | epot = -11.5912920341683 | etot = -9.13334911519047 +687000 ekin = 1.27268261753913 | erot = 1.17407129022592 | epot = -11.5801030230249 | etot = -9.13334911525981 +688000 ekin = 1.2604191440655 | erot = 1.17007604783868 | epot = -11.5638443071319 | etot = -9.13334911522773 +689000 ekin = 1.24287938495423 | erot = 1.16656725574682 | epot = -11.5427957558581 | etot = -9.1333491151571 +690000 ekin = 1.22118240404801 | erot = 1.16336387131456 | epot = -11.5178953904218 | etot = -9.13334911505928 +691000 ekin = 1.19679867225187 | erot = 1.16037339233307 | epot = -11.4905211795311 | etot = -9.13334911494614 +692000 ekin = 1.17139142555457 | erot = 1.15758648593215 | epot = -11.4623270263143 | etot = -9.13334911482758 +693000 ekin = 1.14685376597284 | erot = 1.15519232867469 | epot = -11.4353952091881 | etot = -9.13334911454058 +694000 ekin = 1.12537035278754 | erot = 1.15368599836321 | epot = -11.4124054656034 | etot = -9.13334911445262 +695000 ekin = 1.10824764597546 | erot = 1.15324052660546 | epot = -11.394837286963 | etot = -9.13334911438207 +696000 ekin = 1.09641524899199 | erot = 1.15407441364668 | epot = -11.3838387769731 | etot = -9.13334911433448 +697000 ekin = 1.0904070695983 | erot = 1.15645735234451 | epot = -11.38021353626 | etot = -9.13334911431723 +698000 ekin = 1.09030542376263 | erot = 1.16063392710698 | epot = -11.384288465198 | etot = -9.13334911432841 +699000 ekin = 1.09552536141965 | erot = 1.16669639941866 | epot = -11.3955708752004 | etot = -9.13334911436206 +700000 ekin = 1.10527379803171 | erot = 1.17478862115977 | epot = -11.4134115336272 | etot = -9.13334911443575 +701000 ekin = 1.11851271408081 | erot = 1.18492470948308 | epot = -11.4367865380882 | etot = -9.13334911452431 +702000 ekin = 1.13395549372662 | erot = 1.19694667251851 | epot = -11.4642512808751 | etot = -9.13334911463001 +703000 ekin = 1.15018285433177 | erot = 1.21057055971553 | epot = -11.4941025287918 | etot = -9.13334911474449 +704000 ekin = 1.16576673457734 | erot = 1.2253590806033 | epot = -11.5244749300382 | etot = -9.13334911485753 +705000 ekin = 1.17938915503343 | erot = 1.24076765314262 | epot = -11.5535059231341 | etot = -9.13334911495807 +706000 ekin = 1.18994261306182 | erot = 1.2562234849481 | epot = -11.5795152130455 | etot = -9.1333491150356 +707000 ekin = 1.19660107195375 | erot = 1.271227802675 | epot = -11.6011779897101 | etot = -9.13334911508136 +708000 ekin = 1.19885615186573 | erot = 1.28546332267813 | epot = -11.6176685896339 | etot = -9.13334911509003 +709000 ekin = 1.19651981509382 | erot = 1.29888532038566 | epot = -11.6287542505396 | etot = -9.13334911506012 +710000 ekin = 1.18969957497066 | erot = 1.31177606554459 | epot = -11.6348247555099 | etot = -9.13334911499465 +711000 ekin = 1.17875387602812 | erot = 1.32474791483144 | epot = -11.6368509057608 | etot = -9.13334911490123 +712000 ekin = 1.16423391783899 | erot = 1.3386894522921 | epot = -11.6362724849217 | etot = -9.13334911479056 +713000 ekin = 1.14681758773145 | erot = 1.35466305350745 | epot = -11.6348297559169 | etot = -9.13334911467797 +714000 ekin = 1.12724173590757 | erot = 1.37373509013814 | epot = -11.6343259406232 | etot = -9.13334911457754 +715000 ekin = 1.10624050750108 | erot = 1.39681075797456 | epot = -11.636400379979 | etot = -9.13334911450333 +716000 ekin = 1.08449847089157 | erot = 1.42446438144211 | epot = -11.6423119668 | etot = -9.13334911446637 +717000 ekin = 1.06262586730495 | erot = 1.45678801962731 | epot = -11.652763001406 | etot = -9.13334911447369 +718000 ekin = 1.04116056518022 | erot = 1.49328580498647 | epot = -11.6677954846921 | etot = -9.13334911452545 +719000 ekin = 1.02059756446943 | erot = 1.53283565406262 | epot = -11.6867823331474 | etot = -9.13334911461534 +720000 ekin = 1.00144276091631 | erot = 1.57373478107468 | epot = -11.7085266567205 | etot = -9.13334911472952 +721000 ekin = 0.984282698242522 | erot = 1.61383653730724 | epot = -11.7314683503986 | etot = -9.13334911484888 +722000 ekin = 0.96985633457677 | erot = 1.65076935458374 | epot = -11.7539748041155 | etot = -9.13334911495504 +723000 ekin = 0.959109074098182 | erot = 1.68219090540371 | epot = -11.7746490945239 | etot = -9.13334911502201 +724000 ekin = 0.953206498554131 | erot = 1.70610525279805 | epot = -11.79266086639 | etot = -9.13334911503783 +725000 ekin = 0.953487871460092 | erot = 1.72112406444749 | epot = -11.8079610509059 | etot = -9.13334911499836 +726000 ekin = 0.961348420449859 | erot = 1.72664218755813 | epot = -11.8213397229199 | etot = -9.13334911491192 +727000 ekin = 0.978055187000221 | erot = 1.72290320032193 | epot = -11.8343075021185 | etot = -9.13334911479632 +728000 ekin = 1.00452582497731 | erot = 1.71095374106594 | epot = -11.8488286807165 | etot = -9.13334911467327 +729000 ekin = 1.04110137579929 | erot = 1.6925221534031 | epot = -11.8669726437713 | etot = -9.13334911456892 +730000 ekin = 1.08735958690316 | erot = 1.66981008957492 | epot = -11.8905187909846 | etot = -9.13334911450647 +731000 ekin = 1.14200418375028 | erot = 1.64524141705574 | epot = -11.9205947153098 | etot = -9.13334911450375 +732000 ekin = 1.20285318014175 | erot = 1.62119095712754 | epot = -11.9573932518408 | etot = -9.13334911457154 +733000 ekin = 1.26692596391375 | erot = 1.59976528909609 | epot = -12.000040367713 | etot = -9.13334911470313 +734000 ekin = 1.33064406417852 | erot = 1.58254289880308 | epot = -12.0465360778903 | etot = -9.13334911490874 +735000 ekin = 1.39013484388292 | erot = 1.57032898633086 | epot = -12.0938129453736 | etot = -9.13334911515987 +736000 ekin = 1.44157509139339 | erot = 1.56317476788482 | epot = -12.1380989747065 | etot = -9.13334911542827 +737000 ekin = 1.48157845589432 | erot = 1.56044545881388 | epot = -12.1753730303859 | etot = -9.13334911567766 +738000 ekin = 1.50757504377736 | erot = 1.56100911666946 | epot = -12.2019332763157 | etot = -9.13334911586885 +739000 ekin = 1.51813561812011 | erot = 1.56352092529372 | epot = -12.2150056593802 | etot = -9.13334911596641 +740000 ekin = 1.51318914848911 | erot = 1.56675183784913 | epot = -12.2132901022842 | etot = -9.13334911594593 +741000 ekin = 1.49408865829715 | erot = 1.56989906103857 | epot = -12.1973368351355 | etot = -9.13334911579981 +742000 ekin = 1.4635006153526 | erot = 1.57280025700489 | epot = -12.1696499878992 | etot = -9.13334911554169 +743000 ekin = 1.42512524133545 | erot = 1.57593310600528 | epot = -12.1344074625083 | etot = -9.13334911516759 +744000 ekin = 1.38338487585046 | erot = 1.58054361278105 | epot = -12.097277603429 | etot = -9.13334911479754 +745000 ekin = 1.34281951273833 | erot = 1.58823582840448 | epot = -12.0644044555983 | etot = -9.13334911445548 +746000 ekin = 1.30747334765346 | erot = 1.60047096980711 | epot = -12.0412934316584 | etot = -9.1333491141978 +747000 ekin = 1.28046646005551 | erot = 1.6182176866574 | epot = -12.0320332608057 | etot = -9.13334911409281 +748000 ekin = 1.26367955923863 | erot = 1.64132893143465 | epot = -12.0383576048431 | etot = -9.13334911416987 +749000 ekin = 1.2574293442035 | erot = 1.66831440024557 | epot = -12.0590928588867 | etot = -9.13334911443761 +750000 ekin = 1.26047795508238 | erot = 1.69628448614892 | epot = -12.090111556082 | etot = -9.13334911485068 +751000 ekin = 1.27026186447581 | erot = 1.72133386886134 | epot = -12.1249448486768 | etot = -9.13334911533964 +752000 ekin = 1.283395470868 | erot = 1.73919075505919 | epot = -12.1559353417358 | etot = -9.13334911580862 +753000 ekin = 1.29635957467025 | erot = 1.74596876191974 | epot = -12.1756774528089 | etot = -9.13334911621893 +754000 ekin = 1.30599158741241 | erot = 1.73885024063265 | epot = -12.1781909444329 | etot = -9.13334911638789 +755000 ekin = 1.31024888116356 | erot = 1.71683511467995 | epot = -12.1604331121845 | etot = -9.13334911634101 +756000 ekin = 1.30846938321657 | erot = 1.68097972249338 | epot = -12.1227982218014 | etot = -9.13334911609141 +757000 ekin = 1.30124985041457 | erot = 1.6341900647619 | epot = -12.0687890308653 | etot = -9.13334911568881 +758000 ekin = 1.29019641090553 | erot = 1.5807356338864 | epot = -12.0042811599959 | etot = -9.13334911520393 +759000 ekin = 1.27761222227633 | erot = 1.52554636406109 | epot = -11.9365077010358 | etot = -9.13334911469837 +760000 ekin = 1.26609069506764 | erot = 1.47348693038205 | epot = -11.8729267397083 | etot = -9.13334911425856 +761000 ekin = 1.25808964011641 | erot = 1.42869550462177 | epot = -11.8201342586616 | etot = -9.13334911392337 +762000 ekin = 1.25572222200568 | erot = 1.39407442311013 | epot = -11.7831457588643 | etot = -9.13334911374844 +763000 ekin = 1.26054534569755 | erot = 1.37090045943873 | epot = -11.7647949188315 | etot = -9.13334911369523 +764000 ekin = 1.27353435439963 | erot = 1.3588719908604 | epot = -11.7657554590514 | etot = -9.13334911379134 +765000 ekin = 1.29496682599905 | erot = 1.35616457697868 | epot = -11.7844805169703 | etot = -9.13334911399252 +766000 ekin = 1.32454629042196 | erot = 1.35977679502517 | epot = -11.8176721997099 | etot = -9.13334911426275 +767000 ekin = 1.3616395427185 | erot = 1.36618632223445 | epot = -11.8611749795076 | etot = -9.13334911455462 +768000 ekin = 1.40531019892591 | erot = 1.37181010082889 | epot = -11.9104694145835 | etot = -9.13334911482872 +769000 ekin = 1.45446512869056 | erot = 1.37353498050594 | epot = -11.9613492242367 | etot = -9.13334911504021 +770000 ekin = 1.50793050152324 | erot = 1.3692112564908 | epot = -12.0104908732501 | etot = -9.13334911523604 +771000 ekin = 1.56389616693367 | erot = 1.35775090660325 | epot = -12.0549961887947 | etot = -9.13334911525779 +772000 ekin = 1.62113703504571 | erot = 1.33970323504223 | epot = -12.0941893852765 | etot = -9.1333491151886 +773000 ekin = 1.67872851569619 | erot = 1.31702982988185 | epot = -12.1291074606401 | etot = -9.13334911506207 +774000 ekin = 1.73569257108923 | erot = 1.29264163249645 | epot = -12.1616833185078 | etot = -9.13334911492213 +775000 ekin = 1.79085656133661 | erot = 1.26988000051291 | epot = -12.1940856766607 | etot = -9.13334911481123 +776000 ekin = 1.84276100468295 | erot = 1.25197534037432 | epot = -12.2280854598157 | etot = -9.13334911475846 +777000 ekin = 1.88967118603816 | erot = 1.24159765890997 | epot = -12.26461795972 | etot = -9.13334911477187 +778000 ekin = 1.92971622260738 | erot = 1.24057583214169 | epot = -12.3036411695895 | etot = -9.13334911484046 +779000 ekin = 1.96113164254929 | erot = 1.24980912493184 | epot = -12.3442898824215 | etot = -9.13334911494034 +780000 ekin = 1.98254203386291 | erot = 1.26932045666842 | epot = -12.3852116055749 | etot = -9.13334911504359 +781000 ekin = 1.99321406405731 | erot = 1.29840823518561 | epot = -12.4249714143724 | etot = -9.13334911512944 +782000 ekin = 1.99321095940794 | erot = 1.33580885492146 | epot = -12.4623689295173 | etot = -9.13334911518788 +783000 ekin = 1.98342491293472 | erot = 1.37983642298483 | epot = -12.4966104511371 | etot = -9.13334911521755 +784000 ekin = 1.96551238429988 | erot = 1.4284937162139 | epot = -12.5273552156836 | etot = -9.13334911516984 +785000 ekin = 1.94195910112003 | erot = 1.47961348821968 | epot = -12.5549217045009 | etot = -9.13334911516119 +786000 ekin = 1.91549982326076 | erot = 1.53087711626887 | epot = -12.5797260546657 | etot = -9.13334911513605 +787000 ekin = 1.88902915933118 | erot = 1.57997565975913 | epot = -12.6023539341834 | etot = -9.13334911509308 +788000 ekin = 1.86553746554052 | erot = 1.6247864602542 | epot = -12.6236730408322 | etot = -9.13334911503745 +789000 ekin = 1.84793067284216 | erot = 1.66350572426719 | epot = -12.6447855120736 | etot = -9.13334911496424 +790000 ekin = 1.83884831412187 | erot = 1.69477325871965 | epot = -12.666970687736 | etot = -9.1333491148945 +791000 ekin = 1.84038435201533 | erot = 1.71768127848809 | epot = -12.6914147453587 | etot = -9.13334911485525 +792000 ekin = 1.85374621231307 | erot = 1.7316968379069 | epot = -12.7187921650977 | etot = -9.1333491148777 +793000 ekin = 1.87892178729802 | erot = 1.73653576924509 | epot = -12.7488066715289 | etot = -9.13334911498578 +794000 ekin = 1.9144051004557 | erot = 1.73204169928296 | epot = -12.7797959149174 | etot = -9.1333491151787 +795000 ekin = 1.9572669787258 | erot = 1.7181897621778 | epot = -12.8088058563242 | etot = -9.13334911542062 +796000 ekin = 2.003608517798 | erot = 1.6952533545956 | epot = -12.8322109880412 | etot = -9.13334911564762 +797000 ekin = 2.04914358120503 | erot = 1.66405946742261 | epot = -12.8465521644174 | etot = -9.13334911578975 +798000 ekin = 2.08995546227498 | erot = 1.62623745952976 | epot = -12.8495420376073 | etot = -9.13334911580255 +799000 ekin = 2.12309292251192 | erot = 1.58427028116718 | epot = -12.8407123193656 | etot = -9.1333491156865 +800000 ekin = 2.14682990847424 | erot = 1.5412613855981 | epot = -12.8214404095539 | etot = -9.13334911548158 +801000 ekin = 2.16058282772595 | erot = 1.50048202047544 | epot = -12.794413963447 | etot = -9.13334911524559 +802000 ekin = 2.16461511109201 | erot = 1.46486615503312 | epot = -12.7628303811552 | etot = -9.13334911503007 +803000 ekin = 2.15969104316245 | erot = 1.43661335442493 | epot = -12.7296535124556 | etot = -9.13334911486821 +804000 ekin = 2.14679128687646 | erot = 1.41698988508528 | epot = -12.6971302867205 | etot = -9.1333491147588 +805000 ekin = 2.1269206594369 | erot = 1.40638520515014 | epot = -12.666654979311 | etot = -9.13334911472395 +806000 ekin = 2.1009902826322 | erot = 1.40422932575147 | epot = -12.6385687231441 | etot = -9.1333491147604 +807000 ekin = 2.06982763841558 | erot = 1.40909451158654 | epot = -12.6122712648399 | etot = -9.13334911483777 +808000 ekin = 2.03419092297523 | erot = 1.41919422166642 | epot = -12.5867342595701 | etot = -9.13334911492846 +809000 ekin = 1.99478586655737 | erot = 1.43238858340756 | epot = -12.5605235650175 | etot = -9.13334911505257 +810000 ekin = 1.95230744546423 | erot = 1.44625258192565 | epot = -12.5319091425649 | etot = -9.133349115175 +811000 ekin = 1.90747094188561 | erot = 1.45847148723051 | epot = -12.4992915443988 | etot = -9.13334911528272 +812000 ekin = 1.86102893102452 | erot = 1.46703963548048 | epot = -12.461417681868 | etot = -9.13334911536302 +813000 ekin = 1.81416432243416 | erot = 1.47049868906966 | epot = -12.4180121266398 | etot = -9.13334911513599 +814000 ekin = 1.76902926167563 | erot = 1.4682673931058 | epot = -12.3706457700667 | etot = -9.1333491152853 +815000 ekin = 1.71533069952301 | erot = 1.45797598423648 | epot = -12.3066557947838 | etot = -9.13334911102435 +816000 ekin = 1.68468183703368 | erot = 1.43935942018725 | epot = -12.2573903676285 | etot = -9.13334911040755 +817000 ekin = 1.67569540451894 | erot = 1.42022759192546 | epot = -12.2292721045928 | etot = -9.13334910814843 +818000 ekin = 1.65431804078757 | erot = 1.40071144599652 | epot = -12.1883785945447 | etot = -9.13334910776065 +819000 ekin = 1.63740188371742 | erot = 1.38256931716521 | epot = -12.1533203082681 | etot = -9.13334910738549 +820000 ekin = 1.62512170450766 | erot = 1.3692816885284 | epot = -12.1277525000598 | etot = -9.13334910702377 +821000 ekin = 1.61915909097708 | erot = 1.36404110715986 | epot = -12.1165493048443 | etot = -9.13334910670739 +822000 ekin = 1.62172343976281 | erot = 1.36925913747977 | epot = -12.12433168376 | etot = -9.13334910651737 +823000 ekin = 1.6342749481272 | erot = 1.38616632191067 | epot = -12.1537903765466 | etot = -9.13334910650878 +824000 ekin = 1.65698382617913 | erot = 1.41459711185634 | epot = -12.2049300447282 | etot = -9.13334910669278 +825000 ekin = 1.68854753273329 | erot = 1.4530163184206 | epot = -12.2749129581921 | etot = -9.13334910703822 +826000 ekin = 1.72638863495591 | erot = 1.49875661579891 | epot = -12.3584943582429 | etot = -9.13334910748808 +827000 ekin = 1.76710423380199 | erot = 1.54839439234558 | epot = -12.4488477341237 | etot = -9.13334910797611 +828000 ekin = 1.80698482333474 | erot = 1.59818184901675 | epot = -12.538515780796 | etot = -9.13334910844446 +829000 ekin = 1.84246939969638 | erot = 1.64447465718396 | epot = -12.6202931657257 | etot = -9.13334910884533 +830000 ekin = 1.87048980343092 | erot = 1.68412933439417 | epot = -12.6879682469655 | etot = -9.13334910914043 +831000 ekin = 1.88871335827693 | erot = 1.71486645418453 | epot = -12.7369289217614 | etot = -9.13334910929997 +832000 ekin = 1.89569916791682 | erot = 1.73558694752276 | epot = -12.7646352247443 | etot = -9.13334910930477 +833000 ekin = 1.89096344935487 | erot = 1.7465944755228 | epot = -12.7709070340317 | etot = -9.13334910915404 +834000 ekin = 1.87493429544718 | erot = 1.74964392180754 | epot = -12.757927326144 | etot = -9.13334910888933 +835000 ekin = 1.84878280513965 | erot = 1.74762027308332 | epot = -12.7297521867473 | etot = -9.13334910852438 +836000 ekin = 1.81414476909328 | erot = 1.74421722088915 | epot = -12.6917110981227 | etot = -9.1333491081403 +837000 ekin = 1.77277875467125 | erot = 1.743352851396 | epot = -12.6494807138712 | etot = -9.13334910780394 +838000 ekin = 1.72624445531295 | erot = 1.74841404792614 | epot = -12.6080076108058 | etot = -9.13334910756667 +839000 ekin = 1.67568816110731 | erot = 1.76165550554388 | epot = -12.5706927741064 | etot = -9.13334910745525 +840000 ekin = 1.62179135099408 | erot = 1.78387657045747 | epot = -12.5390170289077 | etot = -9.13334910745614 +841000 ekin = 1.56488441151269 | erot = 1.81456573942591 | epot = -12.5127992584766 | etot = -9.13334910753801 +842000 ekin = 1.5051739956304 | erot = 1.85205645864684 | epot = -12.4905795619746 | etot = -9.13334910769738 +843000 ekin = 1.44300548284026 | erot = 1.89358112522043 | epot = -12.4699357158672 | etot = -9.13334910780648 +844000 ekin = 1.37906620630966 | erot = 1.93639685186046 | epot = -12.4488121660411 | etot = -9.13334910787098 +845000 ekin = 1.3144635283326 | erot = 1.97812996436157 | epot = -12.4259426005652 | etot = -9.13334910787108 +846000 ekin = 1.25068692329337 | erot = 2.01700234953403 | epot = -12.4010383806304 | etot = -9.13334910780299 +847000 ekin = 1.18947724707863 | erot = 2.05204320491501 | epot = -12.3748695596687 | etot = -9.13334910767511 +848000 ekin = 1.13265732504622 | erot = 2.08314733277916 | epot = -12.3491537653295 | etot = -9.13334910750415 +849000 ekin = 1.0819765776989 | erot = 2.11099249694429 | epot = -12.3263181819525 | etot = -9.13334910730936 +850000 ekin = 1.03899924537938 | erot = 2.1368465428431 | epot = -12.309194895335 | etot = -9.13334910711253 +851000 ekin = 1.00503792489605 | erot = 2.1623061869893 | epot = -12.3006932188196 | etot = -9.13334910693424 +852000 ekin = 0.981116857871262 | erot = 2.18901371773129 | epot = -12.303479682395 | etot = -9.13334910679242 +853000 ekin = 0.96794765222281 | erot = 2.21839549972016 | epot = -12.3196922586459 | etot = -9.1333491067029 +854000 ekin = 0.965908910688589 | erot = 2.25145766400397 | epot = -12.3507156813657 | etot = -9.13334910667314 +855000 ekin = 0.975031148292954 | erot = 2.28866143867713 | epot = -12.3970416936757 | etot = -9.13334910670566 +856000 ekin = 0.994993726119038 | erot = 2.32988587265887 | epot = -12.4582287055741 | etot = -9.13334910679616 +857000 ekin = 1.02514000046133 | erot = 2.37447147763838 | epot = -12.5329605850348 | etot = -9.13334910693512 +858000 ekin = 1.06451194043268 | erot = 2.42132581263493 | epot = -12.6191868601774 | etot = -9.13334910710976 +859000 ekin = 1.11189872921292 | erot = 2.4690621764669 | epot = -12.7143100129873 | etot = -9.13334910730746 +860000 ekin = 1.16588800432871 | erot = 2.51613734357213 | epot = -12.8153744554195 | etot = -9.13334910751864 +861000 ekin = 1.22490604809855 | erot = 2.56095681693364 | epot = -12.9192119727711 | etot = -9.13334910773888 +862000 ekin = 1.28723632580607 | erot = 2.60192847236256 | epot = -13.0225139061386 | etot = -9.13334910796994 +863000 ekin = 1.35101431938164 | erot = 2.63746581475179 | epot = -13.1218292423493 | etot = -9.13334910821584 +864000 ekin = 1.41420820518506 | erot = 2.66596355874673 | epot = -13.2135208724115 | etot = -9.13334910847976 +865000 ekin = 1.47460562928568 | erot = 2.68578195464751 | epot = -13.293736692693 | etot = -9.13334910875978 +866000 ekin = 1.52983303720507 | erot = 2.69527584728228 | epot = -13.3584579935323 | etot = -9.13334910904496 +867000 ekin = 1.57743376516521 | erot = 2.69288933097524 | epot = -13.4036722054551 | etot = -9.13334910931467 +868000 ekin = 1.61502389037011 | erot = 2.67731200502193 | epot = -13.4256850049314 | etot = -9.13334910953937 +869000 ekin = 1.64053051307895 | erot = 2.64766625529469 | epot = -13.4215458780593 | etot = -9.13334910968571 +870000 ekin = 1.65249590024763 | erot = 2.60367561918013 | epot = -13.3895206291507 | etot = -9.13334910972294 +871000 ekin = 1.65040511753613 | erot = 2.54576053416164 | epot = -13.3295147613278 | etot = -9.13334910963006 +872000 ekin = 1.63497077370745 | erot = 2.47502461265043 | epot = -13.2433444957602 | etot = -9.13334910940236 +873000 ekin = 1.60829551086259 | erot = 2.3931286467258 | epot = -13.1347732666425 | etot = -9.13334910905411 +874000 ekin = 1.57383856497734 | erot = 2.30208675137617 | epot = -13.009274424972 | etot = -9.13334910861844 +875000 ekin = 1.53613967512497 | erot = 2.20404109166097 | epot = -12.87352987493 | etot = -9.1333491081441 +876000 ekin = 1.50030007471501 | erot = 2.10106901469611 | epot = -12.7347181970994 | etot = -9.13334910768825 +877000 ekin = 1.47128183650081 | erot = 1.99505592487866 | epot = -12.599686868687 | etot = -9.1333491073075 +878000 ekin = 1.45315269234875 | erot = 1.88764504254387 | epot = -12.4741468419377 | etot = -9.13334910704512 +879000 ekin = 1.4484500959242 | erot = 1.78026193725243 | epot = -12.3620611400957 | etot = -9.13334910691912 +880000 ekin = 1.45783397194032 | erot = 1.6742050362216 | epot = -12.2653881150795 | etot = -9.13334910691757 +881000 ekin = 1.48012455416307 | erot = 1.57078382964385 | epot = -12.1842574908083 | etot = -9.13334910700134 +882000 ekin = 1.51270015736555 | erot = 1.47147015192292 | epot = -12.1175194164069 | etot = -9.13334910711841 +883000 ekin = 1.5521156829125 | erot = 1.37801244882818 | epot = -12.0634772389616 | etot = -9.13334910722095 +884000 ekin = 1.59475301549188 | erot = 1.29246300162702 | epot = -12.0205651243982 | etot = -9.13334910727928 +885000 ekin = 1.63734681491784 | erot = 1.21709221484899 | epot = -11.987788137051 | etot = -9.13334910728419 +886000 ekin = 1.67731211299753 | erot = 1.15420415260206 | epot = -11.9648653728432 | etot = -9.13334910724361 +887000 ekin = 1.71288068345211 | erot = 1.10590165063598 | epot = -11.9521314412624 | etot = -9.13334910717432 +888000 ekin = 1.74309500656667 | erot = 1.073858345309 | epot = -11.9503024589714 | etot = -9.13334910709569 +889000 ekin = 1.76770969091059 | erot = 1.05913784424355 | epot = -11.9601966421812 | etot = -9.13334910702711 +890000 ekin = 1.78703240996087 | erot = 1.06207375035243 | epot = -11.9824552673003 | etot = -9.13334910698695 +891000 ekin = 1.80172329224743 | erot = 1.08220747466363 | epot = -12.0172798739031 | etot = -9.13334910699207 +892000 ekin = 1.81257293682698 | erot = 1.11828058018285 | epot = -12.0642026240651 | etot = -9.13334910705524 +893000 ekin = 1.82028982711598 | erot = 1.16828769625041 | epot = -12.1219266305465 | etot = -9.13334910718006 +894000 ekin = 1.82533649728439 | erot = 1.22960280171497 | epot = -12.1882884063595 | etot = -9.13334910736016 +895000 ekin = 1.82785071659798 | erot = 1.29918775470991 | epot = -12.2603875788833 | etot = -9.13334910757539 +896000 ekin = 1.82766966748232 | erot = 1.37387583336083 | epot = -12.3348946086393 | etot = -9.13334910779613 +897000 ekin = 1.82444603808568 | erot = 1.45069893543788 | epot = -12.4084940815126 | etot = -9.13334910798906 +898000 ekin = 1.81781661006261 | erot = 1.52720356355833 | epot = -12.4783692817472 | etot = -9.13334910812629 +899000 ekin = 1.80756915109973 | erot = 1.60168843027914 | epot = -12.5426066895709 | etot = -9.13334910819201 +900000 ekin = 1.79375843956275 | erot = 1.67330364930424 | epot = -12.6004111970548 | etot = -9.13334910818785 +901000 ekin = 1.77674318476286 | erot = 1.74197941464704 | epot = -12.6520717075409 | etot = -9.13334910813097 +902000 ekin = 1.75714245728886 | erot = 1.80819394407444 | epot = -12.6986855094139 | etot = -9.1333491080506 +903000 ekin = 1.73573344441515 | erot = 1.8726332599067 | epot = -12.7417158123006 | etot = -9.13334910797871 +904000 ekin = 1.71332625908481 | erot = 1.93582474192408 | epot = -12.7825001089508 | etot = -9.13334910794195 +905000 ekin = 1.69065428570243 | erot = 1.997832484398 | epot = -12.8218358780556 | etot = -9.13334910795518 +906000 ekin = 1.66831072855943 | erot = 2.05808381417934 | epot = -12.859743650758 | etot = -9.13334910801925 +907000 ekin = 1.64674588303732 | erot = 2.11535919821992 | epot = -12.8954541893767 | etot = -9.13334910811944 +908000 ekin = 1.62631907113895 | erot = 2.16793324010744 | epot = -12.9276014194806 | etot = -9.13334910823417 +909000 ekin = 1.60738004100341 | erot = 2.21381581981552 | epot = -12.9545449691592 | etot = -9.13334910834033 +910000 ekin = 1.59034402491449 | erot = 2.25102295599486 | epot = -12.9747160893305 | etot = -9.13334910842113 +911000 ekin = 1.57572782711068 | erot = 2.27781488081605 | epot = -12.9868918163945 | etot = -9.13334910846772 +912000 ekin = 1.56413054683431 | erot = 2.29287003003294 | epot = -12.9903496853461 | etot = -9.13334910847881 +913000 ekin = 1.55616398737755 | erot = 2.29539983333496 | epot = -12.9849129291696 | etot = -9.13334910845707 +914000 ekin = 1.55235379274356 | erot = 2.28522760386229 | epot = -12.9709305050114 | etot = -9.13334910840559 +915000 ekin = 1.55303636075837 | erot = 2.26284508696368 | epot = -12.9492305560505 | etot = -9.1333491083285 +916000 ekin = 1.558270033732 | erot = 2.2294333936006 | epot = -12.9210525355647 | etot = -9.13334910823207 +917000 ekin = 1.56776924055716 | erot = 2.18681551598127 | epot = -12.8879338646653 | etot = -9.13334910812686 +918000 ekin = 1.58086450735507 | erot = 2.13731406706164 | epot = -12.8515276824452 | etot = -9.13334910802845 +919000 ekin = 1.59649190921421 | erot = 2.08351907893672 | epot = -12.8133600961037 | etot = -9.13334910795277 +920000 ekin = 1.61321892883505 | erot = 2.02800735916499 | epot = -12.7745753959123 | etot = -9.13334910791221 +921000 ekin = 1.62931395437706 | erot = 1.97307497750766 | epot = -12.7357380397973 | etot = -9.13334910791261 +922000 ekin = 1.64286104746755 | erot = 1.92053870341123 | epot = -12.6967488588289 | etot = -9.1333491079501 +923000 ekin = 1.65191234391208 | erot = 1.87163759208356 | epot = -12.6568990440091 | etot = -9.13334910801345 +924000 ekin = 1.6546620620163 | erot = 1.82703710613629 | epot = -12.6150482762386 | etot = -9.13334910808597 +925000 ekin = 1.64962158356488 | erot = 1.78691680128824 | epot = -12.5698874930026 | etot = -9.13334910814945 +926000 ekin = 1.63577435706327 | erot = 1.75111283231059 | epot = -12.5202362975603 | etot = -9.13334910818647 +927000 ekin = 1.61269412581393 | erot = 1.71928618608138 | epot = -12.4653294200783 | etot = -9.13334910818301 +928000 ekin = 1.58061327338809 | erot = 1.69109387513091 | epot = -12.4050562566481 | etot = -9.13334910812912 +929000 ekin = 1.54043465718972 | erot = 1.66634444993707 | epot = -12.3401282151473 | etot = -9.13334910802047 +930000 ekin = 1.49368612297313 | erot = 1.64511875929247 | epot = -12.272153990125 | etot = -9.13334910785945 +931000 ekin = 1.44242020036052 | erot = 1.6278309239395 | epot = -12.2036002319575 | etot = -9.13334910765746 +932000 ekin = 1.38906420478282 | erot = 1.61520048767775 | epot = -12.137613799896 | etot = -9.13334910743542 +933000 ekin = 1.33622958396584 | erot = 1.60811568409894 | epot = -12.0776943752874 | etot = -9.13334910722262 +934000 ekin = 1.28649486983533 | erot = 1.60739378972487 | epot = -12.0272377666147 | etot = -9.13334910705454 +935000 ekin = 1.24218246526101 | erot = 1.6134791908304 | epot = -11.9890107630556 | etot = -9.13334910696424 +936000 ekin = 1.20515312898663 | erot = 1.62614770365626 | epot = -11.9646499396199 | etot = -9.13334910697703 +937000 ekin = 1.17664231217631 | erot = 1.64429583354369 | epot = -11.9542872528244 | etot = -9.13334910710443 +938000 ekin = 1.15716006421835 | erot = 1.66588444174823 | epot = -11.956393613306 | etot = -9.13334910733941 +939000 ekin = 1.14647171712446 | erot = 1.68810326831248 | epot = -11.9679240930837 | etot = -9.1333491076468 +940000 ekin = 1.14367004082762 | erot = 1.70771457433182 | epot = -11.9847337231556 | etot = -9.13334910799618 +941000 ekin = 1.14733884564953 | erot = 1.72149292699345 | epot = -12.0021808809647 | etot = -9.13334910832173 +942000 ekin = 1.15580134682141 | erot = 1.72687300439486 | epot = -12.0160234597784 | etot = -9.13334910856215 +943000 ekin = 1.16743729515031 | erot = 1.7224993662459 | epot = -12.0232857700611 | etot = -9.13334910866491 +944000 ekin = 1.18103106476093 | erot = 1.70858712462871 | epot = -12.0229672979909 | etot = -9.13334910860129 +945000 ekin = 1.19606804455176 | erot = 1.68696892705712 | epot = -12.0163860799919 | etot = -9.133349108383 +946000 ekin = 1.21284058110716 | erot = 1.66075870248008 | epot = -12.0069483916594 | etot = -9.13334910807221 +947000 ekin = 1.2322221057333 | erot = 1.6336701113832 | epot = -11.9992413248876 | etot = -9.1333491077711 +948000 ekin = 1.25509690716023 | erot = 1.60916358070824 | epot = -11.997609595455 | etot = -9.13334910758657 +949000 ekin = 1.28167104221162 | erot = 1.58969080392993 | epot = -12.0047109537215 | etot = -9.13334910757998 +950000 ekin = 1.31105510038426 | erot = 1.57628415673958 | epot = -12.0206883648617 | etot = -9.13334910773781 +951000 ekin = 1.34140314928851 | erot = 1.56859135849483 | epot = -12.043343615766 | etot = -9.13334910798267 +952000 ekin = 1.37054117669026 | erot = 1.56526000759141 | epot = -12.0691502925028 | etot = -9.13334910822116 +953000 ekin = 1.39670348101754 | erot = 1.5644462174252 | epot = -12.0944988068345 | etot = -9.13334910839174 +954000 ekin = 1.41897529237989 | erot = 1.56423287015224 | epot = -12.1165572710139 | etot = -9.13334910848181 +955000 ekin = 1.43729048070498 | erot = 1.56287479953566 | epot = -12.1335143887518 | etot = -9.13334910851119 +956000 ekin = 1.45211066332637 | erot = 1.55892938548462 | epot = -12.1443891573166 | etot = -9.13334910850562 +957000 ekin = 1.46402190623229 | erot = 1.55132217597032 | epot = -12.1486931906856 | etot = -9.13334910848299 +958000 ekin = 1.47342593725725 | erot = 1.53954965712618 | epot = -12.1463247028191 | etot = -9.13334910843566 +959000 ekin = 1.48038578495096 | erot = 1.52394133602091 | epot = -12.1376762293307 | etot = -9.13334910835885 +960000 ekin = 1.48460604034335 | erot = 1.50575363437721 | epot = -12.1237087829657 | etot = -9.13334910824515 +961000 ekin = 1.48549975936425 | erot = 1.48721075412639 | epot = -12.106059621583 | etot = -9.1333491080924 +962000 ekin = 1.48229853496739 | erot = 1.47141202583365 | epot = -12.0870596687075 | etot = -9.13334910790648 +963000 ekin = 1.47417603272498 | erot = 1.4621024086719 | epot = -12.0696275490985 | etot = -9.13334910770162 +964000 ekin = 1.46036644525383 | erot = 1.46332191688609 | epot = -12.0570374696365 | etot = -9.13334910749659 +965000 ekin = 1.44026662182329 | erot = 1.47896324785884 | epot = -12.052578977 | etot = -9.13334910731783 +966000 ekin = 1.4135158340093 | erot = 1.51227943251122 | epot = -12.0591443737113 | etot = -9.13334910719082 +967000 ekin = 1.38005134112541 | erot = 1.56539665061944 | epot = -12.0787970988851 | etot = -9.13334910714022 +968000 ekin = 1.34025482724918 | erot = 1.63885686276601 | epot = -12.1124607971915 | etot = -9.13334910717636 +969000 ekin = 1.29476921981899 | erot = 1.73132793710009 | epot = -12.1594462642422 | etot = -9.13334910732313 +970000 ekin = 1.24442005393169 | erot = 1.83972520711888 | epot = -12.2174943685907 | etot = -9.13334910754013 +971000 ekin = 1.19046696427576 | erot = 1.95943091408832 | epot = -12.2832469861607 | etot = -9.13334910779659 +972000 ekin = 1.13463097113848 | erot = 2.08475088502066 | epot = -12.3527309642089 | etot = -9.1333491080498 +973000 ekin = 1.07911059567929 | erot = 2.20953944501601 | epot = -12.4219991489535 | etot = -9.13334910825824 +974000 ekin = 1.02657367041509 | erot = 2.32774347839951 | epot = -12.4876662572392 | etot = -9.13334910842461 +975000 ekin = 0.979977932766863 | erot = 2.43392801404157 | epot = -12.5472550552954 | etot = -9.13334910848701 +976000 ekin = 0.94230488709895 | erot = 2.52399013955653 | epot = -12.5996441351294 | etot = -9.13334910847391 +977000 ekin = 0.91633529570579 | erot = 2.59517570124248 | epot = -12.6448601053594 | etot = -9.13334910841115 +978000 ekin = 0.90431642289214 | erot = 2.64601698757991 | epot = -12.6836825188045 | etot = -9.13334910833241 +979000 ekin = 0.907654941510261 | erot = 2.6761270404601 | epot = -12.71713109024 | etot = -9.13334910826961 +980000 ekin = 0.926700183438494 | erot = 2.68592744664267 | epot = -12.7459767383264 | etot = -9.13334910824523 +981000 ekin = 0.960659745242717 | erot = 2.67638285527776 | epot = -12.7703917087879 | etot = -9.13334910826741 +982000 ekin = 1.00766017971564 | erot = 2.64879736701281 | epot = -12.7898066550596 | etot = -9.13334910833116 +983000 ekin = 1.06493892794523 | erot = 2.60470505316476 | epot = -12.8029930895281 | etot = -9.13334910841806 +984000 ekin = 1.12913508942421 | erot = 2.54586103455826 | epot = -12.8083452324831 | etot = -9.13334910850068 +985000 ekin = 1.19663599745925 | erot = 2.47431116852314 | epot = -12.8042962745322 | etot = -9.1333491085498 +986000 ekin = 1.26393164267929 | erot = 2.39249159638855 | epot = -12.7897723476083 | etot = -9.13334910854048 +987000 ekin = 1.32792910236438 | erot = 2.30329384117695 | epot = -12.7645720520012 | etot = -9.13334910845985 +988000 ekin = 1.3861859405166 | erot = 2.21003704541747 | epot = -12.7295720942441 | etot = -9.13334910831006 +989000 ekin = 1.43703663165014 | erot = 2.11631776636421 | epot = -12.6867035061226 | etot = -9.13334910810827 +990000 ekin = 1.47960743025892 | erot = 2.02574976476802 | epot = -12.6387063029087 | etot = -9.13334910788175 +991000 ekin = 1.513737246522 | erot = 1.9416427247741 | epot = -12.5887290789572 | etot = -9.13334910766114 +992000 ekin = 1.53983818592274 | erot = 1.86668512516562 | epot = -12.5398724185622 | etot = -9.13334910747385 +993000 ekin = 1.55873490673449 | erot = 1.802689820056 | epot = -12.4947738341302 | etot = -9.13334910733969 +994000 ekin = 1.57151651514591 | erot = 1.75043914206451 | epot = -12.4553047644786 | etot = -9.1333491072682 +995000 ekin = 1.57942173435718 | erot = 1.70964079469539 | epot = -12.4224116363128 | etot = -9.1333491072602 +996000 ekin = 1.58376261672296 | erot = 1.67898574513455 | epot = -12.3960974691663 | etot = -9.13334910730874 +997000 ekin = 1.5858787857511 | erot = 1.65629050261201 | epot = -12.375518395765 | etot = -9.13334910740189 +998000 ekin = 1.58710748471057 | erot = 1.63870906511977 | epot = -12.3591656573538 | etot = -9.13334910752346 +999000 ekin = 1.5887560319907 | erot = 1.62299637539511 | epot = -12.3451015150432 | etot = -9.13334910765744 +1000000 ekin = 1.59207001214641 | erot = 1.60581739808838 | epot = -12.3312365180167 | etot = -9.13334910778188 + 1000000 0.11793111 -1.2674127 0.034288999 -1.0739167 -1.3883882e-05 64000 +Loop time of 12.7173 on 4 procs for 1000000 steps with 10 atoms + +Performance: 67939.084 tau/day, 78633.199 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8787 | 4.0355 | 6.8248 | 81.1 | 31.73 +Bond | 0.17702 | 0.24819 | 0.33387 | 12.1 | 1.95 +Neigh | 0.011662 | 0.011722 | 0.011792 | 0.0 | 0.09 +Comm | 3.0536 | 6.1653 | 7.5423 | 73.5 | 48.48 +Output | 0.074083 | 0.07729 | 0.082929 | 1.2 | 0.61 +Modify | 0.52866 | 0.63564 | 0.74059 | 12.0 | 5.00 +Other | | 1.544 | | | 12.14 + +Nlocal: 2.50000 ave 4 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.50000 ave 9 max 6 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25000 ave 19 max 5 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7000000 +Ave special neighs/atom = 3.6000000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:12 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/data.duplex2 new file mode 100644 index 0000000000..8c985708ca --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file via write_data, version 27 May 2021 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0 +2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0 +3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0 +4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0 +5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0 +6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0 +7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0 +8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0 +9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0 +10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0 +11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0 +12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0 +13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0 +14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0 +15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0 +16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725 +2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215 +3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625 +4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877 +5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292 +6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776 +7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357 +8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032 +9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696 +10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506 +11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418 +12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697 +13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132 +14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759 +15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106 +16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2 similarity index 65% rename from examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 rename to examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2 index 8307d805c3..de0ce851fd 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2 @@ -7,15 +7,15 @@ units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 1 delay 0 check yes read_data data.duplex2 @@ -40,27 +40,16 @@ pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 # NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" +compute quat all property/atom quatw quati quatj quatk compute erot all erotate/asphere compute ekin all ke @@ -71,10 +60,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" run 1000000 -#write_restart config.${number}.* +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 new file mode 100644 index 0000000000..d34e7a16b7 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 @@ -0,0 +1,1173 @@ +LAMMPS (2 Jul 2021) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +set atom * mass 3.1575 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.9560004 + ghost atom cutoff = 3.8 + binsize = 1.4780002, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -21.9967648054699 | etot = -16.4902901461834 +Per MPI rank memory allocation (min/avg/max) = 9.076 | 9.076 | 9.076 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -1.3914531 0.016655298 -1.2057507 5.174549e-05 64000 +1000 ekin = 2.68462004451395 | erot = 2.58605420555131 | epot = -21.8105393794712 | etot = -16.5398651294059 +2000 ekin = 2.60963739095655 | erot = 2.48175619043154 | epot = -21.6459705488588 | etot = -16.5545769674707 +3000 ekin = 2.63989588847182 | erot = 2.46363051573262 | epot = -21.5254922679992 | etot = -16.4219658637948 +4000 ekin = 2.5752038952926 | erot = 2.37178501784054 | epot = -21.4327542438291 | etot = -16.485765330696 +5000 ekin = 2.5044104280733 | erot = 2.08769632851087 | epot = -21.3521450303024 | etot = -16.7600382737182 +6000 ekin = 2.36107642071569 | erot = 2.35003179412404 | epot = -21.2782010260872 | etot = -16.5670928112475 +7000 ekin = 2.37495351372023 | erot = 2.16846238087391 | epot = -21.2534688435259 | etot = -16.7100529489318 +8000 ekin = 2.42775724176586 | erot = 2.14686490397955 | epot = -21.2553298683528 | etot = -16.6807077226074 +9000 ekin = 2.3142246486707 | erot = 1.86378622524029 | epot = -21.2852707364932 | etot = -17.1072598625822 +10000 ekin = 2.3275093348898 | erot = 1.94087852055647 | epot = -21.3429178830636 | etot = -17.0745300276174 +11000 ekin = 2.23983345215335 | erot = 2.16573111806154 | epot = -21.4294123399218 | etot = -17.0238477697069 +12000 ekin = 2.24948652666019 | erot = 2.32563449403283 | epot = -21.5368720528798 | etot = -16.9617510321868 +13000 ekin = 2.31412690264891 | erot = 2.54687184991592 | epot = -21.6246755313501 | etot = -16.7636767787852 +14000 ekin = 2.30456735091103 | erot = 2.82813231901187 | epot = -21.6854822284277 | etot = -16.5527825585048 +15000 ekin = 2.41196948877886 | erot = 2.60315540839479 | epot = -21.7080540027113 | etot = -16.6929291055377 +16000 ekin = 2.32930626459587 | erot = 2.77308393739999 | epot = -21.6887196306943 | etot = -16.5863294286984 +17000 ekin = 2.39617472660395 | erot = 3.03091034756247 | epot = -21.6395184677657 | etot = -16.2124333935992 +18000 ekin = 2.33279500895535 | erot = 3.1434171004899 | epot = -21.574127817026 | etot = -16.0979157075807 +19000 ekin = 2.42845349180333 | erot = 2.98452732659568 | epot = -21.4895578941598 | etot = -16.0765770757608 +20000 ekin = 2.58234763441792 | erot = 3.3325207031799 | epot = -21.3975543217035 | etot = -15.4826859841057 +21000 ekin = 2.64494557638589 | erot = 3.32881968524114 | epot = -21.3229796202748 | etot = -15.3492143586477 +22000 ekin = 2.65030022474653 | erot = 3.26762562263424 | epot = -21.2713919939757 | etot = -15.353466146595 +23000 ekin = 2.74232842321971 | erot = 2.85782586045784 | epot = -21.2433172110302 | etot = -15.6431629273527 +24000 ekin = 2.70913362671027 | erot = 2.56145704641761 | epot = -21.2492397215427 | etot = -15.9786490484148 +25000 ekin = 2.71785549515023 | erot = 2.45020590769015 | epot = -21.2696953560916 | etot = -16.1016339532512 +26000 ekin = 2.80969274934567 | erot = 2.57761600133553 | epot = -21.3121170333525 | etot = -15.9248082826713 +27000 ekin = 2.90228693281852 | erot = 2.52543294446064 | epot = -21.3618959826308 | etot = -15.9341761053517 +28000 ekin = 2.80577992946706 | erot = 2.42942187536898 | epot = -21.4238267965375 | etot = -16.1886249917015 +29000 ekin = 2.84024245066251 | erot = 2.37728970052668 | epot = -21.5220045306242 | etot = -16.304472379435 +30000 ekin = 2.91820846152587 | erot = 2.52858255324276 | epot = -21.6452589795617 | etot = -16.1984679647931 +31000 ekin = 3.01591597087959 | erot = 2.66934437756135 | epot = -21.7837708816785 | etot = -16.0985105332375 +32000 ekin = 3.18554066714549 | erot = 2.70126504453979 | epot = -21.9266237283442 | etot = -16.0398180166589 +33000 ekin = 3.45591097869953 | erot = 3.05486835802111 | epot = -22.0467287622724 | etot = -15.5359494255518 +34000 ekin = 3.47254829729213 | erot = 3.41663527351808 | epot = -22.1468381626759 | etot = -15.2576545918657 +35000 ekin = 3.45946416092998 | erot = 3.21776014393844 | epot = -22.2021645741413 | etot = -15.5249402692728 +36000 ekin = 3.38072119723002 | erot = 2.98891843833273 | epot = -22.2024978629579 | etot = -15.8328582273952 +37000 ekin = 3.29783742910393 | erot = 2.73521555931898 | epot = -22.1657123704833 | etot = -16.1326593820604 +38000 ekin = 3.33959958296015 | erot = 2.61778320328389 | epot = -22.1041970676607 | etot = -16.1468142814167 +39000 ekin = 3.23639805960116 | erot = 2.5837352210672 | epot = -22.009642154348 | etot = -16.1895088736797 +40000 ekin = 3.11586138662867 | erot = 2.1962482086394 | epot = -21.8962581958555 | etot = -16.5841486005874 +41000 ekin = 3.04246623801455 | erot = 2.23321889509941 | epot = -21.8077873635659 | etot = -16.5321022304519 +42000 ekin = 2.84983279602745 | erot = 2.80264211079691 | epot = -21.7482556058168 | etot = -16.0957806989925 +43000 ekin = 2.79124232412404 | erot = 2.40517464805213 | epot = -21.7040912326958 | etot = -16.5076742605196 +44000 ekin = 2.66237577064427 | erot = 2.48075679823098 | epot = -21.6865985692201 | etot = -16.5434660003448 +45000 ekin = 2.579411834329 | erot = 2.5121056113297 | epot = -21.7100580821223 | etot = -16.6185406364636 +46000 ekin = 2.73276177831298 | erot = 2.72002755015629 | epot = -21.7400457171798 | etot = -16.2872563887106 +47000 ekin = 2.64234876254597 | erot = 2.59091566156281 | epot = -21.7975985084292 | etot = -16.5643340843204 +48000 ekin = 2.59173469012523 | erot = 2.43590670780649 | epot = -21.8709604205578 | etot = -16.8433190226261 +49000 ekin = 2.72309795319077 | erot = 2.23156431391332 | epot = -21.9468429014909 | etot = -16.9921806343868 +50000 ekin = 2.84714836170722 | erot = 1.99663528516202 | epot = -22.0121784873832 | etot = -17.168394840514 +51000 ekin = 2.89884791688876 | erot = 1.91491454776672 | epot = -22.0530950349948 | etot = -17.2393325703393 +52000 ekin = 3.03617525579662 | erot = 2.19848391536797 | epot = -22.0866976985223 | etot = -16.8520385273577 +53000 ekin = 2.99175374915047 | erot = 2.39711100098153 | epot = -22.1010575333115 | etot = -16.7121927831795 +54000 ekin = 2.99574935861407 | erot = 2.32745187661854 | epot = -22.1028140124058 | etot = -16.7796127771732 +55000 ekin = 2.99570982560695 | erot = 2.49897185698994 | epot = -22.1057238568571 | etot = -16.6110421742602 +56000 ekin = 2.94925439949793 | erot = 2.44012089769549 | epot = -22.0870769441158 | etot = -16.6977016469224 +57000 ekin = 2.94734500065243 | erot = 2.12984920172195 | epot = -22.0412734212002 | etot = -16.9640792188258 +58000 ekin = 2.81955133884049 | erot = 2.13458872869615 | epot = -21.9788636009449 | etot = -17.0247235334082 +59000 ekin = 2.70811531854742 | erot = 2.38980716247399 | epot = -21.8949081752974 | etot = -16.796985694276 +60000 ekin = 2.70414157935554 | erot = 2.55940091198388 | epot = -21.7861093627117 | etot = -16.5225668713722 +61000 ekin = 2.65859389245701 | erot = 2.53396073555874 | epot = -21.6569039895119 | etot = -16.4643493614962 +62000 ekin = 2.60219558362534 | erot = 2.22515394919036 | epot = -21.5116333689023 | etot = -16.6842838360866 +63000 ekin = 2.63153399947693 | erot = 2.22422110021199 | epot = -21.3652621775791 | etot = -16.5095070778902 +64000 ekin = 2.74532788694554 | erot = 2.18523109551402 | epot = -21.2714335683309 | etot = -16.3408745858713 +65000 ekin = 2.7205493838435 | erot = 2.07343889460204 | epot = -21.2024805852124 | etot = -16.4084923067669 +66000 ekin = 2.58244112846423 | erot = 2.07735193876553 | epot = -21.1764160570954 | etot = -16.5166229898656 +67000 ekin = 2.57755413160872 | erot = 2.44046690225443 | epot = -21.1906023260749 | etot = -16.1725812922118 +68000 ekin = 2.48736395314823 | erot = 2.12758461162304 | epot = -21.2185147422317 | etot = -16.6035661774605 +69000 ekin = 2.41843849956023 | erot = 2.18515112080921 | epot = -21.2498143720114 | etot = -16.6462247516419 +70000 ekin = 2.42405639999479 | erot = 1.9565032993001 | epot = -21.2748182794301 | etot = -16.8942585801352 +71000 ekin = 2.43121308276013 | erot = 1.85632548443178 | epot = -21.3045707498284 | etot = -17.0170321826365 +72000 ekin = 2.5000870368839 | erot = 1.5991945591491 | epot = -21.3493737552796 | etot = -17.2500921592466 +73000 ekin = 2.68616751062557 | erot = 1.88927937064781 | epot = -21.3998788656788 | etot = -16.8244319844054 +74000 ekin = 2.72642650296669 | erot = 1.98526997108517 | epot = -21.439395334657 | etot = -16.7276988606051 +75000 ekin = 2.82872762184213 | erot = 2.08391491924428 | epot = -21.4749344303949 | etot = -16.5622918893085 +76000 ekin = 2.90099143523699 | erot = 2.16095088121795 | epot = -21.4935371507519 | etot = -16.431594834297 +77000 ekin = 3.18544250151153 | erot = 2.00037055601337 | epot = -21.4789486218771 | etot = -16.2931355643522 +78000 ekin = 3.25276485916348 | erot = 2.04037410610699 | epot = -21.4312552501158 | etot = -16.1381162848453 +79000 ekin = 3.31064968204676 | erot = 2.17606310098547 | epot = -21.3489462542885 | etot = -15.8622334712563 +80000 ekin = 3.25017314792773 | erot = 1.78411830235593 | epot = -21.2684346239656 | etot = -16.2341431736819 +81000 ekin = 3.28475664530889 | erot = 1.6269439305135 | epot = -21.2092459483417 | etot = -16.2975453725193 +82000 ekin = 3.22905109952644 | erot = 1.53744252292452 | epot = -21.2050298148135 | etot = -16.4385361923625 +83000 ekin = 3.23231520762086 | erot = 1.77352705563456 | epot = -21.2433468675556 | etot = -16.2375046043002 +84000 ekin = 3.26867693921993 | erot = 1.72038623835529 | epot = -21.2969079823479 | etot = -16.3078448047727 +85000 ekin = 3.24886887492843 | erot = 1.71422228707811 | epot = -21.348730473811 | etot = -16.3856393118045 +86000 ekin = 3.37388966908809 | erot = 2.05166004106914 | epot = -21.4140353196308 | etot = -15.9884856094735 +87000 ekin = 3.32398602808495 | erot = 2.11391553019111 | epot = -21.5044251629371 | etot = -16.0665236046611 +88000 ekin = 3.37321522230425 | erot = 1.88481910803278 | epot = -21.6374519675635 | etot = -16.3794176372264 +89000 ekin = 3.40287848450242 | erot = 1.74012560118449 | epot = -21.7814074383677 | etot = -16.6384033526808 +90000 ekin = 3.56172892861223 | erot = 2.10522136125784 | epot = -21.9615291243628 | etot = -16.2945788344928 +91000 ekin = 3.55669957238093 | erot = 2.42086123522057 | epot = -22.1511779304614 | etot = -16.1736171228599 +92000 ekin = 3.6423779131713 | erot = 2.65970416317374 | epot = -22.3488733671942 | etot = -16.0467912908492 +93000 ekin = 3.71183685172061 | erot = 2.62133287897562 | epot = -22.5092709223126 | etot = -16.1761011916163 +94000 ekin = 3.68157545521779 | erot = 2.4553153988724 | epot = -22.6307602436275 | etot = -16.4938693895373 +95000 ekin = 3.60128502265547 | erot = 2.60141757186749 | epot = -22.7389627643834 | etot = -16.5362601698605 +96000 ekin = 3.53126429160544 | erot = 2.72315885473469 | epot = -22.817764620346 | etot = -16.5633414740059 +97000 ekin = 3.4733587719158 | erot = 2.74980204474205 | epot = -22.8599102318749 | etot = -16.636749415217 +98000 ekin = 3.36569576671696 | erot = 2.64094316029087 | epot = -22.8536591989748 | etot = -16.8470202719669 +99000 ekin = 3.17486973109315 | erot = 2.83643491109138 | epot = -22.8212456182643 | etot = -16.8099409760798 +100000 ekin = 2.98877854809326 | erot = 2.8502739133799 | epot = -22.7838710680404 | etot = -16.9448186065672 +101000 ekin = 2.80581049577973 | erot = 2.78036845929874 | epot = -22.7080420278473 | etot = -17.1218630727688 +102000 ekin = 2.61146211544526 | erot = 3.14391622209059 | epot = -22.5804486115114 | etot = -16.8250702739755 +103000 ekin = 2.52473332619733 | erot = 3.13557205223546 | epot = -22.4165363785398 | etot = -16.756231000107 +104000 ekin = 2.38813618870064 | erot = 2.81177058896972 | epot = -22.253348909294 | etot = -17.0534421316236 +105000 ekin = 2.27037902349684 | erot = 2.38822666643154 | epot = -22.0942448767486 | etot = -17.4356391868202 +106000 ekin = 2.14052224393176 | erot = 2.10858697946665 | epot = -21.9851740201843 | etot = -17.7360647967859 +107000 ekin = 2.0606875579471 | erot = 2.32025367575515 | epot = -21.9181411680675 | etot = -17.5371999343652 +108000 ekin = 2.16310171427444 | erot = 2.45914268610289 | epot = -21.8972466640829 | etot = -17.2750022637055 +109000 ekin = 2.16408281408934 | erot = 2.39028083194269 | epot = -21.9223151975609 | etot = -17.3679515515289 +110000 ekin = 2.27703874503429 | erot = 2.02252280342046 | epot = -21.9984748890034 | etot = -17.6989133405487 +111000 ekin = 2.42168812145148 | erot = 2.08603766327776 | epot = -22.1196725497682 | etot = -17.6119467650389 +112000 ekin = 2.55041354840496 | erot = 2.05316660200933 | epot = -22.2467875616205 | etot = -17.6432074112062 +113000 ekin = 2.65118330223835 | erot = 1.84663307233114 | epot = -22.3714662854257 | etot = -17.8736499108562 +114000 ekin = 2.75066239210875 | erot = 2.06979110412731 | epot = -22.4757786127357 | etot = -17.6553251164996 +115000 ekin = 2.74969592573214 | erot = 2.20672640542628 | epot = -22.5825353241201 | etot = -17.6261129929616 +116000 ekin = 2.83312076133629 | erot = 2.23062165851058 | epot = -22.6813212117304 | etot = -17.6175787918835 +117000 ekin = 2.88175954095811 | erot = 2.38703791420887 | epot = -22.7694466083741 | etot = -17.5006491532071 +118000 ekin = 2.93568625662289 | erot = 2.26039492756773 | epot = -22.8432426400157 | etot = -17.6471614558251 +119000 ekin = 3.19523724062632 | erot = 2.22567760232918 | epot = -22.8880366342743 | etot = -17.4671217913188 +120000 ekin = 3.17008032268755 | erot = 2.25532705796806 | epot = -22.9065026704633 | etot = -17.4810952898077 +121000 ekin = 3.22925408627794 | erot = 2.42139198931066 | epot = -22.9068338710661 | etot = -17.2561877954775 +122000 ekin = 3.16756628646271 | erot = 2.29253955659868 | epot = -22.9100933328212 | etot = -17.4499874897599 +123000 ekin = 3.1388698885873 | erot = 1.87373916792771 | epot = -22.9201354096178 | etot = -17.9075263531028 +124000 ekin = 3.07340133048028 | erot = 2.07486210586024 | epot = -22.9196688561523 | etot = -17.7714054198118 +125000 ekin = 3.01797638857702 | erot = 1.75538270899542 | epot = -22.9139839700497 | etot = -18.1406248724773 +126000 ekin = 2.96636842974594 | erot = 1.89046865067191 | epot = -22.9078794876243 | etot = -18.0510424072065 +127000 ekin = 2.99891017927356 | erot = 1.92488638621193 | epot = -22.8780661376737 | etot = -17.9542695721882 +128000 ekin = 3.07056715413786 | erot = 1.99149347655671 | epot = -22.8571726497157 | etot = -17.7951120190211 +129000 ekin = 3.004345959888 | erot = 1.94814247853281 | epot = -22.8246013230693 | etot = -17.8721128846485 +130000 ekin = 2.83701493144516 | erot = 2.50342892051144 | epot = -22.760915431814 | etot = -17.4204715798574 +131000 ekin = 2.72472484234373 | erot = 2.70734329989557 | epot = -22.6636087699673 | etot = -17.231540627728 +132000 ekin = 2.62389553593816 | erot = 2.52695276027318 | epot = -22.5087045821917 | etot = -17.3578562859804 +133000 ekin = 2.63528199515899 | erot = 2.39127524409793 | epot = -22.2966493236603 | etot = -17.2700920844034 +134000 ekin = 2.50610716876237 | erot = 2.09594811418198 | epot = -22.0718067043304 | etot = -17.469751421386 +135000 ekin = 2.48472772183193 | erot = 2.14881599404776 | epot = -21.8608678335616 | etot = -17.2273241176819 +136000 ekin = 2.53382275845191 | erot = 1.74309578227989 | epot = -21.6765558191783 | etot = -17.3996372784465 +137000 ekin = 2.57036342314515 | erot = 1.7588568598538 | epot = -21.5407454007373 | etot = -17.2115251177384 +138000 ekin = 2.52929445682248 | erot = 1.9194597735102 | epot = -21.4409011955174 | etot = -16.9921469651847 +139000 ekin = 2.57663737105062 | erot = 1.80679457632207 | epot = -21.3860974283602 | etot = -17.0026654809875 +140000 ekin = 2.62053160118783 | erot = 1.51774101989576 | epot = -21.3676503668329 | etot = -17.2293777457493 +141000 ekin = 2.6118920049466 | erot = 1.5506551574555 | epot = -21.3802632860277 | etot = -17.2177161236256 +142000 ekin = 2.51798883678619 | erot = 1.67942283127776 | epot = -21.4214580445684 | etot = -17.2240463765044 +143000 ekin = 2.49892771964518 | erot = 1.52127122899831 | epot = -21.4923083558109 | etot = -17.4721094071674 +144000 ekin = 2.54740250437642 | erot = 1.82241986650803 | epot = -21.6130145049208 | etot = -17.2431921340363 +145000 ekin = 2.56862853368623 | erot = 2.14471322493978 | epot = -21.7452461002774 | etot = -17.0319043416514 +146000 ekin = 2.67329509039847 | erot = 2.25975512947148 | epot = -21.8437012603417 | etot = -16.9106510404717 +147000 ekin = 2.68893868818078 | erot = 2.55718401446969 | epot = -21.9010658016926 | etot = -16.6549430990422 +148000 ekin = 2.81386130771021 | erot = 2.5983058482173 | epot = -21.9210519662198 | etot = -16.5088848102923 +149000 ekin = 2.74990137245699 | erot = 2.32741538507081 | epot = -21.9278539711832 | etot = -16.8505372136554 +150000 ekin = 2.69038170783773 | erot = 2.42676335467449 | epot = -21.8989948167631 | etot = -16.7818497542509 +151000 ekin = 2.66678982895832 | erot = 2.39492028203076 | epot = -21.7008835367967 | etot = -16.6391734258076 +152000 ekin = 2.67029595868374 | erot = 2.53847066662008 | epot = -21.5894578659902 | etot = -16.3806912406864 +153000 ekin = 2.70694158654279 | erot = 2.72265775556547 | epot = -21.7448041240557 | etot = -16.3152047819475 +154000 ekin = 2.79926075391893 | erot = 2.75974679901157 | epot = -21.8203547485971 | etot = -16.2613471956666 +155000 ekin = 2.72511299719383 | erot = 2.88818303221421 | epot = -21.7319777070931 | etot = -16.118681677685 +156000 ekin = 2.65694010664888 | erot = 2.78004189782702 | epot = -21.6308520721295 | etot = -16.1938700676536 +157000 ekin = 2.56365508198589 | erot = 2.71035147954075 | epot = -21.5253087387148 | etot = -16.2513021771881 +158000 ekin = 2.57548107386937 | erot = 2.73764982143024 | epot = -21.438245204372 | etot = -16.1251143090724 +159000 ekin = 2.55799392432019 | erot = 2.92697271834242 | epot = -21.3737314732349 | etot = -15.8887648305723 +160000 ekin = 2.5467948620766 | erot = 2.80531497281545 | epot = -21.3130996693779 | etot = -15.9609898344858 +161000 ekin = 2.47207886924359 | erot = 2.90722613339808 | epot = -21.2672221196596 | etot = -15.8879171170179 +162000 ekin = 2.51623650472988 | erot = 2.57045306394746 | epot = -21.2288584749413 | etot = -16.1421689062639 +163000 ekin = 2.52126404883992 | erot = 2.48352069988724 | epot = -21.2217116449121 | etot = -16.2169268961849 +164000 ekin = 2.53114565385924 | erot = 2.34165200793299 | epot = -21.2429890011705 | etot = -16.3701913393782 +165000 ekin = 2.59660343236104 | erot = 2.12645014227906 | epot = -21.2869963722376 | etot = -16.5639427975975 +166000 ekin = 2.69364521809343 | erot = 2.06502693559814 | epot = -21.3443825816708 | etot = -16.5857104279792 +167000 ekin = 2.72157576348886 | erot = 2.11628142912493 | epot = -21.4170430149546 | etot = -16.5791858223408 +168000 ekin = 2.74006852516302 | erot = 2.16126360687329 | epot = -21.509919793566 | etot = -16.6085876615297 +169000 ekin = 2.84315657816746 | erot = 1.97243923170443 | epot = -21.59492652498 | etot = -16.7793307151081 +170000 ekin = 3.06124015523339 | erot = 1.92459124184589 | epot = -21.6783552680507 | etot = -16.6925238709714 +171000 ekin = 3.21151355702374 | erot = 1.59351420769781 | epot = -21.7622259493219 | etot = -16.9571981846004 +172000 ekin = 3.3654441272643 | erot = 1.67007198308062 | epot = -21.8306762430334 | etot = -16.7951601326884 +173000 ekin = 3.41001134336526 | erot = 1.87953941868167 | epot = -21.8787020007149 | etot = -16.5891512386679 +174000 ekin = 3.46376447230266 | erot = 1.96688973070297 | epot = -21.9078990210444 | etot = -16.4772448180388 +175000 ekin = 3.47678931181566 | erot = 1.55890709488258 | epot = -21.8850180737497 | etot = -16.8493216670515 +176000 ekin = 3.20686196070563 | erot = 1.54933373538606 | epot = -21.833097887743 | etot = -17.0769021916513 +177000 ekin = 3.13331042952683 | erot = 1.28865733070242 | epot = -21.7390998162159 | etot = -17.3171320559867 +178000 ekin = 3.06763392821185 | erot = 1.26897291328759 | epot = -21.6342141405497 | etot = -17.2976072990502 +179000 ekin = 3.02674753152243 | erot = 1.57409428962025 | epot = -21.5270591512612 | etot = -16.9262173301185 +180000 ekin = 3.03569853606404 | erot = 1.67758058394333 | epot = -21.4169893849025 | etot = -16.7037102648951 +181000 ekin = 2.85389178964194 | erot = 1.75333728320479 | epot = -21.3395105909861 | etot = -16.7322815181393 +182000 ekin = 2.74244371300251 | erot = 1.80493411676471 | epot = -21.2869584133412 | etot = -16.739580583574 +183000 ekin = 2.76150374616104 | erot = 1.81761006388012 | epot = -21.2282765342437 | etot = -16.6491627242026 +184000 ekin = 2.6920627409771 | erot = 1.86375380676953 | epot = -21.1764923592868 | etot = -16.6206758115401 +185000 ekin = 2.62052583157023 | erot = 2.07457833425488 | epot = -21.1511718680907 | etot = -16.4560677022656 +186000 ekin = 2.54874716739381 | erot = 2.15191323422238 | epot = -21.1297031986501 | etot = -16.4290427970339 +187000 ekin = 2.47899352285441 | erot = 2.12131864753492 | epot = -21.1527973741678 | etot = -16.5524852037784 +188000 ekin = 2.40242843893261 | erot = 2.28274972847711 | epot = -21.2023943736365 | etot = -16.5172162062268 +189000 ekin = 2.24542511336515 | erot = 2.32237220121109 | epot = -21.2650187542767 | etot = -16.6972214397005 +190000 ekin = 2.27331885209499 | erot = 2.46101053776368 | epot = -21.3641240186243 | etot = -16.6297946287656 +191000 ekin = 2.38811474192599 | erot = 2.65597612519358 | epot = -21.4523608275388 | etot = -16.4082699604192 +192000 ekin = 2.3549239595916 | erot = 3.12866296082007 | epot = -21.5455989503755 | etot = -16.0620120299638 +193000 ekin = 2.33255266209791 | erot = 3.16650140028564 | epot = -21.6305745065442 | etot = -16.1315204441607 +194000 ekin = 2.36641654499892 | erot = 3.75512105430474 | epot = -21.7057940648227 | etot = -15.584256465519 +195000 ekin = 2.27714091943438 | erot = 4.22857583198259 | epot = -21.7506289706187 | etot = -15.2449122192017 +196000 ekin = 2.25022759887657 | erot = 4.197210474691 | epot = -21.7392596229739 | etot = -15.2918215494064 +197000 ekin = 2.13566163028458 | erot = 3.96282097735918 | epot = -21.6861725112142 | etot = -15.5876899035705 +198000 ekin = 2.10026477174317 | erot = 3.46946292854126 | epot = -21.6151658929783 | etot = -16.0454381926939 +199000 ekin = 2.06841069526386 | erot = 3.0262194981423 | epot = -21.5580043865079 | etot = -16.4633741931017 +200000 ekin = 2.07457887577972 | erot = 3.15632875079837 | epot = -21.5271681184488 | etot = -16.2962604918707 +201000 ekin = 2.2286516977074 | erot = 2.68086789208479 | epot = -21.5402772694358 | etot = -16.6307576796436 +202000 ekin = 2.21344680386073 | erot = 2.70841026008594 | epot = -21.5670967607415 | etot = -16.6452396967948 +203000 ekin = 2.29378527554839 | erot = 2.48093430470292 | epot = -21.5962341727993 | etot = -16.821514592548 +204000 ekin = 2.25828607560497 | erot = 2.50063815518557 | epot = -21.6380337966634 | etot = -16.8791095658729 +205000 ekin = 2.39913678175089 | erot = 2.62281981805078 | epot = -21.683813369519 | etot = -16.6618567697173 +206000 ekin = 2.51393947992592 | erot = 2.55239552126193 | epot = -21.7215385309814 | etot = -16.6552035297935 +207000 ekin = 2.55579745831532 | erot = 2.31728514006588 | epot = -21.7786985680233 | etot = -16.9056159696421 +208000 ekin = 2.61391306966581 | erot = 2.1077783534523 | epot = -21.7882764620355 | etot = -17.0665850389174 +209000 ekin = 2.67160585819063 | erot = 2.09388960655155 | epot = -21.8382664978831 | etot = -17.0727710331409 +210000 ekin = 2.82942438299545 | erot = 2.1332798417475 | epot = -21.9979383135581 | etot = -17.0352340888151 +211000 ekin = 2.92049266864331 | erot = 2.12124523148435 | epot = -22.2280513777041 | etot = -17.1863134775764 +212000 ekin = 3.00277061822753 | erot = 2.39488452737936 | epot = -22.4022759841392 | etot = -17.0046208385323 +213000 ekin = 3.13095859457287 | erot = 2.47163847125446 | epot = -22.5628987907077 | etot = -16.9603017248804 +214000 ekin = 3.23740343206459 | erot = 2.34793353448049 | epot = -22.7059476770017 | etot = -17.1206107104567 +215000 ekin = 3.25450904082689 | erot = 2.26222657254672 | epot = -22.8087885080488 | etot = -17.2920528946752 +216000 ekin = 3.33545375500922 | erot = 2.25051135075644 | epot = -22.8910607863362 | etot = -17.3050956805706 +217000 ekin = 3.40631462781493 | erot = 2.45810884416291 | epot = -22.9502612260087 | etot = -17.0858377540309 +218000 ekin = 3.44211621843067 | erot = 2.40223178526927 | epot = -22.9724005123081 | etot = -17.1280525086081 +219000 ekin = 3.35851747520076 | erot = 2.3622312326842 | epot = -22.9879332629404 | etot = -17.2671845550554 +220000 ekin = 3.28339440391154 | erot = 2.48348910158814 | epot = -22.986593738954 | etot = -17.2197102334543 +221000 ekin = 3.198245625619 | erot = 2.63802923468672 | epot = -22.9470020981348 | etot = -17.110727237829 +222000 ekin = 3.05410812074651 | erot = 2.59372727399077 | epot = -22.8798801579579 | etot = -17.2320447632207 +223000 ekin = 3.01415969068794 | erot = 2.70890225393109 | epot = -22.7801464118766 | etot = -17.0570844672575 +224000 ekin = 2.97180261675447 | erot = 2.69506479286081 | epot = -22.6737182851748 | etot = -17.0068508755595 +225000 ekin = 2.90964642881875 | erot = 2.70979121573934 | epot = -22.612285165109 | etot = -16.9928475205509 +226000 ekin = 2.79266706207819 | erot = 2.54927288052965 | epot = -22.6113896624579 | etot = -17.2694497198501 +227000 ekin = 2.76947170660886 | erot = 2.30328015123561 | epot = -22.6467409582567 | etot = -17.5739891004122 +228000 ekin = 2.7832504737585 | erot = 2.27271216177594 | epot = -22.7198790647035 | etot = -17.6639164291691 +229000 ekin = 2.76112130647936 | erot = 2.39217451148943 | epot = -22.800187069951 | etot = -17.6468912519822 +230000 ekin = 2.84369730914533 | erot = 2.42541769291403 | epot = -22.8608578528069 | etot = -17.5917428507475 +231000 ekin = 2.92519379372223 | erot = 2.78019508855845 | epot = -22.8903712559506 | etot = -17.1849823736699 +232000 ekin = 2.92995659411171 | erot = 2.33228808377081 | epot = -22.8760374316386 | etot = -17.6137927537561 +233000 ekin = 2.87287398890689 | erot = 2.17970441616606 | epot = -22.8206945159734 | etot = -17.7681161109005 +234000 ekin = 2.91717500618601 | erot = 2.07964949395221 | epot = -22.7337466562912 | etot = -17.7369221561529 +235000 ekin = 2.88849956347635 | erot = 1.87559177144718 | epot = -22.6649585599089 | etot = -17.9008672249854 +236000 ekin = 2.84502452090031 | erot = 1.92993964719777 | epot = -22.5730839299947 | etot = -17.7981197618967 +237000 ekin = 2.77478670759652 | erot = 2.00862555824023 | epot = -22.4470131017475 | etot = -17.6636008359107 +238000 ekin = 2.77623252972575 | erot = 1.85781358406499 | epot = -22.3442251833764 | etot = -17.7101790695857 +239000 ekin = 2.72624274520992 | erot = 1.82537539862901 | epot = -22.3075370346697 | etot = -17.7559188908307 +240000 ekin = 2.68874575599075 | erot = 2.08791431147569 | epot = -22.3178202354352 | etot = -17.5411601679687 +241000 ekin = 2.71558535720495 | erot = 2.36223789024911 | epot = -22.3776608268974 | etot = -17.2998375794433 +242000 ekin = 2.74214545076415 | erot = 2.69467452470383 | epot = -22.4730205135828 | etot = -17.0362005381148 +243000 ekin = 2.65488365755478 | erot = 3.08626659584903 | epot = -22.605422439735 | etot = -16.8642721863312 +244000 ekin = 2.61050010484592 | erot = 3.05400040440767 | epot = -22.762213943954 | etot = -17.0977134347004 +245000 ekin = 2.51883913658102 | erot = 3.07372030776082 | epot = -22.93079044948 | etot = -17.3382310051381 +246000 ekin = 2.44808144989848 | erot = 2.89693270460537 | epot = -23.0903087154633 | etot = -17.7452945609595 +247000 ekin = 2.37103549600031 | erot = 2.98987101470683 | epot = -23.216715536478 | etot = -17.8558090257709 +248000 ekin = 2.35707290060468 | erot = 2.62430509692226 | epot = -23.3107153472031 | etot = -18.3293373496762 +249000 ekin = 2.34573908311314 | erot = 2.54079763553298 | epot = -23.3554639865934 | etot = -18.4689272679472 +250000 ekin = 2.19516079867438 | erot = 2.53320956727959 | epot = -23.3422435052509 | etot = -18.6138731392969 +251000 ekin = 2.2015799284815 | erot = 2.54497162272742 | epot = -23.289551982172 | etot = -18.5430004309631 +252000 ekin = 2.29455365978426 | erot = 2.27849916282306 | epot = -23.2346327540813 | etot = -18.661579931474 +253000 ekin = 2.24131781303676 | erot = 2.67744517517057 | epot = -23.177227339145 | etot = -18.2584643509377 +254000 ekin = 2.21098192296324 | erot = 2.82095770992414 | epot = -23.1168686504971 | etot = -18.0849290176097 +255000 ekin = 2.19143060711986 | erot = 2.87369415644557 | epot = -23.0553324396615 | etot = -17.990207676096 +256000 ekin = 2.10428673283309 | erot = 2.52844816611576 | epot = -22.9892098264869 | etot = -18.356474927538 +257000 ekin = 2.09018787690756 | erot = 2.57115406533208 | epot = -22.9241936332315 | etot = -18.2628516909919 +258000 ekin = 2.19626617792803 | erot = 2.13919571497513 | epot = -22.8452199017342 | etot = -18.509758008831 +259000 ekin = 2.21294203759043 | erot = 2.07911733890816 | epot = -22.7764097043272 | etot = -18.4843503278286 +260000 ekin = 2.2298812463553 | erot = 1.88363114769134 | epot = -22.7226746972068 | etot = -18.6091623031601 +261000 ekin = 2.23359219993351 | erot = 1.70662190809948 | epot = -22.686593359404 | etot = -18.746379251371 +262000 ekin = 2.41035894748682 | erot = 1.75350704630808 | epot = -22.665573108355 | etot = -18.5017071145601 +263000 ekin = 2.54297814673107 | erot = 1.63910792627695 | epot = -22.6660944245488 | etot = -18.4840083515408 +264000 ekin = 2.6204802717585 | erot = 1.60167126997731 | epot = -22.6963818864547 | etot = -18.4742303447189 +265000 ekin = 2.6339595158455 | erot = 1.61464895664045 | epot = -22.7525488508232 | etot = -18.5039403783373 +266000 ekin = 2.66249523510551 | erot = 1.90346143383776 | epot = -22.8357396370455 | etot = -18.2697829681022 +267000 ekin = 2.84840089865297 | erot = 1.9697381438014 | epot = -22.922895038939 | etot = -18.1047559964847 +268000 ekin = 2.88773992899444 | erot = 2.23404496611545 | epot = -23.0126109152364 | etot = -17.8908260201265 +269000 ekin = 2.95881152251259 | erot = 2.36308023135752 | epot = -23.0806209903755 | etot = -17.7587292365054 +270000 ekin = 3.19922667657043 | erot = 2.31987744595641 | epot = -23.0997207459548 | etot = -17.5806166234279 +271000 ekin = 3.30474443531607 | erot = 2.18146213267909 | epot = -23.0923869412848 | etot = -17.6061803732897 +272000 ekin = 3.38316630950222 | erot = 2.27626381008289 | epot = -23.0565644655524 | etot = -17.3971343459673 +273000 ekin = 3.44314429393663 | erot = 2.33103394910053 | epot = -22.998686348507 | etot = -17.2245081054698 +274000 ekin = 3.29733836463991 | erot = 2.3546068741269 | epot = -22.9061895162167 | etot = -17.2542442774499 +275000 ekin = 3.20483849389297 | erot = 2.17592485213262 | epot = -22.8033610976752 | etot = -17.4225977516496 +276000 ekin = 3.17952696643841 | erot = 2.53631962219384 | epot = -22.6964713302163 | etot = -16.980624741584 +277000 ekin = 3.04779312524477 | erot = 2.63224846283747 | epot = -22.5925250147671 | etot = -16.9124834266848 +278000 ekin = 2.88882241520594 | erot = 2.4429576877197 | epot = -22.5096077221471 | etot = -17.1778276192215 +279000 ekin = 2.7445805924286 | erot = 2.3468901491402 | epot = -22.4433740610139 | etot = -17.3519033194451 +280000 ekin = 2.7554105836729 | erot = 2.4011898984753 | epot = -22.3855374270778 | etot = -17.2289369449296 +281000 ekin = 2.66532300538253 | erot = 2.21704056459403 | epot = -22.3765161892641 | etot = -17.4941526192875 +282000 ekin = 2.60731940802889 | erot = 2.15906154555096 | epot = -22.392902036019 | etot = -17.6265210824392 +283000 ekin = 2.58513425203906 | erot = 2.06481653587231 | epot = -22.4081967019538 | etot = -17.7582459140425 +284000 ekin = 2.54858019457336 | erot = 2.24572478450568 | epot = -22.4445919263858 | etot = -17.6502869473068 +285000 ekin = 2.55758171617774 | erot = 2.76460913859724 | epot = -22.5141586593919 | etot = -17.1919678046169 +286000 ekin = 2.60821734500493 | erot = 3.16634932217225 | epot = -22.5929692498765 | etot = -16.8184025826993 +287000 ekin = 2.49254766601104 | erot = 3.15514661858268 | epot = -22.6449148716492 | etot = -16.9972205870554 +288000 ekin = 2.50066439821538 | erot = 3.4971940395516 | epot = -22.6803477105654 | etot = -16.6824892727984 +289000 ekin = 2.44598353504064 | erot = 3.34215032544757 | epot = -22.6895361095334 | etot = -16.9014022490452 +290000 ekin = 2.39359823072712 | erot = 3.1126844030724 | epot = -22.6698244131813 | etot = -17.1635417793818 +291000 ekin = 2.42617011831441 | erot = 2.85487514428664 | epot = -22.6626122342504 | etot = -17.3815669716493 +292000 ekin = 2.40772687076927 | erot = 2.75801742060114 | epot = -22.6754806613925 | etot = -17.5097363700221 +293000 ekin = 2.42154585346455 | erot = 2.56313321462444 | epot = -22.7028245536538 | etot = -17.7181454855648 +294000 ekin = 2.4728309166701 | erot = 2.92407822599839 | epot = -22.7233881302524 | etot = -17.3264789875839 +295000 ekin = 2.48250330737214 | erot = 2.66001264724756 | epot = -22.7516848410686 | etot = -17.6091688864489 +296000 ekin = 2.50738582337497 | erot = 2.53234484293205 | epot = -22.7873334660358 | etot = -17.7476027997287 +297000 ekin = 2.57517392062601 | erot = 2.82176475993532 | epot = -22.8071785750426 | etot = -17.4102398944812 +298000 ekin = 2.64719948459859 | erot = 2.59986611083047 | epot = -22.8000961016266 | etot = -17.5530305061975 +299000 ekin = 2.57794949271972 | erot = 2.50163391190629 | epot = -22.777423569021 | etot = -17.697840164395 +300000 ekin = 2.54202853433712 | erot = 2.50188796046296 | epot = -22.7359935186374 | etot = -17.6920770238373 +301000 ekin = 2.53853550508107 | erot = 2.33138966267648 | epot = -22.668055568127 | etot = -17.7981304003695 +302000 ekin = 2.54164672579203 | erot = 2.35968144693483 | epot = -22.6002854710846 | etot = -17.6989572983578 +303000 ekin = 2.55152004910016 | erot = 2.25570939719585 | epot = -22.5464912065881 | etot = -17.7392617602921 +304000 ekin = 2.43742201255282 | erot = 1.93302414776497 | epot = -22.4953520351473 | etot = -18.1249058748295 +305000 ekin = 2.37256740983357 | erot = 1.9990668631018 | epot = -22.4852720256447 | etot = -18.1136377527094 +306000 ekin = 2.33394239199429 | erot = 1.95361217330038 | epot = -22.4994393613204 | etot = -18.2118847960258 +307000 ekin = 2.36433385317698 | erot = 2.09819856998282 | epot = -22.5498835871991 | etot = -18.0873511640393 +308000 ekin = 2.39069887757527 | erot = 2.58247807487939 | epot = -22.6356145598509 | etot = -17.6624376073962 +309000 ekin = 2.42870516593962 | erot = 2.50601430493662 | epot = -22.7376993972854 | etot = -17.8029799264091 +310000 ekin = 2.59762961961 | erot = 2.86657561799367 | epot = -22.8270893622475 | etot = -17.3628841246438 +311000 ekin = 2.58045041487711 | erot = 3.2311264730769 | epot = -22.8820505528213 | etot = -17.0704736648673 +312000 ekin = 2.55765290476202 | erot = 3.46227005563475 | epot = -22.8938340197389 | etot = -16.8739110593421 +313000 ekin = 2.559441928848 | erot = 3.26655870580169 | epot = -22.8884040353447 | etot = -17.0624034006951 +314000 ekin = 2.66754752507797 | erot = 3.03950571405875 | epot = -22.8258761802468 | etot = -17.1188229411101 +315000 ekin = 2.73855283007327 | erot = 2.99016186621318 | epot = -22.7272216366889 | etot = -16.9985069404024 +316000 ekin = 2.80269198455227 | erot = 2.86307192976281 | epot = -22.5938909114046 | etot = -16.9281269970896 +317000 ekin = 2.93621184769345 | erot = 2.59361256238012 | epot = -22.4292070317099 | etot = -16.8993826216363 +318000 ekin = 2.89758526069563 | erot = 2.51740962219035 | epot = -22.2783865388305 | etot = -16.8633916559446 +319000 ekin = 2.91605528220969 | erot = 2.46065370098599 | epot = -22.133704436705 | etot = -16.7569954535093 +320000 ekin = 3.07107505335126 | erot = 2.32265497319528 | epot = -21.9969159416467 | etot = -16.6031859151001 +321000 ekin = 3.13741654111418 | erot = 2.10166654249796 | epot = -21.900308219471 | etot = -16.6612251358588 +322000 ekin = 3.25007976010091 | erot = 2.45741622170004 | epot = -21.8520535793255 | etot = -16.1445575975246 +323000 ekin = 3.23909847348115 | erot = 2.5340375320604 | epot = -21.8540021438702 | etot = -16.0808661383287 +324000 ekin = 3.38563358070232 | erot = 2.1731158940233 | epot = -21.9009098604863 | etot = -16.3421603857607 +325000 ekin = 3.34278974993512 | erot = 2.12874487522967 | epot = -21.9500890276596 | etot = -16.4785544024948 +326000 ekin = 3.38095563952734 | erot = 1.87895018746874 | epot = -21.9795682650696 | etot = -16.7196624380736 +327000 ekin = 3.38255419804517 | erot = 2.1588901822408 | epot = -22.0134841360964 | etot = -16.4720397558105 +328000 ekin = 3.40032271527504 | erot = 2.44697536300087 | epot = -22.023450759041 | etot = -16.1761526807651 +329000 ekin = 3.42165866167042 | erot = 2.23397608707607 | epot = -21.9965079843081 | etot = -16.3408732355616 +330000 ekin = 3.40495189589427 | erot = 2.16314285762156 | epot = -21.9196276290174 | etot = -16.3515328755016 +331000 ekin = 3.17548117127382 | erot = 2.09607585596633 | epot = -21.794498989011 | etot = -16.5229419617709 +332000 ekin = 2.98417545246665 | erot = 2.49335753705486 | epot = -21.6758679740327 | etot = -16.1983349845112 +333000 ekin = 2.88789613747813 | erot = 2.2559185916092 | epot = -21.5606249971909 | etot = -16.4168102681035 +334000 ekin = 2.72802815944269 | erot = 2.34583544867011 | epot = -21.5029467999943 | etot = -16.4290831918815 +335000 ekin = 2.67984094653357 | erot = 2.55944269027796 | epot = -21.5037191469947 | etot = -16.2644355101832 +336000 ekin = 2.69835695167784 | erot = 2.67075019722172 | epot = -21.5450631550404 | etot = -16.1759560061409 +337000 ekin = 2.58419106934189 | erot = 3.12853087323264 | epot = -21.643316836933 | etot = -15.9305948943585 +338000 ekin = 2.49996061258828 | erot = 3.1121867329201 | epot = -21.7506422483336 | etot = -16.1384949028252 +339000 ekin = 2.39574216262846 | erot = 3.0806358526705 | epot = -21.8692124850348 | etot = -16.3928344697358 +340000 ekin = 2.49232794145646 | erot = 2.980190991323 | epot = -21.9771878613074 | etot = -16.504668928528 +341000 ekin = 2.49715634905668 | erot = 2.90079807725765 | epot = -22.0570317432504 | etot = -16.6590773169361 +342000 ekin = 2.51716093069969 | erot = 2.82265055007444 | epot = -22.1164185335397 | etot = -16.7766070527655 +343000 ekin = 2.4860981088623 | erot = 2.72316461109174 | epot = -22.1874092656393 | etot = -16.9781465456852 +344000 ekin = 2.59185701101002 | erot = 2.80189377403278 | epot = -22.2240461219157 | etot = -16.8302953368729 +345000 ekin = 2.75203781955695 | erot = 2.78048504556998 | epot = -22.228777643338 | etot = -16.6962547782111 +346000 ekin = 2.81389530494878 | erot = 2.3340730613195 | epot = -22.2248537826432 | etot = -17.0768854163749 +347000 ekin = 2.9391210400536 | erot = 2.50008170041745 | epot = -22.249868336818 | etot = -16.810665596347 +348000 ekin = 2.96773185111312 | erot = 2.74343934252212 | epot = -22.2560808039814 | etot = -16.5449096103462 +349000 ekin = 3.13040986998843 | erot = 2.80190275823786 | epot = -22.2470744750918 | etot = -16.3147618468655 +350000 ekin = 3.08696501979119 | erot = 2.86847264663001 | epot = -22.2200203810508 | etot = -16.2645827146296 +351000 ekin = 3.09062650768665 | erot = 2.55040952388053 | epot = -22.219653345477 | etot = -16.5786173139098 +352000 ekin = 3.11537871248055 | erot = 2.20508138812274 | epot = -22.2132969704675 | etot = -16.8928368698642 +353000 ekin = 3.07156061276484 | erot = 2.27110385815633 | epot = -22.1942519415342 | etot = -16.851587470613 +354000 ekin = 3.03625905361608 | erot = 2.28070870858901 | epot = -22.1756814217729 | etot = -16.8587136595678 +355000 ekin = 3.05199381136594 | erot = 2.27451340050882 | epot = -22.1583132038245 | etot = -16.8318059919498 +356000 ekin = 3.08455685206842 | erot = 2.22987943802129 | epot = -22.1433269864766 | etot = -16.8288906963869 +357000 ekin = 3.05732303271321 | erot = 2.39309407849548 | epot = -22.1193520318396 | etot = -16.6689349206309 +358000 ekin = 3.1711006145134 | erot = 2.70306029074061 | epot = -22.11823298523 | etot = -16.244072079976 +359000 ekin = 3.16486963450204 | erot = 2.78686781955526 | epot = -22.1253692631306 | etot = -16.1736318090733 +360000 ekin = 3.13851448508906 | erot = 2.57867504445972 | epot = -22.1430585034903 | etot = -16.4258689739416 +361000 ekin = 3.1018046044078 | erot = 2.91879652221933 | epot = -22.1488150833326 | etot = -16.1282139567055 +362000 ekin = 3.05062554845306 | erot = 3.01028278746078 | epot = -22.1455190064011 | etot = -16.0846106704873 +363000 ekin = 3.05887916756207 | erot = 2.98286966442435 | epot = -22.1197448021474 | etot = -16.077995970161 +364000 ekin = 2.97835573270391 | erot = 3.15819469882605 | epot = -22.0865889777575 | etot = -15.9500385462276 +365000 ekin = 2.91386725267301 | erot = 3.01797244564511 | epot = -22.036734500504 | etot = -16.1048948021859 +366000 ekin = 2.84923441171881 | erot = 2.78629016923769 | epot = -21.9575039957298 | etot = -16.3219794147733 +367000 ekin = 2.68353251880628 | erot = 2.48104091468962 | epot = -21.89853718758 | etot = -16.7339637540841 +368000 ekin = 2.65983333900818 | erot = 2.52342977423083 | epot = -21.8801683018794 | etot = -16.6969051886404 +369000 ekin = 2.57098271373618 | erot = 2.13783387451323 | epot = -21.8712180667081 | etot = -17.1624014784587 +370000 ekin = 2.46719741991483 | erot = 2.19165130675158 | epot = -21.8880397158873 | etot = -17.2291909892209 +371000 ekin = 2.36101704058599 | erot = 2.37151178551915 | epot = -21.871259635484 | etot = -17.1387308093789 +372000 ekin = 2.35292349616034 | erot = 1.93814576615856 | epot = -21.8337068682175 | etot = -17.5426376058986 +373000 ekin = 2.22654652898943 | erot = 1.97312401893843 | epot = -21.7946812690266 | etot = -17.5950107210988 +374000 ekin = 2.10841533505376 | erot = 2.42321715998303 | epot = -21.7582816122237 | etot = -17.2266491171869 +375000 ekin = 2.09694600146948 | erot = 2.65841461817973 | epot = -21.7455351907437 | etot = -16.9901745710945 +376000 ekin = 2.01640282060124 | erot = 2.94267460873896 | epot = -21.7585878275113 | etot = -16.7995103981711 +377000 ekin = 1.96639420112318 | erot = 3.0881995707428 | epot = -21.7692932541815 | etot = -16.7146994823155 +378000 ekin = 1.8581802807931 | erot = 2.93893488746247 | epot = -21.7888291404588 | etot = -16.9917139722032 +379000 ekin = 1.80977620668707 | erot = 2.89686403333528 | epot = -21.8021607659804 | etot = -17.095520525958 +380000 ekin = 1.73240863049973 | erot = 3.31083227305488 | epot = -21.8040178365907 | etot = -16.7607769330361 +381000 ekin = 1.78593665245924 | erot = 3.0043788778956 | epot = -21.814619015938 | etot = -17.0243034855832 +382000 ekin = 1.81833924259092 | erot = 3.29223624038099 | epot = -21.8338308722139 | etot = -16.723255389242 +383000 ekin = 1.90372822779343 | erot = 3.2223723870211 | epot = -21.8485569566827 | etot = -16.7224563418682 +384000 ekin = 1.84908071228732 | erot = 3.12652639081496 | epot = -21.7977736604942 | etot = -16.8221665573919 +385000 ekin = 1.92406985540242 | erot = 2.87503823935547 | epot = -21.7109558633046 | etot = -16.9118477685467 +386000 ekin = 2.08459192251279 | erot = 2.45881013772448 | epot = -21.8127875838317 | etot = -17.2693855235944 +387000 ekin = 2.14831947455661 | erot = 2.58103233380232 | epot = -21.965778516454 | etot = -17.2364267080951 +388000 ekin = 2.20283399392827 | erot = 2.65764672350552 | epot = -22.0644231935264 | etot = -17.2039424760926 +389000 ekin = 2.20238885724334 | erot = 2.65111850895053 | epot = -22.1516234881391 | etot = -17.2981161219452 +390000 ekin = 2.24047588961197 | erot = 2.79913619901817 | epot = -22.2380523913913 | etot = -17.1984403027612 +391000 ekin = 2.27798913986017 | erot = 2.58277083989429 | epot = -22.3159667090675 | etot = -17.455206729313 +392000 ekin = 2.25449982760673 | erot = 2.37888824458204 | epot = -22.3605850592921 | etot = -17.7271969871034 +393000 ekin = 2.40321868579769 | erot = 2.29619394920021 | epot = -22.4007355614943 | etot = -17.7013229264964 +394000 ekin = 2.38472249136268 | erot = 2.02605124890775 | epot = -22.4166559581036 | etot = -18.0058822178332 +395000 ekin = 2.35870737602683 | erot = 2.13809618093391 | epot = -22.46183889125 | etot = -17.9650353342893 +396000 ekin = 2.36594751638176 | erot = 2.35329585924248 | epot = -22.4900242189752 | etot = -17.770780843351 +397000 ekin = 2.32162964157149 | erot = 2.38815965169872 | epot = -22.5051745520065 | etot = -17.7953852587363 +398000 ekin = 2.2809317117681 | erot = 2.45784979337986 | epot = -22.4904502460558 | etot = -17.7516687409078 +399000 ekin = 2.24440009076072 | erot = 2.20375095522972 | epot = -22.4593286712297 | etot = -18.0111776252393 +400000 ekin = 2.21650351836305 | erot = 2.11035067120488 | epot = -22.4071568047281 | etot = -18.0803026151602 +401000 ekin = 2.18808947871535 | erot = 2.05046808146139 | epot = -22.3505439740505 | etot = -18.1119864138738 +402000 ekin = 2.16649391253901 | erot = 2.14799860386812 | epot = -22.268256251652 | etot = -17.9537637352449 +403000 ekin = 2.28466204544573 | erot = 2.18910683075383 | epot = -22.2050986712119 | etot = -17.7313297950123 +404000 ekin = 2.34692059996724 | erot = 2.09828665659982 | epot = -22.1538027009538 | etot = -17.7085954443867 +405000 ekin = 2.4405679209828 | erot = 1.95202235520055 | epot = -22.1290600615596 | etot = -17.7364697853763 +406000 ekin = 2.51200179837241 | erot = 1.84480550716527 | epot = -22.1228718442874 | etot = -17.7660645387498 +407000 ekin = 2.46779728542654 | erot = 1.95715570890835 | epot = -22.1207033013073 | etot = -17.6957503069724 +408000 ekin = 2.67524377663759 | erot = 2.25989223488927 | epot = -22.1391777417951 | etot = -17.2040417302682 +409000 ekin = 2.66315255700294 | erot = 2.37555491225749 | epot = -22.1303194186109 | etot = -17.0916119493505 +410000 ekin = 2.65203478218384 | erot = 2.35306567100159 | epot = -22.1147712842536 | etot = -17.1096708310682 +411000 ekin = 2.6665921727395 | erot = 2.24630383870687 | epot = -22.1012745566864 | etot = -17.18837854524 +412000 ekin = 2.71788228424455 | erot = 2.0599452609842 | epot = -22.08547529968 | etot = -17.3076477544513 +413000 ekin = 2.9180284813538 | erot = 2.11234467836748 | epot = -22.0711624066711 | etot = -17.0407892469498 +414000 ekin = 2.96559563750791 | erot = 2.00652755440308 | epot = -22.0704517319952 | etot = -17.0983285400842 +415000 ekin = 2.9403339874136 | erot = 2.1506636721416 | epot = -22.0908184253288 | etot = -16.9998207657736 +416000 ekin = 3.01308617564487 | erot = 2.30018045105578 | epot = -22.1467565517931 | etot = -16.8334899250925 +417000 ekin = 2.99189829031787 | erot = 2.38541146259451 | epot = -22.2119953988622 | etot = -16.8346856459498 +418000 ekin = 2.92450258607176 | erot = 2.60659083472735 | epot = -22.2670317375586 | etot = -16.7359383167595 +419000 ekin = 3.02248435904785 | erot = 2.56863874909495 | epot = -22.3092445703347 | etot = -16.7181214621919 +420000 ekin = 3.11629989898236 | erot = 2.19357614992643 | epot = -22.3521371010171 | etot = -17.0422610521083 +421000 ekin = 3.09888957739381 | erot = 2.50768144705348 | epot = -22.4424742155049 | etot = -16.8359031910577 +422000 ekin = 3.22879455450154 | erot = 2.7281466432388 | epot = -22.5663066955684 | etot = -16.609365497828 +423000 ekin = 3.30665671531864 | erot = 2.51591677609467 | epot = -22.6645305507578 | etot = -16.8419570593445 +424000 ekin = 3.37246731972731 | erot = 2.34745055602907 | epot = -22.727642618393 | etot = -17.0077247426366 +425000 ekin = 3.43841525686891 | erot = 2.13655704811661 | epot = -22.7531787907648 | etot = -17.1782064857792 +426000 ekin = 3.39533061745582 | erot = 2.09679686908525 | epot = -22.7598072190452 | etot = -17.2676797325041 +427000 ekin = 3.39111059944188 | erot = 2.09557295937 | epot = -22.7548111473876 | etot = -17.2681275885757 +428000 ekin = 3.31614466866169 | erot = 2.03921223078323 | epot = -22.7608817388065 | etot = -17.4055248393615 +429000 ekin = 3.32919751126109 | erot = 2.28907058183506 | epot = -22.7667239471956 | etot = -17.1484558540995 +430000 ekin = 3.20916903929704 | erot = 2.24711750120359 | epot = -22.7569862329286 | etot = -17.3006996924279 +431000 ekin = 3.21784537917498 | erot = 2.11449131463102 | epot = -22.7330752234491 | etot = -17.4007385296431 +432000 ekin = 3.05825965277366 | erot = 2.1280245777588 | epot = -22.7058311036753 | etot = -17.5195468731428 +433000 ekin = 3.04999159233165 | erot = 2.12377304692495 | epot = -22.6927692042268 | etot = -17.5190045649702 +434000 ekin = 2.97281689578993 | erot = 2.06268809983407 | epot = -22.6735691335098 | etot = -17.6380641378858 +435000 ekin = 2.94081881992646 | erot = 2.27500624558154 | epot = -22.6471201429009 | etot = -17.4312950773929 +436000 ekin = 2.76300260327166 | erot = 2.14872430130916 | epot = -22.6178894405034 | etot = -17.7061625359226 +437000 ekin = 2.59429812875475 | erot = 1.81211382552894 | epot = -22.595485084217 | etot = -18.1890731299333 +438000 ekin = 2.55606503620585 | erot = 2.0179868480706 | epot = -22.5948271221481 | etot = -18.0207752378717 +439000 ekin = 2.53154376315499 | erot = 2.19299208744614 | epot = -22.6163361970742 | etot = -17.891800346473 +440000 ekin = 2.40438990342985 | erot = 2.39730485059928 | epot = -22.6417525467574 | etot = -17.8400577927283 +441000 ekin = 2.39311316134443 | erot = 2.20887829122785 | epot = -22.6584374753817 | etot = -18.0564460228094 +442000 ekin = 2.33774628968778 | erot = 2.27924438602919 | epot = -22.6901952471932 | etot = -18.0732045714763 +443000 ekin = 2.29577071148444 | erot = 2.13681932629555 | epot = -22.7383184381274 | etot = -18.3057284003474 +444000 ekin = 2.23794629484161 | erot = 2.26441379885369 | epot = -22.7861053898433 | etot = -18.2837452961479 +445000 ekin = 2.29545526298793 | erot = 2.21483552932775 | epot = -22.8258649969131 | etot = -18.3155742045974 +446000 ekin = 2.30609557124264 | erot = 2.31380080271873 | epot = -22.8648768729171 | etot = -18.2449804989557 +447000 ekin = 2.3400431119763 | erot = 2.11921527275252 | epot = -22.8964565927018 | etot = -18.437198207973 +448000 ekin = 2.31891408584095 | erot = 1.89336279102554 | epot = -22.9133862874843 | etot = -18.7011094106178 +449000 ekin = 2.50108402662084 | erot = 2.14275389718692 | epot = -22.930633005168 | etot = -18.2867950813603 +450000 ekin = 2.5680115489325 | erot = 2.1703072011048 | epot = -22.9343126165985 | etot = -18.1959938665612 +451000 ekin = 2.56623797742048 | erot = 2.48936702406197 | epot = -22.9565813788787 | etot = -17.9009763773962 +452000 ekin = 2.58271965200715 | erot = 2.71036974079266 | epot = -22.969892761014 | etot = -17.6768033682142 +453000 ekin = 2.57528128095339 | erot = 2.42064719168856 | epot = -22.9718770494986 | etot = -17.9759485768567 +454000 ekin = 2.67501362163761 | erot = 2.16830940597265 | epot = -22.954282826857 | etot = -18.1109597992467 +455000 ekin = 2.56489981687937 | erot = 2.42902486734868 | epot = -22.9396963254752 | etot = -17.9457716412471 +456000 ekin = 2.70565104056166 | erot = 2.41758826939476 | epot = -22.93942784522 | etot = -17.8161885352635 +457000 ekin = 2.6720211004305 | erot = 2.33461800850212 | epot = -22.966154109974 | etot = -17.9595150010414 +458000 ekin = 2.80341163315569 | erot = 2.09116834812238 | epot = -22.9873787877664 | etot = -18.0927988064884 +459000 ekin = 2.88302679195828 | erot = 2.11686421326537 | epot = -22.9983193137535 | etot = -17.9984283085298 +460000 ekin = 2.80959444443701 | erot = 1.91875534890938 | epot = -22.9899489536659 | etot = -18.2615991603195 +461000 ekin = 2.74655544888584 | erot = 2.00712299964627 | epot = -22.9641927476617 | etot = -18.2105142991295 +462000 ekin = 2.69410871293408 | erot = 1.85692462055059 | epot = -22.9396822663687 | etot = -18.388648932884 +463000 ekin = 2.68405751272921 | erot = 1.72122902844385 | epot = -22.920625445423 | etot = -18.51533890425 +464000 ekin = 2.68220436609129 | erot = 1.82183499702516 | epot = -22.902100071716 | etot = -18.3980607085995 +465000 ekin = 2.72690747044742 | erot = 1.76672692428737 | epot = -22.8835808325682 | etot = -18.3899464378335 +466000 ekin = 2.76097376291825 | erot = 1.45315546635129 | epot = -22.8532324895852 | etot = -18.6391032603157 +467000 ekin = 2.70206815185883 | erot = 1.48571966445427 | epot = -22.8038556347775 | etot = -18.6160678184644 +468000 ekin = 2.5468378285447 | erot = 1.46932624584375 | epot = -22.7393489246085 | etot = -18.72318485022 +469000 ekin = 2.57325964052969 | erot = 1.72667647792953 | epot = -22.6884895500973 | etot = -18.3885534316381 +470000 ekin = 2.54097506641283 | erot = 1.39019831696538 | epot = -22.6354294232224 | etot = -18.7042560398442 +471000 ekin = 2.53075144531188 | erot = 1.56973268857361 | epot = -22.5872254672437 | etot = -18.4867413333582 +472000 ekin = 2.48686143209695 | erot = 1.63608646497309 | epot = -22.5386230972985 | etot = -18.4156752002285 +473000 ekin = 2.42292267545319 | erot = 1.87228271405934 | epot = -22.5112867940746 | etot = -18.2160814045621 +474000 ekin = 2.50613933288665 | erot = 2.0952416911658 | epot = -22.5009126606675 | etot = -17.8995316366151 +475000 ekin = 2.45603005290409 | erot = 1.85917779264061 | epot = -22.5137202723094 | etot = -18.1985124267647 +476000 ekin = 2.3346853402221 | erot = 2.0264560210282 | epot = -22.5553111044059 | etot = -18.1941697431556 +477000 ekin = 2.45891726578721 | erot = 2.02023615759308 | epot = -22.6158128757705 | etot = -18.1366594523902 +478000 ekin = 2.41477886253645 | erot = 2.43026093865231 | epot = -22.6679361141587 | etot = -17.8228963129699 +479000 ekin = 2.32198252632126 | erot = 2.32644468281383 | epot = -22.7087553607369 | etot = -18.0603281516018 +480000 ekin = 2.3558894173607 | erot = 2.3595465710013 | epot = -22.7435251879185 | etot = -18.0280891995565 +481000 ekin = 2.284520892779 | erot = 2.2043085242519 | epot = -22.7608284363972 | etot = -18.2719990193663 +482000 ekin = 2.32256646764216 | erot = 2.41557913055296 | epot = -22.7741831402844 | etot = -18.0360375420892 +483000 ekin = 2.27205927409901 | erot = 2.56178717087227 | epot = -22.7728224994831 | etot = -17.9389760545118 +484000 ekin = 2.37993337782981 | erot = 2.66126649810811 | epot = -22.7416478008891 | etot = -17.7004479249512 +485000 ekin = 2.38190748927818 | erot = 2.61854512767477 | epot = -22.7119334579282 | etot = -17.7114808409752 +486000 ekin = 2.3341846650688 | erot = 2.46925253909111 | epot = -22.6824493106805 | etot = -17.8790121065206 +487000 ekin = 2.18094133411115 | erot = 2.69390883740088 | epot = -22.6720546869386 | etot = -17.7972045154266 +488000 ekin = 2.11650686044404 | erot = 2.55325406947426 | epot = -22.6638056402425 | etot = -17.9940447103242 +489000 ekin = 2.21431283780025 | erot = 2.61470772093261 | epot = -22.6573831222825 | etot = -17.8283625635497 +490000 ekin = 2.2177697789255 | erot = 2.23500339456076 | epot = -22.5741440270901 | etot = -18.1213708536038 +491000 ekin = 2.2743268285736 | erot = 1.88817054321361 | epot = -22.4373592688795 | etot = -18.2748618970923 +492000 ekin = 2.53138272091331 | erot = 1.96744277498725 | epot = -22.4175140127838 | etot = -17.9186885168832 +493000 ekin = 2.71682060136924 | erot = 2.08719543513555 | epot = -22.5173229601061 | etot = -17.7133069236013 +494000 ekin = 2.79234310962882 | erot = 1.83822122501509 | epot = -22.5447051999101 | etot = -17.9141408652662 +495000 ekin = 2.76785459319896 | erot = 1.73774545925586 | epot = -22.5287157975834 | etot = -18.0231157451285 +496000 ekin = 2.84739375420049 | erot = 1.56846128670001 | epot = -22.5241542479137 | etot = -18.1082992070132 +497000 ekin = 2.69680214844421 | erot = 1.74348040544602 | epot = -22.5144404613581 | etot = -18.0741579074679 +498000 ekin = 2.62941704239962 | erot = 1.98455622913402 | epot = -22.5178632839582 | etot = -17.9038900124246 +499000 ekin = 2.64804818917005 | erot = 2.28765209546407 | epot = -22.5255155919976 | etot = -17.5898153073635 +500000 ekin = 2.62333387127775 | erot = 2.24107414888815 | epot = -22.5402092035982 | etot = -17.6758011834323 +501000 ekin = 2.58728609470098 | erot = 2.55153168646058 | epot = -22.5581971333472 | etot = -17.4193793521857 +502000 ekin = 2.57438529667224 | erot = 2.59775936587093 | epot = -22.5744776891821 | etot = -17.4023330266389 +503000 ekin = 2.68620055952013 | erot = 2.57830069566415 | epot = -22.5848671752325 | etot = -17.3203659200482 +504000 ekin = 2.70861631349713 | erot = 2.63136597642924 | epot = -22.5422463026807 | etot = -17.2022640127543 +505000 ekin = 2.81322601719058 | erot = 2.35620405508421 | epot = -22.4713277487551 | etot = -17.3018976764803 +506000 ekin = 2.75875978790581 | erot = 2.2811420027319 | epot = -22.4152453500929 | etot = -17.3753435594552 +507000 ekin = 2.76795437715432 | erot = 2.08516805530083 | epot = -22.3599249092895 | etot = -17.5068024768344 +508000 ekin = 2.73683686247801 | erot = 2.23436615836136 | epot = -22.3104902501594 | etot = -17.33928722932 +509000 ekin = 2.78730220151846 | erot = 2.42925226467485 | epot = -22.2669837867327 | etot = -17.0504293205394 +510000 ekin = 2.70408252089242 | erot = 2.30581628327713 | epot = -22.2411716050792 | etot = -17.2312728009097 +511000 ekin = 2.61818706333878 | erot = 2.32198772005124 | epot = -22.2054755882157 | etot = -17.2653008048257 +512000 ekin = 2.6266656789872 | erot = 2.16861742931871 | epot = -22.1496493249526 | etot = -17.3543662166467 +513000 ekin = 2.62864579756464 | erot = 2.28017839888773 | epot = -22.0962074035282 | etot = -17.1873832070758 +514000 ekin = 2.62144790591378 | erot = 2.41032584829392 | epot = -22.0606978370588 | etot = -17.0289240828511 +515000 ekin = 2.4182266596636 | erot = 2.52539385006922 | epot = -22.0307261613953 | etot = -17.0871056516624 +516000 ekin = 2.50897552241983 | erot = 2.78752662759895 | epot = -21.9672371157169 | etot = -16.6707349656981 +517000 ekin = 2.49803351393489 | erot = 2.61327470143936 | epot = -21.8908910019269 | etot = -16.7795827865527 +518000 ekin = 2.40588427132963 | erot = 2.6049652024787 | epot = -21.8271402944051 | etot = -16.8162908205968 +519000 ekin = 2.30783192859372 | erot = 2.28376487382996 | epot = -21.7720265250267 | etot = -17.180429722603 +520000 ekin = 2.2761642305819 | erot = 2.29434994860407 | epot = -21.7128184146401 | etot = -17.1423042354541 +521000 ekin = 2.24914668110677 | erot = 2.36897117879091 | epot = -21.6721321359537 | etot = -17.054014276056 +522000 ekin = 2.35364771784226 | erot = 2.3669509768879 | epot = -21.6628523798145 | etot = -16.9422536850843 +523000 ekin = 2.37618272265833 | erot = 2.13303138965069 | epot = -21.7051372318526 | etot = -17.1959231195436 +524000 ekin = 2.49723384027368 | erot = 2.2402387265416 | epot = -21.782377913726 | etot = -17.0449053469107 +525000 ekin = 2.46375747660483 | erot = 2.51521139084649 | epot = -21.8666578962014 | etot = -16.8876890287501 +526000 ekin = 2.48852380798094 | erot = 2.58777847976814 | epot = -21.9290082944792 | etot = -16.8527060067301 +527000 ekin = 2.56408998824203 | erot = 2.71602192536799 | epot = -21.9877682670139 | etot = -16.7076563534039 +528000 ekin = 2.56498509318779 | erot = 2.76910231594627 | epot = -22.0494190498077 | etot = -16.7153316406737 +529000 ekin = 2.49392950866803 | erot = 2.90081498188824 | epot = -22.0953259392657 | etot = -16.7005814487095 +530000 ekin = 2.55943772908022 | erot = 3.45143762749438 | epot = -22.1238951653049 | etot = -16.1130198087303 +531000 ekin = 2.62008230330594 | erot = 3.4102956933902 | epot = -22.1596065217834 | etot = -16.1292285250873 +532000 ekin = 2.64345831357253 | erot = 3.25189148347864 | epot = -22.2210179597453 | etot = -16.3256681626941 +533000 ekin = 2.66248857759365 | erot = 3.12130181040678 | epot = -22.293854504249 | etot = -16.5100641162486 +534000 ekin = 2.57837832781878 | erot = 3.40672270429757 | epot = -22.3945209938965 | etot = -16.4094199617801 +535000 ekin = 2.54988429096273 | erot = 3.48601096999932 | epot = -22.4965663420717 | etot = -16.4606710811097 +536000 ekin = 2.54332535815076 | erot = 3.38741257391199 | epot = -22.5966447962839 | etot = -16.6659068642212 +537000 ekin = 2.51621672082883 | erot = 3.49541286485898 | epot = -22.7221660584811 | etot = -16.7105364727933 +538000 ekin = 2.55164682489481 | erot = 3.74760630845831 | epot = -22.8591125937166 | etot = -16.5598594603634 +539000 ekin = 2.58092295425592 | erot = 3.80698168734295 | epot = -22.9765606947834 | etot = -16.5886560531845 +540000 ekin = 2.51008871731657 | erot = 3.80582456583147 | epot = -22.9798947810034 | etot = -16.6639814978553 +541000 ekin = 2.46719015764005 | erot = 3.50395862401716 | epot = -22.843108726957 | etot = -16.8719599452998 +542000 ekin = 2.59107475639072 | erot = 3.17066662624118 | epot = -22.8744258545949 | etot = -17.112684471963 +543000 ekin = 2.63620201361468 | erot = 3.06589292292618 | epot = -23.0791931656966 | etot = -17.3770982291557 +544000 ekin = 2.7624303384 | erot = 2.75752131636948 | epot = -23.1902839993582 | etot = -17.6703323445887 +545000 ekin = 2.77751893807181 | erot = 2.90000680655531 | epot = -23.2046062023305 | etot = -17.5270804577034 +546000 ekin = 2.7805950236307 | erot = 2.54289051406649 | epot = -23.2005103103105 | etot = -17.8770247726133 +547000 ekin = 2.81545617905238 | erot = 2.47192481242806 | epot = -23.1718555968601 | etot = -17.8844746053796 +548000 ekin = 2.79144209452802 | erot = 2.80250244565785 | epot = -23.1234791781377 | etot = -17.5295346379518 +549000 ekin = 2.75373348946721 | erot = 2.71813060504065 | epot = -23.0602788235303 | etot = -17.5884147290224 +550000 ekin = 2.68546541277429 | erot = 2.77855841780863 | epot = -22.9807527132684 | etot = -17.5167288826854 +551000 ekin = 2.63458963816036 | erot = 2.84363646369263 | epot = -22.8852605151351 | etot = -17.4070344132821 +552000 ekin = 2.65549146174195 | erot = 2.88006578689767 | epot = -22.7742141173519 | etot = -17.2386568687123 +553000 ekin = 2.61257263960443 | erot = 2.50580069544582 | epot = -22.6366728838902 | etot = -17.5182995488399 +554000 ekin = 2.55042887500034 | erot = 2.45156308445378 | epot = -22.5169799021636 | etot = -17.5149879427095 +555000 ekin = 2.4877174092021 | erot = 2.4195997835835 | epot = -22.4015661830961 | etot = -17.4942489903105 +556000 ekin = 2.43741510652919 | erot = 2.45751361710331 | epot = -22.292881083487 | etot = -17.3979523598545 +557000 ekin = 2.35602361024345 | erot = 2.35108817931542 | epot = -22.2068336513712 | etot = -17.4997218618123 +558000 ekin = 2.29845334881496 | erot = 2.47944197593295 | epot = -22.1269301143066 | etot = -17.3490347895587 +559000 ekin = 2.30547484128393 | erot = 2.43861674436445 | epot = -22.0431486095149 | etot = -17.2990570238665 +560000 ekin = 2.27735914776848 | erot = 2.22067768733756 | epot = -21.9730451699076 | etot = -17.4750083348016 +561000 ekin = 2.29286875562462 | erot = 2.11991684539843 | epot = -21.9034779049411 | etot = -17.490692303918 +562000 ekin = 2.19274483675775 | erot = 2.46930771586795 | epot = -21.8893960999879 | etot = -17.2273435473622 +563000 ekin = 2.25507955004823 | erot = 2.41065657987137 | epot = -21.9034392529016 | etot = -17.237703122982 +564000 ekin = 2.40459323350298 | erot = 2.24328259671745 | epot = -21.9404208075869 | etot = -17.2925449773664 +565000 ekin = 2.45683133378064 | erot = 2.27185510495041 | epot = -22.0074255927212 | etot = -17.2787391539901 +566000 ekin = 2.40141767311459 | erot = 2.21041354599862 | epot = -22.0735209036129 | etot = -17.4616896844997 +567000 ekin = 2.4457477052997 | erot = 2.11328940794165 | epot = -22.1387930635638 | etot = -17.5797559503224 +568000 ekin = 2.42570050072055 | erot = 2.18749548652437 | epot = -22.1800917698723 | etot = -17.5668957826274 +569000 ekin = 2.41454722540317 | erot = 2.10107949642201 | epot = -22.2121048457964 | etot = -17.6964781239712 +570000 ekin = 2.2989763814642 | erot = 2.04752727974981 | epot = -22.2369346580044 | etot = -17.8904309967904 +571000 ekin = 2.37657622585365 | erot = 2.05748511989246 | epot = -22.2528258700709 | etot = -17.8187645243248 +572000 ekin = 2.3168225167925 | erot = 2.58991099215539 | epot = -22.2496997094431 | etot = -17.3429662004952 +573000 ekin = 2.3040067160629 | erot = 2.31011895599928 | epot = -22.2262777020441 | etot = -17.6121520299819 +574000 ekin = 2.2203291203695 | erot = 2.34605820626859 | epot = -22.1986731397123 | etot = -17.6322858130742 +575000 ekin = 2.32899896279942 | erot = 2.14115178550434 | epot = -22.1599463152592 | etot = -17.6897955669555 +576000 ekin = 2.39677965647551 | erot = 2.16319777458983 | epot = -22.1106499071576 | etot = -17.5506724760922 +577000 ekin = 2.34165067357812 | erot = 1.93700136472043 | epot = -22.0653568060897 | etot = -17.7867047677912 +578000 ekin = 2.16459341404791 | erot = 1.94455021171713 | epot = -22.0220297065974 | etot = -17.9128860808324 +579000 ekin = 2.10243284337417 | erot = 1.93292394186435 | epot = -21.9718679160588 | etot = -17.9365111308202 +580000 ekin = 1.99604497344175 | erot = 1.95521625056201 | epot = -21.9148231396271 | etot = -17.9635619156233 +581000 ekin = 1.96384176915015 | erot = 1.99100077453193 | epot = -21.8663464602612 | etot = -17.9115039165791 +582000 ekin = 1.86034078875954 | erot = 1.90507522813595 | epot = -21.8442116641843 | etot = -18.0787956472888 +583000 ekin = 1.71909602928119 | erot = 1.97209600265413 | epot = -21.8622366159147 | etot = -18.1710445839794 +584000 ekin = 1.703647421171 | erot = 1.84090438363609 | epot = -21.9097350864251 | etot = -18.365183281618 +585000 ekin = 1.74431579790209 | erot = 2.03905704940609 | epot = -21.9890373916311 | etot = -18.2056645443229 +586000 ekin = 1.73466674324848 | erot = 1.83902306942848 | epot = -22.0843760980402 | etot = -18.5106862853632 +587000 ekin = 1.69495214035969 | erot = 2.05654584168949 | epot = -22.1748305300913 | etot = -18.4233325480421 +588000 ekin = 1.81991084277846 | erot = 2.03271452479352 | epot = -22.2619123801789 | etot = -18.4092870126069 +589000 ekin = 1.7577411459267 | erot = 2.09107160464902 | epot = -22.3245174454578 | etot = -18.4757046948821 +590000 ekin = 1.72192880825669 | erot = 2.02708321623578 | epot = -22.3712739626591 | etot = -18.6222619381666 +591000 ekin = 1.7680149700417 | erot = 2.19934356351431 | epot = -22.4026553786928 | etot = -18.4352968451368 +592000 ekin = 1.73818904167481 | erot = 2.31753844822573 | epot = -22.4297727542857 | etot = -18.3740452643852 +593000 ekin = 1.74423680346919 | erot = 2.35378967969673 | epot = -22.4309363170804 | etot = -18.3329098339145 +594000 ekin = 1.74360225576695 | erot = 1.98671317855359 | epot = -22.3849580162802 | etot = -18.6546425819596 +595000 ekin = 1.8259762247913 | erot = 2.13309374747876 | epot = -22.3903093107667 | etot = -18.4312393384966 +596000 ekin = 1.88347190280853 | erot = 2.21700247043607 | epot = -22.4390117320798 | etot = -18.3385373588352 +597000 ekin = 1.85682865820145 | erot = 2.22335853873402 | epot = -22.4665965332843 | etot = -18.3864093363488 +598000 ekin = 1.90006820905248 | erot = 2.42053542571092 | epot = -22.4694279641808 | etot = -18.1488243294174 +599000 ekin = 1.90071729874358 | erot = 2.59878396537153 | epot = -22.4910623963927 | etot = -17.9915611322776 +600000 ekin = 1.97752963691671 | erot = 2.72441502124577 | epot = -22.5477576362777 | etot = -17.8458129781152 +601000 ekin = 1.85698550625183 | erot = 2.88505630055983 | epot = -22.601413276632 | etot = -17.8593714698203 +602000 ekin = 1.85670612852391 | erot = 2.9924675577216 | epot = -22.6585474549208 | etot = -17.8093737686753 +603000 ekin = 1.86635938777726 | erot = 2.7946692567766 | epot = -22.7047123446179 | etot = -18.043683700064 +604000 ekin = 1.85627372221482 | erot = 2.96454267326802 | epot = -22.7247435540802 | etot = -17.9039271585974 +605000 ekin = 1.90713526215432 | erot = 2.83334095597306 | epot = -22.7033988480802 | etot = -17.9629226299528 +606000 ekin = 1.97855456734139 | erot = 2.4416881433075 | epot = -22.6272048618402 | etot = -18.2069621511913 +607000 ekin = 2.01266482611061 | erot = 2.45716329068746 | epot = -22.5070850149334 | etot = -18.0372568981353 +608000 ekin = 2.12878560429542 | erot = 2.31425337484033 | epot = -22.3497088958721 | etot = -17.9066699167364 +609000 ekin = 2.06312041868305 | erot = 2.11817811077744 | epot = -22.1990535325682 | etot = -18.0177550031077 +610000 ekin = 2.16915995218525 | erot = 2.15710310478974 | epot = -22.0738713202684 | etot = -17.7476082632935 +611000 ekin = 2.2479062777385 | erot = 2.44524506443981 | epot = -21.9773927987227 | etot = -17.2842414565444 +612000 ekin = 2.33407663304688 | erot = 2.43880885419943 | epot = -21.915819412039 | etot = -17.1429339247927 +613000 ekin = 2.4862713655459 | erot = 2.04564905753212 | epot = -21.9014181358314 | etot = -17.3694977127534 +614000 ekin = 2.63092379207172 | erot = 1.78137353630906 | epot = -21.9268892251557 | etot = -17.514591896775 +615000 ekin = 2.76847753887656 | erot = 1.74704506635928 | epot = -22.0144396036921 | etot = -17.4989169984563 +616000 ekin = 2.91908707455724 | erot = 1.7829061327169 | epot = -22.118601225114 | etot = -17.4166080178398 +617000 ekin = 3.15203249393298 | erot = 1.78303328673794 | epot = -22.2256012419584 | etot = -17.2905354612875 +618000 ekin = 3.31119378517929 | erot = 1.96412968205649 | epot = -22.3133840086656 | etot = -17.0380605414298 +619000 ekin = 3.47590250528842 | erot = 1.76611683746803 | epot = -22.3772219575797 | etot = -17.1352026148232 +620000 ekin = 3.48874988045414 | erot = 1.89528011242398 | epot = -22.4384551139398 | etot = -17.0544251210617 +621000 ekin = 3.6162246198138 | erot = 1.99344049296405 | epot = -22.4893103152157 | etot = -16.8796452024379 +622000 ekin = 3.58399773461891 | erot = 1.74513664213456 | epot = -22.4803416552216 | etot = -17.1512072784681 +623000 ekin = 3.63032006314557 | erot = 1.71430163919976 | epot = -22.4430926293461 | etot = -17.0984709270008 +624000 ekin = 3.65855713197028 | erot = 1.69922484729345 | epot = -22.3868122910147 | etot = -17.0290303117509 +625000 ekin = 3.60887827930814 | erot = 1.53990637330195 | epot = -22.3164178534658 | etot = -17.1676332008557 +626000 ekin = 3.5266046023718 | erot = 1.50586548866505 | epot = -22.2442897351173 | etot = -17.2118196440805 +627000 ekin = 3.50343711770174 | erot = 1.65554299653921 | epot = -22.1699228898753 | etot = -17.0109427756344 +628000 ekin = 3.39027059126337 | erot = 1.7516727323576 | epot = -22.0882385302028 | etot = -16.9462952065818 +629000 ekin = 3.23988150916915 | erot = 1.71907571962443 | epot = -21.9985657464086 | etot = -17.0396085176151 +630000 ekin = 3.19313977959945 | erot = 1.92181644528356 | epot = -21.9264321634453 | etot = -16.8114759385623 +631000 ekin = 3.16387923134672 | erot = 1.95916493180211 | epot = -21.8395694883598 | etot = -16.7165253252109 +632000 ekin = 3.14859471403509 | erot = 1.97621264135338 | epot = -21.7846629506645 | etot = -16.659855595276 +633000 ekin = 3.21562845702806 | erot = 2.00714201834293 | epot = -21.7459219259817 | etot = -16.5231514506108 +634000 ekin = 3.18996985450964 | erot = 2.01201311569096 | epot = -21.7056771658783 | etot = -16.5036941956777 +635000 ekin = 3.09651235720975 | erot = 1.73602275759662 | epot = -21.6544424588022 | etot = -16.8219073439959 +636000 ekin = 2.92860815615002 | erot = 1.85589302961923 | epot = -21.6235143680234 | etot = -16.8390131822541 +637000 ekin = 2.9145049294062 | erot = 1.98660531398791 | epot = -21.619133666584 | etot = -16.7180234231899 +638000 ekin = 2.9886464322491 | erot = 2.52300956640128 | epot = -21.6153555894526 | etot = -16.1036995908022 +639000 ekin = 2.82285402890259 | erot = 2.58031703406081 | epot = -21.5893617816824 | etot = -16.186190718719 +640000 ekin = 2.87726879521924 | erot = 2.71639270851165 | epot = -21.5512867369316 | etot = -15.9576252332007 +641000 ekin = 2.95903007169291 | erot = 2.43559640758676 | epot = -21.5137572402018 | etot = -16.1191307609221 +642000 ekin = 2.9620413382774 | erot = 2.50073908911551 | epot = -21.4303396746003 | etot = -15.9675592472074 +643000 ekin = 2.95135321760972 | erot = 2.18430881955701 | epot = -21.3830067810418 | etot = -16.2473447438751 +644000 ekin = 2.8946147226303 | erot = 2.24797742659791 | epot = -21.3844502347307 | etot = -16.2418580855025 +645000 ekin = 2.95435208333424 | erot = 2.48214942109052 | epot = -21.3637410798343 | etot = -15.9272395754095 +646000 ekin = 2.9055672357566 | erot = 2.30743635404266 | epot = -21.3137753959635 | etot = -16.1007718061642 +647000 ekin = 2.90760512758757 | erot = 2.34216740244697 | epot = -21.2632699171358 | etot = -16.0134973871012 +648000 ekin = 2.85798779133643 | erot = 2.18813680751306 | epot = -21.2316650481513 | etot = -16.1855404493018 +649000 ekin = 2.8011055300675 | erot = 1.99789309268243 | epot = -21.2271459685494 | etot = -16.4281473457995 +650000 ekin = 2.78705126935857 | erot = 2.05433186051859 | epot = -21.2258730978759 | etot = -16.3844899679987 +651000 ekin = 2.82981122207047 | erot = 2.24476751486992 | epot = -21.2549338926243 | etot = -16.1803551556839 +652000 ekin = 2.81187017826173 | erot = 2.46541600128328 | epot = -21.3104029656997 | etot = -16.0331167861547 +653000 ekin = 2.97461611593627 | erot = 2.32074630167001 | epot = -21.3681399998172 | etot = -16.0727775822109 +654000 ekin = 2.88164611559566 | erot = 2.38213902831403 | epot = -21.3981318593913 | etot = -16.1343467154816 +655000 ekin = 2.94913378760669 | erot = 2.34812868784313 | epot = -21.4113698116756 | etot = -16.1141073362258 +656000 ekin = 2.89233729061902 | erot = 2.39374651226493 | epot = -21.4288546902073 | etot = -16.1427708873233 +657000 ekin = 2.77598738951759 | erot = 2.49755521549789 | epot = -21.444950469184 | etot = -16.1714078641686 +658000 ekin = 2.77740080353575 | erot = 2.62230590128066 | epot = -21.4463092301614 | etot = -16.046602525345 +659000 ekin = 2.65259875229085 | erot = 2.75527600584018 | epot = -21.4247610675882 | etot = -16.0168863094572 +660000 ekin = 2.56686955703512 | erot = 2.62037576285298 | epot = -21.3982561329642 | etot = -16.2110108130761 +661000 ekin = 2.65054440121051 | erot = 2.62707264418943 | epot = -21.3903690458673 | etot = -16.1127520004673 +662000 ekin = 2.57957249166943 | erot = 2.57121547805632 | epot = -21.3759360832761 | etot = -16.2251481135504 +663000 ekin = 2.48664501783065 | erot = 2.38657187242597 | epot = -21.3934385678216 | etot = -16.520221677565 +664000 ekin = 2.51645777661058 | erot = 2.20401035947312 | epot = -21.4329380039065 | etot = -16.7124698678228 +665000 ekin = 2.44076978766891 | erot = 2.41816703577445 | epot = -21.4520134506829 | etot = -16.5930766272395 +666000 ekin = 2.35012835368458 | erot = 2.60496616000881 | epot = -21.468608543592 | etot = -16.5135140298986 +667000 ekin = 2.32189657004542 | erot = 2.57250144791893 | epot = -21.493981856009 | etot = -16.5995838380446 +668000 ekin = 2.36116261151376 | erot = 2.41860507877956 | epot = -21.5056838332 | etot = -16.7259161429067 +669000 ekin = 2.31387988694926 | erot = 2.33668050703713 | epot = -21.5343548142385 | etot = -16.8837944202521 +670000 ekin = 2.39198713502114 | erot = 2.44748109573363 | epot = -21.5481637926271 | etot = -16.7086955618724 +671000 ekin = 2.41568039789449 | erot = 2.60129732112569 | epot = -21.6059621481904 | etot = -16.5889844291702 +672000 ekin = 2.55961383121377 | erot = 2.5516494198211 | epot = -21.7089264495916 | etot = -16.5976631985567 +673000 ekin = 2.60207943153982 | erot = 2.89040304008769 | epot = -21.8182919408422 | etot = -16.3258094692147 +674000 ekin = 2.73648569737568 | erot = 2.81855016630383 | epot = -21.9222017117631 | etot = -16.3671658480836 +675000 ekin = 2.91114076539593 | erot = 2.36500632401704 | epot = -22.0018822691695 | etot = -16.7257351797566 +676000 ekin = 2.93341061527324 | erot = 2.28532481615634 | epot = -22.0731286226875 | etot = -16.8543931912579 +677000 ekin = 3.01470682908119 | erot = 2.22858273949015 | epot = -22.1284745680586 | etot = -16.8851849994873 +678000 ekin = 3.14497803943653 | erot = 1.93068246054129 | epot = -22.1456906590932 | etot = -17.0700301591153 +679000 ekin = 3.29461438438575 | erot = 2.1076091211883 | epot = -22.1361806217957 | etot = -16.7339571162216 +680000 ekin = 3.37176530279777 | erot = 2.01104009703978 | epot = -22.1041151314324 | etot = -16.7213097315948 +681000 ekin = 3.45483484720574 | erot = 1.9006745779217 | epot = -22.0463762684206 | etot = -16.6908668432931 +682000 ekin = 3.37894348708773 | erot = 1.72137005878542 | epot = -21.9505620370445 | etot = -16.8502484911713 +683000 ekin = 3.42286368355757 | erot = 1.851267808343 | epot = -21.8191972813593 | etot = -16.5450657894587 +684000 ekin = 3.36291962928464 | erot = 1.78272354471464 | epot = -21.6428884495562 | etot = -16.4972452755569 +685000 ekin = 3.36082871274587 | erot = 1.56476357384128 | epot = -21.4554201037061 | etot = -16.5298278171189 +686000 ekin = 3.29456600954292 | erot = 1.4526614688564 | epot = -21.2708420183485 | etot = -16.5236145399492 +687000 ekin = 3.28683183665641 | erot = 1.05147246964451 | epot = -21.0945257475366 | etot = -16.7562214412357 +688000 ekin = 3.1200573469182 | erot = 1.15864732674202 | epot = -20.9292915494188 | etot = -16.6505868757585 +689000 ekin = 2.98255457232203 | erot = 1.23350933506107 | epot = -20.789156167879 | etot = -16.5730922604959 +690000 ekin = 2.88677394533012 | erot = 1.14959548133369 | epot = -20.6827307127436 | etot = -16.6463612860798 +691000 ekin = 2.85231691921405 | erot = 1.3493894763518 | epot = -20.618749588821 | etot = -16.4170431932552 +692000 ekin = 2.82399536294284 | erot = 1.61591108279221 | epot = -20.5825839292396 | etot = -16.1426774835046 +693000 ekin = 2.78364237671965 | erot = 1.75822822075852 | epot = -20.5907390731048 | etot = -16.0488684756267 +694000 ekin = 2.73371563485489 | erot = 2.0853752693929 | epot = -20.6328696988286 | etot = -15.8137787945808 +695000 ekin = 2.57124739242674 | erot = 2.14630522202577 | epot = -20.6823542908148 | etot = -15.9648016763623 +696000 ekin = 2.51399296936984 | erot = 2.5586711835596 | epot = -20.7367847556415 | etot = -15.664120602712 +697000 ekin = 2.5045480949995 | erot = 2.5021571607765 | epot = -20.7898428219557 | etot = -15.7831375661797 +698000 ekin = 2.36358142640492 | erot = 2.63892421049623 | epot = -20.814814737847 | etot = -15.8123091009459 +699000 ekin = 2.31199340724625 | erot = 2.68625065707107 | epot = -20.7956836949862 | etot = -15.7974396306689 +700000 ekin = 2.14616834772889 | erot = 2.12698342038349 | epot = -20.7725738213778 | etot = -16.4994220532654 +701000 ekin = 2.15539690119064 | erot = 2.17922309078413 | epot = -20.7552775762032 | etot = -16.4206575842285 +702000 ekin = 2.10080573596265 | erot = 2.11876313824413 | epot = -20.7375521816454 | etot = -16.5179833074386 +703000 ekin = 2.11218006165568 | erot = 2.10588532277707 | epot = -20.7475858269107 | etot = -16.529520442478 +704000 ekin = 2.12315820389529 | erot = 2.10220748203651 | epot = -20.7572998532755 | etot = -16.5319341673437 +705000 ekin = 2.15166233402701 | erot = 2.1402299573417 | epot = -20.7941736502213 | etot = -16.5022813588526 +706000 ekin = 2.15163098226693 | erot = 2.26908854153892 | epot = -20.8512276988322 | etot = -16.4305081750263 +707000 ekin = 2.15471286696234 | erot = 2.5265790249537 | epot = -20.952057964416 | etot = -16.2707660725 +708000 ekin = 2.17467467531714 | erot = 2.49469457222147 | epot = -21.0502066736907 | etot = -16.3808374261521 +709000 ekin = 2.2527087542905 | erot = 2.67362934165249 | epot = -21.1795445148264 | etot = -16.2532064188834 +710000 ekin = 2.19946540304098 | erot = 2.99965152220121 | epot = -21.3025369771158 | etot = -16.1034200518737 +711000 ekin = 2.25060849345726 | erot = 2.69455961858579 | epot = -21.3800741765573 | etot = -16.4349060645143 +712000 ekin = 2.31009709048328 | erot = 2.56904053029559 | epot = -21.4438411099749 | etot = -16.5647034891961 +713000 ekin = 2.34856712569268 | erot = 2.67010815786396 | epot = -21.4921710148015 | etot = -16.4734957312449 +714000 ekin = 2.46551783464225 | erot = 2.47127151678511 | epot = -21.4976914761202 | etot = -16.5609021246929 +715000 ekin = 2.51889281585858 | erot = 2.39422134725105 | epot = -21.4732726012175 | etot = -16.5601584381079 +716000 ekin = 2.57715724769765 | erot = 2.54742070298338 | epot = -21.4493966986374 | etot = -16.3248187479563 +717000 ekin = 2.65149378986421 | erot = 2.37788349879642 | epot = -21.4573082004016 | etot = -16.427930911741 +718000 ekin = 2.69352880756017 | erot = 2.62278633313092 | epot = -21.4974593554888 | etot = -16.1811442147977 +719000 ekin = 2.80177184525531 | erot = 2.54312012627467 | epot = -21.5233281256771 | etot = -16.1784361541471 +720000 ekin = 2.69854861927349 | erot = 2.43897381701002 | epot = -21.559021891228 | etot = -16.4214994549445 +721000 ekin = 2.67018557216916 | erot = 2.50608214081748 | epot = -21.6315812717079 | etot = -16.4553135587213 +722000 ekin = 2.6528210671532 | erot = 2.66679722018774 | epot = -21.705637764293 | etot = -16.386019476952 +723000 ekin = 2.65361827522399 | erot = 2.9762220597586 | epot = -21.7797776559588 | etot = -16.1499373209762 +724000 ekin = 2.60569769804332 | erot = 2.7602015007975 | epot = -21.8376307834395 | etot = -16.4717315845987 +725000 ekin = 2.6312786943458 | erot = 2.69399118898632 | epot = -21.8984299962621 | etot = -16.57316011293 +726000 ekin = 2.72545330440858 | erot = 2.64253926181284 | epot = -21.9407919115122 | etot = -16.5727993452907 +727000 ekin = 2.65040284294597 | erot = 2.78538015555903 | epot = -21.9637938172424 | etot = -16.5280108187374 +728000 ekin = 2.4817900390328 | erot = 2.97450520962215 | epot = -21.9479581531627 | etot = -16.4916629045077 +729000 ekin = 2.52972405397769 | erot = 2.90212496736399 | epot = -21.9040262067808 | etot = -16.4721771854391 +730000 ekin = 2.53115260905919 | erot = 2.84472555705129 | epot = -21.8740439587405 | etot = -16.49816579263 +731000 ekin = 2.54145691682368 | erot = 2.59870522768933 | epot = -21.8660177522148 | etot = -16.7258556077018 +732000 ekin = 2.53248561362455 | erot = 2.72510944305534 | epot = -21.8573992551141 | etot = -16.5998041984342 +733000 ekin = 2.62625070581274 | erot = 2.51680047965209 | epot = -21.8396073656004 | etot = -16.6965561801356 +734000 ekin = 2.64998616374939 | erot = 2.72845692103525 | epot = -21.8405294812886 | etot = -16.4620863965039 +735000 ekin = 2.6930620716659 | erot = 3.07169199347478 | epot = -21.8204798153908 | etot = -16.0557257502501 +736000 ekin = 2.7226035182261 | erot = 2.73658566507828 | epot = -21.8062871121353 | etot = -16.3470979288309 +737000 ekin = 2.75870598942315 | erot = 2.61625561790497 | epot = -21.7997278882042 | etot = -16.4247662808761 +738000 ekin = 2.97183711263039 | erot = 2.24889762319117 | epot = -21.8158801485016 | etot = -16.59514541268 +739000 ekin = 3.05953080589944 | erot = 2.09255160152925 | epot = -21.8603696084005 | etot = -16.7082872009718 +740000 ekin = 3.27063059251342 | erot = 2.33629691806491 | epot = -21.9283581824535 | etot = -16.3214306718752 +741000 ekin = 3.35389594882302 | erot = 2.3177523792101 | epot = -21.9905348157484 | etot = -16.3188864877153 +742000 ekin = 3.37765257218107 | erot = 2.24621136389748 | epot = -22.0551085268019 | etot = -16.4312445907234 +743000 ekin = 3.34761803886636 | erot = 2.11604292737006 | epot = -22.1501165805112 | etot = -16.6864556142748 +744000 ekin = 3.45014316044781 | erot = 2.2628373980103 | epot = -22.2301851995834 | etot = -16.5172046411253 +745000 ekin = 3.50577437774123 | erot = 2.18082158773737 | epot = -22.2958892423624 | etot = -16.6092932768838 +746000 ekin = 3.6237956406297 | erot = 2.29172371219975 | epot = -22.3504185189693 | etot = -16.4348991661398 +747000 ekin = 3.66042054954956 | erot = 2.2047502504764 | epot = -22.3851646701836 | etot = -16.5199938701577 +748000 ekin = 3.50974540143194 | erot = 2.40650262572102 | epot = -22.4178592321293 | etot = -16.5016112049764 +749000 ekin = 3.56386965172005 | erot = 2.05758013521468 | epot = -22.4625938818843 | etot = -16.8411440949496 +750000 ekin = 3.49499037119096 | erot = 2.11705320323023 | epot = -22.5182146312729 | etot = -16.9061710568517 +751000 ekin = 3.52059041081212 | erot = 2.16456234667844 | epot = -22.5708671367043 | etot = -16.8857143792137 +752000 ekin = 3.52922989091295 | erot = 2.13328496260202 | epot = -22.6142453819171 | etot = -16.9517305284022 +753000 ekin = 3.54450333705172 | erot = 1.90175527543418 | epot = -22.6772611743004 | etot = -17.2310025618145 +754000 ekin = 3.45153480837564 | erot = 1.87218797414039 | epot = -22.7422768873026 | etot = -17.4185541047866 +755000 ekin = 3.40998140309997 | erot = 1.7976501197847 | epot = -22.7840720762414 | etot = -17.5764405533567 +756000 ekin = 3.34055243015443 | erot = 1.98893101943502 | epot = -22.801524919867 | etot = -17.4720414702775 +757000 ekin = 3.25995163881639 | erot = 2.23144065289767 | epot = -22.8179736050352 | etot = -17.3265813133212 +758000 ekin = 3.16254182007729 | erot = 2.33708167519903 | epot = -22.7968151839708 | etot = -17.2971916886945 +759000 ekin = 3.08959154816134 | erot = 2.90979409874038 | epot = -22.7119241491299 | etot = -16.7125385022282 +760000 ekin = 3.12610940125076 | erot = 2.74386957055392 | epot = -22.5354298293418 | etot = -16.6654508575371 +761000 ekin = 3.01773123261458 | erot = 2.5444184248282 | epot = -22.2878249475343 | etot = -16.7256752900915 +762000 ekin = 2.78676830407828 | erot = 2.45851569401923 | epot = -22.0050811851095 | etot = -16.759797187012 +763000 ekin = 2.66585974802142 | erot = 2.3623113572463 | epot = -21.7220430301031 | etot = -16.6938719248354 +764000 ekin = 2.45269004589322 | erot = 2.21799353565932 | epot = -21.4437328772732 | etot = -16.7730492957207 +765000 ekin = 2.33602063980662 | erot = 2.18630884760025 | epot = -21.2172136821302 | etot = -16.6948841947233 +766000 ekin = 2.29166126734208 | erot = 2.30483974019094 | epot = -21.0282994393417 | etot = -16.4317984318087 +767000 ekin = 2.19131441806538 | erot = 2.03557115351072 | epot = -20.8759897944535 | etot = -16.6491042228774 +768000 ekin = 2.07724554805677 | erot = 2.24966311077002 | epot = -20.7557602191192 | etot = -16.4288515602924 +769000 ekin = 2.05775411195501 | erot = 2.42542434645642 | epot = -20.6955218024995 | etot = -16.212343344088 +770000 ekin = 2.00758682747571 | erot = 2.45906745907325 | epot = -20.6929044608178 | etot = -16.2262501742688 +771000 ekin = 1.98409315586931 | erot = 2.48472564199884 | epot = -20.7734270007245 | etot = -16.3046082028563 +772000 ekin = 1.96669673892092 | erot = 2.78510583323586 | epot = -20.9254659410934 | etot = -16.1736633689366 +773000 ekin = 2.0246104727649 | erot = 2.7825476907091 | epot = -21.1083738193739 | etot = -16.3012156558999 +774000 ekin = 2.11360336305321 | erot = 2.98822109565829 | epot = -21.3029651154825 | etot = -16.201140656771 +775000 ekin = 2.14002916094013 | erot = 3.19368392739269 | epot = -21.5172002816089 | etot = -16.183487193276 +776000 ekin = 2.24832330955206 | erot = 3.06531971326596 | epot = -21.7038275157922 | etot = -16.3901844929741 +777000 ekin = 2.26862051853046 | erot = 3.05204197556552 | epot = -21.8350670013861 | etot = -16.5144045072901 +778000 ekin = 2.28742554048422 | erot = 3.14948640814974 | epot = -21.908697877618 | etot = -16.471785928984 +779000 ekin = 2.3767984920586 | erot = 3.25877776275828 | epot = -21.9331744453781 | etot = -16.2975981905612 +780000 ekin = 2.41113222109191 | erot = 3.41326897160163 | epot = -21.8804415437791 | etot = -16.0560403510855 +781000 ekin = 2.35841060920441 | erot = 3.41692834904078 | epot = -21.7562873535257 | etot = -15.9809483952805 +782000 ekin = 2.33104722618949 | erot = 3.319677867618 | epot = -21.5791021588903 | etot = -15.9283770650828 +783000 ekin = 2.44468610858591 | erot = 3.39120123577045 | epot = -21.3872233744818 | etot = -15.5513360301255 +784000 ekin = 2.470311550305 | erot = 3.16062374063231 | epot = -21.2067959255547 | etot = -15.5758606346174 +785000 ekin = 2.44425304006425 | erot = 2.93358092965286 | epot = -21.066643439754 | etot = -15.6888094700369 +786000 ekin = 2.38361530280068 | erot = 2.4700859723762 | epot = -20.9753503604685 | etot = -16.1216490852916 +787000 ekin = 2.48426374783384 | erot = 2.47298901654076 | epot = -20.8359485090634 | etot = -15.8786957446888 +788000 ekin = 2.6242212902263 | erot = 2.14521403573502 | epot = -20.7277036502939 | etot = -15.9582683243326 +789000 ekin = 2.71455119011441 | erot = 2.24597257975372 | epot = -20.9557602381598 | etot = -15.9952364682917 +790000 ekin = 2.8956628737976 | erot = 2.37559330223004 | epot = -21.3404176331914 | etot = -16.0691614571637 +791000 ekin = 2.93118110717174 | erot = 2.41626490731829 | epot = -21.5892702620177 | etot = -16.2418242475277 +792000 ekin = 2.94573011046952 | erot = 2.50772398358445 | epot = -21.7794479744542 | etot = -16.3259938804002 +793000 ekin = 2.88905153418424 | erot = 2.38272361409125 | epot = -21.9056315911049 | etot = -16.6338564428295 +794000 ekin = 2.80588096705245 | erot = 2.32779825823241 | epot = -21.9743818696617 | etot = -16.8407026443769 +795000 ekin = 2.70597772737488 | erot = 2.07317402356865 | epot = -22.0026881808382 | etot = -17.2235364298946 +796000 ekin = 2.61721688822668 | erot = 2.0877352950794 | epot = -21.991804168953 | etot = -17.286851985647 +797000 ekin = 2.43136202877026 | erot = 1.98048933877632 | epot = -21.9515392836597 | etot = -17.5396879161131 +798000 ekin = 2.3611685869334 | erot = 1.82755970456493 | epot = -21.9000645272965 | etot = -17.7113362357982 +799000 ekin = 2.29297525755987 | erot = 1.5438362356442 | epot = -21.8291726353075 | etot = -17.9923611421034 +800000 ekin = 2.24935465151491 | erot = 1.5446184795202 | epot = -21.7259751888123 | etot = -17.9320020577772 +801000 ekin = 2.14652429984544 | erot = 1.41717049108859 | epot = -21.6384618116251 | etot = -18.0747670206911 +802000 ekin = 2.30260756675948 | erot = 1.51416478035656 | epot = -21.5464279977222 | etot = -17.7296556506061 +803000 ekin = 2.34534628569431 | erot = 1.40949886579115 | epot = -21.5017245308293 | etot = -17.7468793793438 +804000 ekin = 2.31752346956293 | erot = 1.57528351351064 | epot = -21.5228204134078 | etot = -17.6300134303343 +805000 ekin = 2.51908363021985 | erot = 2.02682036822049 | epot = -21.6250345942614 | etot = -17.0791305958211 +806000 ekin = 2.69359804195114 | erot = 2.31785574785011 | epot = -21.7872941337147 | etot = -16.7758403439135 +807000 ekin = 2.78033847998713 | erot = 2.41121019329285 | epot = -21.9922590001463 | etot = -16.8007103268663 +808000 ekin = 2.80619611495204 | erot = 2.63792095913363 | epot = -22.2205031545371 | etot = -16.7763860804514 +809000 ekin = 2.88326450587356 | erot = 2.67886677112831 | epot = -22.4540143776026 | etot = -16.8918831006008 +810000 ekin = 2.91302007052046 | erot = 2.96339278377446 | epot = -22.6564267335948 | etot = -16.7800138792999 +811000 ekin = 3.09829332412426 | erot = 2.61119529725562 | epot = -22.8014808233353 | etot = -17.0919922019554 +812000 ekin = 3.08224679909644 | erot = 2.59515009531282 | epot = -22.8823180456423 | etot = -17.204921151233 +813000 ekin = 3.00916955211487 | erot = 2.7513570465975 | epot = -22.9208796974757 | etot = -17.1603530987634 +814000 ekin = 2.97174307315133 | erot = 2.90525451369445 | epot = -22.9341256772712 | etot = -17.0571280904254 +815000 ekin = 2.96997620607842 | erot = 3.14378750342501 | epot = -22.9208614386057 | etot = -16.8070977291022 +816000 ekin = 2.92448217395719 | erot = 2.88577656649752 | epot = -22.8782094391867 | etot = -17.067950698732 +817000 ekin = 2.88310554429553 | erot = 2.61870439923404 | epot = -22.8398760621413 | etot = -17.3380661186117 +818000 ekin = 2.8186685658087 | erot = 2.51624869438279 | epot = -22.790652874045 | etot = -17.4557356138535 +819000 ekin = 2.69190791098675 | erot = 1.98944862516422 | epot = -22.7267915943545 | etot = -18.0454350582035 +820000 ekin = 2.68723603002879 | erot = 1.98686669393842 | epot = -22.6848562040874 | etot = -18.0107534801202 +821000 ekin = 2.54604202399002 | erot = 2.17140584071642 | epot = -22.6462173351128 | etot = -17.9287694704063 +822000 ekin = 2.51719569259881 | erot = 2.14190227340006 | epot = -22.6036341275869 | etot = -17.944536161588 +823000 ekin = 2.3897594731009 | erot = 2.45514339808758 | epot = -22.5714957893461 | etot = -17.7265929181577 +824000 ekin = 2.31794554365845 | erot = 2.04410509977472 | epot = -22.5460261880528 | etot = -18.1839755446196 +825000 ekin = 2.2413745688521 | erot = 2.02652245530707 | epot = -22.5316621259024 | etot = -18.2637651017432 +826000 ekin = 2.17386448675867 | erot = 1.87577926811458 | epot = -22.5563066825792 | etot = -18.5066629277059 +827000 ekin = 2.15440642655349 | erot = 2.100839050741 | epot = -22.5878061584655 | etot = -18.332560681171 +828000 ekin = 1.93354077156671 | erot = 1.97318227704413 | epot = -22.6117615018474 | etot = -18.7050384532365 +829000 ekin = 1.91274491416172 | erot = 2.31769032262837 | epot = -22.6065942718288 | etot = -18.3761590350387 +830000 ekin = 1.8791033996829 | erot = 2.45880670474272 | epot = -22.612519347576 | etot = -18.2746092431504 +831000 ekin = 1.89725781672108 | erot = 2.49473420733595 | epot = -22.6167165770136 | etot = -18.2247245529566 +832000 ekin = 1.85092425351987 | erot = 2.48066273824477 | epot = -22.6085378559549 | etot = -18.2769508641902 +833000 ekin = 1.79059573863287 | erot = 2.56006070865021 | epot = -22.6126545978152 | etot = -18.2619981505321 +834000 ekin = 1.79399510293591 | erot = 2.4467311322103 | epot = -22.6154861129996 | etot = -18.3747598778534 +835000 ekin = 1.80394510948908 | erot = 2.35964658964164 | epot = -22.6388182435289 | etot = -18.4752265443982 +836000 ekin = 1.69826382101383 | erot = 2.57406388654606 | epot = -22.6545723055334 | etot = -18.3822445979735 +837000 ekin = 1.57085807181323 | erot = 2.4318727074888 | epot = -22.6792499151576 | etot = -18.6765191358556 +838000 ekin = 1.48932995393548 | erot = 2.24165123204968 | epot = -22.6860468687812 | etot = -18.955065682796 +839000 ekin = 1.38743724869555 | erot = 1.7994795781969 | epot = -22.6563653509784 | etot = -19.469448524086 +840000 ekin = 1.45337763400311 | erot = 1.96043695396606 | epot = -22.6075458233742 | etot = -19.193731235405 +841000 ekin = 1.52590522598343 | erot = 2.22694909527787 | epot = -22.5519353417638 | etot = -18.7990810205025 +842000 ekin = 1.46532363485138 | erot = 2.10614026643366 | epot = -22.4887366967109 | etot = -18.9172727954258 +843000 ekin = 1.45281094628277 | erot = 2.17368676107355 | epot = -22.4106869099643 | etot = -18.784189202608 +844000 ekin = 1.49761542714547 | erot = 2.37443717915502 | epot = -22.3449586551429 | etot = -18.4729060488424 +845000 ekin = 1.55104391739263 | erot = 2.37673299844037 | epot = -22.2778376071694 | etot = -18.3500606913364 +846000 ekin = 1.58963047079772 | erot = 2.33696583404051 | epot = -22.1844847216069 | etot = -18.2578884167687 +847000 ekin = 1.54789432070425 | erot = 2.21935266362097 | epot = -22.0782777408795 | etot = -18.3110307565543 +848000 ekin = 1.64518981802254 | erot = 2.25544436718012 | epot = -21.9989181480533 | etot = -18.0982839628507 +849000 ekin = 1.65560014958027 | erot = 2.25710120668683 | epot = -21.9671927272718 | etot = -18.0544913710047 +850000 ekin = 1.64990114979118 | erot = 2.10882779392521 | epot = -21.9923852605708 | etot = -18.2336563168545 +851000 ekin = 1.76413935252599 | erot = 2.19132684842273 | epot = -22.0608745954471 | etot = -18.1054083944984 +852000 ekin = 1.77078332134233 | erot = 2.28186973473967 | epot = -22.1743987365035 | etot = -18.1217456804215 +853000 ekin = 1.88691006136919 | erot = 2.41685663704387 | epot = -22.3155292586367 | etot = -18.0117625602236 +854000 ekin = 1.91928053806185 | erot = 2.8774224065578 | epot = -22.4875387473874 | etot = -17.6908358027677 +855000 ekin = 1.91817487389611 | erot = 2.76992189261422 | epot = -22.6436233810626 | etot = -17.9555266145523 +856000 ekin = 1.88635564274518 | erot = 2.93908057669869 | epot = -22.764714829212 | etot = -17.9392786097681 +857000 ekin = 1.87890917293745 | erot = 2.80324259714404 | epot = -22.8439440601383 | etot = -18.1617922900568 +858000 ekin = 1.76204051430181 | erot = 3.04908239798752 | epot = -22.8707912309211 | etot = -18.0596683186317 +859000 ekin = 1.7989024329101 | erot = 3.00632398338588 | epot = -22.858163621965 | etot = -18.052937205669 +860000 ekin = 1.84913198872632 | erot = 2.5368745453322 | epot = -22.8254155766962 | etot = -18.4394090426377 +861000 ekin = 1.91842166492514 | erot = 2.44106443467542 | epot = -22.7812919779301 | etot = -18.4218058783295 +862000 ekin = 2.03399415900639 | erot = 2.5163072121941 | epot = -22.7187848283737 | etot = -18.1684834571732 +863000 ekin = 2.06594803165259 | erot = 2.19676104809288 | epot = -22.6494648939955 | etot = -18.38675581425 +864000 ekin = 2.14467142649092 | erot = 2.30238631972309 | epot = -22.5816995592198 | etot = -18.1346418130058 +865000 ekin = 2.16190583025574 | erot = 2.29241108749926 | epot = -22.5280905818489 | etot = -18.0737736640939 +866000 ekin = 2.08928464919086 | erot = 2.34809191732007 | epot = -22.4600229326612 | etot = -18.0226463661503 +867000 ekin = 2.13586636899732 | erot = 2.42667521822891 | epot = -22.3898488501335 | etot = -17.8273072629073 +868000 ekin = 2.1954317166317 | erot = 2.34267445579144 | epot = -22.3416768736356 | etot = -17.8035707012125 +869000 ekin = 2.29038273021708 | erot = 1.97935314671745 | epot = -22.3115310066391 | etot = -18.0417951297045 +870000 ekin = 2.32898457121283 | erot = 2.18228869748467 | epot = -22.3276861507295 | etot = -17.816412882032 +871000 ekin = 2.23179297801797 | erot = 2.2459332826014 | epot = -22.3623188812147 | etot = -17.8845926205953 +872000 ekin = 2.29217187589275 | erot = 1.92704010734607 | epot = -22.3920054616901 | etot = -18.1727934784513 +873000 ekin = 2.32174880232822 | erot = 2.05958528502834 | epot = -22.4263932343476 | etot = -18.045059146991 +874000 ekin = 2.31327351953291 | erot = 2.03208404812009 | epot = -22.455443789151 | etot = -18.110086221498 +875000 ekin = 2.36060633411365 | erot = 1.9631506090206 | epot = -22.4715825698401 | etot = -18.1478256267058 +876000 ekin = 2.37581414827156 | erot = 1.68685668202708 | epot = -22.5004013214913 | etot = -18.4377304911927 +877000 ekin = 2.27742755728299 | erot = 1.83322419137898 | epot = -22.532116735846 | etot = -18.421464987184 +878000 ekin = 2.26319377123898 | erot = 1.87116890647667 | epot = -22.5413279545541 | etot = -18.4069652768385 +879000 ekin = 2.23196066439032 | erot = 2.13914596070875 | epot = -22.5501734041016 | etot = -18.1790667790025 +880000 ekin = 2.13938297973388 | erot = 2.29330131769629 | epot = -22.5711782332574 | etot = -18.1384939358272 +881000 ekin = 2.1318680383761 | erot = 2.14219424217023 | epot = -22.5804302674708 | etot = -18.3063679869245 +882000 ekin = 2.07769353958449 | erot = 2.09780809423879 | epot = -22.5758307354899 | etot = -18.4003291016666 +883000 ekin = 2.14813365127776 | erot = 2.3071298666471 | epot = -22.561098149685 | etot = -18.1058346317601 +884000 ekin = 2.07540055241942 | erot = 2.60971216511092 | epot = -22.5339770599324 | etot = -17.8488643424021 +885000 ekin = 2.02469768265883 | erot = 2.37910004807467 | epot = -22.5100762497929 | etot = -18.1062785190594 +886000 ekin = 2.04877327926448 | erot = 2.4920068419659 | epot = -22.4892651846766 | etot = -17.9484850634462 +887000 ekin = 2.04537209931256 | erot = 2.62826263805162 | epot = -22.4798822756914 | etot = -17.8062475383273 +888000 ekin = 1.99171888431611 | erot = 2.59410846730937 | epot = -22.5006414627785 | etot = -17.914814111153 +889000 ekin = 1.98870471402342 | erot = 2.78841340112867 | epot = -22.5468720567938 | etot = -17.7697539416417 +890000 ekin = 1.96284801049735 | erot = 2.75880808828181 | epot = -22.6085064197237 | etot = -17.8868503209446 +891000 ekin = 1.98112231165057 | erot = 3.1373459334429 | epot = -22.6928710534629 | etot = -17.5744028083695 +892000 ekin = 1.98665494216616 | erot = 3.33630831317173 | epot = -22.7519184177234 | etot = -17.4289551623855 +893000 ekin = 2.01620612275651 | erot = 3.24720583676934 | epot = -22.8064098471944 | etot = -17.5429978876685 +894000 ekin = 2.02749033009361 | erot = 3.22400069534531 | epot = -22.8521068920411 | etot = -17.6006158666022 +895000 ekin = 2.00160082448535 | erot = 3.17371669918265 | epot = -22.8614176855647 | etot = -17.6861001618967 +896000 ekin = 1.81339236987639 | erot = 2.84276750235957 | epot = -22.8462163214778 | etot = -18.1900564492418 +897000 ekin = 1.78689182954606 | erot = 2.92738822261576 | epot = -22.8071071587307 | etot = -18.0928271065689 +898000 ekin = 1.79533619439721 | erot = 3.24658999514007 | epot = -22.7264192132158 | etot = -17.6844930236785 +899000 ekin = 1.86159788109296 | erot = 3.45052252234925 | epot = -22.6568068772942 | etot = -17.344686473852 +900000 ekin = 1.871565347733 | erot = 3.32747935577909 | epot = -22.603978413148 | etot = -17.4049337096359 +901000 ekin = 1.92032230964434 | erot = 2.99424285087995 | epot = -22.5603724778797 | etot = -17.6458073173554 +902000 ekin = 1.90371430437561 | erot = 3.42499917647929 | epot = -22.5288190745234 | etot = -17.2001055936685 +903000 ekin = 1.90475417412385 | erot = 2.92419346565474 | epot = -22.481903392252 | etot = -17.6529557524734 +904000 ekin = 1.9042250885605 | erot = 2.83212155923625 | epot = -22.4265338107449 | etot = -17.6901871629482 +905000 ekin = 2.00220741569793 | erot = 2.40991127904267 | epot = -22.3822853443987 | etot = -17.9701666496581 +906000 ekin = 2.01583988806087 | erot = 2.50889047935428 | epot = -22.3419713063768 | etot = -17.8172409389617 +907000 ekin = 2.13017652685615 | erot = 2.70022028195316 | epot = -22.2948001592062 | etot = -17.4644033503968 +908000 ekin = 2.21155735897479 | erot = 2.35139718849896 | epot = -22.2413626180754 | etot = -17.6784080706016 +909000 ekin = 2.1338678778393 | erot = 2.19569541163492 | epot = -22.1827827026496 | etot = -17.8532194131754 +910000 ekin = 2.16567596171951 | erot = 2.22520003505022 | epot = -22.1149129856203 | etot = -17.7240369888505 +911000 ekin = 2.15809222107774 | erot = 2.2903717395524 | epot = -22.0462122442145 | etot = -17.5977482835843 +912000 ekin = 2.22087547394806 | erot = 2.43655350626844 | epot = -21.9749682300971 | etot = -17.3175392498806 +913000 ekin = 2.19758537995934 | erot = 2.46754067556537 | epot = -21.8990451147449 | etot = -17.2339190592201 +914000 ekin = 2.14504994740269 | erot = 2.32786068060022 | epot = -21.8498156381494 | etot = -17.3769050101465 +915000 ekin = 2.15677546734478 | erot = 2.12497444036448 | epot = -21.8141432513078 | etot = -17.5323933435985 +916000 ekin = 2.2160014572559 | erot = 2.25340153292628 | epot = -21.7876876242378 | etot = -17.3182846340556 +917000 ekin = 2.23364693785389 | erot = 2.35177352781133 | epot = -21.7779589013955 | etot = -17.1925384357302 +918000 ekin = 2.08464913851938 | erot = 2.61658836146497 | epot = -21.7825075848243 | etot = -17.08127008484 +919000 ekin = 2.05155719758452 | erot = 2.37138616162095 | epot = -21.8289412030755 | etot = -17.4059978438701 +920000 ekin = 1.99021755546965 | erot = 2.17794976390656 | epot = -21.8761397201475 | etot = -17.7079724007713 +921000 ekin = 2.01039430381082 | erot = 2.29773189624593 | epot = -21.9108483283986 | etot = -17.6027221283418 +922000 ekin = 1.92539579138491 | erot = 2.21469038539231 | epot = -21.9265528183995 | etot = -17.7864666416223 +923000 ekin = 1.89135276318219 | erot = 2.48033290205602 | epot = -21.9147153156562 | etot = -17.5430296504179 +924000 ekin = 1.83373481371766 | erot = 2.30418865946995 | epot = -21.8715535507915 | etot = -17.7336300776039 +925000 ekin = 1.80384785511454 | erot = 2.49787879385034 | epot = -21.8417123497579 | etot = -17.539985700793 +926000 ekin = 1.90546414331473 | erot = 2.28964220950023 | epot = -21.8161106439945 | etot = -17.6210042911796 +927000 ekin = 1.7580003185621 | erot = 2.26185811978829 | epot = -21.8155973506605 | etot = -17.7957389123101 +928000 ekin = 1.73012385728564 | erot = 2.25745755725552 | epot = -21.8415061020356 | etot = -17.8539246874944 +929000 ekin = 1.70181106675635 | erot = 2.24508495229485 | epot = -21.9018319158879 | etot = -17.9549358968367 +930000 ekin = 1.78315203550054 | erot = 2.33522003414065 | epot = -22.0077604163365 | etot = -17.8893883466953 +931000 ekin = 1.77363895925538 | erot = 2.46038215962633 | epot = -22.1457204230464 | etot = -17.9116993041647 +932000 ekin = 1.76667271586465 | erot = 2.59245568108974 | epot = -22.3144614382831 | etot = -17.9553330413287 +933000 ekin = 1.78209785938963 | erot = 2.56752596800069 | epot = -22.4867886743831 | etot = -18.1371648469928 +934000 ekin = 1.87173647679322 | erot = 2.44750687382837 | epot = -22.6262337406975 | etot = -18.3069903900759 +935000 ekin = 1.89665977697722 | erot = 2.59891583987174 | epot = -22.7433040011002 | etot = -18.2477283842512 +936000 ekin = 1.89920259119386 | erot = 2.87375257167893 | epot = -22.8003443005922 | etot = -18.0273891377194 +937000 ekin = 1.86426948560265 | erot = 2.6477908473408 | epot = -22.7873604341046 | etot = -18.2753001011611 +938000 ekin = 1.86665683366312 | erot = 2.42302063492745 | epot = -22.7023246368742 | etot = -18.4126471682836 +939000 ekin = 1.76698390194023 | erot = 2.40739406174174 | epot = -22.5642561328094 | etot = -18.3898781691274 +940000 ekin = 1.75137690733249 | erot = 2.2407642793918 | epot = -22.3713737329341 | etot = -18.3792325462098 +941000 ekin = 1.58963621298461 | erot = 2.27191088485099 | epot = -22.1644304701045 | etot = -18.3028833722689 +942000 ekin = 1.46232602489932 | erot = 2.08408025750091 | epot = -21.9623923454062 | etot = -18.415986063006 +943000 ekin = 1.49840034172783 | erot = 2.09453482021866 | epot = -21.8214517267662 | etot = -18.2285165648197 +944000 ekin = 1.50566445428555 | erot = 2.0804963575743 | epot = -21.7243523604003 | etot = -18.1381915485405 +945000 ekin = 1.52481544863406 | erot = 2.24222261671406 | epot = -21.6950663303363 | etot = -17.9280282649882 +946000 ekin = 1.6705269846928 | erot = 2.20043430064301 | epot = -21.7083474408069 | etot = -17.837386155471 +947000 ekin = 1.75831919417236 | erot = 2.42832255803237 | epot = -21.7266669161379 | etot = -17.5400251639331 +948000 ekin = 1.77052178602355 | erot = 2.24375036337206 | epot = -21.7571925539277 | etot = -17.7429204045321 +949000 ekin = 1.90525688107151 | erot = 2.15107670024899 | epot = -21.7910913830632 | etot = -17.7347578017427 +950000 ekin = 1.99637307838944 | erot = 2.29947036820447 | epot = -21.8702527820815 | etot = -17.5744093354876 +951000 ekin = 2.10483728892661 | erot = 2.30940850407659 | epot = -21.9629695449489 | etot = -17.5487237519457 +952000 ekin = 2.18030789934715 | erot = 2.68842229181026 | epot = -22.0513964726281 | etot = -17.1826662814707 +953000 ekin = 2.29894777100509 | erot = 2.69603811292209 | epot = -22.1773476270753 | etot = -17.1823617431481 +954000 ekin = 2.50427642784842 | erot = 2.51587062326898 | epot = -22.2938756187015 | etot = -17.2737285675841 +955000 ekin = 2.68601007095003 | erot = 2.85595708623568 | epot = -22.4136942236144 | etot = -16.8717270664287 +956000 ekin = 2.86208234199811 | erot = 2.86492575592064 | epot = -22.527658282728 | etot = -16.8006501848093 +957000 ekin = 2.94712002857954 | erot = 3.23864127130547 | epot = -22.6062380946234 | etot = -16.4204767947384 +958000 ekin = 3.09033820658136 | erot = 3.08801001679431 | epot = -22.6118588804753 | etot = -16.4335106570996 +959000 ekin = 3.12093785566108 | erot = 3.07623469356954 | epot = -22.5436503994893 | etot = -16.3464778502587 +960000 ekin = 2.9069016374156 | erot = 3.01090766604238 | epot = -22.3906223678567 | etot = -16.4728130643988 +961000 ekin = 2.88926986935772 | erot = 2.81186239490758 | epot = -22.1509889576314 | etot = -16.4498566933661 +962000 ekin = 2.71651285756864 | erot = 2.69353640054316 | epot = -21.8539054312201 | etot = -16.4438561731083 +963000 ekin = 2.60409923966584 | erot = 2.39582384415016 | epot = -21.5416906703578 | etot = -16.5417675865418 +964000 ekin = 2.40781072012883 | erot = 2.16537437005288 | epot = -21.2330620721338 | etot = -16.6598769819521 +965000 ekin = 2.3377527582572 | erot = 2.03652274723743 | epot = -20.9588727103859 | etot = -16.5845972048913 +966000 ekin = 2.17944465260408 | erot = 2.02332848530725 | epot = -20.7642311299462 | etot = -16.5614579920349 +967000 ekin = 2.07498857026491 | erot = 2.11733282843234 | epot = -20.6152408895115 | etot = -16.4229194908142 +968000 ekin = 1.977515230712 | erot = 2.25496129774362 | epot = -20.5096192481148 | etot = -16.2771427196591 +969000 ekin = 1.99431122494612 | erot = 2.15454095745195 | epot = -20.4866822650025 | etot = -16.3378300826044 +970000 ekin = 2.00624797975466 | erot = 2.31644539427668 | epot = -20.4984368720275 | etot = -16.1757434979961 +971000 ekin = 2.03726182368004 | erot = 2.57406911909556 | epot = -20.5474355193071 | etot = -15.9361045765315 +972000 ekin = 2.11053299316045 | erot = 2.66924970104389 | epot = -20.5957948560729 | etot = -15.8160121618686 +973000 ekin = 2.13909953768404 | erot = 2.79309645313436 | epot = -20.6193111119725 | etot = -15.6871151211541 +974000 ekin = 2.03642559896498 | erot = 2.93377318653239 | epot = -20.614312681758 | etot = -15.6441138962606 +975000 ekin = 1.91630022907467 | erot = 2.56349308712614 | epot = -20.5694430140224 | etot = -16.0896496978216 +976000 ekin = 1.83216235810445 | erot = 2.64204586914641 | epot = -20.5231354926881 | etot = -16.0489272654372 +977000 ekin = 1.76505303121169 | erot = 2.68514846627339 | epot = -20.450057807627 | etot = -15.9998563101419 +978000 ekin = 1.73639184783128 | erot = 2.27119801193581 | epot = -20.3949825706915 | etot = -16.3873927109244 +979000 ekin = 1.81309943455166 | erot = 2.0382217960969 | epot = -20.3578721503554 | etot = -16.5065509197068 +980000 ekin = 1.79425326253144 | erot = 1.72046042714389 | epot = -20.3201056722031 | etot = -16.8053919825278 +981000 ekin = 1.84538588980124 | erot = 1.5997723280769 | epot = -20.3368599575054 | etot = -16.8917017396273 +982000 ekin = 1.9361024609619 | erot = 1.75747204617031 | epot = -20.4060032926331 | etot = -16.7124287855009 +983000 ekin = 1.99928359157551 | erot = 1.98902145591294 | epot = -20.4909781895417 | etot = -16.5026731420533 +984000 ekin = 2.19592051978336 | erot = 2.0961389717365 | epot = -20.625461827793 | etot = -16.3334023362731 +985000 ekin = 2.31254022438617 | erot = 2.24661234767528 | epot = -20.7844444229606 | etot = -16.2252918508992 +986000 ekin = 2.45455647294253 | erot = 2.08651767106892 | epot = -20.9596902957359 | etot = -16.4186161517244 +987000 ekin = 2.56068322151367 | erot = 2.27175324341725 | epot = -21.1348257089466 | etot = -16.3023892440157 +988000 ekin = 2.67201091365387 | erot = 2.31132475520005 | epot = -21.3185263075068 | etot = -16.3351906386529 +989000 ekin = 2.79950226646054 | erot = 2.49566247067108 | epot = -21.4876529502242 | etot = -16.1924882130926 +990000 ekin = 2.90927705603666 | erot = 2.70153575217409 | epot = -21.6276754302458 | etot = -16.0168626220351 +991000 ekin = 3.0768477512586 | erot = 3.08981572487771 | epot = -21.7184165043297 | etot = -15.5517530281934 +992000 ekin = 3.12051956981868 | erot = 3.14725854673712 | epot = -21.7580543270397 | etot = -15.4902762104839 +993000 ekin = 3.1206281076354 | erot = 3.10806695223056 | epot = -21.7488136709546 | etot = -15.5201186110886 +994000 ekin = 3.10341951101567 | erot = 3.39574822230794 | epot = -21.7355411993581 | etot = -15.2363734660345 +995000 ekin = 3.07116945452499 | erot = 3.61798155979366 | epot = -21.7172569404682 | etot = -15.0281059261496 +996000 ekin = 3.08751007567431 | erot = 3.2258719437312 | epot = -21.7092684412539 | etot = -15.3958864218484 +997000 ekin = 3.02133326540191 | erot = 3.2296690929186 | epot = -21.7044711321527 | etot = -15.4534687738322 +998000 ekin = 3.04814833733096 | erot = 3.33574456092159 | epot = -21.6714291500291 | etot = -15.2875362517765 +999000 ekin = 3.13698021613259 | erot = 3.24185323699451 | epot = -21.6125731456074 | etot = -15.2337396924803 +1000000 ekin = 3.12438752705776 | erot = 2.79887049874961 | epot = -21.5300188398266 | etot = -15.6067608140192 + 1000000 0.13886167 -1.3621774 0.016551227 -1.150352 9.5441241e-05 64000 +Loop time of 30.4944 on 1 procs for 1000000 steps with 16 atoms + +Performance: 28333.078 tau/day, 32792.915 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.671 | 24.671 | 24.671 | 0.0 | 80.90 +Bond | 0.87876 | 0.87876 | 0.87876 | 0.0 | 2.88 +Neigh | 0.020568 | 0.020568 | 0.020568 | 0.0 | 0.07 +Comm | 0.3709 | 0.3709 | 0.3709 | 0.0 | 1.22 +Output | 0.15202 | 0.15202 | 0.15202 | 0.0 | 0.50 +Modify | 4.1177 | 4.1177 | 4.1177 | 0.0 | 13.50 +Other | | 0.283 | | | 0.93 + +Nlocal: 16.0000 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 105.000 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 105 +Ave neighs/atom = 6.5625000 +Ave special neighs/atom = 3.7500000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:30 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 new file mode 100644 index 0000000000..4356b9c90d --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 @@ -0,0 +1,1173 @@ +LAMMPS (2 Jul 2021) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +set atom * mass 3.1575 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.9560004 + ghost atom cutoff = 3.8 + binsize = 1.4780002, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -21.9967648054699 | etot = -16.4902901461834 +Per MPI rank memory allocation (min/avg/max) = 8.984 | 9.016 | 9.096 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -1.3914531 0.016655298 -1.2057507 5.174549e-05 64000 +1000 ekin = 2.69992875879531 | erot = 3.03905971783101 | epot = -21.7993424099171 | etot = -16.0603539332907 +2000 ekin = 2.74236013741186 | erot = 2.48566425489664 | epot = -21.5864392778805 | etot = -16.358414885572 +3000 ekin = 2.71406239909253 | erot = 2.2379964617931 | epot = -21.4096440189505 | etot = -16.4575851580649 +4000 ekin = 2.62654210651837 | erot = 2.20187014105975 | epot = -21.2649637920051 | etot = -16.436551544427 +5000 ekin = 2.54619704507768 | erot = 2.19543579497861 | epot = -21.1625272503904 | etot = -16.4208944103341 +6000 ekin = 2.54036074498671 | erot = 2.24575383349946 | epot = -21.1026949544699 | etot = -16.3165803759837 +7000 ekin = 2.54636725719323 | erot = 2.17480262107778 | epot = -21.0944608538479 | etot = -16.3732909755769 +8000 ekin = 2.44266194745414 | erot = 1.89959276882142 | epot = -21.1290547630673 | etot = -16.7868000467917 +9000 ekin = 2.49849768578547 | erot = 1.91590827145359 | epot = -21.2010010008038 | etot = -16.7865950435647 +10000 ekin = 2.60405521154315 | erot = 2.31942457678919 | epot = -21.2714985323704 | etot = -16.3480187440381 +11000 ekin = 2.51729626827439 | erot = 2.60159361363173 | epot = -21.3305509557368 | etot = -16.2116610738307 +12000 ekin = 2.52572671978709 | erot = 2.38660744367415 | epot = -21.4045010372609 | etot = -16.4921668737996 +13000 ekin = 2.6003507735884 | erot = 2.37491144376808 | epot = -21.501501753381 | etot = -16.5262395360245 +14000 ekin = 2.66935763609378 | erot = 2.22902438599211 | epot = -21.5988036534075 | etot = -16.7004216313216 +15000 ekin = 2.71551281751847 | erot = 2.21389248221189 | epot = -21.6990132370777 | etot = -16.7696079373473 +16000 ekin = 2.84978299090939 | erot = 2.43940966993631 | epot = -21.7959192679746 | etot = -16.5067266071289 +17000 ekin = 2.95072779743509 | erot = 2.38947543725578 | epot = -21.8722593940791 | etot = -16.5320561593883 +18000 ekin = 2.85884496438636 | erot = 2.37101194861285 | epot = -21.9018380946369 | etot = -16.6719811816377 +19000 ekin = 2.77343461594062 | erot = 2.33973079907439 | epot = -21.8809702826779 | etot = -16.7678048676629 +20000 ekin = 2.58401274142397 | erot = 2.55272418280189 | epot = -21.8165314333068 | etot = -16.6797945090809 +21000 ekin = 2.51192366343062 | erot = 2.51457779660486 | epot = -21.7320362651688 | etot = -16.7055348051334 +22000 ekin = 2.49083859662966 | erot = 2.52955288592737 | epot = -21.6292667596243 | etot = -16.6088752770672 +23000 ekin = 2.39128650481518 | erot = 2.2075391744556 | epot = -21.5149142799637 | etot = -16.9160886006929 +24000 ekin = 2.35988329046228 | erot = 1.90440982269664 | epot = -21.4005066979858 | etot = -17.1362135848269 +25000 ekin = 2.28215741570376 | erot = 1.9697790536657 | epot = -21.3141881001702 | etot = -17.0622516308007 +26000 ekin = 2.19749762241965 | erot = 2.2783364703954 | epot = -21.263472573334 | etot = -16.7876384805189 +27000 ekin = 2.00825875058883 | erot = 2.19976409135101 | epot = -21.265928423673 | etot = -17.0579055817332 +28000 ekin = 1.84164368193047 | erot = 2.29604978886222 | epot = -21.2913487545157 | etot = -17.153655283723 +29000 ekin = 1.85165645974808 | erot = 2.1316357761727 | epot = -21.3636874932621 | etot = -17.3803952573413 +30000 ekin = 1.81585331071778 | erot = 2.36969485723272 | epot = -21.4672495085949 | etot = -17.2817013406444 +31000 ekin = 1.87586085382615 | erot = 2.30099083087629 | epot = -21.6118799895369 | etot = -17.4350283048345 +32000 ekin = 2.01266417384559 | erot = 2.39241064946051 | epot = -21.7843461993916 | etot = -17.3792713760855 +33000 ekin = 2.10031097060263 | erot = 2.65484725731934 | epot = -21.9744733587441 | etot = -17.2193151308221 +34000 ekin = 2.02466181562198 | erot = 2.84373149584292 | epot = -22.194126260332 | etot = -17.3257329488671 +35000 ekin = 1.97481459340813 | erot = 3.01731663707891 | epot = -22.4189097716656 | etot = -17.4267785411786 +36000 ekin = 2.01233253730944 | erot = 2.9176407320361 | epot = -22.6202547427807 | etot = -17.6902814734351 +37000 ekin = 2.07225850980039 | erot = 3.06834431569997 | epot = -22.8024087727696 | etot = -17.6618059472693 +38000 ekin = 2.05378795549781 | erot = 3.0363867535271 | epot = -22.9460226281607 | etot = -17.8558479191358 +39000 ekin = 2.06863065757201 | erot = 3.09515376673006 | epot = -23.0335342083504 | etot = -17.8697497840484 +40000 ekin = 2.00014415298571 | erot = 3.04584432430158 | epot = -23.0612280460053 | etot = -18.015239568718 +41000 ekin = 2.05172104966417 | erot = 2.77830340889767 | epot = -23.0196796418278 | etot = -18.189655183266 +42000 ekin = 2.05229847533166 | erot = 2.85273348534644 | epot = -22.9340198298525 | etot = -18.0289878691744 +43000 ekin = 1.9375580548129 | erot = 3.046505133258 | epot = -22.820917445214 | etot = -17.8368542571431 +44000 ekin = 1.84663697745675 | erot = 2.93951969808353 | epot = -22.703167317854 | etot = -17.9170106423137 +45000 ekin = 1.72975781399545 | erot = 2.60801842461352 | epot = -22.6010710155897 | etot = -18.2632947769807 +46000 ekin = 1.5918663290664 | erot = 2.62841769679508 | epot = -22.5067814781868 | etot = -18.2864974523253 +47000 ekin = 1.54109228867547 | erot = 2.65380906308329 | epot = -22.4139741210197 | etot = -18.2190727692609 +48000 ekin = 1.52801508900135 | erot = 2.56168528383555 | epot = -22.3146405234587 | etot = -18.2249401506218 +49000 ekin = 1.45236147507209 | erot = 2.19683353122211 | epot = -22.2336496311393 | etot = -18.5844546248451 +50000 ekin = 1.37133529115918 | erot = 2.38139075376814 | epot = -22.1777849612814 | etot = -18.4250589163541 +51000 ekin = 1.37894610429119 | erot = 2.55643955595488 | epot = -22.1214711763546 | etot = -18.1860855161085 +52000 ekin = 1.37307011220264 | erot = 2.64858735385417 | epot = -22.0854715362774 | etot = -18.0638140702206 +53000 ekin = 1.45140505120432 | erot = 2.86325966198773 | epot = -22.0769774994391 | etot = -17.7623127862471 +54000 ekin = 1.49400380215147 | erot = 3.02929024277184 | epot = -22.0888809603766 | etot = -17.5655869154533 +55000 ekin = 1.55040404860755 | erot = 2.51182875106841 | epot = -22.110508190484 | etot = -18.0482753908081 +56000 ekin = 1.49109168917175 | erot = 2.54803153869061 | epot = -22.1366154026192 | etot = -18.0974921747569 +57000 ekin = 1.50050137913426 | erot = 2.41737584414227 | epot = -22.1821202184231 | etot = -18.2642429951466 +58000 ekin = 1.60635589846639 | erot = 2.23996961758249 | epot = -22.2360694135128 | etot = -18.3897438974639 +59000 ekin = 1.72952597734791 | erot = 2.32633058396662 | epot = -22.2901578024364 | etot = -18.2343012411218 +60000 ekin = 1.69244797185259 | erot = 2.40027807279513 | epot = -22.3434040927657 | etot = -18.250678048118 +61000 ekin = 1.72620703032667 | erot = 2.11017860160473 | epot = -22.3831797154275 | etot = -18.5467940834961 +62000 ekin = 1.79594241743978 | erot = 2.21560837695549 | epot = -22.4218397438853 | etot = -18.41028894949 +63000 ekin = 1.77262742266283 | erot = 2.30422369990022 | epot = -22.4467748467827 | etot = -18.3699237242197 +64000 ekin = 1.85527283619093 | erot = 2.3126781136296 | epot = -22.4674777591492 | etot = -18.2995268093287 +65000 ekin = 1.78989203446879 | erot = 1.94802383598239 | epot = -22.4675168623455 | etot = -18.7296009918943 +66000 ekin = 1.77252597290745 | erot = 1.82642026775547 | epot = -22.4502267764221 | etot = -18.8512805357592 +67000 ekin = 1.80939758337874 | erot = 1.93052561353093 | epot = -22.440758264484 | etot = -18.7008350675744 +68000 ekin = 1.89908121763759 | erot = 2.02160808150964 | epot = -22.4404733275273 | etot = -18.5197840283801 +69000 ekin = 1.91605115497137 | erot = 1.99686686402571 | epot = -22.4556690038854 | etot = -18.5427509848884 +70000 ekin = 1.97266986208221 | erot = 1.99525089575647 | epot = -22.4717127742739 | etot = -18.5037920164352 +71000 ekin = 2.00234841846526 | erot = 2.03963009556294 | epot = -22.4872545087286 | etot = -18.4452759947004 +72000 ekin = 2.04989413571925 | erot = 2.251257126901 | epot = -22.5010508598365 | etot = -18.1998995972162 +73000 ekin = 1.96796663525086 | erot = 2.56091060599074 | epot = -22.5094020746161 | etot = -17.9805248333745 +74000 ekin = 1.94071763184331 | erot = 2.25118509796072 | epot = -22.4905641504119 | etot = -18.2986614206078 +75000 ekin = 1.90464776054054 | erot = 2.11018286106258 | epot = -22.4609449840088 | etot = -18.4461143624057 +76000 ekin = 1.96940901357865 | erot = 2.01632288693274 | epot = -22.4274745611146 | etot = -18.4417426606032 +77000 ekin = 1.94486767834805 | erot = 1.90684819966059 | epot = -22.3863373806159 | etot = -18.5346215026073 +78000 ekin = 1.96983919523036 | erot = 1.93099842937097 | epot = -22.344384650684 | etot = -18.4435470260826 +79000 ekin = 1.95938649015114 | erot = 1.86810626994579 | epot = -22.2942796582418 | etot = -18.4667868981449 +80000 ekin = 2.08117502277241 | erot = 1.51004106283071 | epot = -22.2616445282532 | etot = -18.6704284426501 +81000 ekin = 2.12565876638683 | erot = 1.68774361309041 | epot = -22.2503002969457 | etot = -18.4368979174685 +82000 ekin = 2.1024876598189 | erot = 1.68162562422037 | epot = -22.2731769674722 | etot = -18.4890636834329 +83000 ekin = 2.14448498615641 | erot = 1.81975712217532 | epot = -22.304671895878 | etot = -18.3404297875462 +84000 ekin = 2.13258101148045 | erot = 2.02922410781381 | epot = -22.3428808393218 | etot = -18.1810757200275 +85000 ekin = 2.08512493333083 | erot = 2.32083438054863 | epot = -22.3826539010024 | etot = -17.9766945871229 +86000 ekin = 2.17050776391433 | erot = 1.96275338625837 | epot = -22.4224341826942 | etot = -18.2891730325215 +87000 ekin = 2.2398985260089 | erot = 2.23705181642094 | epot = -22.4705294491959 | etot = -17.9935791067661 +88000 ekin = 2.27467140557785 | erot = 2.15326395377642 | epot = -22.513560970712 | etot = -18.0856256113577 +89000 ekin = 2.28843889082878 | erot = 2.12736799131705 | epot = -22.5645528135015 | etot = -18.1487459313557 +90000 ekin = 2.30332724032361 | erot = 2.29619358357547 | epot = -22.621069415243 | etot = -18.021548591344 +91000 ekin = 2.31381008485173 | erot = 2.07740016205537 | epot = -22.6563472804759 | etot = -18.2651370335688 +92000 ekin = 2.37378013130092 | erot = 2.23716627480794 | epot = -22.6690655261852 | etot = -18.0581191200763 +93000 ekin = 2.26456629794214 | erot = 2.65755706511332 | epot = -22.6595495475479 | etot = -17.7374261844924 +94000 ekin = 2.27111991294099 | erot = 2.70843483649312 | epot = -22.6144390606054 | etot = -17.6348843111713 +95000 ekin = 2.16051509784259 | erot = 2.76861411098494 | epot = -22.5458959635297 | etot = -17.6167667547022 +96000 ekin = 2.13622684332841 | erot = 3.00618377960085 | epot = -22.4457322783082 | etot = -17.3033216553789 +97000 ekin = 2.07419989457639 | erot = 2.65264916199247 | epot = -22.3153975468028 | etot = -17.588548490234 +98000 ekin = 2.11485220649791 | erot = 2.62887211771588 | epot = -22.2055031918167 | etot = -17.4617788676029 +99000 ekin = 2.14284693208925 | erot = 2.66222856414602 | epot = -22.1106632337977 | etot = -17.3055877375625 +100000 ekin = 2.1730834183665 | erot = 2.09482283074159 | epot = -22.043708504035 | etot = -17.7758022549269 +101000 ekin = 2.14866231805627 | erot = 2.38819764750835 | epot = -22.0122713210887 | etot = -17.4754113555241 +102000 ekin = 2.16493629238997 | erot = 2.64896606924374 | epot = -22.0210513992314 | etot = -17.2071490375977 +103000 ekin = 2.15114511690207 | erot = 2.56525012972715 | epot = -22.0652696455725 | etot = -17.3488743989433 +104000 ekin = 2.15671515638238 | erot = 2.62706983245359 | epot = -22.1421811666569 | etot = -17.358396177821 +105000 ekin = 2.12719541152403 | erot = 2.65706885533805 | epot = -22.2143972740324 | etot = -17.4301330071703 +106000 ekin = 2.1377470772108 | erot = 2.76654607800828 | epot = -22.2775634673612 | etot = -17.3732703121421 +107000 ekin = 2.20102004108557 | erot = 2.66823836970957 | epot = -22.3043515122748 | etot = -17.4350931014797 +108000 ekin = 2.17638500145548 | erot = 2.80828381708576 | epot = -22.3097186034589 | etot = -17.3250497849176 +109000 ekin = 2.19829684637025 | erot = 2.90666104596411 | epot = -22.282790113145 | etot = -17.1778322208107 +110000 ekin = 2.17152588755655 | erot = 2.81646086297867 | epot = -22.2246380567944 | etot = -17.2366513062592 +111000 ekin = 2.1537343646266 | erot = 2.45540077609881 | epot = -22.1236900284647 | etot = -17.5145548877393 +112000 ekin = 2.13686027679006 | erot = 2.53611388444163 | epot = -21.9714471685635 | etot = -17.2984730073318 +113000 ekin = 2.14753928432348 | erot = 2.38847611973762 | epot = -21.7866419003015 | etot = -17.2506264962404 +114000 ekin = 2.12631244931904 | erot = 2.25317215555341 | epot = -21.5978462560726 | etot = -17.2183616512002 +115000 ekin = 2.10651342910372 | erot = 2.32111327425019 | epot = -21.4106414032646 | etot = -16.9830146999107 +116000 ekin = 2.05857214689201 | erot = 2.34273379327708 | epot = -21.2543641951754 | etot = -16.8530582550063 +117000 ekin = 2.06082171760157 | erot = 2.29311267774735 | epot = -21.1252553707799 | etot = -16.771320975431 +118000 ekin = 2.07134223704075 | erot = 2.26440570108461 | epot = -21.020110076221 | etot = -16.6843621380957 +119000 ekin = 2.06457225589943 | erot = 1.93952258456715 | epot = -20.9769994108546 | etot = -16.972904570388 +120000 ekin = 2.11859853404644 | erot = 1.85164657615878 | epot = -20.9836901114857 | etot = -17.0134450012804 +121000 ekin = 2.16647853751427 | erot = 2.33645973353316 | epot = -21.0297394121115 | etot = -16.5268011410641 +122000 ekin = 2.26904266267125 | erot = 2.41049986821536 | epot = -21.1056070652395 | etot = -16.4260645343529 +123000 ekin = 2.21420535468718 | erot = 2.31638894325154 | epot = -21.1806353306483 | etot = -16.6500410327096 +124000 ekin = 2.25664202990643 | erot = 2.58640626588714 | epot = -21.2735600007682 | etot = -16.4305117049747 +125000 ekin = 2.28621615469859 | erot = 2.48741243437927 | epot = -21.33670340398 | etot = -16.5630748149022 +126000 ekin = 2.35529670025442 | erot = 2.68371862500862 | epot = -21.3743088823657 | etot = -16.3352935571027 +127000 ekin = 2.31727265883053 | erot = 2.65927495810834 | epot = -21.3864411166437 | etot = -16.4098934997048 +128000 ekin = 2.43349491835542 | erot = 2.48790131465779 | epot = -21.3667639128875 | etot = -16.4453676798743 +129000 ekin = 2.39675815548537 | erot = 2.10710860946299 | epot = -21.3539228728258 | etot = -16.8500561078775 +130000 ekin = 2.41755439047172 | erot = 1.81077952884566 | epot = -21.3548853564728 | etot = -17.1265514371554 +131000 ekin = 2.40648552369037 | erot = 1.77591735253035 | epot = -21.3574203976689 | etot = -17.1750175214481 +132000 ekin = 2.40897764408254 | erot = 1.730598467728 | epot = -21.3537520189401 | etot = -17.2141759071296 +133000 ekin = 2.37448540151596 | erot = 1.85880466212885 | epot = -21.3533218886588 | etot = -17.120031825014 +134000 ekin = 2.35796776832177 | erot = 2.06779644045339 | epot = -21.3551168402504 | etot = -16.9293526314752 +135000 ekin = 2.32265431042309 | erot = 2.18050776639534 | epot = -21.3445924581615 | etot = -16.841430381343 +136000 ekin = 2.26143919660737 | erot = 2.06564627363195 | epot = -21.3331599119328 | etot = -17.0060744416935 +137000 ekin = 2.23396906090406 | erot = 2.26473864092821 | epot = -21.3170510126767 | etot = -16.8183433108445 +138000 ekin = 2.25323790872622 | erot = 2.21298196842966 | epot = -21.3256388087684 | etot = -16.8594189316125 +139000 ekin = 2.35354475362125 | erot = 2.11114514997111 | epot = -21.4066516687639 | etot = -16.9419617651716 +140000 ekin = 2.31521381923623 | erot = 2.26671366611825 | epot = -21.4995923309512 | etot = -16.9176648455967 +141000 ekin = 2.33446890243273 | erot = 2.2458560577034 | epot = -21.5117862025255 | etot = -16.9314612423893 +142000 ekin = 2.33661695709308 | erot = 1.99377963333143 | epot = -21.5249788887696 | etot = -17.1945822983451 +143000 ekin = 2.35917698394992 | erot = 1.78177229585752 | epot = -21.5633348907872 | etot = -17.4223856109798 +144000 ekin = 2.41193656560927 | erot = 1.85068539007341 | epot = -21.6190569181184 | etot = -17.3564349624357 +145000 ekin = 2.50328391189521 | erot = 1.97991868781725 | epot = -21.6627615329474 | etot = -17.1795589332349 +146000 ekin = 2.52501086531617 | erot = 1.94890179310193 | epot = -21.7158596570766 | etot = -17.2419469986585 +147000 ekin = 2.55047937715167 | erot = 1.85137728928154 | epot = -21.7917365034049 | etot = -17.3898798369717 +148000 ekin = 2.52990172449131 | erot = 2.00218673263758 | epot = -21.8973033212467 | etot = -17.3652148641178 +149000 ekin = 2.47322709286654 | erot = 2.00142069560529 | epot = -22.0256184185787 | etot = -17.5509706301069 +150000 ekin = 2.55997956203425 | erot = 2.04181533809334 | epot = -22.1371239984736 | etot = -17.535329098346 +151000 ekin = 2.44470695881357 | erot = 2.34031071867535 | epot = -22.2527174105277 | etot = -17.4676997330388 +152000 ekin = 2.44475737305745 | erot = 2.26076754628984 | epot = -22.3351232248327 | etot = -17.6295983054854 +153000 ekin = 2.46166206744171 | erot = 2.17894561391992 | epot = -22.3636879590958 | etot = -17.7230802777341 +154000 ekin = 2.49242904735496 | erot = 2.18959276990461 | epot = -22.3683882355899 | etot = -17.6863664183303 +155000 ekin = 2.44328722883231 | erot = 2.13628761933913 | epot = -22.3356925905996 | etot = -17.7561177424282 +156000 ekin = 2.45031007040204 | erot = 2.26271751825021 | epot = -22.2682169791444 | etot = -17.5551893904921 +157000 ekin = 2.46907480878132 | erot = 1.93271915185536 | epot = -22.2160752580766 | etot = -17.8142812974399 +158000 ekin = 2.47549100134241 | erot = 1.8913430375128 | epot = -22.1750861634876 | etot = -17.8082521246323 +159000 ekin = 2.44378132199929 | erot = 1.82517595680765 | epot = -22.1335445885755 | etot = -17.8645873097686 +160000 ekin = 2.35644874685005 | erot = 1.85678861125791 | epot = -22.1078628335997 | etot = -17.8946254754918 +161000 ekin = 2.44175357097686 | erot = 2.14888928050333 | epot = -22.1031987495152 | etot = -17.512555898035 +162000 ekin = 2.46554036240822 | erot = 2.05333880369385 | epot = -22.1046164027324 | etot = -17.5857372366303 +163000 ekin = 2.36847802529543 | erot = 2.16987713772662 | epot = -22.1331210722207 | etot = -17.5947659091986 +164000 ekin = 2.31295455943998 | erot = 2.1887977205257 | epot = -22.1887776544464 | etot = -17.6870253744808 +165000 ekin = 2.37278415235371 | erot = 2.59415671104245 | epot = -22.269158133539 | etot = -17.3022172701428 +166000 ekin = 2.4571517702507 | erot = 2.91759661846332 | epot = -22.3489659308413 | etot = -16.9742175421273 +167000 ekin = 2.52772481698523 | erot = 2.95707760474977 | epot = -22.4233688575491 | etot = -16.9385664358141 +168000 ekin = 2.38117634975353 | erot = 2.66863240829489 | epot = -22.4863077773179 | etot = -17.4364990192695 +169000 ekin = 2.37442003008243 | erot = 3.02523535510244 | epot = -22.5524544630733 | etot = -17.1527990778884 +170000 ekin = 2.35912346263692 | erot = 3.26723708493091 | epot = -22.5931462410023 | etot = -16.9667856934345 +171000 ekin = 2.30318527402303 | erot = 3.14616282609875 | epot = -22.609006009243 | etot = -17.1596579091213 +172000 ekin = 2.2740316291813 | erot = 3.03566839385151 | epot = -22.5926818968567 | etot = -17.2829818738239 +173000 ekin = 2.2834164296893 | erot = 3.07205239473259 | epot = -22.5825638558613 | etot = -17.2270950314394 +174000 ekin = 2.32458116486063 | erot = 3.00979281518586 | epot = -22.5948442115049 | etot = -17.2604702314584 +175000 ekin = 2.28314539624411 | erot = 2.68632336807997 | epot = -22.6176552757194 | etot = -17.6481865113953 +176000 ekin = 2.39450710620737 | erot = 2.64107287395728 | epot = -22.6667041549035 | etot = -17.6311241747389 +177000 ekin = 2.34061737024895 | erot = 2.84587683178913 | epot = -22.7367147797011 | etot = -17.550220577663 +178000 ekin = 2.37612348031839 | erot = 3.01155432501149 | epot = -22.8363255725682 | etot = -17.4486477672383 +179000 ekin = 2.44543239233025 | erot = 2.86468226567423 | epot = -22.9489860454763 | etot = -17.6388713874718 +180000 ekin = 2.43660202081815 | erot = 2.76977637853855 | epot = -23.0553980647271 | etot = -17.8490196653704 +181000 ekin = 2.48112579799578 | erot = 2.62783914170244 | epot = -23.1486576952534 | etot = -18.0396927555552 +182000 ekin = 2.49495772650956 | erot = 2.4219283767703 | epot = -23.2214385077917 | etot = -18.3045524045118 +183000 ekin = 2.64232135835008 | erot = 2.16689603195343 | epot = -23.2638526717324 | etot = -18.4546352814289 +184000 ekin = 2.60197203740116 | erot = 2.23382360906437 | epot = -23.281896504963 | etot = -18.4461008584975 +185000 ekin = 2.57711189972515 | erot = 2.46016697006761 | epot = -23.3003293492567 | etot = -18.263050479464 +186000 ekin = 2.52186177988752 | erot = 2.57013836767114 | epot = -23.3067390551247 | etot = -18.2147389075661 +187000 ekin = 2.50245214010155 | erot = 2.79417927414254 | epot = -23.2961635629811 | etot = -17.999532148737 +188000 ekin = 2.46480838237763 | erot = 3.04604077517077 | epot = -23.2499789204155 | etot = -17.7391297628671 +189000 ekin = 2.30511335916345 | erot = 2.75740516208171 | epot = -23.1747970843814 | etot = -18.1122785631363 +190000 ekin = 2.21392698297057 | erot = 2.7195569697482 | epot = -23.0904117080343 | etot = -18.1569277553156 +191000 ekin = 2.16967810266233 | erot = 2.75919231540795 | epot = -23.0140192997739 | etot = -18.0851488817036 +192000 ekin = 1.98382084286023 | erot = 3.0342957441601 | epot = -22.932931475377 | etot = -17.9148148883567 +193000 ekin = 1.85970667375602 | erot = 2.92182615510918 | epot = -22.8656246963102 | etot = -18.0840918674449 +194000 ekin = 1.79296966804507 | erot = 2.88349607002158 | epot = -22.8222401649262 | etot = -18.1457744268595 +195000 ekin = 1.64582813172123 | erot = 2.50667314432805 | epot = -22.7522033865825 | etot = -18.5997021105332 +196000 ekin = 1.60167277963834 | erot = 2.389891779398 | epot = -22.6637097277972 | etot = -18.6721451687609 +197000 ekin = 1.71167813407953 | erot = 2.0958900785364 | epot = -22.5747312796683 | etot = -18.7671630670524 +198000 ekin = 1.6477625476503 | erot = 1.92608890072771 | epot = -22.4842649258581 | etot = -18.9104134774801 +199000 ekin = 1.65621021226667 | erot = 2.21876596478764 | epot = -22.4280470542138 | etot = -18.5530708771595 +200000 ekin = 1.68396557470043 | erot = 2.18851360029551 | epot = -22.3792802940388 | etot = -18.5068011190429 +201000 ekin = 1.58452256050707 | erot = 2.76907779285225 | epot = -22.3014443905322 | etot = -17.9478440371729 +202000 ekin = 1.54321939213116 | erot = 2.44655962102416 | epot = -22.2136540120257 | etot = -18.2238749988704 +203000 ekin = 1.49527423056762 | erot = 2.44440846517485 | epot = -22.1231335789825 | etot = -18.18345088324 +204000 ekin = 1.42525079936429 | erot = 2.83745592867434 | epot = -22.0409614513841 | etot = -17.7782547233455 +205000 ekin = 1.42978422295413 | erot = 2.95341773064209 | epot = -21.9571851603537 | etot = -17.5739832067575 +206000 ekin = 1.36049778309753 | erot = 2.83549996707315 | epot = -21.8974335725847 | etot = -17.701435822414 +207000 ekin = 1.29887157812385 | erot = 3.03783363013874 | epot = -21.8430515160585 | etot = -17.5063463077959 +208000 ekin = 1.34341544648367 | erot = 3.11373358018432 | epot = -21.7856032354132 | etot = -17.3284542087452 +209000 ekin = 1.37014771279221 | erot = 2.91335961336079 | epot = -21.7135808557961 | etot = -17.4300735296431 +210000 ekin = 1.42476756889871 | erot = 2.89331189478055 | epot = -21.5850142544314 | etot = -17.2669347907521 +211000 ekin = 1.34927361868025 | erot = 2.68288143618388 | epot = -21.4400426672502 | etot = -17.407887612386 +212000 ekin = 1.49128069580886 | erot = 2.70604382180414 | epot = -21.2914762616266 | etot = -17.0941517440136 +213000 ekin = 1.59986466327348 | erot = 2.65822930237663 | epot = -21.1410448576728 | etot = -16.8829508920227 +214000 ekin = 1.5757095331727 | erot = 2.79629927670816 | epot = -20.9904223688208 | etot = -16.6184135589399 +215000 ekin = 1.63256105235984 | erot = 2.69597024855507 | epot = -20.8601256454149 | etot = -16.5315943445 +216000 ekin = 1.6706438526472 | erot = 2.44739930798256 | epot = -20.7555716480128 | etot = -16.637528487383 +217000 ekin = 1.62188800637991 | erot = 2.43305557283328 | epot = -20.7224133282123 | etot = -16.6674697489991 +218000 ekin = 1.64606636901754 | erot = 2.64869814661889 | epot = -20.7502510322015 | etot = -16.4554865165651 +219000 ekin = 1.70353414409861 | erot = 2.79972211302508 | epot = -20.7845992910569 | etot = -16.2813430339333 +220000 ekin = 1.74880022179267 | erot = 2.64905074347642 | epot = -20.8396457684434 | etot = -16.4417948031743 +221000 ekin = 1.81236487768055 | erot = 2.93669133915729 | epot = -20.9499015869697 | etot = -16.2008453701318 +222000 ekin = 1.8464916185936 | erot = 2.8528717577386 | epot = -21.0927343336171 | etot = -16.3933709572849 +223000 ekin = 1.87441660338496 | erot = 2.96311764811079 | epot = -21.256488559318 | etot = -16.4189543078222 +224000 ekin = 2.099077858395 | erot = 2.75433402152822 | epot = -21.4248183617082 | etot = -16.5714064817849 +225000 ekin = 2.30010533938633 | erot = 2.67454361218696 | epot = -21.6008171170613 | etot = -16.626168165488 +226000 ekin = 2.42689725101247 | erot = 2.70736025408605 | epot = -21.7515066872426 | etot = -16.6172491821441 +227000 ekin = 2.5489592916598 | erot = 2.79460739709124 | epot = -21.8741313055211 | etot = -16.5305646167701 +228000 ekin = 2.61677978890101 | erot = 2.79388359916089 | epot = -21.973054308316 | etot = -16.5623909202541 +229000 ekin = 2.63216772040858 | erot = 2.92346177925241 | epot = -22.0307357525402 | etot = -16.4751062528792 +230000 ekin = 2.58390489345892 | erot = 2.87686964533661 | epot = -22.0461245567339 | etot = -16.5853500179384 +231000 ekin = 2.66188078761021 | erot = 2.60162661808981 | epot = -22.0186848953781 | etot = -16.7551774896781 +232000 ekin = 2.65841421937251 | erot = 2.5895008496799 | epot = -21.952644801982 | etot = -16.7047297329296 +233000 ekin = 2.67013502535664 | erot = 2.39334157986007 | epot = -21.8593772977148 | etot = -16.7959006924981 +234000 ekin = 2.55687226826843 | erot = 2.28743657262095 | epot = -21.7196048549654 | etot = -16.875296014076 +235000 ekin = 2.40908240211938 | erot = 2.18856718834614 | epot = -21.5568246763417 | etot = -16.9591750858761 +236000 ekin = 2.45296495728498 | erot = 1.73228998399408 | epot = -21.3990016680233 | etot = -17.2137467267443 +237000 ekin = 2.45647675573909 | erot = 1.55838299475453 | epot = -21.2711453873863 | etot = -17.2562856368927 +238000 ekin = 2.45085948587478 | erot = 1.73357194764442 | epot = -21.1889221126868 | etot = -17.0044906791676 +239000 ekin = 2.46602609451874 | erot = 1.90065188676605 | epot = -21.166756319606 | etot = -16.8000783383212 +240000 ekin = 2.33796945986692 | erot = 2.10011736609387 | epot = -21.1933792884251 | etot = -16.7552924624643 +241000 ekin = 2.44155086640189 | erot = 2.52942218937962 | epot = -21.2654521458313 | etot = -16.2944790900498 +242000 ekin = 2.43726026146497 | erot = 2.56189785799929 | epot = -21.3596468217689 | etot = -16.3604887023046 +243000 ekin = 2.38527720170892 | erot = 2.92483517968791 | epot = -21.4476955876489 | etot = -16.1375832062521 +244000 ekin = 2.43305152135009 | erot = 3.13030199682032 | epot = -21.5253542662414 | etot = -15.962000748071 +245000 ekin = 2.34248058405637 | erot = 3.39654754017984 | epot = -21.5746719384287 | etot = -15.8356438141925 +246000 ekin = 2.22203010314013 | erot = 3.24539512103687 | epot = -21.6102612139387 | etot = -16.1428359897617 +247000 ekin = 2.18161414825927 | erot = 3.17708625003423 | epot = -21.6121017617733 | etot = -16.2534013634798 +248000 ekin = 2.1478602785734 | erot = 2.93493583442515 | epot = -21.5821175301772 | etot = -16.4993214171787 +249000 ekin = 2.1154622560352 | erot = 2.65676577989598 | epot = -21.5328260462557 | etot = -16.7605980103245 +250000 ekin = 2.08258254452512 | erot = 2.5127810917753 | epot = -21.4612192152784 | etot = -16.865855578978 +251000 ekin = 1.97424894878218 | erot = 2.34806738759122 | epot = -21.3923428532782 | etot = -17.0700265169048 +252000 ekin = 1.97048808369658 | erot = 1.99115759882258 | epot = -21.3271316585962 | etot = -17.365485976077 +253000 ekin = 2.01408243379406 | erot = 2.32755027924602 | epot = -21.2782132891153 | etot = -16.9365805760753 +254000 ekin = 2.08055003788165 | erot = 1.89671800228131 | epot = -21.2526263857111 | etot = -17.2753583455481 +255000 ekin = 2.03693196256137 | erot = 2.07777286412269 | epot = -21.2590218685806 | etot = -17.1443170418966 +256000 ekin = 2.09443852502215 | erot = 1.9307299733728 | epot = -21.2924018193622 | etot = -17.2672333209673 +257000 ekin = 2.15892268396653 | erot = 1.80542946186151 | epot = -21.3549991612156 | etot = -17.3906470153876 +258000 ekin = 2.17985531861447 | erot = 1.78899461221364 | epot = -21.4290810676496 | etot = -17.4602311368214 +259000 ekin = 2.21879481100378 | erot = 2.00042152481937 | epot = -21.5156859416453 | etot = -17.2964696058222 +260000 ekin = 2.23230781087038 | erot = 1.9246911998121 | epot = -21.5739218213468 | etot = -17.4169228106643 +261000 ekin = 2.20725422443409 | erot = 1.9506311297175 | epot = -21.6226626065191 | etot = -17.4647772523675 +262000 ekin = 2.25364220587787 | erot = 1.86806956106366 | epot = -21.6606203978344 | etot = -17.5389086308929 +263000 ekin = 2.27451911244103 | erot = 1.88576182425905 | epot = -21.6707355563002 | etot = -17.5104546196001 +264000 ekin = 2.31743274100668 | erot = 1.89043794607685 | epot = -21.665836761993 | etot = -17.4579660749095 +265000 ekin = 2.34289229985172 | erot = 2.08595197099478 | epot = -21.6767978216755 | etot = -17.247953550829 +266000 ekin = 2.38993006534833 | erot = 2.06541078395749 | epot = -21.7067349963998 | etot = -17.251394147094 +267000 ekin = 2.42913514053654 | erot = 1.90515845127836 | epot = -21.7537718671937 | etot = -17.4194782753788 +268000 ekin = 2.56337406000808 | erot = 1.9262375618368 | epot = -21.8331768183359 | etot = -17.3435651964911 +269000 ekin = 2.61168966394751 | erot = 1.99189529087476 | epot = -21.8974804447419 | etot = -17.2938954899196 +270000 ekin = 2.53639435963124 | erot = 2.18070434963338 | epot = -21.9584187694415 | etot = -17.2413200601769 +271000 ekin = 2.47304999487576 | erot = 2.35836713203746 | epot = -21.9991923760467 | etot = -17.1677752491335 +272000 ekin = 2.47073160362057 | erot = 2.18239415020593 | epot = -22.0193810519898 | etot = -17.3662552981633 +273000 ekin = 2.41611288682344 | erot = 2.11264062363068 | epot = -22.0447361710735 | etot = -17.5159826606194 +274000 ekin = 2.33309205622051 | erot = 2.12677358473254 | epot = -22.0456863660977 | etot = -17.5858207251447 +275000 ekin = 2.2532514977808 | erot = 2.1934534644948 | epot = -21.9873759762877 | etot = -17.5406710140121 +276000 ekin = 2.11579900114231 | erot = 2.01180248953941 | epot = -21.898147992951 | etot = -17.7705465022692 +277000 ekin = 2.01204365223002 | erot = 1.98722100035171 | epot = -21.7960888645597 | etot = -17.796824211978 +278000 ekin = 1.94141858256043 | erot = 2.28521819509407 | epot = -21.7113859217471 | etot = -17.4847491440926 +279000 ekin = 1.83792081872233 | erot = 2.29363129336715 | epot = -21.6511613802401 | etot = -17.5196092681506 +280000 ekin = 1.73807918416884 | erot = 2.50531944195158 | epot = -21.6488609007439 | etot = -17.4054622746235 +281000 ekin = 1.7343274310991 | erot = 2.68378820070505 | epot = -21.6510875258492 | etot = -17.232971894045 +282000 ekin = 1.70745435944703 | erot = 2.46311716439966 | epot = -21.7026331884707 | etot = -17.5320616646241 +283000 ekin = 1.60185741540728 | erot = 2.73972949535769 | epot = -21.7889693093868 | etot = -17.4473823986219 +284000 ekin = 1.45656966763946 | erot = 3.08718988751354 | epot = -21.9109766986026 | etot = -17.3672171434496 +285000 ekin = 1.52336397324813 | erot = 3.23489044535602 | epot = -22.077134823922 | etot = -17.3188804053178 +286000 ekin = 1.52886747117861 | erot = 3.26500488671044 | epot = -22.2419806366666 | etot = -17.4481082787776 +287000 ekin = 1.55827258137914 | erot = 3.21853982890253 | epot = -22.3745806229378 | etot = -17.5977682126562 +288000 ekin = 1.62221220393012 | erot = 3.11944065317533 | epot = -22.4753647550738 | etot = -17.7337118979683 +289000 ekin = 1.6725177195504 | erot = 2.53263586427476 | epot = -22.5286401037665 | etot = -18.3234865199413 +290000 ekin = 1.79922183320684 | erot = 2.60060797838042 | epot = -22.5663935494001 | etot = -18.1665637378129 +291000 ekin = 1.83910683599852 | erot = 2.21931974991997 | epot = -22.5984502564983 | etot = -18.5400236705798 +292000 ekin = 1.94895219983996 | erot = 2.13471584079374 | epot = -22.6223121384565 | etot = -18.5386440978228 +293000 ekin = 2.00848212838236 | erot = 2.19116654326696 | epot = -22.6334508938888 | etot = -18.4338022222395 +294000 ekin = 2.10559198417455 | erot = 1.93202707864317 | epot = -22.6586912703105 | etot = -18.6210722074928 +295000 ekin = 2.21769154753227 | erot = 1.88155097269466 | epot = -22.7095788430015 | etot = -18.6103363227746 +296000 ekin = 2.33458415024599 | erot = 2.23498610265743 | epot = -22.7640278342613 | etot = -18.1944575813579 +297000 ekin = 2.4288563229209 | erot = 1.96776290060617 | epot = -22.8238447137231 | etot = -18.427225490196 +298000 ekin = 2.55470243764216 | erot = 2.23334330823271 | epot = -22.9186285858851 | etot = -18.1305828400102 +299000 ekin = 2.66453185837124 | erot = 2.34987058034016 | epot = -23.0168248151097 | etot = -18.0024223763983 +300000 ekin = 2.72119699302716 | erot = 2.29170874462643 | epot = -23.0901056634067 | etot = -18.0771999257531 +301000 ekin = 2.81586193114724 | erot = 2.13213339022168 | epot = -23.1495883754428 | etot = -18.2015930540739 +302000 ekin = 2.91520994762744 | erot = 1.8827605169696 | epot = -23.1915517299786 | etot = -18.3935812653816 +303000 ekin = 3.00910392441906 | erot = 1.95969044044566 | epot = -23.2200453504933 | etot = -18.2512509856286 +304000 ekin = 3.09252107593619 | erot = 1.6252402693675 | epot = -23.236224750659 | etot = -18.5184634053553 +305000 ekin = 3.18333327783383 | erot = 1.6471076729939 | epot = -23.2396880778629 | etot = -18.4092471270352 +306000 ekin = 3.23038524508787 | erot = 1.86572791579384 | epot = -23.222672281532 | etot = -18.1265591206503 +307000 ekin = 3.17553918919369 | erot = 2.33048974790651 | epot = -23.1930577755999 | etot = -17.6870288384997 +308000 ekin = 3.05565196722459 | erot = 2.12851261980203 | epot = -23.1373688624437 | etot = -17.9532042754171 +309000 ekin = 3.06886265684608 | erot = 2.25716457141466 | epot = -23.0626811521325 | etot = -17.7366539238718 +310000 ekin = 2.91034787850185 | erot = 2.45832048654338 | epot = -23.0039736316975 | etot = -17.6353052666522 +311000 ekin = 2.80209798482135 | erot = 2.69963602433984 | epot = -22.9644587572485 | etot = -17.4627247480873 +312000 ekin = 2.89133577486423 | erot = 2.91057311416264 | epot = -22.9280382115918 | etot = -17.126129322565 +313000 ekin = 2.85188593774405 | erot = 2.647560991136 | epot = -22.9072517674231 | etot = -17.407804838543 +314000 ekin = 2.78595369543581 | erot = 2.70015943474036 | epot = -22.9231273154876 | etot = -17.4370141853114 +315000 ekin = 2.80274029888255 | erot = 2.58977766570975 | epot = -22.9544686180926 | etot = -17.5619506535003 +316000 ekin = 2.8131693061063 | erot = 2.69098007120303 | epot = -22.9778084391865 | etot = -17.4736590618771 +317000 ekin = 2.92747042873615 | erot = 2.60588706069167 | epot = -22.9662401312093 | etot = -17.4328826417815 +318000 ekin = 2.92235999955187 | erot = 2.47590791759846 | epot = -22.9395079234947 | etot = -17.5412400063443 +319000 ekin = 2.95294558428569 | erot = 2.32846959673444 | epot = -22.8862142058978 | etot = -17.6047990248777 +320000 ekin = 2.96034320261015 | erot = 1.9613246232207 | epot = -22.8325608441838 | etot = -17.9108930183529 +321000 ekin = 3.0506123149287 | erot = 1.60256900115909 | epot = -22.7729675622172 | etot = -18.1197862461294 +322000 ekin = 3.06917008169242 | erot = 1.78242384845945 | epot = -22.7183310735855 | etot = -17.8667371434336 +323000 ekin = 3.01773744699225 | erot = 1.54792296048668 | epot = -22.6793347879491 | etot = -18.1136743804702 +324000 ekin = 3.00480822228207 | erot = 1.41906862436121 | epot = -22.6494390826943 | etot = -18.225562236051 +325000 ekin = 2.89783034430756 | erot = 1.53330273244729 | epot = -22.6175860707658 | etot = -18.186452994011 +326000 ekin = 2.86411015648586 | erot = 1.46437933803477 | epot = -22.5787186521105 | etot = -18.2502291575899 +327000 ekin = 2.85311531697703 | erot = 1.586968215819 | epot = -22.5591982819074 | etot = -18.1191147491114 +328000 ekin = 2.86747144026844 | erot = 1.74413948970451 | epot = -22.5408974569851 | etot = -17.9292865270122 +329000 ekin = 2.78611224528683 | erot = 1.59178805962532 | epot = -22.4940152398142 | etot = -18.116114934902 +330000 ekin = 2.69317692812664 | erot = 1.77728472427353 | epot = -22.4199575472594 | etot = -17.9494958948593 +331000 ekin = 2.66550770553886 | erot = 1.86897796248962 | epot = -22.3262951615913 | etot = -17.7918094935628 +332000 ekin = 2.46548011243449 | erot = 1.7863999774723 | epot = -22.2432651292251 | etot = -17.9913850393183 +333000 ekin = 2.38707429510581 | erot = 1.88540525492867 | epot = -22.1912828165259 | etot = -17.9188032664914 +334000 ekin = 2.2984232336711 | erot = 1.9156954724491 | epot = -22.1605657807781 | etot = -17.9464470746579 +335000 ekin = 2.14328705611348 | erot = 1.93351743363523 | epot = -22.1267428568707 | etot = -18.049938367122 +336000 ekin = 2.17230386456888 | erot = 1.84213347788919 | epot = -22.0906093676854 | etot = -18.0761720252273 +337000 ekin = 2.12998408141735 | erot = 1.61504892612894 | epot = -22.0362365245475 | etot = -18.2912035170012 +338000 ekin = 2.2234410055195 | erot = 1.68131888644295 | epot = -21.9914967299634 | etot = -18.0867368380009 +339000 ekin = 2.17397763598084 | erot = 2.04937445475351 | epot = -21.9399664944352 | etot = -17.7166144037009 +340000 ekin = 2.20074652018769 | erot = 2.20161688813931 | epot = -21.9270463566988 | etot = -17.5246829483718 +341000 ekin = 2.27511078184168 | erot = 2.29314361762742 | epot = -21.9408735448824 | etot = -17.3726191454132 +342000 ekin = 2.23496832750102 | erot = 2.56505101253473 | epot = -21.9730675845141 | etot = -17.1730482444784 +343000 ekin = 2.1418080972412 | erot = 2.97675645193228 | epot = -21.9956779914414 | etot = -16.8771134422679 +344000 ekin = 2.21267070166951 | erot = 2.2214319223185 | epot = -22.0021896006044 | etot = -17.5680869766164 +345000 ekin = 2.33078283444885 | erot = 2.24242604297002 | epot = -22.0150204126161 | etot = -17.4418115351972 +346000 ekin = 2.34407159811772 | erot = 1.99201495775964 | epot = -22.0385016930848 | etot = -17.7024151372074 +347000 ekin = 2.44088137371629 | erot = 2.12531879806791 | epot = -22.0618508546084 | etot = -17.4956506828242 +348000 ekin = 2.64914602526502 | erot = 2.46233252053005 | epot = -22.0937551106249 | etot = -16.9822765648298 +349000 ekin = 2.74052569579444 | erot = 2.48588913287134 | epot = -22.1113349203142 | etot = -16.8849200916484 +350000 ekin = 2.63009093889676 | erot = 2.96194682397746 | epot = -22.1188176550616 | etot = -16.5267798921874 +351000 ekin = 2.58934992266522 | erot = 2.8770434785033 | epot = -22.1025806281004 | etot = -16.6361872269319 +352000 ekin = 2.54228487046046 | erot = 2.63361513807466 | epot = -22.0652686765352 | etot = -16.8893686680001 +353000 ekin = 2.53249364323794 | erot = 2.47221948070279 | epot = -22.0318641173351 | etot = -17.0271509933944 +354000 ekin = 2.56206560145027 | erot = 2.34662515218716 | epot = -22.0126143901229 | etot = -17.1039236364855 +355000 ekin = 2.53151865051015 | erot = 2.4113052948177 | epot = -21.9989758809431 | etot = -17.0561519356152 +356000 ekin = 2.38856942051704 | erot = 2.45957154153151 | epot = -21.9929238390891 | etot = -17.1447828770405 +357000 ekin = 2.3850318504501 | erot = 2.38151023524606 | epot = -22.0040942348341 | etot = -17.2375521491379 +358000 ekin = 2.4475851295007 | erot = 2.71803579945329 | epot = -22.0072561961478 | etot = -16.8416352671938 +359000 ekin = 2.38516688439539 | erot = 2.57286490732318 | epot = -21.9670271651238 | etot = -17.0089953734052 +360000 ekin = 2.33663079544671 | erot = 2.56848564652214 | epot = -21.918164841109 | etot = -17.0130483991401 +361000 ekin = 2.42677922379501 | erot = 2.37500774993747 | epot = -21.8672713761358 | etot = -17.0654844024034 +362000 ekin = 2.4605364062408 | erot = 2.49590481611227 | epot = -21.7779995387161 | etot = -16.821558316363 +363000 ekin = 2.55310738370238 | erot = 2.17768318633134 | epot = -21.6776820779023 | etot = -16.9468915078686 +364000 ekin = 2.56780109725782 | erot = 2.16474191665872 | epot = -21.5533633280085 | etot = -16.820820314092 +365000 ekin = 2.59901975131891 | erot = 1.71409893021137 | epot = -21.4252112523553 | etot = -17.1120925708251 +366000 ekin = 2.80245009247375 | erot = 1.44048381506929 | epot = -21.3115965871059 | etot = -17.0686626795629 +367000 ekin = 2.85134090040929 | erot = 1.61253537083185 | epot = -21.2054965437889 | etot = -16.7416202725478 +368000 ekin = 3.00720175661763 | erot = 1.37649145802379 | epot = -21.1143147590192 | etot = -16.7306215443778 +369000 ekin = 3.02782850583648 | erot = 1.29964512201197 | epot = -21.0456750388441 | etot = -16.7182014109956 +370000 ekin = 2.96718136039117 | erot = 1.45830059090199 | epot = -20.9956751371928 | etot = -16.5701931858996 +371000 ekin = 2.97398053523901 | erot = 1.26453322843173 | epot = -20.9819115867117 | etot = -16.7433978230409 +372000 ekin = 2.93284410498009 | erot = 1.41224205422983 | epot = -20.990879656372 | etot = -16.6457934971621 +373000 ekin = 2.88790034010472 | erot = 1.42564554966123 | epot = -21.033892399397 | etot = -16.720346509631 +374000 ekin = 2.82344708085647 | erot = 1.62526123419929 | epot = -21.0946345683056 | etot = -16.6459262532498 +375000 ekin = 2.9048191689212 | erot = 1.74642067705861 | epot = -21.2008783966459 | etot = -16.5496385506661 +376000 ekin = 2.84134799892075 | erot = 1.8767542209254 | epot = -21.3649261105939 | etot = -16.6468238907477 +377000 ekin = 2.86364799078519 | erot = 1.9339338094908 | epot = -21.5406268140668 | etot = -16.7430450137908 +378000 ekin = 2.9048300489525 | erot = 2.17252781549638 | epot = -21.7155346442895 | etot = -16.6381767798406 +379000 ekin = 2.8865075586177 | erot = 1.96118442992092 | epot = -21.8538626049786 | etot = -17.00617061644 +380000 ekin = 2.88651329834493 | erot = 2.08410077478125 | epot = -21.9401095058158 | etot = -16.9694954326896 +381000 ekin = 2.84108364234509 | erot = 2.36602406894656 | epot = -21.9810439461896 | etot = -16.7739362348979 +382000 ekin = 2.65581712933844 | erot = 2.32549072457609 | epot = -21.9604472596471 | etot = -16.9791394057325 +383000 ekin = 2.66697103963134 | erot = 2.19715446258975 | epot = -21.8997743494524 | etot = -17.0356488472313 +384000 ekin = 2.71347175798932 | erot = 2.08604535797532 | epot = -21.8256490214724 | etot = -17.0261319055078 +385000 ekin = 2.5886627289133 | erot = 2.07169637253237 | epot = -21.7588277650259 | etot = -17.0984686635803 +386000 ekin = 2.61416908347419 | erot = 2.12402378221524 | epot = -21.7275890588648 | etot = -16.9893961931754 +387000 ekin = 2.70373372534934 | erot = 2.21149248908639 | epot = -21.7114203261747 | etot = -16.7961941117389 +388000 ekin = 2.74978383236821 | erot = 2.03622128721583 | epot = -21.7171286702607 | etot = -16.9311235506767 +389000 ekin = 2.7587615131327 | erot = 2.35914494269191 | epot = -21.7195350651328 | etot = -16.6016286093082 +390000 ekin = 2.87281151326102 | erot = 2.14919283772492 | epot = -21.7092098874033 | etot = -16.6872055364173 +391000 ekin = 2.88070946214061 | erot = 2.15553640701991 | epot = -21.7308938242004 | etot = -16.6946479550399 +392000 ekin = 2.85350413424044 | erot = 1.95551148082617 | epot = -21.7800211133376 | etot = -16.9710054982709 +393000 ekin = 2.90295298668572 | erot = 2.00031478831759 | epot = -21.8483879920449 | etot = -16.9451202170416 +394000 ekin = 2.87980364418051 | erot = 2.13854428764095 | epot = -21.927891035529 | etot = -16.9095431037075 +395000 ekin = 2.89980834808654 | erot = 2.27975081097515 | epot = -22.0016489908303 | etot = -16.8220898317686 +396000 ekin = 2.93605574834046 | erot = 2.28756221501388 | epot = -22.083719356273 | etot = -16.8601013929187 +397000 ekin = 2.80779171295695 | erot = 2.19257867663266 | epot = -22.1878285992743 | etot = -17.1874582096847 +398000 ekin = 2.65560496560027 | erot = 2.63286768292204 | epot = -22.2927014267366 | etot = -17.0042287782143 +399000 ekin = 2.70831299977891 | erot = 2.28957359120763 | epot = -22.4133968187074 | etot = -17.4155102277209 +400000 ekin = 2.62631472682176 | erot = 2.32258453004918 | epot = -22.5144474162178 | etot = -17.5655481593469 +401000 ekin = 2.61084599477578 | erot = 2.5915842232175 | epot = -22.6219132294945 | etot = -17.4194830115012 +402000 ekin = 2.635885903201 | erot = 2.77714471535857 | epot = -22.7264979351378 | etot = -17.3134673165782 +403000 ekin = 2.57124299169003 | erot = 2.91857224360661 | epot = -22.7998184812975 | etot = -17.3100032460009 +404000 ekin = 2.64669440558066 | erot = 2.93356467106672 | epot = -22.8394282855353 | etot = -17.2591692088879 +405000 ekin = 2.6313696260396 | erot = 3.04830494377478 | epot = -22.8811547071105 | etot = -17.2014801372961 +406000 ekin = 2.57687330940512 | erot = 2.89269043406033 | epot = -22.8904487120533 | etot = -17.4208849685879 +407000 ekin = 2.5618448960505 | erot = 3.08692656736122 | epot = -22.8853592595439 | etot = -17.2365877961322 +408000 ekin = 2.54127249851751 | erot = 3.17601770471241 | epot = -22.9006717760476 | etot = -17.1833815728177 +409000 ekin = 2.53459046783758 | erot = 3.13623300199209 | epot = -22.8968640693003 | etot = -17.2260405994706 +410000 ekin = 2.51587421571662 | erot = 3.14201699757377 | epot = -22.9150990085741 | etot = -17.2572077952837 +411000 ekin = 2.42964978573951 | erot = 3.32305144355791 | epot = -22.9501641087081 | etot = -17.1974628794107 +412000 ekin = 2.36687843567498 | erot = 3.3285504429599 | epot = -22.99567867119 | etot = -17.3002497925551 +413000 ekin = 2.32867643693125 | erot = 3.02147909460678 | epot = -23.0359443059234 | etot = -17.6857887743854 +414000 ekin = 2.2515260449447 | erot = 3.14866247342422 | epot = -23.0379850078343 | etot = -17.6377964894654 +415000 ekin = 2.14860234477144 | erot = 3.14281806599356 | epot = -23.016809711244 | etot = -17.725389300479 +416000 ekin = 2.1332775392394 | erot = 2.78190144921895 | epot = -22.9549412646377 | etot = -18.0397622761793 +417000 ekin = 2.07867029653693 | erot = 2.63891364632679 | epot = -22.8771697337526 | etot = -18.1595857908888 +418000 ekin = 2.01503497087452 | erot = 2.48786384280135 | epot = -22.7881812529124 | etot = -18.2852824392365 +419000 ekin = 1.93436445840309 | erot = 2.56473142390299 | epot = -22.7122209786171 | etot = -18.213125096311 +420000 ekin = 1.86691051962999 | erot = 2.37316247804238 | epot = -22.663644104836 | etot = -18.4235711071637 +421000 ekin = 1.86677256248723 | erot = 2.32313827929405 | epot = -22.6187875829574 | etot = -18.4288767411761 +422000 ekin = 1.82005824158071 | erot = 2.55465763559267 | epot = -22.5903542114936 | etot = -18.2156383343202 +423000 ekin = 1.85196925130395 | erot = 2.5974598823431 | epot = -22.5868190893394 | etot = -18.1373899556924 +424000 ekin = 1.87511106269006 | erot = 2.36649086179881 | epot = -22.5883508404772 | etot = -18.3467489159883 +425000 ekin = 1.85448962199763 | erot = 2.35912334554435 | epot = -22.5825697876888 | etot = -18.3689568201468 +426000 ekin = 1.93877126287049 | erot = 2.34047239554928 | epot = -22.5855644966028 | etot = -18.306320838183 +427000 ekin = 1.98667133586972 | erot = 2.21434059237477 | epot = -22.6165038624105 | etot = -18.415491934166 +428000 ekin = 2.06633462219149 | erot = 2.46308595042594 | epot = -22.6536305130782 | etot = -18.1242099404608 +429000 ekin = 2.06647569478185 | erot = 2.85029146170717 | epot = -22.6734202786045 | etot = -17.7566531221155 +430000 ekin = 2.02119030876775 | erot = 3.03581181604001 | epot = -22.659282107403 | etot = -17.6022799825952 +431000 ekin = 1.92940982496903 | erot = 3.12567479604236 | epot = -22.6051004098157 | etot = -17.5500157888043 +432000 ekin = 1.98926835887559 | erot = 2.96897634192419 | epot = -22.5090519549378 | etot = -17.550807254138 +433000 ekin = 2.041430732461 | erot = 2.85215225860737 | epot = -22.3406443583778 | etot = -17.4470613673094 +434000 ekin = 2.05565692829895 | erot = 2.95627927317659 | epot = -22.1000056035571 | etot = -17.0880694020816 +435000 ekin = 2.08432405496717 | erot = 2.68419048003212 | epot = -21.8308353279851 | etot = -17.0623207929858 +436000 ekin = 2.12772749840159 | erot = 2.84173548840799 | epot = -21.5604223141966 | etot = -16.590959327387 +437000 ekin = 2.04468233985782 | erot = 2.5189263616935 | epot = -21.3171953647823 | etot = -16.753586663231 +438000 ekin = 2.04330796733031 | erot = 2.25039837644757 | epot = -21.1104661155377 | etot = -16.8167597717598 +439000 ekin = 2.1303450962368 | erot = 2.34282002521748 | epot = -20.9455910272725 | etot = -16.4724259058182 +440000 ekin = 2.19070367254229 | erot = 2.15029144838879 | epot = -20.8316849257309 | etot = -16.4906898047998 +441000 ekin = 2.18523324344595 | erot = 2.14329639955517 | epot = -20.7742603417165 | etot = -16.4457306987154 +442000 ekin = 2.35525341099326 | erot = 2.33073585925591 | epot = -20.7921078012968 | etot = -16.1061185310476 +443000 ekin = 2.42381848947146 | erot = 2.29410897800866 | epot = -20.8510039080526 | etot = -16.1330764405725 +444000 ekin = 2.58327001521814 | erot = 2.25550403938057 | epot = -20.9496740359507 | etot = -16.110899981352 +445000 ekin = 2.74914318766584 | erot = 2.36474125562144 | epot = -21.0902773104286 | etot = -15.9763928671413 +446000 ekin = 2.75866465553884 | erot = 2.51903536478378 | epot = -21.2771375903937 | etot = -15.9994375700711 +447000 ekin = 2.81341929589966 | erot = 2.61543912233442 | epot = -21.4943223583146 | etot = -16.0654639400805 +448000 ekin = 2.98791449212417 | erot = 2.686015721345 | epot = -21.6882416455896 | etot = -16.0143114321204 +449000 ekin = 3.02989562281093 | erot = 2.59921391657433 | epot = -21.8625805167009 | etot = -16.2334709773157 +450000 ekin = 3.07584193389835 | erot = 2.74644112742619 | epot = -21.9977284145171 | etot = -16.1754453531925 +451000 ekin = 3.17325103223139 | erot = 2.71318685835069 | epot = -22.0826869675361 | etot = -16.196249076954 +452000 ekin = 3.26804429580737 | erot = 2.87778182303291 | epot = -22.0906838053162 | etot = -15.9448576864759 +453000 ekin = 3.27357354113497 | erot = 2.70771602218269 | epot = -22.0093450685523 | etot = -16.0280555052346 +454000 ekin = 3.19461395199204 | erot = 2.6448969266277 | epot = -21.8896212815607 | etot = -16.050110402941 +455000 ekin = 3.06934448991765 | erot = 2.52112023723169 | epot = -21.7581228733759 | etot = -16.1676581462266 +456000 ekin = 3.00870709873353 | erot = 2.69030125753182 | epot = -21.6192081822491 | etot = -15.9201998259837 +457000 ekin = 2.777216489817 | erot = 2.81809494379019 | epot = -21.5044838205097 | etot = -15.9091723869025 +458000 ekin = 2.72192779143847 | erot = 2.81327589913026 | epot = -21.3991411950549 | etot = -15.8639375044862 +459000 ekin = 2.66716160346718 | erot = 2.91218722489662 | epot = -21.3056824262501 | etot = -15.7263335978863 +460000 ekin = 2.61631308900554 | erot = 2.72088150404113 | epot = -21.2125642789399 | etot = -15.8753696858932 +461000 ekin = 2.52111486337713 | erot = 2.61083643510212 | epot = -21.1320849455669 | etot = -16.0001336470876 +462000 ekin = 2.35496729961921 | erot = 2.5358561099819 | epot = -21.0535223021746 | etot = -16.1626988925735 +463000 ekin = 2.24393433183191 | erot = 2.51761943073286 | epot = -21.0230425923878 | etot = -16.261488829823 +464000 ekin = 2.16264575625711 | erot = 2.67496242735613 | epot = -21.0323536551487 | etot = -16.1947454715355 +465000 ekin = 2.12337820037338 | erot = 2.82456556368798 | epot = -21.0880254572831 | etot = -16.1400816932217 +466000 ekin = 2.04496236125011 | erot = 2.74204868129277 | epot = -21.1490905898122 | etot = -16.3620795472694 +467000 ekin = 2.07076206458635 | erot = 2.74539024720616 | epot = -21.215024164528 | etot = -16.3988718527355 +468000 ekin = 2.08250457485183 | erot = 2.49401005885409 | epot = -21.2895135595468 | etot = -16.7129989258408 +469000 ekin = 2.11940107816922 | erot = 2.73165603901944 | epot = -21.3555553713497 | etot = -16.5044982541611 +470000 ekin = 2.2755450093077 | erot = 2.57556168280448 | epot = -21.4121284090538 | etot = -16.5610217169417 +471000 ekin = 2.2114984621346 | erot = 2.49207243095057 | epot = -21.435732052025 | etot = -16.7321611589398 +472000 ekin = 2.13757463851204 | erot = 2.31011730813802 | epot = -21.4380116997291 | etot = -16.9903197530791 +473000 ekin = 2.06821493877643 | erot = 2.2685003928258 | epot = -21.4114781960858 | etot = -17.0747628644836 +474000 ekin = 1.96490547218431 | erot = 2.35563819582065 | epot = -21.3522336688375 | etot = -17.0316900008326 +475000 ekin = 1.94558586419936 | erot = 2.10680745423891 | epot = -21.2548130597369 | etot = -17.2024197412986 +476000 ekin = 1.94190624501534 | erot = 2.16513825042928 | epot = -21.1595544689155 | etot = -17.0525099734709 +477000 ekin = 1.99924367094436 | erot = 1.80803378013926 | epot = -21.0628461625393 | etot = -17.2555687114557 +478000 ekin = 1.89989927585492 | erot = 1.77183940189901 | epot = -20.9920693922247 | etot = -17.3203307144707 +479000 ekin = 1.84520242098793 | erot = 1.66369715226462 | epot = -20.943197661135 | etot = -17.4342980878825 +480000 ekin = 1.78395227007313 | erot = 1.62380842244011 | epot = -20.9116440658478 | etot = -17.5038833733346 +481000 ekin = 1.80711393748116 | erot = 1.45108120724299 | epot = -20.899809195654 | etot = -17.6416140509299 +482000 ekin = 1.83485472728834 | erot = 1.5899131561371 | epot = -20.9502956349549 | etot = -17.5255277515294 +483000 ekin = 1.74714650944547 | erot = 2.06533056940213 | epot = -21.05982640294 | etot = -17.2473493240924 +484000 ekin = 1.80571868875142 | erot = 2.45785513658362 | epot = -21.2268132327391 | etot = -16.9632394074041 +485000 ekin = 1.97685842465677 | erot = 2.60360246547723 | epot = -21.4062901266649 | etot = -16.8258292365309 +486000 ekin = 2.06309847922673 | erot = 2.90380547812246 | epot = -21.5894655607388 | etot = -16.6225616033897 +487000 ekin = 2.19649216659984 | erot = 2.81883409927295 | epot = -21.7360008549514 | etot = -16.7206745890786 +488000 ekin = 2.27235435120755 | erot = 3.21078167833799 | epot = -21.8710028956708 | etot = -16.3878668661253 +489000 ekin = 2.36365916165255 | erot = 2.98148333833802 | epot = -21.9731809770869 | etot = -16.6280384770963 +490000 ekin = 2.46365572243186 | erot = 3.03413636977556 | epot = -22.0415730890945 | etot = -16.543780996887 +491000 ekin = 2.48043066028394 | erot = 2.95353817719133 | epot = -22.0882801530728 | etot = -16.6543113155975 +492000 ekin = 2.43187986853058 | erot = 2.81942197452495 | epot = -22.1316786946067 | etot = -16.8803768515512 +493000 ekin = 2.43297707751451 | erot = 3.13501618675347 | epot = -22.1516877815826 | etot = -16.5836945173146 +494000 ekin = 2.43547737006958 | erot = 3.22494383304223 | epot = -22.1277792873502 | etot = -16.4673580842384 +495000 ekin = 2.44131017621645 | erot = 3.14764944977832 | epot = -22.0798107226075 | etot = -16.4908510966128 +496000 ekin = 2.44929786442221 | erot = 3.00103698197415 | epot = -22.002928649246 | etot = -16.5525938028496 +497000 ekin = 2.42807342723594 | erot = 2.7881804132664 | epot = -21.8989958230253 | etot = -16.6827419825229 +498000 ekin = 2.43232675717284 | erot = 2.78563195522809 | epot = -21.7990677062023 | etot = -16.5811089938014 +499000 ekin = 2.39683774655034 | erot = 2.52204743265475 | epot = -21.6970829564491 | etot = -16.778197777244 +500000 ekin = 2.39561357168025 | erot = 2.04914490208484 | epot = -21.6057727183568 | etot = -17.1610142445917 +501000 ekin = 2.4901106222084 | erot = 2.09141321522318 | epot = -21.5560066661706 | etot = -16.974482828739 +502000 ekin = 2.50365744754327 | erot = 2.1042025483322 | epot = -21.5549657901232 | etot = -16.9471057942478 +503000 ekin = 2.50788240480081 | erot = 2.30709919674954 | epot = -21.6015443787755 | etot = -16.7865627772251 +504000 ekin = 2.42370070726384 | erot = 1.84999363757408 | epot = -21.6380109735021 | etot = -17.3643166286642 +505000 ekin = 2.3587483485555 | erot = 2.14636862503852 | epot = -21.6689774661088 | etot = -17.1638604925148 +506000 ekin = 2.26228062582653 | erot = 2.45377485636117 | epot = -21.7153954382909 | etot = -16.9993399561032 +507000 ekin = 2.1391923707717 | erot = 2.50319755000138 | epot = -21.7581761618772 | etot = -17.1157862411041 +508000 ekin = 2.1483137387407 | erot = 3.06092132482202 | epot = -21.7763037427611 | etot = -16.5670686791984 +509000 ekin = 2.05180259764866 | erot = 3.39029610338351 | epot = -21.776003585352 | etot = -16.3339048843198 +510000 ekin = 2.04381464635427 | erot = 3.61253858305487 | epot = -21.7386277737458 | etot = -16.0822745443367 +511000 ekin = 2.05816959569107 | erot = 3.10213651349288 | epot = -21.688362376805 | etot = -16.528056267621 +512000 ekin = 1.92422822548454 | erot = 2.79263854517701 | epot = -21.6550102347598 | etot = -16.9381434640982 +513000 ekin = 2.02050703596233 | erot = 2.71259548634818 | epot = -21.6549051178144 | etot = -16.9218025955039 +514000 ekin = 2.07581905977895 | erot = 2.32467594776646 | epot = -21.665556834217 | etot = -17.2650618266716 +515000 ekin = 2.08477825623465 | erot = 2.59404540183163 | epot = -21.7265307260922 | etot = -17.0477070680259 +516000 ekin = 2.15812359163707 | erot = 2.69267871008866 | epot = -21.8093937590764 | etot = -16.9585914573506 +517000 ekin = 2.13934962382492 | erot = 2.84365285719026 | epot = -21.9032983411399 | etot = -16.9202958601247 +518000 ekin = 2.20591925285861 | erot = 3.12936446615936 | epot = -22.0120787399678 | etot = -16.6767950209499 +519000 ekin = 2.26634159461382 | erot = 3.0946506489304 | epot = -22.1371864066205 | etot = -16.7761941630763 +520000 ekin = 2.33395232089105 | erot = 3.16707863806596 | epot = -22.2618368300492 | etot = -16.7608058710922 +521000 ekin = 2.37443913996477 | erot = 2.84321493552052 | epot = -22.3608681173461 | etot = -17.1432140418608 +522000 ekin = 2.38014534564467 | erot = 2.71344764130111 | epot = -22.4471285851319 | etot = -17.3535355981861 +523000 ekin = 2.43082426163835 | erot = 2.87118432179584 | epot = -22.5347499952681 | etot = -17.2327414118339 +524000 ekin = 2.56081842163126 | erot = 3.05550273097465 | epot = -22.6100687346061 | etot = -16.9937475820002 +525000 ekin = 2.55953271858514 | erot = 2.67513220891041 | epot = -22.6739874644368 | etot = -17.4393225369413 +526000 ekin = 2.59958209031031 | erot = 2.95738463024354 | epot = -22.7033728209711 | etot = -17.1464061004173 +527000 ekin = 2.52409384361615 | erot = 2.89851026515122 | epot = -22.7152196639491 | etot = -17.2926155551817 +528000 ekin = 2.57935349807703 | erot = 2.86931301300855 | epot = -22.7061100878871 | etot = -17.2574435768015 +529000 ekin = 2.5449913230182 | erot = 3.03033580941372 | epot = -22.6577883790845 | etot = -17.0824612466525 +530000 ekin = 2.37583920711566 | erot = 3.07767101681233 | epot = -22.5498147001086 | etot = -17.0963044761806 +531000 ekin = 2.28423424660452 | erot = 2.99538223189532 | epot = -22.4172244060317 | etot = -17.1376079275319 +532000 ekin = 2.11092802290005 | erot = 2.62650535715252 | epot = -22.2554156639849 | etot = -17.5179822839324 +533000 ekin = 2.07823067751695 | erot = 2.60462012944299 | epot = -22.0829115643991 | etot = -17.4000607574392 +534000 ekin = 2.08976309920292 | erot = 2.60045035336437 | epot = -21.9117889556573 | etot = -17.22157550309 +535000 ekin = 2.03320809614403 | erot = 2.53673993181143 | epot = -21.7263132935398 | etot = -17.1563652655844 +536000 ekin = 1.97106365765744 | erot = 2.35170112588154 | epot = -21.5718096441991 | etot = -17.2490448606601 +537000 ekin = 1.85757994043449 | erot = 2.1000939316012 | epot = -21.4673782965335 | etot = -17.5097044244978 +538000 ekin = 1.82596102898979 | erot = 2.13846192719758 | epot = -21.3983734318539 | etot = -17.4339504756666 +539000 ekin = 1.73881232516884 | erot = 2.4948493136433 | epot = -21.3425267679341 | etot = -17.1088651291219 +540000 ekin = 1.67447223010914 | erot = 2.77285924634614 | epot = -21.2716590544127 | etot = -16.8243275779574 +541000 ekin = 1.69990418580885 | erot = 2.88110182550538 | epot = -21.1962442587822 | etot = -16.6152382474679 +542000 ekin = 1.71113657497015 | erot = 2.75900359072979 | epot = -21.135597661667 | etot = -16.665457495967 +543000 ekin = 1.78866852977494 | erot = 2.71660471692161 | epot = -21.0866732693148 | etot = -16.5814000226182 +544000 ekin = 1.771817820198 | erot = 2.328771769428 | epot = -21.0413457588288 | etot = -16.9407561692028 +545000 ekin = 1.78667793391233 | erot = 2.11448637898458 | epot = -21.0004042884447 | etot = -17.0992399755478 +546000 ekin = 1.85376909065284 | erot = 1.89612518110719 | epot = -20.9731062289195 | etot = -17.2232119571595 +547000 ekin = 1.886076238392 | erot = 1.67123255058042 | epot = -20.9706093546508 | etot = -17.4133005656784 +548000 ekin = 1.90991638455373 | erot = 1.7881548999802 | epot = -20.9683934987346 | etot = -17.2703222142007 +549000 ekin = 1.93154736700912 | erot = 1.83109029837931 | epot = -20.9876899630373 | etot = -17.2250522976488 +550000 ekin = 1.99815580980597 | erot = 1.56054958425493 | epot = -21.036004232095 | etot = -17.4772988380341 +551000 ekin = 2.06223281194829 | erot = 1.82140531055443 | epot = -21.1099793159587 | etot = -17.226341193456 +552000 ekin = 2.19995559126056 | erot = 1.93328987912288 | epot = -21.1805106953385 | etot = -17.0472652249551 +553000 ekin = 2.16476612655581 | erot = 2.18848299832349 | epot = -21.2339007238634 | etot = -16.8806515989841 +554000 ekin = 2.1925339580923 | erot = 1.9926960214726 | epot = -21.3216202633258 | etot = -17.1363902837609 +555000 ekin = 2.30423346281122 | erot = 1.75126691279995 | epot = -21.4340368938537 | etot = -17.3785365182425 +556000 ekin = 2.4521267330114 | erot = 2.39109930640514 | epot = -21.572517213343 | etot = -16.7292911739264 +557000 ekin = 2.55511582943875 | erot = 2.60632466872853 | epot = -21.7241981903429 | etot = -16.5627576921756 +558000 ekin = 2.67318624692359 | erot = 2.43046608162001 | epot = -21.8811108747484 | etot = -16.7774585462048 +559000 ekin = 2.79102973560867 | erot = 2.67538733153578 | epot = -22.0378553874463 | etot = -16.5714383203018 +560000 ekin = 2.91837921581139 | erot = 2.68572428538372 | epot = -22.1492797858917 | etot = -16.5451762846966 +561000 ekin = 2.8169246804767 | erot = 2.7042344490094 | epot = -22.2164872193212 | etot = -16.6953280898351 +562000 ekin = 2.76503975841354 | erot = 2.53761848613797 | epot = -22.2442970633444 | etot = -16.9416388187929 +563000 ekin = 2.65825040724929 | erot = 2.71023439088386 | epot = -22.2432218230981 | etot = -16.874737024965 +564000 ekin = 2.64808423454385 | erot = 2.70315330750784 | epot = -22.2101649946189 | etot = -16.8589274525672 +565000 ekin = 2.56520347515975 | erot = 2.51222337320417 | epot = -22.1609166692031 | etot = -17.0834898208392 +566000 ekin = 2.49797853328337 | erot = 1.95572936802194 | epot = -22.1122925054573 | etot = -17.658584604152 +567000 ekin = 2.54792607074976 | erot = 1.85729033385369 | epot = -22.0797419433041 | etot = -17.6745255387006 +568000 ekin = 2.60591444007222 | erot = 1.83755900710613 | epot = -22.0644073196278 | etot = -17.6209338724494 +569000 ekin = 2.62362305667833 | erot = 2.09101698674231 | epot = -22.0262950849356 | etot = -17.311655041515 +570000 ekin = 2.59966130338347 | erot = 1.85283577890403 | epot = -21.985297677289 | etot = -17.5328005950015 +571000 ekin = 2.57696065480343 | erot = 2.10053443453256 | epot = -21.9714910967205 | etot = -17.2939960073845 +572000 ekin = 2.61992211526347 | erot = 2.35929604367208 | epot = -21.9659339101479 | etot = -16.9867157512124 +573000 ekin = 2.80765379250771 | erot = 2.64066236878635 | epot = -21.9992362601246 | etot = -16.5509200988305 +574000 ekin = 2.77886407527625 | erot = 2.38672398638091 | epot = -22.0653999532897 | etot = -16.8998118916326 +575000 ekin = 2.68662185812333 | erot = 2.33286464853928 | epot = -22.1404382955657 | etot = -17.120951788903 +576000 ekin = 2.71580008212167 | erot = 2.47248086928729 | epot = -22.2173146829084 | etot = -17.0290337314995 +577000 ekin = 2.73021589278203 | erot = 2.52068341312493 | epot = -22.2907564203179 | etot = -17.039857114411 +578000 ekin = 2.73054357573046 | erot = 2.5578495344155 | epot = -22.3560478485196 | etot = -17.0676547383736 +579000 ekin = 2.66821624836613 | erot = 2.41812757787236 | epot = -22.394402599384 | etot = -17.3080587731455 +580000 ekin = 2.67666651362018 | erot = 2.37337561149719 | epot = -22.3970390424453 | etot = -17.3469969173279 +581000 ekin = 2.50777332809667 | erot = 2.18045458374889 | epot = -22.3739113390241 | etot = -17.6856834271785 +582000 ekin = 2.40279105319001 | erot = 1.89859122534145 | epot = -22.3216073421066 | etot = -18.0202250635751 +583000 ekin = 2.31269263220222 | erot = 1.73074513088258 | epot = -22.257314045486 | etot = -18.2138762824012 +584000 ekin = 2.21239433549828 | erot = 1.75290221167374 | epot = -22.211114941138 | etot = -18.2458183939659 +585000 ekin = 2.15356855038405 | erot = 1.75180079977004 | epot = -22.2293562414396 | etot = -18.3239868912855 +586000 ekin = 2.10262413842075 | erot = 1.85113983993486 | epot = -22.2792098403942 | etot = -18.3254458620385 +587000 ekin = 2.1328837446892 | erot = 2.20890667221829 | epot = -22.3055082909198 | etot = -17.9637178740123 +588000 ekin = 2.14862689118427 | erot = 2.25138259269008 | epot = -22.2976262267024 | etot = -17.897616742828 +589000 ekin = 2.04435421027949 | erot = 2.19255127415941 | epot = -22.2575972691442 | etot = -18.0206917847053 +590000 ekin = 1.97499579796044 | erot = 2.1895582195425 | epot = -22.1946880982505 | etot = -18.0301340807476 +591000 ekin = 1.91372986676128 | erot = 2.00143608804063 | epot = -22.0969708781093 | etot = -18.1818049233073 +592000 ekin = 1.90759584087362 | erot = 1.75955547353167 | epot = -22.0003759984148 | etot = -18.3332246840095 +593000 ekin = 1.85491418079581 | erot = 1.82471441354141 | epot = -21.8971191196309 | etot = -18.2174905252937 +594000 ekin = 1.80279616325959 | erot = 1.89197043010806 | epot = -21.7918103226285 | etot = -18.0970437292608 +595000 ekin = 1.73140057218513 | erot = 1.88940188632514 | epot = -21.6714819005038 | etot = -18.0506794419936 +596000 ekin = 1.6636273955706 | erot = 2.08459374164565 | epot = -21.5484728514096 | etot = -17.8002517141934 +597000 ekin = 1.58837419642041 | erot = 2.25218931046814 | epot = -21.4300614484278 | etot = -17.5894979415393 +598000 ekin = 1.51530311364938 | erot = 2.10564447814212 | epot = -21.3454884805704 | etot = -17.7245408887789 +599000 ekin = 1.51205618459752 | erot = 2.59561573346752 | epot = -21.3001794349524 | etot = -17.1925075168874 +600000 ekin = 1.42420860787909 | erot = 2.66872977571287 | epot = -21.2831261175817 | etot = -17.1901877339898 +601000 ekin = 1.41614052584447 | erot = 2.71409841098224 | epot = -21.2819425817425 | etot = -17.1517036449157 +602000 ekin = 1.39716919100079 | erot = 2.88098133874153 | epot = -21.2738817162048 | etot = -16.9957311864625 +603000 ekin = 1.35362959397666 | erot = 2.47699104027353 | epot = -21.2686606294815 | etot = -17.4380399952313 +604000 ekin = 1.30109941785272 | erot = 2.37915588297089 | epot = -21.2782162294336 | etot = -17.59796092861 +605000 ekin = 1.3347410210722 | erot = 2.45818083278446 | epot = -21.3160026412592 | etot = -17.5230807874025 +606000 ekin = 1.29920725195346 | erot = 2.42086336903906 | epot = -21.37519294939 | etot = -17.6551223283975 +607000 ekin = 1.23411371002999 | erot = 2.51322970316879 | epot = -21.4519931649175 | etot = -17.7046497517188 +608000 ekin = 1.22186321044635 | erot = 2.53110415552155 | epot = -21.5178918639268 | etot = -17.7649244979589 +609000 ekin = 1.29545020421392 | erot = 2.63039876861633 | epot = -21.5664820555049 | etot = -17.6406330826747 +610000 ekin = 1.32833269788873 | erot = 2.69742481429448 | epot = -21.604275256766 | etot = -17.5785177445827 +611000 ekin = 1.37555485576576 | erot = 2.44250786358899 | epot = -21.6325158720195 | etot = -17.8144531526648 +612000 ekin = 1.43492266332439 | erot = 2.48338158304047 | epot = -21.6301768868763 | etot = -17.7118726405114 +613000 ekin = 1.45874940730883 | erot = 2.24888080699426 | epot = -21.6206823260937 | etot = -17.9130521117906 +614000 ekin = 1.55936377690317 | erot = 2.20987492911095 | epot = -21.5983529263254 | etot = -17.8291142203113 +615000 ekin = 1.65618793567238 | erot = 2.06571861106615 | epot = -21.5839674847175 | etot = -17.862060937979 +616000 ekin = 1.69323202132164 | erot = 2.42079239195229 | epot = -21.5767246732261 | etot = -17.4627002599521 +617000 ekin = 1.68010177617037 | erot = 2.37299975949536 | epot = -21.5796207721185 | etot = -17.5265192364528 +618000 ekin = 1.8246344502958 | erot = 2.21376210856673 | epot = -21.5858855133924 | etot = -17.5474889545299 +619000 ekin = 1.82457061205233 | erot = 2.13717697103627 | epot = -21.6086012174157 | etot = -17.6468536343271 +620000 ekin = 1.90243298129573 | erot = 2.026399287695 | epot = -21.6453403015338 | etot = -17.7165080325431 +621000 ekin = 2.00071054813254 | erot = 2.00740169333747 | epot = -21.6932983622006 | etot = -17.6851861207306 +622000 ekin = 2.06294983283443 | erot = 2.33338027747368 | epot = -21.7476105458916 | etot = -17.3512804355835 +623000 ekin = 2.16886474013731 | erot = 2.34052136367693 | epot = -21.8030581053771 | etot = -17.2936720015629 +624000 ekin = 2.27472643943831 | erot = 2.06709867004516 | epot = -21.8339575931657 | etot = -17.4921324836822 +625000 ekin = 2.44743468020715 | erot = 1.92194449605363 | epot = -21.8528539423024 | etot = -17.4834747660416 +626000 ekin = 2.6254852196301 | erot = 1.8914549992757 | epot = -21.8798709040079 | etot = -17.3629306851021 +627000 ekin = 2.68150434400722 | erot = 2.08428883327615 | epot = -21.9107134797374 | etot = -17.144920302454 +628000 ekin = 2.74903675678166 | erot = 1.99441751232837 | epot = -21.9473456387968 | etot = -17.2038913696868 +629000 ekin = 2.86146526790837 | erot = 1.8864966665127 | epot = -21.9845526009202 | etot = -17.2365906664991 +630000 ekin = 2.97219747359881 | erot = 1.94159826713974 | epot = -21.9956245597366 | etot = -17.081828818998 +631000 ekin = 3.02655709138913 | erot = 1.98612431447029 | epot = -21.9867324807645 | etot = -16.9740510749051 +632000 ekin = 2.8924282396145 | erot = 2.07813215947684 | epot = -21.9871217882292 | etot = -17.0165613891379 +633000 ekin = 2.89559354592024 | erot = 2.04782477805557 | epot = -21.9766614082672 | etot = -17.0332430842914 +634000 ekin = 2.83247679377603 | erot = 2.13051755362208 | epot = -21.9597388170748 | etot = -16.9967444696767 +635000 ekin = 2.6371007480047 | erot = 2.23426349035981 | epot = -21.971527434846 | etot = -17.1001631964814 +636000 ekin = 2.58412863450127 | erot = 2.48166310505742 | epot = -21.9758376025014 | etot = -16.9100458629427 +637000 ekin = 2.48413021154078 | erot = 3.05163678747107 | epot = -21.9559270975231 | etot = -16.4201600985112 +638000 ekin = 2.41845843253134 | erot = 3.18487359706622 | epot = -21.921818269157 | etot = -16.3184862395595 +639000 ekin = 2.41474442996945 | erot = 3.07946799577763 | epot = -21.8601538104442 | etot = -16.3659413846971 +640000 ekin = 2.43888704755713 | erot = 3.19916726587331 | epot = -21.7732605714474 | etot = -16.135206258017 +641000 ekin = 2.33318464269015 | erot = 3.52964988306914 | epot = -21.6751385521693 | etot = -15.81230402641 +642000 ekin = 2.2926912747172 | erot = 3.21459747812075 | epot = -21.5762475219887 | etot = -16.0689587691507 +643000 ekin = 2.20009271503132 | erot = 3.27121474420525 | epot = -21.4712567460617 | etot = -15.9999492868251 +644000 ekin = 2.12761393014547 | erot = 3.26891111731317 | epot = -21.348362707749 | etot = -15.9518376602904 +645000 ekin = 2.1428335991833 | erot = 3.15969008283743 | epot = -21.21325186576 | etot = -15.9107281837392 +646000 ekin = 2.06396314958894 | erot = 3.09371999472776 | epot = -21.1127434027894 | etot = -15.9550602584727 +647000 ekin = 2.09494506010988 | erot = 3.01853693183369 | epot = -21.0393545332666 | etot = -15.9258725413231 +648000 ekin = 2.04196638106962 | erot = 2.92354702002768 | epot = -20.9985594175433 | etot = -16.033046016446 +649000 ekin = 2.12312778485914 | erot = 2.76395475216344 | epot = -20.9701414537499 | etot = -16.0830589167274 +650000 ekin = 2.10015809243646 | erot = 2.49008137666262 | epot = -20.9856777615308 | etot = -16.3954382924317 +651000 ekin = 2.17042975668805 | erot = 2.82094735385292 | epot = -21.0172459830267 | etot = -16.0258688724858 +652000 ekin = 2.09384051310296 | erot = 2.85582968797887 | epot = -21.0193054655962 | etot = -16.0696352645143 +653000 ekin = 2.04333185286127 | erot = 2.77890783040049 | epot = -21.0137769463722 | etot = -16.1915372631104 +654000 ekin = 2.08939824491349 | erot = 2.64655974106821 | epot = -20.9895202496129 | etot = -16.2535622636312 +655000 ekin = 2.04966047424328 | erot = 2.69502096883432 | epot = -20.9377501246668 | etot = -16.1930686815892 +656000 ekin = 2.01275055755579 | erot = 2.79546881312587 | epot = -20.8915125736507 | etot = -16.083293202969 +657000 ekin = 2.03431712569043 | erot = 2.53773887631586 | epot = -20.8578047692326 | etot = -16.2857487672263 +658000 ekin = 2.06735385767747 | erot = 2.66675755014667 | epot = -20.8663643114328 | etot = -16.1322529036087 +659000 ekin = 2.06847583306533 | erot = 2.50326478566329 | epot = -20.8825165023757 | etot = -16.3107758836471 +660000 ekin = 2.07870932959752 | erot = 2.81447557231157 | epot = -20.9216042516452 | etot = -16.0284193497362 +661000 ekin = 2.19772022528447 | erot = 2.70676732599835 | epot = -20.955272489222 | etot = -16.0507849379392 +662000 ekin = 2.25232628384317 | erot = 2.75397596508144 | epot = -20.9799482828299 | etot = -15.9736460339053 +663000 ekin = 2.34038951099398 | erot = 2.814307507525 | epot = -21.0068651854295 | etot = -15.8521681669105 +664000 ekin = 2.44930976235149 | erot = 2.91832446463439 | epot = -21.020924392121 | etot = -15.6532901651351 +665000 ekin = 2.62422537382047 | erot = 3.05929629192827 | epot = -21.0148549044024 | etot = -15.3313332386536 +666000 ekin = 2.670006078315 | erot = 3.11170707620248 | epot = -20.9818079036879 | etot = -15.2000947491704 +667000 ekin = 2.64691465550483 | erot = 2.74197391498727 | epot = -20.9087124741422 | etot = -15.5198239036501 +668000 ekin = 2.62658511176402 | erot = 2.5239543546275 | epot = -20.786299632355 | etot = -15.6357601659635 +669000 ekin = 2.54613084896548 | erot = 2.35938084584039 | epot = -20.6443137124917 | etot = -15.7388020176858 +670000 ekin = 2.43931260869762 | erot = 2.38690789091417 | epot = -20.4714500069448 | etot = -15.645229507333 +671000 ekin = 2.36289981273298 | erot = 2.15959347634289 | epot = -20.2658276701857 | etot = -15.7433343811098 +672000 ekin = 2.2910602274596 | erot = 2.06640999933982 | epot = -20.0256672427834 | etot = -15.668197015984 +673000 ekin = 2.10231422621812 | erot = 1.99818617792713 | epot = -19.7891832406039 | etot = -15.6886828364586 +674000 ekin = 1.99734939649369 | erot = 1.85664304782892 | epot = -19.5650277424005 | etot = -15.7110352980778 +675000 ekin = 1.90857669053491 | erot = 1.65889203440098 | epot = -19.3811887348938 | etot = -15.8137200099579 +676000 ekin = 1.77298099338034 | erot = 1.8309437616018 | epot = -19.2510356435177 | etot = -15.6471108885356 +677000 ekin = 1.63736904978552 | erot = 1.99281479568144 | epot = -19.1448234704454 | etot = -15.5146396249784 +678000 ekin = 1.63864208730505 | erot = 2.08161035578974 | epot = -19.105500688407 | etot = -15.3852482453122 +679000 ekin = 1.55282751541948 | erot = 2.3521751505239 | epot = -19.1160594043128 | etot = -15.2110567383695 +680000 ekin = 1.55994958081089 | erot = 2.58133264049645 | epot = -19.1875667436083 | etot = -15.046284522301 +681000 ekin = 1.47247027591437 | erot = 2.65144156511845 | epot = -19.2708019300319 | etot = -15.1468900889991 +682000 ekin = 1.50506312913083 | erot = 2.58308917381129 | epot = -19.3768551123297 | etot = -15.2887028093876 +683000 ekin = 1.58124836058812 | erot = 2.16095218887994 | epot = -19.4911476852349 | etot = -15.7489471357668 +684000 ekin = 1.6001005959995 | erot = 2.67440743177637 | epot = -19.618133888318 | etot = -15.3436258605422 +685000 ekin = 1.74893549928147 | erot = 2.62458073477927 | epot = -19.7359660896817 | etot = -15.362449855621 +686000 ekin = 1.76162153341699 | erot = 2.25978530691164 | epot = -19.8541116154889 | etot = -15.8327047751602 +687000 ekin = 1.82619229946423 | erot = 2.29432044590917 | epot = -19.9622292318958 | etot = -15.8417164865223 +688000 ekin = 1.86359828413827 | erot = 2.16944371769534 | epot = -20.0476865748907 | etot = -16.0146445730571 +689000 ekin = 1.93393905859018 | erot = 2.35498206852836 | epot = -20.1007195797119 | etot = -15.8117984525933 +690000 ekin = 1.97584813479881 | erot = 2.24522756497958 | epot = -20.1288568750709 | etot = -15.9077811752926 +691000 ekin = 1.98048868486336 | erot = 2.14627975778126 | epot = -20.1381110985218 | etot = -16.0113426558772 +692000 ekin = 2.0731346001912 | erot = 1.98008848193517 | epot = -20.1378652364587 | etot = -16.0846421543323 +693000 ekin = 2.19190306917297 | erot = 1.58910242480145 | epot = -20.1350957523462 | etot = -16.3540902583718 +694000 ekin = 2.32090880384981 | erot = 1.6129592713478 | epot = -20.1314162689182 | etot = -16.1975481937205 +695000 ekin = 2.36874640002701 | erot = 1.5905606666644 | epot = -20.1380145179375 | etot = -16.1787074512461 +696000 ekin = 2.44650937280252 | erot = 1.81535925455503 | epot = -20.1652369679559 | etot = -15.9033683405983 +697000 ekin = 2.51545709816397 | erot = 1.68826010240628 | epot = -20.2135933592969 | etot = -16.0098761587266 +698000 ekin = 2.62928708586045 | erot = 1.96628199836588 | epot = -20.2928804390009 | etot = -15.6973113547745 +699000 ekin = 2.71719696170839 | erot = 2.26885524041435 | epot = -20.3980545329771 | etot = -15.4120023308544 +700000 ekin = 2.87208259001985 | erot = 2.42835298004882 | epot = -20.5178291857201 | etot = -15.2173936156514 +701000 ekin = 2.95900259417971 | erot = 2.35931389631808 | epot = -20.6419240268719 | etot = -15.3236075363741 +702000 ekin = 3.02090269085953 | erot = 2.15074914986724 | epot = -20.7704027073332 | etot = -15.5987508666064 +703000 ekin = 2.97785017762568 | erot = 2.21426045315884 | epot = -20.8971176595459 | etot = -15.7050070287614 +704000 ekin = 2.95736377946593 | erot = 2.20998660273298 | epot = -21.0054958631779 | etot = -15.838145480979 +705000 ekin = 2.86750561874265 | erot = 2.27820994963735 | epot = -21.0805981580118 | etot = -15.9348825896318 +706000 ekin = 2.78753231022251 | erot = 2.27865200108248 | epot = -21.1291811901213 | etot = -16.0629968788163 +707000 ekin = 2.82215447573998 | erot = 2.35221981249519 | epot = -21.1609961465472 | etot = -15.986621858312 +708000 ekin = 2.8288482381589 | erot = 2.35861511414917 | epot = -21.1686473578695 | etot = -15.9811840055614 +709000 ekin = 2.83366981826097 | erot = 2.36573692196813 | epot = -21.1360090124629 | etot = -15.9366022722338 +710000 ekin = 2.82063152616624 | erot = 2.46614987505496 | epot = -21.0841357904475 | etot = -15.7973543892263 +711000 ekin = 2.86012277832299 | erot = 2.45669685378256 | epot = -21.0284124029736 | etot = -15.711592770868 +712000 ekin = 2.83900632279951 | erot = 2.58641728570259 | epot = -20.97749537454 | etot = -15.5520717660379 +713000 ekin = 2.81285265683929 | erot = 2.77009227835436 | epot = -20.9479708753276 | etot = -15.365025940134 +714000 ekin = 2.79476769474608 | erot = 2.56608145300981 | epot = -20.9660227808497 | etot = -15.6051736330938 +715000 ekin = 2.88214044419436 | erot = 2.35359704421306 | epot = -21.0023890888555 | etot = -15.7666516004481 +716000 ekin = 2.8062444107519 | erot = 2.44602402366658 | epot = -21.0643399300769 | etot = -15.8120714956584 +717000 ekin = 2.83593496475333 | erot = 1.92271233473007 | epot = -21.141933904549 | etot = -16.3832866050656 +718000 ekin = 3.04347220736712 | erot = 2.09664480466605 | epot = -21.2307953497141 | etot = -16.090678337681 +719000 ekin = 3.12566385858511 | erot = 1.94969815384627 | epot = -21.3369127599911 | etot = -16.2615507475597 +720000 ekin = 3.09860713118126 | erot = 1.90387725838931 | epot = -21.430943204698 | etot = -16.4284588151275 +721000 ekin = 3.12993031147987 | erot = 1.7597447170846 | epot = -21.4934147835513 | etot = -16.6037397549868 +722000 ekin = 3.20199415669046 | erot = 1.70619449649563 | epot = -21.5365621621188 | etot = -16.6283735089327 +723000 ekin = 3.23996165272215 | erot = 1.89914229033929 | epot = -21.5885170205204 | etot = -16.4494130774589 +724000 ekin = 3.2385304661127 | erot = 2.03882621849399 | epot = -21.6296558315724 | etot = -16.3522991469657 +725000 ekin = 3.28185949262493 | erot = 2.37030663171847 | epot = -21.6824484616656 | etot = -16.0302823373222 +726000 ekin = 3.25580607632264 | erot = 2.39086109621883 | epot = -21.7177565383547 | etot = -16.0710893658133 +727000 ekin = 3.19805228999072 | erot = 2.32087178780789 | epot = -21.7371075347428 | etot = -16.2181834569442 +728000 ekin = 3.15990197080524 | erot = 2.25349819703034 | epot = -21.7242195216867 | etot = -16.3108193538511 +729000 ekin = 3.15676540241598 | erot = 2.43628064604805 | epot = -21.6874540329232 | etot = -16.0944079844592 +730000 ekin = 3.09116846008209 | erot = 2.25419507427884 | epot = -21.6463691748075 | etot = -16.3010056404465 +731000 ekin = 3.1348260525846 | erot = 2.37233499175367 | epot = -21.6178854848966 | etot = -16.1107244405583 +732000 ekin = 2.99746260909862 | erot = 2.05794797450074 | epot = -21.6100718510651 | etot = -16.5546612674658 +733000 ekin = 2.96980729498646 | erot = 2.41656769534009 | epot = -21.6212858194831 | etot = -16.2349108291565 +734000 ekin = 2.95805172881307 | erot = 2.41106090290961 | epot = -21.6442325736449 | etot = -16.2751199419222 +735000 ekin = 2.98912645607776 | erot = 2.56433748906623 | epot = -21.6552350758769 | etot = -16.1017711307329 +736000 ekin = 2.98402840956578 | erot = 2.50919943020236 | epot = -21.6382057820196 | etot = -16.1449779422515 +737000 ekin = 2.93444255324219 | erot = 2.46509691619754 | epot = -21.6069075472111 | etot = -16.2073680777713 +738000 ekin = 2.92304716734076 | erot = 2.39086826460992 | epot = -21.5785523296152 | etot = -16.2646368976646 +739000 ekin = 2.87558559566524 | erot = 2.33418319756002 | epot = -21.5767003124474 | etot = -16.3669315192221 +740000 ekin = 2.83334180172276 | erot = 1.96595420169352 | epot = -21.579060146737 | etot = -16.7797641433207 +741000 ekin = 2.90514747722426 | erot = 1.90064280259662 | epot = -21.5882717938202 | etot = -16.7824815139993 +742000 ekin = 2.94949674447586 | erot = 2.10481207661777 | epot = -21.607358114224 | etot = -16.5530492931304 +743000 ekin = 3.04809185048082 | erot = 2.29122955891096 | epot = -21.6217844205865 | etot = -16.2824630111948 +744000 ekin = 2.98636530702456 | erot = 2.18551221916275 | epot = -21.6006673772001 | etot = -16.4287898510128 +745000 ekin = 2.92324621087502 | erot = 2.67370319519931 | epot = -21.5479250866163 | etot = -15.950975680542 +746000 ekin = 2.81108840832447 | erot = 2.60039332109184 | epot = -21.4880495112522 | etot = -16.0765677818358 +747000 ekin = 2.6799138273957 | erot = 2.55252994490126 | epot = -21.4304230755331 | etot = -16.1979793032361 +748000 ekin = 2.53045428101834 | erot = 2.24950736294004 | epot = -21.3737230667369 | etot = -16.5937614227785 +749000 ekin = 2.4521893183736 | erot = 2.14663919598135 | epot = -21.3068166295668 | etot = -16.7079881152118 +750000 ekin = 2.43997409031359 | erot = 2.12137765598021 | epot = -21.26051392318 | etot = -16.6991621768862 +751000 ekin = 2.39722500832643 | erot = 1.84714049259476 | epot = -21.2245204548724 | etot = -16.9801549539512 +752000 ekin = 2.37942582094566 | erot = 1.94578907645433 | epot = -21.2018614145329 | etot = -16.8766465171329 +753000 ekin = 2.28406990648588 | erot = 2.19722525584574 | epot = -21.2075024607032 | etot = -16.7262072983716 +754000 ekin = 2.17408286982644 | erot = 2.09839079215022 | epot = -21.2133775747234 | etot = -16.9409039127468 +755000 ekin = 2.20136426888662 | erot = 2.24067079579293 | epot = -21.2335060459114 | etot = -16.7914709812319 +756000 ekin = 2.12844260913138 | erot = 2.75005545693611 | epot = -21.2581599852214 | etot = -16.3796619191539 +757000 ekin = 2.25743819675586 | erot = 2.52018349756299 | epot = -21.2980084121415 | etot = -16.5203867178226 +758000 ekin = 2.27601870393368 | erot = 2.57559214660628 | epot = -21.3386893542485 | etot = -16.4870785037085 +759000 ekin = 2.36164379748138 | erot = 2.34149147167507 | epot = -21.3861537164028 | etot = -16.6830184472464 +760000 ekin = 2.4675118177957 | erot = 2.29440108117585 | epot = -21.4502954100435 | etot = -16.6883825110719 +761000 ekin = 2.56117979243443 | erot = 2.28528133130907 | epot = -21.5440902713626 | etot = -16.6976291476191 +762000 ekin = 2.73403817269047 | erot = 2.05037676089399 | epot = -21.665528468236 | etot = -16.8811135346516 +763000 ekin = 2.89028863279996 | erot = 1.96997057412352 | epot = -21.7985105959424 | etot = -16.9382513890189 +764000 ekin = 3.07961097460984 | erot = 1.9033768651762 | epot = -21.9231959994996 | etot = -16.9402081597136 +765000 ekin = 3.10823123780416 | erot = 1.87663540264838 | epot = -22.0019892323021 | etot = -17.0171225918495 +766000 ekin = 3.06909048295609 | erot = 2.19611166095393 | epot = -22.0456827970012 | etot = -16.7804806530912 +767000 ekin = 2.95314668625034 | erot = 2.25238187251554 | epot = -22.0265415483726 | etot = -16.8210129896067 +768000 ekin = 2.82146820632443 | erot = 2.14933629194817 | epot = -21.972991691349 | etot = -17.0021871930764 +769000 ekin = 2.77603784529003 | erot = 1.90506312419755 | epot = -21.892293283993 | etot = -17.2111923145055 +770000 ekin = 2.78938661934819 | erot = 1.68105737595234 | epot = -21.7998635345682 | etot = -17.3294195392676 +771000 ekin = 2.69423677840458 | erot = 1.66016415121773 | epot = -21.7233415289997 | etot = -17.3689405993774 +772000 ekin = 2.47513570113057 | erot = 1.55323249560254 | epot = -21.6442608053664 | etot = -17.6158926086333 +773000 ekin = 2.31141180852051 | erot = 1.52117713523274 | epot = -21.5669030975226 | etot = -17.7343141537694 +774000 ekin = 2.17520959919755 | erot = 1.42853024205624 | epot = -21.5199609482922 | etot = -17.9162211070385 +775000 ekin = 2.04944703670502 | erot = 1.48494648755655 | epot = -21.5280933272633 | etot = -17.9936998030017 +776000 ekin = 1.92108310791782 | erot = 1.66205812928437 | epot = -21.5590874070445 | etot = -17.9759461698423 +777000 ekin = 1.71219857932836 | erot = 1.81255070842961 | epot = -21.5756405048094 | etot = -18.0508912170514 +778000 ekin = 1.64975190369177 | erot = 1.77693127539907 | epot = -21.6017623261212 | etot = -18.1750791470304 +779000 ekin = 1.48106773483772 | erot = 1.73996737730562 | epot = -21.6271500213885 | etot = -18.4061149092452 +780000 ekin = 1.42115475189735 | erot = 1.92486733092795 | epot = -21.6544636605774 | etot = -18.3084415777521 +781000 ekin = 1.45929388158725 | erot = 2.37782097649977 | epot = -21.6537823170126 | etot = -17.8166674589255 +782000 ekin = 1.41005089049893 | erot = 2.64330507296433 | epot = -21.6242214819641 | etot = -17.5708655185008 +783000 ekin = 1.48665806788307 | erot = 2.25515514589752 | epot = -21.6087091715109 | etot = -17.8668959577303 +784000 ekin = 1.51747380423224 | erot = 1.88850072498605 | epot = -21.5108011603788 | etot = -18.1048266311605 +785000 ekin = 1.54947682048194 | erot = 1.86706119579432 | epot = -21.3875221209808 | etot = -17.9709841047046 +786000 ekin = 1.54716158992325 | erot = 1.85630977678452 | epot = -21.2539376526395 | etot = -17.8504662859317 +787000 ekin = 1.62670511458602 | erot = 1.68010954051122 | epot = -21.1236984428158 | etot = -17.8168837877186 +788000 ekin = 1.71061295763304 | erot = 1.48079461940059 | epot = -21.0260161605701 | etot = -17.8346085835365 +789000 ekin = 1.75916840317546 | erot = 1.50945935318409 | epot = -21.0009620101452 | etot = -17.7323342537856 +790000 ekin = 1.81745672714458 | erot = 1.42634706359404 | epot = -20.9943086861146 | etot = -17.750504895376 +791000 ekin = 1.94362771134114 | erot = 1.56573593007329 | epot = -21.0261698907264 | etot = -17.516806249312 +792000 ekin = 2.04975276454245 | erot = 1.57988802147755 | epot = -21.07703366781 | etot = -17.44739288179 +793000 ekin = 2.17271315800368 | erot = 1.66062406864755 | epot = -21.1162570840033 | etot = -17.282919857352 +794000 ekin = 2.1333415780368 | erot = 1.76445873405366 | epot = -21.1513206879653 | etot = -17.2535203758748 +795000 ekin = 2.13601408983655 | erot = 1.81116078831877 | epot = -21.1807545548911 | etot = -17.2335796767358 +796000 ekin = 2.17221625803796 | erot = 1.84884046113839 | epot = -21.2058704683359 | etot = -17.1848137491596 +797000 ekin = 2.1463721053049 | erot = 2.21749811105505 | epot = -21.2529195044654 | etot = -16.8890492881055 +798000 ekin = 2.15957642625886 | erot = 2.29275394485755 | epot = -21.2708923889547 | etot = -16.8185620178383 +799000 ekin = 2.08753769092984 | erot = 2.48223892349963 | epot = -21.298877057375 | etot = -16.7291004429455 +800000 ekin = 2.10166063621306 | erot = 2.30451589147627 | epot = -21.3357063804161 | etot = -16.9295298527268 +801000 ekin = 1.98982068448309 | erot = 2.31496031357821 | epot = -21.3630439256785 | etot = -17.0582629276172 +802000 ekin = 1.88852653962954 | erot = 2.53585639899644 | epot = -21.4221529007404 | etot = -16.9977699621144 +803000 ekin = 1.86494899702717 | erot = 2.51258933602113 | epot = -21.5138216867254 | etot = -17.1362833536771 +804000 ekin = 1.83485043700229 | erot = 2.73777283234718 | epot = -21.60675388147 | etot = -17.0341306121205 +805000 ekin = 1.89569263744112 | erot = 2.82042555409346 | epot = -21.7141010846669 | etot = -16.9979828931323 +806000 ekin = 2.03598954392718 | erot = 2.98358468485725 | epot = -21.8550274116334 | etot = -16.8354531828489 +807000 ekin = 2.09814069227244 | erot = 2.8132319353642 | epot = -21.9827325780332 | etot = -17.0713599503965 +808000 ekin = 2.1146277027298 | erot = 2.49693470536621 | epot = -22.0688650799838 | etot = -17.4573026718878 +809000 ekin = 2.13890385092049 | erot = 2.65117639911355 | epot = -22.1082573604101 | etot = -17.318177110376 +810000 ekin = 2.15577455258879 | erot = 2.56739189056133 | epot = -22.0870651879663 | etot = -17.3638987448162 +811000 ekin = 2.17521477004763 | erot = 2.59273676449886 | epot = -22.0068576171901 | etot = -17.2389060826436 +812000 ekin = 2.2138211082672 | erot = 2.2833190373276 | epot = -21.9221481456809 | etot = -17.4250080000861 +813000 ekin = 2.23606377538069 | erot = 2.0667628632266 | epot = -21.8452254459276 | etot = -17.5423988073203 +814000 ekin = 2.31218669650448 | erot = 2.21982956647113 | epot = -21.7734705594004 | etot = -17.2414542964248 +815000 ekin = 2.26166132057992 | erot = 2.05343829873293 | epot = -21.7104605671149 | etot = -17.395360947802 +816000 ekin = 2.29922240842023 | erot = 1.78921729997066 | epot = -21.6731772950091 | etot = -17.5847375866182 +817000 ekin = 2.28546650718359 | erot = 1.75994341757863 | epot = -21.6545632782248 | etot = -17.6091533534626 +818000 ekin = 2.21513678285521 | erot = 1.78656435337588 | epot = -21.6636032884056 | etot = -17.6619021521746 +819000 ekin = 2.2739144098903 | erot = 1.82930333148435 | epot = -21.7137466609641 | etot = -17.6105289195894 +820000 ekin = 2.2428209129448 | erot = 1.73998445300752 | epot = -21.8023021191167 | etot = -17.8194967531644 +821000 ekin = 2.19192382316412 | erot = 2.09893863137338 | epot = -21.9355239556899 | etot = -17.6446615011524 +822000 ekin = 2.23107874912494 | erot = 2.41397800350045 | epot = -22.0937718271939 | etot = -17.4487150745685 +823000 ekin = 2.18728871634498 | erot = 2.89300153500107 | epot = -22.2549565567117 | etot = -17.1746663053656 +824000 ekin = 2.09269007791805 | erot = 3.3277443737517 | epot = -22.4116674984368 | etot = -16.991233046767 +825000 ekin = 2.02686183028574 | erot = 3.16127293746629 | epot = -22.5058824787873 | etot = -17.3177477110353 +826000 ekin = 2.03054435557985 | erot = 3.10016450783322 | epot = -22.5168374475919 | etot = -17.3861285841788 +827000 ekin = 2.01452410392906 | erot = 2.84123064216256 | epot = -22.4710810828109 | etot = -17.6153263367193 +828000 ekin = 1.90238312904183 | erot = 2.71042154497554 | epot = -22.3794911074953 | etot = -17.766686433478 +829000 ekin = 1.90418220366908 | erot = 2.69477669052601 | epot = -22.2643157201658 | etot = -17.6653568259707 +830000 ekin = 1.81997341684275 | erot = 2.54478505747627 | epot = -22.1272898430371 | etot = -17.7625313687181 +831000 ekin = 1.83168283006228 | erot = 2.1167788881342 | epot = -22.0163067804203 | etot = -18.0678450622238 +832000 ekin = 1.95186197623467 | erot = 2.17410981396376 | epot = -21.9377902835795 | etot = -17.8118184933811 +833000 ekin = 2.02730820338377 | erot = 1.91567543746809 | epot = -21.8853858637292 | etot = -17.9424022228773 +834000 ekin = 2.14966587630613 | erot = 1.87948738398654 | epot = -21.8918169629535 | etot = -17.8626637026608 +835000 ekin = 2.11991706020911 | erot = 1.8054541455182 | epot = -21.941723079406 | etot = -18.0163518736787 +836000 ekin = 2.16450787990159 | erot = 1.56947066595225 | epot = -22.0176370617284 | etot = -18.2836585158746 +837000 ekin = 2.22942308740125 | erot = 1.72466381535944 | epot = -22.0834662658134 | etot = -18.1293793630527 +838000 ekin = 2.33805060269789 | erot = 2.18496998632859 | epot = -22.1577664107309 | etot = -17.6347458217044 +839000 ekin = 2.45776270515513 | erot = 2.34137207492852 | epot = -22.2345011792188 | etot = -17.4353663991352 +840000 ekin = 2.44088597010558 | erot = 2.2019351625761 | epot = -22.3102615213255 | etot = -17.6674403886438 +841000 ekin = 2.52217561151199 | erot = 2.11119786335644 | epot = -22.4106870083819 | etot = -17.7773135335135 +842000 ekin = 2.53177717032663 | erot = 2.03329546380518 | epot = -22.5051884058711 | etot = -17.9401157717393 +843000 ekin = 2.46981084627127 | erot = 2.26208096486937 | epot = -22.6073969437417 | etot = -17.8755051326011 +844000 ekin = 2.53343392638509 | erot = 2.2623111116808 | epot = -22.6930988517867 | etot = -17.8973538137208 +845000 ekin = 2.55237006837663 | erot = 2.51402635295059 | epot = -22.7449813491078 | etot = -17.6785849277806 +846000 ekin = 2.43591378572727 | erot = 2.18244993015021 | epot = -22.7598171984306 | etot = -18.1414534825531 +847000 ekin = 2.4748928073951 | erot = 2.44850012169248 | epot = -22.7352494455247 | etot = -17.8118565164371 +848000 ekin = 2.5643357454521 | erot = 2.34872816436968 | epot = -22.6736999531278 | etot = -17.760636043306 +849000 ekin = 2.59586448024849 | erot = 2.26529497804774 | epot = -22.5710185702837 | etot = -17.7098591119875 +850000 ekin = 2.4903961332438 | erot = 2.08374957064487 | epot = -22.4628543871474 | etot = -17.8887086832587 +851000 ekin = 2.488488280051 | erot = 2.15043973705406 | epot = -22.3616397400164 | etot = -17.7227117229113 +852000 ekin = 2.50477194373655 | erot = 2.31551148311398 | epot = -22.2794107361277 | etot = -17.4591273092772 +853000 ekin = 2.48988722576821 | erot = 2.37905944195154 | epot = -22.2174467488412 | etot = -17.3485000811214 +854000 ekin = 2.48068473577124 | erot = 2.18215338513696 | epot = -22.1954265386905 | etot = -17.5325884177823 +855000 ekin = 2.36041825080372 | erot = 2.14907471345932 | epot = -22.229814016814 | etot = -17.7203210525509 +856000 ekin = 2.417358203682 | erot = 2.28663399372911 | epot = -22.3010603003025 | etot = -17.5970681028914 +857000 ekin = 2.30380534498129 | erot = 2.28079843394928 | epot = -22.3899957816153 | etot = -17.8053920026848 +858000 ekin = 2.32374915951241 | erot = 2.52586913415153 | epot = -22.4777730735045 | etot = -17.6281547798405 +859000 ekin = 2.3619482564049 | erot = 2.27489572175724 | epot = -22.5497050266214 | etot = -17.9128610484593 +860000 ekin = 2.2967620573291 | erot = 2.8388989146634 | epot = -22.6025698957187 | etot = -17.4669089237262 +861000 ekin = 2.21161021313974 | erot = 2.99481322410829 | epot = -22.6299245638849 | etot = -17.4235011266369 +862000 ekin = 2.21838183726318 | erot = 3.25000510606081 | epot = -22.6168976032125 | etot = -17.1485106598885 +863000 ekin = 2.13571465170804 | erot = 3.00165601774374 | epot = -22.5766345837815 | etot = -17.4392639143298 +864000 ekin = 2.17821492819622 | erot = 3.24144192927424 | epot = -22.5094500698137 | etot = -17.0897932123433 +865000 ekin = 2.12870821452531 | erot = 3.22322665201182 | epot = -22.4134082795112 | etot = -17.0614734129741 +866000 ekin = 2.03423896588069 | erot = 2.41447107774391 | epot = -22.3090528921738 | etot = -17.8603428485492 +867000 ekin = 1.97183886889236 | erot = 2.4818416043682 | epot = -22.2021182647478 | etot = -17.7484377914873 +868000 ekin = 1.91308044020495 | erot = 2.2465020804263 | epot = -22.1047137256864 | etot = -17.9451312050551 +869000 ekin = 1.86185635878513 | erot = 2.19298136311333 | epot = -22.0509375705501 | etot = -17.9960998486517 +870000 ekin = 1.75992459606909 | erot = 2.27547409061159 | epot = -22.0117595888705 | etot = -17.9763609021898 +871000 ekin = 1.72178818046751 | erot = 1.9657215078554 | epot = -21.980219974492 | etot = -18.2927102861691 +872000 ekin = 1.66903556580815 | erot = 1.9379416782388 | epot = -21.9603990023827 | etot = -18.3534217583358 +873000 ekin = 1.64894346626472 | erot = 1.88450940280994 | epot = -21.9681555430981 | etot = -18.4347026740234 +874000 ekin = 1.57135406761337 | erot = 1.94741453396434 | epot = -21.9765853859777 | etot = -18.4578167843999 +875000 ekin = 1.59516741268935 | erot = 2.23157297797765 | epot = -21.9920927279216 | etot = -18.1653523372546 +876000 ekin = 1.50206798403358 | erot = 2.57780068625252 | epot = -22.0050475608067 | etot = -17.9251788905206 +877000 ekin = 1.52015373136829 | erot = 2.28437163698736 | epot = -22.0218254393268 | etot = -18.2173000709712 +878000 ekin = 1.53387227783086 | erot = 2.27517376879602 | epot = -22.0464155341903 | etot = -18.2373694875634 +879000 ekin = 1.55669077534398 | erot = 2.37565877810974 | epot = -22.0629736571075 | etot = -18.1306241036537 +880000 ekin = 1.60508011630015 | erot = 2.26195551636616 | epot = -22.0724613924566 | etot = -18.2054257597903 +881000 ekin = 1.62558178006308 | erot = 2.31792675005643 | epot = -22.0658818657183 | etot = -18.1223733355988 +882000 ekin = 1.6144910958812 | erot = 2.44866007965463 | epot = -22.0469024278352 | etot = -17.9837512522994 +883000 ekin = 1.63091904234953 | erot = 2.18398402433269 | epot = -22.0252651066238 | etot = -18.2103620399416 +884000 ekin = 1.69681929338547 | erot = 2.21165212418211 | epot = -21.9745385463916 | etot = -18.066067128824 +885000 ekin = 1.75683241806753 | erot = 2.08331167107031 | epot = -21.8927725348196 | etot = -18.0526284456818 +886000 ekin = 1.75713708681619 | erot = 1.80115910431478 | epot = -21.826515750347 | etot = -18.268219559216 +887000 ekin = 1.84458649763971 | erot = 1.6655369970267 | epot = -21.7661815209394 | etot = -18.256058026273 +888000 ekin = 1.88680036415703 | erot = 1.7206520016233 | epot = -21.7110459690312 | etot = -18.1035936032509 +889000 ekin = 1.92232221960098 | erot = 1.56101057590172 | epot = -21.6536565424968 | etot = -18.1703237469941 +890000 ekin = 2.02284103377922 | erot = 1.31029028744492 | epot = -21.5930522300749 | etot = -18.2599209088507 +891000 ekin = 2.0244270161912 | erot = 1.42067034503728 | epot = -21.5472191599552 | etot = -18.1021217987267 +892000 ekin = 2.0362677580668 | erot = 1.6631677107657 | epot = -21.5129190017501 | etot = -17.8134835329176 +893000 ekin = 2.05186124624837 | erot = 1.57527161139243 | epot = -21.4921943128911 | etot = -17.8650614552503 +894000 ekin = 2.09965074001103 | erot = 1.56560345394405 | epot = -21.4743969884808 | etot = -17.8091427945257 +895000 ekin = 2.16252772919196 | erot = 1.54647539834646 | epot = -21.4549689326405 | etot = -17.7459658051021 +896000 ekin = 2.10489706554246 | erot = 1.78263133107092 | epot = -21.4330314423336 | etot = -17.5455030457202 +897000 ekin = 2.15073147494894 | erot = 1.74536300046844 | epot = -21.4239119831837 | etot = -17.5278175077664 +898000 ekin = 2.21697995910659 | erot = 2.06978765869365 | epot = -21.4471718071721 | etot = -17.1604041893719 +899000 ekin = 2.33779396143682 | erot = 2.00733840871154 | epot = -21.4839889813085 | etot = -17.1388566111601 +900000 ekin = 2.41597591914528 | erot = 1.85133754557104 | epot = -21.5274273367598 | etot = -17.2601138720435 +901000 ekin = 2.52644082940032 | erot = 2.19280268194111 | epot = -21.5756266105065 | etot = -16.8563830991651 +902000 ekin = 2.5104307371304 | erot = 1.85686816359485 | epot = -21.6063552107196 | etot = -17.2390563099944 +903000 ekin = 2.62548018500407 | erot = 1.94554509677329 | epot = -21.6466830430359 | etot = -17.0756577612585 +904000 ekin = 2.68604865642036 | erot = 1.82230313014663 | epot = -21.7065646613489 | etot = -17.1982128747819 +905000 ekin = 2.83060251059802 | erot = 2.0169713948485 | epot = -21.7613929111648 | etot = -16.9138190057183 +906000 ekin = 2.94848642766405 | erot = 1.99957930227793 | epot = -21.7999060542919 | etot = -16.8518403243499 +907000 ekin = 2.88672419291402 | erot = 2.19624352905707 | epot = -21.8240702621858 | etot = -16.7411025402147 +908000 ekin = 2.91368680910818 | erot = 2.2752598128973 | epot = -21.8626935205279 | etot = -16.6737468985224 +909000 ekin = 3.03993111338504 | erot = 2.41813386601853 | epot = -21.879736108139 | etot = -16.4216711287354 +910000 ekin = 3.02111394144764 | erot = 2.25653445757713 | epot = -21.8869501318898 | etot = -16.6093017328651 +911000 ekin = 2.99074440603055 | erot = 2.42571768981025 | epot = -21.8911591932141 | etot = -16.4746970973733 +912000 ekin = 2.93883503898899 | erot = 2.54048734112191 | epot = -21.8943632676168 | etot = -16.4150408875059 +913000 ekin = 2.88155815219829 | erot = 2.43333021308706 | epot = -21.8712405715098 | etot = -16.5563522062244 +914000 ekin = 2.78298688988037 | erot = 2.69976035390989 | epot = -21.8286041753375 | etot = -16.3458569315473 +915000 ekin = 2.75144009449231 | erot = 2.66679831130723 | epot = -21.7506323099735 | etot = -16.3323939041739 +916000 ekin = 2.7232885681261 | erot = 2.5321692255797 | epot = -21.6421731788429 | etot = -16.3867153851371 +917000 ekin = 2.69768821710692 | erot = 2.47439052917342 | epot = -21.5733596386738 | etot = -16.4012808923935 +918000 ekin = 2.66995818672244 | erot = 2.09882686301138 | epot = -21.5521619505356 | etot = -16.7833769008018 +919000 ekin = 2.61716147205333 | erot = 2.17918504384239 | epot = -21.5346780530109 | etot = -16.7383315371152 +920000 ekin = 2.4752636050963 | erot = 2.51685127690453 | epot = -21.4991402053981 | etot = -16.5070253233973 +921000 ekin = 2.47056876818124 | erot = 2.49255863309457 | epot = -21.4619591744658 | etot = -16.49883177319 +922000 ekin = 2.58423659960796 | erot = 2.61648914399003 | epot = -21.415611615363 | etot = -16.214885871765 +923000 ekin = 2.49375353891012 | erot = 2.67153957254799 | epot = -21.4001146688761 | etot = -16.2348215574179 +924000 ekin = 2.44602138612021 | erot = 2.68498715701816 | epot = -21.4057397221903 | etot = -16.274731179052 +925000 ekin = 2.4033884662416 | erot = 3.00424602709635 | epot = -21.4434811046198 | etot = -16.0358466112819 +926000 ekin = 2.47488592872591 | erot = 3.17529768125855 | epot = -21.5232565657775 | etot = -15.873072955793 +927000 ekin = 2.40301595960374 | erot = 3.1766285148493 | epot = -21.6300583966364 | etot = -16.0504139221834 +928000 ekin = 2.44990005675536 | erot = 3.45632999664383 | epot = -21.7790682902897 | etot = -15.8728382368905 +929000 ekin = 2.56646836803431 | erot = 3.14534753938374 | epot = -21.9043533033882 | etot = -16.1925373959701 +930000 ekin = 2.53471244466995 | erot = 3.34571877879509 | epot = -21.9769628203927 | etot = -16.0965315969277 +931000 ekin = 2.50104812028332 | erot = 3.03046410574044 | epot = -22.0056915593062 | etot = -16.4741793332825 +932000 ekin = 2.49568433462474 | erot = 2.88794958693699 | epot = -21.9962407011222 | etot = -16.6126067795604 +933000 ekin = 2.38321005752042 | erot = 2.8179651958572 | epot = -21.9635224592414 | etot = -16.7623472058638 +934000 ekin = 2.4631793302924 | erot = 2.48085702084528 | epot = -21.9076116702172 | etot = -16.9635753190795 +935000 ekin = 2.49404269439001 | erot = 2.2680501421832 | epot = -21.8352758876517 | etot = -17.0731830510785 +936000 ekin = 2.54306971323985 | erot = 2.27852041735781 | epot = -21.744631719905 | etot = -16.9230415893073 +937000 ekin = 2.53788333247455 | erot = 2.23194591805544 | epot = -21.6534356613612 | etot = -16.8836064108312 +938000 ekin = 2.56958704064676 | erot = 2.22382492410265 | epot = -21.6129100017677 | etot = -16.8194980370182 +939000 ekin = 2.57422838457825 | erot = 2.07923538706558 | epot = -21.627925471487 | etot = -16.9744616998432 +940000 ekin = 2.60491982052164 | erot = 1.98992236153694 | epot = -21.6750092612145 | etot = -17.0801670791559 +941000 ekin = 2.66373355701882 | erot = 2.32917490630045 | epot = -21.7643701633303 | etot = -16.771461700011 +942000 ekin = 2.69288932722208 | erot = 2.64061927508672 | epot = -21.8851511920178 | etot = -16.551642589709 +943000 ekin = 2.85220624426685 | erot = 2.64758558594824 | epot = -22.0439788566377 | etot = -16.5441870264226 +944000 ekin = 3.06981838443027 | erot = 2.58432650033874 | epot = -22.1868426785127 | etot = -16.5326977937437 +945000 ekin = 3.11977740266157 | erot = 2.76047052292399 | epot = -22.3020466458573 | etot = -16.4217987202717 +946000 ekin = 3.19652619014396 | erot = 2.60532859032593 | epot = -22.384087606966 | etot = -16.5822328264961 +947000 ekin = 3.0878408552909 | erot = 2.30512601523218 | epot = -22.4409982051648 | etot = -17.0480313346417 +948000 ekin = 3.07667922739931 | erot = 2.80704322134861 | epot = -22.4646638948259 | etot = -16.580941446078 +949000 ekin = 3.17062900636055 | erot = 2.74445638705334 | epot = -22.4206065116938 | etot = -16.5055211182799 +950000 ekin = 2.99689212844137 | erot = 2.86552970257333 | epot = -22.3361816450126 | etot = -16.4737598139979 +951000 ekin = 2.97085887473133 | erot = 2.98485442072136 | epot = -22.2080335641936 | etot = -16.252320268741 +952000 ekin = 2.8842631754872 | erot = 2.8809900192572 | epot = -22.0862048890997 | etot = -16.3209516943553 +953000 ekin = 2.7982194729927 | erot = 2.79125510393625 | epot = -21.969725924855 | etot = -16.3802513479261 +954000 ekin = 2.75832450886977 | erot = 2.42390666106181 | epot = -21.8712203511701 | etot = -16.6889891812385 +955000 ekin = 2.87942571582999 | erot = 2.62352115358359 | epot = -21.7827306606124 | etot = -16.2797837911988 +956000 ekin = 2.99654896256558 | erot = 2.37509995935517 | epot = -21.7003789778443 | etot = -16.3287300559236 +957000 ekin = 3.01075252014571 | erot = 2.0959903323952 | epot = -21.6228190260862 | etot = -16.5160761735453 +958000 ekin = 3.08956507051447 | erot = 2.10771389670693 | epot = -21.5884599129524 | etot = -16.391180945731 +959000 ekin = 3.0764993561191 | erot = 2.19950747705666 | epot = -21.6082995757446 | etot = -16.3322927425689 +960000 ekin = 3.10536584557396 | erot = 2.29678872673568 | epot = -21.6407886898385 | etot = -16.2386341175289 +961000 ekin = 3.15824288797319 | erot = 2.14027743718253 | epot = -21.657149423264 | etot = -16.3586290981083 +962000 ekin = 3.14297945524784 | erot = 2.20585989326445 | epot = -21.6669948660148 | etot = -16.3181555175025 +963000 ekin = 3.09592787201277 | erot = 1.84946957131994 | epot = -21.6592309502121 | etot = -16.7138335068794 +964000 ekin = 3.09941791328226 | erot = 2.05420199745743 | epot = -21.6348571714204 | etot = -16.4812372606807 +965000 ekin = 3.05909780025704 | erot = 2.03923495471238 | epot = -21.5780802205104 | etot = -16.479747465541 +966000 ekin = 3.14454176510646 | erot = 2.08245540621271 | epot = -21.4998250637724 | etot = -16.2728278924532 +967000 ekin = 3.03869206876124 | erot = 1.99551102271488 | epot = -21.4455121298548 | etot = -16.4113090383786 +968000 ekin = 2.91377375855432 | erot = 2.20122833628323 | epot = -21.4117922551795 | etot = -16.296790160342 +969000 ekin = 2.99132330213241 | erot = 2.47698235897834 | epot = -21.3565561223408 | etot = -15.8882504612301 +970000 ekin = 2.9592500568048 | erot = 2.48694698427739 | epot = -21.3051309670821 | etot = -15.8589339259999 +971000 ekin = 2.85605976500643 | erot = 2.15308731154091 | epot = -21.2711653081504 | etot = -16.2620182316031 +972000 ekin = 2.87454972615855 | erot = 2.21622270070414 | epot = -21.2533681597897 | etot = -16.162595732927 +973000 ekin = 2.82721122527912 | erot = 2.35000163924687 | epot = -21.2327108232249 | etot = -16.055497958699 +974000 ekin = 2.72683175865898 | erot = 2.83125023318017 | epot = -21.2149243536631 | etot = -15.656842361824 +975000 ekin = 2.70588216363101 | erot = 2.49368474281192 | epot = -21.1936492280788 | etot = -15.9940823216358 +976000 ekin = 2.70041722750338 | erot = 2.45741362546222 | epot = -21.1872755048005 | etot = -16.0294446518349 +977000 ekin = 2.59457836008745 | erot = 2.48585482647431 | epot = -21.1832960991295 | etot = -16.1028629125678 +978000 ekin = 2.59433384768261 | erot = 2.2568529885093 | epot = -21.1912738457585 | etot = -16.3400870095666 +979000 ekin = 2.65907339789715 | erot = 2.14939269259649 | epot = -21.2277961745874 | etot = -16.4193300840938 +980000 ekin = 2.68002582724941 | erot = 2.14623475911327 | epot = -21.2888425661001 | etot = -16.4625819797375 +981000 ekin = 2.64198792972712 | erot = 2.09278957349339 | epot = -21.3758129934796 | etot = -16.6410354902591 +982000 ekin = 2.72135605209082 | erot = 2.104842669207 | epot = -21.4695788294429 | etot = -16.6433801081451 +983000 ekin = 2.63994960139947 | erot = 2.23278066526111 | epot = -21.5361373723971 | etot = -16.6634071057365 +984000 ekin = 2.61481848525047 | erot = 2.09640066338693 | epot = -21.5563728487096 | etot = -16.8451537000722 +985000 ekin = 2.61123661404225 | erot = 2.33711711151793 | epot = -21.5280304280226 | etot = -16.5796767024624 +986000 ekin = 2.53166588530016 | erot = 2.51414944396451 | epot = -21.4598136655134 | etot = -16.4139983362488 +987000 ekin = 2.51681610277364 | erot = 2.15601000139561 | epot = -21.3682813084312 | etot = -16.6954552042619 +988000 ekin = 2.52900907479967 | erot = 1.99810184774674 | epot = -21.2423979763251 | etot = -16.7152870537787 +989000 ekin = 2.46743393431978 | erot = 2.17612647821162 | epot = -21.1081947595189 | etot = -16.4646343469875 +990000 ekin = 2.33679166273261 | erot = 2.21492463068834 | epot = -20.9584920898949 | etot = -16.4067757964739 +991000 ekin = 2.15649617938467 | erot = 2.10512589255922 | epot = -20.8223518284057 | etot = -16.5607297564618 +992000 ekin = 2.1666776200099 | erot = 2.36721990012104 | epot = -20.7043891749962 | etot = -16.1704916548652 +993000 ekin = 2.19208440550422 | erot = 2.60766896726736 | epot = -20.6167811931572 | etot = -15.8170278203856 +994000 ekin = 2.24324320799097 | erot = 2.72045204046688 | epot = -20.5394560681001 | etot = -15.5757608196422 +995000 ekin = 2.30218249346941 | erot = 2.38815652338815 | epot = -20.5055629227559 | etot = -15.8152239058984 +996000 ekin = 2.42068208522293 | erot = 2.25149887670527 | epot = -20.5308517273637 | etot = -15.8586707654355 +997000 ekin = 2.40906609278047 | erot = 2.62359663392259 | epot = -20.6100670630845 | etot = -15.5774043363815 +998000 ekin = 2.47036155438578 | erot = 2.72144206830481 | epot = -20.7420376418528 | etot = -15.5502340191622 +999000 ekin = 2.48386726649711 | erot = 3.06416174290322 | epot = -20.894846886581 | etot = -15.3468178771807 +1000000 ekin = 2.67285546610932 | erot = 3.25707361502085 | epot = -21.0717432309422 | etot = -15.141814149812 + 1000000 0.11879358 -1.3439085 0.026924568 -1.1499305 -8.5339515e-05 64000 +Loop time of 20.1611 on 4 procs for 1000000 steps with 16 atoms + +Performance: 42854.842 tau/day, 49600.511 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.2835 | 7.6895 | 12.253 | 104.5 | 38.14 +Bond | 0.30149 | 0.3467 | 0.39285 | 7.1 | 1.72 +Neigh | 0.013536 | 0.013651 | 0.013755 | 0.1 | 0.07 +Comm | 4.1686 | 8.9506 | 12.543 | 102.1 | 44.40 +Output | 0.091778 | 0.096879 | 0.10816 | 2.1 | 0.48 +Modify | 1.2704 | 1.4599 | 1.6558 | 14.7 | 7.24 +Other | | 1.604 | | | 7.96 + +Nlocal: 4.00000 ave 5 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 12.0000 ave 13 max 11 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 26.2500 ave 54 max 9 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 105 +Ave neighs/atom = 6.5625000 +Ave special neighs/atom = 3.7500000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:20 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring new file mode 100644 index 0000000000..bc30aad2e4 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring @@ -0,0 +1,622 @@ +LAMMPS data file via write_data, version 2 Jul 2021 + +148 atoms +4 atom types +148 bonds +1 bond types +148 ellipsoids + +0 100 xlo xhi +0 100 ylo yhi +0 100 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 24.4563103076585 24.545468489552267 25.008405986404544 1 1 3.7269849963023267 0 0 0 +2 4 24.529799925849524 24.236299729034574 25.438869726984304 1 1 3.7269849963023267 0 0 0 +3 3 24.837268545282573 23.98498105692614 25.841653825869834 1 1 3.7269849963023267 0 0 0 +4 2 25.160243408748546 23.990448143707216 26.252262907702004 1 1 3.7269849963023267 0 0 0 +5 1 25.511800888983288 24.20297091581725 26.46953407064928 1 1 3.7269849963023267 0 0 0 +6 2 25.746069731378416 24.53734405670471 26.70776555674676 1 1 3.7269849963023267 0 0 0 +7 3 25.808044471759384 24.911661509909727 27.06389642784591 1 1 3.7269849963023267 0 0 0 +8 2 25.702150220414598 25.16021735315657 27.552609445175545 1 1 3.7269849963023267 0 0 0 +9 4 25.86583558481563 25.223272838133713 28.134182300485513 1 1 3.7269849963023267 0 0 0 +10 2 25.80332921740182 25.045832983472046 28.610009845867623 1 1 3.7269849963023267 0 0 0 +11 3 25.910927625439783 24.67877553909445 29.01481046441401 1 1 3.7269849963023267 0 0 0 +12 2 26.258738827371122 24.424202368909146 29.31202041427481 1 1 3.7269849963023267 0 0 0 +13 2 26.685861178879446 24.203670648569435 29.53932592988526 1 1 3.7269849963023267 0 0 0 +14 1 27.213655907159712 24.05889335581843 29.529355686667273 1 1 3.7269849963023267 0 0 0 +15 2 27.732458381354213 24.12301887416258 29.465296878682626 1 1 3.7269849963023267 0 0 0 +16 3 28.176435469098767 24.39188111290902 29.295132944313664 1 1 3.7269849963023267 0 0 0 +17 1 28.526140016035093 24.71780561439453 29.306758099194106 1 1 3.7269849963023267 0 0 0 +18 4 28.81297070371788 25.156085631242032 29.41241337896862 1 1 3.7269849963023267 0 0 0 +19 2 29.207268942683253 25.464359514737925 29.764217600427827 1 1 3.7269849963023267 0 0 0 +20 4 29.513927400101824 25.6118524234793 30.245210919346164 1 1 3.7269849963023267 0 0 0 +21 2 30.003254698861596 25.548164315889366 30.532777142800704 1 1 3.7269849963023267 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-0.08634929652338917 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring new file mode 100644 index 0000000000..8f476b9d1f --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring @@ -0,0 +1,72 @@ +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring + +set atom * mass 3.1575 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 new file mode 100644 index 0000000000..0c5a623cc8 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 @@ -0,0 +1,281 @@ +LAMMPS (2 Jul 2021) +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 148 atoms + reading velocities ... + 148 velocities + scanning bonds ... + 1 = max bonds/atom + 148 ellipsoids + reading bonds ... + 148 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +set atom * mass 3.1575 +Setting atom values ... + 148 settings made for mass + +group all type 1 4 +148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 36 36 36 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889 +Per MPI rank memory allocation (min/avg/max) = 9.601 | 9.601 | 9.601 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000 +1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183 +2000 ekin = 20.585620972069 | erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104 +3000 ekin = 20.6239332104642 | erot = 21.5529389082728 | epot = -222.947572771312 | etot = -180.770700652575 +4000 ekin = 20.6395549184482 | erot = 21.6854113323895 | epot = -223.095666904229 | etot = -180.770700653391 +5000 ekin = 20.6295551742564 | erot = 21.7809539301805 | epot = -223.181209757876 | etot = -180.770700653439 +6000 ekin = 20.5959625511847 | erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045 +7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517716 | etot = -180.770700652122 +8000 ekin = 20.4774701419092 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943 +9000 ekin = 20.4074566554238 | erot = 21.8097283692398 | epot = -222.987885674261 | etot = -180.770700649597 +10000 ekin = 20.3427303660296 | erot = 21.7629575866663 | epot = -222.876388600948 | etot = -180.770700648253 +11000 ekin = 20.2927407149577 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189 +12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286 +13000 ekin = 20.2733920359447 | erot = 21.6092715397932 | epot = -222.653364221616 | etot = -180.770700645878 +14000 ekin = 20.319652478907 | erot = 21.558663097499 | epot = -222.649016222075 | etot = -180.770700645669 +15000 ekin = 20.4104009374291 | erot = 21.5031572556304 | epot = -222.684258838857 | etot = -180.770700645798 +16000 ekin = 20.5472869005793 | erot = 21.4346177247038 | epot = -222.752605272036 | etot = -180.770700646753 +17000 ekin = 20.7266657908775 | erot = 21.3426631585214 | epot = -222.840029597232 | etot = -180.770700647833 +18000 ekin = 20.9417612759981 | erot = 21.2178611180923 | epot = -222.930323042997 | etot = -180.770700648907 +19000 ekin = 21.1819308659399 | erot = 21.0532289630289 | epot = -223.00586047892 | etot = -180.770700649951 +20000 ekin = 21.4358169889477 | erot = 20.8473069564703 | epot = -223.053824595387 | etot = -180.770700649969 +21000 ekin = 21.6968513751 | erot = 20.6066744652581 | epot = -223.074226489837 | etot = -180.770700649478 +22000 ekin = 21.9614458442786 | erot = 20.3429420444505 | epot = -223.07508853737 | etot = -180.770700648641 +23000 ekin = 22.2276099755705 | erot = 20.0703385165238 | epot = -223.068649139875 | etot = -180.77070064778 +24000 ekin = 22.4935893196675 | erot = 19.802067172166 | epot = -223.066357139276 | etot = -180.770700647443 +25000 ekin = 22.7566064548228 | erot = 19.5464828008836 | epot = -223.073789902975 | etot = -180.770700647269 +26000 ekin = 23.0126717548399 | erot = 19.3065017718462 | epot = -223.089874174571 | etot = -180.770700647885 +27000 ekin = 23.2550417060594 | erot = 19.0797753474567 | epot = -223.105517701932 | etot = -180.770700648416 +28000 ekin = 23.4774329734805 | erot = 18.8646197299574 | epot = -223.112753352067 | etot = -180.770700648629 +29000 ekin = 23.6747927720663 | erot = 18.6628653411825 | epot = -223.108358761693 | etot = -180.770700648445 +30000 ekin = 23.8432321400247 | erot = 18.4812216983637 | epot = -223.095154486375 | etot = -180.770700647986 +31000 ekin = 23.9793041752229 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647145 +32000 ekin = 24.0810246040235 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646295 +33000 ekin = 24.1468986449398 | erot = 18.1820705445406 | epot = -223.09966983514 | etot = -180.770700645659 +34000 ekin = 24.1756615132863 | erot = 18.2103812210172 | epot = -223.156743379607 | etot = -180.770700645303 +35000 ekin = 24.1663193894652 | erot = 18.3185351073568 | epot = -223.255555142089 | etot = -180.770700645267 +36000 ekin = 24.1167205812964 | erot = 18.5091649894187 | epot = -223.396586216223 | etot = -180.770700645508 +37000 ekin = 24.0274860006135 | erot = 18.7785134320989 | epot = -223.576700078937 | etot = -180.770700646225 +38000 ekin = 23.8991479078985 | erot = 19.1166063146995 | epot = -223.78645486989 | etot = -180.770700647292 +39000 ekin = 23.7326911853236 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648763 +40000 ekin = 23.5294223072121 | erot = 19.9254673141826 | epot = -224.225590272292 | etot = -180.770700650897 +41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045567 | etot = -180.770700653371 +42000 ekin = 23.0154529235024 | erot = 20.7165619564844 | epot = -224.502715535761 | etot = -180.770700655774 +43000 ekin = 22.7111536814278 | erot = 21.0163895622227 | epot = -224.498243901357 | etot = -180.770700657707 +44000 ekin = 22.3710575806356 | erot = 21.2060371289779 | epot = -224.347795365752 | etot = -180.770700656139 +45000 ekin = 22.0515843162889 | erot = 21.2588026881767 | epot = -224.08108764689 | etot = -180.770700642424 +46000 ekin = 21.7855632553132 | erot = 21.2036013766601 | epot = -223.75986526006 | etot = -180.770700628087 +47000 ekin = 21.5167766971454 | erot = 21.0656367023669 | epot = -223.353114011014 | etot = -180.770700611502 +48000 ekin = 21.4540196107332 | erot = 20.8430832424325 | epot = -223.067803499524 | etot = -180.770700646358 +49000 ekin = 21.3647564765273 | erot = 20.5521507191689 | epot = -222.68760781692 | etot = -180.770700621224 +50000 ekin = 21.3125768184616 | erot = 20.2526464671335 | epot = -222.335923904309 | etot = -180.770700618713 +51000 ekin = 21.2949924810833 | erot = 19.9798421626046 | epot = -222.045535260403 | etot = -180.770700616715 +52000 ekin = 21.313714424968 | erot = 19.762769134369 | epot = -221.847184173962 | etot = -180.770700614625 +53000 ekin = 21.3664076685101 | erot = 19.6202359856903 | epot = -221.757344279694 | etot = -180.770700625493 +54000 ekin = 21.4214245524056 | erot = 19.5588232319504 | epot = -221.750948393747 | etot = -180.770700609391 +55000 ekin = 21.5995673396088 | erot = 19.5805214885682 | epot = -221.950789453583 | etot = -180.770700625406 +56000 ekin = 21.7643125668302 | erot = 19.6816042107783 | epot = -222.216617401428 | etot = -180.77070062382 +57000 ekin = 21.922130908444 | erot = 19.8499880475958 | epot = -222.542819582063 | etot = -180.770700626024 +58000 ekin = 22.0666093644387 | erot = 20.0713856445721 | epot = -222.908695636277 | etot = -180.770700627266 +59000 ekin = 22.1910921687945 | erot = 20.3284024096015 | epot = -223.290195207095 | etot = -180.770700628699 +60000 ekin = 22.2920682490233 | erot = 20.6003319531545 | epot = -223.663100832376 | etot = -180.770700630198 +61000 ekin = 22.3680528265786 | erot = 20.8645614198866 | epot = -224.003314878046 | etot = -180.77070063158 +62000 ekin = 22.4198570332631 | erot = 21.0983714926633 | epot = -224.288929158679 | etot = -180.770700632752 +63000 ekin = 22.450080073992 | erot = 21.28155214409 | epot = -224.502332851296 | etot = -180.770700633215 +64000 ekin = 22.4634052763983 | erot = 21.3990470998282 | epot = -224.633153009903 | etot = -180.770700633676 +65000 ekin = 22.4639885390964 | erot = 21.4413332838528 | epot = -224.676022456447 | etot = -180.770700633498 +66000 ekin = 22.4559522488544 | erot = 21.4074154510867 | epot = -224.634068332758 | etot = -180.770700632817 +67000 ekin = 22.4417384097826 | erot = 21.3051580893564 | epot = -224.517597130738 | etot = -180.770700631599 +68000 ekin = 22.421878544646 | erot = 21.1490017805243 | epot = -224.34158095606 | etot = -180.77070063089 +69000 ekin = 22.3954651199576 | erot = 20.9555571676358 | epot = -224.121722917263 | etot = -180.770700629669 +70000 ekin = 22.3613349801193 | erot = 20.7433545871758 | epot = -223.875390195706 | etot = -180.770700628411 +71000 ekin = 22.3171019087139 | erot = 20.5301141425049 | epot = -223.617916679045 | etot = -180.770700627826 +72000 ekin = 22.2595195485147 | erot = 20.3296309382964 | epot = -223.359851114099 | etot = -180.770700627288 +73000 ekin = 22.1869461213877 | erot = 20.1521902584588 | epot = -223.109837006429 | etot = -180.770700626583 +74000 ekin = 22.0990935565683 | erot = 20.0059494138149 | epot = -222.875743596756 | etot = -180.770700626373 +75000 ekin = 21.9959491639282 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795 +76000 ekin = 21.8806005890445 | erot = 19.828424336326 | epot = -222.479725550679 | etot = -180.770700625308 +77000 ekin = 21.7590261899809 | erot = 19.8043252195864 | epot = -222.334052034216 | etot = -180.770700624649 +78000 ekin = 21.6392419839503 | erot = 19.8262630279236 | epot = -222.236205635986 | etot = -180.770700624113 +79000 ekin = 21.5302317519716 | erot = 19.8938812521576 | epot = -222.194813627769 | etot = -180.77070062364 +80000 ekin = 21.4402276725657 | erot = 20.0060100278943 | epot = -222.216938324074 | etot = -180.770700623614 +81000 ekin = 21.3741486759855 | erot = 20.158514479161 | epot = -222.303363779439 | etot = -180.770700624292 +82000 ekin = 21.3325013763505 | erot = 20.3431413542724 | epot = -222.44634335588 | etot = -180.770700625257 +83000 ekin = 21.3128808684037 | erot = 20.548330990772 | epot = -222.631912485779 | etot = -180.770700626604 +84000 ekin = 21.310766170793 | erot = 20.7607919785174 | epot = -222.842258777119 | etot = -180.770700627809 +85000 ekin = 21.3216301567277 | erot = 20.9678418539246 | epot = -223.060172639485 | etot = -180.770700628833 +86000 ekin = 21.3400295156723 | erot = 21.1566564817957 | epot = -223.267386627523 | etot = -180.770700630055 +87000 ekin = 21.3617783036992 | erot = 21.3170902458394 | epot = -223.449569179882 | etot = -180.770700630344 +88000 ekin = 21.3873913218409 | erot = 21.445443991042 | epot = -223.603535942848 | etot = -180.770700629965 +89000 ekin = 21.421574069399 | erot = 21.5439953706456 | epot = -223.736270068948 | etot = -180.770700628904 +90000 ekin = 21.4723781618091 | erot = 21.6216769093347 | epot = -223.86475569847 | etot = -180.770700627326 +91000 ekin = 21.549406625472 | erot = 21.6927202486463 | epot = -224.012827499723 | etot = -180.770700625604 +92000 ekin = 21.6619209347597 | erot = 21.7730744493012 | epot = -224.205696008348 | etot = -180.770700624287 +93000 ekin = 21.8158778641472 | erot = 21.8756732628048 | epot = -224.462251750825 | etot = -180.770700623873 +94000 ekin = 22.0110275730997 | erot = 22.0060799403022 | epot = -224.787808138196 | etot = -180.770700624794 +95000 ekin = 22.2387555838384 | erot = 22.1596167137192 | epot = -225.16907292429 | etot = -180.770700626733 +96000 ekin = 22.4832444899361 | erot = 22.3220202374401 | epot = -225.575965356875 | etot = -180.770700629499 +97000 ekin = 22.7237276202693 | erot = 22.4720556690122 | epot = -225.966483921719 | etot = -180.770700632437 +98000 ekin = 22.9377647716041 | erot = 22.5858660312277 | epot = -226.294331437118 | etot = -180.770700634287 +99000 ekin = 23.1071231637237 | erot = 22.6457411046184 | epot = -226.523564904806 | etot = -180.770700636464 +100000 ekin = 23.2156001924311 | erot = 22.6390310936006 | epot = -226.625331923822 | etot = -180.770700637791 + 100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000 +Loop time of 83.9672 on 1 procs for 100000 steps with 148 atoms + +Performance: 1028.974 tau/day, 1190.942 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 80.885 | 80.885 | 80.885 | 0.0 | 96.33 +Bond | 0.94789 | 0.94789 | 0.94789 | 0.0 | 1.13 +Neigh | 0.011589 | 0.011589 | 0.011589 | 0.0 | 0.01 +Comm | 0.045979 | 0.045979 | 0.045979 | 0.0 | 0.05 +Output | 0.11973 | 0.11973 | 0.11973 | 0.0 | 0.14 +Modify | 1.8641 | 1.8641 | 1.8641 | 0.0 | 2.22 +Other | | 0.09239 | | | 0.11 + +Nlocal: 148.000 ave 148 max 148 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4199.00 ave 4199 max 4199 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4199 +Ave neighs/atom = 28.371622 +Ave special neighs/atom = 6.0000000 +Neighbor list builds = 100 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.5.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:01:23 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 new file mode 100644 index 0000000000..d2a1b84c3d --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 @@ -0,0 +1,281 @@ +LAMMPS (2 Jul 2021) +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 148 atoms + reading velocities ... + 148 velocities + scanning bonds ... + 1 = max bonds/atom + 148 ellipsoids + reading bonds ... + 148 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds + +set atom * mass 3.1575 +Setting atom values ... + 148 settings made for mass + +group all type 1 4 +148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 36 36 36 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889 +Per MPI rank memory allocation (min/avg/max) = 9.383 | 9.432 | 9.506 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000 +1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183 +2000 ekin = 20.585620972069 | erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104 +3000 ekin = 20.6239332104643 | erot = 21.5529389082727 | epot = -222.947572771312 | etot = -180.770700652575 +4000 ekin = 20.6395549184482 | erot = 21.6854113323894 | epot = -223.095666904229 | etot = -180.770700653391 +5000 ekin = 20.6295551742564 | erot = 21.7809539301804 | epot = -223.181209757876 | etot = -180.770700653439 +6000 ekin = 20.5959625511847 | erot = 21.8369756530726 | epot = -223.203638857302 | etot = -180.770700653045 +7000 ekin = 20.5431034482069 | erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652123 +8000 ekin = 20.4774701419093 | erot = 21.8437134145373 | epot = -223.09188420739 | etot = -180.770700650943 +9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649598 +10000 ekin = 20.3427303660297 | erot = 21.7629575866662 | epot = -222.876388600949 | etot = -180.770700648253 +11000 ekin = 20.2927407149578 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.77070064719 +12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383222 | etot = -180.770700646287 +13000 ekin = 20.2733920359447 | erot = 21.6092715397933 | epot = -222.653364221617 | etot = -180.770700645879 +14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.77070064567 +15000 ekin = 20.410400937429 | erot = 21.5031572556307 | epot = -222.684258838858 | etot = -180.770700645799 +16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272037 | etot = -180.770700646753 +17000 ekin = 20.7266657908773 | erot = 21.3426631585218 | epot = -222.840029597232 | etot = -180.770700647833 +18000 ekin = 20.9417612759978 | erot = 21.2178611180927 | epot = -222.930323042998 | etot = -180.770700648907 +19000 ekin = 21.1819308659396 | erot = 21.0532289630294 | epot = -223.005860478921 | etot = -180.770700649952 +20000 ekin = 21.4358169889472 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.77070064997 +21000 ekin = 21.6968513750995 | erot = 20.6066744652585 | epot = -223.074226489837 | etot = -180.770700649479 +22000 ekin = 21.9614458442779 | erot = 20.3429420444508 | epot = -223.075088537371 | etot = -180.770700648642 +23000 ekin = 22.2276099755697 | erot = 20.070338516524 | epot = -223.068649139875 | etot = -180.770700647781 +24000 ekin = 22.4935893196667 | erot = 19.8020671721661 | epot = -223.066357139277 | etot = -180.770700647444 +25000 ekin = 22.756606454822 | erot = 19.5464828008836 | epot = -223.073789902976 | etot = -180.77070064727 +26000 ekin = 23.0126717548391 | erot = 19.3065017718461 | epot = -223.089874174572 | etot = -180.770700647887 +27000 ekin = 23.2550417060586 | erot = 19.0797753474566 | epot = -223.105517701932 | etot = -180.770700648417 +28000 ekin = 23.4774329734797 | erot = 18.8646197299572 | epot = -223.112753352067 | etot = -180.77070064863 +29000 ekin = 23.6747927720654 | erot = 18.6628653411822 | epot = -223.108358761694 | etot = -180.770700648446 +30000 ekin = 23.8432321400238 | erot = 18.4812216983633 | epot = -223.095154486375 | etot = -180.770700647988 +31000 ekin = 23.979304175222 | erot = 18.3307845334015 | epot = -223.08078935577 | etot = -180.770700647146 +32000 ekin = 24.0810246040226 | erot = 18.2261577055998 | epot = -223.077882955919 | etot = -180.770700646297 +33000 ekin = 24.1468986449389 | erot = 18.1820705445401 | epot = -223.09966983514 | etot = -180.770700645661 +34000 ekin = 24.1756615132855 | erot = 18.2103812210167 | epot = -223.156743379607 | etot = -180.770700645304 +35000 ekin = 24.1663193894644 | erot = 18.3185351073563 | epot = -223.255555142089 | etot = -180.770700645269 +36000 ekin = 24.1167205812957 | erot = 18.5091649894184 | epot = -223.396586216223 | etot = -180.770700645509 +37000 ekin = 24.0274860006128 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646226 +38000 ekin = 23.8991479078978 | erot = 19.1166063146994 | epot = -223.786454869891 | etot = -180.770700647293 +39000 ekin = 23.7326911853231 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648764 +40000 ekin = 23.5294223072117 | erot = 19.9254673141828 | epot = -224.225590272293 | etot = -180.770700650899 +41000 ekin = 23.289939614139 | erot = 20.3408097780563 | epot = -224.401450045568 | etot = -180.770700653372 +42000 ekin = 23.0154529235022 | erot = 20.7165619564848 | epot = -224.502715535762 | etot = -180.770700655775 +43000 ekin = 22.7111536814277 | erot = 21.0163895622231 | epot = -224.498243901359 | etot = -180.770700657708 +44000 ekin = 22.3710575806355 | erot = 21.2060371289783 | epot = -224.347795365754 | etot = -180.77070065614 +45000 ekin = 22.0515843162889 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425 +46000 ekin = 21.7855632553133 | erot = 21.20360137666 | epot = -223.759865260062 | etot = -180.770700628089 +47000 ekin = 21.5167766971456 | erot = 21.0656367023667 | epot = -223.353114011016 | etot = -180.770700611503 +48000 ekin = 21.4540196107333 | erot = 20.8430832424321 | epot = -223.067803499525 | etot = -180.77070064636 +49000 ekin = 21.3647564765274 | erot = 20.5521507191682 | epot = -222.687607816922 | etot = -180.770700621226 +50000 ekin = 21.3125768184617 | erot = 20.2526464671325 | epot = -222.33592390431 | etot = -180.770700618715 +51000 ekin = 21.2949924810834 | erot = 19.9798421626035 | epot = -222.045535260404 | etot = -180.770700616717 +52000 ekin = 21.3137144249679 | erot = 19.7627691343679 | epot = -221.847184173963 | etot = -180.770700614627 +53000 ekin = 21.3664076685099 | erot = 19.6202359856891 | epot = -221.757344279695 | etot = -180.770700625496 +54000 ekin = 21.4214245524052 | erot = 19.5588232319492 | epot = -221.750948393748 | etot = -180.770700609393 +55000 ekin = 21.5995673396082 | erot = 19.580521488567 | epot = -221.950789453583 | etot = -180.770700625408 +56000 ekin = 21.7643125668294 | erot = 19.681604210777 | epot = -222.216617401429 | etot = -180.770700623823 +57000 ekin = 21.922130908443 | erot = 19.8499880475945 | epot = -222.542819582064 | etot = -180.770700626026 +58000 ekin = 22.0666093644375 | erot = 20.0713856445709 | epot = -222.908695636278 | etot = -180.770700627269 +59000 ekin = 22.1910921687932 | erot = 20.3284024096003 | epot = -223.290195207095 | etot = -180.770700628702 +60000 ekin = 22.2920682490219 | erot = 20.6003319531534 | epot = -223.663100832376 | etot = -180.770700630201 +61000 ekin = 22.3680528265772 | erot = 20.8645614198856 | epot = -224.003314878046 | etot = -180.770700631583 +62000 ekin = 22.4198570332617 | erot = 21.0983714926625 | epot = -224.288929158679 | etot = -180.770700632755 +63000 ekin = 22.4500800739905 | erot = 21.2815521440892 | epot = -224.502332851297 | etot = -180.770700633217 +64000 ekin = 22.4634052763968 | erot = 21.3990470998276 | epot = -224.633153009904 | etot = -180.770700633679 +65000 ekin = 22.463988539095 | erot = 21.4413332838523 | epot = -224.676022456448 | etot = -180.770700633501 +66000 ekin = 22.4559522488531 | erot = 21.4074154510864 | epot = -224.634068332759 | etot = -180.770700632819 +67000 ekin = 22.4417384097814 | erot = 21.3051580893563 | epot = -224.517597130739 | etot = -180.770700631601 +68000 ekin = 22.4218785446449 | erot = 21.1490017805243 | epot = -224.341580956061 | etot = -180.770700630892 +69000 ekin = 22.3954651199567 | erot = 20.9555571676359 | epot = -224.121722917264 | etot = -180.770700629671 +70000 ekin = 22.3613349801186 | erot = 20.743354587176 | epot = -223.875390195707 | etot = -180.770700628413 +71000 ekin = 22.3171019087134 | erot = 20.5301141425052 | epot = -223.617916679047 | etot = -180.770700627829 +72000 ekin = 22.2595195485144 | erot = 20.3296309382966 | epot = -223.3598511141 | etot = -180.77070062729 +73000 ekin = 22.1869461213875 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626585 +74000 ekin = 22.0990935565682 | erot = 20.0059494138151 | epot = -222.875743596758 | etot = -180.770700626375 +75000 ekin = 21.9959491639282 | erot = 19.8965902063257 | epot = -222.663239996051 | etot = -180.770700625797 +76000 ekin = 21.8806005890446 | erot = 19.8284243363261 | epot = -222.479725550681 | etot = -180.77070062531 +77000 ekin = 21.759026189981 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.770700624651 +78000 ekin = 21.6392419839505 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114 +79000 ekin = 21.5302317519718 | erot = 19.8938812521574 | epot = -222.19481362777 | etot = -180.770700623641 +80000 ekin = 21.4402276725659 | erot = 20.0060100278939 | epot = -222.216938324075 | etot = -180.770700623615 +81000 ekin = 21.3741486759857 | erot = 20.1585144791605 | epot = -222.303363779439 | etot = -180.770700624293 +82000 ekin = 21.3325013763506 | erot = 20.3431413542717 | epot = -222.446343355881 | etot = -180.770700625259 +83000 ekin = 21.3128808684039 | erot = 20.5483309907712 | epot = -222.63191248578 | etot = -180.770700626605 +84000 ekin = 21.3107661707932 | erot = 20.7607919785166 | epot = -222.842258777119 | etot = -180.77070062781 +85000 ekin = 21.3216301567279 | erot = 20.9678418539237 | epot = -223.060172639486 | etot = -180.770700628834 +86000 ekin = 21.3400295156725 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630057 +87000 ekin = 21.3617783036995 | erot = 21.3170902458388 | epot = -223.449569179883 | etot = -180.770700630345 +88000 ekin = 21.3873913218413 | erot = 21.4454439910414 | epot = -223.603535942849 | etot = -180.770700629967 +89000 ekin = 21.4215740693994 | erot = 21.5439953706451 | epot = -223.73627006895 | etot = -180.770700628906 +90000 ekin = 21.4723781618096 | erot = 21.6216769093343 | epot = -223.864755698472 | etot = -180.770700627328 +91000 ekin = 21.5494066254725 | erot = 21.6927202486459 | epot = -224.012827499725 | etot = -180.770700625606 +92000 ekin = 21.6619209347601 | erot = 21.7730744493007 | epot = -224.20569600835 | etot = -180.77070062429 +93000 ekin = 21.8158778641474 | erot = 21.8756732628043 | epot = -224.462251750827 | etot = -180.770700623875 +94000 ekin = 22.0110275730999 | erot = 22.0060799403016 | epot = -224.787808138198 | etot = -180.770700624796 +95000 ekin = 22.2387555838384 | erot = 22.1596167137185 | epot = -225.169072924291 | etot = -180.770700626735 +96000 ekin = 22.4832444899359 | erot = 22.3220202374394 | epot = -225.575965356876 | etot = -180.770700629501 +97000 ekin = 22.7237276202691 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632439 +98000 ekin = 22.9377647716038 | erot = 22.5858660312271 | epot = -226.294331437119 | etot = -180.770700634288 +99000 ekin = 23.1071231637233 | erot = 22.645741104618 | epot = -226.523564904806 | etot = -180.770700636465 +100000 ekin = 23.2156001924307 | erot = 22.6390310936004 | epot = -226.625331923823 | etot = -180.770700637791 + 100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000 +Loop time of 28.0802 on 4 procs for 100000 steps with 148 atoms + +Performance: 3076.899 tau/day, 3561.226 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.209 | 21.356 | 25.248 | 81.3 | 76.05 +Bond | 0.26072 | 0.26526 | 0.27015 | 0.9 | 0.94 +Neigh | 0.005772 | 0.0058625 | 0.005932 | 0.1 | 0.02 +Comm | 1.7227 | 5.6246 | 10.79 | 158.9 | 20.03 +Output | 0.043943 | 0.046855 | 0.048664 | 0.9 | 0.17 +Modify | 0.54715 | 0.55336 | 0.55902 | 0.7 | 1.97 +Other | | 0.2279 | | | 0.81 + +Nlocal: 37.0000 ave 38 max 36 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 111.000 ave 112 max 110 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 1049.75 ave 1270 max 757 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 4199 +Ave neighs/atom = 28.371622 +Ave special neighs/atom = 6.0000000 +Neighbor list builds = 100 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.5.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:28 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 new file mode 100644 index 0000000000..54eb2beaf5 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file via write_data, version 27 May 2021 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0 +2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0 +3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0 +4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0 +5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0 +6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0 +7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0 +8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0 +9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0 +10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397 +2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385 +3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783 +4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775 +5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883 +6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354 +7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567 +8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627 +9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048 +10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 similarity index 65% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 index 6ae8df4ff2..72735fbf5f 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 @@ -2,20 +2,21 @@ variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 +variable rhos equal 0.2 units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 1 delay 0 check yes read_data data.duplex1 @@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 # NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" +compute quat all property/atom quatw quati quatj quatk compute erot all erotate/asphere compute ekin all ke @@ -72,10 +62,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" run 1000000 -#write_restart config.${number}.* +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 new file mode 100644 index 0000000000..c73ab7ca61 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 @@ -0,0 +1,1181 @@ +LAMMPS (2 Jul 2021) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +set atom * mass 3.1575 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -12.298895791142 | etot = -8.37462296864751 +Per MPI rank memory allocation (min/avg/max) = 9.198 | 9.198 | 9.198 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3370157 0.10712616 -1.1190359 -6.6192825e-05 64000 +1000 ekin = 1.07640077431763 | erot = 2.90684392233817 | epot = -12.357867665527 | etot = -8.37462296887116 +2000 ekin = 1.05363107794411 | erot = 2.99414178935849 | epot = -12.4223958364622 | etot = -8.37462296915965 +3000 ekin = 1.04083382823095 | erot = 3.07274362339771 | epot = -12.4882004210899 | etot = -8.37462296946123 +4000 ekin = 1.03780093165924 | erot = 3.13815143503914 | epot = -12.550575336422 | etot = -8.37462296972364 +5000 ekin = 1.04371581655899 | erot = 3.18681185449856 | epot = -12.6051506409707 | etot = -8.37462296991315 +6000 ekin = 1.05738085799295 | erot = 3.21642353087479 | epot = -12.6484273588876 | etot = -8.37462297001983 +7000 ekin = 1.07739394884042 | erot = 3.22597832036696 | epot = -12.677995239256 | etot = -8.37462297004867 +8000 ekin = 1.10226637472087 | erot = 3.21563966301732 | epot = -12.6925290077505 | etot = -8.37462297001231 +9000 ekin = 1.13051291055326 | erot = 3.18656247631366 | epot = -12.6916983567816 | etot = -8.37462296991465 +10000 ekin = 1.16073704358063 | erot = 3.14076972913372 | epot = -12.6761297424775 | etot = -8.37462296976311 +11000 ekin = 1.19170449380505 | erot = 3.08098965164652 | epot = -12.6473171150236 | etot = -8.37462296957204 +12000 ekin = 1.22238189802729 | erot = 3.01040253468266 | epot = -12.6074074020775 | etot = -8.37462296936753 +13000 ekin = 1.25192691881487 | erot = 2.93230261872824 | epot = -12.5588525067181 | etot = -8.37462296917498 +14000 ekin = 1.27963857618757 | erot = 2.84975156813381 | epot = -12.5040131133432 | etot = -8.37462296902179 +15000 ekin = 1.30489368750123 | erot = 2.76534813925014 | epot = -12.444864795638 | etot = -8.37462296888666 +16000 ekin = 1.32709913751461 | erot = 2.6811818478553 | epot = -12.3829039541517 | etot = -8.37462296878182 +17000 ekin = 1.34568132349844 | erot = 2.5986128569079 | epot = -12.3189171492215 | etot = -8.37462296881515 +18000 ekin = 1.36011712604124 | erot = 2.51802979978579 | epot = -12.2527698947086 | etot = -8.37462296888154 +19000 ekin = 1.3700055901564 | erot = 2.43889875259719 | epot = -12.1835273117078 | etot = -8.37462296895424 +20000 ekin = 1.37516683465212 | erot = 2.36049590954913 | epot = -12.1102857132061 | etot = -8.37462296900481 +21000 ekin = 1.37575335509454 | erot = 2.28221618930094 | epot = -12.0325925134033 | etot = -8.37462296900785 +22000 ekin = 1.37235802310946 | erot = 2.20383846967473 | epot = -11.9508194617285 | etot = -8.37462296894431 +23000 ekin = 1.36610326249347 | erot = 2.12570839352804 | epot = -11.8664346248253 | etot = -8.37462296880382 +24000 ekin = 1.35869525710689 | erot = 2.04881568638621 | epot = -11.7821339120795 | etot = -8.3746229685864 +25000 ekin = 1.35242255125593 | erot = 1.97475968439782 | epot = -11.7018052039589 | etot = -8.37462296830517 +26000 ekin = 1.3500701244009 | erot = 1.90560954362746 | epot = -11.6303026360115 | etot = -8.37462296798316 +27000 ekin = 1.35474332970461 | erot = 1.843676291157 | epot = -11.573042588521 | etot = -8.37462296765941 +28000 ekin = 1.36954369410747 | erot = 1.79121252282618 | epot = -11.5353791843194 | etot = -8.37462296738577 +29000 ekin = 1.39711560919894 | erot = 1.75006009044062 | epot = -11.5217986668613 | etot = -8.37462296722172 +30000 ekin = 1.43911092490998 | erot = 1.72127833748021 | epot = -11.5350122296156 | etot = -8.37462296722543 +31000 ekin = 1.49567630461185 | erot = 1.70480588615783 | epot = -11.5751051582055 | etot = -8.37462296743583 +32000 ekin = 1.56511285114173 | erot = 1.69923538983358 | epot = -11.6389712088327 | etot = -8.37462296785736 +33000 ekin = 1.64385110263233 | erot = 1.70198396265071 | epot = -11.7204580336836 | etot = -8.37462296840058 +34000 ekin = 1.72681002365018 | erot = 1.70946314344897 | epot = -11.8108961361853 | etot = -8.37462296908616 +35000 ekin = 1.80812188596362 | erot = 1.71712980816865 | epot = -11.8998746638723 | etot = -8.37462296974007 +36000 ekin = 1.88201893971536 | erot = 1.72067857993906 | epot = -11.9773204899106 | etot = -8.37462297025618 +37000 ekin = 1.94364733336808 | erot = 1.71680208569968 | epot = -12.0350723896309 | etot = -8.37462297056312 +38000 ekin = 1.98961498615624 | erot = 1.70370907929488 | epot = -12.0679470360927 | etot = -8.37462297064162 +39000 ekin = 2.01818359901078 | erot = 1.68126711282219 | epot = -12.0740736823535 | etot = -8.37462297052054 +40000 ekin = 2.02914332282544 | erot = 1.65077260628057 | epot = -12.0545388993641 | etot = -8.37462297025811 +41000 ekin = 2.02349103018079 | erot = 1.61448262351112 | epot = -12.012596623611 | etot = -8.37462296991906 +42000 ekin = 2.00304412554487 | erot = 1.57509121259578 | epot = -11.9527583076989 | etot = -8.37462296955828 +43000 ekin = 1.97008148028931 | erot = 1.5352951062099 | epot = -11.8799995557137 | etot = -8.3746229692145 +44000 ekin = 1.92705109571046 | erot = 1.49750726070831 | epot = -11.7991813253589 | etot = -8.37462296894018 +45000 ekin = 1.87634986385838 | erot = 1.46354390598906 | epot = -11.714516738533 | etot = -8.37462296868559 +46000 ekin = 1.82016797429729 | erot = 1.43491031451222 | epot = -11.6297012572909 | etot = -8.37462296848135 +47000 ekin = 1.76039182008996 | erot = 1.41286016407003 | epot = -11.5478749524839 | etot = -8.37462296832397 +48000 ekin = 1.69856949274756 | erot = 1.39838217522426 | epot = -11.4715746361766 | etot = -8.37462296820474 +49000 ekin = 1.6359395498873 | erot = 1.39228918140579 | epot = -11.4028516994048 | etot = -8.37462296811169 +50000 ekin = 1.57351801537284 | erot = 1.39530041169495 | epot = -11.3434413950981 | etot = -8.37462296803028 +51000 ekin = 1.51222872476347 | erot = 1.40810650340941 | epot = -11.2949581961199 | etot = -8.37462296794708 +52000 ekin = 1.45305245526488 | erot = 1.43140550730924 | epot = -11.2590809304256 | etot = -8.37462296785146 +53000 ekin = 1.39716366086918 | erot = 1.46589567493529 | epot = -11.2376823035411 | etot = -8.37462296773663 +54000 ekin = 1.34602153837047 | erot = 1.51222067984183 | epot = -11.2328651858297 | etot = -8.37462296761736 +55000 ekin = 1.30138436197332 | erot = 1.57077970891814 | epot = -11.2467870384005 | etot = -8.37462296750909 +56000 ekin = 1.26522647192232 | erot = 1.64151101613075 | epot = -11.2813604554938 | etot = -8.37462296744077 +57000 ekin = 1.23956119808437 | erot = 1.72363092633031 | epot = -11.337815091859 | etot = -8.37462296744431 +58000 ekin = 1.22620283906725 | erot = 1.81539828229235 | epot = -11.4162240889032 | etot = -8.3746229675436 +59000 ekin = 1.22652758768648 | erot = 1.91400381193546 | epot = -11.5151543673675 | etot = -8.37462296774558 +60000 ekin = 1.24129579501613 | erot = 2.01564970996742 | epot = -11.6315684730212 | etot = -8.37462296803768 +61000 ekin = 1.27057003505312 | erot = 2.11581304358673 | epot = -11.7610060470473 | etot = -8.37462296840743 +62000 ekin = 1.31372115356085 | erot = 2.20955642503253 | epot = -11.8979005473869 | etot = -8.37462296879357 +63000 ekin = 1.36947667734256 | erot = 2.29224896410242 | epot = -12.0363486106153 | etot = -8.37462296917035 +64000 ekin = 1.43596184816363 | erot = 2.35998108781816 | epot = -12.1705659055152 | etot = -8.37462296953339 +65000 ekin = 1.5108757081497 | erot = 2.40947275989103 | epot = -12.294971437873 | etot = -8.37462296983226 +66000 ekin = 1.59162978656338 | erot = 2.43872351537743 | epot = -12.404976271986 | etot = -8.37462297004522 +67000 ekin = 1.67546349074575 | erot = 2.4472618699926 | epot = -12.4973483309005 | etot = -8.37462297016214 +68000 ekin = 1.75953613825208 | erot = 2.43621057967599 | epot = -12.5703696881156 | etot = -8.37462297018751 +69000 ekin = 1.84098201456571 | erot = 2.40815676459644 | epot = -12.6237617493037 | etot = -8.37462297014158 +70000 ekin = 1.91692810522256 | erot = 2.36682660300834 | epot = -12.6583776782867 | etot = -8.37462297005584 +71000 ekin = 1.98449380473026 | erot = 2.31661131420489 | epot = -12.6757280888525 | etot = -8.37462296991739 +72000 ekin = 2.04081287193495 | erot = 2.26215174487671 | epot = -12.6775875867425 | etot = -8.37462296993079 +73000 ekin = 2.08263291328341 | erot = 2.2074336386418 | epot = -12.6646895218716 | etot = -8.37462296994644 +74000 ekin = 2.10698584150829 | erot = 2.15544421118361 | epot = -12.6370530226944 | etot = -8.37462297000245 +75000 ekin = 2.11136525908711 | erot = 2.10816940675056 | epot = -12.5941576359035 | etot = -8.37462297006578 +76000 ekin = 2.09405873141393 | erot = 2.06669472630755 | epot = -12.535376427811 | etot = -8.37462297008955 +77000 ekin = 2.05455135347901 | erot = 2.03147933575638 | epot = -12.4606536592623 | etot = -8.37462297002688 +78000 ekin = 1.99386684227692 | erot = 2.00268171013299 | epot = -12.3711715222582 | etot = -8.37462296984828 +79000 ekin = 1.91474155283387 | erot = 1.98040758803641 | epot = -12.2697721104227 | etot = -8.37462296955247 +80000 ekin = 1.82155513477569 | erot = 1.96479734780216 | epot = -12.1609754517455 | etot = -8.37462296916766 +81000 ekin = 1.71999782481688 | erot = 1.95595086125338 | epot = -12.0505716548134 | etot = -8.37462296874317 +82000 ekin = 1.61651478139496 | erot = 1.95375810375259 | epot = -11.9448958534856 | etot = -8.37462296833801 +83000 ekin = 1.51761134750078 | erot = 1.9577277486063 | epot = -11.8499620641159 | etot = -8.37462296800882 +84000 ekin = 1.42912416355165 | erot = 1.96688313409194 | epot = -11.7706302654422 | etot = -8.37462296779863 +85000 ekin = 1.35556895555397 | erot = 1.97976517498676 | epot = -11.7099570982742 | etot = -8.37462296773344 +86000 ekin = 1.29966988136848 | erot = 1.99452593271691 | epot = -11.6688187819009 | etot = -8.37462296781547 +87000 ekin = 1.26213747948968 | erot = 2.00910214170779 | epot = -11.6458625892978 | etot = -8.3746229681003 +88000 ekin = 1.24134500163873 | erot = 2.02122064243461 | epot = -11.6371886124846 | etot = -8.37462296841123 +89000 ekin = 1.23421644947624 | erot = 2.02900530500587 | epot = -11.6378447232196 | etot = -8.37462296873754 +90000 ekin = 1.2369060424358 | erot = 2.03136372571833 | epot = -11.6428927371716 | etot = -8.37462296901748 +91000 ekin = 1.24531053049757 | erot = 2.02816188261836 | epot = -11.6480953823213 | etot = -8.37462296920538 +92000 ekin = 1.2556439422707 | erot = 2.02032873397327 | epot = -11.6505956455254 | etot = -8.37462296928141 +93000 ekin = 1.26484018817427 | erot = 2.00975004471085 | epot = -11.6492132021398 | etot = -8.37462296925464 +94000 ekin = 1.27076152680841 | erot = 1.99896253062549 | epot = -11.6443470265804 | etot = -8.3746229691465 +95000 ekin = 1.27224696211181 | erot = 1.99076889271338 | epot = -11.6376388238184 | etot = -8.37462296899321 +96000 ekin = 1.26905385172917 | erot = 1.98776908505807 | epot = -11.6314459056163 | etot = -8.37462296882905 +97000 ekin = 1.26173398384347 | erot = 1.99196117307496 | epot = -11.628318125602 | etot = -8.37462296868355 +98000 ekin = 1.25146122958142 | erot = 2.00445279489013 | epot = -11.6305369930529 | etot = -8.37462296858135 +99000 ekin = 1.23981039935408 | erot = 2.02529911459885 | epot = -11.6397324824951 | etot = -8.37462296854214 +100000 ekin = 1.22848889431686 | erot = 2.05346079777955 | epot = -11.6565726606777 | etot = -8.37462296858124 +101000 ekin = 1.21904296342426 | erot = 2.08686922543178 | epot = -11.6805351575624 | etot = -8.37462296870635 +102000 ekin = 1.21258708443142 | erot = 2.12259257652707 | epot = -11.7098026298712 | etot = -8.37462296891269 +103000 ekin = 1.20962138127609 | erot = 2.15710417867589 | epot = -11.7413485291306 | etot = -8.37462296917863 +104000 ekin = 1.20999435064749 | erot = 2.18665201736524 | epot = -11.7712693374785 | etot = -8.37462296946577 +105000 ekin = 1.21303379771948 | erot = 2.20771017012375 | epot = -11.7953669375665 | etot = -8.37462296972326 +106000 ekin = 1.21781939160539 | erot = 2.21746426398198 | epot = -11.8099066254851 | etot = -8.37462296989777 +107000 ekin = 1.22352668485511 | erot = 2.21425769941191 | epot = -11.8124073542125 | etot = -8.37462296994543 +108000 ekin = 1.22975371616707 | erot = 2.19791821277296 | epot = -11.8022948987809 | etot = -8.37462296984092 +109000 ekin = 1.23675326669538 | erot = 2.16990174522961 | epot = -11.781277981508 | etot = -8.37462296958301 +110000 ekin = 1.24552660594304 | erot = 2.13322593016559 | epot = -11.7533755053021 | etot = -8.37462296919346 +111000 ekin = 1.2577699492819 | erot = 2.09220325002851 | epot = -11.7245961680235 | etot = -8.37462296871309 +112000 ekin = 1.27568807280479 | erot = 2.05200951342181 | epot = -11.7023205544238 | etot = -8.37462296819724 +113000 ekin = 1.30169744977575 | erot = 2.01813224570252 | epot = -11.6944526631898 | etot = -8.37462296771154 +114000 ekin = 1.33804251858973 | erot = 1.99574344242881 | epot = -11.7084089283454 | etot = -8.3746229673269 +115000 ekin = 1.3864743192957 | erot = 1.98903581447781 | epot = -11.750133100834 | etot = -8.37462296706049 +116000 ekin = 1.44876446583433 | erot = 2.00047074173032 | epot = -11.8238581746956 | etot = -8.37462296713092 +117000 ekin = 1.52378581535601 | erot = 2.03044339408209 | epot = -11.9288521768895 | etot = -8.37462296745144 +118000 ekin = 1.60840594184234 | erot = 2.07707436259026 | epot = -12.0601032724464 | etot = -8.3746229680138 +119000 ekin = 1.69804077960537 | erot = 2.13624566567642 | epot = -12.208909414054 | etot = -8.3746229687722 +120000 ekin = 1.78696647862329 | erot = 2.20199105617507 | epot = -12.3635805044452 | etot = -8.37462296964685 +121000 ekin = 1.86883508536353 | erot = 2.26718837407865 | epot = -12.5106464299777 | etot = -8.37462297053554 +122000 ekin = 1.93731263285391 | erot = 2.32446087034982 | epot = -12.6363964745349 | etot = -8.37462297133115 +123000 ekin = 1.98673587945814 | erot = 2.3671448998553 | epot = -12.7285037512518 | etot = -8.37462297193835 +124000 ekin = 2.01268857483506 | erot = 2.39015976226587 | epot = -12.77747130939 | etot = -8.37462297228912 +125000 ekin = 2.01242153120634 | erot = 2.3906292535681 | epot = -12.7776737571268 | etot = -8.37462297235236 +126000 ekin = 1.98507290328086 | erot = 2.36815351492882 | epot = -12.7278493903459 | etot = -8.37462297213621 +127000 ekin = 1.93167931643415 | erot = 2.32470375634614 | epot = -12.6310060444627 | etot = -8.37462297168245 +128000 ekin = 1.85500076916878 | erot = 2.26419178968044 | epot = -12.4938155299045 | etot = -8.37462297105528 +129000 ekin = 1.75920795598134 | erot = 2.19182812292603 | epot = -12.3256590492355 | etot = -8.37462297032817 +130000 ekin = 1.6494941584018 | erot = 2.11340935726337 | epot = -12.1375264852354 | etot = -8.37462296957026 +131000 ekin = 1.5316714306691 | erot = 2.03466319553995 | epot = -11.940957595048 | etot = -8.37462296883898 +132000 ekin = 1.41179399813973 | erot = 1.96073697301916 | epot = -11.747153939335 | etot = -8.37462296817611 +133000 ekin = 1.29582771791038 | erot = 1.89586175533292 | epot = -11.5663124408531 | etot = -8.37462296760982 +134000 ekin = 1.18933366770483 | erot = 1.84313053331003 | epot = -11.407087168276 | etot = -8.37462296726118 +135000 ekin = 1.09698845763049 | erot = 1.80418246558928 | epot = -11.27579389016 | etot = -8.37462296694027 +136000 ekin = 1.0227090445408 | erot = 1.77989195852182 | epot = -11.1772239698136 | etot = -8.37462296675101 +137000 ekin = 0.969402888595114 | erot = 1.77022137974227 | epot = -11.1142472350348 | etot = -8.3746229666974 +138000 ekin = 0.938766242876417 | erot = 1.77423425797178 | epot = -11.0876234676251 | etot = -8.37462296677689 +139000 ekin = 0.931209536918657 | erot = 1.79022284403554 | epot = -11.0960553479296 | etot = -8.37462296697544 +140000 ekin = 0.945902360873822 | erot = 1.81588277986714 | epot = -11.1364081080071 | etot = -8.37462296726611 +141000 ekin = 0.980951010695237 | erot = 1.84854552854019 | epot = -11.2041195068463 | etot = -8.37462296761087 +142000 ekin = 1.03368854660442 | erot = 1.88546172258912 | epot = -11.2937732371596 | etot = -8.37462296796605 +143000 ekin = 1.10102464558818 | erot = 1.92410215903288 | epot = -11.3997497729128 | etot = -8.37462296829172 +144000 ekin = 1.17978371180494 | erot = 1.96241851789353 | epot = -11.5168251982593 | etot = -8.37462296856084 +145000 ekin = 1.26696389973302 | erot = 1.99907135517284 | epot = -11.6406582236461 | etot = -8.37462296874025 +146000 ekin = 1.35987698631762 | erot = 2.03338468070444 | epot = -11.767884635915 | etot = -8.37462296889291 +147000 ekin = 1.45616095203023 | erot = 2.06502561999191 | epot = -11.8958095410392 | etot = -8.37462296901703 +148000 ekin = 1.5536968549114 | erot = 2.09388144715375 | epot = -12.0222012712078 | etot = -8.37462296914268 +149000 ekin = 1.65047924324489 | erot = 2.1197667162033 | epot = -12.1448689287442 | etot = -8.37462296929601 +150000 ekin = 1.74448791629898 | erot = 2.14217867903565 | epot = -12.2612895648267 | etot = -8.37462296949208 +151000 ekin = 1.83359650490197 | erot = 2.16016451670454 | epot = -12.3683839913411 | etot = -8.3746229697346 +152000 ekin = 1.91553611044715 | erot = 2.17231614291486 | epot = -12.4624752233745 | etot = -8.37462297001245 +153000 ekin = 1.98791755611589 | erot = 2.17689716712731 | epot = -12.5394376935492 | etot = -8.37462297030604 +154000 ekin = 2.0483072299909 | erot = 2.17205709329807 | epot = -12.5949872938792 | etot = -8.37462297059021 +155000 ekin = 2.09434778140709 | erot = 2.15608363214675 | epot = -12.6250543843915 | etot = -8.37462297083769 +156000 ekin = 2.12391577783728 | erot = 2.12765251039858 | epot = -12.6261912592573 | etot = -8.37462297102139 +157000 ekin = 2.13531004697561 | erot = 2.08604574913232 | epot = -12.5959787672234 | etot = -8.37462297111547 +158000 ekin = 2.12746223168599 | erot = 2.03132820631849 | epot = -12.5334134091002 | etot = -8.37462297109568 +159000 ekin = 2.10015103339202 | erot = 1.96448478928985 | epot = -12.4392587936245 | etot = -8.37462297094262 +160000 ekin = 2.0541841606366 | erot = 1.88751839461918 | epot = -12.3163255258996 | etot = -8.37462297064381 +161000 ekin = 1.99149541371268 | erot = 1.80350457154626 | epot = -12.1696229554605 | etot = -8.37462297020154 +162000 ekin = 1.91510266104675 | erot = 1.71656915682347 | epot = -12.0062947875074 | etot = -8.37462296963722 +163000 ekin = 1.82889680262201 | erot = 1.63175766791047 | epot = -11.8352774395234 | etot = -8.3746229689909 +164000 ekin = 1.73727850175332 | erot = 1.55477450557411 | epot = -11.6666759756462 | etot = -8.37462296831882 +165000 ekin = 1.64470875439839 | erot = 1.49159241029549 | epot = -11.5109241323761 | etot = -8.37462296768223 +166000 ekin = 1.55526715399568 | erot = 1.44796523954016 | epot = -11.3778553606751 | etot = -8.37462296713925 +167000 ekin = 1.47230568197306 | erot = 1.42890789301289 | epot = -11.2758365417201 | etot = -8.37462296673413 +168000 ekin = 1.39825202215286 | erot = 1.43822523216026 | epot = -11.2111002208049 | etot = -8.3746229664918 +169000 ekin = 1.33457196190104 | erot = 1.47816740254126 | epot = -11.1873623308593 | etot = -8.37462296641698 +170000 ekin = 1.28186404086271 | erot = 1.54925939136745 | epot = -11.2057463987274 | etot = -8.37462296649723 +171000 ekin = 1.24010532837011 | erot = 1.65031493319945 | epot = -11.2650432281453 | etot = -8.37462296657577 +172000 ekin = 1.20973432363878 | erot = 1.77850842430668 | epot = -11.362865714917 | etot = -8.37462296697156 +173000 ekin = 1.18958106737811 | erot = 1.9293947268165 | epot = -11.4935987616334 | etot = -8.37462296743879 +174000 ekin = 1.17780375666777 | erot = 2.09752621801777 | epot = -11.6499529426375 | etot = -8.37462296795192 +175000 ekin = 1.17250284106912 | erot = 2.27682305293096 | epot = -11.8239488624907 | etot = -8.37462296849064 +176000 ekin = 1.17177313417491 | erot = 2.46086230703702 | epot = -12.0072584102488 | etot = -8.37462296903687 +177000 ekin = 1.17372471418875 | erot = 2.64315812275379 | epot = -12.191505806514 | etot = -8.37462296957146 +178000 ekin = 1.17649725816054 | erot = 2.81745378599562 | epot = -12.3685740142275 | etot = -8.37462297007139 +179000 ekin = 1.17828959842921 | erot = 2.97803885665107 | epot = -12.5309514255904 | etot = -8.37462297051008 +180000 ekin = 1.17741681900998 | erot = 3.12008209304855 | epot = -12.6721218829184 | etot = -8.37462297085991 +181000 ekin = 1.17239479280082 | erot = 3.23994177497927 | epot = -12.7869595388779 | etot = -8.37462297109781 +182000 ekin = 1.16204161674185 | erot = 3.33528346670118 | epot = -12.8719480549261 | etot = -8.37462297148306 +183000 ekin = 1.14544700201186 | erot = 3.40346825728235 | epot = -12.9235382308529 | etot = -8.37462297155868 +184000 ekin = 1.12187454429756 | erot = 3.4438269073915 | epot = -12.9403244231946 | etot = -8.37462297150555 +185000 ekin = 1.09113819766574 | erot = 3.45752421108284 | epot = -12.9232853800834 | etot = -8.3746229713348 +186000 ekin = 1.05375177637567 | erot = 3.44681260248443 | epot = -12.8751873499234 | etot = -8.37462297106327 +187000 ekin = 1.01100426926464 | erot = 3.41470705189616 | epot = -12.800334291871 | etot = -8.37462297071016 +188000 ekin = 0.964980950088649 | erot = 3.36467106156785 | epot = -12.7042749819527 | etot = -8.37462297029619 +189000 ekin = 0.918502012521078 | erot = 3.30025095733196 | epot = -12.5933759397276 | etot = -8.3746229698746 +190000 ekin = 0.874955375625722 | erot = 3.22483721777127 | epot = -12.4744155628186 | etot = -8.37462296942164 +191000 ekin = 0.838012694189963 | erot = 3.14179385100163 | epot = -12.3544295141824 | etot = -8.37462296899082 +192000 ekin = 0.811264586710992 | erot = 3.05421641257329 | epot = -12.2401039678969 | etot = -8.37462296861265 +193000 ekin = 0.797833231457456 | erot = 2.96485918306279 | epot = -12.1373153828318 | etot = -8.37462296831155 +194000 ekin = 0.800032366300627 | erot = 2.87610608236578 | epot = -12.0507614167681 | etot = -8.37462296810165 +195000 ekin = 0.819137512919833 | erot = 2.78998115247748 | epot = -11.9837416333826 | etot = -8.37462296798529 +196000 ekin = 0.855301818719356 | erot = 2.70818765526146 | epot = -11.9381124419351 | etot = -8.37462296795424 +197000 ekin = 0.907617485284665 | erot = 2.63215574475441 | epot = -11.9143961980334 | etot = -8.37462296799427 +198000 ekin = 0.974291517584257 | erot = 2.56307623018399 | epot = -11.9119907158566 | etot = -8.37462296808839 +199000 ekin = 1.05288651878767 | erot = 2.50190471363121 | epot = -11.9294142006406 | etot = -8.37462296822169 +200000 ekin = 1.14057530731218 | erot = 2.44933274089538 | epot = -11.9645310165904 | etot = -8.37462296838287 +201000 ekin = 1.23436945655772 | erot = 2.40573577404698 | epot = -12.0147281991691 | etot = -8.37462296856442 +202000 ekin = 1.33129982084466 | erot = 2.37111655194155 | epot = -12.0770393415472 | etot = -8.37462296876096 +203000 ekin = 1.42854451444427 | erot = 2.34506402190567 | epot = -12.1482315053186 | etot = -8.37462296896862 +204000 ekin = 1.52351160571853 | erot = 2.32674290434264 | epot = -12.2248774792437 | etot = -8.37462296918254 +205000 ekin = 1.61388837060062 | erot = 2.31491995505471 | epot = -12.3034312950525 | etot = -8.37462296939715 +206000 ekin = 1.6976677526079 | erot = 2.30802500400466 | epot = -12.3803157262185 | etot = -8.37462296960589 +207000 ekin = 1.7731587468784 | erot = 2.30423562983894 | epot = -12.4520173465218 | etot = -8.37462296980448 +208000 ekin = 1.83898325555922 | erot = 2.30156289475855 | epot = -12.5151691203036 | etot = -8.37462296998581 +209000 ekin = 1.8940606525466 | erot = 2.29797193080362 | epot = -12.5666555534955 | etot = -8.37462297014531 +210000 ekin = 1.93758171355956 | erot = 2.29149245614553 | epot = -12.6036971399837 | etot = -8.37462297027863 +211000 ekin = 1.96897499678811 | erot = 2.28032999988876 | epot = -12.6239279670587 | etot = -8.37462297038181 +212000 ekin = 1.98787057423958 | erot = 2.26297816329946 | epot = -12.6254717079902 | etot = -8.37462297045112 +213000 ekin = 1.9940661531065 | erot = 2.23834847729537 | epot = -12.6070376008835 | etot = -8.37462297048167 +214000 ekin = 1.98749971048334 | erot = 2.20579329600804 | epot = -12.5679159769729 | etot = -8.37462297048154 +215000 ekin = 1.96823269345713 | erot = 2.16512069835555 | epot = -12.50797636226 | etot = -8.37462297044735 +216000 ekin = 1.93645036858781 | erot = 2.11663233289542 | epot = -12.4277056718665 | etot = -8.37462297038329 +217000 ekin = 1.89249565101126 | erot = 2.06105227365498 | epot = -12.3281708949562 | etot = -8.37462297028998 +218000 ekin = 1.83696296100957 | erot = 1.99944931813304 | epot = -12.2110352493002 | etot = -8.37462297015758 +219000 ekin = 1.77087997199992 | erot = 1.93321768349696 | epot = -12.0787206254576 | etot = -8.37462296996071 +220000 ekin = 1.69598414200819 | erot = 1.86416918368551 | epot = -11.9347762953548 | etot = -8.37462296966108 +221000 ekin = 1.61504938765088 | erot = 1.79472971030197 | epot = -11.7844020671754 | etot = -8.37462296922251 +222000 ekin = 1.53214607791996 | erot = 1.72813764736931 | epot = -11.6349066939255 | etot = -8.3746229686362 +223000 ekin = 1.45266240883145 | erot = 1.66846349300071 | epot = -11.4957488697764 | etot = -8.37462296794429 +224000 ekin = 1.38293292450132 | erot = 1.62027927221214 | epot = -11.3778351639601 | etot = -8.37462296724662 +225000 ekin = 1.32944348952763 | erot = 1.58793473617097 | epot = -11.2920011923816 | etot = -8.37462296668304 +226000 ekin = 1.29777350141001 | erot = 1.57457480049465 | epot = -11.2469712682749 | etot = -8.37462296637022 +227000 ekin = 1.2915871154549 | erot = 1.58136206120083 | epot = -11.2475721430407 | etot = -8.37462296638494 +228000 ekin = 1.3119916055049 | erot = 1.60705168356014 | epot = -11.2936662557524 | etot = -8.37462296668736 +229000 ekin = 1.35720775781584 | erot = 1.6487242796873 | epot = -11.3805550048115 | etot = -8.37462296730835 +230000 ekin = 1.42320705813345 | erot = 1.70117239435449 | epot = -11.4990024205433 | etot = -8.37462296805538 +231000 ekin = 1.50467169677602 | erot = 1.75808746579058 | epot = -11.6373821313703 | etot = -8.37462296880375 +232000 ekin = 1.59576180204816 | erot = 1.81345446216761 | epot = -11.7838392336753 | etot = -8.37462296945955 +233000 ekin = 1.69077156764805 | erot = 1.8623377060858 | epot = -11.9277322437063 | etot = -8.37462296997249 +234000 ekin = 1.78453671679948 | erot = 1.90129507954632 | epot = -12.0604547666799 | etot = -8.37462297033413 +235000 ekin = 1.87261122259015 | erot = 1.92842207171143 | epot = -12.1756562648651 | etot = -8.37462297056357 +236000 ekin = 1.95129507586097 | erot = 1.94312673772433 | epot = -12.2690447842764 | etot = -8.37462297069106 +237000 ekin = 2.01688127570934 | erot = 1.945878385496 | epot = -12.3373826321098 | etot = -8.37462297090445 +238000 ekin = 2.06554471096668 | erot = 1.93754713481341 | epot = -12.3777148167617 | etot = -8.37462297098157 +239000 ekin = 2.09498833917127 | erot = 1.91896908743888 | epot = -12.388580397607 | etot = -8.37462297099681 +240000 ekin = 2.10387887335875 | erot = 1.8911406789343 | epot = -12.3696425232258 | etot = -8.3746229709327 +241000 ekin = 2.09205058134753 | erot = 1.85524232773675 | epot = -12.3219158798526 | etot = -8.37462297076831 +242000 ekin = 2.06070692356709 | erot = 1.81270484104086 | epot = -12.2480347350935 | etot = -8.37462297048556 +243000 ekin = 2.01255526288362 | erot = 1.76529169809244 | epot = -12.152469931059 | etot = -8.37462297008292 +244000 ekin = 1.95178746173521 | erot = 1.71512317980711 | epot = -12.0415336111134 | etot = -8.37462296957109 +245000 ekin = 1.88387514784669 | erot = 1.66462101119846 | epot = -11.9231191280349 | etot = -8.37462296898979 +246000 ekin = 1.81512558267746 | erot = 1.61637080971478 | epot = -11.8061193607923 | etot = -8.37462296840006 +247000 ekin = 1.75197548737566 | erot = 1.5728912903863 | epot = -11.6994897456374 | etot = -8.37462296787547 +248000 ekin = 1.70016015194902 | erot = 1.5363664174364 | epot = -11.6111495368736 | etot = -8.37462296748817 +249000 ekin = 1.66404391454297 | erot = 1.50839677555172 | epot = -11.5470636572543 | etot = -8.3746229671596 +250000 ekin = 1.64635032469229 | erot = 1.48977166427928 | epot = -11.5107449561774 | etot = -8.37462296720584 +251000 ekin = 1.64670868822414 | erot = 1.48021150770257 | epot = -11.5015431633557 | etot = -8.37462296742897 +252000 ekin = 1.66264181464383 | erot = 1.47871062656297 | epot = -11.5159754089801 | etot = -8.37462296777332 +253000 ekin = 1.69027564040396 | erot = 1.48380069510011 | epot = -11.5486993036766 | etot = -8.37462296817249 +254000 ekin = 1.72505301291723 | erot = 1.49382397147224 | epot = -11.593499952956 | etot = -8.37462296856652 +255000 ekin = 1.76239471231517 | erot = 1.50720813838028 | epot = -11.6442258196118 | etot = -8.37462296891633 +256000 ekin = 1.79816893498569 | erot = 1.52259254469775 | epot = -11.6953844488861 | etot = -8.37462296920265 +257000 ekin = 1.82895095239692 | erot = 1.53887801863897 | epot = -11.7424519404559 | etot = -8.37462296941997 +258000 ekin = 1.85212386739561 | erot = 1.55528591409788 | epot = -11.7820327510626 | etot = -8.37462296956908 +259000 ekin = 1.86588413888215 | erot = 1.57137656836564 | epot = -11.8118836768993 | etot = -8.37462296965154 +260000 ekin = 1.86922537289867 | erot = 1.58707491263398 | epot = -11.8309232551859 | etot = -8.37462296965327 +261000 ekin = 1.86194745777955 | erot = 1.60277606186355 | epot = -11.8393464893234 | etot = -8.3746229696803 +262000 ekin = 1.84441202421295 | erot = 1.61874454524355 | epot = -11.8377795390081 | etot = -8.37462296955161 +263000 ekin = 1.81775632997606 | erot = 1.63584439963916 | epot = -11.8282236989399 | etot = -8.37462296932469 +264000 ekin = 1.78414336143448 | erot = 1.65581672859407 | epot = -11.8145830590343 | etot = -8.37462296900574 +265000 ekin = 1.74659811333657 | erot = 1.68088156362787 | epot = -11.8021026455966 | etot = -8.37462296863215 +266000 ekin = 1.70875551588584 | erot = 1.71332387538078 | epot = -11.7967023595414 | etot = -8.37462296827477 +267000 ekin = 1.67443624978574 | erot = 1.7550108928448 | epot = -11.8040701106191 | etot = -8.37462296798853 +268000 ekin = 1.64712713207523 | erot = 1.80695733277667 | epot = -11.8287074326935 | etot = -8.37462296784159 +269000 ekin = 1.62949021142684 | erot = 1.8688326756718 | epot = -11.8729458549715 | etot = -8.37462296787285 +270000 ekin = 1.62285159922472 | erot = 1.93872810894281 | epot = -11.9362026762891 | etot = -8.37462296812156 +271000 ekin = 1.6268863104375 | erot = 2.01317767222039 | epot = -12.0146869512063 | etot = -8.37462296854845 +272000 ekin = 1.63981668010415 | erot = 2.08746423747643 | epot = -12.1019038866665 | etot = -8.37462296908593 +273000 ekin = 1.65880091169022 | erot = 2.15626799363764 | epot = -12.1896918749698 | etot = -8.37462296964197 +274000 ekin = 1.68050753849913 | erot = 2.2144872213087 | epot = -12.2696177299304 | etot = -8.37462297012254 +275000 ekin = 1.70172643739792 | erot = 2.25805265702192 | epot = -12.3344020648724 | etot = -8.37462297045251 +276000 ekin = 1.71987527696161 | erot = 2.28456562448906 | epot = -12.3790638720395 | etot = -8.37462297058887 +277000 ekin = 1.73331269261593 | erot = 2.29364905663789 | epot = -12.4015847197774 | etot = -8.37462297052361 +278000 ekin = 1.74143735013745 | erot = 2.28698125838894 | epot = -12.4030415787994 | etot = -8.37462297027302 +279000 ekin = 1.74460802870594 | erot = 2.26806682992263 | epot = -12.3872978285229 | etot = -8.37462296989437 +280000 ekin = 1.74394008412444 | erot = 2.24171314051926 | epot = -12.3602761940829 | etot = -8.37462296943918 +281000 ekin = 1.74088698058183 | erot = 2.21312908436282 | epot = -12.3286390340534 | etot = -8.37462296910875 +282000 ekin = 1.7366965645871 | erot = 2.18704204449556 | epot = -12.2983615778781 | etot = -8.37462296879543 +283000 ekin = 1.732290073716 | erot = 2.16744679622838 | epot = -12.2743598385787 | etot = -8.37462296863431 +284000 ekin = 1.72792109204538 | erot = 2.15675164213738 | epot = -12.2592957028517 | etot = -8.3746229686689 +285000 ekin = 1.72297480902862 | erot = 2.15537559427286 | epot = -12.2529733722001 | etot = -8.37462296889862 +286000 ekin = 1.71598432453039 | erot = 2.16179000838375 | epot = -12.2523973021716 | etot = -8.37462296925743 +287000 ekin = 1.70498524220327 | erot = 2.17315503013707 | epot = -12.2527632419523 | etot = -8.37462296961193 +288000 ekin = 1.68823578051942 | erot = 2.18649203663142 | epot = -12.2493507869533 | etot = -8.37462296980243 +289000 ekin = 1.66510970376211 | erot = 2.19999055777926 | epot = -12.2397232312615 | etot = -8.37462296972011 +290000 ekin = 1.63674302037987 | erot = 2.21381252699345 | epot = -12.2251785167484 | etot = -8.37462296937506 +291000 ekin = 1.60601874197424 | erot = 2.22992661048329 | epot = -12.2105683213541 | etot = -8.37462296889661 +292000 ekin = 1.57682389343777 | erot = 2.25107800691089 | epot = -12.2025248687821 | etot = -8.37462296843347 +293000 ekin = 1.55301992418707 | erot = 2.27950943304611 | epot = -12.2071523254135 | etot = -8.37462296818029 +294000 ekin = 1.53731454048196 | erot = 2.31583078837889 | epot = -12.2277682970271 | etot = -8.37462296816629 +295000 ekin = 1.53083265562523 | erot = 2.35873605655292 | epot = -12.2641916805469 | etot = -8.37462296836872 +296000 ekin = 1.53318706455254 | erot = 2.4052808467906 | epot = -12.3130908800621 | etot = -8.37462296871895 +297000 ekin = 1.54281493583631 | erot = 2.45151931863468 | epot = -12.3689572236285 | etot = -8.37462296915754 +298000 ekin = 1.55733608765133 | erot = 2.49306411731949 | epot = -12.4250231746883 | etot = -8.37462296971744 +299000 ekin = 1.57407386288266 | erot = 2.52498633848769 | epot = -12.473683171534 | etot = -8.37462297016362 +300000 ekin = 1.59001535760027 | erot = 2.54349315182865 | epot = -12.5081314800016 | etot = -8.37462297057271 +301000 ekin = 1.60189886822636 | erot = 2.54585083166192 | epot = -12.5223726708137 | etot = -8.3746229709254 +302000 ekin = 1.60620251585623 | erot = 2.53039812867646 | epot = -12.5112236158409 | etot = -8.37462297130826 +303000 ekin = 1.59914065240599 | erot = 2.49598280993792 | epot = -12.4697464340452 | etot = -8.37462297170129 +304000 ekin = 1.57679795693766 | erot = 2.44177332378527 | epot = -12.3931942527977 | etot = -8.37462297207482 +305000 ekin = 1.53574304374055 | erot = 2.36761905414217 | epot = -12.2779850699661 | etot = -8.37462297208338 +306000 ekin = 1.4739286655962 | erot = 2.27453104047924 | epot = -12.1230826782583 | etot = -8.37462297218286 +307000 ekin = 1.39050823398577 | erot = 2.16376504506915 | epot = -11.9288962509201 | etot = -8.37462297186516 +308000 ekin = 1.28961522980587 | erot = 2.039776672584 | epot = -11.7040148706632 | etot = -8.37462296827334 +309000 ekin = 1.0578293749372 | erot = 1.83361716570652 | epot = -11.2660695010506 | etot = -8.37462296040685 +310000 ekin = 1.14450415449021 | erot = 1.58483272602451 | epot = -11.103959838692 | etot = -8.37462295817728 +311000 ekin = 1.41922601312504 | erot = 1.45460499880731 | epot = -11.2484540448428 | etot = -8.37462303291044 +312000 ekin = 1.45261330232178 | erot = 1.37611906651658 | epot = -11.2033554015526 | etot = -8.37462303271421 +313000 ekin = 1.47884377174098 | erot = 1.31854286229477 | epot = -11.1720096664216 | etot = -8.37462303238585 +314000 ekin = 1.49756299811574 | erot = 1.28320357876905 | epot = -11.1553896088949 | etot = -8.37462303201008 +315000 ekin = 1.51332559187953 | erot = 1.27043025389329 | epot = -11.1583788774965 | etot = -8.37462303172366 +316000 ekin = 1.53080061117969 | erot = 1.27925593275756 | epot = -11.1846795755424 | etot = -8.37462303160514 +317000 ekin = 1.55378721590823 | erot = 1.30719554367504 | epot = -11.2356057912733 | etot = -8.37462303169002 +318000 ekin = 1.58370434541029 | erot = 1.34913652060387 | epot = -11.3074638985376 | etot = -8.37462303252346 +319000 ekin = 1.61943484148203 | erot = 1.39801478359231 | epot = -11.3920726581924 | etot = -8.37462303311802 +320000 ekin = 1.65864783760474 | erot = 1.44696670459029 | epot = -11.4802375759965 | etot = -8.37462303380145 +321000 ekin = 1.69766983847289 | erot = 1.48920524279011 | epot = -11.561498115728 | etot = -8.37462303446499 +322000 ekin = 1.73222385846008 | erot = 1.51888544570663 | epot = -11.6257323391488 | etot = -8.37462303498212 +323000 ekin = 1.75834700852284 | erot = 1.53202956630737 | epot = -11.6649996100693 | etot = -8.37462303523908 +324000 ekin = 1.7732465004629 | erot = 1.5273259702946 | epot = -11.6751955059262 | etot = -8.37462303516874 +325000 ekin = 1.77583924216924 | erot = 1.50655389358375 | epot = -11.6570161705538 | etot = -8.37462303480081 +326000 ekin = 1.76682929376817 | erot = 1.47436928283839 | epot = -11.6158216107554 | etot = -8.37462303414888 +327000 ekin = 1.74834602231073 | erot = 1.4379436720269 | epot = -11.5609127276988 | etot = -8.37462303336115 +328000 ekin = 1.72331109821176 | erot = 1.40578615079664 | epot = -11.5037202815769 | etot = -8.37462303256846 +329000 ekin = 1.69488797673317 | erot = 1.3863558002332 | epot = -11.4558668088442 | etot = -8.37462303187786 +330000 ekin = 1.66566513334694 | erot = 1.38702252391914 | epot = -11.4273106886493 | etot = -8.37462303138319 +331000 ekin = 1.6373218516614 | erot = 1.41331220646666 | epot = -11.4252570892349 | etot = -8.37462303110686 +332000 ekin = 1.61073968003952 | erot = 1.46826665363511 | epot = -11.453629364732 | etot = -8.37462303105739 +333000 ekin = 1.5860523210645 | erot = 1.55220559043164 | epot = -11.5128809427305 | etot = -8.37462303123435 +334000 ekin = 1.56284415922285 | erot = 1.66255678080492 | epot = -11.600023971619 | etot = -8.37462303159123 +335000 ekin = 1.54014240613776 | erot = 1.79443783502794 | epot = -11.7092032732475 | etot = -8.37462303208181 +336000 ekin = 1.5167045521657 | erot = 1.94117931563298 | epot = -11.8325069004484 | etot = -8.3746230326497 +337000 ekin = 1.49128277555494 | erot = 2.09492414345281 | epot = -11.9608299522434 | etot = -8.37462303323563 +338000 ekin = 1.46282625482992 | erot = 2.24735936520941 | epot = -12.0848086538231 | etot = -8.37462303378375 +339000 ekin = 1.43063896798261 | erot = 2.39044100153422 | epot = -12.1957030037649 | etot = -8.37462303424805 +340000 ekin = 1.39448012483982 | erot = 2.51702660359006 | epot = -12.2861297630263 | etot = -8.3746230345964 +341000 ekin = 1.35460313822206 | erot = 2.6213528403744 | epot = -12.3505790134087 | etot = -8.37462303481223 +342000 ekin = 1.31173936863004 | erot = 2.69933546749698 | epot = -12.385697871018 | etot = -8.37462303489103 +343000 ekin = 1.26704159860198 | erot = 2.74871044551737 | epot = -12.390375078956 | etot = -8.37462303483662 +344000 ekin = 1.22200654509472 | erot = 2.76906107654549 | epot = -12.3656906562962 | etot = -8.37462303465604 +345000 ekin = 1.17839357225688 | erot = 2.7617768946551 | epot = -12.3147935012699 | etot = -8.37462303435793 +346000 ekin = 1.13814730560306 | erot = 2.72996678569835 | epot = -12.2427371252557 | etot = -8.37462303395427 +347000 ekin = 1.10331757839143 | erot = 2.67831421953948 | epot = -12.1562548313949 | etot = -8.374623033464 +348000 ekin = 1.07595787263669 | erot = 2.61283600667651 | epot = -12.0634169122313 | etot = -8.37462303291812 +349000 ekin = 1.05798147191732 | erot = 2.54050407789418 | epot = -11.9731085821733 | etot = -8.37462303236178 +350000 ekin = 1.05096760963779 | erot = 2.46871550808003 | epot = -11.8943061495696 | etot = -8.37462303185175 +351000 ekin = 1.055934374293 | erot = 2.40463774698031 | epot = -11.8351951527218 | etot = -8.37462303144848 +352000 ekin = 1.07311971186474 | erot = 2.35449555191691 | epot = -11.802238294989 | etot = -8.37462303120734 +353000 ekin = 1.10182415540774 | erot = 2.32288867128237 | epot = -11.7993358578587 | etot = -8.37462303116861 +354000 ekin = 1.14036300464639 | erot = 2.31223409502398 | epot = -11.8272201310208 | etot = -8.37462303135046 +355000 ekin = 1.18615564007818 | erot = 2.32242185962034 | epot = -11.8832005314415 | etot = -8.37462303174298 +356000 ekin = 1.23595386569849 | erot = 2.35076326964225 | epot = -11.9613401676472 | etot = -8.37462303230647 +357000 ekin = 1.28618457758612 | erot = 2.39228504524977 | epot = -12.0530926558097 | etot = -8.37462303297378 +358000 ekin = 1.33335672484009 | erot = 2.44036693764229 | epot = -12.1483466961434 | etot = -8.37462303366097 +359000 ekin = 1.3744661142348 | erot = 2.48763760748978 | epot = -12.2367267560058 | etot = -8.37462303428119 +360000 ekin = 1.40733698540061 | erot = 2.52696891747122 | epot = -12.3089289376309 | etot = -8.37462303475905 +361000 ekin = 1.4308523011706 | erot = 2.55266032656765 | epot = -12.35813566267 | etot = -8.37462303493178 +362000 ekin = 1.4449802341948 | erot = 2.56161192448427 | epot = -12.3812151936927 | etot = -8.37462303501366 +363000 ekin = 1.45080808015421 | erot = 2.55177253019042 | epot = -12.3772036452516 | etot = -8.37462303490699 +364000 ekin = 1.45046982069901 | erot = 2.52283864584328 | epot = -12.3479315011827 | etot = -8.37462303464038 +365000 ekin = 1.44693366151984 | erot = 2.47609933176712 | epot = -12.2976560275503 | etot = -8.3746230342633 +366000 ekin = 1.44366094468002 | erot = 2.41401126337658 | epot = -12.2322952418937 | etot = -8.37462303383704 +367000 ekin = 1.44416618229162 | erot = 2.33969773429716 | epot = -12.1584869500125 | etot = -8.37462303342374 +368000 ekin = 1.45154164412073 | erot = 2.25648465085064 | epot = -12.0826493280453 | etot = -8.37462303307398 +369000 ekin = 1.46802482611055 | erot = 2.16757470029821 | epot = -12.010222559226 | etot = -8.37462303281721 +370000 ekin = 1.49468484157952 | erot = 2.07591739973062 | epot = -11.9452252739688 | etot = -8.37462303265869 +371000 ekin = 1.53128479294091 | erot = 1.98426522628829 | epot = -11.8901730518129 | etot = -8.37462303258368 +372000 ekin = 1.57634160155613 | erot = 1.8953362606454 | epot = -11.8463008947685 | etot = -8.374623032567 +373000 ekin = 1.62736107596715 | erot = 1.81196417168806 | epot = -11.8139482802385 | etot = -8.37462303258332 +374000 ekin = 1.68119274504245 | erot = 1.73713269144088 | epot = -11.7929484690968 | etot = -8.37462303261351 +375000 ekin = 1.73444043052933 | erot = 1.67385884334656 | epot = -11.7829223065195 | etot = -8.37462303264361 +376000 ekin = 1.78387586144014 | erot = 1.62497473906331 | epot = -11.7834736331733 | etot = -8.37462303266983 +377000 ekin = 1.82648186091977 | erot = 1.59275354369161 | epot = -11.7938584374902 | etot = -8.37462303287884 +378000 ekin = 1.85889028460836 | erot = 1.57838589666623 | epot = -11.8118992141858 | etot = -8.37462303291125 +379000 ekin = 1.87974734421412 | erot = 1.58231910072821 | epot = -11.8366894778907 | etot = -8.37462303294839 +380000 ekin = 1.88876618247971 | erot = 1.6039785204282 | epot = -11.8673677359262 | etot = -8.37462303301827 +381000 ekin = 1.88634387025615 | erot = 1.6416225350766 | epot = -11.9025894384717 | etot = -8.37462303313899 +382000 ekin = 1.87329602399987 | erot = 1.69239968364314 | epot = -11.9403187409513 | etot = -8.37462303330827 +383000 ekin = 1.8506776691208 | erot = 1.75260724973969 | epot = -11.9779079523648 | etot = -8.37462303350427 +384000 ekin = 1.81972884480745 | erot = 1.81808771261031 | epot = -12.0124395911113 | etot = -8.37462303369356 +385000 ekin = 1.78192764776998 | erot = 1.88463133786728 | epot = -12.0411820195034 | etot = -8.37462303386617 +386000 ekin = 1.7389611730154 | erot = 1.94830024178168 | epot = -12.0618844487816 | etot = -8.37462303398448 +387000 ekin = 1.6926170395659 | erot = 2.00550933075364 | epot = -12.0727494044579 | etot = -8.37462303413835 +388000 ekin = 1.64442362564975 | erot = 2.05290262288172 | epot = -12.0719492828229 | etot = -8.3746230342914 +389000 ekin = 1.59562809726233 | erot = 2.08769097010103 | epot = -12.0579421017188 | etot = -8.37462303435545 +390000 ekin = 1.54727258078712 | erot = 2.10804034821868 | epot = -12.0299359634134 | etot = -8.37462303440755 +391000 ekin = 1.5004266868918 | erot = 2.11301685840078 | epot = -11.988066579574 | etot = -8.37462303428138 +392000 ekin = 1.45669956782597 | erot = 2.10352612083869 | epot = -11.934848722603 | etot = -8.37462303393835 +393000 ekin = 1.41857599109012 | erot = 2.08263213471398 | epot = -11.875831159199 | etot = -8.37462303339486 +394000 ekin = 1.38932612627839 | erot = 2.05528425943482 | epot = -11.8192334184618 | etot = -8.37462303274861 +395000 ekin = 1.37246101478421 | erot = 2.02739319427239 | epot = -11.7744772412156 | etot = -8.37462303215901 +396000 ekin = 1.37078907987896 | erot = 2.00445159240664 | epot = -11.7498637040825 | etot = -8.37462303179685 +397000 ekin = 1.38538853999943 | erot = 1.99011302537625 | epot = -11.7501245971575 | etot = -8.37462303178181 +398000 ekin = 1.41490531161701 | erot = 1.98519641778399 | epot = -11.7747247615396 | etot = -8.37462303213862 +399000 ekin = 1.45547085036343 | erot = 1.98743025594767 | epot = -11.8175241391056 | etot = -8.37462303279446 +400000 ekin = 1.50126526406662 | erot = 1.99196444869315 | epot = -11.8678527463724 | etot = -8.3746230336126 +401000 ekin = 1.54549713891549 | erot = 1.99242148352443 | epot = -11.9125416568768 | etot = -8.37462303443686 +402000 ekin = 1.58148802753449 | erot = 1.98217540610574 | epot = -11.9382864687617 | etot = -8.37462303512152 +403000 ekin = 1.60364407572846 | erot = 1.95563446459428 | epot = -11.9339015758638 | etot = -8.37462303554105 +404000 ekin = 1.60823718231449 | erot = 1.90940860688998 | epot = -11.8922688248045 | etot = -8.37462303560003 +405000 ekin = 1.59393186875414 | erot = 1.84321418438518 | epot = -11.8117690883971 | etot = -8.37462303525783 +406000 ekin = 1.56197926550461 | erot = 1.76026394072057 | epot = -11.6968662407814 | etot = -8.37462303455625 +407000 ekin = 1.51595319782289 | erot = 1.66689496115233 | epot = -11.5574711925961 | etot = -8.37462303362087 +408000 ekin = 1.46103089399041 | erot = 1.57144700034374 | epot = -11.4071009269552 | etot = -8.374623032621 +409000 ekin = 1.40302353808214 | erot = 1.48274963105006 | epot = -11.2603962008454 | etot = -8.37462303171318 +410000 ekin = 1.34747963365306 | erot = 1.40871679572282 | epot = -11.1308194603671 | etot = -8.37462303099118 +411000 ekin = 1.2414284292792 | erot = 1.36765891027364 | epot = -10.9837103545922 | etot = -8.37462301503931 +412000 ekin = 1.07606206466598 | erot = 1.44463891804017 | epot = -10.8953239884252 | etot = -8.37462300571905 +413000 ekin = 1.04694922469639 | erot = 1.51102600613188 | epot = -10.9325982588149 | etot = -8.37462302798667 +414000 ekin = 1.03606467090392 | erot = 1.52895884328666 | epot = -10.9396465423142 | etot = -8.37462302812358 +415000 ekin = 1.03698178422018 | erot = 1.56970634086054 | epot = -10.9813111534884 | etot = -8.3746230284077 +416000 ekin = 1.0484279442172 | erot = 1.63005774223143 | epot = -11.0531087152573 | etot = -8.37462302880862 +417000 ekin = 1.06841333535673 | erot = 1.70571770479095 | epot = -11.1487540694421 | etot = -8.37462302929443 +418000 ekin = 1.09444701005109 | erot = 1.79158405306266 | epot = -11.2606540929522 | etot = -8.37462302983849 +419000 ekin = 1.12371544113075 | erot = 1.88200392342424 | epot = -11.3803423949712 | etot = -8.37462303041625 +420000 ekin = 1.15322596863741 | erot = 1.97103956947901 | epot = -11.4988885691128 | etot = -8.37462303099641 +421000 ekin = 1.17996638670221 | erot = 2.05281125535604 | epot = -11.6074006735892 | etot = -8.37462303153091 +422000 ekin = 1.20115062981133 | erot = 2.12197272517915 | epot = -11.6977463869443 | etot = -8.37462303195381 +423000 ekin = 1.21456879342739 | erot = 2.17429924607165 | epot = -11.7634910716972 | etot = -8.37462303219813 +424000 ekin = 1.21895541018794 | erot = 2.20725430505418 | epot = -11.8008327474652 | etot = -8.37462303222309 +425000 ekin = 1.21420953470736 | erot = 2.22030001430874 | epot = -11.8091325810583 | etot = -8.37462303204219 +426000 ekin = 1.20134505265812 | erot = 2.214761428149 | epot = -11.7907295125141 | etot = -8.37462303170695 +427000 ekin = 1.18219319315412 | erot = 2.19340434236676 | epot = -11.7502205668115 | etot = -8.37462303129061 +428000 ekin = 1.15899921940922 | erot = 2.15981652249817 | epot = -11.6934387727657 | etot = -8.37462303085828 +429000 ekin = 1.13415683500802 | erot = 2.11790831243066 | epot = -11.6266881762556 | etot = -8.37462302881691 +430000 ekin = 1.11403963820971 | erot = 2.07460238347228 | epot = -11.5632650504428 | etot = -8.37462302876084 +431000 ekin = 1.10124843427953 | erot = 2.03325324116064 | epot = -11.5091247042084 | etot = -8.37462302876824 +432000 ekin = 1.09509673682051 | erot = 1.99414694703558 | epot = -11.4638667126925 | etot = -8.37462302883644 +433000 ekin = 1.09463609314624 | erot = 1.95711348582247 | epot = -11.4263726079127 | etot = -8.37462302894401 +434000 ekin = 1.0980947201295 | erot = 1.9211128356985 | epot = -11.3938305852091 | etot = -8.37462302938109 +435000 ekin = 1.10341624338792 | erot = 1.88492142830318 | epot = -11.3629607010968 | etot = -8.37462302940571 +436000 ekin = 1.11020757162805 | erot = 1.84854231975901 | epot = -11.3333729208369 | etot = -8.37462302944983 +437000 ekin = 1.11803889537731 | erot = 1.81186902511195 | epot = -11.3045309499979 | etot = -8.37462302950868 +438000 ekin = 1.12642172160223 | erot = 1.77470718111897 | epot = -11.2757519322953 | etot = -8.37462302957406 +439000 ekin = 1.13485148153866 | erot = 1.73686282079482 | epot = -11.2463373319672 | etot = -8.37462302963374 +440000 ekin = 1.14287335820563 | erot = 1.69826079507224 | epot = -11.2157571829505 | etot = -8.37462302967267 +441000 ekin = 1.15016795453003 | erot = 1.65908318343061 | epot = -11.1838741676311 | etot = -8.37462302967045 +442000 ekin = 1.15664284201482 | erot = 1.61992313518266 | epot = -11.1511890068216 | etot = -8.37462302962409 +443000 ekin = 1.16253418069013 | erot = 1.58179210099529 | epot = -11.1189493112082 | etot = -8.37462302952279 +444000 ekin = 1.16846798531266 | erot = 1.5461446661337 | epot = -11.0892356808159 | etot = -8.37462302936959 +445000 ekin = 1.17546820346624 | erot = 1.51479732961039 | epot = -11.0648885622563 | etot = -8.37462302917964 +446000 ekin = 1.18488743024694 | erot = 1.4897380208828 | epot = -11.0492484801105 | etot = -8.37462302898081 +447000 ekin = 1.19824347153649 | erot = 1.47284289980585 | epot = -11.0457094001527 | etot = -8.37462302881034 +448000 ekin = 1.21696535091566 | erot = 1.4655476599557 | epot = -11.0571360395825 | etot = -8.37462302871109 +449000 ekin = 1.24207954598559 | erot = 1.46851271093831 | epot = -11.0852152856444 | etot = -8.37462302872051 +450000 ekin = 1.27389445230352 | erot = 1.48136016742263 | epot = -11.129877648597 | etot = -8.37462302887088 +451000 ekin = 1.31179903842807 | erot = 1.50255470267712 | epot = -11.1889767701161 | etot = -8.37462302901093 +452000 ekin = 1.35460859520386 | erot = 1.52989164327156 | epot = -11.2591232679085 | etot = -8.37462302943311 +453000 ekin = 1.39989469250065 | erot = 1.55983588432741 | epot = -11.3343536067678 | etot = -8.37462302993971 +454000 ekin = 1.4443795754955 | erot = 1.58822152329946 | epot = -11.4072241292536 | etot = -8.37462303045863 +455000 ekin = 1.48456015878112 | erot = 1.6110361600441 | epot = -11.4702193497298 | etot = -8.37462303090461 +456000 ekin = 1.5173332961521 | erot = 1.62510652435415 | epot = -11.5170628516973 | etot = -8.37462303119105 +457000 ekin = 1.54029245797507 | erot = 1.62854015385721 | epot = -11.5434556431077 | etot = -8.37462303127543 +458000 ekin = 1.55209787062638 | erot = 1.62122255615519 | epot = -11.5479434578284 | etot = -8.37462303104684 +459000 ekin = 1.55414659187634 | erot = 1.6057199111291 | epot = -11.5344895335887 | etot = -8.37462303058322 +460000 ekin = 1.54960099436722 | erot = 1.58640018749909 | epot = -11.5106242118337 | etot = -8.37462302996738 +461000 ekin = 1.54273124224815 | erot = 1.56872252266498 | epot = -11.4860767942389 | etot = -8.37462302932575 +462000 ekin = 1.5379558944902 | erot = 1.55825929919717 | epot = -11.4708382224928 | etot = -8.3746230288054 +463000 ekin = 1.53875903307901 | erot = 1.55959299575919 | epot = -11.4729750573654 | etot = -8.37462302852723 +464000 ekin = 1.5468202951179 | erot = 1.5753418689505 | epot = -11.4967851926248 | etot = -8.37462302855638 +465000 ekin = 1.5616294650245 | erot = 1.60564212073123 | epot = -11.5418946146288 | etot = -8.37462302887307 +466000 ekin = 1.58070265304299 | erot = 1.64822662156225 | epot = -11.603552303989 | etot = -8.37462302938373 +467000 ekin = 1.60035208027293 | erot = 1.69905719079097 | epot = -11.6740323010126 | etot = -8.37462302994875 +468000 ekin = 1.61673623107329 | erot = 1.75335443246826 | epot = -11.7447136939725 | etot = -8.37462303043099 +469000 ekin = 1.62683085007104 | erot = 1.80670922025691 | epot = -11.8081631010581 | etot = -8.37462303073019 +470000 ekin = 1.62907239972705 | erot = 1.85596584024091 | epot = -11.8596612707768 | etot = -8.37462303080888 +471000 ekin = 1.62354687373203 | erot = 1.8996612917076 | epot = -11.897831196133 | etot = -8.37462303069334 +472000 ekin = 1.61170510379461 | erot = 1.93800410341077 | epot = -11.9243322376463 | etot = -8.37462303044088 +473000 ekin = 1.59590324450911 | erot = 1.97246730641982 | epot = -11.9429935810563 | etot = -8.37462303012741 +474000 ekin = 1.5788652318122 | erot = 2.00526149881422 | epot = -11.9587497604456 | etot = -8.37462302981915 +475000 ekin = 1.56312071578956 | erot = 2.03882982960352 | epot = -11.97657357496 | etot = -8.37462302956695 +476000 ekin = 1.55063074695145 | erot = 2.07545668637062 | epot = -12.0007104627129 | etot = -8.37462302939086 +477000 ekin = 1.54263588410857 | erot = 2.11704231172364 | epot = -12.0343012251349 | etot = -8.37462302930267 +478000 ekin = 1.53956151542023 | erot = 2.16493101565207 | epot = -12.079115560379 | etot = -8.37462302930667 +479000 ekin = 1.54104337297963 | erot = 2.21977101927418 | epot = -12.1354374216592 | etot = -8.37462302940542 +480000 ekin = 1.54600976096978 | erot = 2.28138261400151 | epot = -12.202015404568 | etot = -8.37462302959675 +481000 ekin = 1.55280606024745 | erot = 2.34867771788771 | epot = -12.2761068080027 | etot = -8.37462302986758 +482000 ekin = 1.55937339634714 | erot = 2.41971772771095 | epot = -12.3537141542431 | etot = -8.37462303018505 +483000 ekin = 1.56350104452682 | erot = 2.49198464322671 | epot = -12.4301087182504 | etot = -8.37462303049682 +484000 ekin = 1.56314467772463 | erot = 2.56280026280356 | epot = -12.5005679712774 | etot = -8.37462303074924 +485000 ekin = 1.55677099189266 | erot = 2.62990187864781 | epot = -12.561295901425 | etot = -8.37462303088452 +486000 ekin = 1.54362230241397 | erot = 2.69196691951125 | epot = -12.6102122528186 | etot = -8.37462303089336 +487000 ekin = 1.52381043791577 | erot = 2.74866369544776 | epot = -12.647097164163 | etot = -8.37462303079951 +488000 ekin = 1.49822858843954 | erot = 2.80041322794242 | epot = -12.6732648470337 | etot = -8.37462303065175 +489000 ekin = 1.46832177710726 | erot = 2.84792010719231 | epot = -12.6908649148032 | etot = -8.37462303050367 +490000 ekin = 1.43580907600697 | erot = 2.89167668868307 | epot = -12.7021087950844 | etot = -8.37462303039437 +491000 ekin = 1.40244626498263 | erot = 2.93162068131092 | epot = -12.7086899766333 | etot = -8.37462303033977 +492000 ekin = 1.36987596423218 | erot = 2.9670311886878 | epot = -12.7115301832547 | etot = -8.3746230303347 +493000 ekin = 1.33956200675526 | erot = 2.99664446239428 | epot = -12.7108294995122 | etot = -8.37462303036264 +494000 ekin = 1.31276816320931 | erot = 3.01889804551771 | epot = -12.7062892391349 | etot = -8.37462303040788 +495000 ekin = 1.29052832589647 | erot = 3.03218505524657 | epot = -12.6973364116076 | etot = -8.3746230304646 +496000 ekin = 1.27356858864311 | erot = 3.035022985778 | epot = -12.683214604961 | etot = -8.37462303053987 +497000 ekin = 1.26217859738859 | erot = 3.02610963123424 | epot = -12.6629112592681 | etot = -8.37462303064528 +498000 ekin = 1.25609176092333 | erot = 3.00437387242381 | epot = -12.63508866407 | etot = -8.37462303072284 +499000 ekin = 1.25448433544043 | erot = 2.96925958209368 | epot = -12.5983669483981 | etot = -8.37462303086403 +500000 ekin = 1.25592311954888 | erot = 2.92052794168088 | epot = -12.5510740922046 | etot = -8.37462303097485 +501000 ekin = 1.25866262015662 | erot = 2.85877857413216 | epot = -12.4920642252914 | etot = -8.37462303100262 +502000 ekin = 1.26101030104231 | erot = 2.78589367847382 | epot = -12.4215270104231 | etot = -8.37462303090696 +503000 ekin = 1.2616822409827 | erot = 2.70525686265705 | epot = -12.341562134315 | etot = -8.37462303067522 +504000 ekin = 1.26006875273123 | erot = 2.62162663921815 | epot = -12.2563184222851 | etot = -8.37462303033575 +505000 ekin = 1.25635230634372 | erot = 2.54066101850671 | epot = -12.1716363547708 | etot = -8.37462302992033 +506000 ekin = 1.25147361583387 | erot = 2.46829686832008 | epot = -12.0943935136487 | etot = -8.37462302949473 +507000 ekin = 1.24695832252401 | erot = 2.40991559866008 | epot = -12.0314969503144 | etot = -8.37462302913032 +508000 ekin = 1.24460011261898 | erot = 2.36947588934082 | epot = -11.9886990309703 | etot = -8.37462302901048 +509000 ekin = 1.24584437165075 | erot = 2.34837731731078 | epot = -11.968844717957 | etot = -8.37462302899552 +510000 ekin = 1.25172041123594 | erot = 2.34550382347416 | epot = -11.9718472639378 | etot = -8.37462302922773 +511000 ekin = 1.26248317250925 | erot = 2.35680066397849 | epot = -11.9939068661987 | etot = -8.37462302971099 +512000 ekin = 1.27739486770368 | erot = 2.37529788848781 | epot = -12.0273157865876 | etot = -8.37462303039607 +513000 ekin = 1.29481021505143 | erot = 2.39185405428337 | epot = -12.0612873005117 | etot = -8.37462303117693 +514000 ekin = 1.31250889880556 | erot = 2.39651406027282 | epot = -12.0836459909757 | etot = -8.37462303189731 +515000 ekin = 1.32825052581694 | erot = 2.38037057725958 | epot = -12.0832441354529 | etot = -8.37462303237642 +516000 ekin = 1.34045831429098 | erot = 2.33760267994488 | epot = -12.052684026695 | etot = -8.37462303245917 +517000 ekin = 1.34883924084267 | erot = 2.26713155444339 | epot = -11.9905938273649 | etot = -8.37462303207887 +518000 ekin = 1.35468550683747 | erot = 2.17326127006768 | epot = -11.9025698082027 | etot = -8.37462303129753 +519000 ekin = 1.36067339624092 | erot = 2.06494828515387 | epot = -11.8002447116851 | etot = -8.37462303029029 +520000 ekin = 1.37018582822474 | erot = 1.95390329836409 | epot = -11.6987121558686 | etot = -8.37462302927973 +521000 ekin = 1.38639579380205 | erot = 1.85221057841339 | epot = -11.6132294006773 | etot = -8.37462302846182 +522000 ekin = 1.41141432490464 | erot = 1.7702244553378 | epot = -11.5562618082023 | etot = -8.37462302795986 +523000 ekin = 1.44572356453295 | erot = 1.71520045870637 | epot = -11.5355470510576 | etot = -8.37462302781823 +524000 ekin = 1.48798145409594 | erot = 1.69073008317732 | epot = -11.5533345652898 | etot = -8.37462302801658 +525000 ekin = 1.53517683781547 | erot = 1.69680296063593 | epot = -11.6066028269467 | etot = -8.37462302849528 +526000 ekin = 1.58304900119082 | erot = 1.73025509475382 | epot = -11.6879271251201 | etot = -8.3746230291755 +527000 ekin = 1.62665879649241 | erot = 1.78540941264132 | epot = -11.7866912391065 | etot = -8.37462302997276 +528000 ekin = 1.66100783108725 | erot = 1.85480654803477 | epot = -11.8904374099227 | etot = -8.37462303080072 +529000 ekin = 1.68163863412719 | erot = 1.93001159413455 | epot = -11.9862732598304 | etot = -8.37462303156867 +530000 ekin = 1.68518623027201 | erot = 2.0025246086571 | epot = -12.0623338711111 | etot = -8.37462303218195 +531000 ekin = 1.66986059685696 | erot = 2.06478669655979 | epot = -12.1092703259673 | etot = -8.3746230325506 +532000 ekin = 1.63581226896246 | erot = 2.11116679184571 | epot = -12.1216020934203 | etot = -8.3746230326121 +533000 ekin = 1.58529617177826 | erot = 2.13870511838797 | epot = -12.0986243225201 | etot = -8.37462303235382 +534000 ekin = 1.52254564095677 | erot = 2.14737698822869 | epot = -12.0445456610105 | etot = -8.37462303182508 +535000 ekin = 1.4533242057691 | erot = 2.13977370493919 | epot = -11.9677209418325 | etot = -8.37462303112417 +536000 ekin = 1.384216910118 | erot = 2.12031314070409 | epot = -11.8791530811922 | etot = -8.37462303037013 +537000 ekin = 1.3218034289985 | erot = 2.09425520394393 | epot = -11.7906816626138 | etot = -8.37462302967138 +538000 ekin = 1.27187743420501 | erot = 2.06681107588913 | epot = -11.7133115391998 | etot = -8.37462302910564 +539000 ekin = 1.23883846279463 | erot = 2.04251647933624 | epot = -11.6559779708478 | etot = -8.3746230287169 +540000 ekin = 1.22531302703342 | erot = 2.02488499742721 | epot = -11.6248210529829 | etot = -8.37462302852225 +541000 ekin = 1.2319988229111 | erot = 2.01625749304557 | epot = -11.6228793444799 | etot = -8.37462302852322 +542000 ekin = 1.25769219451141 | erot = 2.01774880495074 | epot = -11.650064028173 | etot = -8.37462302871088 +543000 ekin = 1.29945731407194 | erot = 2.02924170402309 | epot = -11.7033220471621 | etot = -8.37462302906708 +544000 ekin = 1.35291512122203 | erot = 2.04944893326965 | epot = -11.7769870840475 | etot = -8.37462302955587 +545000 ekin = 1.41265384122183 | erot = 2.07611668223443 | epot = -11.8633935535745 | etot = -8.37462303011828 +546000 ekin = 1.47277167575229 | erot = 2.1064421688077 | epot = -11.95383687523 | etot = -8.37462303067005 +547000 ekin = 1.52754093319581 | erot = 2.13770468829022 | epot = -12.039868652601 | etot = -8.37462303111499 +548000 ekin = 1.57213155238907 | erot = 2.16798237176413 | epot = -12.1147369555225 | etot = -8.37462303136926 +549000 ekin = 1.60327488859484 | erot = 2.1967176749588 | epot = -12.1746155949418 | etot = -8.37462303138818 +550000 ekin = 1.619724343768 | erot = 2.22489244333393 | epot = -12.2192398182844 | etot = -8.37462303118247 +551000 ekin = 1.62240013870625 | erot = 2.2547059313599 | epot = -12.2517291008804 | etot = -8.37462303081428 +552000 ekin = 1.61417495562549 | erot = 2.28884205646996 | epot = -12.2776400424756 | etot = -8.37462303038012 +553000 ekin = 1.59932782091974 | erot = 2.32954987377656 | epot = -12.3035007246854 | etot = -8.37462302998911 +554000 ekin = 1.58274599066962 | erot = 2.37778817613127 | epot = -12.3351571965425 | etot = -8.37462302974158 +555000 ekin = 1.56899856385299 | erot = 2.43263226771681 | epot = -12.3762538612802 | etot = -8.37462302971037 +556000 ekin = 1.56145041157876 | erot = 2.49106505511529 | epot = -12.4271384966192 | etot = -8.37462302992514 +557000 ekin = 1.56197837218949 | erot = 2.54829507223443 | epot = -12.4848964746477 | etot = -8.37462303022382 +558000 ekin = 1.57029216551998 | erot = 2.59810209182206 | epot = -12.5430172882108 | etot = -8.37462303086871 +559000 ekin = 1.58339818321042 | erot = 2.63367391511295 | epot = -12.5916951298608 | etot = -8.37462303153745 +560000 ekin = 1.59712770481254 | erot = 2.64904697988439 | epot = -12.6207977168094 | etot = -8.37462303211248 +561000 ekin = 1.60698123343217 | erot = 2.64009683894273 | epot = -12.6217011048644 | etot = -8.37462303248948 +562000 ekin = 1.60896027782279 | erot = 2.60532700120585 | epot = -12.5889103116224 | etot = -8.37462303259375 +563000 ekin = 1.60023696633189 | erot = 2.54649193869391 | epot = -12.5213519373455 | etot = -8.37462303231966 +564000 ekin = 1.57955774677316 | erot = 2.46891092806073 | epot = -12.4230917066634 | etot = -8.37462303182948 +565000 ekin = 1.54734561566726 | erot = 2.38031455631918 | epot = -12.3022832030954 | etot = -8.37462303110898 +566000 ekin = 1.50554468554416 | erot = 2.29049479450049 | epot = -12.1706625102928 | etot = -8.37462303024818 +567000 ekin = 1.45732250665155 | erot = 2.21025028826054 | epot = -12.0421958242621 | etot = -8.37462302935005 +568000 ekin = 1.40671207380805 | erot = 2.15003703752962 | epot = -11.9313721398968 | etot = -8.37462302855915 +569000 ekin = 1.35794157949082 | erot = 2.11775595086775 | epot = -11.8503205583477 | etot = -8.37462302798917 +570000 ekin = 1.31523212119238 | erot = 2.11799693943009 | epot = -11.8078520883698 | etot = -8.37462302774737 +571000 ekin = 1.28243871604816 | erot = 2.15081941192899 | epot = -11.8078811559402 | etot = -8.37462302796308 +572000 ekin = 1.26220633019077 | erot = 2.21027034249799 | epot = -11.8470997013797 | etot = -8.37462302869095 +573000 ekin = 1.25525341534941 | erot = 2.28456705415308 | epot = -11.9144434992934 | etot = -8.37462302979094 +574000 ekin = 1.26030251433791 | erot = 2.3581378703613 | epot = -11.9930634156822 | etot = -8.37462303098301 +575000 ekin = 1.27473215622843 | erot = 2.41511328226784 | epot = -12.0644684704327 | etot = -8.37462303193643 +576000 ekin = 1.29562562245648 | erot = 2.44294920216499 | epot = -12.113197857112 | etot = -8.37462303249048 +577000 ekin = 1.32065634431855 | erot = 2.43438586780086 | epot = -12.1296652446962 | etot = -8.37462303257683 +578000 ekin = 1.34847271375233 | erot = 2.38804498568671 | epot = -12.1111407317143 | etot = -8.37462303227523 +579000 ekin = 1.37859640731264 | erot = 2.30759327889212 | epot = -12.0608127179336 | etot = -8.37462303172887 +580000 ekin = 1.41115339286314 | erot = 2.20016188412019 | epot = -11.9859383079388 | etot = -8.37462303095542 +581000 ekin = 1.44674776515146 | erot = 2.07475133368212 | epot = -11.8961221291757 | etot = -8.37462303034217 +582000 ekin = 1.4851482181042 | erot = 1.94050793884997 | epot = -11.8002791867466 | etot = -8.37462302979241 +583000 ekin = 1.52576266955557 | erot = 1.80603709651217 | epot = -11.7064227954081 | etot = -8.37462302934032 +584000 ekin = 1.56772288057535 | erot = 1.67887072897699 | epot = -11.6212166385569 | etot = -8.37462302900456 +585000 ekin = 1.60990333958961 | erot = 1.56509115871755 | epot = -11.5496175271043 | etot = -8.37462302879714 +586000 ekin = 1.65096359831956 | erot = 1.46905708282237 | epot = -11.494643709869 | etot = -8.37462302872704 +587000 ekin = 1.689404116345 | erot = 1.39319741551208 | epot = -11.4572245606542 | etot = -8.37462302879712 +588000 ekin = 1.72364170525864 | erot = 1.3379013744288 | epot = -11.4361661086844 | etot = -8.37462302899699 +589000 ekin = 1.75212209151102 | erot = 1.30158756259537 | epot = -11.4283326833828 | etot = -8.37462302927642 +590000 ekin = 1.77348776905869 | erot = 1.281119877253 | epot = -11.4292306759283 | etot = -8.37462302961656 +591000 ekin = 1.78679652583132 | erot = 1.27228388602327 | epot = -11.433703441769 | etot = -8.37462302991442 +592000 ekin = 1.79174476961286 | erot = 1.27074179819946 | epot = -11.4371095979204 | etot = -8.37462303010812 +593000 ekin = 1.78882244318549 | erot = 1.27295060805964 | epot = -11.4363960813905 | etot = -8.37462303014537 +594000 ekin = 1.77931578999136 | erot = 1.27682752829949 | epot = -11.430766348318 | etot = -8.37462303002713 +595000 ekin = 1.76511936071191 | erot = 1.28196044220573 | epot = -11.4217028327169 | etot = -8.37462302979925 +596000 ekin = 1.74839643258959 | erot = 1.28931412525866 | epot = -11.4123335873807 | etot = -8.3746230295325 +597000 ekin = 1.73114837529023 | erot = 1.30076368908084 | epot = -11.4065350936672 | etot = -8.37462302929611 +598000 ekin = 1.71482586357189 | erot = 1.31808503745165 | epot = -11.4075339301729 | etot = -8.37462302914938 +599000 ekin = 1.70035612855402 | erot = 1.34256499056094 | epot = -11.4175441481827 | etot = -8.37462302906774 +600000 ekin = 1.68813838896079 | erot = 1.37518403996459 | epot = -11.4379454579713 | etot = -8.37462302904587 +601000 ekin = 1.6780215527155 | erot = 1.41656361608045 | epot = -11.4692081979194 | etot = -8.37462302912342 +602000 ekin = 1.66952241262375 | erot = 1.46664302734669 | epot = -11.5107884691339 | etot = -8.37462302916344 +603000 ekin = 1.66207455080121 | erot = 1.52486246590722 | epot = -11.5615600460007 | etot = -8.37462302929223 +604000 ekin = 1.65429274424499 | erot = 1.59090716726355 | epot = -11.6198229409005 | etot = -8.37462302939192 +605000 ekin = 1.64513458460608 | erot = 1.66451963176825 | epot = -11.6842772458433 | etot = -8.374623029469 +606000 ekin = 1.63397297141755 | erot = 1.74533329764574 | epot = -11.7539292986231 | etot = -8.37462302955985 +607000 ekin = 1.62046446185742 | erot = 1.8324685241921 | epot = -11.827556015813 | etot = -8.37462302976344 +608000 ekin = 1.60415138615037 | erot = 1.92384516554938 | epot = -11.9026195817859 | etot = -8.37462303008618 +609000 ekin = 1.58416607277154 | erot = 2.01562004721412 | epot = -11.9744091506956 | etot = -8.37462303070992 +610000 ekin = 1.55892234884521 | erot = 2.10126039812687 | epot = -12.0348057783755 | etot = -8.37462303140342 +611000 ekin = 1.52586403282322 | erot = 2.17351542350433 | epot = -12.0740024883762 | etot = -8.37462303204869 +612000 ekin = 1.48252796781519 | erot = 2.22604744671554 | epot = -12.0831984469311 | etot = -8.37462303240035 +613000 ekin = 1.42777710477985 | erot = 2.25549715886549 | epot = -12.0578972959117 | etot = -8.3746230322664 +614000 ekin = 1.36284302676279 | erot = 2.26309761368271 | epot = -12.0005636720648 | etot = -8.3746230316193 +615000 ekin = 1.29166682111691 | erot = 2.25472033316591 | epot = -11.9210101848976 | etot = -8.37462303061475 +616000 ekin = 1.22033159945878 | erot = 2.23929049960089 | epot = -11.8342451285654 | etot = -8.37462302950574 +617000 ekin = 1.15585313013086 | erot = 2.22643765863405 | epot = -11.7569138172924 | etot = -8.37462302852749 +618000 ekin = 1.10482633868692 | erot = 2.22445549379561 | epot = -11.7039048603103 | etot = -8.37462302782772 +619000 ekin = 1.07233800595847 | erot = 2.23915844396541 | epot = -11.6861194773934 | etot = -8.37462302746957 +620000 ekin = 1.06133969548792 | erot = 2.27356598266192 | epot = -11.7095287055648 | etot = -8.37462302741493 +621000 ekin = 1.07250328126192 | erot = 2.32827640438336 | epot = -11.7754027132589 | etot = -8.37462302761364 +622000 ekin = 1.10448299244682 | erot = 2.40202886261783 | epot = -11.8811348830572 | etot = -8.37462302799258 +623000 ekin = 1.15443583440521 | erot = 2.49214268564202 | epot = -12.0212015485468 | etot = -8.37462302849954 +624000 ekin = 1.21858504498163 | erot = 2.59479979276395 | epot = -12.1880078668497 | etot = -8.37462302910413 +625000 ekin = 1.29260009292916 | erot = 2.70513041487836 | epot = -12.3723535376516 | etot = -8.37462302984411 +626000 ekin = 1.37166908701228 | erot = 2.81669294847794 | epot = -12.5629850662659 | etot = -8.37462303077572 +627000 ekin = 1.45036408325867 | erot = 2.92095656625948 | epot = -12.7459436814223 | etot = -8.37462303190418 +628000 ekin = 1.52265779658061 | erot = 3.00738157699388 | epot = -12.9046624066681 | etot = -8.37462303309358 +629000 ekin = 1.58251554245149 | erot = 3.06484099788355 | epot = -13.0219795743843 | etot = -8.37462303404925 +630000 ekin = 1.6251441888068 | erot = 3.08443014421886 | epot = -13.0841973674678 | etot = -8.3746230344421 +631000 ekin = 1.64954255051881 | erot = 3.06336922299652 | epot = -13.0875348072779 | etot = -8.37462303376256 +632000 ekin = 1.65761419154568 | erot = 3.00573585957066 | epot = -13.0379730840985 | etot = -8.37462303298212 +633000 ekin = 1.65174795094007 | erot = 2.9196523277595 | epot = -12.9460233106114 | etot = -8.37462303191187 +634000 ekin = 1.63566753658032 | erot = 2.8160465674089 | epot = -12.8263371348712 | etot = -8.37462303088198 +635000 ekin = 1.61303222684112 | erot = 2.70552755469896 | epot = -12.6931828116467 | etot = -8.37462303010658 +636000 ekin = 1.5864696555612 | erot = 2.59633719497732 | epot = -12.5574298801738 | etot = -8.37462302963529 +637000 ekin = 1.55730595136552 | erot = 2.49385627804114 | epot = -12.4257852588055 | etot = -8.37462302939879 +638000 ekin = 1.52584911625276 | erot = 2.40123459740375 | epot = -12.3017067429401 | etot = -8.37462302928359 +639000 ekin = 1.4919249764131 | erot = 2.32043250457075 | epot = -12.1869805101708 | etot = -8.37462302918699 +640000 ekin = 1.45541378442456 | erot = 2.25314232064305 | epot = -12.0831791341102 | etot = -8.37462302904262 +641000 ekin = 1.41664919926993 | erot = 2.20135144253836 | epot = -11.9926236706323 | etot = -8.37462302882401 +642000 ekin = 1.37663135857242 | erot = 2.16751840710241 | epot = -11.9187727942139 | etot = -8.37462302853903 +643000 ekin = 1.33719601643076 | erot = 2.15436138730409 | epot = -11.8661804319158 | etot = -8.37462302818095 +644000 ekin = 1.3009546006674 | erot = 2.16433354913885 | epot = -11.8399111777162 | etot = -8.37462302790992 +645000 ekin = 1.2700904774084 | erot = 2.19964354153203 | epot = -11.8443570466485 | etot = -8.37462302770811 +646000 ekin = 1.24673444984148 | erot = 2.26154821905495 | epot = -11.8829056965386 | etot = -8.3746230276422 +647000 ekin = 1.23265873216168 | erot = 2.34972644270308 | epot = -11.9570082026438 | etot = -8.37462302777908 +648000 ekin = 1.22854704148088 | erot = 2.46146984669606 | epot = -12.064639916852 | etot = -8.37462302867502 +649000 ekin = 1.23123438276377 | erot = 2.58918284110391 | epot = -12.1950402535071 | etot = -8.37462302963938 +650000 ekin = 1.23733747326785 | erot = 2.72274115030322 | epot = -12.3347016542778 | etot = -8.37462303070677 +651000 ekin = 1.24289918510996 | erot = 2.85114575375504 | epot = -12.4686679705932 | etot = -8.37462303172824 +652000 ekin = 1.24424620799518 | erot = 2.96370857039037 | epot = -12.5825778108493 | etot = -8.37462303246373 +653000 ekin = 1.23918232849171 | erot = 3.05217314602706 | epot = -12.6659785072772 | etot = -8.37462303275843 +654000 ekin = 1.22772861476395 | erot = 3.11212236728239 | epot = -12.7144740146656 | etot = -8.37462303261922 +655000 ekin = 1.21201905899384 | erot = 3.14303840851493 | epot = -12.7296804997022 | etot = -8.37462303219339 +656000 ekin = 1.19543744328548 | erot = 3.1472043556439 | epot = -12.7172648305994 | etot = -8.37462303166998 +657000 ekin = 1.18149305106241 | erot = 3.12826014301058 | epot = -12.6843762252575 | etot = -8.37462303118449 +658000 ekin = 1.17296379520039 | erot = 3.09016086421994 | epot = -12.6377476902088 | etot = -8.37462303078844 +659000 ekin = 1.1715475805743 | erot = 3.03675236921006 | epot = -12.582922980259 | etot = -8.37462303047464 +660000 ekin = 1.17794903027373 | erot = 2.9717237974431 | epot = -12.5242958579367 | etot = -8.37462303021987 +661000 ekin = 1.19217998580356 | erot = 2.89858436847931 | epot = -12.4653873842995 | etot = -8.37462303001659 +662000 ekin = 1.21385724617893 | erot = 2.82043608357553 | epot = -12.4089163596414 | etot = -8.37462302988693 +663000 ekin = 1.24235148672361 | erot = 2.73948706946421 | epot = -12.3564615860687 | etot = -8.37462302988084 +664000 ekin = 1.27672733537722 | erot = 2.65640555000017 | epot = -12.3077559154332 | etot = -8.3746230300558 +665000 ekin = 1.31551337032972 | erot = 2.56977925409673 | epot = -12.2599156548621 | etot = -8.37462303043569 +666000 ekin = 1.3564470832523 | erot = 2.4761038242715 | epot = -12.2071739384876 | etot = -8.37462303096385 +667000 ekin = 1.39640549571929 | erot = 2.37072397309753 | epot = -12.1417525003011 | etot = -8.37462303148432 +668000 ekin = 1.43167926156681 | erot = 2.24978389246185 | epot = -12.0560861858176 | etot = -8.37462303178894 +669000 ekin = 1.45855421041053 | erot = 2.11253877406444 | epot = -11.9457160161991 | etot = -8.37462303172417 +670000 ekin = 1.47395086468889 | erot = 1.96284004635376 | epot = -11.8114139423238 | etot = -8.37462303128116 +671000 ekin = 1.47583917683429 | erot = 1.80887360748459 | epot = -11.659335814911 | etot = -8.37462303059216 +672000 ekin = 1.46334042173463 | erot = 1.66127989926156 | epot = -11.4992433508344 | etot = -8.37462302983822 +673000 ekin = 1.43665130212215 | erot = 1.5307421039891 | epot = -11.3420164352618 | etot = -8.37462302915052 +674000 ekin = 1.3969614764095 | erot = 1.42619748860185 | epot = -11.1977819935876 | etot = -8.37462302857624 +675000 ekin = 1.34640262234059 | erot = 1.35413730294513 | epot = -11.0751629533923 | etot = -8.3746230281066 +676000 ekin = 1.28794616800078 | erot = 1.31873912036178 | epot = -10.9813083160849 | etot = -8.37462302772231 +677000 ekin = 1.22516961115208 | erot = 1.32230065786356 | epot = -10.9220932964383 | etot = -8.37462302742264 +678000 ekin = 1.16189722957944 | erot = 1.36556643966804 | epot = -10.9020866964777 | etot = -8.3746230272302 +679000 ekin = 1.10179124612511 | erot = 1.44777635008945 | epot = -10.924190623401 | etot = -8.37462302718647 +680000 ekin = 1.04797419611956 | erot = 1.56642353037385 | epot = -10.9890207538395 | etot = -8.37462302734611 +681000 ekin = 1.00272279863915 | erot = 1.71676662170497 | epot = -11.0941124481149 | etot = -8.37462302777081 +682000 ekin = 0.967238825853956 | erot = 1.89118238727181 | epot = -11.2330442416428 | etot = -8.37462302851702 +683000 ekin = 0.941511133158685 | erot = 2.07856636781358 | epot = -11.3947005305716 | etot = -8.37462302959932 +684000 ekin = 0.924337639171898 | erot = 2.26421473260418 | epot = -11.5631754027131 | etot = -8.37462303093706 +685000 ekin = 0.913629093907857 | erot = 2.4308049018799 | epot = -11.7190570280991 | etot = -8.37462303231132 +686000 ekin = 0.907072709287811 | erot = 2.56090643971852 | epot = -11.8426021824031 | etot = -8.37462303339673 +687000 ekin = 0.903027971000835 | erot = 2.6406532391868 | epot = -11.9183042440807 | etot = -8.37462303389309 +688000 ekin = 0.90126599734657 | erot = 2.6631528356685 | epot = -11.9390418667022 | etot = -8.37462303368708 +689000 ekin = 0.903127291409964 | erot = 2.62989920641364 | epot = -11.9076495307356 | etot = -8.374623032912 +690000 ekin = 0.911003410961955 | erot = 2.54949432632515 | epot = -11.8351207691396 | etot = -8.37462303185251 +691000 ekin = 0.927482290198902 | erot = 2.43458909333302 | epot = -11.7366944143163 | etot = -8.3746230307844 +692000 ekin = 0.954629968085803 | erot = 2.29871133595714 | epot = -11.6279643338902 | etot = -8.37462302984724 +693000 ekin = 0.993689842548928 | erot = 2.15457291081592 | epot = -11.5228857825806 | etot = -8.37462302921573 +694000 ekin = 1.04477766676298 | erot = 2.01224824489283 | epot = -11.4316489404341 | etot = -8.37462302877829 +695000 ekin = 1.10717972560152 | erot = 1.87902519875999 | epot = -11.3608279528691 | etot = -8.37462302850759 +696000 ekin = 1.17962988094267 | erot = 1.76021636431907 | epot = -11.3144692736454 | etot = -8.37462302838365 +697000 ekin = 1.26034508066981 | erot = 1.65939331949942 | epot = -11.2943614285657 | etot = -8.3746230283965 +698000 ekin = 1.34700634148022 | erot = 1.57856058320643 | epot = -11.3001899532267 | etot = -8.37462302854003 +699000 ekin = 1.43673776972376 | erot = 1.5182938888681 | epot = -11.3296546873967 | etot = -8.37462302880481 +700000 ekin = 1.52614311404677 | erot = 1.47788597100086 | epot = -11.3786521142183 | etot = -8.37462302917067 +701000 ekin = 1.61113170993768 | erot = 1.45542937143776 | epot = -11.4411841111661 | etot = -8.37462302979068 +702000 ekin = 1.68654811959775 | erot = 1.44774835139905 | epot = -11.5089195013108 | etot = -8.37462303031401 +703000 ekin = 1.74804176728588 | erot = 1.45137774866611 | epot = -11.574042546703 | etot = -8.37462303075104 +704000 ekin = 1.79223863051445 | erot = 1.46326677106997 | epot = -11.6301284325956 | etot = -8.37462303101117 +705000 ekin = 1.81722742450332 | erot = 1.48152907261607 | epot = -11.6733795281554 | etot = -8.37462303103604 +706000 ekin = 1.82282717411182 | erot = 1.50598222608154 | epot = -11.703432431022 | etot = -8.3746230308286 +707000 ekin = 1.81047570465579 | erot = 1.53820736290559 | epot = -11.7233060980165 | etot = -8.37462303045516 +708000 ekin = 1.78276828495014 | erot = 1.58105495038929 | epot = -11.738446265359 | etot = -8.3746230300196 +709000 ekin = 1.74282721670583 | erot = 1.63779752304863 | epot = -11.7552477693728 | etot = -8.37462302961834 +710000 ekin = 1.69374790022126 | erot = 1.71129566720286 | epot = -11.7796665967301 | etot = -8.37462302930597 +711000 ekin = 1.6383019339965 | erot = 1.80347448195222 | epot = -11.8163994450386 | etot = -8.37462302908989 +712000 ekin = 1.57892460631464 | erot = 1.91516553832625 | epot = -11.8687131735937 | etot = -8.37462302895278 +713000 ekin = 1.51786752130083 | erot = 2.04613993382096 | epot = -11.9386304840051 | etot = -8.37462302888328 +714000 ekin = 1.45734042325253 | erot = 2.1950944154761 | epot = -12.0270578676235 | etot = -8.37462302889484 +715000 ekin = 1.39951776248721 | erot = 2.35946536295161 | epot = -12.1336061544601 | etot = -8.3746230290213 +716000 ekin = 1.34639246829342 | erot = 2.53511986598189 | epot = -12.2561353635766 | etot = -8.37462302930131 +717000 ekin = 1.29955432270216 | erot = 2.71613012099189 | epot = -12.3903074734231 | etot = -8.3746230297291 +718000 ekin = 1.25989829927652 | erot = 2.89465680806849 | epot = -12.5291781377287 | etot = -8.37462303038367 +719000 ekin = 1.22750607430026 | erot = 3.06092665842397 | epot = -12.6630557638747 | etot = -8.37462303115044 +720000 ekin = 1.20188187066614 | erot = 3.20425006665573 | epot = -12.7807549692619 | etot = -8.37462303194004 +721000 ekin = 1.18220717983373 | erot = 3.3141488243266 | epot = -12.8709790367784 | etot = -8.3746230326181 +722000 ekin = 1.16774608427136 | erot = 3.38185582435497 | epot = -12.9242249417156 | etot = -8.37462303308926 +723000 ekin = 1.15807318397659 | erot = 3.40183188750264 | epot = -12.9345281046214 | etot = -8.37462303314213 +724000 ekin = 1.15381445068157 | erot = 3.37321067522537 | epot = -12.901648158662 | etot = -8.3746230327551 +725000 ekin = 1.15678266077584 | erot = 3.30036671004652 | epot = -12.8317724028189 | etot = -8.37462303199649 +726000 ekin = 1.1696197829831 | erot = 3.19222682083512 | epot = -12.7364696348452 | etot = -8.37462303102701 +727000 ekin = 1.19513165181162 | erot = 3.06063268781758 | epot = -12.6303873696662 | etot = -8.37462303003699 +728000 ekin = 1.23552066624092 | erot = 2.91835949413033 | epot = -12.5285031895567 | etot = -8.37462302918541 +729000 ekin = 1.29175272908879 | erot = 2.77740116858521 | epot = -12.4437769262438 | etot = -8.37462302856975 +730000 ekin = 1.3631967532209 | erot = 2.6478473435432 | epot = -12.3856671249871 | etot = -8.37462302822298 +731000 ekin = 1.44757535461241 | erot = 2.53736869400872 | epot = -12.3595670767507 | etot = -8.37462302812953 +732000 ekin = 1.54119076309627 | erot = 2.4511484979359 | epot = -12.3669622892787 | etot = -8.37462302824654 +733000 ekin = 1.63933166939861 | erot = 2.39205275840952 | epot = -12.406007456334 | etot = -8.37462302852592 +734000 ekin = 1.73673684349519 | erot = 2.3608723595031 | epot = -12.4722322319241 | etot = -8.37462302892585 +735000 ekin = 1.82801503458218 | erot = 2.356559637263 | epot = -12.5591977012566 | etot = -8.37462302941146 +736000 ekin = 1.90799093495898 | erot = 2.37647912513455 | epot = -12.6590930900387 | etot = -8.37462302994521 +737000 ekin = 1.97201607373641 | erot = 2.41675065087087 | epot = -12.7633897550831 | etot = -8.37462303047585 +738000 ekin = 2.01630111185462 | erot = 2.47274745432439 | epot = -12.8636715971181 | etot = -8.37462303093912 +739000 ekin = 2.03827941486831 | erot = 2.53972508206532 | epot = -12.952627528204 | etot = -8.37462303127039 +740000 ekin = 2.03693425612647 | erot = 2.61344505993508 | epot = -13.0250023474894 | etot = -8.37462303142788 +741000 ekin = 2.01297029115182 | erot = 2.69059268985891 | epot = -13.0781860124231 | etot = -8.37462303141239 +742000 ekin = 1.96872639114995 | erot = 2.7688256630284 | epot = -13.1121750854499 | etot = -8.37462303127155 +743000 ekin = 1.90780895371371 | erot = 2.84642411506738 | epot = -13.1288560998655 | etot = -8.37462303108443 +744000 ekin = 1.83452633952077 | erot = 2.92167512844567 | epot = -13.1308244989022 | etot = -8.37462303093574 +745000 ekin = 1.75327142724935 | erot = 2.99223326161803 | epot = -13.1201277197547 | etot = -8.3746230308873 +746000 ekin = 1.66800377362325 | erot = 3.05470990305885 | epot = -13.0973367076415 | etot = -8.37462303095935 +747000 ekin = 1.58193446041842 | erot = 3.10466510764481 | epot = -13.061222599179 | etot = -8.37462303111576 +748000 ekin = 1.49744243756514 | erot = 3.13708170332859 | epot = -13.0091471722146 | etot = -8.37462303132086 +749000 ekin = 1.4161800860191 | erot = 3.14699639332258 | epot = -12.9377995108339 | etot = -8.37462303149226 +750000 ekin = 1.33927892445981 | erot = 3.1303195534607 | epot = -12.8442215094952 | etot = -8.37462303157471 +751000 ekin = 1.26755716712031 | erot = 3.08449081841388 | epot = -12.7266710170761 | etot = -8.37462303154187 +752000 ekin = 1.20166403421531 | erot = 3.00876367724594 | epot = -12.5850507428583 | etot = -8.37462303139709 +753000 ekin = 1.14214671459707 | erot = 2.90415589317233 | epot = -12.4209256389297 | etot = -8.37462303116025 +754000 ekin = 1.08946987137415 | erot = 2.77319742895129 | epot = -12.2372903311776 | etot = -8.37462303085218 +755000 ekin = 1.04403390693365 | erot = 2.61963797727954 | epot = -12.0382949146995 | etot = -8.37462303048628 +756000 ekin = 1.00622473318939 | erot = 2.44820898509878 | epot = -11.8290567483568 | etot = -8.37462303006868 +757000 ekin = 0.976498427349965 | erot = 2.26449263382439 | epot = -11.6156140907484 | etot = -8.37462302957404 +758000 ekin = 0.955485081991406 | erot = 2.07490082913166 | epot = -11.4050089401822 | etot = -8.37462302905912 +759000 ekin = 0.943970421440628 | erot = 1.88597944059249 | epot = -11.2045728906025 | etot = -8.37462302856939 +760000 ekin = 0.942943189126763 | erot = 1.70391676484818 | epot = -11.0214829820775 | etot = -8.3746230281026 +761000 ekin = 0.953636819964326 | erot = 1.53434362883594 | epot = -10.8626034764889 | etot = -8.37462302768861 +762000 ekin = 0.9774394637126 | erot = 1.3819779354708 | epot = -10.7340404265357 | etot = -8.37462302735234 +763000 ekin = 1.01575214957204 | erot = 1.25038414093908 | epot = -10.6407593176234 | etot = -8.37462302711231 +764000 ekin = 1.06980632715056 | erot = 1.14186552721051 | epot = -10.5862948813426 | etot = -8.37462302698152 +765000 ekin = 1.14045321590795 | erot = 1.05746802222152 | epot = -10.5725442650988 | etot = -8.37462302696934 +766000 ekin = 1.22794009365067 | erot = 0.997057737110214 | epot = -10.5996208578434 | etot = -8.37462302708247 +767000 ekin = 1.33169356854964 | erot = 0.959438204818728 | epot = -10.6657548006927 | etot = -8.37462302732435 +768000 ekin = 1.4501370758167 | erot = 0.942489485935825 | epot = -10.7672495894454 | etot = -8.37462302769287 +769000 ekin = 1.58057826605241 | erot = 0.943330765762085 | epot = -10.898532059991 | etot = -8.37462302817651 +770000 ekin = 1.71920830316327 | erot = 0.958522817509944 | epot = -11.052354149423 | etot = -8.37462302874977 +771000 ekin = 1.86125297319058 | erot = 0.984329269146892 | epot = -11.2202052717077 | etot = -8.37462302937024 +772000 ekin = 2.00111996073798 | erot = 1.01706547585179 | epot = -11.3928084666678 | etot = -8.37462303007807 +773000 ekin = 2.13179679392768 | erot = 1.05343215414926 | epot = -11.5598519787697 | etot = -8.3746230306928 +774000 ekin = 2.24724323873895 | erot = 1.09038833142141 | epot = -11.7122546013489 | etot = -8.37462303118857 +775000 ekin = 2.3426359374738 | erot = 1.12564496608179 | epot = -11.8429039350775 | etot = -8.37462303152187 +776000 ekin = 2.41469510966563 | erot = 1.15782091196134 | epot = -11.9471390533043 | etot = -8.37462303167731 +777000 ekin = 2.46195564508681 | erot = 1.1863859033051 | epot = -12.022964580064 | etot = -8.37462303167205 +778000 ekin = 2.48471522536309 | erot = 1.21145891744878 | epot = -12.0707971743639 | etot = -8.37462303155203 +779000 ekin = 2.48466047806976 | erot = 1.23352809684396 | epot = -12.092811606291 | etot = -8.37462303137732 +780000 ekin = 2.46428568677078 | erot = 1.25319615838965 | epot = -12.0921048763578 | etot = -8.37462303119734 +781000 ekin = 2.42632307022413 | erot = 1.27107093313049 | epot = -12.0720170343822 | etot = -8.37462303102754 +782000 ekin = 2.37341747179021 | erot = 1.28787882377792 | epot = -12.0359193264101 | etot = -8.37462303084194 +783000 ekin = 2.30815170371668 | erot = 1.30476531775826 | epot = -11.9875400520692 | etot = -8.37462303059425 +784000 ekin = 2.23331824904064 | erot = 1.32360971124727 | epot = -11.9315509905407 | etot = -8.37462303025285 +785000 ekin = 2.15217666716612 | erot = 1.34711489735354 | epot = -11.8739145943546 | etot = -8.37462302983493 +786000 ekin = 2.06843940785569 | erot = 1.37850506799254 | epot = -11.8215675052575 | etot = -8.37462302940932 +787000 ekin = 1.9858834200417 | erot = 1.42085370631113 | epot = -11.7813601554289 | etot = -8.37462302907609 +788000 ekin = 1.90769396723605 | erot = 1.47626814207218 | epot = -11.7585851382313 | etot = -8.37462302892309 +789000 ekin = 1.83580155857396 | erot = 1.54525606071467 | epot = -11.7556806482778 | etot = -8.3746230289892 +790000 ekin = 1.77050160314611 | erot = 1.62653131912008 | epot = -11.7716559515141 | etot = -8.37462302924791 +791000 ekin = 1.71053482189894 | erot = 1.717315369065 | epot = -11.8024732205846 | etot = -8.37462302962068 +792000 ekin = 1.65360852454738 | erot = 1.81397519201809 | epot = -11.8422067465761 | etot = -8.37462303001059 +793000 ekin = 1.59715988493495 | erot = 1.91273671404254 | epot = -11.8845196293118 | etot = -8.37462303033427 +794000 ekin = 1.53909469766365 | erot = 2.01023412206039 | epot = -11.9239518502785 | etot = -8.37462303055444 +795000 ekin = 1.47829524949757 | erot = 2.103829410215 | epot = -11.9567476903381 | etot = -8.37462303062554 +796000 ekin = 1.41481662089641 | erot = 2.19194291994355 | epot = -11.9813825714076 | etot = -8.37462303056767 +797000 ekin = 1.3498130824975 | erot = 2.27401207106169 | epot = -11.9984481839612 | etot = -8.37462303040201 +798000 ekin = 1.28529636430788 | erot = 2.35042093010669 | epot = -12.010340324573 | etot = -8.37462303015844 +799000 ekin = 1.22381948474078 | erot = 2.42233570221871 | epot = -12.0207782168134 | etot = -8.37462302985392 +800000 ekin = 1.16822785386461 | erot = 2.4914343853454 | epot = -12.0342852688245 | etot = -8.37462302961449 +801000 ekin = 1.12099278642821 | erot = 2.55928816630625 | epot = -12.0549039821744 | etot = -8.37462302943995 +802000 ekin = 1.08396505814352 | erot = 2.62689447863089 | epot = -12.0854825661053 | etot = -8.37462302933093 +803000 ekin = 1.0584163696009 | erot = 2.69442631110622 | epot = -12.1274657101663 | etot = -8.37462302945918 +804000 ekin = 1.04426779801393 | erot = 2.76024770981027 | epot = -12.1791385376415 | etot = -8.37462302981732 +805000 ekin = 1.03995925233861 | erot = 2.820462542343 | epot = -12.2350448251542 | etot = -8.3746230304726 +806000 ekin = 1.04249639914768 | erot = 2.86897163061644 | epot = -12.286091060981 | etot = -8.37462303121685 +807000 ekin = 1.04816653315824 | erot = 2.8985035139628 | epot = -12.3212930790687 | etot = -8.37462303194768 +808000 ekin = 1.05329972431633 | erot = 2.90189493045883 | epot = -12.3298176872637 | etot = -8.37462303248858 +809000 ekin = 1.0551100311715 | erot = 2.87378175152242 | epot = -12.3035148153869 | etot = -8.37462303269303 +810000 ekin = 1.05231348649716 | erot = 2.81208782293683 | epot = -12.2390243420022 | etot = -8.37462303256824 +811000 ekin = 1.04519713626945 | erot = 2.7185412275192 | epot = -12.1383613957983 | etot = -8.37462303200969 +812000 ekin = 1.03556509620936 | erot = 2.59875418167731 | epot = -12.0089423091028 | etot = -8.37462303121614 +813000 ekin = 1.0261737080691 | erot = 2.46123250524489 | epot = -11.8620292436587 | etot = -8.37462303034468 +814000 ekin = 1.0199349938987 | erot = 2.31562695725955 | epot = -11.7101849806875 | etot = -8.37462302952927 +815000 ekin = 1.01938989930425 | erot = 2.17131439138523 | epot = -11.565327319542 | etot = -8.37462302885251 +816000 ekin = 1.02641070194428 | erot = 2.0364324772937 | epot = -11.437466207585 | etot = -8.37462302834705 +817000 ekin = 1.04210163741074 | erot = 1.91741411147782 | epot = -11.3341387769021 | etot = -8.37462302801356 +818000 ekin = 1.06685452879948 | erot = 1.81892194068062 | epot = -11.2603994972665 | etot = -8.37462302778642 +819000 ekin = 1.10044073145771 | erot = 1.74396570048653 | epot = -11.2190294597264 | etot = -8.37462302778212 +820000 ekin = 1.14169134058308 | erot = 1.69367065616412 | epot = -11.2099850246654 | etot = -8.37462302791824 +821000 ekin = 1.18877552115635 | erot = 1.66758281677157 | epot = -11.2309813661153 | etot = -8.3746230281874 +822000 ekin = 1.23927394202738 | erot = 1.66378494635111 | epot = -11.2776819169556 | etot = -8.37462302857712 +823000 ekin = 1.29027861043491 | erot = 1.67905219550407 | epot = -11.3439538348882 | etot = -8.37462302894924 +824000 ekin = 1.33894050069103 | erot = 1.70948347746263 | epot = -11.4230470076179 | etot = -8.37462302946421 +825000 ekin = 1.38220508272949 | erot = 1.7504425333049 | epot = -11.5072706460105 | etot = -8.37462302997613 +826000 ekin = 1.41710294910005 | erot = 1.79708475166576 | epot = -11.588810731177 | etot = -8.37462303041121 +827000 ekin = 1.44127249564728 | erot = 1.84518129446393 | epot = -11.66107682081 | etot = -8.37462303069882 +828000 ekin = 1.45335409116131 | erot = 1.89178230950048 | epot = -11.7197594314505 | etot = -8.37462303078868 +829000 ekin = 1.45330184509051 | erot = 1.93565038630986 | epot = -11.7635752620665 | etot = -8.37462303066615 +830000 ekin = 1.4425358875311 | erot = 1.9773267325415 | epot = -11.7944856504307 | etot = -8.3746230303581 +831000 ekin = 1.42321719807346 | erot = 2.01836652049591 | epot = -11.8162067486375 | etot = -8.37462303006811 +832000 ekin = 1.39798324786963 | erot = 2.06093497421873 | epot = -11.8335412516727 | etot = -8.37462302958432 +833000 ekin = 1.37122558103505 | erot = 2.10801499212763 | epot = -11.8538636023288 | etot = -8.37462302916612 +834000 ekin = 1.34739157346096 | erot = 2.16168408583467 | epot = -11.8836986881931 | etot = -8.37462302889746 +835000 ekin = 1.33033159138483 | erot = 2.22243990039529 | epot = -11.9273945206114 | etot = -8.37462302883124 +836000 ekin = 1.32279692350228 | erot = 2.28888168436561 | epot = -11.9863016368487 | etot = -8.37462302898085 +837000 ekin = 1.32614569946022 | erot = 2.35776552714737 | epot = -12.0585342559267 | etot = -8.37462302931913 +838000 ekin = 1.3403008431359 | erot = 2.42442328377117 | epot = -12.1393471566882 | etot = -8.37462302978115 +839000 ekin = 1.3639577057291 | erot = 2.48350186340837 | epot = -12.2220825994109 | etot = -8.37462303027338 +840000 ekin = 1.39499323416822 | erot = 2.52993036126689 | epot = -12.2995466261263 | etot = -8.37462303069118 +841000 ekin = 1.43098519524823 | erot = 2.55993796917592 | epot = -12.3655461953706 | etot = -8.37462303094641 +842000 ekin = 1.4697160397417 | erot = 2.57185321601787 | epot = -12.416192286756 | etot = -8.37462303099641 +843000 ekin = 1.50953312203678 | erot = 2.56639824287505 | epot = -12.4505543957724 | etot = -8.37462303086053 +844000 ekin = 1.5494822275751 | erot = 2.54631968024221 | epot = -12.4704249384311 | etot = -8.3746230306138 +845000 ekin = 1.58921446589507 | erot = 2.51544731878856 | epot = -12.4792848150415 | etot = -8.3746230303579 +846000 ekin = 1.62874660073367 | erot = 2.47751369443054 | epot = -12.4808833253451 | etot = -8.37462303018089 +847000 ekin = 1.66818957254906 | erot = 2.43516936578216 | epot = -12.4779819684582 | etot = -8.37462303012693 +848000 ekin = 1.70754173431461 | erot = 2.38953851004836 | epot = -12.4717032745481 | etot = -8.37462303018513 +849000 ekin = 1.74659403306467 | erot = 2.34043091651226 | epot = -12.4616479798778 | etot = -8.37462303030089 +850000 ekin = 1.78494345866239 | erot = 2.28706007037795 | epot = -12.4466265594442 | etot = -8.37462303040389 +851000 ekin = 1.82207688727501 | erot = 2.22891420063281 | epot = -12.425614118349 | etot = -8.37462303044114 +852000 ekin = 1.85747606626799 | erot = 2.16637383866296 | epot = -12.398472935331 | etot = -8.37462303040009 +853000 ekin = 1.89070501215685 | erot = 2.10080168938735 | epot = -12.366129731854 | etot = -8.37462303030978 +854000 ekin = 1.9214659857968 | erot = 2.03409194238599 | epot = -12.330180958406 | etot = -8.37462303022316 +855000 ekin = 1.94963553788746 | erot = 1.96792069995055 | epot = -12.2921792680263 | etot = -8.37462303018833 +856000 ekin = 1.97530408452615 | erot = 1.90306034569468 | epot = -12.2529874604462 | etot = -8.37462303022541 +857000 ekin = 1.99898235174409 | erot = 1.83954776716887 | epot = -12.2131531489759 | etot = -8.3746230300629 +858000 ekin = 2.021489668939 | erot = 1.77712472342471 | epot = -12.1732374225848 | etot = -8.37462303022108 +859000 ekin = 2.04332984814827 | erot = 1.71372610059514 | epot = -12.1316789790801 | etot = -8.37462303033664 +860000 ekin = 2.06530510863647 | erot = 1.64761266617994 | epot = -12.0875408051668 | etot = -8.37462303035041 +861000 ekin = 2.08844047523226 | erot = 1.57839130430651 | epot = -12.0414548097765 | etot = -8.37462303023775 +862000 ekin = 2.11372996877535 | erot = 1.50759861505441 | epot = -11.995951613855 | etot = -8.37462303002523 +863000 ekin = 2.14175193680092 | erot = 1.43866072802287 | epot = -11.9550356946146 | etot = -8.37462302979079 +864000 ekin = 2.17225364144349 | erot = 1.37614575517537 | epot = -11.9230224262557 | etot = -8.37462302963687 +865000 ekin = 2.20389689305164 | erot = 1.32450432847655 | epot = -11.9030242511673 | etot = -8.37462302963908 +866000 ekin = 2.23438769161315 | erot = 1.28681328070723 | epot = -11.8958240017944 | etot = -8.37462302947399 +867000 ekin = 2.26151301831573 | erot = 1.26501341500445 | epot = -11.9011494630794 | etot = -8.37462302975918 +868000 ekin = 2.28295312633917 | erot = 1.2587638567001 | epot = -11.9163400130163 | etot = -8.37462302997703 +869000 ekin = 2.2971313908785 | erot = 1.26636363803473 | epot = -11.9381180589604 | etot = -8.37462303004718 +870000 ekin = 2.30388454565948 | erot = 1.28638972777041 | epot = -11.9648973034185 | etot = -8.37462302998857 +871000 ekin = 2.30409365411964 | erot = 1.31787621263464 | epot = -11.9965928971127 | etot = -8.37462303035837 +872000 ekin = 2.29712455306151 | erot = 1.35930276714402 | epot = -12.0310503505619 | etot = -8.37462303035639 +873000 ekin = 2.2827453931599 | erot = 1.40846954678789 | epot = -12.065837970059 | etot = -8.37462303011121 +874000 ekin = 2.26320703627333 | erot = 1.46277950106371 | epot = -12.1006095675609 | etot = -8.3746230302239 +875000 ekin = 2.2400163472838 | erot = 1.51889022328766 | epot = -12.1335296008637 | etot = -8.37462303029222 +876000 ekin = 2.21430830466978 | erot = 1.57348199615719 | epot = -12.1624133311073 | etot = -8.37462303028036 +877000 ekin = 2.18777848573709 | erot = 1.62389020161555 | epot = -12.1862917175042 | etot = -8.3746230301516 +878000 ekin = 2.16252897547841 | erot = 1.66838793091172 | epot = -12.2055399364486 | etot = -8.37462303005844 +879000 ekin = 2.14044753721882 | erot = 1.70571411560968 | epot = -12.2207846828247 | etot = -8.37462302999622 +880000 ekin = 2.12277471002682 | erot = 1.73469967122049 | epot = -12.2320974112761 | etot = -8.37462303002882 +881000 ekin = 2.10977467359972 | erot = 1.75399371449064 | epot = -12.2383914182785 | etot = -8.37462303018811 +882000 ekin = 2.10050164322213 | erot = 1.7618701927401 | epot = -12.2369948664112 | etot = -8.37462303044894 +883000 ekin = 2.0929086771248 | erot = 1.75649694685427 | epot = -12.2240286546981 | etot = -8.37462303071903 +884000 ekin = 2.0843370364501 | erot = 1.7367150045659 | epot = -12.1956750719275 | etot = -8.37462303091147 +885000 ekin = 2.0720290157253 | erot = 1.70282592067542 | epot = -12.1494779673605 | etot = -8.37462303095973 +886000 ekin = 2.05378411491253 | erot = 1.65660476471949 | epot = -12.085011910269 | etot = -8.374623030637 +887000 ekin = 2.02874297420615 | erot = 1.60297409541309 | epot = -12.0063400996919 | etot = -8.37462303007265 +888000 ekin = 1.99720256582679 | erot = 1.54912086824386 | epot = -11.9209464635316 | etot = -8.3746230294609 +889000 ekin = 1.95913963735338 | erot = 1.50198702368973 | epot = -11.8357496899689 | etot = -8.37462302892583 +890000 ekin = 1.91617614841582 | erot = 1.46746689325636 | epot = -11.75826607021 | etot = -8.37462302853783 +891000 ekin = 1.87023137415679 | erot = 1.44931992810141 | epot = -11.694174330585 | etot = -8.37462302832684 +892000 ekin = 1.82316218734301 | erot = 1.44889048228522 | epot = -11.6466756979017 | etot = -8.37462302827347 +893000 ekin = 1.77672781685204 | erot = 1.46538080245969 | epot = -11.6167316476425 | etot = -8.3746230283308 +894000 ekin = 1.73267401007656 | erot = 1.49642015526123 | epot = -11.603717193777 | etot = -8.37462302843919 +895000 ekin = 1.69287615444159 | erot = 1.53876375542575 | epot = -11.6062629384076 | etot = -8.37462302854029 +896000 ekin = 1.6594652881061 | erot = 1.58897281258496 | epot = -11.6230611292876 | etot = -8.37462302859657 +897000 ekin = 1.63484229162877 | erot = 1.64389812681594 | epot = -11.6533634470428 | etot = -8.37462302859813 +898000 ekin = 1.62150447331787 | erot = 1.70104293751506 | epot = -11.6971704394058 | etot = -8.37462302857288 +899000 ekin = 1.62168394146005 | erot = 1.75850368945989 | epot = -11.754810659492 | etot = -8.37462302857205 +900000 ekin = 1.63689346404005 | erot = 1.81470313447866 | epot = -11.8262196271634 | etot = -8.37462302864474 +901000 ekin = 1.66753387742474 | erot = 1.86808611524118 | epot = -11.9102430214842 | etot = -8.37462302881828 +902000 ekin = 1.71269692237879 | erot = 1.91693084841925 | epot = -12.0042507998865 | etot = -8.37462302908844 +903000 ekin = 1.77021838508038 | erot = 1.95934050990336 | epot = -12.1041819244126 | etot = -8.37462302942886 +904000 ekin = 1.83694819296334 | erot = 1.99341312084054 | epot = -12.2049843435877 | etot = -8.37462302978381 +905000 ekin = 1.90914641653746 | erot = 2.0175452764756 | epot = -12.301314723126 | etot = -8.37462303011296 +906000 ekin = 1.98289589688105 | erot = 2.03065122058404 | epot = -12.3881701478506 | etot = -8.37462303038552 +907000 ekin = 2.05443877923752 | erot = 2.03228127523247 | epot = -12.4613430850605 | etot = -8.37462303059052 +908000 ekin = 2.12038320005706 | erot = 2.02259637574775 | epot = -12.5176026065384 | etot = -8.37462303073356 +909000 ekin = 2.17777472065196 | erot = 2.00223868776754 | epot = -12.5546364392486 | etot = -8.37462303082908 +910000 ekin = 2.22407231387502 | erot = 1.97218459089689 | epot = -12.5708799356595 | etot = -8.37462303088757 +911000 ekin = 2.2570988123033 | erot = 1.93367043925279 | epot = -12.565392282463 | etot = -8.37462303090695 +912000 ekin = 2.27504055965447 | erot = 1.88824345124255 | epot = -12.5379070417669 | etot = -8.37462303086985 +913000 ekin = 2.27654326616373 | erot = 1.83792322947823 | epot = -12.4890895263923 | etot = -8.37462303075033 +914000 ekin = 2.26395838706936 | erot = 1.78540897804491 | epot = -12.4239903947897 | etot = -8.37462302967546 +915000 ekin = 2.24045468911864 | erot = 1.7337281006883 | epot = -12.3488058193252 | etot = -8.37462302951822 +916000 ekin = 2.20520370201831 | erot = 1.68615105197114 | epot = -12.2659777833028 | etot = -8.37462302931332 +917000 ekin = 2.15800582905993 | erot = 1.64606783756472 | epot = -12.1786966957294 | etot = -8.37462302910471 +918000 ekin = 2.09921834411119 | erot = 1.61647797760392 | epot = -12.0903193506463 | etot = -8.37462302893123 +919000 ekin = 2.02966476142347 | erot = 1.59954949780366 | epot = -12.0038372880325 | etot = -8.37462302880535 +920000 ekin = 1.95065755949099 | erot = 1.59642144855954 | epot = -11.9217020368486 | etot = -8.37462302879802 +921000 ekin = 1.86366200650715 | erot = 1.6075086608029 | epot = -11.8457936959431 | etot = -8.37462302863303 +922000 ekin = 1.77152243885063 | erot = 1.63263587421854 | epot = -11.7787813414971 | etot = -8.37462302842796 +923000 ekin = 1.67869484032847 | erot = 1.67111175334959 | epot = -11.7244296218669 | etot = -8.3746230281888 +924000 ekin = 1.59024537021156 | erot = 1.72202288865011 | epot = -11.6868912868262 | etot = -8.37462302796453 +925000 ekin = 1.5112393703698 | erot = 1.78411652411382 | epot = -11.6699789223096 | etot = -8.37462302782603 +926000 ekin = 1.44599317764753 | erot = 1.85554834407746 | epot = -11.6761645495494 | etot = -8.37462302782441 +927000 ekin = 1.39752558601309 | erot = 1.93370661236091 | epot = -11.705855226336 | etot = -8.37462302796202 +928000 ekin = 1.36763823809792 | erot = 2.01538770681432 | epot = -11.7576489728028 | etot = -8.37462302789054 +929000 ekin = 1.36100399984171 | erot = 2.09737818238835 | epot = -11.8330052106967 | etot = -8.3746230284666 +930000 ekin = 1.35523134970901 | erot = 2.17722433884352 | epot = -11.9070787109409 | etot = -8.37462302238835 +931000 ekin = 1.39431469298964 | erot = 2.2543562043887 | epot = -12.0232939189524 | etot = -8.37462302157402 +932000 ekin = 1.49280866704539 | erot = 2.31847930194453 | epot = -12.1859109889642 | etot = -8.37462301997426 +933000 ekin = 1.58533340946056 | erot = 2.36490000058681 | epot = -12.3248564302729 | etot = -8.37462302022553 +934000 ekin = 1.68690712098002 | erot = 2.39298221169384 | epot = -12.4545123553122 | etot = -8.37462302263839 +935000 ekin = 1.78473836462927 | erot = 2.39676204061381 | epot = -12.5561234284514 | etot = -8.37462302320833 +936000 ekin = 1.86987725385837 | erot = 2.3725869373384 | epot = -12.6170872147064 | etot = -8.37462302350959 +937000 ekin = 1.93720452637544 | erot = 2.32043568374953 | epot = -12.6322632336339 | etot = -8.37462302350895 +938000 ekin = 1.9838520890903 | erot = 2.24266190734083 | epot = -12.6011370196561 | etot = -8.37462302322501 +939000 ekin = 2.00910923705166 | erot = 2.14379034932815 | epot = -12.5275226091129 | etot = -8.37462302273308 +940000 ekin = 2.01395507289469 | erot = 2.02993348653905 | epot = -12.4185115815289 | etot = -8.37462302209514 +941000 ekin = 2.00103743451551 | erot = 1.90808629517564 | epot = -12.2837467510699 | etot = -8.37462302137876 +942000 ekin = 1.97419824310303 | erot = 1.78546116622366 | epot = -12.1342824299697 | etot = -8.37462302064297 +943000 ekin = 1.93808318009234 | erot = 1.66892069893568 | epot = -11.9816268989622 | etot = -8.37462301993414 +944000 ekin = 1.8977766335859 | erot = 1.5645619851526 | epot = -11.8369616380283 | etot = -8.37462301928981 +945000 ekin = 1.85843605736167 | erot = 1.47742214177585 | epot = -11.7104812178821 | etot = -8.37462301874459 +946000 ekin = 1.82491092897238 | erot = 1.4112458813213 | epot = -11.6107798286296 | etot = -8.37462301833593 +947000 ekin = 1.80134221884099 | erot = 1.36826076777436 | epot = -11.5442260047188 | etot = -8.3746230181035 +948000 ekin = 1.79076227754137 | erot = 1.34894522657638 | epot = -11.5143305222011 | etot = -8.37462301808336 +949000 ekin = 1.79475359820903 | erot = 1.35184135985263 | epot = -11.5212179763541 | etot = -8.3746230182924 +950000 ekin = 1.81326202049733 | erot = 1.37352812801424 | epot = -11.5614131672234 | etot = -8.37462301871185 +951000 ekin = 1.8446612222921 | erot = 1.40888082073615 | epot = -11.6281650623084 | etot = -8.37462301928016 +952000 ekin = 1.88610598518233 | erot = 1.4516699630596 | epot = -11.7123989681437 | etot = -8.37462301990175 +953000 ekin = 1.93415626208905 | erot = 1.49545802208077 | epot = -11.8042373044988 | etot = -8.37462302032895 +954000 ekin = 1.98570845875077 | erot = 1.53486140750072 | epot = -11.8951928870223 | etot = -8.37462302077084 +955000 ekin = 2.03763688300367 | erot = 1.56575119866826 | epot = -11.9780111026998 | etot = -8.37462302102783 +956000 ekin = 2.08752516850609 | erot = 1.58576425991822 | epot = -12.0479124495199 | etot = -8.37462302109557 +957000 ekin = 2.13388693710885 | erot = 1.59443657078623 | epot = -12.1029465289009 | etot = -8.37462302100585 +958000 ekin = 2.17603134876192 | erot = 1.59291217741034 | epot = -12.1435665469851 | etot = -8.37462302081279 +959000 ekin = 2.21381255039506 | erot = 1.58343493106153 | epot = -12.1718705020323 | etot = -8.3746230205757 +960000 ekin = 2.24735101958149 | erot = 1.56876603526881 | epot = -12.1907400751984 | etot = -8.37462302034813 +961000 ekin = 2.27678636585367 | erot = 1.55164507323174 | epot = -12.2030544592552 | etot = -8.37462302016982 +962000 ekin = 2.30208813280194 | erot = 1.53436606871416 | epot = -12.2110772215839 | etot = -8.37462302006782 +963000 ekin = 2.32292955590359 | erot = 1.51849868398086 | epot = -12.2160512599392 | etot = -8.37462302005478 +964000 ekin = 2.33862421267619 | erot = 1.5047615187632 | epot = -12.2180087515685 | etot = -8.37462302012906 +965000 ekin = 2.34813222213658 | erot = 1.49304783092089 | epot = -12.2158030733316 | etot = -8.37462302027411 +966000 ekin = 2.35015122853745 | erot = 1.48260237418168 | epot = -12.2073766231763 | etot = -8.37462302045712 +967000 ekin = 2.34330726066801 | erot = 1.47233774696489 | epot = -12.1902680282645 | etot = -8.37462302063163 +968000 ekin = 2.32644504716153 | erot = 1.46125212630528 | epot = -12.1623201942108 | etot = -8.37462302074401 +969000 ekin = 2.29898771920432 | erot = 1.44887277461825 | epot = -12.1224835145672 | etot = -8.37462302074465 +970000 ekin = 2.26130276214926 | erot = 1.43562016619226 | epot = -12.0715459489416 | etot = -8.37462302060004 +971000 ekin = 2.21499063336789 | erot = 1.42298879008693 | epot = -12.0126024437583 | etot = -8.37462302030352 +972000 ekin = 2.16303757452058 | erot = 1.41348472406632 | epot = -11.951145318372 | etot = -8.37462301978514 +973000 ekin = 2.10950969273521 | erot = 1.41039391551463 | epot = -11.8945266278588 | etot = -8.37462301960897 +974000 ekin = 2.05703199419465 | erot = 1.41732503873172 | epot = -11.8489800520854 | etot = -8.37462301915903 +975000 ekin = 2.01010390574292 | erot = 1.43732066922268 | epot = -11.8220475937212 | etot = -8.37462301875562 +976000 ekin = 1.97340114976778 | erot = 1.47261385396339 | epot = -11.8206380222098 | etot = -8.37462301847868 +977000 ekin = 1.95082006443637 | erot = 1.52416835984564 | epot = -11.8496114426837 | etot = -8.37462301840164 +978000 ekin = 1.9447283226985 | erot = 1.5913101945952 | epot = -11.9106615358701 | etot = -8.3746230185764 +979000 ekin = 1.95538713570238 | erot = 1.67153495870807 | epot = -12.0015451134282 | etot = -8.37462301901775 +980000 ekin = 1.9806772386414 | erot = 1.76051368575892 | epot = -12.115813944186 | etot = -8.37462301978569 +981000 ekin = 2.01579571923818 | erot = 1.852073195397 | epot = -12.242491935286 | etot = -8.3746230206508 +982000 ekin = 2.05441082038431 | erot = 1.93952253756493 | epot = -12.3685563794515 | etot = -8.37462302150224 +983000 ekin = 2.08992138437299 | erot = 2.01671280308907 | epot = -12.4812572096455 | etot = -8.37462302218342 +984000 ekin = 2.11656909820189 | erot = 2.07910696967932 | epot = -12.5702990904574 | etot = -8.37462302257622 +985000 ekin = 2.13033501101521 | erot = 2.12464764347404 | epot = -12.6296056771257 | etot = -8.37462302263646 +986000 ekin = 2.12935596247826 | erot = 2.15403431725829 | epot = -12.6580133021397 | etot = -8.37462302240314 +987000 ekin = 2.11471923987147 | erot = 2.17104098415582 | epot = -12.6603832459134 | etot = -8.37462302188615 +988000 ekin = 2.09119735100847 | erot = 2.18228698931407 | epot = -12.6481073619509 | etot = -8.37462302162839 +989000 ekin = 2.06027968800836 | erot = 2.19075462083354 | epot = -12.6256573302404 | etot = -8.37462302139855 +990000 ekin = 2.02336255788427 | erot = 2.19843813688459 | epot = -12.5964237160094 | etot = -8.37462302124054 +991000 ekin = 1.98188077466453 | erot = 2.2063805572012 | epot = -12.562884353023 | etot = -8.37462302115728 +992000 ekin = 1.93715749695718 | erot = 2.21473069767444 | epot = -12.5265112157552 | etot = -8.3746230211236 +993000 ekin = 1.89038311211529 | erot = 2.2230775987835 | epot = -12.4880837320058 | etot = -8.37462302110698 +994000 ekin = 1.84266575141443 | erot = 2.23084817708077 | epot = -12.4481369495769 | etot = -8.37462302108169 +995000 ekin = 1.79502825849762 | erot = 2.23761065997439 | epot = -12.4072619394952 | etot = -8.37462302102315 +996000 ekin = 1.74865820356561 | erot = 2.24323231086636 | epot = -12.3665135353738 | etot = -8.37462302094188 +997000 ekin = 1.70508150017444 | erot = 2.24765365390765 | epot = -12.3273581749414 | etot = -8.37462302085929 +998000 ekin = 1.66588125244514 | erot = 2.25078611336597 | epot = -12.291290386589 | etot = -8.37462302077789 +999000 ekin = 1.63259998370637 | erot = 2.25262768593191 | epot = -12.2598506903133 | etot = -8.37462302067497 +1000000 ekin = 1.60661879878209 | erot = 2.25373528619522 | epot = -12.2349771055384 | etot = -8.37462302056112 + 1000000 0.1190088 -1.3493654 0.12586767 -1.0628358 0.00017426596 64000 +Loop time of 17.562 on 1 procs for 1000000 steps with 10 atoms + +Performance: 49197.105 tau/day, 56941.094 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.789 | 14.789 | 14.789 | 0.0 | 84.21 +Bond | 0.61289 | 0.61289 | 0.61289 | 0.0 | 3.49 +Neigh | 0.006141 | 0.006141 | 0.006141 | 0.0 | 0.03 +Comm | 0.32905 | 0.32905 | 0.32905 | 0.0 | 1.87 +Output | 0.098357 | 0.098357 | 0.098357 | 0.0 | 0.56 +Modify | 1.4688 | 1.4688 | 1.4688 | 0.0 | 8.36 +Other | | 0.2577 | | | 1.47 + +Nlocal: 10.0000 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37.0000 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7000000 +Ave special neighs/atom = 3.6000000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:17 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 new file mode 100644 index 0000000000..ed20d4c455 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 @@ -0,0 +1,1181 @@ +LAMMPS (2 Jul 2021) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +set atom * mass 3.1575 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -12.298895791142 | etot = -8.37462296864754 +Per MPI rank memory allocation (min/avg/max) = 9.194 | 9.195 | 9.196 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3370157 0.10712616 -1.1190359 -6.6192825e-05 64000 +1000 ekin = 1.07640077431763 | erot = 2.90684392233818 | epot = -12.357867665527 | etot = -8.37462296887121 +2000 ekin = 1.05363107794411 | erot = 2.99414178935848 | epot = -12.4223958364623 | etot = -8.37462296915967 +3000 ekin = 1.04083382823095 | erot = 3.07274362339768 | epot = -12.4882004210899 | etot = -8.37462296946131 +4000 ekin = 1.03780093165925 | erot = 3.13815143503908 | epot = -12.5505753364221 | etot = -8.37462296972372 +5000 ekin = 1.04371581655901 | erot = 3.18681185449848 | epot = -12.6051506409707 | etot = -8.37462296991324 +6000 ekin = 1.05738085799297 | erot = 3.21642353087471 | epot = -12.6484273588875 | etot = -8.37462297001986 +7000 ekin = 1.07739394884044 | erot = 3.22597832036687 | epot = -12.6779952392559 | etot = -8.37462297004859 +8000 ekin = 1.1022663747209 | erot = 3.21563966301724 | epot = -12.6925290077504 | etot = -8.37462297001224 +9000 ekin = 1.13051291055329 | erot = 3.18656247631357 | epot = -12.6916983567815 | etot = -8.37462296991463 +10000 ekin = 1.16073704358066 | erot = 3.14076972913364 | epot = -12.6761297424774 | etot = -8.37462296976313 +11000 ekin = 1.19170449380508 | erot = 3.08098965164645 | epot = -12.6473171150236 | etot = -8.37462296957207 +12000 ekin = 1.22238189802732 | erot = 3.0104025346826 | epot = -12.6074074020774 | etot = -8.37462296936752 +13000 ekin = 1.25192691881491 | erot = 2.9323026187282 | epot = -12.558852506718 | etot = -8.37462296917493 +14000 ekin = 1.27963857618761 | erot = 2.84975156813378 | epot = -12.5040131133431 | etot = -8.37462296902168 +15000 ekin = 1.30489368750127 | erot = 2.76534813925013 | epot = -12.444864795638 | etot = -8.37462296888657 +16000 ekin = 1.32709913751465 | erot = 2.6811818478553 | epot = -12.3829039541517 | etot = -8.3746229687817 +17000 ekin = 1.34568132349848 | erot = 2.59861285690791 | epot = -12.3189171492214 | etot = -8.37462296881501 +18000 ekin = 1.36011712604128 | erot = 2.51802979978581 | epot = -12.2527698947085 | etot = -8.37462296888139 +19000 ekin = 1.37000559015645 | erot = 2.43889875259721 | epot = -12.1835273117077 | etot = -8.37462296895404 +20000 ekin = 1.37516683465218 | erot = 2.36049590954916 | epot = -12.110285713206 | etot = -8.37462296900469 +21000 ekin = 1.37575335509461 | erot = 2.28221618930097 | epot = -12.0325925134032 | etot = -8.37462296900766 +22000 ekin = 1.37235802310954 | erot = 2.20383846967476 | epot = -11.9508194617284 | etot = -8.37462296894406 +23000 ekin = 1.36610326249355 | erot = 2.12570839352806 | epot = -11.8664346248251 | etot = -8.37462296880354 +24000 ekin = 1.35869525710697 | erot = 2.04881568638623 | epot = -11.7821339120793 | etot = -8.37462296858607 +25000 ekin = 1.35242255125602 | erot = 1.97475968439783 | epot = -11.7018052039588 | etot = -8.3746229683049 +26000 ekin = 1.35007012440099 | erot = 1.90560954362747 | epot = -11.6303026360114 | etot = -8.37462296798292 +27000 ekin = 1.3547433297047 | erot = 1.84367629115701 | epot = -11.5730425885209 | etot = -8.37462296765922 +28000 ekin = 1.36954369410757 | erot = 1.79121252282619 | epot = -11.5353791843193 | etot = -8.37462296738557 +29000 ekin = 1.39711560919905 | erot = 1.75006009044063 | epot = -11.5217986668611 | etot = -8.37462296722143 +30000 ekin = 1.4391109249101 | erot = 1.72127833748022 | epot = -11.5350122296155 | etot = -8.37462296722517 +31000 ekin = 1.49567630461198 | erot = 1.70480588615784 | epot = -11.5751051582053 | etot = -8.37462296743552 +32000 ekin = 1.56511285114187 | erot = 1.6992353898336 | epot = -11.6389712088326 | etot = -8.37462296785708 +33000 ekin = 1.64385110263249 | erot = 1.70198396265073 | epot = -11.7204580336835 | etot = -8.37462296840027 +34000 ekin = 1.72681002365037 | erot = 1.709463143449 | epot = -11.8108961361852 | etot = -8.37462296908579 +35000 ekin = 1.80812188596385 | erot = 1.71712980816868 | epot = -11.8998746638723 | etot = -8.37462296973973 +36000 ekin = 1.88201893971562 | erot = 1.72067857993909 | epot = -11.9773204899105 | etot = -8.37462297025577 +37000 ekin = 1.94364733336839 | erot = 1.71680208569971 | epot = -12.0350723896308 | etot = -8.37462297056268 +38000 ekin = 1.98961498615658 | erot = 1.7037090792949 | epot = -12.0679470360926 | etot = -8.37462297064112 +39000 ekin = 2.01818359901117 | erot = 1.6812671128222 | epot = -12.0740736823534 | etot = -8.37462297052003 +40000 ekin = 2.02914332282587 | erot = 1.65077260628056 | epot = -12.054538899364 | etot = -8.37462297025758 +41000 ekin = 2.02349103018124 | erot = 1.6144826235111 | epot = -12.0125966236109 | etot = -8.37462296991857 +42000 ekin = 2.00304412554535 | erot = 1.57509121259575 | epot = -11.9527583076989 | etot = -8.3746229695578 +43000 ekin = 1.97008148028979 | erot = 1.53529510620986 | epot = -11.8799995557137 | etot = -8.37462296921407 +44000 ekin = 1.92705109571092 | erot = 1.49750726070826 | epot = -11.7991813253589 | etot = -8.37462296893973 +45000 ekin = 1.87634986385881 | erot = 1.46354390598901 | epot = -11.714516738533 | etot = -8.37462296868513 +46000 ekin = 1.82016797429767 | erot = 1.43491031451218 | epot = -11.6297012572907 | etot = -8.37462296848089 +47000 ekin = 1.76039182009028 | erot = 1.41286016407 | epot = -11.5478749524838 | etot = -8.37462296832354 +48000 ekin = 1.69856949274782 | erot = 1.39838217522424 | epot = -11.4715746361764 | etot = -8.37462296820431 +49000 ekin = 1.63593954988751 | erot = 1.39228918140577 | epot = -11.4028516994045 | etot = -8.37462296811125 +50000 ekin = 1.573518015373 | erot = 1.39530041169494 | epot = -11.3434413950978 | etot = -8.37462296802981 +51000 ekin = 1.51222872476358 | erot = 1.4081065034094 | epot = -11.2949581961197 | etot = -8.37462296794667 +52000 ekin = 1.45305245526496 | erot = 1.43140550730924 | epot = -11.2590809304253 | etot = -8.37462296785112 +53000 ekin = 1.39716366086923 | erot = 1.4658956749353 | epot = -11.2376823035407 | etot = -8.37462296773616 +54000 ekin = 1.34602153837051 | erot = 1.51222067984185 | epot = -11.2328651858293 | etot = -8.37462296761691 +55000 ekin = 1.30138436197336 | erot = 1.57077970891815 | epot = -11.2467870384001 | etot = -8.37462296750862 +56000 ekin = 1.26522647192236 | erot = 1.64151101613076 | epot = -11.2813604554934 | etot = -8.37462296744032 +57000 ekin = 1.23956119808443 | erot = 1.7236309263303 | epot = -11.3378150918587 | etot = -8.37462296744395 +58000 ekin = 1.22620283906733 | erot = 1.81539828229232 | epot = -11.4162240889028 | etot = -8.37462296754315 +59000 ekin = 1.22652758768657 | erot = 1.9140038119354 | epot = -11.5151543673671 | etot = -8.37462296774508 +60000 ekin = 1.24129579501625 | erot = 2.01564970996732 | epot = -11.6315684730208 | etot = -8.3746229680372 +61000 ekin = 1.27057003505326 | erot = 2.11581304358659 | epot = -11.7610060470469 | etot = -8.374622968407 +62000 ekin = 1.31372115356101 | erot = 2.20955642503236 | epot = -11.8979005473865 | etot = -8.37462296879312 +63000 ekin = 1.36947667734272 | erot = 2.29224896410223 | epot = -12.0363486106148 | etot = -8.37462296916984 +64000 ekin = 1.43596184816382 | erot = 2.35998108781796 | epot = -12.1705659055146 | etot = -8.37462296953284 +65000 ekin = 1.5108757081499 | erot = 2.40947275989084 | epot = -12.2949714378725 | etot = -8.37462296983178 +66000 ekin = 1.59162978656359 | erot = 2.43872351537726 | epot = -12.4049762719856 | etot = -8.37462297004473 +67000 ekin = 1.67546349074597 | erot = 2.44726186999247 | epot = -12.4973483309001 | etot = -8.3746229701617 +68000 ekin = 1.75953613825231 | erot = 2.43621057967589 | epot = -12.5703696881153 | etot = -8.37462297018708 +69000 ekin = 1.84098201456594 | erot = 2.40815676459637 | epot = -12.6237617493034 | etot = -8.37462297014108 +70000 ekin = 1.9169281052228 | erot = 2.36682660300827 | epot = -12.6583776782864 | etot = -8.37462297005529 +71000 ekin = 1.9844938047305 | erot = 2.31661131420484 | epot = -12.6757280888521 | etot = -8.37462296991679 +72000 ekin = 2.04081287193519 | erot = 2.26215174487669 | epot = -12.6775875867421 | etot = -8.37462296993018 +73000 ekin = 2.08263291328363 | erot = 2.2074336386418 | epot = -12.6646895218712 | etot = -8.3746229699458 +74000 ekin = 2.1069858415085 | erot = 2.15544421118363 | epot = -12.6370530226939 | etot = -8.3746229700018 +75000 ekin = 2.11136525908731 | erot = 2.1081694067506 | epot = -12.5941576359031 | etot = -8.37462297006514 +76000 ekin = 2.09405873141411 | erot = 2.06669472630762 | epot = -12.5353764278106 | etot = -8.37462297008889 +77000 ekin = 2.05455135347917 | erot = 2.03147933575646 | epot = -12.4606536592619 | etot = -8.37462297002628 +78000 ekin = 1.99386684227705 | erot = 2.0026817101331 | epot = -12.3711715222579 | etot = -8.37462296984776 +79000 ekin = 1.91474155283397 | erot = 1.98040758803654 | epot = -12.2697721104225 | etot = -8.37462296955195 +80000 ekin = 1.82155513477577 | erot = 1.9647973478023 | epot = -12.1609754517452 | etot = -8.3746229691671 +81000 ekin = 1.71999782481694 | erot = 1.95595086125355 | epot = -12.050571654813 | etot = -8.37462296874256 +82000 ekin = 1.61651478139498 | erot = 1.95375810375277 | epot = -11.9448958534852 | etot = -8.37462296833741 +83000 ekin = 1.51761134750079 | erot = 1.9577277486065 | epot = -11.8499620641155 | etot = -8.37462296800824 +84000 ekin = 1.42912416355166 | erot = 1.96688313409217 | epot = -11.7706302654419 | etot = -8.37462296779805 +85000 ekin = 1.35556895555397 | erot = 1.97976517498703 | epot = -11.7099570982739 | etot = -8.37462296773285 +86000 ekin = 1.29966988136848 | erot = 1.99452593271721 | epot = -11.6688187819006 | etot = -8.37462296781488 +87000 ekin = 1.26213747948969 | erot = 2.00910214170812 | epot = -11.6458625892977 | etot = -8.37462296809987 +88000 ekin = 1.24134500163876 | erot = 2.02122064243495 | epot = -11.6371886124845 | etot = -8.37462296841076 +89000 ekin = 1.23421644947628 | erot = 2.02900530500622 | epot = -11.6378447232196 | etot = -8.37462296873706 +90000 ekin = 1.23690604243587 | erot = 2.03136372571867 | epot = -11.6428927371715 | etot = -8.374622969017 +91000 ekin = 1.24531053049766 | erot = 2.02816188261866 | epot = -11.6480953823212 | etot = -8.37462296920492 +92000 ekin = 1.25564394227081 | erot = 2.02032873397354 | epot = -11.6505956455253 | etot = -8.37462296928095 +93000 ekin = 1.2648401881744 | erot = 2.00975004471106 | epot = -11.6492132021397 | etot = -8.3746229692542 +94000 ekin = 1.27076152680855 | erot = 1.99896253062564 | epot = -11.6443470265802 | etot = -8.374622969146 +95000 ekin = 1.27224696211196 | erot = 1.99076889271348 | epot = -11.6376388238182 | etot = -8.37462296899275 +96000 ekin = 1.26905385172933 | erot = 1.9877690850581 | epot = -11.6314459056159 | etot = -8.3746229688285 +97000 ekin = 1.26173398384364 | erot = 1.99196117307494 | epot = -11.6283181256016 | etot = -8.37462296868301 +98000 ekin = 1.25146122958159 | erot = 2.00445279489008 | epot = -11.6305369930525 | etot = -8.37462296858079 +99000 ekin = 1.23981039935426 | erot = 2.02529911459878 | epot = -11.6397324824947 | etot = -8.37462296854163 +100000 ekin = 1.22848889431703 | erot = 2.05346079777948 | epot = -11.6565726606772 | etot = -8.37462296858067 +101000 ekin = 1.21904296342442 | erot = 2.08686922543173 | epot = -11.6805351575619 | etot = -8.37462296870573 +102000 ekin = 1.21258708443156 | erot = 2.12259257652706 | epot = -11.7098026298707 | etot = -8.37462296891212 +103000 ekin = 1.20962138127621 | erot = 2.15710417867594 | epot = -11.7413485291302 | etot = -8.37462296917809 +104000 ekin = 1.2099943506476 | erot = 2.18665201736537 | epot = -11.7712693374782 | etot = -8.37462296946522 +105000 ekin = 1.21303379771957 | erot = 2.20771017012394 | epot = -11.7953669375663 | etot = -8.37462296972275 +106000 ekin = 1.21781939160547 | erot = 2.21746426398226 | epot = -11.809906625485 | etot = -8.37462296989724 +107000 ekin = 1.22352668485517 | erot = 2.21425769941226 | epot = -11.8124073542123 | etot = -8.37462296994488 +108000 ekin = 1.2297537161671 | erot = 2.19791821277335 | epot = -11.8022948987808 | etot = -8.37462296984036 +109000 ekin = 1.23675326669537 | erot = 2.16990174523003 | epot = -11.7812779815078 | etot = -8.37462296958244 +110000 ekin = 1.24552660594299 | erot = 2.13322593016602 | epot = -11.7533755053018 | etot = -8.37462296919279 +111000 ekin = 1.2577699492818 | erot = 2.09220325002891 | epot = -11.7245961680231 | etot = -8.37462296871236 +112000 ekin = 1.27568807280463 | erot = 2.05200951342218 | epot = -11.7023205544233 | etot = -8.37462296819652 +113000 ekin = 1.30169744977554 | erot = 2.01813224570283 | epot = -11.6944526631891 | etot = -8.37462296771077 +114000 ekin = 1.33804251858946 | erot = 1.99574344242906 | epot = -11.7084089283445 | etot = -8.37462296732602 +115000 ekin = 1.38647431929538 | erot = 1.98903581447797 | epot = -11.7501331008331 | etot = -8.37462296705971 +116000 ekin = 1.44876446583397 | erot = 2.00047074173041 | epot = -11.8238581746945 | etot = -8.37462296713016 +117000 ekin = 1.52378581535561 | erot = 2.03044339408211 | epot = -11.9288521768883 | etot = -8.37462296745063 +118000 ekin = 1.6084059418419 | erot = 2.07707436259023 | epot = -12.0601032724452 | etot = -8.37462296801304 +119000 ekin = 1.69804077960493 | erot = 2.13624566567636 | epot = -12.2089094140527 | etot = -8.37462296877144 +120000 ekin = 1.78696647862287 | erot = 2.20199105617499 | epot = -12.363580504444 | etot = -8.37462296964609 +121000 ekin = 1.86883508536314 | erot = 2.2671883740786 | epot = -12.5106464299765 | etot = -8.37462297053475 +122000 ekin = 1.93731263285359 | erot = 2.32446087034981 | epot = -12.6363964745337 | etot = -8.3746229713303 +123000 ekin = 1.9867358794579 | erot = 2.36714489985536 | epot = -12.7285037512507 | etot = -8.37462297193745 +124000 ekin = 2.01268857483492 | erot = 2.39015976226602 | epot = -12.7774713093892 | etot = -8.37462297228827 +125000 ekin = 2.01242153120629 | erot = 2.39062925356834 | epot = -12.7776737571262 | etot = -8.37462297235156 +126000 ekin = 1.9850729032809 | erot = 2.36815351492914 | epot = -12.7278493903454 | etot = -8.37462297213533 +127000 ekin = 1.93167931643428 | erot = 2.32470375634654 | epot = -12.6310060444623 | etot = -8.37462297168151 +128000 ekin = 1.85500076916896 | erot = 2.26419178968088 | epot = -12.4938155299042 | etot = -8.37462297105431 +129000 ekin = 1.75920795598156 | erot = 2.19182812292651 | epot = -12.3256590492353 | etot = -8.37462297032725 +130000 ekin = 1.64949415840205 | erot = 2.11340935726388 | epot = -12.1375264852353 | etot = -8.37462296956937 +131000 ekin = 1.53167143066935 | erot = 2.03466319554045 | epot = -11.9409575950479 | etot = -8.37462296883812 +132000 ekin = 1.41179399813997 | erot = 1.96073697301965 | epot = -11.7471539393349 | etot = -8.37462296817531 +133000 ekin = 1.29582771791057 | erot = 1.89586175533339 | epot = -11.5663124408529 | etot = -8.37462296760899 +134000 ekin = 1.18933366770496 | erot = 1.84313053331046 | epot = -11.4070871682759 | etot = -8.37462296726045 +135000 ekin = 1.09698845763054 | erot = 1.80418246558968 | epot = -11.2757938901597 | etot = -8.37462296693951 +136000 ekin = 1.02270904454078 | erot = 1.7798919585222 | epot = -11.1772239698133 | etot = -8.37462296675035 +137000 ekin = 0.969402888595009 | erot = 1.77022137974263 | epot = -11.1142472350344 | etot = -8.37462296669672 +138000 ekin = 0.938766242876245 | erot = 1.77423425797214 | epot = -11.0876234676246 | etot = -8.37462296677622 +139000 ekin = 0.931209536918429 | erot = 1.79022284403589 | epot = -11.0960553479291 | etot = -8.37462296697477 +140000 ekin = 0.945902360873547 | erot = 1.81588277986749 | epot = -11.1364081080066 | etot = -8.37462296726554 +141000 ekin = 0.980951010694929 | erot = 1.84854552854054 | epot = -11.2041195068457 | etot = -8.37462296761028 +142000 ekin = 1.03368854660408 | erot = 1.88546172258946 | epot = -11.2937732371591 | etot = -8.37462296796555 +143000 ekin = 1.10102464558782 | erot = 1.92410215903321 | epot = -11.3997497729122 | etot = -8.37462296829122 +144000 ekin = 1.17978371180456 | erot = 1.96241851789384 | epot = -11.5168251982587 | etot = -8.37462296856033 +145000 ekin = 1.26696389973261 | erot = 1.99907135517311 | epot = -11.6406582236455 | etot = -8.37462296873974 +146000 ekin = 1.35987698631718 | erot = 2.03338468070467 | epot = -11.7678846359143 | etot = -8.37462296889242 +147000 ekin = 1.45616095202976 | erot = 2.06502561999209 | epot = -11.8958095410383 | etot = -8.3746229690165 +148000 ekin = 1.5536968549109 | erot = 2.09388144715385 | epot = -12.022201271207 | etot = -8.37462296914221 +149000 ekin = 1.65047924324436 | erot = 2.11976671620332 | epot = -12.1448689287432 | etot = -8.37462296929551 +150000 ekin = 1.74448791629845 | erot = 2.1421786790356 | epot = -12.2612895648256 | etot = -8.37462296949154 +151000 ekin = 1.83359650490145 | erot = 2.16016451670444 | epot = -12.3683839913399 | etot = -8.37462296973401 +152000 ekin = 1.91553611044667 | erot = 2.17231614291472 | epot = -12.4624752233732 | etot = -8.37462297001185 +153000 ekin = 1.98791755611547 | erot = 2.17689716712716 | epot = -12.539437693548 | etot = -8.37462297030538 +154000 ekin = 2.04830722999057 | erot = 2.17205709329794 | epot = -12.5949872938781 | etot = -8.37462297058956 +155000 ekin = 2.09434778140688 | erot = 2.15608363214667 | epot = -12.6250543843906 | etot = -8.37462297083706 +156000 ekin = 2.12391577783721 | erot = 2.12765251039857 | epot = -12.6261912592565 | etot = -8.37462297102076 +157000 ekin = 2.1353100469757 | erot = 2.0860457491324 | epot = -12.5959787672229 | etot = -8.37462297111477 +158000 ekin = 2.12746223168626 | erot = 2.03132820631866 | epot = -12.5334134090999 | etot = -8.37462297109495 +159000 ekin = 2.10015103339247 | erot = 1.96448478929011 | epot = -12.4392587936244 | etot = -8.37462297094182 +160000 ekin = 2.05418416063722 | erot = 1.88751839461952 | epot = -12.3163255258997 | etot = -8.37462297064294 +161000 ekin = 1.99149541371344 | erot = 1.80350457154665 | epot = -12.1696229554607 | etot = -8.37462297020065 +162000 ekin = 1.91510266104762 | erot = 1.71656915682389 | epot = -12.0062947875077 | etot = -8.37462296963622 +163000 ekin = 1.82889680262297 | erot = 1.63175766791089 | epot = -11.8352774395238 | etot = -8.37462296898997 +164000 ekin = 1.73727850175433 | erot = 1.5547745055745 | epot = -11.6666759756467 | etot = -8.37462296831787 +165000 ekin = 1.6447087543994 | erot = 1.49159241029582 | epot = -11.5109241323764 | etot = -8.3746229676812 +166000 ekin = 1.55526715399666 | erot = 1.44796523954041 | epot = -11.3778553606752 | etot = -8.3746229671381 +167000 ekin = 1.47230568197398 | erot = 1.42890789301304 | epot = -11.27583654172 | etot = -8.374622966733 +168000 ekin = 1.39825202215371 | erot = 1.4382252321603 | epot = -11.2111002208047 | etot = -8.37462296649065 +169000 ekin = 1.3345719619018 | erot = 1.4781674025412 | epot = -11.187362330859 | etot = -8.37462296641595 +170000 ekin = 1.28186404086337 | erot = 1.5492593913673 | epot = -11.2057463987267 | etot = -8.37462296649605 +171000 ekin = 1.24010532837069 | erot = 1.65031493319924 | epot = -11.2650432281445 | etot = -8.37462296657455 +172000 ekin = 1.20973432363927 | erot = 1.77850842430643 | epot = -11.3628657149161 | etot = -8.37462296697039 +173000 ekin = 1.18958106737854 | erot = 1.92939472681626 | epot = -11.4935987616323 | etot = -8.37462296743751 +174000 ekin = 1.17780375666815 | erot = 2.09752621801757 | epot = -11.6499529426364 | etot = -8.37462296795064 +175000 ekin = 1.17250284106946 | erot = 2.27682305293081 | epot = -11.8239488624896 | etot = -8.37462296848935 +176000 ekin = 1.17177313417523 | erot = 2.46086230703696 | epot = -12.0072584102478 | etot = -8.37462296903563 +177000 ekin = 1.17372471418906 | erot = 2.64315812275385 | epot = -12.1915058065132 | etot = -8.37462296957025 +178000 ekin = 1.17649725816085 | erot = 2.81745378599582 | epot = -12.3685740142269 | etot = -8.37462297007019 +179000 ekin = 1.17828959842952 | erot = 2.97803885665143 | epot = -12.5309514255899 | etot = -8.37462297050891 +180000 ekin = 1.17741681901028 | erot = 3.12008209304906 | epot = -12.6721218829181 | etot = -8.37462297085878 +181000 ekin = 1.1723947928011 | erot = 3.23994177497995 | epot = -12.7869595388777 | etot = -8.37462297109667 +182000 ekin = 1.1620416167421 | erot = 3.33528346670201 | epot = -12.871948054926 | etot = -8.37462297148189 +183000 ekin = 1.14544700201208 | erot = 3.40346825728336 | epot = -12.9235382308529 | etot = -8.37462297155747 +184000 ekin = 1.12187454429775 | erot = 3.44382690739269 | epot = -12.9403244231948 | etot = -8.3746229715044 +185000 ekin = 1.09113819766591 | erot = 3.45752421108418 | epot = -12.9232853800837 | etot = -8.37462297133365 +186000 ekin = 1.05375177637583 | erot = 3.4468126024859 | epot = -12.8751873499238 | etot = -8.37462297106209 +187000 ekin = 1.01100426926478 | erot = 3.41470705189775 | epot = -12.8003342918715 | etot = -8.37462297070899 +188000 ekin = 0.964980950088774 | erot = 3.36467106156949 | epot = -12.7042749819532 | etot = -8.37462297029496 +189000 ekin = 0.918502012521176 | erot = 3.30025095733366 | epot = -12.5933759397282 | etot = -8.37462296987338 +190000 ekin = 0.874955375625786 | erot = 3.22483721777298 | epot = -12.4744155628192 | etot = -8.37462296942041 +191000 ekin = 0.838012694189986 | erot = 3.14179385100332 | epot = -12.3544295141829 | etot = -8.37462296898962 +192000 ekin = 0.811264586710963 | erot = 3.05421641257493 | epot = -12.2401039678973 | etot = -8.37462296861143 +193000 ekin = 0.797833231457362 | erot = 2.96485918306436 | epot = -12.1373153828321 | etot = -8.37462296831036 +194000 ekin = 0.800032366300468 | erot = 2.87610608236725 | epot = -12.0507614167682 | etot = -8.37462296810044 +195000 ekin = 0.819137512919597 | erot = 2.78998115247884 | epot = -11.9837416333826 | etot = -8.37462296798416 +196000 ekin = 0.855301818719039 | erot = 2.7081876552627 | epot = -11.9381124419349 | etot = -8.37462296795316 +197000 ekin = 0.907617485284263 | erot = 2.6321557447555 | epot = -11.9143961980329 | etot = -8.37462296799313 +198000 ekin = 0.974291517583769 | erot = 2.56307623018493 | epot = -11.911990715856 | etot = -8.37462296808732 +199000 ekin = 1.0528865187871 | erot = 2.50190471363201 | epot = -11.9294142006398 | etot = -8.3746229682207 +200000 ekin = 1.14057530731152 | erot = 2.44933274089605 | epot = -11.9645310165894 | etot = -8.37462296838183 +201000 ekin = 1.23436945655699 | erot = 2.4057357740475 | epot = -12.0147281991679 | etot = -8.37462296856337 +202000 ekin = 1.33129982084388 | erot = 2.37111655194196 | epot = -12.0770393415457 | etot = -8.37462296875989 +203000 ekin = 1.42854451444347 | erot = 2.34506402190598 | epot = -12.148231505317 | etot = -8.37462296896754 +204000 ekin = 1.52351160571773 | erot = 2.32674290434286 | epot = -12.224877479242 | etot = -8.37462296918144 +205000 ekin = 1.61388837059984 | erot = 2.31491995505487 | epot = -12.3034312950507 | etot = -8.37462296939603 +206000 ekin = 1.69766775260718 | erot = 2.3080250040048 | epot = -12.3803157262167 | etot = -8.37462296960474 +207000 ekin = 1.77315874687775 | erot = 2.30423562983907 | epot = -12.4520173465201 | etot = -8.3746229698033 +208000 ekin = 1.83898325555867 | erot = 2.30156289475869 | epot = -12.515169120302 | etot = -8.37462296998464 +209000 ekin = 1.89406065254616 | erot = 2.29797193080379 | epot = -12.5666555534941 | etot = -8.37462297014415 +210000 ekin = 1.93758171355925 | erot = 2.29149245614576 | epot = -12.6036971399825 | etot = -8.37462297027751 +211000 ekin = 1.96897499678795 | erot = 2.28032999988906 | epot = -12.6239279670577 | etot = -8.37462297038067 +212000 ekin = 1.98787057423956 | erot = 2.26297816329984 | epot = -12.6254717079894 | etot = -8.37462297044996 +213000 ekin = 1.99406615310661 | erot = 2.23834847729583 | epot = -12.6070376008829 | etot = -8.3746229704805 +214000 ekin = 1.98749971048357 | erot = 2.20579329600858 | epot = -12.5679159769726 | etot = -8.37462297048041 +215000 ekin = 1.96823269345748 | erot = 2.16512069835616 | epot = -12.5079763622598 | etot = -8.37462297044615 +216000 ekin = 1.93645036858827 | erot = 2.11663233289607 | epot = -12.4277056718664 | etot = -8.37462297038201 +217000 ekin = 1.89249565101184 | erot = 2.06105227365565 | epot = -12.3281708949563 | etot = -8.37462297028879 +218000 ekin = 1.83696296101026 | erot = 1.99944931813373 | epot = -12.2110352493004 | etot = -8.37462297015639 +219000 ekin = 1.77087997200072 | erot = 1.93321768349764 | epot = -12.0787206254579 | etot = -8.37462296995955 +220000 ekin = 1.69598414200906 | erot = 1.86416918368618 | epot = -11.9347762953552 | etot = -8.37462296965996 +221000 ekin = 1.61504938765182 | erot = 1.79472971030261 | epot = -11.7844020671758 | etot = -8.37462296922139 +222000 ekin = 1.53214607792093 | erot = 1.72813764736988 | epot = -11.6349066939258 | etot = -8.37462296863498 +223000 ekin = 1.4526624088324 | erot = 1.66846349300119 | epot = -11.4957488697767 | etot = -8.37462296794309 +224000 ekin = 1.38293292450221 | erot = 1.6202792722125 | epot = -11.3778351639601 | etot = -8.37462296724537 +225000 ekin = 1.32944348952842 | erot = 1.58793473617121 | epot = -11.2920011923814 | etot = -8.37462296668181 +226000 ekin = 1.29777350141066 | erot = 1.57457480049478 | epot = -11.2469712682745 | etot = -8.3746229663691 +227000 ekin = 1.29158711545539 | erot = 1.58136206120086 | epot = -11.24757214304 | etot = -8.37462296638379 +228000 ekin = 1.31199160550521 | erot = 1.60705168356011 | epot = -11.2936662557515 | etot = -8.37462296668622 +229000 ekin = 1.35720775781596 | erot = 1.64872427968725 | epot = -11.3805550048103 | etot = -8.37462296730712 +230000 ekin = 1.42320705813339 | erot = 1.70117239435445 | epot = -11.499002420542 | etot = -8.37462296805411 +231000 ekin = 1.50467169677581 | erot = 1.75808746579057 | epot = -11.6373821313689 | etot = -8.37462296880256 +232000 ekin = 1.59576180204782 | erot = 1.81345446216766 | epot = -11.7838392336738 | etot = -8.37462296945837 +233000 ekin = 1.69077156764762 | erot = 1.86233770608592 | epot = -11.9277322437048 | etot = -8.3746229699713 +234000 ekin = 1.78453671679902 | erot = 1.90129507954651 | epot = -12.0604547666786 | etot = -8.37462297033305 +235000 ekin = 1.87261122258967 | erot = 1.9284220717117 | epot = -12.1756562648638 | etot = -8.37462297056238 +236000 ekin = 1.95129507586051 | erot = 1.94312673772466 | epot = -12.269044784275 | etot = -8.37462297068982 +237000 ekin = 2.01688127570893 | erot = 1.94587838549638 | epot = -12.3373826321085 | etot = -8.37462297090321 +238000 ekin = 2.06554471096635 | erot = 1.93754713481384 | epot = -12.3777148167605 | etot = -8.37462297098031 +239000 ekin = 2.09498833917104 | erot = 1.91896908743933 | epot = -12.3885803976059 | etot = -8.37462297099549 +240000 ekin = 2.10387887335863 | erot = 1.89114067893478 | epot = -12.3696425232248 | etot = -8.37462297093134 +241000 ekin = 2.09205058134751 | erot = 1.85524232773722 | epot = -12.3219158798517 | etot = -8.37462297076695 +242000 ekin = 2.06070692356717 | erot = 1.81270484104131 | epot = -12.2480347350926 | etot = -8.37462297048416 +243000 ekin = 2.01255526288379 | erot = 1.76529169809285 | epot = -12.1524699310582 | etot = -8.37462297008152 +244000 ekin = 1.95178746173543 | erot = 1.71512317980746 | epot = -12.0415336111125 | etot = -8.37462296956963 +245000 ekin = 1.88387514784693 | erot = 1.66462101119872 | epot = -11.923119128034 | etot = -8.37462296898834 +246000 ekin = 1.81512558267768 | erot = 1.61637080971493 | epot = -11.8061193607913 | etot = -8.37462296839864 +247000 ekin = 1.75197548737583 | erot = 1.57289129038632 | epot = -11.6994897456361 | etot = -8.37462296787399 +248000 ekin = 1.70016015194915 | erot = 1.53636641743628 | epot = -11.6111495368723 | etot = -8.37462296748684 +249000 ekin = 1.66404391454307 | erot = 1.50839677555145 | epot = -11.5470636572528 | etot = -8.37462296715831 +250000 ekin = 1.64635032469237 | erot = 1.48977166427888 | epot = -11.5107449561759 | etot = -8.37462296720461 +251000 ekin = 1.64670868822424 | erot = 1.48021150770204 | epot = -11.501543163354 | etot = -8.37462296742773 +252000 ekin = 1.66264181464398 | erot = 1.47871062656233 | epot = -11.5159754089783 | etot = -8.37462296777201 +253000 ekin = 1.69027564040418 | erot = 1.4838006950994 | epot = -11.5486993036748 | etot = -8.37462296817121 +254000 ekin = 1.72505301291753 | erot = 1.49382397147149 | epot = -11.5934999529542 | etot = -8.37462296856521 +255000 ekin = 1.76239471231559 | erot = 1.50720813837951 | epot = -11.6442258196102 | etot = -8.3746229689151 +256000 ekin = 1.79816893498624 | erot = 1.52259254469701 | epot = -11.6953844488847 | etot = -8.37462296920143 +257000 ekin = 1.8289509523976 | erot = 1.53887801863831 | epot = -11.7424519404547 | etot = -8.37462296941884 +258000 ekin = 1.85212386739641 | erot = 1.55528591409732 | epot = -11.7820327510617 | etot = -8.374622969568 +259000 ekin = 1.86588413888306 | erot = 1.57137656836521 | epot = -11.8118836768987 | etot = -8.3746229696504 +260000 ekin = 1.86922537289967 | erot = 1.58707491263371 | epot = -11.8309232551855 | etot = -8.3746229696521 +261000 ekin = 1.8619474577806 | erot = 1.60277606186344 | epot = -11.8393464893232 | etot = -8.37462296967919 +262000 ekin = 1.84441202421402 | erot = 1.61874454524364 | epot = -11.8377795390081 | etot = -8.37462296955045 +263000 ekin = 1.81775632997711 | erot = 1.63584439963944 | epot = -11.8282236989401 | etot = -8.37462296932356 +264000 ekin = 1.78414336143547 | erot = 1.65581672859451 | epot = -11.8145830590346 | etot = -8.37462296900464 +265000 ekin = 1.74659811333744 | erot = 1.68088156362845 | epot = -11.802102645597 | etot = -8.37462296863111 +266000 ekin = 1.70875551588653 | erot = 1.71332387538146 | epot = -11.7967023595417 | etot = -8.37462296827373 +267000 ekin = 1.67443624978621 | erot = 1.75501089284554 | epot = -11.8040701106192 | etot = -8.37462296798742 +268000 ekin = 1.64712713207545 | erot = 1.80695733277743 | epot = -11.8287074326934 | etot = -8.37462296784051 +269000 ekin = 1.62949021142679 | erot = 1.86883267567257 | epot = -11.872945854971 | etot = -8.37462296787168 +270000 ekin = 1.6228515992244 | erot = 1.9387281089436 | epot = -11.9362026762884 | etot = -8.37462296812045 +271000 ekin = 1.62688631043695 | erot = 2.01317767222122 | epot = -12.0146869512055 | etot = -8.37462296854733 +272000 ekin = 1.63981668010343 | erot = 2.08746423747733 | epot = -12.1019038866655 | etot = -8.37462296908471 +273000 ekin = 1.6588009116894 | erot = 2.15626799363862 | epot = -12.1896918749687 | etot = -8.37462296964073 +274000 ekin = 1.68050753849828 | erot = 2.21448722130979 | epot = -12.2696177299294 | etot = -8.3746229701213 +275000 ekin = 1.70172643739711 | erot = 2.25805265702313 | epot = -12.3344020648714 | etot = -8.3746229704512 +276000 ekin = 1.71987527696088 | erot = 2.28456562449038 | epot = -12.3790638720389 | etot = -8.37462297058762 +277000 ekin = 1.73331269261531 | erot = 2.2936490566393 | epot = -12.401584719777 | etot = -8.37462297052239 +278000 ekin = 1.74143735013694 | erot = 2.28698125839038 | epot = -12.403041578799 | etot = -8.37462297027172 +279000 ekin = 1.74460802870554 | erot = 2.26806682992404 | epot = -12.3872978285227 | etot = -8.37462296989315 +280000 ekin = 1.74394008412412 | erot = 2.24171314052056 | epot = -12.3602761940827 | etot = -8.37462296943797 +281000 ekin = 1.74088698058156 | erot = 2.21312908436397 | epot = -12.328639034053 | etot = -8.37462296910752 +282000 ekin = 1.73669656458684 | erot = 2.18704204449651 | epot = -12.2983615778776 | etot = -8.3746229687942 +283000 ekin = 1.73229007371573 | erot = 2.1674467962291 | epot = -12.2743598385779 | etot = -8.37462296863304 +284000 ekin = 1.72792109204508 | erot = 2.15675164213785 | epot = -12.2592957028506 | etot = -8.37462296866769 +285000 ekin = 1.72297480902827 | erot = 2.15537559427311 | epot = -12.2529733721988 | etot = -8.37462296889743 +286000 ekin = 1.71598432453 | erot = 2.16179000838381 | epot = -12.25239730217 | etot = -8.37462296925621 +287000 ekin = 1.70498524220286 | erot = 2.173155030137 | epot = -12.2527632419506 | etot = -8.37462296961069 +288000 ekin = 1.68823578051903 | erot = 2.18649203663127 | epot = -12.2493507869514 | etot = -8.37462296980111 +289000 ekin = 1.66510970376174 | erot = 2.19999055777909 | epot = -12.2397232312596 | etot = -8.37462296971872 +290000 ekin = 1.63674302037954 | erot = 2.21381252699327 | epot = -12.2251785167465 | etot = -8.37462296937372 +291000 ekin = 1.60601874197395 | erot = 2.22992661048312 | epot = -12.2105683213523 | etot = -8.3746229688952 +292000 ekin = 1.57682389343752 | erot = 2.25107800691073 | epot = -12.2025248687803 | etot = -8.37462296843205 +293000 ekin = 1.55301992418683 | erot = 2.27950943304591 | epot = -12.2071523254116 | etot = -8.37462296817889 +294000 ekin = 1.53731454048174 | erot = 2.31583078837865 | epot = -12.2277682970254 | etot = -8.37462296816498 +295000 ekin = 1.53083265562504 | erot = 2.35873605655261 | epot = -12.264191680545 | etot = -8.37462296836736 +296000 ekin = 1.53318706455239 | erot = 2.40528084679021 | epot = -12.3130908800601 | etot = -8.37462296871754 +297000 ekin = 1.54281493583623 | erot = 2.45151931863421 | epot = -12.3689572236265 | etot = -8.37462296915609 +298000 ekin = 1.55733608765135 | erot = 2.49306411731896 | epot = -12.4250231746863 | etot = -8.37462296971601 +299000 ekin = 1.5740738628828 | erot = 2.52498633848713 | epot = -12.473683171532 | etot = -8.37462297016211 +300000 ekin = 1.59001535760057 | erot = 2.5434931518281 | epot = -12.5081314799999 | etot = -8.37462297057123 +301000 ekin = 1.60189886822687 | erot = 2.54585083166139 | epot = -12.5223726708122 | etot = -8.37462297092397 +302000 ekin = 1.606202515857 | erot = 2.53039812867599 | epot = -12.5112236158398 | etot = -8.37462297130681 +303000 ekin = 1.59914065240708 | erot = 2.49598280993758 | epot = -12.4697464340445 | etot = -8.37462297169981 +304000 ekin = 1.57679795693913 | erot = 2.44177332378513 | epot = -12.3931942527976 | etot = -8.37462297207338 +305000 ekin = 1.53574304374243 | erot = 2.3676190541423 | epot = -12.2779850699667 | etot = -8.37462297208197 +306000 ekin = 1.47392866559851 | erot = 2.27453104047969 | epot = -12.1230826782598 | etot = -8.37462297218158 +307000 ekin = 1.39050823398847 | erot = 2.16376504506994 | epot = -11.9288962509223 | etot = -8.37462297186389 +308000 ekin = 1.2896152298086 | erot = 2.03977667258498 | epot = -11.7040148706656 | etot = -8.37462296827207 +309000 ekin = 1.05782937494292 | erot = 1.83361716571104 | epot = -11.2660695010602 | etot = -8.37462296040623 +310000 ekin = 1.14450415447965 | erot = 1.58483272602664 | epot = -11.1039598386832 | etot = -8.37462295817687 +311000 ekin = 1.41922601312442 | erot = 1.45460499880715 | epot = -11.2484540448415 | etot = -8.37462303290993 +312000 ekin = 1.45261330232121 | erot = 1.37611906651637 | epot = -11.2033554015513 | etot = -8.37462303271372 +313000 ekin = 1.4788437717408 | erot = 1.31854286229449 | epot = -11.1720096664207 | etot = -8.37462303238537 +314000 ekin = 1.49756299811591 | erot = 1.28320357876867 | epot = -11.1553896088943 | etot = -8.37462303200971 +315000 ekin = 1.51332559187995 | erot = 1.27043025389279 | epot = -11.158378877496 | etot = -8.37462303172327 +316000 ekin = 1.53080061118026 | erot = 1.27925593275691 | epot = -11.1846795755419 | etot = -8.37462303160469 +317000 ekin = 1.55378721590892 | erot = 1.30719554367425 | epot = -11.2356057912727 | etot = -8.37462303168955 +318000 ekin = 1.58370434541109 | erot = 1.34913652060297 | epot = -11.3074638985371 | etot = -8.374623032523 +319000 ekin = 1.61943484148295 | erot = 1.39801478359137 | epot = -11.3920726581918 | etot = -8.37462303311752 +320000 ekin = 1.65864783760583 | erot = 1.44696670458938 | epot = -11.4802375759962 | etot = -8.37462303380101 +321000 ekin = 1.6976698384742 | erot = 1.48920524278932 | epot = -11.561498115728 | etot = -8.37462303446449 +322000 ekin = 1.73222385846161 | erot = 1.51888544570603 | epot = -11.6257323391493 | etot = -8.37462303498166 +323000 ekin = 1.75834700852462 | erot = 1.53202956630704 | epot = -11.6649996100703 | etot = -8.37462303523864 +324000 ekin = 1.77324650046493 | erot = 1.52732597029455 | epot = -11.6751955059278 | etot = -8.37462303516831 +325000 ekin = 1.77583924217148 | erot = 1.50655389358397 | epot = -11.6570161705558 | etot = -8.37462303480038 +326000 ekin = 1.76682929377058 | erot = 1.47436928283883 | epot = -11.6158216107578 | etot = -8.37462303414843 +327000 ekin = 1.74834602231326 | erot = 1.43794367202746 | epot = -11.5609127277015 | etot = -8.37462303336073 +328000 ekin = 1.72331109821437 | erot = 1.40578615079726 | epot = -11.5037202815796 | etot = -8.37462303256798 +329000 ekin = 1.69488797673583 | erot = 1.38635580023373 | epot = -11.4558668088469 | etot = -8.3746230318773 +330000 ekin = 1.6656651333496 | erot = 1.38702252391951 | epot = -11.4273106886518 | etot = -8.37462303138264 +331000 ekin = 1.63732185166402 | erot = 1.41331220646683 | epot = -11.4252570892371 | etot = -8.37462303110628 +332000 ekin = 1.61073968004208 | erot = 1.46826665363504 | epot = -11.453629364734 | etot = -8.37462303105687 +333000 ekin = 1.58605232106696 | erot = 1.5522055904313 | epot = -11.5128809427321 | etot = -8.37462303123381 +334000 ekin = 1.5628441592252 | erot = 1.66255678080433 | epot = -11.6000239716202 | etot = -8.3746230315907 +335000 ekin = 1.54014240613999 | erot = 1.79443783502711 | epot = -11.7092032732483 | etot = -8.37462303208118 +336000 ekin = 1.51670455216779 | erot = 1.94117931563194 | epot = -11.8325069004488 | etot = -8.37462303264909 +337000 ekin = 1.49128277555691 | erot = 2.0949241434516 | epot = -11.9608299522436 | etot = -8.37462303323505 +338000 ekin = 1.46282625483174 | erot = 2.24735936520808 | epot = -12.084808653823 | etot = -8.37462303378314 +339000 ekin = 1.43063896798429 | erot = 2.39044100153282 | epot = -12.1957030037644 | etot = -8.37462303424733 +340000 ekin = 1.39448012484134 | erot = 2.51702660358864 | epot = -12.2861297630257 | etot = -8.37462303459572 +341000 ekin = 1.35460313822342 | erot = 2.62135284037302 | epot = -12.3505790134079 | etot = -8.37462303481151 +342000 ekin = 1.31173936863123 | erot = 2.69933546749565 | epot = -12.3856978710171 | etot = -8.37462303489026 +343000 ekin = 1.26704159860301 | erot = 2.74871044551612 | epot = -12.390375078955 | etot = -8.3746230348359 +344000 ekin = 1.2220065450956 | erot = 2.76906107654435 | epot = -12.3656906562953 | etot = -8.37462303465534 +345000 ekin = 1.17839357225762 | erot = 2.76177689465409 | epot = -12.314793501269 | etot = -8.37462303435724 +346000 ekin = 1.13814730560366 | erot = 2.72996678569744 | epot = -12.2427371252546 | etot = -8.37462303395354 +347000 ekin = 1.10331757839189 | erot = 2.67831421953866 | epot = -12.1562548313937 | etot = -8.37462303346319 +348000 ekin = 1.07595787263701 | erot = 2.61283600667575 | epot = -12.0634169122301 | etot = -8.37462303291736 +349000 ekin = 1.0579814719175 | erot = 2.54050407789345 | epot = -11.9731085821719 | etot = -8.37462303236099 +350000 ekin = 1.05096760963783 | erot = 2.46871550807927 | epot = -11.8943061495681 | etot = -8.37462303185096 +351000 ekin = 1.05593437429287 | erot = 2.40463774697948 | epot = -11.8351951527201 | etot = -8.3746230314477 +352000 ekin = 1.07311971186445 | erot = 2.35449555191596 | epot = -11.8022382949869 | etot = -8.3746230312065 +353000 ekin = 1.10182415540729 | erot = 2.32288867128129 | epot = -11.7993358578563 | etot = -8.37462303116775 +354000 ekin = 1.1403630046458 | erot = 2.31223409502276 | epot = -11.8272201310181 | etot = -8.37462303134955 +355000 ekin = 1.18615564007747 | erot = 2.32242185961901 | epot = -11.8832005314386 | etot = -8.37462303174213 +356000 ekin = 1.23595386569768 | erot = 2.35076326964089 | epot = -11.9613401676441 | etot = -8.37462303230557 +357000 ekin = 1.28618457758527 | erot = 2.39228504524844 | epot = -12.0530926558067 | etot = -8.37462303297295 +358000 ekin = 1.33335672483922 | erot = 2.44036693764112 | epot = -12.1483466961405 | etot = -8.37462303366018 +359000 ekin = 1.37446611423394 | erot = 2.48763760748888 | epot = -12.2367267560032 | etot = -8.37462303428037 +360000 ekin = 1.4073369853998 | erot = 2.52696891747068 | epot = -12.3089289376288 | etot = -8.3746230347583 +361000 ekin = 1.43085230116985 | erot = 2.55266032656752 | epot = -12.3581356626684 | etot = -8.37462303493106 +362000 ekin = 1.44498023419411 | erot = 2.5616119244846 | epot = -12.3812151936916 | etot = -8.37462303501293 +363000 ekin = 1.45080808015357 | erot = 2.55177253019121 | epot = -12.3772036452511 | etot = -8.37462303490632 +364000 ekin = 1.4504698206984 | erot = 2.52283864584446 | epot = -12.3479315011825 | etot = -8.3746230346396 +365000 ekin = 1.44693366151922 | erot = 2.47609933176865 | epot = -12.2976560275504 | etot = -8.37462303426257 +366000 ekin = 1.44366094467937 | erot = 2.41401126337839 | epot = -12.232295241894 | etot = -8.37462303383623 +367000 ekin = 1.44416618229089 | erot = 2.33969773429917 | epot = -12.158486950013 | etot = -8.37462303342294 +368000 ekin = 1.45154164411989 | erot = 2.25648465085276 | epot = -12.0826493280459 | etot = -8.37462303307324 +369000 ekin = 1.46802482610957 | erot = 2.16757470030039 | epot = -12.0102225592264 | etot = -8.3746230328164 +370000 ekin = 1.4946848415784 | erot = 2.07591739973278 | epot = -11.9452252739691 | etot = -8.3746230326579 +371000 ekin = 1.53128479293964 | erot = 1.9842652262904 | epot = -11.8901730518131 | etot = -8.37462303258308 +372000 ekin = 1.57634160155475 | erot = 1.89533626064742 | epot = -11.8463008947684 | etot = -8.37462303256626 +373000 ekin = 1.62736107596568 | erot = 1.81196417168995 | epot = -11.8139482802383 | etot = -8.37462303258269 +374000 ekin = 1.68119274504092 | erot = 1.73713269144262 | epot = -11.7929484690964 | etot = -8.37462303261285 +375000 ekin = 1.73444043052779 | erot = 1.67385884334812 | epot = -11.7829223065189 | etot = -8.37462303264297 +376000 ekin = 1.78387586143861 | erot = 1.62497473906467 | epot = -11.7834736331725 | etot = -8.37462303266922 +377000 ekin = 1.8264818609183 | erot = 1.59275354369276 | epot = -11.7938584374893 | etot = -8.37462303287821 +378000 ekin = 1.85889028460699 | erot = 1.57838589666717 | epot = -11.8118992141847 | etot = -8.37462303291055 +379000 ekin = 1.87974734421288 | erot = 1.58231910072895 | epot = -11.8366894778896 | etot = -8.37462303294772 +380000 ekin = 1.88876618247863 | erot = 1.60397852042879 | epot = -11.867367735925 | etot = -8.37462303301755 +381000 ekin = 1.88634387025526 | erot = 1.64162253507708 | epot = -11.9025894384705 | etot = -8.3746230331382 +382000 ekin = 1.87329602399917 | erot = 1.69239968364358 | epot = -11.9403187409501 | etot = -8.37462303330739 +383000 ekin = 1.85067766912035 | erot = 1.75260724974017 | epot = -11.9779079523639 | etot = -8.37462303350337 +384000 ekin = 1.81972884480726 | erot = 1.81808771261089 | epot = -12.0124395911108 | etot = -8.37462303369263 +385000 ekin = 1.78192764777005 | erot = 1.88463133786802 | epot = -12.0411820195034 | etot = -8.37462303386534 +386000 ekin = 1.73896117301569 | erot = 1.94830024178261 | epot = -12.061884448782 | etot = -8.37462303398369 +387000 ekin = 1.69261703956642 | erot = 2.00550933075481 | epot = -12.0727494044588 | etot = -8.37462303413753 +388000 ekin = 1.64442362565048 | erot = 2.05290262288317 | epot = -12.0719492828242 | etot = -8.37462303429059 +389000 ekin = 1.59562809726325 | erot = 2.08769097010279 | epot = -12.0579421017207 | etot = -8.37462303435467 +390000 ekin = 1.54727258078821 | erot = 2.10804034822076 | epot = -12.0299359634157 | etot = -8.37462303440669 +391000 ekin = 1.500426686893 | erot = 2.11301685840315 | epot = -11.9880665795767 | etot = -8.37462303428053 +392000 ekin = 1.45669956782719 | erot = 2.10352612084123 | epot = -11.934848722606 | etot = -8.37462303393755 +393000 ekin = 1.41857599109124 | erot = 2.08263213471655 | epot = -11.8758311592018 | etot = -8.37462303339403 +394000 ekin = 1.38932612627926 | erot = 2.05528425943725 | epot = -11.8192334184644 | etot = -8.37462303274791 +395000 ekin = 1.37246101478471 | erot = 2.0273931942745 | epot = -11.7744772412175 | etot = -8.37462303215831 +396000 ekin = 1.37078907987893 | erot = 2.00445159240829 | epot = -11.7498637040834 | etot = -8.37462303179614 +397000 ekin = 1.38538853999881 | erot = 1.99011302537741 | epot = -11.7501245971575 | etot = -8.37462303178123 +398000 ekin = 1.4149053116158 | erot = 1.98519641778469 | epot = -11.7747247615385 | etot = -8.37462303213797 +399000 ekin = 1.45547085036172 | erot = 1.98743025594808 | epot = -11.8175241391037 | etot = -8.37462303279393 +400000 ekin = 1.50126526406456 | erot = 1.99196444869353 | epot = -11.8678527463702 | etot = -8.37462303361212 +401000 ekin = 1.54549713891325 | erot = 1.99242148352504 | epot = -11.9125416568747 | etot = -8.37462303443636 +402000 ekin = 1.58148802753225 | erot = 1.98217540610689 | epot = -11.9382864687602 | etot = -8.37462303512109 +403000 ekin = 1.60364407572636 | erot = 1.95563446459617 | epot = -11.9339015758631 | etot = -8.3746230355406 +404000 ekin = 1.6082371823126 | erot = 1.90940860689276 | epot = -11.892268824805 | etot = -8.37462303559961 +405000 ekin = 1.59393186875248 | erot = 1.84321418438886 | epot = -11.8117690883987 | etot = -8.37462303525732 +406000 ekin = 1.56197926550313 | erot = 1.76026394072503 | epot = -11.696866240784 | etot = -8.37462303455581 +407000 ekin = 1.51595319782147 | erot = 1.66689496115735 | epot = -11.5574711925993 | etot = -8.37462303362048 +408000 ekin = 1.46103089398893 | erot = 1.57144700034909 | epot = -11.4071009269586 | etot = -8.37462303262061 +409000 ekin = 1.40302353808045 | erot = 1.48274963105546 | epot = -11.2603962008488 | etot = -8.37462303171285 +410000 ekin = 1.34747963365107 | erot = 1.40871679572804 | epot = -11.1308194603699 | etot = -8.37462303099076 +411000 ekin = 1.24142842922053 | erot = 1.36765891029395 | epot = -10.9837103545531 | etot = -8.37462301503866 +412000 ekin = 1.07606206464602 | erot = 1.44463891809268 | epot = -10.8953239884568 | etot = -8.37462300571809 +413000 ekin = 1.04694922469337 | erot = 1.5110260061357 | epot = -10.9325982588148 | etot = -8.3746230279857 +414000 ekin = 1.03606467090053 | erot = 1.52895884328951 | epot = -10.9396465423127 | etot = -8.37462302812265 +415000 ekin = 1.03698178421644 | erot = 1.56970634086251 | epot = -10.9813111534857 | etot = -8.37462302840673 +416000 ekin = 1.04842794421315 | erot = 1.63005774223267 | epot = -11.0531087152535 | etot = -8.37462302880764 +417000 ekin = 1.06841333535245 | erot = 1.70571770479165 | epot = -11.1487540694376 | etot = -8.37462302929345 +418000 ekin = 1.0944470100467 | erot = 1.79158405306303 | epot = -11.2606540929472 | etot = -8.37462302983752 +419000 ekin = 1.12371544112636 | erot = 1.88200392342451 | epot = -11.3803423949661 | etot = -8.37462303041528 +420000 ekin = 1.15322596863313 | erot = 1.9710395694794 | epot = -11.498888569108 | etot = -8.37462303099545 +421000 ekin = 1.17996638669817 | erot = 2.05281125535677 | epot = -11.6074006735849 | etot = -8.37462303152993 +422000 ekin = 1.20115062980762 | erot = 2.12197272518036 | epot = -11.6977463869409 | etot = -8.37462303195293 +423000 ekin = 1.2145687934241 | erot = 2.17429924607344 | epot = -11.7634910716948 | etot = -8.37462303219724 +424000 ekin = 1.21895541018511 | erot = 2.20725430505659 | epot = -11.8008327474639 | etot = -8.37462303222225 +425000 ekin = 1.21420953470501 | erot = 2.22030001431169 | epot = -11.8091325810581 | etot = -8.37462303204139 +426000 ekin = 1.20134505265621 | erot = 2.21476142815237 | epot = -11.7907295125147 | etot = -8.3746230317061 +427000 ekin = 1.18219319315261 | erot = 2.19340434237043 | epot = -11.7502205668128 | etot = -8.37462303128977 +428000 ekin = 1.15899921940807 | erot = 2.15981652250199 | epot = -11.6934387727675 | etot = -8.37462303085739 +429000 ekin = 1.13415683500719 | erot = 2.11790831243447 | epot = -11.6266881762577 | etot = -8.37462302881602 +430000 ekin = 1.11403963820914 | erot = 2.07460238347597 | epot = -11.5632650504451 | etot = -8.37462302876001 +431000 ekin = 1.10124843427921 | erot = 2.03325324116416 | epot = -11.5091247042108 | etot = -8.37462302876746 +432000 ekin = 1.09509673682045 | erot = 1.99414694703891 | epot = -11.4638667126951 | etot = -8.37462302883571 +433000 ekin = 1.09463609314644 | erot = 1.95711348582559 | epot = -11.4263726079153 | etot = -8.3746230289433 +434000 ekin = 1.09809472012996 | erot = 1.92111283570137 | epot = -11.3938305852117 | etot = -8.37462302938034 +435000 ekin = 1.10341624338861 | erot = 1.88492142830579 | epot = -11.3629607010994 | etot = -8.37462302940498 +436000 ekin = 1.11020757162892 | erot = 1.84854231976133 | epot = -11.3333729208394 | etot = -8.37462302944915 +437000 ekin = 1.11803889537834 | erot = 1.81186902511391 | epot = -11.3045309500004 | etot = -8.37462302950811 +438000 ekin = 1.12642172160336 | erot = 1.77470718112056 | epot = -11.2757519322974 | etot = -8.37462302957345 +439000 ekin = 1.13485148153982 | erot = 1.73686282079598 | epot = -11.2463373319689 | etot = -8.37462302963315 +440000 ekin = 1.14287335820677 | erot = 1.6982607950729 | epot = -11.2157571829518 | etot = -8.37462302967209 +441000 ekin = 1.15016795453108 | erot = 1.65908318343076 | epot = -11.1838741676317 | etot = -8.37462302966984 +442000 ekin = 1.15664284201572 | erot = 1.61992313518224 | epot = -11.1511890068215 | etot = -8.37462302962353 +443000 ekin = 1.16253418069083 | erot = 1.58179210099427 | epot = -11.1189493112074 | etot = -8.37462302952227 +444000 ekin = 1.16846798531313 | erot = 1.54614466613206 | epot = -11.0892356808142 | etot = -8.37462302936903 +445000 ekin = 1.17546820346648 | erot = 1.51479732960813 | epot = -11.0648885622537 | etot = -8.37462302917911 +446000 ekin = 1.18488743024697 | erot = 1.48973802087996 | epot = -11.0492484801072 | etot = -8.37462302898023 +447000 ekin = 1.19824347153636 | erot = 1.4728428998025 | epot = -11.0457094001486 | etot = -8.37462302880978 +448000 ekin = 1.21696535091544 | erot = 1.46554765995196 | epot = -11.0571360395779 | etot = -8.37462302871048 +449000 ekin = 1.24207954598539 | erot = 1.46851271093431 | epot = -11.0852152856395 | etot = -8.37462302871984 +450000 ekin = 1.27389445230343 | erot = 1.48136016741854 | epot = -11.1298776485921 | etot = -8.37462302887016 +451000 ekin = 1.31179903842818 | erot = 1.50255470267311 | epot = -11.1889767701115 | etot = -8.37462302901019 +452000 ekin = 1.35460859520422 | erot = 1.52989164326772 | epot = -11.2591232679044 | etot = -8.37462302943242 +453000 ekin = 1.39989469250132 | erot = 1.55983588432389 | epot = -11.3343536067643 | etot = -8.37462302993904 +454000 ekin = 1.44437957549653 | erot = 1.58822152329642 | epot = -11.4072241292509 | etot = -8.37462303045796 +455000 ekin = 1.48456015878253 | erot = 1.61103616004163 | epot = -11.470219349728 | etot = -8.37462303090384 +456000 ekin = 1.51733329615388 | erot = 1.62510652435232 | epot = -11.5170628516965 | etot = -8.37462303119029 +457000 ekin = 1.54029245797727 | erot = 1.62854015385607 | epot = -11.5434556431081 | etot = -8.37462303127478 +458000 ekin = 1.55209787062893 | erot = 1.62122255615467 | epot = -11.5479434578297 | etot = -8.37462303104612 +459000 ekin = 1.55414659187908 | erot = 1.60571991112906 | epot = -11.5344895335906 | etot = -8.3746230305825 +460000 ekin = 1.54960099436993 | erot = 1.58640018749931 | epot = -11.5106242118358 | etot = -8.37462302996659 +461000 ekin = 1.54273124225058 | erot = 1.56872252266522 | epot = -11.4860767942407 | etot = -8.37462302932495 +462000 ekin = 1.53795589449209 | erot = 1.55825929919719 | epot = -11.4708382224939 | etot = -8.37462302880462 +463000 ekin = 1.53875903308017 | erot = 1.55959299575885 | epot = -11.4729750573655 | etot = -8.37462302852646 +464000 ekin = 1.54682029511825 | erot = 1.57534186894967 | epot = -11.4967851926235 | etot = -8.37462302855557 +465000 ekin = 1.56162946502409 | erot = 1.60564212072992 | epot = -11.5418946146263 | etot = -8.37462302887232 +466000 ekin = 1.58070265304198 | erot = 1.64822662156059 | epot = -11.6035523039855 | etot = -8.37462302938297 +467000 ekin = 1.60035208027159 | erot = 1.69905719078914 | epot = -11.6740323010087 | etot = -8.37462302994799 +468000 ekin = 1.61673623107193 | erot = 1.75335443246648 | epot = -11.7447136939685 | etot = -8.37462303043008 +469000 ekin = 1.62683085006995 | erot = 1.80670922025537 | epot = -11.8081631010546 | etot = -8.37462303072931 +470000 ekin = 1.62907239972644 | erot = 1.8559658402397 | epot = -11.859661270774 | etot = -8.37462303080784 +471000 ekin = 1.62354687373205 | erot = 1.89966129170666 | epot = -11.8978311961309 | etot = -8.37462303069216 +472000 ekin = 1.61170510379534 | erot = 1.93800410340994 | epot = -11.924332237645 | etot = -8.37462303043972 +473000 ekin = 1.59590324451053 | erot = 1.97246730641883 | epot = -11.9429935810557 | etot = -8.3746230301263 +474000 ekin = 1.57886523181425 | erot = 2.00526149881272 | epot = -11.9587497604451 | etot = -8.37462302981809 +475000 ekin = 1.56312071579209 | erot = 2.03882982960113 | epot = -11.9765735749591 | etot = -8.3746230295659 +476000 ekin = 1.55063074695432 | erot = 2.07545668636699 | epot = -12.0007104627111 | etot = -8.37462302938983 +477000 ekin = 1.54263588411163 | erot = 2.11704231171848 | epot = -12.0343012251317 | etot = -8.37462302930159 +478000 ekin = 1.53956151542339 | erot = 2.16493101564523 | epot = -12.0791155603743 | etot = -8.37462302930564 +479000 ekin = 1.54104337298282 | erot = 2.21977101926569 | epot = -12.1354374216528 | etot = -8.37462302940429 +480000 ekin = 1.546009760973 | erot = 2.28138261399161 | epot = -12.2020154045604 | etot = -8.37462302959578 +481000 ekin = 1.55280606025074 | erot = 2.34867771787686 | epot = -12.2761068079942 | etot = -8.37462302986658 +482000 ekin = 1.55937339635063 | erot = 2.41971772769978 | epot = -12.3537141542343 | etot = -8.37462303018394 +483000 ekin = 1.56350104453064 | erot = 2.49198464321598 | epot = -12.4301087182424 | etot = -8.37462303049574 +484000 ekin = 1.56314467772891 | erot = 2.56280026279411 | epot = -12.5005679712712 | etot = -8.37462303074813 +485000 ekin = 1.55677099189746 | erot = 2.62990187864032 | epot = -12.5612959014211 | etot = -8.37462303088329 +486000 ekin = 1.54362230241928 | erot = 2.69196691950622 | epot = -12.6102122528177 | etot = -8.37462303089216 +487000 ekin = 1.52381043792147 | erot = 2.74866369544547 | epot = -12.6470971641652 | etot = -8.37462303079828 +488000 ekin = 1.49822858844546 | erot = 2.8004132279429 | epot = -12.6732648470389 | etot = -8.37462303065053 +489000 ekin = 1.46832177711314 | erot = 2.84792010719542 | epot = -12.6908649148109 | etot = -8.37462303050238 +490000 ekin = 1.43580907601253 | erot = 2.89167668868852 | epot = -12.702108795094 | etot = -8.37462303039295 +491000 ekin = 1.4024462649876 | erot = 2.93162068131834 | epot = -12.7086899766444 | etot = -8.37462303033848 +492000 ekin = 1.36987596423633 | erot = 2.96703118869674 | epot = -12.7115301832664 | etot = -8.37462303033337 +493000 ekin = 1.33956200675841 | erot = 2.99664446240428 | epot = -12.7108294995239 | etot = -8.37462303036122 +494000 ekin = 1.31276816321137 | erot = 3.0188980455283 | epot = -12.7062892391461 | etot = -8.37462303040639 +495000 ekin = 1.29052832589742 | erot = 3.03218505525729 | epot = -12.6973364116178 | etot = -8.37462303046307 +496000 ekin = 1.27356858864304 | erot = 3.03502298578847 | epot = -12.6832146049698 | etot = -8.37462303053831 +497000 ekin = 1.26217859738771 | erot = 3.02610963124414 | epot = -12.6629112592754 | etot = -8.37462303064359 +498000 ekin = 1.25609176092199 | erot = 3.00437387243302 | epot = -12.6350886640761 | etot = -8.37462303072111 +499000 ekin = 1.25448433543904 | erot = 2.96925958210228 | epot = -12.5983669484037 | etot = -8.37462303086234 +500000 ekin = 1.25592311954784 | erot = 2.92052794168892 | epot = -12.5510740922098 | etot = -8.37462303097309 +501000 ekin = 1.25866262015633 | erot = 2.85877857413965 | epot = -12.4920642252969 | etot = -8.37462303100093 +502000 ekin = 1.26101030104304 | erot = 2.78589367848072 | epot = -12.421527010429 | etot = -8.37462303090524 +503000 ekin = 1.26168224098459 | erot = 2.70525686266326 | epot = -12.3415621343214 | etot = -8.37462303067356 +504000 ekin = 1.2600687527343 | erot = 2.62162663922347 | epot = -12.2563184222917 | etot = -8.37462303033394 +505000 ekin = 1.25635230634784 | erot = 2.54066101851092 | epot = -12.1716363547773 | etot = -8.3746230299186 +506000 ekin = 1.25147361583878 | erot = 2.46829686832302 | epot = -12.0943935136549 | etot = -8.37462302949308 +507000 ekin = 1.24695832252944 | erot = 2.40991559866175 | epot = -12.03149695032 | etot = -8.37462302912881 +508000 ekin = 1.24460011262455 | erot = 2.36947588934127 | epot = -11.9886990309749 | etot = -8.37462302900906 +509000 ekin = 1.24584437165595 | erot = 2.34837731731007 | epot = -11.9688447179601 | etot = -8.37462302899406 +510000 ekin = 1.2517204112405 | erot = 2.34550382347298 | epot = -11.9718472639398 | etot = -8.37462302922633 +511000 ekin = 1.26248317251299 | erot = 2.35680066397777 | epot = -11.9939068662003 | etot = -8.37462302970952 +512000 ekin = 1.27739486770651 | erot = 2.37529788848864 | epot = -12.0273157865898 | etot = -8.3746230303947 +513000 ekin = 1.29481021505335 | erot = 2.39185405428688 | epot = -12.0612873005158 | etot = -8.37462303117561 +514000 ekin = 1.31250889880663 | erot = 2.39651406028005 | epot = -12.0836459909827 | etot = -8.37462303189606 +515000 ekin = 1.3282505258172 | erot = 2.38037057727134 | epot = -12.0832441354637 | etot = -8.37462303237514 +516000 ekin = 1.34045831429047 | erot = 2.3376026799616 | epot = -12.0526840267099 | etot = -8.37462303245782 +517000 ekin = 1.34883924084139 | erot = 2.26713155446507 | epot = -11.9905938273839 | etot = -8.37462303207746 +518000 ekin = 1.35468550683532 | erot = 2.1732612700939 | epot = -11.9025698082252 | etot = -8.37462303129602 +519000 ekin = 1.36067339623777 | erot = 2.06494828518385 | epot = -11.8002447117104 | etot = -8.37462303028879 +520000 ekin = 1.37018582822041 | erot = 1.95390329839677 | epot = -11.6987121558955 | etot = -8.3746230292783 +521000 ekin = 1.38639579379635 | erot = 1.85221057844755 | epot = -11.6132294007042 | etot = -8.37462302846028 +522000 ekin = 1.41141432489743 | erot = 1.77022445537223 | epot = -11.556261808228 | etot = -8.37462302795837 +523000 ekin = 1.44572356452415 | erot = 1.71520045873996 | epot = -11.5355470510809 | etot = -8.37462302781681 +524000 ekin = 1.48798145408556 | erot = 1.69073008320913 | epot = -11.5533345653098 | etot = -8.37462302801515 +525000 ekin = 1.53517683780364 | erot = 1.69680296066522 | epot = -11.6066028269625 | etot = -8.37462302849367 +526000 ekin = 1.58304900117776 | erot = 1.73025509478009 | epot = -11.6879271251317 | etot = -8.37462302917388 +527000 ekin = 1.62665879647842 | erot = 1.78540941266435 | epot = -11.7866912391139 | etot = -8.37462302997112 +528000 ekin = 1.66100783107272 | erot = 1.85480654805457 | epot = -11.8904374099264 | etot = -8.37462303079917 +529000 ekin = 1.68163863411252 | erot = 1.93001159415133 | epot = -11.986273259831 | etot = -8.37462303156715 +530000 ekin = 1.68518623025763 | erot = 2.00252460867122 | epot = -12.0623338711093 | etot = -8.37462303218049 +531000 ekin = 1.66986059684322 | erot = 2.06478669657164 | epot = -12.1092703259641 | etot = -8.37462303254921 +532000 ekin = 1.63581226894962 | erot = 2.11116679185565 | epot = -12.1216020934158 | etot = -8.37462303261058 +533000 ekin = 1.58529617176643 | erot = 2.13870511839619 | epot = -12.098624322515 | etot = -8.37462303235236 +534000 ekin = 1.5225456409459 | erot = 2.14737698823518 | epot = -12.0445456610046 | etot = -8.37462303182352 +535000 ekin = 1.45332420575898 | erot = 2.13977370494377 | epot = -11.9677209418254 | etot = -8.37462303112265 +536000 ekin = 1.38421691010833 | erot = 2.12031314070643 | epot = -11.8791530811833 | etot = -8.3746230303685 +537000 ekin = 1.32180342898888 | erot = 2.09425520394361 | epot = -11.7906816626022 | etot = -8.3746230296697 +538000 ekin = 1.27187743419507 | erot = 2.06681107588574 | epot = -11.713311539185 | etot = -8.37462302910418 +539000 ekin = 1.23883846278406 | erot = 2.04251647932952 | epot = -11.6559779708291 | etot = -8.37462302871551 +540000 ekin = 1.22531302702205 | erot = 2.02488499741709 | epot = -11.6248210529601 | etot = -8.37462302852096 +541000 ekin = 1.23199882289896 | erot = 2.01625749303218 | epot = -11.6228793444531 | etot = -8.37462302852198 +542000 ekin = 1.25769219449867 | erot = 2.01774880493445 | epot = -11.6500640281429 | etot = -8.37462302870979 +543000 ekin = 1.29945731405898 | erot = 2.02924170400448 | epot = -11.7033220471294 | etot = -8.37462302906594 +544000 ekin = 1.35291512120938 | erot = 2.04944893324945 | epot = -11.7769870840134 | etot = -8.37462302955459 +545000 ekin = 1.41265384121013 | erot = 2.07611668221351 | epot = -11.8633935535405 | etot = -8.37462303011689 +546000 ekin = 1.47277167574226 | erot = 2.10644216878695 | epot = -11.9538368751978 | etot = -8.37462303066857 +547000 ekin = 1.52754093318812 | erot = 2.1377046882704 | epot = -12.0398686525721 | etot = -8.37462303111358 +548000 ekin = 1.57213155238435 | erot = 2.16798237174586 | epot = -12.1147369554979 | etot = -8.3746230313677 +549000 ekin = 1.60327488859358 | erot = 2.19671767494249 | epot = -12.1746155949228 | etot = -8.37462303138678 +550000 ekin = 1.61972434377051 | erot = 2.22489244331976 | epot = -12.2192398182714 | etot = -8.37462303118114 +551000 ekin = 1.62240013871266 | erot = 2.25470593134778 | epot = -12.2517291008734 | etot = -8.37462303081292 +552000 ekin = 1.61417495563575 | erot = 2.28884205645968 | epot = -12.2776400424743 | etot = -8.37462303037886 +553000 ekin = 1.59932782093367 | erot = 2.32954987376782 | epot = -12.3035007246893 | etot = -8.37462302998778 +554000 ekin = 1.58274599068694 | erot = 2.37778817612377 | epot = -12.335157196551 | etot = -8.37462302974027 +555000 ekin = 1.56899856387336 | erot = 2.43263226771025 | epot = -12.3762538612928 | etot = -8.37462302970921 +556000 ekin = 1.56145041160178 | erot = 2.49106505510944 | epot = -12.4271384966351 | etot = -8.37462302992391 +557000 ekin = 1.56197837221472 | erot = 2.54829507222914 | epot = -12.4848964746666 | etot = -8.37462303022272 +558000 ekin = 1.57029216554694 | erot = 2.59810209181726 | epot = -12.5430172882317 | etot = -8.37462303086749 +559000 ekin = 1.58339818323854 | erot = 2.63367391510857 | epot = -12.5916951298834 | etot = -8.37462303153627 +560000 ekin = 1.5971277048411 | erot = 2.64904697988052 | epot = -12.6207977168329 | etot = -8.37462303211133 +561000 ekin = 1.60698123346032 | erot = 2.6400968389395 | epot = -12.6217011048881 | etot = -8.37462303248833 +562000 ekin = 1.60896027784962 | erot = 2.6053270012035 | epot = -12.5889103116457 | etot = -8.37462303259261 +563000 ekin = 1.60023696635641 | erot = 2.54649193869282 | epot = -12.5213519373678 | etot = -8.37462303231855 +564000 ekin = 1.57955774679436 | erot = 2.46891092806133 | epot = -12.4230917066839 | etot = -8.37462303182822 +565000 ekin = 1.54734561568422 | erot = 2.38031455632197 | epot = -12.3022832031139 | etot = -8.37462303110775 +566000 ekin = 1.50554468555614 | erot = 2.29049479450585 | epot = -12.170662510309 | etot = -8.37462303024699 +567000 ekin = 1.45732250665802 | erot = 2.21025028826866 | epot = -12.0421958242756 | etot = -8.37462302934893 +568000 ekin = 1.40671207380869 | erot = 2.15003703754034 | epot = -11.9313721399072 | etot = -8.37462302855815 +569000 ekin = 1.35794157948555 | erot = 2.11775595088059 | epot = -11.8503205583542 | etot = -8.37462302798802 +570000 ekin = 1.31523212118133 | erot = 2.11799693944399 | epot = -11.8078520883715 | etot = -8.37462302774614 +571000 ekin = 1.28243871603171 | erot = 2.15081941194262 | epot = -11.8078811559362 | etot = -8.37462302796181 +572000 ekin = 1.26220633016967 | erot = 2.21027034250997 | epot = -11.8470997013693 | etot = -8.37462302868969 +573000 ekin = 1.25525341532478 | erot = 2.28456705416222 | epot = -11.9144434992767 | etot = -8.37462302978965 +574000 ekin = 1.26030251431118 | erot = 2.35813787036682 | epot = -11.9930634156596 | etot = -8.37462303098163 +575000 ekin = 1.2747321562012 | erot = 2.41511328226935 | epot = -12.0644684704057 | etot = -8.37462303193517 +576000 ekin = 1.29562562243032 | erot = 2.44294920216243 | epot = -12.1131978570819 | etot = -8.37462303248916 +577000 ekin = 1.32065634429477 | erot = 2.43438586779435 | epot = -12.1296652446647 | etot = -8.3746230325756 +578000 ekin = 1.34847271373188 | erot = 2.3880449856766 | epot = -12.1111407316826 | etot = -8.3746230322741 +579000 ekin = 1.37859640729612 | erot = 2.30759327887891 | epot = -12.0608127179027 | etot = -8.37462303172765 +580000 ekin = 1.41115339285065 | erot = 2.2001618841045 | epot = -11.9859383079095 | etot = -8.37462303095433 +581000 ekin = 1.44674776514281 | erot = 2.07475133366466 | epot = -11.8961221291487 | etot = -8.37462303034121 +582000 ekin = 1.48514821809916 | erot = 1.94050793883156 | epot = -11.8002791867221 | etot = -8.37462302979136 +583000 ekin = 1.52576266955382 | erot = 1.80603709649357 | epot = -11.7064227953868 | etot = -8.37462302933942 +584000 ekin = 1.56772288057648 | erot = 1.67887072895879 | epot = -11.6212166385388 | etot = -8.37462302900352 +585000 ekin = 1.60990333959317 | erot = 1.56509115870017 | epot = -11.5496175270895 | etot = -8.37462302879619 +586000 ekin = 1.65096359832512 | erot = 1.46905708280604 | epot = -11.4946437098573 | etot = -8.37462302872612 +587000 ekin = 1.68940411635217 | erot = 1.39319741549691 | epot = -11.4572245606452 | etot = -8.37462302879607 +588000 ekin = 1.72364170526714 | erot = 1.33790137441485 | epot = -11.4361661086779 | etot = -8.37462302899591 +589000 ekin = 1.75212209152062 | erot = 1.3015875625827 | epot = -11.4283326833787 | etot = -8.37462302927535 +590000 ekin = 1.77348776906926 | erot = 1.28111987724175 | epot = -11.4292306759265 | etot = -8.37462302961545 +591000 ekin = 1.78679652584279 | erot = 1.2722838860136 | epot = -11.4337034417696 | etot = -8.37462302991325 +592000 ekin = 1.79174476962516 | erot = 1.27074179819159 | epot = -11.4371095979238 | etot = -8.37462303010703 +593000 ekin = 1.78882244319854 | erot = 1.27295060805378 | epot = -11.4363960813967 | etot = -8.37462303014437 +594000 ekin = 1.77931579000502 | erot = 1.2768275282958 | epot = -11.4307663483269 | etot = -8.37462303002605 +595000 ekin = 1.76511936072603 | erot = 1.2819604422043 | epot = -11.4217028327285 | etot = -8.37462302979817 +596000 ekin = 1.74839643260399 | erot = 1.28931412525948 | epot = -11.4123335873949 | etot = -8.37462302953148 +597000 ekin = 1.73114837530465 | erot = 1.30076368908395 | epot = -11.4065350936836 | etot = -8.37462302929503 +598000 ekin = 1.71482586358598 | erot = 1.31808503745678 | epot = -11.4075339301912 | etot = -8.37462302914843 +599000 ekin = 1.70035612856742 | erot = 1.3425649905677 | epot = -11.417544148202 | etot = -8.37462302906685 +600000 ekin = 1.68813838897309 | erot = 1.37518403997246 | epot = -11.4379454579907 | etot = -8.37462302904513 +601000 ekin = 1.67802155272642 | erot = 1.41656361608885 | epot = -11.4692081979379 | etot = -8.37462302912259 +602000 ekin = 1.66952241263303 | erot = 1.46664302735508 | epot = -11.5107884691508 | etot = -8.37462302916268 +603000 ekin = 1.66207455080855 | erot = 1.52486246591497 | epot = -11.5615600460151 | etot = -8.37462302929162 +604000 ekin = 1.6542927442501 | erot = 1.59090716727003 | epot = -11.6198229409115 | etot = -8.37462302939132 +605000 ekin = 1.64513458460873 | erot = 1.6645196317729 | epot = -11.68427724585 | etot = -8.37462302946837 +606000 ekin = 1.63397297141762 | erot = 1.74533329764818 | epot = -11.7539292986251 | etot = -8.37462302955928 +607000 ekin = 1.62046446185494 | erot = 1.83246852419231 | epot = -11.8275560158102 | etot = -8.37462302976293 +608000 ekin = 1.60415138614545 | erot = 1.92384516554779 | epot = -11.9026195817789 | etot = -8.37462303008567 +609000 ekin = 1.58416607276472 | erot = 2.01562004721176 | epot = -11.974409150686 | etot = -8.37462303070949 +610000 ekin = 1.55892234883736 | erot = 2.10126039812532 | epot = -12.0348057783656 | etot = -8.37462303140292 +611000 ekin = 1.52586403281539 | erot = 2.17351542350509 | epot = -12.0740024883685 | etot = -8.37462303204803 +612000 ekin = 1.4825279678083 | erot = 2.22604744671983 | epot = -12.0831984469278 | etot = -8.37462303239972 +613000 ekin = 1.42777710477443 | erot = 2.25549715887384 | epot = -12.057897295914 | etot = -8.37462303226575 +614000 ekin = 1.36284302675892 | erot = 2.26309761369493 | epot = -12.0005636720726 | etot = -8.3746230316187 +615000 ekin = 1.29166682111418 | erot = 2.25472033318116 | epot = -11.9210101849095 | etot = -8.37462303061415 +616000 ekin = 1.22033159945645 | erot = 2.23929049961803 | epot = -11.8342451285797 | etot = -8.3746230295052 +617000 ekin = 1.15585313012806 | erot = 2.22643765865191 | epot = -11.7569138173069 | etot = -8.37462302852692 +618000 ekin = 1.10482633868281 | erot = 2.22445549381317 | epot = -11.703904860323 | etot = -8.37462302782702 +619000 ekin = 1.07233800595233 | erot = 2.23915844398183 | epot = -11.686119477403 | etot = -8.37462302746885 +620000 ekin = 1.06133969547929 | erot = 2.27356598267652 | epot = -11.7095287055701 | etot = -8.37462302741426 +621000 ekin = 1.07250328125059 | erot = 2.3282764043955 | epot = -11.7754027132591 | etot = -8.37462302761301 +622000 ekin = 1.10448299243283 | erot = 2.40202886262695 | epot = -11.8811348830517 | etot = -8.37462302799193 +623000 ekin = 1.15443583438885 | erot = 2.49214268564757 | epot = -12.0212015485354 | etot = -8.37462302849902 +624000 ekin = 1.2185850449635 | erot = 2.59479979276571 | epot = -12.1880078668328 | etot = -8.37462302910356 +625000 ekin = 1.29260009291012 | erot = 2.70513041487662 | epot = -12.3723535376303 | etot = -8.37462302984353 +626000 ekin = 1.37166908699354 | erot = 2.81669294847368 | epot = -12.5629850662423 | etot = -8.37462303077506 +627000 ekin = 1.45036408324169 | erot = 2.92095656625447 | epot = -12.7459436813997 | etot = -8.37462303190359 +628000 ekin = 1.52265779656699 | erot = 3.00738157699049 | epot = -12.9046624066506 | etot = -8.37462303309307 +629000 ekin = 1.58251554244259 | erot = 3.06484099788408 | epot = -13.0219795743754 | etot = -8.37462303404871 +630000 ekin = 1.62514418880337 | erot = 3.08443014422475 | epot = -13.0841973674697 | etot = -8.37462303444157 +631000 ekin = 1.64954255052048 | erot = 3.06336922300758 | epot = -13.0875348072901 | etot = -8.37462303376204 +632000 ekin = 1.65761419155166 | erot = 3.00573585958576 | epot = -13.0379730841191 | etot = -8.37462303298165 +633000 ekin = 1.65174795094912 | erot = 2.91965232777674 | epot = -12.9460233106371 | etot = -8.37462303191122 +634000 ekin = 1.63566753659108 | erot = 2.81604656742636 | epot = -12.8263371348987 | etot = -8.37462303088127 +635000 ekin = 1.61303222685238 | erot = 2.70552755471528 | epot = -12.6931828116736 | etot = -8.37462303010594 +636000 ekin = 1.58646965557207 | erot = 2.59633719499181 | epot = -12.5574298801986 | etot = -8.37462302963469 +637000 ekin = 1.55730595137539 | erot = 2.49385627805374 | epot = -12.4257852588274 | etot = -8.37462302939823 +638000 ekin = 1.52584911626122 | erot = 2.40123459741471 | epot = -12.3017067429588 | etot = -8.37462302928287 +639000 ekin = 1.49192497641984 | erot = 2.32043250458043 | epot = -12.1869805101867 | etot = -8.37462302918644 +640000 ekin = 1.45541378442934 | erot = 2.25314232065171 | epot = -12.083179134123 | etot = -8.37462302904197 +641000 ekin = 1.4166491992725 | erot = 2.20135144254608 | epot = -11.9926236706418 | etot = -8.37462302882326 +642000 ekin = 1.37663135857252 | erot = 2.16751840710901 | epot = -11.9187727942197 | etot = -8.37462302853815 +643000 ekin = 1.33719601642867 | erot = 2.15436138730883 | epot = -11.8661804319178 | etot = -8.37462302818028 +644000 ekin = 1.30095460066298 | erot = 2.16433354914077 | epot = -11.839911177713 | etot = -8.37462302790927 +645000 ekin = 1.27009047740111 | erot = 2.19964354153021 | epot = -11.8443570466387 | etot = -8.37462302770743 +646000 ekin = 1.24673444983097 | erot = 2.26154821904857 | epot = -11.882905696521 | etot = -8.37462302764144 +647000 ekin = 1.23265873214796 | erot = 2.34972644269169 | epot = -11.957008202618 | etot = -8.37462302777833 +648000 ekin = 1.22854704146518 | erot = 2.4614698466802 | epot = -12.0646399168195 | etot = -8.37462302867415 +649000 ekin = 1.23123438274848 | erot = 2.58918284108585 | epot = -12.1950402534729 | etot = -8.37462302963856 +650000 ekin = 1.23733747325548 | erot = 2.72274115028498 | epot = -12.3347016542464 | etot = -8.37462303070591 +651000 ekin = 1.24289918510312 | erot = 2.85114575373848 | epot = -12.4686679705691 | etot = -8.37462303172749 +652000 ekin = 1.24424620799598 | erot = 2.96370857037656 | epot = -12.5825778108355 | etot = -8.37462303246295 +653000 ekin = 1.23918232850118 | erot = 3.05217314601573 | epot = -12.6659785072745 | etot = -8.37462303275754 +654000 ekin = 1.22772861478185 | erot = 3.11212236727186 | epot = -12.7144740146721 | etot = -8.37462303261837 +655000 ekin = 1.21201905901883 | erot = 3.14303840850265 | epot = -12.7296804997141 | etot = -8.37462303219263 +656000 ekin = 1.19543744331557 | erot = 3.1472043556272 | epot = -12.717264830612 | etot = -8.37462303166922 +657000 ekin = 1.1814930510954 | erot = 3.12826014298738 | epot = -12.6843762252665 | etot = -8.37462303118371 +658000 ekin = 1.17296379523421 | erot = 3.09016086418898 | epot = -12.6377476902109 | etot = -8.37462303078768 +659000 ekin = 1.17154758060714 | erot = 3.03675236917095 | epot = -12.5829229802521 | etot = -8.37462303047405 +660000 ekin = 1.17794903030406 | erot = 2.97172379739617 | epot = -12.5242958579197 | etot = -8.37462303021945 +661000 ekin = 1.19217998583019 | erot = 2.89858436842553 | epot = -12.4653873842718 | etot = -8.37462303001611 +662000 ekin = 1.21385724620099 | erot = 2.82043608351658 | epot = -12.4089163596039 | etot = -8.3746230298863 +663000 ekin = 1.24235148674062 | erot = 2.7394870694026 | epot = -12.3564615860234 | etot = -8.37462302988019 +664000 ekin = 1.27672733538917 | erot = 2.65640554993946 | epot = -12.3077559153837 | etot = -8.37462303005511 +665000 ekin = 1.31551337033707 | erot = 2.56977925404147 | epot = -12.2599156548135 | etot = -8.37462303043493 +666000 ekin = 1.35644708325599 | erot = 2.47610382422679 | epot = -12.207173938446 | etot = -8.37462303096323 +667000 ekin = 1.39640549572047 | erot = 2.37072397306798 | epot = -12.141752500272 | etot = -8.37462303148357 +668000 ekin = 1.43167926156656 | erot = 2.24978389245032 | epot = -12.0560861858051 | etot = -8.37462303178822 +669000 ekin = 1.45855421040952 | erot = 2.11253877407092 | epot = -11.9457160162039 | etot = -8.37462303172345 +670000 ekin = 1.47395086468723 | erot = 1.9628400463752 | epot = -11.8114139423427 | etot = -8.37462303128029 +671000 ekin = 1.47583917683162 | erot = 1.80887360751575 | epot = -11.6593358149388 | etot = -8.3746230305914 +672000 ekin = 1.46334042173035 | erot = 1.66127989929634 | epot = -11.4992433508642 | etot = -8.37462302983747 +673000 ekin = 1.43665130211575 | erot = 1.53074210402186 | epot = -11.3420164352874 | etot = -8.3746230291498 +674000 ekin = 1.39696147640067 | erot = 1.42619748862819 | epot = -11.1977819936044 | etot = -8.37462302857559 +675000 ekin = 1.34640262232926 | erot = 1.35413730296204 | epot = -11.0751629533971 | etot = -8.37462302810579 +676000 ekin = 1.28794616798706 | erot = 1.31873912036748 | epot = -10.981308316076 | etot = -8.37462302772149 +677000 ekin = 1.22516961113619 | erot = 1.32230065785723 | epot = -10.9220932964151 | etot = -8.37462302742172 +678000 ekin = 1.16189722956171 | erot = 1.36556643964961 | epot = -10.9020866964405 | etot = -8.37462302722917 +679000 ekin = 1.10179124610589 | erot = 1.44777635005946 | epot = -10.9241906233509 | etot = -8.37462302718558 +680000 ekin = 1.04797419609929 | erot = 1.56642353033359 | epot = -10.9890207537779 | etot = -8.37462302734499 +681000 ekin = 1.00272279861842 | erot = 1.71676662165668 | epot = -11.0941124480449 | etot = -8.37462302776983 +682000 ekin = 0.96723882583355 | erot = 1.89118238721898 | epot = -11.2330442415684 | etot = -8.37462302851591 +683000 ekin = 0.941511133139624 | erot = 2.07856636776108 | epot = -11.394700530499 | etot = -8.37462302959834 +684000 ekin = 0.924337639155355 | erot = 2.26421473255812 | epot = -11.5631754026496 | etot = -8.37462303093609 +685000 ekin = 0.913629093894914 | erot = 2.43080490184677 | epot = -11.719057028052 | etot = -8.37462303231027 +686000 ekin = 0.907072709279063 | erot = 2.56090643970371 | epot = -11.8426021823784 | etot = -8.37462303339564 +687000 ekin = 0.903027970995986 | erot = 2.64065323919292 | epot = -11.9183042440809 | etot = -8.374623033892 +688000 ekin = 0.901265997344289 | erot = 2.66315283569445 | epot = -11.9390418667247 | etot = -8.37462303368598 +689000 ekin = 0.90312729140811 | erot = 2.62989920645488 | epot = -11.907649530774 | etot = -8.37462303291098 +690000 ekin = 0.911003410958121 | erot = 2.54949432637527 | epot = -11.8351207691849 | etot = -8.37462303185154 +691000 ekin = 0.927482290190993 | erot = 2.43458909338556 | epot = -11.7366944143598 | etot = -8.37462303078327 +692000 ekin = 0.954629968072412 | erot = 2.29871133600685 | epot = -11.6279643339253 | etot = -8.37462302984608 +693000 ekin = 0.993689842529491 | erot = 2.15457291085937 | epot = -11.5228857826033 | etot = -8.37462302921447 +694000 ekin = 1.04477766673772 | erot = 2.01224824492835 | epot = -11.431648940443 | etot = -8.37462302877689 +695000 ekin = 1.10717972557134 | erot = 1.87902519878731 | epot = -11.3608279528648 | etot = -8.37462302850611 +696000 ekin = 1.17962988090899 | erot = 1.76021636433897 | epot = -11.3144692736299 | etot = -8.37462302838191 +697000 ekin = 1.26034508063448 | erot = 1.65939331951338 | epot = -11.2943614285427 | etot = -8.37462302839486 +698000 ekin = 1.3470063414454 | erot = 1.57856058321642 | epot = -11.3001899532003 | etot = -8.3746230285385 +699000 ekin = 1.43673776969177 | erot = 1.51829388887638 | epot = -11.3296546873713 | etot = -8.37462302880314 +700000 ekin = 1.52614311401997 | erot = 1.47788597100976 | epot = -11.3786521141988 | etot = -8.37462302916904 +701000 ekin = 1.61113170991832 | erot = 1.45542937144956 | epot = -11.441184111157 | etot = -8.37462302978916 +702000 ekin = 1.68654811958763 | erot = 1.4477483514156 | epot = -11.5089195013157 | etot = -8.37462303031242 +703000 ekin = 1.74804176728602 | erot = 1.45137774868857 | epot = -11.5740425467242 | etot = -8.37462303074958 +704000 ekin = 1.79223863052492 | erot = 1.46326677109846 | epot = -11.6301284326331 | etot = -8.3746230310097 +705000 ekin = 1.81722742452311 | erot = 1.48152907264936 | epot = -11.673379528207 | etot = -8.37462303103458 +706000 ekin = 1.82282717413898 | erot = 1.50598222611714 | epot = -11.7034324310832 | etot = -8.3746230308271 +707000 ekin = 1.81047570468772 | erot = 1.53820736294009 | epot = -11.7233060980815 | etot = -8.37462303045367 +708000 ekin = 1.782768284984 | erot = 1.58105495041898 | epot = -11.738446265421 | etot = -8.37462303001798 +709000 ekin = 1.74282721673902 | erot = 1.63779752307016 | epot = -11.7552477694259 | etot = -8.37462302961672 +710000 ekin = 1.69374790025168 | erot = 1.71129566721375 | epot = -11.7796665967699 | etot = -8.37462302930447 +711000 ekin = 1.63830193402269 | erot = 1.80347448195107 | epot = -11.8163994450621 | etot = -8.37462302908836 +712000 ekin = 1.57892460633575 | erot = 1.91516553831265 | epot = -11.8687131735996 | etot = -8.37462302895119 +713000 ekin = 1.51786752131641 | erot = 2.04613993379542 | epot = -11.9386304839937 | etot = -8.37462302888188 +714000 ekin = 1.45734042326248 | erot = 2.19509441543986 | epot = -12.0270578675957 | etot = -8.37462302889338 +715000 ekin = 1.39951776249161 | erot = 2.35946536290658 | epot = -12.1336061544181 | etot = -8.37462302901989 +716000 ekin = 1.34639246829257 | erot = 2.53511986593063 | epot = -12.2561353635231 | etot = -8.37462302929987 +717000 ekin = 1.29955432269653 | erot = 2.71613012093776 | epot = -12.3903074733622 | etot = -8.37462302972791 +718000 ekin = 1.25989829926672 | erot = 2.89465680801553 | epot = -12.5291781376648 | etot = -8.37462303038252 +719000 ekin = 1.22750607428707 | erot = 3.06092665837673 | epot = -12.663055763813 | etot = -8.37462303114923 +720000 ekin = 1.20188187065045 | erot = 3.20425006661911 | epot = -12.7807549692082 | etot = -8.37462303193865 +721000 ekin = 1.18220717981637 | erot = 3.31414882430528 | epot = -12.8709790367385 | etot = -8.37462303261682 +722000 ekin = 1.167746084253 | erot = 3.38185582435258 | epot = -12.9242249416936 | etot = -8.37462303308801 +723000 ekin = 1.15807318395746 | erot = 3.40183188752098 | epot = -12.9345281046194 | etot = -8.37462303314091 +724000 ekin = 1.15381445066092 | erot = 3.37321067526363 | epot = -12.9016481586785 | etot = -8.37462303275395 +725000 ekin = 1.15678266075217 | erot = 3.3003667101013 | epot = -12.8317724028488 | etot = -8.37462303199533 +726000 ekin = 1.1696197829546 | erot = 3.19222682090122 | epot = -12.7364696348819 | etot = -8.37462303102604 +727000 ekin = 1.19513165177666 | erot = 3.06063268788916 | epot = -12.6303873697018 | etot = -8.37462303003595 +728000 ekin = 1.23552066619851 | erot = 2.91835949420198 | epot = -12.5285031895849 | etot = -8.37462302918443 +729000 ekin = 1.29175272903889 | erot = 2.77740116865265 | epot = -12.4437769262603 | etot = -8.3746230285688 +730000 ekin = 1.3631967531644 | erot = 2.64784734360347 | epot = -12.38566712499 | etot = -8.37462302822212 +731000 ekin = 1.4475753545511 | erot = 2.53736869406004 | epot = -12.3595670767397 | etot = -8.37462302812852 +732000 ekin = 1.54119076303258 | erot = 2.45114849797744 | epot = -12.3669622892558 | etot = -8.37462302824583 +733000 ekin = 1.63933166933537 | erot = 2.39205275844115 | epot = -12.4060074563017 | etot = -8.37462302852523 +734000 ekin = 1.73673684343545 | erot = 2.36087235952521 | epot = -12.4722322318858 | etot = -8.37462302892515 +735000 ekin = 1.82801503452905 | erot = 2.35655963727639 | epot = -12.5591977012161 | etot = -8.37462302941069 +736000 ekin = 1.90799093491543 | erot = 2.37647912514031 | epot = -12.6590930900003 | etot = -8.37462302994453 +737000 ekin = 1.97201607370513 | erot = 2.41675065087033 | epot = -12.7633897550508 | etot = -8.37462303047533 +738000 ekin = 2.01630111183775 | erot = 2.47274745431883 | epot = -12.8636715970953 | etot = -8.37462303093867 +739000 ekin = 2.0382794148672 | erot = 2.53972508205568 | epot = -12.9526275281928 | etot = -8.37462303126992 +740000 ekin = 2.03693425614143 | erot = 2.61344505992171 | epot = -13.0250023474905 | etot = -8.37462303142735 +741000 ekin = 2.01297029118197 | erot = 2.6905926898414 | epot = -13.078186012435 | etot = -8.37462303141167 +742000 ekin = 1.96872639119326 | erot = 2.76882566300566 | epot = -13.1121750854697 | etot = -8.37462303127075 +743000 ekin = 1.90780895376724 | erot = 2.84642411503796 | epot = -13.1288560998889 | etot = -8.37462303108371 +744000 ekin = 1.83452633958094 | erot = 2.92167512840821 | epot = -13.1308244989241 | etot = -8.37462303093494 +745000 ekin = 1.75327142731238 | erot = 2.99223326157179 | epot = -13.1201277197705 | etot = -8.37462303088637 +746000 ekin = 1.66800377368558 | erot = 3.05470990300409 | epot = -13.0973367076481 | etot = -8.37462303095839 +747000 ekin = 1.58193446047701 | erot = 3.10466510758295 | epot = -13.0612225991749 | etot = -8.37462303111489 +748000 ekin = 1.49744243761765 | erot = 3.1370817032622 | epot = -13.0091471721998 | etot = -8.37462303131994 +749000 ekin = 1.41618008606395 | erot = 3.14699639325504 | epot = -12.9377995108104 | etot = -8.37462303149142 +750000 ekin = 1.33927892449615 | erot = 3.13031955339586 | epot = -12.8442215094657 | etot = -8.3746230315737 +751000 ekin = 1.26755716714793 | erot = 3.08449081835569 | epot = -12.7266710170447 | etot = -8.3746230315411 +752000 ekin = 1.20166403423451 | erot = 3.00876367719806 | epot = -12.5850507428289 | etot = -8.37462303139636 +753000 ekin = 1.14214671460853 | erot = 2.90415589313793 | epot = -12.4209256389059 | etot = -8.37462303115941 +754000 ekin = 1.08946987137881 | erot = 2.77319742893274 | epot = -12.237290331163 | etot = -8.37462303085144 +755000 ekin = 1.0440339069326 | erot = 2.61963797727814 | epot = -12.0382949146963 | etot = -8.37462303048555 +756000 ekin = 1.00622473318369 | erot = 2.44820898511458 | epot = -11.8290567483663 | etot = -8.37462303006798 +757000 ekin = 0.976498427340588 | erot = 2.26449263385604 | epot = -11.61561409077 | etot = -8.3746230295734 +758000 ekin = 0.95548508197913 | erot = 2.07490082917664 | epot = -11.4050089402143 | etot = -8.37462302905851 +759000 ekin = 0.943970421426005 | erot = 1.88597944064736 | epot = -11.2045728906421 | etot = -8.37462302856878 +760000 ekin = 0.942943189110147 | erot = 1.7039167649091 | epot = -11.0214829821213 | etot = -8.37462302810203 +761000 ekin = 0.953636819945896 | erot = 1.53434362889912 | epot = -10.8626034765329 | etot = -8.3746230276879 +762000 ekin = 0.97743946369241 | erot = 1.38197793553288 | epot = -10.7340404265768 | etot = -8.3746230273515 +763000 ekin = 1.01575214955006 | erot = 1.25038414099742 | epot = -10.6407593176589 | etot = -8.37462302711139 +764000 ekin = 1.06980632712673 | erot = 1.14186552726324 | epot = -10.5862948813705 | etot = -8.37462302698054 +765000 ekin = 1.14045321588218 | erot = 1.05746802226754 | epot = -10.572544265118 | etot = -8.37462302696826 +766000 ekin = 1.22794009362295 | erot = 0.997057737149038 | epot = -10.5996208578533 | etot = -8.3746230270813 +767000 ekin = 1.33169356851996 | erot = 0.959438204850342 | epot = -10.6657548006934 | etot = -8.37462302732309 +768000 ekin = 1.45013707578519 | erot = 0.942489485960565 | epot = -10.7672495894374 | etot = -8.37462302769164 +769000 ekin = 1.58057826601931 | erot = 0.943330765780494 | epot = -10.8985320599751 | etot = -8.37462302817531 +770000 ekin = 1.71920830312909 | erot = 0.958522817522704 | epot = -11.0523541494005 | etot = -8.3746230287487 +771000 ekin = 1.86125297315597 | erot = 0.984329269154786 | epot = -11.22020527168 | etot = -8.37462302936927 +772000 ekin = 2.00111996070472 | erot = 1.01706547585556 | epot = -11.3928084666374 | etot = -8.37462303007708 +773000 ekin = 2.13179679389825 | erot = 1.05343215415002 | epot = -11.5598519787401 | etot = -8.37462303069187 +774000 ekin = 2.24724323871492 | erot = 1.09038833142067 | epot = -11.7122546013233 | etot = -8.37462303118767 +775000 ekin = 2.34263593745642 | erot = 1.12564496608115 | epot = -11.8429039350586 | etot = -8.37462303152106 +776000 ekin = 2.41469510965557 | erot = 1.15782091196235 | epot = -11.9471390532945 | etot = -8.37462303167661 +777000 ekin = 2.4619556450841 | erot = 1.18638590330911 | epot = -12.0229645800646 | etot = -8.3746230316714 +778000 ekin = 2.48471522536713 | erot = 1.21145891745681 | epot = -12.0707971743752 | etot = -8.37462303155128 +779000 ekin = 2.48466047807948 | erot = 1.23352809685664 | epot = -12.0928116063126 | etot = -8.3746230313765 +780000 ekin = 2.46428568678489 | erot = 1.25319615840711 | epot = -12.0921048763886 | etot = -8.37462303119655 +781000 ekin = 2.4263230702414 | erot = 1.2710709331522 | epot = -12.0720170344205 | etot = -8.37462303102695 +782000 ekin = 2.3734174718094 | erot = 1.28787882380252 | epot = -12.0359193264533 | etot = -8.37462303084136 +783000 ekin = 2.3081517037365 | erot = 1.30476531778341 | epot = -11.9875400521136 | etot = -8.37462303059371 +784000 ekin = 2.23331824905967 | erot = 1.32360971126966 | epot = -11.9315509905816 | etot = -8.37462303025231 +785000 ekin = 2.15217666718282 | erot = 1.34711489736925 | epot = -11.8739145943864 | etot = -8.37462302983438 +786000 ekin = 2.06843940786861 | erot = 1.37850506799765 | epot = -11.821567505275 | etot = -8.37462302940871 +787000 ekin = 1.98588342004993 | erot = 1.42085370630258 | epot = -11.7813601554279 | etot = -8.37462302907537 +788000 ekin = 1.90769396723955 | erot = 1.47626814204841 | epot = -11.7585851382104 | etot = -8.37462302892247 +789000 ekin = 1.83580155857365 | erot = 1.54525606067604 | epot = -11.7556806482382 | etot = -8.37462302898855 +790000 ekin = 1.77050160314379 | erot = 1.62653131906873 | epot = -11.7716559514595 | etot = -8.37462302924703 +791000 ekin = 1.71053482189682 | erot = 1.71731536900441 | epot = -11.8024732205211 | etot = -8.37462302961985 +792000 ekin = 1.65360852454759 | erot = 1.8139751919523 | epot = -11.8422067465096 | etot = -8.37462303000971 +793000 ekin = 1.59715988493912 | erot = 1.91273671397553 | epot = -11.8845196292482 | etot = -8.3746230303335 +794000 ekin = 1.53909469767268 | erot = 2.01023412199548 | epot = -11.9239518502218 | etot = -8.37462303055361 +795000 ekin = 1.47829524951161 | erot = 2.10382941015471 | epot = -11.9567476902912 | etot = -8.37462303062492 +796000 ekin = 1.41481662091498 | erot = 2.19194291988956 | epot = -11.9813825713715 | etot = -8.374623030567 +797000 ekin = 1.34981308251972 | erot = 2.27401207101473 | epot = -11.9984481839359 | etot = -8.37462303040142 +798000 ekin = 1.28529636433261 | erot = 2.35042093006667 | epot = -12.0103403245571 | etot = -8.37462303015777 +799000 ekin = 1.22381948476676 | erot = 2.42233570218471 | epot = -12.0207782168048 | etot = -8.3746230298533 +800000 ekin = 1.16822785389072 | erot = 2.49143438531586 | epot = -12.0342852688204 | etot = -8.3746230296138 +801000 ekin = 1.12099278645327 | erot = 2.55928816627915 | epot = -12.0549039821717 | etot = -8.37462302943928 +802000 ekin = 1.08396505816673 | erot = 2.62689447860425 | epot = -12.0854825661012 | etot = -8.37462302933024 +803000 ekin = 1.05841636962212 | erot = 2.69442631107878 | epot = -12.1274657101593 | etot = -8.37462302945839 +804000 ekin = 1.04426779803363 | erot = 2.76024770978186 | epot = -12.1791385376321 | etot = -8.37462302981661 +805000 ekin = 1.03995925235812 | erot = 2.82046254231515 | epot = -12.2350448251454 | etot = -8.37462303047209 +806000 ekin = 1.04249639916868 | erot = 2.86897163059201 | epot = -12.2860910609771 | etot = -8.37462303121639 +807000 ekin = 1.04816653318231 | erot = 2.89850351394551 | epot = -12.3212930790752 | etot = -8.37462303194734 +808000 ekin = 1.05329972434446 | erot = 2.90189493045252 | epot = -12.3298176872852 | etot = -8.37462303248817 +809000 ekin = 1.05511003120376 | erot = 2.87378175153012 | epot = -12.3035148154265 | etot = -8.37462303269267 +810000 ekin = 1.05231348653264 | erot = 2.81208782296007 | epot = -12.2390243420606 | etot = -8.37462303256789 +811000 ekin = 1.04519713630642 | erot = 2.71854122755763 | epot = -12.1383613958735 | etot = -8.37462303200948 +812000 ekin = 1.03556509624585 | erot = 2.59875418172924 | epot = -12.008942309191 | etot = -8.37462303121596 +813000 ekin = 1.0261737081031 | erot = 2.46123250530751 | epot = -11.8620292437551 | etot = -8.37462303034445 +814000 ekin = 1.01993499392849 | erot = 2.31562695732952 | epot = -11.7101849807871 | etot = -8.37462302952907 +815000 ekin = 1.01938989932849 | erot = 2.17131439145906 | epot = -11.5653273196397 | etot = -8.3746230288521 +816000 ekin = 1.02641070196203 | erot = 2.03643247736796 | epot = -11.4374662076766 | etot = -8.37462302834664 +817000 ekin = 1.04210163742137 | erot = 1.91741411154925 | epot = -11.3341387769838 | etot = -8.37462302801323 +818000 ekin = 1.06685452880261 | erot = 1.81892194074613 | epot = -11.2603994973349 | etot = -8.3746230277862 +819000 ekin = 1.10044073145319 | erot = 1.74396570054325 | epot = -11.2190294597782 | etot = -8.37462302778171 +820000 ekin = 1.14169134057103 | erot = 1.69367065620946 | epot = -11.2099850246983 | etot = -8.37462302791781 +821000 ekin = 1.18877552113715 | erot = 1.66758281680332 | epot = -11.2309813661274 | etot = -8.37462302818695 +822000 ekin = 1.23927394200174 | erot = 1.66378494636768 | epot = -11.2776819169462 | etot = -8.37462302857678 +823000 ekin = 1.29027861040395 | erot = 1.67905219550459 | epot = -11.3439538348575 | etot = -8.37462302894892 +824000 ekin = 1.33894050065628 | erot = 1.70948347744718 | epot = -11.4230470075674 | etot = -8.37462302946389 +825000 ekin = 1.3822050826929 | erot = 1.75044253327451 | epot = -11.5072706459431 | etot = -8.3746230299757 +826000 ekin = 1.41710294906386 | erot = 1.79708475162229 | epot = -11.5888107310971 | etot = -8.37462303041095 +827000 ekin = 1.4412724956138 | erot = 1.84518129440984 | epot = -11.6610768207222 | etot = -8.3746230306986 +828000 ekin = 1.45335409113255 | erot = 1.89178230943845 | epot = -11.7197594313595 | etot = -8.37462303078847 +829000 ekin = 1.45330184506794 | erot = 1.93565038624243 | epot = -11.7635752619764 | etot = -8.37462303066599 +830000 ekin = 1.44253588751545 | erot = 1.97732673247078 | epot = -11.7944856503443 | etot = -8.37462303035807 +831000 ekin = 1.42321719806458 | erot = 2.01836652042357 | epot = -11.8162067485564 | etot = -8.37462303006827 +832000 ekin = 1.39798324786665 | erot = 2.06093497414613 | epot = -11.8335412515971 | etot = -8.37462302958427 +833000 ekin = 1.37122558103672 | erot = 2.10801499205618 | epot = -11.8538636022591 | etot = -8.37462302916623 +834000 ekin = 1.347391573466 | erot = 2.16168408576612 | epot = -11.8836986881298 | etot = -8.37462302889773 +835000 ekin = 1.33033159139224 | erot = 2.22243990033192 | epot = -11.9273945205555 | etot = -8.37462302883135 +836000 ekin = 1.32279692351164 | erot = 2.28888168431024 | epot = -11.9863016368028 | etot = -8.37462302898088 +837000 ekin = 1.32614569947165 | erot = 2.35776552710305 | epot = -12.0585342558939 | etot = -8.37462302931917 +838000 ekin = 1.34030084314995 | erot = 2.42442328374081 | epot = -12.139347156672 | etot = -8.37462302978121 +839000 ekin = 1.36395770574655 | erot = 2.48350186339417 | epot = -12.2220825994143 | etot = -8.37462303027354 +840000 ekin = 1.39499323418974 | erot = 2.52993036126987 | epot = -12.2995466261511 | etot = -8.37462303069152 +841000 ekin = 1.43098519527422 | erot = 2.5599379691956 | epot = -12.3655461954166 | etot = -8.37462303094678 +842000 ekin = 1.46971603977216 | erot = 2.57185321605216 | epot = -12.416192286821 | etot = -8.37462303099667 +843000 ekin = 1.50953312207128 | erot = 2.56639824292026 | epot = -12.4505543958523 | etot = -8.37462303086072 +844000 ekin = 1.54948222761285 | erot = 2.54631968029351 | epot = -12.4704249385206 | etot = -8.37462303061426 +845000 ekin = 1.58921446593512 | erot = 2.51544731884043 | epot = -12.4792848151338 | etot = -8.37462303035821 +846000 ekin = 1.62874660077506 | erot = 2.47751369447731 | epot = -12.4808833254336 | etot = -8.37462303018124 +847000 ekin = 1.66818957259095 | erot = 2.43516936581845 | epot = -12.4779819685369 | etot = -8.37462303012748 +848000 ekin = 1.70754173435641 | erot = 2.38953851006948 | epot = -12.4717032746117 | etot = -8.37462303018578 +849000 ekin = 1.74659403310612 | erot = 2.34043091651457 | epot = -12.4616479799223 | etot = -8.37462303030163 +850000 ekin = 1.78494345870356 | erot = 2.28706007035913 | epot = -12.4466265594671 | etot = -8.37462303040443 +851000 ekin = 1.82207688731629 | erot = 2.228914200592 | epot = -12.42561411835 | etot = -8.3746230304417 +852000 ekin = 1.85747606631012 | erot = 2.16637383860093 | epot = -12.3984729353117 | etot = -8.37462303040065 +853000 ekin = 1.89070501220074 | erot = 2.10080168930645 | epot = -12.3661297318176 | etot = -8.37462303031038 +854000 ekin = 1.9214659858435 | erot = 2.03409194229 | epot = -12.3301809583572 | etot = -8.37462303022366 +855000 ekin = 1.94963553793794 | erot = 1.96792069984453 | epot = -12.2921792679713 | etot = -8.37462303018887 +856000 ekin = 1.97530408458121 | erot = 1.90306034558465 | epot = -12.2529874603915 | etot = -8.37462303022566 +857000 ekin = 1.99898235180446 | erot = 1.83954776706262 | epot = -12.2131531489303 | etot = -8.37462303006319 +858000 ekin = 2.02148966900432 | erot = 1.77712472332923 | epot = -12.1732374225549 | etot = -8.37462303022136 +859000 ekin = 2.0433298482171 | erot = 1.71372610051619 | epot = -12.1316789790703 | etot = -8.37462303033704 +860000 ekin = 2.06530510870649 | erot = 1.64761266612194 | epot = -12.0875408051794 | etot = -8.37462303035096 +861000 ekin = 2.08844047530034 | erot = 1.57839130427194 | epot = -12.0414548098105 | etot = -8.37462303023818 +862000 ekin = 2.11372996883785 | erot = 1.50759861504335 | epot = -11.9959516139068 | etot = -8.37462303002562 +863000 ekin = 2.14175193685403 | erot = 1.43866072803281 | epot = -11.9550356946781 | etot = -8.37462302979131 +864000 ekin = 2.17225364148361 | erot = 1.37614575520133 | epot = -11.923022426322 | etot = -8.37462302963709 +865000 ekin = 2.20389689307595 | erot = 1.32450432851186 | epot = -11.9030242512271 | etot = -8.37462302963933 +866000 ekin = 2.23438769162011 | erot = 1.28681328074455 | epot = -11.8958240018387 | etot = -8.37462302947405 +867000 ekin = 2.26151301830529 | erot = 1.26501341503676 | epot = -11.9011494631015 | etot = -8.37462302975946 +868000 ekin = 2.28295312631386 | erot = 1.25876385672369 | epot = -11.9163400130151 | etot = -8.37462302997758 +869000 ekin = 2.29713139084229 | erot = 1.26636363804849 | epot = -11.9381180589386 | etot = -8.37462303004779 +870000 ekin = 2.30388454561698 | erot = 1.28638972777536 | epot = -11.9648973033815 | etot = -8.37462302998917 +871000 ekin = 2.30409365407575 | erot = 1.31787621263324 | epot = -11.9965928970681 | etot = -8.37462303035909 +872000 ekin = 2.29712455302405 | erot = 1.35930276714017 | epot = -12.0310503505215 | etot = -8.37462303035724 +873000 ekin = 2.28274539313174 | erot = 1.40846954678439 | epot = -12.0658379700283 | etot = -8.37462303011216 +874000 ekin = 2.26320703625639 | erot = 1.46277950106241 | epot = -12.1006095675436 | etot = -8.37462303022481 +875000 ekin = 2.24001634727781 | erot = 1.51889022328921 | epot = -12.1335296008602 | etot = -8.3746230302932 +876000 ekin = 2.21430830467358 | erot = 1.57348199616131 | epot = -12.1624133311162 | etot = -8.37462303028127 +877000 ekin = 2.18777848574912 | erot = 1.62389020162125 | epot = -12.186291717523 | etot = -8.37462303015259 +878000 ekin = 2.1625289754971 | erot = 1.6683879309175 | epot = -12.2055399364741 | etot = -8.37462303005945 +879000 ekin = 2.14044753724287 | erot = 1.70571411561398 | epot = -12.220784682854 | etot = -8.37462302999713 +880000 ekin = 2.12277471005516 | erot = 1.7346996712217 | epot = -12.2320974113065 | etot = -8.37462303002968 +881000 ekin = 2.10977467363156 | erot = 1.75399371448721 | epot = -12.2383914183077 | etot = -8.37462303018896 +882000 ekin = 2.10050164325684 | erot = 1.76187019273065 | epot = -12.2369948664373 | etot = -8.37462303044976 +883000 ekin = 2.09290867716185 | erot = 1.75649694683761 | epot = -12.2240286547192 | etot = -8.37462303071974 +884000 ekin = 2.08433703648905 | erot = 1.7367150045413 | epot = -12.1956750719427 | etot = -8.37462303091231 +885000 ekin = 2.07202901576595 | erot = 1.7028259206429 | epot = -12.1494779673696 | etot = -8.37462303096077 +886000 ekin = 2.05378411495457 | erot = 1.6566047646792 | epot = -12.085011910272 | etot = -8.37462303063819 +887000 ekin = 2.02874297424939 | erot = 1.60297409536587 | epot = -12.0063400996892 | etot = -8.37462303007394 +888000 ekin = 1.99720256587183 | erot = 1.54912086819091 | epot = -11.9209464635251 | etot = -8.37462302946235 +889000 ekin = 1.95913963740047 | erot = 1.50198702363197 | epot = -11.8357496899597 | etot = -8.37462302892728 +890000 ekin = 1.91617614846425 | erot = 1.46746689319387 | epot = -11.7582660701973 | etot = -8.37462302853923 +891000 ekin = 1.87023137420534 | erot = 1.44931992803353 | epot = -11.6941743305672 | etot = -8.37462302832828 +892000 ekin = 1.82316218739014 | erot = 1.44889048221078 | epot = -11.6466756978758 | etot = -8.37462302827483 +893000 ekin = 1.77672781689597 | erot = 1.46538080237729 | epot = -11.6167316476053 | etot = -8.37462302833208 +894000 ekin = 1.73267401011555 | erot = 1.49642015516969 | epot = -11.6037171937257 | etot = -8.37462302844046 +895000 ekin = 1.6928761544742 | erot = 1.53876375532456 | epot = -11.6062629383404 | etot = -8.3746230285416 +896000 ekin = 1.65946528813143 | erot = 1.58897281247465 | epot = -11.623061129204 | etot = -8.3746230285979 +897000 ekin = 1.63484229164664 | erot = 1.64389812669818 | epot = -11.6533634469444 | etot = -8.37462302859954 +898000 ekin = 1.62150447332881 | erot = 1.70104293739242 | epot = -11.6971704392952 | etot = -8.374623028574 +899000 ekin = 1.6216839414652 | erot = 1.75850368933565 | epot = -11.754810659374 | etot = -8.37462302857311 +900000 ekin = 1.63689346404105 | erot = 1.81470313435645 | epot = -11.8262196270434 | etot = -8.37462302864591 +901000 ekin = 1.6675338774235 | erot = 1.86808611512452 | epot = -11.9102430213676 | etot = -8.37462302881957 +902000 ekin = 1.71269692237727 | erot = 1.91693084831131 | epot = -12.0042507997782 | etot = -8.3746230290896 +903000 ekin = 1.77021838508048 | erot = 1.9593405098069 | epot = -12.1041819243172 | etot = -8.37462302942986 +904000 ekin = 1.83694819296679 | erot = 1.9934131207578 | epot = -12.2049843435093 | etot = -8.37462302978473 +905000 ekin = 1.9091464165457 | erot = 2.01754527640836 | epot = -12.3013147230679 | etot = -8.37462303011389 +906000 ekin = 1.98289589689518 | erot = 2.03065122053356 | epot = -12.3881701478152 | etot = -8.37462303038642 +907000 ekin = 2.0544387792582 | erot = 2.03228127519948 | epot = -12.4613430850491 | etot = -8.37462303059146 +908000 ekin = 2.12038320008435 | erot = 2.02259637573229 | epot = -12.5176026065511 | etot = -8.37462303073442 +909000 ekin = 2.17777472068537 | erot = 2.00223868776878 | epot = -12.554636439284 | etot = -8.37462303082986 +910000 ekin = 2.22407231391338 | erot = 1.9721845909131 | epot = -12.5708799357147 | etot = -8.37462303088825 +911000 ekin = 2.25709881234482 | erot = 1.93367043928136 | epot = -12.5653922825338 | etot = -8.37462303090759 +912000 ekin = 2.27504055969691 | erot = 1.88824345128016 | epot = -12.5379070418475 | etot = -8.37462303087045 +913000 ekin = 2.27654326620465 | erot = 1.83792322952128 | epot = -12.489089526477 | etot = -8.3746230307511 +914000 ekin = 2.26395838710281 | erot = 1.78540897808978 | epot = -12.4239903948688 | etot = -8.37462302967619 +915000 ekin = 2.2404546891426 | erot = 1.73372810073202 | epot = -12.3488058193935 | etot = -8.37462302951889 +916000 ekin = 2.20520370203194 | erot = 1.68615105201165 | epot = -12.2659777833575 | etot = -8.37462302931391 +917000 ekin = 2.15800582906335 | erot = 1.64606783760092 | epot = -12.1786966957696 | etot = -8.37462302910529 +918000 ekin = 2.09921834410539 | erot = 1.61647797763549 | epot = -12.0903193506726 | etot = -8.37462302893175 +919000 ekin = 2.02966476141014 | erot = 1.59954949783084 | epot = -12.0038372880469 | etot = -8.3746230288059 +920000 ekin = 1.95065755947246 | erot = 1.59642144858295 | epot = -11.9217020368539 | etot = -8.37462302879853 +921000 ekin = 1.8636620064885 | erot = 1.60750866082269 | epot = -11.8457936959448 | etot = -8.37462302863366 +922000 ekin = 1.77152243883442 | erot = 1.63263587423585 | epot = -11.7787813414987 | etot = -8.3746230284284 +923000 ekin = 1.67869484031726 | erot = 1.67111175336598 | epot = -11.7244296218725 | etot = -8.37462302818924 +924000 ekin = 1.59024537020744 | erot = 1.72202288866753 | epot = -11.6868912868401 | etot = -8.37462302796509 +925000 ekin = 1.51123937037388 | erot = 1.78411652413432 | epot = -11.6699789223347 | etot = -8.37462302782654 +926000 ekin = 1.44599317765939 | erot = 1.85554834410282 | epot = -11.6761645495869 | etot = -8.37462302782471 +927000 ekin = 1.39752558603051 | erot = 1.9337066123923 | epot = -11.7058552263851 | etot = -8.37462302796227 +928000 ekin = 1.36763823811589 | erot = 2.01538770685265 | epot = -11.7576489728592 | etot = -8.37462302789061 +929000 ekin = 1.36100399985385 | erot = 2.09737818243304 | epot = -11.8330052107535 | etot = -8.37462302846664 +930000 ekin = 1.35523134973969 | erot = 2.17722433888997 | epot = -11.9070787110181 | etot = -8.37462302238848 +931000 ekin = 1.39431469293821 | erot = 2.25435620443639 | epot = -12.0232939189487 | etot = -8.37462302157406 +932000 ekin = 1.49280866700354 | erot = 2.31847930199535 | epot = -12.1859109889732 | etot = -8.37462301997432 +933000 ekin = 1.58533340940733 | erot = 2.36490000063033 | epot = -12.3248564302632 | etot = -8.37462302022554 +934000 ekin = 1.6869071209185 | erot = 2.39298221172759 | epot = -12.4545123552844 | etot = -8.37462302263832 +935000 ekin = 1.78473836456431 | erot = 2.39676204063713 | epot = -12.5561234284098 | etot = -8.37462302320837 +936000 ekin = 1.86987725379427 | erot = 2.37258693735196 | epot = -12.6170872146559 | etot = -8.37462302350971 +937000 ekin = 1.93720452631658 | erot = 2.32043568375497 | epot = -12.6322632335806 | etot = -8.37462302350909 +938000 ekin = 1.98385208904068 | erot = 2.24266190734032 | epot = -12.6011370196061 | etot = -8.37462302322507 +939000 ekin = 2.00910923701481 | erot = 2.14379034932402 | epot = -12.5275226090719 | etot = -8.37462302273311 +940000 ekin = 2.01395507287334 | erot = 2.02993348653353 | epot = -12.418511581502 | etot = -8.37462302209516 +941000 ekin = 2.00103743451128 | erot = 1.90808629517054 | epot = -12.2837467510605 | etot = -8.37462302137871 +942000 ekin = 1.97419824311637 | erot = 1.78546116622027 | epot = -12.1342824299796 | etot = -8.37462302064296 +943000 ekin = 1.93808318012258 | erot = 1.66892069893474 | epot = -11.9816268989915 | etot = -8.37462301993416 +944000 ekin = 1.89777663363129 | erot = 1.56456198515432 | epot = -11.8369616380752 | etot = -8.37462301928957 +945000 ekin = 1.8584360574195 | erot = 1.4774221417799 | epot = -11.7104812179438 | etot = -8.3746230187444 +946000 ekin = 1.82491092903916 | erot = 1.4112458813268 | epot = -11.6107798287017 | etot = -8.3746230183357 +947000 ekin = 1.80134221891273 | erot = 1.36826076777987 | epot = -11.544226004796 | etot = -8.37462301810342 +948000 ekin = 1.79076227761391 | erot = 1.34894522657999 | epot = -11.514330522277 | etot = -8.37462301808307 +949000 ekin = 1.79475359827847 | erot = 1.35184135985215 | epot = -11.5212179764226 | etot = -8.37462301829198 +950000 ekin = 1.81326202056042 | erot = 1.37352812800741 | epot = -11.5614131672793 | etot = -8.37462301871149 +951000 ekin = 1.84466122234651 | erot = 1.40888082072085 | epot = -11.6281650623473 | etot = -8.37462301927996 +952000 ekin = 1.88610598522676 | erot = 1.45166996303417 | epot = -11.7123989681623 | etot = -8.37462301990139 +953000 ekin = 1.934156262123 | erot = 1.49545802204409 | epot = -11.8042373044958 | etot = -8.3746230203287 +954000 ekin = 1.98570845877452 | erot = 1.53486140745232 | epot = -11.8951928869974 | etot = -8.37462302077055 +955000 ekin = 2.03763688301833 | erot = 1.56575119860864 | epot = -11.9780111026545 | etot = -8.37462302102751 +956000 ekin = 2.08752516851332 | erot = 1.58576425984886 | epot = -12.0479124494575 | etot = -8.3746230210953 +957000 ekin = 2.13388693711082 | erot = 1.59443657070954 | epot = -12.1029465288261 | etot = -8.37462302100571 +958000 ekin = 2.17603134876119 | erot = 1.59291217732942 | epot = -12.1435665469034 | etot = -8.37462302081277 +959000 ekin = 2.21381255039447 | erot = 1.58343493097992 | epot = -12.1718705019502 | etot = -8.37462302057581 +960000 ekin = 2.24735101958393 | erot = 1.56876603519003 | epot = -12.1907400751222 | etot = -8.37462302034826 +961000 ekin = 2.27678636586191 | erot = 1.55164507315893 | epot = -12.2030544591906 | etot = -8.37462302016977 +962000 ekin = 2.30208813281834 | erot = 1.53436606864973 | epot = -12.2110772215359 | etot = -8.3746230200678 +963000 ekin = 2.32292955592992 | erot = 1.51849868392629 | epot = -12.216051259911 | etot = -8.37462302005475 +964000 ekin = 2.33862421271349 | erot = 1.50476151871897 | epot = -12.2180087515615 | etot = -8.37462302012903 +965000 ekin = 2.34813222218501 | erot = 1.49304783088655 | epot = -12.2158030733455 | etot = -8.37462302027398 +966000 ekin = 2.35015122859632 | erot = 1.48260237415612 | epot = -12.2073766232095 | etot = -8.37462302045703 +967000 ekin = 2.34330726073581 | erot = 1.47233774694663 | epot = -12.1902680283141 | etot = -8.37462302063161 +968000 ekin = 2.32644504723609 | erot = 1.4612521262929 | epot = -12.1623201942732 | etot = -8.3746230207442 +969000 ekin = 2.298987719283 | erot = 1.44887277461076 | epot = -12.1224835146385 | etot = -8.37462302074475 +970000 ekin = 2.26130276222912 | erot = 1.43562016618933 | epot = -12.0715459490187 | etot = -8.37462302060021 +971000 ekin = 2.21499063344576 | erot = 1.42298879008891 | epot = -12.0126024438385 | etot = -8.37462302030381 +972000 ekin = 2.16303757459317 | erot = 1.413484724074 | epot = -11.9511453184525 | etot = -8.37462301978536 +973000 ekin = 2.10950969279595 | erot = 1.41039391552952 | epot = -11.8945266279348 | etot = -8.37462301960932 +974000 ekin = 2.05703199423842 | erot = 1.417325038755 | epot = -11.8489800521527 | etot = -8.37462301915926 +975000 ekin = 2.01010390576686 | erot = 1.43732066925471 | epot = -11.8220475937773 | etot = -8.37462301875575 +976000 ekin = 1.97340114976942 | erot = 1.4726138540038 | epot = -11.820638022252 | etot = -8.37462301847879 +977000 ekin = 1.95082006441383 | erot = 1.52416835989321 | epot = -11.8496114427088 | etot = -8.37462301840173 +978000 ekin = 1.94472832265077 | erot = 1.59131019464789 | epot = -11.9106615358753 | etot = -8.3746230185766 +979000 ekin = 1.95538713562964 | erot = 1.67153495876314 | epot = -12.0015451134109 | etot = -8.37462301901814 +980000 ekin = 1.98067723854538 | erot = 1.76051368581332 | epot = -12.1158139441448 | etot = -8.37462301978612 +981000 ekin = 2.0157957191225 | erot = 1.85207319544778 | epot = -12.2424919352215 | etot = -8.37462302065118 +982000 ekin = 2.05441082025382 | erot = 1.93952253760915 | epot = -12.3685563793656 | etot = -8.37462302150267 +983000 ekin = 2.08992138423356 | erot = 2.0167128031244 | epot = -12.4812572095418 | etot = -8.37462302218386 +984000 ekin = 2.11656909805995 | erot = 2.0791069697044 | epot = -12.5702990903412 | etot = -8.37462302257681 +985000 ekin = 2.13033501087735 | erot = 2.12464764348882 | epot = -12.6296056770033 | etot = -8.37462302263715 +986000 ekin = 2.12935596235087 | erot = 2.15403431726419 | epot = -12.6580133020188 | etot = -8.37462302240378 +987000 ekin = 2.11471923976004 | erot = 2.17104098415556 | epot = -12.6603832458026 | etot = -8.37462302188695 +988000 ekin = 2.0911973509168 | erot = 2.18228698931119 | epot = -12.648107361857 | etot = -8.37462302162897 +989000 ekin = 2.06027968793927 | erot = 2.19075462083259 | epot = -12.6256573301712 | etot = -8.37462302139929 +990000 ekin = 2.02336255783948 | erot = 2.19843813689039 | epot = -12.5964237159713 | etot = -8.3746230212414 +991000 ekin = 1.98188077464448 | erot = 2.20638055721807 | epot = -12.5628843530207 | etot = -8.37462302115815 +992000 ekin = 1.9371574969609 | erot = 2.21473069770544 | epot = -12.526511215791 | etot = -8.37462302112469 +993000 ekin = 1.89038311214042 | erot = 2.22307759882966 | epot = -12.4880837320782 | etot = -8.37462302110816 +994000 ekin = 1.84266575145737 | erot = 2.23084817714076 | epot = -12.4481369496809 | etot = -8.37462302108277 +995000 ekin = 1.79502825855483 | erot = 2.23761066004422 | epot = -12.4072619396231 | etot = -8.37462302102401 +996000 ekin = 1.74865820363213 | erot = 2.24323231093978 | epot = -12.3665135355147 | etot = -8.37462302094276 +997000 ekin = 1.70508150024523 | erot = 2.24765365397734 | epot = -12.3273581750827 | etot = -8.37462302086018 +998000 ekin = 1.66588125251577 | erot = 2.25078611342452 | epot = -12.2912903867191 | etot = -8.37462302077885 +999000 ekin = 1.63259998377321 | erot = 2.25262768597372 | epot = -12.2598506904229 | etot = -8.37462302067593 +1000000 ekin = 1.60661879884278 | erot = 2.25373528621647 | epot = -12.2349771056213 | etot = -8.37462302056205 + 1000000 0.1190088 -1.3493654 0.12586767 -1.0628358 0.00017426596 64000 +Loop time of 13.0812 on 4 procs for 1000000 steps with 10 atoms + +Performance: 66048.962 tau/day, 76445.558 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0631 | 4.6538 | 7.2171 | 72.4 | 35.58 +Bond | 0.17909 | 0.26012 | 0.34382 | 11.7 | 1.99 +Neigh | 0.005471 | 0.005514 | 0.005554 | 0.0 | 0.04 +Comm | 3.0767 | 5.9677 | 7.5973 | 70.7 | 45.62 +Output | 0.072802 | 0.075774 | 0.080905 | 1.1 | 0.58 +Modify | 0.5268 | 0.6169 | 0.72175 | 11.4 | 4.72 +Other | | 1.501 | | | 11.48 + +Nlocal: 2.50000 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.50000 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25000 ave 15 max 2 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7000000 +Ave special neighs/atom = 3.6000000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:13 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 new file mode 100644 index 0000000000..8c985708ca --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file via write_data, version 27 May 2021 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0 +2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0 +3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0 +4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0 +5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0 +6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0 +7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0 +8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0 +9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0 +10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0 +11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0 +12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0 +13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0 +14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0 +15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0 +16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725 +2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215 +3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625 +4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877 +5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292 +6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776 +7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357 +8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032 +9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696 +10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506 +11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418 +12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697 +13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132 +14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759 +15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106 +16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 similarity index 65% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 index 50c1dd3379..b57d5f09c1 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 @@ -2,20 +2,21 @@ variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 +variable rhos equal 0.2 units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 1 delay 0 check yes read_data data.duplex2 @@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 # NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" +compute quat all property/atom quatw quati quatj quatk compute erot all erotate/asphere compute ekin all ke @@ -72,10 +62,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" run 1000000 -#write_restart config.${number}.* +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 new file mode 100644 index 0000000000..ba05c783fb --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 @@ -0,0 +1,1183 @@ +LAMMPS (2 Jul 2021) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +set atom * mass 3.1575 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -21.0482852787267 | etot = -15.5418106194402 +Per MPI rank memory allocation (min/avg/max) = 9.325 | 9.325 | 9.325 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -1.3610384 0.045520537 -1.1464707 5.9660461e-05 64000 +1000 ekin = 2.70391570439002 | erot = 2.60396138194761 | epot = -20.892587006041 | etot = -15.5847099197034 +2000 ekin = 2.64635320949975 | erot = 2.53579824187029 | epot = -20.7791695875995 | etot = -15.5970181362294 +3000 ekin = 2.69752120400807 | erot = 2.55180306746824 | epot = -20.7137659040141 | etot = -15.4644416325378 +4000 ekin = 2.6538821444735 | erot = 2.47641299322465 | epot = -20.679411997643 | etot = -15.5491168599449 +5000 ekin = 2.60025466050757 | erot = 2.2039059393524 | epot = -20.6560408696723 | etot = -15.8518802698123 +6000 ekin = 2.46901398821906 | erot = 2.47310200487734 | epot = -20.6350989412901 | etot = -15.6929829481937 +7000 ekin = 2.51574664182366 | erot = 2.31213437386206 | epot = -20.6631357493118 | etot = -15.835254733626 +8000 ekin = 2.59690047628267 | erot = 2.32317845363664 | epot = -20.7152959922884 | etot = -15.7952170623691 +9000 ekin = 2.48618631858407 | erot = 2.08285633125495 | epot = -20.7950725844518 | etot = -16.2260299346128 +10000 ekin = 2.52115116499232 | erot = 2.20106084795616 | epot = -20.8992442032706 | etot = -16.1770321903222 +11000 ekin = 2.43147539619193 | erot = 2.42927619785951 | epot = -21.0249867006789 | etot = -16.1642351066275 +12000 ekin = 2.45333761568574 | erot = 2.525603071611 | epot = -21.1588492672088 | etot = -16.1799085799121 +13000 ekin = 2.53951720462341 | erot = 2.74654877006482 | epot = -21.2655112796489 | etot = -15.9794453049606 +14000 ekin = 2.52874823012217 | erot = 3.01239544645662 | epot = -21.3374765197331 | etot = -15.7963328431543 +15000 ekin = 2.63126849733541 | erot = 2.75804260501317 | epot = -21.3622375137171 | etot = -15.9729264113685 +16000 ekin = 2.53351081020592 | erot = 2.95152401468654 | epot = -21.3358982910482 | etot = -15.8508634661558 +17000 ekin = 2.57894891181703 | erot = 3.20567182477324 | epot = -21.2708322188654 | etot = -15.4862114822752 +18000 ekin = 2.48912656009906 | erot = 3.305144217587 | epot = -21.185496468772 | etot = -15.391225691086 +19000 ekin = 2.54963746369463 | erot = 3.12775559702558 | epot = -21.0796045258341 | etot = -15.4022114651139 +20000 ekin = 2.70343028147048 | erot = 3.48245634539093 | epot = -20.9620878080506 | etot = -14.7762011811892 +21000 ekin = 2.7400837598076 | erot = 3.493409766499 | epot = -20.8605728519254 | etot = -14.6270793256188 +22000 ekin = 2.70619491966167 | erot = 3.39094503970532 | epot = -20.7832212738354 | etot = -14.6860813144684 +23000 ekin = 2.7697757193537 | erot = 2.96919161110178 | epot = -20.7244407619744 | etot = -14.9854734315189 +24000 ekin = 2.70661582607971 | erot = 2.73688112318632 | epot = -20.7053645378039 | etot = -15.2618675885378 +25000 ekin = 2.68754636497145 | erot = 2.61416599169547 | epot = -20.7064779461664 | etot = -15.4047655894994 +26000 ekin = 2.73235500408328 | erot = 2.73313459064974 | epot = -20.7277379348113 | etot = -15.2622483400783 +27000 ekin = 2.8077624395387 | erot = 2.57060961199337 | epot = -20.7536767854921 | etot = -15.3753047339601 +28000 ekin = 2.72026602469299 | erot = 2.48773762184115 | epot = -20.7972439765033 | etot = -15.5892403299691 +29000 ekin = 2.74993250614264 | erot = 2.4362001954172 | epot = -20.8845224755543 | etot = -15.6983897739944 +30000 ekin = 2.84727011110435 | erot = 2.55872515142543 | epot = -21.0029391367955 | etot = -15.5969438742657 +31000 ekin = 2.9373105145775 | erot = 2.68538653493625 | epot = -21.1441658724037 | etot = -15.52146882289 +32000 ekin = 3.11483472271263 | erot = 2.71833221771894 | epot = -21.3009630690853 | etot = -15.4677961286537 +33000 ekin = 3.42015689623702 | erot = 3.01186958829681 | epot = -21.4445354747605 | etot = -15.0125089902267 +34000 ekin = 3.4571497053447 | erot = 3.34699175671052 | epot = -21.5750227937594 | etot = -14.7708813317042 +35000 ekin = 3.49497749393851 | erot = 3.14001434352617 | epot = -21.6604994386103 | etot = -15.0255076011457 +36000 ekin = 3.47204675153372 | erot = 2.84774400732494 | epot = -21.6891867301232 | etot = -15.3693959712646 +37000 ekin = 3.44180301616544 | erot = 2.56259280720516 | epot = -21.6709924941777 | etot = -15.6665966708071 +38000 ekin = 3.54821034228965 | erot = 2.44212751582536 | epot = -21.6265094810358 | etot = -15.6361716229208 +39000 ekin = 3.46871818671429 | erot = 2.39960208230661 | epot = -21.5379795382885 | etot = -15.6696592692676 +40000 ekin = 3.39697091933591 | erot = 2.06928828303171 | epot = -21.4180869184492 | etot = -15.9518277160816 +41000 ekin = 3.34648089211938 | erot = 2.10977053447759 | epot = -21.3088504303421 | etot = -15.8525990037452 +42000 ekin = 3.14017175730784 | erot = 2.61712762297436 | epot = -21.2075302208961 | etot = -15.4502308406139 +43000 ekin = 3.0541271305486 | erot = 2.16422672116187 | epot = -21.1026514185807 | etot = -15.8842975668702 +44000 ekin = 2.85636525492286 | erot = 2.23456154398502 | epot = -21.0187138708967 | etot = -15.9277870719889 +45000 ekin = 2.71017763793136 | erot = 2.20442798009884 | epot = -20.9688571562277 | etot = -16.0542515381975 +46000 ekin = 2.80228666966609 | erot = 2.3691206574228 | epot = -20.9221917036257 | etot = -15.7507843765369 +47000 ekin = 2.68398029783778 | erot = 2.30787382180577 | epot = -20.9147956898556 | etot = -15.922941570212 +48000 ekin = 2.60361639221643 | erot = 2.16759706121358 | epot = -20.9378819526189 | etot = -16.1666684991889 +49000 ekin = 2.69879527332656 | erot = 1.95331370371646 | epot = -20.9793801292352 | etot = -16.3272711521921 +50000 ekin = 2.78297818082637 | erot = 1.73866705563715 | epot = -21.0239873291857 | etot = -16.5023420927222 +51000 ekin = 2.79226298145992 | erot = 1.75750015205399 | epot = -21.0591817365136 | etot = -16.5094186029996 +52000 ekin = 2.93778678358836 | erot = 2.05248025310421 | epot = -21.1000263829064 | etot = -16.1097593462138 +53000 ekin = 2.93047021956224 | erot = 2.21318598351599 | epot = -21.1408129057595 | etot = -15.9971567026812 +54000 ekin = 2.95313738597263 | erot = 2.20797346738787 | epot = -21.1830307851601 | etot = -16.0219199317996 +55000 ekin = 2.98703149924483 | erot = 2.36965734625007 | epot = -21.2448833674046 | etot = -15.8881945219097 +56000 ekin = 2.99188476268835 | erot = 2.35374933057429 | epot = -21.3017374555428 | etot = -15.9561033622801 +57000 ekin = 3.04248410594252 | erot = 2.10923890188227 | epot = -21.3362725295754 | etot = -16.1845495217507 +58000 ekin = 2.98235297495938 | erot = 2.13409247728305 | epot = -21.3593231655095 | etot = -16.2428777132671 +59000 ekin = 2.91016949839296 | erot = 2.36822905479348 | epot = -21.3622398255744 | etot = -16.083841272388 +60000 ekin = 2.97250779202342 | erot = 2.54263250726513 | epot = -21.3342690818056 | etot = -15.8191287825171 +61000 ekin = 2.96790668494248 | erot = 2.48996902731655 | epot = -21.2724803895842 | etot = -15.8146046773252 +62000 ekin = 2.94610606099048 | erot = 2.18201665175963 | epot = -21.187919461435 | etot = -16.0597967486849 +63000 ekin = 3.0271214705261 | erot = 2.16093889178584 | epot = -21.096658489144 | etot = -15.9085981268321 +64000 ekin = 3.20886369209213 | erot = 2.06931440640059 | epot = -21.0569971647532 | etot = -15.7788190662604 +65000 ekin = 3.22349334555752 | erot = 1.93510092297445 | epot = -21.0349289183418 | etot = -15.8763346498098 +66000 ekin = 3.10418207507129 | erot = 1.94339370515853 | epot = -21.051745388243 | etot = -16.0041696080131 +67000 ekin = 3.12595764700019 | erot = 2.29857726165623 | epot = -21.10762065855 | etot = -15.6830857498936 +68000 ekin = 2.99981867339099 | erot = 2.04147368191603 | epot = -21.181198697827 | etot = -16.13990634252 +69000 ekin = 2.93860333642775 | erot = 2.09583398354869 | epot = -21.2548061558295 | etot = -16.2203688358531 +70000 ekin = 2.9486279695994 | erot = 2.02427035214611 | epot = -21.3225756079773 | etot = -16.3496772862318 +71000 ekin = 2.95485075626806 | erot = 1.98046752535274 | epot = -21.3931478839351 | etot = -16.4578296023143 +72000 ekin = 3.0308352187065 | erot = 1.64033628981958 | epot = -21.468068089369 | etot = -16.7968965808429 +73000 ekin = 3.20193349232367 | erot = 1.82676041495789 | epot = -21.5301957695023 | etot = -16.5015018622208 +74000 ekin = 3.22662444253103 | erot = 1.89227240506012 | epot = -21.5643738418553 | etot = -16.4454769942641 +75000 ekin = 3.28911018830883 | erot = 1.89872323449657 | epot = -21.5810306648803 | etot = -16.3931972420749 +76000 ekin = 3.29558374515743 | erot = 1.87444557500027 | epot = -21.5642338211322 | etot = -16.3942045009745 +77000 ekin = 3.54018909072085 | erot = 1.75729076536995 | epot = -21.5044360245146 | etot = -16.2069561684238 +78000 ekin = 3.54291076978592 | erot = 1.76974361090023 | epot = -21.4006101697986 | etot = -16.0879557891125 +79000 ekin = 3.54987455874821 | erot = 1.91515152695039 | epot = -21.2526696681999 | etot = -15.7876435825013 +80000 ekin = 3.44554692397033 | erot = 1.55785077520358 | epot = -21.1041761178578 | etot = -16.1007784186839 +81000 ekin = 3.39041332540007 | erot = 1.45777024027678 | epot = -20.9764951390216 | etot = -16.1283115733447 +82000 ekin = 3.28164787796656 | erot = 1.38380348431304 | epot = -20.899509162344 | etot = -16.2340578000644 +83000 ekin = 3.27119946746379 | erot = 1.61635220758898 | epot = -20.8682969771061 | etot = -15.9807453020534 +84000 ekin = 3.23767018514775 | erot = 1.58136727778774 | epot = -20.8558733748386 | etot = -16.0368359119031 +85000 ekin = 3.19513864200058 | erot = 1.6431910885888 | epot = -20.8419968518707 | etot = -16.0036671212813 +86000 ekin = 3.24896357270198 | erot = 1.89522046055135 | epot = -20.832806633325 | etot = -15.6886226000717 +87000 ekin = 3.13174021654823 | erot = 1.94306423894159 | epot = -20.8481262288118 | etot = -15.773321773322 +88000 ekin = 3.11122085279115 | erot = 1.78724048339196 | epot = -20.9059531901008 | etot = -16.0074918539177 +89000 ekin = 3.08381661724969 | erot = 1.63584870500641 | epot = -20.9715808309547 | etot = -16.2519155086986 +90000 ekin = 3.20313125753903 | erot = 1.94895881894579 | epot = -21.0671915523152 | etot = -15.9151014758304 +91000 ekin = 3.14651785772312 | erot = 2.26271277860547 | epot = -21.1780568094305 | etot = -15.768826173102 +92000 ekin = 3.23402739820373 | erot = 2.38502646372719 | epot = -21.3058699018424 | etot = -15.6868160399115 +93000 ekin = 3.27864277718335 | erot = 2.22426372598661 | epot = -21.4112218809901 | etot = -15.9083153778202 +94000 ekin = 3.31438607736509 | erot = 2.13604324487186 | epot = -21.5023579935933 | etot = -16.0519286713564 +95000 ekin = 3.27323012344947 | erot = 2.38178684388532 | epot = -21.6160955797709 | etot = -15.9610786124361 +96000 ekin = 3.22326707535017 | erot = 2.54544679505647 | epot = -21.7318191046087 | etot = -15.963105234202 +97000 ekin = 3.23424306839042 | erot = 2.64153427684315 | epot = -21.8458536800775 | etot = -15.9700763348439 +98000 ekin = 3.20883333988349 | erot = 2.67043755850081 | epot = -21.9495446261421 | etot = -16.0702737277578 +99000 ekin = 3.11663851643525 | erot = 2.90733596256664 | epot = -22.0486791427264 | etot = -16.0247046637246 +100000 ekin = 3.03264321501914 | erot = 2.96946233520285 | epot = -22.1457931713674 | etot = -16.1436876211454 +101000 ekin = 2.95046281913209 | erot = 2.88464070608079 | epot = -22.2018281755496 | etot = -16.3667246503367 +102000 ekin = 2.85487641720306 | erot = 3.1835231149768 | epot = -22.1945156997857 | etot = -16.1561161676059 +103000 ekin = 2.83556367487533 | erot = 3.10626911100577 | epot = -22.1286684506118 | etot = -16.1868356647307 +104000 ekin = 2.74206313561178 | erot = 2.764695345083 | epot = -22.0370967342096 | etot = -16.5303382535148 +105000 ekin = 2.68691210569746 | erot = 2.43510424243733 | epot = -21.9227484953522 | etot = -16.8007321472174 +106000 ekin = 2.563230657111 | erot = 2.04976251036808 | epot = -21.8252352950753 | etot = -17.2122421275962 +107000 ekin = 2.45282193090838 | erot = 2.35578840258503 | epot = -21.7394205256344 | etot = -16.930810192141 +108000 ekin = 2.53861743899987 | erot = 2.41441398228763 | epot = -21.6772620188416 | etot = -16.7242305975541 +109000 ekin = 2.47502081207091 | erot = 2.24593310938325 | epot = -21.6325689491034 | etot = -16.9116150276492 +110000 ekin = 2.50321333342882 | erot = 1.86407174946134 | epot = -21.6221361025481 | etot = -17.2548510196579 +111000 ekin = 2.55274947911861 | erot = 1.9335199844403 | epot = -21.6424359547629 | etot = -17.156166491204 +112000 ekin = 2.57554816024176 | erot = 1.85965001180022 | epot = -21.6646307305487 | etot = -17.2294325585067 +113000 ekin = 2.58422184546734 | erot = 1.66612606594662 | epot = -21.6825320885557 | etot = -17.4321841771417 +114000 ekin = 2.63767451071977 | erot = 1.86651684228485 | epot = -21.6875711888383 | etot = -17.1833798358337 +115000 ekin = 2.55850869288988 | erot = 1.95479352013929 | epot = -21.7088690741549 | etot = -17.1955668611257 +116000 ekin = 2.59960484914043 | erot = 1.98515359639087 | epot = -21.7399246709689 | etot = -17.1551662254376 +117000 ekin = 2.6364636182488 | erot = 2.15859263253907 | epot = -21.7790865447414 | etot = -16.9840302939536 +118000 ekin = 2.6722112411998 | erot = 2.07625368130399 | epot = -21.8132075002146 | etot = -17.0647425777108 +119000 ekin = 2.9108516764533 | erot = 1.98818490836516 | epot = -21.8375717289926 | etot = -16.9385351441741 +120000 ekin = 2.93975077154826 | erot = 1.99854094901663 | epot = -21.8494362428877 | etot = -16.9111445223229 +121000 ekin = 3.04700503953791 | erot = 2.15191677123407 | epot = -21.8526361044102 | etot = -16.6537142936382 +122000 ekin = 3.01970065630796 | erot = 2.09092735340917 | epot = -21.8688746811131 | etot = -16.7582466713959 +123000 ekin = 2.9930939614465 | erot = 1.76972828030715 | epot = -21.9045561644836 | etot = -17.14173392273 +124000 ekin = 2.96321679602912 | erot = 1.96464026140171 | epot = -21.9325819137337 | etot = -17.0047248563029 +125000 ekin = 2.98312575423879 | erot = 1.6459259375459 | epot = -21.9608904634477 | etot = -17.331838771663 +126000 ekin = 2.99097949215575 | erot = 1.75618745760134 | epot = -22.009758319428 | etot = -17.2625913696709 +127000 ekin = 3.04267424627598 | erot = 1.84781956231792 | epot = -22.0474977427294 | etot = -17.1570039341355 +128000 ekin = 3.16299477926061 | erot = 1.98570527937047 | epot = -22.1060844986599 | etot = -16.9573844400289 +129000 ekin = 3.16426696344668 | erot = 1.97746137640526 | epot = -22.1606468653278 | etot = -17.0189185254759 +130000 ekin = 3.09082575381668 | erot = 2.52059065203422 | epot = -22.1892702662505 | etot = -16.5778538603996 +131000 ekin = 3.04363359740037 | erot = 2.76905383223605 | epot = -22.1941284862536 | etot = -16.3814410566172 +132000 ekin = 2.97799249868516 | erot = 2.58737442779091 | epot = -22.1487985926417 | etot = -16.5834316661656 +133000 ekin = 3.03410219436435 | erot = 2.49151216637025 | epot = -22.0390476094715 | etot = -16.5134332487369 +134000 ekin = 2.97290518441651 | erot = 2.2795598062273 | epot = -21.9043568760917 | etot = -16.6518918854479 +135000 ekin = 2.97882125899838 | erot = 2.36516672946397 | epot = -21.7588924186334 | etot = -16.4149044301711 +136000 ekin = 3.06225054874148 | erot = 1.85004987442537 | epot = -21.6100365266532 | etot = -16.6977361034863 +137000 ekin = 3.03515949013347 | erot = 1.79133727158631 | epot = -21.4833056014437 | etot = -16.6568088397239 +138000 ekin = 2.9835998684383 | erot = 1.95427111240579 | epot = -21.3692118882268 | etot = -16.4313409073827 +139000 ekin = 3.0063875676428 | erot = 1.75390651791802 | epot = -21.2771971161582 | etot = -16.5169030305974 +140000 ekin = 2.98301520290208 | erot = 1.55293456918089 | epot = -21.2082582422558 | etot = -16.6723084701728 +141000 ekin = 2.8734196918037 | erot = 1.62004287774014 | epot = -21.1593315472341 | etot = -16.6658689776903 +142000 ekin = 2.77198594269102 | erot = 1.82883994332513 | epot = -21.1253786225533 | etot = -16.5245527365371 +143000 ekin = 2.66544385214382 | erot = 1.70763016025286 | epot = -21.1194742186353 | etot = -16.7464002062387 +144000 ekin = 2.64364564452769 | erot = 2.02089778883353 | epot = -21.1558312252306 | etot = -16.4912877918693 +145000 ekin = 2.58320561695123 | erot = 2.33928617610564 | epot = -21.1972194246105 | etot = -16.2747276315536 +146000 ekin = 2.59582465616999 | erot = 2.3913910079826 | epot = -21.2181779484858 | etot = -16.2309622843332 +147000 ekin = 2.57433616776238 | erot = 2.62068830532507 | epot = -21.2035776919776 | etot = -16.0085532188901 +148000 ekin = 2.66661322554065 | erot = 2.64858494989759 | epot = -21.1567312792458 | etot = -15.8415331038076 +149000 ekin = 2.60767807433559 | erot = 2.24435345528447 | epot = -21.1005834026183 | etot = -16.2485518729982 +150000 ekin = 2.54139526377883 | erot = 2.28883985685599 | epot = -21.0349331020295 | etot = -16.2046979813947 +151000 ekin = 2.5432219413665 | erot = 2.35864839828536 | epot = -20.9724639116438 | etot = -16.0705935719919 +152000 ekin = 2.56796491103012 | erot = 2.43023333349202 | epot = -20.9157846601099 | etot = -15.9175864155878 +153000 ekin = 2.51372807626571 | erot = 2.39277188889798 | epot = -20.8708281017583 | etot = -15.9643281365946 +154000 ekin = 2.56425050300779 | erot = 2.55681269376811 | epot = -20.8208061897131 | etot = -15.6997429929373 +155000 ekin = 2.54836883214878 | erot = 2.77382882086472 | epot = -20.7512322840953 | etot = -15.4290346310818 +156000 ekin = 2.50430341115576 | erot = 2.84536424459363 | epot = -20.6831823234819 | etot = -15.3335146677325 +157000 ekin = 2.50400336317688 | erot = 2.74300988092699 | epot = -20.6024983277716 | etot = -15.3554850836678 +158000 ekin = 2.46635677816819 | erot = 2.72725266952981 | epot = -20.3927742179115 | etot = -15.1991647702135 +159000 ekin = 2.41243392896928 | erot = 2.89017327284196 | epot = -20.3716899613963 | etot = -15.069082759585 +160000 ekin = 2.44543789794338 | erot = 2.94805496717089 | epot = -20.5757394278759 | etot = -15.1822465627616 +161000 ekin = 2.48584882392466 | erot = 3.08550000043076 | epot = -20.7243276115622 | etot = -15.1529787872068 +162000 ekin = 2.63092470794183 | erot = 2.8491277718568 | epot = -20.8061639431945 | etot = -15.3261114633959 +163000 ekin = 2.72019716465021 | erot = 2.95674331723642 | epot = -20.9203905101818 | etot = -15.2434500282951 +164000 ekin = 2.85144745755517 | erot = 2.79837544407218 | epot = -21.0599208441751 | etot = -15.4100979425478 +165000 ekin = 3.01926698163447 | erot = 2.57598017599253 | epot = -21.2160748663889 | etot = -15.6208277087619 +166000 ekin = 3.15975032902628 | erot = 2.53424140536866 | epot = -21.3722197077628 | etot = -15.6782279733678 +167000 ekin = 3.28010263683412 | erot = 2.66118639042418 | epot = -21.5168932797697 | etot = -15.5756042525114 +168000 ekin = 3.30088936113461 | erot = 2.6570801564169 | epot = -21.6596207437233 | etot = -15.7016512261718 +169000 ekin = 3.47029246215378 | erot = 2.25395751697315 | epot = -21.7742578136393 | etot = -16.0500078345124 +170000 ekin = 3.70050747267213 | erot = 2.16365167905452 | epot = -21.8748391459109 | etot = -16.0106799941843 +171000 ekin = 3.84839140735074 | erot = 1.87628165448694 | epot = -21.9555399182121 | etot = -16.2308668563744 +172000 ekin = 3.95026415662084 | erot = 1.96481352720165 | epot = -21.9987319268213 | etot = -16.0836542429988 +173000 ekin = 3.92397418949719 | erot = 2.1402486554568 | epot = -21.9962461659818 | etot = -15.9320233210278 +174000 ekin = 3.91787773957962 | erot = 2.15382550531676 | epot = -21.9649412516532 | etot = -15.8932380067568 +175000 ekin = 3.92478898493225 | erot = 1.81413864863455 | epot = -21.886058821032 | etot = -16.1471311874652 +176000 ekin = 3.61843418337262 | erot = 1.68410090365151 | epot = -21.7861032393839 | etot = -16.4835681523597 +177000 ekin = 3.43777437221669 | erot = 1.50869914434539 | epot = -21.6530103766414 | etot = -16.7065368600793 +178000 ekin = 3.29404805426684 | erot = 1.54702143204471 | epot = -21.5151124491371 | etot = -16.6740429628256 +179000 ekin = 3.15559273998197 | erot = 1.83461420036247 | epot = -21.3846264521169 | etot = -16.3944195117725 +180000 ekin = 3.11144262168972 | erot = 1.96187195470713 | epot = -21.2631791815958 | etot = -16.1898646051989 +181000 ekin = 2.86058839708624 | erot = 1.97916662782334 | epot = -21.1736204719049 | etot = -16.3338654469953 +182000 ekin = 2.73358163055363 | erot = 2.08235166110584 | epot = -21.1163854347033 | etot = -16.3004521430438 +183000 ekin = 2.78667823921494 | erot = 2.14955927554286 | epot = -21.0704997912635 | etot = -16.1342622765057 +184000 ekin = 2.74700284417945 | erot = 2.17568363892128 | epot = -21.0417241927555 | etot = -16.1190377096547 +185000 ekin = 2.71206700548405 | erot = 2.43154766133365 | epot = -21.0534073134643 | etot = -15.9097926466466 +186000 ekin = 2.70473969876215 | erot = 2.54763882184454 | epot = -21.0771037789774 | etot = -15.8247252583707 +187000 ekin = 2.69011328843065 | erot = 2.42677059090842 | epot = -21.1334063747328 | etot = -16.0165224953937 +188000 ekin = 2.63139574425889 | erot = 2.47663409366894 | epot = -21.2056416357499 | etot = -16.097611797822 +189000 ekin = 2.52625691649445 | erot = 2.36811030548791 | epot = -21.2763445168886 | etot = -16.3819772949062 +190000 ekin = 2.55070314102272 | erot = 2.46381370096652 | epot = -21.3751397733684 | etot = -16.3606229313791 +191000 ekin = 2.62917079754905 | erot = 2.67833301813017 | epot = -21.4532628428641 | etot = -16.1457590271849 +192000 ekin = 2.58870583923181 | erot = 3.04288815538947 | epot = -21.5216329873865 | etot = -15.8900389927652 +193000 ekin = 2.57473296407422 | erot = 2.98273386984086 | epot = -21.5752070232357 | etot = -16.0177401893207 +194000 ekin = 2.55188197567099 | erot = 3.53664565918049 | epot = -21.6029115846239 | etot = -15.5143839497724 +195000 ekin = 2.37005947654592 | erot = 3.88569194357652 | epot = -21.5199791042833 | etot = -15.2642276841609 +196000 ekin = 2.24643312652487 | erot = 3.89236383309535 | epot = -21.4290282307873 | etot = -15.2902312711671 +197000 ekin = 2.08212744149202 | erot = 3.73392747991439 | epot = -21.3909391389933 | etot = -15.5748842175869 +198000 ekin = 1.99546802101165 | erot = 3.31869767813113 | epot = -21.3106385880563 | etot = -15.9964728889135 +199000 ekin = 1.88808259694764 | erot = 3.05651027418447 | epot = -21.1932358978994 | etot = -16.2486430267673 +200000 ekin = 1.86182600189611 | erot = 3.12152068869523 | epot = -21.1112046099846 | etot = -16.1278579193933 +201000 ekin = 1.97052135402476 | erot = 2.56337970690565 | epot = -21.0818150370229 | etot = -16.5479139760925 +202000 ekin = 1.96444489641634 | erot = 2.52188298721402 | epot = -21.0909969362212 | etot = -16.6046690525908 +203000 ekin = 2.02727163636645 | erot = 2.40435818767017 | epot = -21.1422876293971 | etot = -16.7106578053605 +204000 ekin = 2.08583315864155 | erot = 2.40223613667972 | epot = -21.2224635405406 | etot = -16.7343942452193 +205000 ekin = 2.20775264966623 | erot = 2.45569503503469 | epot = -21.3216506287512 | etot = -16.6582029440503 +206000 ekin = 2.32525581144377 | erot = 2.44338569524376 | epot = -21.4263895154156 | etot = -16.6577480087281 +207000 ekin = 2.39884741653067 | erot = 2.19219588140532 | epot = -21.5586341308418 | etot = -16.9675908329058 +208000 ekin = 2.54174161331668 | erot = 2.0204308648262 | epot = -21.7018700931408 | etot = -17.1396976149979 +209000 ekin = 2.63460295202779 | erot = 2.00847282239007 | epot = -21.8765502984945 | etot = -17.2334745240767 +210000 ekin = 2.81803535020474 | erot = 2.15132327942402 | epot = -22.0655129469125 | etot = -17.0961543172837 +211000 ekin = 2.8544966933982 | erot = 2.00032723609075 | epot = -22.2569212397588 | etot = -17.4020973102698 +212000 ekin = 2.93298840099937 | erot = 2.18896574432212 | epot = -22.4295331026808 | etot = -17.3075789573593 +213000 ekin = 3.04393339596812 | erot = 2.16674803090446 | epot = -22.5865045861157 | etot = -17.3758231592431 +214000 ekin = 3.17687786434378 | erot = 1.93204604450799 | epot = -22.7049386266084 | etot = -17.5960147177566 +215000 ekin = 3.23140803215865 | erot = 1.91093387521926 | epot = -22.7702150399474 | etot = -17.6278731325695 +216000 ekin = 3.2321341050867 | erot = 1.86760943667555 | epot = -22.8077327389956 | etot = -17.7079891972333 +217000 ekin = 3.29951241617977 | erot = 1.99642477225946 | epot = -22.8230103446114 | etot = -17.5270731561722 +218000 ekin = 3.29737584458632 | erot = 1.96274603890206 | epot = -22.8136249789529 | etot = -17.5535030954645 +219000 ekin = 3.23565881897549 | erot = 1.94555976805405 | epot = -22.8103460409257 | etot = -17.6291274538961 +220000 ekin = 3.19248478951655 | erot = 2.14549715461575 | epot = -22.8135403395691 | etot = -17.4755583954368 +221000 ekin = 3.08489658572225 | erot = 2.35182511982449 | epot = -22.7936924594889 | etot = -17.3569707539422 +222000 ekin = 2.98911659742775 | erot = 2.24286093437224 | epot = -22.7593104849621 | etot = -17.5273329531621 +223000 ekin = 2.94028114747166 | erot = 2.45179850593562 | epot = -22.7094689680866 | etot = -17.3173893146793 +224000 ekin = 2.86327223103169 | erot = 2.45496570504129 | epot = -22.6840408073421 | etot = -17.3658028712691 +225000 ekin = 2.86217589447844 | erot = 2.64576978314389 | epot = -22.709459445995 | etot = -17.2015137683726 +226000 ekin = 2.8142175090877 | erot = 2.65054275980917 | epot = -22.7920788909686 | etot = -17.3273186220717 +227000 ekin = 2.76125022534707 | erot = 2.53291854231038 | epot = -22.8714022097528 | etot = -17.5772334420953 +228000 ekin = 2.78877138535082 | erot = 2.36581554390957 | epot = -22.9403431333366 | etot = -17.7857562040762 +229000 ekin = 2.72891406599702 | erot = 2.36761189849136 | epot = -22.9752057147159 | etot = -17.8786797502275 +230000 ekin = 2.73218055588378 | erot = 2.27179336612898 | epot = -22.9619591335889 | etot = -17.9579852115761 +231000 ekin = 2.7823830406074 | erot = 2.56004300399597 | epot = -22.90155406699 | etot = -17.5591280223866 +232000 ekin = 2.70574670734559 | erot = 2.20917728909279 | epot = -22.8024125768837 | etot = -17.8874885804453 +233000 ekin = 2.64840920464763 | erot = 2.10191715204315 | epot = -22.6817951010111 | etot = -17.9314687443204 +234000 ekin = 2.61941879874187 | erot = 1.89218225093214 | epot = -22.5506641543628 | etot = -18.0390631046888 +235000 ekin = 2.59340202709238 | erot = 1.81296941612961 | epot = -22.4559841307523 | etot = -18.0496126875304 +236000 ekin = 2.51387645324674 | erot = 1.87601834806566 | epot = -22.3602077365801 | etot = -17.9703129352677 +237000 ekin = 2.48697606976272 | erot = 1.88725598539924 | epot = -22.2423219253943 | etot = -17.8680898702323 +238000 ekin = 2.4616064489039 | erot = 1.69677740799999 | epot = -22.1532316635744 | etot = -17.9948478066705 +239000 ekin = 2.42201063037743 | erot = 1.70150164392291 | epot = -22.1281108141978 | etot = -18.0045985398974 +240000 ekin = 2.37084323379681 | erot = 1.98736224075244 | epot = -22.1423976045622 | etot = -17.7841921300129 +241000 ekin = 2.37738836540311 | erot = 2.31585984211782 | epot = -22.1830534944813 | etot = -17.4898052869604 +242000 ekin = 2.41676243464672 | erot = 2.55280142063506 | epot = -22.1811996624351 | etot = -17.2116358071533 +243000 ekin = 2.33148792530111 | erot = 2.76551405431882 | epot = -22.1959816056366 | etot = -17.0989796260167 +244000 ekin = 2.38360456402189 | erot = 2.74375775378605 | epot = -22.3530195137562 | etot = -17.2256571959482 +245000 ekin = 2.33752620010225 | erot = 2.63541001293098 | epot = -22.5037249285208 | etot = -17.5307887154876 +246000 ekin = 2.25775984192194 | erot = 2.49145900746147 | epot = -22.6039669429679 | etot = -17.8547480935845 +247000 ekin = 2.20328096321392 | erot = 2.51295988229219 | epot = -22.6897860502887 | etot = -17.9735452047826 +248000 ekin = 2.11215135404835 | erot = 2.38179652938609 | epot = -22.7654961945533 | etot = -18.2715483111189 +249000 ekin = 2.18103243553736 | erot = 2.12199506651676 | epot = -22.8086866218619 | etot = -18.5056591198078 +250000 ekin = 2.00642865007526 | erot = 2.13785268765979 | epot = -22.7981127674599 | etot = -18.6538314297248 +251000 ekin = 2.0081090206787 | erot = 2.15377771615689 | epot = -22.7541924896507 | etot = -18.5923057528151 +252000 ekin = 2.04967696381119 | erot = 2.10564030292916 | epot = -22.7175683002137 | etot = -18.5622510334734 +253000 ekin = 1.97178429049489 | erot = 2.56395759404194 | epot = -22.6833423138514 | etot = -18.1476004293146 +254000 ekin = 1.89998560000768 | erot = 2.76446346254018 | epot = -22.6525507394861 | etot = -17.9881016769382 +255000 ekin = 1.92358808504112 | erot = 2.8232180655232 | epot = -22.6339519254389 | etot = -17.8871457748746 +256000 ekin = 1.88537924827498 | erot = 2.39478935532049 | epot = -22.6063238269833 | etot = -18.3261552233879 +257000 ekin = 1.89017314858349 | erot = 2.47354789341062 | epot = -22.5844642699129 | etot = -18.2207432279188 +258000 ekin = 2.03347535796395 | erot = 2.06391667042751 | epot = -22.5636266221105 | etot = -18.4662345937191 +259000 ekin = 2.08170419875311 | erot = 1.98311262235159 | epot = -22.5595893965744 | etot = -18.4947725754697 +260000 ekin = 2.15465691022503 | erot = 1.92890944309568 | epot = -22.5702550804873 | etot = -18.4866887271666 +261000 ekin = 2.18525908976661 | erot = 1.80668043265703 | epot = -22.599603855669 | etot = -18.6076643332453 +262000 ekin = 2.39558735866003 | erot = 1.77101109907158 | epot = -22.6433503794795 | etot = -18.4767519217479 +263000 ekin = 2.51566381481677 | erot = 1.74502710268516 | epot = -22.7083481578158 | etot = -18.4476572403139 +264000 ekin = 2.61294097754962 | erot = 1.72004349105584 | epot = -22.7870727773709 | etot = -18.4540883087654 +265000 ekin = 2.69751103648214 | erot = 1.73596878524943 | epot = -22.8761138257039 | etot = -18.4426340039723 +266000 ekin = 2.73317595749254 | erot = 2.00190945895257 | epot = -22.9815854287862 | etot = -18.2465000123411 +267000 ekin = 2.88777944401865 | erot = 2.03601396733325 | epot = -23.0741467375982 | etot = -18.1503533262463 +268000 ekin = 2.88428212564762 | erot = 2.39210250452423 | epot = -23.1701763705663 | etot = -17.8937917403945 +269000 ekin = 2.94011387527553 | erot = 2.47436168171166 | epot = -23.2463195301015 | etot = -17.8318439731143 +270000 ekin = 3.16907204765203 | erot = 2.44558507843769 | epot = -23.2623613561913 | etot = -17.6477042301015 +271000 ekin = 3.2333039510145 | erot = 2.22964844922972 | epot = -23.2347949376338 | etot = -17.7718425373896 +272000 ekin = 3.25903447141521 | erot = 2.27670268800702 | epot = -23.1776976604854 | etot = -17.6419605010632 +273000 ekin = 3.33084558602117 | erot = 2.34730506518472 | epot = -23.0897292017612 | etot = -17.4115785505553 +274000 ekin = 3.13365175221781 | erot = 2.2890699134736 | epot = -22.970791629232 | etot = -17.5480699635406 +275000 ekin = 3.06411601298053 | erot = 2.05657284383674 | epot = -22.8411592683854 | etot = -17.7204704115681 +276000 ekin = 3.00284299412694 | erot = 2.41503398631215 | epot = -22.7006548358519 | etot = -17.2827778554128 +277000 ekin = 2.8898853606654 | erot = 2.56679455786094 | epot = -22.5600288715064 | etot = -17.1033489529801 +278000 ekin = 2.79983988341333 | erot = 2.44718365696948 | epot = -22.4337020220077 | etot = -17.1866784816249 +279000 ekin = 2.62025699943826 | erot = 2.34403355986967 | epot = -22.3217153271845 | etot = -17.3574247678766 +280000 ekin = 2.65113378626893 | erot = 2.38211104337873 | epot = -22.2136340723867 | etot = -17.1803892427391 +281000 ekin = 2.56011045257089 | erot = 2.14040765533486 | epot = -22.1467069298693 | etot = -17.4461888219636 +282000 ekin = 2.46937295979447 | erot = 2.08425434958574 | epot = -22.1062066499079 | etot = -17.5525793405277 +283000 ekin = 2.44420819687516 | erot = 1.88047008838871 | epot = -22.0682236162874 | etot = -17.7435453310236 +284000 ekin = 2.39435456980289 | erot = 2.14903249361598 | epot = -22.056902758128 | etot = -17.5135156947092 +285000 ekin = 2.39703522509055 | erot = 2.569646039159 | epot = -22.0888499478259 | etot = -17.1221686835764 +286000 ekin = 2.43717149651546 | erot = 2.84247600307268 | epot = -22.1412346796121 | etot = -16.861587180024 +287000 ekin = 2.31664233692361 | erot = 2.84674819551601 | epot = -22.1861386782236 | etot = -17.0227481457839 +288000 ekin = 2.26607109317395 | erot = 3.21299363478886 | epot = -22.2378784042861 | etot = -16.7588136763232 +289000 ekin = 2.29584076229566 | erot = 3.11249259323235 | epot = -22.2883115241192 | etot = -16.8799781685912 +290000 ekin = 2.23049902061663 | erot = 2.87013105088138 | epot = -22.3143401591494 | etot = -17.2137100876514 +291000 ekin = 2.21755828984435 | erot = 2.71274244030907 | epot = -22.3410646593226 | etot = -17.4107639291691 +292000 ekin = 2.21317296232836 | erot = 2.69582872791188 | epot = -22.3827626255967 | etot = -17.4737609353564 +293000 ekin = 2.23081262903902 | erot = 2.60204748252234 | epot = -22.4352222519775 | etot = -17.6023621404161 +294000 ekin = 2.26311425147062 | erot = 3.03410577179155 | epot = -22.4683441344041 | etot = -17.1711241111419 +295000 ekin = 2.2812207577869 | erot = 2.86887170599452 | epot = -22.4906039301699 | etot = -17.3405114663885 +296000 ekin = 2.26383415546938 | erot = 2.78467774936796 | epot = -22.5129720446774 | etot = -17.46446013984 +297000 ekin = 2.33825045335883 | erot = 2.98513561564366 | epot = -22.5191664894362 | etot = -17.1957804204337 +298000 ekin = 2.37786827340754 | erot = 2.85984647447039 | epot = -22.5058515980845 | etot = -17.2681368502066 +299000 ekin = 2.32052037098645 | erot = 2.6948063398296 | epot = -22.4889248916839 | etot = -17.4735981808679 +300000 ekin = 2.30322327761401 | erot = 2.72939848613212 | epot = -22.4591258064476 | etot = -17.4265040427014 +301000 ekin = 2.29995331731969 | erot = 2.60777958693871 | epot = -22.4102468930599 | etot = -17.5025139888015 +302000 ekin = 2.31454372799517 | erot = 2.67298740529846 | epot = -22.3501115787877 | etot = -17.3625804454941 +303000 ekin = 2.40576357226374 | erot = 2.41520690493574 | epot = -22.2832063980298 | etot = -17.4622359208303 +304000 ekin = 2.35524162584728 | erot = 2.05432603043706 | epot = -22.2112103404661 | etot = -17.8016426841818 +305000 ekin = 2.30537591124535 | erot = 1.98023337779147 | epot = -22.1649123466492 | etot = -17.8793030576124 +306000 ekin = 2.32478727778829 | erot = 1.89519445956113 | epot = -22.1442852026102 | etot = -17.9243034652608 +307000 ekin = 2.41423624130655 | erot = 1.91431870573649 | epot = -22.1548620004642 | etot = -17.8263070534212 +308000 ekin = 2.44675290257479 | erot = 2.31210197406235 | epot = -22.2055558309834 | etot = -17.4467009543463 +309000 ekin = 2.456733741312 | erot = 2.16129470434149 | epot = -22.2742892000813 | etot = -17.6562607544278 +310000 ekin = 2.58167657763234 | erot = 2.4384694301708 | epot = -22.3327423848014 | etot = -17.3125963769982 +311000 ekin = 2.5293944901135 | erot = 2.76106281819497 | epot = -22.3705094869024 | etot = -17.0800521785939 +312000 ekin = 2.52610661112938 | erot = 2.98071467503396 | epot = -22.3866205343165 | etot = -16.8797992481532 +313000 ekin = 2.52405671654842 | erot = 2.80377255965802 | epot = -22.4049055192042 | etot = -17.0770762429978 +314000 ekin = 2.65040443727049 | erot = 2.69900889453174 | epot = -22.3876700619105 | etot = -17.0382567301082 +315000 ekin = 2.74472815623857 | erot = 2.6634099641871 | epot = -22.3592685134382 | etot = -16.9511303930125 +316000 ekin = 2.83270806183629 | erot = 2.6834624018617 | epot = -22.3041387808826 | etot = -16.7879683171846 +317000 ekin = 2.98267354986799 | erot = 2.4999891053122 | epot = -22.2250773416344 | etot = -16.7424146864542 +318000 ekin = 2.95159865011192 | erot = 2.46437525131281 | epot = -22.1605195993969 | etot = -16.7445456979721 +319000 ekin = 2.99544196834495 | erot = 2.37119170515183 | epot = -22.0922506560632 | etot = -16.7256169825664 +320000 ekin = 3.12952415968056 | erot = 2.25302267428086 | epot = -22.0193402840265 | etot = -16.6367934500651 +321000 ekin = 3.21184303812923 | erot = 2.03139593747172 | epot = -21.9793920725106 | etot = -16.7361530969097 +322000 ekin = 3.32994096856511 | erot = 2.3411089367688 | epot = -21.9763192351684 | etot = -16.3052693298345 +323000 ekin = 3.41272790799891 | erot = 2.43631206380498 | epot = -22.014012335423 | etot = -16.1649723636191 +324000 ekin = 3.63714885281377 | erot = 1.94651241761841 | epot = -22.0887358924505 | etot = -16.5050746220183 +325000 ekin = 3.64965023300859 | erot = 1.83594979903826 | epot = -22.1597106232418 | etot = -16.674110591195 +326000 ekin = 3.79931323852483 | erot = 1.60564512903886 | epot = -22.2163199739481 | etot = -16.8113616063844 +327000 ekin = 3.85106864316231 | erot = 1.85449233215436 | epot = -22.2856422481549 | etot = -16.5800812728382 +328000 ekin = 3.95505458701157 | erot = 2.12895030409347 | epot = -22.3412351799646 | etot = -16.2572302888595 +329000 ekin = 3.96560356728839 | erot = 2.0612406639335 | epot = -22.3752736768186 | etot = -16.3484294455967 +330000 ekin = 4.00004269284732 | erot = 2.01808790805441 | epot = -22.3671090028808 | etot = -16.348978401979 +331000 ekin = 3.84205146855946 | erot = 1.89603876125722 | epot = -22.3128837484487 | etot = -16.5747935186321 +332000 ekin = 3.66184063362549 | erot = 2.39349988256161 | epot = -22.257623873614 | etot = -16.2022833574269 +333000 ekin = 3.52628969259453 | erot = 2.20415103930297 | epot = -22.1847867511299 | etot = -16.4543460192324 +334000 ekin = 3.3437779801396 | erot = 2.36266544381992 | epot = -22.1376045131504 | etot = -16.4311610891909 +335000 ekin = 3.23745330446352 | erot = 2.56905504387957 | epot = -22.1187474004986 | etot = -16.3122390521555 +336000 ekin = 3.15020041660106 | erot = 2.76447823600607 | epot = -22.1164491906296 | etot = -16.2017705380225 +337000 ekin = 2.95647753165974 | erot = 3.39203265805615 | epot = -22.1578850568599 | etot = -15.809374867144 +338000 ekin = 2.77494351817581 | erot = 3.38702940437107 | epot = -22.2028615569714 | etot = -16.0408886344245 +339000 ekin = 2.56974792274936 | erot = 3.36393768621225 | epot = -22.2430377961403 | etot = -16.3093521871787 +340000 ekin = 2.54624997134424 | erot = 3.18838906080749 | epot = -22.2696997292606 | etot = -16.5350606971088 +341000 ekin = 2.4668045333309 | erot = 3.23666697035734 | epot = -22.2714054864725 | etot = -16.5679339827843 +342000 ekin = 2.41970796988159 | erot = 3.10075257077742 | epot = -22.2625825508718 | etot = -16.7421220102128 +343000 ekin = 2.39134830962094 | erot = 2.99983011061346 | epot = -22.2626100438681 | etot = -16.8714316236337 +344000 ekin = 2.40072375544815 | erot = 3.07461576439234 | epot = -22.2332671874541 | etot = -16.7579276676136 +345000 ekin = 2.47818664391052 | erot = 3.01878606425649 | epot = -22.1765310886858 | etot = -16.6795583805188 +346000 ekin = 2.42322520039713 | erot = 2.49312120205091 | epot = -22.1072756725379 | etot = -17.1909292700899 +347000 ekin = 2.50705041682168 | erot = 2.52533205787073 | epot = -22.0719334103209 | etot = -17.0395509356285 +348000 ekin = 2.5003068515947 | erot = 2.7382550355115 | epot = -22.027067188238 | etot = -16.7885053011318 +349000 ekin = 2.60963103698124 | erot = 2.7944394998929 | epot = -21.9800449664777 | etot = -16.5759744296036 +350000 ekin = 2.57407872164985 | erot = 2.87849433187398 | epot = -21.9210551857954 | etot = -16.4684821322716 +351000 ekin = 2.60900955228799 | erot = 2.47335254246403 | epot = -21.9029016387199 | etot = -16.8205395439678 +352000 ekin = 2.68632626573655 | erot = 2.16861659144723 | epot = -21.8932933758337 | etot = -17.0383505186499 +353000 ekin = 2.72806527094852 | erot = 2.21631476958764 | epot = -21.8949965382931 | etot = -16.950616497757 +354000 ekin = 2.80926057411796 | erot = 2.29356292718611 | epot = -21.9255698630395 | etot = -16.8227463617354 +355000 ekin = 2.82955370341617 | erot = 2.23886374167674 | epot = -21.9739881370157 | etot = -16.9055706919228 +356000 ekin = 2.95318161283268 | erot = 2.20593846887515 | epot = -22.0378541396085 | etot = -16.8787340579007 +357000 ekin = 3.00516452100387 | erot = 2.39489434202986 | epot = -22.104563588431 | etot = -16.7045047253973 +358000 ekin = 3.14013674094297 | erot = 2.81648025756436 | epot = -22.1940030034409 | etot = -16.2373860049336 +359000 ekin = 3.2489530732029 | erot = 2.89756918684608 | epot = -22.289435624655 | etot = -16.142913364606 +360000 ekin = 3.29499898808924 | erot = 2.69446962924572 | epot = -22.3827935430045 | etot = -16.3933249256695 +361000 ekin = 3.31826252960522 | erot = 3.08121996997403 | epot = -22.3855376265986 | etot = -15.9860551270194 +362000 ekin = 3.22507380499832 | erot = 2.94494755594978 | epot = -22.1939077776838 | etot = -16.0238864167357 +363000 ekin = 3.31998300083389 | erot = 2.84571871387849 | epot = -22.1418339144058 | etot = -15.9761321996935 +364000 ekin = 3.46138826026248 | erot = 3.17267347021574 | epot = -22.2920001905031 | etot = -15.6579384600248 +365000 ekin = 3.41685157685538 | erot = 2.95127990795476 | epot = -22.240326005599 | etot = -15.8721945207889 +366000 ekin = 3.28889153330115 | erot = 2.68298751094344 | epot = -22.0917647614685 | etot = -16.1198857172239 +367000 ekin = 3.13188043782679 | erot = 2.32272362557638 | epot = -21.9624425815398 | etot = -16.5078385181366 +368000 ekin = 3.056352336118 | erot = 2.49179825174104 | epot = -21.8924084965124 | etot = -16.3442579086533 +369000 ekin = 2.97979500179357 | erot = 2.09677594955126 | epot = -21.8535972953644 | etot = -16.7770263440196 +370000 ekin = 2.86265256457624 | erot = 2.27837964431472 | epot = -21.8636474872586 | etot = -16.7226152783677 +371000 ekin = 2.81676366518742 | erot = 2.51005420363864 | epot = -21.8612307947671 | etot = -16.534412925941 +372000 ekin = 2.89056214524153 | erot = 2.17924443857051 | epot = -21.846592680977 | etot = -16.7767860971649 +373000 ekin = 2.85702985814987 | erot = 2.22607119851547 | epot = -21.8235708010662 | etot = -16.7404697444008 +374000 ekin = 2.69116258554349 | erot = 2.54595039875569 | epot = -21.8020300439687 | etot = -16.5649170596695 +375000 ekin = 2.65367735566875 | erot = 2.84882366948588 | epot = -21.7972775666781 | etot = -16.2947765415234 +376000 ekin = 2.56541501684005 | erot = 3.15381436306323 | epot = -21.8007765642063 | etot = -16.081547184303 +377000 ekin = 2.51617117441638 | erot = 3.34506466383927 | epot = -21.778089805669 | etot = -15.9168539674133 +378000 ekin = 2.39886036582834 | erot = 3.14706842402722 | epot = -21.738430489254 | etot = -16.1925016993984 +379000 ekin = 2.32534620585577 | erot = 2.9467038227835 | epot = -21.6782824657579 | etot = -16.4062324371187 +380000 ekin = 2.15266052745912 | erot = 3.43857095246912 | epot = -21.6038294062212 | etot = -16.0125979262929 +381000 ekin = 2.13714114193708 | erot = 3.11249169114175 | epot = -21.5367992698038 | etot = -16.2871664367249 +382000 ekin = 2.05496339747551 | erot = 3.44869747601511 | epot = -21.4764708985239 | etot = -15.9728100250333 +383000 ekin = 2.03169806552591 | erot = 3.38753191033141 | epot = -21.4173191206603 | etot = -15.998089144803 +384000 ekin = 1.9536464992119 | erot = 3.35746983585185 | epot = -21.3597667304038 | etot = -16.0486503953401 +385000 ekin = 1.95295295831838 | erot = 3.20059142565732 | epot = -21.3242192311686 | etot = -16.1706748471929 +386000 ekin = 2.03545459887428 | erot = 2.6333725467863 | epot = -21.3197581171682 | etot = -16.6509309715076 +387000 ekin = 2.08744315207257 | erot = 2.67515413940834 | epot = -21.321978305784 | etot = -16.5593810143031 +388000 ekin = 2.10460844408205 | erot = 2.63750027619817 | epot = -21.3534873824531 | etot = -16.6113786621729 +389000 ekin = 2.13617356384952 | erot = 2.49874264909337 | epot = -21.4010667143317 | etot = -16.7661505013888 +390000 ekin = 2.21418863130661 | erot = 2.61354129728509 | epot = -21.4597800849527 | etot = -16.632050156361 +391000 ekin = 2.30830767897454 | erot = 2.42155138145244 | epot = -21.5215483863443 | etot = -16.7916893259173 +392000 ekin = 2.30978428581462 | erot = 2.2702116622687 | epot = -21.5693953401795 | etot = -16.9893993920962 +393000 ekin = 2.43507049787304 | erot = 2.19525621528521 | epot = -21.6165022301659 | etot = -16.9861755170077 +394000 ekin = 2.48175272100065 | erot = 1.97403757750068 | epot = -21.643553588929 | etot = -17.1877632904276 +395000 ekin = 2.57078024352525 | erot = 1.94477022107785 | epot = -21.7032003447495 | etot = -17.1876498801464 +396000 ekin = 2.63856854694526 | erot = 2.15467094485346 | epot = -21.7518329108741 | etot = -16.9585934190754 +397000 ekin = 2.67333204158292 | erot = 2.10415530221336 | epot = -21.7874922526139 | etot = -17.0100049088176 +398000 ekin = 2.71657217445487 | erot = 2.2726087644269 | epot = -21.7955669580492 | etot = -16.8063860191674 +399000 ekin = 2.74052903415942 | erot = 1.98188508417839 | epot = -21.7850112801671 | etot = -17.0625971618293 +400000 ekin = 2.72461700644057 | erot = 1.79309630627378 | epot = -21.7479203148975 | etot = -17.2302070021832 +401000 ekin = 2.67821010319014 | erot = 1.80652566016257 | epot = -21.698608702759 | etot = -17.2138729394062 +402000 ekin = 2.66678843641911 | erot = 1.99143851830794 | epot = -21.6166886330481 | etot = -16.9584616783211 +403000 ekin = 2.71498615143681 | erot = 2.00496282624719 | epot = -21.5303765730254 | etot = -16.8104275953414 +404000 ekin = 2.72798047530865 | erot = 1.97802766069305 | epot = -21.4249267789288 | etot = -16.7189186429271 +405000 ekin = 2.65655813266499 | erot = 1.93167942695855 | epot = -21.3111486584608 | etot = -16.7229110988373 +406000 ekin = 2.60702986991675 | erot = 1.76285472093913 | epot = -21.1926812354137 | etot = -16.8227966445578 +407000 ekin = 2.48234362601436 | erot = 1.89687727619118 | epot = -21.0701942151549 | etot = -16.6909733129493 +408000 ekin = 2.49227529739515 | erot = 2.21804348518091 | epot = -20.9209091795091 | etot = -16.210590396933 +409000 ekin = 2.28147512963803 | erot = 2.33822783369873 | epot = -20.7906871723621 | etot = -16.1709842090254 +410000 ekin = 2.17062635902643 | erot = 2.33410289107436 | epot = -20.7498754299753 | etot = -16.2451461798745 +411000 ekin = 2.17272870653952 | erot = 2.2156634626659 | epot = -20.7111946304985 | etot = -16.3228024612931 +412000 ekin = 2.18233973422078 | erot = 1.95033555757298 | epot = -20.6834214582718 | etot = -16.5507461664781 +413000 ekin = 2.30890718881924 | erot = 2.0702155403649 | epot = -20.6873588522826 | etot = -16.3082361230984 +414000 ekin = 2.33564543866431 | erot = 1.99840226970565 | epot = -20.7252533334277 | etot = -16.3912056250577 +415000 ekin = 2.38284289900085 | erot = 2.11597172640873 | epot = -20.8097694536977 | etot = -16.3109548282881 +416000 ekin = 2.4891981967793 | erot = 2.33259772891817 | epot = -20.9508447049437 | etot = -16.1290487792462 +417000 ekin = 2.54526036986863 | erot = 2.55910512686791 | epot = -21.1274289862994 | etot = -16.0230634895629 +418000 ekin = 2.51632809206382 | erot = 2.72037030682962 | epot = -21.2997759305311 | etot = -16.0630775316377 +419000 ekin = 2.67295573593477 | erot = 2.7771535580359 | epot = -21.4556263294564 | etot = -16.0055170354857 +420000 ekin = 2.85018483582401 | erot = 2.31598006691945 | epot = -21.598096067305 | etot = -16.4319311645616 +421000 ekin = 2.96837524337278 | erot = 2.62682452529496 | epot = -21.7546670845078 | etot = -16.1594673158401 +422000 ekin = 3.19012922154601 | erot = 2.84396098635259 | epot = -21.9215374215571 | etot = -15.8874472136585 +423000 ekin = 3.3689393550787 | erot = 2.63026872290709 | epot = -22.0572951448105 | etot = -16.0580870668247 +424000 ekin = 3.56949208720973 | erot = 2.47035354176279 | epot = -22.1637806318818 | etot = -16.1239350029093 +425000 ekin = 3.74058915148773 | erot = 2.35112257121746 | epot = -22.2380669505818 | etot = -16.1463552278766 +426000 ekin = 3.80317641902181 | erot = 2.35606913247639 | epot = -22.2959429720038 | etot = -16.1366974205056 +427000 ekin = 3.84305942013411 | erot = 2.33548874740511 | epot = -22.3376365509407 | etot = -16.1590883834015 +428000 ekin = 3.83870631322395 | erot = 2.2350686376018 | epot = -22.3684501057755 | etot = -16.2946751549498 +429000 ekin = 3.88817033525608 | erot = 2.49183581120228 | epot = -22.3756888085917 | etot = -15.9956826621333 +430000 ekin = 3.80889051818672 | erot = 2.40484189761613 | epot = -22.357001863787 | etot = -16.1432694479841 +431000 ekin = 3.77310947248888 | erot = 2.27913524660264 | epot = -22.3205980214879 | etot = -16.2683533023964 +432000 ekin = 3.52274921334614 | erot = 2.24573259199191 | epot = -22.2753655924895 | etot = -16.5068837871515 +433000 ekin = 3.46705236442825 | erot = 2.20376216835505 | epot = -22.2487474226527 | etot = -16.5779328898694 +434000 ekin = 3.31902379467507 | erot = 2.11029295350195 | epot = -22.2098823317898 | etot = -16.7805655836127 +435000 ekin = 3.17487375029743 | erot = 2.50022517053552 | epot = -22.1671631710259 | etot = -16.4920642501929 +436000 ekin = 3.02349956092827 | erot = 2.40764251188789 | epot = -22.1302532198703 | etot = -16.6991111470541 +437000 ekin = 2.82748432721598 | erot = 2.14344362630242 | epot = -22.1006119384222 | etot = -17.1296839849038 +438000 ekin = 2.76339787793433 | erot = 2.41905080521281 | epot = -22.0957010825607 | etot = -16.9132523994136 +439000 ekin = 2.67198886552451 | erot = 2.59491616836501 | epot = -22.1135007428951 | etot = -16.8465957090056 +440000 ekin = 2.51284986257016 | erot = 2.9117422878524 | epot = -22.1427877988882 | etot = -16.7181956484656 +441000 ekin = 2.50780828634469 | erot = 2.72902768068008 | epot = -22.1697146510929 | etot = -16.9328786840681 +442000 ekin = 2.44873015400854 | erot = 2.74922432089635 | epot = -22.2054533182396 | etot = -17.0074988433347 +443000 ekin = 2.38093647463518 | erot = 2.64154199429508 | epot = -22.2472480992725 | etot = -17.2247696303423 +444000 ekin = 2.38366519287148 | erot = 2.67137923733322 | epot = -22.2750222251915 | etot = -17.2199777949868 +445000 ekin = 2.40684373898667 | erot = 2.59567738953131 | epot = -22.2857281482681 | etot = -17.2832070197501 +446000 ekin = 2.36082009501203 | erot = 2.73001014061368 | epot = -22.2789998471504 | etot = -17.1881696115246 +447000 ekin = 2.36605795906938 | erot = 2.58257112672917 | epot = -22.2960840066295 | etot = -17.347454920831 +448000 ekin = 2.32165762068391 | erot = 2.36145535918709 | epot = -22.3211882050735 | etot = -17.6380752252025 +449000 ekin = 2.44203969267578 | erot = 2.62540304636667 | epot = -22.3026387988319 | etot = -17.2351960597895 +450000 ekin = 2.51099258071334 | erot = 2.64840657329913 | epot = -22.2675924392713 | etot = -17.1081932852588 +451000 ekin = 2.50793019457257 | erot = 2.96188202684436 | epot = -22.2417686447221 | etot = -16.7719564233052 +452000 ekin = 2.51543909198824 | erot = 2.97645802250486 | epot = -22.1947639118426 | etot = -16.7028667973495 +453000 ekin = 2.48027617072922 | erot = 2.57675545715309 | epot = -22.1151189784507 | etot = -17.0580873505684 +454000 ekin = 2.53738257378339 | erot = 2.32076068281017 | epot = -22.0114335109919 | etot = -17.1532902543983 +455000 ekin = 2.40824460563833 | erot = 2.52466300048372 | epot = -21.9140685033287 | etot = -16.9811608972066 +456000 ekin = 2.48089669783939 | erot = 2.44995767624588 | epot = -21.8323732399436 | etot = -16.9015188658584 +457000 ekin = 2.41775201722811 | erot = 2.40996718790024 | epot = -21.7728619497133 | etot = -16.9451427445849 +458000 ekin = 2.47981300263295 | erot = 2.17375208123326 | epot = -21.7127229794173 | etot = -17.0591578955511 +459000 ekin = 2.50098429139894 | erot = 2.13049458828857 | epot = -21.6581010444987 | etot = -17.0266221648112 +460000 ekin = 2.38145892905036 | erot = 1.94162891941061 | epot = -21.6082620378711 | etot = -17.2851741894102 +461000 ekin = 2.33337517008642 | erot = 1.98667402531251 | epot = -21.5649964210092 | etot = -17.2449472256103 +462000 ekin = 2.28227781413481 | erot = 1.78636859811692 | epot = -21.553299713964 | etot = -17.4846533017123 +463000 ekin = 2.31407904587683 | erot = 1.75082487007371 | epot = -21.5758125934739 | etot = -17.5109086775234 +464000 ekin = 2.33760733880321 | erot = 1.97752071149075 | epot = -21.6288036107053 | etot = -17.3136755604113 +465000 ekin = 2.35344133595347 | erot = 1.91505497900073 | epot = -21.7041801943292 | etot = -17.435683879375 +466000 ekin = 2.42854776892503 | erot = 1.75072628953244 | epot = -21.7819960540276 | etot = -17.6027219955701 +467000 ekin = 2.46288459947453 | erot = 1.78816598264994 | epot = -21.8507036001179 | etot = -17.5996530179934 +468000 ekin = 2.4396980237813 | erot = 1.72898452339386 | epot = -21.9015694636242 | etot = -17.732886916449 +469000 ekin = 2.54376807882599 | erot = 1.93023555616053 | epot = -21.9541799518692 | etot = -17.4801763168827 +470000 ekin = 2.63326744382486 | erot = 1.50609058500148 | epot = -21.9819116677659 | etot = -17.8425536389396 +471000 ekin = 2.65978116714098 | erot = 1.70311641290876 | epot = -21.998720113699 | etot = -17.6358225336493 +472000 ekin = 2.69971587804179 | erot = 1.80099323522394 | epot = -22.0027803172695 | etot = -17.5020712040038 +473000 ekin = 2.72512699348196 | erot = 2.02324872686535 | epot = -22.0030224491713 | etot = -17.254646728824 +474000 ekin = 2.84072412734433 | erot = 2.2138329031493 | epot = -21.9941738614508 | etot = -16.9396168309571 +475000 ekin = 2.80675445958325 | erot = 1.90220774412446 | epot = -21.9850696381239 | etot = -17.2761074344162 +476000 ekin = 2.72360114140076 | erot = 2.00284464538919 | epot = -21.9892397336864 | etot = -17.2627939468965 +477000 ekin = 2.84056500761862 | erot = 1.91820766145647 | epot = -22.0039582079805 | etot = -17.2451855389054 +478000 ekin = 2.79479136762928 | erot = 2.33508343932093 | epot = -22.0073204493409 | etot = -16.8774456423907 +479000 ekin = 2.68385324315888 | erot = 2.16409914969165 | epot = -21.9972664623628 | etot = -17.1493140695123 +480000 ekin = 2.70919062871945 | erot = 2.2201907483767 | epot = -21.9751418417914 | etot = -17.0457604646952 +481000 ekin = 2.6330738635062 | erot = 1.99280181185983 | epot = -21.9303826423552 | etot = -17.3045069669892 +482000 ekin = 2.59315858027291 | erot = 2.21899648577234 | epot = -21.8738249716004 | etot = -17.0616699055552 +483000 ekin = 2.47046920651463 | erot = 2.31431109078724 | epot = -21.8097795572398 | etot = -17.0249992599379 +484000 ekin = 2.53508822055607 | erot = 2.47424748553176 | epot = -21.7175828393255 | etot = -16.7082471332376 +485000 ekin = 2.50485650643293 | erot = 2.32403296584754 | epot = -21.6361062693728 | etot = -16.8072167970923 +486000 ekin = 2.47721144858964 | erot = 2.13567134935031 | epot = -21.5220454766261 | etot = -16.9091626786862 +487000 ekin = 2.37724853790925 | erot = 2.18943698926396 | epot = -21.3143250794172 | etot = -16.747639552244 +488000 ekin = 2.48818613181863 | erot = 1.88306237250834 | epot = -21.3116084588732 | etot = -16.9403599545463 +489000 ekin = 2.74982657944339 | erot = 1.89187656286075 | epot = -21.4756253900937 | etot = -16.8339222477895 +490000 ekin = 2.84466800424173 | erot = 1.71237058668174 | epot = -21.5263774576827 | etot = -16.9693388667592 +491000 ekin = 2.85737105202628 | erot = 1.55281245576821 | epot = -21.5086751027887 | etot = -17.0984915949942 +492000 ekin = 2.90983632457413 | erot = 1.91497206116242 | epot = -21.5279430025227 | etot = -16.7031346167862 +493000 ekin = 2.89079796015606 | erot = 2.10766085424281 | epot = -21.550840131446 | etot = -16.5523813170471 +494000 ekin = 2.90235816901099 | erot = 1.9402922611658 | epot = -21.5811303529852 | etot = -16.7384799228084 +495000 ekin = 2.87250026921876 | erot = 1.80307251979051 | epot = -21.6111333229179 | etot = -16.9355605339086 +496000 ekin = 2.90478694209697 | erot = 1.72383486079582 | epot = -21.6487754892895 | etot = -17.0201536863967 +497000 ekin = 2.79889384992107 | erot = 1.75660961047752 | epot = -21.6748215786364 | etot = -17.1193181182378 +498000 ekin = 2.74060640404801 | erot = 1.8988825882541 | epot = -21.7102647961433 | etot = -17.0707758038412 +499000 ekin = 2.80294847124193 | erot = 2.31213970127587 | epot = -21.7484718969955 | etot = -16.6333837244777 +500000 ekin = 2.83514351912353 | erot = 2.19332479656699 | epot = -21.7847476520863 | etot = -16.7562793363958 +501000 ekin = 2.85410564762311 | erot = 2.42583012042732 | epot = -21.8174128447106 | etot = -16.5374770766602 +502000 ekin = 2.87283408161098 | erot = 2.50841092791892 | epot = -21.8423925146404 | etot = -16.4611475051105 +503000 ekin = 2.94443013466673 | erot = 2.36313582629975 | epot = -21.8519587007928 | etot = -16.5443927398264 +504000 ekin = 2.98534964558837 | erot = 2.41275211835294 | epot = -21.8136647277171 | etot = -16.4155629637758 +505000 ekin = 3.10846911992697 | erot = 2.13573452517239 | epot = -21.7537837267862 | etot = -16.5095800816869 +506000 ekin = 3.09786641402197 | erot = 2.01700572313873 | epot = -21.7049804656294 | etot = -16.5901083284687 +507000 ekin = 3.16348616847778 | erot = 1.94949346287679 | epot = -21.6672353473611 | etot = -16.5542557160065 +508000 ekin = 3.07061633092948 | erot = 2.13446212006044 | epot = -21.6350846399517 | etot = -16.4300061889618 +509000 ekin = 3.12907466475355 | erot = 2.35272620108291 | epot = -21.6205801924069 | etot = -16.1387793265704 +510000 ekin = 3.0245140017856 | erot = 2.25242701385288 | epot = -21.6251089836152 | etot = -16.3481679679767 +511000 ekin = 2.94040580941495 | erot = 2.31948438934905 | epot = -21.6216965431398 | etot = -16.3618063443758 +512000 ekin = 2.94467119608466 | erot = 2.24306810877183 | epot = -21.5962799069277 | etot = -16.4085406020712 +513000 ekin = 2.87751742568546 | erot = 2.4154144429729 | epot = -21.5773819493344 | etot = -16.284450080676 +514000 ekin = 2.87859810419347 | erot = 2.53612885093564 | epot = -21.588691061236 | etot = -16.1739641061069 +515000 ekin = 2.65152076844924 | erot = 2.70952186913726 | epot = -21.6126230255115 | etot = -16.251580387925 +516000 ekin = 2.77253963034905 | erot = 3.1111688276585 | epot = -21.6107374310228 | etot = -15.7270289730152 +517000 ekin = 2.7657240217945 | erot = 2.98569828005575 | epot = -21.5945323230587 | etot = -15.8431100212085 +518000 ekin = 2.70082064566998 | erot = 2.94453329815957 | epot = -21.5767297354903 | etot = -15.9313757916607 +519000 ekin = 2.54482845466883 | erot = 2.66065301480803 | epot = -21.5508730096676 | etot = -16.3453915401907 +520000 ekin = 2.45944414333559 | erot = 2.6059278317658 | epot = -21.5130137565194 | etot = -16.447641781418 +521000 ekin = 2.40695980994573 | erot = 2.63220992355673 | epot = -21.4828393267851 | etot = -16.4436695932826 +522000 ekin = 2.52378769907125 | erot = 2.56066497083157 | epot = -21.4628073945551 | etot = -16.3783547246523 +523000 ekin = 2.47704387064472 | erot = 2.27847516566714 | epot = -21.3936943383542 | etot = -16.6381753020423 +524000 ekin = 2.45003418957747 | erot = 2.35140218073762 | epot = -21.2843636599225 | etot = -16.4829272896075 +525000 ekin = 2.36142621667719 | erot = 2.56683372922841 | epot = -21.3738770732968 | etot = -16.4456171273912 +526000 ekin = 2.41274041153331 | erot = 2.62143474643862 | epot = -21.5186087776721 | etot = -16.4844336197002 +527000 ekin = 2.51690607418066 | erot = 2.50693092291692 | epot = -21.5243590814513 | etot = -16.5005220843537 +528000 ekin = 2.54770211426161 | erot = 2.53999552090151 | epot = -21.5164154929429 | etot = -16.4287178577798 +529000 ekin = 2.4753674979034 | erot = 2.56875642748162 | epot = -21.5117161086082 | etot = -16.4675921832232 +530000 ekin = 2.5803889742549 | erot = 3.01233807443761 | epot = -21.5190605777288 | etot = -15.9263335290363 +531000 ekin = 2.6505489472462 | erot = 2.80448099540881 | epot = -21.5589351824918 | etot = -16.1039052398368 +532000 ekin = 2.6696524214408 | erot = 2.74119638756006 | epot = -21.6464179501726 | etot = -16.2355691411717 +533000 ekin = 2.72770786142475 | erot = 2.77844536173281 | epot = -21.7626441239329 | etot = -16.2564909007754 +534000 ekin = 2.64182362572746 | erot = 3.16792870118731 | epot = -21.9259934897404 | etot = -16.1162411628256 +535000 ekin = 2.66520124770206 | erot = 3.28791712497576 | epot = -22.0889762146489 | etot = -16.1358578419711 +536000 ekin = 2.62601876922119 | erot = 3.30261897461184 | epot = -22.2457512656675 | etot = -16.3171135218345 +537000 ekin = 2.69839345537191 | erot = 3.42813769244461 | epot = -22.4210021127565 | etot = -16.29447096494 +538000 ekin = 2.66760385526385 | erot = 3.62303132590617 | epot = -22.5913550255155 | etot = -16.3007198443454 +539000 ekin = 2.67321194398858 | erot = 3.60397197005646 | epot = -22.7197786083613 | etot = -16.4425946943163 +540000 ekin = 2.61847962179667 | erot = 3.59814593067319 | epot = -22.8058567264858 | etot = -16.5892311740159 +541000 ekin = 2.67186419743777 | erot = 3.32667413558495 | epot = -22.8335693145217 | etot = -16.835030981499 +542000 ekin = 2.70747491915378 | erot = 3.01115645898026 | epot = -22.8115452943436 | etot = -17.0929139162096 +543000 ekin = 2.54644874759652 | erot = 2.82723025266318 | epot = -22.7664572430855 | etot = -17.3927782428258 +544000 ekin = 2.54639384288721 | erot = 2.5174224919614 | epot = -22.7350779454404 | etot = -17.6712616105918 +545000 ekin = 2.56168013748332 | erot = 2.65611713884728 | epot = -22.7023384195505 | etot = -17.4845411432199 +546000 ekin = 2.58160534092255 | erot = 2.38787600628631 | epot = -22.6704542470138 | etot = -17.7009728998049 +547000 ekin = 2.6121146280375 | erot = 2.34648461296519 | epot = -22.6334663710584 | etot = -17.6748671300557 +548000 ekin = 2.61848748301412 | erot = 2.5516310420712 | epot = -22.6097685172029 | etot = -17.4396499921176 +549000 ekin = 2.67184047302193 | erot = 2.60680496690199 | epot = -22.6113862974877 | etot = -17.3327408575638 +550000 ekin = 2.72277931598642 | erot = 2.65040849078687 | epot = -22.6203600824211 | etot = -17.2471722756478 +551000 ekin = 2.74305353489356 | erot = 2.80075659039589 | epot = -22.6177232617521 | etot = -17.0739131364627 +552000 ekin = 2.81751360269325 | erot = 2.75287635518204 | epot = -22.602311876728 | etot = -17.0319219188527 +553000 ekin = 2.79227730256451 | erot = 2.56192872740975 | epot = -22.5537272638578 | etot = -17.1995212338835 +554000 ekin = 2.73534601403833 | erot = 2.65053323061196 | epot = -22.4791077870334 | etot = -17.0932285423831 +555000 ekin = 2.638870693299 | erot = 2.60099744506951 | epot = -22.3836014529598 | etot = -17.1437333145913 +556000 ekin = 2.5879592273157 | erot = 2.83939231123044 | epot = -22.3242799264679 | etot = -16.8969283879218 +557000 ekin = 2.47840947592946 | erot = 2.83134609082876 | epot = -22.3241590735327 | etot = -17.0144035067744 +558000 ekin = 2.40468725505368 | erot = 2.93322561456073 | epot = -22.2772491751352 | etot = -16.9393363055208 +559000 ekin = 2.41820823948318 | erot = 2.8608918734677 | epot = -22.2036329910434 | etot = -16.9245328780926 +560000 ekin = 2.3966202031316 | erot = 2.57730341735947 | epot = -22.1373821619364 | etot = -17.1634585414453 +561000 ekin = 2.41616568173939 | erot = 2.43139941603537 | epot = -22.0606510286939 | etot = -17.2130859309192 +562000 ekin = 2.32711122790915 | erot = 2.68540878415344 | epot = -22.0362236088755 | etot = -17.0237035968129 +563000 ekin = 2.40105509630183 | erot = 2.62423602861765 | epot = -22.0398518714972 | etot = -17.0145607465777 +564000 ekin = 2.50622664221487 | erot = 2.49283482178932 | epot = -22.0598046960839 | etot = -17.0607432320797 +565000 ekin = 2.51273313956233 | erot = 2.47207361692501 | epot = -22.089921425343 | etot = -17.1051146688556 +566000 ekin = 2.45555537786115 | erot = 2.3082155714912 | epot = -22.1147098672019 | etot = -17.3509389178496 +567000 ekin = 2.48507699437185 | erot = 2.03226369059615 | epot = -22.1483465792771 | etot = -17.6310058943091 +568000 ekin = 2.44600711349212 | erot = 2.16818780091151 | epot = -22.1715613145415 | etot = -17.5573664001379 +569000 ekin = 2.41496567776295 | erot = 2.08307839560002 | epot = -22.1893617136985 | etot = -17.6913176403356 +570000 ekin = 2.31032400356052 | erot = 1.94654984481954 | epot = -22.1972672153819 | etot = -17.9403933670018 +571000 ekin = 2.34174388046968 | erot = 1.90380560996229 | epot = -22.2024778466829 | etot = -17.9569283562509 +572000 ekin = 2.3161224267259 | erot = 2.32477215739614 | epot = -22.1972617700694 | etot = -17.5563671859474 +573000 ekin = 2.33747992651635 | erot = 2.05308190482657 | epot = -22.1742687527247 | etot = -17.7837069213818 +574000 ekin = 2.25296248727395 | erot = 2.15192604028184 | epot = -22.1539412991551 | etot = -17.7490527715993 +575000 ekin = 2.39237411767891 | erot = 2.08020391847446 | epot = -22.1262092875419 | etot = -17.6536312513885 +576000 ekin = 2.39920884793466 | erot = 2.19930885642795 | epot = -22.0840646582165 | etot = -17.4855469538539 +577000 ekin = 2.32808205752383 | erot = 1.94197958979008 | epot = -22.0344723562009 | etot = -17.764410708887 +578000 ekin = 2.17468587063572 | erot = 1.9246103716915 | epot = -21.974741428262 | etot = -17.8754451859348 +579000 ekin = 2.11583896079231 | erot = 1.92936420584513 | epot = -21.9045494517252 | etot = -17.8593462850878 +580000 ekin = 1.98384148142142 | erot = 1.90081955947736 | epot = -21.8148954466249 | etot = -17.9302344057261 +581000 ekin = 1.94016412525864 | erot = 1.93233669573735 | epot = -21.7165439683881 | etot = -17.8440431473921 +582000 ekin = 1.86102518896638 | erot = 1.7934107867181 | epot = -21.6380365856677 | etot = -17.9836006099832 +583000 ekin = 1.68386990762816 | erot = 1.83679042288086 | epot = -21.5992064668102 | etot = -18.0785461363011 +584000 ekin = 1.67261412505274 | erot = 1.65634612158733 | epot = -21.5952053447533 | etot = -18.2662450981132 +585000 ekin = 1.73992925735466 | erot = 1.83366430721896 | epot = -21.6327697441748 | etot = -18.0591761796012 +586000 ekin = 1.7466125540919 | erot = 1.71213201580467 | epot = -21.7000609183771 | etot = -18.2413163484806 +587000 ekin = 1.71710189718411 | erot = 1.97098182988275 | epot = -21.768357454318 | etot = -18.0802737272511 +588000 ekin = 1.86544089524886 | erot = 1.85386980490182 | epot = -21.842568384803 | etot = -18.1232576846523 +589000 ekin = 1.85071717322235 | erot = 1.97068115142872 | epot = -21.9095983694565 | etot = -18.0882000448054 +590000 ekin = 1.83374905828512 | erot = 1.81484654719675 | epot = -21.9582171568561 | etot = -18.3096215513742 +591000 ekin = 1.81469352641546 | erot = 1.99878899767018 | epot = -21.9200659973695 | etot = -18.1065834732838 +592000 ekin = 1.71363100839119 | erot = 2.12573581394757 | epot = -21.9592135376035 | etot = -18.1198467152647 +593000 ekin = 1.72614766500652 | erot = 2.17937588775782 | epot = -22.066408920808 | etot = -18.1608853680437 +594000 ekin = 1.75427689765148 | erot = 1.98826780368093 | epot = -22.097697548866 | etot = -18.3551528475336 +595000 ekin = 1.85406358952635 | erot = 2.20206199980441 | epot = -22.122617669042 | etot = -18.0664920797113 +596000 ekin = 1.84670119316226 | erot = 2.33908153853192 | epot = -22.155983122642 | etot = -17.9702003909479 +597000 ekin = 1.81732138775553 | erot = 2.40005576098704 | epot = -22.1594075236566 | etot = -17.9420303749141 +598000 ekin = 1.86775439707713 | erot = 2.55301581891919 | epot = -22.1595993961167 | etot = -17.7388291801204 +599000 ekin = 1.91773913278386 | erot = 2.67167362163655 | epot = -22.1710888467293 | etot = -17.5816760923089 +600000 ekin = 1.98736665658457 | erot = 2.80063355631871 | epot = -22.2102053911855 | etot = -17.4222051782822 +601000 ekin = 1.90702337725137 | erot = 2.83446711181393 | epot = -22.2420925338084 | etot = -17.5006020447431 +602000 ekin = 1.94976963379135 | erot = 2.90342633891923 | epot = -22.2734691619213 | etot = -17.4202731892107 +603000 ekin = 1.96641425291137 | erot = 2.66529933433871 | epot = -22.2825393460707 | etot = -17.6508257588206 +604000 ekin = 1.91858852447186 | erot = 2.76080776072307 | epot = -22.2678256349419 | etot = -17.5884293497469 +605000 ekin = 1.97193019282266 | erot = 2.54727948628818 | epot = -22.2112173532516 | etot = -17.6920076741407 +606000 ekin = 2.03197193648811 | erot = 2.19902614177691 | epot = -22.116454437631 | etot = -17.885456359366 +607000 ekin = 2.05105280435577 | erot = 2.16675765880345 | epot = -21.9774053858555 | etot = -17.7595949226963 +608000 ekin = 2.17944443921827 | erot = 2.13131743184003 | epot = -21.8153209903606 | etot = -17.5045591193023 +609000 ekin = 2.16101479212578 | erot = 2.06129841109606 | epot = -21.6707988831026 | etot = -17.4484856798808 +610000 ekin = 2.19385705617112 | erot = 2.02131249667451 | epot = -21.5477012163144 | etot = -17.3325316634687 +611000 ekin = 2.19942394637442 | erot = 2.20280786133642 | epot = -21.4384008683113 | etot = -17.0361690606005 +612000 ekin = 2.23163662761472 | erot = 2.17565235563951 | epot = -21.3497883530462 | etot = -16.942499369792 +613000 ekin = 2.34183365034038 | erot = 1.89422502415539 | epot = -21.3091832789111 | etot = -17.0731246044153 +614000 ekin = 2.41074949980773 | erot = 1.66581051947236 | epot = -21.3121685225924 | etot = -17.2356085033123 +615000 ekin = 2.45538962657627 | erot = 1.67175711569401 | epot = -21.3797539205107 | etot = -17.2526071782405 +616000 ekin = 2.54665272757666 | erot = 1.63332091588084 | epot = -21.4744887763243 | etot = -17.2945151328668 +617000 ekin = 2.69386292022066 | erot = 1.67560230924521 | epot = -21.588417959513 | etot = -17.2189527300471 +618000 ekin = 2.87435666564135 | erot = 1.80165459029565 | epot = -21.7048752429668 | etot = -17.0288639870299 +619000 ekin = 3.06032720665911 | erot = 1.65093186491292 | epot = -21.8125402008949 | etot = -17.1012811293228 +620000 ekin = 3.05516944552979 | erot = 1.78567665314242 | epot = -21.9362157730259 | etot = -17.0953696743537 +621000 ekin = 3.19482877288267 | erot = 1.85444292415912 | epot = -22.0590109842187 | etot = -17.0097392871769 +622000 ekin = 3.19833270893114 | erot = 1.64252462622231 | epot = -22.1304552689747 | etot = -17.2895979338213 +623000 ekin = 3.29734758995184 | erot = 1.69707189360923 | epot = -22.1701112545656 | etot = -17.1756917710046 +624000 ekin = 3.37713404636403 | erot = 1.61937249977477 | epot = -22.1901329861865 | etot = -17.1936264400477 +625000 ekin = 3.38380934462709 | erot = 1.549172062804 | epot = -22.1890416607103 | etot = -17.2560602532792 +626000 ekin = 3.32638739446791 | erot = 1.56722148293845 | epot = -22.1785220524129 | etot = -17.2849131750065 +627000 ekin = 3.31569249720213 | erot = 1.71066467192283 | epot = -22.1423640777851 | etot = -17.1160069086602 +628000 ekin = 3.16697776454369 | erot = 1.85806977204786 | epot = -22.011252047656 | etot = -16.9862045110645 +629000 ekin = 2.99094278818936 | erot = 1.8634654411134 | epot = -21.934673140983 | etot = -17.0802649116802 +630000 ekin = 2.90556071918741 | erot = 2.0693130310465 | epot = -21.9350908515797 | etot = -16.9602171013458 +631000 ekin = 2.7996958294494 | erot = 2.05621242567347 | epot = -21.8486045729716 | etot = -16.9926963178487 +632000 ekin = 2.67147709831681 | erot = 2.03262561421969 | epot = -21.7549691244759 | etot = -17.0508664119394 +633000 ekin = 2.65536759972765 | erot = 2.03400136625159 | epot = -21.679933200058 | etot = -16.9905642340788 +634000 ekin = 2.60619207671916 | erot = 2.13546718822646 | epot = -21.6154557479587 | etot = -16.873796483013 +635000 ekin = 2.50701558019073 | erot = 1.74758901075266 | epot = -21.5543249117143 | etot = -17.2997203207709 +636000 ekin = 2.39745600323015 | erot = 1.85247540266627 | epot = -21.5255594300375 | etot = -17.275628024141 +637000 ekin = 2.41790008828863 | erot = 1.89421557823657 | epot = -21.5250233017188 | etot = -17.2129076351937 +638000 ekin = 2.47578971863411 | erot = 2.36571418053383 | epot = -21.5337545659548 | etot = -16.6922506667869 +639000 ekin = 2.35660046082987 | erot = 2.51353605837974 | epot = -21.54109724209 | etot = -16.6709607228804 +640000 ekin = 2.45486082803945 | erot = 2.67800600845136 | epot = -21.55281452089 | etot = -16.4199476843992 +641000 ekin = 2.56928913237036 | erot = 2.42818013926169 | epot = -21.5744429168227 | etot = -16.5769736451907 +642000 ekin = 2.56519022418644 | erot = 2.50858602525862 | epot = -21.5829619563604 | etot = -16.5091857069153 +643000 ekin = 2.61438251477743 | erot = 2.14546404075503 | epot = -21.6040625493726 | etot = -16.8442159938401 +644000 ekin = 2.62186764966541 | erot = 2.14191076230808 | epot = -21.6253516870781 | etot = -16.8615732751046 +645000 ekin = 2.73445879103559 | erot = 2.35765807621328 | epot = -21.6468161631213 | etot = -16.5546992958725 +646000 ekin = 2.74844139127298 | erot = 2.17611353686154 | epot = -21.6394622686015 | etot = -16.714907340467 +647000 ekin = 2.81459539064476 | erot = 2.08632073152515 | epot = -21.6308966078173 | etot = -16.7299804856474 +648000 ekin = 2.8570092687102 | erot = 1.92946433308234 | epot = -21.6388376034712 | etot = -16.8523640016787 +649000 ekin = 2.83442652810374 | erot = 1.81043301746399 | epot = -21.6816093302461 | etot = -17.0367497846784 +650000 ekin = 2.82385635198152 | erot = 1.98060013201552 | epot = -21.7368430060007 | etot = -16.9323865220037 +651000 ekin = 2.9288560289155 | erot = 2.12442721936488 | epot = -21.817286677495 | etot = -16.7640034292146 +652000 ekin = 2.93013307398376 | erot = 2.27578127027579 | epot = -21.8890408405104 | etot = -16.6831264962509 +653000 ekin = 3.0473689812555 | erot = 2.16776847613752 | epot = -21.9486345968612 | etot = -16.7334971394682 +654000 ekin = 2.95795730372489 | erot = 2.21678381714661 | epot = -22.0001869032544 | etot = -16.8254457823829 +655000 ekin = 3.02540562074013 | erot = 2.13692279145244 | epot = -22.0213788097185 | etot = -16.8590503975259 +656000 ekin = 2.93581362686791 | erot = 2.18988187130923 | epot = -22.010975719743 | etot = -16.8852802215659 +657000 ekin = 2.76805340651513 | erot = 2.32463835532636 | epot = -21.9890816986891 | etot = -16.8963899368476 +658000 ekin = 2.72010078264214 | erot = 2.42170769009723 | epot = -21.9346454326183 | etot = -16.792836959879 +659000 ekin = 2.56993867397727 | erot = 2.56748186419784 | epot = -21.8575737943231 | etot = -16.7201532561479 +660000 ekin = 2.47973868672826 | erot = 2.40259679627709 | epot = -21.779567237114 | etot = -16.8972317541087 +661000 ekin = 2.45373542595665 | erot = 2.39904349056725 | epot = -21.7176497643048 | etot = -16.8648708477809 +662000 ekin = 2.31664057269232 | erot = 2.35054704143566 | epot = -21.6537121043302 | etot = -16.9865244902022 +663000 ekin = 2.2406453295341 | erot = 2.17910127912756 | epot = -21.6391536375407 | etot = -17.2194070288791 +664000 ekin = 2.20916362864351 | erot = 2.06262569311492 | epot = -21.6851863902018 | etot = -17.4133970684433 +665000 ekin = 2.13954972476583 | erot = 2.25756057575129 | epot = -21.7455075936899 | etot = -17.3483972931728 +666000 ekin = 2.08532103984046 | erot = 2.53235015645651 | epot = -21.830648816515 | etot = -17.2129776202181 +667000 ekin = 2.0743446863546 | erot = 2.583160243362 | epot = -21.9388099470212 | etot = -17.2813050173046 +668000 ekin = 2.14972707351084 | erot = 2.44036539013565 | epot = -22.0333424314709 | etot = -17.4432499678244 +669000 ekin = 2.14867112158615 | erot = 2.43281409131061 | epot = -22.1304448026363 | etot = -17.5489595897395 +670000 ekin = 2.23890403189199 | erot = 2.5864824921452 | epot = -22.2056814205452 | etot = -17.380294896508 +671000 ekin = 2.31625622499922 | erot = 2.6933385117182 | epot = -22.2796620621828 | etot = -17.2700673254654 +672000 ekin = 2.44586153940035 | erot = 2.5664628061703 | epot = -22.3586952144321 | etot = -17.3463708688615 +673000 ekin = 2.54481735055596 | erot = 2.75556593856597 | epot = -22.4593396425668 | etot = -17.1589563534449 +674000 ekin = 2.71391625159844 | erot = 2.65543084253566 | epot = -22.5584890476539 | etot = -17.1891419535198 +675000 ekin = 2.90764129270645 | erot = 2.2381977509452 | epot = -22.61801770165 | etot = -17.4721786579984 +676000 ekin = 2.92265152568027 | erot = 2.01907422039333 | epot = -22.6419153633297 | etot = -17.7001896172561 +677000 ekin = 2.98331588051324 | erot = 1.94365767388418 | epot = -22.6354363273703 | etot = -17.7084627729728 +678000 ekin = 3.09770353325625 | erot = 1.78984747588675 | epot = -22.5937189533549 | etot = -17.7061679442119 +679000 ekin = 3.25432444248473 | erot = 1.88443631033203 | epot = -22.5317841359598 | etot = -17.393023383143 +680000 ekin = 3.22961887078889 | erot = 1.69909805720003 | epot = -22.4630708250237 | etot = -17.5343538970348 +681000 ekin = 3.29793543712244 | erot = 1.73422658308639 | epot = -22.3946434176701 | etot = -17.3624813974613 +682000 ekin = 3.24199079106598 | erot = 1.59692198561525 | epot = -22.3029193266289 | etot = -17.4640065499476 +683000 ekin = 3.25371946999921 | erot = 1.72202050023483 | epot = -22.1991489993634 | etot = -17.2234090291294 +684000 ekin = 3.19052733109175 | erot = 1.6662268117249 | epot = -22.0655070121609 | etot = -17.2087528693442 +685000 ekin = 3.1235177982566 | erot = 1.51735754830955 | epot = -21.9148242457862 | etot = -17.2739488992201 +686000 ekin = 3.07326489888686 | erot = 1.46555591350557 | epot = -21.7573475582033 | etot = -17.2185267458109 +687000 ekin = 3.06926781943163 | erot = 1.15712044634924 | epot = -21.5962819403317 | etot = -17.3698936745508 +688000 ekin = 2.87390652865996 | erot = 1.40331203652357 | epot = -21.4336822001942 | etot = -17.1564636350106 +689000 ekin = 2.69554492827573 | erot = 1.45829074533159 | epot = -21.2672855389607 | etot = -17.1134498653534 +690000 ekin = 2.61061423011931 | erot = 1.36248966419121 | epot = -21.1045284460287 | etot = -17.1314245517182 +691000 ekin = 2.53848955712385 | erot = 1.51295281726522 | epot = -20.9662406736505 | etot = -16.9147982992614 +692000 ekin = 2.46230747660104 | erot = 1.79517490024313 | epot = -20.8267179895323 | etot = -16.5692356126881 +693000 ekin = 2.33092902932381 | erot = 1.95693255705532 | epot = -20.7214634762692 | etot = -16.4336018898901 +694000 ekin = 2.20499278049206 | erot = 2.26852927145262 | epot = -20.6632308881514 | etot = -16.1897088362067 +695000 ekin = 2.03014457111484 | erot = 2.21386820279707 | epot = -20.6164786812678 | etot = -16.3724659073559 +696000 ekin = 1.90099616141388 | erot = 2.51034651058703 | epot = -20.5979238575911 | etot = -16.1865811855902 +697000 ekin = 1.85444991610563 | erot = 2.53777912909074 | epot = -20.6115349149636 | etot = -16.2193058697672 +698000 ekin = 1.74517859956197 | erot = 2.72238224145333 | epot = -20.6303436251982 | etot = -16.1627827841829 +699000 ekin = 1.75168130890703 | erot = 2.85503588879915 | epot = -20.6320585257891 | etot = -16.0253413280829 +700000 ekin = 1.64369199910964 | erot = 2.34560591480475 | epot = -20.6475139469298 | etot = -16.6582160330154 +701000 ekin = 1.68132533789953 | erot = 2.43909304651544 | epot = -20.6859109282928 | etot = -16.5654925438779 +702000 ekin = 1.70386840970075 | erot = 2.35102704448845 | epot = -20.7376959872522 | etot = -16.6828005330631 +703000 ekin = 1.80305935509228 | erot = 2.30693909538425 | epot = -20.8251011762126 | etot = -16.7151027257361 +704000 ekin = 1.85427679013265 | erot = 2.26509125077347 | epot = -20.9059280513961 | etot = -16.78656001049 +705000 ekin = 1.8833584698334 | erot = 2.19214658824627 | epot = -20.9954367870658 | etot = -16.9199317289861 +706000 ekin = 1.87670234052976 | erot = 2.28719516539754 | epot = -21.0193227576681 | etot = -16.8554252517408 +707000 ekin = 1.93293497142042 | erot = 2.38330202769359 | epot = -21.0638890738314 | etot = -16.7476520747174 +708000 ekin = 2.09065153727169 | erot = 2.35104864418212 | epot = -21.2227908262266 | etot = -16.7810906447728 +709000 ekin = 2.20425730862695 | erot = 2.60124565008625 | epot = -21.3749368892931 | etot = -16.5694339305799 +710000 ekin = 2.15847586521615 | erot = 2.78837422905166 | epot = -21.4537558932195 | etot = -16.5069057989517 +711000 ekin = 2.14738567610619 | erot = 2.55565446850146 | epot = -21.4922752305122 | etot = -16.7892350859046 +712000 ekin = 2.21832534546365 | erot = 2.28378233297843 | epot = -21.5070148685005 | etot = -17.0049071900584 +713000 ekin = 2.23341186047097 | erot = 2.34500428198343 | epot = -21.5008699398633 | etot = -16.9224537974089 +714000 ekin = 2.33230836039941 | erot = 2.19479871425173 | epot = -21.483901980654 | etot = -16.9567949060029 +715000 ekin = 2.33030820573716 | erot = 2.17965051754574 | epot = -21.4553142973933 | etot = -16.9453555741104 +716000 ekin = 2.36748822469763 | erot = 2.35438142347179 | epot = -21.4335845554589 | etot = -16.7117149072895 +717000 ekin = 2.42589072360727 | erot = 2.26035712234886 | epot = -21.4376774007488 | etot = -16.7514295547927 +718000 ekin = 2.38255620505563 | erot = 2.6280597207598 | epot = -21.470981433119 | etot = -16.4603655073036 +719000 ekin = 2.43160380446145 | erot = 2.63972746655475 | epot = -21.49717661689 | etot = -16.4258453458738 +720000 ekin = 2.33769336712164 | erot = 2.55371461534663 | epot = -21.5394919555784 | etot = -16.6480839731101 +721000 ekin = 2.28846155322213 | erot = 2.63462733239702 | epot = -21.618461815108 | etot = -16.6953729294888 +722000 ekin = 2.26257994641476 | erot = 2.84783969674527 | epot = -21.694550270764 | etot = -16.584130627604 +723000 ekin = 2.23304720962004 | erot = 3.06611659822312 | epot = -21.7528202353858 | etot = -16.4536564275427 +724000 ekin = 2.12684507278307 | erot = 2.78432312637068 | epot = -21.7751025516959 | etot = -16.8639343525421 +725000 ekin = 2.06612304118994 | erot = 2.66570087221037 | epot = -21.7772349484671 | etot = -17.0454110350668 +726000 ekin = 2.06015720392015 | erot = 2.53002799423172 | epot = -21.7484309875634 | etot = -17.1582457894116 +727000 ekin = 1.94617710091839 | erot = 2.58809722642007 | epot = -21.6988659423112 | etot = -17.1645916149727 +728000 ekin = 1.79988680762438 | erot = 2.5979160195852 | epot = -21.6244191329758 | etot = -17.2266163057662 +729000 ekin = 1.88959231945985 | erot = 2.45182775661318 | epot = -21.5334662313019 | etot = -17.1920461552289 +730000 ekin = 1.96867512295179 | erot = 2.41054767101822 | epot = -21.4871507299637 | etot = -17.1079279359937 +731000 ekin = 2.04007066021541 | erot = 2.10968471949841 | epot = -21.5107250767904 | etot = -17.3609696970765 +732000 ekin = 2.15156634650388 | erot = 2.21445806294114 | epot = -21.5656945394481 | etot = -17.199670130003 +733000 ekin = 2.35654560078921 | erot = 2.09260206198333 | epot = -21.6365297457679 | etot = -17.1873820829953 +734000 ekin = 2.53299152923288 | erot = 2.37468932984165 | epot = -21.7439901596612 | etot = -16.8363093005867 +735000 ekin = 2.68562697475323 | erot = 2.64165595377583 | epot = -21.8172386752085 | etot = -16.4899557466795 +736000 ekin = 2.79874366040434 | erot = 2.3555672648488 | epot = -21.8745419467365 | etot = -16.7202310214834 +737000 ekin = 2.90595989296537 | erot = 2.41144452276502 | epot = -21.9257424852848 | etot = -16.6083380695544 +738000 ekin = 3.16854231512179 | erot = 2.16995374764134 | epot = -21.9707229821545 | etot = -16.6322269193913 +739000 ekin = 3.23623963268868 | erot = 2.03973592994104 | epot = -22.0157112429487 | etot = -16.739735680319 +740000 ekin = 3.39353868555153 | erot = 2.32580669984048 | epot = -22.0571350158431 | etot = -16.3377896304511 +741000 ekin = 3.45553760108212 | erot = 2.27352146353072 | epot = -22.0707608655516 | etot = -16.3417018009388 +742000 ekin = 3.39019064344739 | erot = 2.25908088551441 | epot = -22.0670611146383 | etot = -16.4177895856765 +743000 ekin = 3.24233276383811 | erot = 2.1839250645018 | epot = -22.0666014745823 | etot = -16.6403436462424 +744000 ekin = 3.20002114728613 | erot = 2.23309952366509 | epot = -22.0285391631713 | etot = -16.59541849222 +745000 ekin = 3.1415194326547 | erot = 2.14368723244866 | epot = -21.964386805698 | etot = -16.6791801405947 +746000 ekin = 3.13633701521512 | erot = 2.2360359398882 | epot = -21.8828728628744 | etot = -16.5104999077711 +747000 ekin = 3.07456220778475 | erot = 2.2658707938338 | epot = -21.7933333887777 | etot = -16.4529003871592 +748000 ekin = 2.89245092613039 | erot = 2.40124088279771 | epot = -21.7426214163831 | etot = -16.448929607455 +749000 ekin = 2.88984722840537 | erot = 2.04545464704744 | epot = -21.7486405812126 | etot = -16.8133387057598 +750000 ekin = 2.90690239667269 | erot = 2.16308193639867 | epot = -21.803785194241 | etot = -16.7338008611696 +751000 ekin = 2.91748713435769 | erot = 2.28652646733639 | epot = -21.8965044368835 | etot = -16.6924908351894 +752000 ekin = 2.973295314377 | erot = 2.21452942544181 | epot = -22.0108702587425 | etot = -16.8230455189237 +753000 ekin = 3.12120975435183 | erot = 2.07420726206789 | epot = -22.1751207133481 | etot = -16.9797036969284 +754000 ekin = 3.10943310281668 | erot = 2.2499210675043 | epot = -22.3612161837256 | etot = -17.0018620134046 +755000 ekin = 3.18094546468904 | erot = 2.11033610484431 | epot = -22.5317563093702 | etot = -17.2404747398369 +756000 ekin = 3.21064051440287 | erot = 2.28479126381456 | epot = -22.6718534245704 | etot = -17.176421646353 +757000 ekin = 3.22246886753978 | erot = 2.44968123087538 | epot = -22.7886247543805 | etot = -17.1164746559654 +758000 ekin = 3.20698410892089 | erot = 2.5094846891231 | epot = -22.8454442004672 | etot = -17.1289754024233 +759000 ekin = 3.2123470068763 | erot = 3.12016624161149 | epot = -22.820120520579 | etot = -16.4876072720912 +760000 ekin = 3.27823245967404 | erot = 2.84290665242014 | epot = -22.678395409203 | etot = -16.5572562971088 +761000 ekin = 3.12453460408373 | erot = 2.62184906422468 | epot = -22.4382001072282 | etot = -16.6918164389198 +762000 ekin = 3.00311895367862 | erot = 2.41644056781974 | epot = -22.1533696227421 | etot = -16.7338101012437 +763000 ekin = 2.78638584214058 | erot = 2.3278167244759 | epot = -21.8612278496175 | etot = -16.747025283001 +764000 ekin = 2.62767890060486 | erot = 2.17189942716293 | epot = -21.5731775254892 | etot = -16.7735991977215 +765000 ekin = 2.51344272364347 | erot = 2.10908907015962 | epot = -21.3425441704373 | etot = -16.7200123766342 +766000 ekin = 2.44393199306001 | erot = 2.31186162861045 | epot = -21.1564464031685 | etot = -16.400652781498 +767000 ekin = 2.31911160677134 | erot = 2.18314082130427 | epot = -20.9627169920037 | etot = -16.460464563928 +768000 ekin = 2.13701069286725 | erot = 2.40318509200869 | epot = -20.8058909702443 | etot = -16.2656951853684 +769000 ekin = 2.10500025579023 | erot = 2.63894895441484 | epot = -20.8353130509949 | etot = -16.0913638407899 +770000 ekin = 2.12136471147768 | erot = 2.65544587845489 | epot = -20.9284031482495 | etot = -16.1515925583169 +771000 ekin = 2.13543144639037 | erot = 2.60537105377022 | epot = -21.0328875238179 | etot = -16.2920850236573 +772000 ekin = 2.24162906957233 | erot = 2.74417889300668 | epot = -21.1929928408453 | etot = -16.2071848782663 +773000 ekin = 2.33155635751522 | erot = 2.6544507323086 | epot = -21.3698964155412 | etot = -16.3838893257173 +774000 ekin = 2.48263962766135 | erot = 2.8220912557924 | epot = -21.5457273132849 | etot = -16.2409964298311 +775000 ekin = 2.54636977687259 | erot = 2.8805310925612 | epot = -21.7219905564994 | etot = -16.2950896870656 +776000 ekin = 2.69100265053998 | erot = 2.71778929652937 | epot = -21.8782095094712 | etot = -16.4694175624019 +777000 ekin = 2.78238726098687 | erot = 2.72823230983043 | epot = -21.9911064717658 | etot = -16.4804869009485 +778000 ekin = 2.78617187411065 | erot = 2.8281579045973 | epot = -22.0683537375471 | etot = -16.4540239588392 +779000 ekin = 2.84892593421593 | erot = 3.03438887674951 | epot = -22.1034747648818 | etot = -16.2201599539164 +780000 ekin = 2.88441601841625 | erot = 3.24511918270346 | epot = -22.0479241425115 | etot = -15.9183889413918 +781000 ekin = 2.79226579266258 | erot = 3.2154845993887 | epot = -21.8915863093268 | etot = -15.8838359172756 +782000 ekin = 2.68974173738947 | erot = 3.17926967086066 | epot = -21.6363560975055 | etot = -15.7673446892554 +783000 ekin = 2.79024932263256 | erot = 2.97774512624287 | epot = -21.2767108150315 | etot = -15.508716366156 +784000 ekin = 2.86449981533265 | erot = 2.69172267164048 | epot = -21.0080507326029 | etot = -15.4518282456298 +785000 ekin = 2.80952796629514 | erot = 2.46781875930137 | epot = -20.8778745868634 | etot = -15.6005278612669 +786000 ekin = 2.68208018815612 | erot = 2.29793991145938 | epot = -20.7982787985711 | etot = -15.8182586989556 +787000 ekin = 2.56813961255804 | erot = 2.41937763036865 | epot = -20.6982631250973 | etot = -15.7107458821706 +788000 ekin = 2.4885142786824 | erot = 2.49924394096823 | epot = -20.6407407229647 | etot = -15.6529825033141 +789000 ekin = 2.3498294671688 | erot = 2.56420624411944 | epot = -20.6454036959724 | etot = -15.7313679846842 +790000 ekin = 2.27171119767482 | erot = 2.49951341291571 | epot = -20.6777685520556 | etot = -15.9065439414651 +791000 ekin = 2.21794673443476 | erot = 2.30373156167342 | epot = -20.7335879448548 | etot = -16.2119096487466 +792000 ekin = 2.11119869207262 | erot = 2.39386074874952 | epot = -20.8097229220293 | etot = -16.3046634812072 +793000 ekin = 2.09149862321906 | erot = 2.33936906711444 | epot = -20.8989593305935 | etot = -16.46809164026 +794000 ekin = 2.07514167963969 | erot = 2.18864817793776 | epot = -21.0024824072391 | etot = -16.7386925496616 +795000 ekin = 2.04599756417535 | erot = 1.93255592397763 | epot = -21.1171979822075 | etot = -17.1386444940546 +796000 ekin = 2.0560011436673 | erot = 2.03200387694222 | epot = -21.2502268612632 | etot = -17.1622218406537 +797000 ekin = 2.02544049585112 | erot = 2.05143967820578 | epot = -21.378370482143 | etot = -17.3014903080861 +798000 ekin = 2.10531554228559 | erot = 1.92029368041684 | epot = -21.4968277215556 | etot = -17.4712184988532 +799000 ekin = 2.1606478877389 | erot = 1.68829576105986 | epot = -21.5739657591762 | etot = -17.7250221103775 +800000 ekin = 2.21578954821239 | erot = 1.79594742030852 | epot = -21.6039560547364 | etot = -17.5922190862155 +801000 ekin = 2.22681551829037 | erot = 1.74309621460745 | epot = -21.6419326028336 | etot = -17.6720208699357 +802000 ekin = 2.43626565180412 | erot = 1.8592236853584 | epot = -21.6656085836152 | etot = -17.3701192464527 +803000 ekin = 2.50783665003003 | erot = 1.58815243555118 | epot = -21.7145730789025 | etot = -17.6185839933213 +804000 ekin = 2.54745667479286 | erot = 1.78752251126699 | epot = -21.8111449940664 | etot = -17.4761658080066 +805000 ekin = 2.80080657856368 | erot = 2.23795086847339 | epot = -21.9683564899642 | etot = -16.9295990429271 +806000 ekin = 3.00571166515339 | erot = 2.5677199981865 | epot = -22.1621480951751 | etot = -16.5887164318352 +807000 ekin = 3.08052739942195 | erot = 2.70802004693301 | epot = -22.38170110091 | etot = -16.593153654555 +808000 ekin = 3.09356150914435 | erot = 2.92145006465354 | epot = -22.5983854951448 | etot = -16.5833739213469 +809000 ekin = 3.13660538877266 | erot = 2.76580118315201 | epot = -22.789892142321 | etot = -16.8874855703963 +810000 ekin = 3.19670438612171 | erot = 3.06033288356123 | epot = -22.9235249464186 | etot = -16.6664876767356 +811000 ekin = 3.24358248709609 | erot = 2.75433145479029 | epot = -22.9913244588516 | etot = -16.9934105169653 +812000 ekin = 3.15387712947307 | erot = 2.67472079387977 | epot = -22.995833823727 | etot = -17.1672359003741 +813000 ekin = 2.94730683854471 | erot = 2.78448217630015 | epot = -22.9500139539581 | etot = -17.2182249391133 +814000 ekin = 2.84152372531229 | erot = 2.94333861884889 | epot = -22.886106332815 | etot = -17.1012439886538 +815000 ekin = 2.76239406868071 | erot = 3.20738232683527 | epot = -22.8152543629747 | etot = -16.8454779674587 +816000 ekin = 2.59996655001222 | erot = 2.95415715753922 | epot = -22.7323176380797 | etot = -17.1781939305283 +817000 ekin = 2.5056850969174 | erot = 2.56873279594443 | epot = -22.6565557161091 | etot = -17.5821378232473 +818000 ekin = 2.36879357411276 | erot = 2.62740710803679 | epot = -22.5771576372442 | etot = -17.5809569550947 +819000 ekin = 2.2213715355314 | erot = 2.20921666744159 | epot = -22.5063000644072 | etot = -18.0757118614342 +820000 ekin = 2.15352101503093 | erot = 2.22634472649342 | epot = -22.4644595926824 | etot = -18.0845938511581 +821000 ekin = 2.02682142410431 | erot = 2.27918504666614 | epot = -22.4285107655757 | etot = -18.1225042948052 +822000 ekin = 1.96590621976957 | erot = 2.11933585708345 | epot = -22.3893132044858 | etot = -18.3040711276327 +823000 ekin = 1.87390236475586 | erot = 2.4383392862657 | epot = -22.3766834300092 | etot = -18.0644417789876 +824000 ekin = 1.76511965451641 | erot = 2.08632973064822 | epot = -22.3846955708834 | etot = -18.5332461857187 +825000 ekin = 1.72275906923827 | erot = 2.05491870773449 | epot = -22.4158544093968 | etot = -18.638176632424 +826000 ekin = 1.6542317303061 | erot = 1.9011808359787 | epot = -22.4865285736257 | etot = -18.9311160073409 +827000 ekin = 1.62203877403882 | erot = 2.11543908972364 | epot = -22.5672947980682 | etot = -18.8298169343057 +828000 ekin = 1.50840521352541 | erot = 1.94184045090041 | epot = -22.6360835929013 | etot = -19.1858379284755 +829000 ekin = 1.53133011832232 | erot = 2.23719923781426 | epot = -22.6642383844121 | etot = -18.8957090282755 +830000 ekin = 1.57674105329983 | erot = 2.32835034572891 | epot = -22.6990636526541 | etot = -18.7939722536254 +831000 ekin = 1.66163281968 | erot = 2.45366313846767 | epot = -22.7282270920055 | etot = -18.6129311338578 +832000 ekin = 1.61575752897166 | erot = 2.36469513945105 | epot = -22.7314805576168 | etot = -18.7510278891941 +833000 ekin = 1.5748462373096 | erot = 2.43716147593346 | epot = -22.7310267178688 | etot = -18.7190190046258 +834000 ekin = 1.61211592879595 | erot = 2.27369578072793 | epot = -22.723107314969 | etot = -18.8372956054451 +835000 ekin = 1.71255063217308 | erot = 2.25145179685536 | epot = -22.7213723561555 | etot = -18.757369927127 +836000 ekin = 1.66410080946976 | erot = 2.36287362112711 | epot = -22.7106963960627 | etot = -18.6837219654658 +837000 ekin = 1.55393537342694 | erot = 2.19682771054845 | epot = -22.7054421830654 | etot = -18.95467909909 +838000 ekin = 1.55395449542858 | erot = 1.97831033841727 | epot = -22.6952408411607 | etot = -19.1629760073149 +839000 ekin = 1.56966734032696 | erot = 1.54356794703242 | epot = -22.6819663107371 | etot = -19.5687310233777 +840000 ekin = 1.67828545417323 | erot = 1.72274710399372 | epot = -22.6537987135736 | etot = -19.2527661554066 +841000 ekin = 1.70756024783427 | erot = 1.86878110711764 | epot = -22.6201854793162 | etot = -19.0438441243643 +842000 ekin = 1.65445531752109 | erot = 1.98969497305258 | epot = -22.583445805341 | etot = -18.9392955147673 +843000 ekin = 1.61813041031379 | erot = 1.94297358984934 | epot = -22.5343209800153 | etot = -18.9732169798522 +844000 ekin = 1.66559589059779 | erot = 2.07459583566505 | epot = -22.4909419629538 | etot = -18.7507502366909 +845000 ekin = 1.67372319184744 | erot = 2.01531047458982 | epot = -22.4486472588292 | etot = -18.759613592392 +846000 ekin = 1.76456308419019 | erot = 2.04286196110417 | epot = -22.3907655586718 | etot = -18.5833405133775 +847000 ekin = 1.68474528716594 | erot = 1.9506218354464 | epot = -22.3219698462716 | etot = -18.6866027236593 +848000 ekin = 1.7769208083991 | erot = 1.9490334388676 | epot = -22.2732219412012 | etot = -18.5472676939345 +849000 ekin = 1.80865478838392 | erot = 1.92750105953155 | epot = -22.254397724897 | etot = -18.5182418769815 +850000 ekin = 1.81902433575234 | erot = 1.83695743097834 | epot = -22.2895798743212 | etot = -18.6335981075905 +851000 ekin = 1.89190920982903 | erot = 1.99438142785482 | epot = -22.3706877386968 | etot = -18.484397101013 +852000 ekin = 1.85572644981354 | erot = 2.08333690914979 | epot = -22.4954803882742 | etot = -18.5564170293108 +853000 ekin = 1.96819950961999 | erot = 2.4652206393425 | epot = -22.6461768022226 | etot = -18.2127566532601 +854000 ekin = 1.99027367747301 | erot = 2.82405245762167 | epot = -22.8233134890242 | etot = -18.0089873539295 +855000 ekin = 2.02041206494319 | erot = 2.76127853932356 | epot = -22.971921387783 | etot = -18.1902307835163 +856000 ekin = 1.98428835568691 | erot = 2.89398807390395 | epot = -23.0688189336956 | etot = -18.1905425041048 +857000 ekin = 1.94437625728123 | erot = 2.75841683957984 | epot = -23.1174862513581 | etot = -18.4146931544971 +858000 ekin = 1.77145748342589 | erot = 2.97613159793736 | epot = -23.092564103994 | etot = -18.3449750226308 +859000 ekin = 1.75449757825296 | erot = 2.94820975918207 | epot = -23.0174946494386 | etot = -18.3147873120036 +860000 ekin = 1.69824130829505 | erot = 2.56619342881162 | epot = -22.913827752011 | etot = -18.6493930149043 +861000 ekin = 1.61723118354539 | erot = 2.60723394433469 | epot = -22.7817384645188 | etot = -18.5572733366387 +862000 ekin = 1.65016805240501 | erot = 2.58826826537521 | epot = -22.6306365080481 | etot = -18.3922001902679 +863000 ekin = 1.62167782718969 | erot = 2.32265511280165 | epot = -22.4833247924562 | etot = -18.5389918524648 +864000 ekin = 1.64443917201354 | erot = 2.41694169973122 | epot = -22.3437317075484 | etot = -18.2823508358037 +865000 ekin = 1.62323607055498 | erot = 2.42797649715591 | epot = -22.2339680949553 | etot = -18.1827555272444 +866000 ekin = 1.52330589260455 | erot = 2.43806006674714 | epot = -22.1297693883002 | etot = -18.1684034289485 +867000 ekin = 1.53921563765445 | erot = 2.563486299306 | epot = -22.0395837686773 | etot = -17.9368818317168 +868000 ekin = 1.51596999193292 | erot = 2.55716270739037 | epot = -21.9937420973996 | etot = -17.9206093980763 +869000 ekin = 1.59814692070021 | erot = 2.15771580624648 | epot = -21.9767818689251 | etot = -18.2209191419784 +870000 ekin = 1.62438751257453 | erot = 2.30366665730433 | epot = -22.0119463158297 | etot = -18.0838921459509 +871000 ekin = 1.64699232624016 | erot = 2.29504943911151 | epot = -22.0696451748842 | etot = -18.1276034095325 +872000 ekin = 1.74936107688413 | erot = 1.9965562018104 | epot = -22.1253859835196 | etot = -18.3794687048251 +873000 ekin = 1.81958663572737 | erot = 2.15311518593397 | epot = -22.1932828259374 | etot = -18.2205810042761 +874000 ekin = 1.81429910947078 | erot = 2.15191422066098 | epot = -22.2521915372879 | etot = -18.2859782071562 +875000 ekin = 1.92774125135583 | erot = 2.09841769816796 | epot = -22.2950199590261 | etot = -18.2688610095023 +876000 ekin = 2.05205383202971 | erot = 1.71112886964838 | epot = -22.3353847724815 | etot = -18.5722020708034 +877000 ekin = 2.00183605232511 | erot = 1.88466440539805 | epot = -22.3587375372386 | etot = -18.4722370795154 +878000 ekin = 1.96978247022157 | erot = 1.9449250442233 | epot = -22.3467650368076 | etot = -18.4320575223628 +879000 ekin = 1.89978467382709 | erot = 2.08488575038812 | epot = -22.3245187946411 | etot = -18.3398483704259 +880000 ekin = 1.79316389452797 | erot = 2.04472659118319 | epot = -22.302273163246 | etot = -18.4643826775348 +881000 ekin = 1.84166442688194 | erot = 1.91254711303943 | epot = -22.2610385402073 | etot = -18.5068270002859 +882000 ekin = 1.8408423266687 | erot = 1.89291352333735 | epot = -22.2058993058574 | etot = -18.4721434558513 +883000 ekin = 1.85228381568774 | erot = 2.04568547305987 | epot = -22.1462287912866 | etot = -18.248259502539 +884000 ekin = 1.74299718480553 | erot = 2.41541515351066 | epot = -22.0952302162198 | etot = -17.9368178779037 +885000 ekin = 1.70113701127997 | erot = 2.12494075622537 | epot = -22.062426804351 | etot = -18.2363490368456 +886000 ekin = 1.65197597470454 | erot = 2.40636683283032 | epot = -22.0395749533763 | etot = -17.9812321458414 +887000 ekin = 1.60780982778138 | erot = 2.52410870186223 | epot = -22.0426576240104 | etot = -17.9107390943668 +888000 ekin = 1.62736239761613 | erot = 2.54417200799014 | epot = -22.0837991546735 | etot = -17.9122647490673 +889000 ekin = 1.56260633740652 | erot = 2.93015784124605 | epot = -22.1644353768148 | etot = -17.6716711981622 +890000 ekin = 1.59045576749902 | erot = 2.98817840520079 | epot = -22.2639211219211 | etot = -17.6852869492213 +891000 ekin = 1.56285966088235 | erot = 3.45684679212867 | epot = -22.3811052217737 | etot = -17.3613987687627 +892000 ekin = 1.54330427837286 | erot = 3.72585516837654 | epot = -22.4833521640577 | etot = -17.2141927173083 +893000 ekin = 1.59146757295502 | erot = 3.57834579864882 | epot = -22.5732593414834 | etot = -17.4034459698796 +894000 ekin = 1.62137337506942 | erot = 3.47314499517383 | epot = -22.6375279090018 | etot = -17.5430095387586 +895000 ekin = 1.66705900653875 | erot = 3.49716948137661 | epot = -22.662497563479 | etot = -17.4982690755636 +896000 ekin = 1.55030206729663 | erot = 3.09080759429039 | epot = -22.6660259737766 | etot = -18.0249163121896 +897000 ekin = 1.59716300254363 | erot = 3.18847114591564 | epot = -22.6447094591962 | etot = -17.8590753107369 +898000 ekin = 1.63846223090733 | erot = 3.52423413884989 | epot = -22.574807009085 | etot = -17.4121106393278 +899000 ekin = 1.76043242630049 | erot = 3.57817463535837 | epot = -22.5017519688559 | etot = -17.163144907197 +900000 ekin = 1.79654660125389 | erot = 3.47500564830083 | epot = -22.4355321588433 | etot = -17.1639799092886 +901000 ekin = 1.90036826124628 | erot = 3.08289582473982 | epot = -22.3778122198785 | etot = -17.3945481338924 +902000 ekin = 1.86184581507154 | erot = 3.53323519892372 | epot = -22.3343178452086 | etot = -16.9392368312133 +903000 ekin = 1.82612532908577 | erot = 2.94106563490189 | epot = -22.2753946825534 | etot = -17.5082037185658 +904000 ekin = 1.83566294124649 | erot = 2.77276060856724 | epot = -22.2178118874787 | etot = -17.609388337665 +905000 ekin = 1.98760022520663 | erot = 2.39033190744944 | epot = -22.1879073477142 | etot = -17.8099752150581 +906000 ekin = 2.03479331668647 | erot = 2.3344228531767 | epot = -22.1683021524764 | etot = -17.7990859826132 +907000 ekin = 2.13854534244443 | erot = 2.49897360264341 | epot = -22.1329919803681 | etot = -17.4954730352803 +908000 ekin = 2.29292980719163 | erot = 2.19971547335618 | epot = -22.0946544988967 | etot = -17.6020092183489 +909000 ekin = 2.26088767533455 | erot = 2.08032511956132 | epot = -22.0656471637075 | etot = -17.7244343688116 +910000 ekin = 2.24374768454178 | erot = 2.05633395261294 | epot = -22.0263801495314 | etot = -17.7262985123767 +911000 ekin = 2.21169387792337 | erot = 2.07671300621837 | epot = -21.9687563877776 | etot = -17.6803495036359 +912000 ekin = 2.26342827869161 | erot = 2.19424965405253 | epot = -21.8985767358688 | etot = -17.4408988031247 +913000 ekin = 2.25810530261834 | erot = 2.15174616543858 | epot = -21.8202885496123 | etot = -17.4104370815554 +914000 ekin = 2.22041757979622 | erot = 2.11296431351484 | epot = -21.7659012518376 | etot = -17.4325193585265 +915000 ekin = 2.305853852629 | erot = 2.01195201885935 | epot = -21.7105872613034 | etot = -17.392781389815 +916000 ekin = 2.31746417556327 | erot = 2.26468835944155 | epot = -21.6446439232134 | etot = -17.0624913882086 +917000 ekin = 2.29083855376978 | erot = 2.35266040877599 | epot = -21.5981818982044 | etot = -16.9546829356586 +918000 ekin = 2.21948812241411 | erot = 2.67757709393344 | epot = -21.5768387043403 | etot = -16.6797734879928 +919000 ekin = 2.17502484144239 | erot = 2.50505023715529 | epot = -21.5962136981092 | etot = -16.9161386195115 +920000 ekin = 2.05225364762306 | erot = 2.28466235959607 | epot = -21.6248903594501 | etot = -17.287974352231 +921000 ekin = 1.95826631852647 | erot = 2.44785811644796 | epot = -21.6449866661346 | etot = -17.2388622311601 +922000 ekin = 1.8871341631229 | erot = 2.20407498665728 | epot = -21.6433309330804 | etot = -17.5521217833002 +923000 ekin = 1.85499144920616 | erot = 2.47959433101658 | epot = -21.6219980061721 | etot = -17.2874122259493 +924000 ekin = 1.82449923254666 | erot = 2.43607326145231 | epot = -21.5811225363952 | etot = -17.3205500423962 +925000 ekin = 1.75365416618008 | erot = 2.67043382132047 | epot = -21.5654424680592 | etot = -17.1413544805586 +926000 ekin = 1.82728938436798 | erot = 2.42568919453246 | epot = -21.5649010983419 | etot = -17.3119225194415 +927000 ekin = 1.71111907930132 | erot = 2.49634793928696 | epot = -21.5869585210727 | etot = -17.3794915024844 +928000 ekin = 1.64740049787453 | erot = 2.53788896245496 | epot = -21.6442370240126 | etot = -17.4589475636831 +929000 ekin = 1.68616483039842 | erot = 2.26272805894195 | epot = -21.7404415309293 | etot = -17.7915486415889 +930000 ekin = 1.8057977284304 | erot = 2.41185782525222 | epot = -21.8766034841673 | etot = -17.6589479304847 +931000 ekin = 1.84540351564131 | erot = 2.51429545093936 | epot = -22.0343594511133 | etot = -17.6746604845327 +932000 ekin = 1.91948716688521 | erot = 2.50789246144377 | epot = -22.2107200997812 | etot = -17.7833404714522 +933000 ekin = 2.08806765098505 | erot = 2.54053118824105 | epot = -22.3857648909732 | etot = -17.7571660517471 +934000 ekin = 2.15790983141932 | erot = 2.35997810661384 | epot = -22.5303312795937 | etot = -18.0124433415605 +935000 ekin = 2.25791486609556 | erot = 2.61090003818589 | epot = -22.6566492075146 | etot = -17.7878343032331 +936000 ekin = 2.2869444991169 | erot = 2.88785018878652 | epot = -22.7387712915836 | etot = -17.5639766036801 +937000 ekin = 2.2598536597864 | erot = 2.68904834283381 | epot = -22.7546509524987 | etot = -17.8057489498784 +938000 ekin = 2.28814448881807 | erot = 2.54450017128294 | epot = -22.6975117726393 | etot = -17.8648671125383 +939000 ekin = 2.22181328679759 | erot = 2.40773891474627 | epot = -22.5724060300531 | etot = -17.9428538285092 +940000 ekin = 2.19047318059934 | erot = 2.24413418480581 | epot = -22.3825999688773 | etot = -17.9479926034721 +941000 ekin = 1.97789684715541 | erot = 2.11351242298739 | epot = -22.1581596355232 | etot = -18.0667503653804 +942000 ekin = 1.82283426551466 | erot = 2.02814504753835 | epot = -21.924507961928 | etot = -18.073528648875 +943000 ekin = 1.77337816859221 | erot = 1.98390662003463 | epot = -21.7436762740981 | etot = -17.9863914854713 +944000 ekin = 1.74129354400305 | erot = 2.0257017281874 | epot = -21.6008012672991 | etot = -17.8338059951087 +945000 ekin = 1.72896560635761 | erot = 2.20997508037831 | epot = -21.5146553493683 | etot = -17.5757146626324 +946000 ekin = 1.90743436358219 | erot = 2.1370577421747 | epot = -21.4832307541302 | etot = -17.4387386483733 +947000 ekin = 2.02837986664296 | erot = 2.29971426385137 | epot = -21.4794165970972 | etot = -17.1513224666028 +948000 ekin = 2.03783072880889 | erot = 2.11465543087132 | epot = -21.4989322229724 | etot = -17.3464460632922 +949000 ekin = 2.16990164235423 | erot = 1.99168801462282 | epot = -21.5364977264078 | etot = -17.3749080694307 +950000 ekin = 2.24527818420086 | erot = 2.12106218398242 | epot = -21.6200851503178 | etot = -17.2537447821345 +951000 ekin = 2.3597779491216 | erot = 2.09437757436112 | epot = -21.7182967003277 | etot = -17.264141176845 +952000 ekin = 2.43036880894168 | erot = 2.60988991207291 | epot = -21.809899640086 | etot = -16.7696409190714 +953000 ekin = 2.58164820046362 | erot = 2.62403788420646 | epot = -21.9145443047519 | etot = -16.7088582200818 +954000 ekin = 2.67569984169079 | erot = 2.49812470218404 | epot = -21.9760951843484 | etot = -16.8022706404736 +955000 ekin = 2.87107117646036 | erot = 2.70877614839088 | epot = -22.0056490566724 | etot = -16.4258017318211 +956000 ekin = 3.09772559509693 | erot = 2.62503444551598 | epot = -21.9996173766588 | etot = -16.2768573360459 +957000 ekin = 3.06387016722013 | erot = 2.8302356311836 | epot = -21.9356950338747 | etot = -16.0415892354709 +958000 ekin = 3.15191228693313 | erot = 2.56018473190256 | epot = -21.7995256048421 | etot = -16.0874285860064 +959000 ekin = 3.17671440940348 | erot = 2.48421513931016 | epot = -21.6207768556515 | etot = -15.9598473069379 +960000 ekin = 3.01275155897339 | erot = 2.43167379369326 | epot = -21.4002125286164 | etot = -15.9557871759497 +961000 ekin = 2.94603084982365 | erot = 2.28503967366068 | epot = -21.1407696110672 | etot = -15.9096990875828 +962000 ekin = 2.87549986152936 | erot = 2.267647953911 | epot = -20.8628900961518 | etot = -15.7197422807115 +963000 ekin = 2.72736350188626 | erot = 2.02845193195215 | epot = -20.6025221949833 | etot = -15.8467067611448 +964000 ekin = 2.55766914748418 | erot = 1.90275324626823 | epot = -20.3671083670073 | etot = -15.9066859732549 +965000 ekin = 2.42945571607617 | erot = 1.87896821137786 | epot = -20.1665878867718 | etot = -15.8581639593178 +966000 ekin = 2.30432659917244 | erot = 2.05976948112514 | epot = -20.0345331150776 | etot = -15.67043703478 +967000 ekin = 2.19239153699628 | erot = 2.23712663138571 | epot = -19.9304749138275 | etot = -15.5009567454455 +968000 ekin = 2.12056467996883 | erot = 2.29258395929203 | epot = -19.8478936102002 | etot = -15.4347449709393 +969000 ekin = 2.03082359465494 | erot = 2.12561043987624 | epot = -19.8204193361233 | etot = -15.6639853015921 +970000 ekin = 2.06263818101753 | erot = 2.20772735706048 | epot = -19.8171007442084 | etot = -15.5467352061304 +971000 ekin = 2.07242738755742 | erot = 2.39359294752823 | epot = -19.8426078132443 | etot = -15.3765874781586 +972000 ekin = 2.13593664400378 | erot = 2.51621155234874 | epot = -19.8711039585162 | etot = -15.2189557621637 +973000 ekin = 2.19239588059205 | erot = 2.7181784623389 | epot = -19.8806125652289 | etot = -14.9700382222979 +974000 ekin = 2.08126353721197 | erot = 2.92742241693149 | epot = -19.8623774194061 | etot = -14.8536914652627 +975000 ekin = 2.01107833245546 | erot = 2.57768138393004 | epot = -19.8162471815015 | etot = -15.227487465116 +976000 ekin = 1.90089112618327 | erot = 2.56071712862275 | epot = -19.7674234084296 | etot = -15.3058151536236 +977000 ekin = 1.82747564686913 | erot = 2.56117528028768 | epot = -19.6916974382103 | etot = -15.3030465110535 +978000 ekin = 1.81823178972961 | erot = 2.21507357950853 | epot = -19.6525909549582 | etot = -15.61928558572 +979000 ekin = 1.86020910008096 | erot = 2.09761460513785 | epot = -19.6622349612071 | etot = -15.7044112559883 +980000 ekin = 1.89813063132926 | erot = 1.86971657434364 | epot = -19.6793196081291 | etot = -15.9114724024562 +981000 ekin = 1.96055767456426 | erot = 1.80588067180873 | epot = -19.7616283768556 | etot = -15.9951900304826 +982000 ekin = 2.04211859099614 | erot = 2.00657086473459 | epot = -19.8926418366081 | etot = -15.8439523808774 +983000 ekin = 2.08434248544596 | erot = 2.13281702823352 | epot = -20.0190963786513 | etot = -15.8019368649718 +984000 ekin = 2.28263945352173 | erot = 2.30206381624253 | epot = -20.1817376775087 | etot = -15.5970344077445 +985000 ekin = 2.33165973691136 | erot = 2.36792674462211 | epot = -20.3496337869149 | etot = -15.6500473053814 +986000 ekin = 2.3684529633035 | erot = 2.40477790490969 | epot = -20.5172631957864 | etot = -15.7440323275732 +987000 ekin = 2.44660573334744 | erot = 2.6065659753273 | epot = -20.6827873919967 | etot = -15.6296156833219 +988000 ekin = 2.48779340096933 | erot = 2.57507657272567 | epot = -20.8472563124355 | etot = -15.7843863387405 +989000 ekin = 2.62562775055464 | erot = 2.78753506888642 | epot = -20.9917314563947 | etot = -15.5785686369537 +990000 ekin = 2.71356724749209 | erot = 3.06120975805148 | epot = -21.1004443459753 | etot = -15.3256673404317 +991000 ekin = 2.84485263345538 | erot = 3.42057995732924 | epot = -21.1508216928481 | etot = -14.8853891020635 +992000 ekin = 2.88616886571365 | erot = 3.47043505670966 | epot = -21.1491979980383 | etot = -14.792594075615 +993000 ekin = 2.86101706988292 | erot = 3.4017274067487 | epot = -21.1075232078294 | etot = -14.8447787311978 +994000 ekin = 2.90016396739777 | erot = 3.68400469179703 | epot = -21.0544509503875 | etot = -14.4702822911927 +995000 ekin = 2.84836922583208 | erot = 3.86724891436252 | epot = -20.9907241498287 | etot = -14.2751060096341 +996000 ekin = 2.87268648345994 | erot = 3.37952872488952 | epot = -20.9186469223171 | etot = -14.6664317139676 +997000 ekin = 2.84260788755105 | erot = 3.24170863045241 | epot = -20.8185896660925 | etot = -14.734273148089 +998000 ekin = 2.86644419268861 | erot = 3.30788437737345 | epot = -20.6892589093676 | etot = -14.5149303393055 +999000 ekin = 2.91762607565484 | erot = 3.19659159186089 | epot = -20.5404731144169 | etot = -14.4262554469012 +1000000 ekin = 2.92466509157894 | erot = 2.67428308534003 | epot = -20.3978646538617 | etot = -14.7989164769428 + 1000000 0.12998512 -1.3075422 0.032675661 -1.092075 0.0002012331 64000 +Loop time of 34.8089 on 1 procs for 1000000 steps with 16 atoms + +Performance: 24821.244 tau/day, 28728.292 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 29.15 | 29.15 | 29.15 | 0.0 | 83.74 +Bond | 0.89192 | 0.89192 | 0.89192 | 0.0 | 2.56 +Neigh | 0.009135 | 0.009135 | 0.009135 | 0.0 | 0.03 +Comm | 0.3491 | 0.3491 | 0.3491 | 0.0 | 1.00 +Output | 0.15275 | 0.15275 | 0.15275 | 0.0 | 0.44 +Modify | 3.9719 | 3.9719 | 3.9719 | 0.0 | 11.41 +Other | | 0.2836 | | | 0.81 + +Nlocal: 16.0000 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 107.000 ave 107 max 107 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875000 +Ave special neighs/atom = 3.7500000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:34 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 new file mode 100644 index 0000000000..037fb5273a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 @@ -0,0 +1,1183 @@ +LAMMPS (2 Jul 2021) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +set atom * mass 3.1575 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -21.0482852787267 | etot = -15.5418106194402 +Per MPI rank memory allocation (min/avg/max) = 9.320 | 9.349 | 9.434 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -1.3610384 0.045520537 -1.1464707 5.9660461e-05 64000 +1000 ekin = 2.72013629959678 | erot = 3.04690178503881 | epot = -20.8790776967073 | etot = -15.1120396120718 +2000 ekin = 2.78009554567455 | erot = 2.50647079931992 | epot = -20.701004729611 | etot = -15.4144383846165 +3000 ekin = 2.76688166744693 | erot = 2.2821949377072 | epot = -20.5676929006559 | etot = -15.5186162955017 +4000 ekin = 2.70260128929368 | erot = 2.27403484282169 | epot = -20.4705557396832 | etot = -15.4939196075678 +5000 ekin = 2.64234178224169 | erot = 2.30733191000246 | epot = -20.4236057646951 | etot = -15.4739320724509 +6000 ekin = 2.65801663486023 | erot = 2.39066626378174 | epot = -20.4246308066932 | etot = -15.3759479080513 +7000 ekin = 2.68316645880462 | erot = 2.33063300072947 | epot = -20.4749165048777 | etot = -15.4611170453436 +8000 ekin = 2.59120591314502 | erot = 2.05477906678441 | epot = -20.5631212612485 | etot = -15.917136281319 +9000 ekin = 2.65376648779415 | erot = 2.11575091090834 | epot = -20.6881173411843 | etot = -15.9185999424818 +10000 ekin = 2.77402134048096 | erot = 2.56538522546417 | epot = -20.812379085734 | etot = -15.4729725197889 +11000 ekin = 2.67401627862025 | erot = 2.88526848066389 | epot = -20.9238620704285 | etot = -15.3645773111444 +12000 ekin = 2.69364271301779 | erot = 2.6669991161831 | epot = -21.0407385357144 | etot = -15.6800967065135 +13000 ekin = 2.78352076266191 | erot = 2.62517780661365 | epot = -21.1720350247763 | etot = -15.7633364555008 +14000 ekin = 2.84595331390102 | erot = 2.43480334086398 | epot = -21.2963503704522 | etot = -16.0155937156872 +15000 ekin = 2.8890700970034 | erot = 2.41912745049439 | epot = -21.4150808543174 | etot = -16.1068833068196 +16000 ekin = 3.00758069356165 | erot = 2.63110801135323 | epot = -21.5261697271624 | etot = -15.8874810222475 +17000 ekin = 3.08749820661837 | erot = 2.53137980117209 | epot = -21.6092998996456 | etot = -15.9904218918551 +18000 ekin = 2.97601119892239 | erot = 2.53805591696759 | epot = -21.6415056622546 | etot = -16.1274385463646 +19000 ekin = 2.88488444737123 | erot = 2.5444118447944 | epot = -21.6205491988715 | etot = -16.1912529067058 +20000 ekin = 2.65941914113237 | erot = 2.80243564233624 | epot = -21.5551870578307 | etot = -16.0933322743621 +21000 ekin = 2.57547433431651 | erot = 2.74965527534454 | epot = -21.4613716405084 | etot = -16.1362420308473 +22000 ekin = 2.53510807627336 | erot = 2.7402974758743 | epot = -21.3396334655203 | etot = -16.0642279133727 +23000 ekin = 2.40091416401759 | erot = 2.4124516066547 | epot = -21.2029723825426 | etot = -16.3896066118703 +24000 ekin = 2.35240654345194 | erot = 2.10101829600973 | epot = -21.0659817341106 | etot = -16.6125568946489 +25000 ekin = 2.24250544456845 | erot = 2.18590508798994 | epot = -20.9513445132092 | etot = -16.5229339806508 +26000 ekin = 2.15423649133118 | erot = 2.45727700237462 | epot = -20.8669379085991 | etot = -16.2554244148933 +27000 ekin = 1.93524632585278 | erot = 2.346503038014 | epot = -20.8326435236231 | etot = -16.5508941597563 +28000 ekin = 1.7694332444345 | erot = 2.4135367579459 | epot = -20.8217433644358 | etot = -16.6387733620554 +29000 ekin = 1.75176430946873 | erot = 2.21029128532635 | epot = -20.8529129923908 | etot = -16.8908573975957 +30000 ekin = 1.69211824889093 | erot = 2.43399158562863 | epot = -20.9103885167126 | etot = -16.784278682193 +31000 ekin = 1.72526028314483 | erot = 2.32450864670446 | epot = -21.0087646424164 | etot = -16.9589957125671 +32000 ekin = 1.85144315905109 | erot = 2.36996515630933 | epot = -21.1366890377948 | etot = -16.9152807224344 +33000 ekin = 1.92914135939683 | erot = 2.5515717658971 | epot = -21.2867811906613 | etot = -16.8060680653674 +34000 ekin = 1.86488201964581 | erot = 2.7040070478884 | epot = -21.4771748939502 | etot = -16.908285826416 +35000 ekin = 1.82452979540547 | erot = 2.88148899883821 | epot = -21.6928620054228 | etot = -16.9868432111791 +36000 ekin = 1.85882387630628 | erot = 2.79217577332792 | epot = -21.8984987105764 | etot = -17.2474990609422 +37000 ekin = 1.92831232163801 | erot = 2.92698521263705 | epot = -22.0979488314928 | etot = -17.2426512972178 +38000 ekin = 1.93581630417405 | erot = 2.90317027989993 | epot = -22.2686450915844 | etot = -17.4296585075104 +39000 ekin = 2.01059319335205 | erot = 2.94480429938119 | epot = -22.3778651261378 | etot = -17.4224676334046 +40000 ekin = 1.97071041215323 | erot = 2.93286391865185 | epot = -22.417858975573 | etot = -17.5142846447679 +41000 ekin = 2.0574643445695 | erot = 2.6824269801062 | epot = -22.3807196920657 | etot = -17.64082836739 +42000 ekin = 2.09112509922765 | erot = 2.69685180517687 | epot = -22.290681194375 | etot = -17.5027042899705 +43000 ekin = 2.01814513009282 | erot = 2.85562815769076 | epot = -22.1601960046645 | etot = -17.286422716881 +44000 ekin = 1.92171799748094 | erot = 2.74064501961463 | epot = -22.0236920121947 | etot = -17.3613289950991 +45000 ekin = 1.81213357146534 | erot = 2.33969637171497 | epot = -21.9013900155102 | etot = -17.7495600723299 +46000 ekin = 1.7043188626816 | erot = 2.39010616929278 | epot = -21.7951136139009 | etot = -17.7006885819265 +47000 ekin = 1.66181647983358 | erot = 2.43237478783471 | epot = -21.6929795780581 | etot = -17.5987883103898 +48000 ekin = 1.60640851287361 | erot = 2.34869900597693 | epot = -21.5897329144351 | etot = -17.6346253955845 +49000 ekin = 1.52653989846239 | erot = 2.00084533105263 | epot = -21.5040522645286 | etot = -17.9766670350135 +50000 ekin = 1.44266718781295 | erot = 2.13453634177559 | epot = -21.4422830581905 | etot = -17.8650795286019 +51000 ekin = 1.43550636726017 | erot = 2.23006562743148 | epot = -21.3792358932285 | etot = -17.7136638985368 +52000 ekin = 1.4191758391953 | erot = 2.33479503366768 | epot = -21.3396501545003 | etot = -17.5856792816373 +53000 ekin = 1.50159149702875 | erot = 2.56353973620709 | epot = -21.3318420135023 | etot = -17.2667107802664 +54000 ekin = 1.53108046116777 | erot = 2.69431714698447 | epot = -21.3427130336451 | etot = -17.1173154254928 +55000 ekin = 1.57204496790938 | erot = 2.27080332163902 | epot = -21.3613604522622 | etot = -17.5185121627138 +56000 ekin = 1.49781857063062 | erot = 2.330860220466 | epot = -21.3901677321074 | etot = -17.5614889410108 +57000 ekin = 1.50326126671596 | erot = 2.187288742759 | epot = -21.4375848454805 | etot = -17.7470348360056 +58000 ekin = 1.56885163164473 | erot = 2.04781187994394 | epot = -21.4901198020449 | etot = -17.8734562904563 +59000 ekin = 1.64456875770868 | erot = 2.09216170303409 | epot = -21.5467238774713 | etot = -17.8099934167286 +60000 ekin = 1.61691925732048 | erot = 2.29542751813002 | epot = -21.6038795960772 | etot = -17.6915328206267 +61000 ekin = 1.65884539872101 | erot = 2.10847349489138 | epot = -21.6559771193386 | etot = -17.8886582257262 +62000 ekin = 1.72309094226649 | erot = 2.30407725612054 | epot = -21.7076104489969 | etot = -17.6804422506099 +63000 ekin = 1.68827086718391 | erot = 2.43329143180642 | epot = -21.7495751902359 | etot = -17.6280128912456 +64000 ekin = 1.77925986833295 | erot = 2.4393196588264 | epot = -21.7824788671424 | etot = -17.563899339983 +65000 ekin = 1.71201207010368 | erot = 2.05565281348585 | epot = -21.8004838491856 | etot = -18.0328189655961 +66000 ekin = 1.72258841195354 | erot = 1.89221111049374 | epot = -21.8042275382219 | etot = -18.1894280157747 +67000 ekin = 1.81093386427603 | erot = 1.97149822718467 | epot = -21.8237244535633 | etot = -18.0412923621026 +68000 ekin = 1.92086731218838 | erot = 2.04627775213357 | epot = -21.8538566840958 | etot = -17.8867116197738 +69000 ekin = 1.95769420352314 | erot = 2.00695954556819 | epot = -21.8959292342321 | etot = -17.9312754851408 +70000 ekin = 2.04640812952288 | erot = 1.99675167399822 | epot = -21.938534738798 | etot = -17.8953749352769 +71000 ekin = 2.09757818208426 | erot = 2.0109977376718 | epot = -21.9790979736474 | etot = -17.8705220538913 +72000 ekin = 2.17178409239857 | erot = 2.18113395841077 | epot = -22.0154687692559 | etot = -17.6625507184466 +73000 ekin = 2.15190632785483 | erot = 2.45126940688765 | epot = -22.0387524357625 | etot = -17.43557670102 +74000 ekin = 2.16265422451121 | erot = 2.15818555561667 | epot = -22.0321747353183 | etot = -17.7113349551904 +75000 ekin = 2.14414193832402 | erot = 1.98187999045808 | epot = -22.016729180432 | etot = -17.8907072516499 +76000 ekin = 2.24692887257273 | erot = 1.89718749935317 | epot = -21.9954563023384 | etot = -17.8513399304125 +77000 ekin = 2.23929641773363 | erot = 1.79331586377885 | epot = -21.9651666845263 | etot = -17.9325544030138 +78000 ekin = 2.25131896609576 | erot = 1.81371170007281 | epot = -21.9326569846906 | etot = -17.867626318522 +79000 ekin = 2.27306161178815 | erot = 1.71185434931877 | epot = -21.8897569865356 | etot = -17.9048410254286 +80000 ekin = 2.39399894443316 | erot = 1.35732464587509 | epot = -21.8616153060319 | etot = -18.1102917157236 +81000 ekin = 2.47373459732179 | erot = 1.54787737363669 | epot = -21.8542089705402 | etot = -17.8325969995817 +82000 ekin = 2.47280496509126 | erot = 1.57756404285385 | epot = -21.8821357876168 | etot = -17.8317667796717 +83000 ekin = 2.48717741782569 | erot = 1.71069094857344 | epot = -21.9195089096536 | etot = -17.7216405432544 +84000 ekin = 2.44796638425883 | erot = 2.01404972344725 | epot = -21.9668916260736 | etot = -17.5048755183675 +85000 ekin = 2.39574083195474 | erot = 2.32413660190237 | epot = -22.0180542299228 | etot = -17.2981767960657 +86000 ekin = 2.48782292320372 | erot = 1.96978488305041 | epot = -22.0725803391445 | etot = -17.6149725328904 +87000 ekin = 2.57930151405763 | erot = 2.25709021389148 | epot = -22.1348945159439 | etot = -17.2985027879948 +88000 ekin = 2.69560248974116 | erot = 2.13715554675384 | epot = -22.1930571194781 | etot = -17.3602990829831 +89000 ekin = 2.72380030029138 | erot = 2.11665976738327 | epot = -22.2588492472982 | etot = -17.4183891796236 +90000 ekin = 2.77758204434581 | erot = 2.30871679266152 | epot = -22.3316634662031 | etot = -17.2453646291958 +91000 ekin = 2.78121426761668 | erot = 2.06238861884246 | epot = -22.3950019314359 | etot = -17.5513990449768 +92000 ekin = 2.82075935404347 | erot = 2.27555189363852 | epot = -22.4458982217014 | etot = -17.3495869740194 +93000 ekin = 2.74234324408907 | erot = 2.73218737047997 | epot = -22.4777668035592 | etot = -17.0032361889902 +94000 ekin = 2.70595529611238 | erot = 2.82191939458418 | epot = -22.4719589759705 | etot = -16.944084285274 +95000 ekin = 2.60066897821245 | erot = 2.87810504187076 | epot = -22.4346047957432 | etot = -16.95583077566 +96000 ekin = 2.62624076118218 | erot = 3.1451658917906 | epot = -22.3619497140361 | etot = -16.5905430610633 +97000 ekin = 2.53528413246974 | erot = 2.79030318337088 | epot = -22.2496930254015 | etot = -16.9241057095608 +98000 ekin = 2.63666210187964 | erot = 2.76857448865095 | epot = -22.149163040074 | etot = -16.7439264495434 +99000 ekin = 2.65483668512625 | erot = 2.78595031296346 | epot = -22.0460055113192 | etot = -16.6052185132295 +100000 ekin = 2.61516760613041 | erot = 2.20131962587004 | epot = -21.9508073892686 | etot = -17.1343201572682 +101000 ekin = 2.54624393295478 | erot = 2.36995664901277 | epot = -21.874080469839 | etot = -16.9578798878715 +102000 ekin = 2.51242302732691 | erot = 2.61025478737434 | epot = -21.821356011813 | etot = -16.6986781971117 +103000 ekin = 2.47093986976506 | erot = 2.46981056153037 | epot = -21.79403310556 | etot = -16.8532826742646 +104000 ekin = 2.46347963016625 | erot = 2.4900807375805 | epot = -21.7873646863929 | etot = -16.8338043186462 +105000 ekin = 2.3862533318021 | erot = 2.6233826819291 | epot = -21.7895340190365 | etot = -16.7798980053053 +106000 ekin = 2.31544255190003 | erot = 2.76529048503058 | epot = -21.7908248307261 | etot = -16.7100917937954 +107000 ekin = 2.35684717555668 | erot = 2.65933844478903 | epot = -21.7713781480756 | etot = -16.7551925277298 +108000 ekin = 2.29901143856413 | erot = 2.67802590245662 | epot = -21.731145444531 | etot = -16.7541081035102 +109000 ekin = 2.32828462660089 | erot = 2.93774189015161 | epot = -21.6703154087737 | etot = -16.4042888920212 +110000 ekin = 2.27463751555908 | erot = 2.84342022670562 | epot = -21.586603103015 | etot = -16.4685453607503 +111000 ekin = 2.1773579490944 | erot = 2.5067816826673 | epot = -21.4648745015602 | etot = -16.7807348697985 +112000 ekin = 2.18549959507201 | erot = 2.55181336139712 | epot = -21.2989895507538 | etot = -16.5616765942846 +113000 ekin = 2.17304263256836 | erot = 2.34739205656804 | epot = -21.1119565159274 | etot = -16.591521826791 +114000 ekin = 2.12510806931591 | erot = 2.37674761233514 | epot = -20.9271632839065 | etot = -16.4253076022555 +115000 ekin = 2.06139325414462 | erot = 2.59024149702718 | epot = -20.7601756973165 | etot = -16.1085409461447 +116000 ekin = 2.00592136714093 | erot = 2.63732939337329 | epot = -20.6295174385157 | etot = -15.9862666780015 +117000 ekin = 2.00329160062505 | erot = 2.56870813228612 | epot = -20.5296446810239 | etot = -15.9576449481127 +118000 ekin = 2.01742809755797 | erot = 2.469445062841 | epot = -20.4506063861922 | etot = -15.9637332257932 +119000 ekin = 1.98594704489151 | erot = 2.26746616716462 | epot = -20.4288828122727 | etot = -16.1754696002165 +120000 ekin = 1.94483011509439 | erot = 2.33696205000848 | epot = -20.4423833948786 | etot = -16.1605912297757 +121000 ekin = 2.12792735290839 | erot = 2.36924962566047 | epot = -20.4991944142889 | etot = -16.0020174357201 +122000 ekin = 2.10495427089311 | erot = 2.48776527931775 | epot = -20.5743254155956 | etot = -15.9816058653848 +123000 ekin = 2.17541547748968 | erot = 2.84180455684321 | epot = -20.6672573168904 | etot = -15.6500372825575 +124000 ekin = 2.1958532357068 | erot = 2.8121953989093 | epot = -20.7617372386156 | etot = -15.7536886039995 +125000 ekin = 2.23956101001647 | erot = 2.84608901602509 | epot = -20.8364418009789 | etot = -15.7507917749374 +126000 ekin = 2.29874303635711 | erot = 3.12890547205367 | epot = -20.8639002292412 | etot = -15.4362517208304 +127000 ekin = 2.34552442074452 | erot = 2.96762996381655 | epot = -20.8482814122637 | etot = -15.5351270277026 +128000 ekin = 2.38042396339137 | erot = 2.39829809100053 | epot = -20.7821422786063 | etot = -16.0034202242144 +129000 ekin = 2.38818705381736 | erot = 2.14510497375848 | epot = -20.7080443781178 | etot = -16.174752350542 +130000 ekin = 2.27293411796485 | erot = 2.06717107329833 | epot = -20.6807223801437 | etot = -16.3406171888805 +131000 ekin = 2.28550173826509 | erot = 1.94055567970244 | epot = -20.6369898880997 | etot = -16.4109324701322 +132000 ekin = 2.26691955879916 | erot = 1.7185353165747 | epot = -20.5775405075239 | etot = -16.59208563215 +133000 ekin = 2.29137866879746 | erot = 1.62868472043511 | epot = -20.5420933212006 | etot = -16.622029931968 +134000 ekin = 2.25290206497444 | erot = 1.68278061233808 | epot = -20.518309736376 | etot = -16.5826270590635 +135000 ekin = 2.14285941072852 | erot = 1.86118396103702 | epot = -20.5054969500187 | etot = -16.5014535782532 +136000 ekin = 2.12990199371937 | erot = 2.0435912460087 | epot = -20.5201047968038 | etot = -16.3466115570758 +137000 ekin = 2.07754853855318 | erot = 1.83088096227382 | epot = -20.5722472452262 | etot = -16.6638177443992 +138000 ekin = 2.15013934154991 | erot = 2.00941220949274 | epot = -20.6677795604911 | etot = -16.5082280094485 +139000 ekin = 2.20517582266495 | erot = 1.94652682269836 | epot = -20.7931525252623 | etot = -16.641449879899 +140000 ekin = 2.33731236767263 | erot = 1.96166026745084 | epot = -20.931086877455 | etot = -16.6321142423315 +141000 ekin = 2.24448516285996 | erot = 2.27879036592838 | epot = -21.0648426319456 | etot = -16.5415671031572 +142000 ekin = 2.19315323753824 | erot = 2.32670116857762 | epot = -21.1877747983341 | etot = -16.6679203922183 +143000 ekin = 2.15154828396331 | erot = 2.38826183428094 | epot = -21.313728726892 | etot = -16.7739186086477 +144000 ekin = 2.10225107667117 | erot = 2.4032470972608 | epot = -21.4354683955926 | etot = -16.9299702216606 +145000 ekin = 2.06221666396515 | erot = 2.32981540966426 | epot = -21.5580653796757 | etot = -17.1660333060463 +146000 ekin = 2.15268481715568 | erot = 2.24715096803357 | epot = -21.6452484907075 | etot = -17.2454127055182 +147000 ekin = 2.13045113501535 | erot = 2.24956262085637 | epot = -21.724100810277 | etot = -17.3440870544053 +148000 ekin = 2.14237927540745 | erot = 2.32388813542669 | epot = -21.8239853334793 | etot = -17.3577179226451 +149000 ekin = 2.13016451804412 | erot = 2.31003298264322 | epot = -21.9413859720017 | etot = -17.5011884713144 +150000 ekin = 2.11189415929176 | erot = 2.27040882248852 | epot = -22.0736176258279 | etot = -17.6913146440477 +151000 ekin = 2.08490791036349 | erot = 2.53796433942563 | epot = -22.1831326518405 | etot = -17.5602604020514 +152000 ekin = 2.05056796581082 | erot = 2.74378211496589 | epot = -22.270737007316 | etot = -17.4763869265393 +153000 ekin = 2.01058950481921 | erot = 2.62970741316335 | epot = -22.3376436760764 | etot = -17.6973467580938 +154000 ekin = 2.01943769577485 | erot = 2.39009828792402 | epot = -22.4001638198036 | etot = -17.9906278361048 +155000 ekin = 2.05430763784557 | erot = 2.40978970203085 | epot = -22.4403746514588 | etot = -17.9762773115824 +156000 ekin = 2.10246203476585 | erot = 2.31628625090994 | epot = -22.394749627823 | etot = -17.9760013421472 +157000 ekin = 2.20121785931646 | erot = 2.26047844907502 | epot = -22.3626746382072 | etot = -17.9009783298157 +158000 ekin = 2.16806247020234 | erot = 2.01859116115329 | epot = -22.3794788142261 | etot = -18.1928251828704 +159000 ekin = 2.20647608921308 | erot = 2.03708981782409 | epot = -22.3933404563958 | etot = -18.1497745493587 +160000 ekin = 2.28482979303704 | erot = 2.066722957277 | epot = -22.3929715093607 | etot = -18.0414187590467 +161000 ekin = 2.3540844152636 | erot = 2.11425691782641 | epot = -22.3845712470916 | etot = -17.9162299140016 +162000 ekin = 2.44383531112357 | erot = 2.0514217263269 | epot = -22.3873594705053 | etot = -17.8921024330549 +163000 ekin = 2.38397054654223 | erot = 2.18088509829515 | epot = -22.40469289024 | etot = -17.8398372454027 +164000 ekin = 2.36323785475508 | erot = 2.24099333696004 | epot = -22.4304254420049 | etot = -17.8261942502898 +165000 ekin = 2.42861068657717 | erot = 2.32334175306815 | epot = -22.4693846686273 | etot = -17.717432228982 +166000 ekin = 2.49646527013115 | erot = 2.76008268343012 | epot = -22.5024150074812 | etot = -17.2458670539199 +167000 ekin = 2.39742733231171 | erot = 2.66606455445543 | epot = -22.5059226951214 | etot = -17.4424308083543 +168000 ekin = 2.48222864422392 | erot = 2.12985047091145 | epot = -22.4839259607868 | etot = -17.8718468456514 +169000 ekin = 2.34389140284733 | erot = 2.23877784986576 | epot = -22.4355001459225 | etot = -17.8528308932094 +170000 ekin = 2.27819176115945 | erot = 2.38937348011867 | epot = -22.3963232925856 | etot = -17.7287580513075 +171000 ekin = 2.26183375697861 | erot = 2.66308813167602 | epot = -22.3493672389156 | etot = -17.4244453502609 +172000 ekin = 2.27023963981114 | erot = 2.54732213285246 | epot = -22.2868682454191 | etot = -17.4693064727555 +173000 ekin = 2.19713801069003 | erot = 2.39492663110728 | epot = -22.2067306662318 | etot = -17.6146660244345 +174000 ekin = 2.08128149693204 | erot = 2.65361881164583 | epot = -22.1239183165144 | etot = -17.3890180079365 +175000 ekin = 2.03179136441166 | erot = 2.65769159317987 | epot = -22.0831649919726 | etot = -17.3936820343811 +176000 ekin = 1.92235220335471 | erot = 2.46758244642915 | epot = -22.0704760764065 | etot = -17.6805414266226 +177000 ekin = 1.87676295332749 | erot = 2.76485058121257 | epot = -22.0943278887429 | etot = -17.4527143542029 +178000 ekin = 1.8196851112204 | erot = 3.06889049439809 | epot = -22.1713258315081 | etot = -17.2827502258896 +179000 ekin = 1.8323945353073 | erot = 2.97256669493282 | epot = -22.3031073057819 | etot = -17.4981460755418 +180000 ekin = 1.7862108322255 | erot = 3.29401414659433 | epot = -22.4701387604057 | etot = -17.3899137815859 +181000 ekin = 1.88518185298461 | erot = 3.13321574647634 | epot = -22.6327591209889 | etot = -17.614361521528 +182000 ekin = 1.91900100882685 | erot = 2.86862183641669 | epot = -22.7815951170127 | etot = -17.9939722717692 +183000 ekin = 2.05132570727835 | erot = 3.08267197262661 | epot = -22.9092206864366 | etot = -17.7752230065317 +184000 ekin = 2.06184088528513 | erot = 3.2007444069869 | epot = -23.026874061216 | etot = -17.764288768944 +185000 ekin = 2.09012289683652 | erot = 3.47009431072618 | epot = -23.1337090395151 | etot = -17.5734918319524 +186000 ekin = 2.23866301207357 | erot = 3.60859469886113 | epot = -23.1738137395736 | etot = -17.3265560286389 +187000 ekin = 2.42181473602157 | erot = 3.85086245359642 | epot = -23.1972395336004 | etot = -16.9245623439824 +188000 ekin = 2.41473791720851 | erot = 4.13943673363425 | epot = -23.3136601494469 | etot = -16.7594854986041 +189000 ekin = 2.40456237424771 | erot = 4.00070701501254 | epot = -23.3710796524501 | etot = -16.9658102631899 +190000 ekin = 2.39275066416795 | erot = 3.65894410977818 | epot = -23.3540165218531 | etot = -17.302321747907 +191000 ekin = 2.40766626916768 | erot = 4.27535474629226 | epot = -23.2939306874287 | etot = -16.6109096719687 +192000 ekin = 2.38476057345238 | erot = 4.12521169410233 | epot = -23.192209272554 | etot = -16.6822370049993 +193000 ekin = 2.26302104637805 | erot = 3.77794026184495 | epot = -23.0633113366603 | etot = -17.0223500284373 +194000 ekin = 2.10155057993348 | erot = 3.49922681191469 | epot = -22.9254751366501 | etot = -17.3246977448019 +195000 ekin = 2.03962481718059 | erot = 3.2525960289961 | epot = -22.7698073537311 | etot = -17.4775865075544 +196000 ekin = 2.06049369787793 | erot = 2.84778946059541 | epot = -22.5997694102264 | etot = -17.6914862517531 +197000 ekin = 2.03160567713315 | erot = 2.3737082845698 | epot = -22.4368418077992 | etot = -18.0315278460962 +198000 ekin = 2.08676704026165 | erot = 2.194825314428 | epot = -22.262282374821 | etot = -17.9806900201313 +199000 ekin = 2.05269408710196 | erot = 2.16400413646385 | epot = -22.1035002649821 | etot = -17.8868020414163 +200000 ekin = 2.01411832170952 | erot = 2.38698541496904 | epot = -21.9546297375273 | etot = -17.5535260008487 +201000 ekin = 2.01209192808751 | erot = 2.38205260132393 | epot = -21.8390879180561 | etot = -17.4449433886447 +202000 ekin = 1.90781796628429 | erot = 2.36530018659066 | epot = -21.7246902929987 | etot = -17.4515721401238 +203000 ekin = 1.80024846565405 | erot = 2.34259351313114 | epot = -21.6159774827442 | etot = -17.473135503959 +204000 ekin = 1.68484818472337 | erot = 2.41487740212517 | epot = -21.5446736069976 | etot = -17.4449480201491 +205000 ekin = 1.62792813458292 | erot = 2.51982872964279 | epot = -21.5011323457792 | etot = -17.3533754815535 +206000 ekin = 1.5541106497836 | erot = 2.69683235574068 | epot = -21.4677288967242 | etot = -17.2167858911999 +207000 ekin = 1.51044177325205 | erot = 2.86067615909032 | epot = -21.441622367489 | etot = -17.0705044351466 +208000 ekin = 1.46178623775167 | erot = 3.09687215817324 | epot = -21.3952301582475 | etot = -16.8365717623226 +209000 ekin = 1.49930719102405 | erot = 2.64986686100826 | epot = -21.3194384463854 | etot = -17.1702643943531 +210000 ekin = 1.48596643994184 | erot = 2.49507203528878 | epot = -21.2123168093856 | etot = -17.231278334155 +211000 ekin = 1.51700235708599 | erot = 2.8598249058151 | epot = -21.0854390229478 | etot = -16.7086117600467 +212000 ekin = 1.4769987196861 | erot = 2.51260914037795 | epot = -20.9565961085738 | etot = -16.9669882485097 +213000 ekin = 1.58916579351318 | erot = 2.6166112188408 | epot = -20.8229216474678 | etot = -16.6171446351139 +214000 ekin = 1.62272322843375 | erot = 2.4227328031145 | epot = -20.7122766474857 | etot = -16.6668206159375 +215000 ekin = 1.66159030501753 | erot = 2.39943071607585 | epot = -20.6287014799335 | etot = -16.5676804588401 +216000 ekin = 1.74578478011186 | erot = 2.33284367785394 | epot = -20.5774611193671 | etot = -16.4988326614013 +217000 ekin = 1.86008672447751 | erot = 2.48365359198229 | epot = -20.5783803604758 | etot = -16.234640044016 +218000 ekin = 1.8869320617951 | erot = 2.6181764126077 | epot = -20.6245681941581 | etot = -16.1194597197553 +219000 ekin = 1.99545846855293 | erot = 2.51280586705981 | epot = -20.6722755262305 | etot = -16.1640111906177 +220000 ekin = 2.07891649227179 | erot = 2.43958393551873 | epot = -20.7460641755863 | etot = -16.2275637477958 +221000 ekin = 2.07405609075884 | erot = 2.36260767845185 | epot = -20.8472863845647 | etot = -16.410622615354 +222000 ekin = 2.10307745764193 | erot = 2.54950611704615 | epot = -20.9726401140735 | etot = -16.3200565393854 +223000 ekin = 2.02990560702866 | erot = 2.36445779587678 | epot = -21.0835627182507 | etot = -16.6891993153453 +224000 ekin = 2.16888148730441 | erot = 2.48643165117696 | epot = -21.1978785829808 | etot = -16.5425654444994 +225000 ekin = 2.30521694661663 | erot = 2.40413284955322 | epot = -21.3143167094639 | etot = -16.604966913294 +226000 ekin = 2.42660104949002 | erot = 2.10961133192976 | epot = -21.4003288303493 | etot = -16.8641164489295 +227000 ekin = 2.51989265457919 | erot = 2.19538124871698 | epot = -21.4710250786465 | etot = -16.7557511753503 +228000 ekin = 2.68551344341405 | erot = 2.30229521160068 | epot = -21.5296149017979 | etot = -16.5418062467832 +229000 ekin = 2.59976522820191 | erot = 2.51681087235226 | epot = -21.5666762700903 | etot = -16.4501001695361 +230000 ekin = 2.58503359291809 | erot = 2.17214995252273 | epot = -21.5872332974481 | etot = -16.8300497520073 +231000 ekin = 2.62353866357513 | erot = 2.17431567394794 | epot = -21.5820516856057 | etot = -16.7841973480826 +232000 ekin = 2.59120478967395 | erot = 2.3400691279725 | epot = -21.567210238379 | etot = -16.6359363207325 +233000 ekin = 2.51791287332684 | erot = 2.16488342987894 | epot = -21.5519147308628 | etot = -16.869118427657 +234000 ekin = 2.48481380355981 | erot = 2.21816982784484 | epot = -21.5223665657166 | etot = -16.8193829343119 +235000 ekin = 2.41086403910156 | erot = 2.10316509959359 | epot = -21.4789613614541 | etot = -16.9649322227589 +236000 ekin = 2.40928284749447 | erot = 1.88888489131684 | epot = -21.4361120637084 | etot = -17.137944324897 +237000 ekin = 2.5630156400106 | erot = 1.7367156365967 | epot = -21.4280913003547 | etot = -17.1283600237474 +238000 ekin = 2.55765653830761 | erot = 1.9091407981951 | epot = -21.4255674324868 | etot = -16.9587700959841 +239000 ekin = 2.62181377631216 | erot = 2.06765286499141 | epot = -21.4529783008629 | etot = -16.7635116595593 +240000 ekin = 2.64076354676114 | erot = 2.31865643186815 | epot = -21.5224999667007 | etot = -16.5630799880714 +241000 ekin = 2.67609348690634 | erot = 2.52623661982357 | epot = -21.6079626104589 | etot = -16.405632503729 +242000 ekin = 2.6355810936148 | erot = 2.91329495494516 | epot = -21.6817125781001 | etot = -16.1328365295402 +243000 ekin = 2.76874739439922 | erot = 3.19547631893862 | epot = -21.7299185420903 | etot = -15.7656948287524 +244000 ekin = 2.76082392607162 | erot = 2.99738855544011 | epot = -21.7654799309604 | etot = -16.0072674494486 +245000 ekin = 2.84856552527555 | erot = 3.55610399773012 | epot = -21.7868813066435 | etot = -15.3822117836379 +246000 ekin = 2.74592112218097 | erot = 3.46897250198827 | epot = -21.7812302083599 | etot = -15.5663365841907 +247000 ekin = 2.62843885877444 | erot = 3.39159127928965 | epot = -21.7507462517777 | etot = -15.7307161137136 +248000 ekin = 2.62657990237121 | erot = 2.96254281821258 | epot = -21.6850863371036 | etot = -16.0959636165198 +249000 ekin = 2.64689987490177 | erot = 2.46750058971842 | epot = -21.6214034121613 | etot = -16.5070029475411 +250000 ekin = 2.59258413901045 | erot = 1.95894591185236 | epot = -21.5523796219696 | etot = -17.0008495711068 +251000 ekin = 2.50508525922234 | erot = 1.94700044531522 | epot = -21.4856406393062 | etot = -17.0335549347686 +252000 ekin = 2.36206141186087 | erot = 2.03422118114506 | epot = -21.4223545940682 | etot = -17.0260720010623 +253000 ekin = 2.30935060528389 | erot = 1.94736645762203 | epot = -21.3716222045376 | etot = -17.1149051416316 +254000 ekin = 2.25274596934999 | erot = 1.98706179687154 | epot = -21.3578828633466 | etot = -17.1180750971251 +255000 ekin = 2.24877704371079 | erot = 1.94793350141006 | epot = -21.3679438916481 | etot = -17.1712333465272 +256000 ekin = 2.15038460246949 | erot = 2.13536641645852 | epot = -21.3873823966766 | etot = -17.1016313777486 +257000 ekin = 2.14820686493285 | erot = 1.95792063838262 | epot = -21.401629803036 | etot = -17.2955022997205 +258000 ekin = 2.21551042205349 | erot = 2.08286212737981 | epot = -21.4265487793699 | etot = -17.1281762299366 +259000 ekin = 2.06173733154787 | erot = 1.93722502209152 | epot = -21.4284901665386 | etot = -17.4295278128993 +260000 ekin = 1.9577918439207 | erot = 2.10071945094404 | epot = -21.4431554356543 | etot = -17.3846441407896 +261000 ekin = 1.8911187304064 | erot = 2.27491420373971 | epot = -21.4742539366704 | etot = -17.3082210025243 +262000 ekin = 1.81155628887096 | erot = 2.76845022524661 | epot = -21.5133565631458 | etot = -16.9333500490283 +263000 ekin = 1.78548461411777 | erot = 2.58995272844153 | epot = -21.5741933378567 | etot = -17.1987559952974 +264000 ekin = 1.70470903910486 | erot = 2.5274072213014 | epot = -21.6543975630333 | etot = -17.4222813026271 +265000 ekin = 1.70456921180777 | erot = 2.91128169616597 | epot = -21.7314640373147 | etot = -17.1156131293409 +266000 ekin = 1.70108763348248 | erot = 3.15353043902158 | epot = -21.8059636436343 | etot = -16.9513455711302 +267000 ekin = 1.68792919988866 | erot = 2.90455900057167 | epot = -21.8707326483041 | etot = -17.2782444478438 +268000 ekin = 1.72057453763242 | erot = 2.62604659087858 | epot = -21.9225381178384 | etot = -17.5759169893274 +269000 ekin = 1.78712640141421 | erot = 2.75599254857452 | epot = -21.9527991628362 | etot = -17.4096802128475 +270000 ekin = 1.72857790804082 | erot = 2.80083154386424 | epot = -21.9488059520794 | etot = -17.4193965001743 +271000 ekin = 1.640994287753 | erot = 2.64687538276781 | epot = -21.9170243489263 | etot = -17.6291546784055 +272000 ekin = 1.58570258321566 | erot = 2.46968320121799 | epot = -21.8446210346507 | etot = -17.7892352502171 +273000 ekin = 1.63767201216311 | erot = 2.19946786706654 | epot = -21.763892987694 | etot = -17.9267531084644 +274000 ekin = 1.59847478128864 | erot = 2.30908990938624 | epot = -21.6682431397428 | etot = -17.760678449068 +275000 ekin = 1.48392569489375 | erot = 2.19949617068957 | epot = -21.5548162861331 | etot = -17.8713944205498 +276000 ekin = 1.39307584924626 | erot = 2.2303953843847 | epot = -21.4256702629284 | etot = -17.8021990292975 +277000 ekin = 1.32228191847657 | erot = 2.1398360682965 | epot = -21.3067538507251 | etot = -17.844635863952 +278000 ekin = 1.28711477346585 | erot = 2.14456329557354 | epot = -21.2240782746279 | etot = -17.7924002055885 +279000 ekin = 1.28936005013421 | erot = 2.38491555516955 | epot = -21.1735485476929 | etot = -17.4992729423892 +280000 ekin = 1.21003074239687 | erot = 2.42890760862485 | epot = -21.1457609661738 | etot = -17.506822615152 +281000 ekin = 1.29885744861012 | erot = 2.42325573855925 | epot = -21.1507776171849 | etot = -17.4286644300155 +282000 ekin = 1.25436778972229 | erot = 2.81925761990967 | epot = -21.1898482264 | etot = -17.1162228167681 +283000 ekin = 1.21194774091207 | erot = 2.81987884081121 | epot = -21.2915251292644 | etot = -17.2596985475411 +284000 ekin = 1.18679083068162 | erot = 2.85260842120881 | epot = -21.4111056079338 | etot = -17.3717063560434 +285000 ekin = 1.15631267773655 | erot = 2.90112491489691 | epot = -21.5215297070963 | etot = -17.4640921144628 +286000 ekin = 1.19279268222577 | erot = 2.85809873900115 | epot = -21.6217291121406 | etot = -17.5708376909137 +287000 ekin = 1.26041360220403 | erot = 2.73020556183284 | epot = -21.6926219129292 | etot = -17.7020027488923 +288000 ekin = 1.28925684516268 | erot = 2.41344019790327 | epot = -21.7395791395394 | etot = -18.0368820964735 +289000 ekin = 1.32958093505198 | erot = 2.27197004074864 | epot = -21.7753244471437 | etot = -18.1737734713431 +290000 ekin = 1.4064267584832 | erot = 1.9557060070415 | epot = -21.8122371335501 | etot = -18.4501043680254 +291000 ekin = 1.43917988615065 | erot = 1.90335102621722 | epot = -21.8672634472313 | etot = -18.5247325348634 +292000 ekin = 1.45457728536597 | erot = 1.91918018244106 | epot = -21.9211778027209 | etot = -18.5474203349139 +293000 ekin = 1.54025708206028 | erot = 1.76739883625601 | epot = -21.9892221465386 | etot = -18.6815662282223 +294000 ekin = 1.63446508682282 | erot = 1.8633883579886 | epot = -22.060866674135 | etot = -18.5630132293236 +295000 ekin = 1.81613674682328 | erot = 1.90284694723315 | epot = -22.1395305108089 | etot = -18.4205468167524 +296000 ekin = 1.90988071284999 | erot = 2.10518814801486 | epot = -22.2099314509302 | etot = -18.1948625900654 +297000 ekin = 1.95608798955025 | erot = 2.5270244388381 | epot = -22.2985651779531 | etot = -17.8154527495648 +298000 ekin = 2.05852737833121 | erot = 2.3890567546875 | epot = -22.3766545803973 | etot = -17.9290704473786 +299000 ekin = 2.18644111379027 | erot = 2.43787113082706 | epot = -22.4274426042906 | etot = -17.8031303596732 +300000 ekin = 2.25246210387413 | erot = 2.26714642530529 | epot = -22.4460120088432 | etot = -17.9264034796638 +301000 ekin = 2.35563337457469 | erot = 1.81807021650501 | epot = -22.457254571189 | etot = -18.2835509801093 +302000 ekin = 2.42168935052551 | erot = 2.12272372548244 | epot = -22.4773288548023 | etot = -17.9329157787943 +303000 ekin = 2.48491149619597 | erot = 1.80440720027877 | epot = -22.4997870994201 | etot = -18.2104684029453 +304000 ekin = 2.57055300825388 | erot = 1.71612576379001 | epot = -22.5136290909673 | etot = -18.2269503189234 +305000 ekin = 2.60127252345939 | erot = 1.60228999221245 | epot = -22.5079813416076 | etot = -18.3044188259357 +306000 ekin = 2.65871790294464 | erot = 1.61152940110762 | epot = -22.4881104545321 | etot = -18.2178631504798 +307000 ekin = 2.67302778478941 | erot = 1.8830323642031 | epot = -22.4558851508275 | etot = -17.899825001835 +308000 ekin = 2.66315429067323 | erot = 2.10086190187504 | epot = -22.4194774636685 | etot = -17.6554612711202 +309000 ekin = 2.6236123571105 | erot = 2.06716291649117 | epot = -22.3854389472788 | etot = -17.6946636736772 +310000 ekin = 2.65346557302719 | erot = 2.43388315560371 | epot = -22.3516578015447 | etot = -17.2643090729138 +311000 ekin = 2.62717610811363 | erot = 2.36697019339695 | epot = -22.3173746471547 | etot = -17.3232283456441 +312000 ekin = 2.76485058199114 | erot = 2.29893166031334 | epot = -22.3073398967793 | etot = -17.2435576544748 +313000 ekin = 2.91401216196316 | erot = 2.42859802814659 | epot = -22.2874024124533 | etot = -16.9447922223436 +314000 ekin = 2.91385799167526 | erot = 1.91396248978007 | epot = -22.2694749773677 | etot = -17.4416544959123 +315000 ekin = 2.93036873457078 | erot = 1.9971654878202 | epot = -22.2742890679514 | etot = -17.3467548455604 +316000 ekin = 3.03268788685593 | erot = 1.92510083916609 | epot = -22.2577485073755 | etot = -17.2999597813535 +317000 ekin = 3.08787594847642 | erot = 1.92578200831372 | epot = -22.2266829567099 | etot = -17.2130249999198 +318000 ekin = 3.13577891188629 | erot = 1.80317853500192 | epot = -22.1919523893648 | etot = -17.2529949424766 +319000 ekin = 3.20520648794486 | erot = 1.70269113516987 | epot = -22.1746193500527 | etot = -17.266721726938 +320000 ekin = 3.29702074479459 | erot = 1.53157782235333 | epot = -22.1625795722849 | etot = -17.3339810051369 +321000 ekin = 3.34504448422807 | erot = 1.62378232552192 | epot = -22.1868841736047 | etot = -17.2180573638547 +322000 ekin = 3.3846016882297 | erot = 1.76562508880768 | epot = -22.2499937572737 | etot = -17.0997669802364 +323000 ekin = 3.30048690012851 | erot = 1.7892216286022 | epot = -22.3245621231126 | etot = -17.2348535943819 +324000 ekin = 3.21996003388849 | erot = 2.07375779111672 | epot = -22.4074947135768 | etot = -17.1137768885716 +325000 ekin = 3.19320065846481 | erot = 2.34417123194123 | epot = -22.4895925051922 | etot = -16.9522206147861 +326000 ekin = 3.13574523293127 | erot = 2.35602865246342 | epot = -22.5449076606478 | etot = -17.0531337752531 +327000 ekin = 3.06250064041735 | erot = 2.56089976464128 | epot = -22.5763641985367 | etot = -16.952963793478 +328000 ekin = 2.98028960475484 | erot = 2.43252122765912 | epot = -22.5713698367084 | etot = -17.1585590042945 +329000 ekin = 3.00073413437882 | erot = 2.54697247273632 | epot = -22.5115486252435 | etot = -16.9638420181284 +330000 ekin = 2.95148018624175 | erot = 2.24389127882674 | epot = -22.4149230401772 | etot = -17.2195515751087 +331000 ekin = 2.81139520815998 | erot = 2.33469163507243 | epot = -22.3023815971863 | etot = -17.1562947539539 +332000 ekin = 2.70201927753227 | erot = 2.23446425932909 | epot = -22.1825698377624 | etot = -17.246086300901 +333000 ekin = 2.67216560815668 | erot = 2.33828838842038 | epot = -22.1081794049507 | etot = -17.0977254083736 +334000 ekin = 2.63564129688349 | erot = 2.38445162200811 | epot = -22.0521006108917 | etot = -17.0320076920001 +335000 ekin = 2.49363748710295 | erot = 2.399272024096 | epot = -21.9997553908813 | etot = -17.1068458796824 +336000 ekin = 2.32703156354334 | erot = 2.49661552302102 | epot = -21.9570264750566 | etot = -17.1333793884923 +337000 ekin = 2.4043791118503 | erot = 2.3478794486252 | epot = -21.9196555873367 | etot = -17.1673970268612 +338000 ekin = 2.41476505798853 | erot = 2.13162500253268 | epot = -21.8968278484038 | etot = -17.3504377878825 +339000 ekin = 2.43793058775615 | erot = 2.41901135922118 | epot = -21.9036252678023 | etot = -17.046683320825 +340000 ekin = 2.49068476405748 | erot = 2.44754202713575 | epot = -21.9103500540913 | etot = -16.9721232628981 +341000 ekin = 2.50472420190452 | erot = 2.6706403885761 | epot = -21.9332795205212 | etot = -16.7579149300406 +342000 ekin = 2.56647086804807 | erot = 2.61525528001598 | epot = -21.9674734299045 | etot = -16.7857472818405 +343000 ekin = 2.51904673868546 | erot = 2.5567658847258 | epot = -21.9948706708333 | etot = -16.919058047422 +344000 ekin = 2.60508290174655 | erot = 2.48137560215981 | epot = -21.9825601130742 | etot = -16.8961016091679 +345000 ekin = 2.63784673980694 | erot = 2.00206586549284 | epot = -21.9580088648428 | etot = -17.318096259543 +346000 ekin = 2.6239789191155 | erot = 2.06342882396958 | epot = -21.9497310194664 | etot = -17.2623232763813 +347000 ekin = 2.65803154655906 | erot = 2.17320914690807 | epot = -21.9288714180667 | etot = -17.0976307245996 +348000 ekin = 2.61080877072533 | erot = 2.24900638089747 | epot = -21.9064648355579 | etot = -17.0466496839351 +349000 ekin = 2.56285615073627 | erot = 2.1937399371138 | epot = -21.9340203469074 | etot = -17.1774242590573 +350000 ekin = 2.52909341929248 | erot = 2.40459665484329 | epot = -21.9698973375557 | etot = -17.0362072634199 +351000 ekin = 2.49713504985968 | erot = 2.44402722640792 | epot = -22.0050349016585 | etot = -17.0638726253909 +352000 ekin = 2.44000815118255 | erot = 2.31901759386448 | epot = -22.0353401663222 | etot = -17.2763144212752 +353000 ekin = 2.43137304156558 | erot = 2.58293559904035 | epot = -22.0473314992666 | etot = -17.0330228586607 +354000 ekin = 2.42872461457106 | erot = 2.20097693718212 | epot = -22.0593257242363 | etot = -17.4296241724831 +355000 ekin = 2.33110822210722 | erot = 2.42063070966282 | epot = -22.0716103668381 | etot = -17.3198714350681 +356000 ekin = 2.3039890517441 | erot = 2.62795866448669 | epot = -22.080434759213 | etot = -17.1484870429822 +357000 ekin = 2.31942397068985 | erot = 2.59655320443803 | epot = -22.0821788434023 | etot = -17.1662016682744 +358000 ekin = 2.31430837414593 | erot = 2.83712652813161 | epot = -22.0725021858678 | etot = -16.9210672835903 +359000 ekin = 2.31455342359143 | erot = 2.75771738371942 | epot = -22.0399086183633 | etot = -16.9676378110525 +360000 ekin = 2.33176210518075 | erot = 2.71178887834453 | epot = -22.0076297483561 | etot = -16.9640787648308 +361000 ekin = 2.27214122387374 | erot = 2.81145339858123 | epot = -21.9599421657392 | etot = -16.8763475432843 +362000 ekin = 2.29940723820844 | erot = 2.47979741361581 | epot = -21.9089639290964 | etot = -17.1297592772721 +363000 ekin = 2.53443578574921 | erot = 2.53169478867003 | epot = -21.8243312678076 | etot = -16.7582006933884 +364000 ekin = 2.6221808903385 | erot = 2.40320793892329 | epot = -21.7324712534028 | etot = -16.707082424141 +365000 ekin = 2.76755808763513 | erot = 1.8947540975541 | epot = -21.6405111096152 | etot = -16.9781989244259 +366000 ekin = 2.83684484493768 | erot = 1.5710285012185 | epot = -21.5686856667024 | etot = -17.1608123205462 +367000 ekin = 2.93599158208369 | erot = 1.35687050095059 | epot = -21.4921061985772 | etot = -17.1992441155429 +368000 ekin = 3.10052552420308 | erot = 1.34392548947254 | epot = -21.4550475057324 | etot = -17.0105964920567 +369000 ekin = 3.32282273578316 | erot = 1.44449669338119 | epot = -21.4696346052349 | etot = -16.7023151760706 +370000 ekin = 3.32440357214618 | erot = 1.32498034754182 | epot = -21.5235244672075 | etot = -16.8741405475195 +371000 ekin = 3.19604825174776 | erot = 1.32912305315216 | epot = -21.6063167417294 | etot = -17.0811454368295 +372000 ekin = 3.24806725016544 | erot = 1.57623327064971 | epot = -21.7023719429116 | etot = -16.8780714220964 +373000 ekin = 3.19541088772603 | erot = 1.59021472687952 | epot = -21.8029802274106 | etot = -17.017354612805 +374000 ekin = 3.26135365290656 | erot = 1.85216595682065 | epot = -21.8950570456544 | etot = -16.7815374359272 +375000 ekin = 3.29383454867952 | erot = 2.06907009365927 | epot = -21.9845454700942 | etot = -16.6216408277554 +376000 ekin = 3.20015592859726 | erot = 2.0735141660112 | epot = -22.0952882395876 | etot = -16.8216181449791 +377000 ekin = 3.09004850922727 | erot = 2.18294615546902 | epot = -22.1887281106778 | etot = -16.9157334459815 +378000 ekin = 3.05043348195272 | erot = 2.5158322509661 | epot = -22.263666143955 | etot = -16.6974004110362 +379000 ekin = 3.1016690882899 | erot = 2.66676931647595 | epot = -22.3392187414395 | etot = -16.5707803366736 +380000 ekin = 3.11503780325994 | erot = 2.60840931269842 | epot = -22.3678930086928 | etot = -16.6444458927345 +381000 ekin = 3.11901255865576 | erot = 2.51316745205276 | epot = -22.3595089455393 | etot = -16.7273289348308 +382000 ekin = 3.08198965968255 | erot = 2.5421648927191 | epot = -22.3171355116317 | etot = -16.6929809592301 +383000 ekin = 3.08529312773613 | erot = 2.60747953716507 | epot = -22.268125758685 | etot = -16.5753530937838 +384000 ekin = 3.06435455473088 | erot = 2.5900830521811 | epot = -22.2008329018472 | etot = -16.5463952949352 +385000 ekin = 2.96902524929805 | erot = 2.39487400705592 | epot = -22.1308203226012 | etot = -16.7669210662472 +386000 ekin = 2.94398257253719 | erot = 2.35624989673771 | epot = -22.097449180614 | etot = -16.7972167113391 +387000 ekin = 2.90022143016868 | erot = 2.26095116124134 | epot = -22.0819030869076 | etot = -16.9207304954976 +388000 ekin = 2.8138912698874 | erot = 2.13357533996898 | epot = -22.1104886391662 | etot = -17.1630220293098 +389000 ekin = 2.86348776127275 | erot = 2.05672668796342 | epot = -22.1951193908387 | etot = -17.2749049416025 +390000 ekin = 2.77165535979993 | erot = 2.15365739500144 | epot = -22.3132389416922 | etot = -17.3879261868909 +391000 ekin = 2.77370479657942 | erot = 2.4364705135603 | epot = -22.4565212308196 | etot = -17.2463459206799 +392000 ekin = 2.76583278927009 | erot = 2.40676865464344 | epot = -22.5818573009823 | etot = -17.4092558570688 +393000 ekin = 2.80900024157666 | erot = 2.37169277236104 | epot = -22.7086594996881 | etot = -17.5279664857504 +394000 ekin = 2.87248081177528 | erot = 2.11617756482181 | epot = -22.817077559155 | etot = -17.8284191825579 +395000 ekin = 2.88095223032725 | erot = 2.05659355426911 | epot = -22.8808764228086 | etot = -17.9433306382122 +396000 ekin = 2.93418192071606 | erot = 2.30478582950603 | epot = -22.909791586559 | etot = -17.6708238363369 +397000 ekin = 2.98163695220519 | erot = 2.0855898498222 | epot = -22.9183417641046 | etot = -17.8511149620772 +398000 ekin = 2.98779262545457 | erot = 2.15192082323126 | epot = -22.9077750506592 | etot = -17.7680616019734 +399000 ekin = 2.9186569326616 | erot = 1.8288713531934 | epot = -22.8818662686362 | etot = -18.1343379827812 +400000 ekin = 2.90983153702367 | erot = 1.84033842076742 | epot = -22.8234620217339 | etot = -18.0732920639428 +401000 ekin = 2.82193337892224 | erot = 1.6578555593453 | epot = -22.7432945990589 | etot = -18.2635056607914 +402000 ekin = 2.71231263059642 | erot = 1.81039261887858 | epot = -22.6593739244624 | etot = -18.1366686749874 +403000 ekin = 2.66036084604537 | erot = 2.02498533176239 | epot = -22.6001656022283 | etot = -17.9148194244206 +404000 ekin = 2.57068790240532 | erot = 1.93095594974712 | epot = -22.5470237392586 | etot = -18.0453798871062 +405000 ekin = 2.56561221793731 | erot = 1.68739793089187 | epot = -22.480605837446 | etot = -18.2275956886168 +406000 ekin = 2.49833625235123 | erot = 1.48188239687454 | epot = -22.4539596863985 | etot = -18.4737410371727 +407000 ekin = 2.49021560270503 | erot = 1.58928602542158 | epot = -22.4700632657781 | etot = -18.3905616376515 +408000 ekin = 2.38021871164252 | erot = 1.73637964468713 | epot = -22.4959988290514 | etot = -18.3794004727217 +409000 ekin = 2.29461436770134 | erot = 1.95814824220593 | epot = -22.5206422995264 | etot = -18.2678796896191 +410000 ekin = 2.25736852989509 | erot = 2.37993089507073 | epot = -22.5486602508665 | etot = -17.9113608259006 +411000 ekin = 2.21596387204284 | erot = 2.74396072623451 | epot = -22.583881506389 | etot = -17.6239569081116 +412000 ekin = 2.20994969108704 | erot = 2.86593591747043 | epot = -22.6211739699294 | etot = -17.5452883613719 +413000 ekin = 2.24794753023264 | erot = 3.00088801127007 | epot = -22.6476708665279 | etot = -17.3988353250252 +414000 ekin = 2.14160819513188 | erot = 3.01120724411838 | epot = -22.6376025284285 | etot = -17.4847870891782 +415000 ekin = 2.14491177835012 | erot = 2.9321520286022 | epot = -22.590258571887 | etot = -17.5131947649346 +416000 ekin = 2.10193769123488 | erot = 2.9810162412694 | epot = -22.5118964710203 | etot = -17.428942538516 +417000 ekin = 2.07066635663257 | erot = 2.60488497680181 | epot = -22.4065047924712 | etot = -17.7309534590368 +418000 ekin = 2.07740574841324 | erot = 2.73315084489172 | epot = -22.2898027885341 | etot = -17.4792461952291 +419000 ekin = 1.98085199943438 | erot = 2.44747426745328 | epot = -22.1631336837142 | etot = -17.7348074168266 +420000 ekin = 1.95880289350343 | erot = 2.55129347690091 | epot = -22.0482798158308 | etot = -17.5381834454264 +421000 ekin = 1.99828966251063 | erot = 2.20799196393452 | epot = -21.939552558565 | etot = -17.7332709321198 +422000 ekin = 1.93529999466693 | erot = 2.35358466371903 | epot = -21.8587107341243 | etot = -17.5698260757383 +423000 ekin = 1.84611594143483 | erot = 2.25228565887447 | epot = -21.8206559909772 | etot = -17.7222543906679 +424000 ekin = 1.92830552207793 | erot = 1.92697824358691 | epot = -21.777972970412 | etot = -17.9226892047471 +425000 ekin = 1.87968918412308 | erot = 2.04838530467779 | epot = -21.7345809752814 | etot = -17.8065064864805 +426000 ekin = 1.8556412970146 | erot = 2.13991381782217 | epot = -21.7013928959338 | etot = -17.705837781097 +427000 ekin = 1.86146118829918 | erot = 2.21385079035769 | epot = -21.6794945474638 | etot = -17.6041825688069 +428000 ekin = 1.93768082509308 | erot = 2.13363270684652 | epot = -21.6773435664085 | etot = -17.6060300344689 +429000 ekin = 1.99945365892738 | erot = 2.19562243163489 | epot = -21.7054036465602 | etot = -17.5103275559979 +430000 ekin = 2.09718842591563 | erot = 2.3463320213618 | epot = -21.7371065581007 | etot = -17.2935861108232 +431000 ekin = 2.17999939901921 | erot = 2.30896770967013 | epot = -21.7414717361359 | etot = -17.2525046274466 +432000 ekin = 2.25849803136377 | erot = 2.37380554728505 | epot = -21.7217776472071 | etot = -17.0894740685582 +433000 ekin = 2.24429029360165 | erot = 2.44429429006342 | epot = -21.7017276929565 | etot = -17.0131431092914 +434000 ekin = 2.35406385747883 | erot = 2.4892079011312 | epot = -21.700781219286 | etot = -16.8575094606759 +435000 ekin = 2.24737880153531 | erot = 2.4659516348531 | epot = -21.7063339873009 | etot = -16.9930035509125 +436000 ekin = 2.23230082302258 | erot = 2.42669718967156 | epot = -21.7123927262194 | etot = -17.0533947135252 +437000 ekin = 2.18383665113533 | erot = 2.24664794927378 | epot = -21.7330413026265 | etot = -17.3025567022174 +438000 ekin = 2.12966913497234 | erot = 2.37196465183249 | epot = -21.7485872315853 | etot = -17.2469534447805 +439000 ekin = 2.09098898533768 | erot = 2.12933040903342 | epot = -21.7361412880266 | etot = -17.5158218936555 +440000 ekin = 2.10148571824467 | erot = 2.27793618592804 | epot = -21.7175254276831 | etot = -17.3381035235104 +441000 ekin = 2.15532867982074 | erot = 2.31865640213706 | epot = -21.6981903134064 | etot = -17.2242052314486 +442000 ekin = 2.09243597225367 | erot = 2.72841000678813 | epot = -21.6523738209046 | etot = -16.8315278418628 +443000 ekin = 2.15730367932181 | erot = 2.62581799220039 | epot = -21.5875809663666 | etot = -16.8044592948444 +444000 ekin = 2.18263017921483 | erot = 2.37014829408738 | epot = -21.504824150884 | etot = -16.9520456775818 +445000 ekin = 2.05145531635821 | erot = 2.17678227962618 | epot = -21.4326062625765 | etot = -17.2043686665921 +446000 ekin = 2.01020948431942 | erot = 2.37374422099264 | epot = -21.3645246084936 | etot = -16.9805709031815 +447000 ekin = 1.89588317933144 | erot = 2.4528908983781 | epot = -21.2952162464884 | etot = -16.9464421687789 +448000 ekin = 1.94918640966662 | erot = 2.39703928139391 | epot = -21.2255467455683 | etot = -16.8793210545077 +449000 ekin = 1.91481408982834 | erot = 2.28318705908368 | epot = -21.1543411876569 | etot = -16.9563400387449 +450000 ekin = 1.87784973555253 | erot = 2.1248579551631 | epot = -21.1046206355142 | etot = -17.1019129447986 +451000 ekin = 1.97352148815437 | erot = 1.86756984773945 | epot = -21.0797511236577 | etot = -17.2386597877639 +452000 ekin = 2.04286189285633 | erot = 1.80786168372332 | epot = -21.0697245816185 | etot = -17.2190010050389 +453000 ekin = 2.1384860647166 | erot = 1.67376501662041 | epot = -21.0904747395762 | etot = -17.2782236582392 +454000 ekin = 2.15164945191103 | erot = 2.04932890222847 | epot = -21.1143650676537 | etot = -16.9133867135142 +455000 ekin = 2.19477985095236 | erot = 2.16695764653243 | epot = -21.1370563835237 | etot = -16.7753188860389 +456000 ekin = 2.19740261168692 | erot = 2.10215601431886 | epot = -21.1403905144291 | etot = -16.8408318884233 +457000 ekin = 2.20601557977637 | erot = 2.13174146926998 | epot = -21.1647757949628 | etot = -16.8270187459165 +458000 ekin = 2.22693497466223 | erot = 2.00297660996761 | epot = -21.2133843445383 | etot = -16.9834727599084 +459000 ekin = 2.40306935261522 | erot = 2.07528469876346 | epot = -21.2759346114691 | etot = -16.7975805600904 +460000 ekin = 2.40922164106694 | erot = 2.23665563054137 | epot = -21.352281719657 | etot = -16.7064044480486 +461000 ekin = 2.42000759716796 | erot = 2.33121048923215 | epot = -21.4035924354774 | etot = -16.6523743490773 +462000 ekin = 2.40697031331563 | erot = 2.14275899197066 | epot = -21.4310008578854 | etot = -16.8812715525991 +463000 ekin = 2.27880926024471 | erot = 1.9450755692431 | epot = -21.4477328212938 | etot = -17.223847991806 +464000 ekin = 2.26372093546448 | erot = 1.71662964564964 | epot = -21.4283876808071 | etot = -17.448037099693 +465000 ekin = 2.24118575319934 | erot = 1.89668392003691 | epot = -21.4003434057031 | etot = -17.2624737324669 +466000 ekin = 2.31013461832327 | erot = 2.00757055155837 | epot = -21.3608207821978 | etot = -17.0431156123162 +467000 ekin = 2.4339696791395 | erot = 2.21874571911994 | epot = -21.3053258443236 | etot = -16.6526104460642 +468000 ekin = 2.41021440017844 | erot = 1.97479498639513 | epot = -21.233460271117 | etot = -16.8484508845435 +469000 ekin = 2.31578531471236 | erot = 1.99784256139238 | epot = -21.1821517028579 | etot = -16.8685238267532 +470000 ekin = 2.20506875315387 | erot = 1.87887773816032 | epot = -21.1430826832857 | etot = -17.0591361919715 +471000 ekin = 2.13628837828128 | erot = 1.99677754816705 | epot = -21.1290504063502 | etot = -16.9959844799019 +472000 ekin = 2.10129418295658 | erot = 2.2405661236519 | epot = -21.1431228234939 | etot = -16.8012625168854 +473000 ekin = 2.15627273414978 | erot = 2.19993171978119 | epot = -21.1733300414642 | etot = -16.8171255875332 +474000 ekin = 2.14076076010815 | erot = 2.25446359877068 | epot = -21.221006263287 | etot = -16.8257819044082 +475000 ekin = 2.13812755485179 | erot = 2.40498819643 | epot = -21.2865391851112 | etot = -16.7434234338294 +476000 ekin = 2.06858808991819 | erot = 2.38860590776937 | epot = -21.3434845601286 | etot = -16.8862905624411 +477000 ekin = 2.07006440492054 | erot = 2.75406570213518 | epot = -21.3922756308481 | etot = -16.5681455237924 +478000 ekin = 2.18444735013641 | erot = 2.70772307923246 | epot = -21.4343815992348 | etot = -16.5422111698659 +479000 ekin = 2.19942421685254 | erot = 3.01662715265702 | epot = -21.4597482066207 | etot = -16.2436968371111 +480000 ekin = 2.0967634494608 | erot = 2.92438195103725 | epot = -21.4845635218897 | etot = -16.4634181213917 +481000 ekin = 2.05435750946167 | erot = 2.89946489225791 | epot = -21.5058659565645 | etot = -16.5520435548449 +482000 ekin = 1.93906176361666 | erot = 2.94002477322929 | epot = -21.5133252549456 | etot = -16.6342387180996 +483000 ekin = 1.92495432631112 | erot = 3.07385412342424 | epot = -21.5077333577219 | etot = -16.5089249079865 +484000 ekin = 1.92789828975046 | erot = 3.32856329414662 | epot = -21.5066449871573 | etot = -16.2501834032602 +485000 ekin = 1.91268771816293 | erot = 3.09586191791501 | epot = -21.4833052647976 | etot = -16.4747556287196 +486000 ekin = 1.78380043967851 | erot = 3.03494358258128 | epot = -21.4585833289245 | etot = -16.6398393066647 +487000 ekin = 1.66173050700684 | erot = 2.86000419946662 | epot = -21.4169307099541 | etot = -16.8951960034807 +488000 ekin = 1.6861803912259 | erot = 2.81632446798658 | epot = -21.3632748840396 | etot = -16.8607700248271 +489000 ekin = 1.70799546417837 | erot = 2.42402499535219 | epot = -21.2867408576365 | etot = -17.1547203981059 +490000 ekin = 1.76758231238948 | erot = 2.12271247808917 | epot = -21.2077046249558 | etot = -17.3174098344771 +491000 ekin = 1.76306663296675 | erot = 2.86063070746491 | epot = -21.1723403735264 | etot = -16.5486430330947 +492000 ekin = 1.76846685645936 | erot = 2.89751715915282 | epot = -21.1637728122907 | etot = -16.4977887966785 +493000 ekin = 1.78426656200509 | erot = 3.00701255652278 | epot = -21.177366494112 | etot = -16.3860873755841 +494000 ekin = 1.86551817373627 | erot = 2.87131917289129 | epot = -21.202525065023 | etot = -16.4656877183955 +495000 ekin = 1.90523259261305 | erot = 3.14209453322629 | epot = -21.199815438883 | etot = -16.1524883130437 +496000 ekin = 1.98335126636148 | erot = 2.98540814212653 | epot = -21.1906478493248 | etot = -16.2218884408368 +497000 ekin = 2.06634825728685 | erot = 2.95896590871823 | epot = -21.1621551542808 | etot = -16.1368409882758 +498000 ekin = 2.1527240028484 | erot = 3.02117382743694 | epot = -21.1193839391164 | etot = -15.9454861088311 +499000 ekin = 2.17953814058362 | erot = 2.7956528806284 | epot = -21.1071993938559 | etot = -16.1320083726439 +500000 ekin = 2.18279625505131 | erot = 2.73392245688628 | epot = -21.1153073171068 | etot = -16.1985886051692 +501000 ekin = 2.14934456304168 | erot = 3.04941214942239 | epot = -21.1511220012823 | etot = -15.9523652888182 +502000 ekin = 2.24815210672164 | erot = 3.29370999045842 | epot = -21.191424172631 | etot = -15.649562075451 +503000 ekin = 2.24373540198307 | erot = 3.32111123848707 | epot = -21.2742763532379 | etot = -15.7094297127677 +504000 ekin = 2.2380398968446 | erot = 3.0991412841911 | epot = -21.3733619536839 | etot = -16.0361807726482 +505000 ekin = 2.30102605486345 | erot = 3.19612982312041 | epot = -21.4437932084701 | etot = -15.9466373304862 +506000 ekin = 2.36370831780387 | erot = 3.19995831891699 | epot = -21.4937378126654 | etot = -15.9300711759445 +507000 ekin = 2.42840177155352 | erot = 2.81713782658399 | epot = -21.5299907326272 | etot = -16.2844511344897 +508000 ekin = 2.3496800529995 | erot = 2.32969767190605 | epot = -21.5629586677094 | etot = -16.8835809428039 +509000 ekin = 2.31587277784011 | erot = 2.32044150422015 | epot = -21.5800976653978 | etot = -16.9437833833375 +510000 ekin = 2.39415651583834 | erot = 2.32489194511628 | epot = -21.5909228684583 | etot = -16.8718744075037 +511000 ekin = 2.37917219486121 | erot = 2.25376804515916 | epot = -21.6001349490033 | etot = -16.967194708983 +512000 ekin = 2.37938693355446 | erot = 1.92023885988138 | epot = -21.6111071917155 | etot = -17.3114813982796 +513000 ekin = 2.4068585795957 | erot = 2.08600293524445 | epot = -21.6155439119537 | etot = -17.1226823971136 +514000 ekin = 2.46724209327195 | erot = 2.20949952828796 | epot = -21.6418209909607 | etot = -16.9650793694008 +515000 ekin = 2.44642692672663 | erot = 2.02689318439863 | epot = -21.6526616938248 | etot = -17.1793415826996 +516000 ekin = 2.34670203308752 | erot = 2.15396125943245 | epot = -21.6543094777108 | etot = -17.1536461851908 +517000 ekin = 2.33878155191648 | erot = 2.33294662418984 | epot = -21.6421766473136 | etot = -16.9704484712073 +518000 ekin = 2.31107655587532 | erot = 2.15491971030968 | epot = -21.6319254773268 | etot = -17.1659292111418 +519000 ekin = 2.29496119138257 | erot = 2.00492803313419 | epot = -21.6347632719486 | etot = -17.3348740474319 +520000 ekin = 2.15339792107183 | erot = 2.04457004756215 | epot = -21.6507830510492 | etot = -17.4528150824152 +521000 ekin = 2.20801983612424 | erot = 2.16352250997097 | epot = -21.6715366002404 | etot = -17.2999942541452 +522000 ekin = 2.28349511901188 | erot = 2.12203826388418 | epot = -21.7067045500198 | etot = -17.3011711671237 +523000 ekin = 2.28326140498731 | erot = 2.24730546524176 | epot = -21.7500540285239 | etot = -17.2194871582948 +524000 ekin = 2.41430391300397 | erot = 2.30243275419766 | epot = -21.7887659971603 | etot = -17.0720293299587 +525000 ekin = 2.46563871852188 | erot = 2.61576568534199 | epot = -21.8311918688001 | etot = -16.7497874649362 +526000 ekin = 2.44766866227825 | erot = 2.73251608599186 | epot = -21.8542594932618 | etot = -16.6740747449916 +527000 ekin = 2.49415128662349 | erot = 2.97647354160827 | epot = -21.8654961412296 | etot = -16.3948713129978 +528000 ekin = 2.63765981818831 | erot = 2.90145202540003 | epot = -21.8539949982376 | etot = -16.3148831546493 +529000 ekin = 2.61312965886424 | erot = 2.63810638896208 | epot = -21.812302902124 | etot = -16.5610668542976 +530000 ekin = 2.61679294703744 | erot = 2.67053467520177 | epot = -21.7690607572615 | etot = -16.4817331350223 +531000 ekin = 2.48476384385704 | erot = 2.71653952081309 | epot = -21.7165365440457 | etot = -16.5152331793756 +532000 ekin = 2.48793546388986 | erot = 2.65738787716549 | epot = -21.6564484956905 | etot = -16.5111251546351 +533000 ekin = 2.41456215119459 | erot = 2.64489299438354 | epot = -21.639072482786 | etot = -16.5796173372078 +534000 ekin = 2.29777827242778 | erot = 2.74873035111879 | epot = -21.6608745386251 | etot = -16.6143659150785 +535000 ekin = 2.26088917727546 | erot = 2.83473610922371 | epot = -21.6981866268834 | etot = -16.6025613403843 +536000 ekin = 2.20131769719344 | erot = 2.88353145322202 | epot = -21.755248482858 | etot = -16.6703993324425 +537000 ekin = 2.13082565508333 | erot = 2.91286112998273 | epot = -21.7996526043394 | etot = -16.7559658192733 +538000 ekin = 2.05764519091759 | erot = 2.95211539945559 | epot = -21.8281285512857 | etot = -16.8183679609125 +539000 ekin = 1.97437084021552 | erot = 2.9097074061232 | epot = -21.8443187140803 | etot = -16.9602404677416 +540000 ekin = 1.95684111980203 | erot = 2.5383191039217 | epot = -21.8503067819182 | etot = -17.3551465581945 +541000 ekin = 2.01269488661909 | erot = 2.53569793957034 | epot = -21.8275993102503 | etot = -17.2792064840608 +542000 ekin = 2.03504454490702 | erot = 2.82348341864015 | epot = -21.8036330964533 | etot = -16.9451051329062 +543000 ekin = 2.03020807235322 | erot = 3.03370589872126 | epot = -21.8016375466952 | etot = -16.7377235756207 +544000 ekin = 2.05269052857014 | erot = 2.58799516983488 | epot = -21.8033388274283 | etot = -17.1626531290233 +545000 ekin = 2.15141870706984 | erot = 2.40428159733159 | epot = -21.8230803043774 | etot = -17.267379999976 +546000 ekin = 2.2730009121937 | erot = 2.20572730047347 | epot = -21.8690779560947 | etot = -17.3903497434275 +547000 ekin = 2.35364033678083 | erot = 2.18498069722327 | epot = -21.9465784737244 | etot = -17.4079574397203 +548000 ekin = 2.43307589906691 | erot = 2.42293816342305 | epot = -22.0303494741984 | etot = -17.1743354117084 +549000 ekin = 2.54088590896235 | erot = 2.9095237719503 | epot = -22.1200487075607 | etot = -16.6696390266481 +550000 ekin = 2.56016664627933 | erot = 2.68398103895175 | epot = -22.1766985156474 | etot = -16.9325508304163 +551000 ekin = 2.72417690556182 | erot = 2.72891308441098 | epot = -22.2176306990374 | etot = -16.7645407090646 +552000 ekin = 2.72596785657269 | erot = 2.42255580538622 | epot = -22.2421241890566 | etot = -17.0936005270977 +553000 ekin = 2.78508615614578 | erot = 2.39994410027753 | epot = -22.2425789733829 | etot = -17.0575487169596 +554000 ekin = 2.81568582164755 | erot = 2.30970996795577 | epot = -22.212027345066 | etot = -17.0866315554627 +555000 ekin = 2.79395520813526 | erot = 2.24542312270129 | epot = -22.1601855930767 | etot = -17.1208072622401 +556000 ekin = 2.81007006192488 | erot = 2.29040711319253 | epot = -22.0853198857605 | etot = -16.9848427106431 +557000 ekin = 2.86720343014862 | erot = 2.06281031141602 | epot = -21.9979009255864 | etot = -17.0678871840218 +558000 ekin = 2.75377155929318 | erot = 2.13725587394243 | epot = -21.8668776496783 | etot = -16.9758502164427 +559000 ekin = 2.72157639522917 | erot = 2.20102610126835 | epot = -21.7194344747873 | etot = -16.7968319782898 +560000 ekin = 2.70961845092833 | erot = 2.59816182534515 | epot = -21.5357151296295 | etot = -16.227934853356 +561000 ekin = 2.57949305004174 | erot = 2.96337390027736 | epot = -21.3145814838314 | etot = -15.7717145335123 +562000 ekin = 2.32107059805592 | erot = 2.51143214075166 | epot = -21.0085235339443 | etot = -16.1760207951367 +563000 ekin = 2.24732443728587 | erot = 2.3879005093821 | epot = -20.8154509884486 | etot = -16.1802260417806 +564000 ekin = 2.33791301852595 | erot = 2.68335523927297 | epot = -20.8066084764155 | etot = -15.7853402186166 +565000 ekin = 2.32510209076373 | erot = 2.8508896099138 | epot = -20.6671406909933 | etot = -15.4911489903158 +566000 ekin = 2.20543771892934 | erot = 2.35706719035764 | epot = -20.5538554522387 | etot = -15.9913505429518 +567000 ekin = 2.11804196373779 | erot = 2.40185685943714 | epot = -20.4713035116105 | etot = -15.9514046884356 +568000 ekin = 2.22268682011225 | erot = 2.33307148175166 | epot = -20.3820924859934 | etot = -15.8263341841295 +569000 ekin = 2.09547585997744 | erot = 2.62261207858624 | epot = -20.2691455782377 | etot = -15.551057639674 +570000 ekin = 2.01580186947893 | erot = 2.33698172151258 | epot = -20.1658958603531 | etot = -15.8131122693616 +571000 ekin = 2.08039178219766 | erot = 2.36534037676708 | epot = -20.0857600662143 | etot = -15.6400279072495 +572000 ekin = 2.11927324959301 | erot = 2.30282149950167 | epot = -20.0451987594363 | etot = -15.6231040103417 +573000 ekin = 2.04663917529184 | erot = 2.3397266793933 | epot = -20.0317480451745 | etot = -15.6453821904893 +574000 ekin = 2.09962922460146 | erot = 2.19990447249075 | epot = -20.0660831814167 | etot = -15.7665494843245 +575000 ekin = 2.2724213043473 | erot = 2.2560950849323 | epot = -20.1489560418924 | etot = -15.6204396526128 +576000 ekin = 2.39016715864533 | erot = 2.22255127128227 | epot = -20.2603613797455 | etot = -15.6476429498179 +577000 ekin = 2.3641256374076 | erot = 2.30198986937696 | epot = -20.3752615554293 | etot = -15.7091460486447 +578000 ekin = 2.49125580710772 | erot = 2.4266078622766 | epot = -20.502520702598 | etot = -15.5846570332137 +579000 ekin = 2.56165048094701 | erot = 2.83228223321267 | epot = -20.636891122234 | etot = -15.2429584080743 +580000 ekin = 2.5985707631887 | erot = 2.86537715884212 | epot = -20.7281657529396 | etot = -15.2642178309088 +581000 ekin = 2.75751410053994 | erot = 3.201023040261 | epot = -20.7812637399727 | etot = -14.8227265991717 +582000 ekin = 2.72186433456447 | erot = 2.73127793091817 | epot = -20.8119294300411 | etot = -15.3587871645585 +583000 ekin = 2.62273499225684 | erot = 2.46109328120281 | epot = -20.82747146712 | etot = -15.7436431936604 +584000 ekin = 2.65791178050006 | erot = 2.52854330537007 | epot = -20.8318022222691 | etot = -15.645347136399 +585000 ekin = 2.61150125120866 | erot = 2.75251814406213 | epot = -20.8423541781131 | etot = -15.4783347828423 +586000 ekin = 2.56490529514568 | erot = 2.76819989101126 | epot = -20.8235905183123 | etot = -15.4904853321554 +587000 ekin = 2.44377479420657 | erot = 2.55313165140451 | epot = -20.787396769062 | etot = -15.7904903234509 +588000 ekin = 2.54600679288766 | erot = 2.00966564099397 | epot = -20.7414898497507 | etot = -16.185817415869 +589000 ekin = 2.42615788479235 | erot = 1.87395944544066 | epot = -20.7098613915245 | etot = -16.4097440612915 +590000 ekin = 2.42016761405663 | erot = 1.71977054763906 | epot = -20.682469148408 | etot = -16.5425309867123 +591000 ekin = 2.38760737800274 | erot = 1.84146371886645 | epot = -20.6722800899364 | etot = -16.4432089930672 +592000 ekin = 2.31657054464672 | erot = 1.96505693643487 | epot = -20.7031666775492 | etot = -16.4215391964676 +593000 ekin = 2.23530102205172 | erot = 1.81162578854723 | epot = -20.7586825210074 | etot = -16.7117557104085 +594000 ekin = 2.21499618339367 | erot = 1.98026347110265 | epot = -20.8347835084303 | etot = -16.6395238539339 +595000 ekin = 2.1735109206856 | erot = 2.27153694538259 | epot = -20.9049251653826 | etot = -16.4598772993144 +596000 ekin = 2.13536721422193 | erot = 2.30838064667278 | epot = -20.9560792436845 | etot = -16.5123313827898 +597000 ekin = 2.05769259414588 | erot = 2.38187665146498 | epot = -20.9894852475388 | etot = -16.5499160019279 +598000 ekin = 2.05674814899196 | erot = 2.42014079217233 | epot = -21.0044596830553 | etot = -16.527570741891 +599000 ekin = 1.95864026709732 | erot = 2.39995075981931 | epot = -20.9740626757897 | etot = -16.6154716488731 +600000 ekin = 1.92217253864592 | erot = 2.27990516657273 | epot = -20.9285242414045 | etot = -16.7264465361859 +601000 ekin = 1.98018146832032 | erot = 2.20890815410652 | epot = -20.8846332261986 | etot = -16.6955436037718 +602000 ekin = 1.9018407158324 | erot = 2.15913830500077 | epot = -20.8542535717533 | etot = -16.7932745509201 +603000 ekin = 1.874147854724 | erot = 2.20472694083471 | epot = -20.8408046427066 | etot = -16.7619298471479 +604000 ekin = 1.8956696755394 | erot = 2.33936411504487 | epot = -20.8324704464838 | etot = -16.5974366558996 +605000 ekin = 1.90221219714077 | erot = 2.24714804248294 | epot = -20.8240875666932 | etot = -16.6747273270695 +606000 ekin = 1.98126421387451 | erot = 2.18362681345851 | epot = -20.831816133263 | etot = -16.6669251059299 +607000 ekin = 1.96256992421002 | erot = 2.31466128891675 | epot = -20.842219228341 | etot = -16.5649880152142 +608000 ekin = 2.00857732853911 | erot = 2.35246654785901 | epot = -20.8480147460981 | etot = -16.4869708696999 +609000 ekin = 1.95325682031733 | erot = 2.81335207348493 | epot = -20.8594200048109 | etot = -16.0928111110087 +610000 ekin = 1.98193326810055 | erot = 2.88259052339692 | epot = -20.8472840007382 | etot = -15.9827602092408 +611000 ekin = 2.04137421596164 | erot = 2.49925666829906 | epot = -20.8306415233202 | etot = -16.2900106390595 +612000 ekin = 2.16269789015095 | erot = 2.70058773214408 | epot = -20.7942268006608 | etot = -15.9309411783658 +613000 ekin = 2.06529168540845 | erot = 2.42568351626004 | epot = -20.7614875640894 | etot = -16.2705123624209 +614000 ekin = 2.13372547058354 | erot = 2.26794536225561 | epot = -20.7223835113478 | etot = -16.3207126785086 +615000 ekin = 2.15900283469833 | erot = 2.41796083425713 | epot = -20.6594009316023 | etot = -16.0824372626469 +616000 ekin = 2.18075700318115 | erot = 2.25199751704729 | epot = -20.6022951429054 | etot = -16.169540622677 +617000 ekin = 2.15965098363287 | erot = 2.22906613418701 | epot = -20.5852528289988 | etot = -16.1965357111789 +618000 ekin = 2.23225625672999 | erot = 2.44686544718971 | epot = -20.610224970018 | etot = -15.9311032660983 +619000 ekin = 2.2697545490367 | erot = 2.3428925387803 | epot = -20.6719638155438 | etot = -16.0593167277268 +620000 ekin = 2.30973430443507 | erot = 2.69227064537985 | epot = -20.7701978809869 | etot = -15.768192931172 +621000 ekin = 2.47203322805299 | erot = 3.06119226990014 | epot = -20.9146158917174 | etot = -15.3813903937642 +622000 ekin = 2.6234827456027 | erot = 3.16275527232546 | epot = -21.0868239893472 | etot = -15.3005859714191 +623000 ekin = 2.67387060573034 | erot = 3.22531872328047 | epot = -21.2795790465567 | etot = -15.3803897175459 +624000 ekin = 2.77334044145805 | erot = 3.19930974567982 | epot = -21.4804753178395 | etot = -15.5078251307016 +625000 ekin = 2.82230466072525 | erot = 2.9747199185102 | epot = -21.6768467596146 | etot = -15.8798221803791 +626000 ekin = 2.97306496702218 | erot = 3.02810006646603 | epot = -21.8368791799807 | etot = -15.8357141464924 +627000 ekin = 2.9396359895921 | erot = 3.11546514885661 | epot = -21.9295648605412 | etot = -15.8744637220925 +628000 ekin = 2.94675401744143 | erot = 2.87563053224012 | epot = -21.9734618105417 | etot = -16.1510772608602 +629000 ekin = 2.93549647211201 | erot = 2.94179551334381 | epot = -21.9629357939838 | etot = -16.085643808528 +630000 ekin = 2.968513495898 | erot = 2.66241758633549 | epot = -21.936706782 | etot = -16.3057756997665 +631000 ekin = 2.97170810029475 | erot = 2.9278488835795 | epot = -21.9408587478556 | etot = -16.0413017639814 +632000 ekin = 3.00915408594527 | erot = 3.03331194667432 | epot = -21.9662975867255 | etot = -15.923831554106 +633000 ekin = 3.15130786380797 | erot = 2.90447111403471 | epot = -21.9802035040982 | etot = -15.9244245262556 +634000 ekin = 3.0872430722561 | erot = 3.06470523223815 | epot = -21.9813618086071 | etot = -15.8294135041129 +635000 ekin = 3.09485256628968 | erot = 3.05293629484995 | epot = -21.9761085643253 | etot = -15.8283197031856 +636000 ekin = 3.18833676246128 | erot = 3.09853352594568 | epot = -21.9262309231053 | etot = -15.6393606346983 +637000 ekin = 3.17249776983439 | erot = 2.76836567164458 | epot = -21.846318761896 | etot = -15.905455320417 +638000 ekin = 3.15773051904035 | erot = 2.74718314777864 | epot = -21.752103466865 | etot = -15.847189800046 +639000 ekin = 3.08619022126289 | erot = 2.75291211878194 | epot = -21.6198807004768 | etot = -15.780778360432 +640000 ekin = 3.13541342359622 | erot = 2.75186869517613 | epot = -21.4236473324242 | etot = -15.5363652136518 +641000 ekin = 2.97070406886304 | erot = 2.53928201823129 | epot = -21.2113872532507 | etot = -15.7014011661563 +642000 ekin = 2.96213641788666 | erot = 2.46548060107455 | epot = -20.9928030195292 | etot = -15.565186000568 +643000 ekin = 2.84219149582808 | erot = 2.30604210385216 | epot = -20.7796379309879 | etot = -15.6314043313077 +644000 ekin = 2.73987448812119 | erot = 1.92488908230349 | epot = -20.5971129650468 | etot = -15.9323493946221 +645000 ekin = 2.66964682664619 | erot = 2.17741731737593 | epot = -20.4501395419023 | etot = -15.6030753978801 +646000 ekin = 2.55685727423959 | erot = 1.94955682330733 | epot = -20.3484174743042 | etot = -15.8420033767573 +647000 ekin = 2.36548817737629 | erot = 2.05467058240502 | epot = -20.2308525146957 | etot = -15.8106937549144 +648000 ekin = 2.31008857244622 | erot = 1.85050053837879 | epot = -20.1170577319191 | etot = -15.9564686210941 +649000 ekin = 2.2820502586928 | erot = 1.71263708698589 | epot = -20.0254728385503 | etot = -16.0307854928716 +650000 ekin = 2.21196677463666 | erot = 1.82025099236574 | epot = -19.9537436999668 | etot = -15.9215259329644 +651000 ekin = 2.17096351970662 | erot = 1.64111059964138 | epot = -19.893946125439 | etot = -16.081872006091 +652000 ekin = 2.24485056260445 | erot = 1.5901592073441 | epot = -19.8559152094387 | etot = -16.0209054394902 +653000 ekin = 2.24348598334208 | erot = 1.56547926791896 | epot = -19.8354995105722 | etot = -16.0265342593112 +654000 ekin = 2.3436705432219 | erot = 1.59100225910908 | epot = -19.8036561058559 | etot = -15.8689833035249 +655000 ekin = 2.33139381348469 | erot = 1.73360745289315 | epot = -19.7790891006602 | etot = -15.7140878342824 +656000 ekin = 2.39082402474884 | erot = 1.66512195058759 | epot = -19.7882728464571 | etot = -15.7323268711207 +657000 ekin = 2.36326494202717 | erot = 1.64634599165851 | epot = -19.8156605115388 | etot = -15.8060495778531 +658000 ekin = 2.37356060304704 | erot = 1.59216090461371 | epot = -19.8647456377851 | etot = -15.8990241301243 +659000 ekin = 2.48069174292956 | erot = 1.49175770497883 | epot = -19.9602607152513 | etot = -15.987811267343 +660000 ekin = 2.43784148373588 | erot = 1.6930424525872 | epot = -20.0982797920099 | etot = -15.9673958556869 +661000 ekin = 2.50127283299443 | erot = 1.90162951574018 | epot = -20.2564772898341 | etot = -15.8535749410995 +662000 ekin = 2.65651409235479 | erot = 1.97694168302421 | epot = -20.4351000172129 | etot = -15.8016442418339 +663000 ekin = 2.59069846598396 | erot = 2.27024751168569 | epot = -20.5951722286015 | etot = -15.7342262509318 +664000 ekin = 2.65199362526649 | erot = 2.41512175478246 | epot = -20.7236956549424 | etot = -15.6565802748934 +665000 ekin = 2.74059693842704 | erot = 2.18558347698565 | epot = -20.836270984044 | etot = -15.9100905686313 +666000 ekin = 2.81567682366713 | erot = 2.34749860597669 | epot = -20.9472815722853 | etot = -15.7841061426415 +667000 ekin = 2.85397277942012 | erot = 2.78444099743799 | epot = -21.051254788865 | etot = -15.4128410120069 +668000 ekin = 2.90295609594963 | erot = 2.67434743985645 | epot = -21.1196454976539 | etot = -15.5423419618478 +669000 ekin = 2.82586988686643 | erot = 2.59996675336095 | epot = -21.1269738870865 | etot = -15.7011372468591 +670000 ekin = 2.79168631386091 | erot = 2.56332899434142 | epot = -21.1062374856384 | etot = -15.7512221774361 +671000 ekin = 2.78377934011114 | erot = 2.65037677108216 | epot = -21.0707534252226 | etot = -15.6365973140293 +672000 ekin = 2.803703333643 | erot = 2.43772748784302 | epot = -21.0308122724576 | etot = -15.7893814509716 +673000 ekin = 2.7691539986881 | erot = 2.51561518037599 | epot = -20.9769263473738 | etot = -15.6921571683097 +674000 ekin = 2.64183624634907 | erot = 2.5509723350789 | epot = -20.9182849770312 | etot = -15.7254763956032 +675000 ekin = 2.62521142757554 | erot = 2.64780321266124 | epot = -20.8750415391238 | etot = -15.602026898887 +676000 ekin = 2.56750452241313 | erot = 2.50976436481691 | epot = -20.8718880077788 | etot = -15.7946191205487 +677000 ekin = 2.54381281980499 | erot = 2.88598144344474 | epot = -20.8743650878296 | etot = -15.4445708245799 +678000 ekin = 2.41460230362231 | erot = 2.74956960106208 | epot = -20.8645099379738 | etot = -15.7003380332894 +679000 ekin = 2.45714396740981 | erot = 2.51630907313239 | epot = -20.8333930763107 | etot = -15.8599400357685 +680000 ekin = 2.39813210053792 | erot = 2.44684074440015 | epot = -20.7887522768163 | etot = -15.9437794318782 +681000 ekin = 2.43918264143157 | erot = 2.34640131965743 | epot = -20.7476808113825 | etot = -15.9620968502935 +682000 ekin = 2.35991514290774 | erot = 2.52582496731663 | epot = -20.6783381667257 | etot = -15.7925980565014 +683000 ekin = 2.52475831935489 | erot = 2.43032542841516 | epot = -20.5982055545538 | etot = -15.6431218067838 +684000 ekin = 2.58660934635455 | erot = 2.11878822836128 | epot = -20.4924135763664 | etot = -15.7870160016506 +685000 ekin = 2.55154119483619 | erot = 1.73486584185217 | epot = -20.382217510981 | etot = -16.0958104742926 +686000 ekin = 2.63111018797726 | erot = 1.47730091117236 | epot = -20.3126109077782 | etot = -16.2041998086286 +687000 ekin = 2.6396968201908 | erot = 1.4733230185728 | epot = -20.2996486685943 | etot = -16.1866288298307 +688000 ekin = 2.7234920794771 | erot = 1.29409931094963 | epot = -20.3234627588047 | etot = -16.305871368378 +689000 ekin = 2.73079979716428 | erot = 1.56006726489594 | epot = -20.4074074566833 | etot = -16.1165403946231 +690000 ekin = 2.8886213899704 | erot = 1.53763438603365 | epot = -20.5271307060396 | etot = -16.1008749300355 +691000 ekin = 2.93184490556377 | erot = 1.68041505604324 | epot = -20.6817002649671 | etot = -16.0694403033601 +692000 ekin = 3.039651675882 | erot = 1.53360102419162 | epot = -20.8394269437995 | etot = -16.2661742437259 +693000 ekin = 3.11332037021243 | erot = 1.78276814996248 | epot = -20.9856322860979 | etot = -16.089543765923 +694000 ekin = 3.26591256423344 | erot = 1.83297982799396 | epot = -21.1162583961221 | etot = -16.0173660038947 +695000 ekin = 3.39944935277107 | erot = 1.85369820811796 | epot = -21.210977736514 | etot = -15.957830175625 +696000 ekin = 3.30343203418313 | erot = 1.83180202140663 | epot = -21.2772827777974 | etot = -16.1420487222076 +697000 ekin = 3.22977317647567 | erot = 1.99511551134629 | epot = -21.3085920420921 | etot = -16.0837033542702 +698000 ekin = 3.36545228088424 | erot = 1.93865151714 | epot = -21.292469671287 | etot = -15.9883658732627 +699000 ekin = 3.26727101649057 | erot = 2.00750907689842 | epot = -21.2347192164131 | etot = -15.9599391230241 +700000 ekin = 3.23373130843466 | erot = 1.9581479646034 | epot = -21.1439766208008 | etot = -15.9520973477627 +701000 ekin = 3.07791756459623 | erot = 1.84629538321642 | epot = -21.0368350139915 | etot = -16.1126220661789 +702000 ekin = 2.95524336171478 | erot = 2.05334887389019 | epot = -20.9320932298122 | etot = -15.9235009942072 +703000 ekin = 2.81685700197359 | erot = 2.30798807393509 | epot = -20.8529482411059 | etot = -15.7281031651972 +704000 ekin = 2.78603745694898 | erot = 2.41032504549238 | epot = -20.7817305926661 | etot = -15.5853680902247 +705000 ekin = 2.82734195960174 | erot = 2.58886515581029 | epot = -20.705486127934 | etot = -15.289279012522 +706000 ekin = 2.69252213631 | erot = 2.87186287347272 | epot = -20.6341395720105 | etot = -15.0697545622277 +707000 ekin = 2.67677781124248 | erot = 2.61015441384283 | epot = -20.5829958432681 | etot = -15.2960636181828 +708000 ekin = 2.61607470121115 | erot = 2.52638154954373 | epot = -20.5707989768076 | etot = -15.4283427260527 +709000 ekin = 2.66476396394733 | erot = 2.77686126060184 | epot = -20.5966805252114 | etot = -15.1550553006623 +710000 ekin = 2.7247375394434 | erot = 3.01436891653811 | epot = -20.6381576133419 | etot = -14.8990511573603 +711000 ekin = 2.73828751365585 | erot = 2.9608710490951 | epot = -20.6834857916291 | etot = -14.9843272288781 +712000 ekin = 2.62321032142597 | erot = 3.36842837276275 | epot = -20.7033938368061 | etot = -14.7117551426174 +713000 ekin = 2.57840853452372 | erot = 3.23870482700691 | epot = -20.7157410164413 | etot = -14.8986276549107 +714000 ekin = 2.57830571481541 | erot = 3.18574747943729 | epot = -20.7368579407289 | etot = -14.9728047464762 +715000 ekin = 2.55353778251667 | erot = 3.06029471484808 | epot = -20.7547414920981 | etot = -15.1409089947334 +716000 ekin = 2.55549921705027 | erot = 2.85756803731154 | epot = -20.7715752448116 | etot = -15.3585079904498 +717000 ekin = 2.66840960058869 | erot = 3.13695167508786 | epot = -20.7817582371968 | etot = -14.9763969615202 +718000 ekin = 2.70162233045717 | erot = 2.88936608298079 | epot = -20.7821953404605 | etot = -15.1912069270225 +719000 ekin = 2.67856075035688 | erot = 3.06593156988589 | epot = -20.7772381096809 | etot = -15.0327457894382 +720000 ekin = 2.73835391684226 | erot = 3.12606615797135 | epot = -20.7642516702525 | etot = -14.8998315954389 +721000 ekin = 2.83298219908753 | erot = 2.86786361439833 | epot = -20.7356626767529 | etot = -15.034816863267 +722000 ekin = 2.84238954774475 | erot = 3.01300544894819 | epot = -20.6952880713171 | etot = -14.8398930746241 +723000 ekin = 2.83841887662262 | erot = 2.85261974479223 | epot = -20.6504830813446 | etot = -14.9594444599298 +724000 ekin = 3.01277617592975 | erot = 3.09042764557505 | epot = -20.6160634840689 | etot = -14.5128596625641 +725000 ekin = 3.17120635017288 | erot = 2.96143140596348 | epot = -20.5877395535627 | etot = -14.4551017974264 +726000 ekin = 3.20454859904884 | erot = 2.97124869107352 | epot = -20.5737408249942 | etot = -14.3979435348719 +727000 ekin = 3.1984655763458 | erot = 2.7778916861742 | epot = -20.5945168300517 | etot = -14.6181595675317 +728000 ekin = 3.28654276144391 | erot = 2.57414717613077 | epot = -20.6404573492144 | etot = -14.7797674116397 +729000 ekin = 3.34397855520275 | erot = 2.60607683819482 | epot = -20.6877535154518 | etot = -14.7376981220543 +730000 ekin = 3.33088715350252 | erot = 2.65576997467214 | epot = -20.7175880662474 | etot = -14.7309309380727 +731000 ekin = 3.33990502646325 | erot = 2.7896619781734 | epot = -20.7385421874518 | etot = -14.6089751828152 +732000 ekin = 3.27037431476568 | erot = 3.1640408813143 | epot = -20.7088668644647 | etot = -14.2744516683848 +733000 ekin = 3.1606234052805 | erot = 3.37415612395548 | epot = -20.6516575424079 | etot = -14.116878013172 +734000 ekin = 3.09953693998359 | erot = 3.25267070419757 | epot = -20.5803936969362 | etot = -14.228186052755 +735000 ekin = 2.94450728592303 | erot = 2.96857162868846 | epot = -20.4729949298549 | etot = -14.5599160152434 +736000 ekin = 2.79584817651803 | erot = 2.92396692050701 | epot = -20.3407691844261 | etot = -14.620954087401 +737000 ekin = 2.72272921166439 | erot = 3.17345753492486 | epot = -20.1979266935858 | etot = -14.3017399469965 +738000 ekin = 2.5433205678578 | erot = 3.29818161761706 | epot = -20.0303847475411 | etot = -14.1888825620663 +739000 ekin = 2.32323875619892 | erot = 2.93500343249736 | epot = -19.8750675706792 | etot = -14.6168253819829 +740000 ekin = 2.15390188391545 | erot = 2.57318962024234 | epot = -19.7116721317167 | etot = -14.9845806275589 +741000 ekin = 1.95437882697973 | erot = 2.32607517304428 | epot = -19.5750053199851 | etot = -15.2945513199611 +742000 ekin = 1.92783578015083 | erot = 2.13064797487013 | epot = -19.4713087417753 | etot = -15.4128249867543 +743000 ekin = 2.04931727768894 | erot = 2.05953320755502 | epot = -19.3808587546544 | etot = -15.2720082694104 +744000 ekin = 1.97574953400554 | erot = 2.06272487174928 | epot = -19.329223801607 | etot = -15.2907493958521 +745000 ekin = 2.04017863714723 | erot = 1.82427330713395 | epot = -19.329462761853 | etot = -15.4650108175718 +746000 ekin = 2.02395159386132 | erot = 1.96899911255016 | epot = -19.3725184887272 | etot = -15.3795677823157 +747000 ekin = 2.09406854938761 | erot = 1.94863482625799 | epot = -19.4739827252225 | etot = -15.4312793495769 +748000 ekin = 2.29815094637996 | erot = 1.90074449731056 | epot = -19.6283880334726 | etot = -15.4294925897821 +749000 ekin = 2.35637166185844 | erot = 1.88187224436566 | epot = -19.8091245759453 | etot = -15.5708806697212 +750000 ekin = 2.46261791012963 | erot = 1.68915240890083 | epot = -20.005990906907 | etot = -15.8542205878765 +751000 ekin = 2.60407300534169 | erot = 1.90400653681749 | epot = -20.20854709803 | etot = -15.7004675558708 +752000 ekin = 2.6908247014245 | erot = 2.30656368674367 | epot = -20.433005538186 | etot = -15.4356171500178 +753000 ekin = 2.86185352213746 | erot = 2.08508944835071 | epot = -20.6608245815303 | etot = -15.7138816110421 +754000 ekin = 2.98333808215654 | erot = 2.53924444651862 | epot = -20.8729357638506 | etot = -15.3503532351755 +755000 ekin = 3.15712054719953 | erot = 2.80998037917447 | epot = -21.0894092143859 | etot = -15.1223082880119 +756000 ekin = 3.33248676900302 | erot = 2.8531869799705 | epot = -21.269924842092 | etot = -15.0842510931185 +757000 ekin = 3.41680611924902 | erot = 2.92784780738217 | epot = -21.4304548340672 | etot = -15.0858009074361 +758000 ekin = 3.39156382871272 | erot = 2.78356707636024 | epot = -21.5766965986288 | etot = -15.4015656935559 +759000 ekin = 3.43155653282481 | erot = 2.83467624438543 | epot = -21.6891769319693 | etot = -15.4229441547591 +760000 ekin = 3.45801219419676 | erot = 2.61557400116959 | epot = -21.7546703090583 | etot = -15.681084113692 +761000 ekin = 3.37717727044754 | erot = 2.89563755209479 | epot = -21.7892028313228 | etot = -15.5163880087804 +762000 ekin = 3.47824550195028 | erot = 2.79188597259482 | epot = -21.7977512926642 | etot = -15.5276198181191 +763000 ekin = 3.47659880804277 | erot = 2.54885516262679 | epot = -21.7781604169457 | etot = -15.7527064462761 +764000 ekin = 3.45277978719479 | erot = 2.64283550756149 | epot = -21.704446978953 | etot = -15.6088316841967 +765000 ekin = 3.39906272086506 | erot = 2.44961754559284 | epot = -21.595031818652 | etot = -15.7463515521941 +766000 ekin = 3.34001470871222 | erot = 2.39682151597909 | epot = -21.4894395399038 | etot = -15.7526033152125 +767000 ekin = 3.45549704932984 | erot = 2.33544666401054 | epot = -21.3866970636423 | etot = -15.595753350302 +768000 ekin = 3.2619807407099 | erot = 2.45762138127385 | epot = -21.2912857370598 | etot = -15.571683615076 +769000 ekin = 3.16082467479752 | erot = 2.36075087935276 | epot = -21.2103530429967 | etot = -15.6887774888465 +770000 ekin = 3.07645918396866 | erot = 2.49259006307431 | epot = -21.1212342627877 | etot = -15.5521850157448 +771000 ekin = 2.92350840414357 | erot = 2.5627524330496 | epot = -21.0363085296099 | etot = -15.5500476924167 +772000 ekin = 2.75979211106249 | erot = 2.44752256772078 | epot = -20.9381586938684 | etot = -15.7308440150851 +773000 ekin = 2.71511621634628 | erot = 2.32937899997693 | epot = -20.8439731838771 | etot = -15.7994779675539 +774000 ekin = 2.55011810434133 | erot = 2.4833205550091 | epot = -20.7658389533283 | etot = -15.7324002939779 +775000 ekin = 2.41197388502347 | erot = 2.62818884118437 | epot = -20.7179622711123 | etot = -15.6777995449045 +776000 ekin = 2.37508963815622 | erot = 2.44136937227733 | epot = -20.7211512138299 | etot = -15.9046922033964 +777000 ekin = 2.34948686881498 | erot = 2.36213131358752 | epot = -20.7370244755334 | etot = -16.0254062931309 +778000 ekin = 2.29585534902512 | erot = 2.73124120723748 | epot = -20.7683121988633 | etot = -15.7412156426007 +779000 ekin = 2.18150396589516 | erot = 2.72210705119083 | epot = -20.8059074416481 | etot = -15.9022964245621 +780000 ekin = 2.26066885699459 | erot = 2.87221231082939 | epot = -20.8394643204864 | etot = -15.7065831526624 +781000 ekin = 2.27461625652605 | erot = 2.81372031403651 | epot = -20.8757314682942 | etot = -15.7873948977317 +782000 ekin = 2.19892592960427 | erot = 2.61785718560358 | epot = -20.896513130731 | etot = -16.0797300155231 +783000 ekin = 2.22941617588637 | erot = 2.47751279799149 | epot = -20.9183852720846 | etot = -16.2114562982067 +784000 ekin = 2.42718924867981 | erot = 2.81382459332938 | epot = -20.9279105230668 | etot = -15.6868966810576 +785000 ekin = 2.38825632563832 | erot = 2.70987963105489 | epot = -20.9108108361698 | etot = -15.8126748794765 +786000 ekin = 2.44404618711738 | erot = 2.52658585483967 | epot = -20.9041006583268 | etot = -15.9334686163698 +787000 ekin = 2.50702113933265 | erot = 2.2829310580732 | epot = -20.8749015767322 | etot = -16.0849493793263 +788000 ekin = 2.449066668908 | erot = 2.41360841664415 | epot = -20.8341700774429 | etot = -15.9714949918908 +789000 ekin = 2.52045486785602 | erot = 2.52744454804461 | epot = -20.7905656205231 | etot = -15.7426662046225 +790000 ekin = 2.52825818807968 | erot = 2.68548159035131 | epot = -20.7575819502236 | etot = -15.5438421717926 +791000 ekin = 2.64995125141669 | erot = 2.7398749354846 | epot = -20.7349773993635 | etot = -15.3451512124622 +792000 ekin = 2.70397080831142 | erot = 2.64980290799399 | epot = -20.7100100046771 | etot = -15.3562362883717 +793000 ekin = 2.75033294845277 | erot = 2.54340061653004 | epot = -20.7078362971787 | etot = -15.4141027321959 +794000 ekin = 2.86533813114897 | erot = 2.55380338833676 | epot = -20.7048471683322 | etot = -15.2857056488465 +795000 ekin = 2.78119650415392 | erot = 2.2671096734503 | epot = -20.7038606047267 | etot = -15.6555544271225 +796000 ekin = 2.75247729659435 | erot = 1.93248690499328 | epot = -20.7002506155577 | etot = -16.0152864139701 +797000 ekin = 2.87695524377374 | erot = 1.75440457751947 | epot = -20.7015802402501 | etot = -16.0702204189569 +798000 ekin = 2.92176058311451 | erot = 1.87424589751703 | epot = -20.7289229999119 | etot = -15.9329165192803 +799000 ekin = 2.84123141391864 | erot = 1.69781273980121 | epot = -20.7536194869373 | etot = -16.2145753332175 +800000 ekin = 2.88647051776051 | erot = 1.88458846794839 | epot = -20.7813888694617 | etot = -16.0103298837528 +801000 ekin = 2.82188707288349 | erot = 1.97533232918811 | epot = -20.785439046684 | etot = -15.9882196446124 +802000 ekin = 2.80670744878582 | erot = 1.9217082384784 | epot = -20.7694229323805 | etot = -16.0410072451162 +803000 ekin = 2.81917409800211 | erot = 1.86293659025173 | epot = -20.7368809564661 | etot = -16.0547702682123 +804000 ekin = 2.81542679490125 | erot = 1.82483816347956 | epot = -20.7049136915728 | etot = -16.064648733192 +805000 ekin = 2.76621025300973 | erot = 1.80656496128526 | epot = -20.6689552876867 | etot = -16.0961800733917 +806000 ekin = 2.65050365938186 | erot = 2.07564631955327 | epot = -20.6394756033499 | etot = -15.9133256244147 +807000 ekin = 2.55624134566849 | erot = 2.16054307897175 | epot = -20.6134778956027 | etot = -15.8966934709625 +808000 ekin = 2.48738013720894 | erot = 2.3214738917894 | epot = -20.5888178207126 | etot = -15.7799637917143 +809000 ekin = 2.4786273298809 | erot = 2.48498826094782 | epot = -20.5619387083683 | etot = -15.5983231175395 +810000 ekin = 2.39703068581702 | erot = 2.81931500773821 | epot = -20.5424309669724 | etot = -15.3260852734171 +811000 ekin = 2.3788728748584 | erot = 2.69438802886514 | epot = -20.5520463788999 | etot = -15.4787854751764 +812000 ekin = 2.28085047814011 | erot = 2.42485138426983 | epot = -20.5550539173041 | etot = -15.8493520548942 +813000 ekin = 2.25229479784333 | erot = 2.55707080478997 | epot = -20.5502753315573 | etot = -15.740909728924 +814000 ekin = 2.22024450946101 | erot = 2.84053382533205 | epot = -20.5291885807552 | etot = -15.4684102459621 +815000 ekin = 2.14652605610512 | erot = 2.67021357483775 | epot = -20.4999623788213 | etot = -15.6832227478784 +816000 ekin = 2.15941760298178 | erot = 2.59153501297961 | epot = -20.4557339217928 | etot = -15.7047813058314 +817000 ekin = 2.16476188533233 | erot = 2.33413354584406 | epot = -20.3878114616857 | etot = -15.8889160305093 +818000 ekin = 2.23169646758985 | erot = 2.16459446462094 | epot = -20.3094264209637 | etot = -15.9131354887529 +819000 ekin = 2.15183597112987 | erot = 1.96236374628708 | epot = -20.2442212233182 | etot = -16.1300215059012 +820000 ekin = 2.15160519820162 | erot = 1.78654941276898 | epot = -20.1685556064365 | etot = -16.2304009954659 +821000 ekin = 2.11411181703442 | erot = 1.59439007001326 | epot = -20.1045081087122 | etot = -16.3960062216645 +822000 ekin = 2.09578590796817 | erot = 1.82458690696508 | epot = -20.0615873148671 | etot = -16.1412144999339 +823000 ekin = 2.08554311077394 | erot = 1.79122152448742 | epot = -20.05426155862 | etot = -16.1774969233586 +824000 ekin = 2.06608530910562 | erot = 1.83488646651511 | epot = -20.0832229529292 | etot = -16.1822511773085 +825000 ekin = 2.12914321441473 | erot = 2.12189619250084 | epot = -20.129726854944 | etot = -15.8786874480284 +826000 ekin = 2.17617898744283 | erot = 2.29556289596582 | epot = -20.1726463529248 | etot = -15.7009044695161 +827000 ekin = 2.15419331300564 | erot = 2.34308143022498 | epot = -20.2056332381731 | etot = -15.7083584949425 +828000 ekin = 2.20039878821187 | erot = 2.41783518802144 | epot = -20.2229965044052 | etot = -15.6047625281719 +829000 ekin = 2.20314847732563 | erot = 2.56607297380303 | epot = -20.2051061030748 | etot = -15.4358846519461 +830000 ekin = 2.30175185120447 | erot = 2.43964061204034 | epot = -20.1552304697959 | etot = -15.4138380065511 +831000 ekin = 2.24000691994535 | erot = 2.16496177189548 | epot = -20.0860391808212 | etot = -15.6810704889804 +832000 ekin = 2.23825638063332 | erot = 2.25483913353678 | epot = -20.0235934169574 | etot = -15.5304979027873 +833000 ekin = 2.16205349111635 | erot = 1.94237500276366 | epot = -19.98792746414 | etot = -15.88349897026 +834000 ekin = 2.16740768022471 | erot = 1.70564999745791 | epot = -19.9844147815713 | etot = -16.1113571038887 +835000 ekin = 2.17278893541038 | erot = 1.56429512699083 | epot = -20.0201055001643 | etot = -16.2830214377631 +836000 ekin = 2.12097731365439 | erot = 1.73560474622193 | epot = -20.0572346764648 | etot = -16.2006526165885 +837000 ekin = 2.13598638451579 | erot = 1.79213525365431 | epot = -20.0629697156965 | etot = -16.1348480775264 +838000 ekin = 2.15523665997388 | erot = 1.65975767864979 | epot = -20.0531324206636 | etot = -16.23813808204 +839000 ekin = 2.18050335550322 | erot = 1.62185210117962 | epot = -20.0624518040171 | etot = -16.2600963473343 +840000 ekin = 2.26003994524067 | erot = 1.64754456826616 | epot = -20.0987090628811 | etot = -16.1911245493743 +841000 ekin = 2.35849160545659 | erot = 1.45991256461148 | epot = -20.1235761929063 | etot = -16.3051720228382 +842000 ekin = 2.30506950612859 | erot = 1.67704941831981 | epot = -20.1403357838886 | etot = -16.1582168594402 +843000 ekin = 2.2500061210523 | erot = 1.57916412105133 | epot = -20.1787490850449 | etot = -16.3495788429413 +844000 ekin = 2.36131993993639 | erot = 1.7422482396807 | epot = -20.2587879559386 | etot = -16.1552197763215 +845000 ekin = 2.37622491879818 | erot = 1.78604993278495 | epot = -20.3527813128756 | etot = -16.1905064612925 +846000 ekin = 2.34115102661073 | erot = 1.84579845054569 | epot = -20.4555275090993 | etot = -16.2685780319429 +847000 ekin = 2.41159198035449 | erot = 1.92961286076146 | epot = -20.5532540909634 | etot = -16.2120492498474 +848000 ekin = 2.31213774862315 | erot = 2.08278486795981 | epot = -20.6337560180198 | etot = -16.2388334014369 +849000 ekin = 2.30336620270284 | erot = 2.04122209248456 | epot = -20.6821032694946 | etot = -16.3375149743072 +850000 ekin = 2.25629668954034 | erot = 2.18270894613907 | epot = -20.7098894953332 | etot = -16.2708838596538 +851000 ekin = 2.29979938433462 | erot = 2.41406540449308 | epot = -20.7044118358106 | etot = -15.9905470469829 +852000 ekin = 2.26390891815814 | erot = 2.16338375104463 | epot = -20.6569849671616 | etot = -16.2296922979588 +853000 ekin = 2.30424571101269 | erot = 1.99747184850889 | epot = -20.5998336497754 | etot = -16.2981160902538 +854000 ekin = 2.36419736155922 | erot = 2.06846824934134 | epot = -20.5204281972685 | etot = -16.087762586368 +855000 ekin = 2.34728028486071 | erot = 1.93310140620006 | epot = -20.4489431066129 | etot = -16.1685614155521 +856000 ekin = 2.30561682537882 | erot = 1.74682255934551 | epot = -20.3871281777728 | etot = -16.3346887930485 +857000 ekin = 2.27745448387204 | erot = 1.83570056454375 | epot = -20.3461722185291 | etot = -16.2330171701133 +858000 ekin = 2.36509593163705 | erot = 1.75581829580632 | epot = -20.3410559181939 | etot = -16.2201416907505 +859000 ekin = 2.38832938274166 | erot = 1.82095166272796 | epot = -20.3690417944101 | etot = -16.1597607489404 +860000 ekin = 2.52181162102379 | erot = 1.95420940577036 | epot = -20.4478015207828 | etot = -15.9717804939886 +861000 ekin = 2.62858628470775 | erot = 1.82148423675541 | epot = -20.5405427960158 | etot = -16.0904722745526 +862000 ekin = 2.69973060754128 | erot = 1.84887576916202 | epot = -20.662955197763 | etot = -16.1143488210597 +863000 ekin = 2.90205526612742 | erot = 1.9505383034712 | epot = -20.7912991546473 | etot = -15.9387055850487 +864000 ekin = 3.12658816228328 | erot = 1.98858429691928 | epot = -20.8929021658141 | etot = -15.7777297066115 +865000 ekin = 3.16945674700263 | erot = 1.86291391059832 | epot = -20.9419832509072 | etot = -15.9096125933062 +866000 ekin = 3.25216934165261 | erot = 1.97645641207194 | epot = -20.9567552239711 | etot = -15.7281294702465 +867000 ekin = 3.2494503723315 | erot = 1.84073824549774 | epot = -20.9282973760209 | etot = -15.8381087581916 +868000 ekin = 3.07999788772614 | erot = 1.92805224835502 | epot = -20.8706478182271 | etot = -15.862597682146 +869000 ekin = 2.91009138976912 | erot = 1.95537175968477 | epot = -20.7577406936844 | etot = -15.8922775442305 +870000 ekin = 2.98633737341233 | erot = 1.74639234614424 | epot = -20.6193203055692 | etot = -15.8865905860126 +871000 ekin = 2.82797025785063 | erot = 2.2221678986274 | epot = -20.5143766346296 | etot = -15.4642384781516 +872000 ekin = 2.75225970096219 | erot = 2.04685014109629 | epot = -20.419745056361 | etot = -15.6206352143025 +873000 ekin = 2.76508179334976 | erot = 2.0780239133508 | epot = -20.3610564187735 | etot = -15.5179507120729 +874000 ekin = 2.70667266094239 | erot = 2.03935635819004 | epot = -20.3167066993027 | etot = -15.5706776801702 +875000 ekin = 2.75331326518739 | erot = 1.87289863150002 | epot = -20.2923067700679 | etot = -15.6660948733804 +876000 ekin = 2.71618421707332 | erot = 1.89637161128803 | epot = -20.2754390470308 | etot = -15.6628832186694 +877000 ekin = 2.71649559901581 | erot = 2.02021579600109 | epot = -20.2646771674153 | etot = -15.5279657723984 +878000 ekin = 2.62749245340236 | erot = 1.88626086619175 | epot = -20.2836933343764 | etot = -15.7699400147823 +879000 ekin = 2.74884813769589 | erot = 1.75263692861076 | epot = -20.3265216122734 | etot = -15.8250365459667 +880000 ekin = 2.71696155764913 | erot = 1.77313431669201 | epot = -20.4055312116441 | etot = -15.9154353373029 +881000 ekin = 2.78382645158938 | erot = 1.81182472346934 | epot = -20.5191596774775 | etot = -15.9235085024187 +882000 ekin = 2.81130894387557 | erot = 2.09576450580371 | epot = -20.6489904734918 | etot = -15.7419170238125 +883000 ekin = 2.88120316600255 | erot = 2.27294351864347 | epot = -20.7888871990884 | etot = -15.6347405144424 +884000 ekin = 2.90293873255487 | erot = 2.48430131570226 | epot = -20.9203204845748 | etot = -15.5330804363176 +885000 ekin = 2.83822193724247 | erot = 2.33567911137719 | epot = -21.0170580718202 | etot = -15.8431570232006 +886000 ekin = 2.79980127208535 | erot = 2.39879132479705 | epot = -21.1056755206464 | etot = -15.907082923764 +887000 ekin = 2.84559753547752 | erot = 2.23279918443311 | epot = -21.1991974917516 | etot = -16.120800771841 +888000 ekin = 2.78048788087594 | erot = 2.21910506766694 | epot = -21.2985745989321 | etot = -16.2989816503892 +889000 ekin = 2.69583578763822 | erot = 2.42515435306365 | epot = -21.3860199387973 | etot = -16.2650297980954 +890000 ekin = 2.58377832307665 | erot = 2.46763021206624 | epot = -21.4668454924046 | etot = -16.4154369572618 +891000 ekin = 2.65145947657465 | erot = 2.54188813630582 | epot = -21.5059683813089 | etot = -16.3126207684284 +892000 ekin = 2.67593216257268 | erot = 2.30931133615791 | epot = -21.5221026652212 | etot = -16.5368591664906 +893000 ekin = 2.63303791081994 | erot = 2.54633069672419 | epot = -21.5431241050783 | etot = -16.3637554975342 +894000 ekin = 2.67500961491449 | erot = 2.62632956964425 | epot = -21.5659877596137 | etot = -16.264648575055 +895000 ekin = 2.69351100875689 | erot = 2.87253630615196 | epot = -21.5608314238545 | etot = -15.9947841089456 +896000 ekin = 2.73971679868387 | erot = 2.8375196836984 | epot = -21.5599160231104 | etot = -15.9826795407282 +897000 ekin = 2.5902415606045 | erot = 3.14999384860249 | epot = -21.516909346574 | etot = -15.776673937367 +898000 ekin = 2.53463691976883 | erot = 2.86279041479487 | epot = -21.4480578810232 | etot = -16.0506305464595 +899000 ekin = 2.47014007897575 | erot = 2.84092875108416 | epot = -21.4001318574341 | etot = -16.0890630273742 +900000 ekin = 2.41396838915872 | erot = 2.6111943771977 | epot = -21.3171783985112 | etot = -16.2920156321548 +901000 ekin = 2.39217135029546 | erot = 2.42887884956528 | epot = -21.2332353575315 | etot = -16.4121851576708 +902000 ekin = 2.35623147489279 | erot = 2.68618153800013 | epot = -21.1565378225643 | etot = -16.1141248096714 +903000 ekin = 2.40445872766433 | erot = 2.65960453389378 | epot = -21.0523977096234 | etot = -15.9883344480653 +904000 ekin = 2.38268859333691 | erot = 2.75563140701143 | epot = -20.925421167619 | etot = -15.7871011672707 +905000 ekin = 2.33859357853536 | erot = 2.74896960744429 | epot = -20.7865758980935 | etot = -15.6990127121138 +906000 ekin = 2.24424050125651 | erot = 2.6721901140042 | epot = -20.6458687615366 | etot = -15.7294381462758 +907000 ekin = 2.11959693796205 | erot = 2.69124042762419 | epot = -20.5218058154346 | etot = -15.7109684498484 +908000 ekin = 1.99538198820349 | erot = 2.73765845183728 | epot = -20.4226667461159 | etot = -15.6896263060752 +909000 ekin = 1.91948050394701 | erot = 2.81092155872986 | epot = -20.3715084186367 | etot = -15.6411063559599 +910000 ekin = 1.8655950428113 | erot = 2.50422584065975 | epot = -20.3542958576836 | etot = -15.9844749742126 +911000 ekin = 1.93700212306605 | erot = 2.70182168284106 | epot = -20.36304703947 | etot = -15.7242232335629 +912000 ekin = 2.01297731830373 | erot = 2.5933346831101 | epot = -20.4016114857558 | etot = -15.795299484342 +913000 ekin = 2.04893253293605 | erot = 2.44335563755528 | epot = -20.4595271951793 | etot = -15.967239024688 +914000 ekin = 2.13522967419267 | erot = 2.04488675557119 | epot = -20.5157656558608 | etot = -16.3356492260969 +915000 ekin = 2.25766070321671 | erot = 1.97393473123396 | epot = -20.6118613948302 | etot = -16.3802659603795 +916000 ekin = 2.21223622141659 | erot = 2.10345838304649 | epot = -20.7544105240985 | etot = -16.4387159196355 +917000 ekin = 2.40651996373637 | erot = 1.99495172303712 | epot = -20.9073170323377 | etot = -16.5058453455642 +918000 ekin = 2.5361573098891 | erot = 2.01638663666306 | epot = -21.0405250498192 | etot = -16.4879811032671 +919000 ekin = 2.65442530964944 | erot = 2.08762135935637 | epot = -21.171971145483 | etot = -16.4299244764772 +920000 ekin = 2.77534951778621 | erot = 2.11359099299359 | epot = -21.2829839475284 | etot = -16.3940434367486 +921000 ekin = 2.91643782768201 | erot = 2.28215815938532 | epot = -21.3691506671597 | etot = -16.1705546800924 +922000 ekin = 2.9556740067861 | erot = 1.92472032499983 | epot = -21.4077235507572 | etot = -16.5273292189713 +923000 ekin = 2.96258486890851 | erot = 1.54690402842656 | epot = -21.3938794896997 | etot = -16.8843905923646 +924000 ekin = 2.92134762613169 | erot = 1.70996406555908 | epot = -21.3449839261319 | etot = -16.7136722344412 +925000 ekin = 2.84653903464837 | erot = 1.92806668586753 | epot = -21.2846325911293 | etot = -16.5100268706134 +926000 ekin = 2.90254254848568 | erot = 2.07364806195503 | epot = -21.2015262749296 | etot = -16.2253356644889 +927000 ekin = 2.91395828926385 | erot = 2.18066099339434 | epot = -21.1200145418058 | etot = -16.0253952591476 +928000 ekin = 2.8451289411599 | erot = 2.48044872209644 | epot = -20.9999796012797 | etot = -15.6744019380233 +929000 ekin = 2.66004165976089 | erot = 2.5177933604696 | epot = -20.8727093584581 | etot = -15.6948743382276 +930000 ekin = 2.65454667829403 | erot = 2.5756927474138 | epot = -20.7556416891762 | etot = -15.5254022634684 +931000 ekin = 2.67423829393911 | erot = 2.88523636975878 | epot = -20.6759551108847 | etot = -15.1164804471868 +932000 ekin = 2.62616449296317 | erot = 2.54798110237906 | epot = -20.6086291233295 | etot = -15.4344835279872 +933000 ekin = 2.69383973705561 | erot = 2.46235736679292 | epot = -20.5456125856306 | etot = -15.389415481782 +934000 ekin = 2.7677642743107 | erot = 2.3410108478683 | epot = -20.4809121018793 | etot = -15.3721369797003 +935000 ekin = 2.72642510821342 | erot = 2.35916469229072 | epot = -20.421116596235 | etot = -15.3355267957309 +936000 ekin = 2.79063797840903 | erot = 2.07475414089676 | epot = -20.3957585636203 | etot = -15.5303664443145 +937000 ekin = 2.98467692525982 | erot = 1.99225267024792 | epot = -20.4024768464836 | etot = -15.4255472509759 +938000 ekin = 3.04156516590295 | erot = 2.13242133064001 | epot = -20.3998804937971 | etot = -15.2258939972542 +939000 ekin = 3.07943235169605 | erot = 2.19292802789723 | epot = -20.3770156967224 | etot = -15.1046553171291 +940000 ekin = 3.11450220916298 | erot = 2.05442808222248 | epot = -20.338662940712 | etot = -15.1697326493265 +941000 ekin = 3.16737235726218 | erot = 2.43340006549767 | epot = -20.276052119725 | etot = -14.6752796969652 +942000 ekin = 3.27652888451136 | erot = 2.440543875825 | epot = -20.1668692973993 | etot = -14.449796537063 +943000 ekin = 3.13900445201095 | erot = 2.17030471354829 | epot = -20.026706304132 | etot = -14.7173971385727 +944000 ekin = 3.115776797146 | erot = 1.97360877260937 | epot = -19.8813791244599 | etot = -14.7919935547045 +945000 ekin = 3.14747064890596 | erot = 1.73794156198896 | epot = -19.73006542878 | etot = -14.8446532178851 +946000 ekin = 3.06500562594201 | erot = 1.59817914677177 | epot = -19.5836319520482 | etot = -14.9204471793344 +947000 ekin = 3.06465941958359 | erot = 1.56394261373872 | epot = -19.4474159558772 | etot = -14.8188139225549 +948000 ekin = 3.07897503028507 | erot = 1.70141948030269 | epot = -19.3426980410742 | etot = -14.5623035304865 +949000 ekin = 2.87406117522915 | erot = 1.60153309498395 | epot = -19.2597755284807 | etot = -14.7841812582676 +950000 ekin = 2.84815804599135 | erot = 1.4271569018952 | epot = -19.2062266956087 | etot = -14.9309117477221 +951000 ekin = 2.78080942687071 | erot = 1.40916295422847 | epot = -19.1985529774587 | etot = -15.0085805963595 +952000 ekin = 2.67957446722111 | erot = 1.63751827005629 | epot = -19.1980674262526 | etot = -14.8809746889752 +953000 ekin = 2.69185316270131 | erot = 1.85029680460115 | epot = -19.2316635394472 | etot = -14.6895135721448 +954000 ekin = 2.64694034455319 | erot = 2.11448729476973 | epot = -19.2977991859257 | etot = -14.5363715466028 +955000 ekin = 2.73224102166805 | erot = 2.37373438935258 | epot = -19.3777324828798 | etot = -14.2717570718591 +956000 ekin = 2.80603458830151 | erot = 2.32665803374313 | epot = -19.4665233130263 | etot = -14.3338306909816 +957000 ekin = 2.73176061747201 | erot = 2.74205596111958 | epot = -19.5249802574393 | etot = -14.0511636788477 +958000 ekin = 2.77128367160812 | erot = 2.70682711528389 | epot = -19.5522596510489 | etot = -14.0741488641569 +959000 ekin = 2.78347654187703 | erot = 2.83940326280204 | epot = -19.5446437759979 | etot = -13.9217639713188 +960000 ekin = 2.63327999523985 | erot = 3.22713050217902 | epot = -19.5114109332441 | etot = -13.6510004358253 +961000 ekin = 2.53039842552533 | erot = 3.04837954363136 | epot = -19.4489807736385 | etot = -13.8702028044818 +962000 ekin = 2.42158405784708 | erot = 2.73764467618042 | epot = -19.3495392486846 | etot = -14.1903105146571 +963000 ekin = 2.35599553488234 | erot = 2.68171440217426 | epot = -19.2270773719364 | etot = -14.1893674348798 +964000 ekin = 2.25219457310666 | erot = 2.53224426940247 | epot = -19.0939126804608 | etot = -14.3094738379516 +965000 ekin = 2.15172115406585 | erot = 2.50742636400585 | epot = -18.965540109871 | etot = -14.3063925917993 +966000 ekin = 2.08836430745308 | erot = 2.10683533981447 | epot = -18.8740473984183 | etot = -14.6788477511507 +967000 ekin = 2.12576981405813 | erot = 2.10554977010201 | epot = -18.8222969563422 | etot = -14.5909773721821 +968000 ekin = 2.1292401689921 | erot = 1.91970464113333 | epot = -18.8304973627001 | etot = -14.7815525525746 +969000 ekin = 2.1744253034849 | erot = 2.16512140090537 | epot = -18.8673529233375 | etot = -14.5278062189472 +970000 ekin = 2.18162741265366 | erot = 2.24508625813671 | epot = -18.9283529594578 | etot = -14.5016392886674 +971000 ekin = 2.1872176318086 | erot = 2.43353633304484 | epot = -19.0277599144679 | etot = -14.4070059496144 +972000 ekin = 2.2705546404458 | erot = 2.03487376489205 | epot = -19.12908661878 | etot = -14.8236582134421 +973000 ekin = 2.33904004605622 | erot = 2.1518392891247 | epot = -19.2366611806893 | etot = -14.7457818455084 +974000 ekin = 2.4184780784401 | erot = 2.34438108784224 | epot = -19.3631184324864 | etot = -14.600259266204 +975000 ekin = 2.46206146488035 | erot = 2.35624199281851 | epot = -19.4736098152942 | etot = -14.6553063575954 +976000 ekin = 2.52456876946493 | erot = 2.27614398265601 | epot = -19.564991557351 | etot = -14.7642788052301 +977000 ekin = 2.60637564524348 | erot = 2.07093705811744 | epot = -19.6101874123269 | etot = -14.932874708966 +978000 ekin = 2.61064269720999 | erot = 2.072025245106 | epot = -19.6294451297035 | etot = -14.9467771873875 +979000 ekin = 2.55561169069442 | erot = 2.18920140876197 | epot = -19.6166445363178 | etot = -14.8718314368614 +980000 ekin = 2.56864273287433 | erot = 2.03395631393331 | epot = -19.6174963338775 | etot = -15.0148972870698 +981000 ekin = 2.66191070196797 | erot = 2.1665909590768 | epot = -19.6250525963032 | etot = -14.7965509352584 +982000 ekin = 2.61731281327803 | erot = 2.24698893274284 | epot = -19.5974740187268 | etot = -14.7331722727059 +983000 ekin = 2.54225454915863 | erot = 2.48926874093363 | epot = -19.5745894051773 | etot = -14.5430661150851 +984000 ekin = 2.50737950403339 | erot = 3.03624865807167 | epot = -19.5602814074042 | etot = -14.0166532452991 +985000 ekin = 2.41525281557154 | erot = 2.79336029081712 | epot = -19.5475069203691 | etot = -14.3388938139804 +986000 ekin = 2.43517645380123 | erot = 2.71437828234949 | epot = -19.5659718124297 | etot = -14.416417076279 +987000 ekin = 2.43635014041211 | erot = 2.70440060167989 | epot = -19.6117703785928 | etot = -14.4710196365008 +988000 ekin = 2.47223137990766 | erot = 3.04012548433551 | epot = -19.6728653378127 | etot = -14.1605084735695 +989000 ekin = 2.57461282782905 | erot = 2.65740086918245 | epot = -19.7180658550378 | etot = -14.4860521580263 +990000 ekin = 2.67359097736915 | erot = 2.60446843961483 | epot = -19.7676266504487 | etot = -14.4895672334648 +991000 ekin = 2.7042668817371 | erot = 2.78857306259774 | epot = -19.8289708825362 | etot = -14.3361309382014 +992000 ekin = 2.77048904951409 | erot = 3.05066231165506 | epot = -19.9192662402546 | etot = -14.0981148790855 +993000 ekin = 2.82958876080101 | erot = 2.65444369525341 | epot = -20.0030938662596 | etot = -14.5190614102052 +994000 ekin = 2.90170601691324 | erot = 2.65673610083159 | epot = -20.0686975144625 | etot = -14.5102553967177 +995000 ekin = 3.03287923230103 | erot = 2.40306030617926 | epot = -20.1412612654703 | etot = -14.70532172699 +996000 ekin = 3.01357004889746 | erot = 1.93970518668616 | epot = -20.2209046421983 | etot = -15.2676294066147 +997000 ekin = 3.16382267303395 | erot = 2.09671009945301 | epot = -20.2929309039621 | etot = -15.0323981314751 +998000 ekin = 3.20277399494116 | erot = 2.11561017239357 | epot = -20.3495982469419 | etot = -15.0312140796072 +999000 ekin = 3.17166482809342 | erot = 2.14572404428907 | epot = -20.3850372708097 | etot = -15.0676483984272 +1000000 ekin = 3.19306217159857 | erot = 2.46621953381515 | epot = -20.4393210047155 | etot = -14.7800392993018 + 1000000 0.14191387 -1.3172305 0.039772926 -1.0778912 3.1162031e-05 64000 +Loop time of 20.4289 on 4 procs for 1000000 steps with 16 atoms + +Performance: 42293.109 tau/day, 48950.357 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.166 | 9.113 | 12.302 | 77.6 | 44.61 +Bond | 0.28759 | 0.35897 | 0.40037 | 7.6 | 1.76 +Neigh | 0.007409 | 0.0075045 | 0.007636 | 0.1 | 0.04 +Comm | 4.5107 | 7.8624 | 10.62 | 83.8 | 38.49 +Output | 0.091711 | 0.096687 | 0.10744 | 2.0 | 0.47 +Modify | 1.2913 | 1.4454 | 1.6019 | 11.5 | 7.08 +Other | | 1.545 | | | 7.56 + +Nlocal: 4.00000 ave 5 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 12.0000 ave 13 max 11 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 26.7500 ave 45 max 11 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875000 +Ave special neighs/atom = 3.7500000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:20 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 new file mode 100644 index 0000000000..d2556f87e9 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 @@ -0,0 +1,68 @@ +LAMMPS data file via write_data, version 27 May 2021 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 1 +2 1 +3 1 +4 1 + +Atoms # hybrid + +1 1 -0.11270997503399371 -0.7862611620723637 1.3165400870544903 1 1 0.060395054525384434 0 0 0 +2 2 -0.16100240482903602 -1.0148422652606093 1.7725173088171975 1 1 0.060395054525384434 0 0 0 +3 3 -0.07298109176865208 -1.2058352049378398 2.2155374630046025 1 1 0.060395054525384434 0 0 0 +4 4 0.20885923193243378 -1.2688318677749852 2.7293157091426354 1 1 0.060395054525384434 0 0 0 +5 1 0.4977080746488808 -1.1877183116613397 3.1217952838980874 1 1 0.060395054525384434 0 0 0 +6 4 -0.2268968274787041 -0.189603020612256 3.1084583050105072 2 1 0.060395054525384434 0 0 0 +7 1 -0.0350302960648884 -0.11245734514413211 2.7014501755341493 2 1 0.060395054525384434 0 0 0 +8 2 0.25244681036675387 -0.03694235704351071 2.3220950502861553 2 1 0.060395054525384434 0 0 0 +9 3 0.6676541258850296 -0.19471246409842435 2.0340464261767104 2 1 0.060395054525384434 0 0 0 +10 4 0.934602266948905 -0.5194117909409754 1.8612193115349325 2 1 0.060395054525384434 0 0 0 + +Velocities + +1 0.7350861197179651 -0.21340767305489933 0.039697389523131524 0.514970941606362 -0.5778402699166201 0.41643574848945447 +2 0.45886825731636693 0.15479323180826426 0.45998155912439004 -0.09532046111956156 -0.028811462065931184 0.1672428695820793 +3 -0.10009582230026307 -0.1356043155573722 -0.1357102030132947 0.512435093836635 0.8794667047362844 -0.4062045597142004 +4 -0.030407148345627223 -0.009119685021467273 0.2894674569635424 -0.22197357320787495 0.46474035192627294 -0.07166539037437039 +5 0.021807141873185235 -0.3544326055489752 0.4440408124043861 -0.019877710182688496 0.008454084203717545 -0.16574323908949498 +6 0.058814594979770644 -0.23964725458291067 0.09430081861001074 -0.16841516333125345 -0.27499692207835863 0.49231682345951117 +7 -0.004278840261670186 0.011171100752661912 -0.10686407869958243 0.3533956051874728 -0.5781793964284943 0.171273466705473 +8 -0.5678723978567293 -0.05635280062816237 -0.12337612014269532 -0.06293014166900977 -0.5548255617488771 -0.3948679676680598 +9 0.07493146865794496 0.37868089841113717 0.11143666048372917 -0.35561925325917687 -0.3453461570214745 -0.5277976799082732 +10 -0.48819053761319386 -0.11027061946453155 0.19465531836187655 0.10340969323917759 0.3809806548307742 0.25623918588602335 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.9824438652148015 -0.023183015026523597 -0.18238525095550406 0.031657854475291056 +2 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.9303156820429525 0.02962373336578937 -0.07607439157272995 0.3575581814380256 +3 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.7912072782182723 -0.043679545103099016 -0.05996218100443608 0.6070318583758278 +4 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.6531869542452552 -0.03659000162837596 0.004181596561545229 0.7563005281201641 +5 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.3249781771672557 0.06207197535108856 0.03689277251937633 0.9429608568635791 +6 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.08029535222204207 0.8726095530830543 -0.46831094470633033 -0.11309325067392484 +7 3.1622776601683795 3.1622776601683795 3.1622776601683795 -0.1303991484205687 0.7764383491760718 -0.6081660772848121 0.10135864274905797 +8 3.1622776601683795 3.1622776601683795 3.1622776601683795 -0.14971034142173664 0.5769499085020084 -0.7973230447846137 0.09482393688465168 +9 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.21130729744233523 -0.37917864508185584 0.8946270178621702 -0.10590221939385809 +10 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.34278400171414436 0.15185237372800306 0.9252984668160771 0.05712032974191834 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 similarity index 65% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 index 8c917321c7..1f6bcc5bef 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 @@ -2,20 +2,21 @@ variable number equal 3 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 +variable rhos equal 0.2 units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 1 delay 0 check yes read_data data.duplex3 @@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 # NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" +compute quat all property/atom quatw quati quatj quatk compute erot all erotate/asphere compute ekin all ke @@ -72,10 +62,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" run 1000000 -#write_restart config.${number}.* +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 new file mode 100644 index 0000000000..db8afff444 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 @@ -0,0 +1,1181 @@ +LAMMPS (2 Jul 2021) +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +set atom * mass 1.0 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.3.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 1.18025158324274 | erot = 2.17908479136507 | epot = -11.4931199991265 | etot = -8.13378362451864 +Per MPI rank memory allocation (min/avg/max) = 9.198 | 9.198 | 9.198 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.087426043 -1.2259004 0.076588446 -1.0312868 -7.7802026e-06 64000 +1000 ekin = 1.08696491147664 | erot = 2.23197650714075 | epot = -11.4527250425129 | etot = -8.13378362389549 +2000 ekin = 1.01265115460252 | erot = 2.29132031278141 | epot = -11.4377550908151 | etot = -8.13378362343119 +3000 ekin = 0.964951920610362 | erot = 2.35614244814783 | epot = -11.4548779921653 | etot = -8.13378362340706 +4000 ekin = 0.945861179227109 | erot = 2.42482489276794 | epot = -11.504469695762 | etot = -8.13378362376699 +5000 ekin = 0.952186940161594 | erot = 2.49508744948287 | epot = -11.5810580140496 | etot = -8.13378362440513 +6000 ekin = 0.976836955567339 | erot = 2.56435791368456 | epot = -11.6749784943528 | etot = -8.13378362510091 +7000 ekin = 1.01151727363105 | erot = 2.63034980765842 | epot = -11.7756507069156 | etot = -8.13378362562616 +8000 ekin = 1.04963768886898 | erot = 2.69159648304404 | epot = -11.8750177977506 | etot = -8.13378362583759 +9000 ekin = 1.08831406483925 | erot = 2.74768757650641 | epot = -11.9697852671577 | etot = -8.13378362581202 +10000 ekin = 1.12769894654433 | erot = 2.79881902231421 | epot = -12.0603015945015 | etot = -8.13378362564291 +11000 ekin = 1.16997706279097 | erot = 2.84539220453504 | epot = -12.1491528928087 | etot = -8.13378362548265 +12000 ekin = 1.21772825403564 | erot = 2.88753582693543 | epot = -12.2390477064186 | etot = -8.13378362544756 +13000 ekin = 1.27247277648631 | erot = 2.92478423931378 | epot = -12.3310406413901 | etot = -8.13378362558998 +14000 ekin = 1.33384628320074 | erot = 2.95599632290763 | epot = -12.423626232019 | etot = -8.13378362591067 +15000 ekin = 1.39936071611664 | erot = 2.97947113417333 | epot = -12.5126154766849 | etot = -8.13378362639496 +16000 ekin = 1.46443870928025 | erot = 2.99312358077431 | epot = -12.5913459174139 | etot = -8.13378362735934 +17000 ekin = 1.52113741921509 | erot = 2.99430260105838 | epot = -12.6492236482455 | etot = -8.13378362797204 +18000 ekin = 1.56143918576787 | erot = 2.98098620608846 | epot = -12.6762090203241 | etot = -8.13378362846779 +19000 ekin = 1.57873438318794 | erot = 2.9520667445456 | epot = -12.6645847564923 | etot = -8.13378362875874 +20000 ekin = 1.56841348053791 | erot = 2.9073514731296 | epot = -12.6095485824455 | etot = -8.133783628778 +21000 ekin = 1.52886464109308 | erot = 2.8476529136898 | epot = -12.5103011832754 | etot = -8.13378362849248 +22000 ekin = 1.46209217703489 | erot = 2.774783976472 | epot = -12.3706597813886 | etot = -8.13378362788177 +23000 ekin = 1.37376733102674 | erot = 2.69155728313727 | epot = -12.1991082412397 | etot = -8.13378362707572 +24000 ekin = 1.27262109890792 | erot = 2.60118350194755 | epot = -12.0075882269997 | etot = -8.13378362614425 +25000 ekin = 1.16926502294376 | erot = 2.50703692695188 | epot = -11.8100855751042 | etot = -8.13378362520854 +26000 ekin = 1.07471489945141 | erot = 2.4123584015281 | epot = -11.6208569253571 | etot = -8.13378362437762 +27000 ekin = 0.998982995755817 | erot = 2.31997753232672 | epot = -11.4527441518066 | etot = -8.13378362372404 +28000 ekin = 0.950065052892328 | erot = 2.23215621537583 | epot = -11.3160048915416 | etot = -8.13378362327344 +29000 ekin = 0.933483801722602 | erot = 2.1505610010297 | epot = -11.2178284257645 | etot = -8.13378362301223 +30000 ekin = 0.952335164336064 | erot = 2.07633501131217 | epot = -11.1624537985556 | etot = -8.13378362290736 +31000 ekin = 1.00761822011319 | erot = 2.01025995539428 | epot = -11.1516617984317 | etot = -8.13378362292422 +32000 ekin = 1.09859027316482 | erot = 1.95287201474925 | epot = -11.1852459109705 | etot = -8.13378362305645 +33000 ekin = 1.22296348257697 | erot = 1.90442653272436 | epot = -11.2611736386122 | etot = -8.13378362331083 +34000 ekin = 1.37683793249585 | erot = 1.86498336105423 | epot = -11.3756049172807 | etot = -8.13378362373066 +35000 ekin = 1.55422271443458 | erot = 1.83436013830184 | epot = -11.5223664771471 | etot = -8.13378362441064 +36000 ekin = 1.74589607048141 | erot = 1.81205442227457 | epot = -11.6917341182485 | etot = -8.13378362549247 +37000 ekin = 1.93777565280859 | erot = 1.79705197600543 | epot = -11.8686112558399 | etot = -8.13378362702585 +38000 ekin = 2.11051089015041 | erot = 1.78782890330229 | epot = -12.0321234221666 | etot = -8.13378362871388 +39000 ekin = 2.24321482588509 | erot = 1.78271510837226 | epot = -12.1597135641243 | etot = -8.1337836298669 +40000 ekin = 2.32146151921643 | erot = 1.7807328300512 | epot = -12.2359779791645 | etot = -8.13378362989691 +41000 ekin = 2.34386750101389 | erot = 1.78241563043109 | epot = -12.2600667603296 | etot = -8.1337836288846 +42000 ekin = 2.32118218527097 | erot = 1.78979050959073 | epot = -12.2447563223396 | etot = -8.13378362747785 +43000 ekin = 2.26309111555158 | erot = 1.8053926207647 | epot = -12.2022673943961 | etot = -8.13378365807986 +44000 ekin = 2.15856242114832 | erot = 1.84609032619604 | epot = -12.1384363880305 | etot = -8.13378364068615 +45000 ekin = 2.08936731003526 | erot = 1.88904724563039 | epot = -12.1121981822921 | etot = -8.1337836266264 +46000 ekin = 1.9964611597006 | erot = 1.93503982400428 | epot = -12.0652846104763 | etot = -8.13378362677143 +47000 ekin = 1.89712577412051 | erot = 1.98806984898587 | epot = -12.0189792501524 | etot = -8.133783627046 +48000 ekin = 1.79036864863103 | erot = 2.04496273496239 | epot = -11.9691150108766 | etot = -8.13378362728318 +49000 ekin = 1.67630116263937 | erot = 2.10216327906913 | epot = -11.9122480690703 | etot = -8.13378362736179 +50000 ekin = 1.55727015247065 | erot = 2.15637892895985 | epot = -11.8474327086501 | etot = -8.13378362721965 +51000 ekin = 1.43817433709145 | erot = 2.205140400327 | epot = -11.7770983642842 | etot = -8.13378362686579 +52000 ekin = 1.32596547232174 | erot = 2.24710946475012 | epot = -11.7068585634502 | etot = -8.13378362637838 +53000 ekin = 1.22848082922914 | erot = 2.28204759210385 | epot = -11.6443120472106 | etot = -8.13378362587756 +54000 ekin = 1.15295119316272 | erot = 2.31049933939892 | epot = -11.597234158045 | etot = -8.13378362548335 +55000 ekin = 1.10463170766329 | erot = 2.33334681406842 | epot = -11.5717621470128 | etot = -8.13378362528111 +56000 ekin = 1.08590799517335 | erot = 2.35139880092331 | epot = -11.5710904214035 | etot = -8.13378362530685 +57000 ekin = 1.09599893485501 | erot = 2.3651115445053 | epot = -11.5948941049136 | etot = -8.1337836255533 +58000 ekin = 1.13119803471016 | erot = 2.37445830578815 | epot = -11.6394399664722 | etot = -8.13378362597388 +59000 ekin = 1.18549837183919 | erot = 2.3789169186323 | epot = -11.6981989169901 | etot = -8.13378362651858 +60000 ekin = 1.25136230662772 | erot = 2.37755306615245 | epot = -11.7626989998985 | etot = -8.13378362711835 +61000 ekin = 1.32065657328813 | erot = 2.36917823379307 | epot = -11.8236184347912 | etot = -8.13378362771004 +62000 ekin = 1.38555350991079 | erot = 2.35258911579049 | epot = -11.8719262538939 | etot = -8.1337836281926 +63000 ekin = 1.43966787267658 | erot = 2.32682848519592 | epot = -11.9002799863548 | etot = -8.13378362848234 +64000 ekin = 1.4790950343818 | erot = 2.29144993715393 | epot = -11.9043286000689 | etot = -8.1337836285332 +65000 ekin = 1.502880497741 | erot = 2.2467096090511 | epot = -11.88337373515 | etot = -8.13378362835793 +66000 ekin = 1.51274507599024 | erot = 2.19359684182996 | epot = -11.8401255458509 | etot = -8.1337836280307 +67000 ekin = 1.51208659633021 | erot = 2.13371356874809 | epot = -11.7795837927184 | etot = -8.1337836276401 +68000 ekin = 1.50462166617951 | erot = 2.06904733139779 | epot = -11.7074526249092 | etot = -8.13378362733192 +69000 ekin = 1.49293889166158 | erot = 2.00167765430522 | epot = -11.6284001731036 | etot = -8.1337836271368 +70000 ekin = 1.47793621174641 | erot = 1.93361210060369 | epot = -11.5453319394055 | etot = -8.13378362705538 +71000 ekin = 1.45891349102845 | erot = 1.86670994694693 | epot = -11.4594070650146 | etot = -8.13378362703918 +72000 ekin = 1.43427842101622 | erot = 1.80270883809016 | epot = -11.3707708861215 | etot = -8.13378362701512 +73000 ekin = 1.40258583891026 | erot = 1.74331039193086 | epot = -11.279679857752 | etot = -8.13378362691089 +74000 ekin = 1.36359371155274 | erot = 1.69025647754912 | epot = -11.187633815782 | etot = -8.13378362668016 +75000 ekin = 1.31886252565205 | erot = 1.6453382071802 | epot = -11.0979843591715 | etot = -8.13378362633928 +76000 ekin = 1.27181692773745 | erot = 1.61030043593585 | epot = -11.0159009896012 | etot = -8.13378362592793 +77000 ekin = 1.22767338921998 | erot = 1.58670952555601 | epot = -10.9481665402833 | etot = -8.13378362550729 +78000 ekin = 1.1918742588197 | erot = 1.57555521121124 | epot = -10.9012130952115 | etot = -8.1337836251806 +79000 ekin = 1.16922470588821 | erot = 1.57716601534084 | epot = -10.880174346204 | etot = -8.13378362497499 +80000 ekin = 1.1635131219374 | erot = 1.59112852775413 | epot = -10.8884252746034 | etot = -8.1337836249119 +81000 ekin = 1.17709123428946 | erot = 1.61633850893092 | epot = -10.927213368212 | etot = -8.13378362499167 +82000 ekin = 1.21064005584029 | erot = 1.65118762576691 | epot = -10.9956113068161 | etot = -8.13378362520887 +83000 ekin = 1.26297331742736 | erot = 1.69382675572846 | epot = -11.0905836987108 | etot = -8.13378362555501 +84000 ekin = 1.33092648687662 | erot = 1.74243133123673 | epot = -11.2071414441142 | etot = -8.13378362600083 +85000 ekin = 1.40961218427365 | erot = 1.7954064033782 | epot = -11.3388022141303 | etot = -8.13378362647841 +86000 ekin = 1.49330005467923 | erot = 1.8515006441401 | epot = -11.478584325705 | etot = -8.13378362688569 +87000 ekin = 1.57653380716703 | erot = 1.90982169886827 | epot = -11.6201391333936 | etot = -8.13378362735832 +88000 ekin = 1.65416408678855 | erot = 1.96971725895485 | epot = -11.7576649732582 | etot = -8.13378362751478 +89000 ekin = 1.72360216634179 | erot = 2.03055934337534 | epot = -11.8879451373045 | etot = -8.13378362758735 +90000 ekin = 1.78500984589395 | erot = 2.09126219979607 | epot = -12.0100556734362 | etot = -8.13378362774619 +91000 ekin = 1.83789001415886 | erot = 2.15001837237363 | epot = -12.1216920145417 | etot = -8.1337836280092 +92000 ekin = 1.87517809322888 | erot = 2.20985483887525 | epot = -12.21881656028 | etot = -8.1337836281759 +93000 ekin = 1.90356384535089 | erot = 2.26204903047957 | epot = -12.2993965046574 | etot = -8.13378362882697 +94000 ekin = 1.9156664167305 | erot = 2.30892488078276 | epot = -12.3583749263607 | etot = -8.13378362884746 +95000 ekin = 1.91095769384008 | erot = 2.34997522030004 | epot = -12.3947165431006 | etot = -8.1337836289605 +96000 ekin = 1.889484024989 | erot = 2.38411475951065 | epot = -12.4073824132802 | etot = -8.1337836287806 +97000 ekin = 1.85343811133898 | erot = 2.41133046292227 | epot = -12.3985522027162 | etot = -8.13378362845492 +98000 ekin = 1.80684275230277 | erot = 2.43203206054831 | epot = -12.372658440891 | etot = -8.13378362803991 +99000 ekin = 1.75478641123179 | erot = 2.44692977736848 | epot = -12.3354998162067 | etot = -8.13378362760647 +100000 ekin = 1.69590911435708 | erot = 2.45386958409534 | epot = -12.2835623848859 | etot = -8.1337836864335 +101000 ekin = 1.68113249375231 | erot = 2.36572534112462 | epot = -12.1806414642138 | etot = -8.13378362933684 +102000 ekin = 1.7267856590017 | erot = 2.35051337712505 | epot = -12.2110826965905 | etot = -8.13378366046373 +103000 ekin = 1.68338599487708 | erot = 2.35411811039611 | epot = -12.1712877656948 | etot = -8.13378366042166 +104000 ekin = 1.64323586412858 | erot = 2.35701648102726 | epot = -12.134036005652 | etot = -8.13378366049613 +105000 ekin = 1.60584113472061 | erot = 2.35932964102255 | epot = -12.0989544363532 | etot = -8.13378366061001 +106000 ekin = 1.57044138011816 | erot = 2.3609277694323 | epot = -12.0651528102264 | etot = -8.13378366067597 +107000 ekin = 1.53705400250982 | erot = 2.36166253248201 | epot = -12.0325001956582 | etot = -8.13378366066635 +108000 ekin = 1.50696391591135 | erot = 2.361285573492 | epot = -12.0020331499847 | etot = -8.13378366058131 +109000 ekin = 1.48244426546665 | erot = 2.35938088271005 | epot = -11.9756088087053 | etot = -8.13378366052861 +110000 ekin = 1.46539913148082 | erot = 2.3553068314616 | epot = -11.9544896235797 | etot = -8.13378366063725 +111000 ekin = 1.45548748017621 | erot = 2.34818065606092 | epot = -11.9374517972409 | etot = -8.13378366100376 +112000 ekin = 1.44872729612956 | erot = 2.33695548266951 | epot = -11.9194664403753 | etot = -8.13378366157622 +113000 ekin = 1.438054955865 | erot = 2.320686955094 | epot = -11.8925255730877 | etot = -8.13378366212873 +114000 ekin = 1.41640788690883 | erot = 2.29883886662114 | epot = -11.8490304158911 | etot = -8.13378366236113 +115000 ekin = 1.38063781822087 | erot = 2.27153218573304 | epot = -11.7859536655161 | etot = -8.13378366156219 +116000 ekin = 1.33630540308419 | erot = 2.23942220246129 | epot = -11.7095112666477 | etot = -8.13378366110223 +117000 ekin = 1.29001229198315 | erot = 2.20380811829907 | epot = -11.6276040708686 | etot = -8.13378366058633 +118000 ekin = 1.24711548834727 | erot = 2.16635124019904 | epot = -11.5472503887779 | etot = -8.13378366023156 +119000 ekin = 1.21073685469435 | erot = 2.12872161390266 | epot = -11.4732421286715 | etot = -8.13378366007448 +120000 ekin = 1.18115748419452 | erot = 2.09256534610069 | epot = -11.4075064903304 | etot = -8.13378366003518 +121000 ekin = 1.15688642101106 | erot = 2.05947511288399 | epot = -11.3501451939313 | etot = -8.13378366003622 +122000 ekin = 1.13593168276773 | erot = 2.03084061403908 | epot = -11.3005559568655 | etot = -8.13378366005868 +123000 ekin = 1.11638811965945 | erot = 2.00761097209064 | epot = -11.2577827519202 | etot = -8.13378366017012 +124000 ekin = 1.09616325371745 | erot = 1.99019695902077 | epot = -11.2201438730114 | etot = -8.13378366027323 +125000 ekin = 1.07358508996133 | erot = 1.97820026039369 | epot = -11.1855690107828 | etot = -8.13378366042783 +126000 ekin = 1.047121989785 | erot = 1.97030937007241 | epot = -11.1512150205173 | etot = -8.13378366065987 +127000 ekin = 1.0156035955053 | erot = 1.96476336054352 | epot = -11.1141506168024 | etot = -8.1337836607536 +128000 ekin = 0.97928184665228 | erot = 1.95990906194963 | epot = -11.0729745693073 | etot = -8.13378366070535 +129000 ekin = 0.940294043229882 | erot = 1.95428772921566 | epot = -11.0283654329011 | etot = -8.13378366045551 +130000 ekin = 0.902735823607268 | erot = 1.94710047764773 | epot = -10.983619961355 | etot = -8.13378366010001 +131000 ekin = 0.872329759139703 | erot = 1.93820575526838 | epot = -10.9443191739569 | etot = -8.13378365954882 +132000 ekin = 0.855045600562256 | erot = 1.92803271303694 | epot = -10.9168619728694 | etot = -8.13378365927017 +133000 ekin = 0.85477556282256 | erot = 1.91694878880971 | epot = -10.9055080107084 | etot = -8.13378365907613 +134000 ekin = 0.873981086378922 | erot = 1.90549522489457 | epot = -10.9132599702531 | etot = -8.13378365897964 +135000 ekin = 0.913690181741819 | erot = 1.89429118508522 | epot = -10.9417650257941 | etot = -8.13378365896708 +136000 ekin = 0.973734451665589 | erot = 1.88395321784242 | epot = -10.9914713285353 | etot = -8.13378365902725 +137000 ekin = 1.05255313135938 | erot = 1.87488800080373 | epot = -11.0612247920055 | etot = -8.13378365984243 +138000 ekin = 1.1443524994853 | erot = 1.8662689721205 | epot = -11.1444051316852 | etot = -8.13378366007936 +139000 ekin = 1.24448357091331 | erot = 1.85821435006753 | epot = -11.2364815813234 | etot = -8.13378366034253 +140000 ekin = 1.34860347563745 | erot = 1.85113522079119 | epot = -11.333522357093 | etot = -8.1337836606644 +141000 ekin = 1.45162669266307 | erot = 1.84534635451924 | epot = -11.430756708267 | etot = -8.13378366108469 +142000 ekin = 1.54663919844505 | erot = 1.84103156950907 | epot = -11.521454429749 | etot = -8.13378366179486 +143000 ekin = 1.6247011023941 | erot = 1.83813053702613 | epot = -11.5966153018863 | etot = -8.13378366246606 +144000 ekin = 1.67710589256285 | erot = 1.83622813336416 | epot = -11.6471176890259 | etot = -8.13378366309886 +145000 ekin = 1.69650852159039 | erot = 1.83477115527459 | epot = -11.6650633403347 | etot = -8.13378366346972 +146000 ekin = 1.67998250270633 | erot = 1.8333430641869 | epot = -11.6471092301922 | etot = -8.13378366329893 +147000 ekin = 1.63255928725478 | erot = 1.83204496823007 | epot = -11.598387917878 | etot = -8.13378366239317 +148000 ekin = 1.56926257377408 | erot = 1.83182914755799 | epot = -11.534875382188 | etot = -8.1337836608559 +149000 ekin = 1.51300824977688 | erot = 1.83452727994329 | epot = -11.4813191889249 | etot = -8.13378365920474 +150000 ekin = 1.48724963784664 | erot = 1.84235837448576 | epot = -11.4633916705171 | etot = -8.13378365818466 +151000 ekin = 1.50619323822939 | erot = 1.85697474829977 | epot = -11.4969516448352 | etot = -8.13378365830607 +152000 ekin = 1.56855992602549 | erot = 1.87847282638512 | epot = -11.5808164119011 | etot = -8.13378365949048 +153000 ekin = 1.65914489646567 | erot = 1.90493735115929 | epot = -11.6978659087714 | etot = -8.13378366114644 +154000 ekin = 1.75680978950735 | erot = 1.93282846213573 | epot = -11.8234219142215 | etot = -8.13378366257846 +155000 ekin = 1.84344901658437 | erot = 1.95802697046849 | epot = -11.9352596504333 | etot = -8.1337836633804 +156000 ekin = 1.90893795388443 | erot = 1.97697594926079 | epot = -12.0196975667215 | etot = -8.13378366357624 +157000 ekin = 1.95061494385932 | erot = 1.98738512433505 | epot = -12.0717837316313 | etot = -8.13378366343689 +158000 ekin = 1.96976178337731 | erot = 1.98837447181476 | epot = -12.0919199183612 | etot = -8.13378366316915 +159000 ekin = 1.96892634677255 | erot = 1.98033790354811 | epot = -12.0830479131018 | etot = -8.13378366278114 +160000 ekin = 1.95167601805979 | erot = 1.96478101829951 | epot = -12.050240698581 | etot = -8.13378366222171 +161000 ekin = 1.92323849263822 | erot = 1.94408396543486 | epot = -12.001106119617 | etot = -8.13378366154392 +162000 ekin = 1.89012785139944 | erot = 1.92106669306913 | epot = -11.94497820536 | etot = -8.13378366089138 +163000 ekin = 1.85873206626408 | erot = 1.89844726529886 | epot = -11.8909629919524 | etot = -8.13378366038947 +164000 ekin = 1.83396756863979 | erot = 1.87841814938175 | epot = -11.8461693781077 | etot = -8.13378366008619 +165000 ekin = 1.81873657814123 | erot = 1.86247026312239 | epot = -11.8149905012202 | etot = -8.1337836599566 +166000 ekin = 1.81415764355357 | erot = 1.85144128795245 | epot = -11.7993825914515 | etot = -8.13378365994553 +167000 ekin = 1.82014338462852 | erot = 1.84569577974681 | epot = -11.7996228243664 | etot = -8.13378365999109 +168000 ekin = 1.83604973591366 | erot = 1.8453491867352 | epot = -11.8151825826933 | etot = -8.13378366004445 +169000 ekin = 1.86118807804061 | erot = 1.850477664299 | epot = -11.8454494024155 | etot = -8.13378366007584 +170000 ekin = 1.89508209492149 | erot = 1.86127600745022 | epot = -11.8901417624555 | etot = -8.13378366008374 +171000 ekin = 1.93739070093832 | erot = 1.8781392722114 | epot = -11.9493136332464 | etot = -8.13378366009671 +172000 ekin = 1.98746465492716 | erot = 1.90165699566161 | epot = -12.0229053107602 | etot = -8.13378366017142 +173000 ekin = 2.04358732260738 | erot = 1.93252470914456 | epot = -12.1098956921178 | etot = -8.13378366036586 +174000 ekin = 2.10212586880685 | erot = 1.97139111366116 | epot = -12.2073006432559 | etot = -8.13378366078787 +175000 ekin = 2.15653164019895 | erot = 2.01868623997428 | epot = -12.3090015416374 | etot = -8.13378366146419 +176000 ekin = 2.19700590631297 | erot = 2.07444517694537 | epot = -12.4052347456343 | etot = -8.13378366237597 +177000 ekin = 2.21275117726728 | erot = 2.13809655452259 | epot = -12.4846313951105 | etot = -8.13378366332058 +178000 ekin = 2.191030841378 | erot = 2.2084963736183 | epot = -12.5333108794519 | etot = -8.1337836644556 +179000 ekin = 2.05002958755708 | erot = 2.27647492405861 | epot = -12.4602881626275 | etot = -8.13378365101178 +180000 ekin = 2.00100366281088 | erot = 2.36086155180537 | epot = -12.4956488860898 | etot = -8.13378367147353 +181000 ekin = 1.82885344502827 | erot = 2.44444025932694 | epot = -12.4070773745335 | etot = -8.13378367017832 +182000 ekin = 1.62724610560602 | erot = 2.53221325513864 | epot = -12.2932430288216 | etot = -8.13378366807689 +183000 ekin = 1.42880501135674 | erot = 2.6254005853434 | epot = -12.1879892625417 | etot = -8.1337836658416 +184000 ekin = 1.26714962832119 | erot = 2.72561981850436 | epot = -12.1265531111179 | etot = -8.13378366429233 +185000 ekin = 1.16606552757954 | erot = 2.83366450732251 | epot = -12.1335136988418 | etot = -8.1337836639398 +186000 ekin = 1.13327188784872 | erot = 2.94811459460534 | epot = -12.2151701472112 | etot = -8.13378366475712 +187000 ekin = 1.16127663962544 | erot = 3.06454091657718 | epot = -12.3596012225469 | etot = -8.13378366634433 +188000 ekin = 1.23275799228605 | erot = 3.17578119614176 | epot = -12.5423228566622 | etot = -8.13378366823443 +189000 ekin = 1.32637276316036 | erot = 3.27316596760519 | epot = -12.733322400823 | etot = -8.1337836700575 +190000 ekin = 1.42100795808774 | erot = 3.34817980173636 | epot = -12.9029714313697 | etot = -8.13378367154559 +191000 ekin = 1.49794111549818 | erot = 3.39410379075351 | epot = -13.0258285788614 | etot = -8.13378367260974 +192000 ekin = 1.54262156679641 | erot = 3.40720165429243 | epot = -13.0836068940667 | etot = -8.13378367297783 +193000 ekin = 1.54797240883498 | erot = 3.38715231466168 | epot = -13.0689083961198 | etot = -8.13378367262315 +194000 ekin = 1.51467582661462 | erot = 3.33705387754773 | epot = -12.9855133757567 | etot = -8.13378367159431 +195000 ekin = 1.45101621748256 | erot = 3.26269312885266 | epot = -12.8474930164477 | etot = -8.13378367011248 +196000 ekin = 1.37083042970796 | erot = 3.17132041678952 | epot = -12.6759345150014 | etot = -8.13378366850388 +197000 ekin = 1.29009120536748 | erot = 3.07036265935845 | epot = -12.4942375317758 | etot = -8.13378366704992 +198000 ekin = 1.22364196643987 | erot = 2.96652382644046 | epot = -12.3239494587839 | etot = -8.13378366590357 +199000 ekin = 1.18307710083285 | erot = 2.86542144217805 | epot = -12.1822822081308 | etot = -8.13378366511989 +200000 ekin = 1.17564340951956 | erot = 2.7715869837879 | epot = -12.0810140580308 | etot = -8.13378366472336 +201000 ekin = 1.2035961939178 | erot = 2.68856918537222 | epot = -12.0259490440303 | etot = -8.13378366474028 +202000 ekin = 1.26374726413821 | erot = 2.61894189740096 | epot = -12.0164728267172 | etot = -8.13378366517806 +203000 ekin = 1.3475159756314 | erot = 2.56419616426486 | epot = -12.0454958058714 | etot = -8.13378366597512 +204000 ekin = 1.44203337890014 | erot = 2.52468734318962 | epot = -12.1005043890649 | etot = -8.13378366697511 +205000 ekin = 1.53246038205354 | erot = 2.49972903140538 | epot = -12.1659730814069 | etot = -8.13378366794802 +206000 ekin = 1.60510558525656 | erot = 2.487934252803 | epot = -12.226823506722 | etot = -8.13378366866242 +207000 ekin = 1.65039556723136 | erot = 2.48771410987755 | epot = -12.2718933460771 | etot = -8.13378366896824 +208000 ekin = 1.66471924263828 | erot = 2.49772662877211 | epot = -12.296229540258 | etot = -8.13378366884764 +209000 ekin = 1.65060780281931 | erot = 2.51706178773899 | epot = -12.3014532589738 | etot = -8.1337836684155 +210000 ekin = 1.61529613530101 | erot = 2.54506818372113 | epot = -12.294147986902 | etot = -8.13378366787983 +211000 ekin = 1.56815998339903 | erot = 2.58088870847291 | epot = -12.2828323593491 | etot = -8.13378366747717 +212000 ekin = 1.51779769211944 | erot = 2.62289115840009 | epot = -12.2744725179132 | etot = -8.13378366739367 +213000 ekin = 1.46970697786409 | erot = 2.66822787294334 | epot = -12.2717185184986 | etot = -8.13378366769122 +214000 ekin = 1.42551121611952 | erot = 2.71271314915572 | epot = -12.2720080334465 | etot = -8.13378366817127 +215000 ekin = 1.38449526701797 | erot = 2.75113858809842 | epot = -12.2694175238339 | etot = -8.13378366871755 +216000 ekin = 1.3461145051069 | erot = 2.77818905444625 | epot = -12.2580872284516 | etot = -8.13378366889847 +217000 ekin = 1.31348152811954 | erot = 2.78964053187663 | epot = -12.2369057285552 | etot = -8.13378366855904 +218000 ekin = 1.29458639919478 | erot = 2.7831914510914 | epot = -12.2115615182393 | etot = -8.13378366795308 +219000 ekin = 1.29978448123104 | erot = 2.7578586549423 | epot = -12.1914268036072 | etot = -8.1337836674339 +220000 ekin = 1.33694784981731 | erot = 2.71363634301963 | epot = -12.1843678601774 | etot = -8.13378366734043 +221000 ekin = 1.40745643921055 | erot = 2.65092088134267 | epot = -12.1921609882709 | etot = -8.13378366771773 +222000 ekin = 1.50572252625935 | erot = 2.57029476952289 | epot = -12.2098009641033 | etot = -8.13378366832109 +223000 ekin = 1.62210843375735 | erot = 2.47289007334103 | epot = -12.2287821759278 | etot = -8.13378366882941 +224000 ekin = 1.746793930229 | erot = 2.36097135919342 | epot = -12.2415489584551 | etot = -8.13378366903269 +225000 ekin = 1.87205636329951 | erot = 2.23842454190523 | epot = -12.2442645742132 | etot = -8.13378366900846 +226000 ekin = 1.99134598106693 | erot = 2.11064622098412 | epot = -12.2357758711294 | etot = -8.13378366907832 +227000 ekin = 2.09586639151715 | erot = 1.98364704051183 | epot = -12.2132971015584 | etot = -8.13378366952941 +228000 ekin = 2.17197666667475 | erot = 1.86293503717791 | epot = -12.1686953741916 | etot = -8.13378367033897 +229000 ekin = 2.20263173192667 | erot = 1.75265294154725 | epot = -12.0890683445911 | etot = -8.13378367111716 +230000 ekin = 2.17321554606937 | erot = 1.65532359970871 | epot = -11.9623228171299 | etot = -8.13378367135177 +231000 ekin = 2.07854920573232 | erot = 1.57213281486727 | epot = -11.7844656913365 | etot = -8.13378367073688 +232000 ekin = 1.9267119502196 | erot = 1.50340464294852 | epot = -11.5639002625325 | etot = -8.13378366936441 +233000 ekin = 1.73729705956053 | erot = 1.44896834770272 | epot = -11.3200490749324 | etot = -8.13378366766914 +234000 ekin = 1.53556953354802 | erot = 1.40834045937527 | epot = -11.0776936590032 | etot = -8.13378366607992 +235000 ekin = 1.34558700580155 | erot = 1.38078818073916 | epot = -10.8601588514749 | etot = -8.13378366493417 +236000 ekin = 1.18525206422596 | erot = 1.3657026321041 | epot = -10.6847383605466 | etot = -8.1337836642165 +237000 ekin = 1.06637029724341 | erot = 1.36251012102854 | epot = -10.5626640820866 | etot = -8.13378366381463 +238000 ekin = 0.995491212021019 | erot = 1.37070429771416 | epot = -10.4999791733993 | etot = -8.13378366366416 +239000 ekin = 0.975031518631579 | erot = 1.3897138412691 | epot = -10.4985290236698 | etot = -8.1337836637691 +240000 ekin = 1.003524239047 | erot = 1.41866034024255 | epot = -10.5559682434628 | etot = -8.13378366417323 +241000 ekin = 1.07556704774179 | erot = 1.45612900246831 | epot = -10.6654797151277 | etot = -8.13378366491761 +242000 ekin = 1.18122375067269 | erot = 1.49994629855486 | epot = -10.8149537152521 | etot = -8.13378366602455 +243000 ekin = 1.30634294707391 | erot = 1.5470333102007 | epot = -10.9871599246153 | etot = -8.13378366734069 +244000 ekin = 1.43466609576103 | erot = 1.59374373480216 | epot = -11.1621934990183 | etot = -8.1337836684551 +245000 ekin = 1.55091944171202 | erot = 1.63606515904626 | epot = -11.3207682704719 | etot = -8.13378366971362 +246000 ekin = 1.63963426714548 | erot = 1.67091688012705 | epot = -11.4443348179091 | etot = -8.13378367063655 +247000 ekin = 1.68912292676081 | erot = 1.69643192578571 | epot = -11.5193385235861 | etot = -8.1337836710396 +248000 ekin = 1.6941862336649 | erot = 1.7122329815499 | epot = -11.5402028860517 | etot = -8.13378367083691 +249000 ekin = 1.65708464249985 | erot = 1.71943097162587 | epot = -11.5102992843203 | etot = -8.13378367019458 +250000 ekin = 1.5863986468533 | erot = 1.72015982289358 | epot = -11.4403421388607 | etot = -8.13378366911384 +251000 ekin = 1.49555936407786 | erot = 1.71716072440045 | epot = -11.3465037564426 | etot = -8.13378366796434 +252000 ekin = 1.39930346630862 | erot = 1.71298107622629 | epot = -11.2460682095268 | etot = -8.13378366699192 +253000 ekin = 1.31034898359547 | erot = 1.70949093459515 | epot = -11.1536235845413 | etot = -8.13378366635073 +254000 ekin = 1.23716194123368 | erot = 1.70776552340092 | epot = -11.0787111307331 | etot = -8.13378366609854 +255000 ekin = 1.18305733845311 | erot = 1.70821467485061 | epot = -11.025055679451 | etot = -8.13378366614725 +256000 ekin = 1.14729363432842 | erot = 1.7106327515816 | epot = -10.9917100522917 | etot = -8.13378366638171 +257000 ekin = 1.12650460108729 | erot = 1.71454195552779 | epot = -10.974830223265 | etot = -8.13378366664996 +258000 ekin = 1.1166971591796 | erot = 1.71938873503289 | epot = -10.9698695610665 | etot = -8.13378366685405 +259000 ekin = 1.11461746403917 | erot = 1.72463904931066 | epot = -10.9730401803372 | etot = -8.13378366698733 +260000 ekin = 1.11796213299311 | erot = 1.72976096813936 | epot = -10.9815067682349 | etot = -8.13378366710241 +261000 ekin = 1.12495929560805 | erot = 1.73429797646796 | epot = -10.9930409392091 | etot = -8.13378366713307 +262000 ekin = 1.13415334886796 | erot = 1.73799782227173 | epot = -11.0059348383754 | etot = -8.13378366723574 +263000 ekin = 1.1441924865775 | erot = 1.74014341283954 | epot = -11.0181195666639 | etot = -8.13378366724682 +264000 ekin = 1.15486713033016 | erot = 1.74014049676713 | epot = -11.0287912942162 | etot = -8.13378366711894 +265000 ekin = 1.16757148072387 | erot = 1.73774643956152 | epot = -11.0391015871619 | etot = -8.13378366687652 +266000 ekin = 1.18492523334604 | erot = 1.73313774545366 | epot = -11.0518466453998 | etot = -8.13378366660006 +267000 ekin = 1.20976553808602 | erot = 1.7268208539035 | epot = -11.0703700583702 | etot = -8.13378366638072 +268000 ekin = 1.24403111905679 | erot = 1.71946869065397 | epot = -11.0972834759949 | etot = -8.13378366628417 +269000 ekin = 1.28796807043007 | erot = 1.71176934564011 | epot = -11.1335210824064 | etot = -8.13378366633624 +270000 ekin = 1.33984072253264 | erot = 1.70434119615532 | epot = -11.1779655852108 | etot = -8.13378366652286 +271000 ekin = 1.39615730896038 | erot = 1.69774776464757 | epot = -11.2276887403839 | etot = -8.13378366677592 +272000 ekin = 1.45234426470337 | erot = 1.69276715684432 | epot = -11.2788950886215 | etot = -8.13378366707379 +273000 ekin = 1.50368133069646 | erot = 1.68992546991196 | epot = -11.3273904679228 | etot = -8.13378366731438 +274000 ekin = 1.54639996325526 | erot = 1.68983337628827 | epot = -11.3700170069557 | etot = -8.13378366741213 +275000 ekin = 1.57877490148631 | erot = 1.69332235277275 | epot = -11.4058809215907 | etot = -8.13378366733162 +276000 ekin = 1.60168052283226 | erot = 1.70138855155399 | epot = -11.436852741484 | etot = -8.13378366709777 +277000 ekin = 1.61832490282934 | erot = 1.71502642603181 | epot = -11.4671349956638 | etot = -8.13378366680269 +278000 ekin = 1.63311060675181 | erot = 1.73495415768007 | epot = -11.5018484310108 | etot = -8.13378366657894 +279000 ekin = 1.64995273994837 | erot = 1.76130541527865 | epot = -11.5450418217717 | etot = -8.1337836665447 +280000 ekin = 1.67073877093407 | erot = 1.79339849893171 | epot = -11.5979209366107 | etot = -8.13378366674486 +281000 ekin = 1.69438407985006 | erot = 1.82970064438533 | epot = -11.6578683914565 | etot = -8.13378366722115 +282000 ekin = 1.71376506080862 | erot = 1.86795891950281 | epot = -11.7155076481303 | etot = -8.13378366781888 +283000 ekin = 1.72224450525371 | erot = 1.9052906854816 | epot = -11.7613188590757 | etot = -8.13378366834034 +284000 ekin = 1.71505262177341 | erot = 1.93881515489551 | epot = -11.7876514453545 | etot = -8.13378366868558 +285000 ekin = 1.68954869056625 | erot = 1.96608819497539 | epot = -11.7894205543634 | etot = -8.13378366882172 +286000 ekin = 1.64555137747819 | erot = 1.98537597121294 | epot = -11.7647110174642 | etot = -8.13378366877303 +287000 ekin = 1.58495470813229 | erot = 1.99578989882443 | epot = -11.7145282755479 | etot = -8.13378366859116 +288000 ekin = 1.51101761585578 | erot = 1.9972977679279 | epot = -11.6420990521131 | etot = -8.13378366832946 +289000 ekin = 1.42766231980942 | erot = 1.99063899576434 | epot = -11.5520849836069 | etot = -8.1337836680331 +290000 ekin = 1.33894501486192 | erot = 1.9771675899912 | epot = -11.4498962725844 | etot = -8.13378366773129 +291000 ekin = 1.24881721188018 | erot = 1.95864649302945 | epot = -11.3412473723313 | etot = -8.13378366742167 +292000 ekin = 1.16137515575687 | erot = 1.93702958191697 | epot = -11.2321884047288 | etot = -8.13378366705499 +293000 ekin = 1.08169833470763 | erot = 1.91427738455186 | epot = -11.1297593858162 | etot = -8.13378366655672 +294000 ekin = 1.01689863826406 | erot = 1.8922324358106 | epot = -11.0429147399714 | etot = -8.13378366589676 +295000 ekin = 0.976377352950502 | erot = 1.8725332495628 | epot = -10.9826942676913 | etot = -8.13378366517798 +296000 ekin = 0.970182395979119 | erot = 1.85650679550227 | epot = -10.9604728561376 | etot = -8.13378366465623 +297000 ekin = 1.00537151817025 | erot = 1.84499118418531 | epot = -10.9841463669809 | etot = -8.13378366462529 +298000 ekin = 1.08200534146773 | erot = 1.8381241771558 | epot = -11.0539131838573 | etot = -8.13378366523378 +299000 ekin = 1.19125189129751 | erot = 1.83519410294181 | epot = -11.1602296606154 | etot = -8.13378366637606 +300000 ekin = 1.31698721061293 | erot = 1.83465168975374 | epot = -11.2854225681136 | etot = -8.13378366774693 +301000 ekin = 1.44008784809228 | erot = 1.83433803115513 | epot = -11.4082095482398 | etot = -8.13378366899243 +302000 ekin = 1.54329548540188 | erot = 1.8319000019686 | epot = -11.5089791572097 | etot = -8.13378366983918 +303000 ekin = 1.61484992407185 | erot = 1.82529439832924 | epot = -11.5739279925551 | etot = -8.13378367015401 +304000 ekin = 1.65011047810347 | erot = 1.81324433416857 | epot = -11.5971384822046 | etot = -8.13378366993254 +305000 ekin = 1.65140814366672 | erot = 1.79549497030458 | epot = -11.5806867832613 | etot = -8.13378366929 +306000 ekin = 1.62643416627335 | erot = 1.77280218914075 | epot = -11.5330200238232 | etot = -8.13378366840907 +307000 ekin = 1.58577500467154 | erot = 1.7466850070844 | epot = -11.4662436792504 | etot = -8.1337836674945 +308000 ekin = 1.54030424866655 | erot = 1.71903801624886 | epot = -11.3931259316301 | etot = -8.13378366671474 +309000 ekin = 1.4990009105044 | erot = 1.69173690592116 | epot = -11.3245214826142 | etot = -8.13378366618868 +310000 ekin = 1.46747597212362 | erot = 1.66636932779771 | epot = -11.2676289658628 | etot = -8.13378366594147 +311000 ekin = 1.44771419446033 | erot = 1.64410448876994 | epot = -11.2256023491826 | etot = -8.13378366595238 +312000 ekin = 1.4383914186309 | erot = 1.62568199896361 | epot = -11.1978570837367 | etot = -8.13378366614219 +313000 ekin = 1.43594352564835 | erot = 1.61150443049618 | epot = -11.1812316225544 | etot = -8.1337836664099 +314000 ekin = 1.43595255616958 | erot = 1.60177116104875 | epot = -11.1715073838745 | etot = -8.13378366665619 +315000 ekin = 1.43500742740479 | erot = 1.59648896098924 | epot = -11.1652800551023 | etot = -8.13378366670831 +316000 ekin = 1.43108473245268 | erot = 1.5956580439379 | epot = -11.1605264431142 | etot = -8.13378366672358 +317000 ekin = 1.42390336283526 | erot = 1.59957952106317 | epot = -11.1572665504279 | etot = -8.13378366652945 +318000 ekin = 1.41631295378262 | erot = 1.60866819207214 | epot = -11.158764812016 | etot = -8.1337836661612 +319000 ekin = 1.41381426232535 | erot = 1.62334142232245 | epot = -11.1709393503702 | etot = -8.13378366572238 +320000 ekin = 1.42315030251777 | erot = 1.64384116840196 | epot = -11.2007751362838 | etot = -8.13378366536404 +321000 ekin = 1.45024845493823 | erot = 1.67003325939981 | epot = -11.2540653795749 | etot = -8.13378366523685 +322000 ekin = 1.49815500536655 | erot = 1.70123818171226 | epot = -11.3331768525206 | etot = -8.13378366544176 +323000 ekin = 1.56569352501989 | erot = 1.73609284126389 | epot = -11.4355700323001 | etot = -8.13378366601634 +324000 ekin = 1.64679224021427 | erot = 1.77264010659823 | epot = -11.553216013806 | etot = -8.13378366699349 +325000 ekin = 1.73163775631264 | erot = 1.80818795205361 | epot = -11.6736093764089 | etot = -8.13378366804261 +326000 ekin = 1.80750329208696 | erot = 1.8398074929546 | epot = -11.7810944543884 | etot = -8.13378366934687 +327000 ekin = 1.85797659457013 | erot = 1.86537346541894 | epot = -11.8571337303148 | etot = -8.13378367032571 +328000 ekin = 1.87027520749331 | erot = 1.88392315073132 | epot = -11.8879820288833 | etot = -8.13378367065868 +329000 ekin = 1.83949589055174 | erot = 1.89597309718727 | epot = -11.869252657917 | etot = -8.13378367017803 +330000 ekin = 1.77117100869305 | erot = 1.90323589019341 | epot = -11.8081905678819 | etot = -8.13378366899542 +331000 ekin = 1.68023517873615 | erot = 1.90771959425362 | epot = -11.7217384405342 | etot = -8.13378366754447 +332000 ekin = 1.58599656571697 | erot = 1.91066851347039 | epot = -11.630448745537 | etot = -8.13378366634961 +333000 ekin = 1.50566649891836 | erot = 1.91203797343616 | epot = -11.5514881380525 | etot = -8.13378366569794 +334000 ekin = 1.44997196059215 | erot = 1.91073772769808 | epot = -11.4944933538505 | etot = -8.13378366556023 +335000 ekin = 1.42175053141052 | erot = 1.90515605628881 | epot = -11.4606902539328 | etot = -8.13378366623347 +336000 ekin = 1.4166253105865 | erot = 1.89330033651205 | epot = -11.443709313723 | etot = -8.13378366662444 +337000 ekin = 1.42902342420092 | erot = 1.87459660541265 | epot = -11.43740369656 | etot = -8.13378366694648 +338000 ekin = 1.45347553474253 | erot = 1.84924982278892 | epot = -11.4365090247033 | etot = -8.13378366717183 +339000 ekin = 1.48532648332336 | erot = 1.81789825388445 | epot = -11.4370084045411 | etot = -8.13378366733326 +340000 ekin = 1.52068113212542 | erot = 1.78131054290141 | epot = -11.4357753425007 | etot = -8.13378366747385 +341000 ekin = 1.5560607012887 | erot = 1.74019406298323 | epot = -11.4300384318859 | etot = -8.13378366761399 +342000 ekin = 1.58819693536409 | erot = 1.69515176482787 | epot = -11.4171323679319 | etot = -8.13378366773989 +343000 ekin = 1.61415529814685 | erot = 1.64675903935067 | epot = -11.3946980053118 | etot = -8.13378366781423 +344000 ekin = 1.63171879307236 | erot = 1.59569319794419 | epot = -11.3611956588172 | etot = -8.13378366780061 +345000 ekin = 1.63976605961489 | erot = 1.5428270420927 | epot = -11.3163767694021 | etot = -8.13378366769448 +346000 ekin = 1.63837200138302 | erot = 1.48918714017029 | epot = -11.2613428090738 | etot = -8.13378366752046 +347000 ekin = 1.62852754177388 | erot = 1.4358735156518 | epot = -11.1981847247562 | etot = -8.13378366733053 +348000 ekin = 1.61158889283549 | erot = 1.38392546940706 | epot = -11.1292980294148 | etot = -8.13378366717223 +349000 ekin = 1.58873557439393 | erot = 1.33422850520796 | epot = -11.0567477466751 | etot = -8.13378366707319 +350000 ekin = 1.56064786721289 | erot = 1.28749851960141 | epot = -10.981930053846 | etot = -8.13378366703173 +351000 ekin = 1.52754191191144 | erot = 1.24434620359675 | epot = -10.9056717825216 | etot = -8.1337836670134 +352000 ekin = 1.48960299203704 | erot = 1.20538641998308 | epot = -10.8287730789798 | etot = -8.13378366695972 +353000 ekin = 1.44778264502695 | erot = 1.17134399709371 | epot = -10.752910308908 | etot = -8.13378366678732 +354000 ekin = 1.4053310095306 | erot = 1.14324844922782 | epot = -10.682363125244 | etot = -8.13378366648559 +355000 ekin = 1.36869095863183 | erot = 1.12250242069477 | epot = -10.6249770453809 | etot = -8.13378366605434 +356000 ekin = 1.34490175995297 | erot = 1.10992990778302 | epot = -10.5886153331823 | etot = -8.13378366544635 +357000 ekin = 1.34315796275824 | erot = 1.10621719879765 | epot = -10.5831588263819 | etot = -8.13378366482602 +358000 ekin = 1.37283801207744 | erot = 1.11171347587857 | epot = -10.6183351524118 | etot = -8.13378366445576 +359000 ekin = 1.43996759058201 | erot = 1.12612871057513 | epot = -10.6998799657442 | etot = -8.13378366458706 +360000 ekin = 1.5438844591394 | erot = 1.14830381564191 | epot = -10.825971940099 | etot = -8.13378366531768 +361000 ekin = 1.67586531509034 | erot = 1.17618905419233 | epot = -10.9858380358531 | etot = -8.13378366657042 +362000 ekin = 1.82005627455383 | erot = 1.20703160753447 | epot = -11.1608715500439 | etot = -8.13378366795558 +363000 ekin = 1.95850583937149 | erot = 1.23798141777832 | epot = -11.3302709261636 | etot = -8.13378366901377 +364000 ekin = 2.0758001766431 | erot = 1.26672677095262 | epot = -11.4763106177177 | etot = -8.13378367012194 +365000 ekin = 2.15891662517416 | erot = 1.29173621495748 | epot = -11.5844365106022 | etot = -8.13378367047059 +366000 ekin = 2.20238380195839 | erot = 1.31262064914847 | epot = -11.6487881213389 | etot = -8.13378367023206 +367000 ekin = 2.2085172727543 | erot = 1.33022857587956 | epot = -11.6725295182442 | etot = -8.13378366961034 +368000 ekin = 2.18513118770686 | erot = 1.34632721320096 | epot = -11.6652420696059 | etot = -8.13378366869811 +369000 ekin = 2.14321144646781 | erot = 1.36315448463404 | epot = -11.6401495989055 | etot = -8.13378366780367 +370000 ekin = 2.0938828241348 | erot = 1.38296858720496 | epot = -11.6106350785167 | etot = -8.1337836671769 +371000 ekin = 2.04539161606818 | erot = 1.40758201280334 | epot = -11.5867572956956 | etot = -8.13378366682413 +372000 ekin = 2.00261126514815 | erot = 1.43827057512772 | epot = -11.574665506942 | etot = -8.13378366666616 +373000 ekin = 1.96798302472993 | erot = 1.475845039439 | epot = -11.5776117307495 | etot = -8.13378366658054 +374000 ekin = 1.94276422015049 | erot = 1.52074221163621 | epot = -11.5972900983351 | etot = -8.13378366654844 +375000 ekin = 1.92741631545133 | erot = 1.57302624843796 | epot = -11.6342262305073 | etot = -8.13378366661803 +376000 ekin = 1.92110841836636 | erot = 1.63232320681275 | epot = -11.6872152920284 | etot = -8.13378366684932 +377000 ekin = 1.92083197489617 | erot = 1.69770894533729 | epot = -11.7523245875363 | etot = -8.1337836673028 +378000 ekin = 1.92097158011965 | erot = 1.76763055654163 | epot = -11.8223858045346 | etot = -8.13378366787334 +379000 ekin = 1.91438056916682 | erot = 1.83964318712893 | epot = -11.887807424947 | etot = -8.13378366865125 +380000 ekin = 1.89241520119269 | erot = 1.91106138176787 | epot = -11.9372602523186 | etot = -8.13378366935807 +381000 ekin = 1.847118431211 | erot = 1.97933543814399 | epot = -11.9602375392212 | etot = -8.13378366986618 +382000 ekin = 1.77364821788507 | erot = 2.04210934439902 | epot = -11.9495412323413 | etot = -8.13378367005726 +383000 ekin = 1.67178472399512 | erot = 2.09754562136631 | epot = -11.903114015185 | etot = -8.13378366982355 +384000 ekin = 1.5470955648132 | erot = 2.1443870823428 | epot = -11.8252663163759 | etot = -8.13378366921985 +385000 ekin = 1.41093432867735 | erot = 2.18184182145047 | epot = -11.7265598182841 | etot = -8.13378366815629 +386000 ekin = 1.27958936994635 | erot = 2.21051340231003 | epot = -11.6238864391457 | etot = -8.13378366688934 +387000 ekin = 1.17137861198704 | erot = 2.23163165239755 | epot = -11.5367939301752 | etot = -8.13378366579065 +388000 ekin = 1.1017978040278 | erot = 2.24634754527518 | epot = -11.4819290145306 | etot = -8.13378366522763 +389000 ekin = 1.07882148969069 | erot = 2.25505587957395 | epot = -11.4676610376653 | etot = -8.1337836684007 +390000 ekin = 1.07051570135882 | erot = 2.26936424221012 | epot = -11.4736636037183 | etot = -8.13378366014933 +391000 ekin = 1.12513305991829 | erot = 2.28557987987778 | epot = -11.5444966077486 | etot = -8.1337836679525 +392000 ekin = 1.21295440172474 | erot = 2.27063670340335 | epot = -11.6173747716335 | etot = -8.13378366650546 +393000 ekin = 1.30924312365477 | erot = 2.24076930893612 | epot = -11.683796099719 | etot = -8.13378366712811 +394000 ekin = 1.40561895760574 | erot = 2.19794335034468 | epot = -11.737345975341 | etot = -8.13378366739058 +395000 ekin = 1.49662707239207 | erot = 2.14293675801956 | epot = -11.7733474977468 | etot = -8.13378366733519 +396000 ekin = 1.58077727991366 | erot = 2.07761988891088 | epot = -11.792180835874 | etot = -8.13378366704947 +397000 ekin = 1.65955042581691 | erot = 2.00469837191009 | epot = -11.7980324643556 | etot = -8.13378366662865 +398000 ekin = 1.73622447988457 | erot = 1.92743077252824 | epot = -11.7974389185588 | etot = -8.13378366614599 +399000 ekin = 1.81471876942085 | erot = 1.84941455049417 | epot = -11.7979169856346 | etot = -8.13378366571955 +400000 ekin = 1.89831345083173 | erot = 1.77428869309119 | epot = -11.8063858093336 | etot = -8.13378366541068 +401000 ekin = 1.98857882165051 | erot = 1.70555701947522 | epot = -11.8279195064034 | etot = -8.13378366527767 +402000 ekin = 2.08469272454806 | erot = 1.64640053761174 | epot = -11.864876927493 | etot = -8.13378366533317 +403000 ekin = 2.18333492883686 | erot = 1.59947809827568 | epot = -11.9165966926833 | etot = -8.13378366557074 +404000 ekin = 2.27899469657634 | erot = 1.56671457666561 | epot = -11.9794929391001 | etot = -8.13378366585815 +405000 ekin = 2.36506409046791 | erot = 1.54904572147161 | epot = -12.0478934783885 | etot = -8.133783666449 +406000 ekin = 2.43306193249953 | erot = 1.5463043441214 | epot = -12.113149943779 | etot = -8.13378366715811 +407000 ekin = 2.47364186380652 | erot = 1.55689186412975 | epot = -12.1643173959552 | etot = -8.13378366801896 +408000 ekin = 2.47760299472659 | erot = 1.57810641384372 | epot = -12.1894930773339 | etot = -8.13378366876364 +409000 ekin = 2.4382285084277 | erot = 1.60664113475376 | epot = -12.1786533122599 | etot = -8.13378366907848 +410000 ekin = 2.35516301280443 | erot = 1.63934184028269 | epot = -12.1282885218174 | etot = -8.13378366873023 +411000 ekin = 2.23661952277391 | erot = 1.67408087730519 | epot = -12.0444840678247 | etot = -8.13378366774563 +412000 ekin = 2.0985126746209 | erot = 1.71012170017462 | epot = -11.9424180412156 | etot = -8.13378366642006 +413000 ekin = 1.9605648479408 | erot = 1.7477880401099 | epot = -11.842136553205 | etot = -8.13378366515434 +414000 ekin = 1.84128090481651 | erot = 1.78771082121978 | epot = -11.7627753903069 | etot = -8.13378366427058 +415000 ekin = 1.75390442336269 | erot = 1.8300910315431 | epot = -11.7177791188322 | etot = -8.1337836639264 +416000 ekin = 1.70439570487947 | erot = 1.8742500828549 | epot = -11.7124294518619 | etot = -8.13378366412758 +417000 ekin = 1.6913155425304 | erot = 1.91850147883522 | epot = -11.7436006861825 | etot = -8.13378366481692 +418000 ekin = 1.70689490031879 | erot = 1.96025799788586 | epot = -11.8009365639622 | etot = -8.13378366575752 +419000 ekin = 1.73962222230418 | erot = 1.99637255840534 | epot = -11.8697784474987 | etot = -8.13378366678922 +420000 ekin = 1.77669286262506 | erot = 2.02357619714827 | epot = -11.9340527274771 | etot = -8.13378366770374 +421000 ekin = 1.80657824082939 | erot = 2.03903049555573 | epot = -11.9793924047129 | etot = -8.13378366832774 +422000 ekin = 1.82111290085882 | erot = 2.04088419799503 | epot = -11.9957807674272 | etot = -8.1337836685733 +423000 ekin = 1.8164858456862 | erot = 2.02865244729792 | epot = -11.9789219614438 | etot = -8.13378366845964 +424000 ekin = 1.79301691785 | erot = 2.00326876348577 | epot = -11.93006934941 | etot = -8.1337836680742 +425000 ekin = 1.7542404696796 | erot = 1.96680784722199 | epot = -11.8548319844099 | etot = -8.13378366750835 +426000 ekin = 1.70601392329041 | erot = 1.92202692837085 | epot = -11.7618245184889 | etot = -8.13378366682768 +427000 ekin = 1.65580906012742 | erot = 1.8718698544119 | epot = -11.6614625806777 | etot = -8.13378366613836 +428000 ekin = 1.61207963969203 | erot = 1.81905558542305 | epot = -11.5649188905514 | etot = -8.13378366543629 +429000 ekin = 1.58339999422577 | erot = 1.76579893171841 | epot = -11.4829825908551 | etot = -8.13378366491096 +430000 ekin = 1.57646033947156 | erot = 1.71346152699463 | epot = -11.4237055311677 | etot = -8.1337836647015 +431000 ekin = 1.59418488210558 | erot = 1.66239892773017 | epot = -11.3903674747255 | etot = -8.13378366488974 +432000 ekin = 1.63452809771572 | erot = 1.61205574804186 | epot = -11.3803675111907 | etot = -8.13378366543315 +433000 ekin = 1.69077410976896 | erot = 1.56136635610719 | epot = -11.3859241320169 | etot = -8.13378366614078 +434000 ekin = 1.75368500742744 | erot = 1.50939558466526 | epot = -11.3968642588279 | etot = -8.13378366673519 +435000 ekin = 1.81477188941387 | erot = 1.45598133800037 | epot = -11.4045368944168 | etot = -8.13378366700251 +436000 ekin = 1.86895151228359 | erot = 1.40204530898162 | epot = -11.4047804881014 | etot = -8.13378366683618 +437000 ekin = 1.91551323813695 | erot = 1.34941425923643 | epot = -11.3987111639621 | etot = -8.1337836665887 +438000 ekin = 1.95545357706326 | erot = 1.30011080733834 | epot = -11.3893480508819 | etot = -8.1337836664803 +439000 ekin = 1.98811153075701 | erot = 1.25557284833992 | epot = -11.3774680457432 | etot = -8.13378366664629 +440000 ekin = 2.00986623436144 | erot = 1.21630204161218 | epot = -11.3599519429689 | etot = -8.1337836669953 +441000 ekin = 2.01530350765885 | erot = 1.18202297032986 | epot = -11.3311101452771 | etot = -8.13378366728841 +442000 ekin = 1.99936349679026 | erot = 1.15207873138338 | epot = -11.285225896028 | etot = -8.13378366785432 +443000 ekin = 1.95696749681617 | erot = 1.12547607064141 | epot = -11.2162272349861 | etot = -8.13378366752857 +444000 ekin = 1.89166490098894 | erot = 1.10194461448034 | epot = -11.1273931823296 | etot = -8.13378366686036 +445000 ekin = 1.81328868644648 | erot = 1.08168732032615 | epot = -11.0287596725666 | etot = -8.13378366579393 +446000 ekin = 1.73577899474597 | erot = 1.06505071492877 | epot = -10.934613374721 | etot = -8.13378366504623 +447000 ekin = 1.67093185588756 | erot = 1.05239705126936 | epot = -10.8571125714687 | etot = -8.13378366431178 +448000 ekin = 1.62911856819551 | erot = 1.04409603312636 | epot = -10.8069982651691 | etot = -8.1337836638472 +449000 ekin = 1.61731626297121 | erot = 1.04041489697142 | epot = -10.791514823704 | etot = -8.13378366376135 +450000 ekin = 1.6371169760582 | erot = 1.04135992229642 | epot = -10.8122605626996 | etot = -8.13378366434497 +451000 ekin = 1.683202581423 | erot = 1.04620824656516 | epot = -10.8631944930217 | etot = -8.13378366503355 +452000 ekin = 1.74581668011809 | erot = 1.05391169410105 | epot = -10.9335120399986 | etot = -8.13378366577951 +453000 ekin = 1.81457146100557 | erot = 1.06335165863438 | epot = -11.0117067861187 | etot = -8.13378366647873 +454000 ekin = 1.87975957938354 | erot = 1.07317402238495 | epot = -11.0867172689043 | etot = -8.13378366713579 +455000 ekin = 1.93251877587718 | erot = 1.08171623325452 | epot = -11.1480186769418 | etot = -8.13378366781011 +456000 ekin = 1.96415416826587 | erot = 1.08704156958762 | epot = -11.1849794063545 | etot = -8.13378366850104 +457000 ekin = 1.96605348076947 | erot = 1.0872339429412 | epot = -11.1870710927812 | etot = -8.13378366907053 +458000 ekin = 1.93127523760885 | erot = 1.08096076790336 | epot = -11.1460196747758 | etot = -8.1337836692636 +459000 ekin = 1.85771594839236 | erot = 1.06809531780637 | epot = -11.0595949350235 | etot = -8.13378366882475 +460000 ekin = 1.75147188083691 | erot = 1.05009293158279 | epot = -10.935348480065 | etot = -8.13378366764531 +461000 ekin = 1.62834142733994 | erot = 1.02990811326384 | epot = -10.7920332065057 | etot = -8.13378366590194 +462000 ekin = 1.51195360648057 | erot = 1.01153881174369 | epot = -10.6572760812005 | etot = -8.13378366297619 +463000 ekin = 1.43011910144001 | erot = 1.00022578453745 | epot = -10.5641285481523 | etot = -8.13378366217487 +464000 ekin = 1.39582910827648 | erot = 0.998198432076844 | epot = -10.5278112022039 | etot = -8.1337836618506 +465000 ekin = 1.41007554850293 | erot = 1.00592009003209 | epot = -10.5497793012381 | etot = -8.13378366270313 +466000 ekin = 1.46251969360747 | erot = 1.02219738030556 | epot = -10.6185007378637 | etot = -8.13378366395071 +467000 ekin = 1.49627186630975 | erot = 1.05472101821045 | epot = -10.6847765488433 | etot = -8.13378366432313 +468000 ekin = 1.51725853676438 | erot = 1.12479885660867 | epot = -10.7758410579087 | etot = -8.13378366453565 +469000 ekin = 1.58140637755938 | erot = 1.16828828959022 | epot = -10.8834783316313 | etot = -8.13378366448166 +470000 ekin = 1.60068578300076 | erot = 1.18114141021406 | epot = -10.9156108575643 | etot = -8.13378366434945 +471000 ekin = 1.59076368328042 | erot = 1.18707237247322 | epot = -10.9116197194539 | etot = -8.13378366370031 +472000 ekin = 1.5612406060142 | erot = 1.18572143101511 | epot = -10.8807456998225 | etot = -8.13378366279316 +473000 ekin = 1.52502097412807 | erot = 1.17792025681444 | epot = -10.8367248927777 | etot = -8.1337836618352 +474000 ekin = 1.49533177226926 | erot = 1.165444462138 | epot = -10.7945598953625 | etot = -8.13378366095528 +475000 ekin = 1.48386630176695 | erot = 1.15068540215814 | epot = -10.7683353641634 | etot = -8.1337836602383 +476000 ekin = 1.49971334633236 | erot = 1.13623821678217 | epot = -10.7697352228581 | etot = -8.13378365974359 +477000 ekin = 1.5487111876978 | erot = 1.12448433353011 | epot = -10.8069791813398 | etot = -8.1337836601119 +478000 ekin = 1.62953491120436 | erot = 1.11764268903856 | epot = -10.8809612604826 | etot = -8.13378366023969 +479000 ekin = 1.73735741643734 | erot = 1.11700620811583 | epot = -10.9881472852193 | etot = -8.13378366066615 +480000 ekin = 1.86556210287678 | erot = 1.12262064775425 | epot = -11.1219664120635 | etot = -8.1337836614325 +481000 ekin = 2.00121026337328 | erot = 1.13364860021549 | epot = -11.2686425499546 | etot = -8.13378368636585 +482000 ekin = 2.04617329760094 | erot = 1.16256926169772 | epot = -11.3425262237857 | etot = -8.13378366448705 +483000 ekin = 2.14335261834056 | erot = 1.21476273129688 | epot = -11.4918990325462 | etot = -8.13378368290878 +484000 ekin = 2.20270995356394 | erot = 1.23147381807205 | epot = -11.5679674446545 | etot = -8.13378367301847 +485000 ekin = 2.20682939441105 | erot = 1.23835798982356 | epot = -11.5789710574867 | etot = -8.13378367325212 +486000 ekin = 2.16589682794375 | erot = 1.24300370552104 | epot = -11.5426842062933 | etot = -8.13378367282848 +487000 ekin = 2.08668888865065 | erot = 1.24625551752377 | epot = -11.4667280780208 | etot = -8.13378367184637 +488000 ekin = 1.98386509125157 | erot = 1.24977318046877 | epot = -11.3674219422435 | etot = -8.13378367052311 +489000 ekin = 1.87707931030795 | erot = 1.25547012773927 | epot = -11.2663331072078 | etot = -8.13378366916055 +490000 ekin = 1.78677596317092 | erot = 1.26490338722197 | epot = -11.1854630185197 | etot = -8.1337836681268 +491000 ekin = 1.72903831214112 | erot = 1.27867004038315 | epot = -11.1414920203231 | etot = -8.13378366779881 +492000 ekin = 1.7103997905776 | erot = 1.29591768107408 | epot = -11.1401011400714 | etot = -8.13378366841973 +493000 ekin = 1.72454317156023 | erot = 1.31423280426865 | epot = -11.1725596457326 | etot = -8.1337836699037 +494000 ekin = 1.75332785015283 | erot = 1.33022406246729 | epot = -11.2173355843424 | etot = -8.13378367172227 +495000 ekin = 1.77349565825339 | erot = 1.34086561473228 | epot = -11.2481449460233 | etot = -8.13378367303767 +496000 ekin = 1.76725059667391 | erot = 1.34512484286612 | epot = -11.246159112691 | etot = -8.13378367315101 +497000 ekin = 1.73127637989022 | erot = 1.34494708212087 | epot = -11.2100071339734 | etot = -8.13378367196233 +498000 ekin = 1.67855000907778 | erot = 1.34489121264346 | epot = -11.1572248917577 | etot = -8.13378367003641 +499000 ekin = 1.63191747119361 | erot = 1.35056727533119 | epot = -11.1162684147384 | etot = -8.13378366821364 +500000 ekin = 1.61378359989808 | erot = 1.36676364681355 | epot = -11.1143309138627 | etot = -8.13378366715105 +501000 ekin = 1.63758101988158 | erot = 1.39609850676573 | epot = -11.1674631937488 | etot = -8.13378366710151 +502000 ekin = 1.70413807541423 | erot = 1.43847493669164 | epot = -11.2763966800733 | etot = -8.13378366796746 +503000 ekin = 1.80268297747941 | erot = 1.49115460253826 | epot = -11.4276212495095 | etot = -8.13378366949188 +504000 ekin = 1.91419549779682 | erot = 1.54914693964081 | epot = -11.5971261088649 | etot = -8.1337836714273 +505000 ekin = 2.01490443998886 | erot = 1.60576406504492 | epot = -11.7544521785742 | etot = -8.13378367354037 +506000 ekin = 2.07966541471917 | erot = 1.65345439354273 | epot = -11.8669034837012 | etot = -8.13378367543934 +507000 ekin = 2.08700353897931 | erot = 1.68517460629698 | epot = -11.9059618217544 | etot = -8.13378367647812 +508000 ekin = 2.02663352664087 | erot = 1.69625747623816 | epot = -11.8566746789476 | etot = -8.13378367606856 +509000 ekin = 1.90589064134532 | erot = 1.68599529702818 | epot = -11.7256696125605 | etot = -8.13378367418702 +510000 ekin = 1.74959091232532 | erot = 1.65787688253333 | epot = -11.5412514663247 | etot = -8.13378367146606 +511000 ekin = 1.59231955658843 | erot = 1.6182626673154 | epot = -11.3443658926804 | etot = -8.13378366877654 +512000 ekin = 1.46755856060292 | erot = 1.57434662380292 | epot = -11.1756888512875 | etot = -8.13378366688171 +513000 ekin = 1.39839916093105 | erot = 1.53234768377481 | epot = -11.0645305108152 | etot = -8.13378366610933 +514000 ekin = 1.39338903686656 | erot = 1.49706258344342 | epot = -11.0242352864652 | etot = -8.13378366615522 +515000 ekin = 1.4449515906223 | erot = 1.47110271002822 | epot = -11.0498379682114 | etot = -8.13378366756091 +516000 ekin = 1.53288312821876 | erot = 1.453570647243 | epot = -11.1202374448478 | etot = -8.133783669386 +517000 ekin = 1.63159033312891 | erot = 1.44224294472704 | epot = -11.2076169492337 | etot = -8.13378367137774 +518000 ekin = 1.7140940145624 | erot = 1.43408399435691 | epot = -11.281961682157 | etot = -8.13378367323773 +519000 ekin = 1.75665192757263 | erot = 1.42579002916731 | epot = -11.316225631737 | etot = -8.13378367499705 +520000 ekin = 1.74187345948359 | erot = 1.41504839774727 | epot = -11.2907055324355 | etot = -8.13378367520464 +521000 ekin = 1.6687170304138 | erot = 1.40071550595613 | epot = -11.2032162101188 | etot = -8.13378367374886 +522000 ekin = 1.55952182856936 | erot = 1.38339983649833 | epot = -11.0767053362068 | etot = -8.13378367113911 +523000 ekin = 1.45114556552355 | erot = 1.36568308064632 | epot = -10.9506123146269 | etot = -8.13378366845702 +524000 ekin = 1.38091842213512 | erot = 1.35134919390609 | epot = -10.8660512824867 | etot = -8.13378366644547 +525000 ekin = 1.37601425592005 | erot = 1.34456662955663 | epot = -10.8543645508867 | etot = -8.13378366541006 +526000 ekin = 1.44870428485565 | erot = 1.34909740178984 | epot = -10.9315853521561 | etot = -8.13378366551062 +527000 ekin = 1.59459863547555 | erot = 1.36714947551734 | epot = -11.0955317779066 | etot = -8.13378366691373 +528000 ekin = 1.79183405482323 | erot = 1.39841904592953 | epot = -11.3240367701711 | etot = -8.1337836694183 +529000 ekin = 2.00478978698341 | erot = 1.43972835787364 | epot = -11.5783018172279 | etot = -8.13378367237083 +530000 ekin = 2.19333795602184 | erot = 1.48552207657583 | epot = -11.8126437074866 | etot = -8.13378367488898 +531000 ekin = 2.32431476966283 | erot = 1.52928747155129 | epot = -11.9873859175035 | etot = -8.13378367628933 +532000 ekin = 2.37971447238976 | erot = 1.56539257217402 | epot = -12.0788907210184 | etot = -8.13378367645461 +533000 ekin = 2.35771666716381 | erot = 1.59048999439669 | epot = -12.0819903372243 | etot = -8.1337836756638 +534000 ekin = 2.26899715449622 | erot = 1.60407394358295 | epot = -12.0068547722117 | etot = -8.13378367413258 +535000 ekin = 2.13365177460143 | erot = 1.60831072461293 | epot = -11.8757461712372 | etot = -8.13378367202286 +536000 ekin = 1.97886376167562 | erot = 1.60719127866692 | epot = -11.7198387100714 | etot = -8.13378366972884 +537000 ekin = 1.83421887314921 | erot = 1.60523898300898 | epot = -11.5732415239224 | etot = -8.13378366776425 +538000 ekin = 1.72531720892395 | erot = 1.60632519288809 | epot = -11.465426068323 | etot = -8.13378366651098 +539000 ekin = 1.66856519905205 | erot = 1.61301472929837 | epot = -11.4153635944735 | etot = -8.13378366612308 +540000 ekin = 1.66907056567389 | erot = 1.62662968764599 | epot = -11.4294839194817 | etot = -8.1337836661618 +541000 ekin = 1.72153495926528 | erot = 1.64788745985663 | epot = -11.5032060864699 | etot = -8.13378366734799 +542000 ekin = 1.80903650496287 | erot = 1.67547869679642 | epot = -11.618298870671 | etot = -8.13378366891172 +543000 ekin = 1.90894616834964 | erot = 1.70734508947333 | epot = -11.7500749283571 | etot = -8.13378367053414 +544000 ekin = 1.99777842838976 | erot = 1.74125357780433 | epot = -11.8728156781126 | etot = -8.13378367191851 +545000 ekin = 2.05546409374046 | erot = 1.77521000036089 | epot = -11.9644577669355 | etot = -8.13378367283414 +546000 ekin = 2.06867595313242 | erot = 1.8077948360879 | epot = -12.0102544623758 | etot = -8.13378367315551 +547000 ekin = 2.03267806245285 | erot = 1.83838588997954 | epot = -12.0048476252993 | etot = -8.13378367286689 +548000 ekin = 1.95148731421026 | erot = 1.86718390882511 | epot = -11.9524548951376 | etot = -8.13378367210227 +549000 ekin = 1.83645042330075 | erot = 1.89487456520008 | epot = -11.8651086595368 | etot = -8.13378367103596 +550000 ekin = 1.70373130495655 | erot = 1.92233248820821 | epot = -11.7598474630408 | etot = -8.13378366987601 +551000 ekin = 1.57139422781638 | erot = 1.9502429186833 | epot = -11.65542081531 | etot = -8.1337836688103 +552000 ekin = 1.45663332558441 | erot = 1.97878558863207 | epot = -11.5692025822092 | etot = -8.13378366799269 +553000 ekin = 1.3733740902053 | erot = 2.00744335365976 | epot = -11.5146011114102 | etot = -8.13378366754517 +554000 ekin = 1.33029485863377 | erot = 2.0349665714564 | epot = -11.4990450976332 | etot = -8.13378366754299 +555000 ekin = 1.32945359626657 | erot = 2.05953157376384 | epot = -11.5227688380265 | etot = -8.13378366799606 +556000 ekin = 1.36589068758086 | erot = 2.07909837609607 | epot = -11.5787727324867 | etot = -8.13378366880977 +557000 ekin = 1.42857577084687 | erot = 2.09193210847203 | epot = -11.6542915491193 | etot = -8.13378366980039 +558000 ekin = 1.50275359964787 | erot = 2.09715314140285 | epot = -11.733690411781 | etot = -8.13378367073029 +559000 ekin = 1.57321830908193 | erot = 2.09511862189589 | epot = -11.8021206023721 | etot = -8.13378367139428 +560000 ekin = 1.62740172364015 | erot = 2.0874549689334 | epot = -11.8486403642998 | etot = -8.13378367172623 +561000 ekin = 1.65692416188407 | erot = 2.07666092047466 | epot = -11.867368754165 | etot = -8.1337836718063 +562000 ekin = 1.65737426356001 | erot = 2.06544534214375 | epot = -11.8566032774352 | etot = -8.13378367173146 +563000 ekin = 1.62727808427686 | erot = 2.0561555503796 | epot = -11.8172173064426 | etot = -8.1337836717861 +564000 ekin = 1.56679933055812 | erot = 2.05047511799406 | epot = -11.7510581199034 | etot = -8.13378367135121 +565000 ekin = 1.48206055328865 | erot = 2.04917576858446 | epot = -11.6650199925185 | etot = -8.13378367064534 +566000 ekin = 1.38423866544416 | erot = 2.05221850150166 | epot = -11.570240836728 | etot = -8.13378366978216 +567000 ekin = 1.28749391779805 | erot = 2.05873429505309 | epot = -11.4800118818356 | etot = -8.1337836689845 +568000 ekin = 1.2057043110348 | erot = 2.06705692033903 | epot = -11.4065448998294 | etot = -8.13378366845561 +569000 ekin = 1.14918558023836 | erot = 2.07495244466027 | epot = -11.3579216931865 | etot = -8.13378366828788 +570000 ekin = 1.12276449647263 | erot = 2.08007272962266 | epot = -11.3366208945389 | etot = -8.13378366844359 +571000 ekin = 1.12567595873366 | erot = 2.08050218013587 | epot = -11.3399618076688 | etot = -8.13378366879922 +572000 ekin = 1.15294903412069 | erot = 2.07519259344981 | epot = -11.3619252967711 | etot = -8.1337836692006 +573000 ekin = 1.19838854920248 | erot = 2.06451015558496 | epot = -11.3966823740142 | etot = -8.13378366922679 +574000 ekin = 1.25460427390538 | erot = 2.04968889738576 | epot = -11.4380768408162 | etot = -8.13378366952507 +575000 ekin = 1.3145473569659 | erot = 2.03199549862714 | epot = -11.4803265251246 | etot = -8.13378366953155 +576000 ekin = 1.37512583612256 | erot = 2.01319845741142 | epot = -11.522107962838 | etot = -8.13378366930401 +577000 ekin = 1.43682760503803 | erot = 1.99528982934627 | epot = -11.5659011033479 | etot = -8.13378366896359 +578000 ekin = 1.50235588202257 | erot = 1.98017269182707 | epot = -11.616312242474 | etot = -8.13378366862437 +579000 ekin = 1.57520818416893 | erot = 1.96938672247183 | epot = -11.6783785749987 | etot = -8.13378366835792 +580000 ekin = 1.65868462492759 | erot = 1.9639024985745 | epot = -11.7563707921412 | etot = -8.13378366863908 +581000 ekin = 1.75247311826172 | erot = 1.96419308534662 | epot = -11.8504498724713 | etot = -8.13378366886299 +582000 ekin = 1.85283782857126 | erot = 1.96967477641562 | epot = -11.9562962743646 | etot = -8.13378366937774 +583000 ekin = 1.95429754596698 | erot = 1.97826405495517 | epot = -12.0663452712462 | etot = -8.13378367032403 +584000 ekin = 2.04662916571296 | erot = 1.98631443704561 | epot = -12.1667272745288 | etot = -8.13378367177025 +585000 ekin = 2.11419694670623 | erot = 1.98862566442644 | epot = -12.2366062846708 | etot = -8.1337836735381 +586000 ekin = 2.13871236987403 | erot = 1.97915340582032 | epot = -12.251649450775 | etot = -8.13378367508065 +587000 ekin = 2.1046578324698 | erot = 1.95256271523913 | epot = -12.1910042235993 | etot = -8.13378367589034 +588000 ekin = 2.00543191748363 | erot = 1.90599988278528 | epot = -12.0452154755461 | etot = -8.13378367527722 +589000 ekin = 1.85115446103327 | erot = 1.84021509337235 | epot = -11.8251532276819 | etot = -8.13378367327628 +590000 ekin = 1.66921622807052 | erot = 1.75933351105154 | epot = -11.5623334095136 | etot = -8.13378367039159 +591000 ekin = 1.49774854837099 | erot = 1.66961531493849 | epot = -11.3011475307967 | etot = -8.13378366748726 +592000 ekin = 1.3741820859932 | erot = 1.57786762200524 | epot = -11.0858333735181 | etot = -8.13378366551967 +593000 ekin = 1.32230765433109 | erot = 1.49017042368474 | epot = -10.9462617430929 | etot = -8.13378366507706 +594000 ekin = 1.34433584580908 | erot = 1.41110289037829 | epot = -10.8892224022229 | etot = -8.13378366603555 +595000 ekin = 1.4231376214122 | erot = 1.34352894995752 | epot = -10.9004502389522 | etot = -8.13378366758252 +596000 ekin = 1.53140640357278 | erot = 1.28905714164113 | epot = -10.9542472149381 | etot = -8.13378366972416 +597000 ekin = 1.63793776665508 | erot = 1.24822708399344 | epot = -11.019948521789 | etot = -8.13378367114047 +598000 ekin = 1.71853369497956 | erot = 1.22042305585484 | epot = -11.0727404229849 | etot = -8.13378367215051 +599000 ekin = 1.75676579673314 | erot = 1.20417119499254 | epot = -11.0947206644607 | etot = -8.13378367273503 +600000 ekin = 1.74415562352347 | erot = 1.1974850125872 | epot = -11.0754243089252 | etot = -8.13378367281453 +601000 ekin = 1.68078686629012 | erot = 1.19842786468538 | epot = -11.012998403262 | etot = -8.13378367228648 +602000 ekin = 1.57592768465659 | erot = 1.20571835984221 | epot = -10.9154297156387 | etot = -8.13378367113989 +603000 ekin = 1.44736021988886 | erot = 1.21906556666659 | epot = -10.8002094561258 | etot = -8.13378366957031 +604000 ekin = 1.31829530124112 | erot = 1.23900632721008 | epot = -10.6910852964351 | etot = -8.13378366798387 +605000 ekin = 1.21203583246966 | erot = 1.26625018196441 | epot = -10.6120696811954 | etot = -8.13378366676136 +606000 ekin = 1.1471788194313 | erot = 1.30114918573804 | epot = -10.5821116711522 | etot = -8.13378366598283 +607000 ekin = 1.13493137969395 | erot = 1.34344256501628 | epot = -10.6121576106217 | etot = -8.13378366591145 +608000 ekin = 1.17769398074537 | erot = 1.39211398655978 | epot = -10.7035916336101 | etot = -8.13378366630492 +609000 ekin = 1.27083042497215 | erot = 1.44572829443106 | epot = -10.8503423864839 | etot = -8.13378366708069 +610000 ekin = 1.40359308953497 | erot = 1.50241692808096 | epot = -11.0397936861262 | etot = -8.13378366851022 +611000 ekin = 1.55996607947089 | erot = 1.55982171139299 | epot = -11.253571460632 | etot = -8.13378366976813 +612000 ekin = 1.72323074885791 | erot = 1.61567444067702 | epot = -11.4726888606289 | etot = -8.13378367109395 +613000 ekin = 1.87623356286535 | erot = 1.66732234623712 | epot = -11.677339581494 | etot = -8.13378367239149 +614000 ekin = 2.00332542687785 | erot = 1.71185786770152 | epot = -11.8489669678998 | etot = -8.13378367332043 +615000 ekin = 2.0938447106911 | erot = 1.74706892485081 | epot = -11.9746973091395 | etot = -8.1337836735976 +616000 ekin = 2.14582652012071 | erot = 1.77208418550063 | epot = -12.0516943786421 | etot = -8.13378367302075 +617000 ekin = 2.16764032551916 | erot = 1.787864761541 | epot = -12.0892887588615 | etot = -8.13378367180135 +618000 ekin = 2.17543321836323 | erot = 1.79702594193641 | epot = -12.1062428306531 | etot = -8.13378367035343 +619000 ekin = 2.18765015125133 | erot = 1.80309631575425 | epot = -12.1245301362281 | etot = -8.13378366922254 +620000 ekin = 2.21827388576285 | erot = 1.80941579610204 | epot = -12.1614733506252 | etot = -8.13378366876028 +621000 ekin = 2.27256724286815 | erot = 1.81817906105655 | epot = -12.2245299729573 | etot = -8.13378366903265 +622000 ekin = 2.34686215369527 | erot = 1.82980019933902 | epot = -12.3104460229224 | etot = -8.13378366988815 +623000 ekin = 2.43079483962716 | erot = 1.8427295467928 | epot = -12.4073080575176 | etot = -8.13378367109765 +624000 ekin = 2.5107485939996 | erot = 1.85365912855095 | epot = -12.4981913948937 | etot = -8.13378367234319 +625000 ekin = 2.57376014758943 | erot = 1.85839628629729 | epot = -12.5659401070791 | etot = -8.13378367319238 +626000 ekin = 2.61178608744741 | erot = 1.85335246050191 | epot = -12.5989222212815 | etot = -8.13378367333221 +627000 ekin = 2.62439666915785 | erot = 1.83675929860322 | epot = -12.5949396406017 | etot = -8.13378367284068 +628000 ekin = 2.61715143116438 | erot = 1.8088329781474 | epot = -12.5597680815328 | etot = -8.13378367222104 +629000 ekin = 2.59614002779832 | erot = 1.77076928021883 | epot = -12.5006929799542 | etot = -8.1337836719371 +630000 ekin = 2.56316564608462 | erot = 1.7236886227231 | epot = -12.4206379408516 | etot = -8.13378367204391 +631000 ekin = 2.51545670839933 | erot = 1.66841938704488 | epot = -12.3176597676938 | etot = -8.13378367224957 +632000 ekin = 2.44898106284144 | erot = 1.60594586085105 | epot = -12.1887105959446 | etot = -8.13378367225213 +633000 ekin = 2.36287257797916 | erot = 1.53782426737236 | epot = -12.0344805167089 | etot = -8.13378367135735 +634000 ekin = 2.26405242524496 | erot = 1.46623278029967 | epot = -11.864068876129 | etot = -8.13378367058439 +635000 ekin = 2.16101755721112 | erot = 1.39475566087583 | epot = -11.6895568877978 | etot = -8.13378366971087 +636000 ekin = 2.06475253332541 | erot = 1.3268650623379 | epot = -11.5254012642585 | etot = -8.13378366859516 +637000 ekin = 1.98973271037715 | erot = 1.26596624428881 | epot = -11.3894826221233 | etot = -8.13378366745732 +638000 ekin = 1.95146778323067 | erot = 1.21514985243714 | epot = -11.3004013023013 | etot = -8.13378366663354 +639000 ekin = 1.96182069136509 | erot = 1.17695161176092 | epot = -11.2725559693112 | etot = -8.13378366618516 +640000 ekin = 2.02679898932797 | erot = 1.15239183903173 | epot = -11.3129744949352 | etot = -8.13378366657551 +641000 ekin = 2.14199910312317 | erot = 1.14071086556715 | epot = -11.4164936363374 | etot = -8.1337836676471 +642000 ekin = 2.2928504631817 | erot = 1.13915186811625 | epot = -11.5657860007561 | etot = -8.13378366945816 +643000 ekin = 2.45552552112345 | erot = 1.1433882823325 | epot = -11.7326974750707 | etot = -8.13378367161478 +644000 ekin = 2.60133752583198 | erot = 1.148353674905 | epot = -11.8834748743264 | etot = -8.13378367358945 +645000 ekin = 2.70371430392256 | erot = 1.14938437136365 | epot = -11.9868823501647 | etot = -8.13378367487845 +646000 ekin = 2.74463607558011 | erot = 1.14332224209556 | epot = -12.0217419928901 | etot = -8.13378367521444 +647000 ekin = 2.71817787235873 | erot = 1.12915792946586 | epot = -11.9811194764579 | etot = -8.13378367463333 +648000 ekin = 2.63028246064842 | erot = 1.10798613625545 | epot = -11.8720522702983 | etot = -8.13378367339448 +649000 ekin = 2.49559189346538 | erot = 1.08245328244055 | epot = -11.7118288477703 | etot = -8.13378367186436 +650000 ekin = 2.33293161554122 | erot = 1.05592857134661 | epot = -11.5226438572585 | etot = -8.13378367037071 +651000 ekin = 2.16312160403312 | erot = 1.03179243267749 | epot = -11.3286977053606 | etot = -8.13378366864995 +652000 ekin = 2.0043776447218 | erot = 1.0126334647444 | epot = -11.1507947775976 | etot = -8.13378366813138 +653000 ekin = 1.86320148187806 | erot = 0.999771298657919 | epot = -10.9967564484937 | etot = -8.13378366795773 +654000 ekin = 1.74159938814614 | erot = 0.993638993388595 | epot = -10.8690220495541 | etot = -8.13378366801934 +655000 ekin = 1.63877614368846 | erot = 0.993961110596709 | epot = -10.7665209224708 | etot = -8.13378366818566 +656000 ekin = 1.5529369639273 | erot = 0.999977751459511 | epot = -10.6866983837148 | etot = -8.13378366832803 +657000 ekin = 1.48301105563479 | erot = 1.01069155837003 | epot = -10.6274862823526 | etot = -8.13378366834774 +658000 ekin = 1.42991653831162 | erot = 1.02511295990344 | epot = -10.5888131664135 | etot = -8.13378366819842 +659000 ekin = 1.39703562131292 | erot = 1.04246417551983 | epot = -10.5732834647419 | etot = -8.13378366790917 +660000 ekin = 1.38964145709155 | erot = 1.06228082946531 | epot = -10.5857059541244 | etot = -8.13378366756751 +661000 ekin = 1.41337783437763 | erot = 1.08434723256434 | epot = -10.6315087343399 | etot = -8.13378366739793 +662000 ekin = 1.47169034615873 | erot = 1.10850483082051 | epot = -10.7139788445335 | etot = -8.13378366755423 +663000 ekin = 1.56097330111581 | erot = 1.13389735843154 | epot = -10.8286543283384 | etot = -8.13378366879109 +664000 ekin = 1.66624490138027 | erot = 1.15850228666392 | epot = -10.9585308577707 | etot = -8.13378366972648 +665000 ekin = 1.77303863682281 | erot = 1.18152952432333 | epot = -11.0883518319623 | etot = -8.13378367081621 +666000 ekin = 1.86640057269355 | erot = 1.20258304574543 | epot = -11.2027672900303 | etot = -8.13378367159136 +667000 ekin = 1.93466412848915 | erot = 1.22193419207378 | epot = -11.2903819923689 | etot = -8.133783671806 +668000 ekin = 1.97306030168019 | erot = 1.24062017116799 | epot = -11.3474641442769 | etot = -8.13378367142873 +669000 ekin = 1.98443783024889 | erot = 1.26004202124057 | epot = -11.3782635221749 | etot = -8.13378367068545 +670000 ekin = 1.97652861972491 | erot = 1.28134194904821 | epot = -11.3916542389563 | etot = -8.13378367018321 +671000 ekin = 1.95649579520902 | erot = 1.30490078083381 | epot = -11.3951802458179 | etot = -8.13378366977503 +672000 ekin = 1.92875532538935 | erot = 1.33065660863181 | epot = -11.3931956035842 | etot = -8.13378366956306 +673000 ekin = 1.89553670248936 | erot = 1.35854540535641 | epot = -11.3878657773159 | etot = -8.13378366947008 +674000 ekin = 1.85764904384443 | erot = 1.38884570045689 | epot = -11.3802784136491 | etot = -8.13378366934781 +675000 ekin = 1.81704545028434 | erot = 1.42228413605295 | epot = -11.373113255601 | etot = -8.13378366926374 +676000 ekin = 1.77505031311568 | erot = 1.45971003523498 | epot = -11.3685440174495 | etot = -8.13378366909886 +677000 ekin = 1.73347451744457 | erot = 1.5019121683338 | epot = -11.3691703547332 | etot = -8.13378366895484 +678000 ekin = 1.69449339360991 | erot = 1.54922606358763 | epot = -11.3775031261173 | etot = -8.13378366891979 +679000 ekin = 1.65969071094775 | erot = 1.60118456838417 | epot = -11.3946589483669 | etot = -8.13378366903495 +680000 ekin = 1.62957005382427 | erot = 1.65634116858805 | epot = -11.4196948917019 | etot = -8.13378366928958 +681000 ekin = 1.60362252577069 | erot = 1.71228358653195 | epot = -11.449689781933 | etot = -8.13378366963035 +682000 ekin = 1.5808307425256 | erot = 1.76582826440389 | epot = -11.4804426769133 | etot = -8.13378366998382 +683000 ekin = 1.56032431135137 | erot = 1.81338479150389 | epot = -11.5074927731382 | etot = -8.13378367028288 +684000 ekin = 1.54183455724318 | erot = 1.85142632174729 | epot = -11.5270445498204 | etot = -8.13378367082992 +685000 ekin = 1.52410759948932 | erot = 1.87642082989206 | epot = -11.5343121005182 | etot = -8.13378367113683 +686000 ekin = 1.50494379429771 | erot = 1.88570070120714 | epot = -11.5244281669092 | etot = -8.13378367140436 +687000 ekin = 1.48208036602607 | erot = 1.87831367885578 | epot = -11.4941777164915 | etot = -8.13378367160967 +688000 ekin = 1.45289287171974 | erot = 1.85497856867545 | epot = -11.4416551120418 | etot = -8.13378367164664 +689000 ekin = 1.41601907826324 | erot = 1.81811437350132 | epot = -11.367917123107 | etot = -8.13378367134249 +690000 ekin = 1.37394775597773 | erot = 1.77166312493213 | epot = -11.2793945514708 | etot = -8.13378367056093 +691000 ekin = 1.33508615018567 | erot = 1.7207149635712 | epot = -11.1895847830922 | etot = -8.13378366933531 +692000 ekin = 1.31344376449331 | erot = 1.67094159750906 | epot = -11.1181690299532 | etot = -8.13378366795085 +693000 ekin = 1.32488046335684 | erot = 1.62783697439007 | epot = -11.0865011046353 | etot = -8.13378366688844 +694000 ekin = 1.38078608495378 | erot = 1.59583179974278 | epot = -11.1104015513257 | etot = -8.13378366662911 +695000 ekin = 1.48192861171659 | erot = 1.57745304983523 | epot = -11.1931653289632 | etot = -8.13378366741139 +696000 ekin = 1.61569966758079 | erot = 1.5727804142449 | epot = -11.32226375092 | etot = -8.13378366909433 +697000 ekin = 1.75843097201211 | erot = 1.57943520717465 | epot = -11.471649850405 | etot = -8.13378367121827 +698000 ekin = 1.88185215219679 | erot = 1.59316882059862 | epot = -11.6088046459831 | etot = -8.13378367318764 +699000 ekin = 1.96106579202292 | erot = 1.60896306337659 | epot = -11.7038125298663 | etot = -8.13378367446684 +700000 ekin = 1.98131680912422 | erot = 1.62236339277023 | epot = -11.7374638766252 | etot = -8.1337836747308 +701000 ekin = 1.94164145669045 | erot = 1.63062825687531 | epot = -11.7060533875203 | etot = -8.1337836739545 +702000 ekin = 1.85450233235201 | erot = 1.63328569356415 | epot = -11.6215716983376 | etot = -8.13378367242146 +703000 ekin = 1.74181404908478 | erot = 1.63189519934157 | epot = -11.5074929188714 | etot = -8.13378367044504 +704000 ekin = 1.62890053406143 | erot = 1.62932624845842 | epot = -11.3920104514131 | etot = -8.13378366889327 +705000 ekin = 1.53704055740013 | erot = 1.62828297752769 | epot = -11.2991072026892 | etot = -8.13378366776141 +706000 ekin = 1.48137553867545 | erot = 1.63090498236421 | epot = -11.2460641881752 | etot = -8.13378366713553 +707000 ekin = 1.47012654302872 | erot = 1.63856880546718 | epot = -11.2424790154444 | etot = -8.13378366694853 +708000 ekin = 1.50545482974759 | erot = 1.65189802616416 | epot = -11.2911365229833 | etot = -8.13378366707157 +709000 ekin = 1.58434919628013 | erot = 1.67079586466944 | epot = -11.3889287286708 | etot = -8.13378366772122 +710000 ekin = 1.69830399772316 | erot = 1.69420639282641 | epot = -11.5262940590572 | etot = -8.13378366850765 +711000 ekin = 1.83638650827484 | erot = 1.72024670599356 | epot = -11.6904168837856 | etot = -8.13378366951719 +712000 ekin = 1.98510691898267 | erot = 1.74609277614869 | epot = -11.8649833659474 | etot = -8.13378367081602 +713000 ekin = 2.12899307619927 | erot = 1.76804611051695 | epot = -12.0308228587679 | etot = -8.13378367205166 +714000 ekin = 2.2537500788108 | erot = 1.78243264236392 | epot = -12.1699663939999 | etot = -8.1337836728252 +715000 ekin = 2.34975342443562 | erot = 1.78632122216762 | epot = -12.2698583199061 | etot = -8.13378367330291 +716000 ekin = 2.41256025264403 | erot = 1.77808812757533 | epot = -12.3244320533944 | etot = -8.13378367317507 +717000 ekin = 2.44474770549548 | erot = 1.75804788177059 | epot = -12.3365792598097 | etot = -8.13378367254361 +718000 ekin = 2.45412216711155 | erot = 1.72831089170459 | epot = -12.3162167308502 | etot = -8.13378367203411 +719000 ekin = 2.44845378812103 | erot = 1.69204638295129 | epot = -12.2742838422468 | etot = -8.13378367117444 +720000 ekin = 2.43656682429823 | erot = 1.65329012912613 | epot = -12.2236406239975 | etot = -8.13378367057317 +721000 ekin = 2.42365620510361 | erot = 1.61605001930567 | epot = -12.1734898947895 | etot = -8.1337836703802 +722000 ekin = 2.40904119934951 | erot = 1.58378410660753 | epot = -12.1266089765548 | etot = -8.13378367059771 +723000 ekin = 2.38647146985516 | erot = 1.55915433554635 | epot = -12.0794094764715 | etot = -8.13378367107003 +724000 ekin = 2.34659230992567 | erot = 1.54397640930162 | epot = -12.0243523907673 | etot = -8.13378367154003 +725000 ekin = 2.28077035570444 | erot = 1.53931973021413 | epot = -11.9538737576625 | etot = -8.13378367174393 +726000 ekin = 2.18489434263528 | erot = 1.54571264605969 | epot = -11.8643906602024 | etot = -8.13378367150746 +727000 ekin = 2.06179491768289 | erot = 1.5633964649543 | epot = -11.758975053444 | etot = -8.13378367080681 +728000 ekin = 1.92142302762616 | erot = 1.59252552389791 | epot = -11.6477322213134 | etot = -8.13378366978937 +729000 ekin = 1.77863161459621 | erot = 1.63318133799978 | epot = -11.5455966213317 | etot = -8.13378366873569 +730000 ekin = 1.64935549787773 | erot = 1.68520345518918 | epot = -11.4683426210493 | etot = -8.13378366798235 +731000 ekin = 1.54617340800501 | erot = 1.74777370763937 | epot = -11.4277307834144 | etot = -8.13378366776999 +732000 ekin = 1.47444012326081 | erot = 1.81876025838909 | epot = -11.4269840497984 | etot = -8.13378366814851 +733000 ekin = 1.43189319814282 | erot = 1.89484027034282 | epot = -11.4605171374877 | etot = -8.13378366900206 +734000 ekin = 1.41017780821054 | erot = 1.97174677425768 | epot = -11.5157082525344 | etot = -8.13378367006618 +735000 ekin = 1.39820849324506 | erot = 2.04483940823445 | epot = -11.5768315724903 | etot = -8.13378367101077 +736000 ekin = 1.38628872342334 | erot = 2.1098536340242 | epot = -11.6299260289958 | etot = -8.13378367154824 +737000 ekin = 1.36961596691125 | erot = 2.16355925927667 | epot = -11.6669588977375 | etot = -8.1337836715496 +738000 ekin = 1.34981044642444 | erot = 2.20404797657021 | epot = -11.6876420941064 | etot = -8.13378367111176 +739000 ekin = 1.3337265319971 | erot = 2.2305539577571 | epot = -11.6980641602564 | etot = -8.13378367050223 +740000 ekin = 1.33016419297185 | erot = 2.24303198932884 | epot = -11.7069798522888 | etot = -8.13378366998815 +741000 ekin = 1.34641052649907 | erot = 2.24189336877249 | epot = -11.7220875649481 | etot = -8.13378366967656 +742000 ekin = 1.38645577649848 | erot = 2.22809836951312 | epot = -11.7483378155403 | etot = -8.13378366952872 +743000 ekin = 1.45103879196092 | erot = 2.20332817129465 | epot = -11.7881506327621 | etot = -8.13378366950656 +744000 ekin = 1.53803120218869 | erot = 2.16985299830622 | epot = -11.8416678701973 | etot = -8.13378366970238 +745000 ekin = 1.64150939164176 | erot = 2.1298859597558 | epot = -11.9051790216537 | etot = -8.13378367025619 +746000 ekin = 1.75074962764572 | erot = 2.08470317829609 | epot = -11.9692364772076 | etot = -8.13378367126575 +747000 ekin = 1.84985303110975 | erot = 2.03398729131598 | epot = -12.0176239950655 | etot = -8.13378367263978 +748000 ekin = 1.91944439123733 | erot = 1.97579729236556 | epot = -12.0290253576753 | etot = -8.13378367407245 +749000 ekin = 1.94080211586985 | erot = 1.90728805389599 | epot = -11.9818738448629 | etot = -8.13378367509709 +750000 ekin = 1.90175708675931 | erot = 1.82602227398106 | epot = -11.8615630358818 | etot = -8.13378367514145 +751000 ekin = 1.80442251329553 | erot = 1.7321012366385 | epot = -11.6703074242626 | etot = -8.1337836743286 +752000 ekin = 1.66438096328611 | erot = 1.62791173822921 | epot = -11.4260763737947 | etot = -8.13378367227942 +753000 ekin = 1.50959112394715 | erot = 1.51791168435181 | epot = -11.1612864778799 | etot = -8.13378366958094 +754000 ekin = 1.37530205556033 | erot = 1.40846180206954 | epot = -10.9175475248713 | etot = -8.13378366724144 +755000 ekin = 1.29223158174908 | erot = 1.30628357856191 | epot = -10.732298826192 | etot = -8.13378366588102 +756000 ekin = 1.27251368864414 | erot = 1.21592403401206 | epot = -10.622221389115 | etot = -8.13378366645877 +757000 ekin = 1.30634776760889 | erot = 1.13861892039714 | epot = -10.5787503559372 | etot = -8.13378366793113 +758000 ekin = 1.37185376254184 | erot = 1.0735107376922 | epot = -10.5791481697226 | etot = -8.13378366948851 +759000 ekin = 1.44617278831012 | erot = 1.01897341841063 | epot = -10.598929877198 | etot = -8.13378367047723 +760000 ekin = 1.51270256479301 | erot = 0.973207034201039 | epot = -10.6196932701125 | etot = -8.13378367111847 +761000 ekin = 1.56039612702868 | erot = 0.934439072309874 | epot = -10.6286188703703 | etot = -8.13378367103177 +762000 ekin = 1.58948756764912 | erot = 0.901622731963184 | epot = -10.6248939700703 | etot = -8.13378367045796 +763000 ekin = 1.60810008603274 | erot = 0.874391507872529 | epot = -10.6162752635795 | etot = -8.13378366967423 +764000 ekin = 1.62768531424286 | erot = 0.852689319785657 | epot = -10.6141583029918 | etot = -8.13378366896324 +765000 ekin = 1.65693698085653 | erot = 0.836745239153095 | epot = -10.6274658895874 | etot = -8.13378366957773 +766000 ekin = 1.70304081025946 | erot = 0.827639758104824 | epot = -10.6644642391125 | etot = -8.13378367074825 +767000 ekin = 1.76603010804921 | erot = 0.819745786931532 | epot = -10.719559566308 | etot = -8.13378367132722 +768000 ekin = 1.83976621727627 | erot = 0.8139156067584 | epot = -10.7874654957375 | etot = -8.13378367170284 +769000 ekin = 1.91953928655908 | erot = 0.809315266595166 | epot = -10.8626382251527 | etot = -8.13378367199848 +770000 ekin = 2.00068337351959 | erot = 0.805269377194069 | epot = -10.9397364229423 | etot = -8.13378367222864 +771000 ekin = 2.07932607088732 | erot = 0.801470015537725 | epot = -11.0145797587942 | etot = -8.13378367236911 +772000 ekin = 2.15218258759755 | erot = 0.797728511840744 | epot = -11.0836947720117 | etot = -8.13378367257343 +773000 ekin = 2.21516346372988 | erot = 0.79376993216211 | epot = -11.1427170688153 | etot = -8.13378367292333 +774000 ekin = 2.26234547301551 | erot = 0.789120208322318 | epot = -11.1852493547456 | etot = -8.13378367340773 +775000 ekin = 2.28747440002057 | erot = 0.782940858117551 | epot = -11.2041989316468 | etot = -8.13378367350871 +776000 ekin = 2.28487294058628 | erot = 0.774236455828425 | epot = -11.1928930694851 | etot = -8.13378367307042 +777000 ekin = 2.25459623260422 | erot = 0.763986238595056 | epot = -11.1523661447081 | etot = -8.13378367350883 +778000 ekin = 2.19483848050509 | erot = 0.752926118473461 | epot = -11.0815482726341 | etot = -8.13378367365559 +779000 ekin = 2.10207554487389 | erot = 0.741428699334343 | epot = -10.9772879179051 | etot = -8.13378367369685 +780000 ekin = 1.975078446677 | erot = 0.730439747656369 | epot = -10.8393018678337 | etot = -8.1337836735003 +781000 ekin = 1.81624237982134 | erot = 0.720681720720675 | epot = -10.6707077731082 | etot = -8.13378367256618 +782000 ekin = 1.63737679983539 | erot = 0.713965531354133 | epot = -10.4851260026601 | etot = -8.13378367147054 +783000 ekin = 1.45327094383719 | erot = 0.712334775523592 | epot = -10.2993893897056 | etot = -8.1337836703448 +784000 ekin = 1.27931304174358 | erot = 0.717795316536906 | epot = -10.1308920276043 | etot = -8.1337836693238 +785000 ekin = 1.12953341815274 | erot = 0.732133377029229 | epot = -9.99545046371264 | etot = -8.13378366853067 +786000 ekin = 1.0148243180478 | erot = 0.75676028118304 | epot = -9.90536826728528 | etot = -8.13378366805444 +787000 ekin = 0.941643963842495 | erot = 0.792599099770748 | epot = -9.86802673154543 | etot = -8.13378366793219 +788000 ekin = 0.91151079635427 | erot = 0.840020856528208 | epot = -9.88531532101941 | etot = -8.13378366813693 +789000 ekin = 0.921376349365235 | erot = 0.89882735727821 | epot = -9.9539873752422 | etot = -8.13378366859875 +790000 ekin = 0.964654482915146 | erot = 0.968273092067122 | epot = -10.0667112442069 | etot = -8.13378366922462 +791000 ekin = 1.03261133425371 | erot = 1.04710148107764 | epot = -10.2134964852549 | etot = -8.13378366992355 +792000 ekin = 1.11580285055926 | erot = 1.13356945355193 | epot = -10.3831559747166 | etot = -8.13378367060541 +793000 ekin = 1.205280651357 | erot = 1.22546277764222 | epot = -10.5645271002539 | etot = -8.13378367125471 +794000 ekin = 1.29310700797017 | erot = 1.32020213138164 | epot = -10.7470928111806 | etot = -8.13378367182877 +795000 ekin = 1.37238467364513 | erot = 1.41513363977019 | epot = -10.9213019889598 | etot = -8.13378367554452 +796000 ekin = 1.40835913067749 | erot = 1.52971390357828 | epot = -11.0718567049054 | etot = -8.1337836706496 +797000 ekin = 1.45167190325167 | erot = 1.62512604236805 | epot = -11.2105816179713 | etot = -8.13378367235159 +798000 ekin = 1.48145722831546 | erot = 1.70064689495284 | epot = -11.315887795747 | etot = -8.13378367247869 +799000 ekin = 1.4955963332668 | erot = 1.76394329939599 | epot = -11.3933233050852 | etot = -8.13378367242244 +800000 ekin = 1.49744893756611 | erot = 1.8132729125825 | epot = -11.4445055223199 | etot = -8.13378367217132 +801000 ekin = 1.49251279282915 | erot = 1.84780559275317 | epot = -11.474102057285 | etot = -8.13378367170271 +802000 ekin = 1.48820480029493 | erot = 1.86779013866868 | epot = -11.4897786100776 | etot = -8.13378367111404 +803000 ekin = 1.49253566042966 | erot = 1.87451451170557 | epot = -11.5008338427234 | etot = -8.13378367058816 +804000 ekin = 1.5116603543289 | erot = 1.86997050315934 | epot = -11.5154145278236 | etot = -8.13378367033537 +805000 ekin = 1.54725262777174 | erot = 1.85635941635703 | epot = -11.5373957146226 | etot = -8.13378367049383 +806000 ekin = 1.59533620641404 | erot = 1.83572111156676 | epot = -11.5648409886255 | etot = -8.13378367064471 +807000 ekin = 1.64925672171952 | erot = 1.81037056531091 | epot = -11.5934109584119 | etot = -8.13378367138148 +808000 ekin = 1.69787116917717 | erot = 1.7813245959011 | epot = -11.6129794371751 | etot = -8.13378367209687 +809000 ekin = 1.73004744235811 | erot = 1.74897468679296 | epot = -11.6128058017335 | etot = -8.13378367258244 +810000 ekin = 1.73831051804067 | erot = 1.71353607859664 | epot = -11.585630270404 | etot = -8.13378367376665 +811000 ekin = 1.71623548899456 | erot = 1.6742846234257 | epot = -11.5243037859369 | etot = -8.13378367351661 +812000 ekin = 1.66416936453534 | erot = 1.63115164435859 | epot = -11.4291046817453 | etot = -8.13378367285134 +813000 ekin = 1.59176171308439 | erot = 1.58513406244348 | epot = -11.3106794473701 | etot = -8.13378367184222 +814000 ekin = 1.51369575693312 | erot = 1.53752063412374 | epot = -11.1850000616877 | etot = -8.13378367063089 +815000 ekin = 1.44735421380678 | erot = 1.48989097525809 | epot = -11.0710288584962 | etot = -8.13378366943134 +816000 ekin = 1.40949972397271 | erot = 1.44406671643183 | epot = -10.9873501088938 | etot = -8.13378366848926 +817000 ekin = 1.41268037619626 | erot = 1.40200084695678 | epot = -10.9484648911707 | etot = -8.13378366801771 +818000 ekin = 1.46212175577427 | erot = 1.36558649858982 | epot = -10.9614919224948 | etot = -8.13378366813073 +819000 ekin = 1.55434977582292 | erot = 1.33645466075966 | epot = -11.0245881053078 | etot = -8.13378366872519 +820000 ekin = 1.67879137032642 | erot = 1.31590146923918 | epot = -11.1284765091463 | etot = -8.1337836695807 +821000 ekin = 1.82107935880473 | erot = 1.30489182434882 | epot = -11.2597548535965 | etot = -8.13378367044299 +822000 ekin = 1.95294466690438 | erot = 1.31620699243495 | epot = -11.4029353289041 | etot = -8.13378366956477 +823000 ekin = 2.0744918329815 | erot = 1.34466437804004 | epot = -11.5529398817614 | etot = -8.13378367073983 +824000 ekin = 2.19907919101152 | erot = 1.36469015649287 | epot = -11.6975530184867 | etot = -8.13378367098235 +825000 ekin = 2.30563380731732 | erot = 1.39476757379007 | epot = -11.8341850523135 | etot = -8.13378367120606 +826000 ekin = 2.39103700934121 | erot = 1.43354131860341 | epot = -11.9583619997622 | etot = -8.13378367181753 +827000 ekin = 2.44908730431562 | erot = 1.47824975110643 | epot = -12.0611207278282 | etot = -8.13378367240619 +828000 ekin = 2.47400495189244 | erot = 1.5253685887777 | epot = -12.1331572137356 | etot = -8.13378367306547 +829000 ekin = 2.46026919524429 | erot = 1.57083290056531 | epot = -12.1648857694093 | etot = -8.13378367359971 +830000 ekin = 2.40417117545801 | erot = 1.61070673373864 | epot = -12.1486615829869 | etot = -8.13378367379024 +831000 ekin = 2.30626797380524 | erot = 1.6420689276996 | epot = -12.0821205749497 | etot = -8.13378367344486 +832000 ekin = 2.17314973457071 | erot = 1.6637889533296 | epot = -11.9707223604975 | etot = -8.13378367259718 +833000 ekin = 2.01667882998926 | erot = 1.67684011591486 | epot = -11.827302617307 | etot = -8.1337836714029 +834000 ekin = 1.85232718441155 | erot = 1.68370832895273 | epot = -11.669819183454 | etot = -8.13378367008967 +835000 ekin = 1.69616282491266 | erot = 1.68768571766349 | epot = -11.5176322116632 | etot = -8.13378366908707 +836000 ekin = 1.56059049290232 | erot = 1.69176136009187 | epot = -11.3861355304323 | etot = -8.13378367743811 +837000 ekin = 1.4649469150044 | erot = 1.67922598577313 | epot = -11.2779565658821 | etot = -8.13378366510453 +838000 ekin = 1.41623376457433 | erot = 1.68359587928439 | epot = -11.2336133181127 | etot = -8.13378367425399 +839000 ekin = 1.38164226012672 | erot = 1.69827238734037 | epot = -11.2136983220805 | etot = -8.13378367461343 +840000 ekin = 1.37281419715513 | erot = 1.71791872248084 | epot = -11.2245165947373 | etot = -8.13378367510138 +841000 ekin = 1.38251849193881 | erot = 1.74222357841543 | epot = -11.2585257459448 | etot = -8.13378367559059 +842000 ekin = 1.40440815942035 | erot = 1.77053653191625 | epot = -11.308728367384 | etot = -8.13378367604745 +843000 ekin = 1.43288889925859 | erot = 1.80208713634726 | epot = -11.3687597120877 | etot = -8.13378367648181 +844000 ekin = 1.46337505814903 | erot = 1.83581425236187 | epot = -11.4329729874354 | etot = -8.13378367692452 +845000 ekin = 1.49225138963089 | erot = 1.87011931155121 | epot = -11.4961543785795 | etot = -8.13378367739744 +846000 ekin = 1.51675477462874 | erot = 1.90271354930936 | epot = -11.5532520018099 | etot = -8.13378367787183 +847000 ekin = 1.53514567571852 | erot = 1.93076451181253 | epot = -11.5996938657532 | etot = -8.13378367822212 +848000 ekin = 1.54758817139767 | erot = 1.95149729782707 | epot = -11.6328691474788 | etot = -8.1337836782541 +849000 ekin = 1.55740275309144 | erot = 1.96313933265 | epot = -11.6543257635983 | etot = -8.13378367785683 +850000 ekin = 1.57132389421101 | erot = 1.96572299084975 | epot = -11.6708305622435 | etot = -8.13378367718269 +851000 ekin = 1.59707563452676 | erot = 1.96110149893909 | epot = -11.6919608101049 | etot = -8.13378367663905 +852000 ekin = 1.6386535081545 | erot = 1.95197424613878 | epot = -11.7244114309664 | etot = -8.13378367667315 +853000 ekin = 1.69191652813023 | erot = 1.94037118809899 | epot = -11.7660713936989 | etot = -8.1337836774697 +854000 ekin = 1.74370784145889 | erot = 1.92645693893931 | epot = -11.8039484591072 | etot = -8.13378367870896 +855000 ekin = 1.77620146948086 | erot = 1.90847432090069 | epot = -11.8184594703326 | etot = -8.13378367995108 +856000 ekin = 1.77433273184065 | erot = 1.88315818057335 | epot = -11.7912745929164 | etot = -8.13378368050239 +857000 ekin = 1.73346273147091 | erot = 1.84735528776312 | epot = -11.7146016992328 | etot = -8.13378367999875 +858000 ekin = 1.66317903315863 | erot = 1.79946643728795 | epot = -11.5964291489817 | etot = -8.13378367853512 +859000 ekin = 1.58513293473523 | erot = 1.74007953905842 | epot = -11.4589961504119 | etot = -8.13378367661827 +860000 ekin = 1.52581941740006 | erot = 1.67168470802684 | epot = -11.3312878003291 | etot = -8.13378367490221 +861000 ekin = 1.50775028679288 | erot = 1.59782760969369 | epot = -11.2393615703528 | etot = -8.1337836738662 +862000 ekin = 1.54306866321957 | erot = 1.52225954467352 | epot = -11.1991118815402 | etot = -8.13378367364711 +863000 ekin = 1.63171594625002 | erot = 1.44845127786619 | epot = -11.2139508982038 | etot = -8.13378367408762 +864000 ekin = 1.76367870712172 | erot = 1.37946094115355 | epot = -11.2769233231883 | etot = -8.13378367491307 +865000 ekin = 1.92306452976728 | erot = 1.31796433815998 | epot = -11.374812543797 | etot = -8.13378367586979 +866000 ekin = 2.09215456373456 | erot = 1.26628926087244 | epot = -11.492227501168 | etot = -8.13378367656101 +867000 ekin = 2.2555870663093 | erot = 1.22649711226227 | epot = -11.6158678558662 | etot = -8.13378367729465 +868000 ekin = 2.40057443573636 | erot = 1.20017706622215 | epot = -11.7345351797559 | etot = -8.13378367779738 +869000 ekin = 2.51819395203098 | erot = 1.18842552010846 | epot = -11.8404031502132 | etot = -8.13378367807373 +870000 ekin = 2.60380767615723 | erot = 1.19178595747267 | epot = -11.9293773118501 | etot = -8.13378367822019 +871000 ekin = 2.65597330530642 | erot = 1.21008900212213 | epot = -11.9998459857543 | etot = -8.13378367832573 +872000 ekin = 2.67413391791353 | erot = 1.24223617503019 | epot = -12.0501537716762 | etot = -8.13378367873251 +873000 ekin = 2.6552381335266 | erot = 1.28590823805749 | epot = -12.0749300509471 | etot = -8.13378367936302 +874000 ekin = 2.59426343772232 | erot = 1.33769628235099 | epot = -12.0657434000994 | etot = -8.13378368002606 +875000 ekin = 2.48661885046081 | erot = 1.39359938817273 | epot = -12.014001918994 | etot = -8.13378368036042 +876000 ekin = 2.33257163459597 | erot = 1.4498598457216 | epot = -11.9162151603149 | etot = -8.13378367999738 +877000 ekin = 2.141517317418 | erot = 1.50380376864633 | epot = -11.7791047648915 | etot = -8.13378367882715 +878000 ekin = 1.93283200512491 | erot = 1.55419737778086 | epot = -11.6208130600935 | etot = -8.13378367718774 +879000 ekin = 1.73117573768839 | erot = 1.60084517567798 | epot = -11.4658045891139 | etot = -8.13378367574752 +880000 ekin = 1.5578715146681 | erot = 1.64373016660559 | epot = -11.3353853563275 | etot = -8.1337836750538 +881000 ekin = 1.42384142296435 | erot = 1.68244604719099 | epot = -11.240071145286 | etot = -8.1337836751306 +882000 ekin = 1.32893688638413 | erot = 1.71640874333306 | epot = -11.1791293052726 | etot = -8.13378367555537 +883000 ekin = 1.26714280251856 | erot = 1.74554143078467 | epot = -11.1464679090328 | etot = -8.13378367572956 +884000 ekin = 1.23268823981684 | erot = 1.77071758435451 | epot = -11.1371895001203 | etot = -8.13378367594895 +885000 ekin = 1.22008849613112 | erot = 1.79312166866591 | epot = -11.1469938409055 | etot = -8.13378367610844 +886000 ekin = 1.22532479936357 | erot = 1.81382116072379 | epot = -11.1729296363289 | etot = -8.13378367624153 +887000 ekin = 1.2449454811134 | erot = 1.83336039664062 | epot = -11.2120895542198 | etot = -8.1337836764658 +888000 ekin = 1.27500212867653 | erot = 1.8516886713632 | epot = -11.2604744767923 | etot = -8.13378367675256 +889000 ekin = 1.31152735186358 | erot = 1.86844690163024 | epot = -11.3137579305996 | etot = -8.13378367710575 +890000 ekin = 1.3498631749174 | erot = 1.88304641091815 | epot = -11.3666932633624 | etot = -8.13378367752689 +891000 ekin = 1.38390530385042 | erot = 1.89468392947328 | epot = -11.412372911412 | etot = -8.13378367808832 +892000 ekin = 1.40569395920114 | erot = 1.9022674868734 | epot = -11.4417451250871 | etot = -8.13378367901258 +893000 ekin = 1.40448288885454 | erot = 1.90432470815783 | epot = -11.4425912767175 | etot = -8.13378367970511 +894000 ekin = 1.37144289301693 | erot = 1.89954369089987 | epot = -11.4047702639074 | etot = -8.1337836799906 +895000 ekin = 1.30348485835023 | erot = 1.88750423026719 | epot = -11.3247727647944 | etot = -8.133783676177 +896000 ekin = 1.22187336940036 | erot = 1.8707106171673 | epot = -11.2263676620824 | etot = -8.13378367551471 +897000 ekin = 1.1475484574015 | erot = 1.8526380388531 | epot = -11.1339701707606 | etot = -8.13378367450598 +898000 ekin = 1.08944016615085 | erot = 1.83653761372357 | epot = -11.0597614537982 | etot = -8.13378367392382 +899000 ekin = 1.05403951137015 | erot = 1.82413022669427 | epot = -11.0119534116562 | etot = -8.13378367359175 +900000 ekin = 1.04500203331437 | erot = 1.81619426355301 | epot = -10.9949799704688 | etot = -8.13378367360146 +901000 ekin = 1.06222206923137 | erot = 1.81234403117871 | epot = -11.0083497743367 | etot = -8.13378367392657 +902000 ekin = 1.10209713925585 | erot = 1.81111462924797 | epot = -11.0469954429571 | etot = -8.13378367445329 +903000 ekin = 1.15876030901198 | erot = 1.81037876583237 | epot = -11.1029227498745 | etot = -8.13378367503018 +904000 ekin = 1.22532881859542 | erot = 1.80797942323846 | epot = -11.1670919178021 | etot = -8.13378367596819 +905000 ekin = 1.29206809095771 | erot = 1.80250391202481 | epot = -11.228355679448 | etot = -8.13378367646547 +906000 ekin = 1.35183435818773 | erot = 1.79300035920579 | epot = -11.2786183941511 | etot = -8.13378367675755 +907000 ekin = 1.39979991832311 | erot = 1.77946415970531 | epot = -11.3130477549902 | etot = -8.13378367696177 +908000 ekin = 1.43268044809292 | erot = 1.76253539552682 | epot = -11.3289995206312 | etot = -8.13378367701141 +909000 ekin = 1.44897967392585 | erot = 1.74341748030413 | epot = -11.3261808311167 | etot = -8.13378367688676 +910000 ekin = 1.44937912518518 | erot = 1.72390580405004 | epot = -11.3070686057931 | etot = -8.13378367655785 +911000 ekin = 1.43727654048153 | erot = 1.70617572376328 | epot = -11.2772359402954 | etot = -8.13378367605061 +912000 ekin = 1.41843448710304 | erot = 1.69263823219248 | epot = -11.2448563947427 | etot = -8.13378367544719 +913000 ekin = 1.40006194636186 | erot = 1.68549440968357 | epot = -11.2193400309129 | etot = -8.1337836748675 +914000 ekin = 1.38958826680245 | erot = 1.68634774644459 | epot = -11.2097196877205 | etot = -8.1337836744735 +915000 ekin = 1.39244842079852 | erot = 1.69595180430484 | epot = -11.2221838995188 | etot = -8.1337836744154 +916000 ekin = 1.41015014913687 | erot = 1.71401831966597 | epot = -11.257952143573 | etot = -8.13378367477015 +917000 ekin = 1.43929629826323 | erot = 1.73916764021605 | epot = -11.3122476139723 | etot = -8.13378367549302 +918000 ekin = 1.4722794295836 | erot = 1.76903078869455 | epot = -11.3750938946781 | etot = -8.1337836764 +919000 ekin = 1.49986621867062 | erot = 1.80052098874725 | epot = -11.4341708846036 | etot = -8.13378367718575 +920000 ekin = 1.51501277168815 | erot = 1.83027923270359 | epot = -11.4790756819828 | etot = -8.13378367759109 +921000 ekin = 1.50567012560593 | erot = 1.85806253143217 | epot = -11.4975163338839 | etot = -8.13378367684584 +922000 ekin = 1.50530570212432 | erot = 1.88405749209565 | epot = -11.5231468708402 | etot = -8.13378367662025 +923000 ekin = 1.51005072163659 | erot = 1.89398296785835 | epot = -11.5378173653492 | etot = -8.13378367585429 +924000 ekin = 1.52928061110808 | erot = 1.89561779723843 | epot = -11.558682083782 | etot = -8.13378367543545 +925000 ekin = 1.56873673242218 | erot = 1.88910082671996 | epot = -11.5916212348592 | etot = -8.13378367571709 +926000 ekin = 1.62371911797747 | erot = 1.87429650796065 | epot = -11.6317993026205 | etot = -8.13378367668236 +927000 ekin = 1.67952368621566 | erot = 1.85068760963458 | epot = -11.663994973807 | etot = -8.13378367795674 +928000 ekin = 1.71651231863953 | erot = 1.81783745906732 | epot = -11.6681334567389 | etot = -8.13378367903208 +929000 ekin = 1.71702542898816 | erot = 1.77614095822328 | epot = -11.6269500667182 | etot = -8.13378367950679 +930000 ekin = 1.67099557122645 | erot = 1.72742889265358 | epot = -11.5322081430821 | etot = -8.13378367920211 +931000 ekin = 1.57874461805286 | erot = 1.67513458336157 | epot = -11.3876628795813 | etot = -8.13378367816685 +932000 ekin = 1.4507920755465 | erot = 1.62392798812581 | epot = -11.2085037402974 | etot = -8.13378367662505 +933000 ekin = 1.30531755369149 | erot = 1.57894109557251 | epot = -11.0180423241588 | etot = -8.13378367489477 +934000 ekin = 1.16422088055465 | erot = 1.54485802719546 | epot = -10.8428625810454 | etot = -8.13378367329525 +935000 ekin = 1.04864497195189 | erot = 1.5250920918049 | epot = -10.7075207359171 | etot = -8.13378367216033 +936000 ekin = 0.974709275907845 | erot = 1.52116328113893 | epot = -10.6296562287295 | etot = -8.13378367168275 +937000 ekin = 0.950462281728795 | erot = 1.53244919754867 | epot = -10.6166951512348 | etot = -8.13378367195737 +938000 ekin = 0.974421294247563 | erot = 1.55616007284456 | epot = -10.6643650400328 | etot = -8.13378367294068 +939000 ekin = 1.03606886914207 | erot = 1.58755449810235 | epot = -10.7574070416974 | etot = -8.13378367445297 +940000 ekin = 1.11826841163644 | erot = 1.62042989252328 | epot = -10.8724819803543 | etot = -8.13378367619459 +941000 ekin = 1.20122028754373 | erot = 1.64794232268583 | epot = -10.9829462880145 | etot = -8.1337836777849 +942000 ekin = 1.26717763871503 | erot = 1.66371924010786 | epot = -11.0646805577046 | etot = -8.1337836788817 +943000 ekin = 1.3050921263636 | erot = 1.66314531322851 | epot = -11.1020211187136 | etot = -8.13378367912151 +944000 ekin = 1.31392378036222 | erot = 1.64449670959754 | epot = -11.0922041684753 | etot = -8.13378367851557 +945000 ekin = 1.30237464583948 | erot = 1.60929976264344 | epot = -11.04545808583 | etot = -8.13378367734709 +946000 ekin = 1.28506402630223 | erot = 1.56181036915073 | epot = -10.9806580715648 | etot = -8.13378367611187 +947000 ekin = 1.27634123347521 | erot = 1.50774431563436 | epot = -10.9178692243886 | etot = -8.133783675279 +948000 ekin = 1.28467886415746 | erot = 1.45281196766794 | epot = -10.8712745068899 | etot = -8.13378367506454 +949000 ekin = 1.31037739981839 | erot = 1.40157240050898 | epot = -10.8457334757007 | etot = -8.13378367537332 +950000 ekin = 1.34722619727445 | erot = 1.35688689258473 | epot = -10.8378967657852 | etot = -8.13378367592597 +951000 ekin = 1.38650860359963 | erot = 1.31991932915849 | epot = -10.8402116091881 | etot = -8.13378367643003 +952000 ekin = 1.42144708600024 | erot = 1.29081153261565 | epot = -10.8460422952464 | etot = -8.13378367663051 +953000 ekin = 1.44882630049243 | erot = 1.26905800932661 | epot = -10.8516679865683 | etot = -8.13378367674927 +954000 ekin = 1.46839021309569 | erot = 1.25288008944085 | epot = -10.8550539791095 | etot = -8.13378367657292 +955000 ekin = 1.48389177819301 | erot = 1.24071488903617 | epot = -10.858390343506 | etot = -8.13378367627686 +956000 ekin = 1.50041048021928 | erot = 1.23152279379181 | epot = -10.8657169500894 | etot = -8.13378367607827 +957000 ekin = 1.52124213198277 | erot = 1.2248104766171 | epot = -10.8798362846954 | etot = -8.13378367609549 +958000 ekin = 1.54632228951779 | erot = 1.22051885586618 | epot = -10.9006248216425 | etot = -8.13378367625849 +959000 ekin = 1.5732429585497 | erot = 1.2189190985513 | epot = -10.9259457334718 | etot = -8.1337836763708 +960000 ekin = 1.59969207484939 | erot = 1.22060655465072 | epot = -10.9540823058879 | etot = -8.13378367638774 +961000 ekin = 1.62253442120938 | erot = 1.22677322860071 | epot = -10.9830913260732 | etot = -8.13378367626306 +962000 ekin = 1.64127230246638 | erot = 1.23851880553052 | epot = -11.0135747841204 | etot = -8.13378367612348 +963000 ekin = 1.65616191530707 | erot = 1.25678968557686 | epot = -11.0467352770293 | etot = -8.13378367614533 +964000 ekin = 1.66566514878509 | erot = 1.28218253465312 | epot = -11.0816313596854 | etot = -8.13378367624715 +965000 ekin = 1.66770285413704 | erot = 1.3145546426696 | epot = -11.1160411733802 | etot = -8.13378367657354 +966000 ekin = 1.65810694801932 | erot = 1.35314679620483 | epot = -11.1450374210337 | etot = -8.13378367680953 +967000 ekin = 1.63401913429882 | erot = 1.39653020162862 | epot = -11.1643330128601 | etot = -8.1337836769327 +968000 ekin = 1.59493849996686 | erot = 1.44254096556363 | epot = -11.1712631425958 | etot = -8.13378367706529 +969000 ekin = 1.54116623449113 | erot = 1.48830566532954 | epot = -11.1632555771591 | etot = -8.13378367733845 +970000 ekin = 1.4719525052895 | erot = 1.53048571058931 | epot = -11.1362218935876 | etot = -8.13378367770882 +971000 ekin = 1.38571362496392 | erot = 1.56593199218658 | epot = -11.0854292947599 | etot = -8.13378367760946 +972000 ekin = 1.28446124080782 | erot = 1.59277024357702 | epot = -11.0110151618351 | etot = -8.13378367745027 +973000 ekin = 1.17320808804033 | erot = 1.61049478778007 | epot = -10.9174865525069 | etot = -8.13378367668655 +974000 ekin = 1.06313421672607 | erot = 1.62023440931496 | epot = -10.8171523014627 | etot = -8.1337836754217 +975000 ekin = 0.970987627773263 | erot = 1.62445058232732 | epot = -10.7292218841971 | etot = -8.13378367409648 +976000 ekin = 0.913517832896917 | erot = 1.62592321152395 | epot = -10.6732247177148 | etot = -8.13378367329392 +977000 ekin = 0.900210296281933 | erot = 1.62660680876215 | epot = -10.6606007784181 | etot = -8.13378367337401 +978000 ekin = 0.928774957734405 | erot = 1.62702793017349 | epot = -10.6895865621565 | etot = -8.13378367424864 +979000 ekin = 0.986309688615544 | erot = 1.62661906277886 | epot = -10.7467124267463 | etot = -8.13378367535186 +980000 ekin = 1.05604184509069 | erot = 1.62477777772944 | epot = -10.8146032989454 | etot = -8.13378367612524 +981000 ekin = 1.12469745172871 | erot = 1.62193499957867 | epot = -10.8804161275922 | etot = -8.13378367628486 +982000 ekin = 1.18655422485744 | erot = 1.61989865506831 | epot = -10.9402365558265 | etot = -8.13378367590075 +983000 ekin = 1.24323393324142 | erot = 1.62138932885757 | epot = -10.9984069373473 | etot = -8.1337836752483 +984000 ekin = 1.30072892338428 | erot = 1.62917854698298 | epot = -11.0636911449926 | etot = -8.13378367462536 +985000 ekin = 1.36575798911899 | erot = 1.64530549626705 | epot = -11.1448471596467 | etot = -8.13378367426062 +986000 ekin = 1.44269014494577 | erot = 1.67060135317286 | epot = -11.2470751724194 | etot = -8.13378367430079 +987000 ekin = 1.53139017700859 | erot = 1.70450616299349 | epot = -11.3696800148167 | etot = -8.13378367481465 +988000 ekin = 1.62542516970506 | erot = 1.74490462806446 | epot = -11.5041134736236 | etot = -8.13378367585409 +989000 ekin = 1.7097331432548 | erot = 1.78758053809196 | epot = -11.6310973585289 | etot = -8.13378367718214 +990000 ekin = 1.7683499056324 | erot = 1.8285480090496 | epot = -11.7306815930646 | etot = -8.13378367838265 +991000 ekin = 1.78717585085268 | erot = 1.86445265595412 | epot = -11.7854121858802 | etot = -8.13378367907336 +992000 ekin = 1.75808068859759 | erot = 1.89344947202214 | epot = -11.7853138396523 | etot = -8.13378367903258 +993000 ekin = 1.68149922524448 | erot = 1.91587778986002 | epot = -11.7311606933815 | etot = -8.13378367827695 +994000 ekin = 1.56634005423023 | erot = 1.93428820616986 | epot = -11.6344119373831 | etot = -8.13378367698301 +995000 ekin = 1.42807354993205 | erot = 1.95281321298946 | epot = -11.5146704383349 | etot = -8.13378367541341 +996000 ekin = 1.28578074359379 | erot = 1.97614374534584 | epot = -11.3957081628235 | etot = -8.1337836738839 +997000 ekin = 1.15849050625869 | erot = 2.00849321119135 | epot = -11.3007673901264 | etot = -8.13378367267635 +998000 ekin = 1.06172554938436 | erot = 2.05288173975883 | epot = -11.248390961091 | etot = -8.13378367194784 +999000 ekin = 1.00534864058225 | erot = 2.1108335144693 | epot = -11.2499658267879 | etot = -8.13378367173635 +1000000 ekin = 0.992888355159924 | erot = 2.18232107200368 | epot = -11.3089930991865 | etot = -8.13378367202294 + 1000000 0.073547286 -1.1520387 0.021139403 -1.0316105 -4.7686302e-05 64000 +Loop time of 16.9184 on 1 procs for 1000000 steps with 10 atoms + +Performance: 51068.728 tau/day, 59107.325 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.164 | 14.164 | 14.164 | 0.0 | 83.72 +Bond | 0.59031 | 0.59031 | 0.59031 | 0.0 | 3.49 +Neigh | 0.006119 | 0.006119 | 0.006119 | 0.0 | 0.04 +Comm | 0.33057 | 0.33057 | 0.33057 | 0.0 | 1.95 +Output | 0.094999 | 0.094999 | 0.094999 | 0.0 | 0.56 +Modify | 1.4671 | 1.4671 | 1.4671 | 0.0 | 8.67 +Other | | 0.265 | | | 1.57 + +Nlocal: 10.0000 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37.0000 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7000000 +Ave special neighs/atom = 3.6000000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.3.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:16 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 new file mode 100644 index 0000000000..a197afadb9 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 @@ -0,0 +1,1181 @@ +LAMMPS (2 Jul 2021) +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +set atom * mass 1.0 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.3.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 1.18025158324274 | erot = 2.17908479136507 | epot = -11.4931199991265 | etot = -8.13378362451868 +Per MPI rank memory allocation (min/avg/max) = 9.194 | 9.195 | 9.196 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.087426043 -1.2259004 0.076588446 -1.0312868 -7.7802026e-06 64000 +1000 ekin = 1.08696491147664 | erot = 2.23197650714075 | epot = -11.452725042513 | etot = -8.13378362389561 +2000 ekin = 1.01265115460251 | erot = 2.29132031278141 | epot = -11.4377550908153 | etot = -8.13378362343137 +3000 ekin = 0.964951920610342 | erot = 2.35614244814783 | epot = -11.4548779921655 | etot = -8.13378362340729 +4000 ekin = 0.945861179227058 | erot = 2.42482489276793 | epot = -11.5044696957622 | etot = -8.13378362376717 +5000 ekin = 0.952186940161504 | erot = 2.49508744948286 | epot = -11.5810580140497 | etot = -8.13378362440532 +6000 ekin = 0.976836955567211 | erot = 2.56435791368455 | epot = -11.6749784943528 | etot = -8.13378362510108 +7000 ekin = 1.01151727363089 | erot = 2.63034980765841 | epot = -11.7756507069157 | etot = -8.13378362562635 +8000 ekin = 1.04963768886881 | erot = 2.69159648304403 | epot = -11.8750177977506 | etot = -8.13378362583779 +9000 ekin = 1.08831406483909 | erot = 2.7476875765064 | epot = -11.9697852671577 | etot = -8.13378362581222 +10000 ekin = 1.1276989465442 | erot = 2.79881902231421 | epot = -12.0603015945015 | etot = -8.13378362564307 +11000 ekin = 1.16997706279087 | erot = 2.84539220453503 | epot = -12.1491528928088 | etot = -8.13378362548286 +12000 ekin = 1.21772825403559 | erot = 2.88753582693542 | epot = -12.2390477064188 | etot = -8.13378362544779 +13000 ekin = 1.27247277648631 | erot = 2.92478423931377 | epot = -12.3310406413903 | etot = -8.13378362559027 +14000 ekin = 1.33384628320076 | erot = 2.95599632290761 | epot = -12.4236262320194 | etot = -8.13378362591099 +15000 ekin = 1.39936071611668 | erot = 2.97947113417331 | epot = -12.5126154766852 | etot = -8.13378362639519 +16000 ekin = 1.46443870928027 | erot = 2.99312358077428 | epot = -12.5913459174141 | etot = -8.13378362735951 +17000 ekin = 1.52113741921511 | erot = 2.99430260105833 | epot = -12.6492236482457 | etot = -8.13378362797221 +18000 ekin = 1.56143918576788 | erot = 2.98098620608842 | epot = -12.6762090203243 | etot = -8.13378362846798 +19000 ekin = 1.57873438318795 | erot = 2.95206674454555 | epot = -12.6645847564925 | etot = -8.13378362875896 +20000 ekin = 1.5684134805379 | erot = 2.90735147312956 | epot = -12.6095485824457 | etot = -8.13378362877826 +21000 ekin = 1.52886464109306 | erot = 2.84765291368977 | epot = -12.5103011832755 | etot = -8.13378362849271 +22000 ekin = 1.46209217703486 | erot = 2.77478397647197 | epot = -12.3706597813888 | etot = -8.13378362788196 +23000 ekin = 1.37376733102671 | erot = 2.69155728313726 | epot = -12.19910824124 | etot = -8.13378362707598 +24000 ekin = 1.2726210989079 | erot = 2.60118350194755 | epot = -12.0075882269999 | etot = -8.13378362614448 +25000 ekin = 1.16926502294374 | erot = 2.50703692695189 | epot = -11.8100855751045 | etot = -8.13378362520882 +26000 ekin = 1.0747148994514 | erot = 2.41235840152813 | epot = -11.6208569253575 | etot = -8.13378362437793 +27000 ekin = 0.998982995755802 | erot = 2.31997753232675 | epot = -11.4527441518068 | etot = -8.13378362372427 +28000 ekin = 0.950065052892287 | erot = 2.23215621537587 | epot = -11.3160048915418 | etot = -8.13378362327369 +29000 ekin = 0.933483801722537 | erot = 2.15056100102974 | epot = -11.2178284257647 | etot = -8.13378362301238 +30000 ekin = 0.952335164335975 | erot = 2.07633501131221 | epot = -11.1624537985557 | etot = -8.13378362290752 +31000 ekin = 1.00761822011308 | erot = 2.01025995539433 | epot = -11.1516617984318 | etot = -8.13378362292438 +32000 ekin = 1.0985902731647 | erot = 1.95287201474931 | epot = -11.1852459109706 | etot = -8.13378362305661 +33000 ekin = 1.22296348257683 | erot = 1.90442653272443 | epot = -11.2611736386123 | etot = -8.13378362331101 +34000 ekin = 1.37683793249572 | erot = 1.86498336105431 | epot = -11.3756049172809 | etot = -8.13378362373086 +35000 ekin = 1.55422271443446 | erot = 1.83436013830194 | epot = -11.5223664771472 | etot = -8.13378362441081 +36000 ekin = 1.74589607048132 | erot = 1.81205442227468 | epot = -11.6917341182487 | etot = -8.13378362549269 +37000 ekin = 1.93777565280851 | erot = 1.79705197600555 | epot = -11.8686112558402 | etot = -8.13378362702612 +38000 ekin = 2.11051089015033 | erot = 1.78782890330243 | epot = -12.0321234221669 | etot = -8.13378362871418 +39000 ekin = 2.243214825885 | erot = 1.78271510837241 | epot = -12.1597135641246 | etot = -8.13378362986722 +40000 ekin = 2.32146151921631 | erot = 1.78073283005134 | epot = -12.2359779791649 | etot = -8.13378362989725 +41000 ekin = 2.34386750101373 | erot = 1.78241563043123 | epot = -12.2600667603299 | etot = -8.13378362888493 +42000 ekin = 2.32118218527075 | erot = 1.78979050959087 | epot = -12.2447563223398 | etot = -8.13378362747816 +43000 ekin = 2.26309111555125 | erot = 1.80539262076482 | epot = -12.2022673943963 | etot = -8.13378365808021 +44000 ekin = 2.15856242114809 | erot = 1.84609032619615 | epot = -12.1384363880308 | etot = -8.13378364068658 +45000 ekin = 2.08936731003487 | erot = 1.88904724563043 | epot = -12.1121981822921 | etot = -8.13378362662681 +46000 ekin = 1.99646115970022 | erot = 1.93503982400429 | epot = -12.0652846104763 | etot = -8.1337836267718 +47000 ekin = 1.89712577412015 | erot = 1.98806984898585 | epot = -12.0189792501524 | etot = -8.13378362704636 +48000 ekin = 1.79036864863072 | erot = 2.04496273496234 | epot = -11.9691150108766 | etot = -8.13378362728355 +49000 ekin = 1.67630116263911 | erot = 2.10216327906906 | epot = -11.9122480690704 | etot = -8.13378362736221 +50000 ekin = 1.55727015247045 | erot = 2.15637892895976 | epot = -11.8474327086503 | etot = -8.13378362722008 +51000 ekin = 1.4381743370913 | erot = 2.20514040032689 | epot = -11.7770983642844 | etot = -8.13378362686622 +52000 ekin = 1.32596547232163 | erot = 2.24710946474999 | epot = -11.7068585634504 | etot = -8.13378362637881 +53000 ekin = 1.22848082922903 | erot = 2.28204759210372 | epot = -11.6443120472107 | etot = -8.13378362587798 +54000 ekin = 1.15295119316259 | erot = 2.3104993393988 | epot = -11.5972341580452 | etot = -8.13378362548376 +55000 ekin = 1.10463170766313 | erot = 2.33334681406831 | epot = -11.571762147013 | etot = -8.13378362528157 +56000 ekin = 1.08590799517315 | erot = 2.35139880092321 | epot = -11.5710904214037 | etot = -8.13378362530734 +57000 ekin = 1.09599893485478 | erot = 2.36511154450522 | epot = -11.5948941049138 | etot = -8.1337836255538 +58000 ekin = 1.13119803470991 | erot = 2.37445830578809 | epot = -11.6394399664723 | etot = -8.13378362597432 +59000 ekin = 1.18549837183894 | erot = 2.37891691863227 | epot = -11.6981989169902 | etot = -8.13378362651899 +60000 ekin = 1.25136230662749 | erot = 2.37755306615245 | epot = -11.7626989998987 | etot = -8.13378362711876 +61000 ekin = 1.32065657328793 | erot = 2.3691782337931 | epot = -11.8236184347914 | etot = -8.13378362771039 +62000 ekin = 1.38555350991065 | erot = 2.35258911579053 | epot = -11.8719262538941 | etot = -8.13378362819294 +63000 ekin = 1.43966787267647 | erot = 2.32682848519598 | epot = -11.9002799863551 | etot = -8.13378362848263 +64000 ekin = 1.47909503438172 | erot = 2.29144993715399 | epot = -11.9043286000692 | etot = -8.13378362853349 +65000 ekin = 1.50288049774094 | erot = 2.24670960905117 | epot = -11.8833737351503 | etot = -8.13378362835817 +66000 ekin = 1.51274507599017 | erot = 2.19359684183002 | epot = -11.8401255458511 | etot = -8.13378362803096 +67000 ekin = 1.51208659633012 | erot = 2.13371356874814 | epot = -11.7795837927186 | etot = -8.13378362764037 +68000 ekin = 1.50462166617941 | erot = 2.06904733139783 | epot = -11.7074526249094 | etot = -8.13378362733216 +69000 ekin = 1.49293889166146 | erot = 2.00167765430525 | epot = -11.6284001731037 | etot = -8.13378362713704 +70000 ekin = 1.47793621174629 | erot = 1.9336121006037 | epot = -11.5453319394057 | etot = -8.13378362705566 +71000 ekin = 1.45891349102836 | erot = 1.86670994694693 | epot = -11.4594070650147 | etot = -8.13378362703941 +72000 ekin = 1.43427842101617 | erot = 1.80270883809016 | epot = -11.3707708861217 | etot = -8.13378362701539 +73000 ekin = 1.40258583891027 | erot = 1.74331039193086 | epot = -11.2796798577523 | etot = -8.13378362691117 +74000 ekin = 1.36359371155278 | erot = 1.69025647754913 | epot = -11.1876338157824 | etot = -8.13378362668049 +75000 ekin = 1.31886252565211 | erot = 1.64533820718023 | epot = -11.0979843591719 | etot = -8.13378362633955 +76000 ekin = 1.2718169277375 | erot = 1.61030043593589 | epot = -11.0159009896016 | etot = -8.13378362592821 +77000 ekin = 1.22767338921997 | erot = 1.58670952555607 | epot = -10.9481665402837 | etot = -8.13378362550769 +78000 ekin = 1.1918742588196 | erot = 1.57555521121131 | epot = -10.9012130952119 | etot = -8.13378362518096 +79000 ekin = 1.16922470588802 | erot = 1.57716601534091 | epot = -10.8801743462043 | etot = -8.13378362497538 +80000 ekin = 1.16351312193714 | erot = 1.5911285277542 | epot = -10.8884252746037 | etot = -8.13378362491238 +81000 ekin = 1.17709123428917 | erot = 1.61633850893099 | epot = -10.9272133682122 | etot = -8.13378362499208 +82000 ekin = 1.21064005584001 | erot = 1.65118762576698 | epot = -10.9956113068163 | etot = -8.13378362520929 +83000 ekin = 1.26297331742712 | erot = 1.69382675572852 | epot = -11.0905836987111 | etot = -8.1337836255555 +84000 ekin = 1.33092648687644 | erot = 1.74243133123679 | epot = -11.2071414441145 | etot = -8.13378362600128 +85000 ekin = 1.40961218427353 | erot = 1.79540640337827 | epot = -11.3388022141306 | etot = -8.13378362647884 +86000 ekin = 1.49330005467918 | erot = 1.85150064414015 | epot = -11.4785843257055 | etot = -8.13378362688614 +87000 ekin = 1.576533807167 | erot = 1.90982169886832 | epot = -11.6201391333941 | etot = -8.13378362735875 +88000 ekin = 1.65416408678852 | erot = 1.96971725895491 | epot = -11.7576649732587 | etot = -8.13378362751531 +89000 ekin = 1.72360216634173 | erot = 2.0305593433754 | epot = -11.8879451373051 | etot = -8.13378362758797 +90000 ekin = 1.78500984589386 | erot = 2.09126219979614 | epot = -12.0100556734368 | etot = -8.1337836277468 +91000 ekin = 1.83789001415873 | erot = 2.15001837237371 | epot = -12.1216920145423 | etot = -8.13378362800981 +92000 ekin = 1.87517809322855 | erot = 2.20985483887557 | epot = -12.2188165602807 | etot = -8.13378362817655 +93000 ekin = 1.90356384535066 | erot = 2.2620490304799 | epot = -12.2993965046582 | etot = -8.13378362882767 +94000 ekin = 1.91566641673035 | erot = 2.30892488078309 | epot = -12.3583749263617 | etot = -8.13378362884821 +95000 ekin = 1.91095769383997 | erot = 2.34997522030035 | epot = -12.3947165431016 | etot = -8.13378362896126 +96000 ekin = 1.88948402498892 | erot = 2.38411475951092 | epot = -12.4073824132812 | etot = -8.13378362878136 +97000 ekin = 1.8534381113389 | erot = 2.4113304629225 | epot = -12.3985522027172 | etot = -8.13378362845576 +98000 ekin = 1.80684275230266 | erot = 2.43203206054847 | epot = -12.3726584408919 | etot = -8.1337836280408 +99000 ekin = 1.75478641123165 | erot = 2.44692977736858 | epot = -12.3354998162076 | etot = -8.13378362760738 +100000 ekin = 1.69590911435643 | erot = 2.45386958409513 | epot = -12.283562384886 | etot = -8.13378368643445 +101000 ekin = 1.6811324937538 | erot = 2.36572534112421 | epot = -12.1806414642157 | etot = -8.13378362933768 +102000 ekin = 1.72678565900148 | erot = 2.35051337712506 | epot = -12.2110826965911 | etot = -8.13378366046458 +103000 ekin = 1.68338599487686 | erot = 2.35411811039608 | epot = -12.1712877656954 | etot = -8.13378366042246 +104000 ekin = 1.64323586412835 | erot = 2.35701648102718 | epot = -12.1340360056525 | etot = -8.13378366049693 +105000 ekin = 1.60584113472038 | erot = 2.35932964102244 | epot = -12.0989544363536 | etot = -8.13378366061083 +106000 ekin = 1.57044138011792 | erot = 2.36092776943215 | epot = -12.0651528102269 | etot = -8.13378366067683 +107000 ekin = 1.53705400250956 | erot = 2.36166253248183 | epot = -12.0325001956586 | etot = -8.13378366066723 +108000 ekin = 1.50696391591104 | erot = 2.3612855734918 | epot = -12.002033149985 | etot = -8.13378366058219 +109000 ekin = 1.48244426546626 | erot = 2.35938088270983 | epot = -11.9756088087055 | etot = -8.13378366052944 +110000 ekin = 1.46539913148031 | erot = 2.35530683146138 | epot = -11.9544896235797 | etot = -8.13378366063801 +111000 ekin = 1.45548748017558 | erot = 2.3481806560607 | epot = -11.9374517972408 | etot = -8.13378366100448 +112000 ekin = 1.4487272961288 | erot = 2.3369554826693 | epot = -11.919466440375 | etot = -8.13378366157695 +113000 ekin = 1.43805495586415 | erot = 2.32068695509381 | epot = -11.8925255730874 | etot = -8.13378366212947 +114000 ekin = 1.41640788690795 | erot = 2.29883886662097 | epot = -11.8490304158908 | etot = -8.13378366236189 +115000 ekin = 1.38063781822003 | erot = 2.2715321857329 | epot = -11.7859536655159 | etot = -8.13378366156294 +116000 ekin = 1.33630540308347 | erot = 2.23942220246118 | epot = -11.7095112666476 | etot = -8.13378366110297 +117000 ekin = 1.29001229198257 | erot = 2.20380811829898 | epot = -11.6276040708685 | etot = -8.13378366058698 +118000 ekin = 1.24711548834684 | erot = 2.16635124019896 | epot = -11.547250388778 | etot = -8.13378366023218 +119000 ekin = 1.21073685469405 | erot = 2.12872161390259 | epot = -11.4732421286718 | etot = -8.13378366007513 +120000 ekin = 1.18115748419431 | erot = 2.09256534610062 | epot = -11.4075064903308 | etot = -8.13378366003586 +121000 ekin = 1.15688642101089 | erot = 2.05947511288393 | epot = -11.3501451939318 | etot = -8.13378366003694 +122000 ekin = 1.13593168276758 | erot = 2.03084061403904 | epot = -11.300555956866 | etot = -8.13378366005934 +123000 ekin = 1.1163881196593 | erot = 2.00761097209062 | epot = -11.2577827519207 | etot = -8.13378366017078 +124000 ekin = 1.09616325371728 | erot = 1.99019695902079 | epot = -11.2201438730119 | etot = -8.13378366027383 +125000 ekin = 1.07358508996113 | erot = 1.97820026039375 | epot = -11.1855690107833 | etot = -8.13378366042845 +126000 ekin = 1.04712198978478 | erot = 1.97030937007251 | epot = -11.1512150205178 | etot = -8.13378366066049 +127000 ekin = 1.01560359550503 | erot = 1.96476336054365 | epot = -11.1141506168029 | etot = -8.1337836607542 +128000 ekin = 0.979281846651978 | erot = 1.95990906194981 | epot = -11.0729745693078 | etot = -8.133783660706 +129000 ekin = 0.940294043229548 | erot = 1.95428772921589 | epot = -11.0283654329015 | etot = -8.1337836604561 +130000 ekin = 0.902735823606936 | erot = 1.947100477648 | epot = -10.9836199613555 | etot = -8.13378366010058 +131000 ekin = 0.872329759139433 | erot = 1.93820575526869 | epot = -10.9443191739575 | etot = -8.1337836595494 +132000 ekin = 0.855045600562102 | erot = 1.92803271303728 | epot = -10.9168619728701 | etot = -8.1337836592707 +133000 ekin = 0.854775562822548 | erot = 1.91694878881008 | epot = -10.9055080107093 | etot = -8.13378365907667 +134000 ekin = 0.873981086379087 | erot = 1.90549522489496 | epot = -10.9132599702542 | etot = -8.13378365898011 +135000 ekin = 0.913690181742188 | erot = 1.89429118508561 | epot = -10.9417650257953 | etot = -8.1337836589675 +136000 ekin = 0.973734451666194 | erot = 1.8839532178428 | epot = -10.9914713285366 | etot = -8.13378365902762 +137000 ekin = 1.05255313136017 | erot = 1.87488800080408 | epot = -11.0612247920069 | etot = -8.13378365984268 +138000 ekin = 1.14435249948622 | erot = 1.86626897212079 | epot = -11.1444051316866 | etot = -8.13378366007961 +139000 ekin = 1.24448357091432 | erot = 1.85821435006774 | epot = -11.2364815813249 | etot = -8.13378366034282 +140000 ekin = 1.34860347563852 | erot = 1.85113522079134 | epot = -11.3335223570946 | etot = -8.13378366066476 +141000 ekin = 1.45162669266417 | erot = 1.84534635451933 | epot = -11.4307567082686 | etot = -8.13378366108508 +142000 ekin = 1.54663919844615 | erot = 1.84103156950911 | epot = -11.5214544297506 | etot = -8.13378366179533 +143000 ekin = 1.6247011023952 | erot = 1.83813053702612 | epot = -11.5966153018878 | etot = -8.13378366246652 +144000 ekin = 1.67710589256394 | erot = 1.83622813336412 | epot = -11.6471176890273 | etot = -8.13378366309928 +145000 ekin = 1.69650852159151 | erot = 1.83477115527455 | epot = -11.6650633403362 | etot = -8.13378366347012 +146000 ekin = 1.67998250270751 | erot = 1.83334306418687 | epot = -11.6471092301937 | etot = -8.13378366329936 +147000 ekin = 1.63255928725608 | erot = 1.83204496823004 | epot = -11.5983879178797 | etot = -8.13378366239362 +148000 ekin = 1.56926257377557 | erot = 1.83182914755798 | epot = -11.5348753821899 | etot = -8.13378366085638 +149000 ekin = 1.51300824977863 | erot = 1.83452727994331 | epot = -11.4813191889272 | etot = -8.13378365920525 +150000 ekin = 1.48724963784866 | erot = 1.84235837448582 | epot = -11.4633916705196 | etot = -8.13378365818515 +151000 ekin = 1.5061932382316 | erot = 1.85697474829986 | epot = -11.496951644838 | etot = -8.13378365830658 +152000 ekin = 1.56855992602772 | erot = 1.87847282638524 | epot = -11.5808164119039 | etot = -8.13378365949099 +153000 ekin = 1.6591448964677 | erot = 1.90493735115943 | epot = -11.697865908774 | etot = -8.13378366114692 +154000 ekin = 1.75680978950899 | erot = 1.93282846213588 | epot = -11.8234219142239 | etot = -8.133783662579 +155000 ekin = 1.84344901658549 | erot = 1.95802697046865 | epot = -11.9352596504351 | etot = -8.13378366338094 +156000 ekin = 1.90893795388493 | erot = 1.97697594926094 | epot = -12.0196975667227 | etot = -8.13378366357679 +157000 ekin = 1.95061494385915 | erot = 1.9873851243352 | epot = -12.0717837316318 | etot = -8.13378366343743 +158000 ekin = 1.96976178337645 | erot = 1.9883744718149 | epot = -12.091919918361 | etot = -8.13378366316969 +159000 ekin = 1.96892634677104 | erot = 1.98033790354824 | epot = -12.0830479131009 | etot = -8.13378366278165 +160000 ekin = 1.95167601805768 | erot = 1.96478101829964 | epot = -12.0502406985796 | etot = -8.13378366222225 +161000 ekin = 1.92323849263564 | erot = 1.94408396543497 | epot = -12.0011061196151 | etot = -8.13378366154445 +162000 ekin = 1.8901278513965 | erot = 1.92106669306924 | epot = -11.9449782053576 | etot = -8.13378366089191 +163000 ekin = 1.85873206626091 | erot = 1.89844726529898 | epot = -11.8909629919499 | etot = -8.13378366038998 +164000 ekin = 1.83396756863653 | erot = 1.87841814938188 | epot = -11.8461693781051 | etot = -8.1337836600867 +165000 ekin = 1.818736578138 | erot = 1.86247026312254 | epot = -11.8149905012176 | etot = -8.13378365995705 +166000 ekin = 1.81415764355048 | erot = 1.85144128795262 | epot = -11.799382591449 | etot = -8.13378365994594 +167000 ekin = 1.82014338462565 | erot = 1.84569577974701 | epot = -11.7996228243641 | etot = -8.13378365999149 +168000 ekin = 1.8360497359111 | erot = 1.84534918673544 | epot = -11.8151825826915 | etot = -8.13378366004491 +169000 ekin = 1.8611880780384 | erot = 1.8504776642993 | epot = -11.845449402414 | etot = -8.13378366007634 +170000 ekin = 1.89508209491969 | erot = 1.8612760074506 | epot = -11.8901417624545 | etot = -8.13378366008421 +171000 ekin = 1.93739070093696 | erot = 1.87813927221188 | epot = -11.949313633246 | etot = -8.1337836600972 +172000 ekin = 1.98746465492625 | erot = 1.90165699566223 | epot = -12.0229053107604 | etot = -8.13378366017191 +173000 ekin = 2.0435873226069 | erot = 1.93252470914531 | epot = -12.1098956921186 | etot = -8.13378366036636 +174000 ekin = 2.10212586880676 | erot = 1.97139111366206 | epot = -12.2073006432572 | etot = -8.13378366078839 +175000 ekin = 2.15653164019917 | erot = 2.0186862399753 | epot = -12.3090015416391 | etot = -8.13378366146463 +176000 ekin = 2.19700590631335 | erot = 2.0744451769465 | epot = -12.4052347456362 | etot = -8.1337836623764 +177000 ekin = 2.21275117726769 | erot = 2.13809655452378 | epot = -12.4846313951125 | etot = -8.13378366332099 +178000 ekin = 2.19103084137828 | erot = 2.20849637361952 | epot = -12.5333108794538 | etot = -8.13378366445596 +179000 ekin = 2.05002958755744 | erot = 2.2764749240598 | epot = -12.4602881626295 | etot = -8.13378365101223 +180000 ekin = 2.00100366281057 | erot = 2.36086155180657 | epot = -12.4956488860912 | etot = -8.13378367147401 +181000 ekin = 1.82885344502769 | erot = 2.44444025932807 | epot = -12.4070773745346 | etot = -8.13378367017883 +182000 ekin = 1.62724610560531 | erot = 2.53221325513969 | epot = -12.2932430288223 | etot = -8.13378366807729 +183000 ekin = 1.42880501135615 | erot = 2.62540058534439 | epot = -12.1879892625424 | etot = -8.13378366584191 +184000 ekin = 1.267149628321 | erot = 2.7256198185053 | epot = -12.1265531111189 | etot = -8.13378366429257 +185000 ekin = 1.16606552757999 | erot = 2.8336645073234 | epot = -12.1335136988434 | etot = -8.13378366393999 +186000 ekin = 1.13327188784992 | erot = 2.94811459460617 | epot = -12.2151701472133 | etot = -8.13378366475719 +187000 ekin = 1.16127663962737 | erot = 3.06454091657788 | epot = -12.3596012225496 | etot = -8.13378366634434 +188000 ekin = 1.2327579922885 | erot = 3.17578119614224 | epot = -12.5423228566653 | etot = -8.13378366823452 +189000 ekin = 1.32637276316298 | erot = 3.27316596760534 | epot = -12.7333224008259 | etot = -8.13378367005761 +190000 ekin = 1.42100795809019 | erot = 3.34817980173611 | epot = -12.902971431372 | etot = -8.13378367154568 +191000 ekin = 1.49794111550009 | erot = 3.39410379075282 | epot = -13.0258285788627 | etot = -8.13378367260982 +192000 ekin = 1.5426215667976 | erot = 3.40720165429128 | epot = -13.0836068940668 | etot = -8.13378367297792 +193000 ekin = 1.54797240883541 | erot = 3.38715231466011 | epot = -13.0689083961188 | etot = -8.13378367262329 +194000 ekin = 1.51467582661435 | erot = 3.33705387754585 | epot = -12.9855133757546 | etot = -8.13378367159441 +195000 ekin = 1.45101621748176 | erot = 3.26269312885055 | epot = -12.8474930164449 | etot = -8.13378367011259 +196000 ekin = 1.37083042970682 | erot = 3.17132041678729 | epot = -12.6759345149981 | etot = -8.133783668504 +197000 ekin = 1.29009120536618 | erot = 3.0703626593562 | epot = -12.4942375317725 | etot = -8.13378366705012 +198000 ekin = 1.22364196643859 | erot = 2.96652382643828 | epot = -12.3239494587807 | etot = -8.13378366590384 +199000 ekin = 1.18307710083175 | erot = 2.865421442176 | epot = -12.1822822081278 | etot = -8.13378366512006 +200000 ekin = 1.1756434095187 | erot = 2.77158698378605 | epot = -12.0810140580283 | etot = -8.13378366472354 +201000 ekin = 1.20359619391725 | erot = 2.6885691853706 | epot = -12.0259490440283 | etot = -8.13378366474049 +202000 ekin = 1.26374726413798 | erot = 2.61894189739959 | epot = -12.016472826716 | etot = -8.13378366517838 +203000 ekin = 1.34751597563146 | erot = 2.56419616426373 | epot = -12.0454958058707 | etot = -8.13378366597546 +204000 ekin = 1.44203337890041 | erot = 2.52468734318871 | epot = -12.1005043890645 | etot = -8.1337836669754 +205000 ekin = 1.53246038205392 | erot = 2.49972903140467 | epot = -12.165973081407 | etot = -8.13378366794836 +206000 ekin = 1.60510558525696 | erot = 2.48793425280246 | epot = -12.2268235067222 | etot = -8.13378366866277 +207000 ekin = 1.65039556723175 | erot = 2.48771410987715 | epot = -12.2718933460776 | etot = -8.13378366896866 +208000 ekin = 1.66471924263863 | erot = 2.49772662877183 | epot = -12.2962295402585 | etot = -8.133783668848 +209000 ekin = 1.65060780281959 | erot = 2.51706178773879 | epot = -12.3014532589743 | etot = -8.13378366841589 +210000 ekin = 1.61529613530122 | erot = 2.54506818372099 | epot = -12.2941479869024 | etot = -8.13378366788021 +211000 ekin = 1.56815998339919 | erot = 2.58088870847282 | epot = -12.2828323593496 | etot = -8.13378366747755 +212000 ekin = 1.51779769211956 | erot = 2.62289115840002 | epot = -12.2744725179137 | etot = -8.13378366739415 +213000 ekin = 1.46970697786419 | erot = 2.66822787294325 | epot = -12.2717185184992 | etot = -8.13378366769171 +214000 ekin = 1.42551121611962 | erot = 2.71271314915558 | epot = -12.272008033447 | etot = -8.1337836681718 +215000 ekin = 1.38449526701816 | erot = 2.75113858809818 | epot = -12.2694175238344 | etot = -8.13378366871808 +216000 ekin = 1.34611450510728 | erot = 2.77818905444589 | epot = -12.2580872284521 | etot = -8.13378366889897 +217000 ekin = 1.3134815281203 | erot = 2.78964053187616 | epot = -12.236905728556 | etot = -8.13378366855957 +218000 ekin = 1.2945863991961 | erot = 2.7831914510908 | epot = -12.2115615182405 | etot = -8.13378366795361 +219000 ekin = 1.29978448123296 | erot = 2.75785865494158 | epot = -12.191426803609 | etot = -8.13378366743447 +220000 ekin = 1.33694784981974 | erot = 2.71363634301879 | epot = -12.1843678601796 | etot = -8.13378366734106 +221000 ekin = 1.4074564392132 | erot = 2.65092088134167 | epot = -12.1921609882732 | etot = -8.13378366771838 +222000 ekin = 1.50572252626187 | erot = 2.57029476952172 | epot = -12.2098009641054 | etot = -8.13378366832179 +223000 ekin = 1.62210843375939 | erot = 2.4728900733397 | epot = -12.2287821759292 | etot = -8.13378366883007 +224000 ekin = 1.74679393023034 | erot = 2.36097135919196 | epot = -12.2415489584556 | etot = -8.13378366903332 +225000 ekin = 1.87205636330007 | erot = 2.23842454190366 | epot = -12.2442645742128 | etot = -8.13378366900908 +226000 ekin = 1.99134598106675 | erot = 2.11064622098247 | epot = -12.2357758711282 | etot = -8.13378366907897 +227000 ekin = 2.09586639151636 | erot = 1.98364704051012 | epot = -12.2132971015565 | etot = -8.13378366953 +228000 ekin = 2.17197666667354 | erot = 1.86293503717618 | epot = -12.1686953741892 | etot = -8.1337836703395 +229000 ekin = 2.20263173192525 | erot = 1.75265294154551 | epot = -12.0890683445884 | etot = -8.13378367111765 +230000 ekin = 2.17321554606792 | erot = 1.65532359970698 | epot = -11.9623228171272 | etot = -8.13378367135228 +231000 ekin = 2.07854920573096 | erot = 1.57213281486555 | epot = -11.7844656913339 | etot = -8.1337836707374 +232000 ekin = 1.92671195021847 | erot = 1.50340464294684 | epot = -11.5639002625302 | etot = -8.13378366936492 +233000 ekin = 1.73729705955971 | erot = 1.44896834770108 | epot = -11.3200490749305 | etot = -8.13378366766967 +234000 ekin = 1.53556953354756 | erot = 1.40834045937372 | epot = -11.0776936590018 | etot = -8.1337836660805 +235000 ekin = 1.34558700580146 | erot = 1.38078818073773 | epot = -10.8601588514738 | etot = -8.13378366493464 +236000 ekin = 1.18525206422628 | erot = 1.36570263210282 | epot = -10.6847383605462 | etot = -8.13378366421707 +237000 ekin = 1.06637029724417 | erot = 1.36251012102743 | epot = -10.5626640820868 | etot = -8.13378366381525 +238000 ekin = 0.995491212022236 | erot = 1.37070429771324 | epot = -10.4999791734002 | etot = -8.13378366366477 +239000 ekin = 0.975031518633231 | erot = 1.38971384126842 | epot = -10.4985290236714 | etot = -8.13378366376973 +240000 ekin = 1.00352423904904 | erot = 1.41866034024213 | epot = -10.5559682434651 | etot = -8.13378366417394 +241000 ekin = 1.07556704774416 | erot = 1.45612900246819 | epot = -10.6654797151307 | etot = -8.13378366491832 +242000 ekin = 1.18122375067533 | erot = 1.49994629855508 | epot = -10.8149537152557 | etot = -8.13378366602531 +243000 ekin = 1.30634294707673 | erot = 1.54703331020128 | epot = -10.9871599246195 | etot = -8.13378366734153 +244000 ekin = 1.43466609576387 | erot = 1.59374373480315 | epot = -11.1621934990229 | etot = -8.13378366845588 +245000 ekin = 1.55091944171472 | erot = 1.63606515904766 | epot = -11.3207682704767 | etot = -8.13378366971433 +246000 ekin = 1.63963426714789 | erot = 1.67091688012884 | epot = -11.4443348179141 | etot = -8.13378367063734 +247000 ekin = 1.68912292676274 | erot = 1.69643192578783 | epot = -11.519338523591 | etot = -8.13378367104043 +248000 ekin = 1.69418623366615 | erot = 1.71223298155225 | epot = -11.5402028860562 | etot = -8.13378367083777 +249000 ekin = 1.65708464250019 | erot = 1.71943097162832 | epot = -11.510299284324 | etot = -8.13378367019547 +250000 ekin = 1.58639864685258 | erot = 1.720159822896 | epot = -11.4403421388633 | etot = -8.13378366911475 +251000 ekin = 1.4955593640759 | erot = 1.7171607244027 | epot = -11.3465037564439 | etot = -8.13378366796528 +252000 ekin = 1.39930346630535 | erot = 1.71298107622824 | epot = -11.2460682095265 | etot = -8.13378366699295 +253000 ekin = 1.31034898359087 | erot = 1.7094909345967 | epot = -11.1536235845393 | etot = -8.13378366635176 +254000 ekin = 1.23716194122791 | erot = 1.70776552340203 | epot = -11.0787111307296 | etot = -8.13378366609963 +255000 ekin = 1.18305733844651 | erot = 1.70821467485129 | epot = -11.0250556794461 | etot = -8.13378366614825 +256000 ekin = 1.14729363432147 | erot = 1.71063275158191 | epot = -10.991710052286 | etot = -8.13378366638265 +257000 ekin = 1.1265046010806 | erot = 1.71454195552783 | epot = -10.9748302232593 | etot = -8.13378366665083 +258000 ekin = 1.11669715917377 | erot = 1.71938873503276 | epot = -10.9698695610614 | etot = -8.13378366685484 +259000 ekin = 1.11461746403468 | erot = 1.72463904931047 | epot = -10.9730401803333 | etot = -8.13378366698814 +260000 ekin = 1.11796213299025 | erot = 1.72976096813917 | epot = -10.9815067682326 | etot = -8.13378366710316 +261000 ekin = 1.12495929560688 | erot = 1.73429797646783 | epot = -10.9930409392085 | etot = -8.1337836671338 +262000 ekin = 1.13415334886842 | erot = 1.73799782227169 | epot = -11.0059348383766 | etot = -8.13378366723648 +263000 ekin = 1.1441924865794 | erot = 1.74014341283961 | epot = -11.0181195666666 | etot = -8.13378366724758 +264000 ekin = 1.15486713033337 | erot = 1.74014049676735 | epot = -11.0287912942205 | etot = -8.13378366711974 +265000 ekin = 1.16757148072827 | erot = 1.73774643956195 | epot = -11.0391015871675 | etot = -8.1337836668773 +266000 ekin = 1.18492523335162 | erot = 1.73313774545438 | epot = -11.0518466454068 | etot = -8.13378366660083 +267000 ekin = 1.20976553809282 | erot = 1.7268208539046 | epot = -11.0703700583789 | etot = -8.13378366638147 +268000 ekin = 1.2440311190649 | erot = 1.71946869065553 | epot = -11.0972834760054 | etot = -8.13378366628496 +269000 ekin = 1.28796807043956 | erot = 1.71176934564224 | epot = -11.1335210824187 | etot = -8.13378366633693 +270000 ekin = 1.33984072254354 | erot = 1.7043411961581 | epot = -11.1779655852252 | etot = -8.13378366652351 +271000 ekin = 1.39615730897264 | erot = 1.69774776465105 | epot = -11.2276887404003 | etot = -8.1337836667766 +272000 ekin = 1.45234426471681 | erot = 1.69276715684855 | epot = -11.2788950886398 | etot = -8.13378366707447 +273000 ekin = 1.50368133071071 | erot = 1.68992546991691 | epot = -11.3273904679427 | etot = -8.1337836673151 +274000 ekin = 1.54639996326974 | erot = 1.68983337629384 | epot = -11.3700170069765 | etot = -8.1337836674129 +275000 ekin = 1.57877490150026 | erot = 1.69332235277881 | epot = -11.4058809216115 | etot = -8.13378366733244 +276000 ekin = 1.60168052284474 | erot = 1.70138855156029 | epot = -11.4368527415036 | etot = -8.13378366709861 +277000 ekin = 1.61832490283932 | erot = 1.7150264260381 | epot = -11.467134995681 | etot = -8.1337836668036 +278000 ekin = 1.63311060675832 | erot = 1.73495415768603 | epot = -11.5018484310241 | etot = -8.13378366657978 +279000 ekin = 1.64995273995069 | erot = 1.76130541528402 | epot = -11.5450418217804 | etot = -8.13378366654569 +280000 ekin = 1.67073877093186 | erot = 1.79339849893625 | epot = -11.5979209366139 | etot = -8.13378366674582 +281000 ekin = 1.69438407984331 | erot = 1.82970064438891 | epot = -11.6578683914543 | etot = -8.13378366722212 +282000 ekin = 1.71376506079771 | erot = 1.86795891950542 | epot = -11.715507648123 | etot = -8.13378366781989 +283000 ekin = 1.72224450523959 | erot = 1.90529068548332 | epot = -11.7613188590643 | etot = -8.13378366834137 +284000 ekin = 1.71505262175737 | erot = 1.93881515489656 | epot = -11.7876514453406 | etot = -8.13378366868666 +285000 ekin = 1.68954869054978 | erot = 1.96608819497607 | epot = -11.7894205543486 | etot = -8.13378366882275 +286000 ekin = 1.64555137746269 | erot = 1.98537597121361 | epot = -11.7647110174504 | etot = -8.1337836687741 +287000 ekin = 1.58495470811888 | erot = 1.99578989882545 | epot = -11.7145282755366 | etot = -8.13378366859229 +288000 ekin = 1.5110176158451 | erot = 1.9972977679296 | epot = -11.6420990521052 | etot = -8.13378366833054 +289000 ekin = 1.42766231980138 | erot = 1.99063899576696 | epot = -11.5520849836022 | etot = -8.13378366803389 +290000 ekin = 1.33894501485583 | erot = 1.97716758999489 | epot = -11.4498962725828 | etot = -8.13378366773207 +291000 ekin = 1.248817211875 | erot = 1.95864649303427 | epot = -11.3412473723318 | etot = -8.13378366742251 +292000 ekin = 1.16137515575165 | erot = 1.9370295819229 | epot = -11.2321884047306 | etot = -8.13378366705601 +293000 ekin = 1.08169833470191 | erot = 1.91427738455886 | epot = -11.1297593858184 | etot = -8.13378366655758 +294000 ekin = 1.01689863825805 | erot = 1.8922324358186 | epot = -11.0429147399744 | etot = -8.13378366589774 +295000 ekin = 0.976377352945052 | erot = 1.87253324957175 | epot = -10.9826942676957 | etot = -8.13378366517893 +296000 ekin = 0.970182395975483 | erot = 1.85650679551204 | epot = -10.9604728561447 | etot = -8.13378366465719 +297000 ekin = 1.0053715181696 | erot = 1.84499118419568 | epot = -10.9841463669915 | etot = -8.13378366462627 +298000 ekin = 1.08200534147073 | erot = 1.83812417716642 | epot = -11.0539131838721 | etot = -8.13378366523492 +299000 ekin = 1.19125189130404 | erot = 1.83519410295209 | epot = -11.1602296606335 | etot = -8.13378366637738 +300000 ekin = 1.31698721062207 | erot = 1.83465168976294 | epot = -11.2854225681332 | etot = -8.13378366774819 +301000 ekin = 1.44008784810256 | erot = 1.83433803116237 | epot = -11.4082095482586 | etot = -8.13378366899367 +302000 ekin = 1.5432954854116 | erot = 1.83190000197301 | epot = -11.508979157225 | etot = -8.13378366984044 +303000 ekin = 1.61484992407947 | erot = 1.82529439833012 | epot = -11.5739279925649 | etot = -8.13378367015528 +304000 ekin = 1.65011047810809 | erot = 1.81324433416556 | epot = -11.5971384822074 | etot = -8.13378366993376 +305000 ekin = 1.6514081436682 | erot = 1.7954949702977 | epot = -11.5806867832572 | etot = -8.13378366929126 +306000 ekin = 1.62643416627235 | erot = 1.77280218913043 | epot = -11.5330200238132 | etot = -8.1337836684104 +307000 ekin = 1.5857750046693 | erot = 1.7466850070714 | epot = -11.4662436792366 | etot = -8.13378366749585 +308000 ekin = 1.54030424866459 | erot = 1.71903801623407 | epot = -11.3931259316147 | etot = -8.13378366671604 +309000 ekin = 1.4990009105043 | erot = 1.69173690590549 | epot = -11.3245214826 | etot = -8.13378366619016 +310000 ekin = 1.46747597212677 | erot = 1.66636932778201 | epot = -11.2676289658518 | etot = -8.13378366594304 +311000 ekin = 1.44771419446782 | erot = 1.64410448875489 | epot = -11.2256023491766 | etot = -8.13378366595387 +312000 ekin = 1.43839141864346 | erot = 1.62568199894977 | epot = -11.1978570837369 | etot = -8.13378366614363 +313000 ekin = 1.43594352566627 | erot = 1.61150443048395 | epot = -11.1812316225614 | etot = -8.13378366641123 +314000 ekin = 1.4359525561927 | erot = 1.6017711610384 | epot = -11.1715073838887 | etot = -8.13378366665756 +315000 ekin = 1.43500742743257 | erot = 1.59648896098093 | epot = -11.1652800551232 | etot = -8.13378366670972 +316000 ekin = 1.43108473248386 | erot = 1.59565804393172 | epot = -11.1605264431406 | etot = -8.13378366672501 +317000 ekin = 1.423903362868 | erot = 1.59957952105914 | epot = -11.157266550458 | etot = -8.13378366653083 +318000 ekin = 1.41631295381457 | erot = 1.6086681920702 | epot = -11.1587648120474 | etot = -8.13378366616265 +319000 ekin = 1.41381426235391 | erot = 1.62334142232249 | epot = -11.1709393504001 | etot = -8.13378366572373 +320000 ekin = 1.42315030254029 | erot = 1.6438411684038 | epot = -11.2007751363095 | etot = -8.13378366536539 +321000 ekin = 1.45024845495236 | erot = 1.67003325940321 | epot = -11.2540653795939 | etot = -8.13378366523836 +322000 ekin = 1.49815500537048 | erot = 1.70123818171696 | epot = -11.3331768525307 | etot = -8.13378366544326 +323000 ekin = 1.56569352501265 | erot = 1.73609284126964 | epot = -11.4355700323001 | etot = -8.13378366601784 +324000 ekin = 1.64679224019604 | erot = 1.77264010660481 | epot = -11.5532160137959 | etot = -8.13378366699503 +325000 ekin = 1.73163775628642 | erot = 1.80818795206065 | epot = -11.6736093763912 | etot = -8.13378366804413 +326000 ekin = 1.807503292055 | erot = 1.8398074929619 | epot = -11.7810944543653 | etot = -8.13378366934842 +327000 ekin = 1.85797659453463 | erot = 1.86537346542643 | epot = -11.8571337302883 | etot = -8.13378367032723 +328000 ekin = 1.87027520745668 | erot = 1.88392315073899 | epot = -11.8879820288559 | etot = -8.13378367066024 +329000 ekin = 1.83949589051625 | erot = 1.89597309719521 | epot = -11.869252657891 | etot = -8.13378367017951 +330000 ekin = 1.77117100866039 | erot = 1.90323589020173 | epot = -11.808190567859 | etot = -8.13378366899683 +331000 ekin = 1.68023517870726 | erot = 1.90771959426241 | epot = -11.7217384405155 | etot = -8.13378366754586 +332000 ekin = 1.58599656569204 | erot = 1.91066851347972 | epot = -11.6304487455228 | etot = -8.133783666351 +333000 ekin = 1.5056664988971 | erot = 1.91203797344599 | epot = -11.5514881380424 | etot = -8.13378366569929 +334000 ekin = 1.44997196057408 | erot = 1.91073772770832 | epot = -11.494493353844 | etot = -8.1337836655616 +335000 ekin = 1.4217505313958 | erot = 1.90515605629965 | epot = -11.4606902539303 | etot = -8.13378366623481 +336000 ekin = 1.41662531057508 | erot = 1.89330033652335 | epot = -11.4437093137243 | etot = -8.13378366662591 +337000 ekin = 1.42902342419243 | erot = 1.87459660542404 | epot = -11.4374036965643 | etot = -8.13378366694779 +338000 ekin = 1.45347553473645 | erot = 1.84924982279989 | epot = -11.4365090247095 | etot = -8.13378366717319 +339000 ekin = 1.48532648331894 | erot = 1.81789825389434 | epot = -11.4370084045478 | etot = -8.1337836673345 +340000 ekin = 1.52068113212175 | erot = 1.78131054290948 | epot = -11.4357753425064 | etot = -8.13378366747516 +341000 ekin = 1.55606070128483 | erot = 1.74019406298873 | epot = -11.4300384318889 | etot = -8.13378366761538 +342000 ekin = 1.58819693535917 | erot = 1.69515176483016 | epot = -11.4171323679306 | etot = -8.13378366774131 +343000 ekin = 1.61415529814034 | erot = 1.64675903934927 | epot = -11.3946980053052 | etot = -8.13378366781557 +344000 ekin = 1.63171879306421 | erot = 1.59569319793894 | epot = -11.3611956588051 | etot = -8.13378366780194 +345000 ekin = 1.63976605960559 | erot = 1.54282704208372 | epot = -11.3163767693851 | etot = -8.13378366769576 +346000 ekin = 1.63837200137359 | erot = 1.48918714015799 | epot = -11.2613428090531 | etot = -8.13378366752157 +347000 ekin = 1.62852754176565 | erot = 1.43587351563677 | epot = -11.1981847247341 | etot = -8.13378366733164 +348000 ekin = 1.61158889282985 | erot = 1.38392546939002 | epot = -11.1292980293931 | etot = -8.13378366717324 +349000 ekin = 1.58873557439206 | erot = 1.33422850518961 | epot = -11.056747746656 | etot = -8.13378366707429 +350000 ekin = 1.56064786721561 | erot = 1.2874985195824 | epot = -10.9819300538308 | etot = -8.13378366703275 +351000 ekin = 1.52754191191907 | erot = 1.24434620357763 | epot = -10.9056717825112 | etot = -8.13378366701453 +352000 ekin = 1.48960299204932 | erot = 1.20538641996432 | epot = -10.8287730789744 | etot = -8.13378366696075 +353000 ekin = 1.44778264504309 | erot = 1.17134399707567 | epot = -10.752910308907 | etot = -8.13378366678829 +354000 ekin = 1.40533100954915 | erot = 1.14324844921071 | epot = -10.6823631252463 | etot = -8.13378366648643 +355000 ekin = 1.36869095865109 | erot = 1.12250242067869 | epot = -10.6249770453852 | etot = -8.13378366605541 +356000 ekin = 1.3449017599716 | erot = 1.1099299077681 | epot = -10.5886153331872 | etot = -8.13378366544746 +357000 ekin = 1.34315796277545 | erot = 1.10621719878399 | epot = -10.5831588263865 | etot = -8.13378366482704 +358000 ekin = 1.37283801209317 | erot = 1.11171347586627 | epot = -10.6183351524161 | etot = -8.13378366445667 +359000 ekin = 1.43996759059677 | erot = 1.12612871056424 | epot = -10.6998799657489 | etot = -8.13378366458786 +360000 ekin = 1.54388445915395 | erot = 1.14830381563242 | epot = -10.825971940105 | etot = -8.13378366531859 +361000 ekin = 1.6758653151051 | erot = 1.1761890541841 | epot = -10.9858380358604 | etot = -8.13378366657118 +362000 ekin = 1.82005627456863 | erot = 1.20703160752722 | epot = -11.160871550052 | etot = -8.1337836679562 +363000 ekin = 1.95850583938559 | erot = 1.23798141777172 | epot = -11.3302709261716 | etot = -8.13378366901432 +364000 ekin = 2.07580017665441 | erot = 1.26672677094628 | epot = -11.4763106177231 | etot = -8.13378367012237 +365000 ekin = 2.15891662518022 | erot = 1.29173621495106 | epot = -11.5844365106023 | etot = -8.13378367047101 +366000 ekin = 2.20238380195836 | erot = 1.31262064914186 | epot = -11.6487881213328 | etot = -8.13378367023257 +367000 ekin = 2.20851727274821 | erot = 1.33022857587286 | epot = -11.6725295182319 | etot = -8.13378366961086 +368000 ekin = 2.18513118769551 | erot = 1.34632721319444 | epot = -11.6652420695885 | etot = -8.13378366869856 +369000 ekin = 2.14321144645259 | erot = 1.36315448462805 | epot = -11.6401495988847 | etot = -8.13378366780407 +370000 ekin = 2.09388282411743 | erot = 1.38296858719989 | epot = -11.6106350784946 | etot = -8.13378366717728 +371000 ekin = 2.04539161605049 | erot = 1.40758201279954 | epot = -11.5867572956745 | etot = -8.13378366682443 +372000 ekin = 2.00261126513199 | erot = 1.4382705751255 | epot = -11.574665506924 | etot = -8.13378366666651 +373000 ekin = 1.96798302471703 | erot = 1.47584503943857 | epot = -11.5776117307364 | etot = -8.13378366658081 +374000 ekin = 1.94276422014241 | erot = 1.52074221163772 | epot = -11.5972900983287 | etot = -8.13378366654861 +375000 ekin = 1.92741631544937 | erot = 1.57302624844148 | epot = -11.634226230509 | etot = -8.13378366661813 +376000 ekin = 1.92110841837139 | erot = 1.63232320681825 | epot = -11.6872152920392 | etot = -8.13378366684957 +377000 ekin = 1.92083197490845 | erot = 1.69770894534465 | epot = -11.7523245875562 | etot = -8.13378366730306 +378000 ekin = 1.92097158013852 | erot = 1.76763055655063 | epot = -11.8223858045628 | etot = -8.13378366787367 +379000 ekin = 1.91438056919013 | erot = 1.83964318713952 | epot = -11.8878074249811 | etot = -8.13378366865147 +380000 ekin = 1.89241520121845 | erot = 1.91106138177954 | epot = -11.9372602523564 | etot = -8.13378366935838 +381000 ekin = 1.8471184312366 | erot = 1.97933543815608 | epot = -11.9602375392593 | etot = -8.13378366986661 +382000 ekin = 1.77364821790758 | erot = 2.04210934441082 | epot = -11.9495412323761 | etot = -8.13378367005771 +383000 ekin = 1.67178472401187 | erot = 2.09754562137713 | epot = -11.903114015213 | etot = -8.13378366982399 +384000 ekin = 1.54709556482222 | erot = 2.14438708235182 | epot = -11.8252663163943 | etot = -8.13378366922026 +385000 ekin = 1.41093432867773 | erot = 2.18184182145731 | epot = -11.7265598182916 | etot = -8.13378366815656 +386000 ekin = 1.27958936993863 | erot = 2.21051340231469 | epot = -11.6238864391429 | etot = -8.13378366688957 +387000 ekin = 1.17137861197302 | erot = 2.2316316524003 | epot = -11.5367939301643 | etot = -8.13378366579099 +388000 ekin = 1.10179780401003 | erot = 2.24634754527649 | epot = -11.4819290145147 | etot = -8.13378366522816 +389000 ekin = 1.0788214896733 | erot = 2.25505587957397 | epot = -11.4676610376486 | etot = -8.13378366840134 +390000 ekin = 1.07051570136181 | erot = 2.26936424219768 | epot = -11.4736636037098 | etot = -8.13378366015027 +391000 ekin = 1.12513305990266 | erot = 2.2855798798667 | epot = -11.5444966077228 | etot = -8.13378366795344 +392000 ekin = 1.21295440171552 | erot = 2.27063670339911 | epot = -11.6173747716209 | etot = -8.13378366650625 +393000 ekin = 1.30924312365021 | erot = 2.24076930893297 | epot = -11.683796099712 | etot = -8.13378366712886 +394000 ekin = 1.40561895760633 | erot = 2.19794335034293 | epot = -11.7373459753404 | etot = -8.13378366739109 +395000 ekin = 1.49662707239774 | erot = 2.14293675801942 | epot = -11.7733474977531 | etot = -8.13378366733589 +396000 ekin = 1.58077727992374 | erot = 2.07761988891243 | epot = -11.7921808358865 | etot = -8.13378366705035 +397000 ekin = 1.65955042583017 | erot = 2.00469837191324 | epot = -11.7980324643728 | etot = -8.13378366662942 +398000 ekin = 1.7362244798993 | erot = 1.92743077253277 | epot = -11.7974389185788 | etot = -8.13378366614676 +399000 ekin = 1.81471876943507 | erot = 1.84941455049975 | epot = -11.7979169856551 | etot = -8.13378366572026 +400000 ekin = 1.89831345084354 | erot = 1.77428869309741 | epot = -11.8063858093523 | etot = -8.13378366541139 +401000 ekin = 1.9885788216584 | erot = 1.70555701948173 | epot = -11.8279195064184 | etot = -8.13378366527829 +402000 ekin = 2.08469272455109 | erot = 1.64640053761827 | epot = -11.8648769275031 | etot = -8.13378366533375 +403000 ekin = 2.1833349288347 | erot = 1.59947809828207 | epot = -11.9165966926882 | etot = -8.13378366557139 +404000 ekin = 2.27899469656911 | erot = 1.56671457667184 | epot = -11.9794929390997 | etot = -8.13378366585873 +405000 ekin = 2.36506409045595 | erot = 1.5490457214777 | epot = -12.0478934783833 | etot = -8.13378366644961 +406000 ekin = 2.43306193248333 | erot = 1.54630434412746 | epot = -12.1131499437695 | etot = -8.13378366715871 +407000 ekin = 2.4736418637867 | erot = 1.55689186413582 | epot = -12.1643173959421 | etot = -8.13378366801955 +408000 ekin = 2.47760299470359 | erot = 1.57810641384991 | epot = -12.1894930773177 | etot = -8.1337836687642 +409000 ekin = 2.43822850840222 | erot = 1.6066411347602 | epot = -12.1786533122416 | etot = -8.13378366907916 +410000 ekin = 2.35516301277751 | erot = 1.63934184028956 | epot = -12.128288521798 | etot = -8.13378366873093 +411000 ekin = 2.236619522747 | erot = 1.67408087731271 | epot = -12.0444840678061 | etot = -8.13378366774637 +412000 ekin = 2.09851267459564 | erot = 1.71012170018305 | epot = -11.9424180411994 | etot = -8.13378366642075 +413000 ekin = 1.96056484791868 | erot = 1.74778804011944 | epot = -11.8421365531932 | etot = -8.13378366515507 +414000 ekin = 1.84128090479855 | erot = 1.78771082123051 | epot = -11.7627753903003 | etot = -8.13378366427126 +415000 ekin = 1.75390442334931 | erot = 1.83009103155497 | epot = -11.7177791188312 | etot = -8.13378366392693 +416000 ekin = 1.70439570487049 | erot = 1.87425008286763 | epot = -11.7124294518662 | etot = -8.13378366412813 +417000 ekin = 1.69131554252525 | erot = 1.91850147884838 | epot = -11.743600686191 | etot = -8.13378366481735 +418000 ekin = 1.7068949003167 | erot = 1.96025799789886 | epot = -11.8009365639737 | etot = -8.1337836657581 +419000 ekin = 1.73962222230422 | erot = 1.99637255841746 | epot = -11.8697784475116 | etot = -8.13378366678987 +420000 ekin = 1.77669286262646 | erot = 2.02357619715879 | epot = -11.9340527274896 | etot = -8.1337836677043 +421000 ekin = 1.80657824083176 | erot = 2.03903049556404 | epot = -11.9793924047241 | etot = -8.13378366832826 +422000 ekin = 1.82111290086227 | erot = 2.04088419800067 | epot = -11.9957807674367 | etot = -8.13378366857376 +423000 ekin = 1.81648584569124 | erot = 2.02865244730067 | epot = -11.978921961452 | etot = -8.1337836684601 +424000 ekin = 1.79301691785737 | erot = 2.00326876348565 | epot = -11.9300693494177 | etot = -8.13378366807468 +425000 ekin = 1.75424046968995 | erot = 1.96680784721923 | epot = -11.854831984418 | etot = -8.13378366750887 +426000 ekin = 1.70601392330414 | erot = 1.92202692836578 | epot = -11.761824518498 | etot = -8.13378366682806 +427000 ekin = 1.65580906014457 | erot = 1.87186985440495 | epot = -11.6614625806883 | etot = -8.13378366613882 +428000 ekin = 1.61207963971218 | erot = 1.81905558541467 | epot = -11.5649188905637 | etot = -8.13378366543682 +429000 ekin = 1.58339999424807 | erot = 1.76579893170898 | epot = -11.4829825908685 | etot = -8.13378366491148 +430000 ekin = 1.57646033949475 | erot = 1.71346152698448 | epot = -11.4237055311813 | etot = -8.13378366470211 +431000 ekin = 1.59418488212815 | erot = 1.66239892771949 | epot = -11.3903674747378 | etot = -8.13378366489016 +432000 ekin = 1.63452809773604 | erot = 1.61205574803078 | epot = -11.3803675112004 | etot = -8.13378366543362 +433000 ekin = 1.6907741097856 | erot = 1.56136635609577 | epot = -11.3859241320225 | etot = -8.13378366614116 +434000 ekin = 1.75368500743944 | erot = 1.50939558465358 | epot = -11.3968642588286 | etot = -8.13378366673553 +435000 ekin = 1.81477188942094 | erot = 1.45598133798856 | epot = -11.4045368944125 | etot = -8.13378366700299 +436000 ekin = 1.868951512286 | erot = 1.40204530896986 | epot = -11.4047804880924 | etot = -8.1337836668365 +437000 ekin = 1.91551323813531 | erot = 1.34941425922493 | epot = -11.3987111639494 | etot = -8.13378366658913 +438000 ekin = 1.95545357705846 | erot = 1.30011080732735 | epot = -11.3893480508668 | etot = -8.13378366648095 +439000 ekin = 1.98811153075007 | erot = 1.25557284832967 | epot = -11.3774680457267 | etot = -8.133783666647 +440000 ekin = 2.0098662343534 | erot = 1.21630204160295 | epot = -11.3599519429522 | etot = -8.13378366699586 +441000 ekin = 2.01530350765085 | erot = 1.18202297032189 | epot = -11.3311101452617 | etot = -8.13378366728898 +442000 ekin = 1.99936349678345 | erot = 1.1520787313769 | epot = -11.2852258960153 | etot = -8.13378366785493 +443000 ekin = 1.95696749681153 | erot = 1.12547607063661 | epot = -11.2162272349774 | etot = -8.13378366752924 +444000 ekin = 1.89166490098686 | erot = 1.10194461447725 | epot = -11.1273931823252 | etot = -8.13378366686104 +445000 ekin = 1.81328868644697 | erot = 1.08168732032465 | epot = -11.0287596725663 | etot = -8.13378366579468 +446000 ekin = 1.73577899474806 | erot = 1.06505071492859 | epot = -10.9346133747235 | etot = -8.13378366504681 +447000 ekin = 1.67093185588937 | erot = 1.0523970512701 | epot = -10.8571125714719 | etot = -8.13378366431241 +448000 ekin = 1.62911856819559 | erot = 1.04409603312767 | epot = -10.8069982651711 | etot = -8.13378366384786 +449000 ekin = 1.61731626296897 | erot = 1.04041489697302 | epot = -10.7915148237039 | etot = -8.13378366376191 +450000 ekin = 1.63711697605421 | erot = 1.04135992229816 | epot = -10.8122605626979 | etot = -8.13378366434548 +451000 ekin = 1.68320258141919 | erot = 1.04620824656711 | epot = -10.8631944930203 | etot = -8.13378366503397 +452000 ekin = 1.7458166801167 | erot = 1.05391169410331 | epot = -10.9335120399999 | etot = -8.13378366577991 +453000 ekin = 1.81457146100864 | erot = 1.0633516586371 | epot = -11.0117067861248 | etot = -8.13378366647908 +454000 ekin = 1.87975957939219 | erot = 1.07317402238826 | epot = -11.0867172689166 | etot = -8.13378366713614 +455000 ekin = 1.93251877589105 | erot = 1.08171623325851 | epot = -11.14801867696 | etot = -8.13378366781044 +456000 ekin = 1.96415416828293 | erot = 1.08704156959223 | epot = -11.1849794063765 | etot = -8.13378366850134 +457000 ekin = 1.96605348078635 | erot = 1.08723394294624 | epot = -11.1870710928035 | etot = -8.13378366907089 +458000 ekin = 1.93127523762167 | erot = 1.08096076790852 | epot = -11.146019674794 | etot = -8.13378366926382 +459000 ekin = 1.85771594839783 | erot = 1.06809531781133 | epot = -11.0595949350342 | etot = -8.13378366882506 +460000 ekin = 1.7514718808334 | erot = 1.05009293158724 | epot = -10.9353484800663 | etot = -8.13378366764562 +461000 ekin = 1.62834142732817 | erot = 1.02990811326759 | epot = -10.792033206498 | etot = -8.13378366590223 +462000 ekin = 1.51195360646361 | erot = 1.01153881174671 | epot = -10.657276081187 | etot = -8.13378366297666 +463000 ekin = 1.43011910142227 | erot = 1.00022578453976 | epot = -10.5641285481373 | etot = -8.13378366217527 +464000 ekin = 1.39582910826184 | erot = 0.99819843207832 | epot = -10.5278112021912 | etot = -8.13378366185106 +465000 ekin = 1.41007554849414 | erot = 1.00592009003254 | epot = -10.5497793012305 | etot = -8.13378366270381 +466000 ekin = 1.46251969360502 | erot = 1.02219738030467 | epot = -10.618500737861 | etot = -8.13378366395135 +467000 ekin = 1.49627186606495 | erot = 1.05472101828711 | epot = -10.6847765486757 | etot = -8.13378366432368 +468000 ekin = 1.5172585367749 | erot = 1.12479885673277 | epot = -10.7758410580437 | etot = -8.13378366453599 +469000 ekin = 1.58140637752447 | erot = 1.16828828956652 | epot = -10.8834783315731 | etot = -8.13378366448215 +470000 ekin = 1.60068578294838 | erot = 1.1811414101898 | epot = -10.9156108574881 | etot = -8.13378366434993 +471000 ekin = 1.59076368321379 | erot = 1.18707237244891 | epot = -10.9116197193634 | etot = -8.13378366370067 +472000 ekin = 1.56124060593966 | erot = 1.18572143099144 | epot = -10.8807456997246 | etot = -8.13378366279351 +473000 ekin = 1.52502097405344 | erot = 1.17792025679204 | epot = -10.8367248926809 | etot = -8.13378366183544 +474000 ekin = 1.49533177220178 | erot = 1.16544446211716 | epot = -10.7945598952744 | etot = -8.13378366095546 +475000 ekin = 1.48386630171196 | erot = 1.15068540213872 | epot = -10.7683353640892 | etot = -8.13378366023852 +476000 ekin = 1.49971334629294 | erot = 1.13623821676371 | epot = -10.7697352228004 | etot = -8.13378365974378 +477000 ekin = 1.5487111876754 | erot = 1.12448433351201 | epot = -10.8069791812994 | etot = -8.13378366011195 +478000 ekin = 1.62953491120082 | erot = 1.11764268902012 | epot = -10.880961260461 | etot = -8.13378366024004 +479000 ekin = 1.73735741645227 | erot = 1.11700620809668 | epot = -10.9881472852153 | etot = -8.13378366066638 +480000 ekin = 1.86556210290876 | erot = 1.12262064773414 | epot = -11.1219664120758 | etot = -8.13378366143285 +481000 ekin = 2.0012102633565 | erot = 1.13364860019954 | epot = -11.2686425499223 | etot = -8.13378368636626 +482000 ekin = 2.04617329746653 | erot = 1.16256926174411 | epot = -11.342526223698 | etot = -8.13378366448739 +483000 ekin = 2.14335261841872 | erot = 1.21476273134234 | epot = -11.4918990326703 | etot = -8.1337836829092 +484000 ekin = 2.2027099535494 | erot = 1.23147381805091 | epot = -11.5679674446188 | etot = -8.13378367301852 +485000 ekin = 2.20682939439848 | erot = 1.23835798980262 | epot = -11.5789710574533 | etot = -8.13378367325215 +486000 ekin = 2.16589682793162 | erot = 1.24300370550065 | epot = -11.5426842062608 | etot = -8.13378367282853 +487000 ekin = 2.08668888863795 | erot = 1.24625551750431 | epot = -11.4667280779886 | etot = -8.13378367184635 +488000 ekin = 1.98386509123788 | erot = 1.24977318045064 | epot = -11.3674219422116 | etot = -8.13378367052306 +489000 ekin = 1.87707931029328 | erot = 1.2554701277229 | epot = -11.2663331071765 | etot = -8.13378366916032 +490000 ekin = 1.78677596315576 | erot = 1.26490338720787 | epot = -11.18546301849 | etot = -8.13378366812638 +491000 ekin = 1.72903831212643 | erot = 1.27867004037192 | epot = -11.1414920202968 | etot = -8.13378366779847 +492000 ekin = 1.71039979056492 | erot = 1.29591768106643 | epot = -11.1401011400508 | etot = -8.13378366841942 +493000 ekin = 1.72454317155186 | erot = 1.31423280426535 | epot = -11.1725596457207 | etot = -8.13378366990352 +494000 ekin = 1.75332785015175 | erot = 1.33022406246905 | epot = -11.2173355843429 | etot = -8.13378367172206 +495000 ekin = 1.77349565826268 | erot = 1.34086561473946 | epot = -11.2481449460395 | etot = -8.13378367303734 +496000 ekin = 1.76725059669556 | erot = 1.34512484287844 | epot = -11.2461591127246 | etot = -8.13378367315062 +497000 ekin = 1.73127637992372 | erot = 1.3449470821372 | epot = -11.2100071340228 | etot = -8.13378367196192 +498000 ekin = 1.67855000911927 | erot = 1.34489121266193 | epot = -11.1572248918172 | etot = -8.13378367003596 +499000 ekin = 1.63191747123612 | erot = 1.35056727534945 | epot = -11.1162684147987 | etot = -8.13378366821311 +500000 ekin = 1.61378359993279 | erot = 1.36676364682918 | epot = -11.1143309139126 | etot = -8.13378366715064 +501000 ekin = 1.63758101989971 | erot = 1.39609850677659 | epot = -11.1674631937776 | etot = -8.13378366710128 +502000 ekin = 1.7041380754091 | erot = 1.43847493669618 | epot = -11.2763966800725 | etot = -8.13378366796721 +503000 ekin = 1.8026829774481 | erot = 1.49115460253573 | epot = -11.4276212494754 | etot = -8.13378366949159 +504000 ekin = 1.91419549774104 | erot = 1.54914693963144 | epot = -11.5971261087994 | etot = -8.13378367142688 +505000 ekin = 2.01490443991482 | erot = 1.60576406503001 | epot = -11.754452178485 | etot = -8.13378367354016 +506000 ekin = 2.07966541463625 | erot = 1.6534543935245 | epot = -11.8669034835998 | etot = -8.13378367543904 +507000 ekin = 2.08700353889804 | erot = 1.68517460627827 | epot = -11.905961821654 | etot = -8.13378367647772 +508000 ekin = 2.02663352657019 | erot = 1.69625747622173 | epot = -11.85667467886 | etot = -8.1337836760681 +509000 ekin = 1.90589064129068 | erot = 1.68599529701607 | epot = -11.7256696124933 | etot = -8.13378367418656 +510000 ekin = 1.74959091228785 | erot = 1.65787688252651 | epot = -11.5412514662799 | etot = -8.1337836714656 +511000 ekin = 1.59231955656531 | erot = 1.61826266731375 | epot = -11.3443658926551 | etot = -8.13378366877608 +512000 ekin = 1.46755856058862 | erot = 1.57434662380559 | epot = -11.1756888512756 | etot = -8.13378366688141 +513000 ekin = 1.3983991609188 | erot = 1.53234768378053 | epot = -11.0645305108086 | etot = -8.13378366610923 +514000 ekin = 1.39338903684995 | erot = 1.49706258345062 | epot = -11.0242352864559 | etot = -8.13378366615529 +515000 ekin = 1.44495159059745 | erot = 1.47110271003594 | epot = -11.0498379681943 | etot = -8.13378366756095 +516000 ekin = 1.53288312818407 | erot = 1.45357064725072 | epot = -11.120237444821 | etot = -8.1337836693862 +517000 ekin = 1.63159033308467 | erot = 1.44224294473458 | epot = -11.2076169491972 | etot = -8.13378367137799 +518000 ekin = 1.71409401451017 | erot = 1.43408399436441 | epot = -11.2819616821124 | etot = -8.1337836732378 +519000 ekin = 1.75665192751476 | erot = 1.42579002917521 | epot = -11.3162256316872 | etot = -8.13378367499721 +520000 ekin = 1.74187345942302 | erot = 1.4150483977562 | epot = -11.290705532384 | etot = -8.13378367520473 +521000 ekin = 1.66871703035345 | erot = 1.40071550596687 | epot = -11.2032162100692 | etot = -8.13378367374886 +522000 ekin = 1.55952182851144 | erot = 1.38339983651153 | epot = -11.076705336162 | etot = -8.13378367113905 +523000 ekin = 1.45114556546891 | erot = 1.36568308066248 | epot = -10.9506123145881 | etot = -8.13378366845668 +524000 ekin = 1.38091842208311 | erot = 1.35134919392548 | epot = -10.8660512824539 | etot = -8.13378366644529 +525000 ekin = 1.37601425586908 | erot = 1.34456662957931 | epot = -10.8543645508583 | etot = -8.13378366540993 +526000 ekin = 1.44870428480397 | erot = 1.3490974018157 | epot = -10.9315853521301 | etot = -8.13378366551039 +527000 ekin = 1.59459863542106 | erot = 1.36714947554628 | epot = -11.0955317778806 | etot = -8.13378366691328 +528000 ekin = 1.79183405476432 | erot = 1.3984190459615 | epot = -11.3240367701436 | etot = -8.13378366941776 +529000 ekin = 2.00478978691934 | erot = 1.43972835790867 | epot = -11.5783018171981 | etot = -8.1337836723701 +530000 ekin = 2.19333795595321 | erot = 1.48552207661414 | epot = -11.8126437074557 | etot = -8.13378367488839 +531000 ekin = 2.32431476959198 | erot = 1.52928747159335 | epot = -11.9873859174739 | etot = -8.1337836762886 +532000 ekin = 2.37971447232121 | erot = 1.56539257222041 | epot = -12.0788907209954 | etot = -8.13378367645378 +533000 ekin = 2.35771666710421 | erot = 1.59048999444787 | epot = -12.0819903372149 | etot = -8.13378367566285 +534000 ekin = 2.26899715445284 | erot = 1.6040739436389 | epot = -12.0068547722234 | etot = -8.13378367413165 +535000 ekin = 2.13365177457976 | erot = 1.60831072467296 | epot = -11.8757461712746 | etot = -8.13378367202191 +536000 ekin = 1.9788637616776 | erot = 1.60719127872978 | epot = -11.7198387101354 | etot = -8.13378366972798 +537000 ekin = 1.8342188731736 | erot = 1.60523898307311 | epot = -11.5732415240101 | etot = -8.13378366776342 +538000 ekin = 1.72531720896728 | erot = 1.60632519295185 | epot = -11.4654260684293 | etot = -8.13378366651021 +539000 ekin = 1.66856519910959 | erot = 1.6130147293602 | epot = -11.4153635945921 | etot = -8.13378366612229 +540000 ekin = 1.66907056573982 | erot = 1.62662968770416 | epot = -11.4294839196051 | etot = -8.13378366616113 +541000 ekin = 1.72153495933529 | erot = 1.64788745991001 | epot = -11.5032060865927 | etot = -8.13378366734736 +542000 ekin = 1.80903650503412 | erot = 1.6754786968445 | epot = -11.6182988707897 | etot = -8.13378366891109 +543000 ekin = 1.90894616841981 | erot = 1.70734508951571 | epot = -11.7500749284691 | etot = -8.13378367053359 +544000 ekin = 1.9977784284566 | erot = 1.7412535778407 | epot = -11.8728156782151 | etot = -8.13378367191784 +545000 ekin = 2.05546409380151 | erot = 1.77521000039075 | epot = -11.9644577670256 | etot = -8.13378367283337 +546000 ekin = 2.06867595318427 | erot = 1.8077948361107 | epot = -12.0102544624496 | etot = -8.13378367315459 +547000 ekin = 2.03267806249103 | erot = 1.83838588999474 | epot = -12.0048476253515 | etot = -8.13378367286575 +548000 ekin = 1.95148731422974 | erot = 1.86718390883231 | epot = -11.9524548951631 | etot = -8.13378367210101 +549000 ekin = 1.83645042329695 | erot = 1.89487456519915 | epot = -11.8651086595307 | etot = -8.13378367103455 +550000 ekin = 1.70373130492655 | erot = 1.92233248819948 | epot = -11.7598474630006 | etot = -8.13378366987457 +551000 ekin = 1.57139422776027 | erot = 1.95024291866776 | epot = -11.6554208152369 | etot = -8.13378366880886 +552000 ekin = 1.45663332550624 | erot = 1.97878558861136 | epot = -11.5692025821088 | etot = -8.13378366799115 +553000 ekin = 1.37337409011331 | erot = 2.00744335363611 | epot = -11.5146011112929 | etot = -8.13378366754347 +554000 ekin = 1.33029485853917 | erot = 2.03496657143245 | epot = -11.4990450975128 | etot = -8.13378366754123 +555000 ekin = 1.32945359618133 | erot = 2.05953157374214 | epot = -11.5227688379176 | etot = -8.13378366799412 +556000 ekin = 1.3658906875148 | erot = 2.07909837607864 | epot = -11.5787727324011 | etot = -8.13378366880768 +557000 ekin = 1.42857577080555 | erot = 2.09193210845994 | epot = -11.654291549064 | etot = -8.13378366979846 +558000 ekin = 1.50275359963189 | erot = 2.0971531413961 | epot = -11.7336904117562 | etot = -8.13378367072818 +559000 ekin = 1.57321830908804 | erot = 2.09511862189364 | epot = -11.8021206023738 | etot = -8.13378367139213 +560000 ekin = 1.62740172366322 | erot = 2.08745496893435 | epot = -11.8486403643216 | etot = -8.13378367172406 +561000 ekin = 1.6569241619188 | erot = 2.07666092047753 | epot = -11.8673687542002 | etot = -8.1337836718039 +562000 ekin = 1.65737426360166 | erot = 2.06544534214746 | epot = -11.8566032774781 | etot = -8.13378367172896 +563000 ekin = 1.62727808432428 | erot = 2.05615555038321 | epot = -11.8172173064911 | etot = -8.13378367178356 +564000 ekin = 1.5667993306087 | erot = 2.05047511799702 | epot = -11.7510581199544 | etot = -8.1337836713487 +565000 ekin = 1.48206055333278 | erot = 2.04917576858652 | epot = -11.6650199925621 | etot = -8.13378367064282 +566000 ekin = 1.3842386654693 | erot = 2.05221850150277 | epot = -11.5702408367517 | etot = -8.13378366977965 +567000 ekin = 1.28749391779178 | erot = 2.05873429505346 | epot = -11.4800118818273 | etot = -8.13378366898202 +568000 ekin = 1.2057043109891 | erot = 2.0670569203391 | epot = -11.4065448997816 | etot = -8.1337836684534 +569000 ekin = 1.14918558015273 | erot = 2.07495244466074 | epot = -11.3579216930989 | etot = -8.1337836682854 +570000 ekin = 1.12276449635449 | erot = 2.0800727296242 | epot = -11.3366208944198 | etot = -8.13378366844112 +571000 ekin = 1.12567595859586 | erot = 2.08050218013897 | epot = -11.3399618075315 | etot = -8.13378366879663 +572000 ekin = 1.1529490339776 | erot = 2.07519259345466 | epot = -11.3619252966304 | etot = -8.13378366919819 +573000 ekin = 1.19838854906436 | erot = 2.06451015559051 | epot = -11.3966823738791 | etot = -8.13378366922423 +574000 ekin = 1.25460427378267 | erot = 2.04968889739192 | epot = -11.4380768406972 | etot = -8.13378366952262 +575000 ekin = 1.31454735686527 | erot = 2.03199549863397 | epot = -11.4803265250284 | etot = -8.13378366952915 +576000 ekin = 1.37512583604677 | erot = 2.01319845741894 | epot = -11.5221079627672 | etot = -8.13378366930153 +577000 ekin = 1.43682760498694 | erot = 1.99528982935438 | epot = -11.5659011033024 | etot = -8.13378366896105 +578000 ekin = 1.50235588199447 | erot = 1.98017269183556 | epot = -11.616312242452 | etot = -8.13378366862198 +579000 ekin = 1.57520818416169 | erot = 1.96938672248033 | epot = -11.6783785749975 | etot = -8.13378366835543 +580000 ekin = 1.65868462493906 | erot = 1.9639024985825 | epot = -11.7563707921581 | etot = -8.13378366863655 +581000 ekin = 1.7524731182851 | erot = 1.96419308535396 | epot = -11.8504498724997 | etot = -8.13378366886061 +582000 ekin = 1.85283782860401 | erot = 1.96967477642142 | epot = -11.9562962744009 | etot = -8.13378366937544 +583000 ekin = 1.95429754600633 | erot = 1.97826405495829 | epot = -12.0663452712864 | etot = -8.13378367032182 +584000 ekin = 2.04662916575505 | erot = 1.98631443704456 | epot = -12.1667272745676 | etot = -8.13378367176799 +585000 ekin = 2.11419694674586 | erot = 1.98862566441948 | epot = -12.2366062847012 | etot = -8.13378367353588 +586000 ekin = 2.13871236990616 | erot = 1.97915340580579 | epot = -12.2516494507903 | etot = -8.13378367507837 +587000 ekin = 2.10465783249031 | erot = 1.95256271521597 | epot = -12.1910042235944 | etot = -8.13378367588808 +588000 ekin = 2.00543191749281 | erot = 1.90599988275355 | epot = -12.0452154755214 | etot = -8.13378367527503 +589000 ekin = 1.8511544610365 | erot = 1.84021509333331 | epot = -11.825153227644 | etot = -8.13378367327421 +590000 ekin = 1.66921622807598 | erot = 1.75933351100741 | epot = -11.5623334094729 | etot = -8.13378367038948 +591000 ekin = 1.49774854838559 | erot = 1.66961531489179 | epot = -11.3011475307624 | etot = -8.13378366748502 +592000 ekin = 1.37418208601873 | erot = 1.57786762195817 | epot = -11.0858333734942 | etot = -8.13378366551733 +593000 ekin = 1.32230765436322 | erot = 1.49017042363896 | epot = -10.9462617430768 | etot = -8.13378366507467 +594000 ekin = 1.34433584584019 | erot = 1.41110289033496 | epot = -10.8892224022084 | etot = -8.13378366603329 +595000 ekin = 1.42313762143471 | erot = 1.34352894991733 | epot = -10.9004502389322 | etot = -8.13378366758016 +596000 ekin = 1.53140640358131 | erot = 1.2890571416043 | epot = -10.9542472149073 | etot = -8.13378366972164 +597000 ekin = 1.63793776664774 | erot = 1.24822708395987 | epot = -11.0199485217458 | etot = -8.13378367113819 +598000 ekin = 1.71853369495733 | erot = 1.22042305582434 | epot = -11.0727404229298 | etot = -8.13378367214814 +599000 ekin = 1.75676579669885 | erot = 1.20417119496498 | epot = -11.0947206643965 | etot = -8.13378367273266 +600000 ekin = 1.74415562348135 | erot = 1.1974850125625 | epot = -11.075424308856 | etot = -8.13378367281218 +601000 ekin = 1.68078686624576 | erot = 1.19842786466352 | epot = -11.0129984031935 | etot = -8.1337836722842 +602000 ekin = 1.57592768461686 | erot = 1.20571835982337 | epot = -10.9154297155778 | etot = -8.13378367113754 +603000 ekin = 1.44736021986067 | erot = 1.219065566651 | epot = -10.8002094560796 | etot = -8.13378366956792 +604000 ekin = 1.31829530122973 | erot = 1.239006327198 | epot = -10.6910852964092 | etot = -8.13378366798146 +605000 ekin = 1.21203583247681 | erot = 1.2662501819561 | epot = -10.6120696811917 | etot = -8.13378366675881 +606000 ekin = 1.14717881945288 | erot = 1.30114918573328 | epot = -10.5821116711666 | etot = -8.13378366598041 +607000 ekin = 1.13493137972343 | erot = 1.34344256501509 | epot = -10.6121576106477 | etot = -8.13378366590919 +608000 ekin = 1.17769398077533 | erot = 1.39211398656236 | epot = -10.7035916336402 | etot = -8.13378366630252 +609000 ekin = 1.27083042499585 | erot = 1.44572829443775 | epot = -10.8503423865119 | etot = -8.13378366707829 +610000 ekin = 1.40359308955129 | erot = 1.50241692809269 | epot = -11.0397936861517 | etot = -8.13378366850774 +611000 ekin = 1.55996607948005 | erot = 1.55982171141016 | epot = -11.2535714606557 | etot = -8.13378366976554 +612000 ekin = 1.72323074886143 | erot = 1.61567444069886 | epot = -11.4726888606515 | etot = -8.13378367109119 +613000 ekin = 1.87623356286683 | erot = 1.66732234626383 | epot = -11.6773395815193 | etot = -8.13378367238861 +614000 ekin = 2.00332542688185 | erot = 1.71185786773203 | epot = -11.8489669679314 | etot = -8.13378367331747 +615000 ekin = 2.09384471070049 | erot = 1.74706892488305 | epot = -11.9746973091783 | etot = -8.13378367359473 +616000 ekin = 2.14582652013453 | erot = 1.77208418553175 | epot = -12.051694378684 | etot = -8.13378367301775 +617000 ekin = 2.16764032553334 | erot = 1.78786476156788 | epot = -12.0892887588997 | etot = -8.1337836717985 +618000 ekin = 2.17543321837147 | erot = 1.79702594195609 | epot = -12.106242830678 | etot = -8.13378367035041 +619000 ekin = 2.18765015124708 | erot = 1.80309631576443 | epot = -12.124530136231 | etot = -8.13378366921951 +620000 ekin = 2.21827388574176 | erot = 1.80941579610145 | epot = -12.1614733506006 | etot = -8.13378366875735 +621000 ekin = 2.27256724282942 | erot = 1.81817906104524 | epot = -12.2245299729043 | etot = -8.13378366902961 +622000 ekin = 2.34686215364278 | erot = 1.82980019931868 | epot = -12.3104460228466 | etot = -8.13378366988515 +623000 ekin = 2.43079483956968 | erot = 1.84272954676688 | epot = -12.407308057431 | etot = -8.13378367109447 +624000 ekin = 2.5107485939494 | erot = 1.85365912852436 | epot = -12.4981913948138 | etot = -8.13378367234005 +625000 ekin = 2.57376014755793 | erot = 1.85839628627515 | epot = -12.5659401070222 | etot = -8.13378367318914 +626000 ekin = 2.61178608743946 | erot = 1.85335246048788 | epot = -12.5989222212562 | etot = -8.1337836733289 +627000 ekin = 2.62439666916913 | erot = 1.83675929859851 | epot = -12.5949396406052 | etot = -8.13378367283753 +628000 ekin = 2.61715143118485 | erot = 1.80883297815135 | epot = -12.5597680815541 | etot = -8.13378367221788 +629000 ekin = 2.5961400278194 | erot = 1.77076928023034 | epot = -12.5006929799836 | etot = -8.1337836719339 +630000 ekin = 2.56316564610313 | erot = 1.72368862274152 | epot = -12.4206379408855 | etot = -8.13378367204083 +631000 ekin = 2.51545670841564 | erot = 1.66841938706966 | epot = -12.3176597677318 | etot = -8.1337836722465 +632000 ekin = 2.44898106285635 | erot = 1.60594586088114 | epot = -12.1887105959866 | etot = -8.13378367224906 +633000 ekin = 2.36287257799253 | erot = 1.53782426740558 | epot = -12.0344805167525 | etot = -8.13378367135442 +634000 ekin = 2.26405242525323 | erot = 1.46623278033278 | epot = -11.8640688761674 | etot = -8.13378367058136 +635000 ekin = 2.16101755721062 | erot = 1.39475566090543 | epot = -11.689556887824 | etot = -8.13378366970794 +636000 ekin = 2.06475253331495 | erot = 1.32686506236116 | epot = -11.5254012642683 | etot = -8.13378366859223 +637000 ekin = 1.98973271035859 | erot = 1.26596624430372 | epot = -11.3894826221168 | etot = -8.13378366745444 +638000 ekin = 1.95146778320796 | erot = 1.21514985244285 | epot = -11.3004013022814 | etot = -8.1337836666306 +639000 ekin = 1.96182069134296 | erot = 1.17695161175767 | epot = -11.2725559692828 | etot = -8.13378366618221 +640000 ekin = 2.02679898931111 | erot = 1.152391839021 | epot = -11.3129744949044 | etot = -8.13378366657234 +641000 ekin = 2.14199910311537 | erot = 1.1407108655517 | epot = -11.4164936363111 | etot = -8.13378366764398 +642000 ekin = 2.29285046318449 | erot = 1.13915186809975 | epot = -11.5657860007392 | etot = -8.133783669455 +643000 ekin = 2.45552552113726 | erot = 1.14338828231893 | epot = -11.732697475068 | etot = -8.13378367161177 +644000 ekin = 2.60133752585675 | erot = 1.14835367489798 | epot = -11.8834748743413 | etot = -8.13378367358661 +645000 ekin = 2.70371430395706 | erot = 1.14938437136576 | epot = -11.9868823501984 | etot = -8.13378367487555 +646000 ekin = 2.7446360756213 | erot = 1.14332224210791 | epot = -12.0217419929408 | etot = -8.13378367521164 +647000 ekin = 2.71817787240185 | erot = 1.12915792948806 | epot = -11.9811194765204 | etot = -8.13378367463047 +648000 ekin = 2.63028246068798 | erot = 1.10798613628602 | epot = -11.8720522703656 | etot = -8.13378367339156 +649000 ekin = 2.49559189349663 | erot = 1.0824532824775 | epot = -11.7118288478354 | etot = -8.13378367186126 +650000 ekin = 2.33293161556148 | erot = 1.05592857138796 | epot = -11.5226438573172 | etot = -8.13378367036778 +651000 ekin = 2.16312160404172 | erot = 1.03179243272167 | epot = -11.3286977054102 | etot = -8.13378366864681 +652000 ekin = 2.00437764472204 | erot = 1.0126334647906 | epot = -11.150794777641 | etot = -8.13378366812837 +653000 ekin = 1.8632014818754 | erot = 0.999771298705831 | epot = -10.9967564485357 | etot = -8.13378366795446 +654000 ekin = 1.74159938814677 | erot = 0.993638993438291 | epot = -10.8690220496012 | etot = -8.13378366801616 +655000 ekin = 1.63877614369834 | erot = 0.99396111064847 | epot = -10.7665209225295 | etot = -8.13378366818269 +656000 ekin = 1.55293696395135 | erot = 0.99997775151372 | epot = -10.6866983837903 | etot = -8.13378366832522 +657000 ekin = 1.48301105567609 | erot = 1.01069155842698 | epot = -10.627486282448 | etot = -8.13378366834489 +658000 ekin = 1.42991653837067 | erot = 1.02511295996319 | epot = -10.5888131665295 | etot = -8.13378366819568 +659000 ekin = 1.39703562138715 | erot = 1.04246417558196 | epot = -10.5732834648756 | etot = -8.13378366790645 +660000 ekin = 1.38964145717507 | erot = 1.06228082952887 | epot = -10.5857059542688 | etot = -8.13378366756489 +661000 ekin = 1.41337783446074 | erot = 1.08434723262789 | epot = -10.6315087344838 | etot = -8.13378366739522 +662000 ekin = 1.47169034623175 | erot = 1.10850483088196 | epot = -10.7139788446653 | etot = -8.13378366755156 +663000 ekin = 1.56097330117258 | erot = 1.13389735848915 | epot = -10.8286543284501 | etot = -8.13378366878835 +664000 ekin = 1.66624490141573 | erot = 1.15850228671561 | epot = -10.9585308578551 | etot = -8.13378366972376 +665000 ekin = 1.77303863683344 | erot = 1.18152952436704 | epot = -11.0883518320138 | etot = -8.13378367081329 +666000 ekin = 1.86640057267678 | erot = 1.20258304577907 | epot = -11.2027672900442 | etot = -8.13378367158832 +667000 ekin = 1.9346641284443 | erot = 1.22193419209587 | epot = -11.290381992343 | etot = -8.13378367180279 +668000 ekin = 1.97306030160823 | erot = 1.24062017117798 | epot = -11.3474641442117 | etot = -8.13378367142545 +669000 ekin = 1.98443783015199 | erot = 1.26004202123897 | epot = -11.3782635220731 | etot = -8.13378367068217 +670000 ekin = 1.97652861960561 | erot = 1.28134194903652 | epot = -11.3916542388221 | etot = -8.13378367017995 +671000 ekin = 1.95649579507403 | erot = 1.30490078081445 | epot = -11.3951802456603 | etot = -8.1337836697718 +672000 ekin = 1.92875532524812 | erot = 1.33065660860772 | epot = -11.3931956034157 | etot = -8.13378366955981 +673000 ekin = 1.89553670234891 | erot = 1.35854540532999 | epot = -11.3878657771455 | etot = -8.13378366946663 +674000 ekin = 1.85764904371203 | erot = 1.38884570042997 | epot = -11.3802784134864 | etot = -8.13378366934444 +675000 ekin = 1.81704545016694 | erot = 1.42228413602671 | epot = -11.3731132554539 | etot = -8.1337836692603 +676000 ekin = 1.7750503130216 | erot = 1.45971003520997 | epot = -11.3685440173268 | etot = -8.1337836690952 +677000 ekin = 1.73347451738065 | erot = 1.50191216830985 | epot = -11.3691703546418 | etot = -8.13378366895131 +678000 ekin = 1.69449339358072 | erot = 1.54922606356397 | epot = -11.3775031260608 | etot = -8.13378366891607 +679000 ekin = 1.65969071095476 | erot = 1.60118456835957 | epot = -11.3946589483456 | etot = -8.13378366903128 +680000 ekin = 1.62957005386514 | erot = 1.65634116856091 | epot = -11.419694891712 | etot = -8.13378366928597 +681000 ekin = 1.60362252583862 | erot = 1.71228358650055 | epot = -11.4496897819657 | etot = -8.13378366962654 +682000 ekin = 1.58083074260915 | erot = 1.76582826436645 | epot = -11.4804426769555 | etot = -8.13378366997985 +683000 ekin = 1.56032431143573 | erot = 1.81338479145877 | epot = -11.5074927731734 | etot = -8.13378367027887 +684000 ekin = 1.54183455731289 | erot = 1.8514263216931 | epot = -11.527044549832 | etot = -8.13378367082606 +685000 ekin = 1.52410759953354 | erot = 1.87642082982803 | epot = -11.5343121004945 | etot = -8.13378367113297 +686000 ekin = 1.5049437943135 | erot = 1.88570070113279 | epot = -11.5244281668467 | etot = -8.13378367140037 +687000 ekin = 1.48208036602091 | erot = 1.87831367877112 | epot = -11.4941777163977 | etot = -8.13378367160572 +688000 ekin = 1.45289287170997 | erot = 1.85497856858115 | epot = -11.4416551119339 | etot = -8.13378367164282 +689000 ekin = 1.41601907826878 | erot = 1.8181143733986 | epot = -11.3679171230061 | etot = -8.13378367133873 +690000 ekin = 1.37394775601603 | erot = 1.77166312482271 | epot = -11.279394551396 | etot = -8.13378367055722 +691000 ekin = 1.33508615026709 | erot = 1.72071496345702 | epot = -11.1895847830556 | etot = -8.1337836693315 +692000 ekin = 1.31344376462008 | erot = 1.6709415973921 | epot = -11.118169029959 | etot = -8.13378366794681 +693000 ekin = 1.32488046352489 | erot = 1.62783697427223 | epot = -11.0865011046813 | etot = -8.13378366688415 +694000 ekin = 1.38078608515558 | erot = 1.59583179962592 | epot = -11.1104015514061 | etot = -8.13378366662458 +695000 ekin = 1.4819286119433 | erot = 1.57745304972118 | epot = -11.1931653290714 | etot = -8.13378366740697 +696000 ekin = 1.61569966782267 | erot = 1.57278041413535 | epot = -11.3222637510478 | etot = -8.13378366908982 +697000 ekin = 1.75843097225773 | erot = 1.5794352070708 | epot = -11.4716498505421 | etot = -8.13378367121361 +698000 ekin = 1.88185215243157 | erot = 1.59316882050077 | epot = -11.6088046461155 | etot = -8.13378367318316 +699000 ekin = 1.96106579222868 | erot = 1.60896306328376 | epot = -11.7038125299747 | etot = -8.13378367446226 +700000 ekin = 1.98131680928092 | erot = 1.62236339268018 | epot = -11.7374638766874 | etot = -8.13378367472627 +701000 ekin = 1.94164145678029 | erot = 1.63062825678504 | epot = -11.7060533875154 | etot = -8.13378367395007 +702000 ekin = 1.85450233236432 | erot = 1.63328569347074 | epot = -11.6215716982522 | etot = -8.13378367241717 +703000 ekin = 1.74181404901883 | erot = 1.63189519924278 | epot = -11.5074929187023 | etot = -8.13378367044066 +704000 ekin = 1.62890053392861 | erot = 1.62932624835339 | epot = -11.3920104511708 | etot = -8.13378366888879 +705000 ekin = 1.53704055722126 | erot = 1.62828297741702 | epot = -11.2991072023952 | etot = -8.13378366775691 +706000 ekin = 1.48137553847377 | erot = 1.63090498224899 | epot = -11.2460641878539 | etot = -8.13378366713111 +707000 ekin = 1.47012654282495 | erot = 1.63856880534838 | epot = -11.2424790151173 | etot = -8.13378366694392 +708000 ekin = 1.50545482955628 | erot = 1.65189802604224 | epot = -11.2911365226655 | etot = -8.13378366706695 +709000 ekin = 1.58434919610858 | erot = 1.67079586454412 | epot = -11.3889287283693 | etot = -8.13378366771659 +710000 ekin = 1.69830399757237 | erot = 1.69420639269681 | epot = -11.5262940587721 | etot = -8.13378366850288 +711000 ekin = 1.83638650813968 | erot = 1.72024670585802 | epot = -11.69041688351 | etot = -8.13378366951231 +712000 ekin = 1.98510691885688 | erot = 1.74609277600621 | epot = -11.8649833656744 | etot = -8.13378367081131 +713000 ekin = 2.12899307607566 | erot = 1.76804611036611 | epot = -12.0308228584888 | etot = -8.133783672047 +714000 ekin = 2.25375007867489 | erot = 1.78243264220262 | epot = -12.1699663936981 | etot = -8.13378367282057 +715000 ekin = 2.34975342428074 | erot = 1.78632122199589 | epot = -12.2698583195751 | etot = -8.13378367329848 +716000 ekin = 2.41256025247786 | erot = 1.77808812739576 | epot = -12.3244320530442 | etot = -8.1337836731706 +717000 ekin = 2.44474770533408 | erot = 1.75804788158726 | epot = -12.3365792594606 | etot = -8.13378367253928 +718000 ekin = 2.45412216699224 | erot = 1.72831089152396 | epot = -12.3162167305459 | etot = -8.13378367202974 +719000 ekin = 2.44845378808475 | erot = 1.69204638277942 | epot = -12.2742838420344 | etot = -8.13378367117019 +720000 ekin = 2.43656682436293 | erot = 1.65329012896632 | epot = -12.2236406238981 | etot = -8.13378367056883 +721000 ekin = 2.42365620527341 | erot = 1.61605001915984 | epot = -12.1734898948091 | etot = -8.13378367037585 +722000 ekin = 2.40904119961221 | erot = 1.58378410647612 | epot = -12.1266089766817 | etot = -8.13378367059338 +723000 ekin = 2.38647147018379 | erot = 1.5591543354285 | epot = -12.0794094766778 | etot = -8.13378367106556 +724000 ekin = 2.34659231028328 | erot = 1.54397640919557 | epot = -12.0243523910145 | etot = -8.13378367153561 +725000 ekin = 2.28077035605073 | erot = 1.53931973011769 | epot = -11.953873757908 | etot = -8.13378367173957 +726000 ekin = 2.18489434293367 | erot = 1.54571264597085 | epot = -11.8643906604075 | etot = -8.13378367150295 +727000 ekin = 2.06179491790743 | erot = 1.56339646487188 | epot = -11.7589750535815 | etot = -8.13378367080221 +728000 ekin = 1.92142302776613 | erot = 1.59252552382201 | epot = -11.6477322213728 | etot = -8.13378366978461 +729000 ekin = 1.7786316146568 | erot = 1.63318133793184 | epot = -11.54559662132 | etot = -8.13378366873134 +730000 ekin = 1.64935549787589 | erot = 1.68520345513118 | epot = -11.4683426209853 | etot = -8.13378366797823 +731000 ekin = 1.54617340796522 | erot = 1.74777370759381 | epot = -11.4277307833247 | etot = -8.13378366776571 +732000 ekin = 1.47444012320943 | erot = 1.8187602583582 | epot = -11.4269840497119 | etot = -8.13378366814423 +733000 ekin = 1.43189319810384 | erot = 1.8948402703279 | epot = -11.4605171374292 | etot = -8.13378366899749 +734000 ekin = 1.41017780820349 | erot = 1.97174677425865 | epot = -11.5157082525239 | etot = -8.1337836700618 +735000 ekin = 1.39820849328343 | erot = 2.04483940824941 | epot = -11.5768315725393 | etot = -8.1337836710065 +736000 ekin = 1.38628872351253 | erot = 2.1098536340491 | epot = -11.6299260291058 | etot = -8.13378367154417 +737000 ekin = 1.3696159670461 | erot = 2.16355925930541 | epot = -11.6669588978971 | etot = -8.13378367154559 +738000 ekin = 1.34981044658826 | erot = 2.20404797659553 | epot = -11.6876420942915 | etot = -8.13378367110774 +739000 ekin = 1.33372653216474 | erot = 2.23055395777236 | epot = -11.6980641604352 | etot = -8.13378367049808 +740000 ekin = 1.33016419311742 | erot = 2.24303198933016 | epot = -11.7069798524316 | etot = -8.13378366998406 +741000 ekin = 1.34641052660523 | erot = 2.2418933687602 | epot = -11.722087565038 | etot = -8.13378366967257 +742000 ekin = 1.38645577656229 | erot = 2.2280983694918 | epot = -11.748337815579 | etot = -8.13378366952496 +743000 ekin = 1.4510387919922 | erot = 2.20332817127167 | epot = -11.7881506327665 | etot = -8.13378366950266 +744000 ekin = 1.53803120220374 | erot = 2.16985299828934 | epot = -11.8416678701917 | etot = -8.13378366969864 +745000 ekin = 1.64150939165489 | erot = 2.12988595975108 | epot = -11.9051790216586 | etot = -8.13378367025267 +746000 ekin = 1.75074962766362 | erot = 2.08470317830682 | epot = -11.9692364772328 | etot = -8.13378367126234 +747000 ekin = 1.84985303113073 | erot = 2.0339872913426 | epot = -12.0176239951097 | etot = -8.13378367263638 +748000 ekin = 1.91944439125361 | erot = 1.97579729240617 | epot = -12.0290253577289 | etot = -8.13378367406914 +749000 ekin = 1.94080211587133 | erot = 1.90728805394724 | epot = -11.9818738449124 | etot = -8.1337836750938 +750000 ekin = 1.90175708673705 | erot = 1.82602227403895 | epot = -11.861563035914 | etot = -8.13378367513804 +751000 ekin = 1.80442251324645 | erot = 1.7321012366993 | epot = -11.670307424271 | etot = -8.13378367432528 +752000 ekin = 1.66438096321275 | erot = 1.62791173828973 | epot = -11.4260763737786 | etot = -8.13378367227611 +753000 ekin = 1.50959112385597 | erot = 1.51791168440983 | epot = -11.1612864778433 | etot = -8.13378366957754 +754000 ekin = 1.37530205546013 | erot = 1.40846180212372 | epot = -10.9175475248216 | etot = -8.13378366723778 +755000 ekin = 1.29223158165298 | erot = 1.30628357861316 | epot = -10.7322988261433 | etot = -8.13378366587714 +756000 ekin = 1.27251368855664 | erot = 1.21592403406034 | epot = -10.622221389072 | etot = -8.13378366645503 +757000 ekin = 1.3063477675277 | erot = 1.13861892044261 | epot = -10.5787503558979 | etot = -8.13378366792755 +758000 ekin = 1.37185376245963 | erot = 1.07351073773517 | epot = -10.5791481696797 | etot = -8.13378366948489 +759000 ekin = 1.44617278821708 | erot = 1.01897341845061 | epot = -10.5989298771412 | etot = -8.13378367047352 +760000 ekin = 1.51270256468479 | erot = 0.973207034238996 | epot = -10.6196932700383 | etot = -8.13378367111452 +761000 ekin = 1.56039612690742 | erot = 0.934439072347236 | epot = -10.6286188702826 | etot = -8.13378367102797 +762000 ekin = 1.58948756751959 | erot = 0.901622732001468 | epot = -10.6248939699753 | etot = -8.13378367045428 +763000 ekin = 1.60810008590181 | erot = 0.874391507913214 | epot = -10.6162752634854 | etot = -8.13378366967037 +764000 ekin = 1.62768531411594 | erot = 0.852689319830039 | epot = -10.6141583029053 | etot = -8.13378366895929 +765000 ekin = 1.65693698081253 | erot = 0.836745239181655 | epot = -10.6274658895677 | etot = -8.13378366957356 +766000 ekin = 1.70304081012829 | erot = 0.827639758152331 | epot = -10.6644642390248 | etot = -8.13378367074414 +767000 ekin = 1.76603010798667 | erot = 0.81974578700517 | epot = -10.7195595663148 | etot = -8.13378367132295 +768000 ekin = 1.83976621723509 | erot = 0.813915606837078 | epot = -10.7874654957709 | etot = -8.13378367169871 +769000 ekin = 1.91953928651817 | erot = 0.809315266677004 | epot = -10.8626382251893 | etot = -8.13378367199416 +770000 ekin = 2.00068337345698 | erot = 0.805269377276929 | epot = -10.9397364229584 | etot = -8.13378367222448 +771000 ekin = 2.07932607078706 | erot = 0.80147001562 | epot = -11.014579758772 | etot = -8.13378367236493 +772000 ekin = 2.15218258745307 | erot = 0.797728511921629 | epot = -11.083694771944 | etot = -8.13378367256931 +773000 ekin = 2.21516346354871 | erot = 0.793769932241683 | epot = -11.1427170687097 | etot = -8.1337836729193 +774000 ekin = 2.26234547281743 | erot = 0.789120208401059 | epot = -11.1852493546222 | etot = -8.13378367340368 +775000 ekin = 2.28747439980972 | erot = 0.782940858199211 | epot = -11.2041989315137 | etot = -8.13378367350475 +776000 ekin = 2.28487294038536 | erot = 0.774236455913865 | epot = -11.1928930693656 | etot = -8.13378367306634 +777000 ekin = 2.25459623244261 | erot = 0.763986238683991 | epot = -11.1523661446313 | etot = -8.13378367350472 +778000 ekin = 2.19483848041185 | erot = 0.752926118565648 | epot = -11.081548272629 | etot = -8.13378367365153 +779000 ekin = 2.10207554487761 | erot = 0.741428699427813 | epot = -10.9772879179982 | etot = -8.13378367369273 +780000 ekin = 1.97507844679113 | erot = 0.730439747748102 | epot = -10.8393018680354 | etot = -8.13378367349615 +781000 ekin = 1.81624238003515 | erot = 0.720681720809312 | epot = -10.6707077734064 | etot = -8.13378367256197 +782000 ekin = 1.63737680012838 | erot = 0.713965531438875 | epot = -10.4851260030337 | etot = -8.13378367146641 +783000 ekin = 1.45327094417962 | erot = 0.712334775603849 | epot = -10.2993893901241 | etot = -8.13378367034059 +784000 ekin = 1.27931304209992 | erot = 0.71779531661219 | epot = -10.1308920280318 | etot = -8.13378366931973 +785000 ekin = 1.12953341848653 | erot = 0.732133377099077 | epot = -9.99545046411213 | etot = -8.13378366852652 +786000 ekin = 1.01482431832703 | erot = 0.756760281246955 | epot = -9.90536826762429 | etot = -8.13378366805031 +787000 ekin = 0.941643964044434 | erot = 0.792599099828181 | epot = -9.86802673180068 | etot = -8.13378366792806 +788000 ekin = 0.91151079646793 | erot = 0.840020856578546 | epot = -9.88531532117945 | etot = -8.13378366813298 +789000 ekin = 0.921376349391728 | erot = 0.898827357320721 | epot = -9.95398737530709 | etot = -8.13378366859464 +790000 ekin = 0.9646544828658 | erot = 0.968273092100882 | epot = -10.0667112441871 | etot = -8.13378366922042 +791000 ekin = 1.03261133414691 | erot = 1.04710148110145 | epot = -10.2134964851676 | etot = -8.13378366991922 +792000 ekin = 1.11580285041638 | erot = 1.13356945356443 | epot = -10.3831559745819 | etot = -8.1337836706011 +793000 ekin = 1.20528065119976 | erot = 1.22546277764171 | epot = -10.564527100092 | etot = -8.13378367125054 +794000 ekin = 1.29310700781807 | erot = 1.32020213136593 | epot = -10.7470928110086 | etot = -8.13378367182458 +795000 ekin = 1.3723846739092 | erot = 1.41513363954107 | epot = -10.9213019889899 | etot = -8.13378367553964 +796000 ekin = 1.40835913128026 | erot = 1.52971390249054 | epot = -11.0718567044156 | etot = -8.13378367064481 +797000 ekin = 1.45167190327184 | erot = 1.62512604238246 | epot = -11.2105816180017 | etot = -8.13378367234739 +798000 ekin = 1.48145722834957 | erot = 1.70064689495111 | epot = -11.3158877957753 | etot = -8.13378367247457 +799000 ekin = 1.49559633330505 | erot = 1.76394329937706 | epot = -11.3933233051004 | etot = -8.13378367241832 +800000 ekin = 1.49744893759607 | erot = 1.81327291254695 | epot = -11.4445055223102 | etot = -8.1337836721672 +801000 ekin = 1.49251279283597 | erot = 1.84780559270302 | epot = -11.4741020572375 | etot = -8.13378367169853 +802000 ekin = 1.48820480026236 | erot = 1.86779013860696 | epot = -11.4897786099793 | etot = -8.13378367110997 +803000 ekin = 1.49253566034238 | erot = 1.87451451163578 | epot = -11.5008338425624 | etot = -8.13378367058421 +804000 ekin = 1.51166035417666 | erot = 1.86997050308506 | epot = -11.5154145275931 | etot = -8.13378367033143 +805000 ekin = 1.54725262755389 | erot = 1.85635941628183 | epot = -11.5373957143256 | etot = -8.13378367048987 +806000 ekin = 1.59533620613465 | erot = 1.83572111149178 | epot = -11.5648409882672 | etot = -8.13378367064076 +807000 ekin = 1.64925672138757 | erot = 1.81037056523643 | epot = -11.5934109580015 | etot = -8.13378367137749 +808000 ekin = 1.69787116881872 | erot = 1.78132459583089 | epot = -11.6129794367426 | etot = -8.13378367209299 +809000 ekin = 1.73004744199967 | erot = 1.74897468672994 | epot = -11.6128058013083 | etot = -8.1337836725787 +810000 ekin = 1.73831051770698 | erot = 1.71353607854315 | epot = -11.5856302700131 | etot = -8.13378367376295 +811000 ekin = 1.7162354887398 | erot = 1.67428462338951 | epot = -11.5243037856423 | etot = -8.133783673513 +812000 ekin = 1.66416936436974 | erot = 1.63115164433668 | epot = -11.4291046815542 | etot = -8.13378367284779 +813000 ekin = 1.59176171300662 | erot = 1.58513406243102 | epot = -11.3106794472763 | etot = -8.13378367183862 +814000 ekin = 1.51369575693279 | erot = 1.53752063411452 | epot = -11.1850000616746 | etot = -8.13378367062732 +815000 ekin = 1.44735421386905 | erot = 1.48989097524506 | epot = -11.071028858542 | etot = -8.13378366942792 +816000 ekin = 1.40949972408348 | erot = 1.44406671640762 | epot = -10.9873501089771 | etot = -8.13378366848597 +817000 ekin = 1.41268037634604 | erot = 1.40200084691418 | epot = -10.9484648912749 | etot = -8.13378366801463 +818000 ekin = 1.46212175596086 | erot = 1.36558649852231 | epot = -10.9614919226108 | etot = -8.1337836681276 +819000 ekin = 1.55434977604764 | erot = 1.33645466066158 | epot = -11.0245881054313 | etot = -8.13378366872208 +820000 ekin = 1.67879137058879 | erot = 1.31590146910598 | epot = -11.1284765092722 | etot = -8.1337836695774 +821000 ekin = 1.82107935909666 | erot = 1.30489182417681 | epot = -11.259754853713 | etot = -8.13378367043957 +822000 ekin = 1.9529446717066 | erot = 1.31620698806857 | epot = -11.4029353293376 | etot = -8.13378366956246 +823000 ekin = 2.07449183435307 | erot = 1.3446643767535 | epot = -11.5529398818435 | etot = -8.13378367073694 +824000 ekin = 2.19907919231085 | erot = 1.36469015519565 | epot = -11.6975530184859 | etot = -8.13378367097939 +825000 ekin = 2.30563380852721 | erot = 1.39476757249072 | epot = -11.8341850522209 | etot = -8.13378367120299 +826000 ekin = 2.39103701046294 | erot = 1.43354131731499 | epot = -11.9583619995925 | etot = -8.13378367181457 +827000 ekin = 2.44908730536611 | erot = 1.47824974984668 | epot = -12.061120727616 | etot = -8.13378367240325 +828000 ekin = 2.4740049529018 | erot = 1.52536858756854 | epot = -12.1331572135331 | etot = -8.13378367306277 +829000 ekin = 2.46026919624821 | erot = 1.57083289943084 | epot = -12.1648857692761 | etot = -8.13378367359711 +830000 ekin = 2.40417117647821 | erot = 1.61070673269887 | epot = -12.1486615829649 | etot = -8.13378367378778 +831000 ekin = 2.3062679748487 | erot = 1.64206892676616 | epot = -12.0821205750573 | etot = -8.13378367344244 +832000 ekin = 2.17314973564168 | erot = 1.66378895251181 | epot = -11.9707223607483 | etot = -8.13378367259479 +833000 ekin = 2.0166788310753 | erot = 1.67684011521384 | epot = -11.8273026176896 | etot = -8.13378367140051 +834000 ekin = 1.85232718548849 | erot = 1.68370832836246 | epot = -11.6698191839383 | etot = -8.13378367008734 +835000 ekin = 1.696162825951 | erot = 1.68768571717172 | epot = -11.5176322122076 | etot = -8.13378366908484 +836000 ekin = 1.56059049397783 | erot = 1.69176135975103 | epot = -11.3861355311657 | etot = -8.13378367743684 +837000 ekin = 1.46494691483958 | erot = 1.67922598600668 | epot = -11.2779565659497 | etot = -8.13378366510345 +838000 ekin = 1.41623376497621 | erot = 1.68359587922025 | epot = -11.2336133184481 | etot = -8.13378367425162 +839000 ekin = 1.38164226048355 | erot = 1.69827238732617 | epot = -11.2136983224206 | etot = -8.13378367461086 +840000 ekin = 1.37281419759143 | erot = 1.71791872251442 | epot = -11.2245165952046 | etot = -8.13378367509872 +841000 ekin = 1.38251849257029 | erot = 1.74222357851784 | epot = -11.2585257466759 | etot = -8.13378367558775 +842000 ekin = 1.40440816037656 | erot = 1.77053653211612 | epot = -11.3087283685373 | etot = -8.13378367604459 +843000 ekin = 1.43288890065947 | erot = 1.80208713667178 | epot = -11.3687597138102 | etot = -8.13378367647898 +844000 ekin = 1.46337506006249 | erot = 1.83581425282211 | epot = -11.4329729898064 | etot = -8.13378367692178 +845000 ekin = 1.49225139202149 | erot = 1.87011931212423 | epot = -11.4961543815405 | etot = -8.13378367739482 +846000 ekin = 1.51675477732079 | erot = 1.90271354992434 | epot = -11.5532520051143 | etot = -8.1337836778692 +847000 ekin = 1.53514567840233 | erot = 1.93076451235142 | epot = -11.5996938689732 | etot = -8.1337836782195 +848000 ekin = 1.54758817369235 | erot = 1.95149729814727 | epot = -11.6328691500911 | etot = -8.1337836782515 +849000 ekin = 1.55740275464435 | erot = 1.96313933262388 | epot = -11.6543257651229 | etot = -8.13378367785465 +850000 ekin = 1.57132389478935 | erot = 1.96572299040244 | epot = -11.6708305623722 | etot = -8.13378367718037 +851000 ekin = 1.59707563407619 | erot = 1.96110149806653 | epot = -11.6919608087796 | etot = -8.13378367663691 +852000 ekin = 1.63865350681412 | erot = 1.95197424490086 | epot = -11.7244114283858 | etot = -8.13378367667083 +853000 ekin = 1.69191652620986 | erot = 1.94037118659739 | epot = -11.7660713902747 | etot = -8.13378367746741 +854000 ekin = 1.74370783938037 | erot = 1.92645693729426 | epot = -11.8039484553812 | etot = -8.13378367870661 +855000 ekin = 1.77620146768418 | erot = 1.90847431922648 | epot = -11.8184594668595 | etot = -8.13378367994886 +856000 ekin = 1.77433273067642 | erot = 1.88315817895787 | epot = -11.7912745901343 | etot = -8.13378368050002 +857000 ekin = 1.73346273112572 | erot = 1.84735528625896 | epot = -11.7146016973811 | etot = -8.13378367999646 +858000 ekin = 1.66317903363266 | erot = 1.7994664359098 | epot = -11.5964291480754 | etot = -8.1337836785329 +859000 ekin = 1.58513293587896 | erot = 1.74007953778942 | epot = -11.4589961502843 | etot = -8.13378367661596 +860000 ekin = 1.52581941899221 | erot = 1.67168470683099 | epot = -11.3312878007233 | etot = -8.13378367490011 +861000 ekin = 1.50775028862609 | erot = 1.59782760852934 | epot = -11.2393615710195 | etot = -8.13378367386411 +862000 ekin = 1.54306866516068 | erot = 1.52225954350351 | epot = -11.1991118823091 | etot = -8.13378367364494 +863000 ekin = 1.63171594825787 | erot = 1.44845127666277 | epot = -11.213950899006 | etot = -8.13378367408539 +864000 ekin = 1.76367870922739 | erot = 1.37946093989893 | epot = -11.2769233240372 | etot = -8.13378367491086 +865000 ekin = 1.92306453203341 | erot = 1.31796433684458 | epot = -11.3748125447456 | etot = -8.13378367586766 +866000 ekin = 2.09215456621248 | erot = 1.26628925949238 | epot = -11.4922275022635 | etot = -8.13378367655859 +867000 ekin = 2.25558706900038 | erot = 1.22649711081648 | epot = -11.6158678571089 | etot = -8.13378367729208 +868000 ekin = 2.40057443855628 | erot = 1.20017706470873 | epot = -11.7345351810599 | etot = -8.13378367779485 +869000 ekin = 2.51819395481234 | erot = 1.18842551852403 | epot = -11.8404031514077 | etot = -8.1337836780713 +870000 ekin = 2.60380767867222 | erot = 1.19178595581356 | epot = -11.9293773127034 | etot = -8.13378367821764 +871000 ekin = 2.65597330736975 | erot = 1.21008900039281 | epot = -11.9998459860857 | etot = -8.13378367832316 +872000 ekin = 2.67413391935025 | erot = 1.24223617324268 | epot = -12.0501537713228 | etot = -8.13378367872988 +873000 ekin = 2.6552381342363 | erot = 1.28590823623526 | epot = -12.074930049832 | etot = -8.13378367936043 +874000 ekin = 2.59426343771486 | erot = 1.33769628052759 | epot = -12.0657433982658 | etot = -8.13378368002336 +875000 ekin = 2.48661884983932 | erot = 1.39359938638622 | epot = -12.0140019165834 | etot = -8.13378368035786 +876000 ekin = 2.33257163351496 | erot = 1.44985984400568 | epot = -11.9162151575154 | etot = -8.13378367999475 +877000 ekin = 2.14151731604679 | erot = 1.50380376702378 | epot = -11.7791047618951 | etot = -8.13378367882451 +878000 ekin = 1.932832003629 | erot = 1.55419737626239 | epot = -11.6208130570763 | etot = -8.13378367718492 +879000 ekin = 1.73117573621979 | erot = 1.60084517426536 | epot = -11.4658045862297 | etot = -8.13378367574457 +880000 ekin = 1.55787151334954 | erot = 1.64373016529537 | epot = -11.3353853536958 | etot = -8.13378367505087 +881000 ekin = 1.42384142186798 | erot = 1.68244604597635 | epot = -11.2400711429721 | etot = -8.1337836751278 +882000 ekin = 1.32893688552342 | erot = 1.71640874220465 | epot = -11.1791293032808 | etot = -8.13378367555272 +883000 ekin = 1.26714280188822 | erot = 1.74554142973579 | epot = -11.1464679073511 | etot = -8.13378367572706 +884000 ekin = 1.23268823939063 | erot = 1.77071758338062 | epot = -11.1371894987175 | etot = -8.13378367594624 +885000 ekin = 1.22008849592431 | erot = 1.793121667761 | epot = -11.1469938397908 | etot = -8.13378367610554 +886000 ekin = 1.22532479940098 | erot = 1.81382115988278 | epot = -11.1729296355223 | etot = -8.13378367623854 +887000 ekin = 1.24494548145927 | erot = 1.83336039585811 | epot = -11.21208955378 | etot = -8.13378367646266 +888000 ekin = 1.27500212940806 | erot = 1.85168867062894 | epot = -11.2604744767863 | etot = -8.13378367674929 +889000 ekin = 1.31152735306242 | erot = 1.86844690092859 | epot = -11.3137579310936 | etot = -8.13378367710254 +890000 ekin = 1.3498631765703 | erot = 1.88304641021545 | epot = -11.3666932643095 | etot = -8.13378367752371 +891000 ekin = 1.38390530587808 | erot = 1.89468392872775 | epot = -11.4123729126909 | etot = -8.13378367808506 +892000 ekin = 1.40569396149735 | erot = 1.9022674860451 | epot = -11.4417451265517 | etot = -8.13378367900926 +893000 ekin = 1.40448289128716 | erot = 1.90432470721805 | epot = -11.4425912782068 | etot = -8.13378367970162 +894000 ekin = 1.37144289541472 | erot = 1.89954368983534 | epot = -11.4047702652371 | etot = -8.13378367998709 +895000 ekin = 1.30348486055177 | erot = 1.88750422908343 | epot = -11.3247727658088 | etot = -8.13378367617357 +896000 ekin = 1.22187337143717 | erot = 1.87071061589499 | epot = -11.2263676628434 | etot = -8.13378367551128 +897000 ekin = 1.14754845934872 | erot = 1.85263803756603 | epot = -11.1339701714171 | etot = -8.13378367450233 +898000 ekin = 1.08944016800739 | erot = 1.83653761246719 | epot = -11.0597614543947 | etot = -8.13378367392007 +899000 ekin = 1.05403951309466 | erot = 1.82413022548821 | epot = -11.0119534121708 | etot = -8.13378367358794 +900000 ekin = 1.04500203485724 | erot = 1.81619426241825 | epot = -10.994979970873 | etot = -8.13378367359756 +901000 ekin = 1.06222207054372 | erot = 1.8123440301414 | epot = -11.0083497746079 | etot = -8.13378367392275 +902000 ekin = 1.10209714029207 | erot = 1.81111462834152 | epot = -11.0469954430829 | etot = -8.13378367444936 +903000 ekin = 1.15876030972024 | erot = 1.81037876509514 | epot = -11.1029227498417 | etot = -8.13378367502628 +904000 ekin = 1.22532881895693 | erot = 1.80797942269356 | epot = -11.1670919176146 | etot = -8.13378367596416 +905000 ekin = 1.29206809096424 | erot = 1.80250391168621 | epot = -11.2283556791119 | etot = -8.13378367646147 +906000 ekin = 1.35183435772567 | erot = 1.79300035909436 | epot = -11.2786183935736 | etot = -8.13378367675354 +907000 ekin = 1.39979991721213 | erot = 1.77946415986595 | epot = -11.3130477540359 | etot = -8.13378367695782 +908000 ekin = 1.43268044609659 | erot = 1.76253539590784 | epot = -11.3289995190119 | etot = -8.13378367700745 +909000 ekin = 1.44897967082509 | erot = 1.74341748083575 | epot = -11.3261808285436 | etot = -8.13378367688281 +910000 ekin = 1.44937912071043 | erot = 1.72390580468978 | epot = -11.307068601954 | etot = -8.13378367655379 +911000 ekin = 1.43727653438468 | erot = 1.70617572444023 | epot = -11.2772359348716 | etot = -8.13378367604669 +912000 ekin = 1.41843447946169 | erot = 1.69263823279422 | epot = -11.2448563876992 | etot = -8.13378367544329 +913000 ekin = 1.40006193727622 | erot = 1.68549441014308 | epot = -11.219340022283 | etot = -8.13378367486371 +914000 ekin = 1.38958825652739 | erot = 1.68634774669615 | epot = -11.2097196776933 | etot = -8.13378367446975 +915000 ekin = 1.39244840974392 | erot = 1.69595180429013 | epot = -11.2221838884456 | etot = -8.13378367441153 +916000 ekin = 1.41015013786076 | erot = 1.71401831934436 | epot = -11.2579521319716 | etot = -8.13378367476645 +917000 ekin = 1.4392962874655 | erot = 1.73916763957947 | epot = -11.3122476025345 | etot = -8.13378367548949 +918000 ekin = 1.47227942008796 | erot = 1.76903078778361 | epot = -11.3750938842682 | etot = -8.13378367639659 +919000 ekin = 1.49986621134982 | erot = 1.80052098765843 | epot = -11.4341708761906 | etot = -8.13378367718234 +920000 ekin = 1.51501276726728 | erot = 1.83027923157205 | epot = -11.479075676427 | etot = -8.13378367758768 +921000 ekin = 1.50567012576534 | erot = 1.85806252988137 | epot = -11.4975163324903 | etot = -8.13378367684357 +922000 ekin = 1.50530570323642 | erot = 1.88405749106785 | epot = -11.5231468709211 | etot = -8.13378367661687 +923000 ekin = 1.51005072433124 | erot = 1.89398296690106 | epot = -11.5378173670833 | etot = -8.13378367585097 +924000 ekin = 1.52928061407801 | erot = 1.89561779618601 | epot = -11.5586820856961 | etot = -8.13378367543205 +925000 ekin = 1.56873673478303 | erot = 1.88910082537247 | epot = -11.5916212358692 | etot = -8.13378367571368 +926000 ekin = 1.623719119736 | erot = 1.87429650615988 | epot = -11.6317993025749 | etot = -8.13378367667902 +927000 ekin = 1.67952368823402 | erot = 1.85068760729924 | epot = -11.6639949734866 | etot = -8.13378367795335 +928000 ekin = 1.71651232215492 | erot = 1.81783745617795 | epot = -11.6681334573616 | etot = -8.13378367902875 +929000 ekin = 1.71702543500849 | erot = 1.7761409547827 | epot = -11.6269500692948 | etot = -8.13378367950356 +930000 ekin = 1.67099558011226 | erot = 1.72742888865563 | epot = -11.5322081479668 | etot = -8.13378367919888 +931000 ekin = 1.57874462940356 | erot = 1.67513457878369 | epot = -11.3876628863509 | etot = -8.13378367816365 +932000 ekin = 1.45079208833672 | erot = 1.62392798294326 | epot = -11.208503747902 | etot = -8.13378367662198 +933000 ekin = 1.30531756655107 | erot = 1.57894108978416 | epot = -11.0180423312269 | etot = -8.1337836748917 +934000 ekin = 1.16422089209607 | erot = 1.54485802085233 | epot = -10.8428625862405 | etot = -8.1337836732921 +935000 ekin = 1.04864498106518 | erot = 1.52509208502931 | epot = -10.7075207382517 | etot = -8.13378367215725 +936000 ekin = 0.97470928197414 | erot = 1.52116327413384 | epot = -10.6296562277879 | etot = -8.13378367167996 +937000 ekin = 0.950462284702358 | erot = 1.53244919059087 | epot = -10.616695147248 | etot = -8.13378367195482 +938000 ekin = 0.974421294583295 | erot = 1.55616006625871 | epot = -10.6643650337801 | etot = -8.13378367293808 +939000 ekin = 1.03606886759094 | erot = 1.58755449221726 | epot = -10.7574070342586 | etot = -8.13378367445039 +940000 ekin = 1.11826840897929 | erot = 1.62042988761827 | epot = -10.8724819727897 | etot = -8.13378367619211 +941000 ekin = 1.20122028436166 | erot = 1.64794231894323 | epot = -10.9829462810871 | etot = -8.13378367778225 +942000 ekin = 1.26717763526718 | erot = 1.66371923758655 | epot = -11.0646805517328 | etot = -8.13378367887906 +943000 ekin = 1.30509212265462 | erot = 1.66314531188336 | epot = -11.1020211136571 | etot = -8.13378367911911 +944000 ekin = 1.3139237763007 | erot = 1.64449670932369 | epot = -11.0922041641376 | etot = -8.13378367851323 +945000 ekin = 1.30237464142681 | erot = 1.60929976332954 | epot = -11.0454580821011 | etot = -8.13378367734473 +946000 ekin = 1.28506402176001 | erot = 1.56181037072794 | epot = -10.9806580685974 | etot = -8.13378367610942 +947000 ekin = 1.27634122926031 | erot = 1.50774431809126 | epot = -10.9178692226282 | etot = -8.13378367527659 +948000 ekin = 1.28467886086298 | erot = 1.45281197104727 | epot = -10.8712745069726 | etot = -8.13378367506231 +949000 ekin = 1.31037739798746 | erot = 1.40157240487559 | epot = -10.8457334782341 | etot = -8.1337836753711 +950000 ekin = 1.34722619716906 | erot = 1.3568868979842 | epot = -10.8378967710771 | etot = -8.13378367592388 +951000 ekin = 1.38650860498497 | erot = 1.31991933557737 | epot = -10.8402116169905 | etot = -8.13378367642818 +952000 ekin = 1.421447087831 | erot = 1.29081153979046 | epot = -10.84604230425 | etot = -8.13378367662858 +953000 ekin = 1.44882630163939 | erot = 1.26905801707694 | epot = -10.8516679954638 | etot = -8.13378367674752 +954000 ekin = 1.46839021225272 | erot = 1.25288009756807 | epot = -10.8550539863921 | etot = -8.13378367657131 +955000 ekin = 1.48389177420735 | erot = 1.24071489729452 | epot = -10.8583903477773 | etot = -8.13378367627542 +956000 ekin = 1.50041047255739 | erot = 1.23152280194284 | epot = -10.865716950577 | etot = -8.13378367607677 +957000 ekin = 1.52124212096693 | erot = 1.22481048447594 | epot = -10.8798362815372 | etot = -8.13378367609429 +958000 ekin = 1.54632227618744 | erot = 1.22051886332113 | epot = -10.9006248157658 | etot = -8.13378367625721 +959000 ekin = 1.57324294423871 | erot = 1.21891910555264 | epot = -10.9259457261608 | etot = -8.1337836763695 +960000 ekin = 1.59969206086875 | erot = 1.22060656116838 | epot = -10.9540822984235 | etot = -8.1337836763864 +961000 ekin = 1.62253440888993 | erot = 1.22677323459116 | epot = -10.9830913197429 | etot = -8.13378367626177 +962000 ekin = 1.64127229281945 | erot = 1.23851881095622 | epot = -11.0135747798977 | etot = -8.133783676122 +963000 ekin = 1.65616190916698 | erot = 1.25678969037885 | epot = -11.0467352756897 | etot = -8.13378367614384 +964000 ekin = 1.66566514666451 | erot = 1.28218253876047 | epot = -11.0816313616704 | etot = -8.13378367624546 +965000 ekin = 1.66770285606757 | erot = 1.31455464601019 | epot = -11.1160411786495 | etot = -8.13378367657176 +966000 ekin = 1.6581069535733 | erot = 1.35314679870501 | epot = -11.145037429086 | etot = -8.13378367680773 +967000 ekin = 1.6340191426093 | erot = 1.39653020323183 | epot = -11.164333022772 | etot = -8.13378367693091 +968000 ekin = 1.59493851000743 | erot = 1.44254096624089 | epot = -11.171263153312 | etot = -8.13378367706365 +969000 ekin = 1.54116624535086 | erot = 1.4883056650783 | epot = -11.1632555877659 | etot = -8.13378367733677 +970000 ekin = 1.47195251630965 | erot = 1.53048570942868 | epot = -11.1362219034456 | etot = -8.13378367770727 +971000 ekin = 1.38571363570397 | erot = 1.56593199014109 | epot = -11.0854293034529 | etot = -8.13378367760786 +972000 ekin = 1.2844612509872 | erot = 1.59277024067381 | epot = -11.0110151691096 | etot = -8.13378367744862 +973000 ekin = 1.17320809752836 | erot = 1.61049478406713 | epot = -10.9174865582804 | etot = -8.13378367668489 +974000 ekin = 1.06313422542289 | erot = 1.62023440485558 | epot = -10.8171523056985 | etot = -8.13378367542 +975000 ekin = 0.97098763557619 | erot = 1.62445057720854 | epot = -10.7292218868794 | etot = -8.13378367409465 +976000 ekin = 0.91351783966156 | erot = 1.62592320586085 | epot = -10.6732247188146 | etot = -8.13378367329216 +977000 ekin = 0.900210301809895 | erot = 1.62660680269658 | epot = -10.6606007778788 | etot = -8.13378367337233 +978000 ekin = 0.928774961855102 | erot = 1.62702792387329 | epot = -10.6895865599753 | etot = -8.13378367424692 +979000 ekin = 0.986309691310116 | erot = 1.62661905645026 | epot = -10.7467124231103 | etot = -8.13378367534995 +980000 ekin = 1.0560418464208 | erot = 1.62477777160401 | epot = -10.8146032941482 | etot = -8.13378367612342 +981000 ekin = 1.12469745191456 | erot = 1.62193499389755 | epot = -10.8804161220952 | etot = -8.1337836762831 +982000 ekin = 1.18655422424979 | erot = 1.61989865006664 | epot = -10.9402365502154 | etot = -8.133783675899 +983000 ekin = 1.24323393226582 | erot = 1.6213893247498 | epot = -10.998406932262 | etot = -8.13378367524638 +984000 ekin = 1.3007289224841 | erot = 1.62917854395174 | epot = -11.0636911410593 | etot = -8.13378367462348 +985000 ekin = 1.3657579887055 | erot = 1.64530549445309 | epot = -11.1448471574172 | etot = -8.13378367425859 +986000 ekin = 1.44269014534723 | erot = 1.67060135266118 | epot = -11.2470751723069 | etot = -8.13378367429852 +987000 ekin = 1.53139017840676 | erot = 1.70450616378661 | epot = -11.3696800170058 | etot = -8.13378367481245 +988000 ekin = 1.62542517207335 | erot = 1.74490463007085 | epot = -11.504113477996 | etot = -8.13378367585183 +989000 ekin = 1.70973314631196 | erot = 1.78758054110428 | epot = -11.6310973645961 | etot = -8.13378367717991 +990000 ekin = 1.76834990883591 | erot = 1.82854801274317 | epot = -11.7306815999595 | etot = -8.13378367838041 +991000 ekin = 1.78717585350667 | erot = 1.86445265992369 | epot = -11.7854121925014 | etot = -8.133783679071 +992000 ekin = 1.75808069003026 | erot = 1.89344947584339 | epot = -11.7853138449038 | etot = -8.13378367903015 +993000 ekin = 1.68149922498393 | erot = 1.91587779315319 | epot = -11.7311606964116 | etot = -8.13378367827449 +994000 ekin = 1.56634005209159 | erot = 1.93428820863977 | epot = -11.6344119377119 | etot = -8.13378367698052 +995000 ekin = 1.4280735459805 | erot = 1.95281321443276 | epot = -11.5146704358241 | etot = -8.13378367541087 +996000 ekin = 1.28578073803757 | erot = 1.97614374563733 | epot = -11.395708157556 | etot = -8.13378367388114 +997000 ekin = 1.15849049936959 | erot = 2.00849321026896 | epot = -11.3007673823119 | etot = -8.13378367267339 +998000 ekin = 1.06172554149893 | erot = 2.05288173761918 | epot = -11.2483909510631 | etot = -8.133783671945 +999000 ekin = 1.00534863216522 | erot = 2.11083351117271 | epot = -11.2499658150715 | etot = -8.13378367173359 +1000000 ekin = 0.992888346872309 | erot = 2.18232106768115 | epot = -11.3089930865736 | etot = -8.1337836720201 + 1000000 0.073547285 -1.1520387 0.021139403 -1.0316105 -4.7686303e-05 64000 +Loop time of 13.756 on 4 procs for 1000000 steps with 10 atoms + +Performance: 62808.788 tau/day, 72695.357 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.0908 | 4.5747 | 7.698 | 93.9 | 33.26 +Bond | 0.21019 | 0.2687 | 0.32615 | 9.6 | 1.95 +Neigh | 0.005636 | 0.0056895 | 0.005729 | 0.0 | 0.04 +Comm | 3.3072 | 6.7911 | 9.3078 | 83.5 | 49.37 +Output | 0.073535 | 0.076852 | 0.083027 | 1.3 | 0.56 +Modify | 0.57149 | 0.61083 | 0.65106 | 4.8 | 4.44 +Other | | 1.428 | | | 10.38 + +Nlocal: 2.50000 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.50000 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25000 ave 16 max 1 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7000000 +Ave special neighs/atom = 3.6000000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.3.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:13 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type new file mode 100644 index 0000000000..7145f65137 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type @@ -0,0 +1,132 @@ +LAMMPS data file via write_data, version 27 May 2021 + +26 atoms +4 atom types +24 bonds +1 bond types +26 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.5974293795290144 -0.47217734566783476 0.1149860099192362 1 1 3.7269849963023267 0 0 0 +2 2 -0.3607975285447209 -0.8084200276362509 0.5005631273908187 1 1 3.7269849963023267 0 0 0 +3 3 -0.1880165420620915 -0.9339012982528754 0.9372222930006777 1 1 3.7269849963023267 0 0 0 +4 4 0.18789028377909187 -0.8807473585891459 1.3080750447260532 1 1 3.7269849963023267 0 0 0 +5 1 0.46680288593900887 -0.6314504249974493 1.6544618495816525 1 1 3.7269849963023267 0 0 0 +6 2 0.6156490001978658 -0.24344915610488765 1.9998398114466447 1 1 3.7269849963023267 0 0 0 +7 3 0.5475869309223161 0.10633006738807783 2.395688109397028 1 1 3.7269849963023267 0 0 0 +8 4 0.3964561058464781 0.33864915662119616 2.855380256681012 1 1 3.7269849963023267 0 0 0 +9 1 0.09151778690925949 0.33572177117709545 3.2793107140407853 1 1 3.7269849963023267 0 0 0 +10 2 -0.260700239272384 0.23452584272483473 3.622064753017485 1 1 3.7269849963023267 0 0 0 +11 3 -0.44049173083867876 -0.04240311520575983 4.057361772274168 1 1 3.7269849963023267 0 0 0 +12 4 -0.48111471327910416 -0.3913669550617015 4.465217350523367 1 1 3.7269849963023267 0 0 0 +13 1 -0.3029890593292223 -0.6218232516387349 4.889919411438907 1 1 3.7269849963023267 0 0 0 +14 4 0.36538593166250877 0.467104033114044 4.885957202043727 2 1 3.7269849963023267 0 0 0 +15 1 0.5837256243756591 0.1432569770282543 4.587937684834979 2 1 3.7269849963023267 0 0 0 +16 2 0.7270895848434721 -0.21648156960230241 4.19127441749994 2 1 3.7269849963023267 0 0 0 +17 3 0.5694364623788377 -0.5971020505771416 3.7905394408535833 2 1 3.7269849963023267 0 0 0 +18 4 0.32183479629572403 -0.7826674384502239 3.3981789941001397 2 1 3.7269849963023267 0 0 0 +19 1 0.027943077828669855 -0.8173952163019756 2.892497591992246 2 1 3.7269849963023267 0 0 0 +20 2 -0.34389471043742403 -0.6801076538339801 2.6010059142333977 2 1 3.7269849963023267 0 0 0 +21 3 -0.5722337592890715 -0.31543771192866543 2.2496367888009035 2 1 3.7269849963023267 0 0 0 +22 4 -0.5243059431454682 -0.018794840926191582 1.6669602274961965 2 1 3.7269849963023267 0 0 0 +23 1 -0.4467049661654279 0.15318137385858244 1.1669311078565738 2 1 3.7269849963023267 0 0 0 +24 2 -0.04279541944801792 0.24071675674438053 0.7924196804793574 2 1 3.7269849963023267 0 0 0 +25 3 0.33688934798342335 0.1390449738629785 0.42004977704361546 2 1 3.7269849963023267 0 0 0 +26 4 0.5381606093378432 -0.28366941895261566 0.04905784853961178 2 1 3.7269849963023267 0 0 0 + +Velocities + +1 -0.1420563695014878 -0.2339928257547227 0.1871716305399088 -0.046333854442252194 0.08160574816172744 0.2791824603833533 +2 0.03390382747481304 0.2912921705525512 -0.1828986721885175 0.09422531767061365 -0.044398236946770545 0.011069519340877812 +3 0.05351747745964457 -0.3700026678535097 -0.01469442373794632 0.10875858697088675 0.2373869034785703 0.15028498953263314 +4 0.1107696836820372 0.012571134739153464 0.23554381030898286 0.11411649786729211 -0.23899527406990237 0.11196343804383825 +5 0.21949033826324368 -0.4153000294565104 0.18426481814713022 0.2497206165366295 0.2505624077277829 -0.35347918243093 +6 -0.24019769428878804 -0.16423570219236758 -0.003762466815720382 0.062008045889015595 0.22340307597010978 -0.38223196779931135 +7 0.12372477399377596 0.10393016373901434 0.08008946447311854 -0.15063203100274558 0.08544129561789665 -0.3233996805084572 +8 0.03216353270652909 -0.1291938805451393 0.1736283537356162 -0.17577447248216746 0.11132849782859955 -0.13659117762014125 +9 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1.173984503142341 1.173984503142341 1.173984503142341 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672 +25 1.173984503142341 1.173984503142341 1.173984503142341 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346 +26 1.173984503142341 1.173984503142341 1.173984503142341 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type similarity index 67% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type index eebc5c6eed..8be01b1b3e 100644 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type @@ -1,33 +1,35 @@ -variable number equal 1 -variable ofreq equal 10000 -variable efreq equal 10000 +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 variable ntype equal 4 variable T equal 0.1 +variable rhos equal 0.2 units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 10 delay 0 check yes read_data data.duplex4.4type + mass * 3.1575 # sets per-type mass if not in data file set atom * mass 3.1575 # sets per-atom mass group all type 1 4 -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 special_bonds lj 0 1 1 @@ -52,28 +54,19 @@ jump in.duplex4.4type loop pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 0.2 0.815 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 # Langevin dynamics fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 -timestep 1e-4 +timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" compute erot all erotate/asphere compute ekin all ke @@ -84,14 +77,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz dump_modify out sort id -dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " - -#restart 10000 config0_restart config1_restart - -run 100000 - -#write_restart config.${number}.* +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" +run 1000000 +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type similarity index 67% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type index 07d3ffc423..3223080aef 100644 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type @@ -1,33 +1,35 @@ -variable number equal 1 -variable ofreq equal 10000 -variable efreq equal 10000 +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 variable ntype equal 8 variable T equal 0.1 +variable rhos equal 0.2 units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 10 delay 0 check yes read_data data.duplex4.8type + mass * 3.1575 # sets per-type mass if not in data file set atom * mass 3.1575 # sets per-atom mass group all type 1 8 -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 special_bonds lj 0 1 1 @@ -52,28 +54,19 @@ jump in.duplex4.8type loop pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 0.2 0.815 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 # Langevin dynamics fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 -timestep 1e-4 +timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" compute erot all erotate/asphere compute ekin all ke @@ -84,14 +77,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz dump_modify out sort id -dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " - -#restart 10000 config0_restart config1_restart - -run 100000 - -#write_restart config.${number}.* +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" +run 1000000 +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 new file mode 100644 index 0000000000..d91037ccc8 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 @@ -0,0 +1,1230 @@ +LAMMPS (2 Jul 2021) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +mass * 3.1575 # sets per-type mass if not in data file +set atom * mass 3.1575 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 4 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.4.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 3.74991604702378 | erot = 3.45272678980464 | epot = -37.374200901142 | etot = -30.1715580643136 +Per MPI rank memory allocation (min/avg/max) = 9.328 | 9.328 | 9.328 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.099997761 -1.4717559 0.03428661 -1.2932417 5.6146609e-05 64000 +1000 ekin = 3.83184879800819 | erot = 3.50203401022062 | epot = -37.4730508915114 | etot = -30.1391680832826 +2000 ekin = 3.82227374831519 | erot = 3.79878100905234 | epot = -37.616191007464 | etot = -29.9951362500965 +3000 ekin = 3.90938932030971 | erot = 4.1584025695072 | epot = -37.7430329723255 | etot = -29.6752410825086 +4000 ekin = 3.82373321902577 | erot = 4.12183047279799 | epot = -37.8313543569025 | etot = -29.8857906650787 +5000 ekin = 3.7245469506492 | erot = 4.29953523687407 | epot = -37.8617217220934 | etot = -29.8376395345701 +6000 ekin = 3.75585156536887 | erot = 4.31270713695362 | epot = -37.8280629310505 | etot = -29.759504228728 +7000 ekin = 3.7932674084105 | erot = 4.16508360466875 | epot = -37.7640947397913 | etot = -29.8057437267121 +8000 ekin = 3.74746489835263 | erot = 4.25243425677967 | epot = -37.6835135449588 | etot = -29.6836143898265 +9000 ekin = 3.70802697723781 | erot = 4.00193184819411 | epot = -37.5899388200959 | etot = -29.879979994664 +10000 ekin = 3.58135597641079 | erot = 3.86411518632772 | epot = -37.5041732418663 | etot = -30.0587020791278 +11000 ekin = 3.45122934445655 | erot = 4.1703535299311 | epot = -37.4859882561369 | etot = -29.8644053817493 +12000 ekin = 3.42435863038453 | erot = 4.21487472538924 | epot = -37.5307136425246 | etot = -29.8914802867508 +13000 ekin = 3.40216979362993 | erot = 4.07292918248782 | epot = -37.6378499557145 | etot = -30.1627509795968 +14000 ekin = 3.2921331552169 | erot = 4.50441987673251 | epot = -37.7761364031321 | etot = -29.9795833711827 +15000 ekin = 3.36883179726036 | erot = 4.91359031415192 | epot = -37.9357367952089 | etot = -29.6533146837966 +16000 ekin = 3.30177911852248 | erot = 5.09593415997444 | epot = -38.143737189117 | etot = -29.7460239106201 +17000 ekin = 3.27867865291038 | erot = 5.45789581601551 | epot = -38.3785999463332 | etot = -29.6420254774073 +18000 ekin = 3.36770908750654 | erot = 5.63036493519878 | epot = -38.5970397067551 | etot = -29.5989656840498 +19000 ekin = 3.29802639540141 | erot = 5.4561639608394 | epot = -38.7810833463914 | etot = -30.0268929901506 +20000 ekin = 3.28760849058064 | erot = 5.26031945979083 | epot = -38.9429500949467 | etot = -30.3950221445752 +21000 ekin = 3.32772748450133 | erot = 5.34990394778077 | epot = -39.0618181252056 | etot = -30.3841866929235 +22000 ekin = 3.34298346296243 | erot = 5.12273250375884 | epot = -39.1360899153793 | etot = -30.670373948658 +23000 ekin = 3.38280280428755 | erot = 5.14933572496698 | epot = -39.1974651493046 | etot = -30.6653266200501 +24000 ekin = 3.43991273776911 | erot = 5.03737353653099 | epot = -39.2427818934622 | etot = -30.7654956191621 +25000 ekin = 3.44382800915666 | erot = 4.56194227438362 | epot = -39.2491545805195 | etot = -31.2433842969792 +26000 ekin = 3.47220361933921 | erot = 4.88028216050135 | epot = -39.2033487475128 | etot = -30.8508629676722 +27000 ekin = 3.47824341108214 | erot = 4.7971367004181 | epot = -39.1340731989048 | etot = -30.8586930874046 +28000 ekin = 3.54835351423501 | erot = 4.65494607739445 | epot = -39.0768463918722 | etot = -30.8735468002427 +29000 ekin = 3.57491058588778 | erot = 4.31737192689192 | epot = -39.0420895500443 | etot = -31.1498070372646 +30000 ekin = 3.51438036654861 | erot = 4.50861299911584 | epot = -39.0276136699747 | etot = -31.0046203043103 +31000 ekin = 3.57650331888545 | erot = 4.40811531091204 | epot = -39.0168289246978 | etot = -31.0322102949003 +32000 ekin = 3.70658082522071 | erot = 4.15949186201363 | epot = -39.017410963825 | etot = -31.1513382765907 +33000 ekin = 3.83721022662003 | erot = 4.05055961618762 | epot = -39.0303039022729 | etot = -31.1425340594653 +34000 ekin = 3.94885880665681 | erot = 3.81495459058985 | epot = -39.0180833389347 | etot = -31.2542699416881 +35000 ekin = 3.97994525138323 | erot = 4.49904715736234 | epot = -38.9543629321032 | etot = -30.4753705233577 +36000 ekin = 3.90049506438266 | erot = 3.99723351860168 | epot = -38.8736492127444 | etot = -30.97592062976 +37000 ekin = 4.00119032736887 | erot = 4.30070706410093 | epot = -38.7576942972653 | etot = -30.4557969057955 +38000 ekin = 4.00581796835647 | erot = 3.82064458204034 | epot = -38.6053485149963 | etot = -30.7788859645995 +39000 ekin = 3.92374370666492 | erot = 3.80679256085696 | epot = -38.4357174066365 | etot = -30.7051811391146 +40000 ekin = 3.81525591020245 | erot = 3.60218215391061 | epot = -38.2889289083718 | etot = -30.8714908442587 +41000 ekin = 3.89801377589297 | erot = 3.52447171643241 | epot = -38.2033074629501 | etot = -30.7808219706247 +42000 ekin = 3.92469802136766 | erot = 3.72207083090906 | epot = -38.1843497161945 | etot = -30.5375808639177 +43000 ekin = 3.90355819056277 | erot = 3.6537526927489 | epot = -38.2197716832792 | etot = -30.6624607999675 +44000 ekin = 3.94906849382533 | erot = 3.48405507068376 | epot = -38.2852323155717 | etot = -30.8521087510626 +45000 ekin = 4.04988136986449 | erot = 3.38338492043337 | epot = -38.379217839749 | etot = -30.9459515494512 +46000 ekin = 4.12456204511554 | erot = 3.52614566674475 | epot = -38.4473213411912 | etot = -30.7966136293309 +47000 ekin = 4.05260082430177 | erot = 3.30110271195184 | epot = -38.4808326895795 | etot = -31.1271291533259 +48000 ekin = 3.94672633965036 | erot = 3.30790944660349 | epot = -38.4845357728861 | etot = -31.2298999866322 +49000 ekin = 3.88681575217735 | erot = 3.78262203823329 | epot = -38.4415128535038 | etot = -30.7720750630932 +50000 ekin = 3.8289998539571 | erot = 3.78573156370326 | epot = -38.3450518110649 | etot = -30.7303203934046 +51000 ekin = 3.84405747033417 | erot = 3.53181676479775 | epot = -38.2059734024445 | etot = -30.8300991673126 +52000 ekin = 3.72257170524986 | erot = 3.44233441463346 | epot = -38.0493176755067 | etot = -30.8844115556233 +53000 ekin = 3.58458805955587 | erot = 3.40175184254418 | epot = -37.8770316144346 | etot = -30.8906917123346 +54000 ekin = 3.42774104644866 | erot = 3.01933445329398 | epot = -37.7242775274776 | etot = -31.277202027735 +55000 ekin = 3.30773758120276 | erot = 3.11354928843072 | epot = -37.584427789289 | etot = -31.1631409196555 +56000 ekin = 3.30267684217518 | erot = 3.36746893036055 | epot = -37.4528615341919 | etot = -30.7827157616562 +57000 ekin = 3.19775481140565 | erot = 3.06235541109217 | epot = -37.3795633131473 | etot = -31.1194530906495 +58000 ekin = 3.11776701522974 | erot = 3.21225050262705 | epot = -37.3545495658646 | etot = -31.0245320480078 +59000 ekin = 3.02660076850687 | erot = 3.05700513362467 | epot = -37.3753385948441 | etot = -31.2917326927126 +60000 ekin = 3.05479252149938 | erot = 3.09854486170695 | epot = -37.4441725320783 | etot = -31.2908351488719 +61000 ekin = 3.01704476791617 | erot = 3.76451997765652 | epot = -37.5384296958521 | etot = -30.7568649502794 +62000 ekin = 3.04313706615776 | erot = 3.65046217125996 | epot = -37.6255736746588 | etot = -30.931974437241 +63000 ekin = 3.01457068009169 | erot = 3.63417424777149 | epot = -37.6954625017369 | etot = -31.0467175738737 +64000 ekin = 2.98716002899804 | erot = 3.66823413077172 | epot = -37.7940816265089 | etot = -31.1386874667392 +65000 ekin = 3.02462936411627 | erot = 3.70957377344584 | epot = -37.8868266007907 | etot = -31.1526234632286 +66000 ekin = 3.04943307417979 | erot = 3.64749592963955 | epot = -37.9385532609816 | etot = -31.2416242571623 +67000 ekin = 3.10664998766834 | erot = 3.9244199235005 | epot = -37.9686488739492 | etot = -30.9375789627803 +68000 ekin = 3.1050854233858 | erot = 3.5178167489996 | epot = -37.983113244155 | etot = -31.3602110717696 +69000 ekin = 3.12460161346418 | erot = 3.45336993587921 | epot = -38.016048039057 | etot = -31.4380764897136 +70000 ekin = 3.27586566025794 | erot = 2.94330488125488 | epot = -38.0712687269606 | etot = -31.8520981854478 +71000 ekin = 3.39211310061258 | erot = 2.74512861011504 | epot = -38.1409313278077 | etot = -32.0036896170801 +72000 ekin = 3.40645093836728 | erot = 2.75927481548157 | epot = -38.2448895790434 | etot = -32.0791638251946 +73000 ekin = 3.52971008848823 | erot = 2.59006671029947 | epot = -38.3559671032089 | etot = -32.2361903044212 +74000 ekin = 3.64539698532476 | erot = 2.94116909218575 | epot = -38.4934235930849 | etot = -31.9068575155744 +75000 ekin = 3.80169679560814 | erot = 3.11004664709647 | epot = -38.6561648833572 | etot = -31.7444214406526 +76000 ekin = 3.86343004207989 | erot = 3.33165114941789 | epot = -38.7892518002904 | etot = -31.5941706087926 +77000 ekin = 3.90472352035116 | erot = 3.31177401193377 | epot = -38.8678679983232 | etot = -31.6513704660382 +78000 ekin = 3.92691530468171 | erot = 3.25784074314341 | epot = -38.8969605625462 | etot = -31.7122045147211 +79000 ekin = 3.93607959529918 | erot = 3.16472395725656 | epot = -38.8636036578363 | etot = -31.7628001052805 +80000 ekin = 3.92375596570385 | erot = 3.03932991445865 | epot = -38.7678348516126 | etot = -31.8047489714501 +81000 ekin = 3.9430777715335 | erot = 2.88134017144298 | epot = -38.6473318824763 | etot = -31.8229139394998 +82000 ekin = 3.86696228915965 | erot = 2.89149309255461 | epot = -38.519943391552 | etot = -31.7614880098377 +83000 ekin = 3.60814275609262 | erot = 2.81572010912293 | epot = -38.3996592376438 | etot = -31.9757963724282 +84000 ekin = 3.71373301448702 | erot = 2.72793818704547 | epot = -38.3011883980015 | etot = -31.859517196469 +85000 ekin = 3.50951070251157 | erot = 2.79348490714939 | epot = -38.2117363909514 | etot = -31.9087407812904 +86000 ekin = 3.47308524750449 | erot = 3.12141964520655 | epot = -38.1244236248806 | etot = -31.5299187321696 +87000 ekin = 3.47440394227043 | erot = 3.04160702571504 | epot = -38.0440539828499 | etot = -31.5280430148644 +88000 ekin = 3.44172477689071 | erot = 2.99907227171085 | epot = -37.9859332104928 | etot = -31.5451361618913 +89000 ekin = 3.46547245050649 | erot = 3.42367325086164 | epot = -37.9432140623315 | etot = -31.0540683609633 +90000 ekin = 3.47276106924413 | erot = 3.41105238494334 | epot = -37.9009776655538 | etot = -31.0171642113663 +91000 ekin = 3.31717291023277 | erot = 4.00503611404981 | epot = -37.8509086765271 | etot = -30.5286996522445 +92000 ekin = 3.30281925189455 | erot = 3.78657692130476 | epot = -37.8308149894367 | etot = -30.7414188162374 +93000 ekin = 3.23932364656722 | erot = 3.46021357148725 | epot = -37.8328101558439 | etot = -31.1332729377895 +94000 ekin = 3.19291152023924 | erot = 3.36401906457231 | epot = -37.8297890174383 | etot = -31.2728584326267 +95000 ekin = 3.11174095364037 | erot = 3.84559531996404 | epot = -37.8285495206063 | etot = -30.8712132470019 +96000 ekin = 3.08253957616709 | erot = 4.19970849347964 | epot = -37.8307056468836 | etot = -30.5484575772369 +97000 ekin = 3.01019162595084 | erot = 4.79435511235213 | epot = -37.8474383063022 | etot = -30.0428915679992 +98000 ekin = 2.95004498340948 | erot = 4.45721895779631 | epot = -37.8489202082855 | etot = -30.4416562670797 +99000 ekin = 2.91563074020306 | erot = 4.14781823161589 | epot = -37.8396252499933 | etot = -30.7761762781743 +100000 ekin = 2.90648603235873 | erot = 3.81215086067838 | epot = -37.7900595351461 | etot = -31.071422642109 +101000 ekin = 2.85218071196321 | erot = 3.48991910340789 | epot = -37.7570245236792 | etot = -31.4149247083081 +102000 ekin = 2.86052427330307 | erot = 3.57587365782269 | epot = -37.7214005697291 | etot = -31.2850026386034 +103000 ekin = 2.88913271922391 | erot = 3.41748118405764 | epot = -37.6983180369495 | etot = -31.3917041336679 +104000 ekin = 2.81650081212179 | erot = 3.64361039549583 | epot = -37.6651320682074 | etot = -31.2050208605898 +105000 ekin = 2.79823699847461 | erot = 3.35865525277725 | epot = -37.6511913094721 | etot = -31.4942990582202 +106000 ekin = 2.78255015161702 | erot = 3.64122601097049 | epot = -37.6357012767034 | etot = -31.2119251141159 +107000 ekin = 2.8853059029881 | erot = 3.80038887689828 | epot = -37.6526611371135 | etot = -30.9669663572271 +108000 ekin = 2.83844762508156 | erot = 3.95272494897009 | epot = -37.7224292501163 | etot = -30.9312566760646 +109000 ekin = 2.91484982662488 | erot = 4.34544884566561 | epot = -37.8436434051328 | etot = -30.5833447328423 +110000 ekin = 2.93667443132402 | erot = 4.67698362049705 | epot = -37.9759529936705 | etot = -30.3622949418494 +111000 ekin = 3.11047864616463 | erot = 4.30694673133228 | epot = -38.1028692919235 | etot = -30.6854439144266 +112000 ekin = 3.32630420939175 | erot = 4.07222830175934 | epot = -38.2330557688864 | etot = -30.8345232577353 +113000 ekin = 3.38238157246173 | erot = 4.25399862575981 | epot = -38.4031841501303 | etot = -30.7668039519087 +114000 ekin = 3.40165200205494 | erot = 4.30744946748772 | epot = -38.6070332241657 | etot = -30.897931754623 +115000 ekin = 3.57685598139985 | erot = 4.55740206723813 | epot = -38.8200433287836 | etot = -30.6857852801457 +116000 ekin = 3.75973031177341 | erot = 4.3615765459289 | epot = -39.0323085624545 | etot = -30.9110017047522 +117000 ekin = 4.08170792820106 | erot = 4.22817627756988 | epot = -39.2374888319016 | etot = -30.9276046261307 +118000 ekin = 4.20730049786356 | erot = 4.45363628574744 | epot = -39.4247594107616 | etot = -30.7638226271506 +119000 ekin = 4.26502745539807 | erot = 4.38707691524353 | epot = -39.5609276649305 | etot = -30.9088232942889 +120000 ekin = 4.18668022830479 | erot = 4.24219249569072 | epot = -39.6276325806844 | etot = -31.1987598566889 +121000 ekin = 4.37673633947889 | erot = 4.44899930150549 | epot = -39.5989335189462 | etot = -30.7731978779619 +122000 ekin = 4.38970640566177 | erot = 4.08524736298491 | epot = -39.5011631447288 | etot = -31.0262093760821 +123000 ekin = 4.42858502015389 | erot = 3.38666748651706 | epot = -39.3700347945817 | etot = -31.5547822879107 +124000 ekin = 4.41843242629728 | erot = 3.29902599884916 | epot = -39.2496495732995 | etot = -31.532191148153 +125000 ekin = 4.2617494523508 | erot = 3.29673673713413 | epot = -39.1012418833314 | etot = -31.5427556938464 +126000 ekin = 4.24892047563245 | erot = 3.36728042977249 | epot = -38.9439369649168 | etot = -31.3277360595119 +127000 ekin = 4.20697642244211 | erot = 3.24776092764451 | epot = -38.7860930134988 | etot = -31.3313556634121 +128000 ekin = 4.051155507125 | erot = 3.47679598409534 | epot = -38.6330582994878 | etot = -31.1051068082675 +129000 ekin = 4.05771564566355 | erot = 3.55109790126639 | epot = -38.5073350485463 | etot = -30.8985215016164 +130000 ekin = 3.96453894213021 | erot = 3.5331352226628 | epot = -38.3915659508259 | etot = -30.8938917860329 +131000 ekin = 3.98900505769183 | erot = 3.64077310067997 | epot = -38.2786451293432 | etot = -30.6488669709714 +132000 ekin = 3.73079609117296 | erot = 3.73126171283414 | epot = -38.1409399456635 | etot = -30.6788821416564 +133000 ekin = 3.65247250435603 | erot = 3.53430985836843 | epot = -38.0235035134258 | etot = -30.8367211507014 +134000 ekin = 3.69649402588234 | erot = 3.97356364722737 | epot = -37.9278485959382 | etot = -30.2577909228285 +135000 ekin = 3.57147615494152 | erot = 4.00472599145964 | epot = -37.8397002442413 | etot = -30.2634980978401 +136000 ekin = 3.54164301577371 | erot = 3.88237062104624 | epot = -37.7460882463413 | etot = -30.3220746095214 +137000 ekin = 3.41247180964224 | erot = 3.32750587829717 | epot = -37.6246112923031 | etot = -30.8846336043637 +138000 ekin = 3.46206567288776 | erot = 3.47277237990382 | epot = -37.562116148782 | etot = -30.6272780959905 +139000 ekin = 3.46179863350053 | erot = 3.29345554522865 | epot = -37.5218039357363 | etot = -30.7665497570071 +140000 ekin = 3.57268233853842 | erot = 3.5202154657235 | epot = -37.4799882832129 | etot = -30.387090478951 +141000 ekin = 3.48030321137913 | erot = 3.69147952189496 | epot = -37.4842309048152 | etot = -30.3124481715411 +142000 ekin = 3.63349703801683 | erot = 3.72222694231707 | epot = -37.5326170636814 | etot = -30.1768930833475 +143000 ekin = 3.71391772492719 | erot = 3.32855653910457 | epot = -37.5715573506384 | etot = -30.5290830866066 +144000 ekin = 3.59876610372647 | erot = 3.57133292531736 | epot = -37.6083426167156 | etot = -30.4382435876717 +145000 ekin = 3.55129898738003 | erot = 3.38442665443505 | epot = -37.645703742064 | etot = -30.7099781002489 +146000 ekin = 3.57274630492872 | erot = 3.74306660671665 | epot = -37.6918399298831 | etot = -30.3760270182377 +147000 ekin = 3.51175180004563 | erot = 4.07506203504851 | epot = -37.7115891932223 | etot = -30.1247753581282 +148000 ekin = 3.52194530375129 | erot = 4.22438638639855 | epot = -37.7453589028593 | etot = -29.9990272127094 +149000 ekin = 3.43829227837986 | erot = 4.25032155928043 | epot = -37.7800675049656 | etot = -30.0914536673053 +150000 ekin = 3.3957375930512 | erot = 4.12519198982275 | epot = -37.7779101405858 | etot = -30.2569805577118 +151000 ekin = 3.38494817974845 | erot = 3.91154836764821 | epot = -37.7346130185547 | etot = -30.4381164711581 +152000 ekin = 3.33928233486053 | erot = 3.82420376901224 | epot = -37.6923063731278 | etot = -30.5288202692551 +153000 ekin = 3.38955645731944 | erot = 3.72251905459199 | epot = -37.6703717263952 | etot = -30.5582962144838 +154000 ekin = 3.4017017115168 | erot = 3.95270448125707 | epot = -37.6783897084388 | etot = -30.3239835156649 +155000 ekin = 3.44581188687106 | erot = 3.52528589615972 | epot = -37.7593041359923 | etot = -30.7882063529615 +156000 ekin = 3.55410349285979 | erot = 3.68359553101924 | epot = -37.8946612865555 | etot = -30.6569622626765 +157000 ekin = 3.67740663285561 | erot = 3.73708949692857 | epot = -38.0406477694046 | etot = -30.6261516396204 +158000 ekin = 3.70912292320982 | erot = 3.62418205239286 | epot = -38.1900046609469 | etot = -30.8566996853442 +159000 ekin = 3.6853282619123 | erot = 3.87298071798083 | epot = -38.2928836797072 | etot = -30.7345746998141 +160000 ekin = 3.72002440516723 | erot = 4.11592492943216 | epot = -38.3652902740973 | etot = -30.5293409394979 +161000 ekin = 3.73388863499069 | erot = 4.42836121024183 | epot = -38.4373191354183 | etot = -30.2750692901858 +162000 ekin = 4.02523829931076 | erot = 4.8680769419056 | epot = -38.4975346699525 | etot = -29.6042194287362 +163000 ekin = 4.03311015138323 | erot = 4.78291233450122 | epot = -38.5597523007635 | etot = -29.7437298148791 +164000 ekin = 4.1335004223363 | erot = 5.01454292769812 | epot = -38.5888368946085 | etot = -29.4407935445741 +165000 ekin = 4.2571846721418 | erot = 4.92225725319176 | epot = -38.5829201612759 | etot = -29.4034782359424 +166000 ekin = 4.11013815046505 | erot = 4.5380600083009 | epot = -38.5467907483033 | etot = -29.8985925895373 +167000 ekin = 4.08710467384593 | erot = 4.20997030650446 | epot = -38.4814936158366 | etot = -30.1844186354862 +168000 ekin = 4.03924000036858 | erot = 3.95993274976396 | epot = -38.3759188508994 | etot = -30.3767461007668 +169000 ekin = 3.94917218886656 | erot = 3.65240127094122 | epot = -38.2594355677076 | etot = -30.6578621078998 +170000 ekin = 3.90935554205321 | erot = 3.78797512477889 | epot = -38.1835201359157 | etot = -30.4861894690836 +171000 ekin = 3.8773250489546 | erot = 4.28652570004448 | epot = -38.1402484566641 | etot = -29.976397707665 +172000 ekin = 3.75957929171828 | erot = 4.02272820820138 | epot = -38.1557340618708 | etot = -30.3734265619512 +173000 ekin = 3.55030915229003 | erot = 4.03115995993296 | epot = -38.2480280629192 | etot = -30.6665589506962 +174000 ekin = 3.61281225750312 | erot = 4.30402685904744 | epot = -38.379508028535 | etot = -30.4626689119845 +175000 ekin = 3.56741376549371 | erot = 4.24945045724339 | epot = -38.5125929458379 | etot = -30.6957287231008 +176000 ekin = 3.69966296688439 | erot = 4.22673264606634 | epot = -38.6131459163278 | etot = -30.6867503033771 +177000 ekin = 3.7232933477479 | erot = 4.39637021744871 | epot = -38.6555013846403 | etot = -30.5358378194437 +178000 ekin = 3.7991935766677 | erot = 4.00194735045329 | epot = -38.6620582075599 | etot = -30.8609172804389 +179000 ekin = 3.78008346787859 | erot = 4.05267692212526 | epot = -38.6224110467893 | etot = -30.7896506567854 +180000 ekin = 3.84388711467645 | erot = 3.70916125532564 | epot = -38.5399848480517 | etot = -30.9869364780496 +181000 ekin = 3.78854199589317 | erot = 3.43025530256468 | epot = -38.4472679874805 | etot = -31.2284706890226 +182000 ekin = 3.65298336461982 | erot = 3.4144670384005 | epot = -38.3421256904839 | etot = -31.2746752874636 +183000 ekin = 3.57592466495272 | erot = 3.54000226366918 | epot = -38.2342661287443 | etot = -31.1183392001224 +184000 ekin = 3.59097293869161 | erot = 3.49764131752706 | epot = -38.1237685559035 | etot = -31.0351542996848 +185000 ekin = 3.59874593561892 | erot = 3.34180949424631 | epot = -38.0345613955437 | etot = -31.0940059656785 +186000 ekin = 3.55637392703387 | erot = 3.60010534755636 | epot = -37.9685691221056 | etot = -30.8120898475154 +187000 ekin = 3.30341471869181 | erot = 3.63282669533297 | epot = -37.9082034969871 | etot = -30.9719620829623 +188000 ekin = 3.25151380843728 | erot = 3.4158708150676 | epot = -37.8374520507023 | etot = -31.1700674271975 +189000 ekin = 3.09888859581603 | erot = 3.51324139411299 | epot = -37.7831379378025 | etot = -31.1710079478735 +190000 ekin = 2.9309664789049 | erot = 3.73100049541724 | epot = -37.7090579094215 | etot = -31.0470909350994 +191000 ekin = 2.7884578953631 | erot = 3.59181404756254 | epot = -37.6234731970084 | etot = -31.2432012540828 +192000 ekin = 2.68708504006426 | erot = 3.91911783313626 | epot = -37.526883385388 | etot = -30.9206805121875 +193000 ekin = 2.65091164661301 | erot = 3.82754219131902 | epot = -37.4213833049326 | etot = -30.9429294670006 +194000 ekin = 2.55372434146215 | erot = 3.81228833556049 | epot = -37.3433541779816 | etot = -30.977341500959 +195000 ekin = 2.54515296633922 | erot = 3.77157425987472 | epot = -37.2550689450336 | etot = -30.9383417188196 +196000 ekin = 2.57228739351393 | erot = 3.48448370430655 | epot = -37.1707275909677 | etot = -31.1139564931472 +197000 ekin = 2.47659034250743 | erot = 3.31788075232347 | epot = -37.1125490303323 | etot = -31.3180779355014 +198000 ekin = 2.47817611131623 | erot = 3.41593598489791 | epot = -37.0628542395745 | etot = -31.1687421433604 +199000 ekin = 2.46398696321861 | erot = 3.79330738397083 | epot = -37.0410272717131 | etot = -30.7837329245237 +200000 ekin = 2.66032750534619 | erot = 3.50045834258033 | epot = -37.0560186461538 | etot = -30.8952327982273 +201000 ekin = 2.82925423269724 | erot = 3.87280363693036 | epot = -37.1094527749141 | etot = -30.4073949052865 +202000 ekin = 2.87690134773435 | erot = 3.73724666810631 | epot = -37.1548849140444 | etot = -30.5407368982037 +203000 ekin = 3.09789929071291 | erot = 3.54687635269494 | epot = -37.1913390618662 | etot = -30.5465634184584 +204000 ekin = 3.2249783082041 | erot = 3.52082166300909 | epot = -37.2064645595876 | etot = -30.4606645883744 +205000 ekin = 3.08968228459873 | erot = 3.62768693137654 | epot = -37.2539593887052 | etot = -30.5365901727299 +206000 ekin = 3.1101415017481 | erot = 3.73856786590981 | epot = -37.3166778706669 | etot = -30.467968503009 +207000 ekin = 3.1829453735338 | erot = 4.25652712659376 | epot = -37.3463184168161 | etot = -29.9068459166886 +208000 ekin = 3.18396090757444 | erot = 4.43896014450663 | epot = -37.3566061410102 | etot = -29.7336850889291 +209000 ekin = 3.31348354672045 | erot = 3.97662877739679 | epot = -37.3764215045056 | etot = -30.0863091803884 +210000 ekin = 3.17486958285119 | erot = 3.68714944924489 | epot = -37.3622513109274 | etot = -30.5002322788313 +211000 ekin = 3.2477738173839 | erot = 3.39112189744197 | epot = -37.3847088569504 | etot = -30.7458131421245 +212000 ekin = 3.12182354729226 | erot = 3.15133571404853 | epot = -37.4262282165348 | etot = -31.153068955194 +213000 ekin = 3.1232309019731 | erot = 3.03298058440268 | epot = -37.4993866522035 | etot = -31.3431751658277 +214000 ekin = 3.02782055391866 | erot = 3.5189307426383 | epot = -37.618739888869 | etot = -31.071988592312 +215000 ekin = 3.08902625374254 | erot = 3.62054952513122 | epot = -37.8003692924875 | etot = -31.0907935136138 +216000 ekin = 3.0402918166672 | erot = 4.36545701920737 | epot = -38.0086846511918 | etot = -30.6029358153172 +217000 ekin = 3.11869416684308 | erot = 4.23835788568589 | epot = -38.1755180741878 | etot = -30.8184660216589 +218000 ekin = 3.12136726795473 | erot = 3.99627368131625 | epot = -38.3382201370155 | etot = -31.2205791877445 +219000 ekin = 3.2474996523994 | erot = 4.03289859762084 | epot = -38.4910930976405 | etot = -31.2106948476203 +220000 ekin = 3.1973165065664 | erot = 4.16726840142166 | epot = -38.6410163306451 | etot = -31.276431422657 +221000 ekin = 3.14591003185424 | erot = 4.4764367328117 | epot = -38.780722121156 | etot = -31.15837535649 +222000 ekin = 3.06194834255767 | erot = 4.40957176775797 | epot = -38.8960295960944 | etot = -31.4245094857787 +223000 ekin = 3.09392792198335 | erot = 4.36929377800867 | epot = -38.9696160320109 | etot = -31.5063943320188 +224000 ekin = 3.18434099924865 | erot = 4.674141260581 | epot = -39.0019773177328 | etot = -31.1434950579031 +225000 ekin = 3.26887097312573 | erot = 4.32849031089069 | epot = -39.0446790784002 | etot = -31.4473177943838 +226000 ekin = 3.21195731331512 | erot = 5.11387401999741 | epot = -39.0947841174991 | etot = -30.7689527841866 +227000 ekin = 3.12036258026498 | erot = 5.06347912205044 | epot = -39.0762383614625 | etot = -30.8923966591471 +228000 ekin = 3.09996729726213 | erot = 5.29564700287486 | epot = -39.0208988713251 | etot = -30.6252845711881 +229000 ekin = 3.03897933795902 | erot = 5.24780237112332 | epot = -38.9575212211327 | etot = -30.6707395120503 +230000 ekin = 3.00051887289146 | erot = 4.62162674048183 | epot = -38.9098464143818 | etot = -31.2877008010086 +231000 ekin = 2.91912781370872 | erot = 4.16321547565937 | epot = -38.8503568044396 | etot = -31.7680135150715 +232000 ekin = 2.80548407611275 | erot = 4.26963451717891 | epot = -38.7971045932123 | etot = -31.7219859999206 +233000 ekin = 2.921352071703 | erot = 4.30663886521625 | epot = -38.7943069633021 | etot = -31.5663160263829 +234000 ekin = 2.8987567571007 | erot = 4.15218445741161 | epot = -38.7953536145697 | etot = -31.7444124000574 +235000 ekin = 2.99243729544443 | erot = 3.66858116296993 | epot = -38.7881689836612 | etot = -32.1271505252468 +236000 ekin = 3.05722012426337 | erot = 3.77007572255967 | epot = -38.8307946718328 | etot = -32.0034988250098 +237000 ekin = 2.93797686036748 | erot = 4.00589644921927 | epot = -38.929946515337 | etot = -31.9860732057502 +238000 ekin = 2.9414435200925 | erot = 3.88111097233617 | epot = -39.0498657472631 | etot = -32.2273112548344 +239000 ekin = 3.10382951223872 | erot = 3.96380163382871 | epot = -39.1526703213401 | etot = -32.0850391752727 +240000 ekin = 3.05998182778604 | erot = 4.32395093282883 | epot = -39.2052189603879 | etot = -31.821286199773 +241000 ekin = 3.07091800265519 | erot = 4.10063821004074 | epot = -39.2356744872187 | etot = -32.0641182745228 +242000 ekin = 2.97211136503677 | erot = 4.19271702506013 | epot = -39.2591861941867 | etot = -32.0943578040898 +243000 ekin = 2.88784895332253 | erot = 4.01063377556442 | epot = -39.2721844581366 | etot = -32.3737017292496 +244000 ekin = 2.72034159299267 | erot = 3.9497078953668 | epot = -39.2969463203695 | etot = -32.62689683201 +245000 ekin = 2.73288139378783 | erot = 4.29552525608627 | epot = -39.3467303394195 | etot = -32.3183236895454 +246000 ekin = 2.68282749729218 | erot = 4.43958709181175 | epot = -39.4036850899301 | etot = -32.2812705008262 +247000 ekin = 2.73156079717717 | erot = 4.29997633507683 | epot = -39.4831744493476 | etot = -32.4516373170936 +248000 ekin = 2.71615239962776 | erot = 4.48384110145867 | epot = -39.5625690361122 | etot = -32.3625755350257 +249000 ekin = 2.72571373834881 | erot = 4.5335019483569 | epot = -39.6161562336935 | etot = -32.3569405469878 +250000 ekin = 2.67302825179683 | erot = 5.17929377782009 | epot = -39.6758534551748 | etot = -31.8235314255579 +251000 ekin = 2.6507365898703 | erot = 5.39364408144172 | epot = -39.7013652486056 | etot = -31.6569845772935 +252000 ekin = 2.81604561937354 | erot = 5.50799647083842 | epot = -39.6939189845586 | etot = -31.3698768943466 +253000 ekin = 2.83629985586585 | erot = 4.91166111825379 | epot = -39.6825773475315 | etot = -31.9346163734119 +254000 ekin = 2.79908189634044 | erot = 4.88281944777383 | epot = -39.6620010988144 | etot = -31.9800997547001 +255000 ekin = 2.84238496514409 | erot = 4.79166487708097 | epot = -39.6680683880925 | etot = -32.0340185458674 +256000 ekin = 2.82611571908347 | erot = 4.38756969310712 | epot = -39.7220228798985 | etot = -32.5083374677079 +257000 ekin = 2.78077325096871 | erot = 4.5642639453855 | epot = -39.7657957602323 | etot = -32.420758563878 +258000 ekin = 2.84466353932841 | erot = 4.94939241805645 | epot = -39.7743058264474 | etot = -31.9802498690625 +259000 ekin = 2.82994372921754 | erot = 4.84156348043289 | epot = -39.7845084321782 | etot = -32.1130012225278 +260000 ekin = 2.84769599243485 | erot = 4.63369709433921 | epot = -39.8060470464454 | etot = -32.3246539596713 +261000 ekin = 2.87237157835352 | erot = 4.51865061212279 | epot = -39.7979847736537 | etot = -32.4069625831774 +262000 ekin = 2.96750612225965 | erot = 4.57561390426948 | epot = -39.7782660470083 | etot = -32.2351460204792 +263000 ekin = 2.9928936584238 | erot = 4.20953311292943 | epot = -39.7453211677642 | etot = -32.542894396411 +264000 ekin = 3.02610258005868 | erot = 4.41804994162532 | epot = -39.7005266944526 | etot = -32.2563741727686 +265000 ekin = 3.02210011112739 | erot = 4.29011549844082 | epot = -39.6578667285885 | etot = -32.3456511190202 +266000 ekin = 2.9552602997359 | erot = 3.9722013360736 | epot = -39.586314373395 | etot = -32.6588527375855 +267000 ekin = 2.96306286479368 | erot = 4.39982365552042 | epot = -39.5117362736935 | etot = -32.1488497533794 +268000 ekin = 2.98837918599768 | erot = 4.59043107838106 | epot = -39.4346030266013 | etot = -31.8557927622225 +269000 ekin = 2.92733730866694 | erot = 4.81492520489307 | epot = -39.3017884762547 | etot = -31.5595259626947 +270000 ekin = 2.90335610024247 | erot = 4.98515255872076 | epot = -39.1437745457484 | etot = -31.2552658867851 +271000 ekin = 2.87611923369216 | erot = 5.02631285080427 | epot = -38.9919498909516 | etot = -31.0895178064552 +272000 ekin = 2.8777026077458 | erot = 4.83651556609768 | epot = -38.8408093950138 | etot = -31.1265912211703 +273000 ekin = 2.77329089721161 | erot = 4.69693225863749 | epot = -38.6610493537941 | etot = -31.190826197945 +274000 ekin = 2.68625637002646 | erot = 4.51669986790578 | epot = -38.450972898294 | etot = -31.2480166603618 +275000 ekin = 2.6033032445429 | erot = 4.20171703621303 | epot = -38.2182499356279 | etot = -31.413229654872 +276000 ekin = 2.57183076311405 | erot = 3.79152446287658 | epot = -38.0174336495132 | etot = -31.6540784235226 +277000 ekin = 2.49975386368552 | erot = 3.59614150828643 | epot = -37.8474968832234 | etot = -31.7516015112514 +278000 ekin = 2.46398069339692 | erot = 3.65098267442651 | epot = -37.6582057642292 | etot = -31.5432423964058 +279000 ekin = 2.48339824565301 | erot = 3.67548575635043 | epot = -37.5048702413578 | etot = -31.3459862393543 +280000 ekin = 2.53376634761115 | erot = 3.55656380463993 | epot = -37.3937621487775 | etot = -31.3034319965264 +281000 ekin = 2.67002406168555 | erot = 3.81689537677439 | epot = -37.3207483356567 | etot = -30.8338288971967 +282000 ekin = 2.63534042744469 | erot = 3.62617225051201 | epot = -37.2561498174831 | etot = -30.9946371395264 +283000 ekin = 2.6220496059321 | erot = 3.60063437351299 | epot = -37.1865464899412 | etot = -30.9638625104961 +284000 ekin = 2.67681575008794 | erot = 3.61566503901023 | epot = -37.1459845078296 | etot = -30.8535037187314 +285000 ekin = 2.71360352201128 | erot = 3.48822466196441 | epot = -37.1436040722677 | etot = -30.941775888292 +286000 ekin = 2.72409949367879 | erot = 3.69046973300079 | epot = -37.1515114688671 | etot = -30.7369422421875 +287000 ekin = 2.78141221541732 | erot = 3.56169254019539 | epot = -37.1836412585713 | etot = -30.8405365029586 +288000 ekin = 2.93111949257226 | erot = 3.8525227571685 | epot = -37.2722312757955 | etot = -30.4885890260548 +289000 ekin = 3.22039073654125 | erot = 3.65796134125549 | epot = -37.4105935842029 | etot = -30.5322415064062 +290000 ekin = 3.45543672952192 | erot = 3.63587074171854 | epot = -37.5601919395408 | etot = -30.4688844683004 +291000 ekin = 3.52760878967926 | erot = 4.20430698093698 | epot = -37.7322836777775 | etot = -30.0003679071612 +292000 ekin = 3.68972381818942 | erot = 4.12076553978665 | epot = -37.9100323199299 | etot = -30.0995429619539 +293000 ekin = 3.83177225674892 | erot = 4.37726484522697 | epot = -38.0821109906697 | etot = -29.8730738886939 +294000 ekin = 4.06640459910211 | erot = 3.74462680595297 | epot = -38.1926156973085 | etot = -30.3815842922535 +295000 ekin = 4.21784736111078 | erot = 3.82616484716752 | epot = -38.2890286287625 | etot = -30.2450164204842 +296000 ekin = 4.26440738773668 | erot = 3.95694734709923 | epot = -38.3824567525616 | etot = -30.1611020177257 +297000 ekin = 4.04618321058719 | erot = 4.11344152769709 | epot = -38.4823151027027 | etot = -30.3226903644185 +298000 ekin = 4.04534420229663 | erot = 4.08413503201891 | epot = -38.5648464298591 | etot = -30.4353671955436 +299000 ekin = 4.0589099673587 | erot = 4.75454163668515 | epot = -38.639463237644 | etot = -29.8260116336001 +300000 ekin = 4.06355522455796 | erot = 4.46292256841625 | epot = -38.7062117520832 | etot = -30.179733959109 +301000 ekin = 4.01853385887688 | erot = 4.67242188374982 | epot = -38.7555551980343 | etot = -30.0645994554076 +302000 ekin = 3.97170308302913 | erot = 4.62245717998414 | epot = -38.7884989680142 | etot = -30.194338705001 +303000 ekin = 4.00670279913523 | erot = 4.89772983741929 | epot = -38.799236313657 | etot = -29.8948036771024 +304000 ekin = 3.81374525151692 | erot = 4.6538936598735 | epot = -38.8327396351166 | etot = -30.3651007237262 +305000 ekin = 3.70792918499072 | erot = 4.53646691129901 | epot = -38.8671341843092 | etot = -30.6227380880195 +306000 ekin = 3.58519135856873 | erot = 4.40317156262038 | epot = -38.8961174826077 | etot = -30.9077545614186 +307000 ekin = 3.52830601019332 | erot = 4.12955816022909 | epot = -38.9381266871201 | etot = -31.2802625166977 +308000 ekin = 3.37444573697916 | erot = 3.65266283146942 | epot = -38.9820449321945 | etot = -31.9549363637459 +309000 ekin = 3.29877896595905 | erot = 4.06788139443827 | epot = -39.0365696198577 | etot = -31.6699092594604 +310000 ekin = 3.27216182566108 | erot = 3.86752279813189 | epot = -39.0649343092171 | etot = -31.9252496854241 +311000 ekin = 3.26050147382307 | erot = 3.90928978323579 | epot = -39.0580520931933 | etot = -31.8882608361345 +312000 ekin = 3.1848300908952 | erot = 3.90959546619215 | epot = -39.0257212693578 | etot = -31.9312957122705 +313000 ekin = 3.09609326591794 | erot = 3.75025646421268 | epot = -38.9535227577836 | etot = -32.107173027653 +314000 ekin = 2.95184537018541 | erot = 4.07381717812352 | epot = -38.8888909934781 | etot = -31.8632284451692 +315000 ekin = 2.92238623527564 | erot = 3.96815066682756 | epot = -38.8370494801766 | etot = -31.9465125780734 +316000 ekin = 2.71301507861594 | erot = 3.8080797893295 | epot = -38.7998345743978 | etot = -32.2787397064523 +317000 ekin = 2.71357150367643 | erot = 4.15190966526588 | epot = -38.7626719044114 | etot = -31.8971907354691 +318000 ekin = 2.62158267835355 | erot = 4.27134701113463 | epot = -38.7271070788674 | etot = -31.8341773893792 +319000 ekin = 2.55366548062856 | erot = 4.41350408683224 | epot = -38.7297464727615 | etot = -31.7625769053007 +320000 ekin = 2.4339724053854 | erot = 4.29070167476865 | epot = -38.7203908826319 | etot = -31.9957168024778 +321000 ekin = 2.40916961938935 | erot = 4.08120981437149 | epot = -38.7041016741434 | etot = -32.2137222403825 +322000 ekin = 2.40921951438688 | erot = 3.84656254092896 | epot = -38.6896664254557 | etot = -32.4338843701398 +323000 ekin = 2.47763175846145 | erot = 3.74024157191546 | epot = -38.6582034756257 | etot = -32.4403301452488 +324000 ekin = 2.50557286685252 | erot = 3.62726015904503 | epot = -38.6277589097221 | etot = -32.4949258838246 +325000 ekin = 2.46128003790462 | erot = 3.30955838055067 | epot = -38.61822105265 | etot = -32.8473826341947 +326000 ekin = 2.50360422224121 | erot = 3.11309077075955 | epot = -38.6155228491476 | etot = -32.9988278561469 +327000 ekin = 2.58559564340003 | erot = 3.03172964208493 | epot = -38.6235874334491 | etot = -33.0062621479641 +328000 ekin = 2.74984266079838 | erot = 3.02808338407911 | epot = -38.6550386035093 | etot = -32.8771125586319 +329000 ekin = 2.91966436364505 | erot = 2.9714434817756 | epot = -38.682045485323 | etot = -32.7909376399024 +330000 ekin = 3.01494295487819 | erot = 3.4413838499053 | epot = -38.7383158304585 | etot = -32.281989025675 +331000 ekin = 3.02442201542022 | erot = 3.78657407910222 | epot = -38.7939596216319 | etot = -31.9829635271095 +332000 ekin = 3.04445691127431 | erot = 3.82788901953126 | epot = -38.8517978078765 | etot = -31.9794518770709 +333000 ekin = 3.03465557138393 | erot = 3.68623317701479 | epot = -38.9019287356725 | etot = -32.1810399872737 +334000 ekin = 2.9809147586341 | erot = 3.87909097065051 | epot = -38.9429458678103 | etot = -32.0829401385257 +335000 ekin = 3.18730692360922 | erot = 3.92298153235814 | epot = -38.9915367606723 | etot = -31.8812483047049 +336000 ekin = 3.28082580011875 | erot = 4.25501923477967 | epot = -39.038294903881 | etot = -31.5024498689825 +337000 ekin = 3.33075954016491 | erot = 4.58632261209059 | epot = -39.0662594017921 | etot = -31.1491772495366 +338000 ekin = 3.31328438683341 | erot = 4.17966745642972 | epot = -39.0415239975115 | etot = -31.5485721542484 +339000 ekin = 3.33917527804132 | erot = 4.28130062815465 | epot = -38.9842917012714 | etot = -31.3638157950754 +340000 ekin = 3.33492148280264 | erot = 4.35651035139105 | epot = -38.8943885223068 | etot = -31.2029566881131 +341000 ekin = 3.3461417209637 | erot = 4.05115720989158 | epot = -38.7823758155587 | etot = -31.3850768847035 +342000 ekin = 3.34251507796689 | erot = 4.42814474655732 | epot = -38.6331517957714 | etot = -30.8624919712472 +343000 ekin = 3.20631341754623 | erot = 3.78967989344565 | epot = -38.4960486393224 | etot = -31.5000553283305 +344000 ekin = 3.07148244251166 | erot = 3.87583965670226 | epot = -38.3948328820768 | etot = -31.4475107828629 +345000 ekin = 3.09789874291718 | erot = 3.9946056524089 | epot = -38.3201974875894 | etot = -31.2276930922633 +346000 ekin = 3.0250008126834 | erot = 3.91508207831934 | epot = -38.2750630613601 | etot = -31.3349801703574 +347000 ekin = 2.94406849477781 | erot = 3.86229670162422 | epot = -38.2289722622904 | etot = -31.4226070658884 +348000 ekin = 2.95641250006446 | erot = 3.72625853383758 | epot = -38.1919210104045 | etot = -31.5092499765025 +349000 ekin = 3.03918076184492 | erot = 3.94202050743572 | epot = -38.1810668298085 | etot = -31.1998655605279 +350000 ekin = 3.09062612520409 | erot = 3.91215331884796 | epot = -38.2023245264387 | etot = -31.1995450823866 +351000 ekin = 3.13831719496483 | erot = 3.99916602553205 | epot = -38.2111529945909 | etot = -31.073669774094 +352000 ekin = 3.10196313130359 | erot = 3.92254342354132 | epot = -38.2543166357449 | etot = -31.2298100809 +353000 ekin = 3.17266611312447 | erot = 3.8947350963975 | epot = -38.3205511283306 | etot = -31.2531499188087 +354000 ekin = 3.20288707130899 | erot = 4.38957454856388 | epot = -38.3888699269269 | etot = -30.7964083070541 +355000 ekin = 3.15965957595978 | erot = 4.27393537405648 | epot = -38.4369161779509 | etot = -31.0033212279347 +356000 ekin = 3.01967844026133 | erot = 4.46559381130412 | epot = -38.4622452099032 | etot = -30.9769729583378 +357000 ekin = 2.97836465744991 | erot = 4.24123654484996 | epot = -38.4340474220208 | etot = -31.214446219721 +358000 ekin = 2.90298621775697 | erot = 4.00214290087714 | epot = -38.3669225243922 | etot = -31.4617934057581 +359000 ekin = 2.89703951576617 | erot = 3.75540528896971 | epot = -38.2596281019021 | etot = -31.6071832971662 +360000 ekin = 2.8951746897939 | erot = 3.69844688179068 | epot = -38.1408983158929 | etot = -31.5472767443083 +361000 ekin = 2.80138616808281 | erot = 3.38323529451493 | epot = -38.0246589917389 | etot = -31.8400375291412 +362000 ekin = 2.77162168417597 | erot = 2.91331523066534 | epot = -37.9398868290147 | etot = -32.2549499141734 +363000 ekin = 2.78539815378419 | erot = 2.68460040337592 | epot = -37.8665635409936 | etot = -32.3965649838335 +364000 ekin = 2.68067812192279 | erot = 2.78677391239245 | epot = -37.7617899033782 | etot = -32.2943378690629 +365000 ekin = 2.54070043685867 | erot = 2.83653994835764 | epot = -37.6554311404473 | etot = -32.278190755231 +366000 ekin = 2.41606481092133 | erot = 2.86609766611194 | epot = -37.5516282283376 | etot = -32.2694657513043 +367000 ekin = 2.46811866465482 | erot = 3.34221140329001 | epot = -37.4475028758825 | etot = -31.6371728079377 +368000 ekin = 2.42926223365496 | erot = 3.33046663396731 | epot = -37.3674460967944 | etot = -31.6077172291721 +369000 ekin = 2.43816169312797 | erot = 3.26459431026922 | epot = -37.3019788371043 | etot = -31.5992228337071 +370000 ekin = 2.46038177337534 | erot = 3.10066469966258 | epot = -37.2626057339964 | etot = -31.7015592609585 +371000 ekin = 2.4406243852624 | erot = 2.87778487491552 | epot = -37.2539180634396 | etot = -31.9355088032617 +372000 ekin = 2.41196438326736 | erot = 3.07515188922142 | epot = -37.3089635753533 | etot = -31.8218473028645 +373000 ekin = 2.48050565170792 | erot = 3.18196875652289 | epot = -37.4397878357734 | etot = -31.7773134275426 +374000 ekin = 2.6353068806194 | erot = 3.59156982435214 | epot = -37.5884648424034 | etot = -31.3615881374319 +375000 ekin = 2.68283894448276 | erot = 3.32451084068228 | epot = -37.7715422578283 | etot = -31.7641924726633 +376000 ekin = 2.79488034579927 | erot = 3.22988532668866 | epot = -38.000903910215 | etot = -31.976138237727 +377000 ekin = 2.97793932778653 | erot = 3.14879447385383 | epot = -38.2360750185569 | etot = -32.1093412169166 +378000 ekin = 3.04959845592839 | erot = 3.49481966296078 | epot = -38.5013695235685 | etot = -31.9569514046793 +379000 ekin = 3.1910641072712 | erot = 3.36561045250094 | epot = -38.7688607813369 | etot = -32.2121862215648 +380000 ekin = 3.25183572215737 | erot = 3.58875776192786 | epot = -39.0288452181145 | etot = -32.1882517340293 +381000 ekin = 3.33794215221605 | erot = 3.6933917756671 | epot = -39.3017064605084 | etot = -32.2703725326252 +382000 ekin = 3.49270190624151 | erot = 3.86829998834037 | epot = -39.5268729273467 | etot = -32.1658710327648 +383000 ekin = 3.55662169084786 | erot = 3.53333329088014 | epot = -39.7267791075158 | etot = -32.6368241257878 +384000 ekin = 3.69351012028553 | erot = 3.28268730044342 | epot = -39.878987472358 | etot = -32.9027900516291 +385000 ekin = 3.6873370603751 | erot = 3.68055641648018 | epot = -39.9998839253488 | etot = -32.6319904484935 +386000 ekin = 3.71694831249288 | erot = 3.79434784508072 | epot = -40.0869801892987 | etot = -32.5756840317251 +387000 ekin = 3.76861509268675 | erot = 3.88558369375098 | epot = -40.1715737743674 | etot = -32.5173749879297 +388000 ekin = 3.83017606883369 | erot = 4.20859412334364 | epot = -40.2007323597246 | etot = -32.1619621675473 +389000 ekin = 3.86768485031755 | erot = 3.99003783907115 | epot = -40.1899129305041 | etot = -32.3321902411154 +390000 ekin = 3.97485559059836 | erot = 3.73907035926323 | epot = -40.1534652302145 | etot = -32.4395392803529 +391000 ekin = 3.99255423920733 | erot = 3.4598541410162 | epot = -40.0955220791988 | etot = -32.6431136989752 +392000 ekin = 4.01983776245659 | erot = 3.68425742647522 | epot = -39.9999647918603 | etot = -32.2958696029285 +393000 ekin = 4.02356764424238 | erot = 3.83787437414739 | epot = -39.8549016020689 | etot = -31.9934595836791 +394000 ekin = 3.93980876114311 | erot = 3.99211744164141 | epot = -39.7011477670265 | etot = -31.769221564242 +395000 ekin = 4.11174368478708 | erot = 3.75033473410268 | epot = -39.5451859148434 | etot = -31.6831074959536 +396000 ekin = 4.20376876107151 | erot = 3.67040632781378 | epot = -39.3948809980869 | etot = -31.5207059092016 +397000 ekin = 4.1363357284298 | erot = 3.65151581957621 | epot = -39.2564297317577 | etot = -31.4685781837517 +398000 ekin = 4.13905245601608 | erot = 3.71620600673377 | epot = -39.093596770216 | etot = -31.2383383074661 +399000 ekin = 4.10332411545508 | erot = 3.71374971681594 | epot = -38.9205234935041 | etot = -31.1034496612331 +400000 ekin = 4.0676601690846 | erot = 3.4213950465438 | epot = -38.7497473150008 | etot = -31.2606920993724 +401000 ekin = 3.9728416411198 | erot = 3.81120481171758 | epot = -38.6001977504162 | etot = -30.8161512975788 +402000 ekin = 3.90587383547448 | erot = 3.5341882621858 | epot = -38.4681757167875 | etot = -31.0281136191273 +403000 ekin = 3.91259869514543 | erot = 3.637386391841 | epot = -38.3230308363683 | etot = -30.7730457493819 +404000 ekin = 3.79936006877817 | erot = 3.32641249272551 | epot = -38.2009092385688 | etot = -31.0751366770651 +405000 ekin = 3.82517596801147 | erot = 3.13064904024263 | epot = -38.1553776059003 | etot = -31.1995525976462 +406000 ekin = 3.73725599382596 | erot = 3.08306268157758 | epot = -38.1316917306566 | etot = -31.3113730552531 +407000 ekin = 3.72651775045891 | erot = 3.09861818078628 | epot = -38.1634910279952 | etot = -31.33835509675 +408000 ekin = 3.79931976439455 | erot = 3.25718386016379 | epot = -38.2217683212397 | etot = -31.1652646966813 +409000 ekin = 3.95093187918723 | erot = 3.43950409776017 | epot = -38.2689453197332 | etot = -30.8785093427858 +410000 ekin = 4.07121708138893 | erot = 3.83760071106065 | epot = -38.3189798432044 | etot = -30.4101620507548 +411000 ekin = 4.2330797855817 | erot = 3.98162063698068 | epot = -38.3721329673505 | etot = -30.1574325447882 +412000 ekin = 4.24117080814308 | erot = 3.9973719347696 | epot = -38.4124767699444 | etot = -30.1739340270317 +413000 ekin = 4.23580670923557 | erot = 3.81064398502802 | epot = -38.4212920990953 | etot = -30.3748414048317 +414000 ekin = 4.27445938143094 | erot = 3.98124541320507 | epot = -38.4106571527343 | etot = -30.1549523580983 +415000 ekin = 4.388994790051 | erot = 3.80279226112407 | epot = -38.3596783722966 | etot = -30.1678913211216 +416000 ekin = 4.45628965411069 | erot = 3.63102956113301 | epot = -38.3042311126169 | etot = -30.2169118973732 +417000 ekin = 4.49028461121071 | erot = 3.62754419666011 | epot = -38.2583198089302 | etot = -30.1404910010594 +418000 ekin = 4.45936601962006 | erot = 3.71144506663867 | epot = -38.1813464675299 | etot = -30.0105353812712 +419000 ekin = 4.38379837521009 | erot = 3.33513327030929 | epot = -38.0724868069421 | etot = -30.3535551614227 +420000 ekin = 4.283111933024 | erot = 3.09826419668627 | epot = -37.9370678690099 | etot = -30.5556917392996 +421000 ekin = 4.15248097510599 | erot = 3.56237827808249 | epot = -37.7709210423884 | etot = -30.0560617891999 +422000 ekin = 3.95490687211586 | erot = 3.47480957997355 | epot = -37.5854884820711 | etot = -30.1557720299817 +423000 ekin = 3.91714305790352 | erot = 3.48476286323411 | epot = -37.3949936437695 | etot = -29.9930877226319 +424000 ekin = 3.84213202460282 | erot = 3.52777059768047 | epot = -37.2158434462619 | etot = -29.8459408239786 +425000 ekin = 3.71924289661379 | erot = 3.3366360966062 | epot = -37.0722526001231 | etot = -30.0163736069031 +426000 ekin = 3.64441997260638 | erot = 3.3622793544102 | epot = -36.9667678357552 | etot = -29.9600685087386 +427000 ekin = 3.75655721345773 | erot = 3.37897054079372 | epot = -36.8611280898054 | etot = -29.725600335554 +428000 ekin = 3.74409443646511 | erot = 3.17732872354239 | epot = -36.742715037602 | etot = -29.8212918775945 +429000 ekin = 3.66329028317848 | erot = 2.78764787478689 | epot = -36.6486255145436 | etot = -30.1976873565782 +430000 ekin = 3.62135290496431 | erot = 2.67337975160585 | epot = -36.5606041515419 | etot = -30.2658714949718 +431000 ekin = 3.61616361793039 | erot = 2.69754710014207 | epot = -36.506732939117 | etot = -30.1930222210445 +432000 ekin = 3.49552617760814 | erot = 3.08491352170466 | epot = -36.485170074763 | etot = -29.9047303754502 +433000 ekin = 3.58020816083934 | erot = 2.88002256286323 | epot = -36.5217696117553 | etot = -30.0615388880528 +434000 ekin = 3.59867849318961 | erot = 3.08407973313556 | epot = -36.6202495320039 | etot = -29.9374913056787 +435000 ekin = 3.67331527289028 | erot = 3.42657552434431 | epot = -36.7488916307825 | etot = -29.6490008335479 +436000 ekin = 3.82088042289265 | erot = 3.6544744236991 | epot = -36.9085622220518 | etot = -29.4332073754601 +437000 ekin = 3.8686942167376 | erot = 3.9547028707988 | epot = -37.0720316005958 | etot = -29.2486345130594 +438000 ekin = 4.11090595842079 | erot = 3.77540801446856 | epot = -37.2088542252226 | etot = -29.3225402523332 +439000 ekin = 4.12926159073598 | erot = 4.06917140325898 | epot = -37.3517590512211 | etot = -29.1533260572261 +440000 ekin = 4.09029177261519 | erot = 4.1498129956529 | epot = -37.4912988817269 | etot = -29.2511941134589 +441000 ekin = 4.14485979348676 | erot = 4.37283240826401 | epot = -37.6181493098546 | etot = -29.1004571081038 +442000 ekin = 4.12304009572835 | erot = 4.39045893698218 | epot = -37.7155315750663 | etot = -29.2020325423558 +443000 ekin = 4.23471751438722 | erot = 4.14989601608929 | epot = -37.768614271265 | etot = -29.3840007407884 +444000 ekin = 4.35772646838213 | erot = 4.52232474512896 | epot = -37.7816885908051 | etot = -28.901637377294 +445000 ekin = 4.39118784053251 | erot = 4.66570824296103 | epot = -37.7439950146597 | etot = -28.6870989311661 +446000 ekin = 4.3967592176502 | erot = 4.46936063153373 | epot = -37.6960851354907 | etot = -28.8299652863068 +447000 ekin = 4.35336664890431 | erot = 4.44173113672768 | epot = -37.6140263912413 | etot = -28.8189286056093 +448000 ekin = 4.28498441172967 | erot = 4.19781838322426 | epot = -37.5090341348628 | etot = -29.0262313399088 +449000 ekin = 4.31763982219639 | erot = 4.52832551746767 | epot = -37.408401745433 | etot = -28.562436405769 +450000 ekin = 4.34138928411246 | erot = 4.4425856403743 | epot = -37.3062489259439 | etot = -28.5222740014571 +451000 ekin = 4.30985185878589 | erot = 4.23825662962939 | epot = -37.1459619150062 | etot = -28.5978534265909 +452000 ekin = 4.32592045036082 | erot = 3.86602766630272 | epot = -36.9847035634509 | etot = -28.7927554467874 +453000 ekin = 4.32845268851047 | erot = 3.54171363095611 | epot = -36.8340779762826 | etot = -28.963911656816 +454000 ekin = 4.31011457813686 | erot = 3.79537837348586 | epot = -36.7199830616561 | etot = -28.6144901100334 +455000 ekin = 4.29550433639196 | erot = 3.85241036204662 | epot = -36.6489739160373 | etot = -28.5010592175987 +456000 ekin = 4.37032742709179 | erot = 4.00721124204766 | epot = -36.6190063800959 | etot = -28.2414677109564 +457000 ekin = 4.3642647028677 | erot = 3.8563715204494 | epot = -36.5969553476855 | etot = -28.3763191243684 +458000 ekin = 4.32567014378598 | erot = 3.50123530464571 | epot = -36.5630453883139 | etot = -28.7361399398822 +459000 ekin = 4.38933815738648 | erot = 3.57401843708542 | epot = -36.5693343587045 | etot = -28.6059777642326 +460000 ekin = 4.31317855607471 | erot = 4.09613513000604 | epot = -36.622903135654 | etot = -28.2135894495732 +461000 ekin = 4.31811012640158 | erot = 4.38273826542212 | epot = -36.7024780237704 | etot = -28.0016296319467 +462000 ekin = 4.3366863876999 | erot = 4.51374491218818 | epot = -36.8227361919452 | etot = -27.9723048920571 +463000 ekin = 4.27564269849647 | erot = 4.86202296781308 | epot = -36.9415310835087 | etot = -27.8038654171991 +464000 ekin = 4.2570485657353 | erot = 4.74085846897254 | epot = -37.0390079052473 | etot = -28.0411008705395 +465000 ekin = 4.27536374407081 | erot = 4.49932366093901 | epot = -37.1090432428535 | etot = -28.3343558378437 +466000 ekin = 4.30607368146059 | erot = 4.23786653917903 | epot = -37.1491605127939 | etot = -28.6052202921542 +467000 ekin = 4.24919786200451 | erot = 4.12771930877703 | epot = -37.1714598423966 | etot = -28.7945426716151 +468000 ekin = 4.39683218085583 | erot = 3.85228521386554 | epot = -37.2088712844975 | etot = -28.9597538897762 +469000 ekin = 4.64124419278975 | erot = 3.80754439193715 | epot = -37.2767302220321 | etot = -28.8279416373053 +470000 ekin = 4.66178408905666 | erot = 3.92065938428506 | epot = -37.3876740781877 | etot = -28.805230604846 +471000 ekin = 4.75392904131979 | erot = 4.24739494727089 | epot = -37.5007122646076 | etot = -28.499388276017 +472000 ekin = 4.78287126449286 | erot = 4.29738258008787 | epot = -37.5977046601012 | etot = -28.5174508155204 +473000 ekin = 4.83746609770177 | erot = 4.38666527032479 | epot = -37.6671790710827 | etot = -28.4430477030562 +474000 ekin = 4.79054197671375 | erot = 4.34169424272135 | epot = -37.6856820094294 | etot = -28.5534457899944 +475000 ekin = 4.83235787688145 | erot = 4.2178840657501 | epot = -37.6508263787863 | etot = -28.6005844361548 +476000 ekin = 4.77650421806816 | erot = 4.23519664592594 | epot = -37.5559363402038 | etot = -28.5442354762097 +477000 ekin = 4.70149228687156 | erot = 3.9495520600404 | epot = -37.4316333722385 | etot = -28.7805890253266 +478000 ekin = 4.6582861234462 | erot = 3.52306589214545 | epot = -37.3056353897914 | etot = -29.1242833741998 +479000 ekin = 4.49034904671764 | erot = 3.69691237093671 | epot = -37.1645007343035 | etot = -28.9772393166492 +480000 ekin = 4.42035953830882 | erot = 3.62614880736061 | epot = -36.985533653495 | etot = -28.9390253078256 +481000 ekin = 4.29236052675561 | erot = 3.46283113670748 | epot = -36.7788376766182 | etot = -29.0236460131551 +482000 ekin = 4.24695006747712 | erot = 3.64617122659712 | epot = -36.5783264764334 | etot = -28.6852051823592 +483000 ekin = 4.27724439911408 | erot = 3.65906944039053 | epot = -36.4031794376631 | etot = -28.4668655981585 +484000 ekin = 4.2785974211618 | erot = 3.80998418987602 | epot = -36.2601336102697 | etot = -28.1715519992319 +485000 ekin = 4.2129183719994 | erot = 3.84278230442229 | epot = -36.1415033158633 | etot = -28.0858026394416 +486000 ekin = 3.98392526407069 | erot = 3.69687119417301 | epot = -36.0420007851878 | etot = -28.3612043269441 +487000 ekin = 3.87685523954233 | erot = 3.52087214489101 | epot = -35.979017993688 | etot = -28.5812906092547 +488000 ekin = 3.74675884240033 | erot = 3.80072807053011 | epot = -35.9652058586036 | etot = -28.4177189456731 +489000 ekin = 3.61099051841836 | erot = 4.09702697313296 | epot = -35.988768679933 | etot = -28.2807511883817 +490000 ekin = 3.72073699277812 | erot = 3.89157882585036 | epot = -36.0103724524786 | etot = -28.3980566338501 +491000 ekin = 3.72740917275109 | erot = 4.01795497893011 | epot = -36.0292354570355 | etot = -28.2838713053543 +492000 ekin = 3.67547789628851 | erot = 3.85969822517323 | epot = -36.0430681478951 | etot = -28.5078920264333 +493000 ekin = 3.65198421841216 | erot = 3.75518718738367 | epot = -36.0824152706774 | etot = -28.6752438648816 +494000 ekin = 3.48528219984848 | erot = 3.81535508778541 | epot = -36.142371045584 | etot = -28.8417337579501 +495000 ekin = 3.31359070882194 | erot = 4.11558724766118 | epot = -36.226868438371 | etot = -28.7976904818878 +496000 ekin = 3.27798311005954 | erot = 3.88806115727325 | epot = -36.3363270902382 | etot = -29.1702828229054 +497000 ekin = 3.23000081873801 | erot = 4.53153851783412 | epot = -36.4817201831143 | etot = -28.7201808465422 +498000 ekin = 3.35490986062519 | erot = 4.76314991175258 | epot = -36.6514686581239 | etot = -28.5334088857461 +499000 ekin = 3.39102564180484 | erot = 4.99058516868931 | epot = -36.8025368986549 | etot = -28.4209260881608 +500000 ekin = 3.44319922277983 | erot = 4.29432196305735 | epot = -36.9177193599233 | etot = -29.1801981740861 +501000 ekin = 3.47746008955494 | erot = 4.28994173802794 | epot = -37.0187053512326 | etot = -29.2513035236497 +502000 ekin = 3.58696948456737 | erot = 4.55410136617397 | epot = -37.1018103829438 | etot = -28.9607395322024 +503000 ekin = 3.68317380855577 | erot = 4.60652443433627 | epot = -37.1620776601797 | etot = -28.8723794172877 +504000 ekin = 3.6885205301443 | erot = 4.67783023002248 | epot = -37.2052759454199 | etot = -28.8389251852531 +505000 ekin = 3.88723268453857 | erot = 4.53079850437648 | epot = -37.2950608294682 | etot = -28.8770296405532 +506000 ekin = 3.80925396925157 | erot = 4.47086505886196 | epot = -37.3479933337837 | etot = -29.0678743056702 +507000 ekin = 3.73248519551987 | erot = 4.21393839264126 | epot = -37.4256513139283 | etot = -29.4792277257672 +508000 ekin = 3.8067276018406 | erot = 3.9370807937698 | epot = -37.4951091449467 | etot = -29.7513007493363 +509000 ekin = 3.8008699116461 | erot = 3.74333566662482 | epot = -37.5406480313394 | etot = -29.9964424530685 +510000 ekin = 3.89850649197984 | erot = 3.97775581109479 | epot = -37.5934385426631 | etot = -29.7171762395885 +511000 ekin = 3.81393185765474 | erot = 4.00469160928629 | epot = -37.6349932199755 | etot = -29.8163697530345 +512000 ekin = 3.76843962846378 | erot = 4.34524756747803 | epot = -37.6787808921542 | etot = -29.5650936962124 +513000 ekin = 3.70769437024756 | erot = 4.19222442242662 | epot = -37.7114576947708 | etot = -29.8115389020966 +514000 ekin = 3.65606306228185 | erot = 4.64296237641009 | epot = -37.7095823242884 | etot = -29.4105568855964 +515000 ekin = 3.50522818557459 | erot = 4.47916848114082 | epot = -37.6783049637299 | etot = -29.6939082970145 +516000 ekin = 3.59266443877116 | erot = 5.02978018029486 | epot = -37.647700985069 | etot = -29.0252563660029 +517000 ekin = 3.53729866959076 | erot = 4.95641997732809 | epot = -37.6445412669913 | etot = -29.1508226200724 +518000 ekin = 3.5534169530515 | erot = 4.5751245967427 | epot = -37.6532745224311 | etot = -29.5247329726369 +519000 ekin = 3.61605940841979 | erot = 4.59842321288977 | epot = -37.7181887221252 | etot = -29.5037061008156 +520000 ekin = 3.6600358073691 | erot = 4.52802897844129 | epot = -37.8184531846625 | etot = -29.6303883988521 +521000 ekin = 3.57990395101953 | erot = 4.58686564429516 | epot = -37.9529160430904 | etot = -29.7861464477757 +522000 ekin = 3.587210173505 | erot = 4.78958389957781 | epot = -38.1056938634056 | etot = -29.7288997903228 +523000 ekin = 3.74553748952041 | erot = 4.82242710318173 | epot = -38.2496598519462 | etot = -29.6816952592441 +524000 ekin = 3.83672965572981 | erot = 5.17806255755526 | epot = -38.3420385705453 | etot = -29.3272463572603 +525000 ekin = 3.97426514986081 | erot = 5.13820563111665 | epot = -38.4306455211978 | etot = -29.3181747402203 +526000 ekin = 4.03278131821155 | erot = 4.61480893928533 | epot = -38.4813375347265 | etot = -29.8337472772296 +527000 ekin = 4.15303805139346 | erot = 4.03339974605304 | epot = -38.4813261438673 | etot = -30.2948883464208 +528000 ekin = 4.34085606106398 | erot = 3.6341604993604 | epot = -38.4621670653442 | etot = -30.4871505049199 +529000 ekin = 4.53593485604716 | erot = 3.72087643644196 | epot = -38.4175016483558 | etot = -30.1606903558667 +530000 ekin = 4.6583694532253 | erot = 3.58233700504177 | epot = -38.3861765288021 | etot = -30.145470070535 +531000 ekin = 4.66519878740331 | erot = 3.4109494773408 | epot = -38.3363103504892 | etot = -30.2601620857451 +532000 ekin = 4.80041164317301 | erot = 3.07760528500131 | epot = -38.3151265786574 | etot = -30.4371096504831 +533000 ekin = 4.73180745168962 | erot = 3.06230961560369 | epot = -38.3468719461379 | etot = -30.5527548788445 +534000 ekin = 4.77276572097031 | erot = 3.01963113043194 | epot = -38.4024212860539 | etot = -30.6100244346517 +535000 ekin = 4.85693928494795 | erot = 2.82516321047269 | epot = -38.5360450508863 | etot = -30.8539425554656 +536000 ekin = 4.79265980947601 | erot = 2.9077544610961 | epot = -38.7196748122559 | etot = -31.0192605416837 +537000 ekin = 4.86947955762472 | erot = 3.00989555981226 | epot = -38.9076102830992 | etot = -31.0282351656622 +538000 ekin = 5.00269155741137 | erot = 2.68875189029913 | epot = -39.0473675460743 | etot = -31.3559240983638 +539000 ekin = 4.98226102919755 | erot = 2.92188829969373 | epot = -39.1655668480607 | etot = -31.2614175191695 +540000 ekin = 4.99147016878249 | erot = 3.35574385805744 | epot = -39.2596960810254 | etot = -30.9124820541854 +541000 ekin = 4.92725844601457 | erot = 3.28345034188324 | epot = -39.3089899760125 | etot = -31.0982811881147 +542000 ekin = 4.77242859226878 | erot = 3.31966912230265 | epot = -39.2902384371049 | etot = -31.1981407225335 +543000 ekin = 4.65726157165108 | erot = 3.56099171692951 | epot = -39.1715392323122 | etot = -30.9532859437317 +544000 ekin = 4.75158561074898 | erot = 2.98586301386343 | epot = -39.0000211966265 | etot = -31.2625725720141 +545000 ekin = 4.71389651780209 | erot = 3.29722166624287 | epot = -38.8124009343345 | etot = -30.8012827502895 +546000 ekin = 4.59452933616222 | erot = 3.65785900566392 | epot = -38.6597531372893 | etot = -30.4073647954631 +547000 ekin = 4.49485576841334 | erot = 3.5222715668964 | epot = -38.5261493757312 | etot = -30.5090220404215 +548000 ekin = 4.49472654055116 | erot = 3.49603087938253 | epot = -38.3944216290947 | etot = -30.403664209161 +549000 ekin = 4.39213180937528 | erot = 3.5322876385525 | epot = -38.2774675964381 | etot = -30.3530481485103 +550000 ekin = 4.36283999146778 | erot = 3.787764410361 | epot = -38.2051317998102 | etot = -30.0545273979814 +551000 ekin = 4.3226010693822 | erot = 4.01133252124214 | epot = -38.1611801425639 | etot = -29.8272465519396 +552000 ekin = 4.3318351566455 | erot = 3.98124414472587 | epot = -38.1537721388025 | etot = -29.8406928374311 +553000 ekin = 4.30534974680463 | erot = 3.81209066755031 | epot = -38.1803693007093 | etot = -30.0629288863544 +554000 ekin = 4.29335219580303 | erot = 3.8021354596393 | epot = -38.2389597407396 | etot = -30.1434720852972 +555000 ekin = 4.45825549052375 | erot = 4.03672150414351 | epot = -38.3296083261043 | etot = -29.834631331437 +556000 ekin = 4.63230188756508 | erot = 3.70797489704063 | epot = -38.4795834327919 | etot = -30.1393066481862 +557000 ekin = 4.70622293985813 | erot = 4.51036732636205 | epot = -38.673884289528 | etot = -29.4572940233078 +558000 ekin = 4.70612532334171 | erot = 4.30314260207033 | epot = -38.9099036274271 | etot = -29.9006357020151 +559000 ekin = 4.85842132468142 | erot = 4.45569884582891 | epot = -39.1571701897086 | etot = -29.8430500191982 +560000 ekin = 4.84667483493845 | erot = 4.2909749826348 | epot = -39.3692871188963 | etot = -30.2316373013231 +561000 ekin = 4.93080663772518 | erot = 4.40964672372494 | epot = -39.5560309503474 | etot = -30.2155775888973 +562000 ekin = 5.02786763240476 | erot = 4.09895267825206 | epot = -39.6620959555469 | etot = -30.53527564489 +563000 ekin = 4.99483060861833 | erot = 4.56393029644419 | epot = -39.7001867829014 | etot = -30.1414258778389 +564000 ekin = 5.01292656089539 | erot = 4.46559434127762 | epot = -39.6969046345991 | etot = -30.2183837324261 +565000 ekin = 4.97924499589812 | erot = 4.5676410286713 | epot = -39.6391307119518 | etot = -30.0922446873824 +566000 ekin = 4.80472039327365 | erot = 4.49618530358125 | epot = -39.5320142538579 | etot = -30.231108557003 +567000 ekin = 4.59721417192406 | erot = 4.44898156673779 | epot = -39.3835091139998 | etot = -30.337313375338 +568000 ekin = 4.59948947791999 | erot = 4.21619266891997 | epot = -39.1697350851652 | etot = -30.3540529383253 +569000 ekin = 4.46814520025957 | erot = 4.13625120915532 | epot = -38.9496016480665 | etot = -30.3452052386516 +570000 ekin = 4.6338057410939 | erot = 3.97471689520409 | epot = -38.718728428018 | etot = -30.11020579172 +571000 ekin = 4.51646555902291 | erot = 3.77943581302538 | epot = -38.5103017941539 | etot = -30.2144004221056 +572000 ekin = 4.44329973394615 | erot = 3.73818983971042 | epot = -38.3513010282128 | etot = -30.1698114545562 +573000 ekin = 4.48138796166313 | erot = 3.67030746094229 | epot = -38.2531080005807 | etot = -30.1014125779753 +574000 ekin = 4.57372019352182 | erot = 3.64740839838085 | epot = -38.1563476897671 | etot = -29.9352190978644 +575000 ekin = 4.81962720354443 | erot = 3.58128135189792 | epot = -38.0780197446128 | etot = -29.6771111891705 +576000 ekin = 4.78739960955902 | erot = 3.1694164956898 | epot = -38.0548669136926 | etot = -30.0980508084438 +577000 ekin = 4.89624137933457 | erot = 3.37301453509222 | epot = -38.0581159208701 | etot = -29.7888600064433 +578000 ekin = 4.89993171052275 | erot = 3.39468878464195 | epot = -38.0636938795356 | etot = -29.7690733843709 +579000 ekin = 4.83297661461382 | erot = 3.08572772864728 | epot = -38.0577731810635 | etot = -30.1390688378024 +580000 ekin = 4.77298411404112 | erot = 3.09603380464131 | epot = -38.0675771405195 | etot = -30.198559221837 +581000 ekin = 4.96965435170546 | erot = 3.06610493080439 | epot = -38.0894896837322 | etot = -30.0537304012223 +582000 ekin = 4.84477580774073 | erot = 2.9927320347077 | epot = -38.1047755328767 | etot = -30.2672676904283 +583000 ekin = 4.80184612340932 | erot = 2.99121545039786 | epot = -38.0992283827672 | etot = -30.30616680896 +584000 ekin = 4.73999729115049 | erot = 2.95820256140574 | epot = -38.1193022601922 | etot = -30.421102407636 +585000 ekin = 4.62963491646152 | erot = 2.99096158598537 | epot = -38.1514766562945 | etot = -30.5308801538476 +586000 ekin = 4.66196804986673 | erot = 3.11428540249498 | epot = -38.1645218154685 | etot = -30.3882683631068 +587000 ekin = 4.58446438916328 | erot = 3.26198289890953 | epot = -38.1451310277745 | etot = -30.2986837397017 +588000 ekin = 4.59050554157104 | erot = 3.3726754228907 | epot = -38.0928945920965 | etot = -30.1297136276347 +589000 ekin = 4.52148456601111 | erot = 3.20426810396365 | epot = -38.0431145518048 | etot = -30.31736188183 +590000 ekin = 4.54292012494668 | erot = 3.17466615888884 | epot = -37.9867331121616 | etot = -30.2691468283261 +591000 ekin = 4.4671534284139 | erot = 3.30654504351686 | epot = -37.9702893954324 | etot = -30.1965909235016 +592000 ekin = 4.47491098921977 | erot = 3.6999642514398 | epot = -37.9696400527198 | etot = -29.7947648120603 +593000 ekin = 4.43506697623667 | erot = 3.70250326611386 | epot = -37.982672172325 | etot = -29.8451019299745 +594000 ekin = 4.36908136306914 | erot = 3.59308231950695 | epot = -38.0038521048194 | etot = -30.0416884222434 +595000 ekin = 4.30615021787055 | erot = 3.60547435881493 | epot = -38.0517692624258 | etot = -30.1401446857403 +596000 ekin = 4.27538703974133 | erot = 3.70718417029047 | epot = -38.1072020006232 | etot = -30.1246307905914 +597000 ekin = 4.09427835861052 | erot = 3.56040857145023 | epot = -38.1368054718235 | etot = -30.4821185417627 +598000 ekin = 4.06772969179112 | erot = 3.98852753231066 | epot = -38.1357675039157 | etot = -30.0795102798139 +599000 ekin = 4.05823661502987 | erot = 3.99204411848289 | epot = -38.094416622612 | etot = -30.0441358890992 +600000 ekin = 4.14000207696597 | erot = 3.69886036268669 | epot = -38.0126500071595 | etot = -30.1737875675069 +601000 ekin = 4.14331251606211 | erot = 4.02012885446817 | epot = -37.8931408419344 | etot = -29.7296994714041 +602000 ekin = 4.19175322865712 | erot = 3.63789752518651 | epot = -37.776838230476 | etot = -29.9471874766323 +603000 ekin = 4.17700109074307 | erot = 3.33190102346871 | epot = -37.6571796612341 | etot = -30.1482775470223 +604000 ekin = 4.32110078335233 | erot = 3.37359972635292 | epot = -37.5481087406156 | etot = -29.8534082309104 +605000 ekin = 4.40829637956691 | erot = 3.12232098209617 | epot = -37.4615593717342 | etot = -29.9309420100711 +606000 ekin = 4.50978571460466 | erot = 2.82903034171751 | epot = -37.4107566252708 | etot = -30.0719405689486 +607000 ekin = 4.64775510562427 | erot = 2.72855004395386 | epot = -37.3886864614938 | etot = -30.0123813119157 +608000 ekin = 4.62515883775198 | erot = 2.69276686565725 | epot = -37.3472679127841 | etot = -30.0293422093749 +609000 ekin = 4.58072072733855 | erot = 2.72618151323734 | epot = -37.321155518993 | etot = -30.0142532784171 +610000 ekin = 4.37064710749545 | erot = 2.94205446769438 | epot = -37.3313655411415 | etot = -30.0186639659516 +611000 ekin = 4.30243700562366 | erot = 2.94482669781544 | epot = -37.3282578261779 | etot = -30.0809941227388 +612000 ekin = 4.37982748485343 | erot = 2.81236690797516 | epot = -37.3366791579241 | etot = -30.1444847650955 +613000 ekin = 4.49298433908216 | erot = 2.9422949922611 | epot = -37.3617837170398 | etot = -29.9265043856965 +614000 ekin = 4.63192250195893 | erot = 2.81948937077719 | epot = -37.3623397651558 | etot = -29.9109278924196 +615000 ekin = 4.56431794922697 | erot = 3.04112038174076 | epot = -37.336047475673 | etot = -29.7306091447052 +616000 ekin = 4.48538645093142 | erot = 2.9863679461823 | epot = -37.2843360454655 | etot = -29.8125816483518 +617000 ekin = 4.35777724185516 | erot = 3.27046740448593 | epot = -37.2149609045279 | etot = -29.5867162581868 +618000 ekin = 4.13929013645538 | erot = 3.31436963968885 | epot = -37.1380165806135 | etot = -29.6843568044692 +619000 ekin = 3.99812604761947 | erot = 3.80697216179629 | epot = -37.0480074184855 | etot = -29.2429092090698 +620000 ekin = 3.75775297824752 | erot = 3.88935078371487 | epot = -37.0016709350122 | etot = -29.3545671730499 +621000 ekin = 3.59837254942666 | erot = 3.36974253347195 | epot = -36.957139996861 | etot = -29.9890249139623 +622000 ekin = 3.52853751549673 | erot = 3.57220920853453 | epot = -36.9826672270778 | etot = -29.8819205030465 +623000 ekin = 3.44776927445729 | erot = 3.68524482792415 | epot = -37.0520182183617 | etot = -29.9190041159803 +624000 ekin = 3.42459051153801 | erot = 4.10039189185601 | epot = -37.1561365046956 | etot = -29.6311541013016 +625000 ekin = 3.47427533928241 | erot = 4.19316198399256 | epot = -37.3128709391509 | etot = -29.6454336158759 +626000 ekin = 3.59243588690051 | erot = 4.25331544595908 | epot = -37.4538356021372 | etot = -29.6080842692777 +627000 ekin = 3.65834270574544 | erot = 3.84587709669875 | epot = -37.5560189371568 | etot = -30.0517991347126 +628000 ekin = 3.70047562334568 | erot = 3.6882110278348 | epot = -37.6346624168372 | etot = -30.2459757656567 +629000 ekin = 3.73516234913422 | erot = 3.92476956261677 | epot = -37.7008434862915 | etot = -30.0409115745406 +630000 ekin = 3.81181204861746 | erot = 3.95913149926753 | epot = -37.7335643601767 | etot = -29.9626208122917 +631000 ekin = 3.81645534702365 | erot = 3.13210702566911 | epot = -37.7706097068458 | etot = -30.822047334153 +632000 ekin = 3.83367227377576 | erot = 3.16390787891888 | epot = -37.8179976528052 | etot = -30.8204175001106 +633000 ekin = 3.78875173101125 | erot = 3.28627876080398 | epot = -37.8551980571897 | etot = -30.7801675653744 +634000 ekin = 3.64435724345663 | erot = 3.54689069849326 | epot = -37.8771184407042 | etot = -30.6858704987543 +635000 ekin = 3.74927918910687 | erot = 3.50067245026001 | epot = -37.9120332365853 | etot = -30.6620815972185 +636000 ekin = 3.89890106913056 | erot = 3.51590480850453 | epot = -37.9883703460318 | etot = -30.5735644683968 +637000 ekin = 3.98051852239104 | erot = 3.51683885701821 | epot = -38.1188954220068 | etot = -30.6215380425976 +638000 ekin = 4.1867925219674 | erot = 3.48363716100457 | epot = -38.3003898519922 | etot = -30.6299601690202 +639000 ekin = 4.29259370089831 | erot = 3.44532403016783 | epot = -38.5009165327295 | etot = -30.7629988016634 +640000 ekin = 4.33862023546758 | erot = 3.61400248687526 | epot = -38.6627935284701 | etot = -30.7101708061272 +641000 ekin = 4.47895119284624 | erot = 3.60758277909094 | epot = -38.7986251266558 | etot = -30.7120911547187 +642000 ekin = 4.48471207018763 | erot = 3.75535910837196 | epot = -38.863620414876 | etot = -30.6235492363164 +643000 ekin = 4.56445558617355 | erot = 3.81552004634157 | epot = -38.8645537025225 | etot = -30.4845780700074 +644000 ekin = 4.73329478475728 | erot = 3.55885168491639 | epot = -38.8054956282291 | etot = -30.5133491585554 +645000 ekin = 4.6912943962558 | erot = 3.28200064721723 | epot = -38.701547429741 | etot = -30.7282523862679 +646000 ekin = 4.58583002001323 | erot = 3.4085956946329 | epot = -38.5478616511678 | etot = -30.5534359365217 +647000 ekin = 4.60741071742923 | erot = 3.38831322436691 | epot = -38.3932861693425 | etot = -30.3975622275464 +648000 ekin = 4.51463144345976 | erot = 3.2427410033314 | epot = -38.2758434893353 | etot = -30.5184710425442 +649000 ekin = 4.55491099792929 | erot = 3.3173810530716 | epot = -38.2201110845429 | etot = -30.347819033542 +650000 ekin = 4.67226589728798 | erot = 3.60950811156257 | epot = -38.2202225605509 | etot = -29.9384485517004 +651000 ekin = 4.60851815831642 | erot = 3.77278937705233 | epot = -38.2536330995444 | etot = -29.8723255641757 +652000 ekin = 4.678459200191 | erot = 3.3937624009624 | epot = -38.2868824175937 | etot = -30.2146608164403 +653000 ekin = 4.66844839257089 | erot = 3.83803199311166 | epot = -38.3235322989536 | etot = -29.817051913271 +654000 ekin = 4.7104895331932 | erot = 3.48299287365129 | epot = -38.3580887397253 | etot = -30.1646063328808 +655000 ekin = 4.59645355598621 | erot = 3.7478202528204 | epot = -38.4145657066933 | etot = -30.0702918978867 +656000 ekin = 4.75902771581097 | erot = 3.81874385847384 | epot = -38.4693742928374 | etot = -29.8916027185526 +657000 ekin = 4.64668020593031 | erot = 3.6665600106013 | epot = -38.4843211797294 | etot = -30.1710809631978 +658000 ekin = 4.5583600187507 | erot = 3.93329833863019 | epot = -38.4803826070965 | etot = -29.9887242497156 +659000 ekin = 4.55537392119719 | erot = 3.6285471602112 | epot = -38.4363459414659 | etot = -30.2524248600575 +660000 ekin = 4.41551333368083 | erot = 3.6539559007289 | epot = -38.3663969488346 | etot = -30.2969277144249 +661000 ekin = 4.32449081576465 | erot = 3.74090915717697 | epot = -38.2884247485437 | etot = -30.2230247756021 +662000 ekin = 4.2382312401034 | erot = 3.58833666048796 | epot = -38.1946280661735 | etot = -30.3680601655822 +663000 ekin = 4.32618520330348 | erot = 3.71369597709409 | epot = -38.0940311251124 | etot = -30.0541499447149 +664000 ekin = 4.30987713127737 | erot = 3.55193027406456 | epot = -38.0118003167729 | etot = -30.149992911431 +665000 ekin = 4.32971268964125 | erot = 3.40416985470638 | epot = -37.9630121098137 | etot = -30.229129565466 +666000 ekin = 4.30397058329232 | erot = 3.24563244836293 | epot = -37.9564459426245 | etot = -30.4068429109692 +667000 ekin = 4.23802718761159 | erot = 3.57923047722682 | epot = -37.911170999797 | etot = -30.0939133349586 +668000 ekin = 4.17750835985169 | erot = 3.42921371885257 | epot = -37.8409684237745 | etot = -30.2342463450703 +669000 ekin = 4.10123021238948 | erot = 3.38759831293412 | epot = -37.7732457913403 | etot = -30.2844172660167 +670000 ekin = 3.96563796265766 | erot = 3.59480187806753 | epot = -37.6965941156386 | etot = -30.1361542749134 +671000 ekin = 3.96406262528469 | erot = 3.64073126780246 | epot = -37.5753442355431 | etot = -29.9705503424559 +672000 ekin = 4.04265318678508 | erot = 3.67979591145804 | epot = -37.4296504342378 | etot = -29.7072013359947 +673000 ekin = 3.99224066234871 | erot = 3.52190422085278 | epot = -37.3047157518844 | etot = -29.7905708686829 +674000 ekin = 3.97681715793532 | erot = 3.75368024393782 | epot = -37.1885781675148 | etot = -29.4580807656416 +675000 ekin = 3.85833621087031 | erot = 3.97050815664581 | epot = -37.1417466549724 | etot = -29.3129022874562 +676000 ekin = 3.77676206895609 | erot = 3.79811590545655 | epot = -37.1253534099231 | etot = -29.5504754355104 +677000 ekin = 3.78226586281953 | erot = 3.88942769355379 | epot = -37.1385629636271 | etot = -29.4668694072538 +678000 ekin = 3.61579087416917 | erot = 3.83629032138248 | epot = -37.1880190743623 | etot = -29.7359378788106 +679000 ekin = 3.59940694058669 | erot = 3.92320694106388 | epot = -37.2411006365046 | etot = -29.7184867548541 +680000 ekin = 3.59936088858661 | erot = 3.59198808770705 | epot = -37.3103059663064 | etot = -30.1189569900128 +681000 ekin = 3.5506817335392 | erot = 3.62032338399699 | epot = -37.397887158622 | etot = -30.2268820410859 +682000 ekin = 3.64312616149454 | erot = 3.63220095729207 | epot = -37.4824268307592 | etot = -30.2070997119726 +683000 ekin = 3.59147144886464 | erot = 4.0054088226964 | epot = -37.5784304648838 | etot = -29.9815501933228 +684000 ekin = 3.72558767154372 | erot = 4.43134049971566 | epot = -37.6663536443173 | etot = -29.5094254730579 +685000 ekin = 3.75700113340408 | erot = 4.42051791074664 | epot = -37.7011506850387 | etot = -29.523631640888 +686000 ekin = 3.68716829673499 | erot = 4.29446170846264 | epot = -37.7134415714993 | etot = -29.7318115663016 +687000 ekin = 3.64818503755748 | erot = 4.53150873331274 | epot = -37.711537143075 | etot = -29.5318433722048 +688000 ekin = 3.65898677055773 | erot = 4.19517143645001 | epot = -37.7179324142981 | etot = -29.8637742072904 +689000 ekin = 3.6205349293849 | erot = 4.90634872884686 | epot = -37.7254294906481 | etot = -29.1985458324163 +690000 ekin = 3.66313798116712 | erot = 4.56796147261006 | epot = -37.7316773182824 | etot = -29.5005778645052 +691000 ekin = 3.71240687811154 | erot = 4.32729443264317 | epot = -37.6986701891451 | etot = -29.6589688783904 +692000 ekin = 3.77937222983674 | erot = 4.25209713638378 | epot = -37.6463069321166 | etot = -29.6148375658961 +693000 ekin = 3.82528389687013 | erot = 4.44391854020428 | epot = -37.5813521083399 | etot = -29.3121496712654 +694000 ekin = 3.77132757417731 | erot = 4.30342910423497 | epot = -37.5292531497342 | etot = -29.454496471322 +695000 ekin = 3.87816824099586 | erot = 3.61664690986648 | epot = -37.4977174174724 | etot = -30.0029022666101 +696000 ekin = 4.03561630547957 | erot = 3.14881777436793 | epot = -37.5165237009968 | etot = -30.3320896211493 +697000 ekin = 4.10221303088947 | erot = 2.74688055821586 | epot = -37.6237315563435 | etot = -30.7746379672381 +698000 ekin = 4.33198843808379 | erot = 2.54448976763408 | epot = -37.8109238872746 | etot = -30.9344456815567 +699000 ekin = 4.45835519306674 | erot = 2.8372756281226 | epot = -38.0765099491828 | etot = -30.7808791279934 +700000 ekin = 4.62566765847138 | erot = 3.20413023616686 | epot = -38.3666686805772 | etot = -30.536870785939 +701000 ekin = 4.71198958041981 | erot = 3.20500762759515 | epot = -38.6531148244764 | etot = -30.7361176164614 +702000 ekin = 4.70320353975512 | erot = 3.49669921722509 | epot = -38.9020142648734 | etot = -30.7021115078932 +703000 ekin = 4.7166659217622 | erot = 3.43605875792423 | epot = -39.0983570180767 | etot = -30.9456323383903 +704000 ekin = 4.81119997223625 | erot = 3.68842954975253 | epot = -39.2326154199855 | etot = -30.7329858979967 +705000 ekin = 4.76635995985854 | erot = 4.27225880905604 | epot = -39.304583019354 | etot = -30.2659642504394 +706000 ekin = 4.6123968900786 | erot = 4.45743851438174 | epot = -39.3303553159895 | etot = -30.2605199115291 +707000 ekin = 4.43392403924413 | erot = 5.00090751066076 | epot = -39.3012148785927 | etot = -29.8663833286878 +708000 ekin = 4.493639803788 | erot = 4.44827137132337 | epot = -39.1855945086319 | etot = -30.2436833335206 +709000 ekin = 4.38087413515987 | erot = 4.33993340713996 | epot = -39.0225667156706 | etot = -30.3017591733707 +710000 ekin = 4.30084034805674 | erot = 4.18416076229495 | epot = -38.8018325665079 | etot = -30.3168314561562 +711000 ekin = 4.16061239283914 | erot = 3.7596460771024 | epot = -38.6119256895403 | etot = -30.6916672195988 +712000 ekin = 4.02785073941548 | erot = 3.91873808556251 | epot = -38.5032151267495 | etot = -30.5566263017715 +713000 ekin = 3.91042694307498 | erot = 4.02474708082426 | epot = -38.4555203424355 | etot = -30.5203463185362 +714000 ekin = 3.91972154955257 | erot = 3.86911398530038 | epot = -38.4391911139339 | etot = -30.650355579081 +715000 ekin = 3.79432885182375 | erot = 3.97493955426887 | epot = -38.4648934882979 | etot = -30.6956250822053 +716000 ekin = 3.81379173421808 | erot = 4.12773796628716 | epot = -38.5344978321895 | etot = -30.5929681316842 +717000 ekin = 3.81338083287853 | erot = 3.91040514076917 | epot = -38.6119475932714 | etot = -30.8881616196237 +718000 ekin = 3.98031853847202 | erot = 3.63481705596704 | epot = -38.678649410417 | etot = -31.0635138159779 +719000 ekin = 3.85667554069524 | erot = 3.54568346865617 | epot = -38.7335222105702 | etot = -31.3311632012187 +720000 ekin = 3.82130999837899 | erot = 3.12899985812958 | epot = -38.800048179352 | etot = -31.8497383228434 +721000 ekin = 3.84625676410583 | erot = 3.33090070721994 | epot = -38.8362758074818 | etot = -31.659118336156 +722000 ekin = 3.79224716661396 | erot = 3.20659617994807 | epot = -38.8301147634646 | etot = -31.8312714169026 +723000 ekin = 3.89270036914644 | erot = 3.09341373486916 | epot = -38.7612142662691 | etot = -31.7751001622535 +724000 ekin = 3.88950015267433 | erot = 3.37593260372111 | epot = -38.6472208331853 | etot = -31.3817880767899 +725000 ekin = 3.89253643906727 | erot = 3.3632565061082 | epot = -38.5278096836431 | etot = -31.2720167384676 +726000 ekin = 3.77207579735126 | erot = 2.95762270097697 | epot = -38.4162496849588 | etot = -31.6865511866306 +727000 ekin = 3.8589508308402 | erot = 2.69741467226751 | epot = -38.3204112624909 | etot = -31.7640457593832 +728000 ekin = 3.95735248448056 | erot = 2.91208862145619 | epot = -38.2269317498774 | etot = -31.3574906439407 +729000 ekin = 3.90116579496193 | erot = 2.68023881807524 | epot = -38.1837112825913 | etot = -31.6023066695542 +730000 ekin = 3.96318220229622 | erot = 2.52640600275291 | epot = -38.1795006550048 | etot = -31.6899124499557 +731000 ekin = 4.07163559325289 | erot = 2.47524828245716 | epot = -38.2208467965997 | etot = -31.6739629208896 +732000 ekin = 4.12331294394785 | erot = 2.59059397612219 | epot = -38.2785246774242 | etot = -31.5646177573541 +733000 ekin = 4.18393032106836 | erot = 2.72580269413632 | epot = -38.3920370437211 | etot = -31.4823040285164 +734000 ekin = 4.22490204001118 | erot = 2.94025387724297 | epot = -38.5577268408556 | etot = -31.3925709236014 +735000 ekin = 4.41637906381283 | erot = 3.39000978300269 | epot = -38.7520895879279 | etot = -30.9457007411124 +736000 ekin = 4.52682105512923 | erot = 3.59384799521502 | epot = -39.0007836443238 | etot = -30.8801145939796 +737000 ekin = 4.54518518822972 | erot = 3.67606395235652 | epot = -39.2431861398732 | etot = -31.021936999287 +738000 ekin = 4.54111831313617 | erot = 3.87514152367601 | epot = -39.4689573474101 | etot = -31.0526975105979 +739000 ekin = 4.64515651334113 | erot = 3.86830954896661 | epot = -39.6580785017875 | etot = -31.1446124394798 +740000 ekin = 4.59721923359584 | erot = 3.83234514918706 | epot = -39.7800787241315 | etot = -31.3505143413486 +741000 ekin = 4.54920694202201 | erot = 4.22873772666781 | epot = -39.8001498706485 | etot = -31.0222052019586 +742000 ekin = 4.37775553859951 | erot = 4.07719515191216 | epot = -39.7729191936198 | etot = -31.3179685031081 +743000 ekin = 4.3556617165815 | erot = 4.19296317409613 | epot = -39.6826493457458 | etot = -31.1340244550682 +744000 ekin = 4.35520781857212 | erot = 4.03027041959878 | epot = -39.5404877687077 | etot = -31.1550095305368 +745000 ekin = 4.22626887984331 | erot = 3.36034348052808 | epot = -39.3612863690872 | etot = -31.7746740087159 +746000 ekin = 4.11995949308923 | erot = 3.27667360498748 | epot = -39.1619120183871 | etot = -31.7652789203104 +747000 ekin = 4.14400839200239 | erot = 3.30199438470026 | epot = -38.9827326721258 | etot = -31.5367298954232 +748000 ekin = 4.00468940718693 | erot = 3.14625781984354 | epot = -38.8044398216778 | etot = -31.6534925946474 +749000 ekin = 3.84115389861465 | erot = 2.95470003366609 | epot = -38.6687005011654 | etot = -31.8728465688846 +750000 ekin = 3.65410258827823 | erot = 3.15459365563754 | epot = -38.5278602215809 | etot = -31.7191639776651 +751000 ekin = 3.60281847230545 | erot = 3.24631581000339 | epot = -38.4153933025755 | etot = -31.5662590202667 +752000 ekin = 3.67731217795128 | erot = 3.63832283099251 | epot = -38.3028409880039 | etot = -30.9872059790601 +753000 ekin = 3.57605485188811 | erot = 3.26752665173291 | epot = -38.2165204041613 | etot = -31.3729389005403 +754000 ekin = 3.69078656100588 | erot = 3.07077330953217 | epot = -38.2008529421062 | etot = -31.4392930715682 +755000 ekin = 3.70168225637986 | erot = 2.97263399944788 | epot = -38.2287093031125 | etot = -31.5543930472847 +756000 ekin = 3.82302121276 | erot = 3.1782689290909 | epot = -38.310131999282 | etot = -31.3088418574311 +757000 ekin = 3.92969183976134 | erot = 3.24398381681734 | epot = -38.4229976799532 | etot = -31.2493220233745 +758000 ekin = 4.01825553851191 | erot = 2.96087889455693 | epot = -38.5603809302421 | etot = -31.5812464971732 +759000 ekin = 4.15945678292269 | erot = 3.31368855914151 | epot = -38.7240687265501 | etot = -31.2509233844859 +760000 ekin = 4.08337495041291 | erot = 3.28527114059579 | epot = -38.8845645171709 | etot = -31.5159184261622 +761000 ekin = 4.14862342701004 | erot = 3.30586771709929 | epot = -38.9896780479041 | etot = -31.5351869037947 +762000 ekin = 4.15291891523591 | erot = 3.21578962032615 | epot = -39.035237071941 | etot = -31.6665285363789 +763000 ekin = 4.13154828483801 | erot = 3.3900507889808 | epot = -39.0640564952969 | etot = -31.5424574214781 +764000 ekin = 4.11445022984107 | erot = 3.78778087021365 | epot = -39.069248399025 | etot = -31.1670172989702 +765000 ekin = 3.94937442988367 | erot = 3.99811330721222 | epot = -39.0421921917084 | etot = -31.0947044546125 +766000 ekin = 3.90772961551845 | erot = 4.0181962192846 | epot = -38.9772379154488 | etot = -31.0513120806457 +767000 ekin = 3.91865092379332 | erot = 3.66675942927299 | epot = -38.8570109636996 | etot = -31.2716006106332 +768000 ekin = 3.90455829915362 | erot = 3.57997769181348 | epot = -38.7106990781797 | etot = -31.2261630872126 +769000 ekin = 3.79614462627826 | erot = 3.72589479531031 | epot = -38.5987325117513 | etot = -31.0766930901627 +770000 ekin = 3.84943042371488 | erot = 3.41445940258812 | epot = -38.524203140241 | etot = -31.260313313938 +771000 ekin = 3.93726861106201 | erot = 3.22573743650855 | epot = -38.4470290210344 | etot = -31.2840229734638 +772000 ekin = 3.96999789478599 | erot = 3.15006319998264 | epot = -38.4433830504296 | etot = -31.3233219556609 +773000 ekin = 3.90264203603893 | erot = 3.08286085672441 | epot = -38.4596433115508 | etot = -31.4741404187875 +774000 ekin = 4.05136357587227 | erot = 3.17001936426344 | epot = -38.5137422973683 | etot = -31.2923593572326 +775000 ekin = 4.11418642080987 | erot = 3.81754399179953 | epot = -38.5927804349062 | etot = -30.6610500222968 +776000 ekin = 4.11481050991315 | erot = 3.55328099460652 | epot = -38.6754580889833 | etot = -31.0073665844636 +777000 ekin = 4.23423405077881 | erot = 3.58108270552595 | epot = -38.76169441768 | etot = -30.9463776613752 +778000 ekin = 4.22244262963946 | erot = 3.64411855451438 | epot = -38.842032142942 | etot = -30.9754709587882 +779000 ekin = 4.20492205038613 | erot = 3.89270804286644 | epot = -38.9009656289588 | etot = -30.8033355357062 +780000 ekin = 4.19457435208234 | erot = 3.98994130977106 | epot = -38.9050369874364 | etot = -30.720521325583 +781000 ekin = 4.33837315790505 | erot = 3.45852422770954 | epot = -38.858660577552 | etot = -31.0617631919374 +782000 ekin = 4.36357496915283 | erot = 3.10010011432268 | epot = -38.7868584055569 | etot = -31.3231833220814 +783000 ekin = 4.42162598039069 | erot = 3.42028138737023 | epot = -38.7233668668895 | etot = -30.8814594991286 +784000 ekin = 4.52915280589068 | erot = 3.46746509226016 | epot = -38.6388342149203 | etot = -30.6422163167695 +785000 ekin = 4.5515940213827 | erot = 3.36141401661281 | epot = -38.5160993571772 | etot = -30.6030913191817 +786000 ekin = 4.4107707826179 | erot = 3.55728141641263 | epot = -38.3921286555455 | etot = -30.424076456515 +787000 ekin = 4.5473982866512 | erot = 3.81681111076943 | epot = -38.2843232861691 | etot = -29.9201138887484 +788000 ekin = 4.51350891647158 | erot = 3.90594890385667 | epot = -38.2029645190101 | etot = -29.7835066986818 +789000 ekin = 4.41183434492804 | erot = 4.01545730842702 | epot = -38.1545360413066 | etot = -29.7272443879516 +790000 ekin = 4.36219296798482 | erot = 4.38022337925401 | epot = -38.1642768248248 | etot = -29.421860477586 +791000 ekin = 4.36856935453186 | erot = 4.10044084346348 | epot = -38.2219055606099 | etot = -29.7528953626145 +792000 ekin = 4.15750522427241 | erot = 4.31220830506829 | epot = -38.3006248567473 | etot = -29.8309113274066 +793000 ekin = 4.04895474142992 | erot = 4.47406069249712 | epot = -38.4166817679429 | etot = -29.8936663340158 +794000 ekin = 4.06782077729031 | erot = 4.54237615913424 | epot = -38.5497403981529 | etot = -29.9395434617283 +795000 ekin = 4.13325369560983 | erot = 4.6766430853343 | epot = -38.7140310649859 | etot = -29.9041342840418 +796000 ekin = 4.24810673699357 | erot = 4.55090018691371 | epot = -38.8628377912581 | etot = -30.0638308673508 +797000 ekin = 4.47820483480053 | erot = 4.37105820701948 | epot = -39.0073103741372 | etot = -30.1580473323172 +798000 ekin = 4.41687882033665 | erot = 4.0319284480101 | epot = -39.1717655165835 | etot = -30.7229582482367 +799000 ekin = 4.51272621151664 | erot = 3.80275615695394 | epot = -39.3264210367218 | etot = -31.0109386682512 +800000 ekin = 4.55406747539997 | erot = 3.86603589563191 | epot = -39.455092115688 | etot = -31.0349887446561 +801000 ekin = 4.71425753043942 | erot = 4.19401636489441 | epot = -39.5455068512898 | etot = -30.637232955956 +802000 ekin = 4.73096724901056 | erot = 4.66018334519229 | epot = -39.597292270086 | etot = -30.2061416758832 +803000 ekin = 4.62379738113321 | erot = 4.84687313016545 | epot = -39.6033097238909 | etot = -30.1326392125923 +804000 ekin = 4.73211781117979 | erot = 4.65405100631752 | epot = -39.5980929919841 | etot = -30.2119241744868 +805000 ekin = 4.74990370273786 | erot = 5.03061291222775 | epot = -39.569498865532 | etot = -29.7889822505664 +806000 ekin = 4.71376969100994 | erot = 4.52737209746845 | epot = -39.5309941756428 | etot = -30.2898523871644 +807000 ekin = 4.86079475139447 | erot = 4.60056901312774 | epot = -39.4997078348834 | etot = -30.0383440703612 +808000 ekin = 4.80209833525365 | erot = 4.45818548395654 | epot = -39.4704788837951 | etot = -30.2101950645849 +809000 ekin = 4.6377001128784 | erot = 4.50410245159993 | epot = -39.4133092695815 | etot = -30.2715067051032 +810000 ekin = 4.58845623547692 | erot = 4.59839740206889 | epot = -39.3630399165046 | etot = -30.1761862789588 +811000 ekin = 4.49885529137753 | erot = 3.98878012931503 | epot = -39.2630135095319 | etot = -30.7753780888393 +812000 ekin = 4.26896362698783 | erot = 3.78568800845445 | epot = -39.1138584925267 | etot = -31.0592068570844 +813000 ekin = 4.13473287838133 | erot = 3.6709761560088 | epot = -38.9684769118808 | etot = -31.1627678774907 +814000 ekin = 3.94776533151714 | erot = 3.9457998277719 | epot = -38.8393181931019 | etot = -30.9457530338129 +815000 ekin = 3.90824876714862 | erot = 4.04132924638677 | epot = -38.7551601823022 | etot = -30.8055821687668 +816000 ekin = 3.78701127768462 | erot = 3.90301930977968 | epot = -38.6978803550943 | etot = -31.00784976763 +817000 ekin = 3.66292511898636 | erot = 3.94682412287945 | epot = -38.6270985077425 | etot = -31.0173492658767 +818000 ekin = 3.57247131276281 | erot = 4.1784329766224 | epot = -38.5581000447571 | etot = -30.8071957553719 +819000 ekin = 3.53877880324498 | erot = 4.11647252852254 | epot = -38.4709987313688 | etot = -30.8157473996013 +820000 ekin = 3.50671598439864 | erot = 4.25631799360866 | epot = -38.3521077332953 | etot = -30.589073755288 +821000 ekin = 3.53103431342861 | erot = 3.63219688182926 | epot = -38.2011634572152 | etot = -31.0379322619573 +822000 ekin = 3.51951391759931 | erot = 3.61259288561798 | epot = -38.0560993175178 | etot = -30.9239925143005 +823000 ekin = 3.57671320020554 | erot = 3.17979253207743 | epot = -37.8872361758755 | etot = -31.1307304435925 +824000 ekin = 3.52000952110921 | erot = 3.12347116703116 | epot = -37.7532307820921 | etot = -31.1097500939517 +825000 ekin = 3.58955759313305 | erot = 3.15061432333252 | epot = -37.6359982536732 | etot = -30.8958263372076 +826000 ekin = 3.67361585241115 | erot = 3.02327306668993 | epot = -37.5692124634555 | etot = -30.8723235443545 +827000 ekin = 3.81109350736604 | erot = 2.85212407416508 | epot = -37.5611625241685 | etot = -30.8979449426374 +828000 ekin = 3.90531542763306 | erot = 2.81227386436724 | epot = -37.5694328663444 | etot = -30.8518435743441 +829000 ekin = 3.84587100054128 | erot = 2.81493449341339 | epot = -37.6070676030481 | etot = -30.9462621090934 +830000 ekin = 3.92673136944209 | erot = 3.15236191191157 | epot = -37.65374691576 | etot = -30.5746536344063 +831000 ekin = 3.93921284330491 | erot = 3.06450076609943 | epot = -37.726173164998 | etot = -30.7224595555937 +832000 ekin = 3.97197612374618 | erot = 3.05649894745004 | epot = -37.8221989970108 | etot = -30.7937239258146 +833000 ekin = 3.93725030890245 | erot = 3.02665836452891 | epot = -37.937171835506 | etot = -30.9732631620746 +834000 ekin = 3.98146697711148 | erot = 3.02136079279377 | epot = -38.0629385880238 | etot = -31.0601108181185 +835000 ekin = 4.05052897985953 | erot = 3.17273406713208 | epot = -38.1835463837721 | etot = -30.9602833367805 +836000 ekin = 4.19040397553796 | erot = 3.26946027032974 | epot = -38.300933644763 | etot = -30.8410693988953 +837000 ekin = 4.23633886579806 | erot = 3.17722972050019 | epot = -38.3895940577245 | etot = -30.9760254714263 +838000 ekin = 4.29790040722482 | erot = 3.15450479842838 | epot = -38.4727069904853 | etot = -31.0203017848321 +839000 ekin = 4.182732050379 | erot = 3.33215565017002 | epot = -38.5543306618494 | etot = -31.0394429613004 +840000 ekin = 4.10684077367696 | erot = 3.38230089969601 | epot = -38.6241675017603 | etot = -31.1350258283873 +841000 ekin = 4.23749853699722 | erot = 4.07451157411683 | epot = -38.6954306161322 | etot = -30.3834205050181 +842000 ekin = 4.2153670799426 | erot = 4.23835126074053 | epot = -38.7619078222528 | etot = -30.3081894815696 +843000 ekin = 4.22215504966699 | erot = 4.35771502414021 | epot = -38.8129398935362 | etot = -30.233069819729 +844000 ekin = 4.30121627933573 | erot = 4.37450016715701 | epot = -38.8385476120776 | etot = -30.1628311655849 +845000 ekin = 4.21550077214609 | erot = 4.14378307005649 | epot = -38.8237568245827 | etot = -30.4644729823801 +846000 ekin = 4.02238016824686 | erot = 4.51654867802952 | epot = -38.7905889780241 | etot = -30.2516601317477 +847000 ekin = 4.01810256512937 | erot = 4.26125017170745 | epot = -38.733957558752 | etot = -30.4546048219152 +848000 ekin = 3.96232133970732 | erot = 4.11983424179405 | epot = -38.6313622633386 | etot = -30.5492066818373 +849000 ekin = 3.80836560854392 | erot = 4.28564223418274 | epot = -38.4895963152699 | etot = -30.3955884725433 +850000 ekin = 3.69578896780274 | erot = 4.39587758868528 | epot = -38.3525607889922 | etot = -30.2608942325042 +851000 ekin = 3.41959969074421 | erot = 4.26064520104062 | epot = -38.1456854690894 | etot = -30.4654405773046 +852000 ekin = 3.30829887930776 | erot = 3.71835542085465 | epot = -37.9409715149428 | etot = -30.9143172147804 +853000 ekin = 3.35508979255713 | erot = 3.37030184945621 | epot = -37.7900455534541 | etot = -31.0646539114407 +854000 ekin = 3.27022944339449 | erot = 3.34212111159852 | epot = -37.7131840806896 | etot = -31.1008335256966 +855000 ekin = 3.19861227193943 | erot = 3.88856216577093 | epot = -37.6928018165187 | etot = -30.6056273788083 +856000 ekin = 3.06768638261934 | erot = 3.98298011021487 | epot = -37.727010473156 | etot = -30.6763439803218 +857000 ekin = 3.02849458271124 | erot = 3.90128373509556 | epot = -37.7894644617561 | etot = -30.8596861439493 +858000 ekin = 3.01766394874133 | erot = 3.81481515545799 | epot = -37.864155422239 | etot = -31.0316763180397 +859000 ekin = 3.04279727315576 | erot = 3.58850792531743 | epot = -37.9147104139937 | etot = -31.2834052155205 +860000 ekin = 3.12250083122182 | erot = 3.47152341944205 | epot = -37.9805991878282 | etot = -31.3865749371643 +861000 ekin = 3.08661234486262 | erot = 3.19104504877429 | epot = -38.04550487435 | etot = -31.7678474807131 +862000 ekin = 3.21284829409286 | erot = 3.29871938445959 | epot = -38.099234844044 | etot = -31.5876671654915 +863000 ekin = 3.30782920492323 | erot = 3.18791577959012 | epot = -38.1747149198294 | etot = -31.678969935316 +864000 ekin = 3.42420257195635 | erot = 2.92388402618494 | epot = -38.2365375033583 | etot = -31.888450905217 +865000 ekin = 3.34466551527704 | erot = 3.0972998859353 | epot = -38.3012083514071 | etot = -31.8592429501948 +866000 ekin = 3.36174635490684 | erot = 3.3198551234471 | epot = -38.3565233653478 | etot = -31.6749218869938 +867000 ekin = 3.42183919685502 | erot = 2.79592217571871 | epot = -38.3877893327297 | etot = -32.1700279601559 +868000 ekin = 3.36274087144656 | erot = 2.53957841641322 | epot = -38.4029375195831 | etot = -32.5006182317234 +869000 ekin = 3.40964507660634 | erot = 2.56691032353942 | epot = -38.3607072506902 | etot = -32.3841518505445 +870000 ekin = 3.53716918539254 | erot = 2.78671187381873 | epot = -38.3296120297666 | etot = -32.0057309705553 +871000 ekin = 3.59594316640842 | erot = 2.64188707611872 | epot = -38.2798157408163 | etot = -32.0419854982892 +872000 ekin = 3.50734679867101 | erot = 2.53533702817691 | epot = -38.2086073023317 | etot = -32.1659234754837 +873000 ekin = 3.49167258379229 | erot = 2.78144827221661 | epot = -38.1271407877645 | etot = -31.8540199317556 +874000 ekin = 3.51303146719815 | erot = 2.71312702979824 | epot = -38.0371921369838 | etot = -31.8110336399874 +875000 ekin = 3.48945347772523 | erot = 2.94850163157185 | epot = -37.9788388329103 | etot = -31.5408837236132 +876000 ekin = 3.56075870692743 | erot = 3.00511197452205 | epot = -37.9138095080298 | etot = -31.3479388265803 +877000 ekin = 3.47758786865167 | erot = 3.16390846334178 | epot = -37.8677942057126 | etot = -31.2262978737192 +878000 ekin = 3.30311825505467 | erot = 3.03452838302444 | epot = -37.8643582436496 | etot = -31.5267116055705 +879000 ekin = 3.24374156245722 | erot = 3.40785973601232 | epot = -37.8934655456588 | etot = -31.2418642471892 +880000 ekin = 3.37573093292725 | erot = 3.29280897525375 | epot = -37.94427513544 | etot = -31.275735227259 +881000 ekin = 3.39840544569004 | erot = 3.55852812717334 | epot = -38.000888118187 | etot = -31.0439545453236 +882000 ekin = 3.5896767073527 | erot = 3.35995074975521 | epot = -38.026551897189 | etot = -31.0769244400811 +883000 ekin = 3.50982611331082 | erot = 2.96694324238039 | epot = -38.0094926569537 | etot = -31.5327233012624 +884000 ekin = 3.40446481074992 | erot = 3.29501620823905 | epot = -37.9974315131722 | etot = -31.2979504941832 +885000 ekin = 3.35965929451973 | erot = 3.11716654513077 | epot = -38.0104898466533 | etot = -31.5336640070028 +886000 ekin = 3.43988208795668 | erot = 3.03035945423276 | epot = -38.069363334615 | etot = -31.5991217924255 +887000 ekin = 3.45628684947244 | erot = 3.13318789403753 | epot = -38.167703435161 | etot = -31.5782286916511 +888000 ekin = 3.56219309594448 | erot = 3.51843891461388 | epot = -38.2809194479115 | etot = -31.2002874373531 +889000 ekin = 3.66415644518205 | erot = 4.27546474777864 | epot = -38.4171028829355 | etot = -30.4774816899748 +890000 ekin = 3.59199164776004 | erot = 4.54716655442247 | epot = -38.5531146541753 | etot = -30.4139564519928 +891000 ekin = 3.4869835078992 | erot = 4.75701182525676 | epot = -38.6580895919222 | etot = -30.4140942587662 +892000 ekin = 3.51562855757933 | erot = 4.92508483334413 | epot = -38.7362622656568 | etot = -30.2955488747333 +893000 ekin = 3.4766111333881 | erot = 5.21569244219365 | epot = -38.7939526432623 | etot = -30.1016490676805 +894000 ekin = 3.33377890272863 | erot = 5.32415823975928 | epot = -38.7809839614906 | etot = -30.1230468190027 +895000 ekin = 3.43478318369578 | erot = 5.410051543616 | epot = -38.7354883491905 | etot = -29.8906536218787 +896000 ekin = 3.35681124753231 | erot = 5.27612600451789 | epot = -38.644144773384 | etot = -30.0112075213338 +897000 ekin = 3.28668538949675 | erot = 5.17803324766013 | epot = -38.5248966927272 | etot = -30.0601780555704 +898000 ekin = 3.28286469703029 | erot = 5.13874374768494 | epot = -38.3749221439187 | etot = -29.9533136992034 +899000 ekin = 3.28106900834711 | erot = 5.02377463132162 | epot = -38.2159550339518 | etot = -29.9111113942831 +900000 ekin = 3.23754877589606 | erot = 4.74128859066625 | epot = -38.0678968923381 | etot = -30.0890595257758 +901000 ekin = 3.13978298302555 | erot = 4.3243129242664 | epot = -37.9137652588163 | etot = -30.4496693515243 +902000 ekin = 3.14110495369385 | erot = 3.63711917032573 | epot = -37.7967183247472 | etot = -31.0184942007276 +903000 ekin = 3.11835106948976 | erot = 3.5835838401184 | epot = -37.7069569192995 | etot = -31.0050220096914 +904000 ekin = 3.07376219479296 | erot = 3.52931006844825 | epot = -37.6597467606241 | etot = -31.0566744973829 +905000 ekin = 3.06812362454372 | erot = 3.78913234205767 | epot = -37.6633180135037 | etot = -30.8060620469023 +906000 ekin = 3.16118254583043 | erot = 3.68210315785564 | epot = -37.7114125889238 | etot = -30.8681268852377 +907000 ekin = 3.05937736690025 | erot = 3.63166351278032 | epot = -37.8094278488435 | etot = -31.118386969163 +908000 ekin = 3.20197665753494 | erot = 3.6441133335068 | epot = -37.8953945586471 | etot = -31.0493045676053 +909000 ekin = 3.13419888287822 | erot = 3.44894287146547 | epot = -37.9553359165693 | etot = -31.3721941622256 +910000 ekin = 3.2011454656304 | erot = 3.42446813676882 | epot = -38.024917947609 | etot = -31.3993043452098 +911000 ekin = 3.183320242491 | erot = 3.30496399638698 | epot = -38.1090485606002 | etot = -31.6207643217223 +912000 ekin = 3.26276595850364 | erot = 3.24471741353574 | epot = -38.2096715613882 | etot = -31.7021881893489 +913000 ekin = 3.2681561913827 | erot = 3.26266624315759 | epot = -38.3821519588598 | etot = -31.8513295243196 +914000 ekin = 3.35412635067755 | erot = 3.33562334375845 | epot = -38.6092123987847 | etot = -31.9194627043487 +915000 ekin = 3.50776663391062 | erot = 3.6091033663435 | epot = -38.8009254120376 | etot = -31.6840554117835 +916000 ekin = 3.5277313901091 | erot = 3.46745309412736 | epot = -38.9707688836112 | etot = -31.9755843993747 +917000 ekin = 3.59076210165264 | erot = 3.41178573512987 | epot = -39.0925719913734 | etot = -32.0900241545909 +918000 ekin = 3.70456853537637 | erot = 3.18226166796491 | epot = -39.1781408185665 | etot = -32.2913106152253 +919000 ekin = 3.78037780426176 | erot = 3.08638967761944 | epot = -39.2569196438486 | etot = -32.3901521619674 +920000 ekin = 3.91060781137684 | erot = 3.28711158692157 | epot = -39.3298863351688 | etot = -32.1321669368704 +921000 ekin = 3.94747979949424 | erot = 3.45337772058887 | epot = -39.3932618134522 | etot = -31.9924042933691 +922000 ekin = 3.94814734356941 | erot = 3.67117615571532 | epot = -39.4429346449514 | etot = -31.8236111456667 +923000 ekin = 3.96148195878582 | erot = 4.16418425189001 | epot = -39.4697891977426 | etot = -31.3441229870668 +924000 ekin = 3.93156231463912 | erot = 4.23364521862771 | epot = -39.4747062603535 | etot = -31.3094987270866 +925000 ekin = 3.98364691406504 | erot = 4.37102519058181 | epot = -39.4559543119553 | etot = -31.1012822073085 +926000 ekin = 3.90165834847865 | erot = 4.5398391765023 | epot = -39.3838686479861 | etot = -30.9423711230052 +927000 ekin = 3.86159556963851 | erot = 4.93409467569006 | epot = -39.3009822835311 | etot = -30.5052920382026 +928000 ekin = 3.88113409255608 | erot = 4.54344659797514 | epot = -39.2237313850886 | etot = -30.7991506945573 +929000 ekin = 3.73601262143371 | erot = 4.54159517313964 | epot = -39.0907845737875 | etot = -30.8131767792141 +930000 ekin = 3.62890283946098 | erot = 4.23223960576937 | epot = -38.9310668930158 | etot = -31.0699244477855 +931000 ekin = 3.51130978751904 | erot = 3.75580234575059 | epot = -38.7496742883208 | etot = -31.4825621550511 +932000 ekin = 3.4360478582467 | erot = 3.85916877458119 | epot = -38.6047820584061 | etot = -31.3095654255782 +933000 ekin = 3.34945134482918 | erot = 4.10711762351073 | epot = -38.510851150919 | etot = -31.0542821825791 +934000 ekin = 3.25407370525901 | erot = 4.02198516513931 | epot = -38.4343657155247 | etot = -31.1583068451264 +935000 ekin = 3.15706754617272 | erot = 3.94213624960972 | epot = -38.3842418910869 | etot = -31.2850380953045 +936000 ekin = 3.00555649828127 | erot = 4.41385590541793 | epot = -38.3669049397814 | etot = -30.9474925360822 +937000 ekin = 2.92065396617262 | erot = 4.74523400801332 | epot = -38.3453538388338 | etot = -30.6794658646479 +938000 ekin = 2.97141948473043 | erot = 4.76974809222722 | epot = -38.3344331957966 | etot = -30.5932656188389 +939000 ekin = 2.94512706992696 | erot = 4.54496818954274 | epot = -38.3244620131108 | etot = -30.8343667536411 +940000 ekin = 2.88288211336379 | erot = 4.33037795313988 | epot = -38.32262444066 | etot = -31.1093643741563 +941000 ekin = 3.0729894973384 | erot = 4.38312166999032 | epot = -38.3472582821346 | etot = -30.8911471148058 +942000 ekin = 3.09399973822793 | erot = 4.23262521183818 | epot = -38.3627707290367 | etot = -31.0361457789706 +943000 ekin = 3.0692834807418 | erot = 4.29810120769341 | epot = -38.3654861580836 | etot = -30.9981014696484 +944000 ekin = 3.05361136554782 | erot = 4.57752136432056 | epot = -38.3891229370226 | etot = -30.7579902071542 +945000 ekin = 3.1053295273393 | erot = 4.63116672909507 | epot = -38.4481824906831 | etot = -30.7116862342487 +946000 ekin = 3.22536073155692 | erot = 4.9775607801974 | epot = -38.5304457687251 | etot = -30.3275242569708 +947000 ekin = 3.22481791886501 | erot = 4.85505897631116 | epot = -38.6306947506549 | etot = -30.5508178554787 +948000 ekin = 3.31258286730489 | erot = 4.40885070504324 | epot = -38.7111926164561 | etot = -30.9897590441079 +949000 ekin = 3.2634175064554 | erot = 4.5080556255622 | epot = -38.7582101439127 | etot = -30.9867370118951 +950000 ekin = 3.38312193033095 | erot = 4.30600402576254 | epot = -38.7909813747404 | etot = -31.1018554186469 +951000 ekin = 3.4587828832488 | erot = 3.92069079490435 | epot = -38.8089483233276 | etot = -31.4294746451744 +952000 ekin = 3.42224118561198 | erot = 3.67807790241698 | epot = -38.8172186174579 | etot = -31.7168995294289 +953000 ekin = 3.5355898130389 | erot = 3.54582501818208 | epot = -38.8376037887756 | etot = -31.7561889575546 +954000 ekin = 3.7408153679097 | erot = 3.65672942044163 | epot = -38.8501623721153 | etot = -31.452617583764 +955000 ekin = 3.71100924365654 | erot = 3.89616377536035 | epot = -38.8864415175113 | etot = -31.2792684984944 +956000 ekin = 3.60593207480462 | erot = 3.6041169004468 | epot = -38.9258365620749 | etot = -31.7157875868235 +957000 ekin = 3.49530434439509 | erot = 3.82410347711554 | epot = -38.946856110473 | etot = -31.6274482889624 +958000 ekin = 3.33025913134877 | erot = 4.09361696296967 | epot = -38.9566069953684 | etot = -31.5327309010499 +959000 ekin = 3.23258633982982 | erot = 4.27749630513793 | epot = -38.9400855462529 | etot = -31.4300029012852 +960000 ekin = 3.31834124707646 | erot = 4.19167538415381 | epot = -38.9006120641386 | etot = -31.3905954329083 +961000 ekin = 3.23354004257472 | erot = 4.33974592386021 | epot = -38.8709462828611 | etot = -31.2976603164261 +962000 ekin = 3.27687420354416 | erot = 4.18251799625536 | epot = -38.8399997192042 | etot = -31.3806075194046 +963000 ekin = 3.18724078299293 | erot = 4.29559449615361 | epot = -38.8215635568147 | etot = -31.3387282776681 +964000 ekin = 3.16628639784342 | erot = 4.17929146419561 | epot = -38.8033314242491 | etot = -31.45775356221 +965000 ekin = 3.23601563824522 | erot = 4.51599223822397 | epot = -38.7801591620089 | etot = -31.0281512855397 +966000 ekin = 3.35348380272848 | erot = 3.96490873951949 | epot = -38.7593006562391 | etot = -31.4409081139911 +967000 ekin = 3.47301428118931 | erot = 3.78771221675296 | epot = -38.7263415939787 | etot = -31.4656150960365 +968000 ekin = 3.5149340684517 | erot = 3.36657292776092 | epot = -38.7364041234236 | etot = -31.854897127211 +969000 ekin = 3.55243037222559 | erot = 3.66068265314151 | epot = -38.7529284526029 | etot = -31.5398154272358 +970000 ekin = 3.63553363347277 | erot = 3.13050605621043 | epot = -38.8016144947092 | etot = -32.035574805026 +971000 ekin = 3.62760421034422 | erot = 3.43775684259623 | epot = -38.8707637872892 | etot = -31.8054027343488 +972000 ekin = 3.66143241862992 | erot = 4.04556663388657 | epot = -38.9794799026745 | etot = -31.272480850158 +973000 ekin = 3.72465898229281 | erot = 3.97416581320678 | epot = -39.0667487302085 | etot = -31.3679239347089 +974000 ekin = 3.99953950913788 | erot = 4.13912764019187 | epot = -39.1431741069699 | etot = -31.0045069576401 +975000 ekin = 4.00465817345125 | erot = 3.9952589646089 | epot = -39.1948973492943 | etot = -31.1949802112341 +976000 ekin = 4.16803719317614 | erot = 4.27607609453617 | epot = -39.2042146461383 | etot = -30.7601013584259 +977000 ekin = 4.27763535208335 | erot = 4.35785374646763 | epot = -39.1647674598219 | etot = -30.529278361271 +978000 ekin = 4.21509832146794 | erot = 3.96978575035236 | epot = -39.0661575270878 | etot = -30.8812734552675 +979000 ekin = 4.11219939771613 | erot = 3.86340161937286 | epot = -38.9126163242263 | etot = -30.9370153071373 +980000 ekin = 4.08548639230655 | erot = 3.71918260809169 | epot = -38.74606503787 | etot = -30.9413960374717 +981000 ekin = 4.02033461236225 | erot = 3.54042819636901 | epot = -38.597187758635 | etot = -31.0364249499038 +982000 ekin = 4.05981657544056 | erot = 3.65178477672051 | epot = -38.4729888125583 | etot = -30.7613874603972 +983000 ekin = 4.15649242216475 | erot = 3.62195027480219 | epot = -38.334259961066 | etot = -30.555817264099 +984000 ekin = 4.1544594314402 | erot = 3.41256983843883 | epot = -38.1946691276125 | etot = -30.6276398577335 +985000 ekin = 3.87659901087172 | erot = 3.4376780504462 | epot = -38.0505436384557 | etot = -30.7362665771378 +986000 ekin = 3.85786856381229 | erot = 3.30334700587324 | epot = -37.8996934133203 | etot = -30.7384778436347 +987000 ekin = 3.87294863787314 | erot = 3.15398232754981 | epot = -37.7929706719646 | etot = -30.7660397065416 +988000 ekin = 3.93790531951915 | erot = 3.08701498108581 | epot = -37.6532967522443 | etot = -30.6283764516394 +989000 ekin = 3.83115351568813 | erot = 3.07802242316603 | epot = -37.5101193189107 | etot = -30.6009433800565 +990000 ekin = 3.81048959043177 | erot = 3.11196082795583 | epot = -37.3832609771669 | etot = -30.4608105587793 +991000 ekin = 3.71517412131507 | erot = 3.09240412040435 | epot = -37.2833659467139 | etot = -30.4757877049945 +992000 ekin = 3.63849701384075 | erot = 2.99887074192591 | epot = -37.1786754428025 | etot = -30.5413076870358 +993000 ekin = 3.63209056043317 | erot = 3.27649085900172 | epot = -37.0906927302529 | etot = -30.182111310818 +994000 ekin = 3.5982839069315 | erot = 3.831697772683 | epot = -37.0255816353104 | etot = -29.5955999556959 +995000 ekin = 3.75927077522078 | erot = 3.45385861701412 | epot = -36.9690811728774 | etot = -29.7559517806425 +996000 ekin = 3.7162823443017 | erot = 3.37243499359166 | epot = -36.9421300931431 | etot = -29.8534127552498 +997000 ekin = 3.60416089411934 | erot = 3.31461433836019 | epot = -36.9528108756411 | etot = -30.0340356431616 +998000 ekin = 3.71457183702544 | erot = 3.42780251384766 | epot = -37.0325234658195 | etot = -29.8901491149464 +999000 ekin = 3.78703773886257 | erot = 3.63993408891207 | epot = -37.1548091593711 | etot = -29.7278373315964 +1000000 ekin = 3.83883486112572 | erot = 3.47192929391945 | epot = -37.2430911050885 | etot = -29.9323269500433 + 1000000 0.10236893 -1.4701186 0.037692055 -1.2847791 5.0290761e-05 64000 +Loop time of 76.6415 on 1 procs for 1000000 steps with 26 atoms + +Performance: 11273.266 tau/day, 13047.762 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 68.018 | 68.018 | 68.018 | 0.0 | 88.75 +Bond | 1.5413 | 1.5413 | 1.5413 | 0.0 | 2.01 +Neigh | 0.015138 | 0.015138 | 0.015138 | 0.0 | 0.02 +Comm | 0.35429 | 0.35429 | 0.35429 | 0.0 | 0.46 +Output | 0.23554 | 0.23554 | 0.23554 | 0.0 | 0.31 +Modify | 6.2843 | 6.2843 | 6.2843 | 0.0 | 8.20 +Other | | 0.1933 | | | 0.25 + +Nlocal: 26.0000 ave 26 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 301.000 ave 301 max 301 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.4.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:01:16 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 new file mode 100644 index 0000000000..0151e42c10 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 @@ -0,0 +1,1230 @@ +LAMMPS (2 Jul 2021) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +mass * 3.1575 # sets per-type mass if not in data file +set atom * mass 3.1575 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 4 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.4.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 3.74991604702378 | erot = 3.45272678980464 | epot = -37.3742009011421 | etot = -30.1715580643137 +Per MPI rank memory allocation (min/avg/max) = 9.321 | 9.322 | 9.323 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.099997761 -1.4717559 0.03428661 -1.2932417 5.6146609e-05 64000 +1000 ekin = 3.92430268570824 | erot = 3.29540971313705 | epot = -37.4816670091169 | etot = -30.2619546102716 +2000 ekin = 3.88644825046428 | erot = 3.58410925014822 | epot = -37.5871874286304 | etot = -30.1166299280179 +3000 ekin = 3.90603224055461 | erot = 3.7820605745286 | epot = -37.7021302921285 | etot = -30.0140374770453 +4000 ekin = 4.02636555552402 | erot = 3.91677901140303 | epot = -37.8027608694504 | etot = -29.8596163025233 +5000 ekin = 4.05442725401043 | erot = 4.07817807460239 | epot = -37.8494362833427 | etot = -29.7168309547299 +6000 ekin = 4.13499768127483 | erot = 4.03873475277248 | epot = -37.8257365098368 | etot = -29.6520040757895 +7000 ekin = 4.08584129662811 | erot = 3.9850289293034 | epot = -37.7447761711061 | etot = -29.6739059451746 +8000 ekin = 4.04473728341538 | erot = 3.70461133282257 | epot = -37.6185211079512 | etot = -29.8691724917133 +9000 ekin = 3.97040375513034 | erot = 3.89171847539017 | epot = -37.4779912856655 | etot = -29.615869055145 +10000 ekin = 4.08064552796876 | erot = 4.10399273710614 | epot = -37.3378150214196 | etot = -29.1531767563447 +11000 ekin = 3.94505548567027 | erot = 4.14758664614568 | epot = -37.2085796341435 | etot = -29.1159375023276 +12000 ekin = 3.88687763742865 | erot = 4.11256727293729 | epot = -37.1168918341091 | etot = -29.1174469237431 +13000 ekin = 3.78376547312033 | erot = 3.94997258779547 | epot = -37.0636475805865 | etot = -29.3299095196707 +14000 ekin = 3.72114827358807 | erot = 3.8386275531307 | epot = -37.053932608354 | etot = -29.4941567816353 +15000 ekin = 3.63885725366143 | erot = 3.37568559083329 | epot = -37.0775134892156 | etot = -30.0629706447209 +16000 ekin = 3.75926862366822 | erot = 3.47832285528774 | epot = -37.1763229835918 | etot = -29.9387315046358 +17000 ekin = 3.80458992549717 | erot = 3.37818714949382 | epot = -37.3270848276042 | etot = -30.1443077526132 +18000 ekin = 3.81685915102047 | erot = 3.82235577807973 | epot = -37.4876996492703 | etot = -29.84848472017 +19000 ekin = 3.80633274630077 | erot = 3.80393283337367 | epot = -37.6386270441083 | etot = -30.0283614644338 +20000 ekin = 3.77027693322166 | erot = 3.97848447130852 | epot = -37.7861726918924 | etot = -30.0374112873623 +21000 ekin = 3.75594248876353 | erot = 3.9040052393667 | epot = -37.9165000666023 | etot = -30.256552338472 +22000 ekin = 3.81729390633802 | erot = 3.70298358069288 | epot = -38.0211478246461 | etot = -30.5008703376152 +23000 ekin = 3.86462773298721 | erot = 3.52903064555356 | epot = -38.0539868057476 | etot = -30.6603284272068 +24000 ekin = 3.84611190496181 | erot = 3.47876891204884 | epot = -38.0524942369902 | etot = -30.7276134199796 +25000 ekin = 3.88431543220182 | erot = 3.80956733596685 | epot = -38.0090041212111 | etot = -30.3151213530425 +26000 ekin = 3.88520717073553 | erot = 4.04667753560885 | epot = -37.9336134642012 | etot = -30.0017287578568 +27000 ekin = 3.83553778749005 | erot = 4.1822230688838 | epot = -37.8633670830473 | etot = -29.8456062266734 +28000 ekin = 3.83638307293675 | erot = 4.13838046178327 | epot = -37.8079901228043 | etot = -29.8332265880843 +29000 ekin = 3.81360349447098 | erot = 4.16358811310883 | epot = -37.7885827024555 | etot = -29.8113910948756 +30000 ekin = 3.89572360919447 | erot = 4.04566996469694 | epot = -37.7874054211311 | etot = -29.8460118472397 +31000 ekin = 3.89393888302725 | erot = 3.55790326104643 | epot = -37.8038131932179 | etot = -30.3519710491442 +32000 ekin = 3.80317271692925 | erot = 3.54273524643289 | epot = -37.8451815180302 | etot = -30.4992735546681 +33000 ekin = 3.78703980355198 | erot = 3.99364624500505 | epot = -37.9406281896735 | etot = -30.1599421411165 +34000 ekin = 3.77142087668814 | erot = 3.88594611308826 | epot = -38.0975843525551 | etot = -30.4402173627787 +35000 ekin = 3.71264930628472 | erot = 3.65225843687428 | epot = -38.2835289304068 | etot = -30.9186211872478 +36000 ekin = 3.74220790707646 | erot = 3.95952222810306 | epot = -38.4596915935923 | etot = -30.7579614584128 +37000 ekin = 3.82423101226182 | erot = 4.44859396622374 | epot = -38.6538277887213 | etot = -30.3810028102358 +38000 ekin = 3.69455547696867 | erot = 4.82722829899239 | epot = -38.8348230288023 | etot = -30.3130392528413 +39000 ekin = 3.59548909658498 | erot = 5.03318978839692 | epot = -38.9632877762134 | etot = -30.3346088912315 +40000 ekin = 3.72390826726257 | erot = 4.77008246177612 | epot = -39.0432740898074 | etot = -30.5492833607687 +41000 ekin = 3.7184513028698 | erot = 4.66721188475367 | epot = -39.0678678855714 | etot = -30.6822046979479 +42000 ekin = 3.54696055158215 | erot = 4.50731751167309 | epot = -39.0616854007739 | etot = -31.0074073375186 +43000 ekin = 3.57495163768253 | erot = 4.94852093613527 | epot = -39.0169365666546 | etot = -30.4934639928368 +44000 ekin = 3.52915394890511 | erot = 5.14481752350043 | epot = -38.9320102816113 | etot = -30.2580388092058 +45000 ekin = 3.36103362047068 | erot = 5.30737062665214 | epot = -38.8074049309155 | etot = -30.1390006837927 +46000 ekin = 3.33204426677162 | erot = 4.63880623753686 | epot = -38.6602813061651 | etot = -30.6894308018567 +47000 ekin = 3.3454696016767 | erot = 4.07237976376904 | epot = -38.5241501078279 | etot = -31.1063007423822 +48000 ekin = 3.40049787952109 | erot = 4.05251615432415 | epot = -38.3938498073684 | etot = -30.9408357735232 +49000 ekin = 3.31008896923646 | erot = 4.20737258711353 | epot = -38.2514760468931 | etot = -30.7340144905431 +50000 ekin = 3.27384446847297 | erot = 3.84861240213725 | epot = -38.0781706006621 | etot = -30.9557137300519 +51000 ekin = 3.28837845708164 | erot = 4.03176750511312 | epot = -37.91245244037 | etot = -30.5923064781752 +52000 ekin = 3.32612610774242 | erot = 3.69449114481266 | epot = -37.7461543084422 | etot = -30.7255370558871 +53000 ekin = 3.24704253260759 | erot = 3.82351300738073 | epot = -37.5996085904177 | etot = -30.5290530504294 +54000 ekin = 3.28722266262309 | erot = 3.86366065026162 | epot = -37.4297798097099 | etot = -30.2788964968252 +55000 ekin = 3.24079189906268 | erot = 3.69908024112645 | epot = -37.2469422361785 | etot = -30.3070700959894 +56000 ekin = 3.18312456980309 | erot = 3.4713329715515 | epot = -37.0860684089786 | etot = -30.4316108676241 +57000 ekin = 3.22541795737972 | erot = 3.05594699251095 | epot = -36.9568071104524 | etot = -30.6754421605617 +58000 ekin = 3.32107899021709 | erot = 2.99608132055998 | epot = -36.8451019319947 | etot = -30.5279416212176 +59000 ekin = 3.37756033387522 | erot = 3.02468556348912 | epot = -36.7527120143503 | etot = -30.3504661169859 +60000 ekin = 3.37838518206593 | erot = 2.80486585978148 | epot = -36.6500489307867 | etot = -30.4667978889392 +61000 ekin = 3.42593058259813 | erot = 2.57336693961351 | epot = -36.5598996921937 | etot = -30.5606021699821 +62000 ekin = 3.38330194206299 | erot = 2.48716523240096 | epot = -36.4917506706074 | etot = -30.6212834961435 +63000 ekin = 3.23944564751904 | erot = 2.68514269262914 | epot = -36.4581690118124 | etot = -30.5335806716642 +64000 ekin = 3.1285734084237 | erot = 2.81379000215892 | epot = -36.4694531808167 | etot = -30.5270897702341 +65000 ekin = 3.09729001722782 | erot = 2.97796742393485 | epot = -36.4999099304855 | etot = -30.4246524893228 +66000 ekin = 3.0253262521451 | erot = 2.98352661182229 | epot = -36.5477137383998 | etot = -30.5388608744324 +67000 ekin = 3.14798260660732 | erot = 3.20065089850766 | epot = -36.632076278664 | etot = -30.283442773549 +68000 ekin = 3.28121216444374 | erot = 3.27703862715895 | epot = -36.7797333797322 | etot = -30.2214825881296 +69000 ekin = 3.391098638729 | erot = 3.49453676740748 | epot = -36.9477169900693 | etot = -30.0620815839328 +70000 ekin = 3.52145416968697 | erot = 3.19663795891383 | epot = -37.1459833247571 | etot = -30.4278911961563 +71000 ekin = 3.72588366820861 | erot = 3.11523594110609 | epot = -37.3394708863319 | etot = -30.4983512770172 +72000 ekin = 3.87053189634938 | erot = 3.51504753627337 | epot = -37.5837173340765 | etot = -30.1981379014537 +73000 ekin = 4.04353464507253 | erot = 3.57819581965 | epot = -37.8491002809692 | etot = -30.2273698162467 +74000 ekin = 4.21655599164692 | erot = 3.67972843708669 | epot = -38.0370200626718 | etot = -30.1407356339382 +75000 ekin = 4.27518037345521 | erot = 3.50148075250718 | epot = -38.1503543696651 | etot = -30.3736932437027 +76000 ekin = 4.3926037838371 | erot = 3.17711135808543 | epot = -38.226977923484 | etot = -30.6572627815614 +77000 ekin = 4.46694156592382 | erot = 3.28356630286398 | epot = -38.2567512319257 | etot = -30.5062433631379 +78000 ekin = 4.58031785764155 | erot = 3.27581240698071 | epot = -38.2501645622443 | etot = -30.3940342976221 +79000 ekin = 4.74132912230465 | erot = 3.40062659497672 | epot = -38.2259226034579 | etot = -30.0839668861765 +80000 ekin = 4.84478519554004 | erot = 3.56980153308305 | epot = -38.1476686101295 | etot = -29.7330818815064 +81000 ekin = 4.71163727716959 | erot = 3.65201658810481 | epot = -38.0489180007763 | etot = -29.6852641355019 +82000 ekin = 4.6231089457345 | erot = 3.61128178949376 | epot = -37.9515873690418 | etot = -29.7171966338136 +83000 ekin = 4.53890753637784 | erot = 3.79707688079965 | epot = -37.8589639327866 | etot = -29.5229795156091 +84000 ekin = 4.51952558800252 | erot = 3.75897913437647 | epot = -37.8043394039476 | etot = -29.5258346815686 +85000 ekin = 4.44986224636033 | erot = 4.10169839029418 | epot = -37.7952059629823 | etot = -29.2436453263278 +86000 ekin = 4.40335859262163 | erot = 4.1830315863789 | epot = -37.8405946712624 | etot = -29.2542044922618 +87000 ekin = 4.34352629789851 | erot = 4.00093225674517 | epot = -37.898177567682 | etot = -29.5537190130383 +88000 ekin = 4.39692532206231 | erot = 3.88765396717278 | epot = -37.9120170018269 | etot = -29.6274377125919 +89000 ekin = 4.35895407807686 | erot = 4.06877052706293 | epot = -37.8812041939536 | etot = -29.4534795888138 +90000 ekin = 4.2071551167368 | erot = 3.96880041117194 | epot = -37.8268382933969 | etot = -29.6508827654882 +91000 ekin = 4.22021993231722 | erot = 4.12841045745293 | epot = -37.7475084891388 | etot = -29.3988780993687 +92000 ekin = 4.13264986882769 | erot = 3.86635436032361 | epot = -37.6428932571545 | etot = -29.6438890280032 +93000 ekin = 4.05697056146709 | erot = 3.48249980793531 | epot = -37.5034004108467 | etot = -29.9639300414443 +94000 ekin = 3.85560920909802 | erot = 3.51617278195618 | epot = -37.3716848222182 | etot = -29.999902831164 +95000 ekin = 3.70696167824248 | erot = 3.74539992686897 | epot = -37.2425364302771 | etot = -29.7901748251656 +96000 ekin = 3.64541489153293 | erot = 3.55177042583762 | epot = -37.1071295289262 | etot = -29.9099442115556 +97000 ekin = 3.59427366044318 | erot = 3.58237376190948 | epot = -36.990331249798 | etot = -29.8136838274454 +98000 ekin = 3.36609732779909 | erot = 3.78920076230077 | epot = -36.8893462899051 | etot = -29.7340481998052 +99000 ekin = 3.24308716626529 | erot = 3.98439513504793 | epot = -36.7958275145338 | etot = -29.5683452132205 +100000 ekin = 3.10105716620534 | erot = 3.88380514199007 | epot = -36.7237148853891 | etot = -29.7388525771937 +101000 ekin = 3.0539281420833 | erot = 3.92712981026617 | epot = -36.7019624525075 | etot = -29.720904500158 +102000 ekin = 3.21793305977278 | erot = 4.11601242104548 | epot = -36.7682713932651 | etot = -29.4343259124469 +103000 ekin = 3.29518049820534 | erot = 4.13622147772537 | epot = -36.8839850328144 | etot = -29.4525830568837 +104000 ekin = 3.38349143563989 | erot = 4.11834556660366 | epot = -37.0170458924467 | etot = -29.5152088902031 +105000 ekin = 3.43063719220731 | erot = 4.19281995644328 | epot = -37.1501255032183 | etot = -29.5266683545677 +106000 ekin = 3.39305878697925 | erot = 4.59139499879988 | epot = -37.2962927183006 | etot = -29.3118389325215 +107000 ekin = 3.49611625167404 | erot = 4.42190170056934 | epot = -37.429825379218 | etot = -29.5118074269746 +108000 ekin = 3.59165643487548 | erot = 4.73333858652907 | epot = -37.4821370449025 | etot = -29.1571420234979 +109000 ekin = 3.59878557010273 | erot = 5.08720641062768 | epot = -37.4454225962912 | etot = -28.7594306155607 +110000 ekin = 3.52607850054496 | erot = 4.92743402067516 | epot = -37.33464551381 | etot = -28.8811329925899 +111000 ekin = 3.52196404281898 | erot = 4.48970120472513 | epot = -37.2166378630308 | etot = -29.2049726154866 +112000 ekin = 3.64094551226764 | erot = 4.18578082474288 | epot = -37.1356107687899 | etot = -29.3088844317794 +113000 ekin = 3.59908785035481 | erot = 3.81929848767576 | epot = -37.1563156196511 | etot = -29.7379292816205 +114000 ekin = 3.73247165614536 | erot = 3.71912191326134 | epot = -37.1841072802385 | etot = -29.7325137108319 +115000 ekin = 3.81386546938822 | erot = 3.49889872890813 | epot = -37.2616543115736 | etot = -29.9488901132773 +116000 ekin = 4.05829999340879 | erot = 3.583906655014 | epot = -37.400300568259 | etot = -29.7580939198362 +117000 ekin = 4.2755011092504 | erot = 3.79076820440129 | epot = -37.5923004712666 | etot = -29.5260311576149 +118000 ekin = 4.45490103530211 | erot = 3.7791518579582 | epot = -37.7846946186124 | etot = -29.5506417253521 +119000 ekin = 4.58790399115629 | erot = 3.86870152715712 | epot = -37.9811558924432 | etot = -29.5245503741297 +120000 ekin = 4.92259141545339 | erot = 3.84940365834989 | epot = -38.1382043293411 | etot = -29.3662092555378 +121000 ekin = 5.13183269148587 | erot = 4.03705087488501 | epot = -38.2560800244006 | etot = -29.0871964580297 +122000 ekin = 5.17140868558149 | erot = 3.61810962674126 | epot = -38.3381390234361 | etot = -29.5486207111134 +123000 ekin = 5.28384467069883 | erot = 4.14897954513985 | epot = -38.3803925391065 | etot = -28.9475683232678 +124000 ekin = 5.45144965935765 | erot = 3.74948516195918 | epot = -38.4152715166926 | etot = -29.2143366953758 +125000 ekin = 5.49907232704439 | erot = 3.62957174075199 | epot = -38.4698081948493 | etot = -29.3411641270529 +126000 ekin = 5.8127555292288 | erot = 3.50370762045619 | epot = -38.5369283444353 | etot = -29.2204651947503 +127000 ekin = 5.71810535961404 | erot = 3.50153411217259 | epot = -38.6097648991191 | etot = -29.3901254273324 +128000 ekin = 5.59769610955136 | erot = 2.99726680348461 | epot = -38.6545287261793 | etot = -30.0595658131433 +129000 ekin = 5.5165718206709 | erot = 3.37515224045301 | epot = -38.6909141535705 | etot = -29.7991900924466 +130000 ekin = 5.46626997343509 | erot = 3.77525421867709 | epot = -38.7059148210798 | etot = -29.4643906289676 +131000 ekin = 5.36987741440168 | erot = 3.92459463488603 | epot = -38.6781199948589 | etot = -29.3836479455712 +132000 ekin = 5.13704854269979 | erot = 3.89365302265496 | epot = -38.6113331110922 | etot = -29.5806315457375 +133000 ekin = 5.04851208372161 | erot = 4.17613618410271 | epot = -38.4969113589743 | etot = -29.2722630911499 +134000 ekin = 4.96335667475928 | erot = 4.28428652813699 | epot = -38.3084161100388 | etot = -29.0607729071425 +135000 ekin = 4.67485522816786 | erot = 3.71485446936997 | epot = -38.043760165967 | etot = -29.6540504684292 +136000 ekin = 4.48906299160435 | erot = 4.19015103736174 | epot = -37.7533241067268 | etot = -29.0741100777607 +137000 ekin = 4.31371561077628 | erot = 3.47925724303279 | epot = -37.4739407743091 | etot = -29.6809679205001 +138000 ekin = 3.96696543473046 | erot = 3.71675428283144 | epot = -37.2042587721449 | etot = -29.520539054583 +139000 ekin = 3.59101315513257 | erot = 3.64278698721023 | epot = -36.9457852108065 | etot = -29.7119850684637 +140000 ekin = 3.44095423425056 | erot = 3.49830537198601 | epot = -36.7203613080885 | etot = -29.7811017018519 +141000 ekin = 3.36296546737416 | erot = 3.56983741924016 | epot = -36.496476745137 | etot = -29.5636738585227 +142000 ekin = 3.18252441669298 | erot = 3.32935464682707 | epot = -36.324475892532 | etot = -29.812596829012 +143000 ekin = 3.18465930443875 | erot = 3.56170045589758 | epot = -36.2215210957517 | etot = -29.4751613354154 +144000 ekin = 3.08106725409761 | erot = 3.50261030291577 | epot = -36.151244725806 | etot = -29.5675671687926 +145000 ekin = 3.0809377636579 | erot = 3.51948185643664 | epot = -36.0863085456325 | etot = -29.4858889255379 +146000 ekin = 3.02030159479372 | erot = 3.37397305462396 | epot = -36.0845314152705 | etot = -29.6902567658529 +147000 ekin = 3.04139072985625 | erot = 3.36603954258544 | epot = -36.1557232229402 | etot = -29.7482929504985 +148000 ekin = 3.14853067203546 | erot = 3.14562859809661 | epot = -36.2494960139436 | etot = -29.9553367438116 +149000 ekin = 3.18195150813254 | erot = 3.58071760906396 | epot = -36.3477640598877 | etot = -29.5850949426912 +150000 ekin = 3.21133048799954 | erot = 3.85389957660273 | epot = -36.4132627454726 | etot = -29.3480326808703 +151000 ekin = 3.34144104231994 | erot = 3.4939153763212 | epot = -36.478294453089 | etot = -29.6429380344479 +152000 ekin = 3.38469121090087 | erot = 3.35926284582863 | epot = -36.5578474424846 | etot = -29.8138933857551 +153000 ekin = 3.52527639525619 | erot = 3.56811727016302 | epot = -36.6674257186119 | etot = -29.5740320531927 +154000 ekin = 3.77924799771019 | erot = 3.52145795256778 | epot = -36.762260192104 | etot = -29.4615542418261 +155000 ekin = 3.83418008764597 | erot = 3.28305394597542 | epot = -36.8282659682366 | etot = -29.7110319346152 +156000 ekin = 3.87517167307501 | erot = 2.75621015438911 | epot = -36.8507311290658 | etot = -30.2193493016017 +157000 ekin = 3.89846784481905 | erot = 3.03513966490474 | epot = -36.8490467787065 | etot = -29.9154392689827 +158000 ekin = 3.86372390524152 | erot = 3.067331408384 | epot = -36.8143502444314 | etot = -29.8832949308059 +159000 ekin = 3.8756082258688 | erot = 2.72238394226933 | epot = -36.772006665376 | etot = -30.1740144972379 +160000 ekin = 3.816595406495 | erot = 2.7916288304199 | epot = -36.7456092138712 | etot = -30.1373849769563 +161000 ekin = 3.90364665450467 | erot = 2.85891130626936 | epot = -36.6767188031102 | etot = -29.9141608423362 +162000 ekin = 3.93432840871765 | erot = 3.23277686088016 | epot = -36.6068502811304 | etot = -29.4397450115325 +163000 ekin = 3.97425577903384 | erot = 2.70754263327067 | epot = -36.5720643915927 | etot = -29.8902659792882 +164000 ekin = 3.91949827572841 | erot = 3.0566880418144 | epot = -36.581283859358 | etot = -29.6050975418151 +165000 ekin = 3.9942517956167 | erot = 3.29785069907587 | epot = -36.6379374004759 | etot = -29.3458349057833 +166000 ekin = 4.02904533815552 | erot = 3.36634066781836 | epot = -36.7340868254039 | etot = -29.33870081943 +167000 ekin = 4.03733260337014 | erot = 3.51733984448515 | epot = -36.8476519248274 | etot = -29.2929794769721 +168000 ekin = 4.01641387278363 | erot = 3.37538682559175 | epot = -36.971098022016 | etot = -29.5792973236406 +169000 ekin = 3.94799788750035 | erot = 3.38842418926848 | epot = -37.1207420196436 | etot = -29.7843199428747 +170000 ekin = 3.98944239104564 | erot = 3.56779767670635 | epot = -37.292260024934 | etot = -29.735019957182 +171000 ekin = 4.04980262307328 | erot = 3.8730831046424 | epot = -37.4956434312018 | etot = -29.5727577034861 +172000 ekin = 4.10498686245119 | erot = 4.24595756362535 | epot = -37.6879527015218 | etot = -29.3370082754453 +173000 ekin = 4.12919710204917 | erot = 4.28575123018794 | epot = -37.8940672883491 | etot = -29.479118956112 +174000 ekin = 4.04607401980725 | erot = 4.41784593637421 | epot = -38.1063274639935 | etot = -29.642407507812 +175000 ekin = 4.13007220306937 | erot = 4.3967913469306 | epot = -38.3139522350313 | etot = -29.7870886850313 +176000 ekin = 4.1414636964047 | erot = 4.25565002500116 | epot = -38.5085743578727 | etot = -30.1114606364668 +177000 ekin = 4.33605278083852 | erot = 4.58687123058771 | epot = -38.663345411644 | etot = -29.7404214002177 +178000 ekin = 4.3268891648432 | erot = 4.50454813785607 | epot = -38.7700089206451 | etot = -29.9385716179458 +179000 ekin = 4.39331384776191 | erot = 4.88121292734115 | epot = -38.8147888868657 | etot = -29.5402621117627 +180000 ekin = 4.36409495919781 | erot = 4.62653667682595 | epot = -38.7920356589674 | etot = -29.8014040229436 +181000 ekin = 4.40002739116619 | erot = 4.26572305349555 | epot = -38.732090098002 | etot = -30.0663396533403 +182000 ekin = 4.38584471768798 | erot = 4.03958660380944 | epot = -38.6652721860918 | etot = -30.2398408645944 +183000 ekin = 4.38872118980235 | erot = 4.03920994265157 | epot = -38.5494953603399 | etot = -30.121564227886 +184000 ekin = 4.58261674670928 | erot = 4.09854761999429 | epot = -38.385824841967 | etot = -29.7046604752634 +185000 ekin = 4.61324410405523 | erot = 4.15998485211153 | epot = -38.1895073749228 | etot = -29.416278418756 +186000 ekin = 4.58712030480541 | erot = 3.80292929559516 | epot = -37.9691363595882 | etot = -29.5790867591876 +187000 ekin = 4.49704057160018 | erot = 3.79953063209063 | epot = -37.7563677349906 | etot = -29.4597965312998 +188000 ekin = 4.67801335458731 | erot = 3.94614018085653 | epot = -37.5596730791519 | etot = -28.9355195437081 +189000 ekin = 4.72635028851209 | erot = 3.97986342680415 | epot = -37.3737961852725 | etot = -28.6675824699563 +190000 ekin = 4.7042288678312 | erot = 3.76567525080941 | epot = -37.196832874262 | etot = -28.7269287556214 +191000 ekin = 4.76615905270403 | erot = 4.11771710042025 | epot = -37.0524866708229 | etot = -28.1686105176986 +192000 ekin = 4.66334615993905 | erot = 4.32180108624872 | epot = -36.9281089002537 | etot = -27.9429616540659 +193000 ekin = 4.54227272612665 | erot = 4.37403333624804 | epot = -36.8106507982267 | etot = -27.894344735852 +194000 ekin = 4.462583886268 | erot = 4.57094153868338 | epot = -36.7126835627942 | etot = -27.6791581378429 +195000 ekin = 4.26009039309661 | erot = 5.10893274622673 | epot = -36.6717506302939 | etot = -27.3027274909705 +196000 ekin = 4.24016895096413 | erot = 4.95101320260786 | epot = -36.6607739952153 | etot = -27.4695918416433 +197000 ekin = 4.07555507933054 | erot = 5.3373115761178 | epot = -36.6886082622519 | etot = -27.2757416068035 +198000 ekin = 3.98091713951368 | erot = 5.37374733968393 | epot = -36.7238260637148 | etot = -27.3691615845172 +199000 ekin = 4.0006733079207 | erot = 5.36035180423053 | epot = -36.7643724815872 | etot = -27.403347369436 +200000 ekin = 3.91652525767982 | erot = 4.88675678602831 | epot = -36.7730308398529 | etot = -27.9697487961448 +201000 ekin = 3.81609915882208 | erot = 4.31400854830159 | epot = -36.7481890160651 | etot = -28.6180813089414 +202000 ekin = 3.71932569397591 | erot = 4.38569878861434 | epot = -36.6956778034205 | etot = -28.5906533208303 +203000 ekin = 3.6429062307207 | erot = 4.3750378945926 | epot = -36.6304609598585 | etot = -28.6125168345452 +204000 ekin = 3.52854777039972 | erot = 4.29732321046263 | epot = -36.5744389849187 | etot = -28.7485680040564 +205000 ekin = 3.47688319826114 | erot = 4.05205396768161 | epot = -36.531456554712 | etot = -29.0025193887692 +206000 ekin = 3.57867350058512 | erot = 4.2868191467488 | epot = -36.5152410045852 | etot = -28.6497483572513 +207000 ekin = 3.67789472949123 | erot = 4.07649115773256 | epot = -36.4807964879222 | etot = -28.7264106006985 +208000 ekin = 3.75162300302636 | erot = 3.99412890438549 | epot = -36.4719013777705 | etot = -28.7261494703586 +209000 ekin = 3.82882555476977 | erot = 4.07806686544388 | epot = -36.5274965379165 | etot = -28.6206041177029 +210000 ekin = 3.9458995738135 | erot = 4.05524037388635 | epot = -36.6356567037899 | etot = -28.6345167560901 +211000 ekin = 4.07654365300251 | erot = 3.99406586158705 | epot = -36.7715123193756 | etot = -28.7009028047861 +212000 ekin = 4.28409313331832 | erot = 4.41351434873083 | epot = -36.9240266223076 | etot = -28.2264191402585 +213000 ekin = 4.49200123945991 | erot = 4.57752549048093 | epot = -37.0744914076607 | etot = -28.0049646777198 +214000 ekin = 4.68170470060552 | erot = 4.83486386570226 | epot = -37.2372407583265 | etot = -27.7206721920187 +215000 ekin = 4.98081379617907 | erot = 4.46606343482571 | epot = -37.4068324828893 | etot = -27.9599552518845 +216000 ekin = 5.16729766417649 | erot = 4.60318830168464 | epot = -37.546455570517 | etot = -27.7759696046559 +217000 ekin = 5.38386929678543 | erot = 4.77752494373566 | epot = -37.6405601527457 | etot = -27.4791659122246 +218000 ekin = 5.7058164504652 | erot = 4.70370884810736 | epot = -37.698401969983 | etot = -27.2888766714105 +219000 ekin = 5.88600523163575 | erot = 4.58694924042826 | epot = -37.7125786046513 | etot = -27.2396241325873 +220000 ekin = 6.15427965488963 | erot = 4.42931316972489 | epot = -37.6846020761394 | etot = -27.1010092515249 +221000 ekin = 6.20955938015943 | erot = 4.54001725187623 | epot = -37.6213945439905 | etot = -26.8718179119549 +222000 ekin = 6.24568472622515 | erot = 4.97311797105802 | epot = -37.5132484834206 | etot = -26.2944457861374 +223000 ekin = 6.23087495739475 | erot = 4.87026240860754 | epot = -37.4093126450282 | etot = -26.3081752790259 +224000 ekin = 6.34215727178104 | erot = 4.95416073100343 | epot = -37.3138628835635 | etot = -26.017544880779 +225000 ekin = 6.34418551658282 | erot = 4.97197547495999 | epot = -37.2296241301023 | etot = -25.9134631385595 +226000 ekin = 6.27234146176753 | erot = 4.712320761698 | epot = -37.16490911443 | etot = -26.1802468909645 +227000 ekin = 6.29782050547387 | erot = 4.64279996368984 | epot = -37.1521034204924 | etot = -26.2114829513287 +228000 ekin = 6.45215375342329 | erot = 4.66543105642573 | epot = -37.1176036705896 | etot = -26.0000188607406 +229000 ekin = 6.57609932445413 | erot = 4.31104294387352 | epot = -37.0319087568376 | etot = -26.1447664885099 +230000 ekin = 6.3941596764924 | erot = 4.16613500609599 | epot = -36.9020701489014 | etot = -26.341775466313 +231000 ekin = 6.06981997767513 | erot = 4.16164382030047 | epot = -36.7672531588279 | etot = -26.5357893608523 +232000 ekin = 6.07851417086582 | erot = 3.92614169635025 | epot = -36.6287349588706 | etot = -26.6240790916545 +233000 ekin = 5.86578448983374 | erot = 3.89415959164517 | epot = -36.465034335415 | etot = -26.7050902539361 +234000 ekin = 5.66525736866247 | erot = 3.89419060194184 | epot = -36.3317105619283 | etot = -26.772262591324 +235000 ekin = 5.45947253618382 | erot = 3.51915643493605 | epot = -36.1877403763664 | etot = -27.2091114052465 +236000 ekin = 5.23839596197748 | erot = 3.35080370425763 | epot = -36.0601413821509 | etot = -27.4709417159157 +237000 ekin = 5.11015038693027 | erot = 3.41418634041097 | epot = -35.9797234474552 | etot = -27.455386720114 +238000 ekin = 5.07705507560246 | erot = 3.55422258848944 | epot = -35.9558941013165 | etot = -27.3246164372246 +239000 ekin = 5.11036683512567 | erot = 3.60903830571379 | epot = -35.9686036709486 | etot = -27.2491985301092 +240000 ekin = 5.05273101840451 | erot = 3.85355249273515 | epot = -36.0380166955248 | etot = -27.1317331843852 +241000 ekin = 5.09369536459292 | erot = 3.6433800043733 | epot = -36.1343234897539 | etot = -27.3972481207877 +242000 ekin = 5.26488817621227 | erot = 4.01055195692897 | epot = -36.2412063129141 | etot = -26.9657661797729 +243000 ekin = 5.23195261672929 | erot = 4.46546566729833 | epot = -36.345605429643 | etot = -26.6481871456153 +244000 ekin = 5.22638739434401 | erot = 4.31088904489896 | epot = -36.4415840114135 | etot = -26.9043075721705 +245000 ekin = 5.44853137039486 | erot = 4.17607977278288 | epot = -36.5182986507189 | etot = -26.8936875075411 +246000 ekin = 5.51456970399734 | erot = 3.7459544203853 | epot = -36.5760003166761 | etot = -27.3154761922935 +247000 ekin = 5.60809096899872 | erot = 4.15307717654149 | epot = -36.6102851986096 | etot = -26.8491170530694 +248000 ekin = 5.44607700345041 | erot = 4.00137483235449 | epot = -36.6173189081378 | etot = -27.1698670723329 +249000 ekin = 5.39824066997391 | erot = 4.00527284085302 | epot = -36.6178595818604 | etot = -27.2143460710335 +250000 ekin = 5.40591864200621 | erot = 3.83152692098389 | epot = -36.5913298844141 | etot = -27.3538843214239 +251000 ekin = 5.42515843147756 | erot = 3.74120297831872 | epot = -36.5372880481644 | etot = -27.3709266383681 +252000 ekin = 5.4712575658911 | erot = 3.93923600749343 | epot = -36.4718103145524 | etot = -27.0613167411679 +253000 ekin = 5.45280164405796 | erot = 4.07788577485834 | epot = -36.3971958399354 | etot = -26.8665084210191 +254000 ekin = 5.351360104931 | erot = 4.05065697891534 | epot = -36.3208515747331 | etot = -26.9188344908867 +255000 ekin = 5.26929844479126 | erot = 3.99546469631013 | epot = -36.2503502909171 | etot = -26.9855871498158 +256000 ekin = 5.28023678974981 | erot = 4.22040986008114 | epot = -36.1946445254556 | etot = -26.6939978756247 +257000 ekin = 5.06048081748237 | erot = 4.23177072887926 | epot = -36.1310700373981 | etot = -26.8388184910365 +258000 ekin = 5.04266904507291 | erot = 4.32321520327971 | epot = -36.0647093578756 | etot = -26.6988251095229 +259000 ekin = 4.83091830266356 | erot = 4.34656742782584 | epot = -36.0089991272069 | etot = -26.8315133967175 +260000 ekin = 4.836699911676 | erot = 4.25709648660297 | epot = -35.96970369746 | etot = -26.875907299181 +261000 ekin = 4.77396719262991 | erot = 4.0929221497623 | epot = -35.9054139064718 | etot = -27.0385245640796 +262000 ekin = 4.6660127085841 | erot = 3.73102576614632 | epot = -35.8157479345105 | etot = -27.4187094597801 +263000 ekin = 4.58027061960237 | erot = 3.74679758350867 | epot = -35.7631254737833 | etot = -27.4360572706722 +264000 ekin = 4.65921569864907 | erot = 3.90501973343979 | epot = -35.7356757776858 | etot = -27.1714403455969 +265000 ekin = 4.67586149937357 | erot = 3.94654925905527 | epot = -35.7049387943769 | etot = -27.0825280359481 +266000 ekin = 4.69584694538616 | erot = 3.98055672084523 | epot = -35.6673176149281 | etot = -26.9909139486967 +267000 ekin = 4.78499421533014 | erot = 4.0364816915833 | epot = -35.6392507408913 | etot = -26.8177748339778 +268000 ekin = 4.84316914009132 | erot = 3.9986077800244 | epot = -35.6448334716871 | etot = -26.8030565515714 +269000 ekin = 4.90837806472402 | erot = 4.04652570535906 | epot = -35.6496420701673 | etot = -26.6947383000842 +270000 ekin = 4.78579400655356 | erot = 4.34179455226934 | epot = -35.6115561484025 | etot = -26.4839675895796 +271000 ekin = 4.85153732395834 | erot = 3.76641259729514 | epot = -35.613775306659 | etot = -26.9958253854055 +272000 ekin = 4.97803664593813 | erot = 4.19853764559888 | epot = -35.66422567808 | etot = -26.487651386543 +273000 ekin = 4.99431287425886 | erot = 4.16775756950246 | epot = -35.7125500141237 | etot = -26.5504795703624 +274000 ekin = 5.02755533075327 | erot = 4.06015777810426 | epot = -35.7335253506941 | etot = -26.6458122418365 +275000 ekin = 4.96372481963275 | erot = 4.27522667590852 | epot = -35.7375976828865 | etot = -26.4986461873452 +276000 ekin = 5.07934127118678 | erot = 4.03884457577036 | epot = -35.7684807851686 | etot = -26.6502949382115 +277000 ekin = 5.11065676525152 | erot = 3.89593355388357 | epot = -35.8299825238668 | etot = -26.8233922047317 +278000 ekin = 5.14434493464948 | erot = 4.10431801630069 | epot = -35.9156424264978 | etot = -26.6669794755476 +279000 ekin = 5.13854043459747 | erot = 3.33687958464002 | epot = -35.9567280939811 | etot = -27.4813080747437 +280000 ekin = 5.13698711985543 | erot = 3.1321095347802 | epot = -35.9663254349012 | etot = -27.6972287802656 +281000 ekin = 5.12014323326354 | erot = 3.01072130069868 | epot = -35.9687821467586 | etot = -27.8379176127964 +282000 ekin = 5.0748729819616 | erot = 2.78222371236629 | epot = -35.9666224009213 | etot = -28.1095257065934 +283000 ekin = 4.93728532174382 | erot = 2.51682526487889 | epot = -36.0092096947433 | etot = -28.5550991081205 +284000 ekin = 5.10799487537326 | erot = 2.34406164243711 | epot = -36.0766867016223 | etot = -28.6246301838119 +285000 ekin = 5.21438921802967 | erot = 2.42355410917311 | epot = -36.1686025783611 | etot = -28.5306592511584 +286000 ekin = 5.22674428893558 | erot = 2.43127546535952 | epot = -36.2811716154217 | etot = -28.6231518611266 +287000 ekin = 5.42842235635899 | erot = 2.80110266939532 | epot = -36.3926299688269 | etot = -28.1631049430726 +288000 ekin = 5.53841609379804 | erot = 3.04198571498546 | epot = -36.5118610231694 | etot = -27.9314592143859 +289000 ekin = 5.3467040301105 | erot = 3.09938875481675 | epot = -36.6304827875393 | etot = -28.184390002612 +290000 ekin = 5.34231674745426 | erot = 3.31160144161375 | epot = -36.7456392368754 | etot = -28.0917210478074 +291000 ekin = 5.36188526202177 | erot = 3.45917476353394 | epot = -36.8302537236161 | etot = -28.0091936980603 +292000 ekin = 5.47780509141152 | erot = 3.77906726321804 | epot = -36.8842491471654 | etot = -27.6273767925359 +293000 ekin = 5.28302000096844 | erot = 3.57818629599035 | epot = -36.8949841799423 | etot = -28.0337778829835 +294000 ekin = 5.30853543438815 | erot = 3.56263204697584 | epot = -36.8825736697856 | etot = -28.0114061884216 +295000 ekin = 5.20536069491162 | erot = 3.77206495855666 | epot = -36.8703913967998 | etot = -27.8929657433315 +296000 ekin = 5.16948391824595 | erot = 3.64242202500107 | epot = -36.8524591521914 | etot = -28.0405532089444 +297000 ekin = 5.14948698293416 | erot = 3.5630007131842 | epot = -36.8077681088433 | etot = -28.095280412725 +298000 ekin = 5.07831718808015 | erot = 3.56647326916591 | epot = -36.7441951556035 | etot = -28.0994046983574 +299000 ekin = 5.07638833142119 | erot = 3.33911289208736 | epot = -36.7050879472261 | etot = -28.2895867237176 +300000 ekin = 5.03413727775465 | erot = 3.74853034027346 | epot = -36.6636621891821 | etot = -27.880994571154 +301000 ekin = 4.97235848835827 | erot = 3.32835758650059 | epot = -36.6711630757898 | etot = -28.370447000931 +302000 ekin = 5.0096895871007 | erot = 3.04854259478463 | epot = -36.7093256921458 | etot = -28.6510935102605 +303000 ekin = 5.12929110471125 | erot = 3.0802372254872 | epot = -36.7951841728067 | etot = -28.5856558426083 +304000 ekin = 5.16690416140484 | erot = 3.34049274708998 | epot = -36.9126194047401 | etot = -28.4052224962453 +305000 ekin = 5.23349789631504 | erot = 3.46551744359714 | epot = -37.0448370009165 | etot = -28.3458216610043 +306000 ekin = 5.2886097452738 | erot = 3.56105103024495 | epot = -37.1811985422466 | etot = -28.3315377667279 +307000 ekin = 5.40125295123197 | erot = 3.87520415097948 | epot = -37.30553234416 | etot = -28.0290752419485 +308000 ekin = 5.46740727789042 | erot = 3.91865002312583 | epot = -37.389277815527 | etot = -28.0032205145107 +309000 ekin = 5.43990046762824 | erot = 4.00265425349909 | epot = -37.4336308324254 | etot = -27.991076111298 +310000 ekin = 5.38744019614249 | erot = 3.91760045067581 | epot = -37.4766997166659 | etot = -28.1716590698476 +311000 ekin = 5.54869794564873 | erot = 3.97913763348747 | epot = -37.5380640420298 | etot = -28.0102284628936 +312000 ekin = 5.71519006739875 | erot = 4.09263126769848 | epot = -37.5745318459452 | etot = -27.766710510848 +313000 ekin = 5.60331607661102 | erot = 3.83543196463859 | epot = -37.6101139619702 | etot = -28.1713659207206 +314000 ekin = 5.5180041708143 | erot = 3.7494474523439 | epot = -37.6279066647949 | etot = -28.3604550416367 +315000 ekin = 5.47833005901007 | erot = 4.08581993263796 | epot = -37.6406124353411 | etot = -28.0764624436931 +316000 ekin = 5.33860837296308 | erot = 4.51116644302033 | epot = -37.6217312448187 | etot = -27.7719564288353 +317000 ekin = 5.23941916557626 | erot = 4.78689518832633 | epot = -37.5731600528525 | etot = -27.5468456989499 +318000 ekin = 5.11187775633088 | erot = 4.8295881268003 | epot = -37.5155006216098 | etot = -27.5740347384786 +319000 ekin = 5.22954347525669 | erot = 4.49457407004892 | epot = -37.4371163833055 | etot = -27.7129988379999 +320000 ekin = 5.30878948863373 | erot = 4.92186054084621 | epot = -37.3586788029377 | etot = -27.1280287734577 +321000 ekin = 5.25051542685368 | erot = 4.81963950413293 | epot = -37.3122945279909 | etot = -27.2421395970043 +322000 ekin = 5.07574443571119 | erot = 4.74007360204251 | epot = -37.2420599117422 | etot = -27.4262418739885 +323000 ekin = 5.0265325350937 | erot = 4.66604787555056 | epot = -37.1620424354779 | etot = -27.4694620248336 +324000 ekin = 5.12999279273048 | erot = 4.55456244400843 | epot = -37.1081993843435 | etot = -27.4236441476046 +325000 ekin = 5.01484863365259 | erot = 5.03270116093541 | epot = -37.0549970668844 | etot = -27.0074472722964 +326000 ekin = 5.15105125743363 | erot = 4.77726330645675 | epot = -37.0062804471437 | etot = -27.0779658832534 +327000 ekin = 5.17373663939357 | erot = 4.75720955177068 | epot = -36.9735735310225 | etot = -27.0426273398583 +328000 ekin = 5.3265809986392 | erot = 4.45847251670634 | epot = -36.9463177254326 | etot = -27.1612642100871 +329000 ekin = 5.28491385975229 | erot = 4.23650020870599 | epot = -36.9151642788529 | etot = -27.3937502103946 +330000 ekin = 5.12552135481235 | erot = 4.79027984581653 | epot = -36.8863179466158 | etot = -26.9705167459869 +331000 ekin = 5.12103290586643 | erot = 5.03778117543898 | epot = -36.841363047454 | etot = -26.6825489661486 +332000 ekin = 5.06929714597605 | erot = 4.90820597157557 | epot = -36.7488012231946 | etot = -26.771298105643 +333000 ekin = 4.96505468499555 | erot = 5.01335794632778 | epot = -36.6271163009911 | etot = -26.6487036696678 +334000 ekin = 4.99343125906659 | erot = 5.01439694959199 | epot = -36.5036049758887 | etot = -26.4957767672301 +335000 ekin = 4.90069371729875 | erot = 4.54385275511657 | epot = -36.3777599646381 | etot = -26.9332134922228 +336000 ekin = 5.07863725672875 | erot = 4.69305135725135 | epot = -36.2629152842756 | etot = -26.4912266702956 +337000 ekin = 4.94799955754133 | erot = 4.52583833193069 | epot = -36.1612360033462 | etot = -26.6873981138742 +338000 ekin = 4.85224868200284 | erot = 4.50041298245555 | epot = -36.0752991866383 | etot = -26.7226375221799 +339000 ekin = 4.72144640536423 | erot = 4.54752039051223 | epot = -35.9970632546972 | etot = -26.7280964588208 +340000 ekin = 4.80943098922164 | erot = 4.34708343509498 | epot = -35.9687361528352 | etot = -26.8122217285186 +341000 ekin = 4.70361214653931 | erot = 4.47793300498463 | epot = -35.9999322617905 | etot = -26.8183871102666 +342000 ekin = 4.76064761481744 | erot = 4.66605256976241 | epot = -36.0433784122729 | etot = -26.616678227693 +343000 ekin = 4.67728032528768 | erot = 4.6610083917642 | epot = -35.9211632159824 | etot = -26.5828744989305 +344000 ekin = 4.96339724601181 | erot = 4.93823124551168 | epot = -36.2212250614817 | etot = -26.3195965699582 +345000 ekin = 4.92216540601158 | erot = 5.10460165774345 | epot = -36.3841924486034 | etot = -26.3574253848484 +346000 ekin = 4.99792813974856 | erot = 4.77882820289903 | epot = -36.4406602112533 | etot = -26.6639038686057 +347000 ekin = 4.97738387739107 | erot = 4.57238123569529 | epot = -36.4353446283208 | etot = -26.8855795152344 +348000 ekin = 4.92451917191307 | erot = 4.32330547944774 | epot = -36.3741726686486 | etot = -27.1263480172878 +349000 ekin = 4.7901834448853 | erot = 4.64955099606445 | epot = -36.2232051796221 | etot = -26.7834707386723 +350000 ekin = 4.74997485376102 | erot = 4.41441619333004 | epot = -36.0086530481284 | etot = -26.8442620010373 +351000 ekin = 4.65861306362097 | erot = 4.54712008187945 | epot = -35.7312651155867 | etot = -26.5255319700863 +352000 ekin = 4.64876538273139 | erot = 4.76138349321515 | epot = -35.4506369361125 | etot = -26.0404880601659 +353000 ekin = 4.59253342080998 | erot = 4.29456686626234 | epot = -35.1553683981332 | etot = -26.2682681110609 +354000 ekin = 4.53810163149175 | erot = 4.43945254667827 | epot = -34.9111484982539 | etot = -25.9335943200839 +355000 ekin = 4.47391617267565 | erot = 4.20275229581248 | epot = -34.7382448152827 | etot = -26.0615763467945 +356000 ekin = 4.33084740359816 | erot = 4.16589789857799 | epot = -34.6459462576645 | etot = -26.1492009554884 +357000 ekin = 4.27639689643504 | erot = 4.49834201135675 | epot = -34.6234093478584 | etot = -25.8486704400666 +358000 ekin = 4.37058163127524 | erot = 4.6282751781028 | epot = -34.6601229270853 | etot = -25.6612661177073 +359000 ekin = 4.33282658147824 | erot = 4.35852771696217 | epot = -34.7355034140381 | etot = -26.0441491155977 +360000 ekin = 4.23025745994598 | erot = 3.7369218729668 | epot = -34.827271441646 | etot = -26.8600921087332 +361000 ekin = 4.32772510308485 | erot = 3.40799158120903 | epot = -34.9260321184264 | etot = -27.1903154341325 +362000 ekin = 4.4377220758705 | erot = 3.92824256651614 | epot = -35.0362517129441 | etot = -26.6702870705575 +363000 ekin = 4.60059512711655 | erot = 3.78527820800773 | epot = -35.149230388508 | etot = -26.7633570533837 +364000 ekin = 4.67620778921741 | erot = 3.65656363116 | epot = -35.2108467629341 | etot = -26.8780753425567 +365000 ekin = 4.68744796027325 | erot = 3.48647035761111 | epot = -35.257929142539 | etot = -27.0840108246547 +366000 ekin = 4.6317169465738 | erot = 3.80732263161735 | epot = -35.3317328424945 | etot = -26.8926932643033 +367000 ekin = 4.58794520776095 | erot = 4.31664541166351 | epot = -35.4114076873989 | etot = -26.5068170679744 +368000 ekin = 4.53697760644319 | erot = 4.37812449310847 | epot = -35.4654560531487 | etot = -26.550353953597 +369000 ekin = 4.50593348762442 | erot = 4.09682529638616 | epot = -35.5029044754857 | etot = -26.9001456914751 +370000 ekin = 4.51011536275109 | erot = 4.41695795738163 | epot = -35.5220659543716 | etot = -26.5949926342389 +371000 ekin = 4.5304986013542 | erot = 4.68112317412985 | epot = -35.5213297387008 | etot = -26.3097079632167 +372000 ekin = 4.42660066351873 | erot = 4.7814861185934 | epot = -35.5227844835438 | etot = -26.3146977014317 +373000 ekin = 4.28146792836394 | erot = 4.87997662616399 | epot = -35.4825501780567 | etot = -26.3211056235288 +374000 ekin = 4.13287464156696 | erot = 4.84001159820223 | epot = -35.452301102515 | etot = -26.4794148627458 +375000 ekin = 4.12545451947128 | erot = 4.81807433824656 | epot = -35.4637375699464 | etot = -26.5202087122286 +376000 ekin = 3.87506271806601 | erot = 5.35141111797735 | epot = -35.4720072259955 | etot = -26.2455333899521 +377000 ekin = 3.79770565908006 | erot = 5.28013401771271 | epot = -35.5177354201972 | etot = -26.4398957434045 +378000 ekin = 3.64048261255644 | erot = 5.4207242379617 | epot = -35.580823638477 | etot = -26.5196167879589 +379000 ekin = 3.5238611157663 | erot = 5.9756700460675 | epot = -35.6532146067628 | etot = -26.153683444929 +380000 ekin = 3.32387900413165 | erot = 6.59135162244908 | epot = -35.7551331169146 | etot = -25.8399024903339 +381000 ekin = 3.31695717077427 | erot = 6.10983514346606 | epot = -35.8815158952865 | etot = -26.4547235810462 +382000 ekin = 3.19546651526091 | erot = 6.36489840257035 | epot = -35.9926058393694 | etot = -26.4322409215381 +383000 ekin = 3.2436816976457 | erot = 6.33114976953688 | epot = -36.0664601033041 | etot = -26.4916286361216 +384000 ekin = 3.20726412806376 | erot = 6.19392941274209 | epot = -36.1325810920204 | etot = -26.7313875512146 +385000 ekin = 3.23885859839745 | erot = 6.31552666314741 | epot = -36.1503271354807 | etot = -26.5959418739358 +386000 ekin = 3.1687441170802 | erot = 5.94413881699916 | epot = -36.1310192334962 | etot = -27.0181362994169 +387000 ekin = 3.15499705249205 | erot = 5.48308596050856 | epot = -36.0714221491833 | etot = -27.4333391361827 +388000 ekin = 3.24907989403005 | erot = 5.58200944567837 | epot = -35.9925882356968 | etot = -27.1614988959884 +389000 ekin = 3.39871525437692 | erot = 5.14342534967113 | epot = -35.926273930772 | etot = -27.384133326724 +390000 ekin = 3.53157771561143 | erot = 5.06601106990858 | epot = -35.9089837935163 | etot = -27.3113950079963 +391000 ekin = 3.6460216873691 | erot = 4.8866150487515 | epot = -35.8854822304094 | etot = -27.3528454942888 +392000 ekin = 3.79325143536293 | erot = 5.07292816992976 | epot = -35.852420754602 | etot = -26.9862411493093 +393000 ekin = 3.89148460233043 | erot = 5.02930522203654 | epot = -35.7951222586314 | etot = -26.8743324342644 +394000 ekin = 3.96458882833113 | erot = 4.47630346760482 | epot = -35.7247928997475 | etot = -27.2839006038116 +395000 ekin = 4.03856036181243 | erot = 4.53784941780784 | epot = -35.6586367417744 | etot = -27.0822269621541 +396000 ekin = 3.9968364670664 | erot = 4.49727898211243 | epot = -35.5718421340363 | etot = -27.0777266848575 +397000 ekin = 4.03872005304064 | erot = 4.03153022392497 | epot = -35.5101946272745 | etot = -27.4399443503089 +398000 ekin = 4.01516330519928 | erot = 4.23226303701212 | epot = -35.4578715559687 | etot = -27.2104452137573 +399000 ekin = 4.0192261656521 | erot = 3.71642260618994 | epot = -35.3548490578809 | etot = -27.6192002860389 +400000 ekin = 4.17225085372021 | erot = 4.04093039429581 | epot = -35.2265510847564 | etot = -27.0133698367403 +401000 ekin = 4.15314996432513 | erot = 3.6480496120942 | epot = -35.0943512868028 | etot = -27.2931517103835 +402000 ekin = 4.20245298417931 | erot = 3.70137380667405 | epot = -34.9745627237165 | etot = -27.0707359328631 +403000 ekin = 4.3413245622893 | erot = 3.62891618665746 | epot = -34.8718657472305 | etot = -26.9016249982838 +404000 ekin = 4.42465890243314 | erot = 3.38938035287092 | epot = -34.7967250831433 | etot = -26.9826858278392 +405000 ekin = 4.6066304195345 | erot = 3.44054758174428 | epot = -34.7925257887169 | etot = -26.7453477874381 +406000 ekin = 4.73346375173105 | erot = 3.27915256113149 | epot = -34.8343083282585 | etot = -26.8216920153959 +407000 ekin = 4.82559135473407 | erot = 3.35253133282278 | epot = -34.90590665538 | etot = -26.7277839678232 +408000 ekin = 4.89298564336973 | erot = 3.47339817729168 | epot = -34.9848536782097 | etot = -26.6184698575483 +409000 ekin = 4.94069048180864 | erot = 3.76649967413614 | epot = -35.0728065521188 | etot = -26.365616396174 +410000 ekin = 5.08376278297818 | erot = 3.48855890171057 | epot = -35.1876079350125 | etot = -26.6152862503238 +411000 ekin = 5.10492342399052 | erot = 3.39152717909368 | epot = -35.2939784996996 | etot = -26.7975278966154 +412000 ekin = 5.21115921489285 | erot = 3.62435455589207 | epot = -35.3853247581666 | etot = -26.5498109873817 +413000 ekin = 5.25687541732564 | erot = 3.76308251202552 | epot = -35.4593584594676 | etot = -26.4394005301164 +414000 ekin = 5.13248472496979 | erot = 3.31025282824712 | epot = -35.5393093363075 | etot = -27.0965717830906 +415000 ekin = 5.09217261574502 | erot = 3.59401320391344 | epot = -35.605161792403 | etot = -26.9189759727445 +416000 ekin = 5.04807348985189 | erot = 3.48392073248403 | epot = -35.6748296719208 | etot = -27.1428354495849 +417000 ekin = 4.99138526936695 | erot = 3.46255923404111 | epot = -35.7531502554479 | etot = -27.2992057520398 +418000 ekin = 5.08999508315071 | erot = 3.44390708246907 | epot = -35.8333696081099 | etot = -27.2994674424901 +419000 ekin = 5.21842750435904 | erot = 3.38325168590942 | epot = -35.8593643490788 | etot = -27.2576851588103 +420000 ekin = 5.28947719533084 | erot = 3.50797044377639 | epot = -35.8848039905135 | etot = -27.0873563514062 +421000 ekin = 5.35268927232105 | erot = 3.36603650801218 | epot = -35.8749221051677 | etot = -27.1561963248345 +422000 ekin = 5.23695191026783 | erot = 3.53841920706918 | epot = -35.889640869454 | etot = -27.114269752117 +423000 ekin = 5.09577504756719 | erot = 3.67923583037255 | epot = -35.9137595336544 | etot = -27.1387486557147 +424000 ekin = 5.01335188112952 | erot = 3.70110718137053 | epot = -35.9185617531992 | etot = -27.2041026906992 +425000 ekin = 5.05206155589202 | erot = 3.57652002072466 | epot = -35.9081181462494 | etot = -27.2795365696328 +426000 ekin = 4.96532396129122 | erot = 3.38938274590579 | epot = -35.8769982527928 | etot = -27.5222915455958 +427000 ekin = 4.77195218714222 | erot = 3.50252627514243 | epot = -35.7935414010633 | etot = -27.5190629387787 +428000 ekin = 4.81068646615363 | erot = 3.51825958765464 | epot = -35.6664317412184 | etot = -27.3374856874101 +429000 ekin = 4.73870321335416 | erot = 3.84986931063865 | epot = -35.4873764559103 | etot = -26.8988039319175 +430000 ekin = 4.602137148251 | erot = 3.45284870606445 | epot = -35.3073410925575 | etot = -27.2523552382421 +431000 ekin = 4.57358006593881 | erot = 3.25422348182542 | epot = -35.136759491896 | etot = -27.3089559441318 +432000 ekin = 4.50724003680402 | erot = 3.29998192315333 | epot = -35.029042571088 | etot = -27.2218206111307 +433000 ekin = 4.3086049570317 | erot = 3.42741416873377 | epot = -34.9513402987258 | etot = -27.2153211729603 +434000 ekin = 4.18610269286836 | erot = 3.55059973000638 | epot = -34.9144648758598 | etot = -27.1777624529851 +435000 ekin = 4.12003359590284 | erot = 3.78033374370934 | epot = -34.8780591099563 | etot = -26.9776917703441 +436000 ekin = 3.97313974106134 | erot = 4.05117020636249 | epot = -34.8427841720092 | etot = -26.8184742245853 +437000 ekin = 3.88596008320786 | erot = 4.32902730055979 | epot = -34.8121331683379 | etot = -26.5971457845702 +438000 ekin = 4.03003221046435 | erot = 4.35508047283409 | epot = -34.7917492531094 | etot = -26.4066365698109 +439000 ekin = 4.04655148511162 | erot = 4.17322604141029 | epot = -34.7786348227556 | etot = -26.5588572962337 +440000 ekin = 4.02801522674504 | erot = 4.13470601724881 | epot = -34.7839930854156 | etot = -26.6212718414218 +441000 ekin = 3.94078147941953 | erot = 4.22144190117307 | epot = -34.8185771480927 | etot = -26.6563537675001 +442000 ekin = 3.97730990695675 | erot = 4.24233406975324 | epot = -34.8718962191135 | etot = -26.6522522424035 +443000 ekin = 3.98508138243256 | erot = 4.16122580291799 | epot = -34.9266782585662 | etot = -26.7803710732156 +444000 ekin = 4.00042709081923 | erot = 4.50741850480102 | epot = -34.9630696153487 | etot = -26.4552240197285 +445000 ekin = 4.02620459576038 | erot = 4.64580325301018 | epot = -34.9893039643637 | etot = -26.3172961155932 +446000 ekin = 4.0145460872058 | erot = 4.89747165518641 | epot = -34.9969089036749 | etot = -26.0848911612827 +447000 ekin = 3.96342694873324 | erot = 4.85867800390665 | epot = -34.9830933662455 | etot = -26.1609884136056 +448000 ekin = 3.74592315828131 | erot = 5.1757843335798 | epot = -34.9638816619608 | etot = -26.0421741700997 +449000 ekin = 3.73316291077384 | erot = 5.18498661281975 | epot = -34.9280438941249 | etot = -26.0098943705313 +450000 ekin = 3.85313039093449 | erot = 4.86926583888879 | epot = -34.8716969798347 | etot = -26.1493007500114 +451000 ekin = 4.06359280531127 | erot = 4.99817049859075 | epot = -34.8377147695099 | etot = -25.7759514656079 +452000 ekin = 4.12215980217286 | erot = 4.58488292412149 | epot = -34.8398353293665 | etot = -26.1327926030721 +453000 ekin = 4.16332842884541 | erot = 4.32671008371143 | epot = -34.8570499988887 | etot = -26.3670114863319 +454000 ekin = 4.11754892618409 | erot = 4.47415692336229 | epot = -34.8913194738514 | etot = -26.299613624305 +455000 ekin = 4.22185774995348 | erot = 4.65517828169311 | epot = -34.9334347985054 | etot = -26.0563987668588 +456000 ekin = 4.30177202276143 | erot = 4.77747798616556 | epot = -35.0188770940117 | etot = -25.9396270850847 +457000 ekin = 4.26451460758689 | erot = 4.69009499467528 | epot = -35.1021143238348 | etot = -26.1475047215727 +458000 ekin = 4.31289289804763 | erot = 4.48148846421258 | epot = -35.1135359976466 | etot = -26.3191546353864 +459000 ekin = 4.40924309472714 | erot = 4.70052929057868 | epot = -35.3709113999309 | etot = -26.2611390146251 +460000 ekin = 4.47691183250296 | erot = 4.50574141189019 | epot = -35.566195356935 | etot = -26.5835421125418 +461000 ekin = 4.43873436995011 | erot = 4.99077626253916 | epot = -35.6310455171599 | etot = -26.2015348846706 +462000 ekin = 4.38932525316365 | erot = 4.94989100042644 | epot = -35.7174404682254 | etot = -26.3782242146353 +463000 ekin = 4.36115268480796 | erot = 5.66229263913986 | epot = -35.782873692384 | etot = -25.7594283684361 +464000 ekin = 4.32411863133124 | erot = 5.21874712372938 | epot = -35.8318174183589 | etot = -26.2889516632982 +465000 ekin = 4.25283049437862 | erot = 4.8931192840781 | epot = -35.8307748329833 | etot = -26.6848250545266 +466000 ekin = 3.97961054012235 | erot = 4.30523919521523 | epot = -35.8019205162808 | etot = -27.5170707809433 +467000 ekin = 3.96957942645156 | erot = 4.02414635207124 | epot = -35.7935881476342 | etot = -27.7998623691114 +468000 ekin = 3.81067149059143 | erot = 3.9131157389001 | epot = -35.819204604463 | etot = -28.0954173749715 +469000 ekin = 3.82956653035967 | erot = 3.76358708523009 | epot = -35.8554657317441 | etot = -28.2623121161543 +470000 ekin = 3.84315155223098 | erot = 3.46319185355978 | epot = -35.9283028420653 | etot = -28.6219594362746 +471000 ekin = 3.8418988592029 | erot = 3.51787257644846 | epot = -36.0370536568195 | etot = -28.6772822211681 +472000 ekin = 3.86861114122384 | erot = 3.36458500068064 | epot = -36.1368322989854 | etot = -28.9036361570809 +473000 ekin = 3.73700168734246 | erot = 3.58329228877727 | epot = -36.2233655143222 | etot = -28.9030715382025 +474000 ekin = 3.82928273613545 | erot = 3.70070391401538 | epot = -36.2919855352844 | etot = -28.7619988851335 +475000 ekin = 3.89544030960044 | erot = 3.76401640046801 | epot = -36.3684307389009 | etot = -28.7089740288324 +476000 ekin = 4.0893276711336 | erot = 3.70907901754989 | epot = -36.4684310716314 | etot = -28.6700243829479 +477000 ekin = 4.15334136664104 | erot = 3.70899967496297 | epot = -36.5311600367348 | etot = -28.6688189951308 +478000 ekin = 4.07512882728816 | erot = 3.80913887771415 | epot = -36.5715417700048 | etot = -28.6872740650025 +479000 ekin = 3.96184225144677 | erot = 3.6758426322944 | epot = -36.6049454628525 | etot = -28.9672605791113 +480000 ekin = 3.86072911979603 | erot = 3.85211085064388 | epot = -36.610629225252 | etot = -28.8977892548121 +481000 ekin = 3.78563823255496 | erot = 4.024314099233 | epot = -36.6044682584304 | etot = -28.7945159266424 +482000 ekin = 3.81986353724786 | erot = 3.94457553240304 | epot = -36.5556242495873 | etot = -28.7911851799364 +483000 ekin = 3.91937069687011 | erot = 3.97985471481356 | epot = -36.4953515335744 | etot = -28.5961261218907 +484000 ekin = 3.90565472316292 | erot = 3.68508276016196 | epot = -36.426514232721 | etot = -28.8357767493961 +485000 ekin = 3.97067640669154 | erot = 3.52818833629947 | epot = -36.3385351029693 | etot = -28.8396703599783 +486000 ekin = 4.08924338068675 | erot = 3.45150371793067 | epot = -36.2407040808296 | etot = -28.6999569822122 +487000 ekin = 4.07761729530311 | erot = 3.69577064304002 | epot = -36.1174543397078 | etot = -28.3440664013647 +488000 ekin = 3.98120330041688 | erot = 4.01179749212345 | epot = -35.9662140009127 | etot = -27.9732132083724 +489000 ekin = 3.94304108511324 | erot = 4.09948585344502 | epot = -35.8365811443688 | etot = -27.7940542058105 +490000 ekin = 3.98200750178142 | erot = 4.19330655565614 | epot = -35.7436522395709 | etot = -27.5683381821333 +491000 ekin = 4.0445360131927 | erot = 4.06864604679586 | epot = -35.6813038605064 | etot = -27.5681218005179 +492000 ekin = 4.10478194610759 | erot = 4.27931273272407 | epot = -35.6201850620984 | etot = -27.2360903832667 +493000 ekin = 4.14218811078688 | erot = 4.30328516243005 | epot = -35.5529321721737 | etot = -27.1074588989568 +494000 ekin = 4.15483197917442 | erot = 4.22087230768742 | epot = -35.5007035923716 | etot = -27.1249993055097 +495000 ekin = 4.26671892357353 | erot = 4.2174513730416 | epot = -35.4450128389817 | etot = -26.9608425423665 +496000 ekin = 4.42373869014864 | erot = 3.65535322096919 | epot = -35.3933064942846 | etot = -27.3142145831668 +497000 ekin = 4.57363309591074 | erot = 3.63766344362461 | epot = -35.3630685420969 | etot = -27.1517720025615 +498000 ekin = 4.7241733979429 | erot = 3.40665904233571 | epot = -35.3570714026405 | etot = -27.2262389623619 +499000 ekin = 4.76806375994884 | erot = 3.58204839805338 | epot = -35.3646341268605 | etot = -27.0145219688582 +500000 ekin = 4.86803273232494 | erot = 3.40069391727077 | epot = -35.4199817543288 | etot = -27.1512551047331 +501000 ekin = 4.96743307602633 | erot = 3.46724128896382 | epot = -35.4970649677138 | etot = -27.0623906027237 +502000 ekin = 4.91929166862602 | erot = 3.57165212036747 | epot = -35.5889625489531 | etot = -27.0980187599596 +503000 ekin = 4.90703913138654 | erot = 3.86458875313982 | epot = -35.6771862828243 | etot = -26.9055583982979 +504000 ekin = 5.13705335061953 | erot = 3.53695462968337 | epot = -35.7347477259475 | etot = -27.0607397456447 +505000 ekin = 5.23249143944192 | erot = 3.46343104093346 | epot = -35.7820571844978 | etot = -27.0861347041225 +506000 ekin = 5.11675278315682 | erot = 3.72067186509955 | epot = -35.8198968197669 | etot = -26.9824721715105 +507000 ekin = 5.18993901387439 | erot = 4.1521508584772 | epot = -35.8269271672407 | etot = -26.4848372948891 +508000 ekin = 4.98597878226577 | erot = 4.11598571894018 | epot = -35.7826195676297 | etot = -26.6806550664237 +509000 ekin = 4.89412425677653 | erot = 4.30807642739921 | epot = -35.6890852058576 | etot = -26.4868845216819 +510000 ekin = 4.89504815268988 | erot = 4.4601383758423 | epot = -35.589321566643 | etot = -26.2341350381108 +511000 ekin = 4.85835750083372 | erot = 4.41721118692769 | epot = -35.4748886415738 | etot = -26.1993199538124 +512000 ekin = 4.85632567301955 | erot = 4.5850146787013 | epot = -35.3170557845391 | etot = -25.8757154328183 +513000 ekin = 4.79088228903384 | erot = 4.41898249223044 | epot = -35.1398620511897 | etot = -25.9299972699254 +514000 ekin = 4.84082723167301 | erot = 4.10048582144458 | epot = -34.9528940279417 | etot = -26.0115809748241 +515000 ekin = 4.66396867258878 | erot = 3.70795325472635 | epot = -34.8081323279138 | etot = -26.4362104005987 +516000 ekin = 4.45203722260375 | erot = 3.7424161749216 | epot = -34.7399422586779 | etot = -26.5454888611526 +517000 ekin = 4.39320763550285 | erot = 3.61293763489201 | epot = -34.7115969229747 | etot = -26.7054516525798 +518000 ekin = 4.33516267423081 | erot = 3.46685163663661 | epot = -34.720559171622 | etot = -26.9185448607546 +519000 ekin = 4.32678001120794 | erot = 3.83331308599435 | epot = -34.7543932584756 | etot = -26.5943001612733 +520000 ekin = 4.16017569753271 | erot = 3.9944210337637 | epot = -34.7797387277814 | etot = -26.625141996485 +521000 ekin = 4.01091284601559 | erot = 4.71227661622668 | epot = -34.8119764016186 | etot = -26.0887869393764 +522000 ekin = 3.92555868149862 | erot = 4.67306017627902 | epot = -34.8638412525405 | etot = -26.2652223947629 +523000 ekin = 4.10629342994171 | erot = 4.23690821219818 | epot = -34.9392637364657 | etot = -26.5960620943258 +524000 ekin = 4.1696440613856 | erot = 4.51539305326675 | epot = -35.0302476439302 | etot = -26.3452105292779 +525000 ekin = 4.14574067413424 | erot = 4.59255192964534 | epot = -35.1665459803978 | etot = -26.4282533766182 +526000 ekin = 4.29635804775357 | erot = 5.38181203699227 | epot = -35.3702076593234 | etot = -25.6920375745776 +527000 ekin = 4.43341423246316 | erot = 5.4208701656537 | epot = -35.5881352754175 | etot = -25.7338508773006 +528000 ekin = 4.65221997264034 | erot = 5.64432261927448 | epot = -35.7907306535607 | etot = -25.4941880616459 +529000 ekin = 4.75833001518884 | erot = 6.22279494556851 | epot = -35.9649272181715 | etot = -24.9838022574141 +530000 ekin = 4.85254900576381 | erot = 6.26630645812944 | epot = -36.1175112827236 | etot = -24.9986558188304 +531000 ekin = 4.88314038497963 | erot = 6.22256761998181 | epot = -36.2218727030893 | etot = -25.1161646981279 +532000 ekin = 4.89429192132453 | erot = 6.19376619305378 | epot = -36.2791850407377 | etot = -25.1911269263594 +533000 ekin = 4.98074956905508 | erot = 6.71246035574299 | epot = -36.2873072492243 | etot = -24.5940973244262 +534000 ekin = 5.05914514163858 | erot = 6.72049132345737 | epot = -36.2541186702092 | etot = -24.4744822051133 +535000 ekin = 4.98307281629278 | erot = 6.60876507020557 | epot = -36.1722591997822 | etot = -24.5804213132839 +536000 ekin = 4.92092214615514 | erot = 6.71824597922614 | epot = -36.0492643890662 | etot = -24.4100962636849 +537000 ekin = 4.73594122849326 | erot = 6.46069540815287 | epot = -35.9116294607657 | etot = -24.7149928241196 +538000 ekin = 4.79280389212897 | erot = 6.10794151385135 | epot = -35.7423046160132 | etot = -24.8415592100329 +539000 ekin = 4.77579753855637 | erot = 5.9721718852028 | epot = -35.533600981652 | etot = -24.7856315578928 +540000 ekin = 4.59343353220661 | erot = 6.02882315943306 | epot = -35.2969540919923 | etot = -24.6746974003527 +541000 ekin = 4.56261508857308 | erot = 5.60884609986364 | epot = -35.0742414984787 | etot = -24.9027803100419 +542000 ekin = 4.42304079078362 | erot = 5.24180126466464 | epot = -34.8728664426876 | etot = -25.2080243872393 +543000 ekin = 4.31458565966317 | erot = 5.30648118805705 | epot = -34.6809264080033 | etot = -25.0598595602831 +544000 ekin = 4.16990383767329 | erot = 5.09480741715239 | epot = -34.5077033118773 | etot = -25.2429920570516 +545000 ekin = 4.0350640414587 | erot = 4.95913193735204 | epot = -34.3738505570895 | etot = -25.3796545782788 +546000 ekin = 4.05283758597051 | erot = 4.62357416672448 | epot = -34.2732549004478 | etot = -25.5968431477528 +547000 ekin = 3.91892476341122 | erot = 4.42471065792707 | epot = -34.1888485564157 | etot = -25.8452131350775 +548000 ekin = 3.85923648383067 | erot = 4.18493881932566 | epot = -34.1251823218199 | etot = -26.0810070186636 +549000 ekin = 3.8927709556134 | erot = 4.20183962759803 | epot = -34.0968256559691 | etot = -26.0022150727577 +550000 ekin = 3.88489313663799 | erot = 4.06987350840239 | epot = -34.0834989925537 | etot = -26.1287323475133 +551000 ekin = 3.87639970039868 | erot = 4.25043058335745 | epot = -34.0931086790782 | etot = -25.966278395322 +552000 ekin = 3.88627319211786 | erot = 4.00102033547709 | epot = -34.1638602914377 | etot = -26.2765667638428 +553000 ekin = 4.05569156373879 | erot = 3.56403629580222 | epot = -34.247483486424 | etot = -26.627755626883 +554000 ekin = 4.2562683800156 | erot = 3.70804766862547 | epot = -34.2954308218039 | etot = -26.3311147731628 +555000 ekin = 4.2648740703529 | erot = 3.78496110408358 | epot = -34.3412268896543 | etot = -26.2913917152178 +556000 ekin = 4.24622902964984 | erot = 4.0345482038853 | epot = -34.3344093396379 | etot = -26.0536321061027 +557000 ekin = 4.07319669837868 | erot = 3.86372668854368 | epot = -34.2640157691761 | etot = -26.3270923822537 +558000 ekin = 3.99489306447001 | erot = 3.82027814531877 | epot = -34.1455461859517 | etot = -26.3303749761629 +559000 ekin = 4.00179663426026 | erot = 3.82651776959122 | epot = -33.9924674804774 | etot = -26.1641530766259 +560000 ekin = 3.90938418270038 | erot = 3.49539199637374 | epot = -33.8018928207122 | etot = -26.3971166416381 +561000 ekin = 3.70375196060242 | erot = 3.38165869548244 | epot = -33.6157331642902 | etot = -26.5303225082053 +562000 ekin = 3.64392595608208 | erot = 3.67997084627168 | epot = -33.4612560312997 | etot = -26.1373592289459 +563000 ekin = 3.59769761679666 | erot = 3.74125845764501 | epot = -33.3480734777506 | etot = -26.0091174033089 +564000 ekin = 3.5872532535469 | erot = 3.35524020938125 | epot = -33.2675171968359 | etot = -26.3250237339077 +565000 ekin = 3.63835964444035 | erot = 3.77402574563864 | epot = -33.2409015523647 | etot = -25.8285161622857 +566000 ekin = 3.64384501808487 | erot = 3.7751512348732 | epot = -33.2503593116355 | etot = -25.8313630586774 +567000 ekin = 3.6321441767138 | erot = 3.8685448978813 | epot = -33.2603190278778 | etot = -25.7596299532827 +568000 ekin = 3.76759211618971 | erot = 3.97321014856349 | epot = -33.2947231384392 | etot = -25.553920873686 +569000 ekin = 3.75607920629668 | erot = 3.9189350411434 | epot = -33.3766443391882 | etot = -25.7016300917481 +570000 ekin = 3.88570178164772 | erot = 3.87013370061556 | epot = -33.4676246266775 | etot = -25.7117891444142 +571000 ekin = 3.91109063039641 | erot = 4.3887336637963 | epot = -33.5301619269295 | etot = -25.2303376327368 +572000 ekin = 3.91357367536979 | erot = 4.54669425634091 | epot = -33.5613071721028 | etot = -25.1010392403921 +573000 ekin = 4.00256460245984 | erot = 4.69928602914621 | epot = -33.5479654090577 | etot = -24.8461147774517 +574000 ekin = 4.04557469411533 | erot = 4.85104808888571 | epot = -33.4823141367214 | etot = -24.5856913537203 +575000 ekin = 4.0199044833131 | erot = 4.48360936846638 | epot = -33.4090682352886 | etot = -24.9055543835092 +576000 ekin = 3.80770420634942 | erot = 4.40902984739946 | epot = -33.3559765416152 | etot = -25.1392424878663 +577000 ekin = 3.6517677072366 | erot = 4.69770290650927 | epot = -33.3414847753623 | etot = -24.9920141616164 +578000 ekin = 3.65416507269722 | erot = 5.09984939028998 | epot = -33.3628873386869 | etot = -24.6088728756997 +579000 ekin = 3.65457514215454 | erot = 4.83085466504592 | epot = -33.4229058723711 | etot = -24.9374760651706 +580000 ekin = 3.61022362260481 | erot = 5.21507039569769 | epot = -33.5257015423975 | etot = -24.700407524095 +581000 ekin = 3.49491427592295 | erot = 5.80898315058308 | epot = -33.6374701054959 | etot = -24.3335726789899 +582000 ekin = 3.45150652331289 | erot = 5.2079729472947 | epot = -33.7413132898281 | etot = -25.0818338192205 +583000 ekin = 3.43883253778232 | erot = 4.99240818298342 | epot = -33.7992206024429 | etot = -25.3679798816772 +584000 ekin = 3.41950743994087 | erot = 5.30429667829858 | epot = -33.8273198616881 | etot = -25.1035157434487 +585000 ekin = 3.52988736379348 | erot = 5.26888625710225 | epot = -33.8562169326849 | etot = -25.0574433117891 +586000 ekin = 3.54522421505718 | erot = 5.15182886320371 | epot = -33.8748034063863 | etot = -25.1777503281254 +587000 ekin = 3.64975640444384 | erot = 4.43116878399003 | epot = -33.8790223191813 | etot = -25.7980971307475 +588000 ekin = 3.85787406303082 | erot = 4.33848995606314 | epot = -33.9012642894904 | etot = -25.7049002703965 +589000 ekin = 3.9487150884209 | erot = 4.36958758855423 | epot = -33.9512157067315 | etot = -25.6329130297563 +590000 ekin = 4.04576150007675 | erot = 4.34777620153069 | epot = -33.9849374243128 | etot = -25.5913997227054 +591000 ekin = 4.13483818439914 | erot = 4.28475308123698 | epot = -33.9975372243776 | etot = -25.5779459587414 +592000 ekin = 4.2556680414864 | erot = 4.00241438742696 | epot = -33.990517302247 | etot = -25.7324348733336 +593000 ekin = 4.26695504286551 | erot = 3.75133860519216 | epot = -33.9824243028376 | etot = -25.9641306547799 +594000 ekin = 4.24513038558056 | erot = 3.88826331815755 | epot = -33.9597952629293 | etot = -25.8264015591912 +595000 ekin = 4.33307108334646 | erot = 3.92609577318174 | epot = -33.9197199407777 | etot = -25.6605530842495 +596000 ekin = 4.23611726585149 | erot = 3.89070717461491 | epot = -33.8740124837561 | etot = -25.7471880432897 +597000 ekin = 4.40233879096614 | erot = 3.9973813082447 | epot = -33.8902431987866 | etot = -25.4905230995758 +598000 ekin = 4.23795477390351 | erot = 4.04526003588007 | epot = -33.9155939268417 | etot = -25.6323791170582 +599000 ekin = 4.13745802989045 | erot = 3.88641709707911 | epot = -33.9296772436184 | etot = -25.9058021166489 +600000 ekin = 4.21239990479469 | erot = 3.82373814742802 | epot = -33.9651236246 | etot = -25.9289855723773 +601000 ekin = 4.3196997334027 | erot = 3.98399943561167 | epot = -34.0172721411615 | etot = -25.7135729721471 +602000 ekin = 4.27803621196727 | erot = 4.02063732656524 | epot = -34.100698422985 | etot = -25.8020248844525 +603000 ekin = 4.31016670434268 | erot = 4.06109056998715 | epot = -34.2290225355021 | etot = -25.8577652611723 +604000 ekin = 4.35436231281196 | erot = 4.27081433433549 | epot = -34.3693989473758 | etot = -25.7442223002283 +605000 ekin = 4.29263786573731 | erot = 4.35816455015996 | epot = -34.5293522620234 | etot = -25.8785498461262 +606000 ekin = 4.23493766333436 | erot = 4.45889694601822 | epot = -34.6959569640143 | etot = -26.0021223546617 +607000 ekin = 4.21589668454932 | erot = 4.35851580050772 | epot = -34.8643734064673 | etot = -26.2899609214103 +608000 ekin = 4.31617609118378 | erot = 4.3711843404177 | epot = -35.0106665625392 | etot = -26.3233061309377 +609000 ekin = 4.40054829762945 | erot = 4.09556922746408 | epot = -35.1090427558591 | etot = -26.6129252307656 +610000 ekin = 4.3836017973497 | erot = 4.43080811091093 | epot = -35.1590130940816 | etot = -26.344603185821 +611000 ekin = 4.30911071721019 | erot = 4.66858603342393 | epot = -35.1997741362033 | etot = -26.2220773855692 +612000 ekin = 4.38115044344101 | erot = 4.62952065066664 | epot = -35.2189008927601 | etot = -26.2082297986524 +613000 ekin = 4.49640333428488 | erot = 4.73033949191661 | epot = -35.2311946320133 | etot = -26.0044518058118 +614000 ekin = 4.42698019674918 | erot = 4.54387450238904 | epot = -35.227024565465 | etot = -26.2561698663268 +615000 ekin = 4.36293882049166 | erot = 4.65167437175536 | epot = -35.250009814436 | etot = -26.235396622189 +616000 ekin = 4.25552094369167 | erot = 3.9677335799062 | epot = -35.262646565401 | etot = -27.0393920418031 +617000 ekin = 4.02844203107201 | erot = 3.93306028038377 | epot = -35.3085438772361 | etot = -27.3470415657803 +618000 ekin = 3.91410624199631 | erot = 3.99915504239052 | epot = -35.3773572154985 | etot = -27.4640959311117 +619000 ekin = 3.92944334041051 | erot = 3.65858234543171 | epot = -35.4549579850513 | etot = -27.8669322992091 +620000 ekin = 3.94632769198491 | erot = 4.05357915876533 | epot = -35.5452298743848 | etot = -27.5453230236346 +621000 ekin = 4.00876452457166 | erot = 4.1855795236138 | epot = -35.6568787558288 | etot = -27.4625347076433 +622000 ekin = 3.97770547832637 | erot = 4.20428409244743 | epot = -35.7853832130653 | etot = -27.6033936422915 +623000 ekin = 3.8762340917962 | erot = 4.44200976918091 | epot = -35.9345595163545 | etot = -27.6163156553774 +624000 ekin = 3.81461749379632 | erot = 4.73413928443226 | epot = -36.0610458736423 | etot = -27.5122890954137 +625000 ekin = 3.8970241751503 | erot = 4.51967995490342 | epot = -36.1593702506674 | etot = -27.7426661206137 +626000 ekin = 4.05285181951198 | erot = 5.1220971455114 | epot = -36.2373709478026 | etot = -27.0624219827792 +627000 ekin = 4.06919694856985 | erot = 5.16853241383701 | epot = -36.2459696084315 | etot = -27.0082402460246 +628000 ekin = 3.97574634490127 | erot = 5.15377915037519 | epot = -36.1860007276685 | etot = -27.0564752323921 +629000 ekin = 3.97847076093846 | erot = 4.98743417354896 | epot = -36.0841602963358 | etot = -27.1182553618484 +630000 ekin = 3.82117049554739 | erot = 4.72915936447924 | epot = -35.9627884752438 | etot = -27.4124586152171 +631000 ekin = 3.86461141431221 | erot = 4.86154549634944 | epot = -35.8061457051957 | etot = -27.079988794534 +632000 ekin = 3.74664734149851 | erot = 4.54810894057643 | epot = -35.6214135997296 | etot = -27.3266573176547 +633000 ekin = 3.70561564688244 | erot = 3.84492477779421 | epot = -35.4366028892501 | etot = -27.8860624645735 +634000 ekin = 3.59215409071661 | erot = 3.93871515972471 | epot = -35.2896538627899 | etot = -27.7587846123486 +635000 ekin = 3.50545587494383 | erot = 4.06717110382211 | epot = -35.1730596180146 | etot = -27.6004326392486 +636000 ekin = 3.3309454150286 | erot = 4.07821458070327 | epot = -35.1077038533349 | etot = -27.6985438576031 +637000 ekin = 3.14505217998963 | erot = 4.05756077132584 | epot = -35.1055524080615 | etot = -27.902939456746 +638000 ekin = 3.09050584392239 | erot = 4.40258652090821 | epot = -35.1570633539889 | etot = -27.6639709891583 +639000 ekin = 3.0768733321709 | erot = 4.16491810908563 | epot = -35.2467836386719 | etot = -28.0049921974154 +640000 ekin = 3.00973730805073 | erot = 4.2692418133335 | epot = -35.3354522376085 | etot = -28.0564731162243 +641000 ekin = 2.94445196408833 | erot = 4.64391413205119 | epot = -35.4644644387967 | etot = -27.8760983426572 +642000 ekin = 2.98442414954633 | erot = 4.9974755612433 | epot = -35.6290057034216 | etot = -27.647105992632 +643000 ekin = 3.2055646953209 | erot = 4.8025531791329 | epot = -35.7795885297939 | etot = -27.7714706553401 +644000 ekin = 3.2748821402377 | erot = 4.64957731616621 | epot = -35.9161733239261 | etot = -27.9917138675222 +645000 ekin = 3.41323831995007 | erot = 4.71321420527612 | epot = -36.0213663956164 | etot = -27.8949138703902 +646000 ekin = 3.56963422518167 | erot = 4.46391006184254 | epot = -36.0597764612018 | etot = -28.0262321741776 +647000 ekin = 3.65146108953765 | erot = 4.34882885781933 | epot = -36.05397385258 | etot = -28.053683905223 +648000 ekin = 3.80589253043839 | erot = 4.22505125234649 | epot = -35.9957895068647 | etot = -27.9648457240799 +649000 ekin = 4.01844415748841 | erot = 4.19109412255817 | epot = -35.9180061331759 | etot = -27.7084678531293 +650000 ekin = 4.03810277748572 | erot = 3.86362623058913 | epot = -35.8260490160444 | etot = -27.9243200079695 +651000 ekin = 4.14203944570719 | erot = 3.56888807374706 | epot = -35.7087423281397 | etot = -27.9978148086855 +652000 ekin = 4.23250261214715 | erot = 3.18710224409382 | epot = -35.6367851174034 | etot = -28.2171802611624 +653000 ekin = 4.36352642926009 | erot = 3.20148998566011 | epot = -35.6464209942557 | etot = -28.0814045793355 +654000 ekin = 4.5279203243997 | erot = 3.02237039454743 | epot = -35.6995719521313 | etot = -28.1492812331841 +655000 ekin = 4.60546960877517 | erot = 2.96007185178719 | epot = -35.8223013228812 | etot = -28.2567598623188 +656000 ekin = 4.78956137676064 | erot = 3.38896158834621 | epot = -35.9826527468557 | etot = -27.8041297817489 +657000 ekin = 4.78481247088243 | erot = 3.67040934516473 | epot = -36.1522101931049 | etot = -27.6969883770578 +658000 ekin = 4.68735602442224 | erot = 4.10635530609359 | epot = -36.3122539915072 | etot = -27.5185426609914 +659000 ekin = 4.79643464434907 | erot = 4.3109166795532 | epot = -36.419822200132 | etot = -27.3124708762297 +660000 ekin = 4.65613606555515 | erot = 4.00182169137307 | epot = -36.5017357753405 | etot = -27.8437780184123 +661000 ekin = 4.53939481189422 | erot = 4.39327864100633 | epot = -36.5522379560179 | etot = -27.6195645031173 +662000 ekin = 4.62075189021993 | erot = 4.64171304234686 | epot = -36.5458752748482 | etot = -27.2834103422814 +663000 ekin = 4.60627251324235 | erot = 4.44191382325803 | epot = -36.5358428119696 | etot = -27.4876564754693 +664000 ekin = 4.53224877457463 | erot = 4.69535654970068 | epot = -36.5440045789042 | etot = -27.3163992546289 +665000 ekin = 4.33791904761007 | erot = 4.79511074251925 | epot = -36.5712979957099 | etot = -27.4382682055805 +666000 ekin = 4.01034004769843 | erot = 5.14475630277467 | epot = -36.6275167021873 | etot = -27.4724203517142 +667000 ekin = 3.92791037721622 | erot = 5.11805894759237 | epot = -36.702269731521 | etot = -27.6563004067124 +668000 ekin = 3.69207242860568 | erot = 4.95115852091685 | epot = -36.7748284431555 | etot = -28.1315974936329 +669000 ekin = 3.52850414694839 | erot = 5.30513713121047 | epot = -36.8468924103841 | etot = -28.0132511322252 +670000 ekin = 3.43685158392413 | erot = 5.67353767341476 | epot = -36.8571678878591 | etot = -27.7467786305202 +671000 ekin = 3.37237891900207 | erot = 4.81383151363256 | epot = -36.7898772614734 | etot = -28.6036668288388 +672000 ekin = 3.4214286448957 | erot = 4.47410705082151 | epot = -36.6509805759937 | etot = -28.7554448802765 +673000 ekin = 3.47620696197726 | erot = 4.53468812753541 | epot = -36.4695914666411 | etot = -28.4586963771284 +674000 ekin = 3.34015467342477 | erot = 4.56003540036704 | epot = -36.2728042740009 | etot = -28.3726142002091 +675000 ekin = 3.26558121431926 | erot = 4.75716318196978 | epot = -36.0812448824919 | etot = -28.0585004862029 +676000 ekin = 3.30557173090095 | erot = 4.66626180335478 | epot = -35.8858133485377 | etot = -27.9139798142819 +677000 ekin = 3.38252137148669 | erot = 4.6897922284426 | epot = -35.7238379181691 | etot = -27.6515243182398 +678000 ekin = 3.33430766992633 | erot = 4.45636421682294 | epot = -35.5898515746333 | etot = -27.799179687884 +679000 ekin = 3.26716522041019 | erot = 4.13643141690213 | epot = -35.528216056043 | etot = -28.1246194187307 +680000 ekin = 3.22330491222221 | erot = 4.11355311991397 | epot = -35.5522418172928 | etot = -28.2153837851566 +681000 ekin = 3.27654998707768 | erot = 4.40088508884104 | epot = -35.6343431031197 | etot = -27.956908027201 +682000 ekin = 3.38403402082966 | erot = 4.64957783602955 | epot = -35.7255960652577 | etot = -27.6919842083985 +683000 ekin = 3.58392532059449 | erot = 4.15499488835506 | epot = -35.8541956283831 | etot = -28.1152754194335 +684000 ekin = 3.63284008875691 | erot = 4.14497212696397 | epot = -36.0448350473496 | etot = -28.2670228316288 +685000 ekin = 3.75538152185656 | erot = 3.95609692494439 | epot = -36.2462524041832 | etot = -28.5347739573822 +686000 ekin = 3.91883145536709 | erot = 3.95298902028767 | epot = -36.4771155861902 | etot = -28.6052951105355 +687000 ekin = 4.05299881159141 | erot = 4.06027810523496 | epot = -36.7169526369127 | etot = -28.6036757200863 +688000 ekin = 4.13599667613283 | erot = 4.1033148925446 | epot = -36.9524101670391 | etot = -28.7130985983616 +689000 ekin = 4.25987754434121 | erot = 4.14481492316592 | epot = -37.19007759108 | etot = -28.7853851235729 +690000 ekin = 4.43074027682468 | erot = 4.04380513304424 | epot = -37.3931354089483 | etot = -28.9185899990794 +691000 ekin = 4.53821721573662 | erot = 3.80503345899004 | epot = -37.5576014163155 | etot = -29.2143507415889 +692000 ekin = 4.6415004277931 | erot = 3.59872997928144 | epot = -37.6895260553275 | etot = -29.449295648253 +693000 ekin = 4.69075885893 | erot = 3.47578918601706 | epot = -37.8114874122422 | etot = -29.6449393672951 +694000 ekin = 4.73822518662626 | erot = 3.8426375014852 | epot = -37.9027003996531 | etot = -29.3218377115416 +695000 ekin = 4.75494194627987 | erot = 3.78113333862433 | epot = -37.9681336831655 | etot = -29.4320583982613 +696000 ekin = 4.69786608199271 | erot = 3.785268211759 | epot = -38.0084908313003 | etot = -29.5253565375486 +697000 ekin = 4.69854328160514 | erot = 3.62432955932676 | epot = -38.0258612384502 | etot = -29.7029883975183 +698000 ekin = 4.71023285872909 | erot = 3.64111389234157 | epot = -38.030154734076 | etot = -29.6788079830054 +699000 ekin = 4.56773244343976 | erot = 3.71983710702499 | epot = -38.0529467082193 | etot = -29.7653771577546 +700000 ekin = 4.43155866208691 | erot = 3.53355461960284 | epot = -38.0685834921134 | etot = -30.1034702104236 +701000 ekin = 4.47548631411736 | erot = 3.38963138436219 | epot = -38.0500116139815 | etot = -30.184893915502 +702000 ekin = 4.46550513016984 | erot = 3.66852889097277 | epot = -38.0164512923402 | etot = -29.8824172711975 +703000 ekin = 4.38742906998813 | erot = 3.97599599383721 | epot = -37.9817705180946 | etot = -29.6183454542693 +704000 ekin = 4.41020682713676 | erot = 3.83147838533281 | epot = -37.9674346241365 | etot = -29.725749411667 +705000 ekin = 4.39308990786441 | erot = 3.75664217186778 | epot = -37.9282520396871 | etot = -29.7785199599549 +706000 ekin = 4.43040906703156 | erot = 4.12756254176888 | epot = -37.8939279543826 | etot = -29.3359563455822 +707000 ekin = 4.51700671633646 | erot = 3.77573523129449 | epot = -37.8444471024437 | etot = -29.5517051548127 +708000 ekin = 4.49065124304534 | erot = 3.88552877104003 | epot = -37.7744800646504 | etot = -29.3983000505651 +709000 ekin = 4.41855498291445 | erot = 3.53582586052311 | epot = -37.6656825257611 | etot = -29.7113016823236 +710000 ekin = 4.40535258977283 | erot = 3.3964950268898 | epot = -37.5466939944653 | etot = -29.7448463778027 +711000 ekin = 4.32709544005249 | erot = 3.54995473848094 | epot = -37.3866324258479 | etot = -29.5095822473145 +712000 ekin = 4.40620309390877 | erot = 3.71557442538528 | epot = -37.1793914331048 | etot = -29.0576139138107 +713000 ekin = 4.39226105260192 | erot = 3.64956114520319 | epot = -36.9592491146157 | etot = -28.9174269168105 +714000 ekin = 4.39459047651044 | erot = 3.58799428596579 | epot = -36.784410906283 | etot = -28.8018261438068 +715000 ekin = 4.41458674942589 | erot = 4.01850565037392 | epot = -36.5924446920393 | etot = -28.1593522922395 +716000 ekin = 4.33665938530708 | erot = 3.50452219695686 | epot = -36.4143425377368 | etot = -28.5731609554728 +717000 ekin = 4.18088462864047 | erot = 3.21190204008997 | epot = -36.2481677379303 | etot = -28.8553810691999 +718000 ekin = 4.03231025467833 | erot = 2.91104295996759 | epot = -36.1402693367142 | etot = -29.1969161220683 +719000 ekin = 3.97260579411823 | erot = 3.29783620298646 | epot = -36.0849771003503 | etot = -28.8145351032456 +720000 ekin = 3.82567789821304 | erot = 3.46218504309262 | epot = -36.1068353452665 | etot = -28.8189724039609 +721000 ekin = 3.83433718059043 | erot = 4.0308403694784 | epot = -36.186895804643 | etot = -28.3217182545742 +722000 ekin = 3.71300872765614 | erot = 3.84736896155716 | epot = -36.2838656104836 | etot = -28.7234879212703 +723000 ekin = 3.74703466957627 | erot = 3.71040850656838 | epot = -36.3812410760549 | etot = -28.9237978999102 +724000 ekin = 3.75607081603381 | erot = 4.0281353287461 | epot = -36.4992818358977 | etot = -28.7150756911178 +725000 ekin = 3.77808990085843 | erot = 4.20966764087112 | epot = -36.6263500488379 | etot = -28.6385925071083 +726000 ekin = 3.99703012102758 | erot = 3.67945861038329 | epot = -36.7651398392481 | etot = -29.0886511078373 +727000 ekin = 4.01741049095323 | erot = 3.72684228835757 | epot = -36.8887239674892 | etot = -29.1444711881784 +728000 ekin = 4.05655244457443 | erot = 3.64411335656443 | epot = -36.9831032192824 | etot = -29.2824374181435 +729000 ekin = 4.15914112670643 | erot = 3.22368867517317 | epot = -37.0758214193941 | etot = -29.6929916175145 +730000 ekin = 4.27496625989451 | erot = 3.03434396509882 | epot = -37.1060663359391 | etot = -29.7967561109457 +731000 ekin = 4.35621946146852 | erot = 3.31453862248439 | epot = -37.0811379025033 | etot = -29.4103798185504 +732000 ekin = 4.31460322853995 | erot = 3.19560214587384 | epot = -37.0358028654706 | etot = -29.5255974910568 +733000 ekin = 4.22952267957096 | erot = 3.20037871938027 | epot = -36.9673423522076 | etot = -29.5374409532564 +734000 ekin = 4.24709820971321 | erot = 3.10598269123747 | epot = -36.8800091287789 | etot = -29.5269282278282 +735000 ekin = 4.1498116292607 | erot = 3.12549638567499 | epot = -36.7838119752137 | etot = -29.508503960278 +736000 ekin = 4.20814181481995 | erot = 2.91522500178923 | epot = -36.7063833852254 | etot = -29.5830165686162 +737000 ekin = 4.01828120268363 | erot = 2.4049581257871 | epot = -36.6589611248556 | etot = -30.2357217963849 +738000 ekin = 4.0109403602871 | erot = 2.68632566149121 | epot = -36.6548343802831 | etot = -29.9575683585048 +739000 ekin = 4.14661584174285 | erot = 2.59506078530653 | epot = -36.6780631105762 | etot = -29.9363864835269 +740000 ekin = 4.08413039711058 | erot = 2.5736582399383 | epot = -36.7021237291572 | etot = -30.0443350921083 +741000 ekin = 4.10845660619335 | erot = 2.78416335535289 | epot = -36.7754492326734 | etot = -29.8828292711272 +742000 ekin = 4.09068760907316 | erot = 3.09866824560678 | epot = -36.8187451874514 | etot = -29.6293893327714 +743000 ekin = 3.96610963094549 | erot = 3.04878673776488 | epot = -36.8535622197271 | etot = -29.8386658510168 +744000 ekin = 3.97087885402889 | erot = 3.04950786237749 | epot = -36.8512621314665 | etot = -29.8308754150601 +745000 ekin = 3.78295099566549 | erot = 3.09154774657218 | epot = -36.8410165021283 | etot = -29.9665177598907 +746000 ekin = 3.88442560568566 | erot = 3.15773579416856 | epot = -36.8645704531052 | etot = -29.822409053251 +747000 ekin = 3.94794600572262 | erot = 3.04363515896638 | epot = -36.9228275975809 | etot = -29.9312464328919 +748000 ekin = 3.94186404778415 | erot = 3.24130800398446 | epot = -37.0438118682001 | etot = -29.8606398164315 +749000 ekin = 3.93262026571698 | erot = 3.71710044171245 | epot = -37.2109632789996 | etot = -29.5612425715701 +750000 ekin = 3.82713052636537 | erot = 4.02486049381798 | epot = -37.3854716207176 | etot = -29.5334806005343 +751000 ekin = 4.02336237200016 | erot = 4.23099342037398 | epot = -37.5518597142044 | etot = -29.2975039218302 +752000 ekin = 4.06152925021086 | erot = 3.76231639564706 | epot = -37.6809132611631 | etot = -29.8570676153051 +753000 ekin = 4.07859449791209 | erot = 3.97018598947917 | epot = -37.7593004103711 | etot = -29.7105199229799 +754000 ekin = 4.26771269586489 | erot = 4.64006960442447 | epot = -37.8141557249927 | etot = -28.9063734247033 +755000 ekin = 4.26666906965385 | erot = 4.77784474773988 | epot = -37.8576299963118 | etot = -28.813116178918 +756000 ekin = 4.29131147009744 | erot = 5.38525988164288 | epot = -37.8917845570813 | etot = -28.215213205341 +757000 ekin = 4.35562563894762 | erot = 5.14819699923428 | epot = -37.8935376948419 | etot = -28.38971505666 +758000 ekin = 4.22616249375219 | erot = 5.19713356473893 | epot = -37.8901713134434 | etot = -28.4668752549522 +759000 ekin = 4.24184449957189 | erot = 5.16496183591595 | epot = -37.8881235068914 | etot = -28.4813171714036 +760000 ekin = 4.23424644958513 | erot = 5.47628298706173 | epot = -37.9000330984186 | etot = -28.1895036617718 +761000 ekin = 4.26448749341646 | erot = 5.45907771030601 | epot = -37.9055730645776 | etot = -28.1820078608551 +762000 ekin = 4.22061932798822 | erot = 5.0436907431348 | epot = -37.9108772679059 | etot = -28.6465671967828 +763000 ekin = 4.09989014592177 | erot = 5.10778066514927 | epot = -37.9045250455563 | etot = -28.6968542344852 +764000 ekin = 4.18374834614789 | erot = 5.46818179899542 | epot = -37.8676566747124 | etot = -28.2157265295691 +765000 ekin = 4.08761418374907 | erot = 5.80858388049076 | epot = -37.8033181876414 | etot = -27.9071201234015 +766000 ekin = 4.03999541680448 | erot = 5.48136006660825 | epot = -37.7411893537014 | etot = -28.2198338702887 +767000 ekin = 4.01701285460389 | erot = 5.31665044278878 | epot = -37.6438611160225 | etot = -28.3101978186298 +768000 ekin = 3.97951625205955 | erot = 5.25792422549902 | epot = -37.5214426737365 | etot = -28.284002196178 +769000 ekin = 3.9904400552571 | erot = 5.21175341266104 | epot = -37.3810973556032 | etot = -28.178903887685 +770000 ekin = 3.99199742512011 | erot = 5.21810902470215 | epot = -37.1986211065215 | etot = -27.9885146566993 +771000 ekin = 3.82567851870023 | erot = 4.95130845103881 | epot = -36.9906650314344 | etot = -28.2136780616954 +772000 ekin = 3.72123202682095 | erot = 4.74084322348095 | epot = -36.744551321368 | etot = -28.2824760710661 +773000 ekin = 3.61186619870346 | erot = 4.4876416941515 | epot = -36.4404296878967 | etot = -28.3409217950418 +774000 ekin = 3.53238563321205 | erot = 4.08515606418301 | epot = -36.143048292969 | etot = -28.5255065955739 +775000 ekin = 3.61960121968344 | erot = 4.03007080844248 | epot = -35.8636424209005 | etot = -28.2139703927746 +776000 ekin = 3.50131397859649 | erot = 3.82783005287515 | epot = -35.5938202085502 | etot = -28.2646761770785 +777000 ekin = 3.40867202048171 | erot = 3.85221546935577 | epot = -35.4006619567299 | etot = -28.1397744668925 +778000 ekin = 3.4583803102866 | erot = 3.51853820068406 | epot = -35.2979750992065 | etot = -28.3210565882358 +779000 ekin = 3.42307480041793 | erot = 3.59321040457274 | epot = -35.2809430031739 | etot = -28.2646577981832 +780000 ekin = 3.42440692402583 | erot = 3.60521054559663 | epot = -35.3411249792456 | etot = -28.3115075096232 +781000 ekin = 3.46934151467013 | erot = 3.84731508491239 | epot = -35.4518670976728 | etot = -28.1352104980902 +782000 ekin = 3.52710406680765 | erot = 4.28376670942223 | epot = -35.5950260565868 | etot = -27.7841552803569 +783000 ekin = 3.61729821660962 | erot = 4.75537078140965 | epot = -35.7562125383786 | etot = -27.3835435403593 +784000 ekin = 3.58366553598354 | erot = 4.11380123135017 | epot = -35.8708728516403 | etot = -28.1734060843065 +785000 ekin = 3.63226984987139 | erot = 4.14613629449623 | epot = -35.9549809353062 | etot = -28.1765747909386 +786000 ekin = 3.55353155352182 | erot = 3.96170523540249 | epot = -36.0104316125791 | etot = -28.4951948236547 +787000 ekin = 3.65679390509465 | erot = 4.13482060006107 | epot = -36.0644977241083 | etot = -28.2728832189526 +788000 ekin = 3.867576992853 | erot = 4.10779053552871 | epot = -36.0997261456394 | etot = -28.1243586172577 +789000 ekin = 3.93645468274948 | erot = 4.27766163431813 | epot = -36.1406694170032 | etot = -27.9265530999356 +790000 ekin = 3.99051031327522 | erot = 3.95340487785031 | epot = -36.2018617372684 | etot = -28.2579465461428 +791000 ekin = 4.10452718423531 | erot = 3.99235351847299 | epot = -36.2624115283464 | etot = -28.1655308256382 +792000 ekin = 4.33302884516796 | erot = 3.8304429162741 | epot = -36.3357012610719 | etot = -28.1722294996298 +793000 ekin = 4.59966330091371 | erot = 3.74212535974473 | epot = -36.4314410279298 | etot = -28.0896523672713 +794000 ekin = 4.70509453521945 | erot = 3.73254571552344 | epot = -36.5039677226904 | etot = -28.0663274719476 +795000 ekin = 4.82373501353496 | erot = 3.69936645898632 | epot = -36.5467302591184 | etot = -28.0236287865971 +796000 ekin = 5.02825099690213 | erot = 3.6584589522484 | epot = -36.5441938749352 | etot = -27.8574839257846 +797000 ekin = 4.98369350470429 | erot = 3.33483563015644 | epot = -36.5302539300584 | etot = -28.2117247951976 +798000 ekin = 5.04627515833427 | erot = 3.25184431558307 | epot = -36.5269098314583 | etot = -28.228790357541 +799000 ekin = 4.96165968599483 | erot = 3.39539196017168 | epot = -36.5580084896252 | etot = -28.2009568434587 +800000 ekin = 4.9608728952381 | erot = 3.5493203329157 | epot = -36.6052154994127 | etot = -28.0950222712589 +801000 ekin = 4.96148873220033 | erot = 3.39995120227754 | epot = -36.6619752973789 | etot = -28.300535362901 +802000 ekin = 4.86744715226313 | erot = 3.35338258088214 | epot = -36.694222464791 | etot = -28.4733927316457 +803000 ekin = 4.75056128639555 | erot = 3.25410486957635 | epot = -36.7045390401487 | etot = -28.6998728841768 +804000 ekin = 4.78109129200104 | erot = 3.07765972882934 | epot = -36.6985265194181 | etot = -28.8397754985877 +805000 ekin = 4.82892493818659 | erot = 3.27499533781792 | epot = -36.6737874267385 | etot = -28.5698671507339 +806000 ekin = 4.74542372520125 | erot = 3.18323237798567 | epot = -36.6406513076366 | etot = -28.7119952044497 +807000 ekin = 4.64766139288033 | erot = 3.38424960796029 | epot = -36.647673088396 | etot = -28.6157620875554 +808000 ekin = 4.457078358644 | erot = 3.35175675914238 | epot = -36.7022500935494 | etot = -28.893414975763 +809000 ekin = 4.3267088759155 | erot = 3.32046355515555 | epot = -36.7741824114205 | etot = -29.1270099803495 +810000 ekin = 4.19642960492136 | erot = 3.20396083815701 | epot = -36.8832195227731 | etot = -29.4828290796948 +811000 ekin = 4.18603442116986 | erot = 3.54097838794745 | epot = -37.0402774324891 | etot = -29.3132646233718 +812000 ekin = 4.33190991624128 | erot = 3.67977508149037 | epot = -37.2334955671968 | etot = -29.2218105694651 +813000 ekin = 4.46701990899902 | erot = 3.84749046887853 | epot = -37.477006312962 | etot = -29.1624959350845 +814000 ekin = 4.70593563863401 | erot = 4.02074050200779 | epot = -37.7739765579915 | etot = -29.0473004173497 +815000 ekin = 4.61635561952674 | erot = 4.30893882425501 | epot = -38.0622407069035 | etot = -29.1369462631217 +816000 ekin = 4.66419241223469 | erot = 4.4334841646702 | epot = -38.3533945439941 | etot = -29.2557179670892 +817000 ekin = 4.61492034782231 | erot = 4.85896836140468 | epot = -38.6054729848482 | etot = -29.1315842756212 +818000 ekin = 4.6936135555876 | erot = 4.57560992803624 | epot = -38.8141140205622 | etot = -29.5448905369383 +819000 ekin = 4.99561997491631 | erot = 4.59057590873874 | epot = -38.9861314653861 | etot = -29.399935581731 +820000 ekin = 5.14251771001315 | erot = 4.38257454602503 | epot = -39.111979352787 | etot = -29.5868870967488 +821000 ekin = 5.21211790511143 | erot = 3.76493639645341 | epot = -39.1791873910091 | etot = -30.2021330894442 +822000 ekin = 5.22763747343407 | erot = 3.81993934721836 | epot = -39.2257832500634 | etot = -30.178206429411 +823000 ekin = 5.20824824630262 | erot = 3.61818509207447 | epot = -39.2577442235127 | etot = -30.4313108851356 +824000 ekin = 5.29481176259064 | erot = 3.61607107182839 | epot = -39.2930045776051 | etot = -30.382121743186 +825000 ekin = 5.34590564278881 | erot = 3.47605801675253 | epot = -39.3020776711429 | etot = -30.4801140116015 +826000 ekin = 5.38005087585683 | erot = 3.56002985231115 | epot = -39.2878928900552 | etot = -30.3478121618872 +827000 ekin = 5.38251681844313 | erot = 3.31581026558491 | epot = -39.2838973283757 | etot = -30.5855702443476 +828000 ekin = 5.30162295798738 | erot = 2.79999506814259 | epot = -39.2990437954941 | etot = -31.1974257693642 +829000 ekin = 5.34935471298468 | erot = 2.63380753851503 | epot = -39.3079384502706 | etot = -31.3247761987709 +830000 ekin = 5.15642397228279 | erot = 2.78944963383064 | epot = -39.3294203636004 | etot = -31.383546757487 +831000 ekin = 5.04271329110575 | erot = 3.07984504895767 | epot = -39.3562191308943 | etot = -31.2336607908309 +832000 ekin = 5.04415123872944 | erot = 3.36917057661257 | epot = -39.3458026730645 | etot = -30.9324808577225 +833000 ekin = 4.97652700754312 | erot = 3.1101682681075 | epot = -39.3003589046715 | etot = -31.2136636290209 +834000 ekin = 4.66785324148465 | erot = 2.98799062968242 | epot = -39.2007615011675 | etot = -31.5449176300004 +835000 ekin = 4.41967948410668 | erot = 3.24754240638231 | epot = -39.0370935965111 | etot = -31.3698717060221 +836000 ekin = 4.19399501172609 | erot = 3.40709899396411 | epot = -38.8824429433975 | etot = -31.2813489377073 +837000 ekin = 4.05102708476564 | erot = 3.50403284169295 | epot = -38.729129846576 | etot = -31.1740699201174 +838000 ekin = 3.94991363719696 | erot = 3.82377156946746 | epot = -38.5557937558051 | etot = -30.7821085491406 +839000 ekin = 3.7432666531872 | erot = 3.97324655976193 | epot = -38.3643816043728 | etot = -30.6478683914237 +840000 ekin = 3.70351574528206 | erot = 3.51244886217305 | epot = -38.1559200259223 | etot = -30.9399554184672 +841000 ekin = 3.60547887438337 | erot = 3.69151206405111 | epot = -37.9552189953845 | etot = -30.65822805695 +842000 ekin = 3.38591284745953 | erot = 3.48115901302697 | epot = -37.764748291951 | etot = -30.8976764314645 +843000 ekin = 3.11807787995847 | erot = 3.24962582172167 | epot = -37.5931200484565 | etot = -31.2254163467764 +844000 ekin = 3.03125896851695 | erot = 3.10915311466782 | epot = -37.405355484813 | etot = -31.2649434016282 +845000 ekin = 2.84759324027358 | erot = 3.53115382226828 | epot = -37.2260086331774 | etot = -30.8472615706355 +846000 ekin = 2.83613069836887 | erot = 3.4149752298821 | epot = -37.0853206047919 | etot = -30.8342146765409 +847000 ekin = 2.82518542790846 | erot = 3.9264613760552 | epot = -36.974096592552 | etot = -30.2224497885884 +848000 ekin = 2.80356101967319 | erot = 3.75897131812122 | epot = -36.8749675315762 | etot = -30.3124351937818 +849000 ekin = 2.84159199816781 | erot = 3.65493979263187 | epot = -36.779890805585 | etot = -30.2833590147853 +850000 ekin = 2.91517374365713 | erot = 3.25543936029208 | epot = -36.7388454898329 | etot = -30.5682323858837 +851000 ekin = 3.08764953673658 | erot = 3.74455145978192 | epot = -36.7223642181885 | etot = -29.89016322167 +852000 ekin = 3.20356705871772 | erot = 3.86422941824802 | epot = -36.7413165099177 | etot = -29.6735200329519 +853000 ekin = 3.25796036952201 | erot = 4.25509323905638 | epot = -36.7658517979722 | etot = -29.2527981893938 +854000 ekin = 3.57244822927054 | erot = 4.18969744123878 | epot = -36.8021340521259 | etot = -29.0399883816166 +855000 ekin = 3.61706783412732 | erot = 4.16292249791896 | epot = -36.8626923862677 | etot = -29.0827020542214 +856000 ekin = 3.78538239755829 | erot = 4.1125355160369 | epot = -36.9244661414311 | etot = -29.0265482278359 +857000 ekin = 3.78178847655943 | erot = 4.13628071929874 | epot = -37.0292483027703 | etot = -29.1111791069121 +858000 ekin = 3.79767899411072 | erot = 4.25390024597238 | epot = -37.1883443366299 | etot = -29.1367650965468 +859000 ekin = 3.79646558910104 | erot = 4.39490149090002 | epot = -37.3423128301936 | etot = -29.1509457501926 +860000 ekin = 3.86711139340656 | erot = 4.91957560544927 | epot = -37.4915022932753 | etot = -28.7048152944195 +861000 ekin = 3.99177075241214 | erot = 4.92589410248027 | epot = -37.5868681074752 | etot = -28.6692032525828 +862000 ekin = 4.09777488770542 | erot = 4.85487231115203 | epot = -37.6175250863673 | etot = -28.6648778875099 +863000 ekin = 4.13925231113358 | erot = 4.50896117392437 | epot = -37.5986086016745 | etot = -28.9503951166166 +864000 ekin = 4.14764866587401 | erot = 4.42487018235784 | epot = -37.5204132439135 | etot = -28.9478943956816 +865000 ekin = 4.14664914911124 | erot = 4.25648196395957 | epot = -37.3939280409712 | etot = -28.9907969279004 +866000 ekin = 4.14214320133623 | erot = 4.18089045470408 | epot = -37.2179460829705 | etot = -28.8949124269302 +867000 ekin = 4.2533355578276 | erot = 3.91180056253338 | epot = -37.0368358637648 | etot = -28.8716997434038 +868000 ekin = 4.25544635673599 | erot = 4.03934502097771 | epot = -36.8925237407717 | etot = -28.597732363058 +869000 ekin = 4.24112681076696 | erot = 4.01454747655037 | epot = -36.8084367274639 | etot = -28.5527624401466 +870000 ekin = 4.33478513327969 | erot = 3.78349131070103 | epot = -36.7681636745506 | etot = -28.6498872305699 +871000 ekin = 4.17502061003877 | erot = 3.95421063050501 | epot = -36.789978024709 | etot = -28.6607467841652 +872000 ekin = 4.17603847735387 | erot = 3.83768938083755 | epot = -36.8688005631079 | etot = -28.8550727049165 +873000 ekin = 4.41693719639055 | erot = 4.07505566261771 | epot = -36.9767379853353 | etot = -28.484745126327 +874000 ekin = 4.41295334009066 | erot = 4.18394759913442 | epot = -37.1369142438402 | etot = -28.5400133046152 +875000 ekin = 4.5295533495583 | erot = 4.19580464695389 | epot = -37.3370998777418 | etot = -28.6117418812297 +876000 ekin = 4.61247068682014 | erot = 4.50897081857259 | epot = -37.524834933576 | etot = -28.4033934281833 +877000 ekin = 4.76533246608885 | erot = 4.08201826719388 | epot = -37.6873606048148 | etot = -28.8400098715321 +878000 ekin = 4.86109701096016 | erot = 4.03315572964805 | epot = -37.8092910984796 | etot = -28.9150383578714 +879000 ekin = 4.93322526419341 | erot = 3.94479688456014 | epot = -37.8433128250789 | etot = -28.9652906763253 +880000 ekin = 4.911777192825 | erot = 3.90966953329923 | epot = -37.7988935874835 | etot = -28.9774468613593 +881000 ekin = 4.87595051611175 | erot = 3.76638474533256 | epot = -37.6791282073065 | etot = -29.0367929458622 +882000 ekin = 4.80398792776511 | erot = 3.52725045147228 | epot = -37.4958553191689 | etot = -29.1646169399315 +883000 ekin = 4.56372183805733 | erot = 3.17268134771393 | epot = -37.3026048485139 | etot = -29.5662016627427 +884000 ekin = 4.38408070690437 | erot = 2.95287988074889 | epot = -37.1164899885621 | etot = -29.7795294009088 +885000 ekin = 4.21401267631408 | erot = 3.28627816384396 | epot = -36.9423946246094 | etot = -29.4421037844513 +886000 ekin = 3.94208450895983 | erot = 3.61827008671944 | epot = -36.8244889717529 | etot = -29.2641343760737 +887000 ekin = 3.76025689669472 | erot = 3.89282193563569 | epot = -36.7542446517053 | etot = -29.1011658193749 +888000 ekin = 3.58518173626078 | erot = 4.10918051627477 | epot = -36.7235080282687 | etot = -29.0291457757332 +889000 ekin = 3.52227905598844 | erot = 4.53948895643707 | epot = -36.742334591686 | etot = -28.6805665792605 +890000 ekin = 3.48725850687346 | erot = 4.91651845671102 | epot = -36.81107494511 | etot = -28.4072979815255 +891000 ekin = 3.51807183016393 | erot = 5.36785996033029 | epot = -36.9187079043872 | etot = -28.0327761138929 +892000 ekin = 3.48651441482314 | erot = 5.25687644163395 | epot = -37.0005216584211 | etot = -28.257130801964 +893000 ekin = 3.51467838154865 | erot = 5.65149044087769 | epot = -37.05944534206 | etot = -27.8932765196337 +894000 ekin = 3.45974654612344 | erot = 5.22169711042801 | epot = -37.1020642679859 | etot = -28.4206206114344 +895000 ekin = 3.57216437063283 | erot = 5.4089506797762 | epot = -37.1028729086242 | etot = -28.1217578582152 +896000 ekin = 3.56655921068021 | erot = 5.69090228219818 | epot = -37.070821741523 | etot = -27.8133602486446 +897000 ekin = 3.57757547802829 | erot = 5.90228049359271 | epot = -36.9859514532974 | etot = -27.5060954816764 +898000 ekin = 3.52295514054008 | erot = 5.84538360240597 | epot = -36.8484715408745 | etot = -27.4801327979284 +899000 ekin = 3.42191869063631 | erot = 5.47174915922289 | epot = -36.6856616378147 | etot = -27.7919937879555 +900000 ekin = 3.45720121516806 | erot = 5.59973772512064 | epot = -36.5148133918258 | etot = -27.4578744515371 +901000 ekin = 3.51607619901442 | erot = 5.88763510779773 | epot = -36.2859464010575 | etot = -26.8822350942454 +902000 ekin = 3.56087621117169 | erot = 5.17399063106742 | epot = -36.0621785767848 | etot = -27.3273117345457 +903000 ekin = 3.56470936099193 | erot = 5.0736169800556 | epot = -35.8794588183624 | etot = -27.2411324773149 +904000 ekin = 3.64294879518613 | erot = 5.28022715353213 | epot = -35.7543216612838 | etot = -26.8311457125655 +905000 ekin = 3.72447152602285 | erot = 5.02657007424527 | epot = -35.6582804909764 | etot = -26.9072388907083 +906000 ekin = 3.75914133677088 | erot = 4.63070748715842 | epot = -35.612999504401 | etot = -27.2231506804717 +907000 ekin = 4.00046169414558 | erot = 4.63743176603131 | epot = -35.6087015116536 | etot = -26.9708080514767 +908000 ekin = 3.98050966425464 | erot = 4.23795607914891 | epot = -35.6020003534147 | etot = -27.3835346100112 +909000 ekin = 4.14488755712815 | erot = 3.77771446920705 | epot = -35.5819012555833 | etot = -27.6592992292481 +910000 ekin = 4.1887889926356 | erot = 3.85878998652561 | epot = -35.5853308204891 | etot = -27.5377518413279 +911000 ekin = 4.15448454864758 | erot = 3.93063753948176 | epot = -35.6075046071718 | etot = -27.5223825190425 +912000 ekin = 4.30922033402802 | erot = 4.53644215925805 | epot = -35.6368602869835 | etot = -26.7911977936974 +913000 ekin = 4.42050627097558 | erot = 4.36559538892952 | epot = -35.6635505470047 | etot = -26.8774488870996 +914000 ekin = 4.6403841670674 | erot = 4.57708989772375 | epot = -35.6621612967527 | etot = -26.4446872319616 +915000 ekin = 4.71121950507705 | erot = 4.34018648406813 | epot = -35.6015140360094 | etot = -26.5501080468642 +916000 ekin = 4.67735943325919 | erot = 4.0723772918886 | epot = -35.4903050476419 | etot = -26.7405683224941 +917000 ekin = 4.78142703705638 | erot = 4.20198791892886 | epot = -35.3917685265256 | etot = -26.4083535705404 +918000 ekin = 4.7742119869693 | erot = 4.42971373988814 | epot = -35.2582637676414 | etot = -26.0543380407839 +919000 ekin = 4.73422216252914 | erot = 4.77044814340051 | epot = -35.0931913565728 | etot = -25.5885210506432 +920000 ekin = 4.64583700129848 | erot = 4.69774436792081 | epot = -34.9395895324837 | etot = -25.5960081632644 +921000 ekin = 4.61516328269964 | erot = 4.43350879426936 | epot = -34.8128426462854 | etot = -25.7641705693164 +922000 ekin = 4.55621337364178 | erot = 4.21768777753525 | epot = -34.731272035168 | etot = -25.957370883991 +923000 ekin = 4.59034826680215 | erot = 4.50920703076205 | epot = -34.7044992141229 | etot = -25.6049439165587 +924000 ekin = 4.58356240196282 | erot = 4.62074320796255 | epot = -34.7126986327434 | etot = -25.5083930228181 +925000 ekin = 4.53220072800684 | erot = 4.79254817721302 | epot = -34.7588998026867 | etot = -25.4341508974668 +926000 ekin = 4.55832715206546 | erot = 5.00471911281283 | epot = -34.8080246038197 | etot = -25.2449783389414 +927000 ekin = 4.62575171089084 | erot = 4.71181044830637 | epot = -34.8667293476369 | etot = -25.5291671884397 +928000 ekin = 4.6865737520682 | erot = 4.76234601746956 | epot = -34.9159498367978 | etot = -25.4670300672601 +929000 ekin = 4.70610289156496 | erot = 5.07097104655825 | epot = -34.9791697926812 | etot = -25.202095854558 +930000 ekin = 4.79474071813525 | erot = 5.21915381885372 | epot = -35.0589708185242 | etot = -25.0450762815352 +931000 ekin = 4.69039359230198 | erot = 5.48593447848963 | epot = -35.1099047138404 | etot = -24.9335766430488 +932000 ekin = 4.7111009460339 | erot = 5.4720468535618 | epot = -35.1612846037869 | etot = -24.9781368041912 +933000 ekin = 4.76369652677887 | erot = 5.41370570081894 | epot = -35.2317575147351 | etot = -25.0543552871373 +934000 ekin = 4.83643894391789 | erot = 5.23508631414153 | epot = -35.3109086744022 | etot = -25.2393834163428 +935000 ekin = 4.76586014730436 | erot = 5.22865540833756 | epot = -35.3670038676071 | etot = -25.3724883119652 +936000 ekin = 4.7459923218933 | erot = 5.40903849081523 | epot = -35.4141584031107 | etot = -25.2591275904022 +937000 ekin = 4.70665366838905 | erot = 5.90535300927779 | epot = -35.4573569432724 | etot = -24.8453502656056 +938000 ekin = 4.73520980048979 | erot = 5.48994015212931 | epot = -35.4717259493596 | etot = -25.2465759967405 +939000 ekin = 4.66471904112519 | erot = 5.58667162801307 | epot = -35.4363389851306 | etot = -25.1849483159923 +940000 ekin = 4.73670308439177 | erot = 5.59502045341229 | epot = -35.3410735898404 | etot = -25.0093500520363 +941000 ekin = 4.56546752366378 | erot = 5.16939612930462 | epot = -35.2196425314963 | etot = -25.4847788785279 +942000 ekin = 4.36600564082669 | erot = 4.55609433699451 | epot = -35.0782455188876 | etot = -26.1561455410664 +943000 ekin = 4.27680501590838 | erot = 4.77186490926422 | epot = -34.9346146494824 | etot = -25.8859447243098 +944000 ekin = 4.17576408254737 | erot = 4.64476704064562 | epot = -34.7936442239135 | etot = -25.9731131007205 +945000 ekin = 4.08165692512371 | erot = 4.64307958398346 | epot = -34.7241648822137 | etot = -25.9994283731065 +946000 ekin = 3.98238337685344 | erot = 4.33903183997964 | epot = -34.7208981880722 | etot = -26.3994829712391 +947000 ekin = 4.11312487406461 | erot = 4.25698162025787 | epot = -34.8023164533948 | etot = -26.4322099590723 +948000 ekin = 4.03905965504869 | erot = 4.28038925266087 | epot = -34.9281986674362 | etot = -26.6087497597266 +949000 ekin = 4.1208125166908 | erot = 4.40083354097111 | epot = -35.1348098866939 | etot = -26.613163829032 +950000 ekin = 4.19947300195128 | erot = 4.46892156642135 | epot = -35.3299547862506 | etot = -26.661560217878 +951000 ekin = 4.28802819218884 | erot = 4.36807424436335 | epot = -35.5595339264246 | etot = -26.9034314898725 +952000 ekin = 4.44618066979578 | erot = 4.88998578448103 | epot = -35.7762645912068 | etot = -26.44009813693 +953000 ekin = 4.5302283554923 | erot = 4.90684636989476 | epot = -35.9402525430858 | etot = -26.5031778176987 +954000 ekin = 4.65793433635961 | erot = 4.95789701943277 | epot = -36.1007223995933 | etot = -26.4848910438009 +955000 ekin = 4.68472849923027 | erot = 4.84778271057312 | epot = -36.2250094081951 | etot = -26.6924981983917 +956000 ekin = 4.83489144923538 | erot = 4.61252423076221 | epot = -36.2912267944712 | etot = -26.8438111144736 +957000 ekin = 4.83158754758409 | erot = 4.0642787483582 | epot = -36.3314048744553 | etot = -27.435538578513 +958000 ekin = 4.95872508890374 | erot = 3.8676428932311 | epot = -36.3554965538545 | etot = -27.5291285717197 +959000 ekin = 4.88220034385472 | erot = 3.76501141985342 | epot = -36.3703754351938 | etot = -27.7231636714857 +960000 ekin = 4.96739750076015 | erot = 3.7014398632156 | epot = -36.3537104260633 | etot = -27.6848730620876 +961000 ekin = 5.05073619222996 | erot = 3.58723306284446 | epot = -36.3292284086296 | etot = -27.6912591535552 +962000 ekin = 5.10220917296366 | erot = 3.43365806618373 | epot = -36.2926607322774 | etot = -27.75679349313 +963000 ekin = 5.25727455724212 | erot = 3.39047088285921 | epot = -36.2233249912223 | etot = -27.575579551121 +964000 ekin = 5.33892942752082 | erot = 3.38850636488331 | epot = -36.1631800361723 | etot = -27.4357442437681 +965000 ekin = 5.2970730958468 | erot = 3.40709075904151 | epot = -36.114647791202 | etot = -27.4104839363137 +966000 ekin = 5.27380254283778 | erot = 3.34984185029643 | epot = -36.0934598827503 | etot = -27.4698154896161 +967000 ekin = 5.19975037009079 | erot = 3.54967607074502 | epot = -36.1222651146807 | etot = -27.3728386738448 +968000 ekin = 5.22098509097155 | erot = 3.3892004067814 | epot = -36.1570868906286 | etot = -27.5469013928757 +969000 ekin = 5.01248198517068 | erot = 3.26201512253228 | epot = -36.2130447987792 | etot = -27.9385476910762 +970000 ekin = 4.97914863237106 | erot = 3.76343819077311 | epot = -36.2895058744145 | etot = -27.5469190512703 +971000 ekin = 5.04224300192785 | erot = 3.59024832311319 | epot = -36.3590409977869 | etot = -27.7265496727458 +972000 ekin = 5.05787332232175 | erot = 3.83558558676151 | epot = -36.3997125264456 | etot = -27.5062536173623 +973000 ekin = 5.01777031588935 | erot = 3.27986497682726 | epot = -36.4166837336011 | etot = -28.1190484408845 +974000 ekin = 4.96186842907979 | erot = 3.23479851019171 | epot = -36.4352005399393 | etot = -28.2385336006678 +975000 ekin = 4.97224363278502 | erot = 3.35077904927888 | epot = -36.4557098060367 | etot = -28.1326871239728 +976000 ekin = 5.0162553138043 | erot = 3.41837200675041 | epot = -36.4643526378271 | etot = -28.0297253172724 +977000 ekin = 5.04359880486583 | erot = 3.40669885598936 | epot = -36.4673967616966 | etot = -28.0170991008414 +978000 ekin = 4.9681411602187 | erot = 3.39885422893789 | epot = -36.4671439769122 | etot = -28.1001485877556 +979000 ekin = 4.68494120169249 | erot = 3.87226166481083 | epot = -36.4696261905049 | etot = -27.9124233240016 +980000 ekin = 4.80514576212701 | erot = 3.73614562894005 | epot = -36.475376838153 | etot = -27.9340854470859 +981000 ekin = 4.85375109376202 | erot = 4.35522911699943 | epot = -36.490277579472 | etot = -27.2812973687106 +982000 ekin = 4.79648806853116 | erot = 4.15595945903746 | epot = -36.5084812040106 | etot = -27.556033676442 +983000 ekin = 4.75907969484057 | erot = 4.43556787871506 | epot = -36.5083539693145 | etot = -27.3137063957588 +984000 ekin = 4.81598118843888 | erot = 4.52957555705298 | epot = -36.5383410952843 | etot = -27.1927843497924 +985000 ekin = 4.87924474650941 | erot = 4.31630979014036 | epot = -36.577700648078 | etot = -27.3821461114282 +986000 ekin = 4.77128314224537 | erot = 4.12408981491498 | epot = -36.5819281400531 | etot = -27.6865551828927 +987000 ekin = 4.70900566206185 | erot = 4.08922713836866 | epot = -36.5892891612732 | etot = -27.7910563608427 +988000 ekin = 4.6968564492698 | erot = 4.03217145235668 | epot = -36.6289948782934 | etot = -27.8999669766669 +989000 ekin = 4.56955203825019 | erot = 4.16364650343056 | epot = -36.6885496975525 | etot = -27.9553511558718 +990000 ekin = 4.56207337974517 | erot = 3.92865148644801 | epot = -36.7375440238776 | etot = -28.2468191576844 +991000 ekin = 4.4586326947315 | erot = 3.99370804360007 | epot = -36.8046932644695 | etot = -28.3523525261379 +992000 ekin = 4.52516169637469 | erot = 4.19036473784407 | epot = -36.9045951669892 | etot = -28.1890687327704 +993000 ekin = 4.26593637770936 | erot = 4.55899726308496 | epot = -37.0283922292365 | etot = -28.2034585884422 +994000 ekin = 4.14968593987806 | erot = 4.67871188882193 | epot = -37.1561829580762 | etot = -28.3277851293762 +995000 ekin = 4.20875361664816 | erot = 4.51127733270458 | epot = -37.285893138091 | etot = -28.5658621887383 +996000 ekin = 4.10968366763525 | erot = 4.25871927923692 | epot = -37.3745810703536 | etot = -29.0061781234814 +997000 ekin = 4.00616178451074 | erot = 4.48911641515844 | epot = -37.4314666701152 | etot = -28.936188470446 +998000 ekin = 4.02180091279274 | erot = 4.35841167717687 | epot = -37.4443636100105 | etot = -29.0641510200409 +999000 ekin = 4.07504562975234 | erot = 4.2623087345041 | epot = -37.4098012996852 | etot = -29.0724469354287 +1000000 ekin = 3.90433765200202 | erot = 4.66881888228247 | epot = -37.3063332342133 | etot = -28.7331766999288 + 1000000 0.10411567 -1.4674304 0.032571422 -1.2846921 -6.6175275e-05 64000 +Loop time of 46.707 on 4 procs for 1000000 steps with 26 atoms + +Performance: 18498.300 tau/day, 21410.069 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.76 | 20.213 | 37.557 | 224.0 | 43.28 +Bond | 0.40923 | 0.55415 | 0.69879 | 19.0 | 1.19 +Neigh | 0.011178 | 0.011362 | 0.011538 | 0.1 | 0.02 +Comm | 5.0567 | 23.133 | 31.358 | 218.8 | 49.53 +Output | 0.11779 | 0.13598 | 0.14356 | 2.9 | 0.29 +Modify | 1.5587 | 2.2266 | 2.8695 | 42.6 | 4.77 +Other | | 0.4324 | | | 0.93 + +Nlocal: 6.50000 ave 10 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 19.5000 ave 23 max 16 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 75.2500 ave 190 max 23 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.4.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:46 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 new file mode 100644 index 0000000000..c3c8dbcc9f --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 @@ -0,0 +1,1272 @@ +LAMMPS (2 Jul 2021) +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +mass * 3.1575 # sets per-type mass if not in data file +set atom * mass 3.1575 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 8 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.8.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 3.74991604702378 | erot = 3.45272678980464 | epot = -37.374200901142 | etot = -30.1715580643136 +Per MPI rank memory allocation (min/avg/max) = 9.328 | 9.328 | 9.328 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.099997761 -1.4717559 0.03428661 -1.2932417 5.6146609e-05 64000 +1000 ekin = 3.83184879800819 | erot = 3.50203401022062 | epot = -37.4730508915114 | etot = -30.1391680832826 +2000 ekin = 3.82227374831519 | erot = 3.79878100905234 | epot = -37.616191007464 | etot = -29.9951362500965 +3000 ekin = 3.90938932030971 | erot = 4.1584025695072 | epot = -37.7430329723255 | etot = -29.6752410825086 +4000 ekin = 3.82373321902577 | erot = 4.12183047279799 | epot = -37.8313543569025 | etot = -29.8857906650787 +5000 ekin = 3.7245469506492 | erot = 4.29953523687407 | epot = -37.8617217220934 | etot = -29.8376395345701 +6000 ekin = 3.75585156536887 | erot = 4.31270713695362 | epot = -37.8280629310505 | etot = -29.759504228728 +7000 ekin = 3.7932674084105 | erot = 4.16508360466875 | epot = -37.7640947397913 | etot = -29.8057437267121 +8000 ekin = 3.74746489835263 | erot = 4.25243425677967 | epot = -37.6835135449588 | etot = -29.6836143898265 +9000 ekin = 3.70802697723781 | erot = 4.00193184819411 | epot = -37.5899388200959 | etot = -29.879979994664 +10000 ekin = 3.58135597641079 | erot = 3.86411518632772 | epot = -37.5041732418663 | etot = -30.0587020791278 +11000 ekin = 3.45122934445655 | erot = 4.1703535299311 | epot = -37.4859882561369 | etot = -29.8644053817493 +12000 ekin = 3.42435863038453 | erot = 4.21487472538924 | epot = -37.5307136425246 | etot = -29.8914802867508 +13000 ekin = 3.40216979362993 | erot = 4.07292918248782 | epot = -37.6378499557145 | etot = -30.1627509795968 +14000 ekin = 3.2921331552169 | erot = 4.50441987673251 | epot = -37.7761364031321 | etot = -29.9795833711827 +15000 ekin = 3.36883179726036 | erot = 4.91359031415192 | epot = -37.9357367952089 | etot = -29.6533146837966 +16000 ekin = 3.30177911852248 | erot = 5.09593415997444 | epot = -38.143737189117 | etot = -29.7460239106201 +17000 ekin = 3.27867865291038 | erot = 5.45789581601551 | epot = -38.3785999463332 | etot = -29.6420254774073 +18000 ekin = 3.36770908750654 | erot = 5.63036493519878 | epot = -38.5970397067551 | etot = -29.5989656840498 +19000 ekin = 3.29802639540141 | erot = 5.4561639608394 | epot = -38.7810833463914 | etot = -30.0268929901506 +20000 ekin = 3.28760849058064 | erot = 5.26031945979083 | epot = -38.9429500949467 | etot = -30.3950221445752 +21000 ekin = 3.32772748450133 | erot = 5.34990394778077 | epot = -39.0618181252056 | etot = -30.3841866929235 +22000 ekin = 3.34298346296243 | erot = 5.12273250375884 | epot = -39.1360899153793 | etot = -30.670373948658 +23000 ekin = 3.38280280428755 | erot = 5.14933572496698 | epot = -39.1974651493046 | etot = -30.6653266200501 +24000 ekin = 3.43991273776911 | erot = 5.03737353653099 | epot = -39.2427818934622 | etot = -30.7654956191621 +25000 ekin = 3.44382800915666 | erot = 4.56194227438362 | epot = -39.2491545805195 | etot = -31.2433842969792 +26000 ekin = 3.47220361933921 | erot = 4.88028216050135 | epot = -39.2033487475128 | etot = -30.8508629676722 +27000 ekin = 3.47824341108214 | erot = 4.7971367004181 | epot = -39.1340731989048 | etot = -30.8586930874046 +28000 ekin = 3.54835351423501 | erot = 4.65494607739445 | epot = -39.0768463918722 | etot = -30.8735468002427 +29000 ekin = 3.57491058588778 | erot = 4.31737192689192 | epot = -39.0420895500443 | etot = -31.1498070372646 +30000 ekin = 3.51438036654861 | erot = 4.50861299911584 | epot = -39.0276136699747 | etot = -31.0046203043103 +31000 ekin = 3.57650331888545 | erot = 4.40811531091204 | epot = -39.0168289246978 | etot = -31.0322102949003 +32000 ekin = 3.70658082522071 | erot = 4.15949186201363 | epot = -39.017410963825 | etot = -31.1513382765907 +33000 ekin = 3.83721022662003 | erot = 4.05055961618762 | epot = -39.0303039022729 | etot = -31.1425340594653 +34000 ekin = 3.94885880665681 | erot = 3.81495459058985 | epot = -39.0180833389347 | etot = -31.2542699416881 +35000 ekin = 3.97994525138323 | erot = 4.49904715736234 | epot = -38.9543629321032 | etot = -30.4753705233577 +36000 ekin = 3.90049506438266 | erot = 3.99723351860168 | epot = -38.8736492127444 | etot = -30.97592062976 +37000 ekin = 4.00119032736887 | erot = 4.30070706410093 | epot = -38.7576942972653 | etot = -30.4557969057955 +38000 ekin = 4.00581796835647 | erot = 3.82064458204034 | epot = -38.6053485149963 | etot = -30.7788859645995 +39000 ekin = 3.92374370666492 | erot = 3.80679256085696 | epot = -38.4357174066365 | etot = -30.7051811391146 +40000 ekin = 3.81525591020245 | erot = 3.60218215391061 | epot = -38.2889289083718 | etot = -30.8714908442587 +41000 ekin = 3.89801377589297 | erot = 3.52447171643241 | epot = -38.2033074629501 | etot = -30.7808219706247 +42000 ekin = 3.92469802136766 | erot = 3.72207083090906 | epot = -38.1843497161945 | etot = -30.5375808639177 +43000 ekin = 3.90355819056277 | erot = 3.6537526927489 | epot = -38.2197716832792 | etot = -30.6624607999675 +44000 ekin = 3.94906849382533 | erot = 3.48405507068376 | epot = -38.2852323155717 | etot = -30.8521087510626 +45000 ekin = 4.04988136986449 | erot = 3.38338492043337 | epot = -38.379217839749 | etot = -30.9459515494512 +46000 ekin = 4.12456204511554 | erot = 3.52614566674475 | epot = -38.4473213411912 | etot = -30.7966136293309 +47000 ekin = 4.05260082430177 | erot = 3.30110271195184 | epot = -38.4808326895795 | etot = -31.1271291533259 +48000 ekin = 3.94672633965036 | erot = 3.30790944660349 | epot = -38.4845357728861 | etot = -31.2298999866322 +49000 ekin = 3.88681575217735 | erot = 3.78262203823329 | epot = -38.4415128535038 | etot = -30.7720750630932 +50000 ekin = 3.8289998539571 | erot = 3.78573156370326 | epot = -38.3450518110649 | etot = -30.7303203934046 +51000 ekin = 3.84405747033417 | erot = 3.53181676479775 | epot = -38.2059734024445 | etot = -30.8300991673126 +52000 ekin = 3.72257170524986 | erot = 3.44233441463346 | epot = -38.0493176755067 | etot = -30.8844115556233 +53000 ekin = 3.58458805955587 | erot = 3.40175184254418 | epot = -37.8770316144346 | etot = -30.8906917123346 +54000 ekin = 3.42774104644866 | erot = 3.01933445329398 | epot = -37.7242775274776 | etot = -31.277202027735 +55000 ekin = 3.30773758120276 | erot = 3.11354928843072 | epot = -37.584427789289 | etot = -31.1631409196555 +56000 ekin = 3.30267684217518 | erot = 3.36746893036055 | epot = -37.4528615341919 | etot = -30.7827157616562 +57000 ekin = 3.19775481140565 | erot = 3.06235541109217 | epot = -37.3795633131473 | etot = -31.1194530906495 +58000 ekin = 3.11776701522974 | erot = 3.21225050262705 | epot = -37.3545495658646 | etot = -31.0245320480078 +59000 ekin = 3.02660076850687 | erot = 3.05700513362467 | epot = -37.3753385948441 | etot = -31.2917326927126 +60000 ekin = 3.05479252149938 | erot = 3.09854486170695 | epot = -37.4441725320783 | etot = -31.2908351488719 +61000 ekin = 3.01704476791617 | erot = 3.76451997765652 | epot = -37.5384296958521 | etot = -30.7568649502794 +62000 ekin = 3.04313706615776 | erot = 3.65046217125996 | epot = -37.6255736746588 | etot = -30.931974437241 +63000 ekin = 3.01457068009169 | erot = 3.63417424777149 | epot = -37.6954625017369 | etot = -31.0467175738737 +64000 ekin = 2.98716002899804 | erot = 3.66823413077172 | epot = -37.7940816265089 | etot = -31.1386874667392 +65000 ekin = 3.02462936411627 | erot = 3.70957377344584 | epot = -37.8868266007907 | etot = -31.1526234632286 +66000 ekin = 3.04943307417979 | erot = 3.64749592963955 | epot = -37.9385532609816 | etot = -31.2416242571623 +67000 ekin = 3.10664998766834 | erot = 3.9244199235005 | epot = -37.9686488739492 | etot = -30.9375789627803 +68000 ekin = 3.1050854233858 | erot = 3.5178167489996 | epot = -37.983113244155 | etot = -31.3602110717696 +69000 ekin = 3.12460161346418 | erot = 3.45336993587921 | epot = -38.016048039057 | etot = -31.4380764897136 +70000 ekin = 3.27586566025794 | erot = 2.94330488125488 | epot = -38.0712687269606 | etot = -31.8520981854478 +71000 ekin = 3.39211310061258 | erot = 2.74512861011504 | epot = -38.1409313278077 | etot = -32.0036896170801 +72000 ekin = 3.40645093836728 | erot = 2.75927481548157 | epot = -38.2448895790434 | etot = -32.0791638251946 +73000 ekin = 3.52971008848823 | erot = 2.59006671029947 | epot = -38.3559671032089 | etot = -32.2361903044212 +74000 ekin = 3.64539698532476 | erot = 2.94116909218575 | epot = -38.4934235930849 | etot = -31.9068575155744 +75000 ekin = 3.80169679560814 | erot = 3.11004664709647 | epot = -38.6561648833572 | etot = -31.7444214406526 +76000 ekin = 3.86343004207989 | erot = 3.33165114941789 | epot = -38.7892518002904 | etot = -31.5941706087926 +77000 ekin = 3.90472352035116 | erot = 3.31177401193377 | epot = -38.8678679983232 | etot = -31.6513704660382 +78000 ekin = 3.92691530468171 | erot = 3.25784074314341 | epot = -38.8969605625462 | etot = -31.7122045147211 +79000 ekin = 3.93607959529918 | erot = 3.16472395725656 | epot = -38.8636036578363 | etot = -31.7628001052805 +80000 ekin = 3.92375596570385 | erot = 3.03932991445865 | epot = -38.7678348516126 | etot = -31.8047489714501 +81000 ekin = 3.9430777715335 | erot = 2.88134017144298 | epot = -38.6473318824763 | etot = -31.8229139394998 +82000 ekin = 3.86696228915965 | erot = 2.89149309255461 | epot = -38.519943391552 | etot = -31.7614880098377 +83000 ekin = 3.60814275609262 | erot = 2.81572010912293 | epot = -38.3996592376438 | etot = -31.9757963724282 +84000 ekin = 3.71373301448702 | erot = 2.72793818704547 | epot = -38.3011883980015 | etot = -31.859517196469 +85000 ekin = 3.50951070251157 | erot = 2.79348490714939 | epot = -38.2117363909514 | etot = -31.9087407812904 +86000 ekin = 3.47308524750449 | erot = 3.12141964520655 | epot = -38.1244236248806 | etot = -31.5299187321696 +87000 ekin = 3.47440394227043 | erot = 3.04160702571504 | epot = -38.0440539828499 | etot = -31.5280430148644 +88000 ekin = 3.44172477689071 | erot = 2.99907227171085 | epot = -37.9859332104928 | etot = -31.5451361618913 +89000 ekin = 3.46547245050649 | erot = 3.42367325086164 | epot = -37.9432140623315 | etot = -31.0540683609633 +90000 ekin = 3.47276106924413 | erot = 3.41105238494334 | epot = -37.9009776655538 | etot = -31.0171642113663 +91000 ekin = 3.31717291023277 | erot = 4.00503611404981 | epot = -37.8509086765271 | etot = -30.5286996522445 +92000 ekin = 3.30281925189455 | erot = 3.78657692130476 | epot = -37.8308149894367 | etot = -30.7414188162374 +93000 ekin = 3.23932364656722 | erot = 3.46021357148725 | epot = -37.8328101558439 | etot = -31.1332729377895 +94000 ekin = 3.19291152023924 | erot = 3.36401906457231 | epot = -37.8297890174383 | etot = -31.2728584326267 +95000 ekin = 3.11174095364037 | erot = 3.84559531996404 | epot = -37.8285495206063 | etot = -30.8712132470019 +96000 ekin = 3.08253957616709 | erot = 4.19970849347964 | epot = -37.8307056468836 | etot = -30.5484575772369 +97000 ekin = 3.01019162595084 | erot = 4.79435511235213 | epot = -37.8474383063022 | etot = -30.0428915679992 +98000 ekin = 2.95004498340948 | erot = 4.45721895779631 | epot = -37.8489202082855 | etot = -30.4416562670797 +99000 ekin = 2.91563074020306 | erot = 4.14781823161589 | epot = -37.8396252499933 | etot = -30.7761762781743 +100000 ekin = 2.90648603235873 | erot = 3.81215086067838 | epot = -37.7900595351461 | etot = -31.071422642109 +101000 ekin = 2.85218071196321 | erot = 3.48991910340789 | epot = -37.7570245236792 | etot = -31.4149247083081 +102000 ekin = 2.86052427330307 | erot = 3.57587365782269 | epot = -37.7214005697291 | etot = -31.2850026386034 +103000 ekin = 2.88913271922391 | erot = 3.41748118405764 | epot = -37.6983180369495 | etot = -31.3917041336679 +104000 ekin = 2.81650081212179 | erot = 3.64361039549583 | epot = -37.6651320682074 | etot = -31.2050208605898 +105000 ekin = 2.79823699847461 | erot = 3.35865525277725 | epot = -37.6511913094721 | etot = -31.4942990582202 +106000 ekin = 2.78255015161702 | erot = 3.64122601097049 | epot = -37.6357012767034 | etot = -31.2119251141159 +107000 ekin = 2.8853059029881 | erot = 3.80038887689828 | epot = -37.6526611371135 | etot = -30.9669663572271 +108000 ekin = 2.83844762508156 | erot = 3.95272494897009 | epot = -37.7224292501163 | etot = -30.9312566760646 +109000 ekin = 2.91484982662488 | erot = 4.34544884566561 | epot = -37.8436434051328 | etot = -30.5833447328423 +110000 ekin = 2.93667443132402 | erot = 4.67698362049705 | epot = -37.9759529936705 | etot = -30.3622949418494 +111000 ekin = 3.11047864616463 | erot = 4.30694673133228 | epot = -38.1028692919235 | etot = -30.6854439144266 +112000 ekin = 3.32630420939175 | erot = 4.07222830175934 | epot = -38.2330557688864 | etot = -30.8345232577353 +113000 ekin = 3.38238157246173 | erot = 4.25399862575981 | epot = -38.4031841501303 | etot = -30.7668039519087 +114000 ekin = 3.40165200205494 | erot = 4.30744946748772 | epot = -38.6070332241657 | etot = -30.897931754623 +115000 ekin = 3.57685598139985 | erot = 4.55740206723813 | epot = -38.8200433287836 | etot = -30.6857852801457 +116000 ekin = 3.75973031177341 | erot = 4.3615765459289 | epot = -39.0323085624545 | etot = -30.9110017047522 +117000 ekin = 4.08170792820106 | erot = 4.22817627756988 | epot = -39.2374888319016 | etot = -30.9276046261307 +118000 ekin = 4.20730049786356 | erot = 4.45363628574744 | epot = -39.4247594107616 | etot = -30.7638226271506 +119000 ekin = 4.26502745539807 | erot = 4.38707691524353 | epot = -39.5609276649305 | etot = -30.9088232942889 +120000 ekin = 4.18668022830479 | erot = 4.24219249569072 | epot = -39.6276325806844 | etot = -31.1987598566889 +121000 ekin = 4.37673633947889 | erot = 4.44899930150549 | epot = -39.5989335189462 | etot = -30.7731978779619 +122000 ekin = 4.38970640566177 | erot = 4.08524736298491 | epot = -39.5011631447288 | etot = -31.0262093760821 +123000 ekin = 4.42858502015389 | erot = 3.38666748651706 | epot = -39.3700347945817 | etot = -31.5547822879107 +124000 ekin = 4.41843242629728 | erot = 3.29902599884916 | epot = -39.2496495732995 | etot = -31.532191148153 +125000 ekin = 4.2617494523508 | erot = 3.29673673713413 | epot = -39.1012418833314 | etot = -31.5427556938464 +126000 ekin = 4.24892047563245 | erot = 3.36728042977249 | epot = -38.9439369649168 | etot = -31.3277360595119 +127000 ekin = 4.20697642244211 | erot = 3.24776092764451 | epot = -38.7860930134988 | etot = -31.3313556634121 +128000 ekin = 4.051155507125 | erot = 3.47679598409534 | epot = -38.6330582994878 | etot = -31.1051068082675 +129000 ekin = 4.05771564566355 | erot = 3.55109790126639 | epot = -38.5073350485463 | etot = -30.8985215016164 +130000 ekin = 3.96453894213021 | erot = 3.5331352226628 | epot = -38.3915659508259 | etot = -30.8938917860329 +131000 ekin = 3.98900505769183 | erot = 3.64077310067997 | epot = -38.2786451293432 | etot = -30.6488669709714 +132000 ekin = 3.73079609117296 | erot = 3.73126171283414 | epot = -38.1409399456635 | etot = -30.6788821416564 +133000 ekin = 3.65247250435603 | erot = 3.53430985836843 | epot = -38.0235035134258 | etot = -30.8367211507014 +134000 ekin = 3.69649402588234 | erot = 3.97356364722737 | epot = -37.9278485959382 | etot = -30.2577909228285 +135000 ekin = 3.57147615494152 | erot = 4.00472599145964 | epot = -37.8397002442413 | etot = -30.2634980978401 +136000 ekin = 3.54164301577371 | erot = 3.88237062104624 | epot = -37.7460882463413 | etot = -30.3220746095214 +137000 ekin = 3.41247180964224 | erot = 3.32750587829717 | epot = -37.6246112923031 | etot = -30.8846336043637 +138000 ekin = 3.46206567288776 | erot = 3.47277237990382 | epot = -37.562116148782 | etot = -30.6272780959905 +139000 ekin = 3.46179863350053 | erot = 3.29345554522865 | epot = -37.5218039357363 | etot = -30.7665497570071 +140000 ekin = 3.57268233853842 | erot = 3.5202154657235 | epot = -37.4799882832129 | etot = -30.387090478951 +141000 ekin = 3.48030321137913 | erot = 3.69147952189496 | epot = -37.4842309048152 | etot = -30.3124481715411 +142000 ekin = 3.63349703801683 | erot = 3.72222694231707 | epot = -37.5326170636814 | etot = -30.1768930833475 +143000 ekin = 3.71391772492719 | erot = 3.32855653910457 | epot = -37.5715573506384 | etot = -30.5290830866066 +144000 ekin = 3.59876610372647 | erot = 3.57133292531736 | epot = -37.6083426167156 | etot = -30.4382435876717 +145000 ekin = 3.55129898738003 | erot = 3.38442665443505 | epot = -37.645703742064 | etot = -30.7099781002489 +146000 ekin = 3.57274630492872 | erot = 3.74306660671665 | epot = -37.6918399298831 | etot = -30.3760270182377 +147000 ekin = 3.51175180004563 | erot = 4.07506203504851 | epot = -37.7115891932223 | etot = -30.1247753581282 +148000 ekin = 3.52194530375129 | erot = 4.22438638639855 | epot = -37.7453589028593 | etot = -29.9990272127094 +149000 ekin = 3.43829227837986 | erot = 4.25032155928043 | epot = -37.7800675049656 | etot = -30.0914536673053 +150000 ekin = 3.3957375930512 | erot = 4.12519198982275 | epot = -37.7779101405858 | etot = -30.2569805577118 +151000 ekin = 3.38494817974845 | erot = 3.91154836764821 | epot = -37.7346130185547 | etot = -30.4381164711581 +152000 ekin = 3.33928233486053 | erot = 3.82420376901224 | epot = -37.6923063731278 | etot = -30.5288202692551 +153000 ekin = 3.38955645731944 | erot = 3.72251905459199 | epot = -37.6703717263952 | etot = -30.5582962144838 +154000 ekin = 3.4017017115168 | erot = 3.95270448125707 | epot = -37.6783897084388 | etot = -30.3239835156649 +155000 ekin = 3.44581188687106 | erot = 3.52528589615972 | epot = -37.7593041359923 | etot = -30.7882063529615 +156000 ekin = 3.55410349285979 | erot = 3.68359553101924 | epot = -37.8946612865555 | etot = -30.6569622626765 +157000 ekin = 3.67740663285561 | erot = 3.73708949692857 | epot = -38.0406477694046 | etot = -30.6261516396204 +158000 ekin = 3.70912292320982 | erot = 3.62418205239286 | epot = -38.1900046609469 | etot = -30.8566996853442 +159000 ekin = 3.6853282619123 | erot = 3.87298071798083 | epot = -38.2928836797072 | etot = -30.7345746998141 +160000 ekin = 3.72002440516723 | erot = 4.11592492943216 | epot = -38.3652902740973 | etot = -30.5293409394979 +161000 ekin = 3.73388863499069 | erot = 4.42836121024183 | epot = -38.4373191354183 | etot = -30.2750692901858 +162000 ekin = 4.02523829931076 | erot = 4.8680769419056 | epot = -38.4975346699525 | etot = -29.6042194287362 +163000 ekin = 4.03311015138323 | erot = 4.78291233450122 | epot = -38.5597523007635 | etot = -29.7437298148791 +164000 ekin = 4.1335004223363 | erot = 5.01454292769812 | epot = -38.5888368946085 | etot = -29.4407935445741 +165000 ekin = 4.2571846721418 | erot = 4.92225725319176 | epot = -38.5829201612759 | etot = -29.4034782359424 +166000 ekin = 4.11013815046505 | erot = 4.5380600083009 | epot = -38.5467907483033 | etot = -29.8985925895373 +167000 ekin = 4.08710467384593 | erot = 4.20997030650446 | epot = -38.4814936158366 | etot = -30.1844186354862 +168000 ekin = 4.03924000036858 | erot = 3.95993274976396 | epot = -38.3759188508994 | etot = -30.3767461007668 +169000 ekin = 3.94917218886656 | erot = 3.65240127094122 | epot = -38.2594355677076 | etot = -30.6578621078998 +170000 ekin = 3.90935554205321 | erot = 3.78797512477889 | epot = -38.1835201359157 | etot = -30.4861894690836 +171000 ekin = 3.8773250489546 | erot = 4.28652570004448 | epot = -38.1402484566641 | etot = -29.976397707665 +172000 ekin = 3.75957929171828 | erot = 4.02272820820138 | epot = -38.1557340618708 | etot = -30.3734265619512 +173000 ekin = 3.55030915229003 | erot = 4.03115995993296 | epot = -38.2480280629192 | etot = -30.6665589506962 +174000 ekin = 3.61281225750312 | erot = 4.30402685904744 | epot = -38.379508028535 | etot = -30.4626689119845 +175000 ekin = 3.56741376549371 | erot = 4.24945045724339 | epot = -38.5125929458379 | etot = -30.6957287231008 +176000 ekin = 3.69966296688439 | erot = 4.22673264606634 | epot = -38.6131459163278 | etot = -30.6867503033771 +177000 ekin = 3.7232933477479 | erot = 4.39637021744871 | epot = -38.6555013846403 | etot = -30.5358378194437 +178000 ekin = 3.7991935766677 | erot = 4.00194735045329 | epot = -38.6620582075599 | etot = -30.8609172804389 +179000 ekin = 3.78008346787859 | erot = 4.05267692212526 | epot = -38.6224110467893 | etot = -30.7896506567854 +180000 ekin = 3.84388711467645 | erot = 3.70916125532564 | epot = -38.5399848480517 | etot = -30.9869364780496 +181000 ekin = 3.78854199589317 | erot = 3.43025530256468 | epot = -38.4472679874805 | etot = -31.2284706890226 +182000 ekin = 3.65298336461982 | erot = 3.4144670384005 | epot = -38.3421256904839 | etot = -31.2746752874636 +183000 ekin = 3.57592466495272 | erot = 3.54000226366918 | epot = -38.2342661287443 | etot = -31.1183392001224 +184000 ekin = 3.59097293869161 | erot = 3.49764131752706 | epot = -38.1237685559035 | etot = -31.0351542996848 +185000 ekin = 3.59874593561892 | erot = 3.34180949424631 | epot = -38.0345613955437 | etot = -31.0940059656785 +186000 ekin = 3.55637392703387 | erot = 3.60010534755636 | epot = -37.9685691221056 | etot = -30.8120898475154 +187000 ekin = 3.30341471869181 | erot = 3.63282669533297 | epot = -37.9082034969871 | etot = -30.9719620829623 +188000 ekin = 3.25151380843728 | erot = 3.4158708150676 | epot = -37.8374520507023 | etot = -31.1700674271975 +189000 ekin = 3.09888859581603 | erot = 3.51324139411299 | epot = -37.7831379378025 | etot = -31.1710079478735 +190000 ekin = 2.9309664789049 | erot = 3.73100049541724 | epot = -37.7090579094215 | etot = -31.0470909350994 +191000 ekin = 2.7884578953631 | erot = 3.59181404756254 | epot = -37.6234731970084 | etot = -31.2432012540828 +192000 ekin = 2.68708504006426 | erot = 3.91911783313626 | epot = -37.526883385388 | etot = -30.9206805121875 +193000 ekin = 2.65091164661301 | erot = 3.82754219131902 | epot = -37.4213833049326 | etot = -30.9429294670006 +194000 ekin = 2.55372434146215 | erot = 3.81228833556049 | epot = -37.3433541779816 | etot = -30.977341500959 +195000 ekin = 2.54515296633922 | erot = 3.77157425987472 | epot = -37.2550689450336 | etot = -30.9383417188196 +196000 ekin = 2.57228739351393 | erot = 3.48448370430655 | epot = -37.1707275909677 | etot = -31.1139564931472 +197000 ekin = 2.47659034250743 | erot = 3.31788075232347 | epot = -37.1125490303323 | etot = -31.3180779355014 +198000 ekin = 2.47817611131623 | erot = 3.41593598489791 | epot = -37.0628542395745 | etot = -31.1687421433604 +199000 ekin = 2.46398696321861 | erot = 3.79330738397083 | epot = -37.0410272717131 | etot = -30.7837329245237 +200000 ekin = 2.66032750534619 | erot = 3.50045834258033 | epot = -37.0560186461538 | etot = -30.8952327982273 +201000 ekin = 2.82925423269724 | erot = 3.87280363693036 | epot = -37.1094527749141 | etot = -30.4073949052865 +202000 ekin = 2.87690134773435 | erot = 3.73724666810631 | epot = -37.1548849140444 | etot = -30.5407368982037 +203000 ekin = 3.09789929071291 | erot = 3.54687635269494 | epot = -37.1913390618662 | etot = -30.5465634184584 +204000 ekin = 3.2249783082041 | erot = 3.52082166300909 | epot = -37.2064645595876 | etot = -30.4606645883744 +205000 ekin = 3.08968228459873 | erot = 3.62768693137654 | epot = -37.2539593887052 | etot = -30.5365901727299 +206000 ekin = 3.1101415017481 | erot = 3.73856786590981 | epot = -37.3166778706669 | etot = -30.467968503009 +207000 ekin = 3.1829453735338 | erot = 4.25652712659376 | epot = -37.3463184168161 | etot = -29.9068459166886 +208000 ekin = 3.18396090757444 | erot = 4.43896014450663 | epot = -37.3566061410102 | etot = -29.7336850889291 +209000 ekin = 3.31348354672045 | erot = 3.97662877739679 | epot = -37.3764215045056 | etot = -30.0863091803884 +210000 ekin = 3.17486958285119 | erot = 3.68714944924489 | epot = -37.3622513109274 | etot = -30.5002322788313 +211000 ekin = 3.2477738173839 | erot = 3.39112189744197 | epot = -37.3847088569504 | etot = -30.7458131421245 +212000 ekin = 3.12182354729226 | erot = 3.15133571404853 | epot = -37.4262282165348 | etot = -31.153068955194 +213000 ekin = 3.1232309019731 | erot = 3.03298058440268 | epot = -37.4993866522035 | etot = -31.3431751658277 +214000 ekin = 3.02782055391866 | erot = 3.5189307426383 | epot = -37.618739888869 | etot = -31.071988592312 +215000 ekin = 3.08902625374254 | erot = 3.62054952513122 | epot = -37.8003692924875 | etot = -31.0907935136138 +216000 ekin = 3.0402918166672 | erot = 4.36545701920737 | epot = -38.0086846511918 | etot = -30.6029358153172 +217000 ekin = 3.11869416684308 | erot = 4.23835788568589 | epot = -38.1755180741878 | etot = -30.8184660216589 +218000 ekin = 3.12136726795473 | erot = 3.99627368131625 | epot = -38.3382201370155 | etot = -31.2205791877445 +219000 ekin = 3.2474996523994 | erot = 4.03289859762084 | epot = -38.4910930976405 | etot = -31.2106948476203 +220000 ekin = 3.1973165065664 | erot = 4.16726840142166 | epot = -38.6410163306451 | etot = -31.276431422657 +221000 ekin = 3.14591003185424 | erot = 4.4764367328117 | epot = -38.780722121156 | etot = -31.15837535649 +222000 ekin = 3.06194834255767 | erot = 4.40957176775797 | epot = -38.8960295960944 | etot = -31.4245094857787 +223000 ekin = 3.09392792198335 | erot = 4.36929377800867 | epot = -38.9696160320109 | etot = -31.5063943320188 +224000 ekin = 3.18434099924865 | erot = 4.674141260581 | epot = -39.0019773177328 | etot = -31.1434950579031 +225000 ekin = 3.26887097312573 | erot = 4.32849031089069 | epot = -39.0446790784002 | etot = -31.4473177943838 +226000 ekin = 3.21195731331512 | erot = 5.11387401999741 | epot = -39.0947841174991 | etot = -30.7689527841866 +227000 ekin = 3.12036258026498 | erot = 5.06347912205044 | epot = -39.0762383614625 | etot = -30.8923966591471 +228000 ekin = 3.09996729726213 | erot = 5.29564700287486 | epot = -39.0208988713251 | etot = -30.6252845711881 +229000 ekin = 3.03897933795902 | erot = 5.24780237112332 | epot = -38.9575212211327 | etot = -30.6707395120503 +230000 ekin = 3.00051887289146 | erot = 4.62162674048183 | epot = -38.9098464143818 | etot = -31.2877008010086 +231000 ekin = 2.91912781370872 | erot = 4.16321547565937 | epot = -38.8503568044396 | etot = -31.7680135150715 +232000 ekin = 2.80548407611275 | erot = 4.26963451717891 | epot = -38.7971045932123 | etot = -31.7219859999206 +233000 ekin = 2.921352071703 | erot = 4.30663886521625 | epot = -38.7943069633021 | etot = -31.5663160263829 +234000 ekin = 2.8987567571007 | erot = 4.15218445741161 | epot = -38.7953536145697 | etot = -31.7444124000574 +235000 ekin = 2.99243729544443 | erot = 3.66858116296993 | epot = -38.7881689836612 | etot = -32.1271505252468 +236000 ekin = 3.05722012426337 | erot = 3.77007572255967 | epot = -38.8307946718328 | etot = -32.0034988250098 +237000 ekin = 2.93797686036748 | erot = 4.00589644921927 | epot = -38.929946515337 | etot = -31.9860732057502 +238000 ekin = 2.9414435200925 | erot = 3.88111097233617 | epot = -39.0498657472631 | etot = -32.2273112548344 +239000 ekin = 3.10382951223872 | erot = 3.96380163382871 | epot = -39.1526703213401 | etot = -32.0850391752727 +240000 ekin = 3.05998182778604 | erot = 4.32395093282883 | epot = -39.2052189603879 | etot = -31.821286199773 +241000 ekin = 3.07091800265519 | erot = 4.10063821004074 | epot = -39.2356744872187 | etot = -32.0641182745228 +242000 ekin = 2.97211136503677 | erot = 4.19271702506013 | epot = -39.2591861941867 | etot = -32.0943578040898 +243000 ekin = 2.88784895332253 | erot = 4.01063377556442 | epot = -39.2721844581366 | etot = -32.3737017292496 +244000 ekin = 2.72034159299267 | erot = 3.9497078953668 | epot = -39.2969463203695 | etot = -32.62689683201 +245000 ekin = 2.73288139378783 | erot = 4.29552525608627 | epot = -39.3467303394195 | etot = -32.3183236895454 +246000 ekin = 2.68282749729218 | erot = 4.43958709181175 | epot = -39.4036850899301 | etot = -32.2812705008262 +247000 ekin = 2.73156079717717 | erot = 4.29997633507683 | epot = -39.4831744493476 | etot = -32.4516373170936 +248000 ekin = 2.71615239962776 | erot = 4.48384110145867 | epot = -39.5625690361122 | etot = -32.3625755350257 +249000 ekin = 2.72571373834881 | erot = 4.5335019483569 | epot = -39.6161562336935 | etot = -32.3569405469878 +250000 ekin = 2.67302825179683 | erot = 5.17929377782009 | epot = -39.6758534551748 | etot = -31.8235314255579 +251000 ekin = 2.6507365898703 | erot = 5.39364408144172 | epot = -39.7013652486056 | etot = -31.6569845772935 +252000 ekin = 2.81604561937354 | erot = 5.50799647083842 | epot = -39.6939189845586 | etot = -31.3698768943466 +253000 ekin = 2.83629985586585 | erot = 4.91166111825379 | epot = -39.6825773475315 | etot = -31.9346163734119 +254000 ekin = 2.79908189634044 | erot = 4.88281944777383 | epot = -39.6620010988144 | etot = -31.9800997547001 +255000 ekin = 2.84238496514409 | erot = 4.79166487708097 | epot = -39.6680683880925 | etot = -32.0340185458674 +256000 ekin = 2.82611571908347 | erot = 4.38756969310712 | epot = -39.7220228798985 | etot = -32.5083374677079 +257000 ekin = 2.78077325096871 | erot = 4.5642639453855 | epot = -39.7657957602323 | etot = -32.420758563878 +258000 ekin = 2.84466353932841 | erot = 4.94939241805645 | epot = -39.7743058264474 | etot = -31.9802498690625 +259000 ekin = 2.82994372921754 | erot = 4.84156348043289 | epot = -39.7845084321782 | etot = -32.1130012225278 +260000 ekin = 2.84769599243485 | erot = 4.63369709433921 | epot = -39.8060470464454 | etot = -32.3246539596713 +261000 ekin = 2.87237157835352 | erot = 4.51865061212279 | epot = -39.7979847736537 | etot = -32.4069625831774 +262000 ekin = 2.96750612225965 | erot = 4.57561390426948 | epot = -39.7782660470083 | etot = -32.2351460204792 +263000 ekin = 2.9928936584238 | erot = 4.20953311292943 | epot = -39.7453211677642 | etot = -32.542894396411 +264000 ekin = 3.02610258005868 | erot = 4.41804994162532 | epot = -39.7005266944526 | etot = -32.2563741727686 +265000 ekin = 3.02210011112739 | erot = 4.29011549844082 | epot = -39.6578667285885 | etot = -32.3456511190202 +266000 ekin = 2.9552602997359 | erot = 3.9722013360736 | epot = -39.586314373395 | etot = -32.6588527375855 +267000 ekin = 2.96306286479368 | erot = 4.39982365552042 | epot = -39.5117362736935 | etot = -32.1488497533794 +268000 ekin = 2.98837918599768 | erot = 4.59043107838106 | epot = -39.4346030266013 | etot = -31.8557927622225 +269000 ekin = 2.92733730866694 | erot = 4.81492520489307 | epot = -39.3017884762547 | etot = -31.5595259626947 +270000 ekin = 2.90335610024247 | erot = 4.98515255872076 | epot = -39.1437745457484 | etot = -31.2552658867851 +271000 ekin = 2.87611923369216 | erot = 5.02631285080427 | epot = -38.9919498909516 | etot = -31.0895178064552 +272000 ekin = 2.8777026077458 | erot = 4.83651556609768 | epot = -38.8408093950138 | etot = -31.1265912211703 +273000 ekin = 2.77329089721161 | erot = 4.69693225863749 | epot = -38.6610493537941 | etot = -31.190826197945 +274000 ekin = 2.68625637002646 | erot = 4.51669986790578 | epot = -38.450972898294 | etot = -31.2480166603618 +275000 ekin = 2.6033032445429 | erot = 4.20171703621303 | epot = -38.2182499356279 | etot = -31.413229654872 +276000 ekin = 2.57183076311405 | erot = 3.79152446287658 | epot = -38.0174336495132 | etot = -31.6540784235226 +277000 ekin = 2.49975386368552 | erot = 3.59614150828643 | epot = -37.8474968832234 | etot = -31.7516015112514 +278000 ekin = 2.46398069339692 | erot = 3.65098267442651 | epot = -37.6582057642292 | etot = -31.5432423964058 +279000 ekin = 2.48339824565301 | erot = 3.67548575635043 | epot = -37.5048702413578 | etot = -31.3459862393543 +280000 ekin = 2.53376634761115 | erot = 3.55656380463993 | epot = -37.3937621487775 | etot = -31.3034319965264 +281000 ekin = 2.67002406168555 | erot = 3.81689537677439 | epot = -37.3207483356567 | etot = -30.8338288971967 +282000 ekin = 2.63534042744469 | erot = 3.62617225051201 | epot = -37.2561498174831 | etot = -30.9946371395264 +283000 ekin = 2.6220496059321 | erot = 3.60063437351299 | epot = -37.1865464899412 | etot = -30.9638625104961 +284000 ekin = 2.67681575008794 | erot = 3.61566503901023 | epot = -37.1459845078296 | etot = -30.8535037187314 +285000 ekin = 2.71360352201128 | erot = 3.48822466196441 | epot = -37.1436040722677 | etot = -30.941775888292 +286000 ekin = 2.72409949367879 | erot = 3.69046973300079 | epot = -37.1515114688671 | etot = -30.7369422421875 +287000 ekin = 2.78141221541732 | erot = 3.56169254019539 | epot = -37.1836412585713 | etot = -30.8405365029586 +288000 ekin = 2.93111949257226 | erot = 3.8525227571685 | epot = -37.2722312757955 | etot = -30.4885890260548 +289000 ekin = 3.22039073654125 | erot = 3.65796134125549 | epot = -37.4105935842029 | etot = -30.5322415064062 +290000 ekin = 3.45543672952192 | erot = 3.63587074171854 | epot = -37.5601919395408 | etot = -30.4688844683004 +291000 ekin = 3.52760878967926 | erot = 4.20430698093698 | epot = -37.7322836777775 | etot = -30.0003679071612 +292000 ekin = 3.68972381818942 | erot = 4.12076553978665 | epot = -37.9100323199299 | etot = -30.0995429619539 +293000 ekin = 3.83177225674892 | erot = 4.37726484522697 | epot = -38.0821109906697 | etot = -29.8730738886939 +294000 ekin = 4.06640459910211 | erot = 3.74462680595297 | epot = -38.1926156973085 | etot = -30.3815842922535 +295000 ekin = 4.21784736111078 | erot = 3.82616484716752 | epot = -38.2890286287625 | etot = -30.2450164204842 +296000 ekin = 4.26440738773668 | erot = 3.95694734709923 | epot = -38.3824567525616 | etot = -30.1611020177257 +297000 ekin = 4.04618321058719 | erot = 4.11344152769709 | epot = -38.4823151027027 | etot = -30.3226903644185 +298000 ekin = 4.04534420229663 | erot = 4.08413503201891 | epot = -38.5648464298591 | etot = -30.4353671955436 +299000 ekin = 4.0589099673587 | erot = 4.75454163668515 | epot = -38.639463237644 | etot = -29.8260116336001 +300000 ekin = 4.06355522455796 | erot = 4.46292256841625 | epot = -38.7062117520832 | etot = -30.179733959109 +301000 ekin = 4.01853385887688 | erot = 4.67242188374982 | epot = -38.7555551980343 | etot = -30.0645994554076 +302000 ekin = 3.97170308302913 | erot = 4.62245717998414 | epot = -38.7884989680142 | etot = -30.194338705001 +303000 ekin = 4.00670279913523 | erot = 4.89772983741929 | epot = -38.799236313657 | etot = -29.8948036771024 +304000 ekin = 3.81374525151692 | erot = 4.6538936598735 | epot = -38.8327396351166 | etot = -30.3651007237262 +305000 ekin = 3.70792918499072 | erot = 4.53646691129901 | epot = -38.8671341843092 | etot = -30.6227380880195 +306000 ekin = 3.58519135856873 | erot = 4.40317156262038 | epot = -38.8961174826077 | etot = -30.9077545614186 +307000 ekin = 3.52830601019332 | erot = 4.12955816022909 | epot = -38.9381266871201 | etot = -31.2802625166977 +308000 ekin = 3.37444573697916 | erot = 3.65266283146942 | epot = -38.9820449321945 | etot = -31.9549363637459 +309000 ekin = 3.29877896595905 | erot = 4.06788139443827 | epot = -39.0365696198577 | etot = -31.6699092594604 +310000 ekin = 3.27216182566108 | erot = 3.86752279813189 | epot = -39.0649343092171 | etot = -31.9252496854241 +311000 ekin = 3.26050147382307 | erot = 3.90928978323579 | epot = -39.0580520931933 | etot = -31.8882608361345 +312000 ekin = 3.1848300908952 | erot = 3.90959546619215 | epot = -39.0257212693578 | etot = -31.9312957122705 +313000 ekin = 3.09609326591794 | erot = 3.75025646421268 | epot = -38.9535227577836 | etot = -32.107173027653 +314000 ekin = 2.95184537018541 | erot = 4.07381717812352 | epot = -38.8888909934781 | etot = -31.8632284451692 +315000 ekin = 2.92238623527564 | erot = 3.96815066682756 | epot = -38.8370494801766 | etot = -31.9465125780734 +316000 ekin = 2.71301507861594 | erot = 3.8080797893295 | epot = -38.7998345743978 | etot = -32.2787397064523 +317000 ekin = 2.71357150367643 | erot = 4.15190966526588 | epot = -38.7626719044114 | etot = -31.8971907354691 +318000 ekin = 2.62158267835355 | erot = 4.27134701113463 | epot = -38.7271070788674 | etot = -31.8341773893792 +319000 ekin = 2.55366548062856 | erot = 4.41350408683224 | epot = -38.7297464727615 | etot = -31.7625769053007 +320000 ekin = 2.4339724053854 | erot = 4.29070167476865 | epot = -38.7203908826319 | etot = -31.9957168024778 +321000 ekin = 2.40916961938935 | erot = 4.08120981437149 | epot = -38.7041016741434 | etot = -32.2137222403825 +322000 ekin = 2.40921951438688 | erot = 3.84656254092896 | epot = -38.6896664254557 | etot = -32.4338843701398 +323000 ekin = 2.47763175846145 | erot = 3.74024157191546 | epot = -38.6582034756257 | etot = -32.4403301452488 +324000 ekin = 2.50557286685252 | erot = 3.62726015904503 | epot = -38.6277589097221 | etot = -32.4949258838246 +325000 ekin = 2.46128003790462 | erot = 3.30955838055067 | epot = -38.61822105265 | etot = -32.8473826341947 +326000 ekin = 2.50360422224121 | erot = 3.11309077075955 | epot = -38.6155228491476 | etot = -32.9988278561469 +327000 ekin = 2.58559564340003 | erot = 3.03172964208493 | epot = -38.6235874334491 | etot = -33.0062621479641 +328000 ekin = 2.74984266079838 | erot = 3.02808338407911 | epot = -38.6550386035093 | etot = -32.8771125586319 +329000 ekin = 2.91966436364505 | erot = 2.9714434817756 | epot = -38.682045485323 | etot = -32.7909376399024 +330000 ekin = 3.01494295487819 | erot = 3.4413838499053 | epot = -38.7383158304585 | etot = -32.281989025675 +331000 ekin = 3.02442201542022 | erot = 3.78657407910222 | epot = -38.7939596216319 | etot = -31.9829635271095 +332000 ekin = 3.04445691127431 | erot = 3.82788901953126 | epot = -38.8517978078765 | etot = -31.9794518770709 +333000 ekin = 3.03465557138393 | erot = 3.68623317701479 | epot = -38.9019287356725 | etot = -32.1810399872737 +334000 ekin = 2.9809147586341 | erot = 3.87909097065051 | epot = -38.9429458678103 | etot = -32.0829401385257 +335000 ekin = 3.18730692360922 | erot = 3.92298153235814 | epot = -38.9915367606723 | etot = -31.8812483047049 +336000 ekin = 3.28082580011875 | erot = 4.25501923477967 | epot = -39.038294903881 | etot = -31.5024498689825 +337000 ekin = 3.33075954016491 | erot = 4.58632261209059 | epot = -39.0662594017921 | etot = -31.1491772495366 +338000 ekin = 3.31328438683341 | erot = 4.17966745642972 | epot = -39.0415239975115 | etot = -31.5485721542484 +339000 ekin = 3.33917527804132 | erot = 4.28130062815465 | epot = -38.9842917012714 | etot = -31.3638157950754 +340000 ekin = 3.33492148280264 | erot = 4.35651035139105 | epot = -38.8943885223068 | etot = -31.2029566881131 +341000 ekin = 3.3461417209637 | erot = 4.05115720989158 | epot = -38.7823758155587 | etot = -31.3850768847035 +342000 ekin = 3.34251507796689 | erot = 4.42814474655732 | epot = -38.6331517957714 | etot = -30.8624919712472 +343000 ekin = 3.20631341754623 | erot = 3.78967989344565 | epot = -38.4960486393224 | etot = -31.5000553283305 +344000 ekin = 3.07148244251166 | erot = 3.87583965670226 | epot = -38.3948328820768 | etot = -31.4475107828629 +345000 ekin = 3.09789874291718 | erot = 3.9946056524089 | epot = -38.3201974875894 | etot = -31.2276930922633 +346000 ekin = 3.0250008126834 | erot = 3.91508207831934 | epot = -38.2750630613601 | etot = -31.3349801703574 +347000 ekin = 2.94406849477781 | erot = 3.86229670162422 | epot = -38.2289722622904 | etot = -31.4226070658884 +348000 ekin = 2.95641250006446 | erot = 3.72625853383758 | epot = -38.1919210104045 | etot = -31.5092499765025 +349000 ekin = 3.03918076184492 | erot = 3.94202050743572 | epot = -38.1810668298085 | etot = -31.1998655605279 +350000 ekin = 3.09062612520409 | erot = 3.91215331884796 | epot = -38.2023245264387 | etot = -31.1995450823866 +351000 ekin = 3.13831719496483 | erot = 3.99916602553205 | epot = -38.2111529945909 | etot = -31.073669774094 +352000 ekin = 3.10196313130359 | erot = 3.92254342354132 | epot = -38.2543166357449 | etot = -31.2298100809 +353000 ekin = 3.17266611312447 | erot = 3.8947350963975 | epot = -38.3205511283306 | etot = -31.2531499188087 +354000 ekin = 3.20288707130899 | erot = 4.38957454856388 | epot = -38.3888699269269 | etot = -30.7964083070541 +355000 ekin = 3.15965957595978 | erot = 4.27393537405648 | epot = -38.4369161779509 | etot = -31.0033212279347 +356000 ekin = 3.01967844026133 | erot = 4.46559381130412 | epot = -38.4622452099032 | etot = -30.9769729583378 +357000 ekin = 2.97836465744991 | erot = 4.24123654484996 | epot = -38.4340474220208 | etot = -31.214446219721 +358000 ekin = 2.90298621775697 | erot = 4.00214290087714 | epot = -38.3669225243922 | etot = -31.4617934057581 +359000 ekin = 2.89703951576617 | erot = 3.75540528896971 | epot = -38.2596281019021 | etot = -31.6071832971662 +360000 ekin = 2.8951746897939 | erot = 3.69844688179068 | epot = -38.1408983158929 | etot = -31.5472767443083 +361000 ekin = 2.80138616808281 | erot = 3.38323529451493 | epot = -38.0246589917389 | etot = -31.8400375291412 +362000 ekin = 2.77162168417597 | erot = 2.91331523066534 | epot = -37.9398868290147 | etot = -32.2549499141734 +363000 ekin = 2.78539815378419 | erot = 2.68460040337592 | epot = -37.8665635409936 | etot = -32.3965649838335 +364000 ekin = 2.68067812192279 | erot = 2.78677391239245 | epot = -37.7617899033782 | etot = -32.2943378690629 +365000 ekin = 2.54070043685867 | erot = 2.83653994835764 | epot = -37.6554311404473 | etot = -32.278190755231 +366000 ekin = 2.41606481092133 | erot = 2.86609766611194 | epot = -37.5516282283376 | etot = -32.2694657513043 +367000 ekin = 2.46811866465482 | erot = 3.34221140329001 | epot = -37.4475028758825 | etot = -31.6371728079377 +368000 ekin = 2.42926223365496 | erot = 3.33046663396731 | epot = -37.3674460967944 | etot = -31.6077172291721 +369000 ekin = 2.43816169312797 | erot = 3.26459431026922 | epot = -37.3019788371043 | etot = -31.5992228337071 +370000 ekin = 2.46038177337534 | erot = 3.10066469966258 | epot = -37.2626057339964 | etot = -31.7015592609585 +371000 ekin = 2.4406243852624 | erot = 2.87778487491552 | epot = -37.2539180634396 | etot = -31.9355088032617 +372000 ekin = 2.41196438326736 | erot = 3.07515188922142 | epot = -37.3089635753533 | etot = -31.8218473028645 +373000 ekin = 2.48050565170792 | erot = 3.18196875652289 | epot = -37.4397878357734 | etot = -31.7773134275426 +374000 ekin = 2.6353068806194 | erot = 3.59156982435214 | epot = -37.5884648424034 | etot = -31.3615881374319 +375000 ekin = 2.68283894448276 | erot = 3.32451084068228 | epot = -37.7715422578283 | etot = -31.7641924726633 +376000 ekin = 2.79488034579927 | erot = 3.22988532668866 | epot = -38.000903910215 | etot = -31.976138237727 +377000 ekin = 2.97793932778653 | erot = 3.14879447385383 | epot = -38.2360750185569 | etot = -32.1093412169166 +378000 ekin = 3.04959845592839 | erot = 3.49481966296078 | epot = -38.5013695235685 | etot = -31.9569514046793 +379000 ekin = 3.1910641072712 | erot = 3.36561045250094 | epot = -38.7688607813369 | etot = -32.2121862215648 +380000 ekin = 3.25183572215737 | erot = 3.58875776192786 | epot = -39.0288452181145 | etot = -32.1882517340293 +381000 ekin = 3.33794215221605 | erot = 3.6933917756671 | epot = -39.3017064605084 | etot = -32.2703725326252 +382000 ekin = 3.49270190624151 | erot = 3.86829998834037 | epot = -39.5268729273467 | etot = -32.1658710327648 +383000 ekin = 3.55662169084786 | erot = 3.53333329088014 | epot = -39.7267791075158 | etot = -32.6368241257878 +384000 ekin = 3.69351012028553 | erot = 3.28268730044342 | epot = -39.878987472358 | etot = -32.9027900516291 +385000 ekin = 3.6873370603751 | erot = 3.68055641648018 | epot = -39.9998839253488 | etot = -32.6319904484935 +386000 ekin = 3.71694831249288 | erot = 3.79434784508072 | epot = -40.0869801892987 | etot = -32.5756840317251 +387000 ekin = 3.76861509268675 | erot = 3.88558369375098 | epot = -40.1715737743674 | etot = -32.5173749879297 +388000 ekin = 3.83017606883369 | erot = 4.20859412334364 | epot = -40.2007323597246 | etot = -32.1619621675473 +389000 ekin = 3.86768485031755 | erot = 3.99003783907115 | epot = -40.1899129305041 | etot = -32.3321902411154 +390000 ekin = 3.97485559059836 | erot = 3.73907035926323 | epot = -40.1534652302145 | etot = -32.4395392803529 +391000 ekin = 3.99255423920733 | erot = 3.4598541410162 | epot = -40.0955220791988 | etot = -32.6431136989752 +392000 ekin = 4.01983776245659 | erot = 3.68425742647522 | epot = -39.9999647918603 | etot = -32.2958696029285 +393000 ekin = 4.02356764424238 | erot = 3.83787437414739 | epot = -39.8549016020689 | etot = -31.9934595836791 +394000 ekin = 3.93980876114311 | erot = 3.99211744164141 | epot = -39.7011477670265 | etot = -31.769221564242 +395000 ekin = 4.11174368478708 | erot = 3.75033473410268 | epot = -39.5451859148434 | etot = -31.6831074959536 +396000 ekin = 4.20376876107151 | erot = 3.67040632781378 | epot = -39.3948809980869 | etot = -31.5207059092016 +397000 ekin = 4.1363357284298 | erot = 3.65151581957621 | epot = -39.2564297317577 | etot = -31.4685781837517 +398000 ekin = 4.13905245601608 | erot = 3.71620600673377 | epot = -39.093596770216 | etot = -31.2383383074661 +399000 ekin = 4.10332411545508 | erot = 3.71374971681594 | epot = -38.9205234935041 | etot = -31.1034496612331 +400000 ekin = 4.0676601690846 | erot = 3.4213950465438 | epot = -38.7497473150008 | etot = -31.2606920993724 +401000 ekin = 3.9728416411198 | erot = 3.81120481171758 | epot = -38.6001977504162 | etot = -30.8161512975788 +402000 ekin = 3.90587383547448 | erot = 3.5341882621858 | epot = -38.4681757167875 | etot = -31.0281136191273 +403000 ekin = 3.91259869514543 | erot = 3.637386391841 | epot = -38.3230308363683 | etot = -30.7730457493819 +404000 ekin = 3.79936006877817 | erot = 3.32641249272551 | epot = -38.2009092385688 | etot = -31.0751366770651 +405000 ekin = 3.82517596801147 | erot = 3.13064904024263 | epot = -38.1553776059003 | etot = -31.1995525976462 +406000 ekin = 3.73725599382596 | erot = 3.08306268157758 | epot = -38.1316917306566 | etot = -31.3113730552531 +407000 ekin = 3.72651775045891 | erot = 3.09861818078628 | epot = -38.1634910279952 | etot = -31.33835509675 +408000 ekin = 3.79931976439455 | erot = 3.25718386016379 | epot = -38.2217683212397 | etot = -31.1652646966813 +409000 ekin = 3.95093187918723 | erot = 3.43950409776017 | epot = -38.2689453197332 | etot = -30.8785093427858 +410000 ekin = 4.07121708138893 | erot = 3.83760071106065 | epot = -38.3189798432044 | etot = -30.4101620507548 +411000 ekin = 4.2330797855817 | erot = 3.98162063698068 | epot = -38.3721329673505 | etot = -30.1574325447882 +412000 ekin = 4.24117080814308 | erot = 3.9973719347696 | epot = -38.4124767699444 | etot = -30.1739340270317 +413000 ekin = 4.23580670923557 | erot = 3.81064398502802 | epot = -38.4212920990953 | etot = -30.3748414048317 +414000 ekin = 4.27445938143094 | erot = 3.98124541320507 | epot = -38.4106571527343 | etot = -30.1549523580983 +415000 ekin = 4.388994790051 | erot = 3.80279226112407 | epot = -38.3596783722966 | etot = -30.1678913211216 +416000 ekin = 4.45628965411069 | erot = 3.63102956113301 | epot = -38.3042311126169 | etot = -30.2169118973732 +417000 ekin = 4.49028461121071 | erot = 3.62754419666011 | epot = -38.2583198089302 | etot = -30.1404910010594 +418000 ekin = 4.45936601962006 | erot = 3.71144506663867 | epot = -38.1813464675299 | etot = -30.0105353812712 +419000 ekin = 4.38379837521009 | erot = 3.33513327030929 | epot = -38.0724868069421 | etot = -30.3535551614227 +420000 ekin = 4.283111933024 | erot = 3.09826419668627 | epot = -37.9370678690099 | etot = -30.5556917392996 +421000 ekin = 4.15248097510599 | erot = 3.56237827808249 | epot = -37.7709210423884 | etot = -30.0560617891999 +422000 ekin = 3.95490687211586 | erot = 3.47480957997355 | epot = -37.5854884820711 | etot = -30.1557720299817 +423000 ekin = 3.91714305790352 | erot = 3.48476286323411 | epot = -37.3949936437695 | etot = -29.9930877226319 +424000 ekin = 3.84213202460282 | erot = 3.52777059768047 | epot = -37.2158434462619 | etot = -29.8459408239786 +425000 ekin = 3.71924289661379 | erot = 3.3366360966062 | epot = -37.0722526001231 | etot = -30.0163736069031 +426000 ekin = 3.64441997260638 | erot = 3.3622793544102 | epot = -36.9667678357552 | etot = -29.9600685087386 +427000 ekin = 3.75655721345773 | erot = 3.37897054079372 | epot = -36.8611280898054 | etot = -29.725600335554 +428000 ekin = 3.74409443646511 | erot = 3.17732872354239 | epot = -36.742715037602 | etot = -29.8212918775945 +429000 ekin = 3.66329028317848 | erot = 2.78764787478689 | epot = -36.6486255145436 | etot = -30.1976873565782 +430000 ekin = 3.62135290496431 | erot = 2.67337975160585 | epot = -36.5606041515419 | etot = -30.2658714949718 +431000 ekin = 3.61616361793039 | erot = 2.69754710014207 | epot = -36.506732939117 | etot = -30.1930222210445 +432000 ekin = 3.49552617760814 | erot = 3.08491352170466 | epot = -36.485170074763 | etot = -29.9047303754502 +433000 ekin = 3.58020816083934 | erot = 2.88002256286323 | epot = -36.5217696117553 | etot = -30.0615388880528 +434000 ekin = 3.59867849318961 | erot = 3.08407973313556 | epot = -36.6202495320039 | etot = -29.9374913056787 +435000 ekin = 3.67331527289028 | erot = 3.42657552434431 | epot = -36.7488916307825 | etot = -29.6490008335479 +436000 ekin = 3.82088042289265 | erot = 3.6544744236991 | epot = -36.9085622220518 | etot = -29.4332073754601 +437000 ekin = 3.8686942167376 | erot = 3.9547028707988 | epot = -37.0720316005958 | etot = -29.2486345130594 +438000 ekin = 4.11090595842079 | erot = 3.77540801446856 | epot = -37.2088542252226 | etot = -29.3225402523332 +439000 ekin = 4.12926159073598 | erot = 4.06917140325898 | epot = -37.3517590512211 | etot = -29.1533260572261 +440000 ekin = 4.09029177261519 | erot = 4.1498129956529 | epot = -37.4912988817269 | etot = -29.2511941134589 +441000 ekin = 4.14485979348676 | erot = 4.37283240826401 | epot = -37.6181493098546 | etot = -29.1004571081038 +442000 ekin = 4.12304009572835 | erot = 4.39045893698218 | epot = -37.7155315750663 | etot = -29.2020325423558 +443000 ekin = 4.23471751438722 | erot = 4.14989601608929 | epot = -37.768614271265 | etot = -29.3840007407884 +444000 ekin = 4.35772646838213 | erot = 4.52232474512896 | epot = -37.7816885908051 | etot = -28.901637377294 +445000 ekin = 4.39118784053251 | erot = 4.66570824296103 | epot = -37.7439950146597 | etot = -28.6870989311661 +446000 ekin = 4.3967592176502 | erot = 4.46936063153373 | epot = -37.6960851354907 | etot = -28.8299652863068 +447000 ekin = 4.35336664890431 | erot = 4.44173113672768 | epot = -37.6140263912413 | etot = -28.8189286056093 +448000 ekin = 4.28498441172967 | erot = 4.19781838322426 | epot = -37.5090341348628 | etot = -29.0262313399088 +449000 ekin = 4.31763982219639 | erot = 4.52832551746767 | epot = -37.408401745433 | etot = -28.562436405769 +450000 ekin = 4.34138928411246 | erot = 4.4425856403743 | epot = -37.3062489259439 | etot = -28.5222740014571 +451000 ekin = 4.30985185878589 | erot = 4.23825662962939 | epot = -37.1459619150062 | etot = -28.5978534265909 +452000 ekin = 4.32592045036082 | erot = 3.86602766630272 | epot = -36.9847035634509 | etot = -28.7927554467874 +453000 ekin = 4.32845268851047 | erot = 3.54171363095611 | epot = -36.8340779762826 | etot = -28.963911656816 +454000 ekin = 4.31011457813686 | erot = 3.79537837348586 | epot = -36.7199830616561 | etot = -28.6144901100334 +455000 ekin = 4.29550433639196 | erot = 3.85241036204662 | epot = -36.6489739160373 | etot = -28.5010592175987 +456000 ekin = 4.37032742709179 | erot = 4.00721124204766 | epot = -36.6190063800959 | etot = -28.2414677109564 +457000 ekin = 4.3642647028677 | erot = 3.8563715204494 | epot = -36.5969553476855 | etot = -28.3763191243684 +458000 ekin = 4.32567014378598 | erot = 3.50123530464571 | epot = -36.5630453883139 | etot = -28.7361399398822 +459000 ekin = 4.38933815738648 | erot = 3.57401843708542 | epot = -36.5693343587045 | etot = -28.6059777642326 +460000 ekin = 4.31317855607471 | erot = 4.09613513000604 | epot = -36.622903135654 | etot = -28.2135894495732 +461000 ekin = 4.31811012640158 | erot = 4.38273826542212 | epot = -36.7024780237704 | etot = -28.0016296319467 +462000 ekin = 4.3366863876999 | erot = 4.51374491218818 | epot = -36.8227361919452 | etot = -27.9723048920571 +463000 ekin = 4.27564269849647 | erot = 4.86202296781308 | epot = -36.9415310835087 | etot = -27.8038654171991 +464000 ekin = 4.2570485657353 | erot = 4.74085846897254 | epot = -37.0390079052473 | etot = -28.0411008705395 +465000 ekin = 4.27536374407081 | erot = 4.49932366093901 | epot = -37.1090432428535 | etot = -28.3343558378437 +466000 ekin = 4.30607368146059 | erot = 4.23786653917903 | epot = -37.1491605127939 | etot = -28.6052202921542 +467000 ekin = 4.24919786200451 | erot = 4.12771930877703 | epot = -37.1714598423966 | etot = -28.7945426716151 +468000 ekin = 4.39683218085583 | erot = 3.85228521386554 | epot = -37.2088712844975 | etot = -28.9597538897762 +469000 ekin = 4.64124419278975 | erot = 3.80754439193715 | epot = -37.2767302220321 | etot = -28.8279416373053 +470000 ekin = 4.66178408905666 | erot = 3.92065938428506 | epot = -37.3876740781877 | etot = -28.805230604846 +471000 ekin = 4.75392904131979 | erot = 4.24739494727089 | epot = -37.5007122646076 | etot = -28.499388276017 +472000 ekin = 4.78287126449286 | erot = 4.29738258008787 | epot = -37.5977046601012 | etot = -28.5174508155204 +473000 ekin = 4.83746609770177 | erot = 4.38666527032479 | epot = -37.6671790710827 | etot = -28.4430477030562 +474000 ekin = 4.79054197671375 | erot = 4.34169424272135 | epot = -37.6856820094294 | etot = -28.5534457899944 +475000 ekin = 4.83235787688145 | erot = 4.2178840657501 | epot = -37.6508263787863 | etot = -28.6005844361548 +476000 ekin = 4.77650421806816 | erot = 4.23519664592594 | epot = -37.5559363402038 | etot = -28.5442354762097 +477000 ekin = 4.70149228687156 | erot = 3.9495520600404 | epot = -37.4316333722385 | etot = -28.7805890253266 +478000 ekin = 4.6582861234462 | erot = 3.52306589214545 | epot = -37.3056353897914 | etot = -29.1242833741998 +479000 ekin = 4.49034904671764 | erot = 3.69691237093671 | epot = -37.1645007343035 | etot = -28.9772393166492 +480000 ekin = 4.42035953830882 | erot = 3.62614880736061 | epot = -36.985533653495 | etot = -28.9390253078256 +481000 ekin = 4.29236052675561 | erot = 3.46283113670748 | epot = -36.7788376766182 | etot = -29.0236460131551 +482000 ekin = 4.24695006747712 | erot = 3.64617122659712 | epot = -36.5783264764334 | etot = -28.6852051823592 +483000 ekin = 4.27724439911408 | erot = 3.65906944039053 | epot = -36.4031794376631 | etot = -28.4668655981585 +484000 ekin = 4.2785974211618 | erot = 3.80998418987602 | epot = -36.2601336102697 | etot = -28.1715519992319 +485000 ekin = 4.2129183719994 | erot = 3.84278230442229 | epot = -36.1415033158633 | etot = -28.0858026394416 +486000 ekin = 3.98392526407069 | erot = 3.69687119417301 | epot = -36.0420007851878 | etot = -28.3612043269441 +487000 ekin = 3.87685523954233 | erot = 3.52087214489101 | epot = -35.979017993688 | etot = -28.5812906092547 +488000 ekin = 3.74675884240033 | erot = 3.80072807053011 | epot = -35.9652058586036 | etot = -28.4177189456731 +489000 ekin = 3.61099051841836 | erot = 4.09702697313296 | epot = -35.988768679933 | etot = -28.2807511883817 +490000 ekin = 3.72073699277812 | erot = 3.89157882585036 | epot = -36.0103724524786 | etot = -28.3980566338501 +491000 ekin = 3.72740917275109 | erot = 4.01795497893011 | epot = -36.0292354570355 | etot = -28.2838713053543 +492000 ekin = 3.67547789628851 | erot = 3.85969822517323 | epot = -36.0430681478951 | etot = -28.5078920264333 +493000 ekin = 3.65198421841216 | erot = 3.75518718738367 | epot = -36.0824152706774 | etot = -28.6752438648816 +494000 ekin = 3.48528219984848 | erot = 3.81535508778541 | epot = -36.142371045584 | etot = -28.8417337579501 +495000 ekin = 3.31359070882194 | erot = 4.11558724766118 | epot = -36.226868438371 | etot = -28.7976904818878 +496000 ekin = 3.27798311005954 | erot = 3.88806115727325 | epot = -36.3363270902382 | etot = -29.1702828229054 +497000 ekin = 3.23000081873801 | erot = 4.53153851783412 | epot = -36.4817201831143 | etot = -28.7201808465422 +498000 ekin = 3.35490986062519 | erot = 4.76314991175258 | epot = -36.6514686581239 | etot = -28.5334088857461 +499000 ekin = 3.39102564180484 | erot = 4.99058516868931 | epot = -36.8025368986549 | etot = -28.4209260881608 +500000 ekin = 3.44319922277983 | erot = 4.29432196305735 | epot = -36.9177193599233 | etot = -29.1801981740861 +501000 ekin = 3.47746008955494 | erot = 4.28994173802794 | epot = -37.0187053512326 | etot = -29.2513035236497 +502000 ekin = 3.58696948456737 | erot = 4.55410136617397 | epot = -37.1018103829438 | etot = -28.9607395322024 +503000 ekin = 3.68317380855577 | erot = 4.60652443433627 | epot = -37.1620776601797 | etot = -28.8723794172877 +504000 ekin = 3.6885205301443 | erot = 4.67783023002248 | epot = -37.2052759454199 | etot = -28.8389251852531 +505000 ekin = 3.88723268453857 | erot = 4.53079850437648 | epot = -37.2950608294682 | etot = -28.8770296405532 +506000 ekin = 3.80925396925157 | erot = 4.47086505886196 | epot = -37.3479933337837 | etot = -29.0678743056702 +507000 ekin = 3.73248519551987 | erot = 4.21393839264126 | epot = -37.4256513139283 | etot = -29.4792277257672 +508000 ekin = 3.8067276018406 | erot = 3.9370807937698 | epot = -37.4951091449467 | etot = -29.7513007493363 +509000 ekin = 3.8008699116461 | erot = 3.74333566662482 | epot = -37.5406480313394 | etot = -29.9964424530685 +510000 ekin = 3.89850649197984 | erot = 3.97775581109479 | epot = -37.5934385426631 | etot = -29.7171762395885 +511000 ekin = 3.81393185765474 | erot = 4.00469160928629 | epot = -37.6349932199755 | etot = -29.8163697530345 +512000 ekin = 3.76843962846378 | erot = 4.34524756747803 | epot = -37.6787808921542 | etot = -29.5650936962124 +513000 ekin = 3.70769437024756 | erot = 4.19222442242662 | epot = -37.7114576947708 | etot = -29.8115389020966 +514000 ekin = 3.65606306228185 | erot = 4.64296237641009 | epot = -37.7095823242884 | etot = -29.4105568855964 +515000 ekin = 3.50522818557459 | erot = 4.47916848114082 | epot = -37.6783049637299 | etot = -29.6939082970145 +516000 ekin = 3.59266443877116 | erot = 5.02978018029486 | epot = -37.647700985069 | etot = -29.0252563660029 +517000 ekin = 3.53729866959076 | erot = 4.95641997732809 | epot = -37.6445412669913 | etot = -29.1508226200724 +518000 ekin = 3.5534169530515 | erot = 4.5751245967427 | epot = -37.6532745224311 | etot = -29.5247329726369 +519000 ekin = 3.61605940841979 | erot = 4.59842321288977 | epot = -37.7181887221252 | etot = -29.5037061008156 +520000 ekin = 3.6600358073691 | erot = 4.52802897844129 | epot = -37.8184531846625 | etot = -29.6303883988521 +521000 ekin = 3.57990395101953 | erot = 4.58686564429516 | epot = -37.9529160430904 | etot = -29.7861464477757 +522000 ekin = 3.587210173505 | erot = 4.78958389957781 | epot = -38.1056938634056 | etot = -29.7288997903228 +523000 ekin = 3.74553748952041 | erot = 4.82242710318173 | epot = -38.2496598519462 | etot = -29.6816952592441 +524000 ekin = 3.83672965572981 | erot = 5.17806255755526 | epot = -38.3420385705453 | etot = -29.3272463572603 +525000 ekin = 3.97426514986081 | erot = 5.13820563111665 | epot = -38.4306455211978 | etot = -29.3181747402203 +526000 ekin = 4.03278131821155 | erot = 4.61480893928533 | epot = -38.4813375347265 | etot = -29.8337472772296 +527000 ekin = 4.15303805139346 | erot = 4.03339974605304 | epot = -38.4813261438673 | etot = -30.2948883464208 +528000 ekin = 4.34085606106398 | erot = 3.6341604993604 | epot = -38.4621670653442 | etot = -30.4871505049199 +529000 ekin = 4.53593485604716 | erot = 3.72087643644196 | epot = -38.4175016483558 | etot = -30.1606903558667 +530000 ekin = 4.6583694532253 | erot = 3.58233700504177 | epot = -38.3861765288021 | etot = -30.145470070535 +531000 ekin = 4.66519878740331 | erot = 3.4109494773408 | epot = -38.3363103504892 | etot = -30.2601620857451 +532000 ekin = 4.80041164317301 | erot = 3.07760528500131 | epot = -38.3151265786574 | etot = -30.4371096504831 +533000 ekin = 4.73180745168962 | erot = 3.06230961560369 | epot = -38.3468719461379 | etot = -30.5527548788445 +534000 ekin = 4.77276572097031 | erot = 3.01963113043194 | epot = -38.4024212860539 | etot = -30.6100244346517 +535000 ekin = 4.85693928494795 | erot = 2.82516321047269 | epot = -38.5360450508863 | etot = -30.8539425554656 +536000 ekin = 4.79265980947601 | erot = 2.9077544610961 | epot = -38.7196748122559 | etot = -31.0192605416837 +537000 ekin = 4.86947955762472 | erot = 3.00989555981226 | epot = -38.9076102830992 | etot = -31.0282351656622 +538000 ekin = 5.00269155741137 | erot = 2.68875189029913 | epot = -39.0473675460743 | etot = -31.3559240983638 +539000 ekin = 4.98226102919755 | erot = 2.92188829969373 | epot = -39.1655668480607 | etot = -31.2614175191695 +540000 ekin = 4.99147016878249 | erot = 3.35574385805744 | epot = -39.2596960810254 | etot = -30.9124820541854 +541000 ekin = 4.92725844601457 | erot = 3.28345034188324 | epot = -39.3089899760125 | etot = -31.0982811881147 +542000 ekin = 4.77242859226878 | erot = 3.31966912230265 | epot = -39.2902384371049 | etot = -31.1981407225335 +543000 ekin = 4.65726157165108 | erot = 3.56099171692951 | epot = -39.1715392323122 | etot = -30.9532859437317 +544000 ekin = 4.75158561074898 | erot = 2.98586301386343 | epot = -39.0000211966265 | etot = -31.2625725720141 +545000 ekin = 4.71389651780209 | erot = 3.29722166624287 | epot = -38.8124009343345 | etot = -30.8012827502895 +546000 ekin = 4.59452933616222 | erot = 3.65785900566392 | epot = -38.6597531372893 | etot = -30.4073647954631 +547000 ekin = 4.49485576841334 | erot = 3.5222715668964 | epot = -38.5261493757312 | etot = -30.5090220404215 +548000 ekin = 4.49472654055116 | erot = 3.49603087938253 | epot = -38.3944216290947 | etot = -30.403664209161 +549000 ekin = 4.39213180937528 | erot = 3.5322876385525 | epot = -38.2774675964381 | etot = -30.3530481485103 +550000 ekin = 4.36283999146778 | erot = 3.787764410361 | epot = -38.2051317998102 | etot = -30.0545273979814 +551000 ekin = 4.3226010693822 | erot = 4.01133252124214 | epot = -38.1611801425639 | etot = -29.8272465519396 +552000 ekin = 4.3318351566455 | erot = 3.98124414472587 | epot = -38.1537721388025 | etot = -29.8406928374311 +553000 ekin = 4.30534974680463 | erot = 3.81209066755031 | epot = -38.1803693007093 | etot = -30.0629288863544 +554000 ekin = 4.29335219580303 | erot = 3.8021354596393 | epot = -38.2389597407396 | etot = -30.1434720852972 +555000 ekin = 4.45825549052375 | erot = 4.03672150414351 | epot = -38.3296083261043 | etot = -29.834631331437 +556000 ekin = 4.63230188756508 | erot = 3.70797489704063 | epot = -38.4795834327919 | etot = -30.1393066481862 +557000 ekin = 4.70622293985813 | erot = 4.51036732636205 | epot = -38.673884289528 | etot = -29.4572940233078 +558000 ekin = 4.70612532334171 | erot = 4.30314260207033 | epot = -38.9099036274271 | etot = -29.9006357020151 +559000 ekin = 4.85842132468142 | erot = 4.45569884582891 | epot = -39.1571701897086 | etot = -29.8430500191982 +560000 ekin = 4.84667483493845 | erot = 4.2909749826348 | epot = -39.3692871188963 | etot = -30.2316373013231 +561000 ekin = 4.93080663772518 | erot = 4.40964672372494 | epot = -39.5560309503474 | etot = -30.2155775888973 +562000 ekin = 5.02786763240476 | erot = 4.09895267825206 | epot = -39.6620959555469 | etot = -30.53527564489 +563000 ekin = 4.99483060861833 | erot = 4.56393029644419 | epot = -39.7001867829014 | etot = -30.1414258778389 +564000 ekin = 5.01292656089539 | erot = 4.46559434127762 | epot = -39.6969046345991 | etot = -30.2183837324261 +565000 ekin = 4.97924499589812 | erot = 4.5676410286713 | epot = -39.6391307119518 | etot = -30.0922446873824 +566000 ekin = 4.80472039327365 | erot = 4.49618530358125 | epot = -39.5320142538579 | etot = -30.231108557003 +567000 ekin = 4.59721417192406 | erot = 4.44898156673779 | epot = -39.3835091139998 | etot = -30.337313375338 +568000 ekin = 4.59948947791999 | erot = 4.21619266891997 | epot = -39.1697350851652 | etot = -30.3540529383253 +569000 ekin = 4.46814520025957 | erot = 4.13625120915532 | epot = -38.9496016480665 | etot = -30.3452052386516 +570000 ekin = 4.6338057410939 | erot = 3.97471689520409 | epot = -38.718728428018 | etot = -30.11020579172 +571000 ekin = 4.51646555902291 | erot = 3.77943581302538 | epot = -38.5103017941539 | etot = -30.2144004221056 +572000 ekin = 4.44329973394615 | erot = 3.73818983971042 | epot = -38.3513010282128 | etot = -30.1698114545562 +573000 ekin = 4.48138796166313 | erot = 3.67030746094229 | epot = -38.2531080005807 | etot = -30.1014125779753 +574000 ekin = 4.57372019352182 | erot = 3.64740839838085 | epot = -38.1563476897671 | etot = -29.9352190978644 +575000 ekin = 4.81962720354443 | erot = 3.58128135189792 | epot = -38.0780197446128 | etot = -29.6771111891705 +576000 ekin = 4.78739960955902 | erot = 3.1694164956898 | epot = -38.0548669136926 | etot = -30.0980508084438 +577000 ekin = 4.89624137933457 | erot = 3.37301453509222 | epot = -38.0581159208701 | etot = -29.7888600064433 +578000 ekin = 4.89993171052275 | erot = 3.39468878464195 | epot = -38.0636938795356 | etot = -29.7690733843709 +579000 ekin = 4.83297661461382 | erot = 3.08572772864728 | epot = -38.0577731810635 | etot = -30.1390688378024 +580000 ekin = 4.77298411404112 | erot = 3.09603380464131 | epot = -38.0675771405195 | etot = -30.198559221837 +581000 ekin = 4.96965435170546 | erot = 3.06610493080439 | epot = -38.0894896837322 | etot = -30.0537304012223 +582000 ekin = 4.84477580774073 | erot = 2.9927320347077 | epot = -38.1047755328767 | etot = -30.2672676904283 +583000 ekin = 4.80184612340932 | erot = 2.99121545039786 | epot = -38.0992283827672 | etot = -30.30616680896 +584000 ekin = 4.73999729115049 | erot = 2.95820256140574 | epot = -38.1193022601922 | etot = -30.421102407636 +585000 ekin = 4.62963491646152 | erot = 2.99096158598537 | epot = -38.1514766562945 | etot = -30.5308801538476 +586000 ekin = 4.66196804986673 | erot = 3.11428540249498 | epot = -38.1645218154685 | etot = -30.3882683631068 +587000 ekin = 4.58446438916328 | erot = 3.26198289890953 | epot = -38.1451310277745 | etot = -30.2986837397017 +588000 ekin = 4.59050554157104 | erot = 3.3726754228907 | epot = -38.0928945920965 | etot = -30.1297136276347 +589000 ekin = 4.52148456601111 | erot = 3.20426810396365 | epot = -38.0431145518048 | etot = -30.31736188183 +590000 ekin = 4.54292012494668 | erot = 3.17466615888884 | epot = -37.9867331121616 | etot = -30.2691468283261 +591000 ekin = 4.4671534284139 | erot = 3.30654504351686 | epot = -37.9702893954324 | etot = -30.1965909235016 +592000 ekin = 4.47491098921977 | erot = 3.6999642514398 | epot = -37.9696400527198 | etot = -29.7947648120603 +593000 ekin = 4.43506697623667 | erot = 3.70250326611386 | epot = -37.982672172325 | etot = -29.8451019299745 +594000 ekin = 4.36908136306914 | erot = 3.59308231950695 | epot = -38.0038521048194 | etot = -30.0416884222434 +595000 ekin = 4.30615021787055 | erot = 3.60547435881493 | epot = -38.0517692624258 | etot = -30.1401446857403 +596000 ekin = 4.27538703974133 | erot = 3.70718417029047 | epot = -38.1072020006232 | etot = -30.1246307905914 +597000 ekin = 4.09427835861052 | erot = 3.56040857145023 | epot = -38.1368054718235 | etot = -30.4821185417627 +598000 ekin = 4.06772969179112 | erot = 3.98852753231066 | epot = -38.1357675039157 | etot = -30.0795102798139 +599000 ekin = 4.05823661502987 | erot = 3.99204411848289 | epot = -38.094416622612 | etot = -30.0441358890992 +600000 ekin = 4.14000207696597 | erot = 3.69886036268669 | epot = -38.0126500071595 | etot = -30.1737875675069 +601000 ekin = 4.14331251606211 | erot = 4.02012885446817 | epot = -37.8931408419344 | etot = -29.7296994714041 +602000 ekin = 4.19175322865712 | erot = 3.63789752518651 | epot = -37.776838230476 | etot = -29.9471874766323 +603000 ekin = 4.17700109074307 | erot = 3.33190102346871 | epot = -37.6571796612341 | etot = -30.1482775470223 +604000 ekin = 4.32110078335233 | erot = 3.37359972635292 | epot = -37.5481087406156 | etot = -29.8534082309104 +605000 ekin = 4.40829637956691 | erot = 3.12232098209617 | epot = -37.4615593717342 | etot = -29.9309420100711 +606000 ekin = 4.50978571460466 | erot = 2.82903034171751 | epot = -37.4107566252708 | etot = -30.0719405689486 +607000 ekin = 4.64775510562427 | erot = 2.72855004395386 | epot = -37.3886864614938 | etot = -30.0123813119157 +608000 ekin = 4.62515883775198 | erot = 2.69276686565725 | epot = -37.3472679127841 | etot = -30.0293422093749 +609000 ekin = 4.58072072733855 | erot = 2.72618151323734 | epot = -37.321155518993 | etot = -30.0142532784171 +610000 ekin = 4.37064710749545 | erot = 2.94205446769438 | epot = -37.3313655411415 | etot = -30.0186639659516 +611000 ekin = 4.30243700562366 | erot = 2.94482669781544 | epot = -37.3282578261779 | etot = -30.0809941227388 +612000 ekin = 4.37982748485343 | erot = 2.81236690797516 | epot = -37.3366791579241 | etot = -30.1444847650955 +613000 ekin = 4.49298433908216 | erot = 2.9422949922611 | epot = -37.3617837170398 | etot = -29.9265043856965 +614000 ekin = 4.63192250195893 | erot = 2.81948937077719 | epot = -37.3623397651558 | etot = -29.9109278924196 +615000 ekin = 4.56431794922697 | erot = 3.04112038174076 | epot = -37.336047475673 | etot = -29.7306091447052 +616000 ekin = 4.48538645093142 | erot = 2.9863679461823 | epot = -37.2843360454655 | etot = -29.8125816483518 +617000 ekin = 4.35777724185516 | erot = 3.27046740448593 | epot = -37.2149609045279 | etot = -29.5867162581868 +618000 ekin = 4.13929013645538 | erot = 3.31436963968885 | epot = -37.1380165806135 | etot = -29.6843568044692 +619000 ekin = 3.99812604761947 | erot = 3.80697216179629 | epot = -37.0480074184855 | etot = -29.2429092090698 +620000 ekin = 3.75775297824752 | erot = 3.88935078371487 | epot = -37.0016709350122 | etot = -29.3545671730499 +621000 ekin = 3.59837254942666 | erot = 3.36974253347195 | epot = -36.957139996861 | etot = -29.9890249139623 +622000 ekin = 3.52853751549673 | erot = 3.57220920853453 | epot = -36.9826672270778 | etot = -29.8819205030465 +623000 ekin = 3.44776927445729 | erot = 3.68524482792415 | epot = -37.0520182183617 | etot = -29.9190041159803 +624000 ekin = 3.42459051153801 | erot = 4.10039189185601 | epot = -37.1561365046956 | etot = -29.6311541013016 +625000 ekin = 3.47427533928241 | erot = 4.19316198399256 | epot = -37.3128709391509 | etot = -29.6454336158759 +626000 ekin = 3.59243588690051 | erot = 4.25331544595908 | epot = -37.4538356021372 | etot = -29.6080842692777 +627000 ekin = 3.65834270574544 | erot = 3.84587709669875 | epot = -37.5560189371568 | etot = -30.0517991347126 +628000 ekin = 3.70047562334568 | erot = 3.6882110278348 | epot = -37.6346624168372 | etot = -30.2459757656567 +629000 ekin = 3.73516234913422 | erot = 3.92476956261677 | epot = -37.7008434862915 | etot = -30.0409115745406 +630000 ekin = 3.81181204861746 | erot = 3.95913149926753 | epot = -37.7335643601767 | etot = -29.9626208122917 +631000 ekin = 3.81645534702365 | erot = 3.13210702566911 | epot = -37.7706097068458 | etot = -30.822047334153 +632000 ekin = 3.83367227377576 | erot = 3.16390787891888 | epot = -37.8179976528052 | etot = -30.8204175001106 +633000 ekin = 3.78875173101125 | erot = 3.28627876080398 | epot = -37.8551980571897 | etot = -30.7801675653744 +634000 ekin = 3.64435724345663 | erot = 3.54689069849326 | epot = -37.8771184407042 | etot = -30.6858704987543 +635000 ekin = 3.74927918910687 | erot = 3.50067245026001 | epot = -37.9120332365853 | etot = -30.6620815972185 +636000 ekin = 3.89890106913056 | erot = 3.51590480850453 | epot = -37.9883703460318 | etot = -30.5735644683968 +637000 ekin = 3.98051852239104 | erot = 3.51683885701821 | epot = -38.1188954220068 | etot = -30.6215380425976 +638000 ekin = 4.1867925219674 | erot = 3.48363716100457 | epot = -38.3003898519922 | etot = -30.6299601690202 +639000 ekin = 4.29259370089831 | erot = 3.44532403016783 | epot = -38.5009165327295 | etot = -30.7629988016634 +640000 ekin = 4.33862023546758 | erot = 3.61400248687526 | epot = -38.6627935284701 | etot = -30.7101708061272 +641000 ekin = 4.47895119284624 | erot = 3.60758277909094 | epot = -38.7986251266558 | etot = -30.7120911547187 +642000 ekin = 4.48471207018763 | erot = 3.75535910837196 | epot = -38.863620414876 | etot = -30.6235492363164 +643000 ekin = 4.56445558617355 | erot = 3.81552004634157 | epot = -38.8645537025225 | etot = -30.4845780700074 +644000 ekin = 4.73329478475728 | erot = 3.55885168491639 | epot = -38.8054956282291 | etot = -30.5133491585554 +645000 ekin = 4.6912943962558 | erot = 3.28200064721723 | epot = -38.701547429741 | etot = -30.7282523862679 +646000 ekin = 4.58583002001323 | erot = 3.4085956946329 | epot = -38.5478616511678 | etot = -30.5534359365217 +647000 ekin = 4.60741071742923 | erot = 3.38831322436691 | epot = -38.3932861693425 | etot = -30.3975622275464 +648000 ekin = 4.51463144345976 | erot = 3.2427410033314 | epot = -38.2758434893353 | etot = -30.5184710425442 +649000 ekin = 4.55491099792929 | erot = 3.3173810530716 | epot = -38.2201110845429 | etot = -30.347819033542 +650000 ekin = 4.67226589728798 | erot = 3.60950811156257 | epot = -38.2202225605509 | etot = -29.9384485517004 +651000 ekin = 4.60851815831642 | erot = 3.77278937705233 | epot = -38.2536330995444 | etot = -29.8723255641757 +652000 ekin = 4.678459200191 | erot = 3.3937624009624 | epot = -38.2868824175937 | etot = -30.2146608164403 +653000 ekin = 4.66844839257089 | erot = 3.83803199311166 | epot = -38.3235322989536 | etot = -29.817051913271 +654000 ekin = 4.7104895331932 | erot = 3.48299287365129 | epot = -38.3580887397253 | etot = -30.1646063328808 +655000 ekin = 4.59645355598621 | erot = 3.7478202528204 | epot = -38.4145657066933 | etot = -30.0702918978867 +656000 ekin = 4.75902771581097 | erot = 3.81874385847384 | epot = -38.4693742928374 | etot = -29.8916027185526 +657000 ekin = 4.64668020593031 | erot = 3.6665600106013 | epot = -38.4843211797294 | etot = -30.1710809631978 +658000 ekin = 4.5583600187507 | erot = 3.93329833863019 | epot = -38.4803826070965 | etot = -29.9887242497156 +659000 ekin = 4.55537392119719 | erot = 3.6285471602112 | epot = -38.4363459414659 | etot = -30.2524248600575 +660000 ekin = 4.41551333368083 | erot = 3.6539559007289 | epot = -38.3663969488346 | etot = -30.2969277144249 +661000 ekin = 4.32449081576465 | erot = 3.74090915717697 | epot = -38.2884247485437 | etot = -30.2230247756021 +662000 ekin = 4.2382312401034 | erot = 3.58833666048796 | epot = -38.1946280661735 | etot = -30.3680601655822 +663000 ekin = 4.32618520330348 | erot = 3.71369597709409 | epot = -38.0940311251124 | etot = -30.0541499447149 +664000 ekin = 4.30987713127737 | erot = 3.55193027406456 | epot = -38.0118003167729 | etot = -30.149992911431 +665000 ekin = 4.32971268964125 | erot = 3.40416985470638 | epot = -37.9630121098137 | etot = -30.229129565466 +666000 ekin = 4.30397058329232 | erot = 3.24563244836293 | epot = -37.9564459426245 | etot = -30.4068429109692 +667000 ekin = 4.23802718761159 | erot = 3.57923047722682 | epot = -37.911170999797 | etot = -30.0939133349586 +668000 ekin = 4.17750835985169 | erot = 3.42921371885257 | epot = -37.8409684237745 | etot = -30.2342463450703 +669000 ekin = 4.10123021238948 | erot = 3.38759831293412 | epot = -37.7732457913403 | etot = -30.2844172660167 +670000 ekin = 3.96563796265766 | erot = 3.59480187806753 | epot = -37.6965941156386 | etot = -30.1361542749134 +671000 ekin = 3.96406262528469 | erot = 3.64073126780246 | epot = -37.5753442355431 | etot = -29.9705503424559 +672000 ekin = 4.04265318678508 | erot = 3.67979591145804 | epot = -37.4296504342378 | etot = -29.7072013359947 +673000 ekin = 3.99224066234871 | erot = 3.52190422085278 | epot = -37.3047157518844 | etot = -29.7905708686829 +674000 ekin = 3.97681715793532 | erot = 3.75368024393782 | epot = -37.1885781675148 | etot = -29.4580807656416 +675000 ekin = 3.85833621087031 | erot = 3.97050815664581 | epot = -37.1417466549724 | etot = -29.3129022874562 +676000 ekin = 3.77676206895609 | erot = 3.79811590545655 | epot = -37.1253534099231 | etot = -29.5504754355104 +677000 ekin = 3.78226586281953 | erot = 3.88942769355379 | epot = -37.1385629636271 | etot = -29.4668694072538 +678000 ekin = 3.61579087416917 | erot = 3.83629032138248 | epot = -37.1880190743623 | etot = -29.7359378788106 +679000 ekin = 3.59940694058669 | erot = 3.92320694106388 | epot = -37.2411006365046 | etot = -29.7184867548541 +680000 ekin = 3.59936088858661 | erot = 3.59198808770705 | epot = -37.3103059663064 | etot = -30.1189569900128 +681000 ekin = 3.5506817335392 | erot = 3.62032338399699 | epot = -37.397887158622 | etot = -30.2268820410859 +682000 ekin = 3.64312616149454 | erot = 3.63220095729207 | epot = -37.4824268307592 | etot = -30.2070997119726 +683000 ekin = 3.59147144886464 | erot = 4.0054088226964 | epot = -37.5784304648838 | etot = -29.9815501933228 +684000 ekin = 3.72558767154372 | erot = 4.43134049971566 | epot = -37.6663536443173 | etot = -29.5094254730579 +685000 ekin = 3.75700113340408 | erot = 4.42051791074664 | epot = -37.7011506850387 | etot = -29.523631640888 +686000 ekin = 3.68716829673499 | erot = 4.29446170846264 | epot = -37.7134415714993 | etot = -29.7318115663016 +687000 ekin = 3.64818503755748 | erot = 4.53150873331274 | epot = -37.711537143075 | etot = -29.5318433722048 +688000 ekin = 3.65898677055773 | erot = 4.19517143645001 | epot = -37.7179324142981 | etot = -29.8637742072904 +689000 ekin = 3.6205349293849 | erot = 4.90634872884686 | epot = -37.7254294906481 | etot = -29.1985458324163 +690000 ekin = 3.66313798116712 | erot = 4.56796147261006 | epot = -37.7316773182824 | etot = -29.5005778645052 +691000 ekin = 3.71240687811154 | erot = 4.32729443264317 | epot = -37.6986701891451 | etot = -29.6589688783904 +692000 ekin = 3.77937222983674 | erot = 4.25209713638378 | epot = -37.6463069321166 | etot = -29.6148375658961 +693000 ekin = 3.82528389687013 | erot = 4.44391854020428 | epot = -37.5813521083399 | etot = -29.3121496712654 +694000 ekin = 3.77132757417731 | erot = 4.30342910423497 | epot = -37.5292531497342 | etot = -29.454496471322 +695000 ekin = 3.87816824099586 | erot = 3.61664690986648 | epot = -37.4977174174724 | etot = -30.0029022666101 +696000 ekin = 4.03561630547957 | erot = 3.14881777436793 | epot = -37.5165237009968 | etot = -30.3320896211493 +697000 ekin = 4.10221303088947 | erot = 2.74688055821586 | epot = -37.6237315563435 | etot = -30.7746379672381 +698000 ekin = 4.33198843808379 | erot = 2.54448976763408 | epot = -37.8109238872746 | etot = -30.9344456815567 +699000 ekin = 4.45835519306674 | erot = 2.8372756281226 | epot = -38.0765099491828 | etot = -30.7808791279934 +700000 ekin = 4.62566765847138 | erot = 3.20413023616686 | epot = -38.3666686805772 | etot = -30.536870785939 +701000 ekin = 4.71198958041981 | erot = 3.20500762759515 | epot = -38.6531148244764 | etot = -30.7361176164614 +702000 ekin = 4.70320353975512 | erot = 3.49669921722509 | epot = -38.9020142648734 | etot = -30.7021115078932 +703000 ekin = 4.7166659217622 | erot = 3.43605875792423 | epot = -39.0983570180767 | etot = -30.9456323383903 +704000 ekin = 4.81119997223625 | erot = 3.68842954975253 | epot = -39.2326154199855 | etot = -30.7329858979967 +705000 ekin = 4.76635995985854 | erot = 4.27225880905604 | epot = -39.304583019354 | etot = -30.2659642504394 +706000 ekin = 4.6123968900786 | erot = 4.45743851438174 | epot = -39.3303553159895 | etot = -30.2605199115291 +707000 ekin = 4.43392403924413 | erot = 5.00090751066076 | epot = -39.3012148785927 | etot = -29.8663833286878 +708000 ekin = 4.493639803788 | erot = 4.44827137132337 | epot = -39.1855945086319 | etot = -30.2436833335206 +709000 ekin = 4.38087413515987 | erot = 4.33993340713996 | epot = -39.0225667156706 | etot = -30.3017591733707 +710000 ekin = 4.30084034805674 | erot = 4.18416076229495 | epot = -38.8018325665079 | etot = -30.3168314561562 +711000 ekin = 4.16061239283914 | erot = 3.7596460771024 | epot = -38.6119256895403 | etot = -30.6916672195988 +712000 ekin = 4.02785073941548 | erot = 3.91873808556251 | epot = -38.5032151267495 | etot = -30.5566263017715 +713000 ekin = 3.91042694307498 | erot = 4.02474708082426 | epot = -38.4555203424355 | etot = -30.5203463185362 +714000 ekin = 3.91972154955257 | erot = 3.86911398530038 | epot = -38.4391911139339 | etot = -30.650355579081 +715000 ekin = 3.79432885182375 | erot = 3.97493955426887 | epot = -38.4648934882979 | etot = -30.6956250822053 +716000 ekin = 3.81379173421808 | erot = 4.12773796628716 | epot = -38.5344978321895 | etot = -30.5929681316842 +717000 ekin = 3.81338083287853 | erot = 3.91040514076917 | epot = -38.6119475932714 | etot = -30.8881616196237 +718000 ekin = 3.98031853847202 | erot = 3.63481705596704 | epot = -38.678649410417 | etot = -31.0635138159779 +719000 ekin = 3.85667554069524 | erot = 3.54568346865617 | epot = -38.7335222105702 | etot = -31.3311632012187 +720000 ekin = 3.82130999837899 | erot = 3.12899985812958 | epot = -38.800048179352 | etot = -31.8497383228434 +721000 ekin = 3.84625676410583 | erot = 3.33090070721994 | epot = -38.8362758074818 | etot = -31.659118336156 +722000 ekin = 3.79224716661396 | erot = 3.20659617994807 | epot = -38.8301147634646 | etot = -31.8312714169026 +723000 ekin = 3.89270036914644 | erot = 3.09341373486916 | epot = -38.7612142662691 | etot = -31.7751001622535 +724000 ekin = 3.88950015267433 | erot = 3.37593260372111 | epot = -38.6472208331853 | etot = -31.3817880767899 +725000 ekin = 3.89253643906727 | erot = 3.3632565061082 | epot = -38.5278096836431 | etot = -31.2720167384676 +726000 ekin = 3.77207579735126 | erot = 2.95762270097697 | epot = -38.4162496849588 | etot = -31.6865511866306 +727000 ekin = 3.8589508308402 | erot = 2.69741467226751 | epot = -38.3204112624909 | etot = -31.7640457593832 +728000 ekin = 3.95735248448056 | erot = 2.91208862145619 | epot = -38.2269317498774 | etot = -31.3574906439407 +729000 ekin = 3.90116579496193 | erot = 2.68023881807524 | epot = -38.1837112825913 | etot = -31.6023066695542 +730000 ekin = 3.96318220229622 | erot = 2.52640600275291 | epot = -38.1795006550048 | etot = -31.6899124499557 +731000 ekin = 4.07163559325289 | erot = 2.47524828245716 | epot = -38.2208467965997 | etot = -31.6739629208896 +732000 ekin = 4.12331294394785 | erot = 2.59059397612219 | epot = -38.2785246774242 | etot = -31.5646177573541 +733000 ekin = 4.18393032106836 | erot = 2.72580269413632 | epot = -38.3920370437211 | etot = -31.4823040285164 +734000 ekin = 4.22490204001118 | erot = 2.94025387724297 | epot = -38.5577268408556 | etot = -31.3925709236014 +735000 ekin = 4.41637906381283 | erot = 3.39000978300269 | epot = -38.7520895879279 | etot = -30.9457007411124 +736000 ekin = 4.52682105512923 | erot = 3.59384799521502 | epot = -39.0007836443238 | etot = -30.8801145939796 +737000 ekin = 4.54518518822972 | erot = 3.67606395235652 | epot = -39.2431861398732 | etot = -31.021936999287 +738000 ekin = 4.54111831313617 | erot = 3.87514152367601 | epot = -39.4689573474101 | etot = -31.0526975105979 +739000 ekin = 4.64515651334113 | erot = 3.86830954896661 | epot = -39.6580785017875 | etot = -31.1446124394798 +740000 ekin = 4.59721923359584 | erot = 3.83234514918706 | epot = -39.7800787241315 | etot = -31.3505143413486 +741000 ekin = 4.54920694202201 | erot = 4.22873772666781 | epot = -39.8001498706485 | etot = -31.0222052019586 +742000 ekin = 4.37775553859951 | erot = 4.07719515191216 | epot = -39.7729191936198 | etot = -31.3179685031081 +743000 ekin = 4.3556617165815 | erot = 4.19296317409613 | epot = -39.6826493457458 | etot = -31.1340244550682 +744000 ekin = 4.35520781857212 | erot = 4.03027041959878 | epot = -39.5404877687077 | etot = -31.1550095305368 +745000 ekin = 4.22626887984331 | erot = 3.36034348052808 | epot = -39.3612863690872 | etot = -31.7746740087159 +746000 ekin = 4.11995949308923 | erot = 3.27667360498748 | epot = -39.1619120183871 | etot = -31.7652789203104 +747000 ekin = 4.14400839200239 | erot = 3.30199438470026 | epot = -38.9827326721258 | etot = -31.5367298954232 +748000 ekin = 4.00468940718693 | erot = 3.14625781984354 | epot = -38.8044398216778 | etot = -31.6534925946474 +749000 ekin = 3.84115389861465 | erot = 2.95470003366609 | epot = -38.6687005011654 | etot = -31.8728465688846 +750000 ekin = 3.65410258827823 | erot = 3.15459365563754 | epot = -38.5278602215809 | etot = -31.7191639776651 +751000 ekin = 3.60281847230545 | erot = 3.24631581000339 | epot = -38.4153933025755 | etot = -31.5662590202667 +752000 ekin = 3.67731217795128 | erot = 3.63832283099251 | epot = -38.3028409880039 | etot = -30.9872059790601 +753000 ekin = 3.57605485188811 | erot = 3.26752665173291 | epot = -38.2165204041613 | etot = -31.3729389005403 +754000 ekin = 3.69078656100588 | erot = 3.07077330953217 | epot = -38.2008529421062 | etot = -31.4392930715682 +755000 ekin = 3.70168225637986 | erot = 2.97263399944788 | epot = -38.2287093031125 | etot = -31.5543930472847 +756000 ekin = 3.82302121276 | erot = 3.1782689290909 | epot = -38.310131999282 | etot = -31.3088418574311 +757000 ekin = 3.92969183976134 | erot = 3.24398381681734 | epot = -38.4229976799532 | etot = -31.2493220233745 +758000 ekin = 4.01825553851191 | erot = 2.96087889455693 | epot = -38.5603809302421 | etot = -31.5812464971732 +759000 ekin = 4.15945678292269 | erot = 3.31368855914151 | epot = -38.7240687265501 | etot = -31.2509233844859 +760000 ekin = 4.08337495041291 | erot = 3.28527114059579 | epot = -38.8845645171709 | etot = -31.5159184261622 +761000 ekin = 4.14862342701004 | erot = 3.30586771709929 | epot = -38.9896780479041 | etot = -31.5351869037947 +762000 ekin = 4.15291891523591 | erot = 3.21578962032615 | epot = -39.035237071941 | etot = -31.6665285363789 +763000 ekin = 4.13154828483801 | erot = 3.3900507889808 | epot = -39.0640564952969 | etot = -31.5424574214781 +764000 ekin = 4.11445022984107 | erot = 3.78778087021365 | epot = -39.069248399025 | etot = -31.1670172989702 +765000 ekin = 3.94937442988367 | erot = 3.99811330721222 | epot = -39.0421921917084 | etot = -31.0947044546125 +766000 ekin = 3.90772961551845 | erot = 4.0181962192846 | epot = -38.9772379154488 | etot = -31.0513120806457 +767000 ekin = 3.91865092379332 | erot = 3.66675942927299 | epot = -38.8570109636996 | etot = -31.2716006106332 +768000 ekin = 3.90455829915362 | erot = 3.57997769181348 | epot = -38.7106990781797 | etot = -31.2261630872126 +769000 ekin = 3.79614462627826 | erot = 3.72589479531031 | epot = -38.5987325117513 | etot = -31.0766930901627 +770000 ekin = 3.84943042371488 | erot = 3.41445940258812 | epot = -38.524203140241 | etot = -31.260313313938 +771000 ekin = 3.93726861106201 | erot = 3.22573743650855 | epot = -38.4470290210344 | etot = -31.2840229734638 +772000 ekin = 3.96999789478599 | erot = 3.15006319998264 | epot = -38.4433830504296 | etot = -31.3233219556609 +773000 ekin = 3.90264203603893 | erot = 3.08286085672441 | epot = -38.4596433115508 | etot = -31.4741404187875 +774000 ekin = 4.05136357587227 | erot = 3.17001936426344 | epot = -38.5137422973683 | etot = -31.2923593572326 +775000 ekin = 4.11418642080987 | erot = 3.81754399179953 | epot = -38.5927804349062 | etot = -30.6610500222968 +776000 ekin = 4.11481050991315 | erot = 3.55328099460652 | epot = -38.6754580889833 | etot = -31.0073665844636 +777000 ekin = 4.23423405077881 | erot = 3.58108270552595 | epot = -38.76169441768 | etot = -30.9463776613752 +778000 ekin = 4.22244262963946 | erot = 3.64411855451438 | epot = -38.842032142942 | etot = -30.9754709587882 +779000 ekin = 4.20492205038613 | erot = 3.89270804286644 | epot = -38.9009656289588 | etot = -30.8033355357062 +780000 ekin = 4.19457435208234 | erot = 3.98994130977106 | epot = -38.9050369874364 | etot = -30.720521325583 +781000 ekin = 4.33837315790505 | erot = 3.45852422770954 | epot = -38.858660577552 | etot = -31.0617631919374 +782000 ekin = 4.36357496915283 | erot = 3.10010011432268 | epot = -38.7868584055569 | etot = -31.3231833220814 +783000 ekin = 4.42162598039069 | erot = 3.42028138737023 | epot = -38.7233668668895 | etot = -30.8814594991286 +784000 ekin = 4.52915280589068 | erot = 3.46746509226016 | epot = -38.6388342149203 | etot = -30.6422163167695 +785000 ekin = 4.5515940213827 | erot = 3.36141401661281 | epot = -38.5160993571772 | etot = -30.6030913191817 +786000 ekin = 4.4107707826179 | erot = 3.55728141641263 | epot = -38.3921286555455 | etot = -30.424076456515 +787000 ekin = 4.5473982866512 | erot = 3.81681111076943 | epot = -38.2843232861691 | etot = -29.9201138887484 +788000 ekin = 4.51350891647158 | erot = 3.90594890385667 | epot = -38.2029645190101 | etot = -29.7835066986818 +789000 ekin = 4.41183434492804 | erot = 4.01545730842702 | epot = -38.1545360413066 | etot = -29.7272443879516 +790000 ekin = 4.36219296798482 | erot = 4.38022337925401 | epot = -38.1642768248248 | etot = -29.421860477586 +791000 ekin = 4.36856935453186 | erot = 4.10044084346348 | epot = -38.2219055606099 | etot = -29.7528953626145 +792000 ekin = 4.15750522427241 | erot = 4.31220830506829 | epot = -38.3006248567473 | etot = -29.8309113274066 +793000 ekin = 4.04895474142992 | erot = 4.47406069249712 | epot = -38.4166817679429 | etot = -29.8936663340158 +794000 ekin = 4.06782077729031 | erot = 4.54237615913424 | epot = -38.5497403981529 | etot = -29.9395434617283 +795000 ekin = 4.13325369560983 | erot = 4.6766430853343 | epot = -38.7140310649859 | etot = -29.9041342840418 +796000 ekin = 4.24810673699357 | erot = 4.55090018691371 | epot = -38.8628377912581 | etot = -30.0638308673508 +797000 ekin = 4.47820483480053 | erot = 4.37105820701948 | epot = -39.0073103741372 | etot = -30.1580473323172 +798000 ekin = 4.41687882033665 | erot = 4.0319284480101 | epot = -39.1717655165835 | etot = -30.7229582482367 +799000 ekin = 4.51272621151664 | erot = 3.80275615695394 | epot = -39.3264210367218 | etot = -31.0109386682512 +800000 ekin = 4.55406747539997 | erot = 3.86603589563191 | epot = -39.455092115688 | etot = -31.0349887446561 +801000 ekin = 4.71425753043942 | erot = 4.19401636489441 | epot = -39.5455068512898 | etot = -30.637232955956 +802000 ekin = 4.73096724901056 | erot = 4.66018334519229 | epot = -39.597292270086 | etot = -30.2061416758832 +803000 ekin = 4.62379738113321 | erot = 4.84687313016545 | epot = -39.6033097238909 | etot = -30.1326392125923 +804000 ekin = 4.73211781117979 | erot = 4.65405100631752 | epot = -39.5980929919841 | etot = -30.2119241744868 +805000 ekin = 4.74990370273786 | erot = 5.03061291222775 | epot = -39.569498865532 | etot = -29.7889822505664 +806000 ekin = 4.71376969100994 | erot = 4.52737209746845 | epot = -39.5309941756428 | etot = -30.2898523871644 +807000 ekin = 4.86079475139447 | erot = 4.60056901312774 | epot = -39.4997078348834 | etot = -30.0383440703612 +808000 ekin = 4.80209833525365 | erot = 4.45818548395654 | epot = -39.4704788837951 | etot = -30.2101950645849 +809000 ekin = 4.6377001128784 | erot = 4.50410245159993 | epot = -39.4133092695815 | etot = -30.2715067051032 +810000 ekin = 4.58845623547692 | erot = 4.59839740206889 | epot = -39.3630399165046 | etot = -30.1761862789588 +811000 ekin = 4.49885529137753 | erot = 3.98878012931503 | epot = -39.2630135095319 | etot = -30.7753780888393 +812000 ekin = 4.26896362698783 | erot = 3.78568800845445 | epot = -39.1138584925267 | etot = -31.0592068570844 +813000 ekin = 4.13473287838133 | erot = 3.6709761560088 | epot = -38.9684769118808 | etot = -31.1627678774907 +814000 ekin = 3.94776533151714 | erot = 3.9457998277719 | epot = -38.8393181931019 | etot = -30.9457530338129 +815000 ekin = 3.90824876714862 | erot = 4.04132924638677 | epot = -38.7551601823022 | etot = -30.8055821687668 +816000 ekin = 3.78701127768462 | erot = 3.90301930977968 | epot = -38.6978803550943 | etot = -31.00784976763 +817000 ekin = 3.66292511898636 | erot = 3.94682412287945 | epot = -38.6270985077425 | etot = -31.0173492658767 +818000 ekin = 3.57247131276281 | erot = 4.1784329766224 | epot = -38.5581000447571 | etot = -30.8071957553719 +819000 ekin = 3.53877880324498 | erot = 4.11647252852254 | epot = -38.4709987313688 | etot = -30.8157473996013 +820000 ekin = 3.50671598439864 | erot = 4.25631799360866 | epot = -38.3521077332953 | etot = -30.589073755288 +821000 ekin = 3.53103431342861 | erot = 3.63219688182926 | epot = -38.2011634572152 | etot = -31.0379322619573 +822000 ekin = 3.51951391759931 | erot = 3.61259288561798 | epot = -38.0560993175178 | etot = -30.9239925143005 +823000 ekin = 3.57671320020554 | erot = 3.17979253207743 | epot = -37.8872361758755 | etot = -31.1307304435925 +824000 ekin = 3.52000952110921 | erot = 3.12347116703116 | epot = -37.7532307820921 | etot = -31.1097500939517 +825000 ekin = 3.58955759313305 | erot = 3.15061432333252 | epot = -37.6359982536732 | etot = -30.8958263372076 +826000 ekin = 3.67361585241115 | erot = 3.02327306668993 | epot = -37.5692124634555 | etot = -30.8723235443545 +827000 ekin = 3.81109350736604 | erot = 2.85212407416508 | epot = -37.5611625241685 | etot = -30.8979449426374 +828000 ekin = 3.90531542763306 | erot = 2.81227386436724 | epot = -37.5694328663444 | etot = -30.8518435743441 +829000 ekin = 3.84587100054128 | erot = 2.81493449341339 | epot = -37.6070676030481 | etot = -30.9462621090934 +830000 ekin = 3.92673136944209 | erot = 3.15236191191157 | epot = -37.65374691576 | etot = -30.5746536344063 +831000 ekin = 3.93921284330491 | erot = 3.06450076609943 | epot = -37.726173164998 | etot = -30.7224595555937 +832000 ekin = 3.97197612374618 | erot = 3.05649894745004 | epot = -37.8221989970108 | etot = -30.7937239258146 +833000 ekin = 3.93725030890245 | erot = 3.02665836452891 | epot = -37.937171835506 | etot = -30.9732631620746 +834000 ekin = 3.98146697711148 | erot = 3.02136079279377 | epot = -38.0629385880238 | etot = -31.0601108181185 +835000 ekin = 4.05052897985953 | erot = 3.17273406713208 | epot = -38.1835463837721 | etot = -30.9602833367805 +836000 ekin = 4.19040397553796 | erot = 3.26946027032974 | epot = -38.300933644763 | etot = -30.8410693988953 +837000 ekin = 4.23633886579806 | erot = 3.17722972050019 | epot = -38.3895940577245 | etot = -30.9760254714263 +838000 ekin = 4.29790040722482 | erot = 3.15450479842838 | epot = -38.4727069904853 | etot = -31.0203017848321 +839000 ekin = 4.182732050379 | erot = 3.33215565017002 | epot = -38.5543306618494 | etot = -31.0394429613004 +840000 ekin = 4.10684077367696 | erot = 3.38230089969601 | epot = -38.6241675017603 | etot = -31.1350258283873 +841000 ekin = 4.23749853699722 | erot = 4.07451157411683 | epot = -38.6954306161322 | etot = -30.3834205050181 +842000 ekin = 4.2153670799426 | erot = 4.23835126074053 | epot = -38.7619078222528 | etot = -30.3081894815696 +843000 ekin = 4.22215504966699 | erot = 4.35771502414021 | epot = -38.8129398935362 | etot = -30.233069819729 +844000 ekin = 4.30121627933573 | erot = 4.37450016715701 | epot = -38.8385476120776 | etot = -30.1628311655849 +845000 ekin = 4.21550077214609 | erot = 4.14378307005649 | epot = -38.8237568245827 | etot = -30.4644729823801 +846000 ekin = 4.02238016824686 | erot = 4.51654867802952 | epot = -38.7905889780241 | etot = -30.2516601317477 +847000 ekin = 4.01810256512937 | erot = 4.26125017170745 | epot = -38.733957558752 | etot = -30.4546048219152 +848000 ekin = 3.96232133970732 | erot = 4.11983424179405 | epot = -38.6313622633386 | etot = -30.5492066818373 +849000 ekin = 3.80836560854392 | erot = 4.28564223418274 | epot = -38.4895963152699 | etot = -30.3955884725433 +850000 ekin = 3.69578896780274 | erot = 4.39587758868528 | epot = -38.3525607889922 | etot = -30.2608942325042 +851000 ekin = 3.41959969074421 | erot = 4.26064520104062 | epot = -38.1456854690894 | etot = -30.4654405773046 +852000 ekin = 3.30829887930776 | erot = 3.71835542085465 | epot = -37.9409715149428 | etot = -30.9143172147804 +853000 ekin = 3.35508979255713 | erot = 3.37030184945621 | epot = -37.7900455534541 | etot = -31.0646539114407 +854000 ekin = 3.27022944339449 | erot = 3.34212111159852 | epot = -37.7131840806896 | etot = -31.1008335256966 +855000 ekin = 3.19861227193943 | erot = 3.88856216577093 | epot = -37.6928018165187 | etot = -30.6056273788083 +856000 ekin = 3.06768638261934 | erot = 3.98298011021487 | epot = -37.727010473156 | etot = -30.6763439803218 +857000 ekin = 3.02849458271124 | erot = 3.90128373509556 | epot = -37.7894644617561 | etot = -30.8596861439493 +858000 ekin = 3.01766394874133 | erot = 3.81481515545799 | epot = -37.864155422239 | etot = -31.0316763180397 +859000 ekin = 3.04279727315576 | erot = 3.58850792531743 | epot = -37.9147104139937 | etot = -31.2834052155205 +860000 ekin = 3.12250083122182 | erot = 3.47152341944205 | epot = -37.9805991878282 | etot = -31.3865749371643 +861000 ekin = 3.08661234486262 | erot = 3.19104504877429 | epot = -38.04550487435 | etot = -31.7678474807131 +862000 ekin = 3.21284829409286 | erot = 3.29871938445959 | epot = -38.099234844044 | etot = -31.5876671654915 +863000 ekin = 3.30782920492323 | erot = 3.18791577959012 | epot = -38.1747149198294 | etot = -31.678969935316 +864000 ekin = 3.42420257195635 | erot = 2.92388402618494 | epot = -38.2365375033583 | etot = -31.888450905217 +865000 ekin = 3.34466551527704 | erot = 3.0972998859353 | epot = -38.3012083514071 | etot = -31.8592429501948 +866000 ekin = 3.36174635490684 | erot = 3.3198551234471 | epot = -38.3565233653478 | etot = -31.6749218869938 +867000 ekin = 3.42183919685502 | erot = 2.79592217571871 | epot = -38.3877893327297 | etot = -32.1700279601559 +868000 ekin = 3.36274087144656 | erot = 2.53957841641322 | epot = -38.4029375195831 | etot = -32.5006182317234 +869000 ekin = 3.40964507660634 | erot = 2.56691032353942 | epot = -38.3607072506902 | etot = -32.3841518505445 +870000 ekin = 3.53716918539254 | erot = 2.78671187381873 | epot = -38.3296120297666 | etot = -32.0057309705553 +871000 ekin = 3.59594316640842 | erot = 2.64188707611872 | epot = -38.2798157408163 | etot = -32.0419854982892 +872000 ekin = 3.50734679867101 | erot = 2.53533702817691 | epot = -38.2086073023317 | etot = -32.1659234754837 +873000 ekin = 3.49167258379229 | erot = 2.78144827221661 | epot = -38.1271407877645 | etot = -31.8540199317556 +874000 ekin = 3.51303146719815 | erot = 2.71312702979824 | epot = -38.0371921369838 | etot = -31.8110336399874 +875000 ekin = 3.48945347772523 | erot = 2.94850163157185 | epot = -37.9788388329103 | etot = -31.5408837236132 +876000 ekin = 3.56075870692743 | erot = 3.00511197452205 | epot = -37.9138095080298 | etot = -31.3479388265803 +877000 ekin = 3.47758786865167 | erot = 3.16390846334178 | epot = -37.8677942057126 | etot = -31.2262978737192 +878000 ekin = 3.30311825505467 | erot = 3.03452838302444 | epot = -37.8643582436496 | etot = -31.5267116055705 +879000 ekin = 3.24374156245722 | erot = 3.40785973601232 | epot = -37.8934655456588 | etot = -31.2418642471892 +880000 ekin = 3.37573093292725 | erot = 3.29280897525375 | epot = -37.94427513544 | etot = -31.275735227259 +881000 ekin = 3.39840544569004 | erot = 3.55852812717334 | epot = -38.000888118187 | etot = -31.0439545453236 +882000 ekin = 3.5896767073527 | erot = 3.35995074975521 | epot = -38.026551897189 | etot = -31.0769244400811 +883000 ekin = 3.50982611331082 | erot = 2.96694324238039 | epot = -38.0094926569537 | etot = -31.5327233012624 +884000 ekin = 3.40446481074992 | erot = 3.29501620823905 | epot = -37.9974315131722 | etot = -31.2979504941832 +885000 ekin = 3.35965929451973 | erot = 3.11716654513077 | epot = -38.0104898466533 | etot = -31.5336640070028 +886000 ekin = 3.43988208795668 | erot = 3.03035945423276 | epot = -38.069363334615 | etot = -31.5991217924255 +887000 ekin = 3.45628684947244 | erot = 3.13318789403753 | epot = -38.167703435161 | etot = -31.5782286916511 +888000 ekin = 3.56219309594448 | erot = 3.51843891461388 | epot = -38.2809194479115 | etot = -31.2002874373531 +889000 ekin = 3.66415644518205 | erot = 4.27546474777864 | epot = -38.4171028829355 | etot = -30.4774816899748 +890000 ekin = 3.59199164776004 | erot = 4.54716655442247 | epot = -38.5531146541753 | etot = -30.4139564519928 +891000 ekin = 3.4869835078992 | erot = 4.75701182525676 | epot = -38.6580895919222 | etot = -30.4140942587662 +892000 ekin = 3.51562855757933 | erot = 4.92508483334413 | epot = -38.7362622656568 | etot = -30.2955488747333 +893000 ekin = 3.4766111333881 | erot = 5.21569244219365 | epot = -38.7939526432623 | etot = -30.1016490676805 +894000 ekin = 3.33377890272863 | erot = 5.32415823975928 | epot = -38.7809839614906 | etot = -30.1230468190027 +895000 ekin = 3.43478318369578 | erot = 5.410051543616 | epot = -38.7354883491905 | etot = -29.8906536218787 +896000 ekin = 3.35681124753231 | erot = 5.27612600451789 | epot = -38.644144773384 | etot = -30.0112075213338 +897000 ekin = 3.28668538949675 | erot = 5.17803324766013 | epot = -38.5248966927272 | etot = -30.0601780555704 +898000 ekin = 3.28286469703029 | erot = 5.13874374768494 | epot = -38.3749221439187 | etot = -29.9533136992034 +899000 ekin = 3.28106900834711 | erot = 5.02377463132162 | epot = -38.2159550339518 | etot = -29.9111113942831 +900000 ekin = 3.23754877589606 | erot = 4.74128859066625 | epot = -38.0678968923381 | etot = -30.0890595257758 +901000 ekin = 3.13978298302555 | erot = 4.3243129242664 | epot = -37.9137652588163 | etot = -30.4496693515243 +902000 ekin = 3.14110495369385 | erot = 3.63711917032573 | epot = -37.7967183247472 | etot = -31.0184942007276 +903000 ekin = 3.11835106948976 | erot = 3.5835838401184 | epot = -37.7069569192995 | etot = -31.0050220096914 +904000 ekin = 3.07376219479296 | erot = 3.52931006844825 | epot = -37.6597467606241 | etot = -31.0566744973829 +905000 ekin = 3.06812362454372 | erot = 3.78913234205767 | epot = -37.6633180135037 | etot = -30.8060620469023 +906000 ekin = 3.16118254583043 | erot = 3.68210315785564 | epot = -37.7114125889238 | etot = -30.8681268852377 +907000 ekin = 3.05937736690025 | erot = 3.63166351278032 | epot = -37.8094278488435 | etot = -31.118386969163 +908000 ekin = 3.20197665753494 | erot = 3.6441133335068 | epot = -37.8953945586471 | etot = -31.0493045676053 +909000 ekin = 3.13419888287822 | erot = 3.44894287146547 | epot = -37.9553359165693 | etot = -31.3721941622256 +910000 ekin = 3.2011454656304 | erot = 3.42446813676882 | epot = -38.024917947609 | etot = -31.3993043452098 +911000 ekin = 3.183320242491 | erot = 3.30496399638698 | epot = -38.1090485606002 | etot = -31.6207643217223 +912000 ekin = 3.26276595850364 | erot = 3.24471741353574 | epot = -38.2096715613882 | etot = -31.7021881893489 +913000 ekin = 3.2681561913827 | erot = 3.26266624315759 | epot = -38.3821519588598 | etot = -31.8513295243196 +914000 ekin = 3.35412635067755 | erot = 3.33562334375845 | epot = -38.6092123987847 | etot = -31.9194627043487 +915000 ekin = 3.50776663391062 | erot = 3.6091033663435 | epot = -38.8009254120376 | etot = -31.6840554117835 +916000 ekin = 3.5277313901091 | erot = 3.46745309412736 | epot = -38.9707688836112 | etot = -31.9755843993747 +917000 ekin = 3.59076210165264 | erot = 3.41178573512987 | epot = -39.0925719913734 | etot = -32.0900241545909 +918000 ekin = 3.70456853537637 | erot = 3.18226166796491 | epot = -39.1781408185665 | etot = -32.2913106152253 +919000 ekin = 3.78037780426176 | erot = 3.08638967761944 | epot = -39.2569196438486 | etot = -32.3901521619674 +920000 ekin = 3.91060781137684 | erot = 3.28711158692157 | epot = -39.3298863351688 | etot = -32.1321669368704 +921000 ekin = 3.94747979949424 | erot = 3.45337772058887 | epot = -39.3932618134522 | etot = -31.9924042933691 +922000 ekin = 3.94814734356941 | erot = 3.67117615571532 | epot = -39.4429346449514 | etot = -31.8236111456667 +923000 ekin = 3.96148195878582 | erot = 4.16418425189001 | epot = -39.4697891977426 | etot = -31.3441229870668 +924000 ekin = 3.93156231463912 | erot = 4.23364521862771 | epot = -39.4747062603535 | etot = -31.3094987270866 +925000 ekin = 3.98364691406504 | erot = 4.37102519058181 | epot = -39.4559543119553 | etot = -31.1012822073085 +926000 ekin = 3.90165834847865 | erot = 4.5398391765023 | epot = -39.3838686479861 | etot = -30.9423711230052 +927000 ekin = 3.86159556963851 | erot = 4.93409467569006 | epot = -39.3009822835311 | etot = -30.5052920382026 +928000 ekin = 3.88113409255608 | erot = 4.54344659797514 | epot = -39.2237313850886 | etot = -30.7991506945573 +929000 ekin = 3.73601262143371 | erot = 4.54159517313964 | epot = -39.0907845737875 | etot = -30.8131767792141 +930000 ekin = 3.62890283946098 | erot = 4.23223960576937 | epot = -38.9310668930158 | etot = -31.0699244477855 +931000 ekin = 3.51130978751904 | erot = 3.75580234575059 | epot = -38.7496742883208 | etot = -31.4825621550511 +932000 ekin = 3.4360478582467 | erot = 3.85916877458119 | epot = -38.6047820584061 | etot = -31.3095654255782 +933000 ekin = 3.34945134482918 | erot = 4.10711762351073 | epot = -38.510851150919 | etot = -31.0542821825791 +934000 ekin = 3.25407370525901 | erot = 4.02198516513931 | epot = -38.4343657155247 | etot = -31.1583068451264 +935000 ekin = 3.15706754617272 | erot = 3.94213624960972 | epot = -38.3842418910869 | etot = -31.2850380953045 +936000 ekin = 3.00555649828127 | erot = 4.41385590541793 | epot = -38.3669049397814 | etot = -30.9474925360822 +937000 ekin = 2.92065396617262 | erot = 4.74523400801332 | epot = -38.3453538388338 | etot = -30.6794658646479 +938000 ekin = 2.97141948473043 | erot = 4.76974809222722 | epot = -38.3344331957966 | etot = -30.5932656188389 +939000 ekin = 2.94512706992696 | erot = 4.54496818954274 | epot = -38.3244620131108 | etot = -30.8343667536411 +940000 ekin = 2.88288211336379 | erot = 4.33037795313988 | epot = -38.32262444066 | etot = -31.1093643741563 +941000 ekin = 3.0729894973384 | erot = 4.38312166999032 | epot = -38.3472582821346 | etot = -30.8911471148058 +942000 ekin = 3.09399973822793 | erot = 4.23262521183818 | epot = -38.3627707290367 | etot = -31.0361457789706 +943000 ekin = 3.0692834807418 | erot = 4.29810120769341 | epot = -38.3654861580836 | etot = -30.9981014696484 +944000 ekin = 3.05361136554782 | erot = 4.57752136432056 | epot = -38.3891229370226 | etot = -30.7579902071542 +945000 ekin = 3.1053295273393 | erot = 4.63116672909507 | epot = -38.4481824906831 | etot = -30.7116862342487 +946000 ekin = 3.22536073155692 | erot = 4.9775607801974 | epot = -38.5304457687251 | etot = -30.3275242569708 +947000 ekin = 3.22481791886501 | erot = 4.85505897631116 | epot = -38.6306947506549 | etot = -30.5508178554787 +948000 ekin = 3.31258286730489 | erot = 4.40885070504324 | epot = -38.7111926164561 | etot = -30.9897590441079 +949000 ekin = 3.2634175064554 | erot = 4.5080556255622 | epot = -38.7582101439127 | etot = -30.9867370118951 +950000 ekin = 3.38312193033095 | erot = 4.30600402576254 | epot = -38.7909813747404 | etot = -31.1018554186469 +951000 ekin = 3.4587828832488 | erot = 3.92069079490435 | epot = -38.8089483233276 | etot = -31.4294746451744 +952000 ekin = 3.42224118561198 | erot = 3.67807790241698 | epot = -38.8172186174579 | etot = -31.7168995294289 +953000 ekin = 3.5355898130389 | erot = 3.54582501818208 | epot = -38.8376037887756 | etot = -31.7561889575546 +954000 ekin = 3.7408153679097 | erot = 3.65672942044163 | epot = -38.8501623721153 | etot = -31.452617583764 +955000 ekin = 3.71100924365654 | erot = 3.89616377536035 | epot = -38.8864415175113 | etot = -31.2792684984944 +956000 ekin = 3.60593207480462 | erot = 3.6041169004468 | epot = -38.9258365620749 | etot = -31.7157875868235 +957000 ekin = 3.49530434439509 | erot = 3.82410347711554 | epot = -38.946856110473 | etot = -31.6274482889624 +958000 ekin = 3.33025913134877 | erot = 4.09361696296967 | epot = -38.9566069953684 | etot = -31.5327309010499 +959000 ekin = 3.23258633982982 | erot = 4.27749630513793 | epot = -38.9400855462529 | etot = -31.4300029012852 +960000 ekin = 3.31834124707646 | erot = 4.19167538415381 | epot = -38.9006120641386 | etot = -31.3905954329083 +961000 ekin = 3.23354004257472 | erot = 4.33974592386021 | epot = -38.8709462828611 | etot = -31.2976603164261 +962000 ekin = 3.27687420354416 | erot = 4.18251799625536 | epot = -38.8399997192042 | etot = -31.3806075194046 +963000 ekin = 3.18724078299293 | erot = 4.29559449615361 | epot = -38.8215635568147 | etot = -31.3387282776681 +964000 ekin = 3.16628639784342 | erot = 4.17929146419561 | epot = -38.8033314242491 | etot = -31.45775356221 +965000 ekin = 3.23601563824522 | erot = 4.51599223822397 | epot = -38.7801591620089 | etot = -31.0281512855397 +966000 ekin = 3.35348380272848 | erot = 3.96490873951949 | epot = -38.7593006562391 | etot = -31.4409081139911 +967000 ekin = 3.47301428118931 | erot = 3.78771221675296 | epot = -38.7263415939787 | etot = -31.4656150960365 +968000 ekin = 3.5149340684517 | erot = 3.36657292776092 | epot = -38.7364041234236 | etot = -31.854897127211 +969000 ekin = 3.55243037222559 | erot = 3.66068265314151 | epot = -38.7529284526029 | etot = -31.5398154272358 +970000 ekin = 3.63553363347277 | erot = 3.13050605621043 | epot = -38.8016144947092 | etot = -32.035574805026 +971000 ekin = 3.62760421034422 | erot = 3.43775684259623 | epot = -38.8707637872892 | etot = -31.8054027343488 +972000 ekin = 3.66143241862992 | erot = 4.04556663388657 | epot = -38.9794799026745 | etot = -31.272480850158 +973000 ekin = 3.72465898229281 | erot = 3.97416581320678 | epot = -39.0667487302085 | etot = -31.3679239347089 +974000 ekin = 3.99953950913788 | erot = 4.13912764019187 | epot = -39.1431741069699 | etot = -31.0045069576401 +975000 ekin = 4.00465817345125 | erot = 3.9952589646089 | epot = -39.1948973492943 | etot = -31.1949802112341 +976000 ekin = 4.16803719317614 | erot = 4.27607609453617 | epot = -39.2042146461383 | etot = -30.7601013584259 +977000 ekin = 4.27763535208335 | erot = 4.35785374646763 | epot = -39.1647674598219 | etot = -30.529278361271 +978000 ekin = 4.21509832146794 | erot = 3.96978575035236 | epot = -39.0661575270878 | etot = -30.8812734552675 +979000 ekin = 4.11219939771613 | erot = 3.86340161937286 | epot = -38.9126163242263 | etot = -30.9370153071373 +980000 ekin = 4.08548639230655 | erot = 3.71918260809169 | epot = -38.74606503787 | etot = -30.9413960374717 +981000 ekin = 4.02033461236225 | erot = 3.54042819636901 | epot = -38.597187758635 | etot = -31.0364249499038 +982000 ekin = 4.05981657544056 | erot = 3.65178477672051 | epot = -38.4729888125583 | etot = -30.7613874603972 +983000 ekin = 4.15649242216475 | erot = 3.62195027480219 | epot = -38.334259961066 | etot = -30.555817264099 +984000 ekin = 4.1544594314402 | erot = 3.41256983843883 | epot = -38.1946691276125 | etot = -30.6276398577335 +985000 ekin = 3.87659901087172 | erot = 3.4376780504462 | epot = -38.0505436384557 | etot = -30.7362665771378 +986000 ekin = 3.85786856381229 | erot = 3.30334700587324 | epot = -37.8996934133203 | etot = -30.7384778436347 +987000 ekin = 3.87294863787314 | erot = 3.15398232754981 | epot = -37.7929706719646 | etot = -30.7660397065416 +988000 ekin = 3.93790531951915 | erot = 3.08701498108581 | epot = -37.6532967522443 | etot = -30.6283764516394 +989000 ekin = 3.83115351568813 | erot = 3.07802242316603 | epot = -37.5101193189107 | etot = -30.6009433800565 +990000 ekin = 3.81048959043177 | erot = 3.11196082795583 | epot = -37.3832609771669 | etot = -30.4608105587793 +991000 ekin = 3.71517412131507 | erot = 3.09240412040435 | epot = -37.2833659467139 | etot = -30.4757877049945 +992000 ekin = 3.63849701384075 | erot = 2.99887074192591 | epot = -37.1786754428025 | etot = -30.5413076870358 +993000 ekin = 3.63209056043317 | erot = 3.27649085900172 | epot = -37.0906927302529 | etot = -30.182111310818 +994000 ekin = 3.5982839069315 | erot = 3.831697772683 | epot = -37.0255816353104 | etot = -29.5955999556959 +995000 ekin = 3.75927077522078 | erot = 3.45385861701412 | epot = -36.9690811728774 | etot = -29.7559517806425 +996000 ekin = 3.7162823443017 | erot = 3.37243499359166 | epot = -36.9421300931431 | etot = -29.8534127552498 +997000 ekin = 3.60416089411934 | erot = 3.31461433836019 | epot = -36.9528108756411 | etot = -30.0340356431616 +998000 ekin = 3.71457183702544 | erot = 3.42780251384766 | epot = -37.0325234658195 | etot = -29.8901491149464 +999000 ekin = 3.78703773886257 | erot = 3.63993408891207 | epot = -37.1548091593711 | etot = -29.7278373315964 +1000000 ekin = 3.83883486112572 | erot = 3.47192929391945 | epot = -37.2430911050885 | etot = -29.9323269500433 + 1000000 0.10236893 -1.4701186 0.037692055 -1.2847791 5.0290761e-05 64000 +Loop time of 84.6254 on 1 procs for 1000000 steps with 26 atoms + +Performance: 10209.700 tau/day, 11816.783 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 75.695 | 75.695 | 75.695 | 0.0 | 89.45 +Bond | 1.6447 | 1.6447 | 1.6447 | 0.0 | 1.94 +Neigh | 0.015217 | 0.015217 | 0.015217 | 0.0 | 0.02 +Comm | 0.36777 | 0.36777 | 0.36777 | 0.0 | 0.43 +Output | 0.23577 | 0.23577 | 0.23577 | 0.0 | 0.28 +Modify | 6.4486 | 6.4486 | 6.4486 | 0.0 | 7.62 +Other | | 0.2182 | | | 0.26 + +Nlocal: 26.0000 ave 26 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 301.000 ave 301 max 301 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.8.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:01:24 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 new file mode 100644 index 0000000000..fb38875e12 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 @@ -0,0 +1,1272 @@ +LAMMPS (2 Jul 2021) +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +mass * 3.1575 # sets per-type mass if not in data file +set atom * mass 3.1575 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 8 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 2.5 457145 angmom 10 +fix 2 all langevin 0.1 0.1 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.8.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 3.74991604702378 | erot = 3.45272678980464 | epot = -37.3742009011421 | etot = -30.1715580643137 +Per MPI rank memory allocation (min/avg/max) = 9.321 | 9.322 | 9.323 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.099997761 -1.4717559 0.03428661 -1.2932417 5.6146609e-05 64000 +1000 ekin = 3.92430268570824 | erot = 3.29540971313705 | epot = -37.4816670091169 | etot = -30.2619546102716 +2000 ekin = 3.88644825046428 | erot = 3.58410925014822 | epot = -37.5871874286304 | etot = -30.1166299280179 +3000 ekin = 3.90603224055461 | erot = 3.7820605745286 | epot = -37.7021302921285 | etot = -30.0140374770453 +4000 ekin = 4.02636555552402 | erot = 3.91677901140303 | epot = -37.8027608694504 | etot = -29.8596163025233 +5000 ekin = 4.05442725401043 | erot = 4.07817807460239 | epot = -37.8494362833427 | etot = -29.7168309547299 +6000 ekin = 4.13499768127483 | erot = 4.03873475277248 | epot = -37.8257365098368 | etot = -29.6520040757895 +7000 ekin = 4.08584129662811 | erot = 3.9850289293034 | epot = -37.7447761711061 | etot = -29.6739059451746 +8000 ekin = 4.04473728341538 | erot = 3.70461133282257 | epot = -37.6185211079512 | etot = -29.8691724917133 +9000 ekin = 3.97040375513034 | erot = 3.89171847539017 | epot = -37.4779912856655 | etot = -29.615869055145 +10000 ekin = 4.08064552796876 | erot = 4.10399273710614 | epot = -37.3378150214196 | etot = -29.1531767563447 +11000 ekin = 3.94505548567027 | erot = 4.14758664614568 | epot = -37.2085796341435 | etot = -29.1159375023276 +12000 ekin = 3.88687763742865 | erot = 4.11256727293729 | epot = -37.1168918341091 | etot = -29.1174469237431 +13000 ekin = 3.78376547312033 | erot = 3.94997258779547 | epot = -37.0636475805865 | etot = -29.3299095196707 +14000 ekin = 3.72114827358807 | erot = 3.8386275531307 | epot = -37.053932608354 | etot = -29.4941567816353 +15000 ekin = 3.63885725366143 | erot = 3.37568559083329 | epot = -37.0775134892156 | etot = -30.0629706447209 +16000 ekin = 3.75926862366822 | erot = 3.47832285528774 | epot = -37.1763229835918 | etot = -29.9387315046358 +17000 ekin = 3.80458992549717 | erot = 3.37818714949382 | epot = -37.3270848276042 | etot = -30.1443077526132 +18000 ekin = 3.81685915102047 | erot = 3.82235577807973 | epot = -37.4876996492703 | etot = -29.84848472017 +19000 ekin = 3.80633274630077 | erot = 3.80393283337367 | epot = -37.6386270441083 | etot = -30.0283614644338 +20000 ekin = 3.77027693322166 | erot = 3.97848447130852 | epot = -37.7861726918924 | etot = -30.0374112873623 +21000 ekin = 3.75594248876353 | erot = 3.9040052393667 | epot = -37.9165000666023 | etot = -30.256552338472 +22000 ekin = 3.81729390633802 | erot = 3.70298358069288 | epot = -38.0211478246461 | etot = -30.5008703376152 +23000 ekin = 3.86462773298721 | erot = 3.52903064555356 | epot = -38.0539868057476 | etot = -30.6603284272068 +24000 ekin = 3.84611190496181 | erot = 3.47876891204884 | epot = -38.0524942369902 | etot = -30.7276134199796 +25000 ekin = 3.88431543220182 | erot = 3.80956733596685 | epot = -38.0090041212111 | etot = -30.3151213530425 +26000 ekin = 3.88520717073553 | erot = 4.04667753560885 | epot = -37.9336134642012 | etot = -30.0017287578568 +27000 ekin = 3.83553778749005 | erot = 4.1822230688838 | epot = -37.8633670830473 | etot = -29.8456062266734 +28000 ekin = 3.83638307293675 | erot = 4.13838046178327 | epot = -37.8079901228043 | etot = -29.8332265880843 +29000 ekin = 3.81360349447098 | erot = 4.16358811310883 | epot = -37.7885827024555 | etot = -29.8113910948756 +30000 ekin = 3.89572360919447 | erot = 4.04566996469694 | epot = -37.7874054211311 | etot = -29.8460118472397 +31000 ekin = 3.89393888302725 | erot = 3.55790326104643 | epot = -37.8038131932179 | etot = -30.3519710491442 +32000 ekin = 3.80317271692925 | erot = 3.54273524643289 | epot = -37.8451815180302 | etot = -30.4992735546681 +33000 ekin = 3.78703980355198 | erot = 3.99364624500505 | epot = -37.9406281896735 | etot = -30.1599421411165 +34000 ekin = 3.77142087668814 | erot = 3.88594611308826 | epot = -38.0975843525551 | etot = -30.4402173627787 +35000 ekin = 3.71264930628472 | erot = 3.65225843687428 | epot = -38.2835289304068 | etot = -30.9186211872478 +36000 ekin = 3.74220790707646 | erot = 3.95952222810306 | epot = -38.4596915935923 | etot = -30.7579614584128 +37000 ekin = 3.82423101226182 | erot = 4.44859396622374 | epot = -38.6538277887213 | etot = -30.3810028102358 +38000 ekin = 3.69455547696867 | erot = 4.82722829899239 | epot = -38.8348230288023 | etot = -30.3130392528413 +39000 ekin = 3.59548909658498 | erot = 5.03318978839692 | epot = -38.9632877762134 | etot = -30.3346088912315 +40000 ekin = 3.72390826726257 | erot = 4.77008246177612 | epot = -39.0432740898074 | etot = -30.5492833607687 +41000 ekin = 3.7184513028698 | erot = 4.66721188475367 | epot = -39.0678678855714 | etot = -30.6822046979479 +42000 ekin = 3.54696055158215 | erot = 4.50731751167309 | epot = -39.0616854007739 | etot = -31.0074073375186 +43000 ekin = 3.57495163768253 | erot = 4.94852093613527 | epot = -39.0169365666546 | etot = -30.4934639928368 +44000 ekin = 3.52915394890511 | erot = 5.14481752350043 | epot = -38.9320102816113 | etot = -30.2580388092058 +45000 ekin = 3.36103362047068 | erot = 5.30737062665214 | epot = -38.8074049309155 | etot = -30.1390006837927 +46000 ekin = 3.33204426677162 | erot = 4.63880623753686 | epot = -38.6602813061651 | etot = -30.6894308018567 +47000 ekin = 3.3454696016767 | erot = 4.07237976376904 | epot = -38.5241501078279 | etot = -31.1063007423822 +48000 ekin = 3.40049787952109 | erot = 4.05251615432415 | epot = -38.3938498073684 | etot = -30.9408357735232 +49000 ekin = 3.31008896923646 | erot = 4.20737258711353 | epot = -38.2514760468931 | etot = -30.7340144905431 +50000 ekin = 3.27384446847297 | erot = 3.84861240213725 | epot = -38.0781706006621 | etot = -30.9557137300519 +51000 ekin = 3.28837845708164 | erot = 4.03176750511312 | epot = -37.91245244037 | etot = -30.5923064781752 +52000 ekin = 3.32612610774242 | erot = 3.69449114481266 | epot = -37.7461543084422 | etot = -30.7255370558871 +53000 ekin = 3.24704253260759 | erot = 3.82351300738073 | epot = -37.5996085904177 | etot = -30.5290530504294 +54000 ekin = 3.28722266262309 | erot = 3.86366065026162 | epot = -37.4297798097099 | etot = -30.2788964968252 +55000 ekin = 3.24079189906268 | erot = 3.69908024112645 | epot = -37.2469422361785 | etot = -30.3070700959894 +56000 ekin = 3.18312456980309 | erot = 3.4713329715515 | epot = -37.0860684089786 | etot = -30.4316108676241 +57000 ekin = 3.22541795737972 | erot = 3.05594699251095 | epot = -36.9568071104524 | etot = -30.6754421605617 +58000 ekin = 3.32107899021709 | erot = 2.99608132055998 | epot = -36.8451019319947 | etot = -30.5279416212176 +59000 ekin = 3.37756033387522 | erot = 3.02468556348912 | epot = -36.7527120143503 | etot = -30.3504661169859 +60000 ekin = 3.37838518206593 | erot = 2.80486585978148 | epot = -36.6500489307867 | etot = -30.4667978889392 +61000 ekin = 3.42593058259813 | erot = 2.57336693961351 | epot = -36.5598996921937 | etot = -30.5606021699821 +62000 ekin = 3.38330194206299 | erot = 2.48716523240096 | epot = -36.4917506706074 | etot = -30.6212834961435 +63000 ekin = 3.23944564751904 | erot = 2.68514269262914 | epot = -36.4581690118124 | etot = -30.5335806716642 +64000 ekin = 3.1285734084237 | erot = 2.81379000215892 | epot = -36.4694531808167 | etot = -30.5270897702341 +65000 ekin = 3.09729001722782 | erot = 2.97796742393485 | epot = -36.4999099304855 | etot = -30.4246524893228 +66000 ekin = 3.0253262521451 | erot = 2.98352661182229 | epot = -36.5477137383998 | etot = -30.5388608744324 +67000 ekin = 3.14798260660732 | erot = 3.20065089850766 | epot = -36.632076278664 | etot = -30.283442773549 +68000 ekin = 3.28121216444374 | erot = 3.27703862715895 | epot = -36.7797333797322 | etot = -30.2214825881296 +69000 ekin = 3.391098638729 | erot = 3.49453676740748 | epot = -36.9477169900693 | etot = -30.0620815839328 +70000 ekin = 3.52145416968697 | erot = 3.19663795891383 | epot = -37.1459833247571 | etot = -30.4278911961563 +71000 ekin = 3.72588366820861 | erot = 3.11523594110609 | epot = -37.3394708863319 | etot = -30.4983512770172 +72000 ekin = 3.87053189634938 | erot = 3.51504753627337 | epot = -37.5837173340765 | etot = -30.1981379014537 +73000 ekin = 4.04353464507253 | erot = 3.57819581965 | epot = -37.8491002809692 | etot = -30.2273698162467 +74000 ekin = 4.21655599164692 | erot = 3.67972843708669 | epot = -38.0370200626718 | etot = -30.1407356339382 +75000 ekin = 4.27518037345521 | erot = 3.50148075250718 | epot = -38.1503543696651 | etot = -30.3736932437027 +76000 ekin = 4.3926037838371 | erot = 3.17711135808543 | epot = -38.226977923484 | etot = -30.6572627815614 +77000 ekin = 4.46694156592382 | erot = 3.28356630286398 | epot = -38.2567512319257 | etot = -30.5062433631379 +78000 ekin = 4.58031785764155 | erot = 3.27581240698071 | epot = -38.2501645622443 | etot = -30.3940342976221 +79000 ekin = 4.74132912230465 | erot = 3.40062659497672 | epot = -38.2259226034579 | etot = -30.0839668861765 +80000 ekin = 4.84478519554004 | erot = 3.56980153308305 | epot = -38.1476686101295 | etot = -29.7330818815064 +81000 ekin = 4.71163727716959 | erot = 3.65201658810481 | epot = -38.0489180007763 | etot = -29.6852641355019 +82000 ekin = 4.6231089457345 | erot = 3.61128178949376 | epot = -37.9515873690418 | etot = -29.7171966338136 +83000 ekin = 4.53890753637784 | erot = 3.79707688079965 | epot = -37.8589639327866 | etot = -29.5229795156091 +84000 ekin = 4.51952558800252 | erot = 3.75897913437647 | epot = -37.8043394039476 | etot = -29.5258346815686 +85000 ekin = 4.44986224636033 | erot = 4.10169839029418 | epot = -37.7952059629823 | etot = -29.2436453263278 +86000 ekin = 4.40335859262163 | erot = 4.1830315863789 | epot = -37.8405946712624 | etot = -29.2542044922618 +87000 ekin = 4.34352629789851 | erot = 4.00093225674517 | epot = -37.898177567682 | etot = -29.5537190130383 +88000 ekin = 4.39692532206231 | erot = 3.88765396717278 | epot = -37.9120170018269 | etot = -29.6274377125919 +89000 ekin = 4.35895407807686 | erot = 4.06877052706293 | epot = -37.8812041939536 | etot = -29.4534795888138 +90000 ekin = 4.2071551167368 | erot = 3.96880041117194 | epot = -37.8268382933969 | etot = -29.6508827654882 +91000 ekin = 4.22021993231722 | erot = 4.12841045745293 | epot = -37.7475084891388 | etot = -29.3988780993687 +92000 ekin = 4.13264986882769 | erot = 3.86635436032361 | epot = -37.6428932571545 | etot = -29.6438890280032 +93000 ekin = 4.05697056146709 | erot = 3.48249980793531 | epot = -37.5034004108467 | etot = -29.9639300414443 +94000 ekin = 3.85560920909802 | erot = 3.51617278195618 | epot = -37.3716848222182 | etot = -29.999902831164 +95000 ekin = 3.70696167824248 | erot = 3.74539992686897 | epot = -37.2425364302771 | etot = -29.7901748251656 +96000 ekin = 3.64541489153293 | erot = 3.55177042583762 | epot = -37.1071295289262 | etot = -29.9099442115556 +97000 ekin = 3.59427366044318 | erot = 3.58237376190948 | epot = -36.990331249798 | etot = -29.8136838274454 +98000 ekin = 3.36609732779909 | erot = 3.78920076230077 | epot = -36.8893462899051 | etot = -29.7340481998052 +99000 ekin = 3.24308716626529 | erot = 3.98439513504793 | epot = -36.7958275145338 | etot = -29.5683452132205 +100000 ekin = 3.10105716620534 | erot = 3.88380514199007 | epot = -36.7237148853891 | etot = -29.7388525771937 +101000 ekin = 3.0539281420833 | erot = 3.92712981026617 | epot = -36.7019624525075 | etot = -29.720904500158 +102000 ekin = 3.21793305977278 | erot = 4.11601242104548 | epot = -36.7682713932651 | etot = -29.4343259124469 +103000 ekin = 3.29518049820534 | erot = 4.13622147772537 | epot = -36.8839850328144 | etot = -29.4525830568837 +104000 ekin = 3.38349143563989 | erot = 4.11834556660366 | epot = -37.0170458924467 | etot = -29.5152088902031 +105000 ekin = 3.43063719220731 | erot = 4.19281995644328 | epot = -37.1501255032183 | etot = -29.5266683545677 +106000 ekin = 3.39305878697925 | erot = 4.59139499879988 | epot = -37.2962927183006 | etot = -29.3118389325215 +107000 ekin = 3.49611625167404 | erot = 4.42190170056934 | epot = -37.429825379218 | etot = -29.5118074269746 +108000 ekin = 3.59165643487548 | erot = 4.73333858652907 | epot = -37.4821370449025 | etot = -29.1571420234979 +109000 ekin = 3.59878557010273 | erot = 5.08720641062768 | epot = -37.4454225962912 | etot = -28.7594306155607 +110000 ekin = 3.52607850054496 | erot = 4.92743402067516 | epot = -37.33464551381 | etot = -28.8811329925899 +111000 ekin = 3.52196404281898 | erot = 4.48970120472513 | epot = -37.2166378630308 | etot = -29.2049726154866 +112000 ekin = 3.64094551226764 | erot = 4.18578082474288 | epot = -37.1356107687899 | etot = -29.3088844317794 +113000 ekin = 3.59908785035481 | erot = 3.81929848767576 | epot = -37.1563156196511 | etot = -29.7379292816205 +114000 ekin = 3.73247165614536 | erot = 3.71912191326134 | epot = -37.1841072802385 | etot = -29.7325137108319 +115000 ekin = 3.81386546938822 | erot = 3.49889872890813 | epot = -37.2616543115736 | etot = -29.9488901132773 +116000 ekin = 4.05829999340879 | erot = 3.583906655014 | epot = -37.400300568259 | etot = -29.7580939198362 +117000 ekin = 4.2755011092504 | erot = 3.79076820440129 | epot = -37.5923004712666 | etot = -29.5260311576149 +118000 ekin = 4.45490103530211 | erot = 3.7791518579582 | epot = -37.7846946186124 | etot = -29.5506417253521 +119000 ekin = 4.58790399115629 | erot = 3.86870152715712 | epot = -37.9811558924432 | etot = -29.5245503741297 +120000 ekin = 4.92259141545339 | erot = 3.84940365834989 | epot = -38.1382043293411 | etot = -29.3662092555378 +121000 ekin = 5.13183269148587 | erot = 4.03705087488501 | epot = -38.2560800244006 | etot = -29.0871964580297 +122000 ekin = 5.17140868558149 | erot = 3.61810962674126 | epot = -38.3381390234361 | etot = -29.5486207111134 +123000 ekin = 5.28384467069883 | erot = 4.14897954513985 | epot = -38.3803925391065 | etot = -28.9475683232678 +124000 ekin = 5.45144965935765 | erot = 3.74948516195918 | epot = -38.4152715166926 | etot = -29.2143366953758 +125000 ekin = 5.49907232704439 | erot = 3.62957174075199 | epot = -38.4698081948493 | etot = -29.3411641270529 +126000 ekin = 5.8127555292288 | erot = 3.50370762045619 | epot = -38.5369283444353 | etot = -29.2204651947503 +127000 ekin = 5.71810535961404 | erot = 3.50153411217259 | epot = -38.6097648991191 | etot = -29.3901254273324 +128000 ekin = 5.59769610955136 | erot = 2.99726680348461 | epot = -38.6545287261793 | etot = -30.0595658131433 +129000 ekin = 5.5165718206709 | erot = 3.37515224045301 | epot = -38.6909141535705 | etot = -29.7991900924466 +130000 ekin = 5.46626997343509 | erot = 3.77525421867709 | epot = -38.7059148210798 | etot = -29.4643906289676 +131000 ekin = 5.36987741440168 | erot = 3.92459463488603 | epot = -38.6781199948589 | etot = -29.3836479455712 +132000 ekin = 5.13704854269979 | erot = 3.89365302265496 | epot = -38.6113331110922 | etot = -29.5806315457375 +133000 ekin = 5.04851208372161 | erot = 4.17613618410271 | epot = -38.4969113589743 | etot = -29.2722630911499 +134000 ekin = 4.96335667475928 | erot = 4.28428652813699 | epot = -38.3084161100388 | etot = -29.0607729071425 +135000 ekin = 4.67485522816786 | erot = 3.71485446936997 | epot = -38.043760165967 | etot = -29.6540504684292 +136000 ekin = 4.48906299160435 | erot = 4.19015103736174 | epot = -37.7533241067268 | etot = -29.0741100777607 +137000 ekin = 4.31371561077628 | erot = 3.47925724303279 | epot = -37.4739407743091 | etot = -29.6809679205001 +138000 ekin = 3.96696543473046 | erot = 3.71675428283144 | epot = -37.2042587721449 | etot = -29.520539054583 +139000 ekin = 3.59101315513257 | erot = 3.64278698721023 | epot = -36.9457852108065 | etot = -29.7119850684637 +140000 ekin = 3.44095423425056 | erot = 3.49830537198601 | epot = -36.7203613080885 | etot = -29.7811017018519 +141000 ekin = 3.36296546737416 | erot = 3.56983741924016 | epot = -36.496476745137 | etot = -29.5636738585227 +142000 ekin = 3.18252441669298 | erot = 3.32935464682707 | epot = -36.324475892532 | etot = -29.812596829012 +143000 ekin = 3.18465930443875 | erot = 3.56170045589758 | epot = -36.2215210957517 | etot = -29.4751613354154 +144000 ekin = 3.08106725409761 | erot = 3.50261030291577 | epot = -36.151244725806 | etot = -29.5675671687926 +145000 ekin = 3.0809377636579 | erot = 3.51948185643664 | epot = -36.0863085456325 | etot = -29.4858889255379 +146000 ekin = 3.02030159479372 | erot = 3.37397305462396 | epot = -36.0845314152705 | etot = -29.6902567658529 +147000 ekin = 3.04139072985625 | erot = 3.36603954258544 | epot = -36.1557232229402 | etot = -29.7482929504985 +148000 ekin = 3.14853067203546 | erot = 3.14562859809661 | epot = -36.2494960139436 | etot = -29.9553367438116 +149000 ekin = 3.18195150813254 | erot = 3.58071760906396 | epot = -36.3477640598877 | etot = -29.5850949426912 +150000 ekin = 3.21133048799954 | erot = 3.85389957660273 | epot = -36.4132627454726 | etot = -29.3480326808703 +151000 ekin = 3.34144104231994 | erot = 3.4939153763212 | epot = -36.478294453089 | etot = -29.6429380344479 +152000 ekin = 3.38469121090087 | erot = 3.35926284582863 | epot = -36.5578474424846 | etot = -29.8138933857551 +153000 ekin = 3.52527639525619 | erot = 3.56811727016302 | epot = -36.6674257186119 | etot = -29.5740320531927 +154000 ekin = 3.77924799771019 | erot = 3.52145795256778 | epot = -36.762260192104 | etot = -29.4615542418261 +155000 ekin = 3.83418008764597 | erot = 3.28305394597542 | epot = -36.8282659682366 | etot = -29.7110319346152 +156000 ekin = 3.87517167307501 | erot = 2.75621015438911 | epot = -36.8507311290658 | etot = -30.2193493016017 +157000 ekin = 3.89846784481905 | erot = 3.03513966490474 | epot = -36.8490467787065 | etot = -29.9154392689827 +158000 ekin = 3.86372390524152 | erot = 3.067331408384 | epot = -36.8143502444314 | etot = -29.8832949308059 +159000 ekin = 3.8756082258688 | erot = 2.72238394226933 | epot = -36.772006665376 | etot = -30.1740144972379 +160000 ekin = 3.816595406495 | erot = 2.7916288304199 | epot = -36.7456092138712 | etot = -30.1373849769563 +161000 ekin = 3.90364665450467 | erot = 2.85891130626936 | epot = -36.6767188031102 | etot = -29.9141608423362 +162000 ekin = 3.93432840871765 | erot = 3.23277686088016 | epot = -36.6068502811304 | etot = -29.4397450115325 +163000 ekin = 3.97425577903384 | erot = 2.70754263327067 | epot = -36.5720643915927 | etot = -29.8902659792882 +164000 ekin = 3.91949827572841 | erot = 3.0566880418144 | epot = -36.581283859358 | etot = -29.6050975418151 +165000 ekin = 3.9942517956167 | erot = 3.29785069907587 | epot = -36.6379374004759 | etot = -29.3458349057833 +166000 ekin = 4.02904533815552 | erot = 3.36634066781836 | epot = -36.7340868254039 | etot = -29.33870081943 +167000 ekin = 4.03733260337014 | erot = 3.51733984448515 | epot = -36.8476519248274 | etot = -29.2929794769721 +168000 ekin = 4.01641387278363 | erot = 3.37538682559175 | epot = -36.971098022016 | etot = -29.5792973236406 +169000 ekin = 3.94799788750035 | erot = 3.38842418926848 | epot = -37.1207420196436 | etot = -29.7843199428747 +170000 ekin = 3.98944239104564 | erot = 3.56779767670635 | epot = -37.292260024934 | etot = -29.735019957182 +171000 ekin = 4.04980262307328 | erot = 3.8730831046424 | epot = -37.4956434312018 | etot = -29.5727577034861 +172000 ekin = 4.10498686245119 | erot = 4.24595756362535 | epot = -37.6879527015218 | etot = -29.3370082754453 +173000 ekin = 4.12919710204917 | erot = 4.28575123018794 | epot = -37.8940672883491 | etot = -29.479118956112 +174000 ekin = 4.04607401980725 | erot = 4.41784593637421 | epot = -38.1063274639935 | etot = -29.642407507812 +175000 ekin = 4.13007220306937 | erot = 4.3967913469306 | epot = -38.3139522350313 | etot = -29.7870886850313 +176000 ekin = 4.1414636964047 | erot = 4.25565002500116 | epot = -38.5085743578727 | etot = -30.1114606364668 +177000 ekin = 4.33605278083852 | erot = 4.58687123058771 | epot = -38.663345411644 | etot = -29.7404214002177 +178000 ekin = 4.3268891648432 | erot = 4.50454813785607 | epot = -38.7700089206451 | etot = -29.9385716179458 +179000 ekin = 4.39331384776191 | erot = 4.88121292734115 | epot = -38.8147888868657 | etot = -29.5402621117627 +180000 ekin = 4.36409495919781 | erot = 4.62653667682595 | epot = -38.7920356589674 | etot = -29.8014040229436 +181000 ekin = 4.40002739116619 | erot = 4.26572305349555 | epot = -38.732090098002 | etot = -30.0663396533403 +182000 ekin = 4.38584471768798 | erot = 4.03958660380944 | epot = -38.6652721860918 | etot = -30.2398408645944 +183000 ekin = 4.38872118980235 | erot = 4.03920994265157 | epot = -38.5494953603399 | etot = -30.121564227886 +184000 ekin = 4.58261674670928 | erot = 4.09854761999429 | epot = -38.385824841967 | etot = -29.7046604752634 +185000 ekin = 4.61324410405523 | erot = 4.15998485211153 | epot = -38.1895073749228 | etot = -29.416278418756 +186000 ekin = 4.58712030480541 | erot = 3.80292929559516 | epot = -37.9691363595882 | etot = -29.5790867591876 +187000 ekin = 4.49704057160018 | erot = 3.79953063209063 | epot = -37.7563677349906 | etot = -29.4597965312998 +188000 ekin = 4.67801335458731 | erot = 3.94614018085653 | epot = -37.5596730791519 | etot = -28.9355195437081 +189000 ekin = 4.72635028851209 | erot = 3.97986342680415 | epot = -37.3737961852725 | etot = -28.6675824699563 +190000 ekin = 4.7042288678312 | erot = 3.76567525080941 | epot = -37.196832874262 | etot = -28.7269287556214 +191000 ekin = 4.76615905270403 | erot = 4.11771710042025 | epot = -37.0524866708229 | etot = -28.1686105176986 +192000 ekin = 4.66334615993905 | erot = 4.32180108624872 | epot = -36.9281089002537 | etot = -27.9429616540659 +193000 ekin = 4.54227272612665 | erot = 4.37403333624804 | epot = -36.8106507982267 | etot = -27.894344735852 +194000 ekin = 4.462583886268 | erot = 4.57094153868338 | epot = -36.7126835627942 | etot = -27.6791581378429 +195000 ekin = 4.26009039309661 | erot = 5.10893274622673 | epot = -36.6717506302939 | etot = -27.3027274909705 +196000 ekin = 4.24016895096413 | erot = 4.95101320260786 | epot = -36.6607739952153 | etot = -27.4695918416433 +197000 ekin = 4.07555507933054 | erot = 5.3373115761178 | epot = -36.6886082622519 | etot = -27.2757416068035 +198000 ekin = 3.98091713951368 | erot = 5.37374733968393 | epot = -36.7238260637148 | etot = -27.3691615845172 +199000 ekin = 4.0006733079207 | erot = 5.36035180423053 | epot = -36.7643724815872 | etot = -27.403347369436 +200000 ekin = 3.91652525767982 | erot = 4.88675678602831 | epot = -36.7730308398529 | etot = -27.9697487961448 +201000 ekin = 3.81609915882208 | erot = 4.31400854830159 | epot = -36.7481890160651 | etot = -28.6180813089414 +202000 ekin = 3.71932569397591 | erot = 4.38569878861434 | epot = -36.6956778034205 | etot = -28.5906533208303 +203000 ekin = 3.6429062307207 | erot = 4.3750378945926 | epot = -36.6304609598585 | etot = -28.6125168345452 +204000 ekin = 3.52854777039972 | erot = 4.29732321046263 | epot = -36.5744389849187 | etot = -28.7485680040564 +205000 ekin = 3.47688319826114 | erot = 4.05205396768161 | epot = -36.531456554712 | etot = -29.0025193887692 +206000 ekin = 3.57867350058512 | erot = 4.2868191467488 | epot = -36.5152410045852 | etot = -28.6497483572513 +207000 ekin = 3.67789472949123 | erot = 4.07649115773256 | epot = -36.4807964879222 | etot = -28.7264106006985 +208000 ekin = 3.75162300302636 | erot = 3.99412890438549 | epot = -36.4719013777705 | etot = -28.7261494703586 +209000 ekin = 3.82882555476977 | erot = 4.07806686544388 | epot = -36.5274965379165 | etot = -28.6206041177029 +210000 ekin = 3.9458995738135 | erot = 4.05524037388635 | epot = -36.6356567037899 | etot = -28.6345167560901 +211000 ekin = 4.07654365300251 | erot = 3.99406586158705 | epot = -36.7715123193756 | etot = -28.7009028047861 +212000 ekin = 4.28409313331832 | erot = 4.41351434873083 | epot = -36.9240266223076 | etot = -28.2264191402585 +213000 ekin = 4.49200123945991 | erot = 4.57752549048093 | epot = -37.0744914076607 | etot = -28.0049646777198 +214000 ekin = 4.68170470060552 | erot = 4.83486386570226 | epot = -37.2372407583265 | etot = -27.7206721920187 +215000 ekin = 4.98081379617907 | erot = 4.46606343482571 | epot = -37.4068324828893 | etot = -27.9599552518845 +216000 ekin = 5.16729766417649 | erot = 4.60318830168464 | epot = -37.546455570517 | etot = -27.7759696046559 +217000 ekin = 5.38386929678543 | erot = 4.77752494373566 | epot = -37.6405601527457 | etot = -27.4791659122246 +218000 ekin = 5.7058164504652 | erot = 4.70370884810736 | epot = -37.698401969983 | etot = -27.2888766714105 +219000 ekin = 5.88600523163575 | erot = 4.58694924042826 | epot = -37.7125786046513 | etot = -27.2396241325873 +220000 ekin = 6.15427965488963 | erot = 4.42931316972489 | epot = -37.6846020761394 | etot = -27.1010092515249 +221000 ekin = 6.20955938015943 | erot = 4.54001725187623 | epot = -37.6213945439905 | etot = -26.8718179119549 +222000 ekin = 6.24568472622515 | erot = 4.97311797105802 | epot = -37.5132484834206 | etot = -26.2944457861374 +223000 ekin = 6.23087495739475 | erot = 4.87026240860754 | epot = -37.4093126450282 | etot = -26.3081752790259 +224000 ekin = 6.34215727178104 | erot = 4.95416073100343 | epot = -37.3138628835635 | etot = -26.017544880779 +225000 ekin = 6.34418551658282 | erot = 4.97197547495999 | epot = -37.2296241301023 | etot = -25.9134631385595 +226000 ekin = 6.27234146176753 | erot = 4.712320761698 | epot = -37.16490911443 | etot = -26.1802468909645 +227000 ekin = 6.29782050547387 | erot = 4.64279996368984 | epot = -37.1521034204924 | etot = -26.2114829513287 +228000 ekin = 6.45215375342329 | erot = 4.66543105642573 | epot = -37.1176036705896 | etot = -26.0000188607406 +229000 ekin = 6.57609932445413 | erot = 4.31104294387352 | epot = -37.0319087568376 | etot = -26.1447664885099 +230000 ekin = 6.3941596764924 | erot = 4.16613500609599 | epot = -36.9020701489014 | etot = -26.341775466313 +231000 ekin = 6.06981997767513 | erot = 4.16164382030047 | epot = -36.7672531588279 | etot = -26.5357893608523 +232000 ekin = 6.07851417086582 | erot = 3.92614169635025 | epot = -36.6287349588706 | etot = -26.6240790916545 +233000 ekin = 5.86578448983374 | erot = 3.89415959164517 | epot = -36.465034335415 | etot = -26.7050902539361 +234000 ekin = 5.66525736866247 | erot = 3.89419060194184 | epot = -36.3317105619283 | etot = -26.772262591324 +235000 ekin = 5.45947253618382 | erot = 3.51915643493605 | epot = -36.1877403763664 | etot = -27.2091114052465 +236000 ekin = 5.23839596197748 | erot = 3.35080370425763 | epot = -36.0601413821509 | etot = -27.4709417159157 +237000 ekin = 5.11015038693027 | erot = 3.41418634041097 | epot = -35.9797234474552 | etot = -27.455386720114 +238000 ekin = 5.07705507560246 | erot = 3.55422258848944 | epot = -35.9558941013165 | etot = -27.3246164372246 +239000 ekin = 5.11036683512567 | erot = 3.60903830571379 | epot = -35.9686036709486 | etot = -27.2491985301092 +240000 ekin = 5.05273101840451 | erot = 3.85355249273515 | epot = -36.0380166955248 | etot = -27.1317331843852 +241000 ekin = 5.09369536459292 | erot = 3.6433800043733 | epot = -36.1343234897539 | etot = -27.3972481207877 +242000 ekin = 5.26488817621227 | erot = 4.01055195692897 | epot = -36.2412063129141 | etot = -26.9657661797729 +243000 ekin = 5.23195261672929 | erot = 4.46546566729833 | epot = -36.345605429643 | etot = -26.6481871456153 +244000 ekin = 5.22638739434401 | erot = 4.31088904489896 | epot = -36.4415840114135 | etot = -26.9043075721705 +245000 ekin = 5.44853137039486 | erot = 4.17607977278288 | epot = -36.5182986507189 | etot = -26.8936875075411 +246000 ekin = 5.51456970399734 | erot = 3.7459544203853 | epot = -36.5760003166761 | etot = -27.3154761922935 +247000 ekin = 5.60809096899872 | erot = 4.15307717654149 | epot = -36.6102851986096 | etot = -26.8491170530694 +248000 ekin = 5.44607700345041 | erot = 4.00137483235449 | epot = -36.6173189081378 | etot = -27.1698670723329 +249000 ekin = 5.39824066997391 | erot = 4.00527284085302 | epot = -36.6178595818604 | etot = -27.2143460710335 +250000 ekin = 5.40591864200621 | erot = 3.83152692098389 | epot = -36.5913298844141 | etot = -27.3538843214239 +251000 ekin = 5.42515843147756 | erot = 3.74120297831872 | epot = -36.5372880481644 | etot = -27.3709266383681 +252000 ekin = 5.4712575658911 | erot = 3.93923600749343 | epot = -36.4718103145524 | etot = -27.0613167411679 +253000 ekin = 5.45280164405796 | erot = 4.07788577485834 | epot = -36.3971958399354 | etot = -26.8665084210191 +254000 ekin = 5.351360104931 | erot = 4.05065697891534 | epot = -36.3208515747331 | etot = -26.9188344908867 +255000 ekin = 5.26929844479126 | erot = 3.99546469631013 | epot = -36.2503502909171 | etot = -26.9855871498158 +256000 ekin = 5.28023678974981 | erot = 4.22040986008114 | epot = -36.1946445254556 | etot = -26.6939978756247 +257000 ekin = 5.06048081748237 | erot = 4.23177072887926 | epot = -36.1310700373981 | etot = -26.8388184910365 +258000 ekin = 5.04266904507291 | erot = 4.32321520327971 | epot = -36.0647093578756 | etot = -26.6988251095229 +259000 ekin = 4.83091830266356 | erot = 4.34656742782584 | epot = -36.0089991272069 | etot = -26.8315133967175 +260000 ekin = 4.836699911676 | erot = 4.25709648660297 | epot = -35.96970369746 | etot = -26.875907299181 +261000 ekin = 4.77396719262991 | erot = 4.0929221497623 | epot = -35.9054139064718 | etot = -27.0385245640796 +262000 ekin = 4.6660127085841 | erot = 3.73102576614632 | epot = -35.8157479345105 | etot = -27.4187094597801 +263000 ekin = 4.58027061960237 | erot = 3.74679758350867 | epot = -35.7631254737833 | etot = -27.4360572706722 +264000 ekin = 4.65921569864907 | erot = 3.90501973343979 | epot = -35.7356757776858 | etot = -27.1714403455969 +265000 ekin = 4.67586149937357 | erot = 3.94654925905527 | epot = -35.7049387943769 | etot = -27.0825280359481 +266000 ekin = 4.69584694538616 | erot = 3.98055672084523 | epot = -35.6673176149281 | etot = -26.9909139486967 +267000 ekin = 4.78499421533014 | erot = 4.0364816915833 | epot = -35.6392507408913 | etot = -26.8177748339778 +268000 ekin = 4.84316914009132 | erot = 3.9986077800244 | epot = -35.6448334716871 | etot = -26.8030565515714 +269000 ekin = 4.90837806472402 | erot = 4.04652570535906 | epot = -35.6496420701673 | etot = -26.6947383000842 +270000 ekin = 4.78579400655356 | erot = 4.34179455226934 | epot = -35.6115561484025 | etot = -26.4839675895796 +271000 ekin = 4.85153732395834 | erot = 3.76641259729514 | epot = -35.613775306659 | etot = -26.9958253854055 +272000 ekin = 4.97803664593813 | erot = 4.19853764559888 | epot = -35.66422567808 | etot = -26.487651386543 +273000 ekin = 4.99431287425886 | erot = 4.16775756950246 | epot = -35.7125500141237 | etot = -26.5504795703624 +274000 ekin = 5.02755533075327 | erot = 4.06015777810426 | epot = -35.7335253506941 | etot = -26.6458122418365 +275000 ekin = 4.96372481963275 | erot = 4.27522667590852 | epot = -35.7375976828865 | etot = -26.4986461873452 +276000 ekin = 5.07934127118678 | erot = 4.03884457577036 | epot = -35.7684807851686 | etot = -26.6502949382115 +277000 ekin = 5.11065676525152 | erot = 3.89593355388357 | epot = -35.8299825238668 | etot = -26.8233922047317 +278000 ekin = 5.14434493464948 | erot = 4.10431801630069 | epot = -35.9156424264978 | etot = -26.6669794755476 +279000 ekin = 5.13854043459747 | erot = 3.33687958464002 | epot = -35.9567280939811 | etot = -27.4813080747437 +280000 ekin = 5.13698711985543 | erot = 3.1321095347802 | epot = -35.9663254349012 | etot = -27.6972287802656 +281000 ekin = 5.12014323326354 | erot = 3.01072130069868 | epot = -35.9687821467586 | etot = -27.8379176127964 +282000 ekin = 5.0748729819616 | erot = 2.78222371236629 | epot = -35.9666224009213 | etot = -28.1095257065934 +283000 ekin = 4.93728532174382 | erot = 2.51682526487889 | epot = -36.0092096947433 | etot = -28.5550991081205 +284000 ekin = 5.10799487537326 | erot = 2.34406164243711 | epot = -36.0766867016223 | etot = -28.6246301838119 +285000 ekin = 5.21438921802967 | erot = 2.42355410917311 | epot = -36.1686025783611 | etot = -28.5306592511584 +286000 ekin = 5.22674428893558 | erot = 2.43127546535952 | epot = -36.2811716154217 | etot = -28.6231518611266 +287000 ekin = 5.42842235635899 | erot = 2.80110266939532 | epot = -36.3926299688269 | etot = -28.1631049430726 +288000 ekin = 5.53841609379804 | erot = 3.04198571498546 | epot = -36.5118610231694 | etot = -27.9314592143859 +289000 ekin = 5.3467040301105 | erot = 3.09938875481675 | epot = -36.6304827875393 | etot = -28.184390002612 +290000 ekin = 5.34231674745426 | erot = 3.31160144161375 | epot = -36.7456392368754 | etot = -28.0917210478074 +291000 ekin = 5.36188526202177 | erot = 3.45917476353394 | epot = -36.8302537236161 | etot = -28.0091936980603 +292000 ekin = 5.47780509141152 | erot = 3.77906726321804 | epot = -36.8842491471654 | etot = -27.6273767925359 +293000 ekin = 5.28302000096844 | erot = 3.57818629599035 | epot = -36.8949841799423 | etot = -28.0337778829835 +294000 ekin = 5.30853543438815 | erot = 3.56263204697584 | epot = -36.8825736697856 | etot = -28.0114061884216 +295000 ekin = 5.20536069491162 | erot = 3.77206495855666 | epot = -36.8703913967998 | etot = -27.8929657433315 +296000 ekin = 5.16948391824595 | erot = 3.64242202500107 | epot = -36.8524591521914 | etot = -28.0405532089444 +297000 ekin = 5.14948698293416 | erot = 3.5630007131842 | epot = -36.8077681088433 | etot = -28.095280412725 +298000 ekin = 5.07831718808015 | erot = 3.56647326916591 | epot = -36.7441951556035 | etot = -28.0994046983574 +299000 ekin = 5.07638833142119 | erot = 3.33911289208736 | epot = -36.7050879472261 | etot = -28.2895867237176 +300000 ekin = 5.03413727775465 | erot = 3.74853034027346 | epot = -36.6636621891821 | etot = -27.880994571154 +301000 ekin = 4.97235848835827 | erot = 3.32835758650059 | epot = -36.6711630757898 | etot = -28.370447000931 +302000 ekin = 5.0096895871007 | erot = 3.04854259478463 | epot = -36.7093256921458 | etot = -28.6510935102605 +303000 ekin = 5.12929110471125 | erot = 3.0802372254872 | epot = -36.7951841728067 | etot = -28.5856558426083 +304000 ekin = 5.16690416140484 | erot = 3.34049274708998 | epot = -36.9126194047401 | etot = -28.4052224962453 +305000 ekin = 5.23349789631504 | erot = 3.46551744359714 | epot = -37.0448370009165 | etot = -28.3458216610043 +306000 ekin = 5.2886097452738 | erot = 3.56105103024495 | epot = -37.1811985422466 | etot = -28.3315377667279 +307000 ekin = 5.40125295123197 | erot = 3.87520415097948 | epot = -37.30553234416 | etot = -28.0290752419485 +308000 ekin = 5.46740727789042 | erot = 3.91865002312583 | epot = -37.389277815527 | etot = -28.0032205145107 +309000 ekin = 5.43990046762824 | erot = 4.00265425349909 | epot = -37.4336308324254 | etot = -27.991076111298 +310000 ekin = 5.38744019614249 | erot = 3.91760045067581 | epot = -37.4766997166659 | etot = -28.1716590698476 +311000 ekin = 5.54869794564873 | erot = 3.97913763348747 | epot = -37.5380640420298 | etot = -28.0102284628936 +312000 ekin = 5.71519006739875 | erot = 4.09263126769848 | epot = -37.5745318459452 | etot = -27.766710510848 +313000 ekin = 5.60331607661102 | erot = 3.83543196463859 | epot = -37.6101139619702 | etot = -28.1713659207206 +314000 ekin = 5.5180041708143 | erot = 3.7494474523439 | epot = -37.6279066647949 | etot = -28.3604550416367 +315000 ekin = 5.47833005901007 | erot = 4.08581993263796 | epot = -37.6406124353411 | etot = -28.0764624436931 +316000 ekin = 5.33860837296308 | erot = 4.51116644302033 | epot = -37.6217312448187 | etot = -27.7719564288353 +317000 ekin = 5.23941916557626 | erot = 4.78689518832633 | epot = -37.5731600528525 | etot = -27.5468456989499 +318000 ekin = 5.11187775633088 | erot = 4.8295881268003 | epot = -37.5155006216098 | etot = -27.5740347384786 +319000 ekin = 5.22954347525669 | erot = 4.49457407004892 | epot = -37.4371163833055 | etot = -27.7129988379999 +320000 ekin = 5.30878948863373 | erot = 4.92186054084621 | epot = -37.3586788029377 | etot = -27.1280287734577 +321000 ekin = 5.25051542685368 | erot = 4.81963950413293 | epot = -37.3122945279909 | etot = -27.2421395970043 +322000 ekin = 5.07574443571119 | erot = 4.74007360204251 | epot = -37.2420599117422 | etot = -27.4262418739885 +323000 ekin = 5.0265325350937 | erot = 4.66604787555056 | epot = -37.1620424354779 | etot = -27.4694620248336 +324000 ekin = 5.12999279273048 | erot = 4.55456244400843 | epot = -37.1081993843435 | etot = -27.4236441476046 +325000 ekin = 5.01484863365259 | erot = 5.03270116093541 | epot = -37.0549970668844 | etot = -27.0074472722964 +326000 ekin = 5.15105125743363 | erot = 4.77726330645675 | epot = -37.0062804471437 | etot = -27.0779658832534 +327000 ekin = 5.17373663939357 | erot = 4.75720955177068 | epot = -36.9735735310225 | etot = -27.0426273398583 +328000 ekin = 5.3265809986392 | erot = 4.45847251670634 | epot = -36.9463177254326 | etot = -27.1612642100871 +329000 ekin = 5.28491385975229 | erot = 4.23650020870599 | epot = -36.9151642788529 | etot = -27.3937502103946 +330000 ekin = 5.12552135481235 | erot = 4.79027984581653 | epot = -36.8863179466158 | etot = -26.9705167459869 +331000 ekin = 5.12103290586643 | erot = 5.03778117543898 | epot = -36.841363047454 | etot = -26.6825489661486 +332000 ekin = 5.06929714597605 | erot = 4.90820597157557 | epot = -36.7488012231946 | etot = -26.771298105643 +333000 ekin = 4.96505468499555 | erot = 5.01335794632778 | epot = -36.6271163009911 | etot = -26.6487036696678 +334000 ekin = 4.99343125906659 | erot = 5.01439694959199 | epot = -36.5036049758887 | etot = -26.4957767672301 +335000 ekin = 4.90069371729875 | erot = 4.54385275511657 | epot = -36.3777599646381 | etot = -26.9332134922228 +336000 ekin = 5.07863725672875 | erot = 4.69305135725135 | epot = -36.2629152842756 | etot = -26.4912266702956 +337000 ekin = 4.94799955754133 | erot = 4.52583833193069 | epot = -36.1612360033462 | etot = -26.6873981138742 +338000 ekin = 4.85224868200284 | erot = 4.50041298245555 | epot = -36.0752991866383 | etot = -26.7226375221799 +339000 ekin = 4.72144640536423 | erot = 4.54752039051223 | epot = -35.9970632546972 | etot = -26.7280964588208 +340000 ekin = 4.80943098922164 | erot = 4.34708343509498 | epot = -35.9687361528352 | etot = -26.8122217285186 +341000 ekin = 4.70361214653931 | erot = 4.47793300498463 | epot = -35.9999322617905 | etot = -26.8183871102666 +342000 ekin = 4.76064761481744 | erot = 4.66605256976241 | epot = -36.0433784122729 | etot = -26.616678227693 +343000 ekin = 4.67728032528768 | erot = 4.6610083917642 | epot = -35.9211632159824 | etot = -26.5828744989305 +344000 ekin = 4.96339724601181 | erot = 4.93823124551168 | epot = -36.2212250614817 | etot = -26.3195965699582 +345000 ekin = 4.92216540601158 | erot = 5.10460165774345 | epot = -36.3841924486034 | etot = -26.3574253848484 +346000 ekin = 4.99792813974856 | erot = 4.77882820289903 | epot = -36.4406602112533 | etot = -26.6639038686057 +347000 ekin = 4.97738387739107 | erot = 4.57238123569529 | epot = -36.4353446283208 | etot = -26.8855795152344 +348000 ekin = 4.92451917191307 | erot = 4.32330547944774 | epot = -36.3741726686486 | etot = -27.1263480172878 +349000 ekin = 4.7901834448853 | erot = 4.64955099606445 | epot = -36.2232051796221 | etot = -26.7834707386723 +350000 ekin = 4.74997485376102 | erot = 4.41441619333004 | epot = -36.0086530481284 | etot = -26.8442620010373 +351000 ekin = 4.65861306362097 | erot = 4.54712008187945 | epot = -35.7312651155867 | etot = -26.5255319700863 +352000 ekin = 4.64876538273139 | erot = 4.76138349321515 | epot = -35.4506369361125 | etot = -26.0404880601659 +353000 ekin = 4.59253342080998 | erot = 4.29456686626234 | epot = -35.1553683981332 | etot = -26.2682681110609 +354000 ekin = 4.53810163149175 | erot = 4.43945254667827 | epot = -34.9111484982539 | etot = -25.9335943200839 +355000 ekin = 4.47391617267565 | erot = 4.20275229581248 | epot = -34.7382448152827 | etot = -26.0615763467945 +356000 ekin = 4.33084740359816 | erot = 4.16589789857799 | epot = -34.6459462576645 | etot = -26.1492009554884 +357000 ekin = 4.27639689643504 | erot = 4.49834201135675 | epot = -34.6234093478584 | etot = -25.8486704400666 +358000 ekin = 4.37058163127524 | erot = 4.6282751781028 | epot = -34.6601229270853 | etot = -25.6612661177073 +359000 ekin = 4.33282658147824 | erot = 4.35852771696217 | epot = -34.7355034140381 | etot = -26.0441491155977 +360000 ekin = 4.23025745994598 | erot = 3.7369218729668 | epot = -34.827271441646 | etot = -26.8600921087332 +361000 ekin = 4.32772510308485 | erot = 3.40799158120903 | epot = -34.9260321184264 | etot = -27.1903154341325 +362000 ekin = 4.4377220758705 | erot = 3.92824256651614 | epot = -35.0362517129441 | etot = -26.6702870705575 +363000 ekin = 4.60059512711655 | erot = 3.78527820800773 | epot = -35.149230388508 | etot = -26.7633570533837 +364000 ekin = 4.67620778921741 | erot = 3.65656363116 | epot = -35.2108467629341 | etot = -26.8780753425567 +365000 ekin = 4.68744796027325 | erot = 3.48647035761111 | epot = -35.257929142539 | etot = -27.0840108246547 +366000 ekin = 4.6317169465738 | erot = 3.80732263161735 | epot = -35.3317328424945 | etot = -26.8926932643033 +367000 ekin = 4.58794520776095 | erot = 4.31664541166351 | epot = -35.4114076873989 | etot = -26.5068170679744 +368000 ekin = 4.53697760644319 | erot = 4.37812449310847 | epot = -35.4654560531487 | etot = -26.550353953597 +369000 ekin = 4.50593348762442 | erot = 4.09682529638616 | epot = -35.5029044754857 | etot = -26.9001456914751 +370000 ekin = 4.51011536275109 | erot = 4.41695795738163 | epot = -35.5220659543716 | etot = -26.5949926342389 +371000 ekin = 4.5304986013542 | erot = 4.68112317412985 | epot = -35.5213297387008 | etot = -26.3097079632167 +372000 ekin = 4.42660066351873 | erot = 4.7814861185934 | epot = -35.5227844835438 | etot = -26.3146977014317 +373000 ekin = 4.28146792836394 | erot = 4.87997662616399 | epot = -35.4825501780567 | etot = -26.3211056235288 +374000 ekin = 4.13287464156696 | erot = 4.84001159820223 | epot = -35.452301102515 | etot = -26.4794148627458 +375000 ekin = 4.12545451947128 | erot = 4.81807433824656 | epot = -35.4637375699464 | etot = -26.5202087122286 +376000 ekin = 3.87506271806601 | erot = 5.35141111797735 | epot = -35.4720072259955 | etot = -26.2455333899521 +377000 ekin = 3.79770565908006 | erot = 5.28013401771271 | epot = -35.5177354201972 | etot = -26.4398957434045 +378000 ekin = 3.64048261255644 | erot = 5.4207242379617 | epot = -35.580823638477 | etot = -26.5196167879589 +379000 ekin = 3.5238611157663 | erot = 5.9756700460675 | epot = -35.6532146067628 | etot = -26.153683444929 +380000 ekin = 3.32387900413165 | erot = 6.59135162244908 | epot = -35.7551331169146 | etot = -25.8399024903339 +381000 ekin = 3.31695717077427 | erot = 6.10983514346606 | epot = -35.8815158952865 | etot = -26.4547235810462 +382000 ekin = 3.19546651526091 | erot = 6.36489840257035 | epot = -35.9926058393694 | etot = -26.4322409215381 +383000 ekin = 3.2436816976457 | erot = 6.33114976953688 | epot = -36.0664601033041 | etot = -26.4916286361216 +384000 ekin = 3.20726412806376 | erot = 6.19392941274209 | epot = -36.1325810920204 | etot = -26.7313875512146 +385000 ekin = 3.23885859839745 | erot = 6.31552666314741 | epot = -36.1503271354807 | etot = -26.5959418739358 +386000 ekin = 3.1687441170802 | erot = 5.94413881699916 | epot = -36.1310192334962 | etot = -27.0181362994169 +387000 ekin = 3.15499705249205 | erot = 5.48308596050856 | epot = -36.0714221491833 | etot = -27.4333391361827 +388000 ekin = 3.24907989403005 | erot = 5.58200944567837 | epot = -35.9925882356968 | etot = -27.1614988959884 +389000 ekin = 3.39871525437692 | erot = 5.14342534967113 | epot = -35.926273930772 | etot = -27.384133326724 +390000 ekin = 3.53157771561143 | erot = 5.06601106990858 | epot = -35.9089837935163 | etot = -27.3113950079963 +391000 ekin = 3.6460216873691 | erot = 4.8866150487515 | epot = -35.8854822304094 | etot = -27.3528454942888 +392000 ekin = 3.79325143536293 | erot = 5.07292816992976 | epot = -35.852420754602 | etot = -26.9862411493093 +393000 ekin = 3.89148460233043 | erot = 5.02930522203654 | epot = -35.7951222586314 | etot = -26.8743324342644 +394000 ekin = 3.96458882833113 | erot = 4.47630346760482 | epot = -35.7247928997475 | etot = -27.2839006038116 +395000 ekin = 4.03856036181243 | erot = 4.53784941780784 | epot = -35.6586367417744 | etot = -27.0822269621541 +396000 ekin = 3.9968364670664 | erot = 4.49727898211243 | epot = -35.5718421340363 | etot = -27.0777266848575 +397000 ekin = 4.03872005304064 | erot = 4.03153022392497 | epot = -35.5101946272745 | etot = -27.4399443503089 +398000 ekin = 4.01516330519928 | erot = 4.23226303701212 | epot = -35.4578715559687 | etot = -27.2104452137573 +399000 ekin = 4.0192261656521 | erot = 3.71642260618994 | epot = -35.3548490578809 | etot = -27.6192002860389 +400000 ekin = 4.17225085372021 | erot = 4.04093039429581 | epot = -35.2265510847564 | etot = -27.0133698367403 +401000 ekin = 4.15314996432513 | erot = 3.6480496120942 | epot = -35.0943512868028 | etot = -27.2931517103835 +402000 ekin = 4.20245298417931 | erot = 3.70137380667405 | epot = -34.9745627237165 | etot = -27.0707359328631 +403000 ekin = 4.3413245622893 | erot = 3.62891618665746 | epot = -34.8718657472305 | etot = -26.9016249982838 +404000 ekin = 4.42465890243314 | erot = 3.38938035287092 | epot = -34.7967250831433 | etot = -26.9826858278392 +405000 ekin = 4.6066304195345 | erot = 3.44054758174428 | epot = -34.7925257887169 | etot = -26.7453477874381 +406000 ekin = 4.73346375173105 | erot = 3.27915256113149 | epot = -34.8343083282585 | etot = -26.8216920153959 +407000 ekin = 4.82559135473407 | erot = 3.35253133282278 | epot = -34.90590665538 | etot = -26.7277839678232 +408000 ekin = 4.89298564336973 | erot = 3.47339817729168 | epot = -34.9848536782097 | etot = -26.6184698575483 +409000 ekin = 4.94069048180864 | erot = 3.76649967413614 | epot = -35.0728065521188 | etot = -26.365616396174 +410000 ekin = 5.08376278297818 | erot = 3.48855890171057 | epot = -35.1876079350125 | etot = -26.6152862503238 +411000 ekin = 5.10492342399052 | erot = 3.39152717909368 | epot = -35.2939784996996 | etot = -26.7975278966154 +412000 ekin = 5.21115921489285 | erot = 3.62435455589207 | epot = -35.3853247581666 | etot = -26.5498109873817 +413000 ekin = 5.25687541732564 | erot = 3.76308251202552 | epot = -35.4593584594676 | etot = -26.4394005301164 +414000 ekin = 5.13248472496979 | erot = 3.31025282824712 | epot = -35.5393093363075 | etot = -27.0965717830906 +415000 ekin = 5.09217261574502 | erot = 3.59401320391344 | epot = -35.605161792403 | etot = -26.9189759727445 +416000 ekin = 5.04807348985189 | erot = 3.48392073248403 | epot = -35.6748296719208 | etot = -27.1428354495849 +417000 ekin = 4.99138526936695 | erot = 3.46255923404111 | epot = -35.7531502554479 | etot = -27.2992057520398 +418000 ekin = 5.08999508315071 | erot = 3.44390708246907 | epot = -35.8333696081099 | etot = -27.2994674424901 +419000 ekin = 5.21842750435904 | erot = 3.38325168590942 | epot = -35.8593643490788 | etot = -27.2576851588103 +420000 ekin = 5.28947719533084 | erot = 3.50797044377639 | epot = -35.8848039905135 | etot = -27.0873563514062 +421000 ekin = 5.35268927232105 | erot = 3.36603650801218 | epot = -35.8749221051677 | etot = -27.1561963248345 +422000 ekin = 5.23695191026783 | erot = 3.53841920706918 | epot = -35.889640869454 | etot = -27.114269752117 +423000 ekin = 5.09577504756719 | erot = 3.67923583037255 | epot = -35.9137595336544 | etot = -27.1387486557147 +424000 ekin = 5.01335188112952 | erot = 3.70110718137053 | epot = -35.9185617531992 | etot = -27.2041026906992 +425000 ekin = 5.05206155589202 | erot = 3.57652002072466 | epot = -35.9081181462494 | etot = -27.2795365696328 +426000 ekin = 4.96532396129122 | erot = 3.38938274590579 | epot = -35.8769982527928 | etot = -27.5222915455958 +427000 ekin = 4.77195218714222 | erot = 3.50252627514243 | epot = -35.7935414010633 | etot = -27.5190629387787 +428000 ekin = 4.81068646615363 | erot = 3.51825958765464 | epot = -35.6664317412184 | etot = -27.3374856874101 +429000 ekin = 4.73870321335416 | erot = 3.84986931063865 | epot = -35.4873764559103 | etot = -26.8988039319175 +430000 ekin = 4.602137148251 | erot = 3.45284870606445 | epot = -35.3073410925575 | etot = -27.2523552382421 +431000 ekin = 4.57358006593881 | erot = 3.25422348182542 | epot = -35.136759491896 | etot = -27.3089559441318 +432000 ekin = 4.50724003680402 | erot = 3.29998192315333 | epot = -35.029042571088 | etot = -27.2218206111307 +433000 ekin = 4.3086049570317 | erot = 3.42741416873377 | epot = -34.9513402987258 | etot = -27.2153211729603 +434000 ekin = 4.18610269286836 | erot = 3.55059973000638 | epot = -34.9144648758598 | etot = -27.1777624529851 +435000 ekin = 4.12003359590284 | erot = 3.78033374370934 | epot = -34.8780591099563 | etot = -26.9776917703441 +436000 ekin = 3.97313974106134 | erot = 4.05117020636249 | epot = -34.8427841720092 | etot = -26.8184742245853 +437000 ekin = 3.88596008320786 | erot = 4.32902730055979 | epot = -34.8121331683379 | etot = -26.5971457845702 +438000 ekin = 4.03003221046435 | erot = 4.35508047283409 | epot = -34.7917492531094 | etot = -26.4066365698109 +439000 ekin = 4.04655148511162 | erot = 4.17322604141029 | epot = -34.7786348227556 | etot = -26.5588572962337 +440000 ekin = 4.02801522674504 | erot = 4.13470601724881 | epot = -34.7839930854156 | etot = -26.6212718414218 +441000 ekin = 3.94078147941953 | erot = 4.22144190117307 | epot = -34.8185771480927 | etot = -26.6563537675001 +442000 ekin = 3.97730990695675 | erot = 4.24233406975324 | epot = -34.8718962191135 | etot = -26.6522522424035 +443000 ekin = 3.98508138243256 | erot = 4.16122580291799 | epot = -34.9266782585662 | etot = -26.7803710732156 +444000 ekin = 4.00042709081923 | erot = 4.50741850480102 | epot = -34.9630696153487 | etot = -26.4552240197285 +445000 ekin = 4.02620459576038 | erot = 4.64580325301018 | epot = -34.9893039643637 | etot = -26.3172961155932 +446000 ekin = 4.0145460872058 | erot = 4.89747165518641 | epot = -34.9969089036749 | etot = -26.0848911612827 +447000 ekin = 3.96342694873324 | erot = 4.85867800390665 | epot = -34.9830933662455 | etot = -26.1609884136056 +448000 ekin = 3.74592315828131 | erot = 5.1757843335798 | epot = -34.9638816619608 | etot = -26.0421741700997 +449000 ekin = 3.73316291077384 | erot = 5.18498661281975 | epot = -34.9280438941249 | etot = -26.0098943705313 +450000 ekin = 3.85313039093449 | erot = 4.86926583888879 | epot = -34.8716969798347 | etot = -26.1493007500114 +451000 ekin = 4.06359280531127 | erot = 4.99817049859075 | epot = -34.8377147695099 | etot = -25.7759514656079 +452000 ekin = 4.12215980217286 | erot = 4.58488292412149 | epot = -34.8398353293665 | etot = -26.1327926030721 +453000 ekin = 4.16332842884541 | erot = 4.32671008371143 | epot = -34.8570499988887 | etot = -26.3670114863319 +454000 ekin = 4.11754892618409 | erot = 4.47415692336229 | epot = -34.8913194738514 | etot = -26.299613624305 +455000 ekin = 4.22185774995348 | erot = 4.65517828169311 | epot = -34.9334347985054 | etot = -26.0563987668588 +456000 ekin = 4.30177202276143 | erot = 4.77747798616556 | epot = -35.0188770940117 | etot = -25.9396270850847 +457000 ekin = 4.26451460758689 | erot = 4.69009499467528 | epot = -35.1021143238348 | etot = -26.1475047215727 +458000 ekin = 4.31289289804763 | erot = 4.48148846421258 | epot = -35.1135359976466 | etot = -26.3191546353864 +459000 ekin = 4.40924309472714 | erot = 4.70052929057868 | epot = -35.3709113999309 | etot = -26.2611390146251 +460000 ekin = 4.47691183250296 | erot = 4.50574141189019 | epot = -35.566195356935 | etot = -26.5835421125418 +461000 ekin = 4.43873436995011 | erot = 4.99077626253916 | epot = -35.6310455171599 | etot = -26.2015348846706 +462000 ekin = 4.38932525316365 | erot = 4.94989100042644 | epot = -35.7174404682254 | etot = -26.3782242146353 +463000 ekin = 4.36115268480796 | erot = 5.66229263913986 | epot = -35.782873692384 | etot = -25.7594283684361 +464000 ekin = 4.32411863133124 | erot = 5.21874712372938 | epot = -35.8318174183589 | etot = -26.2889516632982 +465000 ekin = 4.25283049437862 | erot = 4.8931192840781 | epot = -35.8307748329833 | etot = -26.6848250545266 +466000 ekin = 3.97961054012235 | erot = 4.30523919521523 | epot = -35.8019205162808 | etot = -27.5170707809433 +467000 ekin = 3.96957942645156 | erot = 4.02414635207124 | epot = -35.7935881476342 | etot = -27.7998623691114 +468000 ekin = 3.81067149059143 | erot = 3.9131157389001 | epot = -35.819204604463 | etot = -28.0954173749715 +469000 ekin = 3.82956653035967 | erot = 3.76358708523009 | epot = -35.8554657317441 | etot = -28.2623121161543 +470000 ekin = 3.84315155223098 | erot = 3.46319185355978 | epot = -35.9283028420653 | etot = -28.6219594362746 +471000 ekin = 3.8418988592029 | erot = 3.51787257644846 | epot = -36.0370536568195 | etot = -28.6772822211681 +472000 ekin = 3.86861114122384 | erot = 3.36458500068064 | epot = -36.1368322989854 | etot = -28.9036361570809 +473000 ekin = 3.73700168734246 | erot = 3.58329228877727 | epot = -36.2233655143222 | etot = -28.9030715382025 +474000 ekin = 3.82928273613545 | erot = 3.70070391401538 | epot = -36.2919855352844 | etot = -28.7619988851335 +475000 ekin = 3.89544030960044 | erot = 3.76401640046801 | epot = -36.3684307389009 | etot = -28.7089740288324 +476000 ekin = 4.0893276711336 | erot = 3.70907901754989 | epot = -36.4684310716314 | etot = -28.6700243829479 +477000 ekin = 4.15334136664104 | erot = 3.70899967496297 | epot = -36.5311600367348 | etot = -28.6688189951308 +478000 ekin = 4.07512882728816 | erot = 3.80913887771415 | epot = -36.5715417700048 | etot = -28.6872740650025 +479000 ekin = 3.96184225144677 | erot = 3.6758426322944 | epot = -36.6049454628525 | etot = -28.9672605791113 +480000 ekin = 3.86072911979603 | erot = 3.85211085064388 | epot = -36.610629225252 | etot = -28.8977892548121 +481000 ekin = 3.78563823255496 | erot = 4.024314099233 | epot = -36.6044682584304 | etot = -28.7945159266424 +482000 ekin = 3.81986353724786 | erot = 3.94457553240304 | epot = -36.5556242495873 | etot = -28.7911851799364 +483000 ekin = 3.91937069687011 | erot = 3.97985471481356 | epot = -36.4953515335744 | etot = -28.5961261218907 +484000 ekin = 3.90565472316292 | erot = 3.68508276016196 | epot = -36.426514232721 | etot = -28.8357767493961 +485000 ekin = 3.97067640669154 | erot = 3.52818833629947 | epot = -36.3385351029693 | etot = -28.8396703599783 +486000 ekin = 4.08924338068675 | erot = 3.45150371793067 | epot = -36.2407040808296 | etot = -28.6999569822122 +487000 ekin = 4.07761729530311 | erot = 3.69577064304002 | epot = -36.1174543397078 | etot = -28.3440664013647 +488000 ekin = 3.98120330041688 | erot = 4.01179749212345 | epot = -35.9662140009127 | etot = -27.9732132083724 +489000 ekin = 3.94304108511324 | erot = 4.09948585344502 | epot = -35.8365811443688 | etot = -27.7940542058105 +490000 ekin = 3.98200750178142 | erot = 4.19330655565614 | epot = -35.7436522395709 | etot = -27.5683381821333 +491000 ekin = 4.0445360131927 | erot = 4.06864604679586 | epot = -35.6813038605064 | etot = -27.5681218005179 +492000 ekin = 4.10478194610759 | erot = 4.27931273272407 | epot = -35.6201850620984 | etot = -27.2360903832667 +493000 ekin = 4.14218811078688 | erot = 4.30328516243005 | epot = -35.5529321721737 | etot = -27.1074588989568 +494000 ekin = 4.15483197917442 | erot = 4.22087230768742 | epot = -35.5007035923716 | etot = -27.1249993055097 +495000 ekin = 4.26671892357353 | erot = 4.2174513730416 | epot = -35.4450128389817 | etot = -26.9608425423665 +496000 ekin = 4.42373869014864 | erot = 3.65535322096919 | epot = -35.3933064942846 | etot = -27.3142145831668 +497000 ekin = 4.57363309591074 | erot = 3.63766344362461 | epot = -35.3630685420969 | etot = -27.1517720025615 +498000 ekin = 4.7241733979429 | erot = 3.40665904233571 | epot = -35.3570714026405 | etot = -27.2262389623619 +499000 ekin = 4.76806375994884 | erot = 3.58204839805338 | epot = -35.3646341268605 | etot = -27.0145219688582 +500000 ekin = 4.86803273232494 | erot = 3.40069391727077 | epot = -35.4199817543288 | etot = -27.1512551047331 +501000 ekin = 4.96743307602633 | erot = 3.46724128896382 | epot = -35.4970649677138 | etot = -27.0623906027237 +502000 ekin = 4.91929166862602 | erot = 3.57165212036747 | epot = -35.5889625489531 | etot = -27.0980187599596 +503000 ekin = 4.90703913138654 | erot = 3.86458875313982 | epot = -35.6771862828243 | etot = -26.9055583982979 +504000 ekin = 5.13705335061953 | erot = 3.53695462968337 | epot = -35.7347477259475 | etot = -27.0607397456447 +505000 ekin = 5.23249143944192 | erot = 3.46343104093346 | epot = -35.7820571844978 | etot = -27.0861347041225 +506000 ekin = 5.11675278315682 | erot = 3.72067186509955 | epot = -35.8198968197669 | etot = -26.9824721715105 +507000 ekin = 5.18993901387439 | erot = 4.1521508584772 | epot = -35.8269271672407 | etot = -26.4848372948891 +508000 ekin = 4.98597878226577 | erot = 4.11598571894018 | epot = -35.7826195676297 | etot = -26.6806550664237 +509000 ekin = 4.89412425677653 | erot = 4.30807642739921 | epot = -35.6890852058576 | etot = -26.4868845216819 +510000 ekin = 4.89504815268988 | erot = 4.4601383758423 | epot = -35.589321566643 | etot = -26.2341350381108 +511000 ekin = 4.85835750083372 | erot = 4.41721118692769 | epot = -35.4748886415738 | etot = -26.1993199538124 +512000 ekin = 4.85632567301955 | erot = 4.5850146787013 | epot = -35.3170557845391 | etot = -25.8757154328183 +513000 ekin = 4.79088228903384 | erot = 4.41898249223044 | epot = -35.1398620511897 | etot = -25.9299972699254 +514000 ekin = 4.84082723167301 | erot = 4.10048582144458 | epot = -34.9528940279417 | etot = -26.0115809748241 +515000 ekin = 4.66396867258878 | erot = 3.70795325472635 | epot = -34.8081323279138 | etot = -26.4362104005987 +516000 ekin = 4.45203722260375 | erot = 3.7424161749216 | epot = -34.7399422586779 | etot = -26.5454888611526 +517000 ekin = 4.39320763550285 | erot = 3.61293763489201 | epot = -34.7115969229747 | etot = -26.7054516525798 +518000 ekin = 4.33516267423081 | erot = 3.46685163663661 | epot = -34.720559171622 | etot = -26.9185448607546 +519000 ekin = 4.32678001120794 | erot = 3.83331308599435 | epot = -34.7543932584756 | etot = -26.5943001612733 +520000 ekin = 4.16017569753271 | erot = 3.9944210337637 | epot = -34.7797387277814 | etot = -26.625141996485 +521000 ekin = 4.01091284601559 | erot = 4.71227661622668 | epot = -34.8119764016186 | etot = -26.0887869393764 +522000 ekin = 3.92555868149862 | erot = 4.67306017627902 | epot = -34.8638412525405 | etot = -26.2652223947629 +523000 ekin = 4.10629342994171 | erot = 4.23690821219818 | epot = -34.9392637364657 | etot = -26.5960620943258 +524000 ekin = 4.1696440613856 | erot = 4.51539305326675 | epot = -35.0302476439302 | etot = -26.3452105292779 +525000 ekin = 4.14574067413424 | erot = 4.59255192964534 | epot = -35.1665459803978 | etot = -26.4282533766182 +526000 ekin = 4.29635804775357 | erot = 5.38181203699227 | epot = -35.3702076593234 | etot = -25.6920375745776 +527000 ekin = 4.43341423246316 | erot = 5.4208701656537 | epot = -35.5881352754175 | etot = -25.7338508773006 +528000 ekin = 4.65221997264034 | erot = 5.64432261927448 | epot = -35.7907306535607 | etot = -25.4941880616459 +529000 ekin = 4.75833001518884 | erot = 6.22279494556851 | epot = -35.9649272181715 | etot = -24.9838022574141 +530000 ekin = 4.85254900576381 | erot = 6.26630645812944 | epot = -36.1175112827236 | etot = -24.9986558188304 +531000 ekin = 4.88314038497963 | erot = 6.22256761998181 | epot = -36.2218727030893 | etot = -25.1161646981279 +532000 ekin = 4.89429192132453 | erot = 6.19376619305378 | epot = -36.2791850407377 | etot = -25.1911269263594 +533000 ekin = 4.98074956905508 | erot = 6.71246035574299 | epot = -36.2873072492243 | etot = -24.5940973244262 +534000 ekin = 5.05914514163858 | erot = 6.72049132345737 | epot = -36.2541186702092 | etot = -24.4744822051133 +535000 ekin = 4.98307281629278 | erot = 6.60876507020557 | epot = -36.1722591997822 | etot = -24.5804213132839 +536000 ekin = 4.92092214615514 | erot = 6.71824597922614 | epot = -36.0492643890662 | etot = -24.4100962636849 +537000 ekin = 4.73594122849326 | erot = 6.46069540815287 | epot = -35.9116294607657 | etot = -24.7149928241196 +538000 ekin = 4.79280389212897 | erot = 6.10794151385135 | epot = -35.7423046160132 | etot = -24.8415592100329 +539000 ekin = 4.77579753855637 | erot = 5.9721718852028 | epot = -35.533600981652 | etot = -24.7856315578928 +540000 ekin = 4.59343353220661 | erot = 6.02882315943306 | epot = -35.2969540919923 | etot = -24.6746974003527 +541000 ekin = 4.56261508857308 | erot = 5.60884609986364 | epot = -35.0742414984787 | etot = -24.9027803100419 +542000 ekin = 4.42304079078362 | erot = 5.24180126466464 | epot = -34.8728664426876 | etot = -25.2080243872393 +543000 ekin = 4.31458565966317 | erot = 5.30648118805705 | epot = -34.6809264080033 | etot = -25.0598595602831 +544000 ekin = 4.16990383767329 | erot = 5.09480741715239 | epot = -34.5077033118773 | etot = -25.2429920570516 +545000 ekin = 4.0350640414587 | erot = 4.95913193735204 | epot = -34.3738505570895 | etot = -25.3796545782788 +546000 ekin = 4.05283758597051 | erot = 4.62357416672448 | epot = -34.2732549004478 | etot = -25.5968431477528 +547000 ekin = 3.91892476341122 | erot = 4.42471065792707 | epot = -34.1888485564157 | etot = -25.8452131350775 +548000 ekin = 3.85923648383067 | erot = 4.18493881932566 | epot = -34.1251823218199 | etot = -26.0810070186636 +549000 ekin = 3.8927709556134 | erot = 4.20183962759803 | epot = -34.0968256559691 | etot = -26.0022150727577 +550000 ekin = 3.88489313663799 | erot = 4.06987350840239 | epot = -34.0834989925537 | etot = -26.1287323475133 +551000 ekin = 3.87639970039868 | erot = 4.25043058335745 | epot = -34.0931086790782 | etot = -25.966278395322 +552000 ekin = 3.88627319211786 | erot = 4.00102033547709 | epot = -34.1638602914377 | etot = -26.2765667638428 +553000 ekin = 4.05569156373879 | erot = 3.56403629580222 | epot = -34.247483486424 | etot = -26.627755626883 +554000 ekin = 4.2562683800156 | erot = 3.70804766862547 | epot = -34.2954308218039 | etot = -26.3311147731628 +555000 ekin = 4.2648740703529 | erot = 3.78496110408358 | epot = -34.3412268896543 | etot = -26.2913917152178 +556000 ekin = 4.24622902964984 | erot = 4.0345482038853 | epot = -34.3344093396379 | etot = -26.0536321061027 +557000 ekin = 4.07319669837868 | erot = 3.86372668854368 | epot = -34.2640157691761 | etot = -26.3270923822537 +558000 ekin = 3.99489306447001 | erot = 3.82027814531877 | epot = -34.1455461859517 | etot = -26.3303749761629 +559000 ekin = 4.00179663426026 | erot = 3.82651776959122 | epot = -33.9924674804774 | etot = -26.1641530766259 +560000 ekin = 3.90938418270038 | erot = 3.49539199637374 | epot = -33.8018928207122 | etot = -26.3971166416381 +561000 ekin = 3.70375196060242 | erot = 3.38165869548244 | epot = -33.6157331642902 | etot = -26.5303225082053 +562000 ekin = 3.64392595608208 | erot = 3.67997084627168 | epot = -33.4612560312997 | etot = -26.1373592289459 +563000 ekin = 3.59769761679666 | erot = 3.74125845764501 | epot = -33.3480734777506 | etot = -26.0091174033089 +564000 ekin = 3.5872532535469 | erot = 3.35524020938125 | epot = -33.2675171968359 | etot = -26.3250237339077 +565000 ekin = 3.63835964444035 | erot = 3.77402574563864 | epot = -33.2409015523647 | etot = -25.8285161622857 +566000 ekin = 3.64384501808487 | erot = 3.7751512348732 | epot = -33.2503593116355 | etot = -25.8313630586774 +567000 ekin = 3.6321441767138 | erot = 3.8685448978813 | epot = -33.2603190278778 | etot = -25.7596299532827 +568000 ekin = 3.76759211618971 | erot = 3.97321014856349 | epot = -33.2947231384392 | etot = -25.553920873686 +569000 ekin = 3.75607920629668 | erot = 3.9189350411434 | epot = -33.3766443391882 | etot = -25.7016300917481 +570000 ekin = 3.88570178164772 | erot = 3.87013370061556 | epot = -33.4676246266775 | etot = -25.7117891444142 +571000 ekin = 3.91109063039641 | erot = 4.3887336637963 | epot = -33.5301619269295 | etot = -25.2303376327368 +572000 ekin = 3.91357367536979 | erot = 4.54669425634091 | epot = -33.5613071721028 | etot = -25.1010392403921 +573000 ekin = 4.00256460245984 | erot = 4.69928602914621 | epot = -33.5479654090577 | etot = -24.8461147774517 +574000 ekin = 4.04557469411533 | erot = 4.85104808888571 | epot = -33.4823141367214 | etot = -24.5856913537203 +575000 ekin = 4.0199044833131 | erot = 4.48360936846638 | epot = -33.4090682352886 | etot = -24.9055543835092 +576000 ekin = 3.80770420634942 | erot = 4.40902984739946 | epot = -33.3559765416152 | etot = -25.1392424878663 +577000 ekin = 3.6517677072366 | erot = 4.69770290650927 | epot = -33.3414847753623 | etot = -24.9920141616164 +578000 ekin = 3.65416507269722 | erot = 5.09984939028998 | epot = -33.3628873386869 | etot = -24.6088728756997 +579000 ekin = 3.65457514215454 | erot = 4.83085466504592 | epot = -33.4229058723711 | etot = -24.9374760651706 +580000 ekin = 3.61022362260481 | erot = 5.21507039569769 | epot = -33.5257015423975 | etot = -24.700407524095 +581000 ekin = 3.49491427592295 | erot = 5.80898315058308 | epot = -33.6374701054959 | etot = -24.3335726789899 +582000 ekin = 3.45150652331289 | erot = 5.2079729472947 | epot = -33.7413132898281 | etot = -25.0818338192205 +583000 ekin = 3.43883253778232 | erot = 4.99240818298342 | epot = -33.7992206024429 | etot = -25.3679798816772 +584000 ekin = 3.41950743994087 | erot = 5.30429667829858 | epot = -33.8273198616881 | etot = -25.1035157434487 +585000 ekin = 3.52988736379348 | erot = 5.26888625710225 | epot = -33.8562169326849 | etot = -25.0574433117891 +586000 ekin = 3.54522421505718 | erot = 5.15182886320371 | epot = -33.8748034063863 | etot = -25.1777503281254 +587000 ekin = 3.64975640444384 | erot = 4.43116878399003 | epot = -33.8790223191813 | etot = -25.7980971307475 +588000 ekin = 3.85787406303082 | erot = 4.33848995606314 | epot = -33.9012642894904 | etot = -25.7049002703965 +589000 ekin = 3.9487150884209 | erot = 4.36958758855423 | epot = -33.9512157067315 | etot = -25.6329130297563 +590000 ekin = 4.04576150007675 | erot = 4.34777620153069 | epot = -33.9849374243128 | etot = -25.5913997227054 +591000 ekin = 4.13483818439914 | erot = 4.28475308123698 | epot = -33.9975372243776 | etot = -25.5779459587414 +592000 ekin = 4.2556680414864 | erot = 4.00241438742696 | epot = -33.990517302247 | etot = -25.7324348733336 +593000 ekin = 4.26695504286551 | erot = 3.75133860519216 | epot = -33.9824243028376 | etot = -25.9641306547799 +594000 ekin = 4.24513038558056 | erot = 3.88826331815755 | epot = -33.9597952629293 | etot = -25.8264015591912 +595000 ekin = 4.33307108334646 | erot = 3.92609577318174 | epot = -33.9197199407777 | etot = -25.6605530842495 +596000 ekin = 4.23611726585149 | erot = 3.89070717461491 | epot = -33.8740124837561 | etot = -25.7471880432897 +597000 ekin = 4.40233879096614 | erot = 3.9973813082447 | epot = -33.8902431987866 | etot = -25.4905230995758 +598000 ekin = 4.23795477390351 | erot = 4.04526003588007 | epot = -33.9155939268417 | etot = -25.6323791170582 +599000 ekin = 4.13745802989045 | erot = 3.88641709707911 | epot = -33.9296772436184 | etot = -25.9058021166489 +600000 ekin = 4.21239990479469 | erot = 3.82373814742802 | epot = -33.9651236246 | etot = -25.9289855723773 +601000 ekin = 4.3196997334027 | erot = 3.98399943561167 | epot = -34.0172721411615 | etot = -25.7135729721471 +602000 ekin = 4.27803621196727 | erot = 4.02063732656524 | epot = -34.100698422985 | etot = -25.8020248844525 +603000 ekin = 4.31016670434268 | erot = 4.06109056998715 | epot = -34.2290225355021 | etot = -25.8577652611723 +604000 ekin = 4.35436231281196 | erot = 4.27081433433549 | epot = -34.3693989473758 | etot = -25.7442223002283 +605000 ekin = 4.29263786573731 | erot = 4.35816455015996 | epot = -34.5293522620234 | etot = -25.8785498461262 +606000 ekin = 4.23493766333436 | erot = 4.45889694601822 | epot = -34.6959569640143 | etot = -26.0021223546617 +607000 ekin = 4.21589668454932 | erot = 4.35851580050772 | epot = -34.8643734064673 | etot = -26.2899609214103 +608000 ekin = 4.31617609118378 | erot = 4.3711843404177 | epot = -35.0106665625392 | etot = -26.3233061309377 +609000 ekin = 4.40054829762945 | erot = 4.09556922746408 | epot = -35.1090427558591 | etot = -26.6129252307656 +610000 ekin = 4.3836017973497 | erot = 4.43080811091093 | epot = -35.1590130940816 | etot = -26.344603185821 +611000 ekin = 4.30911071721019 | erot = 4.66858603342393 | epot = -35.1997741362033 | etot = -26.2220773855692 +612000 ekin = 4.38115044344101 | erot = 4.62952065066664 | epot = -35.2189008927601 | etot = -26.2082297986524 +613000 ekin = 4.49640333428488 | erot = 4.73033949191661 | epot = -35.2311946320133 | etot = -26.0044518058118 +614000 ekin = 4.42698019674918 | erot = 4.54387450238904 | epot = -35.227024565465 | etot = -26.2561698663268 +615000 ekin = 4.36293882049166 | erot = 4.65167437175536 | epot = -35.250009814436 | etot = -26.235396622189 +616000 ekin = 4.25552094369167 | erot = 3.9677335799062 | epot = -35.262646565401 | etot = -27.0393920418031 +617000 ekin = 4.02844203107201 | erot = 3.93306028038377 | epot = -35.3085438772361 | etot = -27.3470415657803 +618000 ekin = 3.91410624199631 | erot = 3.99915504239052 | epot = -35.3773572154985 | etot = -27.4640959311117 +619000 ekin = 3.92944334041051 | erot = 3.65858234543171 | epot = -35.4549579850513 | etot = -27.8669322992091 +620000 ekin = 3.94632769198491 | erot = 4.05357915876533 | epot = -35.5452298743848 | etot = -27.5453230236346 +621000 ekin = 4.00876452457166 | erot = 4.1855795236138 | epot = -35.6568787558288 | etot = -27.4625347076433 +622000 ekin = 3.97770547832637 | erot = 4.20428409244743 | epot = -35.7853832130653 | etot = -27.6033936422915 +623000 ekin = 3.8762340917962 | erot = 4.44200976918091 | epot = -35.9345595163545 | etot = -27.6163156553774 +624000 ekin = 3.81461749379632 | erot = 4.73413928443226 | epot = -36.0610458736423 | etot = -27.5122890954137 +625000 ekin = 3.8970241751503 | erot = 4.51967995490342 | epot = -36.1593702506674 | etot = -27.7426661206137 +626000 ekin = 4.05285181951198 | erot = 5.1220971455114 | epot = -36.2373709478026 | etot = -27.0624219827792 +627000 ekin = 4.06919694856985 | erot = 5.16853241383701 | epot = -36.2459696084315 | etot = -27.0082402460246 +628000 ekin = 3.97574634490127 | erot = 5.15377915037519 | epot = -36.1860007276685 | etot = -27.0564752323921 +629000 ekin = 3.97847076093846 | erot = 4.98743417354896 | epot = -36.0841602963358 | etot = -27.1182553618484 +630000 ekin = 3.82117049554739 | erot = 4.72915936447924 | epot = -35.9627884752438 | etot = -27.4124586152171 +631000 ekin = 3.86461141431221 | erot = 4.86154549634944 | epot = -35.8061457051957 | etot = -27.079988794534 +632000 ekin = 3.74664734149851 | erot = 4.54810894057643 | epot = -35.6214135997296 | etot = -27.3266573176547 +633000 ekin = 3.70561564688244 | erot = 3.84492477779421 | epot = -35.4366028892501 | etot = -27.8860624645735 +634000 ekin = 3.59215409071661 | erot = 3.93871515972471 | epot = -35.2896538627899 | etot = -27.7587846123486 +635000 ekin = 3.50545587494383 | erot = 4.06717110382211 | epot = -35.1730596180146 | etot = -27.6004326392486 +636000 ekin = 3.3309454150286 | erot = 4.07821458070327 | epot = -35.1077038533349 | etot = -27.6985438576031 +637000 ekin = 3.14505217998963 | erot = 4.05756077132584 | epot = -35.1055524080615 | etot = -27.902939456746 +638000 ekin = 3.09050584392239 | erot = 4.40258652090821 | epot = -35.1570633539889 | etot = -27.6639709891583 +639000 ekin = 3.0768733321709 | erot = 4.16491810908563 | epot = -35.2467836386719 | etot = -28.0049921974154 +640000 ekin = 3.00973730805073 | erot = 4.2692418133335 | epot = -35.3354522376085 | etot = -28.0564731162243 +641000 ekin = 2.94445196408833 | erot = 4.64391413205119 | epot = -35.4644644387967 | etot = -27.8760983426572 +642000 ekin = 2.98442414954633 | erot = 4.9974755612433 | epot = -35.6290057034216 | etot = -27.647105992632 +643000 ekin = 3.2055646953209 | erot = 4.8025531791329 | epot = -35.7795885297939 | etot = -27.7714706553401 +644000 ekin = 3.2748821402377 | erot = 4.64957731616621 | epot = -35.9161733239261 | etot = -27.9917138675222 +645000 ekin = 3.41323831995007 | erot = 4.71321420527612 | epot = -36.0213663956164 | etot = -27.8949138703902 +646000 ekin = 3.56963422518167 | erot = 4.46391006184254 | epot = -36.0597764612018 | etot = -28.0262321741776 +647000 ekin = 3.65146108953765 | erot = 4.34882885781933 | epot = -36.05397385258 | etot = -28.053683905223 +648000 ekin = 3.80589253043839 | erot = 4.22505125234649 | epot = -35.9957895068647 | etot = -27.9648457240799 +649000 ekin = 4.01844415748841 | erot = 4.19109412255817 | epot = -35.9180061331759 | etot = -27.7084678531293 +650000 ekin = 4.03810277748572 | erot = 3.86362623058913 | epot = -35.8260490160444 | etot = -27.9243200079695 +651000 ekin = 4.14203944570719 | erot = 3.56888807374706 | epot = -35.7087423281397 | etot = -27.9978148086855 +652000 ekin = 4.23250261214715 | erot = 3.18710224409382 | epot = -35.6367851174034 | etot = -28.2171802611624 +653000 ekin = 4.36352642926009 | erot = 3.20148998566011 | epot = -35.6464209942557 | etot = -28.0814045793355 +654000 ekin = 4.5279203243997 | erot = 3.02237039454743 | epot = -35.6995719521313 | etot = -28.1492812331841 +655000 ekin = 4.60546960877517 | erot = 2.96007185178719 | epot = -35.8223013228812 | etot = -28.2567598623188 +656000 ekin = 4.78956137676064 | erot = 3.38896158834621 | epot = -35.9826527468557 | etot = -27.8041297817489 +657000 ekin = 4.78481247088243 | erot = 3.67040934516473 | epot = -36.1522101931049 | etot = -27.6969883770578 +658000 ekin = 4.68735602442224 | erot = 4.10635530609359 | epot = -36.3122539915072 | etot = -27.5185426609914 +659000 ekin = 4.79643464434907 | erot = 4.3109166795532 | epot = -36.419822200132 | etot = -27.3124708762297 +660000 ekin = 4.65613606555515 | erot = 4.00182169137307 | epot = -36.5017357753405 | etot = -27.8437780184123 +661000 ekin = 4.53939481189422 | erot = 4.39327864100633 | epot = -36.5522379560179 | etot = -27.6195645031173 +662000 ekin = 4.62075189021993 | erot = 4.64171304234686 | epot = -36.5458752748482 | etot = -27.2834103422814 +663000 ekin = 4.60627251324235 | erot = 4.44191382325803 | epot = -36.5358428119696 | etot = -27.4876564754693 +664000 ekin = 4.53224877457463 | erot = 4.69535654970068 | epot = -36.5440045789042 | etot = -27.3163992546289 +665000 ekin = 4.33791904761007 | erot = 4.79511074251925 | epot = -36.5712979957099 | etot = -27.4382682055805 +666000 ekin = 4.01034004769843 | erot = 5.14475630277467 | epot = -36.6275167021873 | etot = -27.4724203517142 +667000 ekin = 3.92791037721622 | erot = 5.11805894759237 | epot = -36.702269731521 | etot = -27.6563004067124 +668000 ekin = 3.69207242860568 | erot = 4.95115852091685 | epot = -36.7748284431555 | etot = -28.1315974936329 +669000 ekin = 3.52850414694839 | erot = 5.30513713121047 | epot = -36.8468924103841 | etot = -28.0132511322252 +670000 ekin = 3.43685158392413 | erot = 5.67353767341476 | epot = -36.8571678878591 | etot = -27.7467786305202 +671000 ekin = 3.37237891900207 | erot = 4.81383151363256 | epot = -36.7898772614734 | etot = -28.6036668288388 +672000 ekin = 3.4214286448957 | erot = 4.47410705082151 | epot = -36.6509805759937 | etot = -28.7554448802765 +673000 ekin = 3.47620696197726 | erot = 4.53468812753541 | epot = -36.4695914666411 | etot = -28.4586963771284 +674000 ekin = 3.34015467342477 | erot = 4.56003540036704 | epot = -36.2728042740009 | etot = -28.3726142002091 +675000 ekin = 3.26558121431926 | erot = 4.75716318196978 | epot = -36.0812448824919 | etot = -28.0585004862029 +676000 ekin = 3.30557173090095 | erot = 4.66626180335478 | epot = -35.8858133485377 | etot = -27.9139798142819 +677000 ekin = 3.38252137148669 | erot = 4.6897922284426 | epot = -35.7238379181691 | etot = -27.6515243182398 +678000 ekin = 3.33430766992633 | erot = 4.45636421682294 | epot = -35.5898515746333 | etot = -27.799179687884 +679000 ekin = 3.26716522041019 | erot = 4.13643141690213 | epot = -35.528216056043 | etot = -28.1246194187307 +680000 ekin = 3.22330491222221 | erot = 4.11355311991397 | epot = -35.5522418172928 | etot = -28.2153837851566 +681000 ekin = 3.27654998707768 | erot = 4.40088508884104 | epot = -35.6343431031197 | etot = -27.956908027201 +682000 ekin = 3.38403402082966 | erot = 4.64957783602955 | epot = -35.7255960652577 | etot = -27.6919842083985 +683000 ekin = 3.58392532059449 | erot = 4.15499488835506 | epot = -35.8541956283831 | etot = -28.1152754194335 +684000 ekin = 3.63284008875691 | erot = 4.14497212696397 | epot = -36.0448350473496 | etot = -28.2670228316288 +685000 ekin = 3.75538152185656 | erot = 3.95609692494439 | epot = -36.2462524041832 | etot = -28.5347739573822 +686000 ekin = 3.91883145536709 | erot = 3.95298902028767 | epot = -36.4771155861902 | etot = -28.6052951105355 +687000 ekin = 4.05299881159141 | erot = 4.06027810523496 | epot = -36.7169526369127 | etot = -28.6036757200863 +688000 ekin = 4.13599667613283 | erot = 4.1033148925446 | epot = -36.9524101670391 | etot = -28.7130985983616 +689000 ekin = 4.25987754434121 | erot = 4.14481492316592 | epot = -37.19007759108 | etot = -28.7853851235729 +690000 ekin = 4.43074027682468 | erot = 4.04380513304424 | epot = -37.3931354089483 | etot = -28.9185899990794 +691000 ekin = 4.53821721573662 | erot = 3.80503345899004 | epot = -37.5576014163155 | etot = -29.2143507415889 +692000 ekin = 4.6415004277931 | erot = 3.59872997928144 | epot = -37.6895260553275 | etot = -29.449295648253 +693000 ekin = 4.69075885893 | erot = 3.47578918601706 | epot = -37.8114874122422 | etot = -29.6449393672951 +694000 ekin = 4.73822518662626 | erot = 3.8426375014852 | epot = -37.9027003996531 | etot = -29.3218377115416 +695000 ekin = 4.75494194627987 | erot = 3.78113333862433 | epot = -37.9681336831655 | etot = -29.4320583982613 +696000 ekin = 4.69786608199271 | erot = 3.785268211759 | epot = -38.0084908313003 | etot = -29.5253565375486 +697000 ekin = 4.69854328160514 | erot = 3.62432955932676 | epot = -38.0258612384502 | etot = -29.7029883975183 +698000 ekin = 4.71023285872909 | erot = 3.64111389234157 | epot = -38.030154734076 | etot = -29.6788079830054 +699000 ekin = 4.56773244343976 | erot = 3.71983710702499 | epot = -38.0529467082193 | etot = -29.7653771577546 +700000 ekin = 4.43155866208691 | erot = 3.53355461960284 | epot = -38.0685834921134 | etot = -30.1034702104236 +701000 ekin = 4.47548631411736 | erot = 3.38963138436219 | epot = -38.0500116139815 | etot = -30.184893915502 +702000 ekin = 4.46550513016984 | erot = 3.66852889097277 | epot = -38.0164512923402 | etot = -29.8824172711975 +703000 ekin = 4.38742906998813 | erot = 3.97599599383721 | epot = -37.9817705180946 | etot = -29.6183454542693 +704000 ekin = 4.41020682713676 | erot = 3.83147838533281 | epot = -37.9674346241365 | etot = -29.725749411667 +705000 ekin = 4.39308990786441 | erot = 3.75664217186778 | epot = -37.9282520396871 | etot = -29.7785199599549 +706000 ekin = 4.43040906703156 | erot = 4.12756254176888 | epot = -37.8939279543826 | etot = -29.3359563455822 +707000 ekin = 4.51700671633646 | erot = 3.77573523129449 | epot = -37.8444471024437 | etot = -29.5517051548127 +708000 ekin = 4.49065124304534 | erot = 3.88552877104003 | epot = -37.7744800646504 | etot = -29.3983000505651 +709000 ekin = 4.41855498291445 | erot = 3.53582586052311 | epot = -37.6656825257611 | etot = -29.7113016823236 +710000 ekin = 4.40535258977283 | erot = 3.3964950268898 | epot = -37.5466939944653 | etot = -29.7448463778027 +711000 ekin = 4.32709544005249 | erot = 3.54995473848094 | epot = -37.3866324258479 | etot = -29.5095822473145 +712000 ekin = 4.40620309390877 | erot = 3.71557442538528 | epot = -37.1793914331048 | etot = -29.0576139138107 +713000 ekin = 4.39226105260192 | erot = 3.64956114520319 | epot = -36.9592491146157 | etot = -28.9174269168105 +714000 ekin = 4.39459047651044 | erot = 3.58799428596579 | epot = -36.784410906283 | etot = -28.8018261438068 +715000 ekin = 4.41458674942589 | erot = 4.01850565037392 | epot = -36.5924446920393 | etot = -28.1593522922395 +716000 ekin = 4.33665938530708 | erot = 3.50452219695686 | epot = -36.4143425377368 | etot = -28.5731609554728 +717000 ekin = 4.18088462864047 | erot = 3.21190204008997 | epot = -36.2481677379303 | etot = -28.8553810691999 +718000 ekin = 4.03231025467833 | erot = 2.91104295996759 | epot = -36.1402693367142 | etot = -29.1969161220683 +719000 ekin = 3.97260579411823 | erot = 3.29783620298646 | epot = -36.0849771003503 | etot = -28.8145351032456 +720000 ekin = 3.82567789821304 | erot = 3.46218504309262 | epot = -36.1068353452665 | etot = -28.8189724039609 +721000 ekin = 3.83433718059043 | erot = 4.0308403694784 | epot = -36.186895804643 | etot = -28.3217182545742 +722000 ekin = 3.71300872765614 | erot = 3.84736896155716 | epot = -36.2838656104836 | etot = -28.7234879212703 +723000 ekin = 3.74703466957627 | erot = 3.71040850656838 | epot = -36.3812410760549 | etot = -28.9237978999102 +724000 ekin = 3.75607081603381 | erot = 4.0281353287461 | epot = -36.4992818358977 | etot = -28.7150756911178 +725000 ekin = 3.77808990085843 | erot = 4.20966764087112 | epot = -36.6263500488379 | etot = -28.6385925071083 +726000 ekin = 3.99703012102758 | erot = 3.67945861038329 | epot = -36.7651398392481 | etot = -29.0886511078373 +727000 ekin = 4.01741049095323 | erot = 3.72684228835757 | epot = -36.8887239674892 | etot = -29.1444711881784 +728000 ekin = 4.05655244457443 | erot = 3.64411335656443 | epot = -36.9831032192824 | etot = -29.2824374181435 +729000 ekin = 4.15914112670643 | erot = 3.22368867517317 | epot = -37.0758214193941 | etot = -29.6929916175145 +730000 ekin = 4.27496625989451 | erot = 3.03434396509882 | epot = -37.1060663359391 | etot = -29.7967561109457 +731000 ekin = 4.35621946146852 | erot = 3.31453862248439 | epot = -37.0811379025033 | etot = -29.4103798185504 +732000 ekin = 4.31460322853995 | erot = 3.19560214587384 | epot = -37.0358028654706 | etot = -29.5255974910568 +733000 ekin = 4.22952267957096 | erot = 3.20037871938027 | epot = -36.9673423522076 | etot = -29.5374409532564 +734000 ekin = 4.24709820971321 | erot = 3.10598269123747 | epot = -36.8800091287789 | etot = -29.5269282278282 +735000 ekin = 4.1498116292607 | erot = 3.12549638567499 | epot = -36.7838119752137 | etot = -29.508503960278 +736000 ekin = 4.20814181481995 | erot = 2.91522500178923 | epot = -36.7063833852254 | etot = -29.5830165686162 +737000 ekin = 4.01828120268363 | erot = 2.4049581257871 | epot = -36.6589611248556 | etot = -30.2357217963849 +738000 ekin = 4.0109403602871 | erot = 2.68632566149121 | epot = -36.6548343802831 | etot = -29.9575683585048 +739000 ekin = 4.14661584174285 | erot = 2.59506078530653 | epot = -36.6780631105762 | etot = -29.9363864835269 +740000 ekin = 4.08413039711058 | erot = 2.5736582399383 | epot = -36.7021237291572 | etot = -30.0443350921083 +741000 ekin = 4.10845660619335 | erot = 2.78416335535289 | epot = -36.7754492326734 | etot = -29.8828292711272 +742000 ekin = 4.09068760907316 | erot = 3.09866824560678 | epot = -36.8187451874514 | etot = -29.6293893327714 +743000 ekin = 3.96610963094549 | erot = 3.04878673776488 | epot = -36.8535622197271 | etot = -29.8386658510168 +744000 ekin = 3.97087885402889 | erot = 3.04950786237749 | epot = -36.8512621314665 | etot = -29.8308754150601 +745000 ekin = 3.78295099566549 | erot = 3.09154774657218 | epot = -36.8410165021283 | etot = -29.9665177598907 +746000 ekin = 3.88442560568566 | erot = 3.15773579416856 | epot = -36.8645704531052 | etot = -29.822409053251 +747000 ekin = 3.94794600572262 | erot = 3.04363515896638 | epot = -36.9228275975809 | etot = -29.9312464328919 +748000 ekin = 3.94186404778415 | erot = 3.24130800398446 | epot = -37.0438118682001 | etot = -29.8606398164315 +749000 ekin = 3.93262026571698 | erot = 3.71710044171245 | epot = -37.2109632789996 | etot = -29.5612425715701 +750000 ekin = 3.82713052636537 | erot = 4.02486049381798 | epot = -37.3854716207176 | etot = -29.5334806005343 +751000 ekin = 4.02336237200016 | erot = 4.23099342037398 | epot = -37.5518597142044 | etot = -29.2975039218302 +752000 ekin = 4.06152925021086 | erot = 3.76231639564706 | epot = -37.6809132611631 | etot = -29.8570676153051 +753000 ekin = 4.07859449791209 | erot = 3.97018598947917 | epot = -37.7593004103711 | etot = -29.7105199229799 +754000 ekin = 4.26771269586489 | erot = 4.64006960442447 | epot = -37.8141557249927 | etot = -28.9063734247033 +755000 ekin = 4.26666906965385 | erot = 4.77784474773988 | epot = -37.8576299963118 | etot = -28.813116178918 +756000 ekin = 4.29131147009744 | erot = 5.38525988164288 | epot = -37.8917845570813 | etot = -28.215213205341 +757000 ekin = 4.35562563894762 | erot = 5.14819699923428 | epot = -37.8935376948419 | etot = -28.38971505666 +758000 ekin = 4.22616249375219 | erot = 5.19713356473893 | epot = -37.8901713134434 | etot = -28.4668752549522 +759000 ekin = 4.24184449957189 | erot = 5.16496183591595 | epot = -37.8881235068914 | etot = -28.4813171714036 +760000 ekin = 4.23424644958513 | erot = 5.47628298706173 | epot = -37.9000330984186 | etot = -28.1895036617718 +761000 ekin = 4.26448749341646 | erot = 5.45907771030601 | epot = -37.9055730645776 | etot = -28.1820078608551 +762000 ekin = 4.22061932798822 | erot = 5.0436907431348 | epot = -37.9108772679059 | etot = -28.6465671967828 +763000 ekin = 4.09989014592177 | erot = 5.10778066514927 | epot = -37.9045250455563 | etot = -28.6968542344852 +764000 ekin = 4.18374834614789 | erot = 5.46818179899542 | epot = -37.8676566747124 | etot = -28.2157265295691 +765000 ekin = 4.08761418374907 | erot = 5.80858388049076 | epot = -37.8033181876414 | etot = -27.9071201234015 +766000 ekin = 4.03999541680448 | erot = 5.48136006660825 | epot = -37.7411893537014 | etot = -28.2198338702887 +767000 ekin = 4.01701285460389 | erot = 5.31665044278878 | epot = -37.6438611160225 | etot = -28.3101978186298 +768000 ekin = 3.97951625205955 | erot = 5.25792422549902 | epot = -37.5214426737365 | etot = -28.284002196178 +769000 ekin = 3.9904400552571 | erot = 5.21175341266104 | epot = -37.3810973556032 | etot = -28.178903887685 +770000 ekin = 3.99199742512011 | erot = 5.21810902470215 | epot = -37.1986211065215 | etot = -27.9885146566993 +771000 ekin = 3.82567851870023 | erot = 4.95130845103881 | epot = -36.9906650314344 | etot = -28.2136780616954 +772000 ekin = 3.72123202682095 | erot = 4.74084322348095 | epot = -36.744551321368 | etot = -28.2824760710661 +773000 ekin = 3.61186619870346 | erot = 4.4876416941515 | epot = -36.4404296878967 | etot = -28.3409217950418 +774000 ekin = 3.53238563321205 | erot = 4.08515606418301 | epot = -36.143048292969 | etot = -28.5255065955739 +775000 ekin = 3.61960121968344 | erot = 4.03007080844248 | epot = -35.8636424209005 | etot = -28.2139703927746 +776000 ekin = 3.50131397859649 | erot = 3.82783005287515 | epot = -35.5938202085502 | etot = -28.2646761770785 +777000 ekin = 3.40867202048171 | erot = 3.85221546935577 | epot = -35.4006619567299 | etot = -28.1397744668925 +778000 ekin = 3.4583803102866 | erot = 3.51853820068406 | epot = -35.2979750992065 | etot = -28.3210565882358 +779000 ekin = 3.42307480041793 | erot = 3.59321040457274 | epot = -35.2809430031739 | etot = -28.2646577981832 +780000 ekin = 3.42440692402583 | erot = 3.60521054559663 | epot = -35.3411249792456 | etot = -28.3115075096232 +781000 ekin = 3.46934151467013 | erot = 3.84731508491239 | epot = -35.4518670976728 | etot = -28.1352104980902 +782000 ekin = 3.52710406680765 | erot = 4.28376670942223 | epot = -35.5950260565868 | etot = -27.7841552803569 +783000 ekin = 3.61729821660962 | erot = 4.75537078140965 | epot = -35.7562125383786 | etot = -27.3835435403593 +784000 ekin = 3.58366553598354 | erot = 4.11380123135017 | epot = -35.8708728516403 | etot = -28.1734060843065 +785000 ekin = 3.63226984987139 | erot = 4.14613629449623 | epot = -35.9549809353062 | etot = -28.1765747909386 +786000 ekin = 3.55353155352182 | erot = 3.96170523540249 | epot = -36.0104316125791 | etot = -28.4951948236547 +787000 ekin = 3.65679390509465 | erot = 4.13482060006107 | epot = -36.0644977241083 | etot = -28.2728832189526 +788000 ekin = 3.867576992853 | erot = 4.10779053552871 | epot = -36.0997261456394 | etot = -28.1243586172577 +789000 ekin = 3.93645468274948 | erot = 4.27766163431813 | epot = -36.1406694170032 | etot = -27.9265530999356 +790000 ekin = 3.99051031327522 | erot = 3.95340487785031 | epot = -36.2018617372684 | etot = -28.2579465461428 +791000 ekin = 4.10452718423531 | erot = 3.99235351847299 | epot = -36.2624115283464 | etot = -28.1655308256382 +792000 ekin = 4.33302884516796 | erot = 3.8304429162741 | epot = -36.3357012610719 | etot = -28.1722294996298 +793000 ekin = 4.59966330091371 | erot = 3.74212535974473 | epot = -36.4314410279298 | etot = -28.0896523672713 +794000 ekin = 4.70509453521945 | erot = 3.73254571552344 | epot = -36.5039677226904 | etot = -28.0663274719476 +795000 ekin = 4.82373501353496 | erot = 3.69936645898632 | epot = -36.5467302591184 | etot = -28.0236287865971 +796000 ekin = 5.02825099690213 | erot = 3.6584589522484 | epot = -36.5441938749352 | etot = -27.8574839257846 +797000 ekin = 4.98369350470429 | erot = 3.33483563015644 | epot = -36.5302539300584 | etot = -28.2117247951976 +798000 ekin = 5.04627515833427 | erot = 3.25184431558307 | epot = -36.5269098314583 | etot = -28.228790357541 +799000 ekin = 4.96165968599483 | erot = 3.39539196017168 | epot = -36.5580084896252 | etot = -28.2009568434587 +800000 ekin = 4.9608728952381 | erot = 3.5493203329157 | epot = -36.6052154994127 | etot = -28.0950222712589 +801000 ekin = 4.96148873220033 | erot = 3.39995120227754 | epot = -36.6619752973789 | etot = -28.300535362901 +802000 ekin = 4.86744715226313 | erot = 3.35338258088214 | epot = -36.694222464791 | etot = -28.4733927316457 +803000 ekin = 4.75056128639555 | erot = 3.25410486957635 | epot = -36.7045390401487 | etot = -28.6998728841768 +804000 ekin = 4.78109129200104 | erot = 3.07765972882934 | epot = -36.6985265194181 | etot = -28.8397754985877 +805000 ekin = 4.82892493818659 | erot = 3.27499533781792 | epot = -36.6737874267385 | etot = -28.5698671507339 +806000 ekin = 4.74542372520125 | erot = 3.18323237798567 | epot = -36.6406513076366 | etot = -28.7119952044497 +807000 ekin = 4.64766139288033 | erot = 3.38424960796029 | epot = -36.647673088396 | etot = -28.6157620875554 +808000 ekin = 4.457078358644 | erot = 3.35175675914238 | epot = -36.7022500935494 | etot = -28.893414975763 +809000 ekin = 4.3267088759155 | erot = 3.32046355515555 | epot = -36.7741824114205 | etot = -29.1270099803495 +810000 ekin = 4.19642960492136 | erot = 3.20396083815701 | epot = -36.8832195227731 | etot = -29.4828290796948 +811000 ekin = 4.18603442116986 | erot = 3.54097838794745 | epot = -37.0402774324891 | etot = -29.3132646233718 +812000 ekin = 4.33190991624128 | erot = 3.67977508149037 | epot = -37.2334955671968 | etot = -29.2218105694651 +813000 ekin = 4.46701990899902 | erot = 3.84749046887853 | epot = -37.477006312962 | etot = -29.1624959350845 +814000 ekin = 4.70593563863401 | erot = 4.02074050200779 | epot = -37.7739765579915 | etot = -29.0473004173497 +815000 ekin = 4.61635561952674 | erot = 4.30893882425501 | epot = -38.0622407069035 | etot = -29.1369462631217 +816000 ekin = 4.66419241223469 | erot = 4.4334841646702 | epot = -38.3533945439941 | etot = -29.2557179670892 +817000 ekin = 4.61492034782231 | erot = 4.85896836140468 | epot = -38.6054729848482 | etot = -29.1315842756212 +818000 ekin = 4.6936135555876 | erot = 4.57560992803624 | epot = -38.8141140205622 | etot = -29.5448905369383 +819000 ekin = 4.99561997491631 | erot = 4.59057590873874 | epot = -38.9861314653861 | etot = -29.399935581731 +820000 ekin = 5.14251771001315 | erot = 4.38257454602503 | epot = -39.111979352787 | etot = -29.5868870967488 +821000 ekin = 5.21211790511143 | erot = 3.76493639645341 | epot = -39.1791873910091 | etot = -30.2021330894442 +822000 ekin = 5.22763747343407 | erot = 3.81993934721836 | epot = -39.2257832500634 | etot = -30.178206429411 +823000 ekin = 5.20824824630262 | erot = 3.61818509207447 | epot = -39.2577442235127 | etot = -30.4313108851356 +824000 ekin = 5.29481176259064 | erot = 3.61607107182839 | epot = -39.2930045776051 | etot = -30.382121743186 +825000 ekin = 5.34590564278881 | erot = 3.47605801675253 | epot = -39.3020776711429 | etot = -30.4801140116015 +826000 ekin = 5.38005087585683 | erot = 3.56002985231115 | epot = -39.2878928900552 | etot = -30.3478121618872 +827000 ekin = 5.38251681844313 | erot = 3.31581026558491 | epot = -39.2838973283757 | etot = -30.5855702443476 +828000 ekin = 5.30162295798738 | erot = 2.79999506814259 | epot = -39.2990437954941 | etot = -31.1974257693642 +829000 ekin = 5.34935471298468 | erot = 2.63380753851503 | epot = -39.3079384502706 | etot = -31.3247761987709 +830000 ekin = 5.15642397228279 | erot = 2.78944963383064 | epot = -39.3294203636004 | etot = -31.383546757487 +831000 ekin = 5.04271329110575 | erot = 3.07984504895767 | epot = -39.3562191308943 | etot = -31.2336607908309 +832000 ekin = 5.04415123872944 | erot = 3.36917057661257 | epot = -39.3458026730645 | etot = -30.9324808577225 +833000 ekin = 4.97652700754312 | erot = 3.1101682681075 | epot = -39.3003589046715 | etot = -31.2136636290209 +834000 ekin = 4.66785324148465 | erot = 2.98799062968242 | epot = -39.2007615011675 | etot = -31.5449176300004 +835000 ekin = 4.41967948410668 | erot = 3.24754240638231 | epot = -39.0370935965111 | etot = -31.3698717060221 +836000 ekin = 4.19399501172609 | erot = 3.40709899396411 | epot = -38.8824429433975 | etot = -31.2813489377073 +837000 ekin = 4.05102708476564 | erot = 3.50403284169295 | epot = -38.729129846576 | etot = -31.1740699201174 +838000 ekin = 3.94991363719696 | erot = 3.82377156946746 | epot = -38.5557937558051 | etot = -30.7821085491406 +839000 ekin = 3.7432666531872 | erot = 3.97324655976193 | epot = -38.3643816043728 | etot = -30.6478683914237 +840000 ekin = 3.70351574528206 | erot = 3.51244886217305 | epot = -38.1559200259223 | etot = -30.9399554184672 +841000 ekin = 3.60547887438337 | erot = 3.69151206405111 | epot = -37.9552189953845 | etot = -30.65822805695 +842000 ekin = 3.38591284745953 | erot = 3.48115901302697 | epot = -37.764748291951 | etot = -30.8976764314645 +843000 ekin = 3.11807787995847 | erot = 3.24962582172167 | epot = -37.5931200484565 | etot = -31.2254163467764 +844000 ekin = 3.03125896851695 | erot = 3.10915311466782 | epot = -37.405355484813 | etot = -31.2649434016282 +845000 ekin = 2.84759324027358 | erot = 3.53115382226828 | epot = -37.2260086331774 | etot = -30.8472615706355 +846000 ekin = 2.83613069836887 | erot = 3.4149752298821 | epot = -37.0853206047919 | etot = -30.8342146765409 +847000 ekin = 2.82518542790846 | erot = 3.9264613760552 | epot = -36.974096592552 | etot = -30.2224497885884 +848000 ekin = 2.80356101967319 | erot = 3.75897131812122 | epot = -36.8749675315762 | etot = -30.3124351937818 +849000 ekin = 2.84159199816781 | erot = 3.65493979263187 | epot = -36.779890805585 | etot = -30.2833590147853 +850000 ekin = 2.91517374365713 | erot = 3.25543936029208 | epot = -36.7388454898329 | etot = -30.5682323858837 +851000 ekin = 3.08764953673658 | erot = 3.74455145978192 | epot = -36.7223642181885 | etot = -29.89016322167 +852000 ekin = 3.20356705871772 | erot = 3.86422941824802 | epot = -36.7413165099177 | etot = -29.6735200329519 +853000 ekin = 3.25796036952201 | erot = 4.25509323905638 | epot = -36.7658517979722 | etot = -29.2527981893938 +854000 ekin = 3.57244822927054 | erot = 4.18969744123878 | epot = -36.8021340521259 | etot = -29.0399883816166 +855000 ekin = 3.61706783412732 | erot = 4.16292249791896 | epot = -36.8626923862677 | etot = -29.0827020542214 +856000 ekin = 3.78538239755829 | erot = 4.1125355160369 | epot = -36.9244661414311 | etot = -29.0265482278359 +857000 ekin = 3.78178847655943 | erot = 4.13628071929874 | epot = -37.0292483027703 | etot = -29.1111791069121 +858000 ekin = 3.79767899411072 | erot = 4.25390024597238 | epot = -37.1883443366299 | etot = -29.1367650965468 +859000 ekin = 3.79646558910104 | erot = 4.39490149090002 | epot = -37.3423128301936 | etot = -29.1509457501926 +860000 ekin = 3.86711139340656 | erot = 4.91957560544927 | epot = -37.4915022932753 | etot = -28.7048152944195 +861000 ekin = 3.99177075241214 | erot = 4.92589410248027 | epot = -37.5868681074752 | etot = -28.6692032525828 +862000 ekin = 4.09777488770542 | erot = 4.85487231115203 | epot = -37.6175250863673 | etot = -28.6648778875099 +863000 ekin = 4.13925231113358 | erot = 4.50896117392437 | epot = -37.5986086016745 | etot = -28.9503951166166 +864000 ekin = 4.14764866587401 | erot = 4.42487018235784 | epot = -37.5204132439135 | etot = -28.9478943956816 +865000 ekin = 4.14664914911124 | erot = 4.25648196395957 | epot = -37.3939280409712 | etot = -28.9907969279004 +866000 ekin = 4.14214320133623 | erot = 4.18089045470408 | epot = -37.2179460829705 | etot = -28.8949124269302 +867000 ekin = 4.2533355578276 | erot = 3.91180056253338 | epot = -37.0368358637648 | etot = -28.8716997434038 +868000 ekin = 4.25544635673599 | erot = 4.03934502097771 | epot = -36.8925237407717 | etot = -28.597732363058 +869000 ekin = 4.24112681076696 | erot = 4.01454747655037 | epot = -36.8084367274639 | etot = -28.5527624401466 +870000 ekin = 4.33478513327969 | erot = 3.78349131070103 | epot = -36.7681636745506 | etot = -28.6498872305699 +871000 ekin = 4.17502061003877 | erot = 3.95421063050501 | epot = -36.789978024709 | etot = -28.6607467841652 +872000 ekin = 4.17603847735387 | erot = 3.83768938083755 | epot = -36.8688005631079 | etot = -28.8550727049165 +873000 ekin = 4.41693719639055 | erot = 4.07505566261771 | epot = -36.9767379853353 | etot = -28.484745126327 +874000 ekin = 4.41295334009066 | erot = 4.18394759913442 | epot = -37.1369142438402 | etot = -28.5400133046152 +875000 ekin = 4.5295533495583 | erot = 4.19580464695389 | epot = -37.3370998777418 | etot = -28.6117418812297 +876000 ekin = 4.61247068682014 | erot = 4.50897081857259 | epot = -37.524834933576 | etot = -28.4033934281833 +877000 ekin = 4.76533246608885 | erot = 4.08201826719388 | epot = -37.6873606048148 | etot = -28.8400098715321 +878000 ekin = 4.86109701096016 | erot = 4.03315572964805 | epot = -37.8092910984796 | etot = -28.9150383578714 +879000 ekin = 4.93322526419341 | erot = 3.94479688456014 | epot = -37.8433128250789 | etot = -28.9652906763253 +880000 ekin = 4.911777192825 | erot = 3.90966953329923 | epot = -37.7988935874835 | etot = -28.9774468613593 +881000 ekin = 4.87595051611175 | erot = 3.76638474533256 | epot = -37.6791282073065 | etot = -29.0367929458622 +882000 ekin = 4.80398792776511 | erot = 3.52725045147228 | epot = -37.4958553191689 | etot = -29.1646169399315 +883000 ekin = 4.56372183805733 | erot = 3.17268134771393 | epot = -37.3026048485139 | etot = -29.5662016627427 +884000 ekin = 4.38408070690437 | erot = 2.95287988074889 | epot = -37.1164899885621 | etot = -29.7795294009088 +885000 ekin = 4.21401267631408 | erot = 3.28627816384396 | epot = -36.9423946246094 | etot = -29.4421037844513 +886000 ekin = 3.94208450895983 | erot = 3.61827008671944 | epot = -36.8244889717529 | etot = -29.2641343760737 +887000 ekin = 3.76025689669472 | erot = 3.89282193563569 | epot = -36.7542446517053 | etot = -29.1011658193749 +888000 ekin = 3.58518173626078 | erot = 4.10918051627477 | epot = -36.7235080282687 | etot = -29.0291457757332 +889000 ekin = 3.52227905598844 | erot = 4.53948895643707 | epot = -36.742334591686 | etot = -28.6805665792605 +890000 ekin = 3.48725850687346 | erot = 4.91651845671102 | epot = -36.81107494511 | etot = -28.4072979815255 +891000 ekin = 3.51807183016393 | erot = 5.36785996033029 | epot = -36.9187079043872 | etot = -28.0327761138929 +892000 ekin = 3.48651441482314 | erot = 5.25687644163395 | epot = -37.0005216584211 | etot = -28.257130801964 +893000 ekin = 3.51467838154865 | erot = 5.65149044087769 | epot = -37.05944534206 | etot = -27.8932765196337 +894000 ekin = 3.45974654612344 | erot = 5.22169711042801 | epot = -37.1020642679859 | etot = -28.4206206114344 +895000 ekin = 3.57216437063283 | erot = 5.4089506797762 | epot = -37.1028729086242 | etot = -28.1217578582152 +896000 ekin = 3.56655921068021 | erot = 5.69090228219818 | epot = -37.070821741523 | etot = -27.8133602486446 +897000 ekin = 3.57757547802829 | erot = 5.90228049359271 | epot = -36.9859514532974 | etot = -27.5060954816764 +898000 ekin = 3.52295514054008 | erot = 5.84538360240597 | epot = -36.8484715408745 | etot = -27.4801327979284 +899000 ekin = 3.42191869063631 | erot = 5.47174915922289 | epot = -36.6856616378147 | etot = -27.7919937879555 +900000 ekin = 3.45720121516806 | erot = 5.59973772512064 | epot = -36.5148133918258 | etot = -27.4578744515371 +901000 ekin = 3.51607619901442 | erot = 5.88763510779773 | epot = -36.2859464010575 | etot = -26.8822350942454 +902000 ekin = 3.56087621117169 | erot = 5.17399063106742 | epot = -36.0621785767848 | etot = -27.3273117345457 +903000 ekin = 3.56470936099193 | erot = 5.0736169800556 | epot = -35.8794588183624 | etot = -27.2411324773149 +904000 ekin = 3.64294879518613 | erot = 5.28022715353213 | epot = -35.7543216612838 | etot = -26.8311457125655 +905000 ekin = 3.72447152602285 | erot = 5.02657007424527 | epot = -35.6582804909764 | etot = -26.9072388907083 +906000 ekin = 3.75914133677088 | erot = 4.63070748715842 | epot = -35.612999504401 | etot = -27.2231506804717 +907000 ekin = 4.00046169414558 | erot = 4.63743176603131 | epot = -35.6087015116536 | etot = -26.9708080514767 +908000 ekin = 3.98050966425464 | erot = 4.23795607914891 | epot = -35.6020003534147 | etot = -27.3835346100112 +909000 ekin = 4.14488755712815 | erot = 3.77771446920705 | epot = -35.5819012555833 | etot = -27.6592992292481 +910000 ekin = 4.1887889926356 | erot = 3.85878998652561 | epot = -35.5853308204891 | etot = -27.5377518413279 +911000 ekin = 4.15448454864758 | erot = 3.93063753948176 | epot = -35.6075046071718 | etot = -27.5223825190425 +912000 ekin = 4.30922033402802 | erot = 4.53644215925805 | epot = -35.6368602869835 | etot = -26.7911977936974 +913000 ekin = 4.42050627097558 | erot = 4.36559538892952 | epot = -35.6635505470047 | etot = -26.8774488870996 +914000 ekin = 4.6403841670674 | erot = 4.57708989772375 | epot = -35.6621612967527 | etot = -26.4446872319616 +915000 ekin = 4.71121950507705 | erot = 4.34018648406813 | epot = -35.6015140360094 | etot = -26.5501080468642 +916000 ekin = 4.67735943325919 | erot = 4.0723772918886 | epot = -35.4903050476419 | etot = -26.7405683224941 +917000 ekin = 4.78142703705638 | erot = 4.20198791892886 | epot = -35.3917685265256 | etot = -26.4083535705404 +918000 ekin = 4.7742119869693 | erot = 4.42971373988814 | epot = -35.2582637676414 | etot = -26.0543380407839 +919000 ekin = 4.73422216252914 | erot = 4.77044814340051 | epot = -35.0931913565728 | etot = -25.5885210506432 +920000 ekin = 4.64583700129848 | erot = 4.69774436792081 | epot = -34.9395895324837 | etot = -25.5960081632644 +921000 ekin = 4.61516328269964 | erot = 4.43350879426936 | epot = -34.8128426462854 | etot = -25.7641705693164 +922000 ekin = 4.55621337364178 | erot = 4.21768777753525 | epot = -34.731272035168 | etot = -25.957370883991 +923000 ekin = 4.59034826680215 | erot = 4.50920703076205 | epot = -34.7044992141229 | etot = -25.6049439165587 +924000 ekin = 4.58356240196282 | erot = 4.62074320796255 | epot = -34.7126986327434 | etot = -25.5083930228181 +925000 ekin = 4.53220072800684 | erot = 4.79254817721302 | epot = -34.7588998026867 | etot = -25.4341508974668 +926000 ekin = 4.55832715206546 | erot = 5.00471911281283 | epot = -34.8080246038197 | etot = -25.2449783389414 +927000 ekin = 4.62575171089084 | erot = 4.71181044830637 | epot = -34.8667293476369 | etot = -25.5291671884397 +928000 ekin = 4.6865737520682 | erot = 4.76234601746956 | epot = -34.9159498367978 | etot = -25.4670300672601 +929000 ekin = 4.70610289156496 | erot = 5.07097104655825 | epot = -34.9791697926812 | etot = -25.202095854558 +930000 ekin = 4.79474071813525 | erot = 5.21915381885372 | epot = -35.0589708185242 | etot = -25.0450762815352 +931000 ekin = 4.69039359230198 | erot = 5.48593447848963 | epot = -35.1099047138404 | etot = -24.9335766430488 +932000 ekin = 4.7111009460339 | erot = 5.4720468535618 | epot = -35.1612846037869 | etot = -24.9781368041912 +933000 ekin = 4.76369652677887 | erot = 5.41370570081894 | epot = -35.2317575147351 | etot = -25.0543552871373 +934000 ekin = 4.83643894391789 | erot = 5.23508631414153 | epot = -35.3109086744022 | etot = -25.2393834163428 +935000 ekin = 4.76586014730436 | erot = 5.22865540833756 | epot = -35.3670038676071 | etot = -25.3724883119652 +936000 ekin = 4.7459923218933 | erot = 5.40903849081523 | epot = -35.4141584031107 | etot = -25.2591275904022 +937000 ekin = 4.70665366838905 | erot = 5.90535300927779 | epot = -35.4573569432724 | etot = -24.8453502656056 +938000 ekin = 4.73520980048979 | erot = 5.48994015212931 | epot = -35.4717259493596 | etot = -25.2465759967405 +939000 ekin = 4.66471904112519 | erot = 5.58667162801307 | epot = -35.4363389851306 | etot = -25.1849483159923 +940000 ekin = 4.73670308439177 | erot = 5.59502045341229 | epot = -35.3410735898404 | etot = -25.0093500520363 +941000 ekin = 4.56546752366378 | erot = 5.16939612930462 | epot = -35.2196425314963 | etot = -25.4847788785279 +942000 ekin = 4.36600564082669 | erot = 4.55609433699451 | epot = -35.0782455188876 | etot = -26.1561455410664 +943000 ekin = 4.27680501590838 | erot = 4.77186490926422 | epot = -34.9346146494824 | etot = -25.8859447243098 +944000 ekin = 4.17576408254737 | erot = 4.64476704064562 | epot = -34.7936442239135 | etot = -25.9731131007205 +945000 ekin = 4.08165692512371 | erot = 4.64307958398346 | epot = -34.7241648822137 | etot = -25.9994283731065 +946000 ekin = 3.98238337685344 | erot = 4.33903183997964 | epot = -34.7208981880722 | etot = -26.3994829712391 +947000 ekin = 4.11312487406461 | erot = 4.25698162025787 | epot = -34.8023164533948 | etot = -26.4322099590723 +948000 ekin = 4.03905965504869 | erot = 4.28038925266087 | epot = -34.9281986674362 | etot = -26.6087497597266 +949000 ekin = 4.1208125166908 | erot = 4.40083354097111 | epot = -35.1348098866939 | etot = -26.613163829032 +950000 ekin = 4.19947300195128 | erot = 4.46892156642135 | epot = -35.3299547862506 | etot = -26.661560217878 +951000 ekin = 4.28802819218884 | erot = 4.36807424436335 | epot = -35.5595339264246 | etot = -26.9034314898725 +952000 ekin = 4.44618066979578 | erot = 4.88998578448103 | epot = -35.7762645912068 | etot = -26.44009813693 +953000 ekin = 4.5302283554923 | erot = 4.90684636989476 | epot = -35.9402525430858 | etot = -26.5031778176987 +954000 ekin = 4.65793433635961 | erot = 4.95789701943277 | epot = -36.1007223995933 | etot = -26.4848910438009 +955000 ekin = 4.68472849923027 | erot = 4.84778271057312 | epot = -36.2250094081951 | etot = -26.6924981983917 +956000 ekin = 4.83489144923538 | erot = 4.61252423076221 | epot = -36.2912267944712 | etot = -26.8438111144736 +957000 ekin = 4.83158754758409 | erot = 4.0642787483582 | epot = -36.3314048744553 | etot = -27.435538578513 +958000 ekin = 4.95872508890374 | erot = 3.8676428932311 | epot = -36.3554965538545 | etot = -27.5291285717197 +959000 ekin = 4.88220034385472 | erot = 3.76501141985342 | epot = -36.3703754351938 | etot = -27.7231636714857 +960000 ekin = 4.96739750076015 | erot = 3.7014398632156 | epot = -36.3537104260633 | etot = -27.6848730620876 +961000 ekin = 5.05073619222996 | erot = 3.58723306284446 | epot = -36.3292284086296 | etot = -27.6912591535552 +962000 ekin = 5.10220917296366 | erot = 3.43365806618373 | epot = -36.2926607322774 | etot = -27.75679349313 +963000 ekin = 5.25727455724212 | erot = 3.39047088285921 | epot = -36.2233249912223 | etot = -27.575579551121 +964000 ekin = 5.33892942752082 | erot = 3.38850636488331 | epot = -36.1631800361723 | etot = -27.4357442437681 +965000 ekin = 5.2970730958468 | erot = 3.40709075904151 | epot = -36.114647791202 | etot = -27.4104839363137 +966000 ekin = 5.27380254283778 | erot = 3.34984185029643 | epot = -36.0934598827503 | etot = -27.4698154896161 +967000 ekin = 5.19975037009079 | erot = 3.54967607074502 | epot = -36.1222651146807 | etot = -27.3728386738448 +968000 ekin = 5.22098509097155 | erot = 3.3892004067814 | epot = -36.1570868906286 | etot = -27.5469013928757 +969000 ekin = 5.01248198517068 | erot = 3.26201512253228 | epot = -36.2130447987792 | etot = -27.9385476910762 +970000 ekin = 4.97914863237106 | erot = 3.76343819077311 | epot = -36.2895058744145 | etot = -27.5469190512703 +971000 ekin = 5.04224300192785 | erot = 3.59024832311319 | epot = -36.3590409977869 | etot = -27.7265496727458 +972000 ekin = 5.05787332232175 | erot = 3.83558558676151 | epot = -36.3997125264456 | etot = -27.5062536173623 +973000 ekin = 5.01777031588935 | erot = 3.27986497682726 | epot = -36.4166837336011 | etot = -28.1190484408845 +974000 ekin = 4.96186842907979 | erot = 3.23479851019171 | epot = -36.4352005399393 | etot = -28.2385336006678 +975000 ekin = 4.97224363278502 | erot = 3.35077904927888 | epot = -36.4557098060367 | etot = -28.1326871239728 +976000 ekin = 5.0162553138043 | erot = 3.41837200675041 | epot = -36.4643526378271 | etot = -28.0297253172724 +977000 ekin = 5.04359880486583 | erot = 3.40669885598936 | epot = -36.4673967616966 | etot = -28.0170991008414 +978000 ekin = 4.9681411602187 | erot = 3.39885422893789 | epot = -36.4671439769122 | etot = -28.1001485877556 +979000 ekin = 4.68494120169249 | erot = 3.87226166481083 | epot = -36.4696261905049 | etot = -27.9124233240016 +980000 ekin = 4.80514576212701 | erot = 3.73614562894005 | epot = -36.475376838153 | etot = -27.9340854470859 +981000 ekin = 4.85375109376202 | erot = 4.35522911699943 | epot = -36.490277579472 | etot = -27.2812973687106 +982000 ekin = 4.79648806853116 | erot = 4.15595945903746 | epot = -36.5084812040106 | etot = -27.556033676442 +983000 ekin = 4.75907969484057 | erot = 4.43556787871506 | epot = -36.5083539693145 | etot = -27.3137063957588 +984000 ekin = 4.81598118843888 | erot = 4.52957555705298 | epot = -36.5383410952843 | etot = -27.1927843497924 +985000 ekin = 4.87924474650941 | erot = 4.31630979014036 | epot = -36.577700648078 | etot = -27.3821461114282 +986000 ekin = 4.77128314224537 | erot = 4.12408981491498 | epot = -36.5819281400531 | etot = -27.6865551828927 +987000 ekin = 4.70900566206185 | erot = 4.08922713836866 | epot = -36.5892891612732 | etot = -27.7910563608427 +988000 ekin = 4.6968564492698 | erot = 4.03217145235668 | epot = -36.6289948782934 | etot = -27.8999669766669 +989000 ekin = 4.56955203825019 | erot = 4.16364650343056 | epot = -36.6885496975525 | etot = -27.9553511558718 +990000 ekin = 4.56207337974517 | erot = 3.92865148644801 | epot = -36.7375440238776 | etot = -28.2468191576844 +991000 ekin = 4.4586326947315 | erot = 3.99370804360007 | epot = -36.8046932644695 | etot = -28.3523525261379 +992000 ekin = 4.52516169637469 | erot = 4.19036473784407 | epot = -36.9045951669892 | etot = -28.1890687327704 +993000 ekin = 4.26593637770936 | erot = 4.55899726308496 | epot = -37.0283922292365 | etot = -28.2034585884422 +994000 ekin = 4.14968593987806 | erot = 4.67871188882193 | epot = -37.1561829580762 | etot = -28.3277851293762 +995000 ekin = 4.20875361664816 | erot = 4.51127733270458 | epot = -37.285893138091 | etot = -28.5658621887383 +996000 ekin = 4.10968366763525 | erot = 4.25871927923692 | epot = -37.3745810703536 | etot = -29.0061781234814 +997000 ekin = 4.00616178451074 | erot = 4.48911641515844 | epot = -37.4314666701152 | etot = -28.936188470446 +998000 ekin = 4.02180091279274 | erot = 4.35841167717687 | epot = -37.4443636100105 | etot = -29.0641510200409 +999000 ekin = 4.07504562975234 | erot = 4.2623087345041 | epot = -37.4098012996852 | etot = -29.0724469354287 +1000000 ekin = 3.90433765200202 | erot = 4.66881888228247 | epot = -37.3063332342133 | etot = -28.7331766999288 + 1000000 0.10411567 -1.4674304 0.032571422 -1.2846921 -6.6175275e-05 64000 +Loop time of 46.7814 on 4 procs for 1000000 steps with 26 atoms + +Performance: 18468.870 tau/day, 21376.007 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.74 | 20.221 | 37.61 | 224.5 | 43.22 +Bond | 0.40761 | 0.56838 | 0.7636 | 21.2 | 1.21 +Neigh | 0.009822 | 0.0099905 | 0.010152 | 0.1 | 0.02 +Comm | 5.0791 | 23.235 | 31.502 | 219.3 | 49.67 +Output | 0.11084 | 0.12593 | 0.13167 | 2.5 | 0.27 +Modify | 1.5136 | 2.183 | 2.853 | 44.8 | 4.67 +Other | | 0.4378 | | | 0.94 + +Nlocal: 6.50000 ave 10 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 19.5000 ave 23 max 16 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 75.2500 ave 190 max 23 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.8.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:46 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2 new file mode 100644 index 0000000000..8c985708ca --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file via write_data, version 27 May 2021 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0 +2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0 +3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0 +4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0 +5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0 +6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0 +7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0 +8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0 +9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0 +10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0 +11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0 +12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0 +13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0 +14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0 +15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0 +16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725 +2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215 +3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625 +4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877 +5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292 +6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776 +7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357 +8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032 +9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696 +10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506 +11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418 +12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697 +13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132 +14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759 +15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106 +16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2 similarity index 67% rename from examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 rename to examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2 index 5d5e2cd177..30458a7266 100644 --- a/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 +++ b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2 @@ -1,24 +1,25 @@ -variable number equal 4 +variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 +variable rhos equal 0.5 units lj dimension 3 -newton off +newton on boundary p p p -atom_style hybrid bond ellipsoid +atom_style hybrid bond ellipsoid oxdna atom_modify sort 0 1.0 # Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin +neighbor 2.0 bin neigh_modify every 1 delay 0 check yes -read_data data.duplex4 +read_data data.duplex2 set atom * mass 3.1575 @@ -31,38 +32,27 @@ special_bonds lj 0 1 1 # oxRNA2 pair interactions pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh - pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 -pair_coeff * * oxrna2/dh ${T} 0.5 1.02455 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 # NVE ensemble -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/dot fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 timestep 1e-5 #comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" +compute quat all property/atom quatw quati quatj quatk compute erot all erotate/asphere compute ekin all ke @@ -73,10 +63,11 @@ variable epot equal c_epot variable etot equal c_erot+c_ekin+c_epot fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f" +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" run 1000000 -#write_restart config.${number}.* +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 new file mode 100644 index 0000000000..f02f81d934 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 @@ -0,0 +1,1182 @@ +LAMMPS (2 Jul 2021) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.5 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +set atom * mass 3.1575 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 2.0 0.25 0.761070781051 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 0.1 ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3014979 + ghost atom cutoff = 4.3014979 + binsize = 2.150749, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 4.301497916929199 (../comm.cpp:739) +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -11.1349465280231 | etot = -5.62847186873665 +Per MPI rank memory allocation (min/avg/max) = 9.347 | 9.347 | 9.347 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -0.7299505 0.034016337 -0.52688704 5.1214421e-05 64000 +1000 ekin = 2.74425239815418 | erot = 2.79065458610894 | epot = -11.163378852689 | etot = -5.62847186842591 +2000 ekin = 2.78841691867037 | erot = 2.77992540099535 | epot = -11.1968141877249 | etot = -5.62847186805919 +3000 ekin = 2.83938215410024 | erot = 2.77185117591642 | epot = -11.2397051978033 | etot = -5.62847186778665 +4000 ekin = 2.89876217830266 | erot = 2.76816783884241 | epot = -11.295401884792 | etot = -5.62847186764698 +5000 ekin = 2.96742170720772 | erot = 2.76919345829433 | epot = -11.3650870331989 | etot = -5.62847186769686 +6000 ekin = 3.04563007371043 | erot = 2.77376672268246 | epot = -11.4478686641706 | etot = -5.62847186777771 +7000 ekin = 3.13407886898542 | erot = 2.78065913591454 | epot = -11.5432098726293 | etot = -5.62847186772939 +8000 ekin = 3.23400863287747 | erot = 2.78938863934855 | epot = -11.651869139893 | etot = -5.628471867667 +9000 ekin = 3.34625998930262 | erot = 2.80019523753782 | epot = -11.7749270943235 | etot = -5.62847186748304 +10000 ekin = 3.47220350616338 | erot = 2.8146462281528 | epot = -11.9153216015116 | etot = -5.62847186719541 +11000 ekin = 3.61341090096022 | erot = 2.83541090219848 | epot = -12.0772936703878 | etot = -5.62847186722913 +12000 ekin = 3.76971728921065 | erot = 2.8651661044909 | epot = -12.2633552607298 | etot = -5.62847186702824 +13000 ekin = 3.9410557771447 | erot = 2.90597306806357 | epot = -12.4755007121564 | etot = -5.62847186694818 +14000 ekin = 4.1273074489676 | erot = 2.95952862137382 | epot = -12.7153079373022 | etot = -5.6284718669608 +15000 ekin = 4.32776706381553 | erot = 3.02701108512254 | epot = -12.9832500158853 | etot = -5.62847186694725 +16000 ekin = 4.54139695680688 | erot = 3.10924468066181 | epot = -13.2791135046205 | etot = -5.62847186715177 +17000 ekin = 4.76575661763827 | erot = 3.20604355373095 | epot = -13.60027203892 | etot = -5.62847186755082 +18000 ekin = 4.99700491214688 | erot = 3.31611869568271 | epot = -13.9415954758898 | etot = -5.62847186806023 +19000 ekin = 5.23048108112194 | erot = 3.43700077146765 | epot = -14.2959537213472 | etot = -5.62847186875762 +20000 ekin = 5.4607474251306 | erot = 3.56463156086408 | epot = -14.6538508556013 | etot = -5.62847186960665 +21000 ekin = 5.68087058007138 | erot = 3.69256776681719 | epot = -15.0019102179231 | etot = -5.62847187103449 +22000 ekin = 5.8832761998388 | erot = 3.81252322503561 | epot = -15.3242712967755 | etot = -5.62847187190112 +23000 ekin = 6.06249979951992 | erot = 3.91720950057676 | epot = -15.6081811728147 | etot = -5.62847187271801 +24000 ekin = 6.21449712377438 | erot = 4.00104081543186 | epot = -15.8440098121105 | etot = -5.62847187290421 +25000 ekin = 6.33853277809255 | erot = 4.06184542619886 | epot = -16.0288500769828 | etot = -5.6284718726914 +26000 ekin = 6.43627737187012 | erot = 4.10076278430849 | epot = -16.1655120283938 | etot = -5.6284718722152 +27000 ekin = 6.51092447972028 | erot = 4.12134483746816 | epot = -16.2607411888241 | etot = -5.62847187163566 +28000 ekin = 6.56622100976685 | erot = 4.12827111510823 | epot = -16.3229639959506 | etot = -5.62847187107552 +29000 ekin = 6.60587340002395 | erot = 4.12622173833906 | epot = -16.3605670089491 | etot = -5.62847187058613 +30000 ekin = 6.63335580501832 | erot = 4.11921545444658 | epot = -16.3810431296793 | etot = -5.62847187021444 +31000 ekin = 6.65211888589275 | erot = 4.10999678317536 | epot = -16.3905875389834 | etot = -5.62847186991527 +32000 ekin = 6.66584763664879 | erot = 4.10024297795105 | epot = -16.3945624842072 | etot = -5.62847186960737 +33000 ekin = 6.67923227191035 | erot = 4.0912920741337 | epot = -16.398996215263 | etot = -5.62847186921897 +34000 ekin = 6.69756137216839 | erot = 4.08414768607668 | epot = -16.4101809271346 | etot = -5.62847186888957 +35000 ekin = 6.72589628312089 | erot = 4.07950228497952 | epot = -16.4338704366877 | etot = -5.62847186858733 +36000 ekin = 6.76908557113721 | erot = 4.07778615492113 | epot = -16.4753435944361 | etot = -5.6284718683778 +37000 ekin = 6.8309750621341 | erot = 4.07899014040668 | epot = -16.5384370708782 | etot = -5.62847186833746 +38000 ekin = 6.91354703253178 | erot = 4.08242106390421 | epot = -16.6244399649596 | etot = -5.6284718685236 +39000 ekin = 7.01626065739839 | erot = 4.0865217194279 | epot = -16.731254245777 | etot = -5.62847186895074 +40000 ekin = 7.13573792258335 | erot = 4.08884404540011 | epot = -16.8530538375758 | etot = -5.6284718695923 +41000 ekin = 7.26614194134519 | erot = 4.08627042537778 | epot = -16.9808842370343 | etot = -5.62847187031131 +42000 ekin = 7.40051154120592 | erot = 4.07546023443118 | epot = -17.1044436466276 | etot = -5.62847187099052 +43000 ekin = 7.53157437143693 | erot = 4.05344655359662 | epot = -17.2134927965848 | etot = -5.62847187155127 +44000 ekin = 7.65268317567647 | erot = 4.01819177227262 | epot = -17.2993468198233 | etot = -5.62847187187421 +45000 ekin = 7.7584534330689 | erot = 3.96898510895809 | epot = -17.3559104142065 | etot = -5.62847187217952 +46000 ekin = 7.84504377034641 | erot = 3.90454903064835 | epot = -17.3780646733317 | etot = -5.62847187233695 +47000 ekin = 7.9100239082063 | erot = 3.82478596555242 | epot = -17.3632817459107 | etot = -5.628471872152 +48000 ekin = 7.95195705456506 | erot = 3.73154439390053 | epot = -17.3119733204129 | etot = -5.62847187194729 +49000 ekin = 7.97001825706866 | erot = 3.62752007295095 | epot = -17.2260102016185 | etot = -5.62847187159891 +50000 ekin = 7.96375756700429 | erot = 3.51726958365157 | epot = -17.1094990215452 | etot = -5.62847187088935 +51000 ekin = 7.93280761300438 | erot = 3.40827188497884 | epot = -16.9695513688031 | etot = -5.62847187081985 +52000 ekin = 7.87656811744191 | erot = 3.30207418532579 | epot = -16.8071141735587 | etot = -5.62847187079096 +53000 ekin = 7.79531012541906 | erot = 3.19839984815453 | epot = -16.6221818441148 | etot = -5.62847187054118 +54000 ekin = 7.68952609570334 | erot = 3.09980185481856 | epot = -16.4177998208246 | etot = -5.62847187030271 +55000 ekin = 7.55966222141095 | erot = 3.00897426989566 | epot = -16.19710836145 | etot = -5.62847187014341 +56000 ekin = 7.40594124507999 | erot = 2.92802865182286 | epot = -15.9624417669773 | etot = -5.62847187007443 +57000 ekin = 7.22816598141989 | erot = 2.85836584281815 | epot = -15.715003694348 | etot = -5.62847187010995 +58000 ekin = 7.02573051397604 | erot = 2.80066522322055 | epot = -15.4548676074194 | etot = -5.62847187022284 +59000 ekin = 6.80455077165117 | erot = 2.75651944712048 | epot = -15.1895420860965 | etot = -5.62847186732484 +60000 ekin = 6.57760251691511 | erot = 2.72731501678749 | epot = -14.9333893991692 | etot = -5.6284718654666 +61000 ekin = 5.99884053190006 | erot = 2.6501026979171 | epot = -14.277415033115 | etot = -5.62847180329785 +62000 ekin = 5.82217958652235 | erot = 2.65058478195194 | epot = -14.1012361774607 | etot = -5.62847180898638 +63000 ekin = 6.00993174210252 | erot = 2.7114348346643 | epot = -14.3498384845184 | etot = -5.62847190775156 +64000 ekin = 5.85096985050371 | erot = 2.71173917624744 | epot = -14.1911809366074 | etot = -5.62847190985628 +65000 ekin = 5.67959801442737 | erot = 2.7073163013018 | epot = -14.0153862253963 | etot = -5.62847190966708 +66000 ekin = 5.49812382731708 | erot = 2.69646895132529 | epot = -13.823064688063 | etot = -5.62847190942062 +67000 ekin = 5.31011188753149 | erot = 2.67901331172427 | epot = -13.6175971082582 | etot = -5.6284719090024 +68000 ekin = 5.1196422958259 | erot = 2.65622197273443 | epot = -13.4043361770525 | etot = -5.62847190849221 +69000 ekin = 4.93067975207853 | erot = 2.63014135225736 | epot = -13.1892930124928 | etot = -5.62847190815687 +70000 ekin = 4.74697386617484 | erot = 2.60347312706348 | epot = -12.9789189008748 | etot = -5.62847190763644 +71000 ekin = 4.57222133259566 | erot = 2.57971589798972 | epot = -12.7804091377441 | etot = -5.62847190715871 +72000 ekin = 4.4095964850778 | erot = 2.56228295922532 | epot = -12.6003513510613 | etot = -5.62847190675817 +73000 ekin = 4.26170009573902 | erot = 2.5540607608015 | epot = -12.4442327629946 | etot = -5.62847190645407 +74000 ekin = 4.13052949790817 | erot = 2.55713155841204 | epot = -12.3161329625863 | etot = -5.62847190626611 +75000 ekin = 4.01588192828867 | erot = 2.56608801434087 | epot = -12.2104419139893 | etot = -5.62847197135973 +76000 ekin = 3.95904625854794 | erot = 2.44184942386032 | epot = -12.0293675901709 | etot = -5.62847190776262 +77000 ekin = 4.02755960266364 | erot = 2.46007159499085 | epot = -12.1161031098036 | etot = -5.62847191214915 +78000 ekin = 3.98785439943816 | erot = 2.49596945534639 | epot = -12.1122957670964 | etot = -5.62847191231181 +79000 ekin = 3.96575767721429 | erot = 2.5420084233549 | epot = -12.1362380131152 | etot = -5.62847191254604 +80000 ekin = 3.95961954869556 | erot = 2.59604589435634 | epot = -12.1841373558848 | etot = -5.6284719128329 +81000 ekin = 3.96734100032344 | erot = 2.65577062232391 | epot = -12.2515835357817 | etot = -5.6284719131343 +82000 ekin = 3.98651997822123 | erot = 2.71892569307124 | epot = -12.333917584723 | etot = -5.6284719134305 +83000 ekin = 4.01459300302745 | erot = 2.78352190390239 | epot = -12.4265868206359 | etot = -5.62847191370609 +84000 ekin = 4.04956210608553 | erot = 2.8479662966446 | epot = -12.5260003165344 | etot = -5.62847191380431 +85000 ekin = 4.09049341026869 | erot = 2.91104365381142 | epot = -12.630008978118 | etot = -5.62847191403787 +86000 ekin = 4.13484812560052 | erot = 2.9720116541913 | epot = -12.7353316940203 | etot = -5.6284719142285 +87000 ekin = 4.18003829184658 | erot = 3.03078479878327 | epot = -12.8392950049953 | etot = -5.6284719143655 +88000 ekin = 4.22360704724744 | erot = 3.08796574000362 | epot = -12.9400447017002 | etot = -5.62847191444915 +89000 ekin = 4.26326024607336 | erot = 3.14481288279522 | epot = -13.0365450433359 | etot = -5.62847191446734 +90000 ekin = 4.2958811179063 | erot = 3.20341713777048 | epot = -13.12777017033 | etot = -5.62847191465327 +91000 ekin = 4.31697784577826 | erot = 3.26736040230188 | epot = -13.2128101626457 | etot = -5.62847191456554 +92000 ekin = 4.32507837347591 | erot = 3.3393160194459 | epot = -13.2928663075901 | etot = -5.62847191466833 +93000 ekin = 4.31872212432208 | erot = 3.42036541916806 | epot = -13.3675594581779 | etot = -5.62847191468773 +94000 ekin = 4.29660005793304 | erot = 3.51205694754431 | epot = -13.437128920154 | etot = -5.62847191467669 +95000 ekin = 4.25789021838854 | erot = 3.6160647566687 | epot = -13.5024268896671 | etot = -5.62847191460983 +96000 ekin = 4.20253661926512 | erot = 3.73412422729691 | epot = -13.5651327610313 | etot = -5.62847191446931 +97000 ekin = 4.13146529060029 | erot = 3.86803037439328 | epot = -13.6279675793419 | etot = -5.62847191434832 +98000 ekin = 4.04669071975368 | erot = 4.01885670334762 | epot = -13.6940193371953 | etot = -5.628471914094 +99000 ekin = 3.95128630061913 | erot = 4.18772840013497 | epot = -13.7674866145626 | etot = -5.62847191380852 +100000 ekin = 3.84921784883078 | erot = 4.37558821791315 | epot = -13.8532779802875 | etot = -5.62847191354357 +101000 ekin = 3.74501223923306 | erot = 4.58258429231825 | epot = -13.9560684449147 | etot = -5.62847191336337 +102000 ekin = 3.64330024870574 | erot = 4.80764134110157 | epot = -14.0794135031375 | etot = -5.62847191333017 +103000 ekin = 3.54831662006275 | erot = 5.04811575607591 | epot = -14.2249042896176 | etot = -5.62847191347892 +104000 ekin = 3.46349772064929 | erot = 5.29960820358541 | epot = -14.3915778382038 | etot = -5.62847191396914 +105000 ekin = 3.39136254536257 | erot = 5.55507704360081 | epot = -14.5749115034252 | etot = -5.62847191446186 +106000 ekin = 3.33356403744393 | erot = 5.80718759325027 | epot = -14.7692235454841 | etot = -5.62847191478991 +107000 ekin = 3.29209861353684 | erot = 6.04906687386845 | epot = -14.9696374027456 | etot = -5.62847191534027 +108000 ekin = 3.26748487341094 | erot = 6.27418243659807 | epot = -15.1701392258631 | etot = -5.62847191585406 +109000 ekin = 3.25930506886592 | erot = 6.47585417244427 | epot = -15.3636311580693 | etot = -5.6284719167591 +110000 ekin = 3.26568272829091 | erot = 6.64602097208043 | epot = -15.5401756176987 | etot = -5.62847191732734 +111000 ekin = 3.28520059172616 | erot = 6.77857539600461 | epot = -15.692247905527 | etot = -5.62847191779627 +112000 ekin = 3.31659315707435 | erot = 6.86862760564104 | epot = -15.8136926809253 | etot = -5.62847191820991 +113000 ekin = 3.35860144230934 | erot = 6.91335224014982 | epot = -15.9004256006578 | etot = -5.62847191819866 +114000 ekin = 3.4107346812468 | erot = 6.91406610981361 | epot = -15.9532727088344 | etot = -5.62847191777402 +115000 ekin = 3.47381531534278 | erot = 6.87643065686551 | epot = -15.9787178894079 | etot = -5.62847191719963 +116000 ekin = 3.5488643755877 | erot = 6.80711139529257 | epot = -15.9844476879583 | etot = -5.62847191707805 +117000 ekin = 3.63467409204942 | erot = 6.71320827683716 | epot = -15.9763542854633 | etot = -5.62847191657669 +118000 ekin = 3.72815555523548 | erot = 6.60276001485684 | epot = -15.9593874864267 | etot = -5.62847191633434 +119000 ekin = 3.82420980363903 | erot = 6.48288858478368 | epot = -15.9355703049693 | etot = -5.62847191654655 +120000 ekin = 3.91797748357197 | erot = 6.35662792089921 | epot = -15.9030773212278 | etot = -5.62847191675661 +121000 ekin = 4.00591742044011 | erot = 6.22468993027114 | epot = -15.8590792676427 | etot = -5.62847191693149 +122000 ekin = 4.08550270322343 | erot = 6.08676575288908 | epot = -15.8007403736367 | etot = -5.6284719175242 +123000 ekin = 4.15433540908351 | erot = 5.94071572290345 | epot = -15.7235230494641 | etot = -5.62847191747713 +124000 ekin = 4.21272085203578 | erot = 5.78590733869425 | epot = -15.6271001078547 | etot = -5.62847191712464 +125000 ekin = 4.26325970413163 | erot = 5.62467373686552 | epot = -15.5164053575229 | etot = -5.62847191652571 +126000 ekin = 4.30880597980491 | erot = 5.46113290467086 | epot = -15.3984108007446 | etot = -5.62847191626881 +127000 ekin = 4.35136313111015 | erot = 5.29960307371326 | epot = -15.2794381205808 | etot = -5.62847191575739 +128000 ekin = 4.39391383900498 | erot = 5.14386269106637 | epot = -15.1662484454469 | etot = -5.62847191537554 +129000 ekin = 4.43858036063657 | erot = 4.99693296064704 | epot = -15.0639852363962 | etot = -5.62847191511261 +130000 ekin = 4.48619887382542 | erot = 4.86092637377907 | epot = -14.9755971627245 | etot = -5.62847191512001 +131000 ekin = 4.53629967746126 | erot = 4.73552279955485 | epot = -14.9002943921704 | etot = -5.62847191515428 +132000 ekin = 4.58794392436778 | erot = 4.62012473201905 | epot = -14.8365405715613 | etot = -5.62847191517448 +133000 ekin = 4.63977927970892 | erot = 4.51475331813984 | epot = -14.7830045130169 | etot = -5.62847191516817 +134000 ekin = 4.69096227444668 | erot = 4.4193657152014 | epot = -14.7387999047827 | etot = -5.62847191513464 +135000 ekin = 4.74083332632091 | erot = 4.33399770983663 | epot = -14.7033029512382 | etot = -5.62847191508071 +136000 ekin = 4.78901374177424 | erot = 4.25873574864832 | epot = -14.6762214054337 | etot = -5.62847191501112 +137000 ekin = 4.83519033966293 | erot = 4.19345584709321 | epot = -14.6571181018643 | etot = -5.62847191510819 +138000 ekin = 4.87857190019268 | erot = 4.13759960010504 | epot = -14.6446434153652 | etot = -5.62847191506751 +139000 ekin = 4.91933904268643 | erot = 4.0904184140816 | epot = -14.6382293717809 | etot = -5.62847191501289 +140000 ekin = 4.95802132610714 | erot = 4.05108530565775 | epot = -14.6375785467331 | etot = -5.62847191496819 +141000 ekin = 4.99519923255345 | erot = 4.01864210163631 | epot = -14.6423132491265 | etot = -5.62847191493678 +142000 ekin = 5.0313403186538 | erot = 3.99210960072455 | epot = -14.6519218343063 | etot = -5.62847191492795 +143000 ekin = 5.06663282814597 | erot = 3.9705610087224 | epot = -14.6656657518144 | etot = -5.62847191494604 +144000 ekin = 5.10088003253958 | erot = 3.95318385936644 | epot = -14.6825358068961 | etot = -5.62847191499011 +145000 ekin = 5.13347728619398 | erot = 3.93933318432649 | epot = -14.7012823855749 | etot = -5.62847191505442 +146000 ekin = 5.16346418937014 | erot = 3.92856945833569 | epot = -14.7205055628362 | etot = -5.62847191513039 +147000 ekin = 5.18962884502088 | erot = 3.92067778970105 | epot = -14.738778549931 | etot = -5.62847191520907 +148000 ekin = 5.21063630105009 | erot = 3.91566839447787 | epot = -14.75477661081 | etot = -5.62847191528207 +149000 ekin = 5.22515818277277 | erot = 3.91376203384946 | epot = -14.7673921319647 | etot = -5.62847191534252 +150000 ekin = 5.23199081771404 | erot = 3.91536756918864 | epot = -14.7758303022868 | etot = -5.62847191538416 +151000 ekin = 5.23025857434856 | erot = 3.92102977399562 | epot = -14.7797602637291 | etot = -5.62847191538493 +152000 ekin = 5.21970456277593 | erot = 3.93136599417318 | epot = -14.7795424723186 | etot = -5.6284719153695 +153000 ekin = 5.20020715643906 | erot = 3.94729684643019 | epot = -14.775975918157 | etot = -5.62847191528778 +154000 ekin = 5.17219962280864 | erot = 3.96989664945436 | epot = -14.7705681875096 | etot = -5.62847191524665 +155000 ekin = 5.13597939415166 | erot = 4.00025654377908 | epot = -14.7647078530825 | etot = -5.6284719151518 +156000 ekin = 5.09227456538766 | erot = 4.03969792967894 | epot = -14.7604444100925 | etot = -5.62847191502591 +157000 ekin = 5.04214374655778 | erot = 4.08965648366409 | epot = -14.7602721451215 | etot = -5.62847191489967 +158000 ekin = 4.98664076893679 | erot = 4.15175637520665 | epot = -14.7668690589135 | etot = -5.62847191477004 +159000 ekin = 4.92656708226332 | erot = 4.2269378597674 | epot = -14.7819768568011 | etot = -5.62847191477039 +160000 ekin = 4.86235166664946 | erot = 4.31524574981795 | epot = -14.8060693313525 | etot = -5.62847191488512 +161000 ekin = 4.79340744408374 | erot = 4.41634192155731 | epot = -14.8382212806372 | etot = -5.6284719149962 +162000 ekin = 4.71931679137153 | erot = 4.52911647420334 | epot = -14.8769051807423 | etot = -5.62847191516742 +163000 ekin = 4.63965178837876 | erot = 4.65170333188752 | epot = -14.9198270356111 | etot = -5.62847191534485 +164000 ekin = 4.55406399624281 | erot = 4.78166301740355 | epot = -14.964198929296 | etot = -5.62847191564965 +165000 ekin = 4.46213996067409 | erot = 4.9153027215891 | epot = -15.0059145982043 | etot = -5.62847191594116 +166000 ekin = 4.36388109534828 | erot = 5.04805357548597 | epot = -15.0404065870403 | etot = -5.62847191620602 +167000 ekin = 4.25995046842402 | erot = 5.1751106852227 | epot = -15.0635330700691 | etot = -5.62847191642234 +168000 ekin = 4.15154354282101 | erot = 5.29182746831917 | epot = -15.0718429277119 | etot = -5.62847191657168 +169000 ekin = 4.04026084727475 | erot = 5.39411747728107 | epot = -15.06285024121 | etot = -5.62847191665415 +170000 ekin = 3.92797723838337 | erot = 5.47890367159931 | epot = -15.0353528265942 | etot = -5.62847191661149 +171000 ekin = 3.81680551395843 | erot = 5.54460219961171 | epot = -14.9898796300195 | etot = -5.62847191644934 +172000 ekin = 3.70912194360914 | erot = 5.5911987727273 | epot = -14.9287926324956 | etot = -5.62847191615919 +173000 ekin = 3.60767008610031 | erot = 5.62020496676059 | epot = -14.8563469686169 | etot = -5.62847191575601 +174000 ekin = 3.5159312314275 | erot = 5.63484613588141 | epot = -14.7792492818567 | etot = -5.62847191454778 +175000 ekin = 3.43946966413942 | erot = 5.64148825119161 | epot = -14.7094298295824 | etot = -5.6284719142514 +176000 ekin = 3.3814996434009 | erot = 5.6430458497967 | epot = -14.6530174072231 | etot = -5.62847191402549 +177000 ekin = 3.34426304280398 | erot = 5.64075589500609 | epot = -14.6134908517401 | etot = -5.62847191393005 +178000 ekin = 3.32907821318191 | erot = 5.63429171925387 | epot = -14.5918418466214 | etot = -5.62847191418561 +179000 ekin = 3.33553286829402 | erot = 5.62088708741546 | epot = -14.5848918700479 | etot = -5.62847191433839 +180000 ekin = 3.36333384277286 | erot = 5.59827011329217 | epot = -14.590075870683 | etot = -5.62847191461792 +181000 ekin = 3.41118322744715 | erot = 5.56369949232851 | epot = -14.6033546347479 | etot = -5.6284719149722 +182000 ekin = 3.4766665781393 | erot = 5.5144290911937 | epot = -14.6195675846746 | etot = -5.62847191534156 +183000 ekin = 3.55646627297111 | erot = 5.44847615754721 | epot = -14.6334143461245 | etot = -5.62847191560621 +184000 ekin = 3.64671110623877 | erot = 5.36528131962461 | epot = -14.6404643416891 | etot = -5.62847191582572 +185000 ekin = 3.74294243854212 | erot = 5.26596644090073 | epot = -14.6373807953562 | etot = -5.62847191591336 +186000 ekin = 3.84064021177378 | erot = 5.15359326678875 | epot = -14.6227053944187 | etot = -5.62847191585613 +187000 ekin = 3.93563840594967 | erot = 5.03296537332375 | epot = -14.5970756949468 | etot = -5.62847191567334 +188000 ekin = 4.02444308409251 | erot = 4.91004205202546 | epot = -14.5629570515389 | etot = -5.6284719154209 +189000 ekin = 4.10437481570263 | erot = 4.79101157925906 | epot = -14.5238583101438 | etot = -5.6284719151821 +190000 ekin = 4.17348832619947 | erot = 4.68117061832993 | epot = -14.4831308595823 | etot = -5.62847191505295 +191000 ekin = 4.23028845394399 | erot = 4.5838619279875 | epot = -14.4426222970214 | etot = -5.6284719150899 +192000 ekin = 4.27358054060613 | erot = 4.49984530057472 | epot = -14.4018977564781 | etot = -5.62847191529729 +193000 ekin = 4.2459291199389 | erot = 4.46741799187519 | epot = -14.3418190226901 | etot = -5.628471910876 +194000 ekin = 4.19994174150929 | erot = 4.47173701960579 | epot = -14.300150679366 | etot = -5.62847191825091 +195000 ekin = 4.19981139522189 | erot = 4.40365513590272 | epot = -14.2319384423478 | etot = -5.62847191122323 +196000 ekin = 4.18831859749958 | erot = 4.32821378408475 | epot = -14.1450042928938 | etot = -5.6284719113095 +197000 ekin = 4.16445522600504 | erot = 4.24686919663307 | epot = -14.0397963337814 | etot = -5.62847191114325 +198000 ekin = 4.13074920372969 | erot = 4.15919636754505 | epot = -13.9184174820225 | etot = -5.62847191074777 +199000 ekin = 4.09062074736202 | erot = 4.06700829109767 | epot = -13.7861009486898 | etot = -5.62847191023014 +200000 ekin = 4.0479233868723 | erot = 3.97356549445286 | epot = -13.6499607909688 | etot = -5.62847190964361 +201000 ekin = 4.00668244919801 | erot = 3.88277215508923 | epot = -13.5179265133891 | etot = -5.62847190910191 +202000 ekin = 3.97063392471746 | erot = 3.79828207702036 | epot = -13.3973879104091 | etot = -5.62847190867124 +203000 ekin = 3.94283665189392 | erot = 3.72290259923711 | epot = -13.2942111595166 | etot = -5.62847190838553 +204000 ekin = 3.92540743372156 | erot = 3.6583521626231 | epot = -13.2122315045945 | etot = -5.62847190824983 +205000 ekin = 3.91946432177292 | erot = 3.60562062220845 | epot = -13.1535568521697 | etot = -5.62847190818838 +206000 ekin = 3.92515912499406 | erot = 3.565100627265 | epot = -13.1187316605133 | etot = -5.62847190825423 +207000 ekin = 3.94166066189543 | erot = 3.53643554884992 | epot = -13.1065681191262 | etot = -5.62847190838084 +208000 ekin = 3.9674190465959 | erot = 3.5190928531888 | epot = -13.1149838083199 | etot = -5.6284719085352 +209000 ekin = 3.99456273872588 | erot = 3.50083315850279 | epot = -13.1238678065881 | etot = -5.6284719093594 +210000 ekin = 4.04796401860247 | erot = 3.49168954890823 | epot = -13.1681254815363 | etot = -5.62847191402562 +211000 ekin = 4.09773342715881 | erot = 3.4930481201282 | epot = -13.2192534546321 | etot = -5.62847190734506 +212000 ekin = 4.14205596974231 | erot = 3.50221111647777 | epot = -13.2727389936859 | etot = -5.62847190746587 +213000 ekin = 4.18461227969094 | erot = 3.51992604962354 | epot = -13.3330102373203 | etot = -5.62847190800585 +214000 ekin = 4.22291801220844 | erot = 3.54318058637904 | epot = -13.3945705067363 | etot = -5.62847190814881 +215000 ekin = 4.25639069943864 | erot = 3.57018634832895 | epot = -13.4550489560033 | etot = -5.62847190823574 +216000 ekin = 4.28517056130573 | erot = 3.59920416165346 | epot = -13.512846631277 | etot = -5.6284719083178 +217000 ekin = 4.30951457891135 | erot = 3.62862634730542 | epot = -13.566612834605 | etot = -5.6284719083882 +218000 ekin = 4.33022749097351 | erot = 3.65639118247609 | epot = -13.6150905819282 | etot = -5.62847190847864 +219000 ekin = 4.34822739188558 | erot = 3.68015661121787 | epot = -13.6568559116862 | etot = -5.62847190858279 +220000 ekin = 4.36437280258139 | erot = 3.69755509928789 | epot = -13.6903998105143 | etot = -5.62847190864505 +221000 ekin = 4.37954317243215 | erot = 3.70660976824613 | epot = -13.71462484937 | etot = -5.62847190869167 +222000 ekin = 4.39451292716877 | erot = 3.70596363375719 | epot = -13.7289484695945 | etot = -5.62847190866858 +223000 ekin = 4.41008213188775 | erot = 3.69513355487823 | epot = -13.7336875953398 | etot = -5.62847190857384 +224000 ekin = 4.42678943726018 | erot = 3.67466536393939 | epot = -13.7299267097394 | etot = -5.62847190853985 +225000 ekin = 4.44460701700748 | erot = 3.64600909388419 | epot = -13.7190880192608 | etot = -5.6284719083691 +226000 ekin = 4.47380092382151 | erot = 3.58830814098213 | epot = -13.6905809780337 | etot = -5.62847191323009 +227000 ekin = 4.56056009803568 | erot = 3.47269306832245 | epot = -13.6617250773562 | etot = -5.62847191099804 +228000 ekin = 4.61083327530785 | erot = 3.40803816011397 | epot = -13.6473433475456 | etot = -5.62847191212377 +229000 ekin = 4.63150013167703 | erot = 3.3589814900088 | epot = -13.6189535337029 | etot = -5.62847191201702 +230000 ekin = 4.65431068143757 | erot = 3.31343017818592 | epot = -13.5962127716247 | etot = -5.62847191200126 +231000 ekin = 4.67934821404584 | erot = 3.27332737527277 | epot = -13.5811475014845 | etot = -5.62847191216592 +232000 ekin = 4.70592354946075 | erot = 3.23944506667659 | epot = -13.5738405284593 | etot = -5.62847191232194 +233000 ekin = 4.73271416122328 | erot = 3.21144788525921 | epot = -13.5726339590417 | etot = -5.62847191255916 +234000 ekin = 4.75943444984861 | erot = 3.19078729233698 | epot = -13.5786936545775 | etot = -5.62847191239187 +235000 ekin = 4.78642241817936 | erot = 3.18021193976881 | epot = -13.5951062703943 | etot = -5.62847191244611 +236000 ekin = 4.81315037988097 | erot = 3.18017325334987 | epot = -13.6217955456973 | etot = -5.62847191246644 +237000 ekin = 4.83923297185456 | erot = 3.19145400453496 | epot = -13.6591588888804 | etot = -5.62847191249087 +238000 ekin = 4.86487585931723 | erot = 3.21481908800387 | epot = -13.7081668597346 | etot = -5.62847191241352 +239000 ekin = 4.89063931714873 | erot = 3.25114955282084 | epot = -13.7702607826831 | etot = -5.62847191271357 +240000 ekin = 4.91656145052489 | erot = 3.29901781218922 | epot = -13.8440511754907 | etot = -5.62847191277661 +241000 ekin = 4.94245255089304 | erot = 3.35699698381595 | epot = -13.9279214477117 | etot = -5.62847191300268 +242000 ekin = 4.96767380346102 | erot = 3.42365009425998 | epot = -14.019795810921 | etot = -5.62847191319999 +243000 ekin = 5.00573446225042 | erot = 3.47030260469304 | epot = -14.1045089792028 | etot = -5.62847191225932 +244000 ekin = 5.06987350321221 | erot = 3.50985787352176 | epot = -14.208203293301 | etot = -5.628471916567 +245000 ekin = 5.08405115957638 | erot = 3.57323736718633 | epot = -14.2857604930711 | etot = -5.62847196630839 +246000 ekin = 5.13867281568869 | erot = 3.5302241078675 | epot = -14.2973688418951 | etot = -5.6284719183389 +247000 ekin = 5.24446071734841 | erot = 3.63707192639613 | epot = -14.5100045566459 | etot = -5.62847191290139 +248000 ekin = 5.23528120841762 | erot = 3.74023330973914 | epot = -14.6039864311642 | etot = -5.62847191300749 +249000 ekin = 5.21260078435197 | erot = 3.83729795660079 | epot = -14.6783706538237 | etot = -5.62847191287092 +250000 ekin = 5.17839081250343 | erot = 3.92749000333695 | epot = -14.734352728446 | etot = -5.62847191260562 +251000 ekin = 5.13586036334 | erot = 4.01108345357516 | epot = -14.7754157290646 | etot = -5.62847191214949 +252000 ekin = 5.08918292106492 | erot = 4.09018694184386 | epot = -14.8078417745577 | etot = -5.62847191164893 +253000 ekin = 5.04264218495468 | erot = 4.1675905821178 | epot = -14.8387046782793 | etot = -5.62847191120685 +254000 ekin = 4.99116344078993 | erot = 4.24248912287765 | epot = -14.8621245493497 | etot = -5.6284719856821 +255000 ekin = 4.72637462799972 | erot = 4.2440783766396 | epot = -14.5989249326045 | etot = -5.62847192796514 +256000 ekin = 4.59834109997907 | erot = 4.36369782209805 | epot = -14.5905108364843 | etot = -5.62847191440722 +257000 ekin = 4.77089539876803 | erot = 4.60066315314853 | epot = -15.0000305289764 | etot = -5.62847197705987 +258000 ekin = 4.85704242990004 | erot = 4.66807324376142 | epot = -15.1535875814137 | etot = -5.62847190775219 +259000 ekin = 4.89901811472525 | erot = 4.72718635920727 | epot = -15.2546763808553 | etot = -5.62847190692281 +260000 ekin = 4.94107094739554 | erot = 4.79406863685558 | epot = -15.3636114914093 | etot = -5.62847190715818 +261000 ekin = 4.98242309075096 | erot = 4.86508628580875 | epot = -15.475981284619 | etot = -5.62847190805929 +262000 ekin = 5.01659840998684 | erot = 4.93871137847543 | epot = -15.5837816973622 | etot = -5.62847190889994 +263000 ekin = 5.03982661194632 | erot = 5.00983839411552 | epot = -15.6781369155684 | etot = -5.62847190950657 +264000 ekin = 5.04732696349983 | erot = 5.07389667598511 | epot = -15.7496955495903 | etot = -5.62847191010532 +265000 ekin = 5.03448807085202 | erot = 5.12688367712944 | epot = -15.7898436586188 | etot = -5.62847191063736 +266000 ekin = 4.99773438959737 | erot = 5.16480683531488 | epot = -15.7910131359606 | etot = -5.62847191104833 +267000 ekin = 4.93508497406381 | erot = 5.18388050750012 | epot = -15.7474373928657 | etot = -5.62847191130179 +268000 ekin = 4.84654531471015 | erot = 5.18063468558789 | epot = -15.6556519116809 | etot = -5.62847191138284 +269000 ekin = 4.73423214274795 | erot = 5.15198859731792 | epot = -15.514692651355 | etot = -5.62847191128916 +270000 ekin = 4.60224202248674 | erot = 5.095406888169 | epot = -15.3261208188928 | etot = -5.628471908237 +271000 ekin = 4.45636876655062 | erot = 5.00923317388204 | epot = -15.0940738481985 | etot = -5.6284719077658 +272000 ekin = 4.30375505735574 | erot = 4.89315778304253 | epot = -14.825384747494 | etot = -5.62847190709572 +273000 ekin = 4.15244061479995 | erot = 4.7486264812337 | epot = -14.529539002294 | etot = -5.62847190626033 +274000 ekin = 4.01137482334502 | erot = 4.57896672456475 | epot = -14.2188134532227 | etot = -5.62847190531291 +275000 ekin = 3.87388872892673 | erot = 4.38950805795187 | epot = -13.8918687169909 | etot = -5.62847193011234 +276000 ekin = 3.70828148350286 | erot = 4.1897556795013 | epot = -13.526509065468 | etot = -5.62847190246379 +277000 ekin = 3.74025187940178 | erot = 3.98894405210606 | epot = -13.3576678645654 | etot = -5.62847193305752 +278000 ekin = 3.74221760775414 | erot = 3.77038543692028 | epot = -13.1410749479143 | etot = -5.62847190323988 +279000 ekin = 3.75220115766714 | erot = 3.5579033181485 | epot = -12.9385763794564 | etot = -5.62847190364072 +280000 ekin = 3.77561814014481 | erot = 3.35781654492748 | epot = -12.7619065883798 | etot = -5.62847190330748 +281000 ekin = 3.81272927484688 | erot = 3.17409695196514 | epot = -12.6152981298176 | etot = -5.62847190300556 +282000 ekin = 3.86501988036681 | erot = 3.00952640155211 | epot = -12.5030181842056 | etot = -5.62847190228673 +283000 ekin = 3.93628900406797 | erot = 2.86613168182098 | epot = -12.4308925881245 | etot = -5.62847190223551 +284000 ekin = 4.02702703050139 | erot = 2.74480306500245 | epot = -12.4003019979001 | etot = -5.62847190239626 +285000 ekin = 4.14139706639814 | erot = 2.64599110157964 | epot = -12.4158600691639 | etot = -5.62847190118617 +286000 ekin = 4.28525774918039 | erot = 2.56950762489246 | epot = -12.4832372763193 | etot = -5.62847190224644 +287000 ekin = 4.44987555795468 | erot = 2.51493810068274 | epot = -12.5932855609546 | etot = -5.62847190231714 +288000 ekin = 4.63520922264775 | erot = 2.48100112555536 | epot = -12.7446822515452 | etot = -5.62847190334212 +289000 ekin = 4.83125797005639 | erot = 2.4652724153943 | epot = -12.9250022896853 | etot = -5.6284719042346 +290000 ekin = 5.02763799219575 | erot = 2.46542435681702 | epot = -13.121534254098 | etot = -5.62847190508519 +291000 ekin = 5.21465468575977 | erot = 2.47913524144374 | epot = -13.3222618329671 | etot = -5.62847190576361 +292000 ekin = 5.38472348790369 | erot = 2.50416430328839 | epot = -13.51735969743 | etot = -5.62847190623788 +293000 ekin = 5.53302487063098 | erot = 2.53823701976119 | epot = -13.6997337969533 | etot = -5.62847190656113 +294000 ekin = 5.6571870189969 | erot = 2.57877496352786 | epot = -13.8644338893351 | etot = -5.62847190681034 +295000 ekin = 5.75652780496881 | erot = 2.62269919783882 | epot = -14.0076989098361 | etot = -5.62847190702852 +296000 ekin = 5.83139499491733 | erot = 2.66652171228797 | epot = -14.1263886144125 | etot = -5.62847190720725 +297000 ekin = 5.88282356332479 | erot = 2.70675614329949 | epot = -14.2180516139342 | etot = -5.62847190730991 +298000 ekin = 5.91239748765516 | erot = 2.74048494300649 | epot = -14.2813543379702 | etot = -5.62847190730851 +299000 ekin = 5.92208198046778 | erot = 2.76585299301995 | epot = -14.3164068806927 | etot = -5.62847190720493 +300000 ekin = 5.91390942019086 | erot = 2.78233336188545 | epot = -14.3247146891011 | etot = -5.62847190702474 +301000 ekin = 5.8896213351156 | erot = 2.79074353675879 | epot = -14.3088367786682 | etot = -5.62847190679381 +302000 ekin = 5.85048781421211 | erot = 2.79307875791709 | epot = -14.2720384786514 | etot = -5.62847190652216 +303000 ekin = 5.79743517877222 | erot = 2.79223225552598 | epot = -14.2181393405074 | etot = -5.62847190620923 +304000 ekin = 5.73124340760709 | erot = 2.79262915089303 | epot = -14.1523444641631 | etot = -5.62847190566301 +305000 ekin = 5.65258268469921 | erot = 2.79940899091154 | epot = -14.0804635809916 | etot = -5.62847190538089 +306000 ekin = 5.56254653523101 | erot = 2.81503734235134 | epot = -14.00605578274 | etot = -5.62847190515766 +307000 ekin = 5.46251129680718 | erot = 2.84075892386014 | epot = -13.9317421257007 | etot = -5.62847190503342 +308000 ekin = 5.35391293499786 | erot = 2.87633235163981 | epot = -13.8587171916693 | etot = -5.62847190503159 +309000 ekin = 5.23805007411507 | erot = 2.91996940722959 | epot = -13.7864913863796 | etot = -5.62847190503497 +310000 ekin = 5.11613875822329 | erot = 2.96880482959567 | epot = -13.7134154931044 | etot = -5.62847190528541 +311000 ekin = 4.98925852659202 | erot = 3.01839769775167 | epot = -13.6361281298108 | etot = -5.6284719054671 +312000 ekin = 4.85867326622198 | erot = 3.06421411592835 | epot = -13.5513592877717 | etot = -5.62847190562134 +313000 ekin = 4.7258511266738 | erot = 3.10236590329277 | epot = -13.4566889356297 | etot = -5.62847190566309 +314000 ekin = 4.59293421046375 | erot = 3.13002199528385 | epot = -13.3514281113037 | etot = -5.62847190555615 +315000 ekin = 4.46270669971795 | erot = 3.14588950386969 | epot = -13.2370681089047 | etot = -5.62847190531703 +316000 ekin = 4.33845457034513 | erot = 3.15016989317662 | epot = -13.1170963685062 | etot = -5.62847190498448 +317000 ekin = 4.22370149067671 | erot = 3.14429402986777 | epot = -12.9964674251507 | etot = -5.62847190460621 +318000 ekin = 4.12188681801252 | erot = 3.13056754977849 | epot = -12.8809262720161 | etot = -5.62847190422512 +319000 ekin = 4.03607214172537 | erot = 3.1118418278697 | epot = -12.7763858734651 | etot = -5.62847190387006 +320000 ekin = 3.96873641009652 | erot = 3.0912804861179 | epot = -12.6884887997666 | etot = -5.62847190355219 +321000 ekin = 3.9216779737034 | erot = 3.07226107994149 | epot = -12.622410956915 | etot = -5.62847190327009 +322000 ekin = 3.8960097142375 | erot = 3.05833648374731 | epot = -12.582818101012 | etot = -5.62847190302718 +323000 ekin = 3.89216326553317 | erot = 3.05323078720618 | epot = -12.5738659555752 | etot = -5.62847190283586 +324000 ekin = 3.90971752722326 | erot = 3.06065920137963 | epot = -12.5988486316017 | etot = -5.62847190299881 +325000 ekin = 3.944741977687 | erot = 3.08325557843212 | epot = -12.6564694593672 | etot = -5.62847190324807 +326000 ekin = 3.99225791212997 | erot = 3.12131666196629 | epot = -12.7420464778673 | etot = -5.62847190377102 +327000 ekin = 4.04715751819777 | erot = 3.17277573874003 | epot = -12.8484051615109 | etot = -5.62847190457309 +328000 ekin = 4.10306827950154 | erot = 3.23289809101951 | epot = -12.9644382761215 | etot = -5.62847190560047 +329000 ekin = 4.15294077797066 | erot = 3.2946025468715 | epot = -13.0760152315157 | etot = -5.62847190667354 +330000 ekin = 4.19046086378072 | erot = 3.34957314359328 | epot = -13.1685059148756 | etot = -5.62847190750161 +331000 ekin = 4.21187936703765 | erot = 3.38989153266504 | epot = -13.2302428076701 | etot = -5.62847190796743 +332000 ekin = 4.21589857652274 | erot = 3.41075094374518 | epot = -13.2551214281224 | etot = -5.62847190785444 +333000 ekin = 4.20485265998593 | erot = 3.41174399824388 | epot = -13.2450685654239 | etot = -5.62847190719411 +334000 ekin = 4.18435368274547 | erot = 3.39692225043726 | epot = -13.2097478393409 | etot = -5.62847190615821 +335000 ekin = 4.16205455859871 | erot = 3.3736762359357 | epot = -13.1642026995211 | etot = -5.62847190498668 +336000 ekin = 4.14609491419077 | erot = 3.35093309665757 | epot = -13.1254999147522 | etot = -5.62847190390387 +337000 ekin = 4.14364358929869 | erot = 3.33736964605254 | epot = -13.1094851384224 | etot = -5.62847190307115 +338000 ekin = 4.15982493121681 | erot = 3.33968220642343 | epot = -13.1279790403704 | etot = -5.62847190273015 +339000 ekin = 4.19714166714534 | erot = 3.36120406394183 | epot = -13.1868176336935 | etot = -5.6284719026063 +340000 ekin = 4.25518474379736 | erot = 3.4039445653422 | epot = -13.2876012119385 | etot = -5.62847190279896 +341000 ekin = 4.33079125358751 | erot = 3.46797257818016 | epot = -13.4272357350061 | etot = -5.62847190323847 +342000 ekin = 4.41854745257054 | erot = 3.55173943759712 | epot = -13.5987587940142 | etot = -5.62847190384653 +343000 ekin = 4.51153864836739 | erot = 3.65250494550532 | epot = -13.7925154984198 | etot = -5.62847190454714 +344000 ekin = 4.60219231316128 | erot = 3.76671918647902 | epot = -13.9973834048951 | etot = -5.62847190525479 +345000 ekin = 4.68312343518297 | erot = 3.89042211424549 | epot = -14.202017455332 | etot = -5.6284719059035 +346000 ekin = 4.74786790538276 | erot = 4.01955036383839 | epot = -14.3958901756632 | etot = -5.6284719064421 +347000 ekin = 4.79150376884927 | erot = 4.15019529884136 | epot = -14.5701709744857 | etot = -5.62847190679505 +348000 ekin = 4.81117855584513 | erot = 4.27877359764246 | epot = -14.7184240605368 | etot = -5.62847190704922 +349000 ekin = 4.80564918858542 | erot = 4.40205662692117 | epot = -14.8361777226744 | etot = -5.62847190716779 +350000 ekin = 4.77545945328558 | erot = 4.51714564005014 | epot = -14.9210770005288 | etot = -5.62847190719305 +351000 ekin = 4.72262273321771 | erot = 4.62116010888051 | epot = -14.9722547493024 | etot = -5.62847190720414 +352000 ekin = 4.65007958813981 | erot = 4.71078593020459 | epot = -14.9893374256243 | etot = -5.62847190727988 +353000 ekin = 4.56109157465225 | erot = 4.78180335583209 | epot = -14.9713668379471 | etot = -5.62847190746274 +354000 ekin = 4.4587615124644 | erot = 4.82895979646479 | epot = -14.9161932166522 | etot = -5.62847190772303 +355000 ekin = 4.34584612945451 | erot = 4.84663553107757 | epot = -14.8209535684567 | etot = -5.62847190792459 +356000 ekin = 4.22495470320938 | erot = 4.83038190907635 | epot = -14.6838085201751 | etot = -5.62847190788934 +357000 ekin = 4.09903296594824 | erot = 4.77873075092475 | epot = -14.5062356243553 | etot = -5.6284719074823 +358000 ekin = 3.97178667556097 | erot = 4.69444561048368 | epot = -14.2947041927538 | etot = -5.62847190670913 +359000 ekin = 3.84767298929633 | erot = 4.58431182212489 | epot = -14.0604567171737 | etot = -5.62847190575248 +360000 ekin = 3.73136439808897 | erot = 4.45746613156729 | epot = -13.8173024344143 | etot = -5.62847190475803 +361000 ekin = 3.62758093165782 | erot = 4.32379064504613 | epot = -13.5798434807354 | etot = -5.62847190403148 +362000 ekin = 3.54294892307022 | erot = 4.1935809711395 | epot = -13.365001797887 | etot = -5.62847190367726 +363000 ekin = 3.47837311691809 | erot = 4.07207692081944 | epot = -13.1789219412948 | etot = -5.62847190355725 +364000 ekin = 3.43225009806582 | erot = 3.96193194141563 | epot = -13.0226539430685 | etot = -5.62847190358705 +365000 ekin = 3.40198388464006 | erot = 3.86460642705282 | epot = -12.8950622153777 | etot = -5.62847190368484 +366000 ekin = 3.38451833852889 | erot = 3.78104622244719 | epot = -12.7940364647571 | etot = -5.62847190378102 +367000 ekin = 3.37682483158764 | erot = 3.71218000857488 | epot = -12.7174767440037 | etot = -5.62847190384119 +368000 ekin = 3.37625204139108 | erot = 3.65912147822927 | epot = -12.6638454234731 | etot = -5.62847190385279 +369000 ekin = 3.38074636727291 | erot = 3.62312680344584 | epot = -12.6323450745438 | etot = -5.62847190382506 +370000 ekin = 3.38894636699166 | erot = 3.6053885663718 | epot = -12.622806837183 | etot = -5.62847190381957 +371000 ekin = 3.40011634060361 | erot = 3.60672333638014 | epot = -12.6353115807303 | etot = -5.62847190374657 +372000 ekin = 3.41430323563177 | erot = 3.627489202239 | epot = -12.6702643415689 | etot = -5.62847190369811 +373000 ekin = 3.43217624795848 | erot = 3.66740997408432 | epot = -12.7280581255856 | etot = -5.62847190354281 +374000 ekin = 3.45538314686338 | erot = 3.72532070766139 | epot = -12.809175758152 | etot = -5.62847190362724 +375000 ekin = 3.48458983103553 | erot = 3.79950576965714 | epot = -12.9125675044482 | etot = -5.62847190375552 +376000 ekin = 3.51994630863574 | erot = 3.88772077540834 | epot = -13.0361389879692 | etot = -5.62847190392509 +377000 ekin = 3.5616226323945 | erot = 3.98718032086118 | epot = -13.177274857349 | etot = -5.62847190409328 +378000 ekin = 3.61009229019155 | erot = 4.09470007580574 | epot = -13.3332642703012 | etot = -5.62847190430393 +379000 ekin = 3.66621939252169 | erot = 4.20668278515063 | epot = -13.5013740821146 | etot = -5.62847190444224 +380000 ekin = 3.73222313435093 | erot = 4.31893025304478 | epot = -13.6796252922743 | etot = -5.62847190487858 +381000 ekin = 3.80656943723477 | erot = 4.42661769093527 | epot = -13.8616590336205 | etot = -5.62847190545047 +382000 ekin = 3.88594558525976 | erot = 4.52459411504649 | epot = -14.0390116063896 | etot = -5.62847190608333 +383000 ekin = 3.96695089999416 | erot = 4.60747433893969 | epot = -14.2028971456577 | etot = -5.62847190672383 +384000 ekin = 4.04619645067527 | erot = 4.66967915256735 | epot = -14.3443475105389 | etot = -5.62847190729628 +385000 ekin = 4.12092029137381 | erot = 4.70599192061868 | epot = -14.4553841196618 | etot = -5.62847190766929 +386000 ekin = 4.18945537162624 | erot = 4.71237691680559 | epot = -14.5303041965377 | etot = -5.62847190810589 +387000 ekin = 4.24770733745074 | erot = 4.68531871643827 | epot = -14.5614979619431 | etot = -5.62847190805406 +388000 ekin = 4.29400518232462 | erot = 4.62433064765619 | epot = -14.5468077376914 | etot = -5.62847190771056 +389000 ekin = 4.32973751035554 | erot = 4.53230747815954 | epot = -14.4905168956793 | etot = -5.62847190716421 +390000 ekin = 4.35696496432784 | erot = 4.41432356916359 | epot = -14.3997604400599 | etot = -5.62847190656847 +391000 ekin = 4.3776888846099 | erot = 4.27672755002102 | epot = -14.2828883405675 | etot = -5.6284719059366 +392000 ekin = 4.39398588700783 | erot = 4.1262519122643 | epot = -14.1487097046519 | etot = -5.62847190537976 +393000 ekin = 4.40738241118112 | erot = 3.96936593196882 | epot = -14.0052202479731 | etot = -5.62847190482314 +394000 ekin = 4.41937568155392 | erot = 3.81285278688348 | epot = -13.8607003731001 | etot = -5.62847190466274 +395000 ekin = 4.42988768164223 | erot = 3.66065946576554 | epot = -13.7190190519388 | etot = -5.62847190453102 +396000 ekin = 4.43847476589136 | erot = 3.51525603215626 | epot = -13.5822027024392 | etot = -5.62847190439154 +397000 ekin = 4.44517728396981 | erot = 3.37891512777666 | epot = -13.452564315963 | etot = -5.62847190421658 +398000 ekin = 4.45064950025928 | erot = 3.25392386318185 | epot = -13.3330452674375 | etot = -5.62847190399633 +399000 ekin = 4.45613851377312 | erot = 3.14269651880435 | epot = -13.2273069363759 | etot = -5.62847190379848 +400000 ekin = 4.4629760830569 | erot = 3.04745583063513 | epot = -13.1389038172371 | etot = -5.62847190354509 +401000 ekin = 4.4727554600177 | erot = 2.97053701408792 | epot = -13.0717643774651 | etot = -5.62847190335951 +402000 ekin = 4.48672336701277 | erot = 2.9139652257742 | epot = -13.0291604961274 | etot = -5.62847190334044 +403000 ekin = 4.50482841072929 | erot = 2.87870251806416 | epot = -13.0120028324087 | etot = -5.62847190361521 +404000 ekin = 4.52484325731466 | erot = 2.86379686211144 | epot = -13.0171120236776 | etot = -5.62847190425147 +405000 ekin = 4.54178669954817 | erot = 2.86535120565175 | epot = -13.0356098106769 | etot = -5.62847190547696 +406000 ekin = 4.548121869793 | erot = 2.87565623450054 | epot = -13.0522500108902 | etot = -5.62847190659667 +407000 ekin = 4.5356776566473 | erot = 2.88781666330103 | epot = -13.0519662273702 | etot = -5.62847190742183 +408000 ekin = 4.49806839875348 | erot = 2.89717319271638 | epot = -13.0237134991196 | etot = -5.62847190764973 +409000 ekin = 4.43289041828495 | erot = 2.90293173426126 | epot = -12.964294059822 | etot = -5.62847190727577 +410000 ekin = 4.34222243515046 | erot = 2.90784571760188 | epot = -12.8785400592982 | etot = -5.62847190654581 +411000 ekin = 4.23122328985371 | erot = 2.91632332326885 | epot = -12.7760185189177 | etot = -5.62847190579514 +412000 ekin = 4.10591302472413 | erot = 2.93234263222559 | epot = -12.6667275621851 | etot = -5.62847190523541 +413000 ekin = 3.97147909139413 | erot = 2.95826875334524 | epot = -12.5582197496453 | etot = -5.62847190490591 +414000 ekin = 3.83169645331915 | erot = 2.99487215437287 | epot = -12.4550405124353 | etot = -5.62847190474325 +415000 ekin = 3.68915556889385 | erot = 3.04191716150782 | epot = -12.359544635067 | etot = -5.62847190466537 +416000 ekin = 3.54575553260018 | erot = 3.09878213610913 | epot = -12.2730095733214 | etot = -5.62847190461212 +417000 ekin = 3.40315271148718 | erot = 3.16484246789781 | epot = -12.196467083937 | etot = -5.62847190455201 +418000 ekin = 3.26306253875512 | erot = 3.23960054552672 | epot = -12.1311349887548 | etot = -5.62847190447298 +419000 ekin = 3.12743539448039 | erot = 3.32265867810423 | epot = -12.0785659769574 | etot = -5.62847190437282 +420000 ekin = 2.9985468524975 | erot = 3.41362396345008 | epot = -12.0406427202035 | etot = -5.6284719042559 +421000 ekin = 2.87901712493616 | erot = 3.51197880379036 | epot = -12.0194678328627 | etot = -5.62847190413618 +422000 ekin = 2.77174596053191 | erot = 3.61690112203592 | epot = -12.0171189866093 | etot = -5.62847190404144 +423000 ekin = 2.67973794665325 | erot = 3.72700827486708 | epot = -12.0352181255352 | etot = -5.62847190401484 +424000 ekin = 2.60579870929048 | erot = 3.84002717528967 | epot = -12.0742977886928 | etot = -5.62847190411264 +425000 ekin = 2.55208954527575 | erot = 3.9524416789396 | epot = -12.1330031286141 | etot = -5.62847190439877 +426000 ekin = 2.51954653044551 | erot = 4.05920212807816 | epot = -12.2072205634536 | etot = -5.6284719049299 +427000 ekin = 2.50725893890309 | erot = 4.15363681830485 | epot = -12.289367662923 | etot = -5.62847190571505 +428000 ekin = 2.51210485174572 | erot = 4.22782399614682 | epot = -12.3684007545421 | etot = -5.62847190664956 +429000 ekin = 2.52911833232282 | erot = 4.27377369072579 | epot = -12.431363930529 | etot = -5.62847190748043 +430000 ekin = 2.55284926699967 | erot = 4.28551618826859 | epot = -12.4668373631572 | etot = -5.62847190788893 +431000 ekin = 2.57924139418917 | erot = 4.26142412036958 | epot = -12.4691374222417 | etot = -5.62847190768295 +432000 ekin = 2.60692475465698 | erot = 4.20541068246245 | epot = -12.4408073440566 | etot = -5.62847190693718 +433000 ekin = 2.63712842981307 | erot = 4.12604912501233 | epot = -12.3916494607613 | etot = -5.62847190593589 +434000 ekin = 2.67245542240352 | erot = 4.0340594892126 | epot = -12.3349868166048 | etot = -5.62847190498869 +435000 ekin = 2.7154385463927 | erot = 3.93961255970769 | epot = -12.2835230103846 | etot = -5.62847190428426 +436000 ekin = 2.76760991340479 | erot = 3.85063248523264 | epot = -12.2467143025142 | etot = -5.62847190387679 +437000 ekin = 2.82920515670504 | erot = 3.77223859650537 | epot = -12.2299156569372 | etot = -5.62847190372677 +438000 ekin = 2.89929820057594 | erot = 3.70707509975274 | epot = -12.2348452040968 | etot = -5.62847190376813 +439000 ekin = 2.97609334154046 | erot = 3.65590372389231 | epot = -12.2604689693734 | etot = -5.62847190394063 +440000 ekin = 3.05720906611473 | erot = 3.61815200784066 | epot = -12.3038329781562 | etot = -5.62847190420078 +441000 ekin = 3.13989672827454 | erot = 3.59232302399881 | epot = -12.3606916567915 | etot = -5.62847190451817 +442000 ekin = 3.22119927517245 | erot = 3.57626892520201 | epot = -12.4259401052482 | etot = -5.6284719048737 +443000 ekin = 3.29807867300703 | erot = 3.56737972996171 | epot = -12.4939303082161 | etot = -5.62847190524735 +444000 ekin = 3.36753883942798 | erot = 3.56276348927507 | epot = -12.5587742343218 | etot = -5.62847190561877 +445000 ekin = 3.42676046580105 | erot = 3.55942025919011 | epot = -12.6146526309568 | etot = -5.62847190596565 +446000 ekin = 3.47324383646181 | erot = 3.55443462308996 | epot = -12.6561503658209 | etot = -5.62847190626911 +447000 ekin = 3.5049735437584 | erot = 3.54511419619662 | epot = -12.6785596464618 | etot = -5.62847190650676 +448000 ekin = 3.52056213083121 | erot = 3.52974100709951 | epot = -12.6787750444512 | etot = -5.62847190652048 +449000 ekin = 3.51939696590914 | erot = 3.50705904510649 | epot = -12.6549279176213 | etot = -5.62847190660565 +450000 ekin = 3.50164536053693 | erot = 3.47565071065462 | epot = -12.6057679777917 | etot = -5.62847190660012 +451000 ekin = 3.46824790708062 | erot = 3.43472151201885 | epot = -12.5314413256013 | etot = -5.62847190650187 +452000 ekin = 3.42090312737136 | erot = 3.38414558728552 | epot = -12.4335206209692 | etot = -5.62847190631236 +453000 ekin = 3.36201791829034 | erot = 3.32449206044573 | epot = -12.3149818847727 | etot = -5.62847190603659 +454000 ekin = 3.29463316061277 | erot = 3.25701739818176 | epot = -12.180122464479 | etot = -5.62847190568451 +455000 ekin = 3.2223327489955 | erot = 3.18360703275921 | epot = -12.0344116870245 | etot = -5.62847190526976 +456000 ekin = 3.14914248629495 | erot = 3.10666992197183 | epot = -11.884284313078 | etot = -5.62847190481121 +457000 ekin = 3.07939737173802 | erot = 3.02894564057692 | epot = -11.7368149166547 | etot = -5.6284719043398 +458000 ekin = 3.01756413268755 | erot = 2.95322108561829 | epot = -11.5992571221579 | etot = -5.62847190385206 +459000 ekin = 2.9681063252435 | erot = 2.88249754735552 | epot = -11.4790757760042 | etot = -5.62847190340517 +460000 ekin = 2.93513889003432 | erot = 2.81955267520424 | epot = -11.3831634682736 | etot = -5.62847190303502 +461000 ekin = 2.92205746388812 | erot = 2.76669234907634 | epot = -11.3172217157442 | etot = -5.62847190277971 +462000 ekin = 2.93114290150651 | erot = 2.72556812595624 | epot = -11.2851829301355 | etot = -5.62847190267276 +463000 ekin = 2.96319319680456 | erot = 2.69703193761406 | epot = -11.2886970371553 | etot = -5.6284719027367 +464000 ekin = 3.01726238569007 | erot = 2.6810561513032 | epot = -11.3267904399689 | etot = -5.62847190297563 +465000 ekin = 3.09058398932397 | erot = 2.67674994759312 | epot = -11.3958058402875 | etot = -5.62847190337041 +466000 ekin = 3.17872270900452 | erot = 2.68248866700631 | epot = -11.4896832798918 | etot = -5.628471903881 +467000 ekin = 3.27594114496212 | erot = 2.69614045585922 | epot = -11.6005535052767 | etot = -5.62847190445533 +468000 ekin = 3.37571282133829 | erot = 2.71534026240541 | epot = -11.7195249887838 | etot = -5.62847190504008 +469000 ekin = 3.47128178262645 | erot = 2.73774679763611 | epot = -11.8375004858531 | etot = -5.62847190559053 +470000 ekin = 3.55617737698791 | erot = 2.76123628661821 | epot = -11.9458855696808 | etot = -5.62847190607467 +471000 ekin = 3.62463309399226 | erot = 2.78402790004387 | epot = -12.0371329005057 | etot = -5.62847190646961 +472000 ekin = 3.67190559891852 | erot = 2.80477124779255 | epot = -12.1051487534684 | etot = -5.62847190675733 +473000 ekin = 3.69451868440228 | erot = 2.82263116141548 | epot = -12.1456217527386 | etot = -5.62847190692079 +474000 ekin = 3.69045746330599 | erot = 2.83737882569196 | epot = -12.1563081959442 | etot = -5.62847190694626 +475000 ekin = 3.65932116349867 | erot = 2.84946541727501 | epot = -12.1372584875992 | etot = -5.62847190682555 +476000 ekin = 3.60242486137696 | erot = 2.86004016499145 | epot = -12.0909369329289 | etot = -5.62847190656049 +477000 ekin = 3.52282746239093 | erot = 2.87088465735982 | epot = -12.0221840259131 | etot = -5.62847190616239 +478000 ekin = 3.42525452629137 | erot = 2.88424967270433 | epot = -11.9379761046622 | etot = -5.62847190566652 +479000 ekin = 3.31588349738284 | erot = 2.90254646896319 | epot = -11.8469018714627 | etot = -5.62847190511672 +480000 ekin = 3.20192949245114 | erot = 2.92801081390706 | epot = -11.7584122109372 | etot = -5.62847190457903 +481000 ekin = 3.09102106839942 | erot = 2.96227510040326 | epot = -11.6817680729367 | etot = -5.62847190413407 +482000 ekin = 2.99039932400416 | erot = 3.00590839368512 | epot = -11.6247796215536 | etot = -5.6284719038643 +483000 ekin = 2.9060569334364 | erot = 3.05799802963363 | epot = -11.5925268669061 | etot = -5.62847190383611 +484000 ekin = 2.84200171523445 | erot = 3.11586840862564 | epot = -11.5863420279393 | etot = -5.62847190407919 +485000 ekin = 2.81072036467391 | erot = 3.03665546466979 | epot = -11.4758477218808 | etot = -5.62847189253711 +486000 ekin = 2.99172671785403 | erot = 2.89028588609215 | epot = -11.5104845146741 | etot = -5.62847191072794 +487000 ekin = 3.04661020879821 | erot = 2.89516257155408 | epot = -11.5702446859866 | etot = -5.62847190563434 +488000 ekin = 3.0281344545853 | erot = 2.91755814175983 | epot = -11.5741645018805 | etot = -5.62847190553541 +489000 ekin = 3.02918173186106 | erot = 2.9470327434341 | epot = -11.6046863808974 | etot = -5.62847190560225 +490000 ekin = 3.04920929971604 | erot = 2.98299921440123 | epot = -11.6606804199382 | etot = -5.62847190582094 +491000 ekin = 3.08564623418558 | erot = 3.02458607703473 | epot = -11.7387042173397 | etot = -5.62847190611936 +492000 ekin = 3.13426650211461 | erot = 3.07113014039408 | epot = -11.8338685489468 | etot = -5.62847190643812 +493000 ekin = 3.19024782352769 | erot = 3.12246736377737 | epot = -11.9411870939511 | etot = -5.628471906646 +494000 ekin = 3.24418110398504 | erot = 3.17757093527581 | epot = -12.0502240477778 | etot = -5.62847200851693 +495000 ekin = 3.12930691881382 | erot = 3.12025770004709 | epot = -11.8780365336897 | etot = -5.62847191482878 +496000 ekin = 3.38154400853442 | erot = 3.12702216684199 | epot = -12.1370381395859 | etot = -5.62847196420953 +497000 ekin = 3.537963343002 | erot = 3.21345240187732 | epot = -12.3798876661165 | etot = -5.6284719212372 +498000 ekin = 3.54725242241252 | erot = 3.31274815698128 | epot = -12.4884725006486 | etot = -5.62847192125477 +499000 ekin = 3.54686752389262 | erot = 3.42936350675123 | epot = -12.60470295199 | etot = -5.62847192134617 +500000 ekin = 3.53611629140885 | erot = 3.56214471852909 | epot = -12.7267329314508 | etot = -5.62847192151286 +501000 ekin = 3.51474019580975 | erot = 3.70831240066885 | epot = -12.8515245182369 | etot = -5.62847192175835 +502000 ekin = 3.48291543614181 | erot = 3.86351597862781 | epot = -12.9749033367607 | etot = -5.62847192199109 +503000 ekin = 3.44167367981676 | erot = 4.02200657200069 | epot = -13.0921521741653 | etot = -5.62847192234785 +504000 ekin = 3.39166561935593 | erot = 4.17733332047377 | epot = -13.1974708625707 | etot = -5.62847192274099 +505000 ekin = 3.33344269448486 | erot = 4.32266370132234 | epot = -13.2845783189393 | etot = -5.62847192313209 +506000 ekin = 3.26726906277248 | erot = 4.4515776416869 | epot = -13.3473186278588 | etot = -5.62847192339945 +507000 ekin = 3.1938836164723 | erot = 4.55898983234052 | epot = -13.3813453722982 | etot = -5.62847192348535 +508000 ekin = 3.11462724046553 | erot = 4.6420740647643 | epot = -13.3851732285644 | etot = -5.62847192333461 +509000 ekin = 3.03154551887398 | erot = 4.70083202647774 | epot = -13.3608494683075 | etot = -5.62847192295578 +510000 ekin = 2.94513058608832 | erot = 4.73730594225484 | epot = -13.3109084508294 | etot = -5.62847192248619 +511000 ekin = 2.85640718491609 | erot = 4.75516581385376 | epot = -13.2400449206913 | etot = -5.62847192192149 +512000 ekin = 2.76854482522115 | erot = 4.75962991525362 | epot = -13.1566466618396 | etot = -5.62847192136479 +513000 ekin = 2.68465921480016 | erot = 4.75599513195583 | epot = -13.0691262676546 | etot = -5.62847192089856 +514000 ekin = 2.60745568311009 | erot = 4.7487016866022 | epot = -12.9846292902954 | etot = -5.62847192058309 +515000 ekin = 2.53899080260848 | erot = 4.74082869238206 | epot = -12.9082914153961 | etot = -5.62847192040556 +516000 ekin = 2.48057862893556 | erot = 4.73416754061951 | epot = -12.8432180899117 | etot = -5.62847192035661 +517000 ekin = 2.43281299017177 | erot = 4.72933651070505 | epot = -12.79062142128 | etot = -5.62847192040314 +518000 ekin = 2.39567246197795 | erot = 4.72611868192558 | epot = -12.7502630644083 | etot = -5.62847192050478 +519000 ekin = 2.36868008074725 | erot = 4.72386163456341 | epot = -12.7210136359311 | etot = -5.62847192062046 +520000 ekin = 2.3510906802942 | erot = 4.72186744275436 | epot = -12.7014300437633 | etot = -5.62847192071475 +521000 ekin = 2.3420742612211 | erot = 4.7197022769944 | epot = -12.6902484589817 | etot = -5.62847192076616 +522000 ekin = 2.34085858395192 | erot = 4.71735113727184 | epot = -12.6866816419969 | etot = -5.62847192077317 +523000 ekin = 2.34541603963969 | erot = 4.65571671267266 | epot = -12.6296046827942 | etot = -5.62847193048181 +524000 ekin = 2.39460269537711 | erot = 4.54409239674616 | epot = -12.567167012402 | etot = -5.62847192027872 +525000 ekin = 2.51755565344997 | erot = 4.49060445323463 | epot = -12.636632032409 | etot = -5.62847192572444 +526000 ekin = 2.63891940337868 | erot = 4.49670026128235 | epot = -12.7640916024463 | etot = -5.62847193778531 +527000 ekin = 2.68130557078117 | erot = 4.50503337377532 | epot = -12.8148108746503 | etot = -5.62847193009386 +528000 ekin = 2.71450795010731 | erot = 4.51098798631249 | epot = -12.8539678666136 | etot = -5.62847193019376 +529000 ekin = 2.74727192394566 | erot = 4.51402301144395 | epot = -12.8897668656534 | etot = -5.62847193026377 +530000 ekin = 2.77952118314857 | erot = 4.5125666625393 | epot = -12.920559775978 | etot = -5.62847193029009 +531000 ekin = 2.81130699779759 | erot = 4.50555264767733 | epot = -12.9453315757438 | etot = -5.62847193026884 +532000 ekin = 2.84274553228349 | erot = 4.4925310698098 | epot = -12.963748532302 | etot = -5.62847193020875 +533000 ekin = 2.87393313770274 | erot = 4.47361780233943 | epot = -12.9760228701721 | etot = -5.62847193012992 +534000 ekin = 2.90486933807934 | erot = 4.44928844616361 | epot = -12.9826297142984 | etot = -5.62847193005544 +535000 ekin = 2.93541519865155 | erot = 4.42010482065011 | epot = -12.9839919493031 | etot = -5.62847193000139 +536000 ekin = 2.96529830147131 | erot = 4.38649798395495 | epot = -12.9802682153984 | etot = -5.62847192997214 +537000 ekin = 2.99415467149918 | erot = 4.34867665836394 | epot = -12.9713032598154 | etot = -5.62847192995229 +538000 ekin = 3.02158801647836 | erot = 4.30669342609989 | epot = -12.9567533725302 | etot = -5.62847192995193 +539000 ekin = 3.04722844371598 | erot = 4.26048951905692 | epot = -12.9361898927208 | etot = -5.62847192994795 +540000 ekin = 3.07077963641776 | erot = 4.21000980479747 | epot = -12.9092613711463 | etot = -5.62847192993109 +541000 ekin = 3.09204730614533 | erot = 4.15535061586808 | epot = -12.8758698519099 | etot = -5.62847192989645 +542000 ekin = 3.11094831331283 | erot = 4.09682671839993 | epot = -12.8362469615563 | etot = -5.62847192984357 +543000 ekin = 3.12750284880657 | erot = 4.03499383132477 | epot = -12.7909686099064 | etot = -5.62847192977506 +544000 ekin = 3.14181233916006 | erot = 3.9706269262205 | epot = -12.7409111950808 | etot = -5.62847192970023 +545000 ekin = 3.15402369276438 | erot = 3.90462208418148 | epot = -12.687117706573 | etot = -5.62847192962714 +546000 ekin = 3.16427777375903 | erot = 3.83809465728676 | epot = -12.6308443606047 | etot = -5.62847192955896 +547000 ekin = 3.17263245313991 | erot = 3.77248542238505 | epot = -12.5735898050567 | etot = -5.62847192953171 +548000 ekin = 3.17905114126804 | erot = 3.70842416476335 | epot = -12.5159472355704 | etot = -5.628471929539 +549000 ekin = 3.18335924851645 | erot = 3.64619443423877 | epot = -12.4580256122943 | etot = -5.6284719295391 +550000 ekin = 3.18506506659374 | erot = 3.58603484429188 | epot = -12.3995718405387 | etot = -5.62847192965304 +551000 ekin = 3.18354118865872 | erot = 3.52751972614777 | epot = -12.3395328445982 | etot = -5.62847192979176 +552000 ekin = 3.17814056099981 | erot = 3.46973317229041 | epot = -12.2763456632234 | etot = -5.62847192993316 +553000 ekin = 3.16816249048265 | erot = 3.41187716293338 | epot = -12.2085115834605 | etot = -5.62847193004443 +554000 ekin = 3.15297464057207 | erot = 3.35363386892335 | epot = -12.1350804395834 | etot = -5.62847193008797 +555000 ekin = 3.1321806554361 | erot = 3.29554931591194 | epot = -12.0562019013774 | etot = -5.62847193002936 +556000 ekin = 3.10581995745121 | erot = 3.23932890454018 | epot = -11.9736207918375 | etot = -5.62847192984613 +557000 ekin = 3.07457883900155 | erot = 3.18795403306842 | epot = -11.8910048016006 | etot = -5.62847192953059 +558000 ekin = 3.03998262656473 | erot = 3.14553707334837 | epot = -11.8139916290222 | etot = -5.62847192910913 +559000 ekin = 3.0045037898859 | erot = 3.11693712835399 | epot = -11.7499128468212 | etot = -5.62847192858133 +560000 ekin = 2.97145203626831 | erot = 3.10758181984132 | epot = -11.7075057841324 | etot = -5.62847192802278 +561000 ekin = 2.94451934106521 | erot = 3.12267269751328 | epot = -11.695663966143 | etot = -5.6284719275645 +562000 ekin = 2.92714140962176 | erot = 3.16633554918931 | epot = -11.7219488860595 | etot = -5.62847192724847 +563000 ekin = 2.92206147630413 | erot = 3.24077054349539 | epot = -11.7913039469992 | etot = -5.62847192719971 +564000 ekin = 2.93031627658954 | erot = 3.34563410950147 | epot = -11.9044223135914 | etot = -5.62847192750039 +565000 ekin = 2.95068712295411 | erot = 3.47751232956699 | epot = -12.0566713806754 | etot = -5.62847192815435 +566000 ekin = 2.97962685524118 | erot = 3.62985521349866 | epot = -12.2379539978653 | etot = -5.62847192912545 +567000 ekin = 3.0117159357824 | erot = 3.79324477331537 | epot = -12.4334326394135 | etot = -5.62847193031574 +568000 ekin = 3.04054477450319 | erot = 3.95610049167747 | epot = -12.6251171977687 | etot = -5.62847193158806 +569000 ekin = 3.05981811082524 | erot = 4.10576505730328 | epot = -12.7940551009116 | etot = -5.62847193278313 +570000 ekin = 3.06446758301559 | erot = 4.22987220707428 | epot = -12.9228117238313 | etot = -5.62847193374141 +571000 ekin = 3.0515919104533 | erot = 4.31782950105801 | epot = -12.9978933458373 | etot = -5.62847193432598 +572000 ekin = 3.02108996843848 | erot = 4.36217384042166 | epot = -13.0117357433083 | etot = -5.62847193444813 +573000 ekin = 2.97589592650755 | erot = 4.35953364448391 | epot = -12.9639015050779 | etot = -5.62847193408648 +574000 ekin = 2.92177260951733 | erot = 4.31098813649777 | epot = -12.8612326793134 | etot = -5.62847193329834 +575000 ekin = 2.86675845149345 | erot = 4.22206447606537 | epot = -12.7172948575968 | etot = -5.62847193003794 +576000 ekin = 2.82238695046887 | erot = 4.11002108703335 | epot = -12.5608799670193 | etot = -5.62847192951707 +577000 ekin = 2.79586021289829 | erot = 3.98405314237152 | epot = -12.4083852843567 | etot = -5.62847192908693 +578000 ekin = 2.79062678649988 | erot = 3.84816173903585 | epot = -12.2672604543832 | etot = -5.62847192884748 +579000 ekin = 2.80727876765194 | erot = 3.7063076840155 | epot = -12.1420583804986 | etot = -5.6284719288312 +580000 ekin = 2.84308800283874 | erot = 3.56147502226538 | epot = -12.0330349544021 | etot = -5.62847192929796 +581000 ekin = 2.8927594516754 | erot = 3.41677708041289 | epot = -11.9380084614607 | etot = -5.62847192937237 +582000 ekin = 2.94948274096193 | erot = 3.27852635633959 | epot = -11.8564810267434 | etot = -5.62847192944192 +583000 ekin = 3.00600312777781 | erot = 3.15339507870142 | epot = -11.7878701359047 | etot = -5.62847192942545 +584000 ekin = 3.05615870299363 | erot = 3.04800743036146 | epot = -11.7326380626562 | etot = -5.62847192930113 +585000 ekin = 3.09596263905195 | erot = 2.96828908155839 | epot = -11.6927236497015 | etot = -5.62847192909114 +586000 ekin = 3.12407298196409 | erot = 2.91878541592703 | epot = -11.6713303267181 | etot = -5.62847192882701 +587000 ekin = 3.1417461421883 | erot = 2.90225430097043 | epot = -11.6724723716963 | etot = -5.62847192853757 +588000 ekin = 3.15240031621057 | erot = 2.91960613647359 | epot = -11.7004783809454 | etot = -5.62847192826126 +589000 ekin = 3.16081808256559 | erot = 2.97006448179299 | epot = -11.7593544923991 | etot = -5.62847192804055 +590000 ekin = 3.17204827386215 | erot = 3.05134069933582 | epot = -11.851860901114 | etot = -5.62847192791604 +591000 ekin = 3.19150299841088 | erot = 3.16015018739589 | epot = -11.9801251137996 | etot = -5.62847192799281 +592000 ekin = 3.22264872305427 | erot = 3.2920405752428 | epot = -12.1431612266149 | etot = -5.6284719283178 +593000 ekin = 3.26585695466861 | erot = 3.44092346947024 | epot = -12.335252352998 | etot = -5.62847192885916 +594000 ekin = 3.31918005199199 | erot = 3.59965335611017 | epot = -12.5473053376671 | etot = -5.62847192956493 +595000 ekin = 3.37897127086391 | erot = 3.76045843951842 | epot = -12.7679016406725 | etot = -5.62847193029017 +596000 ekin = 3.43824068582474 | erot = 3.91359738336251 | epot = -12.9803100018126 | etot = -5.62847193262531 +597000 ekin = 3.48744876802135 | erot = 4.0478243787173 | epot = -13.1637450799978 | etot = -5.62847193325914 +598000 ekin = 3.52187002174283 | erot = 4.15698580436678 | epot = -13.307327759723 | etot = -5.62847193361335 +599000 ekin = 3.53831455076447 | erot = 4.23767846722027 | epot = -13.4044649516698 | etot = -5.62847193368508 +600000 ekin = 3.53510970434128 | erot = 4.28920847115898 | epot = -13.4527901090173 | etot = -5.62847193351703 +601000 ekin = 3.51191041821579 | erot = 4.31320178205608 | epot = -13.4535841334509 | etot = -5.62847193317902 +602000 ekin = 3.46937521149507 | erot = 4.31295152750157 | epot = -13.4107986717423 | etot = -5.62847193274563 +603000 ekin = 3.4088222124387 | erot = 4.29270411938567 | epot = -13.3299982641027 | etot = -5.62847193227831 +604000 ekin = 3.33194570984168 | erot = 4.25705245873742 | epot = -13.2174701003966 | etot = -5.62847193181754 +605000 ekin = 3.2406264378913 | erot = 4.21052248047251 | epot = -13.0796208497473 | etot = -5.62847193138353 +606000 ekin = 3.13683319326865 | erot = 4.15735875804854 | epot = -12.9226638822973 | etot = -5.62847193098009 +607000 ekin = 3.02259481110688 | erot = 4.10146703780694 | epot = -12.7525337795153 | etot = -5.62847193060149 +608000 ekin = 2.90001652261395 | erot = 4.04645475164202 | epot = -12.5749432044933 | etot = -5.6284719302373 +609000 ekin = 2.77131728809351 | erot = 3.99571460788032 | epot = -12.3955038258513 | etot = -5.62847192987747 +610000 ekin = 2.63886938891702 | erot = 3.95250622998014 | epot = -12.2198475484129 | etot = -5.62847192951569 +611000 ekin = 2.50524882251801 | erot = 3.920032937849 | epot = -12.053753689229 | etot = -5.62847192886197 +612000 ekin = 2.37382087283167 | erot = 3.90218869860999 | epot = -11.9044814999747 | etot = -5.62847192853301 +613000 ekin = 2.24769613365103 | erot = 3.90186788756939 | epot = -11.7780359494445 | etot = -5.62847192822403 +614000 ekin = 2.12975142865347 | erot = 3.92103062122306 | epot = -11.6792539778537 | etot = -5.62847192797718 +615000 ekin = 2.02283676466854 | erot = 3.96080056836513 | epot = -11.6121092608611 | etot = -5.6284719278274 +616000 ekin = 1.92967019047414 | erot = 4.02099162192593 | epot = -11.5791337402076 | etot = -5.62847192780754 +617000 ekin = 1.85273791862989 | erot = 4.099744744135 | epot = -11.5809545907117 | etot = -5.62847192794679 +618000 ekin = 1.7942029629718 | erot = 4.19322703631862 | epot = -11.6159019275489 | etot = -5.6284719282585 +619000 ekin = 1.75583197431074 | erot = 4.29552606656025 | epot = -11.6798299695989 | etot = -5.62847192872788 +620000 ekin = 1.73895870101793 | erot = 4.39891672383331 | epot = -11.7663473541522 | etot = -5.62847192930098 +621000 ekin = 1.74449834720697 | erot = 4.49462250674119 | epot = -11.8675927838345 | etot = -5.62847192988636 +622000 ekin = 1.77300875733458 | erot = 4.57403518100206 | epot = -11.9755158687144 | etot = -5.62847193037778 +623000 ekin = 1.82476626673924 | erot = 4.63011744403992 | epot = -12.0833556414698 | etot = -5.62847193069065 +624000 ekin = 1.89980556105245 | erot = 4.65854151402706 | epot = -12.1868190058735 | etot = -5.628471930794 +625000 ekin = 1.99788931017694 | erot = 4.65817060170441 | epot = -12.2845318425975 | etot = -5.62847193071619 +626000 ekin = 2.11841939018701 | erot = 4.63077870093506 | epot = -12.3776700216461 | etot = -5.628471930524 +627000 ekin = 2.26034340511523 | erot = 4.5802426839639 | epot = -12.4690580193665 | etot = -5.6284719302874 +628000 ekin = 2.42211143994082 | erot = 4.51161612051721 | epot = -12.5621994905184 | etot = -5.62847193006037 +629000 ekin = 2.60047669423503 | erot = 4.43316974506441 | epot = -12.6621183686995 | etot = -5.62847192940005 +630000 ekin = 2.75035749006496 | erot = 4.31003905739293 | epot = -12.6888685131607 | etot = -5.62847196570277 +631000 ekin = 2.81471524145153 | erot = 4.1177453598379 | epot = -12.5609325370485 | etot = -5.62847193575907 +632000 ekin = 2.95867552227146 | erot = 4.07926707213495 | epot = -12.6664145272728 | etot = -5.62847193286638 +633000 ekin = 3.21010693605695 | erot = 4.20581326830098 | epot = -13.0443921664311 | etot = -5.62847196207314 +634000 ekin = 3.41641131502396 | erot = 4.25928215928574 | epot = -13.3041654106762 | etot = -5.6284719363665 +635000 ekin = 3.57385274076439 | erot = 4.24018711600146 | epot = -13.4425117939027 | etot = -5.62847193713684 +636000 ekin = 3.71894531192015 | erot = 4.21896102702093 | epot = -13.5663782769141 | etot = -5.62847193797298 +637000 ekin = 3.84555962846069 | erot = 4.19009538991242 | epot = -13.6641269570415 | etot = -5.62847193866843 +638000 ekin = 3.94874232720897 | erot = 4.14881281924716 | epot = -13.7260270854934 | etot = -5.62847193903727 +639000 ekin = 4.02564653197239 | erot = 4.09271382118292 | epot = -13.7468322921586 | etot = -5.62847193900331 +640000 ekin = 4.07582551362717 | erot = 4.02260436117536 | epot = -13.7269018134182 | etot = -5.62847193861568 +641000 ekin = 4.10019063758673 | erot = 3.94203419565371 | epot = -13.670696771703 | etot = -5.62847193846252 +642000 ekin = 4.09923585986421 | erot = 3.85569636510016 | epot = -13.5834041628477 | etot = -5.62847193788336 +643000 ekin = 4.07616079969331 | erot = 3.76850329633298 | epot = -13.4731360333853 | etot = -5.62847193735897 +644000 ekin = 4.03483546293706 | erot = 3.68428538411615 | epot = -13.3475927839978 | etot = -5.62847193694458 +645000 ekin = 3.97939693520722 | erot = 3.60521279246359 | epot = -13.2130816642939 | etot = -5.62847193662304 +646000 ekin = 3.91424157378713 | erot = 3.53197746515019 | epot = -13.0746909752778 | etot = -5.62847193634044 +647000 ekin = 3.84412108338865 | erot = 3.46430751174276 | epot = -12.936900531313 | etot = -5.62847193618156 +648000 ekin = 3.77442093435187 | erot = 3.40030625097309 | epot = -12.803199121189 | etot = -5.62847193586402 +649000 ekin = 3.71064844389534 | erot = 3.33902116858815 | epot = -12.6781415480255 | etot = -5.62847193554202 +650000 ekin = 3.65777288951916 | erot = 3.28036981758716 | epot = -12.5666146423759 | etot = -5.62847193526958 +651000 ekin = 3.61962254745685 | erot = 3.22458240432363 | epot = -12.4726768868735 | etot = -5.62847193509302 +652000 ekin = 3.59838866978257 | erot = 3.17201593042838 | epot = -12.3988765352415 | etot = -5.62847193503051 +653000 ekin = 3.59447660060613 | erot = 3.12302902489282 | epot = -12.3459775605645 | etot = -5.62847193506556 +654000 ekin = 3.60674141926014 | erot = 3.07797678374685 | epot = -12.3131901381652 | etot = -5.62847193515817 +655000 ekin = 3.6329884132142 | erot = 3.0372849708598 | epot = -12.298745319343 | etot = -5.62847193526905 +656000 ekin = 3.67052655540377 | erot = 3.00147990310302 | epot = -12.3004783938925 | etot = -5.62847193538567 +657000 ekin = 3.71734630717454 | erot = 2.97084073566211 | epot = -12.3166589782294 | etot = -5.62847193539274 +658000 ekin = 3.75778663127986 | erot = 2.94872940878028 | epot = -12.3349879988478 | etot = -5.62847195878767 +659000 ekin = 3.70128994140422 | erot = 2.99267200720399 | epot = -12.322433884335 | etot = -5.62847193572677 +660000 ekin = 3.77980484716758 | erot = 3.05081678620785 | epot = -12.4590935974502 | etot = -5.62847196407474 +661000 ekin = 3.87674047159649 | erot = 3.02043722452879 | epot = -12.525649641487 | etot = -5.62847194536175 +662000 ekin = 3.96189665337338 | erot = 2.97294510662666 | epot = -12.5633137063048 | etot = -5.62847194630474 +663000 ekin = 4.03233992144667 | erot = 2.90724728966555 | epot = -12.5680591574414 | etot = -5.62847194632914 +664000 ekin = 4.08703350805977 | erot = 2.82371074123732 | epot = -12.5392161951071 | etot = -5.62847194581 +665000 ekin = 4.13016908297309 | erot = 2.72591755760502 | epot = -12.4845585856306 | etot = -5.62847194505245 +666000 ekin = 4.16485763713769 | erot = 2.62158318056703 | epot = -12.4149127617789 | etot = -5.62847194407414 +667000 ekin = 4.19388444252446 | erot = 2.52048046546624 | epot = -12.3428368513066 | etot = -5.62847194331587 +668000 ekin = 4.21970111382924 | erot = 2.43117566525611 | epot = -12.2793487218498 | etot = -5.62847194276442 +669000 ekin = 4.24419480080694 | erot = 2.35970998739347 | epot = -12.2323767306056 | etot = -5.62847194240515 +670000 ekin = 4.26650932858638 | erot = 2.31009212963131 | epot = -12.205073400494 | etot = -5.62847194227631 +671000 ekin = 4.28028750599208 | erot = 2.28394068935258 | epot = -12.1927001375686 | etot = -5.62847194222394 +672000 ekin = 4.28604953834283 | erot = 2.28087700930265 | epot = -12.1953984898335 | etot = -5.62847194218805 +673000 ekin = 4.28538321001861 | erot = 2.29981058099184 | epot = -12.2136657331544 | etot = -5.62847194214396 +674000 ekin = 4.28032637907724 | erot = 2.33931519979736 | epot = -12.2481135209779 | etot = -5.6284719421033 +675000 ekin = 4.27310613165764 | erot = 2.39770546320171 | epot = -12.2992835369734 | etot = -5.62847194211401 +676000 ekin = 4.26563141866178 | erot = 2.4728304784173 | epot = -12.3669338393533 | etot = -5.62847194227417 +677000 ekin = 4.25873601046005 | erot = 2.56159475121792 | epot = -12.4488027043104 | etot = -5.62847194263247 +678000 ekin = 4.25154383428171 | erot = 2.65951246646833 | epot = -12.5395282439892 | etot = -5.62847194323914 +679000 ekin = 4.24120573481474 | erot = 2.76057514733209 | epot = -12.630252826186 | etot = -5.62847194403915 +680000 ekin = 4.22320051194648 | erot = 2.85770689084164 | epot = -12.7093793476574 | etot = -5.62847194486926 +681000 ekin = 4.1924284546272 | erot = 2.94400272523514 | epot = -12.7649031253611 | etot = -5.62847194549873 +682000 ekin = 4.14477706345917 | erot = 3.01435956360772 | epot = -12.7876085728122 | etot = -5.62847194574536 +683000 ekin = 4.07850194585553 | erot = 3.06669689279676 | epot = -12.7736707842126 | etot = -5.62847194556027 +684000 ekin = 3.98766788580418 | erot = 3.09062770615288 | epot = -12.7067675423427 | etot = -5.62847195038565 +685000 ekin = 3.876099760335 | erot = 3.07213118817965 | epot = -12.5767028921904 | etot = -5.6284719436757 +686000 ekin = 3.78865422807076 | erot = 3.05379982502793 | epot = -12.4709259954479 | etot = -5.62847194234925 +687000 ekin = 3.72885638140324 | erot = 3.0512831037603 | epot = -12.4086114323937 | etot = -5.62847194723014 +688000 ekin = 3.65488085471333 | erot = 3.04382149742279 | epot = -12.3271742984754 | etot = -5.62847194633926 +689000 ekin = 3.57606770156701 | erot = 3.03834252482284 | epot = -12.2428821720227 | etot = -5.62847194563281 +690000 ekin = 3.5163442557747 | erot = 3.04775260779204 | epot = -12.1925688086869 | etot = -5.62847194512014 +691000 ekin = 3.479714457667 | erot = 3.07622358468465 | epot = -12.1844099872179 | etot = -5.62847194486626 +692000 ekin = 3.46765181285756 | erot = 3.12642449713322 | epot = -12.2225482549237 | etot = -5.62847194493293 +693000 ekin = 3.47854301585795 | erot = 3.19918358101017 | epot = -12.3061985422019 | etot = -5.62847194533383 +694000 ekin = 3.50760869835413 | erot = 3.2934044105347 | epot = -12.4294850548997 | etot = -5.62847194601086 +695000 ekin = 3.54747029199334 | erot = 3.40637947917737 | epot = -12.5823217180174 | etot = -5.62847194684668 +696000 ekin = 3.58927155200294 | erot = 3.53441505502552 | epot = -12.7521585547315 | etot = -5.62847194770304 +697000 ekin = 3.62399868557179 | erot = 3.6734776731682 | epot = -12.9259483071981 | etot = -5.62847194845815 +698000 ekin = 3.64429609788807 | erot = 3.81929275612903 | epot = -13.0920608031207 | etot = -5.62847194910361 +699000 ekin = 3.64411727681169 | erot = 3.96826912309839 | epot = -13.2408583494292 | etot = -5.62847194951913 +700000 ekin = 3.61972386503995 | erot = 4.11779628938367 | epot = -13.3659921041098 | etot = -5.62847194968622 +701000 ekin = 3.57045543154956 | erot = 4.26605645148198 | epot = -13.4649838327663 | etot = -5.62847194973473 +702000 ekin = 3.49917622968027 | erot = 4.41037029523648 | epot = -13.5380184745267 | etot = -5.62847194960996 +703000 ekin = 3.41079978162148 | erot = 4.54773448504201 | epot = -13.5870062160415 | etot = -5.62847194937802 +704000 ekin = 3.31149657260329 | erot = 4.67560464111897 | epot = -13.6155731628048 | etot = -5.62847194908253 +705000 ekin = 3.2080790304827 | erot = 4.79162132907335 | epot = -13.6281723083369 | etot = -5.62847194878086 +706000 ekin = 3.10702043893943 | erot = 4.89365607518946 | epot = -13.6291484626722 | etot = -5.6284719485433 +707000 ekin = 3.01353531404712 | erot = 4.97967086427614 | epot = -13.6216781267622 | etot = -5.62847194843897 +708000 ekin = 2.93091332937569 | erot = 5.04739802062547 | epot = -13.6067832985163 | etot = -5.6284719485151 +709000 ekin = 2.86026033864142 | erot = 5.09399325394035 | epot = -13.5827255413543 | etot = -5.62847194877252 +710000 ekin = 2.80069789524477 | erot = 5.11589857289861 | epot = -13.545068417301 | etot = -5.62847194915761 +711000 ekin = 2.74994326389775 | erot = 5.10911210220021 | epot = -13.4875273156654 | etot = -5.62847194956741 +712000 ekin = 2.70509857008229 | erot = 5.06990681739858 | epot = -13.4034773373586 | etot = -5.62847194987772 +713000 ekin = 2.66343594223169 | erot = 4.99582282570971 | epot = -13.2877307179238 | etot = -5.62847194998245 +714000 ekin = 2.6229798284771 | erot = 4.88658411810223 | epot = -13.1380358964111 | etot = -5.62847194983175 +715000 ekin = 2.58275404739882 | erot = 4.74456650502127 | epot = -12.955792501868 | etot = -5.62847194944791 +716000 ekin = 2.54267933959134 | erot = 4.57461726456523 | epot = -12.7457685530667 | etot = -5.62847194891013 +717000 ekin = 2.50334691995156 | erot = 4.38348005444583 | epot = -12.5152989223949 | etot = -5.6284719479975 +718000 ekin = 2.46867182026079 | erot = 4.18280619287776 | epot = -12.2799499608795 | etot = -5.62847194774092 +719000 ekin = 2.44027484636896 | erot = 3.97913844269331 | epot = -12.0478852365523 | etot = -5.62847194748998 +720000 ekin = 2.41790751003703 | erot = 3.77617089292149 | epot = -11.8225503502079 | etot = -5.6284719472494 +721000 ekin = 2.40130900294611 | erot = 3.57751641362963 | epot = -11.6072973635973 | etot = -5.62847194702155 +722000 ekin = 2.39001969414016 | erot = 3.38620933334962 | epot = -11.4047009745045 | etot = -5.6284719470147 +723000 ekin = 2.38288808189959 | erot = 3.20447847595442 | epot = -11.2158385045713 | etot = -5.62847194671727 +724000 ekin = 2.3803813723149 | erot = 3.03585463084127 | epot = -11.0447079496027 | etot = -5.62847194644655 +725000 ekin = 2.3833490435995 | erot = 2.88343528869407 | epot = -10.8952562784996 | etot = -5.62847194620604 +726000 ekin = 2.39277988796305 | erot = 2.74974572521145 | epot = -10.7709975591759 | etot = -5.6284719460014 +727000 ekin = 2.40968215723269 | erot = 2.63676770299886 | epot = -10.67492180607 | etot = -5.62847194583841 +728000 ekin = 2.42515137988963 | erot = 2.54412147898368 | epot = -10.5977448182241 | etot = -5.62847195935075 +729000 ekin = 2.40297855332233 | erot = 2.51475999940565 | epot = -10.5462104921551 | etot = -5.62847193942709 +730000 ekin = 2.46310039276272 | erot = 2.54088838264026 | epot = -10.632460714378 | etot = -5.62847193897497 +731000 ekin = 2.53308642089727 | erot = 2.54954386940515 | epot = -10.7111022293682 | etot = -5.62847193906579 +732000 ekin = 2.61398262089544 | erot = 2.58024874599413 | epot = -10.8227033061636 | etot = -5.62847193927408 +733000 ekin = 2.70404858445632 | erot = 2.63167940195199 | epot = -10.9641999260514 | etot = -5.62847193964312 +734000 ekin = 2.80051950068967 | erot = 2.70132929839112 | epot = -11.1303207393002 | etot = -5.62847194021941 +735000 ekin = 2.89941283722633 | erot = 2.78510796762023 | epot = -11.3129927458789 | etot = -5.62847194103234 +736000 ekin = 2.99560133067232 | erot = 2.87741009015498 | epot = -11.5014833619209 | etot = -5.62847194109365 +737000 ekin = 3.08481605494955 | erot = 2.97524489359296 | epot = -11.6885328905225 | etot = -5.62847194198002 +738000 ekin = 3.16217862832009 | erot = 3.07317374868925 | epot = -11.8638243198073 | etot = -5.62847194279795 +739000 ekin = 3.22336037234166 | erot = 3.16493875121252 | epot = -12.0167710668997 | etot = -5.62847194334552 +740000 ekin = 3.26585131643273 | erot = 3.24522139629719 | epot = -12.1395446571587 | etot = -5.62847194442879 +741000 ekin = 3.28375382533968 | erot = 3.29991441187474 | epot = -12.212140181641 | etot = -5.62847194442657 +742000 ekin = 3.27631313182792 | erot = 3.32408611714212 | epot = -12.2288711929082 | etot = -5.62847194393818 +743000 ekin = 3.24737724842533 | erot = 3.32046927282599 | epot = -12.1963184644485 | etot = -5.62847194319719 +744000 ekin = 3.20210603655827 | erot = 3.29401551202302 | epot = -12.1245934909966 | etot = -5.62847194241536 +745000 ekin = 3.14567705942215 | erot = 3.25033567027571 | epot = -12.0244846714081 | etot = -5.62847194171029 +746000 ekin = 3.08279906327067 | erot = 3.19521988713644 | epot = -11.9064908912697 | etot = -5.62847194086257 +747000 ekin = 3.01768881789554 | erot = 3.13473855339626 | epot = -11.780899311672 | etot = -5.62847194038016 +748000 ekin = 2.95302867481637 | erot = 3.07321432169985 | epot = -11.6547149364592 | etot = -5.62847193994297 +749000 ekin = 2.89104396181994 | erot = 3.01469856721782 | epot = -11.534214468566 | etot = -5.62847193952823 +750000 ekin = 2.8337941746493 | erot = 2.96315742669507 | epot = -11.4254235404754 | etot = -5.62847193913108 +751000 ekin = 2.78329891313933 | erot = 2.92241777465506 | epot = -11.334188626555 | etot = -5.62847193876058 +752000 ekin = 2.74156846346743 | erot = 2.89600799329777 | epot = -11.2660483951996 | etot = -5.62847193843439 +753000 ekin = 2.71056677655963 | erot = 2.8869375345651 | epot = -11.2259762493015 | etot = -5.62847193817674 +754000 ekin = 2.69212502675219 | erot = 2.89743125957527 | epot = -11.218028224346 | etot = -5.62847193801851 +755000 ekin = 2.68776538375006 | erot = 2.92849871095324 | epot = -11.2447360327745 | etot = -5.62847193807121 +756000 ekin = 2.69845743043341 | erot = 2.97938409365368 | epot = -11.3063134623189 | etot = -5.62847193823178 +757000 ekin = 2.7245849642024 | erot = 3.04788425624735 | epot = -11.4009411590838 | etot = -5.628471938634 +758000 ekin = 2.76540921284501 | erot = 3.12962823281614 | epot = -11.5235093849758 | etot = -5.62847193931463 +759000 ekin = 2.81868342062832 | erot = 3.2179457539271 | epot = -11.6651011148134 | etot = -5.62847194025796 +760000 ekin = 2.88053746474593 | erot = 3.30429272398516 | epot = -11.8133021300751 | etot = -5.62847194134403 +761000 ekin = 2.94600007667602 | erot = 3.37947250551466 | epot = -11.9539445245137 | etot = -5.628471942323 +762000 ekin = 3.01037281077531 | erot = 3.43568700380028 | epot = -12.074531757463 | etot = -5.62847194288743 +763000 ekin = 3.07103775529337 | erot = 3.4688160008779 | epot = -12.1683256990123 | etot = -5.62847194284105 +764000 ekin = 3.1286639507601 | erot = 3.47975039716702 | epot = -12.2368862901611 | etot = -5.62847194223402 +765000 ekin = 3.18696433131214 | erot = 3.47390232188834 | epot = -12.2893385945311 | etot = -5.62847194133062 +766000 ekin = 3.25112146464065 | erot = 3.45917589108991 | epot = -12.3387692961781 | etot = -5.62847194044749 +767000 ekin = 3.3257732822072 | erot = 3.44357056062516 | epot = -12.3978157826508 | etot = -5.62847193981849 +768000 ekin = 3.41341833403058 | erot = 3.43342634990815 | epot = -12.4753166234905 | etot = -5.62847193955173 +769000 ekin = 3.51361597973961 | erot = 3.43258837752158 | epot = -12.5746762969179 | etot = -5.62847193965668 +770000 ekin = 3.62296220637373 | erot = 3.44225950985554 | epot = -12.69369365631 | etot = -5.6284719400807 +771000 ekin = 3.67754209930831 | erot = 3.42051682773995 | epot = -12.7265308948551 | etot = -5.62847196780683 +772000 ekin = 3.59351734147161 | erot = 3.35849685543844 | epot = -12.5804861304497 | etot = -5.62847193353968 +773000 ekin = 3.58504863518163 | erot = 3.48413941962712 | epot = -12.6976599880777 | etot = -5.62847193326899 +774000 ekin = 3.69556246730569 | erot = 3.75600381589561 | epot = -13.0800382519994 | etot = -5.62847196879806 +775000 ekin = 3.75799647075416 | erot = 3.87395641064186 | epot = -13.2604248539395 | etot = -5.62847197254345 +776000 ekin = 3.7651493109943 | erot = 3.89275295664149 | epot = -13.2863742403519 | etot = -5.62847197271613 +777000 ekin = 3.7485283802971 | erot = 3.88975944451916 | epot = -13.2667597971623 | etot = -5.62847197234605 +778000 ekin = 3.71300754115221 | erot = 3.86527182244794 | epot = -13.2067513352313 | etot = -5.62847197163116 +779000 ekin = 3.66665793168574 | erot = 3.82295167610353 | epot = -13.1180815783184 | etot = -5.62847197052915 +780000 ekin = 3.6197277323346 | erot = 3.76957330549218 | epot = -13.0177730071122 | etot = -5.62847196928545 +781000 ekin = 3.582762426071 | erot = 3.71368279728973 | epot = -12.9249171915596 | etot = -5.62847196819882 +782000 ekin = 3.56434384360535 | erot = 3.66344621659026 | epot = -12.8562620277053 | etot = -5.62847196750966 +783000 ekin = 3.56907083441011 | erot = 3.6245960139525 | epot = -12.8221388158157 | etot = -5.62847196745307 +784000 ekin = 3.5965557822763 | erot = 3.59908724274969 | epot = -12.824114992835 | etot = -5.62847196780897 +785000 ekin = 3.64263842921577 | erot = 3.58559579680112 | epot = -12.8567061945069 | etot = -5.62847196848997 +786000 ekin = 3.70061363597188 | erot = 3.58032714286029 | epot = -12.9094127481158 | etot = -5.62847196928365 +787000 ekin = 3.76290289549889 | erot = 3.5782784647877 | epot = -12.9696533303321 | etot = -5.62847197004554 +788000 ekin = 3.822306912577 | erot = 3.57432079318471 | epot = -13.0250996764347 | etot = -5.628471970673 +789000 ekin = 3.87288356010198 | erot = 3.5640275049411 | epot = -13.0653830361478 | etot = -5.62847197110472 +790000 ekin = 3.91054381117187 | erot = 3.54422213310747 | epot = -13.0832379155458 | etot = -5.62847197126644 +791000 ekin = 3.93344679988893 | erot = 3.51333982536365 | epot = -13.075258596435 | etot = -5.62847197118246 +792000 ekin = 3.94193166980327 | erot = 3.47142235433641 | epot = -13.0418259950432 | etot = -5.6284719709035 +793000 ekin = 3.9380533746213 | erot = 3.41982689800064 | epot = -12.9863522431252 | etot = -5.62847197050325 +794000 ekin = 3.92496167497727 | erot = 3.36081973432835 | epot = -12.9142533793578 | etot = -5.62847197005219 +795000 ekin = 3.90631843193004 | erot = 3.29713731787245 | epot = -12.8319277194087 | etot = -5.62847196960623 +796000 ekin = 3.88587920081752 | erot = 3.23158100763125 | epot = -12.7459321776508 | etot = -5.62847196920202 +797000 ekin = 3.86724402811157 | erot = 3.16668037608652 | epot = -12.6623963730587 | etot = -5.62847196886061 +798000 ekin = 3.85371944439479 | erot = 3.10446220687512 | epot = -12.5866536198586 | etot = -5.62847196858871 +799000 ekin = 3.84821326108177 | erot = 3.04637406837098 | epot = -12.5230592978372 | etot = -5.6284719683845 +800000 ekin = 3.85308746095944 | erot = 2.99338091096299 | epot = -12.4749403401633 | etot = -5.62847196824089 +801000 ekin = 3.8699474209389 | erot = 2.94620265026981 | epot = -12.4446220393607 | etot = -5.62847196815198 +802000 ekin = 3.89938743528548 | erot = 2.90559564184607 | epot = -12.4334550452488 | etot = -5.62847196811729 +803000 ekin = 3.94077451954891 | erot = 2.87255363125875 | epot = -12.4418001189476 | etot = -5.62847196813989 +804000 ekin = 3.99217445515592 | erot = 2.84833794113921 | epot = -12.4689843645178 | etot = -5.62847196822264 +805000 ekin = 4.05048829000735 | erot = 2.83432176411526 | epot = -12.513282022487 | etot = -5.62847196836439 +806000 ekin = 4.1117832972839 | erot = 2.83170980293985 | epot = -12.5719650687838 | etot = -5.62847196856007 +807000 ekin = 4.17172086372807 | erot = 2.84122318399144 | epot = -12.6414160165231 | etot = -5.62847196880358 +808000 ekin = 4.22595471203353 | erot = 2.86283161227628 | epot = -12.7172582934001 | etot = -5.62847196909029 +809000 ekin = 4.27041103452004 | erot = 2.89559061360523 | epot = -12.7944736175402 | etot = -5.62847196941492 +810000 ekin = 4.301435791566 | erot = 2.93761851640051 | epot = -12.8675262777331 | etot = -5.62847196976662 +811000 ekin = 4.31585912497783 | erot = 2.98622782360862 | epot = -12.9305589187105 | etot = -5.62847197012403 +812000 ekin = 4.31104963149467 | erot = 3.03819974723406 | epot = -12.9777213491839 | etot = -5.62847197045514 +813000 ekin = 4.28501152883215 | erot = 3.09015837072237 | epot = -13.0036418702754 | etot = -5.6284719707209 +814000 ekin = 4.23653530291243 | erot = 3.13897206730526 | epot = -13.0039793411017 | etot = -5.62847197088401 +815000 ekin = 4.16537042814435 | erot = 3.18209773847961 | epot = -12.9759401375431 | etot = -5.62847197091918 +816000 ekin = 4.07236517527975 | erot = 3.21779646423656 | epot = -12.9186336103346 | etot = -5.62847197081825 +817000 ekin = 3.95951977497419 | erot = 3.24518380277815 | epot = -12.8331755483459 | etot = -5.62847197059355 +818000 ekin = 3.82991762752959 | erot = 3.2641206689089 | epot = -12.7225102667152 | etot = -5.62847197027671 +819000 ekin = 3.6875335678 | erot = 3.27498902925681 | epot = -12.590994566957 | etot = -5.62847196990016 +820000 ekin = 3.5369910685457 | erot = 3.27842149112395 | epot = -12.4438845291767 | etot = -5.62847196950702 +821000 ekin = 3.38323613921468 | erot = 3.2750550219209 | epot = -12.2867631302651 | etot = -5.6284719691295 +822000 ekin = 3.23123737493016 | erot = 3.26537695384856 | epot = -12.1250862975651 | etot = -5.62847196878637 +823000 ekin = 3.08574116323705 | erot = 3.24970236700643 | epot = -11.9639154987256 | etot = -5.62847196848216 +824000 ekin = 2.95109919875176 | erot = 3.22828590308752 | epot = -11.8078570700471 | etot = -5.62847196820782 +825000 ekin = 2.83117167296028 | erot = 3.20152981124015 | epot = -11.6611734521495 | etot = -5.6284719679491 +826000 ekin = 2.72929448904333 | erot = 3.17021233059984 | epot = -11.5279787873359 | etot = -5.62847196769273 +827000 ekin = 2.64828540246515 | erot = 3.13564460982889 | epot = -11.4124019797295 | etot = -5.62847196743546 +828000 ekin = 2.59045268613421 | erot = 3.09968027912531 | epot = -11.3186049324479 | etot = -5.62847196718838 +829000 ekin = 2.55756748807352 | erot = 3.06454892080937 | epot = -11.2505883758597 | etot = -5.62847196697678 +830000 ekin = 2.55077388167199 | erot = 3.03254604907188 | epot = -11.2117918975783 | etot = -5.62847196683439 +831000 ekin = 2.57043725794491 | erot = 3.00566097499105 | epot = -11.2045701997298 | etot = -5.62847196679385 +832000 ekin = 2.61596870814794 | erot = 2.98524787981802 | epot = -11.2296885548432 | etot = -5.62847196687727 +833000 ekin = 2.68568117521223 | erot = 2.97182255724672 | epot = -11.2859756995487 | etot = -5.62847196708975 +834000 ekin = 2.77673677781702 | erot = 2.96502424361031 | epot = -11.3702329888454 | etot = -5.62847196741803 +835000 ekin = 2.88522063962288 | erot = 2.9637296524443 | epot = -11.4774222599016 | etot = -5.62847196783447 +836000 ekin = 3.00633984255775 | erot = 2.96626860594424 | epot = -11.6010804168059 | etot = -5.62847196830391 +837000 ekin = 3.13471078601861 | erot = 2.97067133313891 | epot = -11.7338540879496 | etot = -5.62847196879203 +838000 ekin = 3.2646797672635 | erot = 2.97489019159131 | epot = -11.8680419281255 | etot = -5.62847196927073 +839000 ekin = 3.39062361880175 | erot = 2.97696578967581 | epot = -11.9960613781968 | etot = -5.6284719697192 +840000 ekin = 3.50719613959126 | erot = 2.97513773551513 | epot = -12.1108058452302 | etot = -5.62847197012377 +841000 ekin = 3.60951430199109 | erot = 2.96792302741424 | epot = -12.2059092998777 | etot = -5.62847197047234 +842000 ekin = 3.69330308165686 | erot = 2.95419217585841 | epot = -12.2759672282673 | etot = -5.62847197075203 +843000 ekin = 3.75502927884949 | erot = 2.9332627309959 | epot = -12.3167639807914 | etot = -5.62847197094604 +844000 ekin = 3.79205095605746 | erot = 2.90501003413473 | epot = -12.3255329612267 | etot = -5.62847197103449 +845000 ekin = 3.8027882686221 | erot = 2.8699770846291 | epot = -12.3012373242501 | etot = -5.62847197099888 +846000 ekin = 3.78689078273148 | erot = 2.82944607301393 | epot = -12.244808826574 | etot = -5.62847197082858 +847000 ekin = 3.74534923688533 | erot = 2.78543388061856 | epot = -12.159255088031 | etot = -5.62847197052711 +848000 ekin = 3.6804896086744 | erot = 2.74058491294141 | epot = -12.0495464917325 | etot = -5.62847197011673 +849000 ekin = 3.59580402254821 | erot = 2.69795473541775 | epot = -11.922230727606 | etot = -5.62847196963999 +850000 ekin = 3.49561211007676 | erot = 2.66069826359753 | epot = -11.7847823428248 | etot = -5.62847196915048 +851000 ekin = 3.38460421182286 | erot = 2.63169879047586 | epot = -11.6447749710046 | etot = -5.62847196870583 +852000 ekin = 3.26735834651863 | erot = 2.6131910553037 | epot = -11.5090213701772 | etot = -5.62847196835484 +853000 ekin = 3.1479297086307 | erot = 2.60644046003564 | epot = -11.3828421367932 | etot = -5.62847196812688 +854000 ekin = 3.02961721531289 | erot = 2.61155167746747 | epot = -11.2696408608016 | etot = -5.62847196802129 +855000 ekin = 2.91497870693846 | erot = 2.62749311928185 | epot = -11.1709437942376 | etot = -5.62847196801727 +856000 ekin = 2.80592683699381 | erot = 2.6522972353592 | epot = -11.0866960404283 | etot = -5.62847196807532 +857000 ekin = 2.70394323168349 | erot = 2.68342637134629 | epot = -11.0158415711826 | etot = -5.62847196815284 +858000 ekin = 2.61028085083429 | erot = 2.71820874447232 | epot = -10.9569615635232 | etot = -5.6284719682166 +859000 ekin = 2.52608469749405 | erot = 2.75423459849491 | epot = -10.9087912642381 | etot = -5.62847196824915 +860000 ekin = 2.45241725402134 | erot = 2.78962480095101 | epot = -10.8705140232205 | etot = -5.62847196824819 +861000 ekin = 2.39021948389612 | erot = 2.82313150310554 | epot = -10.841822955225 | etot = -5.62847196822337 +862000 ekin = 2.340251296173 | erot = 2.85407946345532 | epot = -10.8228027278192 | etot = -5.62847196819083 +863000 ekin = 2.30304188908081 | erot = 2.88219277595577 | epot = -10.8137066332046 | etot = -5.62847196816805 +864000 ekin = 2.2788600614665 | erot = 2.90737073832822 | epot = -10.8147027679653 | etot = -5.62847196817059 +865000 ekin = 2.2677019732128 | erot = 2.92947677434014 | epot = -10.8256507157609 | etot = -5.62847196820794 +866000 ekin = 2.26929189380253 | erot = 2.94819404207217 | epot = -10.8459579041567 | etot = -5.62847196828196 +867000 ekin = 2.28309242314625 | erot = 2.96298089278676 | epot = -10.8745452843195 | etot = -5.6284719683865 +868000 ekin = 2.30832281806483 | erot = 2.97313399071666 | epot = -10.9099287772899 | etot = -5.62847196850837 +869000 ekin = 2.3439813526939 | erot = 2.97793980519836 | epot = -10.9503931265235 | etot = -5.62847196863129 +870000 ekin = 2.38886744866037 | erot = 2.97686809815983 | epot = -10.9942075155616 | etot = -5.62847196874142 +871000 ekin = 2.44159861914831 | erot = 2.96974175433695 | epot = -11.0398123423171 | etot = -5.62847196883185 +872000 ekin = 2.50061961716328 | erot = 2.95681803721471 | epot = -11.0859096232828 | etot = -5.62847196890485 +873000 ekin = 2.56420808255788 | erot = 2.93874614107009 | epot = -11.131426192598 | etot = -5.62847196897004 +874000 ekin = 2.63049127146519 | erot = 2.91641905848208 | epot = -11.1753822989849 | etot = -5.62847196903767 +875000 ekin = 2.69749664575342 | erot = 2.89079069092306 | epot = -11.2167593057862 | etot = -5.62847196910973 +876000 ekin = 2.76325741009686 | erot = 2.8627513866625 | epot = -11.2544807659345 | etot = -5.62847196917517 +877000 ekin = 2.82597857202693 | erot = 2.83312911739798 | epot = -11.2875796586343 | etot = -5.62847196920939 +878000 ekin = 2.88426506170993 | erot = 2.80282960162576 | epot = -11.3155666324696 | etot = -5.62847196913387 +879000 ekin = 2.93899285634575 | erot = 2.77402557834613 | epot = -11.3414904036006 | etot = -5.62847196890876 +880000 ekin = 2.99074429622813 | erot = 2.74904466485448 | epot = -11.3682609300216 | etot = -5.62847196893903 +881000 ekin = 3.03734869108279 | erot = 2.72816458176029 | epot = -11.3939852416205 | etot = -5.6284719687774 +882000 ekin = 3.07935286457197 | erot = 2.71303253602814 | epot = -11.4208573692109 | etot = -5.62847196861077 +883000 ekin = 3.11756797212926 | erot = 2.70517731930176 | epot = -11.4512172599084 | etot = -5.62847196847736 +884000 ekin = 3.15280252977214 | erot = 2.70569769686027 | epot = -11.4869721950348 | etot = -5.62847196840236 +885000 ekin = 3.18571613335284 | erot = 2.71504911614494 | epot = -11.5292372178974 | etot = -5.62847196839963 +886000 ekin = 3.21676773519078 | erot = 2.73290580120412 | epot = -11.5781455048685 | etot = -5.6284719684736 +887000 ekin = 3.24623562557229 | erot = 2.75806669144042 | epot = -11.6327742856409 | etot = -5.6284719686282 +888000 ekin = 3.27425942147032 | erot = 2.78837179695594 | epot = -11.6911031872933 | etot = -5.628471968867 +889000 ekin = 3.30086479023381 | erot = 2.82064068495549 | epot = -11.7499774443771 | etot = -5.62847196918781 +890000 ekin = 3.32596925008795 | erot = 2.85071439956357 | epot = -11.8051556192212 | etot = -5.62847196956963 +891000 ekin = 3.34941253378609 | erot = 2.87373382345107 | epot = -11.8516183271961 | etot = -5.62847196995895 +892000 ekin = 3.37107523704372 | erot = 2.88476437019953 | epot = -11.8843115775119 | etot = -5.62847197026867 +893000 ekin = 3.39111185250974 | erot = 2.87974242636685 | epot = -11.8993262492774 | etot = -5.6284719704008 +894000 ekin = 3.41023213065922 | erot = 2.85650829406247 | epot = -11.8952123950077 | etot = -5.62847197028603 +895000 ekin = 3.42987731018765 | erot = 2.81553499405435 | epot = -11.8738842741643 | etot = -5.6284719699223 +896000 ekin = 3.45214149125935 | erot = 2.76001213076308 | epot = -11.840625591404 | etot = -5.62847196938153 +897000 ekin = 3.47941735763162 | erot = 2.69521466352177 | epot = -11.8031039899337 | etot = -5.62847196878031 +898000 ekin = 3.51352962191391 | erot = 2.62737086743898 | epot = -11.7693724707582 | etot = -5.62847198140534 +899000 ekin = 3.4889391158018 | erot = 2.56291214107266 | epot = -11.6803232263264 | etot = -5.6284719694519 +900000 ekin = 3.45535689463325 | erot = 2.55015985204198 | epot = -11.6339887090223 | etot = -5.62847196234705 +901000 ekin = 3.50186288272102 | erot = 2.58894159326793 | epot = -11.7192764517631 | etot = -5.62847197577414 +902000 ekin = 3.56610213711289 | erot = 2.58196928739602 | epot = -11.7765433970572 | etot = -5.62847197254824 +903000 ekin = 3.62814875925392 | erot = 2.56232070451798 | epot = -11.818941436694 | etot = -5.62847197292212 +904000 ekin = 3.6911239480489 | erot = 2.55247638515041 | epot = -11.8720723066083 | etot = -5.62847197340901 +905000 ekin = 3.75091280495829 | erot = 2.54985569763339 | epot = -11.9292404765093 | etot = -5.62847197391758 +906000 ekin = 3.80322506634537 | erot = 2.55191272481867 | epot = -11.9836097655085 | etot = -5.62847197434447 +907000 ekin = 3.84434228809365 | erot = 2.55683360496833 | epot = -12.0296478676651 | etot = -5.62847197460312 +908000 ekin = 3.87190064076986 | erot = 2.56394104721273 | epot = -12.0643136626345 | etot = -5.62847197465188 +909000 ekin = 3.88547927133989 | erot = 2.57365301113712 | epot = -12.0876042569838 | etot = -5.6284719745068 +910000 ekin = 3.8868045064271 | erot = 2.58702435701482 | epot = -12.1023008376729 | etot = -5.62847197423097 +911000 ekin = 3.8795171994182 | erot = 2.60508796305688 | epot = -12.1130771363803 | etot = -5.62847197390526 +912000 ekin = 3.86859233340828 | erot = 2.6282770139044 | epot = -12.1253413209174 | etot = -5.62847197360469 +913000 ekin = 3.85955912988348 | erot = 2.65612234972595 | epot = -12.1441534529955 | etot = -5.62847197338611 +914000 ekin = 3.85765974078628 | erot = 2.68725904828248 | epot = -12.1733907617502 | etot = -5.6284719726814 +915000 ekin = 3.86988558920738 | erot = 2.72155496053172 | epot = -12.2199125225959 | etot = -5.62847197285679 +916000 ekin = 3.89721211216248 | erot = 2.75899199877689 | epot = -12.284676084202 | etot = -5.62847197326257 +917000 ekin = 3.9359730652043 | erot = 2.79756616812597 | epot = -12.3620112070326 | etot = -5.62847197370231 +918000 ekin = 3.98211349977169 | erot = 2.83523644148149 | epot = -12.445821915401 | etot = -5.62847197414779 +919000 ekin = 4.03109884777409 | erot = 2.86939983471048 | epot = -12.528970658063 | etot = -5.62847197557845 +920000 ekin = 4.07575007487009 | erot = 2.89203459574046 | epot = -12.596256646507 | etot = -5.6284719758965 +921000 ekin = 4.11121320929704 | erot = 2.89963706167902 | epot = -12.6393222476118 | etot = -5.62847197663572 +922000 ekin = 4.1294632990563 | erot = 2.89101491589761 | epot = -12.6489501918611 | etot = -5.62847197690717 +923000 ekin = 4.12574552361613 | erot = 2.86656720235584 | epot = -12.6207847028643 | etot = -5.62847197689231 +924000 ekin = 4.09806256320393 | erot = 2.82817437056367 | epot = -12.5547089103971 | etot = -5.62847197662951 +925000 ekin = 4.04683813531694 | erot = 2.77889166018884 | epot = -12.4542017717231 | etot = -5.62847197621732 +926000 ekin = 3.97415981117782 | erot = 2.7224048538106 | epot = -12.3250366407506 | etot = -5.62847197576223 +927000 ekin = 3.88290109709725 | erot = 2.66247239201842 | epot = -12.1738454644419 | etot = -5.62847197532623 +928000 ekin = 3.7761917256548 | erot = 2.60258196834984 | epot = -12.007245668911 | etot = -5.62847197490635 +929000 ekin = 3.65741733810739 | erot = 2.54590495841865 | epot = -11.8317942709844 | etot = -5.62847197445833 +930000 ekin = 3.53056331173308 | erot = 2.49545263003465 | epot = -11.6544879157075 | etot = -5.6284719739398 +931000 ekin = 3.40054525662893 | erot = 2.45429284446284 | epot = -11.4833100741212 | etot = -5.62847197302942 +932000 ekin = 3.27351307047684 | erot = 2.42812142496917 | epot = -11.330106468077 | etot = -5.62847197263094 +933000 ekin = 3.15479412561102 | erot = 2.4201742848095 | epot = -11.2034403826495 | etot = -5.62847197222898 +934000 ekin = 3.04934556977892 | erot = 2.43124949598185 | epot = -11.1090670376374 | etot = -5.62847197187662 +935000 ekin = 2.96178382525618 | erot = 2.4616517147387 | epot = -11.0519075116135 | etot = -5.62847197161859 +936000 ekin = 2.89581269227129 | erot = 2.51113391188306 | epot = -11.0354185756346 | etot = -5.62847197148024 +937000 ekin = 2.85385879398921 | erot = 2.57889786112038 | epot = -11.0612286265758 | etot = -5.62847197146621 +938000 ekin = 2.83694342931292 | erot = 2.66364816300849 | epot = -11.1290635638871 | etot = -5.6284719715657 +939000 ekin = 2.84476696223264 | erot = 2.76369076866162 | epot = -11.2369297026477 | etot = -5.6284719717534 +940000 ekin = 2.87595320507522 | erot = 2.87707538066995 | epot = -11.3815005577404 | etot = -5.62847197199521 +941000 ekin = 2.92838858222815 | erot = 3.001781599449 | epot = -11.5586421539293 | etot = -5.62847197225216 +942000 ekin = 2.99958691587109 | erot = 3.13593595718877 | epot = -11.763994845549 | etot = -5.62847197248919 +943000 ekin = 3.08701486204183 | erot = 3.27802584272535 | epot = -11.9935126774476 | etot = -5.62847197268037 +944000 ekin = 3.1865868732566 | erot = 3.42629435933061 | epot = -12.2413532064764 | etot = -5.6284719738892 +945000 ekin = 3.29120912267668 | erot = 3.57701253578978 | epot = -12.4966936328758 | etot = -5.62847197440937 +946000 ekin = 3.39621217514857 | erot = 3.72637389469715 | epot = -12.7510580448483 | etot = -5.62847197500261 +947000 ekin = 3.49687303174878 | erot = 3.8697732119292 | epot = -12.995118219371 | etot = -5.62847197569304 +948000 ekin = 3.58827211264809 | erot = 4.00151346864799 | epot = -13.2182575577786 | etot = -5.6284719764825 +949000 ekin = 3.66536645448257 | erot = 4.11475106047836 | epot = -13.4085894922954 | etot = -5.62847197733445 +950000 ekin = 3.72323941899585 | erot = 4.20180191649421 | epot = -13.5535133136576 | etot = -5.62847197816758 +951000 ekin = 3.75754185505713 | erot = 4.25489778055795 | epot = -13.6409116144757 | etot = -5.62847197886061 +952000 ekin = 3.76507381429301 | erot = 4.26734583348333 | epot = -13.6608916270522 | etot = -5.62847197927588 +953000 ekin = 3.74438822080447 | erot = 4.23487585148559 | epot = -13.6077360515863 | etot = -5.62847197929629 +954000 ekin = 3.6962524259717 | erot = 4.15681814968167 | epot = -13.481542554518 | etot = -5.62847197886462 +955000 ekin = 3.62380419842041 | erot = 4.03673171285917 | epot = -13.2890078892873 | etot = -5.62847197800776 +956000 ekin = 3.52555336244235 | erot = 3.88073804718687 | epot = -13.034763389267 | etot = -5.62847197963779 +957000 ekin = 3.39894638511365 | erot = 3.70474137308253 | epot = -12.7321597327766 | etot = -5.6284719745804 +958000 ekin = 3.27782878920333 | erot = 3.53760736955423 | epot = -12.4439081317149 | etot = -5.62847197295739 +959000 ekin = 3.17835028171983 | erot = 3.38602207388545 | epot = -12.1928443304165 | etot = -5.62847197481125 +960000 ekin = 3.0901908743556 | erot = 3.23509493203189 | epot = -11.95375778284 | etot = -5.62847197645248 +961000 ekin = 3.00426258859347 | erot = 3.08248133284665 | epot = -11.7152158969855 | etot = -5.62847197554535 +962000 ekin = 2.92693479517853 | erot = 2.94805480624185 | epot = -11.5034615767523 | etot = -5.6284719753319 +963000 ekin = 2.8597205524796 | erot = 2.83488454346027 | epot = -11.3230770709663 | etot = -5.6284719750264 +964000 ekin = 2.80427359141848 | erot = 2.74583973012051 | epot = -11.1785852963867 | etot = -5.62847197484775 +965000 ekin = 2.76170821784095 | erot = 2.68249826056695 | epot = -11.0726784532017 | etot = -5.62847197479375 +966000 ekin = 2.73254763714389 | erot = 2.64503832984035 | epot = -11.0060579418564 | etot = -5.62847197487214 +967000 ekin = 2.71665521989092 | erot = 2.6321892238601 | epot = -10.9773164188389 | etot = -5.62847197508786 +968000 ekin = 2.71315992408347 | erot = 2.6412436424263 | epot = -10.9828755419371 | etot = -5.62847197542729 +969000 ekin = 2.72046614640552 | erot = 2.66825860722398 | epot = -11.0171967294821 | etot = -5.62847197585261 +970000 ekin = 2.73639579050106 | erot = 2.70848274225803 | epot = -11.073350509069 | etot = -5.62847197630994 +971000 ekin = 2.75849383298582 | erot = 2.75695664288296 | epot = -11.1439224525279 | etot = -5.62847197665908 +972000 ekin = 2.78540546458208 | erot = 2.80984083848411 | epot = -11.2237182799979 | etot = -5.62847197693175 +973000 ekin = 2.81581409071763 | erot = 2.86412704852392 | epot = -11.3084131163579 | etot = -5.62847197711633 +974000 ekin = 2.84847995272243 | erot = 2.91762904371329 | epot = -11.3945809736423 | etot = -5.62847197720655 +975000 ekin = 2.88260770936881 | erot = 2.96920774279544 | epot = -11.4802874293687 | etot = -5.62847197720445 +976000 ekin = 2.90702473502672 | erot = 3.01964919216589 | epot = -11.5551459287789 | etot = -5.62847200158634 +977000 ekin = 2.82994036254706 | erot = 3.1046759626717 | epot = -11.5630883030682 | etot = -5.62847197784941 +978000 ekin = 2.82908362156413 | erot = 3.22546639399175 | epot = -11.6830220192733 | etot = -5.6284720037174 +979000 ekin = 2.83706100064163 | erot = 3.25481872957499 | epot = -11.7203517202847 | etot = -5.62847199006803 +980000 ekin = 2.8360134507332 | erot = 3.2704251144274 | epot = -11.7349105552639 | etot = -5.62847199010325 +981000 ekin = 2.82679467437289 | erot = 3.27908745930583 | epot = -11.7343541238234 | etot = -5.62847199014464 +982000 ekin = 2.8088945699671 | erot = 3.28090658178986 | epot = -11.718273141946 | etot = -5.62847199018903 +983000 ekin = 2.7820889855003 | erot = 3.27578646951999 | epot = -11.6863474452356 | etot = -5.62847199021531 +984000 ekin = 2.74660136776419 | erot = 3.26353952159829 | epot = -11.6386128795509 | etot = -5.62847199018845 +985000 ekin = 2.70333214303226 | erot = 3.24411390737367 | epot = -11.5759180404775 | etot = -5.62847199007155 +986000 ekin = 2.65408912608489 | erot = 3.21786526182798 | epot = -11.5004263777502 | etot = -5.62847198983735 +987000 ekin = 2.57871632965158 | erot = 3.17247279261011 | epot = -11.3796611165783 | etot = -5.62847199431663 +988000 ekin = 2.53018925254918 | erot = 3.15315339399415 | epot = -11.3118146484783 | etot = -5.62847200193499 +989000 ekin = 2.49566277860328 | erot = 3.1295211702859 | epot = -11.253655940825 | etot = -5.62847199193586 +990000 ekin = 2.46227182144369 | erot = 3.09741757416563 | epot = -11.1881613869902 | etot = -5.62847199138088 +991000 ekin = 2.44592298885099 | erot = 3.07158094651789 | epot = -11.1459759264869 | etot = -5.62847199111805 +992000 ekin = 2.4517428121109 | erot = 3.05611048124175 | epot = -11.1363252842705 | etot = -5.62847199091787 +993000 ekin = 2.48099671347122 | erot = 3.05281517837352 | epot = -11.1622838826089 | etot = -5.62847199076417 +994000 ekin = 2.53415669925148 | erot = 3.06359154112299 | epot = -11.2262202310529 | etot = -5.62847199067838 +995000 ekin = 2.6108885303282 | erot = 3.09015398312884 | epot = -11.3295145041275 | etot = -5.62847199067047 +996000 ekin = 2.71011819460966 | erot = 3.13378298490508 | epot = -11.4723731702567 | etot = -5.62847199074198 +997000 ekin = 2.8301560310209 | erot = 3.19515267532744 | epot = -11.6537806972411 | etot = -5.6284719908928 +998000 ekin = 2.96878571502403 | erot = 3.27423191202229 | epot = -11.8714896181783 | etot = -5.62847199113201 +999000 ekin = 3.12322522594026 | erot = 3.37022004592621 | epot = -12.1219172633527 | etot = -5.6284719914862 +1000000 ekin = 3.28990650543485 | erot = 3.48146010603352 | epot = -12.3998386034665 | etot = -5.62847199199813 + 1000000 0.14621807 -0.83009398 0.055104069 -0.56937076 4.8223733e-05 64000 +Loop time of 30.3066 on 1 procs for 1000000 steps with 16 atoms + +Performance: 28508.641 tau/day, 32996.112 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 26.366 | 26.366 | 26.366 | 0.0 | 87.00 +Bond | 0.93995 | 0.93995 | 0.93995 | 0.0 | 3.10 +Neigh | 0.01081 | 0.01081 | 0.01081 | 0.0 | 0.04 +Comm | 0.34184 | 0.34184 | 0.34184 | 0.0 | 1.13 +Output | 0.14946 | 0.14946 | 0.14946 | 0.0 | 0.49 +Modify | 2.2187 | 2.2187 | 2.2187 | 0.0 | 7.32 +Other | | 0.2802 | | | 0.92 + +Nlocal: 16.0000 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 106.000 ave 106 max 106 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 106 +Ave neighs/atom = 6.6250000 +Ave special neighs/atom = 3.7500000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:30 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 new file mode 100644 index 0000000000..a0f683b799 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 @@ -0,0 +1,1182 @@ +LAMMPS (2 Jul 2021) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.5 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-20.000000 -20.000000 -20.000000) to (20.000000 20.000000 20.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds + +set atom * mass 3.1575 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 2.0 0.25 0.761070781051 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 0.1 ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3014979 + ghost atom cutoff = 4.3014979 + binsize = 2.150749, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 4.301497916929199 (../comm.cpp:739) +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -11.1349465280232 | etot = -5.62847186873667 +Per MPI rank memory allocation (min/avg/max) = 9.328 | 9.357 | 9.442 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -0.7299505 0.034016337 -0.52688704 5.1214421e-05 64000 +1000 ekin = 2.74425239815417 | erot = 2.79065458610893 | epot = -11.1633788526891 | etot = -5.62847186842597 +2000 ekin = 2.78841691867035 | erot = 2.77992540099535 | epot = -11.196814187725 | etot = -5.62847186805933 +3000 ekin = 2.83938215410022 | erot = 2.77185117591642 | epot = -11.2397051978034 | etot = -5.62847186778671 +4000 ekin = 2.89876217830263 | erot = 2.76816783884241 | epot = -11.295401884792 | etot = -5.62847186764698 +5000 ekin = 2.96742170720769 | erot = 2.76919345829435 | epot = -11.3650870331989 | etot = -5.62847186769689 +6000 ekin = 3.0456300737104 | erot = 2.77376672268248 | epot = -11.4478686641706 | etot = -5.62847186777773 +7000 ekin = 3.13407886898538 | erot = 2.78065913591457 | epot = -11.5432098726294 | etot = -5.62847186772942 +8000 ekin = 3.23400863287743 | erot = 2.78938863934858 | epot = -11.651869139893 | etot = -5.62847186766703 +9000 ekin = 3.34625998930258 | erot = 2.80019523753785 | epot = -11.7749270943235 | etot = -5.62847186748304 +10000 ekin = 3.47220350616334 | erot = 2.81464622815282 | epot = -11.9153216015116 | etot = -5.62847186719547 +11000 ekin = 3.61341090096018 | erot = 2.83541090219849 | epot = -12.0772936703879 | etot = -5.62847186722922 +12000 ekin = 3.76971728921063 | erot = 2.8651661044909 | epot = -12.26335526073 | etot = -5.62847186702843 +13000 ekin = 3.94105577714468 | erot = 2.90597306806356 | epot = -12.4755007121567 | etot = -5.62847186694845 +14000 ekin = 4.12730744896758 | erot = 2.95952862137381 | epot = -12.7153079373025 | etot = -5.62847186696111 +15000 ekin = 4.32776706381551 | erot = 3.02701108512252 | epot = -12.9832500158855 | etot = -5.62847186694746 +16000 ekin = 4.54139695680685 | erot = 3.10924468066178 | epot = -13.2791135046207 | etot = -5.62847186715204 +17000 ekin = 4.76575661763823 | erot = 3.20604355373091 | epot = -13.6002720389201 | etot = -5.62847186755097 +18000 ekin = 4.99700491214683 | erot = 3.31611869568265 | epot = -13.9415954758899 | etot = -5.62847186806045 +19000 ekin = 5.23048108112189 | erot = 3.43700077146759 | epot = -14.2959537213473 | etot = -5.62847186875782 +20000 ekin = 5.46074742513054 | erot = 3.564631560864 | epot = -14.6538508556015 | etot = -5.62847186960691 +21000 ekin = 5.68087058007131 | erot = 3.69256776681711 | epot = -15.0019102179231 | etot = -5.62847187103466 +22000 ekin = 5.88327619983871 | erot = 3.81252322503551 | epot = -15.3242712967755 | etot = -5.62847187190129 +23000 ekin = 6.0624997995198 | erot = 3.91720950057663 | epot = -15.6081811728146 | etot = -5.62847187271817 +24000 ekin = 6.21449712377425 | erot = 4.00104081543171 | epot = -15.8440098121103 | etot = -5.62847187290434 +25000 ekin = 6.3385327780924 | erot = 4.0618454261987 | epot = -16.0288500769827 | etot = -5.62847187269156 +26000 ekin = 6.43627737186995 | erot = 4.10076278430832 | epot = -16.1655120283937 | etot = -5.6284718722154 +27000 ekin = 6.5109244797201 | erot = 4.12134483746799 | epot = -16.2607411888239 | etot = -5.62847187163586 +28000 ekin = 6.56622100976664 | erot = 4.12827111510807 | epot = -16.3229639959505 | etot = -5.62847187107581 +29000 ekin = 6.60587340002374 | erot = 4.12622173833892 | epot = -16.360567008949 | etot = -5.62847187058635 +30000 ekin = 6.63335580501809 | erot = 4.11921545444646 | epot = -16.3810431296792 | etot = -5.62847187021468 +31000 ekin = 6.65211888589251 | erot = 4.10999678317526 | epot = -16.3905875389831 | etot = -5.62847186991536 +32000 ekin = 6.66584763664854 | erot = 4.10024297795098 | epot = -16.3945624842071 | etot = -5.62847186960759 +33000 ekin = 6.67923227191011 | erot = 4.09129207413365 | epot = -16.398996215263 | etot = -5.62847186921928 +34000 ekin = 6.69756137216815 | erot = 4.08414768607665 | epot = -16.4101809271346 | etot = -5.62847186888976 +35000 ekin = 6.72589628312065 | erot = 4.07950228497949 | epot = -16.4338704366877 | etot = -5.62847186858755 +36000 ekin = 6.76908557113698 | erot = 4.0777861549211 | epot = -16.4753435944362 | etot = -5.6284718683781 +37000 ekin = 6.83097506213388 | erot = 4.07899014040665 | epot = -16.5384370708783 | etot = -5.62847186833779 +38000 ekin = 6.91354703253156 | erot = 4.08242106390417 | epot = -16.6244399649597 | etot = -5.62847186852393 +39000 ekin = 7.01626065739817 | erot = 4.08652171942786 | epot = -16.7312542457771 | etot = -5.6284718689511 +40000 ekin = 7.13573792258313 | erot = 4.08884404540005 | epot = -16.8530538375758 | etot = -5.62847186959263 +41000 ekin = 7.26614194134498 | erot = 4.08627042537768 | epot = -16.9808842370343 | etot = -5.62847187031167 +42000 ekin = 7.40051154120571 | erot = 4.07546023443102 | epot = -17.1044436466276 | etot = -5.62847187099089 +43000 ekin = 7.53157437143672 | erot = 4.0534465535964 | epot = -17.2134927965847 | etot = -5.62847187155159 +44000 ekin = 7.65268317567628 | erot = 4.01819177227234 | epot = -17.2993468198231 | etot = -5.62847187187447 +45000 ekin = 7.75845343306873 | erot = 3.96898510895774 | epot = -17.3559104142063 | etot = -5.62847187217984 +46000 ekin = 7.84504377034629 | erot = 3.90454903064794 | epot = -17.3780646733314 | etot = -5.62847187233718 +47000 ekin = 7.91002390820623 | erot = 3.82478596555196 | epot = -17.3632817459104 | etot = -5.62847187215216 +48000 ekin = 7.95195705456504 | erot = 3.73154439390004 | epot = -17.3119733204126 | etot = -5.62847187194749 +49000 ekin = 7.97001825706871 | erot = 3.62752007295044 | epot = -17.2260102016182 | etot = -5.62847187159909 +50000 ekin = 7.9637575670044 | erot = 3.51726958365106 | epot = -17.109499021545 | etot = -5.62847187088959 +51000 ekin = 7.93280761300456 | erot = 3.40827188497834 | epot = -16.969551368803 | etot = -5.62847187082012 +52000 ekin = 7.87656811744214 | erot = 3.30207418532534 | epot = -16.8071141735587 | etot = -5.6284718707912 +53000 ekin = 7.79531012541934 | erot = 3.19839984815412 | epot = -16.6221818441148 | etot = -5.62847187054138 +54000 ekin = 7.68952609570367 | erot = 3.09980185481821 | epot = -16.4177998208248 | etot = -5.62847187030292 +55000 ekin = 7.55966222141132 | erot = 3.00897426989536 | epot = -16.1971083614502 | etot = -5.62847187014355 +56000 ekin = 7.40594124508039 | erot = 2.92802865182261 | epot = -15.9624417669777 | etot = -5.62847187007472 +57000 ekin = 7.22816598142029 | erot = 2.85836584281794 | epot = -15.7150036943485 | etot = -5.62847187011027 +58000 ekin = 7.02573051397645 | erot = 2.80066522322036 | epot = -15.45486760742 | etot = -5.62847187022319 +59000 ekin = 6.80455077165157 | erot = 2.7565194471203 | epot = -15.189542086097 | etot = -5.62847186732517 +60000 ekin = 6.57760251691547 | erot = 2.7273150167873 | epot = -14.9333893991697 | etot = -5.62847186546698 +61000 ekin = 5.99884053190185 | erot = 2.65010269791718 | epot = -14.2774150331167 | etot = -5.62847180329769 +62000 ekin = 5.82217958652088 | erot = 2.65058478195147 | epot = -14.1012361774588 | etot = -5.62847180898641 +63000 ekin = 6.00993174210273 | erot = 2.71143483466408 | epot = -14.3498384845185 | etot = -5.6284719077517 +64000 ekin = 5.85096985050391 | erot = 2.71173917624715 | epot = -14.1911809366075 | etot = -5.6284719098564 +65000 ekin = 5.67959801442757 | erot = 2.70731630130143 | epot = -14.0153862253962 | etot = -5.62847190966722 +66000 ekin = 5.49812382731728 | erot = 2.69646895132484 | epot = -13.8230646880628 | etot = -5.62847190942073 +67000 ekin = 5.3101118875317 | erot = 2.67901331172375 | epot = -13.617597108258 | etot = -5.62847190900257 +68000 ekin = 5.11964229582613 | erot = 2.65622197273387 | epot = -13.4043361770524 | etot = -5.62847190849237 +69000 ekin = 4.9306797520788 | erot = 2.63014135225676 | epot = -13.1892930124926 | etot = -5.628471908157 +70000 ekin = 4.74697386617514 | erot = 2.60347312706288 | epot = -12.9789189008747 | etot = -5.62847190763669 +71000 ekin = 4.572221332596 | erot = 2.57971589798913 | epot = -12.7804091377441 | etot = -5.62847190715895 +72000 ekin = 4.40959648507817 | erot = 2.56228295922475 | epot = -12.6003513510612 | etot = -5.62847190675832 +73000 ekin = 4.26170009573942 | erot = 2.55406076080096 | epot = -12.4442327629946 | etot = -5.62847190645423 +74000 ekin = 4.13052949790859 | erot = 2.55713155841153 | epot = -12.3161329625864 | etot = -5.62847190626624 +75000 ekin = 4.01588192828932 | erot = 2.56608801434133 | epot = -12.2104419139905 | etot = -5.62847197135984 +76000 ekin = 3.95904625854654 | erot = 2.44184942386114 | epot = -12.0293675901703 | etot = -5.62847190776259 +77000 ekin = 4.0275596026641 | erot = 2.46007159499047 | epot = -12.1161031098037 | etot = -5.6284719121491 +78000 ekin = 3.9878543994386 | erot = 2.49596945534603 | epot = -12.1122957670964 | etot = -5.62847191231177 +79000 ekin = 3.96575767721472 | erot = 2.54200842335453 | epot = -12.1362380131152 | etot = -5.62847191254597 +80000 ekin = 3.95961954869597 | erot = 2.59604589435596 | epot = -12.1841373558848 | etot = -5.62847191283286 +81000 ekin = 3.96734100032382 | erot = 2.65577062232351 | epot = -12.2515835357815 | etot = -5.62847191313418 +82000 ekin = 3.98651997822157 | erot = 2.71892569307082 | epot = -12.3339175847228 | etot = -5.62847191343037 +83000 ekin = 4.01459300302775 | erot = 2.78352190390193 | epot = -12.4265868206356 | etot = -5.62847191370596 +84000 ekin = 4.04956210608577 | erot = 2.84796629664412 | epot = -12.526000316534 | etot = -5.62847191380416 +85000 ekin = 4.09049341026886 | erot = 2.91104365381092 | epot = -12.6300089781176 | etot = -5.62847191403783 +86000 ekin = 4.13484812560062 | erot = 2.97201165419077 | epot = -12.73533169402 | etot = -5.62847191422856 +87000 ekin = 4.18003829184662 | erot = 3.03078479878272 | epot = -12.8392950049949 | etot = -5.62847191436551 +88000 ekin = 4.22360704724742 | erot = 3.08796574000306 | epot = -12.9400447016996 | etot = -5.62847191444908 +89000 ekin = 4.26326024607327 | erot = 3.14481288279466 | epot = -13.0365450433352 | etot = -5.62847191446729 +90000 ekin = 4.29588111790616 | erot = 3.20341713776991 | epot = -13.1277701703293 | etot = -5.62847191465319 +91000 ekin = 4.3169778457781 | erot = 3.26736040230132 | epot = -13.2128101626449 | etot = -5.62847191456548 +92000 ekin = 4.32507837347573 | erot = 3.33931601944534 | epot = -13.2928663075893 | etot = -5.6284719146682 +93000 ekin = 4.31872212432187 | erot = 3.42036541916748 | epot = -13.3675594581769 | etot = -5.62847191468757 +94000 ekin = 4.29660005793282 | erot = 3.51205694754371 | epot = -13.437128920153 | etot = -5.62847191467648 +95000 ekin = 4.2578902183883 | erot = 3.61606475666805 | epot = -13.502426889666 | etot = -5.62847191460968 +96000 ekin = 4.20253661926488 | erot = 3.73412422729619 | epot = -13.5651327610301 | etot = -5.62847191446908 +97000 ekin = 4.13146529060003 | erot = 3.86803037439249 | epot = -13.6279675793406 | etot = -5.62847191434809 +98000 ekin = 4.0466907197534 | erot = 4.01885670334675 | epot = -13.6940193371939 | etot = -5.62847191409377 +99000 ekin = 3.95128630061884 | erot = 4.18772840013401 | epot = -13.7674866145611 | etot = -5.62847191380829 +100000 ekin = 3.84921784883048 | erot = 4.37558821791212 | epot = -13.8532779802859 | etot = -5.62847191354332 +101000 ekin = 3.74501223923274 | erot = 4.58258429231713 | epot = -13.9560684449129 | etot = -5.62847191336305 +102000 ekin = 3.64330024870541 | erot = 4.80764134110039 | epot = -14.0794135031357 | etot = -5.62847191332989 +103000 ekin = 3.54831662006243 | erot = 5.04811575607467 | epot = -14.2249042896159 | etot = -5.6284719134788 +104000 ekin = 3.46349772064897 | erot = 5.29960820358415 | epot = -14.3915778382021 | etot = -5.62847191396902 +105000 ekin = 3.39136254536227 | erot = 5.55507704359958 | epot = -14.5749115034236 | etot = -5.62847191446178 +106000 ekin = 3.33356403744364 | erot = 5.80718759324905 | epot = -14.7692235454826 | etot = -5.62847191478986 +107000 ekin = 3.29209861353655 | erot = 6.04906687386722 | epot = -14.9696374027439 | etot = -5.62847191534016 +108000 ekin = 3.26748487341063 | erot = 6.27418243659677 | epot = -15.1701392258614 | etot = -5.62847191585405 +109000 ekin = 3.25930506886559 | erot = 6.47585417244282 | epot = -15.3636311580676 | etot = -5.62847191675918 +110000 ekin = 3.26568272829054 | erot = 6.64602097207877 | epot = -15.5401756176968 | etot = -5.62847191732745 +111000 ekin = 3.28520059172576 | erot = 6.77857539600264 | epot = -15.6922479055247 | etot = -5.62847191779634 +112000 ekin = 3.3165931570739 | erot = 6.86862760563878 | epot = -15.8136926809227 | etot = -5.62847191821005 +113000 ekin = 3.35860144230889 | erot = 6.91335224014739 | epot = -15.900425600655 | etot = -5.62847191819877 +114000 ekin = 3.41073468124636 | erot = 6.91406610981113 | epot = -15.9532727088316 | etot = -5.62847191777412 +115000 ekin = 3.4738153153424 | erot = 6.87643065686312 | epot = -15.9787178894052 | etot = -5.62847191719965 +116000 ekin = 3.54886437558739 | erot = 6.80711139529042 | epot = -15.9844476879559 | etot = -5.62847191707807 +117000 ekin = 3.6346740920492 | erot = 6.71320827683535 | epot = -15.9763542854612 | etot = -5.62847191657669 +118000 ekin = 3.72815555523539 | erot = 6.60276001485545 | epot = -15.9593874864252 | etot = -5.62847191633435 +119000 ekin = 3.82420980363907 | erot = 6.48288858478273 | epot = -15.9355703049684 | etot = -5.62847191654662 +120000 ekin = 3.91797748357213 | erot = 6.35662792089871 | epot = -15.9030773212275 | etot = -5.62847191675663 +121000 ekin = 4.00591742044035 | erot = 6.22468993027106 | epot = -15.8590792676429 | etot = -5.62847191693151 +122000 ekin = 4.08550270322373 | erot = 6.08676575288936 | epot = -15.8007403736371 | etot = -5.62847191752405 +123000 ekin = 4.15433540908386 | erot = 5.94071572290405 | epot = -15.7235230494649 | etot = -5.62847191747701 +124000 ekin = 4.21272085203614 | erot = 5.78590733869508 | epot = -15.6271001078557 | etot = -5.6284719171245 +125000 ekin = 4.26325970413196 | erot = 5.62467373686651 | epot = -15.516405357524 | etot = -5.62847191652555 +126000 ekin = 4.30880597980506 | erot = 5.46113290467189 | epot = -15.3984108007457 | etot = -5.62847191626874 +127000 ekin = 4.35136313111005 | erot = 5.29960307371424 | epot = -15.2794381205816 | etot = -5.62847191575727 +128000 ekin = 4.39391383900459 | erot = 5.14386269106717 | epot = -15.1662484454472 | etot = -5.62847191537548 +129000 ekin = 4.43858036063586 | erot = 4.99693296064756 | epot = -15.063985236396 | etot = -5.62847191511256 +130000 ekin = 4.48619887382442 | erot = 4.86092637377928 | epot = -14.9755971627238 | etot = -5.62847191512005 +131000 ekin = 4.53629967746003 | erot = 4.73552279955476 | epot = -14.9002943921691 | etot = -5.62847191515434 +132000 ekin = 4.58794392436637 | erot = 4.62012473201875 | epot = -14.8365405715596 | etot = -5.62847191517451 +133000 ekin = 4.63977927970742 | erot = 4.51475331813938 | epot = -14.7830045130149 | etot = -5.62847191516808 +134000 ekin = 4.69096227444516 | erot = 4.41936571520089 | epot = -14.7387999047806 | etot = -5.62847191513459 +135000 ekin = 4.74083332631942 | erot = 4.33399770983613 | epot = -14.7033029512362 | etot = -5.62847191508068 +136000 ekin = 4.78901374177283 | erot = 4.25873574864789 | epot = -14.6762214054318 | etot = -5.62847191501111 +137000 ekin = 4.83519033966162 | erot = 4.19345584709291 | epot = -14.6571181018627 | etot = -5.62847191510818 +138000 ekin = 4.87857190019152 | erot = 4.13759960010489 | epot = -14.6446434153638 | etot = -5.62847191506744 +139000 ekin = 4.91933904268544 | erot = 4.0904184140816 | epot = -14.6382293717798 | etot = -5.62847191501277 +140000 ekin = 4.95802132610631 | erot = 4.05108530565791 | epot = -14.6375785467323 | etot = -5.62847191496811 +141000 ekin = 4.9951992325528 | erot = 4.01864210163659 | epot = -14.6423132491261 | etot = -5.62847191493669 +142000 ekin = 5.03134031865334 | erot = 3.99210960072494 | epot = -14.6519218343061 | etot = -5.62847191492781 +143000 ekin = 5.06663282814571 | erot = 3.97056100872286 | epot = -14.6656657518145 | etot = -5.62847191494595 +144000 ekin = 5.1008800325395 | erot = 3.95318385936693 | epot = -14.6825358068965 | etot = -5.62847191499005 +145000 ekin = 5.1334772861941 | erot = 3.93933318432695 | epot = -14.7012823855755 | etot = -5.62847191505442 +146000 ekin = 5.16346418937044 | erot = 3.92856945833611 | epot = -14.720505562837 | etot = -5.62847191513042 +147000 ekin = 5.18962884502134 | erot = 3.9206777897014 | epot = -14.7387785499319 | etot = -5.62847191520911 +148000 ekin = 5.2106363010507 | erot = 3.91566839447809 | epot = -14.7547766108109 | etot = -5.62847191528212 +149000 ekin = 5.22515818277351 | erot = 3.91376203384954 | epot = -14.7673921319656 | etot = -5.62847191534254 +150000 ekin = 5.23199081771494 | erot = 3.91536756918854 | epot = -14.7758303022877 | etot = -5.62847191538422 +151000 ekin = 5.23025857434957 | erot = 3.92102977399531 | epot = -14.77976026373 | etot = -5.62847191538508 +152000 ekin = 5.21970456277706 | erot = 3.93136599417266 | epot = -14.7795424723193 | etot = -5.62847191536957 +153000 ekin = 5.2002071564403 | erot = 3.94729684642943 | epot = -14.7759759181576 | etot = -5.6284719152879 +154000 ekin = 5.17219962280996 | erot = 3.96989664945337 | epot = -14.7705681875102 | etot = -5.62847191524685 +155000 ekin = 5.13597939415306 | erot = 4.00025654377787 | epot = -14.7647078530828 | etot = -5.62847191515191 +156000 ekin = 5.09227456538914 | erot = 4.03969792967755 | epot = -14.7604444100926 | etot = -5.62847191502592 +157000 ekin = 5.04214374655936 | erot = 4.08965648366256 | epot = -14.7602721451216 | etot = -5.62847191489972 +158000 ekin = 4.98664076893846 | erot = 4.15175637520506 | epot = -14.7668690589136 | etot = -5.62847191477007 +159000 ekin = 4.92656708226507 | erot = 4.22693785976582 | epot = -14.7819768568014 | etot = -5.62847191477047 +160000 ekin = 4.86235166665126 | erot = 4.31524574981647 | epot = -14.806069331353 | etot = -5.62847191488528 +161000 ekin = 4.79340744408557 | erot = 4.416341921556 | epot = -14.8382212806378 | etot = -5.62847191499627 +162000 ekin = 4.71931679137333 | erot = 4.52911647420225 | epot = -14.8769051807431 | etot = -5.62847191516748 +163000 ekin = 4.63965178838048 | erot = 4.65170333188668 | epot = -14.9198270356121 | etot = -5.6284719153449 +164000 ekin = 4.55406399624436 | erot = 4.78166301740298 | epot = -14.9641989292971 | etot = -5.62847191564972 +165000 ekin = 4.46213996067539 | erot = 4.91530272158878 | epot = -15.0059145982053 | etot = -5.62847191594116 +166000 ekin = 4.36388109534925 | erot = 5.04805357548584 | epot = -15.0404065870411 | etot = -5.62847191620604 +167000 ekin = 4.25995046842459 | erot = 5.17511068522271 | epot = -15.0635330700697 | etot = -5.62847191642238 +168000 ekin = 4.15154354282114 | erot = 5.29182746831928 | epot = -15.0718429277122 | etot = -5.62847191657175 +169000 ekin = 4.04026084727441 | erot = 5.3941174772812 | epot = -15.0628502412098 | etot = -5.62847191665417 +170000 ekin = 3.92797723838258 | erot = 5.47890367159942 | epot = -15.0353528265935 | etot = -5.6284719166115 +171000 ekin = 3.81680551395721 | erot = 5.54460219961178 | epot = -14.9898796300184 | etot = -5.62847191644944 +172000 ekin = 3.70912194360758 | erot = 5.59119877272731 | epot = -14.9287926324942 | etot = -5.62847191615928 +173000 ekin = 3.60767008609852 | erot = 5.62020496676055 | epot = -14.8563469686152 | etot = -5.62847191575613 +174000 ekin = 3.51593123142554 | erot = 5.63484613588133 | epot = -14.7792492818548 | etot = -5.6284719145479 +175000 ekin = 3.43946966413739 | erot = 5.64148825119155 | epot = -14.7094298295804 | etot = -5.62847191425149 +176000 ekin = 3.38149964339891 | erot = 5.6430458497967 | epot = -14.6530174072212 | etot = -5.62847191402558 +177000 ekin = 3.34426304280215 | erot = 5.64075589500621 | epot = -14.6134908517385 | etot = -5.62847191393013 +178000 ekin = 3.32907821318033 | erot = 5.63429171925419 | epot = -14.5918418466202 | etot = -5.62847191418564 +179000 ekin = 3.33553286829273 | erot = 5.62088708741604 | epot = -14.5848918700473 | etot = -5.62847191433852 +180000 ekin = 3.36333384277191 | erot = 5.59827011329303 | epot = -14.590075870683 | etot = -5.62847191461804 +181000 ekin = 3.41118322744655 | erot = 5.56369949232961 | epot = -14.6033546347484 | etot = -5.62847191497222 +182000 ekin = 3.47666657813902 | erot = 5.51442909119503 | epot = -14.6195675846756 | etot = -5.62847191534156 +183000 ekin = 3.55646627297111 | erot = 5.44847615754871 | epot = -14.6334143461261 | etot = -5.62847191560626 +184000 ekin = 3.64671110623897 | erot = 5.36528131962616 | epot = -14.640464341691 | etot = -5.62847191582585 +185000 ekin = 3.74294243854247 | erot = 5.26596644090226 | epot = -14.6373807953582 | etot = -5.62847191591345 +186000 ekin = 3.84064021177418 | erot = 5.15359326679018 | epot = -14.6227053944206 | etot = -5.62847191585622 +187000 ekin = 3.93563840595006 | erot = 5.03296537332503 | epot = -14.5970756949485 | etot = -5.6284719156734 +188000 ekin = 4.02444308409283 | erot = 4.9100420520266 | epot = -14.5629570515404 | etot = -5.62847191542098 +189000 ekin = 4.10437481570283 | erot = 4.7910115792601 | epot = -14.5238583101452 | etot = -5.62847191518223 +190000 ekin = 4.17348832619954 | erot = 4.68117061833095 | epot = -14.4831308595836 | etot = -5.62847191505311 +191000 ekin = 4.23028845394395 | erot = 4.58386192798856 | epot = -14.4426222970226 | etot = -5.62847191509009 +192000 ekin = 4.27358054060601 | erot = 4.49984530057589 | epot = -14.4018977564793 | etot = -5.62847191529744 +193000 ekin = 4.24592911993781 | erot = 4.46741799187734 | epot = -14.3418190226914 | etot = -5.62847191087623 +194000 ekin = 4.19994174150889 | erot = 4.47173701960747 | epot = -14.3001506793675 | etot = -5.62847191825111 +195000 ekin = 4.19981139522167 | erot = 4.40365513590425 | epot = -14.2319384423494 | etot = -5.62847191122347 +196000 ekin = 4.18831859749938 | erot = 4.32821378408642 | epot = -14.1450042928957 | etot = -5.62847191130989 +197000 ekin = 4.16445522600488 | erot = 4.24686919663485 | epot = -14.0397963337834 | etot = -5.62847191114363 +198000 ekin = 4.13074920372959 | erot = 4.15919636754691 | epot = -13.9184174820247 | etot = -5.62847191074822 +199000 ekin = 4.090620747362 | erot = 4.06700829109956 | epot = -13.7861009486921 | etot = -5.62847191023056 +200000 ekin = 4.04792338687239 | erot = 3.97356549445473 | epot = -13.6499607909712 | etot = -5.62847190964408 +201000 ekin = 4.00668244919821 | erot = 3.88277215509106 | epot = -13.5179265133916 | etot = -5.62847190910236 +202000 ekin = 3.97063392471778 | erot = 3.79828207702214 | epot = -13.3973879104115 | etot = -5.62847190867159 +203000 ekin = 3.94283665189439 | erot = 3.72290259923884 | epot = -13.2942111595191 | etot = -5.62847190838588 +204000 ekin = 3.92540743372219 | erot = 3.65835216262476 | epot = -13.2122315045971 | etot = -5.62847190825017 +205000 ekin = 3.91946432177371 | erot = 3.60562062221005 | epot = -13.1535568521725 | etot = -5.62847190818872 +206000 ekin = 3.92515912499502 | erot = 3.56510062726653 | epot = -13.1187316605161 | etot = -5.6284719082546 +207000 ekin = 3.94166066189654 | erot = 3.53643554885135 | epot = -13.1065681191291 | etot = -5.62847190838122 +208000 ekin = 3.96741904659715 | erot = 3.51909285319014 | epot = -13.1149838083229 | etot = -5.62847190853559 +209000 ekin = 3.99456273872698 | erot = 3.5008331585032 | epot = -13.12386780659 | etot = -5.62847190935983 +210000 ekin = 4.04796401860469 | erot = 3.49168954890946 | epot = -13.1681254815403 | etot = -5.62847191402609 +211000 ekin = 4.09773342716023 | erot = 3.49304812012899 | epot = -13.2192534546349 | etot = -5.62847190734564 +212000 ekin = 4.14205596974386 | erot = 3.50221111647849 | epot = -13.2727389936889 | etot = -5.6284719074666 +213000 ekin = 4.18461227969266 | erot = 3.51992604962424 | epot = -13.3330102373235 | etot = -5.62847190800659 +214000 ekin = 4.22291801221032 | erot = 3.54318058637976 | epot = -13.3945705067397 | etot = -5.62847190814961 +215000 ekin = 4.25639069944069 | erot = 3.57018634832968 | epot = -13.455048956007 | etot = -5.6284719082366 +216000 ekin = 4.28517056130797 | erot = 3.59920416165413 | epot = -13.5128466312808 | etot = -5.62847190831865 +217000 ekin = 4.30951457891379 | erot = 3.62862634730599 | epot = -13.5666128346089 | etot = -5.62847190838914 +218000 ekin = 4.33022749097613 | erot = 3.65639118247648 | epot = -13.6150905819321 | etot = -5.62847190847947 +219000 ekin = 4.34822739188836 | erot = 3.680156611218 | epot = -13.65685591169 | etot = -5.62847190858365 +220000 ekin = 4.36437280258431 | erot = 3.69755509928772 | epot = -13.6903998105179 | etot = -5.62847190864584 +221000 ekin = 4.37954317243519 | erot = 3.70660976824559 | epot = -13.7146248493731 | etot = -5.62847190869237 +222000 ekin = 4.39451292717191 | erot = 3.70596363375625 | epot = -13.7289484695974 | etot = -5.62847190866922 +223000 ekin = 4.41008213189097 | erot = 3.69513355487692 | epot = -13.7336875953423 | etot = -5.62847190857439 +224000 ekin = 4.42678943726347 | erot = 3.67466536393777 | epot = -13.7299267097417 | etot = -5.6284719085405 +225000 ekin = 4.4446070170108 | erot = 3.64600909388234 | epot = -13.7190880192628 | etot = -5.62847190836967 +226000 ekin = 4.47380092382767 | erot = 3.5883081409745 | epot = -13.6905809780328 | etot = -5.62847191323058 +227000 ekin = 4.56056009804502 | erot = 3.47269306831649 | epot = -13.6617250773597 | etot = -5.6284719109982 +228000 ekin = 4.61083327531104 | erot = 3.40803816011154 | epot = -13.6473433475464 | etot = -5.62847191212383 +229000 ekin = 4.63150013168018 | erot = 3.35898149000663 | epot = -13.6189535337038 | etot = -5.62847191201703 +230000 ekin = 4.65431068144065 | erot = 3.31343017818407 | epot = -13.596212771626 | etot = -5.62847191200131 +231000 ekin = 4.67934821404876 | erot = 3.27332737527121 | epot = -13.5811475014859 | etot = -5.6284719121659 +232000 ekin = 4.70592354946345 | erot = 3.23944506667537 | epot = -13.5738405284608 | etot = -5.62847191232194 +233000 ekin = 4.7327141612257 | erot = 3.21144788525834 | epot = -13.5726339590431 | etot = -5.62847191255906 +234000 ekin = 4.75943444985074 | erot = 3.19078729233646 | epot = -13.578693654579 | etot = -5.6284719123918 +235000 ekin = 4.7864224181812 | erot = 3.18021193976865 | epot = -13.5951062703958 | etot = -5.62847191244599 +236000 ekin = 4.81315037988252 | erot = 3.18017325335007 | epot = -13.621795545699 | etot = -5.62847191246637 +237000 ekin = 4.83923297185582 | erot = 3.19145400453553 | epot = -13.6591588888822 | etot = -5.62847191249082 +238000 ekin = 4.86487585931821 | erot = 3.21481908800481 | epot = -13.7081668597365 | etot = -5.62847191241343 +239000 ekin = 4.89063931714941 | erot = 3.25114955282207 | epot = -13.7702607826849 | etot = -5.62847191271346 +240000 ekin = 4.91656145052528 | erot = 3.29901781219062 | epot = -13.8440511754923 | etot = -5.62847191277639 +241000 ekin = 4.94245255089308 | erot = 3.35699698381743 | epot = -13.9279214477129 | etot = -5.62847191300237 +242000 ekin = 4.9676738034607 | erot = 3.42365009426148 | epot = -14.0197958109218 | etot = -5.62847191319967 +243000 ekin = 5.00573446224949 | erot = 3.4703026046947 | epot = -14.1045089792032 | etot = -5.62847191225906 +244000 ekin = 5.06987350321115 | erot = 3.50985787352289 | epot = -14.2082032933008 | etot = -5.62847191656676 +245000 ekin = 5.08405115957508 | erot = 3.57323736718567 | epot = -14.2857604930688 | etot = -5.62847196630809 +246000 ekin = 5.13867281568972 | erot = 3.53022410786782 | epot = -14.2973688418964 | etot = -5.62847191833886 +247000 ekin = 5.24446071734678 | erot = 3.63707192639729 | epot = -14.5100045566457 | etot = -5.6284719129016 +248000 ekin = 5.23528120841574 | erot = 3.7402333097403 | epot = -14.6039864311637 | etot = -5.6284719130077 +249000 ekin = 5.21260078434991 | erot = 3.83729795660198 | epot = -14.6783706538229 | etot = -5.62847191287103 +250000 ekin = 5.17839081250125 | erot = 3.92749000333825 | epot = -14.7343527284453 | etot = -5.62847191260578 +251000 ekin = 5.13586036333776 | erot = 4.01108345357664 | epot = -14.7754157290639 | etot = -5.62847191214954 +252000 ekin = 5.08918292106269 | erot = 4.0901869418456 | epot = -14.8078417745571 | etot = -5.62847191164886 +253000 ekin = 5.04264218495251 | erot = 4.16759058211992 | epot = -14.8387046782792 | etot = -5.62847191120678 +254000 ekin = 4.99116344078304 | erot = 4.24248912287842 | epot = -14.8621245493434 | etot = -5.62847198568198 +255000 ekin = 4.72637462798313 | erot = 4.24407837663972 | epot = -14.5989249325881 | etot = -5.62847192796522 +256000 ekin = 4.59834109997883 | erot = 4.36369782211094 | epot = -14.5905108364968 | etot = -5.62847191440707 +257000 ekin = 4.77089539876767 | erot = 4.60066315316555 | epot = -15.0000305289929 | etot = -5.62847197705967 +258000 ekin = 4.85704242989329 | erot = 4.66807324377056 | epot = -15.1535875814157 | etot = -5.62847190775189 +259000 ekin = 4.89901811472161 | erot = 4.72718635921493 | epot = -15.254676380859 | etot = -5.62847190692249 +260000 ekin = 4.94107094739191 | erot = 4.79406863686397 | epot = -15.3636114914137 | etot = -5.62847190715783 +261000 ekin = 4.98242309074731 | erot = 4.86508628581783 | epot = -15.475981284624 | etot = -5.62847190805891 +262000 ekin = 5.01659840998324 | erot = 4.93871137848495 | epot = -15.5837816973677 | etot = -5.62847190889948 +263000 ekin = 5.03982661194286 | erot = 5.00983839412499 | epot = -15.678136915574 | etot = -5.62847190950611 +264000 ekin = 5.04732696349651 | erot = 5.07389667599432 | epot = -15.7496955495956 | etot = -5.62847191010476 +265000 ekin = 5.03448807084879 | erot = 5.12688367713822 | epot = -15.7898436586239 | etot = -5.62847191063685 +266000 ekin = 4.99773438959422 | erot = 5.16480683532306 | epot = -15.7910131359651 | etot = -5.62847191104779 +267000 ekin = 4.93508497406072 | erot = 5.18388050750759 | epot = -15.7474373928695 | etot = -5.62847191130122 +268000 ekin = 4.84654531470709 | erot = 5.18063468559457 | epot = -15.6556519116839 | etot = -5.62847191138221 +269000 ekin = 4.73423214274495 | erot = 5.15198859732377 | epot = -15.5146926513573 | etot = -5.62847191128854 +270000 ekin = 4.60224202248383 | erot = 5.09540688817397 | epot = -15.3261208188942 | etot = -5.62847190823643 +271000 ekin = 4.45636876654781 | erot = 5.00923317388611 | epot = -15.0940738481991 | etot = -5.62847190776522 +272000 ekin = 4.30375505735309 | erot = 4.89315778304568 | epot = -14.825384747494 | etot = -5.62847190709522 +273000 ekin = 4.15244061479752 | erot = 4.74862648123594 | epot = -14.5295390022933 | etot = -5.62847190625979 +274000 ekin = 4.01137482334292 | erot = 4.57896672456614 | epot = -14.2188134532213 | etot = -5.62847190531227 +275000 ekin = 3.87388872892428 | erot = 4.38950805795246 | epot = -13.8918687169883 | etot = -5.62847193011159 +276000 ekin = 3.70828148350147 | erot = 4.18975567950129 | epot = -13.5265090654659 | etot = -5.62847190246315 +277000 ekin = 3.74025187940199 | erot = 3.98894405210537 | epot = -13.3576678645646 | etot = -5.62847193305723 +278000 ekin = 3.74221760775445 | erot = 3.7703854369191 | epot = -13.141074947913 | etot = -5.62847190323943 +279000 ekin = 3.75220115766807 | erot = 3.55790331814709 | epot = -12.9385763794555 | etot = -5.62847190364033 +280000 ekin = 3.77561814014637 | erot = 3.35781654492599 | epot = -12.7619065883795 | etot = -5.62847190330715 +281000 ekin = 3.81272927484916 | erot = 3.17409695196373 | epot = -12.6152981298183 | etot = -5.62847190300538 +282000 ekin = 3.86501988036989 | erot = 3.00952640155094 | epot = -12.5030181842073 | etot = -5.62847190228648 +283000 ekin = 3.93628900407196 | erot = 2.86613168182016 | epot = -12.4308925881274 | etot = -5.62847190223531 +284000 ekin = 4.02702703050672 | erot = 2.74480306500215 | epot = -12.400301997905 | etot = -5.62847190239611 +285000 ekin = 4.14139706640362 | erot = 2.64599110158009 | epot = -12.4158600691698 | etot = -5.62847190118607 +286000 ekin = 4.28525774918439 | erot = 2.56950762489372 | epot = -12.4832372763244 | etot = -5.62847190224628 +287000 ekin = 4.44987555795748 | erot = 2.51493810068492 | epot = -12.5932855609593 | etot = -5.6284719023169 +288000 ekin = 4.63520922264933 | erot = 2.48100112555843 | epot = -12.7446822515497 | etot = -5.62847190334196 +289000 ekin = 4.83125797005689 | erot = 2.46527241539821 | epot = -12.9250022896894 | etot = -5.6284719042343 +290000 ekin = 5.02763799219528 | erot = 2.46542435682162 | epot = -13.1215342541017 | etot = -5.62847190508476 +291000 ekin = 5.21465468575846 | erot = 2.47913524144884 | epot = -13.3222618329705 | etot = -5.62847190576323 +292000 ekin = 5.38472348790169 | erot = 2.50416430329376 | epot = -13.5173596974329 | etot = -5.62847190623749 +293000 ekin = 5.53302487062846 | erot = 2.53823701976661 | epot = -13.6997337969559 | etot = -5.62847190656082 +294000 ekin = 5.6571870189941 | erot = 2.5787749635331 | epot = -13.8644338893373 | etot = -5.62847190681011 +295000 ekin = 5.75652780496594 | erot = 2.62269919784364 | epot = -14.0076989098378 | etot = -5.62847190702826 +296000 ekin = 5.83139499491463 | erot = 2.66652171229213 | epot = -14.1263886144138 | etot = -5.62847190720704 +297000 ekin = 5.88282356332242 | erot = 2.70675614330273 | epot = -14.2180516139347 | etot = -5.62847190730956 +298000 ekin = 5.91239748765322 | erot = 2.7404849430086 | epot = -14.28135433797 | etot = -5.62847190730812 +299000 ekin = 5.92208198046631 | erot = 2.7658529930208 | epot = -14.3164068806916 | etot = -5.62847190720453 +300000 ekin = 5.91390942018983 | erot = 2.78233336188499 | epot = -14.3247146890992 | etot = -5.62847190702436 +301000 ekin = 5.88962133511497 | erot = 2.79074353675713 | epot = -14.3088367786655 | etot = -5.6284719067934 +302000 ekin = 5.85048781421181 | erot = 2.79307875791444 | epot = -14.2720384786478 | etot = -5.6284719065216 +303000 ekin = 5.79743517877221 | erot = 2.79223225552269 | epot = -14.2181393405036 | etot = -5.62847190620872 +304000 ekin = 5.73124340760732 | erot = 2.79262915088962 | epot = -14.1523444641594 | etot = -5.62847190566242 +305000 ekin = 5.65258268469963 | erot = 2.79940899090845 | epot = -14.0804635809885 | etot = -5.62847190538042 +306000 ekin = 5.56254653523154 | erot = 2.81503734234889 | epot = -14.0060557827376 | etot = -5.62847190515719 +307000 ekin = 5.46251129680772 | erot = 2.84075892385856 | epot = -13.9317421256993 | etot = -5.628471905033 +308000 ekin = 5.35391293499826 | erot = 2.87633235163923 | epot = -13.8587171916687 | etot = -5.62847190503121 +309000 ekin = 5.23805007411516 | erot = 2.91996940723001 | epot = -13.7864913863797 | etot = -5.62847190503451 +310000 ekin = 5.11613875822289 | erot = 2.96880482959698 | epot = -13.7134154931048 | etot = -5.62847190528492 +311000 ekin = 4.98925852659088 | erot = 3.01839769775364 | epot = -13.6361281298111 | etot = -5.62847190546661 +312000 ekin = 4.85867326621996 | erot = 3.06421411593078 | epot = -13.5513592877715 | etot = -5.6284719056208 +313000 ekin = 4.72585112667078 | erot = 3.10236590329544 | epot = -13.4566889356288 | etot = -5.62847190566256 +314000 ekin = 4.59293421045967 | erot = 3.13002199528656 | epot = -13.3514281113019 | etot = -5.62847190555564 +315000 ekin = 4.46270669971285 | erot = 3.14588950387233 | epot = -13.2370681089016 | etot = -5.62847190531646 +316000 ekin = 4.33845457033907 | erot = 3.15016989317907 | epot = -13.117096368502 | etot = -5.62847190498389 +317000 ekin = 4.22370149066984 | erot = 3.14429402986996 | epot = -12.9964674251454 | etot = -5.62847190460556 +318000 ekin = 4.12188681800496 | erot = 3.13056754978033 | epot = -12.8809262720097 | etot = -5.62847190422441 +319000 ekin = 4.03607214171727 | erot = 3.1118418278711 | epot = -12.7763858734576 | etot = -5.62847190386921 +320000 ekin = 3.96873641008803 | erot = 3.09128048611875 | epot = -12.688488799758 | etot = -5.62847190355117 +321000 ekin = 3.92167797369473 | erot = 3.07226107994169 | epot = -12.6224109569055 | etot = -5.62847190326908 +322000 ekin = 3.89600971422886 | erot = 3.0583364837468 | epot = -12.5828181010019 | etot = -5.62847190302625 +323000 ekin = 3.89216326552489 | erot = 3.05323078720494 | epot = -12.5738659555648 | etot = -5.62847190283501 +324000 ekin = 3.90971752721574 | erot = 3.06065920137769 | epot = -12.5988486315915 | etot = -5.62847190299803 +325000 ekin = 3.94474197768096 | erot = 3.08325557842962 | epot = -12.6564694593579 | etot = -5.62847190324737 +326000 ekin = 3.99225791212593 | erot = 3.12131666196344 | epot = -12.7420464778598 | etot = -5.62847190377039 +327000 ekin = 4.0471575181962 | erot = 3.17277573873705 | epot = -12.8484051615057 | etot = -5.62847190457241 +328000 ekin = 4.10306827950272 | erot = 3.23289809101669 | epot = -12.9644382761191 | etot = -5.62847190559972 +329000 ekin = 4.1529407779747 | erot = 3.29460254686909 | epot = -13.0760152315166 | etot = -5.62847190667283 +330000 ekin = 4.19046086378744 | erot = 3.34957314359153 | epot = -13.1685059148798 | etot = -5.62847190750083 +331000 ekin = 4.21187936704663 | erot = 3.38989153266405 | epot = -13.2302428076773 | etot = -5.6284719079666 +332000 ekin = 4.21589857653334 | erot = 3.41075094374493 | epot = -13.2551214281318 | etot = -5.6284719078535 +333000 ekin = 4.20485265999743 | erot = 3.41174399824419 | epot = -13.2450685654349 | etot = -5.62847190719325 +334000 ekin = 4.18435368275723 | erot = 3.39692225043786 | epot = -13.2097478393525 | etot = -5.62847190615742 +335000 ekin = 4.16205455861025 | erot = 3.37367623593637 | epot = -13.1642026995324 | etot = -5.6284719049858 +336000 ekin = 4.14609491420183 | erot = 3.35093309665819 | epot = -13.1254999147632 | etot = -5.62847190390319 +337000 ekin = 4.14364358930928 | erot = 3.33736964605316 | epot = -13.1094851384328 | etot = -5.6284719030704 +338000 ekin = 4.15982493122721 | erot = 3.33968220642382 | epot = -13.1279790403805 | etot = -5.62847190272943 +339000 ekin = 4.19714166715581 | erot = 3.36120406394198 | epot = -13.1868176337033 | etot = -5.62847190260553 +340000 ekin = 4.25518474380808 | erot = 3.4039445653423 | epot = -13.2876012119485 | etot = -5.62847190279813 +341000 ekin = 4.33079125359858 | erot = 3.46797257818037 | epot = -13.4272357350166 | etot = -5.62847190323766 +342000 ekin = 4.41854745258189 | erot = 3.55173943759755 | epot = -13.5987587940251 | etot = -5.62847190384561 +343000 ekin = 4.51153864837879 | erot = 3.652504945506 | epot = -13.7925154984309 | etot = -5.62847190454609 +344000 ekin = 4.60219231317239 | erot = 3.76671918647997 | epot = -13.997383404906 | etot = -5.62847190525368 +345000 ekin = 4.68312343519334 | erot = 3.89042211424666 | epot = -14.2020174553425 | etot = -5.62847190590253 +346000 ekin = 4.74786790539194 | erot = 4.01955036383976 | epot = -14.3958901756728 | etot = -5.62847190644112 +347000 ekin = 4.79150376885693 | erot = 4.150195298843 | epot = -14.5701709744941 | etot = -5.62847190679421 +348000 ekin = 4.81117855585102 | erot = 4.27877359764447 | epot = -14.7184240605438 | etot = -5.62847190704836 +349000 ekin = 4.80564918858945 | erot = 4.40205662692375 | epot = -14.8361777226801 | etot = -5.62847190716692 +350000 ekin = 4.77545945328785 | erot = 4.51714564005358 | epot = -14.9210770005337 | etot = -5.6284719071923 +351000 ekin = 4.72262273321844 | erot = 4.62116010888509 | epot = -14.9722547493068 | etot = -5.6284719072033 +352000 ekin = 4.65007958813933 | erot = 4.71078593021054 | epot = -14.9893374256289 | etot = -5.62847190727905 +353000 ekin = 4.56109157465084 | erot = 4.7818033558395 | epot = -14.9713668379523 | etot = -5.62847190746193 +354000 ekin = 4.45876151246233 | erot = 4.82895979647354 | epot = -14.9161932166581 | etot = -5.62847190772226 +355000 ekin = 4.34584612945194 | erot = 4.84663553108728 | epot = -14.8209535684629 | etot = -5.62847190792371 +356000 ekin = 4.22495470320642 | erot = 4.83038190908647 | epot = -14.6838085201814 | etot = -5.62847190788853 +357000 ekin = 4.09903296594494 | erot = 4.77873075093466 | epot = -14.5062356243611 | etot = -5.62847190748155 +358000 ekin = 3.9717866755574 | erot = 4.69444561049284 | epot = -14.2947041927586 | etot = -5.62847190670838 +359000 ekin = 3.84767298929259 | erot = 4.58431182213288 | epot = -14.0604567171772 | etot = -5.62847190575173 +360000 ekin = 3.73136439808524 | erot = 4.45746613157388 | epot = -13.8173024344164 | etot = -5.62847190475726 +361000 ekin = 3.62758093165437 | erot = 4.32379064505124 | epot = -13.5798434807365 | etot = -5.62847190403088 +362000 ekin = 3.54294892306734 | erot = 4.19358097114317 | epot = -13.3650017978873 | etot = -5.6284719036768 +363000 ekin = 3.4783731169159 | erot = 4.07207692082171 | epot = -13.1789219412944 | etot = -5.62847190355681 +364000 ekin = 3.43225009806439 | erot = 3.96193194141655 | epot = -13.0226539430675 | etot = -5.62847190358656 +365000 ekin = 3.4019838846394 | erot = 3.86460642705253 | epot = -12.8950622153762 | etot = -5.6284719036843 +366000 ekin = 3.38451833852897 | erot = 3.78104622244587 | epot = -12.7940364647553 | etot = -5.6284719037805 +367000 ekin = 3.37682483158841 | erot = 3.71218000857274 | epot = -12.7174767440016 | etot = -5.62847190384047 +368000 ekin = 3.37625204139247 | erot = 3.65912147822663 | epot = -12.6638454234711 | etot = -5.62847190385203 +369000 ekin = 3.38074636727487 | erot = 3.623126803443 | epot = -12.6323450745421 | etot = -5.62847190382426 +370000 ekin = 3.38894636699412 | erot = 3.60538856636911 | epot = -12.6228068371819 | etot = -5.62847190381867 +371000 ekin = 3.40011634060655 | erot = 3.60672333637796 | epot = -12.6353115807301 | etot = -5.6284719037456 +372000 ekin = 3.41430323563517 | erot = 3.62748920223765 | epot = -12.6702643415699 | etot = -5.62847190369708 +373000 ekin = 3.43217624796222 | erot = 3.66740997408407 | epot = -12.7280581255881 | etot = -5.62847190354183 +374000 ekin = 3.4553831468672 | erot = 3.7253207076625 | epot = -12.8091757581561 | etot = -5.62847190362638 +375000 ekin = 3.48458983103952 | erot = 3.79950576965977 | epot = -12.912567504454 | etot = -5.62847190375469 +376000 ekin = 3.51994630864001 | erot = 3.88772077541255 | epot = -13.0361389879767 | etot = -5.62847190392415 +377000 ekin = 3.56162263239923 | erot = 3.987180320867 | epot = -13.1772748573584 | etot = -5.62847190409221 +378000 ekin = 3.61009229019707 | erot = 4.09470007581313 | epot = -13.3332642703131 | etot = -5.62847190430291 +379000 ekin = 3.66621939252838 | erot = 4.20668278515949 | epot = -13.5013740821291 | etot = -5.62847190444121 +380000 ekin = 3.73222313435908 | erot = 4.31893025305484 | epot = -13.6796252922915 | etot = -5.62847190487763 +381000 ekin = 3.80656943724393 | erot = 4.4266176909461 | epot = -13.8616590336395 | etot = -5.62847190544944 +382000 ekin = 3.88594558526958 | erot = 4.52459411505758 | epot = -14.0390116064095 | etot = -5.6284719060823 +383000 ekin = 3.96695090000421 | erot = 4.60747433895036 | epot = -14.2028971456775 | etot = -5.6284719067229 +384000 ekin = 4.04619645068514 | erot = 4.66967915257686 | epot = -14.3443475105574 | etot = -5.6284719072954 +385000 ekin = 4.1209202913832 | erot = 4.70599192062627 | epot = -14.4553841196779 | etot = -5.6284719076684 +386000 ekin = 4.18945537163468 | erot = 4.71237691681053 | epot = -14.53030419655 | etot = -5.62847190810481 +387000 ekin = 4.24770733745657 | erot = 4.68531871643965 | epot = -14.5614979619493 | etot = -5.62847190805306 +388000 ekin = 4.29400518232787 | erot = 4.62433064765407 | epot = -14.5468077376916 | etot = -5.62847190770962 +389000 ekin = 4.32973751035657 | erot = 4.53230747815447 | epot = -14.4905168956744 | etot = -5.62847190716338 +390000 ekin = 4.35696496432711 | erot = 4.41432356915647 | epot = -14.3997604400514 | etot = -5.62847190656786 +391000 ekin = 4.37768888460796 | erot = 4.27672755001287 | epot = -14.2828883405568 | etot = -5.62847190593597 +392000 ekin = 4.39398588700514 | erot = 4.12625191225617 | epot = -14.1487097046405 | etot = -5.62847190537918 +393000 ekin = 4.407382411178 | erot = 3.96936593196168 | epot = -14.0052202479623 | etot = -5.62847190482259 +394000 ekin = 4.41937568155054 | erot = 3.81285278687815 | epot = -13.8607003730908 | etot = -5.6284719046621 +395000 ekin = 4.42988768163861 | erot = 3.66065946576253 | epot = -13.7190190519313 | etot = -5.6284719045302 +396000 ekin = 4.43847476588742 | erot = 3.515256032156 | epot = -13.5822027024342 | etot = -5.62847190439077 +397000 ekin = 4.44517728396547 | erot = 3.37891512777946 | epot = -13.4525643159608 | etot = -5.62847190421592 +398000 ekin = 4.45064950025449 | erot = 3.25392386318798 | epot = -13.3330452674381 | etot = -5.62847190399563 +399000 ekin = 4.45613851376774 | erot = 3.14269651881402 | epot = -13.2273069363796 | etot = -5.62847190379781 +400000 ekin = 4.46297608305081 | erot = 3.04745583064848 | epot = -13.1389038172436 | etot = -5.62847190354436 +401000 ekin = 4.4727554600107 | erot = 2.97053701410496 | epot = -13.0717643774743 | etot = -5.62847190335867 +402000 ekin = 4.48672336700456 | erot = 2.91396522579477 | epot = -13.0291604961389 | etot = -5.62847190333955 +403000 ekin = 4.50482841071939 | erot = 2.87870251808789 | epot = -13.0120028324216 | etot = -5.62847190361433 +404000 ekin = 4.52484325730244 | erot = 2.86379686213768 | epot = -13.0171120236908 | etot = -5.62847190425068 +405000 ekin = 4.54178669953282 | erot = 2.86535120567948 | epot = -13.0356098106883 | etot = -5.62847190547597 +406000 ekin = 4.54812186977377 | erot = 2.8756562345287 | epot = -13.0522500108982 | etot = -5.62847190659573 +407000 ekin = 4.53567765662368 | erot = 2.88781666332885 | epot = -13.0519662273735 | etot = -5.62847190742095 +408000 ekin = 4.49806839872552 | erot = 2.89717319274354 | epot = -13.0237134991179 | etot = -5.62847190764884 +409000 ekin = 4.43289041825336 | erot = 2.90293173428801 | epot = -12.9642940598164 | etot = -5.628471907275 +410000 ekin = 4.34222243511652 | erot = 2.9078457176288 | epot = -12.8785400592904 | etot = -5.62847190654505 +411000 ekin = 4.23122328981887 | erot = 2.91632332329652 | epot = -12.7760185189097 | etot = -5.62847190579429 +412000 ekin = 4.10591302468972 | erot = 2.93234263225436 | epot = -12.6667275621786 | etot = -5.62847190523456 +413000 ekin = 3.97147909136112 | erot = 2.95826875337514 | epot = -12.5582197496412 | etot = -5.62847190490499 +414000 ekin = 3.8316964532881 | erot = 2.99487215440368 | epot = -12.455040512434 | etot = -5.6284719047422 +415000 ekin = 3.68915556886498 | erot = 3.04191716153914 | epot = -12.3595446350685 | etot = -5.62847190466441 +416000 ekin = 3.54575553257353 | erot = 3.09878213614044 | epot = -12.2730095733252 | etot = -5.62847190461118 +417000 ekin = 3.40315271146257 | erot = 3.16484246792854 | epot = -12.1964670839421 | etot = -5.628471904551 +418000 ekin = 3.26306253873233 | erot = 3.23960054555629 | epot = -12.1311349887606 | etot = -5.62847190447202 +419000 ekin = 3.12743539445919 | erot = 3.3226586781321 | epot = -12.0785659769629 | etot = -5.62847190437166 +420000 ekin = 2.99854685247769 | erot = 3.41362396347574 | epot = -12.0406427202082 | etot = -5.62847190425476 +421000 ekin = 2.87901712491765 | erot = 3.51197880381345 | epot = -12.0194678328662 | etot = -5.62847190413511 +422000 ekin = 2.77174596051471 | erot = 3.61690112205625 | epot = -12.0171189866113 | etot = -5.62847190404032 +423000 ekin = 2.67973794663749 | erot = 3.72700827488463 | epot = -12.0352181255357 | etot = -5.62847190401359 +424000 ekin = 2.60579870927641 | erot = 3.8400271753046 | epot = -12.0742977886923 | etot = -5.6284719041113 +425000 ekin = 2.55208954526361 | erot = 3.95244167895215 | epot = -12.1330031286132 | etot = -5.6284719043974 +426000 ekin = 2.51954653043548 | erot = 4.05920212808865 | epot = -12.2072205634526 | etot = -5.62847190492845 +427000 ekin = 2.50725893889522 | erot = 4.15363681831345 | epot = -12.2893676629222 | etot = -5.62847190571357 +428000 ekin = 2.51210485173988 | erot = 4.22782399615356 | epot = -12.3684007545415 | etot = -5.62847190664806 +429000 ekin = 2.52911833231882 | erot = 4.27377369073059 | epot = -12.4313639305283 | etot = -5.62847190747891 +430000 ekin = 2.55284926699729 | erot = 4.28551618827135 | epot = -12.4668373631561 | etot = -5.62847190788745 +431000 ekin = 2.5792413941883 | erot = 4.26142412037033 | epot = -12.4691374222402 | etot = -5.62847190768156 +432000 ekin = 2.60692475465764 | erot = 4.20541068246136 | epot = -12.4408073440548 | etot = -5.62847190693575 +433000 ekin = 2.63712842981534 | erot = 4.12604912500974 | epot = -12.3916494607596 | etot = -5.62847190593452 +434000 ekin = 2.67245542240745 | erot = 4.03405948920888 | epot = -12.3349868166036 | etot = -5.62847190498728 +435000 ekin = 2.71543854639826 | erot = 3.93961255970321 | epot = -12.2835230103841 | etot = -5.62847190428263 +436000 ekin = 2.76760991341188 | erot = 3.85063248522776 | epot = -12.2467143025148 | etot = -5.62847190387521 +437000 ekin = 2.82920515671347 | erot = 3.77223859650038 | epot = -12.229915656939 | etot = -5.62847190372516 +438000 ekin = 2.89929820058543 | erot = 3.70707509974792 | epot = -12.2348452040997 | etot = -5.62847190376632 +439000 ekin = 2.97609334155065 | erot = 3.65590372388788 | epot = -12.2604689693773 | etot = -5.6284719039388 +440000 ekin = 3.0572090661252 | erot = 3.61815200783681 | epot = -12.3038329781609 | etot = -5.62847190419891 +441000 ekin = 3.13989672828484 | erot = 3.59232302399564 | epot = -12.3606916567967 | etot = -5.62847190451624 +442000 ekin = 3.22119927518209 | erot = 3.5762689251996 | epot = -12.4259401052536 | etot = -5.62847190487189 +443000 ekin = 3.29807867301552 | erot = 3.56737972996007 | epot = -12.4939303082211 | etot = -5.62847190524554 +444000 ekin = 3.36753883943484 | erot = 3.56276348927419 | epot = -12.558774234326 | etot = -5.62847190561699 +445000 ekin = 3.42676046580584 | erot = 3.55942025918996 | epot = -12.6146526309598 | etot = -5.62847190596397 +446000 ekin = 3.47324383646413 | erot = 3.55443462309052 | epot = -12.656150365822 | etot = -5.62847190626738 +447000 ekin = 3.50497354375794 | erot = 3.54511419619786 | epot = -12.6785596464609 | etot = -5.62847190650513 +448000 ekin = 3.52056213082773 | erot = 3.52974100710159 | epot = -12.6787750444482 | etot = -5.62847190651887 +449000 ekin = 3.5193969659025 | erot = 3.5070590451093 | epot = -12.6549279176159 | etot = -5.62847190660407 +450000 ekin = 3.50164536052708 | erot = 3.47565071065802 | epot = -12.6057679777836 | etot = -5.62847190659851 +451000 ekin = 3.46824790706761 | erot = 3.43472151202269 | epot = -12.5314413255905 | etot = -5.62847190650017 +452000 ekin = 3.42090312735532 | erot = 3.3841455872896 | epot = -12.4335206209555 | etot = -5.62847190631062 +453000 ekin = 3.36201791827153 | erot = 3.32449206044985 | epot = -12.3149818847562 | etot = -5.62847190603485 +454000 ekin = 3.29463316059154 | erot = 3.25701739818569 | epot = -12.18012246446 | etot = -5.62847190568276 +455000 ekin = 3.22233274897233 | erot = 3.18360703276273 | epot = -12.034411687003 | etot = -5.62847190526794 +456000 ekin = 3.14914248627045 | erot = 3.10666992197473 | epot = -11.8842843130546 | etot = -5.62847190480945 +457000 ekin = 3.07939737171287 | erot = 3.02894564057903 | epot = -11.7368149166299 | etot = -5.62847190433799 +458000 ekin = 3.01756413266252 | erot = 2.95322108561951 | epot = -11.5992571221324 | etot = -5.62847190385035 +459000 ekin = 2.96810632521944 | erot = 2.88249754735581 | epot = -11.4790757759786 | etot = -5.62847190340336 +460000 ekin = 2.93513889001201 | erot = 2.81955267520362 | epot = -11.3831634682489 | etot = -5.62847190303332 +461000 ekin = 2.92205746386829 | erot = 2.76669234907485 | epot = -11.3172217157212 | etot = -5.62847190277803 +462000 ekin = 2.93114290148975 | erot = 2.72556812595398 | epot = -11.2851829301146 | etot = -5.6284719026709 +463000 ekin = 2.96319319679128 | erot = 2.69703193761113 | epot = -11.2886970371374 | etot = -5.62847190273498 +464000 ekin = 3.01726238568043 | erot = 2.68105615129969 | epot = -11.3267904399539 | etot = -5.62847190297383 +465000 ekin = 3.09058398931785 | erot = 2.67674994758914 | epot = -11.3958058402755 | etot = -5.62847190336855 +466000 ekin = 3.17872270900157 | erot = 2.68248866700197 | epot = -11.4896832798828 | etot = -5.62847190387923 +467000 ekin = 3.2759411449618 | erot = 2.69614045585464 | epot = -11.6005535052698 | etot = -5.62847190445338 +468000 ekin = 3.37571282133989 | erot = 2.71534026240071 | epot = -11.7195249887787 | etot = -5.62847190503812 +469000 ekin = 3.47128178262914 | erot = 2.73774679763144 | epot = -11.8375004858492 | etot = -5.62847190558859 +470000 ekin = 3.55617737699083 | erot = 2.76123628661372 | epot = -11.9458855696774 | etot = -5.62847190607284 +471000 ekin = 3.62463309399455 | erot = 2.78402790003972 | epot = -12.037132900502 | etot = -5.62847190646776 +472000 ekin = 3.67190559891936 | erot = 2.8047712477889 | epot = -12.1051487534637 | etot = -5.62847190675547 +473000 ekin = 3.69451868440097 | erot = 2.82263116141252 | epot = -12.1456217527324 | etot = -5.62847190691896 +474000 ekin = 3.69045746330193 | erot = 2.8373788256899 | epot = -12.1563081959362 | etot = -5.6284719069444 +475000 ekin = 3.65932116349145 | erot = 2.84946541727408 | epot = -12.1372584875892 | etot = -5.62847190682371 +476000 ekin = 3.60242486136646 | erot = 2.86004016499196 | epot = -12.0909369329169 | etot = -5.62847190655849 +477000 ekin = 3.52282746237732 | erot = 2.87088465736214 | epot = -12.0221840258998 | etot = -5.62847190616038 +478000 ekin = 3.42525452627518 | erot = 2.88424967270887 | epot = -11.9379761046485 | etot = -5.62847190566447 +479000 ekin = 3.31588349736502 | erot = 2.90254646897039 | epot = -11.8469018714502 | etot = -5.62847190511476 +480000 ekin = 3.20192949243302 | erot = 2.92801081391733 | epot = -11.7584122109274 | etot = -5.62847190457704 +481000 ekin = 3.09102106838258 | erot = 2.96227510041685 | epot = -11.6817680729317 | etot = -5.62847190413228 +482000 ekin = 2.99039932399026 | erot = 3.00590839370206 | epot = -11.6247796215548 | etot = -5.62847190386249 +483000 ekin = 2.9060569334269 | erot = 3.05799802965361 | epot = -11.5925268669148 | etot = -5.62847190383431 +484000 ekin = 2.8420017152304 | erot = 3.11586840864788 | epot = -11.5863420279555 | etot = -5.62847190407723 +485000 ekin = 2.81072036468127 | erot = 3.0366554646563 | epot = -11.4758477218727 | etot = -5.62847189253513 +486000 ekin = 2.99172671789725 | erot = 2.89028588608556 | epot = -11.5104845147091 | etot = -5.62847191072628 +487000 ekin = 3.04661020882518 | erot = 2.89516257155138 | epot = -11.5702446860095 | etot = -5.62847190563292 +488000 ekin = 3.02813445461698 | erot = 2.91755814175566 | epot = -11.5741645019067 | etot = -5.62847190553406 +489000 ekin = 3.02918173189716 | erot = 2.94703274342865 | epot = -11.6046863809268 | etot = -5.62847190560097 +490000 ekin = 3.04920929975595 | erot = 2.9829992143947 | epot = -11.6606804199702 | etot = -5.62847190581958 +491000 ekin = 3.0856462342284 | erot = 3.02458607702748 | epot = -11.7387042173738 | etot = -5.62847190611796 +492000 ekin = 3.13426650215918 | erot = 3.07113014038627 | epot = -11.8338685489821 | etot = -5.6284719064367 +493000 ekin = 3.19024782357284 | erot = 3.122467363769 | epot = -11.9411870939865 | etot = -5.62847190664467 +494000 ekin = 3.24418110404638 | erot = 3.17757093527559 | epot = -12.0502240478375 | etot = -5.62847200851552 +495000 ekin = 3.12930691887915 | erot = 3.12025770006845 | epot = -11.878036533776 | etot = -5.62847191482835 +496000 ekin = 3.38154400850358 | erot = 3.12702216682433 | epot = -12.137038139537 | etot = -5.62847196420913 +497000 ekin = 3.53796334305638 | erot = 3.21345240185708 | epot = -12.3798876661503 | etot = -5.62847192123686 +498000 ekin = 3.5472524224632 | erot = 3.31274815695996 | epot = -12.4884725006775 | etot = -5.62847192125435 +499000 ekin = 3.54686752393915 | erot = 3.42936350672876 | epot = -12.6047029520135 | etot = -5.62847192134559 +500000 ekin = 3.53611629145095 | erot = 3.56214471850545 | epot = -12.7267329314686 | etot = -5.62847192151223 +501000 ekin = 3.51474019584732 | erot = 3.70831240064401 | epot = -12.8515245182491 | etot = -5.62847192175777 +502000 ekin = 3.48291543617567 | erot = 3.86351597860162 | epot = -12.9749033367677 | etot = -5.62847192199039 +503000 ekin = 3.44167367984815 | erot = 4.02200657197324 | epot = -13.0921521741687 | etot = -5.62847192234736 +504000 ekin = 3.39166561938554 | erot = 4.17733332044561 | epot = -13.1974708625716 | etot = -5.62847192274041 +505000 ekin = 3.33344269451329 | erot = 4.32266370129412 | epot = -13.284578318939 | etot = -5.62847192313161 +506000 ekin = 3.26726906280024 | erot = 4.45157764165941 | epot = -13.3473186278586 | etot = -5.62847192339891 +507000 ekin = 3.19388361650053 | erot = 4.55898983231483 | epot = -13.3813453723001 | etot = -5.62847192348474 +508000 ekin = 3.11462724049546 | erot = 4.64207406474173 | epot = -13.3851732285711 | etot = -5.62847192333393 +509000 ekin = 3.0315455189067 | erot = 4.70083202645973 | epot = -13.3608494683217 | etot = -5.6284719229553 +510000 ekin = 2.9451305861194 | erot = 4.73730594224089 | epot = -13.310908450846 | etot = -5.62847192248573 +511000 ekin = 2.85640718494572 | erot = 4.75516581384411 | epot = -13.2400449207109 | etot = -5.6284719219211 +512000 ekin = 2.76854482524938 | erot = 4.75962991524818 | epot = -13.1566466618619 | etot = -5.62847192136436 +513000 ekin = 2.68465921482692 | erot = 4.75599513195416 | epot = -13.0691262676793 | etot = -5.62847192089823 +514000 ekin = 2.6074556831351 | erot = 4.74870168660358 | epot = -12.9846292903215 | etot = -5.62847192058282 +515000 ekin = 2.53899080263134 | erot = 4.74082869238536 | epot = -12.908291415422 | etot = -5.62847192040532 +516000 ekin = 2.48057862895574 | erot = 4.73416754062336 | epot = -12.8432180899356 | etot = -5.62847192035646 +517000 ekin = 2.43281299018871 | erot = 4.729336510708 | epot = -12.7906214212996 | etot = -5.62847192040289 +518000 ekin = 2.39567246199112 | erot = 4.72611868192627 | epot = -12.7502630644219 | etot = -5.62847192050451 +519000 ekin = 2.3686800807562 | erot = 4.7238616345607 | epot = -12.7210136359372 | etot = -5.62847192062029 +520000 ekin = 2.35109068029861 | erot = 4.72186744274753 | epot = -12.7014300437606 | etot = -5.62847192071449 +521000 ekin = 2.34207426122085 | erot = 4.71970227698317 | epot = -12.6902484589699 | etot = -5.62847192076585 +522000 ekin = 2.34085858394716 | erot = 4.71735113725647 | epot = -12.6866816419765 | etot = -5.62847192077292 +523000 ekin = 2.34541603963217 | erot = 4.65571671261041 | epot = -12.6296046827242 | etot = -5.62847193048164 +524000 ekin = 2.39460269539116 | erot = 4.5440923966837 | epot = -12.5671670123536 | etot = -5.62847192027874 +525000 ekin = 2.51755565348171 | erot = 4.49060445320171 | epot = -12.636632032408 | etot = -5.62847192572459 +526000 ekin = 2.63891940338544 | erot = 4.4967002612617 | epot = -12.7640916024326 | etot = -5.62847193778544 +527000 ekin = 2.68130557076743 | erot = 4.50503337375349 | epot = -12.814810874615 | etot = -5.62847193009407 +528000 ekin = 2.71450795009193 | erot = 4.51098798629199 | epot = -12.8539678665778 | etot = -5.62847193019388 +529000 ekin = 2.74727192392954 | erot = 4.51402301142482 | epot = -12.8897668656182 | etot = -5.62847193026387 +530000 ekin = 2.77952118313263 | erot = 4.51256666252134 | epot = -12.9205597759442 | etot = -5.62847193029021 +531000 ekin = 2.81130699778271 | erot = 4.50555264766032 | epot = -12.9453315757121 | etot = -5.62847193026907 +532000 ekin = 2.84274553227055 | erot = 4.49253106979351 | epot = -12.963748532273 | etot = -5.62847193020897 +533000 ekin = 2.87393313769259 | erot = 4.47361780232379 | epot = -12.9760228701465 | etot = -5.62847193013013 +534000 ekin = 2.90486933807277 | erot = 4.44928844614865 | epot = -12.9826297142772 | etot = -5.62847193005582 +535000 ekin = 2.93541519864921 | erot = 4.42010482063592 | epot = -12.9839919492869 | etot = -5.62847193000178 +536000 ekin = 2.96529830147375 | erot = 4.38649798394161 | epot = -12.9802682153877 | etot = -5.62847192997236 +537000 ekin = 2.99415467150676 | erot = 4.34867665835148 | epot = -12.9713032598109 | etot = -5.62847192995265 +538000 ekin = 3.02158801649127 | erot = 4.30669342608826 | epot = -12.9567533725319 | etot = -5.62847192995239 +539000 ekin = 3.0472284437342 | erot = 4.26048951904593 | epot = -12.9361898927285 | etot = -5.62847192994839 +540000 ekin = 3.07077963644109 | erot = 4.21000980478691 | epot = -12.9092613711594 | etot = -5.62847192993142 +541000 ekin = 3.09204730617341 | erot = 4.15535061585768 | epot = -12.8758698519278 | etot = -5.62847192989669 +542000 ekin = 3.11094831334513 | erot = 4.09682671838946 | epot = -12.8362469615783 | etot = -5.62847192984375 +543000 ekin = 3.12750284884244 | erot = 4.03499383131399 | epot = -12.7909686099319 | etot = -5.62847192977543 +544000 ekin = 3.14181233919874 | erot = 3.97062692620924 | epot = -12.7409111951085 | etot = -5.62847192970057 +545000 ekin = 3.154023692805 | erot = 3.90462208416962 | epot = -12.687117706602 | etot = -5.62847192962739 +546000 ekin = 3.16427777380063 | erot = 3.83809465727444 | epot = -12.6308443606344 | etot = -5.62847192955928 +547000 ekin = 3.17263245318144 | erot = 3.77248542237236 | epot = -12.5735898050858 | etot = -5.62847192953204 +548000 ekin = 3.17905114130834 | erot = 3.70842416475025 | epot = -12.5159472355979 | etot = -5.6284719295393 +549000 ekin = 3.18335924855427 | erot = 3.64619443422522 | epot = -12.4580256123189 | etot = -5.62847192953942 +550000 ekin = 3.18506506662759 | erot = 3.58603484427807 | epot = -12.399571840559 | etot = -5.62847192965338 +551000 ekin = 3.18354118868716 | erot = 3.52751972613345 | epot = -12.3395328446127 | etot = -5.62847192979206 +552000 ekin = 3.17814056102138 | erot = 3.46973317227534 | epot = -12.2763456632303 | etot = -5.62847192993357 +553000 ekin = 3.16816249049593 | erot = 3.4118771629174 | epot = -12.2085115834581 | etot = -5.62847193004478 +554000 ekin = 3.15297464057581 | erot = 3.35363386890657 | epot = -12.1350804395706 | etot = -5.62847193008825 +555000 ekin = 3.13218065542941 | erot = 3.29554931589494 | epot = -12.0562019013542 | etot = -5.62847193002985 +556000 ekin = 3.10581995743369 | erot = 3.23932890452414 | epot = -11.9736207918045 | etot = -5.62847192984666 +557000 ekin = 3.07457883897345 | erot = 3.18795403305513 | epot = -11.8910048015597 | etot = -5.62847192953115 +558000 ekin = 3.039982626527 | erot = 3.14553707333998 | epot = -11.8139916289764 | etot = -5.62847192910947 +559000 ekin = 3.00450378984011 | erot = 3.11693712835302 | epot = -11.7499128467748 | etot = -5.6284719285817 +560000 ekin = 2.97145203621646 | erot = 3.10758181985049 | epot = -11.7075057840903 | etot = -5.62847192802332 +561000 ekin = 2.94451934101013 | erot = 3.12267269753501 | epot = -11.6956639661101 | etot = -5.62847192756497 +562000 ekin = 2.92714140956565 | erot = 3.16633554922539 | epot = -11.7219488860399 | etot = -5.6284719272489 +563000 ekin = 2.92206147624849 | erot = 3.24077054354643 | epot = -11.791303946995 | etot = -5.62847192720009 +564000 ekin = 2.93031627653502 | erot = 3.3456341095667 | epot = -11.9044223136023 | etot = -5.62847192750056 +565000 ekin = 2.95068712290038 | erot = 3.47751232964411 | epot = -12.0566713806991 | etot = -5.62847192815461 +566000 ekin = 2.97962685518711 | erot = 3.62985521358398 | epot = -12.2379539978968 | etot = -5.62847192912568 +567000 ekin = 3.01171593572638 | erot = 3.79324477340409 | epot = -12.4334326394467 | etot = -5.62847193031621 +568000 ekin = 3.04054477444357 | erot = 3.956100491764 | epot = -12.6251171977961 | etot = -5.62847193158857 +569000 ekin = 3.05981811076081 | erot = 4.10576505738188 | epot = -12.7940551009263 | etot = -5.62847193278365 +570000 ekin = 3.06446758294588 | erot = 4.22987220713965 | epot = -12.9228117238275 | etot = -5.62847193374201 +571000 ekin = 3.05159191037886 | erot = 4.31782950110594 | epot = -12.9978933458114 | etot = -5.62847193432658 +572000 ekin = 3.02108996836103 | erot = 4.36217384044962 | epot = -13.0117357432594 | etot = -5.6284719344488 +573000 ekin = 2.97589592642991 | erot = 4.3595336444915 | epot = -12.9639015050087 | etot = -5.6284719340873 +574000 ekin = 2.92177260944326 | erot = 4.31098813648668 | epot = -12.8612326792292 | etot = -5.62847193329925 +575000 ekin = 2.86675845142752 | erot = 4.22206447603994 | epot = -12.7172948575062 | etot = -5.62847193003876 +576000 ekin = 2.82238695041546 | erot = 4.1100210869994 | epot = -12.5608799669327 | etot = -5.62847192951789 +577000 ekin = 2.79586021285995 | erot = 3.98405314233133 | epot = -12.408385284279 | etot = -5.62847192908767 +578000 ekin = 2.7906267864783 | erot = 3.84816173899177 | epot = -12.2672604543186 | etot = -5.62847192884853 +579000 ekin = 2.80727876764756 | erot = 3.70630768396951 | epot = -12.1420583804494 | etot = -5.62847192883231 +580000 ekin = 2.84308800285077 | erot = 3.56147502221966 | epot = -12.0330349543698 | etot = -5.62847192929934 +581000 ekin = 2.89275945170175 | erot = 3.41677708036916 | epot = -11.9380084614447 | etot = -5.62847192937377 +582000 ekin = 2.94948274099937 | erot = 3.27852635629874 | epot = -11.8564810267415 | etot = -5.62847192944344 +583000 ekin = 3.00600312782226 | erot = 3.15339507866366 | epot = -11.7878701359128 | etot = -5.6284719294269 +584000 ekin = 3.05615870304061 | erot = 3.04800743032635 | epot = -11.7326380626692 | etot = -5.62847192930228 +585000 ekin = 3.09596263909699 | erot = 2.96828908152495 | epot = -11.692723649714 | etot = -5.62847192909207 +586000 ekin = 3.12407298200318 | erot = 2.91878541589392 | epot = -11.6713303267248 | etot = -5.62847192882776 +587000 ekin = 3.14174614221827 | erot = 2.90225430093616 | epot = -11.6724723716926 | etot = -5.6284719285382 +588000 ekin = 3.15240031622927 | erot = 2.91960613643676 | epot = -11.7004783809276 | etot = -5.62847192826162 +589000 ekin = 3.16081808257205 | erot = 2.97006448175184 | epot = -11.7593544923648 | etot = -5.62847192804094 +590000 ekin = 3.17204827385661 | erot = 3.05134069928938 | epot = -11.8518609010626 | etot = -5.62847192791657 +591000 ekin = 3.19150299839625 | erot = 3.16015018734539 | epot = -11.980125113735 | etot = -5.62847192799339 +592000 ekin = 3.22264872303177 | erot = 3.29204057518903 | epot = -12.1431612265392 | etot = -5.62847192831836 +593000 ekin = 3.26585695463954 | erot = 3.44092346941412 | epot = -12.3352523529135 | etot = -5.62847192885986 +594000 ekin = 3.31918005195762 | erot = 3.59965335605276 | epot = -12.5473053375762 | etot = -5.62847192956578 +595000 ekin = 3.37897127082535 | erot = 3.76045843946065 | epot = -12.7679016405769 | etot = -5.62847193029094 +596000 ekin = 3.43824068577806 | erot = 3.91359738330063 | epot = -12.9803100017047 | etot = -5.62847193262601 +597000 ekin = 3.48744876796665 | erot = 4.04782437865019 | epot = -13.1637450798766 | etot = -5.62847193325977 +598000 ekin = 3.52187002168153 | erot = 4.15698580429437 | epot = -13.3073277595898 | etot = -5.62847193361392 +599000 ekin = 3.53831455069841 | erot = 4.23767846714294 | epot = -13.404464951527 | etot = -5.62847193368565 +600000 ekin = 3.53510970427265 | erot = 4.28920847107757 | epot = -13.4527901088679 | etot = -5.62847193351773 +601000 ekin = 3.51191041814697 | erot = 4.31320178197176 | epot = -13.4535841332986 | etot = -5.62847193317987 +602000 ekin = 3.46937521142842 | erot = 4.31295152741579 | epot = -13.4107986715908 | etot = -5.62847193274656 +603000 ekin = 3.40882221237635 | erot = 4.29270411929989 | epot = -13.3299982639554 | etot = -5.62847193227922 +604000 ekin = 3.33194570978535 | erot = 4.25705245865312 | epot = -13.2174701002569 | etot = -5.62847193181846 +605000 ekin = 3.24062643784222 | erot = 4.210522480391 | epot = -13.0796208496176 | etot = -5.62847193138435 +606000 ekin = 3.13683319322748 | erot = 4.15735875797083 | epot = -12.9226638821792 | etot = -5.62847193098084 +607000 ekin = 3.02259481107363 | erot = 4.10146703773365 | epot = -12.7525337794094 | etot = -5.62847193060207 +608000 ekin = 2.9000165225881 | erot = 4.04645475157337 | epot = -12.5749432043994 | etot = -5.62847193023795 +609000 ekin = 2.77131728807406 | erot = 3.99571460781604 | epot = -12.3955038257683 | etot = -5.62847192987821 +610000 ekin = 2.63886938890257 | erot = 3.95250622991957 | epot = -12.2198475483386 | etot = -5.62847192951647 +611000 ekin = 2.50524882250675 | erot = 3.92003293779097 | epot = -12.0537536891604 | etot = -5.62847192886263 +612000 ekin = 2.37382087282126 | erot = 3.9021886985529 | epot = -11.9044814999079 | etot = -5.62847192853369 +613000 ekin = 2.24769613363947 | erot = 3.90186788751219 | epot = -11.7780359493765 | etot = -5.6284719282248 +614000 ekin = 2.12975142863874 | erot = 3.92103062116472 | epot = -11.6792539777815 | etot = -5.628471927978 +615000 ekin = 2.02283676464884 | erot = 3.96080056830494 | epot = -11.6121092607819 | etot = -5.62847192782813 +616000 ekin = 1.92967019044788 | erot = 4.02099162186384 | epot = -11.57913374012 | etot = -5.62847192780826 +617000 ekin = 1.8527379185958 | erot = 4.09974474407168 | epot = -11.580954590615 | etot = -5.6284719279475 +618000 ekin = 1.79420296292888 | erot = 4.19322703625556 | epot = -11.6159019274439 | etot = -5.62847192825941 +619000 ekin = 1.75583197425834 | erot = 4.29552606649958 | epot = -11.6798299694868 | etot = -5.62847192872885 +620000 ekin = 1.73895870095566 | erot = 4.39891672377769 | epot = -11.7663473540353 | etot = -5.62847192930197 +621000 ekin = 1.74449834713472 | erot = 4.49462250669341 | epot = -11.8675927837155 | etot = -5.62847192988733 +622000 ekin = 1.77300875725242 | erot = 4.5740351809646 | epot = -11.9755158685958 | etot = -5.6284719303788 +623000 ekin = 1.82476626664742 | erot = 4.63011744401454 | epot = -12.0833556413538 | etot = -5.62847193069181 +624000 ekin = 1.89980556095141 | erot = 4.65854151401442 | epot = -12.1868190057611 | etot = -5.62847193079527 +625000 ekin = 1.99788931006729 | erot = 4.658170601704 | epot = -12.2845318424889 | etot = -5.62847193071759 +626000 ekin = 2.11841939006965 | erot = 4.63077870094526 | epot = -12.3776700215405 | etot = -5.62847193052559 +627000 ekin = 2.26034340499143 | erot = 4.58024268398231 | epot = -12.4690580192627 | etot = -5.62847193028895 +628000 ekin = 2.42211143981235 | erot = 4.51161612054104 | epot = -12.5621994904152 | etot = -5.6284719300618 +629000 ekin = 2.60047669410469 | erot = 4.43316974508954 | epot = -12.6621183685955 | etot = -5.62847192940125 +630000 ekin = 2.75035749002553 | erot = 4.31003905751206 | epot = -12.6888685132419 | etot = -5.6284719657043 +631000 ekin = 2.81471524142372 | erot = 4.11774535992748 | epot = -12.5609325371121 | etot = -5.62847193576093 +632000 ekin = 2.95867552213366 | erot = 4.07926707205796 | epot = -12.6664145270595 | etot = -5.62847193286783 +633000 ekin = 3.21010693588802 | erot = 4.20581326818634 | epot = -13.0443921661487 | etot = -5.62847196207437 +634000 ekin = 3.41641131494308 | erot = 4.25928215931025 | epot = -13.3041654106216 | etot = -5.62847193636831 +635000 ekin = 3.57385274070359 | erot = 4.24018711603685 | epot = -13.4425117938791 | etot = -5.62847193713862 +636000 ekin = 3.71894531188287 | erot = 4.21896102707019 | epot = -13.5663782769278 | etot = -5.62847193797475 +637000 ekin = 3.84555962844877 | erot = 4.19009538997716 | epot = -13.6641269570962 | etot = -5.62847193867029 +638000 ekin = 3.9487423272224 | erot = 4.14881281932708 | epot = -13.7260270855885 | etot = -5.62847193903898 +639000 ekin = 4.02564653200958 | erot = 4.09271382127595 | epot = -13.7468322922904 | etot = -5.62847193900491 +640000 ekin = 4.07582551368556 | erot = 4.02260436127816 | epot = -13.7269018135812 | etot = -5.62847193861744 +641000 ekin = 4.10019063766136 | erot = 3.9420341957623 | epot = -13.6706967718879 | etot = -5.62847193846427 +642000 ekin = 4.09923585995082 | erot = 3.85569636521082 | epot = -13.5834041630469 | etot = -5.62847193788524 +643000 ekin = 4.076160799789 | erot = 3.76850329644278 | epot = -13.4731360335927 | etot = -5.62847193736088 +644000 ekin = 4.03483546303947 | erot = 3.684285384223 | epot = -13.3475927842093 | etot = -5.62847193694681 +645000 ekin = 3.97939693531423 | erot = 3.60521279256606 | epot = -13.2130816645055 | etot = -5.62847193662522 +646000 ekin = 3.91424157389645 | erot = 3.53197746524735 | epot = -13.0746909754864 | etot = -5.62847193634258 +647000 ekin = 3.84412108349711 | erot = 3.46430751183409 | epot = -12.9369005315148 | etot = -5.62847193618361 +648000 ekin = 3.77442093445477 | erot = 3.40030625105817 | epot = -12.803199121379 | etot = -5.62847193586601 +649000 ekin = 3.71064844398661 | erot = 3.33902116866496 | epot = -12.6781415481958 | etot = -5.62847193554422 +650000 ekin = 3.65777288959165 | erot = 3.28036981765265 | epot = -12.566614642516 | etot = -5.62847193527174 +651000 ekin = 3.61962254750334 | erot = 3.22458240437371 | epot = -12.472676886972 | etot = -5.62847193509499 +652000 ekin = 3.59838866979736 | erot = 3.17201593045824 | epot = -12.3988765352881 | etot = -5.62847193503253 +653000 ekin = 3.59447660058636 | erot = 3.12302902489766 | epot = -12.3459775605516 | etot = -5.62847193506762 +654000 ekin = 3.60674141920663 | erot = 3.07797678372272 | epot = -12.3131901380894 | etot = -5.62847193516007 +655000 ekin = 3.6329884131312 | erot = 3.03728497080441 | epot = -12.2987453192067 | etot = -5.62847193527112 +656000 ekin = 3.67052655529805 | erot = 3.0014799030164 | epot = -12.3004783937023 | etot = -5.62847193538784 +657000 ekin = 3.71734630704556 | erot = 2.97084073554921 | epot = -12.3166589779895 | etot = -5.6284719353947 +658000 ekin = 3.75778663136504 | erot = 2.948729408581 | epot = -12.3349879987356 | etot = -5.62847195878952 +659000 ekin = 3.70128994139008 | erot = 2.99267200683485 | epot = -12.3224338839538 | etot = -5.62847193572891 +660000 ekin = 3.77980484686181 | erot = 3.05081678602526 | epot = -12.4590935969641 | etot = -5.62847196407706 +661000 ekin = 3.87674047133219 | erot = 3.02043722445613 | epot = -12.525649641152 | etot = -5.62847194536372 +662000 ekin = 3.96189665312922 | erot = 2.9729451065927 | epot = -12.5633137060284 | etot = -5.62847194630644 +663000 ekin = 4.03233992122775 | erot = 2.90724728967763 | epot = -12.5680591572364 | etot = -5.62847194633099 +664000 ekin = 4.08703350786687 | erot = 2.82371074129416 | epot = -12.5392161949729 | etot = -5.62847194581183 +665000 ekin = 4.13016908280354 | erot = 2.72591755769948 | epot = -12.4845585855571 | etot = -5.62847194505411 +666000 ekin = 4.16485763698556 | erot = 2.62158318068883 | epot = -12.4149127617504 | etot = -5.628471944076 +667000 ekin = 4.1938844423827 | erot = 2.52048046560673 | epot = -12.3428368513072 | etot = -5.6284719433178 +668000 ekin = 4.21970111369211 | erot = 2.43117566540558 | epot = -12.2793487218641 | etot = -5.62847194276645 +669000 ekin = 4.24419480066981 | erot = 2.35970998754456 | epot = -12.2323767306212 | etot = -5.62847194240684 +670000 ekin = 4.26650932844503 | erot = 2.31009212977909 | epot = -12.2050734005021 | etot = -5.62847194227794 +671000 ekin = 4.28028750584352 | erot = 2.28394068949395 | epot = -12.1927001375629 | etot = -5.62847194222542 +672000 ekin = 4.28604953818529 | erot = 2.28087700943569 | epot = -12.1953984898105 | etot = -5.62847194218953 +673000 ekin = 4.28538320985138 | erot = 2.29981058111549 | epot = -12.2136657331125 | etot = -5.62847194214558 +674000 ekin = 4.28032637890109 | erot = 2.33931519991151 | epot = -12.2481135209176 | etot = -5.62847194210497 +675000 ekin = 4.27310613147522 | erot = 2.3977054633075 | epot = -12.2992835368984 | etot = -5.62847194211566 +676000 ekin = 4.26563141847785 | erot = 2.47283047851769 | epot = -12.3669338392713 | etot = -5.62847194227575 +677000 ekin = 4.25873601028162 | erot = 2.5615947513181 | epot = -12.4488027042337 | etot = -5.62847194263396 +678000 ekin = 4.25154383411717 | erot = 2.65951246657549 | epot = -12.5395282439332 | etot = -5.62847194324054 +679000 ekin = 4.24120573467262 | erot = 2.76057514745448 | epot = -12.6302528261675 | etot = -5.62847194404044 +680000 ekin = 4.2232005118335 | erot = 2.85770689098673 | epot = -12.7093793476907 | etot = -5.62847194487046 +681000 ekin = 4.19242845454634 | erot = 2.94400272540728 | epot = -12.7649031254536 | etot = -5.62847194549999 +682000 ekin = 4.14477706340841 | erot = 3.01435956380649 | epot = -12.7876085729617 | etot = -5.62847194574678 +683000 ekin = 4.07850194582787 | erot = 3.06669689301665 | epot = -12.7736707844063 | etot = -5.62847194556178 +684000 ekin = 3.98766788584427 | erot = 3.09062770647999 | epot = -12.7067675427114 | etot = -5.6284719503871 +685000 ekin = 3.87609976033734 | erot = 3.07213118853044 | epot = -12.5767028925454 | etot = -5.62847194367757 +686000 ekin = 3.78865422794909 | erot = 3.05379982528032 | epot = -12.4709259955805 | etot = -5.62847194235105 +687000 ekin = 3.72885638126477 | erot = 3.05128310396259 | epot = -12.4086114324593 | etot = -5.62847194723192 +688000 ekin = 3.65488085468173 | erot = 3.04382149764254 | epot = -12.3271742986651 | etot = -5.62847194634081 +689000 ekin = 3.57606770151101 | erot = 3.03834252499959 | epot = -12.2428821721451 | etot = -5.62847194563445 +690000 ekin = 3.51634425569074 | erot = 3.04775260792024 | epot = -12.1925688087327 | etot = -5.62847194512173 +691000 ekin = 3.47971445755389 | erot = 3.0762235847613 | epot = -12.1844099871832 | etot = -5.62847194486798 +692000 ekin = 3.46765181271641 | erot = 3.12642449715769 | epot = -12.2225482548088 | etot = -5.62847194493469 +693000 ekin = 3.47854301569186 | erot = 3.19918358098414 | epot = -12.3061985420115 | etot = -5.62847194533546 +694000 ekin = 3.50760869816785 | erot = 3.29340441046179 | epot = -12.4294850546422 | etot = -5.62847194601257 +695000 ekin = 3.54747029179261 | erot = 3.4063794790627 | epot = -12.5823217177036 | etot = -5.62847194684826 +696000 ekin = 3.58927155179387 | erot = 3.53441505487526 | epot = -12.7521585543738 | etot = -5.62847194770465 +697000 ekin = 3.62399868536214 | erot = 3.67347767298908 | epot = -12.9259483068109 | etot = -5.62847194845967 +698000 ekin = 3.64429609768408 | erot = 3.81929275592912 | epot = -13.0920608027184 | etot = -5.62847194910516 +699000 ekin = 3.64411727661991 | erot = 3.9682691228859 | epot = -13.2408583490265 | etot = -5.62847194952073 +700000 ekin = 3.61972386486635 | erot = 4.11779628916703 | epot = -13.3659921037213 | etot = -5.62847194968793 +701000 ekin = 3.57045543139896 | erot = 4.2660564512704 | epot = -13.4649838324058 | etot = -5.62847194973641 +702000 ekin = 3.49917622955587 | erot = 4.41037029504254 | epot = -13.5380184742101 | etot = -5.62847194961164 +703000 ekin = 3.41079978152663 | erot = 4.54773448487633 | epot = -13.5870062157827 | etot = -5.62847194937978 +704000 ekin = 3.3114965725397 | erot = 4.6756046409908 | epot = -13.6155731626146 | etot = -5.62847194908408 +705000 ekin = 3.20807903045004 | erot = 4.79162132898958 | epot = -13.6281723082223 | etot = -5.62847194878265 +706000 ekin = 3.10702043893515 | erot = 4.89365607515408 | epot = -13.6291484626345 | etot = -5.62847194854522 +707000 ekin = 3.01353531406683 | erot = 4.97967086429038 | epot = -13.6216781267981 | etot = -5.62847194844094 +708000 ekin = 2.93091332941399 | erot = 5.04739802068841 | epot = -13.6067832986194 | etot = -5.628471948517 +709000 ekin = 2.86026033869288 | erot = 5.09399325404994 | epot = -13.5827255415173 | etot = -5.6284719487745 +710000 ekin = 2.80069789530487 | erot = 5.11589857305232 | epot = -13.5450684175168 | etot = -5.62847194915956 +711000 ekin = 2.74994326396353 | erot = 5.10911210239552 | epot = -13.4875273159283 | etot = -5.62847194956922 +712000 ekin = 2.70509857015251 | erot = 5.06990681763261 | epot = -13.4034773376645 | etot = -5.62847194987941 +713000 ekin = 2.66343594230655 | erot = 4.99582282597876 | epot = -13.2877307182695 | etot = -5.62847194998418 +714000 ekin = 2.62297982855774 | erot = 4.88658411840125 | epot = -13.1380358967925 | etot = -5.62847194983347 +715000 ekin = 2.58275404748664 | erot = 4.74456650534358 | epot = -12.9557925022798 | etot = -5.62847194944956 +716000 ekin = 2.54267933968741 | erot = 4.57461726490259 | epot = -12.7457685535018 | etot = -5.62847194891177 +717000 ekin = 2.50334692005626 | erot = 4.38348005478918 | epot = -12.5152989228446 | etot = -5.62847194799919 +718000 ekin = 2.46867182037462 | erot = 4.18280619321959 | epot = -12.2799499613367 | etot = -5.62847194774247 +719000 ekin = 2.44027484649155 | erot = 3.97913844302635 | epot = -12.0478852370095 | etot = -5.62847194749158 +720000 ekin = 2.41790751016686 | erot = 3.77617089323842 | epot = -11.8225503506562 | etot = -5.62847194725097 +721000 ekin = 2.4013090030809 | erot = 3.57751641392362 | epot = -11.6072973640278 | etot = -5.62847194702331 +722000 ekin = 2.39001969427645 | erot = 3.38620933361414 | epot = -11.4047009749069 | etot = -5.62847194701633 +723000 ekin = 2.38288808203368 | erot = 3.20447847618438 | epot = -11.215838504937 | etot = -5.62847194671893 +724000 ekin = 2.38038137244362 | erot = 3.03585463103371 | epot = -11.0447079499256 | etot = -5.62847194644831 +725000 ekin = 2.38334904372001 | erot = 2.88343528884769 | epot = -10.8952562787756 | etot = -5.62847194620792 +726000 ekin = 2.39277988807282 | erot = 2.74974572532646 | epot = -10.7709975594025 | etot = -5.62847194600324 +727000 ekin = 2.40968215732956 | erot = 2.63676770307688 | epot = -10.6749218062468 | etot = -5.62847194584036 +728000 ekin = 2.42515137983546 | erot = 2.54412147900357 | epot = -10.5977448181919 | etot = -5.62847195935292 +729000 ekin = 2.40297855334107 | erot = 2.5147599996189 | epot = -10.5462104923891 | etot = -5.62847193942917 +730000 ekin = 2.46310039284473 | erot = 2.5408883827304 | epot = -10.6324607145523 | etot = -5.62847193897719 +731000 ekin = 2.53308642097414 | erot = 2.5495438694937 | epot = -10.7111022295357 | etot = -5.62847193906789 +732000 ekin = 2.61398262096627 | erot = 2.58024874608507 | epot = -10.8227033063277 | etot = -5.62847193927639 +733000 ekin = 2.704048584519 | erot = 2.63167940204765 | epot = -10.9641999262121 | etot = -5.62847193964548 +734000 ekin = 2.80051950073999 | erot = 2.70132929849079 | epot = -11.1303207394526 | etot = -5.62847194022178 +735000 ekin = 2.89941283725732 | erot = 2.78510796771905 | epot = -11.3129927460112 | etot = -5.62847194103486 +736000 ekin = 2.99560133067684 | erot = 2.87741009025007 | epot = -11.5014833620231 | etot = -5.62847194109622 +737000 ekin = 3.08481605492428 | erot = 2.97524489368851 | epot = -11.6885328905953 | etot = -5.62847194198254 +738000 ekin = 3.16217862825841 | erot = 3.07317374877763 | epot = -11.8638243198366 | etot = -5.62847194280053 +739000 ekin = 3.2233603722403 | erot = 3.16493875128737 | epot = -12.0167710668757 | etot = -5.62847194334805 +740000 ekin = 3.26585131628546 | erot = 3.24522139633931 | epot = -12.1395446570561 | etot = -5.62847194443136 +741000 ekin = 3.28375382512678 | erot = 3.29991441183865 | epot = -12.2121401813946 | etot = -5.62847194442916 +742000 ekin = 3.27631313155608 | erot = 3.32408611703107 | epot = -12.2288711925279 | etot = -5.62847194394075 +743000 ekin = 3.24737724810676 | erot = 3.32046927265112 | epot = -12.1963184639576 | etot = -5.62847194319976 +744000 ekin = 3.20210603620692 | erot = 3.294015511799 | epot = -12.1245934904241 | etot = -5.62847194241819 +745000 ekin = 3.14567705905112 | erot = 3.25033567001763 | epot = -12.024484670782 | etot = -5.62847194171325 +746000 ekin = 3.08279906289069 | erot = 3.19521988685792 | epot = -11.9064908906143 | etot = -5.62847194086568 +747000 ekin = 3.01768881751512 | erot = 3.13473855311027 | epot = -11.7808993110087 | etot = -5.62847194038335 +748000 ekin = 2.95302867444292 | erot = 3.07321432141834 | epot = -11.6547149358074 | etot = -5.62847193994612 +749000 ekin = 2.89104396146017 | erot = 3.01469856695175 | epot = -11.5342144679434 | etot = -5.62847193953148 +750000 ekin = 2.83379417430944 | erot = 2.96315742645413 | epot = -11.4254235398979 | etot = -5.6284719391343 +751000 ekin = 2.78329891282507 | erot = 2.9224177744474 | epot = -11.3341886260363 | etot = -5.62847193876383 +752000 ekin = 2.74156846318393 | erot = 2.89600799312975 | epot = -11.2660483947513 | etot = -5.62847193843758 +753000 ekin = 2.71056677631148 | erot = 2.88693753444123 | epot = -11.2259762489326 | etot = -5.62847193817986 +754000 ekin = 2.69212502654351 | erot = 2.89743125949813 | epot = -11.2180282240637 | etot = -5.62847193802201 +755000 ekin = 2.6877653835852 | erot = 2.928498710925 | epot = -11.2447360325848 | etot = -5.62847193807463 +756000 ekin = 2.69845743031617 | erot = 2.97938409367356 | epot = -11.306313462225 | etot = -5.62847193823524 +757000 ekin = 2.72458496413561 | erot = 3.04788425631061 | epot = -11.4009411590836 | etot = -5.62847193863741 +758000 ekin = 2.76540921283034 | erot = 3.12962823291443 | epot = -11.5235093850627 | etot = -5.6284719393179 +759000 ekin = 2.81868342066529 | erot = 3.21794575404794 | epot = -11.6651011149743 | etot = -5.62847194026106 +760000 ekin = 2.88053746483065 | erot = 3.30429272411189 | epot = -11.8133021302896 | etot = -5.62847194134709 +761000 ekin = 2.94600007680037 | erot = 3.37947250562756 | epot = -11.953944524754 | etot = -5.6284719423261 +762000 ekin = 3.01037281092737 | erot = 3.43568700387917 | epot = -12.0745317576972 | etot = -5.62847194289063 +763000 ekin = 3.07103775545926 | erot = 3.46881600090596 | epot = -12.1683256992094 | etot = -5.62847194284419 +764000 ekin = 3.12866395092591 | erot = 3.4797503971339 | epot = -12.236886290297 | etot = -5.62847194223723 +765000 ekin = 3.18696433146488 | erot = 3.47390232179098 | epot = -12.2893385945895 | etot = -5.62847194133365 +766000 ekin = 3.25112146476814 | erot = 3.45917589093114 | epot = -12.3387692961499 | etot = -5.62847194045064 +767000 ekin = 3.32577328229762 | erot = 3.44357056041142 | epot = -12.3978157825305 | etot = -5.62847193982147 +768000 ekin = 3.41341833407264 | erot = 3.43342634964742 | epot = -12.475316623275 | etot = -5.62847193955494 +769000 ekin = 3.5136159797232 | erot = 3.43258837722228 | epot = -12.5746762966054 | etot = -5.62847193965994 +770000 ekin = 3.62296220629094 | erot = 3.44225950952588 | epot = -12.6936936559007 | etot = -5.62847194008384 +771000 ekin = 3.67754209912591 | erot = 3.42051682736877 | epot = -12.7265308943046 | etot = -5.62847196780991 +772000 ekin = 3.59351734120376 | erot = 3.3584968550635 | epot = -12.5804861298099 | etot = -5.62847193354268 +773000 ekin = 3.58504863486503 | erot = 3.48413941929351 | epot = -12.6976599874309 | etot = -5.6284719332724 +774000 ekin = 3.69556246693316 | erot = 3.75600381558271 | epot = -13.080038251317 | etot = -5.62847196880115 +775000 ekin = 3.75799647030805 | erot = 3.87395641031774 | epot = -13.2604248531724 | etot = -5.62847197254658 +776000 ekin = 3.76514931049521 | erot = 3.89275295634025 | epot = -13.2863742395547 | etot = -5.62847197271923 +777000 ekin = 3.74852837975917 | erot = 3.88975944424646 | epot = -13.2667597963548 | etot = -5.62847197234917 +778000 ekin = 3.71300754059353 | erot = 3.86527182221224 | epot = -13.2067513344401 | etot = -5.6284719716343 +779000 ekin = 3.66665793112593 | erot = 3.82295167591176 | epot = -13.1180815775701 | etot = -5.62847197053246 +780000 ekin = 3.61972773179476 | erot = 3.76957330535322 | epot = -13.0177730064367 | etot = -5.62847196928869 +781000 ekin = 3.58276242557081 | erot = 3.71368279721232 | epot = -12.9249171909853 | etot = -5.62847196820216 +782000 ekin = 3.56434384316015 | erot = 3.66344621658085 | epot = -12.856262027254 | etot = -5.62847196751304 +783000 ekin = 3.56907083402848 | erot = 3.62459601401305 | epot = -12.8221388154979 | etot = -5.62847196745638 +784000 ekin = 3.59655578195885 | erot = 3.59908724287649 | epot = -12.8241149926476 | etot = -5.62847196781224 +785000 ekin = 3.64263842895723 | erot = 3.58559579698648 | epot = -12.8567061944369 | etot = -5.62847196849322 +786000 ekin = 3.70061363576283 | erot = 3.58032714309407 | epot = -12.9094127481439 | etot = -5.62847196928699 +787000 ekin = 3.76290289532741 | erot = 3.57827846505882 | epot = -12.9696533304352 | etot = -5.62847197004894 +788000 ekin = 3.8223069124302 | erot = 3.5743207934823 | epot = -13.0250996765887 | etot = -5.6284719706762 +789000 ekin = 3.87288355996755 | erot = 3.56402750525542 | epot = -13.0653830363309 | etot = -5.62847197110791 +790000 ekin = 3.91054381103969 | erot = 3.54422213343056 | epot = -13.0832379157399 | etot = -5.62847197126964 +791000 ekin = 3.93344679975163 | erot = 3.51333982568902 | epot = -13.0752585966263 | etot = -5.62847197118567 +792000 ekin = 3.94193166965662 | erot = 3.47142235465919 | epot = -13.0418259952225 | etot = -5.62847197090671 +793000 ekin = 3.93805337446381 | erot = 3.41982689831729 | epot = -12.9863522432875 | etot = -5.62847197050639 +794000 ekin = 3.92496167480954 | erot = 3.36081973463659 | epot = -12.9142533795016 | etot = -5.62847197005551 +795000 ekin = 3.9063184317544 | erot = 3.29713731817139 | epot = -12.8319277195354 | etot = -5.62847196960964 +796000 ekin = 3.88587920063779 | erot = 3.23158100792164 | epot = -12.745932177765 | etot = -5.62847196920561 +797000 ekin = 3.86724402793311 | erot = 3.16668037637107 | epot = -12.6623963731684 | etot = -5.62847196886419 +798000 ekin = 3.85371944422422 | erot = 3.10446220715859 | epot = -12.5866536199751 | etot = -5.62847196859227 +799000 ekin = 3.84821326092654 | erot = 3.04637406866006 | epot = -12.5230592979746 | etot = -5.62847196838804 +800000 ekin = 3.85308746082701 | erot = 2.99338091126559 | epot = -12.474940340337 | etot = -5.62847196824438 +801000 ekin = 3.86994742083567 | erot = 2.94620265059397 | epot = -12.4446220395853 | etot = -5.62847196815562 +802000 ekin = 3.89938743521584 | erot = 2.90559564219863 | epot = -12.4334550455353 | etot = -5.62847196812086 +803000 ekin = 3.94077451951464 | erot = 2.8725536316443 | epot = -12.4418001193023 | etot = -5.62847196814334 +804000 ekin = 3.992174455156 | erot = 2.84833794155936 | epot = -12.4689843649416 | etot = -5.62847196822621 +805000 ekin = 4.05048829003811 | erot = 2.83432176456862 | epot = -12.5132820229749 | etot = -5.62847196836813 +806000 ekin = 4.11178329733929 | erot = 2.83170980342237 | epot = -12.5719650693255 | etot = -5.62847196856381 +807000 ekin = 4.17172086379981 | erot = 2.84122318449694 | epot = -12.6414160171043 | etot = -5.62847196880753 +808000 ekin = 4.22595471211098 | erot = 2.86283161279705 | epot = -12.7172582940025 | etot = -5.62847196909444 +809000 ekin = 4.27041103459019 | erot = 2.89559061413246 | epot = -12.7944736181418 | etot = -5.62847196941918 +810000 ekin = 4.30143579161335 | erot = 2.93761851692464 | epot = -12.8675262783088 | etot = -5.62847196977087 +811000 ekin = 4.31585912498473 | erot = 2.98622782411963 | epot = -12.9305589192329 | etot = -5.62847197012855 +812000 ekin = 4.31104963144209 | erot = 3.03819974772186 | epot = -12.9777213496236 | etot = -5.62847197045961 +813000 ekin = 4.28501152870088 | erot = 3.09015837117713 | epot = -13.0036418706033 | etot = -5.62847197072532 +814000 ekin = 4.23653530268496 | erot = 3.13897206771779 | epot = -13.0039793412913 | etot = -5.6284719708885 +815000 ekin = 4.16537042780704 | erot = 3.18209773884163 | epot = -12.9759401375723 | etot = -5.62847197092361 +816000 ekin = 4.0723651748252 | erot = 3.21779646454099 | epot = -12.9186336101891 | etot = -5.6284719708229 +817000 ekin = 3.95951977440384 | erot = 3.24518380301937 | epot = -12.8331755480214 | etot = -5.62847197059822 +818000 ekin = 3.8299176268559 | erot = 3.26412066908298 | epot = -12.7225102662203 | etot = -5.62847197028138 +819000 ekin = 3.68753356704803 | erot = 3.2749890293617 | epot = -12.5909945663147 | etot = -5.62847196990494 +820000 ekin = 3.53699106775342 | erot = 3.27842149115945 | epot = -12.4438845284247 | etot = -5.62847196951186 +821000 ekin = 3.38323613843139 | erot = 3.27505502188844 | epot = -12.2867631294542 | etot = -5.62847196913438 +822000 ekin = 3.23123737421303 | erot = 3.26537695375067 | epot = -12.1250862967552 | etot = -5.62847196879146 +823000 ekin = 3.08574116264606 | erot = 3.24970236684612 | epot = -11.9639154979793 | etot = -5.62847196848715 +824000 ekin = 2.9510991983436 | erot = 3.22828590286759 | epot = -11.8078570694242 | etot = -5.62847196821301 +825000 ekin = 2.8311716727824 | erot = 3.20152981096286 | epot = -11.6611734516996 | etot = -5.62847196795438 +826000 ekin = 2.72929448912935 | erot = 3.17021233026683 | epot = -11.5279787870942 | etot = -5.62847196769802 +827000 ekin = 2.64828540283224 | erot = 3.13564460944143 | epot = -11.4124019797145 | etot = -5.62847196744083 +828000 ekin = 2.59045268678287 | erot = 3.09968027868469 | epot = -11.3186049326611 | etot = -5.62847196719356 +829000 ekin = 2.55756748898929 | erot = 3.06454892031733 | epot = -11.2505883762886 | etot = -5.62847196698197 +830000 ekin = 2.55077388282834 | erot = 3.03254604853091 | epot = -11.2117918981989 | etot = -5.62847196683961 +831000 ekin = 2.5704372593064 | erot = 3.00566097440441 | epot = -11.2045702005099 | etot = -5.62847196679914 +832000 ekin = 2.61596870967331 | erot = 2.98524787918955 | epot = -11.2296885557457 | etot = -5.6284719668828 +833000 ekin = 2.68568117685698 | erot = 2.97182255658061 | epot = -11.2859757005329 | etot = -5.62847196709536 +834000 ekin = 2.77673677953563 | erot = 2.96502424291077 | epot = -11.3702329898702 | etot = -5.62847196742382 +835000 ekin = 2.88522064137063 | erot = 2.96372965171537 | epot = -11.4774222609262 | etot = -5.62847196784022 +836000 ekin = 3.00633984429238 | erot = 2.9662686051896 | epot = -11.6010804177916 | etot = -5.62847196830963 +837000 ekin = 3.13471078770169 | erot = 2.97067133236171 | epot = -11.7338540888613 | etot = -5.62847196879791 +838000 ekin = 3.2646797688615 | erot = 2.97489019079408 | epot = -11.8680419289321 | etot = -5.6284719692765 +839000 ekin = 3.39062362028674 | erot = 2.97696578886047 | epot = -11.9960613788722 | etot = -5.62847196972498 +840000 ekin = 3.50719614094131 | erot = 2.97513773468309 | epot = -12.110805845754 | etot = -5.62847197012965 +841000 ekin = 3.6095143031902 | erot = 2.96792302656663 | epot = -12.205909300235 | etot = -5.62847197047821 +842000 ekin = 3.69330308269465 | erot = 2.95419217499661 | epot = -12.2759672284492 | etot = -5.62847197075789 +843000 ekin = 3.75502927972068 | erot = 2.93326273012204 | epot = -12.3167639807943 | etot = -5.62847197095162 +844000 ekin = 3.79205095676114 | erot = 2.90501003325241 | epot = -12.3255329610536 | etot = -5.62847197104003 +845000 ekin = 3.80278826916113 | erot = 2.86997708374397 | epot = -12.3012373239095 | etot = -5.6284719710044 +846000 ekin = 3.7868907831117 | erot = 2.82944607213409 | epot = -12.2448088260797 | etot = -5.62847197083392 +847000 ekin = 3.74534923711505 | erot = 2.78543387975461 | epot = -12.1592550874022 | etot = -5.62847197053249 +848000 ekin = 3.68048960876388 | erot = 2.74058491210611 | epot = -12.0495464909921 | etot = -5.6284719701221 +849000 ekin = 3.59580402250911 | erot = 2.6979547346253 | epot = -11.9222307267798 | etot = -5.62847196964534 +850000 ekin = 3.49561210992167 | erot = 2.66069826286262 | epot = -11.7847823419402 | etot = -5.62847196915593 +851000 ekin = 3.38460421156482 | erot = 2.63169878981261 | epot = -11.6447749700886 | etot = -5.62847196871115 +852000 ekin = 3.2673583461708 | erot = 2.61319105472478 | epot = -11.5090213692559 | etot = -5.62847196836028 +853000 ekin = 3.14792970820425 | erot = 2.6064404595508 | epot = -11.3828421358873 | etot = -5.62847196813225 +854000 ekin = 3.02961721482008 | erot = 2.61155167708395 | epot = -11.2696408599309 | etot = -5.62847196802691 +855000 ekin = 2.91497870639192 | erot = 2.62749311900426 | epot = -11.1709437934187 | etot = -5.6284719680225 +856000 ekin = 2.80592683640508 | erot = 2.65229723518904 | epot = -11.0866960396745 | etot = -5.62847196808038 +857000 ekin = 2.70394323106257 | erot = 2.68342637128184 | epot = -11.0158415705022 | etot = -5.62847196815778 +858000 ekin = 2.61028085018917 | erot = 2.7182087445085 | epot = -10.9569615629193 | etot = -5.62847196822162 +859000 ekin = 2.52608469683041 | erot = 2.75423459862355 | epot = -10.9087912637081 | etot = -5.62847196825415 +860000 ekin = 2.45241725334247 | erot = 2.78962480116096 | epot = -10.8705140227566 | etot = -5.62847196825313 +861000 ekin = 2.39021948320316 | erot = 2.82313150338326 | epot = -10.8418229548146 | etot = -5.62847196822818 +862000 ekin = 2.34025129546523 | erot = 2.85407946378513 | epot = -10.822802727446 | etot = -5.62847196819566 +863000 ekin = 2.30304188835595 | erot = 2.88219277632016 | epot = -10.813706632849 | etot = -5.62847196817294 +864000 ekin = 2.27886006072096 | erot = 2.90737073870793 | epot = -10.8147027676044 | etot = -5.62847196817555 +865000 ekin = 2.26770197244177 | erot = 2.92947677471433 | epot = -10.825650715369 | etot = -5.6284719682129 +866000 ekin = 2.26929189300013 | erot = 2.94819404241867 | epot = -10.8459579037059 | etot = -5.62847196828711 +867000 ekin = 2.28309242230586 | erot = 2.96298089308274 | epot = -10.8745452837802 | etot = -5.62847196839164 +868000 ekin = 2.30832281717956 | erot = 2.97313399093992 | epot = -10.9099287766329 | etot = -5.62847196851338 +869000 ekin = 2.34398135175733 | erot = 2.97793980532902 | epot = -10.9503931257227 | etot = -5.62847196863633 +870000 ekin = 2.3888674476675 | erot = 2.97686809818229 | epot = -10.9942075145963 | etot = -5.62847196874653 +871000 ekin = 2.44159861809647 | erot = 2.96974175424173 | epot = -11.0398123411752 | etot = -5.62847196883697 +872000 ekin = 2.500619616053 | erot = 2.95681803699978 | epot = -11.0859096219628 | etot = -5.62847196890998 +873000 ekin = 2.56420808139324 | erot = 2.93874614074125 | epot = -11.1314261911097 | etot = -5.62847196897516 +874000 ekin = 2.63049127025364 | erot = 2.91641905805231 | epot = -11.1753822973487 | etot = -5.62847196904273 +875000 ekin = 2.69749664450509 | erot = 2.89079069041083 | epot = -11.2167593040308 | etot = -5.62847196911489 +876000 ekin = 2.76325740882321 | erot = 2.86275138608941 | epot = -11.2544807640928 | etot = -5.62847196918014 +877000 ekin = 2.82597857073924 | erot = 2.83312911678617 | epot = -11.2875796567397 | etot = -5.62847196921427 +878000 ekin = 2.88426506041778 | erot = 2.80282960099576 | epot = -11.3155666305523 | etot = -5.62847196913875 +879000 ekin = 2.93899285505317 | erot = 2.77402557771481 | epot = -11.3414904016818 | etot = -5.62847196891381 +880000 ekin = 2.99074429493992 | erot = 2.74904466423746 | epot = -11.3682609281216 | etot = -5.62847196894421 +881000 ekin = 3.03734868979927 | erot = 2.72816458116911 | epot = -11.3939852397512 | etot = -5.62847196878281 +882000 ekin = 3.07935286329043 | erot = 2.71303253547246 | epot = -11.4208573673789 | etot = -5.62847196861602 +883000 ekin = 3.11756797084552 | erot = 2.70517731879082 | epot = -11.4512172581187 | etot = -5.62847196848236 +884000 ekin = 3.15280252848168 | erot = 2.70569769640385 | epot = -11.486972193293 | etot = -5.62847196840746 +885000 ekin = 3.18571613205173 | erot = 2.71504911575347 | epot = -11.5292372162097 | etot = -5.62847196840455 +886000 ekin = 3.21676773387613 | erot = 2.7329058008883 | epot = -11.5781455032431 | etot = -5.6284719684787 +887000 ekin = 3.24623562424243 | erot = 2.75806669121019 | epot = -11.6327742840859 | etot = -5.62847196863332 +888000 ekin = 3.27425942012452 | erot = 2.78837179681905 | epot = -11.6911031858155 | etot = -5.62847196887192 +889000 ekin = 3.30086478887179 | erot = 2.82064068491563 | epot = -11.7499774429801 | etot = -5.62847196919267 +890000 ekin = 3.3259692487092 | erot = 2.85071439961825 | epot = -11.805155617902 | etot = -5.62847196957451 +891000 ekin = 3.34941253238938 | erot = 2.87373382358962 | epot = -11.8516183259426 | etot = -5.62847196996364 +892000 ekin = 3.37107523562693 | erot = 2.88476437040179 | epot = -11.8843115763022 | etot = -5.62847197027351 +893000 ekin = 3.39111185107035 | erot = 2.87974242660312 | epot = -11.8993262480791 | etot = -5.62847197040564 +894000 ekin = 3.4102321291952 | erot = 2.85650829429513 | epot = -11.895212393781 | etot = -5.62847197029071 +895000 ekin = 3.4298773086987 | erot = 2.81553499424091 | epot = -11.8738842728666 | etot = -5.62847196992698 +896000 ekin = 3.45214148974819 | erot = 2.76001213086012 | epot = -11.8406255899945 | etot = -5.62847196938618 +897000 ekin = 3.47941735610567 | erot = 2.69521466348942 | epot = -11.8031039883802 | etot = -5.6284719687851 +898000 ekin = 3.51352962041553 | erot = 2.62737086724796 | epot = -11.7693724690737 | etot = -5.62847198141017 +899000 ekin = 3.48893911457665 | erot = 2.56291214065495 | epot = -11.6803232246884 | etot = -5.62847196945683 +900000 ekin = 3.45535689334339 | erot = 2.55015985128176 | epot = -11.6339887069773 | etot = -5.62847196235217 +901000 ekin = 3.50186288143693 | erot = 2.58894159239397 | epot = -11.7192764496102 | etot = -5.62847197577932 +902000 ekin = 3.5661021361054 | erot = 2.58196928658372 | epot = -11.7765433952423 | etot = -5.6284719725532 +903000 ekin = 3.62814875862408 | erot = 2.56232070366863 | epot = -11.8189414352198 | etot = -5.62847197292713 +904000 ekin = 3.69112394796104 | erot = 2.55247638433754 | epot = -11.8720723057126 | etot = -5.62847197341403 +905000 ekin = 3.7509128055889 | erot = 2.54985569692194 | epot = -11.9292404764333 | etot = -5.62847197392247 +906000 ekin = 3.80322506785235 | erot = 2.55191272424328 | epot = -11.9836097664451 | etot = -5.62847197434945 +907000 ekin = 3.8443422905769 | erot = 2.55683360451709 | epot = -12.0296478697021 | etot = -5.62847197460815 +908000 ekin = 3.8719006442339 | erot = 2.56394104682641 | epot = -12.0643136657174 | etot = -5.62847197465711 +909000 ekin = 3.88547927567113 | erot = 2.57365301072747 | epot = -12.0876042609108 | etot = -5.62847197451219 +910000 ekin = 3.88680451139339 | erot = 2.5870243564951 | epot = -12.1023008421247 | etot = -5.62847197423622 +911000 ekin = 3.87951720468961 | erot = 2.6050879623703 | epot = -12.1130771409705 | etot = -5.62847197391058 +912000 ekin = 3.86859233859162 | erot = 2.62827701303798 | epot = -12.1253413252393 | etot = -5.62847197360974 +913000 ekin = 3.85955913456261 | erot = 2.65612234870647 | epot = -12.14415345666 | etot = -5.62847197339095 +914000 ekin = 3.85765974452869 | erot = 2.68725904716219 | epot = -12.173390764377 | etot = -5.62847197268608 +915000 ekin = 3.86988559132831 | erot = 2.72155495896482 | epot = -12.219912523155 | etot = -5.62847197286191 +916000 ekin = 3.89721211279105 | erot = 2.75899199674868 | epot = -12.2846760828075 | etot = -5.62847197326774 +917000 ekin = 3.93597306439209 | erot = 2.79756616560857 | epot = -12.3620112037081 | etot = -5.62847197370745 +918000 ekin = 3.98211349749628 | erot = 2.83523643843263 | epot = -12.4458219100817 | etot = -5.6284719741528 +919000 ekin = 4.03109884414175 | erot = 2.86939983142179 | epot = -12.5289706511467 | etot = -5.62847197558313 +920000 ekin = 4.07575007007163 | erot = 2.89203459277258 | epot = -12.5962566387455 | etot = -5.62847197590126 +921000 ekin = 4.11121320371463 | erot = 2.89963705915855 | epot = -12.6393222395139 | etot = -5.62847197664073 +922000 ekin = 4.12946329331047 | erot = 2.89101491395262 | epot = -12.6489501841751 | etot = -5.62847197691201 +923000 ekin = 4.12574551821064 | erot = 2.86656720110585 | epot = -12.6207846962139 | etot = -5.62847197689736 +924000 ekin = 4.09806255856886 | erot = 2.8281743701107 | epot = -12.5547089053139 | etot = -5.62847197663431 +925000 ekin = 4.04683813175561 | erot = 2.77889166059353 | epot = -12.4542017685711 | etot = -5.62847197622196 +926000 ekin = 3.97415980884028 | erot = 2.72240485506924 | epot = -12.3250366396764 | etot = -5.62847197576684 +927000 ekin = 3.88290109598325 | erot = 2.66247239405016 | epot = -12.1738454653642 | etot = -5.62847197533078 +928000 ekin = 3.77619172564078 | erot = 2.60258197099968 | epot = -12.0072456715511 | etot = -5.62847197491066 +929000 ekin = 3.65741733898654 | erot = 2.54590496147566 | epot = -11.8317942749248 | etot = -5.62847197446256 +930000 ekin = 3.53056331325702 | erot = 2.49545263325868 | epot = -11.6544879204598 | etot = -5.62847197394412 +931000 ekin = 3.4005452585423 | erot = 2.45429284761135 | epot = -11.4833100791872 | etot = -5.62847197303357 +932000 ekin = 3.27351307254188 | erot = 2.42812142781794 | epot = -11.3301064729948 | etot = -5.62847197263502 +933000 ekin = 3.15479412762404 | erot = 2.4201742871754 | epot = -11.2034403870324 | etot = -5.628471972233 +934000 ekin = 3.04934557157637 | erot = 2.43124949772708 | epot = -11.1090670411841 | etot = -5.62847197188061 +935000 ekin = 2.96178382671725 | erot = 2.46165171577527 | epot = -11.0519075141149 | etot = -5.62847197162238 +936000 ekin = 2.89581269331775 | erot = 2.51113391217417 | epot = -11.0354185769758 | etot = -5.6284719714839 +937000 ekin = 2.85385879458329 | erot = 2.57889786067944 | epot = -11.061228626733 | etot = -5.62847197147029 +938000 ekin = 2.83694342945423 | erot = 2.66364816189635 | epot = -11.1290635629205 | etot = -5.6284719715699 +939000 ekin = 2.84476696195415 | erot = 2.76369076698157 | epot = -11.2369297006932 | etot = -5.62847197175744 +940000 ekin = 2.8759532044385 | erot = 2.87707537856042 | epot = -11.3815005549978 | etot = -5.62847197199888 +941000 ekin = 2.92838858131787 | erot = 3.00178159707388 | epot = -11.5586421506475 | etot = -5.62847197225574 +942000 ekin = 2.99958691478888 | erot = 3.13593595472591 | epot = -11.7639948420076 | etot = -5.62847197249282 +943000 ekin = 3.08701486089968 | erot = 3.27802584035403 | epot = -11.9935126739376 | etot = -5.62847197268385 +944000 ekin = 3.186586872159 | erot = 3.42629435721361 | epot = -12.2413532032652 | etot = -5.62847197389261 +945000 ekin = 3.29120912172941 | erot = 3.57701253406485 | epot = -12.496693630207 | etot = -5.6284719744127 +946000 ekin = 3.39621217445015 | erot = 3.72637389347036 | epot = -12.7510580429265 | etot = -5.62847197500597 +947000 ekin = 3.49687303138286 | erot = 3.86977321126905 | epot = -12.9951182183484 | etot = -5.62847197569646 +948000 ekin = 3.58827211267957 | erot = 4.00151346858439 | epot = -13.2182575577498 | etot = -5.62847197648584 +949000 ekin = 3.66536645495548 | erot = 4.11475106100546 | epot = -13.4085894932989 | etot = -5.62847197733792 +950000 ekin = 3.72323941993302 | erot = 4.2018019175768 | epot = -13.553513315681 | etot = -5.62847197817117 +951000 ekin = 3.75754185646123 | erot = 4.25489778213983 | epot = -13.6409116174654 | etot = -5.62847197886429 +952000 ekin = 3.76507381614856 | erot = 4.26734583549593 | epot = -13.6608916309242 | etot = -5.62847197927968 +953000 ekin = 3.74438822307989 | erot = 4.23487585385495 | epot = -13.607736056235 | etot = -5.62847197930019 +954000 ekin = 3.69625242862099 | erot = 4.15681815233244 | epot = -13.4815425598219 | etot = -5.6284719788685 +955000 ekin = 3.62380420138425 | erot = 4.03673171571548 | epot = -13.2890078951114 | etot = -5.62847197801164 +956000 ekin = 3.52555336672213 | erot = 3.88073805038935 | epot = -13.0347633967538 | etot = -5.62847197964228 +957000 ekin = 3.39894639005913 | erot = 3.70474137600897 | epot = -12.7321597406528 | etot = -5.6284719745847 +958000 ekin = 3.27782879331305 | erot = 3.53760737148217 | epot = -12.4439081377568 | etot = -5.62847197296156 +959000 ekin = 3.17835028496736 | erot = 3.38602207543512 | epot = -12.192844335218 | etot = -5.62847197481551 +960000 ekin = 3.09019087769108 | erot = 3.23509493447278 | epot = -11.9537577886205 | etot = -5.62847197645667 +961000 ekin = 3.00426259180557 | erot = 3.0824813352864 | epot = -11.7152159026405 | etot = -5.62847197554848 +962000 ekin = 2.92693479803565 | erot = 2.94805480831314 | epot = -11.5034615816837 | etot = -5.62847197533487 +963000 ekin = 2.85972055487714 | erot = 2.83488454510921 | epot = -11.3230770750156 | etot = -5.62847197502922 +964000 ekin = 2.80427359327328 | erot = 2.74583973131526 | epot = -11.178585299439 | etot = -5.62847197485047 +965000 ekin = 2.76170821909769 | erot = 2.68249826129849 | epot = -11.0726784551929 | etot = -5.62847197479672 +966000 ekin = 2.73254763777982 | erot = 2.64503833012218 | epot = -11.0060579427772 | etot = -5.62847197487522 +967000 ekin = 2.71665521991785 | erot = 2.63218922372615 | epot = -10.9773164187349 | etot = -5.62847197509087 +968000 ekin = 2.71315992354632 | erot = 2.64124364192698 | epot = -10.9828755409038 | etot = -5.62847197543047 +969000 ekin = 2.72046614537744 | erot = 2.66825860642096 | epot = -11.017196727654 | etot = -5.6284719758556 +970000 ekin = 2.73639578907595 | erot = 2.70848274121872 | epot = -11.0733505066075 | etot = -5.62847197631278 +971000 ekin = 2.75849383127184 | erot = 2.75695664167746 | epot = -11.1439224496111 | etot = -5.62847197666182 +972000 ekin = 2.78540546269541 | erot = 2.80984083718468 | epot = -11.2237182768147 | etot = -5.62847197693461 +973000 ekin = 2.81581408876755 | erot = 2.86412704719854 | epot = -11.3084131130852 | etot = -5.62847197711915 +974000 ekin = 2.84847995081039 | erot = 2.91762904242811 | epot = -11.3945809704478 | etot = -5.62847197720934 +975000 ekin = 2.88260770758503 | erot = 2.96920774161524 | epot = -11.4802874264075 | etot = -5.62847197720723 +976000 ekin = 2.90702474113454 | erot = 3.01964919041985 | epot = -11.5551459331455 | etot = -5.62847200159107 +977000 ekin = 2.82994037043752 | erot = 3.10467595319514 | epot = -11.5630883014867 | etot = -5.62847197785407 +978000 ekin = 2.82908362067085 | erot = 3.22546638969981 | epot = -11.6830220140927 | etot = -5.62847200372201 +979000 ekin = 2.8370610010888 | erot = 3.25481873071581 | epot = -11.7203517218855 | etot = -5.62847199008084 +980000 ekin = 2.83601345129769 | erot = 3.27042511574271 | epot = -11.7349105571566 | etot = -5.62847199011619 +981000 ekin = 2.82679467506443 | erot = 3.27908746079809 | epot = -11.7343541260202 | etot = -5.6284719901577 +982000 ekin = 2.80889457079111 | erot = 3.2809065834536 | epot = -11.7182731444468 | etot = -5.62847199020213 +983000 ekin = 2.78208898645713 | erot = 3.27578647134014 | epot = -11.6863474480256 | etot = -5.62847199022831 +984000 ekin = 2.74660136884853 | erot = 3.26353952354967 | epot = -11.6386128825996 | etot = -5.62847199020144 +985000 ekin = 2.70333214423332 | erot = 3.24411390942185 | epot = -11.5759180437397 | etot = -5.62847199008455 +986000 ekin = 2.65408912738725 | erot = 3.21786526393144 | epot = -11.5004263811691 | etot = -5.62847198985045 +987000 ekin = 2.57871632303265 | erot = 3.17247279054186 | epot = -11.3796611079074 | etot = -5.62847199433287 +988000 ekin = 2.53018926050092 | erot = 3.15315340264677 | epot = -11.3118146650989 | etot = -5.62847200195117 +989000 ekin = 2.4956627810317 | erot = 3.12952117262699 | epot = -11.253655945603 | etot = -5.62847199194432 +990000 ekin = 2.46227182390165 | erot = 3.09741757651199 | epot = -11.1881613918028 | etot = -5.62847199138918 +991000 ekin = 2.44592299128019 | erot = 3.07158094882325 | epot = -11.1459759312298 | etot = -5.62847199112639 +992000 ekin = 2.45174281446408 | erot = 3.0561104834769 | epot = -11.1363252888672 | etot = -5.62847199092623 +993000 ekin = 2.48099671570252 | erot = 3.05281518051754 | epot = -11.1622838869926 | etot = -5.62847199077251 +994000 ekin = 2.53415670131493 | erot = 3.06359154316083 | epot = -11.2262202351627 | etot = -5.62847199068692 +995000 ekin = 2.6108885321789 | erot = 3.09015398504997 | epot = -11.3295145079077 | etot = -5.62847199067886 +996000 ekin = 2.71011819620561 | erot = 3.1337829867022 | epot = -11.4723731736583 | etot = -5.62847199075047 +997000 ekin = 2.83015603232536 | erot = 3.19515267699556 | epot = -11.6537807002222 | etot = -5.6284719909013 +998000 ekin = 2.9687857160077 | erot = 3.27423191355817 | epot = -11.8714896207065 | etot = -5.62847199114061 +999000 ekin = 3.12322522658256 | erot = 3.37022004732785 | epot = -12.1219172654051 | etot = -5.62847199149472 +1000000 ekin = 3.2899065057238 | erot = 3.48146010729922 | epot = -12.3998386050297 | etot = -5.62847199200664 + 1000000 0.14621807 -0.83009398 0.055104069 -0.56937076 4.8223734e-05 64000 +Loop time of 19.1599 on 4 procs for 1000000 steps with 16 atoms + +Performance: 45094.124 tau/day, 52192.273 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.6477 | 8.0143 | 10.588 | 80.6 | 41.83 +Bond | 0.24825 | 0.37899 | 0.50101 | 14.6 | 1.98 +Neigh | 0.009732 | 0.0098287 | 0.009891 | 0.1 | 0.05 +Comm | 5.7912 | 8.1786 | 11.805 | 81.8 | 42.69 +Output | 0.096764 | 0.1038 | 0.12074 | 3.1 | 0.54 +Modify | 0.77772 | 0.86731 | 0.96892 | 9.2 | 4.53 +Other | | 1.607 | | | 8.39 + +Nlocal: 4.00000 ave 4 max 4 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 12.0000 ave 12 max 12 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 26.5000 ave 47 max 9 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 106 +Ave neighs/atom = 6.6250000 +Ave special neighs/atom = 3.7500000 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +#write_restart last_config.${number}.* +Total wall time: 0:00:19 diff --git a/examples/PACKAGES/cgdna/examples/test.sh b/examples/PACKAGES/cgdna/examples/test.sh new file mode 100755 index 0000000000..795be9ef88 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/test.sh @@ -0,0 +1,232 @@ +#! /bin/bash + +DATE='2Jul21' +LMPDIR=/Users/ohenrich/Work/code/lammps + +SRCDIR=$LMPDIR/src +EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples + +if [ $# -eq 1 ] && [ $1 = run ]; then + echo '# Compiling executable in' $SRCDIR + + cd $SRCDIR + make clean-all + make -j8 mpi + + ###################################################### + echo '# Running oxDNA duplex1 test' + cd $EXDIR/oxDNA/duplex1 + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex1 . + cp ../data.duplex1 . + + mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null + mv log.lammps log.$DATE.duplex1.g++.1 + grep etot log.$DATE.duplex1.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null + mv log.lammps log.$DATE.duplex1.g++.4 + grep etot log.$DATE.duplex1.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxDNA duplex2 test' + cd $EXDIR/oxDNA/duplex2 + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex2 . + cp ../data.duplex2 . + + mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null + mv log.lammps log.$DATE.duplex2.g++.1 + grep etot log.$DATE.duplex2.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null + mv log.lammps log.$DATE.duplex2.g++.4 + grep etot log.$DATE.duplex2.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxDNA2 duplex1 test' + cd $EXDIR/oxDNA2/duplex1 + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex1 . + cp ../data.duplex1 . + + mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null + mv log.lammps log.$DATE.duplex1.g++.1 + grep etot log.$DATE.duplex1.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null + mv log.lammps log.$DATE.duplex1.g++.4 + grep etot log.$DATE.duplex1.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxDNA2 duplex2 test' + cd $EXDIR/oxDNA2/duplex2 + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex2 . + cp ../data.duplex2 . + + mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null + mv log.lammps log.$DATE.duplex2.g++.1 + grep etot log.$DATE.duplex2.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null + mv log.lammps log.$DATE.duplex2.g++.4 + grep etot log.$DATE.duplex2.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxDNA2 duplex3 test' + cd $EXDIR/oxDNA2/duplex3 + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex3 . + cp ../data.duplex3 . + + mpirun -np 1 ./lmp_mpi < in.duplex3 > /dev/null + mv log.lammps log.$DATE.duplex3.g++.1 + grep etot log.$DATE.duplex3.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex3 > /dev/null + mv log.lammps log.$DATE.duplex3.g++.4 + grep etot log.$DATE.duplex3.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxDNA2 unique_bp test' + cd $EXDIR/oxDNA2/unique_bp + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex4.4type . + cp ../in.duplex4.8type . + cp ../data.duplex4.4type . + cp ../data.duplex4.8type . + + mpirun -np 1 ./lmp_mpi < in.duplex4.4type > /dev/null + mv log.lammps log.$DATE.duplex4.4type.g++.1 + grep etot log.$DATE.duplex4.4type.g++.1 > e_test.dat + grep etot ../log*4type*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex4.4type > /dev/null + mv log.lammps log.$DATE.duplex4.4type.g++.4 + grep etot log.$DATE.duplex4.4type.g++.4 > e_test.dat + grep etot ../log*4type*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 1 ./lmp_mpi < in.duplex4.8type > /dev/null + mv log.lammps log.$DATE.duplex4.8type.g++.1 + grep etot log.$DATE.duplex4.8type.g++.1 > e_test.dat + grep etot ../log*8type*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex4.8type > /dev/null + mv log.lammps log.$DATE.duplex4.8type.g++.4 + grep etot log.$DATE.duplex4.8type.g++.4 > e_test.dat + grep etot ../log*8type*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxDNA2 dsring test' + cd $EXDIR/oxDNA2/dsring + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.dsring . + cp ../data.dsring . + + mpirun -np 1 ./lmp_mpi < in.dsring > /dev/null + mv log.lammps log.$DATE.dsring.g++.1 + grep etot log.$DATE.dsring.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.dsring > /dev/null + mv log.lammps log.$DATE.dsring.g++.4 + grep etot log.$DATE.dsring.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + + ###################################################### + echo '# Running oxRNA2 duplex2 test' + cd $EXDIR/oxRNA2/duplex2 + mkdir test + cd test + cp $SRCDIR/lmp_mpi . + cp ../in.duplex2 . + cp ../data.duplex2 . + + mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null + mv log.lammps log.$DATE.duplex2.g++.1 + grep etot log.$DATE.duplex2.g++.1 > e_test.dat + grep etot ../log*1 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null + mv log.lammps log.$DATE.duplex2.g++.4 + grep etot log.$DATE.duplex2.g++.4 > e_test.dat + grep etot ../log*4 > e_old.dat + ndiff -relerr 1e-8 e_test.dat e_old.dat + + ###################################################### + echo '# Done' + +elif [ $# -eq 1 ] && [ $1 = clean ]; then + echo '# Deleting test directories' + rm -rf $EXDIR/oxDNA/duplex1/test + rm -rf $EXDIR/oxDNA/duplex2/test + rm -rf $EXDIR/oxDNA2/duplex1/test + rm -rf $EXDIR/oxDNA2/duplex2/test + rm -rf $EXDIR/oxDNA2/duplex3/test + rm -rf $EXDIR/oxDNA2/unique_bp/test + rm -rf $EXDIR/oxDNA2/dsring/test + rm -rf $EXDIR/oxRNA2/duplex2/test + echo '# Done' + +else + echo '# Usage:' + echo '# ./test.sh run ... to run test suite' + echo '# ./test.sh clean ... to delete test directories' + +fi diff --git a/examples/USER/cgdna/util/generate.py b/examples/PACKAGES/cgdna/util/generate.py similarity index 100% rename from examples/USER/cgdna/util/generate.py rename to examples/PACKAGES/cgdna/util/generate.py diff --git a/examples/USER/cgdna/util/generate_simple.py b/examples/PACKAGES/cgdna/util/generate_simple.py similarity index 100% rename from examples/USER/cgdna/util/generate_simple.py rename to examples/PACKAGES/cgdna/util/generate_simple.py diff --git a/examples/USER/cgdna/util/input.ref b/examples/PACKAGES/cgdna/util/input.ref similarity index 100% rename from examples/USER/cgdna/util/input.ref rename to examples/PACKAGES/cgdna/util/input.ref diff --git a/examples/USER/cgdna/util/sequence.txt b/examples/PACKAGES/cgdna/util/sequence.txt similarity index 100% rename from examples/USER/cgdna/util/sequence.txt rename to examples/PACKAGES/cgdna/util/sequence.txt diff --git a/examples/USER/cgdna/util/sequence_simple.txt b/examples/PACKAGES/cgdna/util/sequence_simple.txt similarity index 100% rename from examples/USER/cgdna/util/sequence_simple.txt rename to examples/PACKAGES/cgdna/util/sequence_simple.txt diff --git a/examples/USER/cgsdk/README b/examples/PACKAGES/cgsdk/README similarity index 95% rename from examples/USER/cgsdk/README rename to examples/PACKAGES/cgsdk/README index 5d3a493779..09b9b0a8ea 100644 --- a/examples/USER/cgsdk/README +++ b/examples/PACKAGES/cgsdk/README @@ -1,4 +1,4 @@ -LAMMPS USER-CGSDK example problems +LAMMPS CG-SDK example problems Each of these sub-directories contains a sample problem for the SDK coarse grained MD potentials that you can run with LAMMPS. diff --git a/examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz b/examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz similarity index 100% rename from examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz rename to examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz diff --git a/examples/USER/cgsdk/peg-verlet/in.pegc12e8 b/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/in.pegc12e8 rename to examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 diff --git a/examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle b/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle similarity index 100% rename from examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle rename to examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 diff --git a/examples/USER/cgsdk/sds-monolayer/data.sds.gz b/examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/data.sds.gz rename to examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz diff --git a/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid b/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/in.sds-hybrid rename to examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid diff --git a/examples/USER/cgsdk/sds-monolayer/in.sds-regular b/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/in.sds-regular rename to examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 diff --git a/examples/USER/misc/charge_regulation/README b/examples/PACKAGES/charge_regulation/README similarity index 100% rename from examples/USER/misc/charge_regulation/README rename to examples/PACKAGES/charge_regulation/README diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid b/examples/PACKAGES/charge_regulation/data.chreg-acid similarity index 100% rename from examples/USER/misc/charge_regulation/data.chreg-acid rename to examples/PACKAGES/charge_regulation/data.chreg-acid diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid-real b/examples/PACKAGES/charge_regulation/data.chreg-acid-real similarity index 100% rename from examples/USER/misc/charge_regulation/data.chreg-acid-real rename to examples/PACKAGES/charge_regulation/data.chreg-acid-real diff --git a/examples/USER/misc/charge_regulation/data.chreg-polymer b/examples/PACKAGES/charge_regulation/data.chreg-polymer similarity index 100% rename from examples/USER/misc/charge_regulation/data.chreg-polymer rename to examples/PACKAGES/charge_regulation/data.chreg-polymer diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid b/examples/PACKAGES/charge_regulation/in.chreg-acid similarity index 100% rename from examples/USER/misc/charge_regulation/in.chreg-acid rename to examples/PACKAGES/charge_regulation/in.chreg-acid diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/PACKAGES/charge_regulation/in.chreg-acid-real similarity index 100% rename from examples/USER/misc/charge_regulation/in.chreg-acid-real rename to examples/PACKAGES/charge_regulation/in.chreg-acid-real diff --git a/examples/USER/misc/charge_regulation/in.chreg-polymer b/examples/PACKAGES/charge_regulation/in.chreg-polymer similarity index 100% rename from examples/USER/misc/charge_regulation/in.chreg-polymer rename to examples/PACKAGES/charge_regulation/in.chreg-polymer diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 b/examples/PACKAGES/charge_regulation/log.10Feb21.chreg-acid.g++.1 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 rename to examples/PACKAGES/charge_regulation/log.10Feb21.chreg-acid.g++.1 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 b/examples/PACKAGES/charge_regulation/log.10Feb21.chreg-acid.g++.4 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 rename to examples/PACKAGES/charge_regulation/log.10Feb21.chreg-acid.g++.4 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 b/examples/PACKAGES/charge_regulation/log.10Feb21.chreg-polymer.g++.1 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 rename to examples/PACKAGES/charge_regulation/log.10Feb21.chreg-polymer.g++.1 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 b/examples/PACKAGES/charge_regulation/log.10Feb21.chreg-polymer.g++.4 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 rename to examples/PACKAGES/charge_regulation/log.10Feb21.chreg-polymer.g++.4 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/PACKAGES/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 similarity index 100% rename from examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 rename to examples/PACKAGES/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/PACKAGES/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 similarity index 100% rename from examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 rename to examples/PACKAGES/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 diff --git a/examples/USER/misc/cnp/Cu_Mishin1.eam b/examples/PACKAGES/cnp/Cu_Mishin1.eam similarity index 100% rename from examples/USER/misc/cnp/Cu_Mishin1.eam rename to examples/PACKAGES/cnp/Cu_Mishin1.eam diff --git a/examples/USER/misc/cnp/in.cnp b/examples/PACKAGES/cnp/in.cnp similarity index 100% rename from examples/USER/misc/cnp/in.cnp rename to examples/PACKAGES/cnp/in.cnp diff --git a/examples/USER/misc/cnp/log.31May17.cnp.g++.4 b/examples/PACKAGES/cnp/log.31May17.cnp.g++.4 similarity index 100% rename from examples/USER/misc/cnp/log.31May17.cnp.g++.4 rename to examples/PACKAGES/cnp/log.31May17.cnp.g++.4 diff --git a/examples/USER/colvars/data.peptide b/examples/PACKAGES/colvars/data.peptide similarity index 100% rename from examples/USER/colvars/data.peptide rename to examples/PACKAGES/colvars/data.peptide diff --git a/examples/USER/colvars/in.peptide-colvars b/examples/PACKAGES/colvars/in.peptide-colvars similarity index 100% rename from examples/USER/colvars/in.peptide-colvars rename to examples/PACKAGES/colvars/in.peptide-colvars diff --git a/examples/USER/colvars/in.peptide-colvars2 b/examples/PACKAGES/colvars/in.peptide-colvars2 similarity index 100% rename from examples/USER/colvars/in.peptide-colvars2 rename to examples/PACKAGES/colvars/in.peptide-colvars2 diff --git a/examples/USER/colvars/in.peptide-spring b/examples/PACKAGES/colvars/in.peptide-spring similarity index 100% rename from examples/USER/colvars/in.peptide-spring rename to examples/PACKAGES/colvars/in.peptide-spring diff --git a/examples/USER/colvars/in.peptide-spring2 b/examples/PACKAGES/colvars/in.peptide-spring2 similarity index 100% rename from examples/USER/colvars/in.peptide-spring2 rename to examples/PACKAGES/colvars/in.peptide-spring2 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 diff --git a/examples/USER/colvars/out.colvars.state b/examples/PACKAGES/colvars/out.colvars.state similarity index 100% rename from examples/USER/colvars/out.colvars.state rename to examples/PACKAGES/colvars/out.colvars.state diff --git a/examples/USER/colvars/out.colvars.state.old b/examples/PACKAGES/colvars/out.colvars.state.old similarity index 100% rename from examples/USER/colvars/out.colvars.state.old rename to examples/PACKAGES/colvars/out.colvars.state.old diff --git a/examples/USER/colvars/out.colvars.traj b/examples/PACKAGES/colvars/out.colvars.traj similarity index 100% rename from examples/USER/colvars/out.colvars.traj rename to examples/PACKAGES/colvars/out.colvars.traj diff --git a/examples/USER/colvars/out2.colvars.state b/examples/PACKAGES/colvars/out2.colvars.state similarity index 100% rename from examples/USER/colvars/out2.colvars.state rename to examples/PACKAGES/colvars/out2.colvars.state diff --git a/examples/USER/colvars/out2.colvars.traj b/examples/PACKAGES/colvars/out2.colvars.traj similarity index 100% rename from examples/USER/colvars/out2.colvars.traj rename to examples/PACKAGES/colvars/out2.colvars.traj diff --git a/examples/USER/colvars/peptide.colvars b/examples/PACKAGES/colvars/peptide.colvars similarity index 100% rename from examples/USER/colvars/peptide.colvars rename to examples/PACKAGES/colvars/peptide.colvars diff --git a/examples/USER/colvars/peptide.colvars2 b/examples/PACKAGES/colvars/peptide.colvars2 similarity index 100% rename from examples/USER/colvars/peptide.colvars2 rename to examples/PACKAGES/colvars/peptide.colvars2 diff --git a/examples/USER/colvars/peptide.psf b/examples/PACKAGES/colvars/peptide.psf similarity index 100% rename from examples/USER/colvars/peptide.psf rename to examples/PACKAGES/colvars/peptide.psf diff --git a/examples/USER/colvars/peptide2.colvars.state b/examples/PACKAGES/colvars/peptide2.colvars.state similarity index 100% rename from examples/USER/colvars/peptide2.colvars.state rename to examples/PACKAGES/colvars/peptide2.colvars.state diff --git a/examples/USER/colvars/peptide2.colvars.traj b/examples/PACKAGES/colvars/peptide2.colvars.traj similarity index 100% rename from examples/USER/colvars/peptide2.colvars.traj rename to examples/PACKAGES/colvars/peptide2.colvars.traj diff --git a/examples/USER/dielectric/README b/examples/PACKAGES/dielectric/README similarity index 89% rename from examples/USER/dielectric/README rename to examples/PACKAGES/dielectric/README index 6cbb1e204d..1d5f30263c 100644 --- a/examples/USER/dielectric/README +++ b/examples/PACKAGES/dielectric/README @@ -1,4 +1,4 @@ -This folder contains some example data and input scripts for the USER-DIELECTRIC package. Please refer to the following reference for more details: +This folder contains some example data and input scripts for the DIELECTRIC package. Please refer to the following reference for more details: Nguyen TD, Li H, Bagchi D, Solis FJ, Olvera de la Cruz, Incorporating surface polarization effects into large-scale coarse-grained molecular dynamics simulation, Computer Physics Communications 2019, 241, 80--91. @@ -31,9 +31,7 @@ where * epsilon = the local epsilon value at the vertex or at the ion. For real charges, epsilon is the medium dielectric constant, and q is the real (unscaled) charges. - For interface particles: - + if q is zero (zero surface charges), epsilon is set to be 1.0; - + if q is nonzero (charged surfaces), epsilon is set to be em + For interface particles, epsilon is set to be em (the mean dielectric value above). * area_per_patch: the surface area of the patch (element). diff --git a/examples/PACKAGES/dielectric/data.confined b/examples/PACKAGES/dielectric/data.confined new file mode 100644 index 0000000000..2e166151bb --- /dev/null +++ b/examples/PACKAGES/dielectric/data.confined @@ -0,0 +1,4019 @@ +LAMMPS data file: two oppositely charged ions confined between two walls + +4002 atoms +3 atom types + +0.0000000000000000e+00 4.0000006274935302e+01 xlo xhi +0.0000000000000000e+00 4.3301276792816687e+01 ylo yhi +0.0000000000000000e+00 4.0000000000000000e+01 zlo zhi + +Masses + +1 1 +2 1 +3 1 + +Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature + +1 0 1 0 0 0 9.99798 0 0 1 0.866 8 6 6 0 +2 0 1 0 0.500101 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +3 0 1 0 1.0002 0 9.99798 0 0 1 0.866 8 6 6 0 +4 0 1 0 1.5003 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +5 0 1 0 2.0004 0 9.99798 0 0 1 0.866 8 6 6 0 +6 0 1 0 2.50051 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +7 0 1 0 3.00061 0 9.99798 0 0 1 0.866 8 6 6 0 +8 0 1 0 3.50071 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +9 0 1 0 4.00081 0 9.99798 0 0 1 0.866 8 6 6 0 +10 0 1 0 4.50091 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +11 0 1 0 5.00101 0 9.99798 0 0 1 0.866 8 6 6 0 +12 0 1 0 5.50111 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +13 0 1 0 6.00121 0 9.99798 0 0 1 0.866 8 6 6 0 +14 0 1 0 6.50132 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +15 0 1 0 7.00142 0 9.99798 0 0 1 0.866 8 6 6 0 +16 0 1 0 7.50152 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +17 0 1 0 8.00162 0 9.99798 0 0 1 0.866 8 6 6 0 +18 0 1 0 8.50172 0.866201 9.99798 0 0 1 0.866 8 6 6 0 +19 0 1 0 9.00182 0 9.99798 0 0 1 0.866 8 6 6 0 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9.50192 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3861 0 1 0 10.002 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3862 0 1 0 10.5021 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3863 0 1 0 11.0022 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3864 0 1 0 11.5023 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3865 0 1 0 12.0024 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3866 0 1 0 12.5025 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3867 0 1 0 13.0026 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3868 0 1 0 13.5027 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3869 0 1 0 14.0028 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3870 0 1 0 14.5029 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3871 0 1 0 15.003 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3872 0 1 0 15.5031 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3873 0 1 0 16.0032 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3874 0 1 0 16.5033 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3875 0 1 0 17.0034 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3876 0 1 0 17.5035 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3877 0 1 0 18.0036 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3878 0 1 0 18.5037 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3879 0 1 0 19.0038 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3880 0 1 0 19.5039 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3881 0 1 0 20.004 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3882 0 1 0 20.5041 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3883 0 1 0 21.0042 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3884 0 1 0 21.5043 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3885 0 1 0 22.0045 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3886 0 1 0 22.5046 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3887 0 1 0 23.0047 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3888 0 1 0 23.5048 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3889 0 1 0 24.0049 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3890 0 1 0 24.505 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3891 0 1 0 25.0051 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3892 0 1 0 25.5052 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3893 0 1 0 26.0053 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3894 0 1 0 26.5054 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3895 0 1 0 27.0055 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3896 0 1 0 27.5056 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3897 0 1 0 28.0057 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3898 0 1 0 28.5058 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3899 0 1 0 29.0059 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3900 0 1 0 29.506 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3901 0 1 0 30.0061 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3902 0 1 0 30.5062 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3903 0 1 0 31.0063 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3904 0 1 0 31.5064 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3905 0 1 0 32.0065 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3906 0 1 0 32.5066 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3907 0 1 0 33.0067 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3908 0 1 0 33.5068 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3909 0 1 0 34.0069 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3910 0 1 0 34.507 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3911 0 1 0 35.0071 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3912 0 1 0 35.5072 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3913 0 1 0 36.0073 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3914 0 1 0 36.5074 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3915 0 1 0 37.0075 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3916 0 1 0 37.5076 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3917 0 1 0 38.0077 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3918 0 1 0 38.5078 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3919 0 1 0 39.0079 39.8452 30.002 0 0 -1 0.866 8 6 6 0 +3920 0 1 0 39.508 40.7114 30.002 0 0 -1 0.866 8 6 6 0 +3921 0 1 0 0 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3922 0 1 0 0.500101 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3923 0 1 0 1.0002 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3924 0 1 0 1.5003 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3925 0 1 0 2.0004 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3926 0 1 0 2.50051 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3927 0 1 0 3.00061 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3928 0 1 0 3.50071 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3929 0 1 0 4.00081 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3930 0 1 0 4.50091 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3931 0 1 0 5.00101 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3932 0 1 0 5.50111 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3933 0 1 0 6.00121 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3934 0 1 0 6.50132 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3935 0 1 0 7.00142 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3936 0 1 0 7.50152 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3937 0 1 0 8.00162 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3938 0 1 0 8.50172 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3939 0 1 0 9.00182 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3940 0 1 0 9.50192 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3941 0 1 0 10.002 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3942 0 1 0 10.5021 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3943 0 1 0 11.0022 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3944 0 1 0 11.5023 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3945 0 1 0 12.0024 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3946 0 1 0 12.5025 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3947 0 1 0 13.0026 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3948 0 1 0 13.5027 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3949 0 1 0 14.0028 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3950 0 1 0 14.5029 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3951 0 1 0 15.003 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3952 0 1 0 15.5031 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3953 0 1 0 16.0032 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3954 0 1 0 16.5033 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3955 0 1 0 17.0034 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3956 0 1 0 17.5035 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3957 0 1 0 18.0036 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3958 0 1 0 18.5037 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3959 0 1 0 19.0038 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3960 0 1 0 19.5039 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3961 0 1 0 20.004 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3962 0 1 0 20.5041 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3963 0 1 0 21.0042 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3964 0 1 0 21.5043 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3965 0 1 0 22.0045 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3966 0 1 0 22.5046 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3967 0 1 0 23.0047 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3968 0 1 0 23.5048 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3969 0 1 0 24.0049 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3970 0 1 0 24.505 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3971 0 1 0 25.0051 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3972 0 1 0 25.5052 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3973 0 1 0 26.0053 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3974 0 1 0 26.5054 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3975 0 1 0 27.0055 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3976 0 1 0 27.5056 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3977 0 1 0 28.0057 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3978 0 1 0 28.5058 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3979 0 1 0 29.0059 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3980 0 1 0 29.506 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3981 0 1 0 30.0061 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3982 0 1 0 30.5062 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3983 0 1 0 31.0063 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3984 0 1 0 31.5064 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3985 0 1 0 32.0065 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3986 0 1 0 32.5066 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3987 0 1 0 33.0067 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3988 0 1 0 33.5068 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3989 0 1 0 34.0069 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3990 0 1 0 34.507 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3991 0 1 0 35.0071 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3992 0 1 0 35.5072 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3993 0 1 0 36.0073 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3994 0 1 0 36.5074 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3995 0 1 0 37.0075 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3996 0 1 0 37.5076 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3997 0 1 0 38.0077 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +3998 0 1 0 38.5078 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +3999 0 1 0 39.0079 41.5776 30.002 0 0 -1 0.866 8 6 6 0 +4000 0 1 0 39.508 42.4438 30.002 0 0 -1 0.866 8 6 6 0 +4001 0 2 1 15 20 15 0 0 1 0.866 8 6 10 0 +4002 0 3 -1 25 20 25 0 0 1 0.866 8 6 10 0 diff --git a/examples/USER/dielectric/data.sphere b/examples/PACKAGES/dielectric/data.sphere similarity index 74% rename from examples/USER/dielectric/data.sphere rename to examples/PACKAGES/dielectric/data.sphere index 152d5ff41a..3e98e8211f 100644 --- a/examples/USER/dielectric/data.sphere +++ b/examples/PACKAGES/dielectric/data.sphere @@ -16,2567 +16,2567 @@ Masses Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature -1 1 1 0 50 55.2573 41.4935 0 0.525731 -0.850651 0.490491 45 57.5 1 0 -2 1 1 0 50.4064 55.7206 41.8079 0.0406403 0.572055 -0.819208 0.490491 45 57.5 1 0 -3 1 1 0 49.5936 55.7206 41.8079 -0.0406403 0.572055 -0.819208 0.490491 45 57.5 1 0 -4 1 1 0 50.8109 56.1564 42.1616 0.081086 0.615642 -0.783843 0.490491 45 57.5 1 0 -5 1 1 0 50 56.1768 42.1357 0 0.617676 -0.786433 0.490491 45 57.5 1 0 -6 1 1 0 49.1891 56.1564 42.1616 -0.081086 0.615642 -0.783843 0.490491 45 57.5 1 0 -7 1 1 0 51.2114 56.5628 42.5527 0.121144 0.656282 -0.744727 0.490491 45 57.5 1 0 -8 1 1 0 50.4064 56.6088 42.5061 0.0406418 0.660883 -0.749387 0.490491 45 57.5 1 0 -9 1 1 0 51.6062 56.9378 42.9795 0.160622 0.69378 -0.702047 0.490491 45 57.5 1 0 -10 1 1 0 50.8057 57.0062 42.9103 0.0805729 0.700622 -0.708969 0.490491 45 57.5 1 0 -11 1 1 0 50 57.0291 42.8872 0 0.702907 -0.711282 0.490491 45 57.5 1 0 -12 1 1 0 49.5936 56.6088 42.5061 -0.0406418 0.660883 -0.749387 0.490491 45 57.5 1 0 -13 1 1 0 48.7886 56.5628 42.5527 -0.121144 0.656282 -0.744727 0.490491 45 57.5 1 0 -14 1 1 0 49.1943 57.0062 42.9103 -0.0805729 0.700622 -0.708969 0.490491 45 57.5 1 0 -15 1 1 0 48.3938 56.9378 42.9795 -0.160622 0.69378 -0.702047 0.490491 45 57.5 1 0 -16 1 1 0 51.9933 57.2796 43.4399 0.199331 0.727959 -0.656006 0.490491 45 57.5 1 0 -17 1 1 0 51.2119 57.3889 43.3716 0.121192 0.738887 -0.662842 0.490491 45 57.5 1 0 -18 1 1 0 52.3709 57.5865 43.9317 0.237086 0.758652 -0.606825 0.490491 45 57.5 1 0 -19 1 1 0 51.5961 57.7184 43.8454 0.159613 0.771841 -0.615456 0.490491 45 57.5 1 0 -20 1 1 0 50.8114 57.802 43.7976 0.0811417 0.780205 -0.620239 0.490491 45 57.5 1 0 -21 1 1 0 52.7371 57.8572 44.4526 0.273706 0.785715 -0.55474 0.490491 45 57.5 1 0 -22 1 1 0 51.9727 58.015 44.3549 0.197274 0.801504 -0.564513 0.490491 45 57.5 1 0 -23 1 1 0 53.0902 58.0902 45 0.309017 0.809017 -0.5 0.490491 45 57.5 1 0 -24 1 1 0 52.3345 58.2715 44.888 0.233445 0.827147 -0.511205 0.490491 45 57.5 1 0 -25 1 1 0 51.5643 58.4018 44.8074 0.156434 0.840178 -0.519259 0.490491 45 57.5 1 0 -26 1 1 0 51.1908 58.1217 44.2886 0.119078 0.81217 -0.57114 0.490491 45 57.5 1 0 -27 1 1 0 50.4067 58.1752 44.2554 0.040675 0.817523 -0.574458 0.490491 45 57.5 1 0 -28 1 1 0 50.7846 58.4803 44.7589 0.0784592 0.848029 -0.52411 0.490491 45 57.5 1 0 -29 1 1 0 50 58.5065 44.7427 0 0.850651 -0.525731 0.490491 45 57.5 1 0 -30 1 1 0 48.7881 57.3889 43.3716 -0.121192 0.738887 -0.662842 0.490491 45 57.5 1 0 -31 1 1 0 48.0067 57.2796 43.4399 -0.199331 0.727959 -0.656006 0.490491 45 57.5 1 0 -32 1 1 0 49.1886 57.802 43.7976 -0.0811417 0.780205 -0.620239 0.490491 45 57.5 1 0 -33 1 1 0 48.4039 57.7184 43.8454 -0.159613 0.771841 -0.615456 0.490491 45 57.5 1 0 -34 1 1 0 47.6291 57.5865 43.9317 -0.237086 0.758652 -0.606825 0.490491 45 57.5 1 0 -35 1 1 0 49.5933 58.1752 44.2554 -0.040675 0.817523 -0.574458 0.490491 45 57.5 1 0 -36 1 1 0 48.8092 58.1217 44.2886 -0.119078 0.81217 -0.57114 0.490491 45 57.5 1 0 -37 1 1 0 49.2154 58.4803 44.7589 -0.0784592 0.848029 -0.52411 0.490491 45 57.5 1 0 -38 1 1 0 48.4357 58.4018 44.8074 -0.156434 0.840178 -0.519259 0.490491 45 57.5 1 0 -39 1 1 0 48.0273 58.015 44.3549 -0.197274 0.801504 -0.564513 0.490491 45 57.5 1 0 -40 1 1 0 47.2629 57.8572 44.4526 -0.273706 0.785715 -0.55474 0.490491 45 57.5 1 0 -41 1 1 0 47.6655 58.2715 44.888 -0.233445 0.827147 -0.511205 0.490491 45 57.5 1 0 -42 1 1 0 46.9098 58.0902 45 -0.309017 0.809017 -0.5 0.490491 45 57.5 1 0 -43 1 1 0 50.4068 57.435 43.325 0.0406769 0.743496 -0.667502 0.490491 45 57.5 1 0 -44 1 1 0 50 57.8279 43.7771 0 0.782786 -0.622291 0.490491 45 57.5 1 0 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57.5 1 0 -1203 1 1 0 41.1716 53.2486 53.3921 -0.882837 0.324863 0.339209 0.490491 45 57.5 1 0 -1204 1 1 0 41.3733 52.5989 54.3389 -0.862669 0.259892 0.433888 0.490491 45 57.5 1 0 -1205 1 1 0 41.0826 52.6266 53.6852 -0.891742 0.262661 0.368518 0.490491 45 57.5 1 0 -1206 1 1 0 40.8376 52.6408 53.0126 -0.916244 0.264082 0.301258 0.490491 45 57.5 1 0 -1207 1 1 0 40.9417 53.2593 52.7063 -0.905832 0.325929 0.270627 0.490491 45 57.5 1 0 -1208 1 1 0 40.7612 53.2553 52.0119 -0.92388 0.32553 0.201189 0.490491 45 57.5 1 0 -1209 1 1 0 40.6395 52.6415 52.3245 -0.93605 0.264151 0.232455 0.490491 45 57.5 1 0 -1210 1 1 0 40.4894 52.6287 51.6246 -0.951057 0.262865 0.16246 0.490491 45 57.5 1 0 -1211 1 1 0 41.3413 51.9602 54.6027 -0.865871 0.196015 0.460266 0.490491 45 57.5 1 0 -1212 1 1 0 41.036 51.9641 53.9735 -0.896401 0.196412 0.39735 0.490491 45 57.5 1 0 -1213 1 1 0 41.3507 51.312 54.8444 -0.864929 0.1312 0.484441 0.490491 45 57.5 1 0 -1214 1 1 0 41.032 51.3175 54.2236 -0.896801 0.131749 0.422363 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45 57.5 1 0 -1822 1 1 0 44.4758 56.6961 54.9644 -0.552418 0.669612 0.496441 0.490491 45 57.5 1 0 -1823 1 1 0 45.1479 57.0447 55.1797 -0.485208 0.704471 0.51797 0.490491 45 57.5 1 0 -1824 1 1 0 45.8573 57.3501 55.3678 -0.414272 0.735011 0.536784 0.490491 45 57.5 1 0 -1825 1 1 0 43.9252 55.4065 55.8195 -0.607478 0.54065 0.581952 0.490491 45 57.5 1 0 -1826 1 1 0 44.1805 56.0748 55.4065 -0.581952 0.607478 0.54065 0.490491 45 57.5 1 0 -1827 1 1 0 44.5935 55.8195 56.0748 -0.54065 0.581952 0.607478 0.490491 45 57.5 1 0 -1828 1 1 0 51.0649 55.5186 58.2711 0.106494 0.551859 0.82711 0.490491 45 57.5 1 0 -1829 1 1 0 51.4741 55.949 57.9017 0.147413 0.594895 0.79017 0.490491 45 57.5 1 0 -1830 1 1 0 51.8743 56.3458 57.4979 0.187432 0.634579 0.749786 0.490491 45 57.5 1 0 -1831 1 1 0 52.1302 55.7125 57.9265 0.213023 0.571251 0.79265 0.490491 45 57.5 1 0 -1832 1 1 0 51.7253 55.2913 58.3081 0.172532 0.529135 0.830812 0.490491 45 57.5 1 0 -1833 1 1 0 52.3723 55.0421 58.3036 0.237228 0.504209 0.830359 0.490491 45 57.5 1 0 -1834 1 1 0 52.289 56.7232 57.0398 0.228899 0.672319 0.703983 0.490491 45 57.5 1 0 -1835 1 1 0 52.6738 57.0524 56.5662 0.267381 0.705236 0.65662 0.490491 45 57.5 1 0 -1836 1 1 0 52.96 56.4741 57.0231 0.296004 0.647412 0.70231 0.490491 45 57.5 1 0 -1837 1 1 0 53.0521 57.3479 56.0574 0.305212 0.734794 0.605742 0.490491 45 57.5 1 0 -1838 1 1 0 53.4143 57.6041 55.5245 0.341435 0.760406 0.552454 0.490491 45 57.5 1 0 -1839 1 1 0 53.7175 57.0711 56.015 0.371748 0.707107 0.601501 0.490491 45 57.5 1 0 -1840 1 1 0 53.3469 56.7891 56.535 0.334691 0.678913 0.653497 0.490491 45 57.5 1 0 -1841 1 1 0 53.6159 56.1919 56.9704 0.361591 0.619186 0.697037 0.490491 45 57.5 1 0 -1842 1 1 0 53.9977 56.4945 56.4684 0.399769 0.649448 0.64684 0.490491 45 57.5 1 0 -1843 1 1 0 54.2533 55.8779 56.8819 0.425325 0.587785 0.688191 0.490491 45 57.5 1 0 -1844 1 1 0 53.038 54.7623 58.2518 0.303801 0.476225 0.825175 0.490491 45 57.5 1 0 -1845 1 1 0 53.4615 55.1612 57.8345 0.346153 0.516122 0.783452 0.490491 45 57.5 1 0 -1846 1 1 0 53.6603 54.4698 58.1623 0.366027 0.446977 0.816233 0.490491 45 57.5 1 0 -1847 1 1 0 53.8673 55.5337 57.3771 0.38673 0.553372 0.737712 0.490491 45 57.5 1 0 -1848 1 1 0 54.0829 54.8624 57.7258 0.408286 0.48624 0.772575 0.490491 45 57.5 1 0 -1849 1 1 0 54.4826 55.225 57.253 0.448259 0.522499 0.725299 0.490491 45 57.5 1 0 -1850 1 1 0 54.6843 54.5399 57.5794 0.46843 0.45399 0.757936 0.490491 45 57.5 1 0 -1851 1 1 0 54.2713 54.156 58.0302 0.427135 0.415597 0.803016 0.490491 45 57.5 1 0 -1852 1 1 0 54.8571 53.8268 57.859 0.485712 0.382683 0.785899 0.490491 45 57.5 1 0 -1853 1 1 0 52.5518 56.1093 57.4944 0.25518 0.610926 0.749435 0.490491 45 57.5 1 0 -1854 1 1 0 53.2214 55.8369 57.4534 0.322141 0.583692 0.745339 0.490491 45 57.5 1 0 -1855 1 1 0 52.8032 55.4511 57.9011 0.280319 0.545109 0.790112 0.490491 45 57.5 1 0 -1856 1 1 0 53.8268 57.859 54.8571 0.382683 0.785899 0.485712 0.490491 45 57.5 1 0 -1857 1 1 0 54.156 58.0302 54.2713 0.415597 0.803016 0.427135 0.490491 45 57.5 1 0 -1858 1 1 0 54.5399 57.5794 54.6843 0.45399 0.757936 0.46843 0.490491 45 57.5 1 0 -1859 1 1 0 54.4698 58.1623 53.6603 0.446977 0.816233 0.366027 0.490491 45 57.5 1 0 -1860 1 1 0 54.7623 58.2518 53.038 0.476225 0.825175 0.303801 0.490491 45 57.5 1 0 -1861 1 1 0 55.1612 57.8345 53.4615 0.516122 0.783452 0.346153 0.490491 45 57.5 1 0 -1862 1 1 0 54.8624 57.7258 54.0829 0.48624 0.772575 0.408286 0.490491 45 57.5 1 0 -1863 1 1 0 55.225 57.253 54.4826 0.522499 0.725299 0.448259 0.490491 45 57.5 1 0 -1864 1 1 0 55.5337 57.3771 53.8673 0.553372 0.737712 0.38673 0.490491 45 57.5 1 0 -1865 1 1 0 55.8779 56.8819 54.2533 0.587785 0.688191 0.425325 0.490491 45 57.5 1 0 -1866 1 1 0 55.0421 58.3036 52.3723 0.504209 0.830359 0.237228 0.490491 45 57.5 1 0 -1867 1 1 0 55.2913 58.3081 51.7253 0.529135 0.830812 0.172532 0.490491 45 57.5 1 0 -1868 1 1 0 55.7125 57.9265 52.1302 0.571251 0.79265 0.213023 0.490491 45 57.5 1 0 -1869 1 1 0 55.5186 58.2711 51.0649 0.551859 0.82711 0.106494 0.490491 45 57.5 1 0 -1870 1 1 0 55.949 57.9017 51.4741 0.594895 0.79017 0.147413 0.490491 45 57.5 1 0 -1871 1 1 0 56.3458 57.4979 51.8743 0.634579 0.749786 0.187432 0.490491 45 57.5 1 0 -1872 1 1 0 56.1919 56.9704 53.6159 0.619186 0.697037 0.361591 0.490491 45 57.5 1 0 -1873 1 1 0 56.4945 56.4684 53.9977 0.649448 0.64684 0.399769 0.490491 45 57.5 1 0 -1874 1 1 0 56.4741 57.0231 52.96 0.647412 0.70231 0.296004 0.490491 45 57.5 1 0 -1875 1 1 0 56.7891 56.535 53.3469 0.678913 0.653497 0.334691 0.490491 45 57.5 1 0 -1876 1 1 0 57.0711 56.015 53.7175 0.707107 0.601501 0.371748 0.490491 45 57.5 1 0 -1877 1 1 0 56.7232 57.0398 52.289 0.672319 0.703983 0.228899 0.490491 45 57.5 1 0 -1878 1 1 0 57.0524 56.5662 52.6738 0.705236 0.65662 0.267381 0.490491 45 57.5 1 0 -1879 1 1 0 57.3479 56.0574 53.0521 0.734794 0.605742 0.305212 0.490491 45 57.5 1 0 -1880 1 1 0 57.6041 55.5245 53.4143 0.760406 0.552454 0.341435 0.490491 45 57.5 1 0 -1881 1 1 0 55.4511 57.9011 52.8032 0.545109 0.790112 0.280319 0.490491 45 57.5 1 0 -1882 1 1 0 56.1093 57.4944 52.5518 0.610926 0.749435 0.25518 0.490491 45 57.5 1 0 -1883 1 1 0 55.8369 57.4534 53.2214 0.583692 0.745339 0.322141 0.490491 45 57.5 1 0 -1884 1 1 0 55.5245 53.4143 57.6041 0.552454 0.341435 0.760406 0.490491 45 57.5 1 0 -1885 1 1 0 56.015 53.7175 57.0711 0.601501 0.371748 0.707107 0.490491 45 57.5 1 0 -1886 1 1 0 56.0574 53.0521 57.3479 0.605742 0.305212 0.734794 0.490491 45 57.5 1 0 -1887 1 1 0 56.4684 53.9977 56.4945 0.64684 0.399769 0.649448 0.490491 45 57.5 1 0 -1888 1 1 0 56.535 53.3469 56.7891 0.653497 0.334691 0.678913 0.490491 45 57.5 1 0 -1889 1 1 0 56.8819 54.2533 55.8779 0.688191 0.425325 0.587785 0.490491 45 57.5 1 0 -1890 1 1 0 56.9704 53.6159 56.1919 0.697037 0.361591 0.619186 0.490491 45 57.5 1 0 -1891 1 1 0 57.0231 52.96 56.4741 0.70231 0.296004 0.647412 0.490491 45 57.5 1 0 -1892 1 1 0 56.5662 52.6738 57.0524 0.65662 0.267381 0.705236 0.490491 45 57.5 1 0 -1893 1 1 0 57.0398 52.289 56.7232 0.703983 0.228899 0.672319 0.490491 45 57.5 1 0 -1894 1 1 0 57.253 54.4826 55.225 0.725299 0.448259 0.522499 0.490491 45 57.5 1 0 -1895 1 1 0 57.3771 53.8673 55.5337 0.737712 0.38673 0.553372 0.490491 45 57.5 1 0 -1896 1 1 0 57.5794 54.6843 54.5399 0.757936 0.46843 0.45399 0.490491 45 57.5 1 0 -1897 1 1 0 57.7258 54.0829 54.8624 0.772575 0.408286 0.48624 0.490491 45 57.5 1 0 -1898 1 1 0 57.8345 53.4615 55.1612 0.783452 0.346153 0.516122 0.490491 45 57.5 1 0 -1899 1 1 0 57.859 54.8571 53.8268 0.785899 0.485712 0.382683 0.490491 45 57.5 1 0 -1900 1 1 0 58.0302 54.2713 54.156 0.803016 0.427135 0.415597 0.490491 45 57.5 1 0 -1901 1 1 0 58.1623 53.6603 54.4698 0.816233 0.366027 0.446977 0.490491 45 57.5 1 0 -1902 1 1 0 58.2518 53.038 54.7623 0.825175 0.303801 0.476225 0.490491 45 57.5 1 0 -1903 1 1 0 57.4979 51.8743 56.3458 0.749786 0.187432 0.634579 0.490491 45 57.5 1 0 -1904 1 1 0 57.9265 52.1302 55.7125 0.79265 0.213023 0.571251 0.490491 45 57.5 1 0 -1905 1 1 0 57.9017 51.4741 55.949 0.79017 0.147413 0.594895 0.490491 45 57.5 1 0 -1906 1 1 0 58.3036 52.3723 55.0421 0.830359 0.237228 0.504209 0.490491 45 57.5 1 0 -1907 1 1 0 58.3081 51.7253 55.2913 0.830812 0.172532 0.529135 0.490491 45 57.5 1 0 -1908 1 1 0 58.2711 51.0649 55.5186 0.82711 0.106494 0.551859 0.490491 45 57.5 1 0 -1909 1 1 0 57.4534 53.2214 55.8369 0.745339 0.322141 0.583692 0.490491 45 57.5 1 0 -1910 1 1 0 57.9011 52.8032 55.4511 0.790112 0.280319 0.545109 0.490491 45 57.5 1 0 -1911 1 1 0 57.4944 52.5518 56.1093 0.749435 0.25518 0.610926 0.490491 45 57.5 1 0 -1912 1 1 0 54.1427 57.3501 55.3678 0.414272 0.735011 0.536784 0.490491 45 57.5 1 0 -1913 1 1 0 54.8521 57.0447 55.1797 0.485208 0.704471 0.51797 0.490491 45 57.5 1 0 -1914 1 1 0 55.5242 56.6961 54.9644 0.552418 0.669612 0.496441 0.490491 45 57.5 1 0 -1915 1 1 0 55.1338 56.4658 55.6425 0.513375 0.646578 0.564254 0.490491 45 57.5 1 0 -1916 1 1 0 54.4396 56.7898 55.8472 0.443957 0.678977 0.584716 0.490491 45 57.5 1 0 -1917 1 1 0 54.7092 56.1924 56.2831 0.470917 0.619242 0.628313 0.490491 45 57.5 1 0 -1918 1 1 0 56.1924 56.2831 54.7092 0.619242 0.628313 0.470917 0.490491 45 57.5 1 0 -1919 1 1 0 56.7898 55.8472 54.4396 0.678977 0.584716 0.443957 0.490491 45 57.5 1 0 -1920 1 1 0 56.4658 55.6425 55.1338 0.646578 0.564254 0.513375 0.490491 45 57.5 1 0 -1921 1 1 0 57.3501 55.3678 54.1427 0.735011 0.536784 0.414272 0.490491 45 57.5 1 0 -1922 1 1 0 57.0447 55.1797 54.8521 0.704471 0.51797 0.485208 0.490491 45 57.5 1 0 -1923 1 1 0 56.6961 54.9644 55.5242 0.669612 0.496441 0.552418 0.490491 45 57.5 1 0 -1924 1 1 0 54.9644 55.5242 56.6961 0.496441 0.552418 0.669612 0.490491 45 57.5 1 0 -1925 1 1 0 55.6425 55.1338 56.4658 0.564254 0.513375 0.646578 0.490491 45 57.5 1 0 -1926 1 1 0 55.1797 54.8521 57.0447 0.51797 0.485208 0.704471 0.490491 45 57.5 1 0 -1927 1 1 0 56.2831 54.7092 56.1924 0.628313 0.470917 0.619242 0.490491 45 57.5 1 0 -1928 1 1 0 55.8472 54.4396 56.7898 0.584716 0.443957 0.678977 0.490491 45 57.5 1 0 -1929 1 1 0 55.3678 54.1427 57.3501 0.536784 0.414272 0.735011 0.490491 45 57.5 1 0 -1930 1 1 0 55.8195 56.0748 55.4065 0.581952 0.607478 0.54065 0.490491 45 57.5 1 0 -1931 1 1 0 56.0748 55.4065 55.8195 0.607478 0.54065 0.581952 0.490491 45 57.5 1 0 -1932 1 1 0 55.4065 55.8195 56.0748 0.54065 0.581952 0.607478 0.490491 45 57.5 1 0 -1933 1 1 0 48.9351 55.5186 41.7289 -0.106494 0.551859 -0.82711 0.490491 45 57.5 1 0 -1934 1 1 0 48.5259 55.949 42.0983 -0.147413 0.594895 -0.79017 0.490491 45 57.5 1 0 -1935 1 1 0 48.1257 56.3458 42.5021 -0.187432 0.634579 -0.749786 0.490491 45 57.5 1 0 -1936 1 1 0 47.8698 55.7125 42.0735 -0.213023 0.571251 -0.79265 0.490491 45 57.5 1 0 -1937 1 1 0 48.2747 55.2913 41.6919 -0.172532 0.529135 -0.830812 0.490491 45 57.5 1 0 -1938 1 1 0 47.6277 55.0421 41.6964 -0.237228 0.504209 -0.830359 0.490491 45 57.5 1 0 -1939 1 1 0 47.711 56.7232 42.9602 -0.228899 0.672319 -0.703983 0.490491 45 57.5 1 0 -1940 1 1 0 47.3262 57.0524 43.4338 -0.267381 0.705236 -0.65662 0.490491 45 57.5 1 0 -1941 1 1 0 47.04 56.4741 42.9769 -0.296004 0.647412 -0.70231 0.490491 45 57.5 1 0 -1942 1 1 0 46.9479 57.3479 43.9426 -0.305212 0.734794 -0.605742 0.490491 45 57.5 1 0 -1943 1 1 0 46.5857 57.6041 44.4755 -0.341435 0.760406 -0.552454 0.490491 45 57.5 1 0 -1944 1 1 0 46.2825 57.0711 43.985 -0.371748 0.707107 -0.601501 0.490491 45 57.5 1 0 -1945 1 1 0 46.6531 56.7891 43.465 -0.334691 0.678913 -0.653497 0.490491 45 57.5 1 0 -1946 1 1 0 46.3841 56.1919 43.0296 -0.361591 0.619186 -0.697037 0.490491 45 57.5 1 0 -1947 1 1 0 46.0023 56.4945 43.5316 -0.399769 0.649448 -0.64684 0.490491 45 57.5 1 0 -1948 1 1 0 45.7467 55.8779 43.1181 -0.425325 0.587785 -0.688191 0.490491 45 57.5 1 0 -1949 1 1 0 46.962 54.7623 41.7482 -0.303801 0.476225 -0.825175 0.490491 45 57.5 1 0 -1950 1 1 0 46.5385 55.1612 42.1655 -0.346153 0.516122 -0.783452 0.490491 45 57.5 1 0 -1951 1 1 0 46.3397 54.4698 41.8377 -0.366027 0.446977 -0.816233 0.490491 45 57.5 1 0 -1952 1 1 0 46.1327 55.5337 42.6229 -0.38673 0.553372 -0.737712 0.490491 45 57.5 1 0 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0.490491 45 57.5 1 0 -1965 1 1 0 45.2377 58.2518 46.962 -0.476225 0.825175 -0.303801 0.490491 45 57.5 1 0 -1966 1 1 0 44.8388 57.8345 46.5385 -0.516122 0.783452 -0.346153 0.490491 45 57.5 1 0 -1967 1 1 0 45.1376 57.7258 45.9171 -0.48624 0.772575 -0.408286 0.490491 45 57.5 1 0 -1968 1 1 0 44.775 57.253 45.5174 -0.522499 0.725299 -0.448259 0.490491 45 57.5 1 0 -1969 1 1 0 44.4663 57.3771 46.1327 -0.553372 0.737712 -0.38673 0.490491 45 57.5 1 0 -1970 1 1 0 44.1221 56.8819 45.7467 -0.587785 0.688191 -0.425325 0.490491 45 57.5 1 0 -1971 1 1 0 44.9579 58.3036 47.6277 -0.504209 0.830359 -0.237228 0.490491 45 57.5 1 0 -1972 1 1 0 44.7087 58.3081 48.2747 -0.529135 0.830812 -0.172532 0.490491 45 57.5 1 0 -1973 1 1 0 44.2875 57.9265 47.8698 -0.571251 0.79265 -0.213023 0.490491 45 57.5 1 0 -1974 1 1 0 44.4814 58.2711 48.9351 -0.551859 0.82711 -0.106494 0.490491 45 57.5 1 0 -1975 1 1 0 44.051 57.9017 48.5259 -0.594895 0.79017 -0.147413 0.490491 45 57.5 1 0 -1976 1 1 0 43.6542 57.4979 48.1257 -0.634579 0.749786 -0.187432 0.490491 45 57.5 1 0 -1977 1 1 0 43.8081 56.9704 46.3841 -0.619186 0.697037 -0.361591 0.490491 45 57.5 1 0 -1978 1 1 0 43.5055 56.4684 46.0023 -0.649448 0.64684 -0.399769 0.490491 45 57.5 1 0 -1979 1 1 0 43.5259 57.0231 47.04 -0.647412 0.70231 -0.296004 0.490491 45 57.5 1 0 -1980 1 1 0 43.2109 56.535 46.6531 -0.678913 0.653497 -0.334691 0.490491 45 57.5 1 0 -1981 1 1 0 42.9289 56.015 46.2825 -0.707107 0.601501 -0.371748 0.490491 45 57.5 1 0 -1982 1 1 0 43.2768 57.0398 47.711 -0.672319 0.703983 -0.228899 0.490491 45 57.5 1 0 -1983 1 1 0 42.9476 56.5662 47.3262 -0.705236 0.65662 -0.267381 0.490491 45 57.5 1 0 -1984 1 1 0 42.6521 56.0574 46.9479 -0.734794 0.605742 -0.305212 0.490491 45 57.5 1 0 -1985 1 1 0 42.3959 55.5245 46.5857 -0.760406 0.552454 -0.341435 0.490491 45 57.5 1 0 -1986 1 1 0 44.5489 57.9011 47.1968 -0.545109 0.790112 -0.280319 0.490491 45 57.5 1 0 -1987 1 1 0 43.8907 57.4944 47.4482 -0.610926 0.749435 -0.25518 0.490491 45 57.5 1 0 -1988 1 1 0 44.1631 57.4534 46.7786 -0.583692 0.745339 -0.322141 0.490491 45 57.5 1 0 -1989 1 1 0 44.4755 53.4143 42.3959 -0.552454 0.341435 -0.760406 0.490491 45 57.5 1 0 -1990 1 1 0 43.985 53.7175 42.9289 -0.601501 0.371748 -0.707107 0.490491 45 57.5 1 0 -1991 1 1 0 43.9426 53.0521 42.6521 -0.605742 0.305212 -0.734794 0.490491 45 57.5 1 0 -1992 1 1 0 43.5316 53.9977 43.5055 -0.64684 0.399769 -0.649448 0.490491 45 57.5 1 0 -1993 1 1 0 43.465 53.3469 43.2109 -0.653497 0.334691 -0.678913 0.490491 45 57.5 1 0 -1994 1 1 0 43.1181 54.2533 44.1221 -0.688191 0.425325 -0.587785 0.490491 45 57.5 1 0 -1995 1 1 0 43.0296 53.6159 43.8081 -0.697037 0.361591 -0.619186 0.490491 45 57.5 1 0 -1996 1 1 0 42.9769 52.96 43.5259 -0.70231 0.296004 -0.647412 0.490491 45 57.5 1 0 -1997 1 1 0 43.4338 52.6738 42.9476 -0.65662 0.267381 -0.705236 0.490491 45 57.5 1 0 -1998 1 1 0 42.9602 52.289 43.2768 -0.703983 0.228899 -0.672319 0.490491 45 57.5 1 0 -1999 1 1 0 42.747 54.4826 44.775 -0.725299 0.448259 -0.522499 0.490491 45 57.5 1 0 -2000 1 1 0 42.6229 53.8673 44.4663 -0.737712 0.38673 -0.553372 0.490491 45 57.5 1 0 -2001 1 1 0 42.4206 54.6843 45.4601 -0.757936 0.46843 -0.45399 0.490491 45 57.5 1 0 -2002 1 1 0 42.2742 54.0829 45.1376 -0.772575 0.408286 -0.48624 0.490491 45 57.5 1 0 -2003 1 1 0 42.1655 53.4615 44.8388 -0.783452 0.346153 -0.516122 0.490491 45 57.5 1 0 -2004 1 1 0 42.141 54.8571 46.1732 -0.785899 0.485712 -0.382683 0.490491 45 57.5 1 0 -2005 1 1 0 41.9698 54.2713 45.844 -0.803016 0.427135 -0.415597 0.490491 45 57.5 1 0 -2006 1 1 0 41.8377 53.6603 45.5302 -0.816233 0.366027 -0.446977 0.490491 45 57.5 1 0 -2007 1 1 0 41.7482 53.038 45.2377 -0.825175 0.303801 -0.476225 0.490491 45 57.5 1 0 -2008 1 1 0 42.5021 51.8743 43.6542 -0.749786 0.187432 -0.634579 0.490491 45 57.5 1 0 -2009 1 1 0 42.0735 52.1302 44.2875 -0.79265 0.213023 -0.571251 0.490491 45 57.5 1 0 -2010 1 1 0 42.0983 51.4741 44.051 -0.79017 0.147413 -0.594895 0.490491 45 57.5 1 0 -2011 1 1 0 41.6964 52.3723 44.9579 -0.830359 0.237228 -0.504209 0.490491 45 57.5 1 0 -2012 1 1 0 41.6919 51.7253 44.7087 -0.830812 0.172532 -0.529135 0.490491 45 57.5 1 0 -2013 1 1 0 41.7289 51.0649 44.4814 -0.82711 0.106494 -0.551859 0.490491 45 57.5 1 0 -2014 1 1 0 42.5466 53.2214 44.1631 -0.745339 0.322141 -0.583692 0.490491 45 57.5 1 0 -2015 1 1 0 42.0989 52.8032 44.5489 -0.790112 0.280319 -0.545109 0.490491 45 57.5 1 0 -2016 1 1 0 42.5056 52.5518 43.8907 -0.749435 0.25518 -0.610926 0.490491 45 57.5 1 0 -2017 1 1 0 45.8573 57.3501 44.6322 -0.414272 0.735011 -0.536784 0.490491 45 57.5 1 0 -2018 1 1 0 45.1479 57.0447 44.8203 -0.485208 0.704471 -0.51797 0.490491 45 57.5 1 0 -2019 1 1 0 44.4758 56.6961 45.0356 -0.552418 0.669612 -0.496441 0.490491 45 57.5 1 0 -2020 1 1 0 44.8662 56.4658 44.3575 -0.513375 0.646578 -0.564254 0.490491 45 57.5 1 0 -2021 1 1 0 45.5604 56.7898 44.1528 -0.443957 0.678977 -0.584716 0.490491 45 57.5 1 0 -2022 1 1 0 45.2908 56.1924 43.7169 -0.470917 0.619242 -0.628313 0.490491 45 57.5 1 0 -2023 1 1 0 43.8076 56.2831 45.2908 -0.619242 0.628313 -0.470917 0.490491 45 57.5 1 0 -2024 1 1 0 43.2102 55.8472 45.5604 -0.678977 0.584716 -0.443957 0.490491 45 57.5 1 0 -2025 1 1 0 43.5342 55.6425 44.8662 -0.646578 0.564254 -0.513375 0.490491 45 57.5 1 0 -2026 1 1 0 42.6499 55.3678 45.8573 -0.735011 0.536784 -0.414272 0.490491 45 57.5 1 0 -2027 1 1 0 42.9553 55.1797 45.1479 -0.704471 0.51797 -0.485208 0.490491 45 57.5 1 0 -2028 1 1 0 43.3039 54.9644 44.4758 -0.669612 0.496441 -0.552418 0.490491 45 57.5 1 0 -2029 1 1 0 45.0356 55.5242 43.3039 -0.496441 0.552418 -0.669612 0.490491 45 57.5 1 0 -2030 1 1 0 44.3575 55.1338 43.5342 -0.564254 0.513375 -0.646578 0.490491 45 57.5 1 0 -2031 1 1 0 44.8203 54.8521 42.9553 -0.51797 0.485208 -0.704471 0.490491 45 57.5 1 0 -2032 1 1 0 43.7169 54.7092 43.8076 -0.628313 0.470917 -0.619242 0.490491 45 57.5 1 0 -2033 1 1 0 44.1528 54.4396 43.2102 -0.584716 0.443957 -0.678977 0.490491 45 57.5 1 0 -2034 1 1 0 44.6322 54.1427 42.6499 -0.536784 0.414272 -0.735011 0.490491 45 57.5 1 0 -2035 1 1 0 44.1805 56.0748 44.5935 -0.581952 0.607478 -0.54065 0.490491 45 57.5 1 0 -2036 1 1 0 43.9252 55.4065 44.1805 -0.607478 0.54065 -0.581952 0.490491 45 57.5 1 0 -2037 1 1 0 44.5935 55.8195 43.9252 -0.54065 0.581952 -0.607478 0.490491 45 57.5 1 0 -2038 1 1 0 51.0649 55.5186 41.7289 0.106494 0.551859 -0.82711 0.490491 45 57.5 1 0 -2039 1 1 0 51.7253 55.2913 41.6919 0.172532 0.529135 -0.830812 0.490491 45 57.5 1 0 -2040 1 1 0 52.3723 55.0421 41.6964 0.237228 0.504209 -0.830359 0.490491 45 57.5 1 0 -2041 1 1 0 52.1302 55.7125 42.0735 0.213023 0.571251 -0.79265 0.490491 45 57.5 1 0 -2042 1 1 0 51.4741 55.949 42.0983 0.147413 0.594895 -0.79017 0.490491 45 57.5 1 0 -2043 1 1 0 51.8743 56.3458 42.5021 0.187432 0.634579 -0.749786 0.490491 45 57.5 1 0 -2044 1 1 0 53.038 54.7623 41.7482 0.303801 0.476225 -0.825175 0.490491 45 57.5 1 0 -2045 1 1 0 53.6603 54.4698 41.8377 0.366027 0.446977 -0.816233 0.490491 45 57.5 1 0 -2046 1 1 0 53.4615 55.1612 42.1655 0.346153 0.516122 -0.783452 0.490491 45 57.5 1 0 -2047 1 1 0 54.2713 54.156 41.9698 0.427135 0.415597 -0.803016 0.490491 45 57.5 1 0 -2048 1 1 0 54.8571 53.8268 42.141 0.485712 0.382683 -0.785899 0.490491 45 57.5 1 0 -2049 1 1 0 54.6843 54.5399 42.4206 0.46843 0.45399 -0.757936 0.490491 45 57.5 1 0 -2050 1 1 0 54.0829 54.8624 42.2742 0.408286 0.48624 -0.772575 0.490491 45 57.5 1 0 -2051 1 1 0 53.8673 55.5337 42.6229 0.38673 0.553372 -0.737712 0.490491 45 57.5 1 0 -2052 1 1 0 54.4826 55.225 42.747 0.448259 0.522499 -0.725299 0.490491 45 57.5 1 0 -2053 1 1 0 54.2533 55.8779 43.1181 0.425325 0.587785 -0.688191 0.490491 45 57.5 1 0 -2054 1 1 0 52.289 56.7232 42.9602 0.228899 0.672319 -0.703983 0.490491 45 57.5 1 0 -2055 1 1 0 52.96 56.4741 42.9769 0.296004 0.647412 -0.70231 0.490491 45 57.5 1 0 -2056 1 1 0 52.6738 57.0524 43.4338 0.267381 0.705236 -0.65662 0.490491 45 57.5 1 0 -2057 1 1 0 53.6159 56.1919 43.0296 0.361591 0.619186 -0.697037 0.490491 45 57.5 1 0 -2058 1 1 0 53.3469 56.7891 43.465 0.334691 0.678913 -0.653497 0.490491 45 57.5 1 0 -2059 1 1 0 53.9977 56.4945 43.5316 0.399769 0.649448 -0.64684 0.490491 45 57.5 1 0 -2060 1 1 0 53.7175 57.0711 43.985 0.371748 0.707107 -0.601501 0.490491 45 57.5 1 0 -2061 1 1 0 53.0521 57.3479 43.9426 0.305212 0.734794 -0.605742 0.490491 45 57.5 1 0 -2062 1 1 0 53.4143 57.6041 44.4755 0.341435 0.760406 -0.552454 0.490491 45 57.5 1 0 -2063 1 1 0 52.8032 55.4511 42.0989 0.280319 0.545109 -0.790112 0.490491 45 57.5 1 0 -2064 1 1 0 53.2214 55.8369 42.5466 0.322141 0.583692 -0.745339 0.490491 45 57.5 1 0 -2065 1 1 0 52.5518 56.1093 42.5056 0.25518 0.610926 -0.749435 0.490491 45 57.5 1 0 -2066 1 1 0 55.5245 53.4143 42.3959 0.552454 0.341435 -0.760406 0.490491 45 57.5 1 0 -2067 1 1 0 56.0574 53.0521 42.6521 0.605742 0.305212 -0.734794 0.490491 45 57.5 1 0 -2068 1 1 0 56.015 53.7175 42.9289 0.601501 0.371748 -0.707107 0.490491 45 57.5 1 0 -2069 1 1 0 56.5662 52.6738 42.9476 0.65662 0.267381 -0.705236 0.490491 45 57.5 1 0 -2070 1 1 0 57.0398 52.289 43.2768 0.703983 0.228899 -0.672319 0.490491 45 57.5 1 0 -2071 1 1 0 57.0231 52.96 43.5259 0.70231 0.296004 -0.647412 0.490491 45 57.5 1 0 -2072 1 1 0 56.535 53.3469 43.2109 0.653497 0.334691 -0.678913 0.490491 45 57.5 1 0 -2073 1 1 0 56.4684 53.9977 43.5055 0.64684 0.399769 -0.649448 0.490491 45 57.5 1 0 -2074 1 1 0 56.9704 53.6159 43.8081 0.697037 0.361591 -0.619186 0.490491 45 57.5 1 0 -2075 1 1 0 56.8819 54.2533 44.1221 0.688191 0.425325 -0.587785 0.490491 45 57.5 1 0 -2076 1 1 0 57.4979 51.8743 43.6542 0.749786 0.187432 -0.634579 0.490491 45 57.5 1 0 -2077 1 1 0 57.9017 51.4741 44.051 0.79017 0.147413 -0.594895 0.490491 45 57.5 1 0 -2078 1 1 0 57.9265 52.1302 44.2875 0.79265 0.213023 -0.571251 0.490491 45 57.5 1 0 -2079 1 1 0 58.2711 51.0649 44.4814 0.82711 0.106494 -0.551859 0.490491 45 57.5 1 0 -2080 1 1 0 58.3081 51.7253 44.7087 0.830812 0.172532 -0.529135 0.490491 45 57.5 1 0 -2081 1 1 0 58.3036 52.3723 44.9579 0.830359 0.237228 -0.504209 0.490491 45 57.5 1 0 -2082 1 1 0 57.3771 53.8673 44.4663 0.737712 0.38673 -0.553372 0.490491 45 57.5 1 0 -2083 1 1 0 57.253 54.4826 44.775 0.725299 0.448259 -0.522499 0.490491 45 57.5 1 0 -2084 1 1 0 57.8345 53.4615 44.8388 0.783452 0.346153 -0.516122 0.490491 45 57.5 1 0 -2085 1 1 0 57.7258 54.0829 45.1376 0.772575 0.408286 -0.48624 0.490491 45 57.5 1 0 -2086 1 1 0 57.5794 54.6843 45.4601 0.757936 0.46843 -0.45399 0.490491 45 57.5 1 0 -2087 1 1 0 58.2518 53.038 45.2377 0.825175 0.303801 -0.476225 0.490491 45 57.5 1 0 -2088 1 1 0 58.1623 53.6603 45.5302 0.816233 0.366027 -0.446977 0.490491 45 57.5 1 0 -2089 1 1 0 58.0302 54.2713 45.844 0.803016 0.427135 -0.415597 0.490491 45 57.5 1 0 -2090 1 1 0 57.859 54.8571 46.1732 0.785899 0.485712 -0.382683 0.490491 45 57.5 1 0 -2091 1 1 0 57.4944 52.5518 43.8907 0.749435 0.25518 -0.610926 0.490491 45 57.5 1 0 -2092 1 1 0 57.9011 52.8032 44.5489 0.790112 0.280319 -0.545109 0.490491 45 57.5 1 0 -2093 1 1 0 57.4534 53.2214 44.1631 0.745339 0.322141 -0.583692 0.490491 45 57.5 1 0 -2094 1 1 0 53.8268 57.859 45.1429 0.382683 0.785899 -0.485712 0.490491 45 57.5 1 0 -2095 1 1 0 54.5399 57.5794 45.3157 0.45399 0.757936 -0.46843 0.490491 45 57.5 1 0 -2096 1 1 0 54.156 58.0302 45.7287 0.415597 0.803016 -0.427135 0.490491 45 57.5 1 0 -2097 1 1 0 55.225 57.253 45.5174 0.522499 0.725299 -0.448259 0.490491 45 57.5 1 0 -2098 1 1 0 54.8624 57.7258 45.9171 0.48624 0.772575 -0.408286 0.490491 45 57.5 1 0 -2099 1 1 0 55.8779 56.8819 45.7467 0.587785 0.688191 -0.425325 0.490491 45 57.5 1 0 -2100 1 1 0 55.5337 57.3771 46.1327 0.553372 0.737712 -0.38673 0.490491 45 57.5 1 0 -2101 1 1 0 55.1612 57.8345 46.5385 0.516122 0.783452 -0.346153 0.490491 45 57.5 1 0 -2102 1 1 0 54.4698 58.1623 46.3397 0.446977 0.816233 -0.366027 0.490491 45 57.5 1 0 -2103 1 1 0 54.7623 58.2518 46.962 0.476225 0.825175 -0.303801 0.490491 45 57.5 1 0 -2104 1 1 0 56.4945 56.4684 46.0023 0.649448 0.64684 -0.399769 0.490491 45 57.5 1 0 -2105 1 1 0 56.1919 56.9704 46.3841 0.619186 0.697037 -0.361591 0.490491 45 57.5 1 0 -2106 1 1 0 57.0711 56.015 46.2825 0.707107 0.601501 -0.371748 0.490491 45 57.5 1 0 -2107 1 1 0 56.7891 56.535 46.6531 0.678913 0.653497 -0.334691 0.490491 45 57.5 1 0 -2108 1 1 0 56.4741 57.0231 47.04 0.647412 0.70231 -0.296004 0.490491 45 57.5 1 0 -2109 1 1 0 57.6041 55.5245 46.5857 0.760406 0.552454 -0.341435 0.490491 45 57.5 1 0 -2110 1 1 0 57.3479 56.0574 46.9479 0.734794 0.605742 -0.305212 0.490491 45 57.5 1 0 -2111 1 1 0 57.0524 56.5662 47.3262 0.705236 0.65662 -0.267381 0.490491 45 57.5 1 0 -2112 1 1 0 56.7232 57.0398 47.711 0.672319 0.703983 -0.228899 0.490491 45 57.5 1 0 -2113 1 1 0 55.0421 58.3036 47.6277 0.504209 0.830359 -0.237228 0.490491 45 57.5 1 0 -2114 1 1 0 55.7125 57.9265 47.8698 0.571251 0.79265 -0.213023 0.490491 45 57.5 1 0 -2115 1 1 0 55.2913 58.3081 48.2747 0.529135 0.830812 -0.172532 0.490491 45 57.5 1 0 -2116 1 1 0 56.3458 57.4979 48.1257 0.634579 0.749786 -0.187432 0.490491 45 57.5 1 0 -2117 1 1 0 55.949 57.9017 48.5259 0.594895 0.79017 -0.147413 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examples/PACKAGES/drude/ethanol/data.ethanol diff --git a/examples/USER/drude/ethanol/in.ethanol.lang b/examples/PACKAGES/drude/ethanol/in.ethanol.lang similarity index 100% rename from examples/USER/drude/ethanol/in.ethanol.lang rename to examples/PACKAGES/drude/ethanol/in.ethanol.lang diff --git a/examples/USER/drude/ethanol/in.ethanol.nh b/examples/PACKAGES/drude/ethanol/in.ethanol.nh similarity index 100% rename from examples/USER/drude/ethanol/in.ethanol.nh rename to examples/PACKAGES/drude/ethanol/in.ethanol.nh diff --git a/examples/USER/drude/ethanol/in.ethanol.tgnh b/examples/PACKAGES/drude/ethanol/in.ethanol.tgnh similarity index 100% rename from examples/USER/drude/ethanol/in.ethanol.tgnh rename to examples/PACKAGES/drude/ethanol/in.ethanol.tgnh diff --git a/examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1 b/examples/PACKAGES/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1 similarity index 100% rename from examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1 rename to examples/PACKAGES/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1 diff --git a/examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4 b/examples/PACKAGES/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4 similarity index 100% rename from examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4 rename to examples/PACKAGES/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 b/examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 similarity index 100% rename from examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 rename to examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 b/examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 similarity index 100% rename from examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 rename to examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 b/examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 similarity index 100% rename from examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 rename to examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 b/examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 similarity index 100% rename from examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 rename to examples/PACKAGES/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 diff --git a/examples/USER/drude/ethylene_glycol/data.ethylene_glycol b/examples/PACKAGES/drude/ethylene_glycol/data.ethylene_glycol similarity index 100% rename from examples/USER/drude/ethylene_glycol/data.ethylene_glycol rename to examples/PACKAGES/drude/ethylene_glycol/data.ethylene_glycol diff --git a/examples/USER/drude/ethylene_glycol/in.ethylene_glycol b/examples/PACKAGES/drude/ethylene_glycol/in.ethylene_glycol similarity index 100% rename from examples/USER/drude/ethylene_glycol/in.ethylene_glycol rename to examples/PACKAGES/drude/ethylene_glycol/in.ethylene_glycol diff --git a/examples/USER/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.1 b/examples/PACKAGES/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.1 similarity index 100% rename from examples/USER/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.1 rename to examples/PACKAGES/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.1 diff --git a/examples/USER/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.4 b/examples/PACKAGES/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.4 similarity index 100% rename from examples/USER/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.4 rename to examples/PACKAGES/drude/ethylene_glycol/log.18Sep20.ethylene_glycol.g++.4 diff --git a/examples/USER/drude/swm4-ndp/data.swm4-ndp b/examples/PACKAGES/drude/swm4-ndp/data.swm4-ndp similarity index 100% rename from examples/USER/drude/swm4-ndp/data.swm4-ndp rename to examples/PACKAGES/drude/swm4-ndp/data.swm4-ndp diff --git a/examples/USER/drude/swm4-ndp/in.swm4-ndp.lang b/examples/PACKAGES/drude/swm4-ndp/in.swm4-ndp.lang similarity index 100% rename from examples/USER/drude/swm4-ndp/in.swm4-ndp.lang rename to examples/PACKAGES/drude/swm4-ndp/in.swm4-ndp.lang diff --git a/examples/USER/drude/swm4-ndp/in.swm4-ndp.nh b/examples/PACKAGES/drude/swm4-ndp/in.swm4-ndp.nh similarity index 100% rename from examples/USER/drude/swm4-ndp/in.swm4-ndp.nh rename to examples/PACKAGES/drude/swm4-ndp/in.swm4-ndp.nh diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 b/examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 similarity index 100% rename from examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 rename to examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 b/examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 similarity index 100% rename from examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 rename to examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 b/examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 similarity index 100% rename from examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 rename to examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 b/examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 similarity index 100% rename from examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 rename to examples/PACKAGES/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 diff --git a/examples/USER/drude/toluene/data.toluene b/examples/PACKAGES/drude/toluene/data.toluene similarity index 100% rename from examples/USER/drude/toluene/data.toluene rename to examples/PACKAGES/drude/toluene/data.toluene diff --git a/examples/USER/drude/toluene/in.toluene.lang b/examples/PACKAGES/drude/toluene/in.toluene.lang similarity index 100% rename from examples/USER/drude/toluene/in.toluene.lang rename to examples/PACKAGES/drude/toluene/in.toluene.lang diff --git a/examples/USER/drude/toluene/in.toluene.nh b/examples/PACKAGES/drude/toluene/in.toluene.nh similarity index 100% rename from examples/USER/drude/toluene/in.toluene.nh rename to examples/PACKAGES/drude/toluene/in.toluene.nh diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1 b/examples/PACKAGES/drude/toluene/log.7Aug19.toluene.lang.g++.1 similarity index 100% rename from examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1 rename to examples/PACKAGES/drude/toluene/log.7Aug19.toluene.lang.g++.1 diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4 b/examples/PACKAGES/drude/toluene/log.7Aug19.toluene.lang.g++.4 similarity index 100% rename from examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4 rename to examples/PACKAGES/drude/toluene/log.7Aug19.toluene.lang.g++.4 diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1 b/examples/PACKAGES/drude/toluene/log.7Aug19.toluene.nh.g++.1 similarity index 100% rename from examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1 rename to examples/PACKAGES/drude/toluene/log.7Aug19.toluene.nh.g++.1 diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4 b/examples/PACKAGES/drude/toluene/log.7Aug19.toluene.nh.g++.4 similarity index 100% rename from examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4 rename to examples/PACKAGES/drude/toluene/log.7Aug19.toluene.nh.g++.4 diff --git a/examples/USER/misc/e3b/README b/examples/PACKAGES/e3b/README similarity index 100% rename from examples/USER/misc/e3b/README rename to examples/PACKAGES/e3b/README diff --git a/examples/USER/misc/e3b/e3b_box.data b/examples/PACKAGES/e3b/e3b_box.data similarity index 100% rename from examples/USER/misc/e3b/e3b_box.data rename to examples/PACKAGES/e3b/e3b_box.data diff --git a/examples/USER/misc/e3b/in.e3b-tip4p2005 b/examples/PACKAGES/e3b/in.e3b-tip4p2005 similarity index 100% rename from examples/USER/misc/e3b/in.e3b-tip4p2005 rename to examples/PACKAGES/e3b/in.e3b-tip4p2005 diff --git a/examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 b/examples/PACKAGES/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 similarity index 100% rename from examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 rename to examples/PACKAGES/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 diff --git a/examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 b/examples/PACKAGES/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 similarity index 100% rename from examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 rename to examples/PACKAGES/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 diff --git a/examples/USER/misc/edip/Si.edip b/examples/PACKAGES/edip/Si.edip similarity index 100% rename from examples/USER/misc/edip/Si.edip rename to examples/PACKAGES/edip/Si.edip diff --git a/examples/USER/misc/edip/SiC.edip b/examples/PACKAGES/edip/SiC.edip similarity index 100% rename from examples/USER/misc/edip/SiC.edip rename to examples/PACKAGES/edip/SiC.edip diff --git a/examples/USER/misc/edip/data.SiC b/examples/PACKAGES/edip/data.SiC similarity index 100% rename from examples/USER/misc/edip/data.SiC rename to examples/PACKAGES/edip/data.SiC diff --git a/examples/USER/misc/edip/in.edip-Si b/examples/PACKAGES/edip/in.edip-Si similarity index 100% rename from examples/USER/misc/edip/in.edip-Si rename to examples/PACKAGES/edip/in.edip-Si diff --git a/examples/USER/misc/edip/in.edip-Si-multi b/examples/PACKAGES/edip/in.edip-Si-multi similarity index 100% rename from examples/USER/misc/edip/in.edip-Si-multi rename to examples/PACKAGES/edip/in.edip-Si-multi diff --git a/examples/USER/misc/edip/in.edip-SiC b/examples/PACKAGES/edip/in.edip-SiC similarity index 100% rename from examples/USER/misc/edip/in.edip-SiC rename to examples/PACKAGES/edip/in.edip-SiC diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 b/examples/PACKAGES/edip/log.4May2017.g++.edip-Si-multi.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 rename to examples/PACKAGES/edip/log.4May2017.g++.edip-Si-multi.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 b/examples/PACKAGES/edip/log.4May2017.g++.edip-Si-multi.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 rename to examples/PACKAGES/edip/log.4May2017.g++.edip-Si-multi.4 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 b/examples/PACKAGES/edip/log.4May2017.g++.edip-Si.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 rename to examples/PACKAGES/edip/log.4May2017.g++.edip-Si.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 b/examples/PACKAGES/edip/log.4May2017.g++.edip-Si.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 rename to examples/PACKAGES/edip/log.4May2017.g++.edip-Si.4 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 b/examples/PACKAGES/edip/log.4May2017.g++.edip-SiC.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 rename to examples/PACKAGES/edip/log.4May2017.g++.edip-SiC.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 b/examples/PACKAGES/edip/log.4May2017.g++.edip-SiC.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 rename to examples/PACKAGES/edip/log.4May2017.g++.edip-SiC.4 diff --git a/examples/USER/misc/ees/Data_region b/examples/PACKAGES/ees/Data_region similarity 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examples/PACKAGES/ees/log.23Jun17.fix_wall_region.g++.4 diff --git a/examples/USER/eff/Auger-Adamantane/README b/examples/PACKAGES/eff/Auger-Adamantane/README similarity index 100% rename from examples/USER/eff/Auger-Adamantane/README rename to examples/PACKAGES/eff/Auger-Adamantane/README diff --git a/examples/USER/eff/Auger-Adamantane/data.adamantane b/examples/PACKAGES/eff/Auger-Adamantane/data.adamantane similarity index 100% rename from examples/USER/eff/Auger-Adamantane/data.adamantane rename to examples/PACKAGES/eff/Auger-Adamantane/data.adamantane diff --git a/examples/USER/eff/Auger-Adamantane/data.adamantane_ionized b/examples/PACKAGES/eff/Auger-Adamantane/data.adamantane_ionized similarity index 100% rename from examples/USER/eff/Auger-Adamantane/data.adamantane_ionized rename to examples/PACKAGES/eff/Auger-Adamantane/data.adamantane_ionized diff --git a/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve b/examples/PACKAGES/eff/Auger-Adamantane/in.adamantane_ionized.nve similarity index 100% rename from examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve rename to examples/PACKAGES/eff/Auger-Adamantane/in.adamantane_ionized.nve diff --git a/examples/USER/eff/Be-solid/README b/examples/PACKAGES/eff/Be-solid/README similarity index 100% rename from examples/USER/eff/Be-solid/README rename to examples/PACKAGES/eff/Be-solid/README diff --git a/examples/USER/eff/Be-solid/data.Be-solid b/examples/PACKAGES/eff/Be-solid/data.Be-solid similarity index 100% rename from examples/USER/eff/Be-solid/data.Be-solid rename to examples/PACKAGES/eff/Be-solid/data.Be-solid diff --git a/examples/USER/eff/Be-solid/in.Be-solid.spe b/examples/PACKAGES/eff/Be-solid/in.Be-solid.spe similarity index 100% rename from examples/USER/eff/Be-solid/in.Be-solid.spe rename to examples/PACKAGES/eff/Be-solid/in.Be-solid.spe diff --git a/examples/USER/eff/CH4/README b/examples/PACKAGES/eff/CH4/README similarity 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examples/USER/manifold/energy/plot_energies.gpl rename to examples/PACKAGES/manifold/energy/plot_energies.gpl diff --git a/examples/USER/manifold/energy/sphere.data b/examples/PACKAGES/manifold/energy/sphere.data similarity index 100% rename from examples/USER/manifold/energy/sphere.data rename to examples/PACKAGES/manifold/energy/sphere.data diff --git a/examples/USER/manifold/energy/sphere.setup b/examples/PACKAGES/manifold/energy/sphere.setup similarity index 100% rename from examples/USER/manifold/energy/sphere.setup rename to examples/PACKAGES/manifold/energy/sphere.setup diff --git a/examples/USER/manifold/energy/torus.data b/examples/PACKAGES/manifold/energy/torus.data similarity index 100% rename from examples/USER/manifold/energy/torus.data rename to examples/PACKAGES/manifold/energy/torus.data diff --git a/examples/USER/manifold/energy/torus.setup b/examples/PACKAGES/manifold/energy/torus.setup similarity index 100% rename from examples/USER/manifold/energy/torus.setup rename to examples/PACKAGES/manifold/energy/torus.setup diff --git a/examples/USER/manifold/thylakoid/README b/examples/PACKAGES/manifold/thylakoid/README similarity index 100% rename from examples/USER/manifold/thylakoid/README rename to examples/PACKAGES/manifold/thylakoid/README diff --git a/examples/USER/manifold/thylakoid/thylakoid.data b/examples/PACKAGES/manifold/thylakoid/thylakoid.data similarity index 100% rename from examples/USER/manifold/thylakoid/thylakoid.data rename to examples/PACKAGES/manifold/thylakoid/thylakoid.data diff --git a/examples/USER/manifold/thylakoid/thylakoid.in b/examples/PACKAGES/manifold/thylakoid/thylakoid.in similarity index 100% rename from examples/USER/manifold/thylakoid/thylakoid.in rename to examples/PACKAGES/manifold/thylakoid/thylakoid.in diff --git a/examples/USER/manifold/virus/README b/examples/PACKAGES/manifold/virus/README similarity index 100% rename from examples/USER/manifold/virus/README rename to examples/PACKAGES/manifold/virus/README diff --git a/examples/USER/manifold/virus/init.data b/examples/PACKAGES/manifold/virus/init.data similarity index 100% rename from examples/USER/manifold/virus/init.data rename to examples/PACKAGES/manifold/virus/init.data diff --git a/examples/USER/manifold/virus/vir.in b/examples/PACKAGES/manifold/virus/vir.in similarity index 100% rename from examples/USER/manifold/virus/vir.in rename to examples/PACKAGES/manifold/virus/vir.in diff --git a/examples/USER/mdi/README b/examples/PACKAGES/mdi/README similarity index 100% rename from examples/USER/mdi/README rename to examples/PACKAGES/mdi/README diff --git a/examples/USER/mdi/Script.sh b/examples/PACKAGES/mdi/Script.sh similarity index 100% rename from examples/USER/mdi/Script.sh rename to examples/PACKAGES/mdi/Script.sh diff --git a/examples/USER/mdi/driver.py b/examples/PACKAGES/mdi/driver.py similarity index 100% rename from examples/USER/mdi/driver.py rename to examples/PACKAGES/mdi/driver.py diff --git a/examples/USER/mdi/lammps.data b/examples/PACKAGES/mdi/lammps.data similarity index 100% rename from examples/USER/mdi/lammps.data rename to examples/PACKAGES/mdi/lammps.data diff --git a/examples/USER/mdi/lammps.in b/examples/PACKAGES/mdi/lammps.in similarity index 100% rename from examples/USER/mdi/lammps.in rename to examples/PACKAGES/mdi/lammps.in diff --git a/examples/USER/misc/meam_spline/Si_1.meam.spline b/examples/PACKAGES/meam_spline/Si_1.meam.spline similarity index 100% rename from examples/USER/misc/meam_spline/Si_1.meam.spline rename to examples/PACKAGES/meam_spline/Si_1.meam.spline diff --git a/examples/USER/misc/meam_spline/TiO.meam.spline b/examples/PACKAGES/meam_spline/TiO.meam.spline similarity index 100% rename from examples/USER/misc/meam_spline/TiO.meam.spline rename to examples/PACKAGES/meam_spline/TiO.meam.spline diff --git a/examples/USER/misc/meam_spline/in.meam-spline.Si b/examples/PACKAGES/meam_spline/in.meam-spline.Si similarity index 100% rename from examples/USER/misc/meam_spline/in.meam-spline.Si rename to examples/PACKAGES/meam_spline/in.meam-spline.Si diff --git a/examples/USER/misc/meam_spline/in.meam-spline.TiO2 b/examples/PACKAGES/meam_spline/in.meam-spline.TiO2 similarity index 100% rename from examples/USER/misc/meam_spline/in.meam-spline.TiO2 rename to examples/PACKAGES/meam_spline/in.meam-spline.TiO2 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.1 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1 rename to examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.1 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.4 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4 rename to examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.4 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 rename to examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 rename to examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 diff --git a/examples/USER/misc/meam_sw_spline/Si/bcc.in b/examples/PACKAGES/meam_sw_spline/Si/bcc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/bcc.in rename to examples/PACKAGES/meam_sw_spline/Si/bcc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/bcc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/bcc_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/dc.in b/examples/PACKAGES/meam_sw_spline/Si/dc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/dc.in rename to examples/PACKAGES/meam_sw_spline/Si/dc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/dc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/dc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/dc_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/dc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/energy_conservation.meam.sw.in b/examples/PACKAGES/meam_sw_spline/Si/energy_conservation.meam.sw.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/energy_conservation.meam.sw.in rename to examples/PACKAGES/meam_sw_spline/Si/energy_conservation.meam.sw.in diff --git a/examples/USER/misc/meam_sw_spline/Si/fcc.in b/examples/PACKAGES/meam_sw_spline/Si/fcc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/fcc.in rename to examples/PACKAGES/meam_sw_spline/Si/fcc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/fcc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/fcc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/fcc_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/fcc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/hcp_relax.in b/examples/PACKAGES/meam_sw_spline/Si/hcp_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/hcp_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/hcp_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/sc.in b/examples/PACKAGES/meam_sw_spline/Si/sc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/sc.in rename to examples/PACKAGES/meam_sw_spline/Si/sc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/sc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/sc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/sc_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/sc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/single_atom.in b/examples/PACKAGES/meam_sw_spline/Si/single_atom.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/single_atom.in rename to examples/PACKAGES/meam_sw_spline/Si/single_atom.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/alpha.in b/examples/PACKAGES/meam_sw_spline/Ti/alpha.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/alpha.in rename to examples/PACKAGES/meam_sw_spline/Ti/alpha.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/alpha_relaxation.in b/examples/PACKAGES/meam_sw_spline/Ti/alpha_relaxation.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/alpha_relaxation.in rename to examples/PACKAGES/meam_sw_spline/Ti/alpha_relaxation.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/beta.in b/examples/PACKAGES/meam_sw_spline/Ti/beta.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/beta.in rename to examples/PACKAGES/meam_sw_spline/Ti/beta.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/energy_conservation.meam.sw.in b/examples/PACKAGES/meam_sw_spline/Ti/energy_conservation.meam.sw.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/energy_conservation.meam.sw.in rename to examples/PACKAGES/meam_sw_spline/Ti/energy_conservation.meam.sw.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/fcc.in b/examples/PACKAGES/meam_sw_spline/Ti/fcc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/fcc.in rename to examples/PACKAGES/meam_sw_spline/Ti/fcc.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/hexagonal.in b/examples/PACKAGES/meam_sw_spline/Ti/hexagonal.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/hexagonal.in rename to examples/PACKAGES/meam_sw_spline/Ti/hexagonal.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/omega.in b/examples/PACKAGES/meam_sw_spline/Ti/omega.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/omega.in rename to examples/PACKAGES/meam_sw_spline/Ti/omega.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/single_atom.in b/examples/PACKAGES/meam_sw_spline/Ti/single_atom.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/single_atom.in rename to examples/PACKAGES/meam_sw_spline/Ti/single_atom.in diff --git a/examples/USER/mesont/C_10_10.mesocnt b/examples/PACKAGES/mesont/C_10_10.mesocnt similarity index 100% rename from examples/USER/mesont/C_10_10.mesocnt rename to examples/PACKAGES/mesont/C_10_10.mesocnt diff --git a/examples/USER/mesont/README b/examples/PACKAGES/mesont/README similarity index 88% rename from examples/USER/mesont/README rename to examples/PACKAGES/mesont/README index ffbc667120..7d6be7993a 100644 --- a/examples/USER/mesont/README +++ b/examples/PACKAGES/mesont/README @@ -1,8 +1,8 @@ -=== USER-MESONT examples === +=== MESONT examples === =============================== The files in this folder provide examples of using the CNT -mesoscopic force field (USER-MESONT). +mesoscopic force field (MESONT). Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu diff --git a/examples/USER/mesont/TABTP_10_10.mesont b/examples/PACKAGES/mesont/TABTP_10_10.mesont similarity index 100% rename from examples/USER/mesont/TABTP_10_10.mesont rename to examples/PACKAGES/mesont/TABTP_10_10.mesont diff --git a/examples/USER/mesont/cnt.data b/examples/PACKAGES/mesont/cnt.data similarity index 100% rename from examples/USER/mesont/cnt.data rename to examples/PACKAGES/mesont/cnt.data diff --git a/examples/USER/mesont/data.bundle b/examples/PACKAGES/mesont/data.bundle similarity index 100% rename from examples/USER/mesont/data.bundle rename to examples/PACKAGES/mesont/data.bundle diff --git a/examples/USER/mesont/data.film b/examples/PACKAGES/mesont/data.film similarity index 100% rename from examples/USER/mesont/data.film rename to examples/PACKAGES/mesont/data.film diff --git a/examples/USER/mesont/in.bundle b/examples/PACKAGES/mesont/in.bundle similarity index 100% rename from examples/USER/mesont/in.bundle rename to examples/PACKAGES/mesont/in.bundle diff --git a/examples/USER/mesont/in.cnt b/examples/PACKAGES/mesont/in.cnt similarity index 100% rename from examples/USER/mesont/in.cnt rename to examples/PACKAGES/mesont/in.cnt diff --git a/examples/USER/mesont/in.film b/examples/PACKAGES/mesont/in.film similarity index 100% rename from examples/USER/mesont/in.film rename to examples/PACKAGES/mesont/in.film diff --git a/examples/USER/mesont/log.2Jun2020.bundle.g++.1 b/examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.1 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.bundle.g++.1 rename to examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.1 diff --git a/examples/USER/mesont/log.2Jun2020.bundle.g++.4 b/examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.4 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.bundle.g++.4 rename to examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.4 diff --git a/examples/USER/mesont/log.2Jun2020.film.g++.1 b/examples/PACKAGES/mesont/log.2Jun2020.film.g++.1 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.film.g++.1 rename to examples/PACKAGES/mesont/log.2Jun2020.film.g++.1 diff --git a/examples/USER/mesont/log.2Jun2020.film.g++.4 b/examples/PACKAGES/mesont/log.2Jun2020.film.g++.4 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.film.g++.4 rename to examples/PACKAGES/mesont/log.2Jun2020.film.g++.4 diff --git a/examples/USER/mesont/log.9Jan20.cnt.g++.1 b/examples/PACKAGES/mesont/log.9Jan20.cnt.g++.1 similarity index 100% rename from examples/USER/mesont/log.9Jan20.cnt.g++.1 rename to examples/PACKAGES/mesont/log.9Jan20.cnt.g++.1 diff --git a/examples/USER/mesont/log.9Jan20.cnt.g++.4 b/examples/PACKAGES/mesont/log.9Jan20.cnt.g++.4 similarity index 100% rename from examples/USER/mesont/log.9Jan20.cnt.g++.4 rename to examples/PACKAGES/mesont/log.9Jan20.cnt.g++.4 diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.README b/examples/PACKAGES/mgpt/Ta6.8x.mgpt.README similarity index 100% rename from examples/USER/mgpt/Ta6.8x.mgpt.README rename to examples/PACKAGES/mgpt/Ta6.8x.mgpt.README diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.parmin b/examples/PACKAGES/mgpt/Ta6.8x.mgpt.parmin similarity index 100% rename from examples/USER/mgpt/Ta6.8x.mgpt.parmin rename to examples/PACKAGES/mgpt/Ta6.8x.mgpt.parmin diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.potin b/examples/PACKAGES/mgpt/Ta6.8x.mgpt.potin similarity index 100% rename from examples/USER/mgpt/Ta6.8x.mgpt.potin rename to examples/PACKAGES/mgpt/Ta6.8x.mgpt.potin diff --git a/examples/USER/mgpt/in.bcc0 b/examples/PACKAGES/mgpt/in.bcc0 similarity index 100% rename from examples/USER/mgpt/in.bcc0 rename to examples/PACKAGES/mgpt/in.bcc0 diff --git a/examples/USER/mgpt/in.vac0-bcc b/examples/PACKAGES/mgpt/in.vac0-bcc similarity index 100% rename from examples/USER/mgpt/in.vac0-bcc rename to examples/PACKAGES/mgpt/in.vac0-bcc diff --git a/examples/USER/mgpt/in.vacmin-bcc b/examples/PACKAGES/mgpt/in.vacmin-bcc similarity index 100% rename from examples/USER/mgpt/in.vacmin-bcc rename to examples/PACKAGES/mgpt/in.vacmin-bcc diff --git a/examples/USER/mgpt/log.bcc0 b/examples/PACKAGES/mgpt/log.bcc0 similarity index 100% rename from examples/USER/mgpt/log.bcc0 rename to examples/PACKAGES/mgpt/log.bcc0 diff --git a/examples/USER/mgpt/log.vac0-bcc b/examples/PACKAGES/mgpt/log.vac0-bcc similarity index 100% rename from examples/USER/mgpt/log.vac0-bcc rename to examples/PACKAGES/mgpt/log.vac0-bcc diff --git a/examples/USER/mgpt/log.vacmin-bcc b/examples/PACKAGES/mgpt/log.vacmin-bcc similarity index 100% rename from examples/USER/mgpt/log.vacmin-bcc rename to examples/PACKAGES/mgpt/log.vacmin-bcc diff --git a/examples/USER/mofff/hkust1.data b/examples/PACKAGES/mofff/hkust1.data similarity index 100% rename from examples/USER/mofff/hkust1.data rename to examples/PACKAGES/mofff/hkust1.data diff --git a/examples/USER/mofff/in.hkust1 b/examples/PACKAGES/mofff/in.hkust1 similarity index 100% rename from examples/USER/mofff/in.hkust1 rename to examples/PACKAGES/mofff/in.hkust1 diff --git a/examples/USER/mofff/in.hkust1_long b/examples/PACKAGES/mofff/in.hkust1_long similarity index 100% rename from examples/USER/mofff/in.hkust1_long rename to examples/PACKAGES/mofff/in.hkust1_long diff --git a/examples/USER/mofff/log.27Nov18.hkust1.g++.1 b/examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.1 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1.g++.1 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.1 diff --git a/examples/USER/mofff/log.27Nov18.hkust1.g++.4 b/examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.4 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1.g++.4 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.4 diff --git a/examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 b/examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.1 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.1 diff --git a/examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 b/examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.4 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.4 diff --git a/examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs b/examples/PACKAGES/momb/Ag_O1X5.5_O2X0.55.eam.fs similarity index 100% rename from examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs rename to examples/PACKAGES/momb/Ag_O1X5.5_O2X0.55.eam.fs diff --git a/examples/USER/misc/momb/README b/examples/PACKAGES/momb/README similarity index 100% rename from examples/USER/misc/momb/README rename to examples/PACKAGES/momb/README diff --git a/examples/USER/misc/momb/in.system b/examples/PACKAGES/momb/in.system similarity index 100% rename from examples/USER/misc/momb/in.system rename to examples/PACKAGES/momb/in.system diff --git a/examples/USER/misc/momb/log.17Mar2017.system.g++.1 b/examples/PACKAGES/momb/log.17Mar2017.system.g++.1 similarity index 100% rename from examples/USER/misc/momb/log.17Mar2017.system.g++.1 rename to examples/PACKAGES/momb/log.17Mar2017.system.g++.1 diff --git a/examples/USER/misc/momb/log.17Mar2017.system.g++.4 b/examples/PACKAGES/momb/log.17Mar2017.system.g++.4 similarity index 100% rename from examples/USER/misc/momb/log.17Mar2017.system.g++.4 rename to examples/PACKAGES/momb/log.17Mar2017.system.g++.4 diff --git a/examples/USER/misc/momb/system.data b/examples/PACKAGES/momb/system.data similarity index 100% rename from examples/USER/misc/momb/system.data rename to examples/PACKAGES/momb/system.data diff --git a/examples/USER/misc/momentum/in.momentum b/examples/PACKAGES/momentum/in.momentum similarity index 100% rename from examples/USER/misc/momentum/in.momentum rename to examples/PACKAGES/momentum/in.momentum diff --git a/examples/USER/misc/mop/data.mop b/examples/PACKAGES/mop/data.mop similarity index 100% rename from examples/USER/misc/mop/data.mop rename to examples/PACKAGES/mop/data.mop diff --git a/examples/USER/misc/mop/in.compute_stress_mop b/examples/PACKAGES/mop/in.compute_stress_mop similarity index 100% rename from examples/USER/misc/mop/in.compute_stress_mop rename to examples/PACKAGES/mop/in.compute_stress_mop diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 b/examples/PACKAGES/mop/log.5Sep18.compute_stress_mop.g++.1 similarity index 100% rename from examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 rename to examples/PACKAGES/mop/log.5Sep18.compute_stress_mop.g++.1 diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 b/examples/PACKAGES/mop/log.5Sep18.compute_stress_mop.g++.4 similarity index 100% rename from examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 rename to examples/PACKAGES/mop/log.5Sep18.compute_stress_mop.g++.4 diff --git a/examples/USER/misc/mop/moppz.time.reference b/examples/PACKAGES/mop/moppz.time.reference similarity index 100% rename from examples/USER/misc/mop/moppz.time.reference rename to examples/PACKAGES/mop/moppz.time.reference diff --git a/examples/USER/misc/mop/mopz0.time.reference b/examples/PACKAGES/mop/mopz0.time.reference similarity index 100% rename from examples/USER/misc/mop/mopz0.time.reference rename to examples/PACKAGES/mop/mopz0.time.reference diff --git a/examples/PACKAGES/orient_eco/Ni_u3.eam b/examples/PACKAGES/orient_eco/Ni_u3.eam new file mode 120000 index 0000000000..7a9c552e94 --- /dev/null +++ b/examples/PACKAGES/orient_eco/Ni_u3.eam @@ -0,0 +1 @@ +../../../potentials/Ni_u3.eam \ No newline at end of file diff --git a/examples/USER/misc/orient_eco/data.sigma5 b/examples/PACKAGES/orient_eco/data.sigma5 similarity index 100% rename from examples/USER/misc/orient_eco/data.sigma5 rename to examples/PACKAGES/orient_eco/data.sigma5 diff --git a/examples/USER/misc/orient_eco/in.orient_eco b/examples/PACKAGES/orient_eco/in.orient_eco similarity index 100% rename from examples/USER/misc/orient_eco/in.orient_eco rename to examples/PACKAGES/orient_eco/in.orient_eco diff --git a/examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1 b/examples/PACKAGES/orient_eco/log.2Jun2020.orent_eco.g++.1 similarity index 100% rename from examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1 rename to examples/PACKAGES/orient_eco/log.2Jun2020.orent_eco.g++.1 diff --git a/examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4 b/examples/PACKAGES/orient_eco/log.2Jun2020.orent_eco.g++.4 similarity index 100% rename from examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4 rename to examples/PACKAGES/orient_eco/log.2Jun2020.orent_eco.g++.4 diff --git a/examples/USER/misc/orient_eco/sigma5.ori b/examples/PACKAGES/orient_eco/sigma5.ori similarity index 100% rename from examples/USER/misc/orient_eco/sigma5.ori rename to examples/PACKAGES/orient_eco/sigma5.ori diff --git a/examples/USER/pace/Cu-PBE-core-rep.ace b/examples/PACKAGES/pace/Cu-PBE-core-rep.ace similarity index 100% rename from examples/USER/pace/Cu-PBE-core-rep.ace rename to examples/PACKAGES/pace/Cu-PBE-core-rep.ace diff --git a/examples/USER/pace/in.pace.product b/examples/PACKAGES/pace/in.pace.product similarity index 100% rename from examples/USER/pace/in.pace.product rename to examples/PACKAGES/pace/in.pace.product diff --git a/examples/USER/pace/in.pace.recursive b/examples/PACKAGES/pace/in.pace.recursive similarity index 100% rename from examples/USER/pace/in.pace.recursive rename to examples/PACKAGES/pace/in.pace.recursive diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.1 b/examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.1 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.product.g++.1 rename to examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.1 diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.4 b/examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.4 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.product.g++.4 rename to examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.4 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 b/examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.1 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 rename to examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.1 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 b/examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.4 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 rename to examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.4 diff --git a/examples/USER/misc/pafi/.gitignore b/examples/PACKAGES/pafi/.gitignore similarity index 100% rename from examples/USER/misc/pafi/.gitignore rename to examples/PACKAGES/pafi/.gitignore diff --git a/examples/USER/misc/pafi/README b/examples/PACKAGES/pafi/README similarity index 93% rename from examples/USER/misc/pafi/README rename to examples/PACKAGES/pafi/README index c35dff313c..675ce59de4 100644 --- a/examples/USER/misc/pafi/README +++ b/examples/PACKAGES/pafi/README @@ -1,4 +1,4 @@ -Run an example constrained sample for USER-PAFI calculation +Run an example constrained sample for PAFI calculation Author: Thomas Swinburne, CNRS / CINaM, Marseille @@ -21,7 +21,7 @@ allowing the calculation of free energy barriers and minimum free energy paths. To compile: -make yes-user-misc # for PAFI +make yes-misc # for PAFI make yes-manybody # for EAM potential make machine # for binary (machine= e.g. mpi) diff --git a/examples/USER/misc/pafi/in.pafi b/examples/PACKAGES/pafi/in.pafi similarity index 100% rename from examples/USER/misc/pafi/in.pafi rename to examples/PACKAGES/pafi/in.pafi diff --git a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 b/examples/PACKAGES/pafi/log.15Apr20.pafi.g++.1 similarity index 100% rename from examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 rename to examples/PACKAGES/pafi/log.15Apr20.pafi.g++.1 diff --git a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 b/examples/PACKAGES/pafi/log.15Apr20.pafi.g++.4 similarity index 100% rename from examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 rename to examples/PACKAGES/pafi/log.15Apr20.pafi.g++.4 diff --git a/examples/USER/misc/pafi/pafipath.4.data b/examples/PACKAGES/pafi/pafipath.4.data similarity index 100% rename from examples/USER/misc/pafi/pafipath.4.data rename to examples/PACKAGES/pafi/pafipath.4.data diff --git a/examples/USER/phonon/1-1D-mono/README b/examples/PACKAGES/phonon/1-1D-mono/README similarity index 100% rename from examples/USER/phonon/1-1D-mono/README rename to examples/PACKAGES/phonon/1-1D-mono/README diff --git a/examples/USER/phonon/1-1D-mono/data.pos b/examples/PACKAGES/phonon/1-1D-mono/data.pos similarity index 100% rename from examples/USER/phonon/1-1D-mono/data.pos rename to examples/PACKAGES/phonon/1-1D-mono/data.pos diff --git a/examples/USER/phonon/1-1D-mono/disp.dat b/examples/PACKAGES/phonon/1-1D-mono/disp.dat similarity index 100% rename from examples/USER/phonon/1-1D-mono/disp.dat rename to examples/PACKAGES/phonon/1-1D-mono/disp.dat diff --git a/examples/USER/phonon/1-1D-mono/in.Ana b/examples/PACKAGES/phonon/1-1D-mono/in.Ana similarity index 100% rename from examples/USER/phonon/1-1D-mono/in.Ana rename to examples/PACKAGES/phonon/1-1D-mono/in.Ana diff --git a/examples/USER/phonon/1-1D-mono/in.disp b/examples/PACKAGES/phonon/1-1D-mono/in.disp similarity index 100% rename from examples/USER/phonon/1-1D-mono/in.disp rename to examples/PACKAGES/phonon/1-1D-mono/in.disp diff --git a/examples/USER/phonon/1-1D-mono/log.lammps b/examples/PACKAGES/phonon/1-1D-mono/log.lammps similarity index 100% rename from examples/USER/phonon/1-1D-mono/log.lammps rename to examples/PACKAGES/phonon/1-1D-mono/log.lammps diff --git a/examples/USER/phonon/1-1D-mono/map.in b/examples/PACKAGES/phonon/1-1D-mono/map.in similarity index 100% rename from examples/USER/phonon/1-1D-mono/map.in rename to examples/PACKAGES/phonon/1-1D-mono/map.in diff --git a/examples/USER/phonon/1-1D-mono/pdisp.eps b/examples/PACKAGES/phonon/1-1D-mono/pdisp.eps similarity index 100% rename from examples/USER/phonon/1-1D-mono/pdisp.eps rename to examples/PACKAGES/phonon/1-1D-mono/pdisp.eps diff --git a/examples/USER/phonon/1-1D-mono/pdisp.gnuplot b/examples/PACKAGES/phonon/1-1D-mono/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/1-1D-mono/pdisp.gnuplot rename to examples/PACKAGES/phonon/1-1D-mono/pdisp.gnuplot diff --git a/examples/USER/phonon/1-1D-mono/phonon.bin.2000000 b/examples/PACKAGES/phonon/1-1D-mono/phonon.bin.2000000 similarity index 100% rename from examples/USER/phonon/1-1D-mono/phonon.bin.2000000 rename to examples/PACKAGES/phonon/1-1D-mono/phonon.bin.2000000 diff --git a/examples/USER/phonon/1-1D-mono/phonon.log b/examples/PACKAGES/phonon/1-1D-mono/phonon.log similarity index 100% rename from examples/USER/phonon/1-1D-mono/phonon.log rename to examples/PACKAGES/phonon/1-1D-mono/phonon.log diff --git a/examples/USER/phonon/1-1D-mono/plot.disp b/examples/PACKAGES/phonon/1-1D-mono/plot.disp similarity index 100% rename from examples/USER/phonon/1-1D-mono/plot.disp rename to examples/PACKAGES/phonon/1-1D-mono/plot.disp diff --git a/examples/USER/phonon/2-1D-diatomic/README b/examples/PACKAGES/phonon/2-1D-diatomic/README similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/README rename to examples/PACKAGES/phonon/2-1D-diatomic/README diff --git a/examples/USER/phonon/2-1D-diatomic/data.pos b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/data.pos rename to examples/PACKAGES/phonon/2-1D-diatomic/data.pos diff --git a/examples/USER/phonon/2-1D-diatomic/disp.dat b/examples/PACKAGES/phonon/2-1D-diatomic/disp.dat similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/disp.dat rename to examples/PACKAGES/phonon/2-1D-diatomic/disp.dat diff --git a/examples/USER/phonon/2-1D-diatomic/in.Ana b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/in.Ana rename to examples/PACKAGES/phonon/2-1D-diatomic/in.Ana diff --git a/examples/USER/phonon/2-1D-diatomic/in.disp b/examples/PACKAGES/phonon/2-1D-diatomic/in.disp similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/in.disp rename to examples/PACKAGES/phonon/2-1D-diatomic/in.disp diff --git a/examples/USER/phonon/2-1D-diatomic/log.lammps b/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/log.lammps rename to examples/PACKAGES/phonon/2-1D-diatomic/log.lammps diff --git a/examples/USER/phonon/2-1D-diatomic/map.in b/examples/PACKAGES/phonon/2-1D-diatomic/map.in similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/map.in rename to examples/PACKAGES/phonon/2-1D-diatomic/map.in diff --git a/examples/USER/phonon/2-1D-diatomic/pdisp.eps b/examples/PACKAGES/phonon/2-1D-diatomic/pdisp.eps similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/pdisp.eps rename to examples/PACKAGES/phonon/2-1D-diatomic/pdisp.eps diff --git a/examples/USER/phonon/2-1D-diatomic/pdisp.gnuplot b/examples/PACKAGES/phonon/2-1D-diatomic/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/pdisp.gnuplot rename to examples/PACKAGES/phonon/2-1D-diatomic/pdisp.gnuplot diff --git a/examples/USER/phonon/2-1D-diatomic/phonon.bin.2000000 b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/phonon.bin.2000000 rename to examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 diff --git a/examples/USER/phonon/2-1D-diatomic/phonon.log b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/phonon.log rename to examples/PACKAGES/phonon/2-1D-diatomic/phonon.log diff --git a/examples/USER/phonon/2-1D-diatomic/plot.disp b/examples/PACKAGES/phonon/2-1D-diatomic/plot.disp similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/plot.disp rename to examples/PACKAGES/phonon/2-1D-diatomic/plot.disp diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/README similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/README rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/README diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/cuu3.eam similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/cuu3.eam diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/data.pos b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/data.pos similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/data.pos rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/data.pos diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.EAM3D similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.EAM3D diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp2 b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp2 similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp2 rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp2 diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.dos b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.dos similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.dos rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.dos diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/map.in b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/map.in similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/map.in rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/map.in diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.eps similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.eps diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdos.eps similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdos.eps diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.disp similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.disp diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.dos similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.dos diff --git a/examples/USER/phonon/4-Graphene/Graphene.bin.6000000 b/examples/PACKAGES/phonon/4-Graphene/Graphene.bin.6000000 similarity index 100% rename from examples/USER/phonon/4-Graphene/Graphene.bin.6000000 rename to examples/PACKAGES/phonon/4-Graphene/Graphene.bin.6000000 diff --git a/examples/USER/phonon/4-Graphene/Graphene.log b/examples/PACKAGES/phonon/4-Graphene/Graphene.log similarity index 100% rename from examples/USER/phonon/4-Graphene/Graphene.log rename to examples/PACKAGES/phonon/4-Graphene/Graphene.log diff --git a/examples/USER/phonon/4-Graphene/README b/examples/PACKAGES/phonon/4-Graphene/README similarity index 100% rename from examples/USER/phonon/4-Graphene/README rename to examples/PACKAGES/phonon/4-Graphene/README diff --git a/examples/USER/phonon/4-Graphene/SiC.tersoff b/examples/PACKAGES/phonon/4-Graphene/SiC.tersoff similarity index 100% rename from examples/USER/phonon/4-Graphene/SiC.tersoff rename to examples/PACKAGES/phonon/4-Graphene/SiC.tersoff diff --git a/examples/USER/phonon/4-Graphene/data.pos b/examples/PACKAGES/phonon/4-Graphene/data.pos similarity index 100% rename from examples/USER/phonon/4-Graphene/data.pos rename to examples/PACKAGES/phonon/4-Graphene/data.pos diff --git a/examples/USER/phonon/4-Graphene/in.disp b/examples/PACKAGES/phonon/4-Graphene/in.disp similarity index 100% rename from examples/USER/phonon/4-Graphene/in.disp rename to examples/PACKAGES/phonon/4-Graphene/in.disp diff --git a/examples/USER/phonon/4-Graphene/in.graphene b/examples/PACKAGES/phonon/4-Graphene/in.graphene similarity index 100% rename from examples/USER/phonon/4-Graphene/in.graphene rename to examples/PACKAGES/phonon/4-Graphene/in.graphene diff --git a/examples/USER/phonon/4-Graphene/map.in b/examples/PACKAGES/phonon/4-Graphene/map.in similarity index 100% rename from examples/USER/phonon/4-Graphene/map.in rename to examples/PACKAGES/phonon/4-Graphene/map.in diff --git a/examples/USER/phonon/4-Graphene/pdisp.dat b/examples/PACKAGES/phonon/4-Graphene/pdisp.dat similarity index 100% rename from examples/USER/phonon/4-Graphene/pdisp.dat rename to examples/PACKAGES/phonon/4-Graphene/pdisp.dat diff --git a/examples/USER/phonon/4-Graphene/pdisp.eps b/examples/PACKAGES/phonon/4-Graphene/pdisp.eps similarity index 100% rename from examples/USER/phonon/4-Graphene/pdisp.eps rename to examples/PACKAGES/phonon/4-Graphene/pdisp.eps diff --git a/examples/USER/phonon/4-Graphene/pdisp.gnuplot b/examples/PACKAGES/phonon/4-Graphene/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/4-Graphene/pdisp.gnuplot rename to examples/PACKAGES/phonon/4-Graphene/pdisp.gnuplot diff --git a/examples/USER/phonon/4-Graphene/plot.disp b/examples/PACKAGES/phonon/4-Graphene/plot.disp similarity index 100% rename from examples/USER/phonon/4-Graphene/plot.disp rename to examples/PACKAGES/phonon/4-Graphene/plot.disp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/README.md b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/README.md similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/README.md rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/README.md diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/in.silicon similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/in.silicon diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/out.silicon similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/out.silicon diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/python/README.md b/examples/PACKAGES/phonon/dynamical_matrix_command/python/README.md similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/README.md rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/README.md diff --git a/examples/USER/phonon/dynamical_matrix_command/python/SiCGe.tersoff b/examples/PACKAGES/phonon/dynamical_matrix_command/python/SiCGe.tersoff similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/SiCGe.tersoff rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/SiCGe.tersoff diff --git a/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py b/examples/PACKAGES/phonon/dynamical_matrix_command/python/dynmat.py similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/dynmat.py rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/dynmat.py diff --git a/examples/USER/phonon/dynamical_matrix_command/python/ff-silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/python/ff-silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/ff-silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/ff-silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat b/examples/PACKAGES/phonon/dynamical_matrix_command/python/results/dynmat.dat similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/results/dynmat.dat diff --git a/examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt b/examples/PACKAGES/phonon/dynamical_matrix_command/python/results/out.dynamt similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/results/out.dynamt diff --git a/examples/USER/phonon/dynamical_matrix_command/python/silicon_input_file.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/python/silicon_input_file.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/silicon_input_file.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/silicon_input_file.lmp diff --git a/examples/USER/misc/pimd/para-h2/H2.data b/examples/PACKAGES/pimd/para-h2/H2.data similarity index 100% rename from examples/USER/misc/pimd/para-h2/H2.data rename to examples/PACKAGES/pimd/para-h2/H2.data diff --git a/examples/USER/misc/pimd/para-h2/H2.xyz b/examples/PACKAGES/pimd/para-h2/H2.xyz similarity index 100% rename from examples/USER/misc/pimd/para-h2/H2.xyz rename to examples/PACKAGES/pimd/para-h2/H2.xyz diff --git a/examples/USER/misc/pimd/para-h2/NM.info b/examples/PACKAGES/pimd/para-h2/NM.info similarity index 100% rename from examples/USER/misc/pimd/para-h2/NM.info rename to examples/PACKAGES/pimd/para-h2/NM.info diff --git a/examples/USER/misc/pimd/para-h2/in.scp b/examples/PACKAGES/pimd/para-h2/in.scp similarity index 100% rename from examples/USER/misc/pimd/para-h2/in.scp rename to examples/PACKAGES/pimd/para-h2/in.scp diff --git a/examples/USER/misc/pimd/para-h2/pair.table b/examples/PACKAGES/pimd/para-h2/pair.table similarity index 100% rename from examples/USER/misc/pimd/para-h2/pair.table rename to examples/PACKAGES/pimd/para-h2/pair.table diff --git a/examples/USER/misc/pimd/para-h2/run.sh b/examples/PACKAGES/pimd/para-h2/run.sh similarity index 100% rename from examples/USER/misc/pimd/para-h2/run.sh rename to examples/PACKAGES/pimd/para-h2/run.sh diff --git a/examples/USER/misc/pimd/para-h2/vmd.src b/examples/PACKAGES/pimd/para-h2/vmd.src similarity index 100% rename from examples/USER/misc/pimd/para-h2/vmd.src rename to examples/PACKAGES/pimd/para-h2/vmd.src diff --git a/examples/USER/misc/pimd/prot-hairpin/in.scp b/examples/PACKAGES/pimd/prot-hairpin/in.scp similarity index 100% rename from examples/USER/misc/pimd/prot-hairpin/in.scp rename to examples/PACKAGES/pimd/prot-hairpin/in.scp diff --git a/examples/USER/misc/pimd/prot-hairpin/run.sh b/examples/PACKAGES/pimd/prot-hairpin/run.sh similarity index 100% rename from examples/USER/misc/pimd/prot-hairpin/run.sh rename to examples/PACKAGES/pimd/prot-hairpin/run.sh diff --git a/examples/USER/misc/pimd/prot-hairpin/system.data b/examples/PACKAGES/pimd/prot-hairpin/system.data similarity index 100% rename from examples/USER/misc/pimd/prot-hairpin/system.data rename to examples/PACKAGES/pimd/prot-hairpin/system.data diff --git a/examples/USER/misc/temper_npt/data.peptide b/examples/PACKAGES/plumed/data.peptide similarity index 100% rename from examples/USER/misc/temper_npt/data.peptide rename to examples/PACKAGES/plumed/data.peptide diff --git a/examples/USER/plumed/in.peptide-plumed b/examples/PACKAGES/plumed/in.peptide-plumed similarity index 100% rename from examples/USER/plumed/in.peptide-plumed rename to examples/PACKAGES/plumed/in.peptide-plumed diff --git a/examples/USER/plumed/log.4Feb20.peptide-plumed.g++.1 b/examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.1 similarity index 100% rename from examples/USER/plumed/log.4Feb20.peptide-plumed.g++.1 rename to examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.1 diff --git a/examples/USER/plumed/log.4Feb20.peptide-plumed.g++.4 b/examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.4 similarity index 100% rename from examples/USER/plumed/log.4Feb20.peptide-plumed.g++.4 rename to examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.4 diff --git a/examples/USER/plumed/plumed.dat b/examples/PACKAGES/plumed/plumed.dat similarity index 100% rename from examples/USER/plumed/plumed.dat rename to examples/PACKAGES/plumed/plumed.dat diff --git a/examples/USER/plumed/reference/colvar b/examples/PACKAGES/plumed/reference/colvar similarity index 100% rename from examples/USER/plumed/reference/colvar rename to examples/PACKAGES/plumed/reference/colvar diff --git a/examples/USER/plumed/reference/p.log b/examples/PACKAGES/plumed/reference/p.log similarity index 100% rename from examples/USER/plumed/reference/p.log rename to examples/PACKAGES/plumed/reference/p.log diff --git a/examples/USER/ptm/ptm_example.in b/examples/PACKAGES/ptm/ptm_example.in similarity index 100% rename from examples/USER/ptm/ptm_example.in rename to examples/PACKAGES/ptm/ptm_example.in diff --git a/examples/USER/qtb/README b/examples/PACKAGES/qtb/README similarity index 71% rename from examples/USER/qtb/README rename to examples/PACKAGES/qtb/README index 41dec0dea3..80cde6395c 100644 --- a/examples/USER/qtb/README +++ b/examples/PACKAGES/qtb/README @@ -1,5 +1,5 @@ -There are example scripts for using the USER-QTB package. -See its src/USER-QTB/README file for more info on +There are example scripts for using the QTB package. +See its src/QTB/README file for more info on quantum nuclear effects and when they are important to include in your model. diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF diff --git a/examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb b/examples/PACKAGES/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb rename to examples/PACKAGES/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb diff --git a/examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 b/examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 rename to examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 diff --git a/examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 b/examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 rename to examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 diff --git a/examples/USER/qtb/methane_qbmsst/ffield.reax b/examples/PACKAGES/qtb/methane_qbmsst/ffield.reax similarity index 100% rename from examples/USER/qtb/methane_qbmsst/ffield.reax rename to examples/PACKAGES/qtb/methane_qbmsst/ffield.reax diff --git a/examples/USER/qtb/methane_qbmsst/methane_qbmsst.in b/examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in similarity index 100% rename from examples/USER/qtb/methane_qbmsst/methane_qbmsst.in rename to examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in diff --git a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod b/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod similarity index 100% rename from examples/USER/qtb/methane_qbmsst/methane_qtb.mod rename to examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod diff --git a/examples/USER/qtb/methane_qtb/ffield.reax b/examples/PACKAGES/qtb/methane_qtb/ffield.reax similarity index 100% rename from examples/USER/qtb/methane_qtb/ffield.reax rename to examples/PACKAGES/qtb/methane_qtb/ffield.reax diff --git a/examples/USER/qtb/methane_qtb/methane_qtb.in b/examples/PACKAGES/qtb/methane_qtb/methane_qtb.in similarity index 100% rename from examples/USER/qtb/methane_qtb/methane_qtb.in rename to examples/PACKAGES/qtb/methane_qtb/methane_qtb.in diff --git a/examples/USER/quip/data_gap b/examples/PACKAGES/quip/data_gap similarity index 100% rename from examples/USER/quip/data_gap rename to examples/PACKAGES/quip/data_gap diff --git a/examples/USER/quip/data_sw b/examples/PACKAGES/quip/data_sw similarity index 100% rename from examples/USER/quip/data_sw rename to examples/PACKAGES/quip/data_sw diff --git a/examples/USER/quip/gap_example.xml b/examples/PACKAGES/quip/gap_example.xml similarity index 99% rename from examples/USER/quip/gap_example.xml rename to examples/PACKAGES/quip/gap_example.xml index baf9e32bb7..b286925e20 100644 --- a/examples/USER/quip/gap_example.xml +++ b/examples/PACKAGES/quip/gap_example.xml @@ -1,3 +1,4 @@ + diff --git a/examples/USER/quip/gap_example_sparse.dat b/examples/PACKAGES/quip/gap_example_sparse.dat similarity index 100% rename from examples/USER/quip/gap_example_sparse.dat rename to examples/PACKAGES/quip/gap_example_sparse.dat diff --git a/examples/USER/quip/in.gap b/examples/PACKAGES/quip/in.gap similarity index 100% rename from examples/USER/quip/in.gap rename to examples/PACKAGES/quip/in.gap diff --git a/examples/USER/quip/in.molecular b/examples/PACKAGES/quip/in.molecular similarity index 100% rename from examples/USER/quip/in.molecular rename to examples/PACKAGES/quip/in.molecular diff --git a/examples/USER/quip/in.sw b/examples/PACKAGES/quip/in.sw similarity index 100% rename from examples/USER/quip/in.sw rename to examples/PACKAGES/quip/in.sw diff --git a/examples/USER/quip/log.24Jul17.gap.g++.1 b/examples/PACKAGES/quip/log.24Jul17.gap.g++.1 similarity index 100% rename from examples/USER/quip/log.24Jul17.gap.g++.1 rename to examples/PACKAGES/quip/log.24Jul17.gap.g++.1 diff --git a/examples/USER/quip/log.24Jul17.gap.g++.4 b/examples/PACKAGES/quip/log.24Jul17.gap.g++.4 similarity index 100% rename from examples/USER/quip/log.24Jul17.gap.g++.4 rename to examples/PACKAGES/quip/log.24Jul17.gap.g++.4 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.1 b/examples/PACKAGES/quip/log.24Jul17.molecular.g++.1 similarity index 100% rename from examples/USER/quip/log.24Jul17.molecular.g++.1 rename to examples/PACKAGES/quip/log.24Jul17.molecular.g++.1 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.4 b/examples/PACKAGES/quip/log.24Jul17.molecular.g++.4 similarity index 100% rename from examples/USER/quip/log.24Jul17.molecular.g++.4 rename to examples/PACKAGES/quip/log.24Jul17.molecular.g++.4 diff --git a/examples/USER/quip/log.24Jul17.sw.g++.1 b/examples/PACKAGES/quip/log.24Jul17.sw.g++.1 similarity index 100% rename from examples/USER/quip/log.24Jul17.sw.g++.1 rename to examples/PACKAGES/quip/log.24Jul17.sw.g++.1 diff --git a/examples/USER/quip/log.24Jul17.sw.g++.4 b/examples/PACKAGES/quip/log.24Jul17.sw.g++.4 similarity index 100% rename from examples/USER/quip/log.24Jul17.sw.g++.4 rename to examples/PACKAGES/quip/log.24Jul17.sw.g++.4 diff --git a/examples/USER/quip/methane-box-8.data b/examples/PACKAGES/quip/methane-box-8.data similarity index 100% rename from examples/USER/quip/methane-box-8.data rename to examples/PACKAGES/quip/methane-box-8.data diff --git a/examples/USER/quip/out.molecular b/examples/PACKAGES/quip/out.molecular similarity index 100% rename from examples/USER/quip/out.molecular rename to examples/PACKAGES/quip/out.molecular diff --git a/examples/USER/quip/sw_example.xml b/examples/PACKAGES/quip/sw_example.xml similarity index 93% rename from examples/USER/quip/sw_example.xml rename to examples/PACKAGES/quip/sw_example.xml index 8a28a7cd7e..14b829ac34 100644 --- a/examples/USER/quip/sw_example.xml +++ b/examples/PACKAGES/quip/sw_example.xml @@ -1,3 +1,4 @@ + Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements. Ge and Si-Ge from Ethier and Lewis '92 diff --git a/examples/USER/rann/in.rann b/examples/PACKAGES/rann/in.rann similarity index 100% rename from examples/USER/rann/in.rann rename to examples/PACKAGES/rann/in.rann diff --git a/examples/USER/rann/log.22Jun21.rann.g++.1 b/examples/PACKAGES/rann/log.22Jun21.rann.g++.1 similarity index 100% rename from examples/USER/rann/log.22Jun21.rann.g++.1 rename to examples/PACKAGES/rann/log.22Jun21.rann.g++.1 diff --git a/examples/USER/rann/log.22Jun21.rann.g++.4 b/examples/PACKAGES/rann/log.22Jun21.rann.g++.4 similarity index 100% rename from examples/USER/rann/log.22Jun21.rann.g++.4 rename to examples/PACKAGES/rann/log.22Jun21.rann.g++.4 diff --git a/examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene.map similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map rename to examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene.map diff --git a/examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template rename to examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template diff --git a/examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template rename to examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template diff --git a/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene rename to examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene diff --git a/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 rename to examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 diff --git a/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 rename to examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 diff --git a/examples/USER/reaction/create_atoms_polystyrene/trimer.data b/examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/trimer.data rename to examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data diff --git a/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt rename to examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt diff --git a/examples/USER/reaction/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/large_nylon_melt.data.gz rename to examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz diff --git a/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 rename to examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 diff --git a/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 rename to examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_map similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_map diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_map similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_map diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template diff --git a/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized similarity index 100% rename from examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized rename to examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_pre.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_pre.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp2.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp1.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_pre.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_pre.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp2.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp2.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data b/examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data similarity index 100% rename from examples/USER/reaction/tiny_epoxy/tiny_epoxy.data rename to examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized diff --git a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 similarity index 98% rename from examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 rename to examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 index 16e4deef51..57455b04f4 100644 --- a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 +++ b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 @@ -96,8 +96,8 @@ thermo 50 # dump 1 all xyz 1 test_vis.xyz fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined diff --git a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 similarity index 98% rename from examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 index 527d71ce87..b6dcdafc54 100644 --- a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 +++ b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 @@ -96,8 +96,8 @@ thermo 50 # dump 1 all xyz 1 test_vis.xyz fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_map b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_map similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_map rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_map diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp2_map b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_map similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp2_map rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_map diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/tiny_nylon.data b/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data similarity index 100% rename from examples/USER/reaction/tiny_nylon/tiny_nylon.data rename to examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_map b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_map rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_map diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_map b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_map rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_map diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map b/examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_map diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized rename to examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data b/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data rename to examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data diff --git a/examples/USER/misc/rhok/README.md b/examples/PACKAGES/rhok/README.md similarity index 100% rename from examples/USER/misc/rhok/README.md rename to examples/PACKAGES/rhok/README.md diff --git a/examples/USER/misc/rhok/in.crystal b/examples/PACKAGES/rhok/in.crystal similarity index 100% rename from examples/USER/misc/rhok/in.crystal rename to examples/PACKAGES/rhok/in.crystal diff --git a/examples/USER/misc/rhok/in.pinning b/examples/PACKAGES/rhok/in.pinning similarity index 100% rename from examples/USER/misc/rhok/in.pinning rename to examples/PACKAGES/rhok/in.pinning diff --git a/examples/USER/misc/rhok/in.setup b/examples/PACKAGES/rhok/in.setup similarity index 100% rename from examples/USER/misc/rhok/in.setup rename to examples/PACKAGES/rhok/in.setup diff --git a/examples/USER/misc/rhok/log.22Sep2017.crystal.g++.1 b/examples/PACKAGES/rhok/log.22Sep2017.crystal.g++.1 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.crystal.g++.1 rename to examples/PACKAGES/rhok/log.22Sep2017.crystal.g++.1 diff --git a/examples/USER/misc/rhok/log.22Sep2017.crystal.g++.4 b/examples/PACKAGES/rhok/log.22Sep2017.crystal.g++.4 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.crystal.g++.4 rename to examples/PACKAGES/rhok/log.22Sep2017.crystal.g++.4 diff --git a/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.1 b/examples/PACKAGES/rhok/log.22Sep2017.pinning.g++.1 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.pinning.g++.1 rename to examples/PACKAGES/rhok/log.22Sep2017.pinning.g++.1 diff --git a/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4 b/examples/PACKAGES/rhok/log.22Sep2017.pinning.g++.4 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4 rename to examples/PACKAGES/rhok/log.22Sep2017.pinning.g++.4 diff --git a/examples/USER/misc/rhok/log.22Sep2017.setup.g++.1 b/examples/PACKAGES/rhok/log.22Sep2017.setup.g++.1 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.setup.g++.1 rename to examples/PACKAGES/rhok/log.22Sep2017.setup.g++.1 diff --git a/examples/USER/misc/rhok/log.22Sep2017.setup.g++.4 b/examples/PACKAGES/rhok/log.22Sep2017.setup.g++.4 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.setup.g++.4 rename to examples/PACKAGES/rhok/log.22Sep2017.setup.g++.4 diff --git a/examples/USER/scafacos/data.NaCl b/examples/PACKAGES/scafacos/data.NaCl similarity index 100% rename from examples/USER/scafacos/data.NaCl rename to examples/PACKAGES/scafacos/data.NaCl diff --git a/examples/USER/scafacos/data.cloud_wall b/examples/PACKAGES/scafacos/data.cloud_wall similarity index 100% rename from examples/USER/scafacos/data.cloud_wall rename to examples/PACKAGES/scafacos/data.cloud_wall diff --git a/examples/USER/scafacos/data.hammersley_sphere b/examples/PACKAGES/scafacos/data.hammersley_sphere similarity index 100% rename from examples/USER/scafacos/data.hammersley_sphere rename to examples/PACKAGES/scafacos/data.hammersley_sphere diff --git a/examples/USER/scafacos/in.scafacos b/examples/PACKAGES/scafacos/in.scafacos similarity index 100% rename from examples/USER/scafacos/in.scafacos rename to examples/PACKAGES/scafacos/in.scafacos diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/PACKAGES/scafacos/in.scafacos.cw.ewald similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.ewald rename to examples/PACKAGES/scafacos/in.scafacos.cw.ewald diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/PACKAGES/scafacos/in.scafacos.cw.fmm similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.fmm rename to examples/PACKAGES/scafacos/in.scafacos.cw.fmm diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/PACKAGES/scafacos/in.scafacos.cw.p2nfft similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.p2nfft rename to examples/PACKAGES/scafacos/in.scafacos.cw.p2nfft diff --git a/examples/USER/scafacos/in.scafacos.cw.p3m b/examples/PACKAGES/scafacos/in.scafacos.cw.p3m similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.p3m rename to examples/PACKAGES/scafacos/in.scafacos.cw.p3m diff --git a/examples/USER/scafacos/in.scafacos.ewald b/examples/PACKAGES/scafacos/in.scafacos.ewald similarity index 100% rename from examples/USER/scafacos/in.scafacos.ewald rename to examples/PACKAGES/scafacos/in.scafacos.ewald diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/PACKAGES/scafacos/in.scafacos.fmm similarity index 100% rename from examples/USER/scafacos/in.scafacos.fmm rename to examples/PACKAGES/scafacos/in.scafacos.fmm diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/PACKAGES/scafacos/in.scafacos.hsph.direct similarity index 100% rename from examples/USER/scafacos/in.scafacos.hsph.direct rename to examples/PACKAGES/scafacos/in.scafacos.hsph.direct diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/PACKAGES/scafacos/in.scafacos.hsph.fmm similarity index 100% rename from examples/USER/scafacos/in.scafacos.hsph.fmm rename to examples/PACKAGES/scafacos/in.scafacos.hsph.fmm diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/PACKAGES/scafacos/in.scafacos.hsph.p2nfft similarity index 100% rename from examples/USER/scafacos/in.scafacos.hsph.p2nfft rename to examples/PACKAGES/scafacos/in.scafacos.hsph.p2nfft diff --git a/examples/USER/scafacos/in.scafacos.p2nfft b/examples/PACKAGES/scafacos/in.scafacos.p2nfft similarity index 100% rename from examples/USER/scafacos/in.scafacos.p2nfft rename to examples/PACKAGES/scafacos/in.scafacos.p2nfft diff --git a/examples/USER/scafacos/in.scafacos.p3m b/examples/PACKAGES/scafacos/in.scafacos.p3m similarity index 100% rename from examples/USER/scafacos/in.scafacos.p3m rename to examples/PACKAGES/scafacos/in.scafacos.p3m diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 index e0b10de95e..179f3bfcb2 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 index f881ed003a..877cf778fa 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 index 9410529284..8b6cd7d81e 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 index 2dc5c07b2b..2d44371649 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 index e6cd7c506f..a4547054c2 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 index 39e0387491..2036be9b24 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 index 6b36f0ba91..417c8e9f84 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 index 23f55fc5a6..9cad97aa6b 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 index 92e85e072e..3c5a48c251 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 index 18199eca16..4e079da923 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/misc/slater/data.after_equilibration b/examples/PACKAGES/slater/data.after_equilibration similarity index 100% rename from examples/USER/misc/slater/data.after_equilibration rename to examples/PACKAGES/slater/data.after_equilibration diff --git a/examples/USER/misc/slater/data.after_production_run b/examples/PACKAGES/slater/data.after_production_run similarity index 100% rename from examples/USER/misc/slater/data.after_production_run rename to examples/PACKAGES/slater/data.after_production_run diff --git a/examples/USER/misc/slater/in.slater b/examples/PACKAGES/slater/in.slater similarity index 100% rename from examples/USER/misc/slater/in.slater rename to examples/PACKAGES/slater/in.slater diff --git a/examples/USER/misc/slater/log.lammps b/examples/PACKAGES/slater/log.lammps similarity index 100% rename from examples/USER/misc/slater/log.lammps rename to examples/PACKAGES/slater/log.lammps diff --git a/examples/USER/misc/slater/tmp_1_1.rdf b/examples/PACKAGES/slater/tmp_1_1.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_1_1.rdf rename to examples/PACKAGES/slater/tmp_1_1.rdf diff --git a/examples/USER/misc/slater/tmp_1_2.rdf b/examples/PACKAGES/slater/tmp_1_2.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_1_2.rdf rename to examples/PACKAGES/slater/tmp_1_2.rdf diff --git a/examples/USER/misc/slater/tmp_1_3.rdf b/examples/PACKAGES/slater/tmp_1_3.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_1_3.rdf rename to examples/PACKAGES/slater/tmp_1_3.rdf diff --git a/examples/USER/misc/slater/tmp_2_2.rdf b/examples/PACKAGES/slater/tmp_2_2.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_2_2.rdf rename to examples/PACKAGES/slater/tmp_2_2.rdf diff --git a/examples/USER/misc/slater/tmp_2_3.rdf b/examples/PACKAGES/slater/tmp_2_3.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_2_3.rdf rename to examples/PACKAGES/slater/tmp_2_3.rdf diff --git a/examples/USER/misc/slater/tmp_3_3.rdf b/examples/PACKAGES/slater/tmp_3_3.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_3_3.rdf rename to examples/PACKAGES/slater/tmp_3_3.rdf diff --git a/examples/USER/smtbq/data.Alpha b/examples/PACKAGES/smtbq/data.Alpha similarity index 100% rename from examples/USER/smtbq/data.Alpha rename to examples/PACKAGES/smtbq/data.Alpha diff --git a/examples/USER/smtbq/ffield.smtbq.Al b/examples/PACKAGES/smtbq/ffield.smtbq.Al similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.Al rename to examples/PACKAGES/smtbq/ffield.smtbq.Al diff --git a/examples/USER/smtbq/ffield.smtbq.Al2O3 b/examples/PACKAGES/smtbq/ffield.smtbq.Al2O3 similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.Al2O3 rename to examples/PACKAGES/smtbq/ffield.smtbq.Al2O3 diff --git a/examples/USER/smtbq/ffield.smtbq.TiO2 b/examples/PACKAGES/smtbq/ffield.smtbq.TiO2 similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.TiO2 rename to examples/PACKAGES/smtbq/ffield.smtbq.TiO2 diff --git a/examples/USER/smtbq/in.smtbq.Al b/examples/PACKAGES/smtbq/in.smtbq.Al similarity index 100% rename from examples/USER/smtbq/in.smtbq.Al rename to examples/PACKAGES/smtbq/in.smtbq.Al diff --git a/examples/USER/smtbq/in.smtbq.Al2O3 b/examples/PACKAGES/smtbq/in.smtbq.Al2O3 similarity index 100% rename from examples/USER/smtbq/in.smtbq.Al2O3 rename to examples/PACKAGES/smtbq/in.smtbq.Al2O3 diff --git a/examples/USER/smtbq/in.smtbq.TiO2 b/examples/PACKAGES/smtbq/in.smtbq.TiO2 similarity index 100% rename from examples/USER/smtbq/in.smtbq.TiO2 rename to examples/PACKAGES/smtbq/in.smtbq.TiO2 diff --git a/examples/USER/smtbq/log.smtbq.Al.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.Al.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.Al.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.Al.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.Al.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.Al.g++.4 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al2O3.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al2O3.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.4 diff --git a/examples/USER/smtbq/log.smtbq.TiO2.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.TiO2.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.TiO2.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.TiO2.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.4 diff --git a/examples/PACKAGES/sph/README b/examples/PACKAGES/sph/README new file mode 100644 index 0000000000..9df07acab7 --- /dev/null +++ b/examples/PACKAGES/sph/README @@ -0,0 +1 @@ +see the SPH user's guide for a detailed explanation of these examples. diff --git a/examples/USER/sph/cavity_flow/cavity_flow.lmp b/examples/PACKAGES/sph/cavity_flow/cavity_flow.lmp similarity index 100% rename from examples/USER/sph/cavity_flow/cavity_flow.lmp rename to examples/PACKAGES/sph/cavity_flow/cavity_flow.lmp diff --git a/examples/USER/sph/heatconduction/compare_analytic.gpl b/examples/PACKAGES/sph/heatconduction/compare_analytic.gpl similarity index 100% rename from examples/USER/sph/heatconduction/compare_analytic.gpl rename to examples/PACKAGES/sph/heatconduction/compare_analytic.gpl diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp b/examples/PACKAGES/sph/heatconduction/sph_heat_conduction_2d.lmp similarity index 100% rename from examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp rename to examples/PACKAGES/sph/heatconduction/sph_heat_conduction_2d.lmp diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp b/examples/PACKAGES/sph/heatconduction/sph_heat_conduction_3d.lmp similarity index 100% rename from examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp rename to examples/PACKAGES/sph/heatconduction/sph_heat_conduction_3d.lmp diff --git a/examples/USER/sph/shock_tube/compare_exact.gpl b/examples/PACKAGES/sph/shock_tube/compare_exact.gpl similarity index 100% rename from examples/USER/sph/shock_tube/compare_exact.gpl rename to examples/PACKAGES/sph/shock_tube/compare_exact.gpl diff --git a/examples/USER/sph/shock_tube/exact_solution.dat b/examples/PACKAGES/sph/shock_tube/exact_solution.dat similarity index 100% rename from examples/USER/sph/shock_tube/exact_solution.dat rename to examples/PACKAGES/sph/shock_tube/exact_solution.dat diff --git a/examples/USER/sph/shock_tube/shock2d.lmp b/examples/PACKAGES/sph/shock_tube/shock2d.lmp similarity index 100% rename from examples/USER/sph/shock_tube/shock2d.lmp rename to examples/PACKAGES/sph/shock_tube/shock2d.lmp diff --git a/examples/USER/sph/shock_tube/shock3d.lmp b/examples/PACKAGES/sph/shock_tube/shock3d.lmp similarity index 100% rename from examples/USER/sph/shock_tube/shock3d.lmp rename to examples/PACKAGES/sph/shock_tube/shock3d.lmp diff --git a/examples/USER/sph/water_collapse/data.initial b/examples/PACKAGES/sph/water_collapse/data.initial similarity index 100% rename from examples/USER/sph/water_collapse/data.initial rename to examples/PACKAGES/sph/water_collapse/data.initial diff --git a/examples/USER/sph/water_collapse/water_collapse.lmp b/examples/PACKAGES/sph/water_collapse/water_collapse.lmp similarity index 100% rename from examples/USER/sph/water_collapse/water_collapse.lmp rename to examples/PACKAGES/sph/water_collapse/water_collapse.lmp diff --git a/examples/USER/misc/srp/data.chain b/examples/PACKAGES/srp/data.chain similarity index 100% rename from examples/USER/misc/srp/data.chain rename to examples/PACKAGES/srp/data.chain diff --git a/examples/USER/misc/srp/in.srp b/examples/PACKAGES/srp/in.srp similarity index 93% rename from examples/USER/misc/srp/in.srp rename to examples/PACKAGES/srp/in.srp index 018d916292..7f168acbd5 100644 --- a/examples/USER/misc/srp/in.srp +++ b/examples/PACKAGES/srp/in.srp @@ -35,8 +35,8 @@ thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz fix 1 all nve timestep 0.01 -restart 500 mid-run-*.restart +#restart 500 mid-run-*.restart run 1000 -write_restart end-run.restart +#write_restart end-run.restart diff --git a/examples/PACKAGES/srp/log.28Jul2021.srp.g++.1 b/examples/PACKAGES/srp/log.28Jul2021.srp.g++.1 new file mode 100644 index 0000000000..6cf252cba4 --- /dev/null +++ b/examples/PACKAGES/srp/log.28Jul2021.srp.g++.1 @@ -0,0 +1,156 @@ +LAMMPS (28 Jul 2021) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style full +boundary p p p + +special_bonds lj/coul 1 1 1 +newton on on + +# save an extra atom type for bond particles +read_data data.chain +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + reading velocities ... + 3000 velocities + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 2700 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.013 seconds + +neighbor 2.0 bin +neigh_modify every 10 check yes + +bond_style harmonic +bond_coeff * 225.0 0.85 + +comm_modify vel yes +comm_modify cutoff 3.6 + +# must use pair hybrid, since srp bond particles +# do not interact with other atoms types +pair_style hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid +pair_coeff 1 1 dpd 60.0 4.5 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 + +# auto normalization of thermo quantities is turned off by pair srp +# just divide by natoms +variable natoms equal count(all) +variable nPotEng equal c_thermo_pe/v_natoms + +thermo 50 +thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz + +fix 1 all nve +timestep 0.01 + +#restart 500 mid-run-*.restart + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- @Article{Sirk2012 + author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm}, + title = {An enhanced entangled polymer model for dissipative particle dynamics}, + journal = {J.~Chem.~Phys.}, + year = 2012, + volume = 136, + pages = {134903} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Using type 2 for bond particles +Thermo normalization turned off by pair srp (src/MISC/pair_srp.cpp:486) +Neighbor list info ... + update every 10 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3 + ghost atom cutoff = 3.6 + binsize = 1.5, bins = 7 7 7 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair dpd, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair srp, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Removed/inserted 0/2700 bond particles. (src/MISC/fix_srp.cpp:250) +Per MPI rank memory allocation (min/avg/max) = 21.70 | 21.70 | 21.70 Mbytes +Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz + 0 0.98262092 31772.336 10.590779 60.690437 5700 3000 10 10 10 + 50 0.99678169 31789.37 10.596457 61.967133 5700 3000 10 10 10 + 100 1.016953 31770.946 10.590315 61.808425 5700 3000 10 10 10 + 150 1.0151677 31737.965 10.579322 61.034423 5700 3000 10 10 10 + 200 0.99241972 31766.458 10.588819 60.99902 5700 3000 10 10 10 + 250 1.0101747 31816.098 10.605366 61.484391 5700 3000 10 10 10 + 300 1.0058287 31824.98 10.608327 60.656545 5700 3000 10 10 10 + 350 1.0093409 31839.963 10.613321 61.485931 5700 3000 10 10 10 + 400 1.029692 31713.44 10.571147 61.442428 5700 3000 10 10 10 + 450 1.0292264 31739.234 10.579745 61.026996 5700 3000 10 10 10 + 500 1.0141131 31796.032 10.598677 61.099407 5700 3000 10 10 10 + 550 0.99860738 31887.879 10.629293 61.412249 5700 3000 10 10 10 + 600 1.0104436 31830.675 10.610225 60.725018 5700 3000 10 10 10 + 650 1.0060939 31871.441 10.623814 61.12217 5700 3000 10 10 10 + 700 1.0394405 31724.09 10.574697 60.652294 5700 3000 10 10 10 + 750 1.0094386 31827.328 10.609109 61.274573 5700 3000 10 10 10 + 800 0.99986353 31777.205 10.592402 60.652922 5700 3000 10 10 10 + 850 0.9762615 31752.585 10.584195 61.448972 5700 3000 10 10 10 + 900 0.99324534 31794.723 10.598241 61.191199 5700 3000 10 10 10 + 950 1.0139717 31719.123 10.573041 61.876053 5700 3000 10 10 10 + 1000 0.99850758 31774.801 10.5916 60.960607 5700 3000 10 10 10 +Deleted 2700 atoms, new total = 3000 +Loop time of 6.54135 on 1 procs for 1000 steps with 3000 atoms + +Performance: 132082.911 tau/day, 152.874 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.5403 | 4.5403 | 4.5403 | 0.0 | 69.41 +Bond | 0.030682 | 0.030682 | 0.030682 | 0.0 | 0.47 +Neigh | 1.7065 | 1.7065 | 1.7065 | 0.0 | 26.09 +Comm | 0.20647 | 0.20647 | 0.20647 | 0.0 | 3.16 +Output | 0.00084543 | 0.00084543 | 0.00084543 | 0.0 | 0.01 +Modify | 0.034479 | 0.034479 | 0.034479 | 0.0 | 0.53 +Other | | 0.022 | | | 0.34 + +Nlocal: 3000.00 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12269.0 ave 12269 max 12269 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Ave special neighs/atom = 1.8000000 +Neighbor list builds = 21 +Dangerous builds = 0 + +#write_restart end-run.restart +Total wall time: 0:00:06 diff --git a/examples/PACKAGES/srp/log.28Jul2021.srp.g++.4 b/examples/PACKAGES/srp/log.28Jul2021.srp.g++.4 new file mode 100644 index 0000000000..ca41ab915a --- /dev/null +++ b/examples/PACKAGES/srp/log.28Jul2021.srp.g++.4 @@ -0,0 +1,156 @@ +LAMMPS (28 Jul 2021) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style full +boundary p p p + +special_bonds lj/coul 1 1 1 +newton on on + +# save an extra atom type for bond particles +read_data data.chain +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + reading velocities ... + 3000 velocities + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 2700 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +neighbor 2.0 bin +neigh_modify every 10 check yes + +bond_style harmonic +bond_coeff * 225.0 0.85 + +comm_modify vel yes +comm_modify cutoff 3.6 + +# must use pair hybrid, since srp bond particles +# do not interact with other atoms types +pair_style hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid +pair_coeff 1 1 dpd 60.0 4.5 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 + +# auto normalization of thermo quantities is turned off by pair srp +# just divide by natoms +variable natoms equal count(all) +variable nPotEng equal c_thermo_pe/v_natoms + +thermo 50 +thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz + +fix 1 all nve +timestep 0.01 + +#restart 500 mid-run-*.restart + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- @Article{Sirk2012 + author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm}, + title = {An enhanced entangled polymer model for dissipative particle dynamics}, + journal = {J.~Chem.~Phys.}, + year = 2012, + volume = 136, + pages = {134903} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Using type 2 for bond particles +Thermo normalization turned off by pair srp (src/MISC/pair_srp.cpp:486) +Neighbor list info ... + update every 10 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3 + ghost atom cutoff = 3.6 + binsize = 1.5, bins = 7 7 7 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair dpd, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair srp, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Removed/inserted 0/2700 bond particles. (src/MISC/fix_srp.cpp:250) +Per MPI rank memory allocation (min/avg/max) = 10.35 | 10.35 | 10.35 Mbytes +Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz + 0 0.98262092 31772.336 10.590779 60.908146 5700 3000 10 10 10 + 50 1.0094645 31632.293 10.544098 61.107394 5700 3000 10 10 10 + 100 1.0067657 31633.525 10.544508 61.721089 5700 3000 10 10 10 + 150 0.99163624 31751.06 10.583687 60.437789 5700 3000 10 10 10 + 200 0.98701756 31674.754 10.558251 60.897782 5700 3000 10 10 10 + 250 0.99422545 31689.944 10.563315 61.748317 5700 3000 10 10 10 + 300 0.98351268 31756.124 10.585375 61.164735 5700 3000 10 10 10 + 350 0.99570183 31840.098 10.613366 61.210337 5700 3000 10 10 10 + 400 1.0025719 31832.008 10.610669 61.270633 5700 3000 10 10 10 + 450 0.99464256 31812.213 10.604071 60.625168 5700 3000 10 10 10 + 500 0.98753036 31822.577 10.607526 61.007786 5700 3000 10 10 10 + 550 0.98085348 31779.406 10.593135 61.268608 5700 3000 10 10 10 + 600 1.0031999 31849.695 10.616565 61.938464 5700 3000 10 10 10 + 650 1.0102644 31912.564 10.637521 61.298438 5700 3000 10 10 10 + 700 1.0238545 31799.622 10.599874 61.424427 5700 3000 10 10 10 + 750 1.0186874 31781.261 10.593754 60.706143 5700 3000 10 10 10 + 800 1.0245821 31738.473 10.579491 61.550865 5700 3000 10 10 10 + 850 1.0179726 31720.521 10.573507 61.881576 5700 3000 10 10 10 + 900 1.0154591 31760.887 10.586962 61.673156 5700 3000 10 10 10 + 950 0.99349056 31834.644 10.611548 61.624864 5700 3000 10 10 10 + 1000 1.0033121 31820.089 10.606696 60.698277 5700 3000 10 10 10 +Deleted 2700 atoms, new total = 3000 +Loop time of 2.18923 on 4 procs for 1000 steps with 3000 atoms + +Performance: 394659.660 tau/day, 456.782 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2744 | 1.2921 | 1.3222 | 1.6 | 59.02 +Bond | 0.0092027 | 0.0093722 | 0.009696 | 0.2 | 0.43 +Neigh | 0.47767 | 0.47768 | 0.47769 | 0.0 | 21.82 +Comm | 0.34932 | 0.37877 | 0.39403 | 2.9 | 17.30 +Output | 0.001045 | 0.0015711 | 0.003145 | 2.3 | 0.07 +Modify | 0.015498 | 0.016073 | 0.017271 | 0.6 | 0.73 +Other | | 0.01362 | | | 0.62 + +Nlocal: 750.000 ave 754 max 743 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 6941.25 ave 6967 max 6911 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Ave special neighs/atom = 1.8000000 +Neighbor list builds = 21 +Dangerous builds = 0 + +#write_restart end-run.restart +Total wall time: 0:00:02 diff --git a/examples/USER/tally/README b/examples/PACKAGES/tally/README similarity index 84% rename from examples/USER/tally/README rename to examples/PACKAGES/tally/README index fcc58e6e0d..074193b0f2 100644 --- a/examples/USER/tally/README +++ b/examples/PACKAGES/tally/README @@ -1,4 +1,4 @@ -Examples and tests for USER-TALLY compute styles. +Examples and tests for TALLY compute styles. The examples in this directory show where and how compute tally styles are equivalent to other facilities in LAMMPS and thus they can also be diff --git a/examples/USER/tally/data.spce b/examples/PACKAGES/tally/data.spce similarity index 100% rename from examples/USER/tally/data.spce rename to examples/PACKAGES/tally/data.spce diff --git a/examples/USER/tally/in.force b/examples/PACKAGES/tally/in.force similarity index 100% rename from examples/USER/tally/in.force rename to examples/PACKAGES/tally/in.force diff --git a/examples/USER/tally/in.pe b/examples/PACKAGES/tally/in.pe similarity index 100% rename from examples/USER/tally/in.pe rename to examples/PACKAGES/tally/in.pe diff --git a/examples/USER/tally/in.stress b/examples/PACKAGES/tally/in.stress similarity index 100% rename from examples/USER/tally/in.stress rename to examples/PACKAGES/tally/in.stress diff --git a/examples/USER/tally/log.12Jun17.force.1 b/examples/PACKAGES/tally/log.12Jun17.force.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.force.1 rename to examples/PACKAGES/tally/log.12Jun17.force.1 diff --git a/examples/USER/tally/log.12Jun17.force.4 b/examples/PACKAGES/tally/log.12Jun17.force.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.force.4 rename to examples/PACKAGES/tally/log.12Jun17.force.4 diff --git a/examples/USER/tally/log.12Jun17.pe.1 b/examples/PACKAGES/tally/log.12Jun17.pe.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.pe.1 rename to examples/PACKAGES/tally/log.12Jun17.pe.1 diff --git a/examples/USER/tally/log.12Jun17.pe.4 b/examples/PACKAGES/tally/log.12Jun17.pe.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.pe.4 rename to examples/PACKAGES/tally/log.12Jun17.pe.4 diff --git a/examples/USER/tally/log.12Jun17.stress.1 b/examples/PACKAGES/tally/log.12Jun17.stress.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.stress.1 rename to examples/PACKAGES/tally/log.12Jun17.stress.1 diff --git a/examples/USER/tally/log.12Jun17.stress.4 b/examples/PACKAGES/tally/log.12Jun17.stress.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.stress.4 rename to examples/PACKAGES/tally/log.12Jun17.stress.4 diff --git a/examples/USER/plumed/data.peptide b/examples/PACKAGES/temper_npt/data.peptide similarity index 100% rename from examples/USER/plumed/data.peptide rename to examples/PACKAGES/temper_npt/data.peptide diff --git a/examples/USER/misc/temper_npt/in.temper_npt b/examples/PACKAGES/temper_npt/in.temper_npt similarity index 100% rename from examples/USER/misc/temper_npt/in.temper_npt rename to examples/PACKAGES/temper_npt/in.temper_npt diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.0 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.0 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.1 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.1 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.2 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.2 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.3 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.3 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.4 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.4 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.5 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.5 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.6 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.6 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.7 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.7 diff --git a/examples/USER/misc/ti/in.ti_spring b/examples/PACKAGES/ti/in.ti_spring similarity index 100% rename from examples/USER/misc/ti/in.ti_spring rename to examples/PACKAGES/ti/in.ti_spring diff --git a/examples/USER/uef/README b/examples/PACKAGES/uef/README similarity index 92% rename from examples/USER/uef/README rename to examples/PACKAGES/uef/README index aaf53fa2a1..bedffbfb08 100644 --- a/examples/USER/uef/README +++ b/examples/PACKAGES/uef/README @@ -1,4 +1,4 @@ -This directory contains two short example scripts for the USER-UEF +This directory contains two short example scripts for the UEF package. diff --git a/examples/USER/uef/npt_biaxial/data.wca b/examples/PACKAGES/uef/npt_biaxial/data.wca similarity index 100% rename from examples/USER/uef/npt_biaxial/data.wca rename to examples/PACKAGES/uef/npt_biaxial/data.wca diff --git a/examples/USER/uef/npt_biaxial/in.npt_biaxial b/examples/PACKAGES/uef/npt_biaxial/in.npt_biaxial similarity index 100% rename from examples/USER/uef/npt_biaxial/in.npt_biaxial rename to examples/PACKAGES/uef/npt_biaxial/in.npt_biaxial diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 b/examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 similarity index 100% rename from examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 rename to examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 b/examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 similarity index 100% rename from examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 rename to examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 diff --git a/examples/USER/uef/nvt_uniaxial/data.wca b/examples/PACKAGES/uef/nvt_uniaxial/data.wca similarity index 100% rename from examples/USER/uef/nvt_uniaxial/data.wca rename to examples/PACKAGES/uef/nvt_uniaxial/data.wca diff --git a/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial b/examples/PACKAGES/uef/nvt_uniaxial/in.nvt_uniaxial similarity index 100% rename from examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial rename to examples/PACKAGES/uef/nvt_uniaxial/in.nvt_uniaxial diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 b/examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 similarity index 100% rename from examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 rename to examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 b/examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 similarity index 100% rename from examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 rename to examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 diff --git a/examples/USER/vtk/.gitignore b/examples/PACKAGES/vtk/.gitignore similarity index 100% rename from examples/USER/vtk/.gitignore rename to examples/PACKAGES/vtk/.gitignore diff --git a/examples/USER/vtk/in.vtk b/examples/PACKAGES/vtk/in.vtk similarity index 100% rename from examples/USER/vtk/in.vtk rename to examples/PACKAGES/vtk/in.vtk diff --git a/examples/USER/vtk/in.vtp b/examples/PACKAGES/vtk/in.vtp similarity index 100% rename from examples/USER/vtk/in.vtp rename to examples/PACKAGES/vtk/in.vtp diff --git a/examples/USER/yaff/README b/examples/PACKAGES/yaff/README similarity index 100% rename from examples/USER/yaff/README rename to examples/PACKAGES/yaff/README diff --git a/examples/USER/yaff/mil53al/lammps.data b/examples/PACKAGES/yaff/mil53al/lammps.data similarity index 100% rename from examples/USER/yaff/mil53al/lammps.data rename to examples/PACKAGES/yaff/mil53al/lammps.data diff --git a/examples/USER/yaff/mil53al/lammps.in b/examples/PACKAGES/yaff/mil53al/lammps.in similarity index 100% rename from examples/USER/yaff/mil53al/lammps.in rename to examples/PACKAGES/yaff/mil53al/lammps.in diff --git a/examples/USER/yaff/mof5/lammps.data b/examples/PACKAGES/yaff/mof5/lammps.data similarity index 100% rename from examples/USER/yaff/mof5/lammps.data rename to examples/PACKAGES/yaff/mof5/lammps.data diff --git a/examples/USER/yaff/mof5/lammps.in b/examples/PACKAGES/yaff/mof5/lammps.in similarity index 100% rename from examples/USER/yaff/mof5/lammps.in rename to examples/PACKAGES/yaff/mof5/lammps.in diff --git a/examples/README b/examples/README index 9efac36a47..9e873b49b9 100644 --- a/examples/README +++ b/examples/README @@ -5,7 +5,7 @@ problems you can run with LAMMPS. lower-case directories = simple test problems for LAMMPS and its packages upper-case directories = more complex problems -USER directory with its own sub-directories = tests for USER packages +PACKAGES directory with its own sub-directories = tests for styles from specific packages Each is discussed below. @@ -102,7 +102,7 @@ pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration -reax: RDX and TATB and several other models using ReaxFF +reaxff: RDX and TATB and several other models using ReaxFF rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void @@ -170,6 +170,14 @@ The MC directory has an example script for using LAMMPS as an energy-evaluation engine in a iterative Monte Carlo energy-relaxation loop. +The PACKAGES directory contains subdirectories of example scripts for +individual packages or additional individual styles. Most of those are +contributed by the corresponding package or style developers. +See the README files in those directories (if available) or the +corresponding doc page in the manual for more info. See the +https://docs.lammps.org/Build_package.html page for more info about +installing and building packages. + The TIP4P directory has an example for testing forces computed on a GPU. @@ -179,11 +187,6 @@ lj, real, and metal. So that you can see how to scale/unscale input and output values read/written by LAMMPS to verify you are performing the same simulation in different unit systems. -The USER directory contains subdirectories of user-provided example -scripts for ser packages. See the README files in those directories -for more info. See the doc/html/Build_package.html file for more info -about installing and building user packages. - The VISCOSITY directory has example scripts for computing the viscosity of a LJ liquid using 4 different methods. See the VISCOSITY/README file for more info. diff --git a/examples/TIP4P/gpu_dump/data.spce b/examples/TIP4P/gpu_dump/data.spce deleted file mode 120000 index 4c8051fdff..0000000000 --- a/examples/TIP4P/gpu_dump/data.spce +++ /dev/null @@ -1 +0,0 @@ -../../rdf-adf/data.spce \ No newline at end of file diff --git a/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 deleted file mode 100644 index faa6d3c117..0000000000 --- a/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 +++ /dev/null @@ -1,9018 +0,0 @@ -ITEM: TIMESTEP -0 -ITEM: NUMBER OF ATOMS -4500 -ITEM: BOX BOUNDS pp pp pp -2.6450000000000001e-02 3.5532800000000002e+01 -2.6450000000000001e-02 3.5532800000000002e+01 -2.6409999999999999e-02 3.5473599999999998e+01 -ITEM: ATOMS id type x y z fx fy fz -1 1 12.1247 28.092 22.2745 44.3296 17.0725 48.5356 -2 2 12.4974 28.7565 22.854 -24.598 -41.7029 -32.885 -3 2 11.5314 28.5784 21.7021 -26.0334 10.24 -23.1056 -4 1 1.17081 29.3781 23.7307 -74.0189 -7.00332 56.5394 -5 2 1.86259 29.4619 23.0745 28.6874 -4.77355 -53.1747 -6 2 0.455888 28.9379 23.2709 28.8474 14.4006 -7.70694 -7 1 29.6824 14.7369 21.6275 -6.84135 -10.4682 -14.9806 -8 2 30.5192 14.9459 21.2125 -6.0991 2.52794 20.3786 -9 2 29.7669 15.072 22.5202 13.979 5.65532 2.32707 -10 1 10.8733 7.00191 35.1099 71.1535 29.5945 64.996 -11 2 11.0641 6.25389 34.5439 -29.2143 -6.46229 -20.2952 -12 2 9.99418 7.27965 34.8524 -52.7015 -16.0671 -37.9354 -13 1 9.46552 6.437 19.7997 85.2674 -39.8413 10.9994 -14 2 9.09748 6.31006 18.9252 -72.8621 17.4338 -56.4264 -15 2 10.2738 5.92429 19.7966 -6.89627 25.8832 52.2923 -16 1 3.17887 29.6978 22.1201 11.0669 36.9603 2.15921 -17 2 3.20092 30.5775 21.7434 1.96842 -53.5324 1.10468 -18 2 3.38088 29.1173 21.3863 -1.13041 18.9593 -2.63733 -19 1 23.3853 11.3001 30.7823 -23.52 11.4998 -1.78141 -20 2 23.7233 10.5129 31.2094 -10.6549 -69.8744 42.1205 -21 2 24.1635 11.7415 30.442 31.685 49.5553 -38.1127 -22 1 11.0372 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24.1349 44.729 6.0878 18.5114 -41 2 16.0034 22.7047 23.3423 9.45233 -5.41322 19.0748 -42 2 16.6757 22.3276 24.6452 -62.1564 -2.11365 -46.4012 -43 1 13.2926 18.3041 12.3718 -21.6321 35.4491 -10.1185 -44 2 12.5784 18.6431 12.9115 9.10165 -10.6191 6.40125 -45 2 13.218 18.7831 11.5465 14.7856 -26.5319 15.1201 -46 1 20.2739 23.9416 15.503 27.5133 -80.7739 21.5233 -47 2 20.1962 24.62 14.8322 -14.4264 75.5043 -48.974 -48 2 20.6056 23.1764 15.0333 -10.3055 9.55818 35.1212 -49 1 30.1029 10.7821 14.2432 -141.04 -58.2559 25.7885 -50 2 29.4054 10.9741 13.6165 73.7261 15.4355 6.52542 -51 2 29.6831 10.2399 14.911 75.3093 38.8314 -27.5838 -52 1 19.7156 12.9895 25.4049 25.1117 -7.00757 -10.1087 -53 2 20.1589 13.3425 26.1764 19.8361 12.6508 10.0706 -54 2 18.8028 12.8923 25.6761 -46.6998 -11.9636 -2.64236 -55 1 4.22446 18.9933 32.6299 -12.2623 -33.6491 -3.58742 -56 2 4.01977 18.2262 32.0951 -0.65906 11.4759 13.4292 -57 2 3.40273 19.4824 32.6724 -7.13172 6.03869 -1.39336 -58 1 17.6728 30.8673 34.87 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104.714 84.2993 -0.89393 -1880 2 5.78717 34.7455 34.6991 -66.4725 -52.938 1.96992 -1881 2 4.61648 35.4418 34.0383 -42.5934 -34.2834 5.2485 -1882 1 2.50195 12.2818 26.0872 -8.67516 29.7785 -70.3215 -1883 2 3.1341 12.4118 25.3803 -27.1441 -5.8392 34.5663 -1884 2 3.01104 11.8861 26.7947 30.271 -23.377 31.7936 -1885 1 11.0081 34.2904 8.17399 9.42688 -5.7969 97.8947 -1886 2 10.7998 34.3332 9.10726 7.04621 0.417361 -87.1889 -1887 2 11.8825 33.9022 8.14084 -5.45944 4.15781 -5.16582 -1888 1 10.4598 16.7637 26.4131 148.288 90.0257 41.7655 -1889 2 10.4316 17.0754 27.3177 -72.7157 -36.8972 0.248291 -1890 2 11.309 17.0585 26.0841 -70.484 -54.3031 -51.5156 -1891 1 17.2098 4.69875 34.6801 81.246 -30.7191 -41.3973 -1892 2 18.0151 4.45904 34.2214 -71.7257 21.3966 42.2854 -1893 2 16.875 3.87125 35.0255 6.50051 11.5534 -2.108 -1894 1 6.97863 35.1347 32.2629 50.8129 -99.4838 -30.4474 -1895 2 7.56347 34.8235 32.9538 -41.616 46.5075 -25.0214 -1896 2 6.65314 0.469077 32.5846 2.57011 40.1833 47.8232 -1897 1 30.2687 4.69117 18.0464 60.7323 97.3861 -22.0469 -1898 2 29.6025 4.01217 17.9397 -42.0291 -72.8011 18.2538 -1899 2 30.768 4.4187 18.8164 -17.8086 -24.6517 8.15754 -1900 1 14.1597 29.6356 31.6828 30.9419 40.4802 -8.95169 -1901 2 14.4476 30.3966 31.1787 -5.71984 -21.9829 20.3791 -1902 2 13.5545 29.1766 31.1002 -20.3468 -21.2423 -11.9375 -1903 1 22.4062 9.51588 9.73682 -25.0265 24.595 63.1611 -1904 2 22.734 9.37614 10.6252 -11.7157 4.39127 -35.1937 -1905 2 23.0228 9.04451 9.1766 39.1276 -27.1504 -30.8252 -1906 1 22.2407 0.134276 35.413 -42.8239 -41.0374 60.4051 -1907 2 23.1409 0.333643 0.222809 43.4422 17.792 -1.46489 -1908 2 21.8776 35.1647 0.712762 2.03662 22.5692 -45.7042 -1909 1 30.8031 21.1275 11.6291 8.18201 -81.2251 51.4742 -1910 2 31.1578 21.6894 10.9401 18.9684 37.0502 -48.7174 -1911 2 31.4306 20.4081 11.699 -31.726 41.7294 -2.6312 -1912 1 27.4502 5.23285 21.3967 43.0518 -12.2654 10.7167 -1913 2 27.8253 4.72625 22.1171 -28.5647 20.7097 -13.5339 -1914 2 26.5781 5.47904 21.705 -14.103 -7.53663 23.2646 -1915 1 34.2489 16.5307 18.5363 26.9125 -52.6845 -20.1673 -1916 2 34.8827 15.8461 18.7503 10.1132 17.7044 42.0284 -1917 2 33.9212 16.2918 17.6692 -38.1022 30.6955 -21.5306 -1918 1 32.1141 35.0942 16.4825 -0.867004 -48.405 2.84315 -1919 2 32.9623 34.6708 16.6154 -20.9146 28.4235 -14.5239 -1920 2 32.313 0.365179 15.9607 23.3692 9.94143 -6.48738 -1921 1 5.27687 31.5242 24.5907 -41.8155 -32.232 -72.1813 -1922 2 5.60539 31.6007 25.4865 31.5439 41.9211 28.7506 -1923 2 5.5227 32.3499 24.1735 12.1666 -5.48947 41.746 -1924 1 25.7907 25.4154 18.2947 20.8035 21.2797 20.5846 -1925 2 25.4138 24.7122 17.7657 -11.5015 -8.7926 -11.7913 -1926 2 25.758 26.186 17.7278 -5.43932 -10.731 -2.4049 -1927 1 4.9373 22.5181 12.7303 -6.4384 -109.105 57.2178 -1928 2 4.67073 21.7372 13.2154 46.7558 31.8331 -22.6463 -1929 2 4.1183 22.9792 12.549 -49.1964 70.1051 -30.4411 -1930 1 12.3715 3.4068 24.8685 96.9889 -105.459 -2.59257 -1931 2 11.5379 3.78717 25.1454 -78.5271 72.7012 7.46574 -1932 2 12.7376 4.04834 24.2597 -26.2048 27.0425 1.81415 -1933 1 17.2206 21.0678 32.2286 70.9033 -32.4857 -28.922 -1934 2 16.37 21.3218 31.8703 -31.2433 6.59635 -32.464 -1935 2 17.7395 20.8211 31.463 -47.0509 20.4749 43.9242 -1936 1 25.4169 13.6587 27.4317 -0.727949 9.42962 -145.923 -1937 2 25.9517 14.3734 27.0861 -3.23386 -8.44445 54.635 -1938 2 25.0518 13.2348 26.655 1.65215 1.37226 80.6823 -1939 1 31.3457 0.922103 6.09387 93.2805 93.8551 -38.7299 -1940 2 31.5155 0.207477 5.48008 -21.219 -72.6924 -14.0259 -1941 2 31.9625 1.6085 5.83961 -64.7524 -23.8625 51.719 -1942 1 14.5195 27.1466 0.851682 38.6886 37.2405 14.6579 -1943 2 15.053 27.8652 0.512027 -28.0679 -32.9887 -8.99741 -1944 2 14.6072 27.2114 1.80267 -15.0183 -14.128 4.77814 -1945 1 28.877 13.802 31.4018 -4.50288 23.8843 -13.5573 -1946 2 29.2081 14.2631 32.1725 -0.230544 2.07915 -12.4648 -1947 2 28.8087 14.4787 30.7282 1.77038 -19.7831 31.8497 -1948 1 32.2979 1.69743 30.0205 -28.8467 109.78 -38.9645 -1949 2 32.9555 1.84764 29.3413 24.5461 -47.0658 1.39339 -1950 2 31.7668 2.49381 30.0206 1.00965 -60.2251 37.5257 -1951 1 12.623 8.26205 20.3365 -51.0291 54.698 -56.076 -1952 2 12.8038 8.94712 20.98 7.54061 -8.85741 0.764622 -1953 2 12.1346 8.70659 19.6435 47.8511 -55.3633 57.2868 -1954 1 12.529 25.4483 7.87221 -48.9382 -101.6 1.11575 -1955 2 12.9572 24.6439 8.16517 48.6378 37.6284 17.52 -1956 2 11.6948 25.156 7.50493 -0.295674 62.8691 -15.443 -1957 1 1.10092 20.9789 6.76259 27.205 20.4467 -20.553 -1958 2 0.8209 21.0263 5.84848 -7.50941 -2.67192 -4.52081 -1959 2 1.91303 21.4847 6.79139 -30.6585 -22.163 10.0435 -1960 1 4.82409 0.410104 13.4746 -3.61871 -66.6275 45.8026 -1961 2 4.33159 1.13563 13.0908 -33.7684 83.5475 -47.5464 -1962 2 4.1925 35.4689 14.0377 32.5565 -8.9676 -2.20459 -1963 1 7.97943 14.3227 18.3991 -62.6546 39.1623 68.9072 -1964 2 7.48796 15.0929 18.6846 32.7298 -3.02693 -45.5565 -1965 2 7.74856 13.6426 19.0319 33.3077 -26.9346 -30.733 -1966 1 6.57492 10.8376 7.69432 -42.1835 -33.4879 61.6812 -1967 2 6.88034 11.43 7.00728 61.1077 54.5155 -84.4452 -1968 2 5.70739 11.1679 7.92785 -16.8375 -20.6972 23.7848 -1969 1 10.1308 13.458 3.45525 -19.289 -27.8108 18.398 -1970 2 9.47924 14.0224 3.03904 59.8681 9.66437 -14.5467 -1971 2 10.9686 13.7582 3.10271 -46.1431 27.4514 -18.5848 -1972 1 2.78627 23.982 22.6844 61.7668 -37.9237 -21.697 -1973 2 2.23775 23.3518 22.2172 -8.17893 -35.1455 -20.7984 -1974 2 2.17291 24.6441 23.0031 -46.5196 68.0647 37.1881 -1975 1 29.6763 34.0661 9.4221 -25.2085 -34.5053 76.7307 -1976 2 29.4116 33.869 10.3206 -13.3027 -22.4655 -41.4267 -1977 2 30.2063 34.8598 9.49668 49.5961 63.0099 -39.1917 -1978 1 17.3951 25.0142 9.24935 74.1256 -119.972 13.8699 -1979 2 18.0557 25.5131 8.76884 -7.409 57.2755 -19.7204 -1980 2 17.7887 24.1502 9.37149 -78.6001 67.4017 9.86198 -1981 1 11.139 14.0733 32.9523 31.4256 -0.03008 -5.2348 -1982 2 12.066 14.2725 33.0835 -15.5197 6.63618 -14.1202 -1983 2 10.9478 13.388 33.5926 -13.6636 8.48879 -3.5036 -1984 1 1.12572 32.0183 27.5356 24.6266 46.3494 2.8897 -1985 2 0.546692 31.3048 27.8037 -3.08121 -31.7776 -12.0256 -1986 2 1.55521 31.6943 26.7439 -12.2274 -17.2869 5.12609 -1987 1 16.7457 10.366 22.1454 -15.3164 -22.3958 -16.0252 -1988 2 17.6114 10.1816 22.5099 -14.3265 37.126 0.80158 -1989 2 16.5565 11.2637 22.4183 29.9704 0.0490406 16.3066 -1990 1 3.7604 22.8172 16.7231 -94.979 -46.3638 63.4302 -1991 2 3.80199 23.6592 16.2696 52.6252 2.42304 -21.4425 -1992 2 4.60092 22.4005 16.533 37.2062 36.1623 -37.5204 -1993 1 1.85858 2.74219 27.3787 -16.8615 -16.8421 15.8272 -1994 2 2.54214 2.17108 27.7292 -4.59146 35.0941 -40.6374 -1995 2 2.27945 3.20266 26.6527 25.2819 -23.6186 22.0617 -1996 1 20.9735 33.5714 23.8814 -106.803 36.5464 88.0259 -1997 2 21.6236 32.9171 24.1374 45.6079 -11.0665 -63.4639 -1998 2 21.2264 33.8268 22.9943 67.7875 -35.3184 -31.857 -1999 1 14.9346 6.66221 21.3527 -126.314 -3.88715 -82.8474 -2000 2 14.0911 6.81595 20.927 39.2653 62.6904 53.7569 -2001 2 15.1982 5.79131 21.0556 85.678 -53.7307 17.9606 -2002 1 22.2461 5.18918 17.8715 -69.145 -31.4218 -18.0837 -2003 2 21.9344 5.83223 17.2347 -27.7401 11.8107 -16.433 -2004 2 23.137 5.47038 18.0801 108.344 19.9553 34.4799 -2005 1 31.7359 29.9237 26.3736 -84.3482 -146.558 -73.4212 -2006 2 32.1627 30.6728 26.7895 111.481 40.2155 8.28834 -2007 2 32.4462 29.4563 25.9339 -20.9159 104.035 73.147 -2008 1 24.5541 23.2903 6.20562 34.8499 -73.6669 40.9676 -2009 2 25.3233 22.7463 6.0363 -54.9847 54.2625 4.3351 -2010 2 24.1245 22.8728 6.95223 10.9892 27.9336 -36.5991 -2011 1 25.8826 13.3692 31.6978 -39.5587 45.0721 109.942 -2012 2 26.0654 12.9392 30.8624 14.4928 -55.2593 -101.315 -2013 2 26.7459 13.5818 32.0524 34.4682 10.678 13.5079 -2014 1 31.9081 10.2232 30.8508 60.5777 139.069 -26.1959 -2015 2 32.2481 10.7082 31.6027 -21.552 -31.8062 -26.0603 -2016 2 31.6024 9.39393 31.2183 -39.6468 -107.76 57.4176 -2017 1 0.849757 3.66316 11.6882 -66.4227 -77.864 -86.3174 -2018 2 0.839326 4.56785 12.0007 9.47524 78.9317 34.8726 -2019 2 0.14017 3.62253 11.047 60.8788 -7.45935 55.9047 -2020 1 12.6493 6.4064 27.2531 -40.9759 17.8512 -96.8045 -2021 2 11.9988 5.88507 26.7827 30.2874 12.9967 48.5047 -2022 2 12.9203 7.07589 26.6249 2.54534 -39.1725 52.0268 -2023 1 15.9599 7.99333 15.8859 30.1406 -18.388 8.6192 -2024 2 16.7797 7.85417 15.4117 -4.79859 1.07516 10.1564 -2025 2 15.4667 8.60439 15.3385 -20.0761 12.8881 -12.5608 -2026 1 20.0344 20.1357 12.6654 -3.86966 -64.7249 -48.8174 -2027 2 19.4344 20.3202 11.9427 10.3543 13.9442 17.6237 -2028 2 20.3441 19.2454 12.4988 -10.1918 51.4785 29.9814 -2029 1 21.356 6.30633 10.131 -67.0198 -114.109 -5.58798 -2030 2 20.9103 5.53439 10.4799 -7.83167 25.8119 -63.3827 -2031 2 21.891 6.6238 10.8585 85.5245 81.2641 57.4267 -2032 1 35.1559 30.9332 9.83309 61.3262 -2.90007 -69.3354 -2033 2 0.303167 31.6302 9.88912 -24.8958 -15.4978 13.785 -2034 2 34.5934 31.0698 10.5955 -26.5859 21.8525 52.7843 -2035 1 4.27659 27.2552 26.2915 116.968 -151.738 -34.7454 -2036 2 3.39554 27.3768 25.9377 -83.718 52.8428 -4.72735 -2037 2 4.42257 28.0247 26.8419 -28.396 103.456 48.6556 -2038 1 26.8593 19.3342 13.6851 30.7677 67.3413 -148.698 -2039 2 26.0004 19.2038 14.0871 -50.0945 -27.4421 67.323 -2040 2 27.4811 19.0115 14.3374 18.1351 -38.3726 82.2067 -2041 1 7.83885 28.1834 15.8334 16.5365 20.604 -8.56175 -2042 2 7.60386 27.3316 16.2014 -33.7069 20.3127 -2.25908 -2043 2 7.02096 28.6807 15.838 5.21927 -39.3621 14.9074 -2044 1 32.631 18.2249 29.7861 41.9215 38.3318 11.8543 -2045 2 32.1421 17.5039 29.3895 -39.2744 -31.6531 -17.1652 -2046 2 31.957 18.8189 30.1164 -14.576 -4.73824 -0.949144 -2047 1 3.25628 33.4796 7.39391 71.9746 30.5666 -22.4299 -2048 2 4.11434 33.8297 7.63344 -69.5572 -27.2519 -15.9057 -2049 2 3.24436 33.5071 6.43718 -2.52475 -1.44402 31.1707 -2050 1 0.842237 3.50013 3.05753 16.9517 -63.8559 -23.0072 -2051 2 1.37533 4.09985 3.57944 19.8724 20.4219 19.8016 -2052 2 1.42823 2.77011 2.85767 -26.1771 37.5505 12.1175 -2053 1 25.1227 15.9755 21.4703 2.5941 62.4248 -49.2139 -2054 2 25.4287 15.7265 22.3424 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-1824 2 12.8135 11.8841 33.0812 1.80441 -0.0285427 -0.940293 -1825 1 28.1273 28.5701 6.20796 15.569 -1.19954 -3.84549 -1826 2 28.7421 27.8707 6.42982 0.569705 0.69249 1.61013 -1827 2 28.6828 29.3008 5.93649 0.880667 -1.77333 0.445495 -1828 1 9.60977 10.1365 3.09891 -5.94523 16.4753 -3.61789 -1829 2 9.15241 10.5276 3.84329 1.96922 -0.0930667 1.79105 -1830 2 8.91879 9.95189 2.46275 -2.80442 -1.49947 3.15747 -1831 1 14.4197 9.53079 14.3089 -7.16532 7.48911 2.91416 -1832 2 13.6136 9.59909 14.8205 -1.17855 0.294958 -1.49237 -1833 2 14.1507 9.72232 13.4104 0.397574 -1.98121 -0.174343 -1834 1 6.04069 31.1465 20.4566 -9.15708 8.12434 4.89108 -1835 2 6.13395 30.1983 20.3652 -0.244382 1.09085 -0.00860043 -1836 2 5.11224 31.279 20.6481 0.843334 1.97473 -0.0647082 -1837 1 8.7838 13.5803 21.8928 0.217801 17.1488 14.4834 -1838 2 8.51094 14.4978 21.8985 -1.45571 -0.38088 -3.77848 -1839 2 8.24509 13.174 21.2139 6.3086 -2.86453 -1.40498 -1840 1 23.4748 35.2743 4.51161 4.21931 -5.52566 -6.44192 -1841 2 22.7721 35.442 5.13959 1.52363 0.185827 0.842397 -1842 2 24.0271 34.6195 4.93869 0.555595 -0.767624 -1.58782 -1843 1 22.0894 26.5427 21.4562 3.95908 -18.8496 4.23428 -1844 2 22.6255 26.467 22.2455 0.409818 -0.407813 -0.0667319 -1845 2 22.4919 27.2556 20.9601 -0.706819 -0.893449 -0.0692904 -1846 1 1.89498 19.0649 16.666 2.80053 -16.753 0.163504 -1847 2 1.87316 19.9794 16.384 -2.84196 -1.39736 -0.279 -1848 2 2.03554 19.1088 17.6118 -0.829705 -0.704631 -0.796266 -1849 1 23.9684 29.6207 2.08753 -23.7725 14.9997 -17.3986 -1850 2 23.9631 29.2365 1.21082 -2.58409 -0.109131 0.494741 -1851 2 23.5338 30.4669 1.98139 -0.29018 0.110115 1.17243 -1852 1 1.04624 21.6926 30.599 -10.8783 -3.72514 -8.42776 -1853 2 0.112367 21.7513 30.3974 -0.385649 -0.331062 -1.86197 -1854 2 1.46468 21.5314 29.7533 0.951807 4.52263 -0.597105 -1855 1 13.7383 18.7757 16.052 2.06801 4.28003 3.94841 -1856 2 14.0403 19.1264 16.8898 0.614545 -1.93383 0.441892 -1857 2 13.1788 18.0361 16.289 0.955085 -0.158913 -1.28769 -1858 1 15.0232 6.07511 33.936 -1.29508 2.93069 -5.05057 -1859 2 14.7347 5.5858 33.1655 0.234827 -0.161482 0.355153 -1860 2 15.9546 5.86971 34.0159 -1.64187 -4.18189 4.22192 -1861 1 31.8145 4.72505 13.9315 3.51696 2.46284 -9.06312 -1862 2 32.7583 4.70545 14.09 -0.860689 -3.55617 -0.581682 -1863 2 31.7034 4.28385 13.0893 -0.970181 0.0843368 0.95089 -1864 1 24.2418 18.8281 7.32442 19.8697 2.2108 -6.54484 -1865 2 24.4226 18.4746 8.19539 2.81024 2.54724 -0.45717 -1866 2 25.0242 18.62 6.81378 0.970146 1.95667 -0.32899 -1867 1 30.0972 6.70621 9.34508 -7.11575 -10.6459 5.95087 -1868 2 30.6725 6.85653 10.0952 0.385181 0.328039 -2.98084 -1869 2 30.3149 5.82236 9.04901 -0.729241 -1.02843 1.76281 -1870 1 6.44717 22.2065 16.5255 -3.59057 -4.00173 16.1678 -1871 2 6.64259 21.3661 16.94 3.11856 0.683016 0.647408 -1872 2 6.76977 22.1127 15.6292 0.416604 1.37739 1.48251 -1873 1 26.5355 4.89359 31.4896 -7.52384 6.40183 3.48158 -1874 2 26.4108 4.09458 30.9775 1.28288 1.47802 -0.0815147 -1875 2 26.2333 5.59673 30.9148 0.174929 0.381041 0.467201 -1876 1 16.6203 30.9547 12.5759 2.29181 3.31892 0.336466 -1877 2 17.5257 31.2473 12.4718 -0.428516 1.14843 0.686943 -1878 2 16.5321 30.7758 13.5121 -0.928822 -0.936925 -0.848334 -1879 1 4.87322 34.619 34.4415 0.500801 -6.20716 0.421653 -1880 2 5.78673 34.74 34.7005 -1.1578 1.99203 1.93461 -1881 2 4.62688 35.45 34.0352 -2.67178 0.290957 3.74667 -1882 1 2.50149 12.2801 26.0877 -3.61028 1.8033 -1.8975 -1883 2 3.14626 12.3987 25.3903 -1.63452 1.76565 0.0939493 -1884 2 2.99924 11.9029 26.8131 -0.546173 -2.4228 -3.67059 -1885 1 11.0044 34.2914 8.17886 15.9126 -2.73607 2.69613 -1886 2 10.7906 34.3407 9.11057 -2.69506 0.109664 -0.892116 -1887 2 11.8744 33.8931 8.15305 0.922075 0.494336 3.88877 -1888 1 10.4642 16.7648 26.4147 2.80971 1.51282 -9.61072 -1889 2 10.4264 17.0779 27.3185 1.17471 -1.35509 -0.280756 -1890 2 11.3146 17.0636 26.0926 0.590472 -1.32977 -0.414974 -1891 1 17.2152 4.69462 34.6747 11.9213 0.65814 -4.69715 -1892 2 18.0195 4.45625 34.2137 1.04857 -0.57361 0.535519 -1893 2 16.8774 3.86516 35.0125 1.91423 1.04657 2.96864 -1894 1 6.97445 35.1353 32.2671 9.97328 -11.6302 -7.33462 -1895 2 7.55154 34.8288 32.9666 0.774769 -1.62199 -1.46055 -1896 2 6.63884 0.467797 32.5832 1.02155 -1.24749 0.362107 -1897 1 30.2645 4.69075 18.0422 0.694439 -2.46184 2.97624 -1898 2 29.6017 4.00886 17.9326 1.10342 -1.19819 0.759635 -1899 2 30.7589 4.42264 18.8167 -1.07894 2.27368 1.54311 -1900 1 14.1656 29.632 31.6787 5.05867 -0.355939 -0.980506 -1901 2 14.4451 30.4041 31.1867 -0.842964 -0.790639 -0.294246 -1902 2 13.5563 29.1821 31.0933 0.0725257 -1.19259 1.4708 -1903 1 22.4084 9.52165 9.7397 0.735332 -1.67091 -3.93305 -1904 2 22.7212 9.37225 10.6319 -1.09142 1.00002 -0.542777 -1905 2 23.025 9.04279 9.18587 1.34861 1.44662 0.230846 -1906 1 22.2367 0.136878 35.4162 2.39769 -1.00634 11.3877 -1907 2 23.1336 0.346647 0.22933 -0.416125 0.426818 1.11968 -1908 2 21.8755 35.1657 0.715801 -0.0814999 0.0454572 0.682247 -1909 1 30.8013 21.126 11.6255 -3.46793 -5.01909 1.70411 -1910 2 31.1601 21.6971 10.9462 -4.45423 -1.15624 -2.23432 -1911 2 31.4336 20.4108 11.6964 2.44046 2.26421 0.934019 -1912 1 27.4508 5.23152 21.4006 1.74025 1.89877 19.0993 -1913 2 27.8319 4.73772 22.1266 0.4018 0.947765 0.850108 -1914 2 26.5774 5.47438 21.7079 -0.634266 -2.0344 0.72118 -1915 1 34.2517 16.5309 18.5306 0.907524 -6.93269 -4.04601 -1916 2 34.8715 15.8322 18.7399 -0.501769 0.835994 1.04597 -1917 2 33.8909 16.2844 17.6789 -0.976215 1.5179 3.59303 -1918 1 32.115 35.0905 16.482 2.22898 -11.9743 -20.9485 -1919 2 32.966 34.6682 16.5991 -0.636814 -0.495605 0.383446 -1920 2 32.3008 0.353133 15.9431 0.148533 0.858467 3.15742 -1921 1 5.2813 31.5245 24.5891 -0.88265 3.56081 0.527901 -1922 2 5.6102 31.6063 25.4843 2.8911 0.897716 -1.16555 -1923 2 5.50826 32.3562 24.1732 0.0452461 -1.83796 -1.84019 -1924 1 25.7935 25.4126 18.2933 8.42974 5.04501 3.04403 -1925 2 25.4171 24.7186 17.752 -3.18932 0.154086 3.92798 -1926 2 25.7522 26.195 17.7434 -1.62301 -1.62428 -0.262324 -1927 1 4.94055 22.5134 12.7286 -9.04805 -9.98913 0.740441 -1928 2 4.66669 21.7387 13.2196 -2.25032 0.777095 0.693415 -1929 2 4.12797 22.9905 12.5602 2.55025 2.81834 1.88639 -1930 1 12.3705 3.40796 24.8702 -10.2718 -6.94273 4.16449 -1931 2 11.5354 3.79201 25.1374 1.11482 2.05237 1.26765 -1932 2 12.7415 4.04279 24.2574 1.31703 -1.09657 1.0894 -1933 1 17.2229 21.0728 32.2314 -8.179 -5.27121 -18.2871 -1934 2 16.3825 21.3411 31.86 1.15239 -1.37236 -2.54915 -1935 2 17.7485 20.8146 31.4742 0.636225 0.416061 0.167394 -1936 1 25.4211 13.6617 27.4256 -0.423575 1.5864 -14.144 -1937 2 25.9311 14.3939 27.0792 0.209498 -1.21813 2.94262 -1938 2 25.0385 13.2482 26.6517 -1.88498 1.40152 0.678356 -1939 1 31.3452 0.921707 6.09496 5.75289 0.0456399 -1.04313 -1940 2 31.5193 0.206077 5.48357 1.7599 -1.91271 2.66807 -1941 2 31.9558 1.61205 5.83652 -0.775733 -0.136291 -2.46929 -1942 1 14.5238 27.1426 0.855822 -0.28203 -13.8472 13.0001 -1943 2 15.0637 27.8615 0.527327 -2.90129 -0.385453 -1.8344 -1944 2 14.5862 27.2115 1.8085 -1.36301 3.80564 -1.12804 -1945 1 28.8746 13.8014 31.4027 -2.88672 6.47051 7.86952 -1946 2 29.2232 14.2517 32.1721 1.91816 0.252514 -1.72337 -1947 2 28.8041 14.4848 30.7362 -2.55312 0.206489 0.885327 -1948 1 32.2921 1.69364 30.0162 -5.24318 6.11719 0.10458 -1949 2 32.9509 1.85569 29.3409 -1.02656 -2.73336 -0.95222 -1950 2 31.7703 2.49576 30.0398 2.18736 -0.0064308 0.36284 -1951 1 12.6171 8.26014 20.3408 -0.40671 -8.63132 6.16379 -1952 2 12.7962 8.9555 20.9737 1.99194 1.08407 -2.86475 -1953 2 12.1389 8.69542 19.635 2.27749 -2.82959 -1.29442 -1954 1 12.5264 25.4516 7.87552 -4.00904 -0.543437 10.3565 -1955 2 12.9562 24.654 8.18449 -0.215524 -0.0928553 -1.74864 -1956 2 11.705 25.1474 7.48948 4.50811 -0.52052 -4.58555 -1957 1 1.10395 20.9772 6.76689 -12.4418 -4.87906 -17.0173 -1958 2 0.841381 21.0115 5.84704 0.961335 2.29109 -0.167377 -1959 2 1.91806 21.4794 6.80294 -0.662195 -1.08577 2.11991 -1960 1 4.82166 0.411135 13.4723 -6.95497 7.27665 -10.2603 -1961 2 4.31632 1.13144 13.0954 -1.71759 1.5163 4.71861 -1962 2 4.19868 35.4546 14.0325 3.34255 0.282635 2.02706 -1963 1 7.98045 14.3231 18.3954 3.08041 14.4496 -7.04888 -1964 2 7.47829 15.0927 18.6634 -2.22303 -2.54215 1.24386 -1965 2 7.75094 13.6513 19.0374 2.28408 -1.12721 -2.33416 -1966 1 6.57567 10.8403 7.6939 2.74017 2.33053 3.06743 -1967 2 6.87818 11.4306 7.00375 -0.816871 -0.135469 -0.424054 -1968 2 5.69956 11.1571 7.91368 0.353319 -2.48188 -0.273827 -1969 1 10.1296 13.4617 3.4523 -7.92991 7.36607 -13.5551 -1970 2 9.4814 14.0411 3.05172 2.81436 1.47522 -1.87702 -1971 2 10.9658 13.745 3.08241 -0.999119 -0.282534 1.18626 -1972 1 2.78873 23.9803 22.6823 7.39875 -2.15156 -6.43063 -1973 2 2.24341 23.3472 22.2153 1.0523 -1.39215 0.678747 -1974 2 2.17172 24.6381 23.0029 -0.309516 -1.48449 0.660469 -1975 1 29.681 34.0668 9.41834 9.5803 -0.140978 0.198088 -1976 2 29.4023 33.8738 10.3135 -0.39736 4.75337 0.09998 -1977 2 30.2232 34.8514 9.49973 0.132783 -0.224159 -2.50537 -1978 1 17.3964 25.0161 9.25437 -10.6964 6.49204 10.2875 -1979 2 18.0663 25.5133 8.78518 -2.57426 -0.200004 -1.71763 -1980 2 17.7826 24.1488 9.37642 -1.26016 -0.11254 -2.41078 -1981 1 11.1411 14.0768 32.9507 2.74692 8.93145 -23.0737 -1982 2 12.0674 14.2752 33.0877 0.326495 0.0181461 -2.13137 -1983 2 10.9448 13.3932 33.5914 -1.40918 5.092 2.7765 -1984 1 1.12682 32.0133 27.5402 4.517 -1.51145 -4.02069 -1985 2 0.552584 31.2959 27.8081 3.00058 -1.99467 0.131487 -1986 2 1.5621 31.6905 26.7511 1.52551 1.30495 -0.0263278 -1987 1 16.7481 10.3694 22.1507 0.264039 13.0692 4.69918 -1988 2 17.6248 10.1979 22.4946 -0.0377334 0.851346 -4.78636 -1989 2 16.5624 11.2729 22.4066 -1.46932 -0.377234 0.467584 -1990 1 3.76375 22.8172 16.7293 -4.0741 -10.5757 1.02761 -1991 2 3.80151 23.6586 16.2743 -0.690304 1.29329 3.69566 -1992 2 4.5994 22.3969 16.5262 -0.197813 0.973283 -0.721214 -1993 1 1.85399 2.73861 27.3822 3.20071 -7.68688 -3.72082 -1994 2 2.53752 2.17131 27.7389 0.0246343 -1.14856 -1.23911 -1995 2 2.27395 3.18876 26.6492 0.934788 1.93265 2.10385 -1996 1 20.9724 33.5726 23.8784 8.10433 -9.20518 -4.51155 -1997 2 21.6189 32.9194 24.1461 -2.046 -3.87957 -3.38316 -1998 2 21.2405 33.8276 22.9955 0.119388 1.30018 0.791288 -1999 1 14.9356 6.66547 21.3473 -4.32378 2.01425 -5.99167 -2000 2 14.0917 6.81509 20.921 0.850589 0.904261 -2.27949 -2001 2 15.2025 5.79487 21.0522 1.98877 1.97817 -3.72271 -2002 1 22.2485 5.18667 17.87 13.215 -1.9753 -1.37536 -2003 2 21.9401 5.84134 17.2434 -1.85661 0.524428 2.90348 -2004 2 23.1453 5.4526 18.0731 0.178716 1.34064 -2.4977 -2005 1 31.7392 29.9223 26.3752 4.76914 0.177865 5.41636 -2006 2 32.1647 30.6696 26.7955 0.903997 -0.87703 1.20137 -2007 2 32.4505 29.4583 25.9336 0.0227674 -0.433216 0.401033 -2008 1 24.5495 23.287 6.21014 -9.6064 5.24279 8.20718 -2009 2 25.3283 22.7624 6.02443 0.116339 4.39189 1.8768 -2010 2 24.1468 22.8595 6.966 0.2289 -0.0589481 -2.13137 -2011 1 25.8848 13.3641 31.6949 11.7976 1.283 28.4217 -2012 2 26.0644 12.9328 30.8595 -3.81135 -1.20515 1.50928 -2013 2 26.7491 13.586 32.0412 2.1747 1.23594 -3.73301 -2014 1 31.9059 10.2239 30.8521 3.15397 -0.693558 5.50864 -2015 2 32.2432 10.7005 31.6105 -2.64306 -0.474064 1.50947 -2016 2 31.6065 9.38729 31.2082 -1.91976 0.707005 -1.14165 -2017 1 0.84878 3.6625 11.6852 3.82778 -4.24681 3.04899 -2018 2 0.853073 4.56299 12.0097 1.00506 -0.863618 -0.913913 -2019 2 0.134074 3.64014 11.0488 -1.02679 -1.02985 3.07516 -2020 1 12.653 6.40924 27.2569 -10.896 -2.3651 4.67545 -2021 2 12.0107 5.88536 26.7781 -1.95087 -0.422561 2.90655 -2022 2 12.932 7.07765 26.6311 3.33215 -5.37792 -3.19321 -2023 1 15.9575 7.9951 15.8816 6.43964 -4.15323 6.61769 -2024 2 16.7831 7.8467 15.4206 0.588477 2.84349 1.20404 -2025 2 15.4803 8.61195 15.3266 -2.08725 -4.05933 -0.295667 -2026 1 20.0375 20.1391 12.665 -4.11025 1.52341 -3.10314 -2027 2 19.4274 20.3342 11.9537 2.89664 -0.270393 -1.94487 -2028 2 20.3292 19.244 12.4922 -2.13637 -0.289793 3.97752 -2029 1 21.356 6.30845 10.1293 11.8845 -7.32937 -8.40835 -2030 2 20.9041 5.54426 10.4872 -0.836302 1.13214 -0.345734 -2031 2 21.8894 6.63336 10.8547 0.11176 0.0745871 -0.490015 -2032 1 35.1526 30.9366 9.83286 7.59845 5.2547 -1.12957 -2033 2 0.311501 31.622 9.89575 0.964885 -1.25019 -0.233494 -2034 2 34.6019 31.0651 10.6052 0.344797 -0.803576 -0.904465 -2035 1 4.27525 27.2569 26.2869 4.28071 5.72746 7.8462 -2036 2 3.39987 27.3692 25.9163 0.165296 -0.828825 2.86229 -2037 2 4.39971 28.0244 26.8452 0.266735 0.0706906 -1.3371 -2038 1 26.8649 19.3391 13.6882 0.177125 1.61838 2.46927 -2039 2 26.0052 19.1944 14.0834 -0.103725 0.362381 -1.50792 -2040 2 27.4862 19.0117 14.3386 -0.695576 -0.902314 0.251747 -2041 1 7.83542 28.181 15.8382 -13.3943 -2.71551 5.4783 -2042 2 7.57758 27.3247 16.1794 -0.25335 2.11014 -2.48558 -2043 2 7.02351 28.6878 15.8233 1.95232 1.88776 0.576467 -2044 1 32.6262 18.2228 29.791 -14.1882 1.19327 -8.66236 -2045 2 32.1279 17.5186 29.3763 0.458993 0.618559 0.834874 -2046 2 31.9606 18.8321 30.1103 1.27184 -0.0824113 1.15038 -2047 1 3.26267 33.4782 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0.207477 5.48008 -21.219 -72.6924 -14.0259 -1941 2 31.9625 1.6085 5.83961 -64.7524 -23.8625 51.719 -1942 1 14.5195 27.1466 0.851682 38.6886 37.2405 14.6579 -1943 2 15.053 27.8652 0.512027 -28.0679 -32.9887 -8.99741 -1944 2 14.6072 27.2114 1.80267 -15.0183 -14.128 4.77814 -1945 1 28.877 13.802 31.4018 -4.50288 23.8843 -13.5573 -1946 2 29.2081 14.2631 32.1725 -0.230544 2.07915 -12.4648 -1947 2 28.8087 14.4787 30.7282 1.77038 -19.7831 31.8497 -1948 1 32.2979 1.69743 30.0205 -28.8467 109.78 -38.9645 -1949 2 32.9555 1.84764 29.3413 24.5461 -47.0658 1.39339 -1950 2 31.7668 2.49381 30.0206 1.00965 -60.2251 37.5257 -1951 1 12.623 8.26205 20.3365 -51.0291 54.698 -56.076 -1952 2 12.8038 8.94712 20.98 7.54061 -8.85741 0.764622 -1953 2 12.1346 8.70659 19.6435 47.8511 -55.3633 57.2868 -1954 1 12.529 25.4483 7.87221 -48.9382 -101.6 1.11575 -1955 2 12.9572 24.6439 8.16517 48.6378 37.6284 17.52 -1956 2 11.6948 25.156 7.50493 -0.295674 62.8691 -15.443 -1957 1 1.10092 20.9789 6.76259 27.205 20.4467 -20.553 -1958 2 0.8209 21.0263 5.84848 -7.50941 -2.67192 -4.52081 -1959 2 1.91303 21.4847 6.79139 -30.6585 -22.163 10.0435 -1960 1 4.82409 0.410104 13.4746 -3.61871 -66.6275 45.8026 -1961 2 4.33159 1.13563 13.0908 -33.7684 83.5475 -47.5464 -1962 2 4.1925 35.4689 14.0377 32.5565 -8.9676 -2.20459 -1963 1 7.97943 14.3227 18.3991 -62.6546 39.1623 68.9072 -1964 2 7.48796 15.0929 18.6846 32.7298 -3.02693 -45.5565 -1965 2 7.74856 13.6426 19.0319 33.3077 -26.9346 -30.733 -1966 1 6.57492 10.8376 7.69432 -42.1835 -33.4879 61.6812 -1967 2 6.88034 11.43 7.00728 61.1077 54.5155 -84.4452 -1968 2 5.70739 11.1679 7.92785 -16.8375 -20.6972 23.7848 -1969 1 10.1308 13.458 3.45525 -19.289 -27.8108 18.398 -1970 2 9.47924 14.0224 3.03904 59.8681 9.66437 -14.5467 -1971 2 10.9686 13.7582 3.10271 -46.1431 27.4514 -18.5848 -1972 1 2.78627 23.982 22.6844 61.7668 -37.9237 -21.697 -1973 2 2.23775 23.3518 22.2172 -8.17893 -35.1455 -20.7984 -1974 2 2.17291 24.6441 23.0031 -46.5196 68.0647 37.1881 -1975 1 29.6763 34.0661 9.4221 -25.2085 -34.5053 76.7307 -1976 2 29.4116 33.869 10.3206 -13.3027 -22.4655 -41.4267 -1977 2 30.2063 34.8598 9.49668 49.5961 63.0099 -39.1917 -1978 1 17.3951 25.0142 9.24935 74.1256 -119.972 13.8699 -1979 2 18.0557 25.5131 8.76884 -7.409 57.2755 -19.7204 -1980 2 17.7887 24.1502 9.37149 -78.6001 67.4017 9.86198 -1981 1 11.139 14.0733 32.9523 31.4256 -0.03008 -5.2348 -1982 2 12.066 14.2725 33.0835 -15.5197 6.63618 -14.1202 -1983 2 10.9478 13.388 33.5926 -13.6636 8.48879 -3.5036 -1984 1 1.12572 32.0183 27.5356 24.6266 46.3494 2.8897 -1985 2 0.546692 31.3048 27.8037 -3.08121 -31.7776 -12.0256 -1986 2 1.55521 31.6943 26.7439 -12.2274 -17.2869 5.12609 -1987 1 16.7457 10.366 22.1454 -15.3164 -22.3958 -16.0252 -1988 2 17.6114 10.1816 22.5099 -14.3265 37.126 0.80158 -1989 2 16.5565 11.2637 22.4183 29.9704 0.0490406 16.3066 -1990 1 3.7604 22.8172 16.7231 -94.979 -46.3638 63.4302 -1991 2 3.80199 23.6592 16.2696 52.6252 2.42304 -21.4425 -1992 2 4.60092 22.4005 16.533 37.2062 36.1623 -37.5204 -1993 1 1.85858 2.74219 27.3787 -16.8615 -16.8421 15.8272 -1994 2 2.54214 2.17108 27.7292 -4.59146 35.0941 -40.6374 -1995 2 2.27945 3.20266 26.6527 25.2819 -23.6186 22.0617 -1996 1 20.9735 33.5714 23.8814 -106.803 36.5464 88.0259 -1997 2 21.6236 32.9171 24.1374 45.6079 -11.0665 -63.4639 -1998 2 21.2264 33.8268 22.9943 67.7875 -35.3184 -31.857 -1999 1 14.9346 6.66221 21.3527 -126.314 -3.88715 -82.8474 -2000 2 14.0911 6.81595 20.927 39.2653 62.6904 53.7569 -2001 2 15.1982 5.79131 21.0556 85.678 -53.7307 17.9606 -2002 1 22.2461 5.18918 17.8715 -69.145 -31.4218 -18.0837 -2003 2 21.9344 5.83223 17.2347 -27.7401 11.8107 -16.433 -2004 2 23.137 5.47038 18.0801 108.344 19.9553 34.4799 -2005 1 31.7359 29.9237 26.3736 -84.3482 -146.558 -73.4212 -2006 2 32.1627 30.6728 26.7895 111.481 40.2155 8.28834 -2007 2 32.4462 29.4563 25.9339 -20.9159 104.035 73.147 -2008 1 24.5541 23.2903 6.20562 34.8499 -73.6669 40.9676 -2009 2 25.3233 22.7463 6.0363 -54.9847 54.2625 4.3351 -2010 2 24.1245 22.8728 6.95223 10.9892 27.9336 -36.5991 -2011 1 25.8826 13.3692 31.6978 -39.5587 45.0721 109.942 -2012 2 26.0654 12.9392 30.8624 14.4928 -55.2593 -101.315 -2013 2 26.7459 13.5818 32.0524 34.4682 10.678 13.5079 -2014 1 31.9081 10.2232 30.8508 60.5777 139.069 -26.1959 -2015 2 32.2481 10.7082 31.6027 -21.552 -31.8062 -26.0603 -2016 2 31.6024 9.39393 31.2183 -39.6468 -107.76 57.4176 -2017 1 0.849757 3.66316 11.6882 -66.4227 -77.864 -86.3174 -2018 2 0.839326 4.56785 12.0007 9.47524 78.9317 34.8726 -2019 2 0.14017 3.62253 11.047 60.8788 -7.45935 55.9047 -2020 1 12.6493 6.4064 27.2531 -40.9759 17.8512 -96.8045 -2021 2 11.9988 5.88507 26.7827 30.2874 12.9967 48.5047 -2022 2 12.9203 7.07589 26.6249 2.54534 -39.1725 52.0268 -2023 1 15.9599 7.99333 15.8859 30.1406 -18.388 8.6192 -2024 2 16.7797 7.85417 15.4117 -4.79859 1.07516 10.1564 -2025 2 15.4667 8.60439 15.3385 -20.0761 12.8881 -12.5608 -2026 1 20.0344 20.1357 12.6654 -3.86966 -64.7249 -48.8174 -2027 2 19.4344 20.3202 11.9427 10.3543 13.9442 17.6237 -2028 2 20.3441 19.2454 12.4988 -10.1918 51.4785 29.9814 -2029 1 21.356 6.30633 10.131 -67.0198 -114.109 -5.58798 -2030 2 20.9103 5.53439 10.4799 -7.83167 25.8119 -63.3827 -2031 2 21.891 6.6238 10.8585 85.5245 81.2641 57.4267 -2032 1 35.1559 30.9332 9.83309 61.3262 -2.90007 -69.3354 -2033 2 0.303167 31.6302 9.88912 -24.8958 -15.4978 13.785 -2034 2 34.5934 31.0698 10.5955 -26.5859 21.8525 52.7843 -2035 1 4.27659 27.2552 26.2915 116.968 -151.738 -34.7454 -2036 2 3.39554 27.3768 25.9377 -83.718 52.8428 -4.72735 -2037 2 4.42257 28.0247 26.8419 -28.396 103.456 48.6556 -2038 1 26.8593 19.3342 13.6851 30.7677 67.3413 -148.698 -2039 2 26.0004 19.2038 14.0871 -50.0945 -27.4421 67.323 -2040 2 27.4811 19.0115 14.3374 18.1351 -38.3726 82.2067 -2041 1 7.83885 28.1834 15.8334 16.5365 20.604 -8.56175 -2042 2 7.60386 27.3316 16.2014 -33.7069 20.3127 -2.25908 -2043 2 7.02096 28.6807 15.838 5.21927 -39.3621 14.9074 -2044 1 32.631 18.2249 29.7861 41.9215 38.3318 11.8543 -2045 2 32.1421 17.5039 29.3895 -39.2744 -31.6531 -17.1652 -2046 2 31.957 18.8189 30.1164 -14.576 -4.73824 -0.949144 -2047 1 3.25628 33.4796 7.39391 71.9746 30.5666 -22.4299 -2048 2 4.11434 33.8297 7.63344 -69.5572 -27.2519 -15.9057 -2049 2 3.24436 33.5071 6.43718 -2.52475 -1.44402 31.1707 -2050 1 0.842237 3.50013 3.05753 16.9517 -63.8559 -23.0072 -2051 2 1.37533 4.09985 3.57944 19.8724 20.4219 19.8016 -2052 2 1.42823 2.77011 2.85767 -26.1771 37.5505 12.1175 -2053 1 25.1227 15.9755 21.4703 2.5941 62.4248 -49.2139 -2054 2 25.4287 15.7265 22.3424 20.0835 -17.1737 50.8233 -2055 2 25.5184 16.8328 21.3129 -18.0552 -40.9029 7.45317 -2056 1 7.27484 22.2113 14.035 48.561 60.0034 62.6588 -2057 2 7.83751 21.4533 13.8765 -38.0713 -11.7879 -38.4589 -2058 2 6.51927 22.0729 13.4638 0.293443 -44.8648 -32.9729 -2059 1 14.2406 9.72758 11.5631 116.878 81.801 14.5405 -2060 2 13.6867 9.60902 10.7914 -66.2487 -25.9071 -61.3884 -2061 2 14.9707 10.264 11.2543 -53.7978 -46.298 43.148 -2062 1 24.5661 34.1068 22.5037 -12.6784 75.01 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25.7701 32.651 87.3127 -33.674 -49.9122 -2081 2 13.7325 25.6374 32.7874 -23.9657 -5.59064 -20.5018 -2082 2 12.4854 26.1582 33.4696 -48.9202 37.6441 80.1222 -2083 1 30.8723 23.1715 13.4622 -9.11844 -27.0426 17.3174 -2084 2 30.4177 23.0049 14.2879 -11.7763 32.8722 29.883 -2085 2 30.92 22.3151 13.0374 18.8176 -9.0042 -46.3578 -2086 1 9.82399 23.583 1.7494 3.91602 -23.2748 -58.3544 -2087 2 9.72916 23.4277 0.80965 -20.0403 27.4058 -4.72991 -2088 2 10.3677 22.8585 2.05872 18.1457 -16.7879 43.7545 -2089 1 6.8955 12.5745 5.5963 85.8424 -23.1235 -93.8407 -2090 2 7.81182 12.4154 5.36977 -59.0646 18.9114 61.7966 -2091 2 6.4222 12.4672 4.77122 -25.9937 7.60744 34.9584 -2092 1 11.0245 29.5546 32.8142 27.2343 -22.8279 -26.0862 -2093 2 11.5962 29.377 33.5611 -2.51259 4.69703 -3.95931 -2094 2 11.3841 29.0222 32.1047 -13.3466 16.0372 20.0845 -2095 1 5.68503 15.1158 32.9715 71.9243 84.7749 22.2842 -2096 2 6.43529 15.2072 32.3842 -29.722 -48.1256 -23.5074 -2097 2 5.83799 15.7643 33.6589 -49.7197 -21.4736 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11.0044 34.2914 8.17886 15.9126 -2.73607 2.69613 -1886 2 10.7906 34.3407 9.11057 -2.69506 0.109664 -0.892116 -1887 2 11.8744 33.8931 8.15305 0.922075 0.494336 3.88877 -1888 1 10.4642 16.7648 26.4147 2.80971 1.51282 -9.61072 -1889 2 10.4264 17.0779 27.3185 1.17471 -1.35509 -0.280756 -1890 2 11.3146 17.0636 26.0926 0.590472 -1.32977 -0.414974 -1891 1 17.2152 4.69462 34.6747 11.9213 0.65814 -4.69715 -1892 2 18.0195 4.45625 34.2137 1.04857 -0.57361 0.535519 -1893 2 16.8774 3.86516 35.0125 1.91423 1.04657 2.96864 -1894 1 6.97445 35.1353 32.2671 9.97328 -11.6302 -7.33462 -1895 2 7.55154 34.8288 32.9666 0.774769 -1.62199 -1.46055 -1896 2 6.63884 0.467797 32.5832 1.02155 -1.24749 0.362107 -1897 1 30.2645 4.69075 18.0422 0.694439 -2.46184 2.97624 -1898 2 29.6017 4.00886 17.9326 1.10342 -1.19819 0.759635 -1899 2 30.7589 4.42264 18.8167 -1.07894 2.27368 1.54311 -1900 1 14.1656 29.632 31.6787 5.05867 -0.355939 -0.980506 -1901 2 14.4451 30.4041 31.1867 -0.842964 -0.790639 -0.294246 -1902 2 13.5563 29.1821 31.0933 0.0725257 -1.19259 1.4708 -1903 1 22.4084 9.52165 9.7397 0.735332 -1.67091 -3.93305 -1904 2 22.7212 9.37225 10.6319 -1.09142 1.00002 -0.542777 -1905 2 23.025 9.04279 9.18587 1.34861 1.44662 0.230846 -1906 1 22.2367 0.136878 35.4162 2.39769 -1.00634 11.3877 -1907 2 23.1336 0.346647 0.22933 -0.416125 0.426818 1.11968 -1908 2 21.8755 35.1657 0.715801 -0.0814999 0.0454572 0.682247 -1909 1 30.8013 21.126 11.6255 -3.46793 -5.01909 1.70411 -1910 2 31.1601 21.6971 10.9462 -4.45423 -1.15624 -2.23432 -1911 2 31.4336 20.4108 11.6964 2.44046 2.26421 0.934019 -1912 1 27.4508 5.23152 21.4006 1.74025 1.89877 19.0993 -1913 2 27.8319 4.73772 22.1266 0.4018 0.947765 0.850108 -1914 2 26.5774 5.47438 21.7079 -0.634266 -2.0344 0.72118 -1915 1 34.2517 16.5309 18.5306 0.907524 -6.93269 -4.04601 -1916 2 34.8715 15.8322 18.7399 -0.501769 0.835994 1.04597 -1917 2 33.8909 16.2844 17.6789 -0.976215 1.5179 3.59303 -1918 1 32.115 35.0905 16.482 2.22898 -11.9743 -20.9485 -1919 2 32.966 34.6682 16.5991 -0.636814 -0.495605 0.383446 -1920 2 32.3008 0.353133 15.9431 0.148533 0.858467 3.15742 -1921 1 5.2813 31.5245 24.5891 -0.88265 3.56081 0.527901 -1922 2 5.6102 31.6063 25.4843 2.8911 0.897716 -1.16555 -1923 2 5.50826 32.3562 24.1732 0.0452461 -1.83796 -1.84019 -1924 1 25.7935 25.4126 18.2933 8.42974 5.04501 3.04403 -1925 2 25.4171 24.7186 17.752 -3.18932 0.154086 3.92798 -1926 2 25.7522 26.195 17.7434 -1.62301 -1.62428 -0.262324 -1927 1 4.94055 22.5134 12.7286 -9.04805 -9.98913 0.740441 -1928 2 4.66669 21.7387 13.2196 -2.25032 0.777095 0.693415 -1929 2 4.12797 22.9905 12.5602 2.55025 2.81834 1.88639 -1930 1 12.3705 3.40796 24.8702 -10.2718 -6.94273 4.16449 -1931 2 11.5354 3.79201 25.1374 1.11482 2.05237 1.26765 -1932 2 12.7415 4.04279 24.2574 1.31703 -1.09657 1.0894 -1933 1 17.2229 21.0728 32.2314 -8.179 -5.27121 -18.2871 -1934 2 16.3825 21.3411 31.86 1.15239 -1.37236 -2.54915 -1935 2 17.7485 20.8146 31.4742 0.636225 0.416061 0.167394 -1936 1 25.4211 13.6617 27.4256 -0.423575 1.5864 -14.144 -1937 2 25.9311 14.3939 27.0792 0.209498 -1.21813 2.94262 -1938 2 25.0385 13.2482 26.6517 -1.88498 1.40152 0.678356 -1939 1 31.3452 0.921707 6.09496 5.75289 0.0456399 -1.04313 -1940 2 31.5193 0.206077 5.48357 1.7599 -1.91271 2.66807 -1941 2 31.9558 1.61205 5.83652 -0.775733 -0.136291 -2.46929 -1942 1 14.5238 27.1426 0.855822 -0.28203 -13.8472 13.0001 -1943 2 15.0637 27.8615 0.527327 -2.90129 -0.385453 -1.8344 -1944 2 14.5862 27.2115 1.8085 -1.36301 3.80564 -1.12804 -1945 1 28.8746 13.8014 31.4027 -2.88672 6.47051 7.86952 -1946 2 29.2232 14.2517 32.1721 1.91816 0.252514 -1.72337 -1947 2 28.8041 14.4848 30.7362 -2.55312 0.206489 0.885327 -1948 1 32.2921 1.69364 30.0162 -5.24318 6.11719 0.10458 -1949 2 32.9509 1.85569 29.3409 -1.02656 -2.73336 -0.95222 -1950 2 31.7703 2.49576 30.0398 2.18736 -0.0064308 0.36284 -1951 1 12.6171 8.26014 20.3408 -0.40671 -8.63132 6.16379 -1952 2 12.7962 8.9555 20.9737 1.99194 1.08407 -2.86475 -1953 2 12.1389 8.69542 19.635 2.27749 -2.82959 -1.29442 -1954 1 12.5264 25.4516 7.87552 -4.00904 -0.543437 10.3565 -1955 2 12.9562 24.654 8.18449 -0.215524 -0.0928553 -1.74864 -1956 2 11.705 25.1474 7.48948 4.50811 -0.52052 -4.58555 -1957 1 1.10395 20.9772 6.76689 -12.4418 -4.87906 -17.0173 -1958 2 0.841381 21.0115 5.84704 0.961335 2.29109 -0.167377 -1959 2 1.91806 21.4794 6.80294 -0.662195 -1.08577 2.11991 -1960 1 4.82166 0.411135 13.4723 -6.95497 7.27665 -10.2603 -1961 2 4.31632 1.13144 13.0954 -1.71759 1.5163 4.71861 -1962 2 4.19868 35.4546 14.0325 3.34255 0.282635 2.02706 -1963 1 7.98045 14.3231 18.3954 3.08041 14.4496 -7.04888 -1964 2 7.47829 15.0927 18.6634 -2.22303 -2.54215 1.24386 -1965 2 7.75094 13.6513 19.0374 2.28408 -1.12721 -2.33416 -1966 1 6.57567 10.8403 7.6939 2.74017 2.33053 3.06743 -1967 2 6.87818 11.4306 7.00375 -0.816871 -0.135469 -0.424054 -1968 2 5.69956 11.1571 7.91368 0.353319 -2.48188 -0.273827 -1969 1 10.1296 13.4617 3.4523 -7.92991 7.36607 -13.5551 -1970 2 9.4814 14.0411 3.05172 2.81436 1.47522 -1.87702 -1971 2 10.9658 13.745 3.08241 -0.999119 -0.282534 1.18626 -1972 1 2.78873 23.9803 22.6823 7.39875 -2.15156 -6.43063 -1973 2 2.24341 23.3472 22.2153 1.0523 -1.39215 0.678747 -1974 2 2.17172 24.6381 23.0029 -0.309516 -1.48449 0.660469 -1975 1 29.681 34.0668 9.41834 9.5803 -0.140978 0.198088 -1976 2 29.4023 33.8738 10.3135 -0.39736 4.75337 0.09998 -1977 2 30.2232 34.8514 9.49973 0.132783 -0.224159 -2.50537 -1978 1 17.3964 25.0161 9.25437 -10.6964 6.49204 10.2875 -1979 2 18.0663 25.5133 8.78518 -2.57426 -0.200004 -1.71763 -1980 2 17.7826 24.1488 9.37642 -1.26016 -0.11254 -2.41078 -1981 1 11.1411 14.0768 32.9507 2.74692 8.93145 -23.0737 -1982 2 12.0674 14.2752 33.0877 0.326495 0.0181461 -2.13137 -1983 2 10.9448 13.3932 33.5914 -1.40918 5.092 2.7765 -1984 1 1.12682 32.0133 27.5402 4.517 -1.51145 -4.02069 -1985 2 0.552584 31.2959 27.8081 3.00058 -1.99467 0.131487 -1986 2 1.5621 31.6905 26.7511 1.52551 1.30495 -0.0263278 -1987 1 16.7481 10.3694 22.1507 0.264039 13.0692 4.69918 -1988 2 17.6248 10.1979 22.4946 -0.0377334 0.851346 -4.78636 -1989 2 16.5624 11.2729 22.4066 -1.46932 -0.377234 0.467584 -1990 1 3.76375 22.8172 16.7293 -4.0741 -10.5757 1.02761 -1991 2 3.80151 23.6586 16.2743 -0.690304 1.29329 3.69566 -1992 2 4.5994 22.3969 16.5262 -0.197813 0.973283 -0.721214 -1993 1 1.85399 2.73861 27.3822 3.20071 -7.68688 -3.72082 -1994 2 2.53752 2.17131 27.7389 0.0246343 -1.14856 -1.23911 -1995 2 2.27395 3.18876 26.6492 0.934788 1.93265 2.10385 -1996 1 20.9724 33.5726 23.8784 8.10433 -9.20518 -4.51155 -1997 2 21.6189 32.9194 24.1461 -2.046 -3.87957 -3.38316 -1998 2 21.2405 33.8276 22.9955 0.119388 1.30018 0.791288 -1999 1 14.9356 6.66547 21.3473 -4.32378 2.01425 -5.99167 -2000 2 14.0917 6.81509 20.921 0.850589 0.904261 -2.27949 -2001 2 15.2025 5.79487 21.0522 1.98877 1.97817 -3.72271 -2002 1 22.2485 5.18667 17.87 13.215 -1.9753 -1.37536 -2003 2 21.9401 5.84134 17.2434 -1.85661 0.524428 2.90348 -2004 2 23.1453 5.4526 18.0731 0.178716 1.34064 -2.4977 -2005 1 31.7392 29.9223 26.3752 4.76914 0.177865 5.41636 -2006 2 32.1647 30.6696 26.7955 0.903997 -0.87703 1.20137 -2007 2 32.4505 29.4583 25.9336 0.0227674 -0.433216 0.401033 -2008 1 24.5495 23.287 6.21014 -9.6064 5.24279 8.20718 -2009 2 25.3283 22.7624 6.02443 0.116339 4.39189 1.8768 -2010 2 24.1468 22.8595 6.966 0.2289 -0.0589481 -2.13137 -2011 1 25.8848 13.3641 31.6949 11.7976 1.283 28.4217 -2012 2 26.0644 12.9328 30.8595 -3.81135 -1.20515 1.50928 -2013 2 26.7491 13.586 32.0412 2.1747 1.23594 -3.73301 -2014 1 31.9059 10.2239 30.8521 3.15397 -0.693558 5.50864 -2015 2 32.2432 10.7005 31.6105 -2.64306 -0.474064 1.50947 -2016 2 31.6065 9.38729 31.2082 -1.91976 0.707005 -1.14165 -2017 1 0.84878 3.6625 11.6852 3.82778 -4.24681 3.04899 -2018 2 0.853073 4.56299 12.0097 1.00506 -0.863618 -0.913913 -2019 2 0.134074 3.64014 11.0488 -1.02679 -1.02985 3.07516 -2020 1 12.653 6.40924 27.2569 -10.896 -2.3651 4.67545 -2021 2 12.0107 5.88536 26.7781 -1.95087 -0.422561 2.90655 -2022 2 12.932 7.07765 26.6311 3.33215 -5.37792 -3.19321 -2023 1 15.9575 7.9951 15.8816 6.43964 -4.15323 6.61769 -2024 2 16.7831 7.8467 15.4206 0.588477 2.84349 1.20404 -2025 2 15.4803 8.61195 15.3266 -2.08725 -4.05933 -0.295667 -2026 1 20.0375 20.1391 12.665 -4.11025 1.52341 -3.10314 -2027 2 19.4274 20.3342 11.9537 2.89664 -0.270393 -1.94487 -2028 2 20.3292 19.244 12.4922 -2.13637 -0.289793 3.97752 -2029 1 21.356 6.30845 10.1293 11.8845 -7.32937 -8.40835 -2030 2 20.9041 5.54426 10.4872 -0.836302 1.13214 -0.345734 -2031 2 21.8894 6.63336 10.8547 0.11176 0.0745871 -0.490015 -2032 1 35.1526 30.9366 9.83286 7.59845 5.2547 -1.12957 -2033 2 0.311501 31.622 9.89575 0.964885 -1.25019 -0.233494 -2034 2 34.6019 31.0651 10.6052 0.344797 -0.803576 -0.904465 -2035 1 4.27525 27.2569 26.2869 4.28071 5.72746 7.8462 -2036 2 3.39987 27.3692 25.9163 0.165296 -0.828825 2.86229 -2037 2 4.39971 28.0244 26.8452 0.266735 0.0706906 -1.3371 -2038 1 26.8649 19.3391 13.6882 0.177125 1.61838 2.46927 -2039 2 26.0052 19.1944 14.0834 -0.103725 0.362381 -1.50792 -2040 2 27.4862 19.0117 14.3386 -0.695576 -0.902314 0.251747 -2041 1 7.83542 28.181 15.8382 -13.3943 -2.71551 5.4783 -2042 2 7.57758 27.3247 16.1794 -0.25335 2.11014 -2.48558 -2043 2 7.02351 28.6878 15.8233 1.95232 1.88776 0.576467 -2044 1 32.6262 18.2228 29.791 -14.1882 1.19327 -8.66236 -2045 2 32.1279 17.5186 29.3763 0.458993 0.618559 0.834874 -2046 2 31.9606 18.8321 30.1103 1.27184 -0.0824113 1.15038 -2047 1 3.26267 33.4782 7.39241 0.72256 1.05107 -6.58477 -2048 2 4.1177 33.8412 7.62335 -1.20198 1.46048 -0.601021 -2049 2 3.2457 33.4941 6.43549 0.071718 0.812761 -0.0287205 -2050 1 0.844894 3.50214 3.06141 10.9265 -6.46418 5.34726 -2051 2 1.3825 4.10673 3.57296 -1.34547 0.02462 1.3239 -2052 2 1.43348 2.7774 2.85035 0.956803 -0.0258241 1.47884 -2053 1 25.1225 15.9729 21.4727 1.26189 6.66637 7.55006 -2054 2 25.4376 15.7328 22.3441 1.99941 -1.50251 -1.18582 -2055 2 25.5145 16.8296 21.3033 0.649747 -0.161475 0.915999 -2056 1 7.27486 22.2101 14.0385 10.1815 -3.49421 -8.18063 -2057 2 7.84619 21.46 13.8737 1.50039 1.74304 -3.72093 -2058 2 6.53621 22.0846 13.4428 1.08182 3.6941 2.34564 -2059 1 14.2409 9.72949 11.5638 -2.21614 13.7167 -2.62635 -2060 2 13.6906 9.62021 10.7883 -0.22348 -2.43277 0.646692 -2061 2 14.9733 10.2682 11.2645 -0.353329 -0.504752 -2.50308 -2062 1 24.5604 34.1124 22.5076 2.81011 9.56643 12.8028 -2063 2 24.4651 33.192 22.2624 2.76066 3.39389 -3.794 -2064 2 24.909 34.0885 23.3987 -0.0660125 2.15758 -2.31326 -2065 1 28.1787 24.2138 14.4977 2.85163 13.2743 10.1108 -2066 2 28.1314 24.0884 15.4454 -1.95 -0.314329 0.254779 -2067 2 27.5593 23.5776 14.1402 4.78697 -1.19745 -1.90137 -2068 1 35.2086 9.78789 0.994199 1.76044 6.5307 -5.2317 -2069 2 0.557202 10.1754 0.806894 0.418955 -1.44608 0.928967 -2070 2 34.6067 10.532 1.01289 1.59781 1.15857 -0.38696 -2071 1 0.696525 26.2392 12.9981 6.15683 2.43528 1.97356 -2072 2 0.0853603 25.8774 12.3564 0.126465 3.40177 -1.1815 -2073 2 0.827069 27.1459 12.7205 1.01216 -0.0198955 3.9203 -2074 1 22.1927 29.1204 4.3329 10.0155 4.13346 -1.27455 -2075 2 21.5089 28.451 4.35461 1.49845 0.495267 -0.159421 -2076 2 22.908 28.7169 3.84119 -2.47796 1.10379 -2.16302 -2077 1 17.916 28.683 14.989 -2.36263 0.654597 -2.84745 -2078 2 18.4385 28.392 15.7363 -2.11473 0.465722 -0.120026 -2079 2 17.5044 27.8844 14.6585 2.66175 -0.386546 -1.02105 -2080 1 12.7952 25.7665 32.6497 13.9949 3.53752 8.37998 -2081 2 13.7341 25.6434 32.7898 0.325895 -1.85511 0.845326 -2082 2 12.4802 26.1577 33.4645 0.612139 -2.92432 1.79416 -2083 1 30.8742 23.167 13.459 1.42585 -4.1257 6.75052 -2084 2 30.4067 23.0024 14.2778 -1.88886 -0.614314 -1.43999 -2085 2 30.9172 22.3119 13.0311 -1.44327 1.00043 -2.06414 -2086 1 9.82816 23.5848 1.74826 4.09339 -9.25808 -17.9911 -2087 2 9.74381 23.4546 0.803719 0.485579 -1.71759 0.88707 -2088 2 10.3572 22.8448 2.04625 -1.70334 -0.335486 -1.80313 -2089 1 6.89263 12.5722 5.59003 -3.42428 7.18815 0.109591 -2090 2 7.81348 12.4179 5.37924 -0.409968 -0.134661 3.03095 -2091 2 6.43412 12.4627 4.75695 2.18255 -2.57536 -0.0517335 -2092 1 11.0294 29.5516 32.8106 9.33574 -3.0002 -9.362 -2093 2 11.6012 29.3802 33.5589 1.86495 1.52792 -1.29087 -2094 2 11.3895 29.014 32.1053 -0.11513 -1.05364 -0.15456 -2095 1 5.68421 15.1154 32.971 -6.10389 17.5032 9.81276 -2096 2 6.44786 15.1804 32.3976 -2.76176 -5.22659 1.4758 -2097 2 5.84755 15.7576 33.6618 -0.353412 4.33933 -2.88367 -2098 1 21.2619 27.2128 29.9745 13.6163 -5.96544 1.97752 -2099 2 21.1023 27.9709 30.5368 -0.179442 -1.82524 1.45305 -2100 2 20.5969 27.2782 29.2891 0.137903 -0.746035 1.06037 -2101 1 6.19181 8.13957 30.3451 -8.48727 -8.28994 6.01453 -2102 2 6.97701 7.67729 30.0519 -2.03856 -3.21695 4.93459 -2103 2 5.52559 7.45652 30.4214 -1.35773 1.55745 0.920755 -2104 1 32.4099 28.4116 3.86444 -4.18766 8.07464 1.54038 -2105 2 32.5147 27.4665 3.9742 3.5415 2.18598 0.381035 -2106 2 31.5078 28.5858 4.13297 -0.124238 -0.90634 -1.56255 -2107 1 23.9935 26.6237 31.2156 -1.77594 5.02662 -3.69764 -2108 2 23.2047 26.8918 30.7444 0.0659868 -0.69126 -0.258411 -2109 2 24.4759 27.438 31.3587 -2.36725 0.937325 2.90768 -2110 1 28.5047 29.5758 20.8717 -11.8816 10.0842 -0.798304 -2111 2 29.2407 29.9723 20.4054 -1.63534 -5.14698 -5.99675 -2112 2 28.9026 29.1526 21.6325 1.97682 0.775721 -2.26728 -2113 1 27.7507 21.2746 18.519 -2.5653 -10.6239 2.62546 -2114 2 27.4235 20.422 18.2324 0.481061 -0.629309 0.781079 -2115 2 28.2537 21.0848 19.311 -1.00646 0.362905 0.392864 -2116 1 25.2532 27.4363 16.553 -8.60012 2.32024 -6.4729 -2117 2 25.6623 28.3016 16.542 2.83422 -2.12619 2.30998 -2118 2 24.92 27.317 15.6636 5.31661 1.51202 -2.34852 -2119 1 5.61824 2.12637 21.503 -1.17612 0.715888 4.06576 -2120 2 4.8052 2.11258 22.008 1.06061 -0.364635 -2.05514 -2121 2 5.91777 1.21725 21.5055 -2.31637 0.137551 -1.97542 -2122 1 14.2045 17.3028 2.13313 13.8322 -9.9262 14.7443 -2123 2 13.4643 17.6404 1.62874 2.50063 -2.15093 -0.197974 -2124 2 13.9013 17.314 3.04098 -1.33233 -2.7535 0.223921 -2125 1 33.7781 2.9239 0.155769 0.178407 -4.43945 -0.37031 -2126 2 33.4616 3.50802 34.9138 0.119409 -0.168031 0.668625 -2127 2 33.6395 3.41265 0.967026 0.0418614 -0.671587 -0.0553616 -2128 1 0.227757 13.6891 9.35453 3.75917 4.51084 1.19032 -2129 2 0.64664 13.3875 10.1607 -2.554 -4.83332 -1.99438 -2130 2 0.820174 13.4088 8.65689 -2.36288 -2.906 2.52442 -2131 1 27.5718 24.3683 33.9227 11.8758 -14.0536 -0.652827 -2132 2 27.0285 24.2545 33.1429 -0.126379 2.90913 0.147778 -2133 2 28.103 23.573 33.9632 -2.25564 -2.06787 -1.68633 -2134 1 18.7547 23.4368 22.1148 1.76793 -3.43652 -5.89452 -2135 2 17.8334 23.3516 21.8695 0.21508 -0.204651 0.176003 -2136 2 19.1852 23.7587 21.3229 -0.448118 0.043474 -0.389491 -2137 1 2.29221 10.8734 1.51363 3.40588 -1.78065 -4.02462 -2138 2 2.50322 11.7417 1.85678 -0.631189 -1.51747 1.05411 -2139 2 2.85137 10.2765 2.01087 0.643156 1.05988 -1.16649 -2140 1 25.6214 25.899 25.2413 3.03123 -3.73655 12.5526 -2141 2 25.4794 26.589 25.8893 -0.15111 -0.362854 -0.719554 -2142 2 26.3846 25.42 25.5642 0.366269 1.78247 -0.942643 -2143 1 16.9269 16.3234 9.79661 -6.62239 -4.09948 11.2029 -2144 2 17.2235 17.0918 9.30892 4.24477 -4.29454 -0.846488 -2145 2 17.3507 16.4032 10.6511 0.535424 -3.08265 -0.22927 -2146 1 10.4746 17.2104 29.111 0.461956 5.13833 10.1707 -2147 2 10.9241 18.0338 29.3012 -0.703571 0.85844 -2.15095 -2148 2 10.1952 16.8862 29.9673 -1.05192 3.52498 1.46743 -2149 1 16.0666 22.3671 1.6953 -13.4076 -7.95118 -0.708657 -2150 2 15.3907 23.0043 1.46427 1.07175 1.7325 0.439819 -2151 2 16.8399 22.6498 1.20714 1.38044 0.287258 3.91095 -2152 1 16.3357 27.5846 32.8085 2.54571 4.88704 -14.3477 -2153 2 15.9474 26.7327 32.6096 4.10112 -0.695412 1.47727 -2154 2 15.8243 28.2078 32.2925 -3.9931 -1.27178 2.38137 -2155 1 20.4932 11.6283 35.2655 -3.26067 -1.10384 -0.810694 -2156 2 20.9736 12.0663 34.5629 2.17296 -7.5022 -1.79892 -2157 2 19.7289 11.2477 34.8327 1.40006 -3.27805 0.449146 -2158 1 30.4143 26.578 6.51765 1.34698 1.94845 -3.36576 -2159 2 30.1945 26.7453 5.60116 0.455236 -0.800151 0.112693 -2160 2 30.4582 25.6241 6.58369 -2.82519 0.317721 2.06092 -2161 1 12.3779 16.378 4.55641 -4.36421 7.90937 -13.7187 -2162 2 12.3465 15.5702 4.0438 3.23934 2.28262 -2.17386 -2163 2 11.6883 16.9264 4.18253 -0.260462 -0.501236 -2.16943 -2164 1 33.5739 11.9086 21.4588 11.1152 -1.5316 3.49609 -2165 2 33.2115 12.3917 20.7162 3.11323 -0.128176 -0.870749 -2166 2 32.8144 11.6995 22.0027 -1.07419 -0.174326 -2.30381 -2167 1 31.3265 31.2337 1.41157 1.73917 3.01076 -4.26138 -2168 2 31.4705 31.9953 0.849882 -0.517616 -0.645507 0.434596 -2169 2 31.2025 30.5061 0.802147 -2.99133 0.294358 0.258116 -2170 1 28.8718 19.6384 21.2244 5.68955 -4.46505 -10.0472 -2171 2 29.7168 19.4523 20.815 -0.0967467 0.927831 -0.484415 -2172 2 28.8758 20.5854 21.3635 -2.11682 -0.153636 -2.1144 -2173 1 4.42453 23.1716 25.4282 2.90202 2.28962 -12.879 -2174 2 3.9564 23.5331 24.6756 -0.22092 -2.25427 -1.27917 -2175 2 4.52948 22.2427 25.222 -2.16739 -0.10553 2.93245 -2176 1 24.0098 31.996 18.183 -2.49774 3.05067 4.43748 -2177 2 23.2463 32.5536 18.0336 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-0.0840263 -3.07679 -4410 2 25.7332 3.59406 13.2994 -3.10068 -2.3533 4.10846 -4411 1 33.2055 12.6395 8.23391 5.45516 1.9919 5.8193 -4412 2 32.6787 12.8131 9.01402 -0.345731 -1.59928 -1.24485 -4413 2 34.1053 12.8183 8.50726 -0.805487 1.53365 1.78742 -4414 1 29.9023 24.5626 20.7116 3.42295 -6.98403 -0.952027 -4415 2 29.4679 25.4132 20.6473 -0.48284 -2.69496 0.222901 -4416 2 30.2739 24.4166 19.8417 -0.244826 -2.35878 0.7128 -4417 1 15.2998 4.02453 16.4417 -2.15742 4.79241 6.05563 -4418 2 15.7057 4.6226 17.0692 0.191126 1.42105 -2.21766 -4419 2 14.9946 3.28953 16.9736 -0.120429 1.69431 2.26192 -4420 1 31.2753 25.1783 0.424078 -3.05861 -1.08728 17.9787 -4421 2 31.0586 24.4517 35.287 4.05906 -1.40755 1.82856 -4422 2 30.7422 25.0259 1.20438 -1.38424 0.164027 -0.204301 -4423 1 12.1221 3.02324 0.180171 5.54245 -1.23026 6.11818 -4424 2 11.8464 2.17458 35.281 1.14317 0.150516 -0.180026 -4425 2 11.3607 3.34415 0.66332 2.03454 -2.74467 1.9593 -4426 1 32.8431 11.557 14.38 0.147749 2.67556 -1.98289 -4427 2 31.9068 11.5678 14.1811 0.291943 -1.00905 2.75821 -4428 2 32.9664 12.2812 14.9936 1.19966 -2.12497 2.082 -4429 1 20.5645 17.4424 12.4515 6.55406 0.156517 0.559841 -4430 2 19.8459 16.8903 12.1433 -1.42603 2.83887 0.952488 -4431 2 20.6495 17.2292 13.3808 1.56555 -1.24922 -0.696423 -4432 1 15.2816 11.6269 18.8168 5.55975 3.4447 3.66971 -4433 2 14.386 11.8473 19.0727 -0.646747 -2.40537 -4.21442 -4434 2 15.3862 10.7109 19.0741 1.74861 1.0941 -0.195148 -4435 1 29.7377 20.372 3.36652 0.797329 -7.98301 -8.63454 -4436 2 30.4736 19.7997 3.5836 -1.83703 -0.890419 1.54523 -4437 2 29.86 20.5792 2.44008 0.781849 -1.5009 -0.273719 -4438 1 10.4638 28.1009 15.3794 8.14468 4.22684 -0.814723 -4439 2 9.53379 28.2306 15.5652 0.0260372 -2.67835 -1.69305 -4440 2 10.6322 28.642 14.608 -0.570693 -1.3859 -1.11001 -4441 1 16.7704 6.13101 17.944 -0.211983 -1.47772 3.31 -4442 2 17.2683 6.32159 18.7389 1.86764 1.15901 -3.46209 -4443 2 16.6681 6.98075 17.5153 -2.39931 -1.61441 -0.74807 -4444 1 21.5135 0.327334 25.1409 8.66564 11.1895 -11.7105 -4445 2 22.2279 0.15114 25.7531 -4.2921 0.404201 4.61487 -4446 2 21.4118 35.0184 24.6498 0.519456 -0.928846 2.19863 -4447 1 8.71062 23.6629 10.1362 3.05079 1.60887 0.77512 -4448 2 9.03714 24.1011 10.9221 0.259856 1.17771 -1.23482 -4449 2 9.41576 23.0672 9.88307 -1.85123 -1.62472 0.915088 -4450 1 20.2468 3.67222 10.3704 0.4777 5.10365 7.10224 -4451 2 20.359 3.07898 11.1132 -0.765711 0.100413 -2.14552 -4452 2 19.4836 3.33128 9.90403 2.85534 1.08452 -0.754728 -4453 1 5.99164 17.0864 14.8678 -5.37574 3.84131 -0.459775 -4454 2 6.63127 17.7689 14.6646 3.22934 -2.98012 2.44679 -4455 2 5.554 17.396 15.6608 -0.457156 0.512177 -0.289605 -4456 1 9.83882 21.0265 7.18035 5.95081 -1.40299 -8.14061 -4457 2 9.12061 21.5838 6.88056 -2.6067 -3.24929 2.7288 -4458 2 9.85976 21.1517 8.1291 3.24078 0.788148 -1.58199 -4459 1 14.2806 22.3479 30.4744 -5.28704 8.01428 14.3895 -4460 2 13.8253 23.128 30.1575 2.20354 -0.167513 -4.00018 -4461 2 14.4934 21.8556 29.6816 1.73645 -3.40489 3.93134 -4462 1 9.99574 22.3649 18.625 -1.24662 -2.70761 -10.6994 -4463 2 10.4595 21.9481 17.8987 0.183494 1.6516 0.642745 -4464 2 10.6595 22.4657 19.3072 -3.1201 -0.222712 1.57266 -4465 1 13.5444 23.3091 25.3305 6.03923 1.55312 0.42896 -4466 2 13.2633 22.9728 26.1815 -0.932337 -1.00851 -1.27722 -4467 2 14.4265 22.9566 25.2126 -1.02044 -2.61951 -0.48294 -4468 1 20.38 18.6937 28.3968 7.14119 -6.8925 -2.09374 -4469 2 20.0167 18.9886 27.5617 0.316244 -5.43562 -1.75257 -4470 2 21.3206 18.6184 28.2361 0.666353 0.344779 0.815735 -4471 1 31.9689 7.20731 11.1996 7.34708 3.16447 9.75319 -4472 2 31.6099 7.15114 12.0852 0.998483 0.911771 -1.0382 -4473 2 32.8409 6.81882 11.269 -0.906482 -0.425175 -2.58612 -4474 1 3.59826 34.1759 15.1126 -11.7123 -5.68349 5.97393 -4475 2 3.21043 33.454 14.6179 1.39026 0.0576551 1.52481 -4476 2 3.54331 33.8972 16.0267 0.654449 -1.39662 -0.127074 -4477 1 16.7556 18.4081 28.9987 8.31009 -1.52636 -3.73736 -4478 2 17.6307 18.6606 29.2931 -1.43242 0.172472 0.00350369 -4479 2 16.5433 17.6311 29.5158 -4.3853 4.025 1.85791 -4480 1 4.3102 29.9995 27.41 12.3163 -5.69934 9.04024 -4481 2 5.14895 30.4141 27.2079 -1.45489 3.42303 0.773461 -4482 2 3.71946 30.3049 26.7216 -0.489848 -3.13791 0.780952 -4483 1 6.15571 15.7166 24.0745 -10.4675 14.0348 8.09529 -4484 2 5.31022 15.8535 24.5019 -1.15491 -4.01696 -1.7966 -4485 2 6.50126 14.9194 24.4761 0.366863 0.626035 -2.42182 -4486 1 1.16849 28.775 19.8427 0.210476 14.8941 -2.95759 -4487 2 0.55835 28.0645 19.6452 -0.37833 1.16517 1.01041 -4488 2 2.02094 28.3459 19.9163 -1.22217 1.3797 3.29741 -4489 1 23.2346 29.7445 8.55319 -3.19073 0.0591217 -1.71373 -4490 2 24.177 29.8703 8.66448 -1.37464 0.315561 0.0894517 -4491 2 22.981 30.3965 7.89984 0.244518 -1.23007 0.476314 -4492 1 19.4825 19.1594 6.42054 2.91673 9.05689 -8.3853 -4493 2 19.0036 18.5381 5.87205 1.04646 3.76482 -1.27192 -4494 2 18.8796 19.8942 6.5334 2.07477 2.20963 -2.23813 -4495 1 33.0425 24.822 13.641 6.63183 6.2187 -2.78039 -4496 2 33.7809 24.3577 13.2468 -0.641414 -1.92179 0.68381 -4497 2 32.2751 24.3054 13.3949 -0.245517 -1.04267 4.99319 -4498 1 26.0476 6.03912 17.2588 1.74441 -5.97008 8.24573 -4499 2 26.4147 5.4419 17.9106 -0.885223 -2.61028 -1.33276 -4500 2 26.4184 5.74408 16.4271 1.8916 3.73175 0.920143 diff --git a/examples/TIP4P/gpu_dump/in.tip4p b/examples/TIP4P/gpu_dump/in.tip4p deleted file mode 100644 index b31960d203..0000000000 --- a/examples/TIP4P/gpu_dump/in.tip4p +++ /dev/null @@ -1,49 +0,0 @@ -# sample script to compare and debug GPU accelerated tip4p water -# use '-sf gpu' to enables the GPU accelerated pair style -# without it the original lj/cut/tip4p/long from module KSPACE will be used - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -atom_modify map array - -pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 -pair_modify table 0 - -#long-range solver for TIP4P from module KSPACE works on CPU -suffix off -newton on -kspace_style pppm/tip4p 1.0e-5 -suffix on - -read_data data.spce - -pair_coeff * * 0.0 0.0 -pair_coeff 1 1 0.1852 3.1589 - -bond_coeff 1 0.0 0.9572 -angle_coeff 1 0.0 104.52 - -group water type 1 2 - -#maintain the water molecule rigid -fix 1 water shake 1.0e-4 200 0 b 1 a 1 -fix 2 water nve - -thermo 100 -thermo_style custom step etotal ke pe temp evdwl ecoul elong press -thermo_modify format float "%.15g" - -velocity water create 300 123 - -if $(is_active(package,gpu)) & - then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz"& - else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -dump_modify 11 sort id - -timestep 1 - -run 1 diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 deleted file mode 100644 index 57b0db597c..0000000000 --- a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 +++ /dev/null @@ -1,127 +0,0 @@ -LAMMPS (30 Oct 2019) -# - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -atom_modify map array - -pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 -pair_modify table 0 - -#long-range solver for TIP4P from module KSPACE works on CPU -suffix off -newton on -kspace_style pppm/tip4p 1.0e-5 -suffix on - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00143709 secs - read_data CPU = 0.0185545 secs - -pair_coeff * * 0.0 0.0 -pair_coeff 1 1 0.1852 3.1589 - -bond_coeff 1 0.0 0.9572 -angle_coeff 1 0.0 104.52 - -group water type 1 2 -4500 atoms in group water - -#maintain the water molecule rigid -fix 1 water shake 1.0e-4 200 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 water nve - -thermo 100 -thermo_style custom step etotal ke pe temp evdwl ecoul elong press -thermo_modify format float "%.15g" - -velocity water create 300 123 - -if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -if 0 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz -dump_modify 11 sort id - -timestep 1 - -run 1 -PPPM initialization ... - extracting TIP4P info from pair style - using polynomial approximation for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.342797 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00261362 - estimated relative force accuracy = 7.87083e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 79507 46656 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 11.3092 - ghost atom cutoff = 11.3092 - binsize = 5.6546, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/tip4p/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 30.18 | 30.18 | 30.18 Mbytes -Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press - 0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273 - 1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061 -Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms - -Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s -101.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.071838 | 0.071838 | 0.071838 | 0.0 | 76.10 -Bond | 1.974e-06 | 1.974e-06 | 1.974e-06 | 0.0 | 0.00 -Kspace | 0.012686 | 0.012686 | 0.012686 | 0.0 | 13.44 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00012462 | 0.00012462 | 0.00012462 | 0.0 | 0.13 -Output | 0.0093175 | 0.0093175 | 0.0093175 | 0.0 | 9.87 -Modify | 0.00038138 | 0.00038138 | 0.00038138 | 0.0 | 0.40 -Other | | 4.484e-05 | | | 0.05 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 15219 ave 15219 max 15219 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1371514 -Ave neighs/atom = 304.781 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp deleted file mode 100644 index 4441a448da..0000000000 --- a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp +++ /dev/null @@ -1,120 +0,0 @@ -LAMMPS (30 Oct 2019) -package gpu 1 -# - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -atom_modify map array - -pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 -pair_modify table 0 - -#long-range solver for TIP4P from module KSPACE works on CPU -suffix off -newton on -kspace_style pppm/tip4p 1.0e-5 -suffix on - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000921346 secs - read_data CPU = 0.0115216 secs - -pair_coeff * * 0.0 0.0 -pair_coeff 1 1 0.1852 3.1589 - -bond_coeff 1 0.0 0.9572 -angle_coeff 1 0.0 104.52 - -group water type 1 2 -4500 atoms in group water - -#maintain the water molecule rigid -fix 1 water shake 1.0e-4 200 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 water nve - -thermo 100 -thermo_style custom step etotal ke pe temp evdwl ecoul elong press -thermo_modify format float "%.15g" - -velocity water create 300 123 - -if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -if 1 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz -dump_modify 11 sort id - -timestep 1 - -run 1 -PPPM initialization ... - extracting TIP4P info from pair style - using polynomial approximation for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.342797 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00261362 - estimated relative force accuracy = 7.87083e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 79507 46656 -WARNING: Increasing communication cutoff for TIP4P GPU style (../pair_lj_cut_tip4p_long_gpu.cpp:220) -Per MPI rank memory allocation (min/avg/max) = 25.12 | 25.12 | 25.12 Mbytes -Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press - 0 -6581.10980534572 2681.834801985 -9262.94460733072 300 3652.169187345 90723.8782743551 -103638.992069031 20828.2770003278 - 1 -6293.09711304691 1787.55263217221 -8080.64974521913 199.96227554909 3652.6653755458 91910.2042281137 -103643.519348879 20986.203781307 -Loop time of 0.0230916 on 1 procs for 1 steps with 4500 atoms - -Performance: 3.742 ns/day, 6.414 hours/ns, 43.306 timesteps/s -103.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.000606 | 0.000606 | 0.000606 | 0.0 | 2.62 -Bond | 1.682e-06 | 1.682e-06 | 1.682e-06 | 0.0 | 0.01 -Kspace | 0.012588 | 0.012588 | 0.012588 | 0.0 | 54.51 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00015025 | 0.00015025 | 0.00015025 | 0.0 | 0.65 -Output | 0.0093124 | 0.0093124 | 0.0093124 | 0.0 | 40.33 -Modify | 0.00039674 | 0.00039674 | 0.00039674 | 0.0 | 1.72 -Other | | 3.623e-05 | | | 0.16 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 16834 ave 16834 max 16834 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 b/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 deleted file mode 100644 index 0ef671c603..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 +++ /dev/null @@ -1,73 +0,0 @@ -# LAMMPS data file -10 atoms -10 ellipsoids -8 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -Masses - -1 3.1575 -2 3.1575 -3 3.1575 -4 3.1575 - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 -3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 -4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 -5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 -6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1 -7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1 -8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1 -9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1 -10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1 - -# Atom-ID, translational velocity, angular momentum -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 6 7 -6 1 7 8 -7 1 8 9 -8 1 9 10 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1 deleted file mode 100644 index 42c22b9f76..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1 +++ /dev/null @@ -1,1175 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - - - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.9560004 - ghost atom cutoff = 2.5 - binsize = 0.97800022, bins = 41 41 41 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -0 ekin = 0 | erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164 -Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.883 | 7.883 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 -1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.0173888111295073 | erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136619 | erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948556079 | erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.04839505571915 | erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336920643 | erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406440561 | erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563085878 | erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398 -11000 ekin = 0.0965486715045649 | erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229 -12000 ekin = 0.10722146628289 | erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598 -13000 ekin = 0.116672809719548 | erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627 -14000 ekin = 0.12465407373104 | erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151 -15000 ekin = 0.13098393968427 | erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544 -16000 ekin = 0.135553354544872 | erot = 0.669086028489761 | epot = -15.447072628815 | etot = -14.6424332457804 -17000 ekin = 0.138326263958247 | erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935 -18000 ekin = 0.139336096664052 | erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954 -19000 ekin = 0.138678360045177 | erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878 -20000 ekin = 0.136500074655373 | erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773 -21000 ekin = 0.132987065285671 | erot = 0.864912408452581 | epot = -15.6403327194916 | etot = -14.6424332457533 -22000 ekin = 0.128350288213556 | erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311 -23000 ekin = 0.122812385135508 | erot = 0.917661024683965 | epot = -15.6829066555277 | etot = -14.6424332457083 -24000 ekin = 0.116595521408284 | erot = 0.938759014332098 | epot = -15.6977877814267 | etot = -14.6424332456863 -25000 ekin = 0.109911323474816 | erot = 0.956471207347239 | epot = -15.7088157764882 | etot = -14.6424332456662 -26000 ekin = 0.102953426207644 | erot = 0.970893163953205 | epot = -15.7162798358091 | etot = -14.6424332456483 -27000 ekin = 0.0958928250746637 | erot = 0.982114250194058 | epot = -15.7204403209013 | etot = -14.6424332456325 -28000 ekin = 0.0888759410950343 | erot = 0.990219731539854 | epot = -15.7215289182535 | etot = -14.6424332456186 -29000 ekin = 0.0820250748773376 | erot = 0.995296041202929 | epot = -15.719754361686 | etot = -14.6424332456058 -30000 ekin = 0.0754407616839748 | erot = 0.997437949320997 | epot = -15.7153119565981 | etot = -14.6424332455932 -31000 ekin = 0.0692054432610605 | erot = 0.996756332762286 | epot = -15.7083950216035 | etot = -14.6424332455802 -32000 ekin = 0.0633878377978472 | erot = 0.993385345349225 | epot = -15.699206428713 | etot = -14.6424332455659 -33000 ekin = 0.0580474070871663 | erot = 0.987487973309971 | epot = -15.6879686259471 | etot = -14.64243324555 -34000 ekin = 0.0532383791888181 | erot = 0.979259192921751 | epot = -15.6749308176426 | etot = -14.642433245532 -35000 ekin = 0.0490128758307997 | erot = 0.968926197407229 | epot = -15.66037231875 | etot = -14.642433245512 -36000 ekin = 0.0454228081410748 | erot = 0.956745409625975 | epot = -15.6446014632576 | etot = -14.6424332454906 -37000 ekin = 0.0425203357176439 | erot = 0.942996238000726 | epot = -15.6279498191869 | etot = -14.6424332454685 -38000 ekin = 0.0403568280949571 | erot = 0.927971766616668 | epot = -15.6107618401582 | etot = -14.6424332454465 -39000 ekin = 0.0389804214212713 | erot = 0.911966804110017 | epot = -15.5933804709572 | etot = -14.642433245426 -40000 ekin = 0.0384324238856427 | erot = 0.895263959562923 | epot = -15.5761296288567 | etot = -14.6424332454081 -41000 ekin = 0.0387429860408528 | erot = 0.878118672838279 | epot = -15.5592949042733 | etot = -14.6424332453942 -42000 ekin = 0.0399266053637511 | erot = 0.860744395135508 | epot = -15.5431042458848 | etot = -14.6424332453855 -43000 ekin = 0.0419781561011213 | erot = 0.843299365355989 | epot = -15.52771076684 | etot = -14.6424332453829 -44000 ekin = 0.0448701894086714 | erot = 0.82587660331255 | epot = -15.5131800381078 | etot = -14.6424332453866 -45000 ekin = 0.0485521857411517 | erot = 0.808498758184885 | epot = -15.4994841893228 | etot = -14.6424332453968 -46000 ekin = 0.0529522094031971 | erot = 0.791119212186815 | epot = -15.4865046670025 | etot = -14.6424332454125 -47000 ekin = 0.0579809824236746 | erot = 0.773630265882156 | epot = -15.4740444937379 | etot = -14.6424332454321 -48000 ekin = 0.0635377846493077 | erot = 0.755878310836116 | epot = -15.4618493409392 | etot = -14.6424332454537 -49000 ekin = 0.069516912445729 | erot = 0.737684732482671 | epot = -15.4496348904037 | etot = -14.6424332454753 -50000 ekin = 0.0758129058454751 | erot = 0.718870126218106 | epot = -15.4371162775587 | etot = -14.6424332454952 -51000 ekin = 0.0823226638641914 | erot = 0.699278599518873 | epot = -15.4240345088949 | etot = -14.6424332455118 -52000 ekin = 0.0889431481334987 | erot = 0.678798807098492 | epot = -15.4101752007567 | etot = -14.6424332455248 -53000 ekin = 0.0955646689255783 | erot = 0.657379086770007 | epot = -15.3953770012299 | etot = -14.6424332455343 -54000 ekin = 0.102061477509349 | erot = 0.635035489168657 | epot = -15.3795302122191 | etot = -14.6424332455411 -55000 ekin = 0.108282960174 | erot = 0.611853171347175 | epot = -15.362569377067 | etot = -14.6424332455459 -56000 ekin = 0.114049426281782 | erot = 0.587982945924791 | epot = -15.344465617755 | etot = -14.6424332455484 -57000 ekin = 0.119155806186855 | erot = 0.56363525592402 | epot = -15.3252243076595 | etot = -14.6424332455486 -58000 ekin = 0.123384552305435 | erot = 0.539073355224031 | epot = -15.3048911530747 | etot = -14.6424332455452 -59000 ekin = 0.126526300954941 | erot = 0.514606324860987 | epot = -15.2835658713528 | etot = -14.6424332455369 -60000 ekin = 0.128404399836503 | erot = 0.490581338842511 | epot = -15.2614189842015 | etot = -14.6424332455224 -61000 ekin = 0.128898142362337 | erot = 0.467373892403714 | epot = -15.2387052802675 | etot = -14.6424332455015 -62000 ekin = 0.127959880290302 | erot = 0.445374820089113 | epot = -15.2157679458544 | etot = -14.6424332454749 -63000 ekin = 0.125622870624954 | erot = 0.424973765390048 | epot = -15.1930298814588 | etot = -14.6424332454438 -64000 ekin = 0.121999044843202 | erot = 0.406539918574853 | epot = -15.1709722088285 | etot = -14.6424332454104 -65000 ekin = 0.117268056619303 | erot = 0.390401831022836 | epot = -15.1501031330193 | etot = -14.6424332453771 -66000 ekin = 0.111660385257243 | erot = 0.376828594081003 | epot = -15.1309222246847 | etot = -14.6424332453465 -67000 ekin = 0.105437746905135 | erot = 0.366014539812687 | epot = -15.1138855320383 | etot = -14.6424332453205 -68000 ekin = 0.0988737375607857 | erot = 0.358069014156216 | epot = -15.0993759970176 | etot = -14.6424332453006 -69000 ekin = 0.0922368286502244 | erot = 0.353011948772493 | epot = -15.0876820227105 | etot = -14.6424332452877 -70000 ekin = 0.0857769015274457 | erot = 0.350775174164874 | epot = -15.0789853209744 | etot = -14.6424332452821 -71000 ekin = 0.0797156921642124 | erot = 0.35120884424483 | epot = -15.0733577816925 | etot = -14.6424332452834 -72000 ekin = 0.0742409440406404 | erot = 0.354092037745959 | epot = -15.0707662270775 | etot = -14.6424332452909 -73000 ekin = 0.069503749870144 | erot = 0.359146526959529 | epot = -15.0710835221333 | etot = -14.6424332453037 -74000 ekin = 0.0656184497423043 | erot = 0.36605276987658 | epot = -15.0741044649392 | etot = -14.6424332453203 -75000 ekin = 0.0626644690389273 | erot = 0.37446729003154 | epot = -15.07956500441 | etot = -14.6424332453395 -76000 ekin = 0.0606895535086071 | erot = 0.384040683400773 | epot = -15.0871634822692 | etot = -14.6424332453599 -77000 ekin = 0.0597139401235039 | erot = 0.394435495890113 | epot = -15.0965826813933 | etot = -14.6424332453797 -78000 ekin = 0.0597350629869167 | erot = 0.405343151479122 | epot = -15.1075114598641 | etot = -14.6424332453981 -79000 ekin = 0.0607324264355599 | erot = 0.416499017639979 | epot = -15.1196646894891 | etot = -14.6424332454136 -80000 ekin = 0.0626722904949853 | erot = 0.427694630236173 | epot = -15.1328001661567 | etot = -14.6424332454256 -81000 ekin = 0.0655118235328824 | erot = 0.438786127846776 | epot = -15.1467311968131 | etot = -14.6424332454334 -82000 ekin = 0.0692024020835959 | erot = 0.449698113828529 | epot = -15.1613337613492 | etot = -14.6424332454371 -83000 ekin = 0.0736917936906687 | erot = 0.460422490739007 | epot = -15.1765475298665 | etot = -14.6424332454368 -84000 ekin = 0.0789250526546792 | erot = 0.471012272293637 | epot = -15.1923705703818 | etot = -14.6424332454335 -85000 ekin = 0.0848440878750104 | erot = 0.481570908649218 | epot = -15.2088482419521 | etot = -14.6424332454279 -86000 ekin = 0.0913860133254689 | erot = 0.492238169205271 | epot = -15.226057427952 | etot = -14.6424332454213 -87000 ekin = 0.0984805441200107 | erot = 0.503174014616583 | epot = -15.2440878041518 | etot = -14.6424332454152 -88000 ekin = 0.106046830304303 | erot = 0.514542076496116 | epot = -15.2630221522109 | etot = -14.6424332454105 -89000 ekin = 0.113990204127989 | erot = 0.526494309539271 | epot = -15.2829177590758 | etot = -14.6424332454086 -90000 ekin = 0.122199339151899 | erot = 0.539158097285764 | epot = -15.3037906818476 | etot = -14.64243324541 -91000 ekin = 0.130544275971407 | erot = 0.552626637865788 | epot = -15.3256041592523 | etot = -14.6424332454151 -92000 ekin = 0.138875666148818 | erot = 0.566952900962214 | epot = -15.3482618125354 | etot = -14.6424332454244 -93000 ekin = 0.147025440614644 | erot = 0.58214693373749 | epot = -15.3716056197896 | etot = -14.6424332454375 -94000 ekin = 0.154808946847823 | erot = 0.598175891801268 | epot = -15.3954180841032 | etot = -14.6424332454541 -95000 ekin = 0.162028449602152 | erot = 0.6149659424539 | epot = -15.4194276375298 | etot = -14.6424332454737 -96000 ekin = 0.168477779667818 | erot = 0.632405154082103 | epot = -15.4433161792458 | etot = -14.6424332454959 -97000 ekin = 0.173947863026719 | erot = 0.6503466316284 | epot = -15.4667277401751 | etot = -14.64243324552 -98000 ekin = 0.178232875004241 | erot = 0.668611435746027 | epot = -15.4892775562957 | etot = -14.6424332455454 -99000 ekin = 0.181136831926352 | erot = 0.686991165056287 | epot = -15.5105612425543 | etot = -14.6424332455716 -100000 ekin = 0.182480533643596 | erot = 0.705250413407857 | epot = -15.5301641926494 | etot = -14.642433245598 -101000 ekin = 0.182108871451933 | erot = 0.723129571003271 | epot = -15.5476716880789 | etot = -14.6424332456237 -102000 ekin = 0.179898581170267 | erot = 0.740348571090405 | epot = -15.5626803979087 | etot = -14.642433245648 -103000 ekin = 0.175766517608083 | erot = 0.756612167825933 | epot = -15.5748119311038 | etot = -14.6424332456698 -104000 ekin = 0.169678431535444 | erot = 0.771617166851702 | epot = -15.5837288440751 | etot = -14.6424332456879 -105000 ekin = 0.161658036036865 | erot = 0.7850617429621 | epot = -15.5891530246999 | etot = -14.642433245701 -106000 ekin = 0.151795867650478 | erot = 0.796656613424693 | epot = -15.5908857267828 | etot = -14.6424332457076 -107000 ekin = 0.140257112952728 | erot = 0.806137449197324 | epot = -15.5888278078567 | etot = -14.6424332457066 -108000 ekin = 0.127287240201243 | erot = 0.813277564481201 | epot = -15.5829980503796 | etot = -14.6424332456971 -109000 ekin = 0.113214025490919 | erot = 0.817899691734526 | epot = -15.5735469629039 | etot = -14.6424332456785 -110000 ekin = 0.0984444823805245 | erot = 0.819885578054015 | epot = -15.5607633060855 | etot = -14.642433245651 -111000 ekin = 0.0834553769364607 | erot = 0.819182262545871 | epot = -15.5450708850979 | etot = -14.6424332456156 -112000 ekin = 0.0687764915871071 | erot = 0.815804215094497 | epot = -15.5270139522555 | etot = -14.6424332455739 -113000 ekin = 0.0549665904028951 | erot = 0.809830999844525 | epot = -15.5072308357758 | etot = -14.6424332455284 -114000 ekin = 0.0425830583120669 | erot = 0.801400700351035 | epot = -15.4864170041451 | etot = -14.642433245482 -115000 ekin = 0.032147280213268 | erot = 0.790699910049129 | epot = -15.4652804357002 | etot = -14.6424332454378 -116000 ekin = 0.0241087780345819 | erot = 0.777951546674794 | epot = -15.4444935701084 | etot = -14.642433245399 -117000 ekin = 0.0188117102728978 | erot = 0.763402004774129 | epot = -15.4246469604153 | etot = -14.6424332453683 -118000 ekin = 0.0164673894159088 | erot = 0.747309167857022 | epot = -15.4062098026202 | etot = -14.6424332453473 -119000 ekin = 0.0171359296532941 | erot = 0.72993256457545 | epot = -15.3895017395656 | etot = -14.6424332453369 -120000 ekin = 0.0207190822430537 | erot = 0.711526526250299 | epot = -15.3746788538304 | etot = -14.642433245337 -121000 ekin = 0.0269649552319852 | erot = 0.692336677373468 | epot = -15.3617348779521 | etot = -14.6424332453466 -122000 ekin = 0.035483922029777 | erot = 0.67259957021413 | epot = -15.3505167376078 | etot = -14.6424332453639 -123000 ekin = 0.0457738626451396 | erot = 0.652544850165462 | epot = -15.3407519581969 | etot = -14.6424332453863 -124000 ekin = 0.0572521324296494 | erot = 0.632399068066162 | epot = -15.3320844459073 | etot = -14.6424332454115 -125000 ekin = 0.069291373600259 | erot = 0.61239015618606 | epot = -15.324114775223 | etot = -14.6424332454366 -126000 ekin = 0.0812564128172871 | erot = 0.592751635109631 | epot = -15.3164412933861 | etot = -14.6424332454592 -127000 ekin = 0.0925398817823739 | erot = 0.573725774407947 | epot = -15.3086989016674 | etot = -14.642433245477 -128000 ekin = 0.102594692018531 | erot = 0.555565138943754 | epot = -15.3005930764508 | etot = -14.6424332454885 -129000 ekin = 0.110961953873463 | erot = 0.538532171478064 | epot = -15.2919273708439 | etot = -14.6424332454924 -130000 ekin = 0.117293279472126 | erot = 0.522896664453456 | epot = -15.2826231894135 | etot = -14.6424332454879 -131000 ekin = 0.121366644774015 | erot = 0.508931150171097 | epot = -15.2727310404202 | etot = -14.6424332454751 -132000 ekin = 0.123095155538849 | erot = 0.496904390905147 | epot = -15.2624327918983 | etot = -14.6424332454543 -133000 ekin = 0.122528239670492 | erot = 0.48707328299654 | epot = -15.2520347680937 | etot = -14.6424332454267 -134000 ekin = 0.119845042600695 | erot = 0.479673601169304 | epot = -15.2419518891638 | etot = -14.6424332453938 -135000 ekin = 0.115340171966309 | erot = 0.474910093714655 | epot = -15.2326835110385 | etot = -14.6424332453575 -136000 ekin = 0.10940241928465 | erot = 0.472946484072585 | epot = -15.2247821486776 | etot = -14.6424332453204 -137000 ekin = 0.102487634021819 | erot = 0.473895929917062 | epot = -15.2188168092236 | etot = -14.6424332452848 -138000 ekin = 0.0950874634047241 | erot = 0.477812435582801 | epot = -15.2153331442408 | etot = -14.6424332452533 -139000 ekin = 0.0876961121512828 | erot = 0.484683617748065 | epot = -15.2148129751279 | etot = -14.6424332452285 -140000 ekin = 0.0807775418431644 | erot = 0.494425108537532 | epot = -15.2176358955931 | etot = -14.6424332452124 -141000 ekin = 0.0747355681577843 | erot = 0.506876770807999 | epot = -15.2240455841725 | etot = -14.6424332452067 -142000 ekin = 0.0698891098450152 | erot = 0.521800821238859 | epot = -15.2341231762965 | etot = -14.6424332452126 -143000 ekin = 0.0664544171866109 | erot = 0.538881922424141 | epot = -15.2477695848412 | etot = -14.6424332452305 -144000 ekin = 0.0645355104692138 | erot = 0.557729316020268 | epot = -15.2646980717496 | etot = -14.6424332452601 -145000 ekin = 0.0641233595162975 | erot = 0.577881111412676 | epot = -15.2844377162296 | etot = -14.6424332453007 -146000 ekin = 0.065103607751526 | erot = 0.598810893851671 | epot = -15.3063477469538 | etot = -14.6424332453506 -147000 ekin = 0.067271957897368 | erot = 0.619936843681793 | epot = -15.3296420469867 | etot = -14.6424332454076 -148000 ekin = 0.070355749269213 | erot = 0.640633538190949 | epot = -15.3534225329294 | etot = -14.6424332454693 -149000 ekin = 0.0740398128642513 | erot = 0.660246523237734 | epot = -15.3767195816347 | etot = -14.6424332455327 -150000 ekin = 0.0779944201058762 | erot = 0.678109590376207 | epot = -15.398537256077 | etot = -14.6424332455949 -151000 ekin = 0.0819030604172403 | erot = 0.693564488648145 | epot = -15.4179007947184 | etot = -14.642433245653 -152000 ekin = 0.0854878938552698 | erot = 0.705982563003937 | epot = -15.4339037025634 | etot = -14.6424332457042 -153000 ekin = 0.0885310147328597 | erot = 0.714787575382121 | epot = -15.4457518358609 | etot = -14.6424332457459 -154000 ekin = 0.090890101288761 | erot = 0.719478762727545 | epot = -15.4528021097924 | etot = -14.6424332457761 -155000 ekin = 0.0925075703714592 | erot = 0.719653046097743 | epot = -15.4545938622626 | etot = -14.6424332457934 -156000 ekin = 0.0934129479728876 | erot = 0.715025243754007 | epot = -15.4508714375239 | etot = -14.642433245797 -157000 ekin = 0.093718743577964 | erot = 0.705445163946351 | epot = -15.4415971533109 | etot = -14.6424332457866 -158000 ekin = 0.0936106185393401 | erot = 0.690910554325733 | epot = -15.4269544186277 | etot = -14.6424332457627 -159000 ekin = 0.0933330174010976 | erot = 0.67157505165981 | epot = -15.407341314787 | etot = -14.6424332457261 -160000 ekin = 0.0931716565242302 | erot = 0.647750492120669 | epot = -15.3833553943233 | etot = -14.6424332456784 -161000 ekin = 0.093434329623141 | erot = 0.619903194016607 | epot = -15.3557707692612 | etot = -14.6424332456214 -162000 ekin = 0.0944314104804151 | erot = 0.588644098979629 | epot = -15.3255087550172 | etot = -14.6424332455572 -163000 ekin = 0.0964572425739466 | erot = 0.554712943453935 | epot = -15.293603431516 | etot = -14.6424332454881 -164000 ekin = 0.0997733472806099 | erot = 0.51895691856195 | epot = -15.2611635112594 | etot = -14.6424332454168 -165000 ekin = 0.104594102019908 | erot = 0.482304549422441 | epot = -15.2293318967882 | etot = -14.6424332453459 -166000 ekin = 0.111075276516248 | erot = 0.445735768512404 | epot = -15.1992442903064 | etot = -14.6424332452778 -167000 ekin = 0.119305597513578 | erot = 0.410249354728338 | epot = -15.1719881974571 | etot = -14.6424332452152 -168000 ekin = 0.129301354725085 | erot = 0.376829046178766 | epot = -15.1485636460642 | etot = -14.6424332451603 -169000 ekin = 0.141003965789751 | erot = 0.346409702527123 | epot = -15.129846913432 | etot = -14.6424332451151 -170000 ekin = 0.154280377439944 | erot = 0.319844892417983 | epot = -15.1165585149393 | etot = -14.6424332450814 -171000 ekin = 0.168926178621547 | erot = 0.29787722160694 | epot = -15.109236645289 | etot = -14.6424332450605 -172000 ekin = 0.184671319364516 | erot = 0.281112611137265 | epot = -15.1082171755549 | etot = -14.6424332450532 -173000 ekin = 0.201188345437126 | erot = 0.269999595570288 | epot = -15.1136211860671 | etot = -14.6424332450597 -174000 ekin = 0.218103052207045 | erot = 0.264814547402998 | epot = -15.1253508446899 | etot = -14.6424332450799 -175000 ekin = 0.235007413035636 | erot = 0.265653545950127 | epot = -15.1430942040986 | etot = -14.6424332451128 -176000 ekin = 0.25147453426793 | erot = 0.272431389432275 | epot = -15.1663391688573 | etot = -14.642433245157 -177000 ekin = 0.267075225143454 | erot = 0.284887984978814 | epot = -15.1943964553329 | etot = -14.6424332452106 -178000 ekin = 0.281395553895307 | erot = 0.302602030915426 | epot = -15.2264308300819 | etot = -14.6424332452711 -179000 ekin = 0.294054514411889 | erot = 0.325011526057921 | epot = -15.2614992858055 | etot = -14.6424332453357 -180000 ekin = 0.304720692896967 | erot = 0.351440214935869 | epot = -15.2985941532343 | etot = -14.6424332454015 -181000 ekin = 0.313126658918453 | erot = 0.381128639602711 | epot = -15.3366885439866 | etot = -14.6424332454655 -182000 ekin = 0.31907977582365 | erot = 0.413268071114184 | epot = -15.374781092463 | etot = -14.6424332455251 -183000 ekin = 0.322468290005793 | erot = 0.447035301736757 | epot = -15.4119368373208 | etot = -14.6424332455782 -184000 ekin = 0.323261947554702 | erot = 0.48162615508047 | epot = -15.4473213482582 | etot = -14.6424332456231 -185000 ekin = 0.321506983530858 | erot = 0.516285658867847 | epot = -15.4802258880574 | etot = -14.6424332456587 -186000 ekin = 0.317316057633713 | erot = 0.550333132629142 | epot = -15.5100824359478 | etot = -14.642433245685 -187000 ekin = 0.310854440590115 | erot = 0.583180936761995 | epot = -15.5364686230541 | etot = -14.642433245702 -188000 ekin = 0.302324329763978 | erot = 0.614346238385449 | epot = -15.55910381386 | etot = -14.6424332457106 -189000 ekin = 0.291949445197146 | erot = 0.643455779012842 | epot = -15.5778384699217 | etot = -14.6424332457117 -190000 ekin = 0.279961942768283 | erot = 0.670244185704452 | epot = -15.5926393741794 | etot = -14.6424332457066 -191000 ekin = 0.266593185653692 | erot = 0.694546781233374 | epot = -15.6035732125832 | etot = -14.6424332456962 -192000 ekin = 0.25206914162339 | erot = 0.716288088787003 | epot = -15.6107904760917 | etot = -14.6424332456813 -193000 ekin = 0.236610293254171 | erot = 0.73546730224254 | epot = -15.6145108411597 | etot = -14.642433245663 -194000 ekin = 0.220435149405134 | erot = 0.752141943027135 | epot = -15.615010338074 | etot = -14.6424332456418 -195000 ekin = 0.203765880093363 | erot = 0.766410799029957 | epot = -15.6126099247417 | etot = -14.6424332456184 -196000 ekin = 0.186834339037387 | erot = 0.778397083250795 | epot = -15.6076646678817 | etot = -14.6424332455935 -197000 ekin = 0.169886782294202 | erot = 0.788232586070606 | epot = -15.6005526139326 | etot = -14.6424332455678 -198000 ekin = 0.153185871078003 | erot = 0.796043434538988 | epot = -15.5916625511591 | etot = -14.6424332455421 -199000 ekin = 0.137008972987419 | erot = 0.801937915798975 | epot = -15.5813801343039 | etot = -14.6424332455175 -200000 ekin = 0.121642272364818 | erot = 0.80599667326165 | epot = -15.5700721911217 | etot = -14.6424332454952 -201000 ekin = 0.107370722656495 | erot = 0.808265456806725 | epot = -15.5580694249396 | etot = -14.6424332454764 -202000 ekin = 0.0944644042392259 | erot = 0.808750524309999 | epot = -15.5456481740113 | etot = -14.642433245462 -203000 ekin = 0.0831623790894052 | erot = 0.807416772443545 | epot = -15.5330123969864 | etot = -14.6424332454535 -204000 ekin = 0.0736556272335603 | erot = 0.804188725419786 | epot = -15.5202775981049 | etot = -14.6424332454515 -205000 ekin = 0.0660710401675988 | erot = 0.798954607355857 | epot = -15.50745889298 | etot = -14.6424332454565 -206000 ekin = 0.0604586317681712 | erot = 0.791573809424193 | epot = -15.4944656866606 | etot = -14.6424332454683 -207000 ekin = 0.0567840026883055 | erot = 0.781888054798429 | epot = -15.4811053029727 | etot = -14.642433245486 -208000 ekin = 0.0549275971601587 | erot = 0.769736381379669 | epot = -15.4670972240478 | etot = -14.6424332455079 -209000 ekin = 0.0546914447538068 | erot = 0.754973659533921 | epot = -15.4520983498196 | etot = -14.6424332455319 -210000 ekin = 0.0558130126775254 | erot = 0.737491764374774 | epot = -15.4357380226072 | etot = -14.6424332455549 -211000 ekin = 0.0579847210238465 | erot = 0.717241838880044 | epot = -15.417659805478 | etot = -14.6424332455741 -212000 ekin = 0.0608768356205403 | erot = 0.694255492639204 | epot = -15.3975655738466 | etot = -14.6424332455869 -213000 ekin = 0.0641610427083153 | erot = 0.66866247616333 | epot = -15.3752567644623 | etot = -14.6424332455907 -214000 ekin = 0.0675321043587494 | erot = 0.640702495517984 | epot = -15.3506678454611 | etot = -14.6424332455844 -215000 ekin = 0.070725533636796 | erot = 0.610729417267914 | epot = -15.3238881964721 | etot = -14.6424332455674 -216000 ekin = 0.0735300437834149 | erot = 0.579207054837064 | epot = -15.2951703441606 | etot = -14.6424332455401 -217000 ekin = 0.0757943994895872 | erot = 0.54669681320896 | epot = -15.2649244582023 | etot = -14.6424332455037 -218000 ekin = 0.0774290394184588 | erot = 0.513838451215604 | epot = -15.2337007360941 | etot = -14.6424332454601 -219000 ekin = 0.0784033323162054 | erot = 0.481325894960068 | epot = -15.2021624726878 | etot = -14.6424332454115 -220000 ekin = 0.0787395495628487 | erot = 0.449880299616969 | epot = -15.17105309454 | etot = -14.6424332453602 -221000 ekin = 0.0785046319692735 | erot = 0.420222425154563 | epot = -15.1411603024324 | etot = -14.6424332453086 -222000 ekin = 0.0778006814288913 | erot = 0.393045972165166 | epot = -15.113279898853 | etot = -14.642433245259 -223000 ekin = 0.0767549035403158 | erot = 0.368992968905282 | epot = -15.0881811176588 | etot = -14.6424332452132 -224000 ekin = 0.0755095293719617 | erot = 0.348631757026545 | epot = -15.0665745315715 | etot = -14.642433245173 -225000 ekin = 0.0742120885681049 | erot = 0.332437700423087 | epot = -15.0490830341314 | etot = -14.6424332451402 -226000 ekin = 0.0730063028703793 | erot = 0.320776497496347 | epot = -15.0362160454828 | etot = -14.642433245116 -227000 ekin = 0.072023814089001 | erot = 0.313889923623746 | epot = -15.0283469828147 | etot = -14.6424332451019 -228000 ekin = 0.0713769419944288 | erot = 0.311883945242982 | epot = -15.0256941323359 | etot = -14.6424332450985 -229000 ekin = 0.0711526728859999 | erot = 0.314719386436034 | epot = -15.0283053044286 | etot = -14.6424332451066 -230000 ekin = 0.0714080974064536 | erot = 0.322205638587354 | epot = -15.0360469811206 | etot = -14.6424332451268 -231000 ekin = 0.0721675361185164 | erot = 0.333998222200299 | epot = -15.0485990034776 | etot = -14.6424332451587 -232000 ekin = 0.0734216022897964 | erot = 0.349601270465511 | epot = -15.0654561179572 | etot = -14.6424332452019 -233000 ekin = 0.0751284397495126 | erot = 0.368376135876537 | epot = -15.0859378208814 | etot = -14.6424332452553 -234000 ekin = 0.0772173235430297 | erot = 0.389557254435315 | epot = -15.1092078232955 | etot = -14.6424332453172 -235000 ekin = 0.0795947059788122 | erot = 0.412276079792818 | epot = -15.134304031156 | etot = -14.6424332453844 -236000 ekin = 0.0821526186131207 | erot = 0.435593295650776 | epot = -15.1601791597182 | etot = -14.6424332454543 -237000 ekin = 0.0847791014223481 | erot = 0.458538653868279 | epot = -15.1857510008135 | etot = -14.6424332455229 -238000 ekin = 0.0873700423841474 | erot = 0.480156759890556 | epot = -15.2099600478608 | etot = -14.6424332455861 -239000 ekin = 0.0898415153120355 | erot = 0.499556095556555 | epot = -15.2318308565087 | etot = -14.6424332456401 -240000 ekin = 0.0921414623518661 | erot = 0.515957735404873 | epot = -15.250532443438 | etot = -14.6424332456813 -241000 ekin = 0.094259449012787 | erot = 0.528739776890155 | epot = -15.2654324716098 | etot = -14.6424332457068 -242000 ekin = 0.096233280586619 | erot = 0.537473606139462 | epot = -15.276140132441 | etot = -14.6424332457149 -243000 ekin = 0.0981515319325847 | erot = 0.5419487859829 | epot = -15.2825335636204 | etot = -14.642433245705 -244000 ekin = 0.100151482350113 | erot = 0.542184479376325 | epot = -15.2847692074041 | etot = -14.6424332456777 -245000 ekin = 0.102412491094949 | erot = 0.538426702319087 | epot = -15.283272439049 | etot = -14.6424332456349 -246000 ekin = 0.10514539554429 | erot = 0.531132085867033 | epot = -15.2787107269906 | etot = -14.6424332455793 -247000 ekin = 0.108578961411818 | erot = 0.520939994206916 | epot = -15.271952201133 | etot = -14.6424332455143 -248000 ekin = 0.112944688754722 | erot = 0.50863565229477 | epot = -15.2640135864931 | etot = -14.6424332454436 -249000 ekin = 0.118461348905716 | erot = 0.495107336752456 | epot = -15.2560019310293 | etot = -14.6424332453711 -250000 ekin = 0.12532051071417 | erot = 0.481300713195499 | epot = -15.2490544692103 | etot = -14.6424332453007 -251000 ekin = 0.133674056956426 | erot = 0.468173145421963 | epot = -15.2442804476139 | etot = -14.6424332452355 -252000 ekin = 0.143624355874462 | erot = 0.456650355971893 | epot = -15.2427079570251 | etot = -14.6424332451787 -253000 ekin = 0.155217400156355 | erot = 0.447587277163441 | epot = -15.2452379224524 | etot = -14.6424332451326 -254000 ekin = 0.168438906846642 | erot = 0.441734376015304 | epot = -15.2526065279605 | etot = -14.6424332450986 -255000 ekin = 0.183213121646742 | erot = 0.439710227351497 | epot = -15.2653565940763 | etot = -14.642433245078 -256000 ekin = 0.199403908834931 | erot = 0.441980689731482 | epot = -15.283817843638 | etot = -14.6424332450716 -257000 ekin = 0.216817638464837 | erot = 0.448844730303129 | epot = -15.3080956138476 | etot = -14.6424332450796 -258000 ekin = 0.235207399038858 | erot = 0.460426746273211 | epot = -15.3380673904137 | etot = -14.6424332451016 -259000 ekin = 0.254278151369372 | erot = 0.476675120646291 | epot = -15.3733865171527 | etot = -14.642433245137 -260000 ekin = 0.273692576680298 | erot = 0.497366691704061 | epot = -15.4134925135692 | etot = -14.6424332451849 -261000 ekin = 0.293077534076616 | erot = 0.522116767902342 | epot = -15.4576275472227 | etot = -14.6424332452438 -262000 ekin = 0.312031202024067 | erot = 0.550394247117877 | epot = -15.5048586944538 | etot = -14.6424332453119 -263000 ekin = 0.330131107619695 | erot = 0.581541281995867 | epot = -15.5541056350029 | etot = -14.6424332453873 -264000 ekin = 0.346943319973868 | erot = 0.614796773442828 | epot = -15.6041733388843 | etot = -14.6424332454676 -265000 ekin = 0.362033078258367 | erot = 0.649322794992396 | epot = -15.6537891188012 | etot = -14.6424332455505 -266000 ekin = 0.374977027500513 | erot = 0.684232889055324 | epot = -15.7016431621889 | etot = -14.6424332456331 -267000 ekin = 0.385377045185317 | erot = 0.718621072058556 | epot = -15.7464313629566 | etot = -14.6424332457127 -268000 ekin = 0.392875374680224 | erot = 0.75159036946148 | epot = -15.7868989899282 | etot = -14.6424332457865 -269000 ekin = 0.397170471139203 | erot = 0.782279784271994 | epot = -15.8218835012632 | etot = -14.642433245852 -270000 ekin = 0.39803266202809 | erot = 0.80988877167351 | epot = -15.8503546796086 | etot = -14.642433245907 -271000 ekin = 0.395318487598737 | erot = 0.833698516709663 | epot = -15.8714502502579 | etot = -14.6424332459495 -272000 ekin = 0.388982474352171 | erot = 0.853089551908401 | epot = -15.8845052722386 | etot = -14.6424332459781 -273000 ekin = 0.379085147931464 | erot = 0.867555470405014 | epot = -15.8890738643282 | etot = -14.6424332459917 -274000 ekin = 0.365796322193278 | erot = 0.876712662629274 | epot = -15.8849422308128 | etot = -14.6424332459903 -275000 ekin = 0.349393082921568 | erot = 0.880306121913762 | epot = -15.8721324508092 | etot = -14.6424332459739 -276000 ekin = 0.330252358905702 | erot = 0.878211432148943 | epot = -15.8508970369982 | etot = -14.6424332459435 -277000 ekin = 0.308838461220239 | erot = 0.870433084876928 | epot = -15.8217047919976 | etot = -14.6424332459005 -278000 ekin = 0.285686394604133 | erot = 0.857099294885134 | epot = -15.7852189353358 | etot = -14.6424332458465 -279000 ekin = 0.261382042766456 | erot = 0.838453513181018 | epot = -15.7422688017312 | etot = -14.6424332457837 -280000 ekin = 0.236540473325989 | erot = 0.814842890587939 | epot = -15.6938166096284 | etot = -14.6424332457145 -281000 ekin = 0.21178360260805 | erot = 0.78670403285838 | epot = -15.6409208811075 | etot = -14.6424332456411 -282000 ekin = 0.187718337271923 | erot = 0.754546508157667 | epot = -15.5846980909958 | etot = -14.6424332455662 -283000 ekin = 0.164916115090819 | erot = 0.71893470884518 | epot = -15.5262840694281 | etot = -14.6424332454921 -284000 ekin = 0.143894549221734 | erot = 0.680468811939341 | epot = -15.4667966065823 | etot = -14.6424332454212 -285000 ekin = 0.125101678372309 | erot = 0.639765701847639 | epot = -15.4073006255757 | etot = -14.6424332453557 -286000 ekin = 0.108903164107404 | erot = 0.597440790010452 | epot = -15.3487771994147 | etot = -14.6424332452969 -287000 ekin = 0.0955726645551871 | erot = 0.554091668604971 | epot = -15.2920975784065 | etot = -14.6424332452464 -288000 ekin = 0.0852855448006991 | erot = 0.510284456822087 | epot = -15.2380032468277 | etot = -14.6424332452049 -289000 ekin = 0.0781160413102893 | erot = 0.466543535623136 | epot = -15.1870928221065 | etot = -14.6424332451731 -290000 ekin = 0.0740379578618401 | erot = 0.42334512758908 | epot = -15.1398163306018 | etot = -14.6424332451509 -291000 ekin = 0.07292891006337 | erot = 0.381114879437427 | epot = -15.0964770346384 | etot = -14.6424332451376 -292000 ekin = 0.074578035792751 | erot = 0.340229271737877 | epot = -15.0572405526631 | etot = -14.6424332451324 -293000 ekin = 0.0786969407539187 | erot = 0.301020346548478 | epot = -15.0221505324364 | etot = -14.642433245134 -294000 ekin = 0.0849334564702348 | erot = 0.263782947588673 | epot = -14.9911496491996 | etot = -14.6424332451407 -295000 ekin = 0.0928875723607527 | erot = 0.228783448806945 | epot = -14.9641042663184 | etot = -14.6424332451507 -296000 ekin = 0.10212869750719 | erot = 0.19626884038739 | epot = -14.9408307830571 | etot = -14.6424332451625 -297000 ekin = 0.112213252496714 | erot = 0.166475068218874 | epot = -14.92112156589 | etot = -14.6424332451744 -298000 ekin = 0.122701527066799 | erot = 0.139633685446924 | epot = -14.9047684576991 | etot = -14.6424332451854 -299000 ekin = 0.133172792910571 | erot = 0.115976150690183 | epot = -14.8915821887951 | etot = -14.6424332451943 -300000 ekin = 0.14323783970709 | erot = 0.0957354521215423 | epot = -14.8814065370293 | etot = -14.6424332452007 -301000 ekin = 0.152548387988443 | erot = 0.0791450908732833 | epot = -14.8741267240661 | etot = -14.6424332452044 -302000 ekin = 0.16080318429946 | erot = 0.0664357608562006 | epot = -14.8696721903613 | etot = -14.6424332452056 -303000 ekin = 0.167750948486619 | erot = 0.0578302677257533 | epot = -14.868014461417 | etot = -14.6424332452046 -304000 ekin = 0.173190665587062 | erot = 0.0535373136372916 | epot = -14.8691612244265 | etot = -14.6424332452021 -305000 ekin = 0.176969952948875 | erot = 0.053744740290904 | epot = -14.8731479384385 | etot = -14.6424332451987 -306000 ekin = 0.17898236329054 | erot = 0.0586126977876512 | epot = -14.8800283062731 | etot = -14.6424332451949 -307000 ekin = 0.179164502944013 | erot = 0.0682670321056721 | epot = -14.8898647802412 | etot = -14.6424332451915 -308000 ekin = 0.177493763288032 | erot = 0.0827930029186384 | epot = -14.9027200113955 | etot = -14.6424332451889 -309000 ekin = 0.173987301150973 | erot = 0.102229291870626 | epot = -14.9186498382088 | etot = -14.6424332451872 -310000 ekin = 0.168702678647183 | erot = 0.126562162216031 | epot = -14.9376980860501 | etot = -14.6424332451869 -311000 ekin = 0.161740297008921 | erot = 0.155719593406505 | epot = -14.9598931356033 | etot = -14.6424332451879 -312000 ekin = 0.15324744012493 | erot = 0.189565237977707 | epot = -14.985245923293 | etot = -14.6424332451904 -313000 ekin = 0.143423389996968 | erot = 0.227892126760359 | epot = -15.0137487619517 | etot = -14.6424332451944 -314000 ekin = 0.132524706018471 | erot = 0.270416174780379 | epot = -15.0453741259986 | etot = -14.6424332451997 -315000 ekin = 0.120869409552547 | erot = 0.316769708289002 | epot = -15.0800723630487 | etot = -14.6424332452072 -316000 ekin = 0.108838546104732 | erot = 0.3664954379943 | epot = -15.117767229316 | etot = -14.642433245217 -317000 ekin = 0.0968734934277273 | erot = 0.419041536809115 | epot = -15.1583482754667 | etot = -14.6424332452299 -318000 ekin = 0.0854675378549808 | erot = 0.473758725764069 | epot = -15.2016595088657 | etot = -14.6424332452466 -319000 ekin = 0.0751507271451904 | erot = 0.529900497448209 | epot = -15.2474844698619 | etot = -14.6424332452685 -320000 ekin = 0.0664678443364339 | erot = 0.586627760739843 | epot = -15.2955288503729 | etot = -14.6424332452966 -321000 ekin = 0.0599504590563242 | erot = 0.643019202691524 | epot = -15.3454029070797 | etot = -14.6424332453318 -322000 ekin = 0.0560852142799999 | erot = 0.698088453267007 | epot = -15.3966069129217 | etot = -14.6424332453747 -323000 ekin = 0.0552815181248962 | erot = 0.750808639916083 | epot = -15.4485234034659 | etot = -14.6424332454249 -324000 ekin = 0.0578423255205682 | erot = 0.800144112657402 | epot = -15.5004196836594 | etot = -14.6424332454815 -325000 ekin = 0.0639414864634509 | erot = 0.845088070114915 | epot = -15.5514628021208 | etot = -14.6424332455424 -326000 ekin = 0.0736101694210092 | erot = 0.884703689967185 | epot = -15.6007471049934 | etot = -14.6424332456052 -327000 ekin = 0.0867333560897029 | erot = 0.918165419812939 | epot = -15.6473320215696 | etot = -14.642433245667 -328000 ekin = 0.103055779603997 | erot = 0.944796600223848 | epot = -15.6902856255527 | etot = -14.6424332457249 -329000 ekin = 0.122195446170794 | erot = 0.964099781594435 | epot = -15.7287284735416 | etot = -14.6424332457764 -330000 ekin = 0.143662406710256 | erot = 0.975776996237332 | epot = -15.7618726487672 | etot = -14.6424332458196 -331000 ekin = 0.166880785133597 | erot = 0.979738667517973 | epot = -15.7890526985047 | etot = -14.6424332458531 -332000 ekin = 0.191212923969949 | erot = 0.976101405902857 | epot = -15.8097475757491 | etot = -14.6424332458763 -333000 ekin = 0.215985355319607 | erot = 0.965176233539026 | epot = -15.8235948347474 | etot = -14.6424332458887 -334000 ekin = 0.24051665683118 | erot = 0.94744948511249 | epot = -15.8303993878336 | etot = -14.64243324589 -335000 ekin = 0.264146896086271 | erot = 0.923558676868031 | epot = -15.8301388188342 | etot = -14.6424332458799 -336000 ekin = 0.286267467754269 | erot = 0.894265184760613 | epot = -15.8229658983735 | etot = -14.6424332458586 -337000 ekin = 0.306349134750126 | erot = 0.860424939336685 | epot = -15.809207319913 | etot = -14.6424332458262 -338000 ekin = 0.323965497674733 | erot = 0.822957838322781 | epot = -15.7893565817813 | etot = -14.6424332457838 -339000 ekin = 0.338809250789021 | erot = 0.782816380150505 | epot = -15.7640588766724 | etot = -14.6424332457329 -340000 ekin = 0.350699444233775 | erot = 0.74095414130314 | epot = -15.7340868312126 | etot = -14.6424332456757 -341000 ekin = 0.359579293536528 | erot = 0.698295027831883 | epot = -15.7003075669831 | etot = -14.6424332456146 -342000 ekin = 0.365505462154955 | erot = 0.655704542035024 | epot = -15.6636432497426 | etot = -14.6424332455526 -343000 ekin = 0.36863083266141 | erot = 0.613964463465585 | epot = -15.6250285416196 | etot = -14.6424332454926 -344000 ekin = 0.369183369589239 | erot = 0.57375227308083 | epot = -15.5853688881069 | etot = -14.6424332454368 -345000 ekin = 0.367443732824309 | erot = 0.535626361233186 | epot = -15.5455033394448 | etot = -14.6424332453873 -346000 ekin = 0.363723933131786 | erot = 0.500017626276236 | epot = -15.5061748047535 | etot = -14.6424332453455 -347000 ekin = 0.35834870527769 | erot = 0.4672275854273 | epot = -15.468009536017 | etot = -14.642433245312 -348000 ekin = 0.351640582954847 | erot = 0.437432666908131 | epot = -15.4315064951499 | etot = -14.6424332452869 -349000 ekin = 0.34390902469482 | erot = 0.410693986169958 | epot = -15.3970362561344 | etot = -14.6424332452696 -350000 ekin = 0.335443435968795 | erot = 0.386971649880754 | epot = -15.3648483311092 | etot = -14.6424332452597 -351000 ekin = 0.326509584093778 | erot = 0.366142474251534 | epot = -15.3350853036005 | etot = -14.6424332452552 -352000 ekin = 0.317348699022206 | erot = 0.348019930401133 | epot = -15.3078018746784 | etot = -14.642433245255 -353000 ekin = 0.308178466648759 | erot = 0.332375117501959 | epot = -15.2829868294085 | etot = -14.6424332452578 -354000 ekin = 0.299195119854398 | erot = 0.318957598139 | epot = -15.2605859632553 | etot = -14.6424332452619 -355000 ekin = 0.290575888248861 | erot = 0.307515001370351 | epot = -15.2405241348854 | etot = -14.6424332452662 -356000 ekin = 0.282481160312499 | erot = 0.297810406217201 | epot = -15.2227248117992 | etot = -14.6424332452695 -357000 ekin = 0.275055828993794 | erot = 0.289636664277844 | epot = -15.2071257385429 | etot = -14.6424332452713 -358000 ekin = 0.268429427254947 | erot = 0.282827006912201 | epot = -15.1936896794382 | etot = -14.6424332452711 -359000 ekin = 0.262714810201774 | erot = 0.277261507857975 | epot = -15.1824095633287 | etot = -14.642433245269 -360000 ekin = 0.258005302569451 | erot = 0.272869227748628 | epot = -15.1733077755836 | etot = -14.6424332452655 -361000 ekin = 0.2543704006218 | erot = 0.26962613780198 | epot = -15.1664297836851 | etot = -14.6424332452613 -362000 ekin = 0.251850290178673 | erot = 0.267549186087919 | epot = -15.1618327215239 | etot = -14.6424332452573 -363000 ekin = 0.250449609862776 | erot = 0.266687109597444 | epot = -15.159569964715 | etot = -14.6424332452548 -364000 ekin = 0.250131041863364 | erot = 0.267108788857685 | epot = -15.1596730759762 | etot = -14.6424332452551 -365000 ekin = 0.250809442162096 | erot = 0.268890073927981 | epot = -15.1621327613494 | etot = -14.6424332452593 -366000 ekin = 0.252347318763382 | erot = 0.27210007300604 | epot = -15.1668806370379 | etot = -14.6424332452684 -367000 ekin = 0.254552520178544 | erot = 0.276787886819364 | epot = -15.1737736522811 | etot = -14.6424332452832 -368000 ekin = 0.25717899615333 | erot = 0.28297069952372 | epot = -15.1825829409812 | etot = -14.6424332453042 -369000 ekin = 0.259931424908739 | erot = 0.290624011143398 | epot = -15.1929886813831 | etot = -14.642433245331 -370000 ekin = 0.262474349326661 | erot = 0.299674631814961 | epot = -15.2045822265049 | etot = -14.6424332453633 -371000 ekin = 0.264446209428328 | erot = 0.309996869297309 | epot = -15.2168763241252 | etot = -14.6424332453996 -372000 ekin = 0.265478281861457 | erot = 0.321412142686622 | epot = -15.2293236699864 | etot = -14.6424332454383 -373000 ekin = 0.265218028290062 | erot = 0.333692059448684 | epot = -15.2413433332161 | etot = -14.6424332454774 -374000 ekin = 0.263355721247738 | erot = 0.346564809671242 | epot = -15.2523537764331 | etot = -14.6424332455141 -375000 ekin = 0.259652497500791 | erot = 0.359724567998139 | epot = -15.2618103110451 | etot = -14.6424332455462 -376000 ekin = 0.253967268934329 | erot = 0.372843454384676 | epot = -15.2692439688901 | etot = -14.6424332455711 -377000 ekin = 0.246279333497668 | erot = 0.385585491299172 | epot = -15.2742980703837 | etot = -14.6424332455868 -378000 ekin = 0.236703249874173 | erot = 0.397621906702945 | epot = -15.2767584021691 | etot = -14.642433245592 -379000 ekin = 0.225492756940715 | erot = 0.40864706693682 | epot = -15.2765730694637 | etot = -14.6424332455862 -380000 ekin = 0.213031377534926 | erot = 0.418394279001937 | epot = -15.2738589021068 | etot = -14.64243324557 -381000 ekin = 0.199808877311648 | erot = 0.426650676217097 | epot = -15.2688927990735 | etot = -14.6424332455448 -382000 ekin = 0.186384809014953 | erot = 0.433270396060973 | epot = -15.2620884505889 | etot = -14.642433245513 -383000 ekin = 0.173342616140324 | erot = 0.438185279055512 | epot = -15.2539611406731 | etot = -14.6424332454773 -384000 ekin = 0.161239700828068 | erot = 0.441412371407278 | epot = -15.2450853176757 | etot = -14.6424332454403 -385000 ekin = 0.15055995464472 | erot = 0.443057612556829 | epot = -15.2360508126064 | etot = -14.6424332454049 -386000 ekin = 0.141675129696858 | erot = 0.443315241526512 | epot = -15.2274236165962 | etot = -14.6424332453728 -387000 ekin = 0.134820015696242 | erot = 0.442462667351568 | epot = -15.219715928393 | etot = -14.6424332453452 -388000 ekin = 0.130083976412365 | erot = 0.440850813515941 | epot = -15.2133680352507 | etot = -14.6424332453224 -389000 ekin = 0.127418570237209 | erot = 0.438890246280336 | epot = -15.2087420618216 | etot = -14.6424332453041 -390000 ekin = 0.126658423092949 | erot = 0.437033702086702 | epot = -15.2061253704692 | etot = -14.6424332452896 -391000 ekin = 0.127550804261054 | erot = 0.435755902066146 | epot = -15.2057399516053 | etot = -14.6424332452781 -392000 ekin = 0.129788752936042 | erot = 0.435531744058158 | epot = -15.2077537422634 | etot = -14.6424332452692 -393000 ekin = 0.133043055316548 | erot = 0.436814065077171 | epot = -15.2122903656559 | etot = -14.6424332452622 -394000 ekin = 0.13698956146631 | erot = 0.440012156509963 | epot = -15.2194349632336 | etot = -14.6424332452574 -395000 ekin = 0.141329833042578 | erot = 0.445472096884894 | epot = -15.2292351751821 | etot = -14.6424332452547 -396000 ekin = 0.145804542777388 | erot = 0.453459767648299 | epot = -15.2416975556806 | etot = -14.6424332452549 -397000 ekin = 0.150200153188693 | erot = 0.464147173461362 | epot = -15.2567805719085 | etot = -14.6424332452585 -398000 ekin = 0.154350089766171 | erot = 0.477602441558455 | epot = -15.2743857765907 | etot = -14.642433245266 -399000 ekin = 0.158131920622385 | erot = 0.493783661155615 | epot = -15.2943488270562 | etot = -14.6424332452782 -400000 ekin = 0.161462056173815 | erot = 0.512536568006289 | epot = -15.3164318694755 | etot = -14.6424332452954 -401000 ekin = 0.164289301181092 | erot = 0.533595989002424 | epot = -15.3403185355012 | etot = -14.6424332453177 -402000 ekin = 0.166588323050712 | erot = 0.556590928839782 | epot = -15.3656124972355 | etot = -14.642433245345 -403000 ekin = 0.168353810379714 | erot = 0.581053183644432 | epot = -15.3918402394011 | etot = -14.642433245377 -404000 ekin = 0.169595821301209 | erot = 0.606429376023235 | epot = -15.4184584427372 | etot = -14.6424332454128 -405000 ekin = 0.170336578562032 | erot = 0.632096292540657 | epot = -15.444866116554 | etot = -14.6424332454513 -406000 ekin = 0.170608761978825 | erot = 0.65737934451492 | epot = -15.4704213519851 | etot = -14.6424332454913 -407000 ekin = 0.170455178567339 | erot = 0.681573854094692 | epot = -15.4944622781935 | etot = -14.6424332455315 -408000 ekin = 0.169929554809768 | erot = 0.703968692151365 | epot = -15.5163314925311 | etot = -14.64243324557 -409000 ekin = 0.169098093451402 | erot = 0.723871579521667 | epot = -15.5354029185781 | etot = -14.642433245605 -410000 ekin = 0.168041369040766 | erot = 0.740635137248604 | epot = -15.5511097519242 | etot = -14.6424332456348 -411000 ekin = 0.166856102809042 | erot = 0.753682569971378 | epot = -15.5629719184381 | etot = -14.6424332456577 -412000 ekin = 0.165656359033244 | erot = 0.762531725093222 | epot = -15.5706213297988 | etot = -14.6424332456723 -413000 ekin = 0.164573741711754 | erot = 0.766816218739629 | epot = -15.5738232061291 | etot = -14.6424332456777 -414000 ekin = 0.16375624095788 | erot = 0.76630237757158 | epot = -15.5724918642026 | etot = -14.6424332456731 -415000 ekin = 0.163365479945841 | erot = 0.760900920224475 | epot = -15.5666996458289 | etot = -14.6424332456586 -416000 ekin = 0.163572240094564 | erot = 0.750672586698962 | epot = -15.556678072428 | etot = -14.6424332456344 -417000 ekin = 0.164550286199959 | erot = 0.735827297890632 | epot = -15.5428108296923 | etot = -14.6424332456017 -418000 ekin = 0.166468663393417 | erot = 0.716716857299964 | epot = -15.5256187662552 | etot = -14.6424332455618 -419000 ekin = 0.169482781127086 | erot = 0.693821649098622 | epot = -15.5057376757421 | etot = -14.6424332455164 -420000 ekin = 0.173724722667741 | erot = 0.667732191682839 | epot = -15.4838901598183 | etot = -14.6424332454677 -421000 ekin = 0.179293310761204 | erot = 0.639126725581036 | epot = -15.4608532817599 | etot = -14.6424332454176 -422000 ekin = 0.186244514521543 | erot = 0.608746211198846 | epot = -15.4374239710891 | etot = -14.6424332453687 -423000 ekin = 0.19458279814717 | erot = 0.57736816557662 | epot = -15.4143842090468 | etot = -14.642433245323 -424000 ekin = 0.204253993032132 | erot = 0.545780680985193 | epot = -15.3924679192997 | etot = -14.6424332452824 -425000 ekin = 0.215140228919715 | erot = 0.514757766830946 | epot = -15.372331240999 | etot = -14.6424332452483 -426000 ekin = 0.227057395200036 | erot = 0.485036881514114 | epot = -15.3545275219361 | etot = -14.6424332452219 -427000 ekin = 0.239755526228613 | erot = 0.45729922156058 | epot = -15.3394879929935 | etot = -14.6424332452043 -428000 ekin = 0.252922416271937 | erot = 0.432153058133966 | epot = -15.3275087196017 | etot = -14.6424332451958 -429000 ekin = 0.26619066718155 | erot = 0.410120192007268 | epot = -15.318744104385 | etot = -14.6424332451962 -430000 ekin = 0.279148248287638 | erot = 0.391625457761839 | epot = -15.313206951255 | etot = -14.6424332452055 -431000 ekin = 0.291352495295118 | erot = 0.376989149810355 | epot = -15.310774890328 | etot = -14.6424332452226 -432000 ekin = 0.302347287571226 | erot = 0.366422254466054 | epot = -15.3112027872841 | etot = -14.6424332452468 -433000 ekin = 0.311682921771869 | erot = 0.360024429012261 | epot = -15.31414059606 | etot = -14.6424332452759 -434000 ekin = 0.318937954387437 | erot = 0.357784738270616 | epot = -15.3191559379665 | etot = -14.6424332453085 -435000 ekin = 0.323742037714879 | erot = 0.359585207272693 | epot = -15.3257604903309 | etot = -14.6424332453433 -436000 ekin = 0.325798554031361 | erot = 0.365207245305615 | epot = -15.3334390447156 | etot = -14.6424332453787 -437000 ekin = 0.324905697097351 | erot = 0.3743409223498 | epot = -15.3416798648587 | etot = -14.6424332454115 -438000 ekin = 0.320974589858406 | erot = 0.386596930160279 | epot = -15.3500047654589 | etot = -14.6424332454403 -439000 ekin = 0.314043077746411 | erot = 0.401520852185304 | epot = -15.3579971753956 | etot = -14.6424332454639 -440000 ekin = 0.304283988020589 | erot = 0.418609132213777 | epot = -15.3653263657149 | etot = -14.6424332454805 -441000 ekin = 0.292006859111662 | erot = 0.43732591619283 | epot = -15.3717660207935 | etot = -14.642433245489 -442000 ekin = 0.277652365815121 | erot = 0.457119792518649 | epot = -15.3772054038233 | etot = -14.6424332454895 -443000 ekin = 0.261778853590793 | erot = 0.477439412175561 | epot = -15.3816515112488 | etot = -14.6424332454825 -444000 ekin = 0.245040553434287 | erot = 0.497747053376211 | epot = -15.3852208522799 | etot = -14.6424332454694 -445000 ekin = 0.228157260420329 | erot = 0.517529408202232 | epot = -15.3881199140743 | etot = -14.6424332454517 -446000 ekin = 0.21187568172941 | erot = 0.536305196856337 | epot = -15.3906141240179 | etot = -14.6424332454322 -447000 ekin = 0.196923472681482 | erot = 0.553629632753198 | epot = -15.3929863508487 | etot = -14.642433245414 -448000 ekin = 0.183958277880817 | erot = 0.569096233370736 | epot = -15.3954877566523 | etot = -14.6424332454007 -449000 ekin = 0.173515771313228 | erot = 0.5823369471514 | epot = -15.3982859638601 | etot = -14.6424332453955 -450000 ekin = 0.165962361199431 | erot = 0.593021970145669 | epot = -15.4014175767459 | etot = -14.6424332454008 -451000 ekin = 0.161459280835244 | erot = 0.600860851249224 | epot = -15.4047533775022 | etot = -14.6424332454178 -452000 ekin = 0.159944578253892 | erot = 0.605606408076117 | epot = -15.4079842317756 | etot = -14.6424332454456 -453000 ekin = 0.16113765311534 | erot = 0.607062496367839 | epot = -15.410633394965 | etot = -14.6424332454818 -454000 ekin = 0.164567591513356 | erot = 0.605095779305886 | epot = -15.4120966163412 | etot = -14.642433245522 -455000 ekin = 0.169622334209554 | erot = 0.599650455421075 | epot = -15.4117060351916 | etot = -14.642433245561 -456000 ekin = 0.175611802350678 | erot = 0.590763702894336 | epot = -15.4088087508385 | etot = -14.6424332455934 -457000 ekin = 0.18183562198226 | erot = 0.578578749363001 | epot = -15.40284761696 | etot = -14.6424332456148 -458000 ekin = 0.187645727030885 | erot = 0.563352302649156 | epot = -15.3934312753017 | etot = -14.6424332456216 -459000 ekin = 0.192495880384903 | erot = 0.54545371714944 | epot = -15.380382843147 | etot = -14.6424332456127 -460000 ekin = 0.195973381637231 | erot = 0.525354597711837 | epot = -15.3637612249374 | etot = -14.6424332455883 -461000 ekin = 0.19781192099122 | erot = 0.503609203464113 | epot = -15.3438543700065 | etot = -14.6424332455512 -462000 ekin = 0.197887724919132 | erot = 0.48082756028462 | epot = -15.3211485307077 | etot = -14.642433245504 -463000 ekin = 0.196203198485173 | erot = 0.457644248438995 | epot = -15.2962806923752 | etot = -14.642433245451 -464000 ekin = 0.192863034125907 | erot = 0.434686220431767 | epot = -15.2699824999538 | etot = -14.6424332453961 -465000 ekin = 0.188047435822224 | erot = 0.412542760093908 | epot = -15.2430234412587 | etot = -14.6424332453426 -466000 ekin = 0.181986107552777 | erot = 0.391740010674779 | epot = -15.2161593635208 | etot = -14.6424332452933 -467000 ekin = 0.174935400197989 | erot = 0.372721626737635 | epot = -15.1900902721858 | etot = -14.6424332452502 -468000 ekin = 0.167159826102147 | erot = 0.355836258353843 | epot = -15.1654293296706 | etot = -14.6424332452146 -469000 ekin = 0.158918218022594 | erot = 0.341331890767393 | epot = -15.142683353977 | etot = -14.642433245187 -470000 ekin = 0.15045418565321 | erot = 0.329356584635604 | epot = -15.122244015456 | etot = -14.6424332451672 -471000 ekin = 0.141990180749419 | erot = 0.319964871778363 | epot = -15.1043882976826 | etot = -14.6424332451548 -472000 ekin = 0.133724353868213 | erot = 0.313128906246296 | epot = -15.0892865052631 | etot = -14.6424332451486 -473000 ekin = 0.125829398101872 | erot = 0.30875339232503 | epot = -15.0770160355745 | etot = -14.6424332451476 -474000 ekin = 0.118452666363189 | erot = 0.306693264414343 | epot = -15.0675791759279 | etot = -14.6424332451504 -475000 ekin = 0.111716976218893 | erot = 0.306773053291024 | epot = -15.0609232746654 | etot = -14.6424332451555 -476000 ekin = 0.105721655633223 | erot = 0.308806833537924 | epot = -15.0569617343329 | etot = -14.6424332451618 -477000 ekin = 0.100543523675712 | erot = 0.312617617130677 | epot = -15.0555943859742 | etot = -14.6424332451678 -478000 ekin = 0.0962376398644513 | erot = 0.318055055635923 | epot = -15.0567259406731 | etot = -14.6424332451728 -479000 ekin = 0.0928377950023785 | erot = 0.325010357031079 | epot = -15.0602813972093 | etot = -14.6424332451759 -480000 ekin = 0.090356854634411 | erot = 0.33342742776467 | epot = -15.0662175275758 | etot = -14.6424332451768 -481000 ekin = 0.0887871989354817 | erot = 0.343309423711643 | epot = -15.0745298678222 | etot = -14.6424332451751 -482000 ekin = 0.0881016191313876 | erot = 0.354720133059481 | epot = -15.0852549973622 | etot = -14.6424332451713 -483000 ekin = 0.0882551127429665 | erot = 0.367779908275322 | epot = -15.0984682661839 | etot = -14.6424332451656 -484000 ekin = 0.0891880440123839 | erot = 0.382656193510897 | epot = -15.1142774826821 | etot = -14.6424332451588 -485000 ekin = 0.0908310739090705 | erot = 0.399549033149946 | epot = -15.1328133522104 | etot = -14.6424332451514 -486000 ekin = 0.0931120890965814 | erot = 0.418672269927034 | epot = -15.154217604168 | etot = -14.6424332451444 -487000 ekin = 0.095965052636228 | erot = 0.440231422325024 | epot = -15.1786297200999 | etot = -14.6424332451386 -488000 ekin = 0.0993402613831294 | erot = 0.46439945138847 | epot = -15.2061729579066 | etot = -14.642433245135 -489000 ekin = 0.103214957393527 | erot = 0.491291775407073 | epot = -15.2369399779351 | etot = -14.6424332451345 -490000 ekin = 0.107602676592558 | erot = 0.520941965501705 | epot = -15.2709778872323 | etot = -14.6424332451381 -491000 ekin = 0.112559247659628 | erot = 0.553279563920015 | epot = -15.3082720567265 | etot = -14.6424332451469 -492000 ekin = 0.118183136718373 | erot = 0.588111425310959 | epot = -15.3487278071917 | etot = -14.6424332451624 -493000 ekin = 0.124608040121095 | erot = 0.625107908280837 | epot = -15.392149193588 | etot = -14.642433245186 -494000 ekin = 0.131986393307407 | erot = 0.663795156036258 | epot = -15.4382147945633 | etot = -14.6424332452196 -495000 ekin = 0.140463823895335 | erot = 0.703554605722134 | epot = -15.4864516748823 | etot = -14.6424332452649 -496000 ekin = 0.150146408031538 | erot = 0.743630741562818 | epot = -15.5362103949173 | etot = -14.642433245323 -497000 ekin = 0.16106457906771 | erot = 0.783147917316484 | epot = -15.5866457417788 | etot = -14.6424332453946 -498000 ekin = 0.17313921915462 | erot = 0.821136754970969 | epot = -15.6367092196046 | etot = -14.642433245479 -499000 ekin = 0.186156317831562 | erot = 0.856570103854254 | epot = -15.6851596672598 | etot = -14.642433245574 -500000 ekin = 0.199756195068111 | erot = 0.888407758271 | epot = -15.7305971990146 | etot = -14.6424332456755 -501000 ekin = 0.213441517837515 | erot = 0.91564807872929 | epot = -15.7715228423448 | etot = -14.642433245778 -502000 ekin = 0.226605416599129 | erot = 0.937383433645168 | epot = -15.8064220961188 | etot = -14.6424332458745 -503000 ekin = 0.238577508979587 | erot = 0.952855183120512 | epot = -15.833865938058 | etot = -14.6424332459579 -504000 ekin = 0.248682347019072 | erot = 0.961503066783608 | epot = -15.852618659824 | etot = -14.6424332460214 -505000 ekin = 0.256302488972932 | erot = 0.963003656361611 | epot = -15.8617393913938 | etot = -14.6424332460593 -506000 ekin = 0.260937583147984 | erot = 0.957293217915285 | epot = -15.8606640471316 | etot = -14.6424332460684 -507000 ekin = 0.262251679303336 | erot = 0.944571918253111 | epot = -15.849256843604 | etot = -14.6424332460476 -508000 ekin = 0.260103184115659 | erot = 0.925288564928836 | epot = -15.8278249950432 | etot = -14.6424332459987 -509000 ekin = 0.254554875284732 | erot = 0.900107536932193 | epot = -15.7970956581424 | etot = -14.6424332459255 -510000 ekin = 0.245864483352383 | erot = 0.869861717979723 | epot = -15.7581594471658 | etot = -14.6424332458337 -511000 ekin = 0.234458914530911 | erot = 0.835496660120876 | epot = -15.7123888203816 | etot = -14.6424332457298 -512000 ekin = 0.220896820243761 | erot = 0.798011684060442 | epot = -15.6613417499246 | etot = -14.6424332456204 -513000 ekin = 0.205824805091364 | erot = 0.758403224573062 | epot = -15.6066612751764 | etot = -14.642433245512 -514000 ekin = 0.189932244119323 | erot = 0.717614706855288 | epot = -15.5499801963845 | etot = -14.6424332454099 -515000 ekin = 0.17390874820257 | erot = 0.676495918867881 | epot = -15.4928379123889 | etot = -14.6424332453184 -516000 ekin = 0.158407108511426 | erot = 0.635773516021008 | epot = -15.4366138697731 | etot = -14.6424332452406 -517000 ekin = 0.14401335018595 | erot = 0.596033149114218 | epot = -15.3824797444788 | etot = -14.6424332451787 -518000 ekin = 0.131224514119687 | erot = 0.557712825685522 | epot = -15.3313705849381 | etot = -14.6424332451329 -519000 ekin = 0.120434042407135 | erot = 0.521106495594791 | epot = -15.283973783105 | etot = -14.6424332451031 -520000 ekin = 0.111924165177655 | erot = 0.486376443197342 | epot = -15.2407338534629 | etot = -14.6424332450879 -521000 ekin = 0.105864424816476 | erot = 0.453572806058521 | epot = -15.2018704759605 | etot = -14.6424332450855 -522000 ekin = 0.102315362067652 | erot = 0.422658367130085 | epot = -15.1674069742913 | etot = -14.6424332450936 -523000 ekin = 0.101236366465111 | erot = 0.393536647096003 | epot = -15.1372062586706 | etot = -14.6424332451095 -524000 ekin = 0.102496717236374 | erot = 0.366081244307575 | epot = -15.1110112066745 | etot = -14.6424332451305 -525000 ekin = 0.105888887335369 | erot = 0.340164343214287 | epot = -15.0884864757035 | etot = -14.6424332451539 -526000 ekin = 0.111143247849981 | erot = 0.315682368378401 | epot = -15.069258861406 | etot = -14.6424332451776 -527000 ekin = 0.117943398961218 | erot = 0.292576937806713 | epot = -15.0529535819675 | etot = -14.6424332451996 -528000 ekin = 0.12594147425438 | erot = 0.270849598243415 | epot = -15.0392243177162 | etot = -14.6424332452184 -529000 ekin = 0.134772916008765 | erot = 0.250569317238797 | epot = -15.0277754784806 | etot = -14.642433245233 -530000 ekin = 0.144070383401974 | erot = 0.231872340651149 | epot = -15.0183759692965 | etot = -14.6424332452434 -531000 ekin = 0.15347660196879 | erot = 0.214954741433796 | epot = -15.0108645886522 | etot = -14.6424332452496 -532000 ekin = 0.162656054077 | erot = 0.200058697647209 | epot = -15.0051479969762 | etot = -14.642433245252 -533000 ekin = 0.171305419079586 | erot = 0.187454143182299 | epot = -15.0011928075133 | etot = -14.6424332452514 -534000 ekin = 0.179162595538566 | erot = 0.177417842692211 | epot = -14.9990136834797 | etot = -14.6424332452489 -535000 ekin = 0.186014006484961 | erot = 0.170212094440673 | epot = -14.9986593461708 | etot = -14.6424332452451 -536000 ekin = 0.191699759238903 | erot = 0.166065149224394 | epot = -15.0001981537044 | etot = -14.6424332452411 -537000 ekin = 0.196116169930247 | erot = 0.165155084977408 | epot = -15.003704500145 | etot = -14.6424332452374 -538000 ekin = 0.199215220532698 | erot = 0.16759836456926 | epot = -15.0092468303366 | etot = -14.6424332452346 -539000 ekin = 0.201000709668931 | erot = 0.173443713615155 | epot = -15.0168776685175 | etot = -14.6424332452334 -540000 ekin = 0.201521164037735 | erot = 0.182671367030103 | epot = -15.0266257763018 | etot = -14.642433245234 -541000 ekin = 0.200859940141597 | erot = 0.195197211440054 | epot = -15.0384903968184 | etot = -14.6424332452368 -542000 ekin = 0.199123298889485 | erot = 0.210880936221537 | epot = -15.0524374803529 | etot = -14.6424332452419 -543000 ekin = 0.196427519384797 | erot = 0.229537017788178 | epot = -15.0683977824221 | etot = -14.6424332452491 -544000 ekin = 0.192886294946265 | erot = 0.250947202002037 | epot = -15.0862667422075 | etot = -14.6424332452592 -545000 ekin = 0.188599710888657 | erot = 0.274873110236047 | epot = -15.105906066396 | etot = -14.6424332452713 -546000 ekin = 0.183646045244013 | erot = 0.301067663120938 | epot = -15.1271469536504 | etot = -14.6424332452855 -547000 ekin = 0.178077473819967 | erot = 0.329284179376605 | epot = -15.1497948984979 | etot = -14.6424332453014 -548000 ekin = 0.171920510268461 | erot = 0.359282253787744 | epot = -15.1736360093748 | etot = -14.6424332453186 -549000 ekin = 0.165181670578861 | erot = 0.390829837836081 | epot = -15.1984447537512 | etot = -14.6424332453363 -550000 ekin = 0.157858408655945 | erot = 0.423701326923182 | epot = -15.2239929809331 | etot = -14.642433245354 -551000 ekin = 0.149954809005839 | erot = 0.457671882722358 | epot = -15.2500599370991 | etot = -14.6424332453709 -552000 ekin = 0.141500835822421 | erot = 0.492508662666581 | epot = -15.2764427438753 | etot = -14.6424332453863 -553000 ekin = 0.132573145480449 | erot = 0.527960055130409 | epot = -15.3029664460102 | etot = -14.6424332453994 -554000 ekin = 0.123314645146745 | erot = 0.563744383275535 | epot = -15.3294922738321 | etot = -14.6424332454099 -555000 ekin = 0.113949270900184 | erot = 0.599539792629149 | epot = -15.3559223089468 | etot = -14.6424332454175 -556000 ekin = 0.104788088804101 | erot = 0.634977129568617 | epot = -15.3821984637955 | etot = -14.6424332454228 -557000 ekin = 0.096223065473816 | erot = 0.669637513728817 | epot = -15.4082938246293 | etot = -14.6424332454266 -558000 ekin = 0.0887059614381205 | erot = 0.703055990484285 | epot = -15.4341951973531 | etot = -14.6424332454307 -559000 ekin = 0.0827118847691962 | erot = 0.734732129427077 | epot = -15.4598772596334 | etot = -14.6424332454371 -560000 ekin = 0.0786899547209169 | erot = 0.764147748401263 | epot = -15.4852709485701 | etot = -14.6424332454479 -561000 ekin = 0.0770067720584255 | erot = 0.790791153077886 | epot = -15.5102311706012 | etot = -14.6424332454649 -562000 ekin = 0.0778911706718282 | erot = 0.814186471630634 | epot = -15.5345108877914 | etot = -14.6424332454889 -563000 ekin = 0.0813901113631115 | erot = 0.83392592548433 | epot = -15.557749282367 | etot = -14.6424332455196 -564000 ekin = 0.0873448530183196 | erot = 0.849702302566903 | epot = -15.57948040114 | etot = -14.6424332455547 -565000 ekin = 0.0953935152513145 | erot = 0.861338569498428 | epot = -15.5991653303408 | etot = -14.6424332455911 -566000 ekin = 0.105001366117329 | erot = 0.868811531658717 | epot = -15.6162461434001 | etot = -14.642433245624 -567000 ekin = 0.115514789209051 | erot = 0.872266750929858 | epot = -15.6302147857878 | etot = -14.6424332456489 -568000 ekin = 0.126230320989268 | erot = 0.872022546763063 | epot = -15.6406861134137 | etot = -14.6424332456614 -569000 ekin = 0.136467575204541 | erot = 0.868561781940356 | epot = -15.6474626028035 | etot = -14.6424332456586 -570000 ekin = 0.14563482322856 | erot = 0.862511177265558 | epot = -15.6505792461336 | etot = -14.6424332456395 -571000 ekin = 0.153278250259509 | erot = 0.854608991359196 | epot = -15.6503204872237 | etot = -14.642433245605 -572000 ekin = 0.159109636953315 | erot = 0.84566291861986 | epot = -15.6472058011309 | etot = -14.6424332455578 -573000 ekin = 0.163011362016618 | erot = 0.836500892323047 | epot = -15.6419454998422 | etot = -14.6424332455025 -574000 ekin = 0.165021239079159 | erot = 0.827918058208187 | epot = -15.635372542732 | etot = -14.6424332454446 -575000 ekin = 0.165302195907322 | erot = 0.820623479706763 | epot = -15.6283589210038 | etot = -14.6424332453898 -576000 ekin = 0.164102988099574 | erot = 0.815190165400983 | epot = -15.621726398844 | etot = -14.6424332453435 -577000 ekin = 0.161716152385172 | erot = 0.812011817945883 | epot = -15.6161612156416 | etot = -14.6424332453106 -578000 ekin = 0.158438569369477 | erot = 0.811269345695122 | epot = -15.6121411603591 | etot = -14.6424332452945 -579000 ekin = 0.154538688866709 | erot = 0.812909695780285 | epot = -15.6098816299442 | etot = -14.6424332452972 -580000 ekin = 0.150232988451571 | erot = 0.816638977240369 | epot = -15.609305211011 | etot = -14.642433245319 -581000 ekin = 0.145672809811868 | erot = 0.821931135408533 | epot = -15.6100371905791 | etot = -14.6424332453587 -582000 ekin = 0.140941476788303 | erot = 0.828052590347458 | epot = -15.6114273125488 | etot = -14.6424332454131 -583000 ekin = 0.136060602595946 | erot = 0.834102246892096 | epot = -15.6125960949662 | etot = -14.6424332454781 -584000 ekin = 0.131003759893458 | erot = 0.839065139153303 | epot = -15.6125021445952 | etot = -14.6424332455484 -585000 ekin = 0.12571521648007 | erot = 0.841876757443486 | epot = -15.6100252195418 | etot = -14.6424332456182 -586000 ekin = 0.120131224766287 | erot = 0.841493945660819 | epot = -15.6040584161085 | etot = -14.6424332456814 -587000 ekin = 0.11420138056985 | erot = 0.836967317747627 | epot = -15.5936019440499 | etot = -14.6424332457324 -588000 ekin = 0.107907808224915 | erot = 0.827509595977126 | epot = -15.5778506499685 | etot = -14.6424332457665 -589000 ekin = 0.101280337908428 | erot = 0.812554260667712 | epot = -15.5562678443564 | etot = -14.6424332457802 -590000 ekin = 0.0944063548781052 | erot = 0.791799488415071 | epot = -15.5286390890649 | etot = -14.6424332457717 -591000 ekin = 0.0874345511050671 | erot = 0.765233519218362 | epot = -15.4951013160642 | etot = -14.6424332457407 -592000 ekin = 0.0805723392089649 | erot = 0.733139214280964 | epot = -15.4561447991789 | etot = -14.642433245689 -593000 ekin = 0.0740771594091136 | erot = 0.696077455345172 | epot = -15.4125878603738 | etot = -14.6424332456195 -594000 ekin = 0.0682423089615399 | erot = 0.654850963355347 | epot = -15.3655265178539 | etot = -14.642433245537 -595000 ekin = 0.0633782539034779 | erot = 0.610451848321571 | epot = -15.3162633476718 | etot = -14.6424332454467 -596000 ekin = 0.0597906540673611 | erot = 0.563997548399802 | epot = -15.2662214478219 | etot = -14.6424332453547 -597000 ekin = 0.0577565493650921 | erot = 0.516660644083595 | epot = -15.2168504387157 | etot = -14.642433245267 -598000 ekin = 0.0575003158564784 | erot = 0.469598294353525 | epot = -15.1695318553992 | etot = -14.6424332451892 -599000 ekin = 0.0591710965315349 | erot = 0.423886769451421 | epot = -15.125491111109 | etot = -14.6424332451261 -600000 ekin = 0.0628234356919278 | erot = 0.380465849282147 | epot = -15.0857225300552 | etot = -14.6424332450811 -601000 ekin = 0.0684027903404539 | erot = 0.340096852289996 | epot = -15.0509328876871 | etot = -14.6424332450566 -602000 ekin = 0.0757374499151871 | erot = 0.303336891509908 | epot = -15.0215075864782 | etot = -14.6424332450531 -603000 ekin = 0.0845381560125591 | erot = 0.27053072625361 | epot = -14.9975021273357 | etot = -14.6424332450695 -604000 ekin = 0.0944063594091915 | erot = 0.241820347964647 | epot = -14.9786599524771 | etot = -14.6424332451032 -605000 ekin = 0.104851562461362 | erot = 0.217171224792199 | epot = -14.9644560324035 | etot = -14.64243324515 -606000 ekin = 0.115317556390045 | erot = 0.196412930357212 | epot = -14.9541637319514 | etot = -14.6424332452042 -607000 ekin = 0.125216580352904 | erot = 0.179290709848448 | epot = -14.9469405354612 | etot = -14.6424332452598 -608000 ekin = 0.133969542489652 | erot = 0.165523445158619 | epot = -14.9419262329586 | etot = -14.6424332453103 -609000 ekin = 0.141049537027137 | erot = 0.154862582265986 | epot = -14.9383453646425 | etot = -14.6424332453493 -610000 ekin = 0.146025095174201 | erot = 0.147146040889238 | epot = -14.9356043814352 | etot = -14.6424332453717 -611000 ekin = 0.148599079333767 | erot = 0.142341118194411 | epot = -14.933373442902 | etot = -14.6424332453738 -612000 ekin = 0.148639027540153 | erot = 0.140571068728021 | epot = -14.9316433416219 | etot = -14.6424332453538 -613000 ekin = 0.146195193891304 | erot = 0.142121441396014 | epot = -14.9307498805999 | etot = -14.6424332453126 -614000 ekin = 0.141503544703229 | erot = 0.147424293659367 | epot = -14.931361083616 | etot = -14.6424332452534 -615000 ekin = 0.134972482668101 | erot = 0.157020849768253 | epot = -14.9344265776178 | etot = -14.6424332451814 -616000 ekin = 0.127153892886448 | erot = 0.171505679771477 | epot = -14.9410928177618 | etot = -14.6424332451039 -617000 ekin = 0.118700960496736 | erot = 0.191457667913385 | epot = -14.9525918734389 | etot = -14.6424332450288 -618000 ekin = 0.110316794782069 | erot = 0.217364584488849 | epot = -14.9701146242352 | etot = -14.6424332449643 -619000 ekin = 0.10269894266683 | erot = 0.249548776230041 | epot = -14.9946809638151 | etot = -14.6424332449182 -620000 ekin = 0.0964852203328795 | erot = 0.288101317489107 | epot = -15.0270197827187 | etot = -14.6424332448967 -621000 ekin = 0.0922059091544532 | erot = 0.332831044362015 | epot = -15.0674701984206 | etot = -14.6424332449041 -622000 ekin = 0.0902463647123495 | erot = 0.38323345185745 | epot = -15.1159130615123 | etot = -14.6424332449425 -623000 ekin = 0.0908226920728683 | erot = 0.438482716260395 | epot = -15.1717386533448 | etot = -14.6424332450115 -624000 ekin = 0.093971606254935 | erot = 0.497448307332334 | epot = -15.2338531586955 | etot = -14.6424332451083 -625000 ekin = 0.0995541611253139 | erot = 0.558735886776706 | epot = -15.3007232931298 | etot = -14.6424332452277 -626000 ekin = 0.107271859328534 | erot = 0.620750477448395 | epot = -15.3704555821401 | etot = -14.6424332453632 -627000 ekin = 0.116692826740249 | erot = 0.681778220893157 | epot = -15.4409042931398 | etot = -14.6424332455064 -628000 ekin = 0.127285245275924 | erot = 0.740081431761873 | epot = -15.5097999226864 | etot = -14.6424332456486 -629000 ekin = 0.138455039155856 | erot = 0.794000196763613 | epot = -15.5748884817005 | etot = -14.642433245781 -630000 ekin = 0.149584842938721 | erot = 0.842052640234425 | epot = -15.6340707290684 | etot = -14.6424332458952 -631000 ekin = 0.160071499854236 | erot = 0.883025442873649 | epot = -15.6855301887126 | etot = -14.6424332459847 -632000 ekin = 0.169359720293564 | erot = 0.91604650342356 | epot = -15.7278394697617 | etot = -14.6424332460446 -633000 ekin = 0.176970053692923 | erot = 0.940632922939441 | epot = -15.7600362227046 | etot = -14.6424332460723 -634000 ekin = 0.182519961289934 | erot = 0.956709735134031 | epot = -15.7816629424917 | etot = -14.6424332460677 -635000 ekin = 0.185737466035253 | erot = 0.964597760207907 | epot = -15.7927684722764 | etot = -14.6424332460332 -636000 ekin = 0.18646751930257 | erot = 0.964972204259268 | epot = -15.793872969535 | etot = -14.6424332459731 -637000 ekin = 0.184671774603444 | erot = 0.958796660380516 | epot = -15.7859016808771 | etot = -14.6424332458931 -638000 ekin = 0.18042282577675 | erot = 0.947239527077747 | epot = -15.7700955986542 | etot = -14.6424332457997 -639000 ekin = 0.173894119063336 | erot = 0.931581224201453 | epot = -15.7479085889647 | etot = -14.6424332456999 -640000 ekin = 0.165346701826116 | erot = 0.913120838758794 | epot = -15.7209007861851 | etot = -14.6424332456002 -641000 ekin = 0.155113786101916 | erot = 0.89309006009493 | epot = -15.690637091703 | etot = -14.6424332455061 -642000 ekin = 0.143583869242389 | erot = 0.87258071031098 | epot = -15.6585978249756 | etot = -14.6424332454222 -643000 ekin = 0.131182953687747 | erot = 0.852490168058439 | epot = -15.6261063670979 | etot = -14.6424332453517 -644000 ekin = 0.118356305759423 | erot = 0.833486853993461 | epot = -15.5942764050496 | etot = -14.6424332452967 -645000 ekin = 0.105550209083462 | erot = 0.815995971214927 | epot = -15.5639794255562 | etot = -14.6424332452578 -646000 ekin = 0.0931942744180316 | erot = 0.800204061932273 | epot = -15.5358315815851 | etot = -14.6424332452348 -647000 ekin = 0.0816850001788887 | erot = 0.786079744440846 | epot = -15.5101979898461 | etot = -14.6424332452264 -648000 ekin = 0.0713713598428991 | erot = 0.773407243192036 | epot = -15.4872118482655 | etot = -14.6424332452306 -649000 ekin = 0.0625431628711377 | erot = 0.761828976528719 | epot = -15.4668053846447 | etot = -14.6424332452448 -650000 ekin = 0.0554227735500933 | erot = 0.75089345341146 | epot = -15.4487494722279 | etot = -14.6424332452664 -651000 ekin = 0.0501605027659751 | erot = 0.740104978445454 | epot = -15.4326987265037 | etot = -14.6424332452922 -652000 ekin = 0.0468336713668763 | erot = 0.728972100417424 | epot = -15.4182390171038 | etot = -14.6424332453195 -653000 ekin = 0.0454490492582802 | erot = 0.717052285941716 | epot = -15.4049345805454 | etot = -14.6424332453455 -654000 ekin = 0.0459481524955786 | erot = 0.703990869780758 | epot = -15.392372267644 | etot = -14.6424332453677 -655000 ekin = 0.0482147495301334 | erot = 0.689552835103776 | epot = -15.3802008300181 | etot = -14.6424332453842 -656000 ekin = 0.0520838761279773 | erot = 0.673646332746782 | epot = -15.3681634542682 | etot = -14.6424332453934 -657000 ekin = 0.0573516620866903 | erot = 0.656337023113106 | epot = -15.3561219305943 | etot = -14.6424332453945 -658000 ekin = 0.0637853134946501 | erot = 0.637852348217965 | epot = -15.3440709070998 | etot = -14.6424332453872 -659000 ekin = 0.071132670288702 | erot = 0.618574815847019 | epot = -15.3321407315078 | etot = -14.6424332453721 -660000 ekin = 0.0791308828115974 | erot = 0.599023454708769 | epot = -15.3205875828708 | etot = -14.6424332453504 -661000 ekin = 0.0875139366244701 | erot = 0.579822939748188 | epot = -15.3097701216973 | etot = -14.6424332453246 -662000 ekin = 0.0960190004205403 | erot = 0.561660610348952 | epot = -15.3001128560671 | etot = -14.6424332452976 -663000 ekin = 0.104391848885285 | erot = 0.545232746056431 | epot = -15.2920578402148 | etot = -14.642433245273 -664000 ekin = 0.112391863389559 | erot = 0.531182949320054 | epot = -15.2860080579644 | etot = -14.6424332452547 -665000 ekin = 0.119797262719833 | erot = 0.520037124798717 | epot = -15.2822676327648 | etot = -14.6424332452462 -666000 ekin = 0.126411190061272 | erot = 0.512141060962375 | epot = -15.2809854962742 | etot = -14.6424332452505 -667000 ekin = 0.132069035722133 | erot = 0.507607681730257 | epot = -15.2821099627219 | etot = -14.6424332452695 -668000 ekin = 0.136646914538578 | erot = 0.50628131575487 | epot = -15.2853614755967 | etot = -14.6424332453033 -669000 ekin = 0.14007061600892 | erot = 0.507725566171504 | epot = -15.290229427531 | etot = -14.6424332453506 -670000 ekin = 0.142323740902298 | erot = 0.511239425097736 | epot = -15.2959964114079 | etot = -14.6424332454078 -671000 ekin = 0.143453306298631 | erot = 0.515903234043245 | epot = -15.3017897858122 | etot = -14.6424332454703 -672000 ekin = 0.143571012728183 | erot = 0.520652256715692 | epot = -15.3066565149759 | etot = -14.642433245532 -673000 ekin = 0.142848733833163 | erot = 0.524371563353989 | epot = -15.309653542774 | etot = -14.6424332455869 -674000 ekin = 0.141507613274597 | erot = 0.526002362927265 | epot = -15.3099432218308 | etot = -14.6424332456289 -675000 ekin = 0.139801302823325 | erot = 0.52464762902093 | epot = -15.3068821774981 | etot = -14.6424332456538 -676000 ekin = 0.137995095209364 | erot = 0.51966443903789 | epot = -15.3000927799057 | etot = -14.6424332456584 -677000 ekin = 0.136343677284965 | erot = 0.510732098514629 | epot = -15.2895090214414 | etot = -14.6424332456418 -678000 ekin = 0.135070664123434 | erot = 0.497888575253593 | epot = -15.275392484982 | etot = -14.6424332456049 -679000 ekin = 0.134352810446671 | erot = 0.481532294130257 | epot = -15.2583183501274 | etot = -14.6424332455504 -680000 ekin = 0.134310862658399 | erot = 0.462390968603737 | epot = -15.2391350767444 | etot = -14.6424332454823 -681000 ekin = 0.135007638926426 | erot = 0.441462941784009 | epot = -15.2189038261157 | etot = -14.6424332454053 -682000 ekin = 0.136452461528327 | erot = 0.419938865037714 | epot = -15.1988245718906 | etot = -14.6424332453245 -683000 ekin = 0.138609887401881 | erot = 0.399112293315981 | epot = -15.180155425963 | etot = -14.6424332452451 -684000 ekin = 0.141410065652151 | erot = 0.380287181763355 | epot = -15.1641304925875 | etot = -14.642433245172 -685000 ekin = 0.144758102725857 | erot = 0.364688846300657 | epot = -15.1518801941363 | etot = -14.6424332451098 -686000 ekin = 0.148540467122566 | erot = 0.353383275615777 | epot = -15.1443569878012 | etot = -14.6424332450628 -687000 ekin = 0.152627512101214 | erot = 0.347208212231946 | epot = -15.1422689693676 | etot = -14.6424332450344 -688000 ekin = 0.156872371009962 | erot = 0.34671840827179 | epot = -15.1460240243092 | etot = -14.6424332450275 -689000 ekin = 0.161107527975645 | erot = 0.352146941115415 | epot = -15.1556877141346 | etot = -14.6424332450435 -690000 ekin = 0.165141087380615 | erot = 0.363384304941253 | epot = -15.1709586374049 | etot = -14.642433245083 -691000 ekin = 0.16875504264815 | erot = 0.379976931154794 | epot = -15.1911652189476 | etot = -14.6424332451446 -692000 ekin = 0.171707649701913 | erot = 0.401146558394978 | epot = -15.2152874533223 | etot = -14.6424332452254 -693000 ekin = 0.173741393440548 | erot = 0.425831232784737 | epot = -15.242005871546 | etot = -14.6424332453207 -694000 ekin = 0.174597110621582 | erot = 0.452747528135183 | epot = -15.2697778841809 | etot = -14.6424332454241 -695000 ekin = 0.174033757468543 | erot = 0.480471830916593 | epot = -15.2969388339132 | etot = -14.6424332455281 -696000 ekin = 0.171852263360719 | erot = 0.507536398151815 | epot = -15.3218219071368 | etot = -14.6424332456242 -697000 ekin = 0.167921065286729 | erot = 0.532533688686105 | epot = -15.3428879996772 | etot = -14.6424332457043 -698000 ekin = 0.162200409472839 | erot = 0.554220619917834 | epot = -15.3588542751518 | etot = -14.6424332457611 -699000 ekin = 0.154762415711639 | erot = 0.571613361020687 | epot = -15.368809022521 | etot = -14.6424332457887 -700000 ekin = 0.145804230005146 | erot = 0.584063387080839 | epot = -15.3723008628696 | etot = -14.6424332457836 -701000 ekin = 0.13565226955545 | erot = 0.591306922714551 | epot = -15.3693924380152 | etot = -14.6424332457452 -702000 ekin = 0.124756460204928 | erot = 0.593482464342697 | epot = -15.3606721702232 | etot = -14.6424332456756 -703000 ekin = 0.113674325949402 | erot = 0.59111440185125 | epot = -15.3472219733801 | etot = -14.6424332455794 -704000 ekin = 0.103045675944469 | erot = 0.585064323191519 | epot = -15.3305432445998 | etot = -14.6424332454638 -705000 ekin = 0.0935593581959462 | erot = 0.576454826530277 | epot = -15.3124474300635 | etot = -14.6424332453373 -706000 ekin = 0.0859140824288432 | erot = 0.566573150252908 | epot = -15.2949204778911 | etot = -14.6424332452093 -707000 ekin = 0.0807756759568232 | erot = 0.55676342760618 | epot = -15.279972348653 | etot = -14.64243324509 -708000 ekin = 0.0787333622616465 | erot = 0.54831685528832 | epot = -15.2694834625381 | etot = -14.6424332449882 -709000 ekin = 0.0802577669172614 | erot = 0.542368667951201 | epot = -15.2650596797804 | etot = -14.642433244912 -710000 ekin = 0.0856633545554371 | erot = 0.539809747046566 | epot = -15.2679063464696 | etot = -14.6424332448676 -711000 ekin = 0.0950778519056249 | erot = 0.541219180888583 | epot = -15.2787302776533 | etot = -14.642433244859 -712000 ekin = 0.108420876625254 | erot = 0.546822307908553 | epot = -15.2976764294217 | etot = -14.6424332448878 -713000 ekin = 0.125393451698048 | erot = 0.556476834654628 | epot = -15.3243035313057 | etot = -14.642433244953 -714000 ekin = 0.145479367624672 | erot = 0.569687600116107 | epot = -15.3576002127918 | etot = -14.642433245051 -715000 ekin = 0.167958541120004 | erot = 0.585648522299775 | epot = -15.396040308596 | etot = -14.6424332451762 -716000 ekin = 0.191931735854258 | erot = 0.603308292528111 | epot = -15.4376732737035 | etot = -14.6424332453212 -717000 ekin = 0.216355400179739 | erot = 0.621454592033966 | epot = -15.4802432376909 | etot = -14.6424332454772 -718000 ekin = 0.240085056513045 | erot = 0.638810139728873 | epot = -15.5213284418766 | etot = -14.6424332456347 -719000 ekin = 0.261925698577652 | erot = 0.654132895984068 | epot = -15.5584918403458 | etot = -14.6424332457841 -720000 ekin = 0.280687969313521 | erot = 0.666312379865826 | epot = -15.5894335950958 | etot = -14.6424332459165 -721000 ekin = 0.295249345590636 | erot = 0.674454385927398 | epot = -15.6121369775414 | etot = -14.6424332460234 -722000 ekin = 0.304619886334687 | erot = 0.677947410255859 | epot = -15.6250005426882 | etot = -14.6424332460976 -723000 ekin = 0.308011983728321 | erot = 0.676505724572276 | epot = -15.6269509544342 | etot = -14.6424332461336 -724000 ekin = 0.304912667284023 | erot = 0.670186105902545 | epot = -15.6175320193137 | etot = -14.6424332461272 -725000 ekin = 0.295155116710468 | erot = 0.659377522493427 | epot = -15.5969658852801 | etot = -14.6424332460762 -726000 ekin = 0.278983134898227 | erot = 0.644765363163313 | epot = -15.5661817440425 | etot = -14.6424332459809 -727000 ekin = 0.257098790791736 | erot = 0.62727386036856 | epot = -15.5268058970048 | etot = -14.6424332458445 -728000 ekin = 0.230680158271606 | erot = 0.607992016186632 | epot = -15.4811054201315 | etot = -14.6424332456733 -729000 ekin = 0.201354496272774 | erot = 0.58808946404084 | epot = -15.4318772057915 | etot = -14.6424332454779 -730000 ekin = 0.171114103975002 | erot = 0.568729214722098 | epot = -15.3822765639698 | etot = -14.6424332452727 -731000 ekin = 0.142168923907796 | erot = 0.550984135076758 | epot = -15.33558630406 | etot = -14.6424332450754 -732000 ekin = 0.116742007096204 | erot = 0.535763349049472 | epot = -15.2949386010509 | etot = -14.6424332449052 -733000 ekin = 0.096829302753487 | erot = 0.523753647326654 | epot = -15.2630161948605 | etot = -14.6424332447804 -734000 ekin = 0.0839596135584424 | erot = 0.515379592342729 | epot = -15.2417724506162 | etot = -14.642433244715 -735000 ekin = 0.0789983701762927 | erot = 0.510784464199122 | epot = -15.2322160790918 | etot = -14.6424332447164 -736000 ekin = 0.0820355551920711 | erot = 0.509832642268435 | epot = -15.2343014422439 | etot = -14.6424332447834 -737000 ekin = 0.0923827123854171 | erot = 0.512132550856583 | epot = -15.2469485081483 | etot = -14.6424332449063 -738000 ekin = 0.108680448513047 | erot = 0.517077971027771 | epot = -15.2681916646097 | etot = -14.6424332450689 -739000 ekin = 0.12909371568261 | erot = 0.523904364926295 | epot = -15.2954313258598 | etot = -14.6424332452509 -740000 ekin = 0.151555277793257 | erot = 0.531755895778738 | epot = -15.325744419004 | etot = -14.642433245432 -741000 ekin = 0.174012721805987 | erot = 0.539758083452137 | epot = -15.3562040508521 | etot = -14.642433245594 -742000 ekin = 0.194640916830775 | erot = 0.54709054969783 | epot = -15.3841647122517 | etot = -14.6424332457231 -743000 ekin = 0.211995737397994 | erot = 0.55305412533586 | epot = -15.4074831085444 | etot = -14.6424332458105 -744000 ekin = 0.225100508722061 | erot = 0.557126762308091 | epot = -15.4246605168829 | etot = -14.6424332458528 -745000 ekin = 0.233469424485911 | erot = 0.559003260237678 | epot = -15.4349059305744 | etot = -14.6424332458508 -746000 ekin = 0.237079913464194 | erot = 0.558614810498956 | epot = -15.4381279697723 | etot = -14.6424332458091 -747000 ekin = 0.236308652984083 | erot = 0.556125790082259 | epot = -15.4348676888015 | etot = -14.6424332457352 -748000 ekin = 0.231845097887127 | erot = 0.551907079329901 | epot = -15.4261854228554 | etot = -14.6424332456383 -749000 ekin = 0.224593843483487 | erot = 0.5464873600296 | epot = -15.4135144490423 | etot = -14.6424332455292 -750000 ekin = 0.215574369391546 | erot = 0.540486233484958 | epot = -15.3984938482955 | etot = -14.6424332454189 -751000 ekin = 0.20582458342619 | erot = 0.53453535676443 | epot = -15.3827931855088 | etot = -14.6424332453181 -752000 ekin = 0.196313335741677 | erot = 0.52919581521799 | epot = -15.3679423961961 | etot = -14.6424332452364 -753000 ekin = 0.187866475787172 | erot = 0.524881252730799 | epot = -15.3551809736992 | etot = -14.6424332451812 -754000 ekin = 0.181110613625732 | erot = 0.521796491095835 | epot = -15.3453403498786 | etot = -14.642433245157 -755000 ekin = 0.176438042203831 | erot = 0.519900210804112 | epot = -15.338771498173 | etot = -14.6424332451651 -756000 ekin = 0.173994962646518 | erot = 0.518897676281033 | epot = -15.3353258841305 | etot = -14.642433245203 -757000 ekin = 0.173693190270087 | erot = 0.518265706177492 | epot = -15.3343921417126 | etot = -14.642433245265 -758000 ekin = 0.175243155014324 | erot = 0.517307659815626 | epot = -15.3349840601728 | etot = -14.6424332453429 -759000 ekin = 0.178203703092592 | erot = 0.515231902157781 | epot = -15.3358688506772 | etot = -14.6424332454268 -760000 ekin = 0.182042463548471 | erot = 0.511243837941775 | epot = -15.335719546997 | etot = -14.6424332455067 -761000 ekin = 0.186199747761037 | erot = 0.504639825540337 | epot = -15.3332728188748 | etot = -14.6424332455734 -762000 ekin = 0.190149235945093 | erot = 0.494891409026847 | epot = -15.3274738905913 | etot = -14.6424332456194 -763000 ekin = 0.193449921094621 | erot = 0.481710238280717 | epot = -15.3175934050151 | etot = -14.6424332456397 -764000 ekin = 0.195785552426502 | erot = 0.465087294345954 | epot = -15.3033060924046 | etot = -14.6424332456321 -765000 ekin = 0.196989678184887 | erot = 0.445303873487528 | epot = -15.2847267972695 | etot = -14.6424332455971 -766000 ekin = 0.19705591918301 | erot = 0.42291544028873 | epot = -15.2624046050093 | etot = -14.6424332455375 -767000 ekin = 0.196134076494091 | erot = 0.398712320920873 | epot = -15.2372796428729 | etot = -14.642433245458 -768000 ekin = 0.194513096652852 | erot = 0.373662938957262 | epot = -15.2106092809747 | etot = -14.6424332453646 -769000 ekin = 0.192592017627679 | erot = 0.348845887485153 | epot = -15.1838711503774 | etot = -14.6424332452645 -770000 ekin = 0.190840163686972 | erot = 0.325376840212764 | epot = -15.1586502490652 | etot = -14.6424332451654 -771000 ekin = 0.1897483972283 | erot = 0.304335529901141 | epot = -15.1365171722047 | etot = -14.6424332450753 -772000 ekin = 0.189774341851613 | erot = 0.286697153922667 | epot = -15.1189047407758 | etot = -14.6424332450016 -773000 ekin = 0.191286034501537 | erot = 0.27327185783823 | epot = -15.1069911372904 | etot = -14.6424332449506 -774000 ekin = 0.194510000609521 | erot = 0.264655458971911 | epot = -15.1015987045092 | etot = -14.6424332449277 -775000 ekin = 0.199490639679884 | erot = 0.261194193157477 | epot = -15.1031180777726 | etot = -14.6424332449353 -776000 ekin = 0.206067477066043 | erot = 0.262965803936856 | epot = -15.1114665259764 | etot = -14.6424332449735 -777000 ekin = 0.213875019086207 | erot = 0.269778568413728 | epot = -15.1260868325396 | etot = -14.6424332450396 -778000 ekin = 0.222366868965229 | erot = 0.281188790676708 | epot = -15.1459889047703 | etot = -14.6424332451284 -779000 ekin = 0.230862102269011 | erot = 0.296535944175866 | epot = -15.1698312916772 | etot = -14.6424332452323 -780000 ekin = 0.238608567019495 | erot = 0.314993169090641 | epot = -15.1960349814528 | etot = -14.6424332453427 -781000 ekin = 0.244855557741785 | erot = 0.335629445234115 | epot = -15.2229182484261 | etot = -14.6424332454502 -782000 ekin = 0.248927612478623 | erot = 0.357478674283284 | epot = -15.2488395323078 | etot = -14.6424332455459 -783000 ekin = 0.250291897529631 | erot = 0.379610269023857 | epot = -15.2723354121756 | etot = -14.6424332456221 -784000 ekin = 0.248613283253181 | erot = 0.401195731117766 | epot = -15.2922422600437 | etot = -14.6424332456728 -785000 ekin = 0.243793133450733 | erot = 0.421566090460907 | epot = -15.3077924696054 | etot = -14.6424332456938 -786000 ekin = 0.235989501852441 | erot = 0.440255905200996 | epot = -15.3186786527368 | etot = -14.6424332456834 -787000 ekin = 0.225617610784245 | erot = 0.457030673426574 | epot = -15.3250815298531 | etot = -14.6424332456423 -788000 ekin = 0.213330260901315 | erot = 0.471895861690424 | epot = -15.3276593681654 | etot = -14.6424332455737 -789000 ekin = 0.199978499676675 | erot = 0.485087183877963 | epot = -15.3274989290377 | etot = -14.6424332454831 -790000 ekin = 0.186553834702789 | erot = 0.497043141238414 | epot = -15.326030221319 | etot = -14.6424332453778 -791000 ekin = 0.174114766792182 | erot = 0.508362048566067 | epot = -15.3249100606251 | etot = -14.6424332452668 -792000 ekin = 0.163702420431755 | erot = 0.519746739177836 | epot = -15.3258824047693 | etot = -14.6424332451597 -793000 ekin = 0.156252224966481 | erot = 0.531940822987091 | epot = -15.3306262930197 | etot = -14.6424332450661 -794000 ekin = 0.152510350035455 | erot = 0.545660777313313 | epot = -15.3406043723436 | etot = -14.6424332449949 -795000 ekin = 0.152964251159066 | erot = 0.561528326979781 | epot = -15.3569258230916 | etot = -14.6424332449528 -796000 ekin = 0.15779574735844 | erot = 0.580007578777105 | epot = -15.3802365710801 | etot = -14.6424332449446 -797000 ekin = 0.16686245785925 | erot = 0.601351255568902 | epot = -15.4106469584001 | etot = -14.6424332449719 -798000 ekin = 0.179709603433403 | erot = 0.625560121844854 | epot = -15.447702970312 | etot = -14.6424332450337 -799000 ekin = 0.19560996606243 | erot = 0.652359247175797 | epot = -15.4904024583644 | etot = -14.6424332451262 -800000 ekin = 0.213626158791752 | erot = 0.681194021872627 | epot = -15.5372534259076 | etot = -14.6424332452433 -801000 ekin = 0.232687040193831 | erot = 0.711247726385194 | epot = -15.5863680119562 | etot = -14.6424332453772 -802000 ekin = 0.251669429106228 | erot = 0.741480919834361 | epot = -15.6355835944599 | etot = -14.6424332455193 -803000 ekin = 0.269477067858276 | erot = 0.770691008419008 | epot = -15.6826013219375 | etot = -14.6424332456602 -804000 ekin = 0.285110541457411 | erot = 0.797588259155916 | epot = -15.7251320464043 | etot = -14.642433245791 -805000 ekin = 0.297723982505673 | erot = 0.820882528796815 | epot = -15.7610397572057 | etot = -14.6424332459032 -806000 ekin = 0.30666638768647 | erot = 0.839373432910558 | epot = -15.7884730665871 | etot = -14.6424332459901 -807000 ekin = 0.311506975554916 | erot = 0.852035914442971 | epot = -15.8059761360442 | etot = -14.6424332460463 -808000 ekin = 0.312045176252063 | erot = 0.858093398525486 | epot = -15.8125718208464 | etot = -14.6424332460689 -809000 ekin = 0.30830664238606 | erot = 0.857071970756237 | epot = -15.8078118591993 | etot = -14.642433246057 -810000 ekin = 0.300527220558558 | erot = 0.848831113926852 | epot = -15.7917915804976 | etot = -14.6424332460122 -811000 ekin = 0.28912720441781 | erot = 0.833569138620822 | epot = -15.7651295889765 | etot = -14.6424332459379 -812000 ekin = 0.2746784275983 | erot = 0.811804116492284 | epot = -15.7289157899297 | etot = -14.6424332458392 -813000 ekin = 0.257866835579241 | erot = 0.784333459542523 | epot = -15.684633540844 | etot = -14.6424332457223 -814000 ekin = 0.23945308058914 | erot = 0.752176980196793 | epot = -15.63406330638 | etot = -14.6424332455941 -815000 ekin = 0.220233415146368 | erot = 0.716509170267457 | epot = -15.5791758308754 | etot = -14.6424332454616 -816000 ekin = 0.20100275104127 | erot = 0.678586569749112 | epot = -15.5220225661217 | etot = -14.6424332453314 -817000 ekin = 0.182521261074943 | erot = 0.639675603866084 | epot = -15.4646301101505 | etot = -14.6424332452094 -818000 ekin = 0.165485401522765 | erot = 0.600985363832454 | epot = -15.4089040104563 | etot = -14.642433245101 -819000 ekin = 0.150503789775692 | erot = 0.563608719249991 | epot = -15.3565457540359 | etot = -14.6424332450102 -820000 ekin = 0.138078032174242 | erot = 0.528474068972577 | epot = -15.308985346087 | etot = -14.6424332449401 -821000 ekin = 0.128588386726507 | erot = 0.496309093117288 | epot = -15.2673307247366 | etot = -14.6424332448928 -822000 ekin = 0.122284066133886 | erot = 0.467617125514411 | epot = -15.2323344365174 | etot = -14.6424332448691 -823000 ekin = 0.119278020922195 | erot = 0.44266622847641 | epot = -15.2043774942678 | etot = -14.6424332448692 -824000 ekin = 0.119546158602377 | erot = 0.42149068273525 | epot = -15.1834700862294 | etot = -14.6424332448917 -825000 ekin = 0.122931110514134 | erot = 0.403904342219283 | epot = -15.1692686976682 | etot = -14.6424332449348 -826000 ekin = 0.129150803764817 | erot = 0.389525074994505 | epot = -15.1611091237546 | etot = -14.6424332449952 -827000 ekin = 0.137812176400569 | erot = 0.377809252264071 | epot = -15.158054673734 | etot = -14.6424332450694 -828000 ekin = 0.148430331610645 | erot = 0.368094906955542 | epot = -15.1589584837187 | etot = -14.6424332451525 -829000 ekin = 0.160453205764771 | erot = 0.359651737504109 | epot = -15.162538188508 | etot = -14.6424332452391 -830000 ekin = 0.173291382900576 | erot = 0.351735589536987 | epot = -15.1674602177612 | etot = -14.6424332453236 -831000 ekin = 0.186352012967387 | erot = 0.343644456321394 | epot = -15.172429714689 | etot = -14.6424332454002 -832000 ekin = 0.199074924610329 | erot = 0.334772487912646 | epot = -15.1762806579866 | etot = -14.6424332454636 -833000 ekin = 0.210968084885631 | erot = 0.324658115180747 | epot = -15.1780594455754 | etot = -14.6424332455091 -834000 ekin = 0.221638757262098 | erot = 0.313022323434907 | epot = -15.1770943262305 | etot = -14.6424332455335 -835000 ekin = 0.230816330006855 | erot = 0.299793483319955 | epot = -15.1730430588624 | etot = -14.6424332455356 -836000 ekin = 0.238363132178622 | erot = 0.285116039954994 | epot = -15.1659124176498 | etot = -14.6424332455161 -837000 ekin = 0.244270841534611 | erot = 0.269341751254713 | epot = -15.1560458382673 | etot = -14.642433245478 -838000 ekin = 0.248642320238308 | erot = 0.253003904099878 | epot = -15.144079469764 | etot = -14.6424332454258 -839000 ekin = 0.25166156932901 | erot = 0.236776758984113 | epot = -15.1308715736783 | etot = -14.6424332453652 -840000 ekin = 0.253557306828157 | erot = 0.221424057159315 | epot = -15.11741460929 | etot = -14.6424332453026 -841000 ekin = 0.254567562695185 | erot = 0.207741475742172 | epot = -15.1047422836805 | etot = -14.6424332452432 -842000 ekin = 0.254912814680605 | erot = 0.196498262353501 | epot = -15.0938443222254 | etot = -14.6424332451913 -843000 ekin = 0.254783130761291 | erot = 0.18838292178676 | epot = -15.0855992976977 | etot = -14.6424332451496 -844000 ekin = 0.254340789692194 | erot = 0.183956927272137 | epot = -15.0807309620835 | etot = -14.6424332451192 -845000 ekin = 0.253734932885203 | erot = 0.183619247980828 | epot = -15.0797874259659 | etot = -14.6424332450999 -846000 ekin = 0.253120504189253 | erot = 0.187583282240151 | epot = -15.0831370315206 | etot = -14.6424332450911 -847000 ekin = 0.25267165008145 | erot = 0.195866742639383 | epot = -15.0909716378134 | etot = -14.6424332450925 -848000 ekin = 0.252580915304042 | erot = 0.208294222463338 | epot = -15.1033083828718 | etot = -14.6424332451044 -849000 ekin = 0.25303996684305 | erot = 0.224511555531943 | epot = -15.1199847675022 | etot = -14.6424332451272 -850000 ekin = 0.254204001794731 | erot = 0.244010590097857 | epot = -15.1406478370545 | etot = -14.6424332451619 -851000 ekin = 0.256148339024686 | erot = 0.26616256360269 | epot = -15.1647441478359 | etot = -14.6424332452085 -852000 ekin = 0.258829686440298 | erot = 0.290257858698357 | epot = -15.1915207904045 | etot = -14.6424332452658 -853000 ekin = 0.262064657830092 | erot = 0.315549558168062 | epot = -15.2200474613289 | etot = -14.6424332453308 -854000 ekin = 0.265534116125796 | erot = 0.341297947737011 | epot = -15.2492653092615 | etot = -14.6424332453987 -855000 ekin = 0.268815174658096 | erot = 0.366813004431933 | epot = -15.2780614245538 | etot = -14.6424332454637 -856000 ekin = 0.271435486960135 | erot = 0.391492007902975 | epot = -15.3053607403827 | etot = -14.6424332455196 -857000 ekin = 0.272939108069148 | erot = 0.414849750475493 | epot = -15.3302221041057 | etot = -14.642433245561 -858000 ekin = 0.272951155046116 | erot = 0.43653939069067 | epot = -15.3519237913208 | etot = -14.642433245584 -859000 ekin = 0.271229880682587 | erot = 0.456362750062525 | epot = -15.3700258763315 | etot = -14.6424332455864 -860000 ekin = 0.267698633839444 | erot = 0.474269718464337 | epot = -15.3844015978728 | etot = -14.642433245569 -861000 ekin = 0.262455001757546 | erot = 0.490347316011832 | epot = -15.395235563303 | etot = -14.6424332455336 -862000 ekin = 0.255758797180207 | erot = 0.504799761303166 | epot = -15.4029918039675 | etot = -14.6424332454841 -863000 ekin = 0.248003564343611 | erot = 0.517921532816755 | epot = -15.4083583425855 | etot = -14.6424332454251 -864000 ekin = 0.23967765558561 | erot = 0.530065823507455 | epot = -15.4121767244549 | etot = -14.6424332453618 -865000 ekin = 0.23132088944464 | erot = 0.541610953537996 | epot = -15.4153650882815 | etot = -14.6424332452989 -866000 ekin = 0.223481813674061 | erot = 0.552927233335028 | epot = -15.41884229225 | etot = -14.6424332452409 -867000 ekin = 0.216679174488308 | erot = 0.564346499434596 | epot = -15.4234589191144 | etot = -14.6424332451915 -868000 ekin = 0.211369750013263 | erot = 0.576136138940125 | epot = -15.4299391341069 | etot = -14.6424332451535 -869000 ekin = 0.207923502302183 | erot = 0.588478941151671 | epot = -15.4388356885827 | etot = -14.6424332451288 -870000 ekin = 0.206606152993329 | erot = 0.601459626889461 | epot = -15.4504990250012 | etot = -14.6424332451184 -871000 ekin = 0.207568796750739 | erot = 0.615058451103504 | epot = -15.4650604929769 | etot = -14.6424332451226 -872000 ekin = 0.210843969893675 | erot = 0.629151875756264 | epot = -15.4824290907906 | etot = -14.6424332451407 -873000 ekin = 0.216347593110829 | erot = 0.643519970829237 | epot = -15.5023008091114 | etot = -14.6424332451714 -874000 ekin = 0.223886305134919 | erot = 0.657859909725313 | epot = -15.5241794600729 | etot = -14.6424332452126 -875000 ekin = 0.233169807544942 | erot = 0.671804662204777 | epot = -15.5474077150118 | etot = -14.6424332452621 -876000 ekin = 0.243827877956003 | erot = 0.684945735793168 | epot = -15.5712068590658 | etot = -14.6424332453167 -877000 ekin = 0.255431632539201 | erot = 0.696858567347312 | epot = -15.5947234452596 | etot = -14.6424332453731 -878000 ekin = 0.267518408507603 | erot = 0.707128927381253 | epot = -15.6170805813169 | etot = -14.642433245428 -879000 ekin = 0.279619300254697 | erot = 0.715378495713559 | epot = -15.6374310414462 | etot = -14.642433245478 -880000 ekin = 0.291287955017646 | erot = 0.721287639191614 | epot = -15.6550088397293 | etot = -14.64243324552 -881000 ekin = 0.30212877846337 | erot = 0.724613422803328 | epot = -15.6691754468184 | etot = -14.6424332455517 -882000 ekin = 0.31182230406922 | erot = 0.725201068169744 | epot = -15.6794566178103 | etot = -14.6424332455713 -883000 ekin = 0.32014524378975 | erot = 0.722987481097383 | epot = -15.6855659704652 | etot = -14.6424332455781 -884000 ekin = 0.326982762202525 | erot = 0.71799612015275 | epot = -15.6874121279281 | etot = -14.6424332455729 -885000 ekin = 0.332330882217529 | erot = 0.710323349666018 | epot = -15.6850874774407 | etot = -14.6424332455572 -886000 ekin = 0.336287673337269 | erot = 0.700117442970509 | epot = -15.6788383618419 | etot = -14.6424332455341 -887000 ekin = 0.339032964158867 | erot = 0.687552454431532 | epot = -15.6690186640977 | etot = -14.6424332455073 -888000 ekin = 0.340797654552277 | erot = 0.672800100940224 | epot = -15.6560310009735 | etot = -14.642433245481 -889000 ekin = 0.341825106167264 | erot = 0.656003407097172 | epot = -15.6402617587239 | etot = -14.6424332454594 -890000 ekin = 0.34232834758349 | erot = 0.637256013160967 | epot = -15.6220176061905 | etot = -14.642433245446 -891000 ekin = 0.342447730500064 | erot = 0.616590618565621 | epot = -15.6014715945091 | etot = -14.6424332454435 -892000 ekin = 0.342214057419122 | erot = 0.593979026502071 | epot = -15.5786263293741 | etot = -14.6424332454529 -893000 ekin = 0.341522004916641 | erot = 0.569344767729577 | epot = -15.55330001812 | etot = -14.6424332454737 -894000 ekin = 0.34011793412299 | erot = 0.54258751991292 | epot = -15.5251386995396 | etot = -14.6424332455037 -895000 ekin = 0.337605044786632 | erot = 0.513616778977975 | epot = -15.4936550693037 | etot = -14.6424332455391 -896000 ekin = 0.333467462875063 | erot = 0.48239077517222 | epot = -15.4582914836221 | etot = -14.6424332455748 -897000 ekin = 0.327113397523359 | erot = 0.44895570900175 | epot = -15.4185023521299 | etot = -14.6424332456048 -898000 ekin = 0.31793601762133 | erot = 0.413480165458452 | epot = -15.3738494287026 | etot = -14.6424332456228 -899000 ekin = 0.305389123796087 | erot = 0.376280077469223 | epot = -15.3241024468879 | etot = -14.6424332456226 -900000 ekin = 0.289072881395307 | erot = 0.337830752319189 | epot = -15.2693368793129 | etot = -14.6424332455984 -901000 ekin = 0.268822686259832 | erot = 0.298764046957366 | epot = -15.2100199787633 | etot = -14.6424332455461 -902000 ekin = 0.244791653969177 | erot = 0.259850521117947 | epot = -15.1470754205501 | etot = -14.642433245463 -903000 ekin = 0.217514571462771 | erot = 0.2219680472104 | epot = -15.0819158640225 | etot = -14.6424332453494 -904000 ekin = 0.187939204411673 | erot = 0.186059692012536 | epot = -15.0164321416331 | etot = -14.6424332452089 -905000 ekin = 0.157410847731541 | erot = 0.153084564883788 | epot = -14.9529286576644 | etot = -14.642433245049 -906000 ekin = 0.127599356271593 | erot = 0.123965703545267 | epot = -14.8939983046982 | etot = -14.6424332448813 -907000 ekin = 0.100365589130959 | erot = 0.0995389863896934 | epot = -14.8423378202412 | etot = -14.6424332447206 -908000 ekin = 0.0775759855948257 | erot = 0.0805066337401618 | epot = -14.800515863918 | etot = -14.642433244583 -909000 ekin = 0.060887695003573 | erot = 0.0673982354567931 | epot = -14.7707191749444 | etot = -14.642433244484 -910000 ekin = 0.051538292299 | erot = 0.0605415547707063 | epot = -14.7545130915056 | etot = -14.6424332444358 -911000 ekin = 0.0501789452911415 | erot = 0.060044698962114 | epot = -14.7526568886979 | etot = -14.6424332444447 -912000 ekin = 0.0567846925755186 | erot = 0.0657906450223113 | epot = -14.7650085821073 | etot = -14.6424332445095 -913000 ekin = 0.0706603747974273 | erot = 0.0774445361857558 | epot = -14.7905381556057 | etot = -14.6424332446226 -914000 ekin = 0.0905398584141984 | erot = 0.0944735694284727 | epot = -14.8274466726133 | etot = -14.6424332447706 -915000 ekin = 0.114756144633711 | erot = 0.116178630204803 | epot = -14.8733680197762 | etot = -14.6424332449377 -916000 ekin = 0.141447043407485 | erot = 0.141736093135474 | epot = -14.9256163816503 | etot = -14.6424332451073 -917000 ekin = 0.168758535424653 | erot = 0.170247440484187 | epot = -14.9814392211744 | etot = -14.6424332452655 -918000 ekin = 0.195014913443802 | erot = 0.200793639363233 | epot = -15.0382417982084 | etot = -14.6424332454014 -919000 ekin = 0.218837422087009 | erot = 0.232490666330172 | epot = -15.093761333925 | etot = -14.6424332455079 -920000 ekin = 0.239206641026131 | erot = 0.26454226708574 | epot = -15.1461821536939 | etot = -14.642433245582 -921000 ekin = 0.255474577150064 | erot = 0.296286050795975 | epot = -15.1941938735697 | etot = -14.6424332456236 -922000 ekin = 0.267338631216169 | erot = 0.327229363199175 | epot = -15.2370012400502 | etot = -14.6424332456349 -923000 ekin = 0.274791412213632 | erot = 0.357072039931877 | epot = -15.2742966977651 | etot = -14.6424332456196 -924000 ekin = 0.278059017514887 | erot = 0.385714059427459 | epot = -15.3062063225249 | etot = -14.6424332455826 -925000 ekin = 0.277537405166048 | erot = 0.413247220090753 | epot = -15.333217870786 | etot = -14.6424332455292 -926000 ekin = 0.273733135235252 | erot = 0.439931173657219 | epot = -15.3560975543576 | etot = -14.6424332454651 -927000 ekin = 0.267211859637779 | erot = 0.466155363878472 | epot = -15.3758004689124 | etot = -14.6424332453961 -928000 ekin = 0.25855584753175 | erot = 0.492389553499223 | epot = -15.3933786463589 | etot = -14.6424332453279 -929000 ekin = 0.248330567887068 | erot = 0.519126582978688 | epot = -15.4098903961314 | etot = -14.6424332452656 -930000 ekin = 0.237059747160937 | erot = 0.54682171162893 | epot = -15.426314704004 | etot = -14.6424332452141 -931000 ekin = 0.225208144800282 | erot = 0.575833282920741 | epot = -15.4434746728982 | etot = -14.6424332451772 -932000 ekin = 0.213171319360079 | erot = 0.606369490848937 | epot = -15.4619740553667 | etot = -14.6424332451577 -933000 ekin = 0.20127172299004 | erot = 0.63844569037598 | epot = -15.4821506585232 | etot = -14.6424332451571 -934000 ekin = 0.189760460104316 | erot = 0.671856006696139 | epot = -15.5040497119762 | etot = -14.6424332451757 -935000 ekin = 0.178823941832674 | erot = 0.70616199658427 | epot = -15.527419183629 | etot = -14.6424332452121 -936000 ekin = 0.168594479109506 | erot = 0.740699865834002 | epot = -15.5517275902073 | etot = -14.6424332452638 -937000 ekin = 0.159163635629787 | erot = 0.774606336202774 | epot = -15.5762032171595 | etot = -14.6424332453269 -938000 ekin = 0.15059697191027 | erot = 0.806861786792913 | epot = -15.5998920041001 | etot = -14.6424332453969 -939000 ekin = 0.14294871162838 | erot = 0.836347883523471 | epot = -15.6217298406203 | etot = -14.6424332454684 -940000 ekin = 0.136274889167807 | erot = 0.861915676025906 | epot = -15.6406238107299 | etot = -14.6424332455362 -941000 ekin = 0.130643703196332 | erot = 0.882459199117971 | epot = -15.6555361479093 | etot = -14.642433245595 -942000 ekin = 0.126142088158943 | erot = 0.89698906517013 | epot = -15.6655643989695 | etot = -14.6424332456404 -943000 ekin = 0.122877886109216 | erot = 0.904700444357472 | epot = -15.6700115761356 | etot = -14.6424332456689 -944000 ekin = 0.120977407411876 | erot = 0.905030230236174 | epot = -15.6684408833264 | etot = -14.6424332456784 -945000 ekin = 0.120578563691194 | erot = 0.897699054745601 | epot = -15.6607108641049 | etot = -14.6424332456681 -946000 ekin = 0.121820103594628 | erot = 0.88273507092903 | epot = -15.6469884201622 | etot = -14.6424332456386 -947000 ekin = 0.124827761130735 | erot = 0.860477935597424 | epot = -15.6277389423202 | etot = -14.642433245592 -948000 ekin = 0.129698334170688 | erot = 0.831563037039339 | epot = -15.6036946167418 | etot = -14.6424332455318 -949000 ekin = 0.136482857560386 | erot = 0.796887554723775 | epot = -15.5758036577462 | etot = -14.6424332454621 -950000 ekin = 0.145170138933456 | erot = 0.757561255989872 | epot = -15.5451646403111 | etot = -14.6424332453878 -951000 ekin = 0.155672002997282 | erot = 0.714845916095117 | epot = -15.5129511644064 | etot = -14.642433245314 -952000 ekin = 0.167811650838071 | erot = 0.67008783325117 | epot = -15.480332729335 | etot = -14.6424332452457 -953000 ekin = 0.1813165794726 | erot = 0.62464809521225 | epot = -15.4483979198723 | etot = -14.6424332451874 -954000 ekin = 0.19581750070188 | erot = 0.57983508069521 | epot = -15.4180858265396 | etot = -14.6424332451425 -955000 ekin = 0.21085460687665 | erot = 0.536843219767247 | epot = -15.3901310717574 | etot = -14.6424332451135 -956000 ekin = 0.225892299836444 | erot = 0.496701376788955 | epot = -15.3650269217267 | etot = -14.6424332451013 -957000 ekin = 0.240343066496815 | erot = 0.460233438090351 | epot = -15.3430097496926 | etot = -14.6424332451055 -958000 ekin = 0.253600493836713 | erot = 0.428032849889673 | epot = -15.3240665888504 | etot = -14.642433245124 -959000 ekin = 0.26508043374484 | erot = 0.400452005453744 | epot = -15.3079656843521 | etot = -14.6424332451535 -960000 ekin = 0.274268068126469 | erot = 0.3776065494438 | epot = -15.2943078627599 | etot = -14.6424332451896 -961000 ekin = 0.280767177999005 | erot = 0.359393861243336 | epot = -15.2825942844696 | etot = -14.6424332452273 -962000 ekin = 0.284346484058609 | erot = 0.345524198810109 | epot = -15.2723039281299 | etot = -14.6424332452611 -963000 ekin = 0.284976816085041 | erot = 0.335562232322697 | epot = -15.2629722936944 | etot = -14.6424332452867 -964000 ekin = 0.282852494243525 | erot = 0.32897598649065 | epot = -15.2542617260345 | etot = -14.6424332453003 -965000 ekin = 0.278391086611735 | erot = 0.325189577593081 | epot = -15.2460139095051 | etot = -14.6424332453002 -966000 ekin = 0.272207924676681 | erot = 0.32363564014577 | epot = -15.2382768101091 | etot = -14.6424332452866 -967000 ekin = 0.265065367869008 | erot = 0.323803079983236 | epot = -15.2313016931137 | etot = -14.6424332452614 -968000 ekin = 0.25780129371369 | erot = 0.325275872287489 | epot = -15.2255104112296 | etot = -14.6424332452284 -969000 ekin = 0.251245661475409 | erot = 0.327759142573897 | epot = -15.2214380492417 | etot = -14.6424332451924 -970000 ekin = 0.246137008995692 | erot = 0.331089781179722 | epot = -15.2196600353337 | etot = -14.6424332451582 -971000 ekin = 0.243051319619915 | erot = 0.335230325664632 | epot = -15.2207148904151 | etot = -14.6424332451306 -972000 ekin = 0.242353409643559 | erot = 0.340246678804852 | epot = -15.2250333335614 | etot = -14.642433245113 -973000 ekin = 0.244176338167963 | erot = 0.346272190711359 | epot = -15.2328817739871 | etot = -14.6424332451077 -974000 ekin = 0.248428661663719 | erot = 0.353462430362792 | epot = -15.2443243371426 | etot = -14.6424332451161 -975000 ekin = 0.254824314808527 | erot = 0.361946299431624 | epot = -15.2592038593783 | etot = -14.6424332451381 -976000 ekin = 0.262926848825399 | erot = 0.371779749930863 | epot = -15.2771398439293 | etot = -14.6424332451731 -977000 ekin = 0.272199235334822 | erot = 0.382908123264924 | epot = -15.2975406038191 | etot = -14.6424332452194 -978000 ekin = 0.282052066854486 | erot = 0.395142048097982 | epot = -15.3196273602273 | etot = -14.6424332452748 -979000 ekin = 0.291885751915432 | erot = 0.408150081471576 | epot = -15.3424690787237 | etot = -14.6424332453367 -980000 ekin = 0.301125083790032 | erot = 0.421469125222411 | epot = -15.365027454414 | etot = -14.6424332454016 -981000 ekin = 0.309246535916151 | erot = 0.434531423655712 | epot = -15.3862112050375 | etot = -14.6424332454657 -982000 ekin = 0.315799497488435 | erot = 0.446704965615556 | epot = -15.4049377086287 | etot = -14.6424332455247 -983000 ekin = 0.320422573217695 | erot = 0.457342632742344 | epot = -15.4201984515349 | etot = -14.6424332455749 -984000 ekin = 0.322855465254384 | erot = 0.465834622597573 | epot = -15.4311233334643 | etot = -14.6424332456124 -985000 ekin = 0.322946302470594 | erot = 0.471658590972097 | epot = -15.4370381390772 | etot = -14.6424332456345 -986000 ekin = 0.32065391780096 | erot = 0.47442255658858 | epot = -15.437509720029 | etot = -14.6424332456394 -987000 ekin = 0.316044627357463 | erot = 0.473896755513782 | epot = -15.432374628498 | etot = -14.6424332456268 -988000 ekin = 0.309283477264372 | erot = 0.470032116943487 | epot = -15.421748839805 | etot = -14.6424332455972 -989000 ekin = 0.300620522165357 | erot = 0.462964620620384 | epot = -15.4060183883382 | etot = -14.6424332455525 -990000 ekin = 0.290373280688083 | erot = 0.453006262993474 | epot = -15.3858127891769 | etot = -14.6424332454953 -991000 ekin = 0.27890691570339 | erot = 0.440624526217875 | epot = -15.3619646873503 | etot = -14.642433245429 -992000 ekin = 0.266613826413786 | erot = 0.426413006889876 | epot = -15.3354600786606 | etot = -14.642433245357 -993000 ekin = 0.253894212446129 | erot = 0.411056197523116 | epot = -15.3073836552521 | etot = -14.6424332452828 -994000 ekin = 0.241138837000641 | erot = 0.3952913723868 | epot = -15.2788634545973 | etot = -14.6424332452098 -995000 ekin = 0.228714768908433 | erot = 0.379870207853254 | epot = -15.2510182219026 | etot = -14.6424332451409 -996000 ekin = 0.216954417472708 | erot = 0.365522282704992 | epot = -15.2249099452563 | etot = -14.6424332450786 -997000 ekin = 0.206147766459094 | erot = 0.352922066135596 | epot = -15.2015030776196 | etot = -14.6424332450249 -998000 ekin = 0.196537413161582 | erot = 0.342660495987547 | epot = -15.1816311541306 | etot = -14.6424332449815 -999000 ekin = 0.188315843917336 | erot = 0.335221830001114 | epot = -15.1659709188676 | etot = -14.6424332449491 -1000000 ekin = 0.1816243230724 | erot = 0.33096613964385 | epot = -15.155023707645 | etot = -14.6424332449287 - 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 -Loop time of 15.696 on 1 procs for 1000000 steps with 10 atoms - -Performance: 55045.770 tau/day, 63710.382 timesteps/s -99.6% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 11.973 | 11.973 | 11.973 | 0.0 | 76.28 -Bond | 0.57492 | 0.57492 | 0.57492 | 0.0 | 3.66 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.18391 | 0.18391 | 0.18391 | 0.0 | 1.17 -Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00 -Modify | 2.7068 | 2.7068 | 2.7068 | 0.0 | 17.25 -Other | | 0.2573 | | | 1.64 - -Nlocal: 10.0 ave 10.0 max 10.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37.0 ave 37.0 max 37.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 37 -Ave neighs/atom = 3.7 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:15 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4 deleted file mode 100644 index ec5364e4bb..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4 +++ /dev/null @@ -1,1175 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - - - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.003 seconds -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.9560004 - ghost atom cutoff = 2.5 - binsize = 0.97800022, bins = 41 41 41 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -0 ekin = 0 | erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164 -Per MPI rank memory allocation (min/avg/max) = 7.605 | 7.662 | 7.719 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 -1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450840756 | erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.017388811129498 | erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136422 | erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948555727 | erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.0483950557190949 | erot = 0.185086295692109 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336919856 | erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406439518 | erot = 0.288273694501615 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563084574 | erot = 0.343654369293589 | epot = -15.0710491710418 | etot = -14.6424332454398 -11000 ekin = 0.0965486715044103 | erot = 0.400187932108393 | epot = -15.1391698491357 | etot = -14.6424332455229 -12000 ekin = 0.107221466282716 | erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598 -13000 ekin = 0.116672809719361 | erot = 0.512877765427945 | epot = -15.27198382081 | etot = -14.6424332456627 -14000 ekin = 0.124654073730849 | erot = 0.567333962045501 | epot = -15.3344212814915 | etot = -14.6424332457151 -15000 ekin = 0.130983939684084 | erot = 0.619586028257145 | epot = -15.3930032136957 | etot = -14.6424332457544 -16000 ekin = 0.135553354544703 | erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804 -17000 ekin = 0.138326263958104 | erot = 0.715418858086098 | epot = -15.4961783678378 | etot = -14.6424332457936 -18000 ekin = 0.139336096663942 | erot = 0.758296324628463 | epot = -15.5400656670878 | etot = -14.6424332457954 -19000 ekin = 0.138678360045107 | erot = 0.797544234276633 | epot = -15.5786558401095 | etot = -14.6424332457878 -20000 ekin = 0.136500074655344 | erot = 0.833084204411832 | epot = -15.6120175248401 | etot = -14.642433245773 -21000 ekin = 0.13298706528568 | erot = 0.864912408453387 | epot = -15.6403327194924 | etot = -14.6424332457533 -22000 ekin = 0.128350288213599 | erot = 0.893077649558743 | epot = -15.6638611835035 | etot = -14.6424332457311 -23000 ekin = 0.122812385135574 | erot = 0.917661024684626 | epot = -15.6829066555285 | etot = -14.6424332457083 -24000 ekin = 0.116595521408358 | erot = 0.938759014332623 | epot = -15.6977877814273 | etot = -14.6424332456863 -25000 ekin = 0.109911323474882 | erot = 0.956471207347589 | epot = -15.7088157764886 | etot = -14.6424332456661 -26000 ekin = 0.102953426207684 | erot = 0.970893163953319 | epot = -15.7162798358093 | etot = -14.6424332456483 -27000 ekin = 0.0958928250746599 | erot = 0.982114250193934 | epot = -15.7204403209012 | etot = -14.6424332456326 -28000 ekin = 0.0888759410949697 | erot = 0.990219731539457 | epot = -15.721528918253 | etot = -14.6424332456186 -29000 ekin = 0.0820250748771988 | erot = 0.995296041202221 | epot = -15.7197543616852 | etot = -14.6424332456058 -30000 ekin = 0.0754407616837521 | erot = 0.997437949319969 | epot = -15.7153119565969 | etot = -14.6424332455932 -31000 ekin = 0.0692054432607507 | erot = 0.996756332760959 | epot = -15.708395021602 | etot = -14.6424332455803 -32000 ekin = 0.0633878377974527 | erot = 0.993385345347641 | epot = -15.6992064287111 | etot = -14.642433245566 -33000 ekin = 0.0580474070866972 | erot = 0.987487973308198 | epot = -15.6879686259451 | etot = -14.6424332455502 -34000 ekin = 0.0532383791882911 | erot = 0.979259192919845 | epot = -15.6749308176403 | etot = -14.6424332455322 -35000 ekin = 0.0490128758302368 | erot = 0.968926197405304 | epot = -15.6603723187477 | etot = -14.6424332455122 -36000 ekin = 0.0454228081405029 | erot = 0.9567454096241 | epot = -15.6446014632554 | etot = -14.6424332454908 -37000 ekin = 0.0425203357170925 | erot = 0.942996237999004 | epot = -15.6279498191848 | etot = -14.6424332454687 -38000 ekin = 0.0403568280944576 | erot = 0.927971766615168 | epot = -15.6107618401563 | etot = -14.6424332454467 -39000 ekin = 0.0389804214208548 | erot = 0.911966804108811 | epot = -15.5933804709558 | etot = -14.6424332454262 -40000 ekin = 0.0384324238853382 | erot = 0.89526395956208 | epot = -15.5761296288558 | etot = -14.6424332454084 -41000 ekin = 0.038742986040685 | erot = 0.878118672837852 | epot = -15.559294904273 | etot = -14.6424332453944 -42000 ekin = 0.0399266053637394 | erot = 0.860744395135542 | epot = -15.543104245885 | etot = -14.6424332453857 -43000 ekin = 0.0419781561012778 | erot = 0.843299365356476 | epot = -15.5277107668409 | etot = -14.6424332453831 -44000 ekin = 0.044870189409001 | erot = 0.825876603313475 | epot = -15.5131800381094 | etot = -14.6424332453869 -45000 ekin = 0.0485521857416515 | erot = 0.808498758186206 | epot = -15.4994841893249 | etot = -14.642433245397 -46000 ekin = 0.0529522094038557 | erot = 0.791119212188469 | epot = -15.486504667005 | etot = -14.6424332454127 -47000 ekin = 0.0579809824244727 | erot = 0.773630265884061 | epot = -15.4740444937409 | etot = -14.6424332454323 -48000 ekin = 0.063537784650219 | erot = 0.755878310838164 | epot = -15.4618493409424 | etot = -14.642433245454 -49000 ekin = 0.0695169124467211 | erot = 0.737684732484754 | epot = -15.4496348904071 | etot = -14.6424332454756 -50000 ekin = 0.0758129058465106 | erot = 0.71887012622011 | epot = -15.437116277562 | etot = -14.6424332454954 -51000 ekin = 0.0823226638652303 | erot = 0.699278599520668 | epot = -15.424034508898 | etot = -14.6424332455121 -52000 ekin = 0.0889431481345008 | erot = 0.678798807099979 | epot = -15.4101752007595 | etot = -14.642433245525 -53000 ekin = 0.0955646689265035 | erot = 0.657379086771082 | epot = -15.3953770012322 | etot = -14.6424332455346 -54000 ekin = 0.102061477510161 | erot = 0.635035489169246 | epot = -15.3795302122208 | etot = -14.6424332455414 -55000 ekin = 0.108282960174666 | erot = 0.611853171347221 | epot = -15.362569377068 | etot = -14.6424332455461 -56000 ekin = 0.114049426282278 | erot = 0.587982945924278 | epot = -15.3444656177552 | etot = -14.6424332455487 -57000 ekin = 0.119155806187163 | erot = 0.563635255922936 | epot = -15.3252243076589 | etot = -14.6424332455488 -58000 ekin = 0.123384552305545 | erot = 0.539073355222423 | epot = -15.3048911530734 | etot = -14.6424332455455 -59000 ekin = 0.126526300954853 | erot = 0.514606324858908 | epot = -15.2835658713509 | etot = -14.6424332455371 -60000 ekin = 0.128404399836228 | erot = 0.490581338840041 | epot = -15.261418984199 | etot = -14.6424332455227 -61000 ekin = 0.128898142361895 | erot = 0.467373892400967 | epot = -15.2387052802647 | etot = -14.6424332455018 -62000 ekin = 0.127959880289724 | erot = 0.445374820086214 | epot = -15.2157679458512 | etot = -14.6424332454752 -63000 ekin = 0.125622870624276 | erot = 0.424973765387136 | epot = -15.1930298814554 | etot = -14.642433245444 -64000 ekin = 0.121999044842464 | erot = 0.406539918572064 | epot = -15.1709722088251 | etot = -14.6424332454106 -65000 ekin = 0.117268056618549 | erot = 0.390401831020304 | epot = -15.1501031330161 | etot = -14.6424332453772 -66000 ekin = 0.111660385256518 | erot = 0.376828594078844 | epot = -15.1309222246819 | etot = -14.6424332453465 -67000 ekin = 0.105437746904479 | erot = 0.366014539811003 | epot = -15.1138855320359 | etot = -14.6424332453205 -68000 ekin = 0.0988737375602367 | erot = 0.358069014155073 | epot = -15.0993759970159 | etot = -14.6424332453006 -69000 ekin = 0.0922368286498106 | erot = 0.353011948771939 | epot = -15.0876820227094 | etot = -14.6424332452876 -70000 ekin = 0.085776901527188 | erot = 0.350775174164926 | epot = -15.0789853209741 | etot = -14.642433245282 -71000 ekin = 0.0797156921641233 | erot = 0.351208844245479 | epot = -15.0733577816928 | etot = -14.6424332452832 -72000 ekin = 0.0742409440407214 | erot = 0.354092037747167 | epot = -15.0707662270785 | etot = -14.6424332452906 -73000 ekin = 0.0695037498703868 | erot = 0.359146526961236 | epot = -15.0710835221349 | etot = -14.6424332453033 -74000 ekin = 0.0656184497426901 | erot = 0.366052769878701 | epot = -15.0741044649413 | etot = -14.6424332453199 -75000 ekin = 0.0626644690394278 | erot = 0.374467290033983 | epot = -15.0795650044125 | etot = -14.642433245339 -76000 ekin = 0.060689553509186 | erot = 0.384040683403435 | epot = -15.087163482272 | etot = -14.6424332453594 -77000 ekin = 0.0597139401241187 | erot = 0.39443549589289 | epot = -15.0965826813962 | etot = -14.6424332453792 -78000 ekin = 0.0597350629875202 | erot = 0.405343151481915 | epot = -15.107511459867 | etot = -14.6424332453976 -79000 ekin = 0.0607324264361026 | erot = 0.416499017642699 | epot = -15.1196646894919 | etot = -14.6424332454131 -80000 ekin = 0.0626722904954167 | erot = 0.42769463023874 | epot = -15.1328001661592 | etot = -14.6424332454251 -81000 ekin = 0.0655118235331535 | erot = 0.438786127849123 | epot = -15.1467311968152 | etot = -14.6424332454329 -82000 ekin = 0.0692024020836612 | erot = 0.449698113830619 | epot = -15.1613337613509 | etot = -14.6424332454367 -83000 ekin = 0.0736917936904891 | erot = 0.46042249074083 | epot = -15.1765475298676 | etot = -14.6424332454363 -84000 ekin = 0.0789250526542213 | erot = 0.471012272295178 | epot = -15.1923705703823 | etot = -14.6424332454329 -85000 ekin = 0.084844087874249 | erot = 0.481570908650499 | epot = -15.2088482419521 | etot = -14.6424332454274 -86000 ekin = 0.0913860133243872 | erot = 0.492238169206333 | epot = -15.2260574279515 | etot = -14.6424332454208 -87000 ekin = 0.0984805441186009 | erot = 0.503174014617464 | epot = -15.2440878041507 | etot = -14.6424332454146 -88000 ekin = 0.106046830302566 | erot = 0.514542076496851 | epot = -15.2630221522094 | etot = -14.64243324541 -89000 ekin = 0.113990204125935 | erot = 0.526494309539917 | epot = -15.2829177590739 | etot = -14.642433245408 -90000 ekin = 0.122199339149548 | erot = 0.539158097286353 | epot = -15.3037906818453 | etot = -14.6424332454094 -91000 ekin = 0.130544275968788 | erot = 0.552626637866356 | epot = -15.3256041592498 | etot = -14.6424332454146 -92000 ekin = 0.138875666145967 | erot = 0.566952900962782 | epot = -15.3482618125326 | etot = -14.6424332454239 -93000 ekin = 0.147025440611607 | erot = 0.582146933738072 | epot = -15.3716056197866 | etot = -14.642433245437 -94000 ekin = 0.154808946844651 | erot = 0.598175891801872 | epot = -15.3954180841001 | etot = -14.6424332454536 -95000 ekin = 0.162028449598904 | erot = 0.614965942454512 | epot = -15.4194276375267 | etot = -14.6424332454733 -96000 ekin = 0.168477779664558 | erot = 0.632405154082716 | epot = -15.4433161792427 | etot = -14.6424332454954 -97000 ekin = 0.173947863023514 | erot = 0.650346631629012 | epot = -15.466727740172 | etot = -14.6424332455195 -98000 ekin = 0.17823287500116 | erot = 0.668611435746641 | epot = -15.4892775562927 | etot = -14.6424332455449 -99000 ekin = 0.181136831923464 | erot = 0.686991165056919 | epot = -15.5105612425515 | etot = -14.6424332455712 -100000 ekin = 0.182480533640968 | erot = 0.70525041340853 | epot = -15.530164192647 | etot = -14.6424332455975 -101000 ekin = 0.182108871449626 | erot = 0.723129571004015 | epot = -15.5476716880769 | etot = -14.6424332456233 -102000 ekin = 0.179898581168333 | erot = 0.740348571091266 | epot = -15.5626803979072 | etot = -14.6424332456476 -103000 ekin = 0.175766517606564 | erot = 0.756612167826943 | epot = -15.5748119311029 | etot = -14.6424332456694 -104000 ekin = 0.169678431534366 | erot = 0.771617166852901 | epot = -15.5837288440747 | etot = -14.6424332456875 -105000 ekin = 0.16165803603624 | erot = 0.785061742963522 | epot = -15.5891530247003 | etot = -14.6424332457006 -106000 ekin = 0.1517958676503 | erot = 0.79665661342635 | epot = -15.5908857267839 | etot = -14.6424332457072 -107000 ekin = 0.140257112952973 | erot = 0.806137449199221 | epot = -15.5888278078584 | etot = -14.6424332457062 -108000 ekin = 0.12728724020187 | erot = 0.813277564483295 | epot = -15.5829980503819 | etot = -14.6424332456967 -109000 ekin = 0.113214025491873 | erot = 0.817899691736779 | epot = -15.5735469629067 | etot = -14.6424332456781 -110000 ekin = 0.098444482381739 | erot = 0.81988557805637 | epot = -15.5607633060887 | etot = -14.6424332456506 -111000 ekin = 0.0834553769378614 | erot = 0.819182262548248 | epot = -15.5450708851013 | etot = -14.6424332456151 -112000 ekin = 0.0687764915886159 | erot = 0.815804215096793 | epot = -15.5270139522589 | etot = -14.6424332455735 -113000 ekin = 0.0549665904044352 | erot = 0.809830999846637 | epot = -15.5072308357791 | etot = -14.642433245528 -114000 ekin = 0.0425830583135686 | erot = 0.801400700352864 | epot = -15.486417004148 | etot = -14.6424332454816 -115000 ekin = 0.032147280214672 | erot = 0.790699910050555 | epot = -15.4652804357027 | etot = -14.6424332454374 -116000 ekin = 0.0241087780358436 | erot = 0.777951546675731 | epot = -15.4444935701102 | etot = -14.6424332453986 -117000 ekin = 0.0188117102739906 | erot = 0.763402004774535 | epot = -15.4246469604164 | etot = -14.6424332453679 -118000 ekin = 0.0164673894168239 | erot = 0.747309167856823 | epot = -15.4062098026205 | etot = -14.6424332453469 -119000 ekin = 0.0171359296540405 | erot = 0.729932564574684 | epot = -15.3895017395652 | etot = -14.6424332453365 -120000 ekin = 0.0207190822436557 | erot = 0.711526526248979 | epot = -15.3746788538292 | etot = -14.6424332453366 -121000 ekin = 0.0269649552324791 | erot = 0.692336677371669 | epot = -15.3617348779504 | etot = -14.6424332453462 -122000 ekin = 0.0354839220302067 | erot = 0.67259957021192 | epot = -15.3505167376056 | etot = -14.6424332453635 -123000 ekin = 0.0457738626455522 | erot = 0.652544850162972 | epot = -15.3407519581945 | etot = -14.642433245386 -124000 ekin = 0.0572521324300914 | erot = 0.632399068063522 | epot = -15.3320844459048 | etot = -14.6424332454111 -125000 ekin = 0.0692913736007718 | erot = 0.612390156183436 | epot = -15.3241147752205 | etot = -14.6424332454363 -126000 ekin = 0.0812564128179042 | erot = 0.592751635107165 | epot = -15.3164412933838 | etot = -14.6424332454588 -127000 ekin = 0.0925398817831167 | erot = 0.573725774405778 | epot = -15.3086989016655 | etot = -14.6424332454767 -128000 ekin = 0.102594692019408 | erot = 0.555565138942016 | epot = -15.3005930764496 | etot = -14.6424332454881 -129000 ekin = 0.11096195387447 | erot = 0.538532171476867 | epot = -15.2919273708433 | etot = -14.642433245492 -130000 ekin = 0.117293279473245 | erot = 0.522896664452867 | epot = -15.2826231894136 | etot = -14.6424332454875 -131000 ekin = 0.121366644775215 | erot = 0.508931150171148 | epot = -15.2727310404211 | etot = -14.6424332454747 -132000 ekin = 0.123095155540091 | erot = 0.496904390905846 | epot = -15.2624327918999 | etot = -14.642433245454 -133000 ekin = 0.122528239671734 | erot = 0.487073282997867 | epot = -15.2520347680959 | etot = -14.6424332454263 -134000 ekin = 0.119845042601894 | erot = 0.479673601171197 | epot = -15.2419518891665 | etot = -14.6424332453934 -135000 ekin = 0.115340171967421 | erot = 0.474910093717031 | epot = -15.2326835110416 | etot = -14.6424332453571 -136000 ekin = 0.109402419285642 | erot = 0.472946484075328 | epot = -15.224782148681 | etot = -14.64243324532 -137000 ekin = 0.102487634022665 | erot = 0.473895929920059 | epot = -15.2188168092271 | etot = -14.6424332452844 -138000 ekin = 0.0950874634054126 | erot = 0.477812435585917 | epot = -15.2153331442443 | etot = -14.6424332452529 -139000 ekin = 0.0876961121518134 | erot = 0.484683617751174 | epot = -15.2148129751312 | etot = -14.6424332452282 -140000 ekin = 0.0807775418435475 | erot = 0.494425108540512 | epot = -15.2176358955961 | etot = -14.642433245212 -141000 ekin = 0.0747355681580414 | erot = 0.506876770810756 | epot = -15.2240455841751 | etot = -14.6424332452063 -142000 ekin = 0.0698891098451744 | erot = 0.521800821241298 | epot = -15.2341231762987 | etot = -14.6424332452123 -143000 ekin = 0.0664544171867047 | erot = 0.538881922426197 | epot = -15.247769584843 | etot = -14.6424332452301 -144000 ekin = 0.0645355104692778 | erot = 0.557729316021908 | epot = -15.2646980717509 | etot = -14.6424332452598 -145000 ekin = 0.0641233595163661 | erot = 0.577881111413867 | epot = -15.2844377162306 | etot = -14.6424332453003 -146000 ekin = 0.0651036077516285 | erot = 0.598810893852426 | epot = -15.3063477469543 | etot = -14.6424332453502 -147000 ekin = 0.0672719578975283 | erot = 0.619936843682121 | epot = -15.3296420469869 | etot = -14.6424332454073 -148000 ekin = 0.0703557492694452 | erot = 0.640633538190891 | epot = -15.3534225329293 | etot = -14.6424332454689 -149000 ekin = 0.0740398128645613 | erot = 0.66024652323733 | epot = -15.3767195816343 | etot = -14.6424332455324 -150000 ekin = 0.077994420106261 | erot = 0.678109590375523 | epot = -15.3985372560764 | etot = -14.6424332455946 -151000 ekin = 0.0819030604176878 | erot = 0.693564488647254 | epot = -15.4179007947176 | etot = -14.6424332456527 -152000 ekin = 0.08548789385576 | erot = 0.705982563002905 | epot = -15.4339037025625 | etot = -14.6424332457038 -153000 ekin = 0.0885310147333655 | erot = 0.714787575381006 | epot = -15.4457518358599 | etot = -14.6424332457455 -154000 ekin = 0.0908901012892495 | erot = 0.719478762726426 | epot = -15.4528021097914 | etot = -14.6424332457757 -155000 ekin = 0.0925075703718949 | erot = 0.719653046096655 | epot = -15.4545938622616 | etot = -14.642433245793 -156000 ekin = 0.0934129479732331 | erot = 0.71502524375301 | epot = -15.4508714375228 | etot = -14.6424332457966 -157000 ekin = 0.0937187435781837 | erot = 0.7054451639455 | epot = -15.4415971533099 | etot = -14.6424332457862 -158000 ekin = 0.0936106185394034 | erot = 0.690910554325068 | epot = -15.4269544186268 | etot = -14.6424332457623 -159000 ekin = 0.0933330174009798 | erot = 0.671575051659369 | epot = -15.4073413147861 | etot = -14.6424332457258 -160000 ekin = 0.0931716565239132 | erot = 0.647750492120475 | epot = -15.3833553943224 | etot = -14.6424332456781 -161000 ekin = 0.0934343296226144 | erot = 0.619903194016677 | epot = -15.3557707692603 | etot = -14.642433245621 -162000 ekin = 0.0944314104796785 | erot = 0.588644098979961 | epot = -15.3255087550165 | etot = -14.6424332455568 -163000 ekin = 0.0964572425730066 | erot = 0.554712943454524 | epot = -15.2936034315153 | etot = -14.6424332454878 -164000 ekin = 0.0997733472794833 | erot = 0.51895691856277 | epot = -15.2611635112587 | etot = -14.6424332454165 -165000 ekin = 0.104594102018619 | erot = 0.482304549423464 | epot = -15.2293318967876 | etot = -14.6424332453455 -166000 ekin = 0.111075276514824 | erot = 0.445735768513581 | epot = -15.1992442903059 | etot = -14.6424332452775 -167000 ekin = 0.119305597512052 | erot = 0.410249354729612 | epot = -15.1719881974565 | etot = -14.6424332452149 -168000 ekin = 0.12930135472349 | erot = 0.376829046180065 | epot = -15.1485636460635 | etot = -14.64243324516 -169000 ekin = 0.141003965788119 | erot = 0.346409702528372 | epot = -15.1298469134313 | etot = -14.6424332451148 -170000 ekin = 0.154280377438306 | erot = 0.319844892419105 | epot = -15.1165585149385 | etot = -14.6424332450811 -171000 ekin = 0.168926178619928 | erot = 0.297877221607854 | epot = -15.1092366452879 | etot = -14.6424332450601 -172000 ekin = 0.184671319362937 | erot = 0.281112611137901 | epot = -15.1082171755536 | etot = -14.6424332450527 -173000 ekin = 0.201188345435602 | erot = 0.269999595570589 | epot = -15.1136211860655 | etot = -14.6424332450593 -174000 ekin = 0.218103052205587 | erot = 0.264814547402911 | epot = -15.1253508446879 | etot = -14.6424332450794 -175000 ekin = 0.235007413034244 | erot = 0.265653545949627 | epot = -15.1430942040962 | etot = -14.6424332451123 -176000 ekin = 0.251474534266602 | erot = 0.272431389431356 | epot = -15.1663391688545 | etot = -14.6424332451566 -177000 ekin = 0.267075225142183 | erot = 0.284887984977502 | epot = -15.1943964553298 | etot = -14.6424332452101 -178000 ekin = 0.281395553894085 | erot = 0.302602030913778 | epot = -15.2264308300785 | etot = -14.6424332452706 -179000 ekin = 0.294054514410707 | erot = 0.325011526056011 | epot = -15.2614992858019 | etot = -14.6424332453351 -180000 ekin = 0.304720692895811 | erot = 0.351440214933808 | epot = -15.2985941532306 | etot = -14.6424332454009 -181000 ekin = 0.313126658917312 | erot = 0.381128639600623 | epot = -15.3366885439829 | etot = -14.6424332454649 -182000 ekin = 0.319079775822514 | erot = 0.413268071112208 | epot = -15.3747810924592 | etot = -14.6424332455245 -183000 ekin = 0.322468290004655 | erot = 0.447035301735044 | epot = -15.4119368373172 | etot = -14.6424332455775 -184000 ekin = 0.323261947553556 | erot = 0.481626155079162 | epot = -15.4473213482551 | etot = -14.6424332456224 -185000 ekin = 0.321506983529697 | erot = 0.516285658867075 | epot = -15.4802258880548 | etot = -14.642433245658 -186000 ekin = 0.317316057632531 | erot = 0.550333132629024 | epot = -15.5100824359458 | etot = -14.6424332456842 -187000 ekin = 0.310854440588904 | erot = 0.583180936762622 | epot = -15.5364686230528 | etot = -14.6424332457012 -188000 ekin = 0.30232432976273 | erot = 0.614346238386881 | epot = -15.5591038138594 | etot = -14.6424332457098 -189000 ekin = 0.291949445195852 | erot = 0.643455779015098 | epot = -15.5778384699219 | etot = -14.6424332457109 -190000 ekin = 0.279961942766932 | erot = 0.670244185707524 | epot = -15.5926393741803 | etot = -14.6424332457058 -191000 ekin = 0.266593185652274 | erot = 0.694546781237202 | epot = -15.6035732125848 | etot = -14.6424332456953 -192000 ekin = 0.252069141621896 | erot = 0.716288088791507 | epot = -15.6107904760939 | etot = -14.6424332456805 -193000 ekin = 0.2366102932526 | erot = 0.735467302247593 | epot = -15.6145108411624 | etot = -14.6424332456622 -194000 ekin = 0.220435149403491 | erot = 0.75214194303258 | epot = -15.6150103380771 | etot = -14.642433245641 -195000 ekin = 0.203765880091661 | erot = 0.766410799035626 | epot = -15.6126099247449 | etot = -14.6424332456176 -196000 ekin = 0.186834339035651 | erot = 0.778397083256526 | epot = -15.6076646678849 | etot = -14.6424332455927 -197000 ekin = 0.169886782292464 | erot = 0.788232586076187 | epot = -15.6005526139357 | etot = -14.642433245567 -198000 ekin = 0.153185871076301 | erot = 0.796043434544246 | epot = -15.5916625511619 | etot = -14.6424332455413 -199000 ekin = 0.137008972985795 | erot = 0.801937915803759 | epot = -15.5813801343063 | etot = -14.6424332455168 -200000 ekin = 0.121642272363314 | erot = 0.805996673265824 | epot = -15.5700721911236 | etot = -14.6424332454944 -201000 ekin = 0.107370722655147 | erot = 0.808265456810171 | epot = -15.5580694249409 | etot = -14.6424332454756 -202000 ekin = 0.0944644042380589 | erot = 0.808750524312638 | epot = -15.545648174012 | etot = -14.6424332454613 -203000 ekin = 0.0831623790884324 | erot = 0.807416772445363 | epot = -15.5330123969865 | etot = -14.6424332454527 -204000 ekin = 0.0736556272327789 | erot = 0.804188725420783 | epot = -15.5202775981043 | etot = -14.6424332454507 -205000 ekin = 0.066071040166988 | erot = 0.79895460735607 | epot = -15.5074588929788 | etot = -14.6424332454557 -206000 ekin = 0.0604586317676951 | erot = 0.79157380942372 | epot = -15.494465686659 | etot = -14.6424332454675 -207000 ekin = 0.0567840026879156 | erot = 0.781888054797388 | epot = -15.4811053029705 | etot = -14.6424332454852 -208000 ekin = 0.0549275971597975 | erot = 0.769736381378222 | epot = -15.4670972240452 | etot = -14.6424332455072 -209000 ekin = 0.054691444753414 | erot = 0.754973659532252 | epot = -15.4520983498168 | etot = -14.6424332455311 -210000 ekin = 0.0558130126770424 | erot = 0.737491764373083 | epot = -15.4357380226042 | etot = -14.6424332455541 -211000 ekin = 0.0579847210232219 | erot = 0.717241838878542 | epot = -15.4176598054751 | etot = -14.6424332455734 -212000 ekin = 0.0608768356197334 | erot = 0.694255492638095 | epot = -15.3975655738439 | etot = -14.642433245586 -213000 ekin = 0.0641610427072994 | erot = 0.66866247616279 | epot = -15.37525676446 | etot = -14.6424332455899 -214000 ekin = 0.0675321043575128 | erot = 0.64070249551818 | epot = -15.3506678454593 | etot = -14.6424332455836 -215000 ekin = 0.0707255336353422 | erot = 0.610729417268954 | epot = -15.3238881964709 | etot = -14.6424332455666 -216000 ekin = 0.0735300437817614 | erot = 0.579207054839019 | epot = -15.2951703441601 | etot = -14.6424332455393 -217000 ekin = 0.0757943994877641 | erot = 0.546696813211868 | epot = -15.2649244582025 | etot = -14.6424332455029 -218000 ekin = 0.0774290394165078 | erot = 0.51383845121943 | epot = -15.2337007360952 | etot = -14.6424332454593 -219000 ekin = 0.0784033323141758 | erot = 0.481325894964748 | epot = -15.2021624726897 | etot = -14.6424332454108 -220000 ekin = 0.0787395495607948 | erot = 0.449880299622387 | epot = -15.1710530945427 | etot = -14.6424332453595 -221000 ekin = 0.0785046319672525 | erot = 0.420222425160561 | epot = -15.1411603024357 | etot = -14.6424332453079 -222000 ekin = 0.0778006814269618 | erot = 0.393045972171563 | epot = -15.1132798988567 | etot = -14.6424332452582 -223000 ekin = 0.0767549035385332 | erot = 0.368992968911871 | epot = -15.0881811176628 | etot = -14.6424332452124 -224000 ekin = 0.0755095293703771 | erot = 0.348631757033118 | epot = -15.0665745315758 | etot = -14.6424332451723 -225000 ekin = 0.0742120885667612 | erot = 0.332437700429432 | epot = -15.0490830341357 | etot = -14.6424332451395 -226000 ekin = 0.0730063028693098 | erot = 0.320776497502258 | epot = -15.0362160454869 | etot = -14.6424332451153 -227000 ekin = 0.0720238140882299 | erot = 0.313889923629038 | epot = -15.0283469828185 | etot = -14.6424332451012 -228000 ekin = 0.0713769419939713 | erot = 0.311883945247486 | epot = -15.0256941323393 | etot = -14.6424332450978 -229000 ekin = 0.0711526728858612 | erot = 0.314719386439623 | epot = -15.0283053044314 | etot = -14.6424332451059 -230000 ekin = 0.0714080974066282 | erot = 0.32220563858993 | epot = -15.0360469811226 | etot = -14.6424332451261 -231000 ekin = 0.0721675361189904 | erot = 0.333998222201802 | epot = -15.0485990034788 | etot = -14.6424332451581 -232000 ekin = 0.073421602290549 | erot = 0.349601270465942 | epot = -15.0654561179577 | etot = -14.6424332452012 -233000 ekin = 0.0751284397505166 | erot = 0.368376135875933 | epot = -15.0859378208811 | etot = -14.6424332452547 -234000 ekin = 0.0772173235442522 | erot = 0.389557254433757 | epot = -15.1092078232945 | etot = -14.6424332453165 -235000 ekin = 0.0795947059802171 | erot = 0.412276079790421 | epot = -15.1343040311544 | etot = -14.6424332453838 -236000 ekin = 0.0821526186146683 | erot = 0.435593295647697 | epot = -15.160179159716 | etot = -14.6424332454537 -237000 ekin = 0.0847791014239972 | erot = 0.458538653864687 | epot = -15.1857510008109 | etot = -14.6424332455222 -238000 ekin = 0.087370042385855 | erot = 0.480156759886663 | epot = -15.209960047858 | etot = -14.6424332455854 -239000 ekin = 0.0898415153137564 | erot = 0.49955609555256 | epot = -15.2318308565057 | etot = -14.6424332456394 -240000 ekin = 0.0921414623535534 | erot = 0.515957735400968 | epot = -15.2505324434352 | etot = -14.6424332456807 -241000 ekin = 0.094259449014392 | erot = 0.528739776886534 | epot = -15.2654324716071 | etot = -14.6424332457062 -242000 ekin = 0.0962332805880934 | erot = 0.537473606136267 | epot = -15.2761401324386 | etot = -14.6424332457143 -243000 ekin = 0.0981515319338797 | erot = 0.541948785980249 | epot = -15.2825335636184 | etot = -14.6424332457043 -244000 ekin = 0.100151482351181 | erot = 0.542184479374293 | epot = -15.2847692074025 | etot = -14.642433245677 -245000 ekin = 0.102412491095747 | erot = 0.53842670231772 | epot = -15.2832724390477 | etot = -14.6424332456343 -246000 ekin = 0.105145395544779 | erot = 0.531132085866326 | epot = -15.2787107269898 | etot = -14.6424332455787 -247000 ekin = 0.108578961411965 | erot = 0.520939994206832 | epot = -15.2719522011324 | etot = -14.6424332455137 -248000 ekin = 0.112944688754503 | erot = 0.50863565229522 | epot = -15.2640135864927 | etot = -14.6424332454429 -249000 ekin = 0.118461348905117 | erot = 0.495107336753362 | epot = -15.256001931029 | etot = -14.6424332453705 -250000 ekin = 0.125320510713189 | erot = 0.48130071319677 | epot = -15.24905446921 | etot = -14.6424332453 -251000 ekin = 0.13367405695507 | erot = 0.468173145423505 | epot = -15.2442804476135 | etot = -14.6424332452349 -252000 ekin = 0.14362435587275 | erot = 0.456650355973621 | epot = -15.2427079570245 | etot = -14.6424332451781 -253000 ekin = 0.155217400154316 | erot = 0.447587277165273 | epot = -15.2452379224515 | etot = -14.6424332451319 -254000 ekin = 0.168438906844309 | erot = 0.441734376017195 | epot = -15.2526065279595 | etot = -14.642433245098 -255000 ekin = 0.183213121644152 | erot = 0.43971022735342 | epot = -15.265356594075 | etot = -14.6424332450774 -256000 ekin = 0.199403908832121 | erot = 0.441980689733431 | epot = -15.2838178436366 | etot = -14.642433245071 -257000 ekin = 0.216817638461841 | erot = 0.448844730305144 | epot = -15.308095613846 | etot = -14.642433245079 -258000 ekin = 0.235207399035704 | erot = 0.460426746275348 | epot = -15.3380673904121 | etot = -14.642433245101 -259000 ekin = 0.254278151366077 | erot = 0.476675120648602 | epot = -15.3733865171511 | etot = -14.6424332451364 -260000 ekin = 0.27369257667687 | erot = 0.497366691706637 | epot = -15.4134925135677 | etot = -14.6424332451842 -261000 ekin = 0.293077534073047 | erot = 0.522116767905255 | epot = -15.4576275472214 | etot = -14.6424332452431 -262000 ekin = 0.312031202020343 | erot = 0.550394247121191 | epot = -15.5048586944528 | etot = -14.6424332453112 -263000 ekin = 0.330131107615792 | erot = 0.58154128199962 | epot = -15.5541056350021 | etot = -14.6424332453866 -264000 ekin = 0.346943319969756 | erot = 0.61479677344706 | epot = -15.6041733388837 | etot = -14.6424332454669 -265000 ekin = 0.362033078254018 | erot = 0.649322794997101 | epot = -15.6537891188009 | etot = -14.6424332455498 -266000 ekin = 0.374977027495908 | erot = 0.684232889060489 | epot = -15.7016431621888 | etot = -14.6424332456324 -267000 ekin = 0.385377045180443 | erot = 0.718621072064117 | epot = -15.7464313629566 | etot = -14.642433245712 -268000 ekin = 0.392875374675087 | erot = 0.75159036946736 | epot = -15.7868989899283 | etot = -14.6424332457858 -269000 ekin = 0.397170471133826 | erot = 0.782279784278077 | epot = -15.8218835012632 | etot = -14.6424332458513 -270000 ekin = 0.39803266202252 | erot = 0.809888771679688 | epot = -15.8503546796085 | etot = -14.6424332459063 -271000 ekin = 0.395318487593041 | erot = 0.833698516715799 | epot = -15.8714502502577 | etot = -14.6424332459488 -272000 ekin = 0.388982474346436 | erot = 0.85308955191437 | epot = -15.8845052722382 | etot = -14.6424332459774 -273000 ekin = 0.379085147925793 | erot = 0.867555470410658 | epot = -15.8890738643275 | etot = -14.6424332459911 -274000 ekin = 0.365796322187783 | erot = 0.876712662634482 | epot = -15.8849422308119 | etot = -14.6424332459896 -275000 ekin = 0.349393082916365 | erot = 0.880306121918412 | epot = -15.872132450808 | etot = -14.6424332459733 -276000 ekin = 0.330252358900911 | erot = 0.878211432152944 | epot = -15.8508970369967 | etot = -14.6424332459429 -277000 ekin = 0.308838461215969 | erot = 0.87043308488023 | epot = -15.821704791996 | etot = -14.6424332458998 -278000 ekin = 0.285686394600485 | erot = 0.857099294887703 | epot = -15.7852189353341 | etot = -14.6424332458459 -279000 ekin = 0.26138204276351 | erot = 0.838453513182823 | epot = -15.7422688017294 | etot = -14.642433245783 -280000 ekin = 0.236540473323807 | erot = 0.814842890588987 | epot = -15.6938166096265 | etot = -14.6424332457138 -281000 ekin = 0.211783602606672 | erot = 0.786704032858688 | epot = -15.6409208811058 | etot = -14.6424332456404 -282000 ekin = 0.18771833727137 | erot = 0.754546508157259 | epot = -15.5846980909942 | etot = -14.6424332455655 -283000 ekin = 0.164916115091084 | erot = 0.718934708844117 | epot = -15.5262840694266 | etot = -14.6424332454914 -284000 ekin = 0.143894549222789 | erot = 0.680468811937684 | epot = -15.466796606581 | etot = -14.6424332454205 -285000 ekin = 0.125101678374108 | erot = 0.639765701845435 | epot = -15.4073006255745 | etot = -14.642433245355 -286000 ekin = 0.108903164109883 | erot = 0.597440790007762 | epot = -15.3487771994138 | etot = -14.6424332452962 -287000 ekin = 0.0955726645582656 | erot = 0.554091668601873 | epot = -15.2920975784058 | etot = -14.6424332452456 -288000 ekin = 0.0852855448042878 | erot = 0.51028445681865 | epot = -15.2380032468271 | etot = -14.6424332452042 -289000 ekin = 0.0781160413142908 | erot = 0.466543535619429 | epot = -15.187092822106 | etot = -14.6424332451723 -290000 ekin = 0.0740379578661526 | erot = 0.423345127585162 | epot = -15.1398163306014 | etot = -14.6424332451501 -291000 ekin = 0.07292891006789 | erot = 0.38111487943337 | epot = -15.0964770346382 | etot = -14.6424332451369 -292000 ekin = 0.0745780357973755 | erot = 0.340229271733751 | epot = -15.0572405526629 | etot = -14.6424332451317 -293000 ekin = 0.0786969407585494 | erot = 0.301020346544363 | epot = -15.0221505324362 | etot = -14.6424332451333 -294000 ekin = 0.0849334564747798 | erot = 0.263782947584644 | epot = -14.9911496491993 | etot = -14.6424332451399 -295000 ekin = 0.0928875723651302 | erot = 0.22878344880309 | epot = -14.9641042663181 | etot = -14.6424332451499 -296000 ekin = 0.102128697511331 | erot = 0.196268840383788 | epot = -14.9408307830568 | etot = -14.6424332451617 -297000 ekin = 0.11221325250056 | erot = 0.166475068215614 | epot = -14.9211215658898 | etot = -14.6424332451737 -298000 ekin = 0.122701527070309 | erot = 0.139633685444085 | epot = -14.904768457699 | etot = -14.6424332451846 -299000 ekin = 0.133172792913717 | erot = 0.115976150687844 | epot = -14.8915821887951 | etot = -14.6424332451935 -300000 ekin = 0.143237839709864 | erot = 0.0957354521197658 | epot = -14.8814065370295 | etot = -14.6424332451999 -301000 ekin = 0.152548387990851 | erot = 0.07914509087212 | epot = -14.8741267240666 | etot = -14.6424332452037 -302000 ekin = 0.160803184301524 | erot = 0.0664357608556835 | epot = -14.8696721903621 | etot = -14.6424332452049 -303000 ekin = 0.167750948488374 | erot = 0.0578302677258914 | epot = -14.8680144614182 | etot = -14.6424332452039 -304000 ekin = 0.173190665588555 | erot = 0.0535373136380679 | epot = -14.8691612244281 | etot = -14.6424332452015 -305000 ekin = 0.176969952950159 | erot = 0.0537447402922713 | epot = -14.8731479384405 | etot = -14.6424332451981 -306000 ekin = 0.178982363291678 | erot = 0.0586126977895342 | epot = -14.8800283062756 | etot = -14.6424332451944 -307000 ekin = 0.179164502945068 | erot = 0.0682670321079694 | epot = -14.8898647802439 | etot = -14.6424332451909 -308000 ekin = 0.177493763289069 | erot = 0.0827930029212249 | epot = -14.9027200113985 | etot = -14.6424332451882 -309000 ekin = 0.173987301152049 | erot = 0.10222929187336 | epot = -14.918649838212 | etot = -14.6424332451866 -310000 ekin = 0.168702678648352 | erot = 0.126562162218755 | epot = -14.9376980860534 | etot = -14.6424332451863 -311000 ekin = 0.161740297010225 | erot = 0.15571959340906 | epot = -14.9598931356066 | etot = -14.6424332451873 -312000 ekin = 0.153247440126399 | erot = 0.189565237979944 | epot = -14.9852459232961 | etot = -14.6424332451897 -313000 ekin = 0.143423389998623 | erot = 0.227892126762149 | epot = -15.0137487619545 | etot = -14.6424332451937 -314000 ekin = 0.132524706020311 | erot = 0.270416174781616 | epot = -15.045374126001 | etot = -14.6424332451991 -315000 ekin = 0.120869409554559 | erot = 0.31676970828961 | epot = -15.0800723630507 | etot = -14.6424332452065 -316000 ekin = 0.108838546106885 | erot = 0.366495437994255 | epot = -15.1177672293175 | etot = -14.6424332452163 -317000 ekin = 0.0968734934299726 | erot = 0.419041536808435 | epot = -15.1583482754675 | etot = -14.6424332452291 -318000 ekin = 0.0854675378572541 | erot = 0.473758725762824 | epot = -15.201659508866 | etot = -14.6424332452459 -319000 ekin = 0.0751507271474133 | erot = 0.529900497446511 | epot = -15.2474844698617 | etot = -14.6424332452678 -320000 ekin = 0.0664678443385179 | erot = 0.586627760737852 | epot = -15.2955288503723 | etot = -14.6424332452959 -321000 ekin = 0.0599504590581751 | erot = 0.643019202689424 | epot = -15.3454029070787 | etot = -14.6424332453311 -322000 ekin = 0.0560852142815241 | erot = 0.69808845326502 | epot = -15.3966069129205 | etot = -14.642433245374 -323000 ekin = 0.0552815181260046 | erot = 0.750808639914442 | epot = -15.4485234034646 | etot = -14.6424332454242 -324000 ekin = 0.0578423255211838 | erot = 0.800144112656325 | epot = -15.5004196836582 | etot = -14.6424332454807 -325000 ekin = 0.0639414864635107 | erot = 0.845088070114621 | epot = -15.5514628021198 | etot = -14.6424332455416 -326000 ekin = 0.0736101694204692 | erot = 0.884703689967839 | epot = -15.6007471049927 | etot = -14.6424332456044 -327000 ekin = 0.0867333560885398 | erot = 0.918165419814672 | epot = -15.6473320215695 | etot = -14.6424332456662 -328000 ekin = 0.103055779602205 | erot = 0.944796600226729 | epot = -15.690285625553 | etot = -14.6424332457241 -329000 ekin = 0.122195446168384 | erot = 0.964099781598493 | epot = -15.7287284735425 | etot = -14.6424332457756 -330000 ekin = 0.143662406707253 | erot = 0.975776996242511 | epot = -15.7618726487686 | etot = -14.6424332458188 -331000 ekin = 0.16688078513004 | erot = 0.979738667524168 | epot = -15.7890526985066 | etot = -14.6424332458524 -332000 ekin = 0.191212923965886 | erot = 0.976101405909884 | epot = -15.8097475757513 | etot = -14.6424332458756 -333000 ekin = 0.215985355315093 | erot = 0.965176233546684 | epot = -15.8235948347498 | etot = -14.642433245888 -334000 ekin = 0.240516656826274 | erot = 0.947449485120535 | epot = -15.830399387836 | etot = -14.6424332458892 -335000 ekin = 0.26414689608104 | erot = 0.923558676876203 | epot = -15.8301388188364 | etot = -14.6424332458792 -336000 ekin = 0.286267467748786 | erot = 0.89426518476866 | epot = -15.8229658983752 | etot = -14.6424332458578 -337000 ekin = 0.306349134744468 | erot = 0.860424939344321 | epot = -15.8092073199142 | etot = -14.6424332458254 -338000 ekin = 0.323965497668976 | erot = 0.822957838329794 | epot = -15.7893565817818 | etot = -14.642433245783 -339000 ekin = 0.338809250783254 | erot = 0.78281638015672 | epot = -15.7640588766721 | etot = -14.6424332457321 -340000 ekin = 0.35069944422809 | erot = 0.74095414130838 | epot = -15.7340868312114 | etot = -14.6424332456749 -341000 ekin = 0.359579293531018 | erot = 0.698295027836038 | epot = -15.7003075669809 | etot = -14.6424332456139 -342000 ekin = 0.365505462149712 | erot = 0.655704542038074 | epot = -15.6636432497397 | etot = -14.6424332455519 -343000 ekin = 0.368630832656515 | erot = 0.613964463467531 | epot = -15.6250285416158 | etot = -14.6424332454918 -344000 ekin = 0.369183369584766 | erot = 0.573752273081695 | epot = -15.5853688881025 | etot = -14.642433245436 -345000 ekin = 0.367443732820324 | erot = 0.535626361233062 | epot = -15.5455033394399 | etot = -14.6424332453865 -346000 ekin = 0.363723933128335 | erot = 0.500017626275246 | epot = -15.5061748047482 | etot = -14.6424332453447 -347000 ekin = 0.3583487052748 | erot = 0.467227585425602 | epot = -15.4680095360115 | etot = -14.6424332453111 -348000 ekin = 0.351640582952522 | erot = 0.437432666905881 | epot = -15.4315064951445 | etot = -14.6424332452861 -349000 ekin = 0.343909024693046 | erot = 0.41069398616734 | epot = -15.3970362561291 | etot = -14.6424332452687 -350000 ekin = 0.335443435967543 | erot = 0.386971649877949 | epot = -15.3648483311043 | etot = -14.6424332452588 -351000 ekin = 0.326509584093005 | erot = 0.366142474248723 | epot = -15.335085303596 | etot = -14.6424332452543 -352000 ekin = 0.317348699021852 | erot = 0.348019930398485 | epot = -15.3078018746744 | etot = -14.6424332452541 -353000 ekin = 0.30817846664876 | erot = 0.332375117499618 | epot = -15.2829868294052 | etot = -14.6424332452568 -354000 ekin = 0.299195119854683 | erot = 0.318957598137097 | epot = -15.2605859632527 | etot = -14.6424332452609 -355000 ekin = 0.290575888249358 | erot = 0.307515001368969 | epot = -15.2405241348835 | etot = -14.6424332452652 -356000 ekin = 0.282481160313138 | erot = 0.29781040621641 | epot = -15.222724811798 | etot = -14.6424332452685 -357000 ekin = 0.275055828994515 | erot = 0.289636664277668 | epot = -15.2071257385424 | etot = -14.6424332452703 -358000 ekin = 0.268429427255696 | erot = 0.282827006912643 | epot = -15.1936896794384 | etot = -14.6424332452701 -359000 ekin = 0.262714810202509 | erot = 0.277261507859007 | epot = -15.1824095633295 | etot = -14.642433245268 -360000 ekin = 0.258005302570141 | erot = 0.272869227750186 | epot = -15.1733077755848 | etot = -14.6424332452644 -361000 ekin = 0.254370400622431 | erot = 0.269626137803972 | epot = -15.1664297836866 | etot = -14.6424332452602 -362000 ekin = 0.251850290179243 | erot = 0.267549186090239 | epot = -15.1618327215257 | etot = -14.6424332452562 -363000 ekin = 0.250449609863295 | erot = 0.266687109599965 | epot = -15.159569964717 | etot = -14.6424332452537 -364000 ekin = 0.250131041863855 | erot = 0.267108788860278 | epot = -15.1596730759782 | etot = -14.642433245254 -365000 ekin = 0.250809442162592 | erot = 0.268890073930502 | epot = -15.1621327613513 | etot = -14.6424332452582 -366000 ekin = 0.252347318763925 | erot = 0.272100073008351 | epot = -15.1668806370397 | etot = -14.6424332452674 -367000 ekin = 0.254552520179183 | erot = 0.276787886821331 | epot = -15.1737736522827 | etot = -14.6424332452822 -368000 ekin = 0.257178996154117 | erot = 0.282970699525226 | epot = -15.1825829409825 | etot = -14.6424332453031 -369000 ekin = 0.25993142490973 | erot = 0.290624011144342 | epot = -15.1929886813841 | etot = -14.64243324533 -370000 ekin = 0.262474349327911 | erot = 0.299674631815262 | epot = -15.2045822265054 | etot = -14.6424332453622 -371000 ekin = 0.264446209429889 | erot = 0.309996869296908 | epot = -15.2168763241254 | etot = -14.6424332453986 -372000 ekin = 0.265478281863369 | erot = 0.321412142685491 | epot = -15.2293236699861 | etot = -14.6424332454373 -373000 ekin = 0.265218028292355 | erot = 0.333692059446813 | epot = -15.2413433332155 | etot = -14.6424332454763 -374000 ekin = 0.263355721250425 | erot = 0.346564809668647 | epot = -15.2523537764322 | etot = -14.6424332455131 -375000 ekin = 0.259652497503873 | erot = 0.359724567994869 | epot = -15.2618103110439 | etot = -14.6424332455452 -376000 ekin = 0.253967268937784 | erot = 0.372843454380806 | epot = -15.2692439688887 | etot = -14.6424332455701 -377000 ekin = 0.246279333501453 | erot = 0.385585491294785 | epot = -15.274298070382 | etot = -14.6424332455858 -378000 ekin = 0.236703249878221 | erot = 0.397621906698152 | epot = -15.2767584021673 | etot = -14.6424332455909 -379000 ekin = 0.225492756944939 | erot = 0.408647066931743 | epot = -15.2765730694618 | etot = -14.6424332455852 -380000 ekin = 0.213031377539219 | erot = 0.418394278996712 | epot = -15.2738589021049 | etot = -14.642433245569 -381000 ekin = 0.199808877315892 | erot = 0.426650676211857 | epot = -15.2688927990715 | etot = -14.6424332455438 -382000 ekin = 0.186384809019024 | erot = 0.433270396055851 | epot = -15.2620884505868 | etot = -14.642433245512 -383000 ekin = 0.173342616144098 | erot = 0.438185279050645 | epot = -15.253961140671 | etot = -14.6424332454763 -384000 ekin = 0.161239700831436 | erot = 0.441412371402807 | epot = -15.2450853176736 | etot = -14.6424332454394 -385000 ekin = 0.150559954647593 | erot = 0.443057612552847 | epot = -15.2360508126044 | etot = -14.6424332454039 -386000 ekin = 0.141675129699177 | erot = 0.443315241523115 | epot = -15.2274236165942 | etot = -14.6424332453719 -387000 ekin = 0.134820015697985 | erot = 0.442462667348824 | epot = -15.2197159283911 | etot = -14.6424332453443 -388000 ekin = 0.130083976413548 | erot = 0.440850813513903 | epot = -15.2133680352489 | etot = -14.6424332453215 -389000 ekin = 0.127418570237884 | erot = 0.43889024627901 | epot = -15.2087420618201 | etot = -14.6424332453032 -390000 ekin = 0.126658423093201 | erot = 0.437033702086081 | epot = -15.206125370468 | etot = -14.6424332452887 -391000 ekin = 0.127550804260996 | erot = 0.435755902066197 | epot = -15.2057399516044 | etot = -14.6424332452772 -392000 ekin = 0.129788752935801 | erot = 0.435531744058798 | epot = -15.2077537422629 | etot = -14.6424332452683 -393000 ekin = 0.133043055316258 | erot = 0.436814065078314 | epot = -15.2122903656559 | etot = -14.6424332452613 -394000 ekin = 0.136989561466103 | erot = 0.440012156511496 | epot = -15.219434963234 | etot = -14.6424332452564 -395000 ekin = 0.141329833042571 | erot = 0.445472096886692 | epot = -15.2292351751829 | etot = -14.6424332452537 -396000 ekin = 0.145804542777683 | erot = 0.453459767650238 | epot = -15.2416975556817 | etot = -14.6424332452538 -397000 ekin = 0.150200153189368 | erot = 0.464147173463313 | epot = -15.2567805719101 | etot = -14.6424332452574 -398000 ekin = 0.154350089767281 | erot = 0.477602441560301 | epot = -15.2743857765925 | etot = -14.6424332452649 -399000 ekin = 0.158131920623958 | erot = 0.493783661157258 | epot = -15.2943488270584 | etot = -14.6424332452772 -400000 ekin = 0.161462056175852 | erot = 0.512536568007644 | epot = -15.3164318694779 | etot = -14.6424332452944 -401000 ekin = 0.164289301183563 | erot = 0.533595989003439 | epot = -15.3403185355037 | etot = -14.6424332453167 -402000 ekin = 0.166588323053565 | erot = 0.556590928840414 | epot = -15.3656124972379 | etot = -14.642433245344 -403000 ekin = 0.168353810382881 | erot = 0.581053183644676 | epot = -15.3918402394035 | etot = -14.6424332453759 -404000 ekin = 0.169595821304602 | erot = 0.606429376023105 | epot = -15.4184584427394 | etot = -14.6424332454117 -405000 ekin = 0.17033657856555 | erot = 0.632096292540194 | epot = -15.4448661165559 | etot = -14.6424332454502 -406000 ekin = 0.170608761982357 | erot = 0.65737934451417 | epot = -15.4704213519868 | etot = -14.6424332454902 -407000 ekin = 0.170455178570774 | erot = 0.681573854093745 | epot = -15.4944622781949 | etot = -14.6424332455304 -408000 ekin = 0.169929554812993 | erot = 0.703968692150315 | epot = -15.5163314925321 | etot = -14.6424332455688 -409000 ekin = 0.169098093454308 | erot = 0.723871579520606 | epot = -15.5354029185787 | etot = -14.6424332456038 -410000 ekin = 0.168041369043254 | erot = 0.740635137247646 | epot = -15.5511097519244 | etot = -14.6424332456335 -411000 ekin = 0.166856102811026 | erot = 0.753682569970607 | epot = -15.562971918438 | etot = -14.6424332456564 -412000 ekin = 0.165656359034654 | erot = 0.762531725092731 | epot = -15.5706213297983 | etot = -14.642433245671 -413000 ekin = 0.164573741712539 | erot = 0.766816218739469 | epot = -15.5738232061283 | etot = -14.6424332456763 -414000 ekin = 0.163756240958007 | erot = 0.766302377571818 | epot = -15.5724918642016 | etot = -14.6424332456718 -415000 ekin = 0.163365479945299 | erot = 0.760900920225133 | epot = -15.5666996458276 | etot = -14.6424332456572 -416000 ekin = 0.163572240093361 | erot = 0.750672586700048 | epot = -15.5566780724264 | etot = -14.642433245633 -417000 ekin = 0.164550286198126 | erot = 0.735827297892139 | epot = -15.5428108296904 | etot = -14.6424332456002 -418000 ekin = 0.166468663391001 | erot = 0.716716857301867 | epot = -15.525618766253 | etot = -14.6424332455601 -419000 ekin = 0.169482781124152 | erot = 0.69382164910087 | epot = -15.5057376757396 | etot = -14.6424332455146 -420000 ekin = 0.173724722664366 | erot = 0.667732191685369 | epot = -15.4838901598155 | etot = -14.6424332454658 -421000 ekin = 0.179293310757479 | erot = 0.639126725583771 | epot = -15.4608532817569 | etot = -14.6424332454157 -422000 ekin = 0.186244514517565 | erot = 0.608746211201693 | epot = -15.4374239710859 | etot = -14.6424332453666 -423000 ekin = 0.194582798143041 | erot = 0.577368165579506 | epot = -15.4143842090433 | etot = -14.6424332453207 -424000 ekin = 0.204253993027957 | erot = 0.545780680988036 | epot = -15.392467919296 | etot = -14.64243324528 -425000 ekin = 0.215140228915595 | erot = 0.514757766833673 | epot = -15.372331240995 | etot = -14.6424332452458 -426000 ekin = 0.227057395196063 | erot = 0.485036881516669 | epot = -15.354527521932 | etot = -14.6424332452193 -427000 ekin = 0.239755526224872 | erot = 0.457299221562912 | epot = -15.3394879929894 | etot = -14.6424332452017 -428000 ekin = 0.252922416268501 | erot = 0.432153058136047 | epot = -15.3275087195977 | etot = -14.6424332451931 -429000 ekin = 0.266190667178472 | erot = 0.410120192009091 | epot = -15.318744104381 | etot = -14.6424332451935 -430000 ekin = 0.279148248284958 | erot = 0.391625457763427 | epot = -15.3132069512512 | etot = -14.6424332452028 -431000 ekin = 0.291352495292848 | erot = 0.37698914981175 | epot = -15.3107748903245 | etot = -14.6424332452199 -432000 ekin = 0.302347287569357 | erot = 0.36642225446733 | epot = -15.3112027872808 | etot = -14.6424332452441 -433000 ekin = 0.311682921770362 | erot = 0.360024429013509 | epot = -15.314140596057 | etot = -14.6424332452732 -434000 ekin = 0.318937954386234 | erot = 0.357784738271935 | epot = -15.3191559379639 | etot = -14.6424332453058 -435000 ekin = 0.323742037713894 | erot = 0.359585207274212 | epot = -15.3257604903287 | etot = -14.6424332453406 -436000 ekin = 0.325798554030488 | erot = 0.36520724530746 | epot = -15.3334390447139 | etot = -14.642433245376 -437000 ekin = 0.324905697096464 | erot = 0.374340922352109 | epot = -15.3416798648574 | etot = -14.6424332454088 -438000 ekin = 0.32097458985737 | erot = 0.386596930163185 | epot = -15.3500047654581 | etot = -14.6424332454376 -439000 ekin = 0.314043077745088 | erot = 0.401520852188919 | epot = -15.3579971753952 | etot = -14.6424332454612 -440000 ekin = 0.304283988018852 | erot = 0.418609132218188 | epot = -15.3653263657148 | etot = -14.6424332454778 -441000 ekin = 0.292006859109402 | erot = 0.437325916198087 | epot = -15.3717660207938 | etot = -14.6424332454863 -442000 ekin = 0.277652365812265 | erot = 0.457119792524783 | epot = -15.3772054038239 | etot = -14.6424332454868 -443000 ekin = 0.261778853587313 | erot = 0.477439412182564 | epot = -15.3816515112497 | etot = -14.6424332454798 -444000 ekin = 0.245040553430208 | erot = 0.497747053384035 | epot = -15.385220852281 | etot = -14.6424332454667 -445000 ekin = 0.228157260415726 | erot = 0.51752940821079 | epot = -15.3881199140755 | etot = -14.642433245449 -446000 ekin = 0.211875681724409 | erot = 0.536305196865493 | epot = -15.3906141240194 | etot = -14.6424332454295 -447000 ekin = 0.196923472676251 | erot = 0.553629632762795 | epot = -15.3929863508504 | etot = -14.6424332454113 -448000 ekin = 0.183958277875555 | erot = 0.569096233380591 | epot = -15.3954877566542 | etot = -14.642433245398 -449000 ekin = 0.17351577130814 | erot = 0.582336947161301 | epot = -15.3982859638623 | etot = -14.6424332453928 -450000 ekin = 0.165962361194715 | erot = 0.593021970155398 | epot = -15.4014175767483 | etot = -14.6424332453982 -451000 ekin = 0.161459280831074 | erot = 0.600860851258547 | epot = -15.4047533775047 | etot = -14.6424332454151 -452000 ekin = 0.159944578250399 | erot = 0.605606408084822 | epot = -15.4079842317782 | etot = -14.642433245443 -453000 ekin = 0.161137653112611 | erot = 0.607062496375706 | epot = -15.4106333949674 | etot = -14.6424332454791 -454000 ekin = 0.164567591511427 | erot = 0.605095779312731 | epot = -15.4120966163435 | etot = -14.6424332455193 -455000 ekin = 0.169622334208412 | erot = 0.59965045542677 | epot = -15.4117060351935 | etot = -14.6424332455583 -456000 ekin = 0.17561180235027 | erot = 0.590763702898776 | epot = -15.4088087508398 | etot = -14.6424332455907 -457000 ekin = 0.181835621982501 | erot = 0.578578749366117 | epot = -15.4028476169607 | etot = -14.6424332456121 -458000 ekin = 0.187645727031673 | erot = 0.563352302650952 | epot = -15.3934312753015 | etot = -14.6424332456189 -459000 ekin = 0.192495880386129 | erot = 0.545453717149971 | epot = -15.3803828431461 | etot = -14.64243324561 -460000 ekin = 0.195973381638787 | erot = 0.525354597711217 | epot = -15.3637612249357 | etot = -14.6424332455857 -461000 ekin = 0.197811920993003 | erot = 0.503609203462485 | epot = -15.343854370004 | etot = -14.6424332455485 -462000 ekin = 0.197887724921051 | erot = 0.480827560282181 | epot = -15.3211485307045 | etot = -14.6424332455013 -463000 ekin = 0.19620319848715 | erot = 0.457644248435948 | epot = -15.2962806923714 | etot = -14.6424332454483 -464000 ekin = 0.192863034127873 | erot = 0.434686220428325 | epot = -15.2699824999496 | etot = -14.6424332453934 -465000 ekin = 0.188047435824123 | erot = 0.412542760090272 | epot = -15.2430234412543 | etot = -14.6424332453399 -466000 ekin = 0.181986107554568 | erot = 0.391740010671155 | epot = -15.2161593635163 | etot = -14.6424332452906 -467000 ekin = 0.174935400199636 | erot = 0.372721626734198 | epot = -15.1900902721814 | etot = -14.6424332452475 -468000 ekin = 0.167159826103628 | erot = 0.355836258350725 | epot = -15.1654293296662 | etot = -14.6424332452119 -469000 ekin = 0.158918218023891 | erot = 0.341331890764694 | epot = -15.1426833539729 | etot = -14.6424332451843 -470000 ekin = 0.150454185654314 | erot = 0.329356584633373 | epot = -15.1222440154522 | etot = -14.6424332451645 -471000 ekin = 0.141990180750326 | erot = 0.319964871776615 | epot = -15.104388297679 | etot = -14.6424332451521 -472000 ekin = 0.133724353868926 | erot = 0.313128906245008 | epot = -15.0892865052598 | etot = -14.6424332451459 -473000 ekin = 0.125829398102403 | erot = 0.308753392324136 | epot = -15.0770160355714 | etot = -14.6424332451449 -474000 ekin = 0.118452666363553 | erot = 0.306693264413754 | epot = -15.0675791759249 | etot = -14.6424332451476 -475000 ekin = 0.111716976219115 | erot = 0.30677305329061 | epot = -15.0609232746625 | etot = -14.6424332451527 -476000 ekin = 0.105721655633337 | erot = 0.308806833537562 | epot = -15.0569617343299 | etot = -14.642433245159 -477000 ekin = 0.100543523675758 | erot = 0.312617617130229 | epot = -15.0555943859711 | etot = -14.6424332451651 -478000 ekin = 0.0962376398644811 | erot = 0.31805505563526 | epot = -15.0567259406697 | etot = -14.64243324517 -479000 ekin = 0.0928377950024532 | erot = 0.325010357030093 | epot = -15.0602813972057 | etot = -14.6424332451731 -480000 ekin = 0.0903568546345998 | erot = 0.333427427763264 | epot = -15.0662175275719 | etot = -14.642433245174 -481000 ekin = 0.0887871989358601 | erot = 0.343309423709768 | epot = -15.074529867818 | etot = -14.6424332451724 -482000 ekin = 0.0881016191320375 | erot = 0.354720133057113 | epot = -15.0852549973577 | etot = -14.6424332451685 -483000 ekin = 0.0882551127439699 | erot = 0.367779908272474 | epot = -15.0984682661793 | etot = -14.6424332451629 -484000 ekin = 0.0891880440138163 | erot = 0.382656193507622 | epot = -15.1142774826775 | etot = -14.642433245156 -485000 ekin = 0.0908310739109982 | erot = 0.399549033146323 | epot = -15.132813352206 | etot = -14.6424332451486 -486000 ekin = 0.0931120890990551 | erot = 0.41867226992318 | epot = -15.1542176041638 | etot = -14.6424332451416 -487000 ekin = 0.095965052639277 | erot = 0.440231422321074 | epot = -15.1786297200962 | etot = -14.6424332451358 -488000 ekin = 0.0993402613867534 | erot = 0.464399451384565 | epot = -15.2061729579035 | etot = -14.6424332451322 -489000 ekin = 0.103214957397693 | erot = 0.491291775403353 | epot = -15.2369399779327 | etot = -14.6424332451317 -490000 ekin = 0.107602676597199 | erot = 0.520941965498321 | epot = -15.2709778872308 | etot = -14.6424332451353 -491000 ekin = 0.112559247664636 | erot = 0.553279563917093 | epot = -15.3082720567258 | etot = -14.6424332451441 -492000 ekin = 0.11818313672361 | erot = 0.588111425308605 | epot = -15.3487278071918 | etot = -14.6424332451596 -493000 ekin = 0.124608040126391 | erot = 0.625107908279146 | epot = -15.3921491935888 | etot = -14.6424332451833 -494000 ekin = 0.131986393312571 | erot = 0.663795156035298 | epot = -15.4382147945647 | etot = -14.6424332452168 -495000 ekin = 0.140463823900169 | erot = 0.703554605721933 | epot = -15.4864516748842 | etot = -14.6424332452621 -496000 ekin = 0.150146408035849 | erot = 0.743630741563392 | epot = -15.5362103949194 | etot = -14.6424332453202 -497000 ekin = 0.161064579071324 | erot = 0.783147917317811 | epot = -15.586645741781 | etot = -14.6424332453918 -498000 ekin = 0.173139219157391 | erot = 0.821136754973018 | epot = -15.6367092196067 | etot = -14.6424332454763 -499000 ekin = 0.186156317833388 | erot = 0.856570103856968 | epot = -15.6851596672616 | etot = -14.6424332455712 -500000 ekin = 0.199756195068939 | erot = 0.888407758274321 | epot = -15.730597199016 | etot = -14.6424332456728 -501000 ekin = 0.213441517837342 | erot = 0.915648078733143 | epot = -15.7715228423457 | etot = -14.6424332457753 -502000 ekin = 0.226605416598005 | erot = 0.937383433649483 | epot = -15.8064220961193 | etot = -14.6424332458719 -503000 ekin = 0.238577508977599 | erot = 0.952855183125227 | epot = -15.8338659380581 | etot = -14.6424332459553 -504000 ekin = 0.248682347016338 | erot = 0.961503066788675 | epot = -15.8526186598237 | etot = -14.6424332460187 -505000 ekin = 0.256302488969596 | erot = 0.963003656366976 | epot = -15.8617393913932 | etot = -14.6424332460566 -506000 ekin = 0.260937583144194 | erot = 0.957293217920897 | epot = -15.8606640471307 | etot = -14.6424332460656 -507000 ekin = 0.262251679299244 | erot = 0.944571918258912 | epot = -15.849256843603 | etot = -14.6424332460448 -508000 ekin = 0.260103184111408 | erot = 0.925288564934742 | epot = -15.8278249950421 | etot = -14.6424332459959 -509000 ekin = 0.25455487528045 | erot = 0.900107536938111 | epot = -15.7970956581414 | etot = -14.6424332459228 -510000 ekin = 0.245864483348181 | erot = 0.869861717985596 | epot = -15.7581594471648 | etot = -14.642433245831 -511000 ekin = 0.234458914526881 | erot = 0.835496660126654 | epot = -15.7123888203807 | etot = -14.6424332457271 -512000 ekin = 0.220896820239973 | erot = 0.798011684066058 | epot = -15.6613417499238 | etot = -14.6424332456178 -513000 ekin = 0.205824805087872 | erot = 0.758403224578473 | epot = -15.6066612751758 | etot = -14.6424332455094 -514000 ekin = 0.189932244116162 | erot = 0.717614706860426 | epot = -15.5499801963839 | etot = -14.6424332454073 -515000 ekin = 0.173908748199766 | erot = 0.676495918872675 | epot = -15.4928379123882 | etot = -14.6424332453158 -516000 ekin = 0.158407108508993 | erot = 0.635773516025409 | epot = -15.4366138697724 | etot = -14.642433245238 -517000 ekin = 0.144013350183893 | erot = 0.59603314911818 | epot = -15.3824797444781 | etot = -14.642433245176 -518000 ekin = 0.131224514118005 | erot = 0.557712825688994 | epot = -15.3313705849372 | etot = -14.6424332451302 -519000 ekin = 0.120434042405824 | erot = 0.521106495597738 | epot = -15.283973783104 | etot = -14.6424332451004 -520000 ekin = 0.111924165176706 | erot = 0.486376443199764 | epot = -15.2407338534617 | etot = -14.6424332450853 -521000 ekin = 0.105864424815879 | erot = 0.453572806060429 | epot = -15.2018704759591 | etot = -14.6424332450828 -522000 ekin = 0.102315362067395 | erot = 0.422658367131502 | epot = -15.1674069742898 | etot = -14.6424332450909 -523000 ekin = 0.101236366465181 | erot = 0.393536647096984 | epot = -15.137206258669 | etot = -14.6424332451068 -524000 ekin = 0.102496717236757 | erot = 0.366081244308208 | epot = -15.1110112066728 | etot = -14.6424332451278 -525000 ekin = 0.105888887336051 | erot = 0.340164343214671 | epot = -15.0884864757019 | etot = -14.6424332451512 -526000 ekin = 0.111143247850943 | erot = 0.315682368378665 | epot = -15.0692588614045 | etot = -14.6424332451749 -527000 ekin = 0.117943398962438 | erot = 0.29257693780699 | epot = -15.0529535819665 | etot = -14.642433245197 -528000 ekin = 0.12594147425583 | erot = 0.270849598243837 | epot = -15.0392243177155 | etot = -14.6424332452158 -529000 ekin = 0.134772916010411 | erot = 0.250569317239496 | epot = -15.0277754784804 | etot = -14.6424332452305 -530000 ekin = 0.144070383403777 | erot = 0.231872340652232 | epot = -15.0183759692968 | etot = -14.6424332452408 -531000 ekin = 0.153476601970705 | erot = 0.214954741435346 | epot = -15.010864588653 | etot = -14.6424332452469 -532000 ekin = 0.162656054078974 | erot = 0.20005869764927 | epot = -15.0051479969776 | etot = -14.6424332452493 -533000 ekin = 0.171305419081562 | erot = 0.187454143184885 | epot = -15.0011928075152 | etot = -14.6424332452488 -534000 ekin = 0.179162595540481 | erot = 0.1774178426953 | epot = -14.9990136834821 | etot = -14.6424332452463 -535000 ekin = 0.186014006486751 | erot = 0.170212094444198 | epot = -14.9986593461735 | etot = -14.6424332452426 -536000 ekin = 0.191699759240504 | erot = 0.16606514922825 | epot = -15.0001981537073 | etot = -14.6424332452386 -537000 ekin = 0.1961161699316 | erot = 0.165155084981448 | epot = -15.0037045001479 | etot = -14.6424332452348 -538000 ekin = 0.199215220533753 | erot = 0.167598364573304 | epot = -15.0092468303391 | etot = -14.642433245232 -539000 ekin = 0.201000709669645 | erot = 0.173443713619011 | epot = -15.0168776685194 | etot = -14.6424332452308 -540000 ekin = 0.20152116403808 | erot = 0.182671367033565 | epot = -15.0266257763029 | etot = -14.6424332452312 -541000 ekin = 0.200859940141561 | erot = 0.195197211442919 | epot = -15.0384903968184 | etot = -14.642433245234 -542000 ekin = 0.199123298889081 | erot = 0.210880936223622 | epot = -15.0524374803517 | etot = -14.642433245239 -543000 ekin = 0.196427519384058 | erot = 0.229537017789335 | epot = -15.0683977824196 | etot = -14.6424332452462 -544000 ekin = 0.192886294945247 | erot = 0.250947202002153 | epot = -15.0862667422037 | etot = -14.6424332452563 -545000 ekin = 0.18859971088744 | erot = 0.274873110235068 | epot = -15.105906066391 | etot = -14.6424332452685 -546000 ekin = 0.183646045242699 | erot = 0.301067663118862 | epot = -15.1271469536444 | etot = -14.6424332452828 -547000 ekin = 0.178077473818675 | erot = 0.329284179373474 | epot = -15.149794898491 | etot = -14.6424332452988 -548000 ekin = 0.171920510267319 | erot = 0.359282253783652 | epot = -15.173636009367 | etot = -14.642433245316 -549000 ekin = 0.165181670578008 | erot = 0.390829837831177 | epot = -15.1984447537429 | etot = -14.6424332453337 -550000 ekin = 0.157858408655514 | erot = 0.42370132691765 | epot = -15.2239929809246 | etot = -14.6424332453514 -551000 ekin = 0.149954809005953 | erot = 0.457671882716406 | epot = -15.2500599370906 | etot = -14.6424332453683 -552000 ekin = 0.141500835823185 | erot = 0.492508662660431 | epot = -15.2764427438672 | etot = -14.6424332453836 -553000 ekin = 0.132573145481933 | erot = 0.527960055124278 | epot = -15.302966446003 | etot = -14.6424332453968 -554000 ekin = 0.123314645148986 | erot = 0.563744383269626 | epot = -15.3294922738258 | etot = -14.6424332454072 -555000 ekin = 0.113949270903175 | erot = 0.599539792623648 | epot = -15.3559223089416 | etot = -14.6424332454148 -556000 ekin = 0.104788088807786 | erot = 0.634977129563658 | epot = -15.3821984637915 | etot = -14.64243324542 -557000 ekin = 0.0962230654780946 | erot = 0.669637513724504 | epot = -15.4082938246265 | etot = -14.6424332454239 -558000 ekin = 0.0887059614428478 | erot = 0.70305599048067 | epot = -15.4341951973515 | etot = -14.642433245428 -559000 ekin = 0.082711884774194 | erot = 0.734732129424159 | epot = -15.4598772596328 | etot = -14.6424332454344 -560000 ekin = 0.0786899547259911 | erot = 0.764147748398984 | epot = -15.4852709485702 | etot = -14.6424332454453 -561000 ekin = 0.0770067720633791 | erot = 0.790791153076129 | epot = -15.5102311706017 | etot = -14.6424332454622 -562000 ekin = 0.0778911706764789 | erot = 0.814186471629281 | epot = -15.5345108877919 | etot = -14.6424332454862 -563000 ekin = 0.0813901113673084 | erot = 0.83392592548323 | epot = -15.5577492823674 | etot = -14.6424332455168 -564000 ekin = 0.0873448530219544 | erot = 0.849702302565905 | epot = -15.5794804011399 | etot = -14.642433245552 -565000 ekin = 0.0953935152543308 | erot = 0.861338569497384 | epot = -15.59916533034 | etot = -14.6424332455883 -566000 ekin = 0.105001366119722 | erot = 0.868811531657507 | epot = -15.6162461433985 | etot = -14.6424332456212 -567000 ekin = 0.11551478921087 | erot = 0.872266750928371 | epot = -15.6302147857853 | etot = -14.6424332456461 -568000 ekin = 0.126230320990598 | erot = 0.872022546761245 | epot = -15.6406861134104 | etot = -14.6424332456586 -569000 ekin = 0.1364675752055 | erot = 0.868561781938193 | epot = -15.6474626027995 | etot = -14.6424332456558 -570000 ekin = 0.145634823229284 | erot = 0.862511177263077 | epot = -15.650579246129 | etot = -14.6424332456367 -571000 ekin = 0.153278250260132 | erot = 0.854608991356468 | epot = -15.6503204872187 | etot = -14.6424332456021 -572000 ekin = 0.159109636953965 | erot = 0.845662918617004 | epot = -15.6472058011259 | etot = -14.6424332455549 -573000 ekin = 0.163011362017409 | erot = 0.836500892320213 | epot = -15.6419454998373 | etot = -14.6424332454997 -574000 ekin = 0.165021239080183 | erot = 0.82791805820557 | epot = -15.6353725427275 | etot = -14.6424332454418 -575000 ekin = 0.165302195908647 | erot = 0.820623479704516 | epot = -15.6283589210001 | etot = -14.6424332453869 -576000 ekin = 0.164102988101242 | erot = 0.815190165399292 | epot = -15.6217263988412 | etot = -14.6424332453406 -577000 ekin = 0.161716152387198 | erot = 0.812011817944906 | epot = -15.6161612156399 | etot = -14.6424332453078 -578000 ekin = 0.15843856937185 | erot = 0.811269345694985 | epot = -15.6121411603585 | etot = -14.6424332452916 -579000 ekin = 0.154538688869395 | erot = 0.812909695781084 | epot = -15.6098816299448 | etot = -14.6424332452944 -580000 ekin = 0.150232988454514 | erot = 0.816638977242154 | epot = -15.6093052110128 | etot = -14.6424332453162 -581000 ekin = 0.145672809814998 | erot = 0.82193113541131 | epot = -15.6100371905821 | etot = -14.6424332453558 -582000 ekin = 0.140941476791536 | erot = 0.828052590351175 | epot = -15.6114273125529 | etot = -14.6424332454102 -583000 ekin = 0.136060602599188 | erot = 0.834102246896661 | epot = -15.6125960949711 | etot = -14.6424332454752 -584000 ekin = 0.131003759896606 | erot = 0.839065139158589 | epot = -15.6125021446008 | etot = -14.6424332455456 -585000 ekin = 0.125715216483023 | erot = 0.841876757449347 | epot = -15.6100252195477 | etot = -14.6424332456153 -586000 ekin = 0.120131224768948 | erot = 0.841493945667052 | epot = -15.6040584161145 | etot = -14.6424332456785 -587000 ekin = 0.114201380572127 | erot = 0.836967317754023 | epot = -15.5936019440556 | etot = -14.6424332457295 -588000 ekin = 0.10790780822673 | erot = 0.827509595983478 | epot = -15.5778506499738 | etot = -14.6424332457636 -589000 ekin = 0.101280337909716 | erot = 0.812554260673813 | epot = -15.5562678443608 | etot = -14.6424332457773 -590000 ekin = 0.0944063548788227 | erot = 0.791799488420743 | epot = -15.5286390890684 | etot = -14.6424332457688 -591000 ekin = 0.0874345511051893 | erot = 0.765233519223455 | epot = -15.4951013160664 | etot = -14.6424332457378 -592000 ekin = 0.0805723392084907 | erot = 0.733139214285358 | epot = -15.4561447991799 | etot = -14.642433245686 -593000 ekin = 0.0740771594080655 | erot = 0.696077455348817 | epot = -15.4125878603734 | etot = -14.6424332456166 -594000 ekin = 0.0682423089599614 | erot = 0.654850963358217 | epot = -15.3655265178521 | etot = -14.642433245534 -595000 ekin = 0.0633782539014331 | erot = 0.610451848323659 | epot = -15.3162633476688 | etot = -14.6424332454437 -596000 ekin = 0.0597906540649347 | erot = 0.563997548401148 | epot = -15.2662214478178 | etot = -14.6424332453517 -597000 ekin = 0.0577565493623858 | erot = 0.516660644084273 | epot = -15.2168504387106 | etot = -14.642433245264 -598000 ekin = 0.0575003158536081 | erot = 0.469598294353632 | epot = -15.1695318553934 | etot = -14.6424332451862 -599000 ekin = 0.0591710965286251 | erot = 0.423886769451064 | epot = -15.1254911111027 | etot = -14.642433245123 -600000 ekin = 0.0628234356891045 | erot = 0.380465849281436 | epot = -15.0857225300487 | etot = -14.6424332450781 -601000 ekin = 0.0684027903378417 | erot = 0.340096852289044 | epot = -15.0509328876805 | etot = -14.6424332450536 -602000 ekin = 0.0757374499129008 | erot = 0.303336891508804 | epot = -15.0215075864718 | etot = -14.6424332450501 -603000 ekin = 0.0845381560106984 | erot = 0.270530726252426 | epot = -14.9975021273296 | etot = -14.6424332450665 -604000 ekin = 0.0944063594078355 | erot = 0.241820347963454 | epot = -14.9786599524715 | etot = -14.6424332451002 -605000 ekin = 0.104851562460566 | erot = 0.217171224791036 | epot = -14.9644560323985 | etot = -14.6424332451469 -606000 ekin = 0.115317556389835 | erot = 0.196412930356103 | epot = -14.954163731947 | etot = -14.6424332452011 -607000 ekin = 0.125216580353275 | erot = 0.179290709847405 | epot = -14.9469405354574 | etot = -14.6424332452567 -608000 ekin = 0.133969542490564 | erot = 0.165523445157646 | epot = -14.9419262329554 | etot = -14.6424332453072 -609000 ekin = 0.141049537028518 | erot = 0.15486258226509 | epot = -14.9383453646398 | etot = -14.6424332453462 -610000 ekin = 0.146025095175949 | erot = 0.147146040888439 | epot = -14.935604381433 | etot = -14.6424332453686 -611000 ekin = 0.148599079335757 | erot = 0.142341118193739 | epot = -14.9333734429002 | etot = -14.6424332453707 -612000 ekin = 0.148639027542241 | erot = 0.140571068727528 | epot = -14.9316433416205 | etot = -14.6424332453507 -613000 ekin = 0.146195193893338 | erot = 0.142121441395774 | epot = -14.9307498805986 | etot = -14.6424332453095 -614000 ekin = 0.141503544705058 | erot = 0.147424293659482 | epot = -14.9313610836148 | etot = -14.6424332452503 -615000 ekin = 0.134972482669589 | erot = 0.157020849768843 | epot = -14.9344265776168 | etot = -14.6424332451783 -616000 ekin = 0.127153892887477 | erot = 0.17150567977268 | epot = -14.9410928177609 | etot = -14.6424332451008 -617000 ekin = 0.118700960497215 | erot = 0.191457667915335 | epot = -14.9525918734382 | etot = -14.6424332450256 -618000 ekin = 0.110316794781948 | erot = 0.21736458449167 | epot = -14.9701146242348 | etot = -14.6424332449612 -619000 ekin = 0.102698942666097 | erot = 0.249548776233835 | epot = -14.994680963815 | etot = -14.6424332449151 -620000 ekin = 0.0964852203315631 | erot = 0.288101317493937 | epot = -15.0270197827191 | etot = -14.6424332448936 -621000 ekin = 0.0922059091526162 | erot = 0.332831044367888 | epot = -15.0674701984216 | etot = -14.6424332449011 -622000 ekin = 0.090246364710084 | erot = 0.383233451864307 | epot = -15.1159130615138 | etot = -14.6424332449395 -623000 ekin = 0.0908226920702867 | erot = 0.438482716268118 | epot = -15.1717386533468 | etot = -14.6424332450084 -624000 ekin = 0.0939716062521641 | erot = 0.497448307340739 | epot = -15.2338531586981 | etot = -14.6424332451052 -625000 ekin = 0.0995541611224816 | erot = 0.558735886785548 | epot = -15.3007232931327 | etot = -14.6424332452247 -626000 ekin = 0.107271859325762 | erot = 0.620750477457381 | epot = -15.3704555821432 | etot = -14.6424332453601 -627000 ekin = 0.116692826737646 | erot = 0.681778220901968 | epot = -15.440904293143 | etot = -14.6424332455034 -628000 ekin = 0.127285245273582 | erot = 0.740081431770171 | epot = -15.5097999226893 | etot = -14.6424332456456 -629000 ekin = 0.138455039153843 | erot = 0.794000196771077 | epot = -15.5748884817029 | etot = -14.6424332457779 -630000 ekin = 0.149584842937087 | erot = 0.84205264024076 | epot = -15.63407072907 | etot = -14.6424332458922 -631000 ekin = 0.160071499853009 | erot = 0.88302544287862 | epot = -15.6855301887133 | etot = -14.6424332459817 -632000 ekin = 0.169359720292754 | erot = 0.916046503426999 | epot = -15.7278394697613 | etot = -14.6424332460416 -633000 ekin = 0.176970053692527 | erot = 0.94063292294126 | epot = -15.7600362227031 | etot = -14.6424332460693 -634000 ekin = 0.182519961289934 | erot = 0.956709735134238 | epot = -15.7816629424889 | etot = -14.6424332460647 -635000 ekin = 0.185737466035627 | erot = 0.964597760206567 | epot = -15.7927684722724 | etot = -14.6424332460302 -636000 ekin = 0.186467519303287 | erot = 0.964972204256552 | epot = -15.79387296953 | etot = -14.6424332459701 -637000 ekin = 0.184671774604466 | erot = 0.958796660376671 | epot = -15.7859016808713 | etot = -14.6424332458901 -638000 ekin = 0.180422825778035 | erot = 0.947239527073052 | epot = -15.7700955986478 | etot = -14.6424332457967 -639000 ekin = 0.173894119064837 | erot = 0.931581224196235 | epot = -15.747908588958 | etot = -14.642433245697 -640000 ekin = 0.165346701827782 | erot = 0.91312083875339 | epot = -15.7209007861784 | etot = -14.6424332455972 -641000 ekin = 0.155113786103692 | erot = 0.893090060089671 | epot = -15.6906370916964 | etot = -14.6424332455031 -642000 ekin = 0.143583869244217 | erot = 0.872580710306169 | epot = -15.6585978249696 | etot = -14.6424332454192 -643000 ekin = 0.131182953689566 | erot = 0.852490168054334 | epot = -15.6261063670926 | etot = -14.6424332453487 -644000 ekin = 0.118356305761173 | erot = 0.833486853990269 | epot = -15.5942764050451 | etot = -14.6424332452937 -645000 ekin = 0.105550209085081 | erot = 0.815995971212791 | epot = -15.5639794255527 | etot = -14.6424332452548 -646000 ekin = 0.0931942744194625 | erot = 0.800204061931269 | epot = -15.5358315815826 | etot = -14.6424332452318 -647000 ekin = 0.0816850001800769 | erot = 0.786079744440999 | epot = -15.5101979898444 | etot = -14.6424332452233 -648000 ekin = 0.0713713598437978 | erot = 0.773407243193285 | epot = -15.4872118482646 | etot = -14.6424332452275 -649000 ekin = 0.0625431628717075 | erot = 0.761828976530965 | epot = -15.4668053846445 | etot = -14.6424332452418 -650000 ekin = 0.0554227735503044 | erot = 0.750893453414529 | epot = -15.4487494722282 | etot = -14.6424332452633 -651000 ekin = 0.0501605027658098 | erot = 0.74010497844913 | epot = -15.4326987265041 | etot = -14.6424332452892 -652000 ekin = 0.0468336713663308 | erot = 0.728972100421486 | epot = -15.4182390171043 | etot = -14.6424332453165 -653000 ekin = 0.0454490492573673 | erot = 0.717052285945908 | epot = -15.4049345805457 | etot = -14.6424332453424 -654000 ekin = 0.0459481524943306 | erot = 0.703990869784824 | epot = -15.3923722676438 | etot = -14.6424332453647 -655000 ekin = 0.048214749528602 | erot = 0.689552835107499 | epot = -15.3802008300172 | etot = -14.6424332453811 -656000 ekin = 0.0520838761262338 | erot = 0.673646332749968 | epot = -15.3681634542667 | etot = -14.6424332453905 -657000 ekin = 0.0573516620848271 | erot = 0.656337023115609 | epot = -15.356121930592 | etot = -14.6424332453915 -658000 ekin = 0.0637853134927773 | erot = 0.637852348219684 | epot = -15.3440709070967 | etot = -14.6424332453842 -659000 ekin = 0.0711326702869463 | erot = 0.618574815847903 | epot = -15.3321407315039 | etot = -14.642433245369 -660000 ekin = 0.0791308828100933 | erot = 0.59902345470884 | epot = -15.3205875828664 | etot = -14.6424332453475 -661000 ekin = 0.0875139366233532 | erot = 0.57982293974752 | epot = -15.3097701216927 | etot = -14.6424332453218 -662000 ekin = 0.096019000419939 | erot = 0.56166061034769 | epot = -15.3001128560625 | etot = -14.6424332452949 -663000 ekin = 0.104391848885312 | erot = 0.545232746054744 | epot = -15.2920578402104 | etot = -14.6424332452703 -664000 ekin = 0.1123918633903 | erot = 0.531182949318153 | epot = -15.2860080579606 | etot = -14.6424332452521 -665000 ekin = 0.119797262721338 | erot = 0.52003712479683 | epot = -15.2822676327618 | etot = -14.6424332452437 -666000 ekin = 0.126411190063547 | erot = 0.512141060960723 | epot = -15.2809854962723 | etot = -14.642433245248 -667000 ekin = 0.132069035725132 | erot = 0.507607681729055 | epot = -15.2821099627211 | etot = -14.6424332452669 -668000 ekin = 0.136646914542203 | erot = 0.506281315754288 | epot = -15.2853614755971 | etot = -14.6424332453006 -669000 ekin = 0.140070616013021 | erot = 0.50772556617166 | epot = -15.2902294275324 | etot = -14.6424332453477 -670000 ekin = 0.142323740906679 | erot = 0.511239425098687 | epot = -15.2959964114102 | etot = -14.6424332454048 -671000 ekin = 0.143453306303064 | erot = 0.515903234044996 | epot = -15.3017897858152 | etot = -14.6424332454671 -672000 ekin = 0.143571012732418 | erot = 0.520652256718186 | epot = -15.3066565149793 | etot = -14.6424332455287 -673000 ekin = 0.142848733836954 | erot = 0.524371563357074 | epot = -15.3096535427774 | etot = -14.6424332455834 -674000 ekin = 0.141507613277718 | erot = 0.526002362930759 | epot = -15.3099432218339 | etot = -14.6424332456254 -675000 ekin = 0.13980130282559 | erot = 0.524647629024632 | epot = -15.3068821775003 | etot = -14.6424332456501 -676000 ekin = 0.137995095210639 | erot = 0.519664439041565 | epot = -15.3000927799068 | etot = -14.6424332456546 -677000 ekin = 0.136343677285182 | erot = 0.510732098518056 | epot = -15.2895090214411 | etot = -14.6424332456378 -678000 ekin = 0.1350706641226 | erot = 0.49788857525657 | epot = -15.2753924849801 | etot = -14.6424332456009 -679000 ekin = 0.134352810444862 | erot = 0.481532294132637 | epot = -15.2583183501238 | etot = -14.6424332455463 -680000 ekin = 0.13431086265575 | erot = 0.462390968605425 | epot = -15.2391350767393 | etot = -14.6424332454781 -681000 ekin = 0.135007638923122 | erot = 0.441462941784965 | epot = -15.218903826109 | etot = -14.6424332454009 -682000 ekin = 0.136452461524589 | erot = 0.419938865037975 | epot = -15.1988245718825 | etot = -14.6424332453199 -683000 ekin = 0.138609887397947 | erot = 0.399112293315654 | epot = -15.1801554259539 | etot = -14.6424332452403 -684000 ekin = 0.141410065648264 | erot = 0.380287181762594 | epot = -15.1641304925779 | etot = -14.6424332451671 -685000 ekin = 0.144758102722244 | erot = 0.364688846299647 | epot = -15.1518801941267 | etot = -14.6424332451049 -686000 ekin = 0.14854046711943 | erot = 0.353383275614745 | epot = -15.144356987792 | etot = -14.6424332450578 -687000 ekin = 0.152627512098722 | erot = 0.347208212231136 | epot = -15.1422689693591 | etot = -14.6424332450292 -688000 ekin = 0.156872371008243 | erot = 0.346718408271441 | epot = -15.1460240243019 | etot = -14.6424332450222 -689000 ekin = 0.161107527974782 | erot = 0.352146941115747 | epot = -15.1556877141288 | etot = -14.6424332450382 -690000 ekin = 0.16514108738065 | erot = 0.363384304942447 | epot = -15.1709586374008 | etot = -14.6424332450777 -691000 ekin = 0.168755042649082 | erot = 0.379976931156971 | epot = -15.1911652189453 | etot = -14.6424332451393 -692000 ekin = 0.171707649703694 | erot = 0.401146558398203 | epot = -15.2152874533219 | etot = -14.64243324522 -693000 ekin = 0.173741393443093 | erot = 0.425831232789035 | epot = -15.2420058715475 | etot = -14.6424332453154 -694000 ekin = 0.174597110624773 | erot = 0.452747528140487 | epot = -15.2697778841841 | etot = -14.6424332454189 -695000 ekin = 0.174033757472237 | erot = 0.480471830922762 | epot = -15.2969388339179 | etot = -14.6424332455229 -696000 ekin = 0.171852263364752 | erot = 0.50753639815869 | epot = -15.3218219071425 | etot = -14.6424332456191 -697000 ekin = 0.167921065290924 | erot = 0.532533688693483 | epot = -15.3428879996837 | etot = -14.6424332456993 -698000 ekin = 0.162200409477016 | erot = 0.554220619925494 | epot = -15.3588542751586 | etot = -14.6424332457561 -699000 ekin = 0.154762415715625 | erot = 0.571613361028384 | epot = -15.3688090225278 | etot = -14.6424332457837 -700000 ekin = 0.14580423000878 | erot = 0.584063387088342 | epot = -15.3723008628759 | etot = -14.6424332457788 -701000 ekin = 0.135652269558589 | erot = 0.591306922721675 | epot = -15.3693924380207 | etot = -14.6424332457404 -702000 ekin = 0.124756460207458 | erot = 0.593482464349287 | epot = -15.3606721702276 | etot = -14.6424332456708 -703000 ekin = 0.11367432595124 | erot = 0.591114401857202 | epot = -15.3472219733832 | etot = -14.6424332455747 -704000 ekin = 0.10304567594557 | erot = 0.585064323196779 | epot = -15.3305432446014 | etot = -14.6424332454591 -705000 ekin = 0.093559358196298 | erot = 0.576454826534863 | epot = -15.3124474300637 | etot = -14.6424332453326 -706000 ekin = 0.0859140824284676 | erot = 0.566573150256884 | epot = -15.2949204778901 | etot = -14.6424332452047 -707000 ekin = 0.0807756759557719 | erot = 0.556763427609663 | epot = -15.2799723486508 | etot = -14.6424332450854 -708000 ekin = 0.0787333622599937 | erot = 0.548316855291462 | epot = -15.269483462535 | etot = -14.6424332449836 -709000 ekin = 0.0802577669150991 | erot = 0.542368667954137 | epot = -15.2650596797766 | etot = -14.6424332449074 -710000 ekin = 0.0856633545528662 | erot = 0.539809747049451 | epot = -15.2679063464654 | etot = -14.642433244863 -711000 ekin = 0.0950778519027508 | erot = 0.541219180891539 | epot = -15.2787302776488 | etot = -14.6424332448545 -712000 ekin = 0.10842087662218 | erot = 0.546822307911647 | epot = -15.2976764294171 | etot = -14.6424332448833 -713000 ekin = 0.125393451694867 | erot = 0.556476834657881 | epot = -15.3243035313012 | etot = -14.6424332449484 -714000 ekin = 0.145479367621472 | erot = 0.569687600119496 | epot = -15.3576002127874 | etot = -14.6424332450464 -715000 ekin = 0.167958541116859 | erot = 0.585648522303218 | epot = -15.3960403085917 | etot = -14.6424332451716 -716000 ekin = 0.191931735851232 | erot = 0.60330829253147 | epot = -15.4376732736993 | etot = -14.6424332453166 -717000 ekin = 0.216355400176894 | erot = 0.621454592037079 | epot = -15.4802432376866 | etot = -14.6424332454726 -718000 ekin = 0.24008505651044 | erot = 0.638810139731556 | epot = -15.521328441872 | etot = -14.64243324563 -719000 ekin = 0.261925698575349 | erot = 0.654132895986116 | epot = -15.558491840341 | etot = -14.6424332457795 -720000 ekin = 0.280687969311591 | erot = 0.666312379867061 | epot = -15.5894335950905 | etot = -14.6424332459119 -721000 ekin = 0.295249345589153 | erot = 0.674454385927668 | epot = -15.6121369775356 | etot = -14.6424332460188 -722000 ekin = 0.304619886333733 | erot = 0.67794741025506 | epot = -15.6250005426818 | etot = -14.642433246093 -723000 ekin = 0.308011983727977 | erot = 0.676505724570366 | epot = -15.6269509544273 | etot = -14.642433246129 -724000 ekin = 0.304912667284364 | erot = 0.670186105899516 | epot = -15.6175320193064 | etot = -14.6424332461225 -725000 ekin = 0.295155116711556 | erot = 0.659377522489347 | epot = -15.5969658852725 | etot = -14.6424332460716 -726000 ekin = 0.278983134900095 | erot = 0.644765363158316 | epot = -15.5661817440347 | etot = -14.6424332459763 -727000 ekin = 0.257098790794367 | erot = 0.627273860362841 | epot = -15.5268058969971 | etot = -14.6424332458399 -728000 ekin = 0.230680158274935 | erot = 0.607992016180396 | epot = -15.481105420124 | etot = -14.6424332456687 -729000 ekin = 0.201354496276678 | erot = 0.588089464034347 | epot = -15.4318772057843 | etot = -14.6424332454733 -730000 ekin = 0.171114103979303 | erot = 0.568729214715612 | epot = -15.382276563963 | etot = -14.6424332452681 -731000 ekin = 0.142168923912273 | erot = 0.55098413507054 | epot = -15.3355863040536 | etot = -14.6424332450708 -732000 ekin = 0.11674200710062 | erot = 0.535763349043798 | epot = -15.294938601045 | etot = -14.6424332449006 -733000 ekin = 0.096829302757611 | erot = 0.523753647321743 | epot = -15.263016194855 | etot = -14.6424332447757 -734000 ekin = 0.0839596135620853 | erot = 0.515379592338737 | epot = -15.2417724506111 | etot = -14.6424332447103 -735000 ekin = 0.0789983701793321 | erot = 0.510784464196176 | epot = -15.2322160790871 | etot = -14.6424332447116 -736000 ekin = 0.0820355551944618 | erot = 0.509832642266591 | epot = -15.2343014422397 | etot = -14.6424332447787 -737000 ekin = 0.0923827123871921 | erot = 0.51213255085583 | epot = -15.2469485081446 | etot = -14.6424332449015 -738000 ekin = 0.108680448514306 | erot = 0.517077971028045 | epot = -15.2681916646065 | etot = -14.6424332450641 -739000 ekin = 0.12909371568349 | erot = 0.523904364927467 | epot = -15.2954313258571 | etot = -14.6424332452461 -740000 ekin = 0.151555277793912 | erot = 0.531755895780646 | epot = -15.3257444190018 | etot = -14.6424332454272 -741000 ekin = 0.174012721806563 | erot = 0.539758083454575 | epot = -15.3562040508503 | etot = -14.6424332455892 -742000 ekin = 0.194640916831384 | erot = 0.547090549700596 | epot = -15.3841647122502 | etot = -14.6424332457182 -743000 ekin = 0.211995737398717 | erot = 0.553054125338761 | epot = -15.4074831085432 | etot = -14.6424332458057 -744000 ekin = 0.22510050872294 | erot = 0.557126762310943 | epot = -15.4246605168818 | etot = -14.6424332458479 -745000 ekin = 0.233469424486957 | erot = 0.559003260240344 | epot = -15.4349059305732 | etot = -14.6424332458459 -746000 ekin = 0.2370799134654 | erot = 0.558614810501353 | epot = -15.438127969771 | etot = -14.6424332458043 -747000 ekin = 0.236308652985431 | erot = 0.556125790084381 | epot = -15.4348676888002 | etot = -14.6424332457304 -748000 ekin = 0.231845097888603 | erot = 0.551907079331795 | epot = -15.426185422854 | etot = -14.6424332456336 -749000 ekin = 0.224593843485089 | erot = 0.546487360031397 | epot = -15.4135144490409 | etot = -14.6424332455244 -750000 ekin = 0.215574369393293 | erot = 0.540486233486826 | epot = -15.3984938482942 | etot = -14.6424332454141 -751000 ekin = 0.205824583428116 | erot = 0.534535356766581 | epot = -15.382793185508 | etot = -14.6424332453133 -752000 ekin = 0.196313335743831 | erot = 0.529195815220672 | epot = -15.367942396196 | etot = -14.6424332452315 -753000 ekin = 0.187866475789607 | erot = 0.524881252734243 | epot = -15.3551809737002 | etot = -14.6424332451763 -754000 ekin = 0.181110613628491 | erot = 0.521796491100216 | epot = -15.3453403498808 | etot = -14.6424332451521 -755000 ekin = 0.176438042206941 | erot = 0.519900210809565 | epot = -15.3387714981766 | etot = -14.6424332451601 -756000 ekin = 0.173994962649976 | erot = 0.518897676287607 | epot = -15.3353258841355 | etot = -14.642433245198 -757000 ekin = 0.173693190273855 | erot = 0.518265706185164 | epot = -15.334392141719 | etot = -14.6424332452599 -758000 ekin = 0.175243155018327 | erot = 0.517307659824269 | epot = -15.3349840601804 | etot = -14.6424332453378 -759000 ekin = 0.178203703096713 | erot = 0.515231902167182 | epot = -15.3358688506856 | etot = -14.6424332454217 -760000 ekin = 0.182042463552564 | erot = 0.511243837951639 | epot = -15.3357195470058 | etot = -14.6424332455016 -761000 ekin = 0.186199747764933 | erot = 0.504639825550332 | epot = -15.3332728188834 | etot = -14.6424332455682 -762000 ekin = 0.190149235948613 | erot = 0.494891409036607 | epot = -15.3274738905993 | etot = -14.6424332456141 -763000 ekin = 0.193449921097585 | erot = 0.481710238289879 | epot = -15.3175934050219 | etot = -14.6424332456345 -764000 ekin = 0.195785552428752 | erot = 0.465087294354156 | epot = -15.3033060924098 | etot = -14.6424332456268 -765000 ekin = 0.196989678186294 | erot = 0.445303873494492 | epot = -15.2847267972726 | etot = -14.6424332455918 -766000 ekin = 0.197055919183484 | erot = 0.422915440294251 | epot = -15.26240460501 | etot = -14.6424332455322 -767000 ekin = 0.19613407649359 | erot = 0.398712320924831 | epot = -15.2372796428711 | etot = -14.6424332454526 -768000 ekin = 0.194513096651386 | erot = 0.373662938959647 | epot = -15.2106092809703 | etot = -14.6424332453593 -769000 ekin = 0.192592017625304 | erot = 0.348845887486037 | epot = -15.1838711503705 | etot = -14.6424332452592 -770000 ekin = 0.190840163683791 | erot = 0.325376840212305 | epot = -15.1586502490562 | etot = -14.6424332451601 -771000 ekin = 0.189748397224452 | erot = 0.304335529899573 | epot = -15.136517172194 | etot = -14.64243324507 -772000 ekin = 0.189774341847263 | erot = 0.286697153920281 | epot = -15.1189047407638 | etot = -14.6424332449962 -773000 ekin = 0.191286034496866 | erot = 0.273271857835351 | epot = -15.1069911372776 | etot = -14.6424332449453 -774000 ekin = 0.194510000604709 | erot = 0.264655458968876 | epot = -15.101598704496 | etot = -14.6424332449224 -775000 ekin = 0.199490639675106 | erot = 0.261194193154614 | epot = -15.1031180777597 | etot = -14.64243324493 -776000 ekin = 0.206067477061454 | erot = 0.262965803934464 | epot = -15.1114665259641 | etot = -14.6424332449682 -777000 ekin = 0.213875019081943 | erot = 0.269778568412073 | epot = -15.1260868325284 | etot = -14.6424332450344 -778000 ekin = 0.222366868961404 | erot = 0.281188790675987 | epot = -15.1459889047605 | etot = -14.6424332451231 -779000 ekin = 0.230862102265719 | erot = 0.296535944176208 | epot = -15.169831291669 | etot = -14.6424332452271 -780000 ekin = 0.238608567016806 | erot = 0.31499316909211 | epot = -15.1960349814464 | etot = -14.6424332453374 -781000 ekin = 0.244855557739756 | erot = 0.335629445236695 | epot = -15.2229182484214 | etot = -14.6424332454449 -782000 ekin = 0.248927612477286 | erot = 0.357478674286886 | epot = -15.2488395323048 | etot = -14.6424332455406 -783000 ekin = 0.250291897528993 | erot = 0.379610269028342 | epot = -15.2723354121742 | etot = -14.6424332456169 -784000 ekin = 0.248613283253222 | erot = 0.401195731122937 | epot = -15.2922422600437 | etot = -14.6424332456676 -785000 ekin = 0.243793133451402 | erot = 0.421566090466529 | epot = -15.3077924696065 | etot = -14.6424332456886 -786000 ekin = 0.23598950185365 | erot = 0.44025590520682 | epot = -15.3186786527387 | etot = -14.6424332456782 -787000 ekin = 0.225617610785865 | erot = 0.457030673432359 | epot = -15.3250815298553 | etot = -14.6424332456371 -788000 ekin = 0.213330260903178 | erot = 0.471895861695948 | epot = -15.3276593681676 | etot = -14.6424332455685 -789000 ekin = 0.199978499678579 | erot = 0.485087183883026 | epot = -15.3274989290395 | etot = -14.6424332454779 -790000 ekin = 0.186553834704508 | erot = 0.49704314124288 | epot = -15.32603022132 | etot = -14.6424332453726 -791000 ekin = 0.174114766793481 | erot = 0.508362048569847 | epot = -15.3249100606249 | etot = -14.6424332452616 -792000 ekin = 0.163702420432414 | erot = 0.519746739180895 | epot = -15.3258824047679 | etot = -14.6424332451546 -793000 ekin = 0.156252224966309 | erot = 0.53194082298947 | epot = -15.3306262930168 | etot = -14.642433245061 -794000 ekin = 0.152510350034315 | erot = 0.545660777315094 | epot = -15.3406043723391 | etot = -14.6424332449897 -795000 ekin = 0.152964251156891 | erot = 0.5615283269811 | epot = -15.3569258230857 | etot = -14.6424332449477 -796000 ekin = 0.157795747355246 | erot = 0.580007578778131 | epot = -15.3802365710729 | etot = -14.6424332449395 -797000 ekin = 0.166862457855134 | erot = 0.601351255569813 | epot = -15.4106469583918 | etot = -14.6424332449668 -798000 ekin = 0.179709603428539 | erot = 0.62556012184583 | epot = -15.4477029703029 | etot = -14.6424332450285 -799000 ekin = 0.195609966057053 | erot = 0.652359247176983 | epot = -15.490402458355 | etot = -14.642433245121 -800000 ekin = 0.213626158786136 | erot = 0.68119402187417 | epot = -15.5372534258983 | etot = -14.642433245238 -801000 ekin = 0.232687040188266 | erot = 0.711247726387183 | epot = -15.5863680119474 | etot = -14.642433245372 -802000 ekin = 0.251669429100998 | erot = 0.741480919836821 | epot = -15.6355835944519 | etot = -14.642433245514 -803000 ekin = 0.269477067853637 | erot = 0.770691008421927 | epot = -15.6826013219306 | etot = -14.642433245655 -804000 ekin = 0.285110541453573 | erot = 0.797588259159231 | epot = -15.7251320463985 | etot = -14.6424332457857 -805000 ekin = 0.297723982502801 | erot = 0.820882528800413 | epot = -15.7610397572012 | etot = -14.6424332458979 -806000 ekin = 0.306666387684663 | erot = 0.839373432914301 | epot = -15.7884730665838 | etot = -14.6424332459848 -807000 ekin = 0.311506975554225 | erot = 0.852035914446659 | epot = -15.8059761360419 | etot = -14.642433246041 -808000 ekin = 0.312045176252483 | erot = 0.858093398528957 | epot = -15.812571820845 | etot = -14.6424332460636 -809000 ekin = 0.308306642387543 | erot = 0.857071970759347 | epot = -15.8078118591986 | etot = -14.6424332460517 -810000 ekin = 0.300527220561017 | erot = 0.848831113929473 | epot = -15.7917915804974 | etot = -14.6424332460069 -811000 ekin = 0.289127204421129 | erot = 0.833569138622877 | epot = -15.7651295889766 | etot = -14.6424332459326 -812000 ekin = 0.274678427602343 | erot = 0.811804116493732 | epot = -15.72891578993 | etot = -14.6424332458339 -813000 ekin = 0.257866835583857 | erot = 0.784333459543394 | epot = -15.6846335408442 | etot = -14.642433245717 -814000 ekin = 0.23945308059417 | erot = 0.752176980197134 | epot = -15.6340633063801 | etot = -14.6424332455888 -815000 ekin = 0.220233415151649 | erot = 0.716509170267373 | epot = -15.5791758308753 | etot = -14.6424332454563 -816000 ekin = 0.201002751046645 | erot = 0.678586569748774 | epot = -15.5220225661215 | etot = -14.6424332453261 -817000 ekin = 0.182521261080257 | erot = 0.639675603865673 | epot = -15.4646301101501 | etot = -14.6424332452042 -818000 ekin = 0.16548540152787 | erot = 0.600985363832187 | epot = -15.4089040104558 | etot = -14.6424332450958 -819000 ekin = 0.15050378978045 | erot = 0.563608719250084 | epot = -15.3565457540356 | etot = -14.642433245005 -820000 ekin = 0.138078032178526 | erot = 0.528474068973221 | epot = -15.3089853460867 | etot = -14.6424332449349 -821000 ekin = 0.1285883867302 | erot = 0.496309093118672 | epot = -15.2673307247365 | etot = -14.6424332448876 -822000 ekin = 0.12228406613689 | erot = 0.467617125516686 | epot = -15.2323344365175 | etot = -14.6424332448639 -823000 ekin = 0.119278020924427 | erot = 0.442666228479689 | epot = -15.204377494268 | etot = -14.6424332448639 -824000 ekin = 0.119546158603772 | erot = 0.421490682739598 | epot = -15.1834700862299 | etot = -14.6424332448865 -825000 ekin = 0.122931110514646 | erot = 0.403904342224695 | epot = -15.1692686976689 | etot = -14.6424332449295 -826000 ekin = 0.129150803764422 | erot = 0.389525075000924 | epot = -15.1611091237554 | etot = -14.64243324499 -827000 ekin = 0.137812176399265 | erot = 0.377809252271385 | epot = -15.1580546737348 | etot = -14.6424332450642 -828000 ekin = 0.148430331608458 | erot = 0.368094906963596 | epot = -15.1589584837193 | etot = -14.6424332451472 -829000 ekin = 0.160453205761757 | erot = 0.3596517375127 | epot = -15.1625381885084 | etot = -14.6424332452339 -830000 ekin = 0.173291382896823 | erot = 0.351735589545891 | epot = -15.1674602177611 | etot = -14.6424332453184 -831000 ekin = 0.186352012963015 | erot = 0.343644456330365 | epot = -15.1724297146884 | etot = -14.642433245395 -832000 ekin = 0.199074924605492 | erot = 0.334772487921431 | epot = -15.1762806579853 | etot = -14.6424332454584 -833000 ekin = 0.210968084880519 | erot = 0.324658115189106 | epot = -15.1780594455734 | etot = -14.6424332455038 -834000 ekin = 0.22163875725694 | erot = 0.313022323442632 | epot = -15.1770943262278 | etot = -14.6424332455283 -835000 ekin = 0.230816330001906 | erot = 0.299793483326875 | epot = -15.1730430588591 | etot = -14.6424332455304 -836000 ekin = 0.238363132174156 | erot = 0.285116039960992 | epot = -15.165912417646 | etot = -14.6424332455109 -837000 ekin = 0.244270841530906 | erot = 0.269341751259717 | epot = -15.1560458382634 | etot = -14.6424332454728 -838000 ekin = 0.248642320235629 | erot = 0.253003904103877 | epot = -15.1440794697601 | etot = -14.6424332454206 -839000 ekin = 0.251661569327587 | erot = 0.236776758987145 | epot = -15.1308715736748 | etot = -14.6424332453601 -840000 ekin = 0.253557306828163 | erot = 0.221424057161458 | epot = -15.117414609287 | etot = -14.6424332452974 -841000 ekin = 0.254567562696712 | erot = 0.207741475743549 | epot = -15.1047422836783 | etot = -14.642433245238 -842000 ekin = 0.254912814683648 | erot = 0.19649826235426 | epot = -15.093844322224 | etot = -14.6424332451861 -843000 ekin = 0.254783130765732 | erot = 0.18838292178705 | epot = -15.0855992976972 | etot = -14.6424332451444 -844000 ekin = 0.254340789697802 | erot = 0.183956927272122 | epot = -15.0807309620839 | etot = -14.642433245114 -845000 ekin = 0.253734932891637 | erot = 0.183619247980649 | epot = -15.079787425967 | etot = -14.6424332450947 -846000 ekin = 0.25312050419609 | erot = 0.187583282239926 | epot = -15.0831370315219 | etot = -14.6424332450859 -847000 ekin = 0.252671650088207 | erot = 0.195866742639201 | epot = -15.0909716378148 | etot = -14.6424332450873 -848000 ekin = 0.252580915310227 | erot = 0.208294222463247 | epot = -15.1033083828726 | etot = -14.6424332450991 -849000 ekin = 0.253039966848203 | erot = 0.224511555531949 | epot = -15.1199847675021 | etot = -14.642433245122 -850000 ekin = 0.254204001798466 | erot = 0.244010590097926 | epot = -15.1406478370531 | etot = -14.6424332451567 -851000 ekin = 0.25614833902674 | erot = 0.266162563602757 | epot = -15.1647441478328 | etot = -14.6424332452033 -852000 ekin = 0.258829686440543 | erot = 0.290257858698332 | epot = -15.1915207903994 | etot = -14.6424332452605 -853000 ekin = 0.262064657828545 | erot = 0.315549558167831 | epot = -15.2200474613219 | etot = -14.6424332453255 -854000 ekin = 0.265534116122616 | erot = 0.341297947736459 | epot = -15.2492653092525 | etot = -14.6424332453934 -855000 ekin = 0.26881517465356 | erot = 0.366813004430954 | epot = -15.2780614245429 | etot = -14.6424332454584 -856000 ekin = 0.2714354869546 | erot = 0.391492007901482 | epot = -15.3053607403704 | etot = -14.6424332455143 -857000 ekin = 0.272939108063026 | erot = 0.414849750473433 | epot = -15.3302221040922 | etot = -14.6424332455557 -858000 ekin = 0.272951155039827 | erot = 0.436539390688028 | epot = -15.3519237913065 | etot = -14.6424332455787 -859000 ekin = 0.27122988067654 | erot = 0.456362750059338 | epot = -15.370025876317 | etot = -14.6424332455811 -860000 ekin = 0.267698633834005 | erot = 0.474269718460678 | epot = -15.3844015978584 | etot = -14.6424332455637 -861000 ekin = 0.262455001753023 | erot = 0.490347316007822 | epot = -15.3952355632891 | etot = -14.6424332455283 -862000 ekin = 0.255758797176847 | erot = 0.504799761298972 | epot = -15.4029918039546 | etot = -14.6424332454788 -863000 ekin = 0.248003564341593 | erot = 0.517921532812577 | epot = -15.408358342574 | etot = -14.6424332454198 -864000 ekin = 0.239677655585047 | erot = 0.530065823503499 | epot = -15.412176724445 | etot = -14.6424332453565 -865000 ekin = 0.23132088944558 | erot = 0.541610953534477 | epot = -15.4153650882737 | etot = -14.6424332452936 -866000 ekin = 0.223481813676492 | erot = 0.552927233332167 | epot = -15.4188422922443 | etot = -14.6424332452356 -867000 ekin = 0.21667917449216 | erot = 0.564346499432584 | epot = -15.4234589191109 | etot = -14.6424332451862 -868000 ekin = 0.211369750018423 | erot = 0.576136138939141 | epot = -15.4299391341058 | etot = -14.6424332451482 -869000 ekin = 0.207923502308487 | erot = 0.588478941151825 | epot = -15.4388356885839 | etot = -14.6424332451236 -870000 ekin = 0.206606153000579 | erot = 0.601459626890824 | epot = -15.4504990250046 | etot = -14.6424332451132 -871000 ekin = 0.207568796758706 | erot = 0.615058451106102 | epot = -15.4650604929822 | etot = -14.6424332451174 -872000 ekin = 0.210843969902103 | erot = 0.629151875760072 | epot = -15.4824290907977 | etot = -14.6424332451355 -873000 ekin = 0.216347593119445 | erot = 0.643519970834179 | epot = -15.5023008091198 | etot = -14.6424332451662 -874000 ekin = 0.223886305143434 | erot = 0.657859909731246 | epot = -15.5241794600821 | etot = -14.6424332452075 -875000 ekin = 0.233169807553067 | erot = 0.671804662211551 | epot = -15.5474077150215 | etot = -14.6424332452569 -876000 ekin = 0.243827877963456 | erot = 0.684945735800616 | epot = -15.5712068590756 | etot = -14.6424332453115 -877000 ekin = 0.255431632545719 | erot = 0.696858567355222 | epot = -15.5947234452689 | etot = -14.642433245368 -878000 ekin = 0.267518408512945 | erot = 0.707128927389438 | epot = -15.6170805813253 | etot = -14.6424332454229 -879000 ekin = 0.279619300258663 | erot = 0.715378495721848 | epot = -15.6374310414535 | etot = -14.642433245473 -880000 ekin = 0.291287955020082 | erot = 0.721287639199831 | epot = -15.655008839735 | etot = -14.6424332455151 -881000 ekin = 0.302128778464172 | erot = 0.724613422811349 | epot = -15.6691754468222 | etot = -14.6424332455467 -882000 ekin = 0.311822304068348 | erot = 0.72520106817747 | epot = -15.6794566178122 | etot = -14.6424332455663 -883000 ekin = 0.32014524378723 | erot = 0.722987481104759 | epot = -15.6855659704652 | etot = -14.6424332455732 -884000 ekin = 0.326982762198449 | erot = 0.717996120159773 | epot = -15.6874121279262 | etot = -14.642433245568 -885000 ekin = 0.332330882212052 | erot = 0.710323349672674 | epot = -15.6850874774371 | etot = -14.6424332455524 -886000 ekin = 0.336287673330606 | erot = 0.700117442976865 | epot = -15.6788383618368 | etot = -14.6424332455294 -887000 ekin = 0.339032964151287 | erot = 0.687552454437637 | epot = -15.6690186640915 | etot = -14.6424332455026 -888000 ekin = 0.340797654544087 | erot = 0.672800100946149 | epot = -15.6560310009666 | etot = -14.6424332454764 -889000 ekin = 0.341825106158792 | erot = 0.656003407102967 | epot = -15.6402617587166 | etot = -14.6424332454548 -890000 ekin = 0.34232834757507 | erot = 0.637256013166648 | epot = -15.6220176061832 | etot = -14.6424332454415 -891000 ekin = 0.342447730492025 | erot = 0.616590618571196 | epot = -15.6014715945022 | etot = -14.642433245439 -892000 ekin = 0.342214057411764 | erot = 0.593979026507483 | epot = -15.5786263293677 | etot = -14.6424332454484 -893000 ekin = 0.341522004910226 | erot = 0.569344767734754 | epot = -15.5533000181142 | etot = -14.6424332454692 -894000 ekin = 0.340117934117732 | erot = 0.542587519917767 | epot = -15.5251386995347 | etot = -14.6424332454992 -895000 ekin = 0.337605044782691 | erot = 0.513616778982377 | epot = -15.4936550692997 | etot = -14.6424332455346 -896000 ekin = 0.333467462872541 | erot = 0.482390775176039 | epot = -15.4582914836189 | etot = -14.6424332455703 -897000 ekin = 0.327113397522298 | erot = 0.448955709004864 | epot = -15.4185023521275 | etot = -14.6424332456003 -898000 ekin = 0.317936017621705 | erot = 0.413480165460747 | epot = -15.3738494287008 | etot = -14.6424332456183 -899000 ekin = 0.305389123797813 | erot = 0.376280077470634 | epot = -15.3241024468866 | etot = -14.6424332456181 -900000 ekin = 0.289072881398238 | erot = 0.337830752319679 | epot = -15.2693368793119 | etot = -14.642433245594 -901000 ekin = 0.268822686263766 | erot = 0.298764046956941 | epot = -15.2100199787623 | etot = -14.6424332455416 -902000 ekin = 0.244791653973854 | erot = 0.259850521116686 | epot = -15.147075420549 | etot = -14.6424332454585 -903000 ekin = 0.217514571467877 | erot = 0.2219680472084 | epot = -15.0819158640211 | etot = -14.6424332453448 -904000 ekin = 0.187939204416865 | erot = 0.18605969200996 | epot = -15.016432141631 | etot = -14.6424332452042 -905000 ekin = 0.157410847736454 | erot = 0.153084564880819 | epot = -14.9529286576615 | etot = -14.6424332450442 -906000 ekin = 0.127599356275869 | erot = 0.123965703542124 | epot = -14.8939983046943 | etot = -14.6424332448764 -907000 ekin = 0.100365589134273 | erot = 0.0995389863865968 | epot = -14.8423378202365 | etot = -14.6424332447156 -908000 ekin = 0.0775759855969076 | erot = 0.0805066337373332 | epot = -14.8005158639122 | etot = -14.6424332445779 -909000 ekin = 0.060887695004245 | erot = 0.0673982354544352 | epot = -14.7707191749376 | etot = -14.6424332444789 -910000 ekin = 0.051538292298201 | erot = 0.0605415547689986 | epot = -14.7545130914979 | etot = -14.6424332444307 -911000 ekin = 0.0501789452889314 | erot = 0.0600446989611976 | epot = -14.7526568886895 | etot = -14.6424332444394 -912000 ekin = 0.0567846925720761 | erot = 0.0657906450222932 | epot = -14.7650085820985 | etot = -14.6424332445042 -913000 ekin = 0.0706603747930264 | erot = 0.0774445361866898 | epot = -14.7905381555969 | etot = -14.6424332446172 -914000 ekin = 0.0905398584091763 | erot = 0.0944735694303653 | epot = -14.8274466726047 | etot = -14.6424332447652 -915000 ekin = 0.114756144628428 | erot = 0.116178630207615 | epot = -14.8733680197682 | etot = -14.6424332449321 -916000 ekin = 0.141447043402292 | erot = 0.141736093139118 | epot = -14.9256163816431 | etot = -14.6424332451017 -917000 ekin = 0.168758535419861 | erot = 0.170247440488538 | epot = -14.9814392211683 | etot = -14.6424332452599 -918000 ekin = 0.195014913439662 | erot = 0.200793639368136 | epot = -15.0382417982035 | etot = -14.6424332453957 -919000 ekin = 0.218837422083706 | erot = 0.232490666335444 | epot = -15.0937613339213 | etot = -14.6424332455022 -920000 ekin = 0.239206641023781 | erot = 0.264542267091206 | epot = -15.1461821536913 | etot = -14.6424332455763 -921000 ekin = 0.255474577148722 | erot = 0.29628605080145 | epot = -15.1941938735681 | etot = -14.6424332456179 -922000 ekin = 0.26733863121584 | erot = 0.327229363204498 | epot = -15.2370012400495 | etot = -14.6424332456292 -923000 ekin = 0.274791412214288 | erot = 0.357072039936907 | epot = -15.2742966977651 | etot = -14.6424332456139 -924000 ekin = 0.278059017516471 | erot = 0.385714059432095 | epot = -15.3062063225254 | etot = -14.6424332455768 -925000 ekin = 0.277537405168489 | erot = 0.413247220094928 | epot = -15.3332178707869 | etot = -14.6424332455235 -926000 ekin = 0.273733135238468 | erot = 0.439931173660914 | epot = -15.3560975543588 | etot = -14.6424332454594 -927000 ekin = 0.26721185964169 | erot = 0.466155363881716 | epot = -15.3758004689138 | etot = -14.6424332453904 -928000 ekin = 0.258555847536273 | erot = 0.492389553502083 | epot = -15.3933786463605 | etot = -14.6424332453221 -929000 ekin = 0.248330567892114 | erot = 0.519126582981251 | epot = -15.4098903961332 | etot = -14.6424332452599 -930000 ekin = 0.237059747166417 | erot = 0.546821711631313 | epot = -15.4263147040061 | etot = -14.6424332452084 -931000 ekin = 0.225208144806099 | erot = 0.575833282923054 | epot = -15.4434746729006 | etot = -14.6424332451714 -932000 ekin = 0.213171319366128 | erot = 0.606369490851291 | epot = -15.4619740553693 | etot = -14.6424332451519 -933000 ekin = 0.201271722996209 | erot = 0.638445690378466 | epot = -15.482150658526 | etot = -14.6424332451513 -934000 ekin = 0.189760460110485 | erot = 0.671856006698808 | epot = -15.5040497119792 | etot = -14.6424332451699 -935000 ekin = 0.178823941838717 | erot = 0.706161996587126 | epot = -15.5274191836321 | etot = -14.6424332452063 -936000 ekin = 0.168594479115294 | erot = 0.740699865837039 | epot = -15.5517275902103 | etot = -14.6424332452579 -937000 ekin = 0.159163635635195 | erot = 0.774606336205919 | epot = -15.5762032171622 | etot = -14.6424332453211 -938000 ekin = 0.150596971915171 | erot = 0.806861786796075 | epot = -15.5998920041023 | etot = -14.6424332453911 -939000 ekin = 0.142948711632666 | erot = 0.836347883526529 | epot = -15.6217298406219 | etot = -14.6424332454627 -940000 ekin = 0.136274889171384 | erot = 0.861915676028721 | epot = -15.6406238107305 | etot = -14.6424332455304 -941000 ekin = 0.130643703199134 | erot = 0.882459199120404 | epot = -15.6555361479088 | etot = -14.6424332455893 -942000 ekin = 0.126142088160929 | erot = 0.896989065172066 | epot = -15.6655643989677 | etot = -14.6424332456347 -943000 ekin = 0.122877886110378 | erot = 0.904700444358843 | epot = -15.6700115761325 | etot = -14.6424332456633 -944000 ekin = 0.12097740741224 | erot = 0.905030230236918 | epot = -15.6684408833219 | etot = -14.6424332456728 -945000 ekin = 0.120578563690818 | erot = 0.897699054745715 | epot = -15.660710864099 | etot = -14.6424332456625 -946000 ekin = 0.121820103593603 | erot = 0.882735070928584 | epot = -15.6469884201552 | etot = -14.642433245633 -947000 ekin = 0.124827761129181 | erot = 0.860477935596529 | epot = -15.6277389423121 | etot = -14.6424332455864 -948000 ekin = 0.129698334168747 | erot = 0.831563037038142 | epot = -15.6036946167331 | etot = -14.6424332455262 -949000 ekin = 0.136482857558223 | erot = 0.796887554722467 | epot = -15.5758036577371 | etot = -14.6424332454564 -950000 ekin = 0.145170138931244 | erot = 0.757561255988665 | epot = -15.545164640302 | etot = -14.6424332453821 -951000 ekin = 0.155672002995198 | erot = 0.714845916094193 | epot = -15.5129511643977 | etot = -14.6424332453083 -952000 ekin = 0.167811650836288 | erot = 0.670087833250747 | epot = -15.4803327293271 | etot = -14.64243324524 -953000 ekin = 0.181316579471282 | erot = 0.62464809521251 | epot = -15.4483979198655 | etot = -14.6424332451817 -954000 ekin = 0.195817500701168 | erot = 0.579835080696309 | epot = -15.4180858265343 | etot = -14.6424332451368 -955000 ekin = 0.210854606876659 | erot = 0.536843219769282 | epot = -15.3901310717537 | etot = -14.6424332451077 -956000 ekin = 0.225892299837258 | erot = 0.49670137679197 | epot = -15.3650269217247 | etot = -14.6424332450955 -957000 ekin = 0.240343066498473 | erot = 0.460233438094331 | epot = -15.3430097496925 | etot = -14.6424332450997 -958000 ekin = 0.253600493839208 | erot = 0.428032849894538 | epot = -15.324066588852 | etot = -14.6424332451182 -959000 ekin = 0.26508043374811 | erot = 0.400452005459373 | epot = -15.3079656843552 | etot = -14.6424332451478 -960000 ekin = 0.274268068130398 | erot = 0.377606549450015 | epot = -15.2943078627643 | etot = -14.6424332451839 -961000 ekin = 0.280767178003419 | erot = 0.359393861249926 | epot = -15.2825942844748 | etot = -14.6424332452215 -962000 ekin = 0.284346484063279 | erot = 0.345524198816832 | epot = -15.2723039281355 | etot = -14.6424332452554 -963000 ekin = 0.284976816089691 | erot = 0.3355622323293 | epot = -15.2629722936999 | etot = -14.6424332452809 -964000 ekin = 0.282852494247854 | erot = 0.328975986496892 | epot = -15.2542617260392 | etot = -14.6424332452945 -965000 ekin = 0.278391086615428 | erot = 0.325189577598743 | epot = -15.2460139095086 | etot = -14.6424332452944 -966000 ekin = 0.272207924679439 | erot = 0.323635640150665 | epot = -15.2382768101109 | etot = -14.6424332452808 -967000 ekin = 0.265065367870575 | erot = 0.323803079987219 | epot = -15.2313016931133 | etot = -14.6424332452555 -968000 ekin = 0.257801293713888 | erot = 0.325275872290492 | epot = -15.2255104112269 | etot = -14.6424332452225 -969000 ekin = 0.251245661474162 | erot = 0.327759142575902 | epot = -15.2214380492365 | etot = -14.6424332451864 -970000 ekin = 0.24613700899304 | erot = 0.331089781180773 | epot = -15.2196600353261 | etot = -14.6424332451523 -971000 ekin = 0.243051319616021 | erot = 0.335230325664833 | epot = -15.2207148904054 | etot = -14.6424332451246 -972000 ekin = 0.242353409638695 | erot = 0.340246678804358 | epot = -15.22503333355 | etot = -14.6424332451069 -973000 ekin = 0.244176338162489 | erot = 0.346272190710356 | epot = -15.2328817739745 | etot = -14.6424332451017 -974000 ekin = 0.248428661658042 | erot = 0.353462430361478 | epot = -15.2443243371296 | etot = -14.6424332451101 -975000 ekin = 0.254824314803068 | erot = 0.361946299430202 | epot = -15.2592038593654 | etot = -14.6424332451321 -976000 ekin = 0.262926848820545 | erot = 0.371779749929518 | epot = -15.2771398439171 | etot = -14.642433245167 -977000 ekin = 0.27219923533091 | erot = 0.382908123263806 | epot = -15.297540603808 | etot = -14.6424332452133 -978000 ekin = 0.282052066851764 | erot = 0.395142048097211 | epot = -15.3196273602177 | etot = -14.6424332452688 -979000 ekin = 0.291885751914043 | erot = 0.408150081471225 | epot = -15.3424690787159 | etot = -14.6424332453306 -980000 ekin = 0.301125083790016 | erot = 0.421469125222495 | epot = -15.365027454408 | etot = -14.6424332453955 -981000 ekin = 0.309246535917451 | erot = 0.434531423656212 | epot = -15.3862112050333 | etot = -14.6424332454596 -982000 ekin = 0.315799497490911 | erot = 0.446704965616411 | epot = -15.404937708626 | etot = -14.6424332455187 -983000 ekin = 0.32042257322114 | erot = 0.457342632743475 | epot = -15.4201984515335 | etot = -14.6424332455688 -984000 ekin = 0.322855465258551 | erot = 0.465834622598882 | epot = -15.4311233334638 | etot = -14.6424332456063 -985000 ekin = 0.322946302475207 | erot = 0.47165859097348 | epot = -15.4370381390771 | etot = -14.6424332456284 -986000 ekin = 0.320653917805744 | erot = 0.474422556589946 | epot = -15.4375097200291 | etot = -14.6424332456334 -987000 ekin = 0.316044627362153 | erot = 0.473896755515053 | epot = -15.4323746284979 | etot = -14.6424332456207 -988000 ekin = 0.309283477268727 | erot = 0.470032116944613 | epot = -15.4217488398044 | etot = -14.6424332455911 -989000 ekin = 0.300620522169168 | erot = 0.462964620621354 | epot = -15.4060183883369 | etot = -14.6424332455464 -990000 ekin = 0.290373280691188 | erot = 0.453006262994313 | epot = -15.3858127891748 | etot = -14.6424332454893 -991000 ekin = 0.278906915705663 | erot = 0.440624526218637 | epot = -15.3619646873472 | etot = -14.6424332454229 -992000 ekin = 0.266613826415146 | erot = 0.426413006890641 | epot = -15.3354600786566 | etot = -14.6424332453509 -993000 ekin = 0.253894212446534 | erot = 0.411056197524004 | epot = -15.3073836552473 | etot = -14.6424332452767 -994000 ekin = 0.24113883700009 | erot = 0.395291372387941 | epot = -15.2788634545917 | etot = -14.6424332452037 -995000 ekin = 0.22871476890696 | erot = 0.379870207854789 | epot = -15.2510182218965 | etot = -14.6424332451348 -996000 ekin = 0.216954417470376 | erot = 0.365522282707067 | epot = -15.2249099452499 | etot = -14.6424332450725 -997000 ekin = 0.206147766455999 | erot = 0.352922066138332 | epot = -15.2015030776131 | etot = -14.6424332450188 -998000 ekin = 0.196537413157836 | erot = 0.342660495991062 | epot = -15.1816311541242 | etot = -14.6424332449753 -999000 ekin = 0.18831584391307 | erot = 0.335221830005501 | epot = -15.1659709188615 | etot = -14.642433244943 -1000000 ekin = 0.181624323067755 | erot = 0.330966139649165 | epot = -15.1550237076395 | etot = -14.6424332449226 - 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 -Loop time of 16.5005 on 4 procs for 1000000 steps with 10 atoms - -Performance: 52362.058 tau/day, 60604.234 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.51373 | 5.7702 | 10.408 | 174.5 | 34.97 -Bond | 0.084405 | 0.27056 | 0.44162 | 28.3 | 1.64 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.7403 | 2.0946 | 2.4247 | 18.8 | 12.69 -Output | 4e-05 | 6e-05 | 7.1e-05 | 0.0 | 0.00 -Modify | 0.17451 | 0.87938 | 1.53 | 58.2 | 5.33 -Other | | 7.486 | | | 45.37 - -Nlocal: 2.5 ave 5.0 max 0.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10.0 max 5.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 16.0 ave 30.0 max 0.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 64 -Ave neighs/atom = 6.4 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:16 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 b/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 deleted file mode 100644 index 72872d431a..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 +++ /dev/null @@ -1,96 +0,0 @@ -# LAMMPS data file -16 atoms -16 ellipsoids -13 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -Masses - -1 3.1575 -2 3.1575 -3 3.1575 -4 3.1575 - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 -3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 -4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 -5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 -6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1 -7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1 -8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1 -9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1 -10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1 -11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1 -12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1 -13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1 -14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1 -15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1 -16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1 - -# Atom-ID, translational velocity, angular momentum -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00 -11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00 -12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00 -13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00 -14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00 -15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00 -16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 5 6 -6 1 6 7 -7 1 7 8 -8 1 9 10 -9 1 10 11 -10 1 11 12 -11 1 13 14 -12 1 14 15 -13 1 15 16 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1 deleted file mode 100644 index f030e0f93c..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1 +++ /dev/null @@ -1,1176 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 -fix 2 all langevin 0.1 ${T} 0.03 457145 angmom 10 -fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.9560004 - ghost atom cutoff = 2.5 - binsize = 0.97800022, bins = 41 41 41 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -0 ekin = 0 | erot = 0 | epot = -24.5312382023597 | etot = -24.5312382023597 -Per MPI rank memory allocation (min/avg/max) = 8.008 | 8.008 | 8.008 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 -1000 ekin = 1.14690574396998 | erot = 2.51569518930742 | epot = -24.5229788082339 | etot = -20.8603778749565 -2000 ekin = 1.45399965653676 | erot = 2.47529346761995 | epot = -24.5053413112924 | etot = -20.5760481871357 -3000 ekin = 1.98748516841538 | erot = 2.27869060236515 | epot = -24.479432022183 | etot = -20.2132562514025 -4000 ekin = 1.64496816080429 | erot = 1.81579764130658 | epot = -24.4776224042961 | etot = -21.0168566021853 -5000 ekin = 1.84895966245555 | erot = 2.72664609970378 | epot = -24.4004650506536 | etot = -19.8248592884943 -6000 ekin = 2.81982646967251 | erot = 2.27943933047792 | epot = -24.3708804580518 | etot = -19.2716146579014 -7000 ekin = 3.4295488541453 | erot = 3.06244546790251 | epot = -24.2894811609395 | etot = -17.7974868388917 -8000 ekin = 3.46902364328651 | erot = 1.87163076744154 | epot = -24.2046945377415 | etot = -18.8640401270135 -9000 ekin = 3.42624221752733 | erot = 2.19665328890067 | epot = -24.1061295133862 | etot = -18.4832340069582 -10000 ekin = 3.47261688291849 | erot = 2.11359627880933 | epot = -23.9936001795499 | etot = -18.4073870178221 -11000 ekin = 2.94815134012461 | erot = 1.68371787420979 | epot = -23.8824451066212 | etot = -19.2505758922868 -12000 ekin = 2.91661369846828 | erot = 2.44986569301244 | epot = -23.7971038712851 | etot = -18.4306244798044 -13000 ekin = 2.90452877485052 | erot = 3.15041912070996 | epot = -23.7183348836954 | etot = -17.6633869881349 -14000 ekin = 3.03173396911322 | erot = 3.20528252680661 | epot = -23.6395534566822 | etot = -17.4025369607624 -15000 ekin = 3.10924339992056 | erot = 2.34851811722898 | epot = -23.5718810747763 | etot = -18.1141195576268 -16000 ekin = 2.21129165426584 | erot = 2.77310226941398 | epot = -23.4674880203451 | etot = -18.4830940966653 -17000 ekin = 1.64364291226705 | erot = 2.11093006069599 | epot = -23.4464921197588 | etot = -19.6919191467958 -18000 ekin = 1.71575404949661 | erot = 2.18377153128382 | epot = -23.4394231359426 | etot = -19.5398975551621 -19000 ekin = 2.74802968392513 | erot = 3.43483629560937 | epot = -23.451104173519 | etot = -17.2682381939845 -20000 ekin = 2.3643229041162 | erot = 2.97756435312011 | epot = -23.4354516313364 | etot = -18.0935643741001 -21000 ekin = 3.01197341291121 | erot = 2.06047278730446 | epot = -23.4653464733578 | etot = -18.3929002731421 -22000 ekin = 2.72181189461236 | erot = 1.68043760380063 | epot = -23.499010600721 | etot = -19.0967611023081 -23000 ekin = 2.78354866420193 | erot = 2.27555762688526 | epot = -23.4149266394174 | etot = -18.3558203483302 -24000 ekin = 2.70238951268775 | erot = 2.77699460975588 | epot = -23.3727816681014 | etot = -17.8933975456577 -25000 ekin = 2.79329314290743 | erot = 1.72270284379168 | epot = -23.4092634474478 | etot = -18.8932674607487 -26000 ekin = 2.12045088758989 | erot = 2.56536846297423 | epot = -23.4001345199736 | etot = -18.7143151694095 -27000 ekin = 2.13984384122857 | erot = 2.80867896704025 | epot = -23.372540623668 | etot = -18.4240178153992 -28000 ekin = 1.83987887691915 | erot = 1.95066344021761 | epot = -23.3274470842878 | etot = -19.536904767151 -29000 ekin = 1.89211705701482 | erot = 2.1696768345372 | epot = -23.293062192394 | etot = -19.231268300842 -30000 ekin = 2.14849041779036 | erot = 2.16067509784504 | epot = -23.2773582752331 | etot = -18.9681927595977 -31000 ekin = 2.67234738212361 | erot = 2.86863391076037 | epot = -23.2995071870109 | etot = -17.7585258941269 -32000 ekin = 2.53397631055537 | erot = 2.90803809156287 | epot = -23.2362493660415 | etot = -17.7942349639233 -33000 ekin = 3.08856443970765 | erot = 2.77830373791794 | epot = -23.1957127399696 | etot = -17.328844562344 -34000 ekin = 2.34758696559903 | erot = 2.73235573196028 | epot = -23.1859092641964 | etot = -18.1059665666371 -35000 ekin = 2.37656125971695 | erot = 2.21670282442912 | epot = -23.2990352575428 | etot = -18.7057711733968 -36000 ekin = 1.91500165278598 | erot = 2.22479415969906 | epot = -23.3423509866966 | etot = -19.2025551742115 -37000 ekin = 1.90416513806792 | erot = 2.44362474415858 | epot = -23.4523097395397 | etot = -19.1045198573132 -38000 ekin = 2.64855728429901 | erot = 2.6250961281024 | epot = -23.4330562973534 | etot = -18.159402884952 -39000 ekin = 2.47023253086004 | erot = 2.94458438664745 | epot = -23.3886129152296 | etot = -17.9737959977221 -40000 ekin = 2.36649278209599 | erot = 2.21667374563979 | epot = -23.3060594391637 | etot = -18.722892911428 -41000 ekin = 2.11640638984279 | erot = 2.75431236003956 | epot = -23.296637047546 | etot = -18.4259182976636 -42000 ekin = 2.19538989967685 | erot = 2.80995153019434 | epot = -23.3287628829795 | etot = -18.3234214531083 -43000 ekin = 2.28336241709741 | erot = 1.91100961808481 | epot = -23.398154745965 | etot = -19.2037827107827 -44000 ekin = 2.43910444561977 | erot = 2.20967357150541 | epot = -23.3408075599757 | etot = -18.6920295428505 -45000 ekin = 1.99725725495469 | erot = 2.55697923716124 | epot = -23.2988802257869 | etot = -18.744643733671 -46000 ekin = 2.80179143005448 | erot = 3.94591979804991 | epot = -23.2634234091195 | etot = -16.5157121810151 -47000 ekin = 2.00831918922489 | erot = 1.99358498528542 | epot = -23.1997437408908 | etot = -19.1978395663805 -48000 ekin = 2.65343777724262 | erot = 3.19529693167641 | epot = -23.2752277173461 | etot = -17.4264930084271 -49000 ekin = 3.08609210167617 | erot = 3.098444131902 | epot = -23.3331562765622 | etot = -17.148620042984 -50000 ekin = 2.79161045816108 | erot = 3.87280243835105 | epot = -23.283716155905 | etot = -16.6193032593929 -51000 ekin = 2.63041022395737 | erot = 1.73292678860556 | epot = -23.2028735154881 | etot = -18.8395365029252 -52000 ekin = 2.18205853362573 | erot = 2.96101862628972 | epot = -23.1079417719452 | etot = -17.9648646120298 -53000 ekin = 2.3943556604873 | erot = 3.52800628354648 | epot = -23.0586505350936 | etot = -17.1362885910599 -54000 ekin = 2.12390729593688 | erot = 2.48502694765291 | epot = -22.9790932946842 | etot = -18.3701590510944 -55000 ekin = 1.95245465404747 | erot = 2.39606028736228 | epot = -23.0362462549527 | etot = -18.687731313543 -56000 ekin = 2.078586656515 | erot = 2.51006580668827 | epot = -23.0629170158575 | etot = -18.4742645526543 -57000 ekin = 2.60842664676812 | erot = 3.02172637784133 | epot = -23.0307524021856 | etot = -17.4005993775762 -58000 ekin = 2.99447041104738 | erot = 2.32823492888449 | epot = -23.0721969273868 | etot = -17.7494915874549 -59000 ekin = 2.4566598353902 | erot = 2.43942437937462 | epot = -23.0847799943358 | etot = -18.188695779571 -60000 ekin = 2.6971497663209 | erot = 1.66133214228194 | epot = -23.0332753747144 | etot = -18.6747934661116 -61000 ekin = 2.11191914746267 | erot = 1.6204782869367 | epot = -22.9667049822233 | etot = -19.234307547824 -62000 ekin = 2.11717212979171 | erot = 2.47796844210791 | epot = -22.8144212994634 | etot = -18.2192807275637 -63000 ekin = 2.72171812217735 | erot = 2.66368566253267 | epot = -22.7776567061626 | etot = -17.3922529214526 -64000 ekin = 3.22835802379379 | erot = 2.36781220330958 | epot = -22.7933861176758 | etot = -17.1972158905724 -65000 ekin = 3.64756058058813 | erot = 3.15015944023671 | epot = -22.7765851531231 | etot = -15.9788651322982 -66000 ekin = 2.66639386198067 | erot = 2.72112154754982 | epot = -22.7755021487188 | etot = -17.3879867391884 -67000 ekin = 2.38306133316432 | erot = 2.49378542212015 | epot = -22.7973748348603 | etot = -17.9205280795759 -68000 ekin = 2.52481286112851 | erot = 3.23872813661013 | epot = -22.8468557220554 | etot = -17.0833147243168 -69000 ekin = 2.60430769391747 | erot = 3.00968890211103 | epot = -22.8318824138615 | etot = -17.217885817833 -70000 ekin = 2.72529278847958 | erot = 2.96912272855297 | epot = -22.9182544554594 | etot = -17.2238389384268 -71000 ekin = 2.30851064297996 | erot = 2.44510178131689 | epot = -23.110146286175 | etot = -18.3565338618781 -72000 ekin = 1.86333205174444 | erot = 2.21918738219008 | epot = -23.2088713208781 | etot = -19.1263518869436 -73000 ekin = 1.97363737837151 | erot = 2.92039675389546 | epot = -23.3456188157452 | etot = -18.4515846834783 -74000 ekin = 2.03973663696274 | erot = 2.44352827046787 | epot = -23.3706565736274 | etot = -18.8873916661968 -75000 ekin = 2.13029836638111 | erot = 2.25069247013825 | epot = -23.3468514357058 | etot = -18.9658605991864 -76000 ekin = 1.86911909276267 | erot = 1.88174803064112 | epot = -23.3433063511182 | etot = -19.5924392277144 -77000 ekin = 2.8311971230152 | erot = 1.4764600924275 | epot = -23.3736217515866 | etot = -19.0659645361439 -78000 ekin = 3.02331647633308 | erot = 3.49408579644919 | epot = -23.4257428368656 | etot = -16.9083405640833 -79000 ekin = 3.51133596793171 | erot = 2.66043649565033 | epot = -23.4320673594166 | etot = -17.2602948958345 -80000 ekin = 2.88371521187479 | erot = 1.92272084366328 | epot = -23.4437991576283 | etot = -18.6373631020903 -81000 ekin = 2.93345241699417 | erot = 2.30354045717278 | epot = -23.4023767063862 | etot = -18.1653838322193 -82000 ekin = 2.31364693930239 | erot = 1.52107123456185 | epot = -23.332732976686 | etot = -19.4980148028218 -83000 ekin = 2.79964810868887 | erot = 3.01031848157711 | epot = -23.1805490994262 | etot = -17.3705825091602 -84000 ekin = 3.14238697097954 | erot = 2.54443984047462 | epot = -23.0036486008467 | etot = -17.3168217893925 -85000 ekin = 3.11037170652329 | erot = 2.81688612333738 | epot = -22.9040286513178 | etot = -16.9767708214572 -86000 ekin = 3.24614571607055 | erot = 2.4691668527709 | epot = -22.9115348786951 | etot = -17.1962223098536 -87000 ekin = 3.15148333101924 | erot = 2.81476071986705 | epot = -22.88497016051 | etot = -16.9187261096237 -88000 ekin = 2.79204781171839 | erot = 2.11551211421263 | epot = -22.9365333909989 | etot = -18.0289734650679 -89000 ekin = 2.35289392365394 | erot = 3.20722667156868 | epot = -22.838834182654 | etot = -17.2787135874314 -90000 ekin = 2.37582791595297 | erot = 2.35376824711544 | epot = -22.7759716111928 | etot = -18.0463754481244 -91000 ekin = 2.11229902300038 | erot = 2.49991596560396 | epot = -22.7428668079145 | etot = -18.1306518193102 -92000 ekin = 2.18222080456226 | erot = 2.12578389554434 | epot = -22.6742877211503 | etot = -18.3662830210437 -93000 ekin = 2.21095150681925 | erot = 3.26438303982222 | epot = -22.5594438754277 | etot = -17.0841093287862 -94000 ekin = 2.12232737083461 | erot = 3.41982221867449 | epot = -22.5731643271249 | etot = -17.0310147376158 -95000 ekin = 1.85629034286763 | erot = 1.96410759501716 | epot = -22.59538207669 | etot = -18.7749841388052 -96000 ekin = 2.39869119547858 | erot = 2.71927150056489 | epot = -22.6306283736797 | etot = -17.5126656776363 -97000 ekin = 2.66273024813647 | erot = 1.89080412966723 | epot = -22.6359449758314 | etot = -18.0824105980277 -98000 ekin = 2.85072927082227 | erot = 1.60816717415087 | epot = -22.7177273012906 | etot = -18.2588308563174 -99000 ekin = 2.83238909889775 | erot = 2.47205959733049 | epot = -22.8003244534363 | etot = -17.495875757208 -100000 ekin = 2.41865993058067 | erot = 2.0598579213647 | epot = -22.9852243238147 | etot = -18.5067064718694 -101000 ekin = 2.54841697870327 | erot = 2.36461883832458 | epot = -23.0633841926615 | etot = -18.1503483756336 -102000 ekin = 2.54594946615645 | erot = 2.86139475908785 | epot = -23.1098219772669 | etot = -17.7024777520226 -103000 ekin = 2.13582591081888 | erot = 2.12361330514722 | epot = -23.1354410963672 | etot = -18.8760018804011 -104000 ekin = 2.21385815248422 | erot = 2.29274274660023 | epot = -23.0865139718305 | etot = -18.5799130727461 -105000 ekin = 2.44889646860174 | erot = 2.75107727112909 | epot = -23.0544140778533 | etot = -17.8544403381225 -106000 ekin = 1.95956756411726 | erot = 2.3209345631325 | epot = -23.0430612833128 | etot = -18.7625591560631 -107000 ekin = 2.27802020438547 | erot = 2.08909400930221 | epot = -23.0686930034876 | etot = -18.7015787897999 -108000 ekin = 1.90572708538444 | erot = 3.13702334473575 | epot = -23.0271860838353 | etot = -17.9844356537151 -109000 ekin = 2.39380259291066 | erot = 2.22054516746467 | epot = -23.0249223512454 | etot = -18.41057459087 -110000 ekin = 2.26587242950359 | erot = 2.25607481649737 | epot = -23.039981892631 | etot = -18.51803464663 -111000 ekin = 2.15727458703525 | erot = 1.98358283370136 | epot = -23.0767942184013 | etot = -18.9359367976647 -112000 ekin = 2.3828169618658 | erot = 2.69686827828485 | epot = -23.1107895116834 | etot = -18.0311042715327 -113000 ekin = 2.8101781075741 | erot = 2.59950194588724 | epot = -23.0287341179313 | etot = -17.6190540644699 -114000 ekin = 2.35455919019172 | erot = 3.20470938308889 | epot = -22.9694690534849 | etot = -17.4102004802043 -115000 ekin = 2.4406692440432 | erot = 1.89109901084122 | epot = -22.9284259454167 | etot = -18.5966576905323 -116000 ekin = 2.31064767487137 | erot = 2.83979549060621 | epot = -22.9485617435445 | etot = -17.7981185780669 -117000 ekin = 2.08937942523073 | erot = 2.22599804456159 | epot = -22.8649871463364 | etot = -18.5496096765441 -118000 ekin = 2.13839981510475 | erot = 2.6042059558218 | epot = -22.7656872587424 | etot = -18.0230814878159 -119000 ekin = 2.82390266451549 | erot = 2.20939391190357 | epot = -22.7729728906623 | etot = -17.7396763142432 -120000 ekin = 2.01401322106231 | erot = 2.48866024138323 | epot = -22.6353588152779 | etot = -18.1326853528324 -121000 ekin = 2.38145077479306 | erot = 3.12007697133009 | epot = -22.5496980171072 | etot = -17.048170270984 -122000 ekin = 3.27512287434745 | erot = 3.22243197902324 | epot = -22.5766115874577 | etot = -16.079056734087 -123000 ekin = 2.81132514620283 | erot = 2.86307874434964 | epot = -22.6263844574797 | etot = -16.9519805669272 -124000 ekin = 2.19849534367232 | erot = 2.58327740029555 | epot = -22.632926922485 | etot = -17.8511541785171 -125000 ekin = 1.9938456811927 | erot = 1.90953618390393 | epot = -22.6331404835376 | etot = -18.7297586184409 -126000 ekin = 2.42731825528385 | erot = 2.87237001426948 | epot = -22.6106846507781 | etot = -17.3109963812248 -127000 ekin = 1.95505736761304 | erot = 2.81720121527978 | epot = -22.5579301674971 | etot = -17.7856715846043 -128000 ekin = 2.10594260964226 | erot = 2.01356984269814 | epot = -22.4981321684107 | etot = -18.3786197160703 -129000 ekin = 2.55520588445759 | erot = 2.57894735511156 | epot = -22.559207781978 | etot = -17.4250545424089 -130000 ekin = 2.86259834978311 | erot = 2.18965938451607 | epot = -22.5770466332128 | etot = -17.5247888989136 -131000 ekin = 2.86321076870393 | erot = 1.66847645340269 | epot = -22.529949359668 | etot = -17.9982621375613 -132000 ekin = 2.93426604771556 | erot = 3.00425629789163 | epot = -22.5601802720307 | etot = -16.6216579264235 -133000 ekin = 3.65754901201543 | erot = 1.43666262449492 | epot = -22.6237662747263 | etot = -17.529554638216 -134000 ekin = 2.18898923715712 | erot = 2.33049897457535 | epot = -22.7470394091699 | etot = -18.2275511974375 -135000 ekin = 2.03823330514395 | erot = 2.69291476269712 | epot = -22.8900275663634 | etot = -18.1588794985223 -136000 ekin = 2.6538713732039 | erot = 2.40958876583255 | epot = -22.9857440078583 | etot = -17.9222838688218 -137000 ekin = 3.12283566057286 | erot = 3.49983145404452 | epot = -23.0096984445474 | etot = -16.3870313299301 -138000 ekin = 2.45014875520084 | erot = 2.4508647359669 | epot = -23.0794084265037 | etot = -18.178394935336 -139000 ekin = 2.03608492985731 | erot = 1.97462403722722 | epot = -23.178945590097 | etot = -19.1682366230125 -140000 ekin = 2.8375811142686 | erot = 2.49376841321459 | epot = -23.298440206365 | etot = -17.9670906788818 -141000 ekin = 2.83405987670134 | erot = 2.48065309139941 | epot = -23.4226619452758 | etot = -18.107948977175 -142000 ekin = 3.19333498685692 | erot = 3.17336002986012 | epot = -23.3250285546098 | etot = -16.9583335378927 -143000 ekin = 2.2053085459229 | erot = 2.51795869911564 | epot = -23.4007031674318 | etot = -18.6774359223932 -144000 ekin = 3.13477789699627 | erot = 2.69612114268137 | epot = -23.3846120043903 | etot = -17.5537129647126 -145000 ekin = 3.05703751181504 | erot = 2.77857540632303 | epot = -23.3935227778029 | etot = -17.5579098596648 -146000 ekin = 3.56567491078422 | erot = 1.97456126200808 | epot = -23.3912044699534 | etot = -17.8509682971611 -147000 ekin = 2.62692101320613 | erot = 2.7990853604292 | epot = -23.4731299563114 | etot = -18.0471235826761 -148000 ekin = 2.45471110479969 | erot = 1.97948594654501 | epot = -23.5390482551317 | etot = -19.104851203787 -149000 ekin = 2.91425191756495 | erot = 2.34219263228086 | epot = -23.5494392195753 | etot = -18.2929946697295 -150000 ekin = 2.11267470955651 | erot = 3.15139951917672 | epot = -23.456213233303 | etot = -18.1921390045698 -151000 ekin = 1.89283581343662 | erot = 2.39812863380885 | epot = -23.3591999925057 | etot = -19.0682355452602 -152000 ekin = 2.40790737144431 | erot = 2.01427800135936 | epot = -23.2626112351643 | etot = -18.8404258623606 -153000 ekin = 2.05155784053096 | erot = 2.23618306870396 | epot = -23.2634856578898 | etot = -18.9757447486549 -154000 ekin = 2.51778354567736 | erot = 3.20314773898096 | epot = -23.2975528150325 | etot = -17.5766215303742 -155000 ekin = 2.00284429469695 | erot = 2.89937315438495 | epot = -23.3218945133551 | etot = -18.4196770642732 -156000 ekin = 1.91144554872485 | erot = 2.99821559619451 | epot = -23.2209466091476 | etot = -18.3112854642282 -157000 ekin = 2.43182251041877 | erot = 1.62406041783895 | epot = -23.1045847485264 | etot = -19.0487018202686 -158000 ekin = 2.09298289420886 | erot = 2.6766289229666 | epot = -23.031927214759 | etot = -18.2623153975835 -159000 ekin = 2.20764198734381 | erot = 2.83616967442204 | epot = -22.9227666897823 | etot = -17.8789550280164 -160000 ekin = 2.21243983900826 | erot = 2.20003736549807 | epot = -22.9543660393476 | etot = -18.5418888348412 -161000 ekin = 2.45073410895006 | erot = 2.43388496890226 | epot = -22.9636574775946 | etot = -18.0790383997422 -162000 ekin = 2.17367299341061 | erot = 2.69488535843695 | epot = -23.0527030224094 | etot = -18.1841446705618 -163000 ekin = 1.6416624121019 | erot = 2.84097373738807 | epot = -23.1292124278341 | etot = -18.6465762783441 -164000 ekin = 1.67565049116239 | erot = 2.68380704848371 | epot = -23.1590424140942 | etot = -18.7995848744481 -165000 ekin = 2.42206226766745 | erot = 2.72988204300635 | epot = -23.1799778993767 | etot = -18.0280335887029 -166000 ekin = 3.14880802219226 | erot = 2.84384837642053 | epot = -23.2429974571314 | etot = -17.2503410585186 -167000 ekin = 2.25647190185324 | erot = 2.22025584454645 | epot = -23.3152815140534 | etot = -18.8385537676537 -168000 ekin = 2.05307577726746 | erot = 1.92982813234681 | epot = -23.3121709078534 | etot = -19.3292669982392 -169000 ekin = 2.25333032487684 | erot = 2.03837973951729 | epot = -23.3314587534472 | etot = -19.0397486890531 -170000 ekin = 3.24025514660291 | erot = 2.68054613971874 | epot = -23.2656213247604 | etot = -17.3448200384388 -171000 ekin = 3.26091283919611 | erot = 2.31337270355485 | epot = -23.30671463487 | etot = -17.732429092119 -172000 ekin = 3.71728985541098 | erot = 2.37762994657772 | epot = -23.3035184476851 | etot = -17.2085986456964 -173000 ekin = 3.15518229037533 | erot = 2.74844421936228 | epot = -23.2758116201384 | etot = -17.3721851104007 -174000 ekin = 2.99648976213193 | erot = 1.71811302453253 | epot = -23.1981882260451 | etot = -18.4835854393806 -175000 ekin = 2.57240965973333 | erot = 2.55046855203897 | epot = -23.1014541624941 | etot = -17.9785759507218 -176000 ekin = 1.93852156602125 | erot = 2.47332967602318 | epot = -23.1368569455589 | etot = -18.7250057035145 -177000 ekin = 2.80960374115401 | erot = 1.95409121605924 | epot = -23.0982934782514 | etot = -18.3345985210382 -178000 ekin = 2.33244636491393 | erot = 2.27408462832222 | epot = -23.0825224910612 | etot = -18.4759914978251 -179000 ekin = 2.13982176908862 | erot = 2.89346836042849 | epot = -23.0763356798213 | etot = -18.0430455503042 -180000 ekin = 2.207400927993 | erot = 1.5562703232207 | epot = -23.0740416866628 | etot = -19.3103704354491 -181000 ekin = 2.12924843078766 | erot = 3.48717124411563 | epot = -22.9481791847174 | etot = -17.3317595098141 -182000 ekin = 1.86429514249569 | erot = 2.12691540074977 | epot = -22.8573607952401 | etot = -18.8661502519946 -183000 ekin = 2.49432213049246 | erot = 1.94397526976538 | epot = -22.8739996678934 | etot = -18.4357022676356 -184000 ekin = 2.32559536618148 | erot = 2.16188851089671 | epot = -22.8801350202001 | etot = -18.3926511431219 -185000 ekin = 3.43221902743033 | erot = 2.76663819243887 | epot = -22.7961878859294 | etot = -16.5973306660602 -186000 ekin = 3.27655677826301 | erot = 2.10542412812558 | epot = -22.5860615279726 | etot = -17.204080621584 -187000 ekin = 3.21808565073807 | erot = 3.12646745373177 | epot = -22.4680437052799 | etot = -16.1234906008101 -188000 ekin = 3.29470028080779 | erot = 2.71885909254934 | epot = -22.4777213671005 | etot = -16.4641619937434 -189000 ekin = 2.29225438861808 | erot = 2.15238017837044 | epot = -22.4423181907693 | etot = -17.9976836237808 -190000 ekin = 2.31172879251782 | erot = 1.69869193216314 | epot = -22.4421736779848 | etot = -18.4317529533038 -191000 ekin = 2.44737449537105 | erot = 1.95471142288415 | epot = -22.4940636736618 | etot = -18.0919777554066 -192000 ekin = 2.65685760576573 | erot = 2.49493427834054 | epot = -22.551770059613 | etot = -17.3999781755067 -193000 ekin = 2.01491600271975 | erot = 2.53697801257504 | epot = -22.611413796154 | etot = -18.0595197808592 -194000 ekin = 2.13098665262876 | erot = 2.65162788921838 | epot = -22.6516249427401 | etot = -17.869010400893 -195000 ekin = 2.15880156426523 | erot = 2.30285156951273 | epot = -22.6801152411448 | etot = -18.2184621073669 -196000 ekin = 2.26045454251242 | erot = 1.7400410306741 | epot = -22.6243696974319 | etot = -18.6238741242454 -197000 ekin = 2.08353851799175 | erot = 2.84019387252897 | epot = -22.5254653541291 | etot = -17.6017329636084 -198000 ekin = 2.40254425598167 | erot = 1.59510544084176 | epot = -22.4875571568747 | etot = -18.4899074600513 -199000 ekin = 2.32315315727966 | erot = 1.64758309421108 | epot = -22.3940543169462 | etot = -18.4233180654554 -200000 ekin = 1.9344201599962 | erot = 2.09946369983286 | epot = -22.3163824882501 | etot = -18.282498628421 -201000 ekin = 2.25758946372665 | erot = 1.57318447391795 | epot = -22.2162199013465 | etot = -18.3854459637019 -202000 ekin = 2.14286142871167 | erot = 1.84411011823104 | epot = -22.0782645916587 | etot = -18.0912930447159 -203000 ekin = 1.82640790776851 | erot = 3.05975799451598 | epot = -21.9788881819889 | etot = -17.0927222797045 -204000 ekin = 1.62851140603835 | erot = 1.97764157787611 | epot = -21.9332382928783 | etot = -18.3270853089638 -205000 ekin = 1.25482843048893 | erot = 2.20166998646264 | epot = -21.8845360273862 | etot = -18.4280376104346 -206000 ekin = 1.73414183779997 | erot = 1.82150010232861 | epot = -21.8773801883845 | etot = -18.321738248256 -207000 ekin = 1.94750322930568 | erot = 2.48531516705681 | epot = -21.9295431113514 | etot = -17.496724714989 -208000 ekin = 2.09568882924412 | erot = 3.03912830731326 | epot = -22.0166563659434 | etot = -16.881839229386 -209000 ekin = 2.64700139449842 | erot = 2.33696819850967 | epot = -22.1001648259952 | etot = -17.1161952329871 -210000 ekin = 2.84808049130809 | erot = 3.0333180373391 | epot = -22.1925404483828 | etot = -16.3111419197356 -211000 ekin = 1.9735208459781 | erot = 2.67635943704183 | epot = -22.2979529780579 | etot = -17.648072695038 -212000 ekin = 1.60231135436244 | erot = 2.66527693950093 | epot = -22.3334257809678 | etot = -18.0658374871044 -213000 ekin = 1.33634411107147 | erot = 2.64593792571916 | epot = -22.4180515625624 | etot = -18.4357695257718 -214000 ekin = 2.2947085637024 | erot = 1.7654025455793 | epot = -22.5146947473979 | etot = -18.4545836381162 -215000 ekin = 2.54235331845419 | erot = 2.59070032226104 | epot = -22.5977548514775 | etot = -17.4647012107623 -216000 ekin = 2.50726683350059 | erot = 2.07957683306215 | epot = -22.6514435658203 | etot = -18.0645998992575 -217000 ekin = 2.56666688563484 | erot = 2.10721620203285 | epot = -22.7585726045596 | etot = -18.0846895168919 -218000 ekin = 2.3809214758614 | erot = 2.40889946821003 | epot = -22.7858427946485 | etot = -17.996021850577 -219000 ekin = 2.62297703802767 | erot = 1.72015460606372 | epot = -22.8179577818034 | etot = -18.474826137712 -220000 ekin = 2.04452501529803 | erot = 2.48366646228854 | epot = -22.8152593234185 | etot = -18.2870678458319 -221000 ekin = 2.016790382988 | erot = 1.92179513943576 | epot = -22.7675242743918 | etot = -18.8289387519681 -222000 ekin = 2.48246285927141 | erot = 2.69662232500728 | epot = -22.6922041676861 | etot = -17.5131189834074 -223000 ekin = 2.07315316544961 | erot = 2.59399918829032 | epot = -22.6977764075015 | etot = -18.0306240537616 -224000 ekin = 2.13964582929342 | erot = 2.15545737968983 | epot = -22.6791813082171 | etot = -18.3840780992338 -225000 ekin = 2.4443131371706 | erot = 3.02968637363015 | epot = -22.6416871024202 | etot = -17.1676875916194 -226000 ekin = 2.14901519929161 | erot = 2.34793235846519 | epot = -22.69101275787 | etot = -18.1940652001132 -227000 ekin = 2.85261296673757 | erot = 2.16469654263134 | epot = -22.6647959494624 | etot = -17.6474864400935 -228000 ekin = 2.0542557730781 | erot = 2.41859943175188 | epot = -22.648254263469 | etot = -18.175399058639 -229000 ekin = 1.71712866311074 | erot = 2.00134448676601 | epot = -22.656184548909 | etot = -18.9377113990323 -230000 ekin = 2.93835687549904 | erot = 2.52588891439014 | epot = -22.686473096368 | etot = -17.2222273064788 -231000 ekin = 3.65320646645271 | erot = 2.50996334898014 | epot = -22.6663620829857 | etot = -16.5031922675529 -232000 ekin = 2.74858319742744 | erot = 2.15737431011052 | epot = -22.7650781743548 | etot = -17.8591206668168 -233000 ekin = 2.20526469100055 | erot = 1.96946858309177 | epot = -22.808033211882 | etot = -18.6332999377897 -234000 ekin = 3.0329543267647 | erot = 1.91197211768344 | epot = -22.7639916522477 | etot = -17.8190652077996 -235000 ekin = 2.67265278717495 | erot = 2.49323486871604 | epot = -22.8047732486684 | etot = -17.6388855927774 -236000 ekin = 2.45357393436119 | erot = 2.51245746374309 | epot = -22.7782827985553 | etot = -17.812251400451 -237000 ekin = 2.58384683986252 | erot = 2.47764708446689 | epot = -22.8498966602044 | etot = -17.788402735875 -238000 ekin = 2.48850542531642 | erot = 2.95888408934022 | epot = -22.8461058630726 | etot = -17.3987163484159 -239000 ekin = 2.5081973607743 | erot = 2.88284977556179 | epot = -22.8253656494842 | etot = -17.4343185131481 -240000 ekin = 2.80266521029648 | erot = 2.42429156361948 | epot = -22.7822778944155 | etot = -17.5553211204995 -241000 ekin = 2.22400241744572 | erot = 2.47541442439962 | epot = -22.708502965295 | etot = -18.0090861234496 -242000 ekin = 2.1369278840666 | erot = 3.31767605383442 | epot = -22.6765710785147 | etot = -17.2219671406136 -243000 ekin = 2.31455276379189 | erot = 1.97486717843967 | epot = -22.6835713954336 | etot = -18.3941514532021 -244000 ekin = 2.08913537180933 | erot = 2.74057497391117 | epot = -22.6588502228669 | etot = -17.8291398771464 -245000 ekin = 2.13326066848594 | erot = 2.26727722045252 | epot = -22.5891755212551 | etot = -18.1886376323167 -246000 ekin = 1.98597399772947 | erot = 2.24414289909305 | epot = -22.581751166757 | etot = -18.3516342699345 -247000 ekin = 1.7029908245814 | erot = 2.65850843105303 | epot = -22.5730238533539 | etot = -18.2115245977195 -248000 ekin = 2.17045477909461 | erot = 2.21012477326125 | epot = -22.6387048466336 | etot = -18.2581252942777 -249000 ekin = 2.19972531736336 | erot = 2.93804177761671 | epot = -22.667836810757 | etot = -17.530069715777 -250000 ekin = 2.30859844416928 | erot = 2.87484738519315 | epot = -22.7208193440242 | etot = -17.5373735146618 -251000 ekin = 3.15133859857999 | erot = 2.3610033133862 | epot = -22.7532913869796 | etot = -17.2409494750134 -252000 ekin = 2.10711705767907 | erot = 2.93803244308709 | epot = -22.8141998177766 | etot = -17.7690503170104 -253000 ekin = 1.81446587076888 | erot = 3.64847052994272 | epot = -22.7589188116659 | etot = -17.2959824109543 -254000 ekin = 2.38246471864852 | erot = 2.74330406814437 | epot = -22.637470157389 | etot = -17.5117013705961 -255000 ekin = 2.82281981879266 | erot = 2.17751399966926 | epot = -22.6480625048929 | etot = -17.647728686431 -256000 ekin = 2.91721347856852 | erot = 2.29499077181347 | epot = -22.7096621530392 | etot = -17.4974579026573 -257000 ekin = 2.82748375072692 | erot = 3.52099588673786 | epot = -22.6484013012936 | etot = -16.2999216638288 -258000 ekin = 2.19992203178142 | erot = 2.12042549810482 | epot = -22.6612060734149 | etot = -18.3408585435286 -259000 ekin = 2.13920518349551 | erot = 2.2459631658656 | epot = -22.6156265174457 | etot = -18.2304581680846 -260000 ekin = 2.4332113427451 | erot = 2.77503683051912 | epot = -22.6321520875833 | etot = -17.4239039143191 -261000 ekin = 2.05779939929259 | erot = 2.13973837948785 | epot = -22.6823931019282 | etot = -18.4848553231477 -262000 ekin = 2.79110837358257 | erot = 2.25626689025766 | epot = -22.7214681566511 | etot = -17.6740928928109 -263000 ekin = 2.78883106934821 | erot = 1.69356075172848 | epot = -22.7142967476141 | etot = -18.2319049265375 -264000 ekin = 2.20259381207698 | erot = 1.55086518385097 | epot = -22.6762941554802 | etot = -18.9228351595523 -265000 ekin = 2.0317762551793 | erot = 2.12583868325911 | epot = -22.712761701767 | etot = -18.5551467633286 -266000 ekin = 2.50197151162485 | erot = 2.91236336851854 | epot = -22.8558243132671 | etot = -17.4414894331237 -267000 ekin = 2.26171294775303 | erot = 1.4691550288396 | epot = -22.8708165336687 | etot = -19.1399485570761 -268000 ekin = 2.44836854545511 | erot = 2.9937425626706 | epot = -22.7570882008955 | etot = -17.3149770927698 -269000 ekin = 1.58300780634396 | erot = 3.22395730855789 | epot = -22.3907113081099 | etot = -17.5837461932081 -270000 ekin = 2.32322184760979 | erot = 3.06382421219438 | epot = -22.3881691749602 | etot = -17.001123115156 -271000 ekin = 3.60469687596824 | erot = 1.9797358598963 | epot = -22.4683966465291 | etot = -16.8839639106645 -272000 ekin = 3.51923106402285 | erot = 2.03023285354504 | epot = -22.4603583954676 | etot = -16.9108944778997 -273000 ekin = 2.11482184852541 | erot = 2.44627955820304 | epot = -22.3849709951286 | etot = -17.8238695884002 -274000 ekin = 1.92099330523926 | erot = 1.84100701949309 | epot = -22.4079231056523 | etot = -18.64592278092 -275000 ekin = 2.00926480279114 | erot = 2.3425841103212 | epot = -22.5238525372828 | etot = -18.1720036241704 -276000 ekin = 2.63097538006804 | erot = 2.50136285103272 | epot = -22.5353755283889 | etot = -17.4030372972882 -277000 ekin = 1.82015412793384 | erot = 1.70696131852909 | epot = -22.5292430541423 | etot = -19.0021276076793 -278000 ekin = 2.01769954373528 | erot = 2.59890230516084 | epot = -22.5906588225137 | etot = -17.9740569736176 -279000 ekin = 2.25640040624717 | erot = 2.29091139708182 | epot = -22.6277099788414 | etot = -18.0803981755124 -280000 ekin = 3.04018837983384 | erot = 2.20649234309561 | epot = -22.6234289166475 | etot = -17.376748193718 -281000 ekin = 2.26774972276864 | erot = 2.21425432655914 | epot = -22.6813285841657 | etot = -18.1993245348379 -282000 ekin = 2.97313150959962 | erot = 2.86622182739124 | epot = -22.7015431862321 | etot = -16.8621898492412 -283000 ekin = 2.50361895288103 | erot = 3.01017153845275 | epot = -22.6838734010489 | etot = -17.1700829097151 -284000 ekin = 2.07988501520726 | erot = 2.53369538735043 | epot = -22.6244057852699 | etot = -18.0108253827122 -285000 ekin = 2.63544742669395 | erot = 2.22184957642688 | epot = -22.6299704571646 | etot = -17.7726734540438 -286000 ekin = 3.28190504383103 | erot = 2.59924342945106 | epot = -22.6685734662042 | etot = -16.7874249929221 -287000 ekin = 2.5201730496864 | erot = 2.47409649915194 | epot = -22.6647398556855 | etot = -17.6704703068471 -288000 ekin = 1.72383940997515 | erot = 2.2989067867213 | epot = -22.5898062623046 | etot = -18.5670600656082 -289000 ekin = 1.84179788109765 | erot = 2.70369316308707 | epot = -22.47181336009 | etot = -17.9263223159052 -290000 ekin = 1.6715135413566 | erot = 2.58080004878555 | epot = -22.4106998409513 | etot = -18.1583862508092 -291000 ekin = 1.5215220538295 | erot = 2.73428237886897 | epot = -22.3556298896499 | etot = -18.0998254569515 -292000 ekin = 1.80629028335816 | erot = 2.0852735260545 | epot = -22.4535418049614 | etot = -18.5619779955488 -293000 ekin = 2.15472126777205 | erot = 2.19759927977713 | epot = -22.5557303698456 | etot = -18.2034098222964 -294000 ekin = 2.56152704015233 | erot = 2.8613616067162 | epot = -22.6398911758506 | etot = -17.2170025289821 -295000 ekin = 2.371265169146 | erot = 3.38251794814698 | epot = -22.6865354227056 | etot = -16.9327523054126 -296000 ekin = 2.03365878847188 | erot = 2.18393142873388 | epot = -22.6560933682687 | etot = -18.438503151063 -297000 ekin = 2.49621501086621 | erot = 2.10112805919269 | epot = -22.7035635415212 | etot = -18.1062204714623 -298000 ekin = 2.77842269503177 | erot = 3.3772341506228 | epot = -22.7119153133845 | etot = -16.5562584677299 -299000 ekin = 2.67707880841785 | erot = 2.98874558313004 | epot = -22.7666464233606 | etot = -17.1008220318128 -300000 ekin = 2.27178796654212 | erot = 2.26073784829731 | epot = -22.7766831409595 | etot = -18.2441573261201 -301000 ekin = 2.20083021797287 | erot = 3.3890245069517 | epot = -22.7273506022536 | etot = -17.137495877329 -302000 ekin = 2.96489064574833 | erot = 2.84356412203241 | epot = -22.6697893088022 | etot = -16.8613345410215 -303000 ekin = 2.31874098268026 | erot = 2.61961335705569 | epot = -22.6493939125616 | etot = -17.7110395728257 -304000 ekin = 2.72610257159623 | erot = 3.02709946331765 | epot = -22.6952460519591 | etot = -16.9420440170453 -305000 ekin = 2.63459003021214 | erot = 1.919675076019 | epot = -22.6686095819004 | etot = -18.1143444756693 -306000 ekin = 2.27957015123362 | erot = 2.30903194024744 | epot = -22.6205242146107 | etot = -18.0319221231296 -307000 ekin = 2.59039939360351 | erot = 1.72550416449957 | epot = -22.5760437098146 | etot = -18.2601401517115 -308000 ekin = 2.25862282018141 | erot = 2.6613420500591 | epot = -22.4810009931421 | etot = -17.5610361229016 -309000 ekin = 2.58156867056613 | erot = 1.38162183672195 | epot = -22.4520281277666 | etot = -18.4888376204785 -310000 ekin = 2.30199887399085 | erot = 3.49424058278129 | epot = -22.4502933105603 | etot = -16.6540538537882 -311000 ekin = 1.92151496683435 | erot = 3.702621790492 | epot = -22.3972021294092 | etot = -16.7730653720828 -312000 ekin = 1.83005087613798 | erot = 2.19341081660898 | epot = -22.3720470055312 | etot = -18.3485853127842 -313000 ekin = 1.92489041812718 | erot = 1.83277045127814 | epot = -22.490802859931 | etot = -18.7331419905256 -314000 ekin = 2.09288582482849 | erot = 3.1959722998652 | epot = -22.4338118394254 | etot = -17.1449537147317 -315000 ekin = 2.16369102652801 | erot = 2.93597548628521 | epot = -22.4469736533496 | etot = -17.3473071405364 -316000 ekin = 2.09245693384264 | erot = 1.807558537396 | epot = -22.3690695710527 | etot = -18.4690540998141 -317000 ekin = 2.36588943769063 | erot = 1.70568184689724 | epot = -22.3496046632177 | etot = -18.2780333786298 -318000 ekin = 1.83301083634324 | erot = 3.09521659572646 | epot = -22.3586080730087 | etot = -17.430380640939 -319000 ekin = 1.55798533508654 | erot = 2.374400525685 | epot = -22.3769508910799 | etot = -18.4445650303083 -320000 ekin = 2.96087389710191 | erot = 2.89099773614827 | epot = -22.4288122697123 | etot = -16.5769406364621 -321000 ekin = 3.19179841293413 | erot = 2.37305905207938 | epot = -22.5447709145936 | etot = -16.9799134495801 -322000 ekin = 3.10570427346294 | erot = 3.34188038301289 | epot = -22.580443523357 | etot = -16.1328588668812 -323000 ekin = 2.22962685798083 | erot = 2.03306866549118 | epot = -22.5997373536669 | etot = -18.3370418301949 -324000 ekin = 2.28811378374166 | erot = 2.14190372685336 | epot = -22.5597352990857 | etot = -18.1297177884906 -325000 ekin = 2.85757123939544 | erot = 2.33537312761609 | epot = -22.5231085637202 | etot = -17.3301641967086 -326000 ekin = 2.30070347083078 | erot = 2.23549787294263 | epot = -22.5151413151487 | etot = -17.9789399713752 -327000 ekin = 3.29082503272818 | erot = 1.92556360043753 | epot = -22.5231816508473 | etot = -17.3067930176816 -328000 ekin = 2.38165298551354 | erot = 1.63346978078624 | epot = -22.5231376952434 | etot = -18.5080149289436 -329000 ekin = 3.46430064220694 | erot = 2.33095343034691 | epot = -22.4569686289904 | etot = -16.6617145564365 -330000 ekin = 3.03486739022287 | erot = 2.39278089551369 | epot = -22.3332523924126 | etot = -16.905604106676 -331000 ekin = 2.30557375971102 | erot = 2.07089271354998 | epot = -22.2503996798711 | etot = -17.8739332066101 -332000 ekin = 1.60842407147764 | erot = 3.110396890796 | epot = -22.2247256358723 | etot = -17.5059046735987 -333000 ekin = 1.87112469334644 | erot = 3.30899727462101 | epot = -22.130065759788 | etot = -16.9499437918205 -334000 ekin = 2.39344914466899 | erot = 2.11606499087986 | epot = -22.052515122119 | etot = -17.5430009865702 -335000 ekin = 2.58946334556546 | erot = 2.68851920162594 | epot = -21.971164793944 | etot = -16.6931822467526 -336000 ekin = 2.41988877667505 | erot = 2.41525912575628 | epot = -21.8441556082519 | etot = -17.0090077058205 -337000 ekin = 2.33064340197969 | erot = 2.60509084649572 | epot = -21.8962678452425 | etot = -16.9605335967671 -338000 ekin = 1.96206714975463 | erot = 1.65377379268676 | epot = -21.8484931449949 | etot = -18.2326522025535 -339000 ekin = 1.55631939970369 | erot = 2.24373622444027 | epot = -21.8253755182891 | etot = -18.0253198941451 -340000 ekin = 2.70749090548453 | erot = 2.95739933680002 | epot = -21.8243135462175 | etot = -16.1594233039329 -341000 ekin = 2.44634541815133 | erot = 1.84695948440237 | epot = -21.9282158516816 | etot = -17.6349109491279 -342000 ekin = 2.51784295345496 | erot = 2.73626675676614 | epot = -21.9579426326808 | etot = -16.7038329224596 -343000 ekin = 3.41670961674692 | erot = 2.43111012770705 | epot = -21.9935092107186 | etot = -16.1456894662647 -344000 ekin = 2.58780800263767 | erot = 1.6930389050268 | epot = -22.0715354699269 | etot = -17.7906885622624 -345000 ekin = 2.57576456033189 | erot = 1.99487459437559 | epot = -22.1796629942929 | etot = -17.6090238395854 -346000 ekin = 2.40404980880465 | erot = 2.31288728866961 | epot = -22.1855258065435 | etot = -17.4685887090693 -347000 ekin = 2.28146784424865 | erot = 2.74513531512625 | epot = -22.2205619484594 | etot = -17.1939587890845 -348000 ekin = 2.26319568262242 | erot = 2.43454354691427 | epot = -22.2148038230762 | etot = -17.5170645935395 -349000 ekin = 1.98764147715107 | erot = 2.21856918820044 | epot = -22.2333110495202 | etot = -18.0271003841687 -350000 ekin = 2.08440088155067 | erot = 2.55841250738978 | epot = -22.2541078972618 | etot = -17.6112945083214 -351000 ekin = 2.38201758452314 | erot = 2.17974220056875 | epot = -22.2647718284383 | etot = -17.7030120433464 -352000 ekin = 2.75130853950625 | erot = 2.25801401818502 | epot = -22.2226031541769 | etot = -17.2132805964856 -353000 ekin = 2.39316894458245 | erot = 1.9622692189896 | epot = -22.1905585968626 | etot = -17.8351204332906 -354000 ekin = 2.60613964367264 | erot = 2.45699958173639 | epot = -22.0741463551659 | etot = -17.0110071297569 -355000 ekin = 1.80064206533144 | erot = 2.59773518186197 | epot = -22.011221342413 | etot = -17.6128440952196 -356000 ekin = 2.37699640398752 | erot = 3.09710102021834 | epot = -22.0299491911754 | etot = -16.5558517669695 -357000 ekin = 2.50986884955702 | erot = 1.91180399130884 | epot = -22.0481853325197 | etot = -17.6265124916538 -358000 ekin = 2.12558610604631 | erot = 2.6479682554889 | epot = -21.9447638703624 | etot = -17.1712095088272 -359000 ekin = 2.22688919900624 | erot = 2.23931556284384 | epot = -21.8085491928632 | etot = -17.3423444310132 -360000 ekin = 3.13527943466207 | erot = 2.8147567946821 | epot = -21.7902147579702 | etot = -15.840178528626 -361000 ekin = 2.71487331879396 | erot = 2.8877144694031 | epot = -21.8322461119152 | etot = -16.2296583237181 -362000 ekin = 2.515817675735 | erot = 3.0246147355251 | epot = -21.8359960107676 | etot = -16.2955635995075 -363000 ekin = 2.70354655291949 | erot = 2.04948095390169 | epot = -21.8699556802982 | etot = -17.116928173477 -364000 ekin = 2.34554467024059 | erot = 1.36382458642029 | epot = -21.9151567775916 | etot = -18.2057875209307 -365000 ekin = 2.00291957865484 | erot = 2.38153585819252 | epot = -21.8681661882236 | etot = -17.4837107513762 -366000 ekin = 2.16416218280056 | erot = 2.11489166860241 | epot = -21.7862692661643 | etot = -17.5072154147613 -367000 ekin = 2.90642004514044 | erot = 2.66688606213217 | epot = -21.7352532339732 | etot = -16.1619471267006 -368000 ekin = 2.23185601684558 | erot = 2.34205881571908 | epot = -21.7124134746584 | etot = -17.1384986420937 -369000 ekin = 2.15521118053823 | erot = 2.93659164111176 | epot = -21.6437028615637 | etot = -16.5519000399137 -370000 ekin = 2.4198441869984 | erot = 1.73242712802795 | epot = -21.6676625868509 | etot = -17.5153912718245 -371000 ekin = 2.30492028429812 | erot = 2.61127763357756 | epot = -21.6509011744132 | etot = -16.7347032565375 -372000 ekin = 2.96963579911545 | erot = 1.88141866012236 | epot = -21.6391346229962 | etot = -16.7880801637584 -373000 ekin = 3.14075275331208 | erot = 2.93731686024779 | epot = -21.6868881994144 | etot = -15.6088185858545 -374000 ekin = 3.04463795536237 | erot = 3.14447085467475 | epot = -21.7931849017047 | etot = -15.6040760916676 -375000 ekin = 2.39986353169888 | erot = 2.66264703557189 | epot = -21.7551227714398 | etot = -16.692612204169 -376000 ekin = 2.55064647974443 | erot = 2.67473669587464 | epot = -21.696903880931 | etot = -16.4715207053119 -377000 ekin = 2.8852049591096 | erot = 2.18098614239663 | epot = -21.6952272659367 | etot = -16.6290361644304 -378000 ekin = 2.45289138323383 | erot = 2.10679058068883 | epot = -21.7288468051836 | etot = -17.1691648412609 -379000 ekin = 2.53609345690701 | erot = 1.90940679695127 | epot = -21.7506211345922 | etot = -17.3051208807339 -380000 ekin = 2.72283735812631 | erot = 3.24838500978278 | epot = -21.7463635962089 | etot = -15.7751412282998 -381000 ekin = 2.45462865405655 | erot = 2.38504307590766 | epot = -21.7562222022035 | etot = -16.9165504722393 -382000 ekin = 1.80283057853964 | erot = 2.1374935723038 | epot = -21.6701942835523 | etot = -17.7298701327088 -383000 ekin = 1.73467369524417 | erot = 2.3108192426649 | epot = -21.6923619844203 | etot = -17.6468690465113 -384000 ekin = 1.9342846276238 | erot = 2.70905668846398 | epot = -21.7127338523707 | etot = -17.0693925362829 -385000 ekin = 1.68998612656995 | erot = 1.64115683316309 | epot = -21.7718687316805 | etot = -18.4407257719475 -386000 ekin = 1.78400139488241 | erot = 1.74778393778735 | epot = -21.836680877067 | etot = -18.3048955443972 -387000 ekin = 2.07818501197508 | erot = 2.07807279268733 | epot = -21.832055454303 | etot = -17.6757976496406 -388000 ekin = 1.66290950060047 | erot = 2.60797351732765 | epot = -21.8118307069785 | etot = -17.5409476890504 -389000 ekin = 2.21198900204585 | erot = 2.23421390729077 | epot = -21.7427524360538 | etot = -17.2965495267171 -390000 ekin = 1.66652818866883 | erot = 2.31347723913494 | epot = -21.7301442799172 | etot = -17.7501388521135 -391000 ekin = 1.8533948354001 | erot = 3.3132884098265 | epot = -21.8115260458304 | etot = -16.6448428006038 -392000 ekin = 1.58742216104324 | erot = 2.82110846571971 | epot = -21.8293545192998 | etot = -17.4208238925368 -393000 ekin = 2.11722620613808 | erot = 2.34344765418119 | epot = -21.8696915886196 | etot = -17.4090177283003 -394000 ekin = 1.75812741619619 | erot = 2.82419425154452 | epot = -21.8924899919106 | etot = -17.3101683241699 -395000 ekin = 1.65095705493153 | erot = 2.81412301374871 | epot = -21.9536401970573 | etot = -17.488560128377 -396000 ekin = 1.73767503056944 | erot = 2.21765951200349 | epot = -22.1029546817349 | etot = -18.147620139162 -397000 ekin = 1.77674477730128 | erot = 2.32452598687485 | epot = -22.2130001775225 | etot = -18.1117294133464 -398000 ekin = 2.65895177503898 | erot = 2.95633927860974 | epot = -22.2752931466756 | etot = -16.6600020930269 -399000 ekin = 2.03803363665377 | erot = 2.12344232072307 | epot = -22.2652656821057 | etot = -18.1037897247289 -400000 ekin = 2.04555714339347 | erot = 2.27233839044242 | epot = -22.3051350135305 | etot = -17.9872394796946 -401000 ekin = 2.15872349230843 | erot = 2.50519181279082 | epot = -22.3726160012138 | etot = -17.7087006961145 -402000 ekin = 2.37736861330784 | erot = 2.3210196208099 | epot = -22.4002021740759 | etot = -17.7018139399582 -403000 ekin = 2.46021709434135 | erot = 1.94696118347469 | epot = -22.4595514414876 | etot = -18.0523731636716 -404000 ekin = 2.77045691339541 | erot = 2.38769700494278 | epot = -22.6029152684925 | etot = -17.4447613501544 -405000 ekin = 2.3136465567458 | erot = 2.23279102592819 | epot = -22.704170194226 | etot = -18.1577326115521 -406000 ekin = 2.41170890033499 | erot = 2.77109231953927 | epot = -22.779806571174 | etot = -17.5970053512998 -407000 ekin = 2.35942219707683 | erot = 2.74328193450569 | epot = -22.836396275899 | etot = -17.7336921443165 -408000 ekin = 3.24790924688638 | erot = 1.7391244014667 | epot = -22.7651095148446 | etot = -17.7780758664915 -409000 ekin = 2.24830289645136 | erot = 2.34265544739425 | epot = -22.6995454603056 | etot = -18.1085871164599 -410000 ekin = 1.78296326417356 | erot = 2.10343999475669 | epot = -22.7273761758661 | etot = -18.8409729169359 -411000 ekin = 2.40205079722836 | erot = 2.79371172655516 | epot = -22.7437086077248 | etot = -17.5479460839413 -412000 ekin = 2.4827447274903 | erot = 2.66642432537184 | epot = -22.7490438870461 | etot = -17.5998748341839 -413000 ekin = 2.75975825991147 | erot = 1.99252624136793 | epot = -22.7296409338909 | etot = -17.9773564326115 -414000 ekin = 2.46171754591312 | erot = 1.56532549126561 | epot = -22.7020089470024 | etot = -18.6749659098237 -415000 ekin = 2.9412491128766 | erot = 2.93447949050541 | epot = -22.7167297662641 | etot = -16.8410011628821 -416000 ekin = 2.451529226545 | erot = 2.93177240269518 | epot = -22.679285885952 | etot = -17.2959842567118 -417000 ekin = 2.02304677035706 | erot = 2.34845196496212 | epot = -22.6359674216736 | etot = -18.2644686863544 -418000 ekin = 2.27202933065743 | erot = 2.78253971259171 | epot = -22.5709417374616 | etot = -17.5163726942125 -419000 ekin = 3.11399834748007 | erot = 1.5069444804289 | epot = -22.5346711742036 | etot = -17.9137283462946 -420000 ekin = 2.43157626989745 | erot = 2.33553639635962 | epot = -22.5241645646513 | etot = -17.7570518983943 -421000 ekin = 2.52273757815056 | erot = 1.68036667639443 | epot = -22.523670591424 | etot = -18.320566336879 -422000 ekin = 2.28707428015146 | erot = 1.95211017937543 | epot = -22.4864987695302 | etot = -18.2473143100033 -423000 ekin = 2.77128027363906 | erot = 1.83509225830907 | epot = -22.4676364752475 | etot = -17.8612639432993 -424000 ekin = 2.61658126968941 | erot = 1.92044025854228 | epot = -22.5053529183204 | etot = -17.9683313900887 -425000 ekin = 2.25690716213737 | erot = 2.3485630523016 | epot = -22.5471810198293 | etot = -17.9417108053903 -426000 ekin = 2.5401911697216 | erot = 1.58168199076436 | epot = -22.599451551521 | etot = -18.4775783910351 -427000 ekin = 2.61776589335417 | erot = 2.3289376640184 | epot = -22.673196553825 | etot = -17.7264929964524 -428000 ekin = 2.11718463198403 | erot = 3.04652352541351 | epot = -22.7510529806942 | etot = -17.5873448232966 -429000 ekin = 1.69509699892837 | erot = 2.32755685540312 | epot = -22.7391772285581 | etot = -18.7165233742266 -430000 ekin = 2.21470975507857 | erot = 2.51273009568295 | epot = -22.6682263206376 | etot = -17.9407864698761 -431000 ekin = 2.94401624259271 | erot = 2.52065679136838 | epot = -22.6769821981683 | etot = -17.2123091642072 -432000 ekin = 2.86039016721639 | erot = 2.10092531726113 | epot = -22.6856922787856 | etot = -17.7243767943081 -433000 ekin = 2.38577772852308 | erot = 1.92242037772747 | epot = -22.7525956133752 | etot = -18.4443975071246 -434000 ekin = 2.38240431006896 | erot = 2.10745905578944 | epot = -22.7586540042292 | etot = -18.2687906383708 -435000 ekin = 2.12286955240469 | erot = 2.34000354159217 | epot = -22.6319118730511 | etot = -18.1690387790542 -436000 ekin = 2.67385800386604 | erot = 2.59460579166868 | epot = -22.6404996973321 | etot = -17.3720359017973 -437000 ekin = 1.75959740929828 | erot = 2.43720192360986 | epot = -22.7030079938494 | etot = -18.5062086609412 -438000 ekin = 1.75120908430786 | erot = 2.28124118651858 | epot = -22.749190610227 | etot = -18.7167403394005 -439000 ekin = 1.75073242294502 | erot = 2.03624763446663 | epot = -22.7489457185962 | etot = -18.9619656611846 -440000 ekin = 2.07721967183055 | erot = 2.85858063288596 | epot = -22.8109744065491 | etot = -17.8751741018326 -441000 ekin = 1.60202985220682 | erot = 2.85100314352584 | epot = -22.7745689858311 | etot = -18.3215359900984 -442000 ekin = 2.27654314397087 | erot = 3.22274835717702 | epot = -22.7446035204748 | etot = -17.2453120193269 -443000 ekin = 1.93733014307339 | erot = 1.57432763299075 | epot = -22.7272800276947 | etot = -19.2156222516305 -444000 ekin = 1.75731366949631 | erot = 2.25504170254907 | epot = -22.6435278528204 | etot = -18.631172480775 -445000 ekin = 2.09887119167798 | erot = 2.26627204333156 | epot = -22.5193278168198 | etot = -18.1541845818103 -446000 ekin = 2.16625669770322 | erot = 2.62168464822181 | epot = -22.4290479239373 | etot = -17.6411065780122 -447000 ekin = 2.19819598279476 | erot = 2.11162819084596 | epot = -22.3774620810792 | etot = -18.0676379074385 -448000 ekin = 1.7755208645772 | erot = 1.64284712827749 | epot = -22.3894548684582 | etot = -18.9710868756035 -449000 ekin = 2.29637528825017 | erot = 1.5286287774847 | epot = -22.4548388263691 | etot = -18.6298347606342 -450000 ekin = 2.55872726173568 | erot = 1.95244709295837 | epot = -22.4761389570735 | etot = -17.9649646023794 -451000 ekin = 1.93483929977221 | erot = 1.57730203053738 | epot = -22.4721871402484 | etot = -18.9600458099388 -452000 ekin = 1.71591960523824 | erot = 4.15592526681975 | epot = -22.3869204664751 | etot = -16.5150755944171 -453000 ekin = 2.05784261741687 | erot = 2.49754472957529 | epot = -22.4247246256638 | etot = -17.8693372786717 -454000 ekin = 2.37473664452537 | erot = 3.37363200196795 | epot = -22.496641743959 | etot = -16.7482730974657 -455000 ekin = 1.73966540098562 | erot = 3.16990427576242 | epot = -22.3919175950499 | etot = -17.4823479183019 -456000 ekin = 2.41686819433944 | erot = 2.61137211811606 | epot = -22.3203430517439 | etot = -17.2921027392884 -457000 ekin = 2.87348571875052 | erot = 2.67840099268897 | epot = -22.3129445692579 | etot = -16.7610578578184 -458000 ekin = 1.89437239565888 | erot = 2.55463878014183 | epot = -22.4202394049443 | etot = -17.9712282291436 -459000 ekin = 1.87572781245208 | erot = 2.52613531614619 | epot = -22.4249057850463 | etot = -18.023042656448 -460000 ekin = 2.04813188453058 | erot = 2.20089271831971 | epot = -22.4011710022067 | etot = -18.1521463993564 -461000 ekin = 1.47247960021922 | erot = 1.40768398836064 | epot = -22.3586363246324 | etot = -19.4784727360526 -462000 ekin = 1.38503831902219 | erot = 2.34595020862052 | epot = -22.4837409423011 | etot = -18.7527524146584 -463000 ekin = 2.00645645258759 | erot = 1.18165989843029 | epot = -22.4806738518605 | etot = -19.2925575008426 -464000 ekin = 2.08237091480074 | erot = 3.07220535335028 | epot = -22.4836460827449 | etot = -17.3290698145939 -465000 ekin = 2.0456215542015 | erot = 1.86890585180634 | epot = -22.5174143411392 | etot = -18.6028869351313 -466000 ekin = 2.95986717673676 | erot = 2.11178510069291 | epot = -22.6235722981753 | etot = -17.5519200207456 -467000 ekin = 2.20953809644101 | erot = 2.57273746506495 | epot = -22.7571181950953 | etot = -17.9748426335893 -468000 ekin = 1.5902871353447 | erot = 2.01907967468793 | epot = -22.7769947042451 | etot = -19.1676278942124 -469000 ekin = 1.9462052385748 | erot = 2.93750281149461 | epot = -22.7672520333545 | etot = -17.8835439832851 -470000 ekin = 3.38174970242104 | erot = 2.36622797398471 | epot = -22.8494270221486 | etot = -17.1014493457428 -471000 ekin = 2.19235331714116 | erot = 1.88537594669814 | epot = -22.9012671707407 | etot = -18.8235379069014 -472000 ekin = 2.09266734001604 | erot = 2.08181669723127 | epot = -22.9459604070355 | etot = -18.7714763697882 -473000 ekin = 2.36590705985013 | erot = 2.6708545089404 | epot = -23.0062159802477 | etot = -17.9694544114572 -474000 ekin = 2.77035694449384 | erot = 2.3027678515899 | epot = -23.0283042070227 | etot = -17.955179410939 -475000 ekin = 2.81469924529784 | erot = 1.74801606053043 | epot = -22.9818727611313 | etot = -18.419157455303 -476000 ekin = 1.6614371664979 | erot = 2.66895679342948 | epot = -22.9607497426557 | etot = -18.6303557827283 -477000 ekin = 3.4013813766128 | erot = 2.47762083745631 | epot = -22.9863526077737 | etot = -17.1073503937045 -478000 ekin = 2.64900083423483 | erot = 1.91407757255602 | epot = -22.9956967968773 | etot = -18.4326183900864 -479000 ekin = 1.60377176066656 | erot = 2.03690854636729 | epot = -22.9622351913009 | etot = -19.321554884267 -480000 ekin = 2.06361598114192 | erot = 2.38288961387606 | epot = -22.9444711012275 | etot = -18.4979655062095 -481000 ekin = 3.10420446629087 | erot = 2.4564857948581 | epot = -22.8947513649008 | etot = -17.3340611037518 -482000 ekin = 3.72901587351966 | erot = 2.08724672578547 | epot = -22.7565389886474 | etot = -16.9402763893423 -483000 ekin = 2.80051858170061 | erot = 2.88284961334901 | epot = -22.621270459186 | etot = -16.9379022641364 -484000 ekin = 2.0110409785781 | erot = 3.72169931738832 | epot = -22.5566278703519 | etot = -16.8238875743855 -485000 ekin = 1.87367667342341 | erot = 2.09747077779511 | epot = -22.5747713031699 | etot = -18.6036238519514 -486000 ekin = 2.01419066693786 | erot = 1.53376047222564 | epot = -22.6617353485008 | etot = -19.1137842093373 -487000 ekin = 2.62466310274651 | erot = 2.8154565495424 | epot = -22.7635996267058 | etot = -17.3234799744169 -488000 ekin = 2.20017113992739 | erot = 2.63952142846597 | epot = -22.7912824752716 | etot = -17.9515899068783 -489000 ekin = 2.48973425231097 | erot = 1.93887082378345 | epot = -22.7821173566376 | etot = -18.3535122805431 -490000 ekin = 2.82031383172613 | erot = 2.1152704692751 | epot = -22.7439109707737 | etot = -17.8083266697725 -491000 ekin = 2.67150067218103 | erot = 2.60674263371376 | epot = -22.6902612982561 | etot = -17.4120179923614 -492000 ekin = 3.35859725231851 | erot = 2.09917303380754 | epot = -22.6792026914912 | etot = -17.2214324053652 -493000 ekin = 2.92706185972913 | erot = 2.61206418345318 | epot = -22.555890100553 | etot = -17.0167640573707 -494000 ekin = 3.40592557500485 | erot = 2.00651000685379 | epot = -22.4449277885912 | etot = -17.0324922067326 -495000 ekin = 2.82913240855034 | erot = 2.68876281432575 | epot = -22.3431571155508 | etot = -16.8252618926747 -496000 ekin = 2.68873100783268 | erot = 2.65459610018584 | epot = -22.3530288226937 | etot = -17.0097017146752 -497000 ekin = 2.15916102256083 | erot = 2.58178912964776 | epot = -22.3187762548927 | etot = -17.5778261026842 -498000 ekin = 2.1250851017953 | erot = 2.58172095004275 | epot = -22.2888001544895 | etot = -17.5819941026515 -499000 ekin = 2.34130861420783 | erot = 2.33488363451604 | epot = -22.3011081875454 | etot = -17.6249159388215 -500000 ekin = 2.85749511684744 | erot = 1.82527244658259 | epot = -22.3853764151975 | etot = -17.7026088517675 -501000 ekin = 2.41179591621454 | erot = 2.07214655971995 | epot = -22.4198306535951 | etot = -17.9358881776606 -502000 ekin = 2.0580038376515 | erot = 3.03025922314732 | epot = -22.4588141208809 | etot = -17.3705510600821 -503000 ekin = 2.24464497631497 | erot = 2.99486525785898 | epot = -22.4506192513903 | etot = -17.2111090172163 -504000 ekin = 1.80022602455725 | erot = 2.4742601796155 | epot = -22.4453216224399 | etot = -18.1708354182671 -505000 ekin = 2.44409230742744 | erot = 2.02809748474755 | epot = -22.50771443196 | etot = -18.035524639785 -506000 ekin = 2.53466734821408 | erot = 1.74485074876353 | epot = -22.5311895285302 | etot = -18.2516714315526 -507000 ekin = 3.23096993979711 | erot = 2.12667588504341 | epot = -22.5272680080029 | etot = -17.1696221831624 -508000 ekin = 2.87809924914958 | erot = 2.23647435070733 | epot = -22.5735852765105 | etot = -17.4590116766536 -509000 ekin = 3.09666803691483 | erot = 2.01344817227328 | epot = -22.5531322135987 | etot = -17.4430160044106 -510000 ekin = 2.89347551190587 | erot = 1.87907637088166 | epot = -22.5722142851241 | etot = -17.7996624023365 -511000 ekin = 2.89557048228876 | erot = 2.26727517274045 | epot = -22.6021965971202 | etot = -17.439350942091 -512000 ekin = 1.80499322219008 | erot = 2.06104103685542 | epot = -22.5082384805065 | etot = -18.642204221461 -513000 ekin = 1.86582605008159 | erot = 1.80881245799596 | epot = -22.4818731450098 | etot = -18.8072346369322 -514000 ekin = 1.66893021142187 | erot = 2.76856699398954 | epot = -22.5144633272087 | etot = -18.0769661217973 -515000 ekin = 2.16870417972369 | erot = 2.03793643176127 | epot = -22.5725374419723 | etot = -18.3658968304873 -516000 ekin = 1.95862575209641 | erot = 3.55790203033117 | epot = -22.5675974691126 | etot = -17.051069686685 -517000 ekin = 2.10116190921287 | erot = 1.8703746684216 | epot = -22.5643410282357 | etot = -18.5928044506012 -518000 ekin = 2.35762114087238 | erot = 2.34678356890067 | epot = -22.5789498872261 | etot = -17.874545177453 -519000 ekin = 1.4965579156146 | erot = 1.37620919030064 | epot = -22.5775405953339 | etot = -19.7047734894186 -520000 ekin = 2.20583131350858 | erot = 2.06518236580453 | epot = -22.6051420155062 | etot = -18.3341283361931 -521000 ekin = 2.11936831082606 | erot = 1.89313676730226 | epot = -22.6824826885911 | etot = -18.6699776104628 -522000 ekin = 2.43972156166519 | erot = 2.29575985894378 | epot = -22.7597964571688 | etot = -18.0243150365599 -523000 ekin = 2.47148532971583 | erot = 2.62592855606052 | epot = -22.8218100826241 | etot = -17.7243961968478 -524000 ekin = 2.83867159838233 | erot = 1.67228239212566 | epot = -22.9130691352048 | etot = -18.4021151446968 -525000 ekin = 2.33707759686424 | erot = 2.11666157542524 | epot = -22.9343168153401 | etot = -18.4805776430506 -526000 ekin = 2.78556314383173 | erot = 2.12502967301725 | epot = -22.9632272664466 | etot = -18.0526344495976 -527000 ekin = 2.67476397366556 | erot = 2.10678170752056 | epot = -23.0109160127258 | etot = -18.2293703315396 -528000 ekin = 3.11020438334646 | erot = 2.16717572821384 | epot = -23.0743097715177 | etot = -17.7969296599574 -529000 ekin = 1.90071372306354 | erot = 2.29269386063507 | epot = -23.0742513713216 | etot = -18.880843787623 -530000 ekin = 2.54935777739561 | erot = 3.44632009130416 | epot = -22.9815707708391 | etot = -16.9858929021393 -531000 ekin = 1.98646544552742 | erot = 1.84284731266331 | epot = -22.8840867927685 | etot = -19.0547740345778 -532000 ekin = 2.34497208518389 | erot = 2.20242825249901 | epot = -22.958017128877 | etot = -18.4106167911941 -533000 ekin = 2.04465189646124 | erot = 2.5988852213048 | epot = -23.0954673727488 | etot = -18.4519302549827 -534000 ekin = 2.18099982404014 | erot = 2.24509264512596 | epot = -23.1672915876949 | etot = -18.7411991185288 -535000 ekin = 2.46459047030509 | erot = 2.52567370572274 | epot = -23.2601041392818 | etot = -18.269839963254 -536000 ekin = 2.40944341542506 | erot = 3.07014221153817 | epot = -23.3294178896885 | etot = -17.8498322627253 -537000 ekin = 1.46836063591622 | erot = 3.04877831235775 | epot = -23.3582488035726 | etot = -18.8411098552986 -538000 ekin = 2.2322723564918 | erot = 1.93698675675114 | epot = -23.3840280699676 | etot = -19.2147689567247 -539000 ekin = 2.65850305482382 | erot = 1.70915364045623 | epot = -23.4835953822242 | etot = -19.1159386869442 -540000 ekin = 2.15389248554489 | erot = 1.94073382714967 | epot = -23.5227953658549 | etot = -19.4281690531603 -541000 ekin = 2.67641186082159 | erot = 2.24709344305834 | epot = -23.5427111580002 | etot = -18.6192058541203 -542000 ekin = 2.10429644506714 | erot = 2.41109271626466 | epot = -23.504268251071 | etot = -18.9888790897392 -543000 ekin = 1.88696147522521 | erot = 2.545986170319 | epot = -23.4573858832303 | etot = -19.0244382376861 -544000 ekin = 2.53894413626458 | erot = 1.83894339654212 | epot = -23.447037705898 | etot = -19.0691501730913 -545000 ekin = 2.2449929565181 | erot = 3.05817804399732 | epot = -23.6401013875395 | etot = -18.3369303870241 -546000 ekin = 2.38995007911114 | erot = 1.73896404887933 | epot = -23.6250705214727 | etot = -19.4961563934822 -547000 ekin = 2.53772946939786 | erot = 3.02671406060461 | epot = -23.6172206165977 | etot = -18.0527770865952 -548000 ekin = 2.30643053883799 | erot = 2.12291748181918 | epot = -23.6947786726432 | etot = -19.265430651986 -549000 ekin = 2.50325148970644 | erot = 2.43753928660968 | epot = -23.6482202119214 | etot = -18.7074294356052 -550000 ekin = 2.07278457584903 | erot = 1.98823624738949 | epot = -23.6224210624574 | etot = -19.5614002392189 -551000 ekin = 2.20187048094412 | erot = 2.1743107800257 | epot = -23.5352962443151 | etot = -19.1591149833453 -552000 ekin = 2.138048712317 | erot = 2.28135917444489 | epot = -23.5978298104151 | etot = -19.1784219236532 -553000 ekin = 2.42650743515903 | erot = 2.89235296005631 | epot = -23.5454068695436 | etot = -18.2265464743283 -554000 ekin = 2.31243694700819 | erot = 2.73411780294884 | epot = -23.4404612498823 | etot = -18.3939064999252 -555000 ekin = 2.25631450111253 | erot = 2.70826767236547 | epot = -23.3810480325839 | etot = -18.4164658591059 -556000 ekin = 2.42187654466562 | erot = 1.81816757766949 | epot = -23.3335658342219 | etot = -19.0935217118868 -557000 ekin = 2.89583868407859 | erot = 2.59800113316269 | epot = -23.348377375344 | etot = -17.8545375581027 -558000 ekin = 2.65744373001509 | erot = 2.27566901958148 | epot = -23.229384025348 | etot = -18.2962712757514 -559000 ekin = 2.40736894715472 | erot = 3.48404550901825 | epot = -23.2950530086045 | etot = -17.4036385524315 -560000 ekin = 2.51394452480884 | erot = 2.4472528185523 | epot = -23.3548725200314 | etot = -18.3936751766703 -561000 ekin = 2.78696960734098 | erot = 2.18117562469108 | epot = -23.367099011436 | etot = -18.3989537794039 -562000 ekin = 2.60590866354869 | erot = 1.82255499079639 | epot = -23.3670125949106 | etot = -18.9385489405655 -563000 ekin = 2.69475597498162 | erot = 2.75081051570648 | epot = -23.3213805671121 | etot = -17.875814076424 -564000 ekin = 2.62204591899764 | erot = 2.49524198212383 | epot = -23.2345685046841 | etot = -18.1172806035626 -565000 ekin = 2.67044367859168 | erot = 2.01330141540311 | epot = -23.2168974338887 | etot = -18.5331523398939 -566000 ekin = 2.13856275677523 | erot = 3.1447022522953 | epot = -23.162471502403 | etot = -17.8792064933325 -567000 ekin = 2.52010093960199 | erot = 2.13254469832705 | epot = -23.1518584744761 | etot = -18.499212836547 -568000 ekin = 2.28303629721264 | erot = 2.38209001003274 | epot = -23.1558738946393 | etot = -18.4907475873939 -569000 ekin = 3.02199429959192 | erot = 2.33409896439 | epot = -23.098858714014 | etot = -17.742765450032 -570000 ekin = 2.68736138164811 | erot = 2.91449049675473 | epot = -23.0516588224656 | etot = -17.4498069440628 -571000 ekin = 2.4201706123568 | erot = 2.30930147292481 | epot = -22.9494196307347 | etot = -18.2199475454531 -572000 ekin = 1.96101491359208 | erot = 3.17564644151202 | epot = -22.9019671727356 | etot = -17.7653058176315 -573000 ekin = 1.77231254512265 | erot = 3.2959074591727 | epot = -23.0329704228571 | etot = -17.9647504185618 -574000 ekin = 2.45195460796476 | erot = 2.33093773153734 | epot = -23.1880178627738 | etot = -18.4051255232717 -575000 ekin = 2.45020502461256 | erot = 2.4698820279554 | epot = -23.1834275192561 | etot = -18.2633404666881 -576000 ekin = 2.39426958146274 | erot = 2.18334419303673 | epot = -23.165586753046 | etot = -18.5879729785466 -577000 ekin = 2.42087612822122 | erot = 2.8078297015673 | epot = -23.1889846114073 | etot = -17.9602787816187 -578000 ekin = 2.47469593268156 | erot = 2.22291754195604 | epot = -23.1822026147549 | etot = -18.4845891401173 -579000 ekin = 1.99641516200814 | erot = 3.00564689499868 | epot = -23.2220374443818 | etot = -18.219975387375 -580000 ekin = 1.80326364254896 | erot = 2.62493677026808 | epot = -23.2725597079199 | etot = -18.8443592951029 -581000 ekin = 2.54320565466448 | erot = 2.56546557497723 | epot = -23.2936203171846 | etot = -18.1849490875429 -582000 ekin = 2.7760920595553 | erot = 1.7054369481595 | epot = -23.3188805344426 | etot = -18.8373515267278 -583000 ekin = 3.13415689631058 | erot = 2.13862743264097 | epot = -23.4032331278423 | etot = -18.1304487988907 -584000 ekin = 2.79256202281284 | erot = 1.86237066580274 | epot = -23.4507356031754 | etot = -18.7958029145598 -585000 ekin = 2.40352636193977 | erot = 1.43972962791954 | epot = -23.4948475688155 | etot = -19.6515915789562 -586000 ekin = 2.08429136741348 | erot = 2.19251166266265 | epot = -23.4108290375219 | etot = -19.1340260074458 -587000 ekin = 2.94108400136396 | erot = 2.57342077096898 | epot = -23.3540972375961 | etot = -17.8395924652632 -588000 ekin = 2.72217756938907 | erot = 2.61651915812691 | epot = -23.229726324284 | etot = -17.891029596768 -589000 ekin = 2.21949422254638 | erot = 2.3311223729484 | epot = -23.150949548888 | etot = -18.6003329533932 -590000 ekin = 1.81402039776171 | erot = 2.05517606383124 | epot = -23.0478545255486 | etot = -19.1786580639557 -591000 ekin = 1.58417624910412 | erot = 2.41463211542345 | epot = -23.0177633874473 | etot = -19.0189550229197 -592000 ekin = 1.98644093041263 | erot = 1.96551923696644 | epot = -22.9894017313741 | etot = -19.037441563995 -593000 ekin = 1.88204814648092 | erot = 1.95829012430934 | epot = -22.9815982306237 | etot = -19.1412599598334 -594000 ekin = 2.81360399014313 | erot = 2.15645684811238 | epot = -22.9751895785633 | etot = -18.0051287403077 -595000 ekin = 3.09138667876659 | erot = 1.85939570103404 | epot = -22.9585503153314 | etot = -18.0077679355308 -596000 ekin = 2.88475079255431 | erot = 1.99291497545754 | epot = -22.9694795630784 | etot = -18.0918137950666 -597000 ekin = 3.56180105071194 | erot = 2.46630922350926 | epot = -22.9861357432383 | etot = -16.9580254690171 -598000 ekin = 4.25212279079266 | erot = 2.48959233670472 | epot = -23.0214618233768 | etot = -16.2797466958794 -599000 ekin = 3.7244632603479 | erot = 2.76139687839883 | epot = -23.0721196129427 | etot = -16.5862594741959 -600000 ekin = 3.46467571149548 | erot = 1.76392307266267 | epot = -23.1890443898223 | etot = -17.9604456056642 -601000 ekin = 3.0310177628253 | erot = 3.28042241831116 | epot = -23.2392242833269 | etot = -16.9277841021904 -602000 ekin = 2.23251522550048 | erot = 1.93410139388427 | epot = -23.2748311690052 | etot = -19.1082145496205 -603000 ekin = 1.52395184313396 | erot = 2.30579905635095 | epot = -23.3079770801695 | etot = -19.4782261806846 -604000 ekin = 1.80277509473345 | erot = 3.26982922397805 | epot = -23.3021805347927 | etot = -18.2295762160812 -605000 ekin = 1.69061269141421 | erot = 2.90357416013347 | epot = -23.2880125710927 | etot = -18.693825719545 -606000 ekin = 2.35348879310444 | erot = 2.05826930628853 | epot = -23.2259863126357 | etot = -18.8142282132427 -607000 ekin = 2.98750155196662 | erot = 1.93245034618772 | epot = -23.1569905313344 | etot = -18.2370386331801 -608000 ekin = 3.25247562357662 | erot = 2.87367209024389 | epot = -23.1243437665535 | etot = -16.998196052733 -609000 ekin = 2.74562851506243 | erot = 2.46957178784349 | epot = -23.1378453224525 | etot = -17.9226450195466 -610000 ekin = 3.56937899101944 | erot = 1.85394286166138 | epot = -23.1342553563961 | etot = -17.7109335037153 -611000 ekin = 3.25034255711548 | erot = 2.16992689142413 | epot = -23.0420891001313 | etot = -17.6218196515917 -612000 ekin = 2.95654106669507 | erot = 2.13931254426743 | epot = -23.0506038845264 | etot = -17.9547502735639 -613000 ekin = 3.04973095155775 | erot = 1.87979868094329 | epot = -22.9901336683938 | etot = -18.0606040358928 -614000 ekin = 3.00995775064021 | erot = 1.70679828403894 | epot = -23.0067400319172 | etot = -18.2899839972381 -615000 ekin = 2.21837740297639 | erot = 2.65601107560568 | epot = -22.9594109490335 | etot = -18.0850224704514 -616000 ekin = 1.9492997573226 | erot = 2.08809832862859 | epot = -22.9058047688739 | etot = -18.8684066829227 -617000 ekin = 2.34987504209514 | erot = 3.31816085594407 | epot = -22.8092343894311 | etot = -17.1411984913919 -618000 ekin = 2.24263426864651 | erot = 2.25720621146615 | epot = -22.8020578987413 | etot = -18.3022174186286 -619000 ekin = 1.97180881105029 | erot = 2.07875245552439 | epot = -22.7569606401772 | etot = -18.7063993736025 -620000 ekin = 2.39044144530086 | erot = 2.89229500628476 | epot = -22.7088725220114 | etot = -17.4261360704257 -621000 ekin = 2.15150678521736 | erot = 2.30775677443908 | epot = -22.643940119738 | etot = -18.1846765600816 -622000 ekin = 2.0028430350823 | erot = 2.78278646933244 | epot = -22.600112912221 | etot = -17.8144834078063 -623000 ekin = 2.19528283622071 | erot = 2.14002571477316 | epot = -22.666620119306 | etot = -18.3313115683121 -624000 ekin = 2.82040068944897 | erot = 2.57349826686042 | epot = -22.7167317153813 | etot = -17.3228327590719 -625000 ekin = 2.98627918034148 | erot = 1.57679569211939 | epot = -22.7237278324305 | etot = -18.1606529599696 -626000 ekin = 2.37348083921872 | erot = 1.88550722657484 | epot = -22.7032586894344 | etot = -18.4442706236409 -627000 ekin = 2.35195177608881 | erot = 2.01446777503463 | epot = -22.7112770388174 | etot = -18.344857487694 -628000 ekin = 2.50881254425373 | erot = 1.56688558879362 | epot = -22.6405205013867 | etot = -18.5648223683393 -629000 ekin = 2.58514893297873 | erot = 1.70970168729388 | epot = -22.5610370580219 | etot = -18.2661864377493 -630000 ekin = 2.78720199311866 | erot = 2.91114841200295 | epot = -22.4713018556232 | etot = -16.7729514505016 -631000 ekin = 2.4617589215552 | erot = 2.66187466993095 | epot = -22.4061953621981 | etot = -17.282561770712 -632000 ekin = 2.67568812509024 | erot = 2.67916251422212 | epot = -22.3286212206811 | etot = -16.9737705813688 -633000 ekin = 2.42046368116991 | erot = 2.0959495936055 | epot = -22.2764051897282 | etot = -17.7599919149528 -634000 ekin = 2.1766138388507 | erot = 1.75221904598353 | epot = -22.2464672562848 | etot = -18.3176343714506 -635000 ekin = 2.1303374537182 | erot = 2.11558346598702 | epot = -22.1559890122107 | etot = -17.9100680925054 -636000 ekin = 2.03262388834245 | erot = 1.68380166560562 | epot = -22.2457935658938 | etot = -18.5293680119458 -637000 ekin = 2.39791285236697 | erot = 2.55917753311606 | epot = -22.4447998775231 | etot = -17.4877094920401 -638000 ekin = 2.15469983815169 | erot = 3.28400540345815 | epot = -22.4075976338996 | etot = -16.9688923922898 -639000 ekin = 1.81811684885083 | erot = 2.75659290480155 | epot = -22.3748011521987 | etot = -17.8000913985464 -640000 ekin = 1.99907387989529 | erot = 2.08952122746439 | epot = -22.3717813517436 | etot = -18.283186244384 -641000 ekin = 2.66328164143483 | erot = 3.02619691580941 | epot = -22.2647370196577 | etot = -16.5752584624134 -642000 ekin = 2.88967061145595 | erot = 2.59057169345598 | epot = -22.23475748516 | etot = -16.7545151802481 -643000 ekin = 2.79246415244629 | erot = 2.87517098573249 | epot = -22.2468989126934 | etot = -16.5792637745146 -644000 ekin = 2.27988542188579 | erot = 3.04855388745644 | epot = -22.2349136242582 | etot = -16.906474314916 -645000 ekin = 3.01613981708155 | erot = 2.4967822399052 | epot = -22.3345075492296 | etot = -16.8215854922429 -646000 ekin = 2.21704249586791 | erot = 2.60354951531734 | epot = -22.2671914610386 | etot = -17.4465994498533 -647000 ekin = 2.37597087431337 | erot = 2.09971950840957 | epot = -22.4060809913804 | etot = -17.9303906086575 -648000 ekin = 2.4714436262309 | erot = 2.63569146556463 | epot = -22.423642714225 | etot = -17.3165076224295 -649000 ekin = 2.53468077746691 | erot = 2.34586903824308 | epot = -22.358445267116 | etot = -17.477895451406 -650000 ekin = 2.9010220783452 | erot = 2.43748900585602 | epot = -22.235082780767 | etot = -16.8965716965658 -651000 ekin = 2.43937394370796 | erot = 2.32097040047332 | epot = -22.1007717206118 | etot = -17.3404273764305 -652000 ekin = 3.22983264752039 | erot = 1.97644426162264 | epot = -22.1139672910572 | etot = -16.9076903819141 -653000 ekin = 3.42414251849354 | erot = 2.79487810087101 | epot = -22.1558408334809 | etot = -15.9368202141163 -654000 ekin = 2.15889671735112 | erot = 2.36472973550593 | epot = -22.1974951138068 | etot = -17.6738686609497 -655000 ekin = 2.65852679982884 | erot = 1.70572386028398 | epot = -22.2627111956629 | etot = -17.8984605355501 -656000 ekin = 2.48541797006401 | erot = 2.06347531107756 | epot = -22.3150691564122 | etot = -17.7661758752707 -657000 ekin = 2.69778549496517 | erot = 2.20386261244986 | epot = -22.4300467083325 | etot = -17.5283986009175 -658000 ekin = 2.77197513377729 | erot = 2.5072948475956 | epot = -22.5474407814621 | etot = -17.2681708000892 -659000 ekin = 3.66874079211363 | erot = 2.11838086144899 | epot = -22.5519111820512 | etot = -16.7647895284886 -660000 ekin = 2.97388996619018 | erot = 2.92112069101806 | epot = -22.6187600322739 | etot = -16.7237493750657 -661000 ekin = 2.78763059394641 | erot = 2.30401970578286 | epot = -22.7111345560961 | etot = -17.6194842563668 -662000 ekin = 2.98299477151657 | erot = 1.34778890968014 | epot = -22.712605002436 | etot = -18.3818213212393 -663000 ekin = 2.06206406341935 | erot = 2.49091694129999 | epot = -22.6743419399864 | etot = -18.121360935267 -664000 ekin = 1.46165423849889 | erot = 1.88506472859125 | epot = -22.7282890093398 | etot = -19.3815700422497 -665000 ekin = 1.35273695073317 | erot = 2.42195808060362 | epot = -22.7162067017985 | etot = -18.9415116704617 -666000 ekin = 1.89921915483213 | erot = 1.88531092594892 | epot = -22.7370741866503 | etot = -18.9525441058693 -667000 ekin = 2.90243379314502 | erot = 1.97614154053879 | epot = -22.7577380902139 | etot = -17.8791627565301 -668000 ekin = 2.88439733908879 | erot = 3.01316244247058 | epot = -22.6944666694957 | etot = -16.7969068879363 -669000 ekin = 2.54687231970458 | erot = 2.87359405758465 | epot = -22.6569831183116 | etot = -17.2365167410224 -670000 ekin = 2.21301768070541 | erot = 2.27765188013648 | epot = -22.6308484396801 | etot = -18.1401788788382 -671000 ekin = 2.58683275746298 | erot = 2.41409834599394 | epot = -22.7246788592801 | etot = -17.7237477558232 -672000 ekin = 3.29079177090022 | erot = 1.91261376234837 | epot = -22.8001667297379 | etot = -17.5967611964893 -673000 ekin = 2.84673402140676 | erot = 3.00764974897873 | epot = -22.7284025915001 | etot = -16.8740188211146 -674000 ekin = 2.42053568766569 | erot = 2.26590883890938 | epot = -22.6284483786375 | etot = -17.9420038520624 -675000 ekin = 1.96378820155452 | erot = 2.06502777032928 | epot = -22.51415650415 | etot = -18.4853405322662 -676000 ekin = 2.37987332690053 | erot = 1.93897030281589 | epot = -22.4622738554879 | etot = -18.1434302257714 -677000 ekin = 2.62785237684978 | erot = 2.04858248933864 | epot = -22.4668107703719 | etot = -17.7903759041835 -678000 ekin = 2.06360362245241 | erot = 2.31478537085112 | epot = -22.4535526716361 | etot = -18.0751636783326 -679000 ekin = 2.29534664965827 | erot = 3.11695224810765 | epot = -22.5315135213968 | etot = -17.1192146236308 -680000 ekin = 2.77369826886665 | erot = 2.79006418020504 | epot = -22.5458781878731 | etot = -16.9821157388014 -681000 ekin = 2.53921147867385 | erot = 2.45485065209125 | epot = -22.6209291892887 | etot = -17.6268670585236 -682000 ekin = 2.49239283345666 | erot = 2.17277195118013 | epot = -22.5585253944368 | etot = -17.8933606098 -683000 ekin = 2.31649836542777 | erot = 1.55870522096413 | epot = -22.4825872818582 | etot = -18.6073836954663 -684000 ekin = 3.16310193002238 | erot = 2.41685736208791 | epot = -22.523230555191 | etot = -16.9432712630807 -685000 ekin = 3.45688595061428 | erot = 1.65797437511731 | epot = -22.5532406426393 | etot = -17.4383803169077 -686000 ekin = 3.07151502570858 | erot = 2.40426982374968 | epot = -22.5000639933867 | etot = -17.0242791439284 -687000 ekin = 2.88949352966058 | erot = 2.7238056050836 | epot = -22.3550217707533 | etot = -16.7417226360091 -688000 ekin = 1.80054884787415 | erot = 2.30103168557514 | epot = -22.2966882319421 | etot = -18.1951076984928 -689000 ekin = 2.64615904696514 | erot = 2.02804270215569 | epot = -22.2971499666841 | etot = -17.6229482175633 -690000 ekin = 2.74509582020304 | erot = 2.21308151884789 | epot = -22.2232873685679 | etot = -17.2651100295169 -691000 ekin = 3.22973625495416 | erot = 1.79659776362201 | epot = -22.1738233446911 | etot = -17.1474893261149 -692000 ekin = 3.29006251848601 | erot = 2.65455993734058 | epot = -22.1381299825657 | etot = -16.1935075267391 -693000 ekin = 3.00782385068016 | erot = 1.87988611083812 | epot = -22.0870866906686 | etot = -17.1993767291503 -694000 ekin = 2.75349969517394 | erot = 1.96196264346628 | epot = -22.0466569559902 | etot = -17.33119461735 -695000 ekin = 2.74843837441231 | erot = 2.04242579206469 | epot = -22.0120255611129 | etot = -17.2211613946359 -696000 ekin = 2.61118397057101 | erot = 2.51560421142858 | epot = -22.0291666802225 | etot = -16.9023784982229 -697000 ekin = 2.04895161009847 | erot = 2.41377542161681 | epot = -22.0475575829813 | etot = -17.5848305512661 -698000 ekin = 2.33205499894114 | erot = 1.26426607996476 | epot = -22.0891584682771 | etot = -18.4928373893712 -699000 ekin = 2.52365738372774 | erot = 2.88607619964718 | epot = -22.0575161973125 | etot = -16.6477826139376 -700000 ekin = 2.08703154176849 | erot = 3.31918856993651 | epot = -22.043496292523 | etot = -16.637276180818 -701000 ekin = 2.63454496534449 | erot = 1.84779300509081 | epot = -22.0766662152512 | etot = -17.5943282448159 -702000 ekin = 3.08829740869393 | erot = 1.78434998288706 | epot = -22.0748863622431 | etot = -17.2022389706621 -703000 ekin = 2.56007358655962 | erot = 2.26155500183646 | epot = -22.1026908977867 | etot = -17.2810623093906 -704000 ekin = 2.12477400999169 | erot = 2.08457952130484 | epot = -22.1230711325941 | etot = -17.9137176012976 -705000 ekin = 2.23099785424598 | erot = 2.02835190629231 | epot = -22.2359796293319 | etot = -17.9766298687936 -706000 ekin = 2.85888825530194 | erot = 2.83086143547529 | epot = -22.3500389599658 | etot = -16.6602892691886 -707000 ekin = 2.3480098030021 | erot = 2.49047973295143 | epot = -22.4420709095522 | etot = -17.6035813735987 -708000 ekin = 2.15687040039009 | erot = 1.89481927076687 | epot = -22.5427181126696 | etot = -18.4910284415126 -709000 ekin = 2.06126314379796 | erot = 2.64275166601122 | epot = -22.6917747885766 | etot = -17.9877599787674 -710000 ekin = 1.82554938445181 | erot = 2.07235995944929 | epot = -22.8201377385632 | etot = -18.9222283946621 -711000 ekin = 2.12298269627501 | erot = 1.73663135406234 | epot = -22.8023637488401 | etot = -18.9427496985027 -712000 ekin = 1.89441290644275 | erot = 1.81368671766166 | epot = -22.8122394708736 | etot = -19.1041398467692 -713000 ekin = 2.34039314906729 | erot = 2.24025735859079 | epot = -22.739230452663 | etot = -18.1585799450049 -714000 ekin = 2.23394879997726 | erot = 2.28215619335759 | epot = -22.7197007411881 | etot = -18.2035957478533 -715000 ekin = 2.57842687399601 | erot = 2.70596818962316 | epot = -22.7225303697053 | etot = -17.4381353060861 -716000 ekin = 2.777342167833 | erot = 2.9530742807956 | epot = -22.7551711123855 | etot = -17.0247546637569 -717000 ekin = 3.05821476760519 | erot = 1.70402888768233 | epot = -22.805004145031 | etot = -18.0427604897435 -718000 ekin = 2.58403702020119 | erot = 2.7276869575009 | epot = -22.8377652482164 | etot = -17.5260412705143 -719000 ekin = 4.04281043169349 | erot = 2.57288772340244 | epot = -22.765151213101 | etot = -16.1494530580051 -720000 ekin = 2.2626844436645 | erot = 2.05854032263456 | epot = -22.7210270971108 | etot = -18.3998023308117 -721000 ekin = 2.61229526180485 | erot = 1.50190620429945 | epot = -22.6872472176703 | etot = -18.573045751566 -722000 ekin = 2.12130222145933 | erot = 2.47430249425283 | epot = -22.6492037761001 | etot = -18.0535990603879 -723000 ekin = 2.34495921259014 | erot = 2.00001594177129 | epot = -22.6840132581792 | etot = -18.3390381038178 -724000 ekin = 1.60988468746473 | erot = 1.86898213056776 | epot = -22.7229141429322 | etot = -19.2440473248997 -725000 ekin = 1.98873703681155 | erot = 2.69421181813058 | epot = -22.7105382062835 | etot = -18.0275893513414 -726000 ekin = 2.00486594971194 | erot = 1.88744282533496 | epot = -22.7145995160264 | etot = -18.8222907409795 -727000 ekin = 2.36965727388931 | erot = 1.97771456567968 | epot = -22.7738359375483 | etot = -18.4264640979793 -728000 ekin = 3.35107369108538 | erot = 2.66873491563057 | epot = -22.8576831721942 | etot = -16.8378745654783 -729000 ekin = 2.78137391509267 | erot = 2.39427763566612 | epot = -22.9964454563738 | etot = -17.8207939056151 -730000 ekin = 2.94732376078577 | erot = 2.46572632898526 | epot = -23.061543959858 | etot = -17.648493870087 -731000 ekin = 2.3655947471903 | erot = 2.57962564204578 | epot = -23.1418772794081 | etot = -18.196656890172 -732000 ekin = 2.37054326957061 | erot = 2.27737906066013 | epot = -23.1533463942089 | etot = -18.5054240639782 -733000 ekin = 2.84223530802968 | erot = 2.87780967364454 | epot = -23.1651159858109 | etot = -17.4450710041367 -734000 ekin = 2.07281469390073 | erot = 2.84899684376724 | epot = -23.1266412632701 | etot = -18.2048297256022 -735000 ekin = 2.24252699011017 | erot = 2.42167788333885 | epot = -23.081639080379 | etot = -18.41743420693 -736000 ekin = 1.90429954179403 | erot = 2.00615427805272 | epot = -23.0665137080943 | etot = -19.1560598882476 -737000 ekin = 2.52358234623967 | erot = 2.96408613726945 | epot = -23.0498694785062 | etot = -17.562200994997 -738000 ekin = 2.29815228938801 | erot = 2.99337630493273 | epot = -23.0531374110373 | etot = -17.7616088167165 -739000 ekin = 2.10323839566883 | erot = 2.36218654019378 | epot = -23.1209183366636 | etot = -18.655493400801 -740000 ekin = 2.65902408892739 | erot = 2.31758820313662 | epot = -23.0239864631476 | etot = -18.0473741710836 -741000 ekin = 2.88509339134713 | erot = 1.74482801012006 | epot = -22.9368579089963 | etot = -18.3069365075291 -742000 ekin = 2.11922667941259 | erot = 1.93684947156234 | epot = -22.8269253642457 | etot = -18.7708492132708 -743000 ekin = 2.34108734337621 | erot = 2.36593738673209 | epot = -22.783708876953 | etot = -18.0766841468447 -744000 ekin = 2.01297679191398 | erot = 1.65216031512074 | epot = -22.7764820246243 | etot = -19.1113449175895 -745000 ekin = 1.73133017113515 | erot = 1.7176467257586 | epot = -22.6953133444038 | etot = -19.2463364475101 -746000 ekin = 1.93685820803391 | erot = 2.16961525795798 | epot = -22.6422856732894 | etot = -18.5358122072975 -747000 ekin = 2.71054987223223 | erot = 2.52037576286435 | epot = -22.6131171255895 | etot = -17.3821914904929 -748000 ekin = 2.55015048250253 | erot = 2.69537742835584 | epot = -22.6616400107092 | etot = -17.4161120998508 -749000 ekin = 2.4743403066993 | erot = 2.01464607005272 | epot = -22.6951524837167 | etot = -18.2061661069646 -750000 ekin = 2.72230033116892 | erot = 1.60952725065647 | epot = -22.7320627310186 | etot = -18.4002351491932 -751000 ekin = 2.51043142470836 | erot = 1.80224959894129 | epot = -22.6780351335436 | etot = -18.3653541098939 -752000 ekin = 2.63659326252806 | erot = 1.51190288425088 | epot = -22.5566638983436 | etot = -18.4081677515646 -753000 ekin = 2.22777724794013 | erot = 2.36906570543334 | epot = -22.6071335797283 | etot = -18.0102906263549 -754000 ekin = 1.90064002802585 | erot = 2.4987423398728 | epot = -22.5664713331287 | etot = -18.16708896523 -755000 ekin = 1.84097054781323 | erot = 1.81660989632982 | epot = -22.3243978570986 | etot = -18.6668174129556 -756000 ekin = 1.9072977215419 | erot = 3.47869439939258 | epot = -22.3139248457301 | etot = -16.9279327247956 -757000 ekin = 2.92648412859418 | erot = 2.35165714253905 | epot = -22.4032306892798 | etot = -17.1250894181466 -758000 ekin = 2.761119937725 | erot = 2.96029457936289 | epot = -22.4093833044993 | etot = -16.6879687874114 -759000 ekin = 2.05979468653478 | erot = 2.75306043529531 | epot = -22.3978407784686 | etot = -17.5849856566385 -760000 ekin = 3.29448360098896 | erot = 3.86438603184197 | epot = -22.4057510645732 | etot = -15.2468814317423 -761000 ekin = 3.09819348686662 | erot = 1.69735163369829 | epot = -22.3918604222945 | etot = -17.5963153017295 -762000 ekin = 2.8429808573394 | erot = 2.74696984027755 | epot = -22.2799634059086 | etot = -16.6900127082917 -763000 ekin = 2.40587022296419 | erot = 1.99761718955002 | epot = -22.2245473449275 | etot = -17.8210599324133 -764000 ekin = 2.69114689966729 | erot = 2.18706151254182 | epot = -22.1158949498055 | etot = -17.2376865375964 -765000 ekin = 2.02342407409198 | erot = 2.40755354133614 | epot = -22.0801918095988 | etot = -17.6492141941707 -766000 ekin = 2.55386945841861 | erot = 2.2735300120383 | epot = -21.9453814240006 | etot = -17.1179819535437 -767000 ekin = 2.25334005789491 | erot = 3.15616241457377 | epot = -21.9591848457648 | etot = -16.5496823732961 -768000 ekin = 2.00682883228694 | erot = 2.52417129595785 | epot = -21.9372106864373 | etot = -17.4062105581925 -769000 ekin = 2.23813402043546 | erot = 2.85559067422092 | epot = -21.9700652214807 | etot = -16.8763405268243 -770000 ekin = 1.95345812792707 | erot = 1.71037618652205 | epot = -22.0309481387955 | etot = -18.3671138243464 -771000 ekin = 2.03963170914285 | erot = 2.38748698255688 | epot = -22.0082391059021 | etot = -17.5811204142023 -772000 ekin = 2.06112217022411 | erot = 2.70000480403923 | epot = -22.0060196271604 | etot = -17.2448926528971 -773000 ekin = 2.1054473406836 | erot = 2.10438313024729 | epot = -21.9856087815605 | etot = -17.7757783106296 -774000 ekin = 2.20665293417965 | erot = 1.98309808383526 | epot = -21.9846800128842 | etot = -17.7949289948693 -775000 ekin = 1.91373997893468 | erot = 2.82262340642995 | epot = -22.0452968667144 | etot = -17.3089334813498 -776000 ekin = 2.19240734852453 | erot = 2.49078961967547 | epot = -22.091057561943 | etot = -17.407860593743 -777000 ekin = 1.49861623144733 | erot = 1.30695475237057 | epot = -22.160400003221 | etot = -19.3548290194031 -778000 ekin = 1.69531477096896 | erot = 3.17990102703017 | epot = -21.9433338643409 | etot = -17.0681180663417 -779000 ekin = 2.03408275108515 | erot = 2.02083644208248 | epot = -21.8692045577056 | etot = -17.814285364538 -780000 ekin = 2.32186745464909 | erot = 1.59799877907745 | epot = -21.779259403208 | etot = -17.8593931694815 -781000 ekin = 2.81943737654873 | erot = 2.33206120657135 | epot = -21.9280199462268 | etot = -16.7765213631068 -782000 ekin = 2.78999918307152 | erot = 2.82490724099864 | epot = -21.9063368325378 | etot = -16.2914304084676 -783000 ekin = 2.75260781814664 | erot = 1.86132573030769 | epot = -21.9418725483536 | etot = -17.3279389998993 -784000 ekin = 2.98284408884117 | erot = 2.76354560233502 | epot = -21.920715473795 | etot = -16.1743257826188 -785000 ekin = 2.2365893692682 | erot = 1.78861508275494 | epot = -21.8288977108099 | etot = -17.8036932587867 -786000 ekin = 2.14414777981649 | erot = 2.07159716672848 | epot = -21.8686345308374 | etot = -17.6528895842924 -787000 ekin = 2.47319429252999 | erot = 2.28522145597639 | epot = -21.7568224131044 | etot = -16.998406664598 -788000 ekin = 2.2037125656444 | erot = 2.94983992744806 | epot = -21.807401237665 | etot = -16.6538487445726 -789000 ekin = 1.90039797522133 | erot = 2.52747460130211 | epot = -21.733582185717 | etot = -17.3057096091936 -790000 ekin = 1.84303835442002 | erot = 1.52778835767436 | epot = -21.8138250805319 | etot = -18.4429983684375 -791000 ekin = 2.55973906062281 | erot = 2.07623433695467 | epot = -21.8760673428163 | etot = -17.2400939452388 -792000 ekin = 1.64105723574641 | erot = 2.51498077776481 | epot = -21.8705113566728 | etot = -17.7144733431616 -793000 ekin = 2.18354187889159 | erot = 2.48490382483639 | epot = -21.9577315408449 | etot = -17.2892858371169 -794000 ekin = 2.82327663056602 | erot = 3.3208090455501 | epot = -21.9401298111912 | etot = -15.7960441350751 -795000 ekin = 3.35539827663487 | erot = 3.31260020346181 | epot = -21.9264520382708 | etot = -15.2584535581741 -796000 ekin = 2.40740867688621 | erot = 1.57597595059244 | epot = -21.9748654474447 | etot = -17.991480819966 -797000 ekin = 2.79764140160881 | erot = 3.21306683298178 | epot = -21.8960553216211 | etot = -15.8853470870305 -798000 ekin = 2.75235345571032 | erot = 2.16726736660523 | epot = -21.9467263944678 | etot = -17.0271055721522 -799000 ekin = 2.76203245885878 | erot = 2.97689904095233 | epot = -21.8743227138698 | etot = -16.1353912140587 -800000 ekin = 2.81032669767261 | erot = 2.21645039580168 | epot = -21.874383510595 | etot = -16.8476064171207 -801000 ekin = 3.36862076335485 | erot = 2.36357276514919 | epot = -21.8196797425216 | etot = -16.0874862140175 -802000 ekin = 3.17839060401735 | erot = 2.37456159755556 | epot = -21.6942373686297 | etot = -16.1412851670568 -803000 ekin = 2.57363536086741 | erot = 1.72140865671985 | epot = -21.5847418534903 | etot = -17.289697835903 -804000 ekin = 2.40212767593722 | erot = 1.81298666067406 | epot = -21.5293497123863 | etot = -17.314235375775 -805000 ekin = 2.77711079955076 | erot = 2.46558169578922 | epot = -21.6187696645293 | etot = -16.3760771691893 -806000 ekin = 2.55163537095457 | erot = 2.07829064761593 | epot = -21.5175633688748 | etot = -16.8876373503043 -807000 ekin = 2.16828861417546 | erot = 2.14909333685052 | epot = -21.4370785365412 | etot = -17.1196965855152 -808000 ekin = 1.52247178905684 | erot = 2.6826614265022 | epot = -21.3105524860528 | etot = -17.1054192704938 -809000 ekin = 1.92812857984838 | erot = 1.43056331824491 | epot = -21.1839259115906 | etot = -17.8252340134973 -810000 ekin = 2.22251801029333 | erot = 2.58813475636527 | epot = -21.1788629745341 | etot = -16.3682102078755 -811000 ekin = 2.30282325024527 | erot = 1.43949319809354 | epot = -21.1417336792482 | etot = -17.3994172309094 -812000 ekin = 2.15941343791814 | erot = 2.89500994256604 | epot = -21.1419338778617 | etot = -16.0875104973775 -813000 ekin = 2.32954389313432 | erot = 2.41977402200041 | epot = -21.1892335081721 | etot = -16.4399155930374 -814000 ekin = 2.26485001316768 | erot = 1.98538164115157 | epot = -21.1932468666377 | etot = -16.9430152123184 -815000 ekin = 2.41630590364713 | erot = 2.99255527397409 | epot = -21.1098074992862 | etot = -15.700946321665 -816000 ekin = 2.67026011582709 | erot = 2.65041733757061 | epot = -21.1150624925932 | etot = -15.7943850391955 -817000 ekin = 2.26330508431116 | erot = 2.44986465102853 | epot = -21.1331844070825 | etot = -16.4200146717428 -818000 ekin = 2.20996514807098 | erot = 3.727109097134 | epot = -21.1017127717073 | etot = -15.1646385265024 -819000 ekin = 2.57394897351115 | erot = 3.00884410677579 | epot = -21.041932430768 | etot = -15.4591393504811 -820000 ekin = 2.6269546487903 | erot = 2.28213489416385 | epot = -21.0722371160471 | etot = -16.163147573093 -821000 ekin = 2.61364324263858 | erot = 2.35068554002091 | epot = -21.1855362753227 | etot = -16.2212074926632 -822000 ekin = 2.36817941179088 | erot = 2.29408928197165 | epot = -21.224917006927 | etot = -16.5626483131645 -823000 ekin = 2.75982209175738 | erot = 2.28480205814775 | epot = -21.3426772027003 | etot = -16.2980530527951 -824000 ekin = 1.50978044541751 | erot = 2.23801949349373 | epot = -21.3865247649546 | etot = -17.6387248260434 -825000 ekin = 1.83128269423152 | erot = 2.38147378919583 | epot = -21.4614886551422 | etot = -17.2487321717148 -826000 ekin = 2.51131465952168 | erot = 2.83805149504081 | epot = -21.4681680733736 | etot = -16.1188019188111 -827000 ekin = 2.46554499044043 | erot = 2.50199323815042 | epot = -21.4572012069778 | etot = -16.4896629783869 -828000 ekin = 2.41378793908818 | erot = 1.68202937429718 | epot = -21.4539863774251 | etot = -17.3581690640397 -829000 ekin = 2.4681575394398 | erot = 2.76556063553637 | epot = -21.6061033580493 | etot = -16.3723851830731 -830000 ekin = 2.50947351976231 | erot = 1.95946819770171 | epot = -21.6566904098634 | etot = -17.1877486923994 -831000 ekin = 2.69088795720236 | erot = 2.34186880436294 | epot = -21.6751650606748 | etot = -16.6424082991095 -832000 ekin = 1.54455154996055 | erot = 2.80525631028289 | epot = -21.7300917306615 | etot = -17.380283870418 -833000 ekin = 1.60055229673051 | erot = 3.14700223857927 | epot = -21.7718768340911 | etot = -17.0243222987814 -834000 ekin = 1.58616945483838 | erot = 1.86597500790458 | epot = -21.7880513273337 | etot = -18.3359068645908 -835000 ekin = 3.47114373337366 | erot = 2.09781333604001 | epot = -21.8771549098142 | etot = -16.3081978404005 -836000 ekin = 2.71067283785106 | erot = 3.26177139393205 | epot = -22.0614513419415 | etot = -16.0890071101583 -837000 ekin = 2.82278761249275 | erot = 2.64917318251883 | epot = -22.2428744107532 | etot = -16.7709136157417 -838000 ekin = 2.86323560044783 | erot = 2.96285563085687 | epot = -22.3579310822412 | etot = -16.5318398509365 -839000 ekin = 2.91010528600405 | erot = 1.78968409868876 | epot = -22.3931377567277 | etot = -17.6933483720349 -840000 ekin = 2.68501939036542 | erot = 1.84551444209968 | epot = -22.4099858160921 | etot = -17.879451983627 -841000 ekin = 2.78761718016806 | erot = 2.07511139278678 | epot = -22.4502333935977 | etot = -17.5875048206429 -842000 ekin = 2.30765580411605 | erot = 2.05774495041193 | epot = -22.4188744128232 | etot = -18.0534736582952 -843000 ekin = 2.34438101892177 | erot = 2.29420407093426 | epot = -22.4349024679563 | etot = -17.7963173781003 -844000 ekin = 2.00792674828049 | erot = 2.31767327257805 | epot = -22.4786582023913 | etot = -18.1530581815328 -845000 ekin = 2.55136030290324 | erot = 2.34385902090199 | epot = -22.4799883641885 | etot = -17.5847690403832 -846000 ekin = 3.24095798236659 | erot = 2.35217012971054 | epot = -22.5063540497827 | etot = -16.9132259377056 -847000 ekin = 2.03834455975138 | erot = 2.30020941454582 | epot = -22.5309995762754 | etot = -18.1924456019782 -848000 ekin = 2.83373620504456 | erot = 2.13136296315047 | epot = -22.509666561527 | etot = -17.544567393332 -849000 ekin = 2.30412012601641 | erot = 2.33744771805384 | epot = -22.4861027555015 | etot = -17.8445349114312 -850000 ekin = 1.52103738969765 | erot = 2.15323991690878 | epot = -22.5147792441637 | etot = -18.8405019375573 -851000 ekin = 1.85927261161487 | erot = 2.05456043679611 | epot = -22.41752057705 | etot = -18.503687528639 -852000 ekin = 1.35588514515989 | erot = 1.9167555928276 | epot = -22.3689199481736 | etot = -19.0962792101861 -853000 ekin = 2.3850184465024 | erot = 2.13310598794891 | epot = -22.4485532426469 | etot = -17.9304288081955 -854000 ekin = 3.24160358995203 | erot = 2.86289112951559 | epot = -22.5134229014302 | etot = -16.4089281819626 -855000 ekin = 2.13481228779989 | erot = 1.96664100945254 | epot = -22.4546662618353 | etot = -18.3532129645828 -856000 ekin = 2.50184794641609 | erot = 1.67720759103887 | epot = -22.3993038611807 | etot = -18.2202483237257 -857000 ekin = 3.36467068168789 | erot = 2.39681039692234 | epot = -22.3226520614655 | etot = -16.5611709828553 -858000 ekin = 2.48664620814186 | erot = 2.35813115829077 | epot = -22.272278975303 | etot = -17.4275016088704 -859000 ekin = 2.32018019421645 | erot = 2.34139041664418 | epot = -22.2193920346789 | etot = -17.5578214238183 -860000 ekin = 2.22338714949804 | erot = 2.59608961594502 | epot = -22.2078599697903 | etot = -17.3883832043473 -861000 ekin = 2.78084194233445 | erot = 1.92482892867366 | epot = -22.1430552159866 | etot = -17.4373843449785 -862000 ekin = 2.44005485500116 | erot = 2.71281255016884 | epot = -22.1159986211262 | etot = -16.9631312159562 -863000 ekin = 2.24234987838148 | erot = 3.79312130641057 | epot = -22.0841490674594 | etot = -16.0486778826673 -864000 ekin = 3.01456697615184 | erot = 2.29303363412973 | epot = -22.1234826076905 | etot = -16.815881997409 -865000 ekin = 2.16000819632291 | erot = 2.15780299713575 | epot = -22.1287456416268 | etot = -17.8109344481681 -866000 ekin = 1.81163527021121 | erot = 2.32024755104635 | epot = -22.1499759612014 | etot = -18.0180931399439 -867000 ekin = 2.25540445662073 | erot = 3.35667286394567 | epot = -22.1512265495476 | etot = -16.5391492289812 -868000 ekin = 2.12606109236403 | erot = 2.09577443816696 | epot = -22.1889361717519 | etot = -17.9671006412209 -869000 ekin = 3.01588764102674 | erot = 2.28014407542063 | epot = -22.221302584169 | etot = -16.9252708677216 -870000 ekin = 2.40773894902557 | erot = 3.40007074283947 | epot = -22.1952409397611 | etot = -16.387431247896 -871000 ekin = 3.32703715357026 | erot = 3.46064712451054 | epot = -22.207619940406 | etot = -15.4199356623252 -872000 ekin = 2.67470986735512 | erot = 2.18306697620401 | epot = -22.2188283181498 | etot = -17.3610514745907 -873000 ekin = 2.52072696526388 | erot = 2.1369508485849 | epot = -22.2519152847091 | etot = -17.5942374708604 -874000 ekin = 2.27694681653708 | erot = 1.90405870618916 | epot = -22.2119486941003 | etot = -18.0309431713741 -875000 ekin = 3.04326947271929 | erot = 2.81417576356414 | epot = -22.2207355347687 | etot = -16.3632902984853 -876000 ekin = 2.65936305160015 | erot = 2.00688506244317 | epot = -22.2254483507339 | etot = -17.5592002366906 -877000 ekin = 2.1218906050998 | erot = 2.12108610918076 | epot = -22.2199840422449 | etot = -17.9770073279643 -878000 ekin = 2.04330658320778 | erot = 2.19234207701539 | epot = -22.2416061573535 | etot = -18.0059574971303 -879000 ekin = 2.32331088859055 | erot = 1.79314356421366 | epot = -22.2511349493271 | etot = -18.1346804965229 -880000 ekin = 2.7191684680603 | erot = 2.50780771372557 | epot = -22.3211844971675 | etot = -17.0942083153816 -881000 ekin = 1.99457026442112 | erot = 2.42028761684275 | epot = -22.3291049337298 | etot = -17.9142470524659 -882000 ekin = 2.17848471304109 | erot = 2.10936064799446 | epot = -22.4203903692112 | etot = -18.1325450081757 -883000 ekin = 1.77867952654183 | erot = 2.64915979670231 | epot = -22.4714725630276 | etot = -18.0436332397834 -884000 ekin = 2.14335954946475 | erot = 1.84960097278838 | epot = -22.5511502290244 | etot = -18.5581897067713 -885000 ekin = 2.1737296921439 | erot = 1.1224465172794 | epot = -22.6177136264329 | etot = -19.3215374170096 -886000 ekin = 2.42905198250288 | erot = 2.95855698435737 | epot = -22.6235099833459 | etot = -17.2359010164856 -887000 ekin = 2.48421926935623 | erot = 2.38511493603948 | epot = -22.6296650575404 | etot = -17.7603308521447 -888000 ekin = 2.70449841183027 | erot = 2.37632299730154 | epot = -22.6283104195123 | etot = -17.5474890103805 -889000 ekin = 2.16954131372983 | erot = 2.33019249573093 | epot = -22.6936030299779 | etot = -18.1938692205171 -890000 ekin = 2.47926329860922 | erot = 2.33896915658922 | epot = -22.6494572776992 | etot = -17.8312248225007 -891000 ekin = 1.94552918338144 | erot = 2.18077529869467 | epot = -22.6609703311569 | etot = -18.5346658490808 -892000 ekin = 2.28162371339856 | erot = 2.3088525744332 | epot = -22.6825434447643 | etot = -18.0920671569325 -893000 ekin = 2.88680394731139 | erot = 2.10479527485689 | epot = -22.6297583991013 | etot = -17.638159176933 -894000 ekin = 2.22095391000543 | erot = 2.6955566302385 | epot = -22.5465758433209 | etot = -17.6300653030769 -895000 ekin = 2.78422464609227 | erot = 2.65463994767233 | epot = -22.5353839067237 | etot = -17.0965193129591 -896000 ekin = 2.36290673766564 | erot = 2.68569415977408 | epot = -22.5147457657546 | etot = -17.4661448683149 -897000 ekin = 2.78793396360212 | erot = 2.64131273496852 | epot = -22.5414816276965 | etot = -17.1122349291259 -898000 ekin = 2.3402778901712 | erot = 2.19036014594362 | epot = -22.5104750621796 | etot = -17.9798370260648 -899000 ekin = 2.66788181923082 | erot = 2.47623824735052 | epot = -22.4660137235249 | etot = -17.3218936569435 -900000 ekin = 1.59318336723961 | erot = 2.21998911769617 | epot = -22.5347550915857 | etot = -18.7215826066499 -901000 ekin = 2.06417516984273 | erot = 2.10877138148894 | epot = -22.5774386825736 | etot = -18.4044921312419 -902000 ekin = 1.92723308146077 | erot = 2.68515165308711 | epot = -22.5481083061021 | etot = -17.9357235715542 -903000 ekin = 1.80993467873556 | erot = 1.57695529654776 | epot = -22.5323996660651 | etot = -19.1455096907817 -904000 ekin = 1.95575183245312 | erot = 2.60436945067914 | epot = -22.5256682806408 | etot = -17.9655469975085 -905000 ekin = 2.49381768733875 | erot = 1.66773826407627 | epot = -22.4993840902563 | etot = -18.3378281388413 -906000 ekin = 2.70456575671731 | erot = 2.32922683721416 | epot = -22.5151218166898 | etot = -17.4813292227584 -907000 ekin = 3.43903944265671 | erot = 3.0307204788449 | epot = -22.5299571834398 | etot = -16.0601972619382 -908000 ekin = 2.37356952619769 | erot = 2.64936438196245 | epot = -22.516942166439 | etot = -17.4940082582789 -909000 ekin = 2.1860703025731 | erot = 2.13921305901071 | epot = -22.5153521800656 | etot = -18.1900688184818 -910000 ekin = 2.24010023383653 | erot = 1.8514435260008 | epot = -22.5113320632559 | etot = -18.4197883034186 -911000 ekin = 2.67585852173789 | erot = 3.85348226422502 | epot = -22.4699249030924 | etot = -15.9405841171295 -912000 ekin = 3.64657818361083 | erot = 2.2905143551155 | epot = -22.4162004746889 | etot = -16.4791079359625 -913000 ekin = 2.77291999770499 | erot = 2.1022397931402 | epot = -22.2869766697588 | etot = -17.4118168789136 -914000 ekin = 1.89079293131433 | erot = 1.61085972457271 | epot = -22.2125075199665 | etot = -18.7108548640794 -915000 ekin = 2.29207178481568 | erot = 2.8656606451286 | epot = -22.1499813962335 | etot = -16.9922489662893 -916000 ekin = 2.37906860202164 | erot = 2.93218592813836 | epot = -22.1637836439351 | etot = -16.8525291137751 -917000 ekin = 2.59326894380189 | erot = 1.59995350665161 | epot = -22.1382449385233 | etot = -17.9450224880698 -918000 ekin = 2.59372186080417 | erot = 3.48686361915462 | epot = -22.1117393261149 | etot = -16.0311538461561 -919000 ekin = 3.63953975205853 | erot = 2.58422541764726 | epot = -22.1104945479772 | etot = -15.8867293782714 -920000 ekin = 2.78492990282824 | erot = 1.86208025423285 | epot = -22.0733276968689 | etot = -17.4263175398078 -921000 ekin = 3.07307788316298 | erot = 1.56848168882074 | epot = -22.0450316551233 | etot = -17.4034720831396 -922000 ekin = 2.52896264126303 | erot = 2.06804264923523 | epot = -22.0195361349236 | etot = -17.4225308444253 -923000 ekin = 2.61981998522111 | erot = 2.66954469306772 | epot = -22.0457463967354 | etot = -16.7563817184466 -924000 ekin = 2.29381022514437 | erot = 2.49801555366746 | epot = -22.0170239220671 | etot = -17.2251981432553 -925000 ekin = 2.34625944949207 | erot = 3.19587785236191 | epot = -22.028094746344 | etot = -16.4859574444901 -926000 ekin = 2.1499233373865 | erot = 2.05823289292907 | epot = -22.0551986731856 | etot = -17.84704244287 -927000 ekin = 2.70495872901843 | erot = 1.96917479663366 | epot = -22.0956495975482 | etot = -17.4215160718961 -928000 ekin = 2.20438880519295 | erot = 2.76887961394763 | epot = -22.1039091543987 | etot = -17.1306407352581 -929000 ekin = 1.66382307176874 | erot = 2.62906085068005 | epot = -22.1726645871649 | etot = -17.8797806647161 -930000 ekin = 2.44828303043728 | erot = 2.44689226426912 | epot = -22.2529456791372 | etot = -17.3577703844308 -931000 ekin = 2.34172371844874 | erot = 1.78034954048635 | epot = -22.3194053510458 | etot = -18.1973320921107 -932000 ekin = 2.86526138273858 | erot = 3.26408148037739 | epot = -22.3255275519233 | etot = -16.1961846888074 -933000 ekin = 2.82342195482862 | erot = 3.6937351987852 | epot = -22.2580157348403 | etot = -15.7408585812265 -934000 ekin = 2.38157885575329 | erot = 3.09818957660776 | epot = -22.1592884972713 | etot = -16.6795200649102 -935000 ekin = 2.47849108316876 | erot = 1.92075328373161 | epot = -22.0961420624139 | etot = -17.6968976955135 -936000 ekin = 2.49397604910015 | erot = 2.55601396404453 | epot = -22.0064014399899 | etot = -16.9564114268453 -937000 ekin = 2.6918648576103 | erot = 3.47263294076258 | epot = -22.0234522240484 | etot = -15.8589544256755 -938000 ekin = 2.48873697071885 | erot = 2.3615977813032 | epot = -21.9576739595259 | etot = -17.1073392075039 -939000 ekin = 2.7056760578856 | erot = 1.42055121093474 | epot = -22.0193047024759 | etot = -17.8930774336556 -940000 ekin = 2.88189239926779 | erot = 2.54211609996475 | epot = -21.963323771107 | etot = -16.5393152718745 -941000 ekin = 2.44770794558597 | erot = 1.8579190466837 | epot = -21.9343286748115 | etot = -17.6287016825418 -942000 ekin = 2.61959568530468 | erot = 2.22532128272654 | epot = -21.9353530015567 | etot = -17.0904360335255 -943000 ekin = 2.54153612965671 | erot = 2.71959375806095 | epot = -21.9843720500752 | etot = -16.7232421623575 -944000 ekin = 2.57930166684081 | erot = 1.60562519751619 | epot = -21.9098609218899 | etot = -17.7249340575329 -945000 ekin = 2.26017628750984 | erot = 2.67831094836454 | epot = -21.8967586325953 | etot = -16.958271396721 -946000 ekin = 2.56313399941445 | erot = 2.76984355108528 | epot = -21.885121080301 | etot = -16.5521435298013 -947000 ekin = 1.72889278969055 | erot = 1.57454364668031 | epot = -21.8264681047052 | etot = -18.5230316683343 -948000 ekin = 1.42819481646296 | erot = 2.04503560450747 | epot = -21.8391184541439 | etot = -18.3658880331735 -949000 ekin = 1.74199608841338 | erot = 1.96409283987733 | epot = -21.8667949303421 | etot = -18.1607060020513 -950000 ekin = 1.55764652514141 | erot = 2.39695530807616 | epot = -21.8856003991517 | etot = -17.9309985659341 -951000 ekin = 1.63932624900687 | erot = 2.1627973168229 | epot = -21.9503862126057 | etot = -18.1482626467759 -952000 ekin = 1.89086480907742 | erot = 2.49708005969823 | epot = -21.9454729492793 | etot = -17.5575280805036 -953000 ekin = 2.44055170062751 | erot = 2.14431771118738 | epot = -21.8959489835736 | etot = -17.3110795717587 -954000 ekin = 2.14487831289196 | erot = 3.08443398263928 | epot = -21.795825093512 | etot = -16.5665127979808 -955000 ekin = 1.60221367612371 | erot = 3.5308242347527 | epot = -21.6951891429404 | etot = -16.562151232064 -956000 ekin = 2.86347770563429 | erot = 2.69138834272026 | epot = -21.6556631266882 | etot = -16.1007970783337 -957000 ekin = 2.76520094154603 | erot = 2.16152614675844 | epot = -21.6435053042083 | etot = -16.7167782159039 -958000 ekin = 3.29226660028984 | erot = 2.62876087991651 | epot = -21.5934941292417 | etot = -15.6724666490354 -959000 ekin = 2.66337479749112 | erot = 1.93770218849588 | epot = -21.5642990170474 | etot = -16.9632220310604 -960000 ekin = 2.86423754644722 | erot = 2.19410745878017 | epot = -21.5177124722279 | etot = -16.4593674670006 -961000 ekin = 2.48295179178335 | erot = 2.43234834813273 | epot = -21.5213073923115 | etot = -16.6060072523954 -962000 ekin = 1.68087651110994 | erot = 2.11605214746261 | epot = -21.5272991731175 | etot = -17.730370514545 -963000 ekin = 2.12197709458218 | erot = 1.94777002069826 | epot = -21.5235663501543 | etot = -17.4538192348738 -964000 ekin = 2.50733406625421 | erot = 2.86610278796474 | epot = -21.6134414980076 | etot = -16.2400046437886 -965000 ekin = 2.48599183654717 | erot = 1.79499031304665 | epot = -21.5880837540441 | etot = -17.3071016044502 -966000 ekin = 2.00894333039795 | erot = 2.33897690805447 | epot = -21.6770932400157 | etot = -17.3291730015632 -967000 ekin = 2.50955412880022 | erot = 2.78273184372279 | epot = -21.7722886206001 | etot = -16.4800026480771 -968000 ekin = 2.39889345353743 | erot = 2.01767642165489 | epot = -21.8155202641564 | etot = -17.3989503889641 -969000 ekin = 2.28246497162226 | erot = 2.6610436899411 | epot = -21.8367533421236 | etot = -16.8932446805602 -970000 ekin = 2.23203775830392 | erot = 2.52493315465349 | epot = -21.7968010714725 | etot = -17.0398301585151 -971000 ekin = 2.35522817907367 | erot = 3.39194300680609 | epot = -21.8814762448495 | etot = -16.1343050589698 -972000 ekin = 2.92268851492039 | erot = 2.10931174667369 | epot = -21.8978389761888 | etot = -16.8658387145947 -973000 ekin = 2.77937322332655 | erot = 3.20264340638929 | epot = -21.8742816810463 | etot = -15.8922650513305 -974000 ekin = 2.49009389085376 | erot = 2.32800875868964 | epot = -21.7820748340866 | etot = -16.9639721845432 -975000 ekin = 2.72033534996219 | erot = 3.65469302721884 | epot = -21.7224052943306 | etot = -15.3473769171495 -976000 ekin = 2.71017392247357 | erot = 2.02557906552618 | epot = -21.6961182780945 | etot = -16.9603652900947 -977000 ekin = 2.17702730116704 | erot = 2.60235136270384 | epot = -21.6180913127583 | etot = -16.8387126488875 -978000 ekin = 1.77849232321391 | erot = 1.99858920804759 | epot = -21.5849000297842 | etot = -17.8078184985227 -979000 ekin = 2.48810087232518 | erot = 2.63640222059576 | epot = -21.6371898197889 | etot = -16.5126867268679 -980000 ekin = 1.82633711731844 | erot = 2.05813667598699 | epot = -21.6585229341326 | etot = -17.7740491408271 -981000 ekin = 1.91146199713101 | erot = 1.90004529483666 | epot = -21.7219076944834 | etot = -17.9104004025157 -982000 ekin = 1.58901547008885 | erot = 2.3998948195541 | epot = -21.7861972103806 | etot = -17.7972869207376 -983000 ekin = 1.90990791777794 | erot = 2.80966645725473 | epot = -21.7824009478711 | etot = -17.0628265728384 -984000 ekin = 3.04220145268175 | erot = 1.69588850289015 | epot = -21.8411397187458 | etot = -17.1030497631739 -985000 ekin = 2.78368169036401 | erot = 2.92615311813614 | epot = -21.9523851434087 | etot = -16.2425503349085 -986000 ekin = 2.49557629947763 | erot = 3.0544158396407 | epot = -21.9474177819392 | etot = -16.3974256428209 -987000 ekin = 2.94534789449803 | erot = 1.85813505015918 | epot = -21.9308646063833 | etot = -17.1273816617261 -988000 ekin = 3.20975095732697 | erot = 3.54928250010428 | epot = -21.8260823230639 | etot = -15.0670488656326 -989000 ekin = 2.92872893558337 | erot = 2.50053850131553 | epot = -21.7939177563688 | etot = -16.3646503194699 -990000 ekin = 1.94245878607124 | erot = 2.64876037239901 | epot = -21.7891875584096 | etot = -17.1979683999394 -991000 ekin = 2.17972550210194 | erot = 2.86510777418376 | epot = -21.8197503596152 | etot = -16.7749170833296 -992000 ekin = 2.52496188361677 | erot = 2.72509937739588 | epot = -21.7730940251365 | etot = -16.5230327641239 -993000 ekin = 2.06107125732198 | erot = 2.79131355143356 | epot = -21.7326833691733 | etot = -16.8802985604177 -994000 ekin = 2.40031262466104 | erot = 2.5219233481115 | epot = -21.7261274920277 | etot = -16.8038915192551 -995000 ekin = 1.80633536079933 | erot = 2.07468376575716 | epot = -21.7283755003117 | etot = -17.8473563737552 -996000 ekin = 2.61788487499682 | erot = 2.63730746697003 | epot = -21.6837220732346 | etot = -16.4285297312677 -997000 ekin = 3.17513078038726 | erot = 2.07778272001357 | epot = -21.6151676277683 | etot = -16.3622541273675 -998000 ekin = 2.82648577435409 | erot = 2.39219801181103 | epot = -21.4967856271291 | etot = -16.278101840964 -999000 ekin = 2.15841415676437 | erot = 2.8705487674429 | epot = -21.4943522577851 | etot = -16.4653893335778 -1000000 ekin = 2.16735910095287 | erot = 2.44618830827923 | epot = -21.395427974522 | etot = -16.7818805652899 - 1000000 0.096327071 -1.3608937 0.023679494 -1.2017543 -3.298683e-05 -Loop time of 28.7478 on 1 procs for 1000000 steps with 16 atoms - -Performance: 30054.487 tau/day, 34785.286 timesteps/s -99.2% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 23.177 | 23.177 | 23.177 | 0.0 | 80.62 -Bond | 0.9075 | 0.9075 | 0.9075 | 0.0 | 3.16 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.19114 | 0.19114 | 0.19114 | 0.0 | 0.66 -Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00 -Modify | 4.1695 | 4.1695 | 4.1695 | 0.0 | 14.50 -Other | | 0.303 | | | 1.05 - -Nlocal: 16.0 ave 16.0 max 16.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 89.0 ave 89.0 max 89.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 89 -Ave neighs/atom = 5.5625 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:28 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 deleted file mode 100644 index 773305140b..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 +++ /dev/null @@ -1,1176 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.9560004 - ghost atom cutoff = 2.5 - binsize = 0.97800022, bins = 41 41 41 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -0 ekin = 0 | erot = 0 | epot = -24.5312382023598 | etot = -24.5312382023598 -Per MPI rank memory allocation (min/avg/max) = 7.73 | 7.787 | 7.844 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 -1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 -2000 ekin = 2.15911766687235 | erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504 -3000 ekin = 3.26561948796015 | erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198 -4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505 -5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 -6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 -7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 -8000 ekin = 2.51333548501169 | erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614 -9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 -10000 ekin = 2.36632635249862 | erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463 -11000 ekin = 2.03296432220126 | erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202 -12000 ekin = 2.65352743446956 | erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194 -13000 ekin = 1.89067421214403 | erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949 -14000 ekin = 1.90680463918722 | erot = 2.12745987027399 | epot = -23.7545354032947 | etot = -19.7202708938335 -15000 ekin = 2.40428667481004 | erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361 -16000 ekin = 2.7510166356243 | erot = 1.18896277635344 | epot = -23.5745121257654 | etot = -19.6345327137876 -17000 ekin = 2.44090826892662 | erot = 2.38166706806441 | epot = -23.5888433865641 | etot = -18.766268049573 -18000 ekin = 2.16977970545217 | erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939 -19000 ekin = 2.19378610033861 | erot = 2.45183819484609 | epot = -23.5449084745393 | etot = -18.8992841793546 -20000 ekin = 2.07734013817241 | erot = 1.81448496219961 | epot = -23.5782673056893 | etot = -19.6864422053173 -21000 ekin = 2.27781532351243 | erot = 2.76369118136086 | epot = -23.5986545956161 | etot = -18.5571480907428 -22000 ekin = 2.69375785791379 | erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449207 -23000 ekin = 1.99952884103097 | erot = 2.28032953163857 | epot = -23.4448504933921 | etot = -19.1649921207226 -24000 ekin = 2.19993258930349 | erot = 2.97916455146848 | epot = -23.365299008021 | etot = -18.1862018672491 -25000 ekin = 2.28089469652686 | erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537 -26000 ekin = 1.99390998801617 | erot = 2.79250495479074 | epot = -23.1859723519608 | etot = -18.3995574091539 -27000 ekin = 2.00992865272585 | erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421 -28000 ekin = 2.00322172723407 | erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913 -29000 ekin = 2.52361436071784 | erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138 -30000 ekin = 1.94969919616482 | erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198 -31000 ekin = 1.81286761012387 | erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782 -32000 ekin = 1.88389491638451 | erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051 -33000 ekin = 1.78524470387102 | erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434 -34000 ekin = 2.28023843988047 | erot = 3.11357086039974 | epot = -23.0617618407572 | etot = -17.667952540477 -35000 ekin = 2.88795920533174 | erot = 1.81662227096289 | epot = -23.1342233361349 | etot = -18.4296418598403 -36000 ekin = 2.40018487148211 | erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096 -37000 ekin = 2.22699211630433 | erot = 1.73889017332475 | epot = -23.2291614908027 | etot = -19.2632792011737 -38000 ekin = 2.13593461964592 | erot = 3.07590136326315 | epot = -23.1607724763685 | etot = -17.9489364934594 -39000 ekin = 2.08839393640823 | erot = 2.80471150509566 | epot = -23.1352878747759 | etot = -18.242182433272 -40000 ekin = 2.94982054413846 | erot = 2.19484102372241 | epot = -23.1842229043853 | etot = -18.0395613365244 -41000 ekin = 2.47855373480179 | erot = 3.46795094832272 | epot = -23.1698888629099 | etot = -17.2233841797854 -42000 ekin = 2.57225931171306 | erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682 -43000 ekin = 2.16695829201326 | erot = 2.67063324875935 | epot = -22.9841690345739 | etot = -18.1465774938013 -44000 ekin = 2.3251045436594 | erot = 3.31069456451415 | epot = -22.9099977707014 | etot = -17.2741986625279 -45000 ekin = 1.8593572517472 | erot = 3.48256913429864 | epot = -22.7853293556222 | etot = -17.4434029695763 -46000 ekin = 2.59906260222481 | erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741 -47000 ekin = 1.90419350976819 | erot = 3.39352467596445 | epot = -22.5624536061979 | etot = -17.2647354204652 -48000 ekin = 2.46191536162942 | erot = 2.50024189038397 | epot = -22.5888330081063 | etot = -17.6266757560929 -49000 ekin = 3.18008619674969 | erot = 2.18329398142911 | epot = -22.6110647388652 | etot = -17.2476845606864 -50000 ekin = 2.92380640638812 | erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295054 -51000 ekin = 2.8672950322524 | erot = 2.67529217516736 | epot = -22.6748886664557 | etot = -17.132301459036 -52000 ekin = 2.30283827457733 | erot = 1.82645474029551 | epot = -22.6607030819086 | etot = -18.5314100670358 -53000 ekin = 3.18697616339314 | erot = 1.6721126504968 | epot = -22.7158951183044 | etot = -17.8568063044145 -54000 ekin = 2.63274995193147 | erot = 1.96664130685842 | epot = -22.7877787224364 | etot = -18.1883874636465 -55000 ekin = 3.18311630681889 | erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793 -56000 ekin = 2.55275960671528 | erot = 3.05720384772626 | epot = -22.8187750450683 | etot = -17.2088115906267 -57000 ekin = 2.43682051944964 | erot = 3.45782031837858 | epot = -22.7770565571277 | etot = -16.8824157192995 -58000 ekin = 1.93888380963701 | erot = 2.51321017005837 | epot = -22.7135987564736 | etot = -18.2615047767782 -59000 ekin = 2.5584899615086 | erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831 -60000 ekin = 2.80661395039301 | erot = 2.89055248290058 | epot = -22.5801959967487 | etot = -16.8830295634551 -61000 ekin = 2.68598657973729 | erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677 -62000 ekin = 2.74493324548126 | erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319 -63000 ekin = 2.65627195091607 | erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079 -64000 ekin = 2.12379240032878 | erot = 2.79203441675509 | epot = -22.3495990435982 | etot = -17.4337722265143 -65000 ekin = 1.86782238979936 | erot = 2.70277079938777 | epot = -22.3710220966341 | etot = -17.8004289074469 -66000 ekin = 2.74983103317414 | erot = 1.93532287297332 | epot = -22.3642892005434 | etot = -17.679135294396 -67000 ekin = 2.51092055125345 | erot = 2.46618624666166 | epot = -22.3997780561407 | etot = -17.4226712582256 -68000 ekin = 2.95469759114171 | erot = 1.97026833535318 | epot = -22.465077041847 | etot = -17.5401111153521 -69000 ekin = 2.60179538487172 | erot = 2.27022574694886 | epot = -22.4013876082185 | etot = -17.529366476398 -70000 ekin = 2.38624525335422 | erot = 2.82124637267727 | epot = -22.3329612644328 | etot = -17.1254696384013 -71000 ekin = 2.6264191985346 | erot = 2.8933242992384 | epot = -22.3324946257813 | etot = -16.8127511280083 -72000 ekin = 2.93199679301318 | erot = 2.83600213853039 | epot = -22.4418753486332 | etot = -16.6738764170896 -73000 ekin = 2.20521324648382 | erot = 3.05063841714452 | epot = -22.5078076718832 | etot = -17.2519560082549 -74000 ekin = 2.16594519672766 | erot = 2.82993872672919 | epot = -22.5187768617569 | etot = -17.5228929383001 -75000 ekin = 1.52753824412461 | erot = 1.91758574309004 | epot = -22.6434864113427 | etot = -19.198362424128 -76000 ekin = 1.89477517532867 | erot = 2.83145375092216 | epot = -22.7507099037207 | etot = -18.0244809774698 -77000 ekin = 2.84722966394523 | erot = 3.20523918524772 | epot = -22.8263123696514 | etot = -16.7738435204584 -78000 ekin = 2.44900478430451 | erot = 2.80964787966681 | epot = -22.811923730311 | etot = -17.5532710663397 -79000 ekin = 2.16549328835507 | erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255 -80000 ekin = 2.38929173610466 | erot = 2.5835599737549 | epot = -22.7453472674482 | etot = -17.7724955575887 -81000 ekin = 2.74182188149 | erot = 1.92580771183152 | epot = -22.6872721828912 | etot = -18.0196425895697 -82000 ekin = 1.90254633515813 | erot = 1.70958501101744 | epot = -22.5904815431895 | etot = -18.9783501970139 -83000 ekin = 1.63862423461032 | erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292 -84000 ekin = 1.65768128899531 | erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674 -85000 ekin = 2.40787065796921 | erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645 -86000 ekin = 2.51073542405177 | erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608 -87000 ekin = 2.13729284484532 | erot = 1.97886338867606 | epot = -22.4457225556766 | etot = -18.3295663221553 -88000 ekin = 1.7511616822056 | erot = 2.36434608342923 | epot = -22.4232555875235 | etot = -18.3077478218887 -89000 ekin = 1.85498863251071 | erot = 3.29466014836524 | epot = -22.4615925106509 | etot = -17.3119437297749 -90000 ekin = 2.22730928223451 | erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706 -91000 ekin = 2.40026068010467 | erot = 3.13124542611032 | epot = -22.5445138059197 | etot = -17.0130076997047 -92000 ekin = 2.69184894487886 | erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756694 -93000 ekin = 3.04452081584098 | erot = 3.02893158250343 | epot = -22.4857514998612 | etot = -16.4122991015168 -94000 ekin = 3.21054020599498 | erot = 1.87554208928456 | epot = -22.58235617796 | etot = -17.4962738826805 -95000 ekin = 3.49164555041805 | erot = 2.891072597541 | epot = -22.651746211573 | etot = -16.269028063614 -96000 ekin = 2.89611459837769 | erot = 2.3840369162805 | epot = -22.6376886129393 | etot = -17.3575370982811 -97000 ekin = 1.94001816357314 | erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036 -98000 ekin = 2.21812472183551 | erot = 3.66512951907027 | epot = -22.540020786367 | etot = -16.6567665454612 -99000 ekin = 1.96304801418099 | erot = 2.78092002528642 | epot = -22.4500077741119 | etot = -17.7060397346445 -100000 ekin = 1.78146596589238 | erot = 2.66087063973067 | epot = -22.380628502186 | etot = -17.9382918965629 -101000 ekin = 2.13576431486591 | erot = 2.39189697670581 | epot = -22.3671198416411 | etot = -17.8394585500694 -102000 ekin = 1.54265458925823 | erot = 2.31301627489862 | epot = -22.3596033820569 | etot = -18.5039325179 -103000 ekin = 1.6493299781162 | erot = 2.8270014677761 | epot = -22.4044472055819 | etot = -17.9281157596896 -104000 ekin = 1.88425130865015 | erot = 3.36695629589131 | epot = -22.4614117565727 | etot = -17.2102041520312 -105000 ekin = 2.0873628063424 | erot = 1.99902589912496 | epot = -22.4857870795246 | etot = -18.3993983740573 -106000 ekin = 2.85192200005482 | erot = 1.96124421177816 | epot = -22.4885148263279 | etot = -17.6753486144949 -107000 ekin = 2.27699301124082 | erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666 -108000 ekin = 2.43341212242249 | erot = 1.71014523953267 | epot = -22.4750159709764 | etot = -18.3314586090212 -109000 ekin = 2.3240302459673 | erot = 2.92730273400666 | epot = -22.454444740465 | etot = -17.203111760491 -110000 ekin = 2.75939007795593 | erot = 2.37261248457831 | epot = -22.4066316113364 | etot = -17.2746290488021 -111000 ekin = 2.30202775259985 | erot = 2.09098171366695 | epot = -22.340628179725 | etot = -17.9476187134582 -112000 ekin = 2.89672803093986 | erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143 -113000 ekin = 2.80286812020301 | erot = 1.68317583122193 | epot = -22.1739192926258 | etot = -17.6878753412008 -114000 ekin = 3.41134331362354 | erot = 2.66279011393035 | epot = -22.2993892060878 | etot = -16.225255778534 -115000 ekin = 3.04096848543599 | erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327 -116000 ekin = 3.18249263106367 | erot = 3.2187278057963 | epot = -22.376612031037 | etot = -15.975391594177 -117000 ekin = 3.04033644338919 | erot = 2.41632774149289 | epot = -22.3406101341932 | etot = -16.8839459493112 -118000 ekin = 3.22976632794611 | erot = 1.46870208555872 | epot = -22.262910646297 | etot = -17.5644422327922 -119000 ekin = 2.35815331598994 | erot = 3.0746467591689 | epot = -22.21629705762 | etot = -16.7834969824611 -120000 ekin = 1.93901604028919 | erot = 2.21087803685819 | epot = -22.1596747789505 | etot = -18.0097807018031 -121000 ekin = 1.9479198834689 | erot = 3.06697908719323 | epot = -22.1473490758083 | etot = -17.1324501051462 -122000 ekin = 1.69642311218451 | erot = 1.71065948591523 | epot = -22.235021693017 | etot = -18.8279390949172 -123000 ekin = 1.74537927001903 | erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348 -124000 ekin = 2.74229806685693 | erot = 1.94346011848798 | epot = -22.3376426377462 | etot = -17.6518844524013 -125000 ekin = 2.7762803161376 | erot = 1.95737420539166 | epot = -22.3561899601979 | etot = -17.6225354386687 -126000 ekin = 2.05898577806786 | erot = 1.47493157618748 | epot = -22.3918669376121 | etot = -18.8579495833568 -127000 ekin = 1.88620727578863 | erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304 -128000 ekin = 1.65027256647601 | erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694 -129000 ekin = 2.51771860981078 | erot = 2.38745668871878 | epot = -22.3622404512641 | etot = -17.4570651527345 -130000 ekin = 1.60778116741171 | erot = 2.81983062254804 | epot = -22.3043401463427 | etot = -17.8767283563829 -131000 ekin = 2.27966529707091 | erot = 2.29465997580787 | epot = -22.1860056729234 | etot = -17.6116804000446 -132000 ekin = 2.94605151024306 | erot = 2.34727265039698 | epot = -22.1004107829513 | etot = -16.8070866223112 -133000 ekin = 2.00184520718143 | erot = 2.13597622566091 | epot = -22.0860804435183 | etot = -17.948259010676 -134000 ekin = 1.54536260297594 | erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194 -135000 ekin = 1.7899169229158 | erot = 2.40585579784187 | epot = -22.0564792277569 | etot = -17.8607065069993 -136000 ekin = 1.63315069688348 | erot = 2.13968964990471 | epot = -22.0645410751456 | etot = -18.2917007283574 -137000 ekin = 2.36475220491125 | erot = 1.9307510547685 | epot = -22.101884847306 | etot = -17.8063815876263 -138000 ekin = 2.9554682114977 | erot = 1.58329215843879 | epot = -22.1589207193491 | etot = -17.6201603494126 -139000 ekin = 3.18559985564368 | erot = 2.24978247982886 | epot = -22.2766713145626 | etot = -16.84128897909 -140000 ekin = 2.25331500051846 | erot = 3.04264261269698 | epot = -22.4413209794808 | etot = -17.1453633662654 -141000 ekin = 1.8939664036255 | erot = 3.12730191483889 | epot = -22.6943708703896 | etot = -17.6731025519252 -142000 ekin = 2.48698722341786 | erot = 2.50204475841096 | epot = -22.8022645411413 | etot = -17.8132325593125 -143000 ekin = 2.39031114354902 | erot = 2.72027514737476 | epot = -22.7789363640122 | etot = -17.6683500730884 -144000 ekin = 1.93009742932804 | erot = 2.68112648713777 | epot = -22.6600942975093 | etot = -18.0488703810435 -145000 ekin = 1.81543048110687 | erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640414 -146000 ekin = 2.4125202126428 | erot = 2.08569022934172 | epot = -22.5607640770181 | etot = -18.0625536350336 -147000 ekin = 1.44642974398304 | erot = 1.86921415702346 | epot = -22.4437745695726 | etot = -19.1281306685661 -148000 ekin = 1.94224767107088 | erot = 2.57935525538891 | epot = -22.4110987100047 | etot = -17.8894957835449 -149000 ekin = 2.03195649040454 | erot = 3.31786202502785 | epot = -22.312227106758 | etot = -16.9624085913257 -150000 ekin = 2.47792894576432 | erot = 2.68612874200304 | epot = -22.1392843642773 | etot = -16.97522667651 -151000 ekin = 2.75692645092955 | erot = 1.8812256584813 | epot = -21.9329416416723 | etot = -17.2947895322614 -152000 ekin = 2.7753834344323 | erot = 1.78115734250796 | epot = -21.7450724909841 | etot = -17.1885317140438 -153000 ekin = 3.09316888168833 | erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934 -154000 ekin = 2.31433640945477 | erot = 2.19304386678895 | epot = -21.5946356595637 | etot = -17.08725538332 -155000 ekin = 1.94169881401553 | erot = 2.67959698479411 | epot = -21.6941053409437 | etot = -17.072809542134 -156000 ekin = 2.69151609119638 | erot = 2.25048211983204 | epot = -21.7610571974251 | etot = -16.8190589863967 -157000 ekin = 3.89507004263776 | erot = 2.74501587672577 | epot = -21.8157728797743 | etot = -15.1756869604107 -158000 ekin = 2.88173407476086 | erot = 2.69702262693025 | epot = -21.8854957137509 | etot = -16.3067390120598 -159000 ekin = 3.15173323195918 | erot = 2.6174347371013 | epot = -21.8245251626835 | etot = -16.055357193623 -160000 ekin = 2.54983562435716 | erot = 3.26037467643909 | epot = -21.8527884226329 | etot = -16.0425781218367 -161000 ekin = 2.47569624391789 | erot = 2.4441841652721 | epot = -21.7973550812187 | etot = -16.8774746720287 -162000 ekin = 2.94228722137381 | erot = 2.59784970938384 | epot = -21.7813251561029 | etot = -16.2411882253452 -163000 ekin = 3.25812805712344 | erot = 2.25239331007842 | epot = -21.8200893075211 | etot = -16.3095679403192 -164000 ekin = 3.52786799143084 | erot = 2.22392713421412 | epot = -21.7646946348872 | etot = -16.0128995092423 -165000 ekin = 2.47839548873418 | erot = 2.58744140761169 | epot = -21.6790952945041 | etot = -16.6132583981583 -166000 ekin = 2.14435847552792 | erot = 3.04732688845808 | epot = -21.6219995979977 | etot = -16.4303142340117 -167000 ekin = 2.77664659649902 | erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831 -168000 ekin = 1.74464407802389 | erot = 2.78052653338966 | epot = -21.4288999288375 | etot = -16.903729317424 -169000 ekin = 1.8068912909333 | erot = 2.46391033708928 | epot = -21.4128285618694 | etot = -17.1420269338468 -170000 ekin = 1.69498145941511 | erot = 2.88911238881156 | epot = -21.4319269866204 | etot = -16.8478331383937 -171000 ekin = 2.15326316196646 | erot = 1.6134654780187 | epot = -21.2861470779284 | etot = -17.5194184379432 -172000 ekin = 1.67904916339532 | erot = 2.36509147316374 | epot = -21.1250864759441 | etot = -17.080945839385 -173000 ekin = 2.05349972960735 | erot = 2.18864665107749 | epot = -21.0744450592631 | etot = -16.8322986785783 -174000 ekin = 2.49402795941962 | erot = 3.1039231700088 | epot = -20.9332609664625 | etot = -15.335309837034 -175000 ekin = 2.60611029063986 | erot = 2.90993176119179 | epot = -20.8533230180669 | etot = -15.3372809662352 -176000 ekin = 2.14535974511638 | erot = 2.6771051102154 | epot = -20.8508037764829 | etot = -16.0283389211512 -177000 ekin = 2.82654664242577 | erot = 2.8064781965732 | epot = -20.9303681620826 | etot = -15.2973433230837 -178000 ekin = 3.17006270723388 | erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933 -179000 ekin = 2.33834827123179 | erot = 2.84870047825868 | epot = -21.1082901606944 | etot = -15.9212414112039 -180000 ekin = 2.39362550925046 | erot = 2.94575326168225 | epot = -21.1089731290028 | etot = -15.7695943580701 -181000 ekin = 2.78703231260152 | erot = 3.29998898392533 | epot = -21.0761138110654 | etot = -14.9890925145385 -182000 ekin = 3.023383912392 | erot = 2.3253310746288 | epot = -21.0444377426861 | etot = -15.6957227556653 -183000 ekin = 2.44126401356994 | erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424 -184000 ekin = 2.56448211253962 | erot = 2.77267067014069 | epot = -20.6657911214549 | etot = -15.3286383387746 -185000 ekin = 2.16427057092672 | erot = 1.95880146934287 | epot = -20.5647658775173 | etot = -16.4416938372477 -186000 ekin = 2.06536030915311 | erot = 3.1459346313777 | epot = -20.4537584304771 | etot = -15.2424634899463 -187000 ekin = 2.43846121057803 | erot = 1.93593042270706 | epot = -20.4775765627296 | etot = -16.1031849294445 -188000 ekin = 2.28827356508696 | erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372 -189000 ekin = 1.67206333515897 | erot = 3.05807378739725 | epot = -20.6184572736204 | etot = -15.8883201510642 -190000 ekin = 1.96995062226967 | erot = 2.943019674394 | epot = -20.6150380630742 | etot = -15.7020677664105 -191000 ekin = 2.31558303301195 | erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708366 -192000 ekin = 3.58105122568799 | erot = 2.89866835149673 | epot = -20.5550364560059 | etot = -14.0753168788212 -193000 ekin = 2.69738971383614 | erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358 -194000 ekin = 2.65963556416735 | erot = 2.28486501061266 | epot = -20.4488832942326 | etot = -15.5043827194525 -195000 ekin = 1.85289053427901 | erot = 2.65318671222086 | epot = -20.3816844231207 | etot = -15.8756071766209 -196000 ekin = 2.28257181147918 | erot = 2.31175601065464 | epot = -20.4051132325268 | etot = -15.810785410393 -197000 ekin = 2.49770460330585 | erot = 2.55587879440512 | epot = -20.4716020539923 | etot = -15.4180186562813 -198000 ekin = 2.01700960777428 | erot = 1.51922008609382 | epot = -20.4907970823155 | etot = -16.9545673884474 -199000 ekin = 1.50027537520987 | erot = 2.19604462463445 | epot = -20.5138434458212 | etot = -16.8175234459769 -200000 ekin = 1.64850512926723 | erot = 2.45966335482571 | epot = -20.4934420686449 | etot = -16.385273584552 -201000 ekin = 2.62997533994907 | erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916 -202000 ekin = 2.30895175475241 | erot = 2.55653293887659 | epot = -20.6262537118088 | etot = -15.7607690181798 -203000 ekin = 1.64768887888552 | erot = 2.11556417528284 | epot = -20.6617888215465 | etot = -16.8985357673782 -204000 ekin = 2.01924097320136 | erot = 1.97748949636931 | epot = -20.7002685556681 | etot = -16.7035380860975 -205000 ekin = 2.97656554045711 | erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806697 -206000 ekin = 2.56613069661945 | erot = 2.2162424422446 | epot = -21.0621833598182 | etot = -16.2798102209542 -207000 ekin = 3.44850636848559 | erot = 2.48816050856267 | epot = -21.2038849430866 | etot = -15.2672180660384 -208000 ekin = 2.54208934028226 | erot = 2.22605232144503 | epot = -21.3476404533667 | etot = -16.5794987916394 -209000 ekin = 3.84151461096732 | erot = 2.16534559513904 | epot = -21.4932373455843 | etot = -15.486377139478 -210000 ekin = 3.06873591712904 | erot = 2.24760815652572 | epot = -21.6427793540355 | etot = -16.3264352803807 -211000 ekin = 1.64176280869923 | erot = 2.17721976802013 | epot = -21.8130439048271 | etot = -17.9940613281078 -212000 ekin = 2.5985934050661 | erot = 2.41520703335867 | epot = -21.9964648294562 | etot = -16.9826643910315 -213000 ekin = 2.51136104390039 | erot = 1.99503544560739 | epot = -22.161492842604 | etot = -17.6550963530962 -214000 ekin = 2.77089845962619 | erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179 -215000 ekin = 2.53408528186206 | erot = 1.84963848601796 | epot = -22.1148567901871 | etot = -17.7311330223071 -216000 ekin = 2.52671619876928 | erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469 -217000 ekin = 2.50171921508545 | erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455 -218000 ekin = 2.43936294263937 | erot = 2.41974828067302 | epot = -22.2447049583244 | etot = -17.385593735012 -219000 ekin = 2.30221269367205 | erot = 2.65120674162377 | epot = -22.2807164841742 | etot = -17.3272970488784 -220000 ekin = 1.70065256620687 | erot = 2.34758543213917 | epot = -22.2809933538228 | etot = -18.2327553554767 -221000 ekin = 2.09298237125575 | erot = 2.4788648159591 | epot = -22.267957001012 | etot = -17.6961098137972 -222000 ekin = 1.58469709510937 | erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659 -223000 ekin = 1.83926923346352 | erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791 -224000 ekin = 2.59583657132575 | erot = 2.93869915115498 | epot = -22.1425986650605 | etot = -16.6080629425798 -225000 ekin = 3.29351563254165 | erot = 2.84339535814139 | epot = -22.12757310355 | etot = -15.990662112867 -226000 ekin = 3.03135339447922 | erot = 2.08293143143603 | epot = -22.15283624886 | etot = -17.0385514229448 -227000 ekin = 2.50176282992082 | erot = 3.15084128846394 | epot = -22.2250438959745 | etot = -16.5724397775897 -228000 ekin = 2.32013498351673 | erot = 2.67554406359434 | epot = -22.3177515383564 | etot = -17.3220724912453 -229000 ekin = 2.89545450975318 | erot = 2.90735055857064 | epot = -22.4361496683347 | etot = -16.6333446000109 -230000 ekin = 2.28321229485933 | erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863 -231000 ekin = 2.0778632375453 | erot = 3.1067397369644 | epot = -22.5896609633152 | etot = -17.4050579888055 -232000 ekin = 2.1202374109541 | erot = 1.98747810033065 | epot = -22.5738924334392 | etot = -18.4661769221544 -233000 ekin = 2.33571877855589 | erot = 2.83585090202734 | epot = -22.5402065195541 | etot = -17.3686368389708 -234000 ekin = 2.10578223747154 | erot = 2.07381218733635 | epot = -22.5507693150832 | etot = -18.3711748902754 -235000 ekin = 2.44321041214394 | erot = 2.80846352304316 | epot = -22.5606929563186 | etot = -17.3090190211315 -236000 ekin = 2.93630791731799 | erot = 3.06315918531728 | epot = -22.4860653874721 | etot = -16.4865982848368 -237000 ekin = 3.21264879506079 | erot = 3.26866508478298 | epot = -22.3683553437861 | etot = -15.8870414639423 -238000 ekin = 2.46595539123277 | erot = 2.32502019506662 | epot = -22.3144456769666 | etot = -17.5234700906672 -239000 ekin = 2.10325864915823 | erot = 2.47631139904042 | epot = -22.301139292181 | etot = -17.7215692439824 -240000 ekin = 1.77270999777839 | erot = 2.60141429112663 | epot = -22.2344206081543 | etot = -17.8602963192493 -241000 ekin = 1.94952922244078 | erot = 1.39715216866763 | epot = -22.2207225048761 | etot = -18.8740411137677 -242000 ekin = 3.05687991591411 | erot = 2.00862394928705 | epot = -22.2213200390943 | etot = -17.1558161738932 -243000 ekin = 2.86735711945299 | erot = 1.7994811867468 | epot = -22.2697610280427 | etot = -17.6029227218429 -244000 ekin = 2.00525854269389 | erot = 2.36445341214556 | epot = -22.2726788994494 | etot = -17.90296694461 -245000 ekin = 2.28011102404838 | erot = 2.787005205328 | epot = -22.2995433574618 | etot = -17.2324271280854 -246000 ekin = 2.06819738789813 | erot = 2.24624952782284 | epot = -22.2551680110137 | etot = -17.9407210952928 -247000 ekin = 1.69964711256213 | erot = 3.22260619239826 | epot = -22.1916408256116 | etot = -17.2693875206512 -248000 ekin = 1.92997585194759 | erot = 3.61155944514366 | epot = -22.0096484177852 | etot = -16.468113120694 -249000 ekin = 2.16278530892653 | erot = 3.27771891456707 | epot = -21.8856058980726 | etot = -16.445101674579 -250000 ekin = 2.32204054211025 | erot = 2.46317574116849 | epot = -21.8028762710591 | etot = -17.0176599877804 -251000 ekin = 1.23768964067255 | erot = 2.241505337621 | epot = -21.7630657074039 | etot = -18.2838707291104 -252000 ekin = 1.79818833522214 | erot = 2.12556386664128 | epot = -21.7586349357284 | etot = -17.834882733865 -253000 ekin = 2.12809689846393 | erot = 2.59685639208403 | epot = -21.7226495687757 | etot = -16.9976962782278 -254000 ekin = 2.46813261968533 | erot = 2.00391812662871 | epot = -21.7113918037362 | etot = -17.2393410574221 -255000 ekin = 2.31566729087291 | erot = 2.03619058028117 | epot = -21.7265453183256 | etot = -17.3746874471715 -256000 ekin = 2.87223929491326 | erot = 2.61790933826622 | epot = -21.659332511914 | etot = -16.1691838787345 -257000 ekin = 2.85756762932926 | erot = 2.08174673916199 | epot = -21.6161821054731 | etot = -16.6768677369818 -258000 ekin = 2.06111021157734 | erot = 2.32748664972428 | epot = -21.5132485706726 | etot = -17.124651709371 -259000 ekin = 2.23305784057759 | erot = 2.88843859953736 | epot = -21.5040039667854 | etot = -16.3825075266705 -260000 ekin = 2.49862397932476 | erot = 2.3833688584839 | epot = -21.488210637319 | etot = -16.6062177995103 -261000 ekin = 2.09280296934734 | erot = 2.39632540029206 | epot = -21.4325331777953 | etot = -16.9434048081559 -262000 ekin = 2.33576913564289 | erot = 2.67273419354396 | epot = -21.3832241450035 | etot = -16.3747208158166 -263000 ekin = 2.20536189489354 | erot = 2.71530627040564 | epot = -21.4329409070981 | etot = -16.5122727417989 -264000 ekin = 2.2858247573423 | erot = 2.76839346219662 | epot = -21.3931084431599 | etot = -16.338890223621 -265000 ekin = 1.70928536820409 | erot = 1.79395423442895 | epot = -21.2682341921474 | etot = -17.7649945895143 -266000 ekin = 2.48721735474525 | erot = 2.08745460533225 | epot = -21.1746995817337 | etot = -16.6000276216562 -267000 ekin = 2.69283567987773 | erot = 2.10301910407212 | epot = -21.1705161290062 | etot = -16.3746613450563 -268000 ekin = 3.00000233743719 | erot = 2.80954585635721 | epot = -21.1647521126509 | etot = -15.3552039188565 -269000 ekin = 3.50713810468527 | erot = 2.35763817348002 | epot = -21.1537110688983 | etot = -15.288934790733 -270000 ekin = 3.50686942248863 | erot = 1.86462765875889 | epot = -21.1925508822801 | etot = -15.8210538010326 -271000 ekin = 3.57026082273992 | erot = 2.08172467795388 | epot = -21.277581718294 | etot = -15.6255962176003 -272000 ekin = 2.4484752533773 | erot = 3.08466485039763 | epot = -21.3619851902072 | etot = -15.8288450864322 -273000 ekin = 2.39748176307242 | erot = 3.1335505044672 | epot = -21.4386234252579 | etot = -15.9075911577183 -274000 ekin = 2.48208144431864 | erot = 2.00552494041966 | epot = -21.4476232953882 | etot = -16.9600169106499 -275000 ekin = 2.4872108114937 | erot = 3.05413598233607 | epot = -21.4713984309062 | etot = -15.9300516370765 -276000 ekin = 2.82709589676966 | erot = 2.88384306577857 | epot = -21.443459011816 | etot = -15.7325200492678 -277000 ekin = 2.23479555963312 | erot = 2.20310851955639 | epot = -21.3883073251199 | etot = -16.9504032459304 -278000 ekin = 2.81418916407429 | erot = 3.24537052192614 | epot = -21.3155364074003 | etot = -15.2559767213999 -279000 ekin = 2.57366525203698 | erot = 1.81705578305929 | epot = -21.2862101233851 | etot = -16.8954890882888 -280000 ekin = 2.41063464320149 | erot = 1.76282693004732 | epot = -21.254962528096 | etot = -17.0815009548472 -281000 ekin = 2.58126226070487 | erot = 2.29258221702168 | epot = -21.306394928225 | etot = -16.4325504504985 -282000 ekin = 3.02016903398222 | erot = 2.4309452389034 | epot = -21.4340900724633 | etot = -15.9829757995777 -283000 ekin = 2.5926914979033 | erot = 2.11330689541034 | epot = -21.6296517079942 | etot = -16.9236533146805 -284000 ekin = 2.51704243107537 | erot = 3.13156683036759 | epot = -21.7452694753527 | etot = -16.0966602139097 -285000 ekin = 2.4236537221525 | erot = 1.77228258125505 | epot = -21.8557019037769 | etot = -17.6597656003694 -286000 ekin = 1.94467195521662 | erot = 2.03660974116722 | epot = -21.901435736722 | etot = -17.9201540403382 -287000 ekin = 2.56319670376176 | erot = 2.60867050510154 | epot = -21.9067509934901 | etot = -16.7348837846268 -288000 ekin = 2.19574207425736 | erot = 1.69805542160022 | epot = -21.8143855675961 | etot = -17.9205880717385 -289000 ekin = 2.35326278833023 | erot = 1.65840109676148 | epot = -21.6976038565285 | etot = -17.6859399714368 -290000 ekin = 2.35194561775041 | erot = 1.99444238353745 | epot = -21.6551012116075 | etot = -17.3087132103196 -291000 ekin = 1.48585281531713 | erot = 2.66475825861556 | epot = -21.56036793472 | etot = -17.4097568607873 -292000 ekin = 2.1073994475645 | erot = 2.42809824662638 | epot = -21.4451596117638 | etot = -16.9096619175729 -293000 ekin = 2.11618090223715 | erot = 1.86694554151196 | epot = -21.3593625692768 | etot = -17.3762361255277 -294000 ekin = 2.06078090566327 | erot = 2.13941873359473 | epot = -21.232623310094 | etot = -17.032423670836 -295000 ekin = 2.11467178034796 | erot = 2.32673436675183 | epot = -21.1123588667461 | etot = -16.6709527196463 -296000 ekin = 1.53087058859334 | erot = 2.94008409149154 | epot = -21.2112197533848 | etot = -16.7402650732999 -297000 ekin = 2.52732986791201 | erot = 2.18380855337859 | epot = -21.1955190508786 | etot = -16.484380629588 -298000 ekin = 1.89033945823201 | erot = 2.02521913176003 | epot = -21.2593750718295 | etot = -17.3438164818375 -299000 ekin = 1.87142873048437 | erot = 1.6640456322155 | epot = -21.2919162310488 | etot = -17.7564418683489 -300000 ekin = 2.23872615546785 | erot = 1.50807257618898 | epot = -21.3339204593826 | etot = -17.5871217277257 -301000 ekin = 1.99965506724556 | erot = 2.00145094516845 | epot = -21.4707589194324 | etot = -17.4696529070184 -302000 ekin = 1.76370349732521 | erot = 2.2378770890149 | epot = -21.5675275978257 | etot = -17.5659470114856 -303000 ekin = 2.69610887251788 | erot = 1.69957221429742 | epot = -21.5563765448091 | etot = -17.1606954579938 -304000 ekin = 2.55447143501921 | erot = 2.02060813090351 | epot = -21.5692327321341 | etot = -16.9941531662114 -305000 ekin = 2.38230604232715 | erot = 2.31489374428117 | epot = -21.5335950166329 | etot = -16.8363952300246 -306000 ekin = 2.07785475765117 | erot = 2.45230660685968 | epot = -21.4550895345846 | etot = -16.9249281700738 -307000 ekin = 3.17130424567277 | erot = 3.29574614566804 | epot = -21.4151535289883 | etot = -14.9481031376475 -308000 ekin = 3.40959217051674 | erot = 2.68389483402971 | epot = -21.4778643688409 | etot = -15.3843773642944 -309000 ekin = 2.36068264180093 | erot = 2.91715332823343 | epot = -21.5794336507741 | etot = -16.3015976807397 -310000 ekin = 2.49952357229221 | erot = 2.3602895089614 | epot = -21.5982142524176 | etot = -16.738401171164 -311000 ekin = 2.53288726180907 | erot = 2.29596940545853 | epot = -21.6418553661547 | etot = -16.8129986988871 -312000 ekin = 2.05123272208704 | erot = 2.92023923411836 | epot = -21.7377547517075 | etot = -16.7662827955021 -313000 ekin = 1.80834719374889 | erot = 2.29357283142128 | epot = -21.7993116362532 | etot = -17.697391611083 -314000 ekin = 2.30684015099018 | erot = 2.20859462712275 | epot = -21.8029398081388 | etot = -17.2875050300258 -315000 ekin = 1.86413924486173 | erot = 2.14748794238473 | epot = -21.8550418960799 | etot = -17.8434147088335 -316000 ekin = 2.20558056533516 | erot = 3.03447287931581 | epot = -21.8868412075708 | etot = -16.6467877629199 -317000 ekin = 2.4782093112548 | erot = 3.56870099099487 | epot = -21.9902146748518 | etot = -15.9433043726022 -318000 ekin = 2.36582343801679 | erot = 3.01887804681551 | epot = -22.1178732891163 | etot = -16.7331718042839 -319000 ekin = 2.40464629760758 | erot = 3.15910789488741 | epot = -22.2289401281564 | etot = -16.6651859356615 -320000 ekin = 1.80206494109346 | erot = 2.83527990295433 | epot = -22.3120263401861 | etot = -17.6746814961383 -321000 ekin = 2.91146951948762 | erot = 2.25772268449837 | epot = -22.3029455835946 | etot = -17.1337533796087 -322000 ekin = 2.8226351296685 | erot = 2.67950826833979 | epot = -22.3041650189947 | etot = -16.8020216209864 -323000 ekin = 2.067323568424 | erot = 2.31975284775299 | epot = -22.3338840353559 | etot = -17.9468076191789 -324000 ekin = 2.6012747278288 | erot = 2.58351861537749 | epot = -22.3215168526943 | etot = -17.1367235094881 -325000 ekin = 3.45560055552842 | erot = 2.50162515355503 | epot = -22.1825527777624 | etot = -16.2253270686789 -326000 ekin = 3.51422890604519 | erot = 2.8442606101801 | epot = -22.0201095272524 | etot = -15.6616200110271 -327000 ekin = 2.63551490316294 | erot = 2.20570805472232 | epot = -21.9384479867006 | etot = -17.0972250288154 -328000 ekin = 1.8043914440792 | erot = 2.37599512200969 | epot = -21.8619803976419 | etot = -17.681593831553 -329000 ekin = 2.15766181563134 | erot = 2.45286496267961 | epot = -21.8518523862111 | etot = -17.2413256079002 -330000 ekin = 1.8483425992464 | erot = 2.03367429366602 | epot = -21.7684095252419 | etot = -17.8863926323295 -331000 ekin = 2.3531484336258 | erot = 1.80165819621477 | epot = -21.7197009414848 | etot = -17.5648943116442 -332000 ekin = 1.67855936307207 | erot = 2.53341219651311 | epot = -21.733643435588 | etot = -17.5216718760028 -333000 ekin = 1.60376334688456 | erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256 -334000 ekin = 2.2655199008178 | erot = 2.62486254825417 | epot = -21.879497107847 | etot = -16.989114658775 -335000 ekin = 2.91208137486082 | erot = 3.11052870452009 | epot = -21.9161692767171 | etot = -15.8935591973362 -336000 ekin = 2.73132973682385 | erot = 2.56213100489405 | epot = -21.8312488568505 | etot = -16.5377881151326 -337000 ekin = 3.15411918141902 | erot = 3.875128198312 | epot = -21.9061152574783 | etot = -14.8768678777473 -338000 ekin = 2.33141760424507 | erot = 2.13211945089679 | epot = -21.913746111238 | etot = -17.4502090560961 -339000 ekin = 1.71915361945718 | erot = 2.31270220754042 | epot = -21.9042074773719 | etot = -17.8723516503743 -340000 ekin = 1.62199393011805 | erot = 3.16990972384469 | epot = -21.8898233676231 | etot = -17.0979197136604 -341000 ekin = 1.71588704296646 | erot = 3.17642860992462 | epot = -21.8345558128149 | etot = -16.9422401599238 -342000 ekin = 1.82178091247658 | erot = 2.58875985611025 | epot = -21.7161502950572 | etot = -17.3056095264704 -343000 ekin = 3.08559255942693 | erot = 2.94813449265469 | epot = -21.7030445300996 | etot = -15.669317478018 -344000 ekin = 2.95985387154984 | erot = 3.11547515850352 | epot = -21.681548329552 | etot = -15.6062192994986 -345000 ekin = 2.33428072266864 | erot = 2.8804443128302 | epot = -21.6567075042343 | etot = -16.4419824687354 -346000 ekin = 2.02077664062698 | erot = 3.45936833964706 | epot = -21.5877268821218 | etot = -16.1075819018477 -347000 ekin = 2.34924784800441 | erot = 1.93056350805623 | epot = -21.4896151766054 | etot = -17.2098038205448 -348000 ekin = 2.79839267202794 | erot = 2.79408776517961 | epot = -21.4682057474677 | etot = -15.8757253102602 -349000 ekin = 2.33820470114615 | erot = 3.12966318670512 | epot = -21.5603039389198 | etot = -16.0924360510685 -350000 ekin = 2.22383234890832 | erot = 2.3888687038801 | epot = -21.5375784703117 | etot = -16.9248774175232 -351000 ekin = 2.33329735253339 | erot = 2.84447430695177 | epot = -21.5078106306152 | etot = -16.33003897113 -352000 ekin = 2.74923373919409 | erot = 2.76796181793622 | epot = -21.5537134920816 | etot = -16.0365179349513 -353000 ekin = 1.76111836153718 | erot = 2.12255592617517 | epot = -21.5037017999955 | etot = -17.6200275122832 -354000 ekin = 2.29967358188085 | erot = 2.37615363620183 | epot = -21.559257977819 | etot = -16.8834307597363 -355000 ekin = 2.32956787601564 | erot = 2.41406261152025 | epot = -21.5311925684016 | etot = -16.7875620808657 -356000 ekin = 2.99536507165416 | erot = 3.01337867890171 | epot = -21.461213826164 | etot = -15.4524700756081 -357000 ekin = 1.79487551861702 | erot = 2.1478177575683 | epot = -21.4425100027869 | etot = -17.4998167266015 -358000 ekin = 2.06856992699964 | erot = 1.91585051553708 | epot = -21.4597512525557 | etot = -17.475330810019 -359000 ekin = 2.03457633089973 | erot = 2.13725650388116 | epot = -21.4345843672419 | etot = -17.2627515324611 -360000 ekin = 2.64289898809605 | erot = 2.45722294398596 | epot = -21.3798303659972 | etot = -16.2797084339152 -361000 ekin = 2.44681633772951 | erot = 2.40323525392196 | epot = -21.4535746870957 | etot = -16.6035230954443 -362000 ekin = 2.27284400709389 | erot = 2.04866562998477 | epot = -21.4444048899961 | etot = -17.1228952529174 -363000 ekin = 3.23945885057604 | erot = 1.79247859381385 | epot = -21.4992698914106 | etot = -16.4673324470207 -364000 ekin = 3.01124200487832 | erot = 2.16495867321709 | epot = -21.5330648567406 | etot = -16.3568641786452 -365000 ekin = 2.51472285580871 | erot = 2.29864111879032 | epot = -21.6252096459668 | etot = -16.8118456713678 -366000 ekin = 2.59356655410024 | erot = 2.21031948632571 | epot = -21.6397726115723 | etot = -16.8358865711463 -367000 ekin = 2.23422490605625 | erot = 1.85375489374337 | epot = -21.7036464131406 | etot = -17.615666613341 -368000 ekin = 2.4774770785368 | erot = 2.36511710555107 | epot = -21.7442459693683 | etot = -16.9016517852804 -369000 ekin = 2.03854183495617 | erot = 2.80790943599038 | epot = -21.8295461127419 | etot = -16.9830948417954 -370000 ekin = 2.08495509326203 | erot = 2.15717784784086 | epot = -21.8579547558588 | etot = -17.6158218147559 -371000 ekin = 2.1649158804987 | erot = 2.10731342711639 | epot = -21.7507302872469 | etot = -17.4785009796318 -372000 ekin = 1.83416420958724 | erot = 1.90082367490456 | epot = -21.6784224725519 | etot = -17.9434345880601 -373000 ekin = 1.97176482573297 | erot = 1.7779600789095 | epot = -21.6393712386778 | etot = -17.8896463340353 -374000 ekin = 2.89940710658305 | erot = 1.91194262525378 | epot = -21.5337545453635 | etot = -16.7224048135267 -375000 ekin = 2.32339676163341 | erot = 1.92362318361284 | epot = -21.421709102519 | etot = -17.1746891572728 -376000 ekin = 2.59047552311153 | erot = 2.32394149083979 | epot = -21.4139727856534 | etot = -16.4995557717021 -377000 ekin = 2.24598863840517 | erot = 1.65770205797294 | epot = -21.3405339068232 | etot = -17.4368432104451 -378000 ekin = 2.38351514056703 | erot = 2.54156262207208 | epot = -21.3122380587448 | etot = -16.3871602961057 -379000 ekin = 2.08457212928957 | erot = 2.11819645676891 | epot = -21.2663127721437 | etot = -17.0635441860852 -380000 ekin = 2.62168026009058 | erot = 2.36576073073355 | epot = -21.2469701231191 | etot = -16.259529132295 -381000 ekin = 2.42554871977307 | erot = 2.21588725182519 | epot = -21.2594018196931 | etot = -16.6179658480948 -382000 ekin = 2.04454090532122 | erot = 3.35199327879854 | epot = -21.3507561156203 | etot = -15.9542219315006 -383000 ekin = 2.5775676978984 | erot = 1.58356833947096 | epot = -21.4206473136967 | etot = -17.2595112763273 -384000 ekin = 2.32411392435712 | erot = 2.07034159075991 | epot = -21.4254017003271 | etot = -17.0309461852101 -385000 ekin = 1.93815279071873 | erot = 3.2997037447625 | epot = -21.4993838182002 | etot = -16.2615272827189 -386000 ekin = 2.10645704249442 | erot = 2.94380940917573 | epot = -21.5050572923383 | etot = -16.4547908406681 -387000 ekin = 2.28625118399722 | erot = 2.40488022694899 | epot = -21.4350466670762 | etot = -16.74391525613 -388000 ekin = 2.84183807689895 | erot = 2.72440789072404 | epot = -21.448767296848 | etot = -15.882521329225 -389000 ekin = 3.39750799106376 | erot = 3.08194517695383 | epot = -21.6559630447603 | etot = -15.1765098767427 -390000 ekin = 2.82211920760118 | erot = 2.04880343622588 | epot = -21.7229608878358 | etot = -16.8520382440088 -391000 ekin = 2.25113345866118 | erot = 2.45876014532077 | epot = -21.7793475672487 | etot = -17.0694539632668 -392000 ekin = 2.6777973992177 | erot = 2.7527860471579 | epot = -21.9200377033298 | etot = -16.4894542569542 -393000 ekin = 2.07336639249412 | erot = 1.66102921524042 | epot = -22.0500496423093 | etot = -18.3156540345748 -394000 ekin = 2.1138614951422 | erot = 2.4065490584156 | epot = -22.0647062581752 | etot = -17.5442957046174 -395000 ekin = 2.46967791557608 | erot = 2.46187607744979 | epot = -22.0113006362931 | etot = -17.0797466432672 -396000 ekin = 3.17858061422169 | erot = 1.60030928107608 | epot = -21.9570022338792 | etot = -17.1781123385814 -397000 ekin = 2.37483507726777 | erot = 2.17387816921976 | epot = -21.8769234701934 | etot = -17.3282102237059 -398000 ekin = 2.29815779154461 | erot = 2.20148627030488 | epot = -21.8293641014529 | etot = -17.3297200396034 -399000 ekin = 2.66620669497936 | erot = 2.78316441348841 | epot = -21.7420307764657 | etot = -16.2926596679979 -400000 ekin = 1.8196142363994 | erot = 2.77573291920481 | epot = -21.7225828560707 | etot = -17.1272357004665 -401000 ekin = 2.39347596566752 | erot = 3.11237720134103 | epot = -21.763219812775 | etot = -16.2573666457665 -402000 ekin = 4.0137909252526 | erot = 3.58756310879366 | epot = -21.6952307126455 | etot = -14.0938766785993 -403000 ekin = 3.6423872335827 | erot = 3.44210139074532 | epot = -21.6932224157202 | etot = -14.6087337913922 -404000 ekin = 2.52116102522202 | erot = 2.99286839639892 | epot = -21.7395466120138 | etot = -16.2255171903929 -405000 ekin = 2.80514548558626 | erot = 3.09807228440151 | epot = -21.809681120553 | etot = -15.9064633505652 -406000 ekin = 2.32696376764902 | erot = 2.03572639782902 | epot = -21.9111381639248 | etot = -17.5484479984467 -407000 ekin = 2.33504128016394 | erot = 1.91320949168965 | epot = -21.9359478399847 | etot = -17.6876970681311 -408000 ekin = 1.90942025822264 | erot = 2.20375631379572 | epot = -21.9849314014527 | etot = -17.8717548294343 -409000 ekin = 1.98818542800297 | erot = 1.95540808206522 | epot = -22.03783497597 | etot = -18.0942414659018 -410000 ekin = 1.59823476401333 | erot = 1.9127296785249 | epot = -22.0830507565095 | etot = -18.5720863139713 -411000 ekin = 1.87320182179615 | erot = 2.46575148951074 | epot = -22.1911106440467 | etot = -17.8521573327398 -412000 ekin = 2.51909186028136 | erot = 2.65534868642726 | epot = -22.281680067606 | etot = -17.1072395208973 -413000 ekin = 2.80929435327118 | erot = 3.19888285052217 | epot = -22.190767996874 | etot = -16.1825907930807 -414000 ekin = 2.79014519733558 | erot = 2.72515195410933 | epot = -22.1448630242429 | etot = -16.629565872798 -415000 ekin = 2.4678901908732 | erot = 2.24891720770208 | epot = -22.1977268949424 | etot = -17.4809194963671 -416000 ekin = 3.30766536008867 | erot = 1.55878918639504 | epot = -22.1694878213559 | etot = -17.3030332748721 -417000 ekin = 3.95074944679109 | erot = 2.44780201516574 | epot = -22.1018895242094 | etot = -15.7033380622526 -418000 ekin = 2.77340936693416 | erot = 2.68993840817536 | epot = -21.977327562767 | etot = -16.5139797876575 -419000 ekin = 2.38275203991917 | erot = 2.97769109273479 | epot = -21.9010102007428 | etot = -16.5405670680889 -420000 ekin = 1.80397709765343 | erot = 1.82715488758969 | epot = -21.8849019003165 | etot = -18.2537699150733 -421000 ekin = 1.36681295471101 | erot = 1.76825921584578 | epot = -21.8412237154645 | etot = -18.7061515449077 -422000 ekin = 1.39959702132374 | erot = 2.73409619318274 | epot = -21.8826128255667 | etot = -17.7489196110602 -423000 ekin = 1.56944982840735 | erot = 3.0745352163647 | epot = -21.9154707534762 | etot = -17.2714857087042 -424000 ekin = 2.37132681302185 | erot = 2.02827700625919 | epot = -21.9855473914522 | etot = -17.5859435721711 -425000 ekin = 2.32398819807537 | erot = 2.54492547738624 | epot = -22.0336841510595 | etot = -17.1647704755979 -426000 ekin = 2.07554577000492 | erot = 3.12289746501957 | epot = -21.9790717327511 | etot = -16.7806284977266 -427000 ekin = 2.16798189989515 | erot = 2.43592804982976 | epot = -21.8725998895963 | etot = -17.2686899398714 -428000 ekin = 1.81044953925647 | erot = 1.65104945142325 | epot = -21.8530279543937 | etot = -18.391528963714 -429000 ekin = 1.67107266086147 | erot = 2.55773576228634 | epot = -21.8100708745401 | etot = -17.5812624513923 -430000 ekin = 2.68478182527405 | erot = 2.86091245076365 | epot = -21.8410586042845 | etot = -16.2953643282468 -431000 ekin = 2.77628795576833 | erot = 1.57824702797161 | epot = -21.8242269586438 | etot = -17.4696919749038 -432000 ekin = 2.50950337424058 | erot = 1.60698871193856 | epot = -21.7274714752277 | etot = -17.6109793890485 -433000 ekin = 1.86271272714812 | erot = 2.49153826331594 | epot = -21.7782989349596 | etot = -17.4240479444956 -434000 ekin = 2.89451059329443 | erot = 2.7999871143393 | epot = -21.9094190496406 | etot = -16.2149213420069 -435000 ekin = 3.67276301290157 | erot = 1.38568900942255 | epot = -22.090314852724 | etot = -17.0318628303999 -436000 ekin = 3.05559930935247 | erot = 2.0011229579365 | epot = -22.0922696682969 | etot = -17.0355474010079 -437000 ekin = 3.23217703427564 | erot = 1.78362343665461 | epot = -22.1039224603628 | etot = -17.0881219894326 -438000 ekin = 2.86284068923964 | erot = 1.84512171996301 | epot = -22.0628669955697 | etot = -17.3549045863671 -439000 ekin = 2.41223300999623 | erot = 2.70115548536557 | epot = -22.0444627048546 | etot = -16.9310742094928 -440000 ekin = 2.21861950215059 | erot = 3.01743511618684 | epot = -22.068610200563 | etot = -16.8325555822256 -441000 ekin = 2.8932616531564 | erot = 2.87922265473726 | epot = -22.2016049433916 | etot = -16.4291206354979 -442000 ekin = 2.05577486002272 | erot = 1.73545040283799 | epot = -22.2600410881766 | etot = -18.4688158253159 -443000 ekin = 1.86487220517439 | erot = 2.00809914782698 | epot = -22.2983494418706 | etot = -18.4253780888692 -444000 ekin = 2.06067323986939 | erot = 2.15338745019835 | epot = -22.3098473137383 | etot = -18.0957866236705 -445000 ekin = 2.10070768344239 | erot = 2.28023429868874 | epot = -22.3660019273286 | etot = -17.9850599451974 -446000 ekin = 2.41985050727236 | erot = 2.85361119161167 | epot = -22.3957509332304 | etot = -17.1222892343463 -447000 ekin = 2.19943989168951 | erot = 2.98216128214708 | epot = -22.469110173424 | etot = -17.2875089995874 -448000 ekin = 2.35402217188592 | erot = 2.94501347240091 | epot = -22.4864294789763 | etot = -17.1873938346895 -449000 ekin = 2.39054827328709 | erot = 2.92846006473406 | epot = -22.4970387577705 | etot = -17.1780304197493 -450000 ekin = 1.87726152618207 | erot = 1.69631154300644 | epot = -22.4508394587929 | etot = -18.8772663896044 -451000 ekin = 2.02069736260971 | erot = 1.92749635252742 | epot = -22.4770058621559 | etot = -18.5288121470188 -452000 ekin = 1.3666953525299 | erot = 1.87120912975428 | epot = -22.4460428971841 | etot = -19.2081384149 -453000 ekin = 2.05921418622385 | erot = 2.5605072573601 | epot = -22.2726167353286 | etot = -17.6528952917446 -454000 ekin = 1.47363002563146 | erot = 2.19122966699538 | epot = -22.1344003551401 | etot = -18.4695406625132 -455000 ekin = 1.65421215030224 | erot = 2.72189882576686 | epot = -21.9866163127307 | etot = -17.6105053366616 -456000 ekin = 2.34716429715612 | erot = 2.00764007623841 | epot = -21.90677470961 | etot = -17.5519703362155 -457000 ekin = 2.01303704889081 | erot = 2.37161581638612 | epot = -21.8782315807472 | etot = -17.4935787154703 -458000 ekin = 1.72808196373504 | erot = 2.26329030421536 | epot = -21.9079500000029 | etot = -17.9165777320525 -459000 ekin = 2.48364348461731 | erot = 2.3240575427801 | epot = -21.9914965936289 | etot = -17.1837955662315 -460000 ekin = 2.18803460742775 | erot = 2.0007959749913 | epot = -21.9555607076499 | etot = -17.7667301252308 -461000 ekin = 2.27712563450181 | erot = 2.90158501178946 | epot = -21.8847407992378 | etot = -16.7060301529466 -462000 ekin = 2.61279319699133 | erot = 1.79745093921971 | epot = -21.9114284731883 | etot = -17.5011843369773 -463000 ekin = 2.55747204597719 | erot = 3.31219898146397 | epot = -21.8470352327239 | etot = -15.9773642052827 -464000 ekin = 2.15349343963234 | erot = 2.38948322569807 | epot = -21.7801403318396 | etot = -17.2371636665092 -465000 ekin = 2.52543530387722 | erot = 3.61347339076555 | epot = -21.7051172971457 | etot = -15.5662086025029 -466000 ekin = 1.97908646325563 | erot = 2.88692153825727 | epot = -21.7203160444827 | etot = -16.8543080429698 -467000 ekin = 1.62854081734785 | erot = 2.60873315907749 | epot = -21.8060801677334 | etot = -17.568806191308 -468000 ekin = 1.09788716658785 | erot = 3.35078825295795 | epot = -21.8502881604262 | etot = -17.4016127408804 -469000 ekin = 1.70264661426319 | erot = 2.75879477289509 | epot = -21.8645169837194 | etot = -17.4030755965612 -470000 ekin = 1.85887711900485 | erot = 2.87063120254238 | epot = -21.9016760852734 | etot = -17.1721677637262 -471000 ekin = 2.74433347072485 | erot = 2.34940159205027 | epot = -21.9525184591591 | etot = -16.858783396384 -472000 ekin = 2.71861698075021 | erot = 2.13574138468281 | epot = -22.043139657379 | etot = -17.188781291946 -473000 ekin = 2.29393586139762 | erot = 2.07602652007348 | epot = -22.0689471201827 | etot = -17.6989847387116 -474000 ekin = 2.22698015950102 | erot = 2.16459704058481 | epot = -22.0688687972932 | etot = -17.6772915972074 -475000 ekin = 2.49778963349321 | erot = 2.09516395035673 | epot = -22.0493844866031 | etot = -17.4564309027531 -476000 ekin = 2.20247164730207 | erot = 1.76754680635174 | epot = -21.9411609048438 | etot = -17.97114245119 -477000 ekin = 2.45858206017653 | erot = 2.38436547911607 | epot = -21.9035926873371 | etot = -17.0606451480445 -478000 ekin = 1.89904313419097 | erot = 2.04852868041729 | epot = -21.9098024820003 | etot = -17.962230667392 -479000 ekin = 2.27135244904339 | erot = 3.08753180553182 | epot = -21.8855782232971 | etot = -16.5266939687219 -480000 ekin = 1.67006520289894 | erot = 2.76569589720094 | epot = -21.8952512589751 | etot = -17.4594901588753 -481000 ekin = 1.81868654589552 | erot = 2.9414708396822 | epot = -21.8556888607633 | etot = -17.0955314751856 -482000 ekin = 2.1529439710415 | erot = 2.07338062275435 | epot = -21.8139334476411 | etot = -17.5876088538453 -483000 ekin = 1.50003040241525 | erot = 1.99360891760259 | epot = -21.7830178599697 | etot = -18.2893785399518 -484000 ekin = 1.85249475505066 | erot = 2.33993365040866 | epot = -21.8601099434573 | etot = -17.667681537998 -485000 ekin = 1.64683537455249 | erot = 2.50435926395354 | epot = -21.8955949997619 | etot = -17.7444003612559 -486000 ekin = 1.86105919233017 | erot = 2.15998603169225 | epot = -21.8866198023574 | etot = -17.865574578335 -487000 ekin = 2.34642746027526 | erot = 3.11621484615889 | epot = -21.9694478483786 | etot = -16.5068055419444 -488000 ekin = 2.27477353342506 | erot = 3.28151732893999 | epot = -21.9413870028191 | etot = -16.3850961404541 -489000 ekin = 2.38811670508139 | erot = 2.56075035711346 | epot = -21.8588712340667 | etot = -16.9100041718718 -490000 ekin = 2.12967761012957 | erot = 3.54527785345187 | epot = -21.7605939508001 | etot = -16.0856384872187 -491000 ekin = 2.20842614718126 | erot = 2.48924156347248 | epot = -21.6457265496381 | etot = -16.9480588389844 -492000 ekin = 2.4395254440209 | erot = 2.76330603967686 | epot = -21.6220324898892 | etot = -16.4192010061915 -493000 ekin = 1.79410073842211 | erot = 2.29051754332657 | epot = -21.6936080215355 | etot = -17.6089897397868 -494000 ekin = 2.11540109224087 | erot = 3.01314449614681 | epot = -21.7627418159279 | etot = -16.6341962275402 -495000 ekin = 2.15696781071045 | erot = 2.49003984864576 | epot = -21.8774411430157 | etot = -17.2304334836595 -496000 ekin = 2.06056419551912 | erot = 2.60700167900217 | epot = -21.9267578866096 | etot = -17.2591920120883 -497000 ekin = 2.52230078856674 | erot = 1.71004976105951 | epot = -21.8761278437228 | etot = -17.6437772940965 -498000 ekin = 2.15386519150084 | erot = 1.7877582493135 | epot = -21.8235168200552 | etot = -17.8818933792409 -499000 ekin = 3.01273208137282 | erot = 1.73929065213249 | epot = -21.8383204837321 | etot = -17.0862977502268 -500000 ekin = 2.76627013489254 | erot = 2.50177083221038 | epot = -21.8296477468867 | etot = -16.5616067797838 -501000 ekin = 2.69354090483081 | erot = 2.99040340411742 | epot = -21.7028439088855 | etot = -16.0188995999373 -502000 ekin = 1.91653635860025 | erot = 3.89816773432919 | epot = -21.583432763767 | etot = -15.7687286708375 -503000 ekin = 1.8049945577739 | erot = 2.94458962426212 | epot = -21.4077198882804 | etot = -16.6581357062444 -504000 ekin = 1.7007501283395 | erot = 3.04308257832265 | epot = -21.3303407289238 | etot = -16.5865080222617 -505000 ekin = 2.75938082804563 | erot = 2.14633054935697 | epot = -21.3513040286372 | etot = -16.4455926512346 -506000 ekin = 2.29721513417039 | erot = 2.04407050893762 | epot = -21.3782890727133 | etot = -17.0370034296053 -507000 ekin = 3.17630328091397 | erot = 2.42168869077952 | epot = -21.4719630820982 | etot = -15.8739711104047 -508000 ekin = 2.53585993010305 | erot = 2.52795056175584 | epot = -21.6289259001545 | etot = -16.5651154082956 -509000 ekin = 2.12729637924758 | erot = 2.83075478444603 | epot = -21.7770419169527 | etot = -16.8189907532591 -510000 ekin = 2.16130107435063 | erot = 1.4474002808625 | epot = -21.865058134686 | etot = -18.2563567794729 -511000 ekin = 2.54314403873699 | erot = 2.77114415578344 | epot = -21.9659487167511 | etot = -16.6516605222306 -512000 ekin = 2.32805620618464 | erot = 2.80390129625045 | epot = -22.0162636771922 | etot = -16.8843061747571 -513000 ekin = 2.47643071154241 | erot = 2.16996908181989 | epot = -22.0068700128127 | etot = -17.3604702194504 -514000 ekin = 2.76735167549093 | erot = 2.5560945093739 | epot = -22.0884785602195 | etot = -16.7650323753546 -515000 ekin = 2.52241002891622 | erot = 1.82421001167332 | epot = -22.1699357425315 | etot = -17.8233157019419 -516000 ekin = 2.81865025814532 | erot = 2.22273296296804 | epot = -22.2611246405327 | etot = -17.2197414194194 -517000 ekin = 2.03359359720563 | erot = 2.04941720296977 | epot = -22.2784200990267 | etot = -18.1954092988513 -518000 ekin = 2.18715182081959 | erot = 2.76009656526116 | epot = -22.2656600846347 | etot = -17.3184116985539 -519000 ekin = 2.23054901776311 | erot = 2.23031226848963 | epot = -22.3630341627209 | etot = -17.9021728764682 -520000 ekin = 1.88803088032302 | erot = 2.2011880193367 | epot = -22.4543549024555 | etot = -18.3651360027958 -521000 ekin = 2.5788145021642 | erot = 1.87212358693392 | epot = -22.6061072334407 | etot = -18.1551691443426 -522000 ekin = 3.47616129908058 | erot = 1.7772453643546 | epot = -22.6845102288213 | etot = -17.4311035653861 -523000 ekin = 2.84567111920743 | erot = 2.47541358851175 | epot = -22.7265847722155 | etot = -17.4055000644963 -524000 ekin = 2.40295627946642 | erot = 2.37521730874542 | epot = -22.6625181827119 | etot = -17.8843445945001 -525000 ekin = 1.59533356282023 | erot = 2.61484336640372 | epot = -22.5609538171745 | etot = -18.3507768879506 -526000 ekin = 1.67014109396784 | erot = 1.59576537490726 | epot = -22.5093055920857 | etot = -19.2433991232106 -527000 ekin = 2.19651674150708 | erot = 1.9334689520564 | epot = -22.416637825963 | etot = -18.2866521323995 -528000 ekin = 2.6388100641198 | erot = 2.84216954327882 | epot = -22.4260162554832 | etot = -16.9450366480846 -529000 ekin = 2.71709856246059 | erot = 3.01205775167426 | epot = -22.459718422821 | etot = -16.7305621086861 -530000 ekin = 2.59661785995463 | erot = 2.1317538383576 | epot = -22.3199904037947 | etot = -17.5916187054825 -531000 ekin = 2.96824333148625 | erot = 2.35839785116796 | epot = -22.2231381817491 | etot = -16.8964969990948 -532000 ekin = 2.54395795354125 | erot = 2.32264886366187 | epot = -22.2374166013869 | etot = -17.3708097841837 -533000 ekin = 2.47227506927642 | erot = 2.96338827195566 | epot = -22.2425022915258 | etot = -16.8068389502938 -534000 ekin = 2.10485521169123 | erot = 2.03890745270192 | epot = -22.2614710403225 | etot = -18.1177083759294 -535000 ekin = 3.7681160256911 | erot = 2.64691499190425 | epot = -22.2333123161884 | etot = -15.8182812985931 -536000 ekin = 2.78942061222755 | erot = 1.95044966554667 | epot = -22.1701037207896 | etot = -17.4302334430154 -537000 ekin = 2.84557129562433 | erot = 2.62357964692973 | epot = -22.0783833655685 | etot = -16.6092324230145 -538000 ekin = 2.6762341850661 | erot = 2.08962851172352 | epot = -21.9551967105607 | etot = -17.1893340137711 -539000 ekin = 2.73042047481565 | erot = 2.35759238547273 | epot = -22.0351539405022 | etot = -16.9471410802139 -540000 ekin = 2.45519866431123 | erot = 2.4981181890662 | epot = -22.1989060513573 | etot = -17.2455891979799 -541000 ekin = 3.48278591732384 | erot = 2.77790849524953 | epot = -22.293113550245 | etot = -16.0324191376716 -542000 ekin = 2.48972545444614 | erot = 2.87329046778514 | epot = -22.2996895226973 | etot = -16.936673600466 -543000 ekin = 2.34702865402498 | erot = 2.86164606010259 | epot = -22.3019937721979 | etot = -17.0933190580704 -544000 ekin = 2.2292929238022 | erot = 1.46828563141241 | epot = -22.2750271034542 | etot = -18.5774485482396 -545000 ekin = 2.45402962478577 | erot = 2.14177155701245 | epot = -22.2689033162423 | etot = -17.6731021344441 -546000 ekin = 1.98437317503609 | erot = 2.24145066872857 | epot = -22.231451016773 | etot = -18.0056271730083 -547000 ekin = 2.56232506323983 | erot = 1.8957329416699 | epot = -22.2006739415904 | etot = -17.7426159366806 -548000 ekin = 1.72901692707454 | erot = 1.64127805124739 | epot = -22.1889928496838 | etot = -18.8186978713619 -549000 ekin = 1.95693771614146 | erot = 2.64543637333348 | epot = -22.3274020528097 | etot = -17.7250279633348 -550000 ekin = 1.80676199713794 | erot = 1.58556446355636 | epot = -22.4372723150787 | etot = -19.0449458543844 -551000 ekin = 2.19788558810888 | erot = 2.26343688446907 | epot = -22.4937724434742 | etot = -18.0324499708962 -552000 ekin = 2.07444206644618 | erot = 2.4924547779295 | epot = -22.5307066394854 | etot = -17.9638097951097 -553000 ekin = 2.94843364322829 | erot = 2.12309070437467 | epot = -22.5864397604241 | etot = -17.5149154128212 -554000 ekin = 2.8669013077969 | erot = 1.94289309717446 | epot = -22.7547133508173 | etot = -17.944918945846 -555000 ekin = 2.43109245651296 | erot = 2.28708567272124 | epot = -22.8403752960634 | etot = -18.1221971668292 -556000 ekin = 2.31020302439074 | erot = 2.55813703267857 | epot = -22.8772269218695 | etot = -18.0088868648002 -557000 ekin = 2.81362788715375 | erot = 1.42585523952483 | epot = -22.9385956569468 | etot = -18.6991125302682 -558000 ekin = 2.79708127877053 | erot = 1.99543683519586 | epot = -22.9818380573142 | etot = -18.1893199433478 -559000 ekin = 3.34838499070616 | erot = 2.30938187383097 | epot = -23.0552911748694 | etot = -17.3975243103323 -560000 ekin = 3.12573335081966 | erot = 2.33613155247371 | epot = -23.0531044936338 | etot = -17.5912395903404 -561000 ekin = 2.91265639708728 | erot = 2.07460770991413 | epot = -22.9816460067704 | etot = -17.994381899769 -562000 ekin = 3.33014108031755 | erot = 2.52217359738306 | epot = -22.8883444963189 | etot = -17.0360298186183 -563000 ekin = 2.70195061932616 | erot = 1.64767701341235 | epot = -22.8706676277187 | etot = -18.5210399949802 -564000 ekin = 2.82949746353249 | erot = 2.52900091959398 | epot = -22.838139252732 | etot = -17.4796408696055 -565000 ekin = 2.6799458842118 | erot = 2.05094178592405 | epot = -22.7931046586014 | etot = -18.0622169884655 -566000 ekin = 2.32981255203853 | erot = 2.16378765301413 | epot = -22.8021908760777 | etot = -18.308590671025 -567000 ekin = 1.92318241605807 | erot = 2.83258384518153 | epot = -22.7581760555384 | etot = -18.0024097942988 -568000 ekin = 2.17670374071095 | erot = 2.23391142490164 | epot = -22.7850730909043 | etot = -18.3744579252917 -569000 ekin = 2.44198813773898 | erot = 2.6516050247459 | epot = -22.7190926726892 | etot = -17.6254995102043 -570000 ekin = 2.43177788701191 | erot = 1.89766941909699 | epot = -22.6957241348109 | etot = -18.366276828702 -571000 ekin = 2.8616716748476 | erot = 2.96803868526251 | epot = -22.6955740677955 | etot = -16.8658637076854 -572000 ekin = 1.9266829320902 | erot = 3.79132932462474 | epot = -22.6581088104385 | etot = -16.9400965537235 -573000 ekin = 2.4014048576209 | erot = 2.29981222297848 | epot = -22.6359071074265 | etot = -17.9346900268271 -574000 ekin = 1.68882414912167 | erot = 2.32096306897647 | epot = -22.6777773313941 | etot = -18.667990113296 -575000 ekin = 1.85486724354783 | erot = 1.85639491114931 | epot = -22.7438316286092 | etot = -19.0325694739121 -576000 ekin = 3.24777117904094 | erot = 2.95566351376113 | epot = -22.6985695145043 | etot = -16.4951348217022 -577000 ekin = 2.89421636302283 | erot = 2.87485367144017 | epot = -22.6277887766954 | etot = -16.8587187422324 -578000 ekin = 2.40460139915755 | erot = 2.78214210780856 | epot = -22.4342254096835 | etot = -17.2474819027174 -579000 ekin = 2.40583592511148 | erot = 1.99558232802689 | epot = -22.2882462647013 | etot = -17.886828011563 -580000 ekin = 2.69821955230589 | erot = 1.94742609836086 | epot = -22.1748059732807 | etot = -17.529160322614 -581000 ekin = 2.06309002895042 | erot = 2.97622682023057 | epot = -22.0663831943618 | etot = -17.0270663451808 -582000 ekin = 2.33870950534172 | erot = 3.07899815689444 | epot = -21.9472197644711 | etot = -16.529512102235 -583000 ekin = 2.23417742887653 | erot = 2.68476937508274 | epot = -21.8372787545234 | etot = -16.9183319505641 -584000 ekin = 2.94315944829306 | erot = 2.59998006112943 | epot = -21.7510436245968 | etot = -16.2079041151743 -585000 ekin = 2.36063444131441 | erot = 2.49115855857339 | epot = -21.716664566375 | etot = -16.8648715664872 -586000 ekin = 3.56573478158494 | erot = 2.02491202456932 | epot = -21.7701198402972 | etot = -16.1794730341429 -587000 ekin = 3.53722517030309 | erot = 1.97258414970475 | epot = -21.7657911786969 | etot = -16.2559818586891 -588000 ekin = 2.82336660490038 | erot = 1.59341534726277 | epot = -21.7537853332811 | etot = -17.337003381118 -589000 ekin = 2.31627543989202 | erot = 2.20583300708156 | epot = -21.819159896967 | etot = -17.2970514499934 -590000 ekin = 2.5761147615757 | erot = 1.7276907576924 | epot = -21.8419599878986 | etot = -17.5381544686305 -591000 ekin = 1.914719960803 | erot = 3.80606547056266 | epot = -21.9343807003624 | etot = -16.2135952689968 -592000 ekin = 2.11220925054576 | erot = 2.84210516766061 | epot = -21.9632133143301 | etot = -17.0088988961237 -593000 ekin = 1.6646372491541 | erot = 2.46218741166836 | epot = -21.991443017852 | etot = -17.8646183570296 -594000 ekin = 1.86313837200261 | erot = 2.37277652331338 | epot = -22.1142340310892 | etot = -17.8783191357732 -595000 ekin = 1.63972261150116 | erot = 2.14970753455378 | epot = -22.2953930400735 | etot = -18.5059628940186 -596000 ekin = 1.86251521505325 | erot = 1.56938670177389 | epot = -22.4008561933212 | etot = -18.9689542764941 -597000 ekin = 2.21077278172449 | erot = 2.30873590521149 | epot = -22.4593134849654 | etot = -17.9398047980295 -598000 ekin = 1.86600453617805 | erot = 3.02313695685425 | epot = -22.5159510945793 | etot = -17.626809601547 -599000 ekin = 2.86269709275589 | erot = 2.19928983580779 | epot = -22.536034528565 | etot = -17.4740476000013 -600000 ekin = 2.65058373294182 | erot = 2.1453395725597 | epot = -22.4614831887335 | etot = -17.6655598832319 -601000 ekin = 2.97019047275319 | erot = 3.19822787132468 | epot = -22.326632736987 | etot = -16.1582143929091 -602000 ekin = 2.9342181584107 | erot = 2.68627396788675 | epot = -22.2239640230703 | etot = -16.6034718967729 -603000 ekin = 2.59879720190065 | erot = 2.71300694016987 | epot = -22.1699955907165 | etot = -16.8581914486459 -604000 ekin = 1.79062196644622 | erot = 2.11515604890805 | epot = -22.1925738415064 | etot = -18.2867958261521 -605000 ekin = 1.82915557452074 | erot = 2.27656815459633 | epot = -22.2178733165573 | etot = -18.1121495874403 -606000 ekin = 2.33864930282378 | erot = 2.20418036728506 | epot = -22.1612604193817 | etot = -17.6184307492728 -607000 ekin = 2.72666062231761 | erot = 2.97710490441868 | epot = -22.1567890421522 | etot = -16.453023515416 -608000 ekin = 2.45223782114265 | erot = 2.41233206147764 | epot = -22.1258176689204 | etot = -17.2612477863002 -609000 ekin = 1.9103123443041 | erot = 2.62713008552307 | epot = -22.0122680423109 | etot = -17.4748256124837 -610000 ekin = 3.01317318621525 | erot = 2.17099557280212 | epot = -21.9300149409222 | etot = -16.7458461819048 -611000 ekin = 2.44412474588955 | erot = 2.75159898142814 | epot = -21.9253433050474 | etot = -16.7296195777297 -612000 ekin = 2.50268974484936 | erot = 2.16817685060957 | epot = -21.9671518078452 | etot = -17.2962852123863 -613000 ekin = 3.01839912550875 | erot = 2.12784951047117 | epot = -22.0272786909971 | etot = -16.8810300550172 -614000 ekin = 2.25327082296097 | erot = 2.99336372547237 | epot = -22.0696405907525 | etot = -16.8230060423192 -615000 ekin = 1.66371843102219 | erot = 2.63618748290988 | epot = -21.9981136728369 | etot = -17.6982077589049 -616000 ekin = 1.8944933240536 | erot = 2.87324187406682 | epot = -22.0037089747212 | etot = -17.2359737766008 -617000 ekin = 2.14785470202862 | erot = 2.51246772527453 | epot = -22.0246986126974 | etot = -17.3643761853943 -618000 ekin = 3.11173481170738 | erot = 2.74375206798687 | epot = -21.9798263374349 | etot = -16.1243394577406 -619000 ekin = 3.41037360007647 | erot = 2.10617263526643 | epot = -21.9553411920504 | etot = -16.4387949567075 -620000 ekin = 4.28430201323245 | erot = 2.1957191595208 | epot = -21.90292903883 | etot = -15.4229078660767 -621000 ekin = 3.09569620704798 | erot = 2.5579200527576 | epot = -21.8282030152651 | etot = -16.1745867554595 -622000 ekin = 2.76028520250002 | erot = 2.60751645183696 | epot = -21.7454000468333 | etot = -16.3775983924963 -623000 ekin = 2.87264675196573 | erot = 2.90399328536428 | epot = -21.5847888275151 | etot = -15.8081487901851 -624000 ekin = 2.01886304134608 | erot = 3.41825628982886 | epot = -21.4089723845367 | etot = -15.9718530533618 -625000 ekin = 2.87961505977186 | erot = 2.69115058956302 | epot = -21.2853791748084 | etot = -15.7146135254735 -626000 ekin = 2.56085845515984 | erot = 2.15799783992829 | epot = -21.2323395606428 | etot = -16.5134832655546 -627000 ekin = 2.30201253530379 | erot = 2.40176180823354 | epot = -21.2927035084693 | etot = -16.588929164932 -628000 ekin = 2.23995601774104 | erot = 2.75333333919435 | epot = -21.455314974678 | etot = -16.4620256177426 -629000 ekin = 2.20895388847365 | erot = 1.97037787876407 | epot = -21.610417234146 | etot = -17.4310854669083 -630000 ekin = 2.4871462707876 | erot = 2.14054709042105 | epot = -21.6281308139011 | etot = -17.0004374526924 -631000 ekin = 2.05037159551177 | erot = 1.78517593497042 | epot = -21.6331433102589 | etot = -17.7975957797767 -632000 ekin = 1.65441370416735 | erot = 3.2831042715311 | epot = -21.6994880970176 | etot = -16.7619701213191 -633000 ekin = 2.34659059561855 | erot = 2.34109216039932 | epot = -21.8312685537372 | etot = -17.1435857977194 -634000 ekin = 2.31567788282477 | erot = 2.4712780706122 | epot = -21.8809017639924 | etot = -17.0939458105554 -635000 ekin = 1.99067051245485 | erot = 3.35494889731601 | epot = -21.9106362902055 | etot = -16.5650168804346 -636000 ekin = 2.50153790134664 | erot = 2.48847992577269 | epot = -21.8747399591398 | etot = -16.8847221320205 -637000 ekin = 2.76558020651622 | erot = 2.80411296109397 | epot = -21.7869209746905 | etot = -16.2172278070803 -638000 ekin = 2.45491140440701 | erot = 2.8151558595933 | epot = -21.8968446083607 | etot = -16.6267773443604 -639000 ekin = 1.89223426878329 | erot = 2.13319240780509 | epot = -21.9315821506475 | etot = -17.9061554740591 -640000 ekin = 2.12172894611398 | erot = 3.32302900673023 | epot = -21.8803218106497 | etot = -16.4355638578054 -641000 ekin = 2.09554513091345 | erot = 2.23099232244472 | epot = -21.9198354154709 | etot = -17.5932979621127 -642000 ekin = 2.28694261481673 | erot = 2.67379901999301 | epot = -21.9718627423438 | etot = -17.011121107534 -643000 ekin = 2.744472839192 | erot = 2.20403800092058 | epot = -21.9230235464268 | etot = -16.9745127063142 -644000 ekin = 2.87907701459995 | erot = 3.40687801628668 | epot = -21.9412616302816 | etot = -15.655306599395 -645000 ekin = 2.38281186883666 | erot = 2.10846097996387 | epot = -21.8300876925357 | etot = -17.3388148437352 -646000 ekin = 2.68568907435101 | erot = 1.80851531070158 | epot = -21.6847618262214 | etot = -17.1905574411688 -647000 ekin = 2.47722877856152 | erot = 2.03923301171106 | epot = -21.5874044483889 | etot = -17.0709426581163 -648000 ekin = 2.25562229204822 | erot = 1.67565814597326 | epot = -21.6993239289701 | etot = -17.7680434909486 -649000 ekin = 2.58610844989063 | erot = 1.77373064510098 | epot = -21.8575240187191 | etot = -17.4976849237275 -650000 ekin = 2.66588270497851 | erot = 2.18108360585018 | epot = -21.9508135981932 | etot = -17.1038472873645 -651000 ekin = 2.11913643076637 | erot = 3.26412345241467 | epot = -22.0193654333906 | etot = -16.6361055502095 -652000 ekin = 2.32941174826482 | erot = 2.30873319569133 | epot = -22.0419984408252 | etot = -17.4038534968691 -653000 ekin = 2.0648428652661 | erot = 2.14823788524201 | epot = -22.0572931422935 | etot = -17.8442123917854 -654000 ekin = 2.29862160782433 | erot = 1.85805598161352 | epot = -22.0910689230265 | etot = -17.9343913335886 -655000 ekin = 2.10941796901071 | erot = 1.77798843556509 | epot = -22.0694006428864 | etot = -18.1819942383106 -656000 ekin = 2.47625408636497 | erot = 2.33538026369006 | epot = -22.0466976130346 | etot = -17.2350632629796 -657000 ekin = 2.50533498663532 | erot = 2.85849882524471 | epot = -22.0769458799067 | etot = -16.7131120680267 -658000 ekin = 2.50225541618483 | erot = 2.85625932114156 | epot = -22.0511557631718 | etot = -16.6926410258454 -659000 ekin = 3.39371926051805 | erot = 2.76525782770508 | epot = -21.9060640783663 | etot = -15.7470869901432 -660000 ekin = 2.71591740302079 | erot = 2.00360570980063 | epot = -21.7628277690744 | etot = -17.043304656253 -661000 ekin = 2.22252752899417 | erot = 2.53760290280427 | epot = -21.6292254759783 | etot = -16.8690950441799 -662000 ekin = 2.05296914064405 | erot = 2.55185124215154 | epot = -21.5811922241459 | etot = -16.9763718413503 -663000 ekin = 2.25677932682754 | erot = 2.31580178345621 | epot = -21.5535923948076 | etot = -16.9810112845238 -664000 ekin = 2.34856452305364 | erot = 1.86775188552653 | epot = -21.4530740440284 | etot = -17.2367576354483 -665000 ekin = 2.63111504026501 | erot = 2.28726928484771 | epot = -21.3846024000308 | etot = -16.4662180749181 -666000 ekin = 1.64075072082918 | erot = 2.31336726697097 | epot = -21.2830441766066 | etot = -17.3289261888065 -667000 ekin = 1.67151341437157 | erot = 2.82297479485494 | epot = -21.1978062440647 | etot = -16.7033180348382 -668000 ekin = 2.49938009250085 | erot = 3.28711483409768 | epot = -21.0664148636443 | etot = -15.2799199370457 -669000 ekin = 1.62232962120344 | erot = 2.64367899162068 | epot = -20.9834308093409 | etot = -16.7174221965168 -670000 ekin = 2.22815723319758 | erot = 2.60319748550307 | epot = -20.9017148964281 | etot = -16.0703601777275 -671000 ekin = 2.27399198808932 | erot = 2.15907350601013 | epot = -20.8548869535533 | etot = -16.4218214594538 -672000 ekin = 1.96813107327782 | erot = 1.65324359657507 | epot = -20.772525080039 | etot = -17.1511504101861 -673000 ekin = 1.89901466802435 | erot = 2.07212800226185 | epot = -20.7410076393374 | etot = -16.7698649690512 -674000 ekin = 2.08208137777485 | erot = 2.16201236525253 | epot = -20.7653673426948 | etot = -16.5212735996674 -675000 ekin = 2.0453276771275 | erot = 2.48425879615287 | epot = -20.7843939429191 | etot = -16.2548074696387 -676000 ekin = 2.45143986767107 | erot = 2.78633106178593 | epot = -20.8123774066529 | etot = -15.5746064771959 -677000 ekin = 2.19157287399382 | erot = 2.62633282573085 | epot = -20.8265856172367 | etot = -16.008679917512 -678000 ekin = 2.13997346968594 | erot = 2.79122127613926 | epot = -20.7113565112497 | etot = -15.7801617654245 -679000 ekin = 2.16938962390632 | erot = 2.17589740910314 | epot = -20.6051510781816 | etot = -16.2598640451722 -680000 ekin = 2.08639324470195 | erot = 2.68206939589547 | epot = -20.6273390457908 | etot = -15.8588764051934 -681000 ekin = 2.17629732810903 | erot = 1.82420607644455 | epot = -20.7142689529019 | etot = -16.7137655483484 -682000 ekin = 3.02912978468384 | erot = 2.39650400849398 | epot = -20.6940095597209 | etot = -15.268375766543 -683000 ekin = 2.84669773609778 | erot = 2.0986204490286 | epot = -20.7021074415215 | etot = -15.7567892563951 -684000 ekin = 1.96664671503579 | erot = 2.99517270495454 | epot = -20.7465124798198 | etot = -15.7846930598294 -685000 ekin = 1.50234716171427 | erot = 2.04490190725428 | epot = -20.7574586814665 | etot = -17.2102096124979 -686000 ekin = 2.2983326300428 | erot = 2.55614840511419 | epot = -20.7458450763069 | etot = -15.8913640411499 -687000 ekin = 1.8557723170762 | erot = 2.84941631673454 | epot = -20.6738522345032 | etot = -15.9686636006925 -688000 ekin = 2.56405256659889 | erot = 2.23115057372413 | epot = -20.6302627184135 | etot = -15.8350595780904 -689000 ekin = 2.75063212318972 | erot = 2.68162291280505 | epot = -20.7838487483938 | etot = -15.351593712399 -690000 ekin = 2.6815028132868 | erot = 2.52132555802218 | epot = -21.0487980543157 | etot = -15.8459696830068 -691000 ekin = 2.29143802116346 | erot = 2.52222072052105 | epot = -21.2158695525349 | etot = -16.4022108108504 -692000 ekin = 2.4246270425625 | erot = 3.24973814883517 | epot = -21.2444446764855 | etot = -15.5700794850878 -693000 ekin = 2.38038731016142 | erot = 2.9968191678008 | epot = -21.3131544661847 | etot = -15.9359479882225 -694000 ekin = 2.69963794803277 | erot = 2.53306749808314 | epot = -21.5028226467206 | etot = -16.2701172006047 -695000 ekin = 2.49329729781653 | erot = 1.18245567143116 | epot = -21.6798414810252 | etot = -18.0040885117775 -696000 ekin = 1.86320369897189 | erot = 1.46627983716862 | epot = -21.665818352319 | etot = -18.3363348161785 -697000 ekin = 2.40483641810464 | erot = 2.10687269227545 | epot = -21.7015701067683 | etot = -17.1898609963882 -698000 ekin = 2.32104204819312 | erot = 1.91618970993301 | epot = -21.7674602711953 | etot = -17.5302285130692 -699000 ekin = 2.45122174410528 | erot = 2.56320773764919 | epot = -21.7532145628501 | etot = -16.7387850810956 -700000 ekin = 2.13478862711018 | erot = 2.28875108681682 | epot = -21.6619710583027 | etot = -17.2384313443757 -701000 ekin = 2.15430012038637 | erot = 2.18434613511233 | epot = -21.5402240218772 | etot = -17.2015777663785 -702000 ekin = 1.57710248759615 | erot = 1.99882868785594 | epot = -21.49627530475 | etot = -17.9203441292979 -703000 ekin = 2.08893022036769 | erot = 2.17530309960948 | epot = -21.5146124029064 | etot = -17.2503790829292 -704000 ekin = 2.82158558148019 | erot = 1.94529304578916 | epot = -21.5362273629372 | etot = -16.7693487356679 -705000 ekin = 2.80985515279542 | erot = 2.16764072993712 | epot = -21.4883886516798 | etot = -16.5108927689472 -706000 ekin = 1.97469093776246 | erot = 2.31446109128202 | epot = -21.4846235511326 | etot = -17.1954715220882 -707000 ekin = 1.90739234287698 | erot = 2.04402779053621 | epot = -21.5406324629157 | etot = -17.5892123295025 -708000 ekin = 2.48934210084869 | erot = 2.15886534084806 | epot = -21.5617376681341 | etot = -16.9135302264373 -709000 ekin = 2.88909793919243 | erot = 2.58134997867787 | epot = -21.6032655988125 | etot = -16.1328176809422 -710000 ekin = 2.18226376204308 | erot = 2.2781120102664 | epot = -21.5729606480227 | etot = -17.1125848757132 -711000 ekin = 2.31693491167058 | erot = 1.40165937970165 | epot = -21.59486559309 | etot = -17.8762713017178 -712000 ekin = 2.5598074081136 | erot = 2.27261456104693 | epot = -21.7093783142763 | etot = -16.8769563451158 -713000 ekin = 1.95731492543824 | erot = 2.3177907879475 | epot = -21.7925969744163 | etot = -17.5174912610306 -714000 ekin = 2.56349602857406 | erot = 2.10802762811156 | epot = -21.8549579399156 | etot = -17.18343428323 -715000 ekin = 2.42420336547985 | erot = 3.74011705339237 | epot = -21.8363873817813 | etot = -15.6720669629091 -716000 ekin = 2.83424908488974 | erot = 2.84906269643008 | epot = -21.7516725023646 | etot = -16.0683607210448 -717000 ekin = 3.449141155469 | erot = 3.20655139229296 | epot = -21.6556489626088 | etot = -14.9999564148469 -718000 ekin = 3.10544916005123 | erot = 3.94111109893272 | epot = -21.5509268479497 | etot = -14.5043665889657 -719000 ekin = 2.38560143578601 | erot = 2.95196851228004 | epot = -21.5368313311174 | etot = -16.1992613830513 -720000 ekin = 2.22547766761154 | erot = 3.14352355524054 | epot = -21.5280561989878 | etot = -16.1590549761357 -721000 ekin = 1.71648896607559 | erot = 2.23916158851569 | epot = -21.4544704731448 | etot = -17.4988199185535 -722000 ekin = 1.92969886536088 | erot = 2.81516182454304 | epot = -21.4789602411171 | etot = -16.7340995512131 -723000 ekin = 2.37878330622949 | erot = 2.55685717442619 | epot = -21.4258282544299 | etot = -16.4901877737742 -724000 ekin = 1.74694406742187 | erot = 2.45584755221003 | epot = -21.4005294054569 | etot = -17.197737785825 -725000 ekin = 2.29310276841874 | erot = 2.95220863719859 | epot = -21.4633620430606 | etot = -16.2180506374432 -726000 ekin = 1.63448654082141 | erot = 2.30654545762654 | epot = -21.5038765351965 | etot = -17.5628445367485 -727000 ekin = 2.46595168496949 | erot = 3.19849750353943 | epot = -21.5266836250346 | etot = -15.8622344365256 -728000 ekin = 2.21687538357189 | erot = 2.165919089739 | epot = -21.513377733993 | etot = -17.1305832606821 -729000 ekin = 1.89362806269803 | erot = 1.6657813694817 | epot = -21.5533880281027 | etot = -17.993978595923 -730000 ekin = 1.78199630529827 | erot = 2.15399263718836 | epot = -21.5485428072817 | etot = -17.6125538647951 -731000 ekin = 2.16845146601146 | erot = 2.96876326415235 | epot = -21.4849197438583 | etot = -16.3477050136945 -732000 ekin = 2.41098004969989 | erot = 2.27162025823661 | epot = -21.3730972185635 | etot = -16.690496910627 -733000 ekin = 3.04997179731017 | erot = 2.57297105879857 | epot = -21.4193189845269 | etot = -15.7963761284182 -734000 ekin = 2.36878310719472 | erot = 2.04459379545547 | epot = -21.4834058303776 | etot = -17.0700289277274 -735000 ekin = 2.13407288267268 | erot = 1.55092026474352 | epot = -21.5368505426165 | etot = -17.8518573952003 -736000 ekin = 2.1362063540729 | erot = 3.45790946645046 | epot = -21.6430634912022 | etot = -16.0489476706788 -737000 ekin = 1.73554233533154 | erot = 3.58779507650378 | epot = -21.6702622900886 | etot = -16.3469248782532 -738000 ekin = 2.01164487816147 | erot = 2.50514634893196 | epot = -21.6986247134705 | etot = -17.1818334863771 -739000 ekin = 1.85074759845217 | erot = 2.19370944227887 | epot = -21.7133968547419 | etot = -17.6689398140108 -740000 ekin = 2.84699687053757 | erot = 2.7912333503138 | epot = -21.7387373822546 | etot = -16.1005071614032 -741000 ekin = 2.47259234369835 | erot = 2.90849116827955 | epot = -21.7966678254519 | etot = -16.415584313474 -742000 ekin = 2.74165618770735 | erot = 3.26593517824215 | epot = -21.9343343201998 | etot = -15.9267429542503 -743000 ekin = 2.23285850131327 | erot = 3.20738521933767 | epot = -22.0692807008484 | etot = -16.6290369801974 -744000 ekin = 2.0089223878876 | erot = 3.79240058007591 | epot = -22.1503347602461 | etot = -16.3490117922826 -745000 ekin = 3.13933421257374 | erot = 2.32790266093992 | epot = -22.1471844512455 | etot = -16.6799475777318 -746000 ekin = 2.96008666942407 | erot = 2.64881993709762 | epot = -22.122986971371 | etot = -16.5140803648493 -747000 ekin = 2.31606158946103 | erot = 2.05363821834659 | epot = -22.1269013575191 | etot = -17.7572015497115 -748000 ekin = 2.36202846469555 | erot = 2.41533863458708 | epot = -22.1607507396176 | etot = -17.3833836403349 -749000 ekin = 2.07010000324332 | erot = 2.77477767451978 | epot = -22.1615532796329 | etot = -17.3166756018698 -750000 ekin = 1.65856288792329 | erot = 2.38394476194078 | epot = -22.2376789275399 | etot = -18.1951712776758 -751000 ekin = 1.79369238822413 | erot = 2.82711279056287 | epot = -22.3399930058064 | etot = -17.7191878270194 -752000 ekin = 1.3565337369664 | erot = 1.46027272724399 | epot = -22.4259407567778 | etot = -19.6091342925674 -753000 ekin = 1.88677173003379 | erot = 2.44011815977781 | epot = -22.3759237785306 | etot = -18.049033888719 -754000 ekin = 1.74757468714757 | erot = 2.73579703445366 | epot = -22.2777874333258 | etot = -17.7944157117246 -755000 ekin = 2.39540881497791 | erot = 2.40997626783999 | epot = -22.1989471718282 | etot = -17.3935620890103 -756000 ekin = 1.8374249552549 | erot = 2.7898384136326 | epot = -22.1256041210015 | etot = -17.498340752114 -757000 ekin = 1.97252620256626 | erot = 2.57811195064152 | epot = -22.0524369346386 | etot = -17.5017987814308 -758000 ekin = 1.18943353600229 | erot = 2.72305618385831 | epot = -21.9808261825123 | etot = -18.0683364626517 -759000 ekin = 2.16138393466163 | erot = 1.3977782924933 | epot = -21.9922114478071 | etot = -18.4330492206522 -760000 ekin = 2.57272139862155 | erot = 2.33385746622741 | epot = -22.0280808566088 | etot = -17.1215019917599 -761000 ekin = 2.08641160599719 | erot = 2.24969428592799 | epot = -22.1058253802024 | etot = -17.7697194882772 -762000 ekin = 2.1361825080532 | erot = 1.66094626659748 | epot = -22.1311549030111 | etot = -18.3340261283604 -763000 ekin = 2.43010472752659 | erot = 3.36039539289095 | epot = -22.2016765636182 | etot = -16.4111764432007 -764000 ekin = 2.84811842220375 | erot = 2.79168514035599 | epot = -22.2088162305687 | etot = -16.569012668009 -765000 ekin = 1.81453694547676 | erot = 2.77469277969824 | epot = -22.1144835078989 | etot = -17.5252537827239 -766000 ekin = 2.64878768483921 | erot = 2.31374812658081 | epot = -21.9875154152781 | etot = -17.0249796038581 -767000 ekin = 2.58989188969789 | erot = 2.86706483154975 | epot = -21.9043548536665 | etot = -16.4473981324189 -768000 ekin = 1.86368721962895 | erot = 2.78532510291609 | epot = -21.9343474885242 | etot = -17.2853351659791 -769000 ekin = 2.40214820980699 | erot = 2.31347943810898 | epot = -22.0333978303343 | etot = -17.3177701824184 -770000 ekin = 2.49202416232453 | erot = 3.23110904096713 | epot = -22.1402797305012 | etot = -16.4171465272095 -771000 ekin = 2.33292298096755 | erot = 2.27796352597305 | epot = -22.17790877141 | etot = -17.5670222644694 -772000 ekin = 2.29055460354208 | erot = 2.99393464583806 | epot = -22.2735812923856 | etot = -16.9890920430054 -773000 ekin = 2.23134390761289 | erot = 1.82253948832535 | epot = -22.3356201893464 | etot = -18.2817367934081 -774000 ekin = 2.82484138078993 | erot = 2.21081663204023 | epot = -22.3299367088855 | etot = -17.2942786960554 -775000 ekin = 1.82366213720863 | erot = 1.87126548470211 | epot = -22.2720238956272 | etot = -18.5770962737165 -776000 ekin = 1.39176212331748 | erot = 3.16041697920643 | epot = -22.2452599321026 | etot = -17.6930808295787 -777000 ekin = 1.62656494455193 | erot = 2.80889498236168 | epot = -22.1606670215091 | etot = -17.7252070945955 -778000 ekin = 1.49453026929824 | erot = 2.24185784607895 | epot = -22.1729818621132 | etot = -18.436593746736 -779000 ekin = 1.88163725615419 | erot = 1.90711264831679 | epot = -22.2125328330488 | etot = -18.4237829285778 -780000 ekin = 1.70286422785891 | erot = 2.30497222936397 | epot = -22.2799394088718 | etot = -18.2721029516489 -781000 ekin = 2.12678565466725 | erot = 2.5607588088585 | epot = -22.3659184198104 | etot = -17.6783739562846 -782000 ekin = 2.6031276814174 | erot = 1.95727704696267 | epot = -22.2790730674379 | etot = -17.7186683390578 -783000 ekin = 2.1948400081794 | erot = 2.90035247320886 | epot = -22.2007535116304 | etot = -17.1055610302421 -784000 ekin = 2.84936415382249 | erot = 2.24073860376602 | epot = -22.2096265501644 | etot = -17.1195237925759 -785000 ekin = 3.14239456216427 | erot = 2.92883564065743 | epot = -22.250724619048 | etot = -16.1794944162263 -786000 ekin = 2.83302205045547 | erot = 3.44600351958776 | epot = -22.2930098599336 | etot = -16.0139842898904 -787000 ekin = 2.41036243622077 | erot = 3.01402072617264 | epot = -22.2336456938648 | etot = -16.8092625314714 -788000 ekin = 1.99496987344553 | erot = 2.0160805570118 | epot = -22.2004170890862 | etot = -18.1893666586289 -789000 ekin = 2.46197992481173 | erot = 2.27411334262936 | epot = -22.132074772345 | etot = -17.3959815049039 -790000 ekin = 3.57873057583599 | erot = 2.82417596997282 | epot = -22.0695018605637 | etot = -15.6665953147549 -791000 ekin = 3.12331080904155 | erot = 2.42394177795114 | epot = -22.080644982627 | etot = -16.5333923956343 -792000 ekin = 3.95364280137309 | erot = 1.97266999125562 | epot = -22.0153287445499 | etot = -16.0890159519212 -793000 ekin = 2.26819643622963 | erot = 2.58701659000735 | epot = -21.9215549471255 | etot = -17.0663419208885 -794000 ekin = 2.16067669778386 | erot = 2.44301139774416 | epot = -21.7616964244106 | etot = -17.1580083288826 -795000 ekin = 1.62512477760333 | erot = 2.41826409844339 | epot = -21.600959390557 | etot = -17.5575705145103 -796000 ekin = 2.18368115482543 | erot = 2.13083402580691 | epot = -21.4815591943755 | etot = -17.1670440137431 -797000 ekin = 1.81443490468363 | erot = 1.99530711788362 | epot = -21.473386092747 | etot = -17.6636440701797 -798000 ekin = 2.22066977376058 | erot = 2.5136217615585 | epot = -21.5005357102706 | etot = -16.7662441749516 -799000 ekin = 1.89003567281256 | erot = 2.87071760546339 | epot = -21.4707763423861 | etot = -16.7100230641101 -800000 ekin = 2.14249138302219 | erot = 2.35217342569423 | epot = -21.3794335794328 | etot = -16.8847687707164 -801000 ekin = 1.84325206062913 | erot = 1.65490182118709 | epot = -21.2215462073953 | etot = -17.7233923255791 -802000 ekin = 2.20306916659744 | erot = 2.22362280870385 | epot = -21.1078917551145 | etot = -16.6811997798132 -803000 ekin = 2.64756180889851 | erot = 1.90771195713019 | epot = -21.075516629541 | etot = -16.5202428635123 -804000 ekin = 2.34383808048561 | erot = 2.89135072882195 | epot = -21.017800229163 | etot = -15.7826114198554 -805000 ekin = 1.79807471993961 | erot = 2.71703055229461 | epot = -20.8858735264626 | etot = -16.3707682542284 -806000 ekin = 1.74933039138001 | erot = 2.08508375084938 | epot = -20.8501295844101 | etot = -17.0157154421807 -807000 ekin = 1.57086516216332 | erot = 1.70410734557162 | epot = -20.9085753440719 | etot = -17.633602836337 -808000 ekin = 2.08081471116263 | erot = 2.40350759554646 | epot = -20.984850158389 | etot = -16.50052785168 -809000 ekin = 2.61726856088296 | erot = 1.51240481195689 | epot = -20.9779384430211 | etot = -16.8482650701812 -810000 ekin = 3.07307660201955 | erot = 2.65446786899303 | epot = -20.8951461498987 | etot = -15.1676016788862 -811000 ekin = 3.02865521289707 | erot = 3.61705494723141 | epot = -20.938700013487 | etot = -14.2929898533586 -812000 ekin = 2.13828724317889 | erot = 2.79208705150833 | epot = -21.0253177933673 | etot = -16.0949434986801 -813000 ekin = 2.19066742087212 | erot = 3.16148861694095 | epot = -21.2162063121508 | etot = -15.8640502743377 -814000 ekin = 1.70799980950659 | erot = 2.98447609556824 | epot = -21.3083573707191 | etot = -16.6158814656443 -815000 ekin = 2.14655793408327 | erot = 2.27340066456812 | epot = -21.3095101360258 | etot = -16.8895515373744 -816000 ekin = 2.70387013105122 | erot = 1.53091743336716 | epot = -21.3380867226337 | etot = -17.1032991582153 -817000 ekin = 2.55772150346674 | erot = 2.58538498973779 | epot = -21.4687911304725 | etot = -16.325684637268 -818000 ekin = 2.27829227808576 | erot = 2.2610194627647 | epot = -21.51579990444 | etot = -16.9764881635896 -819000 ekin = 2.10478468907764 | erot = 3.02372442904099 | epot = -21.5288267165814 | etot = -16.4003175984628 -820000 ekin = 2.50616680560145 | erot = 2.71768974330904 | epot = -21.5031693602738 | etot = -16.2793128113633 -821000 ekin = 2.62605779655516 | erot = 2.5517168842266 | epot = -21.4782637845704 | etot = -16.3004891037887 -822000 ekin = 3.63911022661674 | erot = 2.20246809596405 | epot = -21.4682605531632 | etot = -15.6266822305824 -823000 ekin = 3.5890614966436 | erot = 2.73568419343317 | epot = -21.4644034772322 | etot = -15.1396577871554 -824000 ekin = 4.11258611216971 | erot = 3.29177083877816 | epot = -21.4054670493164 | etot = -14.0011100983685 -825000 ekin = 2.90574167985894 | erot = 3.46418314252362 | epot = -21.2428648794989 | etot = -14.8729400571163 -826000 ekin = 1.72166879396265 | erot = 1.97031409321974 | epot = -21.0465041377165 | etot = -17.3545212505341 -827000 ekin = 1.9124296633897 | erot = 2.55758046921178 | epot = -20.9198493255665 | etot = -16.449839192965 -828000 ekin = 2.38136751134629 | erot = 2.55567683032446 | epot = -20.8197900136475 | etot = -15.8827456719767 -829000 ekin = 2.24752095426969 | erot = 1.78485397592485 | epot = -20.7078548678742 | etot = -16.6754799376796 -830000 ekin = 2.52760515907096 | erot = 2.34151737044649 | epot = -20.587853056286 | etot = -15.7187305267686 -831000 ekin = 2.68303948249783 | erot = 2.12107955860996 | epot = -20.4986251845811 | etot = -15.6945061434733 -832000 ekin = 2.5995339697481 | erot = 2.01126070882922 | epot = -20.317042202606 | etot = -15.7062475240286 -833000 ekin = 2.41782691161325 | erot = 2.6104596916825 | epot = -20.2071689208773 | etot = -15.1788823175815 -834000 ekin = 2.81812459074308 | erot = 2.32580908472724 | epot = -20.1954682788161 | etot = -15.0515346033458 -835000 ekin = 2.76877914745308 | erot = 2.73409979010148 | epot = -20.2858954358872 | etot = -14.7830164983326 -836000 ekin = 2.56414357027351 | erot = 2.85425200452209 | epot = -20.4214942021634 | etot = -15.0030986273678 -837000 ekin = 1.77982670030629 | erot = 1.97011006317925 | epot = -20.4747752062613 | etot = -16.7248384427758 -838000 ekin = 1.9809448596471 | erot = 2.7884830818994 | epot = -20.4863255993134 | etot = -15.7168976577669 -839000 ekin = 1.99257457422062 | erot = 2.69848359788971 | epot = -20.4692625343629 | etot = -15.7782043622526 -840000 ekin = 1.695727430563 | erot = 2.96442093053147 | epot = -20.5469645302134 | etot = -15.886816169119 -841000 ekin = 2.78747714781483 | erot = 2.84618551296106 | epot = -20.6836589678232 | etot = -15.0499963070473 -842000 ekin = 2.5516108705537 | erot = 2.86967631676814 | epot = -20.7215472760611 | etot = -15.3002600887392 -843000 ekin = 2.00510252228194 | erot = 2.62122625910375 | epot = -20.7126385725957 | etot = -16.08630979121 -844000 ekin = 1.53691661689193 | erot = 1.93035645367874 | epot = -20.7513861721528 | etot = -17.2841131015821 -845000 ekin = 2.30558370867946 | erot = 2.31565535118112 | epot = -20.8631357757407 | etot = -16.2418967158802 -846000 ekin = 2.08834507240676 | erot = 2.32509193883626 | epot = -20.9437811774395 | etot = -16.5303441661965 -847000 ekin = 2.47860773767064 | erot = 2.63825359015714 | epot = -20.9035842025176 | etot = -15.7867228746898 -848000 ekin = 2.15941499449244 | erot = 1.46592084588015 | epot = -20.9421067829749 | etot = -17.3167709426023 -849000 ekin = 2.00792301359513 | erot = 2.48538196855797 | epot = -20.9573985285088 | etot = -16.4640935463557 -850000 ekin = 2.54511466975944 | erot = 2.66862013426066 | epot = -20.9501688277166 | etot = -15.7364340236965 -851000 ekin = 2.16918996810547 | erot = 2.93012028589825 | epot = -20.9578305522532 | etot = -15.8585202982494 -852000 ekin = 2.48734107685338 | erot = 2.46343406489934 | epot = -20.9874894800747 | etot = -16.0367143383219 -853000 ekin = 2.41308828583826 | erot = 2.97804263482415 | epot = -20.9325497268305 | etot = -15.5414188061681 -854000 ekin = 2.35481893706787 | erot = 2.85453301930642 | epot = -20.8448014229524 | etot = -15.6354494665781 -855000 ekin = 2.37449305766123 | erot = 2.06591921004024 | epot = -20.8766751569445 | etot = -16.4362628892431 -856000 ekin = 2.52589522695461 | erot = 2.75200317380097 | epot = -20.7810899349363 | etot = -15.5031915341808 -857000 ekin = 2.56479713152188 | erot = 3.03132159965742 | epot = -20.6741126728545 | etot = -15.0779939416752 -858000 ekin = 3.12600431259895 | erot = 2.14307227855762 | epot = -20.6236416669373 | etot = -15.3545650757807 -859000 ekin = 2.91606538598306 | erot = 2.23743055034025 | epot = -20.6462917973092 | etot = -15.4927958609859 -860000 ekin = 2.88632968266491 | erot = 1.51779320350218 | epot = -20.6690491266306 | etot = -16.2649262404636 -861000 ekin = 2.33646237335095 | erot = 2.84993579191977 | epot = -20.6662989350089 | etot = -15.4799007697382 -862000 ekin = 3.06142360843216 | erot = 1.86714994928413 | epot = -20.7124901286986 | etot = -15.7839165709823 -863000 ekin = 2.88328806598044 | erot = 1.77603258370269 | epot = -20.8185427296306 | etot = -16.1592220799475 -864000 ekin = 2.96121160100481 | erot = 2.65074453444238 | epot = -21.0023810054863 | etot = -15.3904248700391 -865000 ekin = 3.32435720931815 | erot = 2.24357551683278 | epot = -21.1325456190927 | etot = -15.5646128929418 -866000 ekin = 2.85046827088543 | erot = 3.16864534840895 | epot = -21.2188104480758 | etot = -15.1996968287815 -867000 ekin = 2.74121981057393 | erot = 3.09690590629766 | epot = -21.2063169983776 | etot = -15.368191281506 -868000 ekin = 2.19317218320696 | erot = 2.23855212764239 | epot = -21.1598851105383 | etot = -16.728160799689 -869000 ekin = 2.92776187579401 | erot = 2.49696120772198 | epot = -21.1055152241549 | etot = -15.6807921406389 -870000 ekin = 2.48025968092564 | erot = 2.11893759578989 | epot = -21.0847323271701 | etot = -16.4855350504546 -871000 ekin = 2.1845388948614 | erot = 2.3744484320603 | epot = -20.9752554539106 | etot = -16.4162681269889 -872000 ekin = 1.52991727300488 | erot = 2.08936497511662 | epot = -20.9296773909044 | etot = -17.3103951427829 -873000 ekin = 1.39436098333864 | erot = 2.29076078630038 | epot = -20.9970902403712 | etot = -17.3119684707321 -874000 ekin = 1.40847516007258 | erot = 2.77014925513763 | epot = -21.1567852435976 | etot = -16.9781608283874 -875000 ekin = 1.18430169865448 | erot = 2.73096315540972 | epot = -21.2931389111423 | etot = -17.377874057078 -876000 ekin = 1.83112091845917 | erot = 2.99592495330209 | epot = -21.3275375070725 | etot = -16.5004916353113 -877000 ekin = 2.38101871692681 | erot = 2.03701942732192 | epot = -21.413314709608 | etot = -16.9952765653592 -878000 ekin = 2.13057677670605 | erot = 1.75664755774656 | epot = -21.4109592588752 | etot = -17.5237349244226 -879000 ekin = 2.23974599078717 | erot = 2.71277945678049 | epot = -21.3991125430578 | etot = -16.4465870954902 -880000 ekin = 2.68276925988414 | erot = 2.78419511289156 | epot = -21.4451599851349 | etot = -15.9781956123593 -881000 ekin = 2.86954422987714 | erot = 2.35934309050243 | epot = -21.4304898157632 | etot = -16.2016024953836 -882000 ekin = 2.33322673498713 | erot = 2.17176089427924 | epot = -21.3686767563163 | etot = -16.8636891270499 -883000 ekin = 2.36505939156363 | erot = 1.97542469807282 | epot = -21.1740561038168 | etot = -16.8335720141804 -884000 ekin = 2.53970453736975 | erot = 2.25146966956772 | epot = -21.0784914585951 | etot = -16.2873172516576 -885000 ekin = 2.86113216999841 | erot = 2.27428598539185 | epot = -21.0769714000078 | etot = -15.9415532446176 -886000 ekin = 3.16926259480325 | erot = 1.7479502049347 | epot = -21.1261039292057 | etot = -16.2088911294677 -887000 ekin = 2.66032303732719 | erot = 2.49430923572929 | epot = -21.1888853902954 | etot = -16.0342531172389 -888000 ekin = 2.14251397925541 | erot = 2.83067746317048 | epot = -21.2727723297671 | etot = -16.2995808873412 -889000 ekin = 2.13717501491483 | erot = 2.20010872789046 | epot = -21.1879846015514 | etot = -16.8507008587461 -890000 ekin = 1.76445604927834 | erot = 2.97270674684479 | epot = -21.249043049208 | etot = -16.5118802530849 -891000 ekin = 1.64410761916635 | erot = 2.28011654490668 | epot = -21.3725568550826 | etot = -17.4483326910096 -892000 ekin = 1.9736849956493 | erot = 2.35977031841883 | epot = -21.5165660475445 | etot = -17.1831107334764 -893000 ekin = 1.78063715284303 | erot = 1.84016145583949 | epot = -21.5929324441233 | etot = -17.9721338354408 -894000 ekin = 2.80890536765195 | erot = 2.8033716212873 | epot = -21.68691302035 | etot = -16.0746360314107 -895000 ekin = 2.03615797288147 | erot = 2.73640459758099 | epot = -21.7733873211515 | etot = -17.000824750689 -896000 ekin = 1.66692759050852 | erot = 2.55822798781453 | epot = -21.9049846669574 | etot = -17.6798290886343 -897000 ekin = 1.79224531734011 | erot = 2.35948275762719 | epot = -22.0434422253312 | etot = -17.8917141503639 -898000 ekin = 1.83919553961872 | erot = 2.41642222286753 | epot = -22.0758336371865 | etot = -17.8202158747002 -899000 ekin = 1.6636071320686 | erot = 3.06317427040907 | epot = -22.0015388871688 | etot = -17.2747574846912 -900000 ekin = 2.15282039168693 | erot = 2.62540512899952 | epot = -21.9732889613479 | etot = -17.1950634406614 -901000 ekin = 2.43388685834711 | erot = 2.69648861895498 | epot = -22.0420272097224 | etot = -16.9116517324203 -902000 ekin = 2.58083086140289 | erot = 2.40599679938446 | epot = -22.0470185105966 | etot = -17.0601908498092 -903000 ekin = 2.38921046669397 | erot = 2.40351321660547 | epot = -22.0515567722576 | etot = -17.2588330889581 -904000 ekin = 1.99826824339051 | erot = 3.15684651679006 | epot = -22.0749158572968 | etot = -16.9198010971163 -905000 ekin = 2.28113475313044 | erot = 2.2074638316632 | epot = -22.0890181666858 | etot = -17.6004195818921 -906000 ekin = 2.49879330353343 | erot = 1.671102945257 | epot = -22.0615337836095 | etot = -17.8916375348191 -907000 ekin = 2.34107735293828 | erot = 2.16848534916945 | epot = -21.914392426319 | etot = -17.4048297242112 -908000 ekin = 2.83000120831929 | erot = 2.3920412129948 | epot = -21.9351986192177 | etot = -16.7131561979036 -909000 ekin = 3.13472288974739 | erot = 2.07022420849154 | epot = -22.0395372123877 | etot = -16.8345901141488 -910000 ekin = 2.91535724615619 | erot = 3.54296427198744 | epot = -22.17289784711 | etot = -15.7145763289663 -911000 ekin = 1.86266697685629 | erot = 2.75432454240692 | epot = -22.2277400981541 | etot = -17.6107485788909 -912000 ekin = 2.64271590958795 | erot = 1.86909048050939 | epot = -22.2775010562684 | etot = -17.7656946661711 -913000 ekin = 2.45835510175704 | erot = 2.03340616362699 | epot = -22.4008109136254 | etot = -17.9090496482413 -914000 ekin = 2.0168446739852 | erot = 3.01916202272043 | epot = -22.5013367548475 | etot = -17.4653300581419 -915000 ekin = 2.73687318093231 | erot = 2.14033624631652 | epot = -22.5028600755747 | etot = -17.6256506483259 -916000 ekin = 2.38979306224022 | erot = 3.26197451659129 | epot = -22.5263162174438 | etot = -16.8745486386123 -917000 ekin = 2.2132313431686 | erot = 2.24407516775212 | epot = -22.5139668518706 | etot = -18.0566603409499 -918000 ekin = 2.11835073964575 | erot = 2.05693480392619 | epot = -22.4455228128791 | etot = -18.2702372693072 -919000 ekin = 2.66229415880118 | erot = 2.41897705108102 | epot = -22.4796981911192 | etot = -17.398426981237 -920000 ekin = 3.26579644340034 | erot = 2.75572713099831 | epot = -22.5844984666348 | etot = -16.5629748922361 -921000 ekin = 2.7209745531417 | erot = 1.96979925725472 | epot = -22.6385112107694 | etot = -17.9477374003729 -922000 ekin = 1.43413709665673 | erot = 1.52452785259238 | epot = -22.6908688613181 | etot = -19.732203912069 -923000 ekin = 1.67612014861287 | erot = 1.86533200287241 | epot = -22.7504417888943 | etot = -19.208989637409 -924000 ekin = 2.14999846366944 | erot = 1.53353223685726 | epot = -22.7219152384023 | etot = -19.0383845378756 -925000 ekin = 2.27775999892995 | erot = 1.35579588948189 | epot = -22.6313109881577 | etot = -18.9977550997459 -926000 ekin = 2.00325654671082 | erot = 2.07129795862533 | epot = -22.58060449698 | etot = -18.5060499916438 -927000 ekin = 2.51568207758562 | erot = 1.987163454037 | epot = -22.6950313207983 | etot = -18.1921857891757 -928000 ekin = 2.57430073568282 | erot = 2.51446833506414 | epot = -22.8476882631099 | etot = -17.758919192363 -929000 ekin = 2.65883432741931 | erot = 1.82970870115209 | epot = -22.8881462617914 | etot = -18.39960323322 -930000 ekin = 2.41679914385681 | erot = 2.00959752598338 | epot = -22.9005208742364 | etot = -18.4741242043962 -931000 ekin = 3.01841254462055 | erot = 2.11105138843169 | epot = -22.85760539327 | etot = -17.7281414602178 -932000 ekin = 2.34886657046774 | erot = 1.87108210439136 | epot = -22.8977129515892 | etot = -18.6777642767301 -933000 ekin = 2.16783340111898 | erot = 2.83769256871394 | epot = -22.9046776672478 | etot = -17.8991516974149 -934000 ekin = 2.17397600879036 | erot = 2.11893010896207 | epot = -22.9246315138634 | etot = -18.6317253961109 -935000 ekin = 2.35368321763723 | erot = 2.22721731703674 | epot = -22.9148844830612 | etot = -18.3339839483873 -936000 ekin = 2.29404484064883 | erot = 2.52125059394418 | epot = -23.022569346399 | etot = -18.207273911806 -937000 ekin = 2.32419482855967 | erot = 2.82559362345603 | epot = -23.1106534424293 | etot = -17.9608649904136 -938000 ekin = 2.46214257103075 | erot = 1.99597995904795 | epot = -23.1662772746363 | etot = -18.7081547445576 -939000 ekin = 2.9950708934893 | erot = 2.11187711132299 | epot = -23.1593663275129 | etot = -18.0524183227006 -940000 ekin = 3.76806392301913 | erot = 2.67914085708954 | epot = -23.0990741275282 | etot = -16.6518693474195 -941000 ekin = 3.15122194022389 | erot = 2.26598106832925 | epot = -23.0009732777347 | etot = -17.5837702691815 -942000 ekin = 3.50290237899686 | erot = 1.88389191282622 | epot = -22.9638174755667 | etot = -17.5770231837436 -943000 ekin = 3.81981007949588 | erot = 2.71306651628128 | epot = -22.9368745682733 | etot = -16.4039979724962 -944000 ekin = 2.68269000609243 | erot = 2.75597297355549 | epot = -22.9154634627924 | etot = -17.4768004831445 -945000 ekin = 2.5590549123222 | erot = 2.02762890141183 | epot = -22.8197752815545 | etot = -18.2330914678205 -946000 ekin = 2.47577141445405 | erot = 1.66876676951813 | epot = -22.6553996443486 | etot = -18.5108614603764 -947000 ekin = 2.41888872017238 | erot = 1.99290495105536 | epot = -22.5511355353761 | etot = -18.1393418641484 -948000 ekin = 3.55059459316711 | erot = 2.5777258708839 | epot = -22.4076841605954 | etot = -16.2793636965444 -949000 ekin = 2.98580100349108 | erot = 2.44218887595664 | epot = -22.1946740482762 | etot = -16.7666841688284 -950000 ekin = 1.821092375385 | erot = 3.05085494375851 | epot = -22.0411048551924 | etot = -17.1691575360489 -951000 ekin = 2.20017865970828 | erot = 2.37993346919584 | epot = -22.0148953004748 | etot = -17.4347831715707 -952000 ekin = 2.14109063574403 | erot = 1.67049478035644 | epot = -21.9849308950116 | etot = -18.1733454789111 -953000 ekin = 2.29825441833299 | erot = 1.97339930829895 | epot = -21.9506588951235 | etot = -17.6790051684915 -954000 ekin = 1.48812561465813 | erot = 3.35693562507496 | epot = -21.8785232616716 | etot = -17.0334620219385 -955000 ekin = 1.87464515912864 | erot = 2.65909319571748 | epot = -21.7892398748208 | etot = -17.2555015199747 -956000 ekin = 1.69455812204129 | erot = 2.15407102211541 | epot = -21.7240315558968 | etot = -17.8754024117401 -957000 ekin = 1.75583683783662 | erot = 1.6388872433372 | epot = -21.6978461721406 | etot = -18.3031220909668 -958000 ekin = 1.59915972681971 | erot = 2.20119347000054 | epot = -21.6996739320855 | etot = -17.8993207352653 -959000 ekin = 2.58508771526968 | erot = 2.48988894190743 | epot = -21.7128779048797 | etot = -16.6379012477026 -960000 ekin = 2.540004730569 | erot = 2.05993270952562 | epot = -21.7110863197264 | etot = -17.1111488796318 -961000 ekin = 2.28366644951083 | erot = 2.18351789869055 | epot = -21.713158341698 | etot = -17.2459739934967 -962000 ekin = 1.65566986683003 | erot = 3.51395446298371 | epot = -21.7309544663205 | etot = -16.5613301365068 -963000 ekin = 1.99640145079979 | erot = 1.50119578271615 | epot = -21.6827600497459 | etot = -18.1851628162299 -964000 ekin = 2.18656047252606 | erot = 2.27602589879665 | epot = -21.619418671686 | etot = -17.1568323003632 -965000 ekin = 2.1268740717332 | erot = 2.31151575363264 | epot = -21.6000680375134 | etot = -17.1616782121475 -966000 ekin = 3.18082053219097 | erot = 3.42475965115333 | epot = -21.6366484152857 | etot = -15.0310682319414 -967000 ekin = 3.07307267752021 | erot = 2.17494665586724 | epot = -21.5935818966499 | etot = -16.3455625632625 -968000 ekin = 2.08693319857779 | erot = 2.13995709056182 | epot = -21.5217214507964 | etot = -17.2948311616568 -969000 ekin = 2.26980017693321 | erot = 2.21816244485338 | epot = -21.459599392786 | etot = -16.9716367709994 -970000 ekin = 2.49153424363058 | erot = 2.62081062789337 | epot = -21.40624254365 | etot = -16.2938976721261 -971000 ekin = 2.49736294038618 | erot = 2.64542889712536 | epot = -21.3698430243897 | etot = -16.2270511868781 -972000 ekin = 3.20661406309987 | erot = 2.47006567711245 | epot = -21.3129147000401 | etot = -15.6362349598278 -973000 ekin = 3.35896769012794 | erot = 2.62914966754124 | epot = -21.2417754090084 | etot = -15.2536580513392 -974000 ekin = 2.71022162422346 | erot = 2.13950356822279 | epot = -21.1388622732984 | etot = -16.2891370808522 -975000 ekin = 1.81145289576367 | erot = 2.10207160993305 | epot = -21.048316338461 | etot = -17.1347918327643 -976000 ekin = 2.36964932252015 | erot = 1.38498778652618 | epot = -20.9787405486735 | etot = -17.2241034396272 -977000 ekin = 2.83743084482057 | erot = 3.02979079274331 | epot = -21.085451075555 | etot = -15.2182294379911 -978000 ekin = 3.14246219320392 | erot = 3.02811722693053 | epot = -21.1396703506934 | etot = -14.969090930559 -979000 ekin = 3.63780420393836 | erot = 2.4709378582899 | epot = -21.0340146720458 | etot = -14.9252726098175 -980000 ekin = 3.4264538226183 | erot = 3.24172784300214 | epot = -20.9599326810307 | etot = -14.2917510154103 -981000 ekin = 2.92833128833528 | erot = 2.44513741300221 | epot = -20.9990853641094 | etot = -15.6256166627719 -982000 ekin = 2.04564757644964 | erot = 2.21309407620317 | epot = -21.0169476544784 | etot = -16.7582060018256 -983000 ekin = 2.56027499325037 | erot = 1.98413314848097 | epot = -21.0051531932236 | etot = -16.4607450514922 -984000 ekin = 2.31412219695426 | erot = 2.58580887186898 | epot = -21.052483194614 | etot = -16.1525521257907 -985000 ekin = 2.31684810453689 | erot = 2.99962688680855 | epot = -21.126448512153 | etot = -15.8099735208075 -986000 ekin = 2.05087446711593 | erot = 2.15350712572991 | epot = -21.2175956679764 | etot = -17.0132140751306 -987000 ekin = 2.41884444903816 | erot = 1.58397554578725 | epot = -21.1898165062925 | etot = -17.1869965114671 -988000 ekin = 2.75120862227721 | erot = 2.70488585059706 | epot = -21.0891793464809 | etot = -15.6330848736066 -989000 ekin = 2.29399073499349 | erot = 2.85653684714667 | epot = -21.0165729755105 | etot = -15.8660453933703 -990000 ekin = 2.23407391829561 | erot = 2.58986750499253 | epot = -20.9399219780894 | etot = -16.1159805548012 -991000 ekin = 2.2015103509351 | erot = 2.5342789733714 | epot = -20.8272027181399 | etot = -16.0914133938334 -992000 ekin = 1.73506355750681 | erot = 2.49729588452318 | epot = -20.8968748041567 | etot = -16.6645153621267 -993000 ekin = 1.38873426581537 | erot = 1.9682630505033 | epot = -20.9926737588933 | etot = -17.6356764425747 -994000 ekin = 1.48976906105183 | erot = 2.95631655181474 | epot = -21.0595774450851 | etot = -16.6134918322185 -995000 ekin = 2.31357533477074 | erot = 1.67477965585528 | epot = -21.1250456439671 | etot = -17.1366906533411 -996000 ekin = 2.89740155011607 | erot = 2.85049856858161 | epot = -21.0862990854291 | etot = -15.3383989667315 -997000 ekin = 3.12971523768954 | erot = 2.1499509854011 | epot = -21.0771189403087 | etot = -15.7974527172181 -998000 ekin = 2.21576875556996 | erot = 3.03006905150276 | epot = -20.9969954660947 | etot = -15.751157659022 -999000 ekin = 2.60947248329622 | erot = 1.73825748506686 | epot = -20.9115307542595 | etot = -16.5638007858964 -1000000 ekin = 2.32273923275077 | erot = 2.87793771079159 | epot = -20.9050993315882 | etot = -15.7044223880458 - 1000000 0.10323285 -1.3567017 0.050132958 -1.1613975 0.00013807094 -Loop time of 30.2805 on 4 procs for 1000000 steps with 16 atoms - -Performance: 28533.226 tau/day, 33024.567 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.57156 | 10.489 | 19.648 | 266.3 | 34.64 -Bond | 0.087018 | 0.38344 | 0.65455 | 40.7 | 1.27 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.5429 | 2.6691 | 2.7875 | 5.4 | 8.81 -Output | 1.5e-05 | 2.425e-05 | 2.8e-05 | 0.0 | 0.00 -Modify | 0.2134 | 2.6942 | 5.1397 | 131.4 | 8.90 -Other | | 14.05 | | | 46.38 - -Nlocal: 4.0 ave 8.0 max 0.0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 11.0 ave 14.0 max 8.0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 35.5 ave 69.0 max 0.0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 142 -Ave neighs/atom = 8.875 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:30 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 deleted file mode 100644 index 0ef671c603..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 +++ /dev/null @@ -1,73 +0,0 @@ -# LAMMPS data file -10 atoms -10 ellipsoids -8 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -Masses - -1 3.1575 -2 3.1575 -3 3.1575 -4 3.1575 - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 -3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 -4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 -5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 -6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1 -7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1 -8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1 -9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1 -10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1 - -# Atom-ID, translational velocity, angular momentum -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 6 7 -6 1 7 8 -7 1 8 9 -8 1 9 10 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 deleted file mode 100644 index 25cbf1e8a3..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 +++ /dev/null @@ -1,1182 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.003 seconds - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA2 bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA2 pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274048 - ghost atom cutoff = 2.6274048 - binsize = 1.3137024, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -14.6175140343334 | etot = -14.6175140343334 -Per MPI rank memory allocation (min/avg/max) = 8.021 | 8.021 | 8.021 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06 -1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342 -2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675 -3000 ekin = 0.00995035259649285 | erot = 0.0381961780846484 | epot = -14.6656605650904 | etot = -14.6175140344093 -4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659 -5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355 -6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157 -7000 ekin = 0.0483200640564843 | erot = 0.192565862515508 | epot = -14.8583999612756 | etot = -14.6175140347036 -8000 ekin = 0.0604312317605998 | erot = 0.244417870131508 | epot = -14.9223631366883 | etot = -14.6175140347962 -9000 ekin = 0.0727907119671751 | erot = 0.299521949931839 | epot = -14.989826696789 | etot = -14.6175140348899 -10000 ekin = 0.0850022498875221 | erot = 0.356777997217902 | epot = -15.0592942820869 | etot = -14.6175140349815 -11000 ekin = 0.0966857134041704 | erot = 0.415102860829614 | epot = -15.1293026093013 | etot = -14.6175140350675 -12000 ekin = 0.107492790688446 | erot = 0.473466334178045 | epot = -15.1984731600115 | etot = -14.617514035145 -13000 ekin = 0.117121180381715 | erot = 0.530923485009724 | epot = -15.2655587006029 | etot = -14.6175140352115 -14000 ekin = 0.125326348459166 | erot = 0.586641324447693 | epot = -15.329481708172 | etot = -14.6175140352651 -15000 ekin = 0.131930017119452 | erot = 0.639918104234695 | epot = -15.389362156659 | etot = -14.6175140353048 -16000 ekin = 0.136824741331535 | erot = 0.690194029501056 | epot = -15.4445328061632 | etot = -14.6175140353306 -17000 ekin = 0.139974218116303 | erot = 0.73705286614779 | epot = -15.4945411196072 | etot = -14.6175140353432 -18000 ekin = 0.141409342139924 | erot = 0.780214750583505 | epot = -15.5391381280674 | etot = -14.617514035344 -19000 ekin = 0.14122042490348 | erot = 0.819521373491594 | epot = -15.5782558337303 | etot = -14.6175140353352 -20000 ekin = 0.139546371890615 | erot = 0.854915474127934 | epot = -15.6119758813378 | etot = -14.6175140353193 -21000 ekin = 0.136561897558623 | erot = 0.886417110947779 | epot = -15.6404930438051 | etot = -14.6175140352987 -22000 ekin = 0.132464002543739 | erot = 0.914099368829953 | epot = -15.6640774066495 | etot = -14.6175140352758 -23000 ekin = 0.127458921012922 | erot = 0.938065991541773 | epot = -15.6830389478072 | etot = -14.6175140352525 -24000 ekin = 0.121750582423385 | erot = 0.958432936326242 | epot = -15.6976975539802 | etot = -14.6175140352305 -25000 ekin = 0.115531361418989 | erot = 0.97531514293118 | epot = -15.7083605395609 | etot = -14.6175140352107 -26000 ekin = 0.108975565586104 | erot = 0.988819027952036 | epot = -15.7153086287315 | etot = -14.6175140351934 -27000 ekin = 0.102235785319049 | erot = 0.999040485514132 | epot = -15.7187903060115 | etot = -14.6175140351783 -28000 ekin = 0.095441943431881 | erot = 1.00606759140964 | epot = -15.7190235700066 | etot = -14.6175140351651 -29000 ekin = 0.0887026587343887 | erot = 1.00998681843601 | epot = -15.7162035123233 | etot = -14.6175140351529 -30000 ekin = 0.0821083868014372 | erot = 1.01089138149893 | epot = -15.7105138034411 | etot = -14.6175140351407 -31000 ekin = 0.0757357206087773 | erot = 1.00889031641317 | epot = -15.7021400721498 | etot = -14.6175140351278 -32000 ekin = 0.0696522149388972 | erot = 1.00411701389994 | epot = -15.691283263952 | etot = -14.6175140351132 -33000 ekin = 0.0639211300028632 | erot = 0.996736133735177 | epot = -15.6781712988344 | etot = -14.6175140350964 -34000 ekin = 0.0586055597939536 | erot = 0.986948071943124 | epot = -15.6630676668141 | etot = -14.617514035077 -35000 ekin = 0.0537715085519321 | erot = 0.97499041461744 | epot = -15.6462759582244 | etot = -14.617514035055 -36000 ekin = 0.0494895953264297 | erot = 0.961136064967259 | epot = -15.6281396953245 | etot = -14.6175140350308 -37000 ekin = 0.0458351949405726 | erot = 0.945687966086967 | epot = -15.6090371960325 | etot = -14.617514035005 -38000 ekin = 0.0428869588016531 | erot = 0.928970560852795 | epot = -15.5893715546332 | etot = -14.6175140349787 -39000 ekin = 0.0407237982122988 | erot = 0.9113183396798 | epot = -15.5695561728451 | etot = -14.617514034953 -40000 ekin = 0.0394205547754457 | erot = 0.893062038097747 | epot = -15.5499966278026 | etot = -14.6175140349294 -41000 ekin = 0.0390427256107104 | erot = 0.874513269990878 | epot = -15.5310700305109 | etot = -14.6175140349093 -42000 ekin = 0.0396407506458402 | erot = 0.855948622306271 | epot = -15.5131034078461 | etot = -14.617514034894 -43000 ekin = 0.0412444930542154 | erot = 0.837594480923697 | epot = -15.4963530088628 | etot = -14.6175140348849 -44000 ekin = 0.0438586280730372 | erot = 0.819614069272971 | epot = -15.4809867322287 | etot = -14.6175140348826 -45000 ekin = 0.0474596621516281 | erot = 0.802098297010783 | epot = -15.4670719940501 | etot = -14.6175140348877 -46000 ekin = 0.0519951857192148 | erot = 0.785061947877571 | epot = -15.4545711684965 | etot = -14.6175140348997 -47000 ekin = 0.0573856747191636 | erot = 0.76844639238657 | epot = -15.4433461020232 | etot = -14.6175140349174 -48000 ekin = 0.0635286843632004 | erot = 0.75212933501618 | epot = -15.433172054319 | etot = -14.6175140349396 -49000 ekin = 0.070304673538874 | erot = 0.735941123250837 | epot = -15.4237598317539 | etot = -14.6175140349642 -50000 ekin = 0.0775831019857076 | erot = 0.719686007781425 | epot = -15.4147831447563 | etot = -14.6175140349892 -51000 ekin = 0.0852270843845694 | erot = 0.703165726695028 | epot = -15.4059068460928 | etot = -14.6175140350132 -52000 ekin = 0.0930950223451647 | erot = 0.686202231166125 | epot = -15.396811288546 | etot = -14.6175140350347 -53000 ekin = 0.101038429252995 | erot = 0.668656546988927 | epot = -15.3872090112954 | etot = -14.6175140350535 -54000 ekin = 0.10889654098061 | erot = 0.650441726174306 | epot = -15.3768523022246 | etot = -14.6175140350697 -55000 ekin = 0.116489881626234 | erot = 0.631529329348001 | epot = -15.3655332460579 | etot = -14.6175140350836 -56000 ekin = 0.12361610349192 | erot = 0.611950383382611 | epot = -15.35308052197 | etot = -14.6175140350954 -57000 ekin = 0.130051530401153 | erot = 0.591792721317295 | epot = -15.3393582868232 | etot = -14.6175140351048 -58000 ekin = 0.135560625193501 | erot = 0.571196690673292 | epot = -15.3242713509773 | etot = -14.6175140351105 -59000 ekin = 0.139913350827135 | erot = 0.550350463180279 | epot = -15.307777849119 | etot = -14.6175140351115 -60000 ekin = 0.142907875045794 | erot = 0.529485019662529 | epot = -15.2899069298147 | etot = -14.6175140351063 -61000 ekin = 0.144394224777542 | erot = 0.508867904998907 | epot = -15.2707761648706 | etot = -14.6175140350941 -62000 ekin = 0.144294003785763 | erot = 0.488794507592477 | epot = -15.2506025464531 | etot = -14.6175140350748 -63000 ekin = 0.142612256998146 | erot = 0.469576039421557 | epot = -15.2297023314688 | etot = -14.6175140350491 -64000 ekin = 0.139439544726902 | erot = 0.45152434495459 | epot = -15.2084779247003 | etot = -14.6175140350188 -65000 ekin = 0.134944526553566 | erot = 0.434934714913839 | epot = -15.1873932764535 | etot = -14.6175140349861 -66000 ekin = 0.129359146358223 | erot = 0.420068607767106 | epot = -15.1669417890788 | etot = -14.6175140349535 -67000 ekin = 0.122959458764236 | erot = 0.407138362059705 | epot = -15.1476118557469 | etot = -14.617514034923 -68000 ekin = 0.116045210525559 | erot = 0.396295631876262 | epot = -15.1298548772986 | etot = -14.6175140348968 -69000 ekin = 0.108920722072365 | erot = 0.38762458997195 | epot = -15.1140593469202 | etot = -14.6175140348758 -70000 ekin = 0.101878740729572 | erot = 0.381140173640836 | epot = -15.1005329492313 | etot = -14.6175140348609 -71000 ekin = 0.0951880561484016 | erot = 0.376791007701538 | epot = -15.0894930987019 | etot = -14.617514034852 -72000 ekin = 0.0890849677261927 | erot = 0.374466237250371 | epot = -15.0810652398255 | etot = -14.6175140348489 -73000 ekin = 0.0837682427021612 | erot = 0.374005347599889 | epot = -15.0752876251531 | etot = -14.617514034851 -74000 ekin = 0.0793969849744096 | erot = 0.375210076750601 | epot = -15.0721210965825 | etot = -14.6175140348575 -75000 ekin = 0.0760907865069267 | erot = 0.377857644572265 | epot = -15.0714624659463 | etot = -14.6175140348671 -76000 ekin = 0.0739315834908328 | erot = 0.381714646755152 | epot = -15.0731602651247 | etot = -14.6175140348788 -77000 ekin = 0.0729667273608161 | erot = 0.386551032956121 | epot = -15.0770317952083 | etot = -14.6175140348914 -78000 ekin = 0.073212865507933 | erot = 0.392153586683229 | epot = -15.0828804870951 | etot = -14.617514034904 -79000 ekin = 0.074660287835072 | erot = 0.398338263929461 | epot = -15.09051258668 | etot = -14.6175140349155 -80000 ekin = 0.0772774298944847 | erot = 0.404960669863083 | epot = -15.0997521346826 | etot = -14.6175140349251 -81000 ekin = 0.0810152396746107 | erot = 0.411923913359048 | epot = -15.1104531879657 | etot = -14.617514034932 -82000 ekin = 0.0858111278279411 | erot = 0.419183131304986 | epot = -15.1225082940691 | etot = -14.6175140349362 -83000 ekin = 0.0915922459205373 | erot = 0.426746154030553 | epot = -15.1358524348887 | etot = -14.6175140349376 -84000 ekin = 0.0982778862653023 | erot = 0.434670094582779 | epot = -15.1504620157846 | etot = -14.6175140349365 -85000 ekin = 0.105780875252123 | erot = 0.443054055542032 | epot = -15.1663489657278 | etot = -14.6175140349337 -86000 ekin = 0.114007936320491 | erot = 0.452028591870552 | epot = -15.183550563121 | etot = -14.6175140349299 -87000 ekin = 0.122859117093021 | erot = 0.461742961599068 | epot = -15.2021161136185 | etot = -14.6175140349264 -88000 ekin = 0.132226490250365 | erot = 0.472351454260961 | epot = -15.2220919794351 | etot = -14.6175140349238 -89000 ekin = 0.14199243043518 | erot = 0.484000150228927 | epot = -15.2435066155872 | etot = -14.6175140349231 -90000 ekin = 0.152027823848745 | erot = 0.49681531383988 | epot = -15.2663571726137 | etot = -14.6175140349251 -91000 ekin = 0.162190574344125 | erot = 0.510894287760631 | epot = -15.2905988970349 | etot = -14.6175140349302 -92000 ekin = 0.172324730223241 | erot = 0.526299304076712 | epot = -15.3161380692387 | etot = -14.6175140349387 -93000 ekin = 0.182260479602514 | erot = 0.543054150883983 | epot = -15.342828665437 | etot = -14.6175140349505 -94000 ekin = 0.191815166424497 | erot = 0.561143224560487 | epot = -15.3704724259505 | etot = -14.6175140349655 -95000 ekin = 0.200795384589871 | erot = 0.580512230413669 | epot = -15.398821649987 | etot = -14.6175140349834 -96000 ekin = 0.209000133284301 | erot = 0.601069706845445 | epot = -15.4275838751336 | etot = -14.6175140350039 -97000 ekin = 0.216224974983076 | erot = 0.622688639933065 | epot = -15.4564276499427 | etot = -14.6175140350266 -98000 ekin = 0.222267131485452 | erot = 0.645207670246426 | epot = -15.4849888367829 | etot = -14.617514035051 -99000 ekin = 0.226931474008822 | erot = 0.668431711040234 | epot = -15.5128772201258 | etot = -14.6175140350768 -100000 ekin = 0.230037392185194 | erot = 0.692132125756912 | epot = -15.5396835530455 | etot = -14.6175140351034 -101000 ekin = 0.231426538774339 | erot = 0.716046886549487 | epot = -15.5649874604541 | etot = -14.6175140351302 -102000 ekin = 0.230971416186116 | erot = 0.739881303910906 | epot = -15.5883667552535 | etot = -14.6175140351565 -103000 ekin = 0.228584676860968 | erot = 0.763309953365433 | epot = -15.6094086654079 | etot = -14.6175140351815 -104000 ekin = 0.224228843046698 | erot = 0.785980326921886 | epot = -15.6277232051725 | etot = -14.6175140352039 -105000 ekin = 0.217925953180593 | erot = 0.807518535460022 | epot = -15.6429585238635 | etot = -14.6175140352229 -106000 ekin = 0.209766205881976 | erot = 0.827537066837565 | epot = -15.6548173079567 | etot = -14.6175140352372 -107000 ekin = 0.19991466311948 | erot = 0.845644346598459 | epot = -15.6630730449638 | etot = -14.6175140352459 -108000 ekin = 0.188614735691129 | erot = 0.861455562303715 | epot = -15.6675843332431 | etot = -14.6175140352483 -109000 ekin = 0.176187061061687 | erot = 0.874603999194433 | epot = -15.6683050955002 | etot = -14.6175140352441 -110000 ekin = 0.163022626611995 | erot = 0.88475208463374 | epot = -15.6652887464792 | etot = -14.6175140352335 -111000 ekin = 0.14956938211077 | erot = 0.89160140093568 | epot = -15.6586848182637 | etot = -14.6175140352173 -112000 ekin = 0.136312261124986 | erot = 0.8949011206007 | epot = -15.6487274169225 | etot = -14.6175140351968 -113000 ekin = 0.123747404857758 | erot = 0.894454602033368 | epot = -15.6357160420648 | etot = -14.6175140351736 -114000 ekin = 0.112352324429831 | erot = 0.890124196452667 | epot = -15.6199905560322 | etot = -14.6175140351497 -115000 ekin = 0.102554569787556 | erot = 0.881834585426713 | epot = -15.6019031903412 | etot = -14.6175140351269 -116000 ekin = 0.0947020047096738 | erot = 0.869575126614186 | epot = -15.5817911664307 | etot = -14.6175140351068 -117000 ekin = 0.0890378681937318 | erot = 0.853401690493949 | epot = -15.559953593778 | etot = -14.6175140350903 -118000 ekin = 0.0856833736308548 | erot = 0.833438318818926 | epot = -15.5366357275277 | etot = -14.6175140350779 -119000 ekin = 0.0846297171118248 | erot = 0.809878764032089 | epot = -15.5120225162133 | etot = -14.6175140350694 -120000 ekin = 0.0857402026936468 | erot = 0.782987649501416 | epot = -15.4862418872589 | etot = -14.6175140350638 -121000 ekin = 0.088761978164944 | erot = 0.753100709615785 | epot = -15.4593767228408 | etot = -14.61751403506 -122000 ekin = 0.0933458418336512 | erot = 0.720623403982127 | epot = -15.4314832808722 | etot = -14.6175140350564 -123000 ekin = 0.0990718975139699 | erot = 0.68602719834959 | epot = -15.4026131309152 | etot = -14.6175140350516 -124000 ekin = 0.105478567535099 | erot = 0.649842971567299 | epot = -15.3728355741467 | etot = -14.6175140350443 -125000 ekin = 0.112092583657528 | erot = 0.61265130691034 | epot = -15.3422579256011 | etot = -14.6175140350332 -126000 ekin = 0.118457948670349 | erot = 0.575069793125981 | epot = -15.3110417768144 | etot = -14.617514035018 -127000 ekin = 0.124162352097832 | erot = 0.537737821903371 | epot = -15.2794142089993 | etot = -14.6175140349981 -128000 ekin = 0.128860000475183 | erot = 0.501299660072983 | epot = -15.2476736955218 | etot = -14.6175140349736 -129000 ekin = 0.132290197681538 | erot = 0.466386755141783 | epot = -15.2161909877681 | etot = -14.6175140349448 -130000 ekin = 0.134291248323408 | erot = 0.433600287194685 | epot = -15.1854055704302 | etot = -14.6175140349121 -131000 ekin = 0.134809368079367 | erot = 0.403494917851113 | epot = -15.1558183208069 | etot = -14.6175140348764 -132000 ekin = 0.133902311413259 | erot = 0.376564532721602 | epot = -15.1279808789733 | etot = -14.6175140348385 -133000 ekin = 0.131737425950174 | erot = 0.353230559449875 | epot = -15.1024820201993 | etot = -14.6175140347993 -134000 ekin = 0.128583872250139 | erot = 0.333833200745338 | epot = -15.0799311077557 | etot = -14.6175140347602 -135000 ekin = 0.124798858319487 | erot = 0.31862567876175 | epot = -15.0609385718037 | etot = -14.6175140347224 -136000 ekin = 0.12080796695122 | erot = 0.307771366705934 | epot = -15.0460933683448 | etot = -14.6175140346877 -137000 ekin = 0.117080018573556 | erot = 0.301343503849859 | epot = -15.0359375570811 | etot = -14.6175140346577 -138000 ekin = 0.114097404451637 | erot = 0.299327064918768 | epot = -15.0309385040046 | etot = -14.6175140346342 -139000 ekin = 0.112323403877397 | erot = 0.301622293047273 | epot = -15.0314597315437 | etot = -14.6175140346191 -140000 ekin = 0.112168587317134 | erot = 0.308049410073558 | epot = -15.0377320320047 | etot = -14.617514034614 -141000 ekin = 0.113958896787483 | erot = 0.318354084563277 | epot = -15.0498270159712 | etot = -14.6175140346204 -142000 ekin = 0.117908250110044 | erot = 0.332213334114174 | epot = -15.0676356188633 | etot = -14.6175140346391 -143000 ekin = 0.124098500240116 | erot = 0.349241744868859 | epot = -15.0908542797794 | etot = -14.6175140346704 -144000 ekin = 0.132469049162244 | erot = 0.36899804234383 | epot = -15.1189811262199 | etot = -14.6175140347138 -145000 ekin = 0.142817534773294 | erot = 0.390992018433025 | epot = -15.1513235879745 | etot = -14.6175140347682 -146000 ekin = 0.154812002594044 | erot = 0.414692148538822 | epot = -15.1870181859643 | etot = -14.6175140348315 -147000 ekin = 0.168013608208165 | erot = 0.43953414756317 | epot = -15.2250617906724 | etot = -14.6175140349011 -148000 ekin = 0.181907755044192 | erot = 0.46493071599216 | epot = -15.2643525060103 | etot = -14.617514034974 -149000 ekin = 0.195940689918404 | erot = 0.490282644230507 | epot = -15.3037373691959 | etot = -14.6175140350469 -150000 ekin = 0.209558115498161 | erot = 0.514991307802203 | epot = -15.3420634584171 | etot = -14.6175140351168 -151000 ekin = 0.222242375358722 | erot = 0.538472447669863 | epot = -15.3782288582089 | etot = -14.6175140351803 -152000 ekin = 0.233545181100895 | erot = 0.560170967504241 | epot = -15.4112301838403 | etot = -14.6175140352351 -153000 ekin = 0.243113638171897 | erot = 0.579575715963473 | epot = -15.4402033894145 | etot = -14.6175140352791 -154000 ekin = 0.250708030719563 | erot = 0.596234520730074 | epot = -15.4644565867606 | etot = -14.617514035311 -155000 ekin = 0.256210874594961 | erot = 0.609768185048496 | epot = -15.4834930949732 | etot = -14.6175140353298 -156000 ekin = 0.259627463842806 | erot = 0.619882772314079 | epot = -15.4970242714923 | etot = -14.6175140353354 -157000 ekin = 0.26107875673392 | erot = 0.626379517381585 | epot = -15.5049723094438 | etot = -14.6175140353283 -158000 ekin = 0.260787877594978 | erot = 0.629161788909624 | epot = -15.5074637018139 | etot = -14.6175140353093 -159000 ekin = 0.259061752299553 | erot = 0.628238692725195 | epot = -15.5048144803046 | etot = -14.6175140352799 -160000 ekin = 0.256269476948141 | erot = 0.623725097357881 | epot = -15.4975086095477 | etot = -14.6175140352417 -161000 ekin = 0.252818974262866 | erot = 0.615838055765116 | epot = -15.4861710652245 | etot = -14.6175140351965 -162000 ekin = 0.249133354781009 | erot = 0.604889772114047 | epot = -15.4715371620415 | etot = -14.6175140351465 -163000 ekin = 0.245628201594233 | erot = 0.591277407066157 | epot = -15.4544196437542 | etot = -14.6175140350938 -164000 ekin = 0.242690765770646 | erot = 0.5754701254003 | epot = -15.4356749262112 | etot = -14.6175140350402 -165000 ekin = 0.240661818237773 | erot = 0.557993868664013 | epot = -15.4161697218898 | etot = -14.617514034988 -166000 ekin = 0.239820672159938 | erot = 0.539414388849556 | epot = -15.3967490959484 | etot = -14.6175140349389 -167000 ekin = 0.24037368261711 | erot = 0.520319112884873 | epot = -15.3782068303964 | etot = -14.6175140348944 -168000 ekin = 0.24244635767351 | erot = 0.501298426047331 | epot = -15.3612588185771 | etot = -14.6175140348562 -169000 ekin = 0.246079081489649 | erot = 0.482926967022199 | epot = -15.3465200833372 | etot = -14.6175140348253 -170000 ekin = 0.2512263556708 | erot = 0.465745518941327 | epot = -15.334485909415 | etot = -14.6175140348028 -171000 ekin = 0.257759407502687 | erot = 0.450244072412507 | epot = -15.3255175147045 | etot = -14.6175140347893 -172000 ekin = 0.265471962315305 | erot = 0.436846557572436 | epot = -15.3198325546728 | etot = -14.617514034785 -173000 ekin = 0.274088992052948 | erot = 0.425897760801831 | epot = -15.3175007876449 | etot = -14.6175140347901 -174000 ekin = 0.283278228108448 | erot = 0.417652965987037 | epot = -15.3184452288997 | etot = -14.6175140348042 -175000 ekin = 0.292664164217591 | erot = 0.412270652066437 | epot = -15.3224488511105 | etot = -14.6175140348264 -176000 ekin = 0.301844276744599 | erot = 0.409808663992694 | epot = -15.3291669755931 | etot = -14.6175140348558 -177000 ekin = 0.310407103278429 | erot = 0.410224178772685 | epot = -15.3381453169418 | etot = -14.6175140348907 -178000 ekin = 0.317951707449239 | erot = 0.413377690532346 | epot = -15.3488434329111 | etot = -14.6175140349295 -179000 ekin = 0.324107901132174 | erot = 0.419041092198358 | epot = -15.3606630283006 | etot = -14.6175140349701 -180000 ekin = 0.328556397749118 | erot = 0.426909726006353 | epot = -15.3729801587658 | etot = -14.6175140350103 -181000 ekin = 0.331047834154798 | erot = 0.436618006901549 | epot = -15.3851798761042 | etot = -14.6175140350478 -182000 ekin = 0.331419420115411 | erot = 0.447757936313848 | epot = -15.3966913915096 | etot = -14.6175140350804 -183000 ekin = 0.329607792338432 | erot = 0.459899520064776 | epot = -15.4070213475094 | etot = -14.6175140351062 -184000 ekin = 0.325656516855951 | erot = 0.472611792132538 | epot = -15.4157823441122 | etot = -14.6175140351237 -185000 ekin = 0.319716934488103 | erot = 0.485483030926984 | epot = -15.4227140005474 | etot = -14.6175140351323 -186000 ekin = 0.312041347783061 | erot = 0.498138700397667 | epot = -15.4276940833127 | etot = -14.6175140351319 -187000 ekin = 0.302968200961952 | erot = 0.510255791848641 | epot = -15.4307380279341 | etot = -14.6175140351235 -188000 ekin = 0.292899787357099 | erot = 0.521572552051206 | epot = -15.4319863745165 | etot = -14.6175140351082 -189000 ekin = 0.282274048056294 | erot = 0.531893031493142 | epot = -15.4316811146379 | etot = -14.6175140350885 -190000 ekin = 0.271533034589587 | erot = 0.541086413296707 | epot = -15.4301334829529 | etot = -14.6175140350666 -191000 ekin = 0.261091384545769 | erot = 0.54908161018572 | epot = -15.4276870297764 | etot = -14.6175140350449 -192000 ekin = 0.251308489708551 | erot = 0.555858063434352 | epot = -15.4246805881686 | etot = -14.6175140350257 -193000 ekin = 0.242467771120031 | erot = 0.561433978654736 | epot = -15.4214157847852 | etot = -14.6175140350104 -194000 ekin = 0.2347655816246 | erot = 0.565853352187793 | epot = -15.4181329688123 | etot = -14.6175140349999 -195000 ekin = 0.228310848061445 | erot = 0.569173077812631 | epot = -15.4149979608682 | etot = -14.6175140349941 -196000 ekin = 0.223134890550306 | erot = 0.57145120860725 | epot = -15.4121001341502 | etot = -14.6175140349926 -197000 ekin = 0.219209242156003 | erot = 0.572737138233763 | epot = -15.409460415384 | etot = -14.6175140349943 -198000 ekin = 0.216468062809104 | erot = 0.573064123808166 | epot = -15.4070462216152 | etot = -14.6175140349979 -199000 ekin = 0.214831137522652 | erot = 0.572444258403913 | epot = -15.4047894309289 | etot = -14.6175140350023 -200000 ekin = 0.214223573902254 | erot = 0.57086576066316 | epot = -15.4026033695722 | etot = -14.6175140350067 -201000 ekin = 0.214589119166907 | erot = 0.568292309386801 | epot = -15.4003954635645 | etot = -14.6175140350107 -202000 ekin = 0.215895325602457 | erot = 0.564664121433424 | epot = -15.3980734820503 | etot = -14.6175140350145 -203000 ekin = 0.218130347570136 | erot = 0.559900543318492 | epot = -15.395544925907 | etot = -14.6175140350184 -204000 ekin = 0.221292667473869 | erot = 0.553904074217835 | epot = -15.3927107767149 | etot = -14.6175140350232 -205000 ekin = 0.225376258610798 | erot = 0.546565915588112 | epot = -15.3894562092286 | etot = -14.6175140350297 -206000 ekin = 0.230354397529151 | erot = 0.537773288683187 | epot = -15.3856417212507 | etot = -14.6175140350384 -207000 ekin = 0.236165428414771 | erot = 0.527418806929786 | epot = -15.3810982703936 | etot = -14.617514035049 -208000 ekin = 0.242703261860427 | erot = 0.515412077175151 | epot = -15.3756293740966 | etot = -14.617514035061 -209000 ekin = 0.249814382550021 | erot = 0.501693407691568 | epot = -15.3690218253148 | etot = -14.6175140350732 -210000 ekin = 0.257301864855649 | erot = 0.486249049965564 | epot = -15.361064949905 | etot = -14.6175140350838 -211000 ekin = 0.264935635394273 | erot = 0.469126912720557 | epot = -15.3515765832057 | etot = -14.6175140350909 -212000 ekin = 0.272467183646406 | erot = 0.450451153648061 | epot = -15.3404323723872 | etot = -14.6175140350927 -213000 ekin = 0.279646306736793 | erot = 0.430433702677846 | epot = -15.3275940445023 | etot = -14.6175140350876 -214000 ekin = 0.286237611276688 | erot = 0.409381288017783 | epot = -15.3131329343691 | etot = -14.6175140350746 -215000 ekin = 0.292034643872632 | erot = 0.387696263734527 | epot = -15.2972449426606 | etot = -14.6175140350534 -216000 ekin = 0.296870258152624 | erot = 0.365870567411729 | epot = -15.2802548605889 | etot = -14.6175140350245 -217000 ekin = 0.300622666324868 | erot = 0.344472695102956 | epot = -15.2626093964168 | etot = -14.617514034989 -218000 ekin = 0.303217269541043 | erot = 0.324128407398458 | epot = -15.2448597118882 | etot = -14.6175140349487 -219000 ekin = 0.304624843911682 | erot = 0.305496496152239 | epot = -15.2276353749694 | etot = -14.6175140349055 -220000 ekin = 0.304856982073792 | erot = 0.289241221676068 | epot = -15.2116122386118 | etot = -14.6175140348619 -221000 ekin = 0.303959749544065 | erot = 0.276003133762455 | epot = -15.1974769181266 | etot = -14.61751403482 -222000 ekin = 0.302006434070655 | erot = 0.266369862265548 | epot = -15.1858903311184 | etot = -14.6175140347822 -223000 ekin = 0.299090105490396 | erot = 0.260848208954625 | epot = -15.1774523491954 | etot = -14.6175140347503 -224000 ekin = 0.29531650374511 | erot = 0.259838588557332 | epot = -15.1726691270288 | etot = -14.6175140347264 -225000 ekin = 0.290797600317434 | erot = 0.263612591735795 | epot = -15.1719242267649 | etot = -14.6175140347117 -226000 ekin = 0.285646103232653 | erot = 0.272294318080247 | epot = -15.1754544560203 | etot = -14.6175140347074 -227000 ekin = 0.279971018689074 | erot = 0.285846075011501 | epot = -15.1833311284151 | etot = -14.6175140347145 -228000 ekin = 0.273874374727583 | erot = 0.304059069119542 | epot = -15.1954474785804 | etot = -14.6175140347333 -229000 ekin = 0.267449174159942 | erot = 0.326549807965912 | epot = -15.2115130168895 | etot = -14.6175140347636 -230000 ekin = 0.260778614118952 | erot = 0.352763004039877 | epot = -15.2310556529637 | etot = -14.6175140348048 -231000 ekin = 0.253936564976955 | erot = 0.381981763344646 | epot = -15.2534323631772 | etot = -14.6175140348556 -232000 ekin = 0.24698923084228 | erot = 0.413345683736504 | epot = -15.2778489494931 | etot = -14.6175140349143 -233000 ekin = 0.239997814735683 | erot = 0.445877135783545 | epot = -15.3033889854978 | etot = -14.6175140349785 -234000 ekin = 0.233021891669698 | erot = 0.478515439398703 | epot = -15.3290513661138 | etot = -14.6175140350454 -235000 ekin = 0.226123071286244 | erot = 0.510157919201248 | epot = -15.3537950255994 | etot = -14.6175140351119 -236000 ekin = 0.219368436952614 | erot = 0.539706010633753 | epot = -15.3765884827609 | etot = -14.6175140351745 -237000 ekin = 0.212833212708479 | erot = 0.566113832023268 | epot = -15.3964610799618 | etot = -14.6175140352301 -238000 ekin = 0.206602165162757 | erot = 0.588436180449468 | epot = -15.412552380888 | etot = -14.6175140352757 -239000 ekin = 0.200769360307635 | erot = 0.605872583258753 | epot = -15.4241559788757 | etot = -14.6175140353093 -240000 ekin = 0.195436190928488 | erot = 0.617803458378408 | epot = -15.4307536846362 | etot = -14.6175140353293 -241000 ekin = 0.190707920284559 | erot = 0.623817360381655 | epot = -15.4320393160013 | etot = -14.6175140353351 -242000 ekin = 0.186689132523883 | erot = 0.623726737660644 | epot = -15.4279299055112 | etot = -14.6175140353267 -243000 ekin = 0.18347888087463 | erot = 0.61757185737741 | epot = -15.418564773557 | etot = -14.617514035305 -244000 ekin = 0.181166166759762 | erot = 0.60561292371356 | epot = -15.4042931257446 | etot = -14.6175140352713 -245000 ekin = 0.179826690515581 | erot = 0.588311983398978 | epot = -15.3856527091421 | etot = -14.6175140352276 -246000 ekin = 0.179521473344392 | erot = 0.566306329740652 | epot = -15.3633418382609 | etot = -14.6175140351758 -247000 ekin = 0.180297726608685 | erot = 0.54037552872489 | epot = -15.3381872904519 | etot = -14.6175140351184 -248000 ekin = 0.182192022180427 | erot = 0.511404282992934 | epot = -15.3111103402306 | etot = -14.6175140350572 -249000 ekin = 0.185235475058219 | erot = 0.480343275338998 | epot = -15.2830927853917 | etot = -14.6175140349945 -250000 ekin = 0.18946032457762 | erot = 0.448169956263045 | epot = -15.2551443157728 | etot = -14.6175140349321 -251000 ekin = 0.194907020011059 | erot = 0.415851007133659 | epot = -15.2282720620165 | etot = -14.6175140348718 -252000 ekin = 0.201630699422451 | erot = 0.384307951122869 | epot = -15.2034526853603 | etot = -14.617514034815 -253000 ekin = 0.209705815254746 | erot = 0.354387113740477 | epot = -15.1816069637584 | etot = -14.6175140347632 -254000 ekin = 0.219227629545986 | erot = 0.326834860919931 | epot = -15.1635765251836 | etot = -14.6175140347177 -255000 ekin = 0.230309407956005 | erot = 0.302278768995696 | epot = -15.1501022116313 | etot = -14.6175140346796 -256000 ekin = 0.243074422920893 | erot = 0.281215109558497 | epot = -15.1418035671295 | etot = -14.6175140346501 -257000 ekin = 0.257642364628865 | erot = 0.264002762945737 | epot = -15.139159162205 | etot = -14.6175140346304 -258000 ekin = 0.274110461102935 | erot = 0.250863404057276 | epot = -15.1424878997817 | etot = -14.6175140346215 -259000 ekin = 0.292530483428745 | erot = 0.241887528332562 | epot = -15.1519320463858 | etot = -14.6175140346245 -260000 ekin = 0.312883750214262 | erot = 0.237045600990929 | epot = -15.167443385845 | etot = -14.6175140346398 -261000 ekin = 0.335057071665646 | erot = 0.23620332462488 | epot = -15.1887744309582 | etot = -14.6175140346677 -262000 ekin = 0.358823075932977 | erot = 0.239139750883904 | epot = -15.2154768615246 | etot = -14.6175140347077 -263000 ekin = 0.383828346058697 | erot = 0.24556675356939 | epot = -15.2469091343868 | etot = -14.6175140347588 -264000 ekin = 0.409592161639846 | erot = 0.25514829095879 | epot = -15.2822544874178 | etot = -14.6175140348192 -265000 ekin = 0.435517425641053 | erot = 0.267517972446926 | epot = -15.3205494329745 | etot = -14.6175140348865 -266000 ekin = 0.460913759434934 | erot = 0.28229374222826 | epot = -15.3607215366211 | etot = -14.6175140349579 -267000 ekin = 0.485031075314244 | erot = 0.299088986461549 | epot = -15.4016340968062 | etot = -14.6175140350304 -268000 ekin = 0.507100517474285 | erot = 0.317519986657596 | epot = -15.4421345392328 | etot = -14.6175140351009 -269000 ekin = 0.526378761164296 | erot = 0.337210258004039 | epot = -15.4811030543346 | etot = -14.6175140351662 -270000 ekin = 0.542191399558024 | erot = 0.357792786171182 | epot = -15.5174982209533 | etot = -14.6175140352241 -271000 ekin = 0.55397150127625 | erot = 0.378911394713957 | epot = -15.5503969312626 | etot = -14.6175140352724 -272000 ekin = 0.561290243477908 | erot = 0.400222387434508 | epot = -15.579026666222 | etot = -14.6175140353095 -273000 ekin = 0.563877614618956 | erot = 0.421397250044594 | epot = -15.6027888999983 | etot = -14.6175140353347 -274000 ekin = 0.561632338448697 | erot = 0.442126671656052 | epot = -15.6212730454525 | etot = -14.6175140353478 -275000 ekin = 0.554621238225524 | erot = 0.462125606775959 | epot = -15.6342608803503 | etot = -14.6175140353488 -276000 ekin = 0.543069132888247 | erot = 0.481138682332307 | epot = -15.6417218505594 | etot = -14.6175140353389 -277000 ekin = 0.527340979966703 | erot = 0.498945052082944 | epot = -15.6438000673687 | etot = -14.617514035319 -278000 ekin = 0.507918337218215 | erot = 0.515361832412993 | epot = -15.6407942049222 | etot = -14.617514035291 -279000 ekin = 0.485372319602766 | erot = 0.53024547360125 | epot = -15.6331318284605 | etot = -14.6175140352565 -280000 ekin = 0.460335116507262 | erot = 0.543490744710295 | epot = -15.6213398964351 | etot = -14.6175140352175 -281000 ekin = 0.433471859961099 | erot = 0.555027349455695 | epot = -15.606013244593 | etot = -14.6175140351762 -282000 ekin = 0.405454262481042 | erot = 0.564814480005611 | epot = -15.5877827776215 | etot = -14.6175140351348 -283000 ekin = 0.376937038993841 | erot = 0.572833827991569 | epot = -15.56728490208 | etot = -14.6175140350946 -284000 ekin = 0.348537747962758 | erot = 0.579081711929156 | epot = -15.5451334949486 | etot = -14.6175140350567 -285000 ekin = 0.320820372083395 | erot = 0.583561068644996 | epot = -15.5218954757513 | etot = -14.6175140350229 -286000 ekin = 0.294282726921591 | erot = 0.586274110944376 | epot = -15.49807087286 | etot = -14.617514034994 -287000 ekin = 0.269347634013421 | erot = 0.58721647590847 | epot = -15.4740781448926 | etot = -14.6175140349707 -288000 ekin = 0.246357704467551 | erot = 0.586373659771232 | epot = -15.450245399192 | etot = -14.6175140349532 -289000 ekin = 0.22557352214567 | erot = 0.583720426230562 | epot = -15.4268079833179 | etot = -14.6175140349417 -290000 ekin = 0.207174962818393 | erot = 0.57922365744791 | epot = -15.4039126552014 | etot = -14.6175140349351 -291000 ekin = 0.191265313940187 | erot = 0.572848780862473 | epot = -15.3816281297352 | etot = -14.6175140349326 -292000 ekin = 0.177877757396419 | erot = 0.564569470031942 | epot = -15.3599612623613 | etot = -14.617514034933 -293000 ekin = 0.166983649288418 | erot = 0.554379837681261 | epot = -15.3388775219044 | etot = -14.6175140349348 -294000 ekin = 0.158501898150678 | erot = 0.542307895558042 | epot = -15.3183238286452 | etot = -14.6175140349364 -295000 ekin = 0.152308641379645 | erot = 0.528428741575596 | epot = -15.298251417892 | etot = -14.6175140349367 -296000 ekin = 0.148246390134139 | erot = 0.512875830575803 | epot = -15.2786362556445 | etot = -14.6175140349346 -297000 ekin = 0.146131889948737 | erot = 0.495848833634457 | epot = -15.2594947585125 | etot = -14.6175140349293 -298000 ekin = 0.145762142540829 | erot = 0.477616979344766 | epot = -15.2408931568064 | etot = -14.6175140349208 -299000 ekin = 0.146918339842591 | erot = 0.458517327975552 | epot = -15.2229497027275 | etot = -14.6175140349094 -300000 ekin = 0.149367830717969 | erot = 0.438948042713275 | epot = -15.205829908327 | etot = -14.6175140348958 -301000 ekin = 0.152864610233931 | erot = 0.419357266834875 | epot = -15.1897359119496 | etot = -14.6175140348808 -302000 ekin = 0.157149122640062 | erot = 0.400228590599294 | epot = -15.1748917481051 | etot = -14.6175140348658 -303000 ekin = 0.16194834771892 | erot = 0.382064246008704 | epot = -15.1615266285792 | etot = -14.6175140348516 -304000 ekin = 0.166977167327322 | erot = 0.365367110080369 | epot = -15.1498583122469 | etot = -14.6175140348392 -305000 ekin = 0.171941885875759 | erot = 0.350622387002877 | epot = -15.1400783077083 | etot = -14.6175140348297 -306000 ekin = 0.176546522696758 | erot = 0.338279561365245 | epot = -15.1323401188853 | etot = -14.6175140348233 -307000 ekin = 0.180502080572099 | erot = 0.328734935092634 | epot = -15.1267510504853 | etot = -14.6175140348206 -308000 ekin = 0.183539117579173 | erot = 0.32231506851894 | epot = -15.1233682209196 | etot = -14.6175140348214 -309000 ekin = 0.185422589168761 | erot = 0.31926113518105 | epot = -15.1221977591756 | etot = -14.6175140348258 -310000 ekin = 0.18596838252546 | erot = 0.319714556778101 | epot = -15.1231969741369 | etot = -14.6175140348333 -311000 ekin = 0.185060444471766 | erot = 0.323704474533048 | epot = -15.1262789538485 | etot = -14.6175140348436 -312000 ekin = 0.18266705569995 | erot = 0.331137883754578 | epot = -15.1313189743107 | etot = -14.6175140348562 -313000 ekin = 0.178854671448202 | erot = 0.341793554574001 | epot = -15.1381622608926 | etot = -14.6175140348704 -314000 ekin = 0.173797674113419 | erot = 0.355321045101389 | epot = -15.1466327541005 | etot = -14.6175140348857 -315000 ekin = 0.167782440686126 | erot = 0.371246117949507 | epot = -15.1565425935371 | etot = -14.6175140349014 -316000 ekin = 0.161204347699483 | erot = 0.388983636697569 | epot = -15.1677020193138 | etot = -14.6175140349167 -317000 ekin = 0.154556738723145 | erot = 0.407858516720337 | epot = -15.1799292903744 | etot = -14.6175140349309 -318000 ekin = 0.148411457828143 | erot = 0.427134549770667 | epot = -15.1930600425422 | etot = -14.6175140349434 -319000 ekin = 0.143391260343367 | erot = 0.446049980955804 | epot = -15.2069552762529 | etot = -14.6175140349537 -320000 ekin = 0.140135163879429 | erot = 0.463857713006082 | epot = -15.2215069118471 | etot = -14.6175140349616 -321000 ekin = 0.139258496830789 | erot = 0.479867117343116 | epot = -15.2366396491412 | etot = -14.6175140349673 -322000 ekin = 0.141309963686665 | erot = 0.493483840953484 | epot = -15.2523078396112 | etot = -14.6175140349711 -323000 ekin = 0.146728465401823 | erot = 0.504243890594755 | epot = -15.2684863909706 | etot = -14.6175140349741 -324000 ekin = 0.155802740978128 | erot = 0.511838753068286 | epot = -15.285155529024 | etot = -14.6175140349776 -325000 ekin = 0.168637192339279 | erot = 0.516129344219886 | epot = -15.3022805715426 | etot = -14.6175140349834 -326000 ekin = 0.185127492740314 | erot = 0.517147991937071 | epot = -15.31978951967 | etot = -14.6175140349926 -327000 ekin = 0.204949583924698 | erot = 0.515089155112464 | epot = -15.3375527740434 | etot = -14.6175140350062 -328000 ekin = 0.227565145375698 | erot = 0.510290835145397 | epot = -15.3553700155455 | etot = -14.6175140350244 -329000 ekin = 0.252245305620947 | erot = 0.503209396461946 | epot = -15.3729687371292 | etot = -14.6175140350463 -330000 ekin = 0.278112223737838 | erot = 0.494390678508285 | epot = -15.3900169373164 | etot = -14.6175140350703 -331000 ekin = 0.304195517643728 | erot = 0.484439927615862 | epot = -15.4061494803532 | etot = -14.6175140350936 -332000 ekin = 0.329497983391289 | erot = 0.473992405220338 | epot = -15.4210044237253 | etot = -14.6175140351137 -333000 ekin = 0.353063353197021 | erot = 0.463685785197061 | epot = -15.4342631735221 | etot = -14.617514035128 -334000 ekin = 0.374038491014966 | erot = 0.454134842084351 | epot = -15.4456873682339 | etot = -14.6175140351346 -335000 ekin = 0.391723520498624 | erot = 0.44590856262641 | epot = -15.4551461182577 | etot = -14.6175140351327 -336000 ekin = 0.405605581596876 | erot = 0.439509690041266 | epot = -15.4626293067607 | etot = -14.6175140351225 -337000 ekin = 0.415374601836511 | erot = 0.435356764652945 | epot = -15.4682454015947 | etot = -14.6175140351053 -338000 ekin = 0.420921997008494 | erot = 0.4337688621957 | epot = -15.4722048942871 | etot = -14.6175140350829 -339000 ekin = 0.422325110445994 | erot = 0.434953376212245 | epot = -15.4747925217162 | etot = -14.6175140350579 -340000 ekin = 0.419821259879065 | erot = 0.438997304560045 | epot = -15.4763325994719 | etot = -14.6175140350328 -341000 ekin = 0.413775534579932 | erot = 0.445862573585468 | epot = -15.4771521431752 | etot = -14.6175140350098 -342000 ekin = 0.404646174019828 | erot = 0.455385967573506 | epot = -15.4775461765844 | etot = -14.617514034991 -343000 ekin = 0.392950705832007 | erot = 0.467284215126369 | epot = -15.4777489559361 | etot = -14.6175140349777 -344000 ekin = 0.379235231728315 | erot = 0.481164689425287 | epot = -15.4779139561242 | etot = -14.6175140349706 -345000 ekin = 0.364048459932831 | erot = 0.49654196729344 | epot = -15.4781044621959 | etot = -14.6175140349696 -346000 ekin = 0.347921358320248 | erot = 0.512860132814242 | epot = -15.4782955261082 | etot = -14.6175140349738 -347000 ekin = 0.331352665808313 | erot = 0.529520204052381 | epot = -15.4783869048424 | etot = -14.6175140349817 -348000 ekin = 0.314799955037007 | erot = 0.545911447468509 | epot = -15.478225437497 | etot = -14.6175140349915 -349000 ekin = 0.298675493175969 | erot = 0.561444708833552 | epot = -15.4776342370106 | etot = -14.6175140350011 -350000 ekin = 0.28334581552179 | erot = 0.575585348315622 | epot = -15.4764451988457 | etot = -14.6175140350083 -351000 ekin = 0.269133730328657 | erot = 0.587883045338955 | epot = -15.474530810679 | etot = -14.6175140350114 -352000 ekin = 0.256321431306528 | erot = 0.597995738138102 | epot = -15.4718312044538 | etot = -14.6175140350092 -353000 ekin = 0.245153509655857 | erot = 0.605705335206491 | epot = -15.4683728798634 | etot = -14.617514035001 -354000 ekin = 0.235838910987786 | erot = 0.610923562934953 | epot = -15.4642765089099 | etot = -14.6175140349872 -355000 ekin = 0.228551231301984 | erot = 0.613687305426088 | epot = -15.4597525716969 | etot = -14.6175140349688 -356000 ekin = 0.223427131308619 | erot = 0.61414390282533 | epot = -15.4550850690815 | etot = -14.6175140349475 -357000 ekin = 0.220563006919496 | erot = 0.612527933402533 | epot = -15.4506049752473 | etot = -14.6175140349253 -358000 ekin = 0.220010333199303 | erot = 0.609131855544879 | epot = -15.4466562236489 | etot = -14.6175140349047 -359000 ekin = 0.221770268741646 | erot = 0.604273418958276 | epot = -15.443557722588 | etot = -14.6175140348881 -360000 ekin = 0.225788163654918 | erot = 0.598262925571842 | epot = -15.4415651241044 | etot = -14.6175140348777 -361000 ekin = 0.231948578438913 | erot = 0.59137325198523 | epot = -15.4408358652996 | etot = -14.6175140348754 -362000 ekin = 0.240071331019464 | erot = 0.583815109039738 | epot = -15.4414004749418 | etot = -14.6175140348826 -363000 ekin = 0.249908988059078 | erot = 0.575719406612622 | epot = -15.4431424295716 | etot = -14.6175140348999 -364000 ekin = 0.261146140583132 | erot = 0.56712790648618 | epot = -15.4457880819966 | etot = -14.6175140349273 -365000 ekin = 0.273400773646818 | erot = 0.557992653604894 | epot = -15.4489074622159 | etot = -14.6175140349642 -366000 ekin = 0.286228056504663 | erot = 0.548184015757871 | epot = -15.4519261072718 | etot = -14.6175140350093 -367000 ekin = 0.299126926926786 | erot = 0.537506547610907 | epot = -15.4541475095983 | etot = -14.6175140350606 -368000 ekin = 0.311549892639084 | erot = 0.525721330951755 | epot = -15.4547852587065 | etot = -14.6175140351156 -369000 ekin = 0.322916493342769 | erot = 0.512572942753926 | epot = -15.4530034712682 | etot = -14.6175140351715 -370000 ekin = 0.332630833324557 | erot = 0.497818805481132 | epot = -15.4479636740308 | etot = -14.6175140352251 -371000 ekin = 0.340103492446634 | erot = 0.481258447415918 | epot = -15.4388759751356 | etot = -14.6175140352731 -372000 ekin = 0.344777943664193 | erot = 0.462760223983496 | epot = -15.4250522029596 | etot = -14.6175140353119 -373000 ekin = 0.346161332162081 | erot = 0.442283380417406 | epot = -15.405958747918 | etot = -14.6175140353385 -374000 ekin = 0.343859062980667 | erot = 0.419893962766177 | epot = -15.3812670610967 | etot = -14.6175140353498 -375000 ekin = 0.337612023151491 | erot = 0.395773904235502 | epot = -15.35089996273 | etot = -14.617514035343 -376000 ekin = 0.327334336193659 | erot = 0.370223433835828 | epot = -15.3150718053453 | etot = -14.6175140353159 -377000 ekin = 0.313148263712968 | erot = 0.3436575453366 | epot = -15.2743198443167 | etot = -14.6175140352671 -378000 ekin = 0.295411338277735 | erot = 0.316597454537734 | epot = -15.2295228280119 | etot = -14.6175140351964 -379000 ekin = 0.274729408510529 | erot = 0.289657740939432 | epot = -15.1819011845551 | etot = -14.6175140351051 -380000 ekin = 0.251948675267414 | erot = 0.263529414055011 | epot = -15.1329921243187 | etot = -14.6175140349963 -381000 ekin = 0.228120837035203 | erot = 0.238958749468097 | epot = -15.0845936213794 | etot = -14.6175140348761 -382000 ekin = 0.204438854506746 | erot = 0.216721270519329 | epot = -15.0386741597779 | etot = -14.6175140347518 -383000 ekin = 0.182146263755385 | erot = 0.19759188098445 | epot = -14.9972521793722 | etot = -14.6175140346323 -384000 ekin = 0.162429780679522 | erot = 0.182311896924387 | epot = -14.9622557121308 | etot = -14.6175140345269 -385000 ekin = 0.146310622123822 | erot = 0.171555128911536 | epot = -14.9353797854792 | etot = -14.6175140344439 -386000 ekin = 0.134552389652403 | erot = 0.165895597224741 | epot = -14.9179620212657 | etot = -14.6175140343886 -387000 ekin = 0.127600986328395 | erot = 0.165779213534325 | epot = -14.9108942342266 | etot = -14.6175140343639 -388000 ekin = 0.125565151523028 | erot = 0.171500950984996 | epot = -14.9145801368772 | etot = -14.6175140343691 -389000 ekin = 0.128237001096973 | erot = 0.183188026636525 | epot = -14.9289390621349 | etot = -14.6175140344014 -390000 ekin = 0.135143637923168 | erot = 0.200788930663413 | epot = -14.9534466030433 | etot = -14.6175140344567 -391000 ekin = 0.145616156499953 | erot = 0.224068074688611 | epot = -14.9871982657191 | etot = -14.6175140345306 -392000 ekin = 0.158862235246809 | erot = 0.252606362171908 | epot = -15.0289826320371 | etot = -14.6175140346184 -393000 ekin = 0.174032087603698 | erot = 0.285808726839658 | epot = -15.0773548491589 | etot = -14.6175140347155 -394000 ekin = 0.190272707003915 | erot = 0.322920107512839 | epot = -15.1307068493349 | etot = -14.6175140348181 -395000 ekin = 0.206769905102427 | erot = 0.363051013228117 | epot = -15.1873349532527 | etot = -14.6175140349221 -396000 ekin = 0.222780272470673 | erot = 0.405212687947373 | epot = -15.2455069954414 | etot = -14.6175140350234 -397000 ekin = 0.23765569871957 | erot = 0.448360183482314 | epot = -15.3035299173199 | etot = -14.6175140351181 -398000 ekin = 0.250862154070766 | erot = 0.491439914329229 | epot = -15.3598161036022 | etot = -14.6175140352022 -399000 ekin = 0.261993055954332 | erot = 0.533437059170124 | epot = -15.4129441503972 | etot = -14.6175140352727 -400000 ekin = 0.270776550507805 | erot = 0.573417887949055 | epot = -15.4617084737844 | etot = -14.6175140353276 -401000 ekin = 0.277075831016468 | erot = 0.610562842823512 | epot = -15.505152709206 | etot = -14.617514035366 -402000 ekin = 0.280882158892238 | erot = 0.644187798759056 | epot = -15.5425839930397 | etot = -14.6175140353884 -403000 ekin = 0.282301228579434 | erot = 0.673752968641712 | epot = -15.5735682326173 | etot = -14.6175140353962 -404000 ekin = 0.281534519812515 | erot = 0.698860907481931 | epot = -15.5979094626858 | etot = -14.6175140353913 -405000 ekin = 0.278857975737129 | erot = 0.719246574878154 | epot = -15.6156185859915 | etot = -14.6175140353763 -406000 ekin = 0.274600555759475 | erot = 0.73476315739679 | epot = -15.6268777485094 | etot = -14.6175140353531 -407000 ekin = 0.269124923358509 | erot = 0.745367259285065 | epot = -15.6320062179673 | etot = -14.6175140353237 -408000 ekin = 0.262811853165719 | erot = 0.751106276665231 | epot = -15.63143216512 | etot = -14.6175140352891 -409000 ekin = 0.256049112192117 | erot = 0.752109968276187 | epot = -15.6256731157185 | etot = -14.6175140352502 -410000 ekin = 0.249224269809732 | erot = 0.74858433225965 | epot = -15.6153226372768 | etot = -14.6175140352074 -411000 ekin = 0.242720888553437 | erot = 0.740809103918433 | epot = -15.6010440276326 | etot = -14.6175140351607 -412000 ekin = 0.236916379506095 | erot = 0.729136085380854 | epot = -15.5835664999974 | etot = -14.6175140351104 -413000 ekin = 0.232179735243653 | erot = 0.713985498456999 | epot = -15.5636792687578 | etot = -14.6175140350572 -414000 ekin = 0.228867632642243 | erot = 0.695838652585891 | epot = -15.5422203202302 | etot = -14.6175140350021 -415000 ekin = 0.227317772307856 | erot = 0.675225695396218 | epot = -15.5200575026509 | etot = -14.6175140349469 -416000 ekin = 0.227838940777607 | erot = 0.652708261105161 | epot = -15.4980612367764 | etot = -14.6175140348937 -417000 ekin = 0.230697970866891 | erot = 0.628857925336047 | epot = -15.4770699310479 | etot = -14.617514034845 -418000 ekin = 0.236104416120681 | erot = 0.604232291329749 | epot = -15.4578507422538 | etot = -14.6175140348034 -419000 ekin = 0.244194252200401 | erot = 0.579351108945114 | epot = -15.4410593959166 | etot = -14.6175140347711 -420000 ekin = 0.255014214168464 | erot = 0.554674986841152 | epot = -15.4272032357598 | etot = -14.6175140347502 -421000 ekin = 0.268508458340295 | erot = 0.530589008736334 | epot = -15.4166115018185 | etot = -14.6175140347418 -422000 ekin = 0.284509119560496 | erot = 0.507392982380571 | epot = -15.4094161366875 | etot = -14.6175140347464 -423000 ekin = 0.302732060426934 | erot = 0.485299248118979 | epot = -15.4055453433093 | etot = -14.6175140347634 -424000 ekin = 0.322778728051398 | erot = 0.464438075670481 | epot = -15.4047308385137 | etot = -14.6175140347918 -425000 ekin = 0.344144594922637 | erot = 0.444869796712131 | epot = -15.4065284264641 | etot = -14.6175140348293 -426000 ekin = 0.366234204300038 | erot = 0.426602052983704 | epot = -15.4103502921573 | etot = -14.6175140348735 -427000 ekin = 0.388382398339816 | erot = 0.409609962240036 | epot = -15.4155063955013 | etot = -14.6175140349214 -428000 ekin = 0.409880900047524 | erot = 0.393856678091899 | epot = -15.4212516131094 | etot = -14.6175140349699 -429000 ekin = 0.430009061106479 | erot = 0.379311788381591 | epot = -15.4268348845041 | etot = -14.617514035016 -430000 ekin = 0.448067283636575 | erot = 0.3659652824005 | epot = -15.4315466010941 | etot = -14.617514035057 -431000 ekin = 0.463411378723588 | erot = 0.353835411175161 | epot = -15.4347608249895 | etot = -14.6175140350907 -432000 ekin = 0.475485941535269 | erot = 0.342969616703674 | epot = -15.4359695933546 | etot = -14.6175140351156 -433000 ekin = 0.483854704021334 | erot = 0.333438714396283 | epot = -15.4348074535483 | etot = -14.6175140351307 -434000 ekin = 0.488225698519521 | erot = 0.325325491782385 | epot = -15.4310652254377 | etot = -14.6175140351358 -435000 ekin = 0.48846961521868 | erot = 0.318709988965965 | epot = -15.4246936393157 | etot = -14.6175140351311 -436000 ekin = 0.484629100798397 | erot = 0.313653867974891 | epot = -15.4157970038909 | etot = -14.6175140351176 -437000 ekin = 0.476917712285193 | erot = 0.310186654191006 | epot = -15.4046184015729 | etot = -14.6175140350967 -438000 ekin = 0.465707830236428 | erot = 0.308296241623089 | epot = -15.3915181069294 | etot = -14.6175140350699 -439000 ekin = 0.45150753680146 | erot = 0.30792515377069 | epot = -15.3769467256113 | etot = -14.6175140350391 -440000 ekin = 0.434927659014138 | erot = 0.308973010492868 | epot = -15.3614147045135 | etot = -14.6175140350065 -441000 ekin = 0.416641657349937 | erot = 0.311304747383582 | epot = -15.3454604397074 | etot = -14.6175140349739 -442000 ekin = 0.397341542601571 | erot = 0.314762618736297 | epot = -15.3296181962812 | etot = -14.6175140349433 -443000 ekin = 0.377694362715545 | erot = 0.319179725729324 | epot = -15.314388123361 | etot = -14.6175140349161 -444000 ekin = 0.358304425136817 | erot = 0.32439329819003 | epot = -15.3002117582203 | etot = -14.6175140348934 -445000 ekin = 0.339684383335156 | erot = 0.330254911559461 | epot = -15.2874533297707 | etot = -14.6175140348761 -446000 ekin = 0.322237701351822 | erot = 0.336636009508 | epot = -15.2763877457241 | etot = -14.6175140348643 -447000 ekin = 0.30625308658371 | erot = 0.34342824275766 | epot = -15.2671953641993 | etot = -14.6175140348579 -448000 ekin = 0.291909091343975 | erot = 0.350538602019967 | epot = -15.2599617282208 | etot = -14.6175140348568 -449000 ekin = 0.279285717664377 | erot = 0.357880263087886 | epot = -15.254680015613 | etot = -14.6175140348608 -450000 ekin = 0.268379332693754 | erot = 0.365360767815974 | epot = -15.2512541353793 | etot = -14.6175140348696 -451000 ekin = 0.259117719163031 | erot = 0.372869677558793 | epot = -15.2495014316051 | etot = -14.6175140348833 -452000 ekin = 0.251373384973835 | erot = 0.380268095669032 | epot = -15.2491555155445 | etot = -14.6175140349017 -453000 ekin = 0.24497482412797 | erot = 0.387382402362676 | epot = -15.2498712614149 | etot = -14.6175140349243 -454000 ekin = 0.239716691076598 | erot = 0.394004131859313 | epot = -15.251234857886 | etot = -14.6175140349501 -455000 ekin = 0.235370413814522 | erot = 0.399897145639913 | epot = -15.252781594432 | etot = -14.6175140349776 -456000 ekin = 0.231696513790871 | erot = 0.404812188422525 | epot = -15.254022737218 | etot = -14.6175140350046 -457000 ekin = 0.22845901443235 | erot = 0.408507709512969 | epot = -15.2544807589739 | etot = -14.6175140350285 -458000 ekin = 0.225441196082656 | erot = 0.41077470562198 | epot = -15.2537299367515 | etot = -14.6175140350469 -459000 ekin = 0.22246101894078 | erot = 0.411462514810095 | epot = -15.251437568808 | etot = -14.6175140350572 -460000 ekin = 0.219384094438714 | erot = 0.410502136527495 | epot = -15.2474002660241 | etot = -14.6175140350579 -461000 ekin = 0.21613224524022 | erot = 0.40792384413126 | epot = -15.2415701244196 | etot = -14.6175140350481 -462000 ekin = 0.212686361973382 | erot = 0.403866554422734 | epot = -15.2340669514243 | etot = -14.6175140350282 -463000 ekin = 0.209083218482854 | erot = 0.398577486489151 | epot = -15.2251747399712 | etot = -14.6175140349992 -464000 ekin = 0.20540688826373 | erot = 0.392401883856613 | epot = -15.2153228070836 | etot = -14.6175140349633 -465000 ekin = 0.201776197881068 | erot = 0.385763783461919 | epot = -15.2050540162659 | etot = -14.6175140349229 -466000 ekin = 0.198330130961181 | erot = 0.379139817336986 | epot = -15.1949839831793 | etot = -14.6175140348811 -467000 ekin = 0.195213224017124 | erot = 0.373028711257475 | epot = -15.1857559701151 | etot = -14.6175140348405 -468000 ekin = 0.192562810062158 | erot = 0.367919448414916 | epot = -15.1779962932808 | etot = -14.6175140348037 -469000 ekin = 0.190499545154769 | erot = 0.364261004085612 | epot = -15.1722745840131 | etot = -14.6175140347727 -470000 ekin = 0.18912208603274 | erot = 0.362436180586983 | epot = -15.1690723013684 | etot = -14.6175140347487 -471000 ekin = 0.188506156938867 | erot = 0.362741456207278 | epot = -15.1687616478786 | etot = -14.6175140347325 -472000 ekin = 0.188707621222394 | erot = 0.365373993438347 | epot = -15.1715956493845 | etot = -14.6175140347238 -473000 ekin = 0.189768618622282 | erot = 0.370426120543888 | epot = -15.1777087738883 | etot = -14.6175140347222 -474000 ekin = 0.191725397341772 | erot = 0.377886798112635 | epot = -15.1871262301808 | etot = -14.6175140347264 -475000 ekin = 0.194616213071371 | erot = 0.387648901412467 | epot = -15.1997791492193 | etot = -14.6175140347354 -476000 ekin = 0.19848763616133 | erot = 0.399520678155556 | epot = -15.2155223490651 | etot = -14.6175140347483 -477000 ekin = 0.203397790430575 | erot = 0.413239540254448 | epot = -15.234151365449 | etot = -14.617514034764 -478000 ekin = 0.209415519783994 | erot = 0.428486466926518 | epot = -15.2554160214928 | etot = -14.6175140347823 -479000 ekin = 0.216615156595488 | erot = 0.444899686771521 | epot = -15.2790288781697 | etot = -14.6175140348027 -480000 ekin = 0.225067223158495 | erot = 0.462086880017487 | epot = -15.3046681380014 | etot = -14.6175140348255 -481000 ekin = 0.234826185148526 | erot = 0.479635803738694 | epot = -15.3319760237382 | etot = -14.6175140348509 -482000 ekin = 0.24591693935593 | erot = 0.497123799837189 | epot = -15.3605547740723 | etot = -14.6175140348792 -483000 ekin = 0.258322039581471 | erot = 0.514126984880484 | epot = -15.3899630593723 | etot = -14.6175140349103 -484000 ekin = 0.271971667055458 | erot = 0.530229960568097 | epot = -15.4197156625675 | etot = -14.617514034944 -485000 ekin = 0.286738030810237 | erot = 0.545036619609161 | epot = -15.4492886853988 | etot = -14.6175140349794 -486000 ekin = 0.302435294442602 | erot = 0.558182125190157 | epot = -15.4781314546481 | etot = -14.6175140350154 -487000 ekin = 0.318825369858635 | erot = 0.569345540302413 | epot = -15.5056849452114 | etot = -14.6175140350504 -488000 ekin = 0.335629120856599 | erot = 0.578262027782435 | epot = -15.5314051837218 | etot = -14.6175140350827 -489000 ekin = 0.352541803825719 | erot = 0.584733173542254 | epot = -15.5547890124787 | etot = -14.6175140351108 -490000 ekin = 0.369251041133798 | erot = 0.58863390237619 | epot = -15.5753989786432 | etot = -14.6175140351332 -491000 ekin = 0.385455339944008 | erot = 0.589914693970058 | epot = -15.5928840690631 | etot = -14.6175140351491 -492000 ekin = 0.40088115647899 | erot = 0.588598334680754 | epot = -15.6069935263179 | etot = -14.6175140351581 -493000 ekin = 0.415296746377553 | erot = 0.584771169137649 | epot = -15.6175819506758 | etot = -14.6175140351606 -494000 ekin = 0.428521503102931 | erot = 0.578569614095801 | epot = -15.6246051523561 | etot = -14.6175140351573 -495000 ekin = 0.440430011858771 | erot = 0.570163426568569 | epot = -15.6281074735768 | etot = -14.6175140351495 -496000 ekin = 0.450950706316734 | erot = 0.559737766477586 | epot = -15.628202507933 | etot = -14.6175140351387 -497000 ekin = 0.460059581798191 | erot = 0.547476355485745 | epot = -15.6250499724103 | etot = -14.6175140351264 -498000 ekin = 0.467769906492318 | erot = 0.533547985555278 | epot = -15.6188319271617 | etot = -14.6175140351141 -499000 ekin = 0.474119221073082 | erot = 0.518098277332704 | epot = -15.6097315335085 | etot = -14.6175140351027 -500000 ekin = 0.47915510663518 | erot = 0.501247978937513 | epot = -15.5979171206656 | etot = -14.6175140350929 -501000 ekin = 0.482921233338969 | erot = 0.483098304082662 | epot = -15.5835335725064 | etot = -14.6175140350848 -502000 ekin = 0.485445093649088 | erot = 0.463742920559554 | epot = -15.5667020492864 | etot = -14.6175140350777 -503000 ekin = 0.486728599209648 | erot = 0.443285305605623 | epot = -15.5475279398862 | etot = -14.6175140350709 -504000 ekin = 0.486742408087926 | erot = 0.421859374631785 | epot = -15.5261158177828 | etot = -14.6175140350631 -505000 ekin = 0.485424480827694 | erot = 0.399650657768087 | epot = -15.5025891736488 | etot = -14.617514035053 -506000 ekin = 0.48268297341187 | erot = 0.376914939267219 | epot = -15.4771119477182 | etot = -14.6175140350392 -507000 ekin = 0.478403198154612 | erot = 0.353991273961029 | epot = -15.4499085071364 | etot = -14.6175140350208 -508000 ekin = 0.472458052935441 | erot = 0.331306710133916 | epot = -15.4212787980666 | etot = -14.6175140349972 -509000 ekin = 0.46472106285539 | erot = 0.309370883447747 | epot = -15.3916059812718 | etot = -14.6175140349687 -510000 ekin = 0.455081004104095 | erot = 0.288759823578743 | epot = -15.3613548626186 | etot = -14.6175140349358 -511000 ekin = 0.443456979180403 | erot = 0.270089690707411 | epot = -15.3310607047875 | etot = -14.6175140348996 -512000 ekin = 0.429812848219575 | erot = 0.25398253489869 | epot = -15.3013094179802 | etot = -14.6175140348619 -513000 ekin = 0.414169942618988 | erot = 0.241027258547328 | epot = -15.2727112359908 | etot = -14.6175140348245 -514000 ekin = 0.396617122319459 | erot = 0.231739657368316 | epot = -15.245870814477 | etot = -14.6175140347893 -515000 ekin = 0.377317407138787 | erot = 0.226525548757195 | epot = -15.2213569906539 | etot = -14.6175140347579 -516000 ekin = 0.356510629533613 | erot = 0.225650587239684 | epot = -15.1996752515051 | etot = -14.6175140347318 -517000 ekin = 0.334511811731556 | erot = 0.229219509886492 | epot = -15.1812453563299 | etot = -14.6175140347118 -518000 ekin = 0.311705249160021 | erot = 0.23716641592675 | epot = -15.1663856997854 | etot = -14.6175140346987 -519000 ekin = 0.288534562405509 | erot = 0.249256456193826 | epot = -15.1553050532917 | etot = -14.6175140346923 -520000 ekin = 0.265489234982404 | erot = 0.265098165451267 | epot = -15.1481014351262 | etot = -14.6175140346925 -521000 ekin = 0.243088358087729 | erot = 0.284164745160129 | epot = -15.1447671379464 | etot = -14.6175140346986 -522000 ekin = 0.221862437060792 | erot = 0.305821970140486 | epot = -15.1451984419111 | etot = -14.6175140347098 -523000 ekin = 0.202334169776215 | erot = 0.329360070797338 | epot = -15.149208275299 | etot = -14.6175140347255 -524000 ekin = 0.184999091076189 | erot = 0.354026911471086 | epot = -15.1565400372918 | etot = -14.6175140347445 -525000 ekin = 0.170306912739355 | erot = 0.379059948771691 | epot = -15.1668808962774 | etot = -14.6175140347664 -526000 ekin = 0.158644243148445 | erot = 0.403715126925631 | epot = -15.1798734048646 | etot = -14.6175140347905 -527000 ekin = 0.150319367666608 | erot = 0.427291025812717 | epot = -15.1951244282958 | etot = -14.6175140348165 -528000 ekin = 0.145549592055318 | erot = 0.449147424933815 | epot = -15.2122110518333 | etot = -14.6175140348441 -529000 ekin = 0.144451603984815 | erot = 0.46871812185095 | epot = -15.2306837607091 | etot = -14.6175140348734 -530000 ekin = 0.147035267138349 | erot = 0.485518371011605 | epot = -15.2500676730542 | etot = -14.6175140349042 -531000 ekin = 0.153201203684292 | erot = 0.499147835497304 | epot = -15.2698630741182 | etot = -14.6175140349366 -532000 ekin = 0.162742448479717 | erot = 0.509290301682708 | epot = -15.2895467851327 | etot = -14.6175140349702 -533000 ekin = 0.175350354881916 | erot = 0.515711587206721 | epot = -15.3085759770934 | etot = -14.6175140350047 -534000 ekin = 0.190624856013519 | erot = 0.518257146630614 | epot = -15.3263960376834 | etot = -14.6175140350393 -535000 ekin = 0.208088493536824 | erot = 0.516850140104756 | epot = -15.3424526687142 | etot = -14.6175140350726 -536000 ekin = 0.227204325842689 | erot = 0.511491240065728 | epot = -15.3562096010119 | etot = -14.6175140351035 -537000 ekin = 0.247396768812984 | erot = 0.502260311074185 | epot = -15.3671711150173 | etot = -14.6175140351302 -538000 ekin = 0.268074342413392 | erot = 0.489319600961478 | epot = -15.3749079785256 | etot = -14.6175140351508 -539000 ekin = 0.288653182933449 | erot = 0.4729176796722 | epot = -15.3790848977693 | etot = -14.6175140351637 -540000 ekin = 0.308579985825782 | erot = 0.453392904739592 | epot = -15.3794869257329 | etot = -14.6175140351675 -541000 ekin = 0.327353008191246 | erot = 0.431174973010967 | epot = -15.3760420163633 | etot = -14.6175140351611 -542000 ekin = 0.344539853506965 | erot = 0.406783142889028 | epot = -15.3688370315399 | etot = -14.6175140351439 -543000 ekin = 0.359790986513993 | erot = 0.380819988063805 | epot = -15.3581250096939 | etot = -14.6175140351161 -544000 ekin = 0.37284826309085 | erot = 0.353960030672464 | epot = -15.344322328842 | etot = -14.6175140350787 -545000 ekin = 0.383548167009815 | erot = 0.326933212481791 | epot = -15.3279954145248 | etot = -14.6175140350332 -546000 ekin = 0.391819867385749 | erot = 0.300503784237994 | epot = -15.3098376866053 | etot = -14.6175140349815 -547000 ekin = 0.397678590182396 | erot = 0.275445713887096 | epot = -15.2906383389958 | etot = -14.6175140349263 -548000 ekin = 0.401215088504832 | erot = 0.252516050366015 | epot = -15.2712451737408 | etot = -14.6175140348699 -549000 ekin = 0.402582175512791 | erot = 0.232427794767637 | epot = -15.2525240050959 | etot = -14.6175140348155 -550000 ekin = 0.401979352687969 | erot = 0.215823740833009 | epot = -15.2353171282862 | etot = -14.6175140347652 -551000 ekin = 0.399636550193996 | erot = 0.203252510909739 | epot = -15.220403095825 | etot = -14.6175140347213 -552000 ekin = 0.395797934840894 | erot = 0.195147714573778 | epot = -15.2084596841007 | etot = -14.617514034686 -553000 ekin = 0.390706676476196 | erot = 0.191810879117336 | epot = -15.2000315902546 | etot = -14.6175140346611 -554000 ekin = 0.384591526958096 | erot = 0.19339860945437 | epot = -15.1955041710601 | etot = -14.6175140346476 -555000 ekin = 0.377656068332676 | erot = 0.199914362894006 | epot = -15.1950844658734 | etot = -14.6175140346467 -556000 ekin = 0.370071512615683 | erot = 0.211205266307111 | epot = -15.1987908135806 | etot = -14.6175140346578 -557000 ekin = 0.361973939272813 | erot = 0.226964515102972 | epot = -15.2064524890562 | etot = -14.6175140346805 -558000 ekin = 0.353466765020817 | erot = 0.246739996102199 | epot = -15.2177207958362 | etot = -14.6175140347132 -559000 ekin = 0.344628961765223 | erot = 0.269949765670651 | epot = -15.2320927621895 | etot = -14.6175140347536 -560000 ekin = 0.335528980568065 | erot = 0.295904778796298 | epot = -15.248947794163 | etot = -14.6175140347986 -561000 ekin = 0.326243446081694 | erot = 0.32383871490908 | epot = -15.2675961958353 | etot = -14.6175140348445 -562000 ekin = 0.316878486813705 | erot = 0.352943857553535 | epot = -15.2873363792542 | etot = -14.617514034887 -563000 ekin = 0.307590234581993 | erot = 0.382410843957943 | epot = -15.3075151134627 | etot = -14.6175140349227 -564000 ekin = 0.298599911427723 | erot = 0.411468934029848 | epot = -15.3275828804063 | etot = -14.6175140349488 -565000 ekin = 0.290198521501613 | erot = 0.439422606477982 | epot = -15.3471351629436 | etot = -14.617514034964 -566000 ekin = 0.282736992095915 | erot = 0.465680158920146 | epot = -15.3659311859852 | etot = -14.6175140349691 -567000 ekin = 0.276599956454237 | erot = 0.489770841523137 | epot = -15.3838848329439 | etot = -14.6175140349665 -568000 ekin = 0.272165052790849 | erot = 0.51134888782089 | epot = -15.4010279755719 | etot = -14.6175140349602 -569000 ekin = 0.269753809413351 | erot = 0.530185258477429 | epot = -15.4174531028455 | etot = -14.6175140349547 -570000 ekin = 0.269583567607364 | erot = 0.546150320474836 | epot = -15.4332479230362 | etot = -14.617514034954 -571000 ekin = 0.271731068577875 | erot = 0.559192265325752 | epot = -15.4484373688642 | etot = -14.6175140349606 -572000 ekin = 0.276116495687091 | erot = 0.569316321634121 | epot = -15.4629468522959 | etot = -14.6175140349747 -573000 ekin = 0.282512256444534 | erot = 0.576569321998237 | epot = -15.4765956134374 | etot = -14.6175140349946 -574000 ekin = 0.290574483947443 | erot = 0.58103049076154 | epot = -15.4891190097262 | etot = -14.6175140350172 -575000 ekin = 0.299890113326593 | erot = 0.582808418137594 | epot = -15.5002125665028 | etot = -14.6175140350386 -576000 ekin = 0.310029076130859 | erot = 0.582041678954832 | epot = -15.5095847901412 | etot = -14.6175140350555 -577000 ekin = 0.320591144135675 | erot = 0.578899817193377 | epot = -15.5170049963946 | etot = -14.6175140350655 -578000 ekin = 0.331239680817734 | erot = 0.573581904321388 | epot = -15.5223356202072 | etot = -14.6175140350681 -579000 ekin = 0.341718767395713 | erot = 0.566311213814816 | epot = -15.5255440162742 | etot = -14.6175140350637 -580000 ekin = 0.351854361646192 | erot = 0.557326170820746 | epot = -15.5266945675209 | etot = -14.617514035054 -581000 ekin = 0.361543170719959 | erot = 0.546869043111512 | epot = -15.5259262488727 | etot = -14.6175140350412 -582000 ekin = 0.370734291431731 | erot = 0.535174473618127 | epot = -15.5234228000774 | etot = -14.6175140350275 -583000 ekin = 0.37940854514636 | erot = 0.522459863754317 | epot = -15.5193824439152 | etot = -14.6175140350145 -584000 ekin = 0.387559338332064 | erot = 0.50891899993969 | epot = -15.5139923732753 | etot = -14.6175140350036 -585000 ekin = 0.395177418309436 | erot = 0.494719483694829 | epot = -15.5074109369994 | etot = -14.6175140349952 -586000 ekin = 0.402240533516594 | erot = 0.480003760424791 | epot = -15.4997583289309 | etot = -14.6175140349895 -587000 ekin = 0.408707997145263 | erot = 0.464893014294175 | epot = -15.4911150464257 | etot = -14.6175140349862 -588000 ekin = 0.41451954577295 | erot = 0.449492951760516 | epot = -15.4815265325182 | etot = -14.6175140349847 -589000 ekin = 0.419597612555334 | erot = 0.43390048790532 | epot = -15.4710121354448 | etot = -14.6175140349841 -590000 ekin = 0.423852083806567 | erot = 0.418210489542958 | epot = -15.4595766083332 | etot = -14.6175140349837 -591000 ekin = 0.427186671517479 | erot = 0.402521929657892 | epot = -15.447222636158 | etot = -14.6175140349826 -592000 ekin = 0.429506137373686 | erot = 0.386943005728737 | epot = -15.4339631780827 | etot = -14.6175140349802 -593000 ekin = 0.430723706116615 | erot = 0.371594936609099 | epot = -15.4198326777017 | etot = -14.617514034976 -594000 ekin = 0.430768094953839 | erot = 0.356614269836478 | epot = -15.4048963997596 | etot = -14.6175140349693 -595000 ekin = 0.42958966483036 | erot = 0.34215360916983 | epot = -15.3892573089602 | etot = -14.61751403496 -596000 ekin = 0.427165296133674 | erot = 0.328380718540701 | epot = -15.3730600496226 | etot = -14.6175140349482 -597000 ekin = 0.423501658500188 | erot = 0.315475989401846 | epot = -15.3564916828361 | etot = -14.617514034934 -598000 ekin = 0.418636501255824 | erot = 0.30362835958022 | epot = -15.3397788957539 | etot = -14.6175140349178 -599000 ekin = 0.412638207582771 | erot = 0.293029673722298 | epot = -15.3231819162053 | etot = -14.6175140349002 -600000 ekin = 0.405603414753992 | erot = 0.283867637225037 | epot = -15.306985086861 | etot = -14.6175140348819 -601000 ekin = 0.397652939448924 | erot = 0.27631757335997 | epot = -15.2914845476729 | etot = -14.617514034864 -602000 ekin = 0.388926339151977 | erot = 0.270533300127966 | epot = -15.2769736741272 | etot = -14.6175140348472 -603000 ekin = 0.379575547711323 | erot = 0.266637582798157 | epot = -15.2637271653422 | etot = -14.6175140348327 -604000 ekin = 0.369758112224678 | erot = 0.264712769809213 | epot = -15.2519849168553 | etot = -14.6175140348214 -605000 ekin = 0.359630614964776 | erot = 0.264792359550131 | epot = -15.241937009329 | etot = -14.617514034814 -606000 ekin = 0.349342882571482 | erot = 0.266854337886994 | epot = -15.2337112552696 | etot = -14.6175140348111 -607000 ekin = 0.339033558751721 | erot = 0.270817131627805 | epot = -15.2273647251923 | etot = -14.6175140348128 -608000 ekin = 0.328827538259558 | erot = 0.276538908097645 | epot = -15.2228804811762 | etot = -14.617514034819 -609000 ekin = 0.318835621087791 | erot = 0.283820700144912 | epot = -15.2201703560617 | etot = -14.617514034829 -610000 ekin = 0.309156542568471 | erot = 0.292413461056483 | epot = -15.2190840384669 | etot = -14.617514034842 -611000 ekin = 0.29988127210835 | erot = 0.302028697870677 | epot = -15.2194240048356 | etot = -14.6175140348566 -612000 ekin = 0.291099167856382 | erot = 0.312351863790435 | epot = -15.2209650665183 | etot = -14.6175140348715 -613000 ekin = 0.282905257831731 | erot = 0.323057294042835 | epot = -15.2234765867597 | etot = -14.6175140348851 -614000 ekin = 0.275407632339994 | erot = 0.333823223653581 | epot = -15.2267448908899 | etot = -14.6175140348963 -615000 ekin = 0.268733725567278 | erot = 0.344345386321387 | epot = -15.2305931467927 | etot = -14.617514034904 -616000 ekin = 0.263034181136557 | erot = 0.35434787992739 | epot = -15.2348960959719 | etot = -14.6175140349079 -617000 ekin = 0.258483071857821 | erot = 0.363590372787447 | epot = -15.2395874795532 | etot = -14.6175140349079 -618000 ekin = 0.255273496413574 | erot = 0.371871254538827 | epot = -15.2446587858571 | etot = -14.6175140349047 -619000 ekin = 0.253608004174632 | erot = 0.37902692128715 | epot = -15.2501489603613 | etot = -14.6175140348995 -620000 ekin = 0.253683881421992 | erot = 0.384927934513618 | epot = -15.2561258508295 | etot = -14.6175140348939 -621000 ekin = 0.255674023709804 | erot = 0.389473226071993 | epot = -15.2626612846714 | etot = -14.6175140348896 -622000 ekin = 0.25970485336757 | erot = 0.392583779639758 | epot = -15.2698026678959 | etot = -14.6175140348885 -623000 ekin = 0.265833429999403 | erot = 0.394197274405735 | epot = -15.2775447392974 | etot = -14.6175140348923 -624000 ekin = 0.274026439188228 | erot = 0.394265031624551 | epot = -15.2858055057147 | etot = -14.6175140349019 -625000 ekin = 0.284144015738384 | erot = 0.392752285176118 | epot = -15.2944103358322 | etot = -14.6175140349177 -626000 ekin = 0.295931256226139 | erot = 0.389642344380343 | epot = -15.3030876355457 | etot = -14.6175140349392 -627000 ekin = 0.309019727829663 | erot = 0.38494467650416 | epot = -15.3114784392987 | etot = -14.6175140349649 -628000 ekin = 0.322940275279064 | erot = 0.378706350959343 | epot = -15.3191606612307 | etot = -14.6175140349923 -629000 ekin = 0.337147043698277 | erot = 0.37102569897414 | epot = -15.3256867776908 | etot = -14.6175140350184 -630000 ekin = 0.351051052994981 | erot = 0.362066500826367 | epot = -15.3306315888613 | etot = -14.6175140350399 -631000 ekin = 0.364060148819096 | erot = 0.352070586245494 | epot = -15.333644770118 | etot = -14.6175140350534 -632000 ekin = 0.375621025661737 | erot = 0.341366514680777 | epot = -15.3345015753988 | etot = -14.6175140350563 -633000 ekin = 0.385258541224816 | erot = 0.33037209230534 | epot = -15.3331446685769 | etot = -14.6175140350467 -634000 ekin = 0.392607865616762 | erot = 0.31958895649352 | epot = -15.3297108571345 | etot = -14.6175140350242 -635000 ekin = 0.39743609727868 | erot = 0.309588318033271 | epot = -15.3245384503017 | etot = -14.6175140349897 -636000 ekin = 0.399651602685353 | erot = 0.30098809437835 | epot = -15.318153732009 | etot = -14.6175140349453 -637000 ekin = 0.399301141333129 | erot = 0.294422893568983 | epot = -15.3112380697961 | etot = -14.617514034894 -638000 ekin = 0.396556439147407 | erot = 0.290509369489655 | epot = -15.3045798434767 | etot = -14.6175140348397 -639000 ekin = 0.391692975513997 | erot = 0.289810143797434 | epot = -15.2990171540975 | etot = -14.617514034786 -640000 ekin = 0.385064212934161 | erot = 0.292799653113688 | epot = -15.2953779007847 | etot = -14.6175140347369 -641000 ekin = 0.377074355551302 | erot = 0.299834934663062 | epot = -15.2944233249094 | etot = -14.6175140346951 -642000 ekin = 0.368152133961515 | erot = 0.311133625026309 | epot = -15.2967997936509 | etot = -14.6175140346631 -643000 ekin = 0.358727298275111 | erot = 0.326760494743868 | epot = -15.3030018276614 | etot = -14.6175140346424 -644000 ekin = 0.349210670243499 | erot = 0.346622862554325 | epot = -15.3133475674317 | etot = -14.6175140346339 -645000 ekin = 0.339977915474886 | erot = 0.370474376280189 | epot = -15.3279663263927 | etot = -14.6175140346376 -646000 ekin = 0.331356734049287 | erot = 0.397926004729598 | epot = -15.3467967734319 | etot = -14.617514034653 -647000 ekin = 0.323616951062021 | erot = 0.428462692622343 | epot = -15.3695936783637 | etot = -14.6175140346794 -648000 ekin = 0.316962984679749 | erot = 0.461463981264525 | epot = -15.3959410006599 | etot = -14.6175140347156 -649000 ekin = 0.311528303721769 | erot = 0.496226945506609 | epot = -15.4252692839889 | etot = -14.6175140347605 -650000 ekin = 0.307371814502051 | erot = 0.53199011331203 | epot = -15.4568759626267 | etot = -14.6175140348127 -651000 ekin = 0.304476169211528 | erot = 0.567957247023637 | epot = -15.4899474511057 | etot = -14.6175140348705 -652000 ekin = 0.302748327843063 | erot = 0.603320352539344 | epot = -15.523582715315 | etot = -14.6175140349325 -653000 ekin = 0.302022769689561 | erot = 0.637281675063983 | epot = -15.5568184797505 | etot = -14.617514034997 -654000 ekin = 0.302067723594154 | erot = 0.669074745116258 | epot = -15.5886565037723 | etot = -14.6175140350619 -655000 ekin = 0.302594671774775 | erot = 0.697984728110365 | epot = -15.6180934350103 | etot = -14.6175140351252 -656000 ekin = 0.303271161273661 | erot = 0.723368330432067 | epot = -15.6441535268902 | etot = -14.6175140351845 -657000 ekin = 0.303736663270792 | erot = 0.744673311812443 | epot = -15.6659240103206 | etot = -14.6175140352373 -658000 ekin = 0.303620889262384 | erot = 0.761457272710392 | epot = -15.6825921972542 | etot = -14.6175140352814 -659000 ekin = 0.302563666907984 | erot = 0.773404945481054 | epot = -15.6934826477032 | etot = -14.6175140353142 -660000 ekin = 0.300235395695091 | erot = 0.780343280385843 | epot = -15.698092711415 | etot = -14.6175140353341 -661000 ekin = 0.296355710531902 | erot = 0.782250083093143 | epot = -15.6961198289647 | etot = -14.6175140353397 -662000 ekin = 0.290710478297184 | erot = 0.779257959177687 | epot = -15.6874824728051 | etot = -14.6175140353302 -663000 ekin = 0.283165147463639 | erot = 0.77165065199169 | epot = -15.6723298347614 | etot = -14.6175140353061 -664000 ekin = 0.273673427176448 | erot = 0.759850562455872 | epot = -15.6510380249006 | etot = -14.6175140352683 -665000 ekin = 0.262280913452385 | erot = 0.744397727319057 | epot = -15.6241926759903 | etot = -14.6175140352189 -666000 ekin = 0.249123647022483 | erot = 0.7259212317447 | epot = -15.5925589139278 | etot = -14.6175140351606 -667000 ekin = 0.234422061210147 | erot = 0.705104954965032 | epot = -15.5570410512716 | etot = -14.6175140350964 -668000 ekin = 0.218471158369324 | erot = 0.682650243124776 | epot = -15.5186354365237 | etot = -14.6175140350296 -669000 ekin = 0.201627981911843 | erot = 0.659238455806553 | epot = -15.4783804726815 | etot = -14.6175140349632 -670000 ekin = 0.184297501939065 | erot = 0.635496303880898 | epot = -15.43730784072 | etot = -14.6175140349001 -671000 ekin = 0.166917915805004 | erot = 0.611966525748027 | epot = -15.3963984763956 | etot = -14.6175140348426 -672000 ekin = 0.149946120674196 | erot = 0.589085832361493 | epot = -15.3565459878282 | etot = -14.6175140347926 -673000 ekin = 0.133843801904582 | erot = 0.567171306812613 | epot = -15.318529143468 | etot = -14.6175140347508 -674000 ekin = 0.119064262674576 | erot = 0.546415679820867 | epot = -15.2829939772136 | etot = -14.6175140347181 -675000 ekin = 0.106039855017085 | erot = 0.526891195482506 | epot = -15.250445085194 | etot = -14.6175140346944 -676000 ekin = 0.0951697078773878 | erot = 0.508561175678473 | epot = -15.2212449182352 | etot = -14.6175140346793 -677000 ekin = 0.086807451986192 | erot = 0.491297978909966 | epot = -15.1956194655683 | etot = -14.6175140346722 -678000 ekin = 0.0812485969712828 | erot = 0.474905301099178 | epot = -15.1736679327427 | etot = -14.6175140346722 -679000 ekin = 0.0787177619800211 | erot = 0.459143233464763 | epot = -15.1553750301234 | etot = -14.6175140346787 -680000 ekin = 0.0793562024648552 | erot = 0.443753980649329 | epot = -15.140624217805 | etot = -14.6175140346908 -681000 ekin = 0.0832104900789999 | erot = 0.428486254341784 | epot = -15.1292107791285 | etot = -14.6175140347077 -682000 ekin = 0.0902236865225188 | erot = 0.413116880933304 | epot = -15.1208546021847 | etot = -14.6175140347289 -683000 ekin = 0.100230543462408 | erot = 0.397468585264377 | epot = -15.11521316348 | etot = -14.6175140347533 -684000 ekin = 0.112958164258869 | erot = 0.381423459018597 | epot = -15.1118956580574 | etot = -14.6175140347799 -685000 ekin = 0.128033094046148 | erot = 0.364932120277307 | epot = -15.1104792491311 | etot = -14.6175140348076 -686000 ekin = 0.144995008361601 | erot = 0.348018922992647 | epot = -15.1105279661894 | etot = -14.6175140348351 -687000 ekin = 0.163316207854767 | erot = 0.330783730221022 | epot = -15.1116139729365 | etot = -14.6175140348607 -688000 ekin = 0.182425234215551 | erot = 0.313400732953855 | epot = -15.1133400020525 | etot = -14.6175140348831 -689000 ekin = 0.201732335852577 | erot = 0.296114640201443 | epot = -15.1153610109551 | etot = -14.6175140349011 -690000 ekin = 0.220654383891154 | erot = 0.279234374240434 | epot = -15.1174027930453 | etot = -14.6175140349137 -691000 ekin = 0.23863718992453 | erot = 0.263124260136862 | epot = -15.1192754849819 | etot = -14.6175140349205 -692000 ekin = 0.255173895596428 | erot = 0.248192653897472 | epot = -15.1208805844156 | etot = -14.6175140349217 -693000 ekin = 0.269818995118043 | erot = 0.234878024009109 | epot = -15.1222110540446 | etot = -14.6175140349175 -694000 ekin = 0.282198402189113 | erot = 0.223632668706427 | epot = -15.1233451058044 | etot = -14.6175140349089 -695000 ekin = 0.292016609393231 | erot = 0.214904477348993 | epot = -15.124435121639 | etot = -14.6175140348968 -696000 ekin = 0.299062308191112 | erot = 0.209117382947945 | epot = -15.1256937260212 | etot = -14.6175140348821 -697000 ekin = 0.30321380997214 | erot = 0.206651361568493 | epot = -15.1273792064064 | etot = -14.6175140348658 -698000 ekin = 0.30444525619219 | erot = 0.207822979229873 | epot = -15.1297822702705 | etot = -14.6175140348484 -699000 ekin = 0.302833983904948 | erot = 0.212867544425277 | epot = -15.1332155631607 | etot = -14.6175140348305 -700000 ekin = 0.29856859634332 | erot = 0.221923881123336 | epot = -15.1380065122785 | etot = -14.6175140348118 -701000 ekin = 0.291956369738242 | erot = 0.235022588976831 | epot = -15.1444929935074 | etot = -14.6175140347924 -702000 ekin = 0.283427734153835 | erot = 0.252078414121472 | epot = -15.153020183048 | etot = -14.6175140347727 -703000 ekin = 0.273534855576746 | erot = 0.272887068861365 | epot = -15.1639359591909 | etot = -14.6175140347528 -704000 ekin = 0.262941046164233 | erot = 0.297126498876432 | epot = -15.1775815797744 | etot = -14.6175140347337 -705000 ekin = 0.252398060444365 | erot = 0.324362359960393 | epot = -15.194274455122 | etot = -14.6175140347173 -706000 ekin = 0.242709489752073 | erot = 0.354057349893491 | epot = -15.2142808743513 | etot = -14.6175140347058 -707000 ekin = 0.234680465258637 | erot = 0.385584073394242 | epot = -15.2377785733552 | etot = -14.6175140347023 -708000 ekin = 0.229056562326157 | erot = 0.418241319394871 | epot = -15.264811916431 | etot = -14.61751403471 -709000 ekin = 0.226457657533258 | erot = 0.451273895783649 | epot = -15.2952455880485 | etot = -14.6175140347316 -710000 ekin = 0.227314828595311 | erot = 0.483896330830945 | epot = -15.3287251941949 | etot = -14.6175140347687 -711000 ekin = 0.231819479497128 | erot = 0.515320742171203 | epot = -15.3646542564898 | etot = -14.6175140348215 -712000 ekin = 0.239893150548963 | erot = 0.544788749312711 | epot = -15.4021959347498 | etot = -14.6175140348881 -713000 ekin = 0.251183758823288 | erot = 0.571606341188824 | epot = -15.4403041349766 | etot = -14.6175140349645 -714000 ekin = 0.265090036185525 | erot = 0.595179886372787 | epot = -15.4777839576035 | etot = -14.6175140350452 -715000 ekin = 0.280811306968559 | erot = 0.615050345044272 | epot = -15.5133756871366 | etot = -14.6175140351238 -716000 ekin = 0.297415784950407 | erot = 0.630922165703626 | epot = -15.5458519858478 | etot = -14.6175140351937 -717000 ekin = 0.313918116237917 | erot = 0.642683345316706 | epot = -15.5741154968041 | etot = -14.6175140352494 -718000 ekin = 0.329356373327112 | erot = 0.650413757300199 | epot = -15.597284165914 | etot = -14.6175140352867 -719000 ekin = 0.342860093484457 | erot = 0.654380316354483 | epot = -15.6147544451421 | etot = -14.6175140353032 -720000 ekin = 0.353703497403049 | erot = 0.655019233384572 | epot = -15.6262367660863 | etot = -14.6175140352987 -721000 ekin = 0.361340844905849 | erot = 0.652906431496321 | epot = -15.6317613116767 | etot = -14.6175140352745 -722000 ekin = 0.365423978941575 | erot = 0.648719378780931 | epot = -15.6316573929561 | etot = -14.6175140352336 -723000 ekin = 0.365803989072306 | erot = 0.643193727890481 | epot = -15.6265117521426 | etot = -14.6175140351798 -724000 ekin = 0.362520178745313 | erot = 0.637078359573022 | epot = -15.6171125734355 | etot = -14.6175140351172 -725000 ekin = 0.355779938480366 | erot = 0.631092082280502 | epot = -15.604386055811 | etot = -14.6175140350501 -726000 ekin = 0.345932952941823 | erot = 0.625884613514235 | epot = -15.5893316014386 | etot = -14.6175140349825 -727000 ekin = 0.333442641405672 | erot = 0.622003743386422 | epot = -15.5729604197101 | etot = -14.617514034918 -728000 ekin = 0.318857050497248 | erot = 0.619869891937897 | epot = -15.5562409772948 | etot = -14.6175140348596 -729000 ekin = 0.302780724957378 | erot = 0.619758691690217 | epot = -15.5400534514572 | etot = -14.6175140348096 -730000 ekin = 0.285848455041315 | erot = 0.621791770570811 | epot = -15.5251542603814 | etot = -14.6175140347693 -731000 ekin = 0.268701272205162 | erot = 0.625935552811657 | epot = -15.5121508597566 | etot = -14.6175140347398 -732000 ekin = 0.251964649664151 | erot = 0.632007594592174 | epot = -15.5014862789777 | etot = -14.6175140347214 -733000 ekin = 0.236228569496788 | erot = 0.639689689353094 | epot = -15.4934322935639 | etot = -14.617514034714 -734000 ekin = 0.222028960746823 | erot = 0.648546698715163 | epot = -15.4880896941794 | etot = -14.6175140347174 -735000 ekin = 0.209830023527925 | erot = 0.658049804517654 | epot = -15.4853938627761 | etot = -14.6175140347305 -736000 ekin = 0.200007166761159 | erot = 0.667602683399479 | epot = -15.4851238849135 | etot = -14.6175140347528 -737000 ekin = 0.192830719625055 | erot = 0.676569044421098 | epot = -15.4869137988298 | etot = -14.6175140347837 -738000 ekin = 0.188451200585547 | erot = 0.684300102137718 | epot = -15.4902653375453 | etot = -14.6175140348221 -739000 ekin = 0.186887639936592 | erot = 0.690160900651566 | epot = -15.4945625754552 | etot = -14.617514034867 -740000 ekin = 0.188021068410451 | erot = 0.693554915034906 | epot = -15.4990900183625 | etot = -14.6175140349172 -741000 ekin = 0.191595568995028 | erot = 0.693946922730537 | epot = -15.5030565266959 | etot = -14.6175140349703 -742000 ekin = 0.197228843628196 | erot = 0.690884208638673 | epot = -15.5056270872912 | etot = -14.6175140350243 -743000 ekin = 0.20443350363757 | erot = 0.684016821527744 | epot = -15.5059643602408 | etot = -14.6175140350755 -744000 ekin = 0.212648433381533 | erot = 0.673116668202852 | epot = -15.5032791367049 | etot = -14.6175140351205 -745000 ekin = 0.221277722248148 | erot = 0.658094727365387 | epot = -15.496886484769 | etot = -14.6175140351555 -746000 ekin = 0.229733012317517 | erot = 0.639014583781424 | epot = -15.4862616312763 | etot = -14.6175140351774 -747000 ekin = 0.2374740441444 | erot = 0.61610009667291 | epot = -15.4710881760011 | etot = -14.6175140351838 -748000 ekin = 0.244042266762953 | erot = 0.5897348727874 | epot = -15.4512911747243 | etot = -14.617514035174 -749000 ekin = 0.249083597953252 | erot = 0.56045151840338 | epot = -15.4270491515053 | etot = -14.6175140351487 -750000 ekin = 0.252358330147216 | erot = 0.528910066811307 | epot = -15.3987824320685 | etot = -14.61751403511 -751000 ekin = 0.253738423481735 | erot = 0.495866496254582 | epot = -15.3671189547979 | etot = -14.6175140350616 -752000 ekin = 0.253194394015788 | erot = 0.462133785333153 | epot = -15.3328422143563 | etot = -14.6175140350074 -753000 ekin = 0.250775308155868 | erot = 0.428539072350445 | epot = -15.2968284154581 | etot = -14.6175140349518 -754000 ekin = 0.246585878547032 | erot = 0.395880964578706 | epot = -15.2599808780244 | etot = -14.6175140348987 -755000 ekin = 0.240764398113293 | erot = 0.364890850085532 | epot = -15.2231692830501 | etot = -14.6175140348513 -756000 ekin = 0.23346447104344 | erot = 0.33620133003045 | epot = -15.1871798358857 | etot = -14.6175140348118 -757000 ekin = 0.224842467158388 | erot = 0.310323830730243 | epot = -15.1526803326699 | etot = -14.6175140347812 -758000 ekin = 0.215051562421428 | erot = 0.287636293952697 | epot = -15.120201891134 | etot = -14.6175140347599 -759000 ekin = 0.204242275876271 | erot = 0.268380753509857 | epot = -15.0901370641325 | etot = -14.6175140347464 -760000 ekin = 0.192568636065474 | erot = 0.252669695562842 | epot = -15.0627523663679 | etot = -14.6175140347396 -761000 ekin = 0.180198520175885 | erot = 0.240499428911651 | epot = -15.0382119838247 | etot = -14.6175140347371 -762000 ekin = 0.167326299029189 | erot = 0.231768292967787 | epot = -15.0166086267339 | etot = -14.6175140347369 -763000 ekin = 0.154185685901956 | erot = 0.226297425416186 | epot = -14.9979971460548 | etot = -14.6175140347367 -764000 ekin = 0.141060632748886 | erot = 0.22385200334864 | epot = -14.9824266708322 | etot = -14.6175140347347 -765000 ekin = 0.128292252296688 | erot = 0.224161332818126 | epot = -14.9699676198447 | etot = -14.6175140347299 -766000 ekin = 0.116280064488099 | erot = 0.226936813023238 | epot = -14.9607309122326 | etot = -14.6175140347212 -767000 ekin = 0.105476340626969 | erot = 0.23188750727037 | epot = -14.9548778826066 | etot = -14.6175140347093 -768000 ekin = 0.096372890945937 | erot = 0.238733641345087 | epot = -14.9526205669852 | etot = -14.6175140346942 -769000 ekin = 0.0894802427431669 | erot = 0.247218655409017 | epot = -14.9542129328294 | etot = -14.6175140346772 -770000 ekin = 0.0852997361093092 | erot = 0.257120353608164 | epot = -14.9599341243773 | etot = -14.6175140346598 -771000 ekin = 0.0842896183570599 | erot = 0.268261228608835 | epot = -14.9700648816096 | etot = -14.6175140346437 -772000 ekin = 0.0868267987477346 | erot = 0.280517313419992 | epot = -14.9848581467989 | etot = -14.6175140346312 -773000 ekin = 0.0931666172480206 | erot = 0.293824162660099 | epot = -15.0045048145328 | etot = -14.6175140346247 -774000 ekin = 0.103403843826671 | erot = 0.308178073397117 | epot = -15.0290959518505 | etot = -14.6175140346267 -775000 ekin = 0.117439110045757 | erot = 0.323630675217794 | epot = -15.0585838199034 | etot = -14.6175140346399 -776000 ekin = 0.134955835365974 | erot = 0.340275613675452 | epot = -15.0927454837074 | etot = -14.617514034666 -777000 ekin = 0.155413263635979 | erot = 0.358227842745911 | epot = -15.131155141088 | etot = -14.6175140347061 -778000 ekin = 0.178060391221893 | erot = 0.377596905889502 | epot = -15.1731713318714 | etot = -14.61751403476 -779000 ekin = 0.201973803865647 | erot = 0.398457850158065 | epot = -15.2179456888489 | etot = -14.6175140348252 -780000 ekin = 0.226119091214274 | erot = 0.420824480238275 | epot = -15.2644576063504 | etot = -14.6175140348978 -781000 ekin = 0.249431156626622 | erot = 0.444629585314847 | epot = -15.3115747769139 | etot = -14.6175140349725 -782000 ekin = 0.270904470269639 | erot = 0.469715692367583 | epot = -15.3581341976801 | etot = -14.6175140350429 -783000 ekin = 0.289681273783551 | erot = 0.495837747641305 | epot = -15.4030330565279 | etot = -14.617514035103 -784000 ekin = 0.305125009986927 | erot = 0.522676532161923 | epot = -15.445315577297 | etot = -14.6175140351482 -785000 ekin = 0.316868262923434 | erot = 0.549859353707342 | epot = -15.4842416518064 | etot = -14.6175140351756 -786000 ekin = 0.324828845889255 | erot = 0.576983310023016 | epot = -15.5193261910972 | etot = -14.6175140351849 -787000 ekin = 0.32919323387939 | erot = 0.603636505801527 | epot = -15.550343774859 | etot = -14.617514035178 -788000 ekin = 0.330371864852151 | erot = 0.629413875563716 | epot = -15.5772997755747 | etot = -14.6175140351588 -789000 ekin = 0.328934711355495 | erot = 0.653926193132344 | epot = -15.6003749396201 | etot = -14.6175140351322 -790000 ekin = 0.32553731947378 | erot = 0.676802790006292 | epot = -15.6198541445837 | etot = -14.6175140351036 -791000 ekin = 0.320847267933459 | erot = 0.697689943211487 | epot = -15.6360512462227 | etot = -14.6175140350777 -792000 ekin = 0.315479253539392 | erot = 0.716247584423973 | epot = -15.6492408730215 | etot = -14.6175140350582 -793000 ekin = 0.309944490982107 | erot = 0.732146955922051 | epot = -15.6596054819516 | etot = -14.6175140350474 -794000 ekin = 0.304617480925239 | erot = 0.745071299199412 | epot = -15.6672028151708 | etot = -14.6175140350461 -795000 ekin = 0.299720880976423 | erot = 0.754720862084592 | epot = -15.6719557781148 | etot = -14.6175140350538 -796000 ekin = 0.295327396180162 | erot = 0.760822658787278 | epot = -15.6736640900359 | etot = -14.6175140350685 -797000 ekin = 0.291376296851675 | erot = 0.763144639344914 | epot = -15.6720349712838 | etot = -14.6175140350872 -798000 ekin = 0.287701294703707 | erot = 0.761513269131401 | epot = -15.6667285989415 | etot = -14.6175140351064 -799000 ekin = 0.284065979572222 | erot = 0.755832991336602 | epot = -15.6574130060307 | etot = -14.6175140351219 -800000 ekin = 0.280202790631652 | erot = 0.746105645863969 | epot = -15.643822471626 | etot = -14.6175140351304 -801000 ekin = 0.275851560112653 | erot = 0.732447665813264 | epot = -15.6258132610543 | etot = -14.6175140351284 -802000 ekin = 0.270794034433592 | erot = 0.715102809072576 | epot = -15.6034108786199 | etot = -14.6175140351138 -803000 ekin = 0.264881442636465 | erot = 0.694448356025832 | epot = -15.5768438337476 | etot = -14.6175140350853 -804000 ekin = 0.258053167891105 | erot = 0.670993199746629 | epot = -15.5465604026808 | etot = -14.6175140350431 -805000 ekin = 0.250345604728483 | erot = 0.645366941436678 | epot = -15.5132265811537 | etot = -14.6175140349885 -806000 ekin = 0.241890533712104 | erot = 0.618299214644422 | epot = -15.4777037832803 | etot = -14.6175140349238 -807000 ekin = 0.232905655207387 | erot = 0.590591287736433 | epot = -15.4410109777962 | etot = -14.6175140348524 -808000 ekin = 0.223678061733381 | erot = 0.563080896688429 | epot = -15.4042729931999 | etot = -14.6175140347781 -809000 ekin = 0.21454303523099 | erot = 0.536602758842029 | epot = -15.3686598287782 | etot = -14.6175140347052 -810000 ekin = 0.205860488313568 | erot = 0.511947500023896 | epot = -15.3353220229752 | etot = -14.6175140346377 -811000 ekin = 0.197991117806005 | erot = 0.489821758278081 | epot = -15.3053269106636 | etot = -14.6175140345795 -812000 ekin = 0.191273941671524 | erot = 0.470812030934271 | epot = -15.2796000071394 | etot = -14.6175140345336 -813000 ekin = 0.186006404369985 | erot = 0.455354451062655 | epot = -15.2588748899354 | etot = -14.6175140345028 -814000 ekin = 0.18242775371236 | erot = 0.443712201374096 | epot = -15.243653989575 | etot = -14.6175140344885 -815000 ekin = 0.18070598633541 | erot = 0.435961774091635 | epot = -15.234181794919 | etot = -14.617514034492 -816000 ekin = 0.180928373605491 | erot = 0.431988814113314 | epot = -15.2304312222317 | etot = -14.6175140345129 -817000 ekin = 0.183095431234183 | erot = 0.431493858263631 | epot = -15.2321033240486 | etot = -14.6175140345508 -818000 ekin = 0.187118173911464 | erot = 0.434007895069526 | epot = -15.2386401035849 | etot = -14.6175140346039 -819000 ekin = 0.192818568053382 | erot = 0.43891728680681 | epot = -15.2492498895299 | etot = -14.6175140346697 -820000 ekin = 0.199933211814771 | erot = 0.445497181488374 | epot = -15.2629444280486 | etot = -14.6175140347454 -821000 ekin = 0.208120374081953 | erot = 0.452952069483821 | epot = -15.2785864783931 | etot = -14.6175140348273 -822000 ekin = 0.216970558498266 | erot = 0.460461605795678 | epot = -15.2949461992054 | etot = -14.6175140349114 -823000 ekin = 0.226020685629111 | erot = 0.467229260922827 | epot = -15.3107639815452 | etot = -14.6175140349933 -824000 ekin = 0.234771793851546 | erot = 0.47253085821668 | epot = -15.3248166871369 | etot = -14.6175140350687 -825000 ekin = 0.242709867661982 | erot = 0.475759712130438 | epot = -15.3359836149259 | etot = -14.6175140351335 -826000 ekin = 0.249329060857897 | erot = 0.476465014357233 | epot = -15.3433081103994 | etot = -14.6175140351843 -827000 ekin = 0.254156259485738 | erot = 0.474380409602743 | epot = -15.3460507043067 | etot = -14.6175140352182 -828000 ekin = 0.256775693170762 | erot = 0.46944038334452 | epot = -15.3437301117489 | etot = -14.6175140352336 -829000 ekin = 0.256852201216661 | erot = 0.461783092102077 | epot = -15.3361493285486 | etot = -14.6175140352298 -830000 ekin = 0.254151805816721 | erot = 0.451739467041208 | epot = -15.3234053080651 | etot = -14.6175140352072 -831000 ekin = 0.248558416433736 | erot = 0.439809632306583 | epot = -15.3058820839077 | etot = -14.6175140351674 -832000 ekin = 0.240085737091052 | erot = 0.426628719076076 | epot = -15.2842284912797 | etot = -14.6175140351126 -833000 ekin = 0.228883712687689 | erot = 0.412924890624274 | epot = -15.2593226383577 | etot = -14.6175140350458 -834000 ekin = 0.215239082681844 | erot = 0.399472764056086 | epot = -15.2322258817084 | etot = -14.6175140349705 -835000 ekin = 0.199569787294665 | erot = 0.387045440519586 | epot = -15.2041292627046 | etot = -14.6175140348904 -836000 ekin = 0.182413100763772 | erot = 0.376368114580803 | epot = -15.1762952501539 | etot = -14.6175140348093 -837000 ekin = 0.164407483062706 | erot = 0.36807582593139 | epot = -15.1499973437255 | etot = -14.6175140347314 -838000 ekin = 0.146268295773454 | erot = 0.362677435797712 | epot = -15.1264597662312 | etot = -14.61751403466 -839000 ekin = 0.128757768426402 | erot = 0.360527421580405 | epot = -15.1067992246056 | etot = -14.6175140345988 -840000 ekin = 0.112649960717984 | erot = 0.361806618656283 | epot = -15.091970613925 | etot = -14.6175140345507 -841000 ekin = 0.0986919456677054 | erot = 0.366512603929069 | epot = -15.0827185841153 | etot = -14.6175140345185 -842000 ekin = 0.0875630029234395 | erot = 0.374460003555771 | epot = -15.0795370409833 | etot = -14.6175140345041 -843000 ekin = 0.0798341847686366 | erot = 0.385290606532762 | epot = -15.08263882581 | etot = -14.6175140345086 -844000 ekin = 0.0759310929907395 | erot = 0.3984927697296 | epot = -15.0919378972525 | etot = -14.6175140345322 -845000 ekin = 0.076102961020352 | erot = 0.413429207168617 | epot = -15.107046202763 | etot = -14.617514034574 -846000 ekin = 0.0804010613290235 | erot = 0.429371869322532 | epot = -15.1272869652841 | etot = -14.6175140346325 -847000 ekin = 0.0886689809240873 | erot = 0.445542241998021 | epot = -15.1517252576265 | etot = -14.6175140347044 -848000 ekin = 0.100546421459775 | erot = 0.461155038711605 | epot = -15.179215494957 | etot = -14.6175140347856 -849000 ekin = 0.115486960010826 | erot = 0.475462945351677 | epot = -15.208463940234 | etot = -14.6175140348715 -850000 ekin = 0.132788806695669 | erot = 0.487799837752774 | epot = -15.2381026794056 | etot = -14.6175140349571 -851000 ekin = 0.15163622778631 | erot = 0.49761978557658 | epot = -15.2667700483999 | etot = -14.617514035037 -852000 ekin = 0.171148194576093 | erot = 0.5045292426275 | epot = -15.2931914723102 | etot = -14.6175140351066 -853000 ekin = 0.19043015939564 | erot = 0.508310157461229 | epot = -15.3162543520185 | etot = -14.6175140351617 -854000 ekin = 0.208624756899512 | erot = 0.508932337650922 | epot = -15.3350711297497 | etot = -14.6175140351993 -855000 ekin = 0.224957674812131 | erot = 0.506554231539335 | epot = -15.3490259415692 | etot = -14.6175140352178 -856000 ekin = 0.238775816538934 | erot = 0.501512259960027 | epot = -15.3578021117156 | etot = -14.6175140352166 -857000 ekin = 0.249575992233887 | erot = 0.494299801981668 | epot = -15.3613898294122 | etot = -14.6175140351967 -858000 ekin = 0.257023502073677 | erot = 0.485537766821904 | epot = -15.3600753040553 | etot = -14.6175140351598 -859000 ekin = 0.260960921285557 | erot = 0.47593924761589 | epot = -15.3544142040099 | etot = -14.6175140351084 -860000 ekin = 0.261408037072254 | erot = 0.466270984604724 | epot = -15.3451930567227 | etot = -14.6175140350457 -861000 ekin = 0.258554187538227 | erot = 0.457314264403266 | epot = -15.3333824869164 | etot = -14.6175140349749 -862000 ekin = 0.252744258033032 | erot = 0.449827506886351 | epot = -15.3200857998187 | etot = -14.6175140348993 -863000 ekin = 0.24445941779656 | erot = 0.444512141834286 | epot = -15.3064855944532 | etot = -14.6175140348224 -864000 ekin = 0.234293368840191 | erot = 0.441983030939893 | epot = -15.2937904345275 | etot = -14.6175140347474 -865000 ekin = 0.222924696624028 | erot = 0.442744308395087 | epot = -15.2831830396966 | etot = -14.6175140346775 -866000 ekin = 0.211086026109153 | erot = 0.447169652381141 | epot = -15.275769713106 | etot = -14.6175140346157 -867000 ekin = 0.199530465892741 | erot = 0.455487658924214 | epot = -15.2725321593816 | etot = -14.6175140345647 -868000 ekin = 0.188996288427104 | erot = 0.467771811643747 | epot = -15.2742821345979 | etot = -14.6175140345271 -869000 ekin = 0.180171161859106 | erot = 0.483934855626885 | epot = -15.2816200519912 | etot = -14.6175140345052 -870000 ekin = 0.17365741386822 | erot = 0.503727420429673 | epot = -15.2948988687985 | etot = -14.6175140345006 -871000 ekin = 0.169940429081846 | erot = 0.52674119313203 | epot = -15.3141956567285 | etot = -14.6175140345146 -872000 ekin = 0.169362274178155 | erot = 0.552417088945952 | epot = -15.3392933976716 | etot = -14.6175140345475 -873000 ekin = 0.172102391201285 | erot = 0.580058846014358 | epot = -15.3696752718142 | etot = -14.6175140345986 -874000 ekin = 0.17816700290151 | erot = 0.608852557307893 | epot = -15.4045335948759 | etot = -14.6175140346665 -875000 ekin = 0.187388233890407 | erot = 0.637892396630087 | epot = -15.4427946652692 | etot = -14.6175140347487 -876000 ekin = 0.19943318136702 | erot = 0.666212376945529 | epot = -15.4831595931541 | etot = -14.6175140348415 -877000 ekin = 0.213822249050307 | erot = 0.692823325238237 | epot = -15.5241596092293 | etot = -14.6175140349407 -878000 ekin = 0.229955728385699 | erot = 0.71675421264508 | epot = -15.5642239760723 | etot = -14.6175140350415 -879000 ekin = 0.24714610464469 | erot = 0.737095186135096 | epot = -15.6017553259188 | etot = -14.617514035139 -880000 ekin = 0.264653797001986 | erot = 0.753040153406107 | epot = -15.6352079856364 | etot = -14.6175140352283 -881000 ekin = 0.281723784261025 | erot = 0.763926241591362 | epot = -15.6631640611574 | etot = -14.617514035305 -882000 ekin = 0.297620641606497 | erot = 0.769267373447878 | epot = -15.6844020504201 | etot = -14.6175140353657 -883000 ekin = 0.31165996716591 | erot = 0.768779581882635 | epot = -15.6979535844562 | etot = -14.6175140354077 -884000 ekin = 0.32323477376766 | erot = 0.762396270684418 | epot = -15.7031450798815 | etot = -14.6175140354294 -885000 ekin = 0.331836099624976 | erot = 0.750272396067649 | epot = -15.6996225311232 | etot = -14.6175140354305 -886000 ekin = 0.33706775156376 | erot = 0.73277738526586 | epot = -15.6873591722413 | etot = -14.6175140354116 -887000 ekin = 0.33865564976609 | erot = 0.710477420750346 | epot = -15.6666471058906 | etot = -14.6175140353742 -888000 ekin = 0.336452632420724 | erot = 0.684108417156207 | epot = -15.6380750848973 | etot = -14.6175140353203 -889000 ekin = 0.330439768515565 | erot = 0.654541548240145 | epot = -15.6024953520085 | etot = -14.6175140352528 -890000 ekin = 0.320725208484774 | erot = 0.622743520027188 | epot = -15.5609827636863 | etot = -14.6175140351743 -891000 ekin = 0.30754138620901 | erot = 0.589733936087593 | epot = -15.5147893573847 | etot = -14.6175140350881 -892000 ekin = 0.291240998129824 | erot = 0.55654208039805 | epot = -15.4652971135248 | etot = -14.6175140349969 -893000 ekin = 0.272291667891339 | erot = 0.524165278720875 | epot = -15.413970981516 | etot = -14.6175140349038 -894000 ekin = 0.251268620703469 | erot = 0.493530718297772 | epot = -15.3623133738123 | etot = -14.617514034811 -895000 ekin = 0.228844131843647 | erot = 0.465462234286628 | epot = -15.3118204008517 | etot = -14.6175140347214 -896000 ekin = 0.205772103521931 | erot = 0.44065313730724 | epot = -15.2639392754666 | etot = -14.6175140346374 -897000 ekin = 0.182866017803037 | erot = 0.419645693758354 | epot = -15.2200257461231 | etot = -14.6175140345617 -898000 ekin = 0.160968870008541 | erot = 0.402817425242934 | epot = -15.1813003297485 | etot = -14.617514034497 -899000 ekin = 0.140914625128407 | erot = 0.390374024162942 | epot = -15.1488026837377 | etot = -14.6175140344464 -900000 ekin = 0.123482269337592 | erot = 0.382348451689143 | epot = -15.1233447554393 | etot = -14.6175140344126 -901000 ekin = 0.109345484385137 | erot = 0.3786057375543 | epot = -15.1054652563377 | etot = -14.6175140343982 -902000 ekin = 0.0990229789068443 | erot = 0.378853140166087 | epot = -15.0953901534781 | etot = -14.6175140344052 -903000 ekin = 0.0928360184564003 | erot = 0.382655585825594 | epot = -15.0930056387161 | etot = -14.6175140344341 -904000 ekin = 0.0908801123879861 | erot = 0.389456554773426 | epot = -15.0978507016452 | etot = -14.6175140344838 -905000 ekin = 0.0930167096525759 | erot = 0.398604648849945 | epot = -15.109135393054 | etot = -14.6175140345515 -906000 ekin = 0.0988880708462299 | erot = 0.409385812369135 | epot = -15.1257879178477 | etot = -14.6175140346323 -907000 ekin = 0.107954659147321 | erot = 0.421060528764021 | epot = -15.1465292226317 | etot = -14.6175140347203 -908000 ekin = 0.119550305154264 | erot = 0.432904367174404 | epot = -15.1699687071371 | etot = -14.6175140348085 -909000 ekin = 0.132947118364171 | erot = 0.44424923215812 | epot = -15.1947103854124 | etot = -14.6175140348901 -910000 ekin = 0.147420543333256 | erot = 0.454521879656354 | epot = -15.2194564579492 | etot = -14.6175140349595 -911000 ekin = 0.162305506309105 | erot = 0.463275978359162 | epot = -15.243095519681 | etot = -14.6175140350127 -912000 ekin = 0.177037050912775 | erot = 0.470214361754759 | epot = -15.264765447715 | etot = -14.6175140350475 -913000 ekin = 0.191172462463145 | erot = 0.47519909256641 | epot = -15.2838855900937 | etot = -14.6175140350641 -914000 ekin = 0.204395616840717 | erot = 0.478248345048037 | epot = -15.3001579969529 | etot = -14.6175140350642 -915000 ekin = 0.216507238695372 | erot = 0.479520616572283 | epot = -15.3135418903184 | etot = -14.6175140350507 -916000 ekin = 0.227406352399354 | erot = 0.479288139236181 | epot = -15.324208526663 | etot = -14.6175140350275 -917000 ekin = 0.237068358848421 | erot = 0.47790239272317 | epot = -15.3324847865699 | etot = -14.6175140349983 -918000 ekin = 0.245524170399261 | erot = 0.475755244752224 | epot = -15.3387934501184 | etot = -14.6175140349669 -919000 ekin = 0.252843202023974 | erot = 0.473239468155706 | epot = -15.343596705116 | etot = -14.6175140349363 -920000 ekin = 0.259121284815254 | erot = 0.470712244290015 | epot = -15.3473475640143 | etot = -14.617514034909 -921000 ekin = 0.264473144076574 | erot = 0.468464808092157 | epot = -15.3504519870554 | etot = -14.6175140348867 -922000 ekin = 0.269028180853983 | erot = 0.466700668341734 | epot = -15.3532428840659 | etot = -14.6175140348701 -923000 ekin = 0.272927944745736 | erot = 0.465523908452108 | epot = -15.3559658880573 | etot = -14.6175140348595 -924000 ekin = 0.276323793829006 | erot = 0.464938026324777 | epot = -15.3587758550082 | etot = -14.6175140348544 -925000 ekin = 0.279373649323259 | erot = 0.46485472138072 | epot = -15.361742405558 | etot = -14.617514034854 -926000 ekin = 0.282237300897742 | erot = 0.465111106681027 | epot = -15.3648624424358 | etot = -14.617514034857 -927000 ekin = 0.285070250341507 | erot = 0.465493135293317 | epot = -15.368077420497 | etot = -14.6175140348622 -928000 ekin = 0.288016501944515 | erot = 0.465762600718122 | epot = -15.3712931375312 | etot = -14.6175140348685 -929000 ekin = 0.291201026098165 | erot = 0.465684740678949 | epot = -15.3743998016517 | etot = -14.6175140348746 -930000 ekin = 0.294722459178849 | erot = 0.465054261989122 | epot = -15.3772907560474 | etot = -14.6175140348794 -931000 ekin = 0.298646764015069 | erot = 0.463717248452617 | epot = -15.37987804735 | etot = -14.6175140348823 -932000 ekin = 0.303002304639518 | erot = 0.461587311532337 | epot = -15.3821036510548 | etot = -14.6175140348829 -933000 ekin = 0.307776651094703 | erot = 0.458654945590446 | epot = -15.3839456315665 | etot = -14.6175140348813 -934000 ekin = 0.312915338271949 | erot = 0.454989722654232 | epot = -15.3854190958038 | etot = -14.6175140348776 -935000 ekin = 0.318322768321298 | erot = 0.450735625549576 | epot = -15.3865724287433 | etot = -14.6175140348724 -936000 ekin = 0.323865441581078 | erot = 0.4461003856938 | epot = -15.3874798621412 | etot = -14.6175140348663 -937000 ekin = 0.329377658420705 | erot = 0.441340069469478 | epot = -15.3882317627502 | etot = -14.61751403486 -938000 ekin = 0.334669609401419 | erot = 0.43674015463711 | epot = -15.3889237988925 | etot = -14.617514034854 -939000 ekin = 0.339538182698638 | erot = 0.43259572362611 | epot = -15.3896479411737 | etot = -14.6175140348489 -940000 ekin = 0.343779460435286 | erot = 0.429190561371808 | epot = -15.3904840566521 | etot = -14.617514034845 -941000 ekin = 0.347202304174038 | erot = 0.426777065358206 | epot = -15.3914934043749 | etot = -14.6175140348427 -942000 ekin = 0.349642062607923 | erot = 0.425558062624919 | epot = -15.3927141600748 | etot = -14.617514034842 -943000 ekin = 0.350973206935894 | erot = 0.425671371650785 | epot = -15.3941586134297 | etot = -14.617514034843 -944000 ekin = 0.351119786154916 | erot = 0.427178062459289 | epot = -15.3958118834598 | etot = -14.6175140348456 -945000 ekin = 0.350062816508881 | erot = 0.430055404933721 | epot = -15.3976322562924 | etot = -14.6175140348498 -946000 ekin = 0.347844068536826 | erot = 0.43419544779 | epot = -15.399553551182 | etot = -14.6175140348552 -947000 ekin = 0.344566017441624 | erot = 0.439410327984555 | epot = -15.4014903802875 | etot = -14.6175140348614 -948000 ekin = 0.340388212507466 | erot = 0.445444378277408 | epot = -15.4033466256523 | etot = -14.6175140348674 -949000 ekin = 0.335520427168573 | erot = 0.451992965714934 | epot = -15.405027427756 | etot = -14.6175140348725 -950000 ekin = 0.330213181196302 | erot = 0.458727107975965 | epot = -15.4064543240477 | etot = -14.6175140348755 -951000 ekin = 0.32474581655651 | erot = 0.465321341197607 | epot = -15.4075811926297 | etot = -14.6175140348755 -952000 ekin = 0.319412679962215 | erot = 0.471482169177628 | epot = -15.4084088840117 | etot = -14.6175140348718 -953000 ekin = 0.314508037100187 | erot = 0.476974139327395 | epot = -15.4089962112918 | etot = -14.6175140348642 -954000 ekin = 0.310309685024338 | erot = 0.48163943141798 | epot = -15.4094631512954 | etot = -14.6175140348531 -955000 ekin = 0.307061947765172 | erot = 0.485408201613879 | epot = -15.4099841842186 | etot = -14.6175140348396 -956000 ekin = 0.304958921288845 | erot = 0.488297803841432 | epot = -15.4107707599557 | etot = -14.6175140348254 -957000 ekin = 0.304129209168544 | erot = 0.490400499132465 | epot = -15.412043743114 | etot = -14.617514034813 -958000 ekin = 0.30462371461979 | erot = 0.491860923621405 | epot = -15.4139986730458 | etot = -14.6175140348046 -959000 ekin = 0.306408207891338 | erot = 0.492846142548894 | epot = -15.4167683852429 | etot = -14.6175140348027 -960000 ekin = 0.309362278812989 | erot = 0.493512316198202 | epot = -15.4203886298201 | etot = -14.6175140348089 -961000 ekin = 0.313285873784586 | erot = 0.493972653387296 | epot = -15.4247725619958 | etot = -14.6175140348239 -962000 ekin = 0.31791392478401 | erot = 0.494271324762717 | epot = -15.429699284394 | etot = -14.6175140348473 -963000 ekin = 0.322938673952677 | erot = 0.49436733773729 | epot = -15.4348200465674 | etot = -14.6175140348775 -964000 ekin = 0.328038281530642 | erot = 0.494131108238433 | epot = -15.4396834246807 | etot = -14.6175140349116 -965000 ekin = 0.332909295682699 | erot = 0.493354750676295 | epot = -15.4437780813051 | etot = -14.6175140349461 -966000 ekin = 0.33729968976251 | erot = 0.491775167781853 | epot = -15.4465888925212 | etot = -14.6175140349768 -967000 ekin = 0.341038574326505 | erot = 0.489107134739274 | epot = -15.4476597440655 | etot = -14.6175140349998 -968000 ekin = 0.344058508086205 | erot = 0.485082040988283 | epot = -15.446654584086 | etot = -14.6175140350116 -969000 ekin = 0.346406687226292 | erot = 0.479487053292162 | epot = -15.4434077755287 | etot = -14.6175140350102 -970000 ekin = 0.348242259950603 | erot = 0.472199376075359 | epot = -15.4379556710211 | etot = -14.6175140349951 -971000 ekin = 0.34981857790832 | erot = 0.46321104020783 | epot = -15.4305436530838 | etot = -14.6175140349677 -972000 ekin = 0.351451221504254 | erot = 0.452641107454446 | epot = -15.4216063638894 | etot = -14.6175140349307 -973000 ekin = 0.353474851841754 | erot = 0.440734047140903 | epot = -15.4117229338711 | etot = -14.6175140348884 -974000 ekin = 0.356193968986792 | erot = 0.42784496232361 | epot = -15.4015529661561 | etot = -14.6175140348457 -975000 ekin = 0.359834072253393 | erot = 0.414413971021987 | epot = -15.3917620780828 | etot = -14.6175140348074 -976000 ekin = 0.364500158165202 | erot = 0.400933139115816 | epot = -15.3829473320587 | etot = -14.6175140347777 -977000 ekin = 0.370148756532482 | erot = 0.387909813697021 | epot = -15.3755726049891 | etot = -14.6175140347596 -978000 ekin = 0.376577842833215 | erot = 0.375830059083025 | epot = -15.3699219366707 | etot = -14.6175140347545 -979000 ekin = 0.38343628910019 | erot = 0.365125297246779 | epot = -15.3660756211092 | etot = -14.6175140347622 -980000 ekin = 0.390251542223294 | erot = 0.35614439745949 | epot = -15.3639099744643 | etot = -14.6175140347816 -981000 ekin = 0.396471539317082 | erot = 0.349132547197932 | epot = -15.3631181213249 | etot = -14.6175140348099 -982000 ekin = 0.401514997593021 | erot = 0.344217435799683 | epot = -15.3632464682369 | etot = -14.6175140348442 -983000 ekin = 0.40482345877132 | erot = 0.341402706416172 | epot = -15.3637402000689 | etot = -14.6175140348814 -984000 ekin = 0.40590886668651 | erot = 0.340568324597744 | epot = -15.3639912262029 | etot = -14.6175140349187 -985000 ekin = 0.40439180306127 | erot = 0.341477444720355 | epot = -15.3633832827352 | etot = -14.6175140349536 -986000 ekin = 0.400027422801574 | erot = 0.34378943446128 | epot = -15.361330892247 | etot = -14.6175140349842 -987000 ekin = 0.392718180745197 | erot = 0.347078806738211 | epot = -15.3573110224925 | etot = -14.617514035009 -988000 ekin = 0.38251423921461 | erot = 0.35085976914659 | epot = -15.3508880433883 | etot = -14.6175140350271 -989000 ekin = 0.369603726654237 | erot = 0.354615837188711 | epot = -15.3417335988804 | etot = -14.6175140350375 -990000 ekin = 0.354295674461643 | erot = 0.357833454087933 | epot = -15.3296431635888 | etot = -14.6175140350392 -991000 ekin = 0.336998529351755 | erot = 0.360037895318059 | epot = -15.3145504597015 | etot = -14.6175140350317 -992000 ekin = 0.318196763890793 | erot = 0.360829065190808 | epot = -15.2965398640958 | etot = -14.6175140350142 -993000 ekin = 0.298427479538949 | erot = 0.359914303089432 | epot = -15.275855817615 | etot = -14.6175140349866 -994000 ekin = 0.278258203580391 | erot = 0.357135170965373 | epot = -15.2529074094948 | etot = -14.617514034949 -995000 ekin = 0.258266471895345 | erot = 0.352485480212691 | epot = -15.2282659870101 | etot = -14.617514034902 -996000 ekin = 0.239021351636229 | erot = 0.346118523027927 | epot = -15.2026539095112 | etot = -14.617514034847 -997000 ekin = 0.221066818081289 | erot = 0.338342492442898 | epot = -15.1769233453102 | etot = -14.617514034786 -998000 ekin = 0.204906835818331 | erot = 0.329604233509071 | epot = -15.1520251040488 | etot = -14.6175140347214 -999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562 -1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937 - 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05 -Loop time of 17.0535 on 1 procs for 1000000 steps with 10 atoms - -Performance: 50663.947 tau/day, 58638.827 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 13.135 | 13.135 | 13.135 | 0.0 | 77.02 -Bond | 0.6362 | 0.6362 | 0.6362 | 0.0 | 3.73 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.18919 | 0.18919 | 0.18919 | 0.0 | 1.11 -Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00 -Modify | 2.8399 | 2.8399 | 2.8399 | 0.0 | 16.65 -Other | | 0.2536 | | | 1.49 - -Nlocal: 10.0 ave 10.0 max 10.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37.0 ave 37.0 max 37.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 37 -Ave neighs/atom = 3.7 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:17 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 deleted file mode 100644 index 134ef62d8f..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 +++ /dev/null @@ -1,1182 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA2 bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA2 pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274048 - ghost atom cutoff = 2.6274048 - binsize = 1.3137024, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -14.6175140343334 | etot = -14.6175140343334 -Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.96 | 8.018 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06 -1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342 -2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675 -3000 ekin = 0.0099503525964896 | erot = 0.0381961780846439 | epot = -14.6656605650904 | etot = -14.6175140344093 -4000 ekin = 0.0173418024861991 | erot = 0.0669935184860482 | epot = -14.7018493554381 | etot = -14.6175140344659 -5000 ekin = 0.0264109356285965 | erot = 0.102878288094483 | epot = -14.7468032582586 | etot = -14.6175140345355 -6000 ekin = 0.0368533113591267 | erot = 0.14504542056981 | epot = -14.7994127665446 | etot = -14.6175140346157 -7000 ekin = 0.0483200640564583 | erot = 0.192565862515414 | epot = -14.8583999612755 | etot = -14.6175140347036 -8000 ekin = 0.0604312317605635 | erot = 0.244417870131371 | epot = -14.9223631366881 | etot = -14.6175140347962 -9000 ekin = 0.072790711967127 | erot = 0.299521949931656 | epot = -14.9898266967887 | etot = -14.6175140348899 -10000 ekin = 0.0850022498874609 | erot = 0.356777997217668 | epot = -15.0592942820866 | etot = -14.6175140349815 -11000 ekin = 0.0966857134040954 | erot = 0.415102860829322 | epot = -15.1293026093009 | etot = -14.6175140350675 -12000 ekin = 0.107492790688356 | erot = 0.473466334177699 | epot = -15.1984731600111 | etot = -14.617514035145 -13000 ekin = 0.117121180381612 | erot = 0.530923485009329 | epot = -15.2655587006024 | etot = -14.6175140352115 -14000 ekin = 0.125326348459051 | erot = 0.586641324447251 | epot = -15.3294817081714 | etot = -14.6175140352651 -15000 ekin = 0.131930017119328 | erot = 0.63991810423422 | epot = -15.3893621566583 | etot = -14.6175140353048 -16000 ekin = 0.136824741331405 | erot = 0.690194029500566 | epot = -15.4445328061626 | etot = -14.6175140353306 -17000 ekin = 0.139974218116171 | erot = 0.737052866147306 | epot = -15.4945411196066 | etot = -14.6175140353432 -18000 ekin = 0.141409342139797 | erot = 0.780214750583043 | epot = -15.5391381280668 | etot = -14.617514035344 -19000 ekin = 0.141220424903361 | erot = 0.819521373491177 | epot = -15.5782558337298 | etot = -14.6175140353352 -20000 ekin = 0.139546371890511 | erot = 0.854915474127585 | epot = -15.6119758813374 | etot = -14.6175140353193 -21000 ekin = 0.136561897558541 | erot = 0.886417110947522 | epot = -15.6404930438047 | etot = -14.6175140352986 -22000 ekin = 0.132464002543684 | erot = 0.914099368829796 | epot = -15.6640774066492 | etot = -14.6175140352758 -23000 ekin = 0.127458921012898 | erot = 0.938065991541741 | epot = -15.6830389478072 | etot = -14.6175140352525 -24000 ekin = 0.121750582423396 | erot = 0.958432936326346 | epot = -15.6976975539803 | etot = -14.6175140352306 -25000 ekin = 0.115531361419039 | erot = 0.975315142931434 | epot = -15.7083605395612 | etot = -14.6175140352107 -26000 ekin = 0.108975565586195 | erot = 0.988819027952452 | epot = -15.715308628732 | etot = -14.6175140351934 -27000 ekin = 0.102235785319183 | erot = 0.999040485514706 | epot = -15.7187903060122 | etot = -14.6175140351783 -28000 ekin = 0.0954419434320554 | erot = 1.00606759141037 | epot = -15.7190235700075 | etot = -14.6175140351651 -29000 ekin = 0.0887026587346012 | erot = 1.00998681843686 | epot = -15.7162035123244 | etot = -14.6175140351529 -30000 ekin = 0.0821083868016836 | erot = 1.01089138149989 | epot = -15.7105138034423 | etot = -14.6175140351407 -31000 ekin = 0.0757357206090521 | erot = 1.00889031641421 | epot = -15.702140072151 | etot = -14.6175140351278 -32000 ekin = 0.0696522149391935 | erot = 1.00411701390103 | epot = -15.6912832639534 | etot = -14.6175140351132 -33000 ekin = 0.0639211300031737 | erot = 0.996736133736263 | epot = -15.6781712988358 | etot = -14.6175140350964 -34000 ekin = 0.0586055597942697 | erot = 0.986948071944207 | epot = -15.6630676668155 | etot = -14.617514035077 -35000 ekin = 0.0537715085522448 | erot = 0.974990414618501 | epot = -15.6462759582258 | etot = -14.617514035055 -36000 ekin = 0.0494895953267295 | erot = 0.961136064968264 | epot = -15.6281396953257 | etot = -14.6175140350307 -37000 ekin = 0.0458351949408502 | erot = 0.945687966087874 | epot = -15.6090371960337 | etot = -14.617514035005 -38000 ekin = 0.0428869588018996 | erot = 0.928970560853581 | epot = -15.5893715546342 | etot = -14.6175140349787 -39000 ekin = 0.0407237982125063 | erot = 0.911318339680438 | epot = -15.5695561728459 | etot = -14.617514034953 -40000 ekin = 0.0394205547756063 | erot = 0.893062038098217 | epot = -15.5499966278032 | etot = -14.6175140349294 -41000 ekin = 0.0390427256108178 | erot = 0.874513269991183 | epot = -15.5310700305113 | etot = -14.6175140349092 -42000 ekin = 0.0396407506458889 | erot = 0.855948622306388 | epot = -15.5131034078463 | etot = -14.617514034894 -43000 ekin = 0.0412444930542012 | erot = 0.837594480923648 | epot = -15.4963530088627 | etot = -14.6175140348848 -44000 ekin = 0.0438586280729573 | erot = 0.819614069272763 | epot = -15.4809867322283 | etot = -14.6175140348826 -45000 ekin = 0.0474596621514809 | erot = 0.802098297010425 | epot = -15.4670719940496 | etot = -14.6175140348876 -46000 ekin = 0.0519951857190001 | erot = 0.785061947877089 | epot = -15.4545711684958 | etot = -14.6175140348997 -47000 ekin = 0.0573856747188828 | erot = 0.768446392385995 | epot = -15.4433461020223 | etot = -14.6175140349174 -48000 ekin = 0.0635286843628562 | erot = 0.752129335015535 | epot = -15.433172054318 | etot = -14.6175140349396 -49000 ekin = 0.0703046735384702 | erot = 0.735941123250163 | epot = -15.4237598317528 | etot = -14.6175140349642 -50000 ekin = 0.0775831019852491 | erot = 0.719686007780774 | epot = -15.4147831447551 | etot = -14.6175140349891 -51000 ekin = 0.0852270843840623 | erot = 0.703165726694424 | epot = -15.4059068460916 | etot = -14.6175140350132 -52000 ekin = 0.0930950223446157 | erot = 0.686202231165621 | epot = -15.3968112885448 | etot = -14.6175140350346 -53000 ekin = 0.101038429252411 | erot = 0.668656546988554 | epot = -15.3872090112944 | etot = -14.6175140350534 -54000 ekin = 0.108896540979999 | erot = 0.65044172617409 | epot = -15.3768523022237 | etot = -14.6175140350696 -55000 ekin = 0.116489881625605 | erot = 0.631529329347953 | epot = -15.3655332460571 | etot = -14.6175140350836 -56000 ekin = 0.12361610349128 | erot = 0.611950383382754 | epot = -15.3530805219694 | etot = -14.6175140350954 -57000 ekin = 0.130051530400511 | erot = 0.591792721317636 | epot = -15.3393582868229 | etot = -14.6175140351047 -58000 ekin = 0.135560625192868 | erot = 0.571196690673809 | epot = -15.3242713509772 | etot = -14.6175140351105 -59000 ekin = 0.13991335082652 | erot = 0.550350463180971 | epot = -15.307777849119 | etot = -14.6175140351115 -60000 ekin = 0.142907875045205 | erot = 0.529485019663366 | epot = -15.2899069298149 | etot = -14.6175140351063 -61000 ekin = 0.144394224776987 | erot = 0.508867904999859 | epot = -15.2707761648709 | etot = -14.6175140350941 -62000 ekin = 0.14429400378525 | erot = 0.488794507593493 | epot = -15.2506025464535 | etot = -14.6175140350748 -63000 ekin = 0.142612256997681 | erot = 0.469576039422599 | epot = -15.2297023314693 | etot = -14.617514035049 -64000 ekin = 0.139439544726489 | erot = 0.451524344955609 | epot = -15.2084779247008 | etot = -14.6175140350187 -65000 ekin = 0.134944526553205 | erot = 0.434934714914789 | epot = -15.1873932764541 | etot = -14.6175140349861 -66000 ekin = 0.129359146357915 | erot = 0.42006860776795 | epot = -15.1669417890793 | etot = -14.6175140349534 -67000 ekin = 0.122959458763979 | erot = 0.407138362060406 | epot = -15.1476118557473 | etot = -14.6175140349229 -68000 ekin = 0.116045210525348 | erot = 0.396295631876791 | epot = -15.1298548772989 | etot = -14.6175140348967 -69000 ekin = 0.108920722072196 | erot = 0.387624589972286 | epot = -15.1140593469203 | etot = -14.6175140348758 -70000 ekin = 0.10187874072944 | erot = 0.381140173640969 | epot = -15.1005329492312 | etot = -14.6175140348608 -71000 ekin = 0.0951880561483024 | erot = 0.376791007701474 | epot = -15.0894930987017 | etot = -14.6175140348519 -72000 ekin = 0.0890849677261225 | erot = 0.374466237250124 | epot = -15.0810652398251 | etot = -14.6175140348489 -73000 ekin = 0.0837682427021172 | erot = 0.37400534759948 | epot = -15.0752876251526 | etot = -14.617514034851 -74000 ekin = 0.0793969849743902 | erot = 0.375210076750066 | epot = -15.0721210965819 | etot = -14.6175140348574 -75000 ekin = 0.0760907865069309 | erot = 0.377857644571635 | epot = -15.0714624659456 | etot = -14.617514034867 -76000 ekin = 0.073931583490861 | erot = 0.381714646754472 | epot = -15.073160265124 | etot = -14.6175140348787 -77000 ekin = 0.0729667273608691 | erot = 0.386551032955436 | epot = -15.0770317952076 | etot = -14.6175140348913 -78000 ekin = 0.0732128655080132 | erot = 0.392153586682573 | epot = -15.0828804870945 | etot = -14.6175140349039 -79000 ekin = 0.0746602878351816 | erot = 0.398338263928879 | epot = -15.0905125866795 | etot = -14.6175140349154 -80000 ekin = 0.0772774298946258 | erot = 0.404960669862598 | epot = -15.0997521346822 | etot = -14.617514034925 -81000 ekin = 0.0810152396747851 | erot = 0.411923913358685 | epot = -15.1104531879654 | etot = -14.617514034932 -82000 ekin = 0.0858111278281503 | erot = 0.419183131304765 | epot = -15.122508294069 | etot = -14.6175140349361 -83000 ekin = 0.0915922459207823 | erot = 0.426746154030485 | epot = -15.1358524348888 | etot = -14.6175140349375 -84000 ekin = 0.0982778862655832 | erot = 0.434670094582864 | epot = -15.1504620157849 | etot = -14.6175140349364 -85000 ekin = 0.105780875252437 | erot = 0.443054055542249 | epot = -15.1663489657283 | etot = -14.6175140349336 -86000 ekin = 0.114007936320836 | erot = 0.452028591870875 | epot = -15.1835505631216 | etot = -14.6175140349299 -87000 ekin = 0.122859117093393 | erot = 0.461742961599463 | epot = -15.2021161136192 | etot = -14.6175140349264 -88000 ekin = 0.132226490250757 | erot = 0.472351454261397 | epot = -15.2220919794359 | etot = -14.6175140349237 -89000 ekin = 0.141992430435586 | erot = 0.48400015022936 | epot = -15.243506615588 | etot = -14.6175140349231 -90000 ekin = 0.152027823849156 | erot = 0.496815313840275 | epot = -15.2663571726144 | etot = -14.617514034925 -91000 ekin = 0.162190574344531 | erot = 0.510894287760946 | epot = -15.2905988970356 | etot = -14.6175140349301 -92000 ekin = 0.172324730223634 | erot = 0.526299304076921 | epot = -15.3161380692392 | etot = -14.6175140349387 -93000 ekin = 0.182260479602882 | erot = 0.543054150884053 | epot = -15.3428286654374 | etot = -14.6175140349505 -94000 ekin = 0.19181516642483 | erot = 0.561143224560411 | epot = -15.3704724259507 | etot = -14.6175140349654 -95000 ekin = 0.200795384590157 | erot = 0.580512230413436 | epot = -15.398821649987 | etot = -14.6175140349834 -96000 ekin = 0.209000133284529 | erot = 0.601069706845066 | epot = -15.4275838751334 | etot = -14.6175140350038 -97000 ekin = 0.216224974983237 | erot = 0.62268863993255 | epot = -15.4564276499423 | etot = -14.6175140350265 -98000 ekin = 0.222267131485539 | erot = 0.6452076702458 | epot = -15.4849888367823 | etot = -14.617514035051 -99000 ekin = 0.226931474008825 | erot = 0.668431711039527 | epot = -15.5128772201251 | etot = -14.6175140350767 -100000 ekin = 0.230037392185109 | erot = 0.692132125756159 | epot = -15.5396835530446 | etot = -14.6175140351033 -101000 ekin = 0.231426538774162 | erot = 0.716046886548711 | epot = -15.5649874604531 | etot = -14.6175140351302 -102000 ekin = 0.230971416185847 | erot = 0.739881303910146 | epot = -15.5883667552525 | etot = -14.6175140351565 -103000 ekin = 0.228584676860608 | erot = 0.763309953364731 | epot = -15.6094086654068 | etot = -14.6175140351814 -104000 ekin = 0.224228843046253 | erot = 0.78598032692129 | epot = -15.6277232051714 | etot = -14.6175140352039 -105000 ekin = 0.217925953180068 | erot = 0.807518535459536 | epot = -15.6429585238624 | etot = -14.6175140352228 -106000 ekin = 0.209766205881383 | erot = 0.827537066837229 | epot = -15.6548173079557 | etot = -14.6175140352371 -107000 ekin = 0.199914663118832 | erot = 0.845644346598305 | epot = -15.6630730449629 | etot = -14.6175140352458 -108000 ekin = 0.188614735690438 | erot = 0.86145556230374 | epot = -15.6675843332424 | etot = -14.6175140352482 -109000 ekin = 0.176187061060969 | erot = 0.874603999194657 | epot = -15.6683050954996 | etot = -14.617514035244 -110000 ekin = 0.163022626611269 | erot = 0.884752084634178 | epot = -15.6652887464788 | etot = -14.6175140352334 -111000 ekin = 0.149569382110055 | erot = 0.891601400936344 | epot = -15.6586848182636 | etot = -14.6175140352172 -112000 ekin = 0.136312261124298 | erot = 0.894901120601569 | epot = -15.6487274169225 | etot = -14.6175140351967 -113000 ekin = 0.123747404857111 | erot = 0.894454602034433 | epot = -15.635716042065 | etot = -14.6175140351735 -114000 ekin = 0.112352324429236 | erot = 0.89012419645392 | epot = -15.6199905560327 | etot = -14.6175140351496 -115000 ekin = 0.102554569787019 | erot = 0.881834585428133 | epot = -15.601903190342 | etot = -14.6175140351268 -116000 ekin = 0.094702004709198 | erot = 0.869575126615747 | epot = -15.5817911664316 | etot = -14.6175140351067 -117000 ekin = 0.0890378681933156 | erot = 0.853401690495617 | epot = -15.5599535937792 | etot = -14.6175140350902 -118000 ekin = 0.0856833736304911 | erot = 0.833438318820653 | epot = -15.536635727529 | etot = -14.6175140350778 -119000 ekin = 0.0846297171115028 | erot = 0.809878764033866 | epot = -15.5120225162146 | etot = -14.6175140350693 -120000 ekin = 0.0857402026933537 | erot = 0.782987649503194 | epot = -15.4862418872603 | etot = -14.6175140350638 -121000 ekin = 0.0887619781646647 | erot = 0.753100709617513 | epot = -15.4593767228421 | etot = -14.61751403506 -122000 ekin = 0.0933458418333701 | erot = 0.720623403983765 | epot = -15.4314832808735 | etot = -14.6175140350564 -123000 ekin = 0.0990718975136712 | erot = 0.686027198351099 | epot = -15.4026131309163 | etot = -14.6175140350515 -124000 ekin = 0.10547856753477 | erot = 0.649842971568616 | epot = -15.3728355741476 | etot = -14.6175140350442 -125000 ekin = 0.112092583657157 | erot = 0.612651306911466 | epot = -15.3422579256018 | etot = -14.6175140350331 -126000 ekin = 0.118457948669929 | erot = 0.575069793126885 | epot = -15.3110417768148 | etot = -14.6175140350179 -127000 ekin = 0.12416235209736 | erot = 0.537737821904032 | epot = -15.2794142089994 | etot = -14.617514034998 -128000 ekin = 0.12886000047466 | erot = 0.50129966007338 | epot = -15.2476736955216 | etot = -14.6175140349735 -129000 ekin = 0.132290197680968 | erot = 0.466386755141928 | epot = -15.2161909877676 | etot = -14.6175140349447 -130000 ekin = 0.134291248322799 | erot = 0.433600287194598 | epot = -15.1854055704295 | etot = -14.6175140349121 -131000 ekin = 0.134809368078731 | erot = 0.403494917850824 | epot = -15.1558183208059 | etot = -14.6175140348763 -132000 ekin = 0.133902311412609 | erot = 0.376564532721137 | epot = -15.1279808789722 | etot = -14.6175140348384 -133000 ekin = 0.131737425949523 | erot = 0.35323055944927 | epot = -15.102482020198 | etot = -14.6175140347992 -134000 ekin = 0.128583872249503 | erot = 0.333833200744645 | epot = -15.0799311077543 | etot = -14.6175140347601 -135000 ekin = 0.124798858318881 | erot = 0.318625678761018 | epot = -15.0609385718023 | etot = -14.6175140347224 -136000 ekin = 0.120807966950657 | erot = 0.307771366705204 | epot = -15.0460933683435 | etot = -14.6175140346876 -137000 ekin = 0.117080018573046 | erot = 0.301343503849178 | epot = -15.0359375570798 | etot = -14.6175140346576 -138000 ekin = 0.11409740445119 | erot = 0.299327064918184 | epot = -15.0309385040035 | etot = -14.6175140346342 -139000 ekin = 0.112323403877017 | erot = 0.30162229304682 | epot = -15.0314597315429 | etot = -14.6175140346191 -140000 ekin = 0.112168587316825 | erot = 0.308049410073269 | epot = -15.0377320320041 | etot = -14.617514034614 -141000 ekin = 0.113958896787242 | erot = 0.318354084563179 | epot = -15.0498270159708 | etot = -14.6175140346204 -142000 ekin = 0.117908250109871 | erot = 0.332213334114279 | epot = -15.0676356188632 | etot = -14.6175140346391 -143000 ekin = 0.124098500240005 | erot = 0.349241744869171 | epot = -15.0908542797795 | etot = -14.6175140346704 -144000 ekin = 0.132469049162189 | erot = 0.368998042344344 | epot = -15.1189811262203 | etot = -14.6175140347138 -145000 ekin = 0.142817534773286 | erot = 0.390992018433719 | epot = -15.1513235879751 | etot = -14.6175140347681 -146000 ekin = 0.154812002594074 | erot = 0.414692148539669 | epot = -15.1870181859652 | etot = -14.6175140348314 -147000 ekin = 0.168013608208222 | erot = 0.439534147564146 | epot = -15.2250617906734 | etot = -14.617514034901 -148000 ekin = 0.181907755044263 | erot = 0.464930715993231 | epot = -15.2643525060114 | etot = -14.617514034974 -149000 ekin = 0.195940689918476 | erot = 0.490282644231627 | epot = -15.303737369197 | etot = -14.6175140350469 -150000 ekin = 0.209558115498224 | erot = 0.514991307803342 | epot = -15.3420634584183 | etot = -14.6175140351167 -151000 ekin = 0.222242375358764 | erot = 0.538472447670959 | epot = -15.37822885821 | etot = -14.6175140351803 -152000 ekin = 0.233545181100908 | erot = 0.560170967505261 | epot = -15.4112301838413 | etot = -14.6175140352351 -153000 ekin = 0.243113638171877 | erot = 0.579575715964384 | epot = -15.4402033894153 | etot = -14.6175140352791 -154000 ekin = 0.250708030719506 | erot = 0.596234520730852 | epot = -15.4644565867613 | etot = -14.617514035311 -155000 ekin = 0.256210874594867 | erot = 0.60976818504912 | epot = -15.4834930949737 | etot = -14.6175140353297 -156000 ekin = 0.259627463842678 | erot = 0.619882772314523 | epot = -15.4970242714926 | etot = -14.6175140353354 -157000 ekin = 0.261078756733762 | erot = 0.626379517381851 | epot = -15.5049723094439 | etot = -14.6175140353283 -158000 ekin = 0.260787877594799 | erot = 0.629161788909728 | epot = -15.5074637018138 | etot = -14.6175140353093 -159000 ekin = 0.259061752299363 | erot = 0.628238692725143 | epot = -15.5048144803044 | etot = -14.6175140352799 -160000 ekin = 0.256269476947947 | erot = 0.623725097357694 | epot = -15.4975086095473 | etot = -14.6175140352416 -161000 ekin = 0.252818974262676 | erot = 0.615838055764808 | epot = -15.486171065224 | etot = -14.6175140351965 -162000 ekin = 0.249133354780831 | erot = 0.604889772113657 | epot = -15.471537162041 | etot = -14.6175140351465 -163000 ekin = 0.245628201594069 | erot = 0.591277407065719 | epot = -15.4544196437535 | etot = -14.6175140350937 -164000 ekin = 0.242690765770497 | erot = 0.575470125399849 | epot = -15.4356749262106 | etot = -14.6175140350402 -165000 ekin = 0.240661818237638 | erot = 0.557993868663582 | epot = -15.4161697218892 | etot = -14.617514034988 -166000 ekin = 0.239820672159809 | erot = 0.53941438884916 | epot = -15.3967490959478 | etot = -14.6175140349388 -167000 ekin = 0.240373682616981 | erot = 0.520319112884548 | epot = -15.3782068303959 | etot = -14.6175140348944 -168000 ekin = 0.24244635767337 | erot = 0.501298426047094 | epot = -15.3612588185766 | etot = -14.6175140348562 -169000 ekin = 0.246079081489486 | erot = 0.482926967022081 | epot = -15.3465200833369 | etot = -14.6175140348253 -170000 ekin = 0.251226355670601 | erot = 0.465745518941346 | epot = -15.3344859094148 | etot = -14.6175140348028 -171000 ekin = 0.257759407502439 | erot = 0.450244072412675 | epot = -15.3255175147044 | etot = -14.6175140347893 -172000 ekin = 0.265471962314995 | erot = 0.43684655757276 | epot = -15.3198325546728 | etot = -14.617514034785 -173000 ekin = 0.274088992052566 | erot = 0.425897760802307 | epot = -15.317500787645 | etot = -14.6175140347901 -174000 ekin = 0.283278228107989 | erot = 0.417652965987653 | epot = -15.3184452288998 | etot = -14.6175140348041 -175000 ekin = 0.292664164217049 | erot = 0.41227065206718 | epot = -15.3224488511106 | etot = -14.6175140348264 -176000 ekin = 0.301844276743974 | erot = 0.409808663993543 | epot = -15.3291669755933 | etot = -14.6175140348558 -177000 ekin = 0.310407103277722 | erot = 0.410224178773613 | epot = -15.338145316942 | etot = -14.6175140348907 -178000 ekin = 0.317951707448459 | erot = 0.413377690533319 | epot = -15.3488434329112 | etot = -14.6175140349295 -179000 ekin = 0.324107901131331 | erot = 0.419041092199345 | epot = -15.3606630283007 | etot = -14.61751403497 -180000 ekin = 0.328556397748226 | erot = 0.426909726007329 | epot = -15.3729801587658 | etot = -14.6175140350103 -181000 ekin = 0.331047834153872 | erot = 0.436618006902467 | epot = -15.3851798761041 | etot = -14.6175140350478 -182000 ekin = 0.331419420114469 | erot = 0.447757936314679 | epot = -15.3966913915095 | etot = -14.6175140350803 -183000 ekin = 0.32960779233749 | erot = 0.459899520065503 | epot = -15.4070213475091 | etot = -14.6175140351061 -184000 ekin = 0.325656516855028 | erot = 0.472611792133139 | epot = -15.4157823441118 | etot = -14.6175140351236 -185000 ekin = 0.319716934487211 | erot = 0.485483030927449 | epot = -15.4227140005469 | etot = -14.6175140351322 -186000 ekin = 0.312041347782212 | erot = 0.498138700398001 | epot = -15.4276940833121 | etot = -14.6175140351319 -187000 ekin = 0.302968200961153 | erot = 0.510255791848845 | epot = -15.4307380279334 | etot = -14.6175140351234 -188000 ekin = 0.292899787356355 | erot = 0.5215725520513 | epot = -15.4319863745157 | etot = -14.6175140351081 -189000 ekin = 0.282274048055605 | erot = 0.531893031493143 | epot = -15.4316811146372 | etot = -14.6175140350884 -190000 ekin = 0.271533034588949 | erot = 0.541086413296656 | epot = -15.4301334829521 | etot = -14.6175140350665 -191000 ekin = 0.261091384545176 | erot = 0.549081610185661 | epot = -15.4276870297757 | etot = -14.6175140350448 -192000 ekin = 0.251308489707993 | erot = 0.555858063434326 | epot = -15.4246805881679 | etot = -14.6175140350256 -193000 ekin = 0.242467771119499 | erot = 0.561433978654792 | epot = -15.4214157847846 | etot = -14.6175140350103 -194000 ekin = 0.234765581624083 | erot = 0.565853352187983 | epot = -15.4181329688119 | etot = -14.6175140349998 -195000 ekin = 0.228310848060933 | erot = 0.569173077812972 | epot = -15.414997960868 | etot = -14.6175140349941 -196000 ekin = 0.223134890549791 | erot = 0.571451208607789 | epot = -15.4121001341501 | etot = -14.6175140349925 -197000 ekin = 0.219209242155479 | erot = 0.572737138234515 | epot = -15.4094604153842 | etot = -14.6175140349942 -198000 ekin = 0.216468062808567 | erot = 0.573064123809139 | epot = -15.4070462216157 | etot = -14.6175140349979 -199000 ekin = 0.214831137522102 | erot = 0.572444258405115 | epot = -15.4047894309295 | etot = -14.6175140350023 -200000 ekin = 0.214223573901692 | erot = 0.570865760664587 | epot = -15.402603369573 | etot = -14.6175140350067 -201000 ekin = 0.214589119166338 | erot = 0.568292309388425 | epot = -15.4003954635655 | etot = -14.6175140350107 -202000 ekin = 0.215895325601886 | erot = 0.564664121435212 | epot = -15.3980734820515 | etot = -14.6175140350144 -203000 ekin = 0.218130347569574 | erot = 0.559900543320399 | epot = -15.3955449259083 | etot = -14.6175140350184 -204000 ekin = 0.221292667473328 | erot = 0.553904074219812 | epot = -15.3927107767163 | etot = -14.6175140350232 -205000 ekin = 0.225376258610291 | erot = 0.546565915590092 | epot = -15.3894562092301 | etot = -14.6175140350297 -206000 ekin = 0.230354397528691 | erot = 0.537773288685112 | epot = -15.3856417212522 | etot = -14.6175140350384 -207000 ekin = 0.236165428414371 | erot = 0.527418806931585 | epot = -15.3810982703949 | etot = -14.617514035049 -208000 ekin = 0.242703261860097 | erot = 0.515412077176746 | epot = -15.3756293740978 | etot = -14.617514035061 -209000 ekin = 0.249814382549771 | erot = 0.501693407692903 | epot = -15.3690218253159 | etot = -14.6175140350732 -210000 ekin = 0.257301864855487 | erot = 0.486249049966596 | epot = -15.3610649499059 | etot = -14.6175140350838 -211000 ekin = 0.264935635394204 | erot = 0.469126912721243 | epot = -15.3515765832063 | etot = -14.6175140350909 -212000 ekin = 0.272467183646431 | erot = 0.450451153648371 | epot = -15.3404323723875 | etot = -14.6175140350927 -213000 ekin = 0.279646306736912 | erot = 0.430433702677772 | epot = -15.3275940445023 | etot = -14.6175140350876 -214000 ekin = 0.286237611276899 | erot = 0.409381288017331 | epot = -15.3131329343688 | etot = -14.6175140350746 -215000 ekin = 0.29203464387293 | erot = 0.387696263733711 | epot = -15.29724494266 | etot = -14.6175140350534 -216000 ekin = 0.296870258153004 | erot = 0.365870567410591 | epot = -15.2802548605881 | etot = -14.6175140350245 -217000 ekin = 0.300622666325324 | erot = 0.344472695101547 | epot = -15.2626093964159 | etot = -14.617514034989 -218000 ekin = 0.303217269541564 | erot = 0.324128407396835 | epot = -15.244859711887 | etot = -14.6175140349486 -219000 ekin = 0.30462484391226 | erot = 0.305496496150474 | epot = -15.2276353749682 | etot = -14.6175140349055 -220000 ekin = 0.304856982074418 | erot = 0.289241221674229 | epot = -15.2116122386105 | etot = -14.6175140348619 -221000 ekin = 0.303959749544728 | erot = 0.276003133760616 | epot = -15.1974769181253 | etot = -14.61751403482 -222000 ekin = 0.302006434071345 | erot = 0.266369862263779 | epot = -15.1858903311172 | etot = -14.6175140347821 -223000 ekin = 0.299090105491099 | erot = 0.260848208952979 | epot = -15.1774523491944 | etot = -14.6175140347503 -224000 ekin = 0.295316503745815 | erot = 0.259838588555865 | epot = -15.172669127028 | etot = -14.6175140347263 -225000 ekin = 0.29079760031813 | erot = 0.263612591734547 | epot = -15.1719242267643 | etot = -14.6175140347116 -226000 ekin = 0.28564610323333 | erot = 0.272294318079248 | epot = -15.1754544560199 | etot = -14.6175140347074 -227000 ekin = 0.279971018689722 | erot = 0.285846075010758 | epot = -15.1833311284149 | etot = -14.6175140347144 -228000 ekin = 0.27387437472819 | erot = 0.304059069119049 | epot = -15.1954474785804 | etot = -14.6175140347332 -229000 ekin = 0.2674491741605 | erot = 0.326549807965654 | epot = -15.2115130168897 | etot = -14.6175140347636 -230000 ekin = 0.260778614119455 | erot = 0.352763004039831 | epot = -15.2310556529641 | etot = -14.6175140348048 -231000 ekin = 0.253936564977397 | erot = 0.381981763344761 | epot = -15.2534323631777 | etot = -14.6175140348555 -232000 ekin = 0.246989230842658 | erot = 0.413345683736738 | epot = -15.2778489494936 | etot = -14.6175140349142 -233000 ekin = 0.239997814735998 | erot = 0.445877135783837 | epot = -15.3033889854983 | etot = -14.6175140349784 -234000 ekin = 0.233021891669953 | erot = 0.478515439398998 | epot = -15.3290513661143 | etot = -14.6175140350454 -235000 ekin = 0.226123071286445 | erot = 0.510157919201484 | epot = -15.3537950255997 | etot = -14.6175140351118 -236000 ekin = 0.21936843695277 | erot = 0.539706010633891 | epot = -15.3765884827611 | etot = -14.6175140351745 -237000 ekin = 0.212833212708602 | erot = 0.566113832023262 | epot = -15.3964610799619 | etot = -14.61751403523 -238000 ekin = 0.206602165162865 | erot = 0.588436180449287 | epot = -15.4125523808878 | etot = -14.6175140352757 -239000 ekin = 0.200769360307748 | erot = 0.605872583258365 | epot = -15.4241559788754 | etot = -14.6175140353093 -240000 ekin = 0.195436190928625 | erot = 0.61780345837781 | epot = -15.4307536846357 | etot = -14.6175140353293 -241000 ekin = 0.190707920284743 | erot = 0.623817360380854 | epot = -15.4320393160006 | etot = -14.617514035335 -242000 ekin = 0.186689132524135 | erot = 0.623726737659666 | epot = -15.4279299055104 | etot = -14.6175140353266 -243000 ekin = 0.183478880874969 | erot = 0.617571857376273 | epot = -15.4185647735561 | etot = -14.6175140353049 -244000 ekin = 0.181166166760206 | erot = 0.605612923712308 | epot = -15.4042931257437 | etot = -14.6175140352712 -245000 ekin = 0.179826690516145 | erot = 0.588311983397642 | epot = -15.3856527091413 | etot = -14.6175140352275 -246000 ekin = 0.179521473345086 | erot = 0.566306329739288 | epot = -15.3633418382601 | etot = -14.6175140351758 -247000 ekin = 0.180297726609514 | erot = 0.540375528723551 | epot = -15.3381872904514 | etot = -14.6175140351183 -248000 ekin = 0.182192022181392 | erot = 0.511404282991666 | epot = -15.3111103402302 | etot = -14.6175140350572 -249000 ekin = 0.185235475059313 | erot = 0.480343275337858 | epot = -15.2830927853916 | etot = -14.6175140349945 -250000 ekin = 0.189460324578832 | erot = 0.448169956262064 | epot = -15.255144315773 | etot = -14.6175140349321 -251000 ekin = 0.19490702001237 | erot = 0.415851007132868 | epot = -15.228272062017 | etot = -14.6175140348717 -252000 ekin = 0.201630699423836 | erot = 0.384307951122289 | epot = -15.2034526853611 | etot = -14.617514034815 -253000 ekin = 0.209705815256177 | erot = 0.354387113740113 | epot = -15.1816069637594 | etot = -14.6175140347631 -254000 ekin = 0.219227629547432 | erot = 0.326834860919775 | epot = -15.1635765251848 | etot = -14.6175140347176 -255000 ekin = 0.230309407957432 | erot = 0.302278768995733 | epot = -15.1501022116327 | etot = -14.6175140346795 -256000 ekin = 0.243074422922267 | erot = 0.281215109558701 | epot = -15.141803567131 | etot = -14.61751403465 -257000 ekin = 0.257642364630153 | erot = 0.264002762946067 | epot = -15.1391591622066 | etot = -14.6175140346304 -258000 ekin = 0.274110461104108 | erot = 0.250863404057697 | epot = -15.1424878997833 | etot = -14.6175140346215 -259000 ekin = 0.292530483429775 | erot = 0.241887528333024 | epot = -15.1519320463872 | etot = -14.6175140346244 -260000 ekin = 0.312883750215128 | erot = 0.237045600991386 | epot = -15.1674433858462 | etot = -14.6175140346397 -261000 ekin = 0.335057071666333 | erot = 0.236203324625284 | epot = -15.1887744309592 | etot = -14.6175140346676 -262000 ekin = 0.358823075933473 | erot = 0.239139750884213 | epot = -15.2154768615253 | etot = -14.6175140347076 -263000 ekin = 0.383828346058996 | erot = 0.245566753569572 | epot = -15.2469091343872 | etot = -14.6175140347587 -264000 ekin = 0.409592161639947 | erot = 0.255148290958814 | epot = -15.2822544874178 | etot = -14.6175140348191 -265000 ekin = 0.435517425640964 | erot = 0.267517972446782 | epot = -15.3205494329741 | etot = -14.6175140348864 -266000 ekin = 0.460913759434661 | erot = 0.282293742227942 | epot = -15.3607215366204 | etot = -14.6175140349578 -267000 ekin = 0.485031075313793 | erot = 0.299088986461059 | epot = -15.4016340968052 | etot = -14.6175140350303 -268000 ekin = 0.50710051747368 | erot = 0.317519986656956 | epot = -15.4421345392314 | etot = -14.6175140351007 -269000 ekin = 0.526378761163555 | erot = 0.33721025800327 | epot = -15.4811030543329 | etot = -14.6175140351661 -270000 ekin = 0.542191399557166 | erot = 0.357792786170323 | epot = -15.5174982209515 | etot = -14.617514035224 -271000 ekin = 0.553971501275297 | erot = 0.378911394713051 | epot = -15.5503969312606 | etot = -14.6175140352722 -272000 ekin = 0.561290243476884 | erot = 0.400222387433604 | epot = -15.5790266662199 | etot = -14.6175140353094 -273000 ekin = 0.563877614617889 | erot = 0.421397250043755 | epot = -15.6027888999963 | etot = -14.6175140353346 -274000 ekin = 0.561632338447609 | erot = 0.442126671655328 | epot = -15.6212730454506 | etot = -14.6175140353477 -275000 ekin = 0.554621238224436 | erot = 0.462125606775396 | epot = -15.6342608803486 | etot = -14.6175140353487 -276000 ekin = 0.543069132887187 | erot = 0.481138682331962 | epot = -15.6417218505579 | etot = -14.6175140353387 -277000 ekin = 0.527340979965694 | erot = 0.498945052082853 | epot = -15.6438000673675 | etot = -14.6175140353189 -278000 ekin = 0.507918337217276 | erot = 0.515361832413196 | epot = -15.6407942049214 | etot = -14.617514035291 -279000 ekin = 0.485372319601914 | erot = 0.530245473601771 | epot = -15.6331318284601 | etot = -14.6175140352564 -280000 ekin = 0.46033511650651 | erot = 0.543490744711146 | epot = -15.6213398964351 | etot = -14.6175140352175 -281000 ekin = 0.433471859960453 | erot = 0.555027349456868 | epot = -15.6060132445935 | etot = -14.6175140351761 -282000 ekin = 0.405454262480505 | erot = 0.564814480007104 | epot = -15.5877827776223 | etot = -14.6175140351347 -283000 ekin = 0.376937038993415 | erot = 0.572833827993335 | epot = -15.5672849020813 | etot = -14.6175140350945 -284000 ekin = 0.348537747962441 | erot = 0.579081711931139 | epot = -15.5451334949501 | etot = -14.6175140350565 -285000 ekin = 0.320820372083179 | erot = 0.583561068647143 | epot = -15.5218954757531 | etot = -14.6175140350227 -286000 ekin = 0.294282726921465 | erot = 0.586274110946605 | epot = -15.4980708728619 | etot = -14.6175140349939 -287000 ekin = 0.269347634013372 | erot = 0.587216475910704 | epot = -15.4740781448946 | etot = -14.6175140349706 -288000 ekin = 0.246357704467567 | erot = 0.586373659773396 | epot = -15.4502453991941 | etot = -14.6175140349531 -289000 ekin = 0.225573522145737 | erot = 0.583720426232575 | epot = -15.4268079833199 | etot = -14.6175140349416 -290000 ekin = 0.207174962818498 | erot = 0.579223657449698 | epot = -15.4039126552032 | etot = -14.617514034935 -291000 ekin = 0.191265313940317 | erot = 0.57284878086397 | epot = -15.3816281297368 | etot = -14.6175140349325 -292000 ekin = 0.177877757396561 | erot = 0.564569470033103 | epot = -15.3599612623625 | etot = -14.6175140349328 -293000 ekin = 0.166983649288562 | erot = 0.55437983768204 | epot = -15.3388775219052 | etot = -14.6175140349346 -294000 ekin = 0.158501898150816 | erot = 0.542307895558416 | epot = -15.3183238286456 | etot = -14.6175140349363 -295000 ekin = 0.152308641379775 | erot = 0.528428741575564 | epot = -15.2982514178919 | etot = -14.6175140349366 -296000 ekin = 0.14824639013426 | erot = 0.512875830575376 | epot = -15.2786362556441 | etot = -14.6175140349344 -297000 ekin = 0.146131889948848 | erot = 0.49584883363365 | epot = -15.2594947585117 | etot = -14.6175140349292 -298000 ekin = 0.145762142540934 | erot = 0.47761697934363 | epot = -15.2408931568053 | etot = -14.6175140349207 -299000 ekin = 0.146918339842692 | erot = 0.458517327974144 | epot = -15.2229497027261 | etot = -14.6175140349093 -300000 ekin = 0.149367830718069 | erot = 0.438948042711649 | epot = -15.2058299083254 | etot = -14.6175140348957 -301000 ekin = 0.152864610234033 | erot = 0.419357266833102 | epot = -15.1897359119478 | etot = -14.6175140348807 -302000 ekin = 0.157149122640169 | erot = 0.400228590597444 | epot = -15.1748917481033 | etot = -14.6175140348656 -303000 ekin = 0.161948347719032 | erot = 0.382064246006851 | epot = -15.1615266285773 | etot = -14.6175140348514 -304000 ekin = 0.166977167327436 | erot = 0.365367110078575 | epot = -15.1498583122451 | etot = -14.6175140348391 -305000 ekin = 0.171941885875871 | erot = 0.350622387001196 | epot = -15.1400783077067 | etot = -14.6175140348296 -306000 ekin = 0.176546522696863 | erot = 0.338279561363742 | epot = -15.1323401188838 | etot = -14.6175140348232 -307000 ekin = 0.180502080572192 | erot = 0.32873493509135 | epot = -15.126751050484 | etot = -14.6175140348205 -308000 ekin = 0.183539117579248 | erot = 0.322315068517915 | epot = -15.1233682209185 | etot = -14.6175140348213 -309000 ekin = 0.18542258916881 | erot = 0.31926113518031 | epot = -15.1221977591748 | etot = -14.6175140348257 -310000 ekin = 0.185968382525478 | erot = 0.319714556777655 | epot = -15.1231969741364 | etot = -14.6175140348332 -311000 ekin = 0.185060444471749 | erot = 0.323704474532897 | epot = -15.1262789538482 | etot = -14.6175140348435 -312000 ekin = 0.182667055699898 | erot = 0.331137883754702 | epot = -15.1313189743107 | etot = -14.6175140348561 -313000 ekin = 0.178854671448117 | erot = 0.341793554574368 | epot = -15.1381622608928 | etot = -14.6175140348703 -314000 ekin = 0.173797674113305 | erot = 0.355321045101964 | epot = -15.1466327541009 | etot = -14.6175140348857 -315000 ekin = 0.167782440685989 | erot = 0.371246117950244 | epot = -15.1565425935376 | etot = -14.6175140349013 -316000 ekin = 0.161204347699333 | erot = 0.388983636698412 | epot = -15.1677020193144 | etot = -14.6175140349166 -317000 ekin = 0.154556738722997 | erot = 0.407858516721222 | epot = -15.179929290375 | etot = -14.6175140349308 -318000 ekin = 0.148411457828014 | erot = 0.427134549771526 | epot = -15.1930600425429 | etot = -14.6175140349434 -319000 ekin = 0.143391260343274 | erot = 0.446049980956587 | epot = -15.2069552762535 | etot = -14.6175140349536 -320000 ekin = 0.140135163879389 | erot = 0.463857713006731 | epot = -15.2215069118477 | etot = -14.6175140349616 -321000 ekin = 0.13925849683082 | erot = 0.47986711734359 | epot = -15.2366396491416 | etot = -14.6175140349672 -322000 ekin = 0.141309963686786 | erot = 0.493483840953745 | epot = -15.2523078396115 | etot = -14.617514034971 -323000 ekin = 0.146728465402049 | erot = 0.504243890594766 | epot = -15.2684863909708 | etot = -14.617514034974 -324000 ekin = 0.155802740978474 | erot = 0.511838753068047 | epot = -15.2851555290241 | etot = -14.6175140349776 -325000 ekin = 0.168637192339758 | erot = 0.516129344219392 | epot = -15.3022805715425 | etot = -14.6175140349833 -326000 ekin = 0.185127492740937 | erot = 0.517147991936341 | epot = -15.3197895196698 | etot = -14.6175140349925 -327000 ekin = 0.204949583925474 | erot = 0.515089155111526 | epot = -15.3375527740431 | etot = -14.6175140350061 -328000 ekin = 0.227565145376632 | erot = 0.510290835144293 | epot = -15.3553700155453 | etot = -14.6175140350243 -329000 ekin = 0.252245305622037 | erot = 0.503209396460715 | epot = -15.372968737129 | etot = -14.6175140350463 -330000 ekin = 0.278112223739082 | erot = 0.494390678506977 | epot = -15.3900169373163 | etot = -14.6175140350702 -331000 ekin = 0.304195517645115 | erot = 0.484439927614521 | epot = -15.4061494803532 | etot = -14.6175140350935 -332000 ekin = 0.329497983392802 | erot = 0.473992405219011 | epot = -15.4210044237255 | etot = -14.6175140351136 -333000 ekin = 0.353063353198636 | erot = 0.463685785195801 | epot = -15.4342631735224 | etot = -14.617514035128 -334000 ekin = 0.374038491016654 | erot = 0.454134842083192 | epot = -15.4456873682344 | etot = -14.6175140351345 -335000 ekin = 0.391723520500355 | erot = 0.445908562625392 | epot = -15.4551461182584 | etot = -14.6175140351326 -336000 ekin = 0.405605581598612 | erot = 0.439509690040415 | epot = -15.4626293067615 | etot = -14.6175140351225 -337000 ekin = 0.415374601838216 | erot = 0.435356764652285 | epot = -15.4682454015957 | etot = -14.6175140351052 -338000 ekin = 0.42092199701013 | erot = 0.433768862195237 | epot = -15.4722048942883 | etot = -14.6175140350829 -339000 ekin = 0.422325110447523 | erot = 0.434953376211998 | epot = -15.4747925217174 | etot = -14.6175140350579 -340000 ekin = 0.419821259880453 | erot = 0.438997304560007 | epot = -15.4763325994732 | etot = -14.6175140350327 -341000 ekin = 0.413775534581149 | erot = 0.445862573585633 | epot = -15.4771521431765 | etot = -14.6175140350097 -342000 ekin = 0.404646174020848 | erot = 0.455385967573857 | epot = -15.4775461765857 | etot = -14.617514034991 -343000 ekin = 0.39295070583281 | erot = 0.467284215126884 | epot = -15.4777489559374 | etot = -14.6175140349777 -344000 ekin = 0.379235231728883 | erot = 0.481164689425934 | epot = -15.4779139561254 | etot = -14.6175140349706 -345000 ekin = 0.364048459933153 | erot = 0.496541967294177 | epot = -15.4781044621969 | etot = -14.6175140349695 -346000 ekin = 0.347921358320316 | erot = 0.512860132815006 | epot = -15.478295526109 | etot = -14.6175140349737 -347000 ekin = 0.331352665808126 | erot = 0.529520204053122 | epot = -15.4783869048429 | etot = -14.6175140349817 -348000 ekin = 0.314799955036566 | erot = 0.545911447469168 | epot = -15.4782254374972 | etot = -14.6175140349915 -349000 ekin = 0.298675493175281 | erot = 0.561444708834092 | epot = -15.4776342370104 | etot = -14.6175140350011 -350000 ekin = 0.283345815520869 | erot = 0.575585348315993 | epot = -15.4764451988451 | etot = -14.6175140350083 -351000 ekin = 0.269133730327523 | erot = 0.587883045339117 | epot = -15.474530810678 | etot = -14.6175140350114 -352000 ekin = 0.256321431305203 | erot = 0.597995738138039 | epot = -15.4718312044524 | etot = -14.6175140350092 -353000 ekin = 0.24515350965437 | erot = 0.605705335206206 | epot = -15.4683728798616 | etot = -14.617514035001 -354000 ekin = 0.235838910986168 | erot = 0.610923562934476 | epot = -15.4642765089078 | etot = -14.6175140349872 -355000 ekin = 0.228551231300269 | erot = 0.613687305425456 | epot = -15.4597525716945 | etot = -14.6175140349688 -356000 ekin = 0.223427131306842 | erot = 0.61414390282459 | epot = -15.4550850690789 | etot = -14.6175140349475 -357000 ekin = 0.220563006917694 | erot = 0.612527933401747 | epot = -15.4506049752447 | etot = -14.6175140349253 -358000 ekin = 0.22001033319751 | erot = 0.60913185554411 | epot = -15.4466562236463 | etot = -14.6175140349046 -359000 ekin = 0.221770268739896 | erot = 0.604273418957587 | epot = -15.4435577225855 | etot = -14.617514034888 -360000 ekin = 0.225788163653238 | erot = 0.598262925571301 | epot = -15.4415651241022 | etot = -14.6175140348777 -361000 ekin = 0.231948578437327 | erot = 0.591373251984918 | epot = -15.4408358652977 | etot = -14.6175140348754 -362000 ekin = 0.240071331017989 | erot = 0.583815109039703 | epot = -15.4414004749403 | etot = -14.6175140348826 -363000 ekin = 0.249908988057725 | erot = 0.5757194066129 | epot = -15.4431424295705 | etot = -14.6175140348999 -364000 ekin = 0.261146140581906 | erot = 0.567127906486804 | epot = -15.445788081996 | etot = -14.6175140349273 -365000 ekin = 0.273400773645715 | erot = 0.55799265360587 | epot = -15.4489074622158 | etot = -14.6175140349642 -366000 ekin = 0.286228056503678 | erot = 0.548184015759183 | epot = -15.4519261072721 | etot = -14.6175140350092 -367000 ekin = 0.299126926925909 | erot = 0.537506547612528 | epot = -15.454147509599 | etot = -14.6175140350606 -368000 ekin = 0.311549892638302 | erot = 0.525721330953642 | epot = -15.4547852587076 | etot = -14.6175140351156 -369000 ekin = 0.32291649334207 | erot = 0.512572942756027 | epot = -15.4530034712696 | etot = -14.6175140351715 -370000 ekin = 0.332630833323927 | erot = 0.497818805483382 | epot = -15.4479636740324 | etot = -14.6175140352251 -371000 ekin = 0.340103492446064 | erot = 0.481258447418256 | epot = -15.4388759751374 | etot = -14.617514035273 -372000 ekin = 0.344777943663672 | erot = 0.462760223985855 | epot = -15.4250522029614 | etot = -14.6175140353119 -373000 ekin = 0.346161332161602 | erot = 0.442283380419715 | epot = -15.4059587479198 | etot = -14.6175140353385 -374000 ekin = 0.343859062980226 | erot = 0.419893962768359 | epot = -15.3812670610984 | etot = -14.6175140353498 -375000 ekin = 0.337612023151089 | erot = 0.395773904237503 | epot = -15.3508999627316 | etot = -14.617514035343 -376000 ekin = 0.327334336193297 | erot = 0.370223433837585 | epot = -15.3150718053467 | etot = -14.6175140353159 -377000 ekin = 0.31314826371265 | erot = 0.343657545338067 | epot = -15.2743198443178 | etot = -14.6175140352671 -378000 ekin = 0.295411338277465 | erot = 0.316597454538877 | epot = -15.2295228280127 | etot = -14.6175140351964 -379000 ekin = 0.274729408510311 | erot = 0.289657740940239 | epot = -15.1819011845556 | etot = -14.6175140351051 -380000 ekin = 0.251948675267255 | erot = 0.263529414055484 | epot = -15.1329921243191 | etot = -14.6175140349963 -381000 ekin = 0.228120837035106 | erot = 0.238958749468258 | epot = -15.0845936213795 | etot = -14.6175140348762 -382000 ekin = 0.204438854506711 | erot = 0.21672127051921 | epot = -15.0386741597778 | etot = -14.6175140347519 -383000 ekin = 0.182146263755408 | erot = 0.197591880984099 | epot = -14.9972521793719 | etot = -14.6175140346324 -384000 ekin = 0.162429780679591 | erot = 0.182311896923862 | epot = -14.9622557121303 | etot = -14.6175140345269 -385000 ekin = 0.14631062212392 | erot = 0.171555128910903 | epot = -14.9353797854787 | etot = -14.6175140344438 -386000 ekin = 0.134552389652504 | erot = 0.165895597224072 | epot = -14.9179620212652 | etot = -14.6175140343886 -387000 ekin = 0.127600986328474 | erot = 0.165779213533691 | epot = -14.9108942342261 | etot = -14.6175140343639 -388000 ekin = 0.125565151523057 | erot = 0.171500950984465 | epot = -14.9145801368767 | etot = -14.6175140343691 -389000 ekin = 0.128237001096924 | erot = 0.183188026636153 | epot = -14.9289390621345 | etot = -14.6175140344014 -390000 ekin = 0.135143637923019 | erot = 0.200788930663243 | epot = -14.953446603043 | etot = -14.6175140344567 -391000 ekin = 0.145616156499687 | erot = 0.224068074688667 | epot = -14.9871982657189 | etot = -14.6175140345306 -392000 ekin = 0.158862235246419 | erot = 0.252606362172197 | epot = -15.028982632037 | etot = -14.6175140346184 -393000 ekin = 0.174032087603182 | erot = 0.285808726840173 | epot = -15.0773548491589 | etot = -14.6175140347155 -394000 ekin = 0.190272707003279 | erot = 0.32292010751355 | epot = -15.130706849335 | etot = -14.6175140348181 -395000 ekin = 0.206769905101682 | erot = 0.363051013228993 | epot = -15.1873349532528 | etot = -14.6175140349222 -396000 ekin = 0.222780272469837 | erot = 0.405212687948367 | epot = -15.2455069954416 | etot = -14.6175140350234 -397000 ekin = 0.237655698718666 | erot = 0.448360183483368 | epot = -15.3035299173201 | etot = -14.6175140351181 -398000 ekin = 0.250862154069819 | erot = 0.491439914330298 | epot = -15.3598161036023 | etot = -14.6175140352022 -399000 ekin = 0.261993055953367 | erot = 0.533437059171161 | epot = -15.4129441503973 | etot = -14.6175140352727 -400000 ekin = 0.27077655050685 | erot = 0.573417887950022 | epot = -15.4617084737844 | etot = -14.6175140353276 -401000 ekin = 0.277075831015552 | erot = 0.610562842824378 | epot = -15.505152709206 | etot = -14.6175140353661 -402000 ekin = 0.280882158891387 | erot = 0.644187798759806 | epot = -15.5425839930396 | etot = -14.6175140353885 -403000 ekin = 0.282301228578668 | erot = 0.673752968642337 | epot = -15.5735682326172 | etot = -14.6175140353962 -404000 ekin = 0.281534519811851 | erot = 0.698860907482421 | epot = -15.5979094626856 | etot = -14.6175140353913 -405000 ekin = 0.278857975736577 | erot = 0.719246574878491 | epot = -15.6156185859914 | etot = -14.6175140353763 -406000 ekin = 0.27460055575904 | erot = 0.734763157396981 | epot = -15.6268777485092 | etot = -14.6175140353531 -407000 ekin = 0.269124923358191 | erot = 0.745367259285135 | epot = -15.632006217967 | etot = -14.6175140353237 -408000 ekin = 0.262811853165513 | erot = 0.75110627666519 | epot = -15.6314321651198 | etot = -14.6175140352891 -409000 ekin = 0.256049112192014 | erot = 0.752109968276038 | epot = -15.6256731157183 | etot = -14.6175140352503 -410000 ekin = 0.249224269809724 | erot = 0.748584332259421 | epot = -15.6153226372766 | etot = -14.6175140352074 -411000 ekin = 0.242720888553515 | erot = 0.74080910391814 | epot = -15.6010440276324 | etot = -14.6175140351607 -412000 ekin = 0.236916379506249 | erot = 0.729136085380527 | epot = -15.5835664999973 | etot = -14.6175140351105 -413000 ekin = 0.232179735243875 | erot = 0.713985498456682 | epot = -15.5636792687578 | etot = -14.6175140350572 -414000 ekin = 0.228867632642529 | erot = 0.695838652585608 | epot = -15.5422203202303 | etot = -14.6175140350022 -415000 ekin = 0.227317772308198 | erot = 0.675225695396014 | epot = -15.5200575026511 | etot = -14.6175140349469 -416000 ekin = 0.227838940778005 | erot = 0.65270826110506 | epot = -15.4980612367768 | etot = -14.6175140348937 -417000 ekin = 0.23069797086734 | erot = 0.628857925336074 | epot = -15.4770699310485 | etot = -14.6175140348451 -418000 ekin = 0.236104416121177 | erot = 0.604232291329939 | epot = -15.4578507422545 | etot = -14.6175140348034 -419000 ekin = 0.244194252200936 | erot = 0.579351108945467 | epot = -15.4410593959176 | etot = -14.6175140347712 -420000 ekin = 0.255014214169025 | erot = 0.554674986841681 | epot = -15.427203235761 | etot = -14.6175140347503 -421000 ekin = 0.268508458340867 | erot = 0.530589008737006 | epot = -15.4166115018197 | etot = -14.6175140347419 -422000 ekin = 0.284509119561056 | erot = 0.507392982381358 | epot = -15.4094161366888 | etot = -14.6175140347464 -423000 ekin = 0.302732060427453 | erot = 0.485299248119848 | epot = -15.4055453433108 | etot = -14.6175140347635 -424000 ekin = 0.322778728051846 | erot = 0.464438075671392 | epot = -15.4047308385151 | etot = -14.6175140347918 -425000 ekin = 0.344144594922978 | erot = 0.444869796713037 | epot = -15.4065284264654 | etot = -14.6175140348294 -426000 ekin = 0.366234204300236 | erot = 0.426602052984558 | epot = -15.4103502921584 | etot = -14.6175140348736 -427000 ekin = 0.388382398339839 | erot = 0.409609962240785 | epot = -15.4155063955021 | etot = -14.6175140349215 -428000 ekin = 0.409880900047347 | erot = 0.393856678092514 | epot = -15.4212516131098 | etot = -14.61751403497 -429000 ekin = 0.430009061106081 | erot = 0.379311788382045 | epot = -15.4268348845042 | etot = -14.617514035016 -430000 ekin = 0.448067283635938 | erot = 0.365965282400769 | epot = -15.4315466010937 | etot = -14.617514035057 -431000 ekin = 0.463411378722709 | erot = 0.353835411175237 | epot = -15.4347608249887 | etot = -14.6175140350907 -432000 ekin = 0.47548594153415 | erot = 0.342969616703567 | epot = -15.4359695933534 | etot = -14.6175140351157 -433000 ekin = 0.483854704019995 | erot = 0.333438714396017 | epot = -15.4348074535468 | etot = -14.6175140351308 -434000 ekin = 0.488225698517989 | erot = 0.325325491781988 | epot = -15.4310652254358 | etot = -14.6175140351358 -435000 ekin = 0.488469615216989 | erot = 0.318709988965469 | epot = -15.4246936393136 | etot = -14.6175140351312 -436000 ekin = 0.48462910079659 | erot = 0.313653867974335 | epot = -15.4157970038886 | etot = -14.6175140351176 -437000 ekin = 0.476917712283315 | erot = 0.310186654190433 | epot = -15.4046184015705 | etot = -14.6175140350967 -438000 ekin = 0.465707830234525 | erot = 0.308296241622533 | epot = -15.3915181069269 | etot = -14.6175140350699 -439000 ekin = 0.451507536799582 | erot = 0.307925153770196 | epot = -15.376946725609 | etot = -14.6175140350392 -440000 ekin = 0.434927659012326 | erot = 0.308973010492473 | epot = -15.3614147045113 | etot = -14.6175140350065 -441000 ekin = 0.416641657348227 | erot = 0.311304747383323 | epot = -15.3454604397054 | etot = -14.6175140349739 -442000 ekin = 0.397341542599983 | erot = 0.3147626187362 | epot = -15.3296181962795 | etot = -14.6175140349433 -443000 ekin = 0.377694362714098 | erot = 0.319179725729427 | epot = -15.3143881233596 | etot = -14.6175140349161 -444000 ekin = 0.358304425135514 | erot = 0.324393298190365 | epot = -15.3002117582193 | etot = -14.6175140348935 -445000 ekin = 0.339684383333994 | erot = 0.330254911560057 | epot = -15.2874533297702 | etot = -14.6175140348761 -446000 ekin = 0.322237701350787 | erot = 0.336636009508874 | epot = -15.276387745724 | etot = -14.6175140348643 -447000 ekin = 0.306253086582787 | erot = 0.343428242758822 | epot = -15.2671953641996 | etot = -14.617514034858 -448000 ekin = 0.291909091343146 | erot = 0.350538602021414 | epot = -15.2599617282214 | etot = -14.6175140348569 -449000 ekin = 0.279285717663623 | erot = 0.35788026308961 | epot = -15.2546800156141 | etot = -14.6175140348608 -450000 ekin = 0.268379332693062 | erot = 0.365360767817965 | epot = -15.2512541353807 | etot = -14.6175140348697 -451000 ekin = 0.259117719162389 | erot = 0.372869677561009 | epot = -15.2495014316067 | etot = -14.6175140348833 -452000 ekin = 0.251373384973236 | erot = 0.380268095671436 | epot = -15.2491555155464 | etot = -14.6175140349017 -453000 ekin = 0.244974824127414 | erot = 0.387382402365197 | epot = -15.249871261417 | etot = -14.6175140349243 -454000 ekin = 0.239716691076083 | erot = 0.39400413186188 | epot = -15.2512348578882 | etot = -14.6175140349502 -455000 ekin = 0.235370413814051 | erot = 0.399897145642462 | epot = -15.2527815944342 | etot = -14.6175140349777 -456000 ekin = 0.231696513790449 | erot = 0.40481218842498 | epot = -15.2540227372201 | etot = -14.6175140350047 -457000 ekin = 0.228459014431981 | erot = 0.40850770951526 | epot = -15.2544807589758 | etot = -14.6175140350286 -458000 ekin = 0.225441196082345 | erot = 0.410774705624049 | epot = -15.2537299367533 | etot = -14.6175140350469 -459000 ekin = 0.222461018940529 | erot = 0.411462514811891 | epot = -15.2514375688097 | etot = -14.6175140350572 -460000 ekin = 0.219384094438522 | erot = 0.410502136529 | epot = -15.2474002660254 | etot = -14.6175140350579 -461000 ekin = 0.216132245240083 | erot = 0.40792384413244 | epot = -15.2415701244207 | etot = -14.6175140350482 -462000 ekin = 0.212686361973293 | erot = 0.403866554423589 | epot = -15.2340669514251 | etot = -14.6175140350283 -463000 ekin = 0.209083218482802 | erot = 0.398577486489706 | epot = -15.2251747399718 | etot = -14.6175140349993 -464000 ekin = 0.205406888263705 | erot = 0.392401883856904 | epot = -15.2153228070839 | etot = -14.6175140349633 -465000 ekin = 0.201776197881055 | erot = 0.385763783461981 | epot = -15.205054016266 | etot = -14.617514034923 -466000 ekin = 0.198330130961163 | erot = 0.379139817336875 | epot = -15.1949839831792 | etot = -14.6175140348812 -467000 ekin = 0.195213224017084 | erot = 0.373028711257248 | epot = -15.1857559701149 | etot = -14.6175140348406 -468000 ekin = 0.192562810062079 | erot = 0.367919448414624 | epot = -15.1779962932805 | etot = -14.6175140348038 -469000 ekin = 0.190499545154634 | erot = 0.364261004085315 | epot = -15.1722745840127 | etot = -14.6175140347728 -470000 ekin = 0.189122086032537 | erot = 0.362436180586744 | epot = -15.1690723013681 | etot = -14.6175140347488 -471000 ekin = 0.188506156938585 | erot = 0.362741456207124 | epot = -15.1687616478783 | etot = -14.6175140347325 -472000 ekin = 0.188707621222025 | erot = 0.365373993438314 | epot = -15.1715956493842 | etot = -14.6175140347239 -473000 ekin = 0.189768618621823 | erot = 0.370426120543997 | epot = -15.1777087738881 | etot = -14.6175140347222 -474000 ekin = 0.191725397341228 | erot = 0.377886798112909 | epot = -15.1871262301805 | etot = -14.6175140347264 -475000 ekin = 0.194616213070748 | erot = 0.387648901412907 | epot = -15.1997791492191 | etot = -14.6175140347355 -476000 ekin = 0.19848763616064 | erot = 0.39952067815615 | epot = -15.2155223490651 | etot = -14.6175140347483 -477000 ekin = 0.203397790429832 | erot = 0.413239540255182 | epot = -15.2341513654491 | etot = -14.6175140347641 -478000 ekin = 0.209415519783212 | erot = 0.428486466927375 | epot = -15.2554160214929 | etot = -14.6175140347823 -479000 ekin = 0.216615156594683 | erot = 0.444899686772466 | epot = -15.2790288781699 | etot = -14.6175140348028 -480000 ekin = 0.225067223157677 | erot = 0.462086880018489 | epot = -15.3046681380017 | etot = -14.6175140348255 -481000 ekin = 0.234826185147703 | erot = 0.479635803739713 | epot = -15.3319760237384 | etot = -14.617514034851 -482000 ekin = 0.245916939355107 | erot = 0.497123799838186 | epot = -15.3605547740726 | etot = -14.6175140348793 -483000 ekin = 0.258322039580648 | erot = 0.514126984881418 | epot = -15.3899630593725 | etot = -14.6175140349104 -484000 ekin = 0.27197166705463 | erot = 0.530229960568927 | epot = -15.4197156625676 | etot = -14.6175140349441 -485000 ekin = 0.286738030809397 | erot = 0.545036619609846 | epot = -15.4492886853987 | etot = -14.6175140349795 -486000 ekin = 0.302435294441744 | erot = 0.55818212519067 | epot = -15.4781314546478 | etot = -14.6175140350154 -487000 ekin = 0.31882536985775 | erot = 0.569345540302742 | epot = -15.5056849452109 | etot = -14.6175140350504 -488000 ekin = 0.33562912085568 | erot = 0.578262027782569 | epot = -15.531405183721 | etot = -14.6175140350828 -489000 ekin = 0.352541803824768 | erot = 0.584733173542191 | epot = -15.5547890124778 | etot = -14.6175140351108 -490000 ekin = 0.369251041132819 | erot = 0.588633902375943 | epot = -15.575398978642 | etot = -14.6175140351332 -491000 ekin = 0.38545533994301 | erot = 0.589914693969638 | epot = -15.5928840690618 | etot = -14.6175140351491 -492000 ekin = 0.400881156477994 | erot = 0.588598334680196 | epot = -15.6069935263164 | etot = -14.6175140351582 -493000 ekin = 0.41529674637658 | erot = 0.584771169136983 | epot = -15.6175819506742 | etot = -14.6175140351607 -494000 ekin = 0.42852150310201 | erot = 0.578569614095072 | epot = -15.6246051523544 | etot = -14.6175140351573 -495000 ekin = 0.440430011857935 | erot = 0.570163426567811 | epot = -15.6281074735753 | etot = -14.6175140351496 -496000 ekin = 0.45095070631601 | erot = 0.559737766476832 | epot = -15.6282025079316 | etot = -14.6175140351387 -497000 ekin = 0.460059581797609 | erot = 0.547476355485017 | epot = -15.6250499724091 | etot = -14.6175140351264 -498000 ekin = 0.467769906491902 | erot = 0.533547985554597 | epot = -15.6188319271606 | etot = -14.6175140351141 -499000 ekin = 0.474119221072851 | erot = 0.51809827733209 | epot = -15.6097315335077 | etot = -14.6175140351027 -500000 ekin = 0.47915510663515 | erot = 0.501247978936972 | epot = -15.5979171206651 | etot = -14.617514035093 -501000 ekin = 0.482921233339145 | erot = 0.48309830408219 | epot = -15.5835335725062 | etot = -14.6175140350848 -502000 ekin = 0.485445093649468 | erot = 0.463742920559152 | epot = -15.5667020492864 | etot = -14.6175140350778 -503000 ekin = 0.486728599210218 | erot = 0.443285305605287 | epot = -15.5475279398865 | etot = -14.617514035071 -504000 ekin = 0.486742408088666 | erot = 0.421859374631512 | epot = -15.5261158177833 | etot = -14.6175140350632 -505000 ekin = 0.485424480828576 | erot = 0.399650657767878 | epot = -15.5025891736495 | etot = -14.617514035053 -506000 ekin = 0.482682973412862 | erot = 0.376914939267073 | epot = -15.4771119477192 | etot = -14.6175140350392 -507000 ekin = 0.478403198155678 | erot = 0.353991273960951 | epot = -15.4499085071374 | etot = -14.6175140350208 -508000 ekin = 0.472458052936543 | erot = 0.331306710133899 | epot = -15.4212787980677 | etot = -14.6175140349973 -509000 ekin = 0.464721062856492 | erot = 0.309370883447797 | epot = -15.3916059812731 | etot = -14.6175140349688 -510000 ekin = 0.455081004105159 | erot = 0.288759823578861 | epot = -15.3613548626198 | etot = -14.6175140349358 -511000 ekin = 0.443456979181393 | erot = 0.270089690707588 | epot = -15.3310607047887 | etot = -14.6175140348997 -512000 ekin = 0.42981284822046 | erot = 0.253982534898902 | epot = -15.3013094179813 | etot = -14.6175140348619 -513000 ekin = 0.414169942619743 | erot = 0.241027258547542 | epot = -15.2727112359918 | etot = -14.6175140348246 -514000 ekin = 0.396617122320061 | erot = 0.231739657368506 | epot = -15.2458708144779 | etot = -14.6175140347893 -515000 ekin = 0.377317407139222 | erot = 0.226525548757325 | epot = -15.2213569906545 | etot = -14.6175140347579 -516000 ekin = 0.356510629533878 | erot = 0.225650587239722 | epot = -15.1996752515054 | etot = -14.6175140347318 -517000 ekin = 0.334511811731657 | erot = 0.2292195098864 | epot = -15.1812453563299 | etot = -14.6175140347119 -518000 ekin = 0.311705249159968 | erot = 0.237166415926506 | epot = -15.1663856997852 | etot = -14.6175140346987 -519000 ekin = 0.288534562405324 | erot = 0.249256456193412 | epot = -15.1553050532911 | etot = -14.6175140346924 -520000 ekin = 0.265489234982117 | erot = 0.265098165450665 | epot = -15.1481014351253 | etot = -14.6175140346926 -521000 ekin = 0.243088358087376 | erot = 0.28416474515935 | epot = -15.1447671379453 | etot = -14.6175140346986 -522000 ekin = 0.221862437060409 | erot = 0.305821970139557 | epot = -15.1451984419098 | etot = -14.6175140347099 -523000 ekin = 0.202334169775844 | erot = 0.329360070796281 | epot = -15.1492082752976 | etot = -14.6175140347255 -524000 ekin = 0.18499909107587 | erot = 0.354026911469942 | epot = -15.1565400372904 | etot = -14.6175140347446 -525000 ekin = 0.170306912739125 | erot = 0.379059948770509 | epot = -15.1668808962761 | etot = -14.6175140347665 -526000 ekin = 0.158644243148338 | erot = 0.403715126924459 | epot = -15.1798734048633 | etot = -14.6175140347905 -527000 ekin = 0.150319367666652 | erot = 0.427291025811595 | epot = -15.1951244282948 | etot = -14.6175140348166 -528000 ekin = 0.145549592055536 | erot = 0.449147424932796 | epot = -15.2122110518326 | etot = -14.6175140348442 -529000 ekin = 0.144451603985221 | erot = 0.468718121850073 | epot = -15.2306837607087 | etot = -14.6175140348734 -530000 ekin = 0.14703526713895 | erot = 0.485518371010905 | epot = -15.2500676730542 | etot = -14.6175140349043 -531000 ekin = 0.153201203685084 | erot = 0.499147835496798 | epot = -15.2698630741185 | etot = -14.6175140349366 -532000 ekin = 0.162742448480689 | erot = 0.509290301682419 | epot = -15.2895467851334 | etot = -14.6175140349703 -533000 ekin = 0.175350354883052 | erot = 0.515711587206659 | epot = -15.3085759770945 | etot = -14.6175140350048 -534000 ekin = 0.190624856014791 | erot = 0.518257146630773 | epot = -15.3263960376849 | etot = -14.6175140350393 -535000 ekin = 0.2080884935382 | erot = 0.516850140105121 | epot = -15.342452668716 | etot = -14.6175140350727 -536000 ekin = 0.227204325844129 | erot = 0.511491240066285 | epot = -15.356209601014 | etot = -14.6175140351035 -537000 ekin = 0.247396768814447 | erot = 0.502260311074919 | epot = -15.3671711150196 | etot = -14.6175140351302 -538000 ekin = 0.268074342414832 | erot = 0.489319600962367 | epot = -15.374907978528 | etot = -14.6175140351508 -539000 ekin = 0.288653182934819 | erot = 0.472917679673217 | epot = -15.3790848977717 | etot = -14.6175140351637 -540000 ekin = 0.308579985827036 | erot = 0.453392904740712 | epot = -15.3794869257353 | etot = -14.6175140351676 -541000 ekin = 0.32735300819234 | erot = 0.431174973012169 | epot = -15.3760420163656 | etot = -14.6175140351611 -542000 ekin = 0.344539853507862 | erot = 0.406783142890278 | epot = -15.368837031542 | etot = -14.6175140351439 -543000 ekin = 0.359790986514659 | erot = 0.380819988065077 | epot = -15.3581250096959 | etot = -14.6175140351161 -544000 ekin = 0.372848263091261 | erot = 0.353960030673725 | epot = -15.3443223288437 | etot = -14.6175140350787 -545000 ekin = 0.383548167009949 | erot = 0.326933212483018 | epot = -15.3279954145262 | etot = -14.6175140350332 -546000 ekin = 0.391819867385597 | erot = 0.30050378423916 | epot = -15.3098376866063 | etot = -14.6175140349815 -547000 ekin = 0.397678590181961 | erot = 0.275445713888184 | epot = -15.2906383389964 | etot = -14.6175140349263 -548000 ekin = 0.401215088504123 | erot = 0.252516050367 | epot = -15.2712451737411 | etot = -14.6175140348699 -549000 ekin = 0.402582175511822 | erot = 0.232427794768509 | epot = -15.2525240050958 | etot = -14.6175140348155 -550000 ekin = 0.401979352686767 | erot = 0.215823740833757 | epot = -15.2353171282858 | etot = -14.6175140347652 -551000 ekin = 0.399636550192594 | erot = 0.203252510910356 | epot = -15.2204030958242 | etot = -14.6175140347213 -552000 ekin = 0.39579793483933 | erot = 0.19514771457426 | epot = -15.2084596840996 | etot = -14.617514034686 -553000 ekin = 0.390706676474511 | erot = 0.191810879117678 | epot = -15.2000315902533 | etot = -14.6175140346611 -554000 ekin = 0.384591526956334 | erot = 0.193398609454572 | epot = -15.1955041710586 | etot = -14.6175140346477 -555000 ekin = 0.37765606833088 | erot = 0.19991436289407 | epot = -15.1950844658717 | etot = -14.6175140346467 -556000 ekin = 0.370071512613894 | erot = 0.211205266307038 | epot = -15.1987908135787 | etot = -14.6175140346578 -557000 ekin = 0.361973939271072 | erot = 0.22696451510277 | epot = -15.2064524890543 | etot = -14.6175140346805 -558000 ekin = 0.353466765019157 | erot = 0.246739996101886 | epot = -15.2177207958342 | etot = -14.6175140347132 -559000 ekin = 0.344628961763677 | erot = 0.269949765670226 | epot = -15.2320927621875 | etot = -14.6175140347536 -560000 ekin = 0.335528980566657 | erot = 0.295904778795777 | epot = -15.2489477941611 | etot = -14.6175140347987 -561000 ekin = 0.326243446080443 | erot = 0.323838714908469 | epot = -15.2675961958334 | etot = -14.6175140348445 -562000 ekin = 0.31687848681263 | erot = 0.35294385755285 | epot = -15.2873363792525 | etot = -14.617514034887 -563000 ekin = 0.307590234581101 | erot = 0.382410843957197 | epot = -15.3075151134611 | etot = -14.6175140349228 -564000 ekin = 0.298599911427017 | erot = 0.411468934029061 | epot = -15.3275828804049 | etot = -14.6175140349488 -565000 ekin = 0.290198521501092 | erot = 0.439422606477171 | epot = -15.3471351629423 | etot = -14.617514034964 -566000 ekin = 0.282736992095573 | erot = 0.46568015891933 | epot = -15.365931185984 | etot = -14.6175140349691 -567000 ekin = 0.276599956454062 | erot = 0.489770841522339 | epot = -15.3838848329429 | etot = -14.6175140349665 -568000 ekin = 0.272165052790826 | erot = 0.511348887820125 | epot = -15.4010279755712 | etot = -14.6175140349602 -569000 ekin = 0.269753809413461 | erot = 0.530185258476706 | epot = -15.4174531028449 | etot = -14.6175140349547 -570000 ekin = 0.269583567607582 | erot = 0.546150320474166 | epot = -15.4332479230358 | etot = -14.617514034954 -571000 ekin = 0.271731068578169 | erot = 0.559192265325146 | epot = -15.4484373688639 | etot = -14.6175140349606 -572000 ekin = 0.27611649568743 | erot = 0.569316321633573 | epot = -15.4629468522957 | etot = -14.6175140349747 -573000 ekin = 0.282512256444883 | erot = 0.576569321997748 | epot = -15.4765956134373 | etot = -14.6175140349947 -574000 ekin = 0.290574483947772 | erot = 0.581030490761115 | epot = -15.4891190097262 | etot = -14.6175140350173 -575000 ekin = 0.299890113326873 | erot = 0.582808418137228 | epot = -15.5002125665028 | etot = -14.6175140350387 -576000 ekin = 0.310029076131071 | erot = 0.582041678954515 | epot = -15.5095847901411 | etot = -14.6175140350555 -577000 ekin = 0.320591144135804 | erot = 0.578899817193121 | epot = -15.5170049963945 | etot = -14.6175140350656 -578000 ekin = 0.331239680817777 | erot = 0.573581904321184 | epot = -15.5223356202071 | etot = -14.6175140350681 -579000 ekin = 0.341718767395671 | erot = 0.566311213814667 | epot = -15.5255440162741 | etot = -14.6175140350637 -580000 ekin = 0.351854361646072 | erot = 0.557326170820678 | epot = -15.5266945675208 | etot = -14.6175140350541 -581000 ekin = 0.361543170719775 | erot = 0.54686904311153 | epot = -15.5259262488726 | etot = -14.6175140350413 -582000 ekin = 0.370734291431498 | erot = 0.535174473618245 | epot = -15.5234228000773 | etot = -14.6175140350275 -583000 ekin = 0.37940854514609 | erot = 0.522459863754552 | epot = -15.5193824439152 | etot = -14.6175140350145 -584000 ekin = 0.38755933833177 | erot = 0.50891899994006 | epot = -15.5139923732754 | etot = -14.6175140350036 -585000 ekin = 0.395177418309126 | erot = 0.494719483695348 | epot = -15.5074109369997 | etot = -14.6175140349952 -586000 ekin = 0.402240533516271 | erot = 0.480003760425467 | epot = -15.4997583289313 | etot = -14.6175140349896 -587000 ekin = 0.408707997144929 | erot = 0.464893014295021 | epot = -15.4911150464262 | etot = -14.6175140349863 -588000 ekin = 0.414519545772604 | erot = 0.449492951761529 | epot = -15.4815265325189 | etot = -14.6175140349848 -589000 ekin = 0.419597612554971 | erot = 0.433900487906506 | epot = -15.4710121354457 | etot = -14.6175140349842 -590000 ekin = 0.423852083806182 | erot = 0.418210489544302 | epot = -15.4595766083342 | etot = -14.6175140349837 -591000 ekin = 0.42718667151707 | erot = 0.402521929659384 | epot = -15.4472226361591 | etot = -14.6175140349827 -592000 ekin = 0.429506137373247 | erot = 0.386943005730352 | epot = -15.4339631780839 | etot = -14.6175140349803 -593000 ekin = 0.430723706116147 | erot = 0.371594936610811 | epot = -15.4198326777029 | etot = -14.617514034976 -594000 ekin = 0.430768094953345 | erot = 0.356614269838259 | epot = -15.4048963997609 | etot = -14.6175140349693 -595000 ekin = 0.429589664829847 | erot = 0.342153609171636 | epot = -15.3892573089616 | etot = -14.6175140349601 -596000 ekin = 0.427165296133148 | erot = 0.328380718542492 | epot = -15.3730600496239 | etot = -14.6175140349483 -597000 ekin = 0.42350165849966 | erot = 0.315475989403582 | epot = -15.3564916828373 | etot = -14.6175140349341 -598000 ekin = 0.418636501255305 | erot = 0.303628359581859 | epot = -15.339778895755 | etot = -14.6175140349179 -599000 ekin = 0.412638207582272 | erot = 0.293029673723798 | epot = -15.3231819162063 | etot = -14.6175140349002 -600000 ekin = 0.405603414753522 | erot = 0.28386763722636 | epot = -15.3069850868619 | etot = -14.617514034882 -601000 ekin = 0.397652939448492 | erot = 0.276317573361084 | epot = -15.2914845476736 | etot = -14.617514034864 -602000 ekin = 0.388926339151588 | erot = 0.270533300128844 | epot = -15.2769736741277 | etot = -14.6175140348473 -603000 ekin = 0.379575547710976 | erot = 0.266637582798786 | epot = -15.2637271653425 | etot = -14.6175140348328 -604000 ekin = 0.369758112224373 | erot = 0.264712769809576 | epot = -15.2519849168554 | etot = -14.6175140348215 -605000 ekin = 0.35963061496451 | erot = 0.264792359550224 | epot = -15.2419370093288 | etot = -14.6175140348141 -606000 ekin = 0.349342882571248 | erot = 0.266854337886836 | epot = -15.2337112552692 | etot = -14.6175140348112 -607000 ekin = 0.339033558751512 | erot = 0.270817131627415 | epot = -15.2273647251918 | etot = -14.6175140348128 -608000 ekin = 0.32882753825937 | erot = 0.276538908097057 | epot = -15.2228804811754 | etot = -14.617514034819 -609000 ekin = 0.318835621087622 | erot = 0.283820700144174 | epot = -15.2201703560608 | etot = -14.617514034829 -610000 ekin = 0.309156542568317 | erot = 0.292413461055651 | epot = -15.219084038466 | etot = -14.617514034842 -611000 ekin = 0.299881272108214 | erot = 0.302028697869802 | epot = -15.2194240048347 | etot = -14.6175140348566 -612000 ekin = 0.291099167856268 | erot = 0.312351863789569 | epot = -15.2209650665173 | etot = -14.6175140348715 -613000 ekin = 0.282905257831642 | erot = 0.323057294042038 | epot = -15.2234765867589 | etot = -14.6175140348852 -614000 ekin = 0.275407632339941 | erot = 0.333823223652897 | epot = -15.2267448908892 | etot = -14.6175140348963 -615000 ekin = 0.26873372556727 | erot = 0.344345386320857 | epot = -15.2305931467922 | etot = -14.6175140349041 -616000 ekin = 0.263034181136603 | erot = 0.354347879927045 | epot = -15.2348960959716 | etot = -14.617514034908 -617000 ekin = 0.258483071857928 | erot = 0.363590372787296 | epot = -15.2395874795532 | etot = -14.617514034908 -618000 ekin = 0.255273496413749 | erot = 0.371871254538884 | epot = -15.2446587858574 | etot = -14.6175140349047 -619000 ekin = 0.253608004174875 | erot = 0.379026921287401 | epot = -15.2501489603618 | etot = -14.6175140348996 -620000 ekin = 0.253683881422301 | erot = 0.384927934514049 | epot = -15.2561258508302 | etot = -14.6175140348939 -621000 ekin = 0.255674023710173 | erot = 0.389473226072584 | epot = -15.2626612846724 | etot = -14.6175140348896 -622000 ekin = 0.25970485336799 | erot = 0.392583779640473 | epot = -15.269802667897 | etot = -14.6175140348886 -623000 ekin = 0.265833429999859 | erot = 0.394197274406549 | epot = -15.2775447392987 | etot = -14.6175140348923 -624000 ekin = 0.274026439188702 | erot = 0.394265031625425 | epot = -15.2858055057161 | etot = -14.6175140349019 -625000 ekin = 0.28414401573885 | erot = 0.392752285177019 | epot = -15.2944103358336 | etot = -14.6175140349177 -626000 ekin = 0.295931256226573 | erot = 0.389642344381245 | epot = -15.303087635547 | etot = -14.6175140349392 -627000 ekin = 0.309019727830035 | erot = 0.384944676505037 | epot = -15.3114784393 | etot = -14.6175140349649 -628000 ekin = 0.322940275279346 | erot = 0.378706350960174 | epot = -15.3191606612318 | etot = -14.6175140349923 -629000 ekin = 0.337147043698441 | erot = 0.371025698974895 | epot = -15.3256867776918 | etot = -14.6175140350184 -630000 ekin = 0.351051052995002 | erot = 0.362066500827022 | epot = -15.330631588862 | etot = -14.61751403504 -631000 ekin = 0.364060148818953 | erot = 0.352070586246035 | epot = -15.3336447701185 | etot = -14.6175140350535 -632000 ekin = 0.375621025661416 | erot = 0.341366514681189 | epot = -15.334501575399 | etot = -14.6175140350563 -633000 ekin = 0.385258541224309 | erot = 0.330372092305621 | epot = -15.3331446685767 | etot = -14.6175140350468 -634000 ekin = 0.392607865616072 | erot = 0.319588956493667 | epot = -15.329710857134 | etot = -14.6175140350243 -635000 ekin = 0.397436097277817 | erot = 0.309588318033289 | epot = -15.3245384503008 | etot = -14.6175140349897 -636000 ekin = 0.399651602684335 | erot = 0.300988094378234 | epot = -15.3181537320079 | etot = -14.6175140349453 -637000 ekin = 0.399301141331978 | erot = 0.294422893568735 | epot = -15.3112380697947 | etot = -14.617514034894 -638000 ekin = 0.396556439146157 | erot = 0.290509369489293 | epot = -15.3045798434752 | etot = -14.6175140348397 -639000 ekin = 0.391692975512685 | erot = 0.289810143796979 | epot = -15.2990171540957 | etot = -14.6175140347861 -640000 ekin = 0.385064212932825 | erot = 0.29279965311316 | epot = -15.2953779007829 | etot = -14.6175140347369 -641000 ekin = 0.377074355549984 | erot = 0.299834934662478 | epot = -15.2944233249076 | etot = -14.6175140346951 -642000 ekin = 0.368152133960252 | erot = 0.311133625025682 | epot = -15.2967997936491 | etot = -14.6175140346632 -643000 ekin = 0.35872729827394 | erot = 0.326760494743215 | epot = -15.3030018276596 | etot = -14.6175140346425 -644000 ekin = 0.349210670242454 | erot = 0.346622862553666 | epot = -15.3133475674301 | etot = -14.6175140346339 -645000 ekin = 0.339977915473995 | erot = 0.370474376279531 | epot = -15.3279663263912 | etot = -14.6175140346376 -646000 ekin = 0.331356734048571 | erot = 0.397926004728945 | epot = -15.3467967734306 | etot = -14.6175140346531 -647000 ekin = 0.323616951061498 | erot = 0.428462692621698 | epot = -15.3695936783626 | etot = -14.6175140346794 -648000 ekin = 0.316962984679426 | erot = 0.461463981263885 | epot = -15.395941000659 | etot = -14.6175140347157 -649000 ekin = 0.311528303721651 | erot = 0.496226945505972 | epot = -15.4252692839882 | etot = -14.6175140347606 -650000 ekin = 0.307371814502134 | erot = 0.531990113311391 | epot = -15.4568759626263 | etot = -14.6175140348127 -651000 ekin = 0.304476169211803 | erot = 0.567957247022998 | epot = -15.4899474511054 | etot = -14.6175140348706 -652000 ekin = 0.302748327843514 | erot = 0.603320352538697 | epot = -15.5235827153148 | etot = -14.6175140349326 -653000 ekin = 0.302022769690169 | erot = 0.637281675063339 | epot = -15.5568184797505 | etot = -14.617514034997 -654000 ekin = 0.302067723594894 | erot = 0.669074745115614 | epot = -15.5886565037725 | etot = -14.617514035062 -655000 ekin = 0.30259467177562 | erot = 0.697984728109731 | epot = -15.6180934350106 | etot = -14.6175140351253 -656000 ekin = 0.30327116127458 | erot = 0.723368330431443 | epot = -15.6441535268905 | etot = -14.6175140351845 -657000 ekin = 0.303736663271753 | erot = 0.744673311811842 | epot = -15.665924010321 | etot = -14.6175140352374 -658000 ekin = 0.303620889263354 | erot = 0.761457272709825 | epot = -15.6825921972547 | etot = -14.6175140352815 -659000 ekin = 0.302563666908929 | erot = 0.773404945480537 | epot = -15.6934826477038 | etot = -14.6175140353143 -660000 ekin = 0.300235395695977 | erot = 0.780343280385416 | epot = -15.6980927114156 | etot = -14.6175140353342 -661000 ekin = 0.2963557105327 | erot = 0.782250083092817 | epot = -15.6961198289653 | etot = -14.6175140353398 -662000 ekin = 0.290710478297869 | erot = 0.779257959177475 | epot = -15.6874824728057 | etot = -14.6175140353303 -663000 ekin = 0.283165147464189 | erot = 0.771650651991606 | epot = -15.672329834762 | etot = -14.6175140353062 -664000 ekin = 0.27367342717685 | erot = 0.75985056245593 | epot = -15.6510380249012 | etot = -14.6175140352684 -665000 ekin = 0.262280913452633 | erot = 0.744397727319261 | epot = -15.6241926759909 | etot = -14.617514035219 -666000 ekin = 0.249123647022576 | erot = 0.725921231745041 | epot = -15.5925589139283 | etot = -14.6175140351607 -667000 ekin = 0.234422061210095 | erot = 0.705104954965518 | epot = -15.5570410512721 | etot = -14.6175140350965 -668000 ekin = 0.218471158369142 | erot = 0.682650243125394 | epot = -15.5186354365242 | etot = -14.6175140350297 -669000 ekin = 0.201627981911554 | erot = 0.659238455807285 | epot = -15.4783804726821 | etot = -14.6175140349633 -670000 ekin = 0.184297501938695 | erot = 0.635496303881749 | epot = -15.4373078407206 | etot = -14.6175140349002 -671000 ekin = 0.166917915804586 | erot = 0.611966525748987 | epot = -15.3963984763963 | etot = -14.6175140348427 -672000 ekin = 0.149946120673763 | erot = 0.589085832362546 | epot = -15.3565459878289 | etot = -14.6175140347926 -673000 ekin = 0.133843801904168 | erot = 0.567171306813735 | epot = -15.3185291434688 | etot = -14.6175140347509 -674000 ekin = 0.119064262674211 | erot = 0.546415679822031 | epot = -15.2829939772145 | etot = -14.6175140347182 -675000 ekin = 0.106039855016797 | erot = 0.526891195483695 | epot = -15.250445085195 | etot = -14.6175140346945 -676000 ekin = 0.0951697078771964 | erot = 0.508561175679673 | epot = -15.2212449182363 | etot = -14.6175140346794 -677000 ekin = 0.0868074519861108 | erot = 0.491297978911151 | epot = -15.1956194655695 | etot = -14.6175140346723 -678000 ekin = 0.0812485969713162 | erot = 0.47490530110032 | epot = -15.173667932744 | etot = -14.6175140346723 -679000 ekin = 0.0787177619801643 | erot = 0.459143233465844 | epot = -15.1553750301248 | etot = -14.6175140346788 -680000 ekin = 0.079356202465094 | erot = 0.443753980650321 | epot = -15.1406242178063 | etot = -14.6175140346909 -681000 ekin = 0.0832104900793129 | erot = 0.428486254342671 | epot = -15.1292107791298 | etot = -14.6175140347078 -682000 ekin = 0.0902236865228784 | erot = 0.41311688093406 | epot = -15.1208546021859 | etot = -14.617514034729 -683000 ekin = 0.100230543462783 | erot = 0.397468585264983 | epot = -15.1152131634811 | etot = -14.6175140347533 -684000 ekin = 0.112958164259223 | erot = 0.38142345901904 | epot = -15.1118956580582 | etot = -14.61751403478 -685000 ekin = 0.128033094046448 | erot = 0.364932120277571 | epot = -15.1104792491317 | etot = -14.6175140348077 -686000 ekin = 0.144995008361815 | erot = 0.348018922992721 | epot = -15.1105279661897 | etot = -14.6175140348351 -687000 ekin = 0.163316207854869 | erot = 0.330783730220898 | epot = -15.1116139729366 | etot = -14.6175140348608 -688000 ekin = 0.18242523421552 | erot = 0.313400732953528 | epot = -15.1133400020522 | etot = -14.6175140348832 -689000 ekin = 0.201732335852404 | erot = 0.296114640200911 | epot = -15.1153610109544 | etot = -14.6175140349011 -690000 ekin = 0.220654383890837 | erot = 0.2792343742397 | epot = -15.1174027930443 | etot = -14.6175140349138 -691000 ekin = 0.238637189924079 | erot = 0.263124260135935 | epot = -15.1192754849806 | etot = -14.6175140349206 -692000 ekin = 0.255173895595862 | erot = 0.248192653896372 | epot = -15.120880584414 | etot = -14.6175140349217 -693000 ekin = 0.269818995117389 | erot = 0.23487802400786 | epot = -15.1222110540428 | etot = -14.6175140349175 -694000 ekin = 0.282198402188406 | erot = 0.223632668705058 | epot = -15.1233451058024 | etot = -14.6175140349089 -695000 ekin = 0.292016609392508 | erot = 0.214904477347547 | epot = -15.1244351216369 | etot = -14.6175140348968 -696000 ekin = 0.299062308190414 | erot = 0.209117382946464 | epot = -15.125693726019 | etot = -14.6175140348821 -697000 ekin = 0.303213809971508 | erot = 0.20665136156702 | epot = -15.1273792064044 | etot = -14.6175140348658 -698000 ekin = 0.304445256191661 | erot = 0.207822979228463 | epot = -15.1297822702686 | etot = -14.6175140348484 -699000 ekin = 0.302833983904557 | erot = 0.212867544423975 | epot = -15.133215563159 | etot = -14.6175140348305 -700000 ekin = 0.298568596343091 | erot = 0.221923881122192 | epot = -15.1380065122771 | etot = -14.6175140348118 -701000 ekin = 0.291956369738192 | erot = 0.235022588975887 | epot = -15.1444929935065 | etot = -14.6175140347924 -702000 ekin = 0.283427734153971 | erot = 0.252078414120766 | epot = -15.1530201830474 | etot = -14.6175140347727 -703000 ekin = 0.273534855577063 | erot = 0.272887068860917 | epot = -15.1639359591908 | etot = -14.6175140347528 -704000 ekin = 0.262941046164718 | erot = 0.297126498876258 | epot = -15.1775815797747 | etot = -14.6175140347337 -705000 ekin = 0.252398060444993 | erot = 0.324362359960494 | epot = -15.1942744551228 | etot = -14.6175140347173 -706000 ekin = 0.242709489752809 | erot = 0.35405734989386 | epot = -15.2142808743525 | etot = -14.6175140347058 -707000 ekin = 0.23468046525944 | erot = 0.385584073394854 | epot = -15.2377785733566 | etot = -14.6175140347023 -708000 ekin = 0.229056562326985 | erot = 0.418241319395694 | epot = -15.2648119164327 | etot = -14.61751403471 -709000 ekin = 0.226457657534062 | erot = 0.451273895784643 | epot = -15.2952455880503 | etot = -14.6175140347316 -710000 ekin = 0.227314828596047 | erot = 0.483896330832059 | epot = -15.3287251941968 | etot = -14.6175140347687 -711000 ekin = 0.231819479497758 | erot = 0.51532074217238 | epot = -15.3646542564917 | etot = -14.6175140348216 -712000 ekin = 0.239893150549453 | erot = 0.544788749313893 | epot = -15.4021959347515 | etot = -14.6175140348881 -713000 ekin = 0.251183758823612 | erot = 0.571606341189966 | epot = -15.4403041349782 | etot = -14.6175140349646 -714000 ekin = 0.265090036185669 | erot = 0.595179886373849 | epot = -15.4777839576048 | etot = -14.6175140350453 -715000 ekin = 0.280811306968513 | erot = 0.615050345045216 | epot = -15.5133756871376 | etot = -14.6175140351238 -716000 ekin = 0.297415784950172 | erot = 0.63092216570443 | epot = -15.5458519858484 | etot = -14.6175140351938 -717000 ekin = 0.313918116237496 | erot = 0.642683345317361 | epot = -15.5741154968044 | etot = -14.6175140352495 -718000 ekin = 0.329356373326515 | erot = 0.650413757300699 | epot = -15.597284165914 | etot = -14.6175140352868 -719000 ekin = 0.342860093483698 | erot = 0.654380316354833 | epot = -15.6147544451418 | etot = -14.6175140353033 -720000 ekin = 0.353703497402146 | erot = 0.655019233384794 | epot = -15.6262367660857 | etot = -14.6175140352987 -721000 ekin = 0.361340844904821 | erot = 0.652906431496425 | epot = -15.6317613116759 | etot = -14.6175140352746 -722000 ekin = 0.365423978940444 | erot = 0.648719378780955 | epot = -15.6316573929551 | etot = -14.6175140352337 -723000 ekin = 0.365803989071099 | erot = 0.643193727890457 | epot = -15.6265117521414 | etot = -14.6175140351799 -724000 ekin = 0.362520178744054 | erot = 0.637078359572984 | epot = -15.6171125734343 | etot = -14.6175140351172 -725000 ekin = 0.355779938479084 | erot = 0.631092082280464 | epot = -15.6043860558097 | etot = -14.6175140350502 -726000 ekin = 0.345932952940548 | erot = 0.625884613514222 | epot = -15.5893316014373 | etot = -14.6175140349826 -727000 ekin = 0.333442641404433 | erot = 0.622003743386452 | epot = -15.572960419709 | etot = -14.6175140349181 -728000 ekin = 0.31885705049608 | erot = 0.619869891937983 | epot = -15.5562409772938 | etot = -14.6175140348597 -729000 ekin = 0.30278072495631 | erot = 0.61975869169039 | epot = -15.5400534514564 | etot = -14.6175140348097 -730000 ekin = 0.285848455040377 | erot = 0.621791770571061 | epot = -15.5251542603808 | etot = -14.6175140347694 -731000 ekin = 0.26870127220438 | erot = 0.625935552811994 | epot = -15.5121508597562 | etot = -14.6175140347399 -732000 ekin = 0.251964649663544 | erot = 0.632007594592584 | epot = -15.5014862789777 | etot = -14.6175140347215 -733000 ekin = 0.236228569496369 | erot = 0.639689689353592 | epot = -15.4934322935641 | etot = -14.6175140347141 -734000 ekin = 0.2220289607466 | erot = 0.64854669871573 | epot = -15.4880896941798 | etot = -14.6175140347175 -735000 ekin = 0.209830023527896 | erot = 0.658049804518268 | epot = -15.4853938627768 | etot = -14.6175140347306 -736000 ekin = 0.20000716676131 | erot = 0.667602683400117 | epot = -15.4851238849144 | etot = -14.6175140347529 -737000 ekin = 0.192830719625365 | erot = 0.676569044421737 | epot = -15.4869137988309 | etot = -14.6175140347838 -738000 ekin = 0.188451200585985 | erot = 0.684300102138329 | epot = -15.4902653375465 | etot = -14.6175140348222 -739000 ekin = 0.186887639937117 | erot = 0.6901609006521 | epot = -15.4945625754563 | etot = -14.6175140348671 -740000 ekin = 0.18802106841102 | erot = 0.693554915035337 | epot = -15.4990900183636 | etot = -14.6175140349173 -741000 ekin = 0.191595568995591 | erot = 0.693946922730827 | epot = -15.5030565266968 | etot = -14.6175140349704 -742000 ekin = 0.197228843628703 | erot = 0.690884208638806 | epot = -15.5056270872919 | etot = -14.6175140350244 -743000 ekin = 0.204433503637974 | erot = 0.684016821527692 | epot = -15.5059643602413 | etot = -14.6175140350756 -744000 ekin = 0.212648433381792 | erot = 0.673116668202608 | epot = -15.503279136705 | etot = -14.6175140351206 -745000 ekin = 0.221277722248228 | erot = 0.658094727364962 | epot = -15.4968864847688 | etot = -14.6175140351556 -746000 ekin = 0.229733012317398 | erot = 0.639014583780834 | epot = -15.4862616312757 | etot = -14.6175140351775 -747000 ekin = 0.23747404414407 | erot = 0.616100096672176 | epot = -15.4710881760002 | etot = -14.6175140351839 -748000 ekin = 0.244042266762415 | erot = 0.589734872786552 | epot = -15.4512911747231 | etot = -14.6175140351741 -749000 ekin = 0.249083597952522 | erot = 0.560451518402465 | epot = -15.4270491515038 | etot = -14.6175140351488 -750000 ekin = 0.25235833014632 | erot = 0.528910066810374 | epot = -15.3987824320668 | etot = -14.6175140351102 -751000 ekin = 0.253738423480709 | erot = 0.495866496253692 | epot = -15.3671189547962 | etot = -14.6175140350618 -752000 ekin = 0.253194394014668 | erot = 0.462133785332355 | epot = -15.3328422143545 | etot = -14.6175140350075 -753000 ekin = 0.250775308154698 | erot = 0.428539072349797 | epot = -15.2968284154564 | etot = -14.6175140349519 -754000 ekin = 0.246585878545855 | erot = 0.395880964578259 | epot = -15.2599808780229 | etot = -14.6175140348988 -755000 ekin = 0.240764398112151 | erot = 0.364890850085332 | epot = -15.2231692830489 | etot = -14.6175140348514 -756000 ekin = 0.233464471042371 | erot = 0.33620133003052 | epot = -15.1871798358848 | etot = -14.6175140348119 -757000 ekin = 0.224842467157428 | erot = 0.310323830730607 | epot = -15.1526803326694 | etot = -14.6175140347814 -758000 ekin = 0.215051562420606 | erot = 0.287636293953365 | epot = -15.1202018911339 | etot = -14.61751403476 -759000 ekin = 0.204242275875609 | erot = 0.268380753510832 | epot = -15.090137064133 | etot = -14.6175140347465 -760000 ekin = 0.192568636064991 | erot = 0.252669695564108 | epot = -15.0627523663688 | etot = -14.6175140347397 -761000 ekin = 0.180198520175589 | erot = 0.240499428913179 | epot = -15.038211983826 | etot = -14.6175140347373 -762000 ekin = 0.167326299029085 | erot = 0.231768292969539 | epot = -15.0166086267357 | etot = -14.617514034737 -763000 ekin = 0.15418568590204 | erot = 0.226297425418118 | epot = -14.997997146057 | etot = -14.6175140347368 -764000 ekin = 0.141060632749147 | erot = 0.223852003350697 | epot = -14.9824266708347 | etot = -14.6175140347349 -765000 ekin = 0.128292252297103 | erot = 0.224161332820243 | epot = -14.9699676198474 | etot = -14.61751403473 -766000 ekin = 0.116280064488639 | erot = 0.226936813025351 | epot = -14.9607309122354 | etot = -14.6175140347214 -767000 ekin = 0.105476340627594 | erot = 0.231887507272404 | epot = -14.9548778826094 | etot = -14.6175140347094 -768000 ekin = 0.0963728909465988 | erot = 0.23873364134698 | epot = -14.952620566988 | etot = -14.6175140346944 -769000 ekin = 0.0894802427438104 | erot = 0.247218655410706 | epot = -14.9542129328319 | etot = -14.6175140346774 -770000 ekin = 0.0852997361098734 | erot = 0.257120353609604 | epot = -14.9599341243794 | etot = -14.6175140346599 -771000 ekin = 0.0842896183574806 | erot = 0.268261228609983 | epot = -14.9700648816113 | etot = -14.6175140346438 -772000 ekin = 0.0868267987479503 | erot = 0.280517313420827 | epot = -14.9848581468001 | etot = -14.6175140346313 -773000 ekin = 0.0931666172479738 | erot = 0.29382416266062 | epot = -15.0045048145334 | etot = -14.6175140346248 -774000 ekin = 0.103403843826315 | erot = 0.308178073397328 | epot = -15.0290959518505 | etot = -14.6175140346269 -775000 ekin = 0.117439110045059 | erot = 0.323630675217718 | epot = -15.0585838199028 | etot = -14.61751403464 -776000 ekin = 0.134955835364923 | erot = 0.340275613675133 | epot = -15.0927454837062 | etot = -14.6175140346661 -777000 ekin = 0.155413263634583 | erot = 0.3582278427454 | epot = -15.1311551410863 | etot = -14.6175140347063 -778000 ekin = 0.178060391220183 | erot = 0.377596905888865 | epot = -15.1731713318691 | etot = -14.6175140347601 -779000 ekin = 0.201973803863677 | erot = 0.398457850157374 | epot = -15.2179456888463 | etot = -14.6175140348253 -780000 ekin = 0.226119091212116 | erot = 0.420824480237598 | epot = -15.2644576063476 | etot = -14.6175140348979 -781000 ekin = 0.249431156624362 | erot = 0.444629585314245 | epot = -15.3115747769111 | etot = -14.6175140349725 -782000 ekin = 0.27090447026737 | erot = 0.469715692367108 | epot = -15.3581341976774 | etot = -14.617514035043 -783000 ekin = 0.289681273781371 | erot = 0.495837747641005 | epot = -15.4030330565255 | etot = -14.6175140351031 -784000 ekin = 0.305125009984925 | erot = 0.522676532161846 | epot = -15.4453155772951 | etot = -14.6175140351483 -785000 ekin = 0.316868262921689 | erot = 0.549859353707494 | epot = -15.4842416518049 | etot = -14.6175140351757 -786000 ekin = 0.324828845887827 | erot = 0.57698331002341 | epot = -15.5193261910962 | etot = -14.617514035185 -787000 ekin = 0.32919323387832 | erot = 0.60363650580216 | epot = -15.5503437748586 | etot = -14.6175140351781 -788000 ekin = 0.33037186485146 | erot = 0.629413875564563 | epot = -15.5772997755749 | etot = -14.6175140351589 -789000 ekin = 0.328934711355184 | erot = 0.653926193133396 | epot = -15.6003749396209 | etot = -14.6175140351323 -790000 ekin = 0.325537319473833 | erot = 0.676802790007515 | epot = -15.619854144585 | etot = -14.6175140351037 -791000 ekin = 0.320847267933844 | erot = 0.697689943212853 | epot = -15.6360512462245 | etot = -14.6175140350778 -792000 ekin = 0.315479253540059 | erot = 0.716247584425432 | epot = -15.6492408730237 | etot = -14.6175140350582 -793000 ekin = 0.309944490982995 | erot = 0.732146955923568 | epot = -15.659605481954 | etot = -14.6175140350475 -794000 ekin = 0.304617480926279 | erot = 0.745071299200936 | epot = -15.6672028151733 | etot = -14.6175140350461 -795000 ekin = 0.299720880977542 | erot = 0.754720862086076 | epot = -15.6719557781174 | etot = -14.6175140350538 -796000 ekin = 0.295327396181288 | erot = 0.760822658788699 | epot = -15.6736640900385 | etot = -14.6175140350685 -797000 ekin = 0.291376296852734 | erot = 0.763144639346229 | epot = -15.6720349712862 | etot = -14.6175140350872 -798000 ekin = 0.287701294704638 | erot = 0.761513269132583 | epot = -15.6667285989436 | etot = -14.6175140351064 -799000 ekin = 0.284065979572969 | erot = 0.755832991337638 | epot = -15.6574130060325 | etot = -14.6175140351219 -800000 ekin = 0.280202790632173 | erot = 0.746105645864818 | epot = -15.6438224716274 | etot = -14.6175140351304 -801000 ekin = 0.275851560112921 | erot = 0.732447665813908 | epot = -15.6258132610552 | etot = -14.6175140351284 -802000 ekin = 0.270794034433598 | erot = 0.715102809072986 | epot = -15.6034108786203 | etot = -14.6175140351137 -803000 ekin = 0.264881442636211 | erot = 0.694448356025999 | epot = -15.5768438337475 | etot = -14.6175140350853 -804000 ekin = 0.258053167890611 | erot = 0.670993199746564 | epot = -15.5465604026803 | etot = -14.6175140350431 -805000 ekin = 0.250345604727777 | erot = 0.645366941436383 | epot = -15.5132265811527 | etot = -14.6175140349885 -806000 ekin = 0.241890533711227 | erot = 0.618299214643911 | epot = -15.4777037832789 | etot = -14.6175140349238 -807000 ekin = 0.232905655206386 | erot = 0.59059128773573 | epot = -15.4410109777945 | etot = -14.6175140348524 -808000 ekin = 0.223678061732307 | erot = 0.563080896687569 | epot = -15.404272993198 | etot = -14.6175140347781 -809000 ekin = 0.21454303522989 | erot = 0.536602758841035 | epot = -15.3686598287761 | etot = -14.6175140347052 -810000 ekin = 0.205860488312487 | erot = 0.511947500022813 | epot = -15.335322022973 | etot = -14.6175140346377 -811000 ekin = 0.197991117804985 | erot = 0.489821758276953 | epot = -15.3053269106614 | etot = -14.6175140345795 -812000 ekin = 0.191273941670598 | erot = 0.470812030933133 | epot = -15.2796000071373 | etot = -14.6175140345336 -813000 ekin = 0.18600640436918 | erot = 0.455354451061547 | epot = -15.2588748899335 | etot = -14.6175140345028 -814000 ekin = 0.182427753711695 | erot = 0.443712201373049 | epot = -15.2436539895733 | etot = -14.6175140344886 -815000 ekin = 0.180705986334899 | erot = 0.435961774090678 | epot = -15.2341817949176 | etot = -14.617514034492 -816000 ekin = 0.180928373605138 | erot = 0.431988814112469 | epot = -15.2304312222306 | etot = -14.617514034513 -817000 ekin = 0.183095431233989 | erot = 0.431493858262917 | epot = -15.2321033240477 | etot = -14.6175140345508 -818000 ekin = 0.187118173911423 | erot = 0.43400789506895 | epot = -15.2386401035843 | etot = -14.6175140346039 -819000 ekin = 0.192818568053485 | erot = 0.438917286806367 | epot = -15.2492498895297 | etot = -14.6175140346698 -820000 ekin = 0.199933211815007 | erot = 0.445497181488063 | epot = -15.2629444280486 | etot = -14.6175140347455 -821000 ekin = 0.208120374082307 | erot = 0.452952069483619 | epot = -15.2785864783934 | etot = -14.6175140348274 -822000 ekin = 0.216970558498724 | erot = 0.460461605795572 | epot = -15.2949461992058 | etot = -14.6175140349115 -823000 ekin = 0.226020685629653 | erot = 0.467229260922794 | epot = -15.3107639815457 | etot = -14.6175140349933 -824000 ekin = 0.234771793852154 | erot = 0.472530858216694 | epot = -15.3248166871376 | etot = -14.6175140350687 -825000 ekin = 0.242709867662635 | erot = 0.475759712130466 | epot = -15.3359836149267 | etot = -14.6175140351336 -826000 ekin = 0.249329060858575 | erot = 0.476465014357238 | epot = -15.3433081104001 | etot = -14.6175140351843 -827000 ekin = 0.25415625948642 | erot = 0.474380409602698 | epot = -15.3460507043074 | etot = -14.6175140352183 -828000 ekin = 0.256775693171424 | erot = 0.469440383344404 | epot = -15.3437301117495 | etot = -14.6175140352337 -829000 ekin = 0.256852201217284 | erot = 0.46178309210187 | epot = -15.336149328549 | etot = -14.6175140352299 -830000 ekin = 0.254151805817283 | erot = 0.451739467040903 | epot = -15.3234053080654 | etot = -14.6175140352073 -831000 ekin = 0.248558416434218 | erot = 0.439809632306185 | epot = -15.3058820839079 | etot = -14.6175140351675 -832000 ekin = 0.240085737091441 | erot = 0.426628719075599 | epot = -15.2842284912797 | etot = -14.6175140351126 -833000 ekin = 0.228883712687973 | erot = 0.412924890623741 | epot = -15.2593226383575 | etot = -14.6175140350458 -834000 ekin = 0.215239082682017 | erot = 0.399472764055522 | epot = -15.2322258817081 | etot = -14.6175140349705 -835000 ekin = 0.199569787294727 | erot = 0.387045440519038 | epot = -15.2041292627042 | etot = -14.6175140348904 -836000 ekin = 0.182413100763729 | erot = 0.376368114580306 | epot = -15.1762952501535 | etot = -14.6175140348094 -837000 ekin = 0.164407483062571 | erot = 0.368075825930997 | epot = -15.149997343725 | etot = -14.6175140347315 -838000 ekin = 0.146268295773245 | erot = 0.362677435797452 | epot = -15.1264597662308 | etot = -14.6175140346601 -839000 ekin = 0.128757768426142 | erot = 0.360527421580312 | epot = -15.1067992246053 | etot = -14.6175140345989 -840000 ekin = 0.112649960717701 | erot = 0.36180661865639 | epot = -15.0919706139249 | etot = -14.6175140345508 -841000 ekin = 0.0986919456674289 | erot = 0.36651260392939 | epot = -15.0827185841154 | etot = -14.6175140345186 -842000 ekin = 0.0875630029231973 | erot = 0.374460003556307 | epot = -15.0795370409836 | etot = -14.6175140345041 -843000 ekin = 0.0798341847684568 | erot = 0.385290606533499 | epot = -15.0826388258105 | etot = -14.6175140345086 -844000 ekin = 0.0759310929906455 | erot = 0.398492769730518 | epot = -15.0919378972534 | etot = -14.6175140345322 -845000 ekin = 0.0761029610203614 | erot = 0.413429207169692 | epot = -15.1070462027642 | etot = -14.6175140345741 -846000 ekin = 0.0804010613291467 | erot = 0.429371869323724 | epot = -15.1272869652855 | etot = -14.6175140346326 -847000 ekin = 0.0886689809243283 | erot = 0.445542241999283 | epot = -15.151725257628 | etot = -14.6175140347044 -848000 ekin = 0.100546421460129 | erot = 0.46115503871289 | epot = -15.1792154949586 | etot = -14.6175140347856 -849000 ekin = 0.115486960011282 | erot = 0.475462945352927 | epot = -15.2084639402358 | etot = -14.6175140348716 -850000 ekin = 0.132788806696208 | erot = 0.487799837753942 | epot = -15.2381026794073 | etot = -14.6175140349572 -851000 ekin = 0.151636227786906 | erot = 0.497619785577632 | epot = -15.2667700484016 | etot = -14.6175140350371 -852000 ekin = 0.171148194576718 | erot = 0.504529242628412 | epot = -15.2931914723118 | etot = -14.6175140351066 -853000 ekin = 0.190430159396265 | erot = 0.50831015746196 | epot = -15.31625435202 | etot = -14.6175140351617 -854000 ekin = 0.208624756900111 | erot = 0.508932337651449 | epot = -15.3350711297509 | etot = -14.6175140351993 -855000 ekin = 0.224957674812678 | erot = 0.506554231539646 | epot = -15.3490259415702 | etot = -14.6175140352179 -856000 ekin = 0.238775816539412 | erot = 0.501512259960127 | epot = -15.3578021117162 | etot = -14.6175140352167 -857000 ekin = 0.249575992234284 | erot = 0.494299801981541 | epot = -15.3613898294126 | etot = -14.6175140351967 -858000 ekin = 0.257023502073991 | erot = 0.485537766821542 | epot = -15.3600753040553 | etot = -14.6175140351598 -859000 ekin = 0.260960921285794 | erot = 0.475939247615297 | epot = -15.3544142040096 | etot = -14.6175140351085 -860000 ekin = 0.261408037072425 | erot = 0.466270984603931 | epot = -15.3451930567221 | etot = -14.6175140350458 -861000 ekin = 0.258554187538353 | erot = 0.457314264402295 | epot = -15.3333824869156 | etot = -14.6175140349749 -862000 ekin = 0.252744258033141 | erot = 0.449827506885222 | epot = -15.3200857998177 | etot = -14.6175140348993 -863000 ekin = 0.244459417796683 | erot = 0.444512141833012 | epot = -15.3064855944521 | etot = -14.6175140348224 -864000 ekin = 0.23429336884036 | erot = 0.441983030938511 | epot = -15.2937904345263 | etot = -14.6175140347475 -865000 ekin = 0.222924696624272 | erot = 0.442744308393629 | epot = -15.2831830396954 | etot = -14.6175140346775 -866000 ekin = 0.211086026109497 | erot = 0.447169652379628 | epot = -15.2757697131049 | etot = -14.6175140346158 -867000 ekin = 0.199530465893205 | erot = 0.455487658922675 | epot = -15.2725321593806 | etot = -14.6175140345647 -868000 ekin = 0.188996288427701 | erot = 0.467771811642206 | epot = -15.274282134597 | etot = -14.6175140345271 -869000 ekin = 0.180171161859839 | erot = 0.483934855625384 | epot = -15.2816200519904 | etot = -14.6175140345052 -870000 ekin = 0.173657413869083 | erot = 0.503727420428225 | epot = -15.2948988687979 | etot = -14.6175140345006 -871000 ekin = 0.169940429082826 | erot = 0.526741193130643 | epot = -15.3141956567281 | etot = -14.6175140345146 -872000 ekin = 0.169362274179231 | erot = 0.55241708894464 | epot = -15.3392933976713 | etot = -14.6175140345475 -873000 ekin = 0.172102391202432 | erot = 0.580058846013128 | epot = -15.3696752718142 | etot = -14.6175140345986 -874000 ekin = 0.178167002902699 | erot = 0.608852557306752 | epot = -15.404533594876 | etot = -14.6175140346666 -875000 ekin = 0.187388233891608 | erot = 0.637892396629037 | epot = -15.4427946652693 | etot = -14.6175140347487 -876000 ekin = 0.199433181368205 | erot = 0.666212376944565 | epot = -15.4831595931543 | etot = -14.6175140348416 -877000 ekin = 0.213822249051452 | erot = 0.69282332523737 | epot = -15.5241596092296 | etot = -14.6175140349407 -878000 ekin = 0.229955728386783 | erot = 0.716754212644293 | epot = -15.5642239760726 | etot = -14.6175140350415 -879000 ekin = 0.247146104645698 | erot = 0.737095186134375 | epot = -15.6017553259191 | etot = -14.617514035139 -880000 ekin = 0.264653797002906 | erot = 0.753040153405454 | epot = -15.6352079856366 | etot = -14.6175140352283 -881000 ekin = 0.28172378426185 | erot = 0.763926241590771 | epot = -15.6631640611577 | etot = -14.617514035305 -882000 ekin = 0.297620641607227 | erot = 0.769267373447333 | epot = -15.6844020504203 | etot = -14.6175140353657 -883000 ekin = 0.311659967166543 | erot = 0.768779581882131 | epot = -15.6979535844564 | etot = -14.6175140354077 -884000 ekin = 0.323234773768197 | erot = 0.762396270683944 | epot = -15.7031450798816 | etot = -14.6175140354294 -885000 ekin = 0.331836099625417 | erot = 0.750272396067174 | epot = -15.6996225311231 | etot = -14.6175140354305 -886000 ekin = 0.337067751564103 | erot = 0.732777385265373 | epot = -15.6873591722411 | etot = -14.6175140354117 -887000 ekin = 0.338655649766336 | erot = 0.710477420749848 | epot = -15.6666471058904 | etot = -14.6175140353742 -888000 ekin = 0.336452632420875 | erot = 0.684108417155686 | epot = -15.6380750848969 | etot = -14.6175140353203 -889000 ekin = 0.330439768515621 | erot = 0.654541548239603 | epot = -15.602495352008 | etot = -14.6175140352528 -890000 ekin = 0.320725208484741 | erot = 0.62274352002662 | epot = -15.5609827636857 | etot = -14.6175140351743 -891000 ekin = 0.307541386208895 | erot = 0.589733936087021 | epot = -15.514789357384 | etot = -14.6175140350881 -892000 ekin = 0.291240998129636 | erot = 0.556542080397485 | epot = -15.465297113524 | etot = -14.6175140349969 -893000 ekin = 0.272291667891092 | erot = 0.524165278720341 | epot = -15.4139709815152 | etot = -14.6175140349038 -894000 ekin = 0.251268620703177 | erot = 0.493530718297282 | epot = -15.3623133738115 | etot = -14.6175140348111 -895000 ekin = 0.228844131843334 | erot = 0.465462234286213 | epot = -15.311820400851 | etot = -14.6175140347214 -896000 ekin = 0.205772103521623 | erot = 0.440653137306931 | epot = -15.263939275466 | etot = -14.6175140346374 -897000 ekin = 0.18286601780276 | erot = 0.419645693758162 | epot = -15.2200257461227 | etot = -14.6175140345617 -898000 ekin = 0.160968870008327 | erot = 0.40281742524286 | epot = -15.1813003297482 | etot = -14.617514034497 -899000 ekin = 0.140914625128286 | erot = 0.390374024162985 | epot = -15.1488026837377 | etot = -14.6175140344464 -900000 ekin = 0.123482269337591 | erot = 0.382348451689304 | epot = -15.1233447554395 | etot = -14.6175140344126 -901000 ekin = 0.109345484385278 | erot = 0.378605737554559 | epot = -15.1054652563381 | etot = -14.6175140343982 -902000 ekin = 0.0990229789071406 | erot = 0.37885314016642 | epot = -15.0953901534788 | etot = -14.6175140344052 -903000 ekin = 0.0928360184568559 | erot = 0.382655585825979 | epot = -15.093005638717 | etot = -14.6175140344341 -904000 ekin = 0.0908801123885926 | erot = 0.389456554773827 | epot = -15.0978507016463 | etot = -14.6175140344838 -905000 ekin = 0.0930167096533132 | erot = 0.398604648850322 | epot = -15.1091353930552 | etot = -14.6175140345515 -906000 ekin = 0.0988880708470662 | erot = 0.409385812369458 | epot = -15.1257879178489 | etot = -14.6175140346324 -907000 ekin = 0.107954659148216 | erot = 0.421060528764254 | epot = -15.1465292226329 | etot = -14.6175140347204 -908000 ekin = 0.119550305155171 | erot = 0.432904367174519 | epot = -15.1699687071382 | etot = -14.6175140348085 -909000 ekin = 0.132947118365042 | erot = 0.444249232158093 | epot = -15.1947103854133 | etot = -14.6175140348902 -910000 ekin = 0.14742054333404 | erot = 0.45452187965619 | epot = -15.2194564579498 | etot = -14.6175140349596 -911000 ekin = 0.162305506309761 | erot = 0.463275978358842 | epot = -15.2430955196813 | etot = -14.6175140350127 -912000 ekin = 0.177037050913266 | erot = 0.470214361754283 | epot = -15.2647654477151 | etot = -14.6175140350476 -913000 ekin = 0.191172462463443 | erot = 0.475199092565798 | epot = -15.2838855900934 | etot = -14.6175140350642 -914000 ekin = 0.204395616840806 | erot = 0.478248345047313 | epot = -15.3001579969523 | etot = -14.6175140350642 -915000 ekin = 0.21650723869525 | erot = 0.479520616571472 | epot = -15.3135418903175 | etot = -14.6175140350508 -916000 ekin = 0.22740635239903 | erot = 0.479288139235308 | epot = -15.3242085266619 | etot = -14.6175140350276 -917000 ekin = 0.237068358847916 | erot = 0.477902392722287 | epot = -15.3324847865686 | etot = -14.6175140349984 -918000 ekin = 0.245524170398606 | erot = 0.475755244751368 | epot = -15.338793450117 | etot = -14.617514034967 -919000 ekin = 0.252843202023207 | erot = 0.473239468154926 | epot = -15.3435967051145 | etot = -14.6175140349364 -920000 ekin = 0.259121284814418 | erot = 0.470712244289352 | epot = -15.3473475640129 | etot = -14.6175140349091 -921000 ekin = 0.264473144075716 | erot = 0.468464808091652 | epot = -15.3504519870541 | etot = -14.6175140348868 -922000 ekin = 0.269028180853147 | erot = 0.466700668341421 | epot = -15.3532428840648 | etot = -14.6175140348703 -923000 ekin = 0.272927944744965 | erot = 0.465523908452019 | epot = -15.3559658880565 | etot = -14.6175140348596 -924000 ekin = 0.276323793828338 | erot = 0.464938026324942 | epot = -15.3587758550077 | etot = -14.6175140348544 -925000 ekin = 0.279373649322719 | erot = 0.464854721381143 | epot = -15.3617424055579 | etot = -14.6175140348541 -926000 ekin = 0.282237300897349 | erot = 0.465111106681717 | epot = -15.3648624424361 | etot = -14.6175140348571 -927000 ekin = 0.285070250341268 | erot = 0.465493135294266 | epot = -15.3680774204978 | etot = -14.6175140348623 -928000 ekin = 0.288016501944426 | erot = 0.465762600719312 | epot = -15.3712931375323 | etot = -14.6175140348686 -929000 ekin = 0.291201026098215 | erot = 0.465684740680354 | epot = -15.3743998016532 | etot = -14.6175140348747 -930000 ekin = 0.294722459179014 | erot = 0.465054261990702 | epot = -15.3772907560492 | etot = -14.6175140348795 -931000 ekin = 0.29864676401532 | erot = 0.463717248454336 | epot = -15.3798780473521 | etot = -14.6175140348824 -932000 ekin = 0.30300230463982 | erot = 0.461587311534142 | epot = -15.382103651057 | etot = -14.617514034883 -933000 ekin = 0.307776651095021 | erot = 0.458654945592281 | epot = -15.3839456315687 | etot = -14.6175140348814 -934000 ekin = 0.312915338272243 | erot = 0.454989722656041 | epot = -15.385419095806 | etot = -14.6175140348777 -935000 ekin = 0.318322768321537 | erot = 0.4507356255513 | epot = -15.3865724287453 | etot = -14.6175140348725 -936000 ekin = 0.323865441581232 | erot = 0.446100385695392 | epot = -15.3874798621431 | etot = -14.6175140348664 -937000 ekin = 0.329377658420751 | erot = 0.441340069470884 | epot = -15.3882317627517 | etot = -14.6175140348601 -938000 ekin = 0.334669609401342 | erot = 0.436740154638299 | epot = -15.3889237988938 | etot = -14.6175140348541 -939000 ekin = 0.339538182698431 | erot = 0.432595723627041 | epot = -15.3896479411745 | etot = -14.617514034849 -940000 ekin = 0.343779460434951 | erot = 0.429190561372456 | epot = -15.3904840566526 | etot = -14.6175140348452 -941000 ekin = 0.347202304173587 | erot = 0.426777065358565 | epot = -15.391493404375 | etot = -14.6175140348428 -942000 ekin = 0.349642062607373 | erot = 0.425558062624985 | epot = -15.3927141600744 | etot = -14.6175140348421 -943000 ekin = 0.350973206935267 | erot = 0.425671371650545 | epot = -15.3941586134289 | etot = -14.6175140348431 -944000 ekin = 0.351119786154239 | erot = 0.427178062458757 | epot = -15.3958118834587 | etot = -14.6175140348457 -945000 ekin = 0.350062816508182 | erot = 0.430055404932911 | epot = -15.397632256291 | etot = -14.6175140348499 -946000 ekin = 0.347844068536133 | erot = 0.434195447788936 | epot = -15.3995535511804 | etot = -14.6175140348553 -947000 ekin = 0.344566017440968 | erot = 0.439410327983271 | epot = -15.4014903802857 | etot = -14.6175140348614 -948000 ekin = 0.340388212506876 | erot = 0.445444378275944 | epot = -15.4033466256503 | etot = -14.6175140348675 -949000 ekin = 0.335520427168076 | erot = 0.451992965713332 | epot = -15.405027427754 | etot = -14.6175140348726 -950000 ekin = 0.330213181195925 | erot = 0.458727107974287 | epot = -15.4064543240458 | etot = -14.6175140348756 -951000 ekin = 0.324745816556271 | erot = 0.465321341195901 | epot = -15.4075811926278 | etot = -14.6175140348756 -952000 ekin = 0.319412679962131 | erot = 0.471482169175953 | epot = -15.4084088840101 | etot = -14.617514034872 -953000 ekin = 0.314508037100271 | erot = 0.476974139325801 | epot = -15.4089962112904 | etot = -14.6175140348643 -954000 ekin = 0.310309685024597 | erot = 0.481639431416524 | epot = -15.4094631512943 | etot = -14.6175140348532 -955000 ekin = 0.30706194776561 | erot = 0.485408201612597 | epot = -15.4099841842179 | etot = -14.6175140348397 -956000 ekin = 0.304958921289462 | erot = 0.488297803840355 | epot = -15.4107707599554 | etot = -14.6175140348255 -957000 ekin = 0.304129209169334 | erot = 0.490400499131601 | epot = -15.4120437431141 | etot = -14.6175140348131 -958000 ekin = 0.304623714620741 | erot = 0.491860923620763 | epot = -15.4139986730463 | etot = -14.6175140348048 -959000 ekin = 0.306408207892433 | erot = 0.492846142548468 | epot = -15.4167683852438 | etot = -14.6175140348029 -960000 ekin = 0.309362278814204 | erot = 0.493512316197963 | epot = -15.4203886298212 | etot = -14.617514034809 -961000 ekin = 0.313285873785893 | erot = 0.493972653387203 | epot = -15.4247725619971 | etot = -14.617514034824 -962000 ekin = 0.317913924785377 | erot = 0.494271324762721 | epot = -15.4296992843955 | etot = -14.6175140348474 -963000 ekin = 0.322938673954067 | erot = 0.494367337737335 | epot = -15.434820046569 | etot = -14.6175140348776 -964000 ekin = 0.32803828153202 | erot = 0.494131108238476 | epot = -15.4396834246822 | etot = -14.6175140349118 -965000 ekin = 0.332909295684033 | erot = 0.493354750676285 | epot = -15.4437780813066 | etot = -14.6175140349462 -966000 ekin = 0.337299689763766 | erot = 0.491775167781745 | epot = -15.4465888925225 | etot = -14.617514034977 -967000 ekin = 0.341038574327655 | erot = 0.489107134739062 | epot = -15.4476597440666 | etot = -14.6175140349999 -968000 ekin = 0.344058508087222 | erot = 0.485082040987952 | epot = -15.4466545840868 | etot = -14.6175140350117 -969000 ekin = 0.346406687227151 | erot = 0.479487053291702 | epot = -15.4434077755292 | etot = -14.6175140350103 -970000 ekin = 0.348242259951282 | erot = 0.472199376074787 | epot = -15.4379556710213 | etot = -14.6175140349953 -971000 ekin = 0.349818577908804 | erot = 0.463211040207177 | epot = -15.4305436530837 | etot = -14.6175140349678 -972000 ekin = 0.351451221504524 | erot = 0.452641107453752 | epot = -15.4216063638891 | etot = -14.6175140349308 -973000 ekin = 0.3534748518418 | erot = 0.440734047140215 | epot = -15.4117229338706 | etot = -14.6175140348885 -974000 ekin = 0.356193968986606 | erot = 0.427844962322964 | epot = -15.4015529661554 | etot = -14.6175140348458 -975000 ekin = 0.359834072252968 | erot = 0.414413971021433 | epot = -15.3917620780819 | etot = -14.6175140348075 -976000 ekin = 0.364500158164541 | erot = 0.400933139115399 | epot = -15.3829473320578 | etot = -14.6175140347778 -977000 ekin = 0.370148756531594 | erot = 0.387909813696784 | epot = -15.3755726049881 | etot = -14.6175140347597 -978000 ekin = 0.376577842832112 | erot = 0.37583005908299 | epot = -15.3699219366697 | etot = -14.6175140347546 -979000 ekin = 0.383436289098897 | erot = 0.365125297246974 | epot = -15.3660756211082 | etot = -14.6175140347623 -980000 ekin = 0.390251542221838 | erot = 0.356144397459927 | epot = -15.3639099744635 | etot = -14.6175140347817 -981000 ekin = 0.396471539315499 | erot = 0.349132547198626 | epot = -15.3631181213241 | etot = -14.61751403481 -982000 ekin = 0.401514997591354 | erot = 0.344217435800631 | epot = -15.3632464682362 | etot = -14.6175140348443 -983000 ekin = 0.404823458769612 | erot = 0.341402706417366 | epot = -15.3637402000685 | etot = -14.6175140348815 -984000 ekin = 0.405908866684804 | erot = 0.34056832459917 | epot = -15.3639912262027 | etot = -14.6175140349188 -985000 ekin = 0.404391803059605 | erot = 0.341477444721989 | epot = -15.3633832827353 | etot = -14.6175140349537 -986000 ekin = 0.400027422799988 | erot = 0.343789434463081 | epot = -15.3613308922474 | etot = -14.6175140349843 -987000 ekin = 0.392718180743718 | erot = 0.347078806740141 | epot = -15.357311022493 | etot = -14.6175140350092 -988000 ekin = 0.382514239213264 | erot = 0.350859769148604 | epot = -15.3508880433891 | etot = -14.6175140350273 -989000 ekin = 0.36960372665304 | erot = 0.354615837190747 | epot = -15.3417335988814 | etot = -14.6175140350376 -990000 ekin = 0.354295674460603 | erot = 0.357833454089941 | epot = -15.3296431635899 | etot = -14.6175140350393 -991000 ekin = 0.336998529350877 | erot = 0.360037895319979 | epot = -15.3145504597026 | etot = -14.6175140350318 -992000 ekin = 0.318196763890073 | erot = 0.360829065192576 | epot = -15.296539864097 | etot = -14.6175140350143 -993000 ekin = 0.298427479538382 | erot = 0.359914303090994 | epot = -15.2758558176161 | etot = -14.6175140349867 -994000 ekin = 0.278258203579966 | erot = 0.357135170966681 | epot = -15.2529074094957 | etot = -14.6175140349491 -995000 ekin = 0.258266471895044 | erot = 0.352485480213702 | epot = -15.2282659870109 | etot = -14.6175140349022 -996000 ekin = 0.239021351636038 | erot = 0.346118523028621 | epot = -15.2026539095118 | etot = -14.6175140348471 -997000 ekin = 0.221066818081191 | erot = 0.338342492443265 | epot = -15.1769233453106 | etot = -14.6175140347861 -998000 ekin = 0.204906835818307 | erot = 0.329604233509113 | epot = -15.152025104049 | etot = -14.6175140347215 -999000 ekin = 0.190992053959209 | erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563 -1000000 ekin = 0.179708146665587 | erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938 - 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05 -Loop time of 17.7119 on 4 procs for 1000000 steps with 10 atoms - -Performance: 48780.802 tau/day, 56459.261 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.59564 | 6.28 | 11.307 | 181.3 | 35.46 -Bond | 0.083757 | 0.28777 | 0.47668 | 30.6 | 1.62 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.8539 | 2.1875 | 2.4877 | 17.3 | 12.35 -Output | 2.1e-05 | 3.85e-05 | 4.5e-05 | 0.0 | 0.00 -Modify | 0.18254 | 0.92719 | 1.638 | 61.5 | 5.23 -Other | | 8.029 | | | 45.33 - -Nlocal: 2.5 ave 5.0 max 0.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10.0 max 5.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 16.0 ave 30.0 max 0.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 64 -Ave neighs/atom = 6.4 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:17 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 b/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 deleted file mode 100644 index 72872d431a..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 +++ /dev/null @@ -1,96 +0,0 @@ -# LAMMPS data file -16 atoms -16 ellipsoids -13 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -Masses - -1 3.1575 -2 3.1575 -3 3.1575 -4 3.1575 - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 -3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 -4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 -5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 -6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1 -7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1 -8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1 -9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1 -10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1 -11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1 -12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1 -13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1 -14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1 -15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1 -16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1 - -# Atom-ID, translational velocity, angular momentum -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00 -11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00 -12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00 -13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00 -14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00 -15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00 -16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 5 6 -6 1 6 7 -7 1 7 8 -8 1 9 10 -9 1 10 11 -10 1 11 12 -11 1 13 14 -12 1 14 15 -13 1 15 16 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 deleted file mode 100644 index 18df3a8299..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 +++ /dev/null @@ -1,1184 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA2 bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA2 pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274048 - ghost atom cutoff = 2.6274048 - binsize = 1.3137024, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -24.419271289937 | etot = -24.419271289937 -Per MPI rank memory allocation (min/avg/max) = 8.146 | 8.146 | 8.146 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05 -1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817 -2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591 -3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324 -4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247 -5000 ekin = 1.77654023802719 | erot = 2.53418650522101 | epot = -24.1246365663843 | etot = -19.8139098231361 -6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.8863108281781 -7000 ekin = 3.22418765752177 | erot = 2.72037570174022 | epot = -23.9458569915548 | etot = -18.0012936322928 -8000 ekin = 2.83204202112963 | erot = 2.67060276413776 | epot = -23.9211291529766 | etot = -18.4184843677092 -9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833 -10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884567 -11000 ekin = 2.34346978235591 | erot = 2.0608750207871 | epot = -23.5779637301072 | etot = -19.1736189269642 -12000 ekin = 2.71430148816282 | erot = 2.08352509995717 | epot = -23.4639027443831 | etot = -18.6660761562631 -13000 ekin = 2.61978682102879 | erot = 2.37135270083347 | epot = -23.3602247027812 | etot = -18.3690851809189 -14000 ekin = 3.07648218347461 | erot = 2.513719767243 | epot = -23.2345584968309 | etot = -17.6443565461133 -15000 ekin = 2.98155804409324 | erot = 1.87766202539412 | epot = -23.0833749664029 | etot = -18.2241548969156 -16000 ekin = 2.18215330648447 | erot = 2.12621179836828 | epot = -22.9601160092383 | etot = -18.6517509043856 -17000 ekin = 1.85636180329758 | erot = 2.31208745603367 | epot = -22.8022922969143 | etot = -18.633843037583 -18000 ekin = 2.26768559168017 | erot = 1.2389450409061 | epot = -22.668242963885 | etot = -19.1616123312987 -19000 ekin = 2.41605854545852 | erot = 2.44791952321404 | epot = -22.5387095337131 | etot = -17.6747314650405 -20000 ekin = 2.51175765558337 | erot = 2.15047735899709 | epot = -22.3909493829452 | etot = -17.7287143683647 -21000 ekin = 2.9915110961596 | erot = 2.41132105778464 | epot = -22.5047205397251 | etot = -17.1018883857809 -22000 ekin = 3.06067007914886 | erot = 1.83986675392832 | epot = -22.6049739626141 | etot = -17.7044371295369 -23000 ekin = 2.66061083480474 | erot = 2.22251362834379 | epot = -22.5979829967718 | etot = -17.7148585336233 -24000 ekin = 2.65745533322327 | erot = 2.79344397300952 | epot = -22.5688422615674 | etot = -17.1179429553346 -25000 ekin = 2.30064465907917 | erot = 2.20975367009042 | epot = -22.5633453862602 | etot = -18.0529470570906 -26000 ekin = 1.6282588103248 | erot = 2.51914272742421 | epot = -22.6015006270016 | etot = -18.4540990892526 -27000 ekin = 1.76021840072103 | erot = 3.70719293889859 | epot = -22.6409357152274 | etot = -17.1735243756077 -28000 ekin = 2.28064774169505 | erot = 2.34192414128161 | epot = -22.7124772012735 | etot = -18.0899053182968 -29000 ekin = 2.05883865245349 | erot = 1.85387249117169 | epot = -22.7242388348361 | etot = -18.811527691211 -30000 ekin = 2.41090888362676 | erot = 1.86304539977924 | epot = -22.6876650006964 | etot = -18.4137107172904 -31000 ekin = 2.76955959719985 | erot = 2.74117025737249 | epot = -22.6962463526981 | etot = -17.1855164981257 -32000 ekin = 2.08562644954365 | erot = 2.81609166367558 | epot = -22.7309387973059 | etot = -17.8292206840867 -33000 ekin = 2.08306771838837 | erot = 3.6412168312574 | epot = -22.671701882331 | etot = -16.9474173326852 -34000 ekin = 2.32648544880974 | erot = 3.09480128654123 | epot = -22.5637155764017 | etot = -17.1424288410507 -35000 ekin = 2.32492461599899 | erot = 2.02549181832456 | epot = -22.4811871522455 | etot = -18.1307707179219 -36000 ekin = 1.9160219633488 | erot = 1.97655634076097 | epot = -22.3849871062612 | etot = -18.4924088021514 -37000 ekin = 1.57338784336504 | erot = 2.62872199467344 | epot = -22.3528406869297 | etot = -18.1507308488912 -38000 ekin = 2.21547906806797 | erot = 2.89630123965964 | epot = -22.3056616105138 | etot = -17.1938813027862 -39000 ekin = 2.55049061085212 | erot = 2.46486573403212 | epot = -22.2602280028032 | etot = -17.244871657919 -40000 ekin = 2.25628181110086 | erot = 1.87515483835113 | epot = -22.2878959489406 | etot = -18.1564592994886 -41000 ekin = 2.46478791133629 | erot = 2.50742704532316 | epot = -22.3614598606398 | etot = -17.3892449039804 -42000 ekin = 2.69217693496336 | erot = 2.04021031621289 | epot = -22.3505245167544 | etot = -17.6181372655782 -43000 ekin = 2.40211339309477 | erot = 1.6668978842528 | epot = -22.353509525279 | etot = -18.2844982479314 -44000 ekin = 2.30891568897327 | erot = 2.40213237626172 | epot = -22.3871831090405 | etot = -17.6761350438055 -45000 ekin = 1.83275065976638 | erot = 2.26068140262528 | epot = -22.4994702091406 | etot = -18.406038146749 -46000 ekin = 1.97585087518641 | erot = 3.0186371421683 | epot = -22.4902643909032 | etot = -17.4957763735485 -47000 ekin = 1.30702141485601 | erot = 1.99592830992523 | epot = -22.4679405795691 | etot = -19.1649908547879 -48000 ekin = 2.58893650014613 | erot = 1.90050780837457 | epot = -22.5072015009757 | etot = -18.017757192455 -49000 ekin = 2.30293607053961 | erot = 2.71885537559561 | epot = -22.5026363414396 | etot = -17.4808448953044 -50000 ekin = 2.47053682632632 | erot = 3.4216531112208 | epot = -22.415032340787 | etot = -16.5228424032399 -51000 ekin = 2.70972992123879 | erot = 1.4301791663753 | epot = -22.3056750708571 | etot = -18.165765983243 -52000 ekin = 3.01390456844682 | erot = 1.97787470370191 | epot = -22.2827481318966 | etot = -17.2909688597479 -53000 ekin = 2.43796472406694 | erot = 4.25598325759163 | epot = -22.2611961774508 | etot = -15.5672481957922 -54000 ekin = 2.47286167616923 | erot = 2.3677730007818 | epot = -22.243519577301 | etot = -17.40288490035 -55000 ekin = 2.25994505035907 | erot = 1.91872181759988 | epot = -22.2996523252175 | etot = -18.1209854572585 -56000 ekin = 2.3461223108806 | erot = 2.20461695689782 | epot = -22.370356062429 | etot = -17.8196167946505 -57000 ekin = 2.51587877543148 | erot = 2.87451767129977 | epot = -22.4723343857415 | etot = -17.0819379390103 -58000 ekin = 2.49925674722554 | erot = 2.80569508565646 | epot = -22.5303780310556 | etot = -17.2254261981736 -59000 ekin = 2.75080755995156 | erot = 2.17181245800364 | epot = -22.5861118023788 | etot = -17.6634917844236 -60000 ekin = 3.2849676836621 | erot = 1.98487748777051 | epot = -22.5789662701264 | etot = -17.3091210986938 -61000 ekin = 2.4147550327795 | erot = 1.80972454908232 | epot = -22.5207352876114 | etot = -18.2962557057495 -62000 ekin = 2.82665653061546 | erot = 1.68517769072779 | epot = -22.4078181490349 | etot = -17.8959839276917 -63000 ekin = 3.70002607874218 | erot = 1.92704686824234 | epot = -22.2626867402007 | etot = -16.6356137932161 -64000 ekin = 3.61736288982706 | erot = 3.03600982585025 | epot = -22.2659045523542 | etot = -15.6125318366769 -65000 ekin = 3.40363639902008 | erot = 3.89044870099903 | epot = -22.2274777177663 | etot = -14.9333926177472 -66000 ekin = 2.94418257190202 | erot = 2.45963190668857 | epot = -22.1363667635561 | etot = -16.7325522849655 -67000 ekin = 2.60477940218663 | erot = 2.10479080523513 | epot = -22.038362895265 | etot = -17.3287926878432 -68000 ekin = 2.57158327795866 | erot = 2.46431755410219 | epot = -22.0244560205645 | etot = -16.9885551885036 -69000 ekin = 2.43845102321476 | erot = 2.85996177461682 | epot = -22.0620804569545 | etot = -16.7636676591229 -70000 ekin = 3.08348233524936 | erot = 2.49640850205841 | epot = -22.1433186271748 | etot = -16.563427789867 -71000 ekin = 2.5576093427884 | erot = 2.50957641127969 | epot = -22.2697187660694 | etot = -17.2025330120013 -72000 ekin = 1.7831483145096 | erot = 2.52806261120156 | epot = -22.3815818044114 | etot = -18.0703708787002 -73000 ekin = 1.86053585113659 | erot = 2.3350857968737 | epot = -22.4387359493251 | etot = -18.2431143013148 -74000 ekin = 3.14016175467449 | erot = 2.13186507521504 | epot = -22.447062887188 | etot = -17.1750360572984 -75000 ekin = 2.60368665360454 | erot = 2.18680067560206 | epot = -22.4438479629936 | etot = -17.653360633787 -76000 ekin = 1.9633244939079 | erot = 1.96057322365503 | epot = -22.4704022140376 | etot = -18.5465044964747 -77000 ekin = 2.09841107775422 | erot = 2.1471460143176 | epot = -22.4970899098551 | etot = -18.2515328177832 -78000 ekin = 2.49484391610508 | erot = 2.50538853212234 | epot = -22.4472882748805 | etot = -17.4470558266531 -79000 ekin = 3.10058476014063 | erot = 2.47637061915656 | epot = -22.3558276087081 | etot = -16.7788722294109 -80000 ekin = 2.52610159631253 | erot = 1.89085194000216 | epot = -22.2951000287249 | etot = -17.8781464924102 -81000 ekin = 2.34286765202483 | erot = 2.2376810918426 | epot = -22.2933034850974 | etot = -17.71275474123 -82000 ekin = 1.55517061572748 | erot = 2.02195112736337 | epot = -22.2470532436032 | etot = -18.6699315005123 -83000 ekin = 2.27421747802727 | erot = 3.34135950792192 | epot = -22.2406089881454 | etot = -16.6250320021963 -84000 ekin = 2.91603956429582 | erot = 2.09861057599124 | epot = -22.2305865946953 | etot = -17.2159364544083 -85000 ekin = 3.17172070756641 | erot = 2.91883241347319 | epot = -22.2381339647476 | etot = -16.147580843708 -86000 ekin = 3.48918734688943 | erot = 2.79711547316344 | epot = -22.2890012778608 | etot = -16.0026984578079 -87000 ekin = 3.648834525211 | erot = 2.30637362835037 | epot = -22.2817018896603 | etot = -16.3264937360989 -88000 ekin = 3.16156585935194 | erot = 2.24503314085539 | epot = -22.2225172277202 | etot = -16.8159182275129 -89000 ekin = 3.32092350591891 | erot = 1.79966969251215 | epot = -22.1549711261911 | etot = -17.03437792776 -90000 ekin = 2.41383485147934 | erot = 2.22694238351369 | epot = -21.9352492588881 | etot = -17.294472023895 -91000 ekin = 1.87769980964557 | erot = 2.50898156232204 | epot = -21.766796868726 | etot = -17.3801154967584 -92000 ekin = 2.06420930396832 | erot = 2.23853979300919 | epot = -21.6902828653619 | etot = -17.3875337683844 -93000 ekin = 1.94960374605101 | erot = 3.00245663654886 | epot = -21.6771969695753 | etot = -16.7251365869754 -94000 ekin = 2.07633340602167 | erot = 3.38669471112637 | epot = -21.7794316475531 | etot = -16.3164035304051 -95000 ekin = 2.09307446139111 | erot = 2.0811295310408 | epot = -21.9165143849258 | etot = -17.7423103924939 -96000 ekin = 2.66782345206074 | erot = 1.87453507536254 | epot = -21.9748225431664 | etot = -17.4324640157432 -97000 ekin = 1.93962158410337 | erot = 2.81228342262069 | epot = -22.0301811391172 | etot = -17.2782761323932 -98000 ekin = 1.98651083318125 | erot = 2.05358325550364 | epot = -22.1050988415859 | etot = -18.065004752901 -99000 ekin = 2.50729461715162 | erot = 3.55227490812968 | epot = -22.2148658268239 | etot = -16.1552963015426 -100000 ekin = 1.87954195221303 | erot = 2.38994009743578 | epot = -22.3826768493088 | etot = -18.11319479966 -101000 ekin = 1.66917867676911 | erot = 3.61296864361924 | epot = -22.4122779848186 | etot = -17.1301306644303 -102000 ekin = 1.63707836649616 | erot = 3.33958463197985 | epot = -22.3664797586262 | etot = -17.3898167601502 -103000 ekin = 2.00216132457488 | erot = 2.34409134088738 | epot = -22.338100531932 | etot = -17.9918478664698 -104000 ekin = 2.03704734920245 | erot = 2.74903331701925 | epot = -22.3478074938274 | etot = -17.5617268276057 -105000 ekin = 1.85601249652044 | erot = 2.00020228548217 | epot = -22.2937670136133 | etot = -18.4375522316107 -106000 ekin = 1.70582694215149 | erot = 1.90992656339968 | epot = -22.3252996603125 | etot = -18.7095461547614 -107000 ekin = 2.61183521416777 | erot = 1.56756438600251 | epot = -22.3815585845482 | etot = -18.2021589843779 -108000 ekin = 2.13345133147477 | erot = 2.1967764492834 | epot = -22.2873637709221 | etot = -17.9571359901639 -109000 ekin = 2.23517703897427 | erot = 2.12289589403282 | epot = -22.1519605830327 | etot = -17.7938876500256 -110000 ekin = 1.66340581480182 | erot = 2.52573727214601 | epot = -22.1681066766204 | etot = -17.9789635896725 -111000 ekin = 2.28529122032929 | erot = 2.24044883756493 | epot = -22.1711980210611 | etot = -17.6454579631669 -112000 ekin = 2.60405127944181 | erot = 2.43646974545776 | epot = -22.1582164438795 | etot = -17.11769541898 -113000 ekin = 2.40208651796091 | erot = 3.06270264515793 | epot = -22.1587051510952 | etot = -16.6939159879764 -114000 ekin = 2.34302229470158 | erot = 2.30426477746864 | epot = -22.1439772736805 | etot = -17.4966902015103 -115000 ekin = 1.69616053999229 | erot = 3.11049212247371 | epot = -22.1736739038021 | etot = -17.3670212413361 -116000 ekin = 1.51961045217859 | erot = 2.22203808801726 | epot = -22.2355447345615 | etot = -18.4938961943657 -117000 ekin = 1.69355164638512 | erot = 2.33913072714747 | epot = -22.2671845473364 | etot = -18.2345021738038 -118000 ekin = 2.1960991163694 | erot = 2.33815079858085 | epot = -22.2453229868293 | etot = -17.7110730718791 -119000 ekin = 2.55982892523823 | erot = 2.47378749563683 | epot = -22.2824155531543 | etot = -17.2487991322793 -120000 ekin = 1.76091001620491 | erot = 2.1741296357231 | epot = -22.2369948282136 | etot = -18.3019551762855 -121000 ekin = 2.80671234452976 | erot = 2.30128219469303 | epot = -22.2260257995407 | etot = -17.1180312603179 -122000 ekin = 3.23136903340218 | erot = 3.30036165167127 | epot = -22.2515019863338 | etot = -15.7197713012603 -123000 ekin = 2.8561114897291 | erot = 3.24294818442618 | epot = -22.2018342366988 | etot = -16.1027745625435 -124000 ekin = 2.14842162472016 | erot = 2.7693802805091 | epot = -22.0303368839078 | etot = -17.1125349786785 -125000 ekin = 1.83317468651689 | erot = 1.37271219749613 | epot = -21.8885764971633 | etot = -18.6826896131502 -126000 ekin = 2.45181092117661 | erot = 3.08753876167365 | epot = -21.8912653158441 | etot = -16.3519156329938 -127000 ekin = 2.39800706812202 | erot = 2.35255982488708 | epot = -21.8786845575463 | etot = -17.1281176645372 -128000 ekin = 2.74926309150919 | erot = 1.83113656927751 | epot = -21.8947833530885 | etot = -17.3143836923018 -129000 ekin = 2.71720149007507 | erot = 2.89223888586493 | epot = -21.888738829699 | etot = -16.279298453759 -130000 ekin = 3.27436175016883 | erot = 2.48649258221715 | epot = -21.9126051843054 | etot = -16.1517508519195 -131000 ekin = 2.72616313783309 | erot = 2.50345885992118 | epot = -21.9360367126892 | etot = -16.7064147149349 -132000 ekin = 2.62485920187038 | erot = 3.40341903141799 | epot = -21.9656374341347 | etot = -15.9373592008463 -133000 ekin = 2.0325764784668 | erot = 2.89126702157637 | epot = -21.9394295827134 | etot = -17.0155860826702 -134000 ekin = 1.62930019559461 | erot = 1.67001909466596 | epot = -21.900605038258 | etot = -18.6012857479974 -135000 ekin = 2.45037614605464 | erot = 2.12340550038047 | epot = -21.8772864662343 | etot = -17.3035048197992 -136000 ekin = 2.29225558372926 | erot = 3.05501283629331 | epot = -21.7842467542129 | etot = -16.4369783341904 -137000 ekin = 2.71619061857373 | erot = 2.45779692364663 | epot = -21.6204232926258 | etot = -16.4464357504054 -138000 ekin = 3.30410447428295 | erot = 1.73171704445596 | epot = -21.609821441089 | etot = -16.57399992235 -139000 ekin = 2.77055079544968 | erot = 1.72559500013771 | epot = -21.7720020827881 | etot = -17.2758562872007 -140000 ekin = 2.72528465654122 | erot = 2.46411811431296 | epot = -21.8660237331067 | etot = -16.6766209622525 -141000 ekin = 2.78705568892822 | erot = 2.44850479765533 | epot = -21.8731300806739 | etot = -16.6375695940903 -142000 ekin = 3.51931490090282 | erot = 3.48544343137045 | epot = -21.8228511941687 | etot = -14.8180928618954 -143000 ekin = 2.59719776759383 | erot = 2.02350560733262 | epot = -21.8096443263653 | etot = -17.1889409514388 -144000 ekin = 3.74308404358447 | erot = 3.03564456771536 | epot = -21.8085900408448 | etot = -15.029861429545 -145000 ekin = 3.62659723153861 | erot = 2.70926904415538 | epot = -21.7250027836497 | etot = -15.3891365079557 -146000 ekin = 3.87407885398524 | erot = 2.49638573472853 | epot = -21.7001271601514 | etot = -15.3296625714376 -147000 ekin = 3.27961687549993 | erot = 2.08263345163676 | epot = -21.5857141934645 | etot = -16.2234638663278 -148000 ekin = 2.49678519214407 | erot = 1.65068656472224 | epot = -21.3397240410766 | etot = -17.1922522842103 -149000 ekin = 2.74324871192595 | erot = 2.27422609775036 | epot = -21.1619902393526 | etot = -16.1445154296762 -150000 ekin = 2.63493686559431 | erot = 2.89891054679402 | epot = -21.0669519346708 | etot = -15.5331045222825 -151000 ekin = 2.08067982512823 | erot = 2.11598312084942 | epot = -20.9754508944265 | etot = -16.7787879484489 -152000 ekin = 2.41049293269485 | erot = 2.60865966337995 | epot = -20.8324522723453 | etot = -15.8132996762705 -153000 ekin = 2.11771886644781 | erot = 2.2612193836258 | epot = -20.8689010813857 | etot = -16.4899628313121 -154000 ekin = 2.34048807401985 | erot = 2.61000659349907 | epot = -20.9736996291527 | etot = -16.0232049616338 -155000 ekin = 2.06125568994135 | erot = 3.02657060603564 | epot = -20.9977701757737 | etot = -15.9099438797968 -156000 ekin = 2.03103875451807 | erot = 3.1844861824748 | epot = -20.8318196513999 | etot = -15.616294714407 -157000 ekin = 2.34991277428576 | erot = 1.91129748769811 | epot = -20.8011437796089 | etot = -16.539933517625 -158000 ekin = 2.16899004769298 | erot = 2.47810803275591 | epot = -20.8955785127325 | etot = -16.2484804322837 -159000 ekin = 2.86703441642079 | erot = 2.2901833721065 | epot = -21.0162479016245 | etot = -15.8590301130972 -160000 ekin = 2.19810986416329 | erot = 2.37335510649732 | epot = -21.1025044999173 | etot = -16.5310395292567 -161000 ekin = 2.13983549244144 | erot = 2.44280202062021 | epot = -21.204645979403 | etot = -16.6220084663414 -162000 ekin = 1.75007978204456 | erot = 2.67089623079416 | epot = -21.2587160217762 | etot = -16.8377400089375 -163000 ekin = 2.22497705720617 | erot = 2.03752809750894 | epot = -21.4065038175883 | etot = -17.1439986628732 -164000 ekin = 2.74622171092286 | erot = 1.42968886006587 | epot = -21.5464343754361 | etot = -17.3705238044474 -165000 ekin = 2.65892253082074 | erot = 2.28893669468687 | epot = -21.5542883684299 | etot = -16.6064291429223 -166000 ekin = 3.28497940714848 | erot = 2.38441021083685 | epot = -21.4831502209917 | etot = -15.8137606030064 -167000 ekin = 3.03302043173269 | erot = 2.0371493034983 | epot = -21.552220768162 | etot = -16.482051032931 -168000 ekin = 3.16647476932142 | erot = 1.85328814856002 | epot = -21.6005552665342 | etot = -16.5807923486528 -169000 ekin = 2.24705103875432 | erot = 2.66949801663851 | epot = -21.5155875234663 | etot = -16.5990384680735 -170000 ekin = 2.43835864940733 | erot = 2.49651566577791 | epot = -21.3706724967315 | etot = -16.4357981815463 -171000 ekin = 1.91174741927943 | erot = 2.39538037263751 | epot = -21.2808048923853 | etot = -16.9736771004683 -172000 ekin = 2.88344950373025 | erot = 3.21569142102288 | epot = -21.2429879136862 | etot = -15.1438469889331 -173000 ekin = 2.75630897924877 | erot = 2.14100943461477 | epot = -21.2680309804945 | etot = -16.370712566631 -174000 ekin = 2.45420058414632 | erot = 2.2332035837858 | epot = -21.3153962561354 | etot = -16.6279920882033 -175000 ekin = 2.84815372525752 | erot = 2.37845124629735 | epot = -21.2811665321372 | etot = -16.0545615605823 -176000 ekin = 2.13811988096562 | erot = 1.89602404006214 | epot = -21.3483452704796 | etot = -17.3142013494519 -177000 ekin = 2.57845153047441 | erot = 2.74101209600055 | epot = -21.3192781201108 | etot = -15.9998144936358 -178000 ekin = 1.8362026158725 | erot = 2.58532929872161 | epot = -21.2513623538897 | etot = -16.8298304392955 -179000 ekin = 2.51664198429652 | erot = 2.38535598715308 | epot = -21.3137585755744 | etot = -16.4117606041248 -180000 ekin = 1.88870242540222 | erot = 2.46307032082017 | epot = -21.4708809842583 | etot = -17.1191082380359 -181000 ekin = 1.7573063317019 | erot = 3.04206214925082 | epot = -21.4638802199926 | etot = -16.6645117390399 -182000 ekin = 1.56372006631669 | erot = 2.0482446459855 | epot = -21.4014353137661 | etot = -17.7894706014639 -183000 ekin = 2.00375583158539 | erot = 2.82586034021598 | epot = -21.4815637987258 | etot = -16.6519476269244 -184000 ekin = 2.68318475320728 | erot = 2.43685976384415 | epot = -21.5996781237133 | etot = -16.4796336066618 -185000 ekin = 2.99744907214255 | erot = 3.19569112714916 | epot = -21.6712604055259 | etot = -15.4781202062342 -186000 ekin = 3.18086271329103 | erot = 2.43694344502803 | epot = -21.700014527818 | etot = -16.0822083694989 -187000 ekin = 2.64763078555984 | erot = 3.43034775414789 | epot = -21.6568302519365 | etot = -15.5788517122288 -188000 ekin = 2.86104386361227 | erot = 3.05673704653031 | epot = -21.5997264275815 | etot = -15.6819455174389 -189000 ekin = 2.64279940222614 | erot = 1.81959052043828 | epot = -21.5371949170904 | etot = -17.074804994426 -190000 ekin = 2.21943570515013 | erot = 1.84825749826526 | epot = -21.498320200761 | etot = -17.4306269973456 -191000 ekin = 2.27416889747069 | erot = 2.0662909239644 | epot = -21.4373070550835 | etot = -17.0968472336484 -192000 ekin = 2.27339562400024 | erot = 3.1084542715957 | epot = -21.4737141732368 | etot = -16.0918642776409 -193000 ekin = 1.95136295247808 | erot = 1.8894092381771 | epot = -21.4612356964994 | etot = -17.6204635058442 -194000 ekin = 2.46233473019503 | erot = 2.02708794085746 | epot = -21.3374302301573 | etot = -16.8480075591048 -195000 ekin = 3.12435057559399 | erot = 2.09826675864205 | epot = -21.2738979568211 | etot = -16.0512806225851 -196000 ekin = 2.70015718375597 | erot = 2.5128575582669 | epot = -21.1930998936957 | etot = -15.9800851516728 -197000 ekin = 2.55038574692144 | erot = 2.07531410993401 | epot = -21.0258757995296 | etot = -16.4001759426742 -198000 ekin = 2.70688003284557 | erot = 1.79490240776514 | epot = -21.0190268968 | etot = -16.5172444561893 -199000 ekin = 2.5693949791157 | erot = 2.33188600887061 | epot = -21.0320560569424 | etot = -16.1307750689561 -200000 ekin = 2.89114428387874 | erot = 1.42209502781995 | epot = -21.0251552631878 | etot = -16.7119159514891 -201000 ekin = 2.68221791581645 | erot = 1.55638461968673 | epot = -21.0246765678572 | etot = -16.786074032354 -202000 ekin = 2.26600119742896 | erot = 2.24264658465156 | epot = -20.966213452201 | etot = -16.4575656701204 -203000 ekin = 2.11315541926328 | erot = 2.03104522736692 | epot = -20.8925289725737 | etot = -16.7483283259435 -204000 ekin = 2.10598805427349 | erot = 1.8944018028419 | epot = -20.9063507999493 | etot = -16.9059609428339 -205000 ekin = 1.32797127466544 | erot = 2.12796235386513 | epot = -20.9546930460646 | etot = -17.4987594175341 -206000 ekin = 1.38118094354854 | erot = 2.25600442653048 | epot = -20.9248899100655 | etot = -17.2877045399865 -207000 ekin = 1.89847617306066 | erot = 1.80813925076998 | epot = -21.0282211762941 | etot = -17.3216057524635 -208000 ekin = 1.82509354299281 | erot = 3.24652806561536 | epot = -21.2820126865175 | etot = -16.2103910779094 -209000 ekin = 2.8041625285186 | erot = 2.34850039993979 | epot = -21.4041461087816 | etot = -16.2514831803232 -210000 ekin = 3.17398766473313 | erot = 3.11871773439181 | epot = -21.4808635207107 | etot = -15.1881581215857 -211000 ekin = 2.47010820072588 | erot = 2.09528143227157 | epot = -21.6056990668499 | etot = -17.0403094338525 -212000 ekin = 2.36989560577724 | erot = 1.93500906628112 | epot = -21.6842526468772 | etot = -17.3793479748188 -213000 ekin = 1.90065800582391 | erot = 2.51889248061745 | epot = -21.7615899372457 | etot = -17.3420394508043 -214000 ekin = 1.97423172880181 | erot = 2.4980598759111 | epot = -21.7892459673185 | etot = -17.3169543626056 -215000 ekin = 1.97168935774729 | erot = 3.17151545304801 | epot = -21.7903331088791 | etot = -16.6471282980838 -216000 ekin = 1.89146772443534 | erot = 1.88107923457565 | epot = -21.7542848995033 | etot = -17.9817379404923 -217000 ekin = 2.06396631795602 | erot = 1.95272203440507 | epot = -21.8104294829847 | etot = -17.7937411306236 -218000 ekin = 2.31997702749623 | erot = 1.68971395254107 | epot = -21.7623319926371 | etot = -17.7526410125998 -219000 ekin = 2.46685879548778 | erot = 2.20801864234035 | epot = -21.7696248586177 | etot = -17.0947474207895 -220000 ekin = 1.73830824437668 | erot = 3.03764928140501 | epot = -21.7250063140519 | etot = -16.9490487882702 -221000 ekin = 1.77900155382619 | erot = 2.78474425452726 | epot = -21.7358321600373 | etot = -17.1720863516838 -222000 ekin = 2.62686448871845 | erot = 2.86058966709522 | epot = -21.6939796138854 | etot = -16.2065254580717 -223000 ekin = 3.04452612483164 | erot = 1.94024942191071 | epot = -21.7122663420572 | etot = -16.7274907953149 -224000 ekin = 2.718937145138 | erot = 2.42480319358565 | epot = -21.6802900448522 | etot = -16.5365497061286 -225000 ekin = 2.02691300626945 | erot = 3.37602856858266 | epot = -21.6857094668298 | etot = -16.2827678919777 -226000 ekin = 2.36557492667929 | erot = 2.39082460572007 | epot = -21.7553390008386 | etot = -16.9989394684392 -227000 ekin = 2.73620885172714 | erot = 2.63025691267084 | epot = -21.818043188201 | etot = -16.451577423803 -228000 ekin = 2.08980697083006 | erot = 2.26883720629955 | epot = -21.880544956506 | etot = -17.5219007793764 -229000 ekin = 1.80144547388731 | erot = 1.79654911472853 | epot = -21.9628584317261 | etot = -18.3648638431102 -230000 ekin = 2.77451167134285 | erot = 2.22776499369623 | epot = -21.9854420760081 | etot = -16.983165410969 -231000 ekin = 3.15850107875523 | erot = 2.7756116636273 | epot = -21.9726828438209 | etot = -16.0385701014384 -232000 ekin = 1.86960416304709 | erot = 1.70620936865288 | epot = -22.0086347294912 | etot = -18.4328211977913 -233000 ekin = 1.75933775527383 | erot = 1.56532056032101 | epot = -21.9899365513674 | etot = -18.6652782357726 -234000 ekin = 2.33698261677869 | erot = 2.05550388448924 | epot = -21.9120502409319 | etot = -17.5195637396639 -235000 ekin = 1.9573829360185 | erot = 2.52333284033808 | epot = -21.8594642182283 | etot = -17.3787484418717 -236000 ekin = 2.2617849997626 | erot = 1.90928533288046 | epot = -21.8749689452558 | etot = -17.7038986126127 -237000 ekin = 2.48853198845777 | erot = 2.64888724219513 | epot = -21.9453266234327 | etot = -16.8079073927798 -238000 ekin = 2.21038428000156 | erot = 2.7424361712651 | epot = -22.0000238560637 | etot = -17.0472034047971 -239000 ekin = 2.72852713027264 | erot = 2.49133994747208 | epot = -22.0182378682277 | etot = -16.7983707904829 -240000 ekin = 3.10387064960454 | erot = 2.19174616842279 | epot = -21.9254266959964 | etot = -16.629809877969 -241000 ekin = 3.04688823533615 | erot = 2.65417483072321 | epot = -21.8524309009232 | etot = -16.1513678348639 -242000 ekin = 2.22655833358292 | erot = 2.33728691596105 | epot = -21.775606752996 | etot = -17.211761503452 -243000 ekin = 1.53720920161825 | erot = 2.80453969203578 | epot = -21.7184041577432 | etot = -17.3766552640892 -244000 ekin = 1.91538946868823 | erot = 2.4387847070438 | epot = -21.6211228029713 | etot = -17.2669486272392 -245000 ekin = 1.95684890248336 | erot = 2.60788082483666 | epot = -21.4938704859113 | etot = -16.9291407585913 -246000 ekin = 2.07153989492555 | erot = 2.40695304198482 | epot = -21.4521110801275 | etot = -16.9736181432171 -247000 ekin = 1.55669060713796 | erot = 2.27930456834644 | epot = -21.4122603878221 | etot = -17.5762652123377 -248000 ekin = 1.83803563986085 | erot = 2.56773709137239 | epot = -21.4358565123266 | etot = -17.0300837810933 -249000 ekin = 1.79842337395836 | erot = 2.04417900475198 | epot = -21.5079955681831 | etot = -17.6653931894727 -250000 ekin = 1.68165772872533 | erot = 3.39425180338125 | epot = -21.5394505717881 | etot = -16.4635410396816 -251000 ekin = 2.13109176968443 | erot = 3.25918860829495 | epot = -21.5291832995953 | etot = -16.1389029216159 -252000 ekin = 2.053654740928 | erot = 2.53782822604964 | epot = -21.5554268525819 | etot = -16.9639438856043 -253000 ekin = 1.65815317720656 | erot = 3.2103686272941 | epot = -21.5801245998449 | etot = -16.7116027953443 -254000 ekin = 2.32643739073982 | erot = 3.10897981239372 | epot = -21.5778214253297 | etot = -16.1424042221962 -255000 ekin = 2.50573519817545 | erot = 2.76783941653296 | epot = -21.5566198260725 | etot = -16.2830452113641 -256000 ekin = 1.97360306022237 | erot = 2.62555911992843 | epot = -21.5492296987675 | etot = -16.9500675186167 -257000 ekin = 2.23010041401886 | erot = 3.26408085278294 | epot = -21.5699664805037 | etot = -16.0757852137019 -258000 ekin = 2.04489236085684 | erot = 1.84672249628675 | epot = -21.6871004150333 | etot = -17.7954855578897 -259000 ekin = 2.87368351206713 | erot = 2.78936048482183 | epot = -21.79465654858 | etot = -16.131612551691 -260000 ekin = 2.90723740318823 | erot = 2.19282117735075 | epot = -21.8510164466681 | etot = -16.7509578661291 -261000 ekin = 2.76826717813612 | erot = 2.3408102568469 | epot = -21.8996159314726 | etot = -16.7905384964896 -262000 ekin = 3.52272168049175 | erot = 1.77108921100701 | epot = -21.9183679745592 | etot = -16.6245570830604 -263000 ekin = 3.08415540167847 | erot = 2.42542153733818 | epot = -21.8525939259305 | etot = -16.3430169869139 -264000 ekin = 2.24750828021794 | erot = 2.03549249484823 | epot = -21.8644003610158 | etot = -17.5813995859496 -265000 ekin = 1.9256244934252 | erot = 2.50003397851261 | epot = -21.7368613865555 | etot = -17.3112029146177 -266000 ekin = 2.39663137918843 | erot = 3.25281234980079 | epot = -21.6911624005759 | etot = -16.0417186715867 -267000 ekin = 1.71138772864696 | erot = 2.23669516146945 | epot = -21.656773778734 | etot = -17.7086908886176 -268000 ekin = 2.1012342991695 | erot = 3.22431689054768 | epot = -21.6149417342532 | etot = -16.289390544536 -269000 ekin = 1.96288847894507 | erot = 2.78695129937916 | epot = -21.5074378362073 | etot = -16.7575980578831 -270000 ekin = 2.11352321718224 | erot = 2.66970769590072 | epot = -21.4082402788558 | etot = -16.6250093657728 -271000 ekin = 2.187367149063 | erot = 3.10651896358249 | epot = -21.2262888361409 | etot = -15.9324027234954 -272000 ekin = 2.53123659603481 | erot = 2.28031086814788 | epot = -21.0667233503151 | etot = -16.2551758861324 -273000 ekin = 1.93620978534757 | erot = 1.99248019508239 | epot = -21.0024789385132 | etot = -17.0737889580832 -274000 ekin = 1.90995249837777 | erot = 2.21197524437096 | epot = -21.0425035783664 | etot = -16.9205758356177 -275000 ekin = 1.7924862003403 | erot = 3.10053081821809 | epot = -21.0804706135493 | etot = -16.1874535949909 -276000 ekin = 3.35665649861731 | erot = 2.41114048919769 | epot = -21.0250329806457 | etot = -15.2572359928307 -277000 ekin = 2.41733347319127 | erot = 1.50728350741789 | epot = -20.9704854598112 | etot = -17.045868479202 -278000 ekin = 2.53927407792784 | erot = 2.14772203209251 | epot = -20.9597795409701 | etot = -16.2727834309497 -279000 ekin = 1.9086257726176 | erot = 2.39006859456279 | epot = -20.9691625784233 | etot = -16.6704682112429 -280000 ekin = 2.3712715434438 | erot = 3.59520758009785 | epot = -20.8511344732567 | etot = -14.884655349715 -281000 ekin = 1.76900280298917 | erot = 1.79532059184944 | epot = -20.9241533960326 | etot = -17.3598300011939 -282000 ekin = 2.27081772250325 | erot = 3.05002296036257 | epot = -20.8869696699162 | etot = -15.5661289870504 -283000 ekin = 2.18678338225262 | erot = 2.20808584908431 | epot = -20.8425952687799 | etot = -16.4477260374429 -284000 ekin = 1.91967212543913 | erot = 2.20885942937705 | epot = -20.8702716845898 | etot = -16.7417401297736 -285000 ekin = 3.15534421247094 | erot = 1.80733118017555 | epot = -21.0506046634905 | etot = -16.0879292708441 -286000 ekin = 3.87414654801577 | erot = 1.83540293712377 | epot = -21.2318072144161 | etot = -15.5222577292766 -287000 ekin = 3.65199335032365 | erot = 2.91368616965972 | epot = -21.3038992633635 | etot = -14.7382197433801 -288000 ekin = 3.25566938715965 | erot = 1.61414633945368 | epot = -21.2971542306353 | etot = -16.427338504022 -289000 ekin = 2.57263419624199 | erot = 2.78652542009298 | epot = -21.270831111226 | etot = -15.911671494891 -290000 ekin = 2.70850264399552 | erot = 2.41920167874741 | epot = -21.2832461285427 | etot = -16.1555418057998 -291000 ekin = 2.06015522240602 | erot = 2.36096794039798 | epot = -21.2800181616414 | etot = -16.8588949988374 -292000 ekin = 2.28565579809197 | erot = 2.0492309975275 | epot = -21.3390392809808 | etot = -17.0041524853614 -293000 ekin = 2.24969697991474 | erot = 2.35258801570063 | epot = -21.4487457699855 | etot = -16.8464607743701 -294000 ekin = 2.93116374685755 | erot = 2.88908330420809 | epot = -21.5301464521074 | etot = -15.7098994010417 -295000 ekin = 2.66799463567933 | erot = 2.29137040664776 | epot = -21.6929279927361 | etot = -16.733562950409 -296000 ekin = 2.20703557359524 | erot = 2.91779932622371 | epot = -21.745669704948 | etot = -16.6208348051291 -297000 ekin = 2.17709774147519 | erot = 3.31374313109423 | epot = -21.7393959864692 | etot = -16.2485551138997 -298000 ekin = 2.9129468421301 | erot = 2.35672300219859 | epot = -21.6957115365355 | etot = -16.4260416922068 -299000 ekin = 3.16776997287189 | erot = 2.2391818507998 | epot = -21.8064946029841 | etot = -16.3995427793124 -300000 ekin = 3.29561200430319 | erot = 1.38909463218868 | epot = -21.88075107193 | etot = -17.1960444354381 -301000 ekin = 2.38366117761117 | erot = 3.3087020645508 | epot = -21.8991772346975 | etot = -16.2068139925356 -302000 ekin = 2.92578534773873 | erot = 3.24773085922143 | epot = -21.8654359309133 | etot = -15.6919197239531 -303000 ekin = 2.41046706286872 | erot = 2.62044101440911 | epot = -21.8547021809442 | etot = -16.8237941036664 -304000 ekin = 2.22973717088315 | erot = 2.69550632779805 | epot = -21.7935318306645 | etot = -16.8682883319833 -305000 ekin = 2.37917924648061 | erot = 2.39025207841258 | epot = -21.7682058013904 | etot = -16.9987744764972 -306000 ekin = 1.94479260294372 | erot = 2.89926351945751 | epot = -21.7686335450968 | etot = -16.9245774226955 -307000 ekin = 2.51329193607427 | erot = 2.07893464323809 | epot = -21.710948391274 | etot = -17.1187218119617 -308000 ekin = 2.81355602400968 | erot = 2.63100444247636 | epot = -21.7026983871469 | etot = -16.2581379206609 -309000 ekin = 2.33327686418279 | erot = 2.12127029003217 | epot = -21.6762127568296 | etot = -17.2216656026146 -310000 ekin = 2.52298184126179 | erot = 3.21591454963617 | epot = -21.695142164932 | etot = -15.956245774034 -311000 ekin = 2.34923515117596 | erot = 3.03949532400544 | epot = -21.7087574865082 | etot = -16.3200270113268 -312000 ekin = 1.8269200765792 | erot = 3.25879908323384 | epot = -21.581493453196 | etot = -16.495774293383 -313000 ekin = 1.63600964511319 | erot = 2.08094899400482 | epot = -21.606397547734 | etot = -17.889438908616 -314000 ekin = 2.27293762564082 | erot = 2.5685903273234 | epot = -21.6199211148905 | etot = -16.7783931619263 -315000 ekin = 2.5313505044608 | erot = 2.13255412771189 | epot = -21.6994892370102 | etot = -17.0355846048375 -316000 ekin = 1.99528950863063 | erot = 1.8009779719585 | epot = -21.7144101219026 | etot = -17.9181426413135 -317000 ekin = 2.11352183168035 | erot = 2.00935618346838 | epot = -21.702888210866 | etot = -17.5800101957173 -318000 ekin = 2.29665458459675 | erot = 1.9218837801722 | epot = -21.6711519227436 | etot = -17.4526135579747 -319000 ekin = 1.98093881438111 | erot = 1.68246475076764 | epot = -21.5680359341469 | etot = -17.9046323689982 -320000 ekin = 2.46251923881396 | erot = 3.07047264047418 | epot = -21.5096210718397 | etot = -15.9766291925515 -321000 ekin = 1.85318841838943 | erot = 2.6741946235276 | epot = -21.5386927047478 | etot = -17.0113096628308 -322000 ekin = 1.94542919328061 | erot = 3.36132448976007 | epot = -21.462118312038 | etot = -16.1553646289973 -323000 ekin = 1.92568445593302 | erot = 2.08578688156951 | epot = -21.4990899081635 | etot = -17.487618570661 -324000 ekin = 2.21374645511898 | erot = 2.45979330983641 | epot = -21.6010648344435 | etot = -16.9275250694881 -325000 ekin = 2.71973630116966 | erot = 2.37178970012744 | epot = -21.712426807882 | etot = -16.6209008065849 -326000 ekin = 1.88824000887386 | erot = 1.92165807946833 | epot = -21.7667410841736 | etot = -17.9568429958315 -327000 ekin = 3.03069091411613 | erot = 1.66905303717587 | epot = -21.8444186282852 | etot = -17.1446746769932 -328000 ekin = 2.74111841160537 | erot = 1.91707691036631 | epot = -21.8825192055331 | etot = -17.2243238835614 -329000 ekin = 2.94134490087235 | erot = 3.13982603162578 | epot = -21.9373718647512 | etot = -15.8562009322531 -330000 ekin = 2.91659917154128 | erot = 2.01302494652939 | epot = -21.9334919050175 | etot = -17.0038677869468 -331000 ekin = 2.28401437900765 | erot = 2.04959290659006 | epot = -21.9235871145697 | etot = -17.589979828972 -332000 ekin = 2.41477240701933 | erot = 3.18206286535344 | epot = -21.9762685570111 | etot = -16.3794332846383 -333000 ekin = 2.45632306729147 | erot = 2.70981698021117 | epot = -22.0802863854372 | etot = -16.9141463379346 -334000 ekin = 2.37343096192712 | erot = 2.99538841337669 | epot = -22.1169059815891 | etot = -16.7480866062853 -335000 ekin = 2.11258102220993 | erot = 3.56563799589785 | epot = -22.1589708630881 | etot = -16.4807518449803 -336000 ekin = 2.63443561655341 | erot = 2.12835506840877 | epot = -22.135253476801 | etot = -17.3724627918388 -337000 ekin = 2.74032565197819 | erot = 2.73568544119591 | epot = -22.1162186765824 | etot = -16.6402075834083 -338000 ekin = 1.84481246769261 | erot = 2.23462418681718 | epot = -22.1932263562086 | etot = -18.1137897016988 -339000 ekin = 1.56179484671187 | erot = 2.48907003494865 | epot = -22.2362997512502 | etot = -18.1854348695896 -340000 ekin = 1.46400835747893 | erot = 4.0512188877133 | epot = -22.1550062300509 | etot = -16.6397789848587 -341000 ekin = 1.68583362524713 | erot = 2.79345882658496 | epot = -22.1357452359775 | etot = -17.6564527841454 -342000 ekin = 1.96314395645267 | erot = 2.74466248035308 | epot = -22.1973030330981 | etot = -17.4894965962924 -343000 ekin = 2.66788553126356 | erot = 3.18183761806682 | epot = -22.2887136544829 | etot = -16.4389905051526 -344000 ekin = 1.78884972348303 | erot = 2.18066038812641 | epot = -22.3196903631289 | etot = -18.3501802515195 -345000 ekin = 1.54101094076145 | erot = 1.85848281555012 | epot = -22.3637723164297 | etot = -18.9642785601181 -346000 ekin = 1.69292596460904 | erot = 1.8080316670706 | epot = -22.3281555406487 | etot = -18.827197908969 -347000 ekin = 1.37586220035546 | erot = 2.61615920278041 | epot = -22.3502414839316 | etot = -18.3582200807958 -348000 ekin = 2.1379756238867 | erot = 2.8590037384953 | epot = -22.3431546343773 | etot = -17.3461752719953 -349000 ekin = 1.82920941743142 | erot = 1.97683001829644 | epot = -22.358647853278 | etot = -18.5526084175502 -350000 ekin = 1.78940567302629 | erot = 2.50961291060183 | epot = -22.3435711705442 | etot = -18.0445525869161 -351000 ekin = 1.68761490497198 | erot = 2.81740261848487 | epot = -22.413948353252 | etot = -17.9089308297951 -352000 ekin = 2.77021596792832 | erot = 2.15256490237832 | epot = -22.5845859351651 | etot = -17.6618050648585 -353000 ekin = 3.56514294827437 | erot = 1.46623266587274 | epot = -22.6366139885995 | etot = -17.6052383744524 -354000 ekin = 3.44768413783611 | erot = 2.2508741161152 | epot = -22.5521676274445 | etot = -16.8536093734932 -355000 ekin = 2.0339222695118 | erot = 2.90917743936019 | epot = -22.5104712522892 | etot = -17.5673715434172 -356000 ekin = 2.10642401704757 | erot = 3.31919387591753 | epot = -22.5408670189009 | etot = -17.1152491259358 -357000 ekin = 2.76519653125328 | erot = 2.50858960423796 | epot = -22.5185760247454 | etot = -17.2447898892542 -358000 ekin = 2.5374658712045 | erot = 2.2647702680074 | epot = -22.5067305203673 | etot = -17.7044943811554 -359000 ekin = 3.23575918003202 | erot = 2.52804611996866 | epot = -22.5983600193657 | etot = -16.834554719365 -360000 ekin = 2.59182745067507 | erot = 1.97199586910126 | epot = -22.6431957503706 | etot = -18.0793724305942 -361000 ekin = 2.61187422629997 | erot = 2.50384597992352 | epot = -22.6889255875949 | etot = -17.5732053813714 -362000 ekin = 2.38478129908564 | erot = 3.84225576928699 | epot = -22.6416012117121 | etot = -16.4145641433395 -363000 ekin = 2.88499903144359 | erot = 1.98712884581536 | epot = -22.5277585455565 | etot = -17.6556306682975 -364000 ekin = 2.24472586183289 | erot = 1.87849655022233 | epot = -22.4027818145434 | etot = -18.2795594024882 -365000 ekin = 2.04314188489358 | erot = 2.81001232738016 | epot = -22.2276048128305 | etot = -17.3744506005568 -366000 ekin = 2.26658685631362 | erot = 1.95650208645697 | epot = -22.1895525177766 | etot = -17.966463575006 -367000 ekin = 2.81568040956379 | erot = 2.51870737095405 | epot = -22.2465449976265 | etot = -16.9121572171087 -368000 ekin = 2.81607406017701 | erot = 2.1866718839128 | epot = -22.3661835489406 | etot = -17.3634376048508 -369000 ekin = 2.31666862853353 | erot = 2.84859903953565 | epot = -22.4308123375305 | etot = -17.2655446694613 -370000 ekin = 2.66612981804874 | erot = 2.10389084208224 | epot = -22.505799930102 | etot = -17.7357792699711 -371000 ekin = 2.19552758440374 | erot = 3.61117481442869 | epot = -22.5711545036622 | etot = -16.7644521048298 -372000 ekin = 1.77345963407765 | erot = 3.42406482157981 | epot = -22.66405706261 | etot = -17.4665326069525 -373000 ekin = 2.14860861324314 | erot = 2.79097682151395 | epot = -22.7141452937347 | etot = -17.7745598589776 -374000 ekin = 2.69445806056395 | erot = 3.57889438136966 | epot = -22.860153056641 | etot = -16.5868006147074 -375000 ekin = 2.40579827793462 | erot = 2.98564029581681 | epot = -22.9188993843038 | etot = -17.5274608105523 -376000 ekin = 3.36516934625557 | erot = 3.24766546156016 | epot = -22.940715917868 | etot = -16.3278811100523 -377000 ekin = 3.18983781467362 | erot = 2.65450417571542 | epot = -22.8850374180386 | etot = -17.0406954276496 -378000 ekin = 1.54656075265338 | erot = 2.66317423977111 | epot = -22.8855901030291 | etot = -18.6758551106046 -379000 ekin = 1.93839150288505 | erot = 2.54534031143981 | epot = -22.9043634096536 | etot = -18.4206315953288 -380000 ekin = 2.66254728899606 | erot = 2.88892403669479 | epot = -22.9338385289327 | etot = -17.3823672032419 -381000 ekin = 2.95357480274557 | erot = 2.1770881328374 | epot = -22.9777297037143 | etot = -17.8470667681313 -382000 ekin = 2.58828801972808 | erot = 2.01895528744468 | epot = -22.9240694006084 | etot = -18.3168260934356 -383000 ekin = 2.01537544096934 | erot = 2.50444896556415 | epot = -22.9471970402487 | etot = -18.4273726337152 -384000 ekin = 2.1008854766715 | erot = 2.19856058469132 | epot = -22.9599217884816 | etot = -18.6604757271188 -385000 ekin = 1.91384966632105 | erot = 1.63022965207194 | epot = -22.9760629278411 | etot = -19.4319836094481 -386000 ekin = 1.56010650102716 | erot = 1.35861854215736 | epot = -23.0225779741027 | etot = -20.1038529309182 -387000 ekin = 2.21264194719196 | erot = 1.75007226671446 | epot = -23.0228562328387 | etot = -19.0601420189323 -388000 ekin = 1.98740987493218 | erot = 1.95984350341523 | epot = -22.9305477811724 | etot = -18.983294402825 -389000 ekin = 2.54192883121441 | erot = 2.33922416322361 | epot = -22.9249127695712 | etot = -18.0437597751332 -390000 ekin = 2.07846479778646 | erot = 1.88716644515798 | epot = -22.8328701541731 | etot = -18.8672389112287 -391000 ekin = 1.85214179314428 | erot = 2.41299153787073 | epot = -22.7996788423596 | etot = -18.5345455113446 -392000 ekin = 2.1990161201673 | erot = 2.89998817237143 | epot = -22.7987091159473 | etot = -17.6997048234086 -393000 ekin = 2.15260515278705 | erot = 3.19524728171092 | epot = -22.8896620280071 | etot = -17.5418095935092 -394000 ekin = 1.99225032343945 | erot = 2.14729304405154 | epot = -22.8800416390029 | etot = -18.7404982715119 -395000 ekin = 2.03378474286714 | erot = 2.5027536840914 | epot = -22.9316292594111 | etot = -18.3950908324525 -396000 ekin = 2.1438632384243 | erot = 1.95894279389406 | epot = -23.0275362016084 | etot = -18.92473016929 -397000 ekin = 2.3982267029558 | erot = 1.6520465154777 | epot = -23.1343663061977 | etot = -19.0840930877642 -398000 ekin = 3.58481792746973 | erot = 2.51392910802386 | epot = -23.2457545351658 | etot = -17.1470074996722 -399000 ekin = 2.65690049350562 | erot = 1.78819644367598 | epot = -23.3515850649259 | etot = -18.9064881277443 -400000 ekin = 2.51173640894656 | erot = 2.10904826584645 | epot = -23.4207879652203 | etot = -18.8000032904273 -401000 ekin = 2.051233917874 | erot = 2.1536921336815 | epot = -23.4762000730604 | etot = -19.2712740215049 -402000 ekin = 2.43380846674055 | erot = 2.11259263785444 | epot = -23.4648112610383 | etot = -18.9184101564433 -403000 ekin = 2.53609107080855 | erot = 2.81280118329428 | epot = -23.5344895971956 | etot = -18.1855973430928 -404000 ekin = 2.18209195546023 | erot = 2.63706526020475 | epot = -23.6211046727682 | etot = -18.8019474571032 -405000 ekin = 2.45129457425945 | erot = 2.40500271478244 | epot = -23.6324000926426 | etot = -18.7761028036007 -406000 ekin = 2.21962265364597 | erot = 2.24914950938542 | epot = -23.6519777970511 | etot = -19.1832056340197 -407000 ekin = 1.98553912077512 | erot = 2.77856927236326 | epot = -23.557236944138 | etot = -18.7931285509997 -408000 ekin = 2.57635800289226 | erot = 2.58086436198046 | epot = -23.4362831006766 | etot = -18.2790607358039 -409000 ekin = 2.36933136766419 | erot = 2.25922617215654 | epot = -23.3257538962906 | etot = -18.6971963564699 -410000 ekin = 2.02248038283451 | erot = 1.96486213113069 | epot = -23.3085205990924 | etot = -19.3211780851272 -411000 ekin = 1.8788974806599 | erot = 2.6514468933077 | epot = -23.288114132028 | etot = -18.7577697580604 -412000 ekin = 1.99373261308744 | erot = 2.68967710559433 | epot = -23.2520689125676 | etot = -18.5686591938858 -413000 ekin = 2.38901265794743 | erot = 2.64559329464322 | epot = -23.1974799245766 | etot = -18.1628739719859 -414000 ekin = 2.42764537426657 | erot = 1.75171638842505 | epot = -23.1227256481796 | etot = -18.943363885488 -415000 ekin = 2.76411872449006 | erot = 2.44214574701597 | epot = -23.1777400120228 | etot = -17.9714755405168 -416000 ekin = 2.08293620051845 | erot = 2.76581176915863 | epot = -23.186622003278 | etot = -18.337874033601 -417000 ekin = 1.99975250190993 | erot = 1.9578721634496 | epot = -23.1905597787985 | etot = -19.2329351134389 -418000 ekin = 2.38311403931269 | erot = 2.55890369849375 | epot = -23.1547990589628 | etot = -18.2127813211564 -419000 ekin = 2.98411599395291 | erot = 2.57059785409318 | epot = -23.0506701290817 | etot = -17.4959562810356 -420000 ekin = 2.60188910540588 | erot = 2.46051136519661 | epot = -22.9584750453702 | etot = -17.8960745747677 -421000 ekin = 2.51721839958931 | erot = 1.77803097918895 | epot = -22.9478270423399 | etot = -18.6525776635616 -422000 ekin = 2.73215994330404 | erot = 1.67289719515518 | epot = -22.9366997516619 | etot = -18.5316426132027 -423000 ekin = 2.13301592734426 | erot = 2.54982791014141 | epot = -22.8120609726708 | etot = -18.1292171351851 -424000 ekin = 1.90609667850123 | erot = 2.31895806505094 | epot = -22.7750025410849 | etot = -18.5499477975327 -425000 ekin = 2.37363345292966 | erot = 1.95591998920184 | epot = -22.7837602756269 | etot = -18.4542068334954 -426000 ekin = 2.23506150102974 | erot = 2.60957702289923 | epot = -22.8034248715963 | etot = -17.9587863476673 -427000 ekin = 1.8858071920588 | erot = 2.12670154749625 | epot = -22.9703036100131 | etot = -18.957794870458 -428000 ekin = 1.93190556918249 | erot = 2.45435859297294 | epot = -23.1028032345637 | etot = -18.7165390724082 -429000 ekin = 1.72625681322915 | erot = 2.16391616195066 | epot = -23.1169612720762 | etot = -19.2267882968964 -430000 ekin = 2.31229851925652 | erot = 2.14059498772528 | epot = -23.123947656521 | etot = -18.6710541495392 -431000 ekin = 2.45856801873639 | erot = 2.41565239614123 | epot = -23.1343729492306 | etot = -18.260152534353 -432000 ekin = 2.80045086542028 | erot = 2.19133218252703 | epot = -23.1425691977264 | etot = -18.1507861497791 -433000 ekin = 2.20382151693237 | erot = 1.62233615534329 | epot = -23.186811655719 | etot = -19.3606539834433 -434000 ekin = 2.5912014730388 | erot = 2.35257474145033 | epot = -23.2139624944838 | etot = -18.2701862799947 -435000 ekin = 2.292878018016 | erot = 2.54026793769998 | epot = -23.1933803471397 | etot = -18.3602343914237 -436000 ekin = 2.43255475285637 | erot = 2.74965402216776 | epot = -23.2431213562246 | etot = -18.0609125812005 -437000 ekin = 1.64425595993858 | erot = 3.23323066283653 | epot = -23.2344898707627 | etot = -18.3570032479876 -438000 ekin = 1.56118873048903 | erot = 2.60253121414272 | epot = -23.1306562811571 | etot = -18.9669363365254 -439000 ekin = 2.30492577643288 | erot = 1.9389279713903 | epot = -23.1381949153658 | etot = -18.8943411675426 -440000 ekin = 2.52026113610471 | erot = 3.04666677428385 | epot = -23.1986879717886 | etot = -17.6317600614 -441000 ekin = 2.79914634628251 | erot = 2.54581028632591 | epot = -23.1725956938593 | etot = -17.8276390612509 -442000 ekin = 2.93509023618977 | erot = 2.87676477127226 | epot = -23.1159592458781 | etot = -17.304104238416 -443000 ekin = 1.96857488695096 | erot = 1.76444429617767 | epot = -23.0441054580414 | etot = -19.3110862749127 -444000 ekin = 2.00750191739409 | erot = 2.2534047751145 | epot = -22.9735423472635 | etot = -18.712635654755 -445000 ekin = 2.22546986952724 | erot = 2.06326830023309 | epot = -22.8095964231444 | etot = -18.5208582533841 -446000 ekin = 2.4450124715022 | erot = 2.3730159305034 | epot = -22.7149791043001 | etot = -17.8969507022945 -447000 ekin = 2.27692613820669 | erot = 2.40593386102284 | epot = -22.7350457195192 | etot = -18.0521857202897 -448000 ekin = 2.17715994902024 | erot = 1.93996223845971 | epot = -22.8484345777469 | etot = -18.7313123902669 -449000 ekin = 2.2196798712192 | erot = 2.34285870025318 | epot = -22.938199826666 | etot = -18.3756612551936 -450000 ekin = 2.75054977353848 | erot = 1.97938557871968 | epot = -22.8928697422248 | etot = -18.1629343899666 -451000 ekin = 2.21115355148631 | erot = 2.13373186546172 | epot = -22.9268989776618 | etot = -18.5820135607137 -452000 ekin = 2.54346617380347 | erot = 2.35731335928095 | epot = -22.9645722362833 | etot = -18.0637927031988 -453000 ekin = 2.2284644335428 | erot = 1.78504863466535 | epot = -22.9494030803646 | etot = -18.9358900121564 -454000 ekin = 2.43981950788672 | erot = 2.59540327726185 | epot = -22.8784508334485 | etot = -17.8432280482999 -455000 ekin = 2.04589395219366 | erot = 2.7960521140105 | epot = -22.6640287607136 | etot = -17.8220826945095 -456000 ekin = 2.02066497153519 | erot = 2.51421900073603 | epot = -22.4777086012038 | etot = -17.9428246289326 -457000 ekin = 2.62428771899347 | erot = 2.43881206937848 | epot = -22.3598178635714 | etot = -17.2967180751994 -458000 ekin = 2.00990487485324 | erot = 1.99234707595584 | epot = -22.2532334283702 | etot = -18.2509814775611 -459000 ekin = 1.75250109782347 | erot = 2.49689893971802 | epot = -22.2437782516535 | etot = -17.994378214112 -460000 ekin = 1.9190487289221 | erot = 2.07624013444807 | epot = -22.2370852343625 | etot = -18.2417963709923 -461000 ekin = 1.56836892852198 | erot = 1.28974645955658 | epot = -22.2063748439499 | etot = -19.3482594558713 -462000 ekin = 2.45168650095568 | erot = 1.36025556758079 | epot = -22.3059327256893 | etot = -18.4939906571528 -463000 ekin = 2.64349639743884 | erot = 2.07826809667296 | epot = -22.4269210824658 | etot = -17.705156588354 -464000 ekin = 2.67294933942793 | erot = 3.73619931212747 | epot = -22.5513294295021 | etot = -16.1421807779467 -465000 ekin = 1.95387776347697 | erot = 2.23929165445271 | epot = -22.7354276602965 | etot = -18.5422582423668 -466000 ekin = 2.13358131772513 | erot = 2.9628231040371 | epot = -22.8413443832467 | etot = -17.7449399614844 -467000 ekin = 2.46622692687387 | erot = 2.11619893803783 | epot = -23.0236293811154 | etot = -18.4412035162037 -468000 ekin = 1.99045166389675 | erot = 1.6285380006184 | epot = -23.0932840681895 | etot = -19.4742944036743 -469000 ekin = 2.49670871865504 | erot = 2.63664907892974 | epot = -23.1383213964888 | etot = -18.0049635989041 -470000 ekin = 2.92207685554493 | erot = 3.21710942124273 | epot = -23.1429890223789 | etot = -17.0038027455912 -471000 ekin = 2.36481422254557 | erot = 1.72322177619039 | epot = -23.1018283304032 | etot = -19.0137923316673 -472000 ekin = 2.18517765615792 | erot = 2.00241070370021 | epot = -23.0699010011102 | etot = -18.8823126412521 -473000 ekin = 2.37141527291476 | erot = 2.86124879212049 | epot = -23.0301508899776 | etot = -17.7974868249423 -474000 ekin = 2.18573397152438 | erot = 2.60055996125085 | epot = -22.9109845829656 | etot = -18.1246906501904 -475000 ekin = 2.39664419497567 | erot = 2.01359105802913 | epot = -22.8103966693808 | etot = -18.400161416376 -476000 ekin = 2.106779684052 | erot = 2.60326535898524 | epot = -22.8093298667681 | etot = -18.0992848237309 -477000 ekin = 2.53303116397527 | erot = 3.55507509768021 | epot = -22.7929172799516 | etot = -16.7048110182962 -478000 ekin = 2.40644412232746 | erot = 2.73235251079285 | epot = -22.7008644942783 | etot = -17.562067861158 -479000 ekin = 1.2774884884165 | erot = 2.99242202231977 | epot = -22.6580451660686 | etot = -18.3881346553323 -480000 ekin = 1.82378442133505 | erot = 2.13912569674403 | epot = -22.6273806665075 | etot = -18.6644705484284 -481000 ekin = 2.38794676527735 | erot = 3.18394268862154 | epot = -22.652698250081 | etot = -17.0808087961821 -482000 ekin = 3.20103552737715 | erot = 2.41980408559651 | epot = -22.6098898945504 | etot = -16.9890502815768 -483000 ekin = 3.03840673317681 | erot = 2.48624445057528 | epot = -22.5747152180487 | etot = -17.0500640342966 -484000 ekin = 2.70186903599877 | erot = 2.52680102607677 | epot = -22.6043659240374 | etot = -17.3756958619618 -485000 ekin = 3.27237676088605 | erot = 2.42435226331311 | epot = -22.5971021698101 | etot = -16.9003731456109 -486000 ekin = 1.96601696665902 | erot = 1.75893246838797 | epot = -22.6399989280022 | etot = -18.9150494929552 -487000 ekin = 2.62348602949564 | erot = 2.50764223408898 | epot = -22.7315097398775 | etot = -17.6003814762928 -488000 ekin = 1.75208653704965 | erot = 2.64490018417003 | epot = -22.7893685606217 | etot = -18.3923818394021 -489000 ekin = 2.08736451702833 | erot = 2.95231225184179 | epot = -22.8795542371813 | etot = -17.8398774683112 -490000 ekin = 2.30758266641326 | erot = 2.33160202425018 | epot = -22.8824154392574 | etot = -18.2432307485939 -491000 ekin = 2.48198002403303 | erot = 2.59526090835888 | epot = -22.8753520101327 | etot = -17.7981110777408 -492000 ekin = 3.28206840084522 | erot = 2.18523064608534 | epot = -22.8554585939889 | etot = -17.3881595470583 -493000 ekin = 3.37968205627646 | erot = 2.35359230702798 | epot = -22.802471593836 | etot = -17.0691972305315 -494000 ekin = 3.57469694905841 | erot = 2.2485639294812 | epot = -22.8021092664721 | etot = -16.9788483879325 -495000 ekin = 2.5052834294994 | erot = 2.15847696242519 | epot = -22.7974611109899 | etot = -18.1337007190653 -496000 ekin = 1.95424552563439 | erot = 3.58261919463167 | epot = -22.8351163728141 | etot = -17.298251652548 -497000 ekin = 2.22184693843012 | erot = 2.46505638343575 | epot = -22.8411234790096 | etot = -18.1542201571438 -498000 ekin = 1.72646972661644 | erot = 2.39649152448662 | epot = -22.7771984845447 | etot = -18.6542372334417 -499000 ekin = 2.44587532386558 | erot = 2.82724443292545 | epot = -22.7933140861756 | etot = -17.5201943293846 -500000 ekin = 2.78510450558426 | erot = 2.23272713529476 | epot = -22.8971262576266 | etot = -17.8792946167476 -501000 ekin = 2.99437147790547 | erot = 1.97777660143103 | epot = -22.9259326262666 | etot = -17.9537845469301 -502000 ekin = 2.98620318494749 | erot = 1.79968012191087 | epot = -22.9540905110158 | etot = -18.1682072041574 -503000 ekin = 2.51500641896251 | erot = 2.88866029010492 | epot = -22.9837264072572 | etot = -17.5800596981898 -504000 ekin = 2.84385497746759 | erot = 2.69349274825329 | epot = -22.9149904805499 | etot = -17.377642754829 -505000 ekin = 2.95574835602088 | erot = 2.6026753799514 | epot = -22.9888007816538 | etot = -17.4303770456815 -506000 ekin = 2.19820711369971 | erot = 1.96723089641087 | epot = -23.0300125090253 | etot = -18.8645744989147 -507000 ekin = 2.26258673474996 | erot = 2.70466389763239 | epot = -22.9957070923465 | etot = -18.0284564599641 -508000 ekin = 2.63638196787186 | erot = 2.05040146648131 | epot = -23.0074182438498 | etot = -18.3206348094966 -509000 ekin = 2.941534357322 | erot = 2.9116561510807 | epot = -23.0604926861274 | etot = -17.2073021777247 -510000 ekin = 2.26261998090286 | erot = 2.81560695024321 | epot = -23.1751735881193 | etot = -18.0969466569732 -511000 ekin = 2.89882203877689 | erot = 2.15644204743089 | epot = -23.2976829651598 | etot = -18.242418878952 -512000 ekin = 2.18248507908123 | erot = 2.32471465184078 | epot = -23.3729111641778 | etot = -18.8657114332558 -513000 ekin = 1.69088054596992 | erot = 2.87837634409229 | epot = -23.3827433252491 | etot = -18.8134864351869 -514000 ekin = 1.72555879339418 | erot = 2.33322715253437 | epot = -23.3782683624831 | etot = -19.3194824165546 -515000 ekin = 1.99840271010263 | erot = 1.80256652461596 | epot = -23.3732611472924 | etot = -19.5722919125738 -516000 ekin = 3.02857447051151 | erot = 1.5400404903518 | epot = -23.3371239983442 | etot = -18.7685090374808 -517000 ekin = 2.46355229218044 | erot = 2.11387593279357 | epot = -23.3120503202835 | etot = -18.7346220953095 -518000 ekin = 2.03623914203692 | erot = 2.51801359135206 | epot = -23.2489994054059 | etot = -18.6947466720169 -519000 ekin = 1.58667253859857 | erot = 1.63211503072947 | epot = -23.2067561094409 | etot = -19.9879685401128 -520000 ekin = 2.16324608146533 | erot = 1.89657617078696 | epot = -23.2082678544253 | etot = -19.148445602173 -521000 ekin = 1.97686811359425 | erot = 2.0872712571421 | epot = -23.2512754061872 | etot = -19.1871360354508 -522000 ekin = 2.69830866187618 | erot = 2.1956248060682 | epot = -23.3119120700689 | etot = -18.4179786021245 -523000 ekin = 2.24785090987913 | erot = 1.67440253273743 | epot = -23.3589880036331 | etot = -19.4367345610165 -524000 ekin = 2.34889284001673 | erot = 2.1007910786486 | epot = -23.3797580192055 | etot = -18.9300741005401 -525000 ekin = 2.13149576225198 | erot = 2.0723725435025 | epot = -23.4380051055748 | etot = -19.2341367998203 -526000 ekin = 2.50239998087446 | erot = 2.25424985364477 | epot = -23.4972589637756 | etot = -18.7406091292563 -527000 ekin = 3.03515775223167 | erot = 1.80505768055502 | epot = -23.554671119079 | etot = -18.7144556862923 -528000 ekin = 2.5608174763548 | erot = 2.54328225738986 | epot = -23.5720157710688 | etot = -18.4679160373241 -529000 ekin = 2.37506941472445 | erot = 1.93007818421908 | epot = -23.5564414475786 | etot = -19.251293848635 -530000 ekin = 3.3419677281169 | erot = 3.41384036164691 | epot = -23.4493550232615 | etot = -16.6935469334977 -531000 ekin = 2.4235092053109 | erot = 2.35978294499845 | epot = -23.1490536179472 | etot = -18.3657614676379 -532000 ekin = 2.58896799590229 | erot = 1.86978691602605 | epot = -23.165039392045 | etot = -18.7062844801167 -533000 ekin = 2.18027058294701 | erot = 2.16031799038535 | epot = -23.3790946936929 | etot = -19.0385061203605 -534000 ekin = 2.3479868128811 | erot = 2.0385286250955 | epot = -23.4622625656644 | etot = -19.0757471276878 -535000 ekin = 2.3782313722319 | erot = 2.07392590496072 | epot = -23.4816815929821 | etot = -19.0295243157895 -536000 ekin = 2.46212862766406 | erot = 1.89477230721272 | epot = -23.4656032882526 | etot = -19.1087023533758 -537000 ekin = 1.71194009451629 | erot = 2.13445451003515 | epot = -23.5539827524157 | etot = -19.7075881478642 -538000 ekin = 2.16675831406369 | erot = 2.76561566966347 | epot = -23.6593643234718 | etot = -18.7269903397447 -539000 ekin = 2.16624212273309 | erot = 2.29113017698322 | epot = -23.7362705602946 | etot = -19.2788982605782 -540000 ekin = 2.37614209115086 | erot = 1.63783384730145 | epot = -23.7311087126642 | etot = -19.7171327742119 -541000 ekin = 2.61201729538231 | erot = 2.5250031626081 | epot = -23.6609998128446 | etot = -18.5239793548541 -542000 ekin = 2.72899828578995 | erot = 2.10988741791456 | epot = -23.6987729418172 | etot = -18.8598872381126 -543000 ekin = 2.72077400162185 | erot = 1.85643651604112 | epot = -23.6056812049309 | etot = -19.0284706872679 -544000 ekin = 2.11785692900505 | erot = 1.50578231047403 | epot = -23.581427161181 | etot = -19.9577879217019 -545000 ekin = 1.70786262657811 | erot = 2.5699332427333 | epot = -23.5821026874923 | etot = -19.3043068181809 -546000 ekin = 2.38060529409929 | erot = 1.86647004671163 | epot = -23.6101839511561 | etot = -19.3631086103452 -547000 ekin = 2.4524914794752 | erot = 2.45758863876476 | epot = -23.659961725937 | etot = -18.749881607697 -548000 ekin = 2.39048922197387 | erot = 2.39595923181893 | epot = -23.672341518051 | etot = -18.8858930642582 -549000 ekin = 2.59237109487195 | erot = 2.03286301955741 | epot = -23.663402955197 | etot = -19.0381688407676 -550000 ekin = 1.99326412841577 | erot = 1.84900416370414 | epot = -23.6657646794243 | etot = -19.8234963873044 -551000 ekin = 2.44897958881949 | erot = 2.02189459200062 | epot = -23.6223977807006 | etot = -19.1515235998805 -552000 ekin = 2.69506011124378 | erot = 1.4087045289661 | epot = -23.4598817431801 | etot = -19.3561171029703 -553000 ekin = 1.7614112496816 | erot = 2.61025745472483 | epot = -23.2534851194706 | etot = -18.8818164150642 -554000 ekin = 2.30413102985308 | erot = 2.33068531989324 | epot = -23.2170368597895 | etot = -18.5822205100432 -555000 ekin = 3.27044533046142 | erot = 1.64227498681914 | epot = -23.1963457102547 | etot = -18.2836253929742 -556000 ekin = 2.90315678132448 | erot = 2.59895742246943 | epot = -23.1450725642432 | etot = -17.6429583604493 -557000 ekin = 2.91669736278429 | erot = 3.16406737832137 | epot = -23.1449528769861 | etot = -17.0641881358805 -558000 ekin = 2.82900232701285 | erot = 2.71147852622196 | epot = -23.1184803827916 | etot = -17.5779995295568 -559000 ekin = 2.44505587446295 | erot = 3.29469811923283 | epot = -23.1627781618237 | etot = -17.423024168128 -560000 ekin = 2.31904677659936 | erot = 2.34795233137866 | epot = -23.1210700988646 | etot = -18.4540709908866 -561000 ekin = 2.04771931333916 | erot = 2.88228436865011 | epot = -23.024411145941 | etot = -18.0944074639517 -562000 ekin = 2.23091608960519 | erot = 3.71635453668511 | epot = -22.8944164201338 | etot = -16.9471457938435 -563000 ekin = 3.1357852432065 | erot = 2.30361462487037 | epot = -22.9661332369329 | etot = -17.5267333688561 -564000 ekin = 2.43466309429864 | erot = 2.37782011884422 | epot = -22.9389295001135 | etot = -18.1264462869706 -565000 ekin = 2.74708790028088 | erot = 2.07634713087886 | epot = -22.939331551729 | etot = -18.1158965205693 -566000 ekin = 2.4222839122782 | erot = 2.23675738705857 | epot = -22.9632631791452 | etot = -18.3042218798084 -567000 ekin = 2.66083125722037 | erot = 2.00815445030396 | epot = -23.0587738412098 | etot = -18.3897881336855 -568000 ekin = 3.04192088032675 | erot = 1.98454766740893 | epot = -23.1119399549794 | etot = -18.0854714072437 -569000 ekin = 3.57500602366975 | erot = 2.06993473480211 | epot = -23.1169833765643 | etot = -17.4720426180924 -570000 ekin = 2.66021275095562 | erot = 2.34009289778314 | epot = -23.1329733111479 | etot = -18.1326676624092 -571000 ekin = 1.9492727086219 | erot = 2.84215857351434 | epot = -23.059975766874 | etot = -18.2685444847377 -572000 ekin = 2.41534745626505 | erot = 2.40867063666104 | epot = -23.0550186086203 | etot = -18.2310005156942 -573000 ekin = 1.75690848092507 | erot = 2.3167538090557 | epot = -23.1062821980692 | etot = -19.0326199080885 -574000 ekin = 2.10700070451592 | erot = 2.59266019942445 | epot = -23.1953992541668 | etot = -18.4957383502265 -575000 ekin = 2.3766207361603 | erot = 2.79835296504546 | epot = -23.2685471976934 | etot = -18.0935734964876 -576000 ekin = 2.17646651375686 | erot = 3.28542649915204 | epot = -23.3024195314184 | etot = -17.8405265185095 -577000 ekin = 2.48649787916229 | erot = 2.29384528363048 | epot = -23.3336440834232 | etot = -18.5533009206305 -578000 ekin = 2.63489334342406 | erot = 2.38537839776846 | epot = -23.3926914947912 | etot = -18.3724197535987 -579000 ekin = 2.6879639473483 | erot = 1.70827418352421 | epot = -23.3699011030343 | etot = -18.9736629721618 -580000 ekin = 2.35397680707073 | erot = 2.85531289645877 | epot = -23.3791722262718 | etot = -18.1698825227423 -581000 ekin = 2.45623723360352 | erot = 2.60459639714713 | epot = -23.3494339765039 | etot = -18.2886003457532 -582000 ekin = 2.3382526117462 | erot = 3.2061485365379 | epot = -23.4180112490559 | etot = -17.8736101007718 -583000 ekin = 1.96183434404855 | erot = 2.8182320095548 | epot = -23.5859382554133 | etot = -18.80587190181 -584000 ekin = 2.00096532862293 | erot = 1.71661883974024 | epot = -23.6753971791609 | etot = -19.9578130107977 -585000 ekin = 2.26504312453072 | erot = 2.08207426542528 | epot = -23.7221723341546 | etot = -19.3750549441986 -586000 ekin = 2.20198471634668 | erot = 1.96863181734696 | epot = -23.6845937288944 | etot = -19.5139771952007 -587000 ekin = 3.67920423738482 | erot = 1.82482965137738 | epot = -23.6620758789199 | etot = -18.1580419901577 -588000 ekin = 3.48072723000483 | erot = 2.30687784419354 | epot = -23.5628518088072 | etot = -17.7752467346088 -589000 ekin = 2.6301802350708 | erot = 2.97022216183281 | epot = -23.3751519834186 | etot = -17.774749586515 -590000 ekin = 1.60810524494739 | erot = 2.03262567379754 | epot = -23.1930040863614 | etot = -19.5522731676165 -591000 ekin = 1.81653979391832 | erot = 1.75590363843925 | epot = -23.1286401679288 | etot = -19.5561967355713 -592000 ekin = 2.57251131663395 | erot = 2.59255636832343 | epot = -23.1517404198258 | etot = -17.9866727348685 -593000 ekin = 2.43680227955855 | erot = 1.78797812851328 | epot = -23.101945124129 | etot = -18.8771647160572 -594000 ekin = 2.12130372154182 | erot = 2.16319738901753 | epot = -23.0522428105757 | etot = -18.7677417000163 -595000 ekin = 2.61503378317223 | erot = 2.04014237870419 | epot = -23.0400690201979 | etot = -18.3848928583215 -596000 ekin = 2.5838826262171 | erot = 2.12601862315907 | epot = -23.0972897944143 | etot = -18.3873885450381 -597000 ekin = 3.03557942938101 | erot = 3.13923818214656 | epot = -23.0945090272485 | etot = -16.9196914157209 -598000 ekin = 3.44798129544029 | erot = 2.86439798217039 | epot = -23.1511239016259 | etot = -16.8387446240152 -599000 ekin = 2.14574146166173 | erot = 3.49764417749902 | epot = -23.122284004392 | etot = -17.4788983652312 -600000 ekin = 2.20860876734766 | erot = 2.50874056137532 | epot = -23.121641128369 | etot = -18.4042917996461 -601000 ekin = 2.82315501435403 | erot = 2.82784045939002 | epot = -23.0925533117084 | etot = -17.4415578379644 -602000 ekin = 2.33761512592198 | erot = 2.38145173595585 | epot = -23.0579577028674 | etot = -18.3388908409896 -603000 ekin = 1.93160054442741 | erot = 1.95556752436392 | epot = -22.9401029172158 | etot = -19.0529348484245 -604000 ekin = 2.6789810993261 | erot = 3.14412986031109 | epot = -22.910832287093 | etot = -17.0877213274558 -605000 ekin = 2.71997631755228 | erot = 2.06416447860583 | epot = -22.9239871466825 | etot = -18.1398463505244 -606000 ekin = 2.99643636348445 | erot = 2.03201196902714 | epot = -22.8415583488471 | etot = -17.8131100163355 -607000 ekin = 2.88272893636888 | erot = 2.37624693398617 | epot = -22.8254440726334 | etot = -17.5664682022784 -608000 ekin = 3.65630425769789 | erot = 2.4609503215642 | epot = -22.762585585759 | etot = -16.6453310064969 -609000 ekin = 2.67762341692564 | erot = 2.28055578469673 | epot = -22.7828567112764 | etot = -17.824677509654 -610000 ekin = 2.96652133048089 | erot = 2.13934256593668 | epot = -22.7741547643332 | etot = -17.6682908679156 -611000 ekin = 3.84932586877613 | erot = 2.13519046445732 | epot = -22.7544276213926 | etot = -16.7699112881591 -612000 ekin = 2.85989656018767 | erot = 2.46801741609839 | epot = -22.6660352466822 | etot = -17.3381212703962 -613000 ekin = 2.93453113084909 | erot = 2.15612014750899 | epot = -22.6610069845369 | etot = -17.5703557061788 -614000 ekin = 2.80105508963963 | erot = 2.03410273106392 | epot = -22.7348632778619 | etot = -17.8997054571583 -615000 ekin = 2.29275813765167 | erot = 2.37294703205248 | epot = -22.8254873753585 | etot = -18.1597822056544 -616000 ekin = 1.78885710821491 | erot = 2.46510899047625 | epot = -22.9171248890198 | etot = -18.6631587903287 -617000 ekin = 2.58551875410709 | erot = 2.5373402867597 | epot = -22.9360764839305 | etot = -17.8132174430637 -618000 ekin = 2.31892663964202 | erot = 2.68589041417607 | epot = -22.8727518088247 | etot = -17.8679347550066 -619000 ekin = 1.95263551601201 | erot = 2.00547599081928 | epot = -22.8336441658867 | etot = -18.8755326590554 -620000 ekin = 2.93125230382283 | erot = 2.17152517775752 | epot = -22.9083331407927 | etot = -17.8055556592123 -621000 ekin = 2.92256345141131 | erot = 1.69365804073587 | epot = -22.9481701549848 | etot = -18.3319486628377 -622000 ekin = 2.04586667934044 | erot = 2.52349184406704 | epot = -22.8875044323845 | etot = -18.318145908977 -623000 ekin = 1.97950132185482 | erot = 3.07798060074862 | epot = -22.8981219896543 | etot = -17.8406400670509 -624000 ekin = 2.09648418588882 | erot = 2.6543004426831 | epot = -22.9137783443298 | etot = -18.1629937157579 -625000 ekin = 2.53180941807541 | erot = 2.36094945875658 | epot = -22.9713145545226 | etot = -18.0785556776906 -626000 ekin = 2.71470092938691 | erot = 2.03801315634257 | epot = -22.9996382199111 | etot = -18.2469241341817 -627000 ekin = 2.22369596417806 | erot = 2.35283010947608 | epot = -22.9578688816797 | etot = -18.3813428080256 -628000 ekin = 2.27999602854394 | erot = 2.28859122795553 | epot = -22.8528131434533 | etot = -18.2842258869538 -629000 ekin = 2.52123682351367 | erot = 1.89626016629389 | epot = -22.7899249071395 | etot = -18.372427917332 -630000 ekin = 3.09552317576679 | erot = 2.51631689437832 | epot = -22.7146675453805 | etot = -17.1028274752354 -631000 ekin = 2.38490277583395 | erot = 3.31743656633136 | epot = -22.7264783640902 | etot = -17.0241390219248 -632000 ekin = 2.58507904222623 | erot = 2.52764941236063 | epot = -22.679176298765 | etot = -17.5664478441781 -633000 ekin = 2.43449371039936 | erot = 1.90741463354387 | epot = -22.6535443404276 | etot = -18.3116359964843 -634000 ekin = 2.22577214221416 | erot = 2.00782187507303 | epot = -22.5713359353359 | etot = -18.3377419180487 -635000 ekin = 2.21828703186448 | erot = 1.98254572604181 | epot = -22.5412406270617 | etot = -18.3404078691554 -636000 ekin = 2.25203768985671 | erot = 2.77892756814694 | epot = -22.5726302712271 | etot = -17.5416650132235 -637000 ekin = 1.94361631144887 | erot = 2.61217525293607 | epot = -22.6025759792528 | etot = -18.0467844148678 -638000 ekin = 2.53948853675747 | erot = 3.14008150742344 | epot = -22.5816815234452 | etot = -16.9021114792643 -639000 ekin = 2.37754295974937 | erot = 2.49543508367508 | epot = -22.5440763882375 | etot = -17.671098344813 -640000 ekin = 2.08220370718338 | erot = 2.2194194329635 | epot = -22.4524516894458 | etot = -18.1508285492989 -641000 ekin = 2.47978319917432 | erot = 3.55852054823509 | epot = -22.3492008411224 | etot = -16.310897093713 -642000 ekin = 3.38960132344713 | erot = 2.18185754829543 | epot = -22.2381539280913 | etot = -16.6666950563487 -643000 ekin = 2.84882938996105 | erot = 2.41327361032682 | epot = -22.1919035544934 | etot = -16.9298005542056 -644000 ekin = 2.97883864641817 | erot = 1.93798086343986 | epot = -22.1756635530162 | etot = -17.2588440431582 -645000 ekin = 4.12551460905463 | erot = 1.89960199669213 | epot = -22.1698840200029 | etot = -16.1447674142562 -646000 ekin = 2.52696700152244 | erot = 2.00637752228798 | epot = -22.1094379456324 | etot = -17.576093421822 -647000 ekin = 2.55510613012742 | erot = 2.20923063557538 | epot = -22.15306269638 | etot = -17.3887259306772 -648000 ekin = 3.02954161965434 | erot = 2.11327379217002 | epot = -22.1567476137635 | etot = -17.0139322019391 -649000 ekin = 2.58451162799693 | erot = 3.20634164199495 | epot = -22.1331170602233 | etot = -16.3422637902314 -650000 ekin = 3.77201429520633 | erot = 2.43067850654692 | epot = -22.0829669606205 | etot = -15.8802741588673 -651000 ekin = 3.31373950314884 | erot = 2.36225009565165 | epot = -21.9236843158819 | etot = -16.2476947170814 -652000 ekin = 2.49269048046144 | erot = 3.02152130835781 | epot = -21.7248332635395 | etot = -16.2106214747202 -653000 ekin = 2.82562653528407 | erot = 2.5389983180152 | epot = -21.720584398338 | etot = -16.3559595450387 -654000 ekin = 2.35162706281986 | erot = 2.1592221935512 | epot = -21.9212844347389 | etot = -17.4104351783678 -655000 ekin = 2.27465971046838 | erot = 2.12498228082651 | epot = -21.901368818889 | etot = -17.5017268275941 -656000 ekin = 2.33863364839044 | erot = 2.10521355308809 | epot = -21.9220753944062 | etot = -17.4782281929276 -657000 ekin = 2.74434430715418 | erot = 2.19004311145519 | epot = -22.136208072754 | etot = -17.2018206541446 -658000 ekin = 3.04725229200292 | erot = 2.59754076353072 | epot = -22.2930322879088 | etot = -16.6482392323752 -659000 ekin = 2.86433120437707 | erot = 3.42151787717832 | epot = -22.2980196003195 | etot = -16.0121705187641 -660000 ekin = 2.91954234725913 | erot = 1.63326659953276 | epot = -22.3386449739967 | etot = -17.7858360272048 -661000 ekin = 3.21083352573749 | erot = 1.8634965142938 | epot = -22.464255649999 | etot = -17.3899256099677 -662000 ekin = 3.05903745891172 | erot = 2.20029510410105 | epot = -22.5554071532051 | etot = -17.2960745901923 -663000 ekin = 1.91661647748247 | erot = 2.47135637120535 | epot = -22.6199107053331 | etot = -18.2319378566453 -664000 ekin = 1.43090369100425 | erot = 1.36491647540447 | epot = -22.7069611889569 | etot = -19.9111410225482 -665000 ekin = 1.55691746213238 | erot = 2.30942311266534 | epot = -22.7825901033953 | etot = -18.9162495285975 -666000 ekin = 2.44471757511112 | erot = 1.77340988320563 | epot = -22.9221213287866 | etot = -18.7039938704699 -667000 ekin = 2.81231115159421 | erot = 2.33234433996922 | epot = -23.1090557968116 | etot = -17.9644003052482 -668000 ekin = 2.71678052291266 | erot = 3.19300727255308 | epot = -23.1841400059555 | etot = -17.2743522104898 -669000 ekin = 3.42188935289467 | erot = 2.44862028635832 | epot = -23.2319725107707 | etot = -17.3614628715177 -670000 ekin = 2.54095648172786 | erot = 1.9812604087298 | epot = -23.1732308879544 | etot = -18.6510139974967 -671000 ekin = 2.3805663479416 | erot = 2.98378557997481 | epot = -23.1367627748431 | etot = -17.7724108469267 -672000 ekin = 3.02750640268286 | erot = 2.54451073535057 | epot = -23.1209945952621 | etot = -17.5489774572287 -673000 ekin = 3.42534085203218 | erot = 2.36776710166581 | epot = -23.0340816238788 | etot = -17.2409736701808 -674000 ekin = 3.1798335968179 | erot = 2.09974053793233 | epot = -22.9543522982093 | etot = -17.6747781634591 -675000 ekin = 2.35355980125584 | erot = 1.53476738200232 | epot = -22.8483076435154 | etot = -18.9599804602572 -676000 ekin = 2.44776916428191 | erot = 2.24648852028555 | epot = -22.7702475408439 | etot = -18.0759898562764 -677000 ekin = 2.75780413162083 | erot = 1.93135039840676 | epot = -22.8504049108609 | etot = -18.1612503808333 -678000 ekin = 2.86691036183901 | erot = 1.65298998733351 | epot = -22.8624995890271 | etot = -18.3425992398546 -679000 ekin = 2.3422515492929 | erot = 2.69060711211823 | epot = -22.9306443341676 | etot = -17.8977856727565 -680000 ekin = 2.47029457301042 | erot = 2.90804485320413 | epot = -22.9871466954175 | etot = -17.6088072692029 -681000 ekin = 1.90527495083164 | erot = 2.57752516482763 | epot = -22.9202555721454 | etot = -18.4374554564861 -682000 ekin = 2.11691016409813 | erot = 2.69948323324142 | epot = -22.8360698295072 | etot = -18.0196764321677 -683000 ekin = 2.36499416502711 | erot = 2.12378773338609 | epot = -22.7222509077472 | etot = -18.233469009334 -684000 ekin = 2.87417187528689 | erot = 2.65554383853006 | epot = -22.652968937805 | etot = -17.1232532239881 -685000 ekin = 3.04542408260429 | erot = 2.17388790678976 | epot = -22.6211255864198 | etot = -17.4018135970258 -686000 ekin = 2.4572232047866 | erot = 2.42733555780261 | epot = -22.5527218647546 | etot = -17.6681631021654 -687000 ekin = 2.74674649482159 | erot = 1.80406297330729 | epot = -22.4878814460607 | etot = -17.9370719779318 -688000 ekin = 1.79261906898015 | erot = 2.04571284009142 | epot = -22.4053085173396 | etot = -18.566976608268 -689000 ekin = 2.87728983191097 | erot = 1.89493579527769 | epot = -22.4572844245428 | etot = -17.6850587973542 -690000 ekin = 2.12417515140944 | erot = 2.42424686393433 | epot = -22.5714890244145 | etot = -18.0230670090707 -691000 ekin = 2.15969911943639 | erot = 2.52979832764676 | epot = -22.5876082022333 | etot = -17.8981107551501 -692000 ekin = 2.88674525045811 | erot = 2.651929872236 | epot = -22.4776759351877 | etot = -16.9390008124936 -693000 ekin = 2.3092809474595 | erot = 2.51902774155063 | epot = -22.3434837669245 | etot = -17.5151750779144 -694000 ekin = 2.90071779504629 | erot = 2.34205397880616 | epot = -22.2602593853742 | etot = -17.0174876115217 -695000 ekin = 2.95797030089466 | erot = 2.23892898139626 | epot = -22.3013052624001 | etot = -17.1044059801092 -696000 ekin = 2.65789992313128 | erot = 2.33957912785853 | epot = -22.3428209998027 | etot = -17.3453419488129 -697000 ekin = 1.89103531712653 | erot = 1.78294584711428 | epot = -22.3504400882104 | etot = -18.6764589239696 -698000 ekin = 2.22798162215976 | erot = 2.82524697464217 | epot = -22.3736356240205 | etot = -17.3204070272186 -699000 ekin = 2.35365478600885 | erot = 2.0687167283237 | epot = -22.3018254917899 | etot = -17.8794539774573 -700000 ekin = 2.58198996587039 | erot = 2.33085240245665 | epot = -22.2602257590337 | etot = -17.3473833907067 -701000 ekin = 2.99678089142865 | erot = 1.89950599572306 | epot = -22.3219835402767 | etot = -17.425696653125 -702000 ekin = 2.67515901971843 | erot = 2.64727221788161 | epot = -22.3592261887725 | etot = -17.0367949511725 -703000 ekin = 2.02349561650625 | erot = 2.03753398299055 | epot = -22.4335933513225 | etot = -18.3725637518257 -704000 ekin = 1.59653691808601 | erot = 1.63621743826809 | epot = -22.4663049532561 | etot = -19.233550596902 -705000 ekin = 2.34017756427041 | erot = 1.91003662789066 | epot = -22.5429518289027 | etot = -18.2927376367416 -706000 ekin = 2.47923684970646 | erot = 3.2700255708033 | epot = -22.5105468727032 | etot = -16.7612844521934 -707000 ekin = 2.38606338090128 | erot = 2.41702366807843 | epot = -22.6028317136512 | etot = -17.7997446646715 -708000 ekin = 1.68126488203551 | erot = 2.34005210871502 | epot = -22.7455626577094 | etot = -18.7242456669589 -709000 ekin = 1.80997013861619 | erot = 2.57925481113812 | epot = -23.0628207828654 | etot = -18.6735958331111 -710000 ekin = 2.07663470081894 | erot = 1.83621025520769 | epot = -23.1969975442429 | etot = -19.2841525882163 -711000 ekin = 1.95348523042278 | erot = 2.41454584124981 | epot = -23.2350510297748 | etot = -18.8670199581022 -712000 ekin = 2.1336102176431 | erot = 1.78657393325109 | epot = -23.2637922718023 | etot = -19.3436081209081 -713000 ekin = 2.90681618138139 | erot = 1.55095647140783 | epot = -23.1828218540472 | etot = -18.725049201258 -714000 ekin = 2.06612414721503 | erot = 1.86613874365067 | epot = -23.2231257100263 | etot = -19.2908628191606 -715000 ekin = 2.52896020774463 | erot = 1.94259727228635 | epot = -23.1650750564771 | etot = -18.6935175764461 -716000 ekin = 3.03493559712718 | erot = 2.21063194998576 | epot = -23.220942309801 | etot = -17.975374762688 -717000 ekin = 3.0796637775291 | erot = 2.47088132553581 | epot = -23.3632103988425 | etot = -17.8126652957776 -718000 ekin = 3.49698025039097 | erot = 2.2716592270022 | epot = -23.4191136876981 | etot = -17.6504742103049 -719000 ekin = 4.06136594689253 | erot = 3.10418551930051 | epot = -23.4063666180316 | etot = -16.2408151518386 -720000 ekin = 2.49833724515039 | erot = 1.90909716223089 | epot = -23.2614962660793 | etot = -18.854061858698 -721000 ekin = 2.57942252693403 | erot = 1.98570182653287 | epot = -23.1432472967431 | etot = -18.5781229432762 -722000 ekin = 2.01088679016935 | erot = 2.27470118196201 | epot = -23.1033008622402 | etot = -18.8177128901089 -723000 ekin = 2.44107678295511 | erot = 2.07629727323011 | epot = -23.182141318077 | etot = -18.6647672618918 -724000 ekin = 1.90803238982749 | erot = 1.93595857250405 | epot = -23.2369669247167 | etot = -19.3929759623851 -725000 ekin = 2.19380758227312 | erot = 2.80513053743865 | epot = -23.2881919599432 | etot = -18.2892538402315 -726000 ekin = 2.27661543234077 | erot = 2.54381748597239 | epot = -23.3349497821497 | etot = -18.5145168638365 -727000 ekin = 1.72229690120046 | erot = 2.6256783446951 | epot = -23.3699085142538 | etot = -19.0219332683583 -728000 ekin = 2.25091852567842 | erot = 3.59487379729856 | epot = -23.4350255191465 | etot = -17.5892331961695 -729000 ekin = 2.68838496984081 | erot = 1.72110395862725 | epot = -23.4780978913558 | etot = -19.0686089628877 -730000 ekin = 2.53299506461663 | erot = 2.76668907196319 | epot = -23.4895234062855 | etot = -18.1898392697057 -731000 ekin = 2.6760609217159 | erot = 2.04582604734292 | epot = -23.5238636820392 | etot = -18.8019767129804 -732000 ekin = 2.77846316806001 | erot = 1.88433334184077 | epot = -23.5770897435819 | etot = -18.9142932336812 -733000 ekin = 2.18892933871209 | erot = 2.6346843690662 | epot = -23.6104212257528 | etot = -18.7868075179745 -734000 ekin = 1.69459813153559 | erot = 2.30332709760983 | epot = -23.5932285157933 | etot = -19.5953032866479 -735000 ekin = 2.17738229724133 | erot = 2.71615420236581 | epot = -23.5325385675669 | etot = -18.6390020679598 -736000 ekin = 2.29368650601869 | erot = 1.17411705869823 | epot = -23.5029023896105 | etot = -20.0350988248936 -737000 ekin = 2.20822665790328 | erot = 3.11529898775426 | epot = -23.4546507116664 | etot = -18.1311250660089 -738000 ekin = 1.72299649032066 | erot = 2.28748751322147 | epot = -23.3303512731973 | etot = -19.3198672696552 -739000 ekin = 1.39485421458765 | erot = 2.1749073819018 | epot = -23.2849045067521 | etot = -19.7151429102627 -740000 ekin = 1.90421462896905 | erot = 2.27824600991221 | epot = -23.2508192404176 | etot = -19.0683586015364 -741000 ekin = 2.02016004868753 | erot = 2.72072555133488 | epot = -23.1869993966325 | etot = -18.4461137966101 -742000 ekin = 1.97476522388772 | erot = 1.87542520854124 | epot = -23.0922795240436 | etot = -19.2420890916146 -743000 ekin = 1.96482892297271 | erot = 2.7698229839544 | epot = -22.9312319116298 | etot = -18.1965800047027 -744000 ekin = 2.04907219390093 | erot = 2.34374807852806 | epot = -22.8504155274904 | etot = -18.4575952550614 -745000 ekin = 1.66770541517404 | erot = 1.87268797271618 | epot = -22.7970674500482 | etot = -19.256674062158 -746000 ekin = 2.11646191189726 | erot = 2.03543326686021 | epot = -22.7779244301375 | etot = -18.6260292513801 -747000 ekin = 3.07958266175499 | erot = 1.66913380114814 | epot = -22.8031371397658 | etot = -18.0544206768627 -748000 ekin = 3.03808653180953 | erot = 1.85632270757018 | epot = -22.842986346491 | etot = -17.9485771071113 -749000 ekin = 2.53758140749286 | erot = 2.01198418352658 | epot = -22.8596787422339 | etot = -18.3101131512145 -750000 ekin = 2.77211189937696 | erot = 2.32629771282836 | epot = -22.9522411003111 | etot = -17.8538314881058 -751000 ekin = 2.52041553848886 | erot = 2.34908561849257 | epot = -23.012198741928 | etot = -18.1426975849466 -752000 ekin = 2.46415827942669 | erot = 1.68869996421912 | epot = -22.9896556476389 | etot = -18.8367974039931 -753000 ekin = 2.47374307089788 | erot = 1.55777194971628 | epot = -23.1131588644731 | etot = -19.081643843859 -754000 ekin = 2.52796878003787 | erot = 2.29498052924916 | epot = -23.2400216607328 | etot = -18.4170723514458 -755000 ekin = 1.52934821736739 | erot = 2.21323453725358 | epot = -23.2617539322798 | etot = -19.5191711776588 -756000 ekin = 2.10421856984007 | erot = 2.40302151559052 | epot = -23.1682224257729 | etot = -18.6609823403423 -757000 ekin = 2.92556811452857 | erot = 2.06915289798223 | epot = -23.1499528985793 | etot = -18.1552318860685 -758000 ekin = 2.37294922982789 | erot = 2.5136802398028 | epot = -23.0492487158129 | etot = -18.1626192461822 -759000 ekin = 2.60143135392931 | erot = 2.3965867167667 | epot = -22.9022185044006 | etot = -17.9042004337045 -760000 ekin = 3.23086795451839 | erot = 2.77070394347185 | epot = -22.8086083978769 | etot = -16.8070364998867 -761000 ekin = 3.41474520443683 | erot = 1.70182284622131 | epot = -22.7401488061481 | etot = -17.62358075549 -762000 ekin = 3.40874138334159 | erot = 2.5214687610176 | epot = -22.5273378250467 | etot = -16.5971276806875 -763000 ekin = 2.64282337808311 | erot = 1.82465845176878 | epot = -22.3886968592841 | etot = -17.9212150294322 -764000 ekin = 2.38098374928432 | erot = 2.71455514893631 | epot = -22.2306429954919 | etot = -17.1351040972713 -765000 ekin = 2.24220112607173 | erot = 1.94828018292253 | epot = -22.1222898533813 | etot = -17.931808544387 -766000 ekin = 2.50647054308507 | erot = 1.96127686565097 | epot = -21.9854922894721 | etot = -17.5177448807361 -767000 ekin = 2.34036216095461 | erot = 2.64592662901366 | epot = -21.9049052626546 | etot = -16.9186164726863 -768000 ekin = 1.86756150924074 | erot = 2.06140692143859 | epot = -21.8871911578369 | etot = -17.9582227271576 -769000 ekin = 3.0359885140629 | erot = 2.66441888317467 | epot = -21.8245365321496 | etot = -16.124129134912 -770000 ekin = 2.42572833720737 | erot = 1.97830348673474 | epot = -21.8109221594649 | etot = -17.4068903355227 -771000 ekin = 2.20057185883112 | erot = 2.53258595631101 | epot = -21.734014677427 | etot = -17.0008568622849 -772000 ekin = 2.75017737220644 | erot = 1.98404504724256 | epot = -21.81636663385 | etot = -17.082144214401 -773000 ekin = 2.14723700449497 | erot = 2.4151160924984 | epot = -21.9575475647945 | etot = -17.3951944678011 -774000 ekin = 2.20540233527262 | erot = 1.98379632188094 | epot = -22.0437158124788 | etot = -17.8545171553253 -775000 ekin = 2.53159855409247 | erot = 2.82258836068 | epot = -22.2468791717252 | etot = -16.8926922569528 -776000 ekin = 3.15990337350763 | erot = 2.46223603653204 | epot = -22.4204095516686 | etot = -16.7982701416289 -777000 ekin = 1.91544508000443 | erot = 1.75409994742756 | epot = -22.4517072920931 | etot = -18.7821622646612 -778000 ekin = 2.94664557229421 | erot = 2.31806053358263 | epot = -22.4632053661323 | etot = -17.1984992602554 -779000 ekin = 3.10966911142499 | erot = 2.04445735728845 | epot = -22.4851293821807 | etot = -17.3310029134672 -780000 ekin = 2.85217648357475 | erot = 3.13312150331092 | epot = -22.4501336819041 | etot = -16.4648356950184 -781000 ekin = 2.36735214903647 | erot = 3.56398811585504 | epot = -22.4171223027496 | etot = -16.4857820378581 -782000 ekin = 2.32799229473909 | erot = 2.86342068433246 | epot = -22.3437898412805 | etot = -17.1523768622089 -783000 ekin = 1.86441476378237 | erot = 3.05235927245358 | epot = -22.2079503227603 | etot = -17.2911762865243 -784000 ekin = 2.05475171167698 | erot = 2.29789662368463 | epot = -22.1006582038569 | etot = -17.7480098684953 -785000 ekin = 2.03881379634772 | erot = 2.15051381788682 | epot = -22.005618673928 | etot = -17.8162910596935 -786000 ekin = 2.37521569747453 | erot = 2.3215726256904 | epot = -21.9728072887761 | etot = -17.2760189656112 -787000 ekin = 2.76687650937794 | erot = 2.23624710557919 | epot = -21.8969738615634 | etot = -16.8938502466062 -788000 ekin = 2.13321139238913 | erot = 2.25164618737296 | epot = -21.8604412147426 | etot = -17.4755836349805 -789000 ekin = 1.98219933423288 | erot = 1.98059715582116 | epot = -21.8441893392272 | etot = -17.8813928491731 -790000 ekin = 1.67847666786903 | erot = 1.42561139395642 | epot = -21.941381415519 | etot = -18.8372933536936 -791000 ekin = 2.12688741327067 | erot = 2.53203269325841 | epot = -22.0865399118969 | etot = -17.4276198053679 -792000 ekin = 1.72796321880606 | erot = 2.2244832123241 | epot = -22.1855187635199 | etot = -18.2330723323897 -793000 ekin = 3.18410749492954 | erot = 1.94059536299771 | epot = -22.376174949317 | etot = -17.2514720913897 -794000 ekin = 2.49072782508363 | erot = 3.01187609729573 | epot = -22.4316780454308 | etot = -16.9290741230515 -795000 ekin = 2.89848925116022 | erot = 3.07660091365902 | epot = -22.516587410981 | etot = -16.5414972461618 -796000 ekin = 2.32849309170709 | erot = 1.6270978552186 | epot = -22.5662306303253 | etot = -18.6106396833996 -797000 ekin = 2.20767832793875 | erot = 3.65977564474856 | epot = -22.5353770098516 | etot = -16.6679230371643 -798000 ekin = 2.12139192163862 | erot = 2.94416204631962 | epot = -22.5360308536834 | etot = -17.4704768857252 -799000 ekin = 2.48451269034698 | erot = 2.74154593614504 | epot = -22.494267326257 | etot = -17.2682086997649 -800000 ekin = 2.17522042927318 | erot = 2.96479501864727 | epot = -22.3819091222467 | etot = -17.2418936743262 -801000 ekin = 2.54693512060825 | erot = 2.74965360561443 | epot = -22.3009510878525 | etot = -17.0043623616298 -802000 ekin = 3.02825099239106 | erot = 2.89157545074505 | epot = -22.2025114687808 | etot = -16.2826850256447 -803000 ekin = 2.21045049668896 | erot = 2.51592023666071 | epot = -22.1070021550193 | etot = -17.3806314216696 -804000 ekin = 2.91059686956699 | erot = 1.58302660030682 | epot = -22.0840071528844 | etot = -17.5903836830106 -805000 ekin = 2.67761934757361 | erot = 3.069720635569 | epot = -22.0793582077661 | etot = -16.3320182246235 -806000 ekin = 2.75980762879093 | erot = 2.21769953441322 | epot = -22.0550306032646 | etot = -17.0775234400604 -807000 ekin = 2.11045367551317 | erot = 2.83920073001796 | epot = -22.1075830544478 | etot = -17.1579286489166 -808000 ekin = 1.84392497979905 | erot = 2.29793977175805 | epot = -22.0755335570562 | etot = -17.9336688054991 -809000 ekin = 1.93171637862302 | erot = 1.94017253306181 | epot = -22.066928232689 | etot = -18.1950393210042 -810000 ekin = 1.97775979279028 | erot = 2.64727266267807 | epot = -22.1021133187779 | etot = -17.4770808633095 -811000 ekin = 2.24172070509422 | erot = 1.75504577244544 | epot = -22.10631129566 | etot = -18.1095448181203 -812000 ekin = 2.49050572737176 | erot = 2.33987726148268 | epot = -22.1241871902584 | etot = -17.2938042014039 -813000 ekin = 3.01752815471752 | erot = 2.24002143249121 | epot = -22.116807731716 | etot = -16.8592581445073 -814000 ekin = 2.86042310191006 | erot = 2.24117753130618 | epot = -22.1084772529156 | etot = -17.0068766196994 -815000 ekin = 2.57504250841232 | erot = 2.76211504651086 | epot = -21.9950814575784 | etot = -16.6579239026553 -816000 ekin = 2.19959057655107 | erot = 2.59196925340511 | epot = -22.0843867435381 | etot = -17.2928269135819 -817000 ekin = 1.75064707017923 | erot = 2.66165145686199 | epot = -22.3740333039416 | etot = -17.9617347769004 -818000 ekin = 2.24812511950443 | erot = 2.59024748858361 | epot = -22.5610880116939 | etot = -17.7227154036058 -819000 ekin = 2.12541380503016 | erot = 2.59620266733555 | epot = -22.5607008655742 | etot = -17.8390843932085 -820000 ekin = 1.93417567600985 | erot = 2.29084462576239 | epot = -22.4839831235988 | etot = -18.2589628218266 -821000 ekin = 2.11386397679857 | erot = 2.38686655216469 | epot = -22.4763699831312 | etot = -17.9756394541679 -822000 ekin = 2.26135055598867 | erot = 2.12059051821569 | epot = -22.3710179425218 | etot = -17.9890768683174 -823000 ekin = 2.31556864207286 | erot = 2.6035211830053 | epot = -22.4989638717259 | etot = -17.5798740466477 -824000 ekin = 1.73693100722561 | erot = 1.5184813450247 | epot = -22.6200824712308 | etot = -19.3646701189804 -825000 ekin = 1.63610511008412 | erot = 1.97729484626479 | epot = -22.6198519859023 | etot = -19.0064520295534 -826000 ekin = 2.00840924391468 | erot = 2.17848588495273 | epot = -22.5466792805529 | etot = -18.3597841516855 -827000 ekin = 2.18458017496693 | erot = 2.44710855022062 | epot = -22.4005998352674 | etot = -17.7689111100799 -828000 ekin = 1.91041039942926 | erot = 2.73448484092911 | epot = -22.3948766951947 | etot = -17.7499814548364 -829000 ekin = 2.07229941615034 | erot = 2.97135025315954 | epot = -22.434811171522 | etot = -17.3911615022121 -830000 ekin = 1.99297455547369 | erot = 2.1576588802149 | epot = -22.4844092218597 | etot = -18.3337757861711 -831000 ekin = 2.33243999410257 | erot = 2.3763340012213 | epot = -22.5757447430944 | etot = -17.8669707477706 -832000 ekin = 2.02856837401183 | erot = 1.94730405553331 | epot = -22.6670646845116 | etot = -18.6911922549664 -833000 ekin = 2.28622313757813 | erot = 2.15106977742247 | epot = -22.7567197431772 | etot = -18.3194268281767 -834000 ekin = 2.1210378005443 | erot = 1.51167848496405 | epot = -22.7736040844494 | etot = -19.140887798941 -835000 ekin = 2.88530231894867 | erot = 2.74026724638582 | epot = -22.8585460390106 | etot = -17.2329764736761 -836000 ekin = 3.3206881354596 | erot = 2.42232340907521 | epot = -22.8959173733727 | etot = -17.1529058288379 -837000 ekin = 2.74147966492743 | erot = 2.32128866347136 | epot = -22.890688089557 | etot = -17.8279197611582 -838000 ekin = 3.13304582679089 | erot = 3.19831100603569 | epot = -22.9167021580119 | etot = -16.5853453251853 -839000 ekin = 2.73524310738819 | erot = 2.61098784970539 | epot = -22.8499775738039 | etot = -17.5037466167103 -840000 ekin = 2.9714125620732 | erot = 1.43156525093809 | epot = -22.7764096370098 | etot = -18.3734318239986 -841000 ekin = 2.95720011963303 | erot = 2.67281496410328 | epot = -22.74090696109 | etot = -17.1108918773537 -842000 ekin = 2.17222072547984 | erot = 2.30477888514471 | epot = -22.7382739265758 | etot = -18.2612743159512 -843000 ekin = 2.83293093637601 | erot = 2.04166092897363 | epot = -22.7426999769084 | etot = -17.8681081115587 -844000 ekin = 2.95939838423659 | erot = 1.50200392453934 | epot = -22.7837663105733 | etot = -18.3223640017974 -845000 ekin = 3.16075268425023 | erot = 2.28217181916471 | epot = -22.7914034530237 | etot = -17.3484789496088 -846000 ekin = 3.33989324329164 | erot = 2.53602590130801 | epot = -22.7943672716087 | etot = -16.918448127009 -847000 ekin = 2.14144439713513 | erot = 2.75036646754355 | epot = -22.7256188129676 | etot = -17.8338079482889 -848000 ekin = 2.4890850279473 | erot = 2.8187435102158 | epot = -22.5834530760368 | etot = -17.2756245378737 -849000 ekin = 1.98022709854769 | erot = 2.56921409657545 | epot = -22.4587362353358 | etot = -17.9092950402127 -850000 ekin = 2.04755793529054 | erot = 1.80627828287466 | epot = -22.4428719719836 | etot = -18.5890357538184 -851000 ekin = 2.09705201250659 | erot = 1.85768714478959 | epot = -22.4344321769461 | etot = -18.4796930196499 -852000 ekin = 1.70813063193921 | erot = 1.42387240689476 | epot = -22.3764716053444 | etot = -19.2444685665104 -853000 ekin = 2.00143066511545 | erot = 3.04689486443609 | epot = -22.4103416022683 | etot = -17.3620160727168 -854000 ekin = 3.02152778379787 | erot = 2.22991487666191 | epot = -22.4965524184488 | etot = -17.245109757989 -855000 ekin = 2.19608144065262 | erot = 2.83673950685791 | epot = -22.5084193524114 | etot = -17.4755984049009 -856000 ekin = 2.44947147813647 | erot = 1.52884725004682 | epot = -22.4898702614234 | etot = -18.5115515332401 -857000 ekin = 2.53343898625603 | erot = 2.80401080702751 | epot = -22.3987166021506 | etot = -17.0612668088671 -858000 ekin = 2.20262532647404 | erot = 2.8247792069788 | epot = -22.32281615969 | etot = -17.2954116262372 -859000 ekin = 2.30654937158539 | erot = 2.3142791907112 | epot = -22.299521643743 | etot = -17.6786930814465 -860000 ekin = 1.99694898863895 | erot = 1.95028208283263 | epot = -22.3157281013929 | etot = -18.3684970299213 -861000 ekin = 2.69685720778408 | erot = 2.24433692481965 | epot = -22.308684325649 | etot = -17.3674901930452 -862000 ekin = 2.86020772842225 | erot = 2.41684858841926 | epot = -22.2875015844601 | etot = -17.0104452676185 -863000 ekin = 2.60869027955544 | erot = 3.3557429503542 | epot = -22.2313715051009 | etot = -16.2669382751913 -864000 ekin = 2.90975887606274 | erot = 2.2974711132053 | epot = -22.1986440077119 | etot = -16.9914140184438 -865000 ekin = 1.92891179669311 | erot = 2.15731612388581 | epot = -22.0985432850411 | etot = -18.0123153644622 -866000 ekin = 1.96989214479485 | erot = 1.64765168847281 | epot = -21.9980789481616 | etot = -18.380535114894 -867000 ekin = 1.75216909752833 | erot = 3.37220321936945 | epot = -21.9061232860984 | etot = -16.7817509692006 -868000 ekin = 1.82818520973491 | erot = 2.7944755326823 | epot = -21.9402402920261 | etot = -17.3175795496089 -869000 ekin = 2.38093069905802 | erot = 2.38587933771677 | epot = -22.0330352056336 | etot = -17.2662251688588 -870000 ekin = 1.91335987165478 | erot = 3.22058308836822 | epot = -22.0373177401659 | etot = -16.9033747801429 -871000 ekin = 3.11763256544808 | erot = 2.95338164044026 | epot = -21.9586151724215 | etot = -15.8876009665332 -872000 ekin = 2.97998053337799 | erot = 1.38590039691319 | epot = -21.8388889958107 | etot = -17.4730080655196 -873000 ekin = 2.75061349369619 | erot = 2.24383438401082 | epot = -21.7622218517437 | etot = -16.7677739740367 -874000 ekin = 2.42548927431534 | erot = 2.11161436912391 | epot = -21.6727594489541 | etot = -17.1356558055149 -875000 ekin = 2.99029100585666 | erot = 2.74121308538956 | epot = -21.668258099805 | etot = -15.9367540085588 -876000 ekin = 2.13274848736646 | erot = 2.23319212644067 | epot = -21.6688484321843 | etot = -17.3029078183771 -877000 ekin = 1.83070881561166 | erot = 1.60104159742216 | epot = -21.6264522455532 | etot = -18.1947018325194 -878000 ekin = 2.01997766473212 | erot = 2.72068834038241 | epot = -21.6321722158884 | etot = -16.8915062107738 -879000 ekin = 1.43444304741827 | erot = 2.17422518419202 | epot = -21.5502499158235 | etot = -17.9415816842133 -880000 ekin = 2.09181756708376 | erot = 2.57774127759727 | epot = -21.4848386835567 | etot = -16.8152798388756 -881000 ekin = 1.54082374125037 | erot = 1.98591349326851 | epot = -21.5198561888166 | etot = -17.9931189542977 -882000 ekin = 2.20620241649865 | erot = 2.64810056429068 | epot = -21.6150536961203 | etot = -16.760750715331 -883000 ekin = 2.22399673754477 | erot = 2.23146179436218 | epot = -21.6815278641887 | etot = -17.2260693322817 -884000 ekin = 2.78668830976032 | erot = 2.10129457858281 | epot = -21.7273526514588 | etot = -16.8393697631157 -885000 ekin = 1.92363533860365 | erot = 1.77572806384608 | epot = -21.7697843629897 | etot = -18.07042096054 -886000 ekin = 1.99837400493853 | erot = 3.11594950867252 | epot = -21.7880717591464 | etot = -16.6737482455354 -887000 ekin = 1.98879357041702 | erot = 2.81587324889294 | epot = -21.7924289081933 | etot = -16.9877620888833 -888000 ekin = 1.92038081253069 | erot = 2.32529355289366 | epot = -21.8608148998544 | etot = -17.61514053443 -889000 ekin = 1.88062951921479 | erot = 2.46119685782947 | epot = -21.9507114977877 | etot = -17.6088851207434 -890000 ekin = 1.86004220539177 | erot = 2.25705599329311 | epot = -22.0524916675628 | etot = -17.935393468878 -891000 ekin = 2.60383186011201 | erot = 2.35330732153708 | epot = -22.1901610904928 | etot = -17.2330219088437 -892000 ekin = 2.68681495848524 | erot = 2.69191866418566 | epot = -22.2914319616012 | etot = -16.9126983389303 -893000 ekin = 2.1736025604619 | erot = 2.9855340631332 | epot = -22.2913989289332 | etot = -17.1322623053381 -894000 ekin = 2.52599407841049 | erot = 2.45860683847711 | epot = -22.2814390199637 | etot = -17.2968381030761 -895000 ekin = 2.51960337440812 | erot = 2.45850851261114 | epot = -22.3091317035431 | etot = -17.3310198165238 -896000 ekin = 1.83967907235416 | erot = 2.78765565400226 | epot = -22.2817324681859 | etot = -17.6543977418295 -897000 ekin = 2.36174473729441 | erot = 2.02088352475316 | epot = -22.224489906849 | etot = -17.8418616448014 -898000 ekin = 2.11473348088257 | erot = 1.90142069141409 | epot = -22.1399662163227 | etot = -18.123812044026 -899000 ekin = 2.62624378038804 | erot = 2.33607099930376 | epot = -22.0408432520367 | etot = -17.0785284723449 -900000 ekin = 2.11340838535732 | erot = 2.28923228114128 | epot = -22.0429025506397 | etot = -17.6402618841411 -901000 ekin = 1.91566215184365 | erot = 1.81440527703791 | epot = -22.0776473770081 | etot = -18.3475799481266 -902000 ekin = 2.56900020102358 | erot = 2.49857156191872 | epot = -22.0064871081721 | etot = -16.9389153452298 -903000 ekin = 1.85775254721542 | erot = 2.1749013676366 | epot = -21.9440711401438 | etot = -17.9114172252918 -904000 ekin = 1.86494867419599 | erot = 2.32873664886262 | epot = -21.8931245107356 | etot = -17.699439187677 -905000 ekin = 2.31980147940844 | erot = 2.14361807880238 | epot = -21.8243901028494 | etot = -17.3609705446386 -906000 ekin = 2.49848643102806 | erot = 2.24843917975751 | epot = -21.8343535689989 | etot = -17.0874279582134 -907000 ekin = 4.2050438363463 | erot = 2.50213014445972 | epot = -21.9270462870553 | etot = -15.2198723062493 -908000 ekin = 3.27389112705028 | erot = 2.1139773414904 | epot = -22.0852225119256 | etot = -16.697354043385 -909000 ekin = 2.63126952270321 | erot = 1.92588883864824 | epot = -22.2068298128194 | etot = -17.6496714514679 -910000 ekin = 2.59246919961188 | erot = 2.91531362022026 | epot = -22.3084480522696 | etot = -16.8006652324374 -911000 ekin = 2.58543295146612 | erot = 4.35272230096969 | epot = -22.3704507138015 | etot = -15.4322954613657 -912000 ekin = 3.05790216539308 | erot = 3.70627231984866 | epot = -22.3924902932765 | etot = -15.6283158080348 -913000 ekin = 2.8218125632957 | erot = 2.17270533888476 | epot = -22.3593081791921 | etot = -17.3647902770116 -914000 ekin = 2.15501507966989 | erot = 1.21668054480496 | epot = -22.2678655505214 | etot = -18.8961699260465 -915000 ekin = 1.59606056510822 | erot = 2.96269780066395 | epot = -22.1741171670757 | etot = -17.6153588013035 -916000 ekin = 2.59112654939107 | erot = 3.74925924318435 | epot = -22.2377409731947 | etot = -15.8973551806193 -917000 ekin = 3.0493203689855 | erot = 2.87183972423686 | epot = -22.2632355232676 | etot = -16.3420754300453 -918000 ekin = 2.92189281092746 | erot = 2.63335972566601 | epot = -22.258652580422 | etot = -16.7034000438285 -919000 ekin = 3.21078719192946 | erot = 2.75946068538008 | epot = -22.2355180140143 | etot = -16.2652701367047 -920000 ekin = 2.28586788874951 | erot = 2.37332627126475 | epot = -22.2034083137746 | etot = -17.5442141537604 -921000 ekin = 2.38962080413001 | erot = 2.43664225646834 | epot = -22.185112667546 | etot = -17.3588496069477 -922000 ekin = 2.30442218252457 | erot = 2.41447890834928 | epot = -22.1365633702844 | etot = -17.4176622794105 -923000 ekin = 2.49327560684184 | erot = 2.66692243519056 | epot = -22.1215324922228 | etot = -16.9613344501904 -924000 ekin = 1.53749943917136 | erot = 2.96826475564971 | epot = -22.089501289138 | etot = -17.5837370943169 -925000 ekin = 1.85839296627404 | erot = 1.9630089146505 | epot = -22.0261958798282 | etot = -18.2047939989037 -926000 ekin = 1.36443105914384 | erot = 2.1171794932878 | epot = -22.0105979668103 | etot = -18.5289874143787 -927000 ekin = 2.55078266090621 | erot = 2.08770331246949 | epot = -22.0297469966776 | etot = -17.3912610233019 -928000 ekin = 2.08687332975665 | erot = 2.73936175158276 | epot = -22.0655836352027 | etot = -17.2393485538632 -929000 ekin = 1.85843511626749 | erot = 1.85229477009255 | epot = -22.1619339279447 | etot = -18.4512040415846 -930000 ekin = 1.98312827530234 | erot = 2.11072782324153 | epot = -22.148404885232 | etot = -18.0545487866881 -931000 ekin = 2.44404037283661 | erot = 1.87098036863263 | epot = -22.045526835582 | etot = -17.7305060941127 -932000 ekin = 2.74511224055608 | erot = 2.34428828961869 | epot = -22.0610647907213 | etot = -16.9716642605465 -933000 ekin = 3.03612209957546 | erot = 2.51767378960712 | epot = -21.9625270494876 | etot = -16.408731160305 -934000 ekin = 2.94656694542126 | erot = 2.48807264081831 | epot = -21.861447502856 | etot = -16.4268079166164 -935000 ekin = 2.79277367387165 | erot = 2.14683969082916 | epot = -21.8273290607191 | etot = -16.8877156960183 -936000 ekin = 2.97180432771798 | erot = 2.07585566252292 | epot = -21.8285478379897 | etot = -16.7808878477488 -937000 ekin = 3.04681426679838 | erot = 2.34693750557886 | epot = -21.7540345943249 | etot = -16.3602828219476 -938000 ekin = 2.98753455096208 | erot = 2.36094629864927 | epot = -21.669921719463 | etot = -16.3214408698516 -939000 ekin = 2.5815116272011 | erot = 2.28540517977038 | epot = -21.6416685543635 | etot = -16.774751747392 -940000 ekin = 2.64452600431539 | erot = 2.76444843839484 | epot = -21.5519696309499 | etot = -16.1429951882397 -941000 ekin = 2.27120802986608 | erot = 2.60471729926444 | epot = -21.4614510918559 | etot = -16.5855257627254 -942000 ekin = 1.87372160611096 | erot = 2.80847310756688 | epot = -21.3628386356793 | etot = -16.6806439220015 -943000 ekin = 2.47141066321096 | erot = 2.33779379941891 | epot = -21.363618035927 | etot = -16.5544135732972 -944000 ekin = 2.13394139147127 | erot = 1.92151741713676 | epot = -21.3251241131195 | etot = -17.2696653045115 -945000 ekin = 2.55903591944463 | erot = 2.20641057626278 | epot = -21.3689027899513 | etot = -16.6034562942439 -946000 ekin = 2.36057887627665 | erot = 2.87562563403205 | epot = -21.3642844166796 | etot = -16.1280799063709 -947000 ekin = 2.06640868745843 | erot = 1.87129277041451 | epot = -21.361667299016 | etot = -17.423965841143 -948000 ekin = 1.84829667860633 | erot = 1.37748341041347 | epot = -21.4043264064643 | etot = -18.1785463174445 -949000 ekin = 1.76269317475673 | erot = 2.31704682699621 | epot = -21.4241969105702 | etot = -17.3444569088173 -950000 ekin = 1.71597192365278 | erot = 2.24238818867182 | epot = -21.4137382130783 | etot = -17.4553781007537 -951000 ekin = 1.97740353609815 | erot = 2.3235775919709 | epot = -21.4747894560116 | etot = -17.1738083279426 -952000 ekin = 2.93972459147619 | erot = 2.7264267649198 | epot = -21.5184934927053 | etot = -15.8523421363093 -953000 ekin = 2.94580120867627 | erot = 2.3885651029181 | epot = -21.5142900777068 | etot = -16.1799237661125 -954000 ekin = 3.09124464575104 | erot = 1.98545519388255 | epot = -21.4222393978574 | etot = -16.3455395582238 -955000 ekin = 3.57635828612239 | erot = 2.07344149873787 | epot = -21.305651356955 | etot = -15.6558515720948 -956000 ekin = 2.96200909778686 | erot = 3.68175912378205 | epot = -21.157040218368 | etot = -14.5132719967991 -957000 ekin = 2.9934348145403 | erot = 2.66416955872305 | epot = -20.9768827662772 | etot = -15.3192783930138 -958000 ekin = 2.66519549819093 | erot = 2.94296814880089 | epot = -20.7784507090075 | etot = -15.1702870620156 -959000 ekin = 1.92857560759304 | erot = 2.44736991936641 | epot = -20.7023816787833 | etot = -16.3264361518238 -960000 ekin = 1.49450803358212 | erot = 3.13585226423836 | epot = -20.7120144681538 | etot = -16.0816541703333 -961000 ekin = 1.95028642422207 | erot = 2.08600574936454 | epot = -20.7117469089035 | etot = -16.6754547353169 -962000 ekin = 2.02517481382584 | erot = 1.89936067129151 | epot = -20.7773964294488 | etot = -16.8528609443315 -963000 ekin = 1.81867025887159 | erot = 2.47411932412279 | epot = -20.8447579345839 | etot = -16.5519683515895 -964000 ekin = 2.82276496790393 | erot = 2.43516586616438 | epot = -20.903922975909 | etot = -15.6459921418407 -965000 ekin = 2.55108655192476 | erot = 2.29878304255031 | epot = -20.9718606663833 | etot = -16.1219910719082 -966000 ekin = 2.12011039995763 | erot = 2.28469402857006 | epot = -21.0607245253139 | etot = -16.6559200967862 -967000 ekin = 1.58231560351932 | erot = 3.55759001366773 | epot = -21.1226021191741 | etot = -15.982696501987 -968000 ekin = 1.95012246688271 | erot = 2.37521006238884 | epot = -21.1148898184345 | etot = -16.7895572891629 -969000 ekin = 2.19259023755588 | erot = 2.45911390116742 | epot = -21.0842607955297 | etot = -16.4325566568064 -970000 ekin = 1.87048303167747 | erot = 2.95645393326851 | epot = -21.0144108895372 | etot = -16.1874739245912 -971000 ekin = 1.95012477829126 | erot = 3.07172629604582 | epot = -20.9855553455518 | etot = -15.9637042712147 -972000 ekin = 1.93195517458082 | erot = 2.56231250597297 | epot = -20.9701698825601 | etot = -16.4759022020063 -973000 ekin = 2.21533845309822 | erot = 2.92680845685574 | epot = -20.9736039159605 | etot = -15.8314570060066 -974000 ekin = 2.53783851969245 | erot = 2.68951943774763 | epot = -20.9250705852868 | etot = -15.6977126278467 -975000 ekin = 3.38321286183975 | erot = 2.3388937245268 | epot = -20.8976133286568 | etot = -15.1755067422903 -976000 ekin = 2.84642762041042 | erot = 3.11577005329036 | epot = -20.8920682645474 | etot = -14.9298705908466 -977000 ekin = 2.71729658676912 | erot = 2.5084228279903 | epot = -20.8689607108408 | etot = -15.6432412960814 -978000 ekin = 1.79445054300148 | erot = 2.07364967100101 | epot = -20.8420722556647 | etot = -16.9739720416622 -979000 ekin = 1.87118885565252 | erot = 2.21929236157499 | epot = -20.774871884918 | etot = -16.6843906676905 -980000 ekin = 1.92328692629603 | erot = 1.58075146493092 | epot = -20.7450294842512 | etot = -17.2409910930243 -981000 ekin = 1.54380792071409 | erot = 2.05666691648826 | epot = -20.8055779656275 | etot = -17.2051031284252 -982000 ekin = 1.84105485043124 | erot = 1.96437622792518 | epot = -20.9115808211874 | etot = -17.106149742831 -983000 ekin = 2.72418502177569 | erot = 1.79041563369968 | epot = -20.9354223873698 | etot = -16.4208217318945 -984000 ekin = 3.62593140681741 | erot = 2.63360144654398 | epot = -21.0391820820805 | etot = -14.7796492287191 -985000 ekin = 2.94852683897972 | erot = 2.17122506831154 | epot = -21.2107161619268 | etot = -16.0909642546355 -986000 ekin = 2.8730990470673 | erot = 2.17803097743515 | epot = -21.3376467553807 | etot = -16.2865167308783 -987000 ekin = 3.37014034763591 | erot = 2.51986025997469 | epot = -21.4044213003553 | etot = -15.5144206927447 -988000 ekin = 3.46869513961502 | erot = 3.24290721199116 | epot = -21.4574897009989 | etot = -14.7458873493927 -989000 ekin = 2.84166309499202 | erot = 2.20794524768456 | epot = -21.6064619775396 | etot = -16.556853634863 -990000 ekin = 2.7961621760392 | erot = 1.83962335779988 | epot = -21.6050150594377 | etot = -16.9692295255987 -991000 ekin = 3.12373716765057 | erot = 3.19217793832918 | epot = -21.5124956370547 | etot = -15.196580531075 -992000 ekin = 3.28264042603627 | erot = 2.63437573620237 | epot = -21.3974383725657 | etot = -15.4804222103271 -993000 ekin = 3.03843938464914 | erot = 2.2245111821208 | epot = -21.3215565657891 | etot = -16.0586059990192 -994000 ekin = 3.17415651424377 | erot = 2.79358782634793 | epot = -21.2400795485327 | etot = -15.272335207941 -995000 ekin = 3.20647480868909 | erot = 1.72566862077117 | epot = -21.1373044030639 | etot = -16.2051609736037 -996000 ekin = 3.05112273650758 | erot = 3.18000206414337 | epot = -21.0953933909242 | etot = -14.8642685902733 -997000 ekin = 2.95627130723369 | erot = 3.15916576717626 | epot = -21.0582569249376 | etot = -14.9428198505277 -998000 ekin = 3.0660899917632 | erot = 1.97683196852806 | epot = -20.9835503180559 | etot = -15.9406283577646 -999000 ekin = 2.08921397127967 | erot = 2.76365668450607 | epot = -20.9706997536924 | etot = -16.1178290979066 -1000000 ekin = 2.117712793702 | erot = 2.14107266477967 | epot = -20.9100710796761 | etot = -16.6512856211944 - 1000000 0.094120569 -1.3660232 0.059143724 -1.1745224 -3.0717572e-05 -Loop time of 37.9247 on 1 procs for 1000000 steps with 16 atoms - -Performance: 22782.012 tau/day, 26368.069 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 27.061 | 27.061 | 27.061 | 0.0 | 71.36 -Bond | 0.98271 | 0.98271 | 0.98271 | 0.0 | 2.59 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.2053 | 0.2053 | 0.2053 | 0.0 | 0.54 -Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00 -Modify | 9.3814 | 9.3814 | 9.3814 | 0.0 | 24.74 -Other | | 0.2939 | | | 0.77 - -Nlocal: 16.0 ave 16.0 max 16.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 103.0 ave 103.0 max 103.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 103 -Ave neighs/atom = 6.4375 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:37 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 deleted file mode 100644 index 6639b696ed..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 +++ /dev/null @@ -1,1184 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA2 bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA2 pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274048 - ghost atom cutoff = 2.6274048 - binsize = 1.3137024, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -24.419271289937 | etot = -24.419271289937 -Per MPI rank memory allocation (min/avg/max) = 8.028 | 8.085 | 8.143 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05 -1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698 -2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481 -3000 ekin = 3.26433550542939 | erot = 2.76107866472087 | epot = -24.2947953202752 | etot = -18.269381150125 -4000 ekin = 1.9203212531997 | erot = 2.133394384253 | epot = -24.234098584123 | etot = -20.1803829466703 -5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963 -6000 ekin = 2.18974627635306 | erot = 1.73271671162436 | epot = -24.1096616118305 | etot = -20.1871986238531 -7000 ekin = 2.65472853187395 | erot = 1.73258720631297 | epot = -24.0561118130561 | etot = -19.6687960748691 -8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058 -9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658 -10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535 -11000 ekin = 2.03264234985168 | erot = 1.68707706801736 | epot = -23.7396221351636 | etot = -20.0199027172945 -12000 ekin = 2.66329111303325 | erot = 2.49804687909781 | epot = -23.7366995564469 | etot = -18.5753615643158 -13000 ekin = 1.89677055811531 | erot = 2.34624821263612 | epot = -23.6591067615901 | etot = -19.4160879908387 -14000 ekin = 1.91279445145792 | erot = 2.13129118502405 | epot = -23.6468743458148 | etot = -19.6027887093328 -15000 ekin = 2.41876331112169 | erot = 2.07362128417238 | epot = -23.5767792498568 | etot = -19.0843946545628 -16000 ekin = 2.76615310647131 | erot = 1.19495009524763 | epot = -23.4862363509196 | etot = -19.5251331492006 -17000 ekin = 2.45632569069911 | erot = 2.37627186077148 | epot = -23.500787861849 | etot = -18.6681903103784 -18000 ekin = 2.18348858414473 | erot = 2.46933014500077 | epot = -23.5223047738331 | etot = -18.8694860446876 -19000 ekin = 2.2074746303434 | erot = 2.45349372324724 | epot = -23.4618353655003 | etot = -18.8008670119096 -20000 ekin = 2.06964129991908 | erot = 1.80832666230414 | epot = -23.4930879797962 | etot = -19.615120017573 -21000 ekin = 2.26572194434983 | erot = 2.76680470094409 | epot = -23.5023070260553 | etot = -18.4697803807614 -22000 ekin = 2.69295306575102 | erot = 1.86984875574017 | epot = -23.4463493063166 | etot = -18.8835474848254 -23000 ekin = 1.99930153068661 | erot = 2.27735339437466 | epot = -23.3493214662276 | etot = -19.0726665411663 -24000 ekin = 2.20679650752062 | erot = 2.98147599881873 | epot = -23.273517698415 | etot = -18.0852451920757 -25000 ekin = 2.28085541692287 | erot = 2.99165466281124 | epot = -23.2072100929465 | etot = -17.9347000132124 -26000 ekin = 1.9530124305314 | erot = 2.81680126246586 | epot = -23.0636678500934 | etot = -18.2938541570962 -27000 ekin = 1.96948983508855 | erot = 2.69266617300682 | epot = -22.9870601707012 | etot = -18.3249041626058 -28000 ekin = 2.02061868464074 | erot = 2.37038530969117 | epot = -22.9383598315964 | etot = -18.5473558372645 -29000 ekin = 2.51387846128098 | erot = 2.0265039132053 | epot = -22.888959880923 | etot = -18.3485775064367 -30000 ekin = 1.95889729807242 | erot = 2.1170713545074 | epot = -22.7896312662562 | etot = -18.7136626136764 -31000 ekin = 1.81775203419098 | erot = 2.326796842935 | epot = -22.7561124537192 | etot = -18.6115635765932 -32000 ekin = 1.87947265787065 | erot = 2.0009346769358 | epot = -22.8533570528062 | etot = -18.9729497179997 -33000 ekin = 1.77435214491107 | erot = 1.82826131933673 | epot = -22.8632647352802 | etot = -19.2606512710324 -34000 ekin = 2.27098719472917 | erot = 3.11275511420439 | epot = -22.9527052663856 | etot = -17.5689629574521 -35000 ekin = 2.88921171289845 | erot = 1.82538384737236 | epot = -23.0316569923336 | etot = -18.3170614320628 -36000 ekin = 2.40471013682393 | erot = 2.59817148723643 | epot = -23.1277697887139 | etot = -18.1248881646536 -37000 ekin = 2.23499312928139 | erot = 1.74662115184433 | epot = -23.1542126827759 | etot = -19.1725984016501 -38000 ekin = 2.13875747252781 | erot = 3.07733571118648 | epot = -23.0916051545794 | etot = -17.8755119708651 -39000 ekin = 2.08901196654187 | erot = 2.81975762995374 | epot = -23.0796147800379 | etot = -18.1708451835423 -40000 ekin = 2.95155149177527 | erot = 2.19459039829335 | epot = -23.141500571363 | etot = -17.9953586812944 -41000 ekin = 2.49235596566196 | erot = 3.45295839915509 | epot = -23.115526015811 | etot = -17.1702116509939 -42000 ekin = 2.58401591894786 | erot = 3.0976076851145 | epot = -23.0181097727229 | etot = -17.3364861686605 -43000 ekin = 2.17593293893362 | erot = 2.65403748718844 | epot = -22.8962504257564 | etot = -18.0662799996343 -44000 ekin = 2.34068034665607 | erot = 3.294882771572 | epot = -22.8143844644656 | etot = -17.1788213462375 -45000 ekin = 1.87200112415306 | erot = 3.49863859200052 | epot = -22.6989374637074 | etot = -17.3282977475538 -46000 ekin = 2.60943921333194 | erot = 2.23170007842725 | epot = -22.5884035122493 | etot = -17.7472642204901 -47000 ekin = 1.89594756436345 | erot = 3.4002587629387 | epot = -22.4938472923117 | etot = -17.1976409650096 -48000 ekin = 2.49339593279701 | erot = 2.5104785556399 | epot = -22.5372062210456 | etot = -17.5333317326087 -49000 ekin = 3.2041407554348 | erot = 2.17669016194865 | epot = -22.5688036423094 | etot = -17.1879727249259 -50000 ekin = 2.93024070185999 | erot = 1.55416219951966 | epot = -22.6087903765995 | etot = -18.1243874752199 -51000 ekin = 2.8585759501124 | erot = 2.69193261792584 | epot = -22.6228353253324 | etot = -17.0723267572942 -52000 ekin = 2.3079418078843 | erot = 1.84260643306147 | epot = -22.6230480697441 | etot = -18.4724998287983 -53000 ekin = 3.1803685919024 | erot = 1.67451273370508 | epot = -22.6834814309773 | etot = -17.8286001053698 -54000 ekin = 2.6151376953128 | erot = 1.96091197875017 | epot = -22.7484551927013 | etot = -18.1724055186384 -55000 ekin = 3.1639577845443 | erot = 2.86286196426802 | epot = -22.7917236196438 | etot = -16.7649038708315 -56000 ekin = 2.52994034294643 | erot = 3.05544364249365 | epot = -22.7651844773103 | etot = -17.1798004918702 -57000 ekin = 2.40889871674401 | erot = 3.4525690879514 | epot = -22.7113139496974 | etot = -16.849846145002 -58000 ekin = 1.9363727739706 | erot = 2.52762778976703 | epot = -22.6468058892224 | etot = -18.1828053254848 -59000 ekin = 2.55505415922972 | erot = 3.52385701835933 | epot = -22.6037443858311 | etot = -16.5248332082421 -60000 ekin = 2.80945252332612 | erot = 2.88606183204889 | epot = -22.5227874119079 | etot = -16.8272730565329 -61000 ekin = 2.69750183117722 | erot = 2.55373633146433 | epot = -22.4306469225965 | etot = -17.1794087599549 -62000 ekin = 2.74494354639602 | erot = 2.23074517653766 | epot = -22.3675792436719 | etot = -17.3918905207383 -63000 ekin = 2.66335513293138 | erot = 2.46159865380861 | epot = -22.3527707145482 | etot = -17.2278169278082 -64000 ekin = 2.12832019835147 | erot = 2.78772793164811 | epot = -22.3048690294469 | etot = -17.3888208994473 -65000 ekin = 1.88429801911228 | erot = 2.70719871478483 | epot = -22.3342736701749 | etot = -17.7427769362778 -66000 ekin = 2.77106091929282 | erot = 1.94126620531915 | epot = -22.338257942783 | etot = -17.625930818171 -67000 ekin = 2.53561386235746 | erot = 2.45901054739082 | epot = -22.3780784743028 | etot = -17.3834540645545 -68000 ekin = 2.9678648663671 | erot = 1.95502711706149 | epot = -22.4420512915713 | etot = -17.5191593081427 -69000 ekin = 2.61501630036274 | erot = 2.2429513448561 | epot = -22.3607835407198 | etot = -17.502815895501 -70000 ekin = 2.41492598760663 | erot = 2.80885610657203 | epot = -22.2905725083407 | etot = -17.066790414162 -71000 ekin = 2.65062529541957 | erot = 2.88868401392431 | epot = -22.2951070257787 | etot = -16.7557977164349 -72000 ekin = 2.93273744051009 | erot = 2.82552508252073 | epot = -22.4016757930526 | etot = -16.6434132700218 -73000 ekin = 2.18922665452238 | erot = 3.03559183860538 | epot = -22.4509770394845 | etot = -17.2261585463568 -74000 ekin = 2.16074843540078 | erot = 2.83668185121384 | epot = -22.4374624006144 | etot = -17.4400321139998 -75000 ekin = 1.52329638473031 | erot = 1.91520672578907 | epot = -22.5623153080324 | etot = -19.123812197513 -76000 ekin = 1.89250964827726 | erot = 2.83358650938892 | epot = -22.6698326202442 | etot = -17.943736462578 -77000 ekin = 2.82066630152179 | erot = 3.19779433197964 | epot = -22.7402096770599 | etot = -16.7217490435584 -78000 ekin = 2.42603824235662 | erot = 2.82319136688957 | epot = -22.7334053911689 | etot = -17.4841757819227 -79000 ekin = 2.1571494738421 | erot = 1.67722302323495 | epot = -22.7616861631187 | etot = -18.9273136660417 -80000 ekin = 2.3760789053548 | erot = 2.58372913427157 | epot = -22.6889139769023 | etot = -17.729105937276 -81000 ekin = 2.73468961033338 | erot = 1.92748741387075 | epot = -22.6388260929897 | etot = -17.9766490687856 -82000 ekin = 1.90565370838817 | erot = 1.71715050303634 | epot = -22.5547415381056 | etot = -18.9319373266811 -83000 ekin = 1.63698443616271 | erot = 1.88092293220519 | epot = -22.4792739412377 | etot = -18.9613665728698 -84000 ekin = 1.65571812906993 | erot = 2.10290321918187 | epot = -22.4031972735297 | etot = -18.6445759252779 -85000 ekin = 2.40863681830855 | erot = 2.04741059095057 | epot = -22.321221903585 | etot = -17.8651744943259 -86000 ekin = 2.50560893716733 | erot = 1.80624308622105 | epot = -22.3789065133115 | etot = -18.0670544899231 -87000 ekin = 2.13576456371582 | erot = 1.97115993651017 | epot = -22.4335511413526 | etot = -18.3266266411266 -88000 ekin = 1.74897318407528 | erot = 2.37233945814529 | epot = -22.4142028246849 | etot = -18.2928901824643 -89000 ekin = 1.85559683216276 | erot = 3.29559734355419 | epot = -22.4519626048678 | etot = -17.3007684291509 -90000 ekin = 2.22181579992018 | erot = 2.33948779846394 | epot = -22.5289826258985 | etot = -17.9676790275144 -91000 ekin = 2.40596540834273 | erot = 3.11545124680293 | epot = -22.4975752624166 | etot = -16.9761586072709 -92000 ekin = 2.6773157744569 | erot = 3.00279439655287 | epot = -22.4834827179575 | etot = -16.8033725469477 -93000 ekin = 3.0427813598525 | erot = 3.03722776158512 | epot = -22.4121259471479 | etot = -16.3321168257103 -94000 ekin = 3.20507830840023 | erot = 1.86440047317737 | epot = -22.5079833350679 | etot = -17.4385045534903 -95000 ekin = 3.4839955648833 | erot = 2.87934575393031 | epot = -22.5675869456428 | etot = -16.2042456268292 -96000 ekin = 2.8873631080951 | erot = 2.38554372248299 | epot = -22.5453635283434 | etot = -17.2724566977653 -97000 ekin = 1.92899149350272 | erot = 2.09886479790579 | epot = -22.5208382020819 | etot = -18.4929819106733 -98000 ekin = 2.21420868967462 | erot = 3.66528252896999 | epot = -22.4426781355708 | etot = -16.5631869169262 -99000 ekin = 1.98238051924192 | erot = 2.77358159119584 | epot = -22.3579409961467 | etot = -17.6019788857089 -100000 ekin = 1.80278462349605 | erot = 2.65457154995031 | epot = -22.2926900475079 | etot = -17.8353338740616 -101000 ekin = 2.14042196591663 | erot = 2.38610603254675 | epot = -22.2789462117326 | etot = -17.7524182132692 -102000 ekin = 1.54923043145398 | erot = 2.30485616158943 | epot = -22.27519637673 | etot = -18.4211097836866 -103000 ekin = 1.66618004359352 | erot = 2.82192794888076 | epot = -22.3284746660305 | etot = -17.8403666735562 -104000 ekin = 1.8840390723585 | erot = 3.37607054348826 | epot = -22.4068162519772 | etot = -17.1467066361304 -105000 ekin = 2.08970806137592 | erot = 2.01278733908098 | epot = -22.450865561264 | etot = -18.3483701608071 -106000 ekin = 2.87186619049714 | erot = 1.95029477179727 | epot = -22.46479383237 | etot = -17.6426328700756 -107000 ekin = 2.28516102595382 | erot = 1.55115426482475 | epot = -22.420448971169 | etot = -18.5841336803904 -108000 ekin = 2.4440862469061 | erot = 1.71323205815914 | epot = -22.4934628688132 | etot = -18.336144563748 -109000 ekin = 2.33376449416318 | erot = 2.92962175925398 | epot = -22.4792154966925 | etot = -17.2158292432753 -110000 ekin = 2.7815613020599 | erot = 2.36483486971455 | epot = -22.4384263756784 | etot = -17.2920302039039 -111000 ekin = 2.32472851347632 | erot = 2.09554567134105 | epot = -22.3756448055424 | etot = -17.955370620725 -112000 ekin = 2.91126509700492 | erot = 1.8278781240038 | epot = -22.2278235937356 | etot = -17.4886803727269 -113000 ekin = 2.82522334536064 | erot = 1.67936756938672 | epot = -22.2030639545535 | etot = -17.6984730398062 -114000 ekin = 3.42964629994365 | erot = 2.67287683722422 | epot = -22.3274259722919 | etot = -16.224902835124 -115000 ekin = 3.0542495603856 | erot = 1.72370226125566 | epot = -22.3530732875163 | etot = -17.575121465875 -116000 ekin = 3.19934505541307 | erot = 3.20304074939432 | epot = -22.4112422200445 | etot = -16.0088564152371 -117000 ekin = 3.03942349360439 | erot = 2.40720645224432 | epot = -22.3646852618703 | etot = -16.9180553160216 -118000 ekin = 3.21704225120818 | erot = 1.46425401673931 | epot = -22.2864155249032 | etot = -17.6051192569557 -119000 ekin = 2.33989996826882 | erot = 3.07668030790319 | epot = -22.2283862990246 | etot = -16.8118060228526 -120000 ekin = 1.93772242476321 | erot = 2.20130457047854 | epot = -22.1620199969907 | etot = -18.022993001749 -121000 ekin = 1.94013950333198 | erot = 3.08987281123525 | epot = -22.1565667857742 | etot = -17.126554471207 -122000 ekin = 1.68663003450368 | erot = 1.73461876453175 | epot = -22.2565715090021 | etot = -18.8353227099667 -123000 ekin = 1.72841976989173 | erot = 2.32750063038672 | epot = -22.3665160016578 | etot = -18.3105956013793 -124000 ekin = 2.73468934475335 | erot = 1.93313584543739 | epot = -22.378088078826 | etot = -17.7102628886353 -125000 ekin = 2.77507735763211 | erot = 1.95244582221334 | epot = -22.3863676939847 | etot = -17.6588445141392 -126000 ekin = 2.04549959008918 | erot = 1.485897173428 | epot = -22.4226219879524 | etot = -18.8912252244352 -127000 ekin = 1.86410777734907 | erot = 1.58829497411524 | epot = -22.4027380289015 | etot = -18.9503352774372 -128000 ekin = 1.63329448006254 | erot = 1.88032753965974 | epot = -22.3918784566533 | etot = -18.8782564369311 -129000 ekin = 2.51522192674941 | erot = 2.38822614049102 | epot = -22.396225517968 | etot = -17.4927774507275 -130000 ekin = 1.61191166117177 | erot = 2.81688343133435 | epot = -22.341565060394 | etot = -17.9127699678878 -131000 ekin = 2.29569747740708 | erot = 2.2886876976091 | epot = -22.2184139794107 | etot = -17.6340288043945 -132000 ekin = 2.97393694467802 | erot = 2.3613525440602 | epot = -22.1410658382525 | etot = -16.8057763495143 -133000 ekin = 2.01357676743257 | erot = 2.125828419273 | epot = -22.1312019600638 | etot = -17.9917967733582 -134000 ekin = 1.56048037412857 | erot = 2.84208065022547 | epot = -22.0682869067536 | etot = -17.6657258823995 -135000 ekin = 1.79811942319758 | erot = 2.40075843487508 | epot = -22.0853555614258 | etot = -17.8864777033532 -136000 ekin = 1.63631696233012 | erot = 2.13166656554854 | epot = -22.0879615470249 | etot = -18.3199780191463 -137000 ekin = 2.36040439516093 | erot = 1.93785486632901 | epot = -22.1234845924018 | etot = -17.8252253309118 -138000 ekin = 2.94591421775872 | erot = 1.58866111192914 | epot = -22.1783168558241 | etot = -17.6437415261363 -139000 ekin = 3.17560544591524 | erot = 2.24933296614107 | epot = -22.2966418842012 | etot = -16.8717034721449 -140000 ekin = 2.24781162873235 | erot = 3.05934139328612 | epot = -22.4681108223249 | etot = -17.1609578003064 -141000 ekin = 1.89078628042285 | erot = 3.13246933186326 | epot = -22.730922227649 | etot = -17.7076666153629 -142000 ekin = 2.51033894675651 | erot = 2.4942894309123 | epot = -22.8404165502847 | etot = -17.8357881726159 -143000 ekin = 2.40438807844298 | erot = 2.71461817456284 | epot = -22.8207220890738 | etot = -17.7017158360679 -144000 ekin = 1.9307425487964 | erot = 2.67760329085926 | epot = -22.6973757396236 | etot = -18.0890298999679 -145000 ekin = 1.82681171280412 | erot = 1.73674169257736 | epot = -22.6628534675149 | etot = -19.0993000621335 -146000 ekin = 2.42423538163981 | erot = 2.0908776294658 | epot = -22.6072904345337 | etot = -18.0921774234281 -147000 ekin = 1.44607209743073 | erot = 1.8801263906251 | epot = -22.5001275476876 | etot = -19.1739290596318 -148000 ekin = 1.9349809420382 | erot = 2.57774390934154 | epot = -22.4721664357448 | etot = -17.9594415843651 -149000 ekin = 2.02370265642699 | erot = 3.3179576458013 | epot = -22.3745153112138 | etot = -17.0328550089855 -150000 ekin = 2.48124469844233 | erot = 2.68185291250579 | epot = -22.1950329772129 | etot = -17.0319353662648 -151000 ekin = 2.76319440452884 | erot = 1.87355938382631 | epot = -21.986630645846 | etot = -17.3498768574909 -152000 ekin = 2.77453107952051 | erot = 1.77016628972892 | epot = -21.7977108098427 | etot = -17.2530134405933 -153000 ekin = 3.08827014622555 | erot = 1.80976617511255 | epot = -21.6910123469878 | etot = -16.7929760256497 -154000 ekin = 2.32051051770812 | erot = 2.18004857730092 | epot = -21.6406733490634 | etot = -17.1401142540543 -155000 ekin = 1.95766873014157 | erot = 2.67064554154836 | epot = -21.7315745360126 | etot = -17.1032602643227 -156000 ekin = 2.69830438989808 | erot = 2.24987636164771 | epot = -21.7962907570244 | etot = -16.8481100054786 -157000 ekin = 3.89340900899948 | erot = 2.73733315325155 | epot = -21.8437967078712 | etot = -15.2130545456202 -158000 ekin = 2.84737207100033 | erot = 2.70157958556583 | epot = -21.878244439129 | etot = -16.3292927825628 -159000 ekin = 3.1312088996125 | erot = 2.65375527842548 | epot = -21.8350703791794 | etot = -16.0501062011414 -160000 ekin = 2.54316260055464 | erot = 3.27950281054041 | epot = -21.8888467298127 | etot = -16.0661813187176 -161000 ekin = 2.49549109190181 | erot = 2.45028506429479 | epot = -21.8585593359585 | etot = -16.9127831797619 -162000 ekin = 3.05200272259994 | erot = 2.59164651185653 | epot = -21.8439750046483 | etot = -16.2003257701918 -163000 ekin = 3.30374280597553 | erot = 2.24193960212662 | epot = -21.8717863279577 | etot = -16.3261039198555 -164000 ekin = 3.53081155329031 | erot = 2.22419322011391 | epot = -21.8162094860939 | etot = -16.0612047126897 -165000 ekin = 2.48919804649027 | erot = 2.59105984700639 | epot = -21.7395563276218 | etot = -16.6592984341251 -166000 ekin = 2.14880495285182 | erot = 3.05770380831398 | epot = -21.6850566092694 | etot = -16.4785478481036 -167000 ekin = 2.78181890034675 | erot = 2.90402826001928 | epot = -21.5971987360122 | etot = -15.9113515756462 -168000 ekin = 1.74726050172142 | erot = 2.76898886506121 | epot = -21.490566893224 | etot = -16.9743175264414 -169000 ekin = 1.8134289785439 | erot = 2.45780601602371 | epot = -21.4680710936728 | etot = -17.1968360991052 -170000 ekin = 1.69364478039988 | erot = 2.87928997590297 | epot = -21.4668806356843 | etot = -16.8939458793814 -171000 ekin = 2.14879448642638 | erot = 1.61442218455815 | epot = -21.3172106430715 | etot = -17.553993972087 -172000 ekin = 1.68431962963431 | erot = 2.36087816720612 | epot = -21.1539793618528 | etot = -17.1087815650124 -173000 ekin = 2.05784071815669 | erot = 2.17142592689102 | epot = -21.0926393885011 | etot = -16.8633727434534 -174000 ekin = 2.49611606122761 | erot = 3.09665692560806 | epot = -20.9460348670979 | etot = -15.3532618802622 -175000 ekin = 2.61673440848865 | erot = 2.88720331620426 | epot = -20.8525764091519 | etot = -15.348638684459 -176000 ekin = 2.16190213742438 | erot = 2.672518464664 | epot = -20.8442274508468 | etot = -16.0098068487584 -177000 ekin = 2.83236394902013 | erot = 2.81489135382763 | epot = -20.925759607446 | etot = -15.2785043045983 -178000 ekin = 3.17804494293424 | erot = 1.88346790512585 | epot = -21.0677853312893 | etot = -16.0062724832292 -179000 ekin = 2.33267448424065 | erot = 2.85731052069525 | epot = -21.1181390109479 | etot = -15.928154006012 -180000 ekin = 2.39061531304011 | erot = 2.93791308776 | epot = -21.1146449531392 | etot = -15.786116552339 -181000 ekin = 2.79990361156737 | erot = 3.28891520287386 | epot = -21.0834365456108 | etot = -14.9946177311695 -182000 ekin = 3.02616507870526 | erot = 2.3341432703009 | epot = -21.0600545808659 | etot = -15.6997462318597 -183000 ekin = 2.45290144562467 | erot = 2.21141617846262 | epot = -20.911866387917 | etot = -16.2475487638297 -184000 ekin = 2.56560515060991 | erot = 2.7739810551646 | epot = -20.6989716212004 | etot = -15.3593854154259 -185000 ekin = 2.17586139274635 | erot = 1.95913868179524 | epot = -20.5985322435751 | etot = -16.4635321690335 -186000 ekin = 2.07303044902321 | erot = 3.15122816264525 | epot = -20.4965070011281 | etot = -15.2722483894597 -187000 ekin = 2.44319481307615 | erot = 1.92784212082443 | epot = -20.5124982035642 | etot = -16.1414612696636 -188000 ekin = 2.28870879542405 | erot = 2.8871121346017 | epot = -20.6323506293031 | etot = -15.4565296992773 -189000 ekin = 1.68047280237829 | erot = 3.05535775765803 | epot = -20.6378101864803 | etot = -15.901979626444 -190000 ekin = 1.97184665786397 | erot = 2.95271452778009 | epot = -20.6376534135265 | etot = -15.7130922278825 -191000 ekin = 2.30626539196432 | erot = 2.64854814117512 | epot = -20.6037323569656 | etot = -15.6489188238262 -192000 ekin = 3.54976671698926 | erot = 2.91090725702116 | epot = -20.5525508832509 | etot = -14.0918769092405 -193000 ekin = 2.63938438600422 | erot = 3.14409581682352 | epot = -20.5892132844066 | etot = -14.8057330815789 -194000 ekin = 2.67903757365037 | erot = 2.30768318132376 | epot = -20.4753987179501 | etot = -15.488677962976 -195000 ekin = 1.89257615363314 | erot = 2.64508051866103 | epot = -20.4197880125065 | etot = -15.8821313402123 -196000 ekin = 2.29151017050607 | erot = 2.32636787964875 | epot = -20.4440761857987 | etot = -15.8261981356438 -197000 ekin = 2.48344018982905 | erot = 2.5654400941963 | epot = -20.516126938087 | etot = -15.4672466540616 -198000 ekin = 2.01386156849612 | erot = 1.52779840514975 | epot = -20.537160292649 | etot = -16.9955003190031 -199000 ekin = 1.50729232131931 | erot = 2.19878124720506 | epot = -20.5584754599868 | etot = -16.8524018914625 -200000 ekin = 1.64236235330806 | erot = 2.46736341802316 | epot = -20.5387924113648 | etot = -16.4290666400336 -201000 ekin = 2.627066472214 | erot = 2.61321940355396 | epot = -20.6089911163939 | etot = -15.3687052406259 -202000 ekin = 2.3129503751722 | erot = 2.54874856259559 | epot = -20.6732219111123 | etot = -15.8115229733445 -203000 ekin = 1.63961009223968 | erot = 2.10835750593015 | epot = -20.7002051999767 | etot = -16.9522376018069 -204000 ekin = 2.0558049009161 | erot = 1.9161072834091 | epot = -20.8154459612946 | etot = -16.8435337769694 -205000 ekin = 3.04603860094189 | erot = 3.24233043438682 | epot = -20.9297600758299 | etot = -14.6413910405012 -206000 ekin = 2.56775422508359 | erot = 2.20992928465512 | epot = -21.0192669133083 | etot = -16.2415834035696 -207000 ekin = 3.46597997409567 | erot = 2.48427015330086 | epot = -21.151399026488 | etot = -15.2011488990915 -208000 ekin = 2.51159742060494 | erot = 2.22948191756652 | epot = -21.2942477400986 | etot = -16.5531684019271 -209000 ekin = 3.78908644724162 | erot = 2.17660742759513 | epot = -21.4499700336111 | etot = -15.4842761587743 -210000 ekin = 3.03133642129733 | erot = 2.21595982730352 | epot = -21.5648709610245 | etot = -16.3175747124237 -211000 ekin = 1.63075564056512 | erot = 2.12650387194819 | epot = -21.6099552204253 | etot = -17.852695707912 -212000 ekin = 2.67694215598975 | erot = 2.47186432110288 | epot = -21.8481434074352 | etot = -16.6993369303425 -213000 ekin = 2.70688282449408 | erot = 1.96666534072978 | epot = -22.1170796448084 | etot = -17.4435314795845 -214000 ekin = 2.88993887341392 | erot = 3.16392577542175 | epot = -22.1689844550676 | etot = -16.1151198062319 -215000 ekin = 2.59587305508913 | erot = 1.84775314628517 | epot = -22.0799472955547 | etot = -17.6363210941804 -216000 ekin = 2.59710486720184 | erot = 2.79170232594871 | epot = -22.123050002636 | etot = -16.7342428094855 -217000 ekin = 2.50043297628753 | erot = 1.89569946865143 | epot = -22.2232445790842 | etot = -17.8271121341452 -218000 ekin = 2.42608117861514 | erot = 2.42380011003409 | epot = -22.2442965405807 | etot = -17.3944152519314 -219000 ekin = 2.31038806457503 | erot = 2.64910389607574 | epot = -22.2862511100887 | etot = -17.3267591494379 -220000 ekin = 1.69989575631519 | erot = 2.34717348369245 | epot = -22.2936253261379 | etot = -18.2465560861303 -221000 ekin = 2.0597604328414 | erot = 2.4617257870959 | epot = -22.2693428350923 | etot = -17.747856615155 -222000 ekin = 1.56778478035701 | erot = 2.12765432596982 | epot = -22.1639011265163 | etot = -18.4684620201895 -223000 ekin = 1.84761048251748 | erot = 1.88006246465219 | epot = -22.0932628941083 | etot = -18.3655899469387 -224000 ekin = 2.59436846043989 | erot = 2.94714248251079 | epot = -22.1101977210218 | etot = -16.5686867780711 -225000 ekin = 3.30446830369106 | erot = 2.86069163428051 | epot = -22.1130335717329 | etot = -15.9478736337614 -226000 ekin = 3.03148439961004 | erot = 2.0857715841185 | epot = -22.1515480756285 | etot = -17.0342920918999 -227000 ekin = 2.52473737037052 | erot = 3.1515233037479 | epot = -22.2272979755786 | etot = -16.5510373014602 -228000 ekin = 2.32773029487822 | erot = 2.67887550863523 | epot = -22.3289846157579 | etot = -17.3223788122445 -229000 ekin = 2.908632187774 | erot = 2.89972099244786 | epot = -22.4590990625921 | etot = -16.6507458823703 -230000 ekin = 2.30901008738396 | erot = 3.48892218468534 | epot = -22.5811133380347 | etot = -16.7831810659654 -231000 ekin = 2.09445974553368 | erot = 3.10137653837903 | epot = -22.6273628788262 | etot = -17.4315265949135 -232000 ekin = 2.11347252785341 | erot = 1.99214840222577 | epot = -22.6148559367411 | etot = -18.5092350066619 -233000 ekin = 2.31469131808302 | erot = 2.82702779723524 | epot = -22.573468078272 | etot = -17.4317489629538 -234000 ekin = 2.08691986790862 | erot = 2.09006771152617 | epot = -22.5768924885421 | etot = -18.3999049091073 -235000 ekin = 2.43602788311011 | erot = 2.79756094595935 | epot = -22.5841308018507 | etot = -17.3505419727812 -236000 ekin = 2.93232983655883 | erot = 3.05945149934941 | epot = -22.5011281720659 | etot = -16.5093468361576 -237000 ekin = 3.2236915032749 | erot = 3.26810349425041 | epot = -22.3869936414794 | etot = -15.8951986439541 -238000 ekin = 2.4674995923353 | erot = 2.31630563795609 | epot = -22.3210409459325 | etot = -17.5372357156411 -239000 ekin = 2.10887317283391 | erot = 2.47562990634415 | epot = -22.3008221039947 | etot = -17.7163190248166 -240000 ekin = 1.76092230208337 | erot = 2.62077674301801 | epot = -22.2503883436816 | etot = -17.8686892985802 -241000 ekin = 1.93966929781469 | erot = 1.41063904300121 | epot = -22.2367099354244 | etot = -18.8864015946085 -242000 ekin = 3.03220831764684 | erot = 2.02809667614523 | epot = -22.2529237351145 | etot = -17.1926187413224 -243000 ekin = 2.84396619393303 | erot = 1.7910064306681 | epot = -22.2768680265869 | etot = -17.6418954019858 -244000 ekin = 1.94630661585721 | erot = 2.3722540427007 | epot = -22.2272698315535 | etot = -17.9087091729956 -245000 ekin = 2.21268964174709 | erot = 2.75899365563147 | epot = -22.1926413343766 | etot = -17.2209580369981 -246000 ekin = 2.07547606015104 | erot = 2.22089229769683 | epot = -22.119471822751 | etot = -17.8231034649032 -247000 ekin = 1.58341517009487 | erot = 3.06778333448391 | epot = -22.0033087190277 | etot = -17.3521102144489 -248000 ekin = 2.1365138975527 | erot = 3.53502738921423 | epot = -21.8495423719646 | etot = -16.1780010851977 -249000 ekin = 2.17149547481658 | erot = 3.29316066315612 | epot = -21.813933670884 | etot = -16.3492775329113 -250000 ekin = 2.39365756609179 | erot = 2.39580124119371 | epot = -21.767733544404 | etot = -16.9782747371185 -251000 ekin = 1.2828204065042 | erot = 2.24293125468609 | epot = -21.7209613352709 | etot = -18.1952096740806 -252000 ekin = 1.76792385357404 | erot = 2.13774913157991 | epot = -21.715743646839 | etot = -17.8100706616851 -253000 ekin = 2.15844787240193 | erot = 2.59910839140098 | epot = -21.6939194867273 | etot = -16.9363632229244 -254000 ekin = 2.46988601582316 | erot = 1.99393049965303 | epot = -21.6738244724958 | etot = -17.2100079570196 -255000 ekin = 2.31014544453096 | erot = 2.03140480982291 | epot = -21.6888108217887 | etot = -17.3472605674348 -256000 ekin = 2.90570988017011 | erot = 2.61779108741197 | epot = -21.6304219101588 | etot = -16.1069209425767 -257000 ekin = 2.87227426842454 | erot = 2.08598550349753 | epot = -21.5998306482426 | etot = -16.6415708763206 -258000 ekin = 2.06365418401471 | erot = 2.33103720962373 | epot = -21.5019981919811 | etot = -17.1073067983427 -259000 ekin = 2.23106413601668 | erot = 2.88992031738565 | epot = -21.4929751490585 | etot = -16.3719906956562 -260000 ekin = 2.49064109684832 | erot = 2.38083177290805 | epot = -21.4659963710747 | etot = -16.5945235013183 -261000 ekin = 2.09140199827797 | erot = 2.40209752473156 | epot = -21.4076397934529 | etot = -16.9141402704433 -262000 ekin = 2.36091906713393 | erot = 2.66652490187927 | epot = -21.359937125592 | etot = -16.3324931565788 -263000 ekin = 2.2112169796158 | erot = 2.73059503173094 | epot = -21.4187723839513 | etot = -16.4769603726046 -264000 ekin = 2.28961718487933 | erot = 2.75455515229635 | epot = -21.370776058554 | etot = -16.3266037213783 -265000 ekin = 1.71596203334806 | erot = 1.76104932073225 | epot = -21.2034176623527 | etot = -17.7264063082724 -266000 ekin = 2.51424635704546 | erot = 2.09488481391075 | epot = -21.0818656942669 | etot = -16.4727345233107 -267000 ekin = 2.81393895925601 | erot = 2.14232705328249 | epot = -21.1259701200622 | etot = -16.1697041075237 -268000 ekin = 3.10191854871686 | erot = 2.80451383793942 | epot = -21.0933882633302 | etot = -15.1869558766739 -269000 ekin = 3.52550118014125 | erot = 2.35973600910593 | epot = -21.0585255577117 | etot = -15.1732883684645 -270000 ekin = 3.50731584216641 | erot = 1.86855463358785 | epot = -21.093710946541 | etot = -15.7178404707867 -271000 ekin = 3.5675331453682 | erot = 2.0823459971557 | epot = -21.1717850302959 | etot = -15.521905887772 -272000 ekin = 2.43382567191708 | erot = 3.09591378837425 | epot = -21.2584464912718 | etot = -15.7287070309805 -273000 ekin = 2.38177594135517 | erot = 3.14028416008422 | epot = -21.3418702267283 | etot = -15.8198101252889 -274000 ekin = 2.46408091312732 | erot = 2.01407385193325 | epot = -21.3513679347441 | etot = -16.8732131696836 -275000 ekin = 2.45653813926169 | erot = 3.06780010281641 | epot = -21.3769507768006 | etot = -15.8526125347225 -276000 ekin = 2.79508720985829 | erot = 2.87011619931109 | epot = -21.3368600634473 | etot = -15.671656654278 -277000 ekin = 2.21394865880382 | erot = 2.19504097967885 | epot = -21.2606836087454 | etot = -16.8516939702627 -278000 ekin = 2.75723780567064 | erot = 3.25107227641375 | epot = -21.1755556732391 | etot = -15.1672455911547 -279000 ekin = 2.50738352588257 | erot = 1.80312795092014 | epot = -21.119949297869 | etot = -16.8094378210662 -280000 ekin = 2.35419479075042 | erot = 1.7566104351529 | epot = -21.0612865360217 | etot = -16.9504813101184 -281000 ekin = 2.54091624756361 | erot = 2.29354970120309 | epot = -21.0950091005497 | etot = -16.260543151783 -282000 ekin = 2.99712896075656 | erot = 2.42094408338315 | epot = -21.2220089565004 | etot = -15.8039359123607 -283000 ekin = 2.56696810638689 | erot = 2.10068113035835 | epot = -21.403161576838 | etot = -16.7355123400928 -284000 ekin = 2.50149529685552 | erot = 3.12894850572552 | epot = -21.5256946024495 | etot = -15.8952507998684 -285000 ekin = 2.42104861452631 | erot = 1.7773884250687 | epot = -21.6343236201921 | etot = -17.4358865805971 -286000 ekin = 1.95703367775988 | erot = 2.02947038358402 | epot = -21.6777606373854 | etot = -17.6912565760415 -287000 ekin = 2.563069553437 | erot = 2.57822888294094 | epot = -21.7096788412169 | etot = -16.568380404839 -288000 ekin = 2.18408141161779 | erot = 1.69724000161796 | epot = -21.6059228036045 | etot = -17.7246013903687 -289000 ekin = 2.32975723406079 | erot = 1.67288237726622 | epot = -21.4690249265465 | etot = -17.4663853152195 -290000 ekin = 2.22773933829104 | erot = 2.00568808096403 | epot = -21.3936416309443 | etot = -17.1602142116892 -291000 ekin = 1.46140048209222 | erot = 2.68187349132486 | epot = -21.320309661152 | etot = -17.177035687735 -292000 ekin = 2.07752653885401 | erot = 2.42042811850752 | epot = -21.2225710152689 | etot = -16.7246163579074 -293000 ekin = 2.14598735312316 | erot = 1.87232699516306 | epot = -21.1503112105659 | etot = -17.1319968622797 -294000 ekin = 2.15249843510191 | erot = 2.17548638187737 | epot = -21.1209057143321 | etot = -16.7929208973528 -295000 ekin = 2.13417246804068 | erot = 2.31578295657371 | epot = -21.023273761855 | etot = -16.5733183372406 -296000 ekin = 1.52381700282724 | erot = 2.92433462308731 | epot = -21.0839283123442 | etot = -16.6357766864297 -297000 ekin = 2.45165869902145 | erot = 2.17953392904489 | epot = -21.0491333291916 | etot = -16.4179407011252 -298000 ekin = 1.77920935759369 | erot = 2.01251348063453 | epot = -21.0971977522748 | etot = -17.3054749140465 -299000 ekin = 1.87538650376616 | erot = 1.65135039658661 | epot = -21.119277949862 | etot = -17.5925410495092 -300000 ekin = 2.3167056751994 | erot = 1.510902648654 | epot = -21.178913099451 | etot = -17.3513047755976 -301000 ekin = 2.00567209290794 | erot = 2.01270349508404 | epot = -21.2857234594098 | etot = -17.2673478714178 -302000 ekin = 1.78598592595272 | erot = 2.2354055492879 | epot = -21.3905601140029 | etot = -17.3691686387622 -303000 ekin = 2.73278841880507 | erot = 1.64856089415774 | epot = -21.3608973804115 | etot = -16.9795480674487 -304000 ekin = 2.5809493598196 | erot = 2.00558555026353 | epot = -21.400198286629 | etot = -16.8136633765459 -305000 ekin = 2.43647384348742 | erot = 2.28275438290435 | epot = -21.3863075230184 | etot = -16.6670792966266 -306000 ekin = 2.14332823539982 | erot = 2.4338461634411 | epot = -21.3233075109442 | etot = -16.7461331121032 -307000 ekin = 3.21424191196812 | erot = 3.27591538479569 | epot = -21.289790084126 | etot = -14.7996327873622 -308000 ekin = 3.45838026839176 | erot = 2.68116130354006 | epot = -21.3419403426811 | etot = -15.2023987707493 -309000 ekin = 2.38041738433959 | erot = 2.92081370932153 | epot = -21.4463399141034 | etot = -16.1451088204423 -310000 ekin = 2.50977269558789 | erot = 2.34824464102402 | epot = -21.4648074532888 | etot = -16.6067901166769 -311000 ekin = 2.57488628819259 | erot = 2.293754673538 | epot = -21.5151382155269 | etot = -16.6464972537963 -312000 ekin = 2.09623150906876 | erot = 2.93795890592974 | epot = -21.6260240426366 | etot = -16.5918336276381 -313000 ekin = 1.8184499729194 | erot = 2.28463898505893 | epot = -21.6999003790643 | etot = -17.5968114210859 -314000 ekin = 2.3228324174232 | erot = 2.19580475273396 | epot = -21.6870491287185 | etot = -17.1684119585613 -315000 ekin = 1.84546653836013 | erot = 2.13886071139629 | epot = -21.7312132691438 | etot = -17.7468860193873 -316000 ekin = 2.1657114199577 | erot = 3.03124199276298 | epot = -21.7430929234306 | etot = -16.5461395107099 -317000 ekin = 2.42793755919909 | erot = 3.57187833839244 | epot = -21.8303487369249 | etot = -15.8305328393334 -318000 ekin = 2.31418145055206 | erot = 3.02858542885927 | epot = -21.9347898317926 | etot = -16.5920229523813 -319000 ekin = 2.35032973997068 | erot = 3.16078759112674 | epot = -22.0387665246751 | etot = -16.5276491935776 -320000 ekin = 1.78202525445684 | erot = 2.83297321443624 | epot = -22.1187616541783 | etot = -17.5037631852852 -321000 ekin = 2.87441941784728 | erot = 2.26223197636944 | epot = -22.1065455913123 | etot = -16.9698941970956 -322000 ekin = 2.79013397204362 | erot = 2.68769432639935 | epot = -22.1121405540937 | etot = -16.6343122556507 -323000 ekin = 2.070121980457 | erot = 2.31830584817612 | epot = -22.1539458855415 | etot = -17.7655180569083 -324000 ekin = 2.58383941134683 | erot = 2.58296807603305 | epot = -22.1539753505051 | etot = -16.9871678631253 -325000 ekin = 3.43451304817783 | erot = 2.45405386180802 | epot = -21.938960387404 | etot = -16.0503934774181 -326000 ekin = 3.49680929786584 | erot = 2.85196633398113 | epot = -21.8204400999953 | etot = -15.4716644681484 -327000 ekin = 2.68799300805475 | erot = 2.21805195956654 | epot = -21.7892073548558 | etot = -16.8831623872345 -328000 ekin = 1.81477491971657 | erot = 2.35891534842888 | epot = -21.7275637950057 | etot = -17.5538735268602 -329000 ekin = 2.19319322627006 | erot = 2.40717958919081 | epot = -21.6826095784948 | etot = -17.0822367630339 -330000 ekin = 1.87131927244382 | erot = 2.03694340108429 | epot = -21.5934239674847 | etot = -17.6851612939566 -331000 ekin = 2.37197683084608 | erot = 1.80087022346348 | epot = -21.5641185835514 | etot = -17.3912715292419 -332000 ekin = 1.69601394569048 | erot = 2.54947032294377 | epot = -21.5986464339748 | etot = -17.3531621653406 -333000 ekin = 1.59867443991714 | erot = 2.14911483871162 | epot = -21.7162173059518 | etot = -17.9684280273231 -334000 ekin = 2.25811733625553 | erot = 2.62323988136568 | epot = -21.7749416190679 | etot = -16.8935844014467 -335000 ekin = 2.93433632601273 | erot = 3.10350297573268 | epot = -21.7966831809595 | etot = -15.7588438792141 -336000 ekin = 2.76337640462581 | erot = 2.54930710489019 | epot = -21.7180312833467 | etot = -16.4053477738307 -337000 ekin = 3.19235531401951 | erot = 3.87146146874103 | epot = -21.8022396262892 | etot = -14.7384228435286 -338000 ekin = 2.33305125173566 | erot = 2.13094194678887 | epot = -21.8068682042896 | etot = -17.3428750057651 -339000 ekin = 1.71673308889604 | erot = 2.30964121170968 | epot = -21.7941224580796 | etot = -17.7677481574739 -340000 ekin = 1.59424151294027 | erot = 3.16324993863714 | epot = -21.7679173396748 | etot = -17.0104258880973 -341000 ekin = 1.69465464335694 | erot = 3.18694861883744 | epot = -21.7067352043109 | etot = -16.8251319421165 -342000 ekin = 1.81243763026219 | erot = 2.60448215582795 | epot = -21.5993126794634 | etot = -17.1823928933732 -343000 ekin = 3.08243814047349 | erot = 2.9217466333323 | epot = -21.5855979229594 | etot = -15.5814131491536 -344000 ekin = 2.94964594107348 | erot = 3.10231272046816 | epot = -21.5506154266351 | etot = -15.4986567650935 -345000 ekin = 2.34525111670595 | erot = 2.88045261854212 | epot = -21.530734043011 | etot = -16.3050303077629 -346000 ekin = 2.03136740406842 | erot = 3.44352096435563 | epot = -21.4703041890966 | etot = -15.9954158206726 -347000 ekin = 2.34515762081498 | erot = 1.91414074840886 | epot = -21.3488386855954 | etot = -17.0895403163716 -348000 ekin = 2.76763212340836 | erot = 2.78035348102326 | epot = -21.3102796687364 | etot = -15.7622940643048 -349000 ekin = 2.29342234253801 | erot = 3.14526664575919 | epot = -21.3922932631024 | etot = -15.9536042748052 -350000 ekin = 2.17828641691343 | erot = 2.38211689163937 | epot = -21.3570978647003 | etot = -16.7966945561475 -351000 ekin = 2.2787342054874 | erot = 2.85568682453813 | epot = -21.3165609660186 | etot = -16.182139935993 -352000 ekin = 2.70894563927919 | erot = 2.77656375044279 | epot = -21.3565059314145 | etot = -15.8709965416925 -353000 ekin = 1.74748047732915 | erot = 2.14191122851256 | epot = -21.3195625770357 | etot = -17.430170871194 -354000 ekin = 2.30492780756568 | erot = 2.37159952583724 | epot = -21.3742968901642 | etot = -16.6977695567612 -355000 ekin = 2.32493886573112 | erot = 2.38411746089983 | epot = -21.339340741587 | etot = -16.6302844149561 -356000 ekin = 2.9749649543268 | erot = 2.9916655517553 | epot = -21.2468948072712 | etot = -15.2802643011891 -357000 ekin = 1.79541671946026 | erot = 2.13971792108731 | epot = -21.2216819829681 | etot = -17.2865473424205 -358000 ekin = 2.06637919290965 | erot = 1.9076530715578 | epot = -21.2447441674953 | etot = -17.2707119030278 -359000 ekin = 2.02344077580052 | erot = 2.11726163321539 | epot = -21.2183688961264 | etot = -17.0776664871105 -360000 ekin = 2.64012587839158 | erot = 2.43776362828977 | epot = -21.1472477161847 | etot = -16.0693582095033 -361000 ekin = 2.41850555983882 | erot = 2.39054736245265 | epot = -21.2133787743639 | etot = -16.4043258520724 -362000 ekin = 2.2486199222758 | erot = 2.04489136793498 | epot = -21.2088914287919 | etot = -16.9153801385811 -363000 ekin = 3.21904252076974 | erot = 1.79717950163013 | epot = -21.2620537293498 | etot = -16.24583170695 -364000 ekin = 2.9845697448498 | erot = 2.18316673460243 | epot = -21.2883338312843 | etot = -16.120597351832 -365000 ekin = 2.49427392981412 | erot = 2.31205455481896 | epot = -21.4001153296815 | etot = -16.5937868450484 -366000 ekin = 2.61706523565788 | erot = 2.20229130507574 | epot = -21.4506718008962 | etot = -16.6313152601626 -367000 ekin = 2.24650816549397 | erot = 1.87906237362998 | epot = -21.5207044850599 | etot = -17.3951339459359 -368000 ekin = 2.46672276241562 | erot = 2.37638546053105 | epot = -21.5628581383216 | etot = -16.7197499153749 -369000 ekin = 2.03614635149851 | erot = 2.85426887707092 | epot = -21.6803034764487 | etot = -16.7898882478793 -370000 ekin = 2.13410724028005 | erot = 2.17304603842012 | epot = -21.7343761700058 | etot = -17.4272228913057 -371000 ekin = 2.21722409826115 | erot = 2.11058746733929 | epot = -21.6422617131998 | etot = -17.3144501475994 -372000 ekin = 1.88083333566673 | erot = 1.90617172826127 | epot = -21.6005499693118 | etot = -17.8135449053838 -373000 ekin = 1.98298204516521 | erot = 1.78267682128409 | epot = -21.5708808628646 | etot = -17.8052219964153 -374000 ekin = 2.88981201933268 | erot = 1.90326894499807 | epot = -21.4624711307906 | etot = -16.6693901664599 -375000 ekin = 2.31951869092549 | erot = 1.92779670517485 | epot = -21.3521768069862 | etot = -17.1048614108859 -376000 ekin = 2.60113015271722 | erot = 2.31181306588444 | epot = -21.34681055463 | etot = -16.4338673360283 -377000 ekin = 2.23867315344604 | erot = 1.65923992926403 | epot = -21.2611852709131 | etot = -17.363272188203 -378000 ekin = 2.38125181613766 | erot = 2.54002618279121 | epot = -21.2390275318703 | etot = -16.3177495329414 -379000 ekin = 2.06952281308678 | erot = 2.11888196225292 | epot = -21.194025606577 | etot = -17.0056208312373 -380000 ekin = 2.59961269461524 | erot = 2.3751200788503 | epot = -21.1885781090515 | etot = -16.2138453355859 -381000 ekin = 2.42019573552876 | erot = 2.20667402504614 | epot = -21.1989968748535 | etot = -16.5721271142786 -382000 ekin = 2.04746564398744 | erot = 3.34439482672214 | epot = -21.2903574441545 | etot = -15.8984969734449 -383000 ekin = 2.65699216362738 | erot = 1.56546061375907 | epot = -21.3572338418187 | etot = -17.1347810644322 -384000 ekin = 2.43156675693926 | erot = 2.00097327452753 | epot = -21.3434156392382 | etot = -16.9108756077714 -385000 ekin = 1.95152101616516 | erot = 3.28345377140313 | epot = -21.4173973675698 | etot = -16.1824225800015 -386000 ekin = 2.10919215730741 | erot = 2.90700736383436 | epot = -21.3963452767614 | etot = -16.3801457556197 -387000 ekin = 2.34448447096483 | erot = 2.50155013212484 | epot = -21.3487258248084 | etot = -16.5026912217187 -388000 ekin = 2.71771591111729 | erot = 2.76803950274557 | epot = -21.3515918112166 | etot = -15.8658363973537 -389000 ekin = 3.06825183100775 | erot = 3.06148533146046 | epot = -21.4826430036711 | etot = -15.3529058412029 -390000 ekin = 2.56997560639923 | erot = 2.05646161654304 | epot = -21.5623801506968 | etot = -16.9359429277546 -391000 ekin = 2.1110114400687 | erot = 2.44612603817531 | epot = -21.6052888202632 | etot = -17.0481513420191 -392000 ekin = 2.58328475785099 | erot = 2.75249392862464 | epot = -21.7336094646938 | etot = -16.3978307782182 -393000 ekin = 2.03977041996533 | erot = 1.67448219405536 | epot = -21.8740604202474 | etot = -18.1598078062267 -394000 ekin = 2.1229408356241 | erot = 2.43410977254954 | epot = -21.9094739378951 | etot = -17.3524233297214 -395000 ekin = 2.48696003315341 | erot = 2.48225062557349 | epot = -21.8799685903484 | etot = -16.9107579316215 -396000 ekin = 3.18909661029635 | erot = 1.62675064803775 | epot = -21.8520000277039 | etot = -17.0361527693698 -397000 ekin = 2.39161566907255 | erot = 2.17052346752458 | epot = -21.7939512244376 | etot = -17.2318120878404 -398000 ekin = 2.29946433742664 | erot = 2.18115834594542 | epot = -21.7285069861955 | etot = -17.2478843028235 -399000 ekin = 2.65449075133045 | erot = 2.80318185995816 | epot = -21.6503181327212 | etot = -16.1926455214325 -400000 ekin = 1.800915604111 | erot = 2.76596769548035 | epot = -21.6418619272709 | etot = -17.0749786276795 -401000 ekin = 2.35073130822393 | erot = 3.1229922205774 | epot = -21.6675586342212 | etot = -16.1938351054199 -402000 ekin = 3.95550191914708 | erot = 3.58855023837881 | epot = -21.5840051268208 | etot = -14.0399529692949 -403000 ekin = 3.59615502379622 | erot = 3.44558176696768 | epot = -21.5781150073617 | etot = -14.5363782165978 -404000 ekin = 2.50360365952137 | erot = 3.01285184176069 | epot = -21.6258060641303 | etot = -16.1093505628483 -405000 ekin = 2.77241560720113 | erot = 3.10596549510783 | epot = -21.704678917892 | etot = -15.826297815583 -406000 ekin = 2.33934923007339 | erot = 2.04671975867729 | epot = -21.819104286388 | etot = -17.4330352976373 -407000 ekin = 2.34277955096234 | erot = 1.89301717692526 | epot = -21.8450916691373 | etot = -17.6092949412497 -408000 ekin = 1.91561948833426 | erot = 2.19551604353608 | epot = -21.8744041835349 | etot = -17.7632686516646 -409000 ekin = 1.98819074442449 | erot = 1.93870533007334 | epot = -21.921903026697 | etot = -17.9950069521992 -410000 ekin = 1.59047218684375 | erot = 1.93259851333214 | epot = -21.969890787558 | etot = -18.4468200873821 -411000 ekin = 1.88305362601542 | erot = 2.47249081001963 | epot = -22.0985208042931 | etot = -17.742976368258 -412000 ekin = 2.51301623282815 | erot = 2.67550740966365 | epot = -22.2078537029906 | etot = -17.0193300604988 -413000 ekin = 2.81407439938451 | erot = 3.21402559358062 | epot = -22.1310120840187 | etot = -16.1029120910536 -414000 ekin = 2.79247479268938 | erot = 2.73425265524033 | epot = -22.0977113063587 | etot = -16.570983858429 -415000 ekin = 2.47916660937974 | erot = 2.2538291443672 | epot = -22.1646477745644 | etot = -17.4316520208175 -416000 ekin = 3.33232223339091 | erot = 1.56386062957 | epot = -22.1461937000839 | etot = -17.250010837123 -417000 ekin = 3.95877285814837 | erot = 2.43917045295873 | epot = -22.0789469190762 | etot = -15.6810036079691 -418000 ekin = 2.77978041892218 | erot = 2.67961998913593 | epot = -21.9429456651673 | etot = -16.4835452571092 -419000 ekin = 2.38024484823696 | erot = 2.99229133054455 | epot = -21.8677152868896 | etot = -16.4951791081081 -420000 ekin = 1.82267088279317 | erot = 1.83608705422836 | epot = -21.870451160571 | etot = -18.2116932235495 -421000 ekin = 1.36907389827089 | erot = 1.7797704929584 | epot = -21.8376802512791 | etot = -18.6888358600498 -422000 ekin = 1.39969148752264 | erot = 2.73407059574398 | epot = -21.8945647860022 | etot = -17.7608027027356 -423000 ekin = 1.56110844196111 | erot = 3.07614792088633 | epot = -21.9244447660987 | etot = -17.2871884032512 -424000 ekin = 2.34533519268149 | erot = 2.03540102416745 | epot = -21.9949085928942 | etot = -17.6141723760453 -425000 ekin = 2.30531135176125 | erot = 2.5628563075006 | epot = -22.0442964382176 | etot = -17.1761287789557 -426000 ekin = 2.08911806268394 | erot = 3.11967927432985 | epot = -21.9925431949266 | etot = -16.7837458579128 -427000 ekin = 2.15676382580403 | erot = 2.43973499877679 | epot = -21.8818966255662 | etot = -17.2853978009854 -428000 ekin = 1.77792840961357 | erot = 1.65301904457092 | epot = -21.8564247195203 | etot = -18.4254772653358 -429000 ekin = 1.64662621362122 | erot = 2.54748287085176 | epot = -21.8025042608483 | etot = -17.6083951763753 -430000 ekin = 2.65482151975961 | erot = 2.86424448473893 | epot = -21.8233021230657 | etot = -16.3042361185671 -431000 ekin = 2.76450737503174 | erot = 1.57600071919883 | epot = -21.8149424651896 | etot = -17.474434370959 -432000 ekin = 2.55825491646852 | erot = 1.62501657592138 | epot = -21.782511983832 | etot = -17.5992404914421 -433000 ekin = 2.01126969712347 | erot = 2.46583763941079 | epot = -21.8897978226513 | etot = -17.4126904861171 -434000 ekin = 3.04567132520196 | erot = 2.70385575793897 | epot = -22.0064907697329 | etot = -16.256963686592 -435000 ekin = 3.55537447133515 | erot = 1.38977885610833 | epot = -22.1475448623269 | etot = -17.2023915348834 -436000 ekin = 2.99751349357597 | erot = 2.00759426062759 | epot = -22.1521181601551 | etot = -17.1470104059515 -437000 ekin = 3.22719371512018 | erot = 1.7857012571478 | epot = -22.1712823460501 | etot = -17.1583873737822 -438000 ekin = 2.89146439117069 | erot = 1.84455801050198 | epot = -22.1285919294041 | etot = -17.3925695277315 -439000 ekin = 2.4298540579217 | erot = 2.69925899679117 | epot = -22.1231674050022 | etot = -16.9940543502893 -440000 ekin = 2.25394774327534 | erot = 3.00779841178563 | epot = -22.1604171321029 | etot = -16.898670977042 -441000 ekin = 2.90484412816846 | erot = 2.87153501323763 | epot = -22.3059803982533 | etot = -16.5296012568472 -442000 ekin = 2.09031226167651 | erot = 1.73424350391287 | epot = -22.3736918061838 | etot = -18.5491360405944 -443000 ekin = 1.88581876804904 | erot = 2.00333583047903 | epot = -22.4253701402759 | etot = -18.5362155417478 -444000 ekin = 2.07231382818727 | erot = 2.15535274194041 | epot = -22.4449863446106 | etot = -18.2173197744829 -445000 ekin = 2.10994187816787 | erot = 2.27934343705762 | epot = -22.5011906844133 | etot = -18.1119053691878 -446000 ekin = 2.42762161250135 | erot = 2.85815816680871 | epot = -22.5326129135227 | etot = -17.2468331342127 -447000 ekin = 2.18601253591574 | erot = 2.99495256710103 | epot = -22.609768680069 | etot = -17.4288035770523 -448000 ekin = 2.33389346287827 | erot = 2.95385139208094 | epot = -22.6330370332815 | etot = -17.3452921783223 -449000 ekin = 2.34940633774375 | erot = 2.93264896913184 | epot = -22.632810074435 | etot = -17.3507547675594 -450000 ekin = 1.83766660151173 | erot = 1.69672449717286 | epot = -22.577435118717 | etot = -19.0430440200324 -451000 ekin = 1.97812884417234 | erot = 1.92764750146577 | epot = -22.5879223350906 | etot = -18.6821459894525 -452000 ekin = 1.36037939407656 | erot = 1.88463175839662 | epot = -22.5510765694841 | etot = -19.3060654170109 -453000 ekin = 2.08089341129519 | erot = 2.55704963640352 | epot = -22.3855210194734 | etot = -17.7475779717747 -454000 ekin = 1.45876213242879 | erot = 2.19347003321548 | epot = -22.2423919107779 | etot = -18.5901597451336 -455000 ekin = 1.65659111626477 | erot = 2.72276980532162 | epot = -22.0960205273875 | etot = -17.7166596058011 -456000 ekin = 2.34656659310869 | erot = 1.9986137505101 | epot = -22.0123490462426 | etot = -17.6671687026238 -457000 ekin = 2.02190390619673 | erot = 2.36256741542514 | epot = -21.9726531641996 | etot = -17.5881818425778 -458000 ekin = 1.74372434205051 | erot = 2.25707911101456 | epot = -21.9983442618521 | etot = -17.997540808787 -459000 ekin = 2.51332199676583 | erot = 2.31717011174282 | epot = -22.0772270520059 | etot = -17.2467349434973 -460000 ekin = 2.2034722783839 | erot = 2.00072694492175 | epot = -22.0506516825516 | etot = -17.846452459246 -461000 ekin = 2.27677089259524 | erot = 2.92031766851146 | epot = -21.9925449331789 | etot = -16.7954563720722 -462000 ekin = 2.6185812356449 | erot = 1.79402090094851 | epot = -22.0230696595749 | etot = -17.6104675229815 -463000 ekin = 2.59249670562421 | erot = 3.30012727643189 | epot = -21.9571457322291 | etot = -16.064521750173 -464000 ekin = 2.18969352756478 | erot = 2.37346543558646 | epot = -21.8914572439365 | etot = -17.3282982807853 -465000 ekin = 2.55190117035706 | erot = 3.6026040005498 | epot = -21.8125549491858 | etot = -15.6580497782789 -466000 ekin = 1.97953104510473 | erot = 2.88392288093832 | epot = -21.8154103020505 | etot = -16.9519563760074 -467000 ekin = 1.6387129632993 | erot = 2.61654440984279 | epot = -21.8983950281207 | etot = -17.6431376549786 -468000 ekin = 1.11239222475223 | erot = 3.3637902926771 | epot = -21.9583777645662 | etot = -17.4821952471369 -469000 ekin = 1.72382156581199 | erot = 2.77626770299012 | epot = -21.9878353154891 | etot = -17.487746046687 -470000 ekin = 1.8714597310977 | erot = 2.88190687781237 | epot = -22.0448924208381 | etot = -17.291525811928 -471000 ekin = 2.74011620634609 | erot = 2.33779564753422 | epot = -22.0936369539761 | etot = -17.0157251000958 -472000 ekin = 2.69470680116255 | erot = 2.14464177510474 | epot = -22.1704276099478 | etot = -17.3310790336805 -473000 ekin = 2.28376217878235 | erot = 2.08795770091158 | epot = -22.1987443333452 | etot = -17.8270244536512 -474000 ekin = 2.23739040654538 | erot = 2.17996427776831 | epot = -22.2112749348846 | etot = -17.7939202505709 -475000 ekin = 2.52078584565558 | erot = 2.10760071935559 | epot = -22.2127629874904 | etot = -17.5843764224793 -476000 ekin = 2.21655354698253 | erot = 1.76978147174391 | epot = -22.1154823176964 | etot = -18.12914729897 -477000 ekin = 2.49538102143271 | erot = 2.39024231683251 | epot = -22.0840161006559 | etot = -17.1983927623907 -478000 ekin = 1.92447460017176 | erot = 2.05040869255766 | epot = -22.1087248977672 | etot = -18.1338416050377 -479000 ekin = 2.27800579519478 | erot = 3.09893174949893 | epot = -22.0960233927896 | etot = -16.7190858480959 -480000 ekin = 1.67638938499079 | erot = 2.75323401987762 | epot = -22.1000079080955 | etot = -17.6703845032271 -481000 ekin = 1.81944275684786 | erot = 2.94268362469552 | epot = -22.0498104845242 | etot = -17.2876841029808 -482000 ekin = 2.15574027829653 | erot = 2.0725438892243 | epot = -22.0125690425762 | etot = -17.7842848750553 -483000 ekin = 1.49597116676185 | erot = 1.99734627551918 | epot = -21.9777307226356 | etot = -18.4844132803546 -484000 ekin = 1.8484819245566 | erot = 2.33821326463838 | epot = -22.0508318876624 | etot = -17.8641366984674 -485000 ekin = 1.63994328771 | erot = 2.49471615719057 | epot = -22.0805056177628 | etot = -17.9458461728623 -486000 ekin = 1.86887650973413 | erot = 2.15138584351099 | epot = -22.0672609747503 | etot = -18.0469986215052 -487000 ekin = 2.36601044267131 | erot = 3.10120454318392 | epot = -22.1385621074087 | etot = -16.6713471215534 -488000 ekin = 2.28411726066255 | erot = 3.25699291514219 | epot = -22.0925409557863 | etot = -16.5514307799816 -489000 ekin = 2.42268424794998 | erot = 2.54559333727918 | epot = -22.0028229962135 | etot = -17.0345454109843 -490000 ekin = 2.15695777466101 | erot = 3.5405265432528 | epot = -21.8987471713935 | etot = -16.2012628534796 -491000 ekin = 2.21843295915446 | erot = 2.48759605623037 | epot = -21.7849993207689 | etot = -17.0789703053841 -492000 ekin = 2.42523259661774 | erot = 2.76338555140187 | epot = -21.7546976439717 | etot = -16.5660794959521 -493000 ekin = 1.78787643025978 | erot = 2.27566821203155 | epot = -21.8142896153583 | etot = -17.7507449730669 -494000 ekin = 2.08684832766799 | erot = 3.00001715875608 | epot = -21.8562812315893 | etot = -16.7694157451653 -495000 ekin = 2.13573322112433 | erot = 2.49326389133065 | epot = -21.9467671324553 | etot = -17.3177700200003 -496000 ekin = 2.04467628391159 | erot = 2.6162845895522 | epot = -21.9884683374098 | etot = -17.327507463946 -497000 ekin = 2.51418899377052 | erot = 1.70810866993563 | epot = -21.9276447401884 | etot = -17.7053470764823 -498000 ekin = 2.15585318171628 | erot = 1.79538414401099 | epot = -21.8645241799653 | etot = -17.913286854238 -499000 ekin = 3.01701290816369 | erot = 1.75748039597449 | epot = -21.8892368424083 | etot = -17.1147435382701 -500000 ekin = 2.75239118232731 | erot = 2.51840040194924 | epot = -21.8902992314675 | etot = -16.6195076471909 -501000 ekin = 2.67894034986861 | erot = 3.01164832527811 | epot = -21.7709154896334 | etot = -16.0803268144867 -502000 ekin = 1.89316543275823 | erot = 3.89794024057184 | epot = -21.6531840495811 | etot = -15.862078376251 -503000 ekin = 1.79271217239337 | erot = 2.94195973795538 | epot = -21.4642442224488 | etot = -16.7295723121 -504000 ekin = 1.6771855422807 | erot = 3.03652723399754 | epot = -21.3696883509301 | etot = -16.6559755746518 -505000 ekin = 2.71833858397102 | erot = 2.13541162175611 | epot = -21.3703611232649 | etot = -16.5166109175378 -506000 ekin = 2.26393943112 | erot = 2.03997434566047 | epot = -21.3701060081751 | etot = -17.0661922313946 -507000 ekin = 3.13593335317162 | erot = 2.43613799195774 | epot = -21.4594670249601 | etot = -15.8873956798307 -508000 ekin = 2.50977944502594 | erot = 2.54754436309782 | epot = -21.6189261516985 | etot = -16.5616023435747 -509000 ekin = 2.11418702736586 | erot = 2.82587497425585 | epot = -21.7696504732974 | etot = -16.8295884716757 -510000 ekin = 2.14979144320026 | erot = 1.42702348952371 | epot = -21.8372692973069 | etot = -18.2604543645829 -511000 ekin = 2.52507885024672 | erot = 2.75237930607404 | epot = -21.9038675932379 | etot = -16.6264094369171 -512000 ekin = 2.30816398580866 | erot = 2.74440410404474 | epot = -21.9049605915963 | etot = -16.8523925017429 -513000 ekin = 2.48929206456089 | erot = 2.14820879347373 | epot = -21.8691788664222 | etot = -17.2316780083876 -514000 ekin = 2.80085464362196 | erot = 2.54503473578109 | epot = -22.0226541110001 | etot = -16.6767647315971 -515000 ekin = 2.54939499554986 | erot = 1.81858738302198 | epot = -22.114703586072 | etot = -17.7467212075001 -516000 ekin = 2.82421125785514 | erot = 2.22239822832894 | epot = -22.1991501131327 | etot = -17.1525406269486 -517000 ekin = 2.04384407501393 | erot = 2.05286256711726 | epot = -22.223660515307 | etot = -18.1269538731759 -518000 ekin = 2.19097977809323 | erot = 2.75238147912107 | epot = -22.2176385899556 | etot = -17.2742773327413 -519000 ekin = 2.24039331018443 | erot = 2.22517425402749 | epot = -22.3147614078005 | etot = -17.8491938435885 -520000 ekin = 1.89059175672112 | erot = 2.20041051856069 | epot = -22.3991443907322 | etot = -18.3081421154504 -521000 ekin = 2.59226785962331 | erot = 1.8787186288573 | epot = -22.558855864031 | etot = -18.0878693755504 -522000 ekin = 3.47620702193973 | erot = 1.77094959979111 | epot = -22.6529022954593 | etot = -17.4057456737285 -523000 ekin = 2.86949346153076 | erot = 2.45905269319727 | epot = -22.6983641285372 | etot = -17.3698179738092 -524000 ekin = 2.43223643727573 | erot = 2.35710345393931 | epot = -22.6347622840061 | etot = -17.8454223927911 -525000 ekin = 1.58633727726026 | erot = 2.6771932767998 | epot = -22.5981477078776 | etot = -18.3346171538175 -526000 ekin = 1.68956829163897 | erot = 1.56381447059437 | epot = -22.5455188933618 | etot = -19.2921361311285 -527000 ekin = 2.25335664013444 | erot = 1.91897798598234 | epot = -22.438285347212 | etot = -18.2659507210952 -528000 ekin = 2.66417770052522 | erot = 2.81695730712898 | epot = -22.4214392419194 | etot = -16.9403042342652 -529000 ekin = 2.68388271083098 | erot = 3.01210908187864 | epot = -22.4261041670352 | etot = -16.7301123743256 -530000 ekin = 2.58091136149224 | erot = 2.12874327798812 | epot = -22.2849687345625 | etot = -17.5753140950821 -531000 ekin = 2.96791741143998 | erot = 2.35396590663619 | epot = -22.1825114215506 | etot = -16.8606281034744 -532000 ekin = 2.56040610657616 | erot = 2.30869688210952 | epot = -22.1966779750303 | etot = -17.3275749863446 -533000 ekin = 2.47127792277395 | erot = 2.96337405559089 | epot = -22.2034167916881 | etot = -16.7687648133233 -534000 ekin = 2.10109006711395 | erot = 2.06160691104878 | epot = -22.2334884486858 | etot = -18.0707914705231 -535000 ekin = 3.76901503112188 | erot = 2.6463468036932 | epot = -22.2244389422279 | etot = -15.8090771074128 -536000 ekin = 2.76978499488531 | erot = 1.95801212091677 | epot = -22.1621143741426 | etot = -17.4343172583406 -537000 ekin = 2.84173849615256 | erot = 2.62706904536459 | epot = -22.0817906214053 | etot = -16.6129830798882 -538000 ekin = 2.68461551572766 | erot = 2.11438749606247 | epot = -22.0095123737601 | etot = -17.21050936197 -539000 ekin = 2.71441959372568 | erot = 2.40909357772199 | epot = -22.1283805595379 | etot = -17.0048673880902 -540000 ekin = 2.43554469514557 | erot = 2.49366634622684 | epot = -22.2721085965986 | etot = -17.3428975552261 -541000 ekin = 3.40478335851234 | erot = 2.79351301825373 | epot = -22.3438323146239 | etot = -16.1455359378578 -542000 ekin = 2.43305477389315 | erot = 2.89262463310066 | epot = -22.3528484076625 | etot = -17.0271690006687 -543000 ekin = 2.33384318243661 | erot = 2.87812814268662 | epot = -22.3517509549719 | etot = -17.1397796298486 -544000 ekin = 2.20405054763978 | erot = 1.45974147181057 | epot = -22.3200355678433 | etot = -18.656243548393 -545000 ekin = 2.44190363474283 | erot = 2.14425712944393 | epot = -22.3037584455754 | etot = -17.7175976813886 -546000 ekin = 1.97349236865067 | erot = 2.22849747468303 | epot = -22.2610854898172 | etot = -18.0590956464835 -547000 ekin = 2.54002964967593 | erot = 1.88937782138629 | epot = -22.2132220899932 | etot = -17.783814618931 -548000 ekin = 1.68504847096503 | erot = 1.6504983981354 | epot = -22.1188297609737 | etot = -18.7832828918733 -549000 ekin = 1.8698904826159 | erot = 2.68379586673466 | epot = -22.3014742550974 | etot = -17.7477879057469 -550000 ekin = 1.81227590400771 | erot = 1.59168663528122 | epot = -22.4534648123994 | etot = -19.0495022731104 -551000 ekin = 2.18778306678591 | erot = 2.27083852152173 | epot = -22.5132391469467 | etot = -18.0546175586391 -552000 ekin = 2.0524867508114 | erot = 2.50762393323791 | epot = -22.5694064381206 | etot = -18.0092957540712 -553000 ekin = 2.95456875477793 | erot = 2.14561779139538 | epot = -22.6592693777082 | etot = -17.5590828315349 -554000 ekin = 2.82905646744367 | erot = 1.93590782360605 | epot = -22.8091725556775 | etot = -18.0442082646278 -555000 ekin = 2.39158205650881 | erot = 2.26907880603287 | epot = -22.8586370928634 | etot = -18.1979762303218 -556000 ekin = 2.29372548723881 | erot = 2.58079244425137 | epot = -22.9103117359013 | etot = -18.0357938044111 -557000 ekin = 2.83941059371958 | erot = 1.46630907998336 | epot = -22.9934681858733 | etot = -18.6877485121704 -558000 ekin = 2.74456573812684 | erot = 2.01705053511004 | epot = -23.0249165386548 | etot = -18.263300265418 -559000 ekin = 3.32001639007045 | erot = 2.33065957496589 | epot = -23.0702860514081 | etot = -17.4196100863717 -560000 ekin = 3.06548847901962 | erot = 2.32403726670831 | epot = -23.0562195399467 | etot = -17.6666937942187 -561000 ekin = 2.86648091511123 | erot = 2.08496682915783 | epot = -22.9734465855435 | etot = -18.0219988412745 -562000 ekin = 3.27266742525966 | erot = 2.5148755055394 | epot = -22.8741285027176 | etot = -17.0865855719185 -563000 ekin = 2.66038974520286 | erot = 1.64110018949295 | epot = -22.8474543828021 | etot = -18.5459644481063 -564000 ekin = 2.80468636683463 | erot = 2.52664241131886 | epot = -22.8018617517494 | etot = -17.4705329735959 -565000 ekin = 2.64616861412633 | erot = 2.04566022999095 | epot = -22.7506810734506 | etot = -18.0588522293334 -566000 ekin = 2.31863979249599 | erot = 2.17936618392302 | epot = -22.753817383677 | etot = -18.255811407258 -567000 ekin = 1.93243531435252 | erot = 2.8201914219892 | epot = -22.7091974553673 | etot = -17.9565707190256 -568000 ekin = 2.20145087944368 | erot = 2.21735208955968 | epot = -22.7289431019428 | etot = -18.3101401329394 -569000 ekin = 2.47195478734592 | erot = 2.65975337798175 | epot = -22.6704691958401 | etot = -17.5387610305124 -570000 ekin = 2.43702231300343 | erot = 1.88676767986218 | epot = -22.6634145438588 | etot = -18.3396245509932 -571000 ekin = 2.89036429172333 | erot = 2.95615513706037 | epot = -22.6566784173206 | etot = -16.8101589885369 -572000 ekin = 1.93616423502164 | erot = 3.77280866215609 | epot = -22.6161904936583 | etot = -16.9072175964806 -573000 ekin = 2.40449703945409 | erot = 2.31309419006005 | epot = -22.592333216152 | etot = -17.8747419866379 -574000 ekin = 1.69163306749095 | erot = 2.32935369197413 | epot = -22.6465956635078 | etot = -18.6256089040427 -575000 ekin = 1.84139068594293 | erot = 1.86447317795677 | epot = -22.7237799324543 | etot = -19.0179160685546 -576000 ekin = 3.22131124370819 | erot = 2.95816228283025 | epot = -22.6715615977237 | etot = -16.4920880711853 -577000 ekin = 2.86651980816624 | erot = 2.88003300402859 | epot = -22.6040632784101 | etot = -16.8575104662152 -578000 ekin = 2.38036632496091 | erot = 2.76701770395377 | epot = -22.3994142750986 | etot = -17.2520302461839 -579000 ekin = 2.40092915325622 | erot = 1.9941192489901 | epot = -22.2419585433873 | etot = -17.846910141141 -580000 ekin = 2.62012657675686 | erot = 1.97778552777916 | epot = -22.0959374453144 | etot = -17.4980253407783 -581000 ekin = 2.04604501901225 | erot = 3.02029740769394 | epot = -21.969203567202 | etot = -16.9028611404958 -582000 ekin = 2.17538959702762 | erot = 3.10891247706868 | epot = -21.8431272977465 | etot = -16.5588252236502 -583000 ekin = 2.1277994052252 | erot = 2.71423548986473 | epot = -21.8070587526078 | etot = -16.9650238575179 -584000 ekin = 2.99172160795183 | erot = 2.61848378659144 | epot = -21.79936869936 | etot = -16.1891633048167 -585000 ekin = 2.41567815843635 | erot = 2.49971455295247 | epot = -21.7559519530568 | etot = -16.840559241668 -586000 ekin = 3.5784340003808 | erot = 1.99027982649426 | epot = -21.7770294519877 | etot = -16.2083156251126 -587000 ekin = 3.53538631245293 | erot = 1.96660128703793 | epot = -21.754918588089 | etot = -16.2529309885981 -588000 ekin = 2.80370665446806 | erot = 1.58935491344442 | epot = -21.7265541827784 | etot = -17.3334926148659 -589000 ekin = 2.31177964330664 | erot = 2.19607744710081 | epot = -21.7746975125222 | etot = -17.2668404221147 -590000 ekin = 2.5714466329988 | erot = 1.71442868035276 | epot = -21.7777302960456 | etot = -17.491854982694 -591000 ekin = 1.90022629380971 | erot = 3.80795912333789 | epot = -21.8668982157977 | etot = -16.1587127986501 -592000 ekin = 2.10279882895952 | erot = 2.85583901759444 | epot = -21.9108757117546 | etot = -16.9522378652007 -593000 ekin = 1.66307844177278 | erot = 2.45945798543616 | epot = -21.9477120734663 | etot = -17.8251756462574 -594000 ekin = 1.85147702439684 | erot = 2.37601059124117 | epot = -22.0726279896574 | etot = -17.8451403740194 -595000 ekin = 1.62809593102861 | erot = 2.1376140673132 | epot = -22.2629667751952 | etot = -18.4972567768534 -596000 ekin = 1.85098827042652 | erot = 1.55279926082377 | epot = -22.3598865590345 | etot = -18.9560990277842 -597000 ekin = 2.21895198056269 | erot = 2.31253848766694 | epot = -22.4199578312546 | etot = -17.8884673630249 -598000 ekin = 1.87160565114506 | erot = 3.0277507704973 | epot = -22.4911453410919 | etot = -17.5917889194496 -599000 ekin = 2.84158802287444 | erot = 2.1920185610572 | epot = -22.5193833279106 | etot = -17.4857767439789 -600000 ekin = 2.63818657196383 | erot = 2.13278760870029 | epot = -22.4344536662284 | etot = -17.6634794855643 -601000 ekin = 2.95993107274926 | erot = 3.20885509956692 | epot = -22.3072696496284 | etot = -16.1384834773122 -602000 ekin = 2.94299398558342 | erot = 2.68013224377472 | epot = -22.2188520758353 | etot = -16.5957258464772 -603000 ekin = 2.59660369946999 | erot = 2.70989416331592 | epot = -22.1609733489959 | etot = -16.85447548621 -604000 ekin = 1.79240933557438 | erot = 2.1163931677418 | epot = -22.191830604205 | etot = -18.2830281008888 -605000 ekin = 1.83069958852698 | erot = 2.27958589555072 | epot = -22.223893707794 | etot = -18.1136082237163 -606000 ekin = 2.33186424204054 | erot = 2.19630763210353 | epot = -22.1677269529972 | etot = -17.6395550788531 -607000 ekin = 2.71182931402141 | erot = 2.97109858003922 | epot = -22.1521845558164 | etot = -16.4692566617558 -608000 ekin = 2.41997749037237 | erot = 2.41608876723459 | epot = -22.1090787304487 | etot = -17.2730124728417 -609000 ekin = 1.88827272588068 | erot = 2.63293672960969 | epot = -21.998471393382 | etot = -17.4772619378917 -610000 ekin = 3.00352553825308 | erot = 2.17715232945663 | epot = -21.921125149498 | etot = -16.7404472817883 -611000 ekin = 2.45802371980552 | erot = 2.74758446810105 | epot = -21.9175611897393 | etot = -16.7119530018327 -612000 ekin = 2.52205492882348 | erot = 2.13390999483971 | epot = -21.952922358004 | etot = -17.2969574343408 -613000 ekin = 3.0366403087624 | erot = 2.11840093313595 | epot = -22.0002186117394 | etot = -16.8451773698411 -614000 ekin = 2.28547905389303 | erot = 3.00549626246339 | epot = -22.0746950370029 | etot = -16.7837197206465 -615000 ekin = 1.68496895203681 | erot = 2.6238974067784 | epot = -22.0312524650619 | etot = -17.7223861062467 -616000 ekin = 1.93869933628639 | erot = 2.84243572789263 | epot = -22.0598022720905 | etot = -17.2786672079115 -617000 ekin = 2.16688154116712 | erot = 2.51660309412659 | epot = -22.0580971291184 | etot = -17.3746124938247 -618000 ekin = 3.09921969264655 | erot = 2.74549226450141 | epot = -22.0155339259629 | etot = -16.1708219688149 -619000 ekin = 3.43177694169698 | erot = 2.12198343059748 | epot = -21.986089674814 | etot = -16.4323293025195 -620000 ekin = 4.28772375093259 | erot = 2.22706390062221 | epot = -21.9590250230057 | etot = -15.4442373714509 -621000 ekin = 3.0817377949309 | erot = 2.5715302712226 | epot = -21.9009729000649 | etot = -16.2477048339114 -622000 ekin = 2.73165859080048 | erot = 2.62811367428178 | epot = -21.8396158670716 | etot = -16.4798436019893 -623000 ekin = 2.85443766883212 | erot = 2.89934248449797 | epot = -21.6835451183467 | etot = -15.9297649650166 -624000 ekin = 2.03264036935949 | erot = 3.41736745424461 | epot = -21.5163207310271 | etot = -16.066312907423 -625000 ekin = 2.93853121772536 | erot = 2.67773115439888 | epot = -21.3838363274969 | etot = -15.7675739553726 -626000 ekin = 2.62777924734508 | erot = 2.18162282576041 | epot = -21.3730333234904 | etot = -16.5636312503849 -627000 ekin = 2.31990667522995 | erot = 2.39482401666938 | epot = -21.4354987061654 | etot = -16.7207680142661 -628000 ekin = 2.22203953187498 | erot = 2.76412791129531 | epot = -21.5952632825804 | etot = -16.6090958394101 -629000 ekin = 2.21775645889425 | erot = 1.98065436363089 | epot = -21.7562971185524 | etot = -17.5578862960273 -630000 ekin = 2.47359866092386 | erot = 2.13925319586019 | epot = -21.7758191809316 | etot = -17.1629673241476 -631000 ekin = 2.05051856532003 | erot = 1.79291928253663 | epot = -21.7853759251476 | etot = -17.9419380772909 -632000 ekin = 1.64850143430096 | erot = 3.28395498862858 | epot = -21.8317536045469 | etot = -16.8992971816173 -633000 ekin = 2.35005689695082 | erot = 2.3390788040001 | epot = -21.9523909247055 | etot = -17.2632552237546 -634000 ekin = 2.35693540441333 | erot = 2.46483135146881 | epot = -22.0188246134313 | etot = -17.1970578575491 -635000 ekin = 1.98898390231468 | erot = 3.3707265296603 | epot = -22.0674825033302 | etot = -16.7077720713553 -636000 ekin = 2.50980012291046 | erot = 2.48689559173921 | epot = -22.0698487955046 | etot = -17.073153080855 -637000 ekin = 2.77498878878958 | erot = 2.80713853773056 | epot = -21.9907400151913 | etot = -16.4086126886711 -638000 ekin = 2.43806293105884 | erot = 2.79004417520011 | epot = -22.0575076323657 | etot = -16.8294005261068 -639000 ekin = 1.88083948877533 | erot = 2.09676394462429 | epot = -22.048310763883 | etot = -18.0707073304834 -640000 ekin = 2.08188388766029 | erot = 3.35897660071801 | epot = -21.9960574959824 | etot = -16.5551970076041 -641000 ekin = 2.09182696029806 | erot = 2.24096762672331 | epot = -22.0953763111483 | etot = -17.7625817241269 -642000 ekin = 2.29622874060124 | erot = 2.6949832870016 | epot = -22.151409557085 | etot = -17.1601975294822 -643000 ekin = 2.73569648066616 | erot = 2.20073493313118 | epot = -22.0949564882595 | etot = -17.1585250744621 -644000 ekin = 2.8774767032651 | erot = 3.41751476954418 | epot = -22.1298161092011 | etot = -15.8348246363918 -645000 ekin = 2.4290925856966 | erot = 2.10618409243776 | epot = -22.0667334414767 | etot = -17.5314567633423 -646000 ekin = 2.69467422761642 | erot = 1.80008229703286 | epot = -21.8974158987303 | etot = -17.402659374081 -647000 ekin = 2.50876501618975 | erot = 2.02696268329777 | epot = -21.7872910341098 | etot = -17.2515633346223 -648000 ekin = 2.30426131969587 | erot = 1.6458501532655 | epot = -21.8921456933826 | etot = -17.9420342204213 -649000 ekin = 2.59259139367702 | erot = 1.74799625276216 | epot = -22.0338111702567 | etot = -17.6932235238175 -650000 ekin = 2.70418822875775 | erot = 2.18747773876972 | epot = -22.1379356884042 | etot = -17.2462697208768 -651000 ekin = 2.13264787236381 | erot = 3.27713220231 | epot = -22.2140357553834 | etot = -16.8042556807096 -652000 ekin = 2.3441787788075 | erot = 2.31061064519192 | epot = -22.2512463247192 | etot = -17.5964569007197 -653000 ekin = 2.0783895005922 | erot = 2.15412898001082 | epot = -22.2780657745064 | etot = -18.0455472939034 -654000 ekin = 2.30897991961162 | erot = 1.85124051868153 | epot = -22.3104418685982 | etot = -18.150221430305 -655000 ekin = 2.12106061544383 | erot = 1.78500189152084 | epot = -22.2852988882964 | etot = -18.3792363813318 -656000 ekin = 2.4735695444961 | erot = 2.3420013127236 | epot = -22.2660003992253 | etot = -17.4504295420056 -657000 ekin = 2.49468968638545 | erot = 2.86409627910532 | epot = -22.2925124601966 | etot = -16.9337264947059 -658000 ekin = 2.49656210866705 | erot = 2.87057420343463 | epot = -22.2700281258802 | etot = -16.9028918137786 -659000 ekin = 3.4002230119036 | erot = 2.78079262685479 | epot = -22.1392014132181 | etot = -15.9581857744598 -660000 ekin = 2.71468183951524 | erot = 2.00084154317764 | epot = -22.0088760160501 | etot = -17.2933526333572 -661000 ekin = 2.22564214621743 | erot = 2.53966313147986 | epot = -21.8739603827229 | etot = -17.1086551050257 -662000 ekin = 2.02829181839209 | erot = 2.53975139691216 | epot = -21.8209028819505 | etot = -17.2528596666463 -663000 ekin = 2.23525378228906 | erot = 2.31366678132105 | epot = -21.7767349910666 | etot = -17.2278144274565 -664000 ekin = 2.34360790891041 | erot = 1.86434304281456 | epot = -21.6752271215873 | etot = -17.4672761698624 -665000 ekin = 2.6131782266455 | erot = 2.2942197715156 | epot = -21.6042046109401 | etot = -16.696806612779 -666000 ekin = 1.62393527088755 | erot = 2.31134155882296 | epot = -21.5004119311113 | etot = -17.5651351014008 -667000 ekin = 1.67276637494452 | erot = 2.8234547562148 | epot = -21.4092484100762 | etot = -16.9130272789169 -668000 ekin = 2.49690543622955 | erot = 3.27659348221062 | epot = -21.2758920536656 | etot = -15.5023931352255 -669000 ekin = 1.62806554113038 | erot = 2.65931770046313 | epot = -21.2000245357891 | etot = -16.9126412941955 -670000 ekin = 2.23977376187302 | erot = 2.6095972175341 | epot = -21.1325862484852 | etot = -16.2832152690781 -671000 ekin = 2.28188801168356 | erot = 2.16305917244004 | epot = -21.0881674881013 | etot = -16.6432203039777 -672000 ekin = 1.98109020838353 | erot = 1.6545553737063 | epot = -21.0064866117102 | etot = -17.3708410296204 -673000 ekin = 1.94244230895293 | erot = 2.07625571526623 | epot = -20.9829498347911 | etot = -16.964251810572 -674000 ekin = 2.13730353222164 | erot = 2.16737069376511 | epot = -21.0214974795938 | etot = -16.716823253607 -675000 ekin = 2.0738264400087 | erot = 2.48606196350775 | epot = -21.0590224845651 | etot = -16.4991340810486 -676000 ekin = 2.45892166960283 | erot = 2.79866228976047 | epot = -21.091647649138 | etot = -15.8340636897747 -677000 ekin = 2.20625727487218 | erot = 2.63108770232727 | epot = -21.1176354388896 | etot = -16.2802904616901 -678000 ekin = 2.15213590782194 | erot = 2.79904006113487 | epot = -21.0140734470396 | etot = -16.0628974780828 -679000 ekin = 2.18343356480304 | erot = 2.18490396550911 | epot = -20.9181838430532 | etot = -16.549846312741 -680000 ekin = 2.10821203830737 | erot = 2.68505727915271 | epot = -20.9461225832237 | etot = -16.1528532657636 -681000 ekin = 2.19096880009954 | erot = 1.84583521880628 | epot = -21.049747832921 | etot = -17.0129438140152 -682000 ekin = 3.05384884549289 | erot = 2.40296404987894 | epot = -21.0557501140049 | etot = -15.5989372186331 -683000 ekin = 2.86746710745163 | erot = 2.09710011404619 | epot = -21.0757665962385 | etot = -16.1111993747407 -684000 ekin = 1.99137037242252 | erot = 2.9957171615915 | epot = -21.113690638146 | etot = -16.126603104132 -685000 ekin = 1.5741328626647 | erot = 2.03056483786644 | epot = -21.1261282639781 | etot = -17.5214305634469 -686000 ekin = 2.37471898314499 | erot = 2.54238213977475 | epot = -21.1270745420036 | etot = -16.2099734190839 -687000 ekin = 1.90729058124661 | erot = 2.87801884923459 | epot = -21.1165743035804 | etot = -16.3312648730992 -688000 ekin = 2.62048299874671 | erot = 2.25003931366163 | epot = -21.0986223733053 | etot = -16.228100060897 -689000 ekin = 2.68144410783034 | erot = 2.65050786826928 | epot = -21.2128570731653 | etot = -15.8809050970657 -690000 ekin = 2.57020917801037 | erot = 2.48157927371166 | epot = -21.3777687615583 | etot = -16.3259803098363 -691000 ekin = 2.19847693909567 | erot = 2.52609380111695 | epot = -21.4850476477408 | etot = -16.7604769075282 -692000 ekin = 2.34330258125554 | erot = 3.25002655945746 | epot = -21.4986374232228 | etot = -15.9053082825098 -693000 ekin = 2.29392126490893 | erot = 3.00689891870992 | epot = -21.5194889284254 | etot = -16.2186687448065 -694000 ekin = 2.65812969336117 | erot = 2.58735606777937 | epot = -21.7321648892945 | etot = -16.4866791281539 -695000 ekin = 2.4316162204446 | erot = 1.19791474341253 | epot = -21.9242547697609 | etot = -18.2947238059037 -696000 ekin = 1.81693709897036 | erot = 1.47023542418153 | epot = -21.8934819532786 | etot = -18.6063094301267 -697000 ekin = 2.39493869239631 | erot = 2.11395689699314 | epot = -21.9285847092192 | etot = -17.4196891198297 -698000 ekin = 2.35958906151814 | erot = 1.92876427029827 | epot = -22.0159711481531 | etot = -17.7276178163367 -699000 ekin = 2.48368136666702 | erot = 2.56159396613047 | epot = -22.0103910104183 | etot = -16.9651156776208 -700000 ekin = 2.1450801922911 | erot = 2.29917908979014 | epot = -21.922109394496 | etot = -17.4778501124148 -701000 ekin = 2.1745638313557 | erot = 2.20111278634863 | epot = -21.8156387421437 | etot = -17.4399621244394 -702000 ekin = 1.56478756336654 | erot = 2.01119937519508 | epot = -21.7778672436792 | etot = -18.2018803051176 -703000 ekin = 2.06132778292139 | erot = 2.17314611223241 | epot = -21.7930054701539 | etot = -17.5585315750001 -704000 ekin = 2.81983493340982 | erot = 1.94305987211435 | epot = -21.8114535861206 | etot = -17.0485587805964 -705000 ekin = 2.82055978010065 | erot = 2.18251946343581 | epot = -21.766252843205 | etot = -16.7631735996685 -706000 ekin = 1.98110988281637 | erot = 2.32695112193058 | epot = -21.78040819482 | etot = -17.4723471900731 -707000 ekin = 1.91160206821925 | erot = 2.05897248195774 | epot = -21.833053672666 | etot = -17.862479122489 -708000 ekin = 2.49797260430835 | erot = 2.18514664814829 | epot = -21.8432772467022 | etot = -17.1601579942456 -709000 ekin = 2.86869907833219 | erot = 2.56795355151628 | epot = -21.8927607091555 | etot = -16.456108079307 -710000 ekin = 2.19600917748735 | erot = 2.26596247481176 | epot = -21.8688086872618 | etot = -17.4068370349627 -711000 ekin = 2.34017154985874 | erot = 1.44618662245857 | epot = -21.9060063017349 | etot = -18.1196481294176 -712000 ekin = 2.571626566146 | erot = 2.28694259963336 | epot = -22.0214699153591 | etot = -17.1629007495797 -713000 ekin = 1.98520968446438 | erot = 2.33486849904896 | epot = -22.1149578958933 | etot = -17.7948797123799 -714000 ekin = 2.59962138344223 | erot = 2.10724318046303 | epot = -22.1786558411969 | etot = -17.4717912772916 -715000 ekin = 2.4195410390622 | erot = 3.74883662346075 | epot = -22.1475942949397 | etot = -15.9792166324167 -716000 ekin = 2.84279313896907 | erot = 2.86022834631577 | epot = -22.0565535101519 | etot = -16.3535320248671 -717000 ekin = 3.44629592734909 | erot = 3.22665808286196 | epot = -21.9609198250287 | etot = -15.2879658148176 -718000 ekin = 3.10244803746594 | erot = 3.95040927490044 | epot = -21.8593081248118 | etot = -14.8064508124454 -719000 ekin = 2.37775253377205 | erot = 2.95612290233182 | epot = -21.8454876437379 | etot = -16.511612207634 -720000 ekin = 2.21232762300396 | erot = 3.13525351489473 | epot = -21.8232438423991 | etot = -16.4756627045004 -721000 ekin = 1.69400550933915 | erot = 2.23173955948197 | epot = -21.7326772937498 | etot = -17.8069322249286 -722000 ekin = 1.90042078179571 | erot = 2.80431814967802 | epot = -21.7394766818033 | etot = -17.0347377503296 -723000 ekin = 2.36468467929204 | erot = 2.56344225093691 | epot = -21.6720290892733 | etot = -16.7439021590444 -724000 ekin = 1.73517505640396 | erot = 2.45263100900798 | epot = -21.6468054707964 | etot = -17.4589994053844 -725000 ekin = 2.29142999435738 | erot = 2.94537439813943 | epot = -21.7063452187228 | etot = -16.4695408262259 -726000 ekin = 1.63432825555556 | erot = 2.30396244675118 | epot = -21.7456114234691 | etot = -17.8073207211624 -727000 ekin = 2.48133238220639 | erot = 3.20400739682796 | epot = -21.7806560741677 | etot = -16.0953162951334 -728000 ekin = 2.22757813298303 | erot = 2.16464177499475 | epot = -21.7790073705306 | etot = -17.3867874625529 -729000 ekin = 1.89754664123238 | erot = 1.65708384447828 | epot = -21.818793017262 | etot = -18.2641625315513 -730000 ekin = 1.81104622151894 | erot = 2.15772480190845 | epot = -21.8166979693399 | etot = -17.8479269459125 -731000 ekin = 2.20035848812534 | erot = 2.984094437949 | epot = -21.7770198662085 | etot = -16.5925669401341 -732000 ekin = 2.43533262071618 | erot = 2.2714682081237 | epot = -21.6795793034593 | etot = -16.9727784746194 -733000 ekin = 3.07400414774412 | erot = 2.56794551470528 | epot = -21.7282232978635 | etot = -16.0862736354141 -734000 ekin = 2.38495425977383 | erot = 2.02723577856807 | epot = -21.7862523639798 | etot = -17.3740623256379 -735000 ekin = 2.14308578867868 | erot = 1.55617115431814 | epot = -21.8355194712534 | etot = -18.1362625282566 -736000 ekin = 2.14719637814141 | erot = 3.43682718130883 | epot = -21.9432003809582 | etot = -16.359176821508 -737000 ekin = 1.74871923076117 | erot = 3.58265582775873 | epot = -21.961923642904 | etot = -16.6305485843841 -738000 ekin = 2.04024583543123 | erot = 2.50826561687817 | epot = -21.9946639190404 | etot = -17.446152466731 -739000 ekin = 1.85177899677126 | erot = 2.20064138018375 | epot = -22.0123052281368 | etot = -17.9598848511818 -740000 ekin = 2.83857272073312 | erot = 2.79134975714448 | epot = -22.0279140396377 | etot = -16.39799156176 -741000 ekin = 2.46635495152007 | erot = 2.9103294596823 | epot = -22.0794124202159 | etot = -16.7027280090136 -742000 ekin = 2.71465468895042 | erot = 3.27392339093581 | epot = -22.2079531631203 | etot = -16.2193750832341 -743000 ekin = 2.22475007867544 | erot = 3.21169489639582 | epot = -22.3366771138424 | etot = -16.9002321387711 -744000 ekin = 2.01249089419451 | erot = 3.77628990094158 | epot = -22.4195693816618 | etot = -16.6307885865257 -745000 ekin = 3.1550015757828 | erot = 2.315867165247 | epot = -22.4039856366928 | etot = -16.933116895663 -746000 ekin = 2.9760064146713 | erot = 2.63068823711827 | epot = -22.3618535919292 | etot = -16.7551589401397 -747000 ekin = 2.34106182302225 | erot = 2.04664398645464 | epot = -22.354695038859 | etot = -17.9669892293821 -748000 ekin = 2.37138666208783 | erot = 2.40542984904221 | epot = -22.3895155133383 | etot = -17.6126990022083 -749000 ekin = 2.06138370471239 | erot = 2.76626854206187 | epot = -22.3750763140021 | etot = -17.5474240672278 -750000 ekin = 1.64672066604894 | erot = 2.38347386235118 | epot = -22.4369940886927 | etot = -18.4067995602926 -751000 ekin = 1.78177119419735 | erot = 2.81833680350818 | epot = -22.5257071681888 | etot = -17.9255991704833 -752000 ekin = 1.34818171721257 | erot = 1.45846043808637 | epot = -22.6018348796366 | etot = -19.7951927243377 -753000 ekin = 1.87655795218726 | erot = 2.45353295142028 | epot = -22.5520612881159 | etot = -18.2219703845083 -754000 ekin = 1.74975840903648 | erot = 2.74283699647828 | epot = -22.4634749655138 | etot = -17.9708795599991 -755000 ekin = 2.42034607898545 | erot = 2.41190491839854 | epot = -22.3898060492349 | etot = -17.5575550518509 -756000 ekin = 1.85451473741877 | erot = 2.78171703843177 | epot = -22.3128363094556 | etot = -17.6766045336051 -757000 ekin = 1.97510746852342 | erot = 2.51748911462571 | epot = -22.1174762043225 | etot = -17.6248796211734 -758000 ekin = 1.22903408000892 | erot = 2.60716879638028 | epot = -21.9785553297124 | etot = -18.1423524533232 -759000 ekin = 2.21600197663295 | erot = 1.43977874856212 | epot = -22.1451816653321 | etot = -18.4894009401371 -760000 ekin = 2.68031518877979 | erot = 2.41730519207617 | epot = -22.2523665710424 | etot = -17.1547461901865 -761000 ekin = 2.17596592269854 | erot = 2.27182574078646 | epot = -22.3278934724238 | etot = -17.8801018089388 -762000 ekin = 2.18672258558963 | erot = 1.66841951917867 | epot = -22.3560817096941 | etot = -18.5009396049258 -763000 ekin = 2.45624456911328 | erot = 3.353199087397 | epot = -22.4226856635722 | etot = -16.6132420070619 -764000 ekin = 2.82991156680043 | erot = 2.78772749955354 | epot = -22.4168769890428 | etot = -16.7992379226888 -765000 ekin = 1.82695315748762 | erot = 2.76260899367527 | epot = -22.3180874182918 | etot = -17.7285252671289 -766000 ekin = 2.64718727066684 | erot = 2.30809984362825 | epot = -22.1747973384657 | etot = -17.2195102241706 -767000 ekin = 2.57546948652102 | erot = 2.85622460559127 | epot = -22.0792338208857 | etot = -16.6475397287734 -768000 ekin = 1.86461408985655 | erot = 2.77026783876655 | epot = -22.0997460179139 | etot = -17.4648640892908 -769000 ekin = 2.39719072886598 | erot = 2.30714111472591 | epot = -22.1774105238745 | etot = -17.4730786802827 -770000 ekin = 2.47072108127125 | erot = 3.23258521636165 | epot = -22.2814001434105 | etot = -16.5780938457776 -771000 ekin = 2.33036519398503 | erot = 2.29089498051982 | epot = -22.3195270405423 | etot = -17.6982668660374 -772000 ekin = 2.26183241289834 | erot = 3.00933524584073 | epot = -22.4177530473637 | etot = -17.1465853886246 -773000 ekin = 2.23430073882848 | erot = 1.82006063686398 | epot = -22.4857511691573 | etot = -18.4313897934648 -774000 ekin = 2.82253641499965 | erot = 2.20426049452907 | epot = -22.4768371725758 | etot = -17.4500402630471 -775000 ekin = 1.80826097265228 | erot = 1.8594330353803 | epot = -22.4067702410985 | etot = -18.7390762330659 -776000 ekin = 1.40036201749763 | erot = 3.15425759738852 | epot = -22.3648422416548 | etot = -17.8102226267687 -777000 ekin = 1.64191168277988 | erot = 2.80572311301618 | epot = -22.2758078856404 | etot = -17.8281730898443 -778000 ekin = 1.48568750761886 | erot = 2.23411617896699 | epot = -22.2807840878112 | etot = -18.5609804012253 -779000 ekin = 1.86180462326533 | erot = 1.89442532300483 | epot = -22.3101851282869 | etot = -18.5539551820167 -780000 ekin = 1.70083326144506 | erot = 2.31232836878966 | epot = -22.368088335214 | etot = -18.3549267049793 -781000 ekin = 2.10015890171884 | erot = 2.56021799860011 | epot = -22.4467515624801 | etot = -17.7863746621612 -782000 ekin = 2.56555999292579 | erot = 1.95862112685967 | epot = -22.3484071481452 | etot = -17.8242260283597 -783000 ekin = 2.16519753597492 | erot = 2.88346819560595 | epot = -22.2452576468217 | etot = -17.1965919152409 -784000 ekin = 2.82020985681265 | erot = 2.22817695283317 | epot = -22.2217547403593 | etot = -17.1733679307135 -785000 ekin = 3.11754466459225 | erot = 2.90955325829367 | epot = -22.2354545908828 | etot = -16.2083566679969 -786000 ekin = 2.79942218761003 | erot = 3.42875764975157 | epot = -22.250592498505 | etot = -16.0224126611434 -787000 ekin = 2.38458676493535 | erot = 3.01099796177293 | epot = -22.1654452152169 | etot = -16.7698604885087 -788000 ekin = 1.98626456977422 | erot = 2.00275328811937 | epot = -22.1112200648967 | etot = -18.1222022070031 -789000 ekin = 2.44233063979376 | erot = 2.28313889802901 | epot = -22.0447230803812 | etot = -17.3192535425585 -790000 ekin = 3.54880462493947 | erot = 2.80770271341156 | epot = -21.9679846446661 | etot = -15.6114773063151 -791000 ekin = 3.07908349792595 | erot = 2.4183569461896 | epot = -21.9560607901314 | etot = -16.4586203460158 -792000 ekin = 3.91821329297348 | erot = 1.97340936537895 | epot = -21.8852423103708 | etot = -15.9936196520184 -793000 ekin = 2.24372361561433 | erot = 2.58378808209984 | epot = -21.7746367758897 | etot = -16.9471250781755 -794000 ekin = 2.14759663301018 | erot = 2.45362282428674 | epot = -21.6057162069285 | etot = -17.0044967496316 -795000 ekin = 1.62843452575834 | erot = 2.41204885281414 | epot = -21.4428571758252 | etot = -17.4023737972527 -796000 ekin = 2.20611316383669 | erot = 2.13895899282881 | epot = -21.3315860267741 | etot = -16.9865138701086 -797000 ekin = 1.8301274808806 | erot = 1.99903093547351 | epot = -21.3391948873385 | etot = -17.5100364709844 -798000 ekin = 2.25726523935456 | erot = 2.51247281070767 | epot = -21.3769575532967 | etot = -16.6072195032345 -799000 ekin = 1.90933563327017 | erot = 2.87396619489344 | epot = -21.3621013619625 | etot = -16.5787995337988 -800000 ekin = 2.16791860235721 | erot = 2.34759279016547 | epot = -21.2767357657464 | etot = -16.7612243732237 -801000 ekin = 1.87657888051436 | erot = 1.64443435892708 | epot = -21.1205442749523 | etot = -17.5995310355109 -802000 ekin = 2.22680112501959 | erot = 2.21115076271302 | epot = -21.0075202165858 | etot = -16.5695683288532 -803000 ekin = 2.68720281674732 | erot = 1.9055828700456 | epot = -20.9783230569545 | etot = -16.3855373701615 -804000 ekin = 2.34742553306287 | erot = 2.89589931482196 | epot = -20.9208915085851 | etot = -15.6775666607002 -805000 ekin = 1.76090854918944 | erot = 2.71265295620197 | epot = -20.7896819578332 | etot = -16.3161204524417 -806000 ekin = 1.7462870636756 | erot = 2.0675335773069 | epot = -20.7361496593739 | etot = -16.9223290183914 -807000 ekin = 1.56796585063504 | erot = 1.70424554994442 | epot = -20.7915009374418 | etot = -17.5192895368624 -808000 ekin = 2.1089079867654 | erot = 2.39841171836652 | epot = -20.8718914314634 | etot = -16.3645717263314 -809000 ekin = 2.64205233751098 | erot = 1.51708231521757 | epot = -20.860658338686 | etot = -16.7015236859574 -810000 ekin = 3.09559784865049 | erot = 2.66400816236668 | epot = -20.7931361339113 | etot = -15.0335301228942 -811000 ekin = 3.04444079406036 | erot = 3.63356452868707 | epot = -20.8528361945454 | etot = -14.174830871798 -812000 ekin = 2.15160129632237 | erot = 2.79692069084717 | epot = -20.9401885998277 | etot = -15.9916666126582 -813000 ekin = 2.1866812847642 | erot = 3.17352337049868 | epot = -21.140046139319 | etot = -15.7798414840561 -814000 ekin = 1.72120340413861 | erot = 2.99586512288056 | epot = -21.2431304413524 | etot = -16.5260619143332 -815000 ekin = 2.15308486059066 | erot = 2.27039729778303 | epot = -21.2454651427287 | etot = -16.821982984355 -816000 ekin = 2.70853368688568 | erot = 1.52116799452424 | epot = -21.261293152511 | etot = -17.0315914711011 -817000 ekin = 2.58931303514761 | erot = 2.58517904286731 | epot = -21.3952446820623 | etot = -16.2207526040474 -818000 ekin = 2.27857909894085 | erot = 2.24637345033467 | epot = -21.4314613483393 | etot = -16.9065087990638 -819000 ekin = 2.10638790580901 | erot = 3.01120037058918 | epot = -21.4323015928675 | etot = -16.3147133164693 -820000 ekin = 2.45664566148736 | erot = 2.7075790370773 | epot = -21.3792192523262 | etot = -16.2149945537616 -821000 ekin = 2.56775447201567 | erot = 2.5492984098592 | epot = -21.3164894306539 | etot = -16.199436548779 -822000 ekin = 3.57289533285904 | erot = 2.21052116492673 | epot = -21.2854519181088 | etot = -15.502035420323 -823000 ekin = 3.55319917858674 | erot = 2.72446531740647 | epot = -21.2720447371835 | etot = -14.9943802411903 -824000 ekin = 4.11549879731445 | erot = 3.29143140978184 | epot = -21.2030896509282 | etot = -13.7961594438319 -825000 ekin = 2.91512457403517 | erot = 3.47068683775168 | epot = -21.0609871292213 | etot = -14.6751757174345 -826000 ekin = 1.7163898925254 | erot = 1.97834164539342 | epot = -20.8767355772593 | etot = -17.1820040393405 -827000 ekin = 1.87677701795696 | erot = 2.56463384104522 | epot = -20.7854029227346 | etot = -16.3439920637325 -828000 ekin = 2.38062360557162 | erot = 2.54648236886784 | epot = -20.7050759849485 | etot = -15.7779700105091 -829000 ekin = 2.23108302894327 | erot = 1.78470720624501 | epot = -20.6073113475481 | etot = -16.5915211123598 -830000 ekin = 2.54725147866706 | erot = 2.32441333820119 | epot = -20.4877024469931 | etot = -15.6160376301249 -831000 ekin = 2.68575093093387 | erot = 2.09843530086498 | epot = -20.3759551828171 | etot = -15.5917689510182 -832000 ekin = 2.59940424582709 | erot = 2.00750749806411 | epot = -20.1908446114452 | etot = -15.583932867554 -833000 ekin = 2.42127651950715 | erot = 2.60529540830756 | epot = -20.078944485857 | etot = -15.0523725580422 -834000 ekin = 2.84384893680911 | erot = 2.32747318035689 | epot = -20.0706360897591 | etot = -14.8993139725931 -835000 ekin = 2.7678557540129 | erot = 2.75945454275209 | epot = -20.196580890927 | etot = -14.669270594162 -836000 ekin = 2.53473695255286 | erot = 2.86392788167815 | epot = -20.358210381663 | etot = -14.9595455474319 -837000 ekin = 1.73656397849906 | erot = 1.97461102829179 | epot = -20.4142699072864 | etot = -16.7030949004955 -838000 ekin = 1.97190242589771 | erot = 2.78134736415134 | epot = -20.4306923978834 | etot = -15.6774426078343 -839000 ekin = 1.96899626495587 | erot = 2.72126775666989 | epot = -20.4229760480712 | etot = -15.7327120264454 -840000 ekin = 1.7171072647053 | erot = 2.97405496575738 | epot = -20.5310188981682 | etot = -15.8398566677055 -841000 ekin = 2.84263223284519 | erot = 2.84805882649256 | epot = -20.7029997187952 | etot = -15.0123086594574 -842000 ekin = 2.60852389795254 | erot = 2.84079273136912 | epot = -20.7559161264561 | etot = -15.3065994971344 -843000 ekin = 2.05482516428399 | erot = 2.60168054731321 | epot = -20.7398205878817 | etot = -16.0833148762845 -844000 ekin = 1.55484491564895 | erot = 1.93946122833937 | epot = -20.793873895268 | etot = -17.2995677512796 -845000 ekin = 2.34415562398594 | erot = 2.33054915402977 | epot = -20.9292293378503 | etot = -16.2545245598346 -846000 ekin = 2.10828138543307 | erot = 2.31084128804075 | epot = -21.0208568932193 | etot = -16.6017342197455 -847000 ekin = 2.49792342883821 | erot = 2.62762350266534 | epot = -20.9870443583388 | etot = -15.8614974268353 -848000 ekin = 2.16881569142256 | erot = 1.47414765167355 | epot = -21.0272780430065 | etot = -17.3843146999104 -849000 ekin = 2.02577069067687 | erot = 2.48073789957305 | epot = -21.0548829559118 | etot = -16.5483743656619 -850000 ekin = 2.56121323608232 | erot = 2.68216361525941 | epot = -21.0531120198317 | etot = -15.80973516849 -851000 ekin = 2.18318825014005 | erot = 2.93699487251027 | epot = -21.072057934595 | etot = -15.9518748119447 -852000 ekin = 2.47242228011125 | erot = 2.47093974244847 | epot = -21.1036036708141 | etot = -16.1602416482544 -853000 ekin = 2.39779726435527 | erot = 2.98937612414091 | epot = -21.0464025867825 | etot = -15.6592291982864 -854000 ekin = 2.33702117267764 | erot = 2.85284252822427 | epot = -20.9556796853364 | etot = -15.7658159844345 -855000 ekin = 2.34760752254692 | erot = 2.06775496176188 | epot = -20.9732459823191 | etot = -16.5578834980103 -856000 ekin = 2.50439922073455 | erot = 2.74747347867824 | epot = -20.8640767421381 | etot = -15.6122040427253 -857000 ekin = 2.54554426380173 | erot = 3.02043559253138 | epot = -20.7373381265487 | etot = -15.1713582702156 -858000 ekin = 3.06972052097933 | erot = 2.1533020939209 | epot = -20.6779613423402 | etot = -15.45493872744 -859000 ekin = 2.85296234704364 | erot = 2.24390648873861 | epot = -20.6722067614218 | etot = -15.5753379256396 -860000 ekin = 2.81550228271929 | erot = 1.51851082884538 | epot = -20.6725383213113 | etot = -16.3385252097467 -861000 ekin = 2.27514176030031 | erot = 2.84648353799519 | epot = -20.6420712292961 | etot = -15.5204459310006 -862000 ekin = 2.9987675929355 | erot = 1.87057008174782 | epot = -20.6660164836296 | etot = -15.7966788089463 -863000 ekin = 2.82347853622627 | erot = 1.77874439342615 | epot = -20.7576165207476 | etot = -16.1553935910952 -864000 ekin = 2.92188345840032 | erot = 2.64334274850666 | epot = -20.9261206064404 | etot = -15.3608943995334 -865000 ekin = 3.33407052864803 | erot = 2.25520565932836 | epot = -21.0515135151698 | etot = -15.4622373271934 -866000 ekin = 2.86068791662345 | erot = 3.16201991362392 | epot = -21.1397264169455 | etot = -15.1170185866981 -867000 ekin = 2.74707401666422 | erot = 3.06797998358081 | epot = -21.1320468209182 | etot = -15.3169928206732 -868000 ekin = 2.19562503546865 | erot = 2.22513352423332 | epot = -21.0678608919895 | etot = -16.6471023322876 -869000 ekin = 2.92239622436426 | erot = 2.5008962182639 | epot = -21.0133576609085 | etot = -15.5900652182804 -870000 ekin = 2.48942591106965 | erot = 2.13034723792471 | epot = -20.996084603173 | etot = -16.3763114541786 -871000 ekin = 2.19159342044105 | erot = 2.37819238438806 | epot = -20.874805817807 | etot = -16.3050200129778 -872000 ekin = 1.55149762269136 | erot = 2.09773965219071 | epot = -20.8507483226038 | etot = -17.2015110477217 -873000 ekin = 1.39031919518734 | erot = 2.27780516445362 | epot = -20.9245661591995 | etot = -17.2564417995585 -874000 ekin = 1.41307234618125 | erot = 2.76889585749685 | epot = -21.0893130528338 | etot = -16.9073448491557 -875000 ekin = 1.1903759815938 | erot = 2.71897418399016 | epot = -21.2265810734678 | etot = -17.3172309078839 -876000 ekin = 1.81153308354558 | erot = 2.98976206981359 | epot = -21.2471086207564 | etot = -16.4458134673973 -877000 ekin = 2.36285714663855 | erot = 2.036005929661 | epot = -21.3279144058001 | etot = -16.9290513295006 -878000 ekin = 2.12543608141368 | erot = 1.75442210002794 | epot = -21.3225487572348 | etot = -17.4426905757932 -879000 ekin = 2.27283239224876 | erot = 2.70186511894803 | epot = -21.3124243745064 | etot = -16.3377268633096 -880000 ekin = 2.68477293779859 | erot = 2.77341018951834 | epot = -21.3544902274222 | etot = -15.8963071001053 -881000 ekin = 2.87581138753759 | erot = 2.33631707903057 | epot = -21.330399862467 | etot = -16.1182713958988 -882000 ekin = 2.3286795198909 | erot = 2.16799605433164 | epot = -21.25964008372 | etot = -16.7629645094974 -883000 ekin = 2.36016075059912 | erot = 1.97853915282771 | epot = -21.0668204006881 | etot = -16.7281204972613 -884000 ekin = 2.52365942577107 | erot = 2.24976084040446 | epot = -20.9653280828805 | etot = -16.191907816705 -885000 ekin = 2.84734342605207 | erot = 2.26485201008783 | epot = -20.9652017220512 | etot = -15.8530062859113 -886000 ekin = 3.18250292594555 | erot = 1.73451408298307 | epot = -21.0018071240468 | etot = -16.0847901151182 -887000 ekin = 2.68810301741898 | erot = 2.50208813779432 | epot = -21.0684744202113 | etot = -15.878283264998 -888000 ekin = 2.15240565341107 | erot = 2.83219210215604 | epot = -21.1767699295518 | etot = -16.1921721739847 -889000 ekin = 2.16923637104046 | erot = 2.20209706465088 | epot = -21.1021053306932 | etot = -16.7307718950019 -890000 ekin = 1.7855023510616 | erot = 2.98359580087557 | epot = -21.1862135178402 | etot = -16.4171153659031 -891000 ekin = 1.64893562703222 | erot = 2.27727861261825 | epot = -21.3185718288916 | etot = -17.3923575892411 -892000 ekin = 1.96573403811713 | erot = 2.36272783048894 | epot = -21.459073017988 | etot = -17.1306111493819 -893000 ekin = 1.79366158034469 | erot = 1.8414245936827 | epot = -21.5466572595161 | etot = -17.9115710854887 -894000 ekin = 2.81388625610773 | erot = 2.80751276121754 | epot = -21.653645549411 | etot = -16.0322465320857 -895000 ekin = 2.00720208466152 | erot = 2.75365533683677 | epot = -21.7495268499499 | etot = -16.9886694284516 -896000 ekin = 1.6504129469732 | erot = 2.56279209882525 | epot = -21.8921291347682 | etot = -17.6789240889697 -897000 ekin = 1.78028626356388 | erot = 2.35359760186793 | epot = -22.0277295687316 | etot = -17.8938457032998 -898000 ekin = 1.85084740655105 | erot = 2.39311858936893 | epot = -22.0484278013109 | etot = -17.804461805391 -899000 ekin = 1.66159541585127 | erot = 3.04237586636532 | epot = -21.9567167335553 | etot = -17.2527454513387 -900000 ekin = 2.15147578839776 | erot = 2.62380976965387 | epot = -21.9142539059027 | etot = -17.1389683478511 -901000 ekin = 2.41284637562283 | erot = 2.69705294858772 | epot = -21.9824283113928 | etot = -16.8725289871823 -902000 ekin = 2.57612159273654 | erot = 2.40607700278042 | epot = -21.9951115024172 | etot = -17.0129129069002 -903000 ekin = 2.40399270595578 | erot = 2.40563977691886 | epot = -22.0217108129385 | etot = -17.2120783300639 -904000 ekin = 1.99424328949364 | erot = 3.12247316074079 | epot = -22.0941051678023 | etot = -16.9773887175679 -905000 ekin = 2.45187750521127 | erot = 2.11892854013094 | epot = -22.0607781456761 | etot = -17.4899721003339 -906000 ekin = 2.69425177422441 | erot = 1.66991173750643 | epot = -22.0544281667485 | etot = -17.6902646550177 -907000 ekin = 2.57312994796075 | erot = 2.16897016056236 | epot = -22.0362779601713 | etot = -17.2941778516482 -908000 ekin = 2.96409406517859 | erot = 2.4024711800449 | epot = -22.0175634304182 | etot = -16.6509981851947 -909000 ekin = 3.12776536145526 | erot = 2.11994277048498 | epot = -22.0594136296836 | etot = -16.8117054977433 -910000 ekin = 2.92235459450191 | erot = 3.50321314826196 | epot = -22.1261319680945 | etot = -15.7005642253306 -911000 ekin = 1.85367265839013 | erot = 2.7340677155879 | epot = -22.1669720947937 | etot = -17.5792317208157 -912000 ekin = 2.6441002333698 | erot = 1.86322369928707 | epot = -22.1988213519214 | etot = -17.6914974192646 -913000 ekin = 2.46819903214737 | erot = 2.03086240531084 | epot = -22.3188294931139 | etot = -17.8197680556557 -914000 ekin = 2.0189364132938 | erot = 2.94279285834543 | epot = -22.3498562089308 | etot = -17.3881269372916 -915000 ekin = 2.82747738433327 | erot = 2.11633807308138 | epot = -22.3626846124428 | etot = -17.4188691550282 -916000 ekin = 2.54297245214782 | erot = 3.23310309863579 | epot = -22.4639551563544 | etot = -16.6878796055708 -917000 ekin = 2.317284459617 | erot = 2.24259984965456 | epot = -22.4622375561737 | etot = -17.9023532469021 -918000 ekin = 2.08741226822699 | erot = 2.05691148612588 | epot = -22.3736961837371 | etot = -18.2293724293842 -919000 ekin = 2.60375298745589 | erot = 2.38992198070848 | epot = -22.381600437649 | etot = -17.3879254694846 -920000 ekin = 3.21906968424263 | erot = 2.75034755110955 | epot = -22.4644247832706 | etot = -16.4950075479185 -921000 ekin = 2.67870624565115 | erot = 1.98396423697626 | epot = -22.5250790361652 | etot = -17.8624085535378 -922000 ekin = 1.43278887121421 | erot = 1.5212533647767 | epot = -22.5927230801778 | etot = -19.6386808441869 -923000 ekin = 1.69060624417004 | erot = 1.88306141910809 | epot = -22.6640058777009 | etot = -19.0903382144228 -924000 ekin = 2.14344220825837 | erot = 1.52268950055615 | epot = -22.6406273602344 | etot = -18.9744956514199 -925000 ekin = 2.26099137202492 | erot = 1.33050593263702 | epot = -22.5231436368656 | etot = -18.9316463322036 -926000 ekin = 2.00910763305932 | erot = 2.07375747532886 | epot = -22.4432067940419 | etot = -18.3603416856537 -927000 ekin = 2.53244780866363 | erot = 1.99782770480987 | epot = -22.5729932869624 | etot = -18.0427177734889 -928000 ekin = 2.57222338912656 | erot = 2.50502398255852 | epot = -22.7398443943546 | etot = -17.6625970226695 -929000 ekin = 2.6604125156482 | erot = 1.82856993040844 | epot = -22.7887212302343 | etot = -18.2997387841776 -930000 ekin = 2.41305450735431 | erot = 2.00588068310628 | epot = -22.8018421191433 | etot = -18.3829069286827 -931000 ekin = 3.02564328504603 | erot = 2.11587474765859 | epot = -22.7554011904621 | etot = -17.6138831577575 -932000 ekin = 2.345493847807 | erot = 1.88252953078422 | epot = -22.8017329710419 | etot = -18.5737095924506 -933000 ekin = 2.1694502869689 | erot = 2.85662500627744 | epot = -22.8226969360083 | etot = -17.796621642762 -934000 ekin = 2.17146721978253 | erot = 2.11951749144879 | epot = -22.863822849274 | etot = -18.5728381380427 -935000 ekin = 2.34458616912959 | erot = 2.23416576036772 | epot = -22.8574077017674 | etot = -18.2786557722701 -936000 ekin = 2.28175701976408 | erot = 2.53013652057632 | epot = -22.9767476232764 | etot = -18.164854082936 -937000 ekin = 2.30615675948239 | erot = 2.82847988543263 | epot = -23.0701138758201 | etot = -17.9354772309051 -938000 ekin = 2.44231188769576 | erot = 2.0074347584303 | epot = -23.1347662810948 | etot = -18.6850196349687 -939000 ekin = 2.97733385945386 | erot = 2.10203628017719 | epot = -23.1190097237646 | etot = -18.0396395841336 -940000 ekin = 3.7421677147709 | erot = 2.68152697601896 | epot = -23.0475806158046 | etot = -16.6238859250147 -941000 ekin = 3.11295236744588 | erot = 2.28688684379554 | epot = -22.9429748609955 | etot = -17.5431356497541 -942000 ekin = 3.46623937507365 | erot = 1.87520710821393 | epot = -22.9025531718167 | etot = -17.5611066885292 -943000 ekin = 3.79173660111055 | erot = 2.70947594186532 | epot = -22.8673682470227 | etot = -16.3661557040469 -944000 ekin = 2.65981718352589 | erot = 2.74921677045581 | epot = -22.8292657284419 | etot = -17.4202317744602 -945000 ekin = 2.54666185018866 | erot = 2.02257137114126 | epot = -22.723461570169 | etot = -18.154228348839 -946000 ekin = 2.4639439434652 | erot = 1.67047296565225 | epot = -22.5521488157529 | etot = -18.4177319066355 -947000 ekin = 2.40802147360554 | erot = 1.99436728079209 | epot = -22.4558507483505 | etot = -18.0534619939529 -948000 ekin = 3.53638943439814 | erot = 2.58008822568542 | epot = -22.320526737886 | etot = -16.2040490778025 -949000 ekin = 2.98836642878581 | erot = 2.43483192716865 | epot = -22.1062186298424 | etot = -16.6830202738879 -950000 ekin = 1.8506029036585 | erot = 3.01144415000371 | epot = -21.9461665434677 | etot = -17.0841194898055 -951000 ekin = 2.24126333899115 | erot = 2.360964782598 | epot = -21.903362150983 | etot = -17.3011340293938 -952000 ekin = 2.17635665089897 | erot = 1.66171020386367 | epot = -21.8837115918785 | etot = -18.0456447371159 -953000 ekin = 2.32438986511484 | erot = 1.96772774373572 | epot = -21.8620448131731 | etot = -17.5699272043226 -954000 ekin = 1.49063234940533 | erot = 3.34928565739799 | epot = -21.7945452107542 | etot = -16.9546272039509 -955000 ekin = 1.88418951039555 | erot = 2.69014814861619 | epot = -21.7200686498238 | etot = -17.1457309908121 -956000 ekin = 1.69291601426871 | erot = 2.1645662569751 | epot = -21.67000557149 | etot = -17.8125233002462 -957000 ekin = 1.73501465937615 | erot = 1.64299266035092 | epot = -21.6537546166965 | etot = -18.2757472969694 -958000 ekin = 1.60433119962989 | erot = 2.19178936617743 | epot = -21.6456701616229 | etot = -17.8495495958156 -959000 ekin = 2.59325237116392 | erot = 2.48228488776355 | epot = -21.6578286055141 | etot = -16.5822913465866 -960000 ekin = 2.55452313966818 | erot = 2.05772019404723 | epot = -21.6609487080123 | etot = -17.0487053742969 -961000 ekin = 2.2782724554851 | erot = 2.17961583407472 | epot = -21.6530067200073 | etot = -17.1951184304475 -962000 ekin = 1.6603646541701 | erot = 3.50991264012086 | epot = -21.6636215038227 | etot = -16.4933442095318 -963000 ekin = 1.98983107474213 | erot = 1.50487996807377 | epot = -21.607445249844 | etot = -18.1127342070281 -964000 ekin = 2.1801653377091 | erot = 2.29029841094579 | epot = -21.5573031984776 | etot = -17.0868394498227 -965000 ekin = 2.10786877123582 | erot = 2.32216595776003 | epot = -21.5484811250514 | etot = -17.1184463960556 -966000 ekin = 3.14104688246034 | erot = 3.41837947669167 | epot = -21.5824220489405 | etot = -15.0229956897885 -967000 ekin = 3.05692240987348 | erot = 2.17321453760644 | epot = -21.5249732131507 | etot = -16.2948362656708 -968000 ekin = 2.05076027636617 | erot = 2.141245653077 | epot = -21.4468841606018 | etot = -17.2548782311586 -969000 ekin = 2.21533565656662 | erot = 2.21730696558968 | epot = -21.3811315205225 | etot = -16.9484888983662 -970000 ekin = 2.44655838306382 | erot = 2.63914635686249 | epot = -21.3181700854761 | etot = -16.2324653455498 -971000 ekin = 2.47235597423318 | erot = 2.68612281916571 | epot = -21.3025617859469 | etot = -16.1440829925481 -972000 ekin = 3.18960516897918 | erot = 2.4589698172248 | epot = -21.2512287640521 | etot = -15.6026537778481 -973000 ekin = 3.35448615918215 | erot = 2.61012714046349 | epot = -21.181846043468 | etot = -15.2172327438223 -974000 ekin = 2.7109696336397 | erot = 2.1297885006349 | epot = -21.0805156487717 | etot = -16.2397575144971 -975000 ekin = 1.81281242624849 | erot = 2.07588193669119 | epot = -20.9951812472117 | etot = -17.106486884272 -976000 ekin = 2.37607937449446 | erot = 1.37987096361839 | epot = -20.8918377653923 | etot = -17.1358874272794 -977000 ekin = 2.85561145367248 | erot = 3.03617871388547 | epot = -21.0084630734088 | etot = -15.1166729058509 -978000 ekin = 3.13898187042855 | erot = 3.01123432026038 | epot = -21.0722585106273 | etot = -14.9220423199384 -979000 ekin = 3.64209617929686 | erot = 2.4613128172747 | epot = -20.9585875203481 | etot = -14.8551785237765 -980000 ekin = 3.43702129901554 | erot = 3.27336305014796 | epot = -20.899855999005 | etot = -14.1894716498415 -981000 ekin = 2.95818777403214 | erot = 2.46809133944498 | epot = -20.986328819352 | etot = -15.5600497058749 -982000 ekin = 2.05833121455625 | erot = 2.23576836357638 | epot = -21.0416114809553 | etot = -16.7475119028227 -983000 ekin = 2.55525912528627 | erot = 1.97278253435511 | epot = -21.0429704338791 | etot = -16.5149287742377 -984000 ekin = 2.32118186028681 | erot = 2.58283774029526 | epot = -21.0821921217354 | etot = -16.1781725211533 -985000 ekin = 2.30313916872571 | erot = 3.01566259403689 | epot = -21.1725352249725 | etot = -15.8537334622099 -986000 ekin = 2.02463184559008 | erot = 2.17884306421032 | epot = -21.2738965581199 | etot = -17.0704216483195 -987000 ekin = 2.38600679522579 | erot = 1.60423682215952 | epot = -21.2561563051098 | etot = -17.2659126877245 -988000 ekin = 2.73915294843957 | erot = 2.71140680891282 | epot = -21.1542786885715 | etot = -15.7037189312192 -989000 ekin = 2.26683184377889 | erot = 2.87747329962287 | epot = -21.0926545062066 | etot = -15.9483493628049 -990000 ekin = 2.20939931770178 | erot = 2.59683743799389 | epot = -21.0191461353302 | etot = -16.2129093796345 -991000 ekin = 2.18257135988803 | erot = 2.54653688104725 | epot = -20.9118811472645 | etot = -16.1827729063292 -992000 ekin = 1.69790066377666 | erot = 2.49595921156529 | epot = -20.9746634507321 | etot = -16.7808035753901 -993000 ekin = 1.37402706728143 | erot = 1.97741928391721 | epot = -21.0641158581349 | etot = -17.7126695069363 -994000 ekin = 1.46483900547317 | erot = 2.95778549110336 | epot = -21.1249692907517 | etot = -16.7023447941752 -995000 ekin = 2.31288950128446 | erot = 1.68061050856792 | epot = -21.1893866548865 | etot = -17.1958866450341 -996000 ekin = 2.91614737481324 | erot = 2.86807519675625 | epot = -21.1735004751445 | etot = -15.389277903575 -997000 ekin = 3.14120073227004 | erot = 2.13892252916595 | epot = -21.1699471293629 | etot = -15.8898238679269 -998000 ekin = 2.24295362120275 | erot = 3.02318042682039 | epot = -21.1015606373099 | etot = -15.8354265892868 -999000 ekin = 2.61556215485409 | erot = 1.7387146959943 | epot = -21.020005228283 | etot = -16.6657283774346 -1000000 ekin = 2.3401430299422 | erot = 2.86437072240568 | epot = -21.0184376568778 | etot = -15.8139239045299 - 1000000 0.10400636 -1.3745197 0.060867347 -1.1673934 0.00013768636 -Loop time of 34.1939 on 4 procs for 1000000 steps with 16 atoms - -Performance: 25267.628 tau/day, 29244.940 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.63601 | 12.258 | 23.186 | 288.0 | 35.85 -Bond | 0.0885 | 0.40672 | 0.6818 | 42.6 | 1.19 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.65 | 2.786 | 2.9058 | 5.7 | 8.15 -Output | 1.9e-05 | 2.575e-05 | 2.8e-05 | 0.0 | 0.00 -Modify | 0.21592 | 2.7491 | 5.2145 | 132.7 | 8.04 -Other | | 15.99 | | | 46.78 - -Nlocal: 4.0 ave 8.0 max 0.0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 11.0 ave 14.0 max 8.0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 41.75 ave 81.0 max 0.0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 167 -Ave neighs/atom = 10.4375 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:34 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 deleted file mode 100644 index bbd584163b..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 +++ /dev/null @@ -1,73 +0,0 @@ -# LAMMPS data file -10 atoms -10 ellipsoids -8 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -Masses - -1 1.0 -2 1.0 -3 1.0 -4 1.0 - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 -3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 -4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 -5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 -6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1 -7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1 -8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1 -9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1 -10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1 - -# Atom-ID, translational velocity, angular momentum -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 -3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 -4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 -5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 -6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00 -7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00 -8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00 -9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00 -10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 6 7 -6 1 7 8 -7 1 8 9 -8 1 9 10 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 deleted file mode 100644 index 77a368a50b..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 +++ /dev/null @@ -1,1182 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 3 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex3 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds - -set atom * mass 1.0 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA2 bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA2 pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274048 - ghost atom cutoff = 2.6274048 - binsize = 1.3137024, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -14.6249037416652 | etot = -14.6249037416652 -Per MPI rank memory allocation (min/avg/max) = 8.021 | 8.021 | 8.021 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06 -1000 ekin = 0.00366431201929618 | erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679 -2000 ekin = 0.0144775076075466 | erot = 0.00770914672938582 | epot = -14.6470903960565 | etot = -14.6249037417196 -3000 ekin = 0.0319122186081549 | erot = 0.0171972328649101 | epot = -14.6740131932573 | etot = -14.6249037417842 -4000 ekin = 0.0551283043509704 | erot = 0.0302085305548002 | epot = -14.7102405767754 | etot = -14.6249037418696 -5000 ekin = 0.0830285165715823 | erot = 0.0464820547541705 | epot = -14.7544143132963 | etot = -14.6249037419705 -6000 ekin = 0.114331121546757 | erot = 0.0656980211282096 | epot = -14.8049328847556 | etot = -14.6249037420806 -7000 ekin = 0.147653866561892 | erot = 0.0874894888755386 | epot = -14.860047097631 | etot = -14.6249037421936 -8000 ekin = 0.181602099560207 | erot = 0.111456095727703 | epot = -14.9179619375911 | etot = -14.6249037423032 -9000 ekin = 0.214852894725919 | erot = 0.137179311245174 | epot = -14.9769359483746 | etot = -14.6249037424035 -10000 ekin = 0.246227151956033 | erot = 0.164238435218395 | epot = -15.0353693296648 | etot = -14.6249037424904 -11000 ekin = 0.274743080419051 | erot = 0.192226420003239 | epot = -15.0918732429829 | etot = -14.6249037425607 -12000 ekin = 0.2996471417657 | erot = 0.220764512146651 | epot = -15.1453153965252 | etot = -14.6249037426128 -13000 ekin = 0.320421918860966 | erot = 0.249514690530541 | epot = -15.1948403520385 | etot = -14.624903742647 -14000 ekin = 0.33677373488436 | erot = 0.27818893373049 | epot = -15.2398664112793 | etot = -14.6249037426645 -15000 ekin = 0.348605413762901 | erot = 0.306554508009418 | epot = -15.2800636644399 | etot = -14.6249037426675 -16000 ekin = 0.355980829097854 | erot = 0.334434770083744 | epot = -15.3153193418402 | etot = -14.6249037426586 -17000 ekin = 0.35908770105941 | erot = 0.361705441666512 | epot = -15.3456968853664 | etot = -14.6249037426405 -18000 ekin = 0.358203710992239 | erot = 0.388286889516313 | epot = -15.3713943431242 | etot = -14.6249037426156 -19000 ekin = 0.353668912555234 | erot = 0.414133518537107 | epot = -15.3927061736788 | etot = -14.6249037425864 -20000 ekin = 0.345865220775291 | erot = 0.439221805285432 | epot = -15.4099907686153 | etot = -14.6249037425546 -21000 ekin = 0.335201981146472 | erot = 0.463538642606515 | epot = -15.4236443662748 | etot = -14.6249037425218 -22000 ekin = 0.322105588834903 | erot = 0.487071492273063 | epot = -15.4340808235971 | etot = -14.6249037424892 -23000 ekin = 0.307010918596165 | erot = 0.509801406229371 | epot = -15.4417160672832 | etot = -14.6249037424577 -24000 ekin = 0.290352786033169 | erot = 0.531699400501692 | epot = -15.446955928963 | etot = -14.6249037424281 -25000 ekin = 0.272556500902037 | erot = 0.552726088759198 | epot = -15.4501863320622 | etot = -14.624903742401 -26000 ekin = 0.254027484079049 | erot = 0.572834017299018 | epot = -15.4517652437547 | etot = -14.6249037423766 -27000 ekin = 0.23514066521633 | erot = 0.591971851501221 | epot = -15.4520162590729 | etot = -14.6249037423553 -28000 ekin = 0.216230835846198 | erot = 0.610089455964333 | epot = -15.4512240341478 | etot = -14.6249037423373 -29000 ekin = 0.197585285158555 | erot = 0.627142960082633 | epot = -15.4496319875635 | etot = -14.6249037423223 -30000 ekin = 0.179439940173318 | erot = 0.643099062793407 | epot = -15.4474427452769 | etot = -14.6249037423102 -31000 ekin = 0.161979935826124 | erot = 0.657938056392308 | epot = -15.4448217345186 | etot = -14.6249037423001 -32000 ekin = 0.145345108983022 | erot = 0.671655297433962 | epot = -15.4419041487086 | etot = -14.6249037422916 -33000 ekin = 0.12964040034519 | erot = 0.684261083518556 | epot = -15.4388052261475 | etot = -14.6249037422838 -34000 ekin = 0.114950474500008 | erot = 0.695779112936504 | epot = -15.4356333297121 | etot = -14.6249037422756 -35000 ekin = 0.10135710346033 | erot = 0.706243888527894 | epot = -15.4325047342544 | etot = -14.6249037422662 -36000 ekin = 0.088957633457107 | erot = 0.715697403164625 | epot = -15.4295587788764 | etot = -14.6249037422546 -37000 ekin = 0.0778817390290652 | erot = 0.72418563863568 | epot = -15.4269711199052 | etot = -14.6249037422404 -38000 ekin = 0.068303709154812 | erot = 0.731755309647473 | epot = -15.4249627610255 | etot = -14.6249037422232 -39000 ekin = 0.0604476327394706 | erot = 0.738451228922909 | epot = -15.4238026038659 | etot = -14.6249037422035 -40000 ekin = 0.0545835914676979 | erot = 0.7443145576821 | epot = -15.4238018913318 | etot = -14.624903742182 -41000 ekin = 0.0510142787133839 | erot = 0.749382063190735 | epot = -15.4253000840641 | etot = -14.6249037421599 -42000 ekin = 0.0500531571157636 | erot = 0.753686350478931 | epot = -15.428643249734 | etot = -14.6249037421393 -43000 ekin = 0.0519969858278391 | erot = 0.757256889238991 | epot = -15.4341576171885 | etot = -14.6249037421217 -44000 ekin = 0.0570968352184469 | erot = 0.760121540481399 | epot = -15.4421221178085 | etot = -14.6249037421087 -45000 ekin = 0.065532155346979 | erot = 0.762308219230476 | epot = -15.4527441166789 | etot = -14.6249037421014 -46000 ekin = 0.077391880036746 | erot = 0.763846321567568 | epot = -15.4661419437049 | etot = -14.6249037421006 -47000 ekin = 0.0926650518887463 | erot = 0.764767599959976 | epot = -15.4823363939546 | etot = -14.6249037421059 -48000 ekin = 0.111241466891021 | erot = 0.76510628368957 | epot = -15.5012514926977 | etot = -14.6249037421171 -49000 ekin = 0.132920935183101 | erot = 0.764898395951945 | epot = -15.5227230732685 | etot = -14.6249037421334 -50000 ekin = 0.157428432862297 | erot = 0.764180392178817 | epot = -15.5465125671951 | etot = -14.624903742154 -51000 ekin = 0.184431879186394 | erot = 0.762987403181186 | epot = -15.5723230245453 | etot = -14.6249037421777 -52000 ekin = 0.213559336999611 | erot = 0.761351471408957 | epot = -15.5998145506125 | etot = -14.6249037422039 -53000 ekin = 0.244412677541745 | erot = 0.759300175100897 | epot = -15.6286165948748 | etot = -14.6249037422322 -54000 ekin = 0.276574826726797 | erot = 0.756855909736049 | epot = -15.6583344787255 | etot = -14.6249037422626 -55000 ekin = 0.30960770869724 | erot = 0.754035838659133 | epot = -15.6885472896526 | etot = -14.6249037422962 -56000 ekin = 0.343038597242155 | erot = 0.750852192167397 | epot = -15.7187945317444 | etot = -14.6249037423348 -57000 ekin = 0.376334705011604 | erot = 0.747312289063754 | epot = -15.7485507364561 | etot = -14.6249037423808 -58000 ekin = 0.408870193943412 | erot = 0.743417624903535 | epot = -15.7771915612832 | etot = -14.6249037424363 -59000 ekin = 0.439895666476021 | erot = 0.739161690570186 | epot = -15.803961099549 | etot = -14.6249037425028 -60000 ekin = 0.468524372325726 | erot = 0.734526514748657 | epot = -15.8279546296536 | etot = -14.6249037425792 -61000 ekin = 0.493750804630799 | erot = 0.729479048550173 | epot = -15.8481335958428 | etot = -14.6249037426618 -62000 ekin = 0.514511417905549 | erot = 0.723968952963015 | epot = -15.8633841136119 | etot = -14.6249037427433 -63000 ekin = 0.529785687820656 | erot = 0.717929490923262 | epot = -15.8726189215586 | etot = -14.6249037428146 -64000 ekin = 0.538722043349821 | erot = 0.711282639870032 | epot = -15.874908426086 | etot = -14.6249037428661 -65000 ekin = 0.540763046401741 | erot = 0.703948378732647 | epot = -15.8696151680245 | etot = -14.6249037428901 -66000 ekin = 0.535742115226795 | erot = 0.69585678068686 | epot = -15.856502638796 | etot = -14.6249037428824 -67000 ekin = 0.523930969354056 | erot = 0.686960578434575 | epot = -15.8357952906315 | etot = -14.6249037428429 -68000 ekin = 0.506029704478054 | erot = 0.677245632040232 | epot = -15.8081790792936 | etot = -14.6249037427753 -69000 ekin = 0.483104826199992 | erot = 0.666737270644537 | epot = -15.774745839531 | etot = -14.6249037426865 -70000 ekin = 0.456490218293252 | erot = 0.655501536743317 | epot = -15.7368954976212 | etot = -14.6249037425847 -71000 ekin = 0.427669918862549 | erot = 0.643641521526345 | epot = -15.6962151828672 | etot = -14.6249037424783 -72000 ekin = 0.398160338931557 | erot = 0.631289876691081 | epot = -15.654353957998 | etot = -14.6249037423754 -73000 ekin = 0.369405258276815 | erot = 0.618599034382849 | epot = -15.6129080349415 | etot = -14.6249037422819 -74000 ekin = 0.342691749042209 | erot = 0.605730669564501 | epot = -15.5733261608092 | etot = -14.6249037422025 -75000 ekin = 0.31909052680686 | erot = 0.59284563490598 | epot = -15.5368399038529 | etot = -14.62490374214 -76000 ekin = 0.299420611427412 | erot = 0.580095163563671 | epot = -15.5044195170868 | etot = -14.6249037420957 -77000 ekin = 0.284235504574989 | erot = 0.567613716752661 | epot = -15.4767529633973 | etot = -14.6249037420697 -78000 ekin = 0.273826140866561 | erot = 0.555513536864305 | epot = -15.454243419792 | etot = -14.6249037420611 -79000 ekin = 0.268234635497613 | erot = 0.54388078034572 | epot = -15.4370191579124 | etot = -14.624903742069 -80000 ekin = 0.267272602906451 | erot = 0.532773036269929 | epot = -15.4249493812687 | etot = -14.6249037420923 -81000 ekin = 0.270538934182559 | erot = 0.522218059775773 | epot = -15.4176607360884 | etot = -14.6249037421301 -82000 ekin = 0.277434574359295 | erot = 0.512213638248342 | epot = -15.4145519547894 | etot = -14.6249037421818 -83000 ekin = 0.287175732620333 | erot = 0.50272864056942 | epot = -15.414808115436 | etot = -14.6249037422462 -84000 ekin = 0.298811175848678 | erot = 0.493705451301681 | epot = -15.4174203694717 | etot = -14.6249037423214 -85000 ekin = 0.311252369949697 | erot = 0.485064122067565 | epot = -15.4212202344211 | etot = -14.6249037424038 -86000 ekin = 0.323325626375984 | erot = 0.476708618161036 | epot = -15.424937987025 | etot = -14.624903742488 -87000 ekin = 0.333851795518747 | erot = 0.468535420697862 | epot = -15.4272909587828 | etot = -14.6249037425662 -88000 ekin = 0.341751109758396 | erot = 0.460444399763919 | epot = -15.427099252152 | etot = -14.6249037426296 -89000 ekin = 0.346159825920001 | erot = 0.452351304178873 | epot = -15.4234148727693 | etot = -14.6249037426704 -90000 ekin = 0.346534667470265 | erot = 0.444200535918399 | epot = -15.4156389460718 | etot = -14.6249037426831 -91000 ekin = 0.342715665475867 | erot = 0.435976333753397 | epot = -15.4035957418967 | etot = -14.6249037426674 -92000 ekin = 0.3349227158513 | erot = 0.427710377227648 | epot = -15.3875368357071 | etot = -14.6249037426282 -93000 ekin = 0.323677844433752 | erot = 0.419484336039963 | epot = -15.3680659230484 | etot = -14.6249037425747 -94000 ekin = 0.30966978292125 | erot = 0.411426964072553 | epot = -15.3460004895119 | etot = -14.6249037425181 -95000 ekin = 0.293600014861622 | erot = 0.403706586473099 | epot = -15.3222103438021 | etot = -14.6249037424674 -96000 ekin = 0.276058284884091 | erot = 0.396520701306161 | epot = -15.2974827286175 | etot = -14.6249037424272 -97000 ekin = 0.25746445629565 | erot = 0.390084510982946 | epot = -15.2724527096753 | etot = -14.6249037423967 -98000 ekin = 0.238086767082953 | erot = 0.384619533405539 | epot = -15.2476100428595 | etot = -14.624903742371 -99000 ekin = 0.218116994125883 | erot = 0.380342481668092 | epot = -15.2233632181382 | etot = -14.6249037423442 -100000 ekin = 0.197764845956536 | erot = 0.377453964065333 | epot = -15.2001225523339 | etot = -14.624903742312 -101000 ekin = 0.177333852671335 | erot = 0.376126621697227 | epot = -15.1783642166414 | etot = -14.6249037422728 -102000 ekin = 0.157255732179445 | erot = 0.376493003927733 | epot = -15.1586524783356 | etot = -14.6249037422284 -103000 ekin = 0.138079925448889 | erot = 0.378634329970018 | epot = -15.1416179976015 | etot = -14.6249037421826 -104000 ekin = 0.120430234291316 | erot = 0.382571791335251 | epot = -15.1279057677665 | etot = -14.6249037421399 -105000 ekin = 0.10494672239352 | erot = 0.388261944551333 | epot = -15.118112409049 | etot = -14.6249037421041 -106000 ekin = 0.0922291289493497 | erot = 0.395597086392468 | epot = -15.11272995742 | etot = -14.6249037420782 -107000 ekin = 0.0827918191991084 | erot = 0.404410579138465 | epot = -15.112106140401 | etot = -14.6249037420634 -108000 ekin = 0.0770336430609741 | erot = 0.414486225075992 | epot = -15.116423610197 | etot = -14.62490374206 -109000 ekin = 0.075221312117861 | erot = 0.425570202879186 | epot = -15.1256952570646 | etot = -14.6249037420675 -110000 ekin = 0.0774826364247882 | erot = 0.437383858086522 | epot = -15.1397702365965 | etot = -14.6249037420852 -111000 ekin = 0.0838057148048547 | erot = 0.449635759436015 | epot = -15.1583452163526 | etot = -14.6249037421117 -112000 ekin = 0.0940411317710077 | erot = 0.462031808376879 | epot = -15.1809766822946 | etot = -14.6249037421467 -113000 ekin = 0.107905661684195 | erot = 0.474282718869093 | epot = -15.2070921227426 | etot = -14.6249037421893 -114000 ekin = 0.124987416380568 | erot = 0.486108767327343 | epot = -15.2359999259468 | etot = -14.6249037422389 -115000 ekin = 0.14475347442169 | erot = 0.497242253023055 | epot = -15.2668994697394 | etot = -14.6249037422947 -116000 ekin = 0.166561593123301 | erot = 0.507428522971045 | epot = -15.2988938584499 | etot = -14.6249037423555 -117000 ekin = 0.189677527330859 | erot = 0.516426638198687 | epot = -15.3310079079495 | etot = -14.6249037424199 -118000 ekin = 0.213298790897302 | erot = 0.524010758771369 | epot = -15.3622132921543 | etot = -14.6249037424857 -119000 ekin = 0.23658457696156 | erot = 0.529973112381439 | epot = -15.3914614318934 | etot = -14.6249037425504 -120000 ekin = 0.25869030185824 | erot = 0.534129034925715 | epot = -15.4177230793952 | etot = -14.6249037426113 -121000 ekin = 0.278804196532859 | erot = 0.536324108799716 | epot = -15.4400320479982 | etot = -14.6249037426656 -122000 ekin = 0.296182819519396 | erot = 0.536442962870823 | epot = -15.4575295251008 | etot = -14.6249037427106 -123000 ekin = 0.310182446405815 | erot = 0.534418915104236 | epot = -15.4695051042542 | etot = -14.6249037427442 -124000 ekin = 0.320283972930007 | erot = 0.530243389137678 | epot = -15.4754311048322 | etot = -14.6249037427645 -125000 ekin = 0.326110081462184 | erot = 0.523973945236141 | epot = -15.474987769469 | etot = -14.6249037427707 -126000 ekin = 0.327434709614433 | erot = 0.515739832556637 | epot = -15.4680782849335 | etot = -14.6249037427625 -127000 ekin = 0.324186046690112 | erot = 0.505744172152634 | epot = -15.4548339615826 | etot = -14.6249037427399 -128000 ekin = 0.316445106703942 | erot = 0.49426218578474 | epot = -15.4356110351922 | etot = -14.6249037427035 -129000 ekin = 0.304442167762443 | erot = 0.481635256753056 | epot = -15.4109811671698 | etot = -14.6249037426543 -130000 ekin = 0.288552887156219 | erot = 0.468261006625427 | epot = -15.381717636375 | etot = -14.6249037425933 -131000 ekin = 0.269294696165104 | erot = 0.454579955598623 | epot = -15.3487783942857 | etot = -14.624903742522 -132000 ekin = 0.247322351785515 | erot = 0.44105966132284 | epot = -15.3132857555502 | etot = -14.6249037424419 -133000 ekin = 0.223419723871429 | erot = 0.428177456066543 | epot = -15.276500922293 | etot = -14.6249037423551 -134000 ekin = 0.198483666316777 | erot = 0.416402982921072 | epot = -15.2397903915022 | etot = -14.6249037422644 -135000 ekin = 0.173495806295108 | erot = 0.40618164100245 | epot = -15.2045811894712 | etot = -14.6249037421736 -136000 ekin = 0.149479658252647 | erot = 0.397919790440824 | epot = -15.1723031907806 | etot = -14.6249037420871 -137000 ekin = 0.127443476996608 | erot = 0.391972186713592 | epot = -15.1443194057199 | etot = -14.6249037420097 -138000 ekin = 0.10831297052536 | erot = 0.388631700836367 | epot = -15.1218484133082 | etot = -14.6249037419464 -139000 ekin = 0.0928612988418002 | erot = 0.388121053034821 | epot = -15.1058860937783 | etot = -14.6249037419017 -140000 ekin = 0.0816456573910084 | erot = 0.390586148388801 | epot = -15.0971355476587 | etot = -14.6249037418789 -141000 ekin = 0.0749596349872437 | erot = 0.396090706683564 | epot = -15.0959540835505 | etot = -14.6249037418797 -142000 ekin = 0.0728085537690405 | erot = 0.404612196534891 | epot = -15.1023244922084 | etot = -14.6249037419044 -143000 ekin = 0.0749117535383842 | erot = 0.416039504837645 | epot = -15.1158550003269 | etot = -14.6249037419509 -144000 ekin = 0.0807320498020964 | erot = 0.43017313668478 | epot = -15.1358089285024 | etot = -14.6249037420156 -145000 ekin = 0.08952902558338 | erot = 0.446728893938156 | epot = -15.1611616616151 | etot = -14.6249037420935 -146000 ekin = 0.100429851263191 | erot = 0.465345829669622 | epot = -15.1906794231115 | etot = -14.6249037421787 -147000 ekin = 0.112509264558581 | erot = 0.485598823528122 | epot = -15.2230118303515 | etot = -14.6249037422648 -148000 ekin = 0.124869425792591 | erot = 0.507015469189552 | epot = -15.2567886373282 | etot = -14.6249037423461 -149000 ekin = 0.136710750658436 | erot = 0.529096273051187 | epot = -15.290710766127 | etot = -14.6249037424174 -150000 ekin = 0.147386480806171 | erot = 0.551336607352345 | epot = -15.323626830634 | etot = -14.6249037424755 -151000 ekin = 0.156436378416032 | erot = 0.573248570645276 | epot = -15.3545886915794 | etot = -14.6249037425181 -152000 ekin = 0.163597998371653 | erot = 0.594380933602923 | epot = -15.3828826745196 | etot = -14.624903742545 -153000 ekin = 0.168796920199611 | erot = 0.614335653334474 | epot = -15.4080363160912 | etot = -14.6249037425571 -154000 ekin = 0.172119667637745 | erot = 0.63277992909172 | epot = -15.4298033392862 | etot = -14.6249037425567 -155000 ekin = 0.173774602206285 | erot = 0.649453329865168 | epot = -15.448131674618 | etot = -14.6249037425466 -156000 ekin = 0.174046854480021 | erot = 0.664170048550552 | epot = -15.4631206455605 | etot = -14.62490374253 -157000 ekin = 0.173253451016122 | erot = 0.676816762702534 | epot = -15.4749739562284 | etot = -14.6249037425097 -158000 ekin = 0.171704281293749 | erot = 0.687346881268012 | epot = -15.48395490505 | etot = -14.6249037424883 -159000 ekin = 0.169673443699862 | erot = 0.695772131173121 | epot = -15.4903493173403 | etot = -14.6249037424673 -160000 ekin = 0.167383826014546 | erot = 0.702152502586509 | epot = -15.4944400710487 | etot = -14.6249037424476 -161000 ekin = 0.165005624031702 | erot = 0.706585545944493 | epot = -15.4964949124054 | etot = -14.6249037424292 -162000 ekin = 0.162667154471752 | erot = 0.709195914790859 | epot = -15.4967668116741 | etot = -14.6249037424115 -163000 ekin = 0.160474189581485 | erot = 0.710125892129829 | epot = -15.4955038241048 | etot = -14.6249037423935 -164000 ekin = 0.158532578972596 | erot = 0.709527441008927 | epot = -15.4929637623557 | etot = -14.6249037423742 -165000 ekin = 0.156968465370669 | erot = 0.707556101121189 | epot = -15.4894283088449 | etot = -14.624903742353 -166000 ekin = 0.155941053191124 | erot = 0.704366832058078 | epot = -15.4852116275794 | etot = -14.6249037423302 -167000 ekin = 0.155644496809548 | erot = 0.700111698658369 | epot = -15.4806599377741 | etot = -14.6249037423062 -168000 ekin = 0.156297672988182 | erot = 0.694939119112873 | epot = -15.4761405343834 | etot = -14.6249037422823 -169000 ekin = 0.158122923325456 | erot = 0.688994262094025 | epot = -15.4720209276801 | etot = -14.6249037422606 -170000 ekin = 0.161316852937676 | erot = 0.682420091513849 | epot = -15.4686406866943 | etot = -14.6249037422428 -171000 ekin = 0.166017619146822 | erot = 0.675358520304806 | epot = -15.4662798816825 | etot = -14.6249037422309 -172000 ekin = 0.172273671159511 | erot = 0.667951149520835 | epot = -15.4651285629069 | etot = -14.6249037422266 -173000 ekin = 0.180018623556049 | erot = 0.660339136127854 | epot = -15.4652615019149 | etot = -14.624903742231 -174000 ekin = 0.189056055744924 | erot = 0.65266185183192 | epot = -15.4666216498214 | etot = -14.6249037422445 -175000 ekin = 0.199056860650113 | erot = 0.645054167286172 | epot = -15.4690147702031 | etot = -14.6249037422668 -176000 ekin = 0.209570701317552 | erot = 0.637642422787005 | epot = -15.4721168664013 | etot = -14.6249037422967 -177000 ekin = 0.220052442974625 | erot = 0.630539423737628 | epot = -15.4754956090443 | etot = -14.6249037423321 -178000 ekin = 0.229904071991194 | erot = 0.623839102439311 | epot = -15.4786469168001 | etot = -14.6249037423696 -179000 ekin = 0.238532114427982 | erot = 0.617611757777875 | epot = -15.4810476146108 | etot = -14.624903742405 -180000 ekin = 0.245419064060292 | erot = 0.611900922402653 | epot = -15.4822237288957 | etot = -14.6249037424328 -181000 ekin = 0.250203926055771 | erot = 0.606722796615248 | epot = -15.4818304651186 | etot = -14.6249037424476 -182000 ekin = 0.252761402919565 | erot = 0.602068750131856 | epot = -15.4797338954959 | etot = -14.6249037424445 -183000 ekin = 0.253262634974054 | erot = 0.597910660168588 | epot = -15.4760770375641 | etot = -14.6249037424214 -184000 ekin = 0.252195762131878 | erot = 0.594208023726969 | epot = -15.4713075282387 | etot = -14.6249037423799 -185000 ekin = 0.250326113306321 | erot = 0.59091517967259 | epot = -15.4661450353052 | etot = -14.6249037423263 -186000 ekin = 0.248586758541649 | erot = 0.587986907734566 | epot = -15.4614774085478 | etot = -14.6249037422716 -187000 ekin = 0.247909630265846 | erot = 0.585381224303701 | epot = -15.4581945967982 | etot = -14.6249037422286 -188000 ekin = 0.2490290523945 | erot = 0.583059148733781 | epot = -15.4569919433378 | etot = -14.6249037422095 -189000 ekin = 0.252303803181127 | erot = 0.580982165409763 | epot = -15.4581897108128 | etot = -14.6249037422219 -190000 ekin = 0.25760376351551 | erot = 0.579108718145144 | epot = -15.4616162239281 | etot = -14.6249037422675 -191000 ekin = 0.264292655598098 | erot = 0.577391223758838 | epot = -15.4665876216975 | etot = -14.6249037423406 -192000 ekin = 0.271315385056409 | erot = 0.575774831089113 | epot = -15.4719939585751 | etot = -14.6249037424296 -193000 ekin = 0.277374539132748 | erot = 0.574198584868256 | epot = -15.4764768665202 | etot = -14.6249037425192 -194000 ekin = 0.281161076019677 | erot = 0.572598913484698 | epot = -15.478663732098 | etot = -14.6249037425936 -195000 ekin = 0.281592637347121 | erot = 0.570914645865623 | epot = -15.4774110258523 | etot = -14.6249037426396 -196000 ekin = 0.278011867235596 | erot = 0.569092314484759 | epot = -15.4720079243693 | etot = -14.624903742649 -197000 ekin = 0.270307527592762 | erot = 0.567090473639989 | epot = -15.4623017438531 | etot = -14.6249037426204 -198000 ekin = 0.258940359975855 | erot = 0.564882125458807 | epot = -15.4487262279927 | etot = -14.6249037425581 -199000 ekin = 0.244877476699234 | erot = 0.562454912721902 | epot = -15.4322361318925 | etot = -14.6249037424713 -200000 ekin = 0.229456931018641 | erot = 0.559809284042077 | epot = -15.4141699574324 | etot = -14.6249037423716 -201000 ekin = 0.214214012278847 | erot = 0.556955381706859 | epot = -15.3960731362566 | etot = -14.6249037422709 -202000 ekin = 0.200701376135036 | erot = 0.553909032488863 | epot = -15.3795141508034 | etot = -14.6249037421795 -203000 ekin = 0.190329688710817 | erot = 0.550687503827512 | epot = -15.3659209346435 | etot = -14.6249037421052 -204000 ekin = 0.184246973275337 | erot = 0.547306655840007 | epot = -15.356457371168 | etot = -14.6249037420527 -205000 ekin = 0.183262973705813 | erot = 0.543779043729278 | epot = -15.3519457594592 | etot = -14.6249037420241 -206000 ekin = 0.187816949073515 | erot = 0.540113432736619 | epot = -15.3528341238291 | etot = -14.624903742019 -207000 ekin = 0.197980929490512 | erot = 0.536315658388676 | epot = -15.3592003299145 | etot = -14.6249037420353 -208000 ekin = 0.213487612677366 | erot = 0.53239049820727 | epot = -15.3707818529549 | etot = -14.6249037420703 -209000 ekin = 0.233772362712521 | erot = 0.528344018725095 | epot = -15.3870201235584 | etot = -14.6249037421208 -210000 ekin = 0.258021408692355 | erot = 0.524185756556833 | epot = -15.4071109074329 | etot = -14.6249037421837 -211000 ekin = 0.285222208429996 | erot = 0.519930104708342 | epot = -15.4300560553942 | etot = -14.6249037422558 -212000 ekin = 0.314215813604987 | erot = 0.515596398128489 | epot = -15.454715954067 | etot = -14.6249037423335 -213000 ekin = 0.343753634043937 | erot = 0.511207450608882 | epot = -15.4798648270658 | etot = -14.624903742413 -214000 ekin = 0.372561594270316 | erot = 0.506786560075337 | epot = -15.5042518968352 | etot = -14.6249037424895 -215000 ekin = 0.399412456462858 | erot = 0.502353347158712 | epot = -15.5266695461799 | etot = -14.6249037425583 -216000 ekin = 0.423202666203616 | erot = 0.497919155944113 | epot = -15.5460255647623 | etot = -14.6249037426146 -217000 ekin = 0.443025226540025 | erot = 0.493483013679004 | epot = -15.5614119828738 | etot = -14.6249037426548 -218000 ekin = 0.458227302378849 | erot = 0.489029294856436 | epot = -15.5721603399122 | etot = -14.6249037426769 -219000 ekin = 0.46844301918404 | erot = 0.484528125251435 | epot = -15.5778748871159 | etot = -14.6249037426804 -220000 ekin = 0.473598483116685 | erot = 0.479939108990801 | epot = -15.5784413347739 | etot = -14.6249037426664 -221000 ekin = 0.473894168318713 | erot = 0.475218183432529 | epot = -15.5740160943878 | etot = -14.6249037426366 -222000 ekin = 0.46977401404952 | erot = 0.470326483973494 | epot = -15.565004240616 | etot = -14.624903742593 -223000 ekin = 0.461887320397438 | erot = 0.465239349169368 | epot = -15.552030412105 | etot = -14.6249037425382 -224000 ekin = 0.45104133642262 | erot = 0.459953336121611 | epot = -15.5358984150202 | etot = -14.624903742476 -225000 ekin = 0.438137198422833 | erot = 0.454489515561399 | epot = -15.5175304563959 | etot = -14.6249037424116 -226000 ekin = 0.424086332826247 | erot = 0.448892294163513 | epot = -15.4978823693413 | etot = -14.6249037423516 -227000 ekin = 0.409717105195145 | erot = 0.443224250669953 | epot = -15.4778450981665 | etot = -14.6249037423014 -228000 ekin = 0.395692916861505 | erot = 0.437558473222737 | epot = -15.4581551323492 | etot = -14.6249037422649 -229000 ekin = 0.382463318564619 | erot = 0.431970318931211 | epot = -15.4393373797385 | etot = -14.6249037422426 -230000 ekin = 0.370258116730603 | erot = 0.426530223272752 | epot = -15.421692082236 | etot = -14.6249037422326 -231000 ekin = 0.359118625017489 | erot = 0.421298440292615 | epot = -15.4053208075415 | etot = -14.6249037422314 -232000 ekin = 0.348949729121418 | erot = 0.416321816462733 | epot = -15.3901752878198 | etot = -14.6249037422357 -233000 ekin = 0.339575284188205 | erot = 0.411632247273789 | epot = -15.3761112737045 | etot = -14.6249037422425 -234000 ekin = 0.330784909163314 | erot = 0.407246384303571 | epot = -15.362935035717 | etot = -14.6249037422501 -235000 ekin = 0.322367248495157 | erot = 0.403166248673602 | epot = -15.350437239426 | etot = -14.6249037422572 -236000 ekin = 0.314129851889501 | erot = 0.399380677843556 | epot = -15.3384142719966 | etot = -14.6249037422635 -237000 ekin = 0.305908300164827 | erot = 0.395867600047935 | epot = -15.3266796424818 | etot = -14.624903742269 -238000 ekin = 0.297568064657773 | erot = 0.39259715720464 | epot = -15.3150689641361 | etot = -14.6249037422737 -239000 ekin = 0.289002756414808 | erot = 0.389535643317172 | epot = -15.3034421420093 | etot = -14.6249037422773 -240000 ekin = 0.280132201614557 | erot = 0.386650129641611 | epot = -15.291686073536 | etot = -14.6249037422798 -241000 ekin = 0.270903172980175 | erot = 0.383913574227223 | epot = -15.2797204894877 | etot = -14.6249037422803 -242000 ekin = 0.261294311101929 | erot = 0.381310019034114 | epot = -15.2675080724141 | etot = -14.624903742278 -243000 ekin = 0.251325265433967 | erot = 0.378839435319614 | epot = -15.255068443025 | etot = -14.6249037422714 -244000 ekin = 0.241068460184099 | erot = 0.376521662813181 | epot = -15.2424938652571 | etot = -14.6249037422598 -245000 ekin = 0.230660579660543 | erot = 0.374398842117411 | epot = -15.2299631640205 | etot = -14.6249037422425 -246000 ekin = 0.220310176855077 | erot = 0.372535772164605 | epot = -15.2177496912391 | etot = -14.6249037422194 -247000 ekin = 0.21029792040831 | erot = 0.371017759432739 | epot = -15.2062194220324 | etot = -14.6249037421913 -248000 ekin = 0.200966973970282 | erot = 0.369945779906298 | epot = -15.1958164960366 | etot = -14.62490374216 -249000 ekin = 0.19270275205643 | erot = 0.369429135338942 | epot = -15.1870356295232 | etot = -14.6249037421279 -250000 ekin = 0.18590352409262 | erot = 0.369576201101644 | epot = -15.1803834672921 | etot = -14.6249037420978 -251000 ekin = 0.180945546219597 | erot = 0.370484246994953 | epot = -15.1763335352872 | etot = -14.6249037420727 -252000 ekin = 0.178147956309677 | erot = 0.372229589272508 | epot = -15.1752812876371 | etot = -14.624903742055 -253000 ekin = 0.177743031465493 | erot = 0.374859230993345 | epot = -15.1775060045052 | etot = -14.6249037420463 -254000 ekin = 0.179856300055144 | erot = 0.378385037101541 | epot = -15.1831450792041 | etot = -14.6249037420475 -255000 ekin = 0.184498455786623 | erot = 0.382781080046676 | epot = -15.1921832778916 | etot = -14.6249037420583 -256000 ekin = 0.191568141873245 | erot = 0.387983970946509 | epot = -15.2044558548979 | etot = -14.6249037420781 -257000 ekin = 0.200862084874684 | erot = 0.39389562099413 | epot = -15.2196614479746 | etot = -14.6249037421058 -258000 ekin = 0.212087875567067 | erot = 0.400387498987617 | epot = -15.2373791166953 | etot = -14.6249037421406 -259000 ekin = 0.22487530619229 | erot = 0.407305396776974 | epot = -15.2570844451511 | etot = -14.6249037421818 -260000 ekin = 0.238784314763371 | erot = 0.414473950040919 | epot = -15.2781620070334 | etot = -14.6249037422291 -261000 ekin = 0.253310397642053 | erot = 0.42170059668304 | epot = -15.2999147366073 | etot = -14.6249037422822 -262000 ekin = 0.267890750412286 | erot = 0.428779149459046 | epot = -15.3215736422117 | etot = -14.6249037423403 -263000 ekin = 0.281915541777785 | erot = 0.435493571930371 | epot = -15.3423128561102 | etot = -14.6249037424021 -264000 ekin = 0.294748319449044 | erot = 0.441622773940652 | epot = -15.3612748358547 | etot = -14.624903742465 -265000 ekin = 0.305757851305137 | erot = 0.446947232466447 | epot = -15.3776088262971 | etot = -14.6249037425255 -266000 ekin = 0.314361275702132 | erot = 0.451257984268096 | epot = -15.3905230025497 | etot = -14.6249037425794 -267000 ekin = 0.320075758813841 | erot = 0.454368036195507 | epot = -15.3993475376314 | etot = -14.624903742622 -268000 ekin = 0.322573111285627 | erot = 0.456125517716869 | epot = -15.403602371651 | etot = -14.6249037426485 -269000 ekin = 0.321728949456794 | erot = 0.456427019949868 | epot = -15.403059712062 | etot = -14.6249037426553 -270000 ekin = 0.31765519820333 | erot = 0.45522869606994 | epot = -15.3977876369143 | etot = -14.624903742641 -271000 ekin = 0.310703151367432 | erot = 0.452552178355822 | epot = -15.3881590723309 | etot = -14.6249037426077 -272000 ekin = 0.301426233536413 | erot = 0.448482664562071 | epot = -15.3748126406594 | etot = -14.6249037425609 -273000 ekin = 0.290499502093209 | erot = 0.443158007811074 | epot = -15.3585612524138 | etot = -14.6249037425095 -274000 ekin = 0.278606962226069 | erot = 0.436750209657617 | epot = -15.3402609143468 | etot = -14.6249037424631 -275000 ekin = 0.26632348034077 | erot = 0.429443553158618 | epot = -15.3206707759287 | etot = -14.6249037424293 -276000 ekin = 0.254026977158081 | erot = 0.421415402004818 | epot = -15.3003461215739 | etot = -14.624903742411 -277000 ekin = 0.241871064453538 | erot = 0.412825312322111 | epot = -15.2796001191811 | etot = -14.6249037424054 -278000 ekin = 0.229828041579721 | erot = 0.403815416629946 | epot = -15.2585472006151 | etot = -14.6249037424054 -279000 ekin = 0.217786141146189 | erot = 0.394521119096963 | epot = -15.2372110026452 | etot = -14.624903742402 -280000 ekin = 0.205666064593732 | erot = 0.38508770303191 | epot = -15.2156575100133 | etot = -14.6249037423876 -281000 ekin = 0.19351860427424 | erot = 0.375686870762611 | epot = -15.194109217395 | etot = -14.6249037423581 -282000 ekin = 0.181576720747694 | erot = 0.366527860021383 | epot = -15.1730083230829 | etot = -14.6249037423139 -283000 ekin = 0.170254050626048 | erot = 0.357859944223912 | epot = -15.1530177371086 | etot = -14.6249037422586 -284000 ekin = 0.16009863107041 | erot = 0.349965713705531 | epot = -15.1349680869742 | etot = -14.6249037421982 -285000 ekin = 0.151720356670754 | erot = 0.343146625519695 | epot = -15.1197707243297 | etot = -14.6249037421393 -286000 ekin = 0.145712559183906 | erot = 0.337703485420487 | epot = -15.1083197866921 | etot = -14.6249037420877 -287000 ekin = 0.142584250545045 | erot = 0.33391483609244 | epot = -15.1014028286853 | etot = -14.6249037420479 -288000 ekin = 0.14271294134083 | erot = 0.33201595204223 | epot = -15.0996326354053 | etot = -14.6249037420222 -289000 ekin = 0.146320998448773 | erot = 0.332180585089635 | epot = -15.1034053255502 | etot = -14.6249037420118 -290000 ekin = 0.153472816921521 | erot = 0.334506983378674 | epot = -15.1128835423164 | etot = -14.6249037420162 -291000 ekin = 0.16408646566307 | erot = 0.339009144348004 | epot = -15.1279993520452 | etot = -14.6249037420341 -292000 ekin = 0.177952173600894 | erot = 0.345613807734655 | epot = -15.1484697233998 | etot = -14.6249037420642 -293000 ekin = 0.194750859969321 | erot = 0.354163344443058 | epot = -15.1738179465174 | etot = -14.624903742105 -294000 ekin = 0.214068309159694 | erot = 0.364424408222029 | epot = -15.2033964595369 | etot = -14.6249037421551 -295000 ekin = 0.23540371040359 | erot = 0.376101928511103 | epot = -15.2364093811279 | etot = -14.6249037422133 -296000 ekin = 0.258174229753498 | erot = 0.388857685536646 | epot = -15.2719356575678 | etot = -14.6249037422776 -297000 ekin = 0.281719360135706 | erot = 0.402332315571764 | epot = -15.3089554180538 | etot = -14.6249037423463 -298000 ekin = 0.305309684523697 | erot = 0.416169191335652 | epot = -15.3463826182759 | etot = -14.6249037424165 -299000 ekin = 0.328164426016654 | erot = 0.430038291827268 | epot = -15.3831064603292 | etot = -14.6249037424853 -300000 ekin = 0.349480947255048 | erot = 0.443657997414315 | epot = -15.4180426872181 | etot = -14.6249037425488 -301000 ekin = 0.368477349759193 | erot = 0.456812763608568 | epot = -15.4501938559701 | etot = -14.6249037426023 -302000 ekin = 0.384446573101124 | erot = 0.469364841860938 | epot = -15.4787151576043 | etot = -14.6249037426422 -303000 ekin = 0.396817065634558 | erot = 0.481258609604811 | epot = -15.5029794179039 | etot = -14.6249037426646 -304000 ekin = 0.405211709647007 | erot = 0.492516637287636 | epot = -15.5226320896017 | etot = -14.624903742667 -305000 ekin = 0.409494186865868 | erot = 0.503227368870062 | epot = -15.5376252983853 | etot = -14.6249037426493 -306000 ekin = 0.409791521882642 | erot = 0.513525227982917 | epot = -15.5482204924792 | etot = -14.6249037426137 -307000 ekin = 0.406484029567507 | erot = 0.523565033268454 | epot = -15.5549528054007 | etot = -14.6249037425647 -308000 ekin = 0.400159443093576 | erot = 0.533493670193517 | epot = -15.5585568557963 | etot = -14.6249037425092 -309000 ekin = 0.391535685673409 | erot = 0.543422788904487 | epot = -15.5598622170328 | etot = -14.6249037424549 -310000 ekin = 0.381364662749467 | erot = 0.553406603763533 | epot = -15.559675008922 | etot = -14.624903742409 -311000 ekin = 0.370335174700701 | erot = 0.563428434509133 | epot = -15.5586673515868 | etot = -14.624903742377 -312000 ekin = 0.358994462073939 | erot = 0.573398378860855 | epot = -15.5572965832959 | etot = -14.6249037423611 -313000 ekin = 0.347704062021925 | erot = 0.583162598674903 | epot = -15.5557704030573 | etot = -14.6249037423605 -314000 ekin = 0.33663740290675 | erot = 0.592522528333923 | epot = -15.5540636736116 | etot = -14.6249037423709 -315000 ekin = 0.325816357219143 | erot = 0.601260411441213 | epot = -15.5519805110473 | etot = -14.6249037423869 -316000 ekin = 0.31517501281672 | erot = 0.60916645196768 | epot = -15.5492452071863 | etot = -14.6249037424019 -317000 ekin = 0.304633856553889 | erot = 0.616062831072119 | epot = -15.5456004300365 | etot = -14.6249037424105 -318000 ekin = 0.294167456686821 | erot = 0.621820866636781 | epot = -15.5408920657325 | etot = -14.6249037424089 -319000 ekin = 0.283852816310689 | erot = 0.626369338624031 | epot = -15.5351258973307 | etot = -14.6249037423959 -320000 ekin = 0.273891844373646 | erot = 0.62969394858388 | epot = -15.5284895353295 | etot = -14.624903742372 -321000 ekin = 0.264607615830763 | erot = 0.631829520445007 | epot = -15.5213408786157 | etot = -14.6249037423399 -322000 ekin = 0.256418665980724 | erot = 0.632847556381818 | epot = -15.5141699646656 | etot = -14.6249037423031 -323000 ekin = 0.249797892887888 | erot = 0.632842055921319 | epot = -15.5075436910747 | etot = -14.6249037422655 -324000 ekin = 0.245223011939643 | erot = 0.631916211662829 | epot = -15.5020429658332 | etot = -14.6249037422308 -325000 ekin = 0.243124676660885 | erot = 0.630171930979599 | epot = -15.4982003498433 | etot = -14.6249037422029 -326000 ekin = 0.243837159968202 | erot = 0.62770331019607 | epot = -15.4964442123487 | etot = -14.6249037421844 -327000 ekin = 0.247555458534598 | erot = 0.624594349329564 | epot = -15.4970535500418 | etot = -14.6249037421777 -328000 ekin = 0.254302069317208 | erot = 0.620920422826662 | epot = -15.5001262343276 | etot = -14.6249037421837 -329000 ekin = 0.263906382978448 | erot = 0.616752378549749 | epot = -15.5055625037309 | etot = -14.6249037422027 -330000 ekin = 0.275999298196581 | erot = 0.612161709808553 | epot = -15.513064750239 | etot = -14.6249037422339 -331000 ekin = 0.290024872454518 | erot = 0.6072251384784 | epot = -15.5221537532081 | etot = -14.6249037422752 -332000 ekin = 0.305269328205317 | erot = 0.602027230533175 | epot = -15.5322003010622 | etot = -14.6249037423237 -333000 ekin = 0.32090561137506 | erot = 0.59666030333851 | epot = -15.5424696570894 | etot = -14.6249037423759 -334000 ekin = 0.336049438962957 | erot = 0.59122171045733 | epot = -15.5521748918481 | etot = -14.6249037424278 -335000 ekin = 0.349821102707528 | erot = 0.585809355783074 | epot = -15.5605342009664 | etot = -14.6249037424758 -336000 ekin = 0.361406827299004 | erot = 0.580516763971273 | epot = -15.5668273337865 | etot = -14.6249037425162 -337000 ekin = 0.370114335989199 | erot = 0.575429096256477 | epot = -15.570447174792 | etot = -14.6249037425463 -338000 ekin = 0.375418963131835 | erot = 0.570621177508979 | epot = -15.5709438832047 | etot = -14.6249037425639 -339000 ekin = 0.376998306684161 | erot = 0.566157982091391 | epot = -15.5680600313428 | etot = -14.6249037425673 -340000 ekin = 0.374754278532076 | erot = 0.562097189039027 | epot = -15.561755210127 | etot = -14.6249037425559 -341000 ekin = 0.368821588409674 | erot = 0.558493134368603 | epot = -15.5522184653082 | etot = -14.6249037425299 -342000 ekin = 0.359561251230654 | erot = 0.555400700218385 | epot = -15.5398656939398 | etot = -14.6249037424907 -343000 ekin = 0.347537853254552 | erot = 0.552877785918206 | epot = -15.5253193816135 | etot = -14.6249037424408 -344000 ekin = 0.333480374963866 | erot = 0.5509852684009 | epot = -15.5093693857484 | etot = -14.6249037423837 -345000 ekin = 0.318228359784356 | erot = 0.549783918348281 | epot = -15.4929160204566 | etot = -14.6249037423239 -346000 ekin = 0.302667555547469 | erot = 0.549328430110417 | epot = -15.4768997279243 | etot = -14.6249037422664 -347000 ekin = 0.28766105744341 | erot = 0.549659363310447 | epot = -15.4622241629696 | etot = -14.6249037422157 -348000 ekin = 0.273982878354205 | erot = 0.550794243902763 | epot = -15.4496808644331 | etot = -14.6249037421761 -349000 ekin = 0.262260631617843 | erot = 0.552719272009514 | epot = -15.439883645778 | etot = -14.6249037421507 -350000 ekin = 0.252932884528192 | erot = 0.555383042233133 | epot = -15.4332196689026 | etot = -14.6249037421413 -351000 ekin = 0.246225113234617 | erot = 0.55869341876511 | epot = -15.4298222741477 | etot = -14.624903742148 -352000 ekin = 0.242146418558379 | erot = 0.562518344425243 | epot = -15.4295685051533 | etot = -14.6249037421697 -353000 ekin = 0.240507191582831 | erot = 0.566690733134613 | epot = -15.4321016669209 | etot = -14.6249037422035 -354000 ekin = 0.240955911174275 | erot = 0.571016874087082 | epot = -15.4368765275071 | etot = -14.6249037422458 -355000 ekin = 0.243030568944454 | erot = 0.575286990707861 | epot = -15.4432213019444 | etot = -14.624903742292 -356000 ekin = 0.246218336341954 | erot = 0.579286102670435 | epot = -15.4504081813504 | etot = -14.6249037423381 -357000 ekin = 0.250015504867581 | erot = 0.58280308408374 | epot = -15.4577223313315 | etot = -14.6249037423802 -358000 ekin = 0.253980003728839 | erot = 0.585636256510467 | epot = -15.4645200026551 | etot = -14.6249037424158 -359000 ekin = 0.257771924238821 | erot = 0.587595069854197 | epot = -15.4702707365363 | etot = -14.6249037424433 -360000 ekin = 0.261178006692924 | erot = 0.588498175296143 | epot = -15.4745799244512 | etot = -14.6249037424621 -361000 ekin = 0.264121303804436 | erot = 0.588169931158563 | epot = -15.4771949774355 | etot = -14.6249037424725 -362000 ekin = 0.26665626894814 | erot = 0.586437607933123 | epot = -15.4779976193568 | etot = -14.6249037424755 -363000 ekin = 0.268947338174106 | erot = 0.583131261384995 | epot = -15.4769823420322 | etot = -14.6249037424731 -364000 ekin = 0.271226723299596 | erot = 0.578087502910441 | epot = -15.4742179686788 | etot = -14.6249037424688 -365000 ekin = 0.273728224388818 | erot = 0.571157191000725 | epot = -15.469789157857 | etot = -14.6249037424674 -366000 ekin = 0.27660157052003 | erot = 0.562216266683608 | epot = -15.4637215796777 | etot = -14.624903742474 -367000 ekin = 0.279824898676208 | erot = 0.551178529879214 | epot = -15.4559071710475 | etot = -14.6249037424921 -368000 ekin = 0.283144751011421 | erot = 0.538009090150606 | epot = -15.446057583683 | etot = -14.624903742521 -369000 ekin = 0.286073979195429 | erot = 0.522737270878628 | epot = -15.43371499263 | etot = -14.6249037425559 -370000 ekin = 0.287962637923178 | erot = 0.50546765170011 | epot = -15.4183340322108 | etot = -14.6249037425875 -371000 ekin = 0.288129562576893 | erot = 0.486387667907303 | epot = -15.3994209730894 | etot = -14.6249037426052 -372000 ekin = 0.286016270828215 | erot = 0.465769998081936 | epot = -15.3766900115109 | etot = -14.6249037426008 -373000 ekin = 0.281314492917267 | erot = 0.443968246943336 | epot = -15.3501864824312 | etot = -14.6249037425706 -374000 ekin = 0.274029637541304 | erot = 0.421405384813941 | epot = -15.3203387648723 | etot = -14.6249037425171 -375000 ekin = 0.264468317323927 | erot = 0.398555847613352 | epot = -15.2879279073837 | etot = -14.6249037424464 -376000 ekin = 0.253165169267974 | erot = 0.375923572596667 | epot = -15.2539924842319 | etot = -14.6249037423673 -377000 ekin = 0.240780733674519 | erot = 0.354018931407049 | epot = -15.2197034073693 | etot = -14.6249037422878 -378000 ekin = 0.228003530692849 | erot = 0.333337224177657 | epot = -15.1862444970844 | etot = -14.6249037422138 -379000 ekin = 0.215478669427367 | erot = 0.314340303318035 | epot = -15.1547227148943 | etot = -14.6249037421489 -380000 ekin = 0.203769466320298 | erot = 0.297441561967809 | epot = -15.1261147703827 | etot = -14.6249037420946 -381000 ekin = 0.193344913038602 | erot = 0.282993579610754 | epot = -15.1012422347007 | etot = -14.6249037420513 -382000 ekin = 0.1845790971167 | erot = 0.271277560103436 | epot = -15.0807603992401 | etot = -14.62490374202 -383000 ekin = 0.177749902922622 | erot = 0.26249431847454 | epot = -15.0651479633984 | etot = -14.6249037420012 -384000 ekin = 0.173031383434508 | erot = 0.256757595375745 | epot = -15.0546927208059 | etot = -14.6249037419956 -385000 ekin = 0.170483112154869 | erot = 0.254091341095724 | epot = -15.049478195254 | etot = -14.6249037420034 -386000 ekin = 0.170046361592442 | erot = 0.254432809989109 | epot = -15.0493829136049 | etot = -14.6249037420233 -387000 ekin = 0.171558026227206 | erot = 0.257642587604648 | epot = -15.0541043558835 | etot = -14.6249037420517 -388000 ekin = 0.174787865439128 | erot = 0.263521131370077 | epot = -15.0632127388927 | etot = -14.6249037420835 -389000 ekin = 0.179494526901848 | erot = 0.271829477565643 | epot = -15.0762277465811 | etot = -14.6249037421136 -390000 ekin = 0.185484901052496 | erot = 0.282310127810724 | epot = -15.0926987710012 | etot = -14.624903742138 -391000 ekin = 0.192654775276086 | erot = 0.294703495236184 | epot = -15.1122620126683 | etot = -14.624903742156 -392000 ekin = 0.200990711955861 | erot = 0.308756153372879 | epot = -15.1346506074993 | etot = -14.6249037421705 -393000 ekin = 0.210524629688573 | erot = 0.324219483681282 | epot = -15.1596478555577 | etot = -14.6249037421878 -394000 ekin = 0.22125039811835 | erot = 0.340840530849664 | epot = -15.1869946711827 | etot = -14.6249037422146 -395000 ekin = 0.233028912153826 | erot = 0.358349828151301 | epot = -15.2162824825616 | etot = -14.6249037422565 -396000 ekin = 0.2455168348482 | erot = 0.376452447324096 | epot = -15.2468730244869 | etot = -14.6249037423146 -397000 ekin = 0.25814964628924 | erot = 0.394827815017667 | epot = -15.2778812036919 | etot = -14.624903742385 -398000 ekin = 0.270192540270399 | erot = 0.4131410333725 | epot = -15.3082373161018 | etot = -14.6249037424589 -399000 ekin = 0.280849396853854 | erot = 0.431064534842813 | epot = -15.3368176742223 | etot = -14.6249037425256 -400000 ekin = 0.289399657315509 | erot = 0.448305349545533 | epot = -15.3626087494363 | etot = -14.6249037425752 -401000 ekin = 0.295323233787914 | erot = 0.464631356382232 | epot = -15.3848583327717 | etot = -14.6249037426015 -402000 ekin = 0.298377750401429 | erot = 0.479890206670972 | epot = -15.4031716996757 | etot = -14.6249037426033 -403000 ekin = 0.298608046776847 | erot = 0.494016844836358 | epot = -15.4175286341982 | etot = -14.624903742585 -404000 ekin = 0.296288720276099 | erot = 0.507028747324982 | epot = -15.4282212101551 | etot = -14.624903742554 -405000 ekin = 0.29181945089068 | erot = 0.519011022290344 | epot = -15.4357342157007 | etot = -14.6249037425197 -406000 ekin = 0.285604695316787 | erot = 0.530095491696252 | epot = -15.440603929503 | etot = -14.62490374249 -407000 ekin = 0.27795179501284 | erot = 0.540438449781457 | epot = -15.4432939872644 | etot = -14.6249037424701 -408000 ekin = 0.269015012492725 | erot = 0.550201084797105 | epot = -15.4441198397503 | etot = -14.6249037424605 -409000 ekin = 0.258799683406998 | erot = 0.559535019811799 | epot = -15.4432384456764 | etot = -14.6249037424576 -410000 ekin = 0.247223943172304 | erot = 0.568573648692186 | epot = -15.4407013343195 | etot = -14.624903742455 -411000 ekin = 0.234219542826644 | erot = 0.577428429926533 | epot = -15.4365517151989 | etot = -14.6249037424457 -412000 ekin = 0.219842320368382 | erot = 0.5861883861288 | epot = -15.4309344489209 | etot = -14.6249037424237 -413000 ekin = 0.204359948374925 | erot = 0.594920843620856 | epot = -15.4241845343826 | etot = -14.6249037423868 -414000 ekin = 0.188290368309528 | erot = 0.603671832826723 | epot = -15.4168659434726 | etot = -14.6249037423363 -415000 ekin = 0.17237708181679 | erot = 0.612465324291743 | epot = -15.4097461483867 | etot = -14.6249037422781 -416000 ekin = 0.157503657630917 | erot = 0.621301324615619 | epot = -15.4037087244673 | etot = -14.6249037422208 -417000 ekin = 0.144565276806003 | erot = 0.630153567596961 | epot = -15.3996225865765 | etot = -14.6249037421735 -418000 ekin = 0.134326161306162 | erot = 0.638967960411851 | epot = -15.3981978638625 | etot = -14.6249037421445 -419000 ekin = 0.127295713866961 | erot = 0.647663024756136 | epot = -15.3998624807615 | etot = -14.6249037421384 -420000 ekin = 0.123652074078926 | erot = 0.656133267678405 | epot = -15.404689083913 | etot = -14.6249037421557 -421000 ekin = 0.123230332545423 | erot = 0.664256043547052 | epot = -15.4123901182846 | etot = -14.6249037421921 -422000 ekin = 0.125576493084645 | erot = 0.671901405101299 | epot = -15.4223816404261 | etot = -14.6249037422401 -423000 ekin = 0.130051930466291 | erot = 0.678943694027994 | epot = -15.4338993667851 | etot = -14.6249037422908 -424000 ekin = 0.135961143238941 | erot = 0.68527308622734 | epot = -15.4461379718019 | etot = -14.6249037423356 -425000 ekin = 0.142671659965653 | erot = 0.690804983811737 | epot = -15.4583803861463 | etot = -14.6249037423689 -426000 ekin = 0.149699767318955 | erot = 0.69548556134855 | epot = -15.4700890710557 | etot = -14.6249037423882 -427000 ekin = 0.156747049208564 | erot = 0.699292628464386 | epot = -15.4809434200676 | etot = -14.6249037423947 -428000 ekin = 0.163686553654653 | erot = 0.702231990285693 | epot = -15.4908222863327 | etot = -14.6249037423924 -429000 ekin = 0.170509683514881 | erot = 0.704330315301697 | epot = -15.4997437412031 | etot = -14.6249037423865 -430000 ekin = 0.177252892951705 | erot = 0.705626025883602 | epot = -15.5077826612176 | etot = -14.6249037423823 -431000 ekin = 0.183925691222895 | erot = 0.706159951516283 | epot = -15.5149893851227 | etot = -14.6249037423835 -432000 ekin = 0.19045785108011 | erot = 0.705966883793978 | epot = -15.5213284772661 | etot = -14.624903742392 -433000 ekin = 0.196676887389506 | erot = 0.705069371776843 | epot = -15.5266500015735 | etot = -14.6249037424072 -434000 ekin = 0.202317433899842 | erot = 0.703474477741428 | epot = -15.5306956540681 | etot = -14.6249037424269 -435000 ekin = 0.207056046506956 | erot = 0.701173837003811 | epot = -15.5331336259585 | etot = -14.6249037424477 -436000 ekin = 0.210560164857125 | erot = 0.698146912242933 | epot = -15.5336108195661 | etot = -14.6249037424661 -437000 ekin = 0.212539330538931 | erot = 0.694366864819831 | epot = -15.5318099378377 | etot = -14.624903742479 -438000 ekin = 0.212789433625871 | erot = 0.689808070113593 | epot = -15.5275012462235 | etot = -14.624903742484 -439000 ekin = 0.211224885327214 | erot = 0.684454087056214 | epot = -15.5205827148631 | etot = -14.6249037424797 -440000 ekin = 0.207897417438809 | erot = 0.678304934040255 | epot = -15.5111060939441 | etot = -14.624903742465 -441000 ekin = 0.203002684917561 | erot = 0.671382822496918 | epot = -15.4992892498548 | etot = -14.6249037424403 -442000 ekin = 0.196876783893415 | erot = 0.66373594678721 | epot = -15.4855164730867 | etot = -14.6249037424061 -443000 ekin = 0.189984458135294 | erot = 0.655440346227568 | epot = -15.4703285467262 | etot = -14.6249037423634 -444000 ekin = 0.182899715135625 | erot = 0.646600090308741 | epot = -15.4544035477581 | etot = -14.6249037423138 -445000 ekin = 0.176278659807151 | erot = 0.637346059016373 | epot = -15.4385284610832 | etot = -14.6249037422597 -446000 ekin = 0.170824489262207 | erot = 0.627833490901199 | epot = -15.4235617223673 | etot = -14.6249037422039 -447000 ekin = 0.16724611578148 | erot = 0.618238375507256 | epot = -15.4103882334382 | etot = -14.6249037421495 -448000 ekin = 0.166214016011086 | erot = 0.608752709243579 | epot = -15.3998704673542 | etot = -14.6249037420995 -449000 ekin = 0.1683180025474 | erot = 0.599578546514547 | epot = -15.3928002911186 | etot = -14.6249037420567 -450000 ekin = 0.174030350885976 | erot = 0.590920601688637 | epot = -15.3898546945984 | etot = -14.6249037420238 -451000 ekin = 0.183674309612486 | erot = 0.582976972209394 | epot = -15.3915550238252 | etot = -14.6249037420033 -452000 ekin = 0.197394458885248 | erot = 0.575927582956616 | epot = -15.39822578384 | etot = -14.6249037419981 -453000 ekin = 0.215124290963754 | erot = 0.569920414705972 | epot = -15.4099484476811 | etot = -14.6249037420114 -454000 ekin = 0.236549344238332 | erot = 0.565056494271021 | epot = -15.4265095805559 | etot = -14.6249037420465 -455000 ekin = 0.261070666492934 | erot = 0.561375729612865 | epot = -15.4473501382115 | etot = -14.6249037421057 -456000 ekin = 0.287780783019101 | erot = 0.558846520705115 | epot = -15.4715310459133 | etot = -14.6249037421891 -457000 ekin = 0.315469350479039 | erot = 0.557362227354604 | epot = -15.4977353201268 | etot = -14.6249037422931 -458000 ekin = 0.342675461161211 | erot = 0.556746783054113 | epot = -15.5243259866255 | etot = -14.6249037424101 -459000 ekin = 0.367796771324328 | erot = 0.556770049266128 | epot = -15.5494705631189 | etot = -14.6249037425284 -460000 ekin = 0.3892528364295 | erot = 0.557171234683844 | epot = -15.5713278137471 | etot = -14.6249037426338 -461000 ekin = 0.405683830372718 | erot = 0.557686417732241 | epot = -15.5882739908163 | etot = -14.6249037427113 -462000 ekin = 0.416150509763905 | erot = 0.558074591842708 | epot = -15.5991288443566 | etot = -14.6249037427499 -463000 ekin = 0.420292029665246 | erot = 0.558136338549459 | epot = -15.6033321109587 | etot = -14.624903742744 -464000 ekin = 0.418399545178514 | erot = 0.557720582601952 | epot = -15.6010238704768 | etot = -14.6249037426963 -465000 ekin = 0.411377435968826 | erot = 0.55671776612672 | epot = -15.5929989447132 | etot = -14.6249037426177 -466000 ekin = 0.400588481170777 | erot = 0.555041504869193 | epot = -15.5805337285653 | etot = -14.6249037425253 -467000 ekin = 0.387608315925912 | erot = 0.552604267015981 | epot = -15.5651163253807 | etot = -14.6249037424389 -468000 ekin = 0.373939506071419 | erot = 0.549294716065778 | epot = -15.5481379645134 | etot = -14.6249037423762 -469000 ekin = 0.360748545285941 | erot = 0.544964338611031 | epot = -15.5306166262458 | etot = -14.6249037423488 -470000 ekin = 0.348685397522481 | erot = 0.539428754142283 | epot = -15.5130178940239 | etot = -14.6249037423591 -471000 ekin = 0.33782542530965 | erot = 0.53248528288589 | epot = -15.495214450596 | etot = -14.6249037424005 -472000 ekin = 0.327743216876187 | erot = 0.523944004295118 | epot = -15.4765909636299 | etot = -14.6249037424586 -473000 ekin = 0.317695625905249 | erot = 0.513665869846711 | epot = -15.4562652382675 | etot = -14.6249037425155 -474000 ekin = 0.306866206292903 | erot = 0.501599410558902 | epot = -15.4333693594053 | etot = -14.6249037425535 -475000 ekin = 0.294611572516014 | erot = 0.487807694339925 | epot = -15.4073230094157 | etot = -14.6249037425598 -476000 ekin = 0.280654133645735 | erot = 0.472479343853221 | epot = -15.3780372200274 | etot = -14.6249037425284 -477000 ekin = 0.265182667318346 | erot = 0.455920989277164 | epot = -15.3460073990571 | etot = -14.6249037424615 -478000 ekin = 0.248846579355896 | erot = 0.438532535944716 | epot = -15.3122828576688 | etot = -14.6249037423682 -479000 ekin = 0.232654569020801 | erot = 0.420770062233786 | epot = -15.2783283735167 | etot = -14.6249037422621 -480000 ekin = 0.217807844646274 | erot = 0.403103245642895 | epot = -15.2458148324472 | etot = -14.624903742158 -481000 ekin = 0.205508255202274 | erot = 0.385974572360121 | epot = -15.2163865696318 | etot = -14.6249037420694 -482000 ekin = 0.196781566941766 | erot = 0.36976631024765 | epot = -15.1914516191951 | etot = -14.6249037420057 -483000 ekin = 0.19234694356787 | erot = 0.354778814406374 | epot = -15.1720294999463 | etot = -14.6249037419721 -484000 ekin = 0.192548846646396 | erot = 0.341220938396507 | epot = -15.1586735270111 | etot = -14.6249037419682 -485000 ekin = 0.197351634264796 | erot = 0.329210924265182 | epot = -15.1514663005207 | etot = -14.6249037419907 -486000 ekin = 0.206384571112674 | erot = 0.318784712513058 | epot = -15.1500730256597 | etot = -14.624903742034 -487000 ekin = 0.219018661981128 | erot = 0.309908337315953 | epot = -15.1538307413883 | etot = -14.6249037420912 -488000 ekin = 0.234457053485615 | erot = 0.302491737711597 | epot = -15.1618525333532 | etot = -14.6249037421559 -489000 ekin = 0.251825722282228 | erot = 0.296402451840807 | epot = -15.1731319163449 | etot = -14.6249037422219 -490000 ekin = 0.270257579252373 | erot = 0.291478772534408 | epot = -15.1866400940707 | etot = -14.6249037422839 -491000 ekin = 0.288968023940477 | erot = 0.287542686829702 | epot = -15.2014144531066 | etot = -14.6249037423364 -492000 ekin = 0.307321746939982 | erot = 0.28441316533236 | epot = -15.2166386546473 | etot = -14.624903742375 -493000 ekin = 0.32488919226749 | erot = 0.281920128741024 | epot = -15.2317130634052 | etot = -14.6249037423967 -494000 ekin = 0.341487883386483 | erot = 0.279918789013753 | epot = -15.2463104147992 | etot = -14.624903742399 -495000 ekin = 0.35720080106069 | erot = 0.278303167954071 | epot = -15.2604077113969 | etot = -14.6249037423821 -496000 ekin = 0.372363075866133 | erot = 0.277016625443694 | epot = -15.274283443659 | etot = -14.6249037423491 -497000 ekin = 0.387510424729673 | erot = 0.276056483801325 | epot = -15.288470650837 | etot = -14.624903742306 -498000 ekin = 0.403287744735438 | erot = 0.275469725413168 | epot = -15.3036612124104 | etot = -14.6249037422618 -499000 ekin = 0.42032292393259 | erot = 0.275337682298044 | epot = -15.320564348458 | etot = -14.6249037422274 -500000 ekin = 0.43907820686993 | erot = 0.275749832423184 | epot = -15.3397317815074 | etot = -14.6249037422143 -501000 ekin = 0.459699055393576 | erot = 0.27677002458897 | epot = -15.3613728222153 | etot = -14.6249037422327 -502000 ekin = 0.481887975238202 | erot = 0.278401857022776 | epot = -15.3851935745495 | etot = -14.6249037422885 -503000 ekin = 0.504836001700849 | erot = 0.28056227342693 | epot = -15.410302017509 | etot = -14.6249037423813 -504000 ekin = 0.527242963721984 | erot = 0.283072520273731 | epot = -15.4352192264977 | etot = -14.624903742502 -505000 ekin = 0.547444055756082 | erot = 0.285672032586838 | epot = -15.458019830977 | etot = -14.6249037426341 -506000 ekin = 0.563636138784674 | erot = 0.288055811209927 | epot = -15.47659569275 | etot = -14.6249037427554 -507000 ekin = 0.574166796919909 | erot = 0.289928574131153 | epot = -15.4889991138946 | etot = -14.6249037428436 -508000 ekin = 0.577825151301095 | erot = 0.29106332686132 | epot = -15.4937922210437 | etot = -14.6249037428812 -509000 ekin = 0.574066827021787 | erot = 0.291350176078735 | epot = -15.4903207459605 | etot = -14.6249037428599 -510000 ekin = 0.563118031118052 | erot = 0.290823209378379 | epot = -15.478844983279 | etot = -14.6249037427826 -511000 ekin = 0.545937816053849 | erot = 0.289659846600108 | epot = -15.4605014053159 | etot = -14.624903742662 -512000 ekin = 0.524051924661522 | erot = 0.288153919329358 | epot = -15.4371095865082 | etot = -14.6249037425174 -513000 ekin = 0.49930007419802 | erot = 0.286670443869403 | epot = -15.4108742604374 | etot = -14.6249037423699 -514000 ekin = 0.473556830410389 | erot = 0.285593013544029 | epot = -15.3840535861934 | etot = -14.624903742239 -515000 ekin = 0.448481344234872 | erot = 0.285274677057468 | epot = -15.3586597634305 | etot = -14.6249037421382 -516000 ekin = 0.425336124988155 | erot = 0.286000471485139 | epot = -15.3362403385481 | etot = -14.6249037420748 -517000 ekin = 0.404895133580943 | erot = 0.2879658116616 | epot = -15.3177646872915 | etot = -14.6249037420489 -518000 ekin = 0.38744137195972 | erot = 0.291271247088022 | epot = -15.303616361103 | etot = -14.6249037420552 -519000 ekin = 0.372839035852851 | erot = 0.295931281214127 | epot = -15.2936740591517 | etot = -14.6249037420847 -520000 ekin = 0.360656186943069 | erot = 0.301893194868317 | epot = -15.2874531239377 | etot = -14.6249037421263 -521000 ekin = 0.350310207443456 | erot = 0.30906098360489 | epot = -15.284274933218 | etot = -14.6249037421697 -522000 ekin = 0.341208800539667 | erot = 0.3173194084493 | epot = -15.2834319511953 | etot = -14.6249037422063 -523000 ekin = 0.332862997936835 | erot = 0.326553653087588 | epot = -15.284320393256 | etot = -14.6249037422315 -524000 ekin = 0.324955020060083 | erot = 0.336661144000867 | epot = -15.2865199063051 | etot = -14.6249037422441 -525000 ekin = 0.317352570821523 | erot = 0.347553686772997 | epot = -15.2898099998415 | etot = -14.624903742247 -526000 ekin = 0.310071537936527 | erot = 0.359150063852877 | epot = -15.2941253440357 | etot = -14.6249037422463 -527000 ekin = 0.30319969763022 | erot = 0.371361343285068 | epot = -15.2994647831647 | etot = -14.6249037422494 -528000 ekin = 0.296802852838113 | erot = 0.38407297047912 | epot = -15.3057795655799 | etot = -14.6249037422627 -529000 ekin = 0.290839689447243 | erot = 0.397128838352394 | epot = -15.31287227009 | etot = -14.6249037422904 -530000 ekin = 0.285110822260533 | erot = 0.410322608856898 | epot = -15.3203371734496 | etot = -14.6249037423322 -531000 ekin = 0.279260366287321 | erot = 0.423400398731777 | epot = -15.3275645074024 | etot = -14.6249037423833 -532000 ekin = 0.2728357059054 | erot = 0.436076588369062 | epot = -15.3338160367096 | etot = -14.6249037424351 -533000 ekin = 0.265395406955423 | erot = 0.448061330488706 | epot = -15.3383604799205 | etot = -14.6249037424763 -534000 ekin = 0.25664035180014 | erot = 0.45909504502717 | epot = -15.3406391393241 | etot = -14.6249037424968 -535000 ekin = 0.24653363369425 | erot = 0.468982742180589 | epot = -15.3404201183648 | etot = -14.62490374249 -536000 ekin = 0.235373881374767 | erot = 0.477620282696299 | epot = -15.3378979065254 | etot = -14.6249037424543 -537000 ekin = 0.223795203401825 | erot = 0.485006039595742 | epot = -15.3337049853926 | etot = -14.624903742395 -538000 ekin = 0.212682661997717 | erot = 0.491234540507922 | epot = -15.32882094483 | etot = -14.6249037423243 -539000 ekin = 0.203011536568094 | erot = 0.496472671628212 | epot = -15.324387950454 | etot = -14.6249037422577 -540000 ekin = 0.195638496925756 | erot = 0.500922912276288 | epot = -15.3214651514142 | etot = -14.6249037422122 -541000 ekin = 0.191090437373868 | erot = 0.504781043299473 | epot = -15.3207752228743 | etot = -14.624903742201 -542000 ekin = 0.189407567632351 | erot = 0.508197267609666 | epot = -15.3225085774711 | etot = -14.6249037422291 -543000 ekin = 0.190094034780963 | erot = 0.511249275631094 | epot = -15.3262470527038 | etot = -14.6249037422917 -544000 ekin = 0.192205662500001 | erot = 0.513933300996131 | epot = -15.3310427058706 | etot = -14.6249037423745 -545000 ekin = 0.194562943958398 | erot = 0.516174993404786 | epot = -15.3356416798198 | etot = -14.6249037424566 -546000 ekin = 0.196033343259865 | erot = 0.517857026727595 | epot = -15.3387941125054 | etot = -14.624903742518 -547000 ekin = 0.195801439086576 | erot = 0.518856237019659 | epot = -15.3395614186507 | etot = -14.6249037425445 -548000 ekin = 0.193552178457624 | erot = 0.519081068513043 | epot = -15.3375369895016 | etot = -14.6249037425309 -549000 ekin = 0.189527872077782 | erot = 0.518500763845595 | epot = -15.3329323784042 | etot = -14.6249037424808 -550000 ekin = 0.18446469719282 | erot = 0.517160608016848 | epot = -15.326529047614 | etot = -14.6249037424043 -551000 ekin = 0.17944751961377 | erot = 0.515181377053922 | epot = -15.3195326389815 | etot = -14.6249037423138 -552000 ekin = 0.175731062295071 | erot = 0.512744588095586 | epot = -15.3133793926126 | etot = -14.6249037422219 -553000 ekin = 0.174564310046339 | erot = 0.510067400325356 | epot = -15.3095354525118 | etot = -14.6249037421401 -554000 ekin = 0.177036897101121 | erot = 0.507372062614127 | epot = -15.309312701793 | etot = -14.6249037420777 -555000 ekin = 0.183953653121541 | erot = 0.50485506124058 | epot = -15.3137124564044 | etot = -14.6249037420423 -556000 ekin = 0.195740677804154 | erot = 0.502660902828886 | epot = -15.3233053226714 | etot = -14.6249037420384 -557000 ekin = 0.212389174813395 | erot = 0.500864749566249 | epot = -15.3381576664467 | etot = -14.6249037420671 -558000 ekin = 0.233445020972978 | erot = 0.499466731744177 | epot = -15.3578154948427 | etot = -14.6249037421256 -559000 ekin = 0.258048678278145 | erot = 0.498398734229532 | epot = -15.381351154715 | etot = -14.6249037422073 -560000 ekin = 0.285022157939727 | erot = 0.497541950864641 | epot = -15.4074678511075 | etot = -14.6249037423031 -561000 ekin = 0.312990622171893 | erot = 0.496751658908829 | epot = -15.4346460234834 | etot = -14.6249037424027 -562000 ekin = 0.340519848730057 | erot = 0.495884310852853 | epot = -15.461307902079 | etot = -14.6249037424961 -563000 ekin = 0.366249237356341 | erot = 0.494821962715706 | epot = -15.4859749426471 | etot = -14.6249037425751 -564000 ekin = 0.389003340228864 | erot = 0.493490109026347 | epot = -15.5073971918896 | etot = -14.6249037426344 -565000 ekin = 0.407871381975787 | erot = 0.491866632343088 | epot = -15.5246417569901 | etot = -14.6249037426712 -566000 ekin = 0.422251605413063 | erot = 0.489981232303539 | epot = -15.537136580402 | etot = -14.6249037426854 -567000 ekin = 0.431863045464991 | erot = 0.487906470955931 | epot = -15.5446732590994 | etot = -14.6249037426785 -568000 ekin = 0.436733840918529 | erot = 0.485743252286281 | epot = -15.5473808358582 | etot = -14.6249037426534 -569000 ekin = 0.437172173179269 | erot = 0.483603786385196 | epot = -15.5456797021777 | etot = -14.6249037426133 -570000 ekin = 0.43372713864672 | erot = 0.48159597879343 | epot = -15.5402268600018 | etot = -14.6249037425617 -571000 ekin = 0.42714180814445 | erot = 0.479812578148079 | epot = -15.5318581287948 | etot = -14.6249037425023 -572000 ekin = 0.418294466662065 | erot = 0.478326721683348 | epot = -15.5215249307851 | etot = -14.6249037424397 -573000 ekin = 0.408121101336508 | erot = 0.477193277919927 | epot = -15.5102181216365 | etot = -14.6249037423801 -574000 ekin = 0.397514818218918 | erot = 0.476453234966625 | epot = -15.4988717955165 | etot = -14.624903742331 -575000 ekin = 0.387207144490505 | erot = 0.476137354469736 | epot = -15.4882482412605 | etot = -14.6249037423002 -576000 ekin = 0.377649119218454 | erot = 0.476266044932873 | epot = -15.4788189064457 | etot = -14.6249037422944 -577000 ekin = 0.368920817133122 | erot = 0.476844730976094 | epot = -15.4706692904255 | etot = -14.6249037423163 -578000 ekin = 0.360700785231361 | erot = 0.47785688313413 | epot = -15.4634614107286 | etot = -14.6249037423631 -579000 ekin = 0.352319179858645 | erot = 0.479258927576455 | epot = -15.4564818498607 | etot = -14.6249037424256 -580000 ekin = 0.342901425190256 | erot = 0.480981430412058 | epot = -15.4487865980916 | etot = -14.6249037424893 -581000 ekin = 0.331586894252413 | erot = 0.482939076923234 | epot = -15.4394297137118 | etot = -14.6249037425361 -582000 ekin = 0.317784488003658 | erot = 0.485048781538909 | epot = -15.427737012092 | etot = -14.6249037425495 -583000 ekin = 0.301409490235786 | erot = 0.487252029394123 | epot = -15.4135652621474 | etot = -14.6249037425175 -584000 ekin = 0.283039202393456 | erot = 0.489535511255409 | epot = -15.3974784560865 | etot = -14.6249037424376 -585000 ekin = 0.263933313486932 | erot = 0.491944128119358 | epot = -15.3807811839248 | etot = -14.6249037423185 -586000 ekin = 0.245890887800014 | erot = 0.494582820570716 | epot = -15.36537745055 | etot = -14.6249037421793 -587000 ekin = 0.230956405619767 | erot = 0.497607010278002 | epot = -15.3534671579441 | etot = -14.6249037420464 -588000 ekin = 0.221033841917334 | erot = 0.501205839010304 | epot = -15.3471434228726 | etot = -14.6249037419449 -589000 ekin = 0.217504428503198 | erot = 0.505584588307916 | epot = -15.3479927587054 | etot = -14.6249037418943 -590000 ekin = 0.220953423088802 | erot = 0.510952138425678 | epot = -15.3568093034149 | etot = -14.6249037419004 -591000 ekin = 0.231083134064877 | erot = 0.517515644130037 | epot = -15.3735025201503 | etot = -14.6249037419554 -592000 ekin = 0.246829245753809 | erot = 0.525479282586983 | epot = -15.3972122703829 | etot = -14.6249037420421 -593000 ekin = 0.266628949730648 | erot = 0.535039778666154 | epot = -15.4265724705373 | etot = -14.6249037421405 -594000 ekin = 0.288743434935948 | erot = 0.546371032865159 | epot = -15.4600182100359 | etot = -14.6249037422348 -595000 ekin = 0.311533695301854 | erot = 0.559594229359111 | epot = -15.4960316669784 | etot = -14.6249037423174 -596000 ekin = 0.333624348261494 | erot = 0.574736425374244 | epot = -15.5332645160249 | etot = -14.6249037423892 -597000 ekin = 0.353943370598259 | erot = 0.591686591895167 | epot = -15.5705337049495 | etot = -14.6249037424561 -598000 ekin = 0.371670846224399 | erot = 0.610160828223706 | epot = -15.6067354169733 | etot = -14.6249037425252 -599000 ekin = 0.386151688530232 | erot = 0.629687420924543 | epot = -15.6407428520551 | etot = -14.6249037426004 -600000 ekin = 0.396824670884392 | erot = 0.649618644309618 | epot = -15.6713470578743 | etot = -14.6249037426803 -601000 ekin = 0.403202067553724 | erot = 0.669171693344937 | epot = -15.6972775036568 | etot = -14.6249037427581 -602000 ekin = 0.404908528299605 | erot = 0.687495721385225 | epot = -15.7173079925077 | etot = -14.6249037428229 -603000 ekin = 0.401765041348441 | erot = 0.703757265562351 | epot = -15.7304260497729 | etot = -14.6249037428621 -604000 ekin = 0.393886240081566 | erot = 0.717231476889447 | epot = -15.7360214598369 | etot = -14.6249037428659 -605000 ekin = 0.381750384954784 | erot = 0.727382711583162 | epot = -15.7340368393681 | etot = -14.6249037428302 -606000 ekin = 0.366205114567235 | erot = 0.733917584159895 | epot = -15.725026441486 | etot = -14.6249037427589 -607000 ekin = 0.348389460815329 | erot = 0.736798185090343 | epot = -15.7100913885696 | etot = -14.624903742664 -608000 ekin = 0.329579787369629 | erot = 0.73621262347853 | epot = -15.6906961534103 | etot = -14.6249037425622 -609000 ekin = 0.310994196072014 | erot = 0.732511274794253 | epot = -15.6684092133371 | etot = -14.6249037424709 -610000 ekin = 0.29360483588481 | erot = 0.726125549058504 | epot = -15.644634127347 | etot = -14.6249037424037 -611000 ekin = 0.278004208602607 | erot = 0.717488389874772 | epot = -15.6203963408453 | etot = -14.624903742368 -612000 ekin = 0.264353214553523 | erot = 0.706972008379557 | epot = -15.5962289652967 | etot = -14.6249037423637 -613000 ekin = 0.252415280668682 | erot = 0.694851301360247 | epot = -15.5721703244136 | etot = -14.6249037423847 -614000 ekin = 0.241662201717183 | erot = 0.681294462599197 | epot = -15.5478604067366 | etot = -14.6249037424202 -615000 ekin = 0.231427318529533 | erot = 0.666377599991891 | epot = -15.5227086609789 | etot = -14.6249037424574 -616000 ekin = 0.221078258759054 | erot = 0.650117838828839 | epot = -15.496099840071 | etot = -14.6249037424831 -617000 ekin = 0.21018039046722 | erot = 0.632518274251072 | epot = -15.4676024072045 | etot = -14.6249037424862 -618000 ekin = 0.198621509656023 | erot = 0.613617132100535 | epot = -15.4371423842165 | etot = -14.6249037424599 -619000 ekin = 0.18667044221321 | erot = 0.593532504056809 | epot = -15.405106688674 | etot = -14.624903742404 -620000 ekin = 0.174951539061334 | erot = 0.572493952083576 | epot = -15.3723492334691 | etot = -14.6249037423242 -621000 ekin = 0.164335257151748 | erot = 0.550854196820334 | epot = -15.3400931962044 | etot = -14.6249037422324 -622000 ekin = 0.155768039681223 | erot = 0.529078173717901 | epot = -15.3097499555421 | etot = -14.6249037421429 -623000 ekin = 0.150083571178067 | erot = 0.507711807337581 | epot = -15.2826991205843 | etot = -14.6249037420687 -624000 ekin = 0.147843467415026 | erot = 0.487337070698877 | epot = -15.2600842801327 | etot = -14.6249037420188 -625000 ekin = 0.149245521580685 | erot = 0.468521842126521 | epot = -15.2426711057039 | etot = -14.6249037419967 -626000 ekin = 0.154116108891011 | erot = 0.451772481731706 | epot = -15.230792332623 | etot = -14.6249037420003 -627000 ekin = 0.161979086426243 | erot = 0.437494698740521 | epot = -15.2243775271906 | etot = -14.6249037420239 -628000 ekin = 0.172174902879429 | erot = 0.425965324893993 | epot = -15.2230439698331 | etot = -14.6249037420597 -629000 ekin = 0.183995029152745 | erot = 0.417314987668754 | epot = -15.2262137589225 | etot = -14.624903742101 -630000 ekin = 0.196798066695247 | erot = 0.411519917957055 | epot = -15.2332217267955 | etot = -14.6249037421432 -631000 ekin = 0.210082131922237 | erot = 0.408400457424511 | epot = -15.2433863315318 | etot = -14.6249037421851 -632000 ekin = 0.223500184826661 | erot = 0.407624312389748 | epot = -15.2560282394451 | etot = -14.6249037422287 -633000 ekin = 0.236818662197368 | erot = 0.40871410814115 | epot = -15.2704365126172 | etot = -14.6249037422787 -634000 ekin = 0.249833574953511 | erot = 0.411060882467202 | epot = -15.2857981997609 | etot = -14.6249037423402 -635000 ekin = 0.262270239999869 | erot = 0.413946987960319 | epot = -15.3011209703766 | etot = -14.6249037424164 -636000 ekin = 0.273700147362094 | erot = 0.41658241201687 | epot = -15.3151863018853 | etot = -14.6249037425063 -637000 ekin = 0.283507856899951 | erot = 0.418156955202178 | epot = -15.3265685547055 | etot = -14.6249037426034 -638000 ekin = 0.290930324554581 | erot = 0.417906927432974 | epot = -15.3337409946828 | etot = -14.6249037426952 -639000 ekin = 0.295171730169445 | erot = 0.415189912095163 | epot = -15.3352653850311 | etot = -14.6249037427665 -640000 ekin = 0.295573453214757 | erot = 0.409556450349425 | epot = -15.330033646366 | etot = -14.6249037428018 -641000 ekin = 0.291798784614159 | erot = 0.400805216305592 | epot = -15.3175077437094 | etot = -14.6249037427896 -642000 ekin = 0.283982821763191 | erot = 0.389009767281871 | epot = -15.2978963317709 | etot = -14.6249037427259 -643000 ekin = 0.272803834295014 | erot = 0.374510198235057 | epot = -15.2722177751454 | etot = -14.6249037426153 -644000 ekin = 0.259451287281783 | erot = 0.357870303235152 | epot = -15.242225332988 | etot = -14.6249037424711 -645000 ekin = 0.245490538509252 | erot = 0.339807577758131 | epot = -15.2102018585797 | etot = -14.6249037423123 -646000 ekin = 0.232646751226996 | erot = 0.321107525182603 | epot = -15.1786580185706 | etot = -14.624903742161 -647000 ekin = 0.22254581022401 | erot = 0.302534738054871 | epot = -15.1499842903174 | etot = -14.6249037420385 -648000 ekin = 0.216457466201459 | erot = 0.284752019408104 | epot = -15.1261132275716 | etot = -14.624903741962 -649000 ekin = 0.215087078764693 | erot = 0.268256849270417 | epot = -15.1082476699768 | etot = -14.6249037419417 -650000 ekin = 0.218457489209268 | erot = 0.253342374384922 | epot = -15.0967036055725 | etot = -14.6249037419783 -651000 ekin = 0.225910420497663 | erot = 0.240087663214968 | epot = -15.090901825775 | etot = -14.6249037420623 -652000 ekin = 0.236236377394858 | erot = 0.228379019530766 | epot = -15.0895191391013 | etot = -14.6249037421757 -653000 ekin = 0.247915496412395 | erot = 0.217959688822015 | epot = -15.0907789275287 | etot = -14.6249037422943 -654000 ekin = 0.259425494352476 | erot = 0.208500305716241 | epot = -15.0928295424619 | etot = -14.6249037423932 -655000 ekin = 0.26955455820855 | erot = 0.199677958220202 | epot = -15.0941362588805 | etot = -14.6249037424517 -656000 ekin = 0.277652649609351 | erot = 0.191249336850371 | epot = -15.0938057289177 | etot = -14.624903742458 -657000 ekin = 0.283765747905513 | erot = 0.183104207684416 | epot = -15.0917736980008 | etot = -14.6249037424109 -658000 ekin = 0.288620908153495 | erot = 0.175289536735997 | epot = -15.0888141872111 | etot = -14.6249037423216 -659000 ekin = 0.293459924910638 | erot = 0.168001027405567 | epot = -15.0863646945267 | etot = -14.6249037422105 -660000 ekin = 0.299750121924058 | erot = 0.16154591329551 | epot = -15.0861997773236 | etot = -14.624903742104 -661000 ekin = 0.30882794580118 | erot = 0.15628680849445 | epot = -15.0900184963236 | etot = -14.624903742028 -662000 ekin = 0.321550844182007 | erot = 0.152579955314563 | epot = -15.0990345414996 | etot = -14.624903742003 -663000 ekin = 0.338040404322879 | erot = 0.150721656676574 | epot = -15.1136658030369 | etot = -14.6249037420375 -664000 ekin = 0.357588696379433 | erot = 0.150913925254324 | epot = -15.1334063637592 | etot = -14.6249037421255 -665000 ekin = 0.378766116435926 | erot = 0.153254852725576 | epot = -15.1569247114086 | etot = -14.6249037422471 -666000 ekin = 0.399716130930416 | erot = 0.157752003176736 | epot = -15.1823718764813 | etot = -14.6249037423741 -667000 ekin = 0.418564373573455 | erot = 0.164350192887448 | epot = -15.2078183089391 | etot = -14.6249037424782 -668000 ekin = 0.433827740573898 | erot = 0.172960630436554 | epot = -15.2316921135493 | etot = -14.6249037425388 -669000 ekin = 0.444701001629873 | erot = 0.183478145302767 | epot = -15.2530828894839 | etot = -14.6249037425513 -670000 ekin = 0.451136418416049 | erot = 0.195778468141822 | epot = -15.2718186290842 | etot = -14.6249037425263 -671000 ekin = 0.453701004148981 | erot = 0.209695862328768 | epot = -15.2883006089635 | etot = -14.6249037424857 -672000 ekin = 0.453273827001077 | erot = 0.224990306458558 | epot = -15.3031678759134 | etot = -14.6249037424538 -673000 ekin = 0.450699702661522 | erot = 0.241319095058617 | epot = -15.3169225401686 | etot = -14.6249037424485 -674000 ekin = 0.446523488450417 | erot = 0.258227823778676 | epot = -15.3296550547043 | etot = -14.6249037424752 -675000 ekin = 0.44088962459253 | erot = 0.275170305159689 | epot = -15.3409636722772 | etot = -14.624903742525 -676000 ekin = 0.433624481153454 | erot = 0.291558306506453 | epot = -15.350086530239 | etot = -14.6249037425791 -677000 ekin = 0.424453634856828 | erot = 0.306833290383679 | epot = -15.3561906678562 | etot = -14.6249037426157 -678000 ekin = 0.41326517646593 | erot = 0.320546114279227 | epot = -15.3587150333616 | etot = -14.6249037426165 -679000 ekin = 0.400321537247193 | erot = 0.332428088763687 | epot = -15.3576533685842 | etot = -14.6249037425733 -680000 ekin = 0.386341988793522 | erot = 0.342437977068841 | epot = -15.3536837083529 | etot = -14.6249037424906 -681000 ekin = 0.372417408219175 | erot = 0.350774050474234 | epot = -15.3480952010788 | etot = -14.6249037423854 -682000 ekin = 0.35976964508921 | erot = 0.357847594354926 | epot = -15.342520981727 | etot = -14.6249037422829 -683000 ekin = 0.349419724484302 | erot = 0.364223142873746 | epot = -15.3385466095668 | etot = -14.6249037422088 -684000 ekin = 0.341867426589136 | erot = 0.370539083005818 | epot = -15.3373102517758 | etot = -14.6249037421809 -685000 ekin = 0.336892967752833 | erot = 0.37742728588017 | epot = -15.3392239958362 | etot = -14.6249037422032 -686000 ekin = 0.333560575456658 | erot = 0.385449795148896 | epot = -15.343914112869 | etot = -14.6249037422634 -687000 ekin = 0.330440845244727 | erot = 0.395064019974615 | epot = -15.3504086075565 | etot = -14.6249037423372 -688000 ekin = 0.325996654362847 | erot = 0.406617593545496 | epot = -15.3575179903034 | etot = -14.624903742395 -689000 ekin = 0.319023752377333 | erot = 0.420363991129467 | epot = -15.3642914859188 | etot = -14.624903742412 -690000 ekin = 0.309020969988424 | erot = 0.436483939357874 | epot = -15.3704086517213 | etot = -14.624903742375 -691000 ekin = 0.296388973948975 | erot = 0.455097572739774 | epot = -15.3763902889748 | etot = -14.6249037422861 -692000 ekin = 0.282408410636019 | erot = 0.476257707732204 | epot = -15.3835698605304 | etot = -14.6249037421622 -693000 ekin = 0.269008530851688 | erot = 0.499923033173812 | epot = -15.393835306056 | etot = -14.6249037420305 -694000 ekin = 0.258387685788622 | erot = 0.525918285140571 | epot = -15.4092097128506 | etot = -14.6249037419214 -695000 ekin = 0.25257627520821 | erot = 0.553894058809888 | epot = -15.43137407588 | etot = -14.6249037418619 -696000 ekin = 0.253038186235009 | erot = 0.583300660396584 | epot = -15.4612425885012 | etot = -14.6249037418696 -697000 ekin = 0.260392018277579 | erot = 0.613388418368988 | epot = -15.4986841785954 | etot = -14.6249037419489 -698000 ekin = 0.274304391463509 | erot = 0.64324187918294 | epot = -15.5424500127365 | etot = -14.6249037420901 -699000 ekin = 0.293570250406769 | erot = 0.671848180609457 | epot = -15.5903221732877 | etot = -14.6249037422715 -700000 ekin = 0.316355070233514 | erot = 0.698191700483047 | epot = -15.639450513181 | etot = -14.6249037424644 -701000 ekin = 0.340538337282332 | erot = 0.721359481466447 | epot = -15.6868015613885 | etot = -14.6249037426397 -702000 ekin = 0.364075443764615 | erot = 0.740637254695032 | epot = -15.7296164412337 | etot = -14.6249037427741 -703000 ekin = 0.385294321874606 | erot = 0.75557636945477 | epot = -15.7657744341848 | etot = -14.6249037428555 -704000 ekin = 0.40306671671928 | erot = 0.766018576887906 | epot = -15.7939890364911 | etot = -14.6249037428839 -705000 ekin = 0.416833588997184 | erot = 0.772075474100319 | epot = -15.8138128059668 | etot = -14.6249037428693 -706000 ekin = 0.426510451501955 | erot = 0.774072055032491 | epot = -15.8254862493611 | etot = -14.6249037428266 -707000 ekin = 0.432328070473605 | erot = 0.772470813770598 | epot = -15.8297026270152 | etot = -14.624903742771 -708000 ekin = 0.434671210546145 | erot = 0.767794279505844 | epot = -15.8273692327653 | etot = -14.6249037427133 -709000 ekin = 0.433963855683832 | erot = 0.760560754832635 | epot = -15.8194283531753 | etot = -14.6249037426588 -710000 ekin = 0.430621214402396 | erot = 0.751241421805773 | epot = -15.8067663788157 | etot = -14.6249037426076 -711000 ekin = 0.42506102881634 | erot = 0.740240555545717 | epot = -15.7902053269187 | etot = -14.6249037425567 -712000 ekin = 0.417748693286703 | erot = 0.727895913280697 | epot = -15.7705483490698 | etot = -14.6249037425024 -713000 ekin = 0.409245407745788 | erot = 0.714493617369859 | epot = -15.7486427675576 | etot = -14.624903742442 -714000 ekin = 0.400233112897398 | erot = 0.700290376394005 | epot = -15.7254272316667 | etot = -14.6249037423753 -715000 ekin = 0.391499218630518 | erot = 0.685535269234734 | epot = -15.7019382301705 | etot = -14.6249037423053 -716000 ekin = 0.383874653287396 | erot = 0.67048382480872 | epot = -15.6792622203348 | etot = -14.6249037422387 -717000 ekin = 0.378129665172728 | erot = 0.655399296057203 | epot = -15.6584327034143 | etot = -14.6249037421843 -718000 ekin = 0.374843116814185 | erot = 0.640539821856989 | epot = -15.640286680823 | etot = -14.6249037421519 -719000 ekin = 0.374271424141624 | erot = 0.626134666228549 | epot = -15.6253098325193 | etot = -14.6249037421492 -720000 ekin = 0.376249546442097 | erot = 0.612356169201246 | epot = -15.6135094578233 | etot = -14.62490374218 -721000 ekin = 0.380155783156075 | erot = 0.599295758360148 | epot = -15.6043552837583 | etot = -14.6249037422421 -722000 ekin = 0.38496276143876 | erot = 0.586951574249477 | epot = -15.5968180780148 | etot = -14.6249037423265 -723000 ekin = 0.389379823381561 | erot = 0.57523200329734 | epot = -15.5895155690971 | etot = -14.6249037424182 -724000 ekin = 0.392071125783968 | erot = 0.563975606696704 | epot = -15.5809504749797 | etot = -14.624903742499 -725000 ekin = 0.391913283458913 | erot = 0.552983740178136 | epot = -15.5698007661881 | etot = -14.624903742551 -726000 ekin = 0.388241956532947 | erot = 0.542058916015296 | epot = -15.5552046151089 | etot = -14.6249037425607 -727000 ekin = 0.381032991792247 | erot = 0.531040454531364 | epot = -15.5369771888453 | etot = -14.6249037425217 -728000 ekin = 0.370971903191936 | erot = 0.51982908237483 | epot = -15.5157047280045 | etot = -14.6249037424377 -729000 ekin = 0.359388263612697 | erot = 0.508395729808055 | epot = -15.4926877357429 | etot = -14.6249037423222 -730000 ekin = 0.348057580439693 | erot = 0.496773021024349 | epot = -15.4697343436589 | etot = -14.6249037421949 -731000 ekin = 0.338902689199426 | erot = 0.48503267140759 | epot = -15.4488391026866 | etot = -14.6249037420796 -732000 ekin = 0.333649662945475 | erot = 0.473255762296962 | epot = -15.4318091672413 | etot = -14.6249037419988 -733000 ekin = 0.333505576676606 | erot = 0.461504910073432 | epot = -15.4199142287184 | etot = -14.6249037419684 -734000 ekin = 0.338924758984327 | erot = 0.449807254483215 | epot = -15.4136357554618 | etot = -14.6249037419943 -735000 ekin = 0.349515468577354 | erot = 0.438154711902627 | epot = -15.412573922551 | etot = -14.624903742071 -736000 ekin = 0.364111355274983 | erot = 0.426523255164317 | epot = -15.4155383526214 | etot = -14.6249037421821 -737000 ekin = 0.380995719774913 | erot = 0.414906900972836 | epot = -15.4208063630518 | etot = -14.6249037423041 -738000 ekin = 0.398229414671756 | erot = 0.403356227833025 | epot = -15.4264893849167 | etot = -14.6249037424119 -739000 ekin = 0.41400586007365 | erot = 0.392007798568608 | epot = -15.4309174011284 | etot = -14.6249037424862 -740000 ekin = 0.426948743963044 | erot = 0.381091720704502 | epot = -15.4329442071847 | etot = -14.6249037425172 -741000 ekin = 0.436283647683231 | erot = 0.370910229391922 | epot = -15.4320976195822 | etot = -14.6249037425071 -742000 ekin = 0.441850001827036 | erot = 0.361789064611271 | epot = -15.4285428089074 | etot = -14.6249037424691 -743000 ekin = 0.443963491147379 | erot = 0.354012421291793 | epot = -15.4228796548618 | etot = -14.6249037424227 -744000 ekin = 0.443178108515845 | erot = 0.347758127978261 | epot = -15.4158399788819 | etot = -14.6249037423878 -745000 ekin = 0.440021184885117 | erot = 0.343050543545259 | epot = -15.4079754708099 | etot = -14.6249037423795 -746000 ekin = 0.434779146250806 | erot = 0.339744491074207 | epot = -15.3994273797282 | etot = -14.6249037424032 -747000 ekin = 0.427396883605164 | erot = 0.337545938413876 | epot = -15.3898465644715 | etot = -14.6249037424524 -748000 ekin = 0.417523045840964 | erot = 0.336066252171354 | epot = -15.378493040523 | etot = -14.6249037425106 -749000 ekin = 0.404692764111769 | erot = 0.334898725161342 | epot = -15.3644952318284 | etot = -14.6249037425553 -750000 ekin = 0.38859628761696 | erot = 0.333700338300268 | epot = -15.3472003684814 | etot = -14.6249037425641 -751000 ekin = 0.369348367994352 | erot = 0.332259621152217 | epot = -15.3265117316697 | etot = -14.6249037425232 -752000 ekin = 0.347662572337044 | erot = 0.330533807749388 | epot = -15.3031001225185 | etot = -14.6249037424321 -753000 ekin = 0.32485637347094 | erot = 0.328645172901279 | epot = -15.2784052886778 | etot = -14.6249037423055 -754000 ekin = 0.302664104351826 | erot = 0.326836116135493 | epot = -15.2544039626575 | etot = -14.6249037421702 -755000 ekin = 0.282898405306331 | erot = 0.32539267738901 | epot = -15.2331948247533 | etot = -14.6249037420579 -756000 ekin = 0.267052130149665 | erot = 0.324553861438981 | epot = -15.216509733585 | etot = -14.6249037419963 -757000 ekin = 0.255952872034765 | erot = 0.32442748097694 | epot = -15.2052840950137 | etot = -14.624903742002 -758000 ekin = 0.24956686325818 | erot = 0.324931841855881 | epot = -15.1994024471896 | etot = -14.6249037420755 -759000 ekin = 0.247007285742243 | erot = 0.325777353497121 | epot = -15.1976883814409 | etot = -14.6249037422016 -760000 ekin = 0.246749335490674 | erot = 0.326494279608963 | epot = -15.1981473574513 | etot = -14.6249037423517 -761000 ekin = 0.247004464362755 | erot = 0.32650345690093 | epot = -15.1984116637543 | etot = -14.6249037424906 -762000 ekin = 0.246168267682973 | erot = 0.325217160867496 | epot = -15.196289171135 | etot = -14.6249037425846 -763000 ekin = 0.243236270174414 | erot = 0.32214932288445 | epot = -15.1902893356681 | etot = -14.6249037426092 -764000 ekin = 0.238083572627797 | erot = 0.31701054114624 | epot = -15.1799978563308 | etot = -14.6249037425568 -765000 ekin = 0.231530329805837 | erot = 0.309765883620828 | epot = -15.1661999558649 | etot = -14.6249037424383 -766000 ekin = 0.225163449189513 | erot = 0.300642577937803 | epot = -15.1507097694085 | etot = -14.6249037422812 -767000 ekin = 0.22094703764136 | erot = 0.290087936283322 | epot = -15.1359387160482 | etot = -14.6249037421235 -768000 ekin = 0.220714417705591 | erot = 0.278690999515505 | epot = -15.1243091592243 | etot = -14.6249037420032 -769000 ekin = 0.225674230585282 | erot = 0.267090069999639 | epot = -15.1176680425329 | etot = -14.6249037419479 -770000 ekin = 0.236066860406118 | erot = 0.255889903618327 | epot = -15.1168605059916 | etot = -14.6249037419672 -771000 ekin = 0.251070223471381 | erot = 0.245606888556436 | epot = -15.1215808540782 | etot = -14.6249037420503 -772000 ekin = 0.268985032795184 | erot = 0.236650197272858 | epot = -15.130538972238 | etot = -14.6249037421699 -773000 ekin = 0.287649902236207 | erot = 0.229335047808925 | epot = -15.1418886923348 | etot = -14.6249037422896 -774000 ekin = 0.304971347443521 | erot = 0.223914516380439 | epot = -15.1537896061995 | etot = -14.6249037423755 -775000 ekin = 0.319422560281353 | erot = 0.220611402282044 | epot = -15.1649377049685 | etot = -14.6249037424051 -776000 ekin = 0.330375903029014 | erot = 0.219632840721417 | epot = -15.1749124861243 | etot = -14.6249037423739 -777000 ekin = 0.338182326481318 | erot = 0.221157252264488 | epot = -15.1842433210425 | etot = -14.6249037422967 -778000 ekin = 0.34398099350531 | erot = 0.22529363977163 | epot = -15.1941783754801 | etot = -14.6249037422031 -779000 ekin = 0.349294202147492 | erot = 0.232023926337254 | epot = -15.2062218706139 | etot = -14.6249037421291 -780000 ekin = 0.355517983707864 | erot = 0.241146781675322 | epot = -15.2215685074905 | etot = -14.6249037421074 -781000 ekin = 0.36344584750217 | erot = 0.25224414994015 | epot = -15.2405937395998 | etot = -14.6249037421575 -782000 ekin = 0.372957766808887 | erot = 0.264688770758124 | epot = -15.2625502798461 | etot = -14.6249037422791 -783000 ekin = 0.38296926774882 | erot = 0.277702579812121 | epot = -15.2855755900113 | etot = -14.6249037424504 -784000 ekin = 0.391670514066059 | erot = 0.290462881206425 | epot = -15.3070371379046 | etot = -14.6249037426321 -785000 ekin = 0.397003136152363 | erot = 0.302237882822127 | epot = -15.3241447617524 | etot = -14.6249037427779 -786000 ekin = 0.397244540913185 | erot = 0.312520082335045 | epot = -15.3346683660963 | etot = -14.6249037428481 -787000 ekin = 0.391525061079143 | erot = 0.321121025638669 | epot = -15.33754982954 | etot = -14.6249037428222 -788000 ekin = 0.380116514494114 | erot = 0.328198366844194 | epot = -15.3332186240437 | etot = -14.6249037427054 -789000 ekin = 0.364402868102804 | erot = 0.334204933643257 | epot = -15.323511544273 | etot = -14.6249037425269 -790000 ekin = 0.346547882835914 | erot = 0.339772664564402 | epot = -15.3112242897307 | etot = -14.6249037423304 -791000 ekin = 0.328969533926533 | erot = 0.345562661329726 | epot = -15.2994359374168 | etot = -14.6249037421606 -792000 ekin = 0.313783234687151 | erot = 0.352120250332853 | epot = -15.290807227072 | etot = -14.624903742052 -793000 ekin = 0.302371973145348 | erot = 0.359769001653092 | epot = -15.2870447168183 | etot = -14.6249037420198 -794000 ekin = 0.295192752069156 | erot = 0.368565036951925 | epot = -15.2886615310787 | etot = -14.6249037420576 -795000 ekin = 0.291854072001083 | erot = 0.378316728407065 | epot = -15.2950745425492 | etot = -14.624903742141 -796000 ekin = 0.291420477240231 | erot = 0.388659220599418 | epot = -15.3049834400759 | etot = -14.6249037422363 -797000 ekin = 0.292835767594049 | erot = 0.399160677915359 | epot = -15.3169001878201 | etot = -14.6249037423107 -798000 ekin = 0.295321690655136 | erot = 0.40942991973209 | epot = -15.3296553527312 | etot = -14.624903742344 -799000 ekin = 0.298615606685619 | erot = 0.419195269464138 | epot = -15.3427146184843 | etot = -14.6249037423346 -800000 ekin = 0.302963113079283 | erot = 0.428333265393292 | epot = -15.3562001207729 | etot = -14.6249037423003 -801000 ekin = 0.308869807419017 | erot = 0.436842111958073 | epot = -15.3706156616482 | etot = -14.6249037422711 -802000 ekin = 0.316711643346418 | erot = 0.444773620895252 | epot = -15.3863890065178 | etot = -14.6249037422762 -803000 ekin = 0.326365730602249 | erot = 0.452151664704984 | epot = -15.403421137639 | etot = -14.6249037423317 -804000 ekin = 0.337019280358016 | erot = 0.458909057451227 | epot = -15.4208320802433 | etot = -14.6249037424341 -805000 ekin = 0.347244531512768 | erot = 0.464865921886024 | epot = -15.4370141959588 | etot = -14.62490374256 -806000 ekin = 0.355321558015419 | erot = 0.469755825324061 | epot = -15.449981126015 | etot = -14.6249037426755 -807000 ekin = 0.359699244804511 | erot = 0.473288399899576 | epot = -15.457891387451 | etot = -14.6249037427469 -808000 ekin = 0.35944291943687 | erot = 0.475225772200724 | epot = -15.4595724343888 | etot = -14.6249037427512 -809000 ekin = 0.354532149711152 | erot = 0.475448148012716 | epot = -15.4548840404063 | etot = -14.6249037426824 -810000 ekin = 0.34592712151575 | erot = 0.473990365430488 | epot = -15.4448212294989 | etot = -14.6249037425527 -811000 ekin = 0.335391497319932 | erot = 0.47104235524006 | epot = -15.4313375949483 | etot = -14.6249037423883 -812000 ekin = 0.325122479809716 | erot = 0.466917662640269 | epot = -15.4169438846729 | etot = -14.624903742223 -813000 ekin = 0.317281832618796 | erot = 0.462001954841414 | epot = -15.4041875295496 | etot = -14.6249037420894 -814000 ekin = 0.313538689251802 | erot = 0.456696276151744 | epot = -15.3951387074161 | etot = -14.6249037420126 -815000 ekin = 0.314725301427551 | erot = 0.451368238943745 | epot = -15.3909972823755 | etot = -14.6249037420042 -816000 ekin = 0.320674745952841 | erot = 0.446320054204994 | epot = -15.3918985422197 | etot = -14.6249037420619 -817000 ekin = 0.330264402530169 | erot = 0.441777145070237 | epot = -15.3969452897705 | etot = -14.6249037421701 -818000 ekin = 0.341643112116294 | erot = 0.437896324121931 | epot = -15.4044431785426 | etot = -14.6249037423044 -819000 ekin = 0.352584467965985 | erot = 0.434788688971306 | epot = -15.4122768993744 | etot = -14.6249037424371 -820000 ekin = 0.360890006680584 | erot = 0.432549774287109 | epot = -15.4183435235104 | etot = -14.6249037425427 -821000 ekin = 0.364764924967109 | erot = 0.43128829359489 | epot = -15.420956961164 | etot = -14.624903742602 -822000 ekin = 0.363101323048021 | erot = 0.431144612410221 | epot = -15.419149678064 | etot = -14.6249037426058 -823000 ekin = 0.355627506071419 | erot = 0.43229307921143 | epot = -15.4128243278382 | etot = -14.6249037425554 -824000 ekin = 0.342909507999076 | erot = 0.434926118199362 | epot = -15.4027393686599 | etot = -14.6249037424615 -825000 ekin = 0.326218347990279 | erot = 0.439222871854997 | epot = -15.390344962187 | etot = -14.6249037423417 -826000 ekin = 0.307298067026364 | erot = 0.445309293137064 | epot = -15.3775111023799 | etot = -14.6249037422164 -827000 ekin = 0.288081469809457 | erot = 0.453218819733404 | epot = -15.3662040316486 | etot = -14.6249037421057 -828000 ekin = 0.270403517643933 | erot = 0.462862712071296 | epot = -15.358169971741 | etot = -14.6249037420258 -829000 ekin = 0.255756724313351 | erot = 0.474017347276038 | epot = -15.3546778135762 | etot = -14.6249037419868 -830000 ekin = 0.245120383539822 | erot = 0.48633201659407 | epot = -15.3563561421258 | etot = -14.624903741992 -831000 ekin = 0.238883956789673 | erot = 0.499357971990034 | epot = -15.3631456708166 | etot = -14.6249037420369 -832000 ekin = 0.236868645663221 | erot = 0.512595315427615 | epot = -15.3743677032019 | etot = -14.6249037421111 -833000 ekin = 0.238435989569064 | erot = 0.525550909042522 | epot = -15.3888906408114 | etot = -14.6249037421998 -834000 ekin = 0.242658569128244 | erot = 0.537797737790336 | epot = -15.405360049206 | etot = -14.6249037422874 -835000 ekin = 0.248518315376458 | erot = 0.549024910269567 | epot = -15.4224469680061 | etot = -14.62490374236 -836000 ekin = 0.255095050223297 | erot = 0.559068449138061 | epot = -15.4390672417691 | etot = -14.6249037424078 -837000 ekin = 0.261712817640754 | erot = 0.567916383627862 | epot = -15.4545329436951 | etot = -14.6249037424265 -838000 ekin = 0.268023056778799 | erot = 0.575686784519135 | epot = -15.468613583716 | etot = -14.6249037424181 -839000 ekin = 0.274018270323247 | erot = 0.582582979366575 | epot = -15.481504992079 | etot = -14.6249037423892 -840000 ekin = 0.279983100774044 | erot = 0.588834754839254 | epot = -15.493721597963 | etot = -14.6249037423497 -841000 ekin = 0.286398274628748 | erot = 0.594637024330571 | epot = -15.5059390412695 | etot = -14.6249037423102 -842000 ekin = 0.293816650983671 | erot = 0.600098453280244 | epot = -15.5188188465455 | etot = -14.6249037422816 -843000 ekin = 0.302726774569864 | erot = 0.605208920748267 | epot = -15.5328394375906 | etot = -14.6249037422725 -844000 ekin = 0.313421069061913 | erot = 0.609833296484503 | epot = -15.5481581078352 | etot = -14.6249037422888 -845000 ekin = 0.325887895395929 | erot = 0.613733577818103 | epot = -15.5645252155455 | etot = -14.6249037423314 -846000 ekin = 0.33975240096389 | erot = 0.616615984720062 | epot = -15.5812721280797 | etot = -14.6249037423957 -847000 ekin = 0.354292335350613 | erot = 0.618194079532099 | epot = -15.5973901573538 | etot = -14.624903742471 -848000 ekin = 0.368542667425734 | erot = 0.618254639141467 | epot = -15.6117010491094 | etot = -14.6249037425422 -849000 ekin = 0.381474241846711 | erot = 0.616711095272622 | epot = -15.6230890797133 | etot = -14.624903742594 -850000 ekin = 0.392198266664605 | erot = 0.613631554978577 | epot = -15.6307335642585 | etot = -14.6249037426153 -851000 ekin = 0.400129367739792 | erot = 0.609234588534973 | epot = -15.6342676988789 | etot = -14.6249037426041 -852000 ekin = 0.405049998800082 | erot = 0.603854451145949 | epot = -15.6338081925133 | etot = -14.6249037425673 -853000 ekin = 0.407056563943438 | erot = 0.597885334647268 | epot = -15.6298456411094 | etot = -14.6249037425187 -854000 ekin = 0.406415158940066 | erot = 0.591718979209663 | epot = -15.623037880623 | etot = -14.6249037424732 -855000 ekin = 0.403390043513582 | erot = 0.585690332508252 | epot = -15.6139841184641 | etot = -14.6249037424422 -856000 ekin = 0.398116166002876 | erot = 0.580042463524147 | epot = -15.6030623719562 | etot = -14.6249037424292 -857000 ekin = 0.39056801615961 | erot = 0.574915889724005 | epot = -15.5903876483121 | etot = -14.6249037424285 -858000 ekin = 0.380638245095305 | erot = 0.570361176879803 | epot = -15.5759031644036 | etot = -14.6249037424285 -859000 ekin = 0.368297168913566 | erot = 0.566367903414504 | epot = -15.5595688147431 | etot = -14.624903742415 -860000 ekin = 0.353771484485059 | erot = 0.56289933566622 | epot = -15.5415745625294 | etot = -14.6249037423781 -861000 ekin = 0.33766818907467 | erot = 0.559921190515333 | epot = -15.5224931219057 | etot = -14.6249037423157 -862000 ekin = 0.320982687533336 | erot = 0.557415114411014 | epot = -15.5033015441806 | etot = -14.6249037422363 -863000 ekin = 0.304965814690107 | erot = 0.555372641471618 | epot = -15.485242198319 | etot = -14.6249037421573 -864000 ekin = 0.290872653002407 | erot = 0.5537720825734 | epot = -15.4695484776756 | etot = -14.6249037420998 -865000 ekin = 0.27966077424891 | erot = 0.552546988654679 | epot = -15.4571115049861 | etot = -14.6249037420825 -866000 ekin = 0.271730646598884 | erot = 0.551558423385933 | epot = -15.4481928120997 | etot = -14.6249037421148 -867000 ekin = 0.266795961580335 | erot = 0.550582916185739 | epot = -15.442282619959 | etot = -14.6249037421929 -868000 ekin = 0.263936467175558 | erot = 0.549323573879739 | epot = -15.4381637833552 | etot = -14.6249037422999 -869000 ekin = 0.261831470221842 | erot = 0.547444696243082 | epot = -15.4341799088743 | etot = -14.6249037424094 -870000 ekin = 0.259116433169414 | erot = 0.544622620095275 | epot = -15.4286427957584 | etot = -14.6249037424937 -871000 ekin = 0.254766113418661 | erot = 0.540599894777671 | epot = -15.4202697507265 | etot = -14.6249037425302 -872000 ekin = 0.248397230691804 | erot = 0.535228153627548 | epot = -15.4085291268285 | etot = -14.6249037425092 -873000 ekin = 0.240403953826285 | erot = 0.528487826572583 | epot = -15.3937955228344 | etot = -14.6249037424355 -874000 ekin = 0.231884125783745 | erot = 0.520479317821078 | epot = -15.3772671859334 | etot = -14.6249037423285 -875000 ekin = 0.224371090313998 | erot = 0.511388489700788 | epot = -15.3606633222313 | etot = -14.6249037422165 -876000 ekin = 0.219440883380304 | erot = 0.501436812694108 | epot = -15.3457814382033 | etot = -14.6249037421289 -877000 ekin = 0.218302972736541 | erot = 0.490831150818269 | epot = -15.3340378656425 | etot = -14.6249037420877 -878000 ekin = 0.221492456263516 | erot = 0.479728387736696 | epot = -15.3261245861012 | etot = -14.624903742101 -879000 ekin = 0.228756262275047 | erot = 0.468225594693746 | epot = -15.3218855991288 | etot = -14.62490374216 -880000 ekin = 0.23916916008879 | erot = 0.456378166082174 | epot = -15.3204510684128 | etot = -14.6249037422418 -881000 ekin = 0.251443176614632 | erot = 0.444238659513065 | epot = -15.3205855784454 | etot = -14.6249037423177 -882000 ekin = 0.264330844663881 | erot = 0.43190128969608 | epot = -15.3211358767216 | etot = -14.6249037423616 -883000 ekin = 0.276992343361879 | erot = 0.419534292632584 | epot = -15.3214303783539 | etot = -14.6249037423594 -884000 ekin = 0.289210952362963 | erot = 0.407386172192775 | epot = -15.3215008668683 | etot = -14.6249037423126 -885000 ekin = 0.301394205511005 | erot = 0.395760928443894 | epot = -15.3220588761927 | etot = -14.6249037422378 -886000 ekin = 0.31436859920589 | erot = 0.384968165379889 | epot = -15.3242405067469 | etot = -14.6249037421611 -887000 ekin = 0.329038341775477 | erot = 0.375262338090619 | epot = -15.3292044219764 | etot = -14.6249037421103 -888000 ekin = 0.346015111155314 | erot = 0.366788650328168 | epot = -15.3377075035892 | etot = -14.6249037421057 -889000 ekin = 0.365329693883282 | erot = 0.35955094737734 | epot = -15.3497843834164 | etot = -14.6249037421558 -890000 ekin = 0.386310696216818 | erot = 0.353410826838142 | epot = -15.3646252653079 | etot = -14.6249037422529 -891000 ekin = 0.407668087054666 | erot = 0.348119126036796 | epot = -15.3806909554674 | etot = -14.6249037423759 -892000 ekin = 0.427761236102702 | erot = 0.343372786942168 | epot = -15.396037765541 | etot = -14.6249037424962 -893000 ekin = 0.444977236018704 | erot = 0.338883525692821 | epot = -15.4087645042964 | etot = -14.6249037425849 -894000 ekin = 0.458112158679596 | erot = 0.334441343917346 | epot = -15.4174572452184 | etot = -14.6249037426214 -895000 ekin = 0.466648008330968 | erot = 0.329956933565266 | epot = -15.4215086844955 | etot = -14.6249037425992 -896000 ekin = 0.470850232518833 | erot = 0.325472374552695 | epot = -15.421226349598 | etot = -14.6249037425264 -897000 ekin = 0.471664510487189 | erot = 0.321137893833246 | epot = -15.4177061467443 | etot = -14.6249037424239 -898000 ekin = 0.470447771985121 | erot = 0.31716128210791 | epot = -15.4125127964118 | etot = -14.6249037423187 -899000 ekin = 0.468609320535131 | erot = 0.31374324783162 | epot = -15.4072563106044 | etot = -14.6249037422377 -900000 ekin = 0.467255363896452 | erot = 0.311015004595572 | epot = -15.4031741106926 | etot = -14.6249037422006 -901000 ekin = 0.466923299456765 | erot = 0.308993431077939 | epot = -15.4008204727507 | etot = -14.624903742216 -902000 ekin = 0.467466399705909 | erot = 0.307564919774022 | epot = -15.3999350617589 | etot = -14.624903742279 -903000 ekin = 0.468112799245423 | erot = 0.30650258938551 | epot = -15.3995191310034 | etot = -14.6249037423724 -904000 ekin = 0.467682260081114 | erot = 0.305513914729626 | epot = -15.3980999172821 | etot = -14.6249037424714 -905000 ekin = 0.464906903208319 | erot = 0.304308207539406 | epot = -15.3941188532968 | etot = -14.6249037425491 -906000 ekin = 0.458775313350499 | erot = 0.302667437698498 | epot = -15.3863464936332 | etot = -14.6249037425842 -907000 ekin = 0.448811106797387 | erot = 0.300501710925559 | epot = -15.3742165602889 | etot = -14.624903742566 -908000 ekin = 0.435212888278633 | erot = 0.297873922704189 | epot = -15.3579905534804 | etot = -14.6249037424975 -909000 ekin = 0.418821166579361 | erot = 0.294986492955396 | epot = -15.3387114019291 | etot = -14.6249037423944 -910000 ekin = 0.400928155652502 | erot = 0.292134043124591 | epot = -15.3179659410567 | etot = -14.6249037422796 -911000 ekin = 0.38299073131904 | erot = 0.289635345607532 | epot = -15.2975298191036 | etot = -14.624903742177 -912000 ekin = 0.366329155570265 | erot = 0.287762457046 | epot = -15.2789953547218 | etot = -14.6249037421055 -913000 ekin = 0.351888443631644 | erot = 0.286683662572436 | epot = -15.263475848279 | etot = -14.6249037420749 -914000 ekin = 0.340111462795988 | erot = 0.286431278414276 | epot = -15.2514464832956 | etot = -14.6249037420854 -915000 ekin = 0.330936398540546 | erot = 0.286898247266849 | epot = -15.2427383879358 | etot = -14.6249037421284 -916000 ekin = 0.32389927160205 | erot = 0.287861143478129 | epot = -15.2366641572708 | etot = -14.6249037421907 -917000 ekin = 0.318302399047882 | erot = 0.289022784864801 | epot = -15.2322289261694 | etot = -14.6249037422567 -918000 ekin = 0.313403328232211 | erot = 0.290065205370544 | epot = -15.2283722759156 | etot = -14.6249037423128 -919000 ekin = 0.308582994047746 | erot = 0.290702987753655 | epot = -15.2241897241503 | etot = -14.6249037423489 -920000 ekin = 0.303462620955297 | erot = 0.290727692024701 | epot = -15.2190940553404 | etot = -14.6249037423604 -921000 ekin = 0.297952758523176 | erot = 0.290036267627134 | epot = -15.2128927684984 | etot = -14.624903742348 -922000 ekin = 0.292232329167479 | erot = 0.288639696922892 | epot = -15.2057757684081 | etot = -14.6249037423177 -923000 ekin = 0.286668877938219 | erot = 0.286652137103033 | epot = -15.1982247573198 | etot = -14.6249037422785 -924000 ekin = 0.281701868658443 | erot = 0.284264668755385 | epot = -15.1908702796542 | etot = -14.6249037422404 -925000 ekin = 0.277717553237889 | erot = 0.281710557644916 | epot = -15.1843318530949 | etot = -14.6249037422121 -926000 ekin = 0.274945509179126 | erot = 0.279230091666523 | epot = -15.1790793430443 | etot = -14.6249037421987 -927000 ekin = 0.273402631519641 | erot = 0.277042382113033 | epot = -15.1753487558335 | etot = -14.6249037422009 -928000 ekin = 0.272900230271313 | erot = 0.27532923254522 | epot = -15.1731332050308 | etot = -14.6249037422143 -929000 ekin = 0.273115271900815 | erot = 0.274232799537056 | epot = -15.1722518136686 | etot = -14.6249037422307 -930000 ekin = 0.273710515355576 | erot = 0.273865029643896 | epot = -15.1724792872395 | etot = -14.6249037422401 -931000 ekin = 0.274474107139751 | erot = 0.274323617228769 | epot = -15.1737014666023 | etot = -14.6249037422338 -932000 ekin = 0.275440857683152 | erot = 0.275707340216854 | epot = -15.176051940107 | etot = -14.624903742207 -933000 ekin = 0.276957575781874 | erot = 0.278123705988361 | epot = -15.1799850239313 | etot = -14.6249037421611 -934000 ekin = 0.279664435383878 | erot = 0.281683992543418 | epot = -15.1862521700318 | etot = -14.6249037421045 -935000 ekin = 0.284382433296915 | erot = 0.286484503522641 | epot = -15.1957706788708 | etot = -14.6249037420512 -936000 ekin = 0.291920557579979 | erot = 0.292577187598074 | epot = -15.2094014871964 | etot = -14.6249037420184 -937000 ekin = 0.302840159169775 | erot = 0.299936553990588 | epot = -15.2276804551825 | etot = -14.6249037420221 -938000 ekin = 0.317231541763407 | erot = 0.308432066638773 | epot = -15.2505673504752 | etot = -14.6249037420731 -939000 ekin = 0.334562734704664 | erot = 0.317815317270636 | epot = -15.2772817941479 | etot = -14.6249037421726 -940000 ekin = 0.353649521805238 | erot = 0.327729086105133 | epot = -15.3062823502217 | etot = -14.6249037423114 -941000 ekin = 0.372770367646981 | erot = 0.337741122003566 | epot = -15.3354152321204 | etot = -14.6249037424699 -942000 ekin = 0.389915662531947 | erot = 0.347399749799135 | epot = -15.3622191549531 | etot = -14.6249037426221 -943000 ekin = 0.403126345739486 | erot = 0.356302369934052 | epot = -15.3843324584141 | etot = -14.6249037427406 -944000 ekin = 0.410851754406517 | erot = 0.364163156178947 | epot = -15.3999186533885 | etot = -14.624903742803 -945000 ekin = 0.412247920960694 | erot = 0.370864511414574 | epot = -15.4080161751724 | etot = -14.6249037427972 -946000 ekin = 0.407348747780355 | erot = 0.376479254457633 | epot = -15.4087317449614 | etot = -14.6249037427235 -947000 ekin = 0.397071124217177 | erot = 0.381256899558804 | epot = -15.4032317663713 | etot = -14.6249037425953 -948000 ekin = 0.383053455726579 | erot = 0.385576026491136 | epot = -15.3935332246539 | etot = -14.6249037424362 -949000 ekin = 0.367364810070546 | erot = 0.389872987609663 | epot = -15.382141539954 | etot = -14.6249037422738 -950000 ekin = 0.352149150211141 | erot = 0.394562514443112 | epot = -15.371615406789 | etot = -14.6249037421348 -951000 ekin = 0.339280178143099 | erot = 0.399966938641359 | epot = -15.3641508588234 | etot = -14.6249037420389 -952000 ekin = 0.330096120379237 | erot = 0.406268489131811 | epot = -15.3612683515071 | etot = -14.6249037419961 -953000 ekin = 0.325261831669684 | erot = 0.413492937870729 | epot = -15.3636585115451 | etot = -14.6249037420047 -954000 ekin = 0.324774911929383 | erot = 0.421526046053159 | epot = -15.3712047000361 | etot = -14.6249037420535 -955000 ekin = 0.328098170459405 | erot = 0.43015685816017 | epot = -15.3831587707447 | etot = -14.6249037421252 -956000 ekin = 0.334370903123805 | erot = 0.439135698166764 | epot = -15.3984103434923 | etot = -14.6249037422018 -957000 ekin = 0.342633913360331 | erot = 0.448231239799098 | epot = -15.415768895429 | etot = -14.6249037422696 -958000 ekin = 0.352004139469646 | erot = 0.457271615167415 | epot = -15.4341794969597 | etot = -14.6249037423226 -959000 ekin = 0.361755395785228 | erot = 0.466159587643494 | epot = -15.4528187257923 | etot = -14.6249037423635 -960000 ekin = 0.371296348402955 | erot = 0.474860087932416 | epot = -15.4710601787363 | etot = -14.6249037424009 -961000 ekin = 0.380073790912418 | erot = 0.483367158174937 | epot = -15.4883446915324 | etot = -14.624903742445 -962000 ekin = 0.387455548950117 | erot = 0.491663490520803 | epot = -15.5040227819739 | etot = -14.624903742503 -963000 ekin = 0.392654097311874 | erot = 0.49968729563245 | epot = -15.5172451355191 | etot = -14.6249037425748 -964000 ekin = 0.394737939559185 | erot = 0.507318071995981 | epot = -15.5269597542072 | etot = -14.624903742652 -965000 ekin = 0.392748486467115 | erot = 0.514386334667554 | epot = -15.5320385638537 | etot = -14.6249037427191 -966000 ekin = 0.38590547325284 | erot = 0.520705106527849 | epot = -15.5315143225377 | etot = -14.624903742757 -967000 ekin = 0.373852021645421 | erot = 0.526114369234909 | epot = -15.5248701336288 | etot = -14.6249037427485 -968000 ekin = 0.356869417135994 | erot = 0.530525868585158 | epot = -15.5122990284054 | etot = -14.6249037426842 -969000 ekin = 0.335986889834556 | erot = 0.533955228284217 | epot = -15.4948458606857 | etot = -14.624903742567 -970000 ekin = 0.312927788672648 | erot = 0.536531428461786 | epot = -15.4743629595477 | etot = -14.6249037424133 -971000 ekin = 0.289872105907182 | erot = 0.538479668129509 | epot = -15.4532555162878 | etot = -14.6249037422511 -972000 ekin = 0.269070232407033 | erot = 0.540080898361602 | epot = -15.4340548728818 | etot = -14.6249037421131 -973000 ekin = 0.252397022945933 | erot = 0.54161782723094 | epot = -15.4189185922051 | etot = -14.6249037420282 -974000 ekin = 0.240964852823081 | erot = 0.543321042152107 | epot = -15.4091896369882 | etot = -14.624903742013 -975000 ekin = 0.23490216482483 | erot = 0.545328986458791 | epot = -15.4051348933517 | etot = -14.6249037420681 -976000 ekin = 0.233353466622718 | erot = 0.547671994180028 | epot = -15.4059292029808 | etot = -14.624903742178 -977000 ekin = 0.23469220109011 | erot = 0.550284513867316 | epot = -15.4098804572738 | etot = -14.6249037423163 -978000 ekin = 0.236887903181319 | erot = 0.553043053342949 | epot = -15.4148346989756 | etot = -14.6249037424513 -979000 ekin = 0.237945797132614 | erot = 0.555821040963938 | epot = -15.4186705806485 | etot = -14.624903742552 -980000 ekin = 0.236334546964098 | erot = 0.558547250125554 | epot = -15.4197855396836 | etot = -14.624903742594 -981000 ekin = 0.231322843924842 | erot = 0.561252158433111 | epot = -15.4174787449233 | etot = -14.6249037425653 -982000 ekin = 0.223154169545187 | erot = 0.564087592075058 | epot = -15.4121455040898 | etot = -14.6249037424696 -983000 ekin = 0.213008719539848 | erot = 0.567310103887051 | epot = -15.405222565754 | etot = -14.6249037423271 -984000 ekin = 0.202740628548823 | erot = 0.571227590062905 | epot = -15.3988719607832 | etot = -14.6249037421715 -985000 ekin = 0.19443566515497 | erot = 0.576119771488149 | epot = -15.395459178685 | etot = -14.6249037420419 -986000 ekin = 0.189894304519326 | erot = 0.582152858152867 | epot = -15.3969509046438 | etot = -14.6249037419716 -987000 ekin = 0.190182835425093 | erot = 0.589313613953994 | epot = -15.4044001913574 | etot = -14.6249037419783 -988000 ekin = 0.195390213187501 | erot = 0.597385005524193 | epot = -15.4176789607687 | etot = -14.624903742057 -989000 ekin = 0.204671362362471 | erot = 0.605974905403898 | epot = -15.4355500099488 | etot = -14.6249037421824 -990000 ekin = 0.216563394578787 | erot = 0.614593273597699 | epot = -15.4560604104926 | etot = -14.6249037423161 -991000 ekin = 0.229465191862139 | erot = 0.622757127490779 | epot = -15.4771260617733 | etot = -14.6249037424204 -992000 ekin = 0.242114271128949 | erot = 0.630092599917091 | epot = -15.4971106135164 | etot = -14.6249037424704 -993000 ekin = 0.253902581480084 | erot = 0.636403793831659 | epot = -15.5152101177729 | etot = -14.6249037424612 -994000 ekin = 0.264939510335902 | erot = 0.641689105048086 | epot = -15.5315323577919 | etot = -14.6249037424079 -995000 ekin = 0.275864888579236 | erot = 0.646102898208602 | epot = -15.5468715291263 | etot = -14.6249037423384 -996000 ekin = 0.287497820770256 | erot = 0.649877086441226 | epot = -15.5622786494954 | etot = -14.6249037422839 -997000 ekin = 0.300450307467438 | erot = 0.65322742357329 | epot = -15.5785814733092 | etot = -14.6249037422685 -998000 ekin = 0.314829914377602 | erot = 0.656270894957618 | epot = -15.5960045516385 | etot = -14.6249037423033 -999000 ekin = 0.330110494517114 | erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385 -1000000 ekin = 0.345190458650495 | erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498 - 1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06 -Loop time of 16.5683 on 1 procs for 1000000 steps with 10 atoms - -Performance: 52147.644 tau/day, 60356.069 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 12.734 | 12.734 | 12.734 | 0.0 | 76.86 -Bond | 0.62259 | 0.62259 | 0.62259 | 0.0 | 3.76 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.18386 | 0.18386 | 0.18386 | 0.0 | 1.11 -Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 -Modify | 2.7788 | 2.7788 | 2.7788 | 0.0 | 16.77 -Other | | 0.2491 | | | 1.50 - -Nlocal: 10.0 ave 10.0 max 10.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37.0 ave 37.0 max 37.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 37 -Ave neighs/atom = 3.7 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:16 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 deleted file mode 100644 index f798b331e4..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 +++ /dev/null @@ -1,1182 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 3 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex3 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds - -set atom * mass 1.0 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA2 bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA2 pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 1.0 0.815 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274048 - ghost atom cutoff = 2.6274048 - binsize = 1.3137024, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -14.6249037416652 | etot = -14.6249037416652 -Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.96 | 8.018 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06 -1000 ekin = 0.00366431201929595 | erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679 -2000 ekin = 0.0144775076075461 | erot = 0.00770914672939826 | epot = -14.6470903960565 | etot = -14.6249037417196 -3000 ekin = 0.0319122186081537 | erot = 0.017197232864929 | epot = -14.6740131932573 | etot = -14.6249037417842 -4000 ekin = 0.055128304350968 | erot = 0.0302085305548261 | epot = -14.7102405767754 | etot = -14.6249037418696 -5000 ekin = 0.0830285165715777 | erot = 0.0464820547542036 | epot = -14.7544143132963 | etot = -14.6249037419705 -6000 ekin = 0.11433112154675 | erot = 0.0656980211282502 | epot = -14.8049328847556 | etot = -14.6249037420806 -7000 ekin = 0.14765386656188 | erot = 0.0874894888755877 | epot = -14.8600470976311 | etot = -14.6249037421936 -8000 ekin = 0.18160209956019 | erot = 0.111456095727761 | epot = -14.9179619375912 | etot = -14.6249037423032 -9000 ekin = 0.214852894725897 | erot = 0.137179311245239 | epot = -14.9769359483746 | etot = -14.6249037424035 -10000 ekin = 0.246227151956005 | erot = 0.164238435218469 | epot = -15.0353693296649 | etot = -14.6249037424904 -11000 ekin = 0.274743080419017 | erot = 0.192226420003323 | epot = -15.091873242983 | etot = -14.6249037425607 -12000 ekin = 0.299647141765663 | erot = 0.220764512146746 | epot = -15.1453153965252 | etot = -14.6249037426128 -13000 ekin = 0.320421918860927 | erot = 0.249514690530647 | epot = -15.1948403520386 | etot = -14.624903742647 -14000 ekin = 0.336773734884323 | erot = 0.278188933730603 | epot = -15.2398664112794 | etot = -14.6249037426645 -15000 ekin = 0.34860541376287 | erot = 0.306554508009539 | epot = -15.2800636644399 | etot = -14.6249037426675 -16000 ekin = 0.355980829097832 | erot = 0.334434770083873 | epot = -15.3153193418403 | etot = -14.6249037426586 -17000 ekin = 0.359087701059401 | erot = 0.361705441666651 | epot = -15.3456968853665 | etot = -14.6249037426405 -18000 ekin = 0.358203710992248 | erot = 0.388286889516457 | epot = -15.3713943431244 | etot = -14.6249037426157 -19000 ekin = 0.353668912555266 | erot = 0.414133518537258 | epot = -15.3927061736789 | etot = -14.6249037425864 -20000 ekin = 0.345865220775347 | erot = 0.439221805285588 | epot = -15.4099907686155 | etot = -14.6249037425546 -21000 ekin = 0.335201981146553 | erot = 0.463538642606666 | epot = -15.423644366275 | etot = -14.6249037425218 -22000 ekin = 0.322105588835009 | erot = 0.487071492273222 | epot = -15.4340808235974 | etot = -14.6249037424892 -23000 ekin = 0.307010918596293 | erot = 0.509801406229522 | epot = -15.4417160672835 | etot = -14.6249037424577 -24000 ekin = 0.290352786033317 | erot = 0.53169940050183 | epot = -15.4469559289633 | etot = -14.6249037424281 -25000 ekin = 0.272556500902201 | erot = 0.552726088759337 | epot = -15.4501863320625 | etot = -14.624903742401 -26000 ekin = 0.254027484079225 | erot = 0.572834017299149 | epot = -15.451765243755 | etot = -14.6249037423766 -27000 ekin = 0.235140665216512 | erot = 0.591971851501351 | epot = -15.4520162590732 | etot = -14.6249037423553 -28000 ekin = 0.216230835846381 | erot = 0.610089455964456 | epot = -15.4512240341482 | etot = -14.6249037423373 -29000 ekin = 0.197585285158732 | erot = 0.627142960082751 | epot = -15.4496319875638 | etot = -14.6249037423223 -30000 ekin = 0.179439940173485 | erot = 0.643099062793524 | epot = -15.4474427452772 | etot = -14.6249037423102 -31000 ekin = 0.161979935826275 | erot = 0.657938056392414 | epot = -15.4448217345188 | etot = -14.6249037423001 -32000 ekin = 0.145345108983154 | erot = 0.671655297434073 | epot = -15.4419041487088 | etot = -14.6249037422916 -33000 ekin = 0.129640400345301 | erot = 0.684261083518649 | epot = -15.4388052261477 | etot = -14.6249037422838 -34000 ekin = 0.114950474500096 | erot = 0.695779112936577 | epot = -15.4356333297123 | etot = -14.6249037422756 -35000 ekin = 0.101357103460395 | erot = 0.706243888527945 | epot = -15.4325047342545 | etot = -14.6249037422661 -36000 ekin = 0.0889576334571495 | erot = 0.715697403164658 | epot = -15.4295587788764 | etot = -14.6249037422546 -37000 ekin = 0.0778817390290869 | erot = 0.724185638635694 | epot = -15.4269711199052 | etot = -14.6249037422404 -38000 ekin = 0.0683037091548152 | erot = 0.731755309647459 | epot = -15.4249627610255 | etot = -14.6249037422232 -39000 ekin = 0.0604476327394574 | erot = 0.738451228922887 | epot = -15.4238026038658 | etot = -14.6249037422035 -40000 ekin = 0.0545835914676698 | erot = 0.744314557682062 | epot = -15.4238018913317 | etot = -14.624903742182 -41000 ekin = 0.0510142787133431 | erot = 0.749382063190686 | epot = -15.425300084064 | etot = -14.6249037421599 -42000 ekin = 0.0500531571157122 | erot = 0.753686350478873 | epot = -15.4286432497339 | etot = -14.6249037421393 -43000 ekin = 0.0519969858277791 | erot = 0.757256889238925 | epot = -15.4341576171884 | etot = -14.6249037421217 -44000 ekin = 0.0570968352183795 | erot = 0.760121540481331 | epot = -15.4421221178083 | etot = -14.6249037421086 -45000 ekin = 0.0655321553469052 | erot = 0.762308219230389 | epot = -15.4527441166787 | etot = -14.6249037421014 -46000 ekin = 0.077391880036667 | erot = 0.763846321567477 | epot = -15.4661419437046 | etot = -14.6249037421005 -47000 ekin = 0.0926650518886644 | erot = 0.764767599959881 | epot = -15.4823363939543 | etot = -14.6249037421058 -48000 ekin = 0.111241466890937 | erot = 0.765106283689481 | epot = -15.5012514926974 | etot = -14.624903742117 -49000 ekin = 0.132920935183018 | erot = 0.764898395951864 | epot = -15.5227230732682 | etot = -14.6249037421333 -50000 ekin = 0.157428432862217 | erot = 0.764180392178735 | epot = -15.5465125671948 | etot = -14.6249037421538 -51000 ekin = 0.184431879186323 | erot = 0.762987403181098 | epot = -15.572323024545 | etot = -14.6249037421776 -52000 ekin = 0.213559336999553 | erot = 0.761351471408863 | epot = -15.5998145506122 | etot = -14.6249037422038 -53000 ekin = 0.244412677541706 | erot = 0.759300175100794 | epot = -15.6286165948746 | etot = -14.6249037422321 -54000 ekin = 0.276574826726782 | erot = 0.756855909735936 | epot = -15.6583344787253 | etot = -14.6249037422625 -55000 ekin = 0.309607708697251 | erot = 0.754035838659022 | epot = -15.6885472896524 | etot = -14.6249037422961 -56000 ekin = 0.343038597242195 | erot = 0.750852192167276 | epot = -15.7187945317442 | etot = -14.6249037423347 -57000 ekin = 0.376334705011675 | erot = 0.747312289063632 | epot = -15.748550736456 | etot = -14.6249037423806 -58000 ekin = 0.408870193943514 | erot = 0.743417624903406 | epot = -15.7771915612831 | etot = -14.6249037424361 -59000 ekin = 0.439895666476151 | erot = 0.739161690570044 | epot = -15.8039610995489 | etot = -14.6249037425027 -60000 ekin = 0.468524372325882 | erot = 0.734526514748492 | epot = -15.8279546296535 | etot = -14.6249037425791 -61000 ekin = 0.493750804630977 | erot = 0.729479048549992 | epot = -15.8481335958426 | etot = -14.6249037426617 -62000 ekin = 0.514511417905742 | erot = 0.723968952962828 | epot = -15.8633841136118 | etot = -14.6249037427432 -63000 ekin = 0.529785687820863 | erot = 0.717929490923054 | epot = -15.8726189215585 | etot = -14.6249037428146 -64000 ekin = 0.538722043350041 | erot = 0.711282639869802 | epot = -15.8749084260858 | etot = -14.624903742866 -65000 ekin = 0.540763046401972 | erot = 0.703948378732391 | epot = -15.8696151680244 | etot = -14.62490374289 -66000 ekin = 0.535742115227036 | erot = 0.695856780686584 | epot = -15.8565026387959 | etot = -14.6249037428823 -67000 ekin = 0.523930969354304 | erot = 0.68696057843429 | epot = -15.8357952906313 | etot = -14.6249037428428 -68000 ekin = 0.506029704478312 | erot = 0.677245632039928 | epot = -15.8081790792934 | etot = -14.6249037427752 -69000 ekin = 0.483104826200259 | erot = 0.666737270644213 | epot = -15.7747458395309 | etot = -14.6249037426864 -70000 ekin = 0.456490218293525 | erot = 0.655501536742973 | epot = -15.7368954976211 | etot = -14.6249037425846 -71000 ekin = 0.427669918862827 | erot = 0.643641521525979 | epot = -15.696215182867 | etot = -14.6249037424782 -72000 ekin = 0.398160338931837 | erot = 0.631289876690699 | epot = -15.6543539579978 | etot = -14.6249037423753 -73000 ekin = 0.369405258277091 | erot = 0.618599034382457 | epot = -15.6129080349413 | etot = -14.6249037422818 -74000 ekin = 0.342691749042478 | erot = 0.605730669564096 | epot = -15.573326160809 | etot = -14.6249037422024 -75000 ekin = 0.319090526807116 | erot = 0.592845634905565 | epot = -15.5368399038526 | etot = -14.6249037421399 -76000 ekin = 0.299420611427649 | erot = 0.580095163563256 | epot = -15.5044195170865 | etot = -14.6249037420956 -77000 ekin = 0.284235504575202 | erot = 0.567613716752232 | epot = -15.476752963397 | etot = -14.6249037420696 -78000 ekin = 0.273826140866745 | erot = 0.555513536863883 | epot = -15.4542434197916 | etot = -14.624903742061 -79000 ekin = 0.268234635497765 | erot = 0.54388078034531 | epot = -15.437019157912 | etot = -14.6249037420689 -80000 ekin = 0.267272602906572 | erot = 0.532773036269537 | epot = -15.4249493812683 | etot = -14.6249037420922 -81000 ekin = 0.270538934182649 | erot = 0.522218059775401 | epot = -15.417660736088 | etot = -14.62490374213 -82000 ekin = 0.27743457435936 | erot = 0.512213638247992 | epot = -15.414551954789 | etot = -14.6249037421817 -83000 ekin = 0.287175732620383 | erot = 0.502728640569106 | epot = -15.4148081154356 | etot = -14.6249037422461 -84000 ekin = 0.298811175848726 | erot = 0.493705451301405 | epot = -15.4174203694714 | etot = -14.6249037423213 -85000 ekin = 0.311252369949757 | erot = 0.485064122067327 | epot = -15.4212202344208 | etot = -14.6249037424038 -86000 ekin = 0.323325626376074 | erot = 0.476708618160845 | epot = -15.4249379870248 | etot = -14.6249037424879 -87000 ekin = 0.33385179551888 | erot = 0.468535420697723 | epot = -15.4272909587828 | etot = -14.6249037425662 -88000 ekin = 0.341751109758587 | erot = 0.460444399763838 | epot = -15.427099252152 | etot = -14.6249037426296 -89000 ekin = 0.346159825920252 | erot = 0.452351304178841 | epot = -15.4234148727694 | etot = -14.6249037426704 -90000 ekin = 0.346534667470577 | erot = 0.444200535918418 | epot = -15.4156389460721 | etot = -14.6249037426831 -91000 ekin = 0.342715665476236 | erot = 0.435976333753466 | epot = -15.4035957418971 | etot = -14.6249037426674 -92000 ekin = 0.334922715851711 | erot = 0.427710377227768 | epot = -15.3875368357076 | etot = -14.6249037426281 -93000 ekin = 0.323677844434189 | erot = 0.419484336040122 | epot = -15.368065923049 | etot = -14.6249037425747 -94000 ekin = 0.309669782921695 | erot = 0.411426964072737 | epot = -15.3460004895125 | etot = -14.624903742518 -95000 ekin = 0.293600014862055 | erot = 0.403706586473305 | epot = -15.3222103438027 | etot = -14.6249037424673 -96000 ekin = 0.2760582848845 | erot = 0.396520701306389 | epot = -15.297482728618 | etot = -14.6249037424272 -97000 ekin = 0.257464456296026 | erot = 0.390084510983188 | epot = -15.2724527096758 | etot = -14.6249037423966 -98000 ekin = 0.238086767083294 | erot = 0.384619533405776 | epot = -15.24761004286 | etot = -14.6249037423709 -99000 ekin = 0.218116994126189 | erot = 0.380342481668315 | epot = -15.2233632181387 | etot = -14.6249037423442 -100000 ekin = 0.197764845956813 | erot = 0.377453964065525 | epot = -15.2001225523343 | etot = -14.6249037423119 -101000 ekin = 0.177333852671588 | erot = 0.37612662169739 | epot = -15.1783642166417 | etot = -14.6249037422727 -102000 ekin = 0.157255732179676 | erot = 0.376493003927858 | epot = -15.1586524783359 | etot = -14.6249037422283 -103000 ekin = 0.138079925449103 | erot = 0.378634329970109 | epot = -15.1416179976017 | etot = -14.6249037421825 -104000 ekin = 0.120430234291513 | erot = 0.38257179133531 | epot = -15.1279057677667 | etot = -14.6249037421398 -105000 ekin = 0.104946722393699 | erot = 0.388261944551355 | epot = -15.1181124090491 | etot = -14.6249037421041 -106000 ekin = 0.0922291289495077 | erot = 0.395597086392455 | epot = -15.1127299574201 | etot = -14.6249037420781 -107000 ekin = 0.0827918191992449 | erot = 0.404410579138415 | epot = -15.112106140401 | etot = -14.6249037420633 -108000 ekin = 0.0770336430610872 | erot = 0.414486225075909 | epot = -15.116423610197 | etot = -14.62490374206 -109000 ekin = 0.0752213121179505 | erot = 0.425570202879076 | epot = -15.1256952570645 | etot = -14.6249037420675 -110000 ekin = 0.077482636424855 | erot = 0.437383858086389 | epot = -15.1397702365963 | etot = -14.6249037420851 -111000 ekin = 0.0838057148049012 | erot = 0.449635759435866 | epot = -15.1583452163524 | etot = -14.6249037421117 -112000 ekin = 0.094041131771038 | erot = 0.462031808376727 | epot = -15.1809766822944 | etot = -14.6249037421466 -113000 ekin = 0.107905661684216 | erot = 0.47428271886895 | epot = -15.2070921227424 | etot = -14.6249037421893 -114000 ekin = 0.124987416380585 | erot = 0.486108767327206 | epot = -15.2359999259466 | etot = -14.6249037422388 -115000 ekin = 0.144753474421712 | erot = 0.497242253022929 | epot = -15.2668994697393 | etot = -14.6249037422947 -116000 ekin = 0.166561593123338 | erot = 0.507428522970937 | epot = -15.2988938584497 | etot = -14.6249037423555 -117000 ekin = 0.189677527330919 | erot = 0.516426638198595 | epot = -15.3310079079494 | etot = -14.6249037424199 -118000 ekin = 0.213298790897393 | erot = 0.524010758771299 | epot = -15.3622132921543 | etot = -14.6249037424856 -119000 ekin = 0.236584576961686 | erot = 0.529973112381402 | epot = -15.3914614318934 | etot = -14.6249037425503 -120000 ekin = 0.258690301858407 | erot = 0.5341290349257 | epot = -15.4177230793954 | etot = -14.6249037426112 -121000 ekin = 0.278804196533067 | erot = 0.536324108799723 | epot = -15.4400320479983 | etot = -14.6249037426655 -122000 ekin = 0.296182819519644 | erot = 0.536442962870851 | epot = -15.4575295251011 | etot = -14.6249037427106 -123000 ekin = 0.310182446406097 | erot = 0.534418915104283 | epot = -15.4695051042545 | etot = -14.6249037427441 -124000 ekin = 0.320283972930319 | erot = 0.530243389137748 | epot = -15.4754311048325 | etot = -14.6249037427644 -125000 ekin = 0.326110081462518 | erot = 0.523973945236228 | epot = -15.4749877694694 | etot = -14.6249037427707 -126000 ekin = 0.32743470961478 | erot = 0.515739832556742 | epot = -15.468078284934 | etot = -14.6249037427624 -127000 ekin = 0.324186046690464 | erot = 0.505744172152755 | epot = -15.4548339615831 | etot = -14.6249037427398 -128000 ekin = 0.316445106704291 | erot = 0.494262185784872 | epot = -15.4356110351926 | etot = -14.6249037427034 -129000 ekin = 0.304442167762781 | erot = 0.481635256753188 | epot = -15.4109811671702 | etot = -14.6249037426542 -130000 ekin = 0.288552887156539 | erot = 0.468261006625544 | epot = -15.3817176363753 | etot = -14.6249037425933 -131000 ekin = 0.269294696165401 | erot = 0.45457995559872 | epot = -15.3487783942861 | etot = -14.6249037425219 -132000 ekin = 0.247322351785784 | erot = 0.441059661322916 | epot = -15.3132857555505 | etot = -14.6249037424418 -133000 ekin = 0.223419723871666 | erot = 0.428177456066593 | epot = -15.2765009222933 | etot = -14.624903742355 -134000 ekin = 0.19848366631698 | erot = 0.416402982921093 | epot = -15.2397903915024 | etot = -14.6249037422643 -135000 ekin = 0.173495806295277 | erot = 0.406181641002432 | epot = -15.2045811894713 | etot = -14.6249037421736 -136000 ekin = 0.149479658252776 | erot = 0.397919790440761 | epot = -15.1723031907806 | etot = -14.6249037420871 -137000 ekin = 0.127443476996694 | erot = 0.391972186713497 | epot = -15.1443194057198 | etot = -14.6249037420096 -138000 ekin = 0.108312970525399 | erot = 0.38863170083623 | epot = -15.121848413308 | etot = -14.6249037419464 -139000 ekin = 0.0928612988417865 | erot = 0.388121053034643 | epot = -15.1058860937781 | etot = -14.6249037419017 -140000 ekin = 0.0816456573909381 | erot = 0.390586148388578 | epot = -15.0971355476584 | etot = -14.6249037418789 -141000 ekin = 0.074959634987115 | erot = 0.396090706683305 | epot = -15.0959540835502 | etot = -14.6249037418797 -142000 ekin = 0.072808553768854 | erot = 0.404612196534598 | epot = -15.1023244922079 | etot = -14.6249037419044 -143000 ekin = 0.0749117535381453 | erot = 0.416039504837322 | epot = -15.1158550003263 | etot = -14.6249037419509 -144000 ekin = 0.0807320498018154 | erot = 0.430173136684429 | epot = -15.1358089285018 | etot = -14.6249037420155 -145000 ekin = 0.0895290255830711 | erot = 0.44672889393778 | epot = -15.1611616616143 | etot = -14.6249037420935 -146000 ekin = 0.100429851262872 | erot = 0.46534582966922 | epot = -15.1906794231108 | etot = -14.6249037421787 -147000 ekin = 0.112509264558272 | erot = 0.485598823527704 | epot = -15.2230118303508 | etot = -14.6249037422648 -148000 ekin = 0.124869425792311 | erot = 0.507015469189125 | epot = -15.2567886373275 | etot = -14.6249037423461 -149000 ekin = 0.136710750658201 | erot = 0.529096273050756 | epot = -15.2907107661264 | etot = -14.6249037424174 -150000 ekin = 0.147386480805994 | erot = 0.551336607351909 | epot = -15.3236268306334 | etot = -14.6249037424755 -151000 ekin = 0.156436378415923 | erot = 0.573248570644847 | epot = -15.3545886915789 | etot = -14.6249037425181 -152000 ekin = 0.163597998371616 | erot = 0.594380933602504 | epot = -15.3828826745191 | etot = -14.624903742545 -153000 ekin = 0.168796920199645 | erot = 0.614335653334077 | epot = -15.4080363160909 | etot = -14.6249037425571 -154000 ekin = 0.172119667637843 | erot = 0.632779929091333 | epot = -15.4298033392859 | etot = -14.6249037425567 -155000 ekin = 0.173774602206439 | erot = 0.649453329864798 | epot = -15.4481316746178 | etot = -14.6249037425466 -156000 ekin = 0.174046854480218 | erot = 0.664170048550206 | epot = -15.4631206455604 | etot = -14.62490374253 -157000 ekin = 0.17325345101635 | erot = 0.67681676270221 | epot = -15.4749739562283 | etot = -14.6249037425097 -158000 ekin = 0.171704281293994 | erot = 0.687346881267705 | epot = -15.48395490505 | etot = -14.6249037424883 -159000 ekin = 0.169673443700116 | erot = 0.695772131172833 | epot = -15.4903493173403 | etot = -14.6249037424673 -160000 ekin = 0.167383826014799 | erot = 0.702152502586226 | epot = -15.4944400710487 | etot = -14.6249037424476 -161000 ekin = 0.165005624031947 | erot = 0.706585545944227 | epot = -15.4964949124054 | etot = -14.6249037424292 -162000 ekin = 0.162667154471987 | erot = 0.7091959147906 | epot = -15.4967668116741 | etot = -14.6249037424115 -163000 ekin = 0.160474189581708 | erot = 0.710125892129571 | epot = -15.4955038241048 | etot = -14.6249037423935 -164000 ekin = 0.158532578972808 | erot = 0.709527441008673 | epot = -15.4929637623557 | etot = -14.6249037423742 -165000 ekin = 0.156968465370873 | erot = 0.707556101120943 | epot = -15.4894283088449 | etot = -14.624903742353 -166000 ekin = 0.155941053191322 | erot = 0.704366832057858 | epot = -15.4852116275794 | etot = -14.6249037423302 -167000 ekin = 0.15564449680974 | erot = 0.700111698658167 | epot = -15.4806599377741 | etot = -14.6249037423062 -168000 ekin = 0.156297672988367 | erot = 0.694939119112688 | epot = -15.4761405343834 | etot = -14.6249037422823 -169000 ekin = 0.158122923325633 | erot = 0.688994262093866 | epot = -15.4720209276801 | etot = -14.6249037422606 -170000 ekin = 0.161316852937839 | erot = 0.682420091513715 | epot = -15.4686406866943 | etot = -14.6249037422428 -171000 ekin = 0.166017619146964 | erot = 0.675358520304694 | epot = -15.4662798816826 | etot = -14.6249037422309 -172000 ekin = 0.172273671159624 | erot = 0.667951149520755 | epot = -15.465128562907 | etot = -14.6249037422266 -173000 ekin = 0.180018623556126 | erot = 0.660339136127817 | epot = -15.465261501915 | etot = -14.624903742231 -174000 ekin = 0.189056055744959 | erot = 0.652661851831919 | epot = -15.4666216498214 | etot = -14.6249037422446 -175000 ekin = 0.199056860650102 | erot = 0.645054167286212 | epot = -15.4690147702031 | etot = -14.6249037422668 -176000 ekin = 0.209570701317496 | erot = 0.637642422787083 | epot = -15.4721168664013 | etot = -14.6249037422968 -177000 ekin = 0.220052442974529 | erot = 0.630539423737744 | epot = -15.4754956090444 | etot = -14.6249037423321 -178000 ekin = 0.229904071991068 | erot = 0.623839102439468 | epot = -15.4786469168001 | etot = -14.6249037423696 -179000 ekin = 0.238532114427838 | erot = 0.617611757778078 | epot = -15.4810476146109 | etot = -14.624903742405 -180000 ekin = 0.245419064060145 | erot = 0.611900922402911 | epot = -15.4822237288958 | etot = -14.6249037424328 -181000 ekin = 0.250203926055637 | erot = 0.606722796615544 | epot = -15.4818304651187 | etot = -14.6249037424476 -182000 ekin = 0.252761402919458 | erot = 0.602068750132192 | epot = -15.4797338954962 | etot = -14.6249037424445 -183000 ekin = 0.253262634973987 | erot = 0.597910660168958 | epot = -15.4760770375644 | etot = -14.6249037424214 -184000 ekin = 0.252195762131854 | erot = 0.594208023727366 | epot = -15.4713075282391 | etot = -14.6249037423799 -185000 ekin = 0.250326113306337 | erot = 0.590915179672999 | epot = -15.4661450353057 | etot = -14.6249037423263 -186000 ekin = 0.248586758541696 | erot = 0.587986907734991 | epot = -15.4614774085483 | etot = -14.6249037422716 -187000 ekin = 0.247909630265907 | erot = 0.585381224304124 | epot = -15.4581945967987 | etot = -14.6249037422287 -188000 ekin = 0.249029052394555 | erot = 0.583059148734203 | epot = -15.4569919433383 | etot = -14.6249037422095 -189000 ekin = 0.25230380318116 | erot = 0.580982165410166 | epot = -15.4581897108133 | etot = -14.624903742222 -190000 ekin = 0.257603763515512 | erot = 0.579108718145525 | epot = -15.4616162239286 | etot = -14.6249037422675 -191000 ekin = 0.264292655598072 | erot = 0.577391223759195 | epot = -15.4665876216979 | etot = -14.6249037423406 -192000 ekin = 0.271315385056371 | erot = 0.575774831089445 | epot = -15.4719939585754 | etot = -14.6249037424296 -193000 ekin = 0.277374539132726 | erot = 0.574198584868558 | epot = -15.4764768665205 | etot = -14.6249037425192 -194000 ekin = 0.281161076019698 | erot = 0.572598913484966 | epot = -15.4786637320983 | etot = -14.6249037425936 -195000 ekin = 0.28159263734721 | erot = 0.570914645865857 | epot = -15.4774110258526 | etot = -14.6249037426396 -196000 ekin = 0.278011867235767 | erot = 0.569092314484949 | epot = -15.4720079243697 | etot = -14.624903742649 -197000 ekin = 0.270307527593016 | erot = 0.567090473640134 | epot = -15.4623017438535 | etot = -14.6249037426204 -198000 ekin = 0.258940359976181 | erot = 0.564882125458909 | epot = -15.4487262279932 | etot = -14.6249037425581 -199000 ekin = 0.244877476699608 | erot = 0.562454912721969 | epot = -15.432236131893 | etot = -14.6249037424714 -200000 ekin = 0.229456931019031 | erot = 0.559809284042109 | epot = -15.4141699574328 | etot = -14.6249037423717 -201000 ekin = 0.214214012279214 | erot = 0.556955381706857 | epot = -15.396073136257 | etot = -14.6249037422709 -202000 ekin = 0.200701376135343 | erot = 0.553909032488835 | epot = -15.3795141508038 | etot = -14.6249037421796 -203000 ekin = 0.190329688711031 | erot = 0.550687503827458 | epot = -15.3659209346438 | etot = -14.6249037421053 -204000 ekin = 0.184246973275431 | erot = 0.547306655839924 | epot = -15.3564573711681 | etot = -14.6249037420528 -205000 ekin = 0.183262973705765 | erot = 0.543779043729182 | epot = -15.3519457594592 | etot = -14.6249037420242 -206000 ekin = 0.187816949073314 | erot = 0.5401134327365 | epot = -15.3528341238289 | etot = -14.6249037420191 -207000 ekin = 0.197980929490155 | erot = 0.536315658388532 | epot = -15.3592003299141 | etot = -14.6249037420354 -208000 ekin = 0.213487612676859 | erot = 0.532390498207104 | epot = -15.3707818529543 | etot = -14.6249037420704 -209000 ekin = 0.23377236271188 | erot = 0.528344018724915 | epot = -15.3870201235577 | etot = -14.6249037421209 -210000 ekin = 0.258021408691598 | erot = 0.524185756556645 | epot = -15.4071109074321 | etot = -14.6249037421838 -211000 ekin = 0.285222208429149 | erot = 0.519930104708152 | epot = -15.4300560553932 | etot = -14.6249037422559 -212000 ekin = 0.314215813604078 | erot = 0.515596398128299 | epot = -15.454715954066 | etot = -14.6249037423336 -213000 ekin = 0.343753634042999 | erot = 0.511207450608694 | epot = -15.4798648270648 | etot = -14.6249037424131 -214000 ekin = 0.372561594269383 | erot = 0.506786560075164 | epot = -15.5042518968341 | etot = -14.6249037424896 -215000 ekin = 0.399412456461965 | erot = 0.502353347158559 | epot = -15.5266695461789 | etot = -14.6249037425584 -216000 ekin = 0.423202666202795 | erot = 0.497919155943979 | epot = -15.5460255647614 | etot = -14.6249037426146 -217000 ekin = 0.443025226539309 | erot = 0.49348301367888 | epot = -15.561411982873 | etot = -14.6249037426548 -218000 ekin = 0.458227302378268 | erot = 0.48902929485633 | epot = -15.5721603399116 | etot = -14.624903742677 -219000 ekin = 0.468443019183614 | erot = 0.484528125251351 | epot = -15.5778748871154 | etot = -14.6249037426804 -220000 ekin = 0.473598483116428 | erot = 0.479939108990727 | epot = -15.5784413347736 | etot = -14.6249037426664 -221000 ekin = 0.473894168318623 | erot = 0.475218183432471 | epot = -15.5740160943877 | etot = -14.6249037426366 -222000 ekin = 0.469774014049581 | erot = 0.470326483973439 | epot = -15.5650042406161 | etot = -14.6249037425931 -223000 ekin = 0.461887320397625 | erot = 0.465239349169327 | epot = -15.5520304121052 | etot = -14.6249037425383 -224000 ekin = 0.451041336422898 | erot = 0.459953336121568 | epot = -15.5358984150205 | etot = -14.6249037424761 -225000 ekin = 0.438137198423164 | erot = 0.454489515561359 | epot = -15.5175304563962 | etot = -14.6249037424117 -226000 ekin = 0.424086332826599 | erot = 0.448892294163476 | epot = -15.4978823693417 | etot = -14.6249037423516 -227000 ekin = 0.409717105195494 | erot = 0.443224250669919 | epot = -15.4778450981669 | etot = -14.6249037423015 -228000 ekin = 0.395692916861841 | erot = 0.437558473222699 | epot = -15.4581551323495 | etot = -14.624903742265 -229000 ekin = 0.382463318564939 | erot = 0.431970318931165 | epot = -15.4393373797388 | etot = -14.6249037422427 -230000 ekin = 0.37025811673091 | erot = 0.426530223272703 | epot = -15.4216920822363 | etot = -14.6249037422326 -231000 ekin = 0.359118625017792 | erot = 0.42129844029256 | epot = -15.4053208075418 | etot = -14.6249037422314 -232000 ekin = 0.348949729121723 | erot = 0.416321816462675 | epot = -15.3901752878201 | etot = -14.6249037422357 -233000 ekin = 0.339575284188518 | erot = 0.411632247273729 | epot = -15.3761112737048 | etot = -14.6249037422426 -234000 ekin = 0.330784909163637 | erot = 0.407246384303507 | epot = -15.3629350357173 | etot = -14.6249037422502 -235000 ekin = 0.322367248495492 | erot = 0.403166248673538 | epot = -15.3504372394263 | etot = -14.6249037422572 -236000 ekin = 0.314129851889848 | erot = 0.399380677843492 | epot = -15.3384142719969 | etot = -14.6249037422636 -237000 ekin = 0.305908300165184 | erot = 0.395867600047875 | epot = -15.3266796424821 | etot = -14.624903742269 -238000 ekin = 0.297568064658136 | erot = 0.392597157204584 | epot = -15.3150689641364 | etot = -14.6249037422737 -239000 ekin = 0.289002756415172 | erot = 0.389535643317114 | epot = -15.3034421420096 | etot = -14.6249037422774 -240000 ekin = 0.280132201614914 | erot = 0.386650129641556 | epot = -15.2916860735363 | etot = -14.6249037422798 -241000 ekin = 0.270903172980511 | erot = 0.383913574227165 | epot = -15.2797204894881 | etot = -14.6249037422804 -242000 ekin = 0.261294311102232 | erot = 0.381310019034049 | epot = -15.2675080724143 | etot = -14.6249037422781 -243000 ekin = 0.251325265434219 | erot = 0.378839435319532 | epot = -15.2550684430252 | etot = -14.6249037422715 -244000 ekin = 0.241068460184283 | erot = 0.376521662813082 | epot = -15.2424938652572 | etot = -14.6249037422598 -245000 ekin = 0.230660579660644 | erot = 0.374398842117291 | epot = -15.2299631640205 | etot = -14.6249037422425 -246000 ekin = 0.220310176855083 | erot = 0.372535772164452 | epot = -15.217749691239 | etot = -14.6249037422195 -247000 ekin = 0.210297920408214 | erot = 0.371017759432552 | epot = -15.2062194220322 | etot = -14.6249037421914 -248000 ekin = 0.200966973970082 | erot = 0.36994577990608 | epot = -15.1958164960362 | etot = -14.6249037421601 -249000 ekin = 0.192702752056133 | erot = 0.369429135338683 | epot = -15.1870356295227 | etot = -14.6249037421279 -250000 ekin = 0.185903524092239 | erot = 0.369576201101353 | epot = -15.1803834672915 | etot = -14.6249037420979 -251000 ekin = 0.180945546219151 | erot = 0.370484246994623 | epot = -15.1763335352865 | etot = -14.6249037420727 -252000 ekin = 0.178147956309189 | erot = 0.372229589272153 | epot = -15.1752812876364 | etot = -14.624903742055 -253000 ekin = 0.177743031464987 | erot = 0.374859230992971 | epot = -15.1775060045044 | etot = -14.6249037420464 -254000 ekin = 0.179856300054645 | erot = 0.378385037101156 | epot = -15.1831450792033 | etot = -14.6249037420475 -255000 ekin = 0.184498455786156 | erot = 0.382781080046288 | epot = -15.1921832778908 | etot = -14.6249037420584 -256000 ekin = 0.191568141872831 | erot = 0.387983970946124 | epot = -15.2044558548971 | etot = -14.6249037420782 -257000 ekin = 0.20086208487434 | erot = 0.39389562099376 | epot = -15.2196614479739 | etot = -14.6249037421058 -258000 ekin = 0.212087875566807 | erot = 0.400387498987271 | epot = -15.2373791166947 | etot = -14.6249037421406 -259000 ekin = 0.224875306192123 | erot = 0.407305396776656 | epot = -15.2570844451507 | etot = -14.6249037421819 -260000 ekin = 0.238784314763303 | erot = 0.414473950040634 | epot = -15.2781620070332 | etot = -14.6249037422292 -261000 ekin = 0.253310397642086 | erot = 0.421700596682803 | epot = -15.2999147366071 | etot = -14.6249037422822 -262000 ekin = 0.26789075041242 | erot = 0.428779149458854 | epot = -15.3215736422117 | etot = -14.6249037423404 -263000 ekin = 0.281915541778016 | erot = 0.435493571930236 | epot = -15.3423128561104 | etot = -14.6249037424021 -264000 ekin = 0.294748319449364 | erot = 0.441622773940569 | epot = -15.3612748358549 | etot = -14.624903742465 -265000 ekin = 0.305757851305535 | erot = 0.446947232466421 | epot = -15.3776088262975 | etot = -14.6249037425255 -266000 ekin = 0.314361275702592 | erot = 0.451257984268131 | epot = -15.3905230025502 | etot = -14.6249037425794 -267000 ekin = 0.320075758814341 | erot = 0.454368036195608 | epot = -15.399347537632 | etot = -14.624903742622 -268000 ekin = 0.322573111286139 | erot = 0.456125517717021 | epot = -15.4036023716517 | etot = -14.6249037426486 -269000 ekin = 0.321728949457285 | erot = 0.456427019950081 | epot = -15.4030597120627 | etot = -14.6249037426554 -270000 ekin = 0.317655198203759 | erot = 0.455228696070215 | epot = -15.397787636915 | etot = -14.624903742641 -271000 ekin = 0.310703151367757 | erot = 0.452552178356157 | epot = -15.3881590723317 | etot = -14.6249037426077 -272000 ekin = 0.3014262335366 | erot = 0.448482664562447 | epot = -15.37481264066 | etot = -14.624903742561 -273000 ekin = 0.290499502093233 | erot = 0.443158007811504 | epot = -15.3585612524143 | etot = -14.6249037425096 -274000 ekin = 0.278606962225926 | erot = 0.436750209658098 | epot = -15.3402609143472 | etot = -14.6249037424632 -275000 ekin = 0.266323480340475 | erot = 0.429443553159133 | epot = -15.320670775929 | etot = -14.6249037424294 -276000 ekin = 0.254026977157675 | erot = 0.421415402005373 | epot = -15.3003461215741 | etot = -14.6249037424111 -277000 ekin = 0.241871064453077 | erot = 0.412825312322701 | epot = -15.2796001191813 | etot = -14.6249037424055 -278000 ekin = 0.229828041579266 | erot = 0.403815416630584 | epot = -15.2585472006154 | etot = -14.6249037424055 -279000 ekin = 0.217786141145793 | erot = 0.394521119097645 | epot = -15.2372110026455 | etot = -14.6249037424021 -280000 ekin = 0.205666064593437 | erot = 0.385087703032635 | epot = -15.2156575100138 | etot = -14.6249037423877 -281000 ekin = 0.193518604274061 | erot = 0.375686870763365 | epot = -15.1941092173957 | etot = -14.6249037423582 -282000 ekin = 0.18157672074763 | erot = 0.366527860022155 | epot = -15.1730083230837 | etot = -14.624903742314 -283000 ekin = 0.170254050626075 | erot = 0.357859944224688 | epot = -15.1530177371095 | etot = -14.6249037422587 -284000 ekin = 0.160098631070491 | erot = 0.349965713706295 | epot = -15.1349680869751 | etot = -14.6249037421983 -285000 ekin = 0.151720356670846 | erot = 0.34314662552044 | epot = -15.1197707243306 | etot = -14.6249037421394 -286000 ekin = 0.145712559183964 | erot = 0.337703485421193 | epot = -15.1083197866929 | etot = -14.6249037420878 -287000 ekin = 0.142584250545026 | erot = 0.333914836093095 | epot = -15.1014028286861 | etot = -14.624903742048 -288000 ekin = 0.1427129413407 | erot = 0.33201595204283 | epot = -15.0996326354059 | etot = -14.6249037420224 -289000 ekin = 0.146320998448507 | erot = 0.332180585090171 | epot = -15.1034053255506 | etot = -14.6249037420119 -290000 ekin = 0.153472816921105 | erot = 0.334506983379138 | epot = -15.1128835423165 | etot = -14.6249037420163 -291000 ekin = 0.164086465662505 | erot = 0.339009144348392 | epot = -15.1279993520451 | etot = -14.6249037420342 -292000 ekin = 0.177952173600193 | erot = 0.345613807734964 | epot = -15.1484697233995 | etot = -14.6249037420643 -293000 ekin = 0.194750859968512 | erot = 0.354163344443286 | epot = -15.1738179465169 | etot = -14.6249037421051 -294000 ekin = 0.214068309158811 | erot = 0.364424408222176 | epot = -15.2033964595362 | etot = -14.6249037421552 -295000 ekin = 0.235403710402673 | erot = 0.376101928511166 | epot = -15.2364093811272 | etot = -14.6249037422133 -296000 ekin = 0.258174229752594 | erot = 0.388857685536638 | epot = -15.2719356575669 | etot = -14.6249037422777 -297000 ekin = 0.28171936013486 | erot = 0.402332315571688 | epot = -15.308955418053 | etot = -14.6249037423465 -298000 ekin = 0.30530968452295 | erot = 0.416169191335505 | epot = -15.3463826182751 | etot = -14.6249037424166 -299000 ekin = 0.328164426016042 | erot = 0.430038291827055 | epot = -15.3831064603285 | etot = -14.6249037424854 -300000 ekin = 0.349480947254597 | erot = 0.443657997414049 | epot = -15.4180426872175 | etot = -14.6249037425489 -301000 ekin = 0.368477349758915 | erot = 0.456812763608253 | epot = -15.4501938559697 | etot = -14.6249037426025 -302000 ekin = 0.384446573101029 | erot = 0.469364841860584 | epot = -15.478715157604 | etot = -14.6249037426423 -303000 ekin = 0.396817065634643 | erot = 0.481258609604428 | epot = -15.5029794179037 | etot = -14.6249037426647 -304000 ekin = 0.405211709647263 | erot = 0.492516637287232 | epot = -15.5226320896016 | etot = -14.6249037426671 -305000 ekin = 0.409494186866275 | erot = 0.503227368869637 | epot = -15.5376252983854 | etot = -14.6249037426495 -306000 ekin = 0.409791521883174 | erot = 0.513525227982492 | epot = -15.5482204924795 | etot = -14.6249037426138 -307000 ekin = 0.406484029568133 | erot = 0.523565033268022 | epot = -15.554952805401 | etot = -14.6249037425649 -308000 ekin = 0.400159443094258 | erot = 0.533493670193094 | epot = -15.5585568557967 | etot = -14.6249037425093 -309000 ekin = 0.391535685674106 | erot = 0.543422788904079 | epot = -15.5598622170332 | etot = -14.624903742455 -310000 ekin = 0.381364662750139 | erot = 0.553406603763137 | epot = -15.5596750089224 | etot = -14.6249037424091 -311000 ekin = 0.370335174701307 | erot = 0.563428434508751 | epot = -15.5586673515872 | etot = -14.6249037423771 -312000 ekin = 0.358994462074446 | erot = 0.573398378860501 | epot = -15.5572965832962 | etot = -14.6249037423613 -313000 ekin = 0.347704062022306 | erot = 0.583162598674582 | epot = -15.5557704030575 | etot = -14.6249037423606 -314000 ekin = 0.336637402906986 | erot = 0.592522528333631 | epot = -15.5540636736117 | etot = -14.624903742371 -315000 ekin = 0.325816357219225 | erot = 0.601260411440956 | epot = -15.5519805110472 | etot = -14.624903742387 -316000 ekin = 0.315175012816655 | erot = 0.609166451967456 | epot = -15.5492452071862 | etot = -14.6249037424021 -317000 ekin = 0.304633856553691 | erot = 0.616062831071924 | epot = -15.5456004300362 | etot = -14.6249037424106 -318000 ekin = 0.294167456686513 | erot = 0.62182086663663 | epot = -15.5408920657322 | etot = -14.624903742409 -319000 ekin = 0.283852816310304 | erot = 0.626369338623922 | epot = -15.5351258973303 | etot = -14.624903742396 -320000 ekin = 0.273891844373217 | erot = 0.629693948583815 | epot = -15.5284895353292 | etot = -14.6249037423721 -321000 ekin = 0.264607615830326 | erot = 0.631829520444979 | epot = -15.5213408786153 | etot = -14.62490374234 -322000 ekin = 0.256418665980307 | erot = 0.632847556381831 | epot = -15.5141699646654 | etot = -14.6249037423032 -323000 ekin = 0.249797892887523 | erot = 0.632842055921361 | epot = -15.5075436910745 | etot = -14.6249037422657 -324000 ekin = 0.245223011939351 | erot = 0.631916211662891 | epot = -15.5020429658331 | etot = -14.6249037422309 -325000 ekin = 0.243124676660684 | erot = 0.630171930979688 | epot = -15.4982003498434 | etot = -14.624903742203 -326000 ekin = 0.243837159968099 | erot = 0.627703310196172 | epot = -15.4964442123488 | etot = -14.6249037421845 -327000 ekin = 0.247555458534595 | erot = 0.624594349329669 | epot = -15.4970535500421 | etot = -14.6249037421778 -328000 ekin = 0.254302069317299 | erot = 0.620920422826771 | epot = -15.5001262343279 | etot = -14.6249037421838 -329000 ekin = 0.263906382978619 | erot = 0.616752378549859 | epot = -15.5055625037313 | etot = -14.6249037422028 -330000 ekin = 0.275999298196813 | erot = 0.612161709808654 | epot = -15.5130647502395 | etot = -14.624903742234 -331000 ekin = 0.290024872454789 | erot = 0.607225138478484 | epot = -15.5221537532086 | etot = -14.6249037422753 -332000 ekin = 0.305269328205604 | erot = 0.602027230533244 | epot = -15.5322003010627 | etot = -14.6249037423238 -333000 ekin = 0.320905611375339 | erot = 0.596660303338559 | epot = -15.5424696570899 | etot = -14.624903742376 -334000 ekin = 0.33604943896321 | erot = 0.591221710457376 | epot = -15.5521748918485 | etot = -14.6249037424279 -335000 ekin = 0.349821102707738 | erot = 0.585809355783106 | epot = -15.5605342009668 | etot = -14.624903742476 -336000 ekin = 0.361406827299164 | erot = 0.580516763971287 | epot = -15.5668273337868 | etot = -14.6249037425163 -337000 ekin = 0.370114335989308 | erot = 0.575429096256479 | epot = -15.5704471747923 | etot = -14.6249037425465 -338000 ekin = 0.375418963131897 | erot = 0.570621177508977 | epot = -15.5709438832049 | etot = -14.624903742564 -339000 ekin = 0.37699830668418 | erot = 0.566157982091382 | epot = -15.568060031343 | etot = -14.6249037425674 -340000 ekin = 0.374754278532065 | erot = 0.562097189039008 | epot = -15.5617552101272 | etot = -14.6249037425561 -341000 ekin = 0.368821588409643 | erot = 0.558493134368575 | epot = -15.5522184653083 | etot = -14.62490374253 -342000 ekin = 0.359561251230613 | erot = 0.555400700218343 | epot = -15.5398656939398 | etot = -14.6249037424909 -343000 ekin = 0.34753785325451 | erot = 0.55287778591816 | epot = -15.5253193816136 | etot = -14.6249037424409 -344000 ekin = 0.33348037496383 | erot = 0.55098526840084 | epot = -15.5093693857485 | etot = -14.6249037423838 -345000 ekin = 0.318228359784329 | erot = 0.549783918348214 | epot = -15.4929160204567 | etot = -14.6249037423241 -346000 ekin = 0.302667555547452 | erot = 0.54932843011035 | epot = -15.4768997279244 | etot = -14.6249037422666 -347000 ekin = 0.287661057443402 | erot = 0.549659363310377 | epot = -15.4622241629697 | etot = -14.6249037422159 -348000 ekin = 0.273982878354199 | erot = 0.550794243902694 | epot = -15.4496808644332 | etot = -14.6249037421763 -349000 ekin = 0.262260631617831 | erot = 0.552719272009444 | epot = -15.4398836457781 | etot = -14.6249037421509 -350000 ekin = 0.252932884528162 | erot = 0.555383042233064 | epot = -15.4332196689026 | etot = -14.6249037421414 -351000 ekin = 0.246225113234554 | erot = 0.558693418765032 | epot = -15.4298222741477 | etot = -14.6249037421482 -352000 ekin = 0.242146418558272 | erot = 0.56251834442516 | epot = -15.4295685051533 | etot = -14.6249037421699 -353000 ekin = 0.240507191582667 | erot = 0.566690733134521 | epot = -15.4321016669209 | etot = -14.6249037422037 -354000 ekin = 0.240955911174045 | erot = 0.571016874086999 | epot = -15.436876527507 | etot = -14.6249037422459 -355000 ekin = 0.243030568944153 | erot = 0.575286990707781 | epot = -15.4432213019441 | etot = -14.6249037422922 -356000 ekin = 0.246218336341581 | erot = 0.579286102670368 | epot = -15.4504081813502 | etot = -14.6249037423382 -357000 ekin = 0.250015504867143 | erot = 0.582803084083675 | epot = -15.4577223313313 | etot = -14.6249037423804 -358000 ekin = 0.253980003728345 | erot = 0.585636256510411 | epot = -15.4645200026548 | etot = -14.6249037424161 -359000 ekin = 0.257771924238285 | erot = 0.587595069854159 | epot = -15.470270736536 | etot = -14.6249037424435 -360000 ekin = 0.261178006692362 | erot = 0.588498175296126 | epot = -15.4745799244509 | etot = -14.6249037424624 -361000 ekin = 0.264121303803865 | erot = 0.588169931158578 | epot = -15.4771949774352 | etot = -14.6249037424728 -362000 ekin = 0.266656268947586 | erot = 0.586437607933159 | epot = -15.4779976193564 | etot = -14.6249037424757 -363000 ekin = 0.268947338173594 | erot = 0.583131261385069 | epot = -15.4769823420319 | etot = -14.6249037424733 -364000 ekin = 0.271226723299151 | erot = 0.578087502910549 | epot = -15.4742179686787 | etot = -14.624903742469 -365000 ekin = 0.273728224388467 | erot = 0.571157191000871 | epot = -15.4697891578569 | etot = -14.6249037424676 -366000 ekin = 0.276601570519792 | erot = 0.562216266683795 | epot = -15.4637215796778 | etot = -14.6249037424742 -367000 ekin = 0.279824898676098 | erot = 0.551178529879434 | epot = -15.4559071710478 | etot = -14.6249037424923 -368000 ekin = 0.283144751011445 | erot = 0.538009090150866 | epot = -15.4460575836835 | etot = -14.6249037425212 -369000 ekin = 0.286073979195581 | erot = 0.522737270878923 | epot = -15.4337149926306 | etot = -14.6249037425561 -370000 ekin = 0.287962637923446 | erot = 0.505467651700438 | epot = -15.4183340322116 | etot = -14.6249037425877 -371000 ekin = 0.288129562577258 | erot = 0.486387667907668 | epot = -15.3994209730903 | etot = -14.6249037426054 -372000 ekin = 0.286016270828658 | erot = 0.46576999808234 | epot = -15.3766900115119 | etot = -14.6249037426009 -373000 ekin = 0.28131449291777 | erot = 0.44396824694377 | epot = -15.3501864824323 | etot = -14.6249037425708 -374000 ekin = 0.274029637541844 | erot = 0.421405384814399 | epot = -15.3203387648735 | etot = -14.6249037425173 -375000 ekin = 0.264468317324484 | erot = 0.398555847613824 | epot = -15.2879279073849 | etot = -14.6249037424466 -376000 ekin = 0.253165169268526 | erot = 0.375923572597148 | epot = -15.2539924842331 | etot = -14.6249037423675 -377000 ekin = 0.240780733675043 | erot = 0.354018931407531 | epot = -15.2197034073705 | etot = -14.6249037422879 -378000 ekin = 0.228003530693319 | erot = 0.333337224178132 | epot = -15.1862444970855 | etot = -14.624903742214 -379000 ekin = 0.215478669427759 | erot = 0.314340303318484 | epot = -15.1547227148953 | etot = -14.624903742149 -380000 ekin = 0.203769466320592 | erot = 0.297441561968215 | epot = -15.1261147703835 | etot = -14.6249037420947 -381000 ekin = 0.193344913038784 | erot = 0.28299357961111 | epot = -15.1012422347014 | etot = -14.6249037420515 -382000 ekin = 0.184579097116762 | erot = 0.271277560103732 | epot = -15.0807603992407 | etot = -14.6249037420202 -383000 ekin = 0.177749902922565 | erot = 0.262494318474771 | epot = -15.0651479633987 | etot = -14.6249037420014 -384000 ekin = 0.173031383434342 | erot = 0.256757595375907 | epot = -15.0546927208061 | etot = -14.6249037419958 -385000 ekin = 0.170483112154611 | erot = 0.254091341095815 | epot = -15.049478195254 | etot = -14.6249037420036 -386000 ekin = 0.170046361592112 | erot = 0.254432809989126 | epot = -15.0493829136047 | etot = -14.6249037420235 -387000 ekin = 0.171558026226825 | erot = 0.257642587604582 | epot = -15.0541043558832 | etot = -14.6249037420518 -388000 ekin = 0.174787865438713 | erot = 0.263521131369935 | epot = -15.0632127388923 | etot = -14.6249037420836 -389000 ekin = 0.179494526901415 | erot = 0.271829477565432 | epot = -15.0762277465806 | etot = -14.6249037421138 -390000 ekin = 0.185484901052056 | erot = 0.282310127810448 | epot = -15.0926987710007 | etot = -14.6249037421382 -391000 ekin = 0.192654775275645 | erot = 0.294703495235847 | epot = -15.1122620126676 | etot = -14.6249037421561 -392000 ekin = 0.200990711955422 | erot = 0.308756153372483 | epot = -15.1346506074986 | etot = -14.6249037421707 -393000 ekin = 0.210524629688135 | erot = 0.324219483680835 | epot = -15.1596478555569 | etot = -14.624903742188 -394000 ekin = 0.221250398117909 | erot = 0.340840530849171 | epot = -15.1869946711819 | etot = -14.6249037422148 -395000 ekin = 0.233028912153377 | erot = 0.358349828150776 | epot = -15.2162824825608 | etot = -14.6249037422566 -396000 ekin = 0.24551683484774 | erot = 0.376452447323546 | epot = -15.246873024486 | etot = -14.6249037423147 -397000 ekin = 0.258149646288765 | erot = 0.394827815017102 | epot = -15.277881203691 | etot = -14.6249037423851 -398000 ekin = 0.270192540269911 | erot = 0.413141033371924 | epot = -15.3082373161009 | etot = -14.624903742459 -399000 ekin = 0.280849396853359 | erot = 0.431064534842246 | epot = -15.3368176742213 | etot = -14.6249037425257 -400000 ekin = 0.289399657315015 | erot = 0.448305349544995 | epot = -15.3626087494354 | etot = -14.6249037425754 -401000 ekin = 0.295323233787434 | erot = 0.464631356381723 | epot = -15.3848583327708 | etot = -14.6249037426017 -402000 ekin = 0.298377750400983 | erot = 0.479890206670516 | epot = -15.403171699675 | etot = -14.6249037426035 -403000 ekin = 0.298608046776455 | erot = 0.49401684483596 | epot = -15.4175286341975 | etot = -14.6249037425851 -404000 ekin = 0.296288720275777 | erot = 0.507028747324647 | epot = -15.4282212101546 | etot = -14.6249037425541 -405000 ekin = 0.291819450890444 | erot = 0.519011022290083 | epot = -15.4357342157004 | etot = -14.6249037425198 -406000 ekin = 0.285604695316647 | erot = 0.530095491696055 | epot = -15.4406039295028 | etot = -14.6249037424901 -407000 ekin = 0.2779517950128 | erot = 0.540438449781317 | epot = -15.4432939872644 | etot = -14.6249037424703 -408000 ekin = 0.269015012492784 | erot = 0.550201084797022 | epot = -15.4441198397505 | etot = -14.6249037424607 -409000 ekin = 0.258799683407146 | erot = 0.559535019811769 | epot = -15.4432384456767 | etot = -14.6249037424578 -410000 ekin = 0.247223943172528 | erot = 0.568573648692213 | epot = -15.4407013343199 | etot = -14.6249037424552 -411000 ekin = 0.234219542826923 | erot = 0.577428429926601 | epot = -15.4365517151993 | etot = -14.6249037424458 -412000 ekin = 0.219842320368698 | erot = 0.586188386128906 | epot = -15.4309344489214 | etot = -14.6249037424238 -413000 ekin = 0.20435994837526 | erot = 0.594920843620994 | epot = -15.4241845343832 | etot = -14.6249037423869 -414000 ekin = 0.188290368309867 | erot = 0.603671832826878 | epot = -15.4168659434732 | etot = -14.6249037423364 -415000 ekin = 0.17237708181712 | erot = 0.6124653242919 | epot = -15.4097461483873 | etot = -14.6249037422783 -416000 ekin = 0.157503657631228 | erot = 0.621301324615769 | epot = -15.4037087244679 | etot = -14.6249037422209 -417000 ekin = 0.144565276806289 | erot = 0.630153567597092 | epot = -15.399622586577 | etot = -14.6249037421736 -418000 ekin = 0.134326161306418 | erot = 0.638967960411968 | epot = -15.398197863863 | etot = -14.6249037421446 -419000 ekin = 0.127295713867183 | erot = 0.647663024756225 | epot = -15.3998624807619 | etot = -14.6249037421385 -420000 ekin = 0.123652074079106 | erot = 0.656133267678458 | epot = -15.4046890839134 | etot = -14.6249037421558 -421000 ekin = 0.123230332545554 | erot = 0.664256043547071 | epot = -15.4123901182848 | etot = -14.6249037421922 -422000 ekin = 0.125576493084721 | erot = 0.671901405101286 | epot = -15.4223816404263 | etot = -14.6249037422402 -423000 ekin = 0.130051930466301 | erot = 0.678943694027942 | epot = -15.4338993667852 | etot = -14.6249037422909 -424000 ekin = 0.135961143238876 | erot = 0.685273086227244 | epot = -15.4461379718019 | etot = -14.6249037423358 -425000 ekin = 0.142671659965505 | erot = 0.69080498381162 | epot = -15.4583803861461 | etot = -14.624903742369 -426000 ekin = 0.149699767318722 | erot = 0.695485561348404 | epot = -15.4700890710554 | etot = -14.6249037423883 -427000 ekin = 0.156747049208244 | erot = 0.699292628464214 | epot = -15.4809434200673 | etot = -14.6249037423948 -428000 ekin = 0.163686553654253 | erot = 0.702231990285515 | epot = -15.4908222863323 | etot = -14.6249037423925 -429000 ekin = 0.170509683514413 | erot = 0.70433031530151 | epot = -15.4997437412025 | etot = -14.6249037423866 -430000 ekin = 0.177252892951188 | erot = 0.705626025883397 | epot = -15.507782661217 | etot = -14.6249037423824 -431000 ekin = 0.183925691222352 | erot = 0.706159951516081 | epot = -15.5149893851221 | etot = -14.6249037423836 -432000 ekin = 0.190457851079565 | erot = 0.70596688379378 | epot = -15.5213284772654 | etot = -14.6249037423921 -433000 ekin = 0.196676887388984 | erot = 0.705069371776661 | epot = -15.5266500015729 | etot = -14.6249037424073 -434000 ekin = 0.202317433899364 | erot = 0.703474477741261 | epot = -15.5306956540676 | etot = -14.624903742427 -435000 ekin = 0.207056046506538 | erot = 0.701173837003675 | epot = -15.533133625958 | etot = -14.6249037424478 -436000 ekin = 0.210560164856777 | erot = 0.698146912242834 | epot = -15.5336108195658 | etot = -14.6249037424662 -437000 ekin = 0.212539330538657 | erot = 0.69436686481977 | epot = -15.5318099378375 | etot = -14.6249037424791 -438000 ekin = 0.212789433625669 | erot = 0.689808070113577 | epot = -15.5275012462234 | etot = -14.6249037424842 -439000 ekin = 0.211224885327081 | erot = 0.684454087056256 | epot = -15.5205827148631 | etot = -14.6249037424798 -440000 ekin = 0.207897417438738 | erot = 0.678304934040362 | epot = -15.5111060939442 | etot = -14.6249037424651 -441000 ekin = 0.203002684917544 | erot = 0.671382822497087 | epot = -15.4992892498551 | etot = -14.6249037424404 -442000 ekin = 0.196876783893444 | erot = 0.663735946787442 | epot = -15.485516473087 | etot = -14.6249037424062 -443000 ekin = 0.189984458135359 | erot = 0.655440346227863 | epot = -15.4703285467267 | etot = -14.6249037423634 -444000 ekin = 0.182899715135716 | erot = 0.646600090309095 | epot = -15.4544035477587 | etot = -14.6249037423138 -445000 ekin = 0.176278659807256 | erot = 0.637346059016788 | epot = -15.4385284610839 | etot = -14.6249037422598 -446000 ekin = 0.170824489262319 | erot = 0.627833490901675 | epot = -15.4235617223679 | etot = -14.6249037422039 -447000 ekin = 0.167246115781588 | erot = 0.618238375507795 | epot = -15.4103882334389 | etot = -14.6249037421495 -448000 ekin = 0.166214016011178 | erot = 0.608752709244163 | epot = -15.3998704673549 | etot = -14.6249037420996 -449000 ekin = 0.168318002547464 | erot = 0.599578546515158 | epot = -15.3928002911194 | etot = -14.6249037420568 -450000 ekin = 0.174030350885997 | erot = 0.590920601689278 | epot = -15.3898546945991 | etot = -14.6249037420239 -451000 ekin = 0.183674309612449 | erot = 0.582976972210044 | epot = -15.3915550238259 | etot = -14.6249037420034 -452000 ekin = 0.197394458885136 | erot = 0.575927582957288 | epot = -15.3982257838406 | etot = -14.6249037419982 -453000 ekin = 0.21512429096355 | erot = 0.569920414706644 | epot = -15.4099484476817 | etot = -14.6249037420115 -454000 ekin = 0.236549344238021 | erot = 0.565056494271684 | epot = -15.4265095805563 | etot = -14.6249037420466 -455000 ekin = 0.26107066649251 | erot = 0.561375729613514 | epot = -15.4473501382118 | etot = -14.6249037421058 -456000 ekin = 0.287780783018564 | erot = 0.558846520705737 | epot = -15.4715310459135 | etot = -14.6249037421892 -457000 ekin = 0.315469350478398 | erot = 0.557362227355198 | epot = -15.4977353201268 | etot = -14.6249037422932 -458000 ekin = 0.342675461160486 | erot = 0.556746783054669 | epot = -15.5243259866254 | etot = -14.6249037424102 -459000 ekin = 0.367796771323547 | erot = 0.556770049266648 | epot = -15.5494705631187 | etot = -14.6249037425286 -460000 ekin = 0.389252836428699 | erot = 0.557171234684316 | epot = -15.5713278137469 | etot = -14.6249037426338 -461000 ekin = 0.405683830371934 | erot = 0.557686417732654 | epot = -15.588273990816 | etot = -14.6249037427114 -462000 ekin = 0.41615050976317 | erot = 0.558074591843087 | epot = -15.5991288443563 | etot = -14.62490374275 -463000 ekin = 0.420292029664587 | erot = 0.558136338549784 | epot = -15.6033321109585 | etot = -14.6249037427441 -464000 ekin = 0.418399545177946 | erot = 0.557720582602229 | epot = -15.6010238704766 | etot = -14.6249037426964 -465000 ekin = 0.411377435968348 | erot = 0.556717766126943 | epot = -15.592998944713 | etot = -14.6249037426177 -466000 ekin = 0.400588481170385 | erot = 0.555041504869352 | epot = -15.5805337285651 | etot = -14.6249037425254 -467000 ekin = 0.387608315925592 | erot = 0.552604267016079 | epot = -15.5651163253806 | etot = -14.6249037424389 -468000 ekin = 0.373939506071155 | erot = 0.549294716065804 | epot = -15.5481379645132 | etot = -14.6249037423763 -469000 ekin = 0.360748545285724 | erot = 0.544964338610985 | epot = -15.5306166262455 | etot = -14.6249037423488 -470000 ekin = 0.348685397522308 | erot = 0.539428754142175 | epot = -15.5130178940236 | etot = -14.6249037423592 -471000 ekin = 0.337825425309533 | erot = 0.532485282885717 | epot = -15.4952144505958 | etot = -14.6249037424005 -472000 ekin = 0.327743216876142 | erot = 0.523944004294882 | epot = -15.4765909636297 | etot = -14.6249037424587 -473000 ekin = 0.317695625905302 | erot = 0.513665869846428 | epot = -15.4562652382673 | etot = -14.6249037425156 -474000 ekin = 0.306866206293077 | erot = 0.501599410558585 | epot = -15.4333693594052 | etot = -14.6249037425536 -475000 ekin = 0.294611572516325 | erot = 0.487807694339578 | epot = -15.4073230094157 | etot = -14.6249037425598 -476000 ekin = 0.280654133646186 | erot = 0.472479343852861 | epot = -15.3780372200275 | etot = -14.6249037425285 -477000 ekin = 0.265182667318923 | erot = 0.45592098927681 | epot = -15.3460073990573 | etot = -14.6249037424616 -478000 ekin = 0.248846579356572 | erot = 0.438532535944384 | epot = -15.3122828576692 | etot = -14.6249037423683 -479000 ekin = 0.232654569021534 | erot = 0.420770062233477 | epot = -15.2783283735172 | etot = -14.6249037422622 -480000 ekin = 0.217807844647013 | erot = 0.403103245642619 | epot = -15.2458148324477 | etot = -14.6249037421581 -481000 ekin = 0.205508255202962 | erot = 0.385974572359883 | epot = -15.2163865696323 | etot = -14.6249037420695 -482000 ekin = 0.19678156694235 | erot = 0.369766310247464 | epot = -15.1914516191956 | etot = -14.6249037420058 -483000 ekin = 0.192346943568308 | erot = 0.354778814406232 | epot = -15.1720294999467 | etot = -14.6249037419722 -484000 ekin = 0.192548846646656 | erot = 0.341220938396417 | epot = -15.1586735270114 | etot = -14.6249037419683 -485000 ekin = 0.197351634264863 | erot = 0.329210924265139 | epot = -15.1514663005208 | etot = -14.6249037419908 -486000 ekin = 0.20638457111255 | erot = 0.318784712513067 | epot = -15.1500730256597 | etot = -14.6249037420341 -487000 ekin = 0.219018661980825 | erot = 0.30990833731601 | epot = -15.1538307413881 | etot = -14.6249037420913 -488000 ekin = 0.234457053485159 | erot = 0.302491737711703 | epot = -15.1618525333529 | etot = -14.624903742156 -489000 ekin = 0.251825722281652 | erot = 0.296402451840958 | epot = -15.1731319163445 | etot = -14.6249037422219 -490000 ekin = 0.270257579251709 | erot = 0.291478772534598 | epot = -15.1866400940702 | etot = -14.6249037422839 -491000 ekin = 0.288968023939754 | erot = 0.287542686829926 | epot = -15.2014144531061 | etot = -14.6249037423365 -492000 ekin = 0.307321746939228 | erot = 0.284413165332613 | epot = -15.2166386546469 | etot = -14.6249037423751 -493000 ekin = 0.324889192266724 | erot = 0.281920128741297 | epot = -15.2317130634048 | etot = -14.6249037423968 -494000 ekin = 0.34148788338571 | erot = 0.279918789014045 | epot = -15.2463104147988 | etot = -14.6249037423991 -495000 ekin = 0.357200801059907 | erot = 0.27830316795437 | epot = -15.2604077113965 | etot = -14.6249037423822 -496000 ekin = 0.372363075865331 | erot = 0.277016625443997 | epot = -15.2742834436586 | etot = -14.6249037423492 -497000 ekin = 0.387510424728836 | erot = 0.276056483801624 | epot = -15.2884706508366 | etot = -14.6249037423061 -498000 ekin = 0.40328774473455 | erot = 0.275469725413449 | epot = -15.3036612124099 | etot = -14.6249037422619 -499000 ekin = 0.420322923931638 | erot = 0.275337682298311 | epot = -15.3205643484574 | etot = -14.6249037422275 -500000 ekin = 0.439078206868906 | erot = 0.275749832423424 | epot = -15.3397317815068 | etot = -14.6249037422144 -501000 ekin = 0.459699055392479 | erot = 0.27677002458918 | epot = -15.3613728222145 | etot = -14.6249037422328 -502000 ekin = 0.481887975237045 | erot = 0.278401857022953 | epot = -15.3851935745487 | etot = -14.6249037422887 -503000 ekin = 0.504836001699661 | erot = 0.280562273427077 | epot = -15.4103020175081 | etot = -14.6249037423814 -504000 ekin = 0.527242963720809 | erot = 0.283072520273854 | epot = -15.4352192264968 | etot = -14.6249037425021 -505000 ekin = 0.547444055754969 | erot = 0.285672032586941 | epot = -15.4580198309761 | etot = -14.6249037426342 -506000 ekin = 0.563636138783675 | erot = 0.288055811210013 | epot = -15.4765956927492 | etot = -14.6249037427555 -507000 ekin = 0.574166796919079 | erot = 0.289928574131231 | epot = -15.488999113894 | etot = -14.6249037428437 -508000 ekin = 0.57782515130048 | erot = 0.291063326861402 | epot = -15.4937922210432 | etot = -14.6249037428813 -509000 ekin = 0.574066827021413 | erot = 0.291350176078827 | epot = -15.4903207459603 | etot = -14.6249037428601 -510000 ekin = 0.563118031117931 | erot = 0.290823209378486 | epot = -15.4788449832791 | etot = -14.6249037427827 -511000 ekin = 0.545937816053972 | erot = 0.289659846600232 | epot = -15.4605014053163 | etot = -14.6249037426621 -512000 ekin = 0.52405192466186 | erot = 0.2881539193295 | epot = -15.4371095865088 | etot = -14.6249037425175 -513000 ekin = 0.499300074198536 | erot = 0.28667044386956 | epot = -15.4108742604381 | etot = -14.62490374237 -514000 ekin = 0.473556830411034 | erot = 0.285593013544196 | epot = -15.3840535861943 | etot = -14.6249037422391 -515000 ekin = 0.448481344235602 | erot = 0.285274677057636 | epot = -15.3586597634315 | etot = -14.6249037421383 -516000 ekin = 0.425336124988924 | erot = 0.286000471485298 | epot = -15.3362403385491 | etot = -14.6249037420749 -517000 ekin = 0.404895133581714 | erot = 0.287965811661741 | epot = -15.3177646872924 | etot = -14.624903742049 -518000 ekin = 0.387441371960463 | erot = 0.29127124708814 | epot = -15.3036163611039 | etot = -14.6249037420553 -519000 ekin = 0.372839035853544 | erot = 0.295931281214217 | epot = -15.2936740591526 | etot = -14.6249037420848 -520000 ekin = 0.360656186943702 | erot = 0.301893194868378 | epot = -15.2874531239385 | etot = -14.6249037421264 -521000 ekin = 0.350310207444023 | erot = 0.30906098360492 | epot = -15.2842749332187 | etot = -14.6249037421697 -522000 ekin = 0.341208800540165 | erot = 0.317319408449295 | epot = -15.2834319511959 | etot = -14.6249037422064 -523000 ekin = 0.332862997937259 | erot = 0.326553653087547 | epot = -15.2843203932564 | etot = -14.6249037422316 -524000 ekin = 0.324955020060425 | erot = 0.336661144000779 | epot = -15.2865199063054 | etot = -14.6249037422442 -525000 ekin = 0.317352570821777 | erot = 0.347553686772866 | epot = -15.2898099998417 | etot = -14.6249037422471 -526000 ekin = 0.310071537936686 | erot = 0.359150063852697 | epot = -15.2941253440357 | etot = -14.6249037422464 -527000 ekin = 0.30319969763028 | erot = 0.371361343284829 | epot = -15.2994647831646 | etot = -14.6249037422495 -528000 ekin = 0.296802852838071 | erot = 0.384072970478812 | epot = -15.3057795655796 | etot = -14.6249037422627 -529000 ekin = 0.290839689447108 | erot = 0.397128838352017 | epot = -15.3128722700896 | etot = -14.6249037422905 -530000 ekin = 0.285110822260319 | erot = 0.410322608856454 | epot = -15.320337173449 | etot = -14.6249037423323 -531000 ekin = 0.279260366287054 | erot = 0.423400398731268 | epot = -15.3275645074017 | etot = -14.6249037423834 -532000 ekin = 0.272835705905111 | erot = 0.4360765883685 | epot = -15.3338160367088 | etot = -14.6249037424352 -533000 ekin = 0.265395406955148 | erot = 0.448061330488109 | epot = -15.3383604799197 | etot = -14.6249037424764 -534000 ekin = 0.256640351799918 | erot = 0.459095045026538 | epot = -15.3406391393234 | etot = -14.6249037424969 -535000 ekin = 0.246533633694114 | erot = 0.46898274217995 | epot = -15.3404201183641 | etot = -14.62490374249 -536000 ekin = 0.235373881374739 | erot = 0.477620282695672 | epot = -15.3378979065248 | etot = -14.6249037424544 -537000 ekin = 0.223795203401919 | erot = 0.485006039595133 | epot = -15.3337049853922 | etot = -14.6249037423951 -538000 ekin = 0.212682661997928 | erot = 0.491234540507361 | epot = -15.3288209448297 | etot = -14.6249037423244 -539000 ekin = 0.203011536568405 | erot = 0.496472671627705 | epot = -15.3243879504539 | etot = -14.6249037422578 -540000 ekin = 0.195638496926135 | erot = 0.50092291227584 | epot = -15.3214651514142 | etot = -14.6249037422123 -541000 ekin = 0.191090437374276 | erot = 0.504781043299091 | epot = -15.3207752228744 | etot = -14.624903742201 -542000 ekin = 0.189407567632742 | erot = 0.508197267609352 | epot = -15.3225085774713 | etot = -14.6249037422292 -543000 ekin = 0.190094034781292 | erot = 0.511249275630852 | epot = -15.326247052704 | etot = -14.6249037422918 -544000 ekin = 0.192205662500225 | erot = 0.513933300995961 | epot = -15.3310427058708 | etot = -14.6249037423746 -545000 ekin = 0.194562943958487 | erot = 0.516174993404676 | epot = -15.3356416798199 | etot = -14.6249037424567 -546000 ekin = 0.196033343259802 | erot = 0.517857026727554 | epot = -15.3387941125054 | etot = -14.624903742518 -547000 ekin = 0.19580143908636 | erot = 0.518856237019682 | epot = -15.3395614186506 | etot = -14.6249037425445 -548000 ekin = 0.193552178457268 | erot = 0.519081068513129 | epot = -15.3375369895014 | etot = -14.624903742531 -549000 ekin = 0.189527872077315 | erot = 0.518500763845738 | epot = -15.332932378404 | etot = -14.6249037424809 -550000 ekin = 0.184464697192282 | erot = 0.517160608017039 | epot = -15.3265290476137 | etot = -14.6249037424044 -551000 ekin = 0.179447519613205 | erot = 0.515181377054168 | epot = -15.3195326389812 | etot = -14.6249037423139 -552000 ekin = 0.175731062294521 | erot = 0.512744588095886 | epot = -15.3133793926124 | etot = -14.624903742222 -553000 ekin = 0.174564310045835 | erot = 0.510067400325703 | epot = -15.3095354525117 | etot = -14.6249037421402 -554000 ekin = 0.177036897100683 | erot = 0.507372062614515 | epot = -15.309312701793 | etot = -14.6249037420778 -555000 ekin = 0.183953653121175 | erot = 0.504855061241007 | epot = -15.3137124564046 | etot = -14.6249037420424 -556000 ekin = 0.195740677803854 | erot = 0.502660902829331 | epot = -15.3233053226717 | etot = -14.6249037420385 -557000 ekin = 0.212389174813147 | erot = 0.500864749566708 | epot = -15.338157666447 | etot = -14.6249037420672 -558000 ekin = 0.23344502097276 | erot = 0.499466731744655 | epot = -15.357815494843 | etot = -14.6249037421256 -559000 ekin = 0.258048678277938 | erot = 0.498398734230019 | epot = -15.3813511547153 | etot = -14.6249037422074 -560000 ekin = 0.285022157939512 | erot = 0.49754195086514 | epot = -15.4074678511078 | etot = -14.6249037423032 -561000 ekin = 0.312990622171654 | erot = 0.496751658909336 | epot = -15.4346460234837 | etot = -14.6249037424027 -562000 ekin = 0.340519848729776 | erot = 0.495884310853372 | epot = -15.4613079020793 | etot = -14.6249037424961 -563000 ekin = 0.366249237356 | erot = 0.494821962716246 | epot = -15.4859749426474 | etot = -14.6249037425751 -564000 ekin = 0.389003340228442 | erot = 0.493490109026911 | epot = -15.5073971918898 | etot = -14.6249037426344 -565000 ekin = 0.407871381975258 | erot = 0.491866632343677 | epot = -15.5246417569902 | etot = -14.6249037426713 -566000 ekin = 0.422251605412405 | erot = 0.489981232304148 | epot = -15.537136580402 | etot = -14.6249037426854 -567000 ekin = 0.431863045464181 | erot = 0.48790647095657 | epot = -15.5446732590993 | etot = -14.6249037426785 -568000 ekin = 0.436733840917554 | erot = 0.485743252286935 | epot = -15.5473808358579 | etot = -14.6249037426534 -569000 ekin = 0.437172173178126 | erot = 0.483603786385869 | epot = -15.5456797021773 | etot = -14.6249037426133 -570000 ekin = 0.433727138645419 | erot = 0.481595978794116 | epot = -15.5402268600013 | etot = -14.6249037425617 -571000 ekin = 0.427141808143026 | erot = 0.479812578148763 | epot = -15.5318581287941 | etot = -14.6249037425023 -572000 ekin = 0.418294466660563 | erot = 0.478326721684033 | epot = -15.5215249307844 | etot = -14.6249037424398 -573000 ekin = 0.408121101334992 | erot = 0.477193277920611 | epot = -15.5102181216358 | etot = -14.6249037423802 -574000 ekin = 0.397514818217457 | erot = 0.476453234967311 | epot = -15.4988717955158 | etot = -14.6249037423311 -575000 ekin = 0.387207144489171 | erot = 0.476137354470425 | epot = -15.4882482412599 | etot = -14.6249037423003 -576000 ekin = 0.377649119217314 | erot = 0.476266044933562 | epot = -15.4788189064453 | etot = -14.6249037422944 -577000 ekin = 0.368920817132226 | erot = 0.476844730976786 | epot = -15.4706692904254 | etot = -14.6249037423164 -578000 ekin = 0.360700785230741 | erot = 0.477856883134822 | epot = -15.4634614107288 | etot = -14.6249037423632 -579000 ekin = 0.352319179858308 | erot = 0.479258927577157 | epot = -15.4564818498611 | etot = -14.6249037424256 -580000 ekin = 0.342901425190187 | erot = 0.480981430412776 | epot = -15.4487865980922 | etot = -14.6249037424893 -581000 ekin = 0.331586894252575 | erot = 0.482939076923953 | epot = -15.4394297137127 | etot = -14.6249037425362 -582000 ekin = 0.317784488003998 | erot = 0.485048781539638 | epot = -15.4277370120932 | etot = -14.6249037425495 -583000 ekin = 0.301409490236239 | erot = 0.487252029394849 | epot = -15.4135652621486 | etot = -14.6249037425175 -584000 ekin = 0.283039202393957 | erot = 0.489535511256142 | epot = -15.3974784560878 | etot = -14.6249037424377 -585000 ekin = 0.263933313487419 | erot = 0.491944128120081 | epot = -15.380781183926 | etot = -14.6249037423185 -586000 ekin = 0.245890887800433 | erot = 0.494582820571413 | epot = -15.3653774505512 | etot = -14.6249037421793 -587000 ekin = 0.230956405620081 | erot = 0.497607010278675 | epot = -15.3534671579451 | etot = -14.6249037420464 -588000 ekin = 0.221033841917523 | erot = 0.501205839010948 | epot = -15.3471434228734 | etot = -14.624903741945 -589000 ekin = 0.21750442850326 | erot = 0.505584588308524 | epot = -15.3479927587061 | etot = -14.6249037418943 -590000 ekin = 0.220953423088753 | erot = 0.510952138426249 | epot = -15.3568093034155 | etot = -14.6249037419005 -591000 ekin = 0.231083134064746 | erot = 0.517515644130575 | epot = -15.3735025201508 | etot = -14.6249037419554 -592000 ekin = 0.246829245753635 | erot = 0.525479282587494 | epot = -15.3972122703833 | etot = -14.6249037420422 -593000 ekin = 0.26662894973047 | erot = 0.535039778666637 | epot = -15.4265724705377 | etot = -14.6249037421406 -594000 ekin = 0.288743434935807 | erot = 0.546371032865614 | epot = -15.4600182100362 | etot = -14.6249037422348 -595000 ekin = 0.311533695301779 | erot = 0.559594229359546 | epot = -15.4960316669788 | etot = -14.6249037423175 -596000 ekin = 0.3336243482615 | erot = 0.574736425374656 | epot = -15.5332645160253 | etot = -14.6249037423892 -597000 ekin = 0.353943370598348 | erot = 0.591686591895555 | epot = -15.57053370495 | etot = -14.6249037424561 -598000 ekin = 0.371670846224556 | erot = 0.610160828224063 | epot = -15.6067354169738 | etot = -14.6249037425252 -599000 ekin = 0.386151688530433 | erot = 0.629687420924883 | epot = -15.6407428520557 | etot = -14.6249037426004 -600000 ekin = 0.396824670884606 | erot = 0.649618644309941 | epot = -15.6713470578748 | etot = -14.6249037426803 -601000 ekin = 0.403202067553919 | erot = 0.669171693345246 | epot = -15.6972775036573 | etot = -14.6249037427582 -602000 ekin = 0.40490852829975 | erot = 0.687495721385519 | epot = -15.7173079925082 | etot = -14.6249037428229 -603000 ekin = 0.401765041348506 | erot = 0.703757265562631 | epot = -15.7304260497733 | etot = -14.6249037428622 -604000 ekin = 0.393886240081525 | erot = 0.717231476889702 | epot = -15.7360214598372 | etot = -14.624903742866 -605000 ekin = 0.38175038495462 | erot = 0.727382711583425 | epot = -15.7340368393683 | etot = -14.6249037428302 -606000 ekin = 0.366205114566941 | erot = 0.733917584160155 | epot = -15.725026441486 | etot = -14.6249037427589 -607000 ekin = 0.348389460814908 | erot = 0.736798185090599 | epot = -15.7100913885695 | etot = -14.624903742664 -608000 ekin = 0.329579787369096 | erot = 0.736212623478789 | epot = -15.6906961534101 | etot = -14.6249037425622 -609000 ekin = 0.310994196071395 | erot = 0.73251127479451 | epot = -15.6684092133368 | etot = -14.6249037424709 -610000 ekin = 0.293604835884145 | erot = 0.726125549058765 | epot = -15.6446341273466 | etot = -14.6249037424037 -611000 ekin = 0.278004208601941 | erot = 0.717488389875027 | epot = -15.620396340845 | etot = -14.624903742368 -612000 ekin = 0.264353214552908 | erot = 0.706972008379807 | epot = -15.5962289652964 | etot = -14.6249037423637 -613000 ekin = 0.252415280668165 | erot = 0.694851301360494 | epot = -15.5721703244133 | etot = -14.6249037423847 -614000 ekin = 0.241662201716805 | erot = 0.681294462599433 | epot = -15.5478604067365 | etot = -14.6249037424203 -615000 ekin = 0.231427318529322 | erot = 0.666377599992121 | epot = -15.5227086609789 | etot = -14.6249037424574 -616000 ekin = 0.221078258759027 | erot = 0.650117838829056 | epot = -15.4960998400712 | etot = -14.6249037424831 -617000 ekin = 0.210180390467373 | erot = 0.632518274251274 | epot = -15.4676024072048 | etot = -14.6249037424862 -618000 ekin = 0.19862150965634 | erot = 0.61361713210071 | epot = -15.437142384217 | etot = -14.6249037424599 -619000 ekin = 0.186670442213662 | erot = 0.593532504056955 | epot = -15.4051066886746 | etot = -14.6249037424039 -620000 ekin = 0.174951539061879 | erot = 0.572493952083693 | epot = -15.3723492334697 | etot = -14.6249037423241 -621000 ekin = 0.164335257152339 | erot = 0.550854196820419 | epot = -15.3400931962051 | etot = -14.6249037422323 -622000 ekin = 0.15576803968181 | erot = 0.529078173717942 | epot = -15.3097499555427 | etot = -14.6249037421429 -623000 ekin = 0.150083571178598 | erot = 0.507711807337566 | epot = -15.2826991205848 | etot = -14.6249037420687 -624000 ekin = 0.147843467415458 | erot = 0.487337070698791 | epot = -15.2600842801331 | etot = -14.6249037420188 -625000 ekin = 0.149245521580975 | erot = 0.468521842126362 | epot = -15.242671105704 | etot = -14.6249037419967 -626000 ekin = 0.154116108891131 | erot = 0.451772481731462 | epot = -15.2307923326229 | etot = -14.6249037420003 -627000 ekin = 0.161979086426179 | erot = 0.437494698740194 | epot = -15.2243775271902 | etot = -14.6249037420239 -628000 ekin = 0.172174902879175 | erot = 0.425965324893585 | epot = -15.2230439698325 | etot = -14.6249037420598 -629000 ekin = 0.183995029152314 | erot = 0.417314987668265 | epot = -15.2262137589216 | etot = -14.624903742101 -630000 ekin = 0.196798066694665 | erot = 0.411519917956496 | epot = -15.2332217267944 | etot = -14.6249037421432 -631000 ekin = 0.210082131921541 | erot = 0.408400457423892 | epot = -15.2433863315305 | etot = -14.6249037421851 -632000 ekin = 0.223500184825895 | erot = 0.407624312389087 | epot = -15.2560282394437 | etot = -14.6249037422287 -633000 ekin = 0.236818662196578 | erot = 0.408714108140466 | epot = -15.2704365126158 | etot = -14.6249037422787 -634000 ekin = 0.249833574952738 | erot = 0.411060882466515 | epot = -15.2857981997594 | etot = -14.6249037423402 -635000 ekin = 0.262270239999152 | erot = 0.413946987959646 | epot = -15.3011209703752 | etot = -14.6249037424164 -636000 ekin = 0.273700147361468 | erot = 0.416582412016232 | epot = -15.315186301884 | etot = -14.6249037425063 -637000 ekin = 0.283507856899438 | erot = 0.418156955201586 | epot = -15.3265685547044 | etot = -14.6249037426034 -638000 ekin = 0.290930324554196 | erot = 0.417906927432445 | epot = -15.3337409946819 | etot = -14.6249037426952 -639000 ekin = 0.295171730169193 | erot = 0.415189912094696 | epot = -15.3352653850304 | etot = -14.6249037427665 -640000 ekin = 0.29557345321463 | erot = 0.409556450349033 | epot = -15.3300336463655 | etot = -14.6249037428018 -641000 ekin = 0.291798784614145 | erot = 0.400805216305268 | epot = -15.3175077437091 | etot = -14.6249037427896 -642000 ekin = 0.283982821763269 | erot = 0.389009767281603 | epot = -15.2978963317707 | etot = -14.6249037427259 -643000 ekin = 0.272803834295158 | erot = 0.374510198234827 | epot = -15.2722177751453 | etot = -14.6249037426153 -644000 ekin = 0.259451287281963 | erot = 0.35787030323495 | epot = -15.242225332988 | etot = -14.6249037424711 -645000 ekin = 0.24549053850944 | erot = 0.339807577757951 | epot = -15.2102018585798 | etot = -14.6249037423124 -646000 ekin = 0.232646751227162 | erot = 0.321107525182429 | epot = -15.1786580185707 | etot = -14.6249037421611 -647000 ekin = 0.222545810224123 | erot = 0.302534738054695 | epot = -15.1499842903174 | etot = -14.6249037420386 -648000 ekin = 0.216457466201495 | erot = 0.28475201940792 | epot = -15.1261132275715 | etot = -14.624903741962 -649000 ekin = 0.215087078764636 | erot = 0.268256849270223 | epot = -15.1082476699766 | etot = -14.6249037419418 -650000 ekin = 0.218457489209105 | erot = 0.253342374384717 | epot = -15.0967036055721 | etot = -14.6249037419783 -651000 ekin = 0.225910420497396 | erot = 0.240087663214758 | epot = -15.0909018257745 | etot = -14.6249037420624 -652000 ekin = 0.236236377394498 | erot = 0.228379019530553 | epot = -15.0895191391008 | etot = -14.6249037421757 -653000 ekin = 0.247915496411967 | erot = 0.217959688821804 | epot = -15.0907789275281 | etot = -14.6249037422943 -654000 ekin = 0.259425494352017 | erot = 0.20850030571605 | epot = -15.0928295424613 | etot = -14.6249037423932 -655000 ekin = 0.269554558208103 | erot = 0.199677958220037 | epot = -15.0941362588799 | etot = -14.6249037424518 -656000 ekin = 0.277652649608963 | erot = 0.191249336850249 | epot = -15.0938057289172 | etot = -14.624903742458 -657000 ekin = 0.283765747905228 | erot = 0.183104207684344 | epot = -15.0917736980005 | etot = -14.6249037424109 -658000 ekin = 0.288620908153343 | erot = 0.175289536735983 | epot = -15.088814187211 | etot = -14.6249037423216 -659000 ekin = 0.293459924910629 | erot = 0.16800102740562 | epot = -15.0863646945268 | etot = -14.6249037422106 -660000 ekin = 0.299750121924184 | erot = 0.161545913295631 | epot = -15.0861997773238 | etot = -14.624903742104 -661000 ekin = 0.30882794580141 | erot = 0.156286808494636 | epot = -15.0900184963241 | etot = -14.624903742028 -662000 ekin = 0.321550844182293 | erot = 0.152579955314811 | epot = -15.0990345415002 | etot = -14.6249037420031 -663000 ekin = 0.338040404323162 | erot = 0.150721656676881 | epot = -15.1136658030376 | etot = -14.6249037420375 -664000 ekin = 0.35758869637966 | erot = 0.150913925254683 | epot = -15.1334063637598 | etot = -14.6249037421255 -665000 ekin = 0.378766116436051 | erot = 0.153254852725981 | epot = -15.1569247114091 | etot = -14.6249037422471 -666000 ekin = 0.399716130930405 | erot = 0.157752003177184 | epot = -15.1823718764818 | etot = -14.6249037423742 -667000 ekin = 0.418564373573293 | erot = 0.16435019288794 | epot = -15.2078183089394 | etot = -14.6249037424782 -668000 ekin = 0.433827740573583 | erot = 0.172960630437096 | epot = -15.2316921135496 | etot = -14.6249037425389 -669000 ekin = 0.444701001629416 | erot = 0.183478145303361 | epot = -15.2530828894841 | etot = -14.6249037425513 -670000 ekin = 0.451136418415458 | erot = 0.195778468142474 | epot = -15.2718186290843 | etot = -14.6249037425264 -671000 ekin = 0.453701004148267 | erot = 0.209695862329476 | epot = -15.2883006089635 | etot = -14.6249037424858 -672000 ekin = 0.453273827000247 | erot = 0.224990306459319 | epot = -15.3031678759134 | etot = -14.6249037424539 -673000 ekin = 0.450699702660583 | erot = 0.241319095059427 | epot = -15.3169225401685 | etot = -14.6249037424485 -674000 ekin = 0.446523488449384 | erot = 0.258227823779524 | epot = -15.3296550547041 | etot = -14.6249037424752 -675000 ekin = 0.440889624591433 | erot = 0.275170305160563 | epot = -15.3409636722771 | etot = -14.6249037425251 -676000 ekin = 0.43362448115233 | erot = 0.29155830650734 | epot = -15.3500865302388 | etot = -14.6249037425792 -677000 ekin = 0.424453634855728 | erot = 0.306833290384575 | epot = -15.356190667856 | etot = -14.6249037426157 -678000 ekin = 0.413265176464919 | erot = 0.320546114280114 | epot = -15.3587150333616 | etot = -14.6249037426165 -679000 ekin = 0.400321537246337 | erot = 0.33242808876456 | epot = -15.3576533685843 | etot = -14.6249037425734 -680000 ekin = 0.386341988792883 | erot = 0.342437977069693 | epot = -15.3536837083532 | etot = -14.6249037424906 -681000 ekin = 0.372417408218802 | erot = 0.350774050475061 | epot = -15.3480952010793 | etot = -14.6249037423855 -682000 ekin = 0.359769645089127 | erot = 0.357847594355724 | epot = -15.3425209817278 | etot = -14.624903742283 -683000 ekin = 0.349419724484513 | erot = 0.364223142874507 | epot = -15.3385466095678 | etot = -14.6249037422088 -684000 ekin = 0.341867426589617 | erot = 0.370539083006542 | epot = -15.3373102517771 | etot = -14.6249037421809 -685000 ekin = 0.336892967753541 | erot = 0.377427285880855 | epot = -15.3392239958376 | etot = -14.6249037422032 -686000 ekin = 0.333560575457532 | erot = 0.385449795149527 | epot = -15.3439141128706 | etot = -14.6249037422635 -687000 ekin = 0.330440845245698 | erot = 0.395064019975185 | epot = -15.3504086075581 | etot = -14.6249037423373 -688000 ekin = 0.325996654363842 | erot = 0.406617593545993 | epot = -15.3575179903049 | etot = -14.6249037423951 -689000 ekin = 0.31902375237829 | erot = 0.420363991129875 | epot = -15.3642914859202 | etot = -14.6249037424121 -690000 ekin = 0.309020969989285 | erot = 0.436483939358184 | epot = -15.3704086517225 | etot = -14.624903742375 -691000 ekin = 0.296388973949697 | erot = 0.455097572739975 | epot = -15.3763902889758 | etot = -14.6249037422861 -692000 ekin = 0.282408410636572 | erot = 0.476257707732277 | epot = -15.383569860531 | etot = -14.6249037421622 -693000 ekin = 0.26900853085206 | erot = 0.499923033173746 | epot = -15.3938353060564 | etot = -14.6249037420305 -694000 ekin = 0.258387685788816 | erot = 0.525918285140374 | epot = -15.4092097128507 | etot = -14.6249037419215 -695000 ekin = 0.252576275208241 | erot = 0.553894058809539 | epot = -15.4313740758797 | etot = -14.624903741862 -696000 ekin = 0.253038186234903 | erot = 0.583300660396082 | epot = -15.4612425885006 | etot = -14.6249037418696 -697000 ekin = 0.260392018277369 | erot = 0.613388418368354 | epot = -15.4986841785946 | etot = -14.6249037419489 -698000 ekin = 0.274304391463235 | erot = 0.643241879182175 | epot = -15.5424500127355 | etot = -14.6249037420901 -699000 ekin = 0.293570250406476 | erot = 0.671848180608583 | epot = -15.5903221732866 | etot = -14.6249037422715 -700000 ekin = 0.316355070233252 | erot = 0.698191700482076 | epot = -15.6394505131798 | etot = -14.6249037424645 -701000 ekin = 0.340538337282147 | erot = 0.721359481465404 | epot = -15.6868015613873 | etot = -14.6249037426397 -702000 ekin = 0.364075443764542 | erot = 0.740637254693957 | epot = -15.7296164412326 | etot = -14.6249037427741 -703000 ekin = 0.385294321874673 | erot = 0.755576369453691 | epot = -15.7657744341838 | etot = -14.6249037428555 -704000 ekin = 0.403066716719495 | erot = 0.766018576886853 | epot = -15.7939890364902 | etot = -14.6249037428839 -705000 ekin = 0.416833588997526 | erot = 0.772075474099313 | epot = -15.8138128059661 | etot = -14.6249037428693 -706000 ekin = 0.426510451502379 | erot = 0.774072055031553 | epot = -15.8254862493606 | etot = -14.6249037428266 -707000 ekin = 0.432328070474044 | erot = 0.772470813769757 | epot = -15.8297026270148 | etot = -14.624903742771 -708000 ekin = 0.434671210546527 | erot = 0.76779427950511 | epot = -15.827369232765 | etot = -14.6249037427133 -709000 ekin = 0.433963855684076 | erot = 0.760560754832016 | epot = -15.8194283531749 | etot = -14.6249037426588 -710000 ekin = 0.430621214402443 | erot = 0.751241421805289 | epot = -15.8067663788153 | etot = -14.6249037426076 -711000 ekin = 0.425061028816158 | erot = 0.740240555545361 | epot = -15.7902053269182 | etot = -14.6249037425567 -712000 ekin = 0.417748693286293 | erot = 0.727895913280463 | epot = -15.7705483490692 | etot = -14.6249037425024 -713000 ekin = 0.409245407745191 | erot = 0.714493617369743 | epot = -15.748642767557 | etot = -14.624903742442 -714000 ekin = 0.400233112896686 | erot = 0.700290376393996 | epot = -15.725427231666 | etot = -14.6249037423753 -715000 ekin = 0.391499218629782 | erot = 0.685535269234813 | epot = -15.7019382301699 | etot = -14.6249037423053 -716000 ekin = 0.38387465328674 | erot = 0.670483824808895 | epot = -15.6792622203343 | etot = -14.6249037422387 -717000 ekin = 0.37812966517224 | erot = 0.655399296057453 | epot = -15.6584327034141 | etot = -14.6249037421844 -718000 ekin = 0.374843116813924 | erot = 0.640539821857324 | epot = -15.6402866808232 | etot = -14.6249037421519 -719000 ekin = 0.374271424141617 | erot = 0.626134666228947 | epot = -15.6253098325198 | etot = -14.6249037421492 -720000 ekin = 0.376249546442333 | erot = 0.612356169201708 | epot = -15.6135094578241 | etot = -14.62490374218 -721000 ekin = 0.38015578315651 | erot = 0.599295758360665 | epot = -15.6043552837594 | etot = -14.6249037422422 -722000 ekin = 0.384962761439327 | erot = 0.586951574250039 | epot = -15.5968180780159 | etot = -14.6249037423266 -723000 ekin = 0.38937982338218 | erot = 0.575232003297926 | epot = -15.5895155690983 | etot = -14.6249037424182 -724000 ekin = 0.392071125784558 | erot = 0.563975606697306 | epot = -15.5809504749809 | etot = -14.6249037424991 -725000 ekin = 0.391913283459399 | erot = 0.552983740178749 | epot = -15.5698007661892 | etot = -14.6249037425511 -726000 ekin = 0.388241956533271 | erot = 0.542058916015903 | epot = -15.5552046151099 | etot = -14.6249037425608 -727000 ekin = 0.381032991792366 | erot = 0.531040454531963 | epot = -15.5369771888461 | etot = -14.6249037425218 -728000 ekin = 0.370971903191828 | erot = 0.519829082375402 | epot = -15.515704728005 | etot = -14.6249037424378 -729000 ekin = 0.359388263612358 | erot = 0.50839572980859 | epot = -15.4926877357432 | etot = -14.6249037423222 -730000 ekin = 0.348057580439132 | erot = 0.496773021024845 | epot = -15.4697343436589 | etot = -14.6249037421949 -731000 ekin = 0.338902689198661 | erot = 0.485032671408036 | epot = -15.4488391026864 | etot = -14.6249037420797 -732000 ekin = 0.333649662944534 | erot = 0.473255762297357 | epot = -15.4318091672407 | etot = -14.6249037419988 -733000 ekin = 0.333505576675517 | erot = 0.461504910073763 | epot = -15.4199142287177 | etot = -14.6249037419685 -734000 ekin = 0.338924758983124 | erot = 0.44980725448349 | epot = -15.4136357554609 | etot = -14.6249037419943 -735000 ekin = 0.34951546857607 | erot = 0.438154711902834 | epot = -15.41257392255 | etot = -14.6249037420711 -736000 ekin = 0.364111355273647 | erot = 0.426523255164468 | epot = -15.4155383526203 | etot = -14.6249037421822 -737000 ekin = 0.38099571977356 | erot = 0.414906900972945 | epot = -15.4208063630506 | etot = -14.6249037423041 -738000 ekin = 0.398229414670415 | erot = 0.403356227833102 | epot = -15.4264893849155 | etot = -14.624903742412 -739000 ekin = 0.414005860072354 | erot = 0.392007798568672 | epot = -15.4309174011272 | etot = -14.6249037424862 -740000 ekin = 0.426948743961824 | erot = 0.381091720704565 | epot = -15.4329442071836 | etot = -14.6249037425172 -741000 ekin = 0.43628364768211 | erot = 0.370910229391996 | epot = -15.4320976195812 | etot = -14.6249037425071 -742000 ekin = 0.44185000182603 | erot = 0.361789064611378 | epot = -15.4285428089066 | etot = -14.6249037424692 -743000 ekin = 0.443963491146499 | erot = 0.354012421291944 | epot = -15.4228796548611 | etot = -14.6249037424227 -744000 ekin = 0.4431781085151 | erot = 0.347758127978473 | epot = -15.4158399788814 | etot = -14.6249037423879 -745000 ekin = 0.440021184884499 | erot = 0.343050543545547 | epot = -15.4079754708096 | etot = -14.6249037423796 -746000 ekin = 0.434779146250304 | erot = 0.339744491074578 | epot = -15.3994273797281 | etot = -14.6249037424032 -747000 ekin = 0.427396883604757 | erot = 0.337545938414333 | epot = -15.3898465644716 | etot = -14.6249037424525 -748000 ekin = 0.417523045840628 | erot = 0.336066252171896 | epot = -15.3784930405232 | etot = -14.6249037425107 -749000 ekin = 0.404692764111473 | erot = 0.334898725161965 | epot = -15.3644952318288 | etot = -14.6249037425554 -750000 ekin = 0.388596287616679 | erot = 0.333700338300972 | epot = -15.3472003684819 | etot = -14.6249037425642 -751000 ekin = 0.369348367994066 | erot = 0.332259621152988 | epot = -15.3265117316703 | etot = -14.6249037425233 -752000 ekin = 0.347662572336739 | erot = 0.330533807750213 | epot = -15.3031001225191 | etot = -14.6249037424322 -753000 ekin = 0.324856373470614 | erot = 0.328645172902147 | epot = -15.2784052886784 | etot = -14.6249037423056 -754000 ekin = 0.302664104351481 | erot = 0.326836116136386 | epot = -15.2544039626582 | etot = -14.6249037421703 -755000 ekin = 0.28289840530598 | erot = 0.325392677389915 | epot = -15.2331948247539 | etot = -14.624903742058 -756000 ekin = 0.267052130149329 | erot = 0.324553861439878 | epot = -15.2165097335856 | etot = -14.6249037419964 -757000 ekin = 0.255952872034472 | erot = 0.324427480977821 | epot = -15.2052840950144 | etot = -14.6249037420021 -758000 ekin = 0.24956686325796 | erot = 0.324931841856735 | epot = -15.1994024471903 | etot = -14.6249037420756 -759000 ekin = 0.247007285742123 | erot = 0.325777353497946 | epot = -15.1976883814417 | etot = -14.6249037422016 -760000 ekin = 0.246749335490671 | erot = 0.326494279609754 | epot = -15.1981473574522 | etot = -14.6249037423518 -761000 ekin = 0.247004464362874 | erot = 0.326503456901681 | epot = -15.1984116637553 | etot = -14.6249037424907 -762000 ekin = 0.246168267683208 | erot = 0.325217160868209 | epot = -15.1962891711361 | etot = -14.6249037425847 -763000 ekin = 0.243236270174742 | erot = 0.322149322885115 | epot = -15.1902893356692 | etot = -14.6249037426093 -764000 ekin = 0.238083572628182 | erot = 0.31701054114686 | epot = -15.1799978563319 | etot = -14.6249037425569 -765000 ekin = 0.231530329806237 | erot = 0.309765883621403 | epot = -15.166199955866 | etot = -14.6249037424384 -766000 ekin = 0.225163449189886 | erot = 0.300642577938324 | epot = -15.1507097694095 | etot = -14.6249037422813 -767000 ekin = 0.220947037641663 | erot = 0.29008793628379 | epot = -15.1359387160491 | etot = -14.6249037421236 -768000 ekin = 0.220714417705789 | erot = 0.278690999515915 | epot = -15.1243091592251 | etot = -14.6249037420034 -769000 ekin = 0.225674230585351 | erot = 0.267090069999984 | epot = -15.1176680425334 | etot = -14.6249037419481 -770000 ekin = 0.23606686040605 | erot = 0.255889903618604 | epot = -15.1168605059919 | etot = -14.6249037419673 -771000 ekin = 0.251070223471186 | erot = 0.245606888556646 | epot = -15.1215808540782 | etot = -14.6249037420504 -772000 ekin = 0.268985032794879 | erot = 0.236650197272996 | epot = -15.1305389722379 | etot = -14.62490374217 -773000 ekin = 0.287649902235825 | erot = 0.229335047808992 | epot = -15.1418886923345 | etot = -14.6249037422897 -774000 ekin = 0.304971347443094 | erot = 0.223914516380436 | epot = -15.1537896061991 | etot = -14.6249037423756 -775000 ekin = 0.319422560280909 | erot = 0.220611402281974 | epot = -15.1649377049681 | etot = -14.6249037424052 -776000 ekin = 0.330375903028573 | erot = 0.21963284072128 | epot = -15.1749124861238 | etot = -14.624903742374 -777000 ekin = 0.338182326480891 | erot = 0.221157252264285 | epot = -15.184243321042 | etot = -14.6249037422968 -778000 ekin = 0.343980993504904 | erot = 0.225293639771365 | epot = -15.1941783754794 | etot = -14.6249037422032 -779000 ekin = 0.349294202147107 | erot = 0.232023926336935 | epot = -15.2062218706133 | etot = -14.6249037421292 -780000 ekin = 0.355517983707508 | erot = 0.241146781674954 | epot = -15.2215685074899 | etot = -14.6249037421074 -781000 ekin = 0.363445847501857 | erot = 0.252244149939742 | epot = -15.2405937395992 | etot = -14.6249037421576 -782000 ekin = 0.372957766808644 | erot = 0.264688770757683 | epot = -15.2625502798455 | etot = -14.6249037422792 -783000 ekin = 0.382969267748679 | erot = 0.277702579811651 | epot = -15.2855755900109 | etot = -14.6249037424505 -784000 ekin = 0.391670514066047 | erot = 0.290462881205936 | epot = -15.3070371379042 | etot = -14.6249037426322 -785000 ekin = 0.397003136152503 | erot = 0.30223788282162 | epot = -15.3241447617521 | etot = -14.624903742778 -786000 ekin = 0.397244540913489 | erot = 0.312520082334536 | epot = -15.3346683660962 | etot = -14.6249037428482 -787000 ekin = 0.391525061079608 | erot = 0.321121025638165 | epot = -15.3375498295401 | etot = -14.6249037428223 -788000 ekin = 0.380116514494719 | erot = 0.328198366843703 | epot = -15.3332186240439 | etot = -14.6249037427055 -789000 ekin = 0.364402868103514 | erot = 0.334204933642789 | epot = -15.3235115442733 | etot = -14.624903742527 -790000 ekin = 0.34654788283668 | erot = 0.339772664563971 | epot = -15.3112242897311 | etot = -14.6249037423304 -791000 ekin = 0.328969533927298 | erot = 0.345562661329334 | epot = -15.2994359374173 | etot = -14.6249037421606 -792000 ekin = 0.313783234687856 | erot = 0.352120250332508 | epot = -15.2908072270725 | etot = -14.6249037420521 -793000 ekin = 0.302371973145943 | erot = 0.359769001652795 | epot = -15.2870447168187 | etot = -14.6249037420199 -794000 ekin = 0.295192752069597 | erot = 0.368565036951676 | epot = -15.288661531079 | etot = -14.6249037420577 -795000 ekin = 0.291854072001344 | erot = 0.378316728406861 | epot = -15.2950745425493 | etot = -14.6249037421411 -796000 ekin = 0.291420477240303 | erot = 0.388659220599258 | epot = -15.3049834400759 | etot = -14.6249037422364 -797000 ekin = 0.292835767593939 | erot = 0.39916067791523 | epot = -15.3169001878199 | etot = -14.6249037423108 -798000 ekin = 0.295321690654866 | erot = 0.409429919731993 | epot = -15.329655352731 | etot = -14.6249037423441 -799000 ekin = 0.298615606685225 | erot = 0.41919526946406 | epot = -15.3427146184839 | etot = -14.6249037423347 -800000 ekin = 0.302963113078809 | erot = 0.428333265393227 | epot = -15.3562001207724 | etot = -14.6249037423004 -801000 ekin = 0.30886980741851 | erot = 0.436842111958024 | epot = -15.3706156616477 | etot = -14.6249037422712 -802000 ekin = 0.316711643345927 | erot = 0.444773620895207 | epot = -15.3863890065174 | etot = -14.6249037422763 -803000 ekin = 0.326365730601817 | erot = 0.452151664704948 | epot = -15.4034211376386 | etot = -14.6249037423318 -804000 ekin = 0.337019280357668 | erot = 0.458909057451191 | epot = -15.4208320802431 | etot = -14.6249037424342 -805000 ekin = 0.347244531512514 | erot = 0.464865921885975 | epot = -15.4370141959586 | etot = -14.6249037425601 -806000 ekin = 0.355321558015248 | erot = 0.469755825323994 | epot = -15.4499811260149 | etot = -14.6249037426756 -807000 ekin = 0.359699244804389 | erot = 0.47328839989947 | epot = -15.4578913874509 | etot = -14.624903742747 -808000 ekin = 0.359442919436746 | erot = 0.475225772200574 | epot = -15.4595724343886 | etot = -14.6249037427513 -809000 ekin = 0.354532149710961 | erot = 0.475448148012512 | epot = -15.454884040406 | etot = -14.6249037426825 -810000 ekin = 0.345927121515436 | erot = 0.473990365430211 | epot = -15.4448212294985 | etot = -14.6249037425528 -811000 ekin = 0.335391497319453 | erot = 0.471042355239708 | epot = -15.4313375949476 | etot = -14.6249037423884 -812000 ekin = 0.325122479809057 | erot = 0.466917662639856 | epot = -15.416943884672 | etot = -14.6249037422231 -813000 ekin = 0.31728183261798 | erot = 0.462001954840949 | epot = -15.4041875295485 | etot = -14.6249037420896 -814000 ekin = 0.313538689250887 | erot = 0.456696276151244 | epot = -15.3951387074148 | etot = -14.6249037420127 -815000 ekin = 0.314725301426621 | erot = 0.451368238943233 | epot = -15.3909972823742 | etot = -14.6249037420043 -816000 ekin = 0.320674745952002 | erot = 0.446320054204494 | epot = -15.3918985422185 | etot = -14.624903742062 -817000 ekin = 0.330264402529528 | erot = 0.441777145069773 | epot = -15.3969452897695 | etot = -14.6249037421702 -818000 ekin = 0.341643112115936 | erot = 0.437896324121525 | epot = -15.404443178542 | etot = -14.6249037423045 -819000 ekin = 0.352584467965967 | erot = 0.43478868897098 | epot = -15.4122768993742 | etot = -14.6249037424372 -820000 ekin = 0.360890006680921 | erot = 0.432549774286878 | epot = -15.4183435235106 | etot = -14.6249037425428 -821000 ekin = 0.364764924967774 | erot = 0.431288293594747 | epot = -15.4209569611646 | etot = -14.624903742602 -822000 ekin = 0.36310132304895 | erot = 0.431144612410167 | epot = -15.419149678065 | etot = -14.6249037426059 -823000 ekin = 0.355627506072524 | erot = 0.432293079211457 | epot = -15.4128243278395 | etot = -14.6249037425555 -824000 ekin = 0.342909508000251 | erot = 0.43492611819946 | epot = -15.4027393686613 | etot = -14.6249037424616 -825000 ekin = 0.326218347991422 | erot = 0.439222871855163 | epot = -15.3903449621884 | etot = -14.6249037423418 -826000 ekin = 0.307298067027383 | erot = 0.445309293137298 | epot = -15.3775111023813 | etot = -14.6249037422166 -827000 ekin = 0.288081469810276 | erot = 0.453218819733682 | epot = -15.3662040316499 | etot = -14.6249037421059 -828000 ekin = 0.270403517644502 | erot = 0.462862712071626 | epot = -15.358169971742 | etot = -14.6249037420259 -829000 ekin = 0.255756724313645 | erot = 0.474017347276416 | epot = -15.354677813577 | etot = -14.624903741987 -830000 ekin = 0.245120383539843 | erot = 0.486332016594477 | epot = -15.3563561421264 | etot = -14.6249037419921 -831000 ekin = 0.238883956789448 | erot = 0.499357971990473 | epot = -15.3631456708169 | etot = -14.624903742037 -832000 ekin = 0.236868645662797 | erot = 0.512595315428093 | epot = -15.3743677032021 | etot = -14.6249037421112 -833000 ekin = 0.238435989568506 | erot = 0.525550909043033 | epot = -15.3888906408115 | etot = -14.6249037421999 -834000 ekin = 0.242658569127625 | erot = 0.537797737790879 | epot = -15.405360049206 | etot = -14.6249037422875 -835000 ekin = 0.248518315375854 | erot = 0.549024910270133 | epot = -15.4224469680061 | etot = -14.6249037423601 -836000 ekin = 0.255095050222772 | erot = 0.559068449138662 | epot = -15.4390672417693 | etot = -14.6249037424078 -837000 ekin = 0.261712817640357 | erot = 0.567916383628495 | epot = -15.4545329436954 | etot = -14.6249037424265 -838000 ekin = 0.268023056778553 | erot = 0.575686784519793 | epot = -15.4686135837165 | etot = -14.6249037424181 -839000 ekin = 0.27401827032314 | erot = 0.582582979367263 | epot = -15.4815049920797 | etot = -14.6249037423893 -840000 ekin = 0.279983100774025 | erot = 0.588834754839967 | epot = -15.4937215979637 | etot = -14.6249037423497 -841000 ekin = 0.286398274628728 | erot = 0.59463702433131 | epot = -15.5059390412703 | etot = -14.6249037423103 -842000 ekin = 0.293816650983536 | erot = 0.600098453281003 | epot = -15.5188188465462 | etot = -14.6249037422817 -843000 ekin = 0.302726774569486 | erot = 0.605208920749049 | epot = -15.5328394375911 | etot = -14.6249037422726 -844000 ekin = 0.313421069061172 | erot = 0.609833296485301 | epot = -15.5481581078353 | etot = -14.6249037422889 -845000 ekin = 0.325887895394733 | erot = 0.613733577818912 | epot = -15.5645252155452 | etot = -14.6249037423315 -846000 ekin = 0.339752400962196 | erot = 0.616615984720894 | epot = -15.5812721280789 | etot = -14.6249037423958 -847000 ekin = 0.354292335348444 | erot = 0.61819407953295 | epot = -15.5973901573525 | etot = -14.6249037424711 -848000 ekin = 0.368542667423182 | erot = 0.618254639142345 | epot = -15.6117010491079 | etot = -14.6249037425423 -849000 ekin = 0.381474241843926 | erot = 0.616711095273524 | epot = -15.6230890797115 | etot = -14.6249037425941 -850000 ekin = 0.392198266661771 | erot = 0.613631554979492 | epot = -15.6307335642567 | etot = -14.6249037426155 -851000 ekin = 0.40012936773711 | erot = 0.609234588535909 | epot = -15.6342676988772 | etot = -14.6249037426042 -852000 ekin = 0.405049998797733 | erot = 0.603854451146916 | epot = -15.633808192512 | etot = -14.6249037425674 -853000 ekin = 0.407056563941561 | erot = 0.597885334648249 | epot = -15.6298456411086 | etot = -14.6249037425187 -854000 ekin = 0.406415158938748 | erot = 0.591718979210661 | epot = -15.6230378806227 | etot = -14.6249037424733 -855000 ekin = 0.403390043512858 | erot = 0.585690332509252 | epot = -15.6139841184645 | etot = -14.6249037424423 -856000 ekin = 0.398116166002726 | erot = 0.580042463525136 | epot = -15.6030623719571 | etot = -14.6249037424293 -857000 ekin = 0.390568016159967 | erot = 0.574915889724967 | epot = -15.5903876483136 | etot = -14.6249037424286 -858000 ekin = 0.380638245096081 | erot = 0.570361176880736 | epot = -15.5759031644054 | etot = -14.6249037424286 -859000 ekin = 0.368297168914653 | erot = 0.566367903415377 | epot = -15.5595688147452 | etot = -14.6249037424151 -860000 ekin = 0.353771484486348 | erot = 0.56289933566704 | epot = -15.5415745625316 | etot = -14.6249037423782 -861000 ekin = 0.337668189076058 | erot = 0.55992119051608 | epot = -15.522493121908 | etot = -14.6249037423159 -862000 ekin = 0.320982687534733 | erot = 0.55741511441171 | epot = -15.5033015441828 | etot = -14.6249037422364 -863000 ekin = 0.304965814691443 | erot = 0.555372641472256 | epot = -15.4852421983211 | etot = -14.6249037421574 -864000 ekin = 0.290872653003623 | erot = 0.553772082573975 | epot = -15.4695484776774 | etot = -14.6249037420998 -865000 ekin = 0.279660774249956 | erot = 0.552546988655193 | epot = -15.4571115049878 | etot = -14.6249037420826 -866000 ekin = 0.271730646599716 | erot = 0.551558423386406 | epot = -15.448192812101 | etot = -14.6249037421149 -867000 ekin = 0.266795961580917 | erot = 0.550582916186157 | epot = -15.44228261996 | etot = -14.624903742193 -868000 ekin = 0.263936467175858 | erot = 0.549323573880104 | epot = -15.4381637833559 | etot = -14.6249037422999 -869000 ekin = 0.261831470221839 | erot = 0.547444696243376 | epot = -15.4341799088748 | etot = -14.6249037424095 -870000 ekin = 0.259116433169107 | erot = 0.544622620095519 | epot = -15.4286427957584 | etot = -14.6249037424938 -871000 ekin = 0.25476611341807 | erot = 0.540599894777859 | epot = -15.4202697507262 | etot = -14.6249037425303 -872000 ekin = 0.248397230690975 | erot = 0.535228153627688 | epot = -15.4085291268279 | etot = -14.6249037425092 -873000 ekin = 0.240403953825284 | erot = 0.528487826572668 | epot = -15.3937955228335 | etot = -14.6249037424356 -874000 ekin = 0.23188412578265 | erot = 0.52047931782111 | epot = -15.3772671859324 | etot = -14.6249037423286 -875000 ekin = 0.224371090312889 | erot = 0.51138848970078 | epot = -15.3606633222303 | etot = -14.6249037422166 -876000 ekin = 0.219440883379249 | erot = 0.501436812694071 | epot = -15.3457814382023 | etot = -14.624903742129 -877000 ekin = 0.218302972735591 | erot = 0.490831150818216 | epot = -15.3340378656416 | etot = -14.6249037420878 -878000 ekin = 0.221492456262699 | erot = 0.479728387736622 | epot = -15.3261245861005 | etot = -14.6249037421012 -879000 ekin = 0.228756262274367 | erot = 0.468225594693664 | epot = -15.3218855991281 | etot = -14.6249037421601 -880000 ekin = 0.239169160088235 | erot = 0.456378166082075 | epot = -15.3204510684122 | etot = -14.6249037422419 -881000 ekin = 0.251443176614178 | erot = 0.444238659512956 | epot = -15.3205855784449 | etot = -14.6249037423178 -882000 ekin = 0.264330844663498 | erot = 0.431901289695958 | epot = -15.3211358767212 | etot = -14.6249037423617 -883000 ekin = 0.276992343361542 | erot = 0.419534292632451 | epot = -15.3214303783535 | etot = -14.6249037423595 -884000 ekin = 0.289210952362652 | erot = 0.407386172192625 | epot = -15.321500866868 | etot = -14.6249037423127 -885000 ekin = 0.301394205510712 | erot = 0.395760928443729 | epot = -15.3220588761924 | etot = -14.6249037422379 -886000 ekin = 0.314368599205627 | erot = 0.384968165379708 | epot = -15.3242405067466 | etot = -14.6249037421612 -887000 ekin = 0.329038341775269 | erot = 0.375262338090432 | epot = -15.3292044219761 | etot = -14.6249037421104 -888000 ekin = 0.3460151111552 | erot = 0.366788650327974 | epot = -15.337707503589 | etot = -14.6249037421058 -889000 ekin = 0.365329693883301 | erot = 0.359550947377142 | epot = -15.3497843834163 | etot = -14.6249037421559 -890000 ekin = 0.386310696217007 | erot = 0.353410826837943 | epot = -15.364625265308 | etot = -14.6249037422531 -891000 ekin = 0.40766808705505 | erot = 0.348119126036606 | epot = -15.3806909554677 | etot = -14.624903742376 -892000 ekin = 0.427761236103282 | erot = 0.343372786941987 | epot = -15.3960377655415 | etot = -14.6249037424963 -893000 ekin = 0.444977236019449 | erot = 0.33888352569265 | epot = -15.4087645042971 | etot = -14.624903742585 -894000 ekin = 0.458112158680458 | erot = 0.334441343917185 | epot = -15.4174572452192 | etot = -14.6249037426215 -895000 ekin = 0.466648008331883 | erot = 0.329956933565113 | epot = -15.4215086844963 | etot = -14.6249037425993 -896000 ekin = 0.470850232519732 | erot = 0.325472374552551 | epot = -15.4212263495988 | etot = -14.6249037425265 -897000 ekin = 0.471664510488006 | erot = 0.321137893833118 | epot = -15.4177061467451 | etot = -14.624903742424 -898000 ekin = 0.470447771985807 | erot = 0.317161282107798 | epot = -15.4125127964124 | etot = -14.6249037423188 -899000 ekin = 0.468609320535655 | erot = 0.313743247831532 | epot = -15.407256310605 | etot = -14.6249037422378 -900000 ekin = 0.467255363896805 | erot = 0.311015004595507 | epot = -15.403174110693 | etot = -14.6249037422007 -901000 ekin = 0.466923299456955 | erot = 0.308993431077898 | epot = -15.4008204727509 | etot = -14.624903742216 -902000 ekin = 0.467466399705958 | erot = 0.307564919774008 | epot = -15.3999350617591 | etot = -14.6249037422791 -903000 ekin = 0.468112799245358 | erot = 0.306502589385531 | epot = -15.3995191310034 | etot = -14.6249037423725 -904000 ekin = 0.467682260080958 | erot = 0.305513914729679 | epot = -15.398099917282 | etot = -14.6249037424714 -905000 ekin = 0.464906903208091 | erot = 0.304308207539486 | epot = -15.3941188532968 | etot = -14.6249037425492 -906000 ekin = 0.458775313350218 | erot = 0.302667437698602 | epot = -15.386346493633 | etot = -14.6249037425842 -907000 ekin = 0.448811106797068 | erot = 0.300501710925682 | epot = -15.3742165602888 | etot = -14.624903742566 -908000 ekin = 0.435212888278286 | erot = 0.297873922704326 | epot = -15.3579905534802 | etot = -14.6249037424976 -909000 ekin = 0.418821166578994 | erot = 0.294986492955548 | epot = -15.338711401929 | etot = -14.6249037423944 -910000 ekin = 0.400928155652122 | erot = 0.292134043124749 | epot = -15.3179659410565 | etot = -14.6249037422796 -911000 ekin = 0.382990731318649 | erot = 0.289635345607696 | epot = -15.2975298191034 | etot = -14.6249037421771 -912000 ekin = 0.366329155569864 | erot = 0.28776245704618 | epot = -15.2789953547216 | etot = -14.6249037421055 -913000 ekin = 0.351888443631227 | erot = 0.286683662572629 | epot = -15.2634758482788 | etot = -14.624903742075 -914000 ekin = 0.340111462795541 | erot = 0.286431278414487 | epot = -15.2514464832954 | etot = -14.6249037420854 -915000 ekin = 0.330936398540049 | erot = 0.286898247267082 | epot = -15.2427383879356 | etot = -14.6249037421284 -916000 ekin = 0.323899271601486 | erot = 0.287861143478391 | epot = -15.2366641572706 | etot = -14.6249037421907 -917000 ekin = 0.318302399047232 | erot = 0.289022784865087 | epot = -15.2322289261691 | etot = -14.6249037422568 -918000 ekin = 0.313403328231463 | erot = 0.290065205370856 | epot = -15.2283722759152 | etot = -14.6249037423129 -919000 ekin = 0.308582994046901 | erot = 0.290702987753991 | epot = -15.2241897241499 | etot = -14.624903742349 -920000 ekin = 0.303462620954368 | erot = 0.290727692025052 | epot = -15.2190940553399 | etot = -14.6249037423605 -921000 ekin = 0.297952758522196 | erot = 0.290036267627498 | epot = -15.2128927684978 | etot = -14.6249037423481 -922000 ekin = 0.29223232916649 | erot = 0.28863969692327 | epot = -15.2057757684075 | etot = -14.6249037423178 -923000 ekin = 0.286668877937277 | erot = 0.286652137103424 | epot = -15.1982247573193 | etot = -14.6249037422786 -924000 ekin = 0.28170186865761 | erot = 0.28426466875578 | epot = -15.1908702796539 | etot = -14.6249037422405 -925000 ekin = 0.277717553237222 | erot = 0.281710557645316 | epot = -15.1843318530947 | etot = -14.6249037422121 -926000 ekin = 0.274945509178671 | erot = 0.279230091666927 | epot = -15.1790793430443 | etot = -14.6249037421988 -927000 ekin = 0.273402631519431 | erot = 0.277042382113437 | epot = -15.1753487558338 | etot = -14.624903742201 -928000 ekin = 0.272900230271358 | erot = 0.275329232545622 | epot = -15.1731332050314 | etot = -14.6249037422144 -929000 ekin = 0.273115271901108 | erot = 0.274232799537457 | epot = -15.1722518136694 | etot = -14.6249037422308 -930000 ekin = 0.273710515356084 | erot = 0.273865029644295 | epot = -15.1724792872405 | etot = -14.6249037422402 -931000 ekin = 0.274474107140427 | erot = 0.274323617229163 | epot = -15.1737014666035 | etot = -14.6249037422339 -932000 ekin = 0.275440857683932 | erot = 0.275707340217243 | epot = -15.1760519401082 | etot = -14.624903742207 -933000 ekin = 0.276957575782685 | erot = 0.278123705988738 | epot = -15.1799850239326 | etot = -14.6249037421612 -934000 ekin = 0.279664435384645 | erot = 0.281683992543778 | epot = -15.186252170033 | etot = -14.6249037421046 -935000 ekin = 0.284382433297568 | erot = 0.286484503522986 | epot = -15.1957706788719 | etot = -14.6249037420513 -936000 ekin = 0.291920557580458 | erot = 0.292577187598382 | epot = -15.2094014871973 | etot = -14.6249037420184 -937000 ekin = 0.302840159170039 | erot = 0.299936553990847 | epot = -15.2276804551831 | etot = -14.6249037420222 -938000 ekin = 0.317231541763436 | erot = 0.308432066638964 | epot = -15.2505673504756 | etot = -14.6249037420732 -939000 ekin = 0.334562734704465 | erot = 0.317815317270747 | epot = -15.277281794148 | etot = -14.6249037421728 -940000 ekin = 0.35364952180483 | erot = 0.327729086105148 | epot = -15.3062823502215 | etot = -14.6249037423115 -941000 ekin = 0.372770367646405 | erot = 0.337741122003473 | epot = -15.3354152321199 | etot = -14.62490374247 -942000 ekin = 0.389915662531244 | erot = 0.34739974979893 | epot = -15.3622191549524 | etot = -14.6249037426222 -943000 ekin = 0.403126345738701 | erot = 0.356302369933728 | epot = -15.3843324584131 | etot = -14.6249037427407 -944000 ekin = 0.410851754405684 | erot = 0.364163156178504 | epot = -15.3999186533874 | etot = -14.6249037428032 -945000 ekin = 0.41224792095984 | erot = 0.370864511414023 | epot = -15.4080161751712 | etot = -14.6249037427973 -946000 ekin = 0.407348747779498 | erot = 0.376479254456982 | epot = -15.4087317449601 | etot = -14.6249037427236 -947000 ekin = 0.397071124216324 | erot = 0.381256899558077 | epot = -15.4032317663699 | etot = -14.6249037425955 -948000 ekin = 0.38305345572573 | erot = 0.385576026490354 | epot = -15.3935332246524 | etot = -14.6249037424363 -949000 ekin = 0.367364810069699 | erot = 0.389872987608877 | epot = -15.3821415399525 | etot = -14.624903742274 -950000 ekin = 0.352149150210297 | erot = 0.394562514442363 | epot = -15.3716154067876 | etot = -14.6249037421349 -951000 ekin = 0.339280178142264 | erot = 0.399966938640697 | epot = -15.364150858822 | etot = -14.6249037420391 -952000 ekin = 0.330096120378427 | erot = 0.406268489131276 | epot = -15.3612683515059 | etot = -14.6249037419962 -953000 ekin = 0.32526183166892 | erot = 0.413492937870355 | epot = -15.3636585115441 | etot = -14.6249037420048 -954000 ekin = 0.324774911928697 | erot = 0.421526046052984 | epot = -15.3712047000353 | etot = -14.6249037420537 -955000 ekin = 0.328098170458837 | erot = 0.430156858160225 | epot = -15.3831587707443 | etot = -14.6249037421253 -956000 ekin = 0.334370903123397 | erot = 0.439135698167057 | epot = -15.3984103434923 | etot = -14.6249037422019 -957000 ekin = 0.342633913360124 | erot = 0.44823123979963 | epot = -15.4157688954295 | etot = -14.6249037422697 -958000 ekin = 0.352004139469675 | erot = 0.457271615168161 | epot = -15.4341794969606 | etot = -14.6249037423228 -959000 ekin = 0.361755395785515 | erot = 0.466159587644429 | epot = -15.4528187257936 | etot = -14.6249037423637 -960000 ekin = 0.37129634840351 | erot = 0.474860087933521 | epot = -15.4710601787381 | etot = -14.624903742401 -961000 ekin = 0.380073790913227 | erot = 0.483367158176183 | epot = -15.4883446915346 | etot = -14.6249037424452 -962000 ekin = 0.387455548951145 | erot = 0.491663490522134 | epot = -15.5040227819764 | etot = -14.6249037425031 -963000 ekin = 0.392654097313064 | erot = 0.499687295633833 | epot = -15.5172451355218 | etot = -14.6249037425749 -964000 ekin = 0.394737939560465 | erot = 0.507318071997362 | epot = -15.52695975421 | etot = -14.6249037426522 -965000 ekin = 0.392748486468401 | erot = 0.514386334668901 | epot = -15.5320385638565 | etot = -14.6249037427192 -966000 ekin = 0.385905473254046 | erot = 0.520705106529118 | epot = -15.5315143225403 | etot = -14.6249037427571 -967000 ekin = 0.373852021646475 | erot = 0.526114369236053 | epot = -15.5248701336312 | etot = -14.6249037427486 -968000 ekin = 0.356869417136842 | erot = 0.530525868586128 | epot = -15.5122990284073 | etot = -14.6249037426844 -969000 ekin = 0.335986889835165 | erot = 0.533955228285004 | epot = -15.4948458606873 | etot = -14.6249037425671 -970000 ekin = 0.312927788673001 | erot = 0.536531428462375 | epot = -15.4743629595488 | etot = -14.6249037424134 -971000 ekin = 0.289872105907279 | erot = 0.538479668129898 | epot = -15.4532555162884 | etot = -14.6249037422512 -972000 ekin = 0.269070232406882 | erot = 0.5400808983618 | epot = -15.4340548728819 | etot = -14.6249037421133 -973000 ekin = 0.252397022945549 | erot = 0.54161782723096 | epot = -15.4189185922049 | etot = -14.6249037420284 -974000 ekin = 0.240964852822479 | erot = 0.543321042151966 | epot = -15.4091896369876 | etot = -14.6249037420132 -975000 ekin = 0.23490216482404 | erot = 0.545328986458525 | epot = -15.4051348933507 | etot = -14.6249037420682 -976000 ekin = 0.233353466621782 | erot = 0.547671994179659 | epot = -15.4059292029795 | etot = -14.6249037421781 -977000 ekin = 0.234692201089083 | erot = 0.550284513866881 | epot = -15.4098804572724 | etot = -14.6249037423164 -978000 ekin = 0.236887903180263 | erot = 0.553043053342472 | epot = -15.4148346989741 | etot = -14.6249037424514 -979000 ekin = 0.237945797131594 | erot = 0.555821040963433 | epot = -15.4186705806471 | etot = -14.6249037425521 -980000 ekin = 0.236334546963168 | erot = 0.558547250125055 | epot = -15.4197855396823 | etot = -14.6249037425941 -981000 ekin = 0.231322843924042 | erot = 0.561252158432646 | epot = -15.4174787449221 | etot = -14.6249037425654 -982000 ekin = 0.223154169544533 | erot = 0.564087592074629 | epot = -15.4121455040889 | etot = -14.6249037424697 -983000 ekin = 0.213008719539339 | erot = 0.567310103886669 | epot = -15.4052225657532 | etot = -14.6249037423272 -984000 ekin = 0.202740628548441 | erot = 0.571227590062575 | epot = -15.3988719607827 | etot = -14.6249037421716 -985000 ekin = 0.194435665154694 | erot = 0.576119771487871 | epot = -15.3954591786846 | etot = -14.624903742042 -986000 ekin = 0.189894304519126 | erot = 0.58215285815263 | epot = -15.3969509046435 | etot = -14.6249037419717 -987000 ekin = 0.190182835424942 | erot = 0.589313613953793 | epot = -15.4044001913571 | etot = -14.6249037419783 -988000 ekin = 0.195390213187374 | erot = 0.597385005524008 | epot = -15.4176789607685 | etot = -14.6249037420571 -989000 ekin = 0.204671362362343 | erot = 0.605974905403727 | epot = -15.4355500099486 | etot = -14.6249037421825 -990000 ekin = 0.216563394578633 | erot = 0.614593273597528 | epot = -15.4560604104923 | etot = -14.6249037423162 -991000 ekin = 0.229465191861939 | erot = 0.622757127490605 | epot = -15.477126061773 | etot = -14.6249037424204 -992000 ekin = 0.24211427112869 | erot = 0.630092599916922 | epot = -15.4971106135161 | etot = -14.6249037424704 -993000 ekin = 0.253902581479766 | erot = 0.636403793831493 | epot = -15.5152101177725 | etot = -14.6249037424612 -994000 ekin = 0.264939510335544 | erot = 0.641689105047928 | epot = -15.5315323577914 | etot = -14.6249037424079 -995000 ekin = 0.275864888578878 | erot = 0.646102898208469 | epot = -15.5468715291258 | etot = -14.6249037423384 -996000 ekin = 0.287497820769962 | erot = 0.649877086441122 | epot = -15.562278649495 | etot = -14.6249037422839 -997000 ekin = 0.300450307467282 | erot = 0.653227423573226 | epot = -15.578581473309 | etot = -14.6249037422685 -998000 ekin = 0.314829914377661 | erot = 0.656270894957595 | epot = -15.5960045516386 | etot = -14.6249037423033 -999000 ekin = 0.330110494517446 | erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851 -1000000 ekin = 0.345190458651126 | erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498 - 1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06 -Loop time of 17.6535 on 4 procs for 1000000 steps with 10 atoms - -Performance: 48942.073 tau/day, 56645.918 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.58208 | 6.2309 | 11.391 | 182.5 | 35.30 -Bond | 0.087981 | 0.28429 | 0.45668 | 28.3 | 1.61 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.8415 | 2.1564 | 2.4456 | 17.3 | 12.21 -Output | 1.5e-05 | 2.275e-05 | 2.6e-05 | 0.0 | 0.00 -Modify | 0.1751 | 0.91094 | 1.6034 | 60.5 | 5.16 -Other | | 8.071 | | | 45.72 - -Nlocal: 2.5 ave 5.0 max 0.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10.0 max 5.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 16.0 ave 30.0 max 0.0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 64 -Ave neighs/atom = 6.4 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:17 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type deleted file mode 100644 index a8412eef07..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type +++ /dev/null @@ -1,130 +0,0 @@ -# LAMMPS data file -26 atoms -26 ellipsoids -24 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1 -3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1 -4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1 -5 1 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1 -6 2 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1 -7 3 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1 -8 4 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1 -9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1 -10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1 -11 3 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1 -12 4 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1 -13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1 -14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1 -15 1 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1 -16 2 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1 -17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1 -18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1 -19 1 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1 -20 2 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1 -21 3 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1 -22 4 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1 -23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1 -24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1 -25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1 -26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1 - -# Atom-ID, translational, rotational velocity -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01 -11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01 -12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01 -13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01 -14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00 -15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00 -16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00 -17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00 -18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00 -19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00 -20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00 -21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00 -22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00 -23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00 -24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00 -25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00 -26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 5 6 -6 1 6 7 -7 1 7 8 -8 1 8 9 -9 1 9 10 -10 1 10 11 -11 1 11 12 -12 1 12 13 -13 1 14 15 -14 1 15 16 -15 1 16 17 -16 1 17 18 -17 1 18 19 -18 1 19 20 -19 1 20 21 -20 1 21 22 -21 1 22 23 -22 1 23 24 -23 1 24 25 -24 1 25 26 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type deleted file mode 100644 index b4d622ac46..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type +++ /dev/null @@ -1,130 +0,0 @@ -# LAMMPS data file -26 atoms -26 ellipsoids -24 bonds - -8 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1 -3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1 -4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1 -5 5 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1 -6 6 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1 -7 7 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1 -8 8 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1 -9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1 -10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1 -11 7 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1 -12 8 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1 -13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1 -14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1 -15 5 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1 -16 6 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1 -17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1 -18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1 -19 5 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1 -20 6 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1 -21 7 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1 -22 8 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1 -23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1 -24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1 -25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1 -26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1 - -# Atom-ID, translational, rotational velocity -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01 -11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01 -12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01 -13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01 -14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00 -15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00 -16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00 -17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00 -18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00 -19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00 -20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00 -21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00 -22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00 -23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00 -24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00 -25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00 -26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 5 6 -6 1 6 7 -7 1 7 8 -8 1 8 9 -9 1 9 10 -10 1 10 11 -11 1 11 12 -12 1 12 13 -13 1 14 15 -14 1 15 16 -15 1 16 17 -16 1 17 18 -17 1 18 19 -18 1 19 20 -19 1 20 21 -20 1 21 22 -21 1 22 23 -22 1 23 24 -23 1 24 25 -24 1 25 26 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 deleted file mode 100644 index 8f9e9b299e..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 +++ /dev/null @@ -1,244 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 10000 -variable efreq equal 10000 - -variable ntype equal 4 - -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes - -read_data data.duplex4.4type - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 26 atoms - reading velocities ... - 26 velocities - 26 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 24 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.003 seconds -mass * 3.1575 # sets per-type mass if not in data file -set atom * mass 3.1575 # sets per-atom mass - 26 settings made for mass - -group all type 1 4 -26 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - -label loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 1%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+3 -variable comp equal 1+3 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.4type loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 2%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+1 -variable comp equal 2+1 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -next base -jump in.duplex4.4type loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 3%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.4type loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 4%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.4type loop - -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 0.2 0.815 -pair_coeff * * oxdna2/dh 0.1 0.2 0.815 - -# Langevin dynamics -fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 - -timestep 1e-4 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump_modify out sort id -dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " - -#restart 10000 config0_restart config1_restart - -run 100000 -Neighbor list info ... - update every 10 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.6389877 - ghost atom cutoff = 4.6389877 - binsize = 2.3194939, bins = 18 18 18 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448 -Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 -10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211 -20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121 -30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565 -40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372 -50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264 -60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791 -70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404 -80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023 -90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497 -100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413 - 100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014 -Loop time of 7.33046 on 1 procs for 100000 steps with 26 atoms - -Performance: 117864.395 tau/day, 13641.712 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 6.4814 | 6.4814 | 6.4814 | 0.0 | 88.42 -Bond | 0.16262 | 0.16262 | 0.16262 | 0.0 | 2.22 -Neigh | 4.2e-05 | 4.2e-05 | 4.2e-05 | 0.0 | 0.00 -Comm | 0.019555 | 0.019555 | 0.019555 | 0.0 | 0.27 -Output | 0.00131 | 0.00131 | 0.00131 | 0.0 | 0.02 -Modify | 0.64596 | 0.64596 | 0.64596 | 0.0 | 8.81 -Other | | 0.01961 | | | 0.27 - -Nlocal: 26.0 ave 26.0 max 26.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 299.0 ave 299.0 max 299.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 299 -Ave neighs/atom = 11.5 -Ave special neighs/atom = 5.076923076923077 -Neighbor list builds = 2 -Dangerous builds = 0 - -#write_restart config.${number}.* - - -Total wall time: 0:00:07 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 deleted file mode 100644 index ae55b4c3ae..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 +++ /dev/null @@ -1,244 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 10000 -variable efreq equal 10000 - -variable ntype equal 4 - -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes - -read_data data.duplex4.4type - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 26 atoms - reading velocities ... - 26 velocities - 26 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 24 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds -mass * 3.1575 # sets per-type mass if not in data file -set atom * mass 3.1575 # sets per-atom mass - 26 settings made for mass - -group all type 1 4 -26 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - -label loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 1%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+3 -variable comp equal 1+3 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.4type loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 2%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+1 -variable comp equal 2+1 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -next base -jump in.duplex4.4type loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 3%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.4type loop -variable base loop ${ntype} -variable base loop 4 - variable basemod equal ${base}%4 - variable basemod equal 4%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.4type loop - -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 0.2 0.815 -pair_coeff * * oxdna2/dh 0.1 0.2 0.815 - -# Langevin dynamics -fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 - -timestep 1e-4 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump_modify out sort id -dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " - -#restart 10000 config0_restart config1_restart - -run 100000 -Neighbor list info ... - update every 10 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.6389877 - ghost atom cutoff = 4.6389877 - binsize = 2.3194939, bins = 18 18 18 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448 -Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 -10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106 -20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755 -30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902 -40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022 -50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511 -60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784 -70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529 -80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883 -90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149 -100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778 - 100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05 -Loop time of 6.09292 on 4 procs for 100000 steps with 26 atoms - -Performance: 141803.976 tau/day, 16412.497 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.047712 | 2.5625 | 5.2874 | 157.3 | 42.06 -Bond | 0.007398 | 0.053166 | 0.10097 | 19.8 | 0.87 -Neigh | 1.8e-05 | 1.8e-05 | 1.8e-05 | 0.0 | 0.00 -Comm | 0.29205 | 2.9624 | 5.4188 | 143.0 | 48.62 -Output | 0.000866 | 0.00099325 | 0.001303 | 0.0 | 0.02 -Modify | 0.016247 | 0.18354 | 0.37524 | 39.2 | 3.01 -Other | | 0.3303 | | | 5.42 - -Nlocal: 6.5 ave 14.0 max 0.0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 18.5 ave 24.0 max 12.0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 113.75 ave 239.0 max 0.0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 455 -Ave neighs/atom = 17.5 -Ave special neighs/atom = 5.076923076923077 -Neighbor list builds = 1 -Dangerous builds = 0 - -#write_restart config.${number}.* - - -Total wall time: 0:00:06 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 deleted file mode 100644 index 023fef7073..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 +++ /dev/null @@ -1,286 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 10000 -variable efreq equal 10000 - -variable ntype equal 8 - -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes - -read_data data.duplex4.8type - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 26 atoms - reading velocities ... - 26 velocities - 26 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 24 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds -mass * 3.1575 # sets per-type mass if not in data file -set atom * mass 3.1575 # sets per-atom mass - 26 settings made for mass - -group all type 1 8 -26 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - -label loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 1%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+3 -variable comp equal 1+3 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 2%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+1 -variable comp equal 2+1 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 3%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 4%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 5%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+3 -variable comp equal 5+3 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 6%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+1 -variable comp equal 6+1 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 7%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 8%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop - -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 0.2 0.815 -pair_coeff * * oxdna2/dh 0.1 0.2 0.815 - -# Langevin dynamics -fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 - -timestep 1e-4 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump_modify out sort id -dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " - -#restart 10000 config0_restart config1_restart - -run 100000 -Neighbor list info ... - update every 10 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.6389877 - ghost atom cutoff = 4.6389877 - binsize = 2.3194939, bins = 18 18 18 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448 -Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 -10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211 -20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121 -30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565 -40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372 -50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264 -60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791 -70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404 -80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023 -90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497 -100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413 - 100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014 -Loop time of 7.44606 on 1 procs for 100000 steps with 26 atoms - -Performance: 116034.458 tau/day, 13429.914 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 6.5843 | 6.5843 | 6.5843 | 0.0 | 88.43 -Bond | 0.16149 | 0.16149 | 0.16149 | 0.0 | 2.17 -Neigh | 4.3e-05 | 4.3e-05 | 4.3e-05 | 0.0 | 0.00 -Comm | 0.022595 | 0.022595 | 0.022595 | 0.0 | 0.30 -Output | 0.001492 | 0.001492 | 0.001492 | 0.0 | 0.02 -Modify | 0.65313 | 0.65313 | 0.65313 | 0.0 | 8.77 -Other | | 0.02299 | | | 0.31 - -Nlocal: 26.0 ave 26.0 max 26.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 299.0 ave 299.0 max 299.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 299 -Ave neighs/atom = 11.5 -Ave special neighs/atom = 5.076923076923077 -Neighbor list builds = 2 -Dangerous builds = 0 - -#write_restart config.${number}.* - - -Total wall time: 0:00:07 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 deleted file mode 100644 index c8c3f748f9..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 +++ /dev/null @@ -1,286 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 1 -variable ofreq equal 10000 -variable efreq equal 10000 - -variable ntype equal 8 - -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes - -read_data data.duplex4.8type - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 26 atoms - reading velocities ... - 26 velocities - 26 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 24 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds -mass * 3.1575 # sets per-type mass if not in data file -set atom * mass 3.1575 # sets per-atom mass - 26 settings made for mass - -group all type 1 8 -26 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - -label loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 1%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+3 -variable comp equal 1+3 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 2%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+1 -variable comp equal 2+1 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 3%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 4%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 5%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+3 -variable comp equal 5+3 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 6%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -variable comp equal ${base}+1 -variable comp equal 6+1 -pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 7%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop -variable base loop ${ntype} -variable base loop 8 - variable basemod equal ${base}%4 - variable basemod equal 8%4 - if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" - if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" -next base -jump in.duplex4.8type loop - -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh ${T} 0.2 0.815 -pair_coeff * * oxdna2/dh 0.1 0.2 0.815 - -# Langevin dynamics -fix 1 all nve/asphere -fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 -fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 - -timestep 1e-4 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz -dump_modify out sort id -dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " - -#restart 10000 config0_restart config1_restart - -run 100000 -Neighbor list info ... - update every 10 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.6389877 - ghost atom cutoff = 4.6389877 - binsize = 2.3194939, bins = 18 18 18 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448 -Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 -10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106 -20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755 -30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902 -40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022 -50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511 -60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784 -70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529 -80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883 -90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149 -100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778 - 100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05 -Loop time of 6.15993 on 4 procs for 100000 steps with 26 atoms - -Performance: 140261.437 tau/day, 16233.963 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.049533 | 2.573 | 5.3124 | 157.6 | 41.77 -Bond | 0.007709 | 0.055244 | 0.10383 | 20.2 | 0.90 -Neigh | 1.8e-05 | 1.875e-05 | 1.9e-05 | 0.0 | 0.00 -Comm | 0.32774 | 3.0114 | 5.4815 | 142.5 | 48.89 -Output | 0.000925 | 0.0010595 | 0.00137 | 0.6 | 0.02 -Modify | 0.016369 | 0.18492 | 0.37491 | 39.3 | 3.00 -Other | | 0.3343 | | | 5.43 - -Nlocal: 6.5 ave 14.0 max 0.0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 18.5 ave 24.0 max 12.0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 113.75 ave 239.0 max 0.0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 455 -Ave neighs/atom = 17.5 -Ave special neighs/atom = 5.076923076923077 -Neighbor list builds = 1 -Dangerous builds = 0 - -#write_restart config.${number}.* - - -Total wall time: 0:00:06 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 deleted file mode 100644 index 72872d431a..0000000000 --- a/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 +++ /dev/null @@ -1,96 +0,0 @@ -# LAMMPS data file -16 atoms -16 ellipsoids -13 bonds - -4 atom types -1 bond types - -# System size --20.000000 20.000000 xlo xhi --20.000000 20.000000 ylo yhi --20.000000 20.000000 zlo zhi - -Masses - -1 3.1575 -2 3.1575 -3 3.1575 -4 3.1575 - -# Atom-ID, type, position, molecule-ID, ellipsoid flag, density -Atoms - -1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 -2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 -3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 -4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 -5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 -6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1 -7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1 -8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1 -9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1 -10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1 -11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1 -12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1 -13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1 -14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1 -15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1 -16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1 - -# Atom-ID, translational velocity, angular momentum -Velocities - -1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 - -# Atom-ID, shape, quaternion -Ellipsoids - -1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 -3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 -4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 -5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 -6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01 -7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01 -8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01 -9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00 -10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00 -11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00 -12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00 -13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00 -14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00 -15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00 -16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00 - -# Bond topology -Bonds - -1 1 1 2 -2 1 2 3 -3 1 3 4 -4 1 4 5 -5 1 5 6 -6 1 6 7 -7 1 7 8 -8 1 9 10 -9 1 10 11 -10 1 11 12 -11 1 13 14 -12 1 14 15 -13 1 15 16 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 deleted file mode 100644 index 02c9ec0d52..0000000000 --- a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 +++ /dev/null @@ -1,1183 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 4 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex4 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxRNA2 bond interactions - FENE backbone -bond_style oxrna2/fene -bond_coeff * 2.0 0.25 0.761070781051 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxRNA2 pair interactions -pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh - -pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 -pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 -pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 -pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 -pair_coeff * * oxrna2/dh ${T} 0.5 1.02455 -pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 - -# NVE ensemble -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/dot -fix 1 all nve/asphere - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.3014979 - ghost atom cutoff = 3.3014979 - binsize = 1.650749, bins = 25 25 25 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxrna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxrna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxrna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxrna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxrna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxrna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 3.3014979169291987 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -13.282537590974 | etot = -13.282537590974 -Per MPI rank memory allocation (min/avg/max) = 8.071 | 8.071 | 8.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -0.84341458 0.013255977 -0.8301586 -2.0169485e-05 -1000 ekin = 0.00448503054656468 | erot = 0.00825381229611384 | epot = -13.2952764343122 | etot = -13.2825375914695 -2000 ekin = 0.0179027901180511 | erot = 0.0327684151335467 | epot = -13.3332087967732 | etot = -13.2825375915216 -3000 ekin = 0.0401478317723584 | erot = 0.0728240143066062 | epot = -13.3955094376815 | etot = -13.2825375916026 -4000 ekin = 0.0710654348932282 | erot = 0.127292706283096 | epot = -13.4808957328808 | etot = -13.2825375917044 -5000 ekin = 0.110480309743662 | erot = 0.194739074279834 | epot = -13.5877569758405 | etot = -13.282537591817 -6000 ekin = 0.158231230694432 | erot = 0.273546913858903 | epot = -13.7143157364827 | etot = -13.2825375919294 -7000 ekin = 0.214206450831754 | erot = 0.362058396901232 | epot = -13.8588024397642 | etot = -13.2825375920312 -8000 ekin = 0.278374111850069 | erot = 0.458709556672181 | epot = -14.0196212606361 | etot = -13.2825375921138 -9000 ekin = 0.35080209403022 | erot = 0.562145629088178 | epot = -14.1954853152903 | etot = -13.2825375921719 -10000 ekin = 0.431663021447766 | erot = 0.671302139462136 | epot = -14.385502753114 | etot = -13.2825375922041 -11000 ekin = 0.521222365620265 | erot = 0.78544264622411 | epot = -14.5892026040572 | etot = -13.2825375922128 -12000 ekin = 0.61981039873542 | erot = 0.904150888366026 | epot = -14.8064988793055 | etot = -13.2825375922041 -13000 ekin = 0.72778153179885 | erot = 1.02728222251243 | epot = -15.0376013464974 | etot = -13.2825375921861 -14000 ekin = 0.845466747659446 | erot = 1.154885201864 | epot = -15.2828895416915 | etot = -13.2825375921681 -15000 ekin = 0.973515286429446 | erot = 1.28640002432487 | epot = -15.5424529041413 | etot = -13.2825375933869 -16000 ekin = 1.12323013751098 | erot = 1.40387495398598 | epot = -15.8096426839256 | etot = -13.2825375924286 -17000 ekin = 1.2976927283263 | erot = 1.51347784068661 | epot = -16.0937081607397 | etot = -13.2825375917268 -18000 ekin = 1.48565191084531 | erot = 1.63592970999661 | epot = -16.4041192134347 | etot = -13.2825375925928 -19000 ekin = 1.66750911163348 | erot = 1.77940241938721 | epot = -16.7294491246368 | etot = -13.2825375936161 -20000 ekin = 1.84148924290423 | erot = 1.93695511183687 | epot = -17.0609819484057 | etot = -13.2825375936646 -21000 ekin = 2.02307741366163 | erot = 2.09844265792961 | epot = -17.4040576653939 | etot = -13.2825375938027 -22000 ekin = 2.21183606977224 | erot = 2.26260708947302 | epot = -17.7569807531587 | etot = -13.2825375939134 -23000 ekin = 2.40735468792977 | erot = 2.42817202047308 | epot = -18.1180643024997 | etot = -13.2825375940968 -24000 ekin = 2.60896890448861 | erot = 2.59357882573853 | epot = -18.485085324508 | etot = -13.2825375942809 -25000 ekin = 2.81580135477345 | erot = 2.75706655667055 | epot = -18.855405505957 | etot = -13.282537594513 -26000 ekin = 3.02680083558485 | erot = 2.91667946897257 | epot = -19.2260178993271 | etot = -13.2825375947697 -27000 ekin = 3.24067707260308 | erot = 3.07027299756498 | epot = -19.5934876652175 | etot = -13.2825375950495 -28000 ekin = 3.45601412953572 | erot = 3.21560615188039 | epot = -19.9541578767293 | etot = -13.2825375953132 -29000 ekin = 3.6713683081319 | erot = 3.35037905822946 | epot = -20.304284961999 | etot = -13.2825375956376 -30000 ekin = 3.88476027224393 | erot = 3.47208481891837 | epot = -20.639382687185 | etot = -13.2825375960227 -31000 ekin = 4.09387957878895 | erot = 3.57821385032035 | epot = -20.9546310254509 | etot = -13.2825375963416 -32000 ekin = 4.29662185345806 | erot = 3.66648606531138 | epot = -21.2456455154186 | etot = -13.2825375966492 -33000 ekin = 4.49089153394062 | erot = 3.73482555362569 | epot = -21.5082546845018 | etot = -13.2825375969355 -34000 ekin = 4.67464118182276 | erot = 3.78142516888995 | epot = -21.738603947901 | etot = -13.2825375971883 -35000 ekin = 4.84586411782047 | erot = 3.80480460777895 | epot = -21.9332063229962 | etot = -13.2825375973967 -36000 ekin = 5.00270940487365 | erot = 3.8039453503275 | epot = -22.0891923527593 | etot = -13.2825375975582 -37000 ekin = 5.14355281474259 | erot = 3.7783370953036 | epot = -22.204427507712 | etot = -13.2825375976658 -38000 ekin = 5.26699752588855 | erot = 3.72801268545693 | epot = -22.2775478090594 | etot = -13.2825375977139 -39000 ekin = 5.37191151713863 | erot = 3.65359747923659 | epot = -22.3080465940736 | etot = -13.2825375976984 -40000 ekin = 5.45746010972423 | erot = 3.55633701588595 | epot = -22.2963347232305 | etot = -13.2825375976203 -41000 ekin = 5.52312188621308 | erot = 3.43809872369854 | epot = -22.2437582073842 | etot = -13.2825375974726 -42000 ekin = 5.56872044211992 | erot = 3.30135279333163 | epot = -22.1526108327155 | etot = -13.2825375972639 -43000 ekin = 5.59443660082917 | erot = 3.14910305123731 | epot = -22.0260772490691 | etot = -13.2825375970026 -44000 ekin = 5.60078634437692 | erot = 2.98477133565124 | epot = -21.8680952767294 | etot = -13.2825375967012 -45000 ekin = 5.58859564323333 | erot = 2.81204277265316 | epot = -21.6831760122617 | etot = -13.2825375963752 -46000 ekin = 5.55896198288794 | erot = 2.63469562167501 | epot = -21.4761952006007 | etot = -13.2825375960378 -47000 ekin = 5.51320424221946 | erot = 2.45646420183046 | epot = -21.2522060397483 | etot = -13.2825375956984 -48000 ekin = 5.45280176988517 | erot = 2.28095947573118 | epot = -21.0162988409769 | etot = -13.2825375953605 -49000 ekin = 5.37933239946638 | erot = 2.11161440403257 | epot = -20.7734843985446 | etot = -13.2825375950457 -50000 ekin = 5.29440598595185 | erot = 1.95156309993188 | epot = -20.5285066806346 | etot = -13.2825375947508 -51000 ekin = 5.19960275040233 | erot = 1.8036634398305 | epot = -20.2858037847152 | etot = -13.2825375944824 -52000 ekin = 5.0964231996195 | erot = 1.67046877096987 | epot = -20.0494295648281 | etot = -13.2825375942387 -53000 ekin = 4.9862463955433 | erot = 1.55427111116831 | epot = -19.8230551007329 | etot = -13.2825375940213 -54000 ekin = 4.87030445561499 | erot = 1.45710469956877 | epot = -19.6099467490156 | etot = -13.2825375938318 -55000 ekin = 4.74966978520139 | erot = 1.38074642902068 | epot = -19.4129538078748 | etot = -13.2825375936527 -56000 ekin = 4.62525646670949 | erot = 1.32681969001207 | epot = -19.234613750249 | etot = -13.2825375935274 -57000 ekin = 4.49783496228224 | erot = 1.29648861711347 | epot = -19.0768611728237 | etot = -13.282537593428 -58000 ekin = 4.36805832461578 | erot = 1.29057331365797 | epot = -18.9411692316276 | etot = -13.2825375933539 -59000 ekin = 4.2364904586051 | erot = 1.30961007130951 | epot = -18.8286381232177 | etot = -13.2825375933031 -60000 ekin = 4.10363649615144 | erot = 1.35385055377169 | epot = -18.7400246431963 | etot = -13.2825375932731 -61000 ekin = 3.96997203629753 | erot = 1.42326526715546 | epot = -18.6757748967158 | etot = -13.2825375932628 -62000 ekin = 3.83612285735248 | erot = 1.51750909475431 | epot = -18.63616954536 | etot = -13.2825375932532 -63000 ekin = 3.70275913153266 | erot = 1.63593500305368 | epot = -18.6212317278745 | etot = -13.2825375932882 -64000 ekin = 3.57028395426058 | erot = 1.77765695762491 | epot = -18.6304785052259 | etot = -13.2825375933404 -65000 ekin = 3.43939724701796 | erot = 1.94136642645393 | epot = -18.6633012668467 | etot = -13.2825375933748 -66000 ekin = 3.31090885650418 | erot = 2.12543845180125 | epot = -18.7188849017627 | etot = -13.2825375934573 -67000 ekin = 3.18539537800071 | erot = 2.32812634152943 | epot = -18.7960593130806 | etot = -13.2825375935505 -68000 ekin = 3.0635338653798 | erot = 2.54742667497606 | epot = -18.8934981340101 | etot = -13.2825375936542 -69000 ekin = 2.94609585152078 | erot = 2.78109018587171 | epot = -19.0097236311617 | etot = -13.2825375937692 -70000 ekin = 2.83393040716448 | erot = 3.02662959649683 | epot = -19.1430975975577 | etot = -13.2825375938964 -71000 ekin = 2.72793726696335 | erot = 3.2813399428617 | epot = -19.2918148038566 | etot = -13.2825375940315 -72000 ekin = 2.62902971043607 | erot = 3.54239819983169 | epot = -19.4539655044244 | etot = -13.2825375941566 -73000 ekin = 2.53808722042867 | erot = 3.80701983458538 | epot = -19.6276446493623 | etot = -13.2825375943483 -74000 ekin = 2.455928655269 | erot = 4.07171344127425 | epot = -19.8101796911565 | etot = -13.2825375946133 -75000 ekin = 2.3833072864543 | erot = 4.33220600221137 | epot = -19.9980508835341 | etot = -13.2825375948685 -76000 ekin = 2.32085819246822 | erot = 4.58430888321152 | epot = -20.1877046708087 | etot = -13.2825375951289 -77000 ekin = 2.26905284041982 | erot = 4.82394209159272 | epot = -20.3755325274045 | etot = -13.2825375953919 -78000 ekin = 2.2281821557978 | erot = 5.04720004762901 | epot = -20.5579197990814 | etot = -13.2825375956545 -79000 ekin = 2.19835990746566 | erot = 5.25044819004335 | epot = -20.731345693396 | etot = -13.282537595887 -80000 ekin = 2.17954213158759 | erot = 5.43056087724128 | epot = -20.892640604912 | etot = -13.2825375960832 -81000 ekin = 2.17154912845093 | erot = 5.58515654974166 | epot = -21.0392432744259 | etot = -13.2825375962333 -82000 ekin = 2.17396051633407 | erot = 5.7125507021892 | epot = -21.1690488148909 | etot = -13.2825375963676 -83000 ekin = 2.18608268543525 | erot = 5.81159389139857 | epot = -21.2802141733998 | etot = -13.282537596566 -84000 ekin = 2.2069405579712 | erot = 5.88143457462831 | epot = -21.3709127292228 | etot = -13.2825375966233 -85000 ekin = 2.2355007346892 | erot = 5.92248473361667 | epot = -21.440523064944 | etot = -13.2825375966382 -86000 ekin = 2.27071025957252 | erot = 5.93583657914492 | epot = -21.4890844353356 | etot = -13.2825375966181 -87000 ekin = 2.31151705668581 | erot = 5.92306118835155 | epot = -21.5171158416081 | etot = -13.2825375965708 -88000 ekin = 2.35689880582412 | erot = 5.88606517856673 | epot = -21.525501580893 | etot = -13.2825375965021 -89000 ekin = 2.40589192121148 | erot = 5.82697176767419 | epot = -21.5154012853016 | etot = -13.2825375964159 -90000 ekin = 2.45762089189535 | erot = 5.74803678246179 | epot = -21.4881952706708 | etot = -13.2825375963137 -91000 ekin = 2.51132727735695 | erot = 5.65159908896414 | epot = -21.4454639625169 | etot = -13.2825375961958 -92000 ekin = 2.56639616299259 | erot = 5.54005576567966 | epot = -21.3889895247342 | etot = -13.282537596062 -93000 ekin = 2.62237587147962 | erot = 5.41584923925671 | epot = -21.3207627066499 | etot = -13.2825375959136 -94000 ekin = 2.67898536287491 | erot = 5.28145076624188 | epot = -21.2429737248702 | etot = -13.2825375957534 -95000 ekin = 2.73610698777088 | erot = 5.13933222478715 | epot = -21.1579768081439 | etot = -13.2825375955858 -96000 ekin = 2.79376736409348 | erot = 4.991923519611 | epot = -21.0682284791224 | etot = -13.2825375954179 -97000 ekin = 2.8520975917789 | erot = 4.84155102931962 | epot = -20.9761862163567 | etot = -13.2825375952582 -98000 ekin = 2.91128043087791 | erot = 4.69036811429532 | epot = -20.8841861402883 | etot = -13.2825375951151 -99000 ekin = 2.97148865716348 | erot = 4.54028690688379 | epot = -20.7943131590444 | etot = -13.2825375949971 -100000 ekin = 3.03281936548472 | erot = 4.39291958377954 | epot = -20.7082765441749 | etot = -13.2825375949107 -101000 ekin = 3.09523162855504 | erot = 4.24953761553679 | epot = -20.6273068389522 | etot = -13.2825375948604 -102000 ekin = 3.15849350649721 | erot = 4.11105261279871 | epot = -20.5520837141442 | etot = -13.2825375948483 -103000 ekin = 3.22212928739638 | erot = 3.97803233781106 | epot = -20.4826992200828 | etot = -13.2825375948753 -104000 ekin = 3.28539028419999 | erot = 3.85073569994574 | epot = -20.4186635790808 | etot = -13.2825375949351 -105000 ekin = 3.34731475817757 | erot = 3.72912316717803 | epot = -20.3589755203793 | etot = -13.2825375950237 -106000 ekin = 3.4067279473086 | erot = 3.61292637549551 | epot = -20.3021919179394 | etot = -13.2825375951353 -107000 ekin = 3.46228544964883 | erot = 3.5017039548605 | epot = -20.246526999772 | etot = -13.2825375952626 -108000 ekin = 3.51253156080077 | erot = 3.39489824023761 | epot = -20.1899673964364 | etot = -13.2825375953981 -109000 ekin = 3.55597480315873 | erot = 3.29187299703765 | epot = -20.1303853957321 | etot = -13.2825375955357 -110000 ekin = 3.59118238705146 | erot = 3.19193918351245 | epot = -20.0656591662303 | etot = -13.2825375956664 -111000 ekin = 3.61687343778638 | erot = 3.09439958031605 | epot = -19.9938106138842 | etot = -13.2825375957818 -112000 ekin = 3.63202144077084 | erot = 2.99858073408885 | epot = -19.9131397707328 | etot = -13.2825375958731 -113000 ekin = 3.63595677604976 | erot = 2.9038679642207 | epot = -19.8223623362017 | etot = -13.2825375959313 -114000 ekin = 3.62846110509018 | erot = 2.80974594394126 | epot = -19.7207446449798 | etot = -13.2825375959483 -115000 ekin = 3.60984333606122 | erot = 2.71584476484558 | epot = -19.6082256968244 | etot = -13.2825375959176 -116000 ekin = 3.58098592946299 | erot = 2.62198860618916 | epot = -19.4855121314887 | etot = -13.2825375958366 -117000 ekin = 3.54334240221404 | erot = 2.52827901424375 | epot = -19.3541590121477 | etot = -13.2825375956899 -118000 ekin = 3.49891828359516 | erot = 2.43512420844403 | epot = -19.216580087547 | etot = -13.2825375955078 -119000 ekin = 3.45018316481891 | erot = 2.34313144179019 | epot = -19.0758522018958 | etot = -13.2825375952867 -120000 ekin = 3.39991853306434 | erot = 2.25319419875649 | epot = -18.9356503268596 | etot = -13.2825375950388 -121000 ekin = 3.3510515204902 | erot = 2.16646597387207 | epot = -18.800055089141 | etot = -13.2825375947787 -122000 ekin = 3.30648176977496 | erot = 2.08430580540005 | epot = -18.6733251696956 | etot = -13.2825375945206 -123000 ekin = 3.26892966156092 | erot = 2.00820635396395 | epot = -18.5596736098009 | etot = -13.282537594276 -124000 ekin = 3.24083330103916 | erot = 1.93971532774634 | epot = -18.4630862228367 | etot = -13.2825375940512 -125000 ekin = 3.22476145827508 | erot = 1.88029581293259 | epot = -18.3875948633982 | etot = -13.2825375921906 -126000 ekin = 3.14878052704874 | erot = 1.84062475589788 | epot = -18.2719429098057 | etot = -13.282537626859 -127000 ekin = 2.94943277103419 | erot = 1.886595427589 | epot = -18.1185657735804 | etot = -13.2825375749572 -128000 ekin = 3.16220879321477 | erot = 1.96338946783263 | epot = -18.4081359062158 | etot = -13.2825376451684 -129000 ekin = 3.31015030132664 | erot = 1.94720836362437 | epot = -18.5398963214834 | etot = -13.2825376565324 -130000 ekin = 3.4497203872454 | erot = 1.9263351056887 | epot = -18.6585931496325 | etot = -13.2825376566984 -131000 ekin = 3.58872168957069 | erot = 1.90769906106666 | epot = -18.7789584074301 | etot = -13.2825376567928 -132000 ekin = 3.72319125317242 | erot = 1.89293715413342 | epot = -18.8986660641589 | etot = -13.2825376568531 -133000 ekin = 3.84978251755378 | erot = 1.88373597103185 | epot = -19.0160561454729 | etot = -13.2825376568873 -134000 ekin = 3.96557984951709 | erot = 1.88171908502832 | epot = -19.1298365915084 | etot = -13.282537656963 -135000 ekin = 4.06807957718157 | erot = 1.88790714285761 | epot = -19.2385243770752 | etot = -13.282537657036 -136000 ekin = 4.15531911327293 | erot = 1.90286269173109 | epot = -19.340719462101 | etot = -13.282537657097 -137000 ekin = 4.22592766896957 | erot = 1.92681130724409 | epot = -19.4352766333493 | etot = -13.2825376571357 -138000 ekin = 4.27918313097991 | erot = 1.95973390207695 | epot = -19.5214546902016 | etot = -13.2825376571448 -139000 ekin = 4.31500256681567 | erot = 2.00154238231131 | epot = -19.59908260621 | etot = -13.2825376570831 -140000 ekin = 4.33403278412092 | erot = 2.05223040229202 | epot = -19.6688008434056 | etot = -13.2825376569926 -141000 ekin = 4.33751047770786 | erot = 2.11180924821132 | epot = -19.7318573827854 | etot = -13.2825376568662 -142000 ekin = 4.32708478663564 | erot = 2.18042096416689 | epot = -19.7900434075179 | etot = -13.2825376567154 -143000 ekin = 4.30467959787724 | erot = 2.25833701673724 | epot = -19.8455542711563 | etot = -13.2825376565418 -144000 ekin = 4.27235382259247 | erot = 2.34595165411789 | epot = -19.9008431331009 | etot = -13.2825376563906 -145000 ekin = 4.23214636981244 | erot = 2.44344334214718 | epot = -19.9581273682268 | etot = -13.2825376562672 -146000 ekin = 4.18594231916929 | erot = 2.55071340549331 | epot = -20.0191933808486 | etot = -13.2825376561861 -147000 ekin = 4.13537962661592 | erot = 2.66728850163241 | epot = -20.0852057844046 | etot = -13.2825376561563 -148000 ekin = 4.08179900889712 | erot = 2.79223549069442 | epot = -20.1565721557729 | etot = -13.2825376561813 -149000 ekin = 4.02623498472322 | erot = 2.9241198689985 | epot = -20.232892509982 | etot = -13.2825376562603 -150000 ekin = 3.96943958307703 | erot = 3.06100347347629 | epot = -20.3129807129424 | etot = -13.2825376563891 -151000 ekin = 3.91192645323282 | erot = 3.20047132483819 | epot = -20.3949354346329 | etot = -13.2825376565619 -152000 ekin = 3.85402372610883 | erot = 3.33967877480172 | epot = -20.4762401576828 | etot = -13.2825376567723 -153000 ekin = 3.79592773401783 | erot = 3.47541715770412 | epot = -20.5538825487337 | etot = -13.2825376570117 -154000 ekin = 3.73775530704034 | erot = 3.60420547216072 | epot = -20.6244984364701 | etot = -13.282537657269 -155000 ekin = 3.6795979102985 | erot = 3.7224221778291 | epot = -20.6845577456561 | etot = -13.2825376575285 -156000 ekin = 3.62158147939218 | erot = 3.82649073830497 | epot = -20.7306098754663 | etot = -13.2825376577691 -157000 ekin = 3.5639362554113 | erot = 3.91312084630063 | epot = -20.7595947596784 | etot = -13.2825376579665 -158000 ekin = 3.50707329925225 | erot = 3.9795873650006 | epot = -20.7691983223484 | etot = -13.2825376580955 -159000 ekin = 3.45165682738659 | erot = 4.02400734849606 | epot = -20.7582018340186 | etot = -13.282537658136 -160000 ekin = 3.39865532558911 | erot = 4.04555903021673 | epot = -20.7267520138832 | etot = -13.2825376580774 -161000 ekin = 3.34935406486443 | erot = 4.04458967179415 | epot = -20.6764813945808 | etot = -13.2825376579222 -162000 ekin = 3.30532015421541 | erot = 4.02258247379577 | epot = -20.6104402856967 | etot = -13.2825376576855 -163000 ekin = 3.26831809803593 | erot = 3.9819866935813 | epot = -20.5328424490087 | etot = -13.2825376573915 -164000 ekin = 3.24018500158399 | erot = 3.92594872656713 | epot = -20.4486713852208 | etot = -13.2825376570696 -165000 ekin = 3.22267663501631 | erot = 3.85799639398367 | epot = -20.3632106857524 | etot = -13.2825376567524 -166000 ekin = 3.21735668268678 | erot = 3.78179957337381 | epot = -20.2816939123395 | etot = -13.2825376562789 -167000 ekin = 3.22508554133862 | erot = 3.70216421851936 | epot = -20.2097874159612 | etot = -13.2825376561032 -168000 ekin = 3.24596106315348 | erot = 3.62279974210031 | epot = -20.1512984612673 | etot = -13.2825376560135 -169000 ekin = 3.27955383501624 | erot = 3.54538235194483 | epot = -20.1074738429831 | etot = -13.282537656022 -170000 ekin = 3.32466734771662 | erot = 3.47077759716888 | epot = -20.0779826010138 | etot = -13.2825376561283 -171000 ekin = 3.37937800793516 | erot = 3.39904334979718 | epot = -20.0609590140454 | etot = -13.282537656313 -172000 ekin = 3.44119436380901 | erot = 3.32956363469228 | epot = -20.0532956550473 | etot = -13.282537656546 -173000 ekin = 3.50731985302141 | erot = 3.26128359452907 | epot = -20.0511411043353 | etot = -13.2825376567848 -174000 ekin = 3.57497712060583 | erot = 3.19303082809352 | epot = -20.050545605684 | etot = -13.2825376569846 -175000 ekin = 3.64173116724552 | erot = 3.12386956099455 | epot = -20.0481383853484 | etot = -13.2825376571083 -176000 ekin = 3.70574771913082 | erot = 3.05341479574277 | epot = -20.0417001720058 | etot = -13.2825376571322 -177000 ekin = 3.7659388805688 | erot = 2.98204284338451 | epot = -20.0305193810053 | etot = -13.282537657052 -178000 ekin = 3.82196164475694 | erot = 2.91094638159342 | epot = -20.015445683236 | etot = -13.2825376568857 -179000 ekin = 3.87411507697524 | erot = 2.84204110116973 | epot = -19.9986938347994 | etot = -13.2825376566544 -180000 ekin = 3.92317967933193 | erot = 2.7777395342816 | epot = -19.9834568700068 | etot = -13.2825376563932 -181000 ekin = 3.97015764234382 | erot = 2.72070235461324 | epot = -19.9733976530853 | etot = -13.2825376561282 -182000 ekin = 4.01610171617511 | erot = 2.6734984016926 | epot = -19.9721377738014 | etot = -13.2825376559337 -183000 ekin = 4.06177363427731 | erot = 2.63812245871493 | epot = -19.9824337488135 | etot = -13.2825376558213 -184000 ekin = 4.10756653677024 | erot = 2.61575603465066 | epot = -20.0058602272097 | etot = -13.2825376557888 -185000 ekin = 4.15354652964132 | erot = 2.60670565064911 | epot = -20.042789836128 | etot = -13.2825376558376 -186000 ekin = 4.19945391072101 | erot = 2.61036353554316 | epot = -20.0923551022269 | etot = -13.2825376559628 -187000 ekin = 4.24473107430636 | erot = 2.62524898284916 | epot = -20.1525177133095 | etot = -13.282537656154 -188000 ekin = 4.28856799818784 | erot = 2.6491184592848 | epot = -20.2202241138693 | etot = -13.2825376563966 -189000 ekin = 4.33007364399125 | erot = 2.67919947077837 | epot = -20.291810771393 | etot = -13.2825376566233 -190000 ekin = 4.36845326745518 | erot = 2.71241964780781 | epot = -20.3634105721979 | etot = -13.282537656935 -191000 ekin = 4.40242074847429 | erot = 2.74530093921263 | epot = -20.4302593449101 | etot = -13.2825376572232 -192000 ekin = 4.43037880288296 | erot = 2.7745540103848 | epot = -20.4874704712234 | etot = -13.2825376579557 -193000 ekin = 4.44834510305263 | erot = 2.79692081275968 | epot = -20.5278035740366 | etot = -13.2825376582243 -194000 ekin = 4.45438337861284 | erot = 2.80974801333328 | epot = -20.5466690503491 | etot = -13.282537658403 -195000 ekin = 4.44752201417202 | erot = 2.81136444003046 | epot = -20.5414241126779 | etot = -13.2825376584754 -196000 ekin = 4.42737187905048 | erot = 2.80121240437724 | epot = -20.5111219418607 | etot = -13.282537658433 -197000 ekin = 4.39418615090619 | erot = 2.77991547931436 | epot = -20.4566392884965 | etot = -13.282537658276 -198000 ekin = 4.3488852650834 | erot = 2.74924294053029 | epot = -20.3806658636271 | etot = -13.2825376580134 -199000 ekin = 4.29304006378848 | erot = 2.71196807404358 | epot = -20.2875457954965 | etot = -13.2825376576645 -200000 ekin = 4.22880362118172 | erot = 2.67162662745845 | epot = -20.1829679058976 | etot = -13.2825376572574 -201000 ekin = 4.15878346301308 | erot = 2.6321913339107 | epot = -20.0735124537522 | etot = -13.2825376568284 -202000 ekin = 4.08585235174777 | erot = 2.59768848811556 | epot = -19.9660784962823 | etot = -13.2825376564189 -203000 ekin = 4.01290418154392 | erot = 2.5717916467484 | epot = -19.8672334843641 | etot = -13.2825376560718 -204000 ekin = 3.94257872967226 | erot = 2.55743320243961 | epot = -19.7825495879379 | etot = -13.282537655826 -205000 ekin = 3.87698859849794 | erot = 2.55647506167819 | epot = -19.7160013158883 | etot = -13.2825376557122 -206000 ekin = 3.81748743469197 | erot = 2.56947517652852 | epot = -19.6695002669682 | etot = -13.2825376557477 -207000 ekin = 3.76451595610833 | erot = 2.59557970374943 | epot = -19.6426333157917 | etot = -13.2825376559339 -208000 ekin = 3.71755329412155 | erot = 2.63256413547948 | epot = -19.6326550858542 | etot = -13.2825376562531 -209000 ekin = 3.6751895684106 | erot = 2.67704133017555 | epot = -19.6347685552539 | etot = -13.2825376566678 -210000 ekin = 3.63532366958123 | erot = 2.72484401425475 | epot = -19.6427053409575 | etot = -13.2825376571215 -211000 ekin = 3.59547812025537 | erot = 2.77156531006635 | epot = -19.6495810878665 | etot = -13.2825376575447 -212000 ekin = 3.5532013388674 | erot = 2.8131934632015 | epot = -19.648932459936 | etot = -13.2825376578671 -213000 ekin = 3.5064976129211 | erot = 2.84671880107505 | epot = -19.6357540720302 | etot = -13.282537658034 -214000 ekin = 3.45419694129118 | erot = 2.87055671325296 | epot = -19.6072913125676 | etot = -13.2825376580234 -215000 ekin = 3.3961705526571 | erot = 2.8846579012024 | epot = -19.5633661117116 | etot = -13.2825376578521 -216000 ekin = 3.33333457774708 | erot = 2.89027487492533 | epot = -19.5061471102412 | etot = -13.2825376575688 -217000 ekin = 3.26237078851755 | erot = 2.88652329141154 | epot = -19.4314317899048 | etot = -13.2825377099757 -218000 ekin = 3.06041269207635 | erot = 2.81741383451267 | epot = -19.1603641969459 | etot = -13.2825376703568 -219000 ekin = 2.93316276967062 | erot = 2.8446025024716 | epot = -19.0603029343603 | etot = -13.2825376622181 -220000 ekin = 2.96128614843698 | erot = 2.98904145664669 | epot = -19.2328653086382 | etot = -13.2825377035546 -221000 ekin = 2.90913828063349 | erot = 3.0370109417033 | epot = -19.2286868797594 | etot = -13.2825376574226 -222000 ekin = 2.84227376945866 | erot = 3.05603303801694 | epot = -19.1808444650464 | etot = -13.2825376575708 -223000 ekin = 2.78062900949204 | erot = 3.0623214454287 | epot = -19.1254881126305 | etot = -13.2825376577097 -224000 ekin = 2.72480461600036 | erot = 3.05323876331587 | epot = -19.0605810371255 | etot = -13.2825376578093 -225000 ekin = 2.67532541220325 | erot = 3.02684795807176 | epot = -18.9847110281109 | etot = -13.2825376578359 -226000 ekin = 2.63276163036943 | erot = 2.98227164387593 | epot = -18.8975709320212 | etot = -13.2825376577758 -227000 ekin = 2.59776959648577 | erot = 2.91985728396334 | epot = -18.8001645380875 | etot = -13.2825376576384 -228000 ekin = 2.57104335950892 | erot = 2.84110209326691 | epot = -18.6946831102272 | etot = -13.2825376574514 -229000 ekin = 2.55319781380138 | erot = 2.74837649564534 | epot = -18.5841119666977 | etot = -13.282537657251 -230000 ekin = 2.54463522127686 | erot = 2.64454432367535 | epot = -18.4717172020198 | etot = -13.2825376570676 -231000 ekin = 2.54546021784621 | erot = 2.53260284792485 | epot = -18.3606007226861 | etot = -13.282537656915 -232000 ekin = 2.55549307881088 | erot = 2.41545023211296 | epot = -18.2534809677097 | etot = -13.2825376567859 -233000 ekin = 2.57438548648739 | erot = 2.29583418255703 | epot = -18.1527573257026 | etot = -13.2825376566582 -234000 ekin = 2.60178443029265 | erot = 2.17645519655967 | epot = -18.0607772833614 | etot = -13.2825376565091 -235000 ekin = 2.63745218021159 | erot = 2.06012244390588 | epot = -17.9801122804484 | etot = -13.2825376563309 -236000 ekin = 2.68126373962457 | erot = 1.94983176913329 | epot = -17.913633164896 | etot = -13.2825376561382 -237000 ekin = 2.73306880567091 | erot = 1.84868049785708 | epot = -17.8642869594909 | etot = -13.2825376559629 -238000 ekin = 2.79247907581072 | erot = 1.75962709169619 | epot = -17.8346438233477 | etot = -13.2825376558408 -239000 ekin = 2.8586759443782 | erot = 1.68518476454599 | epot = -17.8263983647219 | etot = -13.2825376557977 -240000 ekin = 2.93031183915977 | erot = 1.62715662270393 | epot = -17.8400061177073 | etot = -13.2825376558436 -241000 ekin = 3.00552986743725 | erot = 1.58648515289343 | epot = -17.8745526763034 | etot = -13.2825376559727 -242000 ekin = 3.0820836546572 | erot = 1.56323726723208 | epot = -17.9278585780555 | etot = -13.2825376561662 -243000 ekin = 3.15752262719342 | erot = 1.5567113441869 | epot = -17.9967716277771 | etot = -13.2825376563968 -244000 ekin = 3.22940955213828 | erot = 1.56564064462198 | epot = -18.0775878533929 | etot = -13.2825376566326 -245000 ekin = 3.29554303953914 | erot = 1.58846457359926 | epot = -18.1665452699782 | etot = -13.2825376568398 -246000 ekin = 3.35415939736843 | erot = 1.62363159705077 | epot = -18.2603286514088 | etot = -13.2825376569896 -247000 ekin = 3.40408574270612 | erot = 1.6698832561101 | epot = -18.3565066558791 | etot = -13.2825376570629 -248000 ekin = 3.44481663263181 | erot = 1.72645823945308 | epot = -18.4538125291412 | etot = -13.2825376570563 -249000 ekin = 3.4764966325555 | erot = 1.79316293261092 | epot = -18.5521972221498 | etot = -13.2825376569834 -250000 ekin = 3.4998119290067 | erot = 1.87028571125164 | epot = -18.6526352971293 | etot = -13.2825376568709 -251000 ekin = 3.51581851748171 | erot = 1.95837689015822 | epot = -18.7567330643924 | etot = -13.2825376567524 -252000 ekin = 3.52575126869464 | erot = 2.05795546201286 | epot = -18.8662443873663 | etot = -13.2825376566588 -253000 ekin = 3.53086049262785 | erot = 2.16922084359604 | epot = -18.9826189928353 | etot = -13.2825376566114 -254000 ekin = 3.53230924463609 | erot = 2.29183768672779 | epot = -19.1066845879831 | etot = -13.2825376566192 -255000 ekin = 3.53114146569382 | erot = 2.42483171779584 | epot = -19.2385108401683 | etot = -13.2825376566786 -256000 ekin = 3.5283101054313 | erot = 2.56659937924946 | epot = -19.3774471414593 | etot = -13.2825376567786 -257000 ekin = 3.52473759358279 | erot = 2.71500399460032 | epot = -19.5222792450876 | etot = -13.2825376569044 -258000 ekin = 3.52137545667859 | erot = 2.86751445186624 | epot = -19.6714275655892 | etot = -13.2825376570444 -259000 ekin = 3.51923070409532 | erot = 3.02134046698889 | epot = -19.8231088282769 | etot = -13.2825376571927 -260000 ekin = 3.51933841084553 | erot = 3.17353025732541 | epot = -19.9754063255224 | etot = -13.2825376573514 -261000 ekin = 3.52267851350856 | erot = 3.32101670247704 | epot = -20.1262328735147 | etot = -13.2825376575291 -262000 ekin = 3.53003333480896 | erot = 3.46062452427896 | epot = -20.273195516825 | etot = -13.2825376577371 -263000 ekin = 3.54180424035152 | erot = 3.58907231404775 | epot = -20.413414212382 | etot = -13.2825376579827 -264000 ekin = 3.55787447685305 | erot = 3.70301127793477 | epot = -20.5434234130524 | etot = -13.2825376582646 -265000 ekin = 3.57751330913344 | erot = 3.7991542896344 | epot = -20.659205257334 | etot = -13.2825376585661 -266000 ekin = 3.59938201293793 | erot = 3.87452595150114 | epot = -20.7564456232931 | etot = -13.2825376588541 -267000 ekin = 3.62167235822875 | erot = 3.92682901662434 | epot = -20.8310390339348 | etot = -13.2825376590817 -268000 ekin = 3.64237343768071 | erot = 3.95486700975834 | epot = -20.8797781066388 | etot = -13.2825376591998 -269000 ekin = 3.65961533754883 | erot = 3.95890941485168 | epot = -20.901062411575 | etot = -13.2825376591745 -270000 ekin = 3.67198713217814 | erot = 3.94085700806684 | epot = -20.8953817992463 | etot = -13.2825376590013 -271000 ekin = 3.67872329079258 | erot = 3.90410726329523 | epot = -20.8653682127982 | etot = -13.2825376587104 -272000 ekin = 3.67969720542176 | erot = 3.85312017496781 | epot = -20.8153550387471 | etot = -13.2825376583575 -273000 ekin = 3.67523785304564 | erot = 3.79279347421287 | epot = -20.7505689852647 | etot = -13.2825376580062 -274000 ekin = 3.66585545030596 | erot = 3.72781503527706 | epot = -20.6762081432927 | etot = -13.2825376577096 -275000 ekin = 3.65198266149159 | erot = 3.66213927987052 | epot = -20.5966595988631 | etot = -13.282537657501 -276000 ekin = 3.633806837076 | erot = 3.598661459447 | epot = -20.5150059539148 | etot = -13.2825376573918 -277000 ekin = 3.61121443635146 | erot = 3.53909052619933 | epot = -20.4328426199275 | etot = -13.2825376573767 -278000 ekin = 3.58382533557885 | erot = 3.48398196201195 | epot = -20.3503449550305 | etot = -13.2825376574397 -279000 ekin = 3.55107927466721 | erot = 3.4328876768366 | epot = -20.2665046090618 | etot = -13.282537657558 -280000 ekin = 3.51234648871563 | erot = 3.38459301004919 | epot = -20.1794771564681 | etot = -13.2825376577033 -281000 ekin = 3.46705217022193 | erot = 3.33742016501543 | epot = -20.0870099930804 | etot = -13.282537657843 -282000 ekin = 3.4148174354963 | erot = 3.28957539031067 | epot = -19.98693048375 | etot = -13.2825376579431 -283000 ekin = 3.3556172386103 | erot = 3.23950140187567 | epot = -19.877656298458 | etot = -13.282537657972 -284000 ekin = 3.28993990743714 | erot = 3.18617834963481 | epot = -19.7586559149802 | etot = -13.2825376579083 -285000 ekin = 3.21891605429293 | erot = 3.12930993710548 | epot = -19.6307636491448 | etot = -13.2825376577464 -286000 ekin = 3.14439051761724 | erot = 3.06934998331701 | epot = -19.4962781582955 | etot = -13.2825376573613 -287000 ekin = 3.06960009495595 | erot = 3.00728050107418 | epot = -19.3594182531578 | etot = -13.2825376571276 -288000 ekin = 2.99759349423582 | erot = 2.94413656453561 | epot = -19.2242677156211 | etot = -13.2825376568497 -289000 ekin = 2.9312259032696 | erot = 2.88109280424398 | epot = -19.0948563640673 | etot = -13.2825376565537 -290000 ekin = 2.87364775959538 | erot = 2.81936189019795 | epot = -18.9755473060557 | etot = -13.2825376562624 -291000 ekin = 2.82808392253236 | erot = 2.76008269212129 | epot = -18.8707042706456 | etot = -13.2825376559919 -292000 ekin = 2.79759576436007 | erot = 2.70430482357457 | epot = -18.7844382436883 | etot = -13.2825376557537 -293000 ekin = 2.78483509079594 | erot = 2.65304729582258 | epot = -18.7204200421757 | etot = -13.2825376555571 -294000 ekin = 2.79179688861819 | erot = 2.6073808528377 | epot = -18.6817153968698 | etot = -13.2825376554139 -295000 ekin = 2.81957934527721 | erot = 2.56847294066555 | epot = -18.6705899412834 | etot = -13.2825376553406 -296000 ekin = 2.8680999060561 | erot = 2.53696733690384 | epot = -18.6876048985713 | etot = -13.2825376556114 -297000 ekin = 2.93560102202648 | erot = 2.51254790532835 | epot = -18.7306865831678 | etot = -13.282537655813 -298000 ekin = 3.01880409347916 | erot = 2.49548083197819 | epot = -18.7968225815706 | etot = -13.2825376561132 -299000 ekin = 3.11317674937778 | erot = 2.48585279572497 | epot = -18.8815672015859 | etot = -13.2825376564832 -300000 ekin = 3.21328607489953 | erot = 2.48363458984354 | epot = -18.9794583216121 | etot = -13.2825376568691 -301000 ekin = 3.31333985043737 | erot = 2.48892965616517 | epot = -19.0848071638044 | etot = -13.2825376572019 -302000 ekin = 3.40783628219689 | erot = 2.50232511253499 | epot = -19.1926990521496 | etot = -13.2825376574178 -303000 ekin = 3.49218145837487 | erot = 2.52518642841966 | epot = -19.2999055442772 | etot = -13.2825376574827 -304000 ekin = 3.56312110363183 | erot = 2.55971045465174 | epot = -19.40536921569 | etot = -13.2825376574064 -305000 ekin = 3.61888774143317 | erot = 2.60863169692503 | epot = -19.5100570955986 | etot = -13.2825376572404 -306000 ekin = 3.65906113322132 | erot = 2.67462381277541 | epot = -19.6162226030555 | etot = -13.2825376570587 -307000 ekin = 3.68422703808102 | erot = 2.75956355882423 | epot = -19.7263282538406 | etot = -13.2825376569354 -308000 ekin = 3.69555713019525 | erot = 2.8638613267912 | epot = -19.8419561139128 | etot = -13.2825376569263 -309000 ekin = 3.69442216794192 | erot = 2.98601798220163 | epot = -19.9629778072027 | etot = -13.2825376570592 -310000 ekin = 3.68211177280713 | erot = 3.12248873496362 | epot = -20.0871381651019 | etot = -13.2825376573311 -311000 ekin = 3.65969154495059 | erot = 3.2678638211702 | epot = -20.2100930238326 | etot = -13.2825376577118 -312000 ekin = 3.62799191203365 | erot = 3.41533011396099 | epot = -20.3258596841441 | etot = -13.2825376581495 -313000 ekin = 3.58770577443554 | erot = 3.55735172711468 | epot = -20.4275951601301 | etot = -13.2825376585799 -314000 ekin = 3.53954680683451 | erot = 3.68647834911027 | epot = -20.5085628148818 | etot = -13.282537658937 -315000 ekin = 3.4844173114834 | erot = 3.79616777476322 | epot = -20.5631227454116 | etot = -13.282537659165 -316000 ekin = 3.42353216211074 | erot = 3.88149414080693 | epot = -20.5875639621475 | etot = -13.2825376592299 -317000 ekin = 3.35845872751502 | erot = 3.93962315500785 | epot = -20.5806195416482 | etot = -13.2825376591254 -318000 ekin = 3.2910554651844 | erot = 3.96997627515888 | epot = -20.5435693992165 | etot = -13.2825376588732 -319000 ekin = 3.223320732024 | erot = 3.97407140328373 | epot = -20.479929793824 | etot = -13.2825376585163 -320000 ekin = 3.15718962490234 | erot = 3.9550982666567 | epot = -20.3948255496666 | etot = -13.2825376581075 -321000 ekin = 3.09432530925327 | erot = 3.91739375694779 | epot = -20.2942567238311 | etot = -13.28253765763 -322000 ekin = 3.03585792728448 | erot = 3.86620572599247 | epot = -20.1846013105892 | etot = -13.2825376573123 -323000 ekin = 2.98241823057113 | erot = 3.80588679425271 | epot = -20.0708426818646 | etot = -13.2825376570408 -324000 ekin = 2.93426965651669 | erot = 3.74025042750917 | epot = -19.9570577408439 | etot = -13.2825376568181 -325000 ekin = 2.89141991680417 | erot = 3.67265058789432 | epot = -19.8466081613358 | etot = -13.2825376566373 -326000 ekin = 2.85377350486309 | erot = 3.60592095018933 | epot = -19.7422321115398 | etot = -13.2825376564874 -327000 ekin = 2.82127903352093 | erot = 3.54238718474863 | epot = -19.6462038746274 | etot = -13.2825376563578 -328000 ekin = 2.7940403019229 | erot = 3.4839107987806 | epot = -19.5604887570628 | etot = -13.2825376563592 -329000 ekin = 2.77197949436762 | erot = 3.43169110626222 | epot = -19.4862082569527 | etot = -13.2825376563229 -330000 ekin = 2.75494613632944 | erot = 3.38614869284798 | epot = -19.4236324854868 | etot = -13.2825376563094 -331000 ekin = 2.74315934445212 | erot = 3.34732307626857 | epot = -19.3730200770426 | etot = -13.2825376563219 -332000 ekin = 2.73688271481215 | erot = 3.3148484337223 | epot = -19.3342688048984 | etot = -13.282537656364 -333000 ekin = 2.73633973950942 | erot = 3.28798960596993 | epot = -19.306867001918 | etot = -13.2825376564386 -334000 ekin = 2.74163678826744 | erot = 3.26568447791269 | epot = -19.2898589227258 | etot = -13.2825376565456 -335000 ekin = 2.75270974558534 | erot = 3.24660647154451 | epot = -19.2818538738101 | etot = -13.2825376566802 -336000 ekin = 2.76930297431775 | erot = 3.22925893950186 | epot = -19.2810995706518 | etot = -13.2825376568322 -337000 ekin = 2.79098432744158 | erot = 3.21211025351894 | epot = -19.2856322379462 | etot = -13.2825376569857 -338000 ekin = 2.81719266282506 | erot = 3.19377253885645 | epot = -19.2935028588025 | etot = -13.282537657121 -339000 ekin = 2.84730801445539 | erot = 3.17321131001621 | epot = -19.3030569816891 | etot = -13.2825376572175 -340000 ekin = 2.88072770851369 | erot = 3.14995757252084 | epot = -19.3132229382919 | etot = -13.2825376572574 -341000 ekin = 2.91693042220102 | erot = 3.12427992089927 | epot = -19.3237480003323 | etot = -13.282537657232 -342000 ekin = 2.95550483676992 | erot = 3.09726362719681 | epot = -19.3353061211116 | etot = -13.2825376571449 -343000 ekin = 2.9961267955816 | erot = 3.07075651726459 | epot = -19.3494209698604 | etot = -13.2825376570142 -344000 ekin = 3.03848111852457 | erot = 3.04717169214071 | epot = -19.3681904675347 | etot = -13.2825376568694 -345000 ekin = 3.08214069495797 | erot = 3.02917600552114 | epot = -19.3938543572237 | etot = -13.2825376567446 -346000 ekin = 3.12643023842184 | erot = 3.019323916367 | epot = -19.4282918114614 | etot = -13.2825376566725 -347000 ekin = 3.17030571950563 | erot = 3.01970377197954 | epot = -19.4725471481646 | etot = -13.2825376566794 -348000 ekin = 3.21227615188227 | erot = 3.03164750475753 | epot = -19.5264613134215 | etot = -13.2825376567817 -349000 ekin = 3.25037907572045 | erot = 3.05552302028484 | epot = -19.5884397529928 | etot = -13.2825376569875 -350000 ekin = 3.28221302801698 | erot = 3.090612077422 | epot = -19.655362762734 | etot = -13.282537657295 -351000 ekin = 3.30503586845675 | erot = 3.13508039752096 | epot = -19.7226539236659 | etot = -13.2825376576882 -352000 ekin = 3.31595350171735 | erot = 3.18605925818043 | epot = -19.7845504180312 | etot = -13.2825376581334 -353000 ekin = 3.31222586318789 | erot = 3.2398547104606 | epot = -19.8346182322276 | etot = -13.2825376585791 -354000 ekin = 3.29169173965575 | erot = 3.29228360641242 | epot = -19.8665130050276 | etot = -13.2825376589594 -355000 ekin = 3.25327251248046 | erot = 3.33911881639371 | epot = -19.8749289880786 | etot = -13.2825376592044 -356000 ekin = 3.19745645460935 | erot = 3.37659336434066 | epot = -19.8565874782071 | etot = -13.2825376592571 -357000 ekin = 3.12661218039488 | erot = 3.40186563883939 | epot = -19.8110154783303 | etot = -13.282537659096 -358000 ekin = 3.04496261886749 | erot = 3.41331336007688 | epot = -19.7408136376952 | etot = -13.2825376587508 -359000 ekin = 2.95811577563389 | erot = 3.41055161315594 | epot = -19.65120504709 | etot = -13.2825376583002 -360000 ekin = 2.87219670777466 | erot = 3.39416675335385 | epot = -19.5489011189775 | etot = -13.282537657849 -361000 ekin = 2.79279437102923 | erot = 3.36527462495985 | epot = -19.4406066534821 | etot = -13.282537657493 -362000 ekin = 2.7240341162549 | erot = 3.32507906116193 | epot = -19.331650834705 | etot = -13.2825376572881 -363000 ekin = 2.6680503223993 | erot = 3.27458936074052 | epot = -19.2251773403761 | etot = -13.2825376572363 -364000 ekin = 2.62498064266483 | erot = 3.21457203232936 | epot = -19.1220903322872 | etot = -13.282537657293 -365000 ekin = 2.59341335852256 | erot = 3.14571210015879 | epot = -19.0216631160705 | etot = -13.2825376573892 -366000 ekin = 2.57108401614146 | erot = 3.06888690043657 | epot = -18.9225085740357 | etot = -13.2825376574577 -367000 ekin = 2.55558493490922 | erot = 2.98543100060401 | epot = -18.8235535929648 | etot = -13.2825376574516 -368000 ekin = 2.54491188940874 | erot = 2.89729436784111 | epot = -18.7247439146015 | etot = -13.2825376573517 -369000 ekin = 2.53777310784828 | erot = 2.80704690677514 | epot = -18.6273576717881 | etot = -13.2825376571646 -370000 ekin = 2.53338825950351 | erot = 2.71819995751228 | epot = -18.5341258738832 | etot = -13.2825376568674 -371000 ekin = 2.53146597101795 | erot = 2.63443214139539 | epot = -18.4484357690378 | etot = -13.2825376566244 -372000 ekin = 2.53305224681573 | erot = 2.55818112001752 | epot = -18.3737710231763 | etot = -13.282537656343 -373000 ekin = 2.53983164211189 | erot = 2.49190590621672 | epot = -18.314275204369 | etot = -13.2825376560404 -374000 ekin = 2.5539361342706 | erot = 2.43803861080169 | epot = -18.2745124008035 | etot = -13.2825376557312 -375000 ekin = 2.57759599288755 | erot = 2.39898190221675 | epot = -18.2591155506456 | etot = -13.2825376555413 -376000 ekin = 2.61177868596779 | erot = 2.3771002007207 | epot = -18.2714165420646 | etot = -13.2825376553761 -377000 ekin = 2.65778740675903 | erot = 2.37359397109588 | epot = -18.313919033141 | etot = -13.2825376552861 -378000 ekin = 2.71669984604403 | erot = 2.38881656768454 | epot = -18.3880540690293 | etot = -13.2825376553007 -379000 ekin = 2.78887075408053 | erot = 2.42222171828729 | epot = -18.493630127821 | etot = -13.2825376554532 -380000 ekin = 2.8735893047097 | erot = 2.47221119730624 | epot = -18.6283381577863 | etot = -13.2825376557704 -381000 ekin = 2.96878304795772 | erot = 2.53604633164126 | epot = -18.7873670358596 | etot = -13.2825376562607 -382000 ekin = 3.07087981816342 | erot = 2.60989110069439 | epot = -18.9633085757602 | etot = -13.2825376569024 -383000 ekin = 3.17493836101257 | erot = 2.68903209116691 | epot = -19.1465081098174 | etot = -13.2825376576379 -384000 ekin = 3.27511217440233 | erot = 2.76828123033647 | epot = -19.3259310631177 | etot = -13.2825376583789 -385000 ekin = 3.36541347868712 | erot = 2.84251901104278 | epot = -19.4904701487519 | etot = -13.282537659022 -386000 ekin = 3.44062041949954 | erot = 2.90728609466352 | epot = -19.6304441736393 | etot = -13.2825376594762 -387000 ekin = 3.49708416826315 | erot = 2.95929717263814 | epot = -19.7389190005894 | etot = -13.2825376596881 -388000 ekin = 3.53320899932111 | erot = 2.99676007578797 | epot = -19.8125067347609 | etot = -13.2825376596518 -389000 ekin = 3.5495047719137 | erot = 3.01944441497906 | epot = -19.8514868462961 | etot = -13.2825376594033 -390000 ekin = 3.54826504042848 | erot = 3.02852374317564 | epot = -19.8593264426069 | etot = -13.2825376590028 -391000 ekin = 3.53302701092198 | erot = 3.02626577204788 | epot = -19.8418304414875 | etot = -13.2825376585177 -392000 ekin = 3.50797457908343 | erot = 3.01564117086773 | epot = -19.8061534079638 | etot = -13.2825376580127 -393000 ekin = 3.47739262395909 | erot = 2.99988985775782 | epot = -19.7598201392632 | etot = -13.2825376575463 -394000 ekin = 3.44522282252996 | erot = 2.98206454116529 | epot = -19.7098250208642 | etot = -13.282537657169 -395000 ekin = 3.41473630917387 | erot = 2.9645789212076 | epot = -19.6618528873007 | etot = -13.2825376569193 -396000 ekin = 3.38832727675903 | erot = 2.94881280953917 | epot = -19.6196777431179 | etot = -13.2825376568196 -397000 ekin = 3.36743033117465 | erot = 2.93484808693188 | epot = -19.5848160749774 | etot = -13.2825376568709 -398000 ekin = 3.35256101408384 | erot = 2.92141113768411 | epot = -19.5565098088173 | etot = -13.2825376570493 -399000 ekin = 3.34346845310144 | erot = 2.90607029857573 | epot = -19.5320764089866 | etot = -13.2825376573094 -400000 ekin = 3.33937255609437 | erot = 2.88568094014063 | epot = -19.5075911538258 | etot = -13.2825376575908 -401000 ekin = 3.33924190395899 | erot = 2.85700017339502 | epot = -19.4787797351863 | etot = -13.2825376578323 -402000 ekin = 3.34205998353892 | erot = 2.81733492843204 | epot = -19.441932569956 | etot = -13.282537657985 -403000 ekin = 3.34703246955511 | erot = 2.76507190137545 | epot = -19.394642028952 | etot = -13.2825376580215 -404000 ekin = 3.35370775612911 | erot = 2.69997817544774 | epot = -19.3362235895154 | etot = -13.2825376579385 -405000 ekin = 3.36200495975409 | erot = 2.62323862901266 | epot = -19.2677812465193 | etot = -13.2825376577526 -406000 ekin = 3.37216882210879 | erot = 2.53727277109617 | epot = -19.1919792506971 | etot = -13.2825376574921 -407000 ekin = 3.38467286642281 | erot = 2.44541531528747 | epot = -19.1126258389005 | etot = -13.2825376571902 -408000 ekin = 3.40009251679172 | erot = 2.35154628927638 | epot = -19.0341764629477 | etot = -13.2825376568796 -409000 ekin = 3.41896361161102 | erot = 2.25973253002432 | epot = -18.9612337982252 | etot = -13.2825376565899 -410000 ekin = 3.44163818667578 | erot = 2.17391337707833 | epot = -18.8980892201011 | etot = -13.282537656347 -411000 ekin = 3.46814489278265 | erot = 2.09764003834874 | epot = -18.8483225873038 | etot = -13.2825376561724 -412000 ekin = 3.49806473021384 | erot = 2.03386747107535 | epot = -18.8144698573718 | etot = -13.2825376560826 -413000 ekin = 3.53043538014641 | erot = 1.98479597299823 | epot = -18.7977690092331 | etot = -13.2825376560885 -414000 ekin = 3.5637005865262 | erot = 1.95176512736844 | epot = -18.7980033700874 | etot = -13.2825376561927 -415000 ekin = 3.59572274043577 | erot = 1.93521132484319 | epot = -18.8134717216665 | etot = -13.2825376563875 -416000 ekin = 3.62387476619239 | erot = 1.93470676736698 | epot = -18.8411191902125 | etot = -13.2825376566531 -417000 ekin = 3.64521944272459 | erot = 1.94909657754553 | epot = -18.8768536772273 | etot = -13.2825376569572 -418000 ekin = 3.65676940727035 | erot = 1.97673635559896 | epot = -18.9160434201279 | etot = -13.2825376572586 -419000 ekin = 3.65580092830618 | erot = 2.01580487492028 | epot = -18.9541434607407 | etot = -13.2825376575142 -420000 ekin = 3.64017400050736 | erot = 2.06463212116818 | epot = -18.9873437793641 | etot = -13.2825376576886 -421000 ekin = 3.60860065288865 | erot = 2.12196023054627 | epot = -19.0130985411983 | etot = -13.2825376577633 -422000 ekin = 3.56080810554219 | erot = 2.18705814556919 | epot = -19.0304039088537 | etot = -13.2825376577423 -423000 ekin = 3.49756602992945 | erot = 2.25964754075635 | epot = -19.0397512283355 | etot = -13.2825376576497 -424000 ekin = 3.42057977942507 | erot = 2.33965549129906 | epot = -19.0427729282473 | etot = -13.2825376575231 -425000 ekin = 3.33228159149811 | erot = 2.42686463918893 | epot = -19.0416838880909 | etot = -13.2825376574039 -426000 ekin = 3.2355690960636 | erot = 2.52056283158548 | epot = -19.0386695849744 | etot = -13.2825376573253 -427000 ekin = 3.13354188401682 | erot = 2.61929302170817 | epot = -19.0353725630316 | etot = -13.2825376573066 -428000 ekin = 3.02927593448342 | erot = 2.72077464105999 | epot = -19.0325882328923 | etot = -13.2825376573489 -429000 ekin = 2.92565831326665 | erot = 2.82201873865516 | epot = -19.03021470936 | etot = -13.2825376574382 -430000 ekin = 2.82528572275416 | erot = 2.9196013800765 | epot = -19.0274247603835 | etot = -13.2825376575529 -431000 ekin = 2.73041359107529 | erot = 3.01000711728887 | epot = -19.0229583660374 | etot = -13.2825376576732 -432000 ekin = 2.64293211741183 | erot = 3.08992822754027 | epot = -19.0153980027419 | etot = -13.2825376577898 -433000 ekin = 2.5643487123274 | erot = 3.15643021828688 | epot = -19.0033165885191 | etot = -13.2825376579049 -434000 ekin = 2.49577139885486 | erot = 3.20696626802801 | epot = -18.9852753249085 | etot = -13.2825376580257 -435000 ekin = 2.43791477049345 | erot = 3.23932321271082 | epot = -18.9597756413533 | etot = -13.282537658149 -436000 ekin = 2.39117206292075 | erot = 3.25164920249633 | epot = -18.9253589236664 | etot = -13.2825376582494 -437000 ekin = 2.35579129858636 | erot = 3.24269240916056 | epot = -18.8810213660233 | etot = -13.2825376582763 -438000 ekin = 2.33215137598552 | erot = 3.2122573583515 | epot = -18.8269463925089 | etot = -13.2825376581719 -439000 ekin = 2.32106357051098 | erot = 3.16171527167181 | epot = -18.7653165000812 | etot = -13.2825376578984 -440000 ekin = 2.32396046468774 | erot = 3.09429994298168 | epot = -18.7007980651355 | etot = -13.282537657466 -441000 ekin = 2.34282585391452 | erot = 3.01497153468354 | epot = -18.640335045538 | etot = -13.2825376569399 -442000 ekin = 2.37979980925604 | erot = 2.92981680804556 | epot = -18.592154273725 | etot = -13.2825376564234 -443000 ekin = 2.43656228551105 | erot = 2.84513622245103 | epot = -18.5642361639989 | etot = -13.2825376560368 -444000 ekin = 2.51342571777136 | erot = 2.7665603961214 | epot = -18.5625237697588 | etot = -13.2825376558661 -445000 ekin = 2.60880718707288 | erot = 2.69827998895654 | epot = -18.5896248319851 | etot = -13.2825376559556 -446000 ekin = 2.71906096767751 | erot = 2.64257205052438 | epot = -18.6441706744987 | etot = -13.2825376562969 -447000 ekin = 2.83874401672896 | erot = 2.59965346897449 | epot = -18.7209351425399 | etot = -13.2825376568365 -448000 ekin = 2.96126772415897 | erot = 2.5678148089411 | epot = -18.8116201905962 | etot = -13.2825376574961 -449000 ekin = 3.07973256248984 | erot = 2.54376856118504 | epot = -18.9060387818655 | etot = -13.2825376581906 -450000 ekin = 3.18773299393897 | erot = 2.52315582293486 | epot = -18.9934264757104 | etot = -13.2825376588365 -451000 ekin = 3.28001368753319 | erot = 2.50120181208189 | epot = -19.063753158964 | etot = -13.2825376593489 -452000 ekin = 3.35296274689406 | erot = 2.47353158346045 | epot = -19.1090319899994 | etot = -13.2825376596449 -453000 ekin = 3.40494017429965 | erot = 2.43707428125779 | epot = -19.1245521152213 | etot = -13.2825376596638 -454000 ekin = 3.43637551402205 | erot = 2.39082250837186 | epot = -19.1097356817972 | etot = -13.2825376594033 -455000 ekin = 3.44952760873151 | erot = 2.33613006950087 | epot = -19.0681953371467 | etot = -13.2825376589143 -456000 ekin = 3.44799144671739 | erot = 2.27640153123032 | epot = -19.0069306362556 | etot = -13.2825376583079 -457000 ekin = 3.43601809741101 | erot = 2.21623652990966 | epot = -18.9347922850214 | etot = -13.2825376577007 -458000 ekin = 3.41788845142157 | erot = 2.1603621628938 | epot = -18.8607882715007 | etot = -13.2825376571853 -459000 ekin = 3.39749151939687 | erot = 2.11268532597155 | epot = -18.7927145021832 | etot = -13.2825376568148 -460000 ekin = 3.37812232252718 | erot = 2.07567909161626 | epot = -18.7363390707458 | etot = -13.2825376566023 -461000 ekin = 3.36231617612891 | erot = 2.05042996966763 | epot = -18.695283802365 | etot = -13.2825376565685 -462000 ekin = 3.3516010060682 | erot = 2.03669678982626 | epot = -18.6708354525534 | etot = -13.2825376566589 -463000 ekin = 3.34749626496938 | erot = 2.03201016323612 | epot = -18.6620440849644 | etot = -13.2825376567589 -464000 ekin = 3.35152548102323 | erot = 2.03372508145255 | epot = -18.6677882192986 | etot = -13.2825376568228 -465000 ekin = 3.36505604034897 | erot = 2.03980035193984 | epot = -18.6873940492544 | etot = -13.2825376569656 -466000 ekin = 3.38750814155411 | erot = 2.04917645651097 | epot = -18.7192222551879 | etot = -13.2825376571228 -467000 ekin = 3.41781846537007 | erot = 2.06078922447704 | epot = -18.7611453471536 | etot = -13.2825376573065 -468000 ekin = 3.45442517050212 | erot = 2.07383123667033 | epot = -18.8107940646966 | etot = -13.2825376575241 -469000 ekin = 3.49517146555834 | erot = 2.08763407955762 | epot = -18.8653432028907 | etot = -13.2825376577748 -470000 ekin = 3.53754304391518 | erot = 2.10145518357448 | epot = -18.9215358855326 | etot = -13.2825376580429 -471000 ekin = 3.57898487463084 | erot = 2.11439735084177 | epot = -18.9759198837659 | etot = -13.2825376582933 -472000 ekin = 3.61725786632598 | erot = 2.12555669055681 | epot = -19.0253522153561 | etot = -13.2825376584733 -473000 ekin = 3.65079380576263 | erot = 2.13440730770723 | epot = -19.0677387719965 | etot = -13.2825376585267 -474000 ekin = 3.67897471803139 | erot = 2.14127953357929 | epot = -19.1027919100348 | etot = -13.2825376584241 -475000 ekin = 3.70221628145293 | erot = 2.14765507905513 | epot = -19.1324090186972 | etot = -13.2825376581891 -476000 ekin = 3.72174790903021 | erot = 2.15602304576331 | epot = -19.1603086126937 | etot = -13.2825376579002 -477000 ekin = 3.73912018616709 | erot = 2.16928365664513 | epot = -19.1909415004644 | etot = -13.2825376576521 -478000 ekin = 3.75565100638758 | erot = 2.1899930971983 | epot = -19.2281817610922 | etot = -13.2825376575063 -479000 ekin = 3.77207488928686 | erot = 2.21984602917254 | epot = -19.2744585759276 | etot = -13.2825376574682 -480000 ekin = 3.78851866246341 | erot = 2.25959918548815 | epot = -19.3306555054526 | etot = -13.282537657501 -481000 ekin = 3.80616995061591 | erot = 2.3098465976453 | epot = -19.3985542055315 | etot = -13.2825376572703 -482000 ekin = 3.82906961959049 | erot = 2.37155747933625 | epot = -19.4831647566213 | etot = -13.2825376576945 -483000 ekin = 3.85390461343261 | erot = 2.44250735313214 | epot = -19.5789496246827 | etot = -13.2825376581179 -484000 ekin = 3.87679301499658 | erot = 2.51997841364319 | epot = -19.67930908719 | etot = -13.2825376585502 -485000 ekin = 3.89418558521177 | erot = 2.6008312618536 | epot = -19.7775545060503 | etot = -13.2825376589849 -486000 ekin = 3.90313775339899 | erot = 2.68139032002724 | epot = -19.8670657328067 | etot = -13.2825376593805 -487000 ekin = 3.90177537850701 | erot = 2.75761792311815 | epot = -19.9419309612886 | etot = -13.2825376596635 -488000 ekin = 3.889862131621 | erot = 2.82561628023752 | epot = -19.9980160716145 | etot = -13.282537659756 -489000 ekin = 3.86922231453781 | erot = 2.88229752819473 | epot = -20.0340575023524 | etot = -13.2825376596199 -490000 ekin = 3.84371636435403 | erot = 2.92590481083913 | epot = -20.0521588344865 | etot = -13.2825376592933 -491000 ekin = 3.81858290487071 | erot = 2.9560720610093 | epot = -20.0571926247727 | etot = -13.2825376588927 -492000 ekin = 3.79923632244415 | erot = 2.97333279544435 | epot = -20.0551067764556 | etot = -13.2825376585671 -493000 ekin = 3.78992062784184 | erot = 2.97831679174276 | epot = -20.0507750780124 | etot = -13.2825376584278 -494000 ekin = 3.79229313456423 | erot = 2.9705277109171 | epot = -20.0453585079524 | etot = -13.282537662471 -495000 ekin = 3.79451442394719 | erot = 2.93410724508575 | epot = -20.011159328423 | etot = -13.28253765939 -496000 ekin = 3.81062488236668 | erot = 2.88141942471639 | epot = -19.9745819636242 | etot = -13.2825376565411 -497000 ekin = 3.85788186105167 | erot = 2.8337274407664 | epot = -19.9741469603156 | etot = -13.2825376584975 -498000 ekin = 3.91884579383985 | erot = 2.78115548049834 | epot = -19.9825389376995 | etot = -13.2825376633613 -499000 ekin = 3.96315793686362 | erot = 2.70246806480193 | epot = -19.9481636596236 | etot = -13.2825376579581 -500000 ekin = 4.00272057627429 | erot = 2.6104605460005 | epot = -19.8957187797396 | etot = -13.2825376574648 -501000 ekin = 4.04216054274959 | erot = 2.51312796102747 | epot = -19.8378261606831 | etot = -13.2825376569061 -502000 ekin = 4.08330148514055 | erot = 2.41632704308052 | epot = -19.7821661846333 | etot = -13.2825376564122 -503000 ekin = 4.12765179374079 | erot = 2.32533692996321 | epot = -19.7355263797777 | etot = -13.2825376560737 -504000 ekin = 4.17571661390362 | erot = 2.24418432884543 | epot = -19.7024385986737 | etot = -13.2825376559247 -505000 ekin = 4.22673456415084 | erot = 2.17536462285507 | epot = -19.6846368429506 | etot = -13.2825376559447 -506000 ekin = 4.27886046446231 | erot = 2.11995169726186 | epot = -19.6813498177051 | etot = -13.2825376559809 -507000 ekin = 4.32989839510322 | erot = 2.07798999627042 | epot = -19.6904260476131 | etot = -13.2825376562394 -508000 ekin = 4.3768369745921 | erot = 2.0484622335072 | epot = -19.7078368645372 | etot = -13.2825376564379 -509000 ekin = 4.41701088937313 | erot = 2.0304046125134 | epot = -19.7299531584259 | etot = -13.2825376565393 -510000 ekin = 4.44869291188757 | erot = 2.0233924534456 | epot = -19.7546230218699 | etot = -13.2825376565367 -511000 ekin = 4.47114700664101 | erot = 2.02761863548855 | epot = -19.7813032985787 | etot = -13.2825376564492 -512000 ekin = 4.48448870189135 | erot = 2.04375687850346 | epot = -19.8107832368134 | etot = -13.2825376564186 -513000 ekin = 4.48914630707508 | erot = 2.07205454687262 | epot = -19.8437385103018 | etot = -13.2825376563541 -514000 ekin = 4.48557666179932 | erot = 2.11236294794912 | epot = -19.880477266066 | etot = -13.2825376563175 -515000 ekin = 4.47432723707008 | erot = 2.16436581139646 | epot = -19.9212307047954 | etot = -13.2825376563288 -516000 ekin = 4.45582679665326 | erot = 2.22719069336678 | epot = -19.9655551464159 | etot = -13.2825376563958 -517000 ekin = 4.43030463229704 | erot = 2.29935278530235 | epot = -20.0121950741138 | etot = -13.2825376565144 -518000 ekin = 4.39778184135852 | erot = 2.37880116113811 | epot = -20.0591206591697 | etot = -13.282537656673 -519000 ekin = 4.35811170485676 | erot = 2.46303435402768 | epot = -20.1036837157425 | etot = -13.2825376568581 -520000 ekin = 4.31103971552051 | erot = 2.54924277018622 | epot = -20.1428201427636 | etot = -13.2825376570569 -521000 ekin = 4.25625922128501 | erot = 2.63444730370309 | epot = -20.173244182248 | etot = -13.2825376572599 -522000 ekin = 4.19345339504261 | erot = 2.71562973710984 | epot = -20.1916207896092 | etot = -13.2825376574568 -523000 ekin = 4.12233106589696 | erot = 2.78987661785769 | epot = -20.1947453413877 | etot = -13.2825376576331 -524000 ekin = 4.04267462478795 | erot = 2.85456825314245 | epot = -20.1797805356988 | etot = -13.2825376577684 -525000 ekin = 3.95441508753717 | erot = 2.90762892529157 | epot = -20.1445816706651 | etot = -13.2825376578364 -526000 ekin = 3.85773415549755 | erot = 2.94781757723194 | epot = -20.0880893905407 | etot = -13.2825376578112 -527000 ekin = 3.75317337789126 | erot = 2.97499774805777 | epot = -20.0107087836244 | etot = -13.2825376576754 -528000 ekin = 3.6417156647281 | erot = 2.99029287548742 | epot = -19.9145462004724 | etot = -13.2825376602569 -529000 ekin = 3.5213345798146 | erot = 2.97329981123624 | epot = -19.7771720480706 | etot = -13.2825376570198 -530000 ekin = 3.40524483354961 | erot = 2.93138498576056 | epot = -19.6191674717665 | etot = -13.2825376524564 -531000 ekin = 3.31329586024631 | erot = 2.90771179337398 | epot = -19.503545306618 | etot = -13.2825376529977 -532000 ekin = 3.23028138423145 | erot = 2.91095227687854 | epot = -19.4237713182462 | etot = -13.2825376571362 -533000 ekin = 3.12254472504979 | erot = 2.92159652025145 | epot = -19.3266789030896 | etot = -13.2825376577884 -534000 ekin = 3.01044793877335 | erot = 2.93913625615111 | epot = -19.2321218524839 | etot = -13.2825376575594 -535000 ekin = 2.90665974197989 | erot = 2.96765394779521 | epot = -19.1568513472187 | etot = -13.2825376574435 -536000 ekin = 2.81267447143307 | erot = 3.00750648802701 | epot = -19.1027186169091 | etot = -13.282537657449 -537000 ekin = 2.72954271624314 | erot = 3.05761918512468 | epot = -19.0696995589408 | etot = -13.282537657573 -538000 ekin = 2.65787075123318 | erot = 3.1155333628036 | epot = -19.0559417718371 | etot = -13.2825376578003 -539000 ekin = 2.59787048049701 | erot = 3.17759265897041 | epot = -19.058000797571 | etot = -13.2825376581036 -540000 ekin = 2.54945648890533 | erot = 3.23927692411588 | epot = -19.0712710714641 | etot = -13.2825376584429 -541000 ekin = 2.51237864339879 | erot = 3.29568121874551 | epot = -19.0905975209143 | etot = -13.28253765877 -542000 ekin = 2.48636877597475 | erot = 3.34210880590418 | epot = -19.1110152409131 | etot = -13.2825376590342 -543000 ekin = 2.47126990556773 | erot = 3.37470651251081 | epot = -19.1285140772705 | etot = -13.282537659192 -544000 ekin = 2.46711428277069 | erot = 3.39103758941789 | epot = -19.1406895314063 | etot = -13.2825376592177 -545000 ekin = 2.47411735000801 | erot = 3.39046709617408 | epot = -19.1471221052938 | etot = -13.2825376591117 -546000 ekin = 2.49256786330982 | erot = 3.37425739407446 | epot = -19.1493629162877 | etot = -13.2825376589034 -547000 ekin = 2.52261985355643 | erot = 3.34533431810425 | epot = -19.1504918303061 | etot = -13.2825376586455 -548000 ekin = 2.56402294022763 | erot = 3.30777050324809 | epot = -19.1543311018765 | etot = -13.2825376584007 -549000 ekin = 2.61585467172408 | erot = 3.26610888708041 | epot = -19.1645012170318 | etot = -13.2825376582273 -550000 ekin = 2.67632806502137 | erot = 3.22468583527721 | epot = -19.1835515584625 | etot = -13.2825376581639 -551000 ekin = 2.74273542047784 | erot = 3.18709627675137 | epot = -19.212369355452 | etot = -13.2825376582228 -552000 ekin = 2.81155537633641 | erot = 3.15588528380799 | epot = -19.2499783185349 | etot = -13.2825376583905 -553000 ekin = 2.87870715456312 | erot = 3.13247774360667 | epot = -19.2937225568045 | etot = -13.2825376586348 -554000 ekin = 2.93989960588913 | erot = 3.11729757853032 | epot = -19.3397348433338 | etot = -13.2825376589144 -555000 ekin = 2.99100571713839 | erot = 3.10999728881187 | epot = -19.3835406651408 | etot = -13.2825376591905 -556000 ekin = 3.02839929469222 | erot = 3.10971957917835 | epot = -19.4206565333019 | etot = -13.2825376594313 -557000 ekin = 3.04921300214531 | erot = 3.11533545055502 | epot = -19.4470861123157 | etot = -13.2825376596154 -558000 ekin = 3.05150347330643 | erot = 3.12563190762761 | epot = -19.4596730406651 | etot = -13.282537659731 -559000 ekin = 3.03432873632176 | erot = 3.13944482423642 | epot = -19.4563112203321 | etot = -13.2825376597739 -560000 ekin = 2.99775269247934 | erot = 3.15574356338642 | epot = -19.4360339156122 | etot = -13.2825376597465 -561000 ekin = 2.942791717946 | erot = 3.17367577834175 | epot = -19.399005155943 | etot = -13.2825376596552 -562000 ekin = 2.87131567491456 | erot = 3.19257954674671 | epot = -19.3464328811715 | etot = -13.2825376595102 -563000 ekin = 2.78591370477175 | erot = 3.21196929020305 | epot = -19.280420654299 | etot = -13.2825376593242 -564000 ekin = 2.68973533676632 | erot = 3.2315030248807 | epot = -19.2037760207577 | etot = -13.2825376591107 -565000 ekin = 2.58631900803934 | erot = 3.25094003295475 | epot = -19.119796699877 | etot = -13.2825376588829 -566000 ekin = 2.47942134876985 | erot = 3.27009788588037 | epot = -19.0320568933032 | etot = -13.282537658653 -567000 ekin = 2.37285930824509 | erot = 3.28881390753205 | epot = -18.9442108742075 | etot = -13.2825376584304 -568000 ekin = 2.27037477203514 | erot = 3.30691420257913 | epot = -18.8598266328372 | etot = -13.2825376582229 -569000 ekin = 2.17552646993524 | erot = 3.32418852070849 | epot = -18.7822526486799 | etot = -13.2825376580362 -570000 ekin = 2.0916071735766 | erot = 3.34036686781736 | epot = -18.7145116992692 | etot = -13.2825376578753 -571000 ekin = 2.02157831416005 | erot = 3.35509336874294 | epot = -18.6592093406479 | etot = -13.2825376577449 -572000 ekin = 1.96800973250246 | erot = 3.36789498999432 | epot = -18.6184423801486 | etot = -13.2825376576519 -573000 ekin = 1.93301131086791 | erot = 3.37814685793653 | epot = -18.5936958264077 | etot = -13.2825376576033 -574000 ekin = 1.91814454491553 | erot = 3.38504063675326 | epot = -18.5857228392773 | etot = -13.2825376576086 -575000 ekin = 1.92430832573438 | erot = 3.38756624559585 | epot = -18.5944122290066 | etot = -13.2825376576764 -576000 ekin = 1.9516044746804 | erot = 3.38452119824724 | epot = -18.6186633307411 | etot = -13.2825376578134 -577000 ekin = 1.99920036892028 | erot = 3.37456184631277 | epot = -18.6562998732547 | etot = -13.2825376580217 -578000 ekin = 2.06522335780326 | erot = 3.3563097483278 | epot = -18.7040707644236 | etot = -13.2825376582925 -579000 ekin = 2.14673519282893 | erot = 3.32851940881583 | epot = -18.7577922602505 | etot = -13.2825376586057 -580000 ekin = 2.23983758245539 | erot = 3.29029959753275 | epot = -18.8126748389157 | etot = -13.2825376589276 -581000 ekin = 2.33993889925887 | erot = 3.2413588198074 | epot = -18.8638353782815 | etot = -13.2825376592153 -582000 ekin = 2.44216781901565 | erot = 3.18222403799831 | epot = -18.9069295164397 | etot = -13.2825376594258 -583000 ekin = 2.54186285338052 | erot = 3.1143690597616 | epot = -18.9387695726707 | etot = -13.2825376595286 -584000 ekin = 2.63514321917816 | erot = 3.04016994422167 | epot = -18.9578508227168 | etot = -13.2825376593169 -585000 ekin = 2.72038124549096 | erot = 2.96231486728252 | epot = -18.9652337720559 | etot = -13.2825376592824 -586000 ekin = 2.7952974207905 | erot = 2.88397447346059 | epot = -18.9618095534243 | etot = -13.2825376591732 -587000 ekin = 2.85803030912891 | erot = 2.80849541231913 | epot = -18.9490633804701 | etot = -13.2825376590221 -588000 ekin = 2.90761924156397 | erot = 2.73897208361712 | epot = -18.9291289840422 | etot = -13.2825376588611 -589000 ekin = 2.94382190769964 | erot = 2.67796026302752 | epot = -18.9043198294429 | etot = -13.2825376587158 -590000 ekin = 2.96693832518019 | erot = 2.6272442019698 | epot = -18.8767201857498 | etot = -13.2825376585998 -591000 ekin = 2.9776673784336 | erot = 2.58778349308244 | epot = -18.8479885300359 | etot = -13.2825376585198 -592000 ekin = 2.97699718658232 | erot = 2.55971358412153 | epot = -18.8192484291808 | etot = -13.2825376584769 -593000 ekin = 2.96611919165071 | erot = 2.54241252024637 | epot = -18.7910693703647 | etot = -13.2825376584677 -594000 ekin = 2.94635665290357 | erot = 2.53461934100801 | epot = -18.7635136523971 | etot = -13.2825376584855 -595000 ekin = 2.91908569710317 | erot = 2.53443482988756 | epot = -18.736058185673 | etot = -13.2825376586822 -596000 ekin = 2.88535047381584 | erot = 2.53857982682822 | epot = -18.706467959406 | etot = -13.2825376587619 -597000 ekin = 2.84590859895571 | erot = 2.54482361731877 | epot = -18.6732698750857 | etot = -13.2825376588112 -598000 ekin = 2.80153060629686 | erot = 2.55163242418938 | epot = -18.6357006893087 | etot = -13.2825376588225 -599000 ekin = 2.75300405718648 | erot = 2.55803363009657 | epot = -18.5935753460797 | etot = -13.2825376587966 -600000 ekin = 2.70110632480755 | erot = 2.56364667647513 | epot = -18.5472906600213 | etot = -13.2825376587386 -601000 ekin = 2.64657369870734 | erot = 2.56865533019019 | epot = -18.4977666875495 | etot = -13.282537658652 -602000 ekin = 2.59009198471546 | erot = 2.5737572619282 | epot = -18.4463869051824 | etot = -13.2825376585387 -603000 ekin = 2.532310533728 | erot = 2.58010020265793 | epot = -18.3949483947879 | etot = -13.282537658402 -604000 ekin = 2.47386381071126 | erot = 2.58919184015783 | epot = -18.3455933091172 | etot = -13.2825376582481 -605000 ekin = 2.41538802269351 | erot = 2.60277705144679 | epot = -18.3007027322262 | etot = -13.2825376580859 -606000 ekin = 2.35753010243637 | erot = 2.62269152368394 | epot = -18.2627592840459 | etot = -13.2825376579255 -607000 ekin = 2.30095094646976 | erot = 2.65066096470521 | epot = -18.2341495689621 | etot = -13.2825376577872 -608000 ekin = 2.24632550980833 | erot = 2.68812711798965 | epot = -18.2169902854651 | etot = -13.2825376576671 -609000 ekin = 2.19433984204655 | erot = 2.73619296832811 | epot = -18.2130704679535 | etot = -13.2825376575789 -610000 ekin = 2.1456873411568 | erot = 2.79546287797992 | epot = -18.2236878766662 | etot = -13.2825376575294 -611000 ekin = 2.10106577311586 | erot = 2.86594569746529 | epot = -18.2495491281048 | etot = -13.2825376575236 -612000 ekin = 2.0611756976334 | erot = 2.94698805374731 | epot = -18.2907014089446 | etot = -13.2825376575639 -613000 ekin = 2.02671979093704 | erot = 3.03724338411882 | epot = -18.3465008327059 | etot = -13.28253765765 -614000 ekin = 1.99840061160153 | erot = 3.13468327208674 | epot = -18.4156215414674 | etot = -13.2825376577792 -615000 ekin = 1.97691265350056 | erot = 3.2366575694735 | epot = -18.496107880919 | etot = -13.282537657945 -616000 ekin = 1.96292427457188 | erot = 3.34000833576675 | epot = -18.5854702684777 | etot = -13.2825376581391 -617000 ekin = 1.95704706954883 | erot = 3.44123904148788 | epot = -18.6808237693867 | etot = -13.28253765835 -618000 ekin = 1.959794260624 | erot = 3.53673433570158 | epot = -18.7790662548898 | etot = -13.2825376585642 -619000 ekin = 1.9715343673676 | erot = 3.62301686059804 | epot = -18.8770888867321 | etot = -13.2825376587665 -620000 ekin = 1.99244950084197 | erot = 3.69701656992999 | epot = -18.972003729714 | etot = -13.2825376589421 -621000 ekin = 2.02250680812395 | erot = 3.75631711882003 | epot = -19.0613615860228 | etot = -13.2825376590788 -622000 ekin = 2.06144629221926 | erot = 3.79933797526636 | epot = -19.1433219266566 | etot = -13.2825376591709 -623000 ekin = 2.10878075941396 | erot = 3.8254151393852 | epot = -19.2167335580189 | etot = -13.2825376592197 -624000 ekin = 2.16379839199852 | erot = 3.83475982185834 | epot = -19.2810958730921 | etot = -13.2825376592353 -625000 ekin = 2.22555932783782 | erot = 3.82830035124808 | epot = -19.3363973383196 | etot = -13.2825376592337 -626000 ekin = 2.29288544261924 | erot = 3.8074411034664 | epot = -19.3828642053187 | etot = -13.2825376592331 -627000 ekin = 2.36435394306741 | erot = 3.77379464740524 | epot = -19.4206862497203 | etot = -13.2825376592476 -628000 ekin = 2.4383143267512 | erot = 3.72895154256394 | epot = -19.4498035285972 | etot = -13.2825376592821 -629000 ekin = 2.51294897945051 | erot = 3.67434156157469 | epot = -19.4698282003552 | etot = -13.28253765933 -630000 ekin = 2.58638771765393 | erot = 3.61121141783299 | epot = -19.4801367948617 | etot = -13.2825376593748 -631000 ekin = 2.65686759984471 | erot = 3.54070434321331 | epot = -19.4801096088491 | etot = -13.2825376657911 -632000 ekin = 2.7229119026317 | erot = 3.46399577716167 | epot = -19.4694453501616 | etot = -13.2825376703683 -633000 ekin = 2.78348672610773 | erot = 3.38241264799394 | epot = -19.4484370443956 | etot = -13.2825376702939 -634000 ekin = 2.83810143013093 | erot = 3.29749507667659 | epot = -19.4181341769767 | etot = -13.2825376701692 -635000 ekin = 2.88683118401642 | erot = 3.21096793801023 | epot = -19.3803367920312 | etot = -13.2825376700046 -636000 ekin = 2.93026618629758 | erot = 3.12465298496329 | epot = -19.3374568410755 | etot = -13.2825376698146 -637000 ekin = 2.96941056884663 | erot = 3.04036924656817 | epot = -19.2923174850264 | etot = -13.2825376696116 -638000 ekin = 3.0055616969203 | erot = 2.95987410217464 | epot = -19.2479734684973 | etot = -13.2825376694023 -639000 ekin = 3.04019340863902 | erot = 2.88486846877173 | epot = -19.2075995465998 | etot = -13.282537669189 -640000 ekin = 3.07485121522857 | erot = 2.81704601028329 | epot = -19.1744348944859 | etot = -13.282537668974 -641000 ekin = 3.11105408027351 | erot = 2.75813097964004 | epot = -19.1517227286789 | etot = -13.2825376687654 -642000 ekin = 3.15019312326614 | erot = 2.70984405485486 | epot = -19.1425748467004 | etot = -13.2825376685794 -643000 ekin = 3.19342381263007 | erot = 2.6737639947772 | epot = -19.1497254758466 | etot = -13.2825376684393 -644000 ekin = 3.24155882074965 | erot = 2.65109893593392 | epot = -19.1751954250542 | etot = -13.2825376683706 -645000 ekin = 3.29497575522052 | erot = 2.64241916696972 | epot = -19.2199325905852 | etot = -13.282537668395 -646000 ekin = 3.35355393406662 | erot = 2.6474169032197 | epot = -19.2835085058124 | etot = -13.2825376685261 -647000 ekin = 3.41664956860753 | erot = 2.66474995394781 | epot = -19.3639371913219 | etot = -13.2825376687666 -648000 ekin = 3.48311410605676 | erot = 2.69200913896285 | epot = -19.4576609141254 | etot = -13.2825376691058 -649000 ekin = 3.55135925694157 | erot = 2.72583530733012 | epot = -19.5597322337903 | etot = -13.2825376695186 -650000 ekin = 3.61947301797256 | erot = 2.76220049491302 | epot = -19.66421118285 | etot = -13.2825376699645 -651000 ekin = 3.68538880274599 | erot = 2.7968481634757 | epot = -19.7647746366125 | etot = -13.2825376703908 -652000 ekin = 3.74709908730764 | erot = 2.82584894414338 | epot = -19.8554857021924 | etot = -13.2825376707414 -653000 ekin = 3.80288488877765 | erot = 2.84617490646512 | epot = -19.9315974662116 | etot = -13.2825376709688 -654000 ekin = 3.85151192348354 | erot = 2.8561531933117 | epot = -19.990202787845 | etot = -13.2825376710498 -655000 ekin = 3.89233743676938 | erot = 2.8556624036667 | epot = -20.0305375114281 | etot = -13.282537670992 -656000 ekin = 3.92529306043646 | erot = 2.84600373605527 | epot = -20.0538344673234 | etot = -13.2825376708317 -657000 ekin = 3.95074924371718 | erot = 2.82948452039907 | epot = -20.0627714347384 | etot = -13.2825376706221 -658000 ekin = 3.96930448524318 | erot = 2.8088410501164 | epot = -20.0606832057771 | etot = -13.2825376704176 -659000 ekin = 3.98156254977942 | erot = 2.78666073058104 | epot = -20.0507609506214 | etot = -13.282537670261 -660000 ekin = 3.98794995383628 | erot = 2.76493225942287 | epot = -20.0354198834365 | etot = -13.2825376701774 -661000 ekin = 3.98860416115366 | erot = 2.74479055428754 | epot = -20.015932385614 | etot = -13.2825376701728 -662000 ekin = 3.9833373621284 | erot = 2.72646306735558 | epot = -19.9923380997221 | etot = -13.2825376702381 -663000 ekin = 3.97166196864596 | erot = 2.70938404532092 | epot = -19.963583684321 | etot = -13.2825376703541 -664000 ekin = 3.95286211460538 | erot = 2.69242500163181 | epot = -19.9278247867315 | etot = -13.2825376704943 -665000 ekin = 3.92609780976883 | erot = 2.67418491171738 | epot = -19.8828203921176 | etot = -13.2825376706314 -666000 ekin = 3.89053574203668 | erot = 2.65328635574204 | epot = -19.8263597685171 | etot = -13.2825376707384 -667000 ekin = 3.8455051846995 | erot = 2.62863029044565 | epot = -19.7566731459372 | etot = -13.2825376707921 -668000 ekin = 3.79067534881142 | erot = 2.59957256262293 | epot = -19.6727855822096 | etot = -13.2825376707752 -669000 ekin = 3.7262419486302 | erot = 2.56600183381255 | epot = -19.5747814531206 | etot = -13.2825376706778 -670000 ekin = 3.65309967706656 | erot = 2.52832169427138 | epot = -19.4639590418358 | etot = -13.2825376704979 -671000 ekin = 3.57296811019995 | erot = 2.48736383191386 | epot = -19.342869612354 | etot = -13.2825376702402 -672000 ekin = 3.48843263532053 | erot = 2.44427271264383 | epot = -19.2152430178819 | etot = -13.2825376699176 -673000 ekin = 3.40286035230263 | erot = 2.40039617767022 | epot = -19.0857941995252 | etot = -13.2825376695524 -674000 ekin = 3.32015657281286 | erot = 2.35719425457146 | epot = -18.9598884965615 | etot = -13.2825376691772 -675000 ekin = 3.24436019808318 | erot = 2.3161584141183 | epot = -18.8430562810336 | etot = -13.2825376688321 -676000 ekin = 3.17913583606218 | erot = 2.27873161512007 | epot = -18.7404051197388 | etot = -13.2825376685566 -677000 ekin = 3.12743284478882 | erot = 2.24616920609518 | epot = -18.656139719201 | etot = -13.282537668317 -678000 ekin = 3.09116321203348 | erot = 2.21938913067101 | epot = -18.5930900109803 | etot = -13.2825376682758 -679000 ekin = 3.06996492216854 | erot = 2.19955802308236 | epot = -18.5520606135364 | etot = -13.2825376682855 -680000 ekin = 3.06282540104525 | erot = 2.1876705770889 | epot = -18.5330336464577 | etot = -13.2825376683235 -681000 ekin = 3.06856941757744 | erot = 2.18446333304044 | epot = -18.5355704189915 | etot = -13.2825376683736 -682000 ekin = 3.08614503867108 | erot = 2.19031007374487 | epot = -18.558992780881 | etot = -13.282537668465 -683000 ekin = 3.11401676516072 | erot = 2.20483123960418 | epot = -18.6013856734434 | etot = -13.2825376686785 -684000 ekin = 3.14994970495273 | erot = 2.22703766522701 | epot = -18.6595250391531 | etot = -13.2825376689733 -685000 ekin = 3.19138817293996 | erot = 2.25525783712498 | epot = -18.7291836793918 | etot = -13.2825376693269 -686000 ekin = 3.23553597362021 | erot = 2.28721755219637 | epot = -18.8052911955215 | etot = -13.2825376697049 -687000 ekin = 3.27958856788279 | erot = 2.32030038563253 | epot = -18.8824266235811 | etot = -13.2825376700658 -688000 ekin = 3.32103493723499 | erot = 2.35186996598162 | epot = -18.9554425735786 | etot = -13.282537670362 -689000 ekin = 3.35799818037969 | erot = 2.37963585731743 | epot = -19.0201717082469 | etot = -13.2825376705498 -690000 ekin = 3.38953188175939 | erot = 2.40199807237719 | epot = -19.0740676247395 | etot = -13.2825376706029 -691000 ekin = 3.4157714469421 | erot = 2.41828305274825 | epot = -19.1165921702108 | etot = -13.2825376705204 -692000 ekin = 3.43789562335505 | erot = 2.42879295704677 | epot = -19.1492262507342 | etot = -13.2825376703324 -693000 ekin = 3.45784949823239 | erot = 2.43469159317282 | epot = -19.1750787614881 | etot = -13.2825376700829 -694000 ekin = 3.47795427967203 | erot = 2.43774070867895 | epot = -19.1982326581721 | etot = -13.2825376698211 -695000 ekin = 3.50053093039304 | erot = 2.4399713160839 | epot = -19.2230399160612 | etot = -13.2825376695842 -696000 ekin = 3.52761050730482 | erot = 2.44340337549077 | epot = -19.2535515521878 | etot = -13.2825376693922 -697000 ekin = 3.56079077323185 | erot = 2.44986396553548 | epot = -19.2931924080162 | etot = -13.2825376692489 -698000 ekin = 3.60121696147781 | erot = 2.46089758485735 | epot = -19.344652215487 | etot = -13.2825376691518 -699000 ekin = 3.64961213279439 | erot = 2.47770733426397 | epot = -19.4098571361632 | etot = -13.2825376691048 -700000 ekin = 3.70626748084738 | erot = 2.50104915956855 | epot = -19.4898543095423 | etot = -13.2825376691264 -701000 ekin = 3.77093513696172 | erot = 2.53103621287676 | epot = -19.5845090190851 | etot = -13.2825376692466 -702000 ekin = 3.84262768940316 | erot = 2.56687733849248 | epot = -19.692042697393 | etot = -13.2825376694974 -703000 ekin = 3.91940034762487 | erot = 2.606641106386 | epot = -19.8085791239058 | etot = -13.2825376698949 -704000 ekin = 3.99823585473084 | erot = 2.64716826818578 | epot = -19.9279417933416 | etot = -13.282537670425 -705000 ekin = 4.07514464413388 | erot = 2.68423896185882 | epot = -20.0419212770262 | etot = -13.2825376710335 -706000 ekin = 4.14554203036204 | erot = 2.71304391275063 | epot = -20.1411236147438 | etot = -13.2825376716311 -707000 ekin = 4.20487575193296 | erot = 2.72892533730943 | epot = -20.2163387613507 | etot = -13.2825376721083 -708000 ekin = 4.24938283126103 | erot = 2.72825870748057 | epot = -20.2601792111048 | etot = -13.2825376723632 -709000 ekin = 4.27678612884219 | erot = 2.70926619646602 | epot = -20.2685899976397 | etot = -13.2825376723315 -710000 ekin = 4.28673081640694 | erot = 2.67252621891708 | epot = -20.2417947073323 | etot = -13.2825376720083 -711000 ekin = 4.28082322621957 | erot = 2.62101051796723 | epot = -20.1843714156378 | etot = -13.282537671451 -712000 ekin = 4.26225868778 | erot = 2.55962600084258 | epot = -20.1044223593835 | etot = -13.2825376707609 -713000 ekin = 4.23515498223018 | erot = 2.4944028055444 | epot = -20.0120954578277 | etot = -13.2825376700531 -714000 ekin = 4.20378550521692 | erot = 2.43156567584085 | epot = -19.917888850485 | etot = -13.2825376694272 -715000 ekin = 4.17190188733734 | erot = 2.37671476691363 | epot = -19.8311543232015 | etot = -13.2825376689505 -716000 ekin = 4.14226649349206 | erot = 2.3342523697806 | epot = -19.7590565319274 | etot = -13.2825376686548 -717000 ekin = 4.11642945244376 | erot = 2.30708700175745 | epot = -19.7060541227433 | etot = -13.2825376685421 -718000 ekin = 4.09471959165695 | erot = 2.29657561670706 | epot = -19.6738328769572 | etot = -13.2825376685932 -719000 ekin = 4.07639008592127 | erot = 2.30263774999632 | epot = -19.6615655046944 | etot = -13.2825376687768 -720000 ekin = 4.05985922916209 | erot = 2.32397934765001 | epot = -19.6663762458682 | etot = -13.2825376690561 -721000 ekin = 4.04299880693399 | erot = 2.35837721353457 | epot = -19.6839136898589 | etot = -13.2825376693903 -722000 ekin = 4.02343688315899 | erot = 2.40299878610026 | epot = -19.7089733390021 | etot = -13.2825376697429 -723000 ekin = 3.99884065343804 | erot = 2.45471133767568 | epot = -19.7360896611936 | etot = -13.2825376700799 -724000 ekin = 3.96717167902019 | erot = 2.51036796126357 | epot = -19.7600773106559 | etot = -13.2825376703722 -725000 ekin = 3.92690441967021 | erot = 2.56705586836307 | epot = -19.776497958628 | etot = -13.2825376705947 -726000 ekin = 3.877296379763 | erot = 2.62227216901836 | epot = -19.7821062194432 | etot = -13.2825376706619 -727000 ekin = 3.81909687723751 | erot = 2.67389404657874 | epot = -19.7755285945101 | etot = -13.2825376706939 -728000 ekin = 3.75316507804808 | erot = 2.7209643611948 | epot = -19.7566671098371 | etot = -13.2825376705942 -729000 ekin = 3.68121241124831 | erot = 2.76353487071471 | epot = -19.7272849523308 | etot = -13.2825376703678 -730000 ekin = 3.6059508327336 | erot = 2.8025565644494 | epot = -19.6910450672226 | etot = -13.2825376700396 -731000 ekin = 3.5308358576752 | erot = 2.83972569859104 | epot = -19.653099225923 | etot = -13.2825376696568 -732000 ekin = 3.45966885133483 | erot = 2.87715368835431 | epot = -19.6193602089727 | etot = -13.2825376692835 -733000 ekin = 3.39612153666129 | erot = 2.91688280104535 | epot = -19.5955420066942 | etot = -13.2825376689875 -734000 ekin = 3.34327992468391 | erot = 2.96033658921789 | epot = -19.586154182727 | etot = -13.2825376688252 -735000 ekin = 3.30330112894221 | erot = 3.00783596110657 | epot = -19.5936747588771 | etot = -13.2825376688283 -736000 ekin = 3.27724072963153 | erot = 3.05831043253391 | epot = -19.6180888311626 | etot = -13.2825376689972 -737000 ekin = 3.26506253896072 | erot = 3.10929392283094 | epot = -19.6568941310923 | etot = -13.2825376693006 -738000 ekin = 3.26580566526431 | erot = 3.15723003734709 | epot = -19.7055733722939 | etot = -13.2825376696825 -739000 ekin = 3.27786090585715 | erot = 3.19803615726732 | epot = -19.7584347331987 | etot = -13.2825376700742 -740000 ekin = 3.29929519802999 | erot = 3.22780296867075 | epot = -19.8096358371115 | etot = -13.2825376704108 -741000 ekin = 3.32815980265726 | erot = 3.24345768500962 | epot = -19.8541551583124 | etot = -13.2825376706455 -742000 ekin = 3.36272243968287 | erot = 3.2432241961257 | epot = -19.8884843065695 | etot = -13.282537670761 -743000 ekin = 3.40154954264288 | erot = 3.2265963503818 | epot = -19.910683563855 | etot = -13.2825376708303 -744000 ekin = 3.4435569016163 | erot = 3.19405338784973 | epot = -19.9201479602027 | etot = -13.2825376707366 -745000 ekin = 3.48810285816643 | erot = 3.1476343280298 | epot = -19.9182748567922 | etot = -13.2825376705959 -746000 ekin = 3.53467364483636 | erot = 3.09004249683477 | epot = -19.9072538121133 | etot = -13.2825376704422 -747000 ekin = 3.58273489719278 | erot = 3.02422947594395 | epot = -19.8895020434337 | etot = -13.282537670297 -748000 ekin = 3.63163431992382 | erot = 2.95313859311453 | epot = -19.8673105832095 | etot = -13.2825376701711 -749000 ekin = 3.68055410772631 | erot = 2.87956450536645 | epot = -19.8426562831615 | etot = -13.2825376700687 -750000 ekin = 3.72850264878195 | erot = 2.80607481970415 | epot = -19.8171151384803 | etot = -13.2825376699942 -751000 ekin = 3.77431992735756 | erot = 2.73492674317463 | epot = -19.7917843404902 | etot = -13.282537669958 -752000 ekin = 3.81667135032455 | erot = 2.66792933662917 | epot = -19.7671383569314 | etot = -13.2825376699777 -753000 ekin = 3.85401538818405 | erot = 2.60623951614805 | epot = -19.7427925744073 | etot = -13.2825376700752 -754000 ekin = 3.88455267934827 | erot = 2.55013273026535 | epot = -19.7172230798809 | etot = -13.2825376702673 -755000 ekin = 3.90620090059213 | erot = 2.49884999016387 | epot = -19.6875885613037 | etot = -13.2825376705477 -756000 ekin = 3.91710462659181 | erot = 2.45069600001941 | epot = -19.6503382971558 | etot = -13.2825376705446 -757000 ekin = 3.9172579202584 | erot = 2.40369183428787 | epot = -19.6034874252701 | etot = -13.2825376707238 -758000 ekin = 3.9062285486505 | erot = 2.35617894285691 | epot = -19.5449451622691 | etot = -13.2825376707616 -759000 ekin = 3.88450313649663 | erot = 2.30751185300537 | epot = -19.4745526600901 | etot = -13.2825376705881 -760000 ekin = 3.85399004377755 | erot = 2.25863561783757 | epot = -19.395163331816 | etot = -13.2825376702009 -761000 ekin = 3.81799666982571 | erot = 2.21208980046811 | epot = -19.3126241399681 | etot = -13.2825376696743 -762000 ekin = 3.78022631319321 | erot = 2.17128933430875 | epot = -19.2340533167241 | etot = -13.2825376692221 -763000 ekin = 3.7366180252016 | erot = 2.13809664147806 | epot = -19.1572523356113 | etot = -13.2825376689316 -764000 ekin = 3.68660767297656 | erot = 2.11458113784664 | epot = -19.0837264795493 | etot = -13.2825376687261 -765000 ekin = 3.63152213040596 | erot = 2.10258243850173 | epot = -19.0166422375194 | etot = -13.2825376686117 -766000 ekin = 3.57217194872735 | erot = 2.1031936475929 | epot = -18.9579032648434 | etot = -13.2825376685232 -767000 ekin = 3.50915043230658 | erot = 2.11696161070578 | epot = -18.9086497115305 | etot = -13.2825376685181 -768000 ekin = 3.44287730030143 | erot = 2.14384189418983 | epot = -18.8692568629862 | etot = -13.282537668495 -769000 ekin = 3.37407811668166 | erot = 2.18352203430368 | epot = -18.8401378194328 | etot = -13.2825376684474 -770000 ekin = 3.30402691102912 | erot = 2.23544699328996 | epot = -18.8220115727027 | etot = -13.2825376683836 -771000 ekin = 3.23454927904009 | erot = 2.29870117920768 | epot = -18.8157881266211 | etot = -13.2825376683733 -772000 ekin = 3.16778213081539 | erot = 2.37165603567085 | epot = -18.8219758348638 | etot = -13.2825376683776 -773000 ekin = 3.10585178825157 | erot = 2.45189360020701 | epot = -18.8402830568753 | etot = -13.2825376684167 -774000 ekin = 3.05132445362867 | erot = 2.53742495789882 | epot = -18.871287079784 | etot = -13.2825376682565 -775000 ekin = 3.00630147843413 | erot = 2.62609752201218 | epot = -18.9149366688656 | etot = -13.2825376684193 -776000 ekin = 2.97144443264239 | erot = 2.71477730985895 | epot = -18.9687594110712 | etot = -13.2825376685698 -777000 ekin = 2.94698171102012 | erot = 2.80100976983049 | epot = -19.0305291495212 | etot = -13.2825376686706 -778000 ekin = 2.93288277550831 | erot = 2.88339388730573 | epot = -19.098814331498 | etot = -13.282537668684 -779000 ekin = 2.92910730289328 | erot = 2.96183002798064 | epot = -19.1734749994681 | etot = -13.2825376685942 -780000 ekin = 2.93579388568063 | erot = 3.03750518021602 | epot = -19.2558367343219 | etot = -13.2825376684252 -781000 ekin = 2.95325630950229 | erot = 3.11251463627355 | epot = -19.3483086140145 | etot = -13.2825376682386 -782000 ekin = 2.98176618547997 | erot = 3.18917136100467 | epot = -19.453475214596 | etot = -13.2825376681113 -783000 ekin = 3.02122758220232 | erot = 3.26921648813326 | epot = -19.5729817384412 | etot = -13.2825376681056 -784000 ekin = 3.07089714795214 | erot = 3.35319620066784 | epot = -19.706631016868 | etot = -13.2825376682481 -785000 ekin = 3.12925653034025 | erot = 3.44018487512673 | epot = -19.8519790739953 | etot = -13.2825376685283 -786000 ekin = 3.19405797125446 | erot = 3.52788200321986 | epot = -20.0044776433832 | etot = -13.2825376689089 -787000 ekin = 3.26249776188221 | erot = 3.61297785906456 | epot = -20.1580132902899 | etot = -13.2825376693431 -788000 ekin = 3.33144967160237 | erot = 3.69161943951618 | epot = -20.3056067809067 | etot = -13.2825376697881 -789000 ekin = 3.3977055617303 | erot = 3.7598253120626 | epot = -20.4400685440047 | etot = -13.2825376702118 -790000 ekin = 3.45820395550971 | erot = 3.81377941396282 | epot = -20.5545210400606 | etot = -13.282537670588 -791000 ekin = 3.51015148124692 | erot = 3.85000835168307 | epot = -20.6426975044819 | etot = -13.2825376715519 -792000 ekin = 3.54776564943404 | erot = 3.86447708281896 | epot = -20.6947804042004 | etot = -13.2825376719474 -793000 ekin = 3.56673386234454 | erot = 3.85375177260368 | epot = -20.7030233071259 | etot = -13.2825376721777 -794000 ekin = 3.56535433495117 | erot = 3.8159958528987 | epot = -20.6638878600464 | etot = -13.2825376721966 -795000 ekin = 3.5433642377304 | erot = 3.75111846557778 | epot = -20.5770203752941 | etot = -13.2825376719859 -796000 ekin = 3.50191265631727 | erot = 3.66102926484438 | epot = -20.4454795927271 | etot = -13.2825376715655 -797000 ekin = 3.44331621140757 | erot = 3.54957138818473 | epot = -20.2754252705807 | etot = -13.2825376709884 -798000 ekin = 3.37066053438385 | erot = 3.42213246910246 | epot = -20.0753306738125 | etot = -13.2825376703262 -799000 ekin = 3.28735656783115 | erot = 3.28504268659738 | epot = -19.854936924078 | etot = -13.2825376696495 -800000 ekin = 3.19676141014365 | erot = 3.14491706729739 | epot = -19.6242161464546 | etot = -13.2825376690136 -801000 ekin = 3.1019338834663 | erot = 3.00807795311394 | epot = -19.3925495050332 | etot = -13.282537668453 -802000 ekin = 3.00553736754957 | erot = 2.88012979878413 | epot = -19.1682048343172 | etot = -13.2825376679835 -803000 ekin = 2.90985246624439 | erot = 2.76569078056438 | epot = -18.9580809144186 | etot = -13.2825376676099 -804000 ekin = 2.81683808713677 | erot = 2.66824302179126 | epot = -18.7676187762615 | etot = -13.2825376673335 -805000 ekin = 2.72818412044707 | erot = 2.59005510941686 | epot = -18.6007768970192 | etot = -13.2825376671552 -806000 ekin = 2.64532439255026 | erot = 2.53214862203847 | epot = -18.4600106816661 | etot = -13.2825376670774 -807000 ekin = 2.56941186666319 | erot = 2.49430692057274 | epot = -18.3462564543342 | etot = -13.2825376670982 -808000 ekin = 2.50128142888609 | erot = 2.47514940737337 | epot = -18.2589685034691 | etot = -13.2825376672096 -809000 ekin = 2.44144236795178 | erot = 2.47230913362798 | epot = -18.1962891689485 | etot = -13.2825376673687 -810000 ekin = 2.3901270834084 | erot = 2.48271406544476 | epot = -18.1553788164593 | etot = -13.2825376676061 -811000 ekin = 2.34728664736262 | erot = 2.50269653308012 | epot = -18.1325208483028 | etot = -13.2825376678601 -812000 ekin = 2.31275384401542 | erot = 2.52846132067668 | epot = -18.1237528327934 | etot = -13.2825376681013 -813000 ekin = 2.28637472346317 | erot = 2.55641958964496 | epot = -18.1253319814163 | etot = -13.2825376683081 -814000 ekin = 2.26809634302172 | erot = 2.58342175985524 | epot = -18.1340557713469 | etot = -13.2825376684699 -815000 ekin = 2.25799398108596 | erot = 2.60689379309751 | epot = -18.14742544277 | etot = -13.2825376685865 -816000 ekin = 2.25623692236831 | erot = 2.62489117861678 | epot = -18.1636657696475 | etot = -13.2825376686624 -817000 ekin = 2.26301448165039 | erot = 2.63611346240567 | epot = -18.1816656127584 | etot = -13.2825376687023 -818000 ekin = 2.27845464057391 | erot = 2.63992517487904 | epot = -18.2009174841599 | etot = -13.282537668707 -819000 ekin = 2.30255118255274 | erot = 2.63638076673618 | epot = -18.2214696180233 | etot = -13.2825376687344 -820000 ekin = 2.33498671690695 | erot = 2.62599567772565 | epot = -18.2435200633228 | etot = -13.2825376686902 -821000 ekin = 2.37528893738016 | erot = 2.61008048018772 | epot = -18.2679070861769 | etot = -13.282537668609 -822000 ekin = 2.42285081016729 | erot = 2.59073415646192 | epot = -18.2961226351262 | etot = -13.282537668497 -823000 ekin = 2.47691845696036 | erot = 2.57068820917611 | epot = -18.3301443345042 | etot = -13.2825376683677 -824000 ekin = 2.53658809763989 | erot = 2.55309938374537 | epot = -18.3722251496239 | etot = -13.2825376682387 -825000 ekin = 2.60079770131159 | erot = 2.54128433493742 | epot = -18.4246197043761 | etot = -13.2825376681271 -826000 ekin = 2.66832973198145 | erot = 2.53844971720025 | epot = -18.4893171172274 | etot = -13.2825376680457 -827000 ekin = 2.73783541426217 | erot = 2.54745860095133 | epot = -18.5678316832164 | etot = -13.2825376680029 -828000 ekin = 2.80787353741911 | erot = 2.57063837231064 | epot = -18.6610495777373 | etot = -13.2825376680075 -829000 ekin = 2.87694004141752 | erot = 2.60959914998359 | epot = -18.7690768594751 | etot = -13.282537668074 -830000 ekin = 2.94346318720061 | erot = 2.66502277157491 | epot = -18.8910236269993 | etot = -13.2825376682238 -831000 ekin = 3.00576095292576 | erot = 2.73641402737172 | epot = -19.024712648777 | etot = -13.2825376684795 -832000 ekin = 3.06199003539877 | erot = 2.82186650180169 | epot = -19.1663942060527 | etot = -13.2825376688522 -833000 ekin = 3.110148995619 | erot = 2.91795032491558 | epot = -19.3106369898627 | etot = -13.2825376693281 -834000 ekin = 3.1482044935896 | erot = 3.01984474732963 | epot = -19.4505869107779 | etot = -13.2825376698586 -835000 ekin = 3.17437957900523 | erot = 3.12179257978299 | epot = -19.5787098291524 | etot = -13.2825376703642 -836000 ekin = 3.18757195243324 | erot = 3.21784689829009 | epot = -19.6879565214765 | etot = -13.2825376707532 -837000 ekin = 3.18777327474487 | erot = 3.30274497123895 | epot = -19.7730559169407 | etot = -13.2825376709568 -838000 ekin = 3.17628521735482 | erot = 3.37264530226156 | epot = -19.8314681905769 | etot = -13.2825376709605 -839000 ekin = 3.15554655753644 | erot = 3.42547713956057 | epot = -19.8635613679131 | etot = -13.2825376708161 -840000 ekin = 3.12853906990003 | erot = 3.46080086775206 | epot = -19.8718776082709 | etot = -13.2825376706188 -841000 ekin = 3.09797460324615 | erot = 3.47929817821818 | epot = -19.8598104519234 | etot = -13.2825376704591 -842000 ekin = 3.06563312580165 | erot = 3.48217550738637 | epot = -19.8303463035648 | etot = -13.2825376703768 -843000 ekin = 3.03218078490834 | erot = 3.47078119393998 | epot = -19.7854996491911 | etot = -13.2825376703427 -844000 ekin = 2.99754824930944 | erot = 3.44659665122456 | epot = -19.7266825708132 | etot = -13.2825376702792 -845000 ekin = 2.96164676060981 | erot = 3.41154768665394 | epot = -19.6557321173685 | etot = -13.2825376701047 -846000 ekin = 2.92503739739786 | erot = 3.36840998775599 | epot = -19.5759850549297 | etot = -13.2825376697759 -847000 ekin = 2.88924342096714 | erot = 3.32104931095848 | epot = -19.4928304012251 | etot = -13.2825376692995 -848000 ekin = 2.8566499721658 | erot = 3.27432583403358 | epot = -19.4135134749444 | etot = -13.2825376687451 -849000 ekin = 2.83005143133688 | erot = 3.23330176451346 | epot = -19.345890864224 | etot = -13.2825376683736 -850000 ekin = 2.8120559738006 | erot = 3.20226229426142 | epot = -19.2968559356534 | etot = -13.2825376675913 -851000 ekin = 2.80444558745355 | erot = 3.18500981062576 | epot = -19.2719930659006 | etot = -13.2825376678213 -852000 ekin = 2.80546277462239 | erot = 3.18034603826089 | epot = -19.2683464810845 | etot = -13.2825376682013 -853000 ekin = 2.812441214848 | erot = 3.18510929964103 | epot = -19.280088183191 | etot = -13.282537668702 -854000 ekin = 2.82227167902831 | erot = 3.19468161890284 | epot = -19.2994909671701 | etot = -13.282537669239 -855000 ekin = 2.83221172622116 | erot = 3.20377851191435 | epot = -19.3185279077701 | etot = -13.2825376696346 -856000 ekin = 2.840300530071 | erot = 3.20718605729409 | epot = -19.3300242573945 | etot = -13.2825376700294 -857000 ekin = 2.84404786962661 | erot = 3.20080956079347 | epot = -19.3273951006411 | etot = -13.282537670221 -858000 ekin = 2.84179014641021 | erot = 3.18249842090011 | epot = -19.3068262375301 | etot = -13.2825376702198 -859000 ekin = 2.83276149965023 | erot = 3.15199731414756 | epot = -19.2672964838693 | etot = -13.2825376700715 -860000 ekin = 2.81700723540486 | erot = 3.11046780830085 | epot = -19.2100127135333 | etot = -13.2825376698276 -861000 ekin = 2.79529073709182 | erot = 3.05989039483855 | epot = -19.1377188014554 | etot = -13.282537669525 -862000 ekin = 2.76903178122151 | erot = 3.00259641980569 | epot = -19.0541658702098 | etot = -13.2825376691826 -863000 ekin = 2.74026019036715 | erot = 2.94102587737081 | epot = -18.963823736545 | etot = -13.2825376688071 -864000 ekin = 2.71154390224074 | erot = 2.87766995664925 | epot = -18.8717515272941 | etot = -13.2825376684041 -865000 ekin = 2.68585679375552 | erot = 2.81509451397853 | epot = -18.7834889757203 | etot = -13.2825376679863 -866000 ekin = 2.66591731933855 | erot = 2.75755671058339 | epot = -18.7060116974738 | etot = -13.2825376675519 -867000 ekin = 2.65369684329544 | erot = 2.7083623798959 | epot = -18.6445968906238 | etot = -13.2825376674325 -868000 ekin = 2.65132555301973 | erot = 2.66699243377824 | epot = -18.6008556541371 | etot = -13.2825376673391 -869000 ekin = 2.66041858384405 | erot = 2.63308802762824 | epot = -18.5760442787927 | etot = -13.2825376673204 -870000 ekin = 2.68169704364212 | erot = 2.60613905014957 | epot = -18.5703737612166 | etot = -13.2825376674249 -871000 ekin = 2.714675381147 | erot = 2.58511614863126 | epot = -18.5823291974597 | etot = -13.2825376676815 -872000 ekin = 2.75720487538646 | erot = 2.56766485203678 | epot = -18.6074073957568 | etot = -13.2825376683336 -873000 ekin = 2.803086198203 | erot = 2.54585820174232 | epot = -18.6314820689118 | etot = -13.2825376689665 -874000 ekin = 2.84699852608312 | erot = 2.51460161594881 | epot = -18.6441378114779 | etot = -13.282537669446 -875000 ekin = 2.88482415058241 | erot = 2.47158418781059 | epot = -18.6389460079955 | etot = -13.2825376696025 -876000 ekin = 2.91408523336093 | erot = 2.41771772911331 | epot = -18.6143406317811 | etot = -13.2825376693068 -877000 ekin = 2.93423099085002 | erot = 2.35825815691149 | epot = -18.5750268164393 | etot = -13.2825376686778 -878000 ekin = 2.9475340562781 | erot = 2.30086645375619 | epot = -18.5309381778309 | etot = -13.2825376677966 -879000 ekin = 2.95817730736049 | erot = 2.25490663308305 | epot = -18.4956216073008 | etot = -13.2825376668573 -880000 ekin = 2.97089825195544 | erot = 2.22983196329486 | epot = -18.4832678815106 | etot = -13.2825376662603 -881000 ekin = 2.98893595228507 | erot = 2.2333347502509 | epot = -18.504808368297 | etot = -13.282537665761 -882000 ekin = 3.01519221963423 | erot = 2.27015029167503 | epot = -18.567880176909 | etot = -13.2825376655997 -883000 ekin = 3.050977470883 | erot = 2.3416684229247 | epot = -18.6751835596182 | etot = -13.2825376658105 -884000 ekin = 3.0943568254625 | erot = 2.4464864171533 | epot = -18.8233809089841 | etot = -13.2825376663683 -885000 ekin = 3.14183207195904 | erot = 2.57965576029431 | epot = -19.0040254994221 | etot = -13.2825376671687 -886000 ekin = 3.18914822789967 | erot = 2.73331108133882 | epot = -19.2049969773566 | etot = -13.2825376681181 -887000 ekin = 3.23157512360419 | erot = 2.89766014760895 | epot = -19.4117729403353 | etot = -13.2825376691222 -888000 ekin = 3.26456551809744 | erot = 3.061776633054 | epot = -19.6088798212464 | etot = -13.282537670095 -889000 ekin = 3.28428902019584 | erot = 3.21442460415165 | epot = -19.7812512953062 | etot = -13.2825376709587 -890000 ekin = 3.2880122327761 | erot = 3.34493087267995 | epot = -19.9154807770949 | etot = -13.2825376716389 -891000 ekin = 3.27434561774921 | erot = 3.44412613410496 | epot = -20.0010094239182 | etot = -13.282537672064 -892000 ekin = 3.24338163760107 | erot = 3.50530517060629 | epot = -20.0312244803861 | etot = -13.2825376721787 -893000 ekin = 3.19671556304815 | erot = 3.52503469849065 | epot = -20.0042879335016 | etot = -13.2825376719628 -894000 ekin = 3.13731299174224 | erot = 3.50356986371644 | epot = -19.9234205269042 | etot = -13.2825376714456 -895000 ekin = 3.06920917356845 | erot = 3.44471943345056 | epot = -19.7964662777175 | etot = -13.2825376706985 -896000 ekin = 2.99708420339467 | erot = 3.35519757225323 | epot = -19.6348194454631 | etot = -13.2825376698152 -897000 ekin = 2.92580051783905 | erot = 3.24367712658266 | epot = -19.4520153133086 | etot = -13.2825376688869 -898000 ekin = 2.85975229197938 | erot = 3.12035510150211 | epot = -19.2626450613858 | etot = -13.2825376679043 -899000 ekin = 2.80277954780206 | erot = 2.99561467370083 | epot = -19.080931888693 | etot = -13.2825376671901 -900000 ekin = 2.75771035422124 | erot = 2.87733650110699 | epot = -18.9175845220101 | etot = -13.2825376666818 -901000 ekin = 2.72580329203606 | erot = 2.77189091312759 | epot = -18.7802318714396 | etot = -13.282537666276 -902000 ekin = 2.70770279133312 | erot = 2.68464861430094 | epot = -18.6748890716256 | etot = -13.2825376659915 -903000 ekin = 2.70344494055935 | erot = 2.61971222757332 | epot = -18.6056948339768 | etot = -13.2825376658441 -904000 ekin = 2.71249184745662 | erot = 2.57966599078369 | epot = -18.5746955043654 | etot = -13.282537666125 -905000 ekin = 2.73259472267538 | erot = 2.56420422221153 | epot = -18.5793366115826 | etot = -13.2825376666957 -906000 ekin = 2.7587438798969 | erot = 2.57016719355457 | epot = -18.6114487407342 | etot = -13.2825376672827 -907000 ekin = 2.78650456171834 | erot = 2.59279042980544 | epot = -18.6618326594225 | etot = -13.2825376678987 -908000 ekin = 2.81181709571449 | erot = 2.62665482043733 | epot = -18.7210095845851 | etot = -13.2825376684333 -909000 ekin = 2.83143463248052 | erot = 2.66677850527315 | epot = -18.7807508065458 | etot = -13.2825376687921 -910000 ekin = 2.84337824047693 | erot = 2.70952965399883 | epot = -18.8354455634031 | etot = -13.2825376689274 -911000 ekin = 2.8471370687053 | erot = 2.75311048607181 | epot = -18.8827852236336 | etot = -13.2825376688565 -912000 ekin = 2.84353295186199 | erot = 2.79744224266107 | epot = -18.9235128631783 | etot = -13.2825376686553 -913000 ekin = 2.83428813317848 | erot = 2.8435092291879 | epot = -18.960335030794 | etot = -13.2825376684276 -914000 ekin = 2.82145638452692 | erot = 2.89244132990744 | epot = -18.9964353826995 | etot = -13.2825376682651 -915000 ekin = 2.80692071975216 | erot = 2.94469332949274 | epot = -19.0341517174625 | etot = -13.2825376682176 -916000 ekin = 2.79210576380763 | erot = 2.99958827392467 | epot = -19.074231706018 | etot = -13.2825376682857 -917000 ekin = 2.77794567113789 | erot = 3.05530679534728 | epot = -19.1157901349159 | etot = -13.2825376684308 -918000 ekin = 2.76505338704383 | erot = 3.10923861037682 | epot = -19.1568296660157 | etot = -13.282537668595 -919000 ekin = 2.75398705152147 | erot = 3.15852296699156 | epot = -19.195047687236 | etot = -13.282537668723 -920000 ekin = 2.7454994548339 | erot = 3.2005917707977 | epot = -19.2286288944091 | etot = -13.2825376687775 -921000 ekin = 2.74117522185331 | erot = 3.23390288539821 | epot = -19.257615776068 | etot = -13.2825376688165 -922000 ekin = 2.74423942349208 | erot = 3.25833644681568 | epot = -19.2851135392148 | etot = -13.282537668907 -923000 ekin = 2.75519506145705 | erot = 3.27241102947033 | epot = -19.3101437598841 | etot = -13.2825376689567 -924000 ekin = 2.7739447954554 | erot = 3.27524658464716 | epot = -19.3317290491124 | etot = -13.2825376690098 -925000 ekin = 2.79984975930912 | erot = 3.26648541912473 | epot = -19.3488728475327 | etot = -13.2825376690988 -926000 ekin = 2.83154188646909 | erot = 3.24600163470344 | epot = -19.3600811904065 | etot = -13.282537669234 -927000 ekin = 2.86690921927924 | erot = 3.21375665515251 | epot = -19.3632035438309 | etot = -13.2825376693992 -928000 ekin = 2.90327996746315 | erot = 3.16982824225361 | epot = -19.355645879275 | etot = -13.2825376695582 -929000 ekin = 2.93775285768297 | erot = 3.11459709937969 | epot = -19.3348876267298 | etot = -13.2825376696671 -930000 ekin = 2.96759841379162 | erot = 3.04898886674992 | epot = -19.2991249502297 | etot = -13.2825376696882 -931000 ekin = 2.99062544127955 | erot = 2.97467062306529 | epot = -19.2478337339459 | etot = -13.2825376696011 -932000 ekin = 3.00543704340314 | erot = 2.89412065066031 | epot = -19.1820953634703 | etot = -13.2825376694069 -933000 ekin = 3.01154336745331 | erot = 2.81054368701041 | epot = -19.1046247235875 | etot = -13.2825376691237 -934000 ekin = 3.00929679360139 | erot = 2.72759799680406 | epot = -19.0194324597362 | etot = -13.2825376693307 -935000 ekin = 2.99746134196625 | erot = 2.6462580748832 | epot = -18.9262570860315 | etot = -13.282537669182 -936000 ekin = 2.97526415103787 | erot = 2.56749092791625 | epot = -18.8252927479484 | etot = -13.2825376689942 -937000 ekin = 2.94352512534142 | erot = 2.49335517907333 | epot = -18.7194179731942 | etot = -13.2825376687795 -938000 ekin = 2.90367826460953 | erot = 2.42575018416443 | epot = -18.6119661173247 | etot = -13.2825376685508 -939000 ekin = 2.85762227332947 | erot = 2.36633148508484 | epot = -18.5064914267463 | etot = -13.282537668332 -940000 ekin = 2.80750328433938 | erot = 2.31642989471101 | epot = -18.4064708471881 | etot = -13.2825376681377 -941000 ekin = 2.75550936315199 | erot = 2.27698712574217 | epot = -18.3150341568762 | etot = -13.282537667982 -942000 ekin = 2.70367879381712 | erot = 2.24846537191208 | epot = -18.2346818336126 | etot = -13.2825376678834 -943000 ekin = 2.65376367606827 | erot = 2.23082283410801 | epot = -18.1671241780099 | etot = -13.2825376678336 -944000 ekin = 2.60720594190486 | erot = 2.22360475791271 | epot = -18.1133483676354 | etot = -13.2825376678178 -945000 ekin = 2.56519856453037 | erot = 2.22610144827738 | epot = -18.0738376806168 | etot = -13.282537667809 -946000 ekin = 2.52882759913744 | erot = 2.23758213189974 | epot = -18.0489473988157 | etot = -13.2825376677785 -947000 ekin = 2.49923315497847 | erot = 2.25754573394355 | epot = -18.0393165566274 | etot = -13.2825376677054 -948000 ekin = 2.47771007490038 | erot = 2.28590689257171 | epot = -18.04615463506 | etot = -13.2825376675879 -949000 ekin = 2.46568539864087 | erot = 2.32304174073513 | epot = -18.0712648068282 | etot = -13.2825376674522 -950000 ekin = 2.46454516557792 | erot = 2.36959060782326 | epot = -18.1166734407329 | etot = -13.2825376673317 -951000 ekin = 2.47533994997988 | erot = 2.42623129981836 | epot = -18.1841089170701 | etot = -13.2825376672718 -952000 ekin = 2.49848236352815 | erot = 2.49338196896345 | epot = -18.2744019998023 | etot = -13.2825376673107 -953000 ekin = 2.53348398193916 | erot = 2.57089243328743 | epot = -18.3869140826966 | etot = -13.28253766747 -954000 ekin = 2.57882587532342 | erot = 2.65786416805845 | epot = -18.519227711132 | etot = -13.2825376677502 -955000 ekin = 2.63199527599012 | erot = 2.75261052013185 | epot = -18.6671434642546 | etot = -13.2825376681326 -956000 ekin = 2.68967924815822 | erot = 2.85274255005244 | epot = -18.8249594667971 | etot = -13.2825376685864 -957000 ekin = 2.74806771946834 | erot = 2.95533472441412 | epot = -18.9859401129583 | etot = -13.2825376690759 -958000 ekin = 2.8031986668001 | erot = 3.05711581061144 | epot = -19.1428521469807 | etot = -13.2825376695691 -959000 ekin = 2.85127801275525 | erot = 3.15464148732907 | epot = -19.2884571701257 | etot = -13.2825376700414 -960000 ekin = 2.88892608818491 | erot = 3.24442918289745 | epot = -19.4158929415587 | etot = -13.2825376704763 -961000 ekin = 2.91333465071856 | erot = 3.32306194469326 | epot = -19.5189342662741 | etot = -13.2825376708623 -962000 ekin = 2.922351418879 | erot = 3.3872858534114 | epot = -19.5921749434782 | etot = -13.2825376711878 -963000 ekin = 2.91452965717995 | erot = 3.43412743872974 | epot = -19.6311947673485 | etot = -13.2825376714389 -964000 ekin = 2.88918087862635 | erot = 3.46104482999767 | epot = -19.632763380221 | etot = -13.282537671597 -965000 ekin = 2.84645277180946 | erot = 3.46610960648151 | epot = -19.5951000499324 | etot = -13.2825376716414 -966000 ekin = 2.78809663571847 | erot = 3.44886971922285 | epot = -19.5195040264054 | etot = -13.2825376714641 -967000 ekin = 2.71967964182096 | erot = 3.41234902495006 | epot = -19.4145663381934 | etot = -13.2825376714224 -968000 ekin = 2.64387658032753 | erot = 3.35650459869427 | epot = -19.2829188502389 | etot = -13.2825376712171 -969000 ekin = 2.5636598359908 | erot = 3.28213071774803 | epot = -19.1283282245599 | etot = -13.282537670821 -970000 ekin = 2.48311062142641 | erot = 3.19174642313887 | epot = -18.9573947148006 | etot = -13.2825376702353 -971000 ekin = 2.40743965733721 | erot = 3.08950974407855 | epot = -18.7794870709146 | etot = -13.2825376694988 -972000 ekin = 2.34264905762229 | erot = 2.98071332522745 | epot = -18.6059000516929 | etot = -13.2825376688431 -973000 ekin = 2.29453827360496 | erot = 2.87084836320828 | epot = -18.4479243047972 | etot = -13.282537667984 -974000 ekin = 2.26986492523629 | erot = 2.76590322630273 | epot = -18.3183058187963 | etot = -13.2825376672573 -975000 ekin = 2.27457634340147 | erot = 2.67096736257246 | epot = -18.2280813727252 | etot = -13.2825376667513 -976000 ekin = 2.31300758345889 | erot = 2.58967385348542 | epot = -18.1852191035746 | etot = -13.2825376666303 -977000 ekin = 2.38775385248975 | erot = 2.52429198072532 | epot = -18.1945835001601 | etot = -13.282537666945 -978000 ekin = 2.49343132116534 | erot = 2.47478959071677 | epot = -18.250758581399 | etot = -13.2825376695168 -979000 ekin = 2.63194261796709 | erot = 2.43666985312452 | epot = -18.3511501394741 | etot = -13.2825376683825 -980000 ekin = 2.80143349398027 | erot = 2.41383709773151 | epot = -18.4978082614141 | etot = -13.2825376697023 -981000 ekin = 2.97613228560276 | erot = 2.40353470196688 | epot = -18.6622046578968 | etot = -13.2825376703271 -982000 ekin = 3.15493786386392 | erot = 2.40097885129711 | epot = -18.8384543865171 | etot = -13.2825376713561 -983000 ekin = 3.32895075407343 | erot = 2.40358703807687 | epot = -19.0150754641488 | etot = -13.2825376719985 -984000 ekin = 3.48942626012081 | erot = 2.40902391909424 | epot = -19.1809878517146 | etot = -13.2825376724995 -985000 ekin = 3.63060554065164 | erot = 2.41512886518655 | epot = -19.3282720786893 | etot = -13.2825376728511 -986000 ekin = 3.74861810546827 | erot = 2.42024356026037 | epot = -19.4513993386244 | etot = -13.2825376728957 -987000 ekin = 3.84212741102323 | erot = 2.42421773192364 | epot = -19.5488828158586 | etot = -13.2825376729117 -988000 ekin = 3.91118765036607 | erot = 2.42704295376118 | epot = -19.6207682769566 | etot = -13.2825376728293 -989000 ekin = 3.95686695907234 | erot = 2.42875435934639 | epot = -19.6681589910888 | etot = -13.28253767267 -990000 ekin = 3.98122336719007 | erot = 2.42964012334027 | epot = -19.6934011629788 | etot = -13.2825376724485 -991000 ekin = 3.98715071444002 | erot = 2.43015135461192 | epot = -19.6998397412253 | etot = -13.2825376721734 -992000 ekin = 3.97827672381777 | erot = 2.43082965983246 | epot = -19.6916440567119 | etot = -13.2825376730616 -993000 ekin = 3.95551199283863 | erot = 2.42901824167109 | epot = -19.667067907421 | etot = -13.2825376729113 -994000 ekin = 3.91976370648951 | erot = 2.42191618451507 | epot = -19.6242175637032 | etot = -13.2825376726986 -995000 ekin = 3.87458078794846 | erot = 2.4093277557877 | epot = -19.5664462161636 | etot = -13.2825376724274 -996000 ekin = 3.82377191573499 | erot = 2.39162261227942 | epot = -19.4979322001273 | etot = -13.2825376721129 -997000 ekin = 3.77108738620107 | erot = 2.36980944943232 | epot = -19.4234345074163 | etot = -13.282537671783 -998000 ekin = 3.71986049080444 | erot = 2.34548651217898 | epot = -19.3478846744548 | etot = -13.2825376714714 -999000 ekin = 3.67268794449355 | erot = 2.32066228967754 | epot = -19.2758879053829 | etot = -13.2825376712118 -1000000 ekin = 3.63122130708104 | erot = 2.29747929874878 | epot = -19.2112382768594 | etot = -13.2825376710296 - 1000000 0.16138761 -1.2609484 0.060246044 -0.97375106 -5.5311015e-05 -Loop time of 27.9244 on 1 procs for 1000000 steps with 16 atoms - -Performance: 30940.635 tau/day, 35810.920 timesteps/s -98.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 24.096 | 24.096 | 24.096 | 0.0 | 86.29 -Bond | 0.98737 | 0.98737 | 0.98737 | 0.0 | 3.54 -Neigh | 0.000168 | 0.000168 | 0.000168 | 0.0 | 0.00 -Comm | 0.20002 | 0.20002 | 0.20002 | 0.0 | 0.72 -Output | 1e-05 | 1e-05 | 1e-05 | 0.0 | 0.00 -Modify | 2.3385 | 2.3385 | 2.3385 | 0.0 | 8.37 -Other | | 0.3022 | | | 1.08 - -Nlocal: 16.0 ave 16.0 max 16.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.0 ave 0.0 max 0.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 77.0 ave 77.0 max 77.0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 77 -Ave neighs/atom = 4.8125 -Ave special neighs/atom = 3.75 -Neighbor list builds = 7 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:27 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 deleted file mode 100644 index aa5a15156a..0000000000 --- a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 +++ /dev/null @@ -1,1183 +0,0 @@ -LAMMPS (30 Jun 2020) -variable number equal 4 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156) -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex4 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.004 seconds - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxRNA2 bond interactions - FENE backbone -bond_style oxrna2/fene -bond_coeff * 2.0 0.25 0.761070781051 -special_bonds lj 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# oxRNA2 pair interactions -pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh - -pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 -pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 -pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 -pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 -pair_coeff * * oxrna2/dh ${T} 0.5 1.02455 -pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 - -# NVE ensemble -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/dot -fix 1 all nve/asphere - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb -comm_modify cutoff 2.5 - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.3014979 - ghost atom cutoff = 3.3014979 - binsize = 1.650749, bins = 25 25 25 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxrna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxrna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxrna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxrna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxrna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxrna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -WARNING: Communication cutoff adjusted to 3.3014979169291987 (../comm.cpp:690) -0 ekin = 0 | erot = 0 | epot = -13.282537590974 | etot = -13.282537590974 -Per MPI rank memory allocation (min/avg/max) = 8.005 | 8.062 | 8.119 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -0.84341458 0.013255977 -0.8301586 -2.0169485e-05 -1000 ekin = 0.00448503054655829 | erot = 0.00825381229599554 | epot = -13.2952764343121 | etot = -13.2825375914696 -2000 ekin = 0.0179027901180383 | erot = 0.0327684151333158 | epot = -13.333208796773 | etot = -13.2825375915216 -3000 ekin = 0.0401478317723388 | erot = 0.0728240143062734 | epot = -13.3955094376812 | etot = -13.2825375916026 -4000 ekin = 0.0710654348932012 | erot = 0.127292706282676 | epot = -13.4808957328803 | etot = -13.2825375917044 -5000 ekin = 0.110480309743627 | erot = 0.194739074279345 | epot = -13.58775697584 | etot = -13.282537591817 -6000 ekin = 0.158231230694386 | erot = 0.273546913858364 | epot = -13.7143157364821 | etot = -13.2825375919294 -7000 ekin = 0.214206450831694 | erot = 0.362058396900661 | epot = -13.8588024397635 | etot = -13.2825375920312 -8000 ekin = 0.27837411184999 | erot = 0.458709556671591 | epot = -14.0196212606354 | etot = -13.2825375921138 -9000 ekin = 0.350802094030117 | erot = 0.562145629087582 | epot = -14.1954853152897 | etot = -13.282537592172 -10000 ekin = 0.431663021447632 | erot = 0.671302139461542 | epot = -14.3855027531133 | etot = -13.2825375922041 -11000 ekin = 0.521222365620092 | erot = 0.785442646223518 | epot = -14.5892026040564 | etot = -13.2825375922128 -12000 ekin = 0.619810398735201 | erot = 0.90415088836544 | epot = -14.8064988793047 | etot = -13.2825375922041 -13000 ekin = 0.727781531798581 | erot = 1.02728222251184 | epot = -15.0376013464965 | etot = -13.2825375921861 -14000 ekin = 0.845466747659119 | erot = 1.15488520186341 | epot = -15.2828895416906 | etot = -13.2825375921681 -15000 ekin = 0.973515286429056 | erot = 1.28640002432427 | epot = -15.5424529041403 | etot = -13.282537593387 -16000 ekin = 1.12323013751051 | erot = 1.4038749539854 | epot = -15.8096426839246 | etot = -13.2825375924286 -17000 ekin = 1.29769272832575 | erot = 1.51347784068601 | epot = -16.0937081607386 | etot = -13.2825375917268 -18000 ekin = 1.48565191084472 | erot = 1.63592970999597 | epot = -16.4041192134335 | etot = -13.2825375925929 -19000 ekin = 1.66750911163292 | erot = 1.77940241938649 | epot = -16.7294491246356 | etot = -13.2825375936162 -20000 ekin = 1.84148924290367 | erot = 1.93695511183614 | epot = -17.0609819484045 | etot = -13.2825375936647 -21000 ekin = 2.02307741366106 | erot = 2.09844265792887 | epot = -17.4040576653927 | etot = -13.2825375938028 -22000 ekin = 2.21183606977167 | erot = 2.26260708947227 | epot = -17.7569807531574 | etot = -13.2825375939135 -23000 ekin = 2.40735468792923 | erot = 2.42817202047232 | epot = -18.1180643024984 | etot = -13.2825375940969 -24000 ekin = 2.60896890448811 | erot = 2.59357882573777 | epot = -18.4850853245068 | etot = -13.2825375942809 -25000 ekin = 2.815801354773 | erot = 2.75706655666979 | epot = -18.8554055059558 | etot = -13.282537594513 -26000 ekin = 3.02680083558447 | erot = 2.91667946897181 | epot = -19.2260178993261 | etot = -13.2825375947698 -27000 ekin = 3.24067707260278 | erot = 3.07027299756425 | epot = -19.5934876652165 | etot = -13.2825375950495 -28000 ekin = 3.45601412953551 | erot = 3.21560615187967 | epot = -19.9541578767284 | etot = -13.2825375953133 -29000 ekin = 3.67136830813179 | erot = 3.35037905822876 | epot = -20.3042849619982 | etot = -13.2825375956377 -30000 ekin = 3.88476027224393 | erot = 3.47208481891771 | epot = -20.6393826871844 | etot = -13.2825375960227 -31000 ekin = 4.09387957878907 | erot = 3.57821385031972 | epot = -20.9546310254505 | etot = -13.2825375963417 -32000 ekin = 4.2966218534583 | erot = 3.6664860653108 | epot = -21.2456455154184 | etot = -13.2825375966493 -33000 ekin = 4.49089153394099 | erot = 3.73482555362516 | epot = -21.5082546845017 | etot = -13.2825375969356 -34000 ekin = 4.67464118182325 | erot = 3.78142516888949 | epot = -21.7386039479011 | etot = -13.2825375971883 -35000 ekin = 4.84586411782109 | erot = 3.80480460777856 | epot = -21.9332063229965 | etot = -13.2825375973968 -36000 ekin = 5.0027094048744 | erot = 3.80394535032719 | epot = -22.0891923527598 | etot = -13.2825375975582 -37000 ekin = 5.14355281474345 | erot = 3.77833709530338 | epot = -22.2044275077127 | etot = -13.2825375976659 -38000 ekin = 5.26699752588952 | erot = 3.72801268545681 | epot = -22.2775478090603 | etot = -13.282537597714 -39000 ekin = 5.37191151713971 | erot = 3.65359747923658 | epot = -22.3080465940747 | etot = -13.2825375976984 -40000 ekin = 5.45746010972539 | erot = 3.55633701588603 | epot = -22.2963347232318 | etot = -13.2825375976204 -41000 ekin = 5.52312188621432 | erot = 3.43809872369872 | epot = -22.2437582073857 | etot = -13.2825375974727 -42000 ekin = 5.56872044212123 | erot = 3.3013527933319 | epot = -22.1526108327172 | etot = -13.2825375972641 -43000 ekin = 5.59443660083054 | erot = 3.14910305123766 | epot = -22.0260772490709 | etot = -13.2825375970027 -44000 ekin = 5.60078634437832 | erot = 2.98477133565166 | epot = -21.8680952767313 | etot = -13.2825375967014 -45000 ekin = 5.58859564323475 | erot = 2.81204277265363 | epot = -21.6831760122637 | etot = -13.2825375963753 -46000 ekin = 5.55896198288938 | erot = 2.6346956216755 | epot = -21.4761952006028 | etot = -13.2825375960379 -47000 ekin = 5.51320424222089 | erot = 2.45646420183095 | epot = -21.2522060397504 | etot = -13.2825375956985 -48000 ekin = 5.45280176988658 | erot = 2.28095947573165 | epot = -21.0162988409789 | etot = -13.2825375953606 -49000 ekin = 5.37933239946777 | erot = 2.11161440403301 | epot = -20.7734843985466 | etot = -13.2825375950459 -50000 ekin = 5.29440598595322 | erot = 1.95156309993227 | epot = -20.5285066806364 | etot = -13.2825375947509 -51000 ekin = 5.19960275040365 | erot = 1.80366343983081 | epot = -20.2858037847169 | etot = -13.2825375944825 -52000 ekin = 5.09642319962078 | erot = 1.6704687709701 | epot = -20.0494295648296 | etot = -13.2825375942388 -53000 ekin = 4.98624639554453 | erot = 1.55427111116844 | epot = -19.8230551007342 | etot = -13.2825375940213 -54000 ekin = 4.87030445561618 | erot = 1.4571046995688 | epot = -19.6099467490168 | etot = -13.2825375938318 -55000 ekin = 4.74966978520253 | erot = 1.3807464290206 | epot = -19.4129538078759 | etot = -13.2825375936527 -56000 ekin = 4.62525646671059 | erot = 1.32681969001188 | epot = -19.2346137502498 | etot = -13.2825375935274 -57000 ekin = 4.49783496228329 | erot = 1.29648861711317 | epot = -19.0768611728244 | etot = -13.2825375934279 -58000 ekin = 4.3680583246168 | erot = 1.29057331365756 | epot = -18.9411692316282 | etot = -13.2825375933538 -59000 ekin = 4.23649045860609 | erot = 1.30961007130899 | epot = -18.828638123218 | etot = -13.2825375933029 -60000 ekin = 4.10363649615241 | erot = 1.35385055377105 | epot = -18.7400246431965 | etot = -13.2825375932731 -61000 ekin = 3.96997203629848 | erot = 1.42326526715471 | epot = -18.6757748967159 | etot = -13.2825375932627 -62000 ekin = 3.8361228573534 | erot = 1.51750909475347 | epot = -18.63616954536 | etot = -13.2825375932531 -63000 ekin = 3.70275913153356 | erot = 1.63593500305273 | epot = -18.6212317278744 | etot = -13.2825375932881 -64000 ekin = 3.57028395426148 | erot = 1.77765695762388 | epot = -18.6304785052257 | etot = -13.2825375933403 -65000 ekin = 3.43939724701883 | erot = 1.94136642645281 | epot = -18.6633012668463 | etot = -13.2825375933747 -66000 ekin = 3.31090885650503 | erot = 2.12543845180006 | epot = -18.7188849017622 | etot = -13.2825375934572 -67000 ekin = 3.18539537800154 | erot = 2.32812634152817 | epot = -18.7960593130801 | etot = -13.2825375935504 -68000 ekin = 3.0635338653806 | erot = 2.54742667497474 | epot = -18.8934981340094 | etot = -13.2825375936541 -69000 ekin = 2.94609585152155 | erot = 2.78109018587035 | epot = -19.009723631161 | etot = -13.2825375937691 -70000 ekin = 2.83393040716521 | erot = 3.02662959649543 | epot = -19.1430975975569 | etot = -13.2825375938963 -71000 ekin = 2.72793726696403 | erot = 3.28133994286028 | epot = -19.2918148038557 | etot = -13.2825375940314 -72000 ekin = 2.62902971043669 | erot = 3.54239819983024 | epot = -19.4539655044234 | etot = -13.2825375941565 -73000 ekin = 2.53808722042923 | erot = 3.80701983458394 | epot = -19.6276446493613 | etot = -13.2825375943481 -74000 ekin = 2.45592865526949 | erot = 4.07171344127284 | epot = -19.8101796911555 | etot = -13.2825375946132 -75000 ekin = 2.3833072864547 | erot = 4.33220600221002 | epot = -19.9980508835331 | etot = -13.2825375948683 -76000 ekin = 2.32085819246852 | erot = 4.58430888321027 | epot = -20.1877046708076 | etot = -13.2825375951288 -77000 ekin = 2.26905284042002 | erot = 4.82394209159159 | epot = -20.3755325274035 | etot = -13.2825375953919 -78000 ekin = 2.22818215579792 | erot = 5.04720004762804 | epot = -20.5579197990804 | etot = -13.2825375956544 -79000 ekin = 2.19835990746569 | erot = 5.25044819004257 | epot = -20.7313456933952 | etot = -13.2825375958869 -80000 ekin = 2.17954213158754 | erot = 5.43056087724072 | epot = -20.8926406049113 | etot = -13.2825375960831 -81000 ekin = 2.17154912845079 | erot = 5.58515654974133 | epot = -21.0392432744253 | etot = -13.2825375962332 -82000 ekin = 2.17396051633385 | erot = 5.71255070218911 | epot = -21.1690488148905 | etot = -13.2825375963675 -83000 ekin = 2.18608268543497 | erot = 5.8115938913987 | epot = -21.2802141733995 | etot = -13.2825375965659 -84000 ekin = 2.20694055797086 | erot = 5.88143457462865 | epot = -21.3709127292227 | etot = -13.2825375966232 -85000 ekin = 2.2355007346888 | erot = 5.9224847336172 | epot = -21.440523064944 | etot = -13.282537596638 -86000 ekin = 2.27071025957208 | erot = 5.93583657914561 | epot = -21.4890844353357 | etot = -13.282537596618 -87000 ekin = 2.31151705668532 | erot = 5.92306118835237 | epot = -21.5171158416083 | etot = -13.2825375965707 -88000 ekin = 2.35689880582359 | erot = 5.88606517856767 | epot = -21.5255015808933 | etot = -13.282537596502 -89000 ekin = 2.40589192121093 | erot = 5.82697176767523 | epot = -21.515401285302 | etot = -13.2825375964158 -90000 ekin = 2.45762089189478 | erot = 5.74803678246289 | epot = -21.4881952706713 | etot = -13.2825375963137 -91000 ekin = 2.51132727735637 | erot = 5.65159908896529 | epot = -21.4454639625174 | etot = -13.2825375961958 -92000 ekin = 2.56639616299203 | erot = 5.54005576568085 | epot = -21.3889895247349 | etot = -13.282537596062 -93000 ekin = 2.62237587147907 | erot = 5.41584923925793 | epot = -21.3207627066506 | etot = -13.2825375959136 -94000 ekin = 2.6789853628744 | erot = 5.28145076624312 | epot = -21.242973724871 | etot = -13.2825375957535 -95000 ekin = 2.73610698777042 | erot = 5.1393322247884 | epot = -21.1579768081446 | etot = -13.2825375955858 -96000 ekin = 2.79376736409308 | erot = 4.99192351961226 | epot = -21.0682284791232 | etot = -13.2825375954179 -97000 ekin = 2.85209759177855 | erot = 4.84155102932086 | epot = -20.9761862163575 | etot = -13.2825375952581 -98000 ekin = 2.91128043087762 | erot = 4.69036811429654 | epot = -20.8841861402892 | etot = -13.2825375951151 -99000 ekin = 2.97148865716326 | erot = 4.54028690688497 | epot = -20.7943131590452 | etot = -13.282537594997 -100000 ekin = 3.03281936548454 | erot = 4.39291958378067 | epot = -20.7082765441758 | etot = -13.2825375949106 -101000 ekin = 3.09523162855491 | erot = 4.24953761553784 | epot = -20.6273068389531 | etot = -13.2825375948603 -102000 ekin = 3.15849350649712 | erot = 4.11105261279967 | epot = -20.552083714145 | etot = -13.2825375948482 -103000 ekin = 3.22212928739632 | erot = 3.97803233781191 | epot = -20.4826992200835 | etot = -13.2825375948753 -104000 ekin = 3.28539028419995 | erot = 3.85073569994647 | epot = -20.4186635790814 | etot = -13.282537594935 -105000 ekin = 3.34731475817756 | erot = 3.72912316717864 | epot = -20.3589755203797 | etot = -13.2825375950235 -106000 ekin = 3.40672794730861 | erot = 3.61292637549597 | epot = -20.3021919179397 | etot = -13.2825375951351 -107000 ekin = 3.46228544964886 | erot = 3.50170395486082 | epot = -20.2465269997722 | etot = -13.2825375952625 -108000 ekin = 3.51253156080083 | erot = 3.39489824023779 | epot = -20.1899673964366 | etot = -13.282537595398 -109000 ekin = 3.55597480315881 | erot = 3.2918729970377 | epot = -20.1303853957321 | etot = -13.2825375955356 -110000 ekin = 3.59118238705156 | erot = 3.19193918351237 | epot = -20.0656591662303 | etot = -13.2825375956664 -111000 ekin = 3.6168734377865 | erot = 3.09439958031586 | epot = -19.993810613884 | etot = -13.2825375957817 -112000 ekin = 3.63202144077097 | erot = 2.99858073408855 | epot = -19.9131397707325 | etot = -13.282537595873 -113000 ekin = 3.6359567760499 | erot = 2.90386796422028 | epot = -19.8223623362014 | etot = -13.2825375959312 -114000 ekin = 3.62846110509032 | erot = 2.80974594394075 | epot = -19.7207446449794 | etot = -13.2825375959483 -115000 ekin = 3.60984333606135 | erot = 2.71584476484498 | epot = -19.6082256968239 | etot = -13.2825375959176 -116000 ekin = 3.5809859294631 | erot = 2.62198860618847 | epot = -19.4855121314881 | etot = -13.2825375958365 -117000 ekin = 3.54334240221411 | erot = 2.52827901424299 | epot = -19.354159012147 | etot = -13.2825375956899 -118000 ekin = 3.49891828359518 | erot = 2.43512420844321 | epot = -19.2165800875462 | etot = -13.2825375955078 -119000 ekin = 3.45018316481888 | erot = 2.3431314417893 | epot = -19.0758522018948 | etot = -13.2825375952866 -120000 ekin = 3.39991853306425 | erot = 2.25319419875556 | epot = -18.9356503268585 | etot = -13.2825375950387 -121000 ekin = 3.35105152049006 | erot = 2.1664659738711 | epot = -18.8000550891398 | etot = -13.2825375947787 -122000 ekin = 3.30648176977477 | erot = 2.08430580539905 | epot = -18.6733251696944 | etot = -13.2825375945206 -123000 ekin = 3.2689296615607 | erot = 2.00820635396295 | epot = -18.5596736097996 | etot = -13.282537594276 -124000 ekin = 3.24083330103893 | erot = 1.93971532774534 | epot = -18.4630862228354 | etot = -13.2825375940511 -125000 ekin = 3.22476145827485 | erot = 1.8802958129316 | epot = -18.387594863397 | etot = -13.2825375921905 -126000 ekin = 3.14878052704725 | erot = 1.84062475589711 | epot = -18.2719429098034 | etot = -13.282537626859 -127000 ekin = 2.94943277103416 | erot = 1.88659542758862 | epot = -18.11856577358 | etot = -13.2825375749572 -128000 ekin = 3.16220879321558 | erot = 1.96338946783192 | epot = -18.4081359062159 | etot = -13.2825376451684 -129000 ekin = 3.31015030132692 | erot = 1.94720836362345 | epot = -18.5398963214827 | etot = -13.2825376565323 -130000 ekin = 3.44972038724563 | erot = 1.92633510568783 | epot = -18.6585931496318 | etot = -13.2825376566984 -131000 ekin = 3.58872168957087 | erot = 1.90769906106584 | epot = -18.7789584074295 | etot = -13.2825376567928 -132000 ekin = 3.72319125317256 | erot = 1.89293715413269 | epot = -18.8986660641582 | etot = -13.282537656853 -133000 ekin = 3.8497825175539 | erot = 1.88373597103122 | epot = -19.0160561454723 | etot = -13.2825376568872 -134000 ekin = 3.9655798495172 | erot = 1.8817190850278 | epot = -19.1298365915079 | etot = -13.2825376569629 -135000 ekin = 4.06807957718167 | erot = 1.88790714285721 | epot = -19.2385243770747 | etot = -13.2825376570358 -136000 ekin = 4.15531911327304 | erot = 1.90286269173082 | epot = -19.3407194621007 | etot = -13.2825376570969 -137000 ekin = 4.22592766896971 | erot = 1.92681130724396 | epot = -19.4352766333492 | etot = -13.2825376571355 -138000 ekin = 4.27918313098009 | erot = 1.95973390207694 | epot = -19.5214546902017 | etot = -13.2825376571446 -139000 ekin = 4.31500256681588 | erot = 2.00154238231142 | epot = -19.5990826062102 | etot = -13.2825376570829 -140000 ekin = 4.33403278412117 | erot = 2.05223040229225 | epot = -19.6688008434059 | etot = -13.2825376569925 -141000 ekin = 4.33751047770814 | erot = 2.11180924821164 | epot = -19.7318573827859 | etot = -13.2825376568661 -142000 ekin = 4.32708478663596 | erot = 2.18042096416729 | epot = -19.7900434075185 | etot = -13.2825376567153 -143000 ekin = 4.30467959787758 | erot = 2.25833701673771 | epot = -19.845554271157 | etot = -13.2825376565417 -144000 ekin = 4.27235382259283 | erot = 2.3459516541184 | epot = -19.9008431331017 | etot = -13.2825376563904 -145000 ekin = 4.23214636981281 | erot = 2.44344334214771 | epot = -19.9581273682276 | etot = -13.2825376562671 -146000 ekin = 4.18594231916965 | erot = 2.55071340549387 | epot = -20.0191933808494 | etot = -13.2825376561859 -147000 ekin = 4.13537962661628 | erot = 2.66728850163299 | epot = -20.0852057844054 | etot = -13.2825376561562 -148000 ekin = 4.08179900889746 | erot = 2.79223549069502 | epot = -20.1565721557737 | etot = -13.2825376561812 -149000 ekin = 4.02623498472355 | erot = 2.92411986899913 | epot = -20.2328925099828 | etot = -13.2825376562601 -150000 ekin = 3.96943958307735 | erot = 3.06100347347696 | epot = -20.3129807129432 | etot = -13.2825376563889 -151000 ekin = 3.91192645323312 | erot = 3.20047132483891 | epot = -20.3949354346338 | etot = -13.2825376565618 -152000 ekin = 3.85402372610912 | erot = 3.3396787748025 | epot = -20.4762401576838 | etot = -13.2825376567722 -153000 ekin = 3.79592773401811 | erot = 3.47541715770496 | epot = -20.5538825487347 | etot = -13.2825376570116 -154000 ekin = 3.7377553070406 | erot = 3.60420547216162 | epot = -20.6244984364711 | etot = -13.2825376572689 -155000 ekin = 3.67959791029876 | erot = 3.72242217783006 | epot = -20.6845577456572 | etot = -13.2825376575284 -156000 ekin = 3.62158147939242 | erot = 3.82649073830597 | epot = -20.7306098754674 | etot = -13.282537657769 -157000 ekin = 3.56393625541153 | erot = 3.91312084630165 | epot = -20.7595947596795 | etot = -13.2825376579664 -158000 ekin = 3.50707329925246 | erot = 3.97958736500162 | epot = -20.7691983223494 | etot = -13.2825376580953 -159000 ekin = 3.45165682738677 | erot = 4.02400734849703 | epot = -20.7582018340196 | etot = -13.2825376581358 -160000 ekin = 3.39865532558926 | erot = 4.04555903021762 | epot = -20.7267520138841 | etot = -13.2825376580772 -161000 ekin = 3.34935406486454 | erot = 4.04458967179496 | epot = -20.6764813945816 | etot = -13.2825376579221 -162000 ekin = 3.30532015421547 | erot = 4.02258247379647 | epot = -20.6104402856973 | etot = -13.2825376576853 -163000 ekin = 3.26831809803595 | erot = 3.98198669358187 | epot = -20.5328424490092 | etot = -13.2825376573914 -164000 ekin = 3.24018500158393 | erot = 3.92594872656758 | epot = -20.448671385221 | etot = -13.2825376570695 -165000 ekin = 3.22267663501618 | erot = 3.85799639398401 | epot = -20.3632106857525 | etot = -13.2825376567523 -166000 ekin = 3.21735668268655 | erot = 3.78179957337404 | epot = -20.2816939123394 | etot = -13.2825376562788 -167000 ekin = 3.22508554133831 | erot = 3.70216421851945 | epot = -20.2097874159608 | etot = -13.282537656103 -168000 ekin = 3.24596106315309 | erot = 3.62279974210026 | epot = -20.1512984612667 | etot = -13.2825376560133 -169000 ekin = 3.27955383501576 | erot = 3.54538235194467 | epot = -20.1074738429824 | etot = -13.282537656022 -170000 ekin = 3.32466734771607 | erot = 3.47077759716863 | epot = -20.0779826010129 | etot = -13.2825376561282 -171000 ekin = 3.37937800793454 | erot = 3.39904334979686 | epot = -20.0609590140444 | etot = -13.282537656313 -172000 ekin = 3.44119436380834 | erot = 3.32956363469193 | epot = -20.0532956550461 | etot = -13.2825376565459 -173000 ekin = 3.5073198530207 | erot = 3.2612835945287 | epot = -20.051141104334 | etot = -13.2825376567846 -174000 ekin = 3.57497712060509 | erot = 3.19303082809317 | epot = -20.0505456056827 | etot = -13.2825376569845 -175000 ekin = 3.64173116724473 | erot = 3.12386956099425 | epot = -20.0481383853471 | etot = -13.2825376571082 -176000 ekin = 3.70574771912998 | erot = 3.05341479574251 | epot = -20.0417001720045 | etot = -13.282537657132 -177000 ekin = 3.76593888056791 | erot = 2.98204284338433 | epot = -20.0305193810041 | etot = -13.2825376570519 -178000 ekin = 3.82196164475597 | erot = 2.91094638159331 | epot = -20.0154456832348 | etot = -13.2825376568855 -179000 ekin = 3.87411507697419 | erot = 2.8420411011697 | epot = -19.9986938347981 | etot = -13.2825376566543 -180000 ekin = 3.92317967933079 | erot = 2.77773953428165 | epot = -19.9834568700055 | etot = -13.2825376563931 -181000 ekin = 3.97015764234259 | erot = 2.72070235461336 | epot = -19.973397653084 | etot = -13.2825376561281 -182000 ekin = 4.01610171617377 | erot = 2.67349840169278 | epot = -19.9721377738001 | etot = -13.2825376559335 -183000 ekin = 4.06177363427588 | erot = 2.63812245871518 | epot = -19.9824337488122 | etot = -13.2825376558212 -184000 ekin = 4.10756653676875 | erot = 2.61575603465098 | epot = -20.0058602272084 | etot = -13.2825376557887 -185000 ekin = 4.1535465296398 | erot = 2.60670565064949 | epot = -20.0427898361268 | etot = -13.2825376558375 -186000 ekin = 4.19945391071947 | erot = 2.61036353554361 | epot = -20.0923551022258 | etot = -13.2825376559627 -187000 ekin = 4.24473107430486 | erot = 2.62524898284968 | epot = -20.1525177133085 | etot = -13.282537656154 -188000 ekin = 4.28856799818638 | erot = 2.64911845928539 | epot = -20.2202241138684 | etot = -13.2825376563966 -189000 ekin = 4.33007364398987 | erot = 2.67919947077904 | epot = -20.2918107713923 | etot = -13.2825376566233 -190000 ekin = 4.36845326745392 | erot = 2.71241964780855 | epot = -20.3634105721975 | etot = -13.282537656935 -191000 ekin = 4.40242074847318 | erot = 2.74530093921345 | epot = -20.4302593449098 | etot = -13.2825376572232 -192000 ekin = 4.43037880288196 | erot = 2.77455401038569 | epot = -20.4874704712234 | etot = -13.2825376579557 -193000 ekin = 4.4483451030517 | erot = 2.79692081276062 | epot = -20.5278035740367 | etot = -13.2825376582243 -194000 ekin = 4.45438337861199 | erot = 2.80974801333428 | epot = -20.5466690503493 | etot = -13.282537658403 -195000 ekin = 4.44752201417129 | erot = 2.81136444003151 | epot = -20.5414241126783 | etot = -13.2825376584755 -196000 ekin = 4.4273718790499 | erot = 2.80121240437835 | epot = -20.5111219418613 | etot = -13.2825376584331 -197000 ekin = 4.39418615090579 | erot = 2.77991547931552 | epot = -20.4566392884973 | etot = -13.282537658276 -198000 ekin = 4.3488852650832 | erot = 2.74924294053151 | epot = -20.3806658636282 | etot = -13.2825376580135 -199000 ekin = 4.2930400637885 | erot = 2.71196807404484 | epot = -20.2875457954979 | etot = -13.2825376576645 -200000 ekin = 4.228803621182 | erot = 2.67162662745973 | epot = -20.1829679058993 | etot = -13.2825376572575 -201000 ekin = 4.1587834630136 | erot = 2.63219133391197 | epot = -20.0735124537541 | etot = -13.2825376568285 -202000 ekin = 4.08585235174851 | erot = 2.59768848811678 | epot = -19.9660784962843 | etot = -13.282537656419 -203000 ekin = 4.01290418154487 | erot = 2.57179164674953 | epot = -19.8672334843662 | etot = -13.2825376560718 -204000 ekin = 3.94257872967339 | erot = 2.55743320244059 | epot = -19.7825495879401 | etot = -13.2825376558261 -205000 ekin = 3.8769885984992 | erot = 2.55647506167898 | epot = -19.7160013158905 | etot = -13.2825376557123 -206000 ekin = 3.81748743469334 | erot = 2.56947517652909 | epot = -19.6695002669703 | etot = -13.2825376557479 -207000 ekin = 3.76451595610977 | erot = 2.59557970374973 | epot = -19.6426333157935 | etot = -13.282537655934 -208000 ekin = 3.71755329412301 | erot = 2.63256413547951 | epot = -19.6326550858557 | etot = -13.2825376562532 -209000 ekin = 3.67518956841205 | erot = 2.6770413301753 | epot = -19.6347685552552 | etot = -13.2825376566678 -210000 ekin = 3.63532366958265 | erot = 2.72484401425423 | epot = -19.6427053409585 | etot = -13.2825376571216 -211000 ekin = 3.59547812025674 | erot = 2.7715653100656 | epot = -19.6495810878672 | etot = -13.2825376575449 -212000 ekin = 3.55320133886872 | erot = 2.81319346320055 | epot = -19.6489324599365 | etot = -13.2825376578672 -213000 ekin = 3.50649761292236 | erot = 2.84671880107394 | epot = -19.6357540720304 | etot = -13.2825376580341 -214000 ekin = 3.45419694129236 | erot = 2.87055671325175 | epot = -19.6072913125676 | etot = -13.2825376580235 -215000 ekin = 3.3961705526582 | erot = 2.88465790120113 | epot = -19.5633661117115 | etot = -13.2825376578522 -216000 ekin = 3.33333457774809 | erot = 2.89027487492404 | epot = -19.506147110241 | etot = -13.2825376575688 -217000 ekin = 3.26237078851854 | erot = 2.88652329141029 | epot = -19.4314317899046 | etot = -13.2825377099757 -218000 ekin = 3.0604126920775 | erot = 2.81741383451156 | epot = -19.1603641969459 | etot = -13.2825376703569 -219000 ekin = 2.93316276967125 | erot = 2.84460250247024 | epot = -19.0603029343598 | etot = -13.2825376622183 -220000 ekin = 2.96128614843719 | erot = 2.9890414566452 | epot = -19.2328653086372 | etot = -13.2825377035548 -221000 ekin = 2.90913828063365 | erot = 3.0370109417019 | epot = -19.2286868797585 | etot = -13.2825376574229 -222000 ekin = 2.8422737694587 | erot = 3.05603303801555 | epot = -19.1808444650453 | etot = -13.2825376575711 -223000 ekin = 2.78062900949199 | erot = 3.06232144542732 | epot = -19.1254881126293 | etot = -13.28253765771 -224000 ekin = 2.72480461600021 | erot = 3.05323876331451 | epot = -19.0605810371243 | etot = -13.2825376578096 -225000 ekin = 2.67532541220304 | erot = 3.02684795807043 | epot = -18.9847110281097 | etot = -13.2825376578362 -226000 ekin = 2.63276163036917 | erot = 2.98227164387466 | epot = -18.8975709320199 | etot = -13.2825376577761 -227000 ekin = 2.59776959648546 | erot = 2.91985728396212 | epot = -18.8001645380861 | etot = -13.2825376576386 -228000 ekin = 2.57104335950858 | erot = 2.84110209326577 | epot = -18.694683110226 | etot = -13.2825376574516 -229000 ekin = 2.55319781380102 | erot = 2.74837649564429 | epot = -18.5841119666965 | etot = -13.2825376572512 -230000 ekin = 2.54463522127649 | erot = 2.64454432367442 | epot = -18.4717172020187 | etot = -13.2825376570678 -231000 ekin = 2.54546021784584 | erot = 2.53260284792404 | epot = -18.3606007226851 | etot = -13.2825376569152 -232000 ekin = 2.55549307881052 | erot = 2.41545023211231 | epot = -18.2534809677089 | etot = -13.2825376567861 -233000 ekin = 2.57438548648707 | erot = 2.29583418255659 | epot = -18.1527573257021 | etot = -13.2825376566584 -234000 ekin = 2.60178443029238 | erot = 2.17645519655946 | epot = -18.0607772833611 | etot = -13.2825376565093 -235000 ekin = 2.63745218021138 | erot = 2.06012244390592 | epot = -17.9801122804485 | etot = -13.2825376563312 -236000 ekin = 2.68126373962444 | erot = 1.94983176913362 | epot = -17.9136331648965 | etot = -13.2825376561384 -237000 ekin = 2.73306880567087 | erot = 1.84868049785769 | epot = -17.8642869594917 | etot = -13.2825376559632 -238000 ekin = 2.79247907581076 | erot = 1.75962709169706 | epot = -17.8346438233489 | etot = -13.2825376558411 -239000 ekin = 2.85867594437833 | erot = 1.68518476454709 | epot = -17.8263983647234 | etot = -13.282537655798 -240000 ekin = 2.93031183915998 | erot = 1.62715662270522 | epot = -17.840006117709 | etot = -13.2825376558438 -241000 ekin = 3.00552986743756 | erot = 1.58648515289486 | epot = -17.8745526763053 | etot = -13.2825376559729 -242000 ekin = 3.0820836546576 | erot = 1.5632372672336 | epot = -17.9278585780576 | etot = -13.2825376561664 -243000 ekin = 3.15752262719394 | erot = 1.55671134418848 | epot = -17.9967716277795 | etot = -13.282537656397 -244000 ekin = 3.22940955213892 | erot = 1.56564064462356 | epot = -18.0775878533954 | etot = -13.2825376566329 -245000 ekin = 3.29554303953992 | erot = 1.58846457360084 | epot = -18.1665452699808 | etot = -13.28253765684 -246000 ekin = 3.35415939736937 | erot = 1.6236315970523 | epot = -18.2603286514115 | etot = -13.2825376569898 -247000 ekin = 3.40408574270723 | erot = 1.66988325611156 | epot = -18.3565066558819 | etot = -13.2825376570631 -248000 ekin = 3.4448166326331 | erot = 1.72645823945448 | epot = -18.4538125291441 | etot = -13.2825376570566 -249000 ekin = 3.47649663255696 | erot = 1.79316293261223 | epot = -18.5521972221528 | etot = -13.2825376569836 -250000 ekin = 3.49981192900835 | erot = 1.87028571125288 | epot = -18.6526352971325 | etot = -13.2825376568713 -251000 ekin = 3.51581851748353 | erot = 1.95837689015936 | epot = -18.7567330643956 | etot = -13.2825376567528 -252000 ekin = 3.52575126869662 | erot = 2.05795546201388 | epot = -18.8662443873696 | etot = -13.2825376566591 -253000 ekin = 3.53086049262996 | erot = 2.16922084359695 | epot = -18.9826189928386 | etot = -13.2825376566117 -254000 ekin = 3.5323092446383 | erot = 2.29183768672856 | epot = -19.1066845879863 | etot = -13.2825376566194 -255000 ekin = 3.53114146569609 | erot = 2.42483171779644 | epot = -19.2385108401714 | etot = -13.2825376566788 -256000 ekin = 3.5283101054336 | erot = 2.56659937924988 | epot = -19.3774471414622 | etot = -13.2825376567787 -257000 ekin = 3.52473759358505 | erot = 2.71500399460053 | epot = -19.5222792450903 | etot = -13.2825376569047 -258000 ekin = 3.52137545668075 | erot = 2.86751445186622 | epot = -19.6714275655916 | etot = -13.2825376570446 -259000 ekin = 3.51923070409731 | erot = 3.02134046698861 | epot = -19.8231088282789 | etot = -13.282537657193 -260000 ekin = 3.51933841084731 | erot = 3.17353025732487 | epot = -19.9754063255239 | etot = -13.2825376573517 -261000 ekin = 3.52267851351005 | erot = 3.32101670247621 | epot = -20.1262328735157 | etot = -13.2825376575294 -262000 ekin = 3.53003333481016 | erot = 3.46062452427784 | epot = -20.2731955168254 | etot = -13.2825376577374 -263000 ekin = 3.54180424035237 | erot = 3.58907231404639 | epot = -20.4134142123818 | etot = -13.282537657983 -264000 ekin = 3.55787447685355 | erot = 3.7030112779332 | epot = -20.5434234130516 | etot = -13.2825376582649 -265000 ekin = 3.57751330913366 | erot = 3.7991542896327 | epot = -20.6592052573327 | etot = -13.2825376585664 -266000 ekin = 3.59938201293792 | erot = 3.87452595149942 | epot = -20.7564456232916 | etot = -13.2825376588543 -267000 ekin = 3.62167235822857 | erot = 3.92682901662269 | epot = -20.8310390339333 | etot = -13.282537659082 -268000 ekin = 3.64237343768047 | erot = 3.95486700975685 | epot = -20.8797781066375 | etot = -13.2825376592002 -269000 ekin = 3.6596153375486 | erot = 3.95890941485044 | epot = -20.901062411574 | etot = -13.2825376591749 -270000 ekin = 3.67198713217804 | erot = 3.9408570080659 | epot = -20.8953817992456 | etot = -13.2825376590016 -271000 ekin = 3.67872329079266 | erot = 3.9041072632946 | epot = -20.865368212798 | etot = -13.2825376587107 -272000 ekin = 3.67969720542205 | erot = 3.85312017496749 | epot = -20.8153550387474 | etot = -13.2825376583578 -273000 ekin = 3.67523785304609 | erot = 3.79279347421283 | epot = -20.7505689852654 | etot = -13.2825376580065 -274000 ekin = 3.66585545030655 | erot = 3.72781503527724 | epot = -20.6762081432937 | etot = -13.28253765771 -275000 ekin = 3.65198266149228 | erot = 3.66213927987085 | epot = -20.5966595988644 | etot = -13.2825376575013 -276000 ekin = 3.63380683707674 | erot = 3.59866145944742 | epot = -20.5150059539162 | etot = -13.282537657392 -277000 ekin = 3.61121443635218 | erot = 3.53909052619982 | epot = -20.4328426199289 | etot = -13.2825376573769 -278000 ekin = 3.58382533557949 | erot = 3.48398196201246 | epot = -20.3503449550318 | etot = -13.2825376574399 -279000 ekin = 3.55107927466775 | erot = 3.43288767683711 | epot = -20.266504609063 | etot = -13.2825376575582 -280000 ekin = 3.512346488716 | erot = 3.38459301004971 | epot = -20.1794771564691 | etot = -13.2825376577034 -281000 ekin = 3.46705217022212 | erot = 3.33742016501593 | epot = -20.0870099930813 | etot = -13.2825376578432 -282000 ekin = 3.4148174354963 | erot = 3.28957539031116 | epot = -19.9869304837506 | etot = -13.2825376579432 -283000 ekin = 3.35561723861012 | erot = 3.23950140187618 | epot = -19.8776562984585 | etot = -13.2825376579722 -284000 ekin = 3.28993990743678 | erot = 3.18617834963535 | epot = -19.7586559149806 | etot = -13.2825376579084 -285000 ekin = 3.21891605429242 | erot = 3.12930993710604 | epot = -19.630763649145 | etot = -13.2825376577465 -286000 ekin = 3.14439051761661 | erot = 3.06934998331757 | epot = -19.4962781582957 | etot = -13.2825376573615 -287000 ekin = 3.06960009495524 | erot = 3.00728050107473 | epot = -19.3594182531579 | etot = -13.2825376571279 -288000 ekin = 2.99759349423509 | erot = 2.9441365645361 | epot = -19.2242677156211 | etot = -13.2825376568499 -289000 ekin = 2.93122590326888 | erot = 2.88109280424439 | epot = -19.0948563640672 | etot = -13.2825376565539 -290000 ekin = 2.87364775959469 | erot = 2.81936189019821 | epot = -18.9755473060555 | etot = -13.2825376562626 -291000 ekin = 2.82808392253171 | erot = 2.76008269212137 | epot = -18.8707042706452 | etot = -13.2825376559921 -292000 ekin = 2.79759576435947 | erot = 2.70430482357441 | epot = -18.7844382436877 | etot = -13.2825376557538 -293000 ekin = 2.78483509079536 | erot = 2.65304729582213 | epot = -18.7204200421748 | etot = -13.2825376555573 -294000 ekin = 2.79179688861761 | erot = 2.60738085283692 | epot = -18.6817153968686 | etot = -13.282537655414 -295000 ekin = 2.8195793452766 | erot = 2.56847294066441 | epot = -18.6705899412817 | etot = -13.2825376553407 -296000 ekin = 2.86809990605543 | erot = 2.53696733690238 | epot = -18.6876048985693 | etot = -13.2825376556115 -297000 ekin = 2.93560102202575 | erot = 2.51254790532664 | epot = -18.7306865831654 | etot = -13.2825376558131 -298000 ekin = 3.01880409347839 | erot = 2.49548083197626 | epot = -18.7968225815679 | etot = -13.2825376561133 -299000 ekin = 3.11317674937697 | erot = 2.4858527957229 | epot = -18.8815672015831 | etot = -13.2825376564832 -300000 ekin = 3.21328607489871 | erot = 2.4836345898414 | epot = -18.9794583216092 | etot = -13.2825376568691 -301000 ekin = 3.31333985043658 | erot = 2.48892965616305 | epot = -19.0848071638015 | etot = -13.2825376572019 -302000 ekin = 3.40783628219617 | erot = 2.50232511253297 | epot = -19.192699052147 | etot = -13.2825376574178 -303000 ekin = 3.49218145837423 | erot = 2.52518642841781 | epot = -19.2999055442748 | etot = -13.2825376574828 -304000 ekin = 3.56312110363128 | erot = 2.55971045465009 | epot = -19.4053692156879 | etot = -13.2825376574065 -305000 ekin = 3.6188877414327 | erot = 2.6086316969236 | epot = -19.5100570955968 | etot = -13.2825376572405 -306000 ekin = 3.65906113322095 | erot = 2.67462381277421 | epot = -19.616222603054 | etot = -13.2825376570589 -307000 ekin = 3.68422703808074 | erot = 2.75956355882326 | epot = -19.7263282538395 | etot = -13.2825376569355 -308000 ekin = 3.69555713019506 | erot = 2.86386132679045 | epot = -19.841956113912 | etot = -13.2825376569265 -309000 ekin = 3.6944221679418 | erot = 2.98601798220111 | epot = -19.9629778072023 | etot = -13.2825376570594 -310000 ekin = 3.68211177280709 | erot = 3.12248873496333 | epot = -20.0871381651018 | etot = -13.2825376573313 -311000 ekin = 3.65969154495063 | erot = 3.26786382117018 | epot = -20.2100930238327 | etot = -13.2825376577119 -312000 ekin = 3.62799191203377 | erot = 3.41533011396127 | epot = -20.3258596841446 | etot = -13.2825376581496 -313000 ekin = 3.5877057744357 | erot = 3.5573517271153 | epot = -20.4275951601311 | etot = -13.2825376585801 -314000 ekin = 3.53954680683471 | erot = 3.68647834911128 | epot = -20.5085628148833 | etot = -13.2825376589373 -315000 ekin = 3.48441731148361 | erot = 3.79616777476463 | epot = -20.5631227454135 | etot = -13.2825376591653 -316000 ekin = 3.42353216211093 | erot = 3.88149414080879 | epot = -20.5875639621498 | etot = -13.2825376592301 -317000 ekin = 3.35845872751516 | erot = 3.93962315501014 | epot = -20.5806195416508 | etot = -13.2825376591255 -318000 ekin = 3.29105546518444 | erot = 3.96997627516161 | epot = -20.5435693992194 | etot = -13.2825376588734 -319000 ekin = 3.22332073202391 | erot = 3.97407140328684 | epot = -20.4799297938271 | etot = -13.2825376585164 -320000 ekin = 3.15718962490207 | erot = 3.95509826666012 | epot = -20.3948255496699 | etot = -13.2825376581077 -321000 ekin = 3.09432530925279 | erot = 3.91739375695147 | epot = -20.2942567238344 | etot = -13.2825376576302 -322000 ekin = 3.03585792728377 | erot = 3.86620572599634 | epot = -20.1846013105925 | etot = -13.2825376573124 -323000 ekin = 2.98241823057018 | erot = 3.80588679425669 | epot = -20.0708426818679 | etot = -13.282537657041 -324000 ekin = 2.93426965651548 | erot = 3.74025042751319 | epot = -19.9570577408469 | etot = -13.2825376568183 -325000 ekin = 2.89141991680272 | erot = 3.6726505878983 | epot = -19.8466081613385 | etot = -13.2825376566375 -326000 ekin = 2.85377350486142 | erot = 3.60592095019319 | epot = -19.7422321115423 | etot = -13.2825376564876 -327000 ekin = 2.82127903351907 | erot = 3.54238718475229 | epot = -19.6462038746294 | etot = -13.2825376563581 -328000 ekin = 2.79404030192089 | erot = 3.483910798784 | epot = -19.5604887570644 | etot = -13.2825376563595 -329000 ekin = 2.77197949436551 | erot = 3.43169110626534 | epot = -19.486208256954 | etot = -13.2825376563232 -330000 ekin = 2.75494613632729 | erot = 3.38614869285078 | epot = -19.4236324854878 | etot = -13.2825376563097 -331000 ekin = 2.74315934444998 | erot = 3.34732307627103 | epot = -19.3730200770432 | etot = -13.2825376563222 -332000 ekin = 2.73688271481008 | erot = 3.31484843372441 | epot = -19.3342688048987 | etot = -13.2825376563643 -333000 ekin = 2.73633973950745 | erot = 3.28798960597169 | epot = -19.3068670019181 | etot = -13.282537656439 -334000 ekin = 2.74163678826561 | erot = 3.26568447791409 | epot = -19.2898589227256 | etot = -13.2825376565459 -335000 ekin = 2.75270974558365 | erot = 3.24660647154557 | epot = -19.2818538738098 | etot = -13.2825376566806 -336000 ekin = 2.76930297431622 | erot = 3.22925893950259 | epot = -19.2810995706514 | etot = -13.2825376568326 -337000 ekin = 2.79098432744022 | erot = 3.21211025351937 | epot = -19.2856322379457 | etot = -13.2825376569861 -338000 ekin = 2.81719266282387 | erot = 3.19377253885662 | epot = -19.2935028588019 | etot = -13.2825376571214 -339000 ekin = 2.84730801445438 | erot = 3.17321131001618 | epot = -19.3030569816885 | etot = -13.2825376572179 -340000 ekin = 2.88072770851284 | erot = 3.14995757252068 | epot = -19.3132229382912 | etot = -13.2825376572577 -341000 ekin = 2.91693042220033 | erot = 3.12427992089905 | epot = -19.3237480003317 | etot = -13.2825376572323 -342000 ekin = 2.95550483676937 | erot = 3.09726362719658 | epot = -19.3353061211112 | etot = -13.2825376571453 -343000 ekin = 2.99612679558118 | erot = 3.07075651726445 | epot = -19.3494209698602 | etot = -13.2825376570146 -344000 ekin = 3.03848111852428 | erot = 3.0471716921407 | epot = -19.3681904675347 | etot = -13.2825376568698 -345000 ekin = 3.08214069495779 | erot = 3.02917600552132 | epot = -19.393854357224 | etot = -13.2825376567449 -346000 ekin = 3.12643023842175 | erot = 3.01932391636737 | epot = -19.428291811462 | etot = -13.2825376566729 -347000 ekin = 3.1703057195056 | erot = 3.01970377198013 | epot = -19.4725471481654 | etot = -13.2825376566797 -348000 ekin = 3.21227615188226 | erot = 3.03164750475832 | epot = -19.5264613134225 | etot = -13.282537656782 -349000 ekin = 3.25037907572041 | erot = 3.05552302028579 | epot = -19.588439752994 | etot = -13.2825376569878 -350000 ekin = 3.28221302801688 | erot = 3.09061207742305 | epot = -19.6553627627352 | etot = -13.2825376572953 -351000 ekin = 3.30503586845653 | erot = 3.13508039752205 | epot = -19.722653923667 | etot = -13.2825376576884 -352000 ekin = 3.31595350171697 | erot = 3.1860592581815 | epot = -19.7845504180322 | etot = -13.2825376581337 -353000 ekin = 3.31222586318731 | erot = 3.23985471046157 | epot = -19.8346182322283 | etot = -13.2825376585794 -354000 ekin = 3.29169173965498 | erot = 3.29228360641323 | epot = -19.8665130050279 | etot = -13.2825376589597 -355000 ekin = 3.25327251247953 | erot = 3.33911881639432 | epot = -19.8749289880785 | etot = -13.2825376592046 -356000 ekin = 3.19745645460831 | erot = 3.37659336434106 | epot = -19.8565874782066 | etot = -13.2825376592572 -357000 ekin = 3.12661218039379 | erot = 3.40186563883957 | epot = -19.8110154783295 | etot = -13.2825376590961 -358000 ekin = 3.04496261886646 | erot = 3.41331336007688 | epot = -19.7408136376943 | etot = -13.2825376587509 -359000 ekin = 2.95811577563298 | erot = 3.41055161315579 | epot = -19.651205047089 | etot = -13.2825376583003 -360000 ekin = 2.87219670777394 | erot = 3.39416675335358 | epot = -19.5489011189766 | etot = -13.2825376578491 -361000 ekin = 2.79279437102874 | erot = 3.36527462495952 | epot = -19.4406066534814 | etot = -13.2825376574932 -362000 ekin = 2.72403411625464 | erot = 3.32507906116156 | epot = -19.3316508347044 | etot = -13.2825376572882 -363000 ekin = 2.66805032239925 | erot = 3.27458936074012 | epot = -19.2251773403758 | etot = -13.2825376572364 -364000 ekin = 2.62498064266495 | erot = 3.21457203232894 | epot = -19.1220903322869 | etot = -13.2825376572931 -365000 ekin = 2.5934133585228 | erot = 3.14571210015836 | epot = -19.0216631160704 | etot = -13.2825376573892 -366000 ekin = 2.5710840161418 | erot = 3.06888690043612 | epot = -18.9225085740357 | etot = -13.2825376574577 -367000 ekin = 2.55558493490964 | erot = 2.98543100060352 | epot = -18.8235535929648 | etot = -13.2825376574517 -368000 ekin = 2.54491188940922 | erot = 2.89729436784059 | epot = -18.7247439146015 | etot = -13.2825376573517 -369000 ekin = 2.53777310784879 | erot = 2.80704690677456 | epot = -18.6273576717881 | etot = -13.2825376571647 -370000 ekin = 2.53338825950404 | erot = 2.71819995751166 | epot = -18.5341258738832 | etot = -13.2825376568675 -371000 ekin = 2.53146597101848 | erot = 2.63443214139472 | epot = -18.4484357690377 | etot = -13.2825376566245 -372000 ekin = 2.53305224681624 | erot = 2.55818112001678 | epot = -18.3737710231761 | etot = -13.2825376563431 -373000 ekin = 2.53983164211236 | erot = 2.49190590621591 | epot = -18.3142752043687 | etot = -13.2825376560405 -374000 ekin = 2.55393613427103 | erot = 2.43803861080081 | epot = -18.2745124008031 | etot = -13.2825376557312 -375000 ekin = 2.57759599288795 | erot = 2.39898190221581 | epot = -18.2591155506451 | etot = -13.2825376555413 -376000 ekin = 2.61177868596817 | erot = 2.37710020071972 | epot = -18.2714165420641 | etot = -13.2825376553762 -377000 ekin = 2.6577874067594 | erot = 2.3735939710949 | epot = -18.3139190331406 | etot = -13.2825376552863 -378000 ekin = 2.71669984604439 | erot = 2.38881656768362 | epot = -18.388054069029 | etot = -13.2825376553009 -379000 ekin = 2.78887075408087 | erot = 2.42222171828648 | epot = -18.4936301278208 | etot = -13.2825376554534 -380000 ekin = 2.87358930471002 | erot = 2.47221119730558 | epot = -18.6283381577863 | etot = -13.2825376557707 -381000 ekin = 2.96878304795802 | erot = 2.53604633164079 | epot = -18.7873670358597 | etot = -13.2825376562609 -382000 ekin = 3.07087981816367 | erot = 2.60989110069411 | epot = -18.9633085757604 | etot = -13.2825376569026 -383000 ekin = 3.17493836101278 | erot = 2.68903209116685 | epot = -19.1465081098178 | etot = -13.2825376576382 -384000 ekin = 3.2751121744025 | erot = 2.76828123033664 | epot = -19.3259310631183 | etot = -13.2825376583791 -385000 ekin = 3.36541347868724 | erot = 2.84251901104316 | epot = -19.4904701487526 | etot = -13.2825376590222 -386000 ekin = 3.44062041949959 | erot = 2.90728609466406 | epot = -19.63044417364 | etot = -13.2825376594764 -387000 ekin = 3.49708416826313 | erot = 2.95929717263878 | epot = -19.7389190005902 | etot = -13.2825376596883 -388000 ekin = 3.533208999321 | erot = 2.99676007578866 | epot = -19.8125067347616 | etot = -13.2825376596519 -389000 ekin = 3.54950477191345 | erot = 3.01944441497972 | epot = -19.8514868462967 | etot = -13.2825376594035 -390000 ekin = 3.54826504042807 | erot = 3.0285237431762 | epot = -19.8593264426073 | etot = -13.282537659003 -391000 ekin = 3.53302701092141 | erot = 3.02626577204824 | epot = -19.8418304414874 | etot = -13.2825376585178 -392000 ekin = 3.50797457908268 | erot = 3.01564117086781 | epot = -19.8061534079633 | etot = -13.2825376580128 -393000 ekin = 3.47739262395814 | erot = 2.99988985775754 | epot = -19.7598201392621 | etot = -13.2825376575465 -394000 ekin = 3.44522282252884 | erot = 2.98206454116459 | epot = -19.7098250208625 | etot = -13.2825376571691 -395000 ekin = 3.41473630917259 | erot = 2.96457892120641 | epot = -19.6618528872984 | etot = -13.2825376569194 -396000 ekin = 3.38832727675762 | erot = 2.94881280953746 | epot = -19.6196777431148 | etot = -13.2825376568197 -397000 ekin = 3.36743033117316 | erot = 2.93484808692962 | epot = -19.5848160749737 | etot = -13.2825376568709 -398000 ekin = 3.35256101408232 | erot = 2.92141113768133 | epot = -19.5565098088131 | etot = -13.2825376570494 -399000 ekin = 3.34346845309996 | erot = 2.90607029857247 | epot = -19.5320764089819 | etot = -13.2825376573095 -400000 ekin = 3.33937255609299 | erot = 2.885680940137 | epot = -19.5075911538209 | etot = -13.2825376575909 -401000 ekin = 3.33924190395778 | erot = 2.85700017339113 | epot = -19.4787797351814 | etot = -13.2825376578325 -402000 ekin = 3.34205998353793 | erot = 2.81733492842804 | epot = -19.4419325699511 | etot = -13.2825376579852 -403000 ekin = 3.34703246955441 | erot = 2.76507190137147 | epot = -19.3946420289475 | etot = -13.2825376580217 -404000 ekin = 3.35370775612875 | erot = 2.69997817544394 | epot = -19.3362235895114 | etot = -13.2825376579387 -405000 ekin = 3.36200495975411 | erot = 2.62323862900913 | epot = -19.267781246516 | etot = -13.2825376577527 -406000 ekin = 3.37216882210917 | erot = 2.53727277109297 | epot = -19.1919792506945 | etot = -13.2825376574923 -407000 ekin = 3.38467286642355 | erot = 2.44541531528468 | epot = -19.1126258388987 | etot = -13.2825376571904 -408000 ekin = 3.40009251679279 | erot = 2.351546289274 | epot = -19.0341764629466 | etot = -13.2825376568798 -409000 ekin = 3.41896361161237 | erot = 2.25973253002234 | epot = -18.9612337982248 | etot = -13.2825376565901 -410000 ekin = 3.44163818667736 | erot = 2.17391337707674 | epot = -18.8980892201012 | etot = -13.2825376563471 -411000 ekin = 3.46814489278439 | erot = 2.0976400383475 | epot = -18.8483225873044 | etot = -13.2825376561725 -412000 ekin = 3.49806473021567 | erot = 2.03386747107442 | epot = -18.8144698573729 | etot = -13.2825376560828 -413000 ekin = 3.53043538014826 | erot = 1.98479597299758 | epot = -18.7977690092345 | etot = -13.2825376560887 -414000 ekin = 3.56370058652801 | erot = 1.95176512736805 | epot = -18.7980033700889 | etot = -13.2825376561928 -415000 ekin = 3.59572274043747 | erot = 1.93521132484302 | epot = -18.8134717216681 | etot = -13.2825376563876 -416000 ekin = 3.62387476619394 | erot = 1.93470676736702 | epot = -18.8411191902142 | etot = -13.2825376566532 -417000 ekin = 3.64521944272596 | erot = 1.94909657754577 | epot = -18.876853677229 | etot = -13.2825376569573 -418000 ekin = 3.65676940727155 | erot = 1.97673635559937 | epot = -18.9160434201296 | etot = -13.2825376572587 -419000 ekin = 3.65580092830723 | erot = 2.01580487492087 | epot = -18.9541434607423 | etot = -13.2825376575142 -420000 ekin = 3.64017400050826 | erot = 2.06463212116893 | epot = -18.9873437793658 | etot = -13.2825376576886 -421000 ekin = 3.60860065288942 | erot = 2.12196023054716 | epot = -19.0130985412 | etot = -13.2825376577634 -422000 ekin = 3.56080810554285 | erot = 2.18705814557018 | epot = -19.0304039088553 | etot = -13.2825376577423 -423000 ekin = 3.49756602993001 | erot = 2.2596475407574 | epot = -19.039751228337 | etot = -13.2825376576496 -424000 ekin = 3.42057977942553 | erot = 2.33965549130008 | epot = -19.0427729282486 | etot = -13.282537657523 -425000 ekin = 3.33228159149848 | erot = 2.42686463918984 | epot = -19.041683888092 | etot = -13.2825376574037 -426000 ekin = 3.23556909606388 | erot = 2.52056283158619 | epot = -19.0386695849753 | etot = -13.2825376573252 -427000 ekin = 3.13354188401699 | erot = 2.61929302170861 | epot = -19.0353725630321 | etot = -13.2825376573065 -428000 ekin = 3.0292759344835 | erot = 2.72077464106008 | epot = -19.0325882328924 | etot = -13.2825376573488 -429000 ekin = 2.92565831326667 | erot = 2.82201873865485 | epot = -19.0302147093596 | etot = -13.2825376574381 -430000 ekin = 2.82528572275417 | erot = 2.91960138007576 | epot = -19.0274247603827 | etot = -13.2825376575528 -431000 ekin = 2.73041359107532 | erot = 3.01000711728769 | epot = -19.022958366036 | etot = -13.282537657673 -432000 ekin = 2.64293211741192 | erot = 3.08992822753868 | epot = -19.0153980027402 | etot = -13.2825376577896 -433000 ekin = 2.5643487123276 | erot = 3.15643021828492 | epot = -19.0033165885172 | etot = -13.2825376579047 -434000 ekin = 2.49577139885518 | erot = 3.20696626802576 | epot = -18.9852753249064 | etot = -13.2825376580255 -435000 ekin = 2.43791477049391 | erot = 3.23932321270836 | epot = -18.9597756413512 | etot = -13.2825376581489 -436000 ekin = 2.39117206292133 | erot = 3.25164920249376 | epot = -18.9253589236643 | etot = -13.2825376582492 -437000 ekin = 2.35579129858705 | erot = 3.242692409158 | epot = -18.8810213660213 | etot = -13.2825376582762 -438000 ekin = 2.33215137598627 | erot = 3.2122573583491 | epot = -18.826946392507 | etot = -13.2825376581716 -439000 ekin = 2.32106357051175 | erot = 3.16171527166972 | epot = -18.7653165000796 | etot = -13.2825376578981 -440000 ekin = 2.32396046468846 | erot = 3.09429994298005 | epot = -18.7007980651343 | etot = -13.2825376574658 -441000 ekin = 2.34282585391516 | erot = 3.01497153468249 | epot = -18.6403350455373 | etot = -13.2825376569397 -442000 ekin = 2.37979980925652 | erot = 2.92981680804517 | epot = -18.5921542737248 | etot = -13.2825376564231 -443000 ekin = 2.4365622855113 | erot = 2.84513622245133 | epot = -18.5642361639992 | etot = -13.2825376560366 -444000 ekin = 2.51342571777129 | erot = 2.76656039612237 | epot = -18.5625237697596 | etot = -13.2825376558659 -445000 ekin = 2.60880718707236 | erot = 2.6982799889581 | epot = -18.5896248319859 | etot = -13.2825376559555 -446000 ekin = 2.71906096767643 | erot = 2.64257205052642 | epot = -18.6441706744995 | etot = -13.2825376562967 -447000 ekin = 2.83874401672722 | erot = 2.59965346897689 | epot = -18.7209351425404 | etot = -13.2825376568363 -448000 ekin = 2.9612677241565 | erot = 2.56781480894371 | epot = -18.8116201905961 | etot = -13.2825376574959 -449000 ekin = 3.07973256248662 | erot = 2.54376856118776 | epot = -18.9060387818648 | etot = -13.2825376581905 -450000 ekin = 3.18773299393503 | erot = 2.52315582293758 | epot = -18.9934264757091 | etot = -13.2825376588364 -451000 ekin = 3.28001368752861 | erot = 2.50120181208454 | epot = -19.063753158962 | etot = -13.2825376593488 -452000 ekin = 3.35296274688896 | erot = 2.47353158346301 | epot = -19.1090319899968 | etot = -13.2825376596448 -453000 ekin = 3.40494017429419 | erot = 2.43707428126018 | epot = -19.1245521152182 | etot = -13.2825376596639 -454000 ekin = 3.4363755140164 | erot = 2.39082250837405 | epot = -19.1097356817938 | etot = -13.2825376594033 -455000 ekin = 3.44952760872581 | erot = 2.33613006950283 | epot = -19.068195337143 | etot = -13.2825376589143 -456000 ekin = 3.44799144671178 | erot = 2.27640153123202 | epot = -19.0069306362517 | etot = -13.2825376583079 -457000 ekin = 3.43601809740561 | erot = 2.21623652991106 | epot = -18.9347922850174 | etot = -13.2825376577007 -458000 ekin = 3.41788845141646 | erot = 2.16036216289489 | epot = -18.8607882714966 | etot = -13.2825376571853 -459000 ekin = 3.3974915193921 | erot = 2.1126853259723 | epot = -18.7927145021792 | etot = -13.2825376568148 -460000 ekin = 3.37812232252278 | erot = 2.07567909161665 | epot = -18.7363390707418 | etot = -13.2825376566024 -461000 ekin = 3.36231617612483 | erot = 2.05042996966781 | epot = -18.6952838023611 | etot = -13.2825376565685 -462000 ekin = 3.3516010060643 | erot = 2.03669678982629 | epot = -18.6708354525495 | etot = -13.2825376566589 -463000 ekin = 3.34749626496556 | erot = 2.03201016323594 | epot = -18.6620440849604 | etot = -13.2825376567589 -464000 ekin = 3.35152548101934 | erot = 2.0337250814521 | epot = -18.6677882192943 | etot = -13.2825376568228 -465000 ekin = 3.36505604034505 | erot = 2.03980035193901 | epot = -18.6873940492497 | etot = -13.2825376569656 -466000 ekin = 3.38750814155039 | erot = 2.04917645650973 | epot = -18.719222255183 | etot = -13.2825376571229 -467000 ekin = 3.4178184653666 | erot = 2.06078922447546 | epot = -18.7611453471486 | etot = -13.2825376573065 -468000 ekin = 3.45442517049901 | erot = 2.07383123666845 | epot = -18.8107940646916 | etot = -13.2825376575242 -469000 ekin = 3.49517146555562 | erot = 2.08763407955549 | epot = -18.865343202886 | etot = -13.2825376577749 -470000 ekin = 3.5375430439129 | erot = 2.10145518357207 | epot = -18.9215358855281 | etot = -13.2825376580432 -471000 ekin = 3.578984874629 | erot = 2.11439735083904 | epot = -18.9759198837616 | etot = -13.2825376582935 -472000 ekin = 3.61725786632456 | erot = 2.12555669055365 | epot = -19.0253522153517 | etot = -13.2825376584735 -473000 ekin = 3.65079380576158 | erot = 2.13440730770354 | epot = -19.067738771992 | etot = -13.2825376585269 -474000 ekin = 3.67897471803071 | erot = 2.14127953357501 | epot = -19.1027919100301 | etot = -13.2825376584244 -475000 ekin = 3.70221628145261 | erot = 2.14765507905023 | epot = -19.1324090186923 | etot = -13.2825376581894 -476000 ekin = 3.72174790903032 | erot = 2.15602304575789 | epot = -19.1603086126886 | etot = -13.2825376579004 -477000 ekin = 3.73912018616774 | erot = 2.16928365663934 | epot = -19.1909415004594 | etot = -13.2825376576523 -478000 ekin = 3.7556510063889 | erot = 2.18999309719236 | epot = -19.2281817610876 | etot = -13.2825376575064 -479000 ekin = 3.77207488928898 | erot = 2.21984602916671 | epot = -19.2744585759238 | etot = -13.2825376574681 -480000 ekin = 3.78851866246641 | erot = 2.25959918548264 | epot = -19.33065550545 | etot = -13.2825376575009 -481000 ekin = 3.80616995061892 | erot = 2.30984659763992 | epot = -19.3985542055291 | etot = -13.2825376572702 -482000 ekin = 3.82906961959312 | erot = 2.37155747933105 | epot = -19.4831647566187 | etot = -13.2825376576945 -483000 ekin = 3.85390461343509 | erot = 2.44250735312729 | epot = -19.5789496246803 | etot = -13.2825376581179 -484000 ekin = 3.87679301499903 | erot = 2.51997841363885 | epot = -19.6793090871881 | etot = -13.2825376585502 -485000 ekin = 3.8941855852142 | erot = 2.60083126184978 | epot = -19.7775545060489 | etot = -13.2825376589849 -486000 ekin = 3.9031377534013 | erot = 2.6813903200239 | epot = -19.8670657328057 | etot = -13.2825376593805 -487000 ekin = 3.90177537850899 | erot = 2.75761792311516 | epot = -19.9419309612876 | etot = -13.2825376596634 -488000 ekin = 3.88986213162243 | erot = 2.82561628023474 | epot = -19.9980160716132 | etot = -13.282537659756 -489000 ekin = 3.86922231453849 | erot = 2.88229752819206 | epot = -20.0340575023505 | etot = -13.2825376596199 -490000 ekin = 3.84371636435388 | erot = 2.92590481083659 | epot = -20.0521588344839 | etot = -13.2825376592934 -491000 ekin = 3.8185829048698 | erot = 2.95607206100703 | epot = -20.0571926247696 | etot = -13.2825376588928 -492000 ekin = 3.79923632244268 | erot = 2.97333279544265 | epot = -20.0551067764526 | etot = -13.2825376585672 -493000 ekin = 3.78992062784017 | erot = 2.97831679174203 | epot = -20.0507750780101 | etot = -13.2825376584279 -494000 ekin = 3.7922931345625 | erot = 2.97052771091745 | epot = -20.0453585079511 | etot = -13.2825376624711 -495000 ekin = 3.79451442394532 | erot = 2.9341072450869 | epot = -20.0111593284224 | etot = -13.2825376593901 -496000 ekin = 3.8106248823664 | erot = 2.88141942472008 | epot = -19.9745819636276 | etot = -13.2825376565411 -497000 ekin = 3.85788186105348 | erot = 2.83372744077321 | epot = -19.9741469603241 | etot = -13.2825376584974 -498000 ekin = 3.9188457938421 | erot = 2.78115548050691 | epot = -19.9825389377102 | etot = -13.2825376633612 -499000 ekin = 3.96315793686508 | erot = 2.7024680648114 | epot = -19.9481636596344 | etot = -13.2825376579579 -500000 ekin = 4.0027205762755 | erot = 2.61046054601125 | epot = -19.8957187797513 | etot = -13.2825376574646 -501000 ekin = 4.04216054275046 | erot = 2.51312796103934 | epot = -19.8378261606956 | etot = -13.2825376569058 -502000 ekin = 4.08330148514098 | erot = 2.4163270430933 | epot = -19.7821661846463 | etot = -13.282537656412 -503000 ekin = 4.12765179374065 | erot = 2.32533692997657 | epot = -19.7355263797907 | etot = -13.2825376560735 -504000 ekin = 4.17571661390275 | erot = 2.24418432885896 | epot = -19.7024385986861 | etot = -13.2825376559244 -505000 ekin = 4.22673456414904 | erot = 2.17536462286828 | epot = -19.6846368429618 | etot = -13.2825376559445 -506000 ekin = 4.27886046445946 | erot = 2.11995169727426 | epot = -19.6813498177143 | etot = -13.2825376559806 -507000 ekin = 4.32989839509928 | erot = 2.07798999628154 | epot = -19.69042604762 | etot = -13.2825376562392 -508000 ekin = 4.37683697458704 | erot = 2.04846223351658 | epot = -19.7078368645412 | etot = -13.2825376564376 -509000 ekin = 4.41701088936698 | erot = 2.03040461252071 | epot = -19.7299531584268 | etot = -13.2825376565391 -510000 ekin = 4.44869291188054 | erot = 2.0233924534507 | epot = -19.7546230218677 | etot = -13.2825376565364 -511000 ekin = 4.47114700663339 | erot = 2.02761863549144 | epot = -19.7813032985736 | etot = -13.2825376564488 -512000 ekin = 4.4844887018835 | erot = 2.0437568785043 | epot = -19.8107832368059 | etot = -13.2825376564181 -513000 ekin = 4.48914630706749 | erot = 2.07205454687191 | epot = -19.843738510293 | etot = -13.2825376563536 -514000 ekin = 4.48557666179243 | erot = 2.11236294794722 | epot = -19.8804772660566 | etot = -13.282537656317 -515000 ekin = 4.47432723706423 | erot = 2.1643658113937 | epot = -19.9212307047863 | etot = -13.2825376563284 -516000 ekin = 4.45582679664873 | erot = 2.22719069336347 | epot = -19.9655551464075 | etot = -13.2825376563953 -517000 ekin = 4.43030463229401 | erot = 2.29935278529871 | epot = -20.0121950741066 | etot = -13.2825376565139 -518000 ekin = 4.39778184135702 | erot = 2.37880116113426 | epot = -20.0591206591638 | etot = -13.2825376566725 -519000 ekin = 4.35811170485674 | erot = 2.46303435402364 | epot = -20.1036837157379 | etot = -13.2825376568575 -520000 ekin = 4.31103971552179 | erot = 2.54924277018193 | epot = -20.14282014276 | etot = -13.2825376570563 -521000 ekin = 4.25625922128732 | erot = 2.63444730369841 | epot = -20.1732441822451 | etot = -13.2825376572594 -522000 ekin = 4.19345339504562 | erot = 2.71562973710461 | epot = -20.1916207896065 | etot = -13.2825376574562 -523000 ekin = 4.12233106590031 | erot = 2.78987661785175 | epot = -20.1947453413846 | etot = -13.2825376576325 -524000 ekin = 4.04267462479128 | erot = 2.85456825313573 | epot = -20.1797805356948 | etot = -13.2825376577678 -525000 ekin = 3.95441508754014 | erot = 2.9076289252841 | epot = -20.14458167066 | etot = -13.2825376578358 -526000 ekin = 3.85773415549987 | erot = 2.94781757722392 | epot = -20.0880893905345 | etot = -13.2825376578107 -527000 ekin = 3.75317337789272 | erot = 2.97499774804953 | epot = -20.0107087836172 | etot = -13.282537657675 -528000 ekin = 3.64171566472863 | erot = 2.99029287547963 | epot = -19.9145462004646 | etot = -13.2825376602563 -529000 ekin = 3.52133457981484 | erot = 2.97329981123796 | epot = -19.777172048072 | etot = -13.2825376570192 -530000 ekin = 3.40524483354409 | erot = 2.93138498576302 | epot = -19.619167471763 | etot = -13.2825376524559 -531000 ekin = 3.31329586023445 | erot = 2.90771179337181 | epot = -19.5035453066036 | etot = -13.2825376529973 -532000 ekin = 3.23028138422137 | erot = 2.91095227687559 | epot = -19.4237713182328 | etot = -13.2825376571358 -533000 ekin = 3.12254472504549 | erot = 2.92159652025206 | epot = -19.3266789030856 | etot = -13.282537657788 -534000 ekin = 3.01044793876856 | erot = 2.93913625615421 | epot = -19.2321218524818 | etot = -13.282537657559 -535000 ekin = 2.90665974197478 | erot = 2.96765394780088 | epot = -19.1568513472188 | etot = -13.2825376574432 -536000 ekin = 2.81267447142782 | erot = 3.00750648803519 | epot = -19.1027186169117 | etot = -13.2825376574487 -537000 ekin = 2.72954271623794 | erot = 3.05761918513524 | epot = -19.0696995589458 | etot = -13.2825376575726 -538000 ekin = 2.65787075122818 | erot = 3.11553336281627 | epot = -19.0559417718444 | etot = -13.2825376577999 -539000 ekin = 2.59787048049233 | erot = 3.17759265898484 | epot = -19.0580007975803 | etot = -13.2825376581031 -540000 ekin = 2.54945648890107 | erot = 3.23927692413161 | epot = -19.0712710714752 | etot = -13.2825376584425 -541000 ekin = 2.512378643395 | erot = 3.29568121876202 | epot = -19.0905975209266 | etot = -13.2825376587696 -542000 ekin = 2.48636877597141 | erot = 3.34210880592089 | epot = -19.1110152409261 | etot = -13.2825376590338 -543000 ekin = 2.4712699055648 | erot = 3.3747065125272 | epot = -19.1285140772836 | etot = -13.2825376591916 -544000 ekin = 2.46711428276816 | erot = 3.3910375894335 | epot = -19.1406895314189 | etot = -13.2825376592173 -545000 ekin = 2.4741173500058 | erot = 3.39046709618852 | epot = -19.1471221053056 | etot = -13.2825376591113 -546000 ekin = 2.49256786330789 | erot = 3.37425739408745 | epot = -19.1493629162983 | etot = -13.282537658903 -547000 ekin = 2.52261985355472 | erot = 3.34533431811562 | epot = -19.1504918303153 | etot = -13.282537658645 -548000 ekin = 2.5640229402261 | erot = 3.30777050325775 | epot = -19.1543311018841 | etot = -13.2825376584002 -549000 ekin = 2.61585467172264 | erot = 3.26610888708834 | epot = -19.1645012170377 | etot = -13.2825376582267 -550000 ekin = 2.67632806501996 | erot = 3.22468583528343 | epot = -19.1835515584667 | etot = -13.2825376581633 -551000 ekin = 2.74273542047637 | erot = 3.18709627675594 | epot = -19.2123693554546 | etot = -13.2825376582223 -552000 ekin = 2.81155537633479 | erot = 3.155885283811 | epot = -19.2499783185357 | etot = -13.2825376583899 -553000 ekin = 2.87870715456128 | erot = 3.13247774360817 | epot = -19.2937225568035 | etot = -13.2825376586341 -554000 ekin = 2.93989960588701 | erot = 3.11729757853042 | epot = -19.3397348433313 | etot = -13.2825376589139 -555000 ekin = 2.99100571713598 | erot = 3.10999728881064 | epot = -19.3835406651366 | etot = -13.2825376591899 -556000 ekin = 3.02839929468956 | erot = 3.10971957917588 | epot = -19.4206565332962 | etot = -13.2825376594307 -557000 ekin = 3.04921300214246 | erot = 3.11533545055142 | epot = -19.4470861123087 | etot = -13.2825376596148 -558000 ekin = 3.05150347330348 | erot = 3.12563190762297 | epot = -19.4596730406569 | etot = -13.2825376597304 -559000 ekin = 3.03432873631885 | erot = 3.13944482423083 | epot = -19.456311220323 | etot = -13.2825376597733 -560000 ekin = 2.9977526924766 | erot = 3.15574356337998 | epot = -19.4360339156024 | etot = -13.2825376597459 -561000 ekin = 2.9427917179436 | erot = 3.17367577833455 | epot = -19.3990051559327 | etot = -13.2825376596546 -562000 ekin = 2.87131567491266 | erot = 3.19257954673888 | epot = -19.3464328811612 | etot = -13.2825376595096 -563000 ekin = 2.78591370477051 | erot = 3.2119692901947 | epot = -19.2804206542887 | etot = -13.2825376593235 -564000 ekin = 2.6897353367659 | erot = 3.23150302487196 | epot = -19.2037760207478 | etot = -13.28253765911 -565000 ekin = 2.58631900803989 | erot = 3.25094003294576 | epot = -19.1197966998677 | etot = -13.282537658882 -566000 ekin = 2.47942134877151 | erot = 3.27009788587128 | epot = -19.0320568932949 | etot = -13.2825376586521 -567000 ekin = 2.37285930824791 | erot = 3.28881390752303 | epot = -18.9442108742005 | etot = -13.2825376584296 -568000 ekin = 2.2703747720392 | erot = 3.30691420257032 | epot = -18.8598266328315 | etot = -13.282537658222 -569000 ekin = 2.17552646994053 | erot = 3.32418852070003 | epot = -18.7822526486758 | etot = -13.2825376580353 -570000 ekin = 2.09160717358308 | erot = 3.34036686780938 | epot = -18.7145116992668 | etot = -13.2825376578743 -571000 ekin = 2.02157831416758 | erot = 3.35509336873546 | epot = -18.659209340647 | etot = -13.282537657744 -572000 ekin = 1.96800973251089 | erot = 3.36789498998737 | epot = -18.6184423801492 | etot = -13.2825376576509 -573000 ekin = 1.93301131087701 | erot = 3.37814685793009 | epot = -18.5936958264095 | etot = -13.2825376576024 -574000 ekin = 1.91814454492506 | erot = 3.38504063674726 | epot = -18.5857228392799 | etot = -13.2825376576076 -575000 ekin = 1.92430832574408 | erot = 3.38756624559013 | epot = -18.5944122290096 | etot = -13.2825376576754 -576000 ekin = 1.95160447468999 | erot = 3.38452119824164 | epot = -18.6186633307441 | etot = -13.2825376578125 -577000 ekin = 1.99920036892949 | erot = 3.37456184630709 | epot = -18.6562998732574 | etot = -13.2825376580208 -578000 ekin = 2.06522335781187 | erot = 3.35630974832182 | epot = -18.7040707644253 | etot = -13.2825376582916 -579000 ekin = 2.14673519283674 | erot = 3.32851940880933 | epot = -18.7577922602508 | etot = -13.2825376586048 -580000 ekin = 2.23983758246226 | erot = 3.29029959752555 | epot = -18.8126748389145 | etot = -13.2825376589267 -581000 ekin = 2.33993889926474 | erot = 3.2413588197994 | epot = -18.8638353782784 | etot = -13.2825376592143 -582000 ekin = 2.44216781902051 | erot = 3.18222403798945 | epot = -18.9069295164348 | etot = -13.2825376594248 -583000 ekin = 2.54186285338444 | erot = 3.11436905975195 | epot = -18.938769572664 | etot = -13.2825376595277 -584000 ekin = 2.63514321918155 | erot = 3.04016994421133 | epot = -18.9578508227089 | etot = -13.282537659316 -585000 ekin = 2.72038124549456 | erot = 2.96231486727155 | epot = -18.9652337720477 | etot = -13.2825376592816 -586000 ekin = 2.79529742079441 | erot = 2.88397447344912 | epot = -18.9618095534158 | etot = -13.2825376591723 -587000 ekin = 2.85803030913321 | erot = 2.80849541230731 | epot = -18.9490633804616 | etot = -13.2825376590211 -588000 ekin = 2.90761924156872 | erot = 2.73897208360503 | epot = -18.9291289840339 | etot = -13.2825376588602 -589000 ekin = 2.94382190770487 | erot = 2.67796026301525 | epot = -18.9043198294349 | etot = -13.2825376587148 -590000 ekin = 2.96693832518588 | erot = 2.62724420195739 | epot = -18.8767201857421 | etot = -13.2825376585988 -591000 ekin = 2.97766737843971 | erot = 2.58778349306991 | epot = -18.8479885300284 | etot = -13.2825376585188 -592000 ekin = 2.97699718658878 | erot = 2.55971358410891 | epot = -18.8192484291735 | etot = -13.2825376584758 -593000 ekin = 2.96611919165746 | erot = 2.54241252023367 | epot = -18.7910693703577 | etot = -13.2825376584665 -594000 ekin = 2.94635665291053 | erot = 2.53461934099529 | epot = -18.7635136523902 | etot = -13.2825376584844 -595000 ekin = 2.9190856971103 | erot = 2.53443482987529 | epot = -18.7360581856667 | etot = -13.2825376586811 -596000 ekin = 2.8853504738233 | erot = 2.53857982681691 | epot = -18.706467959401 | etot = -13.2825376587608 -597000 ekin = 2.84590859896362 | erot = 2.54482361730832 | epot = -18.6732698750819 | etot = -13.28253765881 -598000 ekin = 2.80153060630531 | erot = 2.55163242417959 | epot = -18.6357006893061 | etot = -13.2825376588212 -599000 ekin = 2.75300405719548 | erot = 2.55803363008721 | epot = -18.5935753460782 | etot = -13.2825376587955 -600000 ekin = 2.70110632481711 | erot = 2.56364667646595 | epot = -18.5472906600206 | etot = -13.2825376587375 -601000 ekin = 2.64657369871742 | erot = 2.56865533018097 | epot = -18.4977666875493 | etot = -13.2825376586509 -602000 ekin = 2.59009198472601 | erot = 2.57375726191876 | epot = -18.4463869051824 | etot = -13.2825376585376 -603000 ekin = 2.53231053373895 | erot = 2.58010020264817 | epot = -18.394948394788 | etot = -13.2825376584008 -604000 ekin = 2.47386381072251 | erot = 2.58919184014772 | epot = -18.3455933091172 | etot = -13.282537658247 -605000 ekin = 2.41538802270495 | erot = 2.60277705143637 | epot = -18.300702732226 | etot = -13.2825376580847 -606000 ekin = 2.35753010244784 | erot = 2.62269152367331 | epot = -18.2627592840455 | etot = -13.2825376579243 -607000 ekin = 2.30095094648108 | erot = 2.65066096469453 | epot = -18.2341495689615 | etot = -13.2825376577859 -608000 ekin = 2.24632550981926 | erot = 2.68812711797909 | epot = -18.2169902854641 | etot = -13.2825376576658 -609000 ekin = 2.19433984205684 | erot = 2.73619296831783 | epot = -18.2130704679521 | etot = -13.2825376575774 -610000 ekin = 2.14568734116616 | erot = 2.7954628779701 | epot = -18.2236878766643 | etot = -13.2825376575281 -611000 ekin = 2.10106577312396 | erot = 2.8659456974561 | epot = -18.2495491281024 | etot = -13.2825376575223 -612000 ekin = 2.06117569763992 | erot = 2.9469880537389 | epot = -18.2907014089413 | etot = -13.2825376575624 -613000 ekin = 2.02671979094169 | erot = 3.03724338411132 | epot = -18.3465008327016 | etot = -13.2825376576486 -614000 ekin = 1.99840061160405 | erot = 3.13468327208026 | epot = -18.415621541462 | etot = -13.2825376577777 -615000 ekin = 1.97691265350076 | erot = 3.23665756946818 | epot = -18.4961078809123 | etot = -13.2825376579434 -616000 ekin = 1.96292427456966 | erot = 3.34000833576273 | epot = -18.58547026847 | etot = -13.2825376581376 -617000 ekin = 1.95704706954419 | erot = 3.4412390414853 | epot = -18.680823769378 | etot = -13.2825376583485 -618000 ekin = 1.95979426061707 | erot = 3.53673433570056 | epot = -18.7790662548804 | etot = -13.2825376585628 -619000 ekin = 1.97153436735861 | erot = 3.62301686059867 | epot = -18.8770888867224 | etot = -13.2825376587651 -620000 ekin = 1.99244950083126 | erot = 3.69701656993236 | epot = -18.9720037297043 | etot = -13.2825376589407 -621000 ekin = 2.02250680811196 | erot = 3.75631711882421 | epot = -19.0613615860136 | etot = -13.2825376590775 -622000 ekin = 2.06144629220648 | erot = 3.7993379752723 | epot = -19.1433219266483 | etot = -13.2825376591695 -623000 ekin = 2.10878075940092 | erot = 3.82541513939284 | epot = -19.216733558012 | etot = -13.2825376592183 -624000 ekin = 2.16379839198576 | erot = 3.83475982186747 | epot = -19.2810958730871 | etot = -13.2825376592339 -625000 ekin = 2.22555932782583 | erot = 3.82830035125848 | epot = -19.3363973383166 | etot = -13.2825376592323 -626000 ekin = 2.29288544260848 | erot = 3.80744110347782 | epot = -19.3828642053181 | etot = -13.2825376592318 -627000 ekin = 2.36435394305829 | erot = 3.77379464741738 | epot = -19.4206862497219 | etot = -13.2825376592462 -628000 ekin = 2.43831432674405 | erot = 3.72895154257647 | epot = -19.4498035286011 | etot = -13.2825376592806 -629000 ekin = 2.5129489794456 | erot = 3.67434156158729 | epot = -19.4698282003614 | etot = -13.2825376593285 -630000 ekin = 2.58638771765141 | erot = 3.61121141784532 | epot = -19.4801367948702 | etot = -13.2825376593735 -631000 ekin = 2.65686759984465 | erot = 3.54070434322503 | epot = -19.4801096088593 | etot = -13.2825376657897 -632000 ekin = 2.72291190263409 | erot = 3.46399577717246 | epot = -19.4694453501734 | etot = -13.2825376703668 -633000 ekin = 2.78348672611247 | erot = 3.38241264800352 | epot = -19.4484370444086 | etot = -13.2825376702926 -634000 ekin = 2.83810143013786 | erot = 3.29749507668476 | epot = -19.4181341769904 | etot = -13.2825376701678 -635000 ekin = 2.88683118402529 | erot = 3.21096793801688 | epot = -19.3803367920453 | etot = -13.2825376700031 -636000 ekin = 2.93026618630813 | erot = 3.12465298496839 | epot = -19.3374568410897 | etot = -13.2825376698132 -637000 ekin = 2.96941056885858 | erot = 3.0403692465718 | epot = -19.2923174850405 | etot = -13.2825376696101 -638000 ekin = 3.00556169693335 | erot = 2.95987410217697 | epot = -19.2479734685112 | etot = -13.2825376694009 -639000 ekin = 3.04019340865286 | erot = 2.88486846877298 | epot = -19.2075995466134 | etot = -13.2825376691875 -640000 ekin = 3.07485121524287 | erot = 2.81704601028373 | epot = -19.1744348944991 | etot = -13.2825376689725 -641000 ekin = 3.11105408028794 | erot = 2.75813097963992 | epot = -19.1517227286916 | etot = -13.2825376687637 -642000 ekin = 3.15019312328036 | erot = 2.7098440548544 | epot = -19.1425748467125 | etot = -13.2825376685778 -643000 ekin = 3.19342381264373 | erot = 2.67376399477657 | epot = -19.149725475858 | etot = -13.2825376684377 -644000 ekin = 3.2415588207624 | erot = 2.65109893593325 | epot = -19.1751954250647 | etot = -13.282537668369 -645000 ekin = 3.29497575523204 | erot = 2.64241916696914 | epot = -19.2199325905945 | etot = -13.2825376683933 -646000 ekin = 3.35355393407658 | erot = 2.64741690321924 | epot = -19.2835085058203 | etot = -13.2825376685245 -647000 ekin = 3.41664956861565 | erot = 2.66474995394752 | epot = -19.3639371913281 | etot = -13.2825376687649 -648000 ekin = 3.4831141060628 | erot = 2.69200913896267 | epot = -19.4576609141298 | etot = -13.2825376691043 -649000 ekin = 3.55135925694529 | erot = 2.72583530732997 | epot = -19.5597322337925 | etot = -13.2825376695172 -650000 ekin = 3.61947301797377 | erot = 2.76220049491276 | epot = -19.6642111828496 | etot = -13.2825376699631 -651000 ekin = 3.68538880274457 | erot = 2.79684816347516 | epot = -19.764774636609 | etot = -13.2825376703893 -652000 ekin = 3.74709908730354 | erot = 2.82584894414238 | epot = -19.8554857021858 | etot = -13.2825376707399 -653000 ekin = 3.80288488877091 | erot = 2.84617490646358 | epot = -19.9315974662018 | etot = -13.2825376709673 -654000 ekin = 3.85151192347428 | erot = 2.85615319330961 | epot = -19.9902027878321 | etot = -13.2825376710482 -655000 ekin = 3.89233743675784 | erot = 2.85566240366418 | epot = -20.0305375114124 | etot = -13.2825376709904 -656000 ekin = 3.92529306042297 | erot = 2.84600373605249 | epot = -20.0538344673054 | etot = -13.2825376708299 -657000 ekin = 3.9507492437021 | erot = 2.82948452039627 | epot = -20.0627714347188 | etot = -13.2825376706204 -658000 ekin = 3.96930448522689 | erot = 2.80884105011381 | epot = -20.0606832057567 | etot = -13.282537670416 -659000 ekin = 3.98156254976232 | erot = 2.78666073057887 | epot = -20.0507609506005 | etot = -13.2825376702593 -660000 ekin = 3.98794995381879 | erot = 2.76493225942124 | epot = -20.0354198834157 | etot = -13.2825376701757 -661000 ekin = 3.98860416113611 | erot = 2.74479055428647 | epot = -20.0159323855936 | etot = -13.282537670171 -662000 ekin = 3.98333736211109 | erot = 2.72646306735502 | epot = -19.9923380997025 | etot = -13.2825376702364 -663000 ekin = 3.9716619686291 | erot = 2.70938404532074 | epot = -19.9635836843021 | etot = -13.2825376703522 -664000 ekin = 3.95286211458908 | erot = 2.69242500163181 | epot = -19.9278247867134 | etot = -13.2825376704925 -665000 ekin = 3.92609780975317 | erot = 2.67418491171735 | epot = -19.8828203921001 | etot = -13.2825376706295 -666000 ekin = 3.89053574202168 | erot = 2.65328635574181 | epot = -19.8263597684999 | etot = -13.2825376707365 -667000 ekin = 3.84550518468516 | erot = 2.62863029044506 | epot = -19.7566731459204 | etot = -13.2825376707901 -668000 ekin = 3.79067534879777 | erot = 2.59957256262197 | epot = -19.6727855821932 | etot = -13.2825376707734 -669000 ekin = 3.72624194861737 | erot = 2.56600183381133 | epot = -19.5747814531047 | etot = -13.282537670676 -670000 ekin = 3.65309967705475 | erot = 2.52832169427011 | epot = -19.4639590418208 | etot = -13.282537670496 -671000 ekin = 3.57296811018949 | erot = 2.48736383191286 | epot = -19.3428696123407 | etot = -13.2825376702383 -672000 ekin = 3.48843263531181 | erot = 2.44427271264344 | epot = -19.2152430178709 | etot = -13.2825376699157 -673000 ekin = 3.40286035229605 | erot = 2.40039617767075 | epot = -19.0857941995173 | etot = -13.2825376695505 -674000 ekin = 3.32015657280881 | erot = 2.35719425457316 | epot = -18.9598884965573 | etot = -13.2825376691753 -675000 ekin = 3.24436019808196 | erot = 2.31615841412129 | epot = -18.8430562810334 | etot = -13.2825376688302 -676000 ekin = 3.17913583606399 | erot = 2.27873161512438 | epot = -18.740405119743 | etot = -13.2825376685547 -677000 ekin = 3.12743284479367 | erot = 2.24616920610074 | epot = -18.6561397192095 | etot = -13.2825376683151 -678000 ekin = 3.09116321204123 | erot = 2.21938913067767 | epot = -18.5930900109928 | etot = -13.2825376682739 -679000 ekin = 3.06996492217903 | erot = 2.19955802308988 | epot = -18.5520606135526 | etot = -13.2825376682837 -680000 ekin = 3.06282540105824 | erot = 2.18767057709701 | epot = -18.5330336464769 | etot = -13.2825376683217 -681000 ekin = 3.06856941759266 | erot = 2.18446333304883 | epot = -18.5355704190133 | etot = -13.2825376683718 -682000 ekin = 3.08614503868821 | erot = 2.19031007375325 | epot = -18.5589927809047 | etot = -13.2825376684632 -683000 ekin = 3.11401676517912 | erot = 2.20483123961229 | epot = -18.6013856734681 | etot = -13.2825376686767 -684000 ekin = 3.1499497049718 | erot = 2.22703766523478 | epot = -18.6595250391781 | etot = -13.2825376689715 -685000 ekin = 3.1913881729591 | erot = 2.25525783713242 | epot = -18.7291836794166 | etot = -13.2825376693251 -686000 ekin = 3.2355359736388 | erot = 2.28721755220356 | epot = -18.8052911955454 | etot = -13.282537669703 -687000 ekin = 3.27958856790023 | erot = 2.32030038563959 | epot = -18.8824266236037 | etot = -13.2825376700639 -688000 ekin = 3.32103493725068 | erot = 2.35186996598866 | epot = -18.9554425735995 | etot = -13.2825376703601 -689000 ekin = 3.35799818039315 | erot = 2.37963585732459 | epot = -19.0201717082656 | etot = -13.2825376705479 -690000 ekin = 3.38953188177024 | erot = 2.40199807238457 | epot = -19.0740676247556 | etot = -13.2825376706008 -691000 ekin = 3.41577144695012 | erot = 2.41828305275593 | epot = -19.1165921702244 | etot = -13.2825376705183 -692000 ekin = 3.43789562336026 | erot = 2.42879295705483 | epot = -19.1492262507455 | etot = -13.2825376703304 -693000 ekin = 3.45784949823494 | erot = 2.43469159318125 | epot = -19.1750787614971 | etot = -13.2825376700809 -694000 ekin = 3.47795427967228 | erot = 2.43774070868771 | epot = -19.1982326581791 | etot = -13.2825376698191 -695000 ekin = 3.50053093039143 | erot = 2.43997131609287 | epot = -19.2230399160667 | etot = -13.2825376695824 -696000 ekin = 3.52761050730188 | erot = 2.44340337549972 | epot = -19.253551552192 | etot = -13.2825376693904 -697000 ekin = 3.56079077322806 | erot = 2.44986396554409 | epot = -19.2931924080192 | etot = -13.2825376692471 -698000 ekin = 3.60121696147359 | erot = 2.46089758486526 | epot = -19.3446522154888 | etot = -13.28253766915 -699000 ekin = 3.6496121327901 | erot = 2.47770733427071 | epot = -19.4098571361639 | etot = -13.2825376691031 -700000 ekin = 3.70626748084333 | erot = 2.50104915957359 | epot = -19.4898543095415 | etot = -13.2825376691246 -701000 ekin = 3.77093513695816 | erot = 2.53103621287959 | epot = -19.5845090190825 | etot = -13.2825376692448 -702000 ekin = 3.84262768940034 | erot = 2.56687733849262 | epot = -19.6920426973887 | etot = -13.2825376694958 -703000 ekin = 3.91940034762304 | erot = 2.60664110638312 | epot = -19.8085791238994 | etot = -13.2825376698933 -704000 ekin = 3.9982358547303 | erot = 2.64716826817973 | epot = -19.9279417933333 | etot = -13.2825376704233 -705000 ekin = 4.07514464413495 | erot = 2.68423896184971 | epot = -20.0419212770165 | etot = -13.2825376710318 -706000 ekin = 4.14554203036507 | erot = 2.71304391273882 | epot = -20.1411236147333 | etot = -13.2825376716295 -707000 ekin = 4.20487575193823 | erot = 2.7289253372954 | epot = -20.2163387613403 | etot = -13.2825376721067 -708000 ekin = 4.24938283126873 | erot = 2.72825870746495 | epot = -20.2601792110953 | etot = -13.2825376723616 -709000 ekin = 4.27678612885237 | erot = 2.70926619644947 | epot = -20.2685899976319 | etot = -13.2825376723301 -710000 ekin = 4.28673081641948 | erot = 2.67252621890016 | epot = -20.2417947073265 | etot = -13.2825376720069 -711000 ekin = 4.28082322623417 | erot = 2.6210105179504 | epot = -20.1843714156341 | etot = -13.2825376714495 -712000 ekin = 4.26225868779622 | erot = 2.55962600082617 | epot = -20.104422359382 | etot = -13.2825376707596 -713000 ekin = 4.23515498224752 | erot = 2.49440280552867 | epot = -20.0120954578281 | etot = -13.2825376700519 -714000 ekin = 4.20378550523481 | erot = 2.43156567582597 | epot = -19.9178888504867 | etot = -13.282537669426 -715000 ekin = 4.17190188735528 | erot = 2.37671476689976 | epot = -19.8311543232044 | etot = -13.2825376689494 -716000 ekin = 4.14226649350958 | erot = 2.33425236976786 | epot = -19.7590565319311 | etot = -13.2825376686537 -717000 ekin = 4.11642945246045 | erot = 2.30708700174596 | epot = -19.7060541227473 | etot = -13.2825376685409 -718000 ekin = 4.09471959167245 | erot = 2.29657561669689 | epot = -19.6738328769614 | etot = -13.282537668592 -719000 ekin = 4.07639008593528 | erot = 2.30263774998752 | epot = -19.6615655046985 | etot = -13.2825376687757 -720000 ekin = 4.05985922917437 | erot = 2.32397934764256 | epot = -19.666376245872 | etot = -13.2825376690551 -721000 ekin = 4.04299880694437 | erot = 2.35837721352838 | epot = -19.6839136898621 | etot = -13.2825376693893 -722000 ekin = 4.02343688316733 | erot = 2.40299878609526 | epot = -19.7089733390043 | etot = -13.2825376697417 -723000 ekin = 3.99884065344427 | erot = 2.45471133767174 | epot = -19.7360896611947 | etot = -13.2825376700787 -724000 ekin = 3.96717167902435 | erot = 2.51036796126059 | epot = -19.7600773106559 | etot = -13.282537670371 -725000 ekin = 3.92690441967245 | erot = 2.56705586836098 | epot = -19.7764979586269 | etot = -13.2825376705935 -726000 ekin = 3.87729637976355 | erot = 2.62227216901714 | epot = -19.7821062194414 | etot = -13.2825376706607 -727000 ekin = 3.8190968772367 | erot = 2.6738940465784 | epot = -19.7755285945079 | etot = -13.2825376706928 -728000 ekin = 3.75316507804633 | erot = 2.72096436119536 | epot = -19.7566671098349 | etot = -13.2825376705932 -729000 ekin = 3.68121241124607 | erot = 2.76353487071615 | epot = -19.7272849523289 | etot = -13.2825376703667 -730000 ekin = 3.60595083273131 | erot = 2.80255656445165 | epot = -19.6910450672214 | etot = -13.2825376700385 -731000 ekin = 3.53083585767324 | erot = 2.83972569859397 | epot = -19.653099225923 | etot = -13.2825376696558 -732000 ekin = 3.45966885133349 | erot = 2.87715368835778 | epot = -19.6193602089738 | etot = -13.2825376692825 -733000 ekin = 3.39612153666075 | erot = 2.91688280104916 | epot = -19.5955420066965 | etot = -13.2825376689866 -734000 ekin = 3.34327992468431 | erot = 2.96033658922183 | epot = -19.5861541827305 | etot = -13.2825376688244 -735000 ekin = 3.3033011289436 | erot = 3.00783596111042 | epot = -19.5936747588816 | etot = -13.2825376688276 -736000 ekin = 3.27724072963395 | erot = 3.05831043253752 | epot = -19.6180888311677 | etot = -13.2825376689963 -737000 ekin = 3.26506253896415 | erot = 3.10929392283416 | epot = -19.656894131098 | etot = -13.2825376692997 -738000 ekin = 3.26580566526871 | erot = 3.15723003734976 | epot = -19.7055733723001 | etot = -13.2825376696816 -739000 ekin = 3.27786090586245 | erot = 3.19803615726929 | epot = -19.7584347332053 | etot = -13.2825376700736 -740000 ekin = 3.29929519803613 | erot = 3.22780296867189 | epot = -19.8096358371181 | etot = -13.2825376704101 -741000 ekin = 3.3281598026641 | erot = 3.2434576850098 | epot = -19.8541551583189 | etot = -13.282537670645 -742000 ekin = 3.36272243969023 | erot = 3.24322419612484 | epot = -19.8884843065754 | etot = -13.2825376707603 -743000 ekin = 3.40154954265053 | erot = 3.22659635037975 | epot = -19.91068356386 | etot = -13.2825376708298 -744000 ekin = 3.44355690162401 | erot = 3.19405338784643 | epot = -19.9201479602064 | etot = -13.282537670736 -745000 ekin = 3.48810285817397 | erot = 3.14763432802534 | epot = -19.9182748567946 | etot = -13.2825376705953 -746000 ekin = 3.53467364484348 | erot = 3.09004249682931 | epot = -19.9072538121143 | etot = -13.2825376704415 -747000 ekin = 3.58273489719928 | erot = 3.02422947593768 | epot = -19.8895020434333 | etot = -13.2825376702963 -748000 ekin = 3.63163431992952 | erot = 2.95313859310771 | epot = -19.8673105832079 | etot = -13.2825376701706 -749000 ekin = 3.68055410773111 | erot = 2.87956450535935 | epot = -19.8426562831586 | etot = -13.2825376700682 -750000 ekin = 3.7285026487858 | erot = 2.80607481969708 | epot = -19.8171151384766 | etot = -13.2825376699938 -751000 ekin = 3.77431992736046 | erot = 2.73492674316789 | epot = -19.7917843404859 | etot = -13.2825376699576 -752000 ekin = 3.81667135032658 | erot = 2.66792933662307 | epot = -19.7671383569269 | etot = -13.2825376699773 -753000 ekin = 3.85401538818531 | erot = 2.6062395161429 | epot = -19.7427925744031 | etot = -13.2825376700749 -754000 ekin = 3.88455267934887 | erot = 2.5501327302614 | epot = -19.7172230798774 | etot = -13.2825376702671 -755000 ekin = 3.90620090059213 | erot = 2.49884999016135 | epot = -19.6875885613011 | etot = -13.2825376705476 -756000 ekin = 3.91710462659123 | erot = 2.4506960000184 | epot = -19.6503382971539 | etot = -13.2825376705443 -757000 ekin = 3.91725792025721 | erot = 2.40369183428835 | epot = -19.6034874252691 | etot = -13.2825376707236 -758000 ekin = 3.90622854864869 | erot = 2.35617894285865 | epot = -19.5449451622686 | etot = -13.2825376707613 -759000 ekin = 3.88450313649421 | erot = 2.307511853008 | epot = -19.47455266009 | etot = -13.2825376705877 -760000 ekin = 3.85399004377457 | erot = 2.25863561784068 | epot = -19.3951633318159 | etot = -13.2825376702006 -761000 ekin = 3.81799666982234 | erot = 2.2120898004713 | epot = -19.3126241399677 | etot = -13.2825376696741 -762000 ekin = 3.78022631318949 | erot = 2.17128933431168 | epot = -19.2340533167231 | etot = -13.2825376692219 -763000 ekin = 3.73661802519724 | erot = 2.13809664148039 | epot = -19.157252335609 | etot = -13.2825376689313 -764000 ekin = 3.68660767297181 | erot = 2.11458113784821 | epot = -19.0837264795458 | etot = -13.2825376687258 -765000 ekin = 3.63152213040114 | erot = 2.10258243850245 | epot = -19.016642237515 | etot = -13.2825376686114 -766000 ekin = 3.57217194872271 | erot = 2.10319364759271 | epot = -18.9579032648383 | etot = -13.2825376685229 -767000 ekin = 3.50915043230235 | erot = 2.11696161070464 | epot = -18.9086497115248 | etot = -13.2825376685178 -768000 ekin = 3.44287730029771 | erot = 2.14384189418764 | epot = -18.8692568629801 | etot = -13.2825376684947 -769000 ekin = 3.3740781166784 | erot = 2.18352203430037 | epot = -18.8401378194259 | etot = -13.2825376684472 -770000 ekin = 3.3040269110262 | erot = 2.2354469932855 | epot = -18.8220115726952 | etot = -13.2825376683835 -771000 ekin = 3.23454927903731 | erot = 2.29870117920211 | epot = -18.8157881266126 | etot = -13.2825376683732 -772000 ekin = 3.16778213081256 | erot = 2.37165603566442 | epot = -18.8219758348544 | etot = -13.2825376683774 -773000 ekin = 3.10585178824851 | erot = 2.45189360020004 | epot = -18.840283056865 | etot = -13.2825376684165 -774000 ekin = 3.05132445362518 | erot = 2.53742495789156 | epot = -18.8712870797731 | etot = -13.2825376682564 -775000 ekin = 3.00630147843012 | erot = 2.62609752200496 | epot = -18.9149366688542 | etot = -13.2825376684191 -776000 ekin = 2.97144443263784 | erot = 2.71477730985204 | epot = -18.9687594110596 | etot = -13.2825376685697 -777000 ekin = 2.94698171101505 | erot = 2.80100976982407 | epot = -19.0305291495095 | etot = -13.2825376686704 -778000 ekin = 2.93288277550281 | erot = 2.8833938872999 | epot = -19.0988143314864 | etot = -13.2825376686837 -779000 ekin = 2.9291073028875 | erot = 2.9618300279754 | epot = -19.1734749994569 | etot = -13.282537668594 -780000 ekin = 2.93579388567472 | erot = 3.03750518021137 | epot = -19.2558367343112 | etot = -13.2825376684251 -781000 ekin = 2.95325630949646 | erot = 3.11251463626943 | epot = -19.3483086140044 | etot = -13.2825376682385 -782000 ekin = 2.98176618547441 | erot = 3.189171361001 | epot = -19.4534752145867 | etot = -13.2825376681113 -783000 ekin = 3.02122758219725 | erot = 3.26921648812991 | epot = -19.5729817384327 | etot = -13.2825376681056 -784000 ekin = 3.07089714794778 | erot = 3.35319620066463 | epot = -19.7066310168605 | etot = -13.2825376682481 -785000 ekin = 3.12925653033684 | erot = 3.44018487512351 | epot = -19.8519790739888 | etot = -13.2825376685285 -786000 ekin = 3.19405797125228 | erot = 3.52788200321648 | epot = -20.0044776433779 | etot = -13.2825376689092 -787000 ekin = 3.26249776188156 | erot = 3.61297785906092 | epot = -20.1580132902857 | etot = -13.2825376693433 -788000 ekin = 3.33144967160353 | erot = 3.69161943951225 | epot = -20.305606780904 | etot = -13.2825376697883 -789000 ekin = 3.39770556173349 | erot = 3.75982531205833 | epot = -20.4400685440038 | etot = -13.282537670212 -790000 ekin = 3.45820395551511 | erot = 3.81377941395818 | epot = -20.5545210400615 | etot = -13.2825376705882 -791000 ekin = 3.51015148125463 | erot = 3.85000835167799 | epot = -20.6426975044847 | etot = -13.2825376715521 -792000 ekin = 3.5477656494443 | erot = 3.86447708281342 | epot = -20.6947804042054 | etot = -13.2825376719477 -793000 ekin = 3.56673386235719 | erot = 3.85375177259752 | epot = -20.7030233071327 | etot = -13.282537672178 -794000 ekin = 3.56535433496591 | erot = 3.81599585289175 | epot = -20.6638878600545 | etot = -13.2825376721968 -795000 ekin = 3.54336423774681 | erot = 3.75111846556983 | epot = -20.5770203753028 | etot = -13.2825376719862 -796000 ekin = 3.50191265633486 | erot = 3.66102926483526 | epot = -20.445479592736 | etot = -13.2825376715658 -797000 ekin = 3.44331621142581 | erot = 3.54957138817431 | epot = -20.275425270589 | etot = -13.2825376709889 -798000 ekin = 3.37066053440221 | erot = 3.42213246909072 | epot = -20.0753306738195 | etot = -13.2825376703266 -799000 ekin = 3.28735656784917 | erot = 3.28504268658437 | epot = -19.8549369240833 | etot = -13.2825376696498 -800000 ekin = 3.1967614101609 | erot = 3.14491706728329 | epot = -19.6242161464581 | etot = -13.2825376690139 -801000 ekin = 3.10193388348241 | erot = 3.008077953099 | epot = -19.3925495050348 | etot = -13.2825376684534 -802000 ekin = 3.00553736756426 | erot = 2.88012979876869 | epot = -19.1682048343169 | etot = -13.2825376679839 -803000 ekin = 2.90985246625746 | erot = 2.76569078054883 | epot = -18.9580809144165 | etot = -13.2825376676103 -804000 ekin = 2.81683808714811 | erot = 2.66824302177604 | epot = -18.767618776258 | etot = -13.2825376673338 -805000 ekin = 2.72818412045662 | erot = 2.59005510940243 | epot = -18.6007768970147 | etot = -13.2825376671557 -806000 ekin = 2.64532439255801 | erot = 2.53214862202529 | epot = -18.460010681661 | etot = -13.2825376670777 -807000 ekin = 2.56941186666917 | erot = 2.49430692056124 | epot = -18.3462564543289 | etot = -13.2825376670985 -808000 ekin = 2.50128142889036 | erot = 2.4751494073639 | epot = -18.2589685034643 | etot = -13.2825376672101 -809000 ekin = 2.44144236795443 | erot = 2.47230913362086 | epot = -18.1962891689445 | etot = -13.2825376673692 -810000 ekin = 2.39012708340952 | erot = 2.48271406544018 | epot = -18.1553788164563 | etot = -13.2825376676066 -811000 ekin = 2.34728664736234 | erot = 2.50269653307823 | epot = -18.1325208483013 | etot = -13.2825376678607 -812000 ekin = 2.31275384401392 | erot = 2.5284613206776 | epot = -18.1237528327934 | etot = -13.2825376681019 -813000 ekin = 2.28637472346062 | erot = 2.55641958964873 | epot = -18.1253319814181 | etot = -13.2825376683087 -814000 ekin = 2.2680963430183 | erot = 2.58342175986192 | epot = -18.1340557713507 | etot = -13.2825376684705 -815000 ekin = 2.25799398108187 | erot = 2.60689379310711 | epot = -18.147425442776 | etot = -13.282537668587 -816000 ekin = 2.25623692236378 | erot = 2.6248911786293 | epot = -18.1636657696559 | etot = -13.2825376686629 -817000 ekin = 2.26301448164562 | erot = 2.63611346242108 | epot = -18.1816656127696 | etot = -13.2825376687029 -818000 ekin = 2.27845464056916 | erot = 2.63992517489727 | epot = -18.200917484174 | etot = -13.2825376687075 -819000 ekin = 2.30255118254824 | erot = 2.63638076675709 | epot = -18.2214696180403 | etot = -13.2825376687349 -820000 ekin = 2.33498671690288 | erot = 2.62599567774902 | epot = -18.2435200633427 | etot = -13.2825376686908 -821000 ekin = 2.37528893737676 | erot = 2.61008048021327 | epot = -18.2679070861996 | etot = -13.2825376686096 -822000 ekin = 2.42285081016476 | erot = 2.59073415648932 | epot = -18.2961226351515 | etot = -13.2825376684974 -823000 ekin = 2.47691845695884 | erot = 2.57068820920496 | epot = -18.330144334532 | etot = -13.2825376683682 -824000 ekin = 2.53658809763949 | erot = 2.55309938377513 | epot = -18.3722251496539 | etot = -13.2825376682393 -825000 ekin = 2.60079770131234 | erot = 2.54128433496743 | epot = -18.4246197044077 | etot = -13.2825376681279 -826000 ekin = 2.6683297319833 | erot = 2.53844971722971 | epot = -18.4893171172594 | etot = -13.2825376680464 -827000 ekin = 2.73783541426496 | erot = 2.54745860097927 | epot = -18.5678316832478 | etot = -13.2825376680036 -828000 ekin = 2.8078735374226 | erot = 2.570638372336 | epot = -18.6610495777666 | etot = -13.282537668008 -829000 ekin = 2.87694004142142 | erot = 2.6095991500053 | epot = -18.7690768595013 | etot = -13.2825376680745 -830000 ekin = 2.94346318720465 | erot = 2.66502277159192 | epot = -18.8910236270209 | etot = -13.2825376682243 -831000 ekin = 3.00576095292962 | erot = 2.73641402738311 | epot = -19.0247126487928 | etot = -13.28253766848 -832000 ekin = 3.0619900354022 | erot = 2.82186650180673 | epot = -19.1663942060617 | etot = -13.2825376688528 -833000 ekin = 3.11014899562178 | erot = 2.9179503249138 | epot = -19.3106369898642 | etot = -13.2825376693286 -834000 ekin = 3.14820449359153 | erot = 3.01984474732083 | epot = -19.4505869107716 | etot = -13.2825376698592 -835000 ekin = 3.17437957900616 | erot = 3.12179257976731 | epot = -19.5787098291384 | etot = -13.2825376703649 -836000 ekin = 3.18757195243303 | erot = 3.217846898268 | epot = -19.687956521455 | etot = -13.282537670754 -837000 ekin = 3.18777327474339 | erot = 3.30274497121124 | epot = -19.7730559169123 | etot = -13.2825376709577 -838000 ekin = 3.17628521735201 | erot = 3.37264530222933 | epot = -19.8314681905428 | etot = -13.2825376709614 -839000 ekin = 3.15554655753232 | erot = 3.42547713952516 | epot = -19.8635613678745 | etot = -13.282537670817 -840000 ekin = 3.12853906989481 | erot = 3.46080086771501 | epot = -19.8718776082294 | etot = -13.2825376706196 -841000 ekin = 3.09797460324027 | erot = 3.47929817818113 | epot = -19.8598104518813 | etot = -13.2825376704599 -842000 ekin = 3.06563312579573 | erot = 3.48217550735097 | epot = -19.8303463035245 | etot = -13.2825376703778 -843000 ekin = 3.0321807849032 | erot = 3.47078119390777 | epot = -19.7854996491548 | etot = -13.2825376703438 -844000 ekin = 2.99754824930587 | erot = 3.44659665119674 | epot = -19.7266825707828 | etot = -13.2825376702802 -845000 ekin = 2.96164676060849 | erot = 3.41154768663129 | epot = -19.6557321173456 | etot = -13.2825376701058 -846000 ekin = 2.92503739739917 | erot = 3.3684099877387 | epot = -19.5759850549147 | etot = -13.2825376697769 -847000 ekin = 2.88924342097115 | erot = 3.32104931094625 | epot = -19.4928304012178 | etot = -13.2825376693004 -848000 ekin = 2.85664997217234 | erot = 3.2743258340256 | epot = -19.413513474944 | etot = -13.282537668746 -849000 ekin = 2.83005143134554 | erot = 3.23330176450845 | epot = -19.3458908642286 | etot = -13.2825376683746 -850000 ekin = 2.81205597381057 | erot = 3.20226229425748 | epot = -19.2968559356605 | etot = -13.2825376675925 -851000 ekin = 2.80444558746427 | erot = 3.18500981062148 | epot = -19.2719930659083 | etot = -13.2825376678225 -852000 ekin = 2.80546277463363 | erot = 3.18034603825546 | epot = -19.2683464810916 | etot = -13.2825376682025 -853000 ekin = 2.81244121485968 | erot = 3.18510929963401 | epot = -19.280088183197 | etot = -13.2825376687033 -854000 ekin = 2.82227167904044 | erot = 3.19468161889413 | epot = -19.2994909671748 | etot = -13.2825376692403 -855000 ekin = 2.83221172623428 | erot = 3.20377851190415 | epot = -19.3185279077744 | etot = -13.282537669636 -856000 ekin = 2.84030053008536 | erot = 3.20718605728263 | epot = -19.3300242573987 | etot = -13.2825376700307 -857000 ekin = 2.84404786964225 | erot = 3.20080956078108 | epot = -19.3273951006455 | etot = -13.2825376702222 -858000 ekin = 2.84179014642712 | erot = 3.18249842088716 | epot = -19.3068262375353 | etot = -13.282537670221 -859000 ekin = 2.8327614996683 | erot = 3.15199731413447 | epot = -19.2672964838756 | etot = -13.2825376700728 -860000 ekin = 2.8170072354239 | erot = 3.110467808288 | epot = -19.2100127135406 | etot = -13.2825376698287 -861000 ekin = 2.79529073711156 | erot = 3.0598903948263 | epot = -19.1377188014641 | etot = -13.2825376695262 -862000 ekin = 2.76903178124154 | erot = 3.00259641979431 | epot = -19.0541658702196 | etot = -13.2825376691838 -863000 ekin = 2.740260190387 | erot = 2.94102587736042 | epot = -18.9638237365556 | etot = -13.2825376688082 -864000 ekin = 2.71154390225988 | erot = 2.8776699566398 | epot = -18.8717515273048 | etot = -13.2825376684052 -865000 ekin = 2.68585679377337 | erot = 2.81509451396977 | epot = -18.7834889757305 | etot = -13.2825376679873 -866000 ekin = 2.66591731935461 | erot = 2.75755671057519 | epot = -18.7060116974828 | etot = -13.282537667553 -867000 ekin = 2.65369684330944 | erot = 2.70836237988842 | epot = -18.6445968906315 | etot = -13.2825376674336 -868000 ekin = 2.65132555303167 | erot = 2.66699243377126 | epot = -18.6008556541432 | etot = -13.2825376673403 -869000 ekin = 2.6604185838541 | erot = 2.63308802762149 | epot = -18.5760442787973 | etot = -13.2825376673217 -870000 ekin = 2.68169704365066 | erot = 2.60613905014281 | epot = -18.5703737612197 | etot = -13.2825376674262 -871000 ekin = 2.71467538115452 | erot = 2.58511614862431 | epot = -18.5823291974616 | etot = -13.2825376676827 -872000 ekin = 2.75720487539373 | erot = 2.56766485202981 | epot = -18.6074073957583 | etot = -13.2825376683347 -873000 ekin = 2.80308619821104 | erot = 2.54585820173567 | epot = -18.6314820689143 | etot = -13.2825376689676 -874000 ekin = 2.84699852609265 | erot = 2.51460161594248 | epot = -18.6441378114824 | etot = -13.2825376694472 -875000 ekin = 2.88482415059394 | erot = 2.47158418780442 | epot = -18.638946008002 | etot = -13.2825376696036 -876000 ekin = 2.91408523337446 | erot = 2.4177177291072 | epot = -18.6143406317896 | etot = -13.2825376693079 -877000 ekin = 2.93423099086519 | erot = 2.35825815690521 | epot = -18.5750268164492 | etot = -13.2825376686788 -878000 ekin = 2.94753405629445 | erot = 2.3008664537491 | epot = -18.5309381778413 | etot = -13.2825376677977 -879000 ekin = 2.95817730737743 | erot = 2.25490663307461 | epot = -18.4956216073104 | etot = -13.2825376668584 -880000 ekin = 2.97089825197214 | erot = 2.22983196328469 | epot = -18.4832678815182 | etot = -13.2825376662614 -881000 ekin = 2.98893595230079 | erot = 2.2333347502388 | epot = -18.5048083683019 | etot = -13.2825376657623 -882000 ekin = 3.01519221964841 | erot = 2.27015029166098 | epot = -18.5678801769104 | etot = -13.282537665601 -883000 ekin = 3.05097747089527 | erot = 2.3416684229089 | epot = -18.6751835596161 | etot = -13.2825376658119 -884000 ekin = 3.09435682547256 | erot = 2.4464864171362 | epot = -18.8233809089785 | etot = -13.2825376663698 -885000 ekin = 3.14183207196681 | erot = 2.57965576027657 | epot = -19.0040254994135 | etot = -13.2825376671702 -886000 ekin = 3.1891482279053 | erot = 2.73331108132125 | epot = -19.2049969773462 | etot = -13.2825376681197 -887000 ekin = 3.23157512360801 | erot = 2.89766014759257 | epot = -19.4117729403243 | etot = -13.2825376691237 -888000 ekin = 3.2645655180999 | erot = 3.06177663304004 | epot = -19.6088798212365 | etot = -13.2825376700966 -889000 ekin = 3.28428902019744 | erot = 3.21442460414138 | epot = -19.7812512952993 | etot = -13.2825376709605 -890000 ekin = 3.28801223277735 | erot = 3.34493087267462 | epot = -19.9154807770927 | etot = -13.2825376716407 -891000 ekin = 3.27434561775047 | erot = 3.44412613410549 | epot = -20.0010094239219 | etot = -13.2825376720659 -892000 ekin = 3.24338163760246 | erot = 3.5053051706131 | epot = -20.031224480396 | etot = -13.2825376721805 -893000 ekin = 3.19671556304953 | erot = 3.52503469850342 | epot = -20.0042879335176 | etot = -13.2825376719647 -894000 ekin = 3.13731299174319 | erot = 3.50356986373413 | epot = -19.9234205269247 | etot = -13.2825376714474 -895000 ekin = 3.06920917356835 | erot = 3.44471943347162 | epot = -19.7964662777404 | etot = -13.2825376707004 -896000 ekin = 2.99708420339286 | erot = 3.35519757227584 | epot = -19.6348194454858 | etot = -13.2825376698171 -897000 ekin = 2.92580051783491 | erot = 3.24367712660513 | epot = -19.4520153133288 | etot = -13.2825376688887 -898000 ekin = 2.85975229197251 | erot = 3.12035510152301 | epot = -19.2626450614017 | etot = -13.2825376679062 -899000 ekin = 2.80277954779219 | erot = 2.9956146737193 | epot = -19.0809318887035 | etot = -13.282537667192 -900000 ekin = 2.75771035420834 | erot = 2.87733650112268 | epot = -18.9175845220148 | etot = -13.2825376666838 -901000 ekin = 2.72580329202024 | erot = 2.77189091314049 | epot = -18.7802318714387 | etot = -13.282537666278 -902000 ekin = 2.70770279131466 | erot = 2.6846486143113 | epot = -18.6748890716194 | etot = -13.2825376659935 -903000 ekin = 2.7034449405386 | erot = 2.61971222758158 | epot = -18.6056948339661 | etot = -13.282537665846 -904000 ekin = 2.712491847434 | erot = 2.57966599079039 | epot = -18.5746955043512 | etot = -13.2825376661268 -905000 ekin = 2.73259472265153 | erot = 2.56420422221706 | epot = -18.5793366115661 | etot = -13.2825376666975 -906000 ekin = 2.75874387987261 | erot = 2.57016719355954 | epot = -18.6114487407167 | etot = -13.2825376672845 -907000 ekin = 2.78650456169418 | erot = 2.5927904298105 | epot = -18.6618326594052 | etot = -13.2825376679006 -908000 ekin = 2.81181709569093 | erot = 2.62665482044298 | epot = -18.7210095845691 | etot = -13.2825376684352 -909000 ekin = 2.83143463245786 | erot = 2.66677850527972 | epot = -18.7807508065316 | etot = -13.282537668794 -910000 ekin = 2.84337824045527 | erot = 2.70952965400631 | epot = -18.8354455633909 | etot = -13.2825376689293 -911000 ekin = 2.84713706868452 | erot = 2.75311048607999 | epot = -18.882785223623 | etot = -13.2825376688585 -912000 ekin = 2.8435329518418 | erot = 2.79744224266951 | epot = -18.9235128631685 | etot = -13.2825376686572 -913000 ekin = 2.83428813315847 | erot = 2.84350922919611 | epot = -18.9603350307843 | etot = -13.2825376684297 -914000 ekin = 2.82145638450671 | erot = 2.89244132991502 | epot = -18.996435382689 | etot = -13.2825376682672 -915000 ekin = 2.80692071973142 | erot = 2.94469332949939 | epot = -19.0341517174505 | etot = -13.2825376682197 -916000 ekin = 2.79210576378607 | erot = 2.99958827393019 | epot = -19.074231706004 | etot = -13.2825376682877 -917000 ekin = 2.77794567111531 | erot = 3.05530679535158 | epot = -19.1157901348997 | etot = -13.2825376684328 -918000 ekin = 2.76505338702007 | erot = 3.1092386103798 | epot = -19.156829665997 | etot = -13.2825376685971 -919000 ekin = 2.75398705149648 | erot = 3.15852296699312 | epot = -19.1950476872148 | etot = -13.2825376687252 -920000 ekin = 2.74549945480772 | erot = 3.2005917707978 | epot = -19.2286288943852 | etot = -13.2825376687797 -921000 ekin = 2.74117522182622 | erot = 3.23390288539695 | epot = -19.2576157760415 | etot = -13.2825376688183 -922000 ekin = 2.74423942346447 | erot = 3.25833644681322 | epot = -19.2851135391865 | etot = -13.2825376689088 -923000 ekin = 2.75519506142942 | erot = 3.27241102946701 | epot = -19.310143759855 | etot = -13.2825376689586 -924000 ekin = 2.77394479542841 | erot = 3.27524658464355 | epot = -19.3317290490837 | etot = -13.2825376690117 -925000 ekin = 2.79984975928351 | erot = 3.26648541912167 | epot = -19.3488728475058 | etot = -13.2825376691007 -926000 ekin = 2.83154188644563 | erot = 3.24600163470182 | epot = -19.3600811903832 | etot = -13.2825376692358 -927000 ekin = 2.86690921925873 | erot = 3.21375665515305 | epot = -19.3632035438127 | etot = -13.2825376694009 -928000 ekin = 2.90327996744615 | erot = 3.1698282422568 | epot = -19.3556458792629 | etot = -13.28253766956 -929000 ekin = 2.9377528576698 | erot = 3.11459709938568 | epot = -19.3348876267244 | etot = -13.2825376696689 -930000 ekin = 2.96759841378242 | erot = 3.04898886675846 | epot = -19.2991249502308 | etot = -13.28253766969 -931000 ekin = 2.99062544127426 | erot = 2.97467062307573 | epot = -19.2478337339529 | etot = -13.2825376696029 -932000 ekin = 3.00543704340162 | erot = 2.89412065067177 | epot = -19.182095363482 | etot = -13.2825376694086 -933000 ekin = 3.01154336745542 | erot = 2.81054368702195 | epot = -19.1046247236028 | etot = -13.2825376691254 -934000 ekin = 3.009296793607 | erot = 2.72759799681476 | epot = -19.0194324597542 | etot = -13.2825376693324 -935000 ekin = 2.997461341975 | erot = 2.64625807489206 | epot = -18.9262570860507 | etot = -13.2825376691836 -936000 ekin = 2.97526415104969 | erot = 2.56749092792282 | epot = -18.8252927479684 | etot = -13.2825376689959 -937000 ekin = 2.94352512535629 | erot = 2.49335517907744 | epot = -18.7194179732148 | etot = -13.2825376687811 -938000 ekin = 2.90367826462751 | erot = 2.42575018416626 | epot = -18.611966117346 | etot = -13.2825376685523 -939000 ekin = 2.85762227335056 | erot = 2.36633148508481 | epot = -18.5064914267688 | etot = -13.2825376683334 -940000 ekin = 2.80750328436355 | erot = 2.31642989470971 | epot = -18.4064708472124 | etot = -13.2825376681392 -941000 ekin = 2.75550936317914 | erot = 2.27698712574035 | epot = -18.315034156903 | etot = -13.2825376679835 -942000 ekin = 2.70367879384707 | erot = 2.24846537191054 | epot = -18.2346818336424 | etot = -13.2825376678848 -943000 ekin = 2.65376367610072 | erot = 2.23082283410755 | epot = -18.1671241780433 | etot = -13.282537667835 -944000 ekin = 2.60720594193945 | erot = 2.22360475791407 | epot = -18.1133483676727 | etot = -13.2825376678192 -945000 ekin = 2.56519856456668 | erot = 2.2261014482812 | epot = -18.0738376806584 | etot = -13.2825376678105 -946000 ekin = 2.52882759917491 | erot = 2.23758213190646 | epot = -18.0489473988614 | etot = -13.28253766778 -947000 ekin = 2.49923315501652 | erot = 2.25754573395336 | epot = -18.0393165566767 | etot = -13.2825376677068 -948000 ekin = 2.47771007493837 | erot = 2.28590689258452 | epot = -18.0461546351121 | etot = -13.2825376675892 -949000 ekin = 2.46568539867815 | erot = 2.32304174075055 | epot = -18.0712648068822 | etot = -13.2825376674535 -950000 ekin = 2.46454516561394 | erot = 2.36959060784074 | epot = -18.1166734407876 | etot = -13.2825376673329 -951000 ekin = 2.47533995001422 | erot = 2.42623129983711 | epot = -18.1841089171244 | etot = -13.2825376672731 -952000 ekin = 2.49848236356054 | erot = 2.49338196898259 | epot = -18.2744019998551 | etot = -13.282537667312 -953000 ekin = 2.53348398196953 | erot = 2.57089243330607 | epot = -18.3869140827469 | etot = -13.2825376674713 -954000 ekin = 2.57882587535192 | erot = 2.65786416807577 | epot = -18.5192277111793 | etot = -13.2825376677516 -955000 ekin = 2.63199527601701 | erot = 2.75261052014717 | epot = -18.6671434642983 | etot = -13.2825376681341 -956000 ekin = 2.68967924818385 | erot = 2.85274255006523 | epot = -18.824959466837 | etot = -13.2825376685879 -957000 ekin = 2.74806771949303 | erot = 2.95533472442408 | epot = -18.9859401129945 | etot = -13.2825376690774 -958000 ekin = 2.80319866682411 | erot = 3.05711581061847 | epot = -19.1428521470133 | etot = -13.2825376695707 -959000 ekin = 2.85127801277871 | erot = 3.15464148733328 | epot = -19.2884571701549 | etot = -13.2825376700429 -960000 ekin = 2.88892608820776 | erot = 3.24442918289906 | epot = -19.4158929415847 | etot = -13.2825376704779 -961000 ekin = 2.91333465074054 | erot = 3.32306194469256 | epot = -19.5189342662969 | etot = -13.2825376708638 -962000 ekin = 2.92235141889966 | erot = 3.38728585340868 | epot = -19.5921749434977 | etot = -13.2825376711894 -963000 ekin = 2.91452965719862 | erot = 3.43412743872512 | epot = -19.631194767364 | etot = -13.2825376714403 -964000 ekin = 2.88918087864217 | erot = 3.46104482999107 | epot = -19.6327633802318 | etot = -13.2825376715986 -965000 ekin = 2.84645277182146 | erot = 3.46610960647262 | epot = -19.595100049937 | etot = -13.282537671643 -966000 ekin = 2.78809663572529 | erot = 3.4488697192109 | epot = -19.5195040264019 | etot = -13.2825376714657 -967000 ekin = 2.71967964182158 | erot = 3.41234902493455 | epot = -19.4145663381801 | etot = -13.2825376714239 -968000 ekin = 2.64387658032148 | erot = 3.35650459867512 | epot = -19.2829188502152 | etot = -13.2825376712186 -969000 ekin = 2.56365983597794 | erot = 3.2821307177253 | epot = -19.1283282245258 | etot = -13.2825376708226 -970000 ekin = 2.48311062140704 | erot = 3.19174642311281 | epot = -18.9573947147568 | etot = -13.282537670237 -971000 ekin = 2.4074396573122 | erot = 3.08950974404967 | epot = -18.7794870708623 | etot = -13.2825376695004 -972000 ekin = 2.34264905759316 | erot = 2.98071332519642 | epot = -18.6059000516343 | etot = -13.2825376688447 -973000 ekin = 2.29453827357382 | erot = 2.87084836317583 | epot = -18.4479243047352 | etot = -13.2825376679856 -974000 ekin = 2.26986492520578 | erot = 2.76590322626965 | epot = -18.3183058187343 | etot = -13.2825376672589 -975000 ekin = 2.27457634337442 | erot = 2.67096736253948 | epot = -18.2280813726668 | etot = -13.2825376667529 -976000 ekin = 2.31300758343906 | erot = 2.58967385345333 | epot = -18.1852191035243 | etot = -13.2825376666319 -977000 ekin = 2.38775385247815 | erot = 2.52429198069488 | epot = -18.1945835001196 | etot = -13.2825376669466 -978000 ekin = 2.4934313211563 | erot = 2.47478959068606 | epot = -18.2507585813607 | etot = -13.2825376695183 -979000 ekin = 2.63194261798452 | erot = 2.43666985309478 | epot = -18.3511501394633 | etot = -13.282537668384 -980000 ekin = 2.80143349399528 | erot = 2.41383709770836 | epot = -18.4978082614077 | etot = -13.282537669704 -981000 ekin = 2.97613228562078 | erot = 2.40353470194656 | epot = -18.6622046578964 | etot = -13.2825376703291 -982000 ekin = 3.15493786388404 | erot = 2.40097885128001 | epot = -18.8384543865222 | etot = -13.2825376713581 -983000 ekin = 3.32895075409049 | erot = 2.40358703806397 | epot = -19.0150754641548 | etot = -13.2825376720003 -984000 ekin = 3.48942626013249 | erot = 2.40902391908617 | epot = -19.18098785172 | etot = -13.2825376725014 -985000 ekin = 3.6306055406564 | erot = 2.41512886518398 | epot = -19.3282720786933 | etot = -13.2825376728529 -986000 ekin = 3.74861810546546 | erot = 2.42024356026412 | epot = -19.4513993386271 | etot = -13.2825376728975 -987000 ekin = 3.84212741101313 | erot = 2.42421773193476 | epot = -19.5488828158614 | etot = -13.2825376729136 -988000 ekin = 3.9111876503493 | erot = 2.42704295378038 | epot = -19.6207682769609 | etot = -13.2825376728312 -989000 ekin = 3.95686695904995 | erot = 2.42875435937409 | epot = -19.668158991096 | etot = -13.282537672672 -990000 ekin = 3.98122336716337 | erot = 2.42964012337661 | epot = -19.6934011629903 | etot = -13.2825376724504 -991000 ekin = 3.98715071441045 | erot = 2.43015135465657 | epot = -19.6998397412425 | etot = -13.2825376721755 -992000 ekin = 3.97827672378661 | erot = 2.43082965988458 | epot = -19.6916440567348 | etot = -13.2825376730636 -993000 ekin = 3.95551199280445 | erot = 2.42901824172678 | epot = -19.6670679074445 | etot = -13.2825376729133 -994000 ekin = 3.91976370645273 | erot = 2.42191618457207 | epot = -19.6242175637255 | etot = -13.2825376727007 -995000 ekin = 3.87458078790943 | erot = 2.40932775584377 | epot = -19.5664462161828 | etot = -13.2825376724296 -996000 ekin = 3.82377191569406 | erot = 2.39162261233252 | epot = -19.4979322001416 | etot = -13.282537672115 -997000 ekin = 3.77108738615857 | erot = 2.36980944948075 | epot = -19.4234345074243 | etot = -13.282537671785 -998000 ekin = 3.71986049076073 | erot = 2.34548651222161 | epot = -19.3478846744559 | etot = -13.2825376714735 -999000 ekin = 3.6726879444491 | erot = 2.32066228971374 | epot = -19.2758879053768 | etot = -13.282537671214 -1000000 ekin = 3.63122130703635 | erot = 2.29747929877849 | epot = -19.2112382768466 | etot = -13.2825376710318 - 1000000 0.16138761 -1.2609484 0.060246044 -0.97375106 -5.5311015e-05 -Loop time of 26.5666 on 4 procs for 1000000 steps with 16 atoms - -Performance: 32522.039 tau/day, 37641.249 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.3902 | 10.546 | 19.399 | 188.7 | 39.70 -Bond | 0.18541 | 0.40208 | 0.71402 | 31.3 | 1.51 -Neigh | 0.000147 | 0.000155 | 0.000163 | 0.0 | 0.00 -Comm | 2.6792 | 2.8295 | 2.994 | 7.2 | 10.65 -Output | 3.1e-05 | 3.425e-05 | 3.6e-05 | 0.0 | 0.00 -Modify | 0.37735 | 0.81798 | 1.4614 | 45.1 | 3.08 -Other | | 11.97 | | | 45.06 - -Nlocal: 4.0 ave 8.0 max 1.0 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Nghost: 10.5 ave 12.0 max 8.0 min -Histogram: 1 0 0 0 0 0 0 2 0 1 -Neighs: 31.75 ave 55.0 max 9.0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 - -Total # of neighbors = 127 -Ave neighs/atom = 7.9375 -Ave special neighs/atom = 3.75 -Neighbor list builds = 7 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:26 diff --git a/examples/USER/dielectric/data.confined b/examples/USER/dielectric/data.confined deleted file mode 100644 index 52afc2cf62..0000000000 --- a/examples/USER/dielectric/data.confined +++ /dev/null @@ -1,4019 +0,0 @@ -LAMMPS data file: two oppositely charged ions confined between two walls - -4002 atoms -3 atom types - -0.0000000000000000e+00 4.0000006274935302e+01 xlo xhi -0.0000000000000000e+00 4.3301276792816687e+01 ylo yhi -0.0000000000000000e+00 4.0000000000000000e+01 zlo zhi - -Masses - -1 1 -2 1 -3 1 - -Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature - -1 0 1 0 0 0 9.99798 0 0 1 0.866 8 6 1 0 -2 0 1 0 0.500101 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -3 0 1 0 1.0002 0 9.99798 0 0 1 0.866 8 6 1 0 -4 0 1 0 1.5003 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -5 0 1 0 2.0004 0 9.99798 0 0 1 0.866 8 6 1 0 -6 0 1 0 2.50051 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -7 0 1 0 3.00061 0 9.99798 0 0 1 0.866 8 6 1 0 -8 0 1 0 3.50071 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -9 0 1 0 4.00081 0 9.99798 0 0 1 0.866 8 6 1 0 -10 0 1 0 4.50091 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -11 0 1 0 5.00101 0 9.99798 0 0 1 0.866 8 6 1 0 -12 0 1 0 5.50111 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -13 0 1 0 6.00121 0 9.99798 0 0 1 0.866 8 6 1 0 -14 0 1 0 6.50132 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -15 0 1 0 7.00142 0 9.99798 0 0 1 0.866 8 6 1 0 -16 0 1 0 7.50152 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -17 0 1 0 8.00162 0 9.99798 0 0 1 0.866 8 6 1 0 -18 0 1 0 8.50172 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -19 0 1 0 9.00182 0 9.99798 0 0 1 0.866 8 6 1 0 -20 0 1 0 9.50192 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -21 0 1 0 10.002 0 9.99798 0 0 1 0.866 8 6 1 0 -22 0 1 0 10.5021 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -23 0 1 0 11.0022 0 9.99798 0 0 1 0.866 8 6 1 0 -24 0 1 0 11.5023 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -25 0 1 0 12.0024 0 9.99798 0 0 1 0.866 8 6 1 0 -26 0 1 0 12.5025 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -27 0 1 0 13.0026 0 9.99798 0 0 1 0.866 8 6 1 0 -28 0 1 0 13.5027 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -29 0 1 0 14.0028 0 9.99798 0 0 1 0.866 8 6 1 0 -30 0 1 0 14.5029 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -31 0 1 0 15.003 0 9.99798 0 0 1 0.866 8 6 1 0 -32 0 1 0 15.5031 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -33 0 1 0 16.0032 0 9.99798 0 0 1 0.866 8 6 1 0 -34 0 1 0 16.5033 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -35 0 1 0 17.0034 0 9.99798 0 0 1 0.866 8 6 1 0 -36 0 1 0 17.5035 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -37 0 1 0 18.0036 0 9.99798 0 0 1 0.866 8 6 1 0 -38 0 1 0 18.5037 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -39 0 1 0 19.0038 0 9.99798 0 0 1 0.866 8 6 1 0 -40 0 1 0 19.5039 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -41 0 1 0 20.004 0 9.99798 0 0 1 0.866 8 6 1 0 -42 0 1 0 20.5041 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -43 0 1 0 21.0042 0 9.99798 0 0 1 0.866 8 6 1 0 -44 0 1 0 21.5043 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -45 0 1 0 22.0045 0 9.99798 0 0 1 0.866 8 6 1 0 -46 0 1 0 22.5046 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -47 0 1 0 23.0047 0 9.99798 0 0 1 0.866 8 6 1 0 -48 0 1 0 23.5048 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -49 0 1 0 24.0049 0 9.99798 0 0 1 0.866 8 6 1 0 -50 0 1 0 24.505 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -51 0 1 0 25.0051 0 9.99798 0 0 1 0.866 8 6 1 0 -52 0 1 0 25.5052 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -53 0 1 0 26.0053 0 9.99798 0 0 1 0.866 8 6 1 0 -54 0 1 0 26.5054 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -55 0 1 0 27.0055 0 9.99798 0 0 1 0.866 8 6 1 0 -56 0 1 0 27.5056 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -57 0 1 0 28.0057 0 9.99798 0 0 1 0.866 8 6 1 0 -58 0 1 0 28.5058 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -59 0 1 0 29.0059 0 9.99798 0 0 1 0.866 8 6 1 0 -60 0 1 0 29.506 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -61 0 1 0 30.0061 0 9.99798 0 0 1 0.866 8 6 1 0 -62 0 1 0 30.5062 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -63 0 1 0 31.0063 0 9.99798 0 0 1 0.866 8 6 1 0 -64 0 1 0 31.5064 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -65 0 1 0 32.0065 0 9.99798 0 0 1 0.866 8 6 1 0 -66 0 1 0 32.5066 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -67 0 1 0 33.0067 0 9.99798 0 0 1 0.866 8 6 1 0 -68 0 1 0 33.5068 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -69 0 1 0 34.0069 0 9.99798 0 0 1 0.866 8 6 1 0 -70 0 1 0 34.507 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -71 0 1 0 35.0071 0 9.99798 0 0 1 0.866 8 6 1 0 -72 0 1 0 35.5072 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -73 0 1 0 36.0073 0 9.99798 0 0 1 0.866 8 6 1 0 -74 0 1 0 36.5074 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -75 0 1 0 37.0075 0 9.99798 0 0 1 0.866 8 6 1 0 -76 0 1 0 37.5076 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -77 0 1 0 38.0077 0 9.99798 0 0 1 0.866 8 6 1 0 -78 0 1 0 38.5078 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -79 0 1 0 39.0079 0 9.99798 0 0 1 0.866 8 6 1 0 -80 0 1 0 39.508 0.866201 9.99798 0 0 1 0.866 8 6 1 0 -81 0 1 0 0 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -82 0 1 0 0.500101 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -83 0 1 0 1.0002 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -84 0 1 0 1.5003 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -85 0 1 0 2.0004 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -86 0 1 0 2.50051 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -87 0 1 0 3.00061 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -88 0 1 0 3.50071 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -89 0 1 0 4.00081 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -90 0 1 0 4.50091 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -91 0 1 0 5.00101 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -92 0 1 0 5.50111 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -93 0 1 0 6.00121 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -94 0 1 0 6.50132 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -95 0 1 0 7.00142 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -96 0 1 0 7.50152 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -97 0 1 0 8.00162 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -98 0 1 0 8.50172 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -99 0 1 0 9.00182 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -100 0 1 0 9.50192 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -101 0 1 0 10.002 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -102 0 1 0 10.5021 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -103 0 1 0 11.0022 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -104 0 1 0 11.5023 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -105 0 1 0 12.0024 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -106 0 1 0 12.5025 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -107 0 1 0 13.0026 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -108 0 1 0 13.5027 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -109 0 1 0 14.0028 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -110 0 1 0 14.5029 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -111 0 1 0 15.003 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -112 0 1 0 15.5031 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -113 0 1 0 16.0032 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -114 0 1 0 16.5033 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -115 0 1 0 17.0034 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -116 0 1 0 17.5035 2.5986 9.99798 0 0 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27.0055 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -136 0 1 0 27.5056 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -137 0 1 0 28.0057 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -138 0 1 0 28.5058 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -139 0 1 0 29.0059 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -140 0 1 0 29.506 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -141 0 1 0 30.0061 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -142 0 1 0 30.5062 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -143 0 1 0 31.0063 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -144 0 1 0 31.5064 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -145 0 1 0 32.0065 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -146 0 1 0 32.5066 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -147 0 1 0 33.0067 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -148 0 1 0 33.5068 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -149 0 1 0 34.0069 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -150 0 1 0 34.507 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -151 0 1 0 35.0071 1.7324 9.99798 0 0 1 0.866 8 6 1 0 -152 0 1 0 35.5072 2.5986 9.99798 0 0 1 0.866 8 6 1 0 -153 0 1 0 36.0073 1.7324 9.99798 0 0 1 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0 0 1 0.866 8 6 1 0 -1178 0 1 0 28.5058 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1179 0 1 0 29.0059 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1180 0 1 0 29.506 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1181 0 1 0 30.0061 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1182 0 1 0 30.5062 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1183 0 1 0 31.0063 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1184 0 1 0 31.5064 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1185 0 1 0 32.0065 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1186 0 1 0 32.5066 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1187 0 1 0 33.0067 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1188 0 1 0 33.5068 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1189 0 1 0 34.0069 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1190 0 1 0 34.507 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1191 0 1 0 35.0071 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1192 0 1 0 35.5072 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1193 0 1 0 36.0073 24.2536 9.99798 0 0 1 0.866 8 6 1 0 -1194 0 1 0 36.5074 25.1198 9.99798 0 0 1 0.866 8 6 1 0 -1195 0 1 0 37.0075 24.2536 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0 0 1 0.866 8 6 1 0 -1214 0 1 0 6.50132 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1215 0 1 0 7.00142 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1216 0 1 0 7.50152 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1217 0 1 0 8.00162 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1218 0 1 0 8.50172 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1219 0 1 0 9.00182 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1220 0 1 0 9.50192 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1221 0 1 0 10.002 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1222 0 1 0 10.5021 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1223 0 1 0 11.0022 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1224 0 1 0 11.5023 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1225 0 1 0 12.0024 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1226 0 1 0 12.5025 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1227 0 1 0 13.0026 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1228 0 1 0 13.5027 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1229 0 1 0 14.0028 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1230 0 1 0 14.5029 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1231 0 1 0 15.003 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1232 0 1 0 15.5031 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1233 0 1 0 16.0032 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1234 0 1 0 16.5033 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1235 0 1 0 17.0034 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1236 0 1 0 17.5035 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1237 0 1 0 18.0036 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1238 0 1 0 18.5037 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1239 0 1 0 19.0038 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1240 0 1 0 19.5039 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1241 0 1 0 20.004 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1242 0 1 0 20.5041 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1243 0 1 0 21.0042 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1244 0 1 0 21.5043 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1245 0 1 0 22.0045 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1246 0 1 0 22.5046 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1247 0 1 0 23.0047 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1248 0 1 0 23.5048 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1249 0 1 0 24.0049 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1250 0 1 0 24.505 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1251 0 1 0 25.0051 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1252 0 1 0 25.5052 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1253 0 1 0 26.0053 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1254 0 1 0 26.5054 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1255 0 1 0 27.0055 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1256 0 1 0 27.5056 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1257 0 1 0 28.0057 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1258 0 1 0 28.5058 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1259 0 1 0 29.0059 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1260 0 1 0 29.506 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1261 0 1 0 30.0061 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1262 0 1 0 30.5062 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1263 0 1 0 31.0063 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1264 0 1 0 31.5064 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1265 0 1 0 32.0065 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1266 0 1 0 32.5066 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1267 0 1 0 33.0067 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1268 0 1 0 33.5068 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1269 0 1 0 34.0069 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1270 0 1 0 34.507 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1271 0 1 0 35.0071 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1272 0 1 0 35.5072 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1273 0 1 0 36.0073 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1274 0 1 0 36.5074 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1275 0 1 0 37.0075 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1276 0 1 0 37.5076 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1277 0 1 0 38.0077 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1278 0 1 0 38.5078 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1279 0 1 0 39.0079 25.986 9.99798 0 0 1 0.866 8 6 1 0 -1280 0 1 0 39.508 26.8522 9.99798 0 0 1 0.866 8 6 1 0 -1281 0 1 0 0 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1282 0 1 0 0.500101 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1283 0 1 0 1.0002 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1284 0 1 0 1.5003 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1285 0 1 0 2.0004 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1286 0 1 0 2.50051 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1287 0 1 0 3.00061 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1288 0 1 0 3.50071 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1289 0 1 0 4.00081 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1290 0 1 0 4.50091 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1291 0 1 0 5.00101 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1292 0 1 0 5.50111 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1293 0 1 0 6.00121 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1294 0 1 0 6.50132 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1295 0 1 0 7.00142 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1296 0 1 0 7.50152 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1297 0 1 0 8.00162 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1298 0 1 0 8.50172 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1299 0 1 0 9.00182 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1300 0 1 0 9.50192 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1301 0 1 0 10.002 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1302 0 1 0 10.5021 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1303 0 1 0 11.0022 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1304 0 1 0 11.5023 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1305 0 1 0 12.0024 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1306 0 1 0 12.5025 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1307 0 1 0 13.0026 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1308 0 1 0 13.5027 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1309 0 1 0 14.0028 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1310 0 1 0 14.5029 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1311 0 1 0 15.003 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1312 0 1 0 15.5031 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1313 0 1 0 16.0032 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1314 0 1 0 16.5033 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1315 0 1 0 17.0034 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1316 0 1 0 17.5035 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1317 0 1 0 18.0036 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1318 0 1 0 18.5037 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1319 0 1 0 19.0038 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1320 0 1 0 19.5039 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1321 0 1 0 20.004 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1322 0 1 0 20.5041 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1323 0 1 0 21.0042 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1324 0 1 0 21.5043 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1325 0 1 0 22.0045 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1326 0 1 0 22.5046 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1327 0 1 0 23.0047 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1328 0 1 0 23.5048 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1329 0 1 0 24.0049 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1330 0 1 0 24.505 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1331 0 1 0 25.0051 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1332 0 1 0 25.5052 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1333 0 1 0 26.0053 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1334 0 1 0 26.5054 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1335 0 1 0 27.0055 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1336 0 1 0 27.5056 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1337 0 1 0 28.0057 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1338 0 1 0 28.5058 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1339 0 1 0 29.0059 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1340 0 1 0 29.506 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1341 0 1 0 30.0061 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1342 0 1 0 30.5062 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1343 0 1 0 31.0063 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1344 0 1 0 31.5064 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1345 0 1 0 32.0065 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1346 0 1 0 32.5066 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1347 0 1 0 33.0067 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1348 0 1 0 33.5068 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1349 0 1 0 34.0069 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1350 0 1 0 34.507 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1351 0 1 0 35.0071 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1352 0 1 0 35.5072 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1353 0 1 0 36.0073 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1354 0 1 0 36.5074 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1355 0 1 0 37.0075 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1356 0 1 0 37.5076 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1357 0 1 0 38.0077 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1358 0 1 0 38.5078 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1359 0 1 0 39.0079 27.7184 9.99798 0 0 1 0.866 8 6 1 0 -1360 0 1 0 39.508 28.5846 9.99798 0 0 1 0.866 8 6 1 0 -1361 0 1 0 0 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1362 0 1 0 0.500101 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1363 0 1 0 1.0002 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1364 0 1 0 1.5003 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1365 0 1 0 2.0004 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1366 0 1 0 2.50051 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1367 0 1 0 3.00061 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1368 0 1 0 3.50071 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1369 0 1 0 4.00081 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1370 0 1 0 4.50091 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1371 0 1 0 5.00101 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1372 0 1 0 5.50111 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1373 0 1 0 6.00121 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1374 0 1 0 6.50132 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1375 0 1 0 7.00142 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1376 0 1 0 7.50152 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1377 0 1 0 8.00162 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1378 0 1 0 8.50172 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1379 0 1 0 9.00182 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1380 0 1 0 9.50192 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1381 0 1 0 10.002 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1382 0 1 0 10.5021 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1383 0 1 0 11.0022 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1384 0 1 0 11.5023 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1385 0 1 0 12.0024 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1386 0 1 0 12.5025 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1387 0 1 0 13.0026 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1388 0 1 0 13.5027 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1389 0 1 0 14.0028 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1390 0 1 0 14.5029 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1391 0 1 0 15.003 29.4508 9.99798 0 0 1 0.866 8 6 1 0 -1392 0 1 0 15.5031 30.317 9.99798 0 0 1 0.866 8 6 1 0 -1393 0 1 0 16.0032 29.4508 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-3933 0 1 0 6.00121 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3934 0 1 0 6.50132 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3935 0 1 0 7.00142 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3936 0 1 0 7.50152 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3937 0 1 0 8.00162 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3938 0 1 0 8.50172 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3939 0 1 0 9.00182 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3940 0 1 0 9.50192 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3941 0 1 0 10.002 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3942 0 1 0 10.5021 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3943 0 1 0 11.0022 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3944 0 1 0 11.5023 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3945 0 1 0 12.0024 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3946 0 1 0 12.5025 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3947 0 1 0 13.0026 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3948 0 1 0 13.5027 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3949 0 1 0 14.0028 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3950 0 1 0 14.5029 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3951 0 1 0 15.003 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3952 0 1 0 15.5031 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3953 0 1 0 16.0032 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3954 0 1 0 16.5033 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3955 0 1 0 17.0034 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3956 0 1 0 17.5035 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3957 0 1 0 18.0036 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3958 0 1 0 18.5037 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3959 0 1 0 19.0038 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3960 0 1 0 19.5039 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3961 0 1 0 20.004 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3962 0 1 0 20.5041 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3963 0 1 0 21.0042 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3964 0 1 0 21.5043 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3965 0 1 0 22.0045 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3966 0 1 0 22.5046 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3967 0 1 0 23.0047 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3968 0 1 0 23.5048 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3969 0 1 0 24.0049 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3970 0 1 0 24.505 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3971 0 1 0 25.0051 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3972 0 1 0 25.5052 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3973 0 1 0 26.0053 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3974 0 1 0 26.5054 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3975 0 1 0 27.0055 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3976 0 1 0 27.5056 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3977 0 1 0 28.0057 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3978 0 1 0 28.5058 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3979 0 1 0 29.0059 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3980 0 1 0 29.506 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3981 0 1 0 30.0061 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3982 0 1 0 30.5062 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3983 0 1 0 31.0063 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3984 0 1 0 31.5064 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3985 0 1 0 32.0065 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3986 0 1 0 32.5066 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3987 0 1 0 33.0067 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3988 0 1 0 33.5068 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3989 0 1 0 34.0069 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3990 0 1 0 34.507 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3991 0 1 0 35.0071 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3992 0 1 0 35.5072 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3993 0 1 0 36.0073 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3994 0 1 0 36.5074 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3995 0 1 0 37.0075 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3996 0 1 0 37.5076 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3997 0 1 0 38.0077 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -3998 0 1 0 38.5078 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -3999 0 1 0 39.0079 41.5776 30.002 0 0 -1 0.866 8 6 1 0 -4000 0 1 0 39.508 42.4438 30.002 0 0 -1 0.866 8 6 1 0 -4001 0 2 1 15 20 15 0 0 1 0.866 8 6 10 0 -4002 0 3 -1 25 20 25 0 0 1 0.866 8 6 10 0 diff --git a/examples/USER/misc/cauchy/NiAlH_jea.eam.alloy b/examples/USER/misc/cauchy/NiAlH_jea.eam.alloy deleted file mode 120000 index 9d763bffe4..0000000000 --- a/examples/USER/misc/cauchy/NiAlH_jea.eam.alloy +++ /dev/null @@ -1 +0,0 @@ -../../../../potentials/NiAlH_jea.eam.alloy \ No newline at end of file diff --git a/examples/USER/misc/electron_stopping/Si.sw b/examples/USER/misc/electron_stopping/Si.sw deleted file mode 120000 index e575921334..0000000000 --- a/examples/USER/misc/electron_stopping/Si.sw +++ /dev/null @@ -1 +0,0 @@ -../../../../potentials/Si.sw \ No newline at end of file diff --git a/examples/USER/misc/orient_eco/Ni_u3.eam b/examples/USER/misc/orient_eco/Ni_u3.eam deleted file mode 120000 index 0abe5fb328..0000000000 --- a/examples/USER/misc/orient_eco/Ni_u3.eam +++ /dev/null @@ -1 +0,0 @@ -../../../../potentials/Ni_u3.eam \ No newline at end of file diff --git a/examples/USER/sph/README b/examples/USER/sph/README deleted file mode 100644 index b5a1acc614..0000000000 --- a/examples/USER/sph/README +++ /dev/null @@ -1 +0,0 @@ -see the USER-SPH user's guide for a detailed explanation of these examples. diff --git a/examples/meam/in.meamc b/examples/meam/in.meam similarity index 96% rename from examples/meam/in.meamc rename to examples/meam/in.meam index f6815cd7d4..b4463be365 100644 --- a/examples/meam/in.meamc +++ b/examples/meam/in.meam @@ -7,7 +7,7 @@ atom_style atomic read_data data.meam -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C neighbor 0.3 bin diff --git a/examples/meam/in.meamc.shear b/examples/meam/in.meamc.shear deleted file mode 100644 index e4584d9744..0000000000 --- a/examples/meam/in.meamc.shear +++ /dev/null @@ -1,79 +0,0 @@ -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box - -lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 & - origin 0.5 0 0 -create_atoms 1 box - -pair_style meam/c -pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 0.9 INF INF -region upper block INF INF 6.1 INF INF INF -group lower region lower -group upper region upper -group boundary union lower upper -group mobile subtract all boundary - -set group lower type 2 -set group upper type 3 - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -compute new3d mobile temp -compute new2d mobile temp/partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -#dump 1 all atom 500 dump.meam.shear - -#dump 2 all image 100 image.*.jpg type type & -# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 2 pad 4 - -#dump 3 all movie 100 movie.mpg type type & -# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 3 pad 4 - -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 diff --git a/examples/meam/log.27Nov18.meamc.g++.1 b/examples/meam/log.27Nov18.meam.g++.1 similarity index 97% rename from examples/meam/log.27Nov18.meamc.g++.1 rename to examples/meam/log.27Nov18.meam.g++.1 index 2fcd24077b..40f999c00a 100644 --- a/examples/meam/log.27Nov18.meamc.g++.1 +++ b/examples/meam/log.27Nov18.meam.g++.1 @@ -13,7 +13,7 @@ read_data data.meam reading atoms ... 128 atoms -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 @@ -41,12 +41,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.g++.4 b/examples/meam/log.27Nov18.meam.g++.4 similarity index 97% rename from examples/meam/log.27Nov18.meamc.g++.4 rename to examples/meam/log.27Nov18.meam.g++.4 index b97f18b25c..8a8070b28a 100644 --- a/examples/meam/log.27Nov18.meamc.g++.4 +++ b/examples/meam/log.27Nov18.meam.g++.4 @@ -13,7 +13,7 @@ read_data data.meam reading atoms ... 128 atoms -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 @@ -41,12 +41,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.shear.g++.1 b/examples/meam/log.27Nov18.meam.shear.g++.1 similarity index 98% rename from examples/meam/log.27Nov18.meamc.shear.g++.1 rename to examples/meam/log.27Nov18.meam.shear.g++.1 index 4aff7d2399..e183bc698a 100644 --- a/examples/meam/log.27Nov18.meamc.shear.g++.1 +++ b/examples/meam/log.27Nov18.meam.shear.g++.1 @@ -19,7 +19,7 @@ create_atoms 1 box Created 1912 atoms Time spent = 0.000667334 secs -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -75,12 +75,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 27 17 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.shear.g++.4 b/examples/meam/log.27Nov18.meam.shear.g++.4 similarity index 98% rename from examples/meam/log.27Nov18.meamc.shear.g++.4 rename to examples/meam/log.27Nov18.meam.shear.g++.4 index 702e13f554..63f6adf8a1 100644 --- a/examples/meam/log.27Nov18.meamc.shear.g++.4 +++ b/examples/meam/log.27Nov18.meam.shear.g++.4 @@ -19,7 +19,7 @@ create_atoms 1 box Created 1912 atoms Time spent = 0.000405788 secs -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -75,12 +75,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 27 17 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt index 6e29676530..59c2802b45 100644 --- a/examples/plugins/CMakeLists.txt +++ b/examples/plugins/CMakeLists.txt @@ -31,6 +31,11 @@ endif() set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) +# Need -restrict with Intel compilers +if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") +endif() + # bail out on windows if(CMAKE_SYSTEM_NAME STREQUAL Windows) message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows") @@ -44,7 +49,7 @@ include(LAMMPSInterfaceCXX) # building the plugins add_library(morse2plugin MODULE morse2plugin.cpp pair_morse2.cpp pair_morse2_omp.cpp) -target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/USER-OMP") +target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/OPENMP") target_link_libraries(morse2plugin PRIVATE lammps) add_library(nve2plugin MODULE nve2plugin.cpp fix_nve2.cpp) diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index f4d8b41086..c342742740 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -1,5 +1,5 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/OPENMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp DSOEXT=.so diff --git a/examples/plugins/Makefile.macos b/examples/plugins/Makefile.macos index a7c20ff90f..c890314cd4 100644 --- a/examples/plugins/Makefile.macos +++ b/examples/plugins/Makefile.macos @@ -1,5 +1,5 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/OPENMP LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup DSOEXT=.dylib diff --git a/examples/plugins/Makefile.serial b/examples/plugins/Makefile.serial index ecc7631a05..fff7d99a2e 100644 --- a/examples/plugins/Makefile.serial +++ b/examples/plugins/Makefile.serial @@ -1,5 +1,5 @@ CXX=g++ -CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/OPENMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp DSOEXT=.so diff --git a/examples/qeq/buck.inc b/examples/qeq/buck.inc new file mode 100644 index 0000000000..af3fe3dfb6 --- /dev/null +++ b/examples/qeq/buck.inc @@ -0,0 +1,22 @@ + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve diff --git a/examples/qeq/in.qeq.buck b/examples/qeq/in.qeq.buck index 2258a9e2ae..4b74b44186 100644 --- a/examples/qeq/in.qeq.buck +++ b/examples/qeq/in.qeq.buck @@ -1,41 +1,68 @@ # This example demonstrates the use of various fix qeq variants with -# that defines and uses charges, in this case pair_style buck/coul/long +# a pair style using charges, in this case pair_style buck/coul/long units metal atom_style charge read_data data.aC -replicate 2 2 2 +#replicate 2 2 2 pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 pair_coeff 1 2 18003 .2052124 133.5381 pair_coeff 1 1 0 .1 0 -kspace_style ewald 1e-6 -neighbor 1.0 bin -neigh_modify delay 0 every 1 check yes +fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2 -group type1 type 1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 -variable qtot equal count(type1)*c_q1+count(type2)*c_q2 - -thermo_style custom step pe c_q1 c_q2 v_qtot -thermo 10 - -timestep 0.0001 +include buck.inc velocity all create 300.0 1281937 -fix 1 all nve +run 0 post no -#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2 -fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 +write_restart qeq.restart -run 100 +clear + +print "Using fix qeq/point" +read_restart qeq.restart +fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +run 100 + +clear + +print "Using fix qeq/shielded" +read_restart qeq.restart +fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +run 100 + + +clear + +print "Using fix qeq/slater" +read_restart qeq.restart +fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +run 100 + +clear + +print "Using fix qeq/dynamic" +read_restart qeq.restart +fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2 +include buck.inc + +run 100 + +clear + +print "Using fix qeq/fire" +read_restart qeq.restart +fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2 +include buck.inc + +run 100 diff --git a/examples/qeq/log.20Apr21.qeq.buck.g++.1 b/examples/qeq/log.20Apr21.qeq.buck.g++.1 new file mode 100644 index 0000000000..d5b41867b1 --- /dev/null +++ b/examples/qeq/log.20Apr21.qeq.buck.g++.1 @@ -0,0 +1,650 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# This example demonstrates the use of various fix qeq variants with +# a pair style using charges, in this case pair_style buck/coul/long + +units metal +atom_style charge + +read_data data.aC +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + read_data CPU = 0.009 seconds +#replicate 2 2 2 + +pair_style buck/coul/long 12.0 +pair_coeff 2 2 1388.77 .3623188 175.0 +pair_coeff 1 2 18003 .2052124 133.5381 +pair_coeff 1 1 0 .1 0 + +fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2 + +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +velocity all create 300.0 1281937 +run 0 post no +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.30705229 + grid = 48 48 54 + stencil order = 5 + estimated absolute RMS force accuracy = 1.8909403e-05 + estimated relative force accuracy = 1.3131854e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 184525 124416 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Fix qeq CG convergence failed (4.357840257025601e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410) +WARNING: Fix qeq CG convergence failed (5.274094378414531e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410) +Per MPI rank memory allocation (min/avg/max) = 38.75 | 38.75 | 38.75 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10 +Loop time of 1.66893e-06 on 1 procs for 0 steps with 1200 atoms + + +write_restart qeq.restart +System init for write_restart ... +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 42772 21870 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/point" +Using fix qeq/point +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 1 by 1 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 42772 21870 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/point, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3 + 10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8 + 20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8 + 30 -3568.22095 0.86767937 -0.43383969 0.000000000001 8 + 40 -3633.24956 0.87335551 -0.43667775 0.000000000000 8 + 50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8 + 60 -3784.36769 0.88402303 -0.44201151 -0.000000000000 8 + 70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8 + 80 -3965.29722 0.89431515 -0.44715757 -0.000000000001 8 + 90 -4048.36764 0.89698588 -0.44849294 0.000000000000 8 + 100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8 +Loop time of 11.5935 on 1 procs for 100 steps with 1200 atoms + +Performance: 0.075 ns/day, 322.041 hours/ns, 8.626 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8257 | 2.8257 | 2.8257 | 0.0 | 24.37 +Kspace | 1.2136 | 1.2136 | 1.2136 | 0.0 | 10.47 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.015541 | 0.015541 | 0.015541 | 0.0 | 0.13 +Output | 0.0014489 | 0.0014489 | 0.0014489 | 0.0 | 0.01 +Modify | 7.5351 | 7.5351 | 7.5351 | 0.0 | 64.99 +Other | | 0.00206 | | | 0.02 + +Nlocal: 1200.00 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8100.00 ave 8100 max 8100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 367600.0 ave 367600 max 367600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 735200.0 ave 735200 max 735200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 735200 +Ave neighs/atom = 612.66667 +Neighbor list builds = 0 +Dangerous builds = 0 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/shielded" +Using fix qeq/shielded +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 1 by 1 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 42772 21870 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3 + 10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2 + 20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2 + 30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1 + 40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1 + 50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2 + 60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2 + 70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2 + 80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1 + 90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2 + 100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2 +Loop time of 7.93936 on 1 procs for 100 steps with 1200 atoms + +Performance: 0.109 ns/day, 220.538 hours/ns, 12.595 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8061 | 2.8061 | 2.8061 | 0.0 | 35.34 +Kspace | 1.2176 | 1.2176 | 1.2176 | 0.0 | 15.34 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.015528 | 0.015528 | 0.015528 | 0.0 | 0.20 +Output | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 0.02 +Modify | 3.8966 | 3.8966 | 3.8966 | 0.0 | 49.08 +Other | | 0.002076 | | | 0.03 + +Nlocal: 1200.00 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8100.00 ave 8100 max 8100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 367600.0 ave 367600 max 367600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 735200.0 ave 735200 max 735200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 735200 +Ave neighs/atom = 612.66667 +Neighbor list builds = 0 +Dangerous builds = 0 + + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/slater" +Using fix qeq/slater +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 1 by 1 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 42772 21870 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3 + 10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2 + 20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2 + 30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1 + 40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1 + 50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2 + 60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2 + 70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2 + 80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1 + 90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2 + 100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2 +Loop time of 7.9652 on 1 procs for 100 steps with 1200 atoms + +Performance: 0.108 ns/day, 221.256 hours/ns, 12.555 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.809 | 2.809 | 2.809 | 0.0 | 35.27 +Kspace | 1.2214 | 1.2214 | 1.2214 | 0.0 | 15.33 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.015635 | 0.015635 | 0.015635 | 0.0 | 0.20 +Output | 0.0014393 | 0.0014393 | 0.0014393 | 0.0 | 0.02 +Modify | 3.9157 | 3.9157 | 3.9157 | 0.0 | 49.16 +Other | | 0.002091 | | | 0.03 + +Nlocal: 1200.00 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8100.00 ave 8100 max 8100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 367600.0 ave 367600 max 367600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 735200.0 ave 735200 max 735200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 735200 +Ave neighs/atom = 612.66667 +Neighbor list builds = 0 +Dangerous builds = 0 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/dynamic" +Using fix qeq/dynamic +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 1 by 1 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 42772 21870 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix qeq/dynamic, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -3432.38094 0.85231286 -0.42615643 0.000000000001 43 + 10 -3452.05217 0.85475894 -0.42737947 -0.000000000001 17 + 20 -3497.8643 0.85999180 -0.42999590 -0.000000000007 22 + 30 -3568.53169 0.86772479 -0.43386239 -0.000000000006 22 + 40 -3633.43753 0.87338291 -0.43669146 -0.000000000006 22 + 50 -3700.27953 0.87807632 -0.43903816 -0.000000000005 22 + 60 -3784.4004 0.88402822 -0.44201411 0.000000000002 17 + 70 -3877.73706 0.89012201 -0.44506100 0.000000000002 22 + 80 -3965.36111 0.89432486 -0.44716243 0.000000000008 17 + 90 -4048.57901 0.89701688 -0.44850844 -0.000000000004 22 + 100 -4118.62736 0.89718691 -0.44859346 -0.000000000026 17 +Loop time of 18.5333 on 1 procs for 100 steps with 1200 atoms + +Performance: 0.047 ns/day, 514.815 hours/ns, 5.396 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8268 | 2.8268 | 2.8268 | 0.0 | 15.25 +Kspace | 1.2138 | 1.2138 | 1.2138 | 0.0 | 6.55 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.015407 | 0.015407 | 0.015407 | 0.0 | 0.08 +Output | 0.0014303 | 0.0014303 | 0.0014303 | 0.0 | 0.01 +Modify | 14.474 | 14.474 | 14.474 | 0.0 | 78.10 +Other | | 0.001973 | | | 0.01 + +Nlocal: 1200.00 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8100.00 ave 8100 max 8100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 367600.0 ave 367600 max 367600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 367600 +Ave neighs/atom = 306.33333 +Neighbor list builds = 0 +Dangerous builds = 0 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/fire" +Using fix qeq/fire +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 1 by 1 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 42772 21870 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix qeq/fire, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -3432.06113 0.85226679 -0.42613339 0.000000000004 37 + 10 -3452.0494 0.85475813 -0.42737906 0.000000000001 10 + 20 -3497.83503 0.85998739 -0.42999370 0.000000000003 13 + 30 -3568.47507 0.86771599 -0.43385799 0.000000000004 13 + 40 -3633.35368 0.87337029 -0.43668514 0.000000000004 13 + 50 -3700.15601 0.87805847 -0.43902924 0.000000000005 13 + 60 -3784.32042 0.88401635 -0.44200818 0.000000000000 11 + 70 -3877.59818 0.89010162 -0.44505081 0.000000000000 13 + 80 -3965.28426 0.89431356 -0.44715678 0.000000000000 11 + 90 -4048.3338 0.89698069 -0.44849034 0.000000000001 13 + 100 -4118.63638 0.89718818 -0.44859409 0.000000000003 12 +Loop time of 13.0492 on 1 procs for 100 steps with 1200 atoms + +Performance: 0.066 ns/day, 362.479 hours/ns, 7.663 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7996 | 2.7996 | 2.7996 | 0.0 | 21.45 +Kspace | 1.2141 | 1.2141 | 1.2141 | 0.0 | 9.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.015527 | 0.015527 | 0.015527 | 0.0 | 0.12 +Output | 0.0014405 | 0.0014405 | 0.0014405 | 0.0 | 0.01 +Modify | 9.0166 | 9.0166 | 9.0166 | 0.0 | 69.10 +Other | | 0.001981 | | | 0.02 + +Nlocal: 1200.00 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8100.00 ave 8100 max 8100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 367600.0 ave 367600 max 367600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 367600 +Ave neighs/atom = 306.33333 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:00 diff --git a/examples/qeq/log.20Apr21.qeq.buck.g++.4 b/examples/qeq/log.20Apr21.qeq.buck.g++.4 new file mode 100644 index 0000000000..cafa94bae9 --- /dev/null +++ b/examples/qeq/log.20Apr21.qeq.buck.g++.4 @@ -0,0 +1,650 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# This example demonstrates the use of various fix qeq variants with +# a pair style using charges, in this case pair_style buck/coul/long + +units metal +atom_style charge + +read_data data.aC +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1200 atoms + read_data CPU = 0.009 seconds +#replicate 2 2 2 + +pair_style buck/coul/long 12.0 +pair_coeff 2 2 1388.77 .3623188 175.0 +pair_coeff 1 2 18003 .2052124 133.5381 +pair_coeff 1 1 0 .1 0 + +fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2 + +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +velocity all create 300.0 1281937 +run 0 post no +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.30705229 + grid = 48 48 54 + stencil order = 5 + estimated absolute RMS force accuracy = 1.8909403e-05 + estimated relative force accuracy = 1.3131854e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 57970 32256 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Fix qeq CG convergence failed (4.299911728887494e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410) +WARNING: Fix qeq CG convergence failed (5.273380778822746e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410) +Per MPI rank memory allocation (min/avg/max) = 14.97 | 15.02 | 15.08 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10 +Loop time of 3.33786e-06 on 4 procs for 0 steps with 1200 atoms + + +write_restart qeq.restart +System init for write_restart ... +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 14960 5832 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/point" +Using fix qeq/point +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 2 by 2 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 14960 5832 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/point, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3 + 10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8 + 20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8 + 30 -3568.22095 0.86767937 -0.43383969 0.000000000000 8 + 40 -3633.24956 0.87335551 -0.43667775 -0.000000000000 8 + 50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8 + 60 -3784.36769 0.88402303 -0.44201151 0.000000000000 8 + 70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8 + 80 -3965.29722 0.89431515 -0.44715757 0.000000000000 8 + 90 -4048.36764 0.89698588 -0.44849294 -0.000000000000 8 + 100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8 +Loop time of 3.30911 on 4 procs for 100 steps with 1200 atoms + +Performance: 0.261 ns/day, 91.920 hours/ns, 30.220 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.67613 | 0.68904 | 0.71562 | 1.9 | 20.82 +Kspace | 0.36056 | 0.3881 | 0.39892 | 2.6 | 11.73 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013339 | 0.017982 | 0.019974 | 2.0 | 0.54 +Output | 0.0006721 | 0.00099713 | 0.0019572 | 0.0 | 0.03 +Modify | 2.2109 | 2.211 | 2.211 | 0.0 | 66.81 +Other | | 0.002041 | | | 0.06 + +Nlocal: 300.000 ave 300 max 300 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4875.00 ave 4880 max 4870 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 91900.0 ave 91900 max 91900 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 183800.0 ave 183800 max 183800 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 735200 +Ave neighs/atom = 612.66667 +Neighbor list builds = 0 +Dangerous builds = 0 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/shielded" +Using fix qeq/shielded +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 2 by 2 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.006 seconds +fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 14960 5832 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3 + 10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2 + 20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2 + 30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1 + 40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1 + 50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2 + 60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2 + 70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2 + 80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1 + 90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2 + 100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2 +Loop time of 2.25559 on 4 procs for 100 steps with 1200 atoms + +Performance: 0.383 ns/day, 62.655 hours/ns, 44.334 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.67442 | 0.69181 | 0.70907 | 2.0 | 30.67 +Kspace | 0.39381 | 0.41151 | 0.43023 | 2.6 | 18.24 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012851 | 0.01426 | 0.015146 | 0.7 | 0.63 +Output | 0.00066686 | 0.00098681 | 0.0019395 | 0.0 | 0.04 +Modify | 1.1349 | 1.135 | 1.135 | 0.0 | 50.32 +Other | | 0.002035 | | | 0.09 + +Nlocal: 300.000 ave 300 max 300 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4875.00 ave 4880 max 4870 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 91900.0 ave 91900 max 91900 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 183800.0 ave 183800 max 183800 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 735200 +Ave neighs/atom = 612.66667 +Neighbor list builds = 0 +Dangerous builds = 0 + + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/slater" +Using fix qeq/slater +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 2 by 2 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.012 seconds +fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 14960 5832 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3 + 10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2 + 20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2 + 30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1 + 40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1 + 50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2 + 60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2 + 70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2 + 80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1 + 90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2 + 100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2 +Loop time of 2.39249 on 4 procs for 100 steps with 1200 atoms + +Performance: 0.361 ns/day, 66.458 hours/ns, 41.797 timesteps/s +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.6751 | 0.70301 | 0.71919 | 2.1 | 29.38 +Kspace | 0.45569 | 0.47315 | 0.49885 | 2.6 | 19.78 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012967 | 0.018681 | 0.020909 | 2.4 | 0.78 +Output | 0.00066733 | 0.00099397 | 0.0019579 | 0.0 | 0.04 +Modify | 1.1945 | 1.1946 | 1.1947 | 0.0 | 49.93 +Other | | 0.002046 | | | 0.09 + +Nlocal: 300.000 ave 300 max 300 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4875.00 ave 4880 max 4870 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 91900.0 ave 91900 max 91900 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 183800.0 ave 183800 max 183800 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 735200 +Ave neighs/atom = 612.66667 +Neighbor list builds = 0 +Dangerous builds = 0 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/dynamic" +Using fix qeq/dynamic +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 2 by 2 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.002 seconds +fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 14960 5832 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix qeq/dynamic, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -3432.38094 0.85231286 -0.42615643 -0.000000000001 43 + 10 -3452.05217 0.85475894 -0.42737947 -0.000000000003 17 + 20 -3497.8643 0.85999180 -0.42999590 0.000000000000 22 + 30 -3568.53169 0.86772479 -0.43386239 -0.000000000000 22 + 40 -3633.43753 0.87338291 -0.43669146 0.000000000006 22 + 50 -3700.27953 0.87807632 -0.43903816 0.000000000003 22 + 60 -3784.4004 0.88402822 -0.44201411 0.000000000009 17 + 70 -3877.73706 0.89012201 -0.44506100 0.000000000010 22 + 80 -3965.36111 0.89432486 -0.44716243 0.000000000011 17 + 90 -4048.57901 0.89701688 -0.44850844 0.000000000012 22 + 100 -4118.62736 0.89718691 -0.44859346 0.000000000013 17 +Loop time of 5.27704 on 4 procs for 100 steps with 1200 atoms + +Performance: 0.164 ns/day, 146.584 hours/ns, 18.950 timesteps/s +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.68437 | 0.69096 | 0.69826 | 0.7 | 13.09 +Kspace | 0.38484 | 0.38941 | 0.39524 | 0.7 | 7.38 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012609 | 0.01529 | 0.016842 | 1.3 | 0.29 +Output | 0.00067735 | 0.0010006 | 0.0019588 | 1.7 | 0.02 +Modify | 4.1783 | 4.1783 | 4.1784 | 0.0 | 79.18 +Other | | 0.002027 | | | 0.04 + +Nlocal: 300.000 ave 300 max 300 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4875.00 ave 4880 max 4870 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 91900.0 ave 93081 max 90719 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 367600 +Ave neighs/atom = 306.33333 +Neighbor list builds = 0 +Dangerous builds = 0 + +clear + using 1 OpenMP thread(s) per MPI task + +print "Using fix qeq/fire" +Using fix qeq/fire +read_restart qeq.restart +Reading restart file ... + restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021 + restoring atom style charge from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256) + 1 by 2 by 2 MPI processor grid + restoring pair style buck/coul/long from restart + 1200 atoms + read_restart CPU = 0.001 seconds +fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2 +include buck.inc + +kspace_style pppm 1e-6 + +neighbor 1.0 bin +neigh_modify delay 0 every 1 check yes + +group type1 type 1 +400 atoms in group type1 +compute charge1 type1 property/atom q +compute q1 type1 reduce ave c_charge1 +group type2 type 2 +800 atoms in group type2 +compute charge2 type2 property/atom q +compute q2 type2 reduce ave c_charge2 +variable qtot equal count(type1)*c_q1+count(type2)*c_q2 +variable nqeq equal f_2 + +thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq +thermo 10 +thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f" + +timestep 0.0001 + +fix 1 all nve + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.27644401 + grid = 27 27 30 + stencil order = 5 + estimated absolute RMS force accuracy = 1.4502702e-05 + estimated relative force accuracy = 1.0071569e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 14960 5832 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13 + ghost atom cutoff = 13 + binsize = 6.5, bins = 4 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix qeq/fire, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes +Step PotEng c_q1 c_q2 v_qtot v_nqeq + 0 -3432.05316 0.85226679 -0.42613339 0.000000000001 37 + 10 -3452.04937 0.85475813 -0.42737906 0.000000000001 10 + 20 -3497.83659 0.85998739 -0.42999370 0.000000000002 13 + 30 -3568.47793 0.86771599 -0.43385799 0.000000000002 13 + 40 -3633.35326 0.87337029 -0.43668514 0.000000000002 13 + 50 -3700.16079 0.87805847 -0.43902924 0.000000000000 13 + 60 -3784.31906 0.88401635 -0.44200818 -0.000000000001 11 + 70 -3877.60163 0.89010162 -0.44505081 -0.000000000000 13 + 80 -3965.28179 0.89431356 -0.44715678 0.000000000001 11 + 90 -4048.33861 0.89698069 -0.44849034 0.000000000001 13 + 100 -4118.63861 0.89718818 -0.44859409 0.000000000002 12 +Loop time of 3.88026 on 4 procs for 100 steps with 1200 atoms + +Performance: 0.223 ns/day, 107.785 hours/ns, 25.771 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.68424 | 0.69912 | 0.73572 | 2.5 | 18.02 +Kspace | 0.38093 | 0.41715 | 0.43168 | 3.2 | 10.75 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012711 | 0.013318 | 0.014003 | 0.4 | 0.34 +Output | 0.00066566 | 0.00098735 | 0.0019317 | 0.0 | 0.03 +Modify | 2.7477 | 2.7477 | 2.7477 | 0.0 | 70.81 +Other | | 0.002004 | | | 0.05 + +Nlocal: 300.000 ave 300 max 300 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4875.00 ave 4880 max 4870 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 91900.0 ave 93081 max 90719 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 367600 +Ave neighs/atom = 306.33333 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:17 diff --git a/examples/qeq/log.27Nov18.qeq.buck.g++.1 b/examples/qeq/log.27Nov18.qeq.buck.g++.1 deleted file mode 100644 index 4d5225ccc3..0000000000 --- a/examples/qeq/log.27Nov18.qeq.buck.g++.1 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# This example demonstrates the use of various fix qeq variants with -# that defines and uses charges, in this case pair_style buck/coul/long - -units metal -atom_style charge - -read_data data.aC - orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms -replicate 2 2 2 - orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) - 1 by 1 by 1 MPI processor grid - 9600 atoms - Time spent = 0.00114894 secs - -pair_style buck/coul/long 12.0 -pair_coeff 2 2 1388.77 .3623188 175.0 -pair_coeff 1 2 18003 .2052124 133.5381 -pair_coeff 1 1 0 .1 0 -kspace_style ewald 1e-6 - -neighbor 1.0 bin -neigh_modify delay 0 every 1 check yes - -group type1 type 1 -3200 atoms in group type1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -6400 atoms in group type2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 -variable qtot equal count(type1)*c_q1+count(type2)*c_q2 - -thermo_style custom step pe c_q1 c_q2 v_qtot spcpu -thermo 10 - -timestep 0.0001 - -velocity all create 300.0 1281937 -fix 1 all nve - -#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2 -fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 - -run 100 -Ewald initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - G vector (1/distance) = 0.305064 - estimated absolute RMS force accuracy = 2.07629e-05 - estimated relative force accuracy = 1.44191e-06 - KSpace vectors: actual max1d max3d = 13556 20 34460 - kxmax kymax kzmax = 18 18 20 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13 - ghost atom cutoff = 13 - binsize = 6.5, bins = 8 8 9 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair buck/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix qeq/fire, perpetual, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes -Step PotEng c_q1 c_q2 v_qtot S/CPU - 0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0 - 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877 - 20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179 - 30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643 - 40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341 - 50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127 - 60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762 - 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546 - 80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079 - 90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419 - 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001 -Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms - -Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48 -Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01 -Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00 -Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11 -Other | | 0.007197 | | | 0.00 - -Nlocal: 9600 ave 9600 max 9600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 22125 ave 22125 max 22125 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.9408e+06 ave 2.9408e+06 max 2.9408e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2940800 -Ave neighs/atom = 306.333 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:03:01 diff --git a/examples/qeq/log.27Nov18.qeq.buck.g++.4 b/examples/qeq/log.27Nov18.qeq.buck.g++.4 deleted file mode 100644 index 947c3caeaf..0000000000 --- a/examples/qeq/log.27Nov18.qeq.buck.g++.4 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# This example demonstrates the use of various fix qeq variants with -# that defines and uses charges, in this case pair_style buck/coul/long - -units metal -atom_style charge - -read_data data.aC - orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 1200 atoms -replicate 2 2 2 - orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) - 1 by 2 by 2 MPI processor grid - 9600 atoms - Time spent = 0.000675201 secs - -pair_style buck/coul/long 12.0 -pair_coeff 2 2 1388.77 .3623188 175.0 -pair_coeff 1 2 18003 .2052124 133.5381 -pair_coeff 1 1 0 .1 0 -kspace_style ewald 1e-6 - -neighbor 1.0 bin -neigh_modify delay 0 every 1 check yes - -group type1 type 1 -3200 atoms in group type1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -6400 atoms in group type2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 -variable qtot equal count(type1)*c_q1+count(type2)*c_q2 - -thermo_style custom step pe c_q1 c_q2 v_qtot spcpu -thermo 10 - -timestep 0.0001 - -velocity all create 300.0 1281937 -fix 1 all nve - -#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2 -#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2 -fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 - -run 100 -Ewald initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - G vector (1/distance) = 0.305064 - estimated absolute RMS force accuracy = 2.07629e-05 - estimated relative force accuracy = 1.44191e-06 - KSpace vectors: actual max1d max3d = 13556 20 34460 - kxmax kymax kzmax = 18 18 20 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13 - ghost atom cutoff = 13 - binsize = 6.5, bins = 8 8 9 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair buck/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix qeq/fire, perpetual, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes -Step PotEng c_q1 c_q2 v_qtot S/CPU - 0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0 - 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312 - 20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316 - 30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335 - 40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139 - 50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263 - 60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722 - 70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406 - 80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813 - 90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145 - 100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486 -Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms - -Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s -97.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22 -Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75 -Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00 -Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03 -Other | | 0.01409 | | | 0.03 - -Nlocal: 2400 ave 2400 max 2400 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 11550 ave 11550 max 11550 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 735200 ave 740758 max 729642 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 2940800 -Ave neighs/atom = 306.333 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:49 diff --git a/examples/qeq/param.qeq1 b/examples/qeq/param.qeq1 index 9c8514b021..b49705194c 100644 --- a/examples/qeq/param.qeq1 +++ b/examples/qeq/param.qeq1 @@ -1,3 +1,4 @@ +# UNITS: real 1 5.3200 14.8732 1.0206 0.0 0.0 2 5.8678 14.0000 0.9000 0.0 0.0 3 8.5000 17.9978 1.0503 0.0 0.0 diff --git a/examples/qeq/param.qeq2 b/examples/qeq/param.qeq2 index 7e2fdeb8f2..1d77b7d3a6 100644 --- a/examples/qeq/param.qeq2 +++ b/examples/qeq/param.qeq2 @@ -1,2 +1,3 @@ +# UNITS: metal 1 0.00000 7.25028 0.01 0.772871 0.000000 2 11.26882 15.37920 0.01 0.243072 0.000000 diff --git a/examples/reax/in.reaxc.rdx b/examples/reax/in.reaxc.rdx deleted file mode 100644 index 4874ea2dbb..0000000000 --- a/examples/reax/in.reaxc.rdx +++ /dev/null @@ -1,52 +0,0 @@ -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press & - v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & - v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 diff --git a/examples/reax/in.reaxc.rdx-shielded b/examples/reax/in.reaxc.rdx-shielded deleted file mode 100644 index 3354b92eab..0000000000 --- a/examples/reax/in.reaxc.rdx-shielded +++ /dev/null @@ -1,52 +0,0 @@ -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press & - v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & - v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 diff --git a/examples/reax/in.reaxc.tatb b/examples/reax/in.reaxc.tatb deleted file mode 100644 index a166613b85..0000000000 --- a/examples/reax/in.reaxc.tatb +++ /dev/null @@ -1,55 +0,0 @@ -# ReaxFF potential for TATB system -# this run is equivalent to reax/in.reax.tatb, - -units real - -atom_style charge -read_data data.tatb - -pair_style reax/c control.reax_c.tatb -pair_coeff * * ffield.reax C H O N - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c -fix 4 all reax/c/bonds 5 bonds.reaxc - -thermo 5 -thermo_style custom step temp epair etotal press & - v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & - v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reaxc.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 3 all reax/c/species 1 5 5 species.tatb - -run 25 diff --git a/examples/reax/in.reaxc.tatb-shielded b/examples/reax/in.reaxc.tatb-shielded deleted file mode 100644 index 2ff4d34f7a..0000000000 --- a/examples/reax/in.reaxc.tatb-shielded +++ /dev/null @@ -1,55 +0,0 @@ -# ReaxFF potential for TATB system -# this run is equivalent to reax/in.reax.tatb, - -units real - -atom_style charge -read_data data.tatb - -pair_style reax/c control.reax_c.tatb -pair_coeff * * ffield.reax C H O N - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve -fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c -fix 4 all reax/c/bonds 5 bonds.reaxc - -thermo 5 -thermo_style custom step temp epair etotal press & - v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & - v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reaxc.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 3 all reax/c/species 1 5 5 species.tatb - -run 25 diff --git a/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1 b/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1 deleted file mode 100644 index 9e991a5d6e..0000000000 --- a/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1 +++ /dev/null @@ -1,116 +0,0 @@ -LAMMPS (4 Jan 2019) -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 21 atoms - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 3 3 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/shielded, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 15.54 | 15.54 | 15.54 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79939 0 168.88404 - 10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934 - 20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512 - 30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749 - 40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085 - 50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995 - 60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414 - 70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648 - 80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464 - 90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914 - 100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951 -Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms - -Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.59308 | 0.59308 | 0.59308 | 0.0 | 90.21 -Neigh | 0.020665 | 0.020665 | 0.020665 | 0.0 | 3.14 -Comm | 0.0015757 | 0.0015757 | 0.0015757 | 0.0 | 0.24 -Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.06 -Modify | 0.04156 | 0.04156 | 0.04156 | 0.0 | 6.32 -Other | | 0.000154 | | | 0.02 - -Nlocal: 21 ave 21 max 21 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 546 ave 546 max 546 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1096 ave 1096 max 1096 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 1306 ave 1306 max 1306 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1306 -Ave neighs/atom = 62.1905 -Neighbor list builds = 10 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4 b/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4 deleted file mode 100644 index 1492865c17..0000000000 --- a/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4 +++ /dev/null @@ -1,116 +0,0 @@ -LAMMPS (4 Jan 2019) -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 21 atoms - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 3 3 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/shielded, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.62 | 12.08 | 13.84 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452 - 10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934 - 20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929 - 30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706 - 40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076 - 50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999 - 60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412 - 70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967 - 80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525 - 90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126 - 100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944 -Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms - -Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s -93.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.53395 | 0.5352 | 0.53805 | 0.2 | 84.37 -Neigh | 0.0088253 | 0.012023 | 0.016203 | 2.4 | 1.90 -Comm | 0.0051677 | 0.0081 | 0.0093861 | 1.9 | 1.28 -Output | 0.00049353 | 0.00054371 | 0.00058222 | 0.0 | 0.09 -Modify | 0.074155 | 0.078299 | 0.081472 | 0.9 | 12.34 -Other | | 0.0001715 | | | 0.03 - -Nlocal: 5.25 ave 15 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 355.5 ave 432 max 282 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 298.75 ave 822 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -FullNghs: 326.5 ave 927 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 1306 -Ave neighs/atom = 62.1905 -Neighbor list builds = 10 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1 b/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1 deleted file mode 100644 index 86dc1c323a..0000000000 --- a/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1 +++ /dev/null @@ -1,114 +0,0 @@ -LAMMPS (4 Jan 2019) -# ReaxFF potential for TATB system -# this run is equivalent to reax/in.reax.tatb, - -units real - -atom_style charge -read_data data.tatb - triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 384 atoms - -pair_style reax/c control.reax_c.tatb -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve -fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c -fix 4 all reax/c/bonds 5 bonds.reaxc - -thermo 5 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reaxc.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 3 all reax/c/species 1 5 5 species.tatb - -run 25 -Neighbor list info ... - update every 5 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 5 4 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/shielded, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 169.6 | 169.6 | 169.6 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 - 5 0.61603942 -44761.698 -44760.994 8934.628 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 - 10 2.3525549 -44763.227 -44760.541 12288.614 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9684 0 6381.7061 - 15 4.9013311 -44766.36 -44760.764 17716.982 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2449 0 6370.4111 - 20 7.8294673 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5142 0 6355.2654 - 25 10.697904 -44772.904 -44760.691 34232.821 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3541 0 6336.8349 -Loop time of 7.80985 on 1 procs for 25 steps with 384 atoms - -Performance: 0.017 ns/day, 1388.418 hours/ns, 3.201 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.003 | 5.003 | 5.003 | 0.0 | 64.06 -Neigh | 1.1164 | 1.1164 | 1.1164 | 0.0 | 14.29 -Comm | 0.0065806 | 0.0065806 | 0.0065806 | 0.0 | 0.08 -Output | 0.00029969 | 0.00029969 | 0.00029969 | 0.0 | 0.00 -Modify | 1.6831 | 1.6831 | 1.6831 | 0.0 | 21.55 -Other | | 0.0004976 | | | 0.01 - -Nlocal: 384 ave 384 max 384 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7559 ave 7559 max 7559 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 286828 ave 286828 max 286828 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 336304 ave 336304 max 336304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 336304 -Ave neighs/atom = 875.792 -Neighbor list builds = 5 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:08 diff --git a/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4 b/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4 deleted file mode 100644 index 7dc9867f5a..0000000000 --- a/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4 +++ /dev/null @@ -1,114 +0,0 @@ -LAMMPS (4 Jan 2019) -# ReaxFF potential for TATB system -# this run is equivalent to reax/in.reax.tatb, - -units real - -atom_style charge -read_data data.tatb - triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 384 atoms - -pair_style reax/c control.reax_c.tatb -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve -fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c -fix 4 all reax/c/bonds 5 bonds.reaxc - -thermo 5 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reaxc.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 3 all reax/c/species 1 5 5 species.tatb - -run 25 -Neighbor list info ... - update every 5 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 5 4 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/shielded, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 - 5 0.61603968 -44761.698 -44760.994 8934.6336 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 - 10 2.3525543 -44763.227 -44760.541 12288.588 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9756 0 6381.7133 - 15 4.9013233 -44766.36 -44760.764 17716.934 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2627 0 6370.4289 - 20 7.8294615 -44769.686 -44760.747 25205.586 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4958 0 6355.2471 - 25 10.697919 -44772.904 -44760.691 34232.898 -61069.308 490.25887 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3285 0 6336.8093 -Loop time of 4.34178 on 4 procs for 25 steps with 384 atoms - -Performance: 0.031 ns/day, 771.872 hours/ns, 5.758 timesteps/s -96.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.1756 | 3.1763 | 3.1771 | 0.0 | 73.16 -Neigh | 0.58917 | 0.59661 | 0.6035 | 0.9 | 13.74 -Comm | 0.0088837 | 0.010178 | 0.011116 | 0.8 | 0.23 -Output | 0.00036407 | 0.0019013 | 0.003552 | 2.7 | 0.04 -Modify | 0.54882 | 0.55637 | 0.56413 | 0.8 | 12.81 -Other | | 0.0004123 | | | 0.01 - -Nlocal: 96 ave 96 max 96 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 5118 ave 5118 max 5118 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 79754 ave 79754 max 79754 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 84076 ave 84076 max 84076 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 336304 -Ave neighs/atom = 875.792 -Neighbor list builds = 5 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:04 diff --git a/examples/reax/log.8March18.reaxc.rdx.g++.1 b/examples/reax/log.8March18.reaxc.rdx.g++.1 deleted file mode 100644 index 4ae10e3f52..0000000000 --- a/examples/reax/log.8March18.reaxc.rdx.g++.1 +++ /dev/null @@ -1,115 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 21 atoms - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 3 3 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/reax, perpetual, copy from (1) - attributes: half, newton off, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 15.28 | 15.28 | 15.28 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79937 0 168.88402 - 10 1288.6114 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43322 0 107.75935 - 20 538.95849 -1942.7037 -1910.5731 -10725.658 -2803.7395 7.9078331 0.077926702 0 81.610043 0.22951937 -57.557104 0 30.331203 -10.178049 878.99015 -159.69092 0 89.315159 - 30 463.09542 -1933.5765 -1905.9685 -33255.507 -2749.8591 -8.0154628 0.027628767 0 81.627403 0.11972403 -50.262284 0 20.82032 -9.6327022 851.88722 -149.495 0 79.205731 - 40 885.49449 -1958.9126 -1906.1228 -4814.7123 -2795.644 9.1506221 0.1374749 0 70.948046 0.24360579 -57.8627 0 19.076515 -11.141211 873.73892 -159.9939 0 92.434059 - 50 861.1646 -1954.4599 -1903.1206 -1896.7387 -2784.8446 3.8269113 0.1579328 0 79.851775 3.3492107 -78.066127 0 32.628975 -7.9565255 872.81826 -190.98565 0 114.75994 - 60 1167.785 -1971.8432 -1902.2243 -3482.6975 -2705.8638 -17.121582 0.22749067 0 44.507705 7.856069 -74.788959 0 16.256519 -4.6046602 835.8308 -188.33691 0 114.19414 - 70 1439.9947 -1989.3024 -1903.4554 23845.067 -2890.7896 31.958874 0.26671735 0 85.758608 3.1803486 -71.002907 0 24.357106 -10.311315 905.86799 -175.38482 0 106.79659 - 80 502.40024 -1930.7547 -1900.8035 -20356.557 -2703.8096 -18.663105 0.11286226 0 99.803799 2.0329394 -76.171387 0 19.236609 -6.2786041 826.47358 -166.03157 0 92.539694 - 90 749.09267 -1946.9834 -1902.3254 17798.812 -2863.7586 42.068927 0.24338042 0 96.18195 0.96181754 -69.955528 0 24.61541 -11.58277 903.68895 -190.13838 0 120.69139 - 100 1109.7046 -1968.5875 -1902.4311 -4490.6736 -2755.8953 -7.1235173 0.21757663 0 61.806405 7.0825933 -75.645487 0 20.114745 -6.2371664 863.56285 -198.56939 0 122.09923 -Loop time of 0.395195 on 1 procs for 100 steps with 21 atoms - -Performance: 21.863 ns/day, 1.098 hours/ns, 253.039 timesteps/s -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.3722 | 0.3722 | 0.3722 | 0.0 | 94.18 -Neigh | 0.0098455 | 0.0098455 | 0.0098455 | 0.0 | 2.49 -Comm | 0.00047445 | 0.00047445 | 0.00047445 | 0.0 | 0.12 -Output | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.09 -Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 3.08 -Other | | 0.0001521 | | | 0.04 - -Nlocal: 21 ave 21 max 21 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 546 ave 546 max 546 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1096 ave 1096 max 1096 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1096 -Ave neighs/atom = 52.1905 -Neighbor list builds = 10 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reaxc.rdx.g++.4 b/examples/reax/log.8March18.reaxc.rdx.g++.4 deleted file mode 100644 index 6ea4835402..0000000000 --- a/examples/reax/log.8March18.reaxc.rdx.g++.4 +++ /dev/null @@ -1,115 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 21 atoms - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 3 3 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/reax, perpetual, copy from (1) - attributes: half, newton off, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 10.37 | 11.76 | 13.34 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79988 0 168.88453 - 10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252286 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934 - 20 538.95818 -1942.7037 -1910.5731 -10725.623 -2803.7394 7.9078307 0.077926702 0 81.61005 0.22951942 -57.557107 0 30.331206 -10.178049 878.9901 -159.68951 0 89.313749 - 30 463.09514 -1933.5765 -1905.9685 -33255.525 -2749.859 -8.0154737 0.027628797 0 81.627408 0.11972402 -50.262283 0 20.82031 -9.6327021 851.88715 -149.49499 0 79.205724 - 40 885.49412 -1958.9125 -1906.1227 -4814.6606 -2795.6439 9.150622 0.13747487 0 70.948029 0.24360517 -57.862679 0 19.076509 -11.141214 873.7389 -159.99392 0 92.434078 - 50 861.16393 -1954.46 -1903.1207 -1896.7323 -2784.8449 3.8270197 0.1579328 0 79.851743 3.3492115 -78.066132 0 32.628992 -7.9565379 872.81841 -190.98568 0 114.75996 - 60 1167.7846 -1971.8432 -1902.2243 -3482.8111 -2705.8633 -17.121657 0.2274907 0 44.507681 7.8560366 -74.788989 0 16.256493 -4.6046537 835.8305 -188.33687 0 114.1941 - 70 1439.9942 -1989.3023 -1903.4554 23845.444 -2890.7894 31.958784 0.26671721 0 85.758586 3.1803655 -71.002918 0 24.357158 -10.311304 905.86792 -175.38481 0 106.79657 - 80 502.3975 -1930.7546 -1900.8036 -20356.439 -2703.8105 -18.662812 0.11286123 0 99.80391 2.0329293 -76.171334 0 19.236803 -6.2786439 826.47397 -166.03141 0 92.539551 - 90 749.09048 -1946.9837 -1902.3258 17798.718 -2863.7582 42.068719 0.24338057 0 96.181773 0.96183581 -69.955529 0 24.615414 -11.582758 903.68862 -190.1384 0 120.69139 - 100 1109.6999 -1968.5875 -1902.4314 -4490.3728 -2755.8964 -7.1231468 0.21757685 0 61.806149 7.0826648 -75.645428 0 20.115002 -6.2371958 863.56343 -198.56957 0 122.09942 -Loop time of 0.329552 on 4 procs for 100 steps with 21 atoms - -Performance: 26.217 ns/day, 0.915 hours/ns, 303.443 timesteps/s -96.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.26372 | 0.26499 | 0.26754 | 0.3 | 80.41 -Neigh | 0.0045478 | 0.0062494 | 0.0076699 | 1.5 | 1.90 -Comm | 0.0041637 | 0.0064691 | 0.0080271 | 1.8 | 1.96 -Output | 0.00054169 | 0.00056636 | 0.00060368 | 0.0 | 0.17 -Modify | 0.049433 | 0.051134 | 0.05311 | 0.6 | 15.52 -Other | | 0.000141 | | | 0.04 - -Nlocal: 5.25 ave 15 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 355.5 ave 432 max 282 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 298.75 ave 822 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 1195 -Ave neighs/atom = 56.9048 -Neighbor list builds = 10 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reaxc.tatb.g++.1 b/examples/reax/log.8March18.reaxc.tatb.g++.1 deleted file mode 100644 index ac5537bba4..0000000000 --- a/examples/reax/log.8March18.reaxc.tatb.g++.1 +++ /dev/null @@ -1,113 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for TATB system -# this run is equivalent to reax/in.reax.tatb, - -units real - -atom_style charge -read_data data.tatb - triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 384 atoms - -pair_style reax/c control.reax_c.tatb -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c -fix 4 all reax/c/bonds 5 bonds.reaxc - -thermo 5 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reaxc.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 3 all reax/c/species 1 5 5 species.tatb - -run 25 -Neighbor list info ... - update every 5 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 5 4 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/reax, perpetual, copy from (1) - attributes: half, newton off, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 176.7 | 176.7 | 176.7 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275 - 5 0.61603968 -44761.698 -44760.994 8934.6347 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 - 10 2.3525551 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9768 0 6381.7146 - 15 4.9013279 -44766.36 -44760.764 17717.01 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2375 0 6370.4038 - 20 7.8294645 -44769.686 -44760.747 25205.624 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4889 0 6355.2402 - 25 10.697904 -44772.904 -44760.691 34232.965 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3125 0 6336.7934 -Loop time of 4.72562 on 1 procs for 25 steps with 384 atoms - -Performance: 0.029 ns/day, 840.110 hours/ns, 5.290 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.775 | 3.775 | 3.775 | 0.0 | 79.88 -Neigh | 0.47047 | 0.47047 | 0.47047 | 0.0 | 9.96 -Comm | 0.0025151 | 0.0025151 | 0.0025151 | 0.0 | 0.05 -Output | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.01 -Modify | 0.47676 | 0.47676 | 0.47676 | 0.0 | 10.09 -Other | | 0.0005293 | | | 0.01 - -Nlocal: 384 ave 384 max 384 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7559 ave 7559 max 7559 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 286828 ave 286828 max 286828 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 286828 -Ave neighs/atom = 746.948 -Neighbor list builds = 5 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:05 diff --git a/examples/reax/log.8March18.reaxc.tatb.g++.4 b/examples/reax/log.8March18.reaxc.tatb.g++.4 deleted file mode 100644 index 12558be68a..0000000000 --- a/examples/reax/log.8March18.reaxc.tatb.g++.4 +++ /dev/null @@ -1,113 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for TATB system -# this run is equivalent to reax/in.reax.tatb, - -units real - -atom_style charge -read_data data.tatb - triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 384 atoms - -pair_style reax/c control.reax_c.tatb -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c -fix 4 all reax/c/bonds 5 bonds.reaxc - -thermo 5 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reaxc.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 3 all reax/c/species 1 5 5 species.tatb - -run 25 -Neighbor list info ... - update every 5 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 5 4 3 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/reax, perpetual, copy from (1) - attributes: half, newton off, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 118 | 118 | 118 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 - 5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 - 10 2.3525544 -44763.227 -44760.541 12288.587 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9764 0 6381.7141 - 15 4.9013311 -44766.36 -44760.764 17716.955 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2558 0 6370.4221 - 20 7.8294715 -44769.686 -44760.747 25205.613 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4906 0 6355.2419 - 25 10.697924 -44772.904 -44760.691 34232.794 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91376 -1582.3261 253.82253 -653.53183 18791.975 -8684.3641 0 6336.8449 -Loop time of 2.84068 on 4 procs for 25 steps with 384 atoms - -Performance: 0.048 ns/day, 505.009 hours/ns, 8.801 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.3253 | 2.328 | 2.3305 | 0.2 | 81.95 -Neigh | 0.2589 | 0.26458 | 0.26897 | 0.7 | 9.31 -Comm | 0.0094428 | 0.012062 | 0.014872 | 2.3 | 0.42 -Output | 0.00043392 | 0.0042209 | 0.0054941 | 3.4 | 0.15 -Modify | 0.22563 | 0.23134 | 0.23579 | 0.8 | 8.14 -Other | | 0.0005122 | | | 0.02 - -Nlocal: 96 ave 96 max 96 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 5118 ave 5118 max 5118 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 79754 ave 79754 max 79754 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 319016 -Ave neighs/atom = 830.771 -Neighbor list builds = 5 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/reax/AB/README b/examples/reaxff/AB/README similarity index 100% rename from examples/reax/AB/README rename to examples/reaxff/AB/README diff --git a/examples/reax/AB/data.AB b/examples/reaxff/AB/data.AB similarity index 100% rename from examples/reax/AB/data.AB rename to examples/reaxff/AB/data.AB diff --git a/examples/reax/AB/ffield.reax.AB b/examples/reaxff/AB/ffield.reax.AB similarity index 100% rename from examples/reax/AB/ffield.reax.AB rename to examples/reaxff/AB/ffield.reax.AB diff --git a/examples/reax/AB/in.AB b/examples/reaxff/AB/in.AB similarity index 100% rename from examples/reax/AB/in.AB rename to examples/reaxff/AB/in.AB diff --git a/examples/reax/AB/lmp_control b/examples/reaxff/AB/lmp_control similarity index 100% rename from examples/reax/AB/lmp_control rename to examples/reaxff/AB/lmp_control diff --git a/examples/reax/AB/log.8Mar18.AB.g++.1 b/examples/reaxff/AB/log.8Mar18.AB.g++.1 similarity index 100% rename from examples/reax/AB/log.8Mar18.AB.g++.1 rename to examples/reaxff/AB/log.8Mar18.AB.g++.1 diff --git a/examples/reax/AB/log.8Mar18.AB.g++.4 b/examples/reaxff/AB/log.8Mar18.AB.g++.4 similarity index 100% rename from examples/reax/AB/log.8Mar18.AB.g++.4 rename to examples/reaxff/AB/log.8Mar18.AB.g++.4 diff --git a/examples/reax/AB/param.qeq b/examples/reaxff/AB/param.qeq similarity index 100% rename from examples/reax/AB/param.qeq rename to examples/reaxff/AB/param.qeq diff --git a/examples/reax/AuO/README b/examples/reaxff/AuO/README similarity index 100% rename from examples/reax/AuO/README rename to examples/reaxff/AuO/README diff --git a/examples/reax/AuO/data.AuO b/examples/reaxff/AuO/data.AuO similarity index 100% rename from examples/reax/AuO/data.AuO rename to examples/reaxff/AuO/data.AuO diff --git a/examples/reax/AuO/ffield.reax.AuO b/examples/reaxff/AuO/ffield.reax.AuO similarity index 100% rename from examples/reax/AuO/ffield.reax.AuO rename to examples/reaxff/AuO/ffield.reax.AuO diff --git a/examples/reax/AuO/in.AuO b/examples/reaxff/AuO/in.AuO similarity index 100% rename from examples/reax/AuO/in.AuO rename to examples/reaxff/AuO/in.AuO diff --git a/examples/reax/AuO/lmp_control b/examples/reaxff/AuO/lmp_control similarity index 100% rename from examples/reax/AuO/lmp_control rename to examples/reaxff/AuO/lmp_control diff --git a/examples/reax/AuO/log.8Mar18.AuO.g++.1 b/examples/reaxff/AuO/log.8Mar18.AuO.g++.1 similarity index 100% rename from examples/reax/AuO/log.8Mar18.AuO.g++.1 rename to examples/reaxff/AuO/log.8Mar18.AuO.g++.1 diff --git a/examples/reax/AuO/log.8Mar18.AuO.g++.4 b/examples/reaxff/AuO/log.8Mar18.AuO.g++.4 similarity index 100% rename from examples/reax/AuO/log.8Mar18.AuO.g++.4 rename to examples/reaxff/AuO/log.8Mar18.AuO.g++.4 diff --git a/examples/reax/AuO/param.qeq b/examples/reaxff/AuO/param.qeq similarity index 100% rename from examples/reax/AuO/param.qeq rename to examples/reaxff/AuO/param.qeq diff --git a/examples/reax/CHO/README b/examples/reaxff/CHO/README similarity index 100% rename from examples/reax/CHO/README rename to examples/reaxff/CHO/README diff --git a/examples/reax/CHO/data.CHO b/examples/reaxff/CHO/data.CHO similarity index 100% rename from examples/reax/CHO/data.CHO rename to examples/reaxff/CHO/data.CHO diff --git a/examples/reax/CHO/ffield.reax.cho b/examples/reaxff/CHO/ffield.reax.cho similarity index 100% rename from examples/reax/CHO/ffield.reax.cho rename to examples/reaxff/CHO/ffield.reax.cho diff --git a/examples/reax/CHO/in.CHO b/examples/reaxff/CHO/in.CHO similarity index 100% rename from examples/reax/CHO/in.CHO rename to examples/reaxff/CHO/in.CHO diff --git a/examples/reax/CHO/lmp_control b/examples/reaxff/CHO/lmp_control similarity index 100% rename from examples/reax/CHO/lmp_control rename to examples/reaxff/CHO/lmp_control diff --git a/examples/reax/CHO/log.8Mar18.CHO.g++.1 b/examples/reaxff/CHO/log.8Mar18.CHO.g++.1 similarity index 100% rename from examples/reax/CHO/log.8Mar18.CHO.g++.1 rename to examples/reaxff/CHO/log.8Mar18.CHO.g++.1 diff --git a/examples/reax/CHO/log.8Mar18.CHO.g++.4 b/examples/reaxff/CHO/log.8Mar18.CHO.g++.4 similarity index 100% rename from examples/reax/CHO/log.8Mar18.CHO.g++.4 rename to examples/reaxff/CHO/log.8Mar18.CHO.g++.4 diff --git a/examples/reax/CHO/param.qeq b/examples/reaxff/CHO/param.qeq similarity index 100% rename from examples/reax/CHO/param.qeq rename to examples/reaxff/CHO/param.qeq diff --git a/examples/reax/FC/README b/examples/reaxff/FC/README similarity index 100% rename from examples/reax/FC/README rename to examples/reaxff/FC/README diff --git a/examples/reax/FC/data.FC b/examples/reaxff/FC/data.FC similarity index 100% rename from examples/reax/FC/data.FC rename to examples/reaxff/FC/data.FC diff --git a/examples/reax/FC/ffield.reax.FC b/examples/reaxff/FC/ffield.reax.FC similarity index 100% rename from examples/reax/FC/ffield.reax.FC rename to examples/reaxff/FC/ffield.reax.FC diff --git a/examples/reax/FC/in.FC b/examples/reaxff/FC/in.FC similarity index 100% rename from examples/reax/FC/in.FC rename to examples/reaxff/FC/in.FC diff --git a/examples/reax/FC/log.8Mar18.FC.g++.1 b/examples/reaxff/FC/log.8Mar18.FC.g++.1 similarity index 100% rename from examples/reax/FC/log.8Mar18.FC.g++.1 rename to examples/reaxff/FC/log.8Mar18.FC.g++.1 diff --git a/examples/reax/FC/log.8Mar18.FC.g++.4 b/examples/reaxff/FC/log.8Mar18.FC.g++.4 similarity index 100% rename from examples/reax/FC/log.8Mar18.FC.g++.4 rename to examples/reaxff/FC/log.8Mar18.FC.g++.4 diff --git a/examples/reax/FeOH3/README b/examples/reaxff/FeOH3/README similarity index 100% rename from examples/reax/FeOH3/README rename to examples/reaxff/FeOH3/README diff --git a/examples/reax/FeOH3/data.FeOH3 b/examples/reaxff/FeOH3/data.FeOH3 similarity index 100% rename from examples/reax/FeOH3/data.FeOH3 rename to examples/reaxff/FeOH3/data.FeOH3 diff --git a/examples/reax/FeOH3/ffield.reax.Fe_O_C_H b/examples/reaxff/FeOH3/ffield.reax.Fe_O_C_H similarity index 100% rename from examples/reax/FeOH3/ffield.reax.Fe_O_C_H rename to examples/reaxff/FeOH3/ffield.reax.Fe_O_C_H diff --git a/examples/reax/FeOH3/in.FeOH3 b/examples/reaxff/FeOH3/in.FeOH3 similarity index 100% rename from examples/reax/FeOH3/in.FeOH3 rename to examples/reaxff/FeOH3/in.FeOH3 diff --git a/examples/reax/FeOH3/lmp_control b/examples/reaxff/FeOH3/lmp_control similarity index 100% rename from examples/reax/FeOH3/lmp_control rename to examples/reaxff/FeOH3/lmp_control diff --git a/examples/reax/FeOH3/log.5Oct16.FeOH3.g++.1 b/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1 similarity index 100% rename from examples/reax/FeOH3/log.5Oct16.FeOH3.g++.1 rename to examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1 diff --git a/examples/reax/FeOH3/log.5Oct16.FeOH3.g++.4 b/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.4 similarity index 100% rename from examples/reax/FeOH3/log.5Oct16.FeOH3.g++.4 rename to examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.4 diff --git a/examples/reax/FeOH3/param.qeq b/examples/reaxff/FeOH3/param.qeq similarity index 100% rename from examples/reax/FeOH3/param.qeq rename to examples/reaxff/FeOH3/param.qeq diff --git a/examples/reax/HNS/README.txt b/examples/reaxff/HNS/README.txt similarity index 100% rename from examples/reax/HNS/README.txt rename to examples/reaxff/HNS/README.txt diff --git a/examples/reax/HNS/data.hns-equil b/examples/reaxff/HNS/data.hns-equil similarity index 100% rename from examples/reax/HNS/data.hns-equil rename to examples/reaxff/HNS/data.hns-equil diff --git a/examples/reax/HNS/ffield.reax.hns b/examples/reaxff/HNS/ffield.reax.hns similarity index 100% rename from examples/reax/HNS/ffield.reax.hns rename to examples/reaxff/HNS/ffield.reax.hns diff --git a/examples/reax/HNS/in.reaxc.hns b/examples/reaxff/HNS/in.reaxc.hns similarity index 100% rename from examples/reax/HNS/in.reaxc.hns rename to examples/reaxff/HNS/in.reaxc.hns diff --git a/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 b/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1 similarity index 100% rename from examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 rename to examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1 diff --git a/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 b/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4 similarity index 100% rename from examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 rename to examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4 diff --git a/examples/reax/RDX/README b/examples/reaxff/RDX/README similarity index 100% rename from examples/reax/RDX/README rename to examples/reaxff/RDX/README diff --git a/examples/reax/RDX/data.RDX b/examples/reaxff/RDX/data.RDX similarity index 100% rename from examples/reax/RDX/data.RDX rename to examples/reaxff/RDX/data.RDX diff --git a/examples/reax/RDX/ffield.reax.rdx b/examples/reaxff/RDX/ffield.reax.rdx similarity index 100% rename from examples/reax/RDX/ffield.reax.rdx rename to examples/reaxff/RDX/ffield.reax.rdx diff --git a/examples/reax/RDX/in.RDX b/examples/reaxff/RDX/in.RDX similarity index 100% rename from examples/reax/RDX/in.RDX rename to examples/reaxff/RDX/in.RDX diff --git a/examples/reax/RDX/lmp_control b/examples/reaxff/RDX/lmp_control similarity index 100% rename from examples/reax/RDX/lmp_control rename to examples/reaxff/RDX/lmp_control diff --git a/examples/reax/RDX/log.8Mar18.RDX.g++.1 b/examples/reaxff/RDX/log.8Mar18.RDX.g++.1 similarity index 100% rename from examples/reax/RDX/log.8Mar18.RDX.g++.1 rename to examples/reaxff/RDX/log.8Mar18.RDX.g++.1 diff --git a/examples/reax/RDX/log.8Mar18.RDX.g++.4 b/examples/reaxff/RDX/log.8Mar18.RDX.g++.4 similarity index 100% rename from examples/reax/RDX/log.8Mar18.RDX.g++.4 rename to examples/reaxff/RDX/log.8Mar18.RDX.g++.4 diff --git a/examples/reax/RDX/param.qeq b/examples/reaxff/RDX/param.qeq similarity index 100% rename from examples/reax/RDX/param.qeq rename to examples/reaxff/RDX/param.qeq diff --git a/examples/reax/README b/examples/reaxff/README similarity index 100% rename from examples/reax/README rename to examples/reaxff/README diff --git a/examples/reax/VOH/README b/examples/reaxff/VOH/README similarity index 100% rename from examples/reax/VOH/README rename to examples/reaxff/VOH/README diff --git a/examples/reax/VOH/data.VOH b/examples/reaxff/VOH/data.VOH similarity index 100% rename from examples/reax/VOH/data.VOH rename to examples/reaxff/VOH/data.VOH diff --git a/examples/reax/VOH/ffield.reax.V_O_C_H b/examples/reaxff/VOH/ffield.reax.V_O_C_H similarity index 100% rename from examples/reax/VOH/ffield.reax.V_O_C_H rename to examples/reaxff/VOH/ffield.reax.V_O_C_H diff --git a/examples/reax/VOH/in.VOH b/examples/reaxff/VOH/in.VOH similarity index 100% rename from examples/reax/VOH/in.VOH rename to examples/reaxff/VOH/in.VOH diff --git a/examples/reax/VOH/lmp_control b/examples/reaxff/VOH/lmp_control similarity index 100% rename from examples/reax/VOH/lmp_control rename to examples/reaxff/VOH/lmp_control diff --git a/examples/reax/VOH/log.8Mar18.VOH.g++.1 b/examples/reaxff/VOH/log.8Mar18.VOH.g++.1 similarity index 100% rename from examples/reax/VOH/log.8Mar18.VOH.g++.1 rename to examples/reaxff/VOH/log.8Mar18.VOH.g++.1 diff --git a/examples/reax/VOH/log.8Mar18.VOH.g++.4 b/examples/reaxff/VOH/log.8Mar18.VOH.g++.4 similarity index 100% rename from examples/reax/VOH/log.8Mar18.VOH.g++.4 rename to examples/reaxff/VOH/log.8Mar18.VOH.g++.4 diff --git a/examples/reax/VOH/param.qeq b/examples/reaxff/VOH/param.qeq similarity index 100% rename from examples/reax/VOH/param.qeq rename to examples/reaxff/VOH/param.qeq diff --git a/examples/reax/ZnOH2/README b/examples/reaxff/ZnOH2/README similarity index 100% rename from examples/reax/ZnOH2/README rename to examples/reaxff/ZnOH2/README diff --git a/examples/reax/ZnOH2/data.ZnOH2 b/examples/reaxff/ZnOH2/data.ZnOH2 similarity index 100% rename from examples/reax/ZnOH2/data.ZnOH2 rename to examples/reaxff/ZnOH2/data.ZnOH2 diff --git a/examples/reax/ZnOH2/ffield.reax.ZnOH b/examples/reaxff/ZnOH2/ffield.reax.ZnOH similarity index 100% rename from examples/reax/ZnOH2/ffield.reax.ZnOH rename to examples/reaxff/ZnOH2/ffield.reax.ZnOH diff --git a/examples/reax/ZnOH2/in.ZnOH2 b/examples/reaxff/ZnOH2/in.ZnOH2 similarity index 100% rename from examples/reax/ZnOH2/in.ZnOH2 rename to examples/reaxff/ZnOH2/in.ZnOH2 diff --git a/examples/reax/ZnOH2/lmp_control b/examples/reaxff/ZnOH2/lmp_control similarity index 100% rename from examples/reax/ZnOH2/lmp_control rename to examples/reaxff/ZnOH2/lmp_control diff --git a/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1 b/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.1 similarity index 100% rename from examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1 rename to examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.1 diff --git a/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4 b/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.4 similarity index 100% rename from examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4 rename to examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.4 diff --git a/examples/reax/ZnOH2/param.qeq b/examples/reaxff/ZnOH2/param.qeq similarity index 100% rename from examples/reax/ZnOH2/param.qeq rename to examples/reaxff/ZnOH2/param.qeq diff --git a/examples/reax/ci-reaxFF/CH4.dat b/examples/reaxff/ci-reaxFF/CH4.dat similarity index 100% rename from examples/reax/ci-reaxFF/CH4.dat rename to examples/reaxff/ci-reaxFF/CH4.dat diff --git a/examples/reax/ci-reaxFF/ci-reaxFF_ZBL.dat b/examples/reaxff/ci-reaxFF/ci-reaxFF_ZBL.dat similarity index 100% rename from examples/reax/ci-reaxFF/ci-reaxFF_ZBL.dat rename to examples/reaxff/ci-reaxFF/ci-reaxFF_ZBL.dat diff --git a/examples/reax/ci-reaxFF/control b/examples/reaxff/ci-reaxFF/control similarity index 100% rename from examples/reax/ci-reaxFF/control rename to examples/reaxff/ci-reaxFF/control diff --git a/examples/reax/ci-reaxFF/ffield.ci-reax.CH b/examples/reaxff/ci-reaxFF/ffield.ci-reax.CH similarity index 100% rename from examples/reax/ci-reaxFF/ffield.ci-reax.CH rename to examples/reaxff/ci-reaxFF/ffield.ci-reax.CH diff --git a/examples/reax/ci-reaxFF/in.ci-reax.CH b/examples/reaxff/ci-reaxFF/in.ci-reax.CH similarity index 100% rename from examples/reax/ci-reaxFF/in.ci-reax.CH rename to examples/reaxff/ci-reaxFF/in.ci-reax.CH diff --git a/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 b/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 similarity index 100% rename from examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 rename to examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 diff --git a/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 b/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 similarity index 100% rename from examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 rename to examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 diff --git a/examples/reax/control.reax_c.rdx b/examples/reaxff/control.reax_c.rdx similarity index 100% rename from examples/reax/control.reax_c.rdx rename to examples/reaxff/control.reax_c.rdx diff --git a/examples/reax/control.reax_c.tatb b/examples/reaxff/control.reax_c.tatb similarity index 100% rename from examples/reax/control.reax_c.tatb rename to examples/reaxff/control.reax_c.tatb diff --git a/examples/reax/data.rdx b/examples/reaxff/data.rdx similarity index 100% rename from examples/reax/data.rdx rename to examples/reaxff/data.rdx diff --git a/examples/reax/data.tatb b/examples/reaxff/data.tatb similarity index 100% rename from examples/reax/data.tatb rename to examples/reaxff/data.tatb diff --git a/examples/reax/ffield.reax b/examples/reaxff/ffield.reax similarity index 100% rename from examples/reax/ffield.reax rename to examples/reaxff/ffield.reax diff --git a/examples/reaxff/in.reaxff.rdx b/examples/reaxff/in.reaxff.rdx new file mode 100644 index 0000000000..82a582e958 --- /dev/null +++ b/examples/reaxff/in.reaxff.rdx @@ -0,0 +1,53 @@ +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx + +pair_style reaxff control.reax_c.rdx +pair_coeff * * ffield.reax C H O N + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff + +variable nqeq equal f_2 + +thermo 10 +thermo_style custom step temp epair etotal press & + v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & + v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxff.rdx + +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 diff --git a/examples/reaxff/in.reaxff.rdx-shielded b/examples/reaxff/in.reaxff.rdx-shielded new file mode 100644 index 0000000000..d1a5f0beaa --- /dev/null +++ b/examples/reaxff/in.reaxff.rdx-shielded @@ -0,0 +1,52 @@ +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx + +pair_style reaxff control.reax_c.rdx +pair_coeff * * ffield.reax C H O N + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff +variable nqeq equal f_2 + +thermo 10 +thermo_style custom step temp epair etotal press & + v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & + v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxff.rdx + +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 diff --git a/examples/reaxff/in.reaxff.tatb b/examples/reaxff/in.reaxff.tatb new file mode 100644 index 0000000000..6cf7828cf1 --- /dev/null +++ b/examples/reaxff/in.reaxff.tatb @@ -0,0 +1,55 @@ +# ReaxFF potential for TATB system + +units real + +atom_style charge +read_data data.tatb + +pair_style reaxff control.reax_c.tatb +pair_coeff * * ffield.reax C H O N + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff +fix 4 all reaxff/bonds 5 bonds.reaxff +variable nqeq equal f_2 + +thermo 5 +thermo_style custom step temp epair etotal press & + v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & + v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxff.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reaxff/species 1 5 5 species.tatb + +run 25 diff --git a/examples/reaxff/in.reaxff.tatb-shielded b/examples/reaxff/in.reaxff.tatb-shielded new file mode 100644 index 0000000000..5a809ecdd2 --- /dev/null +++ b/examples/reaxff/in.reaxff.tatb-shielded @@ -0,0 +1,55 @@ +# ReaxFF potential for TATB system + +units real + +atom_style charge +read_data data.tatb + +pair_style reaxff control.reax_c.tatb +pair_coeff * * ffield.reax C H O N + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff +fix 4 all reaxff/bonds 5 bonds.reaxff +variable nqeq equal f_2 + +thermo 5 +thermo_style custom step temp epair etotal press & + v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & + v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxff.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reaxff/species 1 5 5 species.tatb + +run 25 diff --git a/examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.1 b/examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.1 new file mode 100644 index 0000000000..7a0fcf53b5 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.1 @@ -0,0 +1,144 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx +Reading data file ... + orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 21 atoms + read_data CPU = 0.001 seconds + +pair_style reaxff control.reax_c.rdx +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff +variable nqeq equal f_2 + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxff.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12 + 10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8 + 20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7 + 30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8 + 40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11 + 50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10 + 60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10 + 70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10 + 80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9 + 90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11 + 100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10 +Loop time of 0.23792 on 1 procs for 100 steps with 21 atoms + +Performance: 36.315 ns/day, 0.661 hours/ns, 420.310 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.21046 | 0.21046 | 0.21046 | 0.0 | 88.46 +Neigh | 0.010947 | 0.010947 | 0.010947 | 0.0 | 4.60 +Comm | 0.00060345 | 0.00060345 | 0.00060345 | 0.0 | 0.25 +Output | 0.00071705 | 0.00071705 | 0.00071705 | 0.0 | 0.30 +Modify | 0.014873 | 0.014873 | 0.014873 | 0.0 | 6.25 +Other | | 0.0003213 | | | 0.14 + +Nlocal: 21.0000 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 546.000 ave 546 max 546 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1096.00 ave 1096 max 1096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1306.00 ave 1306 max 1306 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1306 +Ave neighs/atom = 62.190476 +Neighbor list builds = 10 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.4 b/examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.4 new file mode 100644 index 0000000000..4840b5fa2b --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.4 @@ -0,0 +1,144 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx +Reading data file ... + orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 21 atoms + read_data CPU = 0.003 seconds + +pair_style reaxff control.reax_c.rdx +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff +variable nqeq equal f_2 + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxff.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12 + 10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8 + 20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6 + 30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8 + 40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11 + 50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10 + 60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10 + 70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10 + 80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9 + 90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11 + 100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10 +Loop time of 0.427646 on 4 procs for 100 steps with 21 atoms + +Performance: 20.204 ns/day, 1.188 hours/ns, 233.838 timesteps/s +88.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1373 | 0.20047 | 0.27938 | 11.8 | 46.88 +Neigh | 0.0067 | 0.009334 | 0.01249 | 2.1 | 2.18 +Comm | 0.057132 | 0.13685 | 0.19972 | 14.4 | 32.00 +Output | 0.00078935 | 0.0013884 | 0.0031266 | 2.7 | 0.32 +Modify | 0.075213 | 0.079164 | 0.082556 | 0.9 | 18.51 +Other | | 0.0004359 | | | 0.10 + +Nlocal: 5.25000 ave 15 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 355.500 ave 432 max 282 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 298.750 ave 822 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +FullNghs: 326.500 ave 927 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 1306 +Ave neighs/atom = 62.190476 +Neighbor list builds = 10 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/reaxff/log.21Jul21.reaxff.rdx.g++.1 b/examples/reaxff/log.21Jul21.reaxff.rdx.g++.1 new file mode 100644 index 0000000000..89e5c606c2 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.rdx.g++.1 @@ -0,0 +1,154 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx +Reading data file ... + orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 21 atoms + read_data CPU = 0.001 seconds + +pair_style reaxff control.reax_c.rdx +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff + +variable nqeq equal f_2 + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxff.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +- fix qeq/reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/reaxff, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 13.36 | 13.36 | 13.36 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5 + 10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8 + 20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7 + 30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8 + 40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11 + 50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10 + 60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10 + 70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10 + 80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9 + 90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11 + 100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5 +Loop time of 0.231802 on 1 procs for 100 steps with 21 atoms + +Performance: 37.273 ns/day, 0.644 hours/ns, 431.402 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.20857 | 0.20857 | 0.20857 | 0.0 | 89.98 +Neigh | 0.010489 | 0.010489 | 0.010489 | 0.0 | 4.52 +Comm | 0.00059632 | 0.00059632 | 0.00059632 | 0.0 | 0.26 +Output | 0.00067498 | 0.00067498 | 0.00067498 | 0.0 | 0.29 +Modify | 0.011161 | 0.011161 | 0.011161 | 0.0 | 4.82 +Other | | 0.000307 | | | 0.13 + +Nlocal: 21.0000 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 546.000 ave 546 max 546 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1096.00 ave 1096 max 1096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1096 +Ave neighs/atom = 52.190476 +Neighbor list builds = 10 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/reaxff/log.21Jul21.reaxff.rdx.g++.4 b/examples/reaxff/log.21Jul21.reaxff.rdx.g++.4 new file mode 100644 index 0000000000..29c36c54f0 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.rdx.g++.4 @@ -0,0 +1,154 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx +Reading data file ... + orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 21 atoms + read_data CPU = 0.001 seconds + +pair_style reaxff control.reax_c.rdx +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff + +variable nqeq equal f_2 + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxff.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +- fix qeq/reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/reaxff, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.353 | 10.52 | 11.73 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418 12 + 10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252292 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8 + 20 538.95847 -1942.7037 -1910.5731 -10725.668 -2803.7395 7.9078328 0.077926688 0 81.610045 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69262 0 89.316856 7 + 30 463.09521 -1933.5765 -1905.9685 -33255.503 -2749.8591 -8.0154614 0.027628708 0 81.627408 0.11972393 -50.262275 0 20.820319 -9.6327031 851.88721 -149.49497 0 79.205707 8 + 40 885.49559 -1958.9126 -1906.1227 -4814.661 -2795.644 9.1506103 0.13747486 0 70.948058 0.24360549 -57.862693 0 19.076514 -11.141211 873.73894 -159.9939 0 92.434063 11 + 50 861.16222 -1954.4601 -1903.1209 -1896.7328 -2784.8449 3.8269573 0.15793301 0 79.851661 3.3492101 -78.066131 0 32.628939 -7.9565311 872.81847 -190.9857 0 114.75999 10 + 60 1167.7838 -1971.8434 -1902.2246 -3482.8253 -2705.8639 -17.121553 0.22749078 0 44.507707 7.8560156 -74.789002 0 16.256509 -4.6046674 835.83076 -188.33689 0 114.19413 10 + 70 1439.9922 -1989.3024 -1903.4556 23845.682 -2890.7894 31.958742 0.26671722 0 85.758402 3.1803955 -71.002937 0 24.357176 -10.311293 905.86805 -175.38494 0 106.79668 10 + 80 502.39847 -1930.7549 -1900.8038 -20356.357 -2703.8111 -18.662668 0.11286141 0 99.803668 2.0329484 -76.17132 0 19.236866 -6.2786536 826.47435 -166.03145 0 92.539587 9 + 90 749.0857 -1946.984 -1902.3263 17798.657 -2863.7584 42.068704 0.24338054 0 96.181666 0.96183837 -69.955527 0 24.615445 -11.58275 903.68864 -190.13828 0 120.69127 11 + 100 1109.695 -1968.5879 -1902.4321 -4490.3441 -2755.8984 -7.1226574 0.21757683 0 61.806014 7.0826278 -75.645456 0 20.115306 -6.2372466 863.56451 -198.56953 0 122.09941 10.5 +Loop time of 0.371707 on 4 procs for 100 steps with 21 atoms + +Performance: 23.244 ns/day, 1.033 hours/ns, 269.029 timesteps/s +91.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13518 | 0.19123 | 0.24947 | 9.7 | 51.45 +Neigh | 0.0073075 | 0.0096968 | 0.012228 | 1.8 | 2.61 +Comm | 0.034511 | 0.093329 | 0.14912 | 14.0 | 25.11 +Output | 0.00081416 | 0.0011345 | 0.0019655 | 1.4 | 0.31 +Modify | 0.073177 | 0.075449 | 0.078618 | 0.7 | 20.30 +Other | | 0.0008711 | | | 0.23 + +Nlocal: 5.25000 ave 15 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 355.500 ave 432 max 282 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 298.750 ave 822 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 1195 +Ave neighs/atom = 56.904762 +Neighbor list builds = 10 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.1 b/examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.1 new file mode 100644 index 0000000000..4c84081d44 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for TATB system + +units real + +atom_style charge +read_data data.tatb +Reading data file ... + triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 384 atoms + read_data CPU = 0.002 seconds + +pair_style reaxff control.reax_c.tatb +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff +fix 4 all reaxff/bonds 5 bonds.reaxff +variable nqeq equal f_2 + +thermo 5 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxff.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reaxff/species 1 5 5 species.tatb + +run 25 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 5 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 141.3 | 141.3 | 141.3 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275 31 + 5 0.61603968 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665 8 + 10 2.3525543 -44763.227 -44760.541 12288.589 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714 10 + 15 4.9013256 -44766.36 -44760.764 17716.957 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2536 0 6370.4198 9 + 20 7.8294699 -44769.686 -44760.747 25205.552 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5055 0 6355.2567 8 + 25 10.697916 -44772.904 -44760.691 34232.955 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.308 0 6336.7889 7 +Loop time of 3.31728 on 1 procs for 25 steps with 384 atoms + +Performance: 0.041 ns/day, 589.738 hours/ns, 7.536 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9321 | 1.9321 | 1.9321 | 0.0 | 58.24 +Neigh | 0.6452 | 0.6452 | 0.6452 | 0.0 | 19.45 +Comm | 0.0020122 | 0.0020122 | 0.0020122 | 0.0 | 0.06 +Output | 0.00030173 | 0.00030173 | 0.00030173 | 0.0 | 0.01 +Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 22.22 +Other | | 0.0003829 | | | 0.01 + +Nlocal: 384.000 ave 384 max 384 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7559.00 ave 7559 max 7559 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 286828.0 ave 286828 max 286828 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 336304.0 ave 336304 max 336304 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 336304 +Ave neighs/atom = 875.79167 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:03 diff --git a/examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.4 b/examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.4 new file mode 100644 index 0000000000..d4cb8a0190 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for TATB system + +units real + +atom_style charge +read_data data.tatb +Reading data file ... + triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 384 atoms + read_data CPU = 0.004 seconds + +pair_style reaxff control.reax_c.tatb +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff +fix 4 all reaxff/bonds 5 bonds.reaxff +variable nqeq equal f_2 + +thermo 5 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxff.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reaxff/species 1 5 5 species.tatb + +run 25 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 5 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 94.50 | 94.50 | 94.50 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -44760.998 -44760.998 7827.7865 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0278 31 + 5 0.61603964 -44761.698 -44760.994 8934.6344 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9 + 10 2.3525559 -44763.227 -44760.541 12288.611 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9712 0 6381.7089 11 + 15 4.9013319 -44766.36 -44760.764 17716.965 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2514 0 6370.4176 9 + 20 7.8294706 -44769.686 -44760.747 25205.511 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5196 0 6355.2708 7 + 25 10.69792 -44772.904 -44760.691 34232.831 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.353 0 6336.8339 11 +Loop time of 2.66226 on 4 procs for 25 steps with 384 atoms + +Performance: 0.051 ns/day, 473.290 hours/ns, 9.391 timesteps/s +96.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.7311 | 1.7619 | 1.794 | 2.0 | 66.18 +Neigh | 0.46483 | 0.46901 | 0.47348 | 0.5 | 17.62 +Comm | 0.039253 | 0.073989 | 0.10705 | 10.7 | 2.78 +Output | 0.0012206 | 0.0080282 | 0.010299 | 4.4 | 0.30 +Modify | 0.34359 | 0.3488 | 0.36264 | 1.4 | 13.10 +Other | | 0.0005529 | | | 0.02 + +Nlocal: 96.0000 ave 96 max 96 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5118.00 ave 5118 max 5118 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 79754.0 ave 79754 max 79754 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 84076.0 ave 84076 max 84076 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 336304 +Ave neighs/atom = 875.79167 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:03 diff --git a/examples/reaxff/log.21Jul21.reaxff.tatb.g++.1 b/examples/reaxff/log.21Jul21.reaxff.tatb.g++.1 new file mode 100644 index 0000000000..2e1c7a5b26 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.tatb.g++.1 @@ -0,0 +1,151 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for TATB system + +units real + +atom_style charge +read_data data.tatb +Reading data file ... + triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 384 atoms + read_data CPU = 0.008 seconds + +pair_style reaxff control.reax_c.tatb +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff +fix 4 all reaxff/bonds 5 bonds.reaxff +variable nqeq equal f_2 + +thermo 5 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxff.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reaxff/species 1 5 5 species.tatb + +run 25 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +- fix qeq/reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 5 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/reaxff, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 148.1 | 148.1 | 148.1 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -44760.998 -44760.998 7827.7878 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 31.5 + 5 0.61603968 -44761.698 -44760.994 8934.6346 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9 + 10 2.3525552 -44763.227 -44760.541 12288.581 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9765 0 6381.7142 10.5 + 15 4.9013309 -44766.36 -44760.764 17716.918 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2622 0 6370.4284 9.5 + 20 7.829469 -44769.686 -44760.747 25205.568 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.5126 0 6355.2639 8 + 25 10.697899 -44772.904 -44760.691 34232.788 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3619 0 6336.8427 11 +Loop time of 2.91659 on 1 procs for 25 steps with 384 atoms + +Performance: 0.046 ns/day, 518.504 hours/ns, 8.572 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9139 | 1.9139 | 1.9139 | 0.0 | 65.62 +Neigh | 0.5948 | 0.5948 | 0.5948 | 0.0 | 20.39 +Comm | 0.0020205 | 0.0020205 | 0.0020205 | 0.0 | 0.07 +Output | 0.00031287 | 0.00031287 | 0.00031287 | 0.0 | 0.01 +Modify | 0.40513 | 0.40513 | 0.40513 | 0.0 | 13.89 +Other | | 0.0003856 | | | 0.01 + +Nlocal: 384.000 ave 384 max 384 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7559.00 ave 7559 max 7559 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 286828.0 ave 286828 max 286828 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 286828 +Ave neighs/atom = 746.94792 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:03 diff --git a/examples/reaxff/log.21Jul21.reaxff.tatb.g++.4 b/examples/reaxff/log.21Jul21.reaxff.tatb.g++.4 new file mode 100644 index 0000000000..100c2f7ca4 --- /dev/null +++ b/examples/reaxff/log.21Jul21.reaxff.tatb.g++.4 @@ -0,0 +1,151 @@ +LAMMPS (2 Jul 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for TATB system + +units real + +atom_style charge +read_data data.tatb +Reading data file ... + triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 384 atoms + read_data CPU = 0.002 seconds + +pair_style reaxff control.reax_c.tatb +WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97) +WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113) +WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97) +WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97) +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reaxff + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff +fix 4 all reaxff/bonds 5 bonds.reaxff +variable nqeq equal f_2 + +thermo 5 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxff.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reaxff/species 1 5 5 species.tatb + +run 25 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +- fix qeq/reaxff command: + +@Article{Aktulga12, + author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, + title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 5 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeq/reaxff, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 99.27 | 99.27 | 99.27 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq + 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 31 + 5 0.61603941 -44761.698 -44760.994 8934.6279 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 10 + 10 2.352555 -44763.227 -44760.541 12288.61 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9686 0 6381.7064 9 + 15 4.9013339 -44766.36 -44760.764 17716.995 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2413 0 6370.4076 10.5 + 20 7.8294636 -44769.686 -44760.747 25205.611 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4966 0 6355.2478 10 + 25 10.6979 -44772.904 -44760.691 34232.798 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3574 0 6336.8382 10.5 +Loop time of 2.53633 on 4 procs for 25 steps with 384 atoms + +Performance: 0.053 ns/day, 450.902 hours/ns, 9.857 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.7343 | 1.7637 | 1.815 | 2.4 | 69.54 +Neigh | 0.44441 | 0.44869 | 0.45403 | 0.6 | 17.69 +Comm | 0.025287 | 0.074702 | 0.10592 | 11.9 | 2.95 +Output | 0.0016916 | 0.0080527 | 0.010178 | 4.1 | 0.32 +Modify | 0.23126 | 0.24065 | 0.25706 | 2.1 | 9.49 +Other | | 0.000566 | | | 0.02 + +Nlocal: 96.0000 ave 96 max 96 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5118.00 ave 5118 max 5118 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 79754.0 ave 79754 max 79754 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 319016 +Ave neighs/atom = 830.77083 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:02 diff --git a/examples/snap/Ni_Zuo_JPCA2020.quadratic.snapcoeff b/examples/snap/Ni_Zuo_JPCA2020.quadratic.snapcoeff new file mode 120000 index 0000000000..9401393007 --- /dev/null +++ b/examples/snap/Ni_Zuo_JPCA2020.quadratic.snapcoeff @@ -0,0 +1 @@ +../../potentials/Ni_Zuo_JPCA2020.quadratic.snapcoeff \ No newline at end of file diff --git a/examples/snap/Ni_Zuo_JPCA2020.quadratic.snapparam b/examples/snap/Ni_Zuo_JPCA2020.quadratic.snapparam new file mode 120000 index 0000000000..a47ada019b --- /dev/null +++ b/examples/snap/Ni_Zuo_JPCA2020.quadratic.snapparam @@ -0,0 +1 @@ +../../potentials/Ni_Zuo_JPCA2020.quadratic.snapparam \ No newline at end of file diff --git a/examples/snap/Ni_Zuo_JPCA2020.snapcoeff b/examples/snap/Ni_Zuo_JPCA2020.snapcoeff new file mode 120000 index 0000000000..7211856b43 --- /dev/null +++ b/examples/snap/Ni_Zuo_JPCA2020.snapcoeff @@ -0,0 +1 @@ +../../potentials/Ni_Zuo_JPCA2020.snapcoeff \ No newline at end of file diff --git a/examples/snap/Ni_Zuo_JPCA2020.snapparam b/examples/snap/Ni_Zuo_JPCA2020.snapparam new file mode 120000 index 0000000000..b7fc095fab --- /dev/null +++ b/examples/snap/Ni_Zuo_JPCA2020.snapparam @@ -0,0 +1 @@ +../../potentials/Ni_Zuo_JPCA2020.snapparam \ No newline at end of file diff --git a/examples/snap/in.snap.scale.Ni_Zuo_JCPA2020 b/examples/snap/in.snap.scale.Ni_Zuo_JCPA2020 new file mode 100644 index 0000000000..ee195c11f3 --- /dev/null +++ b/examples/snap/in.snap.scale.Ni_Zuo_JCPA2020 @@ -0,0 +1,53 @@ +# Toy demonstration of SNAP "scale" parameter, using fix/adapt and hybrid/overlay +# Mixing linear and quadratic SNAP Ni potentials by Zuo et al. JCPA 2020 + +# mixing parameter + +variable lambda equal 0.2 + + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 3 +variable a equal 3.52 +units metal + +# generate the box and atom positions using a FCC lattice +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice fcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 34. + +# choose bundled SNAP Ni potential from Zuo et al. JCPA 2020 +pair_style hybrid/overlay snap snap +pair_coeff * * snap 1 Ni_Zuo_JPCA2020.snapcoeff Ni_Zuo_JPCA2020.snapparam Ni +pair_coeff * * snap 2 Ni_Zuo_JPCA2020.quadratic.snapcoeff Ni_Zuo_JPCA2020.quadratic.snapparam Ni + +# scale according to mixing parameter +variable l1 equal ${lambda} +variable l2 equal 1.0-${lambda} +fix scale1 all adapt 1 pair snap:1 scale * * v_l1 +fix scale2 all adapt 1 pair snap:2 scale * * v_l2 + +# Setup output +thermo 1 +thermo_modify norm yes + +# Set up NVE run +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +# Run MD +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} diff --git a/examples/tracker/contact_history.dat b/examples/tracker/contact_history.dat new file mode 100644 index 0000000000..898aab4ef6 --- /dev/null +++ b/examples/tracker/contact_history.dat @@ -0,0 +1,8122 @@ +16 68 0 0.5 +17 37 0 0.5 +162 210 0 0.5 +174 163 0 0.5 +179 255 0 0.5 +96 161 0 0.505 +111 162 0 0.505 +156 231 0 0.505 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4.125 4.805 +210 227 0 4.805 +234 233 0 4.805 +245 254 0.785 4.805 +57 11 2.19 4.81 +127 187 0.95 4.81 +129 141 3.95 4.81 +156 22 4.13 4.81 +180 245 0.585 4.81 +210 21 2.905 4.81 +211 24 2.95 4.81 +18 24 0 4.815 +18 99 0.67 4.815 +49 41 3.44 4.815 +72 76 3.045 4.815 +111 95 0 4.815 +111 148 1.91 4.815 +139 22 4.16 4.815 +173 100 2.735 4.815 +181 129 1.175 4.815 +192 141 3.985 4.815 +194 215 0 4.815 +249 246 0 4.815 +251 84 4.16 4.815 +55 103 4.26 4.82 +58 14 1.535 4.82 +60 102 3.23 4.82 +62 34 3.955 4.82 +80 160 4.26 4.82 +159 203 2.52 4.82 +168 49 2.85 4.82 +189 62 2.25 4.82 +21 10 3.73 4.825 +51 119 2.84 4.825 +150 233 0 4.825 +173 110 1.14 4.825 +181 168 0 4.825 +61 15 4.16 4.83 +106 102 0 4.83 +120 40 0.21 4.83 +134 213 0 4.83 +157 206 3.845 4.83 +174 224 2.955 4.83 +204 93 1.91 4.83 +218 22 3.44 4.83 +226 62 4.295 4.83 +245 195 3.615 4.83 +82 162 3.195 4.835 +88 108 3.99 4.835 +126 137 4.225 4.835 +127 181 3.905 4.835 +138 80 0 4.835 +169 165 0 4.835 +206 175 2.7 4.835 +219 93 1.01 4.835 +249 100 3.975 4.835 +7 28 1.4 4.84 +16 19 3.725 4.84 +88 172 3.16 4.84 +112 119 0.265 4.84 +166 169 0 4.84 +168 185 4.325 4.84 +233 239 2.875 4.84 +234 201 1.49 4.84 +238 248 4.145 4.84 +239 47 0 4.84 +29 70 3.145 4.845 +97 162 1.965 4.845 +101 107 3.825 4.845 +109 110 0 4.845 +155 217 0 4.845 +170 100 2.515 4.845 +171 207 3.77 4.845 +171 61 3.415 4.845 +178 213 4.315 4.845 +194 28 4.055 4.845 +222 235 0 4.845 +222 253 2.27 4.845 +223 81 1.79 4.845 +23 230 3.865 4.85 +60 39 3.4 4.85 +75 96 1.96 4.85 +146 172 2.87 4.85 +165 184 2.735 4.85 +211 41 2.6 4.85 +219 32 3.605 4.85 +254 30 3.8 4.85 +11 138 0.505 4.855 +25 91 3.995 4.855 +29 86 2.045 4.855 +73 91 0 4.855 +101 172 3.855 4.855 +238 62 0 4.855 +45 10 1.975 4.86 +69 183 3.925 4.86 +100 61 2.87 4.86 +108 117 0 4.86 +118 153 4.355 4.86 +126 80 0 4.86 +136 194 0 4.86 +151 194 4.31 4.86 +167 218 0 4.86 +168 133 4.03 4.86 +171 184 3.25 4.86 +171 230 4.22 4.86 +182 243 4.34 4.86 +201 118 3.5 4.86 +226 246 3.845 4.86 +31 154 3.25 4.865 +54 39 0.135 4.865 +88 104 0 4.865 +145 237 2.845 4.865 +183 246 0 4.865 +188 186 3.51 4.865 +215 197 0 4.865 +24 107 4.29 4.87 +36 84 3.67 4.87 +55 104 0 4.87 +57 39 0 4.87 +59 120 3.175 4.87 +147 200 3.11 4.87 +214 235 2.87 4.87 +218 235 0 4.87 +240 184 3.625 4.87 +241 143 3.885 4.87 +249 185 4.3 4.87 +8 21 0 4.875 +126 202 4.26 4.875 +132 194 0 4.875 +170 79 2.44 4.875 +176 13 3.04 4.875 +207 206 3.58 4.875 +209 17 0 4.875 +235 30 4.37 4.875 +23 45 4.205 4.88 +25 126 3.905 4.88 +30 44 4.215 4.88 +50 223 4.29 4.88 +77 192 4.285 4.88 +159 93 2.555 4.88 +173 224 0.2 4.88 +211 231 3.175 4.88 +230 21 3.405 4.88 +244 34 3.625 4.88 +17 85 2.995 4.885 +33 34 4.04 4.885 +34 162 3.765 4.885 +60 75 3.335 4.885 +82 98 0 4.885 +88 34 4.29 4.885 +94 99 0 4.885 +109 44 3.955 4.885 +136 179 0.585 4.885 +147 229 2.395 4.885 +168 243 4.37 4.885 +254 13 0 4.885 +4 212 1.175 4.89 +7 153 2.405 4.89 +48 228 2.195 4.89 +58 59 0 4.89 +74 86 2.53 4.89 +101 177 2.325 4.89 +140 217 0 4.89 +146 189 4.1 4.89 +167 171 4.38 4.89 +174 222 0.285 4.89 +191 62 3.695 4.89 +221 61 4.325 4.89 +222 93 4.12 4.89 +57 122 3.01 4.895 +94 97 0 4.895 +165 249 1.915 4.895 +207 13 0 4.895 +227 235 3.395 4.895 +5 76 3.39 4.9 +51 8 2.39 4.9 +92 155 3.15 4.9 +110 162 4.275 4.9 +167 227 1.835 4.9 +188 201 4.115 4.9 +206 196 0 4.9 +244 116 3.72 4.9 +140 206 2.975 4.905 +143 222 4.35 4.905 +222 206 2.605 4.905 +228 47 0 4.905 +229 235 3.88 4.905 +237 184 3.535 4.905 +246 5 0.57 4.905 +13 50 3.81 4.91 +13 56 4.33 4.91 +18 101 4.3 4.91 +21 27 2.605 4.91 +45 93 4.01 4.91 +63 84 2.84 4.91 +69 135 3.205 4.91 +129 13 4.155 4.91 +130 143 1.385 4.91 +130 179 3.88 4.91 +151 179 4.29 4.91 +156 140 0 4.91 +161 175 0 4.91 +194 208 4.365 4.91 +203 93 1.885 4.91 +204 23 3.775 4.91 +236 1 4.17 4.91 +239 42 4.235 4.91 +242 62 3.81 4.91 +46 47 0 4.915 +59 115 3.875 4.915 +98 238 3.16 4.915 +106 99 3.98 4.915 +112 249 4.105 4.915 +116 72 3.665 4.915 +132 151 4.15 4.915 +140 135 0 4.915 +171 205 3.58 4.915 +188 135 0 4.915 +208 16 0 4.915 +215 222 3.91 4.915 +25 153 3.815 4.92 +50 2 0 4.92 +57 201 0.2 4.92 +68 125 4.42 4.92 +140 201 0 4.92 +188 144 0 4.92 +206 45 4.405 4.92 +226 255 1.235 4.92 +227 248 4.38 4.92 +234 251 4.25 4.92 +6 121 4.4 4.925 +119 188 0 4.925 +144 159 2.29 4.925 +146 241 1.65 4.925 +192 67 1.645 4.925 +214 194 3.37 4.925 +217 194 1.425 4.925 +239 61 0 4.925 +239 27 3.74 4.925 +51 118 0 4.93 +69 241 3.635 4.93 +70 76 0 4.93 +88 99 0 4.93 +91 140 0 4.93 +94 161 4.405 4.93 +128 100 1.505 4.93 +194 220 3.73 4.93 +222 45 0 4.93 +253 60 3.27 4.93 +9 23 0 4.935 +14 6 2.565 4.935 +14 11 0 4.935 +43 60 3.405 4.935 +58 54 4.09 4.935 +130 148 1.54 4.935 +164 221 2.92 4.935 +170 127 0 4.935 +187 67 3.735 4.935 +206 212 3.485 4.935 +219 230 2 4.935 +15 93 0 4.94 +22 45 2.505 4.94 +30 99 2.495 4.94 +39 115 3.89 4.94 +67 148 3.19 4.94 +101 166 0 4.94 +103 104 0 4.94 +210 212 0 4.94 +215 23 0 4.94 +219 21 4.39 4.94 +223 2 0 4.94 +225 223 4.27 4.94 +235 29 0 4.94 +29 154 3.385 4.945 +54 166 1.9 4.945 +63 75 2.865 4.945 +69 245 3.995 4.945 +89 124 1.73 4.945 +132 2 4.37 4.945 +152 209 0 4.945 +162 67 4.245 4.945 +173 39 4.375 4.945 +201 14 2.23 4.945 +210 179 3.625 4.945 +232 255 1.52 4.945 +239 235 0 4.945 +29 107 4.33 4.95 +55 107 4.105 4.95 +59 123 0.755 4.95 +60 34 4.445 4.95 +113 162 0 4.95 +143 148 1.645 4.95 +150 249 3.065 4.95 +159 4 3.37 4.95 +211 219 4.385 4.95 +110 177 4.31 4.955 +119 186 4.445 4.955 +121 52 4.37 4.955 +126 91 2.36 4.955 +128 180 4.445 4.955 +163 248 4.365 4.955 +208 28 4.01 4.955 +219 154 4.44 4.955 +8 92 4.285 4.96 +46 125 2.485 4.96 +56 34 0 4.96 +67 144 3.715 4.96 +68 99 3.95 4.96 +98 241 2.59 4.96 +107 117 4.02 4.96 +115 137 2.06 4.96 +171 48 4.19 4.96 +208 90 3.91 4.96 +239 125 2.56 4.96 +243 246 0 4.96 +24 255 4.2 4.965 +40 112 3.32 4.965 +82 104 3 4.965 +96 187 3.665 4.965 +108 184 3.36 4.965 +128 170 0 4.965 +149 132 0.915 4.965 +164 241 4.225 4.965 +199 59 0.76 4.965 +217 200 4.075 4.965 +40 249 4.04 4.97 +140 204 0 4.97 +164 240 3.57 4.97 +171 252 2.74 4.97 +215 171 4.43 4.97 +232 35 4.04 4.97 +234 247 0 4.97 +237 26 4.425 4.97 +254 256 0 4.97 +25 70 0 4.975 +56 209 4.355 4.975 +83 132 1.02 4.975 +129 255 1.71 4.975 +132 152 0 4.975 +132 216 4.25 4.975 +140 179 3.14 4.975 +174 180 2.195 4.975 +205 1 3.865 4.975 +216 33 4.425 4.975 +226 205 3.99 4.975 +244 120 3.64 4.975 +62 1 4.08 4.98 +128 96 4.35 4.98 +143 147 2.82 4.98 +187 184 2.48 4.98 +199 25 2.225 4.98 +21 55 3.735 4.985 +59 119 0.655 4.985 +71 151 1.04 4.985 +123 135 3.86 4.985 +147 211 0 4.985 +163 227 4.325 4.985 +204 45 4.395 4.985 +209 22 4.435 4.985 +212 81 1.115 4.985 +213 195 4.455 4.985 +215 221 3.62 4.985 +7 121 1.435 4.99 +10 124 3.72 4.99 +31 27 0 4.99 +78 96 4.14 4.99 +87 146 4.045 4.99 +101 115 3.9 4.99 +174 176 0 4.99 +183 139 0 4.99 +192 252 4.145 4.99 +194 70 3.91 4.99 +209 194 3.675 4.99 +209 70 4.435 4.99 +210 220 4.37 4.99 +239 253 0 4.99 +23 208 4.21 4.995 +30 255 3.88 4.995 +31 28 2.215 4.995 +42 39 2.19 4.995 +65 134 4.395 4.995 +104 238 3.9 4.995 +138 188 3.86 4.995 +174 188 0.71 4.995 +203 16 4.45 4.995 +65 70 4.49 5 +80 161 4.445 5 +75 117 4.385 5 +190 162 3.75 5 +202 224 0 5 +164 180 0 5 +234 58 2.415 5 +196 51 4.145 5 +9 221 3.92 5 +221 45 0 5 diff --git a/examples/tracker/in.track b/examples/tracker/in.track new file mode 100644 index 0000000000..01da9933be --- /dev/null +++ b/examples/tracker/in.track @@ -0,0 +1,34 @@ +# 3d Lennard-Jones melt with tracking + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 4 0 4 0 4 +create_box 2 box +create_atoms 2 box +mass 1 1.0 +mass 2 1.0 +velocity all create 2.0 87287 loop geom + +pair_style hybrid/overlay lj/cut 2.5 tracker +pair_coeff * * lj/cut 1.0 1.0 2.5 +pair_coeff * * tracker 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve +fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5 +fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat + +dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4] +dump_modify 1 header no + +# compute 1 all property/local patom1 patom2 +# dump 2 all local 1 pairs.dat c_1[1] c_1[2] + +# dump 3 all atom 1 atoms.dat + +thermo 50 +run 1000 #0 diff --git a/examples/tracker/lifetime_hist.dat b/examples/tracker/lifetime_hist.dat new file mode 100644 index 0000000000..002e269896 --- /dev/null +++ b/examples/tracker/lifetime_hist.dat @@ -0,0 +1,65 @@ +# Histogrammed data for fix 3 +# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value +# Bin Coord Count Count/Total +0 30 0 0 1e+20 -1e+20 +1 0.1 0 0 +2 0.3 0 0 +3 0.5 0 0 +4 0.7 0 0 +5 0.9 0 0 +6 1.1 0 0 +7 1.3 0 0 +8 1.5 0 0 +9 1.7 0 0 +10 1.9 0 0 +11 2.1 0 0 +12 2.3 0 0 +13 2.5 0 0 +14 2.7 0 0 +15 2.9 0 0 +16 3.1 0 0 +17 3.3 0 0 +18 3.5 0 0 +19 3.7 0 0 +20 3.9 0 0 +21 4.1 0 0 +22 4.3 0 0 +23 4.5 0 0 +24 4.7 0 0 +25 4.9 0 0 +26 5.1 0 0 +27 5.3 0 0 +28 5.5 0 0 +29 5.7 0 0 +30 5.9 0 0 +1000 30 8122 0 0.5 5 +1 0.1 0 0 +2 0.3 0 0 +3 0.5 910 0.112041 +4 0.7 1253 0.154272 +5 0.9 953 0.117336 +6 1.1 747 0.0919724 +7 1.3 559 0.0688254 +8 1.5 501 0.0616843 +9 1.7 421 0.0518345 +10 1.9 356 0.0438316 +11 2.1 300 0.0369367 +12 2.3 281 0.0345974 +13 2.5 242 0.0297956 +14 2.7 226 0.0278257 +15 2.9 175 0.0215464 +16 3.1 168 0.0206846 +17 3.3 162 0.0199458 +18 3.5 129 0.0158828 +19 3.7 151 0.0185915 +20 3.9 137 0.0168678 +21 4.1 98 0.012066 +22 4.3 104 0.0128047 +23 4.5 83 0.0102192 +24 4.7 77 0.00948042 +25 4.9 86 0.0105885 +26 5.1 3 0.000369367 +27 5.3 0 0 +28 5.5 0 0 +29 5.7 0 0 +30 5.9 0 0 diff --git a/examples/tracker/log.8Apr21.tracker.g++.1 b/examples/tracker/log.8Apr21.tracker.g++.1 new file mode 100644 index 0000000000..e654558061 --- /dev/null +++ b/examples/tracker/log.8Apr21.tracker.g++.1 @@ -0,0 +1,107 @@ +LAMMPS (8 Apr 2021) +# 3d Lennard-Jones melt with tracking + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848) + 1 by 1 by 1 MPI processor grid +create_atoms 2 box +Created 256 atoms + create_atoms CPU = 0.001 seconds +mass 1 1.0 +mass 2 1.0 +velocity all create 2.0 87287 loop geom + +pair_style hybrid/overlay lj/cut 2.5 tracker +pair_coeff * * lj/cut 1.0 1.0 2.5 +pair_coeff * * tracker 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve +fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5 +fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat + +dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4] +dump_modify 1 header no + +# compute 1 all property/local patom1 patom2 +# dump 2 all local 1 pairs.dat c_1[1] c_1[2] + +# dump 3 all atom 1 atoms.dat + +thermo 50 +run 1000 #0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) pair tracker, perpetual + attributes: half, newton on, history + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 2 -6.7733681 0 -3.7850868 -4.5535126 + 50 1.0540428 -5.3670859 0 -3.7921977 2.3386375 + 100 1.0402713 -5.3493439 0 -3.7950323 2.4553748 + 150 1.0570745 -5.3738961 0 -3.7944781 2.3767396 + 200 1.0431846 -5.3518647 0 -3.7932002 2.5010135 + 250 1.070121 -5.3902744 0 -3.791363 2.4908658 + 300 1.0667723 -5.3866302 0 -3.7927224 2.3589344 + 350 1.000601 -5.2859643 0 -3.7909257 2.9065274 + 400 0.99256113 -5.2738812 0 -3.7908553 2.8595867 + 450 1.0482542 -5.357452 0 -3.7912128 2.4707397 + 500 1.0196176 -5.3123538 0 -3.7889017 2.7230338 + 550 0.98274535 -5.2586303 0 -3.7902706 2.9156947 + 600 1.0683914 -5.3863229 0 -3.789996 2.3002719 + 650 1.0130779 -5.303917 0 -3.7902362 2.8726423 + 700 1.0583333 -5.3737358 0 -3.792437 2.5770307 + 750 0.98274506 -5.2612464 0 -3.792887 2.9447027 + 800 1.0294191 -5.332001 0 -3.7939042 2.5293193 + 850 0.99240027 -5.2735754 0 -3.7907899 2.7672711 + 900 1.0293488 -5.3306241 0 -3.7926323 2.6054041 + 950 0.97137182 -5.2424403 0 -3.7910742 3.129989 + 1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598 +Loop time of 0.310363 on 1 procs for 1000 steps with 256 atoms + +Performance: 1391918.252 tau/day, 3222.033 timesteps/s +100.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.22132 | 0.22132 | 0.22132 | 0.0 | 71.31 +Neigh | 0.03458 | 0.03458 | 0.03458 | 0.0 | 11.14 +Comm | 0.0087938 | 0.0087938 | 0.0087938 | 0.0 | 2.83 +Output | 0.014075 | 0.014075 | 0.014075 | 0.0 | 4.54 +Modify | 0.02818 | 0.02818 | 0.02818 | 0.0 | 9.08 +Other | | 0.003411 | | | 1.10 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1327.00 ave 1327 max 1327 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9612.00 ave 9612 max 9612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9612 +Ave neighs/atom = 37.546875 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/tracker/reference/contact_history.dat b/examples/tracker/reference/contact_history.dat new file mode 100644 index 0000000000..8ae3885e5c --- /dev/null +++ b/examples/tracker/reference/contact_history.dat @@ -0,0 +1,8122 @@ +16 36 0 0.5 +64 193 0 0.505 +175 194 0 0.505 +63 80 0 0.51 +31 50 0 0.51 +12 188 0 0.515 +18 135 0 0.515 +22 166 0 0.515 +82 70 0 0.515 +61 26 0 0.525 +90 80 0 0.525 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4 +75 110 2.91 4.005 +197 120 3.215 4.005 +220 247 2.38 4.01 +226 207 0 4.01 +157 244 2.205 4.015 +215 235 2.16 4.015 +240 29 2.82 4.015 +238 239 0 4.02 +111 97 0 4.025 +158 138 0.175 4.03 +157 138 3.425 4.035 +229 140 2.955 4.035 +256 108 3.45 4.04 +248 132 1.54 4.04 +200 236 0.715 4.04 +240 26 2.48 4.04 +215 231 2.91 4.045 +215 247 0 4.05 +235 138 0 4.05 +103 183 1.785 4.055 +254 146 1.865 4.06 +229 24 1.65 4.06 +203 215 1.37 4.065 +103 130 2.605 4.065 +226 120 2.54 4.07 +226 247 1.17 4.07 +47 210 0 4.07 +234 140 3.445 4.075 +238 116 1.45 4.075 +238 243 3.485 4.075 +250 153 3.065 4.085 +248 184 1.53 4.09 +253 27 3.39 4.09 +111 146 0.655 4.09 +144 32 0 4.095 +200 140 3.025 4.095 +256 190 3.565 4.1 +234 107 2.705 4.1 +154 45 2.62 4.105 +203 141 3.445 4.105 +224 210 1.62 4.11 +223 141 2.76 4.115 +203 247 3.22 4.12 +47 84 3.34 4.12 +256 243 1.74 4.125 +255 14 0.66 4.125 +253 107 3.325 4.125 +195 231 2.7 4.125 +252 150 3.55 4.125 +245 134 2.66 4.125 +237 236 2.925 4.13 +238 125 2.81 4.135 +200 243 0 4.14 +230 27 2.96 4.14 +200 146 2.8 4.145 +47 66 0 4.145 +248 149 0 4.15 +154 192 2.645 4.15 +245 231 0 4.15 +253 192 3.62 4.155 +250 98 2.97 4.155 +200 134 2.995 4.16 +248 130 0 4.165 +249 231 0 4.165 +76 98 0.985 4.165 +212 142 3.655 4.17 +231 18 0 4.17 +249 232 0.83 4.17 +212 255 0 4.18 +234 251 0 4.18 +232 149 0 4.185 +236 135 3.56 4.185 +47 100 1.19 4.185 +214 80 0.6 4.19 +103 244 0.97 4.19 +204 247 0 4.195 +245 5 1.055 4.195 +235 27 2.89 4.2 +47 91 0.845 4.2 +200 26 2.66 4.205 +195 249 3.005 4.205 +242 5 0 4.205 +65 117 2.795 4.21 +242 103 3.315 4.21 +243 131 2.855 4.21 +245 145 2.485 4.21 +109 108 3.275 4.215 +241 243 0 4.215 +144 27 1.815 4.22 +253 105 2.35 4.22 +65 152 3.395 4.22 +235 250 0.05 4.22 +240 228 0 4.22 +242 19 3.355 4.22 +245 255 2.385 4.22 +248 182 0.8 4.225 +146 8 2.29 4.23 +248 140 0.515 4.245 +229 18 1.705 4.245 +65 83 2.86 4.25 +232 140 2.495 4.25 +214 250 3.47 4.26 +157 232 2.79 4.26 +216 98 0 4.26 +230 134 0 4.265 +248 6 2.765 4.27 +157 149 3.625 4.27 +203 214 3.1 4.27 +203 250 3.095 4.27 +240 255 0 4.27 +242 33 3.685 4.27 +236 173 3.61 4.275 +245 109 3.145 4.275 +253 29 3.48 4.28 +234 215 0 4.28 +211 232 2.235 4.29 +242 98 0 4.29 +243 143 2.83 4.29 +103 2 1.925 4.295 +133 30 3.675 4.295 +158 177 0 4.3 +103 104 0 4.3 +240 250 0 4.3 +224 65 0 4.31 +252 155 3.565 4.31 +242 127 2.56 4.31 +242 113 3.05 4.31 +243 1 0 4.31 +194 232 3.285 4.315 +226 249 3.23 4.32 +252 182 0.27 4.32 +103 99 2.23 4.32 +13 178 3.385 4.32 +232 130 0 4.325 +234 153 3.115 4.33 +242 17 1.535 4.33 +243 177 2.84 4.33 +107 16 0 4.335 +249 236 0 4.335 +197 220 2.345 4.34 +157 154 3.52 4.345 +103 23 0.14 4.345 +214 108 3.62 4.35 +253 189 3.005 4.355 +153 138 0 4.355 +208 154 3.01 4.36 +248 7 2.63 4.365 +146 6 0.625 4.365 +252 139 3.605 4.365 +232 244 0.76 4.365 +250 255 0 4.37 +252 186 3.655 4.37 +234 156 3.5 4.37 +229 134 0 4.37 +76 96 3.84 4.37 +254 149 2.87 4.38 +253 153 3.1 4.38 +223 239 0 4.38 +223 255 3.55 4.39 +103 22 3.635 4.39 +229 243 1.91 4.39 +254 231 3.07 4.395 +214 121 1.405 4.395 +219 71 3.86 4.395 +252 151 3.595 4.395 +144 62 1.065 4.4 +208 141 3.41 4.4 +194 229 3.165 4.4 +69 121 2.955 4.4 +248 17 2.955 4.405 +109 149 3.785 4.41 +252 138 0 4.41 +245 103 0 4.41 +76 119 0 4.41 +153 160 2.47 4.41 +194 228 3.265 4.415 +195 212 1.845 4.42 +231 132 2.66 4.42 +208 255 1.95 4.425 +65 80 3.92 4.425 +158 62 3.385 4.435 +146 23 2.21 4.435 +144 192 0.655 4.44 +223 256 3.92 4.445 +105 160 3.765 4.445 +35 106 3.935 4.445 +154 112 3.845 4.45 +256 189 3.895 4.455 +154 123 3.46 4.455 +67 121 2.345 4.455 +245 229 0 4.455 +231 152 3.715 4.46 +221 250 0.33 4.46 +35 113 3.445 4.46 +69 68 3.78 4.465 +13 17 0.585 4.465 +146 19 3.84 4.47 +240 124 2.735 4.475 +146 22 3.83 4.485 +109 9 3.205 4.49 +241 107 3.985 4.49 +247 28 3.875 4.49 +221 244 2.185 4.495 +235 153 3.11 4.495 +240 247 3.7 4.495 +199 231 0 4.5 +154 110 3.74 4.5 +250 251 0 4.5 +144 145 0.63 4.505 +208 236 2.88 4.505 +35 114 3.15 4.51 +238 144 0.92 4.515 +248 99 3.765 4.52 +144 132 3.885 4.525 +145 20 1.4 4.525 +154 4 3.825 4.525 +157 250 0 4.525 +224 157 2.3 4.525 +238 255 0 4.525 +144 255 0.66 4.53 +208 158 2.94 4.53 +238 65 4.015 4.53 +75 109 3.28 4.535 +242 246 0 4.54 +248 5 0 4.545 +200 242 3.94 4.545 +250 46 3.97 4.545 +65 98 0 4.55 +221 232 3.19 4.555 +238 210 3.98 4.555 +248 244 0 4.56 +238 111 0.105 4.56 +111 95 3.335 4.565 +208 79 3.01 4.565 +142 132 0 4.565 +214 219 0 4.575 +238 109 3.63 4.58 +142 232 1.565 4.58 +15 123 3.995 4.58 +248 154 4.03 4.585 +47 108 3.96 4.585 +142 131 0 4.585 +224 107 0 4.59 +219 9 4.095 4.595 +221 144 3.515 4.595 +232 132 1.635 4.595 +242 211 0 4.595 +243 159 2.435 4.595 +248 147 0.82 4.6 +224 250 0 4.6 +245 244 0.61 4.6 +215 230 0 4.605 +232 147 3.77 4.605 +247 29 3.78 4.605 +221 251 3.72 4.61 +247 144 3.835 4.61 +76 117 0 4.615 +212 157 2.28 4.62 +238 242 3.685 4.62 +234 102 3.675 4.625 +103 15 4.1 4.625 +194 242 4.1 4.63 +235 156 3.805 4.63 +232 242 1.9 4.635 +197 230 0 4.64 +252 108 3.96 4.645 +241 255 0 4.645 +219 108 3.47 4.65 +249 219 3.855 4.65 +228 242 4.09 4.65 +243 184 3.92 4.655 +242 153 4.075 4.66 +215 242 4 4.665 +221 107 3.38 4.665 +246 134 1.975 4.665 +154 46 3.11 4.675 +133 2 3.335 4.675 +195 245 1.71 4.68 +220 47 3.6 4.68 +238 245 2.44 4.68 +35 107 3.725 4.68 +200 210 3.98 4.685 +208 216 3.37 4.69 +47 241 3.825 4.69 +236 13 4.165 4.7 +75 67 4.2 4.705 +195 142 3.79 4.71 +153 5 1.615 4.71 +111 255 0 4.72 +69 226 3.925 4.725 +238 204 4.075 4.725 +256 139 3.74 4.73 +109 110 0 4.73 +203 47 3.785 4.73 +226 247 4.16 4.73 +164 47 3.675 4.73 +254 143 3.6 4.735 +75 101 0.12 4.735 +75 153 3.04 4.74 +250 127 3.985 4.74 +164 220 3.52 4.745 +241 68 3.91 4.745 +47 102 3.975 4.745 +228 30 0 4.745 +109 46 3.94 4.75 +154 108 1.545 4.75 +194 69 3.86 4.75 +236 182 3.525 4.75 +35 110 3.43 4.75 +232 158 2.28 4.755 +254 159 3.345 4.76 +75 146 0.945 4.76 +224 241 3.315 4.765 +214 117 1.36 4.775 +26 57 3.715 4.78 +109 14 1.565 4.79 +142 19 3.965 4.79 +111 250 2.355 4.795 +144 140 3.97 4.8 +75 117 4.165 4.8 +203 233 0 4.805 +223 242 4.125 4.805 +234 233 0 4.805 +35 96 4.195 4.805 +245 254 0.785 4.805 +212 245 0.585 4.81 +153 11 2.19 4.81 +65 77 3.95 4.81 +145 137 3.44 4.815 +75 22 4.16 4.815 +224 77 3.985 4.815 +249 246 0 4.815 +251 52 4.16 4.815 +200 145 2.85 4.82 +154 14 1.535 4.82 +221 158 2.25 4.82 +157 15 4.16 4.83 +226 158 4.295 4.83 +245 99 3.615 4.83 +249 164 3.975 4.835 +200 217 4.325 4.84 +234 105 1.49 4.84 +238 248 4.145 4.84 +203 111 3.77 4.845 +203 157 3.415 4.845 +210 117 4.315 4.845 +254 30 3.8 4.85 +197 216 2.735 4.85 +238 158 0 4.855 +200 69 4.03 4.86 +214 243 4.34 4.86 +203 216 3.25 4.86 +203 230 4.22 4.86 +226 246 3.845 4.86 +164 157 2.87 4.86 +215 246 0 4.865 +220 218 3.51 4.865 +153 135 0 4.87 +249 217 4.3 4.87 +240 216 3.625 4.87 +241 79 3.885 4.87 +111 110 3.58 4.875 +208 13 3.04 4.875 +235 30 4.37 4.875 +146 127 4.29 4.88 +230 21 3.405 4.88 +254 13 0 4.885 +200 243 4.37 4.885 +129 130 4.04 4.885 +144 228 2.195 4.89 +154 155 0 4.89 +223 158 3.695 4.89 +76 121 0 4.89 +111 13 0 4.895 +153 186 3.01 4.895 +197 249 1.915 4.895 +220 105 4.115 4.9 +199 227 1.835 4.9 +244 180 3.72 4.9 +246 5 0.57 4.905 +76 110 2.975 4.905 +228 143 0 4.905 +229 235 3.88 4.905 +13 146 3.81 4.91 +13 152 4.33 4.91 +65 13 4.155 4.91 +236 1 4.17 4.91 +242 158 3.81 4.91 +107 61 1.885 4.91 +203 109 3.58 4.915 +220 71 0 4.915 +142 143 0 4.915 +76 71 0 4.915 +153 105 0.2 4.92 +146 2 0 4.92 +220 80 0 4.92 +226 255 1.235 4.92 +234 251 4.25 4.92 +76 105 0 4.92 +224 35 1.645 4.925 +253 156 3.27 4.93 +154 150 4.09 4.935 +219 35 3.735 4.935 +235 29 0 4.94 +35 84 3.19 4.94 +194 35 4.245 4.945 +232 255 1.52 4.945 +195 248 4.365 4.955 +203 144 4.19 4.96 +35 80 3.715 4.96 +243 246 0 4.96 +142 189 2.485 4.96 +152 130 0 4.96 +103 155 0.76 4.965 +254 256 0 4.97 +203 252 2.74 4.97 +232 131 4.04 4.97 +234 247 0 4.97 +76 108 0 4.97 +109 1 3.865 4.975 +65 255 1.71 4.975 +226 109 3.99 4.975 +76 211 3.14 4.975 +152 113 4.355 4.975 +244 184 3.64 4.975 +219 216 2.48 4.98 +103 25 2.225 4.98 +195 227 4.325 4.985 +215 75 0 4.99 +224 252 4.145 4.99 +107 16 4.45 4.995 +234 154 2.415 5 diff --git a/examples/tracker/reference/lifetime_hist.dat b/examples/tracker/reference/lifetime_hist.dat new file mode 100644 index 0000000000..002e269896 --- /dev/null +++ b/examples/tracker/reference/lifetime_hist.dat @@ -0,0 +1,65 @@ +# Histogrammed data for fix 3 +# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value +# Bin Coord Count Count/Total +0 30 0 0 1e+20 -1e+20 +1 0.1 0 0 +2 0.3 0 0 +3 0.5 0 0 +4 0.7 0 0 +5 0.9 0 0 +6 1.1 0 0 +7 1.3 0 0 +8 1.5 0 0 +9 1.7 0 0 +10 1.9 0 0 +11 2.1 0 0 +12 2.3 0 0 +13 2.5 0 0 +14 2.7 0 0 +15 2.9 0 0 +16 3.1 0 0 +17 3.3 0 0 +18 3.5 0 0 +19 3.7 0 0 +20 3.9 0 0 +21 4.1 0 0 +22 4.3 0 0 +23 4.5 0 0 +24 4.7 0 0 +25 4.9 0 0 +26 5.1 0 0 +27 5.3 0 0 +28 5.5 0 0 +29 5.7 0 0 +30 5.9 0 0 +1000 30 8122 0 0.5 5 +1 0.1 0 0 +2 0.3 0 0 +3 0.5 910 0.112041 +4 0.7 1253 0.154272 +5 0.9 953 0.117336 +6 1.1 747 0.0919724 +7 1.3 559 0.0688254 +8 1.5 501 0.0616843 +9 1.7 421 0.0518345 +10 1.9 356 0.0438316 +11 2.1 300 0.0369367 +12 2.3 281 0.0345974 +13 2.5 242 0.0297956 +14 2.7 226 0.0278257 +15 2.9 175 0.0215464 +16 3.1 168 0.0206846 +17 3.3 162 0.0199458 +18 3.5 129 0.0158828 +19 3.7 151 0.0185915 +20 3.9 137 0.0168678 +21 4.1 98 0.012066 +22 4.3 104 0.0128047 +23 4.5 83 0.0102192 +24 4.7 77 0.00948042 +25 4.9 86 0.0105885 +26 5.1 3 0.000369367 +27 5.3 0 0 +28 5.5 0 0 +29 5.7 0 0 +30 5.9 0 0 diff --git a/fortran/lammps.f90 b/fortran/lammps.f90 index 21909e1288..2e78cdd00b 100644 --- a/fortran/lammps.f90 +++ b/fortran/lammps.f90 @@ -76,17 +76,15 @@ MODULE LIBLAMMPS TYPE(c_ptr), VALUE :: handle END SUBROUTINE lammps_close - SUBROUTINE lammps_mpi_init(handle) BIND(C, name='lammps_mpi_init') - IMPORT :: c_ptr - TYPE(c_ptr), VALUE :: handle + SUBROUTINE lammps_mpi_init() BIND(C, name='lammps_mpi_init') END SUBROUTINE lammps_mpi_init - SUBROUTINE lammps_mpi_finalize(handle) & - BIND(C, name='lammps_mpi_finalize') - IMPORT :: c_ptr - TYPE(c_ptr), VALUE :: handle + SUBROUTINE lammps_mpi_finalize() BIND(C, name='lammps_mpi_finalize') END SUBROUTINE lammps_mpi_finalize + SUBROUTINE lammps_kokkos_finalize() BIND(C, name='lammps_kokkos_finalize') + END SUBROUTINE lammps_kokkos_finalize + SUBROUTINE lammps_file(handle,filename) BIND(C, name='lammps_file') IMPORT :: c_ptr TYPE(c_ptr), VALUE :: handle @@ -188,7 +186,8 @@ CONTAINS IF (PRESENT(finalize)) THEN IF (finalize) THEN - CALL lammps_mpi_finalize(self%handle) + CALL lammps_kokkos_finalize() + CALL lammps_mpi_finalize() END IF END IF END SUBROUTINE lmp_close diff --git a/lib/Install.py b/lib/Install.py index 284ef6888b..0a0979c2ee 100644 --- a/lib/Install.py +++ b/lib/Install.py @@ -26,7 +26,7 @@ specify -m and optionally -e, order does not matter Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src -make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ diff --git a/lib/README b/lib/README index 2b7a38f5db..75fca5c185 100644 --- a/lib/README +++ b/lib/README @@ -15,7 +15,7 @@ one of the provided Makefiles to make it suitable for your machine. The libraries in this directory are the following: -atc atomistic-to-continuum methods, USER-ATC package +atc atomistic-to-continuum methods, ATC package from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia) awpmd antisymmetrized wave packet molecular dynamics, AWPMD package from Ilya Valuev (JIHT RAS) @@ -27,17 +27,17 @@ gpu general GPU routines, GPU package from Mike Brown (ORNL) h5md ch5md library for output of MD data in HDF5 format from Pierre de Buyl (KU Leuven) -hdnnp hooks to n2p2, neural network potential package, used by USER-HDNNP +hdnnp hooks to n2p2, neural network potential package, used by ML-HDNNP from Andreas Singraber kim hooks to the KIM library, used by KIM package from Ryan Elliott and Ellad Tadmor (U Minn) kokkos Kokkos package for GPU and many-core acceleration from Kokkos development team (Sandia) -linalg set of BLAS and LAPACK routines needed by USER-ATC package +linalg set of BLAS and LAPACK routines needed by ATC package from Axel Kohlmeyer (Temple U) message client/server communication library via MPI, sockets, files from Steve Plimpton (Sandia) -molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package +molfile hooks to VMD molfile plugins, used by the MOLFILE package from Axel Kohlmeyer (Temple U) and the VMD development team mscg hooks to the MSCG library, used by fix_mscg command from Jacob Wagner and Greg Voth group (U Chicago) @@ -51,9 +51,9 @@ python hooks to the system Python library, used by the PYTHON package from the LAMMPS development team qmmm quantum mechanics/molecular mechanics coupling interface from Axel Kohlmeyer (Temple U) -quip interface to QUIP/libAtoms framework, USER-QUIP package +quip interface to QUIP/libAtoms framework, ML-QUIP package from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) -smd hooks to Eigen library, used by USER-SMD package +machdyn hooks to Eigen library, used by MACHDYN package from Georg Ganzenmueller (Ernst Mach Institute, Germany) voronoi hooks to the Voro++ library, used by compute voronoi/atom command from Daniel Schwen (LANL) diff --git a/lib/atc/Makefile.lammps.empty b/lib/atc/Makefile.lammps.empty index 49cab486a9..8624fdcadb 100644 --- a/lib/atc/Makefile.lammps.empty +++ b/lib/atc/Makefile.lammps.empty @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-atc_SYSINC = -user-atc_SYSLIB = -user-atc_SYSPATH = +atc_SYSINC = +atc_SYSLIB = +atc_SYSPATH = diff --git a/lib/atc/Makefile.lammps.installed b/lib/atc/Makefile.lammps.installed index c8cd66af26..223f41cd08 100644 --- a/lib/atc/Makefile.lammps.installed +++ b/lib/atc/Makefile.lammps.installed @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-atc_SYSINC = -user-atc_SYSLIB = -lblas -llapack -user-atc_SYSPATH = +atc_SYSINC = +atc_SYSLIB = -lblas -llapack +atc_SYSPATH = diff --git a/lib/atc/Makefile.lammps.linalg b/lib/atc/Makefile.lammps.linalg index 5d92fd8cfb..930ee6357b 100644 --- a/lib/atc/Makefile.lammps.linalg +++ b/lib/atc/Makefile.lammps.linalg @@ -1,6 +1,6 @@ # Settings that the LAMMPS build will import when this package library is used -user-atc_SYSINC = -user-atc_SYSLIB = -llinalg -lgfortran -user-atc_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) +atc_SYSINC = +atc_SYSLIB = -llinalg -lgfortran +atc_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/atc/README b/lib/atc/README index d3adfdafe4..70a83e5c8f 100644 --- a/lib/atc/README +++ b/lib/atc/README @@ -10,7 +10,7 @@ estimation and molecular dynamics-finite element coupling methods. ------------------------------------------------- This directory has source files to build a library that LAMMPS -links against when using the USER-ATC package. +links against when using the ATC package. This library must be built with a C++ compiler, before LAMMPS is built, so LAMMPS can link against it. diff --git a/lib/awpmd/Makefile.lammps.empty b/lib/awpmd/Makefile.lammps.empty index d80c517f3d..551267720e 100644 --- a/lib/awpmd/Makefile.lammps.empty +++ b/lib/awpmd/Makefile.lammps.empty @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-awpmd_SYSINC = -user-awpmd_SYSLIB = -user-awpmd_SYSPATH = +awpmd_SYSINC = +awpmd_SYSLIB = +awpmd_SYSPATH = diff --git a/lib/awpmd/Makefile.lammps.installed b/lib/awpmd/Makefile.lammps.installed index 6b089784a0..975133e429 100644 --- a/lib/awpmd/Makefile.lammps.installed +++ b/lib/awpmd/Makefile.lammps.installed @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-awpmd_SYSINC = -user-awpmd_SYSLIB = -lblas -llapack -user-awpmd_SYSPATH = +awpmd_SYSINC = +awpmd_SYSLIB = -lblas -llapack +awpmd_SYSPATH = diff --git a/lib/awpmd/Makefile.lammps.linalg b/lib/awpmd/Makefile.lammps.linalg index a30f4a821d..1d986da5d7 100644 --- a/lib/awpmd/Makefile.lammps.linalg +++ b/lib/awpmd/Makefile.lammps.linalg @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-awpmd_SYSINC = -user-awpmd_SYSLIB = -llinalg -lgfortran -user-awpmd_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) +awpmd_SYSINC = +awpmd_SYSLIB = -llinalg -lgfortran +awpmd_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/awpmd/README b/lib/awpmd/README index 20e142f74c..d829361a1b 100644 --- a/lib/awpmd/README +++ b/lib/awpmd/README @@ -14,7 +14,7 @@ of wxWidgets Library License (see license directory for details). ------------------------------------------------- This directory has source files to build a library that LAMMPS -links against when using the USER-AWPMD package. +links against when using the AWPMD package. This library must be built with a C++ compiler, before LAMMPS is built, so LAMMPS can link against it. diff --git a/lib/awpmd/ivutils/include/pairhash.h b/lib/awpmd/ivutils/include/pairhash.h index 401b7b91e3..ea598e9f4d 100644 --- a/lib/awpmd/ivutils/include/pairhash.h +++ b/lib/awpmd/ivutils/include/pairhash.h @@ -11,7 +11,7 @@ /*e**************************************************************************** * $Log: pairhash.h,v $ * Revision 1.3 2011/06/11 18:18:50 morozov - * USER-AWPMD compiles on Linux now! + * AWPMD compiles on Linux now! * * Revision 1.2 2011/06/11 16:53:55 valuev * sync with LAMMPS diff --git a/lib/colvars/Makefile.common b/lib/colvars/Makefile.common index ce501dc5f3..5743507507 100644 --- a/lib/colvars/Makefile.common +++ b/lib/colvars/Makefile.common @@ -30,6 +30,7 @@ COLVARS_SRCS = \ colvarbias_histogram.cpp \ colvarbias_meta.cpp \ colvarbias_restraint.cpp \ + colvarcomp_alchlambda.cpp \ colvarcomp_angles.cpp \ colvarcomp_apath.cpp \ colvarcomp_coordnums.cpp \ diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps index 78e8768edd..cdf948a471 100644 --- a/lib/colvars/Makefile.deps +++ b/lib/colvars/Makefile.deps @@ -86,6 +86,20 @@ $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h +$(COLVARS_OBJ_DIR)colvarcomp_alchlambda.o: colvarcomp_alchlambda.cpp \ + colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \ + colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ + lepton/include/lepton/ExpressionTreeNode.h \ + lepton/include/lepton/windowsIncludes.h \ + lepton/include/lepton/CustomFunction.h \ + lepton/include/lepton/ExpressionProgram.h \ + lepton/include/lepton/ExpressionTreeNode.h \ + lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ + lepton/include/lepton/Exception.h \ + lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ + colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \ colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \ colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \ @@ -285,7 +299,7 @@ $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarscript_commands.h colvarscript_commands_colvar.h \ - colvarscript_commands_bias.h colvaratoms.h + colvarscript_commands_bias.h colvaratoms.h colvarmodule_utils.h $(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h @@ -294,7 +308,8 @@ $(COLVARS_OBJ_DIR)colvarproxy_tcl.o: colvarproxy_tcl.cpp colvarmodule.h \ colvarproxy_tcl.h colvarproxy_volmaps.h colvaratoms.h colvarparse.h \ colvarparams.h colvardeps.h $(COLVARS_OBJ_DIR)colvarproxy_volmaps.o: colvarproxy_volmaps.cpp \ - colvarmodule.h colvars_version.h colvarproxy_volmaps.h + colvarmodule.h colvars_version.h colvarproxy_volmaps.h \ + colvarmodule_utils.h $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \ colvarmodule.h colvars_version.h colvartypes.h colvarvalue.h \ colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \ diff --git a/lib/colvars/README b/lib/colvars/README index cd6e59511a..eeba557ce3 100644 --- a/lib/colvars/README +++ b/lib/colvars/README @@ -49,7 +49,7 @@ C++11-only features. ## How to build (CMake) This is the recommended build recipe: no additional settings are normally -needed besides "-D PKG_USER-COLVARS=yes". +needed besides "-D PKG_COLVARS=yes". Building and linking of Lepton (or other C++11-only features) is enabled automatically when compilation is carried out with C++11 support, and disabled diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index ed6fec1ac5..54e11aaa75 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -96,7 +96,7 @@ int colvar::init(std::string const &conf) "", colvarparse::parse_silent)) { enable(f_cv_scripted); - cvm::log("This colvar uses scripted function \"" + scripted_function + "\"."); + cvm::log("This colvar uses scripted function \"" + scripted_function + "\".\n"); std::string type_str; get_keyval(conf, "scriptedFunctionType", type_str, "scalar"); @@ -134,7 +134,7 @@ int colvar::init(std::string const &conf) std::sort(cvcs.begin(), cvcs.end(), compare); if(cvcs.size() > 1) { - cvm::log("Sorted list of components for this scripted colvar:"); + cvm::log("Sorted list of components for this scripted colvar:\n"); for (i = 0; i < cvcs.size(); i++) { cvm::log(cvm::to_str(i+1) + " " + cvcs[i]->name); } @@ -298,6 +298,11 @@ int colvar::init(std::string const &conf) error_code |= init_extended_Lagrangian(conf); error_code |= init_output_flags(conf); + // Detect if we have one component that is an alchemical lambda + if (is_enabled(f_cv_single_cvc) && cvcs[0]->function_type == "alch_lambda") { + enable(f_cv_external); + } + // Now that the children are defined we can solve dependencies enable(f_cv_active); @@ -636,7 +641,6 @@ int colvar::init_extended_Lagrangian(std::string const &conf) x_ext.type(colvarvalue::type_notset); v_ext.type(value()); fr.type(value()); - const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature()); if (temp <= 0.0) { if (found) @@ -654,7 +658,7 @@ int colvar::init_extended_Lagrangian(std::string const &conf) return INPUT_ERROR; } ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance); - cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " [E]/U^2"); + cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " [E]/U^2\n"); get_keyval(conf, "extendedTimeConstant", extended_period, 200.0); if (extended_period <= 0.0) { @@ -662,7 +666,7 @@ int colvar::init_extended_Lagrangian(std::string const &conf) } ext_mass = (cvm::boltzmann() * temp * extended_period * extended_period) / (4.0 * PI * PI * tolerance * tolerance); - cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " [E]/(U/fs)^2 (U: colvar unit)"); + cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " [E]/(U/fs)^2 (U: colvar unit)\n"); { bool b_output_energy; @@ -770,7 +774,9 @@ template int colvar::init_components_type(std::string c if ( (cvcp->function_type != std::string("distance_z")) && (cvcp->function_type != std::string("dihedral")) && (cvcp->function_type != std::string("polar_phi")) && - (cvcp->function_type != std::string("spin_angle")) ) { + (cvcp->function_type != std::string("spin_angle")) && + (cvcp->function_type != std::string("euler_phi")) && + (cvcp->function_type != std::string("euler_psi"))) { cvm::error("Error: invalid use of period and/or " "wrapAround in a \""+ std::string(def_config_key)+ @@ -860,6 +866,7 @@ int colvar::init_components(std::string const &conf) "inertia", "inertia"); error_code |= init_components_type(conf, "moment of inertia around an axis", "inertiaZ"); error_code |= init_components_type(conf, "eigenvector", "eigenvector"); + error_code |= init_components_type(conf, "alchemical coupling parameter", "alchLambda"); error_code |= init_components_type(conf, "geometrical path collective variables (s)", "gspath"); error_code |= init_components_type(conf, "geometrical path collective variables (z)", "gzpath"); error_code |= init_components_type(conf, "linear combination of other collective variables", "linearCombination"); @@ -867,6 +874,9 @@ int colvar::init_components(std::string const &conf) error_code |= init_components_type(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV"); error_code |= init_components_type(conf, "arithmetic path collective variables (s) for other CVs", "aspathCV"); error_code |= init_components_type(conf, "arithmetic path collective variables (s) for other CVs", "azpathCV"); + error_code |= init_components_type(conf, "euler phi angle of the optimal orientation", "eulerPhi"); + error_code |= init_components_type(conf, "euler psi angle of the optimal orientation", "eulerPsi"); + error_code |= init_components_type(conf, "euler theta angle of the optimal orientation", "eulerTheta"); error_code |= init_components_type(conf, "total value of atomic map", "mapTotal"); @@ -1074,6 +1084,7 @@ int colvar::init_dependencies() { init_feature(f_cv_hide_Jacobian, "hide_Jacobian_force", f_type_user); require_feature_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated + exclude_feature_self(f_cv_hide_Jacobian, f_cv_extended_Lagrangian); init_feature(f_cv_extended_Lagrangian, "extended_Lagrangian", f_type_user); require_feature_self(f_cv_extended_Lagrangian, f_cv_scalar); @@ -1082,6 +1093,9 @@ int colvar::init_dependencies() { init_feature(f_cv_Langevin, "Langevin_dynamics", f_type_user); require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian); + init_feature(f_cv_external, "external", f_type_user); + require_feature_self(f_cv_external, f_cv_single_cvc); + init_feature(f_cv_single_cvc, "single_component", f_type_static); init_feature(f_cv_linear, "linear", f_type_static); @@ -1195,6 +1209,21 @@ std::vector > colvar::get_atom_lists() } +std::vector const &colvar::get_volmap_ids() +{ + volmap_ids_.resize(cvcs.size()); + for (size_t i = 0; i < cvcs.size(); i++) { + if (cvcs[i]->param_exists("mapID") == COLVARS_OK) { + volmap_ids_[i] = + *(reinterpret_cast(cvcs[i]->get_param_ptr("mapID"))); + } else { + volmap_ids_[i] = -1; + } + } + return volmap_ids_; +} + + colvar::~colvar() { // There is no need to call free_children_deps() here @@ -1552,9 +1581,11 @@ int colvar::collect_cvc_total_forces() } } - if (!is_enabled(f_cv_hide_Jacobian)) { + if (!(is_enabled(f_cv_hide_Jacobian) && is_enabled(f_cv_subtract_applied_force))) { // add the Jacobian force to the total force, and don't apply any silent // correction internally: biases such as colvarbias_abf will handle it + // If f_cv_hide_Jacobian is enabled, a force of -fj is present in ft due to the + // Jacobian-compensating force ft += fj; } } @@ -1687,14 +1718,16 @@ cvm::real colvar::update_forces_energy() // add the biases' force, which at this point should already have // been summed over each bias using this colvar + // fb is already multiplied by the relevant time step factor for each bias f += fb; if (is_enabled(f_cv_Jacobian)) { // the instantaneous Jacobian force was not included in the reported total force; // instead, it is subtracted from the applied force (silent Jacobian correction) // This requires the Jacobian term for the *current* timestep + // Need to scale it for impulse MTS if (is_enabled(f_cv_hide_Jacobian)) - f -= fj; + f -= fj * cvm::real(time_step_factor); } // At this point f is the force f from external biases that will be applied to the @@ -1727,26 +1760,44 @@ cvm::real colvar::update_forces_energy() colvarvalue f_ext(fr.type()); // force acting on the extended variable f_ext.reset(); - // the total force is applied to the fictitious mass, while the - // atoms only feel the harmonic force + wall force - // fr: bias force on extended variable (without harmonic spring), for output in trajectory - // f_ext: total force on extended variable (including harmonic spring) - // f: - initially, external biasing force - // - after this code block, colvar force to be applied to atomic coordinates - // ie. spring force (fb_actual will be added just below) + if (is_enabled(f_cv_external)) { + // There are no forces on the "actual colvar" bc there is no gradient wrt atomic coordinates + // So we apply this to the extended DOF + f += fb_actual; + } + fr = f; // External force has been scaled for a 1-timestep impulse, scale it back because we will // integrate it with the colvar's own timestep factor f_ext = f / cvm::real(time_step_factor); - f_ext += (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x); - f = (-0.5 * ext_force_k) * this->dist2_rgrad(x_ext, x); - // Coupling force is a slow force, to be applied to atomic coords impulse-style - f *= cvm::real(time_step_factor); + + colvarvalue f_system(fr.type()); // force exterted by the system on the extended DOF + + if (is_enabled(f_cv_external)) { + // Add "alchemical" force from external variable + f_system = cvcs[0]->total_force(); + // f is now irrelevant because we are not applying atomic forces in the simulation + // just driving the external variable lambda + } else { + // the total force is applied to the fictitious mass, while the + // atoms only feel the harmonic force + wall force + // fr: bias force on extended variable (without harmonic spring), for output in trajectory + // f_ext: total force on extended variable (including harmonic spring) + // f: - initially, external biasing force + // - after this code block, colvar force to be applied to atomic coordinates + // ie. spring force (fb_actual will be added just below) + f_system = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x); + f = -1.0 * f_system; + // Coupling force is a slow force, to be applied to atomic coords impulse-style + // over a single MD timestep + f *= cvm::real(time_step_factor); + } + f_ext += f_system; if (is_enabled(f_cv_subtract_applied_force)) { // Report a "system" force without the biases on this colvar - // that is, just the spring force - ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x); + // that is, just the spring force (or alchemical force) + ft_reported = f_system; } else { // The total force acting on the extended variable is f_ext // This will be used in the next timestep @@ -1778,10 +1829,19 @@ cvm::real colvar::update_forces_energy() (is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) { x_ext -= 2.0 * delta; v_ext *= -1.0; + if ((is_enabled(f_cv_reflecting_lower_boundary) && (delta = x_ext - lower_boundary) < 0) || + (is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) { + cvm::error("Error: extended coordinate value " + cvm::to_str(x_ext) + " is still outside boundaries after reflection.\n"); + } } x_ext.apply_constraints(); this->wrap(x_ext); + if (is_enabled(f_cv_external)) { + // Colvar value is constrained to the extended value + x = x_ext; + cvcs[0]->set_value(x_ext); + } } else { // If this is a postprocessing run (eg. in VMD), the extended DOF // is equal to the actual coordinate @@ -1789,9 +1849,11 @@ cvm::real colvar::update_forces_energy() } } - // Now adding the force on the actual colvar (for those biases that - // bypass the extended Lagrangian mass) - f += fb_actual; + if (!is_enabled(f_cv_external)) { + // Now adding the force on the actual colvar (for those biases that + // bypass the extended Lagrangian mass) + f += fb_actual; + } if (cvm::debug()) cvm::log("Done updating colvar \""+this->name+"\".\n"); @@ -1954,7 +2016,7 @@ int colvar::update_cvc_flags() int colvar::update_cvc_config(std::vector const &confs) { - cvm::log("Updating configuration for colvar \""+name+"\""); + cvm::log("Updating configuration for colvar \""+name+"\"\n"); if (confs.size() != cvcs.size()) { return cvm::error("Error: Wrong number of CVC config strings. " @@ -2076,6 +2138,15 @@ bool colvar::periodic_boundaries() const cvm::real colvar::dist2(colvarvalue const &x1, colvarvalue const &x2) const { + if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { + if (is_enabled(f_cv_periodic) && is_enabled(f_cv_scalar)) { + cvm::real diff = x1.real_value - x2.real_value; + const cvm::real period_lower_boundary = wrap_center - period / 2.0; + const cvm::real period_upper_boundary = wrap_center + period / 2.0; + diff = (diff < period_lower_boundary ? diff + period : ( diff > period_upper_boundary ? diff - period : diff)); + return diff * diff; + } + } if (is_enabled(f_cv_homogeneous)) { return (cvcs[0])->dist2(x1, x2); } else { @@ -2086,6 +2157,15 @@ cvm::real colvar::dist2(colvarvalue const &x1, colvarvalue colvar::dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const { + if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { + if (is_enabled(f_cv_periodic) && is_enabled(f_cv_scalar)) { + cvm::real diff = x1.real_value - x2.real_value; + const cvm::real period_lower_boundary = wrap_center - period / 2.0; + const cvm::real period_upper_boundary = wrap_center + period / 2.0; + diff = (diff < period_lower_boundary ? diff + period : ( diff > period_upper_boundary ? diff - period : diff)); + return 2.0 * diff; + } + } if (is_enabled(f_cv_homogeneous)) { return (cvcs[0])->dist2_lgrad(x1, x2); } else { @@ -2096,6 +2176,15 @@ colvarvalue colvar::dist2_lgrad(colvarvalue const &x1, colvarvalue colvar::dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const { + if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { + if (is_enabled(f_cv_periodic) && is_enabled(f_cv_scalar)) { + cvm::real diff = x1.real_value - x2.real_value; + const cvm::real period_lower_boundary = wrap_center - period / 2.0; + const cvm::real period_upper_boundary = wrap_center + period / 2.0; + diff = (diff < period_lower_boundary ? diff + period : ( diff > period_upper_boundary ? diff - period : diff)); + return (-2.0) * diff; + } + } if (is_enabled(f_cv_homogeneous)) { return (cvcs[0])->dist2_rgrad(x1, x2); } else { @@ -2302,7 +2391,7 @@ std::ostream & colvar::write_traj_label(std::ostream & os) os << " " << cvm::wrap_string(this->name, this_cv_width); - if (is_enabled(f_cv_extended_Lagrangian)) { + if (is_enabled(f_cv_extended_Lagrangian) && !is_enabled(f_cv_external)) { // extended DOF os << " r_" << cvm::wrap_string(this->name, this_cv_width-2); @@ -2314,7 +2403,7 @@ std::ostream & colvar::write_traj_label(std::ostream & os) os << " v_" << cvm::wrap_string(this->name, this_cv_width-2); - if (is_enabled(f_cv_extended_Lagrangian)) { + if (is_enabled(f_cv_extended_Lagrangian) && !is_enabled(f_cv_external)) { // extended DOF os << " vr_" << cvm::wrap_string(this->name, this_cv_width-3); @@ -2347,7 +2436,7 @@ std::ostream & colvar::write_traj(std::ostream &os) os << " "; if (is_enabled(f_cv_output_value)) { - if (is_enabled(f_cv_extended_Lagrangian)) { + if (is_enabled(f_cv_extended_Lagrangian) && !is_enabled(f_cv_external)) { os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << x; @@ -2360,7 +2449,7 @@ std::ostream & colvar::write_traj(std::ostream &os) if (is_enabled(f_cv_output_velocity)) { - if (is_enabled(f_cv_extended_Lagrangian)) { + if (is_enabled(f_cv_extended_Lagrangian) && !is_enabled(f_cv_external)) { os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << v_fdiff; diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 5cf0077a39..2856170727 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -192,7 +192,7 @@ protected: /// Amplitude of Gaussian white noise for Langevin extended dynamics cvm::real ext_sigma; - /// \brief Harmonic restraint force + /// \brief Applied force on extended DOF, for output (unscaled if using MTS) colvarvalue fr; /// \brief Jacobian force, when Jacobian_force is enabled @@ -591,6 +591,7 @@ public: class alpha_dihedrals; class alpha_angles; class dihedPC; + class alch_lambda; class componentDisabled; class CartesianBasedPath; class gspath; @@ -601,6 +602,9 @@ public: class gzpathCV; class aspathCV; class azpathCV; + class euler_phi; + class euler_psi; + class euler_theta; // non-scalar components class distance_vec; @@ -658,6 +662,9 @@ protected: static std::map> global_cvc_map; #endif + /// Volmap numeric IDs, one for each CVC (-1 if not available) + std::vector volmap_ids_; + public: /// \brief Sorted array of (zero-based) IDs for all atoms involved @@ -670,6 +677,10 @@ public: /// \brief Get vector of vectors of atom IDs for all atom groups virtual std::vector > get_atom_lists(); + + /// Volmap numeric IDs, one for each CVC (-1 if not available) + std::vector const &get_volmap_ids(); + }; diff --git a/lib/colvars/colvar_arithmeticpath.h b/lib/colvars/colvar_arithmeticpath.h index 552edf23e3..cf613af389 100644 --- a/lib/colvars/colvar_arithmeticpath.h +++ b/lib/colvars/colvar_arithmeticpath.h @@ -7,6 +7,7 @@ #include #include #include +#include namespace ArithmeticPathCV { @@ -24,6 +25,7 @@ public: virtual void computeValue(); virtual void computeDerivatives(); virtual void compute(); + virtual void reComputeLambda(const vector& rmsd_between_refs); protected: scalar_type lambda; vector weights; @@ -124,6 +126,16 @@ void ArithmeticPathBase::computeDerivative } } +template +void ArithmeticPathBase::reComputeLambda(const vector& rmsd_between_refs) { + scalar_type mean_square_displacements = 0.0; + for (size_t i_frame = 1; i_frame < total_frames; ++i_frame) { + cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n")); + mean_square_displacements += rmsd_between_refs[i_frame - 1] * rmsd_between_refs[i_frame - 1]; + } + mean_square_displacements /= scalar_type(total_frames - 1); + lambda = 1.0 / mean_square_displacements; +} } #endif // ARITHMETICPATHCV_H diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index 1a4280a202..9bbd91cf05 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -37,6 +37,7 @@ cvm::atom::atom(int atom_number) } id = p->get_atom_id(index); update_mass(); + update_charge(); reset_data(); } @@ -53,6 +54,7 @@ cvm::atom::atom(cvm::residue_id const &residue, } id = p->get_atom_id(index); update_mass(); + update_charge(); reset_data(); } @@ -62,6 +64,7 @@ cvm::atom::atom(atom const &a) { id = (cvm::proxy)->get_atom_id(index); update_mass(); + update_charge(); reset_data(); } @@ -214,8 +217,6 @@ int cvm::atom_group::init() index = -1; b_dummy = false; - b_center = false; - b_rotate = false; b_user_defined_fit = false; fitting_group = NULL; @@ -240,8 +241,9 @@ int cvm::atom_group::init_dependencies() { } init_feature(f_ag_active, "active", f_type_dynamic); - init_feature(f_ag_center, "translational_fit", f_type_static); - init_feature(f_ag_rotate, "rotational_fit", f_type_static); + init_feature(f_ag_center, "center_to_reference", f_type_user); + init_feature(f_ag_center_origin, "center_to_origin", f_type_user); + init_feature(f_ag_rotate, "rotate_to_origin", f_type_user); init_feature(f_ag_fitting_group, "fitting_group", f_type_static); init_feature(f_ag_explicit_gradient, "explicit_atom_gradient", f_type_dynamic); init_feature(f_ag_fit_gradients, "fit_gradients", f_type_user); @@ -272,6 +274,10 @@ int cvm::atom_group::init_dependencies() { // Features that are implemented (or not) by all atom groups feature_states[f_ag_active].available = true; + feature_states[f_ag_center].available = true; + feature_states[f_ag_center_origin].available = true; + feature_states[f_ag_rotate].available = true; + // f_ag_scalable_com is provided by the CVC iff it is COM-based feature_states[f_ag_scalable_com].available = false; // TODO make f_ag_scalable depend on f_ag_scalable_com (or something else) @@ -317,6 +323,9 @@ void cvm::atom_group::update_total_mass() total_mass += ai->mass; } } + if (total_mass < 1e-15) { + cvm::error("ERROR: " + description + " has zero total mass.\n"); + } } @@ -381,12 +390,22 @@ int cvm::atom_group::parse(std::string const &group_conf) // We need to know about fitting to decide whether the group is scalable // and we need to know about scalability before adding atoms - bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false); - bool b_defined_rotate = get_keyval(group_conf, "rotateReference", b_rotate, false); + bool b_defined_center = get_keyval_feature(this, group_conf, "centerToOrigin", f_ag_center_origin, false); + // Legacy alias + b_defined_center |= get_keyval_feature(this, group_conf, "centerReference", f_ag_center, is_enabled(f_ag_center_origin), parse_deprecated); + b_defined_center |= get_keyval_feature(this, group_conf, "centerToReference", f_ag_center, is_enabled(f_ag_center)); + + if (is_enabled(f_ag_center_origin) && ! is_enabled(f_ag_center)) { + return cvm::error("centerToReference may not be disabled if centerToOrigin is enabled.\n"); + } + // Legacy alias + bool b_defined_rotate = get_keyval_feature(this, group_conf, "rotateReference", f_ag_rotate, false, parse_deprecated); + b_defined_rotate |= get_keyval_feature(this, group_conf, "rotateToReference", f_ag_rotate, is_enabled(f_ag_rotate)); + // is the user setting explicit options? b_user_defined_fit = b_defined_center || b_defined_rotate; - if (is_available(f_ag_scalable_com) && !b_rotate && !b_center) { + if (is_available(f_ag_scalable_com) && !is_enabled(f_ag_rotate) && !is_enabled(f_ag_center)) { enable(f_ag_scalable_com); enable(f_ag_scalable); } @@ -507,12 +526,8 @@ int cvm::atom_group::parse(std::string const &group_conf) // whether these atoms will ever receive forces or not bool enable_forces = true; - // disableForces is deprecated - if (get_keyval(group_conf, "enableForces", enable_forces, true)) { - noforce = !enable_forces; - } else { - get_keyval(group_conf, "disableForces", noforce, false, colvarparse::parse_silent); - } + get_keyval(group_conf, "enableForces", enable_forces, true, colvarparse::parse_silent); + noforce = !enable_forces; } // Now that atoms are defined we can parse the detailed fitting options @@ -760,10 +775,10 @@ std::string const cvm::atom_group::print_atom_ids() const int cvm::atom_group::parse_fitting_options(std::string const &group_conf) { - if (b_center || b_rotate) { + if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) { if (b_dummy) - cvm::error("Error: centerReference or rotateReference " + cvm::error("Error: centerToReference or rotateToReference " "cannot be defined for a dummy atom.\n"); bool b_ref_pos_group = false; @@ -827,7 +842,7 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) if (ref_pos.size()) { - if (b_rotate) { + if (is_enabled(f_ag_rotate)) { if (ref_pos.size() != group_for_fit->size()) cvm::error("Error: the number of reference positions provided("+ cvm::to_str(ref_pos.size())+ @@ -846,7 +861,7 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) return COLVARS_ERROR; } - if (b_rotate && !noforce) { + if (is_enabled(f_ag_rotate) && !noforce) { cvm::log("Warning: atom group \""+key+ "\" will be aligned to a fixed orientation given by the reference positions provided. " "If the internal structure of the group changes too much (i.e. its RMSD is comparable " @@ -865,7 +880,7 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) bool b_fit_gradients; get_keyval(group_conf, "enableFitGradients", b_fit_gradients, true); - if (b_fit_gradients && (b_center || b_rotate)) { + if (b_fit_gradients && (is_enabled(f_ag_center) || is_enabled(f_ag_rotate))) { enable(f_ag_fit_gradients); } } @@ -879,7 +894,7 @@ void cvm::atom_group::do_feature_side_effects(int id) // If enabled features are changed upstream, the features below should be refreshed switch (id) { case f_ag_fit_gradients: - if (b_center || b_rotate) { + if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) { atom_group *group_for_fit = fitting_group ? fitting_group : this; group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::atom_pos(0.0, 0.0, 0.0)); rot.request_group1_gradients(group_for_fit->size()); @@ -971,7 +986,7 @@ int cvm::atom_group::calc_required_properties() calc_center_of_geometry(); if (!is_enabled(f_ag_scalable)) { - if (b_center || b_rotate) { + if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) { if (fitting_group) { fitting_group->calc_center_of_geometry(); } @@ -1001,7 +1016,7 @@ void cvm::atom_group::calc_apply_roto_translation() fitting_group->cog_orig = fitting_group->center_of_geometry(); } - if (b_center) { + if (is_enabled(f_ag_center)) { // center on the origin first cvm::atom_pos const rpg_cog = fitting_group ? fitting_group->center_of_geometry() : this->center_of_geometry(); @@ -1011,9 +1026,9 @@ void cvm::atom_group::calc_apply_roto_translation() } } - if (b_rotate) { - // rotate the group (around the center of geometry if b_center is - // true, around the origin otherwise) + if (is_enabled(f_ag_rotate)) { + // rotate the group (around the center of geometry if f_ag_center is + // enabled, around the origin otherwise) rot.calc_optimal_rotation(fitting_group ? fitting_group->positions() : this->positions(), @@ -1030,7 +1045,7 @@ void cvm::atom_group::calc_apply_roto_translation() } } - if (b_center) { + if (is_enabled(f_ag_center) && !is_enabled(f_ag_center_origin)) { // align with the center of geometry of ref_pos apply_translation(ref_pos_cog); if (fitting_group) { @@ -1063,7 +1078,7 @@ void cvm::atom_group::read_velocities() { if (b_dummy) return; - if (b_rotate) { + if (is_enabled(f_ag_rotate)) { for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->read_velocity(); @@ -1084,7 +1099,7 @@ void cvm::atom_group::read_total_forces() { if (b_dummy) return; - if (b_rotate) { + if (is_enabled(f_ag_rotate)) { for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->read_total_force(); @@ -1172,14 +1187,14 @@ void cvm::atom_group::calc_fit_gradients() cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - if (b_center) { + if (is_enabled(f_ag_center)) { // add the center of geometry contribution to the gradients cvm::rvector atom_grad; for (size_t i = 0; i < this->size(); i++) { atom_grad += atoms[i].grad; } - if (b_rotate) atom_grad = (rot.inverse()).rotate(atom_grad); + if (is_enabled(f_ag_rotate)) atom_grad = (rot.inverse()).rotate(atom_grad); atom_grad *= (-1.0)/(cvm::real(group_for_fit->size())); for (size_t j = 0; j < group_for_fit->size(); j++) { @@ -1187,7 +1202,7 @@ void cvm::atom_group::calc_fit_gradients() } } - if (b_rotate) { + if (is_enabled(f_ag_rotate)) { // add the rotation matrix contribution to the gradients cvm::rotation const rot_inv = rot.inverse(); @@ -1196,7 +1211,7 @@ void cvm::atom_group::calc_fit_gradients() // compute centered, unrotated position cvm::atom_pos const pos_orig = - rot_inv.rotate((b_center ? (atoms[i].pos - ref_pos_cog) : (atoms[i].pos))); + rot_inv.rotate((is_enabled(f_ag_center) ? (atoms[i].pos - ref_pos_cog) : (atoms[i].pos))); // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i cvm::quaternion const dxdq = @@ -1340,7 +1355,7 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force) return; } - if (b_rotate) { + if (is_enabled(f_ag_rotate)) { // rotate forces back to the original frame cvm::rotation const rot_inv = rot.inverse(); @@ -1355,7 +1370,7 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force) } } - if ((b_center || b_rotate) && is_enabled(f_ag_fit_gradients)) { + if ((is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) && is_enabled(f_ag_fit_gradients)) { atom_group *group_for_fit = fitting_group ? fitting_group : this; @@ -1386,7 +1401,7 @@ void cvm::atom_group::apply_force(cvm::rvector const &force) return; } - if (b_rotate) { + if (is_enabled(f_ag_rotate)) { cvm::rotation const rot_inv = rot.inverse(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index af6a529f8a..490b008d06 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -101,18 +101,14 @@ public: inline void update_mass() { colvarproxy *p = cvm::proxy; - if (p->updated_masses()) { - mass = p->get_atom_mass(index); - } + mass = p->get_atom_mass(index); } /// Get the latest value of the charge inline void update_charge() { colvarproxy *p = cvm::proxy; - if (p->updated_charges()) { - charge = p->get_atom_charge(index); - } + charge = p->get_atom_charge(index); } /// Get the current position @@ -328,35 +324,23 @@ public: /// If yes, returns 1-based number of a common atom; else, returns 0 static int overlap(const atom_group &g1, const atom_group &g2); - /// \brief When updating atomic coordinates, translate them to align with the - /// center of mass of the reference coordinates - bool b_center; - - /// \brief When updating atom coordinates (and after - /// centering them if b_center is set), rotate the group to - /// align with the reference coordinates. - /// - /// Note: gradients will be calculated in the rotated frame: when - /// forces will be applied, they will rotated back to the original - /// frame - bool b_rotate; - /// The rotation calculated automatically if b_rotate is defined + /// The rotation calculated automatically if f_ag_rotate is defined cvm::rotation rot; - /// \brief Indicates that the user has explicitly set centerReference or + /// \brief Indicates that the user has explicitly set centerToReference or /// rotateReference, and the corresponding reference: /// cvc's (eg rmsd, eigenvector) will not override the user's choice bool b_user_defined_fit; - /// \brief use reference coordinates for b_center or b_rotate + /// \brief use reference coordinates for f_ag_center or f_ag_rotate std::vector ref_pos; /// \brief Center of geometry of the reference coordinates; regardless - /// of whether b_center is true, ref_pos is centered to zero at + /// of whether f_ag_center is true, ref_pos is centered to zero at /// initialization, and ref_pos_cog serves to center the positions cvm::atom_pos ref_pos_cog; - /// \brief If b_center or b_rotate is true, use this group to + /// \brief If f_ag_center or f_ag_rotate is true, use this group to /// define the transformation (default: this group itself) atom_group *fitting_group; @@ -395,12 +379,12 @@ public: void apply_translation(cvm::rvector const &t); /// \brief Get the current velocities; this must be called always - /// *after* read_positions(); if b_rotate is defined, the same + /// *after* read_positions(); if f_ag_rotate is defined, the same /// rotation applied to the coordinates will be used void read_velocities(); /// \brief Get the current total_forces; this must be called always - /// *after* read_positions(); if b_rotate is defined, the same + /// *after* read_positions(); if f_ag_rotate is defined, the same /// rotation applied to the coordinates will be used void read_total_forces(); diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index a84ec358dd..4893ceb46d 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -136,10 +136,11 @@ int colvarbias_abf::init(std::string const &conf) colvars[i]->enable(f_cv_hide_Jacobian); } - // If any colvar is extended-system, we need to collect the extended - // system gradient - if (colvars[i]->is_enabled(f_cv_extended_Lagrangian)) + // If any colvar is extended-system (restrained style, not external with constraint), we are running eABF + if (colvars[i]->is_enabled(f_cv_extended_Lagrangian) + && !colvars[i]->is_enabled(f_cv_external)) { b_extended = true; + } // Cannot mix and match coarse time steps with ABF because it gives // wrong total force averages - total force needs to be averaged over @@ -475,7 +476,7 @@ int colvarbias_abf::update() last_gradients->copy_grid(*gradients); last_samples->copy_grid(*samples); shared_last_step = cvm::step_absolute(); - cvm::log("Prepared sample and gradient buffers at step "+cvm::to_str(cvm::step_absolute())+"."); + cvm::log("Prepared sample and gradient buffers at step "+cvm::to_str(cvm::step_absolute())+".\n"); } // update UI estimator every step @@ -812,8 +813,10 @@ int colvarbias_abf::write_output_files() cvm::log("ABF bias trying to write gradients and samples to disk"); } - if (shared_on && cvm::main()->proxy->replica_index() > 0) { + if (shared_on && cvm::main()->proxy->replica_index() > 0 + && ! (b_CZAR_estimator || b_UI_estimator) ) { // No need to report the same data as replica 0, let it do the I/O job + // except if using an eABF FE estimator return COLVARS_OK; } diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h index 15c81e9466..3a3120a058 100644 --- a/lib/colvars/colvarbias_abf.h +++ b/lib/colvars/colvarbias_abf.h @@ -121,6 +121,8 @@ private: } else { system_force[i] = colvars[i]->total_force().real_value - colvar_forces[i].real_value; + // If hideJacobian is active then total_force has an extra term of -fj + // which is the Jacobian-compensating force at the colvar level } if (cvm::debug()) cvm::log("ABF System force calc: cv " + cvm::to_str(i) + diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp index 3efe0b0acc..92cc112845 100644 --- a/lib/colvars/colvarbias_histogram.cpp +++ b/lib/colvars/colvarbias_histogram.cpp @@ -129,14 +129,14 @@ int colvarbias_histogram::update() // output_prefix is unset during the constructor if (cvm::step_relative() == 0) { out_name = cvm::output_prefix() + "." + this->name + ".dat"; - cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\""); + cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\"\n"); } } if (out_name_dx.size() == 0) { if (cvm::step_relative() == 0) { out_name_dx = cvm::output_prefix() + "." + this->name + ".dx"; - cvm::log("Histogram " + this->name + " will be written to file \"" + out_name_dx + "\""); + cvm::log("Histogram " + this->name + " will be written to file \"" + out_name_dx + "\"\n"); } } diff --git a/lib/colvars/colvarbias_histogram.h b/lib/colvars/colvarbias_histogram.h index 2e6c6884fb..6044fa189e 100644 --- a/lib/colvars/colvarbias_histogram.h +++ b/lib/colvars/colvarbias_histogram.h @@ -35,7 +35,6 @@ protected: colvar_grid_scalar *grid; std::vector bin; std::string out_name, out_name_dx; - size_t output_freq; /// If one or more of the variables are \link colvarvalue::type_vector \endlink, treat them as arrays of this length size_t colvar_array_size; diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp index d448b1f2e4..ccbd6c406f 100644 --- a/lib/colvars/colvarbias_meta.cpp +++ b/lib/colvars/colvarbias_meta.cpp @@ -50,6 +50,7 @@ colvarbias_meta::colvarbias_meta(char const *key) dump_fes = true; keep_hills = false; + restart_keep_hills = false; dump_fes_save = false; dump_replica_fes = false; @@ -902,7 +903,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, count++) { size_t i; for (i = 0; i < num_variables(); i++) { - new_colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i); + new_colvar_values[i] = he->bin_to_value_scalar(he_ix[i], i); } // loop over the hills and increment the energy grid locally @@ -934,40 +935,12 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, } } else { - - // TODO delete this (never used) - - // simpler version, with just the energy - - for ( ; (he->index_ok(he_ix)); ) { - - for (size_t i = 0; i < num_variables(); i++) { - new_colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i); - } - - hills_energy_here = 0.0; - calc_hills(h_first, h_last, hills_energy_here, &new_colvar_values); - he->acc_value(he_ix, hills_energy_here); - - he->incr(he_ix); - - count++; - if ((count % print_frequency) == 0) { - if (print_progress) { - cvm::real const progress = cvm::real(count) / cvm::real(he->number_of_points()); - std::ostringstream os; - os.setf(std::ios::fixed, std::ios::floatfield); - os << std::setw(6) << std::setprecision(2) - << 100.0 * progress - << "% done."; - cvm::log(os.str()); - } - } - } + cvm::error("No grid object provided in metadynamics::project_hills()\n", + BUG_ERROR); } if (print_progress) { - cvm::log("100.00% done."); + cvm::log("100.00% done.\n"); } if (! keep_hills) { @@ -1281,9 +1254,25 @@ int colvarbias_meta::set_state_params(std::string const &state_conf) return error_code; } + colvarparse::get_keyval(state_conf, "keepHills", restart_keep_hills, false, + colvarparse::parse_restart); + + if ((!restart_keep_hills) && (cvm::main()->restart_version_number() < 20210604)) { + if (keep_hills) { + cvm::log("Warning: could not ensure that keepHills was enabled when " + "this state file was written; because it is enabled now, " + "it is assumed that it was also then, but please verify.\n"); + restart_keep_hills = true; + } + } else { + if (restart_keep_hills) { + cvm::log("This state file/stream contains explicit hills.\n"); + } + } + std::string check_replica = ""; if (colvarparse::get_keyval(state_conf, "replicaID", check_replica, - std::string(""), colvarparse::parse_silent) && + std::string(""), colvarparse::parse_restart) && (check_replica != this->replica_id)) { return cvm::error("Error: in the state file , the " "\"metadynamics\" block has a different replicaID ("+ @@ -1297,8 +1286,6 @@ int colvarbias_meta::set_state_params(std::string const &state_conf) std::istream & colvarbias_meta::read_state_data(std::istream& is) { - bool grids_from_restart_file = use_grids; - if (use_grids) { if (expand_grids) { @@ -1343,7 +1330,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) !(hills_energy->read_restart(is))) { is.clear(); is.seekg(hills_energy_pos, std::ios::beg); - grids_from_restart_file = false; if (!rebin_grids) { if (hills_energy_backup == NULL) cvm::fatal_error("Error: couldn't read the free energy grid for metadynamics bias \""+ @@ -1381,7 +1367,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) !(hills_energy_gradients->read_restart(is))) { is.clear(); is.seekg(hills_energy_gradients_pos, std::ios::beg); - grids_from_restart_file = false; if (!rebin_grids) { if (hills_energy_backup == NULL) cvm::fatal_error("Error: couldn't read the free energy gradients grid for metadynamics bias \""+ @@ -1419,28 +1404,29 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) } } + // Save references to the end of the list of existing hills, so that it can + // be cleared if hills are read successfully state bool const existing_hills = !hills.empty(); size_t const old_hills_size = hills.size(); hill_iter old_hills_end = hills.end(); hill_iter old_hills_off_grid_end = hills_off_grid.end(); - // read the hills explicitly written (if there are any) + // Read any hills following the grid data (if any) while (read_hill(is)) { - if (cvm::debug()) + if (cvm::debug()) { cvm::log("Read a previously saved hill under the " "metadynamics bias \""+ this->name+"\", created at step "+ cvm::to_str((hills.back()).it)+".\n"); + } } is.clear(); new_hills_begin = hills.end(); - if (grids_from_restart_file) { - if (hills.size() > old_hills_size) - cvm::log("Read "+cvm::to_str(hills.size())+ - " hills in addition to the grids.\n"); - } else { - if (!hills.empty()) - cvm::log("Read "+cvm::to_str(hills.size())+" hills.\n"); + cvm::log("Read "+cvm::to_str(hills.size() - old_hills_size)+" hills.\n"); + + if (existing_hills) { + hills.erase(hills.begin(), old_hills_end); + hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end); } if (rebin_grids) { @@ -1454,7 +1440,16 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) colvar_grid_gradient *new_hills_energy_gradients = new colvar_grid_gradient(colvars); - if (!grids_from_restart_file || (keep_hills && !hills.empty())) { + if (cvm::debug()) { + std::ostringstream tmp_os; + tmp_os << "hills_energy parameters:\n"; + hills_energy->write_params(tmp_os); + tmp_os << "new_hills_energy parameters:\n"; + new_hills_energy->write_params(tmp_os); + cvm::log(tmp_os.str()); + } + + if (restart_keep_hills && !hills.empty()) { // if there are hills, recompute the new grids from them cvm::log("Rebinning the energy and forces grids from "+ cvm::to_str(hills.size())+" hills (this may take a while)...\n"); @@ -1494,11 +1489,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) if (cvm::debug()) cvm::log("colvarbias_meta::read_restart() done\n"); - if (existing_hills) { - hills.erase(hills.begin(), old_hills_end); - hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end); - } - has_data = true; if (comm != single_replica) { @@ -1509,6 +1499,15 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) } +inline std::istream & reset_istream(std::istream &is, size_t start_pos) +{ + is.clear(); + is.seekg(start_pos, std::ios::beg); + is.setstate(std::ios::failbit); + return is; +} + + std::istream & colvarbias_meta::read_hill(std::istream &is) { if (!is) return is; // do nothing if failbit is set @@ -1518,45 +1517,72 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) std::string data; if ( !(is >> read_block("hill", &data)) ) { - is.clear(); - is.seekg(start_pos, std::ios::beg); - is.setstate(std::ios::failbit); - return is; + return reset_istream(is, start_pos); } + std::istringstream data_is(data); + cvm::step_number h_it = 0L; - get_keyval(data, "step", h_it, h_it, parse_restart); - if (h_it <= state_file_step) { - if (cvm::debug()) - cvm::log("Skipping a hill older than the state file for metadynamics bias \""+ - this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+"\n"); - return is; - } - cvm::real h_weight; - get_keyval(data, "weight", h_weight, hill_weight, parse_restart); - std::vector h_centers(num_variables()); for (i = 0; i < num_variables(); i++) { h_centers[i].type(variables(i)->value()); } - get_keyval(data, "centers", h_centers, h_centers, parse_restart); - std::vector h_sigmas(num_variables()); - get_keyval(data, "widths", h_sigmas, h_sigmas, parse_restart); - for (i = 0; i < num_variables(); i++) { - // For backward compatibility, read the widths instead of the sigmas - h_sigmas[i] /= 2.0; - } + std::string h_replica; - std::string h_replica = ""; - if (comm != single_replica) { - get_keyval(data, "replicaID", h_replica, replica_id, parse_restart); - if (h_replica != replica_id) - cvm::fatal_error("Error: trying to read a hill created by replica \""+h_replica+ - "\" for replica \""+replica_id+ - "\"; did you swap output files?\n"); + std::string keyword; + while (data_is >> keyword) { + + if (keyword == "step") { + if ( !(data_is >> h_it)) { + return reset_istream(is, start_pos); + } + if ((h_it <= state_file_step) && !restart_keep_hills) { + if (cvm::debug()) + cvm::log("Skipping a hill older than the state file for metadynamics bias \""+ + this->name+"\""+ + ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+"\n"); + return is; + } + } + + if (keyword == "weight") { + if ( !(data_is >> h_weight)) { + return reset_istream(is, start_pos); + } + } + + if (keyword == "centers") { + for (i = 0; i < num_variables(); i++) { + if ( !(data_is >> h_centers[i])) { + return reset_istream(is, start_pos); + } + } + } + + if (keyword == "widths") { + for (i = 0; i < num_variables(); i++) { + if ( !(data_is >> h_sigmas[i])) { + return reset_istream(is, start_pos); + } + // For backward compatibility, read the widths instead of the sigmas + h_sigmas[i] /= 2.0; + } + } + + if (comm != single_replica) { + if (keyword == "replicaID") { + if ( !(data_is >> h_replica)) { + return reset_istream(is, start_pos); + } + if (h_replica != replica_id) { + cvm::error("Error: trying to read a hill created by replica \""+ + h_replica+"\" for replica \""+replica_id+ + "\"; did you swap output files?\n", INPUT_ERROR); + } + } + } } hill_iter const hills_end = hills.end(); @@ -1699,8 +1725,12 @@ std::string const colvarbias_meta::hills_traj_file_name() const std::string const colvarbias_meta::get_state_params() const { std::ostringstream os; - if (this->comm != single_replica) + if (keep_hills) { + os << "keepHills on" << "\n"; + } + if (this->comm != single_replica) { os << "replicaID " << this->replica_id << "\n"; + } return (colvarbias::get_state_params() + os.str()); } @@ -1944,6 +1974,7 @@ colvarbias_meta::hill::hill(cvm::step_number it_in, sigmas(cv_values.size()), replica(replica_in) { + hill_value = 0.0; for (size_t i = 0; i < cv_values.size(); i++) { centers[i].type(cv_values[i]); centers[i] = cv_values[i]; @@ -1967,7 +1998,9 @@ colvarbias_meta::hill::hill(colvarbias_meta::hill const &h) centers(h.centers), sigmas(h.sigmas), replica(h.replica) -{} +{ + hill_value = 0.0; +} colvarbias_meta::hill::~hill() diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h index 2f34abcc77..bf1710170e 100644 --- a/lib/colvars/colvarbias_meta.h +++ b/lib/colvars/colvarbias_meta.h @@ -155,10 +155,12 @@ protected: /// \brief How often the hills should be projected onto the grids size_t grids_freq; - /// \brief Whether to keep the hills in the restart file (e.g. to do - /// meaningful accurate rebinning afterwards) + /// Keep hills in the restart file (e.g. to accurately rebin later) bool keep_hills; + /// value of keepHills saved in the most recent restart file + bool restart_keep_hills; + /// \brief Dump the free energy surface (.pmf file) every restartFrequency bool dump_fes; diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index a1542d05bf..8938e64a0e 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -51,7 +51,7 @@ int colvar::cvc::init(std::string const &conf) std::string const old_name(name); if (name.size() > 0) { - cvm::log("Updating configuration for component \""+name+"\""); + cvm::log("Updating configuration for component \""+name+"\"\n"); } if (get_keyval(conf, "name", name, name)) { @@ -112,7 +112,7 @@ int colvar::cvc::init_total_force_params(std::string const &conf) } if (get_keyval_feature(this, conf, "oneSiteTotalForce", f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) { - cvm::log("Computing total force on group 1 only"); + cvm::log("Computing total force on group 1 only\n"); } if (! is_enabled(f_cvc_one_site_total_force)) { @@ -426,7 +426,7 @@ void colvar::cvc::collect_gradients(std::vector const &atom_ids, std::vecto // If necessary, apply inverse rotation to get atomic // gradient in the laboratory frame - if (ag.b_rotate) { + if (ag.is_enabled(f_ag_rotate)) { cvm::rotation const rot_inv = ag.rot.inverse(); for (size_t k = 0; k < ag.size(); k++) { @@ -505,7 +505,7 @@ void colvar::cvc::debug_gradients() cvm::atom_pos fit_gradient_sum, gradient_sum; // print the values of the fit gradients - if (group->b_rotate || group->b_center) { + if (group->is_enabled(f_ag_center) || group->is_enabled(f_ag_rotate)) { if (group->is_enabled(f_ag_fit_gradients)) { size_t j; @@ -514,7 +514,7 @@ void colvar::cvc::debug_gradients() for (j = 0; j < group_for_fit->fit_gradients.size(); j++) { cvm::log((group->fitting_group ? std::string("refPosGroup") : group->key) + "[" + cvm::to_str(j) + "] = " + - (group->b_rotate ? + (group->is_enabled(f_ag_rotate) ? cvm::to_str(rot_0.rotate(group_for_fit->fit_gradients[j])) : cvm::to_str(group_for_fit->fit_gradients[j]))); } @@ -525,7 +525,7 @@ void colvar::cvc::debug_gradients() for (size_t ia = 0; ia < group->size(); ia++) { // tests are best conducted in the unrotated (simulation) frame - cvm::rvector const atom_grad = (group->b_rotate ? + cvm::rvector const atom_grad = (group->is_enabled(f_ag_rotate) ? rot_inv.rotate((*group)[ia].grad) : (*group)[ia].grad); gradient_sum += atom_grad; diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index 57df68ab6e..2f68ac6abc 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -271,6 +271,12 @@ public: /// \brief Whether or not this CVC will be computed in parallel whenever possible bool b_try_scalable; + /// Forcibly set value of CVC - useful for driving an external coordinate, + /// eg. lambda dynamics + inline void set_value(colvarvalue const &new_value) { + x = new_value; + } + protected: /// \brief Cached value @@ -1344,6 +1350,71 @@ public: }; +class colvar::euler_phi + : public colvar::orientation +{ +public: + euler_phi(std::string const &conf); + euler_phi(); + virtual int init(std::string const &conf); + virtual ~euler_phi() {} + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); + virtual cvm::real dist2(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + /// Redefined to handle the 2*PI periodicity + virtual void wrap(colvarvalue &x_unwrapped) const; +}; + + +class colvar::euler_psi + : public colvar::orientation +{ +public: + euler_psi(std::string const &conf); + euler_psi(); + virtual int init(std::string const &conf); + virtual ~euler_psi() {} + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); + virtual cvm::real dist2(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + /// Redefined to handle the 2*PI periodicity + virtual void wrap(colvarvalue &x_unwrapped) const; +}; + + +class colvar::euler_theta + : public colvar::orientation +{ +public: + euler_theta(std::string const &conf); + euler_theta(); + virtual int init(std::string const &conf); + virtual ~euler_theta() {} + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); + // theta angle is a scalar variable and not periodic + // we need to override the virtual functions from orientation + virtual cvm::real dist2(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const; +}; + /// \brief Colvar component: root mean square deviation (RMSD) of a /// group with respect to a set of reference coordinates; uses \link @@ -1406,6 +1477,28 @@ public: }; +// \brief Colvar component: alch_lambda +// To communicate value with back-end in lambda-dynamics +class colvar::alch_lambda + : public colvar::cvc +{ +protected: + // No atom groups needed +public: + alch_lambda(std::string const &conf); + alch_lambda(); + virtual ~alch_lambda() {} + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); + virtual cvm::real dist2(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const; +}; + class colvar::componentDisabled : public colvar::cvc @@ -1681,11 +1774,20 @@ public: protected: - /// Identifier of the map object (as used by the simulation engine) - std::string map_name; + /// String identifier of the map object (as used by the simulation engine) + std::string volmap_name; + + /// Numeric identifier of the map object (as used by the simulation engine) + int volmap_id; /// Index of the map objet in the proxy arrays int volmap_index; + + /// Group of atoms selected internally (optional) + cvm::atom_group *atoms; + + /// Weights assigned to each atom (default: uniform weights) + std::vector atom_weights; }; diff --git a/lib/colvars/colvarcomp_alchlambda.cpp b/lib/colvars/colvarcomp_alchlambda.cpp new file mode 100644 index 0000000000..5e10a1dab5 --- /dev/null +++ b/lib/colvars/colvarcomp_alchlambda.cpp @@ -0,0 +1,56 @@ +// -*- c++ -*- + +// This file is part of the Collective Variables module (Colvars). +// The original version of Colvars and its updates are located at: +// https://github.com/Colvars/colvars +// Please update all Colvars source files before making any changes. +// If you wish to distribute your changes, please submit them to the +// Colvars repository at GitHub. + + +#include + +#include "colvarmodule.h" +#include "colvarvalue.h" +#include "colvarparse.h" +#include "colvar.h" +#include "colvarcomp.h" + + +colvar::alch_lambda::alch_lambda(std::string const &conf) + : cvc(conf) +{ + function_type = "alch_lambda"; + + disable(f_cvc_explicit_gradient); + disable(f_cvc_gradient); + + x.type(colvarvalue::type_scalar); + // Query initial value from back-end + cvm::proxy->get_alch_lambda(&x.real_value); +} + + +void colvar::alch_lambda::calc_value() +{ + // Special workflow: + // at the beginning of the timestep we get a force instead of calculating the value + + cvm::proxy->get_dE_dLambda(&ft.real_value); + ft.real_value *= -1.0; // Energy derivative to force +} + + +void colvar::alch_lambda::calc_gradients() +{ +} + + +void colvar::alch_lambda::apply_force(colvarvalue const &force) +{ + // Special workflow: + // at the end of the time step we send a new value + cvm::proxy->set_alch_lambda(&x.real_value); +} + +simple_scalar_dist_functions(alch_lambda) diff --git a/lib/colvars/colvarcomp_apath.cpp b/lib/colvars/colvarcomp_apath.cpp index 591d8d0012..a4d1df9e50 100644 --- a/lib/colvars/colvarcomp_apath.cpp +++ b/lib/colvars/colvarcomp_apath.cpp @@ -19,17 +19,8 @@ colvar::aspathCV::aspathCV(std::string const &conf): CVBasedPath(conf) { get_keyval(conf, "weights", p_weights, std::vector(cv.size(), 1.0)); x.type(colvarvalue::type_scalar); use_explicit_gradients = true; - std::vector rmsd_between_refs(total_reference_frames - 1, 0.0); - computeDistanceBetweenReferenceFrames(rmsd_between_refs); - cvm::real mean_square_displacements = 0.0; - for (size_t i_frame = 1; i_frame < total_reference_frames; ++i_frame) { - cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n")); - mean_square_displacements += rmsd_between_refs[i_frame - 1] * rmsd_between_refs[i_frame - 1]; - } - mean_square_displacements /= cvm::real(total_reference_frames - 1); - cvm::real suggested_lambda = 1.0 / mean_square_displacements; cvm::real p_lambda; - get_keyval(conf, "lambda", p_lambda, suggested_lambda); + get_keyval(conf, "lambda", p_lambda, -1.0); ArithmeticPathCV::ArithmeticPathBase::initialize(cv.size(), total_reference_frames, p_lambda, ref_cv[0], p_weights); cvm::log(std::string("Lambda is ") + cvm::to_str(lambda) + std::string("\n")); for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { @@ -58,6 +49,16 @@ void colvar::aspathCV::updateDistanceToReferenceFrames() { } void colvar::aspathCV::calc_value() { + if (lambda < 0) { + // this implies that the user may not set a valid lambda value + // so recompute it by the suggested value in Parrinello's paper + cvm::log("A non-positive value of lambda is detected, which implies that it may not set in the configuration.\n"); + cvm::log("This component (aspathCV) will recompute a value for lambda following the suggestion in the origin paper.\n"); + std::vector rmsd_between_refs(total_reference_frames - 1, 0.0); + computeDistanceBetweenReferenceFrames(rmsd_between_refs); + reComputeLambda(rmsd_between_refs); + cvm::log("Ok, the value of lambda is updated to " + cvm::to_str(lambda)); + } computeValue(); x = s; } @@ -107,17 +108,8 @@ colvar::azpathCV::azpathCV(std::string const &conf): CVBasedPath(conf) { get_keyval(conf, "weights", p_weights, std::vector(cv.size(), 1.0)); x.type(colvarvalue::type_scalar); use_explicit_gradients = true; - std::vector rmsd_between_refs(total_reference_frames - 1, 0.0); - computeDistanceBetweenReferenceFrames(rmsd_between_refs); - cvm::real mean_square_displacements = 0.0; - for (size_t i_frame = 1; i_frame < total_reference_frames; ++i_frame) { - cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n")); - mean_square_displacements += rmsd_between_refs[i_frame - 1] * rmsd_between_refs[i_frame - 1]; - } - mean_square_displacements /= cvm::real(total_reference_frames - 1); - cvm::real suggested_lambda = 1.0 / mean_square_displacements; cvm::real p_lambda; - get_keyval(conf, "lambda", p_lambda, suggested_lambda); + get_keyval(conf, "lambda", p_lambda, -1.0); ArithmeticPathCV::ArithmeticPathBase::initialize(cv.size(), total_reference_frames, p_lambda, ref_cv[0], p_weights); cvm::log(std::string("Lambda is ") + cvm::to_str(lambda) + std::string("\n")); for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { @@ -146,6 +138,16 @@ void colvar::azpathCV::updateDistanceToReferenceFrames() { } void colvar::azpathCV::calc_value() { + if (lambda < 0) { + // this implies that the user may not set a valid lambda value + // so recompute it by the suggested value in Parrinello's paper + cvm::log("A non-positive value of lambda is detected, which implies that it may not set in the configuration.\n"); + cvm::log("This component (azpathCV) will recompute a value for lambda following the suggestion in the origin paper.\n"); + std::vector rmsd_between_refs(total_reference_frames - 1, 0.0); + computeDistanceBetweenReferenceFrames(rmsd_between_refs); + reComputeLambda(rmsd_between_refs); + cvm::log("Ok, the value of lambda is updated to " + cvm::to_str(lambda)); + } computeValue(); x = z; } diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index 1b1b295ff1..c044da86b3 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -194,10 +194,10 @@ colvar::distance_z::distance_z(std::string const &conf) ref2 = parse_group(conf, "ref2", true); if ( ref2 ) { - cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\""); + cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"\n"); fixed_axis = false; if (key_lookup(conf, "axis")) - cvm::log("Warning: explicit axis definition will be ignored!"); + cvm::log("Warning: explicit axis definition will be ignored!\n"); } else { if (get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0))) { if (axis.norm2() == 0.0) { @@ -808,9 +808,9 @@ colvar::gyration::gyration(std::string const &conf) atoms = parse_group(conf, "atoms"); if (atoms->b_user_defined_fit) { - cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\"."); + cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\".\n"); } else { - atoms->b_center = true; + atoms->enable(f_ag_center); atoms->ref_pos.assign(1, cvm::atom_pos(0.0, 0.0, 0.0)); atoms->fit_gradients.assign(atoms->size(), cvm::rvector(0.0, 0.0, 0.0)); } @@ -1025,13 +1025,13 @@ colvar::rmsd::rmsd(std::string const &conf) } if (atoms->b_user_defined_fit) { - cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\"."); + cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\".\n"); } else { // Default: fit everything - cvm::log("Enabling \"centerReference\" and \"rotateReference\", to minimize RMSD before calculating it as a variable: " + cvm::log("Enabling \"centerToReference\" and \"rotateToReference\", to minimize RMSD before calculating it as a variable: " "if this is not the desired behavior, disable them explicitly within the \"atoms\" block.\n"); - atoms->b_center = true; - atoms->b_rotate = true; + atoms->enable(f_ag_center); + atoms->enable(f_ag_rotate); // default case: reference positions for calculating the rmsd are also those used // for fitting atoms->ref_pos = ref_pos; @@ -1156,7 +1156,7 @@ void colvar::rmsd::calc_Jacobian_derivative() cvm::real rotation_term = 0.0; // The rotation term only applies is coordinates are rotated - if (atoms->b_rotate) { + if (atoms->is_enabled(f_ag_rotate)) { // gradient of the rotation matrix cvm::matrix2d grad_rot_mat(3, 3); @@ -1202,7 +1202,7 @@ void colvar::rmsd::calc_Jacobian_derivative() } // The translation term only applies is coordinates are centered - cvm::real translation_term = atoms->b_center ? 3.0 : 0.0; + cvm::real translation_term = atoms->is_enabled(f_ag_center) ? 3.0 : 0.0; jd.real_value = x.real_value > 0.0 ? (3.0 * atoms->size() - 1.0 - translation_term - rotation_term) / x.real_value : @@ -1284,10 +1284,10 @@ colvar::eigenvector::eigenvector(std::string const &conf) cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\".\n"); } else { // default: fit everything - cvm::log("Enabling \"centerReference\" and \"rotateReference\", to minimize RMSD before calculating the vector projection: " + cvm::log("Enabling \"centerToReference\" and \"rotateToReference\", to minimize RMSD before calculating the vector projection: " "if this is not the desired behavior, disable them explicitly within the \"atoms\" block.\n"); - atoms->b_center = true; - atoms->b_rotate = true; + atoms->enable(f_ag_center); + atoms->enable(f_ag_rotate); atoms->ref_pos = ref_pos; atoms->center_ref_pos(); atoms->disable(f_ag_fit_gradients); // cancel out if group is fitted on itself @@ -1355,14 +1355,14 @@ colvar::eigenvector::eigenvector(std::string const &conf) if (b_difference_vector) { - if (atoms->b_center) { + if (atoms->is_enabled(f_ag_center)) { // both sets should be centered on the origin for fitting for (size_t i = 0; i < atoms->size(); i++) { eigenvec[i] -= eig_center; ref_pos[i] -= ref_pos_center; } } - if (atoms->b_rotate) { + if (atoms->is_enabled(f_ag_rotate)) { atoms->rot.calc_optimal_rotation(eigenvec, ref_pos); for (size_t i = 0; i < atoms->size(); i++) { eigenvec[i] = atoms->rot.rotate(eigenvec[i]); @@ -1372,7 +1372,7 @@ colvar::eigenvector::eigenvector(std::string const &conf) for (size_t i = 0; i < atoms->size(); i++) { eigenvec[i] -= ref_pos[i]; } - if (atoms->b_center) { + if (atoms->is_enabled(f_ag_center)) { // bring back the ref positions to where they were for (size_t i = 0; i < atoms->size(); i++) { ref_pos[i] += ref_pos_center; @@ -1521,7 +1521,8 @@ colvar::cartesian::cartesian(std::string const &conf) x.type(colvarvalue::type_vector); disable(f_cvc_explicit_gradient); - x.vector1d_value.resize(atoms->size() * axes.size()); + // Don't try to access atoms if creation of the atom group failed + if (atoms != NULL) x.vector1d_value.resize(atoms->size() * axes.size()); } diff --git a/lib/colvars/colvarcomp_gpath.cpp b/lib/colvars/colvarcomp_gpath.cpp index 8849f9dbe4..884dfdaee9 100644 --- a/lib/colvars/colvarcomp_gpath.cpp +++ b/lib/colvars/colvarcomp_gpath.cpp @@ -65,8 +65,8 @@ colvar::CartesianBasedPath::CartesianBasedPath(std::string const &conf): cvc(con cvm::atom_group* tmp_atoms = parse_group(conf, "atoms"); if (!has_user_defined_fitting) { // Swipe from the rmsd class - tmp_atoms->b_center = true; - tmp_atoms->b_rotate = true; + tmp_atoms->enable(f_ag_center); + tmp_atoms->enable(f_ag_rotate); tmp_atoms->ref_pos = reference_frames[i_frame]; tmp_atoms->center_ref_pos(); tmp_atoms->enable(f_ag_fit_gradients); @@ -87,8 +87,8 @@ colvar::CartesianBasedPath::CartesianBasedPath(std::string const &conf): cvc(con std::vector reference_fitting_position(tmp_fitting_atoms->size()); cvm::load_coords(reference_position_filename.c_str(), &reference_fitting_position, tmp_fitting_atoms, reference_column, reference_column_value); // setup the atom group for calculating - tmp_atoms->b_center = true; - tmp_atoms->b_rotate = true; + tmp_atoms->enable(f_ag_center); + tmp_atoms->enable(f_ag_rotate); tmp_atoms->b_user_defined_fit = true; tmp_atoms->disable(f_ag_scalable); tmp_atoms->disable(f_ag_scalable_com); diff --git a/lib/colvars/colvarcomp_rotations.cpp b/lib/colvars/colvarcomp_rotations.cpp index c7a414b006..fbf572b3f3 100644 --- a/lib/colvars/colvarcomp_rotations.cpp +++ b/lib/colvars/colvarcomp_rotations.cpp @@ -442,3 +442,335 @@ void colvar::spin_angle::wrap(colvarvalue &x_unwrapped) const return; } + + +colvar::euler_phi::euler_phi(std::string const &conf) + : orientation() +{ + function_type = "euler_phi"; + period = 360.0; + enable(f_cvc_periodic); + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); + init(conf); +} + + +colvar::euler_phi::euler_phi() + : orientation() +{ + function_type = "euler_phi"; + period = 360.0; + enable(f_cvc_periodic); + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); +} + + +int colvar::euler_phi::init(std::string const &conf) +{ + int error_code = COLVARS_OK; + error_code |= orientation::init(conf); + return error_code; +} + + +void colvar::euler_phi::calc_value() +{ + atoms_cog = atoms->center_of_geometry(); + + rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog)); + + const cvm::real& q0 = rot.q.q0; + const cvm::real& q1 = rot.q.q1; + const cvm::real& q2 = rot.q.q2; + const cvm::real& q3 = rot.q.q3; + const cvm::real tmp_y = 2 * (q0 * q1 + q2 * q3); + const cvm::real tmp_x = 1 - 2 * (q1 * q1 + q2 * q2); + x.real_value = cvm::atan2(tmp_y, tmp_x) * (180.0/PI); +} + + +void colvar::euler_phi::calc_gradients() +{ + const cvm::real& q0 = rot.q.q0; + const cvm::real& q1 = rot.q.q1; + const cvm::real& q2 = rot.q.q2; + const cvm::real& q3 = rot.q.q3; + const cvm::real denominator = (2 * q0 * q1 + 2 * q2 * q3) * (2 * q0 * q1 + 2 * q2 * q3) + (-2 * q1 * q1 - 2 * q2 * q2 + 1) * (-2 * q1 * q1 - 2 * q2 * q2 + 1); + const cvm::real dxdq0 = (180.0/PI) * 2 * q1 * (-2 * q1 * q1 - 2 * q2 * q2 + 1) / denominator; + const cvm::real dxdq1 = (180.0/PI) * (2 * q0 * (-2 * q1 * q1 - 2 * q2 * q2 + 1) - 4 * q1 * (-2 * q0 * q1 - 2 * q2 * q3)) / denominator; + const cvm::real dxdq2 = (180.0/PI) * (-4 * q2 * (-2 * q0 * q1 - 2 * q2 * q3) + 2 * q3 * (-2 * q1 * q1 - 2 * q2 * q2 + 1)) / denominator; + const cvm::real dxdq3 = (180.0/PI) * 2 * q2 * (-2 * q1 * q1 - 2 * q2 * q2 + 1) / denominator; + for (size_t ia = 0; ia < atoms->size(); ia++) { + (*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]) + + (dxdq1 * (rot.dQ0_2[ia])[1]) + + (dxdq2 * (rot.dQ0_2[ia])[2]) + + (dxdq3 * (rot.dQ0_2[ia])[3]); + } +} + + +void colvar::euler_phi::apply_force(colvarvalue const &force) +{ + cvm::real const &fw = force.real_value; + if (!atoms->noforce) { + atoms->apply_colvar_force(fw); + } +} + + +cvm::real colvar::euler_phi::dist2(colvarvalue const &x1, + colvarvalue const &x2) const +{ + cvm::real diff = x1.real_value - x2.real_value; + diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff)); + return diff * diff; +} + + +colvarvalue colvar::euler_phi::dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + cvm::real diff = x1.real_value - x2.real_value; + diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff)); + return 2.0 * diff; +} + + +colvarvalue colvar::euler_phi::dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + cvm::real diff = x1.real_value - x2.real_value; + diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff)); + return (-2.0) * diff; +} + + +void colvar::euler_phi::wrap(colvarvalue &x_unwrapped) const +{ + if ((x_unwrapped.real_value - wrap_center) >= 180.0) { + x_unwrapped.real_value -= 360.0; + return; + } + + if ((x_unwrapped.real_value - wrap_center) < -180.0) { + x_unwrapped.real_value += 360.0; + return; + } + + return; +} + + +colvar::euler_psi::euler_psi(std::string const &conf) + : orientation() +{ + function_type = "euler_psi"; + period = 360.0; + enable(f_cvc_periodic); + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); + init(conf); +} + + +colvar::euler_psi::euler_psi() + : orientation() +{ + function_type = "euler_psi"; + period = 360.0; + enable(f_cvc_periodic); + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); +} + + +int colvar::euler_psi::init(std::string const &conf) +{ + int error_code = COLVARS_OK; + error_code |= orientation::init(conf); + return error_code; +} + + +void colvar::euler_psi::calc_value() +{ + atoms_cog = atoms->center_of_geometry(); + + rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog)); + + const cvm::real& q0 = rot.q.q0; + const cvm::real& q1 = rot.q.q1; + const cvm::real& q2 = rot.q.q2; + const cvm::real& q3 = rot.q.q3; + const cvm::real tmp_y = 2 * (q0 * q3 + q1 * q2); + const cvm::real tmp_x = 1 - 2 * (q2 * q2 + q3 * q3); + x.real_value = cvm::atan2(tmp_y, tmp_x) * (180.0/PI); +} + + +void colvar::euler_psi::calc_gradients() +{ + const cvm::real& q0 = rot.q.q0; + const cvm::real& q1 = rot.q.q1; + const cvm::real& q2 = rot.q.q2; + const cvm::real& q3 = rot.q.q3; + const cvm::real denominator = (2 * q0 * q3 + 2 * q1 * q2) * (2 * q0 * q3 + 2 * q1 * q2) + (-2 * q2 * q2 - 2 * q3 * q3 + 1) * (-2 * q2 * q2 - 2 * q3 * q3 + 1); + const cvm::real dxdq0 = (180.0/PI) * 2 * q3 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) / denominator; + const cvm::real dxdq1 = (180.0/PI) * 2 * q2 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) / denominator; + const cvm::real dxdq2 = (180.0/PI) * (2 * q1 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) - 4 * q2 * (-2 * q0 * q3 - 2 * q1 * q2)) / denominator; + const cvm::real dxdq3 = (180.0/PI) * (2 * q0 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) - 4 * q3 * (-2 * q0 * q3 - 2 * q1 * q2)) / denominator; + for (size_t ia = 0; ia < atoms->size(); ia++) { + (*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]) + + (dxdq1 * (rot.dQ0_2[ia])[1]) + + (dxdq2 * (rot.dQ0_2[ia])[2]) + + (dxdq3 * (rot.dQ0_2[ia])[3]); + } +} + + +void colvar::euler_psi::apply_force(colvarvalue const &force) +{ + cvm::real const &fw = force.real_value; + if (!atoms->noforce) { + atoms->apply_colvar_force(fw); + } +} + + +cvm::real colvar::euler_psi::dist2(colvarvalue const &x1, + colvarvalue const &x2) const +{ + cvm::real diff = x1.real_value - x2.real_value; + diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff)); + return diff * diff; +} + + +colvarvalue colvar::euler_psi::dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + cvm::real diff = x1.real_value - x2.real_value; + diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff)); + return 2.0 * diff; +} + + +colvarvalue colvar::euler_psi::dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + cvm::real diff = x1.real_value - x2.real_value; + diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff)); + return (-2.0) * diff; +} + + +void colvar::euler_psi::wrap(colvarvalue &x_unwrapped) const +{ + if ((x_unwrapped.real_value - wrap_center) >= 180.0) { + x_unwrapped.real_value -= 360.0; + return; + } + + if ((x_unwrapped.real_value - wrap_center) < -180.0) { + x_unwrapped.real_value += 360.0; + return; + } + + return; +} + + +colvar::euler_theta::euler_theta(std::string const &conf) + : orientation() +{ + function_type = "euler_theta"; + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); + init(conf); +} + + +colvar::euler_theta::euler_theta() + : orientation() +{ + function_type = "euler_theta"; + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); +} + + +int colvar::euler_theta::init(std::string const &conf) +{ + int error_code = COLVARS_OK; + error_code |= orientation::init(conf); + return error_code; +} + + +void colvar::euler_theta::calc_value() +{ + atoms_cog = atoms->center_of_geometry(); + + rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog)); + + const cvm::real& q0 = rot.q.q0; + const cvm::real& q1 = rot.q.q1; + const cvm::real& q2 = rot.q.q2; + const cvm::real& q3 = rot.q.q3; + x.real_value = cvm::asin(2 * (q0 * q2 - q3 * q1)) * (180.0/PI); +} + + +void colvar::euler_theta::calc_gradients() +{ + const cvm::real& q0 = rot.q.q0; + const cvm::real& q1 = rot.q.q1; + const cvm::real& q2 = rot.q.q2; + const cvm::real& q3 = rot.q.q3; + const cvm::real denominator = cvm::sqrt(1 - (2 * q0 * q2 - 2 * q1 * q3) * (2 * q0 * q2 - 2 * q1 * q3)); + const cvm::real dxdq0 = (180.0/PI) * 2 * q2 / denominator; + const cvm::real dxdq1 = (180.0/PI) * -2 * q3 / denominator; + const cvm::real dxdq2 = (180.0/PI) * 2 * q0 / denominator; + const cvm::real dxdq3 = (180.0/PI) * -2 * q1 / denominator; + for (size_t ia = 0; ia < atoms->size(); ia++) { + (*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]) + + (dxdq1 * (rot.dQ0_2[ia])[1]) + + (dxdq2 * (rot.dQ0_2[ia])[2]) + + (dxdq3 * (rot.dQ0_2[ia])[3]); + } +} + + +void colvar::euler_theta::apply_force(colvarvalue const &force) +{ + cvm::real const &fw = force.real_value; + if (!atoms->noforce) { + atoms->apply_colvar_force(fw); + } +} + + +cvm::real colvar::euler_theta::dist2(colvarvalue const &x1, + colvarvalue const &x2) const +{ + // theta angle is not periodic + return cvc::dist2(x1, x2); +} + + +colvarvalue colvar::euler_theta::dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + // theta angle is not periodic + return cvc::dist2_lgrad(x1, x2); +} + + +colvarvalue colvar::euler_theta::dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + // theta angle is not periodic + return cvc::dist2_rgrad(x1, x2); +} diff --git a/lib/colvars/colvarcomp_volmaps.cpp b/lib/colvars/colvarcomp_volmaps.cpp index 8ea2b76de4..865500dfeb 100644 --- a/lib/colvars/colvarcomp_volmaps.cpp +++ b/lib/colvars/colvarcomp_volmaps.cpp @@ -19,6 +19,9 @@ colvar::map_total::map_total() : cvc(), volmap_index(-1) { function_type = "map_total"; + volmap_id = -1; + volmap_index = -1; + atoms = NULL; x.type(colvarvalue::type_scalar); } @@ -27,6 +30,9 @@ colvar::map_total::map_total(std::string const &conf) : cvc(), volmap_index(-1) { function_type = "map_total"; + volmap_id = -1; + volmap_index = -1; + atoms = NULL; x.type(colvarvalue::type_scalar); map_total::init(conf); } @@ -35,26 +41,101 @@ colvar::map_total::map_total(std::string const &conf) int colvar::map_total::init(std::string const &conf) { int error_code = cvc::init(conf); - get_keyval(conf, "mapName", map_name, map_name); - volmap_index = (cvm::proxy)->init_volmap(map_name); - error_code |= volmap_index > 0 ? COLVARS_OK : INPUT_ERROR; + colvarproxy *proxy = cvm::main()->proxy; + get_keyval(conf, "mapName", volmap_name, volmap_name); + get_keyval(conf, "mapID", volmap_id, volmap_id); + register_param("mapID", reinterpret_cast(&volmap_id)); + + if ((volmap_name.size() > 0) && (volmap_id >= 0)) { + error_code |= + cvm::error("Error: mapName and mapID are mutually exclusive.\n"); + } + + // Parse optional group + atoms = parse_group(conf, "atoms", true); + if (atoms != NULL) { + + // Using internal selection + if (volmap_name.size()) { + error_code |= proxy->check_volmap_by_name(volmap_name); + } + if (volmap_id >= 0) { + error_code |= proxy->check_volmap_by_id(volmap_id); + } + + } else { + + // Using selection from the MD engine + if (volmap_name.size()) { + volmap_index = proxy->init_volmap_by_name(volmap_name); + } + if (volmap_id >= 0) { + volmap_index = proxy->init_volmap_by_id(volmap_id); + } + error_code |= volmap_index > 0 ? COLVARS_OK : INPUT_ERROR; + } + + if (get_keyval(conf, "atomWeights", atom_weights, atom_weights)) { + if (atoms == NULL) { + error_code |= cvm::error("Error: weights can only be assigned when atoms " + "are selected explicitly in Colvars.\n", + INPUT_ERROR); + } else { + if (atoms->size() != atom_weights.size()) { + error_code |= cvm::error("Error: if defined, the number of weights ("+ + cvm::to_str(atom_weights.size())+ + ") must equal the number of atoms ("+ + cvm::to_str(atoms->size())+ + ").\n", INPUT_ERROR); + } + } + } + + if (volmap_name.size() > 0) { + volmap_id = proxy->get_volmap_id_from_name(volmap_name.c_str()); + } + return error_code; } void colvar::map_total::calc_value() { - x.real_value = (cvm::proxy)->get_volmap_value(volmap_index); + colvarproxy *proxy = cvm::main()->proxy; + int flags = is_enabled(f_cvc_gradient) ? colvarproxy::volmap_flag_gradients : + colvarproxy::volmap_flag_null; + + if (atoms != NULL) { + // Compute the map inside Colvars + x.real_value = 0.0; + + cvm::real *w = NULL; + if (atom_weights.size() > 0) { + flags |= colvarproxy::volmap_flag_use_atom_field; + w = &(atom_weights[0]); + } + proxy->compute_volmap(flags, volmap_id, atoms->begin(), atoms->end(), + &(x.real_value), w); + } else { + // Get the externally computed value + x.real_value = proxy->get_volmap_value(volmap_index); + } } void colvar::map_total::calc_gradients() { - // Atomic coordinates are not available here + // Computed in calc_value() or by the MD engine } void colvar::map_total::apply_force(colvarvalue const &force) { - (cvm::proxy)->apply_volmap_force(volmap_index, force.real_value); + colvarproxy *proxy = cvm::main()->proxy; + if (atoms) { + if (!atoms->noforce) + atoms->apply_colvar_force(force.real_value); + } else { + proxy->apply_volmap_force(volmap_index, force.real_value); + } } diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index 94c5cfbda7..c240ce5a96 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -49,7 +49,7 @@ void colvardeps::free_children_deps() { // Cannot be in the base class destructor because it needs the derived class features() size_t i,j,fid; - if (cvm::debug()) cvm::log("DEPS: freeing children deps for " + description); + if (cvm::debug()) cvm::log("DEPS: freeing children deps for " + description + "\n"); cvm::increase_depth(); for (fid = 0; fid < feature_states.size(); fid++) { @@ -58,7 +58,7 @@ void colvardeps::free_children_deps() { int g = features()[fid]->requires_children[i]; for (j=0; jfeatures()[g]->description); + + children[j]->features()[g]->description + "\n"); children[j]->decr_ref_count(g); } } @@ -80,7 +80,7 @@ void colvardeps::restore_children_deps() { int g = features()[fid]->requires_children[i]; for (j=0; jfeatures()[g]->description); + + children[j]->features()[g]->description + "\n"); children[j]->enable(g, false, false); } } @@ -135,7 +135,7 @@ int colvardeps::enable(int feature_id, if (cvm::debug()) { cvm::log("DEPS: " + description + (dry_run ? " testing " : " enabling ") + - "\"" + f->description +"\""); + "\"" + f->description +"\"\n"); } if (fs->enabled) { @@ -144,7 +144,7 @@ int colvardeps::enable(int feature_id, // as requirement is enabled fs->ref_count++; if (cvm::debug()) - cvm::log("DEPS: bumping ref_count to " + cvm::to_str(fs->ref_count)); + cvm::log("DEPS: bumping ref_count to " + cvm::to_str(fs->ref_count) + "\n"); } // Do not try to further resolve deps return COLVARS_OK; @@ -243,7 +243,7 @@ int colvardeps::enable(int feature_id, enable(g, false, false); // Just for printing error output } cvm::decrease_depth(); - cvm::log("-----------------------------------------"); + cvm::log("-----------------------------------------\n"); if (toplevel) { cvm::error("Error: Failed dependency in " + description + "."); } @@ -285,7 +285,7 @@ int colvardeps::enable(int feature_id, do_feature_side_effects(feature_id); if (cvm::debug()) cvm::log("DEPS: feature \"" + f->description + "\" in " - + description + " enabled, ref_count = 1."); + + description + " enabled, ref_count = 1." + "\n"); } return COLVARS_OK; } @@ -297,7 +297,7 @@ int colvardeps::disable(int feature_id) { feature_state *fs = &feature_states[feature_id]; if (cvm::debug()) cvm::log("DEPS: disabling feature \"" - + f->description + "\" in " + description); + + f->description + "\" in " + description + "\n"); if (fs->enabled == false) { return COLVARS_OK; @@ -313,14 +313,14 @@ int colvardeps::disable(int feature_id) { // internal deps (self) for (i=0; irequires_self.size(); i++) { if (cvm::debug()) cvm::log("DEPS: dereferencing self " - + features()[f->requires_self[i]]->description); + + features()[f->requires_self[i]]->description + "\n"); decr_ref_count(f->requires_self[i]); } // alternates for (i=0; ialternate_refs.size(); i++) { if (cvm::debug()) cvm::log("DEPS: dereferencing alt " - + features()[fs->alternate_refs[i]]->description); + + features()[fs->alternate_refs[i]]->description + "\n"); decr_ref_count(fs->alternate_refs[i]); } // Forget these, now that they are dereferenced @@ -337,7 +337,7 @@ int colvardeps::disable(int feature_id) { int g = f->requires_children[i]; for (j=0; jfeatures()[g]->description); + + children[j]->features()[g]->description + "\n"); children[j]->decr_ref_count(g); } } @@ -430,11 +430,13 @@ void colvardeps::require_feature_alt(int f, int g, int h, int i, int j) { void colvardeps::print_state() { size_t i; - cvm::log("Features of \"" + description + "\" ON/OFF (refcount)"); + cvm::log("Features of \"" + description + "\" (refcount)\n"); for (i = 0; i < feature_states.size(); i++) { - std::string onoff = is_enabled(i) ? "ON" : "OFF"; - cvm::log("- " + features()[i]->description + " " + onoff + " (" - + cvm::to_str(feature_states[i].ref_count) + ")"); + std::string onoff = is_enabled(i) ? "ON " : " "; + // Only display refcount if non-zero for less clutter + std::string refcount = feature_states[i].ref_count != 0 ? + " (" + cvm::to_str(feature_states[i].ref_count) + ") " : ""; + cvm::log("- " + onoff + features()[i]->description + refcount + "\n"); } cvm::increase_depth(); for (i=0; irequires_children.size(); i++) { int g = features()[fid]->requires_children[i]; if (cvm::debug()) cvm::log("DEPS: re-enabling children's " - + child->features()[g]->description); + + child->features()[g]->description + "\n"); child->enable(g, false, false); } } diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h index f4f543f336..9fd441ffec 100644 --- a/lib/colvars/colvardeps.h +++ b/lib/colvars/colvardeps.h @@ -283,6 +283,10 @@ public: /// center with fictitious mass; bias forces will be applied to /// the center f_cv_extended_Lagrangian, + /// \brief An extended variable that sets an external variable in the + /// back-end (eg. an alchemical coupling parameter for lambda-dynamics) + /// Can have a single component + f_cv_external, /// \brief The extended system coordinate undergoes Langevin dynamics f_cv_Langevin, /// \brief Output the potential and kinetic energies @@ -375,6 +379,7 @@ public: enum features_atomgroup { f_ag_active, f_ag_center, + f_ag_center_origin, f_ag_rotate, f_ag_fitting_group, /// Perform a standard minimum msd fit for given atoms diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index df122b1be4..b3768a47f6 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -122,17 +122,91 @@ cvm::real colvar_grid_scalar::entropy() const colvar_grid_gradient::colvar_grid_gradient() - : colvar_grid(), samples(NULL) + : colvar_grid(), + samples(NULL), + weights(NULL) {} colvar_grid_gradient::colvar_grid_gradient(std::vector const &nx_i) - : colvar_grid(nx_i, 0.0, nx_i.size()), samples(NULL) + : colvar_grid(nx_i, 0.0, nx_i.size()), + samples(NULL), + weights(NULL) {} colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars) - : colvar_grid(colvars, 0.0, colvars.size()), samples(NULL) + : colvar_grid(colvars, 0.0, colvars.size()), + samples(NULL), + weights(NULL) {} + +colvar_grid_gradient::colvar_grid_gradient(std::string &filename) + : colvar_grid(), + samples(NULL), + weights(NULL) +{ + std::ifstream is; + is.open(filename.c_str()); + if (!is.is_open()) { + cvm::error("Error opening multicol gradient file " + filename + " for reading.\n"); + return; + } + + // Data in the header: nColvars, then for each + // xiMin, dXi, nPoints, periodic flag + + std::string hash; + size_t i; + + if ( !(is >> hash) || (hash != "#") ) { + cvm::error("Error reading grid at position "+ + cvm::to_str(static_cast(is.tellg()))+ + " in stream(read \"" + hash + "\")\n"); + return; + } + + is >> nd; + + if (nd > 50) { + cvm::error("Error: excessive number of dimensions in file \""+ + filename+"\". Please ensure that the file is not corrupt.\n", + INPUT_ERROR); + return; + } + + mult = nd; + std::vector lower_in(nd), widths_in(nd); + std::vector nx_in(nd); + std::vector periodic_in(nd); + + for (i = 0; i < nd; i++ ) { + if ( !(is >> hash) || (hash != "#") ) { + cvm::error("Error reading grid at position "+ + cvm::to_str(static_cast(is.tellg()))+ + " in stream(read \"" + hash + "\")\n"); + return; + } + + is >> lower_in[i] >> widths_in[i] >> nx_in[i] >> periodic_in[i]; + } + + this->setup(nx_in, 0., mult); + + widths = widths_in; + + for (i = 0; i < nd; i++ ) { + lower_boundaries.push_back(colvarvalue(lower_in[i])); + periodic.push_back(static_cast(periodic_in[i])); + } + + // Reset the istream for read_multicol, which expects the whole file + is.clear(); + is.seekg(0); + read_multicol(is); + is.close(); +} + + void colvar_grid_gradient::write_1D_integral(std::ostream &os) { cvm::real bin, min, integral; @@ -202,7 +276,7 @@ integrate_potential::integrate_potential(std::vector &colvars, colvar_ // Compute inverse of Laplacian diagonal for Jacobi preconditioning // For now all code related to preconditioning is commented out // until a method better than Jacobi is implemented -// cvm::log("Preparing inverse diagonal for preconditioning..."); +// cvm::log("Preparing inverse diagonal for preconditioning...\n"); // inv_lap_diag.resize(nt); // std::vector id(nt), lap_col(nt); // for (int i = 0; i < nt; i++) { @@ -213,7 +287,30 @@ integrate_potential::integrate_potential(std::vector &colvars, colvar_ // id[i] = 0.; // inv_lap_diag[i] = 1. / lap_col[i]; // } -// cvm::log("Done."); +// cvm::log("Done.\n"); + } +} + + +integrate_potential::integrate_potential(colvar_grid_gradient * gradients) + : gradients(gradients) +{ + nd = gradients->num_variables(); + nx = gradients->number_of_points_vec(); + widths = gradients->widths; + periodic = gradients->periodic; + + // Expand grid by 1 bin in non-periodic dimensions + for (size_t i = 0; i < nd; i++ ) { + if (!periodic[i]) nx[i]++; + // Shift the grid by half the bin width (values at edges instead of center of bins) + lower_boundaries.push_back(gradients->lower_boundaries[i].real_value - 0.5 * widths[i]); + } + + setup(nx); + + if (nd > 1) { + divergence.resize(nt); } } @@ -246,7 +343,7 @@ int integrate_potential::integrate(const int itmax, const cvm::real &tol, cvm::r } else if (nd <= 3) { nr_linbcg_sym(divergence, data, tol, itmax, iter, err); - cvm::log("Integrated in " + cvm::to_str(iter) + " steps, error: " + cvm::to_str(err)); + cvm::log("Integrated in " + cvm::to_str(iter) + " steps, error: " + cvm::to_str(err) + "\n"); } else { cvm::error("Cannot integrate PMF in dimension > 3\n"); diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h index 17d049a6eb..3642ae387c 100644 --- a/lib/colvars/colvargrid.h +++ b/lib/colvars/colvargrid.h @@ -102,6 +102,12 @@ public: return nd; } + /// Return the numbers of points in all dimensions + inline std::vector const &number_of_points_vec() const + { + return nx; + } + /// Return the number of points in the i-th direction, if provided, or /// the total number inline size_t number_of_points(int const icv = -1) const @@ -199,6 +205,7 @@ public: { nd = nt = 0; mult = 1; + has_parent_data = false; this->setup(); } @@ -222,9 +229,9 @@ public: hard_lower_boundaries(g.hard_lower_boundaries), hard_upper_boundaries(g.hard_upper_boundaries), widths(g.widths), + has_parent_data(false), has_data(false) - { - } + {} /// \brief Constructor from explicit grid sizes \param nx_i Number /// of grid points along each dimension \param t Initial value for @@ -233,7 +240,7 @@ public: colvar_grid(std::vector const &nx_i, T const &t = T(), size_t mult_i = 1) - : has_data(false) + : has_parent_data(false), has_data(false) { this->setup(nx_i, t, mult_i); } @@ -245,7 +252,7 @@ public: T const &t = T(), size_t mult_i = 1, bool add_extra_bin = false) - : has_data(false) + : has_parent_data(false), has_data(false) { this->init_from_colvars(colvars, t, mult_i, add_extra_bin); } @@ -1066,8 +1073,8 @@ public: std::vector nx_read; std::vector bin; - if ( cv.size() != nd ) { - cvm::error("Cannot read grid file: missing reference to colvars."); + if ( cv.size() > 0 && cv.size() != nd ) { + cvm::error("Cannot read grid file: number of variables in file differs from number referenced by grid.\n"); return is; } @@ -1525,6 +1532,9 @@ public: /// Constructor from a vector of colvars colvar_grid_gradient(std::vector &colvars); + /// Constructor from a multicol file + colvar_grid_gradient(std::string &filename); + /// \brief Get a vector with the binned value(s) indexed by ix, normalized if applicable inline void vector_value(std::vector const &ix, std::vector &v) const { @@ -1658,10 +1668,13 @@ class integrate_potential : public colvar_grid_scalar {} /// Constructor from a vector of colvars + gradient grid - integrate_potential (std::vector &colvars, colvar_grid_gradient * gradients); + integrate_potential(std::vector &colvars, colvar_grid_gradient * gradients); + + /// Constructor from a gradient grid (for processing grid files without a Colvars config) + integrate_potential(colvar_grid_gradient * gradients); /// \brief Calculate potential from divergence (in 2D); return number of steps - int integrate (const int itmax, const cvm::real & tol, cvm::real & err); + int integrate(const int itmax, const cvm::real & tol, cvm::real & err); /// \brief Update matrix containing divergence and boundary conditions /// based on new gradient point value, in neighboring bins diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp index 95d42560fc..405c68244b 100644 --- a/lib/colvars/colvarmodule.cpp +++ b/lib/colvars/colvarmodule.cpp @@ -34,6 +34,9 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) xyz_reader_use_count = 0; + restart_version_str.clear(); + restart_version_int = 0; + if (proxy == NULL) { proxy = proxy_in; // Pointer to the proxy object parse = new colvarparse(); // Parsing object for global options @@ -48,7 +51,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) cvm::log(cvm::line_marker); cvm::log("Initializing the collective variables module, version "+ - cvm::to_str(COLVARS_VERSION)+".\n"); + version()+".\n"); cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n " "https://dx.doi.org/10.1080/00268976.2013.813594\n" "in any publication based on this calculation.\n"); @@ -58,7 +61,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) } #if (__cplusplus >= 201103L) - cvm::log("This version was built with the C++11 standard or higher."); + cvm::log("This version was built with the C++11 standard or higher.\n"); #else cvm::log("This version was built without the C++11 standard: some features are disabled.\n" "Please see the following link for details:\n" @@ -186,6 +189,7 @@ std::istream & colvarmodule::getline(std::istream &is, std::string &line) size_t const sz = l.size(); if (sz > 0) { if (l[sz-1] == '\r' ) { + // Replace Windows newlines with Unix newlines line = l.substr(0, sz-1); } else { line = l; @@ -200,6 +204,7 @@ std::istream & colvarmodule::getline(std::istream &is, std::string &line) int colvarmodule::parse_config(std::string &conf) { + // Auto-generated additional configuration extra_conf.clear(); // Check that the input has matching braces @@ -208,6 +213,9 @@ int colvarmodule::parse_config(std::string &conf) INPUT_ERROR); } + // Check that the input has only ASCII characters, and warn otherwise + colvarparse::check_ascii(conf); + // Parse global options if (catch_input_errors(parse_global_params(conf))) { return get_error(); @@ -472,7 +480,7 @@ int colvarmodule::parse_biases(std::string const &conf) if (use_scripted_forces) { cvm::log(cvm::line_marker); cvm::increase_depth(); - cvm::log("User forces script will be run at each bias update."); + cvm::log("User forces script will be run at each bias update.\n"); cvm::decrease_depth(); } @@ -754,6 +762,9 @@ int colvarmodule::calc() error_code |= end_of_step(); + // TODO move this to a base-class proxy method that calls this function + error_code |= proxy->end_of_step(); + return error_code; } @@ -1311,21 +1322,23 @@ std::istream & colvarmodule::read_restart(std::istream &is) colvarparse::parse_restart); it = it_restart; - std::string restart_version; - int restart_version_int = 0; + restart_version_str.clear(); + restart_version_int = 0; parse->get_keyval(restart_conf, "version", - restart_version, std::string(""), + restart_version_str, std::string(""), colvarparse::parse_restart); - if (restart_version.size()) { - if (restart_version != std::string(COLVARS_VERSION)) { - cvm::log("This state file was generated with version "+ - restart_version+"\n"); - } + if (restart_version_str.size()) { + // Initialize integer version number of this restart file restart_version_int = - proxy->get_version_from_string(restart_version.c_str()); + proxy->get_version_from_string(restart_version_str.c_str()); } - if (restart_version_int < 20160810) { + if (restart_version() != version()) { + cvm::log("This state file was generated with version "+ + restart_version()+"\n"); + } + + if (restart_version_number() < 20160810) { // check for total force change if (proxy->total_forces_enabled()) { warn_total_forces = true; @@ -1769,6 +1782,8 @@ int cvm::read_index_file(char const *filename) cvm::error("Error: in opening index file \""+ std::string(filename)+"\".\n", FILE_ERROR); + } else { + index_file_names.push_back(std::string(filename)); } while (is.good()) { @@ -1861,6 +1876,7 @@ int colvarmodule::reset_index_groups() } index_group_names.clear(); index_groups.clear(); + index_file_names.clear(); return COLVARS_OK; } @@ -1924,48 +1940,75 @@ int cvm::load_coords_xyz(char const *filename, std::string line; cvm::real x = 0.0, y = 0.0, z = 0.0; + std::string const error_msg("Error: cannot parse XYZ file \""+ + std::string(filename)+"\".\n"); + if ( ! (xyz_is >> natoms) ) { - cvm::error("Error: cannot parse XYZ file " - + std::string(filename) + ".\n", INPUT_ERROR); + return cvm::error(error_msg, INPUT_ERROR); } ++xyz_reader_use_count; if (xyz_reader_use_count < 2) { - cvm::log("Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units."); + cvm::log("Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units.\n"); } - // skip comment line - cvm::getline(xyz_is, line); - cvm::getline(xyz_is, line); - xyz_is.width(255); - std::vector::iterator pos_i = pos->begin(); + if (xyz_is.good()) { + // skip comment line + cvm::getline(xyz_is, line); + cvm::getline(xyz_is, line); + xyz_is.width(255); + } else { + return cvm::error(error_msg, INPUT_ERROR); + } + std::vector::iterator pos_i = pos->begin(); + size_t xyz_natoms = 0; if (pos->size() != natoms) { // Use specified indices int next = 0; // indices are zero-based std::vector::const_iterator index = atoms->sorted_ids().begin(); - for ( ; pos_i != pos->end() ; pos_i++, index++) { + for ( ; pos_i != pos->end() ; pos_i++, index++) { while ( next < *index ) { cvm::getline(xyz_is, line); next++; } - xyz_is >> symbol; - xyz_is >> x >> y >> z; - // XYZ files are assumed to be in Angstrom (as eg. VMD will) - (*pos_i)[0] = proxy->angstrom_to_internal(x); - (*pos_i)[1] = proxy->angstrom_to_internal(y); - (*pos_i)[2] = proxy->angstrom_to_internal(z); + if (xyz_is.good()) { + xyz_is >> symbol; + xyz_is >> x >> y >> z; + // XYZ files are assumed to be in Angstrom (as eg. VMD will) + (*pos_i)[0] = proxy->angstrom_to_internal(x); + (*pos_i)[1] = proxy->angstrom_to_internal(y); + (*pos_i)[2] = proxy->angstrom_to_internal(z); + xyz_natoms++; + } else { + return cvm::error(error_msg, INPUT_ERROR); + } } + } else { // Use all positions + for ( ; pos_i != pos->end() ; pos_i++) { - xyz_is >> symbol; - xyz_is >> x >> y >> z; - (*pos_i)[0] = proxy->angstrom_to_internal(x); - (*pos_i)[1] = proxy->angstrom_to_internal(y); - (*pos_i)[2] = proxy->angstrom_to_internal(z); + if (xyz_is.good()) { + xyz_is >> symbol; + xyz_is >> x >> y >> z; + (*pos_i)[0] = proxy->angstrom_to_internal(x); + (*pos_i)[1] = proxy->angstrom_to_internal(y); + (*pos_i)[2] = proxy->angstrom_to_internal(z); + xyz_natoms++; + } else { + return cvm::error(error_msg, INPUT_ERROR); + } } } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + + if (xyz_natoms != pos->size()) { + return cvm::error("Error: The number of positions read from file \""+ + std::string(filename)+"\" does not match the number of "+ + "positions required: "+cvm::to_str(xyz_natoms)+" vs. "+ + cvm::to_str(pos->size())+".\n", INPUT_ERROR); + } + + return COLVARS_OK; } diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 1cad4195d6..3d4296a4c9 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -81,6 +81,12 @@ private: public: + /// Get the version string (YYYY-MM-DD format) + std::string version() const + { + return std::string(COLVARS_VERSION); + } + /// Get the version number (higher = more recent) int version_number() const { @@ -150,6 +156,12 @@ public: return ::cos(static_cast(x)); } + /// Reimplemented to work around MS compiler issues + static inline real asin(real const &x) + { + return ::asin(static_cast(x)); + } + /// Reimplemented to work around MS compiler issues static inline real acos(real const &x) { @@ -685,6 +697,9 @@ public: static rvector position_distance(atom_pos const &pos1, atom_pos const &pos2); + /// \brief Names of .ndx files that have been loaded + std::vector index_file_names; + /// \brief Names of groups from one or more Gromacs .ndx files std::vector index_group_names; @@ -758,7 +773,11 @@ protected: /// Write labels at the next iteration bool cv_traj_write_labels; -private: + /// Version of the most recent state file read + std::string restart_version_str; + + /// Integer version of the most recent state file read + int restart_version_int; /// Counter for the current depth in the object hierarchy (useg e.g. in output) size_t depth_s; @@ -771,6 +790,18 @@ private: public: + /// Version of the most recent state file read + inline std::string restart_version() const + { + return restart_version_str; + } + + /// Integer version of the most recent state file read + inline int restart_version_number() const + { + return restart_version_int; + } + /// Get the current object depth in the hierarchy static size_t & depth(); diff --git a/lib/colvars/colvarmodule_utils.h b/lib/colvars/colvarmodule_utils.h new file mode 100644 index 0000000000..a7004edd92 --- /dev/null +++ b/lib/colvars/colvarmodule_utils.h @@ -0,0 +1,80 @@ +// -*- c++ -*- + +// This file is part of the Collective Variables module (Colvars). +// The original version of Colvars and its updates are located at: +// https://github.com/Colvars/colvars +// Please update all Colvars source files before making any changes. +// If you wish to distribute your changes, please submit them to the +// Colvars repository at GitHub. + + +#ifndef COLVARMODULE_UTILS_H +#define COLVARMODULE_UTILS_H + + +#include "colvarmodule.h" + + +template +cvm::real get_force_norm2(T const &x) +{ + return x.norm2(); +} + + +template <> +inline cvm::real get_force_norm2(cvm::real const &x) +{ + return x*x; +} + + +template +cvm::real compute_norm2_stats(std::vector const &v, + int *minmax_index = NULL) +{ + cvm::real result = 0.0; + if (flag == -1) { + // Initialize for minimum search, using approx. largest float32 value + result = 1.0e38; + } + + typename std::vector::const_iterator xi = v.begin(); + size_t i = 0; + + if (get_index) *minmax_index = -1; // Let's not assume minmax_index is initialized to -1 + + for ( ; xi != v.end(); xi++, i++) { + cvm::real const norm2 = get_force_norm2(*xi); + if (flag == 0) { + result += norm2; + } + if (flag == 1) { + if (norm2 > result) { + result = norm2; + if (get_index) *minmax_index = i; + } + } + if (flag == -1) { + if (norm2 < result) { + result = norm2; + if (get_index) *minmax_index = i; + } + } + } + + size_t const n = v.size(); + + if (flag == 0) { + if (n > 0) { + result /= cvm::real(n); + } + } + + result = cvm::sqrt(result); + + return result; +} + + +#endif diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp index cbe19c1914..3449a681f3 100644 --- a/lib/colvars/colvarparse.cpp +++ b/lib/colvars/colvarparse.cpp @@ -125,6 +125,10 @@ void colvarparse::mark_key_set_user(std::string const &key_str, cvm::log("# "+key_str+" = "+cvm::to_str(value)+"\n", cvm::log_user_params()); } + if (parse_mode & parse_deprecation_warning) { + cvm::log("Warning: keyword "+key_str+ + " is deprecated. Check the documentation for the current equivalent.\n"); + } } @@ -919,6 +923,26 @@ int colvarparse::check_braces(std::string const &conf, return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK; } + +int colvarparse::check_ascii(std::string const &conf) +{ + // Check for non-ASCII characters + std::string line; + std::istringstream is(conf); + while (cvm::getline(is, line)) { + unsigned char const * const uchars = + reinterpret_cast(line.c_str()); + for (size_t i = 0; i < line.size(); i++) { + if (uchars[i] & 0x80U) { + cvm::log("Warning: non-ASCII character detected in this line: \""+ + line+"\".\n"); + } + } + } + return COLVARS_OK; +} + + void colvarparse::split_string(const std::string& data, const std::string& delim, std::vector& dest) { size_t index = 0, new_index = 0; std::string tmpstr; diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h index b7d42fdffa..8e35896f89 100644 --- a/lib/colvars/colvarparse.h +++ b/lib/colvars/colvarparse.h @@ -56,6 +56,8 @@ public: parse_echo = (1<<1), /// Print the default value of a keyword, if it is NOT given parse_echo_default = (1<<2), + /// Print a deprecation warning if the keyword is given + parse_deprecation_warning = (1<<3), /// Do not print the keyword parse_silent = 0, /// Raise error if the keyword is not provided @@ -66,7 +68,9 @@ public: /// The call is being executed from a read_restart() function parse_restart = (1<<18), /// Alias for old default behavior (should be phased out) - parse_normal = (1<<2) | (1<<1) | (1<<17) + parse_normal = (1<<2) | (1<<1) | (1<<17), + /// Settings for a deprecated keyword + parse_deprecated = (1<<1) | (1<<3) | (1<<17) }; /// \brief Check that all the keywords within "conf" are in the list @@ -317,6 +321,10 @@ public: /// from this position static int check_braces(std::string const &conf, size_t const start_pos); + /// \brief Check that a config string contains non-ASCII characters + /// \param conf The configuration string + static int check_ascii(std::string const &conf); + /// \brief Split a string with a specified delimiter into a vector /// \param data The string to be splitted /// \param delim A delimiter diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index 24f833f857..d0f83c70a7 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -24,12 +24,15 @@ #include "colvarproxy.h" #include "colvarscript.h" #include "colvaratoms.h" +#include "colvarmodule_utils.h" colvarproxy_system::colvarproxy_system() { angstrom_value = 0.0; + kcal_mol_value = 0.0; + boundaries_type = boundaries_unsupported; total_force_requested = false; reset_pbc_lattice(); } @@ -38,6 +41,46 @@ colvarproxy_system::colvarproxy_system() colvarproxy_system::~colvarproxy_system() {} +int colvarproxy_system::set_unit_system(std::string const & /* units */, + bool /* check_only */) +{ + return COLVARS_NOT_IMPLEMENTED; +} + + +cvm::real colvarproxy_system::backend_angstrom_value() +{ + return 1.0; +} + + +cvm::real colvarproxy_system::boltzmann() +{ + return 0.001987191; +} + + +cvm::real colvarproxy_system::temperature() +{ + // TODO define, document and implement a user method to set the value of this + return 300.0; +} + + +cvm::real colvarproxy_system::dt() +{ + // TODO define, document and implement a user method to set the value of this + return 1.0; +} + + +cvm::real colvarproxy_system::rand_gaussian() +{ + // TODO define, document and implement a user method to set the value of this + return 0.0; +} + + void colvarproxy_system::add_energy(cvm::real /* energy */) {} @@ -139,9 +182,31 @@ int colvarproxy_system::get_molid(int &) } +int colvarproxy_system::get_alch_lambda(cvm::real* lambda) +{ + return cvm::error("Error in get_alch_lambda: alchemical lambda dynamics is not supported by this build.", + COLVARS_NOT_IMPLEMENTED); +} + + +int colvarproxy_system::set_alch_lambda(cvm::real* lambda) +{ + return cvm::error("Error in set_alch_lambda: alchemical lambda dynamics is not supported by this build.", + COLVARS_NOT_IMPLEMENTED); +} + + +int colvarproxy_system::get_dE_dLambda(cvm::real* force) +{ + return cvm::error("Error in get_dE_dLambda: alchemical lambda dynamics is not supported by this build.", + COLVARS_NOT_IMPLEMENTED); +} + colvarproxy_atoms::colvarproxy_atoms() { + atoms_rms_applied_force_ = atoms_max_applied_force_ = 0.0; + atoms_max_applied_force_id_ = -1; updated_masses_ = updated_charges_ = false; } @@ -178,6 +243,18 @@ int colvarproxy_atoms::add_atom_slot(int atom_id) } +int colvarproxy_atoms::init_atom(int /* atom_number */) +{ + return COLVARS_NOT_IMPLEMENTED; +} + + +int colvarproxy_atoms::check_atom_id(int /* atom_number */) +{ + return COLVARS_NOT_IMPLEMENTED; +} + + int colvarproxy_atoms::init_atom(cvm::residue_id const & /* residue */, std::string const & /* atom_name */, std::string const & /* segment_id */) @@ -232,8 +309,39 @@ int colvarproxy_atoms::load_coords(char const * /* filename */, } +void colvarproxy_atoms::compute_rms_atoms_applied_force() +{ + atoms_rms_applied_force_ = + compute_norm2_stats(atoms_new_colvar_forces); +} -colvarproxy_atom_groups::colvarproxy_atom_groups() {} + +void colvarproxy_atoms::compute_max_atoms_applied_force() +{ + int minmax_index = -1; + size_t const n_atoms_ids = atoms_ids.size(); + if ((n_atoms_ids > 0) && (n_atoms_ids == atoms_new_colvar_forces.size())) { + atoms_max_applied_force_ = + compute_norm2_stats(atoms_new_colvar_forces, + &minmax_index); + if (minmax_index >= 0) { + atoms_max_applied_force_id_ = atoms_ids[minmax_index]; + } else { + atoms_max_applied_force_id_ = -1; + } + } else { + atoms_max_applied_force_ = + compute_norm2_stats(atoms_new_colvar_forces); + atoms_max_applied_force_id_ = -1; + } +} + + + +colvarproxy_atom_groups::colvarproxy_atom_groups() +{ + atom_groups_rms_applied_force_ = atom_groups_max_applied_force_ = 0.0; +} colvarproxy_atom_groups::~colvarproxy_atom_groups() @@ -296,6 +404,20 @@ void colvarproxy_atom_groups::clear_atom_group(int index) } +void colvarproxy_atom_groups::compute_rms_atom_groups_applied_force() +{ + atom_groups_rms_applied_force_ = + compute_norm2_stats(atom_groups_new_colvar_forces); +} + + +void colvarproxy_atom_groups::compute_max_atom_groups_applied_force() +{ + atom_groups_max_applied_force_ = + compute_norm2_stats(atom_groups_new_colvar_forces); +} + + colvarproxy_smp::colvarproxy_smp() { @@ -464,28 +586,14 @@ int colvarproxy_smp::smp_unlock() colvarproxy_script::colvarproxy_script() { script = NULL; + force_script_defined = false; + have_scripts = false; } colvarproxy_script::~colvarproxy_script() {} -char const *colvarproxy_script::script_obj_to_str(unsigned char *obj) -{ - cvm::error("Error: trying to print a script object without a scripting " - "language interface.\n", BUG_ERROR); - return reinterpret_cast(obj); -} - - -std::vector colvarproxy_script::script_obj_to_str_vector(unsigned char * /* obj */) -{ - cvm::error("Error: trying to print a script object without a scripting " - "language interface.\n", BUG_ERROR); - return std::vector(); -} - - int colvarproxy_script::run_force_callback() { return COLVARS_NOT_IMPLEMENTED; @@ -512,6 +620,7 @@ int colvarproxy_script::run_colvar_gradient_callback(std::string const & /* name colvarproxy_io::colvarproxy_io() { input_buffer_ = NULL; + restart_frequency_engine = 0; } @@ -660,6 +769,23 @@ int colvarproxy::update_output() } +int colvarproxy::end_of_step() +{ + // Disable flags that Colvars doesn't need any more + updated_masses_ = updated_charges_ = false; + + // Compute force statistics + compute_rms_atoms_applied_force(); + compute_max_atoms_applied_force(); + compute_rms_atom_groups_applied_force(); + compute_max_atom_groups_applied_force(); + compute_rms_volmaps_applied_force(); + compute_max_volmaps_applied_force(); + + return COLVARS_OK; +} + + int colvarproxy::post_run() { int error_code = COLVARS_OK; @@ -672,6 +798,19 @@ int colvarproxy::post_run() } +void colvarproxy::log(std::string const &message) +{ + fprintf(stdout, "colvars: %s", message.c_str()); +} + + +void colvarproxy::error(std::string const &message) +{ + // TODO handle errors? + colvarproxy::log(message); +} + + void colvarproxy::add_error_msg(std::string const &message) { std::istringstream is(message); diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index 7a60292092..c9841ebdf4 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -59,7 +59,7 @@ public: std::string units; /// \brief Request to set the units used internally by Colvars - virtual int set_unit_system(std::string const &units, bool check_only) = 0; + virtual int set_unit_system(std::string const &units, bool check_only); /// \brief Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates /// * defaults to 0. in the base class; derived proxy classes must set it @@ -68,7 +68,7 @@ public: cvm::real angstrom_value; /// \brief Value of 1 Angstrom in the backend's unit for atomic coordinates - virtual cvm::real backend_angstrom_value() = 0; + virtual cvm::real backend_angstrom_value(); /// \brief Value of 1 kcal/mol in the internal Colvars unit for energy cvm::real kcal_mol_value; @@ -79,6 +79,12 @@ public: return l * angstrom_value; } + /// \brief Convert a length from internal to Angstrom + inline cvm::real internal_to_angstrom(cvm::real l) const + { + return l / angstrom_value; + } + // /// \brief Convert a length from back-end unit to internal // inline cvm::real back_end_to_internal_unit(cvm::real l) { // if (angstrom_value == 0.) { @@ -88,19 +94,19 @@ public: // } /// \brief Boltzmann constant in internal Colvars units - virtual cvm::real boltzmann() = 0; + virtual cvm::real boltzmann(); /// \brief Target temperature of the simulation (K units) - virtual cvm::real temperature() = 0; + virtual cvm::real temperature(); /// \brief Time step of the simulation (fs) - virtual cvm::real dt() = 0; + virtual cvm::real dt(); /// \brief Pseudo-random number with Gaussian distribution - virtual cvm::real rand_gaussian(void) = 0; + virtual cvm::real rand_gaussian(void); /// Pass restraint energy value for current timestep to MD engine - virtual void add_energy(cvm::real energy) = 0; + virtual void add_energy(cvm::real energy); /// \brief Get the PBC-aware distance vector between two positions virtual cvm::rvector position_distance(cvm::atom_pos const &pos1, @@ -126,6 +132,15 @@ public: /// \param molid Set this argument equal to the current VMD molid virtual int get_molid(int &molid); + /// Get value of alchemical lambda parameter from back-end (if available) + virtual int get_alch_lambda(cvm::real* lambda); + + /// Set value of alchemical lambda parameter in back-end (if available) + virtual int set_alch_lambda(cvm::real* lambda); + + /// Get energy derivative with respect to lambda (if available) + virtual int get_dE_dLambda(cvm::real* force); + protected: /// Whether the total forces have been requested @@ -167,11 +182,11 @@ public: /// Prepare this atom for collective variables calculation, selecting it by /// numeric index (1-based) - virtual int init_atom(int atom_number) = 0; + virtual int init_atom(int atom_number); /// Check that this atom number is valid, but do not initialize the /// corresponding atom yet - virtual int check_atom_id(int atom_number) = 0; + virtual int check_atom_id(int atom_number); /// Select this atom for collective variables calculation, using name and /// residue number. Not all programs support this: leave this function as @@ -262,11 +277,16 @@ public: return cvm::rvector(0.0); } - inline std::vector *modify_atom_ids() + inline std::vector const *get_atom_ids() const { return &atoms_ids; } + inline std::vector const *get_atom_masses() const + { + return &atoms_masses; + } + inline std::vector *modify_atom_masses() { // assume that we are requesting masses to change them @@ -274,6 +294,11 @@ public: return &atoms_masses; } + inline std::vector const *get_atom_charges() + { + return &atoms_charges; + } + inline std::vector *modify_atom_charges() { // assume that we are requesting charges to change them @@ -281,21 +306,60 @@ public: return &atoms_charges; } + inline std::vector const *get_atom_positions() const + { + return &atoms_positions; + } + inline std::vector *modify_atom_positions() { return &atoms_positions; } + inline std::vector const *get_atom_total_forces() const + { + return &atoms_total_forces; + } + inline std::vector *modify_atom_total_forces() { return &atoms_total_forces; } - inline std::vector *modify_atom_new_colvar_forces() + inline std::vector const *get_atom_applied_forces() const { return &atoms_new_colvar_forces; } + inline std::vector *modify_atom_applied_forces() + { + return &atoms_new_colvar_forces; + } + + /// Compute the root-mean-square of the applied forces + void compute_rms_atoms_applied_force(); + + /// Compute the maximum norm among all applied forces + void compute_max_atoms_applied_force(); + + /// Get the root-mean-square of the applied forces + inline cvm::real rms_atoms_applied_force() const + { + return atoms_rms_applied_force_; + } + + /// Get the maximum norm among all applied forces + inline cvm::real max_atoms_applied_force() const + { + return atoms_max_applied_force_; + } + + /// Get the atom ID with the largest applied force + inline int max_atoms_applied_force_id() const + { + return atoms_max_applied_force_id_; + } + /// Record whether masses have been updated inline bool updated_masses() const { @@ -326,6 +390,15 @@ protected: /// \brief Forces applied from colvars, to be communicated to the MD integrator std::vector atoms_new_colvar_forces; + /// Root-mean-square of the applied forces + cvm::real atoms_rms_applied_force_; + + /// Maximum norm among all applied forces + cvm::real atoms_max_applied_force_; + + /// ID of the atom with the maximum norm among all applied forces + int atoms_max_applied_force_id_; + /// Whether the masses and charges have been updated from the host code bool updated_masses_, updated_charges_; @@ -404,6 +477,56 @@ public: return cvm::rvector(0.0); } + inline std::vector const *get_atom_group_ids() const + { + return &atom_groups_ids; + } + + inline std::vector *modify_atom_group_masses() + { + // TODO updated_masses + return &atom_groups_masses; + } + + inline std::vector *modify_atom_group_charges() + { + // TODO updated masses + return &atom_groups_charges; + } + + inline std::vector *modify_atom_group_positions() + { + return &atom_groups_coms; + } + + inline std::vector *modify_atom_group_total_forces() + { + return &atom_groups_total_forces; + } + + inline std::vector *modify_atom_group_applied_forces() + { + return &atom_groups_new_colvar_forces; + } + + /// Compute the root-mean-square of the applied forces + void compute_rms_atom_groups_applied_force(); + + /// Compute the maximum norm among all applied forces + void compute_max_atom_groups_applied_force(); + + /// Get the root-mean-square of the applied forces + inline cvm::real rms_atom_groups_applied_force() const + { + return atom_groups_rms_applied_force_; + } + + /// Get the maximum norm among all applied forces + inline cvm::real max_atom_groups_applied_force() const + { + return atom_groups_max_applied_force_; + } + protected: /// \brief Array of 0-based integers used to uniquely associate atom groups @@ -422,6 +545,12 @@ protected: /// \brief Forces applied from colvars, to be communicated to the MD integrator std::vector atom_groups_new_colvar_forces; + /// Root-mean-square of the applied group forces + cvm::real atom_groups_rms_applied_force_; + + /// Maximum norm among all applied group forces + cvm::real atom_groups_max_applied_force_; + /// Used by all init_atom_group() functions: create a slot for an atom group not requested yet int add_atom_group_slot(int atom_group_id); }; @@ -519,12 +648,6 @@ public: /// Destructor virtual ~colvarproxy_script(); - /// Convert a script object (Tcl or Python call argument) to a C string - virtual char const *script_obj_to_str(unsigned char *obj); - - /// Convert a script object (Tcl or Python call argument) to a vector of strings - virtual std::vector script_obj_to_str_vector(unsigned char *obj); - /// Pointer to the scripting interface object /// (does not need to be allocated in a new interface) colvarscript *script; @@ -706,11 +829,14 @@ public: /// \brief Update data based from the results of a module update (e.g. send forces) virtual int update_output(); + /// Carry out operations needed before next step is run + int end_of_step(); + /// Print a message to the main log - virtual void log(std::string const &message) = 0; + virtual void log(std::string const &message); /// Print a message to the main log and/or let the host code know about it - virtual void error(std::string const &message) = 0; + virtual void error(std::string const &message); /// Record error message (used by VMD to collect them after a script call) void add_error_msg(std::string const &message); diff --git a/lib/colvars/colvarproxy_tcl.cpp b/lib/colvars/colvarproxy_tcl.cpp index a799bead7d..0a5473cae9 100644 --- a/lib/colvars/colvarproxy_tcl.cpp +++ b/lib/colvars/colvarproxy_tcl.cpp @@ -11,6 +11,8 @@ #if defined(NAMD_TCL) || defined(VMDTCL) #define COLVARS_TCL +#endif +#ifdef COLVARS_TCL #include #endif diff --git a/lib/colvars/colvarproxy_tcl.h b/lib/colvars/colvarproxy_tcl.h index 371b3c0224..badb62f900 100644 --- a/lib/colvars/colvarproxy_tcl.h +++ b/lib/colvars/colvarproxy_tcl.h @@ -27,7 +27,7 @@ public: /// Is Tcl available? (trigger initialization if needed) int tcl_available(); - /// Tcl implementation of script_obj_to_str() + /// Get a string representation of the Tcl object pointed to by obj char const *tcl_get_str(void *obj); /// Tcl implementation of run_force_callback() @@ -51,6 +51,12 @@ public: return tcl_interp_; } + /// Set the pointer to the Tcl interpreter + inline void set_tcl_interp(void *interp) + { + tcl_interp_ = interp; + } + protected: /// Pointer to Tcl interpreter object diff --git a/lib/colvars/colvarproxy_volmaps.cpp b/lib/colvars/colvarproxy_volmaps.cpp index fc665eec99..03e5d303d1 100644 --- a/lib/colvars/colvarproxy_volmaps.cpp +++ b/lib/colvars/colvarproxy_volmaps.cpp @@ -9,9 +9,13 @@ #include "colvarmodule.h" #include "colvarproxy_volmaps.h" +#include "colvarmodule_utils.h" -colvarproxy_volmaps::colvarproxy_volmaps() {} +colvarproxy_volmaps::colvarproxy_volmaps() +{ + volmaps_rms_applied_force_ = volmaps_max_applied_force_ = 0.0; +} colvarproxy_volmaps::~colvarproxy_volmaps() {} @@ -46,25 +50,41 @@ int colvarproxy_volmaps::add_volmap_slot(int volmap_id) } -int colvarproxy_volmaps::init_volmap(int volmap_id) +int colvarproxy_volmaps::check_volmap_by_id(int /* volmap_id */) { - return cvm::error("Error: access to volumetric maps is unavailable " - "in this build.\n", + return cvm::error("Error: selecting volumetric maps is not available.\n", COLVARS_NOT_IMPLEMENTED); } -int colvarproxy_volmaps::init_volmap(const char *volmap_name) +int colvarproxy_volmaps::check_volmap_by_name(const char * /* volmap_name */) { - return cvm::error("Error: access to volumetric maps is unavailable " - "in this build.\n", - COLVARS_NOT_IMPLEMENTED); + return cvm::error("Error: selecting volumetric maps by name is not " + "available.\n", COLVARS_NOT_IMPLEMENTED); } -int colvarproxy_volmaps::init_volmap(const std::string &volmap_name) +int colvarproxy_volmaps::init_volmap_by_name(char const *volmap_name) { - return init_volmap(volmap_name.c_str()); + return -1; +} + + +int colvarproxy_volmaps::init_volmap_by_id(int volmap_id) +{ + return -1; +} + + +int colvarproxy_volmaps::init_volmap_by_name(std::string const &volmap_name) +{ + return init_volmap_by_name(volmap_name.c_str()); +} + + +int colvarproxy_volmaps::check_volmap_by_name(std::string const &volmap_name) +{ + return check_volmap_by_name(volmap_name.c_str()); } @@ -79,3 +99,36 @@ void colvarproxy_volmaps::clear_volmap(int index) volmaps_ncopies[index] -= 1; } } + + +int colvarproxy_volmaps::get_volmap_id_from_name(char const *volmap_name) +{ + // Raise error + colvarproxy_volmaps::check_volmap_by_name(volmap_name); + return -1; +} + + +int colvarproxy_volmaps::compute_volmap(int /* flags */, + int /* volmap_id */, + cvm::atom_iter /* atom_begin */, + cvm::atom_iter /* atom_end */, + cvm::real * /* value */, + cvm::real * /* atom_field */) +{ + return COLVARS_NOT_IMPLEMENTED; +} + + +void colvarproxy_volmaps::compute_rms_volmaps_applied_force() +{ + volmaps_rms_applied_force_ = + compute_norm2_stats(volmaps_new_colvar_forces); +} + + +void colvarproxy_volmaps::compute_max_volmaps_applied_force() +{ + volmaps_max_applied_force_ = + compute_norm2_stats(volmaps_new_colvar_forces); +} diff --git a/lib/colvars/colvarproxy_volmaps.h b/lib/colvars/colvarproxy_volmaps.h index 67cbb2cd2d..6e88ee83f9 100644 --- a/lib/colvars/colvarproxy_volmaps.h +++ b/lib/colvars/colvarproxy_volmaps.h @@ -25,17 +25,37 @@ public: int add_volmap_slot(int volmap_id); /// Request and prepare this volumetric map for use by Colvars - virtual int init_volmap(int volmap_id); + /// \param volmap_id Numeric ID used by the MD engine + /// \returns Index of the map in the colvarproxy arrays + virtual int init_volmap_by_id(int volmap_id); /// Request and prepare this volumetric map for use by Colvars - virtual int init_volmap(char const *volmap_name); + /// \param volmap_name Name used by the MD engine + /// \returns Index of the map in the colvarproxy arrays + virtual int init_volmap_by_name(char const *volmap_name); + + /// Check that the given volmap ID is valid (return COLVARS_OK if it is) + /// \param volmap_id Numeric ID used by the MD engine + /// \returns Error code + virtual int check_volmap_by_id(int volmap_id); + + /// Check that the given volmap name is valid (return COLVARS_OK if it is) + /// \param volmap_name Name used by the MD engine + /// \returns Error code + virtual int check_volmap_by_name(char const *volmap_name); /// Request and prepare this volumetric map for use by Colvars - int init_volmap(std::string const &volmap_name); + int init_volmap_by_name(std::string const &volmap_name); + + /// Check that the given volmap name is valid (return COLVARS_OK if it is) + int check_volmap_by_name(std::string const &volmap_name); /// \brief Used by the CVC destructors virtual void clear_volmap(int index); + /// Get the numeric ID of the given volumetric map (for the MD program) + virtual int get_volmap_id_from_name(char const *volmap_name); + /// Get the numeric ID of the given volumetric map (for the MD program) inline int get_volmap_id(int index) const { @@ -54,6 +74,32 @@ public: volmaps_new_colvar_forces[index] += new_force; } + /// Re-weigh an atomic field (e.g. a colvar) by the value of a volumetric map + /// \param flags Combination of flags + /// \param volmap_id Numeric index of the map (no need to request it) + /// \param atom_begin Iterator pointing to first atom + /// \param atom_end Iterator pointing past the last atom + /// \param value Pointer to location of total to increment + /// \param atom_field Array of atomic field values (if NULL, ones are used) + virtual int compute_volmap(int flags, + int volmap_id, + cvm::atom_iter atom_begin, + cvm::atom_iter atom_end, + cvm::real *value, + cvm::real *atom_field); + + /// Flags controlling what computation is done on the map + enum { + volmap_flag_null = 0, + volmap_flag_gradients = 1, + volmap_flag_use_atom_field = (1<<8) + }; + + /// Compute the root-mean-square of the applied forces + void compute_rms_volmaps_applied_force(); + + /// Compute the maximum norm among all applied forces + void compute_max_volmaps_applied_force(); protected: @@ -70,6 +116,12 @@ protected: /// \brief Forces applied from colvars, to be communicated to the MD /// integrator std::vector volmaps_new_colvar_forces; + + /// Root-mean-square of the the applied forces + cvm::real volmaps_rms_applied_force_; + + /// Maximum norm among all applied forces + cvm::real volmaps_max_applied_force_; }; diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index 33e05d72d1..dd56c39f3a 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2020-09-17" +#define COLVARS_VERSION "2021-08-06" #endif diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp index ebd52b10ad..490ff6e81c 100644 --- a/lib/colvars/colvarscript.cpp +++ b/lib/colvars/colvarscript.cpp @@ -13,6 +13,8 @@ #if defined(NAMD_TCL) || defined(VMDTCL) #define COLVARS_TCL +#endif +#ifdef COLVARS_TCL #include #endif @@ -23,6 +25,19 @@ +#ifdef COLVARS_TCL +/// Run the script API via Tcl command-line interface +/// \param clientData Not used +/// \param my_interp Pointer to Tcl_Interp object (read from Colvars if NULL) +/// \param objc Number of Tcl command parameters +/// \param objv Array of command parameters +/// \return Result of the script command +extern "C" int tcl_run_colvarscript_command(ClientData clientData, + Tcl_Interp *interp_in, + int objc, Tcl_Obj *const objv[]); +#endif + + colvarscript::colvarscript(colvarproxy *p) : proxy_(p), colvars(p->colvars), @@ -57,9 +72,11 @@ int colvarscript::init_commands() } cmd_help.resize(colvarscript::cv_n_commands); + cmd_rethelp.resize(colvarscript::cv_n_commands); cmd_n_args_min.resize(colvarscript::cv_n_commands); cmd_n_args_max.resize(colvarscript::cv_n_commands); cmd_arghelp.resize(colvarscript::cv_n_commands); + cmd_full_help.resize(colvarscript::cv_n_commands); cmd_fns.resize(colvarscript::cv_n_commands); if (cmd_names) { @@ -95,24 +112,60 @@ int colvarscript::init_command(colvarscript::command const &comm, { cmd_str_map[std::string(name)] = comm; cmd_names[comm] = name; - cmd_help[comm] = help; + + // Initialize short help string and return-value help string (if present) + { + std::string const help_str(help); + std::istringstream is(help_str); + std::string line; + std::getline(is, line); + cmd_help[comm] = line; + cmd_rethelp[comm] = ""; + while (std::getline(is, line)) { + cmd_rethelp[comm] += line + "\n"; + } + } + + // Initialize arguments' help strings cmd_n_args_min[comm] = n_args_min; cmd_n_args_max[comm] = n_args_max; - std::string const arghelp_str(arghelp); - std::istringstream is(arghelp_str); - std::string line; - for (int iarg = 0; iarg < n_args_max; iarg++) { - if (! std::getline(is, line)) { - return cvm::error("Error: could not initialize help string for scripting " - "command \""+std::string(name)+"\".\n", BUG_ERROR); + { + std::string const arghelp_str(arghelp); + std::istringstream is(arghelp_str); + std::string line; + for (int iarg = 0; iarg < n_args_max; iarg++) { + if (! std::getline(is, line)) { + return cvm::error("Error: could not initialize help string for scripting " + "command \""+std::string(name)+"\".\n", BUG_ERROR); + } + cmd_arghelp[comm].push_back(line); } - cmd_arghelp[comm].push_back(line); } + + cmd_full_help[comm] = cmd_help[comm]+"\n"; + if (cmd_n_args_min[comm] > 0) { + cmd_full_help[comm] += "\nParameters\n"; + cmd_full_help[comm] += "----------\n\n"; + size_t i; + for (i = 0; i < cmd_n_args_min[comm]; i++) { + cmd_full_help[comm] += cmd_arghelp[comm][i]+"\n"; + } + for (i = cmd_n_args_min[comm]; i < cmd_n_args_max[comm]; i++) { + cmd_full_help[comm] += cmd_arghelp[comm][i]+" (optional)\n"; + } + } + if (cmd_rethelp[comm].size() > 0) { + cmd_full_help[comm] += "\nReturns\n"; + cmd_full_help[comm] += "-------\n\n"; + cmd_full_help[comm] += cmd_rethelp[comm]+"\n"; + } + cmd_fns[comm] = fn; if (cvm::debug()) { cvm::log("Defined command \""+std::string(name)+"\", with help string:\n"); - cvm::log(get_command_help(name)); + cvm::log(get_command_full_help(name)); } + return COLVARS_OK; } @@ -133,27 +186,76 @@ std::string colvarscript::get_cmd_prefix(colvarscript::Object_type t) } -std::string colvarscript::get_command_help(char const *cmd) + +char const *colvarscript::get_command_help(char const *cmd) { if (cmd_str_map.count(cmd) > 0) { colvarscript::command const c = cmd_str_map[std::string(cmd)]; - std::string new_result(cmd_help[c]+"\n"); - if (cmd_n_args_max[c] == 0) return new_result; - new_result += "\nParameters\n"; - new_result += "----------\n\n"; - size_t i; - for (i = 0; i < cmd_n_args_min[c]; i++) { - new_result += cmd_arghelp[c][i]+"\n"; - } - for (i = cmd_n_args_min[c]; i < cmd_n_args_max[c]; i++) { - new_result += cmd_arghelp[c][i]+" (optional)\n"; - } - return new_result; + return cmd_help[c].c_str(); } - cvm::error("Error: command "+std::string(cmd)+ " is not implemented.\n", INPUT_ERROR); - return std::string(""); + return NULL; +} + + +char const *colvarscript::get_command_rethelp(char const *cmd) +{ + if (cmd_str_map.count(cmd) > 0) { + colvarscript::command const c = cmd_str_map[std::string(cmd)]; + return cmd_rethelp[c].c_str(); + } + cvm::error("Error: command "+std::string(cmd)+ + " is not implemented.\n", INPUT_ERROR); + return NULL; +} + + +char const *colvarscript::get_command_arghelp(char const *cmd, int i) +{ + if (cmd_str_map.count(cmd) > 0) { + colvarscript::command const c = cmd_str_map[std::string(cmd)]; + return cmd_arghelp[c][i].c_str(); + } + cvm::error("Error: command "+std::string(cmd)+ + " is not implemented.\n", INPUT_ERROR); + return NULL; +} + + +int colvarscript::get_command_n_args_min(char const *cmd) +{ + if (cmd_str_map.count(cmd) > 0) { + colvarscript::command const c = cmd_str_map[std::string(cmd)]; + return cmd_n_args_min[c]; + } + cvm::error("Error: command "+std::string(cmd)+ + " is not implemented.\n", INPUT_ERROR); + return -1; +} + + +int colvarscript::get_command_n_args_max(char const *cmd) +{ + if (cmd_str_map.count(cmd) > 0) { + colvarscript::command const c = cmd_str_map[std::string(cmd)]; + return cmd_n_args_max[c]; + } + cvm::error("Error: command "+std::string(cmd)+ + " is not implemented.\n", INPUT_ERROR); + return -1; +} + + +char const *colvarscript::get_command_full_help(char const *cmd) +{ + if (cmd_str_map.count(cmd) > 0) { + colvarscript::command const c = cmd_str_map[std::string(cmd)]; + return cmd_full_help[c].c_str(); + } + cvm::error("Error: command "+std::string(cmd)+ + " is not implemented.\n", INPUT_ERROR); + return NULL; } @@ -234,7 +336,7 @@ std::string colvarscript::get_command_cmdline_help(colvarscript::Object_type t, if (cmd_str_map.count(cmdkey) > 0) { command const c = cmd_str_map[cmdkey]; return get_command_cmdline_syntax(t, c)+"\n\n"+ - get_command_help(cmd_names[c]); + get_command_full_help(cmd_names[c]); } cvm::error("Error: could not find scripting command \""+cmd+"\".", INPUT_ERROR); @@ -244,7 +346,7 @@ std::string colvarscript::get_command_cmdline_help(colvarscript::Object_type t, int colvarscript::run(int objc, unsigned char *const objv[]) { - result.clear(); + clear_str_result(); if (cvm::debug()) { cvm::log("Called script run with " + cvm::to_str(objc) + " args:"); @@ -346,6 +448,60 @@ int colvarscript::run(int objc, unsigned char *const objv[]) } +char *colvarscript::obj_to_str(unsigned char *obj) +{ + char *strobj = reinterpret_cast(obj); + if (cvm::debug()) { + cvm::log("Using simple-cast script::obj_to_str(): result = \"" + + (strobj ? std::string(strobj) : std::string("(null)")) + "\""); + } + return strobj; +} + + +std::vector colvarscript::obj_to_str_vector(unsigned char *obj) +{ + if (cvm::debug()) { + cvm::log("Using simple-cast colvarscript::obj_to_str_vector().\n"); + } + + std::vector new_result; + std::string const str(reinterpret_cast(obj)); + + // TODO get rid of this once colvarscript can handle both fix_modify and Tcl? + // LAMMPS has a nicer function in the utils class + + for (size_t i = 0; i < str.length(); i++) { + char const c = str[i]; + if (c == '\"') { + i++; + if (i >= str.length()) { + cvm::error("Error: could not split the following string:\n"+ + str+"\n", INPUT_ERROR); + break; + } + new_result.push_back(std::string("")); + while (str[i] != '\"') { + new_result.back().append(1, str[i]); + if (i >= str.length()) { + cvm::error("Error: could not split the following string:\n"+ + str+"\n", INPUT_ERROR); + break; + } else { + i++; + } + } + } + } + + if (cvm::debug()) { + cvm::log("result = "+cvm::to_str(new_result)+".\n"); + } + + return new_result; +} + + int colvarscript::proc_features(colvardeps *obj, int objc, unsigned char *const objv[]) { @@ -428,9 +584,9 @@ int colvarscript::set_result_str(std::string const &s) { if (cvm::get_error() != COLVARS_OK) { // Avoid overwriting the error message - result += s; + modify_str_result() += s; } else { - result = s; + modify_str_result() = s; } return COLVARS_OK; } @@ -438,17 +594,17 @@ int colvarscript::set_result_str(std::string const &s) void colvarscript::add_error_msg(std::string const &s) { - result += s; + modify_str_result() += s; // Ensure terminating newlines if (s[s.size()-1] != '\n') { - result += "\n"; + modify_str_result() += "\n"; } } int colvarscript::clear_str_result() { - result.clear(); + modify_str_result().clear(); return COLVARS_OK; } @@ -487,32 +643,69 @@ const char * get_colvarscript_result() int tcl_colvars_vmd_init(Tcl_Interp *interp, int molid); #endif -extern "C" -int tcl_run_colvarscript_command(ClientData /* clientData */, - Tcl_Interp *my_interp, - int objc, Tcl_Obj *const objv[]) +#if !defined(VMDTCL) && !defined(NAMD_TCL) +extern "C" { + int Colvars_Init(Tcl_Interp *interp) { + colvarproxy *proxy = new colvarproxy(); + colvarmodule *colvars = new colvarmodule(proxy); + proxy->set_tcl_interp(reinterpret_cast(interp)); + proxy->colvars = colvars; + proxy->script = new colvarscript(proxy); + Tcl_CreateObjCommand(interp, "cv", tcl_run_colvarscript_command, + (ClientData *) NULL, (Tcl_CmdDeleteProc *) NULL); + Tcl_EvalEx(interp, "package provide colvars", -1, 0); + return TCL_OK; + } +} +#endif + + +extern "C" int tcl_run_colvarscript_command(ClientData /* clientData */, + Tcl_Interp *my_interp, + int objc, Tcl_Obj *const objv[]) { colvarmodule *colvars = cvm::main(); if (!colvars) { #if defined(VMDTCL) + + if (objc == 2) { + if (!strcmp(Tcl_GetString(objv[1]), "molid")) { + // return invalid molid + Tcl_SetResult(my_interp, (char *) "-1", TCL_STATIC); + } + if (!strcmp(Tcl_GetString(objv[1]), "delete") || + !strcmp(Tcl_GetString(objv[1]), "reset")) { + // nothing to delete or reset + Tcl_SetResult(my_interp, NULL, TCL_STATIC); + } + if (!strcmp(Tcl_GetString(objv[1]), "help")) { + // print message + Tcl_SetResult(my_interp, + (char *) "First, setup the Colvars module with: " + "cv molid |top", TCL_STATIC); + } + return TCL_OK; + } + if (objc >= 3) { // require a molid to create the module if (!strcmp(Tcl_GetString(objv[1]), "molid")) { - int molid = -1; + int molid = -(1<<16); // This value is used to indicate "top" if (strcmp(Tcl_GetString(objv[2]), "top")) { // If this is not "top", get the integer value Tcl_GetIntFromObj(my_interp, objv[2], &molid); } return tcl_colvars_vmd_init(my_interp, molid); } else { - // TODO allow calling cv help after this - Tcl_SetResult(my_interp, (char *) "Syntax error.", TCL_STATIC); + Tcl_SetResult(my_interp, (char *) "Syntax error. First, setup the Colvars module with cv molid |top", TCL_STATIC); return TCL_ERROR; } } + Tcl_SetResult(my_interp, (char *) "First, setup the Colvars module with: " - "cv molid ", TCL_STATIC); + "cv molid |top", TCL_STATIC); + #else Tcl_SetResult(my_interp, const_cast("Error: Colvars module not yet initialized"), @@ -534,10 +727,19 @@ int tcl_run_colvarscript_command(ClientData /* clientData */, cvm::clear_error(); - int retval = script->run(objc, - reinterpret_cast(objv)); + unsigned char * arg_pointers_[100]; + if (objc > 100) { + std::string const errstr = "Too many positional arguments ("+ + cvm::to_str(objc)+") passed to the \"cv\" command.\n"; + Tcl_SetResult(interp, const_cast(errstr.c_str()), TCL_VOLATILE); + return TCL_ERROR; + } + for (int i = 0; i < objc; i++) { + arg_pointers_[i] = reinterpret_cast(const_cast(proxy->tcl_get_str(objv[i]))); + } + int retval = script->run(objc, arg_pointers_); - std::string result = proxy->get_error_msgs() + script->result; + std::string result = proxy->get_error_msgs() + script->str_result(); Tcl_SetResult(interp, const_cast(result.c_str()), TCL_VOLATILE); @@ -558,3 +760,162 @@ int tcl_run_colvarscript_command(ClientData /* clientData */, } #endif // #if defined(COLVARS_TCL) + + + + +int colvarscript::set_result_text_from_str(std::string const &x_str, + unsigned char *obj) { + if (obj) { + strcpy(reinterpret_cast(obj), x_str.c_str()); + } else { + set_result_str(x_str); + } + return COLVARS_OK; +} + +// Template to convert everything to string and use the above + +template +int colvarscript::set_result_text(T const &x, unsigned char *obj) { + std::string const x_str = x.to_simple_string(); + return set_result_text_from_str(x_str, obj); +} + + +template +int colvarscript::pack_vector_elements_text(std::vector const &x, + std::string &x_str) { + x_str.clear(); + for (size_t i = 0; i < x.size(); ++i) { + if (i > 0) x_str.append(1, ' '); + x_str += cvm::to_str(x[i]); + } + return COLVARS_OK; +} + + +// Specializations for plain old data types that don't have a stringifier member + +template <> +int colvarscript::set_result_text(int const &x, unsigned char *obj) { + std::string const x_str = cvm::to_str(x); + return set_result_text_from_str(x_str, obj); +} + +template <> +int colvarscript::set_result_text(std::vector const &x, + unsigned char *obj) { + std::string x_str(""); + pack_vector_elements_text(x, x_str); + return set_result_text_from_str(x_str, obj); +} + + +template <> +int colvarscript::set_result_text(long int const &x, unsigned char *obj) { + std::string const x_str = cvm::to_str(x); + return set_result_text_from_str(x_str, obj); +} + +template <> +int colvarscript::set_result_text(std::vector const &x, + unsigned char *obj) { + std::string x_str(""); + pack_vector_elements_text(x, x_str); + return set_result_text_from_str(x_str, obj); +} + + +template <> +int colvarscript::set_result_text(cvm::real const &x, unsigned char *obj) { + std::string const x_str = cvm::to_str(x); + return set_result_text_from_str(x_str, obj); +} + +template <> +int colvarscript::set_result_text(std::vector const &x, + unsigned char *obj) { + std::string x_str(""); + pack_vector_elements_text(x, x_str); + return set_result_text_from_str(x_str, obj); +} + + +// TODO these can be removed after the Tcl backend is ready (otherwise, the +// default template syntax may break scripts or the Dashboard) + +template <> +int colvarscript::set_result_text(std::vector const &x, + unsigned char *obj) { + std::string x_str(""); + for (size_t i = 0; i < x.size(); i++) { + if (i > 0) x_str.append(1, ' '); + x_str += "{ "+x[i].to_simple_string()+" }"; + } + return set_result_text_from_str(x_str, obj); +} + +template <> +int colvarscript::set_result_text(std::vector const &x, + unsigned char *obj) { + std::string x_str(""); + for (size_t i = 0; i < x.size(); i++) { + if (i > 0) x_str.append(1, ' '); + x_str += "{ "+x[i].to_simple_string()+" }"; + } + return set_result_text_from_str(x_str, obj); +} + + +// Member functions to set script results for each typexc + +int colvarscript::set_result_int(int const &x, unsigned char *obj) { + return set_result_text(x, obj); +} + +int colvarscript::set_result_int_vec(std::vector const &x, + unsigned char *obj) { + return set_result_text< std::vector >(x, obj); +} + + +int colvarscript::set_result_long_int(long int const &x, unsigned char *obj) { + return set_result_text(x, obj); +} + +int colvarscript::set_result_long_int_vec(std::vector const &x, + unsigned char *obj) { + return set_result_text< std::vector >(x, obj); +} + + +int colvarscript::set_result_real(cvm::real const &x, unsigned char *obj) { + return set_result_text(x, obj); +} + +int colvarscript::set_result_real_vec(std::vector const &x, + unsigned char *obj) { + return set_result_text< std::vector >(x, obj); +} + + +int colvarscript::set_result_rvector(cvm::rvector const &x, unsigned char *obj) { + return set_result_text(x, obj); +} + +int colvarscript::set_result_rvector_vec(std::vector const &x, + unsigned char *obj) { + return set_result_text< std::vector >(x, obj); +} + + +int colvarscript::set_result_colvarvalue(colvarvalue const &x, + unsigned char *obj) { + return set_result_text(x, obj); +} + +int colvarscript::set_result_colvarvalue_vec(std::vector const &x, + unsigned char *obj) { + return set_result_text< std::vector >(x, obj); +} diff --git a/lib/colvars/colvarscript.h b/lib/colvars/colvarscript.h index d6f77668e6..7eac15c09d 100644 --- a/lib/colvars/colvarscript.h +++ b/lib/colvars/colvarscript.h @@ -46,9 +46,8 @@ public: /// COLVARSCRIPT_ERROR int proxy_error; - /// If an error is returned by one of the methods, it should set this to the - /// error message - std::string result; + /// String representation of the result of a script call + std::string str_result_; /// Run a script command with space-separated positional arguments (objects) int run(int objc, unsigned char *const objv[]); @@ -56,13 +55,13 @@ public: /// Get the string result of the current scripting call inline std::string const &str_result() const { - return result; + return str_result_; } /// Modify the string result of the current scripting call inline std::string &modify_str_result() { - return result; + return str_result_; } /// Set the return value to the given string @@ -137,21 +136,38 @@ public: template int cmd_arg_shift(); - /// Use scripting language to get the string representation of an object - inline char const *obj_to_str(unsigned char *const obj) - { - return (obj == NULL ? NULL : proxy_->script_obj_to_str(obj)); - } - /// Get names of all commands inline char const **get_command_names() const { return cmd_names; } + /// Get one-line help summary for a command + /// \param cmd Name of the command's function (e.g. "cv_units") + char const *get_command_help(char const *cmd); + + /// Get description of the return value of a command + /// \param cmd Name of the command's function (e.g. "cv_units") + char const *get_command_rethelp(char const *cmd); + + /// Get description of the argument of a command (excluding prefix) + /// \param cmd Name of the command's function (e.g. "cv_units") + /// \param i Index of the argument; 0 is the first argument after the + /// prefix, e.g. "value" has an index of 0 in the array of arguments: + /// { "cv", "colvar", "xi", "value" } + char const *get_command_arghelp(char const *cmd, int i); + + /// Get number of required arguments (excluding prefix) + /// \param cmd Name of the command's function (e.g. "cv_units") + int get_command_n_args_min(char const *cmd); + + /// Get number of total arguments (excluding prefix) + /// \param cmd Name of the command's function (e.g. "cv_units") + int get_command_n_args_max(char const *cmd); + /// Get help string for a command (does not specify how it is launched) /// \param cmd Name of the command's function (e.g. "cv_units") - std::string get_command_help(char const *cmd); + char const *get_command_full_help(char const *cmd); /// Get summary of command line syntax for all commands of a given context /// \param t One of use_module, use_colvar or use_bias @@ -182,6 +198,53 @@ public: return this->proxy_; } + // Input functions - get the string reps of script argument objects + + /// Get the string representation of an object (by default, a simple cast) + char *obj_to_str(unsigned char *obj); + + /// Get a list of strings from an object (does not work with a simple cast) + std::vector obj_to_str_vector(unsigned char *obj); + + + // Output functions - convert internal objects to representations suitable + // for use in the scripting language. At the moment only conversion to C + // strings is supported, and obj is assumed to be a char * pointer. + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_int(int const &x, unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_int_vec(std::vector const &x, unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_long_int(long int const &x, unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_long_int_vec(std::vector const &x, + unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_real(cvm::real const &x, unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_real_vec(std::vector const &x, + unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_rvector(cvm::rvector const &x, unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_rvector_vec(std::vector const &x, + unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_colvarvalue(colvarvalue const &x, unsigned char *obj = NULL); + + /// Copy x into obj if not NULL, or into the script object's result otherwise + int set_result_colvarvalue_vec(std::vector const &x, + unsigned char *obj = NULL); + private: /// Set up all script API functions @@ -193,14 +256,6 @@ private: int n_args_min, int n_args_max, char const *arghelp, int (*fn)(void *, int, unsigned char * const *)); - /// Execute a script command - inline int exec_command(command c, - void *pobj, - int objc, unsigned char * const *objv) - { - return (*(cmd_fns[c]))(pobj, objc, objv); - } - public: // TODO this function will be removed soon /// Run subcommands on base colvardeps object (colvar, bias, ...) @@ -218,6 +273,9 @@ private: // TODO /// Help strings for each command std::vector cmd_help; + /// Description of the return values of each command (may be empty) + std::vector cmd_rethelp; + /// Minimum number of arguments for each command std::vector cmd_n_args_min; @@ -227,6 +285,9 @@ private: // TODO /// Help strings for each command argument std::vector< std::vector > cmd_arghelp; + /// Full help strings for each command + std::vector cmd_full_help; + /// Implementations of each command std::vector cmd_fns; @@ -241,6 +302,18 @@ private: // TODO return NULL; } + /// Set obj equal to x, using its string representation + template + int set_result_text(T const &x, unsigned char *obj); + + /// Code reused by instances of set_result_text() + template + int pack_vector_elements_text(std::vector const &x, std::string &x_str); + + /// Code reused by all instances of set_result_text() + int set_result_text_from_str(std::string const &x_str, unsigned char *obj); + + }; @@ -305,13 +378,15 @@ int colvarscript::check_cmd_nargs(char const *cmd, { int const shift = cmd_arg_shift(); if (objc < shift+n_args_min) { - add_error_msg("Missing arguments for script function \""+std::string(cmd)+ - "\":\n"+get_command_help(cmd)); + add_error_msg("Insufficient number of arguments ("+cvm::to_str(objc)+ + ") for script function \""+std::string(cmd)+ + "\":\n"+get_command_full_help(cmd)); return COLVARSCRIPT_ERROR; } if (objc > shift+n_args_max) { - add_error_msg("Too many arguments for script function \""+std::string(cmd)+ - "\":\n"+get_command_help(cmd)); + add_error_msg("Too many arguments ("+cvm::to_str(objc)+ + ") for script function \""+std::string(cmd)+ + "\":\n"+get_command_full_help(cmd)); return COLVARSCRIPT_ERROR; } return COLVARSCRIPT_OK; @@ -364,18 +439,6 @@ int colvarscript::cmd_arg_shift() extern "C" { -#if defined(COLVARS_TCL) - /// Run the script API via Tcl command-line interface - /// \param clientData Not used - /// \param my_interp Pointer to Tcl_Interp object (read from Colvars if NULL) - /// \param objc Number of Tcl command parameters - /// \param objv Array of command parameters - /// \return Result of the script command - int tcl_run_colvarscript_command(ClientData clientData, - Tcl_Interp *interp_in, - int objc, Tcl_Obj *const objv[]); -#endif // #if defined(COLVARS_TCL) - /// Generic wrapper for string-based scripting int run_colvarscript_command(int objc, unsigned char *const objv[]); diff --git a/lib/colvars/colvarscript_commands.cpp b/lib/colvars/colvarscript_commands.cpp index c74663d2fd..0029979912 100644 --- a/lib/colvars/colvarscript_commands.cpp +++ b/lib/colvars/colvarscript_commands.cpp @@ -33,6 +33,54 @@ char const **cvscript_command_names() } +extern "C" +char const *cvscript_command_help(char const *c) +{ + colvarscript *script = colvarscript_obj(); + return script->get_command_help(c); +} + + +extern "C" +char const *cvscript_command_rethelp(char const *c) +{ + colvarscript *script = colvarscript_obj(); + return script->get_command_rethelp(c); +} + + +extern "C" +char const *cvscript_command_arghelp(char const *c, int i) +{ + colvarscript *script = colvarscript_obj(); + return script->get_command_arghelp(c, i); +} + + +extern "C" +char const *cvscript_command_full_help(char const *c) +{ + colvarscript *script = colvarscript_obj(); + return script->get_command_full_help(c); +} + + +extern "C" +int cvscript_command_n_args_min(char const *c) +{ + colvarscript *script = colvarscript_obj(); + return script->get_command_n_args_min(c); +} + + +extern "C" +int cvscript_command_n_args_max(char const *c) +{ + colvarscript *script = colvarscript_obj(); + return script->get_command_n_args_max(c); +} + + // Instantiate the body of all script commands #define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \ diff --git a/lib/colvars/colvarscript_commands.h b/lib/colvars/colvarscript_commands.h index d90a3ac422..021aae1cc6 100644 --- a/lib/colvars/colvarscript_commands.h +++ b/lib/colvars/colvarscript_commands.h @@ -25,7 +25,8 @@ // COMM = the id of the command (must be a member of colvarscript::command) -// HELP = a one-line description (C string literal) for the command +// HELP = short description (C string literal) for the command; the second line +// is optional, and documents the return value (if any) // N_ARGS_MIN = the lowest number of arguments allowed @@ -68,6 +69,33 @@ extern "C" { /// Get the names of all commands (array of strings) char const ** cvscript_command_names(); + /// Get the help summary of the given command + /// \param cmd Name of the command's function (e.g. "cv_units") + char const *cvscript_command_help(char const *cmd); + + /// Get description of the return value of a command + /// \param cmd Name of the command's function (e.g. "cv_units") + char const *cvscript_command_rethelp(char const *cmd); + + /// Get description of the arguments of a command (excluding prefix) + /// \param cmd Name of the command's function (e.g. "cv_units") + /// \param i Index of the argument; 0 is the first argument after the + /// prefix, e.g. "value" has an index of 0 in the array of arguments: + /// { "cv", "colvar", "xi", "value" } + char const *cvscript_command_arghelp(char const *cmd, int i); + + /// Get the full help string of a command + /// \param cmd Name of the command's function (e.g. "cv_units") + char const *cvscript_command_full_help(char const *cmd); + + /// Get number of required arguments (excluding prefix) + /// \param cmd Name of the command's function (e.g. "cv_units") + int cvscript_command_n_args_min(char const *cmd); + + /// Get number of total arguments (excluding prefix) + /// \param cmd Name of the command's function (e.g. "cv_units") + int cvscript_command_n_args_max(char const *cmd); + } #endif @@ -135,7 +163,8 @@ CVSCRIPT(cv_delete, ) CVSCRIPT(cv_frame, - "Get or set current frame number (VMD only)", + "Get or set current frame number (VMD only)\n" + "frame : integer - Frame number", 0, 1, "frame : integer - Frame number", char const *arg = @@ -143,7 +172,7 @@ CVSCRIPT(cv_frame, if (arg == NULL) { long int f = -1; if (script->proxy()->get_frame(f) == COLVARS_OK) { - script->set_result_str(cvm::to_str(f)); + script->set_result_long_int(f); return COLVARS_OK; } else { script->add_error_msg("Frame number is not available"); @@ -161,8 +190,90 @@ CVSCRIPT(cv_frame, return COLVARS_OK; ) +CVSCRIPT(cv_getatomappliedforces, + "Get the list of forces applied by Colvars to atoms\n" + "forces : array of arrays of floats - Atomic forces", + 0, 0, + "", + script->set_result_rvector_vec(*(script->proxy()->get_atom_applied_forces())); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatomappliedforcesmax, + "Get the maximum norm of forces applied by Colvars to atoms\n" + "force : float - Maximum atomic force", + 0, 0, + "", + script->set_result_real(script->proxy()->max_atoms_applied_force()); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatomappliedforcesmaxid, + "Get the atom ID with the largest applied force\n" + "id : int - ID of the atom with the maximum atomic force", + 0, 0, + "", + script->set_result_int(script->proxy()->max_atoms_applied_force_id()); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatomappliedforcesrms, + "Get the root-mean-square norm of forces applied by Colvars to atoms\n" + "force : float - RMS atomic force", + 0, 0, + "", + script->set_result_real(script->proxy()->rms_atoms_applied_force()); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatomids, + "Get the list of indices of atoms used in Colvars\n" + "indices : array of ints - Atomic indices", + 0, 0, + "", + script->set_result_int_vec(*(script->proxy()->get_atom_ids())); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatomcharges, + "Get the list of charges of atoms used in Colvars\n" + "charges : array of floats - Atomic charges", + 0, 0, + "", + script->set_result_real_vec(*(script->proxy()->get_atom_charges())); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatommasses, + "Get the list of masses of atoms used in Colvars\n" + "masses : array of floats - Atomic masses", + 0, 0, + "", + script->set_result_real_vec(*(script->proxy()->get_atom_masses())); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatompositions, + "Get the list of cached positions of atoms used in Colvars\n" + "positions : array of arrays of floats - Atomic positions", + 0, 0, + "", + script->set_result_rvector_vec(*(script->proxy()->get_atom_positions())); + return COLVARS_OK; + ) + +CVSCRIPT(cv_getatomtotalforces, + "Get the list of cached total forces of atoms used in Colvars\n" + "forces : array of arrays of floats - Atomic total foces", + 0, 0, + "", + script->set_result_rvector_vec(*(script->proxy()->get_atom_total_forces())); + return COLVARS_OK; + ) + CVSCRIPT(cv_getconfig, - "Get the module's configuration string read so far", + "Get the module's configuration string read so far\n" + "conf : string - Current configuration string", 0, 0, "", script->set_result_str(cvm::main()->get_config()); @@ -170,15 +281,17 @@ CVSCRIPT(cv_getconfig, ) CVSCRIPT(cv_getenergy, - "Get the current Colvars energy", + "Get the current Colvars energy\n" + "E : float - Amount of energy (internal units)", 0, 0, "", - script->set_result_str(cvm::to_str(cvm::main()->total_bias_energy)); + script->set_result_real(cvm::main()->total_bias_energy); return COLVARS_OK; ) CVSCRIPT(cv_help, - "Get the help string of the Colvars scripting interface", + "Get the help string of the Colvars scripting interface\n" + "help : string - Help string", 0, 1, "command : string - Get the help string of this specific command", unsigned char *const cmdobj = @@ -205,7 +318,8 @@ CVSCRIPT(cv_help, ) CVSCRIPT(cv_list, - "Return a list of all variables or biases", + "Return a list of all variables or biases\n" + "list : sequence of strings - List of elements", 0, 1, "param : string - \"colvars\" or \"biases\"; default is \"colvars\"", std::string res; @@ -235,7 +349,8 @@ CVSCRIPT(cv_list, ) CVSCRIPT(cv_listcommands, - "Get the list of script functions, prefixed with \"cv_\", \"colvar_\" or \"bias_\"", + "Get the list of script functions, prefixed with \"cv_\", \"colvar_\" or \"bias_\"\n" + "list : sequence of strings - List of commands", 0, 0, "", int const n_commands = cvscript_n_commands(); @@ -249,6 +364,20 @@ CVSCRIPT(cv_listcommands, return COLVARS_OK; ) +CVSCRIPT(cv_listindexfiles, + "Get a list of the index files loaded in this session", + 0, 0, + "", + int const n_files = script->module()->index_file_names.size(); + std::string result; + for (int i = 0; i < n_files; i++) { + if (i > 0) result.append(1, ' '); + result.append(script->module()->index_file_names[i]); + } + script->set_result_str(result); + return COLVARS_OK; + ) + CVSCRIPT(cv_load, "Load data from a state file into all matching colvars and biases", 1, 1, @@ -280,15 +409,16 @@ CVSCRIPT(cv_loadfromstring, ) CVSCRIPT(cv_molid, - "Get or set the molecule ID on which Colvars is defined (VMD only)", + "Get or set the molecule ID on which Colvars is defined (VMD only)\n" + "molid : integer - Current molecule ID", 0, 1, - "molid : integer - Molecule ID; -1 means undefined", + "molid : integer - New molecule ID; -1 means undefined", char const *arg = script->obj_to_str(script->get_module_cmd_arg(0, objc, objv)); if (arg == NULL) { int molid = -1; script->proxy()->get_molid(molid); - script->set_result_str(cvm::to_str(molid)); + script->set_result_int(molid); return COLVARS_OK; } else { script->add_error_msg("Error: To change the molecule ID in VMD, use cv delete first."); @@ -297,7 +427,8 @@ CVSCRIPT(cv_molid, ) CVSCRIPT(cv_printframe, - "Return the values that would be written to colvars.traj", + "Return the values that would be written to colvars.traj\n" + "values : string - The values\n", 0, 0, "", std::ostringstream os; @@ -307,7 +438,8 @@ CVSCRIPT(cv_printframe, ) CVSCRIPT(cv_printframelabels, - "Return the labels that would be written to colvars.traj", + "Return the labels that would be written to colvars.traj\n" + "Labels : string - The labels", 0, 0, "", std::ostringstream os; @@ -348,14 +480,16 @@ CVSCRIPT(cv_save, ) CVSCRIPT(cv_savetostring, - "Write the Colvars state to a string and return it", + "Write the Colvars state to a string and return it\n" + "state : string - The saved state", 0, 0, "", return script->module()->write_restart_string(script->modify_str_result()); ) CVSCRIPT(cv_units, - "Get or set the current Colvars unit system", + "Get or set the current Colvars unit system\n" + "units : string - The current unit system", 0, 1, "units : string - The new unit system", char const *argstr = @@ -390,7 +524,8 @@ CVSCRIPT(cv_update, ) CVSCRIPT(cv_version, - "Get the Colvars Module version number", + "Get the Colvars Module version number\n" + "version : string - Colvars version", 0, 0, "", script->set_result_str(COLVARS_VERSION); diff --git a/lib/colvars/colvarscript_commands_bias.h b/lib/colvars/colvarscript_commands_bias.h index 990902e239..f83b3422ff 100644 --- a/lib/colvars/colvarscript_commands_bias.h +++ b/lib/colvars/colvarscript_commands_bias.h @@ -9,15 +9,17 @@ CVSCRIPT(bias_bin, - "Get the current grid bin index (1D ABF only for now)", + "Get the current grid bin index (1D ABF only for now)\n" + "bin : integer - Bin index", 0, 0, "", - script->set_result_str(cvm::to_str(this_bias->current_bin())); + script->set_result_int(this_bias->current_bin()); return COLVARS_OK; ) CVSCRIPT(bias_bincount, - "Get the number of samples at the given grid bin (1D ABF only for now)", + "Get the number of samples at the given grid bin (1D ABF only for now)\n" + "samples : integer - Number of samples", 0, 1, "index : integer - Grid index; defaults to current bin", int index = this_bias->current_bin(); @@ -30,12 +32,13 @@ CVSCRIPT(bias_bincount, return COLVARSCRIPT_ERROR; } } - script->set_result_str(cvm::to_str(this_bias->bin_count(index))); + script->set_result_int(this_bias->bin_count(index)); return COLVARS_OK; ) CVSCRIPT(bias_binnum, - "Get the total number of grid points of this bias (1D ABF only for now)", + "Get the total number of grid points of this bias (1D ABF only for now)\n" + "Bins : integer - Number of grid points", 0, 0, "", int r = this_bias->bin_num(); @@ -44,7 +47,7 @@ CVSCRIPT(bias_binnum, this_bias->name); return COLVARSCRIPT_ERROR; } - script->set_result_str(cvm::to_str(r)); + script->set_result_int(r); return COLVARS_OK; ) @@ -57,22 +60,25 @@ CVSCRIPT(bias_delete, ) CVSCRIPT(bias_energy, - "Get the current energy of this bias", + "Get the current energy of this bias\n" + "E : float - Energy value", 0, 0, "", - script->set_result_str(cvm::to_str(this_bias->get_energy())); + script->set_result_real(this_bias->get_energy()); return COLVARS_OK; ) CVSCRIPT(bias_get, - "Get the value of the given feature for this bias", + "Get the value of the given feature for this bias\n" + "state : 1/0 - State of the given feature", 1, 1, "feature : string - Name of the feature", return script->proc_features(this_bias, objc, objv); ) CVSCRIPT(bias_getconfig, - "Return the configuration string of this bias", + "Return the configuration string of this bias\n" + "conf : string - Current configuration string", 0, 0, "", script->set_result_str(this_bias->get_config()); @@ -80,7 +86,8 @@ CVSCRIPT(bias_getconfig, ) CVSCRIPT(bias_help, - "Get a help summary or the help string of one bias subcommand", + "Get a help summary or the help string of one bias subcommand\n" + "help : string - Help string", 0, 1, "command : string - Get the help string of this specific command", unsigned char *const cmdobj = @@ -129,7 +136,8 @@ CVSCRIPT(bias_save, ) CVSCRIPT(bias_savetostring, - "Save data from this bias into a string and return it", + "Save data from this bias into a string and return it\n" + "state : string - The bias state", 0, 0, "", return this_bias->write_state_string(script->modify_str_result()); @@ -156,7 +164,8 @@ CVSCRIPT(bias_share, ) CVSCRIPT(bias_state, - "Print a string representation of the feature state of this bias", + "Print a string representation of the feature state of this bias\n" + "state : string - String representation of the bias features", 0, 0, "", this_bias->print_state(); @@ -164,10 +173,11 @@ CVSCRIPT(bias_state, ) CVSCRIPT(bias_update, - "Recompute this bias and return its up-to-date energy", + "Recompute this bias and return its up-to-date energy\n" + "E : float - Energy value", 0, 0, "", this_bias->update(); - script->set_result_str(cvm::to_str(this_bias->get_energy())); + script->set_result_colvarvalue(this_bias->get_energy()); return COLVARS_OK; ) diff --git a/lib/colvars/colvarscript_commands_colvar.h b/lib/colvars/colvarscript_commands_colvar.h index b880b5b8be..7c4c2d67f7 100644 --- a/lib/colvars/colvarscript_commands_colvar.h +++ b/lib/colvars/colvarscript_commands_colvar.h @@ -9,7 +9,8 @@ CVSCRIPT(colvar_addforce, - "Apply the given force onto this colvar and return the same", + "Apply the given force onto this colvar and return the same\n" + "force : float or array - Applied force; matches colvar dimensionality", 1, 1, "force : float or array - Applied force; must match colvar dimensionality", std::string const f_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv))); @@ -23,7 +24,7 @@ CVSCRIPT(colvar_addforce, return COLVARSCRIPT_ERROR; } this_colvar->add_bias_force(force); - script->set_result_str(force.to_simple_string()); + script->set_result_colvarvalue(force); return COLVARS_OK; ) @@ -56,22 +57,25 @@ CVSCRIPT(colvar_delete, ) CVSCRIPT(colvar_get, - "Get the value of the given feature for this colvar", + "Get the value of the given feature for this colvar\n" + "state : 1/0 - State of the given feature", 1, 1, "feature : string - Name of the feature", return script->proc_features(this_colvar, objc, objv); ) CVSCRIPT(colvar_getappliedforce, - "Return the total of the forces applied to this colvar", + "Return the total of the forces applied to this colvar\n" + "force : float - Applied force; matches the colvar dimensionality", 0, 0, "", - script->set_result_str((this_colvar->applied_force()).to_simple_string()); + script->set_result_colvarvalue(this_colvar->applied_force()); return COLVARS_OK; ) CVSCRIPT(colvar_getatomgroups, - "Return the atom indices used by this colvar as a list of lists", + "Return the atom indices used by this colvar as a list of lists\n" + "groups : array of arrays of ints - Atom indices", 0, 0, "", std::string result; @@ -91,21 +95,17 @@ CVSCRIPT(colvar_getatomgroups, ) CVSCRIPT(colvar_getatomids, - "Return the list of atom indices used by this colvar", + "Return the list of atom indices used by this colvar\n" + "indices : array of ints - Atom indices", 0, 0, "", - std::string result; - std::vector::iterator li = this_colvar->atom_ids.begin(); - for ( ; li != this_colvar->atom_ids.end(); ++li) { - result += cvm::to_str(*li); - result += " "; - } - script->set_result_str(result); + script->set_result_int_vec(this_colvar->atom_ids); return COLVARS_OK; ) CVSCRIPT(colvar_getconfig, - "Return the configuration string of this colvar", + "Return the configuration string of this colvar\n" + "conf : string - Current configuration string", 0, 0, "", script->set_result_str(this_colvar->get_config()); @@ -113,35 +113,34 @@ CVSCRIPT(colvar_getconfig, ) CVSCRIPT(colvar_getgradients, - "Return the atomic gradients of this colvar", + "Return the atomic gradients of this colvar\n" + "gradients : array of arrays of floats - Atomic gradients", 0, 0, "", - std::string result; - std::vector::iterator li = - this_colvar->atomic_gradients.begin(); - for ( ; li != this_colvar->atomic_gradients.end(); ++li) { - result += "{"; - int j; - for (j = 0; j < 3; ++j) { - result += cvm::to_str((*li)[j]); - result += " "; - } - result += "} "; - } - script->set_result_str(result); + script->set_result_rvector_vec(this_colvar->atomic_gradients); return COLVARS_OK; ) CVSCRIPT(colvar_gettotalforce, - "Return the sum of internal and external forces to this colvar", + "Return the sum of internal and external forces to this colvar\n" + "force : float - Total force; matches the colvar dimensionality", 0, 0, "", - script->set_result_str((this_colvar->total_force()).to_simple_string()); + script->set_result_colvarvalue(this_colvar->total_force()); + return COLVARS_OK; + ) + +CVSCRIPT(colvar_getvolmapids, + "Return the list of volumetric map indices used by this colvar", + 0, 0, + "", + script->set_result_int_vec(this_colvar->get_volmap_ids()); return COLVARS_OK; ) CVSCRIPT(colvar_help, - "Get a help summary or the help string of one colvar subcommand", + "Get a help summary or the help string of one colvar subcommand\n" + "help : string - Help string", 0, 1, "command : string - Get the help string of this specific command", unsigned char *const cmdobj = @@ -167,7 +166,7 @@ CVSCRIPT(colvar_modifycvcs, "Modify configuration of individual components by passing string arguments", 1, 1, "confs : sequence of strings - New configurations; empty strings are skipped", - std::vector const confs(script->proxy()->script_obj_to_str_vector(script->get_colvar_cmd_arg(0, objc, objv))); + std::vector const confs(script->obj_to_str_vector(script->get_colvar_cmd_arg(0, objc, objv))); cvm::increase_depth(); int res = this_colvar->update_cvc_config(confs); cvm::decrease_depth(); @@ -180,10 +179,11 @@ CVSCRIPT(colvar_modifycvcs, ) CVSCRIPT(colvar_run_ave, - "Get the current running average of the value of this colvar", + "Get the current running average of the value of this colvar\n" + "value : float or array - Averaged value; matches the colvar dimensionality", 0, 0, "", - script->set_result_str(this_colvar->run_ave().to_simple_string()); + script->set_result_colvarvalue(this_colvar->run_ave()); return COLVARS_OK; ) @@ -196,7 +196,8 @@ CVSCRIPT(colvar_set, ) CVSCRIPT(colvar_state, - "Print a string representation of the feature state of this colvar", + "Print a string representation of the feature state of this colvar\n" + "state : string - The feature state", 0, 0, "", this_colvar->print_state(); @@ -204,7 +205,8 @@ CVSCRIPT(colvar_state, ) CVSCRIPT(colvar_type, - "Get the type description of this colvar", + "Get the type description of this colvar\n" + "type : string - Type description", 0, 0, "", script->set_result_str(this_colvar->value().type_desc(this_colvar->value().value_type)); @@ -212,25 +214,28 @@ CVSCRIPT(colvar_type, ) CVSCRIPT(colvar_update, - "Recompute this colvar and return its up-to-date value", + "Recompute this colvar and return its up-to-date value\n" + "value : float or array - Current value; matches the colvar dimensionality", 0, 0, "", this_colvar->calc(); this_colvar->update_forces_energy(); - script->set_result_str((this_colvar->value()).to_simple_string()); + script->set_result_colvarvalue(this_colvar->value()); return COLVARS_OK; ) CVSCRIPT(colvar_value, - "Get the current value of this colvar", + "Get the current value of this colvar\n" + "value : float or array - Current value; matches the colvar dimensionality", 0, 0, "", - script->set_result_str(this_colvar->value().to_simple_string()); + script->set_result_colvarvalue(this_colvar->value()); return COLVARS_OK; ) CVSCRIPT(colvar_width, - "Get the width of this colvar", + "Get the width of this colvar\n" + "width : float - Value of the width", 0, 0, "", script->set_result_str(cvm::to_str(this_colvar->width, 0, diff --git a/lib/colvars/colvartypes.cpp b/lib/colvars/colvartypes.cpp index 3cbaed63a8..4117a7a68f 100644 --- a/lib/colvars/colvartypes.cpp +++ b/lib/colvars/colvartypes.cpp @@ -256,6 +256,7 @@ namespace { colvarmodule::rotation::rotation() { b_debug_gradients = false; + lambda = 0.0; #ifdef COLVARS_LAMMPS jacobi = new_Jacobi_solver(4); #else @@ -268,6 +269,7 @@ colvarmodule::rotation::rotation(cvm::quaternion const &qi) : q(qi) { b_debug_gradients = false; + lambda = 0.0; #ifdef COLVARS_LAMMPS jacobi = new_Jacobi_solver(4); #else @@ -283,6 +285,7 @@ colvarmodule::rotation::rotation(cvm::real angle, cvm::rvector const &axis) cvm::real const sina = cvm::sin(angle/2.0); q = cvm::quaternion(cvm::cos(angle/2.0), sina * axis_n.x, sina * axis_n.y, sina * axis_n.z); + lambda = 0.0; #ifdef COLVARS_LAMMPS jacobi = new_Jacobi_solver(4); #else diff --git a/lib/colvars/colvarvalue.cpp b/lib/colvars/colvarvalue.cpp index 7ab617bc44..24a2790f6e 100644 --- a/lib/colvars/colvarvalue.cpp +++ b/lib/colvars/colvarvalue.cpp @@ -224,7 +224,7 @@ void colvarvalue::is_derivative() colvarvalue::colvarvalue(colvarvalue const &x) - : value_type(x.type()) + : value_type(x.type()), real_value(0.0) { switch (x.type()) { case type_scalar: @@ -252,6 +252,7 @@ colvarvalue::colvarvalue(colvarvalue const &x) colvarvalue::colvarvalue(cvm::vector1d const &v, Type vti) + : real_value(0.0) { if ((vti != type_vector) && (v.size() != num_dimensions(vti))) { cvm::error("Error: trying to initialize a variable of type \""+type_desc(vti)+ @@ -579,16 +580,7 @@ colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const cvm::rvector const &v1 = this->rvector_value; cvm::rvector const &v2 = x2.rvector_value; cvm::real const cos_t = v1 * v2; - cvm::real const sin_t = cvm::sqrt(1.0 - cos_t*cos_t); - return colvarvalue( 2.0 * sin_t * - cvm::rvector((-1.0) * sin_t * v2.x + - cos_t/sin_t * (v1.x - cos_t*v2.x), - (-1.0) * sin_t * v2.y + - cos_t/sin_t * (v1.y - cos_t*v2.y), - (-1.0) * sin_t * v2.z + - cos_t/sin_t * (v1.z - cos_t*v2.z) - ), - colvarvalue::type_unit3vectorderiv ); + return colvarvalue(2.0 * (cos_t * v1 - v2), colvarvalue::type_unit3vectorderiv); } case colvarvalue::type_quaternion: case colvarvalue::type_quaternionderiv: diff --git a/lib/colvars/colvarvalue.h b/lib/colvars/colvarvalue.h index ca367dd43f..3f26c35df4 100644 --- a/lib/colvars/colvarvalue.h +++ b/lib/colvars/colvarvalue.h @@ -124,7 +124,7 @@ public: /// Constructor from a type specification inline colvarvalue(Type const &vti) - : value_type(vti) + : value_type(vti), real_value(0.0) { reset(); } @@ -138,12 +138,12 @@ public: /// by default a type \link type_3vector \endlink , if you want a /// \link type_unit3vector \endlink you must set it explicitly) inline colvarvalue(cvm::rvector const &v, Type vti = type_3vector) - : value_type(vti), rvector_value(v) + : value_type(vti), real_value(0.0), rvector_value(v) {} /// \brief Copy constructor from quaternion base type inline colvarvalue(cvm::quaternion const &q, Type vti = type_quaternion) - : value_type(vti), quaternion_value(q) + : value_type(vti), real_value(0.0), quaternion_value(q) {} /// Copy constructor from vector1d base type diff --git a/lib/h5md/README b/lib/h5md/README index 4768b50697..a6d4d8206b 100644 --- a/lib/h5md/README +++ b/lib/h5md/README @@ -1,6 +1,6 @@ This directory contains the ch5md library, which is bundled with LAMMPS under its own BSD license; see below. This library is used -when the USER-H5MD package is included in a LAMMPS build and the dump +when the H5MD package is included in a LAMMPS build and the dump h5md command is invoked in a LAMMPS input script. You can type "make lib-h5md" from the src directory to see help on how @@ -25,7 +25,7 @@ license that can be found in the file LICENSE. To use the h5md dump style in lammps, execute make -f Makefile.h5cc in this directory then -make yes-user-h5md +make yes-h5md in the src directory of LAMMPS to rebuild LAMMPS. Note that you must have the h5cc compiler installed to use diff --git a/lib/hdnnp/README b/lib/hdnnp/README index ed61f211ea..708f36c179 100644 --- a/lib/hdnnp/README +++ b/lib/hdnnp/README @@ -1,4 +1,4 @@ -The USER-HDNNP package requires access to pre-compiled libraries of the n2p2 +The ML-HDNNP package requires access to pre-compiled libraries of the n2p2 package (https://github.com/CompPhysVienna/n2p2). More precisely, the n2p2 core library ("libnnp"), the interface library ("libnnpif"), some headers and extra build helper files are needed. These files will be created automatically during @@ -6,7 +6,7 @@ the n2p2 build process. This file gives some basic instructions on how to compile n2p2 manually. How to integrate it then in the LAMMPS build process or how to use the automatic -download and build option is described in detail on the USER-HDNNP build +download and build option is described in detail on the ML-HDNNP build instructions page of the LAMMPS documentation. IMPORTANT: The n2p2 version must be "v2.1.4" or higher. @@ -25,7 +25,7 @@ After downloading n2p2, change to the "src" directory and simply execute make libnnpif -which should create the following files needed by the USER-HDNNP package: +which should create the following files needed by the ML-HDNNP package: * "n2p2/lib/libnnp.a" * "n2p2/lib/libnnpif.a" @@ -48,7 +48,7 @@ also available (e.g. "makefile.intel") and can be activated by supplying the Please make sure that your compiler settings for n2p2 and LAMMPS are compatible (avoid mixing different compilers). -If you want to build a serial version of LAMMPS with USER-HDNNP package n2p2 must +If you want to build a serial version of LAMMPS with ML-HDNNP package n2p2 must also be built with MPI disabled. This can be achieved with a preprocessor flag (-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in the provided compiler-specific settings makefiles. For example, if you use the GNU @@ -64,10 +64,10 @@ For more information about the n2p2 build process please visit https://compphysvienna.github.io/n2p2/topics/build.html or ask questions on the Github issue page (https://github.com/CompPhysVienna/n2p2/issues). -Testing a successful build of LAMMPS with USER-HDNNP +Testing a successful build of LAMMPS with ML-HDNNP ==================================================== -An example is provided in the LAMMPS directory "examples/USER/hdnnp" which runs +An example is provided in the LAMMPS directory "examples/PACKAGES/hdnnp" which runs 10 timesteps with 360 water molecules. The neural network potential is defined via files in the "hdnnp-data" subdirectory. Use the "in.hdnnp" LAMMPS script file to run the simulation. You should see a large output of the n2p2 library when diff --git a/lib/linalg/README b/lib/linalg/README index 725df86c4c..de2d83dcbd 100644 --- a/lib/linalg/README +++ b/lib/linalg/README @@ -1,10 +1,10 @@ -This directory has BLAS and LAPACK files needed by the USER-ATC and -USER-AWPMD packages, and possibly by other packages in the future. +This directory has BLAS and LAPACK files needed by the ATC and +AWPMD packages, and possibly by other packages in the future. Note that this is an *incomplete* subset of full BLAS/LAPACK. You should only need to build and use the library in this directory if -you want to build LAMMPS with the USER-ATC and/or USER-AWPMD packages +you want to build LAMMPS with the ATC and/or AWPMD packages AND you do not have any other suitable BLAS and LAPACK libraries installed on your system. E.g. ATLAS, GOTO-BLAS, OpenBLAS, ACML, or MKL. diff --git a/lib/smd/.gitignore b/lib/machdyn/.gitignore similarity index 100% rename from lib/smd/.gitignore rename to lib/machdyn/.gitignore diff --git a/lib/smd/Install.py b/lib/machdyn/Install.py similarity index 97% rename from lib/smd/Install.py rename to lib/machdyn/Install.py index 16dd3038a8..2e90c9ca0f 100644 --- a/lib/smd/Install.py +++ b/lib/machdyn/Install.py @@ -17,11 +17,12 @@ parser = ArgumentParser(prog='Install.py', # settings -version = '3.3.7' +version = '3.3.9' tarball = "eigen.tar.gz" # known checksums for different Eigen versions. used to validate the download. checksums = { \ + '3.3.9' : '609286804b0f79be622ccf7f9ff2b660', \ '3.3.7' : '9e30f67e8531477de4117506fe44669b' \ } diff --git a/lib/machdyn/Makefile.lammps b/lib/machdyn/Makefile.lammps new file mode 100644 index 0000000000..71db4fd4bc --- /dev/null +++ b/lib/machdyn/Makefile.lammps @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +machdyn_SYSINC = +machdyn_SYSLIB = +machdyn_SYSPATH = diff --git a/lib/smd/README b/lib/machdyn/README similarity index 94% rename from lib/smd/README rename to lib/machdyn/README index 1bd5902a1f..38a2957648 100644 --- a/lib/smd/README +++ b/lib/machdyn/README @@ -1,5 +1,5 @@ This directory contains links to the Eigen library which is required -to use the USER-SMD package in a LAMMPS input script. +to use the MACHDYN package in a LAMMPS input script. The Eigen library is available at http://eigen.tuxfamily.org. It's a general C++ template library for linear algebra. @@ -26,10 +26,10 @@ Instructions: % ln -s /home/sjplimp/tools/eigen includelink When these steps are complete you can build LAMMPS -with the USER-SMD package installed: +with the MACHDYN package installed: % cd lammps/src -% make yes-user-smd +% make yes-machdyn % make g++ (or whatever target you wish) Note that if you download and unpack a new LAMMPS tarball, the diff --git a/lib/mdi/Install.py b/lib/mdi/Install.py index 1c411d349e..d67437d0ce 100644 --- a/lib/mdi/Install.py +++ b/lib/mdi/Install.py @@ -28,7 +28,7 @@ specify -m and optionally -e, order does not matter Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src -make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ diff --git a/lib/mesont/Install.py b/lib/mesont/Install.py index 284ef6888b..0a0979c2ee 100644 --- a/lib/mesont/Install.py +++ b/lib/mesont/Install.py @@ -26,7 +26,7 @@ specify -m and optionally -e, order does not matter Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src -make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ diff --git a/lib/mesont/README b/lib/mesont/README index 886263ddb3..3ed47bf218 100644 --- a/lib/mesont/README +++ b/lib/mesont/README @@ -1,4 +1,4 @@ -USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon +MESONT is a LAMMPS package for simulation of nanomechanics of carbon nanotubes (CNTs). The model is based on a coarse-grained representation of CNTs as "flexible cylinders" consisting of a variable number of segments. Internal interactions within a CNT and the van der Waals diff --git a/lib/molfile/Makefile.lammps b/lib/molfile/Makefile.lammps index a181f48aec..55a0487a9f 100644 --- a/lib/molfile/Makefile.lammps +++ b/lib/molfile/Makefile.lammps @@ -3,7 +3,7 @@ # # http://www.ks.uiuc.edu/Research/vmd/plugins/molfile # -# When you build LAMMPS with the USER-MOLFILE package installed, it will +# When you build LAMMPS with the MOLFILE package installed, it will # use the 3 settings in this file. They should be set as follows. # # The molfile_SYSINC setting is to point to the folder with the VMD diff --git a/lib/molfile/README b/lib/molfile/README index 9e8260c202..9960b5a836 100644 --- a/lib/molfile/README +++ b/lib/molfile/README @@ -1,6 +1,6 @@ This directory has a Makefile.lammps file with settings that allows LAMMPS to dynamically link to the VMD molfile library. This is -required to use the USER-MOLFILE package and its interface to the dump +required to use the MOLFILE package and its interface to the dump and write_dump commands in a LAMMPS input script. More information about the VMD molfile plugins can be found at diff --git a/lib/mscg/README b/lib/mscg/README index 329eebba96..5e3cfe4452 100755 --- a/lib/mscg/README +++ b/lib/mscg/README @@ -51,7 +51,7 @@ When these steps are complete you can build LAMMPS with the MS-CG package installed: % cd lammps/src -% make yes-USER-MSCG +% make yes-MSCG % make g++ (or whatever target you wish) Note that if you download and unpack a new LAMMPS tarball, the diff --git a/lib/netcdf/README b/lib/netcdf/README index b18ea1d276..c23b7fbb06 100644 --- a/lib/netcdf/README +++ b/lib/netcdf/README @@ -1,6 +1,6 @@ The Makefile.lammps file in this directory is used when building LAMMPS with packages that make use of the NetCDF library or its -parallel version. For example, the USER-NETCDF package which adds +parallel version. For example, the NETCDF package which adds dump netcdf and dump netcdf/mpiio commands. The file has several settings needed to compile diff --git a/lib/pace/Makefile b/lib/pace/Makefile index c2e1892ddd..ac9f3a3151 100644 --- a/lib/pace/Makefile +++ b/lib/pace/Makefile @@ -2,8 +2,8 @@ SHELL = /bin/sh # ------ FILES ------ -SRC_FILES = $(wildcard src/USER-PACE/*.cpp) -SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES)) +SRC_FILES = $(wildcard src/ML-PACE/*.cpp) +SRC = $(filter-out src/ML-PACE/pair_pace.cpp, $(SRC_FILES)) # ------ DEFINITIONS ------ @@ -12,7 +12,7 @@ OBJ = $(SRC:.cpp=.o) # ------ SETTINGS ------ -CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE +CXXFLAGS = -O3 -fPIC -Isrc/ML-PACE ARCHIVE = ar ARCHFLAG = -rc diff --git a/lib/pace/Makefile.lammps b/lib/pace/Makefile.lammps index 17820716df..89761c1b4b 100644 --- a/lib/pace/Makefile.lammps +++ b/lib/pace/Makefile.lammps @@ -1,3 +1,3 @@ -pace_SYSINC =-I../../lib/pace/src/USER-PACE +pace_SYSINC =-I../../lib/pace/src/ML-PACE pace_SYSLIB = -L../../lib/pace/ -lpace pace_SYSPATH = diff --git a/lib/pace/README b/lib/pace/README index ddc6f7f7a7..1cbc9fad68 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -1,18 +1,14 @@ -This directory contains files required to use the USER-PACE package, -which provides the pace pair style, an efficient implementation of -the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. -This package was written by Yury Lysogorskiy and others -at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, -Ruhr University Bochum, Germany, http://www.icams.de +This directory contains files required to use the ML-PACE package, which +provides the pace pair style, an efficient implementation of the Atomic +Cluster Expansion potential (ACE). ACE is a methodology for deriving a +highly accurate classical potential fit to a large archive of quantum +mechanical (DFT) data. This package was written by Yury Lysogorskiy and +others at ICAMS, the Interdisciplinary Centre for Advanced Materials +Simulation, Ruhr University Bochum, Germany, http://www.icams.de -You can type "make lib-pace" from the src directory to see help on -how to download and build this library via make commands, or you can -do the same thing by typing "python Install.py" from within this -directory. +You can type "make lib-pace" from the src directory to see help on how +to download and build this library via make commands, or you can do the +same thing by typing "python Install.py" from within this directory. -More information about the USER-PACE implementation of ACE -is available here: - -https://github.com/ICAMS/lammps-user-pace +More information about the ML-PACE implementation of ACE is available +here: https://github.com/ICAMS/lammps-user-pace diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index e3858b39d3..548e51a5bc 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -53,6 +53,7 @@ checksums = { \ '2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \ '2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \ '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \ + '2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \ } # parse and process arguments diff --git a/lib/plumed/README b/lib/plumed/README index 6b9b22bbce..a21b40ced1 100644 --- a/lib/plumed/README +++ b/lib/plumed/README @@ -51,6 +51,6 @@ When these steps are complete you can build LAMMPS with the PLUMED package installed: % cd lammps/src -% make yes-user-plumed +% make yes-plumed % make mpi (or whatever target you wish) diff --git a/lib/qmmm/README b/lib/qmmm/README index 196aa4d7e0..7e9f30d692 100644 --- a/lib/qmmm/README +++ b/lib/qmmm/README @@ -21,7 +21,7 @@ and also an interface layer into the QM code similar to the one in QE. LAMMPS has support for two build systems, the traditional make based one and a newer one based on CMake. You have to build LAMMPS as a -library with the USER-QMMM package included and for that you need to +library with the QMMM package included and for that you need to also build the libqmmm.a library in this folder. Below you will find some description of the steps needed in either case. @@ -55,7 +55,7 @@ build configuration with CMake: mkdir build-qmmm cd build-qmmm - cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \ + cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \ -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake make make install @@ -139,7 +139,7 @@ this library exist. Step 2) Build a standalone LAMMPS executable as described in the LAMMPS -documentation and include the USER-QMMM package. This executable +documentation and include the QMMM package. This executable is not functional for QM/MM, but it will usually be needed to run all MM calculations for equilibration and testing and also to confirm that the classical part of the code is set up correctly. @@ -147,7 +147,7 @@ Also build a the LAMMPS library. This can be a static library or a shared library. For example for a static library with the minimum set of packages required for the examples here: - make yes-molecule yes-kspace yes-rigid yes-user-qmmm + make yes-molecule yes-kspace yes-rigid yes-qmmm make mpi make mode=lib mpi diff --git a/lib/quip/README b/lib/quip/README index 5e737db11d..7b74dc2d7e 100644 --- a/lib/quip/README +++ b/lib/quip/README @@ -76,15 +76,17 @@ and QUIP_ARCH should be autodetected, even without having to set the environment variables. Otherwise export the environment variables as shown above or edit Makefile.lammps -LAMMPS ships with a user package containing the interface necessary +LAMMPS ships with a package containing the interface necessary to use QUIP potentials, but it needs to be added to the compilation -first. To do that, enter the LAMMPS source directory and type: +first. To do that, either enter the LAMMPS source directory and type: -$ make yes-user-quip +$ make yes-ml-quip + +or use -DPKG_ML-QUIP=yes when configuring LAMMPS for compilation with CMake. 2.2) Build LAMMPS according to the instructions on the LAMMPS website. -3) There are three example sets in examples/USER/quip: +3) There are three example sets in examples/PACKAGES/quip: - a set of input files to compute the energy of an 8-atom cubic diamond cell of silicon with the Stillinger-Weber potential. Use diff --git a/lib/smd/Makefile.lammps b/lib/smd/Makefile.lammps deleted file mode 100644 index 6951a1394c..0000000000 --- a/lib/smd/Makefile.lammps +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -user-smd_SYSINC = -I../../lib/includelink/eigen3 -user-smd_SYSLIB = -user-smd_SYSPATH = diff --git a/lib/vtk/README b/lib/vtk/README index 61e2a40c23..d0e2481f6f 100644 --- a/lib/vtk/README +++ b/lib/vtk/README @@ -1,5 +1,5 @@ The Makefile.lammps file in this directory is used when building -LAMMPS with its USER-VTK package installed. The file has several +LAMMPS with its VTK package installed. The file has several settings needed to compile and link LAMMPS with the VTK library. You should choose a Makefile.lammps.* file compatible with your system and your version of VTK, and copy it to Makefile.lammps before building @@ -23,7 +23,7 @@ vtk_SYSINC refers to the include directory of the installed VTK library vtk_SYSLIB refers to the libraries needed to link to from an application (LAMMPS in this case) to "embed" VTK in the application. VTK consists of multiple shared libraries which are -needed when using the USER-VTK package. +needed when using the VTK package. vtk_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the VTK library can be found. You may not need this setting if the path is diff --git a/potentials/README b/potentials/README index fbc49f8613..4df315a7f2 100644 --- a/potentials/README +++ b/potentials/README @@ -84,18 +84,18 @@ Au_u3 = Gold universal 3 The suffix of each file indicates the pair style it is used with: adp ADP angular dependent potential -airebo AI-REBO and REBO potentials +airebo AI-REBO and REBO potentials bop.table BOP potential, tabulated form cdeam concentration-dependent EAM comb COMB potential comb3 COMB3 potential -eam embedded atom method (EAM) single element, DYNAMO funcfl format +eam embedded atom method (EAM) single element, DYNAMO funcfl format eam.alloy EAM multi-element alloy, DYNAMO setfl format -eam.fs Finnis-Sinclair EAM format (single element or alloy) +eam.fs Finnis-Sinclair EAM format (single element or alloy) edip EDIP potential for silicon-based materials eim embedded-ion method (EIM) potential lcbop LCBOP long-range bond-order potential -meam modified EAM (MEAM) library and individual elements/alloys +meam modified EAM (MEAM) library and individual elements/alloys meam.spline modified EAM (MEAM) spline potential meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential mesocnt mesoscopic carbon nanotube (CNT) potential @@ -105,14 +105,14 @@ mliap.descriptor MLIAP potential descriptor mliap.model MLIAP potential model nb3b.harmonic nonbonded 3-body harmonic potential poly polymorphic 3-body potential -reax ReaxFF potential (see README.reax for more info) +reax ReaxFF potential (see README.reax for more info) smtbq second moment tight binding QEq (SMTBQ) potential snap SNAP potential snapcoeff SNAP potential snapparam SNAP potential streitz Coulombic portion of Streitz-Mintmire potential -sw Stillinger-Weber potential -tersoff Tersoff potential +sw Stillinger-Weber potential +tersoff Tersoff potential tersoff.mod modified Tersoff potential tersoff.zbl Tersoff with ZBL core vashishta Vashishta 2-body and 3-body potential diff --git a/potentials/SiGeH.sw.quip b/potentials/SiGeH.sw.quip new file mode 100644 index 0000000000..d6cd5c7688 --- /dev/null +++ b/potentials/SiGeH.sw.quip @@ -0,0 +1,47 @@ + + + UNITS: metal DATE: 2015-02-24 CITATION: Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements. Ge and Si-Ge from Ethier and Lewis '92 + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/python/examples/pylammps/README.md b/python/examples/pylammps/README.md index 7ee8c8ac90..e66f5a2a8e 100644 --- a/python/examples/pylammps/README.md +++ b/python/examples/pylammps/README.md @@ -51,7 +51,7 @@ which has both LAMMPS and its Python package installed: 6. Configure LAMMPS compilation (CMake) ```shell - (myenv)$ cmake -C ../cmake/presets/minimal.cmake \ + (myenv)$ cmake -C ../cmake/presets/basic.cmake \ -D BUILD_SHARED_LIBS=on \ -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on \ -D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \ diff --git a/python/lammps/core.py b/python/lammps/core.py index 88eba735b0..7dea6e5e6e 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -201,6 +201,9 @@ class lammps(object): [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_scatter_atoms_subset.restype = None + self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p] + self.lib.lammps_gather_bonds.restype = None + self.lib.lammps_gather.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather.restype = None @@ -295,9 +298,16 @@ class lammps(object): self.lib.lammps_extract_variable.argtypes = [c_void_p, c_char_p, c_char_p] - # TODO: NOT IMPLEMENTED IN PYTHON WRAPPER - self.lib.lammps_fix_external_set_energy_global = [c_void_p, c_char_p, c_double] - self.lib.lammps_fix_external_set_virial_global = [c_void_p, c_char_p, POINTER(c_double)] + self.lib.lammps_fix_external_get_force.argtypes = [c_void_p, c_char_p] + self.lib.lammps_fix_external_get_force.restype = POINTER(POINTER(c_double)) + + self.lib.lammps_fix_external_set_energy_global.argtypes = [c_void_p, c_char_p, c_double] + self.lib.lammps_fix_external_set_virial_global.argtypes = [c_void_p, c_char_p, POINTER(c_double)] + self.lib.lammps_fix_external_set_energy_peratom.argtypes = [c_void_p, c_char_p, POINTER(c_double)] + self.lib.lammps_fix_external_set_virial_peratom.argtypes = [c_void_p, c_char_p, POINTER(POINTER(c_double))] + + self.lib.lammps_fix_external_set_vector_length.argtypes = [c_void_p, c_char_p, c_int] + self.lib.lammps_fix_external_set_vector.argtypes = [c_void_p, c_char_p, c_int, c_double] # detect if Python is using a version of mpi4py that can pass communicators # only needed if LAMMPS has been compiled with MPI support. @@ -460,10 +470,16 @@ class lammps(object): # ------------------------------------------------------------------------- def finalize(self): - """Shut down the MPI communication through the library interface by calling :cpp:func:`lammps_finalize`. + """Shut down the MPI communication and Kokkos environment (if active) through the + library interface by calling :cpp:func:`lammps_mpi_finalize` and + :cpp:func:`lammps_kokkos_finalize`. + + You cannot create or use any LAMMPS instances after this function is called + unless LAMMPS was compiled without MPI and without Kokkos support. """ self.close() - self.lib.lammps_finalize() + self.lib.lammps_kokkos_finalize() + self.lib.lammps_mpi_finalize() # ------------------------------------------------------------------------- @@ -1193,6 +1209,32 @@ class lammps(object): with ExceptionCheck(self): self.lib.lammps_scatter_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data) + + # ------------------------------------------------------------------------- + + def gather_bonds(self): + """Retrieve global list of bonds + + This is a wrapper around the :cpp:func:`lammps_gather_bonds` + function of the C-library interface. + + This function returns a tuple with the number of bonds and a + flat list of ctypes integer values with the bond type, bond atom1, + bond atom2 for each bond. + + .. versionadded:: 28Jul2021 + + :return: a tuple with the number of bonds and a list of c_int or c_long + :rtype: (int, 3*nbonds*c_tagint) + """ + nbonds = self.extract_global("nbonds") + with ExceptionCheck(self): + data = ((3*nbonds)*self.c_tagint)() + self.lib.lammps_gather_bonds(self.lmp,data) + return nbonds,data + + # ------------------------------------------------------------------------- + # return vector of atom/compute/fix properties gathered across procs # 3 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() @@ -1351,7 +1393,7 @@ class lammps(object): id_lmp = (self.c_tagint*n)() try: id_lmp[:] = id[0:n] - except: # lgtm [py/catch-base-exception] + except ValueError: return 0 else: id_lmp = None @@ -1359,21 +1401,21 @@ class lammps(object): type_lmp = (c_int*n)() try: type_lmp[:] = type[0:n] - except: # lgtm [py/catch-base-exception] + except ValueError: return 0 three_n = 3*n x_lmp = (c_double*three_n)() try: x_lmp[:] = x[0:three_n] - except: # lgtm [py/catch-base-exception] + except ValueError: return 0 if v: v_lmp = (c_double*(three_n))() try: v_lmp[:] = v[0:three_n] - except: # lgtm [py/catch-base-exception] + except ValueError: return 0 else: v_lmp = None @@ -1382,7 +1424,7 @@ class lammps(object): img_lmp = (self.c_imageint*n)() try: img_lmp[:] = image[0:n] - except: # lgtm [py/catch-base-exception] + except ValueError: return 0 else: img_lmp = None @@ -1536,7 +1578,7 @@ class lammps(object): """ result = {} - for p in ['GPU', 'KOKKOS', 'USER-INTEL', 'USER-OMP']: + for p in ['GPU', 'KOKKOS', 'INTEL', 'OPENMP']: result[p] = {} c = 'api' result[p][c] = [] @@ -1719,7 +1761,35 @@ class lammps(object): # ------------------------------------------------------------------------- - def set_fix_external_callback(self, fix_name, callback, caller=None): + def set_fix_external_callback(self, fix_id, callback, caller=None): + """Set the callback function for a fix external instance with a given fix ID. + + Optionally also set a reference to the calling object. + + This is a wrapper around the :cpp:func:`lammps_set_fix_external_callback` function + of the C-library interface. However this is set up to call a Python function with + the following arguments. + + .. code-block: python + + def func(object, ntimestep, nlocal, tag, x, f): + + - object is the value of the "caller" argument + - ntimestep is the current timestep + - nlocal is the number of local atoms on the current MPI process + - tag is a 1d NumPy array of integers representing the atom IDs of the local atoms + - x is a 2d NumPy array of doubles of the coordinates of the local atoms + - f is a 2d NumPy array of doubles of the forces on the local atoms that will be added + + .. versionchanged:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param callback: Python function that will be called from fix external + :type: function + :param caller: reference to some object passed to the callback function + :type: object, optional + """ import numpy as np def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr): @@ -1731,10 +1801,161 @@ class lammps(object): cFunc = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper) cCaller = caller - self.callback[fix_name] = { 'function': cFunc, 'caller': caller } + self.callback[fix_id] = { 'function': cFunc, 'caller': caller } with ExceptionCheck(self): - self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller) + self.lib.lammps_set_fix_external_callback(self.lmp, fix_id.encode(), cFunc, cCaller) + # ------------------------------------------------------------------------- + + def fix_external_get_force(self, fix_id): + """Get access to the array with per-atom forces of a fix external instance with a given fix ID. + + This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :return: requested data + :rtype: ctypes.POINTER(ctypes.POINTER(ctypes.double)) + """ + + with ExceptionCheck(self): + return self.lib.lammps_fix_external_get_force(self.lmp, fix_id.encode()) + + # ------------------------------------------------------------------------- + + def fix_external_set_energy_global(self, fix_id, eng): + """Set the global energy contribution for a fix external instance with the given ID. + + This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param eng: potential energy value to be added by fix external + :type: float + """ + + with ExceptionCheck(self): + return self.lib.lammps_fix_external_set_energy_global(self.lmp, fix_id.encode(), eng) + + # ------------------------------------------------------------------------- + + def fix_external_set_virial_global(self, fix_id, virial): + """Set the global virial contribution for a fix external instance with the given ID. + + This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param eng: list of 6 floating point numbers with the virial to be added by fix external + :type: float + """ + + cvirial = (6*c_double)(*virial) + with ExceptionCheck(self): + return self.lib.lammps_fix_external_set_virial_global(self.lmp, fix_id.encode(), cvirial) + + # ------------------------------------------------------------------------- + + def fix_external_set_energy_peratom(self, fix_id, eatom): + """Set the per-atom energy contribution for a fix external instance with the given ID. + + This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param eatom: list of potential energy values for local atoms to be added by fix external + :type: float + """ + + nlocal = self.extract_setting('nlocal') + if len(eatom) < nlocal: + raise Exception('per-atom energy list length must be at least nlocal') + ceatom = (nlocal*c_double)(*eatom) + with ExceptionCheck(self): + return self.lib.lammps_fix_external_set_energy_peratom(self.lmp, fix_id.encode(), ceatom) + + # ------------------------------------------------------------------------- + + def fix_external_set_virial_peratom(self, fix_id, vatom): + """Set the per-atom virial contribution for a fix external instance with the given ID. + + This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param vatom: list of natoms lists with 6 floating point numbers to be added by fix external + :type: float + """ + + # copy virial data to C compatible buffer + nlocal = self.extract_setting('nlocal') + if len(vatom) < nlocal: + raise Exception('per-atom virial first dimension must be at least nlocal') + if len(vatom[0]) != 6: + raise Exception('per-atom virial second dimension must be 6') + vbuf = (c_double * 6) + vptr = POINTER(c_double) + c_virial = (vptr * nlocal)() + for i in range(nlocal): + c_virial[i] = vbuf() + for j in range(6): + c_virial[i][j] = vatom[i][j] + + with ExceptionCheck(self): + return self.lib.lammps_fix_external_set_virial_peratom(self.lmp, fix_id.encode(), c_virial) + + # ------------------------------------------------------------------------- + def fix_external_set_vector_length(self, fix_id, length): + """Set the vector length for a global vector stored with fix external for analysis + + This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param length: length of the global vector + :type: int + """ + + with ExceptionCheck(self): + return self.lib.lammps_fix_external_set_vector_length(self.lmp, fix_id.encode(), length) + + # ------------------------------------------------------------------------- + def fix_external_set_vector(self, fix_id, idx, val): + """Store a global vector value for a fix external instance with the given ID. + + This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function + of the C-library interface. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param idx: 1-based index of the value in the global vector + :type: int + :param val: value to be stored in the global vector + :type: float + """ + + with ExceptionCheck(self): + return self.lib.lammps_fix_external_set_vector(self.lmp, fix_id.encode(), idx, val) # ------------------------------------------------------------------------- diff --git a/python/lammps/mliap/loader.py b/python/lammps/mliap/loader.py index 8588c2b4bf..dff791bfc1 100644 --- a/python/lammps/mliap/loader.py +++ b/python/lammps/mliap/loader.py @@ -39,13 +39,13 @@ def activate_mliappy(lmp): # End Importlib magic to find the embedded python module except Exception as ee: - raise ImportError("Could not load MLIAP python coupling module.") from ee + raise ImportError("Could not load ML-IAP python coupling module.") from ee def load_model(model): try: import mliap_model_python_couple except ImportError as ie: - raise ImportError("MLIAP python module must be activated before loading\n" + raise ImportError("ML-IAP python module must be activated before loading\n" "the pair style. Call lammps.mliap.activate_mliappy(lmp)." ) from ie mliap_model_python_couple.load_from_python(model) diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index 20fdf4cc68..2f0f74594e 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -17,7 +17,7 @@ ################################################################################ import warnings -from ctypes import POINTER, c_double, c_int, c_int32, c_int64, cast +from ctypes import POINTER, c_void_p, c_char_p, c_double, c_int, c_int32, c_int64, cast from .constants import * # lgtm [py/polluting-import] @@ -246,7 +246,109 @@ class numpy_wrapper: return np.ctypeslib.as_array(value) return value - # ------------------------------------------------------------------------- + # ------------------------------------------------------------------------- + + def gather_bonds(self): + """Retrieve global list of bonds as NumPy array + + This is a wrapper around :py:meth:`lammps.gather_bonds() ` + It behaves the same as the original method, but returns a NumPy array instead + of a ``ctypes`` list. + + .. versionadded:: 28Jul2021 + + :return: the requested data as a 2d-integer numpy array + :rtype: numpy.array(nbonds,3) + """ + import numpy as np + nbonds, value = self.lmp.gather_bonds() + return np.ctypeslib.as_array(value).reshape(nbonds,3) + + # ------------------------------------------------------------------------- + + def fix_external_get_force(self, fix_id): + """Get access to the array with per-atom forces of a fix external instance with a given fix ID. + + This function is a wrapper around the + :py:meth:`lammps.fix_external_get_force() ` + method. It behaves the same as the original method, but returns a NumPy array instead + of a ``ctypes`` pointer. + + .. versionchanged:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :return: requested data + :rtype: numpy.array + """ + import numpy as np + nlocal = self.lmp.extract_setting('nlocal') + value = self.lmp.fix_external_get_force(fix_id) + return self.darray(value,nlocal,3) + + # ------------------------------------------------------------------------- + + def fix_external_set_energy_peratom(self, fix_id, eatom): + """Set the per-atom energy contribution for a fix external instance with the given ID. + + This function is an alternative to + :py:meth:`lammps.fix_external_set_energy_peratom() ` + method. It behaves the same as the original method, but accepts a NumPy array + instead of a list as argument. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param eatom: per-atom potential energy + :type: numpy.array + """ + import numpy as np + nlocal = self.lmp.extract_setting('nlocal') + if len(eatom) < nlocal: + raise Exception('per-atom energy dimension must be at least nlocal') + + c_double_p = POINTER(c_double) + value = eatom.astype(np.double) + return self.lmp.lib.lammps_fix_external_set_energy_peratom(self.lmp.lmp, fix_id.encode(), + value.ctypes.data_as(c_double_p)) + + # ------------------------------------------------------------------------- + + def fix_external_set_virial_peratom(self, fix_id, vatom): + """Set the per-atom virial contribution for a fix external instance with the given ID. + + This function is an alternative to + :py:meth:`lammps.fix_external_set_virial_peratom() ` + method. It behaves the same as the original method, but accepts a NumPy array + instead of a list as argument. + + .. versionadded:: 28Jul2021 + + :param fix_id: Fix-ID of a fix external instance + :type: string + :param eatom: per-atom potential energy + :type: numpy.array + """ + import numpy as np + nlocal = self.lmp.extract_setting('nlocal') + if len(vatom) < nlocal: + raise Exception('per-atom virial first dimension must be at least nlocal') + if len(vatom[0]) != 6: + raise Exception('per-atom virial second dimension must be 6') + + c_double_pp = np.ctypeslib.ndpointer(dtype=np.uintp, ndim=1, flags='C') + + # recast numpy array to be compatible with library interface + value = (vatom.__array_interface__['data'][0] + + np.arange(vatom.shape[0])*vatom.strides[0]).astype(np.uintp) + + # change prototype to our custom type + self.lmp.lib.lammps_fix_external_set_virial_peratom.argtypes = [ c_void_p, c_char_p, c_double_pp ] + + self.lmp.lib.lammps_fix_external_set_virial_peratom(self.lmp.lmp, fix_id.encode(), value) + + # ------------------------------------------------------------------------- def get_neighlist(self, idx): """Returns an instance of :class:`NumPyNeighList` which wraps access to the neighbor list with the given index diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index f9bdd1720a..a89791a02e 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -240,7 +240,8 @@ class Atom2D(Atom): @property def position(self): - """ + """Access to coordinates of an atom + :getter: Return position of atom :setter: Set position of atom :type: tuple (float, float) @@ -255,7 +256,7 @@ class Atom2D(Atom): @property def velocity(self): - """ + """Access to velocity of an atom :getter: Return velocity of atom :setter: Set velocity of atom :type: tuple (float, float) @@ -270,8 +271,7 @@ class Atom2D(Atom): @property def force(self): - """ - Return the total force acting on the atom + """Access to force of an atom :type: tuple (float, float) """ diff --git a/src/.gitignore b/src/.gitignore index 37955b454d..6c0a838c1b 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -52,7 +52,7 @@ /*_dielectric.cpp /*_dielectric.h /compute_efield_atom.cpp -/compute_efield_atom.j +/compute_efield_atom.h /superpose3d.h @@ -70,13 +70,14 @@ /meam*.h /meam*.cpp -/pair_meamc.cpp -/pair_meamc.h +/pair_meam.cpp +/pair_meam.h /compute_mliap.cpp /compute_mliap.h /mliap_*.cpp /mliap_*.h +/mliap_model_python_couple.pyx /pair_mliap.cpp /pair_mliap.h @@ -250,6 +251,68 @@ /pair_mesont_tpm.cpp /pair_mesont_tpm.h +/compute_adf.cpp +/compute_adf.h +/compute_contact_atom.cpp +/compute_contact_atom.h +/compute_hexorder_atom.cpp +/compute_hexorder_atom.h +/dump_dcd.cpp +/dump_dcd.h +/fix_controller.cpp +/fix_controller.h +/fix_drag.cpp +/fix_drag.h +/fix_numdiff.cpp +/fix_numdiff.h +/fix_nve_noforce.cpp +/fix_nve_noforce.h +/fix_spring_rg.cpp +/fix_spring_rg.h +/fix_temp_csld.cpp +/fix_temp_csld.h +/fix_temp_csvr.cpp +/fix_temp_csvr.h +/fix_tmd.cpp +/fix_tmd.h +/pair_beck.cpp +/pair_beck.h +/pair_born_coul_dsf.cpp +/pair_born_coul_dsf.h +/pair_born_coul_wolf.cpp +/pair_born_coul_wolf.h +/pair_coul_cut_global.cpp +/pair_coul_cut_global.h +/pair_coul_streitz.cpp +/pair_coul_streitz.h +/pair_gauss.cpp +/pair_gauss.h +/pair_lj96_cut.cpp +/pair_lj96_cut.h +/pair_lj_cubic.cpp +/pair_lj_cubic.h +/pair_lj_cubic_const.h +/pair_lj_cut_coul_debye.cpp +/pair_lj_cut_coul_debye.h +/pair_lj_cut_coul_dsf.cpp +/pair_lj_cut_coul_dsf.h +/pair_lj_cut_coul_wolf.cpp +/pair_lj_cut_coul_wolf.h +/pair_lj_gromacs.cpp +/pair_lj_gromacs.h +/pair_lj_gromacs_coul_gromacs.cpp +/pair_lj_gromacs_coul_gromacs.h +/pair_lj_relres.cpp +/pair_lj_relres.h +/pair_lj_smooth.cpp +/pair_lj_smooth.h +/pair_lj_smooth_linear.cpp +/pair_lj_smooth_linear.h +/pair_mie_cut.cpp +/pair_mie_cut.h +/pair_ufm.cpp +/pair_ufm.h + /angle_cg_cmm.cpp /angle_cg_cmm.h /angle_charmm.cpp @@ -314,6 +377,8 @@ /atom_vec_granular.h /atom_vec_molecular.cpp /atom_vec_molecular.h +/atom_vec_oxdna.cpp +/atom_vec_oxdna.h /atom_vec_peri.cpp /atom_vec_peri.h /atom_vec_template.cpp @@ -386,6 +451,8 @@ /compute_erotate_rigid.h /compute_event_displace.cpp /compute_event_displace.h +/compute_fabric.cpp +/compute_fabric.h /compute_fep.cpp /compute_fep.h /compute_force_tally.cpp @@ -574,12 +641,8 @@ /fix_client_md.h /fix_cmap.cpp /fix_cmap.h -/fix_deposit.cpp -/fix_deposit.h /fix_dpd_energy.cpp /fix_dpd_energy.h -/fix_efield.cpp -/fix_efield.h /fix_electron_stopping.cpp /fix_electron_stopping.h /fix_electron_stopping_fit.cpp @@ -588,8 +651,6 @@ /fix_eos_cv.h /fix_eos_table.cpp /fix_eos_table.h -/fix_evaporate.cpp -/fix_evaporate.h /fix_ffl.cpp /fix_ffl.h /fix_filter_corotate.cpp @@ -718,6 +779,8 @@ /fix_orient_eco.h /fix_orient_fcc.cpp /fix_orient_fcc.h +/fix_pair_tracker.cpp +/fix_pair_tracker.h /fix_peri_neigh.cpp /fix_peri_neigh.h /fix_phonon.cpp @@ -728,18 +791,18 @@ /fix_pour.h /fix_qeq_comb.cpp /fix_qeq_comb.h -/fix_qeq_reax.cpp /fix_qeq_fire.cpp /fix_qeq_fire.h -/fix_qeq_reax.h +/fix_qeq_reaxff.cpp +/fix_qeq_reaxff.h /fix_qmmm.cpp /fix_qmmm.h -/fix_reaxc.cpp -/fix_reaxc.h -/fix_reaxc_bonds.cpp -/fix_reaxc_bonds.h -/fix_reaxc_species.cpp -/fix_reaxc_species.h +/fix_reaxff.cpp +/fix_reaxff.h +/fix_reaxff_bonds.cpp +/fix_reaxff_bonds.h +/fix_reaxff_species.cpp +/fix_reaxff_species.h /fix_rhok.cpp /fix_rhok.h /fix_rigid.cpp @@ -791,8 +854,6 @@ /fix_tgnpt_drude.h /fix_tgnvt_drude.cpp /fix_tgnvt_drude.h -/fix_thermal_conductivity.cpp -/fix_thermal_conductivity.h /fix_ti_rs.cpp /fix_ti_rs.h /fix_ti_spring.cpp @@ -1129,8 +1190,8 @@ /pair_peri_ves.h /pair_quip.cpp /pair_quip.h -/pair_reaxc.cpp -/pair_reaxc.h +/pair_reaxff.cpp +/pair_reaxff.h /pair_rebo.cpp /pair_rebo.h /pair_resquared.cpp @@ -1167,6 +1228,8 @@ /pair_tip4p_long.h /pair_tip4p_long_soft.cpp /pair_tip4p_long_soft.h +/pair_tracker.h +/pair_tracker.cpp /pair_tri_lj.cpp /pair_tri_lj.h /pair_yukawa_colloid.cpp @@ -1215,50 +1278,27 @@ /reader_adios.h /reader_molfile.cpp /reader_molfile.h -/reaxc_allocate.cpp -/reaxc_allocate.h -/reaxc_basic_comm.cpp -/reaxc_basic_comm.h -/reaxc_bond_orders.cpp -/reaxc_bond_orders.h -/reaxc_bonds.cpp -/reaxc_bonds.h -/reaxc_control.cpp -/reaxc_control.h -/reaxc_defs.h -/reaxc_ffield.cpp -/reaxc_ffield.h -/reaxc_forces.cpp -/reaxc_forces.h -/reaxc_hydrogen_bonds.cpp -/reaxc_hydrogen_bonds.h -/reaxc_init_md.cpp -/reaxc_init_md.h -/reaxc_io_tools.cpp -/reaxc_io_tools.h -/reaxc_list.cpp -/reaxc_list.h -/reaxc_lookup.cpp -/reaxc_lookup.h -/reaxc_multi_body.cpp -/reaxc_multi_body.h -/reaxc_nonbonded.cpp -/reaxc_nonbonded.h -/reaxc_reset_tools.cpp -/reaxc_reset_tools.h -/reaxc_system_props.cpp -/reaxc_system_props.h -/reaxc_tool_box.cpp -/reaxc_tool_box.h -/reaxc_torsion_angles.cpp -/reaxc_torsion_angles.h -/reaxc_traj.cpp -/reaxc_traj.h -/reaxc_types.h -/reaxc_valence_angles.cpp -/reaxc_valence_angles.h -/reaxc_vector.cpp -/reaxc_vector.h +/reaxff_allocate.cpp +/reaxff_bond_orders.cpp +/reaxff_bonds.cpp +/reaxff_control.cpp +/reaxff_ffield.cpp +/reaxff_forces.cpp +/reaxff_hydrogen_bonds.cpp +/reaxff_init_md.cpp +/reaxff_list.cpp +/reaxff_lookup.cpp +/reaxff_multi_body.cpp +/reaxff_nonbonded.cpp +/reaxff_reset_tools.cpp +/reaxff_tool_box.cpp +/reaxff_torsion_angles.cpp +/reaxff_valence_angles.cpp +/reaxff_api.h +/reaxff_defs.h +/reaxff_inline.h +/reaxff_omp.h +/reaxff_types.h /remap.cpp /remap.h /remap_wrap.cpp @@ -1429,6 +1469,10 @@ /pair_thole.h /pair_buck_mdf.cpp /pair_buck_mdf.h +/pair_dpd.cpp +/pair_dpd.h +/pair_dpd_tstat.cpp +/pair_dpd_tstat.h /pair_dpd_ext.cpp /pair_dpd_ext.h /pair_dpd_ext_tstat.cpp diff --git a/src/USER-ADIOS/Install.sh b/src/ADIOS/Install.sh similarity index 98% rename from src/USER-ADIOS/Install.sh rename to src/ADIOS/Install.sh index b8a2f1f9a9..ddca8c6efe 100644 --- a/src/USER-ADIOS/Install.sh +++ b/src/ADIOS/Install.sh @@ -72,7 +72,7 @@ adios_SYSLIB=${ADIOS2_LIB} sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ../USER-ADIOS/Makefile.lammps +include ../ADIOS/Makefile.lammps ' ../Makefile.package.settings fi fi diff --git a/src/USER-ADIOS/README b/src/ADIOS/README similarity index 95% rename from src/USER-ADIOS/README rename to src/ADIOS/README index 2b66f27f6b..18f4a8aed4 100644 --- a/src/USER-ADIOS/README +++ b/src/ADIOS/README @@ -8,7 +8,7 @@ Configure LAMMPS with CMake ADIOS2_DIR to the ADIOS 2.x installation path b. use the cmake option - -D PKG_USER-ADIOS=yes + -D PKG_ADIOS=yes The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory); If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket. diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/ADIOS/dump_atom_adios.cpp similarity index 100% rename from src/USER-ADIOS/dump_atom_adios.cpp rename to src/ADIOS/dump_atom_adios.cpp diff --git a/src/USER-ADIOS/dump_atom_adios.h b/src/ADIOS/dump_atom_adios.h similarity index 100% rename from src/USER-ADIOS/dump_atom_adios.h rename to src/ADIOS/dump_atom_adios.h diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/ADIOS/dump_custom_adios.cpp similarity index 100% rename from src/USER-ADIOS/dump_custom_adios.cpp rename to src/ADIOS/dump_custom_adios.cpp diff --git a/src/USER-ADIOS/dump_custom_adios.h b/src/ADIOS/dump_custom_adios.h similarity index 100% rename from src/USER-ADIOS/dump_custom_adios.h rename to src/ADIOS/dump_custom_adios.h diff --git a/src/USER-ADIOS/reader_adios.cpp b/src/ADIOS/reader_adios.cpp similarity index 100% rename from src/USER-ADIOS/reader_adios.cpp rename to src/ADIOS/reader_adios.cpp diff --git a/src/USER-ADIOS/reader_adios.h b/src/ADIOS/reader_adios.h similarity index 100% rename from src/USER-ADIOS/reader_adios.h rename to src/ADIOS/reader_adios.h diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index 5c0602a453..23ec79fa98 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,32 +17,31 @@ #include "pair_resquared.h" -#include -#include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairRESquared::PairRESquared(LAMMPS *lmp) : Pair(lmp), - cr60(pow(60.0,1.0/3.0)), - b_alpha(45.0/56.0) +PairRESquared::PairRESquared(LAMMPS *lmp) : + Pair(lmp), cr60(pow(60.0, 1.0 / 3.0)), b_alpha(45.0 / 56.0) { single_enable = 0; - cr60 = pow(60.0,1.0/3.0); - b_alpha = 45.0/56.0; - solv_f_a = 3.0/(16.0*atan(1.0)*-36.0); - solv_f_r = 3.0/(16.0*atan(1.0)*2025.0); + cr60 = pow(60.0, 1.0 / 3.0); + b_alpha = 45.0 / 56.0; + solv_f_a = 3.0 / (16.0 * atan(1.0) * -36.0); + solv_f_r = 3.0 / (16.0 * atan(1.0) * 2025.0); } /* ---------------------------------------------------------------------- @@ -68,8 +66,8 @@ PairRESquared::~PairRESquared() memory->destroy(lj3); memory->destroy(lj4); memory->destroy(offset); - delete [] lshape; - delete [] setwell; + delete[] lshape; + delete[] setwell; } } @@ -77,14 +75,14 @@ PairRESquared::~PairRESquared() void PairRESquared::compute(int eflag, int vflag) { - int i,j,ii,jj,inum,jnum,itype,jtype; - double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj; - double fforce[3],ttor[3],rtor[3],r12[3]; - int *ilist,*jlist,*numneigh,**firstneigh; - RE2Vars wi,wj; + int i, j, ii, jj, inum, jnum, itype, jtype; + double evdwl, one_eng, rsq, r2inv, r6inv, forcelj, factor_lj; + double fforce[3], ttor[3], rtor[3], r12[3]; + int *ilist, *jlist, *numneigh, **firstneigh; + RE2Vars wi, wj; evdwl = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -107,7 +105,7 @@ void PairRESquared::compute(int eflag, int vflag) // not a LJ sphere - if (lshape[itype] != 0.0) precompute_i(i,wi); + if (lshape[itype] != 0.0) precompute_i(i, wi); jlist = firstneigh[i]; jnum = numneigh[i]; @@ -119,10 +117,10 @@ void PairRESquared::compute(int eflag, int vflag) // r12 = center to center vector - r12[0] = x[j][0]-x[i][0]; - r12[1] = x[j][1]-x[i][1]; - r12[2] = x[j][2]-x[i][2]; - rsq = MathExtra::dot3(r12,r12); + r12[0] = x[j][0] - x[i][0]; + r12[1] = x[j][1] - x[i][1]; + r12[2] = x[j][2] - x[i][2]; + rsq = MathExtra::dot3(r12, r12); jtype = type[j]; // compute if less than cutoff @@ -132,49 +130,50 @@ void PairRESquared::compute(int eflag, int vflag) switch (form[itype][jtype]) { - case SPHERE_SPHERE: - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - forcelj *= -r2inv; - if (eflag) one_eng = - r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) - - offset[itype][jtype]; - fforce[0] = r12[0]*forcelj; - fforce[1] = r12[1]*forcelj; - fforce[2] = r12[2]*forcelj; - break; + case SPHERE_SPHERE: + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); + forcelj *= -r2inv; + if (eflag) { + one_eng = r6inv * (r6inv * lj3[itype][jtype] - lj4[itype][jtype]); + one_eng -= offset[itype][jtype]; + } + fforce[0] = r12[0] * forcelj; + fforce[1] = r12[1] * forcelj; + fforce[2] = r12[2] * forcelj; + break; - case SPHERE_ELLIPSE: - precompute_i(j,wj); - if (newton_pair || j < nlocal) { - one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,true); - tor[j][0] += rtor[0]*factor_lj; - tor[j][1] += rtor[1]*factor_lj; - tor[j][2] += rtor[2]*factor_lj; - } else - one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,false); - break; + case SPHERE_ELLIPSE: + precompute_i(j, wj); + if (newton_pair || j < nlocal) { + one_eng = resquared_lj(j, i, wj, r12, rsq, fforce, rtor, true); + tor[j][0] += rtor[0] * factor_lj; + tor[j][1] += rtor[1] * factor_lj; + tor[j][2] += rtor[2] * factor_lj; + } else + one_eng = resquared_lj(j, i, wj, r12, rsq, fforce, rtor, false); + break; - case ELLIPSE_SPHERE: - one_eng = resquared_lj(i,j,wi,r12,rsq,fforce,ttor,true); - tor[i][0] += ttor[0]*factor_lj; - tor[i][1] += ttor[1]*factor_lj; - tor[i][2] += ttor[2]*factor_lj; - break; + case ELLIPSE_SPHERE: + one_eng = resquared_lj(i, j, wi, r12, rsq, fforce, ttor, true); + tor[i][0] += ttor[0] * factor_lj; + tor[i][1] += ttor[1] * factor_lj; + tor[i][2] += ttor[2] * factor_lj; + break; - default: - precompute_i(j,wj); - one_eng = resquared_analytic(i,j,wi,wj,r12,rsq,fforce,ttor,rtor); - tor[i][0] += ttor[0]*factor_lj; - tor[i][1] += ttor[1]*factor_lj; - tor[i][2] += ttor[2]*factor_lj; - if (newton_pair || j < nlocal) { - tor[j][0] += rtor[0]*factor_lj; - tor[j][1] += rtor[1]*factor_lj; - tor[j][2] += rtor[2]*factor_lj; - } - break; + default: + precompute_i(j, wj); + one_eng = resquared_analytic(i, j, wi, wj, r12, rsq, fforce, ttor, rtor); + tor[i][0] += ttor[0] * factor_lj; + tor[i][1] += ttor[1] * factor_lj; + tor[i][2] += ttor[2] * factor_lj; + if (newton_pair || j < nlocal) { + tor[j][0] += rtor[0] * factor_lj; + tor[j][1] += rtor[1] * factor_lj; + tor[j][2] += rtor[2] * factor_lj; + } + break; } fforce[0] *= factor_lj; @@ -190,11 +189,11 @@ void PairRESquared::compute(int eflag, int vflag) f[j][2] -= fforce[2]; } - if (eflag) evdwl = factor_lj*one_eng; + if (eflag) evdwl = factor_lj * one_eng; - if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,0.0,fforce[0],fforce[1],fforce[2], - -r12[0],-r12[1],-r12[2]); + if (evflag) + ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fforce[0], fforce[1], fforce[2], + -r12[0], -r12[1], -r12[2]); } } } @@ -209,31 +208,30 @@ void PairRESquared::compute(int eflag, int vflag) void PairRESquared::allocate() { allocated = 1; - int n = atom->ntypes; + const int n = atom->ntypes + 1; - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + memory->create(setflag, n, n, "pair:setflag"); + for (int i = 1; i < n; i++) + for (int j = i; j < n; j++) setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutsq, n, n, "pair:cutsq"); - memory->create(form,n+1,n+1,"pair:form"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(shape1,n+1,3,"pair:shape1"); - memory->create(shape2,n+1,3,"pair:shape2"); - memory->create(well,n+1,3,"pair:well"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); - memory->create(offset,n+1,n+1,"pair:offset"); + memory->create(form, n, n, "pair:form"); + memory->create(epsilon, n, n, "pair:epsilon"); + memory->create(sigma, n, n, "pair:sigma"); + memory->create(shape1, n, 3, "pair:shape1"); + memory->create(shape2, n, 3, "pair:shape2"); + memory->create(well, n, 3, "pair:well"); + memory->create(cut, n, n, "pair:cut"); + memory->create(lj1, n, n, "pair:lj1"); + memory->create(lj2, n, n, "pair:lj2"); + memory->create(lj3, n, n, "pair:lj3"); + memory->create(lj4, n, n, "pair:lj4"); + memory->create(offset, n, n, "pair:offset"); - lshape = new double[n+1]; - setwell = new int[n+1]; - for (int i = 1; i <= n; i++) setwell[i] = 0; + lshape = new double[n]; + setwell = new int[n]; + for (int i = 1; i < n; i++) setwell[i] = 0; } /* ---------------------------------------------------------------------- @@ -242,14 +240,14 @@ void PairRESquared::allocate() void PairRESquared::settings(int narg, char **arg) { - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); - cut_global = utils::numeric(FLERR,arg[0],false,lmp); + cut_global = utils::numeric(FLERR, arg[0], false, lmp); // reset cutoffs that have been explicitly set if (allocated) { - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) if (setflag[i][j]) cut[i][j] = cut_global; @@ -262,29 +260,28 @@ void PairRESquared::settings(int narg, char **arg) void PairRESquared::coeff(int narg, char **arg) { - if (narg < 10 || narg > 11) - error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 10 || narg > 11) error->all(FLERR, "Incorrect args for pair coefficients"); if (!allocated) allocate(); - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); - double epsilon_one = utils::numeric(FLERR,arg[2],false,lmp); - double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); - double eia_one = utils::numeric(FLERR,arg[4],false,lmp); - double eib_one = utils::numeric(FLERR,arg[5],false,lmp); - double eic_one = utils::numeric(FLERR,arg[6],false,lmp); - double eja_one = utils::numeric(FLERR,arg[7],false,lmp); - double ejb_one = utils::numeric(FLERR,arg[8],false,lmp); - double ejc_one = utils::numeric(FLERR,arg[9],false,lmp); + double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp); + double sigma_one = utils::numeric(FLERR, arg[3], false, lmp); + double eia_one = utils::numeric(FLERR, arg[4], false, lmp); + double eib_one = utils::numeric(FLERR, arg[5], false, lmp); + double eic_one = utils::numeric(FLERR, arg[6], false, lmp); + double eja_one = utils::numeric(FLERR, arg[7], false, lmp); + double ejb_one = utils::numeric(FLERR, arg[8], false, lmp); + double ejc_one = utils::numeric(FLERR, arg[9], false, lmp); double cut_one = cut_global; - if (narg == 11) cut_one = utils::numeric(FLERR,arg[10],false,lmp); + if (narg == 11) cut_one = utils::numeric(FLERR, arg[10], false, lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { epsilon[i][j] = epsilon_one; sigma[i][j] = sigma_one; cut[i][j] = cut_one; @@ -292,22 +289,26 @@ void PairRESquared::coeff(int narg, char **arg) well[i][0] = eia_one; well[i][1] = eib_one; well[i][2] = eic_one; - if (eia_one == 1.0 && eib_one == 1.0 && eic_one == 1.0) setwell[i] = 2; - else setwell[i] = 1; + if (eia_one == 1.0 && eib_one == 1.0 && eic_one == 1.0) + setwell[i] = 2; + else + setwell[i] = 1; } if (eja_one != 0.0 || ejb_one != 0.0 || ejc_one != 0.0) { well[j][0] = eja_one; well[j][1] = ejb_one; well[j][2] = ejc_one; - if (eja_one == 1.0 && ejb_one == 1.0 && ejc_one == 1.0) setwell[j] = 2; - else setwell[j] = 1; + if (eja_one == 1.0 && ejb_one == 1.0 && ejc_one == 1.0) + setwell[j] = 2; + else + setwell[j] = 1; } setflag[i][j] = 1; count++; } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -317,21 +318,21 @@ void PairRESquared::coeff(int narg, char **arg) void PairRESquared::init_style() { avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); - if (!avec) error->all(FLERR,"Pair resquared requires atom style ellipsoid"); + if (!avec) error->all(FLERR, "Pair resquared requires atom style ellipsoid"); - neighbor->request(this,instance_me); + neighbor->request(this, instance_me); // per-type shape precalculations // require that atom shapes are identical within each type for (int i = 1; i <= atom->ntypes; i++) { - if (!atom->shape_consistency(i,shape1[i][0],shape1[i][1],shape1[i][2])) - error->all(FLERR,"Pair resquared requires atoms with same type have same shape"); + if (!atom->shape_consistency(i, shape1[i][0], shape1[i][1], shape1[i][2])) + error->all(FLERR, "Pair resquared requires atoms with same type have same shape"); if (setwell[i]) { - shape2[i][0] = shape1[i][0]*shape1[i][0]; - shape2[i][1] = shape1[i][1]*shape1[i][1]; - shape2[i][2] = shape1[i][2]*shape1[i][2]; - lshape[i] = shape1[i][0]*shape1[i][1]*shape1[i][2]; + shape2[i][0] = shape1[i][0] * shape1[i][0]; + shape2[i][1] = shape1[i][1] * shape1[i][1]; + shape2[i][2] = shape1[i][2] * shape1[i][2]; + lshape[i] = shape1[i][0] * shape1[i][1] * shape1[i][2]; } } } @@ -343,14 +344,12 @@ void PairRESquared::init_style() double PairRESquared::init_one(int i, int j) { if (setwell[i] == 0 || setwell[j] == 0) - error->all(FLERR,"Pair resquared epsilon a,b,c coeffs are not all set"); + error->all(FLERR, "Pair resquared epsilon a,b,c coeffs are not all set"); int ishape = 0; - if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0) - ishape = 1; + if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0) ishape = 1; int jshape = 0; - if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0) - jshape = 1; + if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0) jshape = 1; if (ishape == 0 && jshape == 0) { form[i][j] = SPHERE_SPHERE; @@ -371,28 +370,27 @@ double PairRESquared::init_one(int i, int j) if (setflag[i][j] == 0) { if (setflag[j][i] == 0) { if (ishape == 0 && jshape == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]); + cut[i][j] = mix_distance(cut[i][i], cut[j][j]); } else - error->all(FLERR, - "Pair resquared epsilon and sigma coeffs are not all set"); + error->all(FLERR, "Pair resquared epsilon and sigma coeffs are not all set"); } epsilon[i][j] = epsilon[j][i]; sigma[i][j] = sigma[j][i]; cut[i][j] = cut[j][i]; } - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); if (offset_flag && (cut[i][j] > 0.0)) { double ratio = sigma[i][j] / cut[i][j]; - offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0)); - } else offset[i][j] = 0.0; + offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio, 12.0) - pow(ratio, 6.0)); + } else + offset[i][j] = 0.0; epsilon[j][i] = epsilon[i][j]; sigma[j][i] = sigma[i][j]; @@ -413,16 +411,16 @@ void PairRESquared::write_restart(FILE *fp) { write_restart_settings(fp); - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) { - fwrite(&setwell[i],sizeof(int),1,fp); - if (setwell[i]) fwrite(&well[i][0],sizeof(double),3,fp); + fwrite(&setwell[i], sizeof(int), 1, fp); + if (setwell[i]) fwrite(&well[i][0], sizeof(double), 3, fp); for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); + fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { - fwrite(&epsilon[i][j],sizeof(double),1,fp); - fwrite(&sigma[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); } } } @@ -437,27 +435,27 @@ void PairRESquared::read_restart(FILE *fp) read_restart_settings(fp); allocate(); - int i,j; + int i, j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { - if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setwell[i],1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &setwell[i], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setwell[i], 1, MPI_INT, 0, world); if (setwell[i]) { - if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,nullptr,error); - MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world); + if (me == 0) utils::sfread(FLERR, &well[i][0], sizeof(double), 3, fp, nullptr, error); + MPI_Bcast(&well[i][0], 3, MPI_DOUBLE, 0, world); } for (j = i; j <= atom->ntypes; j++) { - if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } - MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -469,8 +467,8 @@ void PairRESquared::read_restart(FILE *fp) void PairRESquared::write_restart_settings(FILE *fp) { - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); } /* ---------------------------------------------------------------------- @@ -481,34 +479,34 @@ void PairRESquared::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); } - MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); } /* ---------------------------------------------------------------------- Precompute per-particle temporaries for RE-squared calculation ------------------------------------------------------------------------- */ -void PairRESquared::precompute_i(const int i,RE2Vars &ws) +void PairRESquared::precompute_i(const int i, RE2Vars &ws) { - double aTs[3][3]; // A1'*S1^2 + double aTs[3][3]; // A1'*S1^2 int *ellipsoid = atom->ellipsoid; AtomVecEllipsoid::Bonus *bonus = avec->bonus; - MathExtra::quat_to_mat_trans(bonus[ellipsoid[i]].quat,ws.A); - MathExtra::transpose_diag3(ws.A,well[atom->type[i]],ws.aTe); - MathExtra::transpose_diag3(ws.A,shape2[atom->type[i]],aTs); - MathExtra::diag_times3(shape2[atom->type[i]],ws.A,ws.sa); - MathExtra::times3(aTs,ws.A,ws.gamma); - MathExtra::rotation_generator_x(ws.A,ws.lA[0]); - MathExtra::rotation_generator_y(ws.A,ws.lA[1]); - MathExtra::rotation_generator_z(ws.A,ws.lA[2]); - for (int i=0; i<3; i++) { - MathExtra::times3(aTs,ws.lA[i],ws.lAtwo[i]); - MathExtra::transpose_times3(ws.lA[i],ws.sa,ws.lAsa[i]); - MathExtra::plus3(ws.lAsa[i],ws.lAtwo[i],ws.lAsa[i]); + MathExtra::quat_to_mat_trans(bonus[ellipsoid[i]].quat, ws.A); + MathExtra::transpose_diag3(ws.A, well[atom->type[i]], ws.aTe); + MathExtra::transpose_diag3(ws.A, shape2[atom->type[i]], aTs); + MathExtra::diag_times3(shape2[atom->type[i]], ws.A, ws.sa); + MathExtra::times3(aTs, ws.A, ws.gamma); + MathExtra::rotation_generator_x(ws.A, ws.lA[0]); + MathExtra::rotation_generator_y(ws.A, ws.lA[1]); + MathExtra::rotation_generator_z(ws.A, ws.lA[2]); + for (int m = 0; m < 3; m++) { + MathExtra::times3(aTs, ws.lA[m], ws.lAtwo[m]); + MathExtra::transpose_times3(ws.lA[m], ws.sa, ws.lAsa[m]); + MathExtra::plus3(ws.lAsa[m], ws.lAtwo[m], ws.lAsa[m]); } } @@ -517,6 +515,7 @@ void PairRESquared::precompute_i(const int i,RE2Vars &ws) derivative of m (m2) ------------------------------------------------------------------------- */ +// clang-format off double PairRESquared::det_prime(const double m[3][3], const double m2[3][3]) { double ans; @@ -531,458 +530,441 @@ double PairRESquared::det_prime(const double m[3][3], const double m2[3][3]) m2[2][0]*m[0][1]*m[1][2] - m2[2][0]*m[0][2]*m[1][1]; return ans; } +// clang-format on /* ---------------------------------------------------------------------- Compute the energy, force, torque for a pair (INTEGRATED-INTEGRATED) ------------------------------------------------------------------------- */ -double PairRESquared::resquared_analytic(const int i, const int j, - const RE2Vars &wi, const RE2Vars &wj, - const double *r, const double rsq, - double *fforce, double *ttor, - double *rtor) +double PairRESquared::resquared_analytic(const int i, const int j, const RE2Vars &wi, + const RE2Vars &wj, const double *r, const double rsq, + double *fforce, double *ttor, double *rtor) { int *type = atom->type; // pair computations for energy, force, torque - double z1[3],z2[3]; // A1*rhat # don't need to store - double v1[3],v2[3]; // inv(S1^2)*z1 # don't need to store - double sigma1,sigma2; // 1/sqrt(z1'*v1) - double sigma1p2,sigma2p2; // sigma1^2 - double rnorm; // L2 norm of r - double rhat[3]; // r/rnorm - double s[3]; // inv(gamma1+gamma2)*rhat - double sigma12; // 1/sqrt(0.5*s'*rhat) - double H12[3][3]; // gamma1/sigma1+gamma2/sigma2 - double dH; // det(H12) - double lambda; // dS1/sigma1p2+dS2/sigma2p2 - double nu; // sqrt(dH/(sigma1+sigma2)) - double w[3]; // inv(A1'*E1*A1+A2'*E2*A2)*rhat - double h12; // rnorm-sigma12; - double eta; // lambda/nu - double chi; // 2*rhat'*w - double sprod; // dS1*dS2 - double sigh; // sigma/h12 - double tprod; // eta*chi*sigh - double Ua,Ur; // attractive/repulsive parts of potential + double z1[3], z2[3]; // A1*rhat # don't need to store + double v1[3], v2[3]; // inv(S1^2)*z1 # don't need to store + double sigma1, sigma2; // 1/sqrt(z1'*v1) + double sigma1p2, sigma2p2; // sigma1^2 + double rnorm; // L2 norm of r + double rhat[3]; // r/rnorm + double s[3]; // inv(gamma1+gamma2)*rhat + double sigma12; // 1/sqrt(0.5*s'*rhat) + double H12[3][3]; // gamma1/sigma1+gamma2/sigma2 + double dH; // det(H12) + double lambda; // dS1/sigma1p2+dS2/sigma2p2 + double nu; // sqrt(dH/(sigma1+sigma2)) + double w[3]; // inv(A1'*E1*A1+A2'*E2*A2)*rhat + double h12; // rnorm-sigma12; + double eta; // lambda/nu + double chi; // 2*rhat'*w + double sprod; // dS1*dS2 + double sigh; // sigma/h12 + double tprod; // eta*chi*sigh + double Ua, Ur; // attractive/repulsive parts of potential // pair computations for force, torque - double sec; // sigma*eta*chi - double sigma1p3, sigma2p3; // sigma1^3 - double vsigma1[3], vsigma2[3]; // sigma1^3*v1; - double sigma12p3; // sigma12^3 - double gsigma1[3][3], gsigma2[3][3]; // -gamma1/sigma1^2 - double tsig1sig2; // eta/(2*(sigma1+sigma2)) - double tdH; // eta/(2*dH) - double teta1,teta2; // 2*eta/lambda*dS1/sigma1p3 - double fourw[3]; // 4*w; - double spr[3]; // 0.5*sigma12^3*s - double hsec; // h12+[3,b_alpha]*sec - double dspu; // 1/h12 - 1/hsec + temp - double pbsu; // 3*sigma/hsec - double dspr; // 7/h12-1/hsec+temp - double pbsr; // b_alpha*sigma/hsec; - double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm - double u1[3],u2[3]; // A1*u - double dsigma1,dsigma2; // u1'*vsigma1 (force) p'*vsigma1 (tor) - double dH12[3][3]; // dsigma1*gsigma1 + dsigma2*gsigma2 - double ddH; // derivative of det(H12) - double deta,dchi,dh12; // derivatives of eta,chi,h12 - double dUr,dUa; // derivatives of Ua,Ur + double sec; // sigma*eta*chi + double sigma1p3, sigma2p3; // sigma1^3 + double vsigma1[3], vsigma2[3]; // sigma1^3*v1; + double sigma12p3; // sigma12^3 + double gsigma1[3][3], gsigma2[3][3]; // -gamma1/sigma1^2 + double tsig1sig2; // eta/(2*(sigma1+sigma2)) + double tdH; // eta/(2*dH) + double teta1, teta2; // 2*eta/lambda*dS1/sigma1p3 + double fourw[3]; // 4*w; + double spr[3]; // 0.5*sigma12^3*s + double hsec; // h12+[3,b_alpha]*sec + double dspu; // 1/h12 - 1/hsec + temp + double pbsu; // 3*sigma/hsec + double dspr; // 7/h12-1/hsec+temp + double pbsr; // b_alpha*sigma/hsec; + double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm + double u1[3], u2[3]; // A1*u + double dsigma1, dsigma2; // u1'*vsigma1 (force) p'*vsigma1 (tor) + double dH12[3][3]; // dsigma1*gsigma1 + dsigma2*gsigma2 + double ddH; // derivative of det(H12) + double deta, dchi, dh12; // derivatives of eta,chi,h12 + double dUr, dUa; // derivatives of Ua,Ur // pair computations for torque - double fwae[3]; // -fourw'*aTe - double p[3]; // lA*rhat + double fwae[3]; // -fourw'*aTe + double p[3]; // lA*rhat rnorm = sqrt(rsq); - rhat[0] = r[0]/rnorm; - rhat[1] = r[1]/rnorm; - rhat[2] = r[2]/rnorm; + rhat[0] = r[0] / rnorm; + rhat[1] = r[1] / rnorm; + rhat[2] = r[2] / rnorm; // energy double temp[3][3]; - MathExtra::plus3(wi.gamma,wj.gamma,temp); - int ierror = MathExtra::mldivide3(temp,rhat,s); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + MathExtra::plus3(wi.gamma, wj.gamma, temp); + int ierror = MathExtra::mldivide3(temp, rhat, s); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - sigma12 = 1.0/sqrt(0.5*MathExtra::dot3(s,rhat)); - MathExtra::matvec(wi.A,rhat,z1); - MathExtra::matvec(wj.A,rhat,z2); - v1[0] = z1[0]/shape2[type[i]][0]; - v1[1] = z1[1]/shape2[type[i]][1]; - v1[2] = z1[2]/shape2[type[i]][2]; - v2[0] = z2[0]/shape2[type[j]][0]; - v2[1] = z2[1]/shape2[type[j]][1]; - v2[2] = z2[2]/shape2[type[j]][2]; - sigma1 = 1.0/sqrt(MathExtra::dot3(z1,v1)); - sigma2 = 1.0/sqrt(MathExtra::dot3(z2,v2)); - H12[0][0] = wi.gamma[0][0]/sigma1+wj.gamma[0][0]/sigma2; - H12[0][1] = wi.gamma[0][1]/sigma1+wj.gamma[0][1]/sigma2; - H12[0][2] = wi.gamma[0][2]/sigma1+wj.gamma[0][2]/sigma2; - H12[1][0] = wi.gamma[1][0]/sigma1+wj.gamma[1][0]/sigma2; - H12[1][1] = wi.gamma[1][1]/sigma1+wj.gamma[1][1]/sigma2; - H12[1][2] = wi.gamma[1][2]/sigma1+wj.gamma[1][2]/sigma2; - H12[2][0] = wi.gamma[2][0]/sigma1+wj.gamma[2][0]/sigma2; - H12[2][1] = wi.gamma[2][1]/sigma1+wj.gamma[2][1]/sigma2; - H12[2][2] = wi.gamma[2][2]/sigma1+wj.gamma[2][2]/sigma2; - dH=MathExtra::det3(H12); - sigma1p2 = sigma1*sigma1; - sigma2p2 = sigma2*sigma2; - lambda = lshape[type[i]]/sigma1p2 + lshape[type[j]]/sigma2p2; - nu = sqrt(dH/(sigma1+sigma2)); - MathExtra::times3(wi.aTe,wi.A,temp); + sigma12 = 1.0 / sqrt(0.5 * MathExtra::dot3(s, rhat)); + MathExtra::matvec(wi.A, rhat, z1); + MathExtra::matvec(wj.A, rhat, z2); + v1[0] = z1[0] / shape2[type[i]][0]; + v1[1] = z1[1] / shape2[type[i]][1]; + v1[2] = z1[2] / shape2[type[i]][2]; + v2[0] = z2[0] / shape2[type[j]][0]; + v2[1] = z2[1] / shape2[type[j]][1]; + v2[2] = z2[2] / shape2[type[j]][2]; + sigma1 = 1.0 / sqrt(MathExtra::dot3(z1, v1)); + sigma2 = 1.0 / sqrt(MathExtra::dot3(z2, v2)); + H12[0][0] = wi.gamma[0][0] / sigma1 + wj.gamma[0][0] / sigma2; + H12[0][1] = wi.gamma[0][1] / sigma1 + wj.gamma[0][1] / sigma2; + H12[0][2] = wi.gamma[0][2] / sigma1 + wj.gamma[0][2] / sigma2; + H12[1][0] = wi.gamma[1][0] / sigma1 + wj.gamma[1][0] / sigma2; + H12[1][1] = wi.gamma[1][1] / sigma1 + wj.gamma[1][1] / sigma2; + H12[1][2] = wi.gamma[1][2] / sigma1 + wj.gamma[1][2] / sigma2; + H12[2][0] = wi.gamma[2][0] / sigma1 + wj.gamma[2][0] / sigma2; + H12[2][1] = wi.gamma[2][1] / sigma1 + wj.gamma[2][1] / sigma2; + H12[2][2] = wi.gamma[2][2] / sigma1 + wj.gamma[2][2] / sigma2; + dH = MathExtra::det3(H12); + sigma1p2 = sigma1 * sigma1; + sigma2p2 = sigma2 * sigma2; + lambda = lshape[type[i]] / sigma1p2 + lshape[type[j]] / sigma2p2; + nu = sqrt(dH / (sigma1 + sigma2)); + MathExtra::times3(wi.aTe, wi.A, temp); double temp2[3][3]; - MathExtra::times3(wj.aTe,wj.A,temp2); - MathExtra::plus3(temp,temp2,temp); - ierror = MathExtra::mldivide3(temp,rhat,w); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + MathExtra::times3(wj.aTe, wj.A, temp2); + MathExtra::plus3(temp, temp2, temp); + ierror = MathExtra::mldivide3(temp, rhat, w); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - h12 = rnorm-sigma12; - eta = lambda/nu; - chi = 2.0*MathExtra::dot3(rhat,w); + h12 = rnorm - sigma12; + eta = lambda / nu; + chi = 2.0 * MathExtra::dot3(rhat, w); sprod = lshape[type[i]] * lshape[type[j]]; - sigh = sigma[type[i]][type[j]]/h12; - tprod = eta*chi*sigh; + sigh = sigma[type[i]][type[j]] / h12; + tprod = eta * chi * sigh; - double stemp = h12/2.0; - Ua = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*(shape1[type[j]][0]+stemp)* - (shape1[type[j]][1]+stemp)*(shape1[type[j]][2]+stemp); - Ua = (1.0+3.0*tprod)*sprod/Ua; - Ua = epsilon[type[i]][type[j]]*Ua/-36.0; + double stemp = h12 / 2.0; + Ua = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + (shape1[type[j]][0] + stemp) * (shape1[type[j]][1] + stemp) * (shape1[type[j]][2] + stemp); + Ua = (1.0 + 3.0 * tprod) * sprod / Ua; + Ua = epsilon[type[i]][type[j]] * Ua / -36.0; - stemp = h12/cr60; - Ur = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*(shape1[type[j]][0]+stemp)* - (shape1[type[j]][1]+stemp)*(shape1[type[j]][2]+stemp); - Ur = (1.0+b_alpha*tprod)*sprod/Ur; - Ur = epsilon[type[i]][type[j]]*Ur*pow(sigh,6.0)/2025.0; + stemp = h12 / cr60; + Ur = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + (shape1[type[j]][0] + stemp) * (shape1[type[j]][1] + stemp) * (shape1[type[j]][2] + stemp); + Ur = (1.0 + b_alpha * tprod) * sprod / Ur; + Ur = epsilon[type[i]][type[j]] * Ur * pow(sigh, 6.0) / 2025.0; // force - sec = sigma[type[i]][type[j]]*eta*chi; - sigma12p3 = pow(sigma12,3.0); - sigma1p3 = sigma1p2*sigma1; - sigma2p3 = sigma2p2*sigma2; - vsigma1[0] = -sigma1p3*v1[0]; - vsigma1[1] = -sigma1p3*v1[1]; - vsigma1[2] = -sigma1p3*v1[2]; - vsigma2[0] = -sigma2p3*v2[0]; - vsigma2[1] = -sigma2p3*v2[1]; - vsigma2[2] = -sigma2p3*v2[2]; - gsigma1[0][0] = -wi.gamma[0][0]/sigma1p2; - gsigma1[0][1] = -wi.gamma[0][1]/sigma1p2; - gsigma1[0][2] = -wi.gamma[0][2]/sigma1p2; - gsigma1[1][0] = -wi.gamma[1][0]/sigma1p2; - gsigma1[1][1] = -wi.gamma[1][1]/sigma1p2; - gsigma1[1][2] = -wi.gamma[1][2]/sigma1p2; - gsigma1[2][0] = -wi.gamma[2][0]/sigma1p2; - gsigma1[2][1] = -wi.gamma[2][1]/sigma1p2; - gsigma1[2][2] = -wi.gamma[2][2]/sigma1p2; - gsigma2[0][0] = -wj.gamma[0][0]/sigma2p2; - gsigma2[0][1] = -wj.gamma[0][1]/sigma2p2; - gsigma2[0][2] = -wj.gamma[0][2]/sigma2p2; - gsigma2[1][0] = -wj.gamma[1][0]/sigma2p2; - gsigma2[1][1] = -wj.gamma[1][1]/sigma2p2; - gsigma2[1][2] = -wj.gamma[1][2]/sigma2p2; - gsigma2[2][0] = -wj.gamma[2][0]/sigma2p2; - gsigma2[2][1] = -wj.gamma[2][1]/sigma2p2; - gsigma2[2][2] = -wj.gamma[2][2]/sigma2p2; - tsig1sig2 = eta/(2.0*(sigma1+sigma2)); - tdH = eta/(2.0*dH); - teta1 = 2.0*eta/lambda; - teta2 = teta1*lshape[type[j]]/sigma2p3; - teta1 = teta1*lshape[type[i]]/sigma1p3; - fourw[0] = 4.0*w[0]; - fourw[1] = 4.0*w[1]; - fourw[2] = 4.0*w[2]; - spr[0] = 0.5*sigma12p3*s[0]; - spr[1] = 0.5*sigma12p3*s[1]; - spr[2] = 0.5*sigma12p3*s[2]; + sec = sigma[type[i]][type[j]] * eta * chi; + sigma12p3 = pow(sigma12, 3.0); + sigma1p3 = sigma1p2 * sigma1; + sigma2p3 = sigma2p2 * sigma2; + vsigma1[0] = -sigma1p3 * v1[0]; + vsigma1[1] = -sigma1p3 * v1[1]; + vsigma1[2] = -sigma1p3 * v1[2]; + vsigma2[0] = -sigma2p3 * v2[0]; + vsigma2[1] = -sigma2p3 * v2[1]; + vsigma2[2] = -sigma2p3 * v2[2]; + gsigma1[0][0] = -wi.gamma[0][0] / sigma1p2; + gsigma1[0][1] = -wi.gamma[0][1] / sigma1p2; + gsigma1[0][2] = -wi.gamma[0][2] / sigma1p2; + gsigma1[1][0] = -wi.gamma[1][0] / sigma1p2; + gsigma1[1][1] = -wi.gamma[1][1] / sigma1p2; + gsigma1[1][2] = -wi.gamma[1][2] / sigma1p2; + gsigma1[2][0] = -wi.gamma[2][0] / sigma1p2; + gsigma1[2][1] = -wi.gamma[2][1] / sigma1p2; + gsigma1[2][2] = -wi.gamma[2][2] / sigma1p2; + gsigma2[0][0] = -wj.gamma[0][0] / sigma2p2; + gsigma2[0][1] = -wj.gamma[0][1] / sigma2p2; + gsigma2[0][2] = -wj.gamma[0][2] / sigma2p2; + gsigma2[1][0] = -wj.gamma[1][0] / sigma2p2; + gsigma2[1][1] = -wj.gamma[1][1] / sigma2p2; + gsigma2[1][2] = -wj.gamma[1][2] / sigma2p2; + gsigma2[2][0] = -wj.gamma[2][0] / sigma2p2; + gsigma2[2][1] = -wj.gamma[2][1] / sigma2p2; + gsigma2[2][2] = -wj.gamma[2][2] / sigma2p2; + tsig1sig2 = eta / (2.0 * (sigma1 + sigma2)); + tdH = eta / (2.0 * dH); + teta1 = 2.0 * eta / lambda; + teta2 = teta1 * lshape[type[j]] / sigma2p3; + teta1 = teta1 * lshape[type[i]] / sigma1p3; + fourw[0] = 4.0 * w[0]; + fourw[1] = 4.0 * w[1]; + fourw[2] = 4.0 * w[2]; + spr[0] = 0.5 * sigma12p3 * s[0]; + spr[1] = 0.5 * sigma12p3 * s[1]; + spr[2] = 0.5 * sigma12p3 * s[2]; - stemp = 1.0/(shape1[type[i]][0]*2.0+h12)+ - 1.0/(shape1[type[i]][1]*2.0+h12)+ - 1.0/(shape1[type[i]][2]*2.0+h12)+ - 1.0/(shape1[type[j]][0]*2.0+h12)+ - 1.0/(shape1[type[j]][1]*2.0+h12)+ - 1.0/(shape1[type[j]][2]*2.0+h12); - hsec = h12+3.0*sec; - dspu = 1.0/h12-1.0/hsec+stemp; - pbsu = 3.0*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * 2.0 + h12) + 1.0 / (shape1[type[i]][1] * 2.0 + h12) + + 1.0 / (shape1[type[i]][2] * 2.0 + h12) + 1.0 / (shape1[type[j]][0] * 2.0 + h12) + + 1.0 / (shape1[type[j]][1] * 2.0 + h12) + 1.0 / (shape1[type[j]][2] * 2.0 + h12); + hsec = h12 + 3.0 * sec; + dspu = 1.0 / h12 - 1.0 / hsec + stemp; + pbsu = 3.0 * sigma[type[i]][type[j]] / hsec; - stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+ - 1.0/(shape1[type[i]][1]*cr60+h12)+ - 1.0/(shape1[type[i]][2]*cr60+h12)+ - 1.0/(shape1[type[j]][0]*cr60+h12)+ - 1.0/(shape1[type[j]][1]*cr60+h12)+ - 1.0/(shape1[type[j]][2]*cr60+h12); - hsec = h12+b_alpha*sec; - dspr = 7.0/h12-1.0/hsec+stemp; - pbsr = b_alpha*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * cr60 + h12) + 1.0 / (shape1[type[i]][1] * cr60 + h12) + + 1.0 / (shape1[type[i]][2] * cr60 + h12) + 1.0 / (shape1[type[j]][0] * cr60 + h12) + + 1.0 / (shape1[type[j]][1] * cr60 + h12) + 1.0 / (shape1[type[j]][2] * cr60 + h12); + hsec = h12 + b_alpha * sec; + dspr = 7.0 / h12 - 1.0 / hsec + stemp; + pbsr = b_alpha * sigma[type[i]][type[j]] / hsec; - for (int i=0; i<3; i++) { - u[0] = -rhat[i]*rhat[0]; - u[1] = -rhat[i]*rhat[1]; - u[2] = -rhat[i]*rhat[2]; - u[i] += 1.0; + for (int m = 0; m < 3; m++) { + u[0] = -rhat[m] * rhat[0]; + u[1] = -rhat[m] * rhat[1]; + u[2] = -rhat[m] * rhat[2]; + u[m] += 1.0; u[0] /= rnorm; u[1] /= rnorm; u[2] /= rnorm; - MathExtra::matvec(wi.A,u,u1); - MathExtra::matvec(wj.A,u,u2); - dsigma1=MathExtra::dot3(u1,vsigma1); - dsigma2=MathExtra::dot3(u2,vsigma2); - dH12[0][0] = dsigma1*gsigma1[0][0]+dsigma2*gsigma2[0][0]; - dH12[0][1] = dsigma1*gsigma1[0][1]+dsigma2*gsigma2[0][1]; - dH12[0][2] = dsigma1*gsigma1[0][2]+dsigma2*gsigma2[0][2]; - dH12[1][0] = dsigma1*gsigma1[1][0]+dsigma2*gsigma2[1][0]; - dH12[1][1] = dsigma1*gsigma1[1][1]+dsigma2*gsigma2[1][1]; - dH12[1][2] = dsigma1*gsigma1[1][2]+dsigma2*gsigma2[1][2]; - dH12[2][0] = dsigma1*gsigma1[2][0]+dsigma2*gsigma2[2][0]; - dH12[2][1] = dsigma1*gsigma1[2][1]+dsigma2*gsigma2[2][1]; - dH12[2][2] = dsigma1*gsigma1[2][2]+dsigma2*gsigma2[2][2]; - ddH = det_prime(H12,dH12); - deta = (dsigma1+dsigma2)*tsig1sig2; - deta -= ddH*tdH; - deta -= dsigma1*teta1+dsigma2*teta2; - dchi = MathExtra::dot3(u,fourw); - dh12 = rhat[i]+MathExtra::dot3(u,spr); - dUa = pbsu*(eta*dchi+deta*chi)-dh12*dspu; - dUr = pbsr*(eta*dchi+deta*chi)-dh12*dspr; - fforce[i]=dUr*Ur+dUa*Ua; + MathExtra::matvec(wi.A, u, u1); + MathExtra::matvec(wj.A, u, u2); + dsigma1 = MathExtra::dot3(u1, vsigma1); + dsigma2 = MathExtra::dot3(u2, vsigma2); + dH12[0][0] = dsigma1 * gsigma1[0][0] + dsigma2 * gsigma2[0][0]; + dH12[0][1] = dsigma1 * gsigma1[0][1] + dsigma2 * gsigma2[0][1]; + dH12[0][2] = dsigma1 * gsigma1[0][2] + dsigma2 * gsigma2[0][2]; + dH12[1][0] = dsigma1 * gsigma1[1][0] + dsigma2 * gsigma2[1][0]; + dH12[1][1] = dsigma1 * gsigma1[1][1] + dsigma2 * gsigma2[1][1]; + dH12[1][2] = dsigma1 * gsigma1[1][2] + dsigma2 * gsigma2[1][2]; + dH12[2][0] = dsigma1 * gsigma1[2][0] + dsigma2 * gsigma2[2][0]; + dH12[2][1] = dsigma1 * gsigma1[2][1] + dsigma2 * gsigma2[2][1]; + dH12[2][2] = dsigma1 * gsigma1[2][2] + dsigma2 * gsigma2[2][2]; + ddH = det_prime(H12, dH12); + deta = (dsigma1 + dsigma2) * tsig1sig2; + deta -= ddH * tdH; + deta -= dsigma1 * teta1 + dsigma2 * teta2; + dchi = MathExtra::dot3(u, fourw); + dh12 = rhat[m] + MathExtra::dot3(u, spr); + dUa = pbsu * (eta * dchi + deta * chi) - dh12 * dspu; + dUr = pbsr * (eta * dchi + deta * chi) - dh12 * dspr; + fforce[m] = dUr * Ur + dUa * Ua; } // torque on i - MathExtra::vecmat(fourw,wi.aTe,fwae); + MathExtra::vecmat(fourw, wi.aTe, fwae); - for (int i=0; i<3; i++) { - MathExtra::matvec(wi.lA[i],rhat,p); - dsigma1 = MathExtra::dot3(p,vsigma1); - dH12[0][0] = wi.lAsa[i][0][0]/sigma1+dsigma1*gsigma1[0][0]; - dH12[0][1] = wi.lAsa[i][0][1]/sigma1+dsigma1*gsigma1[0][1]; - dH12[0][2] = wi.lAsa[i][0][2]/sigma1+dsigma1*gsigma1[0][2]; - dH12[1][0] = wi.lAsa[i][1][0]/sigma1+dsigma1*gsigma1[1][0]; - dH12[1][1] = wi.lAsa[i][1][1]/sigma1+dsigma1*gsigma1[1][1]; - dH12[1][2] = wi.lAsa[i][1][2]/sigma1+dsigma1*gsigma1[1][2]; - dH12[2][0] = wi.lAsa[i][2][0]/sigma1+dsigma1*gsigma1[2][0]; - dH12[2][1] = wi.lAsa[i][2][1]/sigma1+dsigma1*gsigma1[2][1]; - dH12[2][2] = wi.lAsa[i][2][2]/sigma1+dsigma1*gsigma1[2][2]; - ddH = det_prime(H12,dH12); - deta = tsig1sig2*dsigma1-tdH*ddH; - deta -= teta1*dsigma1; + for (int i = 0; i < 3; i++) { + MathExtra::matvec(wi.lA[i], rhat, p); + dsigma1 = MathExtra::dot3(p, vsigma1); + dH12[0][0] = wi.lAsa[i][0][0] / sigma1 + dsigma1 * gsigma1[0][0]; + dH12[0][1] = wi.lAsa[i][0][1] / sigma1 + dsigma1 * gsigma1[0][1]; + dH12[0][2] = wi.lAsa[i][0][2] / sigma1 + dsigma1 * gsigma1[0][2]; + dH12[1][0] = wi.lAsa[i][1][0] / sigma1 + dsigma1 * gsigma1[1][0]; + dH12[1][1] = wi.lAsa[i][1][1] / sigma1 + dsigma1 * gsigma1[1][1]; + dH12[1][2] = wi.lAsa[i][1][2] / sigma1 + dsigma1 * gsigma1[1][2]; + dH12[2][0] = wi.lAsa[i][2][0] / sigma1 + dsigma1 * gsigma1[2][0]; + dH12[2][1] = wi.lAsa[i][2][1] / sigma1 + dsigma1 * gsigma1[2][1]; + dH12[2][2] = wi.lAsa[i][2][2] / sigma1 + dsigma1 * gsigma1[2][2]; + ddH = det_prime(H12, dH12); + deta = tsig1sig2 * dsigma1 - tdH * ddH; + deta -= teta1 * dsigma1; double tempv[3]; - MathExtra::matvec(wi.lA[i],w,tempv); - dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(wi.lAtwo[i],spr,tempv); - dh12 = -MathExtra::dot3(s,tempv); + MathExtra::matvec(wi.lA[i], w, tempv); + dchi = -MathExtra::dot3(fwae, tempv); + MathExtra::matvec(wi.lAtwo[i], spr, tempv); + dh12 = -MathExtra::dot3(s, tempv); - dUa = pbsu*(eta*dchi + deta*chi)-dh12*dspu; - dUr = pbsr*(eta*dchi + deta*chi)-dh12*dspr; - ttor[i] = -(dUa*Ua+dUr*Ur); + dUa = pbsu * (eta * dchi + deta * chi) - dh12 * dspu; + dUr = pbsr * (eta * dchi + deta * chi) - dh12 * dspr; + ttor[i] = -(dUa * Ua + dUr * Ur); } // torque on j - if (!(force->newton_pair || j < atom->nlocal)) - return Ua+Ur; + if (!(force->newton_pair || j < atom->nlocal)) return Ua + Ur; - MathExtra::vecmat(fourw,wj.aTe,fwae); + MathExtra::vecmat(fourw, wj.aTe, fwae); - for (int i=0; i<3; i++) { - MathExtra::matvec(wj.lA[i],rhat,p); - dsigma2 = MathExtra::dot3(p,vsigma2); - dH12[0][0] = wj.lAsa[i][0][0]/sigma2+dsigma2*gsigma2[0][0]; - dH12[0][1] = wj.lAsa[i][0][1]/sigma2+dsigma2*gsigma2[0][1]; - dH12[0][2] = wj.lAsa[i][0][2]/sigma2+dsigma2*gsigma2[0][2]; - dH12[1][0] = wj.lAsa[i][1][0]/sigma2+dsigma2*gsigma2[1][0]; - dH12[1][1] = wj.lAsa[i][1][1]/sigma2+dsigma2*gsigma2[1][1]; - dH12[1][2] = wj.lAsa[i][1][2]/sigma2+dsigma2*gsigma2[1][2]; - dH12[2][0] = wj.lAsa[i][2][0]/sigma2+dsigma2*gsigma2[2][0]; - dH12[2][1] = wj.lAsa[i][2][1]/sigma2+dsigma2*gsigma2[2][1]; - dH12[2][2] = wj.lAsa[i][2][2]/sigma2+dsigma2*gsigma2[2][2]; - ddH = det_prime(H12,dH12); - deta = tsig1sig2*dsigma2-tdH*ddH; - deta -= teta2*dsigma2; + for (int i = 0; i < 3; i++) { + MathExtra::matvec(wj.lA[i], rhat, p); + dsigma2 = MathExtra::dot3(p, vsigma2); + dH12[0][0] = wj.lAsa[i][0][0] / sigma2 + dsigma2 * gsigma2[0][0]; + dH12[0][1] = wj.lAsa[i][0][1] / sigma2 + dsigma2 * gsigma2[0][1]; + dH12[0][2] = wj.lAsa[i][0][2] / sigma2 + dsigma2 * gsigma2[0][2]; + dH12[1][0] = wj.lAsa[i][1][0] / sigma2 + dsigma2 * gsigma2[1][0]; + dH12[1][1] = wj.lAsa[i][1][1] / sigma2 + dsigma2 * gsigma2[1][1]; + dH12[1][2] = wj.lAsa[i][1][2] / sigma2 + dsigma2 * gsigma2[1][2]; + dH12[2][0] = wj.lAsa[i][2][0] / sigma2 + dsigma2 * gsigma2[2][0]; + dH12[2][1] = wj.lAsa[i][2][1] / sigma2 + dsigma2 * gsigma2[2][1]; + dH12[2][2] = wj.lAsa[i][2][2] / sigma2 + dsigma2 * gsigma2[2][2]; + ddH = det_prime(H12, dH12); + deta = tsig1sig2 * dsigma2 - tdH * ddH; + deta -= teta2 * dsigma2; double tempv[3]; - MathExtra::matvec(wj.lA[i],w,tempv); - dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(wj.lAtwo[i],spr,tempv); - dh12 = -MathExtra::dot3(s,tempv); + MathExtra::matvec(wj.lA[i], w, tempv); + dchi = -MathExtra::dot3(fwae, tempv); + MathExtra::matvec(wj.lAtwo[i], spr, tempv); + dh12 = -MathExtra::dot3(s, tempv); - dUa = pbsu*(eta*dchi + deta*chi)-dh12*dspu; - dUr = pbsr*(eta*dchi + deta*chi)-dh12*dspr; - rtor[i] = -(dUa*Ua+dUr*Ur); + dUa = pbsu * (eta * dchi + deta * chi) - dh12 * dspu; + dUr = pbsr * (eta * dchi + deta * chi) - dh12 * dspr; + rtor[i] = -(dUa * Ua + dUr * Ur); } - return Ua+Ur; + return Ua + Ur; } /* ---------------------------------------------------------------------- Compute the energy, force, torque for a pair (INTEGRATED-LJ) ------------------------------------------------------------------------- */ -double PairRESquared::resquared_lj(const int i, const int j, - const RE2Vars &wi, const double *r, - const double rsq, double *fforce, - double *ttor, bool calc_torque) +double PairRESquared::resquared_lj(const int i, const int j, const RE2Vars &wi, const double *r, + const double rsq, double *fforce, double *ttor, bool calc_torque) { int *type = atom->type; // pair computations for energy, force, torque - double rnorm; // L2 norm of r - double rhat[3]; // r/rnorm - double s[3]; // inv(gamma1)*rhat - double sigma12; // 1/sqrt(0.5*s'*rhat) - double w[3]; // inv(A1'*E1*A1+I)*rhat - double h12; // rnorm-sigma12; - double chi; // 2*rhat'*w - double sigh; // sigma/h12 - double tprod; // chi*sigh - double Ua,Ur; // attractive/repulsive parts of potential + double rnorm; // L2 norm of r + double rhat[3]; // r/rnorm + double s[3]; // inv(gamma1)*rhat + double sigma12; // 1/sqrt(0.5*s'*rhat) + double w[3]; // inv(A1'*E1*A1+I)*rhat + double h12; // rnorm-sigma12; + double chi; // 2*rhat'*w + double sigh; // sigma/h12 + double tprod; // chi*sigh + double Ua, Ur; // attractive/repulsive parts of potential // pair computations for force, torque - double sec; // sigma*chi - double sigma12p3; // sigma12^3 - double fourw[3]; // 4*w; - double spr[3]; // 0.5*sigma12^3*s - double hsec; // h12+[3,b_alpha]*sec - double dspu; // 1/h12 - 1/hsec + temp - double pbsu; // 3*sigma/hsec - double dspr; // 7/h12-1/hsec+temp - double pbsr; // b_alpha*sigma/hsec; - double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm - double dchi,dh12; // derivatives of chi,h12 - double dUr,dUa; // derivatives of Ua,Ur - double h12p3; // h12^3 + double sec; // sigma*chi + double sigma12p3; // sigma12^3 + double fourw[3]; // 4*w; + double spr[3]; // 0.5*sigma12^3*s + double hsec; // h12+[3,b_alpha]*sec + double dspu; // 1/h12 - 1/hsec + temp + double pbsu; // 3*sigma/hsec + double dspr; // 7/h12-1/hsec+temp + double pbsr; // b_alpha*sigma/hsec; + double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm + double dchi, dh12; // derivatives of chi,h12 + double dUr, dUa; // derivatives of Ua,Ur + double h12p3; // h12^3 // pair computations for torque - double fwae[3]; // -fourw'*aTe - double p[3]; // lA*rhat + double fwae[3]; // -fourw'*aTe + double p[3]; // lA*rhat // distance of closest approach correction - double aTs[3][3]; // A1'*S1^2 - double gamma[3][3]; // A1'*S1^2*A - double lAtwo[3][3][3]; // A1'*S1^2*wi.lA + double aTs[3][3]; // A1'*S1^2 + double gamma[3][3]; // A1'*S1^2*A + double lAtwo[3][3][3]; // A1'*S1^2*wi.lA double scorrect[3]; - double half_sigma=sigma[type[i]][type[j]] / 2.0; - scorrect[0] = shape1[type[i]][0]+half_sigma; - scorrect[1] = shape1[type[i]][1]+half_sigma; - scorrect[2] = shape1[type[i]][2]+half_sigma; + double half_sigma = sigma[type[i]][type[j]] / 2.0; + scorrect[0] = shape1[type[i]][0] + half_sigma; + scorrect[1] = shape1[type[i]][1] + half_sigma; + scorrect[2] = shape1[type[i]][2] + half_sigma; scorrect[0] = scorrect[0] * scorrect[0] / 2.0; scorrect[1] = scorrect[1] * scorrect[1] / 2.0; scorrect[2] = scorrect[2] * scorrect[2] / 2.0; - MathExtra::transpose_diag3(wi.A,scorrect,aTs); - MathExtra::times3(aTs,wi.A,gamma); - for (int ii=0; ii<3; ii++) - MathExtra::times3(aTs,wi.lA[ii],lAtwo[ii]); + MathExtra::transpose_diag3(wi.A, scorrect, aTs); + MathExtra::times3(aTs, wi.A, gamma); + for (int ii = 0; ii < 3; ii++) MathExtra::times3(aTs, wi.lA[ii], lAtwo[ii]); - rnorm=sqrt(rsq); - rhat[0] = r[0]/rnorm; - rhat[1] = r[1]/rnorm; - rhat[2] = r[2]/rnorm; + rnorm = sqrt(rsq); + rhat[0] = r[0] / rnorm; + rhat[1] = r[1] / rnorm; + rhat[2] = r[2] / rnorm; // energy - int ierror = MathExtra::mldivide3(gamma,rhat,s); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + int ierror = MathExtra::mldivide3(gamma, rhat, s); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - sigma12 = 1.0/sqrt(0.5*MathExtra::dot3(s,rhat)); + sigma12 = 1.0 / sqrt(0.5 * MathExtra::dot3(s, rhat)); double temp[3][3]; - MathExtra::times3(wi.aTe,wi.A,temp); + MathExtra::times3(wi.aTe, wi.A, temp); temp[0][0] += 1.0; temp[1][1] += 1.0; temp[2][2] += 1.0; - ierror = MathExtra::mldivide3(temp,rhat,w); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + ierror = MathExtra::mldivide3(temp, rhat, w); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - h12 = rnorm-sigma12; - chi = 2.0*MathExtra::dot3(rhat,w); - sigh = sigma[type[i]][type[j]]/h12; - tprod = chi*sigh; + h12 = rnorm - sigma12; + chi = 2.0 * MathExtra::dot3(rhat, w); + sigh = sigma[type[i]][type[j]] / h12; + tprod = chi * sigh; - h12p3 = pow(h12,3.0); - double sigmap3 = pow(sigma[type[i]][type[j]],3.0); - double stemp = h12/2.0; - Ua = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*h12p3/8.0; - Ua = (1.0+3.0*tprod)*lshape[type[i]]/Ua; - Ua = epsilon[type[i]][type[j]]*Ua*sigmap3*solv_f_a; + h12p3 = pow(h12, 3.0); + double sigmap3 = pow(sigma[type[i]][type[j]], 3.0); + double stemp = h12 / 2.0; + Ua = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + h12p3 / 8.0; + Ua = (1.0 + 3.0 * tprod) * lshape[type[i]] / Ua; + Ua = epsilon[type[i]][type[j]] * Ua * sigmap3 * solv_f_a; - stemp = h12/cr60; - Ur = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*h12p3/60.0; - Ur = (1.0+b_alpha*tprod)*lshape[type[i]]/Ur; - Ur = epsilon[type[i]][type[j]]*Ur*sigmap3*pow(sigh,6.0)*solv_f_r; + stemp = h12 / cr60; + Ur = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + h12p3 / 60.0; + Ur = (1.0 + b_alpha * tprod) * lshape[type[i]] / Ur; + Ur = epsilon[type[i]][type[j]] * Ur * sigmap3 * pow(sigh, 6.0) * solv_f_r; // force - sec = sigma[type[i]][type[j]]*chi; - sigma12p3 = pow(sigma12,3.0); - fourw[0] = 4.0*w[0]; - fourw[1] = 4.0*w[1]; - fourw[2] = 4.0*w[2]; - spr[0] = 0.5*sigma12p3*s[0]; - spr[1] = 0.5*sigma12p3*s[1]; - spr[2] = 0.5*sigma12p3*s[2]; + sec = sigma[type[i]][type[j]] * chi; + sigma12p3 = pow(sigma12, 3.0); + fourw[0] = 4.0 * w[0]; + fourw[1] = 4.0 * w[1]; + fourw[2] = 4.0 * w[2]; + spr[0] = 0.5 * sigma12p3 * s[0]; + spr[1] = 0.5 * sigma12p3 * s[1]; + spr[2] = 0.5 * sigma12p3 * s[2]; - stemp = 1.0/(shape1[type[i]][0]*2.0+h12)+ - 1.0/(shape1[type[i]][1]*2.0+h12)+ - 1.0/(shape1[type[i]][2]*2.0+h12)+ - 3.0/h12; - hsec = h12+3.0*sec; - dspu = 1.0/h12-1.0/hsec+stemp; - pbsu = 3.0*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * 2.0 + h12) + 1.0 / (shape1[type[i]][1] * 2.0 + h12) + + 1.0 / (shape1[type[i]][2] * 2.0 + h12) + 3.0 / h12; + hsec = h12 + 3.0 * sec; + dspu = 1.0 / h12 - 1.0 / hsec + stemp; + pbsu = 3.0 * sigma[type[i]][type[j]] / hsec; - stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+ - 1.0/(shape1[type[i]][1]*cr60+h12)+ - 1.0/(shape1[type[i]][2]*cr60+h12)+ - 3.0/h12; - hsec = h12+b_alpha*sec; - dspr = 7.0/h12-1.0/hsec+stemp; - pbsr = b_alpha*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * cr60 + h12) + 1.0 / (shape1[type[i]][1] * cr60 + h12) + + 1.0 / (shape1[type[i]][2] * cr60 + h12) + 3.0 / h12; + hsec = h12 + b_alpha * sec; + dspr = 7.0 / h12 - 1.0 / hsec + stemp; + pbsr = b_alpha * sigma[type[i]][type[j]] / hsec; - for (int i=0; i<3; i++) { - u[0] = -rhat[i]*rhat[0]; - u[1] = -rhat[i]*rhat[1]; - u[2] = -rhat[i]*rhat[2]; - u[i] += 1.0; + for (int m = 0; m < 3; m++) { + u[0] = -rhat[m] * rhat[0]; + u[1] = -rhat[m] * rhat[1]; + u[2] = -rhat[m] * rhat[2]; + u[m] += 1.0; u[0] /= rnorm; u[1] /= rnorm; u[2] /= rnorm; - dchi = MathExtra::dot3(u,fourw); - dh12 = rhat[i]+MathExtra::dot3(u,spr); - dUa = pbsu*dchi-dh12*dspu; - dUr = pbsr*dchi-dh12*dspr; - fforce[i]=dUr*Ur+dUa*Ua; + dchi = MathExtra::dot3(u, fourw); + dh12 = rhat[m] + MathExtra::dot3(u, spr); + dUa = pbsu * dchi - dh12 * dspu; + dUr = pbsr * dchi - dh12 * dspr; + fforce[m] = dUr * Ur + dUa * Ua; } // torque on i if (calc_torque) { - MathExtra::vecmat(fourw,wi.aTe,fwae); + MathExtra::vecmat(fourw, wi.aTe, fwae); - for (int i=0; i<3; i++) { - MathExtra::matvec(wi.lA[i],rhat,p); + for (int m = 0; m < 3; m++) { + MathExtra::matvec(wi.lA[m], rhat, p); double tempv[3]; - MathExtra::matvec(wi.lA[i],w,tempv); - dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(lAtwo[i],spr,tempv); - dh12 = -MathExtra::dot3(s,tempv); + MathExtra::matvec(wi.lA[m], w, tempv); + dchi = -MathExtra::dot3(fwae, tempv); + MathExtra::matvec(lAtwo[m], spr, tempv); + dh12 = -MathExtra::dot3(s, tempv); - dUa = pbsu*dchi-dh12*dspu; - dUr = pbsr*dchi-dh12*dspr; - ttor[i] = -(dUa*Ua+dUr*Ur); + dUa = pbsu * dchi - dh12 * dspu; + dUr = pbsr * dchi - dh12 * dspr; + ttor[m] = -(dUa * Ua + dUr * Ur); } } - return Ua+Ur; + return Ua + Ur; } diff --git a/src/USER-ATC/Install.sh b/src/ATC/Install.sh similarity index 86% rename from src/USER-ATC/Install.sh rename to src/ATC/Install.sh index f241f92065..e1dacdd7d6 100755 --- a/src/USER-ATC/Install.sh +++ b/src/ATC/Install.sh @@ -31,7 +31,7 @@ action () { if (test $1 = 1) then if (test ! -e ../pair_eam.cpp) then - echo "Must install MANYBODY package with USER-ATC" + echo "Must install MANYBODY package with ATC" exit 1 fi fi @@ -54,9 +54,9 @@ if (test $1 = 1) then # sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/atc |' ../Makefile.package # sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/atc$(LIBSOBJDIR) |' ../Makefile.package sed -i -e 's|^PKG_LIB =[ \t]*|&-latc |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-atc_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-atc_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(atc_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(atc_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(atc_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then diff --git a/src/USER-ATC/README b/src/ATC/README similarity index 93% rename from src/USER-ATC/README rename to src/ATC/README index 06ab91ed80..0a6475236e 100644 --- a/src/USER-ATC/README +++ b/src/ATC/README @@ -7,7 +7,7 @@ See the doc page for the fix atc command to get started. At the bottom of the doc page are many links to additional documentation contained in the doc/USER/atc directory. -There are example scripts for using this package in examples/USER/atc. +There are example scripts for using this package in examples/PACKAGES/atc. This package uses an external library in lib/atc which must be compiled before making LAMMPS. See the lib/atc/README file and the diff --git a/src/USER-ATC/fix_atc.cpp b/src/ATC/fix_atc.cpp similarity index 98% rename from src/USER-ATC/fix_atc.cpp rename to src/ATC/fix_atc.cpp index b4f5b1eade..21306e01bd 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/ATC/fix_atc.cpp @@ -37,7 +37,7 @@ using namespace FixConst; using std::string; #ifdef LAMMPS_BIGBIG -#error "The USER-ATC package is not compatible with -DLAMMPS_BIGBIG" +#error "The ATC package is not compatible with -DLAMMPS_BIGBIG" #endif // main page of doxygen documentation @@ -700,20 +700,17 @@ int FixATC::size_restart(int /* nlocal */) { void FixATC::write_restart(FILE * /* fp */) { - char ** args = new char*[2]; - args[0] = new char[50]; - args[1] = new char[50]; - sprintf(args[0],"write_restart"); - sprintf(args[1],"ATC.restart"); + char *args[2]; + args[0] = utils::strdup("write_restart"); + args[1] = utils::strdup("ATC.restart"); // Then call all objects I own to write their data if (comm->me == 0) { atc_->modify(2,args); } - delete [] args[0]; - delete [] args[1]; - delete [] args; + delete[] args[0]; + delete[] args[1]; } /* ---------------------------------------------------------------------- @@ -722,20 +719,17 @@ void FixATC::write_restart(FILE * /* fp */) { void FixATC::restart(char * /* buf */) { - char ** args = new char*[2]; - args[0] = new char[50]; - args[1] = new char[50]; - sprintf(args[0],"read_restart"); - sprintf(args[1],"ATC.restart"); + char *args[2]; + args[0] = utils::strdup("read_restart"); + args[1] = utils::strdup("ATC.restart"); // Then call all objects I own to write their data if (comm->me == 0) { atc_->modify(2,args); } - delete [] args[0]; - delete [] args[1]; - delete [] args; + delete[] args[0]; + delete[] args[1]; } /* ---------------------------------------------------------------------- diff --git a/src/USER-ATC/fix_atc.h b/src/ATC/fix_atc.h similarity index 100% rename from src/USER-ATC/fix_atc.h rename to src/ATC/fix_atc.h diff --git a/src/USER-AWPMD/Install.sh b/src/AWPMD/Install.sh similarity index 90% rename from src/USER-AWPMD/Install.sh rename to src/AWPMD/Install.sh index 094e10c157..70e87c3fbc 100755 --- a/src/USER-AWPMD/Install.sh +++ b/src/AWPMD/Install.sh @@ -41,8 +41,8 @@ if (test $1 = 1) then sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/awpmd/ivutils/include -I../../lib/awpmd/systems/interact |' ../Makefile.package sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/awpmd |' ../Makefile.package sed -i -e 's|^PKG_LIB =[ \t]*|&-lawpmd |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-awpmd_SYSPATH) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-awpmd_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(awpmd_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(awpmd_SYSLIB) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then diff --git a/src/USER-AWPMD/README b/src/AWPMD/README similarity index 97% rename from src/USER-AWPMD/README rename to src/AWPMD/README index 6d8e8d032d..82ce245ab1 100644 --- a/src/USER-AWPMD/README +++ b/src/AWPMD/README @@ -4,7 +4,7 @@ Wave Packet Molecular Dynamics (AWPMD) method. See the doc page for the pair_style awpmd/cut command to get started. There are example scripts for using this package in -examples/USER/awpmd. +examples/PACKAGES/awpmd. This package uses an external library in lib/awpmd which must be compiled before making LAMMPS. See the lib/awpmd/README file and the diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/AWPMD/atom_vec_wavepacket.cpp similarity index 100% rename from src/USER-AWPMD/atom_vec_wavepacket.cpp rename to src/AWPMD/atom_vec_wavepacket.cpp diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/AWPMD/atom_vec_wavepacket.h similarity index 100% rename from src/USER-AWPMD/atom_vec_wavepacket.h rename to src/AWPMD/atom_vec_wavepacket.h diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/AWPMD/fix_nve_awpmd.cpp similarity index 100% rename from src/USER-AWPMD/fix_nve_awpmd.cpp rename to src/AWPMD/fix_nve_awpmd.cpp diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/AWPMD/fix_nve_awpmd.h similarity index 100% rename from src/USER-AWPMD/fix_nve_awpmd.h rename to src/AWPMD/fix_nve_awpmd.h diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/AWPMD/pair_awpmd_cut.cpp similarity index 100% rename from src/USER-AWPMD/pair_awpmd_cut.cpp rename to src/AWPMD/pair_awpmd_cut.cpp diff --git a/src/USER-AWPMD/pair_awpmd_cut.h b/src/AWPMD/pair_awpmd_cut.h similarity index 100% rename from src/USER-AWPMD/pair_awpmd_cut.h rename to src/AWPMD/pair_awpmd_cut.h diff --git a/src/USER-BOCS/README b/src/BOCS/README similarity index 81% rename from src/USER-BOCS/README rename to src/BOCS/README index 45aecc278c..b8cd001031 100644 --- a/src/USER-BOCS/README +++ b/src/BOCS/README @@ -7,7 +7,7 @@ molecular liquids," J. Chem. Phys. 143, 243148 (2015). doi: 10.1063/1.4937383 -The USER-BOCS user package for LAMMPS is part of the BOCS software package: +The BOCS user package for LAMMPS is part of the BOCS software package: https://github.com/noid-group/BOCS See the following reference for information about the entire package: @@ -16,4 +16,4 @@ Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. "BOCS: Bottom-Up Open-Source Coarse-Graining Software." J. Phys. Chem. B. 122, 13, 3363-3377 (2018). -Example inputs are in the examples/USER/bocs folder. +Example inputs are in the examples/PACKAGES/bocs folder. diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/BOCS/compute_pressure_bocs.cpp similarity index 99% rename from src/USER-BOCS/compute_pressure_bocs.cpp rename to src/BOCS/compute_pressure_bocs.cpp index b62d7cd1bf..8d891006b2 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/BOCS/compute_pressure_bocs.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/BOCS/compute_pressure_bocs.h similarity index 98% rename from src/USER-BOCS/compute_pressure_bocs.h rename to src/BOCS/compute_pressure_bocs.h index d5d4b1a7b9..ccae6ce0e3 100644 --- a/src/USER-BOCS/compute_pressure_bocs.h +++ b/src/BOCS/compute_pressure_bocs.h @@ -10,7 +10,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/BOCS/fix_bocs.cpp similarity index 99% rename from src/USER-BOCS/fix_bocs.cpp rename to src/BOCS/fix_bocs.cpp index 4f773e7c65..89ff3d8e4e 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/BOCS/fix_bocs.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; using namespace FixConst; static const char cite_user_bocs_package[] = - "USER-BOCS package:\n\n" + "BOCS package:\n\n" "@Article{Dunn2018,\n" " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n" " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n" @@ -1100,7 +1100,12 @@ void FixBocs::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/) nve_x(); if (pstat_flag) remap(); } +} +/* ---------------------------------------------------------------------- */ + +void FixBocs::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/) +{ // if barostat, redo KSpace coeffs at outermost level, // since volume has changed diff --git a/src/USER-BOCS/fix_bocs.h b/src/BOCS/fix_bocs.h similarity index 98% rename from src/USER-BOCS/fix_bocs.h rename to src/BOCS/fix_bocs.h index fd1e09115d..69b32d4cd0 100644 --- a/src/USER-BOCS/fix_bocs.h +++ b/src/BOCS/fix_bocs.h @@ -10,7 +10,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ @@ -37,6 +37,7 @@ class FixBocs : public Fix { virtual void initial_integrate(int); virtual void final_integrate(); void initial_integrate_respa(int, int, int); + void pre_force_respa(int, int, int); void final_integrate_respa(int, int); virtual void pre_exchange(); double compute_scalar(); diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 7dc7956586..23a4da7f07 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -21,21 +21,21 @@ #include "pair_body_rounded_polygon.h" -#include -#include -#include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polygon.h" #include "comm.h" -#include "force.h" -#include "fix.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 65179ecb80..6deb06aafb 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -23,22 +23,22 @@ #include "pair_body_rounded_polyhedron.h" -#include -#include #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" #include "comm.h" -#include "force.h" -#include "fix.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "math_extra.h" +#include "fix.h" +#include "force.h" #include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -1212,10 +1212,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody, contact_list[num_contacts].unique = 1; num_contacts++; } - } else { - } - return interact; } diff --git a/src/USER-BROWNIAN/fix_brownian.cpp b/src/BROWNIAN/fix_brownian.cpp similarity index 98% rename from src/USER-BROWNIAN/fix_brownian.cpp rename to src/BROWNIAN/fix_brownian.cpp index fc6b434080..b811ede721 100644 --- a/src/USER-BROWNIAN/fix_brownian.cpp +++ b/src/BROWNIAN/fix_brownian.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian.h b/src/BROWNIAN/fix_brownian.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian.h rename to src/BROWNIAN/fix_brownian.h diff --git a/src/USER-BROWNIAN/fix_brownian_asphere.cpp b/src/BROWNIAN/fix_brownian_asphere.cpp similarity index 99% rename from src/USER-BROWNIAN/fix_brownian_asphere.cpp rename to src/BROWNIAN/fix_brownian_asphere.cpp index ef0c246508..fccc6b5040 100644 --- a/src/USER-BROWNIAN/fix_brownian_asphere.cpp +++ b/src/BROWNIAN/fix_brownian_asphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_asphere.h b/src/BROWNIAN/fix_brownian_asphere.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian_asphere.h rename to src/BROWNIAN/fix_brownian_asphere.h diff --git a/src/USER-BROWNIAN/fix_brownian_base.cpp b/src/BROWNIAN/fix_brownian_base.cpp similarity index 99% rename from src/USER-BROWNIAN/fix_brownian_base.cpp rename to src/BROWNIAN/fix_brownian_base.cpp index fd5d1f5df7..0fa928bebf 100644 --- a/src/USER-BROWNIAN/fix_brownian_base.cpp +++ b/src/BROWNIAN/fix_brownian_base.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_base.h b/src/BROWNIAN/fix_brownian_base.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian_base.h rename to src/BROWNIAN/fix_brownian_base.h diff --git a/src/USER-BROWNIAN/fix_brownian_sphere.cpp b/src/BROWNIAN/fix_brownian_sphere.cpp similarity index 98% rename from src/USER-BROWNIAN/fix_brownian_sphere.cpp rename to src/BROWNIAN/fix_brownian_sphere.cpp index 4621be595f..cf835dcdc1 100644 --- a/src/USER-BROWNIAN/fix_brownian_sphere.cpp +++ b/src/BROWNIAN/fix_brownian_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_sphere.h b/src/BROWNIAN/fix_brownian_sphere.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian_sphere.h rename to src/BROWNIAN/fix_brownian_sphere.h diff --git a/src/USER-BROWNIAN/fix_propel_self.cpp b/src/BROWNIAN/fix_propel_self.cpp similarity index 100% rename from src/USER-BROWNIAN/fix_propel_self.cpp rename to src/BROWNIAN/fix_propel_self.cpp diff --git a/src/USER-BROWNIAN/fix_propel_self.h b/src/BROWNIAN/fix_propel_self.h similarity index 100% rename from src/USER-BROWNIAN/fix_propel_self.h rename to src/BROWNIAN/fix_propel_self.h diff --git a/src/USER-CGDNA/Install.sh b/src/CG-DNA/Install.sh similarity index 85% rename from src/USER-CGDNA/Install.sh rename to src/CG-DNA/Install.sh index 9ef10d3f62..3c65fac787 100755 --- a/src/USER-CGDNA/Install.sh +++ b/src/CG-DNA/Install.sh @@ -26,8 +26,25 @@ action () { fi } +# the CG-DNA package cannot be used without +# the MOLECULE and ASPHERE packages installed. + +if (test $1 = 1) then + if (test ! -e ../bond_harmonic.cpp) then + echo "Must install MOLECULE package with CG-DNA" + exit 1 + fi + if (test ! -e ../fix_nve_asphere.cpp) then + echo "Must install ASPHERE package with CG-DNA" + exit 1 + fi +fi + + # list of files with dependcies +action atom_vec_oxdna.cpp +action atom_vec_oxdna.h action bond_oxdna_fene.cpp bond_fene.h action bond_oxdna2_fene.cpp bond_fene.h action bond_oxrna2_fene.cpp bond_fene.h diff --git a/src/USER-CGDNA/README.md b/src/CG-DNA/README.md similarity index 96% rename from src/USER-CGDNA/README.md rename to src/CG-DNA/README.md index 015c1db188..bd3799a060 100644 --- a/src/USER-CGDNA/README.md +++ b/src/CG-DNA/README.md @@ -40,13 +40,13 @@ gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 144114 (2015). Example input and data files can be found in -/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. +examples/PACKAGES/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. Python setup tools which create single straight or helical DNA or RNA strands as well as DNA or RNA duplexes or arrays of duplexes can be -found in /examples/USER/cgdna/util/. A technical report with more +found in examples/PACKAGES/cgdna/util/. A technical report with more general information on the model, its implementation and performance as well as the structure of the data and input file can be found -in /doc/src/PDF/USER-CGDNA.pdf. +in doc/src/PDF/CG-DNA.pdf. IMPORTANT NOTE: This package can only be used if LAMMPS is compiled with the MOLECULE and ASPHERE packages. These should be included in diff --git a/src/CG-DNA/atom_vec_oxdna.cpp b/src/CG-DNA/atom_vec_oxdna.cpp new file mode 100644 index 0000000000..f5d56eef31 --- /dev/null +++ b/src/CG-DNA/atom_vec_oxdna.cpp @@ -0,0 +1,95 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "atom_vec_oxdna.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ +AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp) +{ + molecular = Atom::MOLECULAR; + bonds_allow = 1; + mass_type = PER_TYPE; + + atom->molecule_flag = 1; + + // strings with peratom variables to include in each AtomVec method + // strings cannot contain fields in corresponding AtomVec default strings + // order of fields in a string does not matter + // except: fields_data_atom & fields_data_vel must match data file + + fields_grow = (char *) "id5p"; + fields_copy = (char *) "id5p"; + fields_comm = (char *) ""; + fields_comm_vel = (char *) ""; + fields_reverse = (char *) ""; + fields_border = (char *) "id5p"; + fields_border_vel = (char *) ""; + fields_exchange = (char *) "id5p"; + fields_restart = (char *) "id5p"; + fields_create = (char *) ""; + fields_data_atom = (char *) "id type x"; + fields_data_vel = (char *) "id v"; + + setup_fields(); + + if(!force->newton_bond) error->warning(FLERR,"Write_data command requires newton on to preserve 3'->5' bond polarity"); +} + +/* ---------------------------------------------------------------------- */ +AtomVecOxdna::~AtomVecOxdna() {} + +/* ---------------------------------------------------------------------- + set local copies of all grow ptrs used by this class, except defaults + needed in replicate when 2 atom classes exist and it calls pack_restart() +------------------------------------------------------------------------- */ + +void AtomVecOxdna::grow_pointers() +{ + id5p = atom->id5p; +} + +/* ---------------------------------------------------------------------- + initialize atom quantity 5' partner +------------------------------------------------------------------------- */ + +void AtomVecOxdna::data_atom_post(int ilocal) +{ + tagint *id5p = atom->id5p; + id5p[ilocal] = -1; +} + +/* ---------------------------------------------------------------------- + process bond information as per data file + store 5' partner to inform 3'->5' bond directionality +------------------------------------------------------------------------- */ + +void AtomVecOxdna::data_bonds_post(int /*m*/, int /*num_bond*/, tagint atom1, tagint atom2, + tagint id_offset) +{ + int n; + tagint *id5p = atom->id5p; + + if (id_offset) { + atom1 += id_offset; + atom2 += id_offset; + } + + if ((n = atom->map(atom1)) >= 0) { id5p[n] = atom2; } +} diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.h b/src/CG-DNA/atom_vec_oxdna.h similarity index 58% rename from src/KOKKOS/fix_reaxc_species_kokkos.h rename to src/CG-DNA/atom_vec_oxdna.h index 1a5f204132..f05f6d2013 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.h +++ b/src/CG-DNA/atom_vec_oxdna.h @@ -1,4 +1,3 @@ -// clang-format off /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -12,33 +11,37 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifdef FIX_CLASS +#ifdef ATOM_CLASS // clang-format off -FixStyle(reax/c/species/kk,FixReaxCSpeciesKokkos); -FixStyle(reax/c/species/kk/device,FixReaxCSpeciesKokkos); -FixStyle(reax/c/species/kk/host,FixReaxCSpeciesKokkos); +AtomStyle(oxdna,AtomVecOxdna); // clang-format on #else -#ifndef LMP_FIX_REAXC_SPECIES_KOKKOS_H -#define LMP_FIX_REAXC_SPECIES_KOKKOS_H +#ifndef LMP_ATOM_VEC_OXDNA_H +#define LMP_ATOM_VEC_OXDNA_H -#include "fix_reaxc_species.h" - -#define BUFLEN 1000 +#include "atom_vec.h" namespace LAMMPS_NS { -class FixReaxCSpeciesKokkos : public FixReaxCSpecies { +class AtomVecOxdna : public AtomVec { public: - FixReaxCSpeciesKokkos(class LAMMPS *, int, char **); - virtual ~FixReaxCSpeciesKokkos(); - void init(); + AtomVecOxdna(class LAMMPS *); + ~AtomVecOxdna(); + + void grow_pointers(); + void data_atom_post(int); + void data_bonds_post(int, int, tagint, tagint, tagint); private: - void FindMolecule(); + tagint *id5p; }; -} + +} // namespace LAMMPS_NS #endif #endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/CG-DNA/bond_oxdna2_fene.cpp similarity index 71% rename from src/USER-CGDNA/bond_oxdna2_fene.cpp rename to src/CG-DNA/bond_oxdna2_fene.cpp index 0fad5bfaae..54f2dab9d2 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/CG-DNA/bond_oxdna2_fene.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,30 +18,16 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -BondOxdna2Fene::BondOxdna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -BondOxdna2Fene::~BondOxdna2Fene() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxDNA2 ------------------------------------------------------------------------- */ -void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], - double /*e3*/[3], double r[3]) +void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], + double r[3]) const { - double d_cs_x=-0.34, d_cs_y=+0.3408; - - r[0] = d_cs_x*e1[0] + d_cs_y*e2[0]; - r[1] = d_cs_x*e1[1] + d_cs_y*e2[1]; - r[2] = d_cs_x*e1[2] + d_cs_y*e2[2]; + constexpr double d_cs_x = -0.34; + constexpr double d_cs_y = +0.3408; + r[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; + r[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; + r[2] = d_cs_x * e1[2] + d_cs_y * e2[2]; } diff --git a/src/USER-CGDNA/bond_oxdna2_fene.h b/src/CG-DNA/bond_oxdna2_fene.h similarity index 93% rename from src/USER-CGDNA/bond_oxdna2_fene.h rename to src/CG-DNA/bond_oxdna2_fene.h index 98a74e3551..6c932f9421 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.h +++ b/src/CG-DNA/bond_oxdna2_fene.h @@ -26,9 +26,9 @@ namespace LAMMPS_NS { class BondOxdna2Fene : public BondOxdnaFene { public: - BondOxdna2Fene(class LAMMPS *); - virtual ~BondOxdna2Fene(); - virtual void compute_interaction_sites(double *, double *, double *, double *); + BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {} + virtual ~BondOxdna2Fene() {} + virtual void compute_interaction_sites(double *, double *, double *, double *) const; }; } // namespace LAMMPS_NS diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp similarity index 94% rename from src/USER-CGDNA/bond_oxdna_fene.cpp rename to src/CG-DNA/bond_oxdna_fene.cpp index 483e54e809..5a332a0b8c 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -17,7 +16,6 @@ #include "bond_oxdna_fene.h" -#include #include "atom.h" #include "neighbor.h" #include "comm.h" @@ -29,26 +27,19 @@ #include "atom_vec_ellipsoid.h" #include "math_extra.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - BondOxdnaFene::~BondOxdnaFene() { if (allocated) { - memory->destroy(setflag); memory->destroy(k); memory->destroy(Delta); memory->destroy(r0); - } } @@ -57,14 +48,13 @@ BondOxdnaFene::~BondOxdnaFene() compute vector COM-sugar-phosphate backbone interaction site in oxDNA ------------------------------------------------------------------------- */ void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3], - double /*e3*/[3], double r[3]) + double /*e3*/[3], double r[3]) const { - double d_cs=-0.4; + constexpr double d_cs=-0.4; r[0] = d_cs*e1[0]; r[1] = d_cs*e1[1]; r[2] = d_cs*e1[2]; - } /* ---------------------------------------------------------------------- @@ -218,11 +208,8 @@ void BondOxdnaFene::compute(int eflag, int vflag) // if r > 2*Delta something serious is wrong, abort if (rlogarg < 0.1) { - char str[128]; - sprintf(str,"FENE bond too long: " BIGINT_FORMAT " " - TAGINT_FORMAT " " TAGINT_FORMAT " %g", - update->ntimestep,atom->tag[a],atom->tag[b],r); - error->warning(FLERR,str); + error->warning(FLERR,"FENE bond too long: {} {} {} {}", + update->ntimestep,atom->tag[a],atom->tag[b],r); rlogarg = 0.1; } @@ -398,10 +385,8 @@ double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/, // if r > 2*Delta something serious is wrong, abort if (rlogarg < 0.1) { - char str[128]; - sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g", - update->ntimestep,sqrt(rsq)); - error->warning(FLERR,str); + error->warning(FLERR,"FENE bond too long: {} {:.8}", + update->ntimestep,sqrt(rsq)); rlogarg = 0.1; } diff --git a/src/USER-CGDNA/bond_oxdna_fene.h b/src/CG-DNA/bond_oxdna_fene.h similarity index 96% rename from src/USER-CGDNA/bond_oxdna_fene.h rename to src/CG-DNA/bond_oxdna_fene.h index d0151da4af..42b542a6fb 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.h +++ b/src/CG-DNA/bond_oxdna_fene.h @@ -26,9 +26,9 @@ namespace LAMMPS_NS { class BondOxdnaFene : public Bond { public: - BondOxdnaFene(class LAMMPS *); + BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {} virtual ~BondOxdnaFene(); - virtual void compute_interaction_sites(double *, double *, double *, double *); + virtual void compute_interaction_sites(double *, double *, double *, double *) const; virtual void compute(int, int); void coeff(int, char **); void init_style(); diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/CG-DNA/bond_oxrna2_fene.cpp similarity index 71% rename from src/USER-CGDNA/bond_oxrna2_fene.cpp rename to src/CG-DNA/bond_oxrna2_fene.cpp index 71c5d9edf3..24de5f7714 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.cpp +++ b/src/CG-DNA/bond_oxrna2_fene.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,30 +18,17 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -BondOxrna2Fene::~BondOxrna2Fene() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 ------------------------------------------------------------------------- */ -void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], - double e3[3], double r[3]) + +void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], + double r[3]) const { - double d_cs_x=-0.4, d_cs_z=+0.2; - - r[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; - r[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; - r[2] = d_cs_x*e1[2] + d_cs_z*e3[2]; + constexpr double d_cs_x = -0.4; + constexpr double d_cs_z = +0.2; + r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; + r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; + r[2] = d_cs_x * e1[2] + d_cs_z * e3[2]; } diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/CG-DNA/bond_oxrna2_fene.h similarity index 93% rename from src/USER-CGDNA/bond_oxrna2_fene.h rename to src/CG-DNA/bond_oxrna2_fene.h index 901daf2eb0..a805cd005f 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.h +++ b/src/CG-DNA/bond_oxrna2_fene.h @@ -26,9 +26,10 @@ namespace LAMMPS_NS { class BondOxrna2Fene : public BondOxdnaFene { public: - BondOxrna2Fene(class LAMMPS *); - virtual ~BondOxrna2Fene(); - virtual void compute_interaction_sites(double *, double *, double *, double *); + BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {} + virtual ~BondOxrna2Fene() {} + + virtual void compute_interaction_sites(double *, double *, double *, double *) const; }; } // namespace LAMMPS_NS diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/CG-DNA/fix_nve_dot.cpp similarity index 100% rename from src/USER-CGDNA/fix_nve_dot.cpp rename to src/CG-DNA/fix_nve_dot.cpp diff --git a/src/USER-CGDNA/fix_nve_dot.h b/src/CG-DNA/fix_nve_dot.h similarity index 100% rename from src/USER-CGDNA/fix_nve_dot.h rename to src/CG-DNA/fix_nve_dot.h diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/CG-DNA/fix_nve_dotc_langevin.cpp similarity index 100% rename from src/USER-CGDNA/fix_nve_dotc_langevin.cpp rename to src/CG-DNA/fix_nve_dotc_langevin.cpp diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.h b/src/CG-DNA/fix_nve_dotc_langevin.h similarity index 100% rename from src/USER-CGDNA/fix_nve_dotc_langevin.h rename to src/CG-DNA/fix_nve_dotc_langevin.h diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/CG-DNA/mf_oxdna.h similarity index 100% rename from src/USER-CGDNA/mf_oxdna.h rename to src/CG-DNA/mf_oxdna.h diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_coaxstk.cpp rename to src/CG-DNA/pair_oxdna2_coaxstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/CG-DNA/pair_oxdna2_coaxstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_coaxstk.h rename to src/CG-DNA/pair_oxdna2_coaxstk.h diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_dh.cpp rename to src/CG-DNA/pair_oxdna2_dh.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/CG-DNA/pair_oxdna2_dh.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_dh.h rename to src/CG-DNA/pair_oxdna2_dh.h diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/CG-DNA/pair_oxdna2_excv.cpp similarity index 67% rename from src/USER-CGDNA/pair_oxdna2_excv.cpp rename to src/CG-DNA/pair_oxdna2_excv.cpp index 2197fceb76..cde2af65da 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/CG-DNA/pair_oxdna2_excv.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,34 +18,19 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -PairOxdna2Excv::PairOxdna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -PairOxdna2Excv::~PairOxdna2Excv() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-excluded volume interaction sites in oxDNA2 ------------------------------------------------------------------------- */ -void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], - double /*e3*/[3], double rs[3], double rb[3]) +void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], + double rs[3], double rb[3]) { - double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4; + double d_cs_x = -0.34, d_cs_y = +0.3408, d_cb = +0.4; - rs[0] = d_cs_x*e1[0] + d_cs_y*e2[0]; - rs[1] = d_cs_x*e1[1] + d_cs_y*e2[1]; - rs[2] = d_cs_x*e1[2] + d_cs_y*e2[2]; - - rb[0] = d_cb*e1[0]; - rb[1] = d_cb*e1[1]; - rb[2] = d_cb*e1[2]; + rs[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; + rs[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; + rs[2] = d_cs_x * e1[2] + d_cs_y * e2[2]; + rb[0] = d_cb * e1[0]; + rb[1] = d_cb * e1[1]; + rb[2] = d_cb * e1[2]; } diff --git a/src/USER-CGDNA/pair_oxdna2_excv.h b/src/CG-DNA/pair_oxdna2_excv.h similarity index 93% rename from src/USER-CGDNA/pair_oxdna2_excv.h rename to src/CG-DNA/pair_oxdna2_excv.h index e5fc3a3a26..0fc51406ad 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.h +++ b/src/CG-DNA/pair_oxdna2_excv.h @@ -26,8 +26,8 @@ namespace LAMMPS_NS { class PairOxdna2Excv : public PairOxdnaExcv { public: - PairOxdna2Excv(class LAMMPS *); - virtual ~PairOxdna2Excv(); + PairOxdna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {} + virtual ~PairOxdna2Excv() {} virtual void compute_interaction_sites(double *, double *, double *, double *, double *); }; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_coaxstk.cpp rename to src/CG-DNA/pair_oxdna_coaxstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/CG-DNA/pair_oxdna_coaxstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_coaxstk.h rename to src/CG-DNA/pair_oxdna_coaxstk.h diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_excv.cpp rename to src/CG-DNA/pair_oxdna_excv.cpp diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/CG-DNA/pair_oxdna_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_excv.h rename to src/CG-DNA/pair_oxdna_excv.h diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_hbond.cpp rename to src/CG-DNA/pair_oxdna_hbond.cpp diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/CG-DNA/pair_oxdna_hbond.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_hbond.h rename to src/CG-DNA/pair_oxdna_hbond.h diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp similarity index 90% rename from src/USER-CGDNA/pair_oxdna_stk.cpp rename to src/CG-DNA/pair_oxdna_stk.cpp index 25521fd1e0..2f1a0bf1b6 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/CG-DNA/pair_oxdna_stk.cpp @@ -17,19 +17,20 @@ #include "pair_oxdna_stk.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "atom_vec_oxdna.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neighbor.h" + #include #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MFOxdna; @@ -42,26 +43,26 @@ PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp) writedata = 1; // sequence-specific stacking strength - // A:0 C:1 G:2 T:3, 5'- [i][j] -3' + // A:0 C:1 G:2 T:3, 3'- [i][j] -5' eta_st[0][0] = 1.11960; - eta_st[0][1] = 1.00852; - eta_st[0][2] = 0.96950; - eta_st[0][3] = 0.99632; + eta_st[1][0] = 1.00852; + eta_st[2][0] = 0.96950; + eta_st[3][0] = 0.99632; - eta_st[1][0] = 1.01889; + eta_st[0][1] = 1.01889; eta_st[1][1] = 0.97804; - eta_st[1][2] = 1.02681; - eta_st[1][3] = 0.96950; + eta_st[2][1] = 1.02681; + eta_st[3][1] = 0.96950; - eta_st[2][0] = 0.98169; - eta_st[2][1] = 1.05913; + eta_st[0][2] = 0.98169; + eta_st[1][2] = 1.05913; eta_st[2][2] = 0.97804; - eta_st[2][3] = 1.00852; + eta_st[3][2] = 1.00852; - eta_st[3][0] = 0.94694; - eta_st[3][1] = 0.98169; - eta_st[3][2] = 1.01889; + eta_st[0][3] = 0.94694; + eta_st[1][3] = 0.98169; + eta_st[2][3] = 1.01889; eta_st[3][3] = 0.96383; } @@ -244,15 +245,16 @@ void PairOxdnaStk::compute(int eflag, int vflag) int **bondlist = neighbor->bondlist; int nbondlist = neighbor->nbondlist; + tagint *id5p = atom->id5p; + AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); AtomVecEllipsoid::Bonus *bonus = avec->bonus; int *ellipsoid = atom->ellipsoid; - int a,b,in,atype,btype; + int a,b,btemp,in,atype,btype; double f1,f4t4,f4t5,f4t6,f5c1,f5c2; double df1,df4t4,df4t5,df4t6,df5c1,df5c2; - double tptofp; evdwl = 0.0; ev_init(eflag,vflag); @@ -261,8 +263,19 @@ void PairOxdnaStk::compute(int eflag, int vflag) for (in = 0; in < nbondlist; in++) { - a = bondlist[in][1]; - b = bondlist[in][0]; + a = bondlist[in][0]; + b = bondlist[in][1]; + + // directionality test: a -> b is 3' -> 5' + if(atom->tag[b] != id5p[a]) { + + btemp = b; + b = a; + a = btemp; + + } + + // a now in 3' direction, b in 5' direction qa=bonus[ellipsoid[a]].quat; MathExtra::q_to_exyz(qa,ax,ay,az); @@ -279,30 +292,11 @@ void PairOxdnaStk::compute(int eflag, int vflag) rb_cst[1] = d_cst*bx[1]; rb_cst[2] = d_cst*bx[2]; - // vector stacking site b to a - delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0]; - delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1]; - delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2]; + // vector stacking site a to b + delr_st[0] = x[b][0] + rb_cst[0] - x[a][0] - ra_cst[0]; + delr_st[1] = x[b][1] + rb_cst[1] - x[a][1] - ra_cst[1]; + delr_st[2] = x[b][2] + rb_cst[2] - x[a][2] - ra_cst[2]; - // test for directionality of vector b to a - tptofp = MFOxdna::is_3pto5p(delr_st,bz); - - // if b to a is 5' to 3' we need to swap roles of a and b - if (tptofp == -1) { - - std::swap(a,b); - std::swap(ax,bx); - std::swap(ay,by); - std::swap(az,bz); - std::swap(ra_cst,rb_cst); - - delr_st[0] *= -1; - delr_st[1] *= -1; - delr_st[2] *= -1; - - } - - // a now in 5' direction, b in 3' direction atype = type[a]; btype = type[b]; @@ -325,9 +319,9 @@ void PairOxdnaStk::compute(int eflag, int vflag) rb_cs[2] = d_cs*bx[2]; // vector backbone site b to a - delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]); - delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]); - delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]); + delr_ss[0] = (x[b][0] + rb_cs[0] - x[a][0] - ra_cs[0]); + delr_ss[1] = (x[b][1] + rb_cs[1] - x[a][1] - ra_cs[1]); + delr_ss[2] = (x[b][2] + rb_cs[2] - x[a][2] - ra_cs[2]); rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2]; r_ss = sqrt(rsq_ss); @@ -345,7 +339,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (f1) { // theta4 angle and correction - cost4 = MathExtra::dot3(az,bz); + cost4 = MathExtra::dot3(bz,az); if (cost4 > 1.0) cost4 = 1.0; if (cost4 < -1.0) cost4 = -1.0; theta4 = acos(cost4); @@ -357,7 +351,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (f4t4) { // theta5 angle and correction - cost5p = MathExtra::dot3(delr_st_norm,az); + cost5p = MathExtra::dot3(delr_st_norm,bz); if (cost5p > 1.0) cost5p = 1.0; if (cost5p < -1.0) cost5p = -1.0; theta5p = acos(cost5p); @@ -368,16 +362,16 @@ void PairOxdnaStk::compute(int eflag, int vflag) // early rejection criterium if (f4t5) { - cost6p = MathExtra::dot3(delr_st_norm,bz); + cost6p = MathExtra::dot3(delr_st_norm,az); if (cost6p > 1.0) cost6p = 1.0; if (cost6p < -1.0) cost6p = -1.0; theta6p = acos(cost6p); - cosphi1 = MathExtra::dot3(delr_ss_norm,ay); + cosphi1 = MathExtra::dot3(delr_ss_norm,by); if (cosphi1 > 1.0) cosphi1 = 1.0; if (cosphi1 < -1.0) cosphi1 = -1.0; - cosphi2 = MathExtra::dot3(delr_ss_norm,by); + cosphi2 = MathExtra::dot3(delr_ss_norm,ay); if (cosphi2 > 1.0) cosphi2 = 1.0; if (cosphi2 < -1.0) cosphi2 = -1.0; @@ -385,11 +379,10 @@ void PairOxdnaStk::compute(int eflag, int vflag) b_st6[atype][btype], dtheta_st6_c[atype][btype]); f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype], - cosphi_st1_c[atype][btype]); + -cosphi_st1_c[atype][btype]); f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype], - cosphi_st2_c[atype][btype]); - + -cosphi_st2_c[atype][btype]); evdwl = f1 * f4t4 * f4t5 * f4t6 * f5c1 * f5c2; @@ -410,10 +403,10 @@ void PairOxdnaStk::compute(int eflag, int vflag) b_st6[atype][btype], dtheta_st6_c[atype][btype])/sin(theta6p); df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype], - cosphi_st1_c[atype][btype]); + -cosphi_st1_c[atype][btype]); df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype], - cosphi_st2_c[atype][btype]); + -cosphi_st2_c[atype][btype]); // force, torque and virial contribution for forces between stacking sites @@ -446,9 +439,9 @@ void PairOxdnaStk::compute(int eflag, int vflag) finc = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2 * rinv_st; fpair += finc; - delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc; - delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc; - delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc; + delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc; + delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc; + delf[2] += (delr_st_norm[2]*cost5p - bz[2]) * finc; } @@ -458,28 +451,27 @@ void PairOxdnaStk::compute(int eflag, int vflag) finc = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2 * rinv_st; fpair += finc; - delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc; - delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc; - delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc; + delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc; + delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc; + delf[2] += (delr_st_norm[2]*cost6p - az[2]) * finc; } // increment forces and torques - if (newton_bond || a < nlocal) { - f[a][0] += delf[0]; - f[a][1] += delf[1]; - f[a][2] += delf[2]; + f[a][0] -= delf[0]; + f[a][1] -= delf[1]; + f[a][2] -= delf[2]; MathExtra::cross3(ra_cst,delf,delta); } if (newton_bond || b < nlocal) { - f[b][0] -= delf[0]; - f[b][1] -= delf[1]; - f[b][2] -= delf[2]; + f[b][0] += delf[0]; + f[b][1] += delf[1]; + f[b][2] += delf[2]; MathExtra::cross3(rb_cst,delf,deltb); @@ -487,16 +479,16 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (newton_bond || a < nlocal) { - torque[a][0] += delta[0]; - torque[a][1] += delta[1]; - torque[a][2] += delta[2]; + torque[a][0] -= delta[0]; + torque[a][1] -= delta[1]; + torque[a][2] -= delta[2]; } if (newton_bond || b < nlocal) { - torque[b][0] -= deltb[0]; - torque[b][1] -= deltb[1]; - torque[b][2] -= deltb[2]; + torque[b][0] += deltb[0]; + torque[b][1] += deltb[1]; + torque[b][2] += deltb[2]; } @@ -505,7 +497,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl, - delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]); // force, torque and virial contribution for forces between backbone sites @@ -529,9 +521,9 @@ void PairOxdnaStk::compute(int eflag, int vflag) finc = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2 * rinv_ss; fpair += finc; - delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc; - delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc; - delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc; + delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc; + delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc; + delf[2] += (delr_ss_norm[2]*cosphi1 - by[2]) * finc; } @@ -541,28 +533,27 @@ void PairOxdnaStk::compute(int eflag, int vflag) finc = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2 * rinv_ss; fpair += finc; - delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc; - delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc; - delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc; + delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc; + delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc; + delf[2] += (delr_ss_norm[2]*cosphi2 - ay[2]) * finc; } // increment forces and torques - if (newton_bond || a < nlocal) { - f[a][0] += delf[0]; - f[a][1] += delf[1]; - f[a][2] += delf[2]; + f[a][0] -= delf[0]; + f[a][1] -= delf[1]; + f[a][2] -= delf[2]; MathExtra::cross3(ra_cs,delf,delta); } if (newton_bond || b < nlocal) { - f[b][0] -= delf[0]; - f[b][1] -= delf[1]; - f[b][2] -= delf[2]; + f[b][0] += delf[0]; + f[b][1] += delf[1]; + f[b][2] += delf[2]; MathExtra::cross3(rb_cs,delf,deltb); @@ -570,22 +561,22 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (newton_bond || a < nlocal) { - torque[a][0] += delta[0]; - torque[a][1] += delta[1]; - torque[a][2] += delta[2]; + torque[a][0] -= delta[0]; + torque[a][1] -= delta[1]; + torque[a][2] -= delta[2]; } if (newton_bond || b < nlocal) { - torque[b][0] -= deltb[0]; - torque[b][1] -= deltb[1]; - torque[b][2] -= deltb[2]; + torque[b][0] += deltb[0]; + torque[b][1] += deltb[1]; + torque[b][2] += deltb[2]; } // increment virial only if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0, - delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]); // pure torques not expressible as r x f @@ -600,7 +591,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (theta4) { tpair = -f1 * df4t4 * f4t5 * f4t6 * f5c1 * f5c2; - MathExtra::cross3(bz,az,t4dir); + MathExtra::cross3(az,bz,t4dir); delta[0] += t4dir[0]*tpair; delta[1] += t4dir[1]*tpair; @@ -616,11 +607,11 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (theta5p) { tpair = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2; - MathExtra::cross3(delr_st_norm,az,t5pdir); + MathExtra::cross3(delr_st_norm,bz,t5pdir); - delta[0] += t5pdir[0] * tpair; - delta[1] += t5pdir[1] * tpair; - delta[2] += t5pdir[2] * tpair; + deltb[0] += t5pdir[0] * tpair; + deltb[1] += t5pdir[1] * tpair; + deltb[2] += t5pdir[2] * tpair; } @@ -628,11 +619,11 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (theta6p) { tpair = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2; - MathExtra::cross3(delr_st_norm,bz,t6pdir); + MathExtra::cross3(delr_st_norm,az,t6pdir); - deltb[0] -= t6pdir[0] * tpair; - deltb[1] -= t6pdir[1] * tpair; - deltb[2] -= t6pdir[2] * tpair; + delta[0] -= t6pdir[0] * tpair; + delta[1] -= t6pdir[1] * tpair; + delta[2] -= t6pdir[2] * tpair; } @@ -640,11 +631,11 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (cosphi1) { tpair = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2; - MathExtra::cross3(delr_ss_norm,ay,cosphi1dir); + MathExtra::cross3(delr_ss_norm,by,cosphi1dir); - delta[0] += cosphi1dir[0] * tpair; - delta[1] += cosphi1dir[1] * tpair; - delta[2] += cosphi1dir[2] * tpair; + deltb[0] += cosphi1dir[0] * tpair; + deltb[1] += cosphi1dir[1] * tpair; + deltb[2] += cosphi1dir[2] * tpair; } @@ -652,27 +643,27 @@ void PairOxdnaStk::compute(int eflag, int vflag) if (cosphi2) { tpair = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2; - MathExtra::cross3(delr_ss_norm,by,cosphi2dir); + MathExtra::cross3(delr_ss_norm,ay,cosphi2dir); - deltb[0] -= cosphi2dir[0] * tpair; - deltb[1] -= cosphi2dir[1] * tpair; - deltb[2] -= cosphi2dir[2] * tpair; + delta[0] -= cosphi2dir[0] * tpair; + delta[1] -= cosphi2dir[1] * tpair; + delta[2] -= cosphi2dir[2] * tpair; } // increment torques if (newton_bond || a < nlocal) { - torque[a][0] += delta[0]; - torque[a][1] += delta[1]; - torque[a][2] += delta[2]; + torque[a][0] -= delta[0]; + torque[a][1] -= delta[1]; + torque[a][2] -= delta[2]; } if (newton_bond || b < nlocal) { - torque[b][0] -= deltb[0]; - torque[b][1] -= deltb[1]; - torque[b][2] -= deltb[2]; + torque[b][0] += deltb[0]; + torque[b][1] += deltb[1]; + torque[b][2] += deltb[2]; } @@ -935,6 +926,17 @@ void PairOxdnaStk::coeff(int narg, char **arg) } +/* ---------------------------------------------------------------------- + atom_style hybrid bond ellipsoid oxdna required +------------------------------------------------------------------------- */ + +void PairOxdnaStk::init_style() +{ + if (!atom->style_match("oxdna")) { + error->all(FLERR,"Must use 'atom_style hybrid bond ellipsoid oxdna' with pair style oxdna/stk, oxdna2/stk or oxrna2/stk"); + } +} + /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/CG-DNA/pair_oxdna_stk.h similarity index 99% rename from src/USER-CGDNA/pair_oxdna_stk.h rename to src/CG-DNA/pair_oxdna_stk.h index 3d6c22d909..8695f8fd36 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.h +++ b/src/CG-DNA/pair_oxdna_stk.h @@ -32,6 +32,7 @@ class PairOxdnaStk : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); + void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_xstk.cpp rename to src/CG-DNA/pair_oxdna_xstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/CG-DNA/pair_oxdna_xstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_xstk.h rename to src/CG-DNA/pair_oxdna_xstk.h diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/CG-DNA/pair_oxrna2_dh.cpp similarity index 71% rename from src/USER-CGDNA/pair_oxrna2_dh.cpp rename to src/CG-DNA/pair_oxrna2_dh.cpp index 9ebbabbd1a..f19dbb249b 100644 --- a/src/USER-CGDNA/pair_oxrna2_dh.cpp +++ b/src/CG-DNA/pair_oxrna2_dh.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,30 +18,15 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -PairOxrna2Dh::PairOxrna2Dh(LAMMPS *lmp) : PairOxdna2Dh(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -PairOxrna2Dh::~PairOxrna2Dh() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 ------------------------------------------------------------------------- */ -void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], - double e3[3], double r[3]) +void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], + double r[3]) { - double d_cs_x=-0.4, d_cs_z=+0.2; - - r[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; - r[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; - r[2] = d_cs_x*e1[2] + d_cs_z*e3[2]; + double d_cs_x = -0.4, d_cs_z = +0.2; + r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; + r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; + r[2] = d_cs_x * e1[2] + d_cs_z * e3[2]; } diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/CG-DNA/pair_oxrna2_dh.h similarity index 94% rename from src/USER-CGDNA/pair_oxrna2_dh.h rename to src/CG-DNA/pair_oxrna2_dh.h index 1b66cd82ca..3008b4cc8c 100644 --- a/src/USER-CGDNA/pair_oxrna2_dh.h +++ b/src/CG-DNA/pair_oxrna2_dh.h @@ -26,8 +26,8 @@ namespace LAMMPS_NS { class PairOxrna2Dh : public PairOxdna2Dh { public: - PairOxrna2Dh(class LAMMPS *); - virtual ~PairOxrna2Dh(); + PairOxrna2Dh(class LAMMPS *lmp) : PairOxdna2Dh(lmp) {} + virtual ~PairOxrna2Dh() {} virtual void compute_interaction_sites(double *, double *, double *, double *); }; diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/CG-DNA/pair_oxrna2_excv.cpp similarity index 85% rename from src/USER-CGDNA/pair_oxrna2_excv.cpp rename to src/CG-DNA/pair_oxrna2_excv.cpp index 0e0535f0a0..2c1e4ca89f 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.cpp +++ b/src/CG-DNA/pair_oxrna2_excv.cpp @@ -21,20 +21,6 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -PairOxrna2Excv::PairOxrna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -PairOxrna2Excv::~PairOxrna2Excv() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-excluded volume interaction sites in oxRNA2 ------------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/CG-DNA/pair_oxrna2_excv.h similarity index 93% rename from src/USER-CGDNA/pair_oxrna2_excv.h rename to src/CG-DNA/pair_oxrna2_excv.h index 90537f865e..4f404ef103 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.h +++ b/src/CG-DNA/pair_oxrna2_excv.h @@ -26,8 +26,8 @@ namespace LAMMPS_NS { class PairOxrna2Excv : public PairOxdnaExcv { public: - PairOxrna2Excv(class LAMMPS *); - virtual ~PairOxrna2Excv(); + PairOxrna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {} + virtual ~PairOxrna2Excv() {} virtual void compute_interaction_sites(double *, double *, double *, double *, double *); }; diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/CG-DNA/pair_oxrna2_hbond.cpp similarity index 92% rename from src/USER-CGDNA/pair_oxrna2_hbond.cpp rename to src/CG-DNA/pair_oxrna2_hbond.cpp index 31f50816aa..dfa9997af3 100644 --- a/src/USER-CGDNA/pair_oxrna2_hbond.cpp +++ b/src/CG-DNA/pair_oxrna2_hbond.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -48,12 +47,4 @@ PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp) alpha_hb[3][1] = 1.00000; alpha_hb[3][2] = 0.58655; alpha_hb[3][3] = 1.00000; - -} - -/* ---------------------------------------------------------------------- */ - -PairOxrna2Hbond::~PairOxrna2Hbond() -{ - } diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/CG-DNA/pair_oxrna2_hbond.h similarity index 97% rename from src/USER-CGDNA/pair_oxrna2_hbond.h rename to src/CG-DNA/pair_oxrna2_hbond.h index ed96bda744..fe213c5615 100644 --- a/src/USER-CGDNA/pair_oxrna2_hbond.h +++ b/src/CG-DNA/pair_oxrna2_hbond.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PairOxrna2Hbond : public PairOxdnaHbond { public: PairOxrna2Hbond(class LAMMPS *); - virtual ~PairOxrna2Hbond(); + virtual ~PairOxrna2Hbond() {} }; } // namespace LAMMPS_NS diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/CG-DNA/pair_oxrna2_stk.cpp similarity index 88% rename from src/USER-CGDNA/pair_oxrna2_stk.cpp rename to src/CG-DNA/pair_oxrna2_stk.cpp index 8353a22463..4d733f53b5 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/CG-DNA/pair_oxrna2_stk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "atom_vec_ellipsoid.h" +#include "atom_vec_oxdna.h" #include "comm.h" #include "error.h" #include "force.h" @@ -44,26 +45,26 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp) writedata = 1; // sequence-specific stacking strength - // A:0 C:1 G:2 U:3, 5'- [i][j] -3' + // A:0 C:1 G:2 U:3, 3'- [i][j] -5' eta_st[0][0] = 0.93851; - eta_st[0][1] = 1.12901; - eta_st[0][2] = 1.15626; - eta_st[0][3] = 0.88850; + eta_st[1][0] = 1.12901; + eta_st[2][0] = 1.15626; + eta_st[3][0] = 0.88850; - eta_st[1][0] = 0.86331; + eta_st[0][1] = 0.86331; eta_st[1][1] = 1.05060; - eta_st[1][2] = 0.90982; - eta_st[1][3] = 0.83252; + eta_st[2][1] = 0.90982; + eta_st[3][1] = 0.83252; - eta_st[2][0] = 0.99407; - eta_st[2][1] = 1.14333; + eta_st[0][2] = 0.99407; + eta_st[1][2] = 1.14333; eta_st[2][2] = 1.06573; - eta_st[2][3] = 0.91705; + eta_st[3][2] = 0.91705; - eta_st[3][0] = 0.98804; - eta_st[3][1] = 1.04949; - eta_st[3][2] = 1.12063; + eta_st[0][3] = 0.98804; + eta_st[1][3] = 1.04949; + eta_st[2][3] = 1.12063; eta_st[3][3] = 0.83818; } @@ -261,15 +262,16 @@ void PairOxrna2Stk::compute(int eflag, int vflag) int **bondlist = neighbor->bondlist; int nbondlist = neighbor->nbondlist; + tagint *id5p = atom->id5p; + AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); AtomVecEllipsoid::Bonus *bonus = avec->bonus; int *ellipsoid = atom->ellipsoid; - int a,b,in,atype,btype; + int a,b,btemp,in,atype,btype; double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2; double df1,df4t5,df4t6,df4t9,df4t10,df5c1,df5c2; - double tptofp; evdwl = 0.0; ev_init(eflag,vflag); @@ -278,62 +280,43 @@ void PairOxrna2Stk::compute(int eflag, int vflag) for (in = 0; in < nbondlist; in++) { - a = bondlist[in][1]; - b = bondlist[in][0]; + a = bondlist[in][0]; + b = bondlist[in][1]; + + // directionality test: a -> b is 3' -> 5' + if(atom->tag[b] != id5p[a]) { + + btemp = b; + b = a; + a = btemp; + + } + + // a now in 3' direction, b in 5' direction qa=bonus[ellipsoid[a]].quat; MathExtra::q_to_exyz(qa,ax,ay,az); qb=bonus[ellipsoid[b]].quat; MathExtra::q_to_exyz(qb,bx,by,bz); - // vector COM a - 3'-stacking site a - ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0]; - ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1]; - ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2]; + // vector COM a - 5'-stacking site a + ra_cst[0] = d_cst_x_5p*ax[0] + d_cst_y_5p*ay[0]; + ra_cst[1] = d_cst_x_5p*ax[1] + d_cst_y_5p*ay[1]; + ra_cst[2] = d_cst_x_5p*ax[2] + d_cst_y_5p*ay[2]; - // vector COM b - 5'-stacking site b - rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0]; - rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1]; - rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2]; + // vector COM b - 3'-stacking site b + rb_cst[0] = d_cst_x_3p*bx[0] + d_cst_y_3p*by[0]; + rb_cst[1] = d_cst_x_3p*bx[1] + d_cst_y_3p*by[1]; + rb_cst[2] = d_cst_x_3p*bx[2] + d_cst_y_3p*by[2]; - // vector 5'-stacking site b to 3'-stacking site a - delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0]; - delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1]; - delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2]; + // vector 5'-stacking site a to 3'-stacking site b + delr_st[0] = x[b][0] + rb_cst[0] - x[a][0] - ra_cst[0]; + delr_st[1] = x[b][1] + rb_cst[1] - x[a][1] - ra_cst[1]; + delr_st[2] = x[b][2] + rb_cst[2] - x[a][2] - ra_cst[2]; - // test for directionality of vector b to a - tptofp = MFOxdna::is_3pto5p(delr_st,bz); - - // if b to a is 5' to 3' we need to swap roles of a and b - if (tptofp == -1) { - - std::swap(a,b); - std::swap(ax,bx); - std::swap(ay,by); - std::swap(az,bz); - - } - - // a now in 5' direction, b in 3' direction atype = type[a]; btype = type[b]; - // calculate again - // vector COM a - 3'-stacking site a - ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0]; - ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1]; - ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2]; - - // vector COM b - 5'-stacking site b - rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0]; - rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1]; - rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2]; - - // vector 5'-stacking site b to 3'-stacking site a - delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0]; - delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1]; - delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2]; - rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2]; r_st = sqrt(rsq_st); rinv_st = 1.0/r_st; @@ -352,10 +335,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag) rb_cs[1] = d_cs_x*bx[1] + d_cs_z*bz[1]; rb_cs[2] = d_cs_x*bx[2] + d_cs_z*bz[2]; - // vector backbone site b to a - delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]); - delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]); - delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]); + // vector backbone site a to b + delr_ss[0] = (x[b][0] + rb_cs[0] - x[a][0] - ra_cs[0]); + delr_ss[1] = (x[b][1] + rb_cs[1] - x[a][1] - ra_cs[1]); + delr_ss[2] = (x[b][2] + rb_cs[2] - x[a][2] - ra_cs[2]); rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2]; r_ss = sqrt(rsq_ss); @@ -373,7 +356,7 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (f1) { // theta5 angle and correction - cost5p = MathExtra::dot3(delr_st_norm,az); + cost5p = MathExtra::dot3(delr_st_norm,bz); if (cost5p > 1.0) cost5p = 1.0; if (cost5p < -1.0) cost5p = -1.0; theta5p = acos(cost5p); @@ -384,18 +367,18 @@ void PairOxrna2Stk::compute(int eflag, int vflag) // early rejection criterium if (f4t5) { - cost6p = MathExtra::dot3(delr_st_norm,bz); + cost6p = MathExtra::dot3(delr_st_norm,az); if (cost6p > 1.0) cost6p = 1.0; if (cost6p < -1.0) cost6p = -1.0; theta6p = acos(cost6p); - aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; - aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1]; - aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2]; + aux5p[0] = d5p_x * ax[0] + d5p_y * ay[0] + d5p_z * az[0]; + aux5p[1] = d5p_x * ax[1] + d5p_y * ay[1] + d5p_z * az[1]; + aux5p[2] = d5p_x * ax[2] + d5p_y * ay[2] + d5p_z * az[2]; - aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0]; - aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1]; - aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2]; + aux3p[0] = d3p_x * bx[0] + d3p_y * by[0] + d3p_z * bz[0]; + aux3p[1] = d3p_x * bx[1] + d3p_y * by[1] + d3p_z * bz[1]; + aux3p[2] = d3p_x * bx[2] + d3p_y * by[2] + d3p_z * bz[2]; cost9 = MathExtra::dot3(delr_ss_norm,aux3p); if (cost9 > 1.0) cost9 = 1.0; @@ -407,11 +390,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (cost10 < -1.0) cost10 = -1.0; theta10 = acos(cost10); - cosphi1 = MathExtra::dot3(delr_ss_norm,ay); + cosphi1 = MathExtra::dot3(delr_ss_norm,by); if (cosphi1 > 1.0) cosphi1 = 1.0; if (cosphi1 < -1.0) cosphi1 = -1.0; - cosphi2 = MathExtra::dot3(delr_ss_norm,by); + cosphi2 = MathExtra::dot3(delr_ss_norm,ay); if (cosphi2 > 1.0) cosphi2 = 1.0; if (cosphi2 < -1.0) cosphi2 = -1.0; @@ -425,10 +408,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag) b_st10[atype][btype], dtheta_st10_c[atype][btype]); f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype], - cosphi_st1_c[atype][btype]); + -cosphi_st1_c[atype][btype]); f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype], - cosphi_st2_c[atype][btype]); + -cosphi_st2_c[atype][btype]); evdwl = f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2; @@ -453,10 +436,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag) b_st10[atype][btype], dtheta_st10_c[atype][btype])/sin(theta10); df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype], - cosphi_st1_c[atype][btype]); + -cosphi_st1_c[atype][btype]); df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype], - cosphi_st2_c[atype][btype]); + -cosphi_st2_c[atype][btype]); // force, torque and virial contribution for forces between stacking sites @@ -489,9 +472,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag) finc = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st; fpair += finc; - delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc; - delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc; - delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc; + delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc; + delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc; + delf[2] += (delr_st_norm[2]*cost5p - bz[2]) * finc; } @@ -501,28 +484,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag) finc = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st; fpair += finc; - delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc; - delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc; - delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc; + delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc; + delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc; + delf[2] += (delr_st_norm[2]*cost6p - az[2]) * finc; } // increment forces and torques - if (newton_bond || a < nlocal) { - f[a][0] += delf[0]; - f[a][1] += delf[1]; - f[a][2] += delf[2]; + f[a][0] -= delf[0]; + f[a][1] -= delf[1]; + f[a][2] -= delf[2]; MathExtra::cross3(ra_cst,delf,delta); } if (newton_bond || b < nlocal) { - f[b][0] -= delf[0]; - f[b][1] -= delf[1]; - f[b][2] -= delf[2]; + f[b][0] += delf[0]; + f[b][1] += delf[1]; + f[b][2] += delf[2]; MathExtra::cross3(rb_cst,delf,deltb); @@ -530,16 +512,16 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (newton_bond || a < nlocal) { - torque[a][0] += delta[0]; - torque[a][1] += delta[1]; - torque[a][2] += delta[2]; + torque[a][0] -= delta[0]; + torque[a][1] -= delta[1]; + torque[a][2] -= delta[2]; } if (newton_bond || b < nlocal) { - torque[b][0] -= deltb[0]; - torque[b][1] -= deltb[1]; - torque[b][2] -= deltb[2]; + torque[b][0] += deltb[0]; + torque[b][1] += deltb[1]; + torque[b][2] += deltb[2]; } @@ -547,8 +529,8 @@ void PairOxrna2Stk::compute(int eflag, int vflag) // NOTE: The virial is calculated on the 'molecular' basis. // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) - if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl, - delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + if (evflag) ev_tally_xyz(b,a,nlocal,newton_bond,evdwl, + delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]); // force, torque and virial contribution for forces between backbone sites @@ -596,9 +578,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag) finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss; fpair += finc; - delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc; - delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc; - delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc; + delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc; + delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc; + delf[2] += (delr_ss_norm[2]*cosphi1 - by[2]) * finc; } @@ -608,28 +590,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag) finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss; fpair += finc; - delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc; - delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc; - delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc; + delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc; + delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc; + delf[2] += (delr_ss_norm[2]*cosphi2 - ay[2]) * finc; } // increment forces and torques - if (newton_bond || a < nlocal) { - f[a][0] += delf[0]; - f[a][1] += delf[1]; - f[a][2] += delf[2]; + f[a][0] -= delf[0]; + f[a][1] -= delf[1]; + f[a][2] -= delf[2]; MathExtra::cross3(ra_cs,delf,delta); } if (newton_bond || b < nlocal) { - f[b][0] -= delf[0]; - f[b][1] -= delf[1]; - f[b][2] -= delf[2]; + f[b][0] += delf[0]; + f[b][1] += delf[1]; + f[b][2] += delf[2]; MathExtra::cross3(rb_cs,delf,deltb); @@ -637,22 +618,22 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (newton_bond || a < nlocal) { - torque[a][0] += delta[0]; - torque[a][1] += delta[1]; - torque[a][2] += delta[2]; + torque[a][0] -= delta[0]; + torque[a][1] -= delta[1]; + torque[a][2] -= delta[2]; } if (newton_bond || b < nlocal) { - torque[b][0] -= deltb[0]; - torque[b][1] -= deltb[1]; - torque[b][2] -= deltb[2]; + torque[b][0] += deltb[0]; + torque[b][1] += deltb[1]; + torque[b][2] += deltb[2]; } // increment virial only - if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0, - delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + if (evflag) ev_tally_xyz(b,a,nlocal,newton_bond,0.0, + delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]); // pure torques not expressible as r x f @@ -667,11 +648,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (theta5p) { tpair = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2; - MathExtra::cross3(delr_st_norm,az,t5pdir); + MathExtra::cross3(delr_st_norm,bz,t5pdir); - delta[0] += t5pdir[0] * tpair; - delta[1] += t5pdir[1] * tpair; - delta[2] += t5pdir[2] * tpair; + deltb[0] += t5pdir[0] * tpair; + deltb[1] += t5pdir[1] * tpair; + deltb[2] += t5pdir[2] * tpair; } @@ -679,11 +660,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (theta6p) { tpair = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2; - MathExtra::cross3(delr_st_norm,bz,t6pdir); + MathExtra::cross3(delr_st_norm,az,t6pdir); - deltb[0] -= t6pdir[0] * tpair; - deltb[1] -= t6pdir[1] * tpair; - deltb[2] -= t6pdir[2] * tpair; + delta[0] -= t6pdir[0] * tpair; + delta[1] -= t6pdir[1] * tpair; + delta[2] -= t6pdir[2] * tpair; } @@ -693,9 +674,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag) tpair = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2; MathExtra::cross3(delr_ss_norm,aux3p,t9dir); - delta[0] += t9dir[0] * tpair; - delta[1] += t9dir[1] * tpair; - delta[2] += t9dir[2] * tpair; + deltb[0] += t9dir[0] * tpair; + deltb[1] += t9dir[1] * tpair; + deltb[2] += t9dir[2] * tpair; } @@ -705,9 +686,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag) tpair = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2; MathExtra::cross3(delr_ss_norm,aux5p,t10dir); - deltb[0] -= t10dir[0] * tpair; - deltb[1] -= t10dir[1] * tpair; - deltb[2] -= t10dir[2] * tpair; + delta[0] -= t10dir[0] * tpair; + delta[1] -= t10dir[1] * tpair; + delta[2] -= t10dir[2] * tpair; } @@ -715,11 +696,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (cosphi1) { tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2; - MathExtra::cross3(delr_ss_norm,ay,cosphi1dir); + MathExtra::cross3(delr_ss_norm,by,cosphi1dir); - delta[0] += cosphi1dir[0] * tpair; - delta[1] += cosphi1dir[1] * tpair; - delta[2] += cosphi1dir[2] * tpair; + deltb[0] += cosphi1dir[0] * tpair; + deltb[1] += cosphi1dir[1] * tpair; + deltb[2] += cosphi1dir[2] * tpair; } @@ -727,27 +708,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (cosphi2) { tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2; - MathExtra::cross3(delr_ss_norm,by,cosphi2dir); + MathExtra::cross3(delr_ss_norm,ay,cosphi2dir); - deltb[0] -= cosphi2dir[0] * tpair; - deltb[1] -= cosphi2dir[1] * tpair; - deltb[2] -= cosphi2dir[2] * tpair; + delta[0] -= cosphi2dir[0] * tpair; + delta[1] -= cosphi2dir[1] * tpair; + delta[2] -= cosphi2dir[2] * tpair; } // increment torques if (newton_bond || a < nlocal) { - torque[a][0] += delta[0]; - torque[a][1] += delta[1]; - torque[a][2] += delta[2]; + torque[a][0] -= delta[0]; + torque[a][1] -= delta[1]; + torque[a][2] -= delta[2]; } if (newton_bond || b < nlocal) { - torque[b][0] -= deltb[0]; - torque[b][1] -= deltb[1]; - torque[b][2] -= deltb[2]; + torque[b][0] += deltb[0]; + torque[b][1] += deltb[1]; + torque[b][2] += deltb[2]; } @@ -1027,6 +1008,17 @@ void PairOxrna2Stk::coeff(int narg, char **arg) } +/* ---------------------------------------------------------------------- + atom_style hybrid bond ellipsoid oxdna required +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::init_style() +{ + if (!atom->style_match("oxdna")) { + error->all(FLERR,"Must use 'atom_style hybrid bond ellipsoid oxdna' with pair style oxdna/stk, oxdna2/stk or oxrna2/stk"); + } +} + /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/CG-DNA/pair_oxrna2_stk.h similarity index 99% rename from src/USER-CGDNA/pair_oxrna2_stk.h rename to src/CG-DNA/pair_oxrna2_stk.h index 7648dd207d..23650c98b5 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.h +++ b/src/CG-DNA/pair_oxrna2_stk.h @@ -31,6 +31,7 @@ class PairOxrna2Stk : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); + void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_xstk.cpp rename to src/CG-DNA/pair_oxrna2_xstk.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/CG-DNA/pair_oxrna2_xstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_xstk.h rename to src/CG-DNA/pair_oxrna2_xstk.h diff --git a/src/USER-CGSDK/Install.sh b/src/CG-SDK/Install.sh similarity index 100% rename from src/USER-CGSDK/Install.sh rename to src/CG-SDK/Install.sh diff --git a/src/USER-CGSDK/README b/src/CG-SDK/README similarity index 91% rename from src/USER-CGSDK/README rename to src/CG-SDK/README index 3d5cae9b20..c6bd90531e 100644 --- a/src/USER-CGSDK/README +++ b/src/CG-SDK/README @@ -1,8 +1,9 @@ -This package implements 3 commands which can be used in a LAMMPS input +This package implements 4 commands which can be used in a LAMMPS input script: pair_style lj/sdk pair_style lj/sdk/coul/long +pair_style lj/sdk/coul/msm angle_style sdk These styles allow coarse grained MD simulations with the @@ -13,7 +14,7 @@ lipids and charged amino acids. See the doc pages for these commands for details. There are example scripts for using this package in -examples/USER/cgsdk +examples/PACKAGES/cgsdk This is the second generation implementation reducing the the clutter of the previous version. For many systems with long range diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/CG-SDK/angle_sdk.cpp similarity index 100% rename from src/USER-CGSDK/angle_sdk.cpp rename to src/CG-SDK/angle_sdk.cpp diff --git a/src/USER-CGSDK/angle_sdk.h b/src/CG-SDK/angle_sdk.h similarity index 100% rename from src/USER-CGSDK/angle_sdk.h rename to src/CG-SDK/angle_sdk.h diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/CG-SDK/lj_sdk_common.h similarity index 100% rename from src/USER-CGSDK/lj_sdk_common.h rename to src/CG-SDK/lj_sdk_common.h diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/CG-SDK/pair_lj_sdk.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk.cpp rename to src/CG-SDK/pair_lj_sdk.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/CG-SDK/pair_lj_sdk.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk.h rename to src/CG-SDK/pair_lj_sdk.h diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/CG-SDK/pair_lj_sdk_coul_long.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_long.cpp rename to src/CG-SDK/pair_lj_sdk_coul_long.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.h b/src/CG-SDK/pair_lj_sdk_coul_long.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_long.h rename to src/CG-SDK/pair_lj_sdk_coul_long.h diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/CG-SDK/pair_lj_sdk_coul_msm.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp rename to src/CG-SDK/pair_lj_sdk_coul_msm.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.h b/src/CG-SDK/pair_lj_sdk_coul_msm.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_msm.h rename to src/CG-SDK/pair_lj_sdk_coul_msm.h diff --git a/src/USER-COLVARS/Install.sh b/src/COLVARS/Install.sh similarity index 100% rename from src/USER-COLVARS/Install.sh rename to src/COLVARS/Install.sh diff --git a/src/USER-COLVARS/README b/src/COLVARS/README similarity index 92% rename from src/USER-COLVARS/README rename to src/COLVARS/README index 6627bc9ec4..eebaecf4a8 100644 --- a/src/USER-COLVARS/README +++ b/src/COLVARS/README @@ -13,7 +13,7 @@ on building LAMMPS with external libraries. The settings in the Makefile.lammps file in that directory must be correct for LAMMPS to build correctly with this package installed. -The files in the USER-COLVARS package folder implement an interface +The files in the COLVARS package folder implement an interface between LAMMPS and Colvars, originally written by Axel Kohlmeyer (akohlmey@gmail.com) and maintained by Giacomo Fiorin (giacomo.fiorin@gmail.com). @@ -36,7 +36,7 @@ which also includes citations to the articles documenting the various methods that make use Colvars. There are also example scripts for using this package in the folder -examples/USER/colvars, as well as the GitHub page for Colvars. +examples/PACKAGES/colvars, as well as the GitHub page for Colvars. Please contact Giacomo Fiorin (giacomo.fiorin@gmail.com) for questions regarding this package. diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/COLVARS/colvarproxy_lammps.cpp similarity index 100% rename from src/USER-COLVARS/colvarproxy_lammps.cpp rename to src/COLVARS/colvarproxy_lammps.cpp diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/COLVARS/colvarproxy_lammps.h similarity index 100% rename from src/USER-COLVARS/colvarproxy_lammps.h rename to src/COLVARS/colvarproxy_lammps.h diff --git a/src/COLVARS/colvarproxy_lammps_version.h b/src/COLVARS/colvarproxy_lammps_version.h new file mode 100644 index 0000000000..0399595533 --- /dev/null +++ b/src/COLVARS/colvarproxy_lammps_version.h @@ -0,0 +1,3 @@ +#ifndef COLVARPROXY_VERSION +#define COLVARPROXY_VERSION "2021-03-02" +#endif diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/COLVARS/fix_colvars.cpp similarity index 99% rename from src/USER-COLVARS/fix_colvars.cpp rename to src/COLVARS/fix_colvars.cpp index f4f6974c70..45e12951bb 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/COLVARS/fix_colvars.cpp @@ -480,7 +480,7 @@ void FixColvars::one_time_init() memory->create(force_buf,3*num_coords,"colvars:force_buf"); if (me == 0) { - std::vector &tl = *(proxy->modify_atom_ids()); + std::vector const &tl = *(proxy->get_atom_ids()); inthash_t *hashtable=new inthash_t; inthash_init(hashtable, num_coords); idmap = (void *)hashtable; @@ -563,7 +563,7 @@ void FixColvars::setup(int vflag) if (me == 0) { - std::vector &id = *(proxy->modify_atom_ids()); + std::vector const &id = *(proxy->get_atom_ids()); std::vector &tp = *(proxy->modify_atom_types()); std::vector &cd = *(proxy->modify_atom_positions()); std::vector &of = *(proxy->modify_atom_total_forces()); @@ -836,7 +836,7 @@ void FixColvars::post_force(int /*vflag*/) if (me == 0) { - std::vector &fo = *(proxy->modify_atom_new_colvar_forces()); + std::vector &fo = *(proxy->modify_atom_applied_forces()); double *fbuf = force_buf; for (int j=0; j < num_coords; ++j) { diff --git a/src/USER-COLVARS/fix_colvars.h b/src/COLVARS/fix_colvars.h similarity index 100% rename from src/USER-COLVARS/fix_colvars.h rename to src/COLVARS/fix_colvars.h diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/COLVARS/group_ndx.cpp similarity index 100% rename from src/USER-COLVARS/group_ndx.cpp rename to src/COLVARS/group_ndx.cpp diff --git a/src/USER-COLVARS/group_ndx.h b/src/COLVARS/group_ndx.h similarity index 100% rename from src/USER-COLVARS/group_ndx.h rename to src/COLVARS/group_ndx.h diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/COLVARS/ndx_group.cpp similarity index 100% rename from src/USER-COLVARS/ndx_group.cpp rename to src/COLVARS/ndx_group.cpp diff --git a/src/USER-COLVARS/ndx_group.h b/src/COLVARS/ndx_group.h similarity index 100% rename from src/USER-COLVARS/ndx_group.h rename to src/COLVARS/ndx_group.h diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h index 9161e3f902..3789d52122 100644 --- a/src/COMPRESS/zstd_file_writer.h +++ b/src/COMPRESS/zstd_file_writer.h @@ -25,6 +25,11 @@ #include #include +#if ZSTD_VERSION_NUMBER < 10400 +#error must have at least zstd version 1.4 to compile with -DLAMMPS_ZSTD +#endif + + namespace LAMMPS_NS { class ZstdFileWriter : public FileWriter { diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index ed6634f4b0..04c7a743d8 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -19,19 +19,19 @@ #include "compute_temp_cs.h" -#include - #include "atom.h" #include "atom_vec.h" +#include "comm.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "fix_store.h" #include "force.h" #include "group.h" -#include "modify.h" -#include "fix_store.h" -#include "comm.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -74,8 +74,7 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) : strcpy(id_fix,fixcmd.c_str()); fixcmd += fmt::format(" {} STORE peratom 0 1", group->names[igroup]); - modify->add_fix(fixcmd); - fix = (FixStore *) modify->fix[modify->nfix-1]; + fix = (FixStore *)modify->add_fix(fixcmd); // set fix store values = 0 for now // fill them in via setup() once Comm::borders() has been called diff --git a/src/USER-DIELECTRIC/Install.sh b/src/DIELECTRIC/Install.sh similarity index 75% rename from src/USER-DIELECTRIC/Install.sh rename to src/DIELECTRIC/Install.sh index fd540f3c7e..2505eb1a59 100644 --- a/src/USER-DIELECTRIC/Install.sh +++ b/src/DIELECTRIC/Install.sh @@ -30,8 +30,12 @@ action () { # are installed, which in turn requires KSPACE if (test $1 = 1) then - if (test ! -e ../ppp.cpp) then - echo "Must install KSPACE package with USER-DIELECTRIC" + if (test ! -e ../pppm.cpp) then + echo "Must install KSPACE package with DIELECTRIC package" + exit 1 + fi + if (test ! -e ../pair_lj_cut_coul_debye.cpp) then + echo "Must install EXTRA-PAIR package with DIELECTRIC package" exit 1 fi fi diff --git a/src/USER-DIELECTRIC/README b/src/DIELECTRIC/README similarity index 85% rename from src/USER-DIELECTRIC/README rename to src/DIELECTRIC/README index 11e9bde03f..37a9d673bf 100644 --- a/src/USER-DIELECTRIC/README +++ b/src/DIELECTRIC/README @@ -1,4 +1,4 @@ -The USER-DIELECTRIC package provides several solvers for computing surface induced charges +The DIELECTRIC package provides several solvers for computing surface induced charges at the interface between two media with different dielectric constants: * the boundary element solver using the GMRES algorithm (fix polarize/bem/gmres), @@ -10,7 +10,7 @@ or mobile (for example, dielectric colloids in a solvent). See the header of the source files for more details on the references of the methods. -The USER-DIELECTRIC package was created by Trung Nguyen while at Northwestern. +The DIELECTRIC package was created by Trung Nguyen while at Northwestern. Questions can be addressed to Trung Nguyen (ndactrung@gmail.com). * Citation @@ -23,6 +23,6 @@ Molecular Dynamics simulation", Computer Physics Communications 241, 80--91 (201 * Examples -Example input scripts and data files can be found under examples/USER/dielectric: +Example input scripts and data files can be found under examples/PACKAGES/dielectric: mpirun -np 8 ../../../src/lmp_mpi -in in.confined diff --git a/src/USER-DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp similarity index 99% rename from src/USER-DIELECTRIC/atom_vec_dielectric.cpp rename to src/DIELECTRIC/atom_vec_dielectric.cpp index b0e3487807..cc182251e9 100644 --- a/src/USER-DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -20,7 +20,7 @@ using namespace LAMMPS_NS; static const char cite_user_dielectric_package[] = - "USER-DIELECTRIC package:\n\n" + "DIELECTRIC package:\n\n" "@Article{TrungCPC19,\n" " author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi," " Francisco J. Solis, Monica Olvera de la Cruz,\n" diff --git a/src/USER-DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/atom_vec_dielectric.h rename to src/DIELECTRIC/atom_vec_dielectric.h diff --git a/src/USER-DIELECTRIC/compute_efield_atom.cpp b/src/DIELECTRIC/compute_efield_atom.cpp similarity index 100% rename from src/USER-DIELECTRIC/compute_efield_atom.cpp rename to src/DIELECTRIC/compute_efield_atom.cpp diff --git a/src/USER-DIELECTRIC/compute_efield_atom.h b/src/DIELECTRIC/compute_efield_atom.h similarity index 100% rename from src/USER-DIELECTRIC/compute_efield_atom.h rename to src/DIELECTRIC/compute_efield_atom.h diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp similarity index 98% rename from src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp rename to src/DIELECTRIC/fix_polarize_bem_gmres.cpp index b25c7ce7b7..667f0efc26 100644 --- a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp @@ -431,7 +431,7 @@ void FixPolarizeBEMGMRES::gmres_solve(double *x, double *r) // fill up h with zero - memset(h, 0, (mr + 1) * mr * sizeof(double)); + memset(h, 0, (size_t)(mr + 1) * mr * sizeof(double)); // the inner loop k = 1..(n-1) // build up the k-th Krylov space, @@ -523,13 +523,9 @@ void FixPolarizeBEMGMRES::gmres_solve(double *x, double *r) rho = fabs(g[k]); #ifdef _POLARIZE_DEBUG - if (comm->me == 0) { - char message[256]; - sprintf(message, "itr = %d: k = %d, norm(r) = %g norm(b) = %g", itr, k, rho, normb); - error->warning(FLERR, message); - } + if (comm->me == 0) + error->warning(FLERR,"itr = {}: k = {}, norm(r) = {} norm(b) = {}", itr, k, rho, normb); #endif - if (rho <= rho_tol && rho <= tol_abs) break; } @@ -560,11 +556,8 @@ void FixPolarizeBEMGMRES::gmres_solve(double *x, double *r) rho = sqrt(vec_dot(r, r, n)); #ifdef _POLARIZE_DEBUG - if (comm->me == 0) { - char message[256]; - sprintf(message, "itr = %d: norm(r) = %g norm(b) = %g", itr, rho, normb); - error->warning(FLERR, message); - } + if (comm->me == 0) + error->warning(FLERR, "itr = {}: norm(r) = {} norm(b) = {}", itr, rho, normb); #endif // Barros et al. suggested the condition: norm(r) < EPSILON norm(b) @@ -756,11 +749,11 @@ double FixPolarizeBEMGMRES::memory_usage() bytes += atom->nmax * sizeof(double); // q_backup bytes += mr * sizeof(double); // c bytes += (mr + 1) * sizeof(double); // g - bytes += (mr + 1) * mr * sizeof(double); // h + bytes += (double) (mr + 1) * mr * sizeof(double); // h bytes += mat_dim * sizeof(double); // r - bytes += mr * (mr + 1) * sizeof(double); // s + bytes += (double) mr * (mr + 1) * sizeof(double); // s bytes += mat_dim * sizeof(double); // v - bytes += (mr + 1) * mr * sizeof(double); // y + bytes += (double) (mr + 1) * mr * sizeof(double); // y return bytes; } diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.h b/src/DIELECTRIC/fix_polarize_bem_gmres.h similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_gmres.h rename to src/DIELECTRIC/fix_polarize_bem_gmres.h diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp rename to src/DIELECTRIC/fix_polarize_bem_icc.cpp diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_icc.h b/src/DIELECTRIC/fix_polarize_bem_icc.h similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_icc.h rename to src/DIELECTRIC/fix_polarize_bem_icc.h diff --git a/src/USER-DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp similarity index 97% rename from src/USER-DIELECTRIC/fix_polarize_functional.cpp rename to src/DIELECTRIC/fix_polarize_functional.cpp index 4ca2de43d0..e082ba79ce 100644 --- a/src/USER-DIELECTRIC/fix_polarize_functional.cpp +++ b/src/DIELECTRIC/fix_polarize_functional.cpp @@ -37,6 +37,7 @@ #include "kspace.h" #include "math_const.h" #include "math_extra.h" +#include "math_special.h" #include "memory.h" #include "modify.h" #include "msm_dielectric.h" @@ -60,6 +61,7 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathExtra; using namespace MathConst; +using namespace MathSpecial; enum { REAL2SCALED = 0, SCALED2REAL = 1 }; @@ -589,21 +591,21 @@ void FixPolarizeFunctional::set_arrays(int i) double FixPolarizeFunctional::memory_usage() { double bytes = 0; - bytes += num_induced_charges * num_induced_charges * sizeof(double); // inverse_matrix - bytes += num_induced_charges * num_induced_charges * sizeof(double); // Rww - bytes += num_induced_charges * num_induced_charges * sizeof(double); // G1ww - bytes += num_induced_charges * num_induced_charges * sizeof(double); // ndotGww - bytes += num_induced_charges * num_induced_charges * sizeof(double); // G2ww - bytes += num_induced_charges * num_induced_charges * sizeof(double); // G3ww - bytes += num_induced_charges * sizeof(double); // qiRqwVector - bytes += num_induced_charges * sizeof(double); // sum2G2wq - bytes += num_induced_charges * sizeof(double); // sum1G2qw - bytes += num_induced_charges * sizeof(double); // sum1G1qw_epsilon - bytes += num_induced_charges * sizeof(double); // sum2ndotGwq_epsilon - bytes += num_ions * num_induced_charges * sizeof(double); // G1qw_real - bytes += nmax * sizeof(int); // induced_charge_idx - bytes += nmax * sizeof(int); // ion_idx - bytes += num_induced_charges * sizeof(double); // induced_charges + bytes += square(num_induced_charges) * sizeof(double); // inverse_matrix + bytes += square(num_induced_charges) * sizeof(double); // Rww + bytes += square(num_induced_charges) * sizeof(double); // G1ww + bytes += square(num_induced_charges) * sizeof(double); // ndotGww + bytes += square(num_induced_charges) * sizeof(double); // G2ww + bytes += square(num_induced_charges) * sizeof(double); // G3ww + bytes += num_induced_charges * sizeof(double); // qiRqwVector + bytes += num_induced_charges * sizeof(double); // sum2G2wq + bytes += num_induced_charges * sizeof(double); // sum1G2qw + bytes += num_induced_charges * sizeof(double); // sum1G1qw_epsilon + bytes += num_induced_charges * sizeof(double); // sum2ndotGwq_epsilon + bytes += (double)num_ions * num_induced_charges * sizeof(double); // G1qw_real + bytes += nmax * sizeof(int); // induced_charge_idx + bytes += nmax * sizeof(int); // ion_idx + bytes += num_induced_charges * sizeof(double); // induced_charges return bytes; } @@ -1115,9 +1117,6 @@ void FixPolarizeFunctional::calculate_grad_greens_ewald(double *vec, double dx, void FixPolarizeFunctional::calculate_matrix_multiply_vector(double **matrix, double *in_vec, double *out_vec, int M) { -#if defined(OPENMP) -#pragma parallel omp for -#endif for (int k = 0; k < M; ++k) { double temp = 0.0; for (int l = 0; l < M; ++l) { temp += matrix[k][l] * in_vec[l]; } diff --git a/src/USER-DIELECTRIC/fix_polarize_functional.h b/src/DIELECTRIC/fix_polarize_functional.h similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_functional.h rename to src/DIELECTRIC/fix_polarize_functional.h diff --git a/src/USER-DIELECTRIC/msm_dielectric.cpp b/src/DIELECTRIC/msm_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/msm_dielectric.cpp rename to src/DIELECTRIC/msm_dielectric.cpp diff --git a/src/USER-DIELECTRIC/msm_dielectric.h b/src/DIELECTRIC/msm_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/msm_dielectric.h rename to src/DIELECTRIC/msm_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp b/src/DIELECTRIC/pair_coul_cut_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp rename to src/DIELECTRIC/pair_coul_cut_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_coul_cut_dielectric.h b/src/DIELECTRIC/pair_coul_cut_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_cut_dielectric.h rename to src/DIELECTRIC/pair_coul_cut_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_coul_long_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_long_dielectric.cpp rename to src/DIELECTRIC/pair_coul_long_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_coul_long_dielectric.h b/src/DIELECTRIC/pair_coul_long_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_long_dielectric.h rename to src/DIELECTRIC/pair_coul_long_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp similarity index 99% rename from src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp rename to src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp index ef326b5316..0d0c7074bb 100644 --- a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp +++ b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp @@ -53,9 +53,9 @@ using namespace MathExtra; PairLJLongCoulLongDielectric::PairLJLongCoulLongDielectric(LAMMPS *lmp) : PairLJLongCoulLong(lmp) { respa_enable = 0; - cut_respa = NULL; - efield = NULL; - epot = NULL; + cut_respa = nullptr; + efield = nullptr; + epot = nullptr; nmax = 0; } diff --git a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.h b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.h rename to src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h diff --git a/src/USER-DIELECTRIC/pppm_dielectric.cpp b/src/DIELECTRIC/pppm_dielectric.cpp similarity index 98% rename from src/USER-DIELECTRIC/pppm_dielectric.cpp rename to src/DIELECTRIC/pppm_dielectric.cpp index 7fdb0b76c4..88c0e4c449 100644 --- a/src/USER-DIELECTRIC/pppm_dielectric.cpp +++ b/src/DIELECTRIC/pppm_dielectric.cpp @@ -469,21 +469,19 @@ void PPPMDielectric::slabcorr() } /* ---------------------------------------------------------------------- - compute qsum,qsqsum,q2 and give error/warning if not charge neutral - called initially, when particle count changes, when charges are changed + compute qsum,qsqsum,q2 and ignore error/warning if not charge neutral + called whenever charges are changed ------------------------------------------------------------------------- */ void PPPMDielectric::qsum_qsq() { const double * const q = atom->q; - const double * const eps = atom->epsilon; const int nlocal = atom->nlocal; double qsum_local(0.0), qsqsum_local(0.0); for (int i = 0; i < nlocal; i++) { - double qtmp = eps[i]*q[i]; - qsum_local += qtmp; - qsqsum_local += qtmp*qtmp; + qsum_local += q[i]; + qsqsum_local += q[i]*q[i]; } MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); diff --git a/src/USER-DIELECTRIC/pppm_dielectric.h b/src/DIELECTRIC/pppm_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pppm_dielectric.h rename to src/DIELECTRIC/pppm_dielectric.h diff --git a/src/DIELECTRIC/pppm_disp_dielectric.cpp b/src/DIELECTRIC/pppm_disp_dielectric.cpp new file mode 100644 index 0000000000..944225dd43 --- /dev/null +++ b/src/DIELECTRIC/pppm_disp_dielectric.cpp @@ -0,0 +1,866 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Trung Nguyen (Northwestern) +------------------------------------------------------------------------- */ + +#include "pppm_disp_dielectric.h" + +#include "angle.h" +#include "atom.h" +#include "atom_vec_dielectric.h" +#include "bond.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" +#include "gridcomm.h" +#include "math_const.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" +#include "remap_wrap.h" + +#include +#include + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define MAXORDER 7 +#define OFFSET 16384 +#define SMALL 0.00001 +#define LARGE 10000.0 +#define EPS_HOC 1.0e-7 + +enum{REVERSE_RHO,REVERSE_RHO_GEOM,REVERSE_RHO_ARITH,REVERSE_RHO_NONE}; +enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM, + FORWARD_IK_GEOM,FORWARD_AD_GEOM, + FORWARD_IK_PERATOM_GEOM,FORWARD_AD_PERATOM_GEOM, + FORWARD_IK_ARITH,FORWARD_AD_ARITH, + FORWARD_IK_PERATOM_ARITH,FORWARD_AD_PERATOM_ARITH, + FORWARD_IK_NONE,FORWARD_AD_NONE,FORWARD_IK_PERATOM_NONE, + FORWARD_AD_PERATOM_NONE}; + +#ifdef FFT_SINGLE +#define ZEROF 0.0f +#define ONEF 1.0f +#else +#define ZEROF 0.0 +#define ONEF 1.0 +#endif + +/* ---------------------------------------------------------------------- */ + +PPPMDispDielectric::PPPMDispDielectric(LAMMPS *lmp) : PPPMDisp(lmp) +{ + dipoleflag = 0; // turned off for now, until dipole works + group_group_enable = 0; + + mu_flag = 0; + + efield = nullptr; + phi = nullptr; + potflag = 0; + + avec = (AtomVecDielectric *) atom->style_match("dielectric"); + if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric"); +} + +/* ---------------------------------------------------------------------- */ + +PPPMDispDielectric::~PPPMDispDielectric() +{ + memory->destroy(efield); + memory->destroy(phi); +} + +/* ---------------------------------------------------------------------- + compute the PPPM long-range force, energy, virial +------------------------------------------------------------------------- */ + +void PPPMDispDielectric::compute(int eflag, int vflag) +{ + + int i; + + // set energy/virial flags + // invoke allocate_peratom() if needed for first time + + ev_init(eflag,vflag); + + if (evflag_atom && !peratom_allocate_flag) allocate_peratom(); + + // convert atoms from box to lamda coords + + if (triclinic == 0) boxlo = domain->boxlo; + else { + boxlo = domain->boxlo_lamda; + domain->x2lamda(atom->nlocal); + } + // extend size of per-atom arrays if necessary + + if (atom->nmax > nmax) { + + if (function[0]) { + memory->destroy(part2grid); + memory->destroy(efield); + memory->destroy(phi); + } + if (function[1] + function[2] + function[3]) memory->destroy(part2grid_6); + nmax = atom->nmax; + if (function[0]) { + memory->create(part2grid,nmax,3,"pppm/disp:part2grid"); + memory->create(efield,nmax,3,"pppm/disp:efield"); + memory->create(phi,nmax,"pppm/disp:phi"); + } + if (function[1] + function[2] + function[3]) + memory->create(part2grid_6,nmax,3,"pppm/disp:part2grid_6"); + } + + energy = 0.0; + energy_1 = 0.0; + energy_6 = 0.0; + if (vflag) for (i = 0; i < 6; i++) virial_6[i] = virial_1[i] = 0.0; + + // find grid points for all my particles + // distribute partcles' charges/dispersion coefficients on the grid + // communication between processors and remapping two fft + // Solution of poissons equation in k-space and backtransformation + // communication between processors + // calculation of forces + + if (function[0]) { + + // perform calculations for coulomb interactions only + + particle_map_c(delxinv,delyinv,delzinv,shift,part2grid,nupper,nlower, + nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out); + + make_rho_c(); + + gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO, + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + + brick2fft(nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in, + density_brick,density_fft,work1,remap); + + if (differentiation_flag == 1) { + poisson_ad(work1,work2,density_fft,fft1,fft2, + nx_pppm,ny_pppm,nz_pppm,nfft, + nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft, + nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in, + energy_1,greensfn, + virial_1,vg,vg2, + u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick); + + gc->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD, + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + + fieldforce_c_ad(); + + if (vflag_atom) + gc->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM, + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + + } else { + poisson_ik(work1,work2,density_fft,fft1,fft2, + nx_pppm,ny_pppm,nz_pppm,nfft, + nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft, + nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in, + energy_1,greensfn, + fkx,fky,fkz,fkx2,fky2,fkz2, + vdx_brick,vdy_brick,vdz_brick,virial_1,vg,vg2, + u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick); + + gc->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK, + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + + fieldforce_c_ik(); + + if (evflag_atom) + gc->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM, + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + } + + if (evflag_atom) fieldforce_c_peratom(); + } + + if (function[1]) { + + // perform calculations for geometric mixing + + particle_map(delxinv_6,delyinv_6,delzinv_6,shift_6,part2grid_6, + nupper_6,nlower_6, + nxlo_out_6,nylo_out_6,nzlo_out_6, + nxhi_out_6,nyhi_out_6,nzhi_out_6); + + make_rho_g(); + + gc6->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO_GEOM, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + brick2fft(nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, + density_brick_g,density_fft_g,work1_6,remap_6); + + if (differentiation_flag == 1) { + poisson_ad(work1_6,work2_6,density_fft_g,fft1_6,fft2_6, + nx_pppm_6,ny_pppm_6,nz_pppm_6,nfft_6, + nxlo_fft_6,nylo_fft_6,nzlo_fft_6,nxhi_fft_6,nyhi_fft_6,nzhi_fft_6, + nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, + energy_6,greensfn_6, + virial_6,vg_6,vg2_6, + u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g, + v3_brick_g,v4_brick_g,v5_brick_g); + + gc6->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD_GEOM, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + fieldforce_g_ad(); + + if (vflag_atom) + gc6->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM_GEOM, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + } else { + poisson_ik(work1_6,work2_6,density_fft_g,fft1_6,fft2_6, + nx_pppm_6,ny_pppm_6,nz_pppm_6,nfft_6, + nxlo_fft_6,nylo_fft_6,nzlo_fft_6,nxhi_fft_6,nyhi_fft_6,nzhi_fft_6, + nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, + energy_6,greensfn_6, + fkx_6,fky_6,fkz_6,fkx2_6,fky2_6,fkz2_6, + vdx_brick_g,vdy_brick_g,vdz_brick_g,virial_6,vg_6,vg2_6, + u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g, + v3_brick_g,v4_brick_g,v5_brick_g); + + gc6->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK_GEOM, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + fieldforce_g_ik(); + + if (evflag_atom) + gc6->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM_GEOM, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + } + + if (evflag_atom) fieldforce_g_peratom(); + } + + if (function[2]) { + + // perform calculations for arithmetic mixing + + particle_map(delxinv_6,delyinv_6,delzinv_6,shift_6,part2grid_6, + nupper_6,nlower_6, + nxlo_out_6,nylo_out_6,nzlo_out_6, + nxhi_out_6,nyhi_out_6,nzhi_out_6); + + make_rho_a(); + + gc6->reverse_comm_kspace(this,7,sizeof(FFT_SCALAR),REVERSE_RHO_ARITH, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + brick2fft_a(); + + if (differentiation_flag == 1) { + poisson_ad(work1_6,work2_6,density_fft_a3,fft1_6,fft2_6, + nx_pppm_6,ny_pppm_6,nz_pppm_6,nfft_6, + nxlo_fft_6,nylo_fft_6,nzlo_fft_6,nxhi_fft_6,nyhi_fft_6,nzhi_fft_6, + nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, + energy_6,greensfn_6, + virial_6,vg_6,vg2_6, + u_brick_a3,v0_brick_a3,v1_brick_a3,v2_brick_a3, + v3_brick_a3,v4_brick_a3,v5_brick_a3); + poisson_2s_ad(density_fft_a0,density_fft_a6, + u_brick_a0,v0_brick_a0,v1_brick_a0,v2_brick_a0, + v3_brick_a0,v4_brick_a0,v5_brick_a0, + u_brick_a6,v0_brick_a6,v1_brick_a6,v2_brick_a6, + v3_brick_a6,v4_brick_a6,v5_brick_a6); + poisson_2s_ad(density_fft_a1,density_fft_a5, + u_brick_a1,v0_brick_a1,v1_brick_a1,v2_brick_a1, + v3_brick_a1,v4_brick_a1,v5_brick_a1, + u_brick_a5,v0_brick_a5,v1_brick_a5,v2_brick_a5, + v3_brick_a5,v4_brick_a5,v5_brick_a5); + poisson_2s_ad(density_fft_a2,density_fft_a4, + u_brick_a2,v0_brick_a2,v1_brick_a2,v2_brick_a2, + v3_brick_a2,v4_brick_a2,v5_brick_a2, + u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4, + v3_brick_a4,v4_brick_a4,v5_brick_a4); + + gc6->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_AD_ARITH, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + fieldforce_a_ad(); + + if (evflag_atom) + gc6->forward_comm_kspace(this,42,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM_ARITH, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + } else { + poisson_ik(work1_6,work2_6,density_fft_a3,fft1_6,fft2_6, + nx_pppm_6,ny_pppm_6,nz_pppm_6,nfft_6, + nxlo_fft_6,nylo_fft_6,nzlo_fft_6,nxhi_fft_6,nyhi_fft_6,nzhi_fft_6, + nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, + energy_6,greensfn_6, + fkx_6,fky_6,fkz_6,fkx2_6,fky2_6,fkz2_6, + vdx_brick_a3,vdy_brick_a3,vdz_brick_a3,virial_6,vg_6,vg2_6, + u_brick_a3,v0_brick_a3,v1_brick_a3,v2_brick_a3, + v3_brick_a3,v4_brick_a3,v5_brick_a3); + poisson_2s_ik(density_fft_a0,density_fft_a6, + vdx_brick_a0,vdy_brick_a0,vdz_brick_a0, + vdx_brick_a6,vdy_brick_a6,vdz_brick_a6, + u_brick_a0,v0_brick_a0,v1_brick_a0,v2_brick_a0, + v3_brick_a0,v4_brick_a0,v5_brick_a0, + u_brick_a6,v0_brick_a6,v1_brick_a6,v2_brick_a6, + v3_brick_a6,v4_brick_a6,v5_brick_a6); + poisson_2s_ik(density_fft_a1,density_fft_a5, + vdx_brick_a1,vdy_brick_a1,vdz_brick_a1, + vdx_brick_a5,vdy_brick_a5,vdz_brick_a5, + u_brick_a1,v0_brick_a1,v1_brick_a1,v2_brick_a1, + v3_brick_a1,v4_brick_a1,v5_brick_a1, + u_brick_a5,v0_brick_a5,v1_brick_a5,v2_brick_a5, + v3_brick_a5,v4_brick_a5,v5_brick_a5); + poisson_2s_ik(density_fft_a2,density_fft_a4, + vdx_brick_a2,vdy_brick_a2,vdz_brick_a2, + vdx_brick_a4,vdy_brick_a4,vdz_brick_a4, + u_brick_a2,v0_brick_a2,v1_brick_a2,v2_brick_a2, + v3_brick_a2,v4_brick_a2,v5_brick_a2, + u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4, + v3_brick_a4,v4_brick_a4,v5_brick_a4); + + gc6->forward_comm_kspace(this,21,sizeof(FFT_SCALAR),FORWARD_IK_ARITH, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + fieldforce_a_ik(); + + if (evflag_atom) + gc6->forward_comm_kspace(this,49,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM_ARITH, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + } + + if (evflag_atom) fieldforce_a_peratom(); + } + + if (function[3]) { + + // perform calculations if no mixing rule applies + + particle_map(delxinv_6,delyinv_6,delzinv_6,shift_6,part2grid_6, + nupper_6,nlower_6, + nxlo_out_6,nylo_out_6,nzlo_out_6, + nxhi_out_6,nyhi_out_6,nzhi_out_6); + + make_rho_none(); + + gc6->reverse_comm_kspace(this,nsplit_alloc,sizeof(FFT_SCALAR),REVERSE_RHO_NONE, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + brick2fft_none(); + + if (differentiation_flag == 1) { + int n = 0; + for (int k = 0; k < nsplit_alloc/2; k++) { + poisson_none_ad(n,n+1,density_fft_none[n],density_fft_none[n+1], + u_brick_none[n],u_brick_none[n+1], + v0_brick_none,v1_brick_none,v2_brick_none, + v3_brick_none,v4_brick_none,v5_brick_none); + n += 2; + } + + gc6->forward_comm_kspace(this,1*nsplit_alloc,sizeof(FFT_SCALAR), + FORWARD_AD_NONE, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + fieldforce_none_ad(); + + if (vflag_atom) + gc6->forward_comm_kspace(this,6*nsplit_alloc,sizeof(FFT_SCALAR), + FORWARD_AD_PERATOM_NONE, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + } else { + int n = 0; + for (int k = 0; k < nsplit_alloc/2; k++) { + poisson_none_ik(n,n+1,density_fft_none[n],density_fft_none[n+1], + vdx_brick_none[n],vdy_brick_none[n],vdz_brick_none[n], + vdx_brick_none[n+1],vdy_brick_none[n+1],vdz_brick_none[n+1], + u_brick_none,v0_brick_none,v1_brick_none,v2_brick_none, + v3_brick_none,v4_brick_none,v5_brick_none); + n += 2; + } + + gc6->forward_comm_kspace(this,3*nsplit_alloc,sizeof(FFT_SCALAR), + FORWARD_IK_NONE, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + + fieldforce_none_ik(); + + if (evflag_atom) + gc6->forward_comm_kspace(this,7*nsplit_alloc,sizeof(FFT_SCALAR), + FORWARD_IK_PERATOM_NONE, + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + } + + if (evflag_atom) fieldforce_none_peratom(); + } + + // update qsum and qsqsum, if atom count has changed and energy needed + + if ((eflag_global || eflag_atom) && atom->natoms != natoms_original) { + qsum_qsq(); + natoms_original = atom->natoms; + } + + // sum energy across procs and add in volume-dependent term + + const double qscale = force->qqrd2e * scale; + + if (eflag_global) { + double energy_all; + MPI_Allreduce(&energy_1,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); + energy_1 = energy_all; + MPI_Allreduce(&energy_6,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); + energy_6 = energy_all; + + energy_1 *= 0.5*volume; + energy_6 *= 0.5*volume; + + energy_1 -= g_ewald*qsqsum/MY_PIS + + MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume); + energy_6 += - MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumij + + 1.0/12.0*pow(g_ewald_6,6)*csum; + energy_1 *= qscale; + } + + // sum virial across procs + + if (vflag_global) { + double virial_all[6]; + MPI_Allreduce(virial_1,virial_all,6,MPI_DOUBLE,MPI_SUM,world); + for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i]; + MPI_Allreduce(virial_6,virial_all,6,MPI_DOUBLE,MPI_SUM,world); + for (i = 0; i < 6; i++) virial[i] += 0.5*volume*virial_all[i]; + if (function[1]+function[2]+function[3]) { + double a = MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumij; + virial[0] -= a; + virial[1] -= a; + virial[2] -= a; + } + } + + if (eflag_atom) { + if (function[0]) { + double *q = atom->q; + // coulomb self energy correction + for (i = 0; i < atom->nlocal; i++) { + eatom[i] -= qscale*g_ewald*q[i]*q[i]/MY_PIS + + qscale*MY_PI2*q[i]*qsum / (g_ewald*g_ewald*volume); + } + } + if (function[1] + function[2] + function[3]) { + int tmp; + for (i = 0; i < atom->nlocal; i++) { + tmp = atom->type[i]; + eatom[i] += - MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumi[tmp] + + 1.0/12.0*pow(g_ewald_6,6)*cii[tmp]; + } + } + } + + if (vflag_atom) { + if (function[1] + function[2] + function[3]) { + int tmp; + // dispersion self virial correction + for (i = 0; i < atom->nlocal; i++) { + tmp = atom->type[i]; + for (int n = 0; n < 3; n++) + vatom[i][n] -= MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumi[tmp]; + } + } + } + + // 2d slab correction + + if (slabflag) slabcorr(eflag); + if (function[0]) energy += energy_1; + if (function[1] + function[2] + function[3]) energy += energy_6; + + // convert atoms back from lamda to box coords + + if (triclinic) domain->lamda2x(atom->nlocal); +} + +/* ---------------------------------------------------------------------- + interpolate from grid to get electric field & force on my particles + for ik scheme +------------------------------------------------------------------------- */ + +void PPPMDispDielectric::fieldforce_c_ik() +{ + int i,l,m,n,nx,ny,nz,mx,my,mz; + FFT_SCALAR dx,dy,dz,x0,y0,z0; + FFT_SCALAR ekx,eky,ekz,u; + + // loop over my charges, interpolate electric field from nearby grid points + // (nx,ny,nz) = global coords of grid pt to "lower left" of charge + // (dx,dy,dz) = distance to "lower left" grid pt + // (mx,my,mz) = global coords of moving stencil pt + // ek = 3 components of E-field on particle + + double *q = atom->q; + double **x = atom->x; + double **f = atom->f; + double *eps = atom->epsilon; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) { + nx = part2grid[i][0]; + ny = part2grid[i][1]; + nz = part2grid[i][2]; + dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv; + dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv; + dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv; + + compute_rho1d(dx,dy,dz, order, rho_coeff, rho1d); + + u = ekx = eky = ekz = ZEROF; + for (n = nlower; n <= nupper; n++) { + mz = n+nz; + z0 = rho1d[2][n]; + for (m = nlower; m <= nupper; m++) { + my = m+ny; + y0 = z0*rho1d[1][m]; + for (l = nlower; l <= nupper; l++) { + mx = l+nx; + x0 = y0*rho1d[0][l]; + if (potflag) u += x0*u_brick[mz][my][mx]; + ekx -= x0*vdx_brick[mz][my][mx]; + eky -= x0*vdy_brick[mz][my][mx]; + ekz -= x0*vdz_brick[mz][my][mx]; + } + } + } + + // electrostatic potential + + if (potflag) phi[i] = u; + + // convert E-field to force + + const double efactor = scale * eps[i]; + efield[i][0] = efactor*ekx; + efield[i][1] = efactor*eky; + efield[i][2] = efactor*ekz; + + // convert E-field to force + + const double qfactor = force->qqrd2e * scale * q[i]; + f[i][0] += qfactor*ekx; + f[i][1] += qfactor*eky; + if (slabflag != 2) f[i][2] += qfactor*ekz; + } +} +/* ---------------------------------------------------------------------- + interpolate from grid to get electric field & force on my particles + for ad scheme +------------------------------------------------------------------------- */ + +void PPPMDispDielectric::fieldforce_c_ad() +{ + int i,l,m,n,nx,ny,nz,mx,my,mz; + FFT_SCALAR dx,dy,dz; + FFT_SCALAR ekx,eky,ekz,u; + double s1,s2,s3; + double sf = 0.0; + + double *prd; + + if (triclinic == 0) prd = domain->prd; + else prd = domain->prd_lamda; + + double xprd = prd[0]; + double yprd = prd[1]; + double zprd = prd[2]; + double zprd_slab = zprd*slab_volfactor; + + double hx_inv = nx_pppm/xprd; + double hy_inv = ny_pppm/yprd; + double hz_inv = nz_pppm/zprd_slab; + + // loop over my charges, interpolate electric field from nearby grid points + // (nx,ny,nz) = global coords of grid pt to "lower left" of charge + // (dx,dy,dz) = distance to "lower left" grid pt + // (mx,my,mz) = global coords of moving stencil pt + // ek = 3 components of E-field on particle + + double *q = atom->q; + double **x = atom->x; + double **f = atom->f; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) { + nx = part2grid[i][0]; + ny = part2grid[i][1]; + nz = part2grid[i][2]; + dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv; + dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv; + dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv; + + compute_rho1d(dx,dy,dz, order, rho_coeff, rho1d); + compute_drho1d(dx,dy,dz, order, drho_coeff, drho1d); + + u = ekx = eky = ekz = ZEROF; + for (n = nlower; n <= nupper; n++) { + mz = n+nz; + for (m = nlower; m <= nupper; m++) { + my = m+ny; + for (l = nlower; l <= nupper; l++) { + mx = l+nx; + u += rho1d[0][l]*rho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx]; + ekx += drho1d[0][l]*rho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx]; + eky += rho1d[0][l]*drho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx]; + ekz += rho1d[0][l]*rho1d[1][m]*drho1d[2][n]*u_brick[mz][my][mx]; + } + } + } + ekx *= hx_inv; + eky *= hy_inv; + ekz *= hz_inv; + + // electrical potential + + if (potflag) phi[i] = u; + + // convert E-field to force and substract self forces + const double qfactor = qqrd2e * scale; + + s1 = x[i][0]*hx_inv; + s2 = x[i][1]*hy_inv; + s3 = x[i][2]*hz_inv; + sf = sf_coeff[0]*sin(2*MY_PI*s1); + sf += sf_coeff[1]*sin(4*MY_PI*s1); + sf *= 2*q[i]*q[i]; + f[i][0] += qfactor*(ekx*q[i] - sf); + + sf = sf_coeff[2]*sin(2*MY_PI*s2); + sf += sf_coeff[3]*sin(4*MY_PI*s2); + sf *= 2*q[i]*q[i]; + f[i][1] += qfactor*(eky*q[i] - sf); + + sf = sf_coeff[4]*sin(2*MY_PI*s3); + sf += sf_coeff[5]*sin(4*MY_PI*s3); + sf *= 2*q[i]*q[i]; + if (slabflag != 2) f[i][2] += qfactor*(ekz*q[i] - sf); + } +} + +/* ---------------------------------------------------------------------- + interpolate from grid to get electric field & force on my particles +------------------------------------------------------------------------- */ + +void PPPMDispDielectric::fieldforce_c_peratom() +{ + int i,l,m,n,nx,ny,nz,mx,my,mz; + FFT_SCALAR dx,dy,dz,x0,y0,z0; + FFT_SCALAR u_pa,v0,v1,v2,v3,v4,v5; + + // loop over my charges, interpolate electric field from nearby grid points + // (nx,ny,nz) = global coords of grid pt to "lower left" of charge + // (dx,dy,dz) = distance to "lower left" grid pt + // (mx,my,mz) = global coords of moving stencil pt + // ek = 3 components of E-field on particle + + double *q = atom->q; + double **x = atom->x; + + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) { + nx = part2grid[i][0]; + ny = part2grid[i][1]; + nz = part2grid[i][2]; + dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv; + dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv; + dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv; + + compute_rho1d(dx,dy,dz, order, rho_coeff, rho1d); + + u_pa = v0 = v1 = v2 = v3 = v4 = v5 = ZEROF; + for (n = nlower; n <= nupper; n++) { + mz = n+nz; + z0 = rho1d[2][n]; + for (m = nlower; m <= nupper; m++) { + my = m+ny; + y0 = z0*rho1d[1][m]; + for (l = nlower; l <= nupper; l++) { + mx = l+nx; + x0 = y0*rho1d[0][l]; + if (eflag_atom) u_pa += x0*u_brick[mz][my][mx]; + if (vflag_atom) { + v0 += x0*v0_brick[mz][my][mx]; + v1 += x0*v1_brick[mz][my][mx]; + v2 += x0*v2_brick[mz][my][mx]; + v3 += x0*v3_brick[mz][my][mx]; + v4 += x0*v4_brick[mz][my][mx]; + v5 += x0*v5_brick[mz][my][mx]; + } + } + } + } + + // electrostatic potential + + phi[i] = u_pa; + + // convert E-field to force + + const double qfactor = 0.5*force->qqrd2e * scale * q[i]; + + if (eflag_atom) eatom[i] += u_pa*qfactor; + if (vflag_atom) { + vatom[i][0] += v0*qfactor; + vatom[i][1] += v1*qfactor; + vatom[i][2] += v2*qfactor; + vatom[i][3] += v3*qfactor; + vatom[i][4] += v4*qfactor; + vatom[i][5] += v5*qfactor; + } + } +} + +/* ---------------------------------------------------------------------- + Slab-geometry correction term to dampen inter-slab interactions between + periodically repeating slabs. Yields good approximation to 2D Ewald if + adequate empty space is left between repeating slabs (J. Chem. Phys. + 111, 3155). Slabs defined here to be parallel to the xy plane. Also + extended to non-neutral systems (J. Chem. Phys. 131, 094107). +------------------------------------------------------------------------- */ + +void PPPMDispDielectric::slabcorr(int /*eflag*/) +{ + // compute local contribution to global dipole moment + + double *q = atom->q; + double **x = atom->x; + double *eps = atom->epsilon; + double zprd = domain->zprd; + int nlocal = atom->nlocal; + + double dipole = 0.0; + for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2]; + + if (mu_flag) { + double **mu = atom->mu; + for (int i = 0; i < nlocal; i++) dipole += mu[i][2]; + } + + // sum local contributions to get global dipole moment + + double dipole_all; + MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world); + + // need to make non-neutral systems and/or + // per-atom energy translationally invariant + + double dipole_r2 = 0.0; + if (eflag_atom || fabs(qsum) > SMALL) { + + if (mu_flag) + error->all(FLERR,"Cannot (yet) use kspace slab correction with " + "long-range dipoles and non-neutral systems or per-atom energy"); + + for (int i = 0; i < nlocal; i++) + dipole_r2 += q[i]*x[i][2]*x[i][2]; + + // sum local contributions + + double tmp; + MPI_Allreduce(&dipole_r2,&tmp,1,MPI_DOUBLE,MPI_SUM,world); + dipole_r2 = tmp; + } + + // compute corrections + + const double e_slabcorr = MY_2PI*(dipole_all*dipole_all - + qsum*dipole_r2 - qsum*qsum*zprd*zprd/12.0)/volume; + const double qscale = qqrd2e * scale; + + if (eflag_global) energy += qscale * e_slabcorr; + + // per-atom energy + + if (eflag_atom) { + double efact = qscale * MY_2PI/volume; + for (int i = 0; i < nlocal; i++) + eatom[i] += efact * eps[i]*q[i]*(x[i][2]*dipole_all - 0.5*(dipole_r2 + + qsum*x[i][2]*x[i][2]) - qsum*zprd*zprd/12.0); + } + + // add on force corrections + + double ffact = qscale * (-4.0*MY_PI/volume); + double **f = atom->f; + + for (int i = 0; i < nlocal; i++) { + f[i][2] += ffact * eps[i]*q[i]*(dipole_all - qsum*x[i][2]); + efield[i][2] += ffact * eps[i]*(dipole_all - qsum*x[i][2]); + } + + // add on torque corrections + + if (mu_flag && atom->torque) { + double **mu = atom->mu; + double **torque = atom->torque; + for (int i = 0; i < nlocal; i++) { + torque[i][0] += ffact * dipole_all * mu[i][1]; + torque[i][1] += -ffact * dipole_all * mu[i][0]; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local arrays +------------------------------------------------------------------------- */ + +double PPPMDispDielectric::memory_usage() +{ + double bytes = PPPMDisp::memory_usage(); + bytes += nmax*3 * sizeof(double); + bytes += nmax * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + compute qsum,qsqsum,q2 and give error/warning if not charge neutral + called initially, when particle count changes, when charges are changed +------------------------------------------------------------------------- */ + +void PPPMDispDielectric::qsum_qsq() +{ + const double * const q = atom->q; + const int nlocal = atom->nlocal; + double qsum_local(0.0), qsqsum_local(0.0); + + for (int i = 0; i < nlocal; i++) { + qsum_local += q[i]; + qsqsum_local += q[i]*q[i]; + } + + MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world); + + q2 = qsqsum * force->qqrd2e; +} diff --git a/src/DIELECTRIC/pppm_disp_dielectric.h b/src/DIELECTRIC/pppm_disp_dielectric.h new file mode 100644 index 0000000000..8f0476ab40 --- /dev/null +++ b/src/DIELECTRIC/pppm_disp_dielectric.h @@ -0,0 +1,62 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef KSPACE_CLASS +// clang-format off +KSpaceStyle(pppm/disp/dielectric,PPPMDispDielectric); +// clang-format on +#else + +#ifndef LMP_PPPM_DISP_DIELECTRIC_H +#define LMP_PPPM_DISP_DIELECTRIC_H + +#include "pppm_disp.h" + +namespace LAMMPS_NS { + +class PPPMDispDielectric : public PPPMDisp { + public: + PPPMDispDielectric(class LAMMPS *); + virtual ~PPPMDispDielectric(); + virtual double memory_usage(); + virtual void compute(int, int); + void qsum_qsq(); + void slabcorr(int); + + double **efield; + double *phi; + int potflag; // 1/0 if per-atom electrostatic potential phi is needed + + protected: + virtual void fieldforce_c_ik(); + virtual void fieldforce_c_ad(); + virtual void fieldforce_c_peratom(); + + class AtomVecDielectric *avec; + int mu_flag; +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/USER-DIFFRACTION/README b/src/DIFFRACTION/README similarity index 98% rename from src/USER-DIFFRACTION/README rename to src/DIFFRACTION/README index fb36011960..a9a8ad523e 100644 --- a/src/USER-DIFFRACTION/README +++ b/src/DIFFRACTION/README @@ -42,7 +42,7 @@ User-diffraction includes: See the doc pages for these commands for detailed usage instructions. There are example scripts for using this package in -examples/USER/diffraction. +examples/PACKAGES/diffraction. --------------------------------- diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/DIFFRACTION/compute_saed.cpp similarity index 100% rename from src/USER-DIFFRACTION/compute_saed.cpp rename to src/DIFFRACTION/compute_saed.cpp diff --git a/src/USER-DIFFRACTION/compute_saed.h b/src/DIFFRACTION/compute_saed.h similarity index 100% rename from src/USER-DIFFRACTION/compute_saed.h rename to src/DIFFRACTION/compute_saed.h diff --git a/src/USER-DIFFRACTION/compute_saed_consts.h b/src/DIFFRACTION/compute_saed_consts.h similarity index 100% rename from src/USER-DIFFRACTION/compute_saed_consts.h rename to src/DIFFRACTION/compute_saed_consts.h diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/DIFFRACTION/compute_xrd.cpp similarity index 100% rename from src/USER-DIFFRACTION/compute_xrd.cpp rename to src/DIFFRACTION/compute_xrd.cpp diff --git a/src/USER-DIFFRACTION/compute_xrd.h b/src/DIFFRACTION/compute_xrd.h similarity index 100% rename from src/USER-DIFFRACTION/compute_xrd.h rename to src/DIFFRACTION/compute_xrd.h diff --git a/src/USER-DIFFRACTION/compute_xrd_consts.h b/src/DIFFRACTION/compute_xrd_consts.h similarity index 100% rename from src/USER-DIFFRACTION/compute_xrd_consts.h rename to src/DIFFRACTION/compute_xrd_consts.h diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/DIFFRACTION/fix_saed_vtk.cpp similarity index 100% rename from src/USER-DIFFRACTION/fix_saed_vtk.cpp rename to src/DIFFRACTION/fix_saed_vtk.cpp diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/DIFFRACTION/fix_saed_vtk.h similarity index 100% rename from src/USER-DIFFRACTION/fix_saed_vtk.h rename to src/DIFFRACTION/fix_saed_vtk.h diff --git a/src/USER-MISC/angle_dipole.cpp b/src/DIPOLE/angle_dipole.cpp similarity index 60% rename from src/USER-MISC/angle_dipole.cpp rename to src/DIPOLE/angle_dipole.cpp index 38f13a47bd..f7724e2b56 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/DIPOLE/angle_dipole.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,16 +17,16 @@ #include "angle_dipole.h" -#include #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -55,16 +54,16 @@ AngleDipole::~AngleDipole() void AngleDipole::compute(int eflag, int vflag) { - int iRef,iDip,iDummy,n,type; - double delx,dely,delz; - double eangle,tangle,fi[3],fj[3]; - double r,cosGamma,deltaGamma,kdg,rmu; + int iRef, iDip, iDummy, n, type; + double delx, dely, delz; + double eangle, tangle, fi[3], fj[3]; + double r, cosGamma, deltaGamma, kdg, rmu; eangle = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); - double **x = atom->x; // position vector - double **mu = atom->mu; // point-dipole components and moment magnitude + double **x = atom->x; // position vector + double **mu = atom->mu; // point-dipole components and moment magnitude double **torque = atom->torque; int **anglelist = neighbor->anglelist; int nanglelist = neighbor->nanglelist; @@ -75,45 +74,44 @@ void AngleDipole::compute(int eflag, int vflag) double delTx, delTy, delTz; double fx, fy, fz, fmod, fmod_sqrtff; - if (!newton_bond) - error->all(FLERR,"'newton' flag for bonded interactions must be 'on'"); + if (!newton_bond) error->all(FLERR, "'newton' flag for bonded interactions must be 'on'"); for (n = 0; n < nanglelist; n++) { - iDip = anglelist[n][0]; // dipole whose orientation is to be restrained - iRef = anglelist[n][1]; // reference atom toward which dipole will point - iDummy = anglelist[n][2]; // dummy atom - irrelevant to the interaction + iDip = anglelist[n][0]; // dipole whose orientation is to be restrained + iRef = anglelist[n][1]; // reference atom toward which dipole will point + iDummy = anglelist[n][2]; // dummy atom - irrelevant to the interaction type = anglelist[n][3]; delx = x[iRef][0] - x[iDip][0]; dely = x[iRef][1] - x[iDip][1]; delz = x[iRef][2] - x[iDip][2]; - r = sqrt(delx*delx + dely*dely + delz*delz); + r = sqrt(delx * delx + dely * dely + delz * delz); rmu = r * mu[iDip][3]; - cosGamma = (mu[iDip][0]*delx+mu[iDip][1]*dely+mu[iDip][2]*delz) / rmu; + cosGamma = (mu[iDip][0] * delx + mu[iDip][1] * dely + mu[iDip][2] * delz) / rmu; deltaGamma = cosGamma - cos(gamma0[type]); kdg = k[type] * deltaGamma; - if (eflag) eangle = kdg * deltaGamma; // energy + if (eflag) eangle = kdg * deltaGamma; // energy tangle = 2.0 * kdg / rmu; - delTx = tangle * (dely*mu[iDip][2] - delz*mu[iDip][1]); - delTy = tangle * (delz*mu[iDip][0] - delx*mu[iDip][2]); - delTz = tangle * (delx*mu[iDip][1] - dely*mu[iDip][0]); + delTx = tangle * (dely * mu[iDip][2] - delz * mu[iDip][1]); + delTy = tangle * (delz * mu[iDip][0] - delx * mu[iDip][2]); + delTz = tangle * (delx * mu[iDip][1] - dely * mu[iDip][0]); torque[iDip][0] += delTx; torque[iDip][1] += delTy; torque[iDip][2] += delTz; // Force couple that counterbalances dipolar torque - fx = dely*delTz - delz*delTy; // direction (fi): - r x (-T) - fy = delz*delTx - delx*delTz; - fz = delx*delTy - dely*delTx; + fx = dely * delTz - delz * delTy; // direction (fi): - r x (-T) + fy = delz * delTx - delx * delTz; + fz = delx * delTy - dely * delTx; - fmod = sqrt(delTx*delTx + delTy*delTy + delTz*delTz) / r; // magnitude - fmod_sqrtff = fmod / sqrt(fx*fx + fy*fy + fz*fz); + fmod = sqrt(delTx * delTx + delTy * delTy + delTz * delTz) / r; // magnitude + fmod_sqrtff = fmod / sqrt(fx * fx + fy * fy + fz * fz); fi[0] = fx * fmod_sqrtff; fi[1] = fy * fmod_sqrtff; @@ -131,9 +129,9 @@ void AngleDipole::compute(int eflag, int vflag) f[iRef][1] += fi[1]; f[iRef][2] += fi[2]; - if (evflag) // virial = rij.fi = 0 (fj = -fi & fk = 0) - ev_tally(iRef,iDip,iDummy,nlocal,newton_bond,eangle,fj,fi, - 0.0,0.0,0.0,0.0,0.0,0.0); + if (evflag) // virial = rij.fi = 0 (fj = -fi & fk = 0) + ev_tally(iRef, iDip, iDummy, nlocal, newton_bond, eangle, fj, fi, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0); } } @@ -144,10 +142,10 @@ void AngleDipole::allocate() allocated = 1; int n = atom->nangletypes; - memory->create(k,n+1,"angle:k"); - memory->create(gamma0,n+1,"angle:gamma0"); + memory->create(k, n + 1, "angle:k"); + memory->create(gamma0, n + 1, "angle:gamma0"); - memory->create(setflag,n+1,"angle:setflag"); + memory->create(setflag, n + 1, "angle:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; } @@ -157,26 +155,36 @@ void AngleDipole::allocate() void AngleDipole::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients"); if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error); - double k_one = utils::numeric(FLERR,arg[1],false,lmp); - double gamma0_one = utils::numeric(FLERR,arg[2],false,lmp); + double k_one = utils::numeric(FLERR, arg[1], false, lmp); + double gamma0_one = utils::numeric(FLERR, arg[2], false, lmp); // convert gamma0 from degrees to radians int count = 0; for (int i = ilo; i <= ihi; i++) { k[i] = k_one; - gamma0[i] = gamma0_one/180.0 * MY_PI; + gamma0[i] = gamma0_one / 180.0 * MY_PI; setflag[i] = 1; count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void AngleDipole::init_style() +{ + if (!atom->mu_flag || !atom->torque_flag) + error->all(FLERR,"Angle style dipole requires atom attributes mu and torque"); } /* ---------------------------------------------------------------------- @@ -194,8 +202,8 @@ double AngleDipole::equilibrium_angle(int i) void AngleDipole::write_restart(FILE *fp) { - fwrite(&k[1],sizeof(double),atom->nangletypes,fp); - fwrite(&gamma0[1],sizeof(double),atom->nangletypes,fp); + fwrite(&k[1], sizeof(double), atom->nangletypes, fp); + fwrite(&gamma0[1], sizeof(double), atom->nangletypes, fp); } /* ---------------------------------------------------------------------- @@ -207,11 +215,11 @@ void AngleDipole::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error); - utils::sfread(FLERR,&gamma0[1],sizeof(double),atom->nangletypes,fp,nullptr,error); + utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error); + utils::sfread(FLERR, &gamma0[1], sizeof(double), atom->nangletypes, fp, nullptr, error); } - MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); - MPI_Bcast(&gamma0[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&gamma0[1], atom->nangletypes, MPI_DOUBLE, 0, world); for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; } @@ -222,8 +230,7 @@ void AngleDipole::read_restart(FILE *fp) void AngleDipole::write_data(FILE *fp) { - for (int i = 1; i <= atom->nangletypes; i++) - fprintf(fp,"%d %g %g\n",i,k[i],gamma0[i]); + for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g %g\n", i, k[i], gamma0[i]); } /* ---------------------------------------------------------------------- @@ -232,20 +239,20 @@ void AngleDipole::write_data(FILE *fp) double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/) { - double **x = atom->x; // position vector - double **mu = atom->mu; // point-dipole components and moment magnitude + double **x = atom->x; // position vector + double **mu = atom->mu; // point-dipole components and moment magnitude double delx = x[iRef][0] - x[iDip][0]; double dely = x[iRef][1] - x[iDip][1]; double delz = x[iRef][2] - x[iDip][2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(delx, dely, delz); - double r = sqrt(delx*delx + dely*dely + delz*delz); + double r = sqrt(delx * delx + dely * dely + delz * delz); double rmu = r * mu[iDip][3]; - double cosGamma = (mu[iDip][0]*delx+mu[iDip][1]*dely+mu[iDip][2]*delz) / rmu; + double cosGamma = (mu[iDip][0] * delx + mu[iDip][1] * dely + mu[iDip][2] * delz) / rmu; double deltaGamma = cosGamma - cos(gamma0[type]); double kdg = k[type] * deltaGamma; - return kdg * deltaGamma; // energy + return kdg * deltaGamma; // energy } diff --git a/src/USER-MISC/angle_dipole.h b/src/DIPOLE/angle_dipole.h similarity index 82% rename from src/USER-MISC/angle_dipole.h rename to src/DIPOLE/angle_dipole.h index e74947da9e..d94315c5aa 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/DIPOLE/angle_dipole.h @@ -29,12 +29,13 @@ class AngleDipole : public Angle { AngleDipole(class LAMMPS *); virtual ~AngleDipole(); virtual void compute(int, int); - void coeff(int, char **); - double equilibrium_angle(int); - void write_restart(FILE *); - void read_restart(FILE *); - void write_data(FILE *); - double single(int, int, int, int); + virtual void init_style(); + virtual void coeff(int, char **); + virtual double equilibrium_angle(int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_data(FILE *); + virtual double single(int, int, int, int); protected: double *k, *gamma0; diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/DIPOLE/pair_lj_sf_dipole_sf.cpp similarity index 100% rename from src/USER-MISC/pair_lj_sf_dipole_sf.cpp rename to src/DIPOLE/pair_lj_sf_dipole_sf.cpp diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.h b/src/DIPOLE/pair_lj_sf_dipole_sf.h similarity index 100% rename from src/USER-MISC/pair_lj_sf_dipole_sf.h rename to src/DIPOLE/pair_lj_sf_dipole_sf.h diff --git a/src/pair_dpd.cpp b/src/DPD-BASIC/pair_dpd.cpp similarity index 100% rename from src/pair_dpd.cpp rename to src/DPD-BASIC/pair_dpd.cpp diff --git a/src/pair_dpd.h b/src/DPD-BASIC/pair_dpd.h similarity index 100% rename from src/pair_dpd.h rename to src/DPD-BASIC/pair_dpd.h diff --git a/src/USER-MISC/pair_dpd_ext.cpp b/src/DPD-BASIC/pair_dpd_ext.cpp similarity index 100% rename from src/USER-MISC/pair_dpd_ext.cpp rename to src/DPD-BASIC/pair_dpd_ext.cpp diff --git a/src/USER-MISC/pair_dpd_ext.h b/src/DPD-BASIC/pair_dpd_ext.h similarity index 100% rename from src/USER-MISC/pair_dpd_ext.h rename to src/DPD-BASIC/pair_dpd_ext.h diff --git a/src/USER-MISC/pair_dpd_ext_tstat.cpp b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp similarity index 100% rename from src/USER-MISC/pair_dpd_ext_tstat.cpp rename to src/DPD-BASIC/pair_dpd_ext_tstat.cpp diff --git a/src/USER-MISC/pair_dpd_ext_tstat.h b/src/DPD-BASIC/pair_dpd_ext_tstat.h similarity index 100% rename from src/USER-MISC/pair_dpd_ext_tstat.h rename to src/DPD-BASIC/pair_dpd_ext_tstat.h diff --git a/src/pair_dpd_tstat.cpp b/src/DPD-BASIC/pair_dpd_tstat.cpp similarity index 100% rename from src/pair_dpd_tstat.cpp rename to src/DPD-BASIC/pair_dpd_tstat.cpp diff --git a/src/pair_dpd_tstat.h b/src/DPD-BASIC/pair_dpd_tstat.h similarity index 100% rename from src/pair_dpd_tstat.h rename to src/DPD-BASIC/pair_dpd_tstat.h diff --git a/src/USER-MESODPD/README b/src/DPD-MESO/README similarity index 98% rename from src/USER-MESODPD/README rename to src/DPD-MESO/README index 0119fdb9f8..c2d4904808 100644 --- a/src/USER-MESODPD/README +++ b/src/DPD-MESO/README @@ -43,7 +43,7 @@ started. At the bottom of the doc pages are many links to additional documentation contained in the doc/USER/meso directory. There are example scripts for using this package in -examples/USER/meso. +examples/PACKAGES/meso. The person who created this package is Zhen Li (zhen_li at brown.edu) at Division of Applied Mathematics, Brown University, USA. Contact him diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/DPD-MESO/atom_vec_edpd.cpp similarity index 100% rename from src/USER-MESODPD/atom_vec_edpd.cpp rename to src/DPD-MESO/atom_vec_edpd.cpp diff --git a/src/USER-MESODPD/atom_vec_edpd.h b/src/DPD-MESO/atom_vec_edpd.h similarity index 100% rename from src/USER-MESODPD/atom_vec_edpd.h rename to src/DPD-MESO/atom_vec_edpd.h diff --git a/src/USER-MESODPD/atom_vec_mdpd.cpp b/src/DPD-MESO/atom_vec_mdpd.cpp similarity index 100% rename from src/USER-MESODPD/atom_vec_mdpd.cpp rename to src/DPD-MESO/atom_vec_mdpd.cpp diff --git a/src/USER-MESODPD/atom_vec_mdpd.h b/src/DPD-MESO/atom_vec_mdpd.h similarity index 100% rename from src/USER-MESODPD/atom_vec_mdpd.h rename to src/DPD-MESO/atom_vec_mdpd.h diff --git a/src/USER-MESODPD/atom_vec_tdpd.cpp b/src/DPD-MESO/atom_vec_tdpd.cpp similarity index 100% rename from src/USER-MESODPD/atom_vec_tdpd.cpp rename to src/DPD-MESO/atom_vec_tdpd.cpp diff --git a/src/USER-MESODPD/atom_vec_tdpd.h b/src/DPD-MESO/atom_vec_tdpd.h similarity index 100% rename from src/USER-MESODPD/atom_vec_tdpd.h rename to src/DPD-MESO/atom_vec_tdpd.h diff --git a/src/USER-MESODPD/compute_edpd_temp_atom.cpp b/src/DPD-MESO/compute_edpd_temp_atom.cpp similarity index 100% rename from src/USER-MESODPD/compute_edpd_temp_atom.cpp rename to src/DPD-MESO/compute_edpd_temp_atom.cpp diff --git a/src/USER-MESODPD/compute_edpd_temp_atom.h b/src/DPD-MESO/compute_edpd_temp_atom.h similarity index 100% rename from src/USER-MESODPD/compute_edpd_temp_atom.h rename to src/DPD-MESO/compute_edpd_temp_atom.h diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp b/src/DPD-MESO/compute_tdpd_cc_atom.cpp similarity index 100% rename from src/USER-MESODPD/compute_tdpd_cc_atom.cpp rename to src/DPD-MESO/compute_tdpd_cc_atom.cpp diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.h b/src/DPD-MESO/compute_tdpd_cc_atom.h similarity index 100% rename from src/USER-MESODPD/compute_tdpd_cc_atom.h rename to src/DPD-MESO/compute_tdpd_cc_atom.h diff --git a/src/USER-MESODPD/fix_edpd_source.cpp b/src/DPD-MESO/fix_edpd_source.cpp similarity index 100% rename from src/USER-MESODPD/fix_edpd_source.cpp rename to src/DPD-MESO/fix_edpd_source.cpp diff --git a/src/USER-MESODPD/fix_edpd_source.h b/src/DPD-MESO/fix_edpd_source.h similarity index 100% rename from src/USER-MESODPD/fix_edpd_source.h rename to src/DPD-MESO/fix_edpd_source.h diff --git a/src/USER-MESODPD/fix_mvv_dpd.cpp b/src/DPD-MESO/fix_mvv_dpd.cpp similarity index 100% rename from src/USER-MESODPD/fix_mvv_dpd.cpp rename to src/DPD-MESO/fix_mvv_dpd.cpp diff --git a/src/USER-MESODPD/fix_mvv_dpd.h b/src/DPD-MESO/fix_mvv_dpd.h similarity index 100% rename from src/USER-MESODPD/fix_mvv_dpd.h rename to src/DPD-MESO/fix_mvv_dpd.h diff --git a/src/USER-MESODPD/fix_mvv_edpd.cpp b/src/DPD-MESO/fix_mvv_edpd.cpp similarity index 100% rename from src/USER-MESODPD/fix_mvv_edpd.cpp rename to src/DPD-MESO/fix_mvv_edpd.cpp diff --git a/src/USER-MESODPD/fix_mvv_edpd.h b/src/DPD-MESO/fix_mvv_edpd.h similarity index 100% rename from src/USER-MESODPD/fix_mvv_edpd.h rename to src/DPD-MESO/fix_mvv_edpd.h diff --git a/src/USER-MESODPD/fix_mvv_tdpd.cpp b/src/DPD-MESO/fix_mvv_tdpd.cpp similarity index 100% rename from src/USER-MESODPD/fix_mvv_tdpd.cpp rename to src/DPD-MESO/fix_mvv_tdpd.cpp diff --git a/src/USER-MESODPD/fix_mvv_tdpd.h b/src/DPD-MESO/fix_mvv_tdpd.h similarity index 100% rename from src/USER-MESODPD/fix_mvv_tdpd.h rename to src/DPD-MESO/fix_mvv_tdpd.h diff --git a/src/USER-MESODPD/fix_tdpd_source.cpp b/src/DPD-MESO/fix_tdpd_source.cpp similarity index 100% rename from src/USER-MESODPD/fix_tdpd_source.cpp rename to src/DPD-MESO/fix_tdpd_source.cpp diff --git a/src/USER-MESODPD/fix_tdpd_source.h b/src/DPD-MESO/fix_tdpd_source.h similarity index 100% rename from src/USER-MESODPD/fix_tdpd_source.h rename to src/DPD-MESO/fix_tdpd_source.h diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/DPD-MESO/pair_edpd.cpp similarity index 100% rename from src/USER-MESODPD/pair_edpd.cpp rename to src/DPD-MESO/pair_edpd.cpp diff --git a/src/USER-MESODPD/pair_edpd.h b/src/DPD-MESO/pair_edpd.h similarity index 100% rename from src/USER-MESODPD/pair_edpd.h rename to src/DPD-MESO/pair_edpd.h diff --git a/src/USER-MESODPD/pair_mdpd.cpp b/src/DPD-MESO/pair_mdpd.cpp similarity index 100% rename from src/USER-MESODPD/pair_mdpd.cpp rename to src/DPD-MESO/pair_mdpd.cpp diff --git a/src/USER-MESODPD/pair_mdpd.h b/src/DPD-MESO/pair_mdpd.h similarity index 100% rename from src/USER-MESODPD/pair_mdpd.h rename to src/DPD-MESO/pair_mdpd.h diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/DPD-MESO/pair_mdpd_rhosum.cpp similarity index 100% rename from src/USER-MESODPD/pair_mdpd_rhosum.cpp rename to src/DPD-MESO/pair_mdpd_rhosum.cpp diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.h b/src/DPD-MESO/pair_mdpd_rhosum.h similarity index 100% rename from src/USER-MESODPD/pair_mdpd_rhosum.h rename to src/DPD-MESO/pair_mdpd_rhosum.h diff --git a/src/USER-MESODPD/pair_tdpd.cpp b/src/DPD-MESO/pair_tdpd.cpp similarity index 100% rename from src/USER-MESODPD/pair_tdpd.cpp rename to src/DPD-MESO/pair_tdpd.cpp diff --git a/src/USER-MESODPD/pair_tdpd.h b/src/DPD-MESO/pair_tdpd.h similarity index 100% rename from src/USER-MESODPD/pair_tdpd.h rename to src/DPD-MESO/pair_tdpd.h diff --git a/src/USER-DPD/README b/src/DPD-REACT/README similarity index 94% rename from src/USER-DPD/README rename to src/DPD-REACT/README index ef895bef2a..c79a2455b0 100644 --- a/src/USER-DPD/README +++ b/src/DPD-REACT/README @@ -27,7 +27,7 @@ dpd/conservative" and "pair dpd/fdt" and "pair dpd/fdt/energy" commands to get started. At the bottom of the doc page are many links to additional documentation contained in the doc/USER/dpd directory. -There are example scripts for using this package in examples/USER/dpd. +There are example scripts for using this package in examples/PACKAGES/dpd-react. The primary people who created this package are James Larentzos (james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/DPD-REACT/atom_vec_dpd.cpp similarity index 100% rename from src/USER-DPD/atom_vec_dpd.cpp rename to src/DPD-REACT/atom_vec_dpd.cpp diff --git a/src/USER-DPD/atom_vec_dpd.h b/src/DPD-REACT/atom_vec_dpd.h similarity index 100% rename from src/USER-DPD/atom_vec_dpd.h rename to src/DPD-REACT/atom_vec_dpd.h diff --git a/src/USER-DPD/compute_dpd.cpp b/src/DPD-REACT/compute_dpd.cpp similarity index 100% rename from src/USER-DPD/compute_dpd.cpp rename to src/DPD-REACT/compute_dpd.cpp diff --git a/src/USER-DPD/compute_dpd.h b/src/DPD-REACT/compute_dpd.h similarity index 100% rename from src/USER-DPD/compute_dpd.h rename to src/DPD-REACT/compute_dpd.h diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/DPD-REACT/compute_dpd_atom.cpp similarity index 100% rename from src/USER-DPD/compute_dpd_atom.cpp rename to src/DPD-REACT/compute_dpd_atom.cpp diff --git a/src/USER-DPD/compute_dpd_atom.h b/src/DPD-REACT/compute_dpd_atom.h similarity index 100% rename from src/USER-DPD/compute_dpd_atom.h rename to src/DPD-REACT/compute_dpd_atom.h diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/DPD-REACT/fix_dpd_energy.cpp similarity index 100% rename from src/USER-DPD/fix_dpd_energy.cpp rename to src/DPD-REACT/fix_dpd_energy.cpp diff --git a/src/USER-DPD/fix_dpd_energy.h b/src/DPD-REACT/fix_dpd_energy.h similarity index 100% rename from src/USER-DPD/fix_dpd_energy.h rename to src/DPD-REACT/fix_dpd_energy.h diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/DPD-REACT/fix_eos_cv.cpp similarity index 100% rename from src/USER-DPD/fix_eos_cv.cpp rename to src/DPD-REACT/fix_eos_cv.cpp diff --git a/src/USER-DPD/fix_eos_cv.h b/src/DPD-REACT/fix_eos_cv.h similarity index 100% rename from src/USER-DPD/fix_eos_cv.h rename to src/DPD-REACT/fix_eos_cv.h diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/DPD-REACT/fix_eos_table.cpp similarity index 100% rename from src/USER-DPD/fix_eos_table.cpp rename to src/DPD-REACT/fix_eos_table.cpp diff --git a/src/USER-DPD/fix_eos_table.h b/src/DPD-REACT/fix_eos_table.h similarity index 100% rename from src/USER-DPD/fix_eos_table.h rename to src/DPD-REACT/fix_eos_table.h diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/DPD-REACT/fix_eos_table_rx.cpp similarity index 100% rename from src/USER-DPD/fix_eos_table_rx.cpp rename to src/DPD-REACT/fix_eos_table_rx.cpp diff --git a/src/USER-DPD/fix_eos_table_rx.h b/src/DPD-REACT/fix_eos_table_rx.h similarity index 100% rename from src/USER-DPD/fix_eos_table_rx.h rename to src/DPD-REACT/fix_eos_table_rx.h diff --git a/src/USER-DPD/fix_rx.cpp b/src/DPD-REACT/fix_rx.cpp similarity index 99% rename from src/USER-DPD/fix_rx.cpp rename to src/DPD-REACT/fix_rx.cpp index 52dcaaf2d5..e50e145853 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/DPD-REACT/fix_rx.cpp @@ -18,6 +18,7 @@ #include "comm.h" #include "domain.h" #include "error.h" +#include "fix_property_atom.h" #include "force.h" #include "group.h" #include "math_special.h" @@ -344,12 +345,9 @@ void FixRX::post_constructor() newcmd1 += " ghost yes"; newcmd2 += " ghost yes"; - modify->add_fix(newcmd1); - fix_species = (FixPropertyAtom *) modify->fix[modify->nfix-1]; - restartFlag = modify->fix[modify->nfix-1]->restart_reset; - - modify->add_fix(newcmd2); - fix_species_old = (FixPropertyAtom *) modify->fix[modify->nfix-1]; + fix_species = (FixPropertyAtom *) modify->add_fix(newcmd1); + restartFlag = fix_species->restart_reset; + fix_species_old = (FixPropertyAtom *) modify->add_fix(newcmd2); if (nspecies==0) error->all(FLERR,"There are no rx species specified."); diff --git a/src/USER-DPD/fix_rx.h b/src/DPD-REACT/fix_rx.h similarity index 99% rename from src/USER-DPD/fix_rx.h rename to src/DPD-REACT/fix_rx.h index debf4d911e..1d65c4c09e 100644 --- a/src/USER-DPD/fix_rx.h +++ b/src/DPD-REACT/fix_rx.h @@ -136,7 +136,7 @@ class FixRX : public Fix { //!< ODE Solver diagnostics. void odeDiagnostics(void); - private: + protected: char *kineticsFile; char *id_fix_species, *id_fix_species_old; class FixPropertyAtom *fix_species, *fix_species_old; diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/DPD-REACT/fix_shardlow.cpp similarity index 99% rename from src/USER-DPD/fix_shardlow.cpp rename to src/DPD-REACT/fix_shardlow.cpp index 0881edd468..65fa14daeb 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/DPD-REACT/fix_shardlow.cpp @@ -158,7 +158,7 @@ void FixShardlow::setup(int /*vflag*/) for (int i = 0; i < modify->nfix; i++) if (strstr(modify->fix[i]->style,"nvt") || strstr(modify->fix[i]->style,"npt") || strstr(modify->fix[i]->style,"gle") || strstr(modify->fix[i]->style,"gld")) - error->all(FLERR,"Cannot use constant temperature integration routines with USER-DPD."); + error->all(FLERR,"Cannot use constant temperature integration routines with DPD-REACT."); for (int i = 0; i < modify->nfix; i++) { if (utils::strmatch(modify->fix[i]->style,"^shardlow")) fixShardlow = true; diff --git a/src/USER-DPD/fix_shardlow.h b/src/DPD-REACT/fix_shardlow.h similarity index 100% rename from src/USER-DPD/fix_shardlow.h rename to src/DPD-REACT/fix_shardlow.h diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/DPD-REACT/nbin_ssa.cpp similarity index 100% rename from src/USER-DPD/nbin_ssa.cpp rename to src/DPD-REACT/nbin_ssa.cpp diff --git a/src/USER-DPD/nbin_ssa.h b/src/DPD-REACT/nbin_ssa.h similarity index 100% rename from src/USER-DPD/nbin_ssa.h rename to src/DPD-REACT/nbin_ssa.h diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/DPD-REACT/npair_half_bin_newton_ssa.cpp similarity index 100% rename from src/USER-DPD/npair_half_bin_newton_ssa.cpp rename to src/DPD-REACT/npair_half_bin_newton_ssa.cpp diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.h b/src/DPD-REACT/npair_half_bin_newton_ssa.h similarity index 100% rename from src/USER-DPD/npair_half_bin_newton_ssa.h rename to src/DPD-REACT/npair_half_bin_newton_ssa.h diff --git a/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp b/src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp similarity index 100% rename from src/USER-DPD/nstencil_half_bin_2d_ssa.cpp rename to src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp diff --git a/src/USER-DPD/nstencil_half_bin_2d_ssa.h b/src/DPD-REACT/nstencil_half_bin_2d_ssa.h similarity index 100% rename from src/USER-DPD/nstencil_half_bin_2d_ssa.h rename to src/DPD-REACT/nstencil_half_bin_2d_ssa.h diff --git a/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp b/src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp similarity index 100% rename from src/USER-DPD/nstencil_half_bin_3d_ssa.cpp rename to src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp diff --git a/src/USER-DPD/nstencil_half_bin_3d_ssa.h b/src/DPD-REACT/nstencil_half_bin_3d_ssa.h similarity index 100% rename from src/USER-DPD/nstencil_half_bin_3d_ssa.h rename to src/DPD-REACT/nstencil_half_bin_3d_ssa.h diff --git a/src/USER-DPD/nstencil_ssa.h b/src/DPD-REACT/nstencil_ssa.h similarity index 100% rename from src/USER-DPD/nstencil_ssa.h rename to src/DPD-REACT/nstencil_ssa.h diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/DPD-REACT/pair_dpd_fdt.cpp similarity index 100% rename from src/USER-DPD/pair_dpd_fdt.cpp rename to src/DPD-REACT/pair_dpd_fdt.cpp diff --git a/src/USER-DPD/pair_dpd_fdt.h b/src/DPD-REACT/pair_dpd_fdt.h similarity index 100% rename from src/USER-DPD/pair_dpd_fdt.h rename to src/DPD-REACT/pair_dpd_fdt.h diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/DPD-REACT/pair_dpd_fdt_energy.cpp similarity index 100% rename from src/USER-DPD/pair_dpd_fdt_energy.cpp rename to src/DPD-REACT/pair_dpd_fdt_energy.cpp diff --git a/src/USER-DPD/pair_dpd_fdt_energy.h b/src/DPD-REACT/pair_dpd_fdt_energy.h similarity index 100% rename from src/USER-DPD/pair_dpd_fdt_energy.h rename to src/DPD-REACT/pair_dpd_fdt_energy.h diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/DPD-REACT/pair_exp6_rx.cpp similarity index 99% rename from src/USER-DPD/pair_exp6_rx.cpp rename to src/DPD-REACT/pair_exp6_rx.cpp index f5adfac7a1..8240cb88b7 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/DPD-REACT/pair_exp6_rx.cpp @@ -617,8 +617,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site1,"1fluid") == 0) isite1 = oneFluidApproxParameter; - else - { + else { int isp; for (isp = 0; isp < nspecies; isp++) if (strcmp(site1, &atom->dname[isp][0]) == 0) break; @@ -631,8 +630,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site2,"1fluid") == 0) isite2 = oneFluidApproxParameter; - else - { + else { int isp; for (isp = 0; isp < nspecies; isp++) if (strcmp(site2, &atom->dname[isp][0]) == 0) break; @@ -644,8 +642,7 @@ void PairExp6rx::coeff(int narg, char **arg) } // Set the interaction potential type to the enumerated type. - for (int iparam = 0; iparam < nparams; ++iparam) - { + for (int iparam = 0; iparam < nparams; ++iparam) { if (strcmp( params[iparam].potential, "exp6") == 0) params[iparam].potentialType = exp6PotentialType; else @@ -663,7 +660,6 @@ void PairExp6rx::coeff(int narg, char **arg) scalingFlag = EXPONENT; exponentR = utils::numeric(FLERR,arg[6],false,lmp); exponentEpsilon = utils::numeric(FLERR,arg[7],false,lmp); - if (narg > 9) error->all(FLERR,"Incorrect args for pair coefficients"); if (narg == 9) cut_one = utils::numeric(FLERR,arg[8],false,lmp); } else if (strcmp(arg[5],"polynomial") == 0) { scalingFlag = POLYNOMIAL; diff --git a/src/USER-DPD/pair_exp6_rx.h b/src/DPD-REACT/pair_exp6_rx.h similarity index 100% rename from src/USER-DPD/pair_exp6_rx.h rename to src/DPD-REACT/pair_exp6_rx.h diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/DPD-REACT/pair_multi_lucy.cpp similarity index 100% rename from src/USER-DPD/pair_multi_lucy.cpp rename to src/DPD-REACT/pair_multi_lucy.cpp diff --git a/src/USER-DPD/pair_multi_lucy.h b/src/DPD-REACT/pair_multi_lucy.h similarity index 100% rename from src/USER-DPD/pair_multi_lucy.h rename to src/DPD-REACT/pair_multi_lucy.h diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/DPD-REACT/pair_multi_lucy_rx.cpp similarity index 100% rename from src/USER-DPD/pair_multi_lucy_rx.cpp rename to src/DPD-REACT/pair_multi_lucy_rx.cpp diff --git a/src/USER-DPD/pair_multi_lucy_rx.h b/src/DPD-REACT/pair_multi_lucy_rx.h similarity index 100% rename from src/USER-DPD/pair_multi_lucy_rx.h rename to src/DPD-REACT/pair_multi_lucy_rx.h diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/DPD-REACT/pair_table_rx.cpp similarity index 100% rename from src/USER-DPD/pair_table_rx.cpp rename to src/DPD-REACT/pair_table_rx.cpp diff --git a/src/USER-DPD/pair_table_rx.h b/src/DPD-REACT/pair_table_rx.h similarity index 100% rename from src/USER-DPD/pair_table_rx.h rename to src/DPD-REACT/pair_table_rx.h diff --git a/src/USER-DPD/random_external_state.h b/src/DPD-REACT/random_external_state.h similarity index 100% rename from src/USER-DPD/random_external_state.h rename to src/DPD-REACT/random_external_state.h diff --git a/src/USER-SDPD/Install.sh b/src/DPD-SMOOTH/Install.sh similarity index 100% rename from src/USER-SDPD/Install.sh rename to src/DPD-SMOOTH/Install.sh diff --git a/src/USER-SDPD/README b/src/DPD-SMOOTH/README similarity index 100% rename from src/USER-SDPD/README rename to src/DPD-SMOOTH/README diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/DPD-SMOOTH/fix_meso_move.cpp similarity index 99% rename from src/USER-SDPD/fix_meso_move.cpp rename to src/DPD-SMOOTH/fix_meso_move.cpp index 220019ea98..85eee5ffbe 100644 --- a/src/USER-SDPD/fix_meso_move.cpp +++ b/src/DPD-SMOOTH/fix_meso_move.cpp @@ -68,7 +68,7 @@ FixMesoMove::FixMesoMove (LAMMPS *lmp, int narg, char **arg) : // parse args - int iarg; + int iarg = narg; if (strcmp(arg[3],"linear") == 0) { if (narg < 7) error->all(FLERR,"Illegal fix meso/move command"); diff --git a/src/USER-SDPD/fix_meso_move.h b/src/DPD-SMOOTH/fix_meso_move.h similarity index 100% rename from src/USER-SDPD/fix_meso_move.h rename to src/DPD-SMOOTH/fix_meso_move.h diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/DPD-SMOOTH/fix_rigid_meso.cpp similarity index 100% rename from src/USER-SDPD/fix_rigid_meso.cpp rename to src/DPD-SMOOTH/fix_rigid_meso.cpp diff --git a/src/USER-SDPD/fix_rigid_meso.h b/src/DPD-SMOOTH/fix_rigid_meso.h similarity index 100% rename from src/USER-SDPD/fix_rigid_meso.h rename to src/DPD-SMOOTH/fix_rigid_meso.h diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp similarity index 100% rename from src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp rename to src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h similarity index 100% rename from src/USER-SDPD/pair_sdpd_taitwater_isothermal.h rename to src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h diff --git a/src/USER-DRUDE/README b/src/DRUDE/README similarity index 92% rename from src/USER-DRUDE/README rename to src/DRUDE/README index 540e74279e..e6ee049a99 100644 --- a/src/USER-DRUDE/README +++ b/src/DRUDE/README @@ -13,7 +13,7 @@ See the file doc/drude_tutorial.html for getting started. There are auxiliary tools for using this package in tools/drude. -There are example scripts for using this package in examples/USER/drude. +There are example scripts for using this package in examples/PACKAGES/drude. The person who created this package is Alain Dequidt at the Chemistry Institute of Clermont-Ferrand, Clermont University, France diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/DRUDE/compute_temp_drude.cpp similarity index 100% rename from src/USER-DRUDE/compute_temp_drude.cpp rename to src/DRUDE/compute_temp_drude.cpp diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/DRUDE/compute_temp_drude.h similarity index 100% rename from src/USER-DRUDE/compute_temp_drude.h rename to src/DRUDE/compute_temp_drude.h diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/DRUDE/fix_drude.cpp similarity index 94% rename from src/USER-DRUDE/fix_drude.cpp rename to src/DRUDE/fix_drude.cpp index 1856b5455c..e0b313c35e 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/DRUDE/fix_drude.cpp @@ -14,16 +14,16 @@ #include "fix_drude.h" -#include -#include #include "atom.h" +#include "atom_vec.h" #include "comm.h" -#include "modify.h" #include "error.h" #include "memory.h" +#include "modify.h" #include "molecule.h" -#include "atom_vec.h" +#include +#include #include #include @@ -311,20 +311,17 @@ void FixDrude::rebuild_special() { //build_drudeid(); // Log info - if (comm->me == 0) { - if (screen) fprintf(screen, "Rebuild special list taking Drude particles into account\n"); - if (logfile) fprintf(logfile, "Rebuild special list taking Drude particles into account\n"); - } + if (comm->me == 0) + utils::logmesg(lmp, "Rebuild special list taking Drude particles into account\n"); + int nspecmax, nspecmax_old, nspecmax_loc; nspecmax_loc = 0; for (int i=0; ime == 0) { - if (screen) fprintf(screen, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old); - if (logfile) fprintf(logfile, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old); - } + if (comm->me == 0) + utils::logmesg(lmp, "Old max number of 1-2 to 1-4 neighbors: {}\n", nspecmax_old); // Build lists of drude and core-drude pairs std::vector drude_vec, core_drude_vec, core_special_vec; @@ -351,15 +348,11 @@ void FixDrude::rebuild_special() { if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2]; } MPI_Allreduce(&nspecmax_loc, &nspecmax, 1, MPI_INT, MPI_MAX, world); - if (comm->me == 0) { - if (screen) fprintf(screen, "New max number of 1-2 to 1-4 neighbors: %d (+%d)\n", nspecmax, nspecmax - nspecmax_old); - if (logfile) fprintf(logfile, "New max number of 1-2 to 1-4 neighbors: %d (+%d)\n", nspecmax, nspecmax - nspecmax_old); - } - if (atom->maxspecial < nspecmax) { - char str[1024]; - sprintf(str, "Not enough space in special: extra/special/per/atom should be at least %d", nspecmax - nspecmax_old); - error->all(FLERR, str); - } + if (comm->me == 0) + utils::logmesg(lmp, "New max number of 1-2 to 1-4 neighbors: {} (+{})\n", nspecmax, nspecmax - nspecmax_old); + + if (atom->maxspecial < nspecmax) + error->all(FLERR, "Not enough space in special: extra/special/per/atom should be at least {}", nspecmax - nspecmax_old); // Build list of cores' special lists to communicate to ghost drude particles for (int i=0; ime == 0) { - char str[128]; - sprintf(str,"Too many neighbors in CNP for %d atoms",nerrorall); - error->warning(FLERR,str); - } + if (nerrorall && comm->me == 0) + error->warning(FLERR,"Too many neighbors in CNP for {} atoms",nerrorall); // compute CNP value for each atom in group // only performed if # of nearest neighbors = 12 or 14 (fcc,hcp) @@ -311,11 +308,8 @@ void ComputeCNPAtom::compute_peratom() // warning message MPI_Allreduce(&nerror,&nerrorall,1,MPI_INT,MPI_SUM,world); - if (nerrorall && comm->me == 0) { - char str[128]; - sprintf(str,"Too many common neighbors in CNP %d times",nerrorall); - error->warning(FLERR,str); - } + if (nerrorall && comm->me == 0) + error->warning(FLERR,"Too many common neighbors in CNP {} times",nerrorall); } /* ---------------------------------------------------------------------- diff --git a/src/USER-MISC/compute_cnp_atom.h b/src/EXTRA-COMPUTE/compute_cnp_atom.h similarity index 100% rename from src/USER-MISC/compute_cnp_atom.h rename to src/EXTRA-COMPUTE/compute_cnp_atom.h diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/EXTRA-COMPUTE/compute_entropy_atom.cpp similarity index 100% rename from src/USER-MISC/compute_entropy_atom.cpp rename to src/EXTRA-COMPUTE/compute_entropy_atom.cpp diff --git a/src/USER-MISC/compute_entropy_atom.h b/src/EXTRA-COMPUTE/compute_entropy_atom.h similarity index 100% rename from src/USER-MISC/compute_entropy_atom.h rename to src/EXTRA-COMPUTE/compute_entropy_atom.h diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/EXTRA-COMPUTE/compute_gyration_shape.cpp similarity index 97% rename from src/USER-MISC/compute_gyration_shape.cpp rename to src/EXTRA-COMPUTE/compute_gyration_shape.cpp index d64594d219..47c94ac48d 100644 --- a/src/USER-MISC/compute_gyration_shape.cpp +++ b/src/EXTRA-COMPUTE/compute_gyration_shape.cpp @@ -92,8 +92,8 @@ void ComputeGyrationShape::compute_vector() ione[1][1] = gyration_tensor[1]; ione[2][2] = gyration_tensor[2]; ione[0][1] = ione[1][0] = gyration_tensor[3]; - ione[1][2] = ione[2][1] = gyration_tensor[4]; - ione[0][2] = ione[2][0] = gyration_tensor[5]; + ione[0][2] = ione[2][0] = gyration_tensor[4]; + ione[1][2] = ione[2][1] = gyration_tensor[5]; int ierror = MathEigen::jacobi3(ione,evalues,evectors); if (ierror) error->all(FLERR, "Insufficient Jacobi rotations " diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/EXTRA-COMPUTE/compute_gyration_shape.h similarity index 100% rename from src/USER-MISC/compute_gyration_shape.h rename to src/EXTRA-COMPUTE/compute_gyration_shape.h diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp similarity index 100% rename from src/USER-MISC/compute_gyration_shape_chunk.cpp rename to src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp diff --git a/src/USER-MISC/compute_gyration_shape_chunk.h b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h similarity index 100% rename from src/USER-MISC/compute_gyration_shape_chunk.h rename to src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h diff --git a/src/compute_hexorder_atom.cpp b/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp similarity index 100% rename from src/compute_hexorder_atom.cpp rename to src/EXTRA-COMPUTE/compute_hexorder_atom.cpp diff --git a/src/compute_hexorder_atom.h b/src/EXTRA-COMPUTE/compute_hexorder_atom.h similarity index 100% rename from src/compute_hexorder_atom.h rename to src/EXTRA-COMPUTE/compute_hexorder_atom.h diff --git a/src/USER-MISC/compute_hma.cpp b/src/EXTRA-COMPUTE/compute_hma.cpp similarity index 95% rename from src/USER-MISC/compute_hma.cpp rename to src/EXTRA-COMPUTE/compute_hma.cpp index b74280a8e5..043dcec6cf 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/EXTRA-COMPUTE/compute_hma.cpp @@ -91,9 +91,8 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : // our new fix's group = same as compute group id_fix = utils::strdup(std::string(id)+"_COMPUTE_STORE"); - modify->add_fix(fmt::format("{} {} STORE peratom 1 3", - id_fix, group->names[igroup])); - fix = (FixStore *) modify->fix[modify->nfix-1]; + fix = (FixStore *)modify->add_fix(fmt::format("{} {} STORE peratom 1 3", + id_fix, group->names[igroup])); // calculate xu,yu,zu for fix store array // skip if reset from restart file @@ -116,7 +115,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : computeU = computeP = computeCv = -1; returnAnharmonic = 0; size_vector = 0; - memory->create(extlist, 3, "hma:extlist"); + extlist = new int[3]; for (int iarg=4; iarg-1) continue; @@ -145,20 +144,11 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : } } - if (size_vector == 0) { - error->all(FLERR,"Illegal compute hma command"); - } - if (size_vector<3) { - memory->grow(extlist, size_vector, "hma:extlist"); - } - memory->create(vector, size_vector, "hma:vector"); + if (size_vector == 0) error->all(FLERR,"Illegal compute hma command"); + vector = new double[size_vector]; - if (computeU>-1 || computeCv>-1) { - peflag = 1; - } - if (computeP>-1) { - pressflag = 1; - } + if (computeU>-1 || computeCv>-1) peflag = 1; + if (computeP>-1) pressflag = 1; nmax = 0; } @@ -170,10 +160,11 @@ ComputeHMA::~ComputeHMA() // check nfix in case all fixes have already been deleted if (modify->nfix) modify->delete_fix(id_fix); - delete [] id_fix; - delete [] id_temp; - memory->destroy(extlist); - memory->destroy(vector); + delete[] id_fix; + delete[] id_temp; + delete[] extlist; + delete[] vector; + memory->destroy(deltaR); } diff --git a/src/USER-MISC/compute_hma.h b/src/EXTRA-COMPUTE/compute_hma.h similarity index 100% rename from src/USER-MISC/compute_hma.h rename to src/EXTRA-COMPUTE/compute_hma.h diff --git a/src/USER-MISC/compute_momentum.cpp b/src/EXTRA-COMPUTE/compute_momentum.cpp similarity index 100% rename from src/USER-MISC/compute_momentum.cpp rename to src/EXTRA-COMPUTE/compute_momentum.cpp diff --git a/src/USER-MISC/compute_momentum.h b/src/EXTRA-COMPUTE/compute_momentum.h similarity index 100% rename from src/USER-MISC/compute_momentum.h rename to src/EXTRA-COMPUTE/compute_momentum.h diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp similarity index 100% rename from src/MISC/compute_msd_nongauss.cpp rename to src/EXTRA-COMPUTE/compute_msd_nongauss.cpp diff --git a/src/MISC/compute_msd_nongauss.h b/src/EXTRA-COMPUTE/compute_msd_nongauss.h similarity index 100% rename from src/MISC/compute_msd_nongauss.h rename to src/EXTRA-COMPUTE/compute_msd_nongauss.h diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/EXTRA-COMPUTE/compute_pressure_cylinder.cpp similarity index 100% rename from src/USER-MISC/compute_pressure_cylinder.cpp rename to src/EXTRA-COMPUTE/compute_pressure_cylinder.cpp diff --git a/src/USER-MISC/compute_pressure_cylinder.h b/src/EXTRA-COMPUTE/compute_pressure_cylinder.h similarity index 100% rename from src/USER-MISC/compute_pressure_cylinder.h rename to src/EXTRA-COMPUTE/compute_pressure_cylinder.h diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp similarity index 100% rename from src/USER-MISC/compute_stress_mop.cpp rename to src/EXTRA-COMPUTE/compute_stress_mop.cpp diff --git a/src/USER-MISC/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h similarity index 100% rename from src/USER-MISC/compute_stress_mop.h rename to src/EXTRA-COMPUTE/compute_stress_mop.h diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp similarity index 100% rename from src/USER-MISC/compute_stress_mop_profile.cpp rename to src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp diff --git a/src/USER-MISC/compute_stress_mop_profile.h b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h similarity index 100% rename from src/USER-MISC/compute_stress_mop_profile.h rename to src/EXTRA-COMPUTE/compute_stress_mop_profile.h diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/EXTRA-COMPUTE/compute_temp_rotate.cpp similarity index 100% rename from src/USER-MISC/compute_temp_rotate.cpp rename to src/EXTRA-COMPUTE/compute_temp_rotate.cpp diff --git a/src/USER-MISC/compute_temp_rotate.h b/src/EXTRA-COMPUTE/compute_temp_rotate.h similarity index 100% rename from src/USER-MISC/compute_temp_rotate.h rename to src/EXTRA-COMPUTE/compute_temp_rotate.h diff --git a/src/MISC/compute_ti.cpp b/src/EXTRA-COMPUTE/compute_ti.cpp similarity index 100% rename from src/MISC/compute_ti.cpp rename to src/EXTRA-COMPUTE/compute_ti.cpp diff --git a/src/MISC/compute_ti.h b/src/EXTRA-COMPUTE/compute_ti.h similarity index 100% rename from src/MISC/compute_ti.h rename to src/EXTRA-COMPUTE/compute_ti.h diff --git a/src/dump_dcd.cpp b/src/EXTRA-DUMP/dump_dcd.cpp similarity index 100% rename from src/dump_dcd.cpp rename to src/EXTRA-DUMP/dump_dcd.cpp diff --git a/src/dump_dcd.h b/src/EXTRA-DUMP/dump_dcd.h similarity index 100% rename from src/dump_dcd.h rename to src/EXTRA-DUMP/dump_dcd.h diff --git a/src/MISC/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp similarity index 100% rename from src/MISC/dump_xtc.cpp rename to src/EXTRA-DUMP/dump_xtc.cpp diff --git a/src/MISC/dump_xtc.h b/src/EXTRA-DUMP/dump_xtc.h similarity index 100% rename from src/MISC/dump_xtc.h rename to src/EXTRA-DUMP/dump_xtc.h diff --git a/src/MISC/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp similarity index 100% rename from src/MISC/xdr_compat.cpp rename to src/EXTRA-DUMP/xdr_compat.cpp diff --git a/src/MISC/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h similarity index 100% rename from src/MISC/xdr_compat.h rename to src/EXTRA-DUMP/xdr_compat.h diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/EXTRA-FIX/fix_addtorque.cpp similarity index 100% rename from src/USER-MISC/fix_addtorque.cpp rename to src/EXTRA-FIX/fix_addtorque.cpp diff --git a/src/USER-MISC/fix_addtorque.h b/src/EXTRA-FIX/fix_addtorque.h similarity index 100% rename from src/USER-MISC/fix_addtorque.h rename to src/EXTRA-FIX/fix_addtorque.h diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/EXTRA-FIX/fix_ave_correlate_long.cpp similarity index 99% rename from src/USER-MISC/fix_ave_correlate_long.cpp rename to src/EXTRA-FIX/fix_ave_correlate_long.cpp index b45823d509..32a304d08f 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/EXTRA-FIX/fix_ave_correlate_long.cpp @@ -145,11 +145,9 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): error->all(FLERR,"Illegal fix ave/correlate/long command"); if (me == 0) { fp = fopen(arg[iarg+1],"w"); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open fix ave/correlate/long file %s",arg[iarg+1]); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open fix ave/correlate/long file {}: {}", + arg[iarg+1],utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"overwrite") == 0) { diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/EXTRA-FIX/fix_ave_correlate_long.h similarity index 100% rename from src/USER-MISC/fix_ave_correlate_long.h rename to src/EXTRA-FIX/fix_ave_correlate_long.h diff --git a/src/fix_controller.cpp b/src/EXTRA-FIX/fix_controller.cpp similarity index 100% rename from src/fix_controller.cpp rename to src/EXTRA-FIX/fix_controller.cpp diff --git a/src/fix_controller.h b/src/EXTRA-FIX/fix_controller.h similarity index 100% rename from src/fix_controller.h rename to src/EXTRA-FIX/fix_controller.h diff --git a/src/fix_drag.cpp b/src/EXTRA-FIX/fix_drag.cpp similarity index 100% rename from src/fix_drag.cpp rename to src/EXTRA-FIX/fix_drag.cpp diff --git a/src/fix_drag.h b/src/EXTRA-FIX/fix_drag.h similarity index 100% rename from src/fix_drag.h rename to src/EXTRA-FIX/fix_drag.h diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/EXTRA-FIX/fix_electron_stopping.cpp similarity index 98% rename from src/USER-MISC/fix_electron_stopping.cpp rename to src/EXTRA-FIX/fix_electron_stopping.cpp index e6aedb014b..bd54fea97d 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/EXTRA-FIX/fix_electron_stopping.cpp @@ -243,11 +243,8 @@ void FixElectronStopping::read_table(const char *file) char line[MAXLINE]; FILE *fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str, 128, "Cannot open stopping range table %s", file); - error->one(FLERR, str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open stopping range table {}: {}", file, utils::getsyserror()); const int ncol = atom->ntypes + 1; diff --git a/src/USER-MISC/fix_electron_stopping.h b/src/EXTRA-FIX/fix_electron_stopping.h similarity index 100% rename from src/USER-MISC/fix_electron_stopping.h rename to src/EXTRA-FIX/fix_electron_stopping.h diff --git a/src/USER-MISC/fix_electron_stopping_fit.cpp b/src/EXTRA-FIX/fix_electron_stopping_fit.cpp similarity index 100% rename from src/USER-MISC/fix_electron_stopping_fit.cpp rename to src/EXTRA-FIX/fix_electron_stopping_fit.cpp diff --git a/src/USER-MISC/fix_electron_stopping_fit.h b/src/EXTRA-FIX/fix_electron_stopping_fit.h similarity index 100% rename from src/USER-MISC/fix_electron_stopping_fit.h rename to src/EXTRA-FIX/fix_electron_stopping_fit.h diff --git a/src/USER-MISC/fix_ffl.cpp b/src/EXTRA-FIX/fix_ffl.cpp similarity index 100% rename from src/USER-MISC/fix_ffl.cpp rename to src/EXTRA-FIX/fix_ffl.cpp diff --git a/src/USER-MISC/fix_ffl.h b/src/EXTRA-FIX/fix_ffl.h similarity index 100% rename from src/USER-MISC/fix_ffl.h rename to src/EXTRA-FIX/fix_ffl.h diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/EXTRA-FIX/fix_filter_corotate.cpp similarity index 100% rename from src/USER-MISC/fix_filter_corotate.cpp rename to src/EXTRA-FIX/fix_filter_corotate.cpp diff --git a/src/USER-MISC/fix_filter_corotate.h b/src/EXTRA-FIX/fix_filter_corotate.h similarity index 100% rename from src/USER-MISC/fix_filter_corotate.h rename to src/EXTRA-FIX/fix_filter_corotate.h diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/EXTRA-FIX/fix_flow_gauss.cpp similarity index 100% rename from src/USER-MISC/fix_flow_gauss.cpp rename to src/EXTRA-FIX/fix_flow_gauss.cpp diff --git a/src/USER-MISC/fix_flow_gauss.h b/src/EXTRA-FIX/fix_flow_gauss.h similarity index 100% rename from src/USER-MISC/fix_flow_gauss.h rename to src/EXTRA-FIX/fix_flow_gauss.h diff --git a/src/MISC/fix_gld.cpp b/src/EXTRA-FIX/fix_gld.cpp similarity index 99% rename from src/MISC/fix_gld.cpp rename to src/EXTRA-FIX/fix_gld.cpp index 34ed43301e..2e30882206 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/EXTRA-FIX/fix_gld.cpp @@ -132,6 +132,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Illegal fix gld command"); } if (strcmp(arg[iarg+1],"no") == 0) { + zeroflag = 0; } else if (strcmp(arg[iarg+1],"yes") == 0) { zeroflag = 1; } else { @@ -144,6 +145,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Illegal fix gld command"); } if (strcmp(arg[iarg+1],"no") == 0) { + freezeflag = 0; } else if (strcmp(arg[iarg+1],"yes") == 0) { freezeflag = 1; for (int i = 0; i < atom->nlocal; i++) { diff --git a/src/MISC/fix_gld.h b/src/EXTRA-FIX/fix_gld.h similarity index 100% rename from src/MISC/fix_gld.h rename to src/EXTRA-FIX/fix_gld.h diff --git a/src/USER-MISC/fix_gle.cpp b/src/EXTRA-FIX/fix_gle.cpp similarity index 97% rename from src/USER-MISC/fix_gle.cpp rename to src/EXTRA-FIX/fix_gle.cpp index 782ea89792..563295d8c1 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/EXTRA-FIX/fix_gle.cpp @@ -19,18 +19,18 @@ #include "fix_gle.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "random_mars.h" +#include "respa.h" +#include "update.h" + #include #include -#include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "comm.h" -#include "random_mars.h" -#include "memory.h" -#include "error.h" - using namespace LAMMPS_NS; using namespace FixConst; @@ -225,13 +225,9 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) : char *fname = arg[7]; if (comm->me == 0) { fgle = utils::open_potential(fname,lmp,nullptr); - if (fgle == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open A-matrix file %s",fname); - error->one(FLERR,str); - } - if (screen) fprintf(screen,"Reading A-matrix from %s\n", fname); - if (logfile) fprintf(logfile,"Reading A-matrix from %s\n", fname); + if (fgle == nullptr) + error->one(FLERR,"Cannot open A-matrix file {}: {}",fname, utils::getsyserror()); + utils::logmesg(lmp,"Reading A-matrix from {}\n", fname); } // read each line of the file, skipping blank lines or leading '#' @@ -295,15 +291,9 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) : } else { if (comm->me == 0) { fgle = utils::open_potential(fname,lmp,nullptr); - if (fgle == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open C-matrix file %s",fname); - error->one(FLERR,str); - } - if (screen) - fprintf(screen,"Reading C-matrix from %s\n", fname); - if (logfile) - fprintf(logfile,"Reading C-matrix from %s\n", fname); + if (fgle == nullptr) + error->one(FLERR,"Cannot open C-matrix file {}: {}",fname, utils::getsyserror()); + utils::logmesg(lmp,"Reading C-matrix from {}\n", fname); } // read each line of the file, skipping blank lines or leading '#' diff --git a/src/USER-MISC/fix_gle.h b/src/EXTRA-FIX/fix_gle.h similarity index 100% rename from src/USER-MISC/fix_gle.h rename to src/EXTRA-FIX/fix_gle.h diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/EXTRA-FIX/fix_momentum_chunk.cpp similarity index 100% rename from src/USER-MISC/fix_momentum_chunk.cpp rename to src/EXTRA-FIX/fix_momentum_chunk.cpp diff --git a/src/USER-MISC/fix_momentum_chunk.h b/src/EXTRA-FIX/fix_momentum_chunk.h similarity index 100% rename from src/USER-MISC/fix_momentum_chunk.h rename to src/EXTRA-FIX/fix_momentum_chunk.h diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/EXTRA-FIX/fix_npt_cauchy.cpp similarity index 99% rename from src/USER-MISC/fix_npt_cauchy.cpp rename to src/EXTRA-FIX/fix_npt_cauchy.cpp index 2390872631..e58632635f 100644 --- a/src/USER-MISC/fix_npt_cauchy.cpp +++ b/src/EXTRA-FIX/fix_npt_cauchy.cpp @@ -671,6 +671,7 @@ int FixNPTCauchy::setmask() mask |= INITIAL_INTEGRATE; mask |= FINAL_INTEGRATE; mask |= INITIAL_INTEGRATE_RESPA; + mask |= PRE_FORCE_RESPA; mask |= FINAL_INTEGRATE_RESPA; if (pre_exchange_flag) mask |= PRE_EXCHANGE; return mask; @@ -1032,7 +1033,12 @@ void FixNPTCauchy::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloo nve_x(); if (pstat_flag) remap(); } +} +/* ---------------------------------------------------------------------- */ + +void FixNPTCauchy::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/) +{ // if barostat, redo KSpace coeffs at outermost level, // since volume has changed diff --git a/src/USER-MISC/fix_npt_cauchy.h b/src/EXTRA-FIX/fix_npt_cauchy.h similarity index 99% rename from src/USER-MISC/fix_npt_cauchy.h rename to src/EXTRA-FIX/fix_npt_cauchy.h index 1348b1bce4..80122ad0ac 100644 --- a/src/USER-MISC/fix_npt_cauchy.h +++ b/src/EXTRA-FIX/fix_npt_cauchy.h @@ -35,6 +35,7 @@ class FixNPTCauchy : public Fix { virtual void initial_integrate(int); virtual void final_integrate(); void initial_integrate_respa(int, int, int); + void pre_force_respa(int, int, int); void final_integrate_respa(int, int); virtual void pre_exchange(); double compute_scalar(); diff --git a/src/fix_numdiff.cpp b/src/EXTRA-FIX/fix_numdiff.cpp similarity index 100% rename from src/fix_numdiff.cpp rename to src/EXTRA-FIX/fix_numdiff.cpp diff --git a/src/fix_numdiff.h b/src/EXTRA-FIX/fix_numdiff.h similarity index 100% rename from src/fix_numdiff.h rename to src/EXTRA-FIX/fix_numdiff.h diff --git a/src/USER-MISC/fix_nvk.cpp b/src/EXTRA-FIX/fix_nvk.cpp similarity index 100% rename from src/USER-MISC/fix_nvk.cpp rename to src/EXTRA-FIX/fix_nvk.cpp diff --git a/src/USER-MISC/fix_nvk.h b/src/EXTRA-FIX/fix_nvk.h similarity index 100% rename from src/USER-MISC/fix_nvk.h rename to src/EXTRA-FIX/fix_nvk.h diff --git a/src/MISC/fix_oneway.cpp b/src/EXTRA-FIX/fix_oneway.cpp similarity index 100% rename from src/MISC/fix_oneway.cpp rename to src/EXTRA-FIX/fix_oneway.cpp diff --git a/src/MISC/fix_oneway.h b/src/EXTRA-FIX/fix_oneway.h similarity index 100% rename from src/MISC/fix_oneway.h rename to src/EXTRA-FIX/fix_oneway.h diff --git a/src/USER-MISC/fix_pafi.cpp b/src/EXTRA-FIX/fix_pafi.cpp similarity index 100% rename from src/USER-MISC/fix_pafi.cpp rename to src/EXTRA-FIX/fix_pafi.cpp diff --git a/src/USER-MISC/fix_pafi.h b/src/EXTRA-FIX/fix_pafi.h similarity index 100% rename from src/USER-MISC/fix_pafi.h rename to src/EXTRA-FIX/fix_pafi.h diff --git a/src/USER-MISC/fix_rhok.cpp b/src/EXTRA-FIX/fix_rhok.cpp similarity index 100% rename from src/USER-MISC/fix_rhok.cpp rename to src/EXTRA-FIX/fix_rhok.cpp diff --git a/src/USER-MISC/fix_rhok.h b/src/EXTRA-FIX/fix_rhok.h similarity index 100% rename from src/USER-MISC/fix_rhok.h rename to src/EXTRA-FIX/fix_rhok.h diff --git a/src/USER-MISC/fix_smd.cpp b/src/EXTRA-FIX/fix_smd.cpp similarity index 100% rename from src/USER-MISC/fix_smd.cpp rename to src/EXTRA-FIX/fix_smd.cpp diff --git a/src/USER-MISC/fix_smd.h b/src/EXTRA-FIX/fix_smd.h similarity index 100% rename from src/USER-MISC/fix_smd.h rename to src/EXTRA-FIX/fix_smd.h diff --git a/src/fix_spring_rg.cpp b/src/EXTRA-FIX/fix_spring_rg.cpp similarity index 100% rename from src/fix_spring_rg.cpp rename to src/EXTRA-FIX/fix_spring_rg.cpp diff --git a/src/fix_spring_rg.h b/src/EXTRA-FIX/fix_spring_rg.h similarity index 100% rename from src/fix_spring_rg.h rename to src/EXTRA-FIX/fix_spring_rg.h diff --git a/src/fix_temp_csld.cpp b/src/EXTRA-FIX/fix_temp_csld.cpp similarity index 100% rename from src/fix_temp_csld.cpp rename to src/EXTRA-FIX/fix_temp_csld.cpp diff --git a/src/fix_temp_csld.h b/src/EXTRA-FIX/fix_temp_csld.h similarity index 100% rename from src/fix_temp_csld.h rename to src/EXTRA-FIX/fix_temp_csld.h diff --git a/src/fix_temp_csvr.cpp b/src/EXTRA-FIX/fix_temp_csvr.cpp similarity index 100% rename from src/fix_temp_csvr.cpp rename to src/EXTRA-FIX/fix_temp_csvr.cpp diff --git a/src/fix_temp_csvr.h b/src/EXTRA-FIX/fix_temp_csvr.h similarity index 100% rename from src/fix_temp_csvr.h rename to src/EXTRA-FIX/fix_temp_csvr.h diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/EXTRA-FIX/fix_ti_spring.cpp similarity index 100% rename from src/USER-MISC/fix_ti_spring.cpp rename to src/EXTRA-FIX/fix_ti_spring.cpp diff --git a/src/USER-MISC/fix_ti_spring.h b/src/EXTRA-FIX/fix_ti_spring.h similarity index 100% rename from src/USER-MISC/fix_ti_spring.h rename to src/EXTRA-FIX/fix_ti_spring.h diff --git a/src/fix_tmd.cpp b/src/EXTRA-FIX/fix_tmd.cpp similarity index 98% rename from src/fix_tmd.cpp rename to src/EXTRA-FIX/fix_tmd.cpp index c8dd39910b..335c1a5e6b 100644 --- a/src/fix_tmd.cpp +++ b/src/EXTRA-FIX/fix_tmd.cpp @@ -75,8 +75,7 @@ nfileevery(0), fp(nullptr), xf(nullptr), xold(nullptr) if (me == 0) { fp = fopen(arg[6],"w"); if (fp == nullptr) - error->one(FLERR,"Cannot open fix tmd file {}: {}", - arg[6], utils::getsyserror()); + error->one(FLERR,"Cannot open fix tmd file {}: {}", arg[6], utils::getsyserror()); fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back", "gamma_forward lambda work_lambda work_analytical"); } @@ -381,7 +380,7 @@ int FixTMD::unpack_exchange(int nlocal, double *buf) void FixTMD::readfile(char *file) { if (me == 0) { - if (screen) fprintf(screen,"Reading TMD target file %s ...\n",file); + utils::logmesg(lmp,"Reading TMD target file {} ...\n",file); open(file); } @@ -541,8 +540,7 @@ void FixTMD::open(char *file) } if (fp == nullptr) - error->one(FLERR,"Cannot open file {}: {}", - file, utils::getsyserror()); + error->one(FLERR,"Cannot open file {}: {}",file, utils::getsyserror()); } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_tmd.h b/src/EXTRA-FIX/fix_tmd.h similarity index 100% rename from src/fix_tmd.h rename to src/EXTRA-FIX/fix_tmd.h diff --git a/src/MISC/fix_ttm.cpp b/src/EXTRA-FIX/fix_ttm.cpp similarity index 100% rename from src/MISC/fix_ttm.cpp rename to src/EXTRA-FIX/fix_ttm.cpp diff --git a/src/MISC/fix_ttm.h b/src/EXTRA-FIX/fix_ttm.h similarity index 100% rename from src/MISC/fix_ttm.h rename to src/EXTRA-FIX/fix_ttm.h diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/EXTRA-FIX/fix_ttm_mod.cpp similarity index 99% rename from src/USER-MISC/fix_ttm_mod.cpp rename to src/EXTRA-FIX/fix_ttm_mod.cpp index 211b2eadb2..7d89d89e6f 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/EXTRA-FIX/fix_ttm_mod.cpp @@ -20,22 +20,21 @@ #include "fix_ttm_mod.h" +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "random_mars.h" +#include "respa.h" +#include "tokenizer.h" +#include "update.h" + #include #include -#include "atom.h" -#include "force.h" -#include "update.h" -#include "domain.h" -#include "respa.h" -#include "comm.h" -#include "random_mars.h" -#include "memory.h" -#include "error.h" -#include "citeme.h" -#include "math_const.h" - - -#include "tokenizer.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -104,11 +103,8 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : if (narg != 11) error->all(FLERR,"Illegal fix ttm/mod command"); if (comm->me == 0) { fp = fopen(arg[10],"w"); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open fix ttm/mod file %s",arg[10]); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open fix ttm/mod file {}: {}",arg[10],utils::getsyserror()); } } diff --git a/src/USER-MISC/fix_ttm_mod.h b/src/EXTRA-FIX/fix_ttm_mod.h similarity index 100% rename from src/USER-MISC/fix_ttm_mod.h rename to src/EXTRA-FIX/fix_ttm_mod.h diff --git a/src/MISC/fix_viscosity.cpp b/src/EXTRA-FIX/fix_viscosity.cpp similarity index 100% rename from src/MISC/fix_viscosity.cpp rename to src/EXTRA-FIX/fix_viscosity.cpp diff --git a/src/MISC/fix_viscosity.h b/src/EXTRA-FIX/fix_viscosity.h similarity index 100% rename from src/MISC/fix_viscosity.h rename to src/EXTRA-FIX/fix_viscosity.h diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/EXTRA-FIX/fix_wall_ees.cpp similarity index 100% rename from src/USER-MISC/fix_wall_ees.cpp rename to src/EXTRA-FIX/fix_wall_ees.cpp diff --git a/src/USER-MISC/fix_wall_ees.h b/src/EXTRA-FIX/fix_wall_ees.h similarity index 100% rename from src/USER-MISC/fix_wall_ees.h rename to src/EXTRA-FIX/fix_wall_ees.h diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp similarity index 100% rename from src/USER-MISC/fix_wall_reflect_stochastic.cpp rename to src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.h b/src/EXTRA-FIX/fix_wall_reflect_stochastic.h similarity index 100% rename from src/USER-MISC/fix_wall_reflect_stochastic.h rename to src/EXTRA-FIX/fix_wall_reflect_stochastic.h diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/EXTRA-FIX/fix_wall_region_ees.cpp similarity index 100% rename from src/USER-MISC/fix_wall_region_ees.cpp rename to src/EXTRA-FIX/fix_wall_region_ees.cpp diff --git a/src/USER-MISC/fix_wall_region_ees.h b/src/EXTRA-FIX/fix_wall_region_ees.h similarity index 100% rename from src/USER-MISC/fix_wall_region_ees.h rename to src/EXTRA-FIX/fix_wall_region_ees.h diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/EXTRA-MOLECULE/angle_cosine_delta.cpp similarity index 100% rename from src/MOLECULE/angle_cosine_delta.cpp rename to src/EXTRA-MOLECULE/angle_cosine_delta.cpp diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/EXTRA-MOLECULE/angle_cosine_delta.h similarity index 100% rename from src/MOLECULE/angle_cosine_delta.h rename to src/EXTRA-MOLECULE/angle_cosine_delta.h diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp similarity index 100% rename from src/MOLECULE/angle_cosine_periodic.cpp rename to src/EXTRA-MOLECULE/angle_cosine_periodic.cpp diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/EXTRA-MOLECULE/angle_cosine_periodic.h similarity index 100% rename from src/MOLECULE/angle_cosine_periodic.h rename to src/EXTRA-MOLECULE/angle_cosine_periodic.h diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp similarity index 100% rename from src/USER-MISC/angle_cosine_shift.cpp rename to src/EXTRA-MOLECULE/angle_cosine_shift.cpp diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/EXTRA-MOLECULE/angle_cosine_shift.h similarity index 100% rename from src/USER-MISC/angle_cosine_shift.h rename to src/EXTRA-MOLECULE/angle_cosine_shift.h diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp similarity index 100% rename from src/USER-MISC/angle_cosine_shift_exp.cpp rename to src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.h similarity index 100% rename from src/USER-MISC/angle_cosine_shift_exp.h rename to src/EXTRA-MOLECULE/angle_cosine_shift_exp.h diff --git a/src/USER-MISC/angle_fourier.cpp b/src/EXTRA-MOLECULE/angle_fourier.cpp similarity index 100% rename from src/USER-MISC/angle_fourier.cpp rename to src/EXTRA-MOLECULE/angle_fourier.cpp diff --git a/src/USER-MISC/angle_fourier.h b/src/EXTRA-MOLECULE/angle_fourier.h similarity index 100% rename from src/USER-MISC/angle_fourier.h rename to src/EXTRA-MOLECULE/angle_fourier.h diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp similarity index 64% rename from src/USER-MISC/angle_fourier_simple.cpp rename to src/EXTRA-MOLECULE/angle_fourier_simple.cpp index d69da70a57..4f76c68281 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,21 +18,21 @@ #include "angle_fourier_simple.h" -#include #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; using namespace MathConst; -#define SMALL 0.001 +#define SMALL 0.0001 /* ---------------------------------------------------------------------- */ @@ -60,14 +59,14 @@ AngleFourierSimple::~AngleFourierSimple() void AngleFourierSimple::compute(int eflag, int vflag) { - int i1,i2,i3,n,type; - double delx1,dely1,delz1,delx2,dely2,delz2; - double eangle,f1[3],f3[3]; - double term,sgn; - double rsq1,rsq2,r1,r2,c,cn,th,nth,a,a11,a12,a22; + int i1, i2, i3, n, type; + double delx1, dely1, delz1, delx2, dely2, delz2; + double eangle, f1[3], f3[3]; + double term, sgn; + double rsq1, rsq2, r1, r2, c, cn, th, nth, a, a11, a12, a22; eangle = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -88,7 +87,7 @@ void AngleFourierSimple::compute(int eflag, int vflag) dely1 = x[i1][1] - x[i2][1]; delz1 = x[i1][2] - x[i2][2]; - rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1; r1 = sqrt(rsq1); // 2nd bond @@ -97,13 +96,13 @@ void AngleFourierSimple::compute(int eflag, int vflag) dely2 = x[i3][1] - x[i2][1]; delz2 = x[i3][2] - x[i2][2]; - rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2; r2 = sqrt(rsq2); // angle (cos and sin) - c = delx1*delx2 + dely1*dely2 + delz1*delz2; - c /= r1*r2; + c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; @@ -111,38 +110,38 @@ void AngleFourierSimple::compute(int eflag, int vflag) // force & energy th = acos(c); - nth = N[type]*acos(c); + nth = N[type] * acos(c); cn = cos(nth); - term = k[type]*(1.0+C[type]*cn); + term = k[type] * (1.0 + C[type] * cn); if (eflag) eangle = term; // handle sin(n th)/sin(th) singulatiries - if (fabs(c)-1.0 > 0.0001) { - a = k[type]*C[type]*N[type]*sin(nth)/sin(th); + if (fabs(c) - 1.0 > SMALL) { + a = k[type] * C[type] * N[type] * sin(nth) / sin(th); } else { if (c >= 0.0) { term = 1.0 - c; sgn = 1.0; } else { term = 1.0 + c; - sgn = ( fmodf((float)(N[type]),2.0) == 0.0f )?-1.0:1.0; + sgn = (fmod(N[type], 2.0) == 0.0) ? -1.0 : 1.0; } - a = N[type]+N[type]*(1.0-N[type]*N[type])*term/3.0; - a = k[type]*C[type]*N[type]*(double)(sgn)*a; + a = N[type] + N[type] * (1.0 - N[type] * N[type]) * term / 3.0; + a = k[type] * C[type] * N[type] * sgn * a; } - a11 = a*c / rsq1; - a12 = -a / (r1*r2); - a22 = a*c / rsq2; + a11 = a * c / rsq1; + a12 = -a / (r1 * r2); + a22 = a * c / rsq2; - f1[0] = a11*delx1 + a12*delx2; - f1[1] = a11*dely1 + a12*dely2; - f1[2] = a11*delz1 + a12*delz2; - f3[0] = a22*delx2 + a12*delx1; - f3[1] = a22*dely2 + a12*dely1; - f3[2] = a22*delz2 + a12*delz1; + f1[0] = a11 * delx1 + a12 * delx2; + f1[1] = a11 * dely1 + a12 * dely2; + f1[2] = a11 * delz1 + a12 * delz2; + f3[0] = a22 * delx2 + a12 * delx1; + f3[1] = a22 * dely2 + a12 * dely1; + f3[2] = a22 * delz2 + a12 * delz1; // apply force to each of 3 atoms @@ -164,8 +163,9 @@ void AngleFourierSimple::compute(int eflag, int vflag) f[i3][2] += f3[2]; } - if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3, - delx1,dely1,delz1,delx2,dely2,delz2); + if (evflag) + ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2, + delz2); } } @@ -176,11 +176,11 @@ void AngleFourierSimple::allocate() allocated = 1; int n = atom->nangletypes; - memory->create(k,n+1,"angle:k"); - memory->create(C,n+1,"angle:C"); - memory->create(N,n+1,"angle:N"); + memory->create(k, n + 1, "angle:k"); + memory->create(C, n + 1, "angle:C"); + memory->create(N, n + 1, "angle:N"); - memory->create(setflag,n+1,"angle:setflag"); + memory->create(setflag, n + 1, "angle:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; } @@ -190,15 +190,15 @@ void AngleFourierSimple::allocate() void AngleFourierSimple::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for angle coefficients"); if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error); - double k_one = utils::numeric(FLERR,arg[1],false,lmp); - double C_one = utils::numeric(FLERR,arg[2],false,lmp); - double N_one = utils::numeric(FLERR,arg[3],false,lmp); + double k_one = utils::numeric(FLERR, arg[1], false, lmp); + double C_one = utils::numeric(FLERR, arg[2], false, lmp); + double N_one = utils::numeric(FLERR, arg[3], false, lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -209,14 +209,14 @@ void AngleFourierSimple::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); } /* ---------------------------------------------------------------------- */ double AngleFourierSimple::equilibrium_angle(int i) { - return (MY_PI/N[i]); + return (MY_PI / N[i]); } /* ---------------------------------------------------------------------- @@ -225,9 +225,9 @@ double AngleFourierSimple::equilibrium_angle(int i) void AngleFourierSimple::write_restart(FILE *fp) { - fwrite(&k[1],sizeof(double),atom->nangletypes,fp); - fwrite(&C[1],sizeof(double),atom->nangletypes,fp); - fwrite(&N[1],sizeof(double),atom->nangletypes,fp); + fwrite(&k[1], sizeof(double), atom->nangletypes, fp); + fwrite(&C[1], sizeof(double), atom->nangletypes, fp); + fwrite(&N[1], sizeof(double), atom->nangletypes, fp); } /* ---------------------------------------------------------------------- @@ -239,13 +239,13 @@ void AngleFourierSimple::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error); - utils::sfread(FLERR,&C[1],sizeof(double),atom->nangletypes,fp,nullptr,error); - utils::sfread(FLERR,&N[1],sizeof(double),atom->nangletypes,fp,nullptr,error); + utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error); + utils::sfread(FLERR, &C[1], sizeof(double), atom->nangletypes, fp, nullptr, error); + utils::sfread(FLERR, &N[1], sizeof(double), atom->nangletypes, fp, nullptr, error); } - MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); - MPI_Bcast(&C[1],atom->nangletypes,MPI_DOUBLE,0,world); - MPI_Bcast(&N[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&C[1], atom->nangletypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&N[1], atom->nangletypes, MPI_DOUBLE, 0, world); for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; } @@ -256,8 +256,7 @@ void AngleFourierSimple::read_restart(FILE *fp) void AngleFourierSimple::write_data(FILE *fp) { - for (int i = 1; i <= atom->nangletypes; i++) - fprintf(fp,"%d %g %g %g\n",i,k[i],C[i],N[i]); + for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g %g %g\n", i, k[i], C[i], N[i]); } /* ---------------------------------------------------------------------- */ @@ -269,21 +268,21 @@ double AngleFourierSimple::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); - double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + domain->minimum_image(delx1, dely1, delz1); + double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); - double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + domain->minimum_image(delx2, dely2, delz2); + double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); - double c = delx1*delx2 + dely1*dely2 + delz1*delz2; - c /= r1*r2; + double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; - double cn = cos(N[type]*acos(c)); + double cn = cos(N[type] * acos(c)); - double eng = k[type]*(1.0+C[type]*cn); + double eng = k[type] * (1.0 + C[type] * cn); return eng; } diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/EXTRA-MOLECULE/angle_fourier_simple.h similarity index 100% rename from src/USER-MISC/angle_fourier_simple.h rename to src/EXTRA-MOLECULE/angle_fourier_simple.h diff --git a/src/USER-MISC/angle_gaussian.cpp b/src/EXTRA-MOLECULE/angle_gaussian.cpp similarity index 100% rename from src/USER-MISC/angle_gaussian.cpp rename to src/EXTRA-MOLECULE/angle_gaussian.cpp diff --git a/src/USER-MISC/angle_gaussian.h b/src/EXTRA-MOLECULE/angle_gaussian.h similarity index 100% rename from src/USER-MISC/angle_gaussian.h rename to src/EXTRA-MOLECULE/angle_gaussian.h diff --git a/src/USER-MISC/angle_quartic.cpp b/src/EXTRA-MOLECULE/angle_quartic.cpp similarity index 100% rename from src/USER-MISC/angle_quartic.cpp rename to src/EXTRA-MOLECULE/angle_quartic.cpp diff --git a/src/USER-MISC/angle_quartic.h b/src/EXTRA-MOLECULE/angle_quartic.h similarity index 100% rename from src/USER-MISC/angle_quartic.h rename to src/EXTRA-MOLECULE/angle_quartic.h diff --git a/src/USER-MISC/bond_gaussian.cpp b/src/EXTRA-MOLECULE/bond_gaussian.cpp similarity index 100% rename from src/USER-MISC/bond_gaussian.cpp rename to src/EXTRA-MOLECULE/bond_gaussian.cpp diff --git a/src/USER-MISC/bond_gaussian.h b/src/EXTRA-MOLECULE/bond_gaussian.h similarity index 100% rename from src/USER-MISC/bond_gaussian.h rename to src/EXTRA-MOLECULE/bond_gaussian.h diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp similarity index 100% rename from src/USER-MISC/bond_harmonic_shift.cpp rename to src/EXTRA-MOLECULE/bond_harmonic_shift.cpp diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/EXTRA-MOLECULE/bond_harmonic_shift.h similarity index 100% rename from src/USER-MISC/bond_harmonic_shift.h rename to src/EXTRA-MOLECULE/bond_harmonic_shift.h diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp similarity index 100% rename from src/USER-MISC/bond_harmonic_shift_cut.cpp rename to src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h similarity index 100% rename from src/USER-MISC/bond_harmonic_shift_cut.h rename to src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/EXTRA-MOLECULE/bond_nonlinear.cpp similarity index 100% rename from src/MOLECULE/bond_nonlinear.cpp rename to src/EXTRA-MOLECULE/bond_nonlinear.cpp diff --git a/src/MOLECULE/bond_nonlinear.h b/src/EXTRA-MOLECULE/bond_nonlinear.h similarity index 100% rename from src/MOLECULE/bond_nonlinear.h rename to src/EXTRA-MOLECULE/bond_nonlinear.h diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp similarity index 100% rename from src/USER-MISC/dihedral_cosine_shift_exp.cpp rename to src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h similarity index 100% rename from src/USER-MISC/dihedral_cosine_shift_exp.h rename to src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/EXTRA-MOLECULE/dihedral_fourier.cpp similarity index 100% rename from src/USER-MISC/dihedral_fourier.cpp rename to src/EXTRA-MOLECULE/dihedral_fourier.cpp diff --git a/src/USER-MISC/dihedral_fourier.h b/src/EXTRA-MOLECULE/dihedral_fourier.h similarity index 100% rename from src/USER-MISC/dihedral_fourier.h rename to src/EXTRA-MOLECULE/dihedral_fourier.h diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/EXTRA-MOLECULE/dihedral_helix.cpp similarity index 100% rename from src/MOLECULE/dihedral_helix.cpp rename to src/EXTRA-MOLECULE/dihedral_helix.cpp diff --git a/src/MOLECULE/dihedral_helix.h b/src/EXTRA-MOLECULE/dihedral_helix.h similarity index 100% rename from src/MOLECULE/dihedral_helix.h rename to src/EXTRA-MOLECULE/dihedral_helix.h diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp similarity index 100% rename from src/USER-MISC/dihedral_nharmonic.cpp rename to src/EXTRA-MOLECULE/dihedral_nharmonic.cpp diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/EXTRA-MOLECULE/dihedral_nharmonic.h similarity index 100% rename from src/USER-MISC/dihedral_nharmonic.h rename to src/EXTRA-MOLECULE/dihedral_nharmonic.h diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp similarity index 100% rename from src/USER-MISC/dihedral_quadratic.cpp rename to src/EXTRA-MOLECULE/dihedral_quadratic.cpp diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/EXTRA-MOLECULE/dihedral_quadratic.h similarity index 100% rename from src/USER-MISC/dihedral_quadratic.h rename to src/EXTRA-MOLECULE/dihedral_quadratic.h diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/EXTRA-MOLECULE/dihedral_spherical.cpp similarity index 100% rename from src/USER-MISC/dihedral_spherical.cpp rename to src/EXTRA-MOLECULE/dihedral_spherical.cpp diff --git a/src/USER-MISC/dihedral_spherical.h b/src/EXTRA-MOLECULE/dihedral_spherical.h similarity index 100% rename from src/USER-MISC/dihedral_spherical.h rename to src/EXTRA-MOLECULE/dihedral_spherical.h diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp similarity index 100% rename from src/USER-MISC/dihedral_table_cut.cpp rename to src/EXTRA-MOLECULE/dihedral_table_cut.cpp diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/EXTRA-MOLECULE/dihedral_table_cut.h similarity index 100% rename from src/USER-MISC/dihedral_table_cut.h rename to src/EXTRA-MOLECULE/dihedral_table_cut.h diff --git a/src/USER-MISC/improper_cossq.cpp b/src/EXTRA-MOLECULE/improper_cossq.cpp similarity index 100% rename from src/USER-MISC/improper_cossq.cpp rename to src/EXTRA-MOLECULE/improper_cossq.cpp diff --git a/src/USER-MISC/improper_cossq.h b/src/EXTRA-MOLECULE/improper_cossq.h similarity index 100% rename from src/USER-MISC/improper_cossq.h rename to src/EXTRA-MOLECULE/improper_cossq.h diff --git a/src/USER-MISC/improper_distance.cpp b/src/EXTRA-MOLECULE/improper_distance.cpp similarity index 100% rename from src/USER-MISC/improper_distance.cpp rename to src/EXTRA-MOLECULE/improper_distance.cpp diff --git a/src/USER-MISC/improper_distance.h b/src/EXTRA-MOLECULE/improper_distance.h similarity index 100% rename from src/USER-MISC/improper_distance.h rename to src/EXTRA-MOLECULE/improper_distance.h diff --git a/src/USER-MISC/improper_fourier.cpp b/src/EXTRA-MOLECULE/improper_fourier.cpp similarity index 100% rename from src/USER-MISC/improper_fourier.cpp rename to src/EXTRA-MOLECULE/improper_fourier.cpp diff --git a/src/USER-MISC/improper_fourier.h b/src/EXTRA-MOLECULE/improper_fourier.h similarity index 100% rename from src/USER-MISC/improper_fourier.h rename to src/EXTRA-MOLECULE/improper_fourier.h diff --git a/src/USER-MISC/improper_ring.cpp b/src/EXTRA-MOLECULE/improper_ring.cpp similarity index 100% rename from src/USER-MISC/improper_ring.cpp rename to src/EXTRA-MOLECULE/improper_ring.cpp diff --git a/src/USER-MISC/improper_ring.h b/src/EXTRA-MOLECULE/improper_ring.h similarity index 100% rename from src/USER-MISC/improper_ring.h rename to src/EXTRA-MOLECULE/improper_ring.h diff --git a/src/pair_beck.cpp b/src/EXTRA-PAIR/pair_beck.cpp similarity index 100% rename from src/pair_beck.cpp rename to src/EXTRA-PAIR/pair_beck.cpp diff --git a/src/pair_beck.h b/src/EXTRA-PAIR/pair_beck.h similarity index 100% rename from src/pair_beck.h rename to src/EXTRA-PAIR/pair_beck.h diff --git a/src/pair_born_coul_dsf.cpp b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp similarity index 100% rename from src/pair_born_coul_dsf.cpp rename to src/EXTRA-PAIR/pair_born_coul_dsf.cpp diff --git a/src/pair_born_coul_dsf.h b/src/EXTRA-PAIR/pair_born_coul_dsf.h similarity index 100% rename from src/pair_born_coul_dsf.h rename to src/EXTRA-PAIR/pair_born_coul_dsf.h diff --git a/src/pair_born_coul_wolf.cpp b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp similarity index 100% rename from src/pair_born_coul_wolf.cpp rename to src/EXTRA-PAIR/pair_born_coul_wolf.cpp diff --git a/src/pair_born_coul_wolf.h b/src/EXTRA-PAIR/pair_born_coul_wolf.h similarity index 100% rename from src/pair_born_coul_wolf.h rename to src/EXTRA-PAIR/pair_born_coul_wolf.h diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/EXTRA-PAIR/pair_buck_mdf.cpp similarity index 100% rename from src/USER-MISC/pair_buck_mdf.cpp rename to src/EXTRA-PAIR/pair_buck_mdf.cpp diff --git a/src/USER-MISC/pair_buck_mdf.h b/src/EXTRA-PAIR/pair_buck_mdf.h similarity index 100% rename from src/USER-MISC/pair_buck_mdf.h rename to src/EXTRA-PAIR/pair_buck_mdf.h diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/EXTRA-PAIR/pair_cosine_squared.cpp similarity index 100% rename from src/USER-MISC/pair_cosine_squared.cpp rename to src/EXTRA-PAIR/pair_cosine_squared.cpp diff --git a/src/USER-MISC/pair_cosine_squared.h b/src/EXTRA-PAIR/pair_cosine_squared.h similarity index 100% rename from src/USER-MISC/pair_cosine_squared.h rename to src/EXTRA-PAIR/pair_cosine_squared.h diff --git a/src/pair_coul_cut_global.cpp b/src/EXTRA-PAIR/pair_coul_cut_global.cpp similarity index 100% rename from src/pair_coul_cut_global.cpp rename to src/EXTRA-PAIR/pair_coul_cut_global.cpp diff --git a/src/pair_coul_cut_global.h b/src/EXTRA-PAIR/pair_coul_cut_global.h similarity index 100% rename from src/pair_coul_cut_global.h rename to src/EXTRA-PAIR/pair_coul_cut_global.h diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/EXTRA-PAIR/pair_coul_diel.cpp similarity index 100% rename from src/USER-MISC/pair_coul_diel.cpp rename to src/EXTRA-PAIR/pair_coul_diel.cpp diff --git a/src/USER-MISC/pair_coul_diel.h b/src/EXTRA-PAIR/pair_coul_diel.h similarity index 100% rename from src/USER-MISC/pair_coul_diel.h rename to src/EXTRA-PAIR/pair_coul_diel.h diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/EXTRA-PAIR/pair_coul_slater_cut.cpp similarity index 100% rename from src/USER-MISC/pair_coul_slater_cut.cpp rename to src/EXTRA-PAIR/pair_coul_slater_cut.cpp diff --git a/src/USER-MISC/pair_coul_slater_cut.h b/src/EXTRA-PAIR/pair_coul_slater_cut.h similarity index 100% rename from src/USER-MISC/pair_coul_slater_cut.h rename to src/EXTRA-PAIR/pair_coul_slater_cut.h diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/EXTRA-PAIR/pair_coul_slater_long.cpp similarity index 100% rename from src/USER-MISC/pair_coul_slater_long.cpp rename to src/EXTRA-PAIR/pair_coul_slater_long.cpp diff --git a/src/USER-MISC/pair_coul_slater_long.h b/src/EXTRA-PAIR/pair_coul_slater_long.h similarity index 100% rename from src/USER-MISC/pair_coul_slater_long.h rename to src/EXTRA-PAIR/pair_coul_slater_long.h diff --git a/src/EXTRA-PAIR/pair_e3b.cpp b/src/EXTRA-PAIR/pair_e3b.cpp new file mode 100644 index 0000000000..a904939e42 --- /dev/null +++ b/src/EXTRA-PAIR/pair_e3b.cpp @@ -0,0 +1,655 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + + contributing authors: Steven E Strong and Nicholas J Hestand + contact: stevene.strong at gmail dot com +------------------------------------------------------------------------- */ + +#include "pair_e3b.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "update.h" + +#include +#include + +//these are defined here to avoid confusing hardcoded indices, but +//they do not allow flexibility. If they are changed the code will break +#define DIM 3 +#define NUMH 2 //number of hydrogen atoms per water molecule +#define NUMO 2 //number of oxygen atoms per pair of water molecules +#define BOND_DELTA 1.01 //buffer for OH bonds that aren't perfectly rigid + +static constexpr double NOT_SET = 1.024e300; + +using namespace LAMMPS_NS; +/* ---------------------------------------------------------------------- */ + +PairE3B::PairE3B(LAMMPS *lmp) : Pair(lmp), pairPerAtom(10) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + nextra = 4; //store and tally pot energy terms eA, eB, eC, and e2 + pvector = new double[nextra]; + + allocatedE3B = false; + pairO = nullptr; + pairH = nullptr; + exps = nullptr; + del3 = nullptr; + fpair3 = nullptr; + sumExp = nullptr; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairE3B::~PairE3B() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } + if (allocatedE3B) { + memory->destroy(pairO); + memory->destroy(pairH); + memory->destroy(exps); + memory->destroy(del3); + memory->destroy(fpair3); + memory->destroy(sumExp); + } + + delete[] pvector; +} + +/* ---------------------------------------------------------------------- */ + +void PairE3B::compute(int eflag, int vflag) +{ + int i, j, k, h, ii, jj, hh, kk, inum, jnum, otherO; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair, rsq, tmpexp; + double fxtmp, fytmp, fztmp, fix, fiy, fiz; + double delxh, delyh, delzh, rsqh, tmpr; + double scFact1, scFact2, scEng, scDer; + int *ilist, *jlist, *numneigh, **firstneigh; + bool addedH; + + if (natoms != atom->natoms) error->all(FLERR, "pair E3B requires a fixed number of atoms"); + + ev_init(eflag, vflag); + //clear sumExp array + memset(sumExp, 0.0, nbytes); + + evdwl = 0.0; + pvector[0] = pvector[1] = pvector[2] = pvector[3] = 0.0; + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + int npair = 0; + // loop over half neighbor list of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (type[i] != typeO) continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + fix = fiy = fiz = 0.0; + + // two-body interactions + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + //skip unless O-O interaction + if (type[j] != typeO) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; //OO distance + + //two body interaction + //not shifted b/c k2=4.87/A, so at cutoff (5.2A) e^(-kr) = 1e-11 + if (rsq < rc2sq) { + tmpr = sqrt(rsq); + tmpexp = e2 * exp(-k2 * tmpr); + fpair = k2 * tmpexp / tmpr; + + fxtmp = delx * fpair; + fytmp = dely * fpair; + fztmp = delz * fpair; + fix += fxtmp; + fiy += fytmp; + fiz += fztmp; + f[j][0] -= fxtmp; + f[j][1] -= fytmp; + f[j][2] -= fztmp; + + if (evflag) { + ev_tally(i, j, nlocal, newton_pair, tmpexp, 0.0, fpair, delx, dely, delz); + pvector[0] += tmpexp; + } + } //end if rsqmap(tag[otherO] + hh + 1); + //if hydrogen atom is missing, bond potential or shake will + //catch this, so don't need to check here + //if (h<0) + // error->one(FLERR,"hydrogen atom missing"); + h = domain->closest_image(otherO, h); + pairH[npair][kk][hh] = h; + + delxh = x[k][0] - x[h][0]; + delyh = x[k][1] - x[h][1]; + delzh = x[k][2] - x[h][2]; + rsqh = delxh * delxh + delyh * delyh + delzh * delzh; + + if (rsqh < rc3sq) { + + tmpr = sqrt(rsqh); + tmpexp = exp(-k3 * tmpr); + if (tmpr > rs) { + scFact1 = rc3 - tmpr; + scFact2 = sc_num + 2 * tmpr; + scEng = scFact1 * scFact1 * scFact2 * sc_denom; + scDer = k3 * scEng - 6 * scFact1 * (rs - tmpr) * sc_denom; + } else { + scDer = k3; + scEng = 1.0; + } + + //need to keep fpair3 separate from del3 for virial + fpair3[npair][kk][hh] = scDer * tmpexp / tmpr; + tmpexp *= scEng; + exps[npair][kk][hh] = tmpexp; + del3[npair][kk][hh][0] = delxh; + del3[npair][kk][hh][1] = delyh; + del3[npair][kk][hh][2] = delzh; + + //accumulate global vector of sum(e^kr) + //tags start at 1, so subtract one to index sumExp + sumExp[tag[k] - 1] += tmpexp; + sumExp[tag[h] - 1] += tmpexp; + + addedH = true; + } else { + exps[npair][kk][hh] = 0.0; + fpair3[npair][kk][hh] = 0.0; + } //if < rc3sq + } //end loop through 2 Hs + } //end for kk in NUMO + //if added a pair, check if array is too small and grow + if (addedH) { + npair++; + if (npair >= pairmax) error->one(FLERR, "neigh is too small"); + } + } //end if < rc3deltaSq + } //end for jj neigh + + //add 2-body forces on i + f[i][0] += fix; + f[i][1] += fiy; + f[i][2] += fiz; + } //end for ii + + //communicate sumExp array + //tested that no change in speed with MPI_IN_PLACE + MPI_Allreduce(MPI_IN_PLACE, sumExp, maxID, MPI_DOUBLE, MPI_SUM, world); + + //now loop through list of pairs, calculating 3body forces + int j2, otherH; + double partA, partB, partC; + for (ii = 0; ii < npair; ii++) { + + for (kk = 0; kk < NUMO; kk++) { + i = pairO[ii][kk]; + otherO = (kk + 1) % 2; + partB = eb * + (sumExp[tag[pairO[ii][otherO]] - 1] + sumExp[tag[pairH[ii][otherO][0]] - 1] + + sumExp[tag[pairH[ii][otherO][1]] - 1] - 2 * (exps[ii][otherO][0] + exps[ii][otherO][1])); + partC = ec * (sumExp[tag[i] - 1] - exps[ii][kk][0] - exps[ii][kk][1]); + + for (hh = 0; hh < NUMH; hh++) { + j = pairH[ii][kk][hh]; + + //type A + otherH = (hh + 1) % 2; + j2 = pairH[ii][kk][otherH]; + + partA = ea * (sumExp[tag[j2] - 1] - exps[ii][kk][otherH]); //not full energy yet + fpair = partA * fpair3[ii][kk][hh]; + fxtmp = fpair * del3[ii][kk][hh][0]; + fytmp = fpair * del3[ii][kk][hh][1]; + fztmp = fpair * del3[ii][kk][hh][2]; + + f[i][0] += fxtmp; + f[i][1] += fytmp; + f[i][2] += fztmp; + f[j][0] -= fxtmp; + f[j][1] -= fytmp; + f[j][2] -= fztmp; + + if (evflag) { + evdwl = partA * exps[ii][kk][hh] * 0.5; //mult by exp on this H + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, del3[ii][kk][hh][0], + del3[ii][kk][hh][1], del3[ii][kk][hh][2]); + pvector[1] += evdwl; + } + + //type B + fpair = partB * fpair3[ii][kk][hh]; + fxtmp = fpair * del3[ii][kk][hh][0]; + fytmp = fpair * del3[ii][kk][hh][1]; + fztmp = fpair * del3[ii][kk][hh][2]; + + f[i][0] += fxtmp; + f[i][1] += fytmp; + f[i][2] += fztmp; + f[j][0] -= fxtmp; + f[j][1] -= fytmp; + f[j][2] -= fztmp; + + if (evflag) { + evdwl = partB * exps[ii][kk][hh] * 0.5; //mult by exp on this H + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, del3[ii][kk][hh][0], + del3[ii][kk][hh][1], del3[ii][kk][hh][2]); + pvector[2] += evdwl; + } + + //type C + fpair = partC * fpair3[ii][kk][hh]; + fxtmp = fpair * del3[ii][kk][hh][0]; + fytmp = fpair * del3[ii][kk][hh][1]; + fztmp = fpair * del3[ii][kk][hh][2]; + + f[i][0] += fxtmp; + f[i][1] += fytmp; + f[i][2] += fztmp; + f[j][0] -= fxtmp; + f[j][1] -= fytmp; + f[j][2] -= fztmp; + + if (evflag) { + evdwl = partC * exps[ii][kk][hh] * 0.5; //mult by exp on this H + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, del3[ii][kk][hh][0], + del3[ii][kk][hh][1], del3[ii][kk][hh][2]); + pvector[3] += evdwl; + } + } //end for hh in NUMH + } //end for kk in NUMO + } //end for ii in npairs + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairE3B::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); +} + +void PairE3B::allocateE3B() +{ + allocatedE3B = true; + + //TODO: get memory->grow working for 4d arrays + pairmax = atom->nlocal * pairPerAtom; //initial guess for size of pair lists + memory->create(pairO, pairmax, NUMO, "pair:pairO"); + memory->create(pairH, pairmax, NUMO, NUMH, "pair:pairH"); + memory->create(exps, pairmax, NUMO, NUMH, "pair:exps"); + memory->create(fpair3, pairmax, NUMO, NUMH, "pair:fpair3"); + memory->create(del3, pairmax, NUMO, NUMH, DIM, "pair:del3"); + + //set del3 to zero to silence valgrind memcheck errors + //don't need to do this in every call to compute() because we set + //exps and fpair3 to zero, and all uses of del3 are multiplied by one of those + int ii, jj, kk, ll; + for (ii = 0; ii < pairmax; ii++) + for (jj = 0; jj < NUMO; jj++) + for (kk = 0; kk < NUMH; kk++) + for (ll = 0; ll < DIM; ll++) del3[ii][jj][kk][ll] = 0.0; + + natoms = atom->natoms; + maxID = find_maxID(); + if (!natoms) error->all(FLERR, "No atoms found"); + memory->create(sumExp, maxID, "pair:sumExp"); + nbytes = sizeof(double) * maxID; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairE3B::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); + typeO = utils::inumeric(FLERR, arg[0], false, lmp); +} + +/* ---------------------------------------------------------------------- + coeffs must be * * keyword/value + keyword/values set the potential parameters +------------------------------------------------------------------------- */ +void PairE3B::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + //1=* 2=* 3/4=1st keyword/value + if (narg < 4) error->all(FLERR, "There must be at least one keyword given to pair_coeff"); + + // clear setflag since coeff() called once with I,J = * * + int n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) setflag[i][j] = 0; + + setflag[typeO][typeO] = 1; + + //parse keyword/value pairs + double bondL = 0.0; //OH bond length + bool repeatFlag = false; + + //clear parameters + e2 = ea = eb = ec = k3 = k2 = NOT_SET; + rs = rc3 = rc2 = 0.0; + + int iarg = 2; //beginning of keyword/value pairs + while (iarg < narg) { + char *keyword = arg[iarg++]; + if (checkKeyword(keyword, "Ea", 1, narg - iarg)) + ea = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "Eb", 1, narg - iarg)) + eb = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "Ec", 1, narg - iarg)) + ec = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "K3", 1, narg - iarg)) + k3 = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "Rs", 1, narg - iarg)) + rs = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "Rc3", 1, narg - iarg)) + rc3 = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "Rc2", 1, narg - iarg)) + rc2 = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "bondL", 1, narg - iarg)) + bondL = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "E2", 1, narg - iarg)) + e2 = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "K2", 1, narg - iarg)) + k2 = utils::numeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "neigh", 1, narg - iarg)) + pairPerAtom = utils::inumeric(FLERR, arg[iarg++], false, lmp); + else if (checkKeyword(keyword, "preset", 1, narg - iarg)) { + int presetFlag = utils::inumeric(FLERR, arg[iarg++], false, lmp); + presetParam(presetFlag, repeatFlag, bondL); + } else + error->all(FLERR, "Keyword {} is unknown", keyword); + } + + checkInputs(bondL); + + //cutmax for neighbor listing + cutmax = MAX(rc2, rc3); + rc2sq = rc2 * rc2; + rc3sq = rc3 * rc3; + rc3deltaSq = (rc3 + bondL) * (rc3 + bondL); + + double tmpfact = 1.0 / (rc3 - rs); + sc_denom = tmpfact * tmpfact * tmpfact; + sc_num = rc3 - 3 * rs; +} + +/* ---------------------------------------------------------------------- + init specific to this pair styles +------------------------------------------------------------------------- */ + +void PairE3B::init_style() +{ + if (atom->tag_enable == 0) error->all(FLERR, "Pair style E3B requires atom IDs"); + if (force->newton_pair == 0) error->all(FLERR, "Pair style E3B requires newton pair on"); + if (typeO < 1 || typeO > atom->ntypes) error->all(FLERR, "Invalid Otype: out of bounds"); + + // need a half neighbor list + neighbor->request(this, instance_me); + + if (!force->pair_match("tip4p", false, 0)) + if (comm->me == 0) + error->warning(FLERR, "E3B pair_style is designed for use with hybrid/overlay tip4p style"); + + if (!allocatedE3B) allocateE3B(); +} + +static const char cite_E3B1[] = + "Explicit Three-Body (E3B) potential for water:\n\n" + "@article{kumar_water_2008,\n" + "title = {Water Simulation Model with Explicit Three-Molecule Interactions},\n" + "volume = {112},\n" + "doi = {10.1021/jp8009468},\n" + "number = {28},\n" + "journal = {J Phys. Chem. B},\n" + "author = {Kumar, R. and Skinner, J. L.},\n" + "year = {2008},\n" + "pages = {8311--8318}\n" + "}\n\n"; + +static const char cite_E3B2[] = + "Explicit Three-Body (E3B) potential for water:\n\n" + "@article{tainter_robust_2011,\n" + "title = {Robust three-body water simulation model},\n" + "volume = {134},\n" + "doi = {10.1063/1.3587053},\n" + "number = {18},\n" + "journal = {J. Chem. Phys},\n" + "author = {Tainter, C. J. and Pieniazek, P. A. and Lin, Y.-S. and Skinner, J. L.},\n" + "year = {2011},\n" + "pages = {184501}\n" + "}\n\n"; + +static const char cite_E3B3[] = + "Explicit Three-Body (E3B) potential for water:\n\n" + "@article{tainter_reparametrized_2015,\n" + "title = {Reparametrized {E3B} (Explicit Three-Body) Water Model Using the {TIP4P/2005} Model " + "as a Reference},\n" + "volume = {11},\n" + "doi = {10.1021/acs.jctc.5b00117},\n" + "number = {5},\n" + "journal = {J. Chem. Theory Comput.},\n" + "author = {Tainter, Craig J. and Shi, Liang and Skinner, James L.},\n" + "year = {2015},\n" + "pages = {2268--2277}\n" + "}\n\n"; + +void PairE3B::presetParam(const int flag, bool &repeatFlag, double &bondL) +{ + if (repeatFlag) error->all(FLERR, "Cannot request two different sets of preset parameters"); + repeatFlag = true; + + if (ea != NOT_SET || eb != NOT_SET || ec != NOT_SET || e2 != NOT_SET || k3 != NOT_SET || + k2 != NOT_SET || bondL != 0.0 || rs != 0.0 || rc3 != 0.0 || rc2 != 0.0) + error->all(FLERR, "Preset keyword will overwrite another keyword setting"); + + double econv = 1.0, lconv = 1.0; + if (strcmp(update->unit_style, "real") == 0) { + econv = 1.0 / 4.184; + lconv = 1.0; + } else if (strcmp(update->unit_style, "metal") == 0) { + econv = 0.103653271; + lconv = 1.0; + } else if (strcmp(update->unit_style, "si") == 0) { + econv = 1.660578e-21; + lconv = 1e-10; + } else if (strcmp(update->unit_style, "cgs") == 0) { + econv = 1.660578e-14; + lconv = 1e-8; + } else + error->all(FLERR, "Pre-defined E3B parameters have not been set for {} units.", + update->unit_style); + + //here parameters are defined in kJ/mol and A + //they will be converted to the lammps units after + if (flag == 2008) { + error->all(FLERR, + "'preset 2008' is not yet supported, because this would require distinct k3 " + "coefficients, use 'preset 2011' or 'preset 2015'"); + if (lmp->citeme) lmp->citeme->add(cite_E3B1); + ea = 4699.6; + eb = -2152.9; + ec = 1312.7; + //ka = 1.0/1.88; + //kb = 1.0/1.71; + //kc = 1.0/1.56; + e2 = 1.925e6; + k2 = 4.67; + rs = 5.0; + rc3 = 5.2; + rc2 = 5.2; + bondL = 0.9572; + } else if (flag == 2011) { + if (lmp->citeme) lmp->citeme->add(cite_E3B2); + ea = 1745.7; + eb = -4565.0; + ec = 7606.8; + k3 = 1.907; + e2 = 2.349e6; + k2 = 4.872; + rs = 5.0; + rc3 = 5.2; + rc2 = 5.2; + bondL = 0.9572; + } else if (flag == 2015) { + if (lmp->citeme) lmp->citeme->add(cite_E3B3); + ea = 150.0; + eb = -1005.0; + ec = 1880.0; + k3 = 1.907; + e2 = 0.453e6; + k2 = 4.872; + rs = 5.0; + rc3 = 5.2; + rc2 = 5.2; + bondL = 0.9572; + } else + error->all(FLERR, "Unknown argument: preset only takes 2011 or 2015 as arguments"); + + //convert units + ea *= econv; + eb *= econv; + ec *= econv; + e2 *= econv; + k3 /= lconv; + k2 /= lconv; + rs *= lconv; + rc2 *= lconv; + rc3 *= lconv; + bondL *= lconv * BOND_DELTA; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ +//pair.cpp::init uses this to set cutsq array, used for neighboring, etc +double PairE3B::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + + return cutmax; +} + +bool PairE3B::checkKeyword(const char *thiskey, const char *test, const int nVal, const int nRem) +{ + if (strcmp(thiskey, test) == 0) { + if (nRem < nVal) error->all(FLERR, "Too few arguments to '{}' keyword.", test); + return true; + } + return false; +} + +//find max atom ID for all atoms +//from fix_deposit.cpp +tagint PairE3B::find_maxID() +{ + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + + tagint max = 0; + tagint maxID; + for (int i = 0; i < nlocal; i++) max = MAX(max, tag[i]); + MPI_Allreduce(&max, &maxID, 1, MPI_LMP_TAGINT, MPI_MAX, world); + + return maxID; +} + +void PairE3B::checkInputs(const double &bondL) +{ + //first check that all necessary values were set + if (rc2 == 0.0) error->all(FLERR, "rc2 keyword missing"); + if (rs == 0.0) error->all(FLERR, "Rs keyword missing"); + if (rc3 == 0.0) error->all(FLERR, "Rc3 keyword missing"); + if (bondL == 0.0) error->all(FLERR, "bondL keyword missing"); + if (ea == NOT_SET) error->all(FLERR, "Ea keyword missing"); + if (eb == NOT_SET) error->all(FLERR, "Eb keyword missing"); + if (ec == NOT_SET) error->all(FLERR, "Ec keyword missing"); + if (k3 == NOT_SET) error->all(FLERR, "K3 keyword missing"); + if (e2 == NOT_SET) error->all(FLERR, "E2 keyword missing"); + if (k2 == NOT_SET) error->all(FLERR, "K2 keyword missing"); + + //now test that values are within acceptable ranges + if (k2 < 0.0 or k3 < 0.0) error->all(FLERR, "exponential decay is negative"); + if (bondL < 0.0) error->all(FLERR, "OH bond length is negative"); + if (rc2 < 0.0 || rc3 < 0.0 || rs < 0.0) error->all(FLERR, "potential cutoff is negative"); + if (rs > rc3) error->all(FLERR, "potential switching distance is larger than cutoff"); + if (rs == rc3) + error->warning(FLERR, + "potential switching distance is equal to cutoff: this is untested and not " + "conserve energy"); + if (pairPerAtom < 0) error->all(FLERR, "neigh is negative"); +} diff --git a/src/USER-MISC/pair_e3b.h b/src/EXTRA-PAIR/pair_e3b.h similarity index 100% rename from src/USER-MISC/pair_e3b.h rename to src/EXTRA-PAIR/pair_e3b.h diff --git a/src/pair_gauss.cpp b/src/EXTRA-PAIR/pair_gauss.cpp similarity index 100% rename from src/pair_gauss.cpp rename to src/EXTRA-PAIR/pair_gauss.cpp diff --git a/src/pair_gauss.h b/src/EXTRA-PAIR/pair_gauss.h similarity index 100% rename from src/pair_gauss.h rename to src/EXTRA-PAIR/pair_gauss.h diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/EXTRA-PAIR/pair_gauss_cut.cpp similarity index 100% rename from src/USER-MISC/pair_gauss_cut.cpp rename to src/EXTRA-PAIR/pair_gauss_cut.cpp diff --git a/src/USER-MISC/pair_gauss_cut.h b/src/EXTRA-PAIR/pair_gauss_cut.h similarity index 100% rename from src/USER-MISC/pair_gauss_cut.h rename to src/EXTRA-PAIR/pair_gauss_cut.h diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/EXTRA-PAIR/pair_lennard_mdf.cpp similarity index 100% rename from src/USER-MISC/pair_lennard_mdf.cpp rename to src/EXTRA-PAIR/pair_lennard_mdf.cpp diff --git a/src/USER-MISC/pair_lennard_mdf.h b/src/EXTRA-PAIR/pair_lennard_mdf.h similarity index 100% rename from src/USER-MISC/pair_lennard_mdf.h rename to src/EXTRA-PAIR/pair_lennard_mdf.h diff --git a/src/pair_lj96_cut.cpp b/src/EXTRA-PAIR/pair_lj96_cut.cpp similarity index 100% rename from src/pair_lj96_cut.cpp rename to src/EXTRA-PAIR/pair_lj96_cut.cpp diff --git a/src/pair_lj96_cut.h b/src/EXTRA-PAIR/pair_lj96_cut.h similarity index 100% rename from src/pair_lj96_cut.h rename to src/EXTRA-PAIR/pair_lj96_cut.h diff --git a/src/pair_lj_cubic.cpp b/src/EXTRA-PAIR/pair_lj_cubic.cpp similarity index 100% rename from src/pair_lj_cubic.cpp rename to src/EXTRA-PAIR/pair_lj_cubic.cpp diff --git a/src/pair_lj_cubic.h b/src/EXTRA-PAIR/pair_lj_cubic.h similarity index 100% rename from src/pair_lj_cubic.h rename to src/EXTRA-PAIR/pair_lj_cubic.h diff --git a/src/pair_lj_cubic_const.h b/src/EXTRA-PAIR/pair_lj_cubic_const.h similarity index 100% rename from src/pair_lj_cubic_const.h rename to src/EXTRA-PAIR/pair_lj_cubic_const.h diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp similarity index 100% rename from src/pair_lj_cut_coul_debye.cpp rename to src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp diff --git a/src/pair_lj_cut_coul_debye.h b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.h similarity index 100% rename from src/pair_lj_cut_coul_debye.h rename to src/EXTRA-PAIR/pair_lj_cut_coul_debye.h diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp similarity index 100% rename from src/pair_lj_cut_coul_dsf.cpp rename to src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp diff --git a/src/pair_lj_cut_coul_dsf.h b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h similarity index 100% rename from src/pair_lj_cut_coul_dsf.h rename to src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp similarity index 100% rename from src/pair_lj_cut_coul_wolf.cpp rename to src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp diff --git a/src/pair_lj_cut_coul_wolf.h b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h similarity index 100% rename from src/pair_lj_cut_coul_wolf.h rename to src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp similarity index 100% rename from src/USER-MISC/pair_lj_expand_coul_long.cpp rename to src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp diff --git a/src/USER-MISC/pair_lj_expand_coul_long.h b/src/EXTRA-PAIR/pair_lj_expand_coul_long.h similarity index 100% rename from src/USER-MISC/pair_lj_expand_coul_long.h rename to src/EXTRA-PAIR/pair_lj_expand_coul_long.h diff --git a/src/pair_lj_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs.cpp similarity index 100% rename from src/pair_lj_gromacs.cpp rename to src/EXTRA-PAIR/pair_lj_gromacs.cpp diff --git a/src/pair_lj_gromacs.h b/src/EXTRA-PAIR/pair_lj_gromacs.h similarity index 100% rename from src/pair_lj_gromacs.h rename to src/EXTRA-PAIR/pair_lj_gromacs.h diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp similarity index 100% rename from src/pair_lj_gromacs_coul_gromacs.cpp rename to src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp diff --git a/src/pair_lj_gromacs_coul_gromacs.h b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h similarity index 100% rename from src/pair_lj_gromacs_coul_gromacs.h rename to src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/EXTRA-PAIR/pair_lj_mdf.cpp similarity index 100% rename from src/USER-MISC/pair_lj_mdf.cpp rename to src/EXTRA-PAIR/pair_lj_mdf.cpp diff --git a/src/USER-MISC/pair_lj_mdf.h b/src/EXTRA-PAIR/pair_lj_mdf.h similarity index 100% rename from src/USER-MISC/pair_lj_mdf.h rename to src/EXTRA-PAIR/pair_lj_mdf.h diff --git a/src/pair_lj_relres.cpp b/src/EXTRA-PAIR/pair_lj_relres.cpp similarity index 100% rename from src/pair_lj_relres.cpp rename to src/EXTRA-PAIR/pair_lj_relres.cpp diff --git a/src/pair_lj_relres.h b/src/EXTRA-PAIR/pair_lj_relres.h similarity index 100% rename from src/pair_lj_relres.h rename to src/EXTRA-PAIR/pair_lj_relres.h diff --git a/src/pair_lj_smooth.cpp b/src/EXTRA-PAIR/pair_lj_smooth.cpp similarity index 100% rename from src/pair_lj_smooth.cpp rename to src/EXTRA-PAIR/pair_lj_smooth.cpp diff --git a/src/pair_lj_smooth.h b/src/EXTRA-PAIR/pair_lj_smooth.h similarity index 100% rename from src/pair_lj_smooth.h rename to src/EXTRA-PAIR/pair_lj_smooth.h diff --git a/src/pair_lj_smooth_linear.cpp b/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp similarity index 100% rename from src/pair_lj_smooth_linear.cpp rename to src/EXTRA-PAIR/pair_lj_smooth_linear.cpp diff --git a/src/pair_lj_smooth_linear.h b/src/EXTRA-PAIR/pair_lj_smooth_linear.h similarity index 100% rename from src/pair_lj_smooth_linear.h rename to src/EXTRA-PAIR/pair_lj_smooth_linear.h diff --git a/src/pair_mie_cut.cpp b/src/EXTRA-PAIR/pair_mie_cut.cpp similarity index 100% rename from src/pair_mie_cut.cpp rename to src/EXTRA-PAIR/pair_mie_cut.cpp diff --git a/src/pair_mie_cut.h b/src/EXTRA-PAIR/pair_mie_cut.h similarity index 100% rename from src/pair_mie_cut.h rename to src/EXTRA-PAIR/pair_mie_cut.h diff --git a/src/USER-MISC/pair_momb.cpp b/src/EXTRA-PAIR/pair_momb.cpp similarity index 100% rename from src/USER-MISC/pair_momb.cpp rename to src/EXTRA-PAIR/pair_momb.cpp diff --git a/src/USER-MISC/pair_momb.h b/src/EXTRA-PAIR/pair_momb.h similarity index 100% rename from src/USER-MISC/pair_momb.h rename to src/EXTRA-PAIR/pair_momb.h diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp similarity index 100% rename from src/USER-MISC/pair_morse_smooth_linear.cpp rename to src/EXTRA-PAIR/pair_morse_smooth_linear.cpp diff --git a/src/USER-MISC/pair_morse_smooth_linear.h b/src/EXTRA-PAIR/pair_morse_smooth_linear.h similarity index 100% rename from src/USER-MISC/pair_morse_smooth_linear.h rename to src/EXTRA-PAIR/pair_morse_smooth_linear.h diff --git a/src/MISC/pair_nm_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut.cpp similarity index 100% rename from src/MISC/pair_nm_cut.cpp rename to src/EXTRA-PAIR/pair_nm_cut.cpp diff --git a/src/MISC/pair_nm_cut.h b/src/EXTRA-PAIR/pair_nm_cut.h similarity index 100% rename from src/MISC/pair_nm_cut.h rename to src/EXTRA-PAIR/pair_nm_cut.h diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp similarity index 100% rename from src/MISC/pair_nm_cut_coul_cut.cpp rename to src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp diff --git a/src/MISC/pair_nm_cut_coul_cut.h b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h similarity index 100% rename from src/MISC/pair_nm_cut_coul_cut.h rename to src/EXTRA-PAIR/pair_nm_cut_coul_cut.h diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp similarity index 100% rename from src/MISC/pair_nm_cut_coul_long.cpp rename to src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp diff --git a/src/MISC/pair_nm_cut_coul_long.h b/src/EXTRA-PAIR/pair_nm_cut_coul_long.h similarity index 100% rename from src/MISC/pair_nm_cut_coul_long.h rename to src/EXTRA-PAIR/pair_nm_cut_coul_long.h diff --git a/src/pair_ufm.cpp b/src/EXTRA-PAIR/pair_ufm.cpp similarity index 100% rename from src/pair_ufm.cpp rename to src/EXTRA-PAIR/pair_ufm.cpp diff --git a/src/pair_ufm.h b/src/EXTRA-PAIR/pair_ufm.h similarity index 100% rename from src/pair_ufm.h rename to src/EXTRA-PAIR/pair_ufm.h diff --git a/src/USER-MISC/pair_wf_cut.cpp b/src/EXTRA-PAIR/pair_wf_cut.cpp similarity index 99% rename from src/USER-MISC/pair_wf_cut.cpp rename to src/EXTRA-PAIR/pair_wf_cut.cpp index cf2813ab5a..2fb363a161 100644 --- a/src/USER-MISC/pair_wf_cut.cpp +++ b/src/EXTRA-PAIR/pair_wf_cut.cpp @@ -15,6 +15,7 @@ /* ---------------------------------------------------------------------- Contributing Author: Xipeng Wang, Simon Ramirez-Hinestrosa ------------------------------------------------------------------------- */ + #include "pair_wf_cut.h" #include "atom.h" @@ -391,5 +392,5 @@ void *PairWFCut::extract(const char *str, int &dim) if (strcmp(str,"sigma") == 0) return (void *) sigma; if (strcmp(str,"nu") == 0) return (void *) nu; if (strcmp(str,"mu") == 0) return (void *) mu; - return NULL; + return nullptr; } diff --git a/src/USER-MISC/pair_wf_cut.h b/src/EXTRA-PAIR/pair_wf_cut.h similarity index 100% rename from src/USER-MISC/pair_wf_cut.h rename to src/EXTRA-PAIR/pair_wf_cut.h diff --git a/src/USER-FEP/Install.sh b/src/FEP/Install.sh similarity index 100% rename from src/USER-FEP/Install.sh rename to src/FEP/Install.sh diff --git a/src/USER-FEP/README b/src/FEP/README similarity index 97% rename from src/USER-FEP/README rename to src/FEP/README index 3ed5a52b44..00b6ac518f 100644 --- a/src/USER-FEP/README +++ b/src/FEP/README @@ -4,7 +4,7 @@ simulations with soft-core pair potentials in LAMMPS. See the doc page for the fix adapt/fep command to get started. There are example scripts for using this package in -examples/USER/fep. +examples/PACKAGES/fep. There are auxiliary tools for using this package in tools/fep. diff --git a/src/USER-FEP/compute_fep.cpp b/src/FEP/compute_fep.cpp similarity index 100% rename from src/USER-FEP/compute_fep.cpp rename to src/FEP/compute_fep.cpp diff --git a/src/USER-FEP/compute_fep.h b/src/FEP/compute_fep.h similarity index 100% rename from src/USER-FEP/compute_fep.h rename to src/FEP/compute_fep.h diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/FEP/fix_adapt_fep.cpp similarity index 98% rename from src/USER-FEP/fix_adapt_fep.cpp rename to src/FEP/fix_adapt_fep.cpp index b5aad03887..3b4290f2c9 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/FEP/fix_adapt_fep.cpp @@ -216,10 +216,8 @@ void FixAdaptFEP::post_constructor() id_fix_chg = nullptr; if (diamflag) { - auto cmd = fmt::format("{}_FIX_STORE_DIAM {} STORE peratom 1 1", - group->names[igroup]); - modify->add_fix(cmd); - fix_diam = (FixStore *) modify->fix[modify->nfix-1]; + auto cmd = fmt::format("{}_FIX_STORE_DIAM {} STORE peratom 1 1", group->names[igroup]); + fix_diam = (FixStore *) modify->add_fix(cmd); if (fix_diam->restart_reset) fix_diam->restart_reset = 0; else { @@ -236,10 +234,8 @@ void FixAdaptFEP::post_constructor() } if (chgflag) { - auto cmd = fmt::format("{}_FIX_STORE_CHG {} STORE peratom 1 1", - group->names[igroup]); - modify->add_fix(cmd); - fix_chg = (FixStore *) modify->fix[modify->nfix-1]; + auto cmd = fmt::format("{}_FIX_STORE_CHG {} STORE peratom 1 1", group->names[igroup]); + fix_chg = (FixStore *) modify->add_fix(cmd); if (fix_chg->restart_reset) fix_chg->restart_reset = 0; else { diff --git a/src/USER-FEP/fix_adapt_fep.h b/src/FEP/fix_adapt_fep.h similarity index 100% rename from src/USER-FEP/fix_adapt_fep.h rename to src/FEP/fix_adapt_fep.h diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/FEP/pair_coul_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_coul_cut_soft.cpp rename to src/FEP/pair_coul_cut_soft.cpp diff --git a/src/USER-FEP/pair_coul_cut_soft.h b/src/FEP/pair_coul_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_coul_cut_soft.h rename to src/FEP/pair_coul_cut_soft.h diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/FEP/pair_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_coul_long_soft.cpp rename to src/FEP/pair_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_coul_long_soft.h b/src/FEP/pair_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_coul_long_soft.h rename to src/FEP/pair_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/FEP/pair_lj_charmm_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp rename to src/FEP/pair_lj_charmm_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.h b/src/FEP/pair_lj_charmm_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_charmm_coul_long_soft.h rename to src/FEP/pair_lj_charmm_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/FEP/pair_lj_class2_coul_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp rename to src/FEP/pair_lj_class2_coul_cut_soft.cpp diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.h b/src/FEP/pair_lj_class2_coul_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_cut_soft.h rename to src/FEP/pair_lj_class2_coul_cut_soft.h diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/FEP/pair_lj_class2_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_long_soft.cpp rename to src/FEP/pair_lj_class2_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.h b/src/FEP/pair_lj_class2_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_long_soft.h rename to src/FEP/pair_lj_class2_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/FEP/pair_lj_class2_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_class2_soft.cpp rename to src/FEP/pair_lj_class2_soft.cpp diff --git a/src/USER-FEP/pair_lj_class2_soft.h b/src/FEP/pair_lj_class2_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_class2_soft.h rename to src/FEP/pair_lj_class2_soft.h diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/FEP/pair_lj_cut_coul_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp rename to src/FEP/pair_lj_cut_coul_cut_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.h b/src/FEP/pair_lj_cut_coul_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_cut_soft.h rename to src/FEP/pair_lj_cut_coul_cut_soft.h diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/FEP/pair_lj_cut_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_long_soft.cpp rename to src/FEP/pair_lj_cut_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.h b/src/FEP/pair_lj_cut_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_long_soft.h rename to src/FEP/pair_lj_cut_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/FEP/pair_lj_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_soft.cpp rename to src/FEP/pair_lj_cut_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_soft.h b/src/FEP/pair_lj_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_soft.h rename to src/FEP/pair_lj_cut_soft.h diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/FEP/pair_lj_cut_tip4p_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp rename to src/FEP/pair_lj_cut_tip4p_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.h b/src/FEP/pair_lj_cut_tip4p_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_tip4p_long_soft.h rename to src/FEP/pair_lj_cut_tip4p_long_soft.h diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/FEP/pair_morse_soft.cpp similarity index 98% rename from src/USER-FEP/pair_morse_soft.cpp rename to src/FEP/pair_morse_soft.cpp index 2e228ef2ca..db7c4eca6c 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/FEP/pair_morse_soft.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,8 +13,6 @@ #include "pair_morse_soft.h" -#include -#include #include "atom.h" #include "comm.h" #include "force.h" @@ -24,6 +21,8 @@ #include "math_special.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; @@ -165,7 +164,6 @@ void PairMorseSoft::allocate() PairMorse::allocate(); int n = atom->ntypes; memory->create(lambda,n+1,n+1,"pair:lambda"); - } /* ---------------------------------------------------------------------- @@ -344,6 +342,7 @@ void PairMorseSoft::write_restart_settings(FILE *fp) fwrite(&shift_range,sizeof(double),1,fp); fwrite(&cut_global,sizeof(double),1,fp); fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- @@ -358,11 +357,13 @@ void PairMorseSoft::read_restart_settings(FILE *fp) utils::sfread(FLERR,&shift_range,sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&shift_range,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } @@ -385,8 +386,8 @@ void PairMorseSoft::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) - fprintf(fp,"%d %g %g %g %g\n",i,d0[i][j],alpha[i][j],r0[i][j], - lambda[i][j]); + fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,d0[i][j],alpha[i][j],r0[i][j], + lambda[i][j],cut[i][j]); } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-FEP/pair_morse_soft.h b/src/FEP/pair_morse_soft.h similarity index 86% rename from src/USER-FEP/pair_morse_soft.h rename to src/FEP/pair_morse_soft.h index e15658bfc0..f6ec254a44 100644 --- a/src/USER-FEP/pair_morse_soft.h +++ b/src/FEP/pair_morse_soft.h @@ -29,7 +29,8 @@ namespace LAMMPS_NS { class PairMorseSoft : public PairMorse { public: - PairMorseSoft(class LAMMPS *lmp) : PairMorse(lmp), lambda(nullptr){}; + PairMorseSoft(class LAMMPS *lmp) : + PairMorse(lmp), lambda(nullptr), nlambda(0), shift_range(1.0){}; virtual ~PairMorseSoft(); virtual void compute(int, int); @@ -41,10 +42,10 @@ class PairMorseSoft : public PairMorse { virtual void write_restart_settings(FILE *); virtual void read_restart_settings(FILE *); - void write_data(FILE *); - void write_data_all(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); virtual double single(int, int, int, int, double, double, double, double &); - void *extract(const char *, int &); + virtual void *extract(const char *, int &); protected: double **lambda; @@ -52,7 +53,7 @@ class PairMorseSoft : public PairMorse { int nlambda; double shift_range; - void allocate(); + virtual void allocate(); }; } // namespace LAMMPS_NS diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/FEP/pair_tip4p_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_tip4p_long_soft.cpp rename to src/FEP/pair_tip4p_long_soft.cpp diff --git a/src/USER-FEP/pair_tip4p_long_soft.h b/src/FEP/pair_tip4p_long_soft.h similarity index 100% rename from src/USER-FEP/pair_tip4p_long_soft.h rename to src/FEP/pair_tip4p_long_soft.h diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index 8d55cd5857..a87d2165d9 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -41,14 +41,14 @@ action fix_npt_gpu.cpp action fix_nve_asphere_gpu.h fix_nve_asphere.h action fix_nve_asphere_gpu.cpp fix_nve_asphere.cpp action gpu_extra.h -action pair_beck_gpu.cpp -action pair_beck_gpu.h +action pair_beck_gpu.cpp pair_beck.cpp +action pair_beck_gpu.h pair_beck.h action pair_born_coul_long_gpu.cpp pair_born_coul_long.cpp action pair_born_coul_long_gpu.h pair_born_coul_long.cpp action pair_born_coul_long_cs_gpu.cpp pair_born_coul_long_cs.cpp action pair_born_coul_long_cs_gpu.h pair_born_coul_long_cs.cpp -action pair_born_coul_wolf_gpu.cpp -action pair_born_coul_wolf_gpu.h +action pair_born_coul_wolf_gpu.cpp pair_born_coul_wolf.cpp +action pair_born_coul_wolf_gpu.h pair_born_coul_wolf.h action pair_born_coul_wolf_cs_gpu.cpp pair_born_coul_wolf_cs.cpp action pair_born_coul_wolf_cs_gpu.h pair_born_coul_wolf_cs.cpp action pair_born_gpu.cpp @@ -71,10 +71,10 @@ action pair_coul_long_gpu.cpp pair_coul_long.cpp action pair_coul_long_gpu.h pair_coul_long.cpp action pair_coul_long_cs_gpu.cpp pair_coul_long_cs.cpp action pair_coul_long_cs_gpu.h pair_coul_long_cs.cpp -action pair_dpd_gpu.cpp -action pair_dpd_gpu.h -action pair_dpd_tstat_gpu.cpp -action pair_dpd_tstat_gpu.h +action pair_dpd_gpu.cpp pair_dpd.cpp +action pair_dpd_gpu.h pair_dpd.h +action pair_dpd_tstat_gpu.cpp pair_dpd_tstat.cpp +action pair_dpd_tstat_gpu.h pair_dpd_tstat.h action pair_lj_cut_dipole_cut_gpu.cpp pair_lj_cut_dipole_cut.cpp action pair_lj_cut_dipole_cut_gpu.h pair_lj_cut_dipole_cut.cpp action pair_lj_sf_dipole_sf_gpu.cpp pair_lj_sf_dipole_sf.cpp @@ -85,12 +85,12 @@ action pair_eam_fs_gpu.cpp pair_eam.cpp action pair_eam_fs_gpu.h pair_eam.cpp action pair_eam_gpu.cpp pair_eam.cpp action pair_eam_gpu.h pair_eam.cpp -action pair_gauss_gpu.cpp -action pair_gauss_gpu.h +action pair_gauss_gpu.cpp pair_gauss.cpp +action pair_gauss_gpu.h pair_gauss.h action pair_gayberne_gpu.cpp pair_gayberne.cpp action pair_gayberne_gpu.h pair_gayberne.cpp -action pair_lj96_cut_gpu.cpp -action pair_lj96_cut_gpu.h +action pair_lj96_cut_gpu.cpp pair_lj96_cut.cpp +action pair_lj96_cut_gpu.h pair_lj96_cut.h action pair_lj_charmm_coul_long_gpu.cpp pair_lj_charmm_coul_long.cpp action pair_lj_charmm_coul_long_gpu.h pair_lj_charmm_coul_long.cpp action pair_lj_charmm_coul_charmm_gpu.cpp pair_lj_charmm_coul_charmm.cpp @@ -99,34 +99,34 @@ action pair_lj_class2_coul_long_gpu.cpp pair_lj_class2_coul_long.cpp action pair_lj_class2_coul_long_gpu.h pair_lj_class2_coul_long.cpp action pair_lj_class2_gpu.cpp pair_lj_class2.cpp action pair_lj_class2_gpu.h pair_lj_class2.cpp -action pair_lj_cubic_gpu.cpp -action pair_lj_cubic_gpu.h +action pair_lj_cubic_gpu.cpp pair_lj_cubic.cpp +action pair_lj_cubic_gpu.h pair_lj_cubic.h action pair_lj_cut_coul_cut_gpu.cpp action pair_lj_cut_coul_cut_gpu.h -action pair_lj_cut_coul_debye_gpu.cpp -action pair_lj_cut_coul_debye_gpu.h -action pair_lj_cut_coul_dsf_gpu.cpp -action pair_lj_cut_coul_dsf_gpu.h +action pair_lj_cut_coul_debye_gpu.cpp pair_lj_cut_coul_debye.cpp +action pair_lj_cut_coul_debye_gpu.h pair_lj_cut_coul_debye.h +action pair_lj_cut_coul_dsf_gpu.cpp pair_lj_cut_coul_dsf.cpp +action pair_lj_cut_coul_dsf_gpu.h pair_lj_cut_coul_dsf.h action pair_lj_cut_coul_long_gpu.cpp pair_lj_cut_coul_long.cpp action pair_lj_cut_coul_long_gpu.h pair_lj_cut_coul_long.cpp action pair_lj_cut_coul_msm_gpu.cpp pair_lj_cut_coul_msm.cpp action pair_lj_cut_coul_msm_gpu.h pair_lj_cut_coul_msm.h action pair_lj_cut_gpu.cpp action pair_lj_cut_gpu.h -action pair_lj_smooth_gpu.cpp -action pair_lj_smooth_gpu.h +action pair_lj_smooth_gpu.cpp pair_lj_smooth.cpp +action pair_lj_smooth_gpu.h pair_lj_smooth.h action pair_lj_expand_gpu.cpp action pair_lj_expand_gpu.h action pair_lj_expand_coul_long_gpu.cpp pair_lj_expand_coul_long.cpp action pair_lj_expand_coul_long_gpu.h pair_lj_expand_coul_long.cpp -action pair_lj_gromacs_gpu.cpp -action pair_lj_gromacs_gpu.h +action pair_lj_gromacs_gpu.cpp pair_lj_gromacs.cpp +action pair_lj_gromacs_gpu.h pair_lj_gromacs.h action pair_lj_sdk_coul_long_gpu.cpp pair_lj_sdk_coul_long.cpp action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp action pair_lj_sdk_gpu.h pair_lj_sdk.cpp -action pair_mie_cut_gpu.cpp -action pair_mie_cut_gpu.h +action pair_mie_cut_gpu.cpp pair_mie_cut.cpp +action pair_mie_cut_gpu.h pair_mie_cut.h action pair_morse_gpu.cpp action pair_morse_gpu.h action pair_resquared_gpu.cpp pair_resquared.cpp @@ -153,8 +153,8 @@ action pair_zbl_gpu.cpp action pair_zbl_gpu.h action pppm_gpu.cpp pppm.cpp action pppm_gpu.h pppm.cpp -action pair_ufm_gpu.cpp -action pair_ufm_gpu.h +action pair_ufm_gpu.cpp pair_ufm.cpp +action pair_ufm_gpu.h pair_ufm.h action pair_lj_cut_dipole_long_gpu.cpp pair_lj_cut_dipole_long.cpp action pair_lj_cut_dipole_long_gpu.h pair_lj_cut_dipole_long.cpp action pair_lj_cut_tip4p_long_gpu.h pair_lj_cut_tip4p_long.cpp diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index b98b105045..8e3ec2ace8 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -106,6 +106,8 @@ PPPMGPU::PPPMGPU(LAMMPS *lmp) : PPPM(lmp) PPPMGPU::~PPPMGPU() { PPPM_GPU_API(clear)(poisson_time); + destroy_3d_offset(density_brick_gpu,nzlo_out,nylo_out); + destroy_3d_offset(vd_brick,nzlo_out,nylo_out); } /* ---------------------------------------------------------------------- diff --git a/src/compute_contact_atom.cpp b/src/GRANULAR/compute_contact_atom.cpp similarity index 100% rename from src/compute_contact_atom.cpp rename to src/GRANULAR/compute_contact_atom.cpp diff --git a/src/compute_contact_atom.h b/src/GRANULAR/compute_contact_atom.h similarity index 100% rename from src/compute_contact_atom.h rename to src/GRANULAR/compute_contact_atom.h diff --git a/src/GRANULAR/compute_fabric.cpp b/src/GRANULAR/compute_fabric.cpp new file mode 100644 index 0000000000..a09327e2d5 --- /dev/null +++ b/src/GRANULAR/compute_fabric.cpp @@ -0,0 +1,595 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_fabric.h" + +#include "atom.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + +enum { OTHER, GRANULAR }; +enum { TYPE, RADIUS }; +enum { CN, BR, FN, FT }; + +/* ---------------------------------------------------------------------- */ + +ComputeFabric::ComputeFabric(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), tensor_style(NULL) +{ + if (narg < 3) error->all(FLERR, "Illegal compute fabric command"); + + if (strcmp(arg[3], "type") == 0) + cutstyle = TYPE; + else if (strcmp(arg[3], "radius") == 0) + cutstyle = RADIUS; + else + error->all(FLERR, "Illegal compute fabric command"); + + if (cutstyle == RADIUS && !atom->radius_flag) + error->all(FLERR, "Compute fabric radius style requires atom attribute radius"); + + // If optional arguments included, this will be oversized + ntensors = narg - 4; + tensor_style = new int[ntensors]; + + cn_flag = 0; + br_flag = 0; + fn_flag = 0; + ft_flag = 0; + type_filter = nullptr; + + ntensors = 0; + int iarg = 4; + while (iarg < narg) { + if (strcmp(arg[iarg], "contact") == 0) { + cn_flag = 1; + tensor_style[ntensors++] = CN; + } else if (strcmp(arg[iarg], "branch") == 0) { + br_flag = 1; + tensor_style[ntensors++] = BR; + } else if (strcmp(arg[iarg], "force/normal") == 0) { + fn_flag = 1; + tensor_style[ntensors++] = FN; + } else if (strcmp(arg[iarg], "force/tangential") == 0) { + ft_flag = 1; + tensor_style[ntensors++] = FT; + } else if (strcmp(arg[iarg], "type/include") == 0) { + if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in compute fabric command"); + int ntypes = atom->ntypes; + + int i, j, itype, jtype, in, jn, infield, jnfield; + int inlo, inhi, jnlo, jnhi; + char *istr, *jstr; + if (!type_filter) { + memory->create(type_filter, ntypes + 1, ntypes + 1, "compute/fabric:type_filter"); + + for (i = 0; i <= ntypes; i++) { + for (j = 0; j <= ntypes; j++) { type_filter[i][j] = 0; } + } + } + + in = strlen(arg[iarg + 1]) + 1; + istr = new char[in]; + strcpy(istr, arg[iarg + 1]); + std::vector iwords = Tokenizer(istr, ",").as_vector(); + infield = iwords.size(); + + jn = strlen(arg[iarg + 2]) + 1; + jstr = new char[jn]; + strcpy(jstr, arg[iarg + 2]); + std::vector jwords = Tokenizer(jstr, ",").as_vector(); + jnfield = jwords.size(); + + for (i = 0; i < infield; i++) { + const char *ifield = iwords[i].c_str(); + utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error); + + for (j = 0; j < jnfield; j++) { + const char *jfield = jwords[j].c_str(); + utils::bounds(FLERR, jfield, 1, ntypes, jnlo, jnhi, error); + + for (itype = inlo; itype <= inhi; itype++) { + for (jtype = jnlo; jtype <= jnhi; jtype++) { + type_filter[itype][jtype] = 1; + type_filter[jtype][itype] = 1; + } + } + } + } + + delete[] istr; + delete[] jstr; + + iarg += 2; + } else + error->all(FLERR, "Illegal compute fabric command"); + iarg++; + } + + vector_flag = 1; + size_vector = ntensors * 6; + extvector = 0; + + scalar_flag = 1; + extscalar = 1; + + vector = new double[size_vector]; +} + +/* ---------------------------------------------------------------------- */ + +ComputeFabric::~ComputeFabric() +{ + delete[] vector; + delete[] tensor_style; + memory->destroy(type_filter); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeFabric::init() +{ + if (force->pair == NULL) error->all(FLERR, "No pair style is defined for compute fabric"); + if (force->pair->single_enable == 0 && (fn_flag || ft_flag)) + error->all(FLERR, "Pair style does not support compute fabric normal or tangential force"); + + // Find if granular or gran + pstyle = OTHER; + if (force->pair_match("^granular", 0) || force->pair_match("^gran/", 0)) pstyle = GRANULAR; + + if (pstyle != GRANULAR && ft_flag) + error->all(FLERR, "Pair style does not calculate tangential forces for compute fabric"); + + if (force->pair->beyond_contact) + error->all(FLERR, "Compute fabric does not support pair styles that extend beyond contact"); + + // need an occasional half neighbor list + // set size to same value as request made by force->pair + // this should enable it to always be a copy list (e.g. for granular pstyle) + + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; + NeighRequest *pairrequest = neighbor->find_request((void *) force->pair); + if (pairrequest) neighbor->requests[irequest]->size = pairrequest->size; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeFabric::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeFabric::compute_vector() +{ + invoked_vector = update->ntimestep; + + int i, j, ii, jj, inum, jnum, itype, jtype; + tagint itag, jtag; + double xtmp, ytmp, ztmp, delx, dely, delz; + double r, rinv, rsq, radsum, fpair; + + double nx, ny, nz; + double ncinv, denom, fn, ft, prefactor; + double br_tensor[6], ft_tensor[6], fn_tensor[6]; + double trace_phi, trace_D, trace_Xfn, trace_Xft; + double phi_ij[6] = {0.0}; + double Ac_ij[6] = {0.0}; + double D_ij[6] = {0.0}; + double Xfn_ij[6] = {0.0}; + double Xft_ij[6] = {0.0}; + double temp_dbl[6]; + + int *ilist, *jlist, *numneigh, **firstneigh; + + double **x = atom->x; + double *radius = atom->radius; + tagint *tag = atom->tag; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + Pair *pair = force->pair; + double **cutsq = force->pair->cutsq; + + // invoke compute_scalar() to update the number of contacts, if needed + nc = compute_scalar(); + + // If no contacts, everything will be zero + if (nc == 0) { + for (i = 0; i < size_vector; i++) vector[i] = 0.0; + return; + } + ncinv = 1.0 / nc; + + // First loop through and calculate contact fabric tensor + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (!(mask[i] & groupbit)) continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itag = tag[i]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + if (!(mask[j] & groupbit)) continue; + + // itag = jtag is possible for long cutoffs that include images of self + + if (newton_pair == 0 && j >= nlocal) { + jtag = tag[j]; + if (itag > jtag) { + if ((itag + jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag + jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + } + + jtype = type[j]; + + if (type_filter) + if (type_filter[itype][jtype] == 0) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + + if (cutstyle == TYPE) { + if (rsq >= cutsq[itype][jtype]) continue; + } else { + radsum = radius[i] + radius[j]; + if (rsq >= radsum * radsum) continue; + } + + r = sqrt(rsq); + rinv = 1.0 / r; + nx = delx * rinv; + ny = dely * rinv; + nz = delz * rinv; + + phi_ij[0] += nx * nx; + phi_ij[1] += ny * ny; + phi_ij[2] += nz * nz; + phi_ij[3] += nx * ny; + phi_ij[4] += nx * nz; + phi_ij[5] += ny * nz; + } + } + + //Sum phi across processors + MPI_Allreduce(phi_ij, temp_dbl, 6, MPI_DOUBLE, MPI_SUM, world); + for (i = 0; i < 6; i++) phi_ij[i] = temp_dbl[i] * ncinv; + + trace_phi = (1.0 / 3.0) * (phi_ij[0] + phi_ij[1] + phi_ij[2]); + + Ac_ij[0] = (15.0 / 2.0) * (phi_ij[0] - trace_phi); + Ac_ij[1] = (15.0 / 2.0) * (phi_ij[1] - trace_phi); + Ac_ij[2] = (15.0 / 2.0) * (phi_ij[2] - trace_phi); + Ac_ij[3] = (15.0 / 2.0) * (phi_ij[3]); + Ac_ij[4] = (15.0 / 2.0) * (phi_ij[4]); + Ac_ij[5] = (15.0 / 2.0) * (phi_ij[5]); + + // If needed, loop through and calculate other fabric tensors + if (br_flag || fn_flag || ft_flag) { + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (!(mask[i] & groupbit)) continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itag = tag[i]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + if (!(mask[j] & groupbit)) continue; + + // itag = jtag is possible for long cutoffs that include images of self + + if (newton_pair == 0 && j >= nlocal) { + jtag = tag[j]; + if (itag > jtag) { + if ((itag + jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag + jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + } + + jtype = type[j]; + + if (type_filter) + if (type_filter[itype][jtype] == 0) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + + if (cutstyle == TYPE) { + if (rsq >= cutsq[itype][jtype]) continue; + } else { + radsum = radius[i] + radius[j]; + if (rsq >= radsum * radsum) continue; + } + + if (fn_flag || ft_flag) pair->single(i, j, itype, jtype, rsq, 1.0, 1.0, fpair); + + r = sqrt(rsq); + rinv = 1.0 / r; + nx = delx * rinv; + ny = dely * rinv; + nz = delz * rinv; + + denom = 1 + Ac_ij[0] * nx * nx + Ac_ij[1] * ny * ny + Ac_ij[2] * nz * nz; + denom += 2 * Ac_ij[3] * nx * ny + 2 * Ac_ij[4] * nx * nz + 2 * Ac_ij[5] * ny * nz; + prefactor = ncinv / denom; + + if (br_flag) { + D_ij[0] += prefactor * nx * nx * r; + D_ij[1] += prefactor * ny * ny * r; + D_ij[2] += prefactor * nz * nz * r; + D_ij[3] += prefactor * nx * ny * r; + D_ij[4] += prefactor * nx * nz * r; + D_ij[5] += prefactor * ny * nz * r; + } + + if (fn_flag || ft_flag) { + fn = r * fpair; + + Xfn_ij[0] += prefactor * nx * nx * fn; + Xfn_ij[1] += prefactor * ny * ny * fn; + Xfn_ij[2] += prefactor * nz * nz * fn; + Xfn_ij[3] += prefactor * nx * ny * fn; + Xfn_ij[4] += prefactor * nx * nz * fn; + Xfn_ij[5] += prefactor * ny * nz * fn; + + if (ft_flag) { + ft = force->pair->svector[3]; + + Xft_ij[0] += prefactor * nx * nx * ft; + Xft_ij[1] += prefactor * ny * ny * ft; + Xft_ij[2] += prefactor * nz * nz * ft; + Xft_ij[3] += prefactor * nx * ny * ft; + Xft_ij[4] += prefactor * nx * nz * ft; + Xft_ij[5] += prefactor * ny * nz * ft; + } + } + } + } + } + + // Output results + + if (cn_flag) { + for (i = 0; i < ntensors; i++) { + if (tensor_style[i] == CN) { + for (j = 0; j < 6; j++) vector[6 * i + j] = Ac_ij[j]; + } + } + } + + if (br_flag) { + MPI_Allreduce(D_ij, temp_dbl, 6, MPI_DOUBLE, MPI_SUM, world); + for (i = 0; i < 6; i++) D_ij[i] = temp_dbl[i]; + + trace_D = (1.0 / 3.0) * (D_ij[0] + D_ij[1] + D_ij[2]); + + br_tensor[0] = (15.0 / (6.0 * trace_D)) * (D_ij[0] - trace_D); + br_tensor[1] = (15.0 / (6.0 * trace_D)) * (D_ij[1] - trace_D); + br_tensor[2] = (15.0 / (6.0 * trace_D)) * (D_ij[2] - trace_D); + br_tensor[3] = (15.0 / (6.0 * trace_D)) * (D_ij[3]); + br_tensor[4] = (15.0 / (6.0 * trace_D)) * (D_ij[4]); + br_tensor[5] = (15.0 / (6.0 * trace_D)) * (D_ij[5]); + + for (i = 0; i < ntensors; i++) { + if (tensor_style[i] == BR) { + for (j = 0; j < 6; j++) vector[6 * i + j] = br_tensor[j]; + } + } + } + + if (fn_flag || ft_flag) { + MPI_Allreduce(Xfn_ij, temp_dbl, 6, MPI_DOUBLE, MPI_SUM, world); + for (i = 0; i < 6; i++) Xfn_ij[i] = temp_dbl[i]; + + trace_Xfn = (1.0 / 3.0) * (Xfn_ij[0] + Xfn_ij[1] + Xfn_ij[2]); + } + + if (fn_flag) { + + fn_tensor[0] = (15.0 / (6.0 * trace_Xfn)) * (Xfn_ij[0] - trace_Xfn); + fn_tensor[1] = (15.0 / (6.0 * trace_Xfn)) * (Xfn_ij[1] - trace_Xfn); + fn_tensor[2] = (15.0 / (6.0 * trace_Xfn)) * (Xfn_ij[2] - trace_Xfn); + fn_tensor[3] = (15.0 / (6.0 * trace_Xfn)) * (Xfn_ij[3]); + fn_tensor[4] = (15.0 / (6.0 * trace_Xfn)) * (Xfn_ij[4]); + fn_tensor[5] = (15.0 / (6.0 * trace_Xfn)) * (Xfn_ij[5]); + + for (i = 0; i < ntensors; i++) { + if (tensor_style[i] == FN) { + for (j = 0; j < 6; j++) vector[6 * i + j] = fn_tensor[j]; + } + } + } + + if (ft_flag) { + MPI_Allreduce(Xft_ij, temp_dbl, 6, MPI_DOUBLE, MPI_SUM, world); + for (i = 0; i < 6; i++) Xft_ij[i] = temp_dbl[i]; + + trace_Xft = (1.0 / 3.0) * (Xft_ij[0] + Xft_ij[1] + Xft_ij[2]); + + ft_tensor[0] = (15.0 / (9.0 * trace_Xfn)) * (Xft_ij[0] - trace_Xft); + ft_tensor[1] = (15.0 / (9.0 * trace_Xfn)) * (Xft_ij[1] - trace_Xft); + ft_tensor[2] = (15.0 / (9.0 * trace_Xfn)) * (Xft_ij[2] - trace_Xft); + ft_tensor[3] = (15.0 / (9.0 * trace_Xfn)) * (Xft_ij[3]); + ft_tensor[4] = (15.0 / (9.0 * trace_Xfn)) * (Xft_ij[4]); + ft_tensor[5] = (15.0 / (9.0 * trace_Xfn)) * (Xft_ij[5]); + + for (i = 0; i < ntensors; i++) { + if (tensor_style[i] == FT) { + for (j = 0; j < 6; j++) vector[6 * i + j] = ft_tensor[j]; + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +double ComputeFabric::compute_scalar() +{ + // Skip if already calculated on this timestep + if (invoked_scalar == update->ntimestep) return nc; + + invoked_scalar = update->ntimestep; + + int i, j, ii, jj, inum, jnum, itype, jtype; + tagint itag, jtag; + double xtmp, ytmp, ztmp, delx, dely, delz; + double rsq, radsum, temp_dbl; + + int *ilist, *jlist, *numneigh, **firstneigh; + + double **x = atom->x; + double *radius = atom->radius; + tagint *tag = atom->tag; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + double **cutsq = force->pair->cutsq; + + // First loop through and calculate contact fabric tensor + nc = 0; + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (!(mask[i] & groupbit)) continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itag = tag[i]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + if (!(mask[j] & groupbit)) continue; + + // itag = jtag is possible for long cutoffs that include images of self + + if (newton_pair == 0 && j >= nlocal) { + jtag = tag[j]; + if (itag > jtag) { + if ((itag + jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag + jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + } + + jtype = type[j]; + + if (type_filter) + if (type_filter[itype][jtype] == 0) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + + if (cutstyle == TYPE) { + if (rsq >= cutsq[itype][jtype]) continue; + } else { + radsum = radius[i] + radius[j]; + if (rsq >= radsum * radsum) continue; + } + + nc += 1.0; + } + } + //Count total contacts across processors + MPI_Allreduce(&nc, &temp_dbl, 1, MPI_DOUBLE, MPI_SUM, world); + nc = temp_dbl; + + scalar = nc; + return nc; +} + diff --git a/src/GRANULAR/compute_fabric.h b/src/GRANULAR/compute_fabric.h new file mode 100644 index 0000000000..5e20ea6562 --- /dev/null +++ b/src/GRANULAR/compute_fabric.h @@ -0,0 +1,79 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(fabric,ComputeFabric); +// clang-format on +#else + +#ifndef LMP_COMPUTE_FABRIC_H +#define LMP_COMPUTE_FABRIC_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeFabric : public Compute { + public: + ComputeFabric(class LAMMPS *, int, char **); + ~ComputeFabric(); + void init(); + void init_list(int, class NeighList *); + void compute_vector(); + double compute_scalar(); + + private: + int ntensors, pstyle, cutstyle; + double nc; + int *tensor_style; + int **type_filter; + class NeighList *list; + + int cn_flag, br_flag, fn_flag, ft_flag; +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Compute fabric radius style requires atom attribute radius + +Self-explanatory. + +E: No pair style is defined for compute fabric + +Self-explanatory. + +E: Pair style does not support compute fabric normal or tangential force + +Pair style must be single enabled to calculate the normal or tangential force tensors + +E: Pair style does not calculate tangential forces for compute fabric + +The tangential force tensor can only be calculated for granular pair styles with tangential forces + +E: Compute fabric does not support pair styles that extend beyond contact + +Granular pair styles that extend beyond contact such as JKR or DMT are not supported + +*/ diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 52311f64a7..5f16176e49 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -437,7 +437,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : // register with Atom class history_one = nullptr; - grow_arrays(atom->nmax); + FixWallGran::grow_arrays(atom->nmax); atom->add_callback(Atom::GROW); atom->add_callback(Atom::RESTART); @@ -1193,7 +1193,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, knfac = E; //Hooke a = sqrt(dR); Fne = knfac*delta; - if (normal_model != HOOKE) { + if (normal_model != NORMAL_HOOKE) { Fne *= a; knfac *= a; } @@ -1555,8 +1555,7 @@ double FixWallGran::memory_usage() void FixWallGran::grow_arrays(int nmax) { - if (use_history) memory->grow(history_one,nmax,size_history, - "fix_wall_gran:history_one"); + if (use_history) memory->grow(history_one,nmax,size_history,"fix_wall_gran:history_one"); if (peratom_flag) { memory->grow(array_atom,nmax,size_peratom_cols,"fix_wall_gran:array_atom"); } diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 0a92bac543..37afe9632c 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -62,7 +62,7 @@ FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) : ncontact = nullptr; walls = nullptr; history_many = nullptr; - grow_arrays(atom->nmax); + FixWallGranRegion::grow_arrays(atom->nmax); // initialize shear history as if particle is not touching region @@ -355,8 +355,7 @@ void FixWallGranRegion::grow_arrays(int nmax) if (use_history) { memory->grow(ncontact,nmax,"fix_wall_gran:ncontact"); memory->grow(walls,nmax,tmax,"fix_wall_gran:walls"); - memory->grow(history_many,nmax,tmax,size_history, - "fix_wall_gran:history_many"); + memory->grow(history_many,nmax,tmax,size_history,"fix_wall_gran:history_many"); } if (peratom_flag) memory->grow(array_atom,nmax,size_peratom_cols,"fix_wall_gran:array_atom"); diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 753cceb247..e6013b9940 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -68,8 +67,8 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp) // this is so final order of Modify:fix will conform to input script fix_history = nullptr; - modify->add_fix("NEIGH_HISTORY_HH_DUMMY all DUMMY"); - fix_dummy = (FixDummy *) modify->fix[modify->nfix-1]; + fix_dummy = (FixDummy *) modify->add_fix("NEIGH_HISTORY_HH_DUMMY" + + std::to_string(instance_me) + " all DUMMY"); } /* ---------------------------------------------------------------------- */ @@ -80,8 +79,8 @@ PairGranHookeHistory::~PairGranHookeHistory() delete [] svector; - if (!fix_history) modify->delete_fix("NEIGH_HISTORY_HH_DUMMY"); - else modify->delete_fix("NEIGH_HISTORY_HH"); + if (!fix_history) modify->delete_fix("NEIGH_HISTORY_HH_DUMMY"+std::to_string(instance_me)); + else modify->delete_fix("NEIGH_HISTORY_HH"+std::to_string(instance_me)); if (allocated) { memory->destroy(setflag); @@ -436,22 +435,20 @@ void PairGranHookeHistory::init_style() // this is so its order in the fix list is preserved if (history && (fix_history == nullptr)) { - auto cmd = fmt::format("NEIGH_HISTORY_HH all NEIGH_HISTORY {}", - size_history); - modify->replace_fix("NEIGH_HISTORY_HH_DUMMY",cmd,1); - int ifix = modify->find_fix("NEIGH_HISTORY_HH"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; + auto cmd = fmt::format("NEIGH_HISTORY_HH{} all NEIGH_HISTORY {}", instance_me, size_history); + fix_history = (FixNeighHistory *) modify->replace_fix("NEIGH_HISTORY_HH_DUMMY" + + std::to_string(instance_me),cmd,1); fix_history->pair = this; } // check for FixFreeze and set freeze_group_bit - for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"freeze") == 0) break; - if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit; - else freeze_group_bit = 0; + int ifreeze = modify->find_fix_by_style("^freeze"); + if (ifreeze < 0) freeze_group_bit = 0; + else freeze_group_bit = modify->fix[ifreeze]->groupbit; // check for FixRigid so can extract rigid body masses + // FIXME: this only catches the first rigid fix, there may be multiple. fix_rigid = nullptr; for (i = 0; i < modify->nfix; i++) @@ -460,15 +457,8 @@ void PairGranHookeHistory::init_style() // check for FixPour and FixDeposit so can extract particle radii - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; - - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; + int ipour = modify->find_fix_by_style("^pour"); + int idep = modify->find_fix_by_style("^deposit"); // set maxrad_dynamic and maxrad_frozen for each type // include future FixPour and FixDeposit particles as dynamic @@ -499,15 +489,13 @@ void PairGranHookeHistory::init_style() else onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius[i]); - MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes, - MPI_DOUBLE,MPI_MAX,world); - MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes, - MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes,MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes,MPI_DOUBLE,MPI_MAX,world); // set fix which stores history info if (history) { - int ifix = modify->find_fix("NEIGH_HISTORY_HH"); + int ifix = modify->find_fix("NEIGH_HISTORY_HH"+std::to_string(instance_me)); if (ifix < 0) error->all(FLERR,"Could not find pair fix neigh history ID"); fix_history = (FixNeighHistory *) modify->fix[ifix]; } diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index cca349b819..2846403e4c 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -20,25 +20,24 @@ #include "pair_granular.h" -#include -#include - #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" +#include "comm.h" +#include "error.h" #include "fix.h" #include "fix_dummy.h" #include "fix_neigh_history.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "force.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -103,15 +102,15 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) // this is so final order of Modify:fix will conform to input script fix_history = nullptr; - modify->add_fix("NEIGH_HISTORY_GRANULAR_DUMMY all DUMMY"); - fix_dummy = (FixDummy *) modify->fix[modify->nfix-1]; + fix_dummy = (FixDummy *) modify->add_fix("NEIGH_HISTORY_GRANULAR_DUMMY all DUMMY"); } /* ---------------------------------------------------------------------- */ PairGranular::~PairGranular() { - delete [] svector; + delete[] svector; + delete[] history_transfer_factors; if (!fix_history) modify->delete_fix("NEIGH_HISTORY_GRANULAR_DUMMY"); else modify->delete_fix("NEIGH_HISTORY_GRANULAR"); @@ -1122,21 +1121,21 @@ void PairGranular::init_style() // this is so its order in the fix list is preserved if (use_history && fix_history == nullptr) { - modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY","NEIGH_HISTORY_GRANULAR" - " all NEIGH_HISTORY " + std::to_string(size_history),1); - int ifix = modify->find_fix("NEIGH_HISTORY_GRANULAR"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; + fix_history = (FixNeighHistory *) modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY", + "NEIGH_HISTORY_GRANULAR" + " all NEIGH_HISTORY " + + std::to_string(size_history),1); fix_history->pair = this; } // check for FixFreeze and set freeze_group_bit - for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"freeze") == 0) break; - if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit; - else freeze_group_bit = 0; + int ifix = modify->find_fix_by_style("^freeze"); + if (ifix < 0) freeze_group_bit = 0; + else freeze_group_bit = modify->fix[ifix]->groupbit; // check for FixRigid so can extract rigid body masses + // FIXME: this only catches the first rigid fix, there may be multiple. fix_rigid = nullptr; for (i = 0; i < modify->nfix; i++) @@ -1145,15 +1144,8 @@ void PairGranular::init_style() // check for FixPour and FixDeposit so can extract particle radii - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; - - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; + int ipour = modify->find_fix_by_style("^pour"); + int idep = modify->find_fix_by_style("^deposit"); // set maxrad_dynamic and maxrad_frozen for each type // include future FixPour and FixDeposit particles as dynamic @@ -1187,10 +1179,8 @@ void PairGranular::init_style() } } - MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes, - MPI_DOUBLE,MPI_MAX,world); - MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes, - MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes,MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes,MPI_DOUBLE,MPI_MAX,world); // set fix which stores history info diff --git a/src/USER-H5MD/Install.sh b/src/H5MD/Install.sh similarity index 100% rename from src/USER-H5MD/Install.sh rename to src/H5MD/Install.sh diff --git a/src/USER-H5MD/README b/src/H5MD/README similarity index 100% rename from src/USER-H5MD/README rename to src/H5MD/README diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/H5MD/dump_h5md.cpp similarity index 100% rename from src/USER-H5MD/dump_h5md.cpp rename to src/H5MD/dump_h5md.cpp diff --git a/src/USER-H5MD/dump_h5md.h b/src/H5MD/dump_h5md.h similarity index 100% rename from src/USER-H5MD/dump_h5md.h rename to src/H5MD/dump_h5md.h diff --git a/src/USER-INTEL/Install.sh b/src/INTEL/Install.sh similarity index 95% rename from src/USER-INTEL/Install.sh rename to src/INTEL/Install.sh index 8c291f0ae2..94d967b194 100755 --- a/src/USER-INTEL/Install.sh +++ b/src/INTEL/Install.sh @@ -56,7 +56,7 @@ if (test $mode = 1) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*INTEL[^ \t]* //' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_USER_INTEL |' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_INTEL |' ../Makefile.package fi elif (test $mode = 0) then diff --git a/src/USER-INTEL/README b/src/INTEL/README similarity index 98% rename from src/USER-INTEL/README rename to src/INTEL/README index 650e2c3a2d..b59b0619b3 100644 --- a/src/USER-INTEL/README +++ b/src/INTEL/README @@ -42,8 +42,8 @@ be added or changed in the Makefile depending on the version: ----------------------------------------------------------------------------- When using the suffix command with "intel", intel styles will be used if they -exist. If the suffix command is used with "hybrid intel omp" and the USER-OMP -is installed, USER-OMP styles will be used whenever USER-INTEL styles are not +exist. If the suffix command is used with "hybrid intel omp" and the OPENMP +is installed, OPENMP styles will be used whenever INTEL styles are not available. This allow for running most styles in LAMMPS with threading. ----------------------------------------------------------------------------- diff --git a/src/USER-INTEL/TEST/README b/src/INTEL/TEST/README similarity index 95% rename from src/USER-INTEL/TEST/README rename to src/INTEL/TEST/README index fdc92b363d..a3eee3f69c 100644 --- a/src/USER-INTEL/TEST/README +++ b/src/INTEL/TEST/README @@ -32,7 +32,7 @@ ############################################################################# ############################################################################# -# For Skylake server (Xeon) architectures, see notes in the USER-INTEL/README +# For Skylake server (Xeon) architectures, see notes in the INTEL/README # for build flags that should be used. ############################################################################# @@ -62,7 +62,7 @@ # -v N off # newton off # # The default is on for all of the benchmarks except for LJ where the off -# setting performs best with the USER-INTEL package +# setting performs best with the INTEL package ############################################################################# # Example for running benchmarks (see run_benchmarks.sh for script): @@ -106,17 +106,17 @@ export bench=in.intel.lj mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -v N on ############################################################################# -# To run with USER-OMP package +# To run with OPENMP package ############################################################################# mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk omp 0 -sf omp -v N on ############################################################################# -# To run with USER-INTEL package and no coprocessor +# To run with INTEL package and no coprocessor ############################################################################# mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 0 -sf intel ############################################################################# -# To run with USER-INTEL and automatic load balancing to 1 coprocessor +# To run with INTEL and automatic load balancing to 1 coprocessor ############################################################################# mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 1 -sf intel diff --git a/src/USER-INTEL/TEST/in.intel.airebo b/src/INTEL/TEST/in.intel.airebo similarity index 100% rename from src/USER-INTEL/TEST/in.intel.airebo rename to src/INTEL/TEST/in.intel.airebo diff --git a/src/USER-INTEL/TEST/in.intel.dpd b/src/INTEL/TEST/in.intel.dpd similarity index 100% rename from src/USER-INTEL/TEST/in.intel.dpd rename to src/INTEL/TEST/in.intel.dpd diff --git a/src/USER-INTEL/TEST/in.intel.eam b/src/INTEL/TEST/in.intel.eam similarity index 100% rename from src/USER-INTEL/TEST/in.intel.eam rename to src/INTEL/TEST/in.intel.eam diff --git a/src/USER-INTEL/TEST/in.intel.lc b/src/INTEL/TEST/in.intel.lc similarity index 100% rename from src/USER-INTEL/TEST/in.intel.lc rename to src/INTEL/TEST/in.intel.lc diff --git a/src/USER-INTEL/TEST/in.intel.lj b/src/INTEL/TEST/in.intel.lj similarity index 100% rename from src/USER-INTEL/TEST/in.intel.lj rename to src/INTEL/TEST/in.intel.lj diff --git a/src/USER-INTEL/TEST/in.intel.rhodo b/src/INTEL/TEST/in.intel.rhodo similarity index 100% rename from src/USER-INTEL/TEST/in.intel.rhodo rename to src/INTEL/TEST/in.intel.rhodo diff --git a/src/USER-INTEL/TEST/in.intel.sw b/src/INTEL/TEST/in.intel.sw similarity index 100% rename from src/USER-INTEL/TEST/in.intel.sw rename to src/INTEL/TEST/in.intel.sw diff --git a/src/USER-INTEL/TEST/in.intel.tersoff b/src/INTEL/TEST/in.intel.tersoff similarity index 100% rename from src/USER-INTEL/TEST/in.intel.tersoff rename to src/INTEL/TEST/in.intel.tersoff diff --git a/src/USER-INTEL/TEST/in.intel.water b/src/INTEL/TEST/in.intel.water similarity index 100% rename from src/USER-INTEL/TEST/in.intel.water rename to src/INTEL/TEST/in.intel.water diff --git a/src/USER-INTEL/TEST/in.lc_generate_restart b/src/INTEL/TEST/in.lc_generate_restart similarity index 100% rename from src/USER-INTEL/TEST/in.lc_generate_restart rename to src/INTEL/TEST/in.lc_generate_restart diff --git a/src/USER-INTEL/TEST/mW.sw b/src/INTEL/TEST/mW.sw similarity index 100% rename from src/USER-INTEL/TEST/mW.sw rename to src/INTEL/TEST/mW.sw diff --git a/src/USER-INTEL/TEST/mW_32k_cube.data b/src/INTEL/TEST/mW_32k_cube.data similarity index 100% rename from src/USER-INTEL/TEST/mW_32k_cube.data rename to src/INTEL/TEST/mW_32k_cube.data diff --git a/src/USER-INTEL/TEST/run_benchmarks.sh b/src/INTEL/TEST/run_benchmarks.sh similarity index 100% rename from src/USER-INTEL/TEST/run_benchmarks.sh rename to src/INTEL/TEST/run_benchmarks.sh diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/INTEL/angle_charmm_intel.cpp similarity index 97% rename from src/USER-INTEL/angle_charmm_intel.cpp rename to src/INTEL/angle_charmm_intel.cpp index 9284150522..26943934be 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/INTEL/angle_charmm_intel.cpp @@ -83,7 +83,7 @@ void AngleCharmmIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -162,7 +162,11 @@ void AngleCharmmIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:seangle, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:seangle, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -246,7 +250,11 @@ void AngleCharmmIntel::eval(const int vflag, // apply force to each of 3 atoms #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/INTEL/angle_charmm_intel.h similarity index 100% rename from src/USER-INTEL/angle_charmm_intel.h rename to src/INTEL/angle_charmm_intel.h diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/INTEL/angle_harmonic_intel.cpp similarity index 97% rename from src/USER-INTEL/angle_harmonic_intel.cpp rename to src/INTEL/angle_harmonic_intel.cpp index 6a7a5c2fe2..e392730edc 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/INTEL/angle_harmonic_intel.cpp @@ -83,7 +83,7 @@ void AngleHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -162,7 +162,11 @@ void AngleHarmonicIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:seangle, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:seangle, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -228,7 +232,11 @@ void AngleHarmonicIntel::eval(const int vflag, // apply force to each of 3 atoms #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/INTEL/angle_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/angle_harmonic_intel.h rename to src/INTEL/angle_harmonic_intel.h diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/INTEL/bond_fene_intel.cpp similarity index 97% rename from src/USER-INTEL/bond_fene_intel.cpp rename to src/INTEL/bond_fene_intel.cpp index 0efcdafaef..1ab8da68d9 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/INTEL/bond_fene_intel.cpp @@ -82,7 +82,7 @@ void BondFENEIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -158,7 +158,11 @@ void BondFENEIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:sebond, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:sebond, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -215,7 +219,11 @@ void BondFENEIntel::eval(const int vflag, // apply force to each of 2 atoms #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/INTEL/bond_fene_intel.h similarity index 100% rename from src/USER-INTEL/bond_fene_intel.h rename to src/INTEL/bond_fene_intel.h diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/INTEL/bond_harmonic_intel.cpp similarity index 97% rename from src/USER-INTEL/bond_harmonic_intel.cpp rename to src/INTEL/bond_harmonic_intel.cpp index db531ee650..35b194f0fa 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/INTEL/bond_harmonic_intel.cpp @@ -79,7 +79,7 @@ void BondHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -155,7 +155,11 @@ void BondHarmonicIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:sebond, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:sebond, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -184,7 +188,11 @@ void BondHarmonicIntel::eval(const int vflag, // apply force to each of 2 atoms #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/INTEL/bond_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/bond_harmonic_intel.h rename to src/INTEL/bond_harmonic_intel.h diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/INTEL/dihedral_charmm_intel.cpp similarity index 98% rename from src/USER-INTEL/dihedral_charmm_intel.cpp rename to src/INTEL/dihedral_charmm_intel.cpp index c49768afe6..4116d9134f 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/INTEL/dihedral_charmm_intel.cpp @@ -88,7 +88,7 @@ void DihedralCharmmIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); // insure pair->ev_tally() will use 1-4 virial contribution @@ -181,9 +181,16 @@ void DihedralCharmmIntel::eval(const int vflag, } #if defined(LMP_SIMD_COMPILER_TEST) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:sedihedral, sevdwl, secoul, sv0, sv1, sv2, \ + sv3, sv4, sv5, spv0, spv1, spv2, spv3, spv4, \ + spv5) +#else #pragma simd reduction(+:sedihedral, sevdwl, secoul, sv0, sv1, sv2, \ - sv3, sv4, sv5, spv0, spv1, spv2, spv3, spv4, spv5) + sv3, sv4, sv5, spv0, spv1, spv2, spv3, spv4, \ + spv5) +#endif + #pragma vector aligned for (int n = nfrom; n < nto; n++) { #endif for (int n = nfrom; n < nto; n += npl) { @@ -329,7 +336,11 @@ void DihedralCharmmIntel::eval(const int vflag, #if defined(LMP_SIMD_COMPILER_TEST) +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i2 < nlocal) { @@ -408,7 +419,11 @@ void DihedralCharmmIntel::eval(const int vflag, // apply force to each of 4 atoms #if defined(LMP_SIMD_COMPILER_TEST) +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/dihedral_charmm_intel.h b/src/INTEL/dihedral_charmm_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_charmm_intel.h rename to src/INTEL/dihedral_charmm_intel.h diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/INTEL/dihedral_fourier_intel.cpp similarity index 98% rename from src/USER-INTEL/dihedral_fourier_intel.cpp rename to src/INTEL/dihedral_fourier_intel.cpp index d8a500b40e..d952ac7506 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/INTEL/dihedral_fourier_intel.cpp @@ -77,7 +77,7 @@ void DihedralFourierIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -154,7 +154,11 @@ void DihedralFourierIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -304,7 +308,11 @@ void DihedralFourierIntel::eval(const int vflag, } #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/dihedral_fourier_intel.h b/src/INTEL/dihedral_fourier_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_fourier_intel.h rename to src/INTEL/dihedral_fourier_intel.h diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/INTEL/dihedral_harmonic_intel.cpp similarity index 97% rename from src/USER-INTEL/dihedral_harmonic_intel.cpp rename to src/INTEL/dihedral_harmonic_intel.cpp index 82eb87e90f..df9304b6ba 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/INTEL/dihedral_harmonic_intel.cpp @@ -77,7 +77,7 @@ void DihedralHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -154,7 +154,11 @@ void DihedralHarmonicIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -299,7 +303,11 @@ void DihedralHarmonicIntel::eval(const int vflag, } #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/dihedral_harmonic_intel.h b/src/INTEL/dihedral_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_harmonic_intel.h rename to src/INTEL/dihedral_harmonic_intel.h diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/INTEL/dihedral_opls_intel.cpp similarity index 98% rename from src/USER-INTEL/dihedral_opls_intel.cpp rename to src/INTEL/dihedral_opls_intel.cpp index a19482a2d8..89f06773d5 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/INTEL/dihedral_opls_intel.cpp @@ -81,7 +81,7 @@ void DihedralOPLSIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -158,7 +158,11 @@ void DihedralOPLSIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n ++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -319,7 +323,11 @@ void DihedralOPLSIntel::eval(const int vflag, } #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/dihedral_opls_intel.h b/src/INTEL/dihedral_opls_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_opls_intel.h rename to src/INTEL/dihedral_opls_intel.h diff --git a/src/USER-INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp similarity index 97% rename from src/USER-INTEL/fix_intel.cpp rename to src/INTEL/fix_intel.cpp index edec1f0c42..d0633d7791 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/INTEL/fix_intel.cpp @@ -510,7 +510,7 @@ void FixIntel::bond_init_check() if ((_offload_balance != 0.0) && (atom->molecular != Atom::ATOMIC) && (force->newton_pair != force->newton_bond)) error->all(FLERR, - "USER-INTEL package requires same setting for newton bond and non-bond."); + "INTEL package requires same setting for newton bond and non-bond."); int intel_pair = 0; if (force->pair_match("/intel$", 0) != nullptr) @@ -557,12 +557,12 @@ void FixIntel::check_neighbor_intel() if (neighbor->requests[i]->skip && _offload_balance != 0.0) error->all(FLERR, "Cannot yet use hybrid styles with Intel offload."); - // avoid flagging a neighbor list as both USER-INTEL and USER-OMP + // avoid flagging a neighbor list as both INTEL and OPENMP if (neighbor->requests[i]->intel) neighbor->requests[i]->omp = 0; } #else - // avoid flagging a neighbor list as both USER-INTEL and USER-OMP + // avoid flagging a neighbor list as both INTEL and OPENMP const int nrequest = neighbor->nrequest; for (int i = 0; i < nrequest; ++i) if (neighbor->requests[i]->intel) @@ -635,19 +635,31 @@ void FixIntel::reduce_results(acc_t * _noalias const f_scalar) if (_nthreads == 4) { acc_t *f_scalar3 = f_scalar2 + f_stride4; acc_t *f_scalar4 = f_scalar3 + f_stride4; - _use_simd_pragma("vector aligned") - _use_simd_pragma("simd") + #if defined(USE_OMP_SIMD) + #pragma omp simd aligned(f_scalar,f_scalar2,f_scalar3,f_scalar4:64) + #elif defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma simd + #endif for (int n = 0; n < o_range; n++) f_scalar[n] += f_scalar2[n] + f_scalar3[n] + f_scalar4[n]; } else if (_nthreads == 2) { - _use_simd_pragma("vector aligned") - _use_simd_pragma("simd") + #if defined(USE_OMP_SIMD) + #pragma omp simd aligned(f_scalar,f_scalar2:64) + #elif defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma simd + #endif for (int n = 0; n < o_range; n++) f_scalar[n] += f_scalar2[n]; } else { acc_t *f_scalar3 = f_scalar2 + f_stride4; - _use_simd_pragma("vector aligned") - _use_simd_pragma("simd") + #if defined(USE_OMP_SIMD) + #pragma omp simd aligned(f_scalar,f_scalar2,f_scalar3:64) + #elif defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma simd + #endif for (int n = 0; n < o_range; n++) f_scalar[n] += f_scalar2[n] + f_scalar3[n]; } @@ -662,8 +674,12 @@ void FixIntel::reduce_results(acc_t * _noalias const f_scalar) acc_t *f_scalar2 = f_scalar + f_stride4; for (int t = 1; t < _nthreads; t++) { - _use_simd_pragma("vector aligned") - _use_simd_pragma("simd") + #if defined(USE_OMP_SIMD) + #pragma omp simd aligned(f_scalar,f_scalar2:64) + #elif defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma simd + #endif for (int n = iifrom; n < iito; n++) f_scalar[n] += f_scalar2[n]; f_scalar2 += f_stride4; diff --git a/src/USER-INTEL/fix_intel.h b/src/INTEL/fix_intel.h similarity index 98% rename from src/USER-INTEL/fix_intel.h rename to src/INTEL/fix_intel.h index 8bc3e80780..8e5d2b524d 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/INTEL/fix_intel.h @@ -541,19 +541,19 @@ W: More MPI tasks/OpenMP threads than available cores Using more MPI tasks/OpenMP threads than available cores will typically decrease performance. -E: USER-INTEL package requires same setting for newton bond and non-bond. +E: INTEL package requires same setting for newton bond and non-bond. The newton setting must be the same for both pairwise and bonded forces. E: Intel styles for bond/angle/dihedral/improper require intel pair style." -You cannot use the USER-INTEL package for bond calculations without a -USER-INTEL supported pair style. +You cannot use the INTEL package for bond calculations without a +INTEL supported pair style. E: Intel styles for kspace require intel pair style. -You cannot use the USER-INTEL package for kspace calculations without a -USER-INTEL supported pair style. +You cannot use the INTEL package for kspace calculations without a +INTEL supported pair style. E: Cannot currently get per-atom virials with intel package. diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/INTEL/fix_nh_intel.cpp similarity index 95% rename from src/USER-INTEL/fix_nh_intel.cpp rename to src/INTEL/fix_nh_intel.cpp index 5370e3a13f..a4fdecbd96 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/INTEL/fix_nh_intel.cpp @@ -99,8 +99,12 @@ void FixNHIntel::remap() if (allremap) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { const double d0 = x[i].x - b0; @@ -112,8 +116,12 @@ void FixNHIntel::remap() } } else { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { if (mask[i] & dilate_group_bit) { @@ -278,8 +286,12 @@ void FixNHIntel::remap() if (allremap) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { x[i].x = h0*x[i].x + h5*x[i].y + h4*x[i].z + nb0; @@ -288,8 +300,12 @@ void FixNHIntel::remap() } } else { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { if (mask[i] & dilate_group_bit) { @@ -415,8 +431,12 @@ void FixNHIntel::nh_v_press() if (igroup == 0) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { v[i].x *= f0; @@ -425,8 +445,12 @@ void FixNHIntel::nh_v_press() } } else { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -448,8 +472,12 @@ void FixNHIntel::nve_v() double * _noalias const v = atom->v[0]; const double * _noalias const f = atom->f[0]; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) v[i] += _dtfm[i] * f[i]; @@ -468,15 +496,23 @@ void FixNHIntel::nve_x() if (igroup == 0) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) x[i] += dtv * v[i]; } else { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { if (_dtfm[i] != 0.0) @@ -500,15 +536,23 @@ void FixNHIntel::nh_v_temp() if (igroup == 0) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) v[i] *= factor_eta; } else { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { if (_dtfm[i] != 0.0) diff --git a/src/USER-INTEL/fix_nh_intel.h b/src/INTEL/fix_nh_intel.h similarity index 100% rename from src/USER-INTEL/fix_nh_intel.h rename to src/INTEL/fix_nh_intel.h diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/INTEL/fix_npt_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_npt_intel.cpp rename to src/INTEL/fix_npt_intel.cpp diff --git a/src/USER-INTEL/fix_npt_intel.h b/src/INTEL/fix_npt_intel.h similarity index 100% rename from src/USER-INTEL/fix_npt_intel.h rename to src/INTEL/fix_npt_intel.h diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/INTEL/fix_nve_asphere_intel.cpp similarity index 96% rename from src/USER-INTEL/fix_nve_asphere_intel.cpp rename to src/INTEL/fix_nve_asphere_intel.cpp index 78504c237a..eda8b48a67 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/INTEL/fix_nve_asphere_intel.cpp @@ -97,8 +97,12 @@ void FixNVEAsphereIntel::initial_integrate(int /*vflag*/) dtq = 0.5 * dtv; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { v[i] += _dtfm[i] * f[i]; @@ -108,8 +112,12 @@ void FixNVEAsphereIntel::initial_integrate(int /*vflag*/) // update angular momentum by 1/2 step if (igroup == 0) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { double *quat = bonus[ellipsoid[i]].quat; @@ -118,8 +126,12 @@ void FixNVEAsphereIntel::initial_integrate(int /*vflag*/) } } else { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -143,8 +155,12 @@ void FixNVEAsphereIntel::final_integrate() const double * _noalias const torque = atom->torque[0]; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { v[i] += _dtfm[i] * f[i]; diff --git a/src/USER-INTEL/fix_nve_asphere_intel.h b/src/INTEL/fix_nve_asphere_intel.h similarity index 100% rename from src/USER-INTEL/fix_nve_asphere_intel.h rename to src/INTEL/fix_nve_asphere_intel.h diff --git a/src/USER-INTEL/fix_nve_intel.cpp b/src/INTEL/fix_nve_intel.cpp similarity index 94% rename from src/USER-INTEL/fix_nve_intel.cpp rename to src/INTEL/fix_nve_intel.cpp index fb90946da0..9670af65c2 100644 --- a/src/USER-INTEL/fix_nve_intel.cpp +++ b/src/INTEL/fix_nve_intel.cpp @@ -68,8 +68,12 @@ void FixNVEIntel::initial_integrate(int /*vflag*/) if (igroup == 0 && atom->ntypes == 1 && !atom->rmass) { const double dtfm = dtf / atom->mass[1]; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { v[i] += dtfm * f[i]; @@ -78,8 +82,12 @@ void FixNVEIntel::initial_integrate(int /*vflag*/) } else if (igroup == 0) { if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { v[i] += _dtfm[i] * f[i]; @@ -88,8 +96,12 @@ void FixNVEIntel::initial_integrate(int /*vflag*/) } else { if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { if (_dtfm[i] != 0.0) { @@ -112,16 +124,24 @@ void FixNVEIntel::final_integrate() _nlocal3 = 3 * atom->nlocal; const double dtfm = dtf / atom->mass[1]; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) v[i] += dtfm * f[i]; } else if (igroup == 0) { if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) { v[i] += _dtfm[i] * f[i]; @@ -129,8 +149,12 @@ void FixNVEIntel::final_integrate() } else { if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int i = 0; i < _nlocal3; i++) v[i] += _dtfm[i] * f[i]; diff --git a/src/USER-INTEL/fix_nve_intel.h b/src/INTEL/fix_nve_intel.h similarity index 100% rename from src/USER-INTEL/fix_nve_intel.h rename to src/INTEL/fix_nve_intel.h diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/INTEL/fix_nvt_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nvt_intel.cpp rename to src/INTEL/fix_nvt_intel.cpp diff --git a/src/USER-INTEL/fix_nvt_intel.h b/src/INTEL/fix_nvt_intel.h similarity index 100% rename from src/USER-INTEL/fix_nvt_intel.h rename to src/INTEL/fix_nvt_intel.h diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/INTEL/fix_nvt_sllod_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nvt_sllod_intel.cpp rename to src/INTEL/fix_nvt_sllod_intel.cpp diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.h b/src/INTEL/fix_nvt_sllod_intel.h similarity index 100% rename from src/USER-INTEL/fix_nvt_sllod_intel.h rename to src/INTEL/fix_nvt_sllod_intel.h diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/INTEL/improper_cvff_intel.cpp similarity index 97% rename from src/USER-INTEL/improper_cvff_intel.cpp rename to src/INTEL/improper_cvff_intel.cpp index 9fe1ad8eb1..4d473de7aa 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/INTEL/improper_cvff_intel.cpp @@ -87,7 +87,7 @@ void ImproperCvffIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -165,7 +165,11 @@ void ImproperCvffIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:seimproper, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:seimproper, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -247,7 +251,11 @@ void ImproperCvffIntel::eval(const int vflag, flt_t p, pd; #ifdef LMP_INTEL_USE_SIMDOFF_FIX +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (m == 2) { @@ -319,7 +327,11 @@ void ImproperCvffIntel::eval(const int vflag, // apply force to each of 4 atoms #ifdef LMP_INTEL_USE_SIMDOFF_FIX +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/INTEL/improper_cvff_intel.h similarity index 100% rename from src/USER-INTEL/improper_cvff_intel.h rename to src/INTEL/improper_cvff_intel.h diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/INTEL/improper_harmonic_intel.cpp similarity index 97% rename from src/USER-INTEL/improper_harmonic_intel.cpp rename to src/INTEL/improper_harmonic_intel.cpp index c5bf84b2d5..1a637fa1a6 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/INTEL/improper_harmonic_intel.cpp @@ -89,7 +89,7 @@ void ImproperHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { @@ -167,7 +167,11 @@ void ImproperHarmonicIntel::eval(const int vflag, if (VFLAG && vflag) { sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0; } +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:seimproper, sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:seimproper, sv0, sv1, sv2, sv3, sv4, sv5) +#endif for (int n = nfrom; n < nto; n++) { #else for (int n = nfrom; n < nto; n += npl) { @@ -276,7 +280,11 @@ void ImproperHarmonicIntel::eval(const int vflag, // apply force to each of 4 atoms #ifdef LMP_INTEL_USE_SIMDOFF +#if defined(USE_OMP_SIMD) + #pragma omp ordered simd +#else #pragma simdoff +#endif #endif { if (NEWTON_BOND || i1 < nlocal) { diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/INTEL/improper_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/improper_harmonic_intel.h rename to src/INTEL/improper_harmonic_intel.h diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/INTEL/intel_buffers.cpp similarity index 100% rename from src/USER-INTEL/intel_buffers.cpp rename to src/INTEL/intel_buffers.cpp diff --git a/src/USER-INTEL/intel_buffers.h b/src/INTEL/intel_buffers.h similarity index 100% rename from src/USER-INTEL/intel_buffers.h rename to src/INTEL/intel_buffers.h diff --git a/src/USER-INTEL/intel_intrinsics.h b/src/INTEL/intel_intrinsics.h similarity index 99% rename from src/USER-INTEL/intel_intrinsics.h rename to src/INTEL/intel_intrinsics.h index a17cc2859a..fef7be2968 100644 --- a/src/USER-INTEL/intel_intrinsics.h +++ b/src/INTEL/intel_intrinsics.h @@ -85,7 +85,11 @@ struct vector_ops {}; // Intrinsic routines for IMCI and AVX-512 #if defined(__MIC__) || defined(__AVX512F__) // Integer vector class +#ifdef __INTEL_LLVM_COMPILER +#pragma pack(push,16) +#else #pragma pack(push,64) +#endif struct ivec32x16 { __m512i vec; ivec32x16() {} @@ -113,7 +117,7 @@ struct vector_ops { typedef double fscal; typedef F64vec8 fvec; typedef ivec32x16 ivec; - typedef __mmask bvec; + typedef __mmask16 bvec; typedef double farr[8] __attribute__((aligned(64))); typedef int iarr[16] __attribute__((aligned(64))); static fvec recip(const fvec &a) { return _mm512_recip_pd(a); } @@ -123,7 +127,8 @@ struct vector_ops { } template static fvec gather(const fvec &from, bvec mask, const ivec &idx, const void *base) { - return _mm512_mask_i32logather_pd(from, mask, idx, base, scale); + return _mm512_mask_i32gather_pd(from, mask, _mm512_castsi512_si256(idx), + base, scale); } static fvec blend(const bvec &mask, const fvec &a, const fvec &b) { return _mm512_mask_blend_pd(mask, a, b); @@ -250,7 +255,7 @@ struct vector_ops { typedef float fscal; typedef F32vec16 fvec; typedef ivec32x16 ivec; - typedef __mmask bvec; + typedef __mmask16 bvec; typedef float farr[16] __attribute__((aligned(64))); typedef int iarr[16] __attribute__((aligned(64))); static const bvec full_mask = 0xFFFF; @@ -380,16 +385,18 @@ struct vector_ops { *r3 = gather<4>(*r3, mask, idxs, reinterpret_cast(base) + 12); } // Additional routines needed for the implementation of mixed precision - static fvec cvtdown(const vector_ops::fvec &lo, const vector_ops::fvec &hi) { + static fvec cvtdown(const vector_ops::fvec &lo, + const vector_ops::fvec &hi) { __m512 t1 = _mm512_cvtpd_pslo(lo); __m512 t2 = _mm512_cvtpd_pslo(hi); - return _mm512_mask_permute4f128_ps(t1, 0xFF00, t2, _MM_PERM_BADC); + return _mm512_mask_shuffle_f32x4(_mm512_undefined_ps(), 0xFF00, t2, t2, + 0x4E); } static vector_ops::fvec cvtup_lo(const fvec &a) { return _mm512_cvtpslo_pd(a); } static vector_ops::fvec cvtup_hi(const fvec &a) { - return _mm512_cvtpslo_pd(_mm512_permute4f128_ps(a, _MM_PERM_BADC)); // permute DCBA -> BADC + return _mm512_cvtpslo_pd(_mm512_shuffle_f32x4(a, a, 0x4E)); } static void mask_cvtup(const bvec &a, vector_ops::bvec *blo, vector_ops::bvec *bhi) { *blo = a & 0xFF; @@ -1692,7 +1699,7 @@ struct vector_ops { typedef flt_t fscal; typedef flt_t fvec; typedef int ivec; - typedef bool bvec; + typedef int bvec; typedef flt_t farr[1]; typedef int iarr[1]; static fvec recip(const fvec &a) { diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/INTEL/intel_intrinsics_airebo.h similarity index 98% rename from src/USER-INTEL/intel_intrinsics_airebo.h rename to src/INTEL/intel_intrinsics_airebo.h index f49abbaf3d..5a7959c683 100644 --- a/src/USER-INTEL/intel_intrinsics_airebo.h +++ b/src/INTEL/intel_intrinsics_airebo.h @@ -511,7 +511,8 @@ public: const int scale) { assert(scale == sizeof(FVEC_SCAL_T)); # if FVEC_LEN==8 - return FVEC_SUFFIX(_mm512_i32logather_)(idx.val_, mem, sizeof(FVEC_SCAL_T)); + return FVEC_SUFFIX(_mm512_i32gather_)(_mm512_castsi512_si256(idx.val_), + mem, sizeof(FVEC_SCAL_T)); # else return FVEC_SUFFIX(_mm512_i32gather_)(idx.val_, mem, sizeof(FVEC_SCAL_T)); # endif @@ -522,8 +523,8 @@ public: ) { assert(scale == sizeof(FVEC_SCAL_T)); # if FVEC_LEN==8 - return FVEC_SUFFIX(_mm512_mask_i32logather_)(src.val_, mask.val_, idx.val_, - mem, sizeof(FVEC_SCAL_T)); + return FVEC_SUFFIX(_mm512_mask_i32gather_)(src.val_, mask.val_, + _mm512_castsi512_si256(idx.val_), mem, sizeof(FVEC_SCAL_T)); # else return FVEC_SUFFIX(_mm512_mask_i32gather_)(src.val_, mask.val_, idx.val_, mem, sizeof(FVEC_SCAL_T)); @@ -609,8 +610,8 @@ public: ) { assert(scale == sizeof(FVEC_SCAL_T)); # if FVEC_LEN==8 - return FVEC_SUFFIX(_mm512_mask_i32logather_)(src.val_, mask.val_, idx.val_, - mem, sizeof(FVEC_SCAL_T)); + return FVEC_SUFFIX(_mm512_mask_i32gather_)(src.val_, mask.val_, + _mm512_castsi512_si256(idx.val_), mem, sizeof(FVEC_SCAL_T)); # else return FVEC_SUFFIX(_mm512_mask_i32gather_)(src.val_, mask.val_, idx.val_, mem, sizeof(FVEC_SCAL_T)); @@ -622,8 +623,9 @@ public: ) { assert(scale == sizeof(FVEC_SCAL_T)); # if FVEC_LEN==8 - FVEC_SUFFIX(_mm512_mask_i32loscatter_)(mem, mask.val_, idx.val_, a.val_, - sizeof(FVEC_SCAL_T)); + FVEC_SUFFIX(_mm512_mask_i32scatter_)(mem, mask.val_, + _mm512_castsi512_si256(idx.val_), + a.val_, sizeof(FVEC_SCAL_T)); # else FVEC_SUFFIX(_mm512_mask_i32scatter_)(mem, mask.val_, idx.val_, a.val_, sizeof(FVEC_SCAL_T)); @@ -651,12 +653,12 @@ class avec16pd { return a >> 8; } VEC_INLINE static __m512i get_ivec_hi(__m512i a) { - return _mm512_permute4f128_epi32(a, _MM_PERM_BADC); + return _mm512_shuffle_i32x4(a, a, 0x4E); } public: VEC_INLINE avec16pd(const FVEC_NAME &a) { lo_ = _mm512_cvtpslo_pd(a.val_); - hi_ = _mm512_cvtpslo_pd(_mm512_permute4f128_ps(a.val_, _MM_PERM_BADC)); + hi_ = _mm512_cvtpslo_pd(_mm512_shuffle_f32x4(a.val_, a.val_, 0x4E)); } VEC_INLINE static avec16pd undefined() { return avec16pd(_mm512_undefined_pd(), _mm512_undefined_pd()); @@ -666,11 +668,11 @@ public: const double * mem, const int scale ) { assert(scale == sizeof(double)); - __m512d lo = _mm512_mask_i32logather_pd(src.lo_, mask.val_, idx.val_, mem, - sizeof(double)); - __m512d hi = _mm512_mask_i32logather_pd(src.hi_, get_bvec_hi(mask.val_), - get_ivec_hi(idx.val_), mem, - sizeof(double)); + __m512d lo = _mm512_mask_i32gather_pd(src.lo_, mask.val_, + _mm512_castsi512_si256(idx.val_), + mem, sizeof(double)); + __m512d hi = _mm512_mask_i32gather_pd(src.hi_, get_bvec_hi(mask.val_), + _mm512_castsi512_si256(get_ivec_hi(idx.val_)), mem, sizeof(double)); return avec16pd(lo, hi); } VEC_INLINE static void mask_i32loscatter( @@ -678,10 +680,12 @@ public: const avec16pd &a, const int scale ) { assert(scale == sizeof(double)); - _mm512_mask_i32loscatter_pd(mem, mask.val_, idx.val_, a.lo_, - sizeof(double)); - _mm512_mask_i32loscatter_pd(mem, get_bvec_hi(mask.val_), - get_ivec_hi(idx.val_), a.hi_, sizeof(double)); + _mm512_mask_i32scatter_pd(mem, mask.val_, + _mm512_castsi512_si256(idx.val_), a.lo_, + sizeof(double)); + _mm512_mask_i32scatter_pd(mem, get_bvec_hi(mask.val_), + _mm512_castsi512_si256(get_ivec_hi(idx.val_)), + a.hi_, sizeof(double)); } #define AVEC2_BINOP(the_sym, the_name) \ diff --git a/src/USER-INTEL/intel_preprocess.h b/src/INTEL/intel_preprocess.h similarity index 79% rename from src/USER-INTEL/intel_preprocess.h rename to src/INTEL/intel_preprocess.h index c082bb237f..27daa5f3d2 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/INTEL/intel_preprocess.h @@ -16,6 +16,16 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ +#ifdef __INTEL_LLVM_COMPILER +#define USE_OMP_SIMD +#define __INTEL_COMPILER __INTEL_LLVM_COMPILER +#define __INTEL_COMPILER_BUILD_DATE __INTEL_LLVM_COMPILER +#define _MM_SCALE_1 1 +#define _MM_SCALE_2 2 +#define _MM_SCALE_4 4 +#define _MM_SCALE_8 8 +#endif + #ifdef __INTEL_COMPILER #define LMP_SIMD_COMPILER #if (__INTEL_COMPILER_BUILD_DATE > 20160720) @@ -40,10 +50,10 @@ #ifndef LMP_INTEL_PREPROCESS_H #define LMP_INTEL_PREPROCESS_H -// LAMMPS_MEMALIGN is set to 64 by default for -DLMP_USER_INTEL +// LAMMPS_MEMALIGN is set to 64 by default for -DLMP_INTEL // so we only need to error out in case of a different alignment #if LAMMPS_MEMALIGN && (LAMMPS_MEMALIGN != 64) -#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS of your LAMMPS makefile for USER-INTEL package +#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS of your LAMMPS makefile for INTEL package #endif #if defined(_OPENMP) @@ -327,6 +337,9 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, #endif +// TO BE DEPRECATED +#ifndef USE_OMP_SIMD + #define IP_PRE_fdotr_acc_force_l5(lf, lt, minlocal, nthreads, f_start, \ f_stride, pos, ov0, ov1, ov2, \ ov3, ov4, ov5) \ @@ -521,6 +534,198 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, } \ } +#else + +#define IP_PRE_fdotr_acc_force_l5(lf, lt, minlocal, nthreads, f_start, \ + f_stride, pos, ov0, ov1, ov2, \ + ov3, ov4, ov5) \ +{ \ + acc_t *f_scalar = &f_start[0].x; \ + flt_t *x_scalar = &pos[minlocal].x; \ + int f_stride4 = f_stride * 4; \ + _alignvar(acc_t ovv[16],64); \ + int vwidth; \ + if (sizeof(acc_t) == sizeof(double)) \ + vwidth = INTEL_COMPILE_WIDTH/2; \ + else \ + vwidth = INTEL_COMPILE_WIDTH; \ + if (vwidth < 4) vwidth = 4; \ + _use_simd_pragma("omp simd aligned(ovv:64)") \ + for (int v = 0; v < vwidth; v++) ovv[v] = (acc_t)0.0; \ + int remainder = lt % vwidth; \ + if (lf > lt) remainder = 0; \ + const int v_range = lt - remainder; \ + if (nthreads == 2) { \ + acc_t *f_scalar2 = f_scalar + f_stride4; \ + for (int n = lf; n < v_range; n += vwidth) { \ + _use_simd_pragma("omp simd aligned(f_scalar,f_scalar2,ovv,x_scalar:64)")\ + for (int v = 0; v < vwidth; v++) { \ + f_scalar[n+v] += f_scalar2[n+v]; \ + ovv[v] += f_scalar[n+v] * x_scalar[n+v]; \ + } \ + ov3 += f_scalar[n+1] * x_scalar[n+0]; \ + ov4 += f_scalar[n+2] * x_scalar[n+0]; \ + ov5 += f_scalar[n+2] * x_scalar[n+1]; \ + if (vwidth > 4) { \ + ov3 += f_scalar[n+5] * x_scalar[n+4]; \ + ov4 += f_scalar[n+6] * x_scalar[n+4]; \ + ov5 += f_scalar[n+6] * x_scalar[n+5]; \ + } \ + if (vwidth > 8) { \ + ov3 += f_scalar[n+9] * x_scalar[n+8]; \ + ov3 += f_scalar[n+13] * x_scalar[n+12]; \ + ov4 += f_scalar[n+10] * x_scalar[n+8]; \ + ov4 += f_scalar[n+14] * x_scalar[n+12]; \ + ov5 += f_scalar[n+10] * x_scalar[n+9]; \ + ov5 += f_scalar[n+14] * x_scalar[n+13]; \ + } \ + } \ + _use_simd_pragma("vector aligned") \ + _use_simd_pragma("ivdep") \ + _use_simd_pragma("loop_count min(4) max(INTEL_COMPILE_WIDTH)") \ + for (int n = v_range; n < lt; n++) \ + f_scalar[n] += f_scalar2[n]; \ + } else if (nthreads==4) { \ + acc_t *f_scalar2 = f_scalar + f_stride4; \ + acc_t *f_scalar3 = f_scalar2 + f_stride4; \ + acc_t *f_scalar4 = f_scalar3 + f_stride4; \ + for (int n = lf; n < v_range; n += vwidth) { \ + _use_simd_pragma("omp simd aligned(f_scalar,f_scalar2,f_scalar3,f_scalar4,ovv:64)") \ + for (int v = 0; v < vwidth; v++) { \ + f_scalar[n+v] += f_scalar2[n+v] + f_scalar3[n+v] + \ + f_scalar4[n+v]; \ + ovv[v] += f_scalar[n+v] * x_scalar[n+v]; \ + } \ + ov3 += f_scalar[n+1] * x_scalar[n+0]; \ + ov4 += f_scalar[n+2] * x_scalar[n+0]; \ + ov5 += f_scalar[n+2] * x_scalar[n+1]; \ + if (vwidth > 4) { \ + ov3 += f_scalar[n+5] * x_scalar[n+4]; \ + ov4 += f_scalar[n+6] * x_scalar[n+4]; \ + ov5 += f_scalar[n+6] * x_scalar[n+5]; \ + } \ + if (vwidth > 8) { \ + ov3 += f_scalar[n+9] * x_scalar[n+8]; \ + ov3 += f_scalar[n+13] * x_scalar[n+12]; \ + ov4 += f_scalar[n+10] * x_scalar[n+8]; \ + ov4 += f_scalar[n+14] * x_scalar[n+12]; \ + ov5 += f_scalar[n+10] * x_scalar[n+9]; \ + ov5 += f_scalar[n+14] * x_scalar[n+13]; \ + } \ + } \ + _use_simd_pragma("vector aligned") \ + _use_simd_pragma("ivdep") \ + _use_simd_pragma("loop_count min(4) max(INTEL_COMPILE_WIDTH)") \ + for (int n = v_range; n < lt; n++) \ + f_scalar[n] += f_scalar2[n] + f_scalar3[n] + f_scalar4[n]; \ + } else if (nthreads==1) { \ + for (int n = lf; n < v_range; n += vwidth) { \ + _use_simd_pragma("omp simd aligned(ovv,f_scalar,x_scalar:64)") \ + for (int v = 0; v < vwidth; v++) \ + ovv[v] += f_scalar[n+v] * x_scalar[n+v]; \ + ov3 += f_scalar[n+1] * x_scalar[n+0]; \ + ov4 += f_scalar[n+2] * x_scalar[n+0]; \ + ov5 += f_scalar[n+2] * x_scalar[n+1]; \ + if (vwidth > 4) { \ + ov3 += f_scalar[n+5] * x_scalar[n+4]; \ + ov4 += f_scalar[n+6] * x_scalar[n+4]; \ + ov5 += f_scalar[n+6] * x_scalar[n+5]; \ + } \ + if (vwidth > 8) { \ + ov3 += f_scalar[n+9] * x_scalar[n+8]; \ + ov3 += f_scalar[n+13] * x_scalar[n+12]; \ + ov4 += f_scalar[n+10] * x_scalar[n+8]; \ + ov4 += f_scalar[n+14] * x_scalar[n+12]; \ + ov5 += f_scalar[n+10] * x_scalar[n+9]; \ + ov5 += f_scalar[n+14] * x_scalar[n+13]; \ + } \ + } \ + } else if (nthreads==3) { \ + acc_t *f_scalar2 = f_scalar + f_stride4; \ + acc_t *f_scalar3 = f_scalar2 + f_stride4; \ + for (int n = lf; n < v_range; n += vwidth) { \ + _use_simd_pragma("omp simd aligned(f_scalar,f_scalar2,f_scalar3,ovv,x_scalar:64)") \ + for (int v = 0; v < vwidth; v++) { \ + f_scalar[n+v] += f_scalar2[n+v] + f_scalar3[n+v]; \ + ovv[v] += f_scalar[n+v] * x_scalar[n+v]; \ + } \ + ov3 += f_scalar[n+1] * x_scalar[n+0]; \ + ov4 += f_scalar[n+2] * x_scalar[n+0]; \ + ov5 += f_scalar[n+2] * x_scalar[n+1]; \ + if (vwidth > 4) { \ + ov3 += f_scalar[n+5] * x_scalar[n+4]; \ + ov4 += f_scalar[n+6] * x_scalar[n+4]; \ + ov5 += f_scalar[n+6] * x_scalar[n+5]; \ + } \ + if (vwidth > 8) { \ + ov3 += f_scalar[n+9] * x_scalar[n+8]; \ + ov3 += f_scalar[n+13] * x_scalar[n+12]; \ + ov4 += f_scalar[n+10] * x_scalar[n+8]; \ + ov4 += f_scalar[n+14] * x_scalar[n+12]; \ + ov5 += f_scalar[n+10] * x_scalar[n+9]; \ + ov5 += f_scalar[n+14] * x_scalar[n+13]; \ + } \ + } \ + _use_simd_pragma("vector aligned") \ + _use_simd_pragma("ivdep") \ + _use_simd_pragma("loop_count min(4) max(INTEL_COMPILE_WIDTH)") \ + for (int n = v_range; n < lt; n++) \ + f_scalar[n] += f_scalar2[n] + f_scalar3[n]; \ + } \ + for (int n = v_range; n < lt; n += 4) { \ + _use_simd_pragma("vector aligned") \ + _use_simd_pragma("ivdep") \ + for (int v = 0; v < 4; v++) \ + ovv[v] += f_scalar[n+v] * x_scalar[n+v]; \ + ov3 += f_scalar[n+1] * x_scalar[n+0]; \ + ov4 += f_scalar[n+2] * x_scalar[n+0]; \ + ov5 += f_scalar[n+2] * x_scalar[n+1]; \ + } \ + ov0 += ovv[0]; \ + ov1 += ovv[1]; \ + ov2 += ovv[2]; \ + if (vwidth > 4) { \ + ov0 += ovv[4]; \ + ov1 += ovv[5]; \ + ov2 += ovv[6]; \ + } \ + if (vwidth > 8) { \ + ov0 += ovv[8] + ovv[12]; \ + ov1 += ovv[9] + ovv[13]; \ + ov2 += ovv[10] + ovv[14]; \ + } \ +} + +#define IP_PRE_fdotr_acc_force(nall, minlocal, nthreads, f_start, \ + f_stride, pos, offload, vflag, ov0, ov1, \ + ov2, ov3, ov4, ov5) \ +{ \ + int o_range = (nall - minlocal) * 4; \ + IP_PRE_omp_range_id_align(iifrom, iito, tid, o_range, nthreads, \ + sizeof(acc_t)); \ + \ + acc_t *f_scalar = &f_start[0].x; \ + int f_stride4 = f_stride * 4; \ + int t; \ + if (vflag == VIRIAL_FDOTR) t = 4; else t = 1; \ + acc_t *f_scalar2 = f_scalar + f_stride4 * t; \ + for ( ; t < nthreads; t++) { \ + _use_simd_pragma("omp simd aligned(f_scalar,f_scalar2:64)") \ + for (int n = iifrom; n < iito; n++) \ + f_scalar[n] += f_scalar2[n]; \ + f_scalar2 += f_stride4; \ + } \ + \ + if (vflag == VIRIAL_FDOTR) { \ + int nt_min = MIN(4,nthreads); \ + IP_PRE_fdotr_acc_force_l5(iifrom, iito, minlocal, nt_min, f_start, \ + f_stride, pos, ov0, ov1, ov2, ov3, ov4, \ + ov5); \ + } \ +} + +#endif + #ifdef _LMP_INTEL_OFFLOAD #include diff --git a/src/USER-INTEL/intel_simd.h b/src/INTEL/intel_simd.h similarity index 88% rename from src/USER-INTEL/intel_simd.h rename to src/INTEL/intel_simd.h index 165455a33d..2affa6a394 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/INTEL/intel_simd.h @@ -173,7 +173,7 @@ namespace ip_simd { } inline SIMD_double SIMD_gather(const double *p, const SIMD_int &i) { - return _mm512_i32logather_pd(i, p, _MM_SCALE_8); + return _mm512_i32gather_pd(_mm512_castsi512_si256(i), p, _MM_SCALE_8); } inline SIMD_int SIMD_gather(const SIMD_mask &m, const int *p, @@ -190,8 +190,8 @@ namespace ip_simd { inline SIMD_double SIMD_gather(const SIMD_mask &m, const double *p, const SIMD_int &i) { - return _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, p, - _MM_SCALE_8); + return _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), p, _MM_SCALE_8); } template @@ -227,8 +227,8 @@ namespace ip_simd { inline SIMD_double SIMD_gatherz(const SIMD_mask &m, const double *p, const SIMD_int &i) { - return _mm512_mask_i32logather_pd( _mm512_set1_pd(0.0), m, i, p, - _MM_SCALE_8); + return _mm512_mask_i32gather_pd( _mm512_set1_pd(0.0), m, + _mm512_castsi512_si256(i),p, _MM_SCALE_8); } // ------- Store Operations @@ -257,7 +257,8 @@ namespace ip_simd { inline void SIMD_scatter(const SIMD_mask &m, double *p, const SIMD_int &i, const SIMD_double &vec) { - _mm512_mask_i32loscatter_pd(p, m, i, vec, _MM_SCALE_8); + _mm512_mask_i32scatter_pd(p, m, _mm512_castsi512_si256(i), vec, + _MM_SCALE_8); } // ------- Arithmetic Operations @@ -834,23 +835,29 @@ namespace ip_simd { inline void SIMD_atom_gather(const SIMD_mask &m, const double *atom, const SIMD_int &i, SIMD_double &x, SIMD_double &y, SIMD_double &z) { - x = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, atom, - _MM_SCALE_2); - y = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, atom+1, - _MM_SCALE_2); - z = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, atom+2, - _MM_SCALE_2); + x = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), atom, + _MM_SCALE_2); + y = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), atom+1, + _MM_SCALE_2); + z = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), atom+2, + _MM_SCALE_2); } inline void SIMD_atom_gather(const SIMD_mask &m, const double *atom, const SIMD_int &i, SIMD_double &x, SIMD_double &y, SIMD_double &z, SIMD_int &type) { - x = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, atom, - _MM_SCALE_2); - y = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, atom+1, - _MM_SCALE_2); - z = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, atom+2, - _MM_SCALE_2); + x = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), atom, + _MM_SCALE_2); + y = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), atom+1, + _MM_SCALE_2); + z = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), atom+2, + _MM_SCALE_2); type = _mm512_mask_i32gather_epi32(_mm512_undefined_epi32(), m, i, atom+3, _MM_SCALE_2); } @@ -888,10 +895,12 @@ namespace ip_simd { const SIMD_int &joffset, SIMD_double &eng) { SIMD_double jeng; SIMD_conflict_pi_reduce1(rmask, joffset, eng); - jeng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask, joffset, - force, _MM_SCALE_2); + jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask, + _mm512_castsi512_si256(joffset), + force, _MM_SCALE_2); jeng = jeng + eng; - _mm512_mask_i32loscatter_pd(force, rmask, joffset, jeng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, rmask, _mm512_castsi512_si256(joffset), + jeng, _MM_SCALE_2); } inline void SIMD_jeng_update(const SIMD_mask &rmask, double *force, @@ -899,20 +908,24 @@ namespace ip_simd { SIMD_double engd, jeng; engd = _mm512_cvtps_pd(_mm512_castps512_ps256(eng)); SIMD_conflict_pi_reduce1(rmask, joffset, engd); - jeng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask, joffset, - force, _MM_SCALE_2); + jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask, + _mm512_castsi512_si256(joffset), + force, _MM_SCALE_2); jeng = jeng + engd; - _mm512_mask_i32loscatter_pd(force, rmask, joffset, jeng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, rmask, _mm512_castsi512_si256(joffset), + jeng, _MM_SCALE_2); SIMD_mask rmask2 = rmask >> 8; engd = _mm512_cvtps_pd(_mm512_castps512_ps256( _mm512_shuffle_f32x4(eng,eng,238))); SIMD_int joffset2 = _mm512_shuffle_i32x4(joffset, joffset, 238); SIMD_conflict_pi_reduce1(rmask2, joffset2, engd); - jeng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask2, joffset2, - force, _MM_SCALE_2); + jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2, + _mm512_castsi512_si256(joffset2), + force, _MM_SCALE_2); jeng = jeng + engd; - _mm512_mask_i32loscatter_pd(force, rmask2, joffset2, jeng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, rmask2, _mm512_castsi512_si256(joffset2), + jeng, _MM_SCALE_2); } inline void SIMD_jeng_update_hi(const SIMD_mask &mask, float *force, @@ -926,10 +939,12 @@ namespace ip_simd { SIMD_double jeng; SIMD_conflict_pi_reduce1(rmask, joffset, eng); - jeng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask, joffset, - force, _MM_SCALE_2); + jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask, + _mm512_castsi512_si256(joffset), + force, _MM_SCALE_2); jeng = jeng + eng; - _mm512_mask_i32loscatter_pd(force, rmask, joffset, jeng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, rmask, _mm512_castsi512_si256(joffset), + jeng, _MM_SCALE_2); } inline void SIMD_safe_jforce(const SIMD_mask &m, float *force, @@ -956,18 +971,24 @@ namespace ip_simd { SIMD_double &fy, SIMD_double &fz) { SIMD_conflict_pi_reduce3(m, i, fx, fy, fz); SIMD_double jfrc; - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force, - _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force, + _MM_SCALE_2); jfrc = jfrc + fx; - _mm512_mask_i32loscatter_pd(force, m, i, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force + 1, - _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force + 1, + _MM_SCALE_2); jfrc = jfrc + fy; - _mm512_mask_i32loscatter_pd(force+1, m, i, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force + 2, - _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+1, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force + 2, + _MM_SCALE_2); jfrc = jfrc + fz; - _mm512_mask_i32loscatter_pd(force+2, m, i, jfrc, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+2, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); } inline void SIMD_safe_jforce(const SIMD_mask &rmask, double *force, @@ -979,40 +1000,54 @@ namespace ip_simd { amzd = _mm512_cvtps_pd(_mm512_castps512_ps256(amz)); SIMD_conflict_pi_reduce3(rmask, joffset, amxd, amyd, amzd); SIMD_double jfrc; - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask, joffset, - force, _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask, + _mm512_castsi512_si256(joffset), + force, _MM_SCALE_2); jfrc = jfrc + amxd; - _mm512_mask_i32loscatter_pd(force, rmask, joffset, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask, joffset, - force + 1, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, rmask, _mm512_castsi512_si256(joffset), + jfrc, _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask, + _mm512_castsi512_si256(joffset), + force + 1, _MM_SCALE_2); jfrc = jfrc + amyd; - _mm512_mask_i32loscatter_pd(force+1, rmask, joffset, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask, joffset, - force + 2, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+1, rmask, _mm512_castsi512_si256(joffset), + jfrc, _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask, + _mm512_castsi512_si256(joffset), + force + 2, _MM_SCALE_2); jfrc = jfrc + amzd; - _mm512_mask_i32loscatter_pd(force+2, rmask, joffset, jfrc, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+2, rmask, _mm512_castsi512_si256(joffset), + jfrc, _MM_SCALE_2); SIMD_mask rmask2 = rmask >> 8; amxd = _mm512_cvtps_pd(_mm512_castps512_ps256( - _mm512_shuffle_f32x4(amx,amx,238))); + _mm512_shuffle_f32x4(amx,amx,238))); amyd = _mm512_cvtps_pd(_mm512_castps512_ps256( - _mm512_shuffle_f32x4(amy,amy,238))); + _mm512_shuffle_f32x4(amy,amy,238))); amzd = _mm512_cvtps_pd(_mm512_castps512_ps256( - _mm512_shuffle_f32x4(amz,amz,238))); + _mm512_shuffle_f32x4(amz,amz,238))); SIMD_int joffset2 = _mm512_shuffle_i32x4(joffset, joffset, 238); SIMD_conflict_pi_reduce3(rmask2, joffset2, amxd, amyd, amzd); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask2, joffset2, - force, _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2, + _mm512_castsi512_si256(joffset2), + force, _MM_SCALE_2); jfrc = jfrc + amxd; - _mm512_mask_i32loscatter_pd(force, rmask2, joffset2, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask2, joffset2, - force + 1, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, rmask2, _mm512_castsi512_si256(joffset2), + jfrc, _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2, + _mm512_castsi512_si256(joffset2), + force + 1, _MM_SCALE_2); jfrc = jfrc + amyd; - _mm512_mask_i32loscatter_pd(force+1, rmask2, joffset2, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), rmask2, joffset2, - force + 2, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+1, rmask2, + _mm512_castsi512_si256(joffset2), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2, + _mm512_castsi512_si256(joffset2), + force + 2, _MM_SCALE_2); jfrc = jfrc + amzd; - _mm512_mask_i32loscatter_pd(force+2, rmask2, joffset2, jfrc, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+2, rmask2, + _mm512_castsi512_si256(joffset2), jfrc, + _MM_SCALE_2); } inline void SIMD_jforce_update(const SIMD_mask &m, float *force, @@ -1064,18 +1099,24 @@ namespace ip_simd { const SIMD_int &i, const SIMD_double &fx, const SIMD_double &fy, const SIMD_double &fz) { SIMD_double jfrc; - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force, - _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force, + _MM_SCALE_2); jfrc = jfrc - fx; - _mm512_mask_i32loscatter_pd(force, m, i, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force + 1, - _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force + 1, + _MM_SCALE_2); jfrc = jfrc - fy; - _mm512_mask_i32loscatter_pd(force+1, m, i, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force + 2, - _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+1, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force + 2, + _MM_SCALE_2); jfrc = jfrc - fz; - _mm512_mask_i32loscatter_pd(force+2, m, i, jfrc, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+2, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); } inline void SIMD_jforce_update(const SIMD_mask &rmask, @@ -1502,11 +1543,12 @@ namespace ip_simd { fwtmp = SIMD_add(fwtmp, hmask, fwtmp, hevdwl); fjtmp = SIMD_add(fjtmp, hmask, fjtmp, hevdwl); SIMD_conflict_pi_reduce1(hmask, k, hevdwl); - SIMD_double keng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), - hmask, k, force + 3, - _MM_SCALE_2); + SIMD_double keng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), hmask, + _mm512_castsi512_si256(k), + force + 3, _MM_SCALE_2); keng = keng + hevdwl; - _mm512_mask_i32loscatter_pd(force + 3, hmask, k, keng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force + 3, hmask, _mm512_castsi512_si256(k), + keng, _MM_SCALE_2); } } @@ -1523,11 +1565,12 @@ namespace ip_simd { fwtmp = SIMD_add(fwtmp, hmask, fwtmp, hevdwl); fjtmp = SIMD_add(fjtmp, hmask, fjtmp, hevdwl); SIMD_conflict_pi_reduce1(hmask, k, hevdwl); - SIMD_double keng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), - hmask, k, force + 3, - _MM_SCALE_2); + SIMD_double keng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), hmask, + _mm512_castsi512_si256(k), + force + 3, _MM_SCALE_2); keng = keng + hevdwl; - _mm512_mask_i32loscatter_pd(force + 3, hmask, k, keng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force + 3, hmask, _mm512_castsi512_si256(k), + keng, _MM_SCALE_2); } SIMD_mask hmask2 = hmask >> 8; facradd = _mm512_cvtps_pd(_mm512_castps512_ps256( @@ -1539,11 +1582,13 @@ namespace ip_simd { fjtmp2 = SIMD_add(fjtmp2, hmask2, fjtmp2, hevdwl); SIMD_int k2 = _mm512_shuffle_i32x4(k, k, 238); SIMD_conflict_pi_reduce1(hmask2, k2, hevdwl); - SIMD_double keng = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), - hmask2, k2, force + 3, - _MM_SCALE_2); + SIMD_double keng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), + hmask2, + _mm512_castsi512_si256(k2), + force + 3, _MM_SCALE_2); keng = keng + hevdwl; - _mm512_mask_i32loscatter_pd(force + 3, hmask2, k2, keng, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force + 3, hmask2, _mm512_castsi512_si256(k2), + keng, _MM_SCALE_2); } } @@ -1815,24 +1860,32 @@ namespace ip_simd { const int EFLAG, const int eatom, const SIMD_double &fwtmp) { SIMD_double jfrc; - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force, - _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force, + _MM_SCALE_2); jfrc = jfrc + fx; - _mm512_mask_i32loscatter_pd(force, m, i, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force + 1, - _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force + 1, + _MM_SCALE_2); jfrc = jfrc + fy; - _mm512_mask_i32loscatter_pd(force+1, m, i, jfrc, _MM_SCALE_2); - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, force + 2, - _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+1, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), force + 2, + _MM_SCALE_2); jfrc = jfrc + fz; - _mm512_mask_i32loscatter_pd(force+2, m, i, jfrc, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+2, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); if (EFLAG) { if (eatom) { - jfrc = _mm512_mask_i32logather_pd(_mm512_undefined_pd(), m, i, - force + 3, _MM_SCALE_2); + jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m, + _mm512_castsi512_si256(i), + force + 3, _MM_SCALE_2); jfrc = jfrc + fwtmp; - _mm512_mask_i32loscatter_pd(force+3, m, i, jfrc, _MM_SCALE_2); + _mm512_mask_i32scatter_pd(force+3, m, _mm512_castsi512_si256(i), jfrc, + _MM_SCALE_2); } } } diff --git a/src/USER-INTEL/math_extra_intel.h b/src/INTEL/math_extra_intel.h similarity index 100% rename from src/USER-INTEL/math_extra_intel.h rename to src/INTEL/math_extra_intel.h diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/INTEL/nbin_intel.cpp similarity index 99% rename from src/USER-INTEL/nbin_intel.cpp rename to src/INTEL/nbin_intel.cpp index 5227b6c521..94f18002a0 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/INTEL/nbin_intel.cpp @@ -68,7 +68,7 @@ NBinIntel::~NBinIntel() { void NBinIntel::bin_atoms_setup(int nall) { // binhead = per-bin vector, mbins in length - // add 1 bin for USER-INTEL package + // add 1 bin for INTEL package if (mbins > maxbin) { #ifdef _LMP_INTEL_OFFLOAD diff --git a/src/USER-INTEL/nbin_intel.h b/src/INTEL/nbin_intel.h similarity index 100% rename from src/USER-INTEL/nbin_intel.h rename to src/INTEL/nbin_intel.h diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/INTEL/npair_full_bin_ghost_intel.cpp similarity index 97% rename from src/USER-INTEL/npair_full_bin_ghost_intel.cpp rename to src/INTEL/npair_full_bin_ghost_intel.cpp index 50f98bf746..e96f2c713d 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/INTEL/npair_full_bin_ghost_intel.cpp @@ -42,11 +42,11 @@ void NPairFullBinGhostIntel::build(NeighList *list) #ifdef _LMP_INTEL_OFFLOAD if (_fix->offload_noghost()) error->all(FLERR, - "The 'ghost no' option cannot be used with this USER-INTEL pair style."); + "The 'ghost no' option cannot be used with this INTEL pair style."); #endif if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) @@ -324,7 +324,11 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const int bstart = binhead[ibin + binstart[k]]; const int bend = binhead[ibin + binend[k]]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int jj = bstart; jj < bend; jj++) tj[ncount++] = binpacked[jj]; @@ -345,15 +349,23 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const int bstart = binhead[ibin + stencil[k]]; const int bend = binhead[ibin + stencil[k] + 1]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int jj = bstart; jj < bend; jj++) tj[ncount++] = binpacked[jj]; } } // if i < nlocal #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int u = 0; u < ncount; u++) { const int j = tj[u]; @@ -425,12 +437,16 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int alln = n; n = 0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned #ifdef LMP_INTEL_NBOR_COMPAT #pragma ivdep #else +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif + #pragma vector aligned #endif for (int u = 0; u < alln; u++) { int which; @@ -454,12 +470,16 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, alln = n2; n2 = maxnbors * 2; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned #ifdef LMP_INTEL_NBOR_COMPAT #pragma ivdep #else +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif + #pragma vector aligned #endif for (int u = n2; u < alln; u++) { int which; diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.h b/src/INTEL/npair_full_bin_ghost_intel.h similarity index 100% rename from src/USER-INTEL/npair_full_bin_ghost_intel.h rename to src/INTEL/npair_full_bin_ghost_intel.h diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/INTEL/npair_full_bin_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_full_bin_intel.cpp rename to src/INTEL/npair_full_bin_intel.cpp index 4b84c72081..82c73ec940 100644 --- a/src/USER-INTEL/npair_full_bin_intel.cpp +++ b/src/INTEL/npair_full_bin_intel.cpp @@ -37,7 +37,7 @@ NPairFullBinIntel::NPairFullBinIntel(LAMMPS *lmp) : NPairIntel(lmp) {} void NPairFullBinIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_full_bin_intel.h b/src/INTEL/npair_full_bin_intel.h similarity index 100% rename from src/USER-INTEL/npair_full_bin_intel.h rename to src/INTEL/npair_full_bin_intel.h diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/INTEL/npair_half_bin_newton_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_half_bin_newton_intel.cpp rename to src/INTEL/npair_half_bin_newton_intel.cpp index abaddde84c..21145ad647 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp +++ b/src/INTEL/npair_half_bin_newton_intel.cpp @@ -39,7 +39,7 @@ NPairHalfBinNewtonIntel::NPairHalfBinNewtonIntel(LAMMPS *lmp) : void NPairHalfBinNewtonIntel::build(NeighList *list) { if (nstencil / 2 > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.h b/src/INTEL/npair_half_bin_newton_intel.h similarity index 100% rename from src/USER-INTEL/npair_half_bin_newton_intel.h rename to src/INTEL/npair_half_bin_newton_intel.h diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/INTEL/npair_half_bin_newton_tri_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp rename to src/INTEL/npair_half_bin_newton_tri_intel.cpp index 264407b1bf..1ad4d5fc68 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/INTEL/npair_half_bin_newton_tri_intel.cpp @@ -39,7 +39,7 @@ NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) : void NPairHalfBinNewtonTriIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.h b/src/INTEL/npair_half_bin_newton_tri_intel.h similarity index 100% rename from src/USER-INTEL/npair_half_bin_newton_tri_intel.h rename to src/INTEL/npair_half_bin_newton_tri_intel.h diff --git a/src/USER-INTEL/npair_halffull_newtoff_intel.h b/src/INTEL/npair_halffull_newtoff_intel.h similarity index 100% rename from src/USER-INTEL/npair_halffull_newtoff_intel.h rename to src/INTEL/npair_halffull_newtoff_intel.h diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/INTEL/npair_halffull_newton_intel.cpp similarity index 100% rename from src/USER-INTEL/npair_halffull_newton_intel.cpp rename to src/INTEL/npair_halffull_newton_intel.cpp diff --git a/src/USER-INTEL/npair_halffull_newton_intel.h b/src/INTEL/npair_halffull_newton_intel.h similarity index 100% rename from src/USER-INTEL/npair_halffull_newton_intel.h rename to src/INTEL/npair_halffull_newton_intel.h diff --git a/src/USER-INTEL/npair_intel.cpp b/src/INTEL/npair_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_intel.cpp rename to src/INTEL/npair_intel.cpp index 643ceff8f3..395e50006c 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/INTEL/npair_intel.cpp @@ -344,14 +344,22 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, const int bstart = binhead[ibin + binstart[k]]; const int bend = binhead[ibin + binend[k]]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int jj = bstart; jj < bend; jj++) tj[ncount++] = binpacked[jj]; } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int u = 0; u < ncount; u++) { const int j = tj[u]; @@ -375,7 +383,11 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, const int bstart = binhead[ibin]; const int bend = binhead[ibin + 1]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int jj = bstart; jj < bend; jj++) { const int j = binpacked[jj]; @@ -533,12 +545,16 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, n = pack_offset; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned #ifdef LMP_INTEL_NBOR_COMPAT #pragma ivdep #else +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif + #pragma vector aligned #endif for (int u = n; u < alln; u++) { int which; @@ -566,12 +582,16 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, n2 = pack_offset + maxnbors; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned #ifdef LMP_INTEL_NBOR_COMPAT #pragma ivdep #else +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif + #pragma vector aligned #endif for (int u = n2; u < alln; u++) { int which; @@ -737,8 +757,14 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int jnum = numneigh[i]; if (!THREE) IP_PRE_neighbor_pad(jnum, offload); #if __INTEL_COMPILER+0 > 1499 +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(max:vlmax,vgmax) \ + reduction(min:vlmin, vgmin) +#else + #pragma simd reduction(max:vlmax,vgmax) \ + reduction(min:vlmin, vgmin) +#endif #pragma vector aligned - #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin) #endif for (int jj = 0; jj < jnum; jj++) { const int j = jlist[jj] & NEIGHMASK; @@ -782,8 +808,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int jnum = numneigh[i]; if (!THREE) IP_PRE_neighbor_pad(jnum, offload); int jj = 0; - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned for (jj = 0; jj < jnum; jj++) { const int which = jlist[jj] >> SBBITS & 3; const int j = jlist[jj] & NEIGHMASK; diff --git a/src/USER-INTEL/npair_intel.h b/src/INTEL/npair_intel.h similarity index 98% rename from src/USER-INTEL/npair_intel.h rename to src/INTEL/npair_intel.h index 7c21e683ad..8035f6f9be 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/INTEL/npair_intel.h @@ -113,7 +113,7 @@ E: The 'package intel' command is required for /intel styles Self explanatory. -E: Too many neighbor bins for USER-INTEL package. +E: Too many neighbor bins for INTEL package. The number of bins used in the stencil to check for neighboring atoms is too high for the Intel package. Either increase the bin size in the input script diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/INTEL/npair_skip_intel.cpp similarity index 100% rename from src/USER-INTEL/npair_skip_intel.cpp rename to src/INTEL/npair_skip_intel.cpp diff --git a/src/USER-INTEL/npair_skip_intel.h b/src/INTEL/npair_skip_intel.h similarity index 100% rename from src/USER-INTEL/npair_skip_intel.h rename to src/INTEL/npair_skip_intel.h diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/INTEL/pair_airebo_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_airebo_intel.cpp rename to src/INTEL/pair_airebo_intel.cpp index 12afce046b..be38bbe418 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/INTEL/pair_airebo_intel.cpp @@ -180,12 +180,10 @@ PairAIREBOIntel::~PairAIREBOIntel() void PairAIREBOIntel::init_style() { PairAIREBO::init_style(); - neighbor->requests[neighbor->nrequest-1]->intel = 1; + neighbor->find_request(this)->intel = 1; - const int nrequest = neighbor->nrequest; - for (int i = 0; i < nrequest; ++i) - if (neighbor->requests[i]->skip) - error->all(FLERR, "Cannot yet use airebo/intel with hybrid."); + if (utils::strmatch(force->pair_style,"^hybrid")) + error->all(FLERR, "Cannot yet use airebo/intel with hybrid."); int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -293,7 +291,10 @@ void PairAIREBOIntel::compute( ) { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); pvector[0] = pvector[1] = pvector[2] = 0.0; @@ -2332,7 +2333,7 @@ static void aut_rebo_neigh(KernelArgsAIREBOT * ka) { int n_skin = 0; int lowest_idx; - #pragma unroll(4) + //#pragma unroll(4) for (lowest_idx = 0; lowest_idx < jnum; lowest_idx += fvec::VL) { bvec j_mask = bvec::full(); if (lowest_idx + fvec::VL > jnum) j_mask = bvec::only(jnum - lowest_idx); diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/INTEL/pair_airebo_intel.h similarity index 100% rename from src/USER-INTEL/pair_airebo_intel.h rename to src/INTEL/pair_airebo_intel.h diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/INTEL/pair_airebo_morse_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_airebo_morse_intel.cpp rename to src/INTEL/pair_airebo_morse_intel.cpp diff --git a/src/USER-INTEL/pair_airebo_morse_intel.h b/src/INTEL/pair_airebo_morse_intel.h similarity index 100% rename from src/USER-INTEL/pair_airebo_morse_intel.h rename to src/INTEL/pair_airebo_morse_intel.h diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/INTEL/pair_buck_coul_cut_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_buck_coul_cut_intel.cpp rename to src/INTEL/pair_buck_coul_cut_intel.cpp index e2ff70e392..2633fd4ab2 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/INTEL/pair_buck_coul_cut_intel.cpp @@ -16,25 +16,25 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_buck_coul_cut_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "force.h" #include "group.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "suffix.h" -#include "force.h" #include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -76,7 +76,10 @@ void PairBuckCoulCutIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -246,12 +249,18 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, fxtmp = fytmp = fztmp = (acc_t)0; if (EFLAG) fwtmp = sevdwl = secoul = (acc_t)0; if (NEWTON_PAIR == 0) - if (vflag == VIRIAL_PAIR) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0; + if (vflag == VIRIAL_PAIR) + sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ sv0, sv1, sv2, sv3, sv4, sv5) +#endif + #pragma vector aligned #endif for (int jj = 0; jj < jnum; jj++) { flt_t forcecoul, forcebuck, evdwl, ecoul; @@ -403,11 +412,12 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, void PairBuckCoulCutIntel::init_style() { PairBuckCoulCut::init_style(); + auto request = neighbor->find_request(this); if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -494,7 +504,8 @@ void PairBuckCoulCutIntel::ForceConst::set_ntypes(const int ntypes, const int ntable, Memory *memory, const int cop) { - if ((ntypes != _ntypes || ntable != _ntable)) { + if (memory != nullptr) _memory = memory; + if ((ntypes != _ntypes) || (ntable != _ntable)) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -516,13 +527,12 @@ void PairBuckCoulCutIntel::ForceConst::set_ntypes(const int ntypes, _memory->destroy(c_force); _memory->destroy(c_energy); _memory->destroy(c_cut); - } if (ntypes > 0) { _cop = cop; - memory->create(c_force,ntypes,ntypes,"fc.c_force"); - memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); - memory->create(c_cut,ntypes,ntypes,"fc.c_cut"); + _memory->create(c_force,ntypes,ntypes,"fc.c_force"); + _memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); + _memory->create(c_cut,ntypes,ntypes,"fc.c_cut"); #ifdef _LMP_INTEL_OFFLOAD @@ -548,5 +558,4 @@ void PairBuckCoulCutIntel::ForceConst::set_ntypes(const int ntypes, } _ntypes=ntypes; _ntable=ntable; - _memory=memory; } diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.h b/src/INTEL/pair_buck_coul_cut_intel.h similarity index 100% rename from src/USER-INTEL/pair_buck_coul_cut_intel.h rename to src/INTEL/pair_buck_coul_cut_intel.h diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/INTEL/pair_buck_coul_long_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_buck_coul_long_intel.cpp rename to src/INTEL/pair_buck_coul_long_intel.cpp index 689a874bce..d9d618e4a8 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/INTEL/pair_buck_coul_long_intel.cpp @@ -16,25 +16,25 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_buck_coul_long_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "force.h" #include "group.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "suffix.h" -#include "force.h" #include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -76,7 +76,10 @@ void PairBuckCoulLongIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -307,9 +310,14 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#else + #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#endif #pragma vector aligned - #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, secoul, \ - sv0, sv1, sv2, sv3, sv4, sv5) #endif for (int jj = 0; jj < ej; jj++) { flt_t forcecoul, forcebuck, evdwl, ecoul; @@ -479,11 +487,13 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, void PairBuckCoulLongIntel::init_style() { PairBuckCoulLong::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -605,7 +615,8 @@ void PairBuckCoulLongIntel::ForceConst::set_ntypes(const int ntypes, const int ntable, Memory *memory, const int cop) { - if ((ntypes != _ntypes || ntable != _ntable)) { + if (memory != nullptr) _memory = memory; + if ((ntypes != _ntypes) || (ntable != _ntable)) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -642,14 +653,14 @@ void PairBuckCoulLongIntel::ForceConst::set_ntypes(const int ntypes, } if (ntypes > 0) { _cop = cop; - memory->create(c_force,ntypes,ntypes,"fc.c_force"); - memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); - memory->create(rho_inv,ntypes,ntypes,"fc.rho_inv"); - memory->create(table,ntable,"pair:fc.table"); - memory->create(etable,ntable,"pair:fc.etable"); - memory->create(detable,ntable,"pair:fc.detable"); - memory->create(ctable,ntable,"pair:fc.ctable"); - memory->create(dctable,ntable,"pair:fc.dctable"); + _memory->create(c_force,ntypes,ntypes,"fc.c_force"); + _memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); + _memory->create(rho_inv,ntypes,ntypes,"fc.rho_inv"); + _memory->create(table,ntable,"pair:fc.table"); + _memory->create(etable,ntable,"pair:fc.etable"); + _memory->create(detable,ntable,"pair:fc.detable"); + _memory->create(ctable,ntable,"pair:fc.ctable"); + _memory->create(dctable,ntable,"pair:fc.dctable"); #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -682,7 +693,6 @@ void PairBuckCoulLongIntel::ForceConst::set_ntypes(const int ntypes, } _ntypes=ntypes; _ntable=ntable; - _memory=memory; } diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.h b/src/INTEL/pair_buck_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_buck_coul_long_intel.h rename to src/INTEL/pair_buck_coul_long_intel.h diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/INTEL/pair_buck_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_buck_intel.cpp rename to src/INTEL/pair_buck_intel.cpp index 017774f8f6..9bad314fcf 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/INTEL/pair_buck_intel.cpp @@ -69,7 +69,10 @@ void PairBuckIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -228,12 +231,18 @@ void PairBuckIntel::eval(const int offload, const int vflag, fxtmp = fytmp = fztmp = (acc_t)0; if (EFLAG) fwtmp = sevdwl = (acc_t)0; if (NEWTON_PAIR == 0) - if (vflag == VIRIAL_PAIR) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0; + if (vflag == VIRIAL_PAIR) + sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ sv0, sv1, sv2, sv3, sv4, sv5) +#endif + #pragma vector aligned #endif for (int jj = 0; jj < jnum; jj++) { @@ -363,11 +372,14 @@ void PairBuckIntel::eval(const int offload, const int vflag, void PairBuckIntel::init_style() { PairBuck::init_style(); + + // augment neighbor list request + auto request = neighbor->find_request(this); if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -443,6 +455,7 @@ template void PairBuckIntel::ForceConst::set_ntypes(const int ntypes, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if ((ntypes != _ntypes )) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD @@ -465,9 +478,8 @@ void PairBuckIntel::ForceConst::set_ntypes(const int ntypes, } if (ntypes > 0) { _cop = cop; - memory->create(c_force,ntypes,ntypes,"fc.c_force"); - memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); - + _memory->create(c_force,ntypes,ntypes,"fc.c_force"); + _memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -487,7 +499,6 @@ void PairBuckIntel::ForceConst::set_ntypes(const int ntypes, } } _ntypes=ntypes; - _memory=memory; } diff --git a/src/USER-INTEL/pair_buck_intel.h b/src/INTEL/pair_buck_intel.h similarity index 100% rename from src/USER-INTEL/pair_buck_intel.h rename to src/INTEL/pair_buck_intel.h diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/INTEL/pair_dpd_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_dpd_intel.cpp rename to src/INTEL/pair_dpd_intel.cpp index 18c039572b..e6ffd1ca44 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/INTEL/pair_dpd_intel.cpp @@ -14,17 +14,20 @@ Shun Xu (Computer Network Information Center, CAS) ------------------------------------------------------------------------- */ -#include #include "pair_dpd_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" + +#include + using namespace LAMMPS_NS; #define LMP_MKL_RNG VSL_BRNG_MT19937 @@ -85,7 +88,10 @@ void PairDPDIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -284,9 +290,14 @@ void PairDPDIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ - sv0, sv1, sv2, sv3, sv4, sv5) + sv0, sv1, sv2, sv3, sv4, sv5) +#endif + #pragma vector aligned #endif for (int jj = 0; jj < jnum; jj++) { flt_t forcelj, evdwl; @@ -469,11 +480,13 @@ void PairDPDIntel::settings(int narg, char **arg) { void PairDPDIntel::init_style() { PairDPD::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -545,6 +558,7 @@ void PairDPDIntel::ForceConst::set_ntypes(const int ntypes, const int max_nbors, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if (ntypes != _ntypes) { if (_ntypes > 0) { _memory->destroy(param); @@ -553,15 +567,14 @@ void PairDPDIntel::ForceConst::set_ntypes(const int ntypes, } if (ntypes > 0) { _cop = cop; - memory->create(param,ntypes,ntypes,"fc.param"); - memory->create(rand_buffer_thread, nthreads, max_nbors, + _memory->create(param,ntypes,ntypes,"fc.param"); + _memory->create(rand_buffer_thread, nthreads, max_nbors, "fc.rand_buffer_thread"); - memory->create(rngi,nthreads,"fc.param"); + _memory->create(rngi,nthreads,"fc.param"); for (int i = 0; i < nthreads; i++) rngi[i] = max_nbors; } } _ntypes = ntypes; - _memory = memory; } /* ---------------------------------------------------------------------- diff --git a/src/USER-INTEL/pair_dpd_intel.h b/src/INTEL/pair_dpd_intel.h similarity index 100% rename from src/USER-INTEL/pair_dpd_intel.h rename to src/INTEL/pair_dpd_intel.h diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/INTEL/pair_eam_alloy_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_eam_alloy_intel.cpp rename to src/INTEL/pair_eam_alloy_intel.cpp diff --git a/src/USER-INTEL/pair_eam_alloy_intel.h b/src/INTEL/pair_eam_alloy_intel.h similarity index 100% rename from src/USER-INTEL/pair_eam_alloy_intel.h rename to src/INTEL/pair_eam_alloy_intel.h diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/INTEL/pair_eam_fs_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_eam_fs_intel.cpp rename to src/INTEL/pair_eam_fs_intel.cpp diff --git a/src/USER-INTEL/pair_eam_fs_intel.h b/src/INTEL/pair_eam_fs_intel.h similarity index 100% rename from src/USER-INTEL/pair_eam_fs_intel.h rename to src/INTEL/pair_eam_fs_intel.h diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/INTEL/pair_eam_intel.cpp similarity index 94% rename from src/USER-INTEL/pair_eam_intel.cpp rename to src/INTEL/pair_eam_intel.cpp index 58573eca5f..8a42e6bbaa 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/INTEL/pair_eam_intel.cpp @@ -81,7 +81,10 @@ void PairEAMIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -306,7 +309,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, acc_t rhoi = (acc_t)0.0; int ej = 0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s + #pragma vector aligned #pragma ivdep #endif for (int jj = 0; jj < jnum; jj++) { @@ -325,8 +328,12 @@ void PairEAMIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:rhoi) +#else #pragma simd reduction(+:rhoi) +#endif + #pragma vector aligned #endif for (int jj = 0; jj < ej; jj++) { int jtype; @@ -367,23 +374,35 @@ void PairEAMIntel::eval(const int offload, const int vflag, const int rcount = nall; if (nthreads == 2) { double *trho2 = rho + nmax; - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned for (int n = 0; n < rcount; n++) rho[n] += trho2[n]; } else if (nthreads == 4) { double *trho2 = rho + nmax; double *trho3 = trho2 + nmax; double *trho4 = trho3 + nmax; - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned for (int n = 0; n < rcount; n++) rho[n] += trho2[n] + trho3[n] + trho4[n]; } else { double *trhon = rho + nmax; for (int t = 1; t < nthreads; t++) { - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned for (int n = 0; n < rcount; n++) rho[n] += trhon[n]; trhon += nmax; @@ -412,8 +431,12 @@ void PairEAMIntel::eval(const int offload, const int vflag, if (EFLAG) tevdwl = (acc_t)0.0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:tevdwl) +#else #pragma simd reduction(+:tevdwl) +#endif + #pragma vector aligned #endif for (int ii = iifrom; ii < iito; ++ii) { const int i = ilist[ii]; @@ -486,7 +509,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, int ej = 0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s + #pragma vector aligned #pragma ivdep #endif for (int jj = 0; jj < jnum; jj++) { @@ -508,9 +531,14 @@ void PairEAMIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + sv0, sv1, sv2, sv3, sv4, sv5) +#else #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ - sv0, sv1, sv2, sv3, sv4, sv5) + sv0, sv1, sv2, sv3, sv4, sv5) +#endif + #pragma vector aligned #endif for (int jj = 0; jj < ej; jj++) { int jtype; @@ -638,11 +666,13 @@ void PairEAMIntel::eval(const int offload, const int vflag, void PairEAMIntel::init_style() { PairEAM::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -751,7 +781,8 @@ void PairEAMIntel::ForceConst::set_ntypes(const int ntypes, const int nr, const int nrho, Memory *memory, const int cop) { - if (ntypes != _ntypes || nr + 1 > _nr || nrho + 1 > _nrho) { + if (memory != nullptr) _memory = memory; + if ((ntypes != _ntypes) || (nr + 1 > _nr) || (nrho + 1 > _nrho)) { if (_ntypes > 0) { _memory->destroy(rhor_spline_f); _memory->destroy(rhor_spline_e); @@ -764,18 +795,17 @@ void PairEAMIntel::ForceConst::set_ntypes(const int ntypes, _cop = cop; _nr = nr + 1; IP_PRE_edge_align(_nr, sizeof(flt_t)); - memory->create(rhor_spline_f,ntypes*ntypes*_nr,"fc.rhor_spline_f"); - memory->create(rhor_spline_e,ntypes*ntypes*_nr,"fc.rhor_spline_e"); - memory->create(z2r_spline_t,ntypes*ntypes*_nr,"fc.z2r_spline_t"); + _memory->create(rhor_spline_f,ntypes*ntypes*_nr,"fc.rhor_spline_f"); + _memory->create(rhor_spline_e,ntypes*ntypes*_nr,"fc.rhor_spline_e"); + _memory->create(z2r_spline_t,ntypes*ntypes*_nr,"fc.z2r_spline_t"); _nrho = nrho + 1; IP_PRE_edge_align(_nrho, sizeof(flt_t)); - memory->create(frho_spline_f,ntypes*_nrho,"fc.frho_spline_f"); - memory->create(frho_spline_e,ntypes*_nrho,"fc.frho_spline_e"); - memory->create(scale_f,ntypes,ntypes,"fc.scale_f"); + _memory->create(frho_spline_f,ntypes*_nrho,"fc.frho_spline_f"); + _memory->create(frho_spline_e,ntypes*_nrho,"fc.frho_spline_e"); + _memory->create(scale_f,ntypes,ntypes,"fc.scale_f"); } } _ntypes = ntypes; - _memory = memory; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/INTEL/pair_eam_intel.h similarity index 100% rename from src/USER-INTEL/pair_eam_intel.h rename to src/INTEL/pair_eam_intel.h diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/INTEL/pair_gayberne_intel.cpp similarity index 96% rename from src/USER-INTEL/pair_gayberne_intel.cpp rename to src/INTEL/pair_gayberne_intel.cpp index e51b7758e6..139792e543 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/INTEL/pair_gayberne_intel.cpp @@ -25,16 +25,16 @@ #endif #include "atom.h" -#include "comm.h" #include "atom_vec_ellipsoid.h" +#include "comm.h" #include "force.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" - +#include "neighbor.h" #include "suffix.h" + using namespace LAMMPS_NS; #define FC_PACKED1_T typename ForceConst::fc_packed1 @@ -75,7 +75,10 @@ void PairGayBerneIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nall = atom->nlocal + atom->nghost; @@ -447,9 +450,14 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, __assume(packed_j % INTEL_MIC_VECTOR_WIDTH == 0); #endif #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp,fytmp,fztmp,fwtmp,t1tmp,t2tmp, \ + t3tmp,sevdwl,sv0,sv1,sv2,sv3,sv4,sv5) +#else + #pragma simd reduction(+:fxtmp,fytmp,fztmp,fwtmp,t1tmp,t2tmp, \ + t3tmp,sevdwl,sv0,sv1,sv2,sv3,sv4,sv5) +#endif #pragma vector aligned - #pragma simd reduction(+:fxtmp,fytmp,fztmp,fwtmp,t1tmp,t2tmp,t3tmp, \ - sevdwl,sv0,sv1,sv2,sv3,sv4,sv5) #endif for (int jj = 0; jj < packed_j; jj++) { flt_t a2_0, a2_1, a2_2, a2_3, a2_4, a2_5, a2_6, a2_7, a2_8; @@ -804,8 +812,12 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, acc_t *f_scalar2 = f_scalar + fst4; for (int t = 1; t < nthreads; t++) { #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma vector aligned #endif for (int n = iifrom * 8; n < sto; n++) f_scalar[n] += f_scalar2[n]; @@ -874,11 +886,13 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, void PairGayBerneIntel::init_style() { PairGayBerne::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -976,6 +990,7 @@ void PairGayBerneIntel::ForceConst::set_ntypes(const int ntypes, const int nthreads, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if (ntypes != _ntypes) { if (_ntypes > 0) { fc_packed3 *oic = ic; @@ -1015,15 +1030,15 @@ void PairGayBerneIntel::ForceConst::set_ntypes(const int ntypes, if (ntypes > 0) { _cop = cop; - memory->create(ijc, ntypes, ntypes, "fc.ijc"); - memory->create(lj34, ntypes, ntypes, "fc.lj34"); - memory->create(ic, ntypes, "fc.ic"); - memory->create(rsq_form, nthreads, one_length, "rsq_form"); - memory->create(delx_form, nthreads, one_length, "delx_form"); - memory->create(dely_form, nthreads, one_length, "dely_form"); - memory->create(delz_form, nthreads, one_length, "delz_form"); - memory->create(jtype_form, nthreads, one_length, "jtype_form"); - memory->create(jlist_form, nthreads, one_length, "jlist_form"); + _memory->create(ijc, ntypes, ntypes, "fc.ijc"); + _memory->create(lj34, ntypes, ntypes, "fc.lj34"); + _memory->create(ic, ntypes, "fc.ic"); + _memory->create(rsq_form, nthreads, one_length, "rsq_form"); + _memory->create(delx_form, nthreads, one_length, "delx_form"); + _memory->create(dely_form, nthreads, one_length, "dely_form"); + _memory->create(delz_form, nthreads, one_length, "delz_form"); + _memory->create(jtype_form, nthreads, one_length, "jtype_form"); + _memory->create(jlist_form, nthreads, one_length, "jlist_form"); for (int zn = 0; zn < nthreads; zn++) for (int zo = 0; zo < one_length; zo++) { @@ -1068,5 +1083,4 @@ void PairGayBerneIntel::ForceConst::set_ntypes(const int ntypes, } } _ntypes = ntypes; - _memory = memory; } diff --git a/src/USER-INTEL/pair_gayberne_intel.h b/src/INTEL/pair_gayberne_intel.h similarity index 100% rename from src/USER-INTEL/pair_gayberne_intel.h rename to src/INTEL/pair_gayberne_intel.h diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp similarity index 96% rename from src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp rename to src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 59809cc839..23e357516f 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -72,7 +72,10 @@ void PairLJCharmmCoulCharmmIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -292,9 +295,14 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#else + #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#endif #pragma vector aligned - #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, secoul, \ - sv0, sv1, sv2, sv3, sv4, sv5) #endif for (int jj = 0; jj < ej; jj++) { flt_t forcecoul, forcelj, evdwl; @@ -448,11 +456,13 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, void PairLJCharmmCoulCharmmIntel::init_style() { PairLJCharmmCoulCharmm::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -549,6 +559,7 @@ void PairLJCharmmCoulCharmmIntel::pack_force_const(ForceConst &fc, template void PairLJCharmmCoulCharmmIntel::ForceConst::set_ntypes( const int ntypes, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if (ntypes != _ntypes) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD @@ -569,8 +580,8 @@ void PairLJCharmmCoulCharmmIntel::ForceConst::set_ntypes( } if (ntypes > 0) { _cop = cop; - memory->create(cutsq,ntypes,ntypes,"fc.cutsq"); - memory->create(lj,ntypes,ntypes,"fc.lj"); + _memory->create(cutsq,ntypes,ntypes,"fc.cutsq"); + _memory->create(lj,ntypes,ntypes,"fc.lj"); #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -589,5 +600,4 @@ void PairLJCharmmCoulCharmmIntel::ForceConst::set_ntypes( } } _ntypes=ntypes; - _memory=memory; } diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h b/src/INTEL/pair_lj_charmm_coul_charmm_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h rename to src/INTEL/pair_lj_charmm_coul_charmm_intel.h diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp rename to src/INTEL/pair_lj_charmm_coul_long_intel.cpp index 0ce7e1e1fd..696f5948ac 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -13,20 +13,23 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_charmm_coul_long_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "group.h" #include "kspace.h" #include "memory.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" + +#include + using namespace LAMMPS_NS; #define LJ_T typename IntelBuffers::vec2_t @@ -73,7 +76,10 @@ void PairLJCharmmCoulLongIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -309,9 +315,14 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#else + #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#endif #pragma vector aligned - #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, secoul, \ - sv0, sv1, sv2, sv3, sv4, sv5) #endif for (int jj = 0; jj < ej; jj++) { flt_t forcecoul, forcelj, evdwl, ecoul; @@ -510,11 +521,13 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, void PairLJCharmmCoulLongIntel::init_style() { PairLJCharmmCoulLong::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -641,7 +654,8 @@ void PairLJCharmmCoulLongIntel::ForceConst::set_ntypes(const int ntypes, const int ntable, Memory *memory, const int cop) { - if ((ntypes != _ntypes || ntable != _ntable)) { + if (memory != nullptr) _memory = memory; + if ((ntypes != _ntypes) || (ntable != _ntable)) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -675,13 +689,13 @@ void PairLJCharmmCoulLongIntel::ForceConst::set_ntypes(const int ntypes, } if (ntypes > 0) { _cop = cop; - memory->create(cutsq,ntypes,ntypes,"fc.cutsq"); - memory->create(lj,ntypes,ntypes,"fc.lj"); - memory->create(table,ntable,"pair:fc.table"); - memory->create(etable,ntable,"pair:fc.etable"); - memory->create(detable,ntable,"pair:fc.detable"); - memory->create(ctable,ntable,"pair:fc.ctable"); - memory->create(dctable,ntable,"pair:fc.dctable"); + _memory->create(cutsq,ntypes,ntypes,"fc.cutsq"); + _memory->create(lj,ntypes,ntypes,"fc.lj"); + _memory->create(table,ntable,"pair:fc.table"); + _memory->create(etable,ntable,"pair:fc.etable"); + _memory->create(detable,ntable,"pair:fc.detable"); + _memory->create(ctable,ntable,"pair:fc.ctable"); + _memory->create(dctable,ntable,"pair:fc.dctable"); #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -711,5 +725,4 @@ void PairLJCharmmCoulLongIntel::ForceConst::set_ntypes(const int ntypes, } _ntypes=ntypes; _ntable=ntable; - _memory=memory; } diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h b/src/INTEL/pair_lj_charmm_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_charmm_coul_long_intel.h rename to src/INTEL/pair_lj_charmm_coul_long_intel.h diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/INTEL/pair_lj_cut_coul_long_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp rename to src/INTEL/pair_lj_cut_coul_long_intel.cpp index 9e024b35c8..f78f579a9a 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_cut_coul_long_intel.cpp @@ -75,7 +75,10 @@ void PairLJCutCoulLongIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -303,9 +306,14 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#else + #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + secoul, sv0, sv1, sv2, sv3, sv4, sv5) +#endif #pragma vector aligned - #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, secoul, \ - sv0, sv1, sv2, sv3, sv4, sv5) #endif for (int jj = 0; jj < ej; jj++) { flt_t forcecoul, forcelj, evdwl, ecoul; @@ -476,11 +484,13 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, void PairLJCutCoulLongIntel::init_style() { PairLJCutCoulLong::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -600,7 +610,8 @@ void PairLJCutCoulLongIntel::ForceConst::set_ntypes(const int ntypes, const int ntable, Memory *memory, const int cop) { - if ((ntypes != _ntypes || ntable != _ntable)) { + if (memory != nullptr) _memory = memory; + if ((ntypes != _ntypes) || (ntable != _ntable)) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -634,13 +645,13 @@ void PairLJCutCoulLongIntel::ForceConst::set_ntypes(const int ntypes, } if (ntypes > 0) { _cop = cop; - memory->create(c_force,ntypes,ntypes,"fc.c_force"); - memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); - memory->create(table,ntable,"pair:fc.table"); - memory->create(etable,ntable,"pair:fc.etable"); - memory->create(detable,ntable,"pair:fc.detable"); - memory->create(ctable,ntable,"pair:fc.ctable"); - memory->create(dctable,ntable,"pair:fc.dctable"); + _memory->create(c_force,ntypes,ntypes,"fc.c_force"); + _memory->create(c_energy,ntypes,ntypes,"fc.c_energy"); + _memory->create(table,ntable,"pair:fc.table"); + _memory->create(etable,ntable,"pair:fc.etable"); + _memory->create(detable,ntable,"pair:fc.detable"); + _memory->create(ctable,ntable,"pair:fc.ctable"); + _memory->create(dctable,ntable,"pair:fc.dctable"); #ifdef _LMP_INTEL_OFFLOAD flt_t * ospecial_lj = special_lj; @@ -671,5 +682,4 @@ void PairLJCutCoulLongIntel::ForceConst::set_ntypes(const int ntypes, } _ntypes=ntypes; _ntable=ntable; - _memory=memory; } diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.h b/src/INTEL/pair_lj_cut_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_cut_coul_long_intel.h rename to src/INTEL/pair_lj_cut_coul_long_intel.h diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/INTEL/pair_lj_cut_intel.cpp similarity index 95% rename from src/USER-INTEL/pair_lj_cut_intel.cpp rename to src/INTEL/pair_lj_cut_intel.cpp index 029b1eca5b..afd01e9919 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/INTEL/pair_lj_cut_intel.cpp @@ -13,18 +13,20 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" - +#include "neighbor.h" #include "suffix.h" + +#include + using namespace LAMMPS_NS; #define FC_PACKED1_T typename ForceConst::fc_packed1 @@ -65,7 +67,10 @@ void PairLJCutIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -237,9 +242,15 @@ void PairLJCutIntel::eval(const int offload, const int vflag, if (vflag == VIRIAL_PAIR) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned nog2s +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ + sv0, sv1, sv2, sv3, sv4, sv5) \ + aligned(jlist,x,ljc12oi,special_lj,f,lj34i:64) +#else #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ sv0, sv1, sv2, sv3, sv4, sv5) + #pragma vector aligned +#endif #endif for (int jj = 0; jj < jnum; jj++) { flt_t forcelj, evdwl; @@ -380,11 +391,13 @@ void PairLJCutIntel::eval(const int offload, const int vflag, void PairLJCutIntel::init_style() { PairLJCut::init_style(); + auto request = neighbor->find_request(this); + if (force->newton_pair == 0) { - neighbor->requests[neighbor->nrequest-1]->half = 0; - neighbor->requests[neighbor->nrequest-1]->full = 1; + request->half = 0; + request->full = 1; } - neighbor->requests[neighbor->nrequest-1]->intel = 1; + request->intel = 1; int ifix = modify->find_fix("package_intel"); if (ifix < 0) @@ -458,6 +471,7 @@ template void PairLJCutIntel::ForceConst::set_ntypes(const int ntypes, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if (ntypes != _ntypes) { if (_ntypes > 0) { _memory->destroy(ljc12o); @@ -465,10 +479,9 @@ void PairLJCutIntel::ForceConst::set_ntypes(const int ntypes, } if (ntypes > 0) { _cop = cop; - memory->create(ljc12o,ntypes,ntypes,"fc.c12o"); - memory->create(lj34,ntypes,ntypes,"fc.lj34"); + _memory->create(ljc12o,ntypes,ntypes,"fc.c12o"); + _memory->create(lj34,ntypes,ntypes,"fc.lj34"); } } _ntypes = ntypes; - _memory = memory; } diff --git a/src/USER-INTEL/pair_lj_cut_intel.h b/src/INTEL/pair_lj_cut_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_cut_intel.h rename to src/INTEL/pair_lj_cut_intel.h diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/INTEL/pair_lj_long_coul_long_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_lj_long_coul_long_intel.cpp rename to src/INTEL/pair_lj_long_coul_long_intel.cpp diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.h b/src/INTEL/pair_lj_long_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_long_coul_long_intel.h rename to src/INTEL/pair_lj_long_coul_long_intel.h diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/INTEL/pair_rebo_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_rebo_intel.cpp rename to src/INTEL/pair_rebo_intel.cpp diff --git a/src/USER-INTEL/pair_rebo_intel.h b/src/INTEL/pair_rebo_intel.h similarity index 100% rename from src/USER-INTEL/pair_rebo_intel.h rename to src/INTEL/pair_rebo_intel.h diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/INTEL/pair_sw_intel.cpp similarity index 98% rename from src/USER-INTEL/pair_sw_intel.cpp rename to src/INTEL/pair_sw_intel.cpp index b7c92bf1ee..0a7e3baca0 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/INTEL/pair_sw_intel.cpp @@ -96,7 +96,10 @@ void PairSWIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -369,8 +372,12 @@ void PairSWIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl) +#else #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl) +#endif + #pragma vector aligned #endif for (int jj = 0; jj < ejnum_pad; jj++) { acc_t fjxtmp, fjytmp, fjztmp, fjtmp; @@ -1102,7 +1109,8 @@ void PairSWIntel::allocate() void PairSWIntel::init_style() { PairSW::init_style(); - neighbor->requests[neighbor->nrequest-1]->intel = 1; + neighbor->find_request(this)->intel = 1; + map[0] = map[1]; int ifix = modify->find_fix("package_intel"); @@ -1269,6 +1277,7 @@ template void PairSWIntel::ForceConst::set_ntypes(const int ntypes, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if (ntypes != _ntypes) { if (_ntypes > 0) { fc_packed0 *op2 = p2[0]; @@ -1285,19 +1294,19 @@ void PairSWIntel::ForceConst::set_ntypes(const int ntypes, } #endif - memory->destroy(p2); - memory->destroy(p2f); - memory->destroy(p2f2); - memory->destroy(p2e); - memory->destroy(p3); + _memory->destroy(p2); + _memory->destroy(p2f); + _memory->destroy(p2f2); + _memory->destroy(p2e); + _memory->destroy(p3); } if (ntypes > 0) { _cop = cop; - memory->create(p2,ntypes,ntypes,"fc.p2"); - memory->create(p2f,ntypes,ntypes,"fc.p2f"); - memory->create(p2f2,ntypes,ntypes,"fc.p2f2"); - memory->create(p2e,ntypes,ntypes,"fc.p2e"); - memory->create(p3,ntypes,ntypes,ntypes,"fc.p3"); + _memory->create(p2,ntypes,ntypes,"fc.p2"); + _memory->create(p2f,ntypes,ntypes,"fc.p2f"); + _memory->create(p2f2,ntypes,ntypes,"fc.p2f2"); + _memory->create(p2e,ntypes,ntypes,"fc.p2e"); + _memory->create(p3,ntypes,ntypes,ntypes,"fc.p3"); #ifdef _LMP_INTEL_OFFLOAD fc_packed0 *op2 = p2[0]; @@ -1317,5 +1326,4 @@ void PairSWIntel::ForceConst::set_ntypes(const int ntypes, } } _ntypes = ntypes; - _memory = memory; } diff --git a/src/USER-INTEL/pair_sw_intel.h b/src/INTEL/pair_sw_intel.h similarity index 100% rename from src/USER-INTEL/pair_sw_intel.h rename to src/INTEL/pair_sw_intel.h diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/INTEL/pair_tersoff_intel.cpp similarity index 94% rename from src/USER-INTEL/pair_tersoff_intel.cpp rename to src/INTEL/pair_tersoff_intel.cpp index 975b600bfa..3c963cb850 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/INTEL/pair_tersoff_intel.cpp @@ -16,11 +16,8 @@ Contributing author: Markus Höhnerbach (RWTH) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_tersoff_intel.h" + #include "atom.h" #include "neighbor.h" #include "neigh_list.h" @@ -30,30 +27,13 @@ #include "memory.h" #include "error.h" -// Currently Intel compiler is required for this pair style. -// For convenience, base class routines are called if not using Intel compiler. -#ifndef __INTEL_COMPILER +#include +#include + using namespace LAMMPS_NS; -PairTersoffIntel::PairTersoffIntel(LAMMPS *lmp) : PairTersoff(lmp) -{ -} - -void PairTersoffIntel::compute(int eflag, int vflag) -{ - PairTersoff::compute(eflag, vflag); -} - -void PairTersoffIntel::init_style() -{ - if (comm->me == 0) { - error->warning(FLERR, "Tersoff/intel currently requires intel compiler. " - "Using MANYBODY version."); - } - PairTersoff::init_style(); -} - -#else +// Currently the Intel compiler is required for this pair style. +#ifdef __INTEL_COMPILER #ifdef _LMP_INTEL_OFFLOAD #pragma offload_attribute(push,target(mic)) @@ -110,7 +90,10 @@ void PairTersoffIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); + if (vflag && !vflag_fdotr && force->newton_pair) + error->all(FLERR,"INTEL package does not support pair_modify nofdotr " + "with newton on"); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -367,11 +350,11 @@ void PairTersoffIntel::eval(const int offload, const int vflag, lmp_intel::vector_traits::support_integer_and_gather_ops; bool use_scalar = VL < 4; if (use_scalar) { - IntelKernelTersoff::kernel(ARGS); + IntelKernelTersoff::template kernel(ARGS); } else if (pack_i) { - IntelKernelTersoff::kernel(ARGS); + IntelKernelTersoff::template kernel(ARGS); } else { - IntelKernelTersoff::kernel(ARGS); + IntelKernelTersoff::template kernel(ARGS); } if (EFLAG) oevdwl += sevdwl; } @@ -567,6 +550,7 @@ template void PairTersoffIntel::ForceConst::set_ntypes(const int ntypes, Memory *memory, const int cop) { + if (memory != nullptr) _memory = memory; if ((ntypes != _ntypes)) { if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD @@ -598,13 +582,13 @@ void PairTersoffIntel::ForceConst::set_ntypes(const int ntypes, _cop = cop; size_t VL = 512 / 8 / sizeof(flt_t); int ntypes_pad = ntypes + VL - ntypes % VL; - memory->create(c_first_loop,ntypes,ntypes,"fc.c_first_loop"); - memory->create(c_second_loop,ntypes,ntypes,"fc.c_second_loop"); - memory->create(c_cutoff_outer,ntypes,ntypes,"fc.c_cutoff_outer"); - memory->create(c_inner_loop,ntypes,ntypes,ntypes,"fc.c_inner_loop"); - memory->create(c_cutoff_inner,ntypes,ntypes,ntypes_pad,"fc.c_cutoff_inner"); - memory->create(c_inner,ntypes,ntypes,ntypes,"fc.c_inner"); - memory->create(c_outer,ntypes,ntypes,"fc.c_outer"); + _memory->create(c_first_loop,ntypes,ntypes,"fc.c_first_loop"); + _memory->create(c_second_loop,ntypes,ntypes,"fc.c_second_loop"); + _memory->create(c_cutoff_outer,ntypes,ntypes,"fc.c_cutoff_outer"); + _memory->create(c_inner_loop,ntypes,ntypes,ntypes,"fc.c_inner_loop"); + _memory->create(c_cutoff_inner,ntypes,ntypes,ntypes_pad,"fc.c_cutoff_inner"); + _memory->create(c_inner,ntypes,ntypes,ntypes,"fc.c_inner"); + _memory->create(c_outer,ntypes,ntypes,"fc.c_outer"); #ifdef _LMP_INTEL_OFFLOAD c_first_loop_t * oc_first_loop = c_first_loop[0]; c_second_loop_t * oc_second_loop = c_second_loop[0]; @@ -631,7 +615,6 @@ void PairTersoffIntel::ForceConst::set_ntypes(const int ntypes, } } _ntypes=ntypes; - _memory=memory; } #ifdef _LMP_INTEL_OFFLOAD @@ -691,7 +674,8 @@ void IntelKernelTersoff::kernel_step( fvec vrijsq = vdx_ij * vdx_ij + vdy_ij * vdy_ij + vdz_ij * vdz_ij; fvec vrij = sqrt(vrijsq); ivec vis_orig = v::int_load_vl(is); - ivec vnumneigh_i = v::int_gather<4>(v_i0, vmask, vis_orig, numneigh); + ivec vnumneigh_i = v::template int_gather<4>(v_i0, vmask, vis_orig, + numneigh); ivec vc_idx_ij = v::int_mullo(v_i4floats, vw_j + v::int_mullo(v_i_ntypes, vw_i)); fvec vzeta = v::zero(); @@ -718,14 +702,16 @@ void IntelKernelTersoff::kernel_step( while (! v::mask_testz(vactive_mask) && cache_idx < N_CACHE) { bvec vnew_mask = vactive_mask & ~ veff_old_mask; vks = v::int_mullo(v_i4floats, v_i_NEIGHMASK & - v::int_gather<4>(vks, vactive_mask, vkks + vcnumneigh_i, firstneigh)); + (v::template int_gather<4>(vks, vactive_mask, + vkks + vcnumneigh_i, + firstneigh))); v::gather_x(vks, vnew_mask, x, &vx_k, &vy_k, &vz_k, &vw_k); fvec vdx_ik = (vx_k - vx_i); fvec vdy_ik = (vy_k - vy_i); fvec vdz_ik = (vz_k - vz_i); fvec vrsq = vdx_ik * vdx_ik + vdy_ik * vdy_ik + vdz_ik * vdz_ik; ivec vc_idx = v::int_mullo(v_i4floats, vw_k) + v::int_mullo(v_i_ntypes, vc_idx_ij); - vcutsq = v::gather<4>(vcutsq, vnew_mask, vc_idx, c_inner); + vcutsq = v::template gather<4>(vcutsq, vnew_mask, vc_idx, c_inner); bvec vcutoff_mask = v::cmplt(vrsq, vcutsq); bvec vsame_mask = v::int_cmpneq(vjs, vks); bvec veff_mask = vcutoff_mask & vsame_mask & vactive_mask; @@ -769,14 +755,16 @@ void IntelKernelTersoff::kernel_step( while (! v::mask_testz(vactive_mask)) { bvec vnew_mask = vactive_mask & ~ veff_old_mask; vks = v::int_mullo(v_i4floats, v_i_NEIGHMASK & - v::int_gather<4>(vks, vactive_mask, vkks + vcnumneigh_i, firstneigh)); + (v::template int_gather<4>(vks, vactive_mask, + vkks + vcnumneigh_i, + firstneigh))); v::gather_x(vks, vnew_mask, x, &vx_k, &vy_k, &vz_k, &vw_k); fvec vdx_ik = (vx_k - vx_i); fvec vdy_ik = (vy_k - vy_i); fvec vdz_ik = (vz_k - vz_i); fvec vrsq = vdx_ik * vdx_ik + vdy_ik * vdy_ik + vdz_ik * vdz_ik; ivec vc_idx = v::int_mullo(v_i4floats, vw_k) + v::int_mullo(v_i_ntypes, vc_idx_ij); - vcutsq = v::gather<4>(vcutsq, vnew_mask, vc_idx, c_inner); + vcutsq = v::template gather<4>(vcutsq, vnew_mask, vc_idx, c_inner); bvec vcutoff_mask = v::cmplt(vrsq, vcutsq); bvec vsame_mask = v::int_cmpneq(vjs, vks); bvec veff_mask = vcutoff_mask & vsame_mask & vactive_mask; @@ -836,14 +824,16 @@ void IntelKernelTersoff::kernel_step( while (! v::mask_testz(vactive_mask)) { bvec vnew_mask = vactive_mask & ~ veff_old_mask; vks = v::int_mullo(v_i4floats, v_i_NEIGHMASK & - v::int_gather<4>(vks, vactive_mask, vkks + vcnumneigh_i, firstneigh)); + (v::template int_gather<4>(vks, vactive_mask, + vkks + vcnumneigh_i, + firstneigh))); v::gather_x(vks, vnew_mask, x, &vx_k, &vy_k, &vz_k, &vw_k); fvec vdx_ik = vx_k - vx_i; fvec vdy_ik = vy_k - vy_i; fvec vdz_ik = vz_k - vz_i; fvec vrsq = vdx_ik * vdx_ik + vdy_ik * vdy_ik + vdz_ik * vdz_ik; ivec vc_idx = v::int_mullo(v_i4floats, vw_k) + v::int_mullo(v_i_ntypes, vc_idx_ij); - vcutsq = v::gather<4>(vcutsq, vnew_mask, vc_idx, c_inner); + vcutsq = v::template gather<4>(vcutsq, vnew_mask, vc_idx, c_inner); bvec vcutoff_mask = v::cmplt(vrsq, vcutsq); bvec vsame_mask = v::int_cmpneq(vjs, vks); bvec veff_mask = vcutoff_mask & vsame_mask & vactive_mask; @@ -991,7 +981,7 @@ void IntelKernelTersoff::kernel_step_const_i( fvec vdy_ik = vy_k - vy_i; fvec vdz_ik = vz_k - vz_i; fvec vrsq = vdx_ik * vdx_ik + vdy_ik * vdy_ik + vdz_ik * vdz_ik; - fvec vcutsq = v::gather<4>(v::zero(), vmask, vc_idx_j_ntypes, &c_inner[ntypes * ntypes * w_i + w_k]); + fvec vcutsq = v::template gather<4>(v::zero(), vmask, vc_idx_j_ntypes, &c_inner[ntypes * ntypes * w_i + w_k]); bvec vcutoff_mask = v::cmplt(vrsq, vcutsq); bvec vsame_mask = v::int_cmpneq(vjs, ivec(static_cast(4 * sizeof(typename v::fscal) * k))); bvec veff_mask = vcutoff_mask & vsame_mask & vmask; @@ -1035,7 +1025,7 @@ void IntelKernelTersoff::kernel_step_const_i( fvec vdy_ik = vy_k - vy_i; fvec vdz_ik = vz_k - vz_i; fvec vrsq = vdx_ik * vdx_ik + vdy_ik * vdy_ik + vdz_ik * vdz_ik; - fvec vcutsq = v::gather<4>(v::zero(), vmask, vc_idx_j_ntypes, &c_inner[ntypes * ntypes * w_i + w_k]); + fvec vcutsq = v::template gather<4>(v::zero(), vmask, vc_idx_j_ntypes, &c_inner[ntypes * ntypes * w_i + w_k]); bvec vcutoff_mask = v::cmplt(vrsq, vcutsq); bvec vsame_mask = v::int_cmpneq(vjs, ivec(static_cast(4 * sizeof(typename v::fscal) * k))); bvec veff_mask = vcutoff_mask & vsame_mask & vmask; @@ -1082,7 +1072,7 @@ void IntelKernelTersoff::kernel_step_const_i( fvec vdy_ik = vy_k - vy_i; fvec vdz_ik = vz_k - vz_i; fvec vrsq = vdx_ik * vdx_ik + vdy_ik * vdy_ik + vdz_ik * vdz_ik; - fvec vcutsq = v::gather<4>(v::zero(), vmask, vc_idx_j_ntypes, &c_inner[ntypes * ntypes * w_i + w_k].cutsq); + fvec vcutsq = v::template gather<4>(v::zero(), vmask, vc_idx_j_ntypes, &c_inner[ntypes * ntypes * w_i + w_k].cutsq); bvec vcutoff_mask = v::cmplt(vrsq, vcutsq); bvec vsame_mask = v::int_cmpneq(vjs, ivec(static_cast(4 * sizeof(typename v::fscal) * k))); bvec veff_mask = vcutoff_mask & vsame_mask & vmask; @@ -1228,7 +1218,7 @@ void IntelKernelTersoff::kernel( template -IntelKernelTersoff::fvec IntelKernelTersoff::zeta_vector( +typename IntelKernelTersoff::fvec IntelKernelTersoff::zeta_vector( const c_inner_t * param, ivec xjw, bvec mask, fvec vrij, fvec rsq2, @@ -1354,6 +1344,8 @@ void IntelKernelTersoff::force_zeta_vector( } } +#define BCF lmp_intel::vector_routines + template template void IntelKernelTersoff::attractive_vector( @@ -1393,7 +1385,7 @@ void IntelKernelTersoff::attractive_vector( fvec varg3 = varg1 * varg1 * varg1; bvec mask_ex = v::cmpeq(vppowermint, fvec(3.)); fvec varg = v::blend(mask_ex, varg1, varg3); - fvec vex_delr = min(fvec(1.e30), exp(varg)); + fvec vex_delr = BCF::min(fvec(1.e30), exp(varg)); fvec vex_delr_d_factor = v::blend(mask_ex, v_1_0, fvec(3.0) * varg1 * varg1); fvec vex_delr_d = vplam3 * vex_delr_d_factor * vex_delr; bvec vmask_need_sine = v::cmpnle(vrik, vpbigr - vpbigd) & mask; @@ -1413,12 +1405,12 @@ void IntelKernelTersoff::attractive_vector( if (ZETA) *zeta = vfc * vgijk * vex_delr; fvec vminus_costheta = - vcostheta; - fvec vdcosdrjx = vrijinv * fmadd(vminus_costheta, vrij_hatx, rik_hatx); - fvec vdcosdrjy = vrijinv * fmadd(vminus_costheta, vrij_haty, rik_haty); - fvec vdcosdrjz = vrijinv * fmadd(vminus_costheta, vrij_hatz, rik_hatz); - fvec vdcosdrkx = rikinv * fmadd(vminus_costheta, rik_hatx, vrij_hatx); - fvec vdcosdrky = rikinv * fmadd(vminus_costheta, rik_haty, vrij_haty); - fvec vdcosdrkz = rikinv * fmadd(vminus_costheta, rik_hatz, vrij_hatz); + fvec vdcosdrjx = vrijinv * BCF::fmadd(vminus_costheta, vrij_hatx, rik_hatx); + fvec vdcosdrjy = vrijinv * BCF::fmadd(vminus_costheta, vrij_haty, rik_haty); + fvec vdcosdrjz = vrijinv * BCF::fmadd(vminus_costheta, vrij_hatz, rik_hatz); + fvec vdcosdrkx = rikinv * BCF::fmadd(vminus_costheta, rik_hatx, vrij_hatx); + fvec vdcosdrky = rikinv * BCF::fmadd(vminus_costheta, rik_haty, vrij_haty); + fvec vdcosdrkz = rikinv * BCF::fmadd(vminus_costheta, rik_hatz, vrij_hatz); fvec vdcosdrix = -(vdcosdrjx + vdcosdrkx); fvec vdcosdriy = -(vdcosdrjy + vdcosdrky); fvec vdcosdriz = -(vdcosdrjz + vdcosdrkz); @@ -1439,4 +1431,4 @@ void IntelKernelTersoff::attractive_vector( #pragma offload_attribute(pop) #endif -#endif +#endif // __INTEL_COMPILER diff --git a/src/USER-INTEL/pair_tersoff_intel.h b/src/INTEL/pair_tersoff_intel.h similarity index 97% rename from src/USER-INTEL/pair_tersoff_intel.h rename to src/INTEL/pair_tersoff_intel.h index b613a00194..b40ce19787 100644 --- a/src/USER-INTEL/pair_tersoff_intel.h +++ b/src/INTEL/pair_tersoff_intel.h @@ -14,7 +14,10 @@ #ifdef PAIR_CLASS // clang-format off +// Currently the Intel compilers are required for this pair style. +#ifdef __INTEL_COMPILER PairStyle(tersoff/intel,PairTersoffIntel); +#endif // clang-format on #else @@ -25,6 +28,8 @@ PairStyle(tersoff/intel,PairTersoffIntel); #include "fix_intel.h" #include "pair_tersoff.h" +#ifdef __INTEL_COMPILER + namespace LAMMPS_NS { class PairTersoffIntel : public PairTersoff { @@ -33,7 +38,6 @@ class PairTersoffIntel : public PairTersoff { virtual void compute(int, int); void init_style(); -#ifdef __INTEL_COMPILER protected: typedef struct { float x,y,z; int w; } sng4_t; @@ -88,10 +92,10 @@ class PairTersoffIntel : public PairTersoff { template void pack_force_const(ForceConst &fc, IntelBuffers *buffers); -#endif // __INTEL_COMPILER }; } +#endif // __INTEL_COMPILER #endif #endif diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp similarity index 97% rename from src/USER-INTEL/pppm_disp_intel.cpp rename to src/INTEL/pppm_disp_intel.cpp index ff045983db..6b732ccfac 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/INTEL/pppm_disp_intel.cpp @@ -160,7 +160,7 @@ void PPPMDispIntel::init() precompute_rho(); } if (order > INTEL_P3M_MAXORDER) - error->all(FLERR,"PPPM order greater than supported by USER-INTEL\n"); + error->all(FLERR,"PPPM order greater than supported by INTEL\n"); } /* ---------------------------------------------------------------------- @@ -770,8 +770,12 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz, IP_PRE_omp_range_id_align(iifrom, iito, tid, nlocal, nthr, sizeof(ATOM_T)); #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:flag) +#else #pragma simd reduction(+:flag) +#endif + #pragma vector aligned #endif for (int i = iifrom; i < iito; i++) { @@ -876,7 +880,11 @@ void PPPMDispIntel::make_rho_c(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho_lookup[idx][k]; @@ -885,7 +893,11 @@ void PPPMDispIntel::make_rho_c(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower; k <= nupper; k++) { FFT_SCALAR r1,r2,r3; @@ -917,8 +929,12 @@ void PPPMDispIntel::make_rho_c(IntelBuffers * /*buffers*/) int mzy = m*nix + mz; FFT_SCALAR x0 = y0*rho[1][m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mzyx = l + mzy; @@ -939,7 +955,11 @@ void PPPMDispIntel::make_rho_c(IntelBuffers * /*buffers*/) IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, nthr); #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { for (int j = 1; j < nthr; j++) { @@ -1025,7 +1045,11 @@ void PPPMDispIntel::make_rho_g(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho6_lookup[idx][k]; @@ -1034,7 +1058,11 @@ void PPPMDispIntel::make_rho_g(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1,r2,r3; @@ -1067,8 +1095,12 @@ void PPPMDispIntel::make_rho_g(IntelBuffers * /*buffers*/) int mzy = m*nix + mz; FFT_SCALAR x0 = y0*rho[1][m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mzyx = l + mzy; @@ -1089,7 +1121,11 @@ void PPPMDispIntel::make_rho_g(IntelBuffers * /*buffers*/) IP_PRE_omp_range_id(ifrom, ito, tid, ngrid_6, nthr); #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { for (int j = 1; j < nthr; j++) { @@ -1173,7 +1209,11 @@ void PPPMDispIntel::make_rho_a(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho6_lookup[idx][k]; @@ -1182,7 +1222,11 @@ void PPPMDispIntel::make_rho_a(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1,r2,r3; @@ -1215,8 +1259,12 @@ void PPPMDispIntel::make_rho_a(IntelBuffers * /*buffers*/) int my = m + nysum; FFT_SCALAR x0 = y0*rho[1][m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l + nxsum; @@ -1307,7 +1355,11 @@ void PPPMDispIntel::make_rho_none(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho6_lookup[idx][k]; @@ -1316,7 +1368,11 @@ void PPPMDispIntel::make_rho_none(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1,r2,r3; @@ -1349,8 +1405,12 @@ void PPPMDispIntel::make_rho_none(IntelBuffers * /*buffers*/) int mzy = m*nix + mz; FFT_SCALAR x0 = y0*rho[1][m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mzyx = l + mzy; @@ -1373,7 +1433,11 @@ void PPPMDispIntel::make_rho_none(IntelBuffers * /*buffers*/) IP_PRE_omp_range_id(ifrom, ito, tid, ngrid_6*nsplit, nthr); #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { for (int j = 1; j < nthr; j++) { @@ -1454,7 +1518,11 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho0[k] = rho_lookup[idx][k]; @@ -1463,7 +1531,11 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower; k <= nupper; k++) { FFT_SCALAR r1 = rho_coeff[order-1][k]; @@ -1498,8 +1570,12 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers * /*buffers*/) int my = m+nysum; FFT_SCALAR y0 = z0*rho1[m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l+nxsum; @@ -1624,7 +1700,11 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers * /*buffers*/) int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho_lookup[idx][k]; @@ -1636,7 +1716,11 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower; k <= nupper; k++) { FFT_SCALAR r1,r2,r3,dr1,dr2,dr3; @@ -1680,8 +1764,12 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers * /*buffers*/) FFT_SCALAR eky_p = drho[1][m] * rho[2][n]; FFT_SCALAR ekz_p = rho[1][m] * drho[2][n]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l + nxsum; @@ -1702,7 +1790,11 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers * /*buffers*/) } } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { particle_ekx[i] *= hx_inv; @@ -1802,7 +1894,11 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho0[k] = rho6_lookup[idx][k]; @@ -1811,7 +1907,11 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1 = rho_coeff_6[order_6-1][k]; @@ -1846,8 +1946,12 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers * /*buffers*/) int my = m+nysum; FFT_SCALAR y0 = z0*rho1[m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l+nxsum; @@ -1967,7 +2071,11 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers * /*buffers*/) int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho6_lookup[idx][k]; @@ -1979,7 +2087,11 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1,r2,r3,dr1,dr2,dr3; @@ -2023,8 +2135,12 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers * /*buffers*/) FFT_SCALAR eky_p = drho[1][m] * rho[2][n]; FFT_SCALAR ekz_p = rho[1][m] * drho[2][n]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l + nxsum; @@ -2045,7 +2161,11 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers * /*buffers*/) } } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { particle_ekx[i] *= hx_inv; @@ -2143,7 +2263,11 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho0[k] = rho6_lookup[idx][k]; @@ -2152,7 +2276,11 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1 = rho_coeff_6[order_6-1][k]; @@ -2206,8 +2334,12 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers * /*buffers*/) int my = m+nysum; FFT_SCALAR y0 = z0*rho1[m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l+nxsum; @@ -2398,7 +2530,11 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers * /*buffers*/) int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho6_lookup[idx][k]; @@ -2410,7 +2546,11 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1,r2,r3,dr1,dr2,dr3; @@ -2479,8 +2619,12 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers * /*buffers*/) FFT_SCALAR eky_p = drho[1][m] * rho[2][n]; FFT_SCALAR ekz_p = rho[1][m] * drho[2][n]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l + nxsum; @@ -2541,7 +2685,11 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers * /*buffers*/) } } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { particle_ekx0[i] *= hx_inv; @@ -2671,7 +2819,11 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers * /*buffers*/) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho0[k] = rho6_lookup[idx][k]; @@ -2680,7 +2832,11 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1 = rho_coeff_6[order_6-1][k]; @@ -2721,8 +2877,12 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers * /*buffers*/) int my = m+nysum; FFT_SCALAR y0 = z0*rho1[m]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l+nxsum; @@ -2848,7 +3008,11 @@ void PPPMDispIntel::fieldforce_none_ad(IntelBuffers * /*buffers*/) int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho6_lookup[idx][k]; @@ -2860,7 +3024,11 @@ void PPPMDispIntel::fieldforce_none_ad(IntelBuffers * /*buffers*/) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower_6; k <= nupper_6; k++) { FFT_SCALAR r1,r2,r3,dr1,dr2,dr3; @@ -2909,8 +3077,12 @@ void PPPMDispIntel::fieldforce_none_ad(IntelBuffers * /*buffers*/) FFT_SCALAR eky_p = drho[1][m] * rho[2][n]; FFT_SCALAR ekz_p = rho[1][m] * drho[2][n]; #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif + #pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7) #endif for (int l = 0; l < order; l++) { int mx = l + nxsum; @@ -2992,7 +3164,11 @@ void PPPMDispIntel::precompute_rho() for (int i = 0; i < rho_points; i++) { FFT_SCALAR dx = -1. + 1./half_rho_scale * (FFT_SCALAR)i; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k=nlower; k<=nupper;k++) { FFT_SCALAR r1 = ZEROF; @@ -3006,7 +3182,11 @@ void PPPMDispIntel::precompute_rho() } if (differentiation_flag == 1) { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k=nlower; k<=nupper;k++) { FFT_SCALAR r1 = ZEROF; @@ -3026,7 +3206,11 @@ void PPPMDispIntel::precompute_rho() for (int i = 0; i < rho_points; i++) { FFT_SCALAR dx = -1. + 1./half_rho_scale * (FFT_SCALAR)i; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k=nlower_6; k<=nupper_6;k++) { FFT_SCALAR r1 = ZEROF; @@ -3040,7 +3224,11 @@ void PPPMDispIntel::precompute_rho() } if (differentiation_flag == 1) { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k=nlower_6; k<=nupper_6;k++) { FFT_SCALAR r1 = ZEROF; diff --git a/src/USER-INTEL/pppm_disp_intel.h b/src/INTEL/pppm_disp_intel.h similarity index 100% rename from src/USER-INTEL/pppm_disp_intel.h rename to src/INTEL/pppm_disp_intel.h diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/INTEL/pppm_intel.cpp similarity index 97% rename from src/USER-INTEL/pppm_intel.cpp rename to src/INTEL/pppm_intel.cpp index b369e25284..8041709ebc 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/INTEL/pppm_intel.cpp @@ -135,7 +135,7 @@ void PPPMIntel::init() } if (order > INTEL_P3M_MAXORDER) - error->all(FLERR,"PPPM order greater than supported by USER-INTEL\n"); + error->all(FLERR,"PPPM order greater than supported by INTEL\n"); } @@ -394,8 +394,12 @@ void PPPMIntel::particle_map(IntelBuffers *buffers) IP_PRE_omp_range_id_align(iifrom, iito, tid, nlocal, nthr, sizeof(ATOM_T)); #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned +#if defined(USE_OMP_SIMD) + #pragma omp simd reduction(+:flag) +#else #pragma simd reduction(+:flag) +#endif + #pragma vector aligned #endif for (int i = iifrom; i < iito; i++) { @@ -500,7 +504,11 @@ void PPPMIntel::make_rho(IntelBuffers *buffers) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho_lookup[idx][k]; @@ -509,7 +517,11 @@ void PPPMIntel::make_rho(IntelBuffers *buffers) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower; k <= nupper; k++) { FFT_SCALAR r1,r2,r3; @@ -541,7 +553,11 @@ void PPPMIntel::make_rho(IntelBuffers *buffers) int mzy = m*nix + mz; FFT_SCALAR x0 = y0*rho[1][m]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int l = 0; l < INTEL_P3M_ALIGNED_MAXORDER; l++) { int mzyx = l + mzy; @@ -563,7 +579,11 @@ void PPPMIntel::make_rho(IntelBuffers *buffers) IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, nthr); #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { for (int j = 1; j < nthr; j++) { @@ -645,7 +665,11 @@ void PPPMIntel::fieldforce_ik(IntelBuffers *buffers) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho0[k] = rho_lookup[idx][k]; @@ -654,7 +678,11 @@ void PPPMIntel::fieldforce_ik(IntelBuffers *buffers) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower; k <= nupper; k++) { FFT_SCALAR r1 = rho_coeff[order-1][k]; @@ -690,7 +718,11 @@ void PPPMIntel::fieldforce_ik(IntelBuffers *buffers) int my = m+nysum; FFT_SCALAR y0 = z0*rho1[m]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int l = 0; l < INTEL_P3M_ALIGNED_MAXORDER; l++) { int mx = l+nxsum; @@ -813,7 +845,11 @@ void PPPMIntel::fieldforce_ad(IntelBuffers *buffers) dz = dz*half_rho_scale + half_rho_scale_plus; int idz = dz; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) { rho[0][k] = rho_lookup[idx][k]; @@ -825,7 +861,11 @@ void PPPMIntel::fieldforce_ad(IntelBuffers *buffers) } } else { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k = nlower; k <= nupper; k++) { FFT_SCALAR r1,r2,r3,dr1,dr2,dr3; @@ -871,7 +911,11 @@ void PPPMIntel::fieldforce_ad(IntelBuffers *buffers) FFT_SCALAR eky_p = drho[1][m] * rho[2][n]; FFT_SCALAR ekz_p = rho[1][m] * drho[2][n]; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int l = 0; l < INTEL_P3M_ALIGNED_MAXORDER; l++) { int mx = l + nxsum; @@ -893,7 +937,11 @@ void PPPMIntel::fieldforce_ad(IntelBuffers *buffers) } #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int i = ifrom; i < ito; i++) { particle_ekx[i] *= hx_inv; @@ -942,7 +990,11 @@ void PPPMIntel::precompute_rho() for (int i = 0; i < rho_points; i++) { FFT_SCALAR dx = -1. + 1./half_rho_scale * (FFT_SCALAR)i; #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k=nlower; k<=nupper;k++) { FFT_SCALAR r1 = ZEROF; @@ -956,7 +1008,11 @@ void PPPMIntel::precompute_rho() } if (differentiation_flag == 1) { #if defined(LMP_SIMD_COMPILER) +#if defined(USE_OMP_SIMD) + #pragma omp simd +#else #pragma simd +#endif #endif for (int k=nlower; k<=nupper;k++) { FFT_SCALAR r1 = ZEROF; diff --git a/src/USER-INTEL/pppm_intel.h b/src/INTEL/pppm_intel.h similarity index 96% rename from src/USER-INTEL/pppm_intel.h rename to src/INTEL/pppm_intel.h index b6ffe206b1..c0e66996c1 100644 --- a/src/USER-INTEL/pppm_intel.h +++ b/src/INTEL/pppm_intel.h @@ -116,9 +116,9 @@ class PPPMIntel : public PPPM { /* ERROR/WARNING messages: -E: PPPM order greater than supported by USER-INTEL +E: PPPM order greater than supported by INTEL There is a compile time limit on the maximum order for PPPM -in the USER-INTEL package that might be different from LAMMPS +in the INTEL package that might be different from LAMMPS */ diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/INTEL/verlet_lrt_intel.cpp similarity index 100% rename from src/USER-INTEL/verlet_lrt_intel.cpp rename to src/INTEL/verlet_lrt_intel.cpp diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/INTEL/verlet_lrt_intel.h similarity index 100% rename from src/USER-INTEL/verlet_lrt_intel.h rename to src/INTEL/verlet_lrt_intel.h diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/INTERLAYER/pair_coul_shield.cpp similarity index 59% rename from src/USER-MISC/pair_coul_shield.cpp rename to src/INTERLAYER/pair_coul_shield.cpp index 2cda85ead6..dbb12abf2e 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/INTERLAYER/pair_coul_shield.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -20,22 +19,24 @@ ------------------------------------------------------------------------- */ #include "pair_coul_shield.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "math_special.h" #include "error.h" +#include "force.h" +#include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairCoulShield::PairCoulShield(LAMMPS *lmp) : Pair(lmp) { +PairCoulShield::PairCoulShield(LAMMPS *lmp) : Pair(lmp) +{ tap_flag = 1; } @@ -57,13 +58,13 @@ PairCoulShield::~PairCoulShield() void PairCoulShield::compute(int eflag, int vflag) { - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,Tap,dTap; - double rsq,r,r3,rarg,th,depsdr,epsr,forcecoul,factor_coul,Vc,fvc; - int *ilist,*jlist,*numneigh,**firstneigh; + int i, j, ii, jj, inum, jnum, itype, jtype; + double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, ecoul, fpair, Tap, dTap; + double rsq, r, r3, rarg, th, depsdr, epsr, forcecoul, factor_coul, Vc, fvc; + int *ilist, *jlist, *numneigh, **firstneigh; ecoul = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -100,47 +101,51 @@ void PairCoulShield::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + rsq = delx * delx + dely * dely + delz * delz; jtype = type[j]; // only include the interaction between different layers if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { r = sqrt(rsq); - r3 = rsq*r; - rarg = 1.0/sigmae[itype][jtype]; + r3 = rsq * r; + rarg = 1.0 / sigmae[itype][jtype]; th = r3 + MathSpecial::cube(rarg); - epsr = 1.0/pow(th,0.333333333333333333333333); + epsr = 1.0 / pow(th, 1.0 / 3.0); depsdr = MathSpecial::square(epsr); depsdr *= depsdr; - Vc = qqrd2e*qtmp*q[j]*epsr; + Vc = qqrd2e * qtmp * q[j] * epsr; // turn on/off taper function if (tap_flag) { - Tap = calc_Tap(r,cut[itype][jtype]); - dTap = calc_dTap(r,cut[itype][jtype]); - } else {Tap = 1.0; dTap = 0.0;} + Tap = calc_Tap(r, cut[itype][jtype]); + dTap = calc_dTap(r, cut[itype][jtype]); + } else { + Tap = 1.0; + dTap = 0.0; + } - forcecoul = qqrd2e*qtmp*q[j]*r*depsdr; - fvc = forcecoul*Tap - Vc*dTap/r; - fpair = factor_coul*fvc; + forcecoul = qqrd2e * qtmp * q[j] * r * depsdr; + fvc = forcecoul * Tap - Vc * dTap / r; + fpair = factor_coul * fvc; - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; + f[i][0] += delx * fpair; + f[i][1] += dely * fpair; + f[i][2] += delz * fpair; if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; + f[j][0] -= delx * fpair; + f[j][1] -= dely * fpair; + f[j][2] -= delz * fpair; } if (eflag) { - if (tap_flag) ecoul = Vc*Tap; - else ecoul = Vc - offset[itype][jtype]; + if (tap_flag) + ecoul = Vc * Tap; + else + ecoul = Vc - offset[itype][jtype]; ecoul *= factor_coul; } - if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0, - ecoul,fpair,delx,dely,delz); + if (evflag) ev_tally(i, j, nlocal, newton_pair, 0.0, ecoul, fpair, delx, dely, delz); } } } @@ -157,15 +162,14 @@ void PairCoulShield::allocate() allocated = 1; int n = atom->ntypes; - memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(setflag, n + 1, n + 1, "pair:setflag"); for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + for (int j = i; j <= n; j++) setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(sigmae,n+1,n+1,"pair:sigmae"); - memory->create(offset,n+1,n+1,"pair:offset"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(cut, n + 1, n + 1, "pair:cut"); + memory->create(sigmae, n + 1, n + 1, "pair:sigmae"); + memory->create(offset, n + 1, n + 1, "pair:offset"); } /* ---------------------------------------------------------------------- @@ -174,17 +178,17 @@ void PairCoulShield::allocate() void PairCoulShield::settings(int narg, char **arg) { - if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); + if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command"); - cut_global = utils::numeric(FLERR,arg[0],false,lmp); - if (narg == 2) tap_flag = utils::numeric(FLERR,arg[1],false,lmp); + cut_global = utils::numeric(FLERR, arg[0], false, lmp); + if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp); // reset cutoffs that have been explicitly set if (allocated) { - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) - for (j = i+1; j <= atom->ntypes; j++) + for (j = i + 1; j <= atom->ntypes; j++) if (setflag[i][j]) cut[i][j] = cut_global; } } @@ -195,21 +199,21 @@ void PairCoulShield::settings(int narg, char **arg) void PairCoulShield::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients"); if (!allocated) allocate(); - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); - double sigmae_one = utils::numeric(FLERR,arg[2],false,lmp); + double sigmae_one = utils::numeric(FLERR, arg[2], false, lmp); double cut_one = cut_global; - if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); + if (narg == 4) cut_one = utils::numeric(FLERR, arg[3], false, lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { sigmae[i][j] = sigmae_one; cut[i][j] = cut_one; setflag[i][j] = 1; @@ -217,22 +221,20 @@ void PairCoulShield::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } - /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairCoulShield::init_style() { - if (!atom->q_flag) - error->all(FLERR,"Pair style coul/shield requires atom attribute q"); + if (!atom->q_flag) error->all(FLERR, "Pair style coul/shield requires atom attribute q"); if (!atom->molecule_flag) - error->all(FLERR,"Pair style coul/shield requires atom attribute molecule"); + error->all(FLERR, "Pair style coul/shield requires atom attribute molecule"); - neighbor->request(this,instance_me); + neighbor->request(this, instance_me); } /* ---------------------------------------------------------------------- @@ -242,22 +244,23 @@ void PairCoulShield::init_style() double PairCoulShield::init_one(int i, int j) { if (setflag[i][j] == 0) { - error->all(FLERR,"for pair style coul/shield, parameters need to be set explicitly for all pairs."); + error->all(FLERR, + "for pair style coul/shield, parameters need to be set explicitly for all pairs."); } double *q = atom->q; double qqrd2e = force->qqrd2e; - double r,r3,rarg,th,epsr; + double r, r3, rarg, th, epsr; if (offset_flag) { - r = cut[i][j]; - r3 = r*r*r; - rarg = 1.0/sigmae[i][j]; - th = r3 + MathSpecial::cube(rarg); - epsr = 1.0/pow(th,0.333333333333333333); - offset[i][j] = qqrd2e*q[i]*q[j]*epsr; - } else offset[i][j] = 0.0; - + r = cut[i][j]; + r3 = r * r * r; + rarg = 1.0 / sigmae[i][j]; + th = r3 + MathSpecial::cube(rarg); + epsr = 1.0 / pow(th, 1.0/3.0); + offset[i][j] = qqrd2e * q[i] * q[j] * epsr; + } else + offset[i][j] = 0.0; sigmae[j][i] = sigmae[i][j]; offset[j][i] = offset[i][j]; @@ -274,13 +277,13 @@ void PairCoulShield::write_restart(FILE *fp) { write_restart_settings(fp); - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); + fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { - fwrite(&sigmae[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&sigmae[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); } } } @@ -294,19 +297,19 @@ void PairCoulShield::read_restart(FILE *fp) read_restart_settings(fp); allocate(); - int i,j; + int i, j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - utils::sfread(FLERR,&sigmae[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR, &sigmae[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } - MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigmae[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -317,9 +320,9 @@ void PairCoulShield::read_restart(FILE *fp) void PairCoulShield::write_restart_settings(FILE *fp) { - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&offset_flag, sizeof(int), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); } /* ---------------------------------------------------------------------- @@ -329,23 +332,22 @@ void PairCoulShield::write_restart_settings(FILE *fp) void PairCoulShield::read_restart_settings(FILE *fp) { if (comm->me == 0) { - utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); } - MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&offset_flag,1,MPI_INT,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); } /* ---------------------------------------------------------------------- */ -double PairCoulShield::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double /*factor_lj*/, - double &fforce) +double PairCoulShield::single(int i, int j, int itype, int jtype, double rsq, double factor_coul, + double /*factor_lj*/, double &fforce) { - double r, rarg,Vc,fvc,forcecoul,phishieldec; - double r3,th,epsr,depsdr,Tap,dTap; + double r, rarg, Vc, fvc, forcecoul, phishieldec; + double r3, th, epsr, depsdr, Tap, dTap; double *q = atom->q; double qqrd2e = force->qqrd2e; @@ -357,25 +359,30 @@ double PairCoulShield::single(int i, int j, int itype, int jtype, } r = sqrt(rsq); - r3 = rsq*r; - rarg = 1.0/sigmae[itype][jtype]; + r3 = rsq * r; + rarg = 1.0 / sigmae[itype][jtype]; th = r3 + MathSpecial::cube(rarg); - epsr = 1.0/pow(th,0.333333333333333333); - depsdr = epsr*epsr; + epsr = 1.0 / pow(th, 1.0/3.0); + depsdr = epsr * epsr; depsdr *= depsdr; - Vc = qqrd2e*q[i]*q[j]*epsr; + Vc = qqrd2e * q[i] * q[j] * epsr; // turn on/off taper function if (tap_flag) { - Tap = calc_Tap(r,cut[itype][jtype]); - dTap = calc_dTap(r,cut[itype][jtype]); - } else {Tap = 1.0; dTap = 0.0;} + Tap = calc_Tap(r, cut[itype][jtype]); + dTap = calc_dTap(r, cut[itype][jtype]); + } else { + Tap = 1.0; + dTap = 0.0; + } - forcecoul = qqrd2e*q[i]*q[j]*r*depsdr; - fvc = forcecoul*Tap - Vc*dTap/r; - fforce = factor_coul*fvc; + forcecoul = qqrd2e * q[i] * q[j] * r * depsdr; + fvc = forcecoul * Tap - Vc * dTap / r; + fforce = factor_coul * fvc; - if (tap_flag) phishieldec = Vc*Tap; - else phishieldec = Vc - offset[itype][jtype]; - return factor_coul*phishieldec; + if (tap_flag) + phishieldec = Vc * Tap; + else + phishieldec = Vc - offset[itype][jtype]; + return factor_coul * phishieldec; } diff --git a/src/USER-MISC/pair_coul_shield.h b/src/INTERLAYER/pair_coul_shield.h similarity index 100% rename from src/USER-MISC/pair_coul_shield.h rename to src/INTERLAYER/pair_coul_shield.h diff --git a/src/USER-MISC/pair_drip.cpp b/src/INTERLAYER/pair_drip.cpp similarity index 97% rename from src/USER-MISC/pair_drip.cpp rename to src/INTERLAYER/pair_drip.cpp index 97f5ca439e..71281623ac 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/INTERLAYER/pair_drip.cpp @@ -161,11 +161,8 @@ void PairDRIP::read_file(char *filename) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open DRIP potential file %s",filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open DRIP potential file {}: {}",filename,utils::getsyserror()); } // read each line out of file, skipping blank lines or leading '#' @@ -366,10 +363,7 @@ void PairDRIP::compute(int eflag, int vflag) f[j][0] += fj[0]; f[j][1] += fj[1]; f[j][2] += fj[2]; - - // multiply 2 since v_tally has a 0.5 coeff - fj[0] *= 2; fj[1] *= 2; fj[2] *= 2; - if (vflag_atom) v_tally(j, fj, x[j]); + if (vflag_either) v_tally2_newton(j, fj, x[j]); } } //loop over jj @@ -377,10 +371,7 @@ void PairDRIP::compute(int eflag, int vflag) f[i][0] += fi[0]; f[i][1] += fi[1]; f[i][2] += fi[2]; - - // multiply 2 since v_tally has a 0.5 coeff - fi[0] *= 2; fi[1] *= 2; fi[2] *= 2; - if (vflag_atom) v_tally(i, fi, x[i]); + if (vflag_either) v_tally2_newton(i, fi, x[i]); } // loop over ii @@ -529,22 +520,13 @@ double PairDRIP::calc_repulsive(int const i, int const j, Param& p, f[nbj3][k] += fnbj3[k]; } - if (vflag_atom) { - // multiply since v_tally has a 0.5 coeff - for (int k = 0; k < DIM; k++) { - fnbi1[k] *= 2; - fnbi2[k] *= 2; - fnbi3[k] *= 2; - fnbj1[k] *= 2; - fnbj2[k] *= 2; - fnbj3[k] *= 2; - } - v_tally(nbi1, fnbi1, x[nbi1]); - v_tally(nbi2, fnbi2, x[nbi2]); - v_tally(nbi3, fnbi3, x[nbi3]); - v_tally(nbj1, fnbj1, x[nbj1]); - v_tally(nbj2, fnbj2, x[nbj2]); - v_tally(nbj3, fnbj3, x[nbj3]); + if (vflag_either) { + v_tally2_newton(nbi1, fnbi1, x[nbi1]); + v_tally2_newton(nbi2, fnbi2, x[nbi2]); + v_tally2_newton(nbi3, fnbi3, x[nbi3]); + v_tally2_newton(nbj1, fnbj1, x[nbj1]); + v_tally2_newton(nbj2, fnbj2, x[nbj2]); + v_tally2_newton(nbj3, fnbj3, x[nbj3]); } return phi; diff --git a/src/USER-MISC/pair_drip.h b/src/INTERLAYER/pair_drip.h similarity index 100% rename from src/USER-MISC/pair_drip.h rename to src/INTERLAYER/pair_drip.h diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp similarity index 99% rename from src/USER-MISC/pair_ilp_graphene_hbn.cpp rename to src/INTERLAYER/pair_ilp_graphene_hbn.cpp index 8317567f69..3a35c281c1 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp @@ -202,11 +202,8 @@ void PairILPGrapheneHBN::read_file(char *filename) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open ILP potential file %s",filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open ILP potential file {}: {}",filename,utils::getsyserror()); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/INTERLAYER/pair_ilp_graphene_hbn.h similarity index 100% rename from src/USER-MISC/pair_ilp_graphene_hbn.h rename to src/INTERLAYER/pair_ilp_graphene_hbn.h diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp similarity index 99% rename from src/USER-MISC/pair_kolmogorov_crespi_full.cpp rename to src/INTERLAYER/pair_kolmogorov_crespi_full.cpp index c5a2781762..bd5050401e 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp @@ -203,11 +203,8 @@ void PairKolmogorovCrespiFull::read_file(char *filename) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open KC potential file %s",filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open KC potential file {}: {}",filename,utils::getsyserror()); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/INTERLAYER/pair_kolmogorov_crespi_full.h similarity index 100% rename from src/USER-MISC/pair_kolmogorov_crespi_full.h rename to src/INTERLAYER/pair_kolmogorov_crespi_full.h diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp similarity index 98% rename from src/USER-MISC/pair_kolmogorov_crespi_z.cpp rename to src/INTERLAYER/pair_kolmogorov_crespi_z.cpp index d5a60bd2c9..481e9f6604 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp @@ -280,11 +280,8 @@ void PairKolmogorovCrespiZ::read_file(char *filename) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open KC potential file %s",filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open KC potential file {}: {}",filename, utils::getsyserror()); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/INTERLAYER/pair_kolmogorov_crespi_z.h similarity index 100% rename from src/USER-MISC/pair_kolmogorov_crespi_z.h rename to src/INTERLAYER/pair_kolmogorov_crespi_z.h diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/INTERLAYER/pair_lebedeva_z.cpp similarity index 98% rename from src/USER-MISC/pair_lebedeva_z.cpp rename to src/INTERLAYER/pair_lebedeva_z.cpp index 57e9535a1c..13a7797534 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/INTERLAYER/pair_lebedeva_z.cpp @@ -187,8 +187,8 @@ void PairLebedevaZ::allocate() void PairLebedevaZ::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - if (strcmp(force->pair_style,"hybrid/overlay")!=0) - error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); + if (!utils::strmatch(force->pair_style,"^hybrid/overlay")) + error->all(FLERR,"Pair style lebedeva/z requires using hybrid/overlay"); cut_global = utils::numeric(FLERR,arg[0],false,lmp); diff --git a/src/USER-MISC/pair_lebedeva_z.h b/src/INTERLAYER/pair_lebedeva_z.h similarity index 100% rename from src/USER-MISC/pair_lebedeva_z.h rename to src/INTERLAYER/pair_lebedeva_z.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 0ac90a53f2..5e7285a75f 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -55,6 +55,7 @@ action angle_harmonic_kokkos.cpp angle_harmonic.cpp action angle_harmonic_kokkos.h angle_harmonic.h action atom_kokkos.cpp action atom_kokkos.h +action atom_map_kokkos.cpp action atom_vec_angle_kokkos.cpp atom_vec_angle.cpp action atom_vec_angle_kokkos.h atom_vec_angle.h action atom_vec_atomic_kokkos.cpp @@ -136,12 +137,12 @@ action fix_nvt_kokkos.cpp action fix_nvt_kokkos.h action fix_property_atom_kokkos.cpp action fix_property_atom_kokkos.h -action fix_qeq_reax_kokkos.cpp fix_qeq_reax.cpp -action fix_qeq_reax_kokkos.h fix_qeq_reax.h -action fix_reaxc_bonds_kokkos.cpp fix_reaxc_bonds.cpp -action fix_reaxc_bonds_kokkos.h fix_reaxc_bonds.h -action fix_reaxc_species_kokkos.cpp fix_reaxc_species.cpp -action fix_reaxc_species_kokkos.h fix_reaxc_species.h +action fix_qeq_reaxff_kokkos.cpp fix_qeq_reaxff.cpp +action fix_qeq_reaxff_kokkos.h fix_qeq_reaxff.h +action fix_reaxff_bonds_kokkos.cpp fix_reaxff_bonds.cpp +action fix_reaxff_bonds_kokkos.h fix_reaxff_bonds.h +action fix_reaxff_species_kokkos.cpp fix_reaxff_species.cpp +action fix_reaxff_species_kokkos.h fix_reaxff_species.h action fix_setforce_kokkos.cpp action fix_setforce_kokkos.h action fix_shake_kokkos.cpp fix_shake.cpp @@ -250,28 +251,28 @@ action pair_lj_class2_kokkos.cpp pair_lj_class2.cpp action pair_lj_class2_kokkos.h pair_lj_class2.h action pair_lj_cut_coul_cut_kokkos.cpp action pair_lj_cut_coul_cut_kokkos.h -action pair_lj_cut_coul_debye_kokkos.cpp -action pair_lj_cut_coul_debye_kokkos.h -action pair_lj_cut_coul_dsf_kokkos.cpp -action pair_lj_cut_coul_dsf_kokkos.h +action pair_lj_cut_coul_debye_kokkos.cpp pair_lj_cut_coul_debye.cpp +action pair_lj_cut_coul_debye_kokkos.h pair_lj_cut_coul_debye.h +action pair_lj_cut_coul_dsf_kokkos.cpp pair_lj_cut_coul_dsf.cpp +action pair_lj_cut_coul_dsf_kokkos.h pair_lj_cut_coul_dsf.h action pair_lj_cut_coul_long_kokkos.cpp pair_lj_cut_coul_long.cpp action pair_lj_cut_coul_long_kokkos.h pair_lj_cut_coul_long.h action pair_lj_cut_kokkos.cpp action pair_lj_cut_kokkos.h action pair_lj_expand_kokkos.cpp action pair_lj_expand_kokkos.h -action pair_lj_gromacs_coul_gromacs_kokkos.cpp -action pair_lj_gromacs_coul_gromacs_kokkos.h -action pair_lj_gromacs_kokkos.cpp -action pair_lj_gromacs_kokkos.h +action pair_lj_gromacs_coul_gromacs_kokkos.cpp pair_lj_gromacs_coul_gromacs.cpp +action pair_lj_gromacs_coul_gromacs_kokkos.h pair_lj_gromacs_coul_gromacs.h +action pair_lj_gromacs_kokkos.cpp pair_lj_gromacs.cpp +action pair_lj_gromacs_kokkos.h pair_lj_gromacs.h action pair_lj_sdk_kokkos.cpp pair_lj_sdk.cpp action pair_lj_sdk_kokkos.h pair_lj_sdk.h action pair_morse_kokkos.cpp action pair_morse_kokkos.h action pair_multi_lucy_rx_kokkos.cpp pair_multi_lucy_rx.cpp action pair_multi_lucy_rx_kokkos.h pair_multi_lucy_rx.h -action pair_reaxc_kokkos.cpp pair_reaxc.cpp -action pair_reaxc_kokkos.h pair_reaxc.h +action pair_reaxff_kokkos.cpp pair_reaxff.cpp +action pair_reaxff_kokkos.h pair_reaxff.h action pair_snap_kokkos.cpp pair_snap.cpp action pair_snap_kokkos.h pair_snap.h action pair_snap_kokkos_impl.h pair_snap.cpp diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index a8527989d7..02cd4ea708 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -13,23 +12,25 @@ ------------------------------------------------------------------------- */ #include "atom_kokkos.h" -#include + +#include "atom_masks.h" #include "atom_vec.h" #include "atom_vec_kokkos.h" #include "comm_kokkos.h" -#include "update.h" #include "domain.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" #include "kokkos.h" -#include "atom_masks.h" +#include "memory_kokkos.h" +#include "update.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp) {} +AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp) +{ + k_error_flag = DAT::tdual_int_scalar("atom:error_flag"); +} /* ---------------------------------------------------------------------- */ @@ -77,23 +78,25 @@ AtomKokkos::~AtomKokkos() memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3); memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4); + AtomKokkos::map_delete(); + // SPIN package memoryKK->destroy_kokkos(k_sp, sp); memoryKK->destroy_kokkos(k_fm, fm); memoryKK->destroy_kokkos(k_fm_long, fm_long); - // USER-DPD package - memoryKK->destroy_kokkos(k_uCond,uCond); - memoryKK->destroy_kokkos(k_uMech,uMech); - memoryKK->destroy_kokkos(k_uChem,uChem); - memoryKK->destroy_kokkos(k_uCG,uCG); - memoryKK->destroy_kokkos(k_uCGnew,uCGnew); - memoryKK->destroy_kokkos(k_rho,rho); - memoryKK->destroy_kokkos(k_dpdTheta,dpdTheta); - memoryKK->destroy_kokkos(k_duChem,duChem); + // DPD-REACT package + memoryKK->destroy_kokkos(k_uCond, uCond); + memoryKK->destroy_kokkos(k_uMech, uMech); + memoryKK->destroy_kokkos(k_uChem, uChem); + memoryKK->destroy_kokkos(k_uCG, uCG); + memoryKK->destroy_kokkos(k_uCGnew, uCGnew); + memoryKK->destroy_kokkos(k_rho, rho); + memoryKK->destroy_kokkos(k_dpdTheta, dpdTheta); + memoryKK->destroy_kokkos(k_duChem, duChem); - memoryKK->destroy_kokkos(k_dvector,dvector); + memoryKK->destroy_kokkos(k_dvector, dvector); dvector = nullptr; } @@ -101,34 +104,32 @@ AtomKokkos::~AtomKokkos() void AtomKokkos::sync(const ExecutionSpace space, unsigned int mask) { - if (space == Device && lmp->kokkos->auto_sync) - ((AtomVecKokkos *) avec)->modified(Host,mask); + if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->modified(Host, mask); - ((AtomVecKokkos *) avec)->sync(space,mask); + ((AtomVecKokkos *) avec)->sync(space, mask); } /* ---------------------------------------------------------------------- */ void AtomKokkos::modified(const ExecutionSpace space, unsigned int mask) { - ((AtomVecKokkos *) avec)->modified(space,mask); + ((AtomVecKokkos *) avec)->modified(space, mask); - if (space == Device && lmp->kokkos->auto_sync) - ((AtomVecKokkos *) avec)->sync(Host,mask); + if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->sync(Host, mask); } void AtomKokkos::sync_overlapping_device(const ExecutionSpace space, unsigned int mask) { - ((AtomVecKokkos *) avec)->sync_overlapping_device(space,mask); + ((AtomVecKokkos *) avec)->sync_overlapping_device(space, mask); } /* ---------------------------------------------------------------------- */ void AtomKokkos::allocate_type_arrays() { if (avec->mass_type == AtomVec::PER_TYPE) { - k_mass = DAT::tdual_float_1d("Mass",ntypes+1); + k_mass = DAT::tdual_float_1d("Mass", ntypes + 1); mass = k_mass.h_view.data(); - mass_setflag = new int[ntypes+1]; + mass_setflag = new int[ntypes + 1]; for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0; k_mass.modify(); } @@ -138,11 +139,11 @@ void AtomKokkos::allocate_type_arrays() void AtomKokkos::sort() { - int i,m,n,ix,iy,iz,ibin,empty; + int i, m, n, ix, iy, iz, ibin, empty; // set next timestep for sorting to take place - nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq; + nextsort = (update->ntimestep / sortfreq) * sortfreq + sortfreq; // re-setup sort bins if needed @@ -155,33 +156,33 @@ void AtomKokkos::sort() memory->destroy(next); memory->destroy(permute); maxnext = atom->nmax; - memory->create(next,maxnext,"atom:next"); - memory->create(permute,maxnext,"atom:permute"); + memory->create(next, maxnext, "atom:next"); + memory->create(permute, maxnext, "atom:permute"); } // insure there is one extra atom location at end of arrays for swaps if (nlocal == nmax) avec->grow(0); - sync(Host,ALL_MASK); - modified(Host,ALL_MASK); + sync(Host, ALL_MASK); + modified(Host, ALL_MASK); // bin atoms in reverse order so linked list will be in forward order for (i = 0; i < nbins; i++) binhead[i] = -1; HAT::t_x_array_const h_x = k_x.view(); - for (i = nlocal-1; i >= 0; i--) { - ix = static_cast ((h_x(i,0)-bboxlo[0])*bininvx); - iy = static_cast ((h_x(i,1)-bboxlo[1])*bininvy); - iz = static_cast ((h_x(i,2)-bboxlo[2])*bininvz); - ix = MAX(ix,0); - iy = MAX(iy,0); - iz = MAX(iz,0); - ix = MIN(ix,nbinx-1); - iy = MIN(iy,nbiny-1); - iz = MIN(iz,nbinz-1); - ibin = iz*nbiny*nbinx + iy*nbinx + ix; + for (i = nlocal - 1; i >= 0; i--) { + ix = static_cast((h_x(i, 0) - bboxlo[0]) * bininvx); + iy = static_cast((h_x(i, 1) - bboxlo[1]) * bininvy); + iz = static_cast((h_x(i, 2) - bboxlo[2]) * bininvz); + ix = MAX(ix, 0); + iy = MAX(iy, 0); + iz = MAX(iz, 0); + ix = MIN(ix, nbinx - 1); + iy = MIN(iy, nbiny - 1); + iz = MIN(iz, nbinz - 1); + ibin = iz * nbiny * nbinx + iy * nbinx + ix; next[i] = binhead[ibin]; binhead[ibin] = i; } @@ -213,13 +214,13 @@ void AtomKokkos::sort() for (i = 0; i < nlocal; i++) { if (current[i] == permute[i]) continue; - avec->copy(i,nlocal,0); + avec->copy(i, nlocal, 0); empty = i; while (permute[empty] != i) { - avec->copy(permute[empty],empty,0); + avec->copy(permute[empty], empty, 0); empty = current[empty] = permute[empty]; } - avec->copy(nlocal,empty,0); + avec->copy(nlocal, empty, 0); current[empty] = permute[empty]; } @@ -237,13 +238,14 @@ void AtomKokkos::sort() reallocate memory to the pointer selected by the mask ------------------------------------------------------------------------- */ -void AtomKokkos::grow(unsigned int mask) { +void AtomKokkos::grow(unsigned int mask) +{ if (mask & SPECIAL_MASK) { memoryKK->destroy_kokkos(k_special, special); sync(Device, mask); modified(Device, mask); - memoryKK->grow_kokkos(k_special,special,nmax,maxspecial,"atom:special"); + memoryKK->grow_kokkos(k_special, special, nmax, maxspecial, "atom:special"); avec->grow_pointers(); sync(Host, mask); } @@ -262,22 +264,18 @@ int AtomKokkos::add_custom(const char *name, int flag) if (flag == 0) { index = nivector; nivector++; - iname = (char **) memory->srealloc(iname,nivector*sizeof(char *), - "atom:iname"); + iname = (char **) memory->srealloc(iname, nivector * sizeof(char *), "atom:iname"); iname[index] = utils::strdup(name); - ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *), - "atom:ivector"); - memory->create(ivector[index],nmax,"atom:ivector"); + ivector = (int **) memory->srealloc(ivector, nivector * sizeof(int *), "atom:ivector"); + memory->create(ivector[index], nmax, "atom:ivector"); } else { index = ndvector; ndvector++; - dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *), - "atom:dname"); + dname = (char **) memory->srealloc(dname, ndvector * sizeof(char *), "atom:dname"); dname[index] = utils::strdup(name); - this->sync(Device,DVECTOR_MASK); - memoryKK->grow_kokkos(k_dvector,dvector,ndvector,nmax, - "atom:dvector"); - this->modified(Device,DVECTOR_MASK); + this->sync(Device, DVECTOR_MASK); + memoryKK->grow_kokkos(k_dvector, dvector, ndvector, nmax, "atom:dvector"); + this->modified(Device, DVECTOR_MASK); } return index; @@ -294,12 +292,12 @@ void AtomKokkos::remove_custom(int flag, int index) if (flag == 0) { memory->destroy(ivector[index]); ivector[index] = nullptr; - delete [] iname[index]; + delete[] iname[index]; iname[index] = nullptr; } else { //memoryKK->destroy_kokkos(dvector); dvector[index] = nullptr; - delete [] dname[index]; + delete[] dname[index]; dname[index] = nullptr; } } @@ -335,19 +333,16 @@ void AtomKokkos::deallocate_topology() done at higher levels (Verlet,Modify,etc) ------------------------------------------------------------------------- */ -void AtomKokkos::sync_modify(ExecutionSpace execution_space, - unsigned int datamask_read, +void AtomKokkos::sync_modify(ExecutionSpace execution_space, unsigned int datamask_read, unsigned int datamask_modify) { - sync(execution_space,datamask_read); - modified(execution_space,datamask_modify); + sync(execution_space, datamask_read); + modified(execution_space, datamask_modify); } -AtomVec *AtomKokkos::new_avec(const std::string &style, - int trysuffix, int &sflag) +AtomVec *AtomKokkos::new_avec(const std::string &style, int trysuffix, int &sflag) { - AtomVec* avec = Atom::new_avec(style,trysuffix,sflag); - if (!avec->kokkosable) - error->all(FLERR,"KOKKOS package requires a kokkos enabled atom_style"); + AtomVec *avec = Atom::new_avec(style, trysuffix, sflag); + if (!avec->kokkosable) error->all(FLERR, "KOKKOS package requires a kokkos enabled atom_style"); return avec; } diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index e807180f35..6cf91a5ddc 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -61,13 +61,49 @@ class AtomKokkos : public Atom { DAT::tdual_f_array k_fm; DAT::tdual_f_array k_fm_long; -// USER-DPD package +// DPD-REACT package DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew, k_rho,k_dpdTheta,k_duChem; AtomKokkos(class LAMMPS *); - ~AtomKokkos(); + virtual ~AtomKokkos(); + + void map_init(int check = 1); + void map_set(); + void map_delete(); + + DAT::tdual_int_1d k_sametag; + DAT::tdual_int_1d k_map_array; + DAT::tdual_int_scalar k_error_flag; + dual_hash_type k_map_hash; + + // map lookup function inlined for efficiency + // return -1 if no map defined + + template + KOKKOS_INLINE_FUNCTION + static int map_kokkos(tagint global, int map_style, DAT::tdual_int_1d k_map_array, dual_hash_type k_map_hash) + { + if (map_style == 1) + return k_map_array.view()(global); + else if (map_style == 2) + return AtomKokkos::map_find_hash_kokkos(global,k_map_hash); + else + return -1; + } + + template + KOKKOS_INLINE_FUNCTION + static int map_find_hash_kokkos(tagint global, dual_hash_type &k_map_hash) + { + int local = -1; + auto d_map_hash = k_map_hash.view(); + auto index = d_map_hash.find(global); + if (d_map_hash.valid_at(index)) + local = d_map_hash.value_at(index); + return local; + } virtual void allocate_type_arrays(); void sync(const ExecutionSpace space, unsigned int mask); diff --git a/src/KOKKOS/atom_map_kokkos.cpp b/src/KOKKOS/atom_map_kokkos.cpp new file mode 100644 index 0000000000..8d0d1243ac --- /dev/null +++ b/src/KOKKOS/atom_map_kokkos.cpp @@ -0,0 +1,288 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "atom_kokkos.h" + +#include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "neighbor_kokkos.h" + +#include + +using namespace LAMMPS_NS; + +#define EXTRA 1000 + +/* ---------------------------------------------------------------------- + allocate and initialize array or hash table for global -> local map + for array option: + array length = 1 to map_tag_max + set entire array to -1 as initial values + for hash option: + map_nhash = length of hash table + map_nbucket = # of hash buckets, prime larger than map_nhash * 2 + so buckets will only be filled with 0 or 1 atoms on average +------------------------------------------------------------------------- */ + +void AtomKokkos::map_init(int check) +{ + // check for new map style if max atomID changed (check = 1 = default) + // recreate = 1 if must delete old map and create new map + // recreate = 0 if can re-use old map w/out realloc and just adjust settings + // map_maxarray/map_nhash initially -1, to force recreate even when no atoms + + int recreate = 0; + if (check) recreate = map_style_set(); + + if (map_style == MAP_ARRAY && map_tag_max > map_maxarray) + recreate = 1; + else if (map_style == MAP_HASH && nlocal + nghost > map_nhash) + recreate = 1; + + // if not recreating: + // for array, initialize current map_tag_max values + // for hash, set all buckets to empty, put all entries in free list + + if (!recreate) { + if (map_style == MAP_ARRAY) { + for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1; + } else { + for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1; + map_nused = 0; + map_free = 0; + for (int i = 0; i < map_nhash; i++) map_hash[i].next = i + 1; + if (map_nhash > 0) map_hash[map_nhash - 1].next = -1; + } + + // recreating: delete old map and create new one for array or hash + + } else { + map_delete(); + + if (map_style == MAP_ARRAY) { + map_maxarray = map_tag_max; + memoryKK->create_kokkos(k_map_array, map_array, map_maxarray + 1, "atom:map_array"); + for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1; + + } else { + + // map_nhash = max # of atoms that can be hashed on this proc + // set to max of ave atoms/proc or atoms I can store + // multiply by 2, require at least 1000 + // doubling means hash table will need to be re-init only rarely + + int nper = static_cast(natoms / comm->nprocs); + map_nhash = MAX(nper, nmax); + map_nhash *= 2; + map_nhash = MAX(map_nhash, 1000); + + // map_nbucket = prime just larger than map_nhash + // next_prime() should be fast enough, + // about 10% of odd integers are prime above 1M + + map_nbucket = next_prime(map_nhash); + + // set all buckets to empty + // set hash to map_nhash in length + // put all hash entries in free list and point them to each other + + map_bucket = new int[map_nbucket]; + for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1; + + map_hash = new HashElem[map_nhash]; + map_nused = 0; + map_free = 0; + for (int i = 0; i < map_nhash; i++) map_hash[i].next = i + 1; + map_hash[map_nhash - 1].next = -1; + + // use "view" template method to avoid unnecessary deep_copy + + auto h_map_hash = k_map_hash.view(); // get type + h_map_hash = decltype(h_map_hash)(map_nhash); + k_map_hash.view() = h_map_hash; + } + } + + k_sametag.modify_host(); + if (map_style == Atom::MAP_ARRAY) k_map_array.modify_host(); +} + +/* ---------------------------------------------------------------------- + set global -> local map for all of my own and ghost atoms + loop in reverse order so that nearby images take precedence over far ones + and owned atoms take precedence over images + this enables valid lookups of bond topology atoms + for hash table option: + if hash table too small, re-init + global ID may already be in table if image atom was set +------------------------------------------------------------------------- */ + +void AtomKokkos::map_set() +{ + int nall = nlocal + nghost; + + atomKK->sync(Host, TAG_MASK); + + k_sametag.sync_host(); + if (map_style == Atom::MAP_ARRAY) k_map_array.sync_host(); + + if (map_style == MAP_ARRAY) { + + // possible reallocation of sametag must come before loop over atoms + // since loop sets sametag + + if (nall > max_same) { + max_same = nall + EXTRA; + memoryKK->destroy_kokkos(k_sametag, sametag); + memoryKK->create_kokkos(k_sametag, sametag, max_same, "atom:sametag"); + } + + for (int i = nall - 1; i >= 0; i--) { + sametag[i] = map_array[tag[i]]; + map_array[tag[i]] = i; + } + + } else { + + // if this proc has more atoms than hash table size, call map_init() + // call with 0 since max atomID in system has not changed + // possible reallocation of sametag must come after map_init(), + // b/c map_init() may invoke map_delete(), whacking sametag + + if (nall > map_nhash) map_init(0); + if (nall > max_same) { + max_same = nall + EXTRA; + memoryKK->destroy_kokkos(k_sametag, sametag); + memoryKK->create_kokkos(k_sametag, sametag, max_same, "atom:sametag"); + } + + int previous, ibucket, index; + tagint global; + + for (int i = nall - 1; i >= 0; i--) { + sametag[i] = map_find_hash(tag[i]); + + // search for key + // if found it, just overwrite local value with index + + previous = -1; + global = tag[i]; + ibucket = global % map_nbucket; + index = map_bucket[ibucket]; + while (index > -1) { + if (map_hash[index].global == global) break; + previous = index; + index = map_hash[index].next; + } + if (index > -1) { + map_hash[index].local = i; + continue; + } + + // take one entry from free list + // add the new global/local pair as entry at end of bucket list + // special logic if this entry is 1st in bucket + + index = map_free; + map_free = map_hash[map_free].next; + if (previous == -1) + map_bucket[ibucket] = index; + else + map_hash[previous].next = index; + map_hash[index].global = global; + map_hash[index].local = i; + map_hash[index].next = -1; + map_nused++; + } + + // Copy to Kokkos hash + + // use "view" template method to avoid unnecessary deep_copy + + auto h_map_hash = k_map_hash.view(); + h_map_hash.clear(); + + for (int i = nall - 1; i >= 0; i--) { + + // search for key + // if don't find it, done + + previous = -1; + global = tag[i]; + ibucket = global % map_nbucket; + index = map_bucket[ibucket]; + while (index > -1) { + if (map_hash[index].global == global) break; + previous = index; + index = map_hash[index].next; + } + if (index == -1) continue; + + int local = map_hash[index].local; + + auto insert_result = h_map_hash.insert(global, local); + if (insert_result.failed()) error->one(FLERR, "Kokkos::UnorderedMap insertion failed"); + } + } + + k_sametag.modify_host(); + if (map_style == Atom::MAP_ARRAY) + k_map_array.modify_host(); + else if (map_style == Atom::MAP_HASH) { + + // use "view" template method to avoid unnecessary deep_copy + + auto h_map_hash = k_map_hash.view(); + auto d_map_hash = k_map_hash.view(); + + // check if fix shake or neigh bond needs a device hash + + int device_hash_flag = 0; + + auto neighborKK = (NeighborKokkos *) neighbor; + if (neighborKK->device_flag) device_hash_flag = 1; + + for (int n = 0; n < modify->nfix; n++) + if (utils::strmatch(modify->fix[n]->style, "^shake")) + if (modify->fix[n]->execution_space == Device) device_hash_flag = 1; + + if (device_hash_flag) { + Kokkos::deep_copy(d_map_hash,h_map_hash); + k_map_hash.view() = d_map_hash; + } + } +} + +/* ---------------------------------------------------------------------- + free the array or hash table for global to local mapping +------------------------------------------------------------------------- */ + +void AtomKokkos::map_delete() +{ + memoryKK->destroy_kokkos(k_sametag, sametag); + sametag = nullptr; + + if (map_style == MAP_ARRAY) { + memoryKK->destroy_kokkos(k_map_array, map_array); + map_array = nullptr; + } else { + k_map_hash.h_view = host_hash_type(); + k_map_hash.d_view = hash_type(); + } + + Atom::map_delete(); +} diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 4358a49358..e02631f89e 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -13,15 +13,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_dpd_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 45ce316d3f..cd5316cc73 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -13,15 +13,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_full_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index fd5318e1d1..588ff94d73 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -1128,9 +1128,10 @@ void CommKokkos::borders_device() { max = MAX(maxforward*rmax,maxreverse*smax); if (max > maxrecv) grow_recv_kokkos(max); + atomKK->modified(exec_space,ALL_MASK); + // reset global->local map - atomKK->modified(exec_space,ALL_MASK); if (map_style != Atom::MAP_NONE) { atomKK->sync(Host,TAG_MASK); atom->map_set(); diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reaxff_kokkos.cpp similarity index 81% rename from src/KOKKOS/fix_qeq_reax_kokkos.cpp rename to src/KOKKOS/fix_qeq_reaxff_kokkos.cpp index cace20c098..77bd013ad4 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reaxff_kokkos.cpp @@ -17,7 +17,7 @@ Kamesh Arumugam (NVIDIA) ------------------------------------------------------------------------- */ -#include "fix_qeq_reax_kokkos.h" +#include "fix_qeq_reaxff_kokkos.h" #include "atom.h" #include "atom_kokkos.h" @@ -43,9 +43,9 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ template -FixQEqReaxKokkos:: -FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg) : - FixQEqReax(lmp, narg, arg) +FixQEqReaxFFKokkos:: +FixQEqReaxFFKokkos(LAMMPS *lmp, int narg, char **arg) : + FixQEqReaxFF(lmp, narg, arg) { kokkosable = 1; forward_comm_device = 1; @@ -69,7 +69,7 @@ FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ template -FixQEqReaxKokkos::~FixQEqReaxKokkos() +FixQEqReaxFFKokkos::~FixQEqReaxFFKokkos() { if (copymode) return; @@ -80,11 +80,11 @@ FixQEqReaxKokkos::~FixQEqReaxKokkos() /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::init() +void FixQEqReaxFFKokkos::init() { atomKK->sync(execution_space,Q_MASK); - FixQEqReax::init(); + FixQEqReaxFF::init(); neighflag = lmp->kokkos->neighflag_qeq; int irequest = neighbor->nrequest - 1; @@ -110,7 +110,7 @@ void FixQEqReaxKokkos::init() int ntypes = atom->ntypes; k_params = Kokkos::DualView - ("FixQEqReax::params",ntypes+1); + ("FixQEqReaxFF::params",ntypes+1); params = k_params.template view(); for (int n = 1; n <= ntypes; n++) { @@ -131,7 +131,7 @@ void FixQEqReaxKokkos::init() /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::init_shielding_k() +void FixQEqReaxFFKokkos::init_shielding_k() { int i,j; int ntypes = atom->ntypes; @@ -141,7 +141,7 @@ void FixQEqReaxKokkos::init_shielding_k() for (i = 1; i <= ntypes; ++i) for (j = 1; j <= ntypes; ++j) - k_shield.h_view(i,j) = pow( gamma[i] * gamma[j], -1.5 ); + k_shield.h_view(i,j) = pow(gamma[i] * gamma[j], -1.5); k_shield.template modify(); k_shield.template sync(); @@ -159,7 +159,7 @@ void FixQEqReaxKokkos::init_shielding_k() /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::init_hist() +void FixQEqReaxFFKokkos::init_hist() { k_s_hist.clear_sync_state(); k_t_hist.clear_sync_state(); @@ -174,7 +174,7 @@ void FixQEqReaxKokkos::init_hist() /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::setup_pre_force(int vflag) +void FixQEqReaxFFKokkos::setup_pre_force(int vflag) { //neighbor->build_one(list); @@ -184,7 +184,7 @@ void FixQEqReaxKokkos::setup_pre_force(int vflag) /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::pre_force(int /*vflag*/) +void FixQEqReaxFFKokkos::pre_force(int /*vflag*/) { if (update->ntimestep % nevery) return; @@ -228,10 +228,10 @@ void FixQEqReaxKokkos::pre_force(int /*vflag*/) if (execution_space == Host) { // CPU if (neighflag == FULL) { - FixQEqReaxKokkosComputeHFunctor computeH_functor(this); + FixQEqReaxFFKokkosComputeHFunctor computeH_functor(this); Kokkos::parallel_scan(inum,computeH_functor); } else { // HALF and HALFTHREAD are the same - FixQEqReaxKokkosComputeHFunctor computeH_functor(this); + FixQEqReaxFFKokkosComputeHFunctor computeH_functor(this); Kokkos::parallel_scan(inum,computeH_functor); } } else { // GPU, use teams @@ -244,11 +244,11 @@ void FixQEqReaxKokkos::pre_force(int /*vflag*/) Kokkos::TeamPolicy policy(num_teams, atoms_per_team, vector_length); if (neighflag == FULL) { - FixQEqReaxKokkosComputeHFunctor computeH_functor( + FixQEqReaxFFKokkosComputeHFunctor computeH_functor( this, atoms_per_team, vector_length); Kokkos::parallel_for(policy, computeH_functor); } else { // HALF and HALFTHREAD are the same - FixQEqReaxKokkosComputeHFunctor computeH_functor( + FixQEqReaxFFKokkosComputeHFunctor computeH_functor( this, atoms_per_team, vector_length); Kokkos::parallel_for(policy, computeH_functor); } @@ -258,16 +258,16 @@ void FixQEqReaxKokkos::pre_force(int /*vflag*/) k_s_hist.template sync(); k_t_hist.template sync(); - FixQEqReaxKokkosMatVecFunctor matvec_functor(this); + FixQEqReaxFFKokkosMatVecFunctor matvec_functor(this); Kokkos::parallel_for(inum,matvec_functor); - // comm->forward_comm_fix(this); //Dist_vector( s ); + // comm->forward_comm_fix(this); //Dist_vector(s); pack_flag = 2; k_s.template modify(); comm->forward_comm_fix(this); k_s.template sync(); - // comm->forward_comm_fix(this); //Dist_vector( t ); + // comm->forward_comm_fix(this); //Dist_vector(t); pack_flag = 3; k_t.template modify(); comm->forward_comm_fix(this); @@ -282,11 +282,11 @@ void FixQEqReaxKokkos::pre_force(int /*vflag*/) // 1st cg solve over b_s, s - cg_solve1(); + matvecs = cg_solve1(); // 2nd cg solve over b_t, t - cg_solve2(); + matvecs += cg_solve2(); // calculate_Q(); @@ -313,7 +313,7 @@ void FixQEqReaxKokkos::pre_force(int /*vflag*/) template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::num_neigh_item(int ii, int &maxneigh) const +void FixQEqReaxFFKokkos::num_neigh_item(int ii, int &maxneigh) const { const int i = d_ilist[ii]; maxneigh += d_numneigh[i]; @@ -322,7 +322,7 @@ void FixQEqReaxKokkos::num_neigh_item(int ii, int &maxneigh) const /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::allocate_matrix() +void FixQEqReaxFFKokkos::allocate_matrix() { const int inum = list->inum; @@ -331,7 +331,7 @@ void FixQEqReaxKokkos::allocate_matrix() // determine the total space for the H matrix m_cap = 0; - FixQEqReaxKokkosNumNeighFunctor neigh_functor(this); + FixQEqReaxFFKokkosNumNeighFunctor neigh_functor(this); Kokkos::parallel_reduce(inum,neigh_functor,m_cap); d_firstnbr = typename AT::t_int_1d("qeq/kk:firstnbr",nmax); @@ -343,7 +343,7 @@ void FixQEqReaxKokkos::allocate_matrix() /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::allocate_array() +void FixQEqReaxFFKokkos::allocate_array() { if (atom->nmax > nmax) { nmax = atom->nmax; @@ -377,7 +377,7 @@ void FixQEqReaxKokkos::allocate_array() // init_storage - FixQEqReaxKokkosZeroFunctor zero_functor(this); + FixQEqReaxFFKokkosZeroFunctor zero_functor(this); Kokkos::parallel_for(ignum,zero_functor); } @@ -385,7 +385,7 @@ void FixQEqReaxKokkos::allocate_array() template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::zero_item(int ii) const +void FixQEqReaxFFKokkos::zero_item(int ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -409,7 +409,7 @@ void FixQEqReaxKokkos::zero_item(int ii) const template template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::compute_h_item(int ii, int &m_fill, const bool &final) const +void FixQEqReaxFFKokkos::compute_h_item(int ii, int &m_fill, const bool &final) const { const int i = d_ilist[ii]; int j,jj,jtype; @@ -477,7 +477,7 @@ void FixQEqReaxKokkos::compute_h_item(int ii, int &m_fill, const boo template template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::compute_h_team( +void FixQEqReaxFFKokkos::compute_h_team( const typename Kokkos::TeamPolicy::member_type &team, int atoms_per_team, int vector_length) const { @@ -682,7 +682,7 @@ void FixQEqReaxKokkos::compute_h_team( template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::calculate_H_k(const F_FLOAT &r, const F_FLOAT &shld) const +double FixQEqReaxFFKokkos::calculate_H_k(const F_FLOAT &r, const F_FLOAT &shld) const { F_FLOAT taper, denom; @@ -704,7 +704,7 @@ double FixQEqReaxKokkos::calculate_H_k(const F_FLOAT &r, const F_FLO template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::matvec_item(int ii) const +void FixQEqReaxFFKokkos::matvec_item(int ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -722,7 +722,7 @@ void FixQEqReaxKokkos::matvec_item(int ii) const /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::cg_solve1() +int FixQEqReaxFFKokkos::cg_solve1() // b = b_s, x = s; { const int inum = list->inum; @@ -732,16 +732,16 @@ void FixQEqReaxKokkos::cg_solve1() if (execution_space == Host) teamsize = 1; else teamsize = 128; - // sparse_matvec( &H, x, q ); - FixQEqReaxKokkosSparse12Functor sparse12_functor(this); + // sparse_matvec(&H, x, q); + FixQEqReaxFFKokkosSparse12Functor sparse12_functor(this); Kokkos::parallel_for(inum,sparse12_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(inum,ignum),*this); if (neighflag == HALF) { - FixQEqReaxKokkosSparse13Functor sparse13_functor(this); + FixQEqReaxFFKokkosSparse13Functor sparse13_functor(this); Kokkos::parallel_for(inum,sparse13_functor); } else if (neighflag == HALFTHREAD) { - FixQEqReaxKokkosSparse13Functor sparse13_functor(this); + FixQEqReaxFFKokkosSparse13Functor sparse13_functor(this); Kokkos::parallel_for(inum,sparse13_functor); } if (need_dup) @@ -752,49 +752,49 @@ void FixQEqReaxKokkos::cg_solve1() if (neighflag != FULL) { k_o.template modify(); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->reverse_comm_fix(this); //Coll_vector(q); k_o.template sync(); } - // vector_sum( r , 1., b, -1., q, nn ); + // vector_sum(r , 1., b, -1., q, nn); // preconditioning: d[j] = r[j] * Hdia_inv[j]; - // b_norm = parallel_norm( b, nn ); + // b_norm = parallel_norm(b, nn); F_FLOAT my_norm = 0.0; - FixQEqReaxKokkosNorm1Functor norm1_functor(this); + FixQEqReaxFFKokkosNorm1Functor norm1_functor(this); Kokkos::parallel_reduce(inum,norm1_functor,my_norm); F_FLOAT norm_sqr = 0.0; - MPI_Allreduce( &my_norm, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_norm, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world); b_norm = sqrt(norm_sqr); - // sig_new = parallel_dot( r, d, nn); + // sig_new = parallel_dot(r, d, nn); F_FLOAT my_dot = 0.0; - FixQEqReaxKokkosDot1Functor dot1_functor(this); + FixQEqReaxFFKokkosDot1Functor dot1_functor(this); Kokkos::parallel_reduce(inum,dot1_functor,my_dot); F_FLOAT dot_sqr = 0.0; - MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world); F_FLOAT sig_new = dot_sqr; int loop; for (loop = 1; (loop < imax) && (sqrt(sig_new)/b_norm > tolerance); loop++) { - // comm->forward_comm_fix(this); //Dist_vector( d ); + // comm->forward_comm_fix(this); //Dist_vector(d); pack_flag = 1; k_d.template modify(); comm->forward_comm_fix(this); k_d.template sync(); - // sparse_matvec( &H, d, q ); - FixQEqReaxKokkosSparse22Functor sparse22_functor(this); + // sparse_matvec(&H, d, q); + FixQEqReaxFFKokkosSparse22Functor sparse22_functor(this); Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(inum,ignum),*this); if (need_dup) dup_o.reset_except(d_o); if (neighflag == HALF) { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + FixQEqReaxFFKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); } else if (neighflag == HALFTHREAD) { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + FixQEqReaxFFKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); } if (need_dup) @@ -805,54 +805,52 @@ void FixQEqReaxKokkos::cg_solve1() if (neighflag != FULL) { k_o.template modify(); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->reverse_comm_fix(this); //Coll_vector(q); k_o.template sync(); } - // tmp = parallel_dot( d, q, nn); + // tmp = parallel_dot(d, q, nn); my_dot = dot_sqr = 0.0; - FixQEqReaxKokkosDot2Functor dot2_functor(this); + FixQEqReaxFFKokkosDot2Functor dot2_functor(this); Kokkos::parallel_reduce(inum,dot2_functor,my_dot); - MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world); tmp = dot_sqr; alpha = sig_new / tmp; sig_old = sig_new; - // vector_add( s, alpha, d, nn ); - // vector_add( r, -alpha, q, nn ); + // vector_add(s, alpha, d, nn); + // vector_add(r, -alpha, q, nn); my_dot = dot_sqr = 0.0; - FixQEqReaxKokkosPrecon1Functor precon1_functor(this); + FixQEqReaxFFKokkosPrecon1Functor precon1_functor(this); Kokkos::parallel_for(inum,precon1_functor); // preconditioning: p[j] = r[j] * Hdia_inv[j]; - // sig_new = parallel_dot( r, p, nn); - FixQEqReaxKokkosPreconFunctor precon_functor(this); + // sig_new = parallel_dot(r, p, nn); + FixQEqReaxFFKokkosPreconFunctor precon_functor(this); Kokkos::parallel_reduce(inum,precon_functor,my_dot); - MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world); sig_new = dot_sqr; beta = sig_new / sig_old; - // vector_sum( d, 1., p, beta, d, nn ); - FixQEqReaxKokkosVecSum2Functor vecsum2_functor(this); + // vector_sum(d, 1., p, beta, d, nn); + FixQEqReaxFFKokkosVecSum2Functor vecsum2_functor(this); Kokkos::parallel_for(inum,vecsum2_functor); } - if (loop >= imax && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq/reax cg_solve1 convergence failed after %d iterations " - "at " BIGINT_FORMAT " step: %f",loop,update->ntimestep,sqrt(sig_new)/b_norm); - error->warning(FLERR,str); - //error->all(FLERR,str); - } - + if ((loop >= imax) && maxwarn && (comm->me == 0)) + error->warning(FLERR,fmt::format("Fix qeq/reaxff/kk cg_solve1 convergence " + "failed after {} iterations at step {}: " + "{}", loop, update->ntimestep, + sqrt(sig_new)/b_norm)); + return loop; } /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::cg_solve2() +int FixQEqReaxFFKokkos::cg_solve2() // b = b_t, x = t; { const int inum = list->inum; @@ -862,18 +860,18 @@ void FixQEqReaxKokkos::cg_solve2() if (execution_space == Host) teamsize = 1; else teamsize = 128; - // sparse_matvec( &H, x, q ); - FixQEqReaxKokkosSparse32Functor sparse32_functor(this); + // sparse_matvec(&H, x, q); + FixQEqReaxFFKokkosSparse32Functor sparse32_functor(this); Kokkos::parallel_for(inum,sparse32_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(inum,ignum),*this); if (need_dup) dup_o.reset_except(d_o); if (neighflag == HALF) { - FixQEqReaxKokkosSparse33Functor sparse33_functor(this); + FixQEqReaxFFKokkosSparse33Functor sparse33_functor(this); Kokkos::parallel_for(inum,sparse33_functor); } else if (neighflag == HALFTHREAD) { - FixQEqReaxKokkosSparse33Functor sparse33_functor(this); + FixQEqReaxFFKokkosSparse33Functor sparse33_functor(this); Kokkos::parallel_for(inum,sparse33_functor); } if (need_dup) @@ -884,49 +882,49 @@ void FixQEqReaxKokkos::cg_solve2() if (neighflag != FULL) { k_o.template modify(); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->reverse_comm_fix(this); //Coll_vector(q); k_o.template sync(); } - // vector_sum( r , 1., b, -1., q, nn ); + // vector_sum(r , 1., b, -1., q, nn); // preconditioning: d[j] = r[j] * Hdia_inv[j]; - // b_norm = parallel_norm( b, nn ); + // b_norm = parallel_norm(b, nn); F_FLOAT my_norm = 0.0; - FixQEqReaxKokkosNorm2Functor norm2_functor(this); + FixQEqReaxFFKokkosNorm2Functor norm2_functor(this); Kokkos::parallel_reduce(inum,norm2_functor,my_norm); F_FLOAT norm_sqr = 0.0; - MPI_Allreduce( &my_norm, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_norm, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world); b_norm = sqrt(norm_sqr); - // sig_new = parallel_dot( r, d, nn); + // sig_new = parallel_dot(r, d, nn); F_FLOAT my_dot = 0.0; - FixQEqReaxKokkosDot1Functor dot1_functor(this); + FixQEqReaxFFKokkosDot1Functor dot1_functor(this); Kokkos::parallel_reduce(inum,dot1_functor,my_dot); F_FLOAT dot_sqr = 0.0; - MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world); F_FLOAT sig_new = dot_sqr; int loop; for (loop = 1; (loop < imax) && (sqrt(sig_new)/b_norm > tolerance); loop++) { - // comm->forward_comm_fix(this); //Dist_vector( d ); + // comm->forward_comm_fix(this); //Dist_vector(d); pack_flag = 1; k_d.template modify(); comm->forward_comm_fix(this); k_d.template sync(); - // sparse_matvec( &H, d, q ); - FixQEqReaxKokkosSparse22Functor sparse22_functor(this); + // sparse_matvec(&H, d, q); + FixQEqReaxFFKokkosSparse22Functor sparse22_functor(this); Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(inum,ignum),*this); if (need_dup) dup_o.reset_except(d_o); if (neighflag == HALF) { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + FixQEqReaxFFKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); } else if (neighflag == HALFTHREAD) { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + FixQEqReaxFFKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); } if (need_dup) @@ -937,82 +935,80 @@ void FixQEqReaxKokkos::cg_solve2() if (neighflag != FULL) { k_o.template modify(); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->reverse_comm_fix(this); //Coll_vector(q); k_o.template sync(); } - // tmp = parallel_dot( d, q, nn); + // tmp = parallel_dot(d, q, nn); my_dot = dot_sqr = 0.0; - FixQEqReaxKokkosDot2Functor dot2_functor(this); + FixQEqReaxFFKokkosDot2Functor dot2_functor(this); Kokkos::parallel_reduce(inum,dot2_functor,my_dot); - MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world); tmp = dot_sqr; alpha = sig_new / tmp; sig_old = sig_new; - // vector_add( t, alpha, d, nn ); - // vector_add( r, -alpha, q, nn ); + // vector_add(t, alpha, d, nn); + // vector_add(r, -alpha, q, nn); my_dot = dot_sqr = 0.0; - FixQEqReaxKokkosPrecon2Functor precon2_functor(this); + FixQEqReaxFFKokkosPrecon2Functor precon2_functor(this); Kokkos::parallel_for(inum,precon2_functor); // preconditioning: p[j] = r[j] * Hdia_inv[j]; - // sig_new = parallel_dot( r, p, nn); - FixQEqReaxKokkosPreconFunctor precon_functor(this); + // sig_new = parallel_dot(r, p, nn); + FixQEqReaxFFKokkosPreconFunctor precon_functor(this); Kokkos::parallel_reduce(inum,precon_functor,my_dot); - MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world); sig_new = dot_sqr; beta = sig_new / sig_old; - // vector_sum( d, 1., p, beta, d, nn ); - FixQEqReaxKokkosVecSum2Functor vecsum2_functor(this); + // vector_sum(d, 1., p, beta, d, nn); + FixQEqReaxFFKokkosVecSum2Functor vecsum2_functor(this); Kokkos::parallel_for(inum,vecsum2_functor); } - if (loop >= imax && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq/reax cg_solve2 convergence failed after %d iterations " - "at " BIGINT_FORMAT " step: %f",loop,update->ntimestep,sqrt(sig_new)/b_norm); - error->warning(FLERR,str); - //error->all(FLERR,str); - } - + if ((loop >= imax) && maxwarn && (comm->me == 0)) + error->warning(FLERR,fmt::format("Fix qeq/reaxff/kk cg_solve2 convergence " + "failed after {} iterations at step {}: " + "{}", loop, update->ntimestep, + sqrt(sig_new)/b_norm)); + return loop; } /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::calculate_q() +void FixQEqReaxFFKokkos::calculate_q() { F_FLOAT sum, sum_all; const int inum = list->inum; - // s_sum = parallel_vector_acc( s, nn ); + // s_sum = parallel_vector_acc(s, nn); sum = sum_all = 0.0; - FixQEqReaxKokkosVecAcc1Functor vecacc1_functor(this); + FixQEqReaxFFKokkosVecAcc1Functor vecacc1_functor(this); Kokkos::parallel_reduce(inum,vecacc1_functor,sum); - MPI_Allreduce(&sum, &sum_all, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&sum, &sum_all, 1, MPI_DOUBLE, MPI_SUM, world); const F_FLOAT s_sum = sum_all; - // t_sum = parallel_vector_acc( t, nn); + // t_sum = parallel_vector_acc(t, nn); sum = sum_all = 0.0; - FixQEqReaxKokkosVecAcc2Functor vecacc2_functor(this); + FixQEqReaxFFKokkosVecAcc2Functor vecacc2_functor(this); Kokkos::parallel_reduce(inum,vecacc2_functor,sum); - MPI_Allreduce(&sum, &sum_all, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&sum, &sum_all, 1, MPI_DOUBLE, MPI_SUM, world); const F_FLOAT t_sum = sum_all; // u = s_sum / t_sum; delta = s_sum/t_sum; // q[i] = s[i] - u * t[i]; - FixQEqReaxKokkosCalculateQFunctor calculateQ_functor(this); + FixQEqReaxFFKokkosCalculateQFunctor calculateQ_functor(this); Kokkos::parallel_for(inum,calculateQ_functor); atomKK->modified(execution_space,Q_MASK); pack_flag = 4; - //comm->forward_comm_fix( this ); //Dist_vector( atom->q ); + //comm->forward_comm_fix(this); //Dist_vector(atom->q); comm->forward_comm_fix(this); } @@ -1020,7 +1016,7 @@ void FixQEqReaxKokkos::calculate_q() template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::sparse12_item(int ii) const +void FixQEqReaxFFKokkos::sparse12_item(int ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -1034,7 +1030,7 @@ void FixQEqReaxKokkos::sparse12_item(int ii) const template template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::sparse13_item(int ii) const +void FixQEqReaxFFKokkos::sparse13_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); @@ -1056,7 +1052,7 @@ void FixQEqReaxKokkos::sparse13_item(int ii) const template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::operator() (TagSparseMatvec1, const membertype1 &team) const +void FixQEqReaxFFKokkos::operator() (TagSparseMatvec1, const membertype1 &team) const { const int i = d_ilist[team.league_rank()]; if (mask[i] & groupbit) { @@ -1073,7 +1069,7 @@ void FixQEqReaxKokkos::operator() (TagSparseMatvec1, const membertyp template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::sparse22_item(int ii) const +void FixQEqReaxFFKokkos::sparse22_item(int ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -1087,7 +1083,7 @@ void FixQEqReaxKokkos::sparse22_item(int ii) const template template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::sparse23_item(int ii) const +void FixQEqReaxFFKokkos::sparse23_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); @@ -1109,7 +1105,7 @@ void FixQEqReaxKokkos::sparse23_item(int ii) const template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::operator() (TagSparseMatvec2, const membertype2 &team) const +void FixQEqReaxFFKokkos::operator() (TagSparseMatvec2, const membertype2 &team) const { const int i = d_ilist[team.league_rank()]; if (mask[i] & groupbit) { @@ -1124,7 +1120,7 @@ void FixQEqReaxKokkos::operator() (TagSparseMatvec2, const membertyp template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::operator() (TagZeroQGhosts, const int &i) const +void FixQEqReaxFFKokkos::operator() (TagZeroQGhosts, const int &i) const { if (mask[i] & groupbit) d_o[i] = 0.0; @@ -1134,7 +1130,7 @@ void FixQEqReaxKokkos::operator() (TagZeroQGhosts, const int &i) con template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::sparse32_item(int ii) const +void FixQEqReaxFFKokkos::sparse32_item(int ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -1147,7 +1143,7 @@ void FixQEqReaxKokkos::sparse32_item(int ii) const template template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::sparse33_item(int ii) const +void FixQEqReaxFFKokkos::sparse33_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); @@ -1169,7 +1165,7 @@ void FixQEqReaxKokkos::sparse33_item(int ii) const template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::operator() (TagSparseMatvec3, const membertype3 &team) const +void FixQEqReaxFFKokkos::operator() (TagSparseMatvec3, const membertype3 &team) const { const int i = d_ilist[team.league_rank()]; if (mask[i] & groupbit) { @@ -1186,7 +1182,7 @@ void FixQEqReaxKokkos::operator() (TagSparseMatvec3, const membertyp template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::vecsum2_item(int ii) const +void FixQEqReaxFFKokkos::vecsum2_item(int ii) const { const int i = d_ilist[ii]; if (mask[i] & groupbit) @@ -1197,7 +1193,7 @@ void FixQEqReaxKokkos::vecsum2_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::norm1_item(int ii) const +double FixQEqReaxFFKokkos::norm1_item(int ii) const { F_FLOAT tmp = 0; const int i = d_ilist[ii]; @@ -1213,7 +1209,7 @@ double FixQEqReaxKokkos::norm1_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::norm2_item(int ii) const +double FixQEqReaxFFKokkos::norm2_item(int ii) const { F_FLOAT tmp = 0; const int i = d_ilist[ii]; @@ -1229,7 +1225,7 @@ double FixQEqReaxKokkos::norm2_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::dot1_item(int ii) const +double FixQEqReaxFFKokkos::dot1_item(int ii) const { F_FLOAT tmp = 0.0; const int i = d_ilist[ii]; @@ -1242,7 +1238,7 @@ double FixQEqReaxKokkos::dot1_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::dot2_item(int ii) const +double FixQEqReaxFFKokkos::dot2_item(int ii) const { double tmp = 0.0; const int i = d_ilist[ii]; @@ -1256,7 +1252,7 @@ double FixQEqReaxKokkos::dot2_item(int ii) const template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::precon1_item(int ii) const +void FixQEqReaxFFKokkos::precon1_item(int ii) const { const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -1269,7 +1265,7 @@ void FixQEqReaxKokkos::precon1_item(int ii) const template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::precon2_item(int ii) const +void FixQEqReaxFFKokkos::precon2_item(int ii) const { const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -1282,7 +1278,7 @@ void FixQEqReaxKokkos::precon2_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::precon_item(int ii) const +double FixQEqReaxFFKokkos::precon_item(int ii) const { F_FLOAT tmp = 0.0; const int i = d_ilist[ii]; @@ -1297,7 +1293,7 @@ double FixQEqReaxKokkos::precon_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::vecacc1_item(int ii) const +double FixQEqReaxFFKokkos::vecacc1_item(int ii) const { F_FLOAT tmp = 0.0; const int i = d_ilist[ii]; @@ -1310,7 +1306,7 @@ double FixQEqReaxKokkos::vecacc1_item(int ii) const template KOKKOS_INLINE_FUNCTION -double FixQEqReaxKokkos::vecacc2_item(int ii) const +double FixQEqReaxFFKokkos::vecacc2_item(int ii) const { F_FLOAT tmp = 0.0; const int i = d_ilist[ii]; @@ -1324,7 +1320,7 @@ double FixQEqReaxKokkos::vecacc2_item(int ii) const template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::calculate_q_item(int ii) const +void FixQEqReaxFFKokkos::calculate_q_item(int ii) const { const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -1343,20 +1339,20 @@ void FixQEqReaxKokkos::calculate_q_item(int ii) const /* ---------------------------------------------------------------------- */ template -int FixQEqReaxKokkos::pack_forward_comm_fix_kokkos(int n, DAT::tdual_int_2d k_sendlist, +int FixQEqReaxFFKokkos::pack_forward_comm_fix_kokkos(int n, DAT::tdual_int_2d k_sendlist, int iswap_in, DAT::tdual_xfloat_1d &k_buf, int /*pbc_flag*/, int * /*pbc*/) { d_sendlist = k_sendlist.view(); iswap = iswap_in; d_buf = k_buf.view(); - Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); + Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); return n; } template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::operator()(TagFixQEqReaxPackForwardComm, const int &i) const { +void FixQEqReaxFFKokkos::operator()(TagFixQEqReaxFFPackForwardComm, const int &i) const { int j = d_sendlist(iswap, i); if (pack_flag == 1) @@ -1372,11 +1368,11 @@ void FixQEqReaxKokkos::operator()(TagFixQEqReaxPackForwardComm, cons /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::unpack_forward_comm_fix_kokkos(int n, int first_in, DAT::tdual_xfloat_1d &buf) +void FixQEqReaxFFKokkos::unpack_forward_comm_fix_kokkos(int n, int first_in, DAT::tdual_xfloat_1d &buf) { first = first_in; d_buf = buf.view(); - Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); + Kokkos::parallel_for(Kokkos::RangePolicy(0,n),*this); if (pack_flag == 4) atomKK->modified(execution_space,Q_MASK); // needed for auto_sync @@ -1384,14 +1380,14 @@ void FixQEqReaxKokkos::unpack_forward_comm_fix_kokkos(int n, int fir template KOKKOS_INLINE_FUNCTION -void FixQEqReaxKokkos::operator()(TagFixQEqReaxUnpackForwardComm, const int &i) const { +void FixQEqReaxFFKokkos::operator()(TagFixQEqReaxFFUnpackForwardComm, const int &i) const { if (pack_flag == 1) d_d[i + first] = d_buf[i]; - else if ( pack_flag == 2) + else if (pack_flag == 2) d_s[i + first] = d_buf[i]; - else if ( pack_flag == 3) + else if (pack_flag == 3) d_t[i + first] = d_buf[i]; - else if ( pack_flag == 4) + else if (pack_flag == 4) q[i + first] = d_buf[i]; } @@ -1399,7 +1395,7 @@ void FixQEqReaxKokkos::operator()(TagFixQEqReaxUnpackForwardComm, co /* ---------------------------------------------------------------------- */ template -int FixQEqReaxKokkos::pack_forward_comm(int n, int *list, double *buf, +int FixQEqReaxFFKokkos::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int m; @@ -1424,7 +1420,7 @@ int FixQEqReaxKokkos::pack_forward_comm(int n, int *list, double *bu /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::unpack_forward_comm(int n, int first, double *buf) +void FixQEqReaxFFKokkos::unpack_forward_comm(int n, int first, double *buf) { int i, m; @@ -1450,7 +1446,7 @@ void FixQEqReaxKokkos::unpack_forward_comm(int n, int first, double /* ---------------------------------------------------------------------- */ template -int FixQEqReaxKokkos::pack_reverse_comm(int n, int first, double *buf) +int FixQEqReaxFFKokkos::pack_reverse_comm(int n, int first, double *buf) { k_o.sync_host(); @@ -1464,7 +1460,7 @@ int FixQEqReaxKokkos::pack_reverse_comm(int n, int first, double *bu /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::unpack_reverse_comm(int n, int *list, double *buf) +void FixQEqReaxFFKokkos::unpack_reverse_comm(int n, int *list, double *buf) { k_o.sync_host(); @@ -1478,7 +1474,7 @@ void FixQEqReaxKokkos::unpack_reverse_comm(int n, int *list, double /* ---------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::cleanup_copy() +void FixQEqReaxFFKokkos::cleanup_copy() { id = style = nullptr; } @@ -1488,7 +1484,7 @@ void FixQEqReaxKokkos::cleanup_copy() ------------------------------------------------------------------------- */ template -double FixQEqReaxKokkos::memory_usage() +double FixQEqReaxFFKokkos::memory_usage() { double bytes; @@ -1506,7 +1502,7 @@ double FixQEqReaxKokkos::memory_usage() ------------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::grow_arrays(int nmax) +void FixQEqReaxFFKokkos::grow_arrays(int nmax) { k_s_hist.template sync(); k_t_hist.template sync(); @@ -1529,7 +1525,7 @@ void FixQEqReaxKokkos::grow_arrays(int nmax) ------------------------------------------------------------------------- */ template -void FixQEqReaxKokkos::copy_arrays(int i, int j, int /*delflag*/) +void FixQEqReaxFFKokkos::copy_arrays(int i, int j, int /*delflag*/) { k_s_hist.template sync(); k_t_hist.template sync(); @@ -1548,7 +1544,7 @@ void FixQEqReaxKokkos::copy_arrays(int i, int j, int /*delflag*/) ------------------------------------------------------------------------- */ template -int FixQEqReaxKokkos::pack_exchange(int i, double *buf) +int FixQEqReaxFFKokkos::pack_exchange(int i, double *buf) { k_s_hist.template sync(); k_t_hist.template sync(); @@ -1563,7 +1559,7 @@ int FixQEqReaxKokkos::pack_exchange(int i, double *buf) ------------------------------------------------------------------------- */ template -int FixQEqReaxKokkos::unpack_exchange(int nlocal, double *buf) +int FixQEqReaxFFKokkos::unpack_exchange(int nlocal, double *buf) { k_s_hist.template sync(); k_t_hist.template sync(); @@ -1580,8 +1576,8 @@ int FixQEqReaxKokkos::unpack_exchange(int nlocal, double *buf) /* ---------------------------------------------------------------------- */ namespace LAMMPS_NS { -template class FixQEqReaxKokkos; +template class FixQEqReaxFFKokkos; #ifdef LMP_KOKKOS_GPU -template class FixQEqReaxKokkos; +template class FixQEqReaxFFKokkos; #endif } diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reaxff_kokkos.h similarity index 74% rename from src/KOKKOS/fix_qeq_reax_kokkos.h rename to src/KOKKOS/fix_qeq_reaxff_kokkos.h index aa4ae354cd..71c0808b0f 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reaxff_kokkos.h @@ -14,16 +14,19 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(qeq/reax/kk,FixQEqReaxKokkos); -FixStyle(qeq/reax/kk/device,FixQEqReaxKokkos); -FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos); +FixStyle(qeq/reaxff/kk,FixQEqReaxFFKokkos); +FixStyle(qeq/reaxff/kk/device,FixQEqReaxFFKokkos); +FixStyle(qeq/reaxff/kk/host,FixQEqReaxFFKokkos); +FixStyle(qeq/reax/kk,FixQEqReaxFFKokkos); +FixStyle(qeq/reax/kk/device,FixQEqReaxFFKokkos); +FixStyle(qeq/reax/kk/host,FixQEqReaxFFKokkos); // clang-format on #else -#ifndef LMP_FIX_QEQ_REAX_KOKKOS_H -#define LMP_FIX_QEQ_REAX_KOKKOS_H +#ifndef LMP_FIX_QEQ_REAXFF_KOKKOS_H +#define LMP_FIX_QEQ_REAXFF_KOKKOS_H -#include "fix_qeq_reax.h" +#include "fix_qeq_reaxff.h" #include "kokkos_type.h" #include "neigh_list.h" #include "neigh_list_kokkos.h" @@ -35,16 +38,16 @@ struct TagSparseMatvec1 {}; struct TagSparseMatvec2 {}; struct TagSparseMatvec3 {}; struct TagZeroQGhosts{}; -struct TagFixQEqReaxPackForwardComm {}; -struct TagFixQEqReaxUnpackForwardComm {}; +struct TagFixQEqReaxFFPackForwardComm {}; +struct TagFixQEqReaxFFUnpackForwardComm {}; template -class FixQEqReaxKokkos : public FixQEqReax, public KokkosBase { +class FixQEqReaxFFKokkos : public FixQEqReaxFF, public KokkosBase { public: typedef DeviceType device_type; typedef ArrayTypes AT; - FixQEqReaxKokkos(class LAMMPS *, int, char **); - ~FixQEqReaxKokkos(); + FixQEqReaxFFKokkos(class LAMMPS *, int, char **); + ~FixQEqReaxFFKokkos(); void cleanup_copy(); void init(); @@ -141,10 +144,10 @@ class FixQEqReaxKokkos : public FixQEqReax, public KokkosBase { double calculate_H_k(const F_FLOAT &r, const F_FLOAT &shld) const; KOKKOS_INLINE_FUNCTION - void operator()(TagFixQEqReaxPackForwardComm, const int&) const; + void operator()(TagFixQEqReaxFFPackForwardComm, const int&) const; KOKKOS_INLINE_FUNCTION - void operator()(TagFixQEqReaxUnpackForwardComm, const int&) const; + void operator()(TagFixQEqReaxFFUnpackForwardComm, const int&) const; struct params_qeq{ KOKKOS_INLINE_FUNCTION @@ -225,8 +228,8 @@ class FixQEqReaxKokkos : public FixQEqReax, public KokkosBase { void init_hist(); void allocate_matrix(); void allocate_array(); - void cg_solve1(); - void cg_solve2(); + int cg_solve1(); + int cg_solve2(); void calculate_q(); int neighflag, pack_flag; @@ -241,11 +244,11 @@ class FixQEqReaxKokkos : public FixQEqReax, public KokkosBase { }; template -struct FixQEqReaxKokkosNumNeighFunctor { +struct FixQEqReaxFFKokkosNumNeighFunctor { typedef DeviceType device_type ; typedef int value_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosNumNeighFunctor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosNumNeighFunctor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -255,10 +258,10 @@ struct FixQEqReaxKokkosNumNeighFunctor { }; template -struct FixQEqReaxKokkosMatVecFunctor { +struct FixQEqReaxFFKokkosMatVecFunctor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosMatVecFunctor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosMatVecFunctor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -268,17 +271,17 @@ struct FixQEqReaxKokkosMatVecFunctor { }; template -struct FixQEqReaxKokkosComputeHFunctor { +struct FixQEqReaxFFKokkosComputeHFunctor { int atoms_per_team, vector_length; typedef int value_type; typedef Kokkos::ScratchMemorySpace scratch_space; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; - FixQEqReaxKokkosComputeHFunctor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosComputeHFunctor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; - FixQEqReaxKokkosComputeHFunctor(FixQEqReaxKokkos *c_ptr, + FixQEqReaxFFKokkosComputeHFunctor(FixQEqReaxFFKokkos *c_ptr, int _atoms_per_team, int _vector_length) : atoms_per_team(_atoms_per_team), vector_length(_vector_length), c(*c_ptr) { c.cleanup_copy(); @@ -315,10 +318,10 @@ struct FixQEqReaxKokkosComputeHFunctor { }; template -struct FixQEqReaxKokkosZeroFunctor { +struct FixQEqReaxFFKokkosZeroFunctor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosZeroFunctor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosZeroFunctor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -328,10 +331,10 @@ struct FixQEqReaxKokkosZeroFunctor { }; template -struct FixQEqReaxKokkosSparse12Functor { +struct FixQEqReaxFFKokkosSparse12Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosSparse12Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosSparse12Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -341,10 +344,10 @@ struct FixQEqReaxKokkosSparse12Functor { }; template -struct FixQEqReaxKokkosSparse13Functor { +struct FixQEqReaxFFKokkosSparse13Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosSparse13Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosSparse13Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -354,10 +357,10 @@ struct FixQEqReaxKokkosSparse13Functor { }; template -struct FixQEqReaxKokkosSparse22Functor { +struct FixQEqReaxFFKokkosSparse22Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosSparse22Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosSparse22Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -367,10 +370,10 @@ struct FixQEqReaxKokkosSparse22Functor { }; template -struct FixQEqReaxKokkosSparse23Functor { +struct FixQEqReaxFFKokkosSparse23Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosSparse23Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosSparse23Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -380,10 +383,10 @@ struct FixQEqReaxKokkosSparse23Functor { }; template -struct FixQEqReaxKokkosSparse32Functor { +struct FixQEqReaxFFKokkosSparse32Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosSparse32Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosSparse32Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -393,10 +396,10 @@ struct FixQEqReaxKokkosSparse32Functor { }; template -struct FixQEqReaxKokkosSparse33Functor { +struct FixQEqReaxFFKokkosSparse33Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosSparse33Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosSparse33Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -406,10 +409,10 @@ struct FixQEqReaxKokkosSparse33Functor { }; template -struct FixQEqReaxKokkosVecSum2Functor { +struct FixQEqReaxFFKokkosVecSum2Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosVecSum2Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosVecSum2Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -419,11 +422,11 @@ struct FixQEqReaxKokkosVecSum2Functor { }; template -struct FixQEqReaxKokkosNorm1Functor { +struct FixQEqReaxFFKokkosNorm1Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosNorm1Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosNorm1Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -433,11 +436,11 @@ struct FixQEqReaxKokkosNorm1Functor { }; template -struct FixQEqReaxKokkosNorm2Functor { +struct FixQEqReaxFFKokkosNorm2Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosNorm2Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosNorm2Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -447,11 +450,11 @@ struct FixQEqReaxKokkosNorm2Functor { }; template -struct FixQEqReaxKokkosDot1Functor { +struct FixQEqReaxFFKokkosDot1Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosDot1Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosDot1Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -461,11 +464,11 @@ struct FixQEqReaxKokkosDot1Functor { }; template -struct FixQEqReaxKokkosDot2Functor { +struct FixQEqReaxFFKokkosDot2Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosDot2Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosDot2Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -475,10 +478,10 @@ struct FixQEqReaxKokkosDot2Functor { }; template -struct FixQEqReaxKokkosPrecon1Functor { +struct FixQEqReaxFFKokkosPrecon1Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosPrecon1Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosPrecon1Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -488,10 +491,10 @@ struct FixQEqReaxKokkosPrecon1Functor { }; template -struct FixQEqReaxKokkosPrecon2Functor { +struct FixQEqReaxFFKokkosPrecon2Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosPrecon2Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosPrecon2Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -501,11 +504,11 @@ struct FixQEqReaxKokkosPrecon2Functor { }; template -struct FixQEqReaxKokkosPreconFunctor { +struct FixQEqReaxFFKokkosPreconFunctor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosPreconFunctor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosPreconFunctor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -515,11 +518,11 @@ struct FixQEqReaxKokkosPreconFunctor { }; template -struct FixQEqReaxKokkosVecAcc1Functor { +struct FixQEqReaxFFKokkosVecAcc1Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosVecAcc1Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosVecAcc1Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -529,11 +532,11 @@ struct FixQEqReaxKokkosVecAcc1Functor { }; template -struct FixQEqReaxKokkosVecAcc2Functor { +struct FixQEqReaxFFKokkosVecAcc2Functor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; + FixQEqReaxFFKokkos c; typedef double value_type; - FixQEqReaxKokkosVecAcc2Functor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkosVecAcc2Functor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION @@ -543,10 +546,10 @@ struct FixQEqReaxKokkosVecAcc2Functor { }; template -struct FixQEqReaxKokkosCalculateQFunctor { +struct FixQEqReaxFFKokkosCalculateQFunctor { typedef DeviceType device_type ; - FixQEqReaxKokkos c; - FixQEqReaxKokkosCalculateQFunctor(FixQEqReaxKokkos* c_ptr):c(*c_ptr) { + FixQEqReaxFFKokkos c; + FixQEqReaxFFKokkosCalculateQFunctor(FixQEqReaxFFKokkos* c_ptr):c(*c_ptr) { c.cleanup_copy(); }; KOKKOS_INLINE_FUNCTION diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxff_bonds_kokkos.cpp similarity index 69% rename from src/KOKKOS/fix_reaxc_bonds_kokkos.cpp rename to src/KOKKOS/fix_reaxff_bonds_kokkos.cpp index 3da59ce972..2fc7d4639d 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxff_bonds_kokkos.cpp @@ -16,22 +16,22 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include "fix_reaxc_bonds_kokkos.h" +#include "fix_reaxff_bonds_kokkos.h" #include "atom.h" #include "atom_masks.h" #include "error.h" #include "force.h" #include "memory_kokkos.h" -#include "pair_reaxc_kokkos.h" +#include "pair_reaxff_kokkos.h" using namespace LAMMPS_NS; using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixReaxCBondsKokkos::FixReaxCBondsKokkos(LAMMPS *lmp, int narg, char **arg) : - FixReaxCBonds(lmp, narg, arg) +FixReaxFFBondsKokkos::FixReaxFFBondsKokkos(LAMMPS *lmp, int narg, char **arg) : + FixReaxFFBonds(lmp, narg, arg) { kokkosable = 1; atomKK = (AtomKokkos *) atom; @@ -42,25 +42,25 @@ FixReaxCBondsKokkos::FixReaxCBondsKokkos(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixReaxCBondsKokkos::~FixReaxCBondsKokkos() +FixReaxFFBondsKokkos::~FixReaxFFBondsKokkos() { } /* ---------------------------------------------------------------------- */ -void FixReaxCBondsKokkos::init() +void FixReaxFFBondsKokkos::init() { - Pair *pair_kk = force->pair_match("reax/c/kk",0); - if (pair_kk == nullptr) error->all(FLERR,"Cannot use fix reax/c/bonds without " - "pair_style reax/c/kk"); + Pair *pair_kk = force->pair_match("^reax../kk",0); + if (pair_kk == nullptr) error->all(FLERR,"Cannot use fix reaxff/bonds without " + "pair_style reaxff/kk"); - FixReaxCBonds::init(); + FixReaxFFBonds::init(); } /* ---------------------------------------------------------------------- */ -void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/) +void FixReaxFFBondsKokkos::Output_ReaxFF_Bonds() { int nbuf_local; @@ -72,23 +72,23 @@ void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/ int nlocal_tot = static_cast (atom->natoms); numbonds = 0; - if (reaxc->execution_space == Device) - ((PairReaxCKokkos*) reaxc)->FindBond(numbonds); + if (reaxff->execution_space == Device) + ((PairReaxFFKokkos*) reaxff)->FindBond(numbonds); else - ((PairReaxCKokkos*) reaxc)->FindBond(numbonds); + ((PairReaxFFKokkos*) reaxff)->FindBond(numbonds); // allocate a temporary buffer for the snapshot info MPI_Allreduce(&numbonds,&numbonds_max,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&nlocal,&nlocal_max,1,MPI_INT,MPI_MAX,world); nbuf = 1+(numbonds_max*2+10)*nlocal_max; - memoryKK->create_kokkos(k_buf,buf,nbuf,"reax/c/bonds:buf"); + memoryKK->create_kokkos(k_buf,buf,nbuf,"reaxff/bonds:buf"); // Pass information to buffer - if (reaxc->execution_space == Device) - ((PairReaxCKokkos*) reaxc)->PackBondBuffer(k_buf,nbuf_local); + if (reaxff->execution_space == Device) + ((PairReaxFFKokkos*) reaxff)->PackBondBuffer(k_buf,nbuf_local); else - ((PairReaxCKokkos*) reaxc)->PackBondBuffer(k_buf,nbuf_local); + ((PairReaxFFKokkos*) reaxff)->PackBondBuffer(k_buf,nbuf_local); buf[0] = nlocal; // Receive information from buffer for output @@ -99,12 +99,12 @@ void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/ /* ---------------------------------------------------------------------- */ -double FixReaxCBondsKokkos::memory_usage() +double FixReaxFFBondsKokkos::memory_usage() { double bytes; bytes = nbuf*sizeof(double); - // These are accounted for in PairReaxCKokkos: + // These are accounted for in PairReaxFFKokkos: //bytes += nmax*sizeof(int); //bytes += 1.0*nmax*MAXREAXBOND*sizeof(double); //bytes += 1.0*nmax*MAXREAXBOND*sizeof(int); diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.h b/src/KOKKOS/fix_reaxff_bonds_kokkos.h similarity index 59% rename from src/KOKKOS/fix_reaxc_bonds_kokkos.h rename to src/KOKKOS/fix_reaxff_bonds_kokkos.h index 8c1bb9bef9..b39dfa3c17 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.h +++ b/src/KOKKOS/fix_reaxff_bonds_kokkos.h @@ -14,29 +14,32 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(reax/c/bonds/kk,FixReaxCBondsKokkos); -FixStyle(reax/c/bonds/kk/device,FixReaxCBondsKokkos); -FixStyle(reax/c/bonds/kk/host,FixReaxCBondsKokkos); +FixStyle(reaxff/bonds/kk,FixReaxFFBondsKokkos); +FixStyle(reaxff/bonds/kk/device,FixReaxFFBondsKokkos); +FixStyle(reaxff/bonds/kk/host,FixReaxFFBondsKokkos); +FixStyle(reax/c/bonds/kk,FixReaxFFBondsKokkos); +FixStyle(reax/c/bonds/kk/device,FixReaxFFBondsKokkos); +FixStyle(reax/c/bonds/kk/host,FixReaxFFBondsKokkos); // clang-format on #else -#ifndef LMP_FIX_REAXC_BONDS_KOKKOS_H -#define LMP_FIX_REAXC_BONDS_KOKKOS_H +#ifndef LMP_FIX_REAXFF_BONDS_KOKKOS_H +#define LMP_FIX_REAXFF_BONDS_KOKKOS_H -#include "fix_reaxc_bonds.h" +#include "fix_reaxff_bonds.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class FixReaxCBondsKokkos : public FixReaxCBonds { +class FixReaxFFBondsKokkos : public FixReaxFFBonds { public: - FixReaxCBondsKokkos(class LAMMPS *, int, char **); - virtual ~FixReaxCBondsKokkos(); + FixReaxFFBondsKokkos(class LAMMPS *, int, char **); + virtual ~FixReaxFFBondsKokkos(); void init(); private: int nbuf; - void Output_ReaxC_Bonds(bigint, FILE *); + void Output_ReaxFF_Bonds(); double memory_usage(); }; } diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxff_species_kokkos.cpp similarity index 82% rename from src/KOKKOS/fix_reaxc_species_kokkos.cpp rename to src/KOKKOS/fix_reaxff_species_kokkos.cpp index 85cd3b23ba..d3d913eda8 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxff_species_kokkos.cpp @@ -16,27 +16,29 @@ Contributing authors: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include "fix_reaxc_species_kokkos.h" +#include "fix_reaxff_species_kokkos.h" + #include "atom.h" -#include "fix_ave_atom.h" -#include "reaxc_defs.h" -#include "pair_reaxc_kokkos.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" #include "input.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neigh_list.h" +#include "neigh_request.h" + +#include "fix_ave_atom.h" +#include "pair_reaxff_kokkos.h" +#include "reaxff_defs.h" using namespace LAMMPS_NS; using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixReaxCSpeciesKokkos::FixReaxCSpeciesKokkos(LAMMPS *lmp, int narg, char **arg) : - FixReaxCSpecies(lmp, narg, arg) +FixReaxFFSpeciesKokkos::FixReaxFFSpeciesKokkos(LAMMPS *lmp, int narg, char **arg) : + FixReaxFFSpecies(lmp, narg, arg) { kokkosable = 1; atomKK = (AtomKokkos *) atom; @@ -49,25 +51,25 @@ FixReaxCSpeciesKokkos::FixReaxCSpeciesKokkos(LAMMPS *lmp, int narg, char **arg) /* ---------------------------------------------------------------------- */ -FixReaxCSpeciesKokkos::~FixReaxCSpeciesKokkos() +FixReaxFFSpeciesKokkos::~FixReaxFFSpeciesKokkos() { } /* ---------------------------------------------------------------------- */ -void FixReaxCSpeciesKokkos::init() +void FixReaxFFSpeciesKokkos::init() { - Pair* pair_kk = force->pair_match("reax/c/kk",0); - if (pair_kk == nullptr) error->all(FLERR,"Cannot use fix reax/c/species/kk without " - "pair_style reax/c/kk"); + Pair* pair_kk = force->pair_match("^reax../kk",0); + if (pair_kk == nullptr) error->all(FLERR,"Cannot use fix reaxff/species/kk without " + "pair_style reaxff/kk"); - FixReaxCSpecies::init(); + FixReaxFFSpecies::init(); } /* ---------------------------------------------------------------------- */ -void FixReaxCSpeciesKokkos::FindMolecule() +void FixReaxFFSpeciesKokkos::FindMolecule() { int i,j,ii,jj,inum,itype,jtype,loop,looptot; int change,done,anychange; @@ -75,14 +77,14 @@ void FixReaxCSpeciesKokkos::FindMolecule() double bo_tmp,bo_cut; double **spec_atom = f_SPECBOND->array_atom; - inum = reaxc->list->inum; + inum = reaxff->list->inum; typename ArrayTypes::t_int_1d ilist; - if (reaxc->execution_space == Host) { - NeighListKokkos* k_list = static_cast*>(reaxc->list); + if (reaxff->execution_space == Host) { + NeighListKokkos* k_list = static_cast*>(reaxff->list); k_list->k_ilist.sync(); ilist = k_list->k_ilist.h_view; } else { - NeighListKokkos* k_list = static_cast*>(reaxc->list); + NeighListKokkos* k_list = static_cast*>(reaxff->list); k_list->k_ilist.sync(); ilist = k_list->k_ilist.h_view; } @@ -114,7 +116,7 @@ void FixReaxCSpeciesKokkos::FindMolecule() itype = atom->type[i]; for (jj = 0; jj < MAXSPECBOND; jj++) { - j = reaxc->tmpid[i][jj]; + j = reaxff->tmpid[i][jj]; if ((j == 0) && (j < i)) continue; if (!(mask[j] & groupbit)) continue; diff --git a/src/KOKKOS/fix_reaxff_species_kokkos.h b/src/KOKKOS/fix_reaxff_species_kokkos.h new file mode 100644 index 0000000000..ad9d02319d --- /dev/null +++ b/src/KOKKOS/fix_reaxff_species_kokkos.h @@ -0,0 +1,47 @@ +// clang-format off +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(reaxff/species/kk,FixReaxFFSpeciesKokkos); +FixStyle(reaxff/species/kk/device,FixReaxFFSpeciesKokkos); +FixStyle(reaxff/species/kk/host,FixReaxFFSpeciesKokkos); +FixStyle(reax/c/species/kk,FixReaxFFSpeciesKokkos); +FixStyle(reax/c/species/kk/device,FixReaxFFSpeciesKokkos); +FixStyle(reax/c/species/kk/host,FixReaxFFSpeciesKokkos); +// clang-format on +#else + +#ifndef LMP_FIX_REAXFF_SPECIES_KOKKOS_H +#define LMP_FIX_REAXFF_SPECIES_KOKKOS_H + +#include "fix_reaxff_species.h" + +#define BUFLEN 1000 + +namespace LAMMPS_NS { + +class FixReaxFFSpeciesKokkos : public FixReaxFFSpecies { + public: + FixReaxFFSpeciesKokkos(class LAMMPS *, int, char **); + virtual ~FixReaxFFSpeciesKokkos(); + void init(); + + private: + void FindMolecule(); +}; +} + +#endif +#endif diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 7bc7bf95c3..15b4a39849 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -13,24 +13,25 @@ ------------------------------------------------------------------------- */ #include "fix_rx_kokkos.h" -#include -#include "atom_masks.h" + #include "atom_kokkos.h" -#include "force.h" -#include "memory_kokkos.h" -#include "update.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list_kokkos.h" -#include "neigh_request.h" -#include "error.h" -#include "math_special_kokkos.h" +#include "atom_masks.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix_property_atom.h" +#include "force.h" #include "kokkos.h" - +#include "math_special_kokkos.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "neigh_list_kokkos.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" #include // DBL_EPSILON +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -104,7 +105,7 @@ void FixRxKokkos::post_constructor() FixRX::post_constructor(); // Need a copy of this - this->my_restartFlag = modify->fix[modify->nfix-1]->restart_reset; + this->my_restartFlag = fix_species->restart_reset; } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/fix_shake_kokkos.cpp b/src/KOKKOS/fix_shake_kokkos.cpp index 804da9fd22..91d8458d21 100644 --- a/src/KOKKOS/fix_shake_kokkos.cpp +++ b/src/KOKKOS/fix_shake_kokkos.cpp @@ -201,6 +201,14 @@ void FixShakeKokkos::pre_neighbor() type = atom->type; nlocal = atom->nlocal; + map_style = atom->map_style; + if (map_style == Atom::MAP_ARRAY) { + k_map_array = atomKK->k_map_array; + k_map_array.template sync(); + } else if (map_style == Atom::MAP_HASH) { + k_map_hash = atomKK->k_map_hash; + } + k_shake_flag.sync(); k_shake_atom.sync(); @@ -213,21 +221,16 @@ void FixShakeKokkos::pre_neighbor() d_list = k_list.view(); } - // don't yet have atom_map_kokkos routines, so move data from host to device + // Atom Map - if (atom->map_style != Atom::MAP_ARRAY) - error->all(FLERR,"Must use atom map style array with Kokkos"); + map_style = atom->map_style; - int* map_array_host = atom->get_map_array(); - int map_size = atom->get_map_size(); - int map_maxarray = atom->get_map_maxarray(); - if (map_maxarray > (int)k_map_array.extent(0)) - k_map_array = DAT::tdual_int_1d("NeighBond:map_array",map_maxarray); - for (int i=0; i(); - k_map_array.template sync(); - map_array = k_map_array.view(); + if (map_style == Atom::MAP_ARRAY) { + k_map_array = atomKK->k_map_array; + k_map_array.template sync(); + } else if (map_style == Atom::MAP_HASH) { + k_map_hash = atomKK->k_map_hash; + } // build list of SHAKE clusters I compute @@ -241,14 +244,16 @@ void FixShakeKokkos::pre_neighbor() auto d_list = this->d_list; auto d_error_flag = this->d_error_flag; auto d_nlist = this->d_nlist; - auto map_array = this->map_array; + auto map_style = atom->map_style; + auto k_map_array = this->k_map_array; + auto k_map_hash = this->k_map_hash; Kokkos::parallel_for(Kokkos::RangePolicy(0,nlocal), LAMMPS_LAMBDA(const int& i) { if (d_shake_flag[i]) { if (d_shake_flag[i] == 2) { - const int atom1 = map_array(d_shake_atom(i,0)); - const int atom2 = map_array(d_shake_atom(i,1)); + const int atom1 = AtomKokkos::map_kokkos(d_shake_atom(i,0),map_style,k_map_array,k_map_hash); + const int atom2 = AtomKokkos::map_kokkos(d_shake_atom(i,1),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1) { d_error_flag() = 1; } @@ -257,9 +262,9 @@ void FixShakeKokkos::pre_neighbor() d_list[nlist] = i; } } else if (d_shake_flag[i] % 2 == 1) { - const int atom1 = map_array(d_shake_atom(i,0)); - const int atom2 = map_array(d_shake_atom(i,1)); - const int atom3 = map_array(d_shake_atom(i,2)); + const int atom1 = AtomKokkos::map_kokkos(d_shake_atom(i,0),map_style,k_map_array,k_map_hash); + const int atom2 = AtomKokkos::map_kokkos(d_shake_atom(i,1),map_style,k_map_array,k_map_hash); + const int atom3 = AtomKokkos::map_kokkos(d_shake_atom(i,2),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1) d_error_flag() = 1; if (i <= atom1 && i <= atom2 && i <= atom3) { @@ -267,10 +272,10 @@ void FixShakeKokkos::pre_neighbor() d_list[nlist] = i; } } else { - const int atom1 = map_array(d_shake_atom(i,0)); - const int atom2 = map_array(d_shake_atom(i,1)); - const int atom3 = map_array(d_shake_atom(i,2)); - const int atom4 = map_array(d_shake_atom(i,3)); + const int atom1 = AtomKokkos::map_kokkos(d_shake_atom(i,0),map_style,k_map_array,k_map_hash); + const int atom2 = AtomKokkos::map_kokkos(d_shake_atom(i,1),map_style,k_map_array,k_map_hash); + const int atom3 = AtomKokkos::map_kokkos(d_shake_atom(i,2),map_style,k_map_array,k_map_hash); + const int atom4 = AtomKokkos::map_kokkos(d_shake_atom(i,3),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) d_error_flag() = 1; if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4) { @@ -307,6 +312,14 @@ void FixShakeKokkos::post_force(int vflag) d_mass = atomKK->k_mass.view(); nlocal = atomKK->nlocal; + map_style = atom->map_style; + if (map_style == Atom::MAP_ARRAY) { + k_map_array = atomKK->k_map_array; + k_map_array.template sync(); + } else if (map_style == Atom::MAP_HASH) { + k_map_hash = atomKK->k_map_hash; + } + if (d_rmass.data()) atomKK->sync(execution_space,X_MASK|F_MASK|RMASS_MASK); else @@ -586,8 +599,8 @@ void FixShakeKokkos::shake(int m, EV_FLOAT& ev) const // local atom IDs and constraint distances - int i0 = map_array(d_shake_atom(m,0)); - int i1 = map_array(d_shake_atom(m,1)); + int i0 = AtomKokkos::map_kokkos(d_shake_atom(m,0),map_style,k_map_array,k_map_hash); + int i1 = AtomKokkos::map_kokkos(d_shake_atom(m,1),map_style,k_map_array,k_map_hash); double bond1 = d_bond_distance[d_shake_type(m,0)]; // r01 = distance vec between atoms, with PBC @@ -697,9 +710,9 @@ void FixShakeKokkos::shake3(int m, EV_FLOAT& ev) const // local atom IDs and constraint distances - int i0 = map_array(d_shake_atom(m,0)); - int i1 = map_array(d_shake_atom(m,1)); - int i2 = map_array(d_shake_atom(m,2)); + int i0 = AtomKokkos::map_kokkos(d_shake_atom(m,0),map_style,k_map_array,k_map_hash); + int i1 = AtomKokkos::map_kokkos(d_shake_atom(m,1),map_style,k_map_array,k_map_hash); + int i2 = AtomKokkos::map_kokkos(d_shake_atom(m,2),map_style,k_map_array,k_map_hash); double bond1 = d_bond_distance[d_shake_type(m,0)]; double bond2 = d_bond_distance[d_shake_type(m,1)]; @@ -880,10 +893,10 @@ void FixShakeKokkos::shake4(int m, EV_FLOAT& ev) const // local atom IDs and constraint distances - int i0 = map_array(d_shake_atom(m,0)); - int i1 = map_array(d_shake_atom(m,1)); - int i2 = map_array(d_shake_atom(m,2)); - int i3 = map_array(d_shake_atom(m,3)); + int i0 = AtomKokkos::map_kokkos(d_shake_atom(m,0),map_style,k_map_array,k_map_hash); + int i1 = AtomKokkos::map_kokkos(d_shake_atom(m,1),map_style,k_map_array,k_map_hash); + int i2 = AtomKokkos::map_kokkos(d_shake_atom(m,2),map_style,k_map_array,k_map_hash); + int i3 = AtomKokkos::map_kokkos(d_shake_atom(m,3),map_style,k_map_array,k_map_hash); double bond1 = d_bond_distance[d_shake_type(m,0)]; double bond2 = d_bond_distance[d_shake_type(m,1)]; double bond3 = d_bond_distance[d_shake_type(m,2)]; @@ -1142,9 +1155,9 @@ void FixShakeKokkos::shake3angle(int m, EV_FLOAT& ev) const // local atom IDs and constraint distances - int i0 = map_array(d_shake_atom(m,0)); - int i1 = map_array(d_shake_atom(m,1)); - int i2 = map_array(d_shake_atom(m,2)); + int i0 = AtomKokkos::map_kokkos(d_shake_atom(m,0),map_style,k_map_array,k_map_hash); + int i1 = AtomKokkos::map_kokkos(d_shake_atom(m,1),map_style,k_map_array,k_map_hash); + int i2 = AtomKokkos::map_kokkos(d_shake_atom(m,2),map_style,k_map_array,k_map_hash); double bond1 = d_bond_distance[d_shake_type(m,0)]; double bond2 = d_bond_distance[d_shake_type(m,1)]; double bond12 = d_angle_distance[d_shake_type(m,2)]; diff --git a/src/KOKKOS/fix_shake_kokkos.h b/src/KOKKOS/fix_shake_kokkos.h index b95c042ac1..12e082a903 100644 --- a/src/KOKKOS/fix_shake_kokkos.h +++ b/src/KOKKOS/fix_shake_kokkos.h @@ -26,6 +26,7 @@ FixStyle(shake/kk/host,FixShakeKokkos); #include "fix_shake.h" #include "kokkos_type.h" #include "kokkos_base.h" +#include namespace LAMMPS_NS { @@ -172,9 +173,6 @@ class FixShakeKokkos : public FixShake, public KokkosBase { KOKKOS_INLINE_FUNCTION void v_tally(EV_FLOAT&, int, int *, double, double *) const; - DAT::tdual_int_1d k_map_array; - typename AT::t_int_1d_randomread map_array; - int iswap; int first; typename AT::t_int_2d d_sendlist; @@ -185,6 +183,10 @@ class FixShakeKokkos : public FixShake, public KokkosBase { tagint **shake_atom_tmp; int **shake_type_tmp; + int map_style; + DAT::tdual_int_1d k_map_array; + dual_hash_type k_map_hash; + // copied from Domain KOKKOS_INLINE_FUNCTION diff --git a/src/KOKKOS/kissfft_kokkos.cpp b/src/KOKKOS/kissfft_kokkos.cpp deleted file mode 100644 index f0695edb10..0000000000 --- a/src/KOKKOS/kissfft_kokkos.cpp +++ /dev/null @@ -1,21 +0,0 @@ -// clang-format off -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - - -namespace LAMMPS_NS { -template class KissFFTKokkos; -#ifdef LMP_KOKKOS_GPU -template class KissFFTKokkos; -#endif -} diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index fd171b61af..aa435d5b0b 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -69,6 +69,10 @@ GPU_AWARE_UNKNOWN using namespace LAMMPS_NS; +Kokkos::InitArguments KokkosLMP::args{-1, -1, -1, false}; +int KokkosLMP::is_finalized = 0; +int KokkosLMP::init_ngpus = 0; + /* ---------------------------------------------------------------------- */ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) @@ -155,6 +159,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } else if (strcmp(arg[iarg],"t") == 0 || strcmp(arg[iarg],"threads") == 0) { nthreads = atoi(arg[iarg+1]); + + if (nthreads <= 0) + error->all(FLERR,"Invalid number of threads requested for Kokkos: must be 1 or greater"); + iarg += 2; } else if (strcmp(arg[iarg],"n") == 0 || @@ -165,13 +173,27 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } else error->all(FLERR,"Invalid Kokkos command-line args"); } - // initialize Kokkos + // Initialize Kokkos. However, we cannot change any + // Kokkos library parameters after the first initalization - if (me == 0) { - if (screen) fprintf(screen," will use up to %d GPU(s) per node\n",ngpus); - if (logfile) fprintf(logfile," will use up to %d GPU(s) per node\n",ngpus); + if (args.num_threads != -1) { + if (args.num_threads != nthreads || args.num_numa != numa || args.device_id != device) + if (me == 0) + error->warning(FLERR,"Kokkos package already initalized, cannot reinitialize with different parameters"); + nthreads = args.num_threads; + numa = args.num_numa; + device = args.device_id; + ngpus = init_ngpus; + } else { + args.num_threads = nthreads; + args.num_numa = numa; + args.device_id = device; + init_ngpus = ngpus; } + if (me == 0) + utils::logmesg(lmp, " will use up to {} GPU(s) per node\n",ngpus); + #ifdef LMP_KOKKOS_GPU if (ngpus <= 0) error->all(FLERR,"Kokkos has been compiled for CUDA, HIP, or SYCL but no GPUs are requested"); @@ -184,12 +206,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) "than the OpenMP backend"); #endif - Kokkos::InitArguments args; - args.num_threads = nthreads; - args.num_numa = numa; - args.device_id = device; - - Kokkos::initialize(args); + KokkosLMP::initialize(args,error); // default settings for package kokkos command @@ -276,9 +293,14 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) error->warning(FLERR,"MVAPICH2 'MV2_USE_CUDA' environment variable is not set. Disabling GPU-aware MPI"); // pure MPICH or some unsupported MPICH derivative #elif defined(MPICH) && !defined(MVAPICH2_VERSION) - if (me == 0) - error->warning(FLERR,"Detected MPICH. Disabling GPU-aware MPI"); + char* str; gpu_aware_flag = 0; + if ((str = getenv("MPICH_GPU_SUPPORT_ENABLED"))) + if ((strcmp(str,"1") == 0)) + gpu_aware_flag = 1; + + if (!gpu_aware_flag && me == 0) + error->warning(FLERR,"Detected MPICH. Disabling GPU-aware MPI"); #else if (me == 0) error->warning(FLERR,"Kokkos with CUDA, HIP, or SYCL assumes CUDA-aware MPI is available," @@ -299,9 +321,27 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) KokkosLMP::~KokkosLMP() { - // finalize Kokkos - Kokkos::finalize(); +} + +/* ---------------------------------------------------------------------- */ + +void KokkosLMP::initialize(Kokkos::InitArguments args, Error *error) +{ + if (!Kokkos::is_initialized()) { + if (is_finalized) + error->all(FLERR,"Kokkos package already finalized, cannot re-initialize"); + Kokkos::initialize(args); + } +} + +/* ---------------------------------------------------------------------- */ + +void KokkosLMP::finalize() +{ + if (Kokkos::is_initialized() && !is_finalized) + Kokkos::finalize(); + is_finalized = 1; } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 22060ecc09..65990544ad 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -49,8 +49,14 @@ class KokkosLMP : protected Pointers { int newtonflag; double binsize; + static int is_finalized; + static Kokkos::InitArguments args; + static int init_ngpus; + KokkosLMP(class LAMMPS *, int, char **); ~KokkosLMP(); + static void initialize(Kokkos::InitArguments, Error *); + static void finalize(); void accelerator(int, char **); int neigh_count(int); @@ -84,13 +90,21 @@ because MPI library not recognized The local MPI rank was not found in one of four supported environment variables. +E: Invalid number of threads requested for Kokkos: must be 1 or greater + +Self-explanatory. + E: GPUs are requested but Kokkos has not been compiled for CUDA Recompile Kokkos with CUDA support to use GPUs. -E: Kokkos has been compiled for CUDA but no GPUs are requested +E: Kokkos has been compiled for CUDA, HIP, or SYCL but no GPUs are requested -One or more GPUs must be used when Kokkos is compiled for CUDA. +One or more GPUs must be used when Kokkos is compiled for CUDA/HIP/SYCL. + +W: Kokkos package already initalized, cannot reinitialize with different parameters + +Self-explanatory. E: Illegal ... command diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index c9e5736410..05c839db3f 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -23,6 +23,7 @@ #include #include #include +#include enum{FULL=1u,HALFTHREAD=2u,HALF=4u}; @@ -45,7 +46,9 @@ enum{FULL=1u,HALFTHREAD=2u,HALF=4u}; static constexpr LAMMPS_NS::bigint LMP_KOKKOS_AV_DELTA = 10; namespace Kokkos { - using NoInit = ViewAllocateWithoutInitializing; + static auto NoInit = [](std::string const& label) { + return Kokkos::view_alloc(Kokkos::WithoutInitializing, label); + }; } struct lmp_float3 { @@ -551,6 +554,23 @@ typedef int T_INT; // LAMMPS types +typedef Kokkos::UnorderedMap hash_type; +typedef hash_type::HostMirror host_hash_type; + +struct dual_hash_type { + hash_type d_view; + host_hash_type h_view; + + template + KOKKOS_INLINE_FUNCTION + std::enable_if_t<(std::is_same::value || Kokkos::SpaceAccessibility::accessible),hash_type&> view() {return d_view;} + + template + KOKKOS_INLINE_FUNCTION + std::enable_if_t::value || Kokkos::SpaceAccessibility::accessible),host_hash_type&> view() {return h_view;} + +}; + template struct ArrayTypes; diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index aaf883c881..715d77f293 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -348,7 +348,7 @@ void MinKokkos::setup_minimal(int flag) void MinKokkos::run(int n) { if (nextra_atom) - error->all(FLERR,"Cannot yet use extra atom DOFs (e.g. USER-AWPMD and USER-EFF packages) " + error->all(FLERR,"Cannot yet use extra atom DOFs (e.g. AWPMD and EFF packages) " "with Kokkos minimize"); // minimizer iterations diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index eed0026af3..a4cb6e7d40 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -190,15 +190,13 @@ void NeighBondKokkos::init_topology_kk() { /* ---------------------------------------------------------------------- build all topology neighbor lists every few timesteps - normally built with pair lists, but USER-CUDA separates them + normally built with pair lists, but CUDA separates them ------------------------------------------------------------------------- */ template void NeighBondKokkos::build_topology_kk() { atomKK->sync(execution_space, X_MASK | TAG_MASK); - int nall = atom->nlocal + atom->nghost; - int nmax = atom->nmax; nlocal = atom->nlocal; x = atomKK->k_x.view(); @@ -207,30 +205,7 @@ void NeighBondKokkos::build_topology_kk() lostbond = output->thermo->lostbond; - // don't yet have atom_map_kokkos routines, so move data from host to device - - if (atom->map_style != Atom::MAP_ARRAY) - error->all(FLERR,"Must use atom map style array with Kokkos"); - - int* map_array_host = atom->get_map_array(); - int map_size = atom->get_map_size(); - int map_maxarray = atom->get_map_maxarray(); - if (map_maxarray > (int)k_map_array.extent(0)) - k_map_array = DAT::tdual_int_1d("NeighBond:map_array",map_maxarray); - for (int i=0; i(); - k_map_array.template sync(); - map_array = k_map_array.view(); - - int* sametag_host = atomKK->sametag; - if (nmax > (int)k_sametag.extent(0)) - k_sametag = DAT::tdual_int_1d("NeighBond:sametag",nmax); - for (int i=0; i(); - k_sametag.template sync(); - sametag = k_sametag.view(); + update_class_variables(); if (force->bond) (this->*bond_build_kk)(); if (force->angle) (this->*angle_build_kk)(); @@ -306,7 +281,7 @@ template KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondBondAll, const int &i, int &nmissing) const { for (int m = 0; m < num_bond[i]; m++) { - int atom1 = map_array(bond_atom(i,m)); + int atom1 = AtomKokkos::map_kokkos(bond_atom(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -394,7 +369,7 @@ KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondBondPartial, const int &i, int &nmissing) const { for (int m = 0; m < num_bond[i]; m++) { if (bond_type(i,m) <= 0) continue; - int atom1 = map_array(bond_atom(i,m)); + int atom1 = AtomKokkos::map_kokkos(bond_atom(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -420,7 +395,6 @@ void NeighBondKokkos::bond_check() { int flag = 0; - update_domain_variables(); atomKK->sync(execution_space, X_MASK); k_bondlist.sync(); @@ -507,9 +481,9 @@ template KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondAngleAll, const int &i, int &nmissing) const { for (int m = 0; m < num_angle[i]; m++) { - int atom1 = map_array(angle_atom1(i,m)); - int atom2 = map_array(angle_atom2(i,m)); - int atom3 = map_array(angle_atom3(i,m)); + int atom1 = AtomKokkos::map_kokkos(angle_atom1(i,m),map_style,k_map_array,k_map_hash); + int atom2 = AtomKokkos::map_kokkos(angle_atom2(i,m),map_style,k_map_array,k_map_hash); + int atom3 = AtomKokkos::map_kokkos(angle_atom3(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -602,9 +576,9 @@ KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondAnglePartial, const int &i, int &nmissing) const { for (int m = 0; m < num_angle[i]; m++) { if (angle_type(i,m) <= 0) continue; - int atom1 = map_array(angle_atom1(i,m)); - int atom2 = map_array(angle_atom2(i,m)); - int atom3 = map_array(angle_atom3(i,m)); + int atom1 = AtomKokkos::map_kokkos(angle_atom1(i,m),map_style,k_map_array,k_map_hash); + int atom2 = AtomKokkos::map_kokkos(angle_atom2(i,m),map_style,k_map_array,k_map_hash); + int atom3 = AtomKokkos::map_kokkos(angle_atom3(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -636,7 +610,6 @@ void NeighBondKokkos::angle_check() // check all 3 distances // in case angle potential computes any of them - update_domain_variables(); atomKK->sync(execution_space, X_MASK); k_anglelist.sync(); @@ -735,10 +708,10 @@ template KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondDihedralAll, const int &i, int &nmissing) const { for (int m = 0; m < num_dihedral[i]; m++) { - int atom1 = map_array(dihedral_atom1(i,m)); - int atom2 = map_array(dihedral_atom2(i,m)); - int atom3 = map_array(dihedral_atom3(i,m)); - int atom4 = map_array(dihedral_atom4(i,m)); + int atom1 = AtomKokkos::map_kokkos(dihedral_atom1(i,m),map_style,k_map_array,k_map_hash); + int atom2 = AtomKokkos::map_kokkos(dihedral_atom2(i,m),map_style,k_map_array,k_map_hash); + int atom3 = AtomKokkos::map_kokkos(dihedral_atom3(i,m),map_style,k_map_array,k_map_hash); + int atom4 = AtomKokkos::map_kokkos(dihedral_atom4(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -835,10 +808,10 @@ KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondDihedralPartial, const int &i, int &nmissing) const { for (int m = 0; m < num_dihedral[i]; m++) { if (dihedral_type(i,m) <= 0) continue; - int atom1 = map_array(dihedral_atom1(i,m)); - int atom2 = map_array(dihedral_atom2(i,m)); - int atom3 = map_array(dihedral_atom3(i,m)); - int atom4 = map_array(dihedral_atom4(i,m)); + int atom1 = AtomKokkos::map_kokkos(dihedral_atom1(i,m),map_style,k_map_array,k_map_hash); + int atom2 = AtomKokkos::map_kokkos(dihedral_atom2(i,m),map_style,k_map_array,k_map_hash); + int atom3 = AtomKokkos::map_kokkos(dihedral_atom3(i,m),map_style,k_map_array,k_map_hash); + int atom4 = AtomKokkos::map_kokkos(dihedral_atom4(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -874,7 +847,6 @@ void NeighBondKokkos::dihedral_check(int nlist, typename AT::t_int_2 // check all 6 distances // in case dihedral/improper potential computes any of them - update_domain_variables(); atomKK->sync(execution_space, X_MASK); k_dihedrallist.sync(); @@ -990,10 +962,10 @@ template KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondImproperAll, const int &i, int &nmissing) const { for (int m = 0; m < num_improper[i]; m++) { - int atom1 = map_array(improper_atom1(i,m)); - int atom2 = map_array(improper_atom2(i,m)); - int atom3 = map_array(improper_atom3(i,m)); - int atom4 = map_array(improper_atom4(i,m)); + int atom1 = AtomKokkos::map_kokkos(improper_atom1(i,m),map_style,k_map_array,k_map_hash); + int atom2 = AtomKokkos::map_kokkos(improper_atom2(i,m),map_style,k_map_array,k_map_hash); + int atom3 = AtomKokkos::map_kokkos(improper_atom3(i,m),map_style,k_map_array,k_map_hash); + int atom4 = AtomKokkos::map_kokkos(improper_atom4(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -1090,10 +1062,10 @@ KOKKOS_INLINE_FUNCTION void NeighBondKokkos::operator()(TagNeighBondImproperPartial, const int &i, int &nmissing) const { for (int m = 0; m < num_improper[i]; m++) { if (improper_type(i,m) <= 0) continue; - int atom1 = map_array(improper_atom1(i,m)); - int atom2 = map_array(improper_atom2(i,m)); - int atom3 = map_array(improper_atom3(i,m)); - int atom4 = map_array(improper_atom4(i,m)); + int atom1 = AtomKokkos::map_kokkos(improper_atom1(i,m),map_style,k_map_array,k_map_hash); + int atom2 = AtomKokkos::map_kokkos(improper_atom2(i,m),map_style,k_map_array,k_map_hash); + int atom3 = AtomKokkos::map_kokkos(improper_atom3(i,m),map_style,k_map_array,k_map_hash); + int atom4 = AtomKokkos::map_kokkos(improper_atom4(i,m),map_style,k_map_array,k_map_hash); if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) return; @@ -1137,8 +1109,8 @@ int NeighBondKokkos::closest_image(const int i, int j) const X_FLOAT rsqmin = delx*delx + dely*dely + delz*delz; X_FLOAT rsq; - while (sametag[j] >= 0) { - j = sametag[j]; + while (d_sametag[j] >= 0) { + j = d_sametag[j]; delx = xi0 - x(j,0); dely = xi1 - x(j,1); delz = xi2 - x(j,2); @@ -1218,8 +1190,10 @@ void NeighBondKokkos::minimum_image(X_FLOAT &dx, X_FLOAT &dy, X_FLOA /* ---------------------------------------------------------------------- */ template -void NeighBondKokkos::update_domain_variables() +void NeighBondKokkos::update_class_variables() { + // Domain + triclinic = domain->triclinic; xperiodic = domain->xperiodic; xprd_half = domain->xprd_half; @@ -1233,6 +1207,21 @@ void NeighBondKokkos::update_domain_variables() xy = domain->xy; xz = domain->xz; yz = domain->yz; + + // Atom Map + + map_style = atom->map_style; + + k_sametag = atomKK->k_sametag; + k_sametag.template sync(); + d_sametag = k_sametag.view(); + + if (map_style == Atom::MAP_ARRAY) { + k_map_array = atomKK->k_map_array; + k_map_array.template sync(); + } else if (map_style == Atom::MAP_HASH) { + k_map_hash = atomKK->k_map_hash; + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/neigh_bond_kokkos.h b/src/KOKKOS/neigh_bond_kokkos.h index 887ead95f6..d2e5d0fc62 100644 --- a/src/KOKKOS/neigh_bond_kokkos.h +++ b/src/KOKKOS/neigh_bond_kokkos.h @@ -19,6 +19,7 @@ #include "kokkos_type.h" #include "domain_kokkos.h" #include "pointers.h" +#include namespace LAMMPS_NS { @@ -81,13 +82,11 @@ class NeighBondKokkos : protected Pointers { int me,nprocs; private: - - - DAT::tdual_int_1d k_map_array; - typename AT::t_int_1d_randomread map_array; - + int map_style; DAT::tdual_int_1d k_sametag; - typename AT::t_int_1d_randomread sametag; + typename AT::t_int_1d d_sametag; + DAT::tdual_int_1d k_map_array; + dual_hash_type k_map_hash; typename AT::t_int_2d v_bondlist; typename AT::t_int_2d v_anglelist; @@ -130,7 +129,7 @@ class NeighBondKokkos : protected Pointers { KOKKOS_INLINE_FUNCTION void minimum_image(X_FLOAT &dx, X_FLOAT &dy, X_FLOAT &dz) const; - void update_domain_variables(); + void update_class_variables(); // topology build functions @@ -174,10 +173,6 @@ class NeighBondKokkos : protected Pointers { /* ERROR/WARNING messages: -E: Must use atom map style array with Kokkos - -See the atom_modify map command. - E: Bond atoms missing on proc %d at step %ld The 2nd atom needed to compute a particular bond is missing on this diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index e4a2b02cc0..207ff7501b 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -226,7 +226,7 @@ void NeighborKokkos::operator()(TagNeighborCheckDistance, const int /* ---------------------------------------------------------------------- build perpetuals neighbor lists called at setup and every few timesteps during run or minimization - topology lists also built if topoflag = 1, USER-CUDA calls with topoflag = 0 + topology lists also built if topoflag = 1, CUDA calls with topoflag = 0 ------------------------------------------------------------------------- */ @@ -377,7 +377,7 @@ void NeighborKokkos::init_topology() { /* ---------------------------------------------------------------------- build all topology neighbor lists every few timesteps - normally built with pair lists, but USER-CUDA separates them + normally built with pair lists, but CUDA separates them ------------------------------------------------------------------------- */ void NeighborKokkos::build_topology() { diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 1a560e2129..ef885535ed 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -64,13 +64,14 @@ class NeighborKokkos : public Neighbor { DAT::tdual_int_2d k_dihedrallist; DAT::tdual_int_2d k_improperlist; + int device_flag; + private: DAT::tdual_x_array x; DAT::tdual_x_array xhold; X_FLOAT deltasq; - int device_flag; void init_cutneighsq_kokkos(int); void create_kokkos_list(int); diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 7d6a39abe5..1110aef4a6 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -610,7 +610,9 @@ void NeighborKokkosExecute::build_ItemGPU(typename Kokkos::TeamPolic if (test) return; #else - dev.team_barrier(); + int not_done = (i >= 0 && i <= nlocal); + dev.team_reduce(Kokkos::Max(not_done)); + if(not_done == 0) return; #endif if (i >= 0 && i < nlocal) { @@ -1053,13 +1055,14 @@ void NeighborKokkosExecute::build_ItemSizeGPU(typename Kokkos::TeamP other_x[MY_II + 4 * atoms_per_bin] = radi; } other_id[MY_II] = i; - // FIXME_SYCL #ifndef KOKKOS_ENABLE_SYCL int test = (__syncthreads_count(i >= 0 && i <= nlocal) == 0); if (test) return; #else - dev.team_barrier(); + int not_done = (i >= 0 && i <= nlocal); + dev.team_reduce(Kokkos::Max(not_done)); + if(not_done == 0) return; #endif if (i >= 0 && i < nlocal) { diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index 93f8e37006..fab33d0ec7 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -13,17 +13,18 @@ ------------------------------------------------------------------------- */ #include "pair_gran_hooke_history_kokkos.h" -#include "kokkos.h" + #include "atom_kokkos.h" #include "atom_masks.h" -#include "memory_kokkos.h" +#include "error.h" +#include "fix_neigh_history_kokkos.h" #include "force.h" -#include "neighbor.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "modify.h" #include "neigh_list.h" #include "neigh_request.h" -#include "error.h" -#include "modify.h" -#include "fix_neigh_history_kokkos.h" +#include "neighbor.h" #include "update.h" using namespace LAMMPS_NS; @@ -67,20 +68,13 @@ void PairGranHookeHistoryKokkos::init_style() // this is so its order in the fix list is preserved if (history && fix_history == nullptr) { - char dnumstr[16]; - sprintf(dnumstr,"%d",3); - char **fixarg = new char*[4]; - fixarg[0] = (char *) "NEIGH_HISTORY_HH"; - fixarg[1] = (char *) "all"; + auto cmd = std::string("NEIGH_HISTORY_HH") + std::to_string(instance_me) + " all "; if (execution_space == Device) - fixarg[2] = (char *) "NEIGH_HISTORY/KK/DEVICE"; + cmd += "NEIGH_HISTORY/KK/DEVICE 3"; else - fixarg[2] = (char *) "NEIGH_HISTORY/KK/HOST"; - fixarg[3] = dnumstr; - modify->replace_fix("NEIGH_HISTORY_HH_DUMMY",4,fixarg,1); - delete [] fixarg; - int ifix = modify->find_fix("NEIGH_HISTORY_HH"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; + cmd += "NEIGH_HISTORY/KK/HOST 3"; + fix_history = (FixNeighHistory *) + modify->replace_fix("NEIGH_HISTORY_HH_DUMMY"+std::to_string(instance_me),cmd,1); fix_history->pair = this; fix_historyKK = (FixNeighHistoryKokkos *)fix_history; } diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxff_kokkos.cpp similarity index 84% rename from src/KOKKOS/pair_reaxc_kokkos.cpp rename to src/KOKKOS/pair_reaxff_kokkos.cpp index de707fba3b..aac0229f87 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxff_kokkos.cpp @@ -16,7 +16,7 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include "pair_reaxc_kokkos.h" +#include "pair_reaxff_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" @@ -28,23 +28,23 @@ #include "math_special.h" #include "neigh_request.h" #include "neighbor.h" -#include "reaxc_defs.h" -#include "reaxc_lookup.h" -#include "reaxc_tool_box.h" + +#include "reaxff_api.h" #include - #define TEAMSIZE 128 /* ---------------------------------------------------------------------- */ +using namespace ReaxFF; + namespace LAMMPS_NS { using namespace MathConst; using namespace MathSpecial; template -PairReaxCKokkos::PairReaxCKokkos(LAMMPS *lmp) : PairReaxC(lmp) +PairReaxFFKokkos::PairReaxFFKokkos(LAMMPS *lmp) : PairReaxFF(lmp) { respa_enable = 0; @@ -73,7 +73,7 @@ PairReaxCKokkos::PairReaxCKokkos(LAMMPS *lmp) : PairReaxC(lmp) /* ---------------------------------------------------------------------- */ template -PairReaxCKokkos::~PairReaxCKokkos() +PairReaxFFKokkos::~PairReaxFFKokkos() { if (copymode) return; @@ -100,28 +100,28 @@ PairReaxCKokkos::~PairReaxCKokkos() /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::allocate() +void PairReaxFFKokkos::allocate() { int n = atom->ntypes; k_params_sing = Kokkos::DualView - ("PairReaxC::params_sing",n+1); + ("PairReaxFF::params_sing",n+1); paramssing = k_params_sing.template view(); k_params_twbp = Kokkos::DualView - ("PairReaxC::params_twbp",n+1,n+1); + ("PairReaxFF::params_twbp",n+1,n+1); paramstwbp = k_params_twbp.template view(); k_params_thbp = Kokkos::DualView - ("PairReaxC::params_thbp",n+1,n+1,n+1); + ("PairReaxFF::params_thbp",n+1,n+1,n+1); paramsthbp = k_params_thbp.template view(); k_params_fbp = Kokkos::DualView - ("PairReaxC::params_fbp",n+1,n+1,n+1,n+1); + ("PairReaxFF::params_fbp",n+1,n+1,n+1,n+1); paramsfbp = k_params_fbp.template view(); k_params_hbp = Kokkos::DualView - ("PairReaxC::params_hbp",n+1,n+1,n+1); + ("PairReaxFF::params_hbp",n+1,n+1,n+1); paramshbp = k_params_hbp.template view(); k_tap = DAT::tdual_ffloat_1d("pair:tap",8); @@ -135,11 +135,11 @@ void PairReaxCKokkos::allocate() ------------------------------------------------------------------------- */ template -void PairReaxCKokkos::init_style() +void PairReaxFFKokkos::init_style() { - PairReaxC::init_style(); - if (fix_reax) modify->delete_fix(fix_id); // not needed in the Kokkos version - fix_reax = nullptr; + PairReaxFF::init_style(); + if (fix_reaxff) modify->delete_fix(fix_id); // not needed in the Kokkos version + fix_reaxff = nullptr; // irequest = neigh request made by parent class @@ -157,7 +157,7 @@ void PairReaxCKokkos::init_style() neighbor->requests[irequest]->half = 1; neighbor->requests[irequest]->ghost = 1; } else { - error->all(FLERR,"Must use half neighbor list with pair style reax/c/kk"); + error->all(FLERR,"Must use half neighbor list with pair style reaxff/kk"); } allocate(); @@ -168,21 +168,21 @@ void PairReaxCKokkos::init_style() /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::setup() +void PairReaxFFKokkos::setup() { int i,j,k,m; int n = atom->ntypes; // general parameters for (i = 0; i < 39; i ++) - gp[i] = system->reax_param.gp.l[i]; + gp[i] = api->system->reax_param.gp.l[i]; p_boc1 = gp[0]; p_boc2 = gp[1]; // vdw parameters - vdwflag = system->reax_param.gp.vdw_type; - lgflag = control->lgflag; + vdwflag = api->system->reax_param.gp.vdw_type; + lgflag = api->control->lgflag; // atom, bond, angle, dihedral, H-bond specific parameters two_body_parameters *twbp; @@ -202,38 +202,38 @@ void PairReaxCKokkos::setup() if (map[i] == -1) continue; // general - k_params_sing.h_view(i).mass = system->reax_param.sbp[map[i]].mass; + k_params_sing.h_view(i).mass = api->system->reax_param.sbp[map[i]].mass; // polarization - k_params_sing.h_view(i).chi = system->reax_param.sbp[map[i]].chi; - k_params_sing.h_view(i).eta = system->reax_param.sbp[map[i]].eta; + k_params_sing.h_view(i).chi = api->system->reax_param.sbp[map[i]].chi; + k_params_sing.h_view(i).eta = api->system->reax_param.sbp[map[i]].eta; // bond order - k_params_sing.h_view(i).r_s = system->reax_param.sbp[map[i]].r_s; - k_params_sing.h_view(i).r_pi = system->reax_param.sbp[map[i]].r_pi; - k_params_sing.h_view(i).r_pi2 = system->reax_param.sbp[map[i]].r_pi_pi; - k_params_sing.h_view(i).valency = system->reax_param.sbp[map[i]].valency; - k_params_sing.h_view(i).valency_val = system->reax_param.sbp[map[i]].valency_val; - k_params_sing.h_view(i).valency_boc = system->reax_param.sbp[map[i]].valency_boc; - k_params_sing.h_view(i).valency_e = system->reax_param.sbp[map[i]].valency_e; - k_params_sing.h_view(i).nlp_opt = system->reax_param.sbp[map[i]].nlp_opt; + k_params_sing.h_view(i).r_s = api->system->reax_param.sbp[map[i]].r_s; + k_params_sing.h_view(i).r_pi = api->system->reax_param.sbp[map[i]].r_pi; + k_params_sing.h_view(i).r_pi2 = api->system->reax_param.sbp[map[i]].r_pi_pi; + k_params_sing.h_view(i).valency = api->system->reax_param.sbp[map[i]].valency; + k_params_sing.h_view(i).valency_val = api->system->reax_param.sbp[map[i]].valency_val; + k_params_sing.h_view(i).valency_boc = api->system->reax_param.sbp[map[i]].valency_boc; + k_params_sing.h_view(i).valency_e = api->system->reax_param.sbp[map[i]].valency_e; + k_params_sing.h_view(i).nlp_opt = api->system->reax_param.sbp[map[i]].nlp_opt; // multibody - k_params_sing.h_view(i).p_lp2 = system->reax_param.sbp[map[i]].p_lp2; - k_params_sing.h_view(i).p_ovun2 = system->reax_param.sbp[map[i]].p_ovun2; - k_params_sing.h_view(i).p_ovun5 = system->reax_param.sbp[map[i]].p_ovun5; + k_params_sing.h_view(i).p_lp2 = api->system->reax_param.sbp[map[i]].p_lp2; + k_params_sing.h_view(i).p_ovun2 = api->system->reax_param.sbp[map[i]].p_ovun2; + k_params_sing.h_view(i).p_ovun5 = api->system->reax_param.sbp[map[i]].p_ovun5; // angular - k_params_sing.h_view(i).p_val3 = system->reax_param.sbp[map[i]].p_val3; - k_params_sing.h_view(i).p_val5 = system->reax_param.sbp[map[i]].p_val5; + k_params_sing.h_view(i).p_val3 = api->system->reax_param.sbp[map[i]].p_val3; + k_params_sing.h_view(i).p_val5 = api->system->reax_param.sbp[map[i]].p_val5; // hydrogen bond - k_params_sing.h_view(i).p_hbond = system->reax_param.sbp[map[i]].p_hbond; + k_params_sing.h_view(i).p_hbond = api->system->reax_param.sbp[map[i]].p_hbond; for (j = 1; j <= n; j++) { if (map[j] == -1) continue; - twbp = &(system->reax_param.tbp[map[i]][map[j]]); + twbp = &(api->system->reax_param.tbp[map[i]][map[j]]); // vdW k_params_twbp.h_view(i,j).gamma = twbp->gamma; @@ -277,7 +277,7 @@ void PairReaxCKokkos::setup() if (map[k] == -1) continue; // Angular - thbh = &(system->reax_param.thbp[map[i]][map[j]][map[k]]); + thbh = &(api->system->reax_param.thbp[map[i]][map[j]][map[k]]); thbp = &(thbh->prm[0]); k_params_thbp.h_view(i,j,k).cnt = thbh->cnt; k_params_thbp.h_view(i,j,k).theta_00 = thbp->theta_00; @@ -289,7 +289,7 @@ void PairReaxCKokkos::setup() k_params_thbp.h_view(i,j,k).p_coa1 = thbp->p_coa1; // Hydrogen Bond - hbp = &(system->reax_param.hbp[map[i]][map[j]][map[k]]); + hbp = &(api->system->reax_param.hbp[map[i]][map[j]][map[k]]); k_params_hbp.h_view(i,j,k).p_hb1 = hbp->p_hb1; k_params_hbp.h_view(i,j,k).p_hb2 = hbp->p_hb2; k_params_hbp.h_view(i,j,k).p_hb3 = hbp->p_hb3; @@ -299,7 +299,7 @@ void PairReaxCKokkos::setup() if (map[m] == -1) continue; // Torsion - fbh = &(system->reax_param.fbp[map[i]][map[j]][map[k]][map[m]]); + fbh = &(api->system->reax_param.fbp[map[i]][map[j]][map[k]][map[m]]); fbp = &(fbh->prm[0]); k_params_fbp.h_view(i,j,k,m).p_tor1 = fbp->p_tor1; k_params_fbp.h_view(i,j,k,m).p_cot1 = fbp->p_cot1; @@ -317,13 +317,13 @@ void PairReaxCKokkos::setup() k_params_hbp.template modify(); // cutoffs - cut_nbsq = control->nonb_cut * control->nonb_cut; - cut_hbsq = control->hbond_cut * control->hbond_cut; - cut_bosq = control->bond_cut * control->bond_cut; + cut_nbsq = api->control->nonb_cut * api->control->nonb_cut; + cut_hbsq = api->control->hbond_cut * api->control->hbond_cut; + cut_bosq = api->control->bond_cut * api->control->bond_cut; // bond order cutoffs bo_cut = 0.01 * gp[29]; - thb_cut = control->thb_cut; + thb_cut = api->control->thb_cut; thb_cutsq = 0.000010; //thb_cut*thb_cut; if (atom->nmax > nmax) { @@ -335,26 +335,24 @@ void PairReaxCKokkos::setup() /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::init_md() +void PairReaxFFKokkos::init_md() { // init_taper() F_FLOAT d1, d7, swa, swa2, swa3, swb, swb2, swb3; - LR_lookup_table ** & LR = system->LR; + LR_lookup_table ** & LR = api->system->LR; - swa = control->nonb_low; - swb = control->nonb_cut; - enobondsflag = control->enobondsflag; + swa = api->control->nonb_low; + swb = api->control->nonb_cut; + enobondsflag = api->control->enobondsflag; - if (fabs(swa) > 0.01 ) + if (fabs(swa) > 0.01) error->warning(FLERR,"Warning: non-zero lower Taper-radius cutoff"); if (swb < 0) error->one(FLERR,"Negative upper Taper-radius cutoff"); - else if (swb < 5) { - char str[128]; - sprintf(str,"Warning: very low Taper-radius cutoff: %f\n", swb); - error->one(FLERR,str); - } + else if (swb < 5) + error->one(FLERR,fmt::format("Warning: very low Taper-radius cutoff: " + "{}\n", swb)); d1 = swb - swa; d7 = powint(d1,7); @@ -366,18 +364,18 @@ void PairReaxCKokkos::init_md() k_tap.h_view(7) = 20.0/d7; k_tap.h_view(6) = -70.0 * (swa + swb) / d7; k_tap.h_view(5) = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7; - k_tap.h_view(4) = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3 ) / d7; - k_tap.h_view(3) = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7; + k_tap.h_view(4) = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3) / d7; + k_tap.h_view(3) = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3) / d7; k_tap.h_view(2) =-210.0 * (swa3*swb2 + swa2*swb3) / d7; k_tap.h_view(1) = 140.0 * swa3 * swb3 / d7; k_tap.h_view(0) = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 - - 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7; + 7.0*swa*swb3*swb3 + swb3*swb3*swb) / d7; k_tap.template modify(); k_tap.template sync(); - if (control->tabulate) { + if (api->control->tabulate) { int ntypes = atom->ntypes; Init_Lookup_Tables(); @@ -432,14 +430,14 @@ void PairReaxCKokkos::init_md() /* ---------------------------------------------------------------------- */ template -int PairReaxCKokkos::Init_Lookup_Tables() +int PairReaxFFKokkos::Init_Lookup_Tables() { int i, j, r; int num_atom_types; double dr; double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; double v0_vdw, v0_ele, vlast_vdw, vlast_ele; - LR_lookup_table ** & LR = system->LR; + LR_lookup_table ** & LR = api->system->LR; /* initializations */ v0_vdw = 0; @@ -448,49 +446,49 @@ int PairReaxCKokkos::Init_Lookup_Tables() vlast_ele = 0; num_atom_types = atom->ntypes; - dr = control->nonb_cut / control->tabulate; + dr = api->control->nonb_cut / api->control->tabulate; h = (double*) - smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h"); + smalloc(api->control->error_ptr, (api->control->tabulate+2) * sizeof(double), "lookup:h"); fh = (double*) - smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh"); + smalloc(api->control->error_ptr, (api->control->tabulate+2) * sizeof(double), "lookup:fh"); fvdw = (double*) - smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw"); + smalloc(api->control->error_ptr, (api->control->tabulate+2) * sizeof(double), "lookup:fvdw"); fCEvd = (double*) - smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd"); + smalloc(api->control->error_ptr, (api->control->tabulate+2) * sizeof(double), "lookup:fCEvd"); fele = (double*) - smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele"); + smalloc(api->control->error_ptr, (api->control->tabulate+2) * sizeof(double), "lookup:fele"); fCEclmb = (double*) - smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); + smalloc(api->control->error_ptr, (api->control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); LR = (LR_lookup_table**) - scalloc( control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table*), "lookup:LR"); + scalloc(api->control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table*), "lookup:LR"); for (i = 0; i < num_atom_types+1; ++i) LR[i] = (LR_lookup_table*) - scalloc( control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table), "lookup:LR[i]"); + scalloc(api->control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table), "lookup:LR[i]"); for (i = 1; i <= num_atom_types; ++i) { for (j = i; j <= num_atom_types; ++j) { LR[i][j].xmin = 0; - LR[i][j].xmax = control->nonb_cut; - LR[i][j].n = control->tabulate + 2; + LR[i][j].xmax = api->control->nonb_cut; + LR[i][j].n = api->control->tabulate + 2; LR[i][j].dx = dr; - LR[i][j].inv_dx = control->tabulate / control->nonb_cut; + LR[i][j].inv_dx = api->control->tabulate / api->control->nonb_cut; LR[i][j].y = (LR_data*) - smalloc( control->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); + smalloc(api->control->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); LR[i][j].H = (cubic_spline_coef*) - smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); + smalloc(api->control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); LR[i][j].vdW = (cubic_spline_coef*) - smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); + smalloc(api->control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); LR[i][j].CEvd = (cubic_spline_coef*) - smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); + smalloc(api->control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); LR[i][j].ele = (cubic_spline_coef*) - smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); + smalloc(api->control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); LR[i][j].CEclmb = (cubic_spline_coef*) - smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), + smalloc(api->control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), "lookup:LR[i,j].CEclmb"); - for (r = 1; r <= control->tabulate; ++r) { - LR_vdW_Coulomb(i, j, r * dr, &(LR[i][j].y[r]) ); + for (r = 1; r <= api->control->tabulate; ++r) { + LR_vdW_Coulomb(i, j, r * dr, &(LR[i][j].y[r])); h[r] = LR[i][j].dx; fh[r] = LR[i][j].y[r].H; fvdw[r] = LR[i][j].y[r].e_vdW; @@ -511,20 +509,20 @@ int PairReaxCKokkos::Init_Lookup_Tables() vlast_vdw = fCEvd[r-1]; vlast_ele = fele[r-1]; - Natural_Cubic_Spline( control->error_ptr, &h[1], &fh[1], - &(LR[i][j].H[1]), control->tabulate+1 ); + Natural_Cubic_Spline(api->control->error_ptr, &h[1], &fh[1], + &(LR[i][j].H[1]), api->control->tabulate+1); - Complete_Cubic_Spline( control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, - &(LR[i][j].vdW[1]), control->tabulate+1 ); + Complete_Cubic_Spline(api->control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, + &(LR[i][j].vdW[1]), api->control->tabulate+1); - Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEvd[1], - &(LR[i][j].CEvd[1]), control->tabulate+1 ); + Natural_Cubic_Spline(api->control->error_ptr, &h[1], &fCEvd[1], + &(LR[i][j].CEvd[1]), api->control->tabulate+1); - Complete_Cubic_Spline( control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, - &(LR[i][j].ele[1]), control->tabulate+1 ); + Complete_Cubic_Spline(api->control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, + &(LR[i][j].ele[1]), api->control->tabulate+1); - Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEclmb[1], - &(LR[i][j].CEclmb[1]), control->tabulate+1 ); + Natural_Cubic_Spline(api->control->error_ptr, &h[1], &fCEclmb[1], + &(LR[i][j].CEclmb[1]), api->control->tabulate+1); } } free(h); @@ -540,11 +538,11 @@ int PairReaxCKokkos::Init_Lookup_Tables() /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::Deallocate_Lookup_Tables() +void PairReaxFFKokkos::Deallocate_Lookup_Tables() { int i, j; int ntypes; - LR_lookup_table ** & LR = system->LR; + LR_lookup_table ** & LR = api->system->LR; ntypes = atom->ntypes; @@ -553,25 +551,25 @@ void PairReaxCKokkos::Deallocate_Lookup_Tables() for (j = i; j <= ntypes; ++j) { if (map[i] == -1) continue; if (LR[i][j].n) { - sfree( control->error_ptr, LR[i][j].y, "LR[i,j].y" ); - sfree( control->error_ptr, LR[i][j].H, "LR[i,j].H" ); - sfree( control->error_ptr, LR[i][j].vdW, "LR[i,j].vdW" ); - sfree( control->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd" ); - sfree( control->error_ptr, LR[i][j].ele, "LR[i,j].ele" ); - sfree( control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" ); + sfree(api->control->error_ptr, LR[i][j].y, "LR[i,j].y"); + sfree(api->control->error_ptr, LR[i][j].H, "LR[i,j].H"); + sfree(api->control->error_ptr, LR[i][j].vdW, "LR[i,j].vdW"); + sfree(api->control->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd"); + sfree(api->control->error_ptr, LR[i][j].ele, "LR[i,j].ele"); + sfree(api->control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb"); } } - sfree( control->error_ptr, LR[i], "LR[i]" ); + sfree(api->control->error_ptr, LR[i], "LR[i]"); } - sfree( control->error_ptr, LR, "LR" ); + sfree(api->control->error_ptr, LR, "LR"); } /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_data *lr ) +void PairReaxFFKokkos::LR_vdW_Coulomb(int i, int j, double r_ij, LR_data *lr) { - double p_vdW1 = system->reax_param.gp.l[28]; + double p_vdW1 = api->system->reax_param.gp.l[28]; double p_vdW1i = 1.0 / p_vdW1; double powr_vdW1, powgi_vdW1; double tmp, fn13, exp1, exp2; @@ -581,7 +579,7 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ double e_lg, de_lg, r_ij5, r_ij6, re6; two_body_parameters *twbp; - twbp = &(system->reax_param.tbp[map[i]][map[j]]); + twbp = &(api->system->reax_param.tbp[map[i]][map[j]]); e_core = 0; de_core = 0; e_lg = de_lg = 0.0; @@ -603,32 +601,32 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ dTap += k_tap.h_view[1]/r_ij; /*vdWaals Calculations*/ - if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) + if (api->system->reax_param.gp.vdw_type==1 || api->system->reax_param.gp.vdw_type==3) { // shielding powr_vdW1 = pow(r_ij, p_vdW1); - powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1); + powgi_vdW1 = pow(1.0 / twbp->gamma_w, p_vdW1); - fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i ); - exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); + fn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i); + exp1 = exp(twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2); - dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i-1.0) * pow(r_ij, p_vdW1-2.0); + dfn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i-1.0) * pow(r_ij, p_vdW1-2.0); lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } else { // no shielding - exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); + exp1 = exp(twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2); lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; } - if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) + if (api->system->reax_param.gp.vdw_type==2 || api->system->reax_param.gp.vdw_type==3) { // inner wall e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); lr->e_vdW += Tap * e_core; @@ -637,14 +635,14 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ lr->CEvd += dTap * e_core + Tap * de_core / r_ij; // lg correction, only if lgvdw is yes - if (control->lgflag) { - r_ij5 = powint( r_ij, 5 ); - r_ij6 = powint( r_ij, 6 ); - re6 = powint( twbp->lgre, 6 ); - e_lg = -(twbp->lgcij/( r_ij6 + re6 )); + if (api->control->lgflag) { + r_ij5 = powint(r_ij, 5); + r_ij6 = powint(r_ij, 6); + re6 = powint(twbp->lgre, 6); + e_lg = -(twbp->lgcij/(r_ij6 + re6)); lr->e_vdW += Tap * e_lg; - de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ; + de_lg = -6.0 * e_lg * r_ij5 / (r_ij6 + re6) ; lr->CEvd += dTap * e_lg + Tap * de_lg/r_ij; } @@ -652,20 +650,20 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ /* Coulomb calculations */ - dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma ); - dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); + dr3gamij_1 = (r_ij * r_ij * r_ij + twbp->gamma); + dr3gamij_3 = pow(dr3gamij_1 , 0.33333333333333); tmp = Tap / dr3gamij_3; lr->H = EV_to_KCALpMOL * tmp; lr->e_ele = C_ele * tmp; - lr->CEclmb = C_ele * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; + lr->CEclmb = C_ele * (dTap - Tap * r_ij / dr3gamij_1) / dr3gamij_3; } /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::compute(int eflag_in, int vflag_in) +void PairReaxFFKokkos::compute(int eflag_in, int vflag_in) { copymode = 1; @@ -726,42 +724,42 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // Polarization (self) if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); } else { //if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); } ev_all += ev; pvector[13] = ev.ecoul; // LJ + Coulomb - if (control->tabulate) { + if (api->control->tabulate) { if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); } else if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); } } else { if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); } else if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); } } ev_all += ev; @@ -855,34 +853,34 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // Bond energy if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; pvector[0] = ev.evdwl; } else { //if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; pvector[0] = ev.evdwl; } // Multi-body corrections if (neighflag == HALF) { - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } else { //if (neighflag == HALFTHREAD) { - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } pvector[2] = ev.ereax[0]; @@ -893,15 +891,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // Angular if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } else { //if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } pvector[4] = ev.ereax[3]; @@ -912,15 +910,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // Torsion if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } else { //if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } pvector[8] = ev.ereax[6]; @@ -931,15 +929,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (cut_hbsq > 0.0) { if (neighflag == HALF) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } else { //if (neighflag == HALFTHREAD) { if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,inum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,inum),*this); ev_all += ev; } } @@ -971,9 +969,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) //} if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); ev_all += ev; pvector[0] += ev.evdwl; } else { //if (neighflag == HALFTHREAD) { @@ -987,9 +985,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) //} if (evflag) - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); ev_all += ev; pvector[0] += ev.evdwl; } @@ -1051,7 +1049,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputePolar, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputePolar, const int &ii, EV_FLOAT_REAX& ev) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -1069,9 +1067,9 @@ void PairReaxCKokkos::operator()(PairReaxComputePolar template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputePolar, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputePolar, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputePolar(), ii, ev); + this->template operator()(PairReaxFFComputePolar(), ii, ev); } @@ -1080,7 +1078,7 @@ void PairReaxCKokkos::operator()(PairReaxComputePolar template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial @@ -1222,9 +1220,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeLJCoulomb, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeLJCoulomb(), ii, ev); + this->template operator()(PairReaxFFComputeLJCoulomb(), ii, ev); } /* ---------------------------------------------------------------------- */ @@ -1232,7 +1230,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeTabulatedLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial @@ -1279,8 +1277,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb cut_nbsq) continue; const F_FLOAT rij = sqrt(rsq); - const int tmin = MIN( itype, jtype ); - const int tmax = MAX( itype, jtype ); + const int tmin = MIN(itype, jtype); + const int tmax = MAX(itype, jtype); const LR_lookup_table_kk& t = d_LR(tmin,tmax); @@ -1329,84 +1327,84 @@ void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeTabulatedLJCoulomb, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeTabulatedLJCoulomb(), ii, ev); + this->template operator()(PairReaxFFComputeTabulatedLJCoulomb(), ii, ev); } /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::allocate_array() +void PairReaxFFKokkos::allocate_array() { if (cut_hbsq > 0.0) { - d_hb_first = typename AT::t_int_1d("reax/c/kk:hb_first",nmax); - d_hb_num = typename AT::t_int_1d("reax/c/kk:hb_num",nmax); - d_hb_list = typename AT::t_int_1d("reax/c/kk:hb_list",nmax*maxhb); + d_hb_first = typename AT::t_int_1d("reaxff/kk:hb_first",nmax); + d_hb_num = typename AT::t_int_1d("reaxff/kk:hb_num",nmax); + d_hb_list = typename AT::t_int_1d("reaxff/kk:hb_list",nmax*maxhb); } - d_bo_first = typename AT::t_int_1d("reax/c/kk:bo_first",nmax); - d_bo_num = typename AT::t_int_1d("reax/c/kk:bo_num",nmax); - d_bo_list = typename AT::t_int_1d("reax/c/kk:bo_list",nmax*maxbo); + d_bo_first = typename AT::t_int_1d("reaxff/kk:bo_first",nmax); + d_bo_num = typename AT::t_int_1d("reaxff/kk:bo_num",nmax); + d_bo_list = typename AT::t_int_1d("reaxff/kk:bo_list",nmax*maxbo); - d_BO = typename AT::t_ffloat_2d_dl("reax/c/kk:BO",nmax,maxbo); - d_BO_s = typename AT::t_ffloat_2d_dl("reax/c/kk:BO",nmax,maxbo); - d_BO_pi = typename AT::t_ffloat_2d_dl("reax/c/kk:BO_pi",nmax,maxbo); - d_BO_pi2 = typename AT::t_ffloat_2d_dl("reax/c/kk:BO_pi2",nmax,maxbo); + d_BO = typename AT::t_ffloat_2d_dl("reaxff/kk:BO",nmax,maxbo); + d_BO_s = typename AT::t_ffloat_2d_dl("reaxff/kk:BO",nmax,maxbo); + d_BO_pi = typename AT::t_ffloat_2d_dl("reaxff/kk:BO_pi",nmax,maxbo); + d_BO_pi2 = typename AT::t_ffloat_2d_dl("reaxff/kk:BO_pi2",nmax,maxbo); - d_dln_BOp_pix = typename AT::t_ffloat_2d_dl("reax/c/kk:d_dln_BOp_pix",nmax,maxbo); - d_dln_BOp_piy = typename AT::t_ffloat_2d_dl("reax/c/kk:d_dln_BOp_piy",nmax,maxbo); - d_dln_BOp_piz = typename AT::t_ffloat_2d_dl("reax/c/kk:d_dln_BOp_piz",nmax,maxbo); + d_dln_BOp_pix = typename AT::t_ffloat_2d_dl("reaxff/kk:d_dln_BOp_pix",nmax,maxbo); + d_dln_BOp_piy = typename AT::t_ffloat_2d_dl("reaxff/kk:d_dln_BOp_piy",nmax,maxbo); + d_dln_BOp_piz = typename AT::t_ffloat_2d_dl("reaxff/kk:d_dln_BOp_piz",nmax,maxbo); - d_dln_BOp_pi2x = typename AT::t_ffloat_2d_dl("reax/c/kk:d_dln_BOp_pi2x",nmax,maxbo); - d_dln_BOp_pi2y = typename AT::t_ffloat_2d_dl("reax/c/kk:d_dln_BOp_pi2y",nmax,maxbo); - d_dln_BOp_pi2z = typename AT::t_ffloat_2d_dl("reax/c/kk:d_dln_BOp_pi2z",nmax,maxbo); + d_dln_BOp_pi2x = typename AT::t_ffloat_2d_dl("reaxff/kk:d_dln_BOp_pi2x",nmax,maxbo); + d_dln_BOp_pi2y = typename AT::t_ffloat_2d_dl("reaxff/kk:d_dln_BOp_pi2y",nmax,maxbo); + d_dln_BOp_pi2z = typename AT::t_ffloat_2d_dl("reaxff/kk:d_dln_BOp_pi2z",nmax,maxbo); - d_C1dbo = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C1dbo",nmax,maxbo); - d_C2dbo = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C2dbo",nmax,maxbo); - d_C3dbo = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C3dbo",nmax,maxbo); + d_C1dbo = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C1dbo",nmax,maxbo); + d_C2dbo = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C2dbo",nmax,maxbo); + d_C3dbo = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C3dbo",nmax,maxbo); - d_C1dbopi = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C1dbopi",nmax,maxbo); - d_C2dbopi = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C2dbopi",nmax,maxbo); - d_C3dbopi = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C3dbopi",nmax,maxbo); - d_C4dbopi = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C4dbopi",nmax,maxbo); + d_C1dbopi = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C1dbopi",nmax,maxbo); + d_C2dbopi = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C2dbopi",nmax,maxbo); + d_C3dbopi = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C3dbopi",nmax,maxbo); + d_C4dbopi = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C4dbopi",nmax,maxbo); - d_C1dbopi2 = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C1dbopi2",nmax,maxbo); - d_C2dbopi2 = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C2dbopi2",nmax,maxbo); - d_C3dbopi2 = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C3dbopi2",nmax,maxbo); - d_C4dbopi2 = typename AT::t_ffloat_2d_dl("reax/c/kk:d_C4dbopi2",nmax,maxbo); + d_C1dbopi2 = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C1dbopi2",nmax,maxbo); + d_C2dbopi2 = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C2dbopi2",nmax,maxbo); + d_C3dbopi2 = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C3dbopi2",nmax,maxbo); + d_C4dbopi2 = typename AT::t_ffloat_2d_dl("reaxff/kk:d_C4dbopi2",nmax,maxbo); - d_dBOpx = typename AT::t_ffloat_2d_dl("reax/c/kk:dBOpx",nmax,maxbo); - d_dBOpy = typename AT::t_ffloat_2d_dl("reax/c/kk:dBOpy",nmax,maxbo); - d_dBOpz = typename AT::t_ffloat_2d_dl("reax/c/kk:dBOpz",nmax,maxbo); + d_dBOpx = typename AT::t_ffloat_2d_dl("reaxff/kk:dBOpx",nmax,maxbo); + d_dBOpy = typename AT::t_ffloat_2d_dl("reaxff/kk:dBOpy",nmax,maxbo); + d_dBOpz = typename AT::t_ffloat_2d_dl("reaxff/kk:dBOpz",nmax,maxbo); - d_dDeltap_self = typename AT::t_ffloat_2d_dl("reax/c/kk:dDeltap_self",nmax,3); - d_Deltap_boc = typename AT::t_ffloat_1d("reax/c/kk:Deltap_boc",nmax); - d_Deltap = typename AT::t_ffloat_1d("reax/c/kk:Deltap",nmax); - d_total_bo = typename AT::t_ffloat_1d("reax/c/kk:total_bo",nmax); + d_dDeltap_self = typename AT::t_ffloat_2d_dl("reaxff/kk:dDeltap_self",nmax,3); + d_Deltap_boc = typename AT::t_ffloat_1d("reaxff/kk:Deltap_boc",nmax); + d_Deltap = typename AT::t_ffloat_1d("reaxff/kk:Deltap",nmax); + d_total_bo = typename AT::t_ffloat_1d("reaxff/kk:total_bo",nmax); - d_Cdbo = typename AT::t_ffloat_2d_dl("reax/c/kk:Cdbo",nmax,3*maxbo); - d_Cdbopi = typename AT::t_ffloat_2d_dl("reax/c/kk:Cdbopi",nmax,3*maxbo); - d_Cdbopi2 = typename AT::t_ffloat_2d_dl("reax/c/kk:Cdbopi2",nmax,3*maxbo); + d_Cdbo = typename AT::t_ffloat_2d_dl("reaxff/kk:Cdbo",nmax,3*maxbo); + d_Cdbopi = typename AT::t_ffloat_2d_dl("reaxff/kk:Cdbopi",nmax,3*maxbo); + d_Cdbopi2 = typename AT::t_ffloat_2d_dl("reaxff/kk:Cdbopi2",nmax,3*maxbo); - d_Delta = typename AT::t_ffloat_1d("reax/c/kk:Delta",nmax); - d_Delta_boc = typename AT::t_ffloat_1d("reax/c/kk:Delta_boc",nmax); - d_dDelta_lp = typename AT::t_ffloat_1d("reax/c/kk:dDelta_lp",nmax); - d_Delta_lp = typename AT::t_ffloat_1d("reax/c/kk:Delta_lp",nmax); - d_Delta_lp_temp = typename AT::t_ffloat_1d("reax/c/kk:Delta_lp_temp",nmax); - d_CdDelta = typename AT::t_ffloat_1d("reax/c/kk:CdDelta",nmax); - d_sum_ovun = typename AT::t_ffloat_2d_dl("reax/c/kk:sum_ovun",nmax,3); + d_Delta = typename AT::t_ffloat_1d("reaxff/kk:Delta",nmax); + d_Delta_boc = typename AT::t_ffloat_1d("reaxff/kk:Delta_boc",nmax); + d_dDelta_lp = typename AT::t_ffloat_1d("reaxff/kk:dDelta_lp",nmax); + d_Delta_lp = typename AT::t_ffloat_1d("reaxff/kk:Delta_lp",nmax); + d_Delta_lp_temp = typename AT::t_ffloat_1d("reaxff/kk:Delta_lp_temp",nmax); + d_CdDelta = typename AT::t_ffloat_1d("reaxff/kk:CdDelta",nmax); + d_sum_ovun = typename AT::t_ffloat_2d_dl("reaxff/kk:sum_ovun",nmax,3); - // FixReaxCBonds - d_abo = typename AT::t_ffloat_2d("reax/c/kk:abo",nmax,maxbo); - d_neighid = typename AT::t_tagint_2d("reax/c/kk:neighid",nmax,maxbo); - d_numneigh_bonds = typename AT::t_int_1d("reax/c/kk:numneigh_bonds",nmax); + // FixReaxFFBonds + d_abo = typename AT::t_ffloat_2d("reaxff/kk:abo",nmax,maxbo); + d_neighid = typename AT::t_tagint_2d("reaxff/kk:neighid",nmax,maxbo); + d_numneigh_bonds = typename AT::t_int_1d("reaxff/kk:numneigh_bonds",nmax); } /* ---------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxZero, const int &n) const { +void PairReaxFFKokkos::operator()(PairReaxZero, const int &n) const { d_total_bo(n) = 0.0; d_CdDelta(n) = 0.0; d_bo_num(n) = 0.0; @@ -1417,13 +1415,13 @@ void PairReaxCKokkos::operator()(PairReaxZero, const int &n) const { template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxZeroEAtom, const int &i) const { +void PairReaxFFKokkos::operator()(PairReaxZeroEAtom, const int &i) const { d_eatom(i) = 0.0; } template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxZeroVAtom, const int &i) const { +void PairReaxFFKokkos::operator()(PairReaxZeroVAtom, const int &i) const { d_vatom(i,0) = 0.0; d_vatom(i,1) = 0.0; d_vatom(i,2) = 0.0; @@ -1436,7 +1434,7 @@ void PairReaxCKokkos::operator()(PairReaxZeroVAtom, const int &i) co template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxBuildListsFull, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxBuildListsFull, const int &ii) const { if (d_resize_bo() || d_resize_hb()) return; @@ -1594,7 +1592,7 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsFull, const int & template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxBuildListsHalf, const int &ii) const { if (d_resize_bo() || d_resize_hb()) return; @@ -1668,7 +1666,7 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, } d_hb_list[j_index] = j; - } else if ( j < nlocal && ihb == 2 && jhb == 1) { + } else if (j < nlocal && ihb == 2 && jhb == 1) { if (NEIGHFLAG == HALF) { i_index = d_hb_first[j] + d_hb_num[j]; d_hb_num[j]++; @@ -1807,7 +1805,7 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxBondOrder1, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxBondOrder1, const int &ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -1821,7 +1819,7 @@ void PairReaxCKokkos::operator()(PairReaxBondOrder1, const int &ii) template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxBondOrder2, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxBondOrder2, const int &ii) const { F_FLOAT exp_p1i, exp_p2i, exp_p1j, exp_p2j, f1, f2, f3, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji; F_FLOAT f4, f5, exp_f4, exp_f5, f4f5, Cf45_ij, Cf45_ji; @@ -1883,7 +1881,7 @@ void PairReaxCKokkos::operator()(PairReaxBondOrder2, const int &ii) (-p_boc1 * exp_p1i + exp_p2i / (exp_p2i + exp_p2j)) + -p_boc1 * exp_p1i / u1_ji - ((val_j+f2) / (u1_ji*u1_ji)) * (-p_boc1 * exp_p1i + exp_p2i / (exp_p2i + exp_p2j))); - Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j + Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j ); + Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j + Cf1B_ij * exp_p2j / (exp_p2i + exp_p2j); } else { f1 = 1.0; Cf1_ij = Cf1_ji = 0.0; @@ -1955,7 +1953,7 @@ void PairReaxCKokkos::operator()(PairReaxBondOrder2, const int &ii) template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxBondOrder3, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxBondOrder3, const int &ii) const { // bot part of BO() const int i = d_ilist[ii]; @@ -1991,7 +1989,7 @@ void PairReaxCKokkos::operator()(PairReaxBondOrder3, const int &ii) template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeMulti1, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeMulti1, const int &ii) const { const int i = d_ilist[ii]; const int itype = type(i); @@ -2025,7 +2023,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti1 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); auto a_CdDelta = v_CdDelta.template access::value>(); @@ -2053,7 +2051,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2::operator()(PairReaxComputeMulti2template e_tally(ev,i,i,e_lp); // over coordination - const F_FLOAT exp_ovun1 = p_ovun3 * exp( p_ovun4 * d_sum_ovun(i,2) ); + const F_FLOAT exp_ovun1 = p_ovun3 * exp(p_ovun4 * d_sum_ovun(i,2)); const F_FLOAT inv_exp_ovun1 = 1.0 / (1 + exp_ovun1); const F_FLOAT Delta_lpcorr = d_Delta[i] - (dfvl * d_Delta_lp_temp[i]) * inv_exp_ovun1; - const F_FLOAT exp_ovun2 = exp( p_ovun2 * Delta_lpcorr ); + const F_FLOAT exp_ovun2 = exp(p_ovun2 * Delta_lpcorr); const F_FLOAT inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2); const F_FLOAT DlpVi = 1.0 / (Delta_lpcorr + val_i + 1e-8); @@ -2088,14 +2086,14 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2template e_tally(ev,i,i,e_ov); CEover2 = d_sum_ovun(i,1) * DlpVi * inv_exp_ovun2 * - (1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 )); - CEover3 = CEover2 * (1.0 - dfvl * d_dDelta_lp[i] * inv_exp_ovun1 ); + (1.0 - Delta_lpcorr * (DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2)); + CEover3 = CEover2 * (1.0 - dfvl * d_dDelta_lp[i] * inv_exp_ovun1); CEover4 = CEover2 * (dfvl * d_Delta_lp_temp[i]) * p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1); // under coordination const F_FLOAT exp_ovun2n = 1.0 / exp_ovun2; - const F_FLOAT exp_ovun6 = exp( p_ovun6 * Delta_lpcorr ); + const F_FLOAT exp_ovun6 = exp(p_ovun6 * Delta_lpcorr); const F_FLOAT exp_ovun8 = p_ovun7 * exp(p_ovun8 * d_sum_ovun(i,2)); const F_FLOAT inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n); const F_FLOAT inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8); @@ -2109,7 +2107,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2template e_tally(ev,i,i,e_un); CEunder1 = inv_exp_ovun2n * - ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 + p_ovun2 * e_un * exp_ovun2n ); + (p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 + p_ovun2 * e_un * exp_ovun2n); CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8; CEunder3 = CEunder1 * (1.0 - dfvl * d_dDelta_lp[i] * inv_exp_ovun1); CEunder4 = CEunder1 * (dfvl * d_Delta_lp_temp[i]) * @@ -2166,9 +2164,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeMulti2, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeMulti2(), ii, ev); + this->template operator()(PairReaxFFComputeMulti2(), ii, ev); } @@ -2177,7 +2175,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -2245,7 +2243,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular::operator()(PairReaxComputeAngular 0.0 && SBO <= 1.0) { - SBO2 = pow( SBO, p_val9 ); - CSBO2 = p_val9 * pow( SBO, p_val9 - 1.0 ); + SBO2 = pow(SBO, p_val9); + CSBO2 = p_val9 * pow(SBO, p_val9 - 1.0); } else if (SBO > 1.0 && SBO < 2.0) { - SBO2 = 2.0 - pow( 2.0-SBO, p_val9 ); - CSBO2 = p_val9 * pow( 2.0 - SBO, p_val9 - 1.0 ); + SBO2 = 2.0 - pow(2.0-SBO, p_val9); + CSBO2 = p_val9 * pow(2.0 - SBO, p_val9 - 1.0); } else { SBO2 = 2.0; CSBO2 = 0.0; } - expval6 = exp( p_val6 * d_Delta_boc[i] ); + expval6 = exp(p_val6 * d_Delta_boc[i]); F_FLOAT CdDelta_i = 0.0; F_FLOAT fitmp[3],fjtmp[3]; @@ -2352,21 +2350,21 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular= 0) expval12theta = p_val1 * (1.0 - expval2theta); else // To avoid linear Me-H-Me angles (6/6/06) @@ -2376,7 +2374,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular::operator()(PairReaxComputeAngular::operator()(PairReaxComputeAngular::operator()(PairReaxComputeAngular template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeAngular, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeAngular(), ii, ev); + this->template operator()(PairReaxFFComputeAngular(), ii, ev); } @@ -2489,7 +2487,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeTorsion, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeTorsion, const int &ii, EV_FLOAT_REAX& ev) const { auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -2499,7 +2497,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion::value,Kokkos::MemoryTraits::value> > a_Cdbo = d_Cdbo; //auto a_Cdbo = dup_Cdbo.template access::value>(); - // in reaxc_torsion_angles: j = i, k = j, i = k; + // in reaxff_torsion_angles: j = i, k = j, i = k; F_FLOAT Delta_i, Delta_j, bo_ij, bo_ik, bo_jl, BOA_ij, BOA_ik, BOA_jl; F_FLOAT p_tor1, p_cot1, V1, V2, V3; @@ -2566,10 +2564,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion::operator()(PairReaxComputeTorsion= 0 && sin_ijk <= 1e-10) tan_ijk_i = cos_ijk / 1e-10; else if (sin_ijk <= 0 && sin_ijk >= -1e-10) tan_ijk_i = -cos_ijk / 1e-10; else tan_ijk_i = cos_ijk / sin_ijk; - exp_tor2_ik = exp( -p_tor2 * BOA_ik ); - exp_cot2_ik = exp( -p_cot2 * SQR(BOA_ik -1.5) ); + exp_tor2_ik = exp(-p_tor2 * BOA_ik); + exp_cot2_ik = exp(-p_cot2 * SQR(BOA_ik -1.5)); for (int l = 0; l < 3; l++) fktmp[l] = 0.0; @@ -2651,7 +2649,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion= 0 && sin_jil <= 1e-10) tan_jil_i = cos_jil / 1e-10; else if (sin_jil <= 0 && sin_jil >= -1e-10) @@ -2679,13 +2677,13 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion::operator()(PairReaxComputeTorsion::operator()(PairReaxComputeTorsion::operator()(PairReaxComputeTorsion template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeTorsion, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeTorsion, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeTorsion(), ii, ev); + this->template operator()(PairReaxFFComputeTorsion(), ii, ev); } @@ -2864,7 +2862,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -3000,9 +2998,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeHydrogen template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeHydrogen, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeHydrogen(), ii, ev); + this->template operator()(PairReaxFFComputeHydrogen(), ii, ev); } @@ -3011,7 +3009,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeHydrogen template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxUpdateBond, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxUpdateBond, const int &ii) const { Kokkos::View::value,Kokkos::MemoryTraits::value> > a_Cdbo = d_Cdbo; Kokkos::View::value,Kokkos::MemoryTraits::value> > a_Cdbopi = d_Cdbopi; @@ -3063,10 +3061,9 @@ void PairReaxCKokkos::operator()(PairReaxUpdateBond, cons template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeBond1, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeBond1, const int &ii, EV_FLOAT_REAX& ev) const { auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); - auto a_f = v_f.template access::value>(); auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); auto a_CdDelta = v_CdDelta.template access::value>(); @@ -3139,7 +3136,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1= 1.00) { if (gp[37] == 2 || (imass == 12.0000 && jmass == 15.9990) || (jmass == 12.0000 && imass == 15.9990)) { - const F_FLOAT exphu = exp(-gp[7] * SQR(BO_i - 2.50) ); + const F_FLOAT exphu = exp(-gp[7] * SQR(BO_i - 2.50)); const F_FLOAT exphua1 = exp(-gp[3] * (d_total_bo[i]-BO_i)); const F_FLOAT exphub1 = exp(-gp[3] * (d_total_bo[j]-BO_i)); const F_FLOAT exphuov = exp(gp[4] * (d_Delta[i] + d_Delta[j])); @@ -3151,7 +3148,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1template e_tally(ev,i,j,estriph); const F_FLOAT decobdbo = gp[10] * exphu * hulpov * (exphua1 + exphub1) * - ( gp[3] - 2.0 * gp[7] * (BO_i-2.50) ); + (gp[3] - 2.0 * gp[7] * (BO_i-2.50)); const F_FLOAT decobdboua = -gp[10] * exphu * hulpov * (gp[3]*exphua1 + 25.0*gp[4]*exphuov*hulpov*(exphua1+exphub1)); const F_FLOAT decobdboub = -gp[10] * exphu * hulpov * @@ -3171,9 +3168,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeBond1, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeBond1, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeBond1(), ii, ev); + this->template operator()(PairReaxFFComputeBond1(), ii, ev); } @@ -3182,7 +3179,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -3372,9 +3369,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond2 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii) const { +void PairReaxFFKokkos::operator()(PairReaxFFComputeBond2, const int &ii) const { EV_FLOAT_REAX ev; - this->template operator()(PairReaxComputeBond2(), ii, ev); + this->template operator()(PairReaxFFComputeBond2(), ii, ev); } @@ -3383,7 +3380,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond2 template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, const int &j, +void PairReaxFFKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, const int &j, const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const { @@ -3442,7 +3439,7 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::e_tally(EV_FLOAT_REAX & /*ev*/, const int &i, const int &j, +void PairReaxFFKokkos::e_tally(EV_FLOAT_REAX & /*ev*/, const int &i, const int &j, const F_FLOAT &epair) const { @@ -3464,7 +3461,7 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX & /*ev*/, const int &i, template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX & /*ev*/, const int &i, +void PairReaxFFKokkos::e_tally_single(EV_FLOAT_REAX & /*ev*/, const int &i, const F_FLOAT &epair) const { // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial @@ -3479,7 +3476,7 @@ void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX & /*ev*/, const i template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, +void PairReaxFFKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, F_FLOAT *fi, F_FLOAT *drij) const { @@ -3515,7 +3512,7 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, const int &j, const int &k, +void PairReaxFFKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { @@ -3557,7 +3554,7 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons template template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, const int &j, const int &k, +void PairReaxFFKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, const int &j, const int &k, const int &l, F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *dril, F_FLOAT *drjl, F_FLOAT *drkl) const { @@ -3601,7 +3598,7 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::v_tally3_atom(EV_FLOAT_REAX &ev, const int &i, const int & /*j*/, +void PairReaxFFKokkos::v_tally3_atom(EV_FLOAT_REAX &ev, const int &i, const int & /*j*/, const int & /*k*/, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const { @@ -3637,7 +3634,7 @@ void PairReaxCKokkos::v_tally3_atom(EV_FLOAT_REAX &ev, const int &i, ------------------------------------------------------------------------- */ template -void PairReaxCKokkos::ev_setup(int eflag, int vflag, int) +void PairReaxFFKokkos::ev_setup(int eflag, int vflag, int) { int i; @@ -3692,7 +3689,7 @@ void PairReaxCKokkos::ev_setup(int eflag, int vflag, int) /* ---------------------------------------------------------------------- */ template -double PairReaxCKokkos::memory_usage() +double PairReaxFFKokkos::memory_usage() { double bytes = 0.0; @@ -3706,13 +3703,13 @@ double PairReaxCKokkos::memory_usage() bytes += (double)nmax*17*sizeof(F_FLOAT); bytes += (double)maxbo*nmax*34*sizeof(F_FLOAT); - // FixReaxCSpecies + // FixReaxFFSpecies if (fixspecies_flag) { bytes += (double)MAXSPECBOND*nmax*sizeof(tagint); bytes += (double)MAXSPECBOND*nmax*sizeof(F_FLOAT); } - // FixReaxCBonds + // FixReaxFFBonds bytes += (double)maxbo*nmax*sizeof(tagint); bytes += (double)maxbo*nmax*sizeof(F_FLOAT); bytes += (double)nmax*sizeof(int); @@ -3723,12 +3720,12 @@ double PairReaxCKokkos::memory_usage() /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::FindBond(int &numbonds) +void PairReaxFFKokkos::FindBond(int &numbonds) { copymode = 1; Kokkos::parallel_for(Kokkos::RangePolicy(0,nmax),*this); - bo_cut_bond = control->bg_cut; + bo_cut_bond = api->control->bg_cut; atomKK->sync(execution_space,TAG_MASK); tag = atomKK->k_tag.view(); @@ -3738,14 +3735,14 @@ void PairReaxCKokkos::FindBond(int &numbonds) d_ilist = k_list->d_ilist; numbonds = 0; - PairReaxCKokkosFindBondFunctor find_bond_functor(this); + PairReaxFFKokkosFindBondFunctor find_bond_functor(this); Kokkos::parallel_reduce(inum,find_bond_functor,numbonds); copymode = 0; } template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxFindBondZero, const int &i) const { +void PairReaxFFKokkos::operator()(PairReaxFindBondZero, const int &i) const { d_numneigh_bonds[i] = 0; for (int j = 0; j < maxbo; j++) { d_neighid(i,j) = 0; @@ -3755,7 +3752,7 @@ void PairReaxCKokkos::operator()(PairReaxFindBondZero, const int &i) template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::calculate_find_bond_item(int ii, int &numbonds) const +void PairReaxFFKokkos::calculate_find_bond_item(int ii, int &numbonds) const { const int i = d_ilist[ii]; int nj = 0; @@ -3782,7 +3779,7 @@ void PairReaxCKokkos::calculate_find_bond_item(int ii, int &numbonds /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::PackBondBuffer(DAT::tdual_ffloat_1d k_buf, int &nbuf_local) +void PairReaxFFKokkos::PackBondBuffer(DAT::tdual_ffloat_1d k_buf, int &nbuf_local) { d_buf = k_buf.view(); k_params_sing.template sync(); @@ -3796,7 +3793,7 @@ void PairReaxCKokkos::PackBondBuffer(DAT::tdual_ffloat_1d k_buf, int copymode = 1; nlocal = atomKK->nlocal; - PairReaxCKokkosPackBondBufferFunctor pack_bond_buffer_functor(this); + PairReaxFFKokkosPackBondBufferFunctor pack_bond_buffer_functor(this); Kokkos::parallel_scan(nlocal,pack_bond_buffer_functor); copymode = 0; @@ -3810,7 +3807,7 @@ void PairReaxCKokkos::PackBondBuffer(DAT::tdual_ffloat_1d k_buf, int template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::pack_bond_buffer_item(int i, int &j, const bool &final) const +void PairReaxFFKokkos::pack_bond_buffer_item(int i, int &j, const bool &final) const { if (i == 0) j += 2; @@ -3852,7 +3849,7 @@ void PairReaxCKokkos::pack_bond_buffer_item(int i, int &j, const boo /* ---------------------------------------------------------------------- */ template -void PairReaxCKokkos::FindBondSpecies() +void PairReaxFFKokkos::FindBondSpecies() { if (nmax > (int)k_tmpid.extent(0)) { @@ -3880,12 +3877,12 @@ void PairReaxCKokkos::FindBondSpecies() k_error_flag.sync(); if (k_error_flag.h_view()) - error->all(FLERR,"Increase MAXSPECBOND in reaxc_defs.h"); + error->all(FLERR,"Increase MAXSPECBOND in reaxff_defs.h"); } template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxFindBondSpeciesZero, const int &i) const { +void PairReaxFFKokkos::operator()(PairReaxFindBondSpeciesZero, const int &i) const { for (int j = 0; j < MAXSPECBOND; j++) { k_tmpbo.view()(i,j) = 0.0; k_tmpid.view()(i,j) = 0; @@ -3894,7 +3891,7 @@ void PairReaxCKokkos::operator()(PairReaxFindBondSpeciesZero, const template KOKKOS_INLINE_FUNCTION -void PairReaxCKokkos::operator()(PairReaxFindBondSpecies, const int &i) const { +void PairReaxFFKokkos::operator()(PairReaxFindBondSpecies, const int &i) const { int nj = 0; const int j_start = d_bo_first[i]; @@ -3916,8 +3913,8 @@ void PairReaxCKokkos::operator()(PairReaxFindBondSpecies, const int } } -template class PairReaxCKokkos; +template class PairReaxFFKokkos; #ifdef LMP_KOKKOS_GPU -template class PairReaxCKokkos; +template class PairReaxFFKokkos; #endif } diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxff_kokkos.h similarity index 85% rename from src/KOKKOS/pair_reaxc_kokkos.h rename to src/KOKKOS/pair_reaxff_kokkos.h index 7caa270a80..e60533f61e 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxff_kokkos.h @@ -15,9 +15,12 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(reax/c/kk,PairReaxCKokkos); -PairStyle(reax/c/kk/device,PairReaxCKokkos); -PairStyle(reax/c/kk/host,PairReaxCKokkos); +PairStyle(reaxff/kk,PairReaxFFKokkos); +PairStyle(reaxff/kk/device,PairReaxFFKokkos); +PairStyle(reaxff/kk/host,PairReaxFFKokkos); +PairStyle(reax/c/kk,PairReaxFFKokkos); +PairStyle(reax/c/kk/device,PairReaxFFKokkos); +PairStyle(reax/c/kk/host,PairReaxFFKokkos); // clang-format on #else @@ -25,9 +28,8 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos); #define LMP_PAIR_REAXC_KOKKOS_H #include "pair_kokkos.h" -#include "pair_reaxc.h" +#include "pair_reaxff.h" #include "neigh_list_kokkos.h" -#include "reaxc_types.h" #define C_ele 332.06371 #define SMALL 0.0001 @@ -37,12 +39,14 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos); #define SQR(x) ((x)*(x)) +#include "reaxff_inline.h" + namespace LAMMPS_NS { template struct LR_lookup_table_kk { - typedef Kokkos::DualView tdual_cubic_spline_coef_1d; + typedef Kokkos::DualView tdual_cubic_spline_coef_1d; typedef typename tdual_cubic_spline_coef_1d::t_dev t_cubic_spline_coef_1d; double dx, inv_dx; @@ -52,13 +56,13 @@ struct LR_lookup_table_kk }; template -struct PairReaxComputePolar{}; +struct PairReaxFFComputePolar{}; template -struct PairReaxComputeLJCoulomb{}; +struct PairReaxFFComputeLJCoulomb{}; template -struct PairReaxComputeTabulatedLJCoulomb{}; +struct PairReaxFFComputeTabulatedLJCoulomb{}; struct PairReaxBuildListsFull{}; @@ -81,25 +85,25 @@ template struct PairReaxUpdateBond{}; template -struct PairReaxComputeBond1{}; +struct PairReaxFFComputeBond1{}; template -struct PairReaxComputeBond2{}; +struct PairReaxFFComputeBond2{}; template -struct PairReaxComputeMulti1{}; +struct PairReaxFFComputeMulti1{}; template -struct PairReaxComputeMulti2{}; +struct PairReaxFFComputeMulti2{}; template -struct PairReaxComputeAngular{}; +struct PairReaxFFComputeAngular{}; template -struct PairReaxComputeTorsion{}; +struct PairReaxFFComputeTorsion{}; template -struct PairReaxComputeHydrogen{}; +struct PairReaxFFComputeHydrogen{}; struct PairReaxFindBondZero{}; @@ -109,7 +113,7 @@ struct PairReaxFindBondSpecies{}; template -class PairReaxCKokkos : public PairReaxC { +class PairReaxFFKokkos : public PairReaxFF { public: enum {EnabledNeighFlags=FULL|HALF|HALFTHREAD}; enum {COUL_FLAG=1}; @@ -117,8 +121,8 @@ class PairReaxCKokkos : public PairReaxC { typedef ArrayTypes AT; typedef EV_FLOAT_REAX value_type; - PairReaxCKokkos(class LAMMPS *); - virtual ~PairReaxCKokkos(); + PairReaxFFKokkos(class LAMMPS *); + virtual ~PairReaxFFKokkos(); void ev_setup(int, int, int alloc = 1); void compute(int, int); @@ -130,27 +134,27 @@ class PairReaxCKokkos : public PairReaxC { template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputePolar, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputePolar, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputePolar, const int&) const; + void operator()(PairReaxFFComputePolar, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeLJCoulomb, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeLJCoulomb, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeLJCoulomb, const int&) const; + void operator()(PairReaxFFComputeLJCoulomb, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeTabulatedLJCoulomb, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeTabulatedLJCoulomb, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeTabulatedLJCoulomb, const int&) const; + void operator()(PairReaxFFComputeTabulatedLJCoulomb, const int&) const; KOKKOS_INLINE_FUNCTION void operator()(PairReaxBuildListsFull, const int&) const; @@ -183,55 +187,55 @@ class PairReaxCKokkos : public PairReaxC { template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeBond1, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeBond1, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeBond1, const int&) const; + void operator()(PairReaxFFComputeBond1, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeBond2, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeBond2, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeBond2, const int&) const; + void operator()(PairReaxFFComputeBond2, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeMulti1, const int&) const; + void operator()(PairReaxFFComputeMulti1, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeMulti2, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeMulti2, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeMulti2, const int&) const; + void operator()(PairReaxFFComputeMulti2, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeAngular, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeAngular, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeAngular, const int&) const; + void operator()(PairReaxFFComputeAngular, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeTorsion, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeTorsion, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeTorsion, const int&) const; + void operator()(PairReaxFFComputeTorsion, const int&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeHydrogen, const int&, EV_FLOAT_REAX&) const; + void operator()(PairReaxFFComputeHydrogen, const int&, EV_FLOAT_REAX&) const; template KOKKOS_INLINE_FUNCTION - void operator()(PairReaxComputeHydrogen, const int&) const; + void operator()(PairReaxFFComputeHydrogen, const int&) const; KOKKOS_INLINE_FUNCTION void operator()(PairReaxFindBondZero, const int&) const; @@ -338,7 +342,7 @@ class PairReaxCKokkos : public PairReaxC { void init_md(); int Init_Lookup_Tables(); void Deallocate_Lookup_Tables(); - void LR_vdW_Coulomb( int i, int j, double r_ij, LR_data *lr ); + void LR_vdW_Coulomb(int i, int j, double r_ij, ReaxFF::LR_data *lr); typedef Kokkos::DualView tdual_int_1d; Kokkos::DualView k_params_sing; @@ -432,7 +436,7 @@ class PairReaxCKokkos : public PairReaxC { int vdwflag, lgflag; F_FLOAT gp[39], p_boc1, p_boc2; - friend void pair_virial_fdotr_compute(PairReaxCKokkos*); + friend void pair_virial_fdotr_compute(PairReaxFFKokkos*); int bocnt,hbcnt,enobondsflag; @@ -457,11 +461,11 @@ class PairReaxCKokkos : public PairReaxC { }; template -struct PairReaxCKokkosFindBondFunctor { +struct PairReaxFFKokkosFindBondFunctor { typedef DeviceType device_type; typedef int value_type; - PairReaxCKokkos c; - PairReaxCKokkosFindBondFunctor(PairReaxCKokkos* c_ptr):c(*c_ptr) {}; + PairReaxFFKokkos c; + PairReaxFFKokkosFindBondFunctor(PairReaxFFKokkos* c_ptr):c(*c_ptr) {}; KOKKOS_INLINE_FUNCTION void join(volatile int &dst, @@ -476,11 +480,11 @@ struct PairReaxCKokkosFindBondFunctor { }; template -struct PairReaxCKokkosPackBondBufferFunctor { +struct PairReaxFFKokkosPackBondBufferFunctor { typedef DeviceType device_type; typedef int value_type; - PairReaxCKokkos c; - PairReaxCKokkosPackBondBufferFunctor(PairReaxCKokkos* c_ptr):c(*c_ptr) {}; + PairReaxFFKokkos c; + PairReaxFFKokkosPackBondBufferFunctor(PairReaxFFKokkos* c_ptr):c(*c_ptr) {}; KOKKOS_INLINE_FUNCTION void operator()(const int ii, int &j, const bool &final) const { diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 34dffacca8..30a4082711 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -30,6 +30,7 @@ #include "neighbor_kokkos.h" #include "kokkos.h" #include "sna.h" +#include "comm.h" #define MAXLINE 1024 #define MAXWORD 3 @@ -86,6 +87,16 @@ PairSNAPKokkos::~PairSNAPKokkos() template void PairSNAPKokkos::init_style() { + if (host_flag) { + if (lmp->kokkos->nthreads > 1) + if (comm->me == 0) + utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " + "CPU thread, even if more threads are requested\n"); + + PairSNAP::init_style(); + return; + } + if (force->newton_pair == 0) error->all(FLERR,"Pair style SNAP requires newton pair on"); @@ -133,6 +144,13 @@ struct FindMaxNumNeighs { template void PairSNAPKokkos::compute(int eflag_in, int vflag_in) { + if (host_flag) { + atomKK->sync(Host,X_MASK|TYPE_MASK); + PairSNAP::compute(eflag_in,vflag_in); + atomKK->modified(Host,F_MASK); + return; + } + eflag = eflag_in; vflag = vflag_in; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 2385d1977a..dbda29d807 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -1532,7 +1532,7 @@ void PPPMKokkos::operator()(TagPPPM_make_rho_atomic, const int &i) c template KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator() (TagPPPM_make_rho, typename Kokkos::TeamPolicy::member_type dev) const { - // adapted from USER-OMP/pppm.cpp: + // adapted from OPENMP/pppm.cpp: // determine range of grid points handled by this thread int tid = dev.league_rank(); diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 492eac3e49..909c6930cf 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -76,12 +76,12 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) : void VerletKokkos::setup(int flag) { if (comm->me == 0 && screen) { - fprintf(screen,"Setting up Verlet run ...\n"); + fputs("Setting up Verlet run ...\n",screen); if (flag) { - fprintf(screen," Unit style : %s\n", update->unit_style); - fprintf(screen," Current step : " BIGINT_FORMAT "\n", - update->ntimestep); - fprintf(screen," Time step : %g\n", update->dt); + fmt::print(screen," Unit style : {}\n" + " Current step : {}\n" + " Time step : {}\n", + update->unit_style,update->ntimestep,update->dt); timer->print_timeout(screen); } } @@ -132,6 +132,7 @@ void VerletKokkos::setup(int flag) // compute all forces + force->setup(); ev_set(update->ntimestep); force_clear(); modify->setup_pre_force(vflag); @@ -140,11 +141,10 @@ void VerletKokkos::setup(int flag) atomKK->sync(force->pair->execution_space,force->pair->datamask_read); force->pair->compute(eflag,vflag); atomKK->modified(force->pair->execution_space,force->pair->datamask_modify); - timer->stamp(Timer::PAIR); } else if (force->pair) force->pair->compute_dummy(eflag,vflag); - if (atomKK->molecular) { + if (atomKK->molecular != Atom::ATOMIC) { if (force->bond) { atomKK->sync(force->bond->execution_space,force->bond->datamask_read); force->bond->compute(eflag,vflag); @@ -165,7 +165,6 @@ void VerletKokkos::setup(int flag) force->improper->compute(eflag,vflag); atomKK->modified(force->improper->execution_space,force->improper->datamask_modify); } - timer->stamp(Timer::BOND); } if (force->kspace) { @@ -174,9 +173,10 @@ void VerletKokkos::setup(int flag) atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read); force->kspace->compute(eflag,vflag); atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify); - timer->stamp(Timer::KSPACE); } else force->kspace->compute_dummy(eflag,vflag); } + + modify->setup_pre_reverse(eflag,vflag); if (force->newton) comm->reverse_comm(); lmp->kokkos->auto_sync = 0; @@ -244,11 +244,10 @@ void VerletKokkos::setup_minimal(int flag) atomKK->sync(force->pair->execution_space,force->pair->datamask_read); force->pair->compute(eflag,vflag); atomKK->modified(force->pair->execution_space,force->pair->datamask_modify); - timer->stamp(Timer::PAIR); } else if (force->pair) force->pair->compute_dummy(eflag,vflag); - if (atomKK->molecular) { + if (atomKK->molecular != Atom::ATOMIC) { if (force->bond) { atomKK->sync(force->bond->execution_space,force->bond->datamask_read); force->bond->compute(eflag,vflag); @@ -269,7 +268,6 @@ void VerletKokkos::setup_minimal(int flag) force->improper->compute(eflag,vflag); atomKK->modified(force->improper->execution_space,force->improper->datamask_modify); } - timer->stamp(Timer::BOND); } if (force->kspace) { @@ -278,10 +276,10 @@ void VerletKokkos::setup_minimal(int flag) atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read); force->kspace->compute(eflag,vflag); atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify); - timer->stamp(Timer::KSPACE); } else force->kspace->compute_dummy(eflag,vflag); } + modify->setup_pre_reverse(eflag,vflag); if (force->newton) comm->reverse_comm(); lmp->kokkos->auto_sync = 0; @@ -302,6 +300,7 @@ void VerletKokkos::run(int n) int n_post_integrate = modify->n_post_integrate; int n_pre_exchange = modify->n_pre_exchange; int n_pre_neighbor = modify->n_pre_neighbor; + int n_post_neighbor = modify->n_post_neighbor; int n_pre_force = modify->n_pre_force; int n_pre_reverse = modify->n_pre_reverse; int n_post_force = modify->n_post_force; @@ -320,11 +319,11 @@ void VerletKokkos::run(int n) timer->init_timeout(); for (int i = 0; i < n; i++) { - if (timer->check_timeout(i)) { update->nsteps = i; break; } + ntimestep = ++update->ntimestep; ev_set(ntimestep); @@ -388,6 +387,10 @@ void VerletKokkos::run(int n) } neighbor->build(1); timer->stamp(Timer::NEIGH); + if (n_post_neighbor) { + modify->post_neighbor(); + timer->stamp(Timer::MODIFY); + } } // force computations @@ -648,5 +651,3 @@ void VerletKokkos::force_clear() } } } - - diff --git a/src/pair_coul_streitz.cpp b/src/KSPACE/pair_coul_streitz.cpp similarity index 100% rename from src/pair_coul_streitz.cpp rename to src/KSPACE/pair_coul_streitz.cpp diff --git a/src/pair_coul_streitz.h b/src/KSPACE/pair_coul_streitz.h similarity index 100% rename from src/pair_coul_streitz.h rename to src/KSPACE/pair_coul_streitz.h diff --git a/src/USER-LB/README b/src/LATBOLTZ/README similarity index 98% rename from src/USER-LB/README rename to src/LATBOLTZ/README index 4f22986d84..6f2e06178c 100644 --- a/src/USER-LB/README +++ b/src/LATBOLTZ/README @@ -16,7 +16,7 @@ brief descriptions of other fixes below, each of which have their own doc page. There are example scripts for using this package in -examples/USER/lb. +examples/PACKAGES/latboltz. IMPORTANT NOTE: This package can only be used if LAMMPS is compiled with MPI (i.e. the serial makefile should not be used to compile the diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/LATBOLTZ/fix_lb_fluid.cpp similarity index 100% rename from src/USER-LB/fix_lb_fluid.cpp rename to src/LATBOLTZ/fix_lb_fluid.cpp diff --git a/src/USER-LB/fix_lb_fluid.h b/src/LATBOLTZ/fix_lb_fluid.h similarity index 98% rename from src/USER-LB/fix_lb_fluid.h rename to src/LATBOLTZ/fix_lb_fluid.h index 3b0ce872ba..0842acbe64 100644 --- a/src/USER-LB/fix_lb_fluid.h +++ b/src/LATBOLTZ/fix_lb_fluid.h @@ -23,7 +23,7 @@ FixStyle(lb/fluid,FixLbFluid); #include "fix.h" #if defined(MPI_STUBS) -#error "The USER-LB package cannot be compiled in serial with MPI STUBS" +#error "The LATBOLTZ package cannot be compiled in serial with MPI STUBS" #endif namespace LAMMPS_NS { diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/LATBOLTZ/fix_lb_momentum.cpp similarity index 100% rename from src/USER-LB/fix_lb_momentum.cpp rename to src/LATBOLTZ/fix_lb_momentum.cpp diff --git a/src/USER-LB/fix_lb_momentum.h b/src/LATBOLTZ/fix_lb_momentum.h similarity index 100% rename from src/USER-LB/fix_lb_momentum.h rename to src/LATBOLTZ/fix_lb_momentum.h diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/LATBOLTZ/fix_lb_pc.cpp similarity index 100% rename from src/USER-LB/fix_lb_pc.cpp rename to src/LATBOLTZ/fix_lb_pc.cpp diff --git a/src/USER-LB/fix_lb_pc.h b/src/LATBOLTZ/fix_lb_pc.h similarity index 100% rename from src/USER-LB/fix_lb_pc.h rename to src/LATBOLTZ/fix_lb_pc.h diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/LATBOLTZ/fix_lb_rigid_pc_sphere.cpp similarity index 100% rename from src/USER-LB/fix_lb_rigid_pc_sphere.cpp rename to src/LATBOLTZ/fix_lb_rigid_pc_sphere.cpp diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.h b/src/LATBOLTZ/fix_lb_rigid_pc_sphere.h similarity index 100% rename from src/USER-LB/fix_lb_rigid_pc_sphere.h rename to src/LATBOLTZ/fix_lb_rigid_pc_sphere.h diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/LATBOLTZ/fix_lb_viscous.cpp similarity index 100% rename from src/USER-LB/fix_lb_viscous.cpp rename to src/LATBOLTZ/fix_lb_viscous.cpp diff --git a/src/USER-LB/fix_lb_viscous.h b/src/LATBOLTZ/fix_lb_viscous.h similarity index 100% rename from src/USER-LB/fix_lb_viscous.h rename to src/LATBOLTZ/fix_lb_viscous.h diff --git a/src/USER-SMD/Install.sh b/src/MACHDYN/Install.sh similarity index 61% rename from src/USER-SMD/Install.sh rename to src/MACHDYN/Install.sh index cb9aa5452b..bf18c332f3 100755 --- a/src/USER-SMD/Install.sh +++ b/src/MACHDYN/Install.sh @@ -37,29 +37,29 @@ done if (test $1 = 1) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*smd[^ \t]* //g' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/smd/includelink |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-smd_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-smd_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-smd_SYSPATH) |' ../Makefile.package + sed -i -e 's/[^ \t]*machdyn[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/machdyn/includelink |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(machdyn_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(machdyn_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(machdyn_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*smd.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ..\/..\/lib\/smd\/Makefile.lammps +include ..\/..\/lib\/machdyn\/Makefile.lammps ' ../Makefile.package.settings fi elif (test $1 = 0) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*smd[^ \t]* //g' ../Makefile.package + sed -i -e 's/[^ \t]*machdyn[^ \t]* //g' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*smd.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings fi fi diff --git a/src/USER-SMD/README b/src/MACHDYN/README similarity index 92% rename from src/USER-SMD/README rename to src/MACHDYN/README index 924157ac97..4bbf3cb3a9 100644 --- a/src/USER-SMD/README +++ b/src/MACHDYN/README @@ -19,7 +19,7 @@ from *.STL files. See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started. -There are example scripts for using this package in examples/USER/smd. +There are example scripts for using this package in examples/PACKAGES/machdyn. The person who created this package is Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp similarity index 99% rename from src/USER-SMD/atom_vec_smd.cpp rename to src/MACHDYN/atom_vec_smd.cpp index 2cae7517ec..b798425e19 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/atom_vec_smd.h b/src/MACHDYN/atom_vec_smd.h similarity index 97% rename from src/USER-SMD/atom_vec_smd.h rename to src/MACHDYN/atom_vec_smd.h index 8ad6448bba..ada2c2c936 100644 --- a/src/USER-SMD/atom_vec_smd.h +++ b/src/MACHDYN/atom_vec_smd.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/MACHDYN/compute_smd_contact_radius.cpp similarity index 98% rename from src/USER-SMD/compute_smd_contact_radius.cpp rename to src/MACHDYN/compute_smd_contact_radius.cpp index 82186c96b4..7a10b563f8 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/MACHDYN/compute_smd_contact_radius.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_contact_radius.h b/src/MACHDYN/compute_smd_contact_radius.h similarity index 96% rename from src/USER-SMD/compute_smd_contact_radius.h rename to src/MACHDYN/compute_smd_contact_radius.h index 503ae386a7..87f3208dd3 100644 --- a/src/USER-SMD/compute_smd_contact_radius.h +++ b/src/MACHDYN/compute_smd_contact_radius.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/MACHDYN/compute_smd_damage.cpp similarity index 98% rename from src/USER-SMD/compute_smd_damage.cpp rename to src/MACHDYN/compute_smd_damage.cpp index 23a74123bf..f3b52ccfce 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/MACHDYN/compute_smd_damage.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_damage.h b/src/MACHDYN/compute_smd_damage.h similarity index 96% rename from src/USER-SMD/compute_smd_damage.h rename to src/MACHDYN/compute_smd_damage.h index 21956c9819..ac1fcb1bb4 100644 --- a/src/USER-SMD/compute_smd_damage.h +++ b/src/MACHDYN/compute_smd_damage.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/MACHDYN/compute_smd_hourglass_error.cpp similarity index 98% rename from src/USER-SMD/compute_smd_hourglass_error.cpp rename to src/MACHDYN/compute_smd_hourglass_error.cpp index 53289c6d12..b0d01d2b14 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.cpp +++ b/src/MACHDYN/compute_smd_hourglass_error.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_hourglass_error.h b/src/MACHDYN/compute_smd_hourglass_error.h similarity index 96% rename from src/USER-SMD/compute_smd_hourglass_error.h rename to src/MACHDYN/compute_smd_hourglass_error.h index b7e513f182..32b5b90d56 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.h +++ b/src/MACHDYN/compute_smd_hourglass_error.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/MACHDYN/compute_smd_internal_energy.cpp similarity index 98% rename from src/USER-SMD/compute_smd_internal_energy.cpp rename to src/MACHDYN/compute_smd_internal_energy.cpp index aa59d7cc00..0d17588b13 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/MACHDYN/compute_smd_internal_energy.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_internal_energy.h b/src/MACHDYN/compute_smd_internal_energy.h similarity index 96% rename from src/USER-SMD/compute_smd_internal_energy.h rename to src/MACHDYN/compute_smd_internal_energy.h index 3277bf028c..b4aaaf6b40 100644 --- a/src/USER-SMD/compute_smd_internal_energy.h +++ b/src/MACHDYN/compute_smd_internal_energy.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/MACHDYN/compute_smd_plastic_strain.cpp similarity index 98% rename from src/USER-SMD/compute_smd_plastic_strain.cpp rename to src/MACHDYN/compute_smd_plastic_strain.cpp index 5d98650226..3f5fbdf090 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/MACHDYN/compute_smd_plastic_strain.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain.h b/src/MACHDYN/compute_smd_plastic_strain.h similarity index 96% rename from src/USER-SMD/compute_smd_plastic_strain.h rename to src/MACHDYN/compute_smd_plastic_strain.h index 92409afbf8..7e319610a3 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.h +++ b/src/MACHDYN/compute_smd_plastic_strain.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/MACHDYN/compute_smd_plastic_strain_rate.cpp similarity index 98% rename from src/USER-SMD/compute_smd_plastic_strain_rate.cpp rename to src/MACHDYN/compute_smd_plastic_strain_rate.cpp index da9f4846cc..d215b0e321 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_plastic_strain_rate.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.h b/src/MACHDYN/compute_smd_plastic_strain_rate.h similarity index 96% rename from src/USER-SMD/compute_smd_plastic_strain_rate.h rename to src/MACHDYN/compute_smd_plastic_strain_rate.h index 745b9ed3cc..d0ea09af26 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.h +++ b/src/MACHDYN/compute_smd_plastic_strain_rate.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/MACHDYN/compute_smd_rho.cpp similarity index 98% rename from src/USER-SMD/compute_smd_rho.cpp rename to src/MACHDYN/compute_smd_rho.cpp index cffe71ade3..f05c7c6e83 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/MACHDYN/compute_smd_rho.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_rho.h b/src/MACHDYN/compute_smd_rho.h similarity index 96% rename from src/USER-SMD/compute_smd_rho.h rename to src/MACHDYN/compute_smd_rho.h index 85335bbce8..954caade5d 100644 --- a/src/USER-SMD/compute_smd_rho.h +++ b/src/MACHDYN/compute_smd_rho.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/MACHDYN/compute_smd_tlsph_defgrad.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_defgrad.cpp rename to src/MACHDYN/compute_smd_tlsph_defgrad.cpp index 0611dab47b..e8c78821dc 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/MACHDYN/compute_smd_tlsph_defgrad.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.h b/src/MACHDYN/compute_smd_tlsph_defgrad.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_defgrad.h rename to src/MACHDYN/compute_smd_tlsph_defgrad.h index ece997771b..eed4066867 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.h +++ b/src/MACHDYN/compute_smd_tlsph_defgrad.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/MACHDYN/compute_smd_tlsph_dt.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_dt.cpp rename to src/MACHDYN/compute_smd_tlsph_dt.cpp index 8000de9c59..ca1973309f 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.cpp +++ b/src/MACHDYN/compute_smd_tlsph_dt.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_dt.h b/src/MACHDYN/compute_smd_tlsph_dt.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_dt.h rename to src/MACHDYN/compute_smd_tlsph_dt.h index 1fedd6d36d..e57db2dd74 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.h +++ b/src/MACHDYN/compute_smd_tlsph_dt.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_num_neighs.cpp rename to src/MACHDYN/compute_smd_tlsph_num_neighs.cpp index f7d95410ae..230a5946f8 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp +++ b/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.h b/src/MACHDYN/compute_smd_tlsph_num_neighs.h similarity index 97% rename from src/USER-SMD/compute_smd_tlsph_num_neighs.h rename to src/MACHDYN/compute_smd_tlsph_num_neighs.h index ad6311d60d..e3531a47ea 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.h +++ b/src/MACHDYN/compute_smd_tlsph_num_neighs.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/MACHDYN/compute_smd_tlsph_shape.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_shape.cpp rename to src/MACHDYN/compute_smd_tlsph_shape.cpp index b2d38b2af2..1887de683c 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/MACHDYN/compute_smd_tlsph_shape.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_shape.h b/src/MACHDYN/compute_smd_tlsph_shape.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_shape.h rename to src/MACHDYN/compute_smd_tlsph_shape.h index c1b9b69bfb..76298cf30c 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.h +++ b/src/MACHDYN/compute_smd_tlsph_shape.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/MACHDYN/compute_smd_tlsph_strain.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_strain.cpp rename to src/MACHDYN/compute_smd_tlsph_strain.cpp index 19ce976509..30f158a3f1 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/MACHDYN/compute_smd_tlsph_strain.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain.h b/src/MACHDYN/compute_smd_tlsph_strain.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_strain.h rename to src/MACHDYN/compute_smd_tlsph_strain.h index f94385b7fe..426cb6dea9 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.h +++ b/src/MACHDYN/compute_smd_tlsph_strain.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_strain_rate.cpp rename to src/MACHDYN/compute_smd_tlsph_strain_rate.cpp index adb0bbcf6d..1889cbcc0f 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.h b/src/MACHDYN/compute_smd_tlsph_strain_rate.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_strain_rate.h rename to src/MACHDYN/compute_smd_tlsph_strain_rate.h index 35d2a80519..7fd851725c 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.h +++ b/src/MACHDYN/compute_smd_tlsph_strain_rate.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/MACHDYN/compute_smd_tlsph_stress.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_stress.cpp rename to src/MACHDYN/compute_smd_tlsph_stress.cpp index 75a06a45e9..038e09a3c0 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/MACHDYN/compute_smd_tlsph_stress.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_stress.h b/src/MACHDYN/compute_smd_tlsph_stress.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_stress.h rename to src/MACHDYN/compute_smd_tlsph_stress.h index 7bb0250620..4ef4199e48 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.h +++ b/src/MACHDYN/compute_smd_tlsph_stress.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/MACHDYN/compute_smd_triangle_vertices.cpp similarity index 98% rename from src/USER-SMD/compute_smd_triangle_vertices.cpp rename to src/MACHDYN/compute_smd_triangle_vertices.cpp index c4b832faa3..016ae3e85f 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.cpp +++ b/src/MACHDYN/compute_smd_triangle_vertices.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_triangle_vertices.h b/src/MACHDYN/compute_smd_triangle_vertices.h similarity index 96% rename from src/USER-SMD/compute_smd_triangle_vertices.h rename to src/MACHDYN/compute_smd_triangle_vertices.h index fe369580aa..06be1a4e1a 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.h +++ b/src/MACHDYN/compute_smd_triangle_vertices.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/MACHDYN/compute_smd_ulsph_effm.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_effm.cpp rename to src/MACHDYN/compute_smd_ulsph_effm.cpp index edf9355f20..24cae6b14e 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.cpp +++ b/src/MACHDYN/compute_smd_ulsph_effm.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_effm.h b/src/MACHDYN/compute_smd_ulsph_effm.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_effm.h rename to src/MACHDYN/compute_smd_ulsph_effm.h index 8839f1dcbc..836a3d2a74 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.h +++ b/src/MACHDYN/compute_smd_ulsph_effm.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_num_neighs.cpp rename to src/MACHDYN/compute_smd_ulsph_num_neighs.cpp index 5b900fc15d..7c181a6a82 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp +++ b/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.h b/src/MACHDYN/compute_smd_ulsph_num_neighs.h similarity index 97% rename from src/USER-SMD/compute_smd_ulsph_num_neighs.h rename to src/MACHDYN/compute_smd_ulsph_num_neighs.h index 75217d7685..527ba17737 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.h +++ b/src/MACHDYN/compute_smd_ulsph_num_neighs.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/MACHDYN/compute_smd_ulsph_strain.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_strain.cpp rename to src/MACHDYN/compute_smd_ulsph_strain.cpp index 3dbfc02391..eed26821b0 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/MACHDYN/compute_smd_ulsph_strain.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain.h b/src/MACHDYN/compute_smd_ulsph_strain.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_strain.h rename to src/MACHDYN/compute_smd_ulsph_strain.h index 6265a9ab5e..54f53f6782 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.h +++ b/src/MACHDYN/compute_smd_ulsph_strain.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_strain_rate.cpp rename to src/MACHDYN/compute_smd_ulsph_strain_rate.cpp index d44a6bac70..9e2709eb0a 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.h b/src/MACHDYN/compute_smd_ulsph_strain_rate.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_strain_rate.h rename to src/MACHDYN/compute_smd_ulsph_strain_rate.h index 8ccd5695c1..ab97d7a924 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.h +++ b/src/MACHDYN/compute_smd_ulsph_strain_rate.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/MACHDYN/compute_smd_ulsph_stress.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_stress.cpp rename to src/MACHDYN/compute_smd_ulsph_stress.cpp index eadfbfc1b0..9aa75b76e8 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/MACHDYN/compute_smd_ulsph_stress.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_stress.h b/src/MACHDYN/compute_smd_ulsph_stress.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_stress.h rename to src/MACHDYN/compute_smd_ulsph_stress.h index bcb6098b64..6f3182f5f4 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.h +++ b/src/MACHDYN/compute_smd_ulsph_stress.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/MACHDYN/compute_smd_vol.cpp similarity index 98% rename from src/USER-SMD/compute_smd_vol.cpp rename to src/MACHDYN/compute_smd_vol.cpp index 873699a591..2fdc4e34d2 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/MACHDYN/compute_smd_vol.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_vol.h b/src/MACHDYN/compute_smd_vol.h similarity index 96% rename from src/USER-SMD/compute_smd_vol.h rename to src/MACHDYN/compute_smd_vol.h index ab9143d41c..c0fd4550b4 100644 --- a/src/USER-SMD/compute_smd_vol.h +++ b/src/MACHDYN/compute_smd_vol.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/MACHDYN/fix_smd_adjust_dt.cpp similarity index 99% rename from src/USER-SMD/fix_smd_adjust_dt.cpp rename to src/MACHDYN/fix_smd_adjust_dt.cpp index dc5dbd08a9..f45364713a 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/MACHDYN/fix_smd_adjust_dt.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_adjust_dt.h b/src/MACHDYN/fix_smd_adjust_dt.h similarity index 97% rename from src/USER-SMD/fix_smd_adjust_dt.h rename to src/MACHDYN/fix_smd_adjust_dt.h index 5f6b350be3..41203cf472 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.h +++ b/src/MACHDYN/fix_smd_adjust_dt.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/MACHDYN/fix_smd_integrate_tlsph.cpp similarity index 99% rename from src/USER-SMD/fix_smd_integrate_tlsph.cpp rename to src/MACHDYN/fix_smd_integrate_tlsph.cpp index a8257dfebe..8bde3b3d07 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/MACHDYN/fix_smd_integrate_tlsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.h b/src/MACHDYN/fix_smd_integrate_tlsph.h similarity index 97% rename from src/USER-SMD/fix_smd_integrate_tlsph.h rename to src/MACHDYN/fix_smd_integrate_tlsph.h index c5f86092a4..582b4588a4 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.h +++ b/src/MACHDYN/fix_smd_integrate_tlsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/MACHDYN/fix_smd_integrate_ulsph.cpp similarity index 99% rename from src/USER-SMD/fix_smd_integrate_ulsph.cpp rename to src/MACHDYN/fix_smd_integrate_ulsph.cpp index 2c9b71c400..967cf33095 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/MACHDYN/fix_smd_integrate_ulsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/MACHDYN/fix_smd_integrate_ulsph.h similarity index 96% rename from src/USER-SMD/fix_smd_integrate_ulsph.h rename to src/MACHDYN/fix_smd_integrate_ulsph.h index 36afceeaaa..af75685a4b 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.h +++ b/src/MACHDYN/fix_smd_integrate_ulsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/MACHDYN/fix_smd_move_triangulated_surface.cpp similarity index 99% rename from src/USER-SMD/fix_smd_move_triangulated_surface.cpp rename to src/MACHDYN/fix_smd_move_triangulated_surface.cpp index 15ba0ef828..c790720e99 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/MACHDYN/fix_smd_move_triangulated_surface.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.h b/src/MACHDYN/fix_smd_move_triangulated_surface.h similarity index 97% rename from src/USER-SMD/fix_smd_move_triangulated_surface.h rename to src/MACHDYN/fix_smd_move_triangulated_surface.h index 8fce159121..aec2fcb688 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.h +++ b/src/MACHDYN/fix_smd_move_triangulated_surface.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/MACHDYN/fix_smd_setvel.cpp similarity index 99% rename from src/USER-SMD/fix_smd_setvel.cpp rename to src/MACHDYN/fix_smd_setvel.cpp index c0c0fccd46..7b76e08ec6 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/MACHDYN/fix_smd_setvel.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/MACHDYN/fix_smd_setvel.h similarity index 97% rename from src/USER-SMD/fix_smd_setvel.h rename to src/MACHDYN/fix_smd_setvel.h index 8791d58c3f..1e91a8d602 100644 --- a/src/USER-SMD/fix_smd_setvel.h +++ b/src/MACHDYN/fix_smd_setvel.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp similarity index 99% rename from src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp rename to src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp index 77d8bcc804..32d96e3d7f 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/MACHDYN/fix_smd_tlsph_reference_configuration.h similarity index 97% rename from src/USER-SMD/fix_smd_tlsph_reference_configuration.h rename to src/MACHDYN/fix_smd_tlsph_reference_configuration.h index a5a26797e0..98108b8ffd 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/MACHDYN/fix_smd_wall_surface.cpp similarity index 100% rename from src/USER-SMD/fix_smd_wall_surface.cpp rename to src/MACHDYN/fix_smd_wall_surface.cpp diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/MACHDYN/fix_smd_wall_surface.h similarity index 100% rename from src/USER-SMD/fix_smd_wall_surface.h rename to src/MACHDYN/fix_smd_wall_surface.h diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/MACHDYN/pair_smd_hertz.cpp similarity index 99% rename from src/USER-SMD/pair_smd_hertz.cpp rename to src/MACHDYN/pair_smd_hertz.cpp index 24e6802a14..a5355e46e0 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/MACHDYN/pair_smd_hertz.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_hertz.h b/src/MACHDYN/pair_smd_hertz.h similarity index 97% rename from src/USER-SMD/pair_smd_hertz.h rename to src/MACHDYN/pair_smd_hertz.h index 0d3c5b880b..b736764de3 100644 --- a/src/USER-SMD/pair_smd_hertz.h +++ b/src/MACHDYN/pair_smd_hertz.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/MACHDYN/pair_smd_tlsph.cpp similarity index 99% rename from src/USER-SMD/pair_smd_tlsph.cpp rename to src/MACHDYN/pair_smd_tlsph.cpp index 62e8e5e1c1..280e0173e3 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/MACHDYN/pair_smd_tlsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/MACHDYN/pair_smd_tlsph.h similarity index 99% rename from src/USER-SMD/pair_smd_tlsph.h rename to src/MACHDYN/pair_smd_tlsph.h index b641ca71e5..86e2bbe52b 100644 --- a/src/USER-SMD/pair_smd_tlsph.h +++ b/src/MACHDYN/pair_smd_tlsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/MACHDYN/pair_smd_triangulated_surface.cpp similarity index 99% rename from src/USER-SMD/pair_smd_triangulated_surface.cpp rename to src/MACHDYN/pair_smd_triangulated_surface.cpp index 36a34b5f1c..0d6abb6dfb 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/MACHDYN/pair_smd_triangulated_surface.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_triangulated_surface.h b/src/MACHDYN/pair_smd_triangulated_surface.h similarity index 97% rename from src/USER-SMD/pair_smd_triangulated_surface.h rename to src/MACHDYN/pair_smd_triangulated_surface.h index 5e2c8e3fc4..57865e7983 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.h +++ b/src/MACHDYN/pair_smd_triangulated_surface.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/MACHDYN/pair_smd_ulsph.cpp similarity index 99% rename from src/USER-SMD/pair_smd_ulsph.cpp rename to src/MACHDYN/pair_smd_ulsph.cpp index 38a80195e9..0958cbc7c3 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/MACHDYN/pair_smd_ulsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_ulsph.h b/src/MACHDYN/pair_smd_ulsph.h similarity index 98% rename from src/USER-SMD/pair_smd_ulsph.h rename to src/MACHDYN/pair_smd_ulsph.h index b9ae311917..6d58168b5a 100644 --- a/src/USER-SMD/pair_smd_ulsph.h +++ b/src/MACHDYN/pair_smd_ulsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_kernels.h b/src/MACHDYN/smd_kernels.h similarity index 98% rename from src/USER-SMD/smd_kernels.h rename to src/MACHDYN/smd_kernels.h index 67244b64d3..07155f13a5 100644 --- a/src/USER-SMD/smd_kernels.h +++ b/src/MACHDYN/smd_kernels.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_material_models.cpp b/src/MACHDYN/smd_material_models.cpp similarity index 99% rename from src/USER-SMD/smd_material_models.cpp rename to src/MACHDYN/smd_material_models.cpp index a49b5b034d..cee0a3822e 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/MACHDYN/smd_material_models.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_material_models.h b/src/MACHDYN/smd_material_models.h similarity index 98% rename from src/USER-SMD/smd_material_models.h rename to src/MACHDYN/smd_material_models.h index 89dca2155a..df1d830445 100644 --- a/src/USER-SMD/smd_material_models.h +++ b/src/MACHDYN/smd_material_models.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_math.h b/src/MACHDYN/smd_math.h similarity index 99% rename from src/USER-SMD/smd_math.h rename to src/MACHDYN/smd_math.h index de8658b59c..369adb2321 100644 --- a/src/USER-SMD/smd_math.h +++ b/src/MACHDYN/smd_math.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/MAKE/OPTIONS/Makefile.intel_coprocessor b/src/MAKE/OPTIONS/Makefile.intel_coprocessor index b11256baa1..2b66c20f4a 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_coprocessor +++ b/src/MAKE/OPTIONS/Makefile.intel_coprocessor @@ -1,4 +1,4 @@ -# intel_coprocessor = USER-INTEL package with Phi offload support, Intel MPI, MKL FFT +# intel_coprocessor = INTEL package with Phi offload support, Intel MPI, MKL FFT SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi index 4adc427d91..04ec1fdc64 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi @@ -1,4 +1,4 @@ -# intel_cpu_intelmpi = USER-INTEL package, Intel MPI, MKL FFT +# intel_cpu_intelmpi = INTEL package, Intel MPI, MKL FFT SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich index 762899722c..dece0092f1 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich @@ -1,4 +1,4 @@ -# intel_cpu_mpich = USER-INTEL package, MPICH with compiler set to Intel icc +# intel_cpu_mpich = INTEL package, MPICH with compiler set to Intel icc SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi index 9adb5b1af2..0053aef20a 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi @@ -1,4 +1,4 @@ -# intel_cpu_openmpi = USER-INTEL package, OpenMPI with compiler set to Intel icc +# intel_cpu_openmpi = INTEL package, OpenMPI with compiler set to Intel icc SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.mgptfast b/src/MAKE/OPTIONS/Makefile.mgptfast index dc8682c3a6..da10701a9a 100644 --- a/src/MAKE/OPTIONS/Makefile.mgptfast +++ b/src/MAKE/OPTIONS/Makefile.mgptfast @@ -1,4 +1,4 @@ -# mgptfast = MPI with its default compiler, optimizations for USER-MGPT +# mgptfast = MPI with its default compiler, optimizations for MGPT SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.omp b/src/MAKE/OPTIONS/Makefile.omp index a6b45f7a31..0f49cdb15c 100644 --- a/src/MAKE/OPTIONS/Makefile.omp +++ b/src/MAKE/OPTIONS/Makefile.omp @@ -1,4 +1,4 @@ -# omp = USER-OMP package, MPI with its default compiler +# omp = OPENMP package, MPI with its default compiler SHELL = /bin/sh diff --git a/src/MAKE/README b/src/MAKE/README index 95f6c72a1a..bd883948a2 100644 --- a/src/MAKE/README +++ b/src/MAKE/README @@ -44,7 +44,7 @@ These Makefiles derive from src/MAKE/Makefile.mpi with added settings to illustrate how they can be added to any Makefile. Makefile.big use of -DLAMMPS_BIGBIG setting -Makefile.fastmgpt optimzations for USER-MGPT package +Makefile.fastmgpt optimzations for MGPT package Makefile.fftw FFTW support for long-range Coulombics (PPPM) Makefile.jpeg JPEG support for dump image Makefile.png PNG support for dump image @@ -63,14 +63,14 @@ the compiler wrapped by mpicxx. Setting this requires a different syntax for different MPIs. Makefile.opt OPT package, using default MPI -Makefile.omp USER-OMP package, using default MPI +Makefile.omp OPENMP package, using default MPI Makefile.gpu GPU package, using default MPI -Makefile.intel_cpu_intelmpi USER-INTEL package for CPU with Intel MPI -Makefile.intel_cpu_mpich USER-INTEL package for CPU with MPICH -Makefile.intel_cpu_openmpi USER-INTEL package for CPU with OpenMPI -Makefile.intel_coprocessor USER-INTEL package with Xeon Phi support -Makefile.knl USER-INTEL package with KNL support +Makefile.intel_cpu_intelmpi INTEL package for CPU with Intel MPI +Makefile.intel_cpu_mpich INTEL package for CPU with MPICH +Makefile.intel_cpu_openmpi INTEL package for CPU with OpenMPI +Makefile.intel_coprocessor INTEL package with Xeon Phi support +Makefile.knl INTEL package with KNL support Makefile.kokkos_cuda_mpich KOKKOS package with GPU support for MPICH Makefile.kokkos_cuda_openmpi KOKKOS package with GPU support for OpenMPI diff --git a/src/USER-MANIFOLD/README b/src/MANIFOLD/README similarity index 97% rename from src/USER-MANIFOLD/README rename to src/MANIFOLD/README index 24c645232d..3dd496ad03 100644 --- a/src/USER-MANIFOLD/README +++ b/src/MANIFOLD/README @@ -1,5 +1,5 @@ +==============================================================================+ -This file is a part of the USER-MANIFOLD package. +This file is a part of the MANIFOLD package. This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation @@ -21,7 +21,7 @@ This software is distributed under the GNU General Public License. +==============================================================================+ At the moment we have a few manifolds available, extending them is very easy: -To add a new manifold, do the following in the "USER-MANIFOLD" directory: +To add a new manifold, do the following in the "MANIFOLD" directory: 0. Create a new pair of source/header files, and name them "manifold_*.cpp/h", where you should replace '*' with some (descriptive) name. @@ -69,7 +69,7 @@ a relatively simple manifold. With those things in place, the install script should be able to add your manifold to LAMMPS without any extra work, so just running -make yes-user-manifold +make yes-manifold make should (re)compile LAMMPS with the manifolds added. diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/MANIFOLD/fix_manifoldforce.cpp similarity index 100% rename from src/USER-MANIFOLD/fix_manifoldforce.cpp rename to src/MANIFOLD/fix_manifoldforce.cpp diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/MANIFOLD/fix_manifoldforce.h similarity index 97% rename from src/USER-MANIFOLD/fix_manifoldforce.h rename to src/MANIFOLD/fix_manifoldforce.h index 285fcd5578..d58fe6001b 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/MANIFOLD/fix_manifoldforce.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2015) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/MANIFOLD/fix_nve_manifold_rattle.cpp similarity index 99% rename from src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp rename to src/MANIFOLD/fix_nve_manifold_rattle.cpp index b340869ea9..b4644a1350 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/MANIFOLD/fix_nve_manifold_rattle.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/MANIFOLD/fix_nve_manifold_rattle.h similarity index 98% rename from src/USER-MANIFOLD/fix_nve_manifold_rattle.h rename to src/MANIFOLD/fix_nve_manifold_rattle.h index e112b9bc7e..e2bf6b5639 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/MANIFOLD/fix_nve_manifold_rattle.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/MANIFOLD/fix_nvt_manifold_rattle.cpp similarity index 99% rename from src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp rename to src/MANIFOLD/fix_nvt_manifold_rattle.cpp index 57ae8ef109..f675cdff73 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h b/src/MANIFOLD/fix_nvt_manifold_rattle.h similarity index 98% rename from src/USER-MANIFOLD/fix_nvt_manifold_rattle.h rename to src/MANIFOLD/fix_nvt_manifold_rattle.h index 2e6115e692..d8439b1ad0 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h +++ b/src/MANIFOLD/fix_nvt_manifold_rattle.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/manifold.h b/src/MANIFOLD/manifold.h similarity index 98% rename from src/USER-MANIFOLD/manifold.h rename to src/MANIFOLD/manifold.h index f2f46a6647..92a5a02222 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/MANIFOLD/manifold.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation diff --git a/src/USER-MANIFOLD/manifold_cylinder.cpp b/src/MANIFOLD/manifold_cylinder.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder.cpp rename to src/MANIFOLD/manifold_cylinder.cpp diff --git a/src/USER-MANIFOLD/manifold_cylinder.h b/src/MANIFOLD/manifold_cylinder.h similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder.h rename to src/MANIFOLD/manifold_cylinder.h diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/MANIFOLD/manifold_cylinder_dent.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder_dent.cpp rename to src/MANIFOLD/manifold_cylinder_dent.cpp diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.h b/src/MANIFOLD/manifold_cylinder_dent.h similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder_dent.h rename to src/MANIFOLD/manifold_cylinder_dent.h diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/MANIFOLD/manifold_dumbbell.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_dumbbell.cpp rename to src/MANIFOLD/manifold_dumbbell.cpp diff --git a/src/USER-MANIFOLD/manifold_dumbbell.h b/src/MANIFOLD/manifold_dumbbell.h similarity index 100% rename from src/USER-MANIFOLD/manifold_dumbbell.h rename to src/MANIFOLD/manifold_dumbbell.h diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.cpp b/src/MANIFOLD/manifold_ellipsoid.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_ellipsoid.cpp rename to src/MANIFOLD/manifold_ellipsoid.cpp diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.h b/src/MANIFOLD/manifold_ellipsoid.h similarity index 100% rename from src/USER-MANIFOLD/manifold_ellipsoid.h rename to src/MANIFOLD/manifold_ellipsoid.h diff --git a/src/USER-MANIFOLD/manifold_factory.cpp b/src/MANIFOLD/manifold_factory.cpp similarity index 98% rename from src/USER-MANIFOLD/manifold_factory.cpp rename to src/MANIFOLD/manifold_factory.cpp index 8b3e3d02d0..6fa73643b5 100644 --- a/src/USER-MANIFOLD/manifold_factory.cpp +++ b/src/MANIFOLD/manifold_factory.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/MANIFOLD/manifold_factory.h similarity index 97% rename from src/USER-MANIFOLD/manifold_factory.h rename to src/MANIFOLD/manifold_factory.h index ddaf965169..4cf27b0b83 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/MANIFOLD/manifold_factory.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/MANIFOLD/manifold_gaussian_bump.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_gaussian_bump.cpp rename to src/MANIFOLD/manifold_gaussian_bump.cpp diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.h b/src/MANIFOLD/manifold_gaussian_bump.h similarity index 98% rename from src/USER-MANIFOLD/manifold_gaussian_bump.h rename to src/MANIFOLD/manifold_gaussian_bump.h index 75c0ce6644..8c72db080f 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.h +++ b/src/MANIFOLD/manifold_gaussian_bump.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/MANIFOLD/manifold_plane.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_plane.cpp rename to src/MANIFOLD/manifold_plane.cpp diff --git a/src/USER-MANIFOLD/manifold_plane.h b/src/MANIFOLD/manifold_plane.h similarity index 100% rename from src/USER-MANIFOLD/manifold_plane.h rename to src/MANIFOLD/manifold_plane.h diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/MANIFOLD/manifold_plane_wiggle.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_plane_wiggle.cpp rename to src/MANIFOLD/manifold_plane_wiggle.cpp diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.h b/src/MANIFOLD/manifold_plane_wiggle.h similarity index 100% rename from src/USER-MANIFOLD/manifold_plane_wiggle.h rename to src/MANIFOLD/manifold_plane_wiggle.h diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/MANIFOLD/manifold_sphere.h similarity index 100% rename from src/USER-MANIFOLD/manifold_sphere.h rename to src/MANIFOLD/manifold_sphere.h diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/MANIFOLD/manifold_spine.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_spine.cpp rename to src/MANIFOLD/manifold_spine.cpp diff --git a/src/USER-MANIFOLD/manifold_spine.h b/src/MANIFOLD/manifold_spine.h similarity index 100% rename from src/USER-MANIFOLD/manifold_spine.h rename to src/MANIFOLD/manifold_spine.h diff --git a/src/USER-MANIFOLD/manifold_supersphere.h b/src/MANIFOLD/manifold_supersphere.h similarity index 100% rename from src/USER-MANIFOLD/manifold_supersphere.h rename to src/MANIFOLD/manifold_supersphere.h diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/MANIFOLD/manifold_thylakoid.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid.cpp rename to src/MANIFOLD/manifold_thylakoid.cpp diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/MANIFOLD/manifold_thylakoid.h similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid.h rename to src/MANIFOLD/manifold_thylakoid.h diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/MANIFOLD/manifold_thylakoid_shared.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid_shared.cpp rename to src/MANIFOLD/manifold_thylakoid_shared.cpp diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.h b/src/MANIFOLD/manifold_thylakoid_shared.h similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid_shared.h rename to src/MANIFOLD/manifold_thylakoid_shared.h diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/MANIFOLD/manifold_torus.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_torus.cpp rename to src/MANIFOLD/manifold_torus.cpp diff --git a/src/USER-MANIFOLD/manifold_torus.h b/src/MANIFOLD/manifold_torus.h similarity index 100% rename from src/USER-MANIFOLD/manifold_torus.h rename to src/MANIFOLD/manifold_torus.h diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index b18dbfef90..67ff81d4a3 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -85,10 +85,10 @@ PairAIREBO::~PairAIREBO() { memory->destroy(REBO_numneigh); memory->sfree(REBO_firstneigh); - delete [] ipage; + delete[] ipage; memory->destroy(nC); memory->destroy(nH); - delete [] pvector; + delete[] pvector; if (allocated) { memory->destroy(setflag); @@ -100,7 +100,7 @@ PairAIREBO::~PairAIREBO() memory->destroy(lj2); memory->destroy(lj3); memory->destroy(lj4); - delete [] map; + delete[] map; } } @@ -112,9 +112,9 @@ void PairAIREBO::compute(int eflag, int vflag) pvector[0] = pvector[1] = pvector[2] = 0.0; REBO_neigh(); - FREBO(eflag,vflag); - if (ljflag) FLJ(eflag,vflag); - if (torflag) TORSION(eflag,vflag); + FREBO(eflag); + if (ljflag) FLJ(eflag); + if (torflag) TORSION(eflag); if (vflag_fdotr) virial_fdotr_compute(); } @@ -252,7 +252,7 @@ void PairAIREBO::init_style() if (oneatom != neighbor->oneatom) create = 1; if (create) { - delete [] ipage; + delete[] ipage; pgsize = neighbor->pgsize; oneatom = neighbor->oneatom; @@ -421,7 +421,7 @@ void PairAIREBO::REBO_neigh() REBO forces and energy ------------------------------------------------------------------------- */ -void PairAIREBO::FREBO(int eflag, int /*vflag*/) +void PairAIREBO::FREBO(int eflag) { int i,j,k,m,ii,inum,itype,jtype; tagint itag,jtag; @@ -497,7 +497,7 @@ void PairAIREBO::FREBO(int eflag, int /*vflag*/) del[0] = delx; del[1] = dely; del[2] = delz; - bij = bondorder(i,j,del,rij,VA,f,vflag_atom); + bij = bondorder(i,j,del,rij,VA,f); dVAdi = bij*dVA; fpair = -(dVRdi+dVAdi) / rij; @@ -520,7 +520,7 @@ void PairAIREBO::FREBO(int eflag, int /*vflag*/) find 3- and 4-step paths between atoms I,J via REBO neighbor lists ------------------------------------------------------------------------- */ -void PairAIREBO::FLJ(int eflag, int /*vflag*/) +void PairAIREBO::FLJ(int eflag) { int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype; int atomi,atomj,atomk,atomm; @@ -786,8 +786,7 @@ void PairAIREBO::FLJ(int eflag, int /*vflag*/) delscale[0] = scale * delij[0]; delscale[1] = scale * delij[1]; delscale[2] = scale * delij[2]; - Stb = bondorderLJ(i,j,delscale,rcmin[itype][jtype],VA, - delij,rij,f,vflag_atom); + Stb = bondorderLJ(i,j,delscale,rcmin[itype][jtype],VA,delij,rij,f); } else Stb = 0.0; fpair = -(dStr * (Stb*cij*VLJ - cij*VLJ) + @@ -815,7 +814,7 @@ void PairAIREBO::FLJ(int eflag, int /*vflag*/) f[atomj][1] -= delij[1]*fpair; f[atomj][2] -= delij[2]*fpair; - if (vflag_atom) v_tally2(atomi,atomj,fpair,delij); + if (vflag_either) v_tally2(atomi,atomj,fpair,delij); } else if (npath == 3) { fpair1 = dC*dwikS*wkjS / rikS; @@ -837,7 +836,7 @@ void PairAIREBO::FLJ(int eflag, int /*vflag*/) f[atomk][1] -= fi[1] + fj[1]; f[atomk][2] -= fi[2] + fj[2]; - if (vflag_atom) + if (vflag_either) v_tally3(atomi,atomj,atomk,fi,fj,delikS,deljkS); } else if (npath == 4) { @@ -873,7 +872,7 @@ void PairAIREBO::FLJ(int eflag, int /*vflag*/) f[atomm][1] += fm[1]; f[atomm][2] += fm[2]; - if (vflag_atom) { + if (vflag_either) { delimS[0] = delikS[0] + delkmS[0]; delimS[1] = delikS[1] + delkmS[1]; delimS[2] = delikS[2] + delkmS[2]; @@ -889,7 +888,7 @@ void PairAIREBO::FLJ(int eflag, int /*vflag*/) torsional forces and energy ------------------------------------------------------------------------- */ -void PairAIREBO::TORSION(int eflag, int /*vflag*/) +void PairAIREBO::TORSION(int eflag) { int i,j,k,l,ii,inum; tagint itag,jtag; @@ -1249,9 +1248,7 @@ void PairAIREBO::TORSION(int eflag, int /*vflag*/) Bij function ------------------------------------------------------------------------- */ -double PairAIREBO::bondorder(int i, int j, double rij[3], - double rijmag, double VA, - double **f, int vflag_atom) +double PairAIREBO::bondorder(int i, int j, double rij[3], double rijmag, double VA, double **f) { int atomi,atomj,k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4; int itype,jtype,ktype,ltype,ntype; @@ -1435,7 +1432,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2]; - if (vflag_atom) { + if (vflag_either) { rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2]; rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2]; v_tally3(atomi,atomj,atomk,fj,fk,rji,rki); @@ -1577,7 +1574,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2]; - if (vflag_atom) { + if (vflag_either) { rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2]; v_tally3(atomi,atomj,atoml,fi,fl,rij,rlj); } @@ -1613,7 +1610,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -1627,7 +1624,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -1649,7 +1646,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn); + if (vflag_either) v_tally2(atomk,atomn,-tmp2,rkn); } } } @@ -1680,7 +1677,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -1694,7 +1691,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -1716,7 +1713,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln); + if (vflag_either) v_tally2(atoml,atomn,-tmp2,rln); } } } @@ -1928,7 +1925,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atom4][0] += f4[0]; f[atom4][1] += f4[1]; f[atom4][2] += f4[2]; - if (vflag_atom) { + if (vflag_either) { r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2]; r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2]; v_tally4(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43); @@ -1964,7 +1961,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -1978,7 +1975,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -2000,7 +1997,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn); + if (vflag_either) v_tally2(atomk,atomn,-tmp2,rkn); } } } @@ -2031,7 +2028,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -2045,7 +2042,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -2067,7 +2064,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln); + if (vflag_either) v_tally2(atoml,atomn,-tmp2,rln); } } } @@ -2113,8 +2110,7 @@ but of the vector r_ij. */ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rijmag_mod, - double VA, double rij[3], double rijmag, - double **f, int vflag_atom) + double VA, double rij[3], double rijmag, double **f) { int atomi,atomj,k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4; int itype,jtype,ktype,ltype,ntype; @@ -2438,7 +2434,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2]; - if (vflag_atom) { + if (vflag_either) { rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2]; rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2]; v_tally3(atomi,atomj,atomk,fj,fk,rji,rki); @@ -2542,7 +2538,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2]; - if (vflag_atom) { + if (vflag_either) { rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2]; v_tally3(atomi,atomj,atoml,fi,fl,rij,rlj); } @@ -2577,7 +2573,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -2591,7 +2587,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -2613,7 +2609,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn); + if (vflag_either) v_tally2(atomk,atomn,-tmp2,rkn); } } } @@ -2644,7 +2640,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -2658,7 +2654,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -2680,7 +2676,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln); + if (vflag_either) v_tally2(atoml,atomn,-tmp2,rln); } } } @@ -2885,7 +2881,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atom4][0] += f4[0]; f[atom4][1] += f4[1]; f[atom4][2] += f4[2]; - if (vflag_atom) { + if (vflag_either) { r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2]; r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2]; v_tally4(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43); @@ -2919,7 +2915,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -2933,7 +2929,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik); + if (vflag_either) v_tally2(atomi,atomk,-tmp2,rik); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -2955,7 +2951,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn); + if (vflag_either) v_tally2(atomk,atomn,-tmp2,rkn); } } } @@ -2986,7 +2982,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -3000,7 +2996,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl); + if (vflag_either) v_tally2(atomj,atoml,-tmp2,rjl); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -3022,7 +3018,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rij f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln); + if (vflag_either) v_tally2(atoml,atomn,-tmp2,rln); } } } diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index fa1572b1e4..fc511b7bb0 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -96,12 +96,12 @@ class PairAIREBO : public Pair { double Tf[5][5][10], Tdfdx[5][5][10], Tdfdy[5][5][10], Tdfdz[5][5][10]; void REBO_neigh(); - void FREBO(int, int); - void FLJ(int, int); - void TORSION(int, int); + void FREBO(int); + void FLJ(int); + void TORSION(int); - double bondorder(int, int, double *, double, double, double **, int); - double bondorderLJ(int, int, double *, double, double, double *, double, double **, int); + double bondorder(int, int, double *, double, double, double **); + double bondorderLJ(int, int, double *, double, double, double *, double, double **); double gSpline(double, double, int, double *, double *); double PijSpline(double, double, int, int, double *); diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 0dbcb1de15..e2a677c2a0 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -251,10 +251,8 @@ void PairBOP::compute(int eflag, int vflag) f[j][1] -= ftmp2; f[j][2] -= ftmp3; dE = pl_ij.rep - 2.0*pl_ij.betaS*sigB_0 - 2.0*pl_ij.betaP*piB_0; - if (evflag) { - ev_tally(i,j,nlocal,newton_pair, dE, 0.0, dpr1, - pl_ij.dis[0],pl_ij.dis[1],pl_ij.dis[2]); - } + if (evflag) ev_tally(i,j,nlocal,newton_pair, dE, 0.0, -dpr1, + pl_ij.dis[0],pl_ij.dis[1],pl_ij.dis[2]); } nlisti = BOP_total2[i]; for (jj = 0; jj < nlisti; jj++) { @@ -274,10 +272,8 @@ void PairBOP::compute(int eflag, int vflag) f[j][1] -= ftmp2; f[j][2] -= ftmp3; dE = -p2_ij.rep; - if (evflag) { - ev_tally(i,j,nlocal,newton_pair, dE, 0.0, dpr2, - p2_ij.dis[0],p2_ij.dis[1],p2_ij.dis[2]); - } + if (evflag) ev_tally(i,j,nlocal,newton_pair, dE, 0.0, -dpr2, + p2_ij.dis[0],p2_ij.dis[1],p2_ij.dis[2]); } } if (vflag_fdotr) virial_fdotr_compute(); @@ -1142,10 +1138,8 @@ double PairBOP::SigmaBo(int itmp, int jtmp) f[bt_i][n] -= ftmp[n]; f[bt_j][n] += ftmp[n]; } - if (evflag) { - ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0, - ftmp[0],ftmp[1],ftmp[2],xtmp[0],xtmp[1],xtmp[2]); - } + if (evflag) ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0, + -ftmp[0],-ftmp[1],-ftmp[2],xtmp[0],xtmp[1],xtmp[2]); } else { for (int n = 0; n < 3; n++) { bt_sg[loop].dSigB[n] = dsigB*part2*bt_sg[loop].dSigB1[n] - @@ -1157,10 +1151,8 @@ double PairBOP::SigmaBo(int itmp, int jtmp) f[bt_i][n] -= ftmp[n]; f[bt_j][n] += ftmp[n]; } - if (evflag) { - ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0, - ftmp[0],ftmp[1],ftmp[2],xtmp[0],xtmp[1],xtmp[2]); - } + if (evflag) ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0, + -ftmp[0],-ftmp[1],-ftmp[2],xtmp[0],xtmp[1],xtmp[2]); } } return(sigB); @@ -1841,10 +1833,8 @@ double PairBOP::PiBo(int itmp, int jtmp) f[bt_i][n] -= ftmp[n]; f[bt_j][n] += ftmp[n]; } - if (evflag) { - ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0,ftmp[0],ftmp[1], - ftmp[2],xtmp[0],xtmp[1],xtmp[2]); - } + if (evflag) ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0, + -ftmp[0],-ftmp[1],-ftmp[2],xtmp[0],xtmp[1],xtmp[2]); } return(piB); } diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index fd278d1488..689ba992d8 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -394,7 +394,7 @@ void PairComb::compute(int eflag, int vflag) if (evflag) ev_tally(i,j,nlocal,newton_pair,elp_ij,0.0,0.0,0.0,0.0,0.0); - if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2); + if (vflag_either) v_tally3(i,j,k,fj,fk,delr1,delr2); } } diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index c3d9c3043f..eee97849b9 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -1294,7 +1294,7 @@ void PairComb3::compute(int eflag, int vflag) if (evflag) ev_tally(i,j,nlocal,newton_pair,ep6p_ij,0.0,0.0,0.0,0.0,0.0); - if (vflag_atom) + if (vflag_either) v_tally3(i,j,k,fj,fk,delrj,delrk); } // k-loop @@ -1387,7 +1387,7 @@ void PairComb3::compute(int eflag, int vflag) } } - if (vflag_atom) + if (vflag_either) v_tally3(j,i,l,fi,fl,delrl,delrk); } } diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 5ec89cbe7e..2b206689d6 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -28,7 +28,7 @@ class PairEAM : public Pair { public: friend class FixSemiGrandCanonicalMC; // Alex Stukowski option - // public variables so USER-ATC package can access them + // public variables so ATC package can access them double cutmax; diff --git a/src/USER-MISC/pair_edip.cpp b/src/MANYBODY/pair_edip.cpp similarity index 52% rename from src/USER-MISC/pair_edip.cpp rename to src/MANYBODY/pair_edip.cpp index 3f80609853..5efc5b7980 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/MANYBODY/pair_edip.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -34,8 +33,8 @@ #include "neighbor.h" #include -#include #include +#include using namespace LAMMPS_NS; @@ -52,12 +51,11 @@ static constexpr int leadDimInteractionList = 64; /* ---------------------------------------------------------------------- */ PairEDIP::PairEDIP(LAMMPS *lmp) : - Pair(lmp), preInvR_ij(nullptr), preExp3B_ij(nullptr), preExp3BDerived_ij(nullptr), - preExp2B_ij(nullptr), preExp2BDerived_ij(nullptr), prePow2B_ij(nullptr), - preForceCoord(nullptr), cutoffFunction(nullptr), cutoffFunctionDerived(nullptr), - pow2B(nullptr), exp2B(nullptr), exp3B(nullptr), qFunctionGrid(nullptr), - expMinusBetaZeta_iZeta_iGrid(nullptr), tauFunctionGrid(nullptr), - tauFunctionDerivedGrid(nullptr) + Pair(lmp), preInvR_ij(nullptr), preExp3B_ij(nullptr), preExp3BDerived_ij(nullptr), + preExp2B_ij(nullptr), preExp2BDerived_ij(nullptr), prePow2B_ij(nullptr), preForceCoord(nullptr), + cutoffFunction(nullptr), cutoffFunctionDerived(nullptr), pow2B(nullptr), exp2B(nullptr), + exp3B(nullptr), qFunctionGrid(nullptr), expMinusBetaZeta_iZeta_iGrid(nullptr), + tauFunctionGrid(nullptr), tauFunctionDerivedGrid(nullptr) { single_enable = 0; restartinfo = 0; @@ -90,10 +88,10 @@ PairEDIP::~PairEDIP() void PairEDIP::compute(int eflag, int vflag) { - int i,j,k,ii,inum,jnum; - int itype,jtype,ktype,ijparam,ikparam; - double xtmp,ytmp,ztmp,evdwl; - int *ilist,*jlist,*numneigh,**firstneigh; + int i, j, k, ii, inum, jnum; + int itype, jtype, ktype, ijparam, ikparam; + double xtmp, ytmp, ztmp, evdwl; + int *ilist, *jlist, *numneigh, **firstneigh; int preForceCoord_counter; double invR_ij; @@ -149,7 +147,7 @@ void PairEDIP::compute(int eflag, int vflag) double potential2B_factor; evdwl = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -180,86 +178,82 @@ void PairEDIP::compute(int eflag, int vflag) // pre-loop to compute environment coordination f(Z) for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { - j = jlist[neighbor_j]; - j &= NEIGHMASK; + j = jlist[neighbor_j]; + j &= NEIGHMASK; - double dr_ij[3], r_ij; + double dr_ij[3], r_ij; - dr_ij[0] = xtmp - x[j][0]; - dr_ij[1] = ytmp - x[j][1]; - dr_ij[2] = ztmp - x[j][2]; - r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; + dr_ij[0] = xtmp - x[j][0]; + dr_ij[1] = ytmp - x[j][1]; + dr_ij[2] = ztmp - x[j][2]; + r_ij = dr_ij[0] * dr_ij[0] + dr_ij[1] * dr_ij[1] + dr_ij[2] * dr_ij[2]; - jtype = map[type[j]]; - ijparam = elem3param[itype][jtype][jtype]; - if (r_ij > params[ijparam].cutsq) continue; + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + if (r_ij > params[ijparam].cutsq) continue; - r_ij = sqrt(r_ij); + r_ij = sqrt(r_ij); - invR_ij = 1.0 / r_ij; - preInvR_ij[neighbor_j] = invR_ij; + invR_ij = 1.0 / r_ij; + preInvR_ij[neighbor_j] = invR_ij; - invRMinusCutoffA = 1.0 / (r_ij - cutoffA); - sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA; - gammInvRMinusCutoffA = gamm * invRMinusCutoffA; + invRMinusCutoffA = 1.0 / (r_ij - cutoffA); + sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA; + gammInvRMinusCutoffA = gamm * invRMinusCutoffA; - interpolDeltaX = r_ij - GRIDSTART; - interpolTMP = (interpolDeltaX * GRIDDENSITY); - interpolIDX = (int) interpolTMP; + interpolDeltaX = r_ij - GRIDSTART; + interpolTMP = (interpolDeltaX * GRIDDENSITY); + interpolIDX = (int) interpolTMP; - interpolY1 = exp3B[interpolIDX]; - interpolY2 = exp3B[interpolIDX+1]; - exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY1 = exp3B[interpolIDX]; + interpolY2 = exp3B[interpolIDX + 1]; + exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); - exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA; + exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA; - preExp3B_ij[neighbor_j] = exp3B_ij; - preExp3BDerived_ij[neighbor_j] = exp3BDerived_ij; + preExp3B_ij[neighbor_j] = exp3B_ij; + preExp3BDerived_ij[neighbor_j] = exp3BDerived_ij; - interpolY1 = exp2B[interpolIDX]; - interpolY2 = exp2B[interpolIDX+1]; - exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY1 = exp2B[interpolIDX]; + interpolY2 = exp2B[interpolIDX + 1]; + exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); - exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA; + exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA; - preExp2B_ij[neighbor_j] = exp2B_ij; - preExp2BDerived_ij[neighbor_j] = exp2BDerived_ij; + preExp2B_ij[neighbor_j] = exp2B_ij; + preExp2BDerived_ij[neighbor_j] = exp2BDerived_ij; - interpolY1 = pow2B[interpolIDX]; - interpolY2 = pow2B[interpolIDX+1]; - pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY1 = pow2B[interpolIDX]; + interpolY2 = pow2B[interpolIDX + 1]; + pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); - prePow2B_ij[neighbor_j] = pow2B_ij; + prePow2B_ij[neighbor_j] = pow2B_ij; - // zeta and its derivative + // zeta and its derivative - if (r_ij < cutoffC) zeta_i += 1.0; - else { - interpolY1 = cutoffFunction[interpolIDX]; - interpolY2 = cutoffFunction[interpolIDX+1]; - cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + if (r_ij < cutoffC) + zeta_i += 1.0; + else { + interpolY1 = cutoffFunction[interpolIDX]; + interpolY2 = cutoffFunction[interpolIDX + 1]; + cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); - zeta_i += cutoffFunction_ij; + zeta_i += cutoffFunction_ij; - interpolY1 = cutoffFunctionDerived[interpolIDX]; - interpolY2 = cutoffFunctionDerived[interpolIDX+1]; - zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY1 = cutoffFunctionDerived[interpolIDX]; + interpolY2 = cutoffFunctionDerived[interpolIDX + 1]; + zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); - zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij; + zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij; - preForceCoord_counter=numForceCoordPairs*5; - preForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij; - preForceCoord[preForceCoord_counter+1]=dr_ij[0]; - preForceCoord[preForceCoord_counter+2]=dr_ij[1]; - preForceCoord[preForceCoord_counter+3]=dr_ij[2]; - preForceCoord[preForceCoord_counter+4]=j; - numForceCoordPairs++; - } + preForceCoord_counter = numForceCoordPairs * 5; + preForceCoord[preForceCoord_counter + 0] = zeta_iDerivedInvR_ij; + preForceCoord[preForceCoord_counter + 1] = dr_ij[0]; + preForceCoord[preForceCoord_counter + 2] = dr_ij[1]; + preForceCoord[preForceCoord_counter + 3] = dr_ij[2]; + preForceCoord[preForceCoord_counter + 4] = j; + numForceCoordPairs++; + } } // quantities depending on zeta_i @@ -269,24 +263,20 @@ void PairEDIP::compute(int eflag, int vflag) interpolIDX = (int) interpolTMP; interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX]; - interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1]; - expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX + 1]; + expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); interpolY1 = qFunctionGrid[interpolIDX]; - interpolY2 = qFunctionGrid[interpolIDX+1]; - qFunction = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY2 = qFunctionGrid[interpolIDX + 1]; + qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); interpolY1 = tauFunctionGrid[interpolIDX]; - interpolY2 = tauFunctionGrid[interpolIDX+1]; - tauFunction = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY2 = tauFunctionGrid[interpolIDX + 1]; + tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); interpolY1 = tauFunctionDerivedGrid[interpolIDX]; - interpolY2 = tauFunctionDerivedGrid[interpolIDX+1]; - tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); + interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1]; + tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i; @@ -303,7 +293,7 @@ void PairEDIP::compute(int eflag, int vflag) dr_ij[0] = x[j][0] - xtmp; dr_ij[1] = x[j][1] - ytmp; dr_ij[2] = x[j][2] - ztmp; - r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; + r_ij = dr_ij[0] * dr_ij[0] + dr_ij[1] * dr_ij[1] + dr_ij[2] * dr_ij[2]; jtype = map[type[j]]; ijparam = elem3param[itype][jtype][jtype]; @@ -318,13 +308,12 @@ void PairEDIP::compute(int eflag, int vflag) exp2B_ij = preExp2B_ij[neighbor_j]; - pow2BDerived_ij = - rho * invR_ij * pow2B_ij; + pow2BDerived_ij = -rho * invR_ij * pow2B_ij; - forceModCoord += (forceModCoord_factor*exp2B_ij); + forceModCoord += (forceModCoord_factor * exp2B_ij); exp2BDerived_ij = preExp2BDerived_ij[neighbor_j]; - forceMod2B = exp2BDerived_ij * potential2B_factor + - exp2B_ij * pow2BDerived_ij; + forceMod2B = exp2BDerived_ij * potential2B_factor + exp2B_ij * pow2BDerived_ij; directorCos_ij_x = invR_ij * dr_ij[0]; directorCos_ij_y = invR_ij * dr_ij[1]; @@ -349,136 +338,123 @@ void PairEDIP::compute(int eflag, int vflag) evdwl = (exp2B_ij * potential2B_factor); - if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, - -forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2]); + if (evflag) + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, -forceMod2B * invR_ij, dr_ij[0], dr_ij[1], + dr_ij[2]); // three-body Forces for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) { - double dr_ik[3], r_ik, f_ik[3]; + double dr_ik[3], r_ik, f_ik[3]; - k = jlist[neighbor_k]; - k &= NEIGHMASK; - ktype = map[type[k]]; - ikparam = elem3param[itype][ktype][ktype]; + k = jlist[neighbor_k]; + k &= NEIGHMASK; + ktype = map[type[k]]; + ikparam = elem3param[itype][ktype][ktype]; - dr_ik[0] = x[k][0] - xtmp; - dr_ik[1] = x[k][1] - ytmp; - dr_ik[2] = x[k][2] - ztmp; - r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2]; + dr_ik[0] = x[k][0] - xtmp; + dr_ik[1] = x[k][1] - ytmp; + dr_ik[2] = x[k][2] - ztmp; + r_ik = dr_ik[0] * dr_ik[0] + dr_ik[1] * dr_ik[1] + dr_ik[2] * dr_ik[2]; - if (r_ik > params[ikparam].cutsq) continue; + if (r_ik > params[ikparam].cutsq) continue; - r_ik = sqrt(r_ik); + r_ik = sqrt(r_ik); - invR_ik = preInvR_ij[neighbor_k]; + invR_ik = preInvR_ij[neighbor_k]; - directorCos_ik_x = invR_ik * dr_ik[0]; - directorCos_ik_y = invR_ik * dr_ik[1]; - directorCos_ik_z = invR_ik * dr_ik[2]; + directorCos_ik_x = invR_ik * dr_ik[0]; + directorCos_ik_y = invR_ik * dr_ik[1]; + directorCos_ik_z = invR_ik * dr_ik[2]; - cosTeta = directorCos_ij_x * directorCos_ik_x + - directorCos_ij_y * directorCos_ik_y + + cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z; - cosTetaDiff = cosTeta + tauFunction; - cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff; - qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction; - expMinusQFunctionCosTetaDiffCosTetaDiff = - exp(-qFunctionCosTetaDiffCosTetaDiff); + cosTetaDiff = cosTeta + tauFunction; + cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff; + qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction; + expMinusQFunctionCosTetaDiffCosTetaDiff = exp(-qFunctionCosTetaDiffCosTetaDiff); - potentia3B_factor = lambda * + potentia3B_factor = lambda * ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) + eta * qFunctionCosTetaDiffCosTetaDiff); - exp3B_ik = preExp3B_ij[neighbor_k]; - exp3BDerived_ik = preExp3BDerived_ij[neighbor_k]; + exp3B_ik = preExp3B_ij[neighbor_k]; + exp3BDerived_ik = preExp3BDerived_ij[neighbor_k]; - forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik * - potentia3B_factor; - forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik * - qFunction * cosTetaDiff * + forceMod3B_factor1_ij = -exp3BDerived_ij * exp3B_ik * potentia3B_factor; + forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik * qFunction * cosTetaDiff * (eta + expMinusQFunctionCosTetaDiffCosTetaDiff); - forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij; + forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij; - f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x + - forceMod3B_factor2_ij * - (cosTeta * directorCos_ij_x - directorCos_ik_x); - f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y + - forceMod3B_factor2_ij * - (cosTeta * directorCos_ij_y - directorCos_ik_y); - f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z + - forceMod3B_factor2_ij * - (cosTeta * directorCos_ij_z - directorCos_ik_z); + f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x + + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_x - directorCos_ik_x); + f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y + + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_y - directorCos_ik_y); + f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z + + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_z - directorCos_ik_z); - forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij * - potentia3B_factor; - forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik; + forceMod3B_factor1_ik = -exp3BDerived_ik * exp3B_ij * potentia3B_factor; + forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik; - f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x + - forceMod3B_factor2_ik * - (cosTeta * directorCos_ik_x - directorCos_ij_x); - f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y + - forceMod3B_factor2_ik * - (cosTeta * directorCos_ik_y - directorCos_ij_y); - f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z + - forceMod3B_factor2_ik * - (cosTeta * directorCos_ik_z - directorCos_ij_z); + f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x + + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_x - directorCos_ij_x); + f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y + + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_y - directorCos_ij_y); + f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z + + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_z - directorCos_ij_z); - forceModCoord += (forceMod3B_factor2 * - (tauFunctionDerived - 0.5 * mu * cosTetaDiff)); + forceModCoord += (forceMod3B_factor2 * (tauFunctionDerived - 0.5 * mu * cosTetaDiff)); - f[j][0] += f_ij[0]; - f[j][1] += f_ij[1]; - f[j][2] += f_ij[2]; + f[j][0] += f_ij[0]; + f[j][1] += f_ij[1]; + f[j][2] += f_ij[2]; - f[k][0] += f_ik[0]; - f[k][1] += f_ik[1]; - f[k][2] += f_ik[2]; + f[k][0] += f_ik[0]; + f[k][1] += f_ik[1]; + f[k][2] += f_ik[2]; - f[i][0] -= f_ij[0] + f_ik[0]; - f[i][1] -= f_ij[1] + f_ik[1]; - f[i][2] -= f_ij[2] + f_ik[2]; + f[i][0] -= f_ij[0] + f_ik[0]; + f[i][1] -= f_ij[1] + f_ik[1]; + f[i][2] -= f_ij[2] + f_ik[2]; - // potential energy + // potential energy - evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor); + evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor); - if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik); + if (evflag) ev_tally3(i, j, k, evdwl, 0.0, f_ij, f_ik, dr_ij, dr_ik); } } // forces due to environment coordination f(Z) for (int idx = 0; idx < numForceCoordPairs; idx++) { - double dr_ij[3],f_ij[3]; + double dr_ij[3], f_ij[3]; - preForceCoord_counter = idx * 5; - zeta_iDerivedInvR_ij=preForceCoord[preForceCoord_counter+0]; - dr_ij[0]=preForceCoord[preForceCoord_counter+1]; - dr_ij[1]=preForceCoord[preForceCoord_counter+2]; - dr_ij[2]=preForceCoord[preForceCoord_counter+3]; - j = static_cast (preForceCoord[preForceCoord_counter+4]); + preForceCoord_counter = idx * 5; + zeta_iDerivedInvR_ij = preForceCoord[preForceCoord_counter + 0]; + dr_ij[0] = preForceCoord[preForceCoord_counter + 1]; + dr_ij[1] = preForceCoord[preForceCoord_counter + 2]; + dr_ij[2] = preForceCoord[preForceCoord_counter + 3]; + j = static_cast(preForceCoord[preForceCoord_counter + 4]); - forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij; + forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij; - f_ij[0] = forceModCoord_ij * dr_ij[0]; - f_ij[1] = forceModCoord_ij * dr_ij[1]; - f_ij[2] = forceModCoord_ij * dr_ij[2]; + f_ij[0] = forceModCoord_ij * dr_ij[0]; + f_ij[1] = forceModCoord_ij * dr_ij[1]; + f_ij[2] = forceModCoord_ij * dr_ij[2]; - f[i][0] -= f_ij[0]; - f[i][1] -= f_ij[1]; - f[i][2] -= f_ij[2]; + f[i][0] -= f_ij[0]; + f[i][1] -= f_ij[1]; + f[i][2] -= f_ij[2]; - f[j][0] += f_ij[0]; - f[j][1] += f_ij[1]; - f[j][2] += f_ij[2]; + f[j][0] += f_ij[0]; + f[j][1] += f_ij[1]; + f[j][2] += f_ij[2]; - // potential energy - - evdwl = 0.0; - if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, - -forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]); + if (evflag) + ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, -forceModCoord_ij, dr_ij[0], dr_ij[1], + dr_ij[2]); } } @@ -500,58 +476,51 @@ void PairEDIP::allocateGrids(void) double maxArgumentTauFunctionGrid; double maxArgumentQFunctionGrid; double maxArgumentExpMinusBetaZeta_iZeta_i; - double const leftLimitToZero = -DBL_MIN * 1000.0; + double const leftLimitToZero = -std::numeric_limits::min() * 1000.0; deallocateGrids(); // tauFunctionGrid maxArgumentTauFunctionGrid = leadDimInteractionList; - numGridPointsTauFunctionGrid = (int) - ((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2; + numGridPointsTauFunctionGrid = (int) ((maxArgumentTauFunctionGrid) *GRIDDENSITY) + 2; - memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid, - "edip:tauFunctionGrid"); - memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid, + memory->create(tauFunctionGrid, numGridPointsTauFunctionGrid, "edip:tauFunctionGrid"); + memory->create(tauFunctionDerivedGrid, numGridPointsTauFunctionGrid, "edip:tauFunctionDerivedGrid"); // expMinusBetaZeta_iZeta_iGrid maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList; - numGridPointsExpMinusBetaZeta_iZeta_i = (int) - ((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2; - memory->create(expMinusBetaZeta_iZeta_iGrid, - numGridPointsExpMinusBetaZeta_iZeta_i, + numGridPointsExpMinusBetaZeta_iZeta_i = + (int) ((maxArgumentExpMinusBetaZeta_iZeta_i) *GRIDDENSITY) + 2; + memory->create(expMinusBetaZeta_iZeta_iGrid, numGridPointsExpMinusBetaZeta_iZeta_i, "edip:expMinusBetaZeta_iZeta_iGrid"); // qFunctionGrid maxArgumentQFunctionGrid = leadDimInteractionList; - numGridPointsQFunctionGrid = (int) - ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2; - memory->create(qFunctionGrid,numGridPointsQFunctionGrid,"edip:qFunctionGrid"); + numGridPointsQFunctionGrid = (int) ((maxArgumentQFunctionGrid) *GRIDDENSITY) + 2; + memory->create(qFunctionGrid, numGridPointsQFunctionGrid, "edip:qFunctionGrid"); // cutoffFunction numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY); - numGridPointsNotOneCutoffFunction = (int) ((cutoffA-cutoffC) * GRIDDENSITY); - numGridPointsCutoffFunction = numGridPointsOneCutoffFunction + - numGridPointsNotOneCutoffFunction+2; + numGridPointsNotOneCutoffFunction = (int) ((cutoffA - cutoffC) * GRIDDENSITY); + numGridPointsCutoffFunction = + numGridPointsOneCutoffFunction + numGridPointsNotOneCutoffFunction + 2; - memory->create(cutoffFunction,numGridPointsCutoffFunction, - "edip:cutoffFunction"); - memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction, - "edip:cutoffFunctionDerived"); + memory->create(cutoffFunction, numGridPointsCutoffFunction, "edip:cutoffFunction"); + memory->create(cutoffFunctionDerived, numGridPointsCutoffFunction, "edip:cutoffFunctionDerived"); // pow2B - numGridPointsR = (int) - ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY); + numGridPointsR = (int) ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY); numGridPointsRTotal = numGridPointsR + 2; - memory->create(pow2B,numGridPointsRTotal,"edip:pow2B"); - memory->create(exp2B,numGridPointsRTotal,"edip:exp2B"); - memory->create(exp3B,numGridPointsRTotal,"edip:exp3B"); + memory->create(pow2B, numGridPointsRTotal, "edip:pow2B"); + memory->create(exp2B, numGridPointsRTotal, "edip:exp2B"); + memory->create(exp3B, numGridPointsRTotal, "edip:exp3B"); } /* ---------------------------------------------------------------------- @@ -563,15 +532,13 @@ void PairEDIP::allocatePreLoops(void) int nthreads = comm->nthreads; deallocatePreLoops(); - memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij"); - memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij"); - memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList, - "edip:preExp3BDerived_ij"); - memory->create(preExp2B_ij,nthreads*leadDimInteractionList,"edip:preExp2B_ij"); - memory->create(preExp2BDerived_ij,nthreads*leadDimInteractionList, - "edip:preExp2BDerived_ij"); - memory->create(prePow2B_ij,nthreads*leadDimInteractionList,"edip:prePow2B_ij"); - memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord"); + memory->create(preInvR_ij, nthreads * leadDimInteractionList, "edip:preInvR_ij"); + memory->create(preExp3B_ij, nthreads * leadDimInteractionList, "edip:preExp3B_ij"); + memory->create(preExp3BDerived_ij, nthreads * leadDimInteractionList, "edip:preExp3BDerived_ij"); + memory->create(preExp2B_ij, nthreads * leadDimInteractionList, "edip:preExp2B_ij"); + memory->create(preExp2BDerived_ij, nthreads * leadDimInteractionList, "edip:preExp2BDerived_ij"); + memory->create(prePow2B_ij, nthreads * leadDimInteractionList, "edip:prePow2B_ij"); + memory->create(preForceCoord, 5 * nthreads * leadDimInteractionList, "edip:preForceCoord"); } /* ---------------------------------------------------------------------- @@ -613,19 +580,19 @@ void PairEDIP::allocate() allocated = 1; int n = atom->ntypes; - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); - map = new int[n+1]; + map = new int[n + 1]; } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ -void PairEDIP::settings(int narg, char **/*arg*/) +void PairEDIP::settings(int narg, char ** /*arg*/) { - if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + if (narg != 0) error->all(FLERR, "Illegal pair_style command"); } /* ---------------------------------------------------------------------- */ @@ -652,105 +619,97 @@ void PairEDIP::initGrids(void) double deltaArgumentQFunctionGrid; double deltaArgumentTauFunctionGrid; double deltaArgumentExpMinusBetaZeta_iZeta_i; - double const leftLimitToZero = -DBL_MIN * 1000.0; + double const leftLimitToZero = -std::numeric_limits::min() * 1000.0; // tauFunctionGrid maxArgumentTauFunctionGrid = leadDimInteractionList; - numGridPointsTauFunctionGrid = (int) - ((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2; + numGridPointsTauFunctionGrid = (int) ((maxArgumentTauFunctionGrid) *GRIDDENSITY) + 2; r = 0.0; deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY; for (l = 0; l < numGridPointsTauFunctionGrid; l++) { - tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) - - u2 * exp(-2.0 * u4 * r); - tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) + - 2.0 * u2 * u4 * exp(-2.0 * u4 * r); - r += deltaArgumentTauFunctionGrid; + tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) - u2 * exp(-2.0 * u4 * r); + tauFunctionDerivedGrid[l] = -u2 * u3 * u4 * exp(-u4 * r) + 2.0 * u2 * u4 * exp(-2.0 * u4 * r); + r += deltaArgumentTauFunctionGrid; } // expMinusBetaZeta_iZeta_iGrid maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList; - numGridPointsExpMinusBetaZeta_iZeta_i = (int) - ((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2; + numGridPointsExpMinusBetaZeta_iZeta_i = + (int) ((maxArgumentExpMinusBetaZeta_iZeta_i) *GRIDDENSITY) + 2; r = 0.0; deltaArgumentExpMinusBetaZeta_iZeta_i = 1.0 / GRIDDENSITY; for (l = 0; l < numGridPointsExpMinusBetaZeta_iZeta_i; l++) { - expMinusBetaZeta_iZeta_iGrid[l] = exp(-beta * r * r); - r += deltaArgumentExpMinusBetaZeta_iZeta_i; + expMinusBetaZeta_iZeta_iGrid[l] = exp(-beta * r * r); + r += deltaArgumentExpMinusBetaZeta_iZeta_i; } // qFunctionGrid maxArgumentQFunctionGrid = leadDimInteractionList; - numGridPointsQFunctionGrid = - (int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2; + numGridPointsQFunctionGrid = (int) ((maxArgumentQFunctionGrid) *GRIDDENSITY) + 2; r = 0.0; deltaArgumentQFunctionGrid = 1.0 / GRIDDENSITY; for (l = 0; l < numGridPointsQFunctionGrid; l++) { - qFunctionGrid[l] = Q0 * exp(-mu * r); - r += deltaArgumentQFunctionGrid; + qFunctionGrid[l] = Q0 * exp(-mu * r); + r += deltaArgumentQFunctionGrid; } // cutoffFunction - numGridPointsOneCutoffFunction = - (int) ((cutoffC - GRIDSTART) * GRIDDENSITY); - numGridPointsNotOneCutoffFunction = - (int) ((cutoffA-cutoffC) * GRIDDENSITY); + numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY); + numGridPointsNotOneCutoffFunction = (int) ((cutoffA - cutoffC) * GRIDDENSITY); numGridPointsCutoffFunction = - numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2; + numGridPointsOneCutoffFunction + numGridPointsNotOneCutoffFunction + 2; r = GRIDSTART; deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY; for (l = 0; l < numGridPointsOneCutoffFunction; l++) { - cutoffFunction[l] = 1.0; - cutoffFunctionDerived[l] = 0.0; - r += deltaArgumentCutoffFunction; + cutoffFunction[l] = 1.0; + cutoffFunctionDerived[l] = 0.0; + r += deltaArgumentCutoffFunction; } - for (l = numGridPointsOneCutoffFunction; - l < numGridPointsCutoffFunction; l++) { - temp = (cutoffA - cutoffC)/(r - cutoffC); - temp3 = temp * temp * temp; - temp4 = temp3 * temp; - cutoffFunction[l] = exp(alpha/(1.0-temp3)); - cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) * - (temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3)); - r += deltaArgumentCutoffFunction; + for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) { + temp = (cutoffA - cutoffC) / (r - cutoffC); + temp3 = temp * temp * temp; + temp4 = temp3 * temp; + cutoffFunction[l] = exp(alpha / (1.0 - temp3)); + cutoffFunctionDerived[l] = (-3 * alpha / (cutoffA - cutoffC)) * + (temp4 / ((1 - temp3) * (1 - temp3))) * exp(alpha / (1.0 - temp3)); + r += deltaArgumentCutoffFunction; } // pow2B - numGridPointsR = (int) - ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY); + numGridPointsR = (int) ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY); r = GRIDSTART; deltaArgumentR = 1.0 / GRIDDENSITY; for (l = 0; l < numGridPointsR; l++) { - pow2B[l] = pow((B/r),rho); - exp2B[l] = A * exp(sigma/(r-cutoffA)); - exp3B[l] = exp(gamm/(r-cutoffA)); - r += deltaArgumentR; + pow2B[l] = pow((B / r), rho); + exp2B[l] = A * exp(sigma / (r - cutoffA)); + exp3B[l] = exp(gamm / (r - cutoffA)); + r += deltaArgumentR; } - pow2B[numGridPointsR] = pow((B/r),rho); - exp2B[numGridPointsR]=0; - exp3B[numGridPointsR]=0; + pow2B[numGridPointsR] = pow((B / r), rho); + exp2B[numGridPointsR] = 0; + exp3B[numGridPointsR] = 0; r += deltaArgumentR; - pow2B[numGridPointsR+1] = pow((B/r),rho); - exp2B[numGridPointsR+1]=0; - exp3B[numGridPointsR+1]=0; + pow2B[numGridPointsR + 1] = pow((B / r), rho); + exp2B[numGridPointsR + 1] = 0; + exp3B[numGridPointsR + 1] = 0; } /* ---------------------------------------------------------------------- @@ -761,9 +720,8 @@ void PairEDIP::coeff(int narg, char **arg) { if (!allocated) allocate(); - map_element2type(narg-3,arg+3); - if (nelements != 1) - error->all(FLERR,"Pair style edip only supports single element potentials"); + map_element2type(narg - 3, arg + 3); + if (nelements != 1) error->all(FLERR, "Pair style edip only supports single element potentials"); // read potential file and initialize potential parameters @@ -783,12 +741,11 @@ void PairEDIP::coeff(int narg, char **arg) void PairEDIP::init_style() { - if (force->newton_pair == 0) - error->all(FLERR,"Pair style edip requires newton pair on"); + if (force->newton_pair == 0) error->all(FLERR, "Pair style edip requires newton pair on"); // need a full neighbor list - int irequest = neighbor->request(this,instance_me); + int irequest = neighbor->request(this, instance_me); neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; } @@ -799,7 +756,7 @@ void PairEDIP::init_style() double PairEDIP::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); return cutmax; } @@ -809,7 +766,7 @@ double PairEDIP::init_one(int i, int j) void PairEDIP::read_file(char *file) { int params_per_line = 20; - char **words = new char*[params_per_line+1]; + char **words = new char *[params_per_line + 1]; memory->sfree(params); params = nullptr; @@ -819,38 +776,36 @@ void PairEDIP::read_file(char *file) FILE *fp; if (comm->me == 0) { - fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open EDIP potential file %s",file); - error->one(FLERR,str); - } + fp = utils::open_potential(file, lmp, nullptr); + if (fp == nullptr) + error->one(FLERR,"Cannot open EDIP potential file {}: {}", file,utils::getsyserror()); } // read each set of params from potential file // one set of params can span multiple lines // store params if all 3 element tags are in element list - int n,nwords,ielement,jelement,kelement; - char line[MAXLINE],*ptr; + int n, nwords, ielement, jelement, kelement; + char line[MAXLINE], *ptr; int eof = 0; while (1) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); + ptr = fgets(line, MAXLINE, fp); if (ptr == nullptr) { eof = 1; fclose(fp); - } else n = strlen(line) + 1; + } else + n = strlen(line) + 1; } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + MPI_Bcast(&n, 1, MPI_INT, 0, world); + MPI_Bcast(line, n, MPI_CHAR, 0, world); // strip comment, skip line if blank - if ((ptr = strchr(line,'#'))) *ptr = '\0'; + if ((ptr = strchr(line, '#'))) *ptr = '\0'; nwords = utils::count_words(line); if (nwords == 0) continue; @@ -859,54 +814,53 @@ void PairEDIP::read_file(char *file) while (nwords < params_per_line) { n = strlen(line); if (comm->me == 0) { - ptr = fgets(&line[n],MAXLINE-n,fp); + ptr = fgets(&line[n], MAXLINE - n, fp); if (ptr == nullptr) { eof = 1; fclose(fp); - } else n = strlen(line) + 1; + } else + n = strlen(line) + 1; } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - if ((ptr = strchr(line,'#'))) *ptr = '\0'; + MPI_Bcast(&n, 1, MPI_INT, 0, world); + MPI_Bcast(line, n, MPI_CHAR, 0, world); + if ((ptr = strchr(line, '#'))) *ptr = '\0'; nwords = utils::count_words(line); } - if (nwords != params_per_line) - error->all(FLERR,"Incorrect format in EDIP potential file"); + if (nwords != params_per_line) error->all(FLERR, "Incorrect format in EDIP potential file"); // words = ptrs to all words in line nwords = 0; - words[nwords++] = strtok(line," \t\n\r\f"); - while ((words[nwords++] = strtok(nullptr," \t\n\r\f"))) continue; + words[nwords++] = strtok(line, " \t\n\r\f"); + while ((words[nwords++] = strtok(nullptr, " \t\n\r\f"))) continue; // ielement,jelement,kelement = 1st args // if all 3 args are in element list, then parse this line // else skip to next entry in file for (ielement = 0; ielement < nelements; ielement++) - if (strcmp(words[0],elements[ielement]) == 0) break; + if (strcmp(words[0], elements[ielement]) == 0) break; if (ielement == nelements) continue; for (jelement = 0; jelement < nelements; jelement++) - if (strcmp(words[1],elements[jelement]) == 0) break; + if (strcmp(words[1], elements[jelement]) == 0) break; if (jelement == nelements) continue; for (kelement = 0; kelement < nelements; kelement++) - if (strcmp(words[2],elements[kelement]) == 0) break; + if (strcmp(words[2], elements[kelement]) == 0) break; if (kelement == nelements) continue; // load up parameter settings and error check their values if (nparams == maxparam) { maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); + params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params"); // make certain all addional allocated storage is initialized // to avoid false positives when checking with valgrind - memset(params + nparams, 0, DELTA*sizeof(Param)); + memset(params + nparams, 0, DELTA * sizeof(Param)); } params[nparams].ielement = ielement; @@ -930,25 +884,24 @@ void PairEDIP::read_file(char *file) params[nparams].u3 = atof(words[18]); params[nparams].u4 = atof(words[19]); - if (params[nparams].A < 0.0 || params[nparams].B < 0.0 || - params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 || - params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 || - params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 || - params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 || - params[nparams].rho < 0.0 || params[nparams].sigma < 0.0) - error->all(FLERR,"Illegal EDIP parameter"); + if (params[nparams].A < 0.0 || params[nparams].B < 0.0 || params[nparams].cutoffA < 0.0 || + params[nparams].cutoffC < 0.0 || params[nparams].alpha < 0.0 || + params[nparams].beta < 0.0 || params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 || + params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 || params[nparams].rho < 0.0 || + params[nparams].sigma < 0.0) + error->all(FLERR, "Illegal EDIP parameter"); nparams++; } - delete [] words; + delete[] words; } /* ---------------------------------------------------------------------- */ void PairEDIP::setup_params() { - int i,j,k,m,n; + int i, j, k, m, n; double rtmp; // set elem3param for all triplet combinations @@ -956,28 +909,25 @@ void PairEDIP::setup_params() // do not allow for ACB in place of ABC memory->destroy(elem3param); - memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); + memory->create(elem3param, nelements, nelements, nelements, "pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) for (k = 0; k < nelements; k++) { n = -1; for (m = 0; m < nparams; m++) { - if (i == params[m].ielement && j == params[m].jelement && - k == params[m].kelement) { - if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + if (i == params[m].ielement && j == params[m].jelement && k == params[m].kelement) { + if (n >= 0) error->all(FLERR, "Potential file has duplicate entry"); n = m; } } - if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + if (n < 0) error->all(FLERR, "Potential file is missing an entry"); elem3param[i][j][k] = n; } // set cutoff square - for (m = 0; m < nparams; m++) { - params[m].cutsq = params[m].cutoffA*params[m].cutoffA; - } + for (m = 0; m < nparams; m++) { params[m].cutsq = params[m].cutoffA * params[m].cutoffA; } // set cutmax to max of all params diff --git a/src/USER-MISC/pair_edip.h b/src/MANYBODY/pair_edip.h similarity index 100% rename from src/USER-MISC/pair_edip.h rename to src/MANYBODY/pair_edip.h diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/MANYBODY/pair_edip_multi.cpp similarity index 99% rename from src/USER-MISC/pair_edip_multi.cpp rename to src/MANYBODY/pair_edip_multi.cpp index 73cc1ef1f9..47cc5a90fa 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/MANYBODY/pair_edip_multi.cpp @@ -590,11 +590,8 @@ void PairEDIPMulti::read_file(char *file) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open EDIP potential file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open EDIP potential file {}: {}",file,utils::getsyserror()); } // read each set of params from potential file diff --git a/src/USER-MISC/pair_edip_multi.h b/src/MANYBODY/pair_edip_multi.h similarity index 100% rename from src/USER-MISC/pair_edip_multi.h rename to src/MANYBODY/pair_edip_multi.h diff --git a/src/USER-MISC/pair_extep.cpp b/src/MANYBODY/pair_extep.cpp similarity index 99% rename from src/USER-MISC/pair_extep.cpp rename to src/MANYBODY/pair_extep.cpp index 554aafe8ee..bc96a40c57 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/MANYBODY/pair_extep.cpp @@ -354,6 +354,7 @@ void PairExTeP::compute(int eflag, int vflag) f[k][0] -= fc_prefac_ik * delr2[0]; f[k][1] -= fc_prefac_ik * delr2[1]; f[k][2] -= fc_prefac_ik * delr2[2]; + if (vflag_either) v_tally2(i,k,-fc_prefac_ik,delr2); if (itype != ktype) { fc_prefac_ik = dFc_dNdij * fc_prefac_ik_0; f[i][0] += fc_prefac_ik * delr2[0]; @@ -362,6 +363,7 @@ void PairExTeP::compute(int eflag, int vflag) f[k][0] -= fc_prefac_ik * delr2[0]; f[k][1] -= fc_prefac_ik * delr2[1]; f[k][2] -= fc_prefac_ik * delr2[2]; + if (vflag_either) v_tally2(i,k,-fc_prefac_ik,delr2); } /* END F_IJ (2) */ @@ -410,7 +412,7 @@ void PairExTeP::compute(int eflag, int vflag) f[k][1] += fk[1]; f[k][2] += fk[2]; - if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2); + if (vflag_either) v_tally3(i,j,k,fj,fk,delr1,delr2); } } } @@ -527,11 +529,8 @@ void PairExTeP::read_file(char *file) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open ExTeP potential file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open ExTeP potential file {}: {}",file,utils::getsyserror()); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/USER-MISC/pair_extep.h b/src/MANYBODY/pair_extep.h similarity index 100% rename from src/USER-MISC/pair_extep.h rename to src/MANYBODY/pair_extep.h diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 71a0038bb6..98826f98f6 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -227,7 +227,7 @@ void PairGW::compute(int eflag, int vflag) f[k][1] += fk[1]; f[k][2] += fk[2]; - if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2); + if (vflag_either) v_tally3(i,j,k,fj,fk,delr1,delr2); } // kk } // jj } // ii diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 1af884d814..3c6f08a7e7 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -67,7 +67,7 @@ PairLCBOP::~PairLCBOP() { memory->destroy(SR_numneigh); memory->sfree(SR_firstneigh); - delete [] ipage; + delete[] ipage; memory->destroy(N); memory->destroy(M); @@ -167,7 +167,7 @@ void PairLCBOP::init_style() if (oneatom != neighbor->oneatom) create = 1; if (create) { - delete [] ipage; + delete[] ipage; pgsize = neighbor->pgsize; oneatom = neighbor->oneatom; @@ -386,7 +386,7 @@ void PairLCBOP::FSR(int eflag, int /*vflag*/) del[0] = delx; del[1] = dely; del[2] = delz; - Bij = bondorder(i,j,del,rijmag,VA,f,vflag_atom); + Bij = bondorder(i,j,del,rijmag,VA,f); dVAdi = Bij*dVA; // F = (dVRdi+dVAdi)*(-grad rijmag) @@ -402,8 +402,7 @@ void PairLCBOP::FSR(int eflag, int /*vflag*/) double evdwl=0.0; if (eflag) evdwl = VR - Bij*VA; - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); } } } @@ -493,8 +492,7 @@ void PairLCBOP::FLR(int eflag, int /*vflag*/) double evdwl=0.0; if (eflag) evdwl = V; - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); } } } @@ -503,7 +501,7 @@ void PairLCBOP::FLR(int eflag, int /*vflag*/) forces for Nij and Mij ------------------------------------------------------------------------- */ -void PairLCBOP::FNij( int i, int j, double factor, double **f, int vflag_atom) { +void PairLCBOP::FNij( int i, int j, double factor, double **f) { int atomi = i; int atomj = j; int *SR_neighs = SR_firstneigh[i]; @@ -532,7 +530,7 @@ void PairLCBOP::FNij( int i, int j, double factor, double **f, int vflag_atom) { f[atomk][1] -= rik[1]*fpair; f[atomk][2] -= rik[2]*fpair; - if (vflag_atom) v_tally2(atomi,atomk,fpair,rik); + if (vflag_either) v_tally2(atomi,atomk,fpair,rik); } } } @@ -540,7 +538,7 @@ void PairLCBOP::FNij( int i, int j, double factor, double **f, int vflag_atom) { /* ---------------------------------------------------------------------- */ -void PairLCBOP::FMij( int i, int j, double factor, double **f, int vflag_atom) { +void PairLCBOP::FMij( int i, int j, double factor, double **f) { int atomi = i; int atomj = j; int *SR_neighs = SR_firstneigh[i]; @@ -573,12 +571,12 @@ void PairLCBOP::FMij( int i, int j, double factor, double **f, int vflag_atom) { f[atomk][0] -= rik[0]*fpair; f[atomk][1] -= rik[1]*fpair; f[atomk][2] -= rik[2]*fpair; - if (vflag_atom) v_tally2(atomi,atomk,fpair,rik); + if (vflag_either) v_tally2(atomi,atomk,fpair,rik); } if (dF > TOL) { double factor2 = factor*f_c_ik*dF; - FNij( atomk, atomi, factor2, f, vflag_atom ); + FNij(atomk, atomi, factor2, f); } } } @@ -588,17 +586,15 @@ void PairLCBOP::FMij( int i, int j, double factor, double **f, int vflag_atom) { Bij function ------------------------------------------------------------------------- */ -double PairLCBOP::bondorder(int i, int j, double rij[3], - double rijmag, double VA, - double **f, int vflag_atom) +double PairLCBOP::bondorder(int i, int j, double rij[3],double rijmag, double VA,double **f) { double bij, bji; /* bij & bji */{ double rji[3]; rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2]; - bij = b(i,j,rij,rijmag,VA,f,vflag_atom); - bji = b(j,i,rji,rijmag,VA,f,vflag_atom); + bij = b(i,j,rij,rijmag,VA,f); + bji = b(j,i,rji,rijmag,VA,f); } double Fij_conj; @@ -663,31 +659,30 @@ double PairLCBOP::bondorder(int i, int j, double rij[3], } double dF_dNij, dF_dNji, dF_dNconj; - Fij_conj = F_conj( Nij, Nji, Nconj, &dF_dNij, &dF_dNji, &dF_dNconj ); + Fij_conj = F_conj(Nij, Nji, Nconj, &dF_dNij, &dF_dNji, &dF_dNconj); /*forces for Nij*/ if (3-Nij > TOL) { - double factor = -VA*0.5*( dF_dNij + dF_dNconj*( dNconj_dNij + dNconj_dNel*dNij_el_dNij ) ); - FNij( i, j, factor, f, vflag_atom ); + double factor = -VA*0.5*(dF_dNij + dF_dNconj*(dNconj_dNij + dNconj_dNel*dNij_el_dNij)); + FNij(i, j, factor, f); } /*forces for Nji*/ if (3-Nji > TOL) { - double factor = -VA*0.5*( dF_dNji + dF_dNconj*( dNconj_dNji + dNconj_dNel*dNji_el_dNji ) ); - FNij( j, i, factor, f, vflag_atom ); + double factor = -VA*0.5*(dF_dNji + dF_dNconj*(dNconj_dNji + dNconj_dNel*dNji_el_dNji)); + FNij(j, i, factor, f); } /*forces for Mij*/ if (3-Mij > TOL) { - double factor = -VA*0.5*( dF_dNconj*dNconj_dNel*dNij_el_dMij ); - FMij( i, j, factor, f, vflag_atom ); + double factor = -VA*0.5*(dF_dNconj*dNconj_dNel*dNij_el_dMij); + FMij(i, j, factor, f); } if (3-Mji > TOL) { - double factor = -VA*0.5*( dF_dNconj*dNconj_dNel*dNji_el_dMji ); - FMij( j, i, factor, f, vflag_atom ); + double factor = -VA*0.5*(dF_dNconj*dNconj_dNel*dNji_el_dMji); + FMij(j,i,factor,f); } } - - double Bij = 0.5*( bij + bji + Fij_conj ); + double Bij = 0.5*(bij + bji + Fij_conj); return Bij; } @@ -695,9 +690,7 @@ double PairLCBOP::bondorder(int i, int j, double rij[3], bij function ------------------------------------------------------------------------- */ -double PairLCBOP::b(int i, int j, double rij[3], - double rijmag, double VA, - double **f, int vflag_atom) { +double PairLCBOP::b(int i, int j, double rij[3], double rijmag, double VA, double **f) { int *SR_neighs = SR_firstneigh[i]; double **x = atom->x; int atomi = i; @@ -818,7 +811,7 @@ double PairLCBOP::b(int i, int j, double rij[3], f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2]; - if (vflag_atom) { + if (vflag_either) { double rji[3], rki[3]; rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2]; rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2]; @@ -937,11 +930,8 @@ void PairLCBOP::read_file(char *filename) if (comm->me == 0) { FILE *fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open LCBOP potential file %s",filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open LCBOP potential file {}: {}",filename,utils::getsyserror()); // skip initial comment lines diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index 9350283f18..836e66e160 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -76,10 +76,10 @@ class PairLCBOP : public Pair { void FSR(int, int); void FLR(int, int); - void FNij(int, int, double, double **, int); - void FMij(int, int, double, double **, int); - double bondorder(int, int, double *, double, double, double **, int); - double b(int, int, double *, double, double, double **, int); + void FNij(int, int, double, double **); + void FMij(int, int, double, double **); + double bondorder(int, int, double *, double, double, double **); + double b(int, int, double *, double, double, double **); double gSpline(double, double *); double hSpline(double, double *); diff --git a/src/USER-MISC/pair_local_density.cpp b/src/MANYBODY/pair_local_density.cpp similarity index 97% rename from src/USER-MISC/pair_local_density.cpp rename to src/MANYBODY/pair_local_density.cpp index f5944ac826..5fefd33dea 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/MANYBODY/pair_local_density.cpp @@ -663,29 +663,25 @@ void PairLocalDensity::parse_file(char *filename) { char line[MAXLINE]; double ratio, lc2, uc2, denom; - if (me == 0) { fptr = fopen(filename, "r"); - if (fptr == nullptr) { - char str[128]; - sprintf(str,"Cannot open Local Density potential file %s",filename); - error->one(FLERR,str); - } + if (fptr == nullptr) + error->one(FLERR,"Cannot open Local Density potential file {}: {}",filename,utils::getsyserror()); } - double *ftmp; // tmp var to extract the complete 2D frho array from file + double *ftmp; // tmp var to extract the complete 2D frho array from file - // broadcast number of LD potentials and number of (rho,frho) pairs - if (me == 0) { + // broadcast number of LD potentials and number of (rho,frho) pairs + if (me == 0) { - // first 2 comment lines ignored - utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); - utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + // first 2 comment lines ignored + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); - // extract number of potentials and number of (frho, rho) points - utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); - sscanf(line, "%d %d", &nLD, &nrho); - utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + // extract number of potentials and number of (frho, rho) points + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + sscanf(line, "%d %d", &nLD, &nrho); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); } MPI_Bcast(&nLD,1,MPI_INT,0,world); diff --git a/src/USER-MISC/pair_local_density.h b/src/MANYBODY/pair_local_density.h similarity index 100% rename from src/USER-MISC/pair_local_density.h rename to src/MANYBODY/pair_local_density.h diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/MANYBODY/pair_meam_spline.cpp similarity index 99% rename from src/USER-MISC/pair_meam_spline.cpp rename to src/MANYBODY/pair_meam_spline.cpp index a63b61c7b2..0425fbcc8e 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/MANYBODY/pair_meam_spline.cpp @@ -445,11 +445,8 @@ void PairMEAMSpline::read_file(const char* filename) if (comm->me == 0) { FILE *fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[1024]; - snprintf(str,128,"Cannot open spline MEAM potential file %s", filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open spline MEAM potential file {}: {}", filename,utils::getsyserror()); // Skip first line of file. It's a comment. char line[MAXLINE]; diff --git a/src/USER-MISC/pair_meam_spline.h b/src/MANYBODY/pair_meam_spline.h similarity index 100% rename from src/USER-MISC/pair_meam_spline.h rename to src/MANYBODY/pair_meam_spline.h diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/MANYBODY/pair_meam_sw_spline.cpp similarity index 99% rename from src/USER-MISC/pair_meam_sw_spline.cpp rename to src/MANYBODY/pair_meam_sw_spline.cpp index 74437b70f6..b74b2a01de 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/MANYBODY/pair_meam_sw_spline.cpp @@ -399,11 +399,8 @@ void PairMEAMSWSpline::read_file(const char* filename) { if (comm->me == 0) { FILE *fp = utils::open_potential(filename,lmp,nullptr); - if (fp == nullptr) { - char str[1024]; - snprintf(str,1024,"Cannot open spline MEAM potential file %s", filename); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,"Cannot open spline MEAM potential file {}: {}", filename,utils::getsyserror()); // Skip first line of file. char line[MAXLINE]; diff --git a/src/USER-MISC/pair_meam_sw_spline.h b/src/MANYBODY/pair_meam_sw_spline.h similarity index 100% rename from src/USER-MISC/pair_meam_sw_spline.h rename to src/MANYBODY/pair_meam_sw_spline.h diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 319f0dde8f..aa269ae6ea 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -293,8 +293,7 @@ void PairPolymorphic::compute(int eflag, int vflag) f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); } if (eta == 1) { @@ -352,7 +351,7 @@ void PairPolymorphic::compute(int eflag, int vflag) f[k][1] -= delr2[1]*fpair; f[k][2] -= delr2[2]*fpair; - if (vflag_atom) v_tally2(i, k, -fpair, delr2); + if (vflag_either) v_tally2(i, k, -fpair, delr2); } } @@ -419,8 +418,8 @@ void PairPolymorphic::compute(int eflag, int vflag) f[j][1] -= delr1[1]*fpair; f[j][2] -= delr1[2]*fpair; - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]); + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0, + -fpair,-delr1[0],-delr1[1],-delr1[2]); // attractive term via loop over k @@ -451,7 +450,7 @@ void PairPolymorphic::compute(int eflag, int vflag) f[k][1] += fk[1]; f[k][2] += fk[2]; - if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2); + if (vflag_either) v_tally3(i,j,k,fj,fk,delr1,delr2); } } } diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 33682ce3fa..f21c3bffca 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -88,10 +88,10 @@ void PairTersoff::compute(int eflag, int vflag) if (shift_flag) { if (evflag) { if (eflag) { - if (vflag_atom) eval<1,1,1,1>(); + if (vflag_either) eval<1,1,1,1>(); else eval<1,1,1,0>(); } else { - if (vflag_atom) eval<1,1,0,1>(); + if (vflag_either) eval<1,1,0,1>(); else eval<1,1,0,0>(); } } else eval<1,0,0,0>(); @@ -100,17 +100,17 @@ void PairTersoff::compute(int eflag, int vflag) if (evflag) { if (eflag) { - if (vflag_atom) eval<0,1,1,1>(); + if (vflag_either) eval<0,1,1,1>(); else eval<0,1,1,0>(); } else { - if (vflag_atom) eval<0,1,0,1>(); + if (vflag_either) eval<0,1,0,1>(); else eval<0,1,0,0>(); } } else eval<0,0,0,0>(); } } -template +template void PairTersoff::eval() { int i,j,k,ii,jj,kk,inum,jnum; @@ -315,7 +315,7 @@ void PairTersoff::eval() f[k][1] += fk[1]; f[k][2] += fk[2]; - if (VFLAG_ATOM) v_tally3(i,j,k,fj,fk,delr1,delr2); + if (VFLAG_EITHER) v_tally3(i,j,k,fj,fk,delr1,delr2); } f[j][0] += fjxtmp; f[j][1] += fjytmp; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/MANYBODY/pair_tersoff_table.cpp similarity index 97% rename from src/USER-MISC/pair_tersoff_table.cpp rename to src/MANYBODY/pair_tersoff_table.cpp index 016213e505..94c4d88b09 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/MANYBODY/pair_tersoff_table.cpp @@ -91,7 +91,7 @@ PairTersoffTable::~PairTersoffTable() memory->destroy(cutsq); } deallocateGrids(); - deallocatePreLoops(); + PairTersoffTable::deallocatePreLoops(); } /* ---------------------------------------------------------------------- */ @@ -145,13 +145,10 @@ void PairTersoffTable::compute(int eflag, int vflag) jlist = firstneigh[i]; jnum = numneigh[i]; - if (jnum > leadingDimensionInteractionList) { - char errmsg[256]; - sprintf(errmsg,"Too many neighbors for interaction list: %d vs %d.\n" - "Check your system or increase 'leadingDimensionInteractionList'", - jnum, leadingDimensionInteractionList); - error->one(FLERR,errmsg); - } + if (jnum > leadingDimensionInteractionList) + error->one(FLERR,"Too many neighbors for interaction list: {} vs {}.\n" + "Check your system or increase 'leadingDimensionInteractionList'", + jnum, leadingDimensionInteractionList); // Pre-calculate gteta and cutoff function for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { @@ -434,10 +431,7 @@ void PairTersoffTable::compute(int eflag, int vflag) fytmp += f_ij[1] + f_ik[1]; fztmp += f_ij[2] + f_ik[2]; - // potential energy - evdwl = 0.0; - - if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik); + if (vflag_either) v_tally3(i,j,k,f_ij,f_ik,dr_ij,dr_ik); } // second loop over neighbors of atom i except j, forces and virial only - part 2/2 @@ -499,11 +493,7 @@ void PairTersoffTable::compute(int eflag, int vflag) fytmp += f_ij[1] + f_ik[1]; fztmp += f_ij[2] + f_ik[2]; - // potential energy - evdwl = 0.0; - - if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik); - + if (vflag_either) v_tally3(i,j,k,f_ij,f_ik,dr_ij,dr_ik); } } // loop on J f[i][0] += fxtmp; @@ -755,7 +745,7 @@ void PairTersoffTable::coeff(int narg, char **arg) void PairTersoffTable::init_style() { if (force->newton_pair == 0) - error->all(FLERR,"Pair style Tersoff requires newton pair on"); + error->all(FLERR,"Pair style tersoff/table requires newton pair on"); // need a full neighbor list @@ -888,9 +878,8 @@ void PairTersoffTable::read_file(char *file) MPI_Bcast(&nparams, 1, MPI_INT, 0, world); MPI_Bcast(&maxparam, 1, MPI_INT, 0, world); - if (comm->me != 0) { + if (comm->me != 0) params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); - } MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); } diff --git a/src/USER-MISC/pair_tersoff_table.h b/src/MANYBODY/pair_tersoff_table.h similarity index 100% rename from src/USER-MISC/pair_tersoff_table.h rename to src/MANYBODY/pair_tersoff_table.h diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index d6d7f82dbd..0b24f21e2d 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -290,8 +290,9 @@ void FixBondSwap::post_integrate() // inext,jnext must be on-processor (inext,jnext < nlocal) // inext,jnext must be in fix group // inext,jnext must have same molecule IDs - // for use case 1 (above): this insures chain length is preserved - // for use case 2: always satisfied b/c fix group = bond-able atoms + // in use cases above ... + // for case 1: this insures chain length is preserved + // for case 2: always satisfied b/c fix group = bond-able atoms // 4 atoms must be unique (no duplicates): inext != jnext, inext != j // already know i != inext, j != jnext // all 4 old and new bonds must have length < cutoff @@ -440,7 +441,7 @@ void FixBondSwap::post_integrate() done: - // trigger immediate reneighboring if any swaps occurred + // trigger immediate reneighboring if swaps occurred on one or more procs int accept_any; MPI_Allreduce(&accept,&accept_any,1,MPI_INT,MPI_SUM,world); diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index e275cd8c11..fc1b1c03db 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -1230,7 +1230,7 @@ void FixGCMC::attempt_molecule_deletion() // work-around to avoid n=0 problem with fix rigid/nvt/small - if (ngas == natoms_per_molecule) return; + if (rigidflag && ngas == natoms_per_molecule) return; tagint deletion_molecule = pick_random_gas_molecule(); if (deletion_molecule == -1) return; @@ -1900,7 +1900,7 @@ void FixGCMC::attempt_molecule_deletion_full() // work-around to avoid n=0 problem with fix rigid/nvt/small - if (ngas == natoms_per_molecule) return; + if (rigidflag && ngas == natoms_per_molecule) return; tagint deletion_molecule = pick_random_gas_molecule(); if (deletion_molecule == -1) return; @@ -2315,7 +2315,7 @@ double FixGCMC::energy_full() // unlike Verlet, not performing a reverse_comm() or forces here // b/c GCMC does not care about forces // don't think it will mess up energy due to any post_force() fixes - // but Modify::pre_reverse() is needed for USER-INTEL + // but Modify::pre_reverse() is needed for INTEL if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag); if (modify->n_post_force) modify->post_force(vflag); diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 3dd0d2d3c9..7b4a749f2e 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -1049,7 +1049,7 @@ double FixWidom::energy_full() // unlike Verlet, not performing a reverse_comm() or forces here // b/c Widom does not care about forces // don't think it will mess up energy due to any post_force() fixes - // but Modify::pre_reverse() is needed for USER-INTEL + // but Modify::pre_reverse() is needed for INTEL if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag); if (modify->n_pre_force) modify->pre_force(vflag); diff --git a/src/USER-MDI/Install.sh b/src/MDI/Install.sh similarity index 96% rename from src/USER-MDI/Install.sh rename to src/MDI/Install.sh index 4f1ea6dfba..bc19162a17 100755 --- a/src/USER-MDI/Install.sh +++ b/src/MDI/Install.sh @@ -40,7 +40,7 @@ if (test $1 = 1) then sed -i -e 's/[^ \t]*mdi[^ \t]* //g' ../Makefile.package sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/mdi/includelink |' ../Makefile.package sed -i -e 's/[^ \t]*MDI[^ \t]* //' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_USER_MDI |' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_MDI |' ../Makefile.package sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mdi/liblink |' ../Makefile.package sed -i -e 's|^PKG_LIB =[ \t]*|&-lmdi |' ../Makefile.package sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(mdi_SYSINC) |' ../Makefile.package diff --git a/src/USER-MDI/README b/src/MDI/README similarity index 93% rename from src/USER-MDI/README rename to src/MDI/README index 045fbea518..cad9ae3f39 100644 --- a/src/USER-MDI/README +++ b/src/MDI/README @@ -1,4 +1,4 @@ -The USER-MDI package adds an mdi/engine command which enables LAMMPS +The MDI package adds an mdi/engine command which enables LAMMPS to operate as a MolSSI Driver Interface (MDI) engine, responding to commands from an external MDI driver. diff --git a/src/USER-MDI/fix_mdi_engine.cpp b/src/MDI/fix_mdi_engine.cpp similarity index 98% rename from src/USER-MDI/fix_mdi_engine.cpp rename to src/MDI/fix_mdi_engine.cpp index db9e114488..81eb87a0f3 100644 --- a/src/USER-MDI/fix_mdi_engine.cpp +++ b/src/MDI/fix_mdi_engine.cpp @@ -554,7 +554,7 @@ void FixMDIEngine::send_charges(Error *error) void FixMDIEngine::send_energy(Error *error) { // get conversion factor to atomic units - double energy_conv; + double energy_conv = 1.0; if (lmpunits == REAL) { double kelvin_to_hartree; MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree); @@ -884,10 +884,9 @@ void FixMDIEngine::receive_cell(Error *error) // ensure that the new cell vector is orthogonal double small = std::numeric_limits::min(); - if (abs(celldata[1]) > small or abs(celldata[2]) > small or abs(celldata[3]) > small or - abs(celldata[5]) > small or abs(celldata[6]) > small or abs(celldata[7]) > small) { - error->all(FLERR, - "MDI: LAMMPS currently only supports the >CELL command for orthogonal cell vectors"); + if (fabs(celldata[1]) > small or fabs(celldata[2]) > small or fabs(celldata[3]) > small or + fabs(celldata[5]) > small or fabs(celldata[6]) > small or fabs(celldata[7]) > small) { + error->all(FLERR, "MDI: LAMMPS currently only supports the >CELL command for orthogonal cell vectors"); } // set the new LAMMPS cell dimensions diff --git a/src/USER-MDI/fix_mdi_engine.h b/src/MDI/fix_mdi_engine.h similarity index 100% rename from src/USER-MDI/fix_mdi_engine.h rename to src/MDI/fix_mdi_engine.h diff --git a/src/USER-MDI/library_mdi.cpp b/src/MDI/library_mdi.cpp similarity index 100% rename from src/USER-MDI/library_mdi.cpp rename to src/MDI/library_mdi.cpp diff --git a/src/USER-MDI/library_mdi.h b/src/MDI/library_mdi.h similarity index 100% rename from src/USER-MDI/library_mdi.h rename to src/MDI/library_mdi.h diff --git a/src/USER-MDI/mdi_engine.cpp b/src/MDI/mdi_engine.cpp similarity index 100% rename from src/USER-MDI/mdi_engine.cpp rename to src/MDI/mdi_engine.cpp diff --git a/src/USER-MDI/mdi_engine.h b/src/MDI/mdi_engine.h similarity index 100% rename from src/USER-MDI/mdi_engine.h rename to src/MDI/mdi_engine.h diff --git a/src/MEAM/README b/src/MEAM/README new file mode 100644 index 0000000000..8015f6c699 --- /dev/null +++ b/src/MEAM/README @@ -0,0 +1,26 @@ +This package implements the MEAM potential as a LAMMPS pair style. + +============================================================================== + +This package is a translation and extension of the Fortran MEAM +package to native C++. + +Translation by + Sebastian Hütter, sebastian.huetter@ovgu.de + Institute of Materials and Joining Technology + Otto-von-Guericke University Magdeburg, Germany + +The original Fortran implementation was created by + Greg Wagner (while at Sandia, now at Northwestern U). + +============================================================================== + +Use "make yes-meam" to enable this package or use +-DPKG_MEAM=on when configuring building LAMMPS + + +In your LAMMPS input script, specify + pair_style meam +to enable the use of this implementation. parameters, input files and +outputs are compatible to those for the Fortran version of pair_style meam. + diff --git a/src/USER-MEAMC/meam.h b/src/MEAM/meam.h similarity index 98% rename from src/USER-MEAMC/meam.h rename to src/MEAM/meam.h index d41e5f6aed..5205e01ec8 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/MEAM/meam.h @@ -294,10 +294,10 @@ class MEAM { void meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double *eng_vdwl, double *eatom, int ntype, int *type, int *fmap, double **scale, int &errorflag); - void meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, + void meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int vflag_atom, double *eng_vdwl, double *eatom, int ntype, int *type, int *fmap, double **scale, double **x, int numneigh, int *firstneigh, int numneigh_full, - int *firstneigh_full, int fnoffset, double **f, double **vatom); + int *firstneigh_full, int fnoffset, double **f, double **vatom, double *virial); }; // Functions we need for compat diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/MEAM/meam_dens_final.cpp similarity index 100% rename from src/USER-MEAMC/meam_dens_final.cpp rename to src/MEAM/meam_dens_final.cpp diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/MEAM/meam_dens_init.cpp similarity index 100% rename from src/USER-MEAMC/meam_dens_init.cpp rename to src/MEAM/meam_dens_init.cpp diff --git a/src/USER-MEAMC/meam_force.cpp b/src/MEAM/meam_force.cpp similarity index 94% rename from src/USER-MEAMC/meam_force.cpp rename to src/MEAM/meam_force.cpp index ab72d3c6c8..88b6140f80 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/MEAM/meam_force.cpp @@ -21,12 +21,15 @@ using namespace LAMMPS_NS; void -MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl, - double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh, - int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom) +MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int vflag_atom, + double* eng_vdwl, double* eatom, int /*ntype*/, int* type, int* fmap, + double** scale, double** x, int numneigh, int* firstneigh, int numneigh_full, + int* firstneigh_full, int fnoffset, double** f, double** vatom, double *virial) { int j, jn, k, kn, kk, m, n, p, q; int nv2, nv3, elti, eltj, eltk, ind; + int eflag_either = eflag_atom || eflag_global; + int vflag_either = vflag_atom || vflag_global; double xitmp, yitmp, zitmp, delij[3], rij2, rij, rij3; double v[6], fi[3], fj[3]; double third, sixth; @@ -414,7 +417,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int // Tabulate per-atom virial as symmetrized stress tensor - if (vflag_atom != 0) { + if (vflag_either) { fi[0] = delij[0] * force + dUdrijm[0]; fi[1] = delij[1] * force + dUdrijm[1]; fi[2] = delij[2] * force + dUdrijm[2]; @@ -425,9 +428,16 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int v[4] = -0.25 * (delij[0] * fi[2] + delij[2] * fi[0]); v[5] = -0.25 * (delij[1] * fi[2] + delij[2] * fi[1]); - for (m = 0; m < 6; m++) { - vatom[i][m] = vatom[i][m] + v[m]; - vatom[j][m] = vatom[j][m] + v[m]; + if (vflag_global) { + for (m = 0; m < 6; m++) { + virial[m] += 2.0*v[m]; + } + } + if (vflag_atom) { + for (m = 0; m < 6; m++) { + vatom[i][m] += v[m]; + vatom[j][m] += v[m]; + } } } @@ -499,7 +509,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int // Tabulate per-atom virial as symmetrized stress tensor - if (vflag_atom != 0) { + if (vflag_either) { fi[0] = force1 * dxik; fi[1] = force1 * dyik; fi[2] = force1 * dzik; @@ -513,10 +523,18 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int v[4] = -sixth * (dxik * fi[2] + dxjk * fj[2] + dzik * fi[0] + dzjk * fj[0]); v[5] = -sixth * (dyik * fi[2] + dyjk * fj[2] + dzik * fi[1] + dzjk * fj[1]); - for (m = 0; m < 6; m++) { - vatom[i][m] = vatom[i][m] + v[m]; - vatom[j][m] = vatom[j][m] + v[m]; - vatom[k][m] = vatom[k][m] + v[m]; + if (vflag_global) { + for (m = 0; m < 6; m++) { + virial[m] += 3.0*v[m]; + } + } + + if (vflag_atom) { + for (m = 0; m < 6; m++) { + vatom[i][m] += v[m]; + vatom[j][m] += v[m]; + vatom[k][m] += v[m]; + } } } } diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/MEAM/meam_funcs.cpp similarity index 100% rename from src/USER-MEAMC/meam_funcs.cpp rename to src/MEAM/meam_funcs.cpp diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/MEAM/meam_impl.cpp similarity index 100% rename from src/USER-MEAMC/meam_impl.cpp rename to src/MEAM/meam_impl.cpp diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/MEAM/meam_setup_done.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_done.cpp rename to src/MEAM/meam_setup_done.cpp diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/MEAM/meam_setup_global.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_global.cpp rename to src/MEAM/meam_setup_global.cpp diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/MEAM/meam_setup_param.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_param.cpp rename to src/MEAM/meam_setup_param.cpp diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/MEAM/pair_meam.cpp similarity index 94% rename from src/USER-MEAMC/pair_meamc.cpp rename to src/MEAM/pair_meam.cpp index a4ea3abdce..2acf58f738 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/MEAM/pair_meam.cpp @@ -16,7 +16,7 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include "pair_meamc.h" +#include "pair_meam.h" #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ static const char *keywords[] = { /* ---------------------------------------------------------------------- */ -PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) +PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; restartinfo = 0; @@ -72,7 +72,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ -PairMEAMC::~PairMEAMC() +PairMEAM::~PairMEAM() { delete meam_inst; @@ -85,7 +85,7 @@ PairMEAMC::~PairMEAMC() /* ---------------------------------------------------------------------- */ -void PairMEAMC::compute(int eflag, int vflag) +void PairMEAM::compute(int eflag, int vflag) { int i,ii,n,inum_half,errorflag; int *ilist_half,*numneigh_half,**firstneigh_half; @@ -154,17 +154,16 @@ void PairMEAMC::compute(int eflag, int vflag) // vptr is first value in vatom if it will be used by meam_force() // else vatom may not exist, so pass dummy ptr - double **vptr; + double **vptr = nullptr; if (vflag_atom) vptr = vatom; - else vptr = nullptr; for (ii = 0; ii < inum_half; ii++) { i = ilist_half[ii]; - meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom, - vflag_atom,&eng_vdwl,eatom,ntype,type,map,scale,x, - numneigh_half[i],firstneigh_half[i], - numneigh_full[i],firstneigh_full[i], - offset,f,vptr); + meam_inst->meam_force(i,eflag_global,eflag_atom,vflag_global, + vflag_atom,&eng_vdwl,eatom,ntype,type,map,scale,x, + numneigh_half[i],firstneigh_half[i], + numneigh_full[i],firstneigh_full[i], + offset,f,vptr,virial); offset += numneigh_half[i]; } @@ -173,7 +172,7 @@ void PairMEAMC::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void PairMEAMC::allocate() +void PairMEAM::allocate() { allocated = 1; int n = atom->ntypes; @@ -189,7 +188,7 @@ void PairMEAMC::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAMC::settings(int narg, char ** /*arg*/) +void PairMEAM::settings(int narg, char ** /*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -198,7 +197,7 @@ void PairMEAMC::settings(int narg, char ** /*arg*/) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairMEAMC::coeff(int narg, char **arg) +void PairMEAM::coeff(int narg, char **arg) { int m,n; @@ -309,7 +308,7 @@ void PairMEAMC::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairMEAMC::init_style() +void PairMEAM::init_style() { if (force->newton_pair == 0) error->all(FLERR,"Pair style MEAM requires newton pair on"); @@ -329,7 +328,7 @@ void PairMEAMC::init_style() half or full ------------------------------------------------------------------------- */ -void PairMEAMC::init_list(int id, NeighList *ptr) +void PairMEAM::init_list(int id, NeighList *ptr) { if (id == 1) listfull = ptr; else if (id == 2) listhalf = ptr; @@ -339,7 +338,7 @@ void PairMEAMC::init_list(int id, NeighList *ptr) init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAMC::init_one(int i, int j) +double PairMEAM::init_one(int i, int j) { if (setflag[i][j] == 0) scale[i][j] = 1.0; scale[j][i] = scale[i][j]; @@ -348,16 +347,16 @@ double PairMEAMC::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_files(const std::string &globalfile, +void PairMEAM::read_files(const std::string &globalfile, const std::string &userfile) { - read_global_meamc_file(globalfile); - read_user_meamc_file(userfile); + read_global_meam_file(globalfile); + read_user_meam_file(userfile); } /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_global_meamc_file(const std::string &globalfile) +void PairMEAM::read_global_meam_file(const std::string &globalfile) { // allocate parameter arrays std::vector lat(nlibelements); @@ -498,7 +497,7 @@ void PairMEAMC::read_global_meamc_file(const std::string &globalfile) /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_user_meamc_file(const std::string &userfile) +void PairMEAM::read_user_meam_file(const std::string &userfile) { // done if user param file is "NULL" @@ -577,7 +576,7 @@ void PairMEAMC::read_user_meamc_file(const std::string &userfile) /* ---------------------------------------------------------------------- */ -int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, +int PairMEAM::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m; @@ -621,7 +620,7 @@ int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ -void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) +void PairMEAM::unpack_forward_comm(int n, int first, double *buf) { int i,k,m,last; @@ -662,7 +661,7 @@ void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) +int PairMEAM::pack_reverse_comm(int n, int first, double *buf) { int i,k,m,last; @@ -697,7 +696,7 @@ int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) +void PairMEAM::unpack_reverse_comm(int n, int *list, double *buf) { int i,j,k,m; @@ -732,7 +731,7 @@ void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double PairMEAMC::memory_usage() +double PairMEAM::memory_usage() { double bytes = 11 * meam_inst->nmax * sizeof(double); bytes += (double)(3 + 6 + 10 + 3 + 3 + 3) * meam_inst->nmax * sizeof(double); @@ -747,7 +746,7 @@ double PairMEAMC::memory_usage() done once per reneighbor so that neigh_f2c and neigh_c2f don't see them ------------------------------------------------------------------------- */ -void PairMEAMC::neigh_strip(int inum, int *ilist, +void PairMEAM::neigh_strip(int inum, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jnum; @@ -763,7 +762,7 @@ void PairMEAMC::neigh_strip(int inum, int *ilist, /* ---------------------------------------------------------------------- */ -void *PairMEAMC::extract(const char *str, int &dim) +void *PairMEAM::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"scale") == 0) return (void *) scale; diff --git a/src/USER-MEAMC/pair_meamc.h b/src/MEAM/pair_meam.h similarity index 92% rename from src/USER-MEAMC/pair_meamc.h rename to src/MEAM/pair_meam.h index 08166c7bd7..06be670eb9 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/MEAM/pair_meam.h @@ -13,13 +13,13 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(meam/c,PairMEAMC); -PairStyle(meam,PairMEAMC); +PairStyle(meam,PairMEAM); +PairStyle(meam/c,PairMEAM); // clang-format on #else -#ifndef LMP_PAIR_MEAMC_H -#define LMP_PAIR_MEAMC_H +#ifndef LMP_PAIR_MEAM_H +#define LMP_PAIR_MEAM_H #include "pair.h" @@ -27,10 +27,10 @@ PairStyle(meam,PairMEAMC); namespace LAMMPS_NS { -class PairMEAMC : public Pair { +class PairMEAM : public Pair { public: - PairMEAMC(class LAMMPS *); - ~PairMEAMC(); + PairMEAM(class LAMMPS *); + ~PairMEAM(); void compute(int, int); void settings(int, char **); void coeff(int, char **); @@ -56,8 +56,8 @@ class PairMEAMC : public Pair { void allocate(); void read_files(const std::string &, const std::string &); - void read_global_meamc_file(const std::string &); - void read_user_meamc_file(const std::string &); + void read_global_meam_file(const std::string &); + void read_user_meam_file(const std::string &); void neigh_strip(int, int *, int *, int **); }; diff --git a/src/USER-MESONT/Install.sh b/src/MESONT/Install.sh similarity index 100% rename from src/USER-MESONT/Install.sh rename to src/MESONT/Install.sh diff --git a/src/USER-MESONT/README b/src/MESONT/README similarity index 97% rename from src/USER-MESONT/README rename to src/MESONT/README index ce08731734..0c66cb7b82 100644 --- a/src/USER-MESONT/README +++ b/src/MESONT/README @@ -1,4 +1,4 @@ -USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon +MESONT is a LAMMPS package for simulation of nanomechanics of carbon nanotubes (CNTs). The model is based on a coarse-grained representation of CNTs as "flexible cylinders" consisting of a variable number of segments. Internal interactions within a CNT and the van der Waals @@ -22,7 +22,7 @@ The following commands are contained in this package: atom_style mesont This command enables mesont atom_style containing variables used for - further commands in USER-MESONT. + further commands in MESONT. pair_style mesont/tpm cut table_path BendingMode TPMType This command activates a pair_style describing CNT mesoscopic tubular diff --git a/src/USER-MESONT/atom_vec_mesont.cpp b/src/MESONT/atom_vec_mesont.cpp similarity index 100% rename from src/USER-MESONT/atom_vec_mesont.cpp rename to src/MESONT/atom_vec_mesont.cpp diff --git a/src/USER-MESONT/atom_vec_mesont.h b/src/MESONT/atom_vec_mesont.h similarity index 100% rename from src/USER-MESONT/atom_vec_mesont.h rename to src/MESONT/atom_vec_mesont.h diff --git a/src/USER-MESONT/compute_mesont.cpp b/src/MESONT/compute_mesont.cpp similarity index 100% rename from src/USER-MESONT/compute_mesont.cpp rename to src/MESONT/compute_mesont.cpp diff --git a/src/USER-MESONT/compute_mesont.h b/src/MESONT/compute_mesont.h similarity index 100% rename from src/USER-MESONT/compute_mesont.h rename to src/MESONT/compute_mesont.h diff --git a/src/USER-MESONT/export_mesont.h b/src/MESONT/export_mesont.h similarity index 100% rename from src/USER-MESONT/export_mesont.h rename to src/MESONT/export_mesont.h diff --git a/src/USER-MESONT/pair_mesocnt.cpp b/src/MESONT/pair_mesocnt.cpp similarity index 100% rename from src/USER-MESONT/pair_mesocnt.cpp rename to src/MESONT/pair_mesocnt.cpp diff --git a/src/USER-MESONT/pair_mesocnt.h b/src/MESONT/pair_mesocnt.h similarity index 100% rename from src/USER-MESONT/pair_mesocnt.h rename to src/MESONT/pair_mesocnt.h diff --git a/src/USER-MESONT/pair_mesont_tpm.cpp b/src/MESONT/pair_mesont_tpm.cpp similarity index 100% rename from src/USER-MESONT/pair_mesont_tpm.cpp rename to src/MESONT/pair_mesont_tpm.cpp diff --git a/src/USER-MESONT/pair_mesont_tpm.h b/src/MESONT/pair_mesont_tpm.h similarity index 100% rename from src/USER-MESONT/pair_mesont_tpm.h rename to src/MESONT/pair_mesont_tpm.h diff --git a/src/USER-MESONT/potentials.txt b/src/MESONT/potentials.txt similarity index 100% rename from src/USER-MESONT/potentials.txt rename to src/MESONT/potentials.txt diff --git a/src/USER-MGPT/README b/src/MGPT/README similarity index 92% rename from src/USER-MGPT/README rename to src/MGPT/README index 151bd02b5d..1f29a68385 100644 --- a/src/USER-MGPT/README +++ b/src/MGPT/README @@ -17,7 +17,7 @@ See the doc page for the pair_style mgpt command for full details on using this package in LAMMPS. In particular, the user should note that the MGPT potentials are explicitly volume dependent, requiring special attention in their application. Useful example scripts are given in -the "examples/USER/mgpt" directory. These scripts show the necessary +the "examples/PACKAGES/mgpt" directory. These scripts show the necessary steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations. @@ -28,6 +28,6 @@ vanadium (V6.1 potentials) are contained in the LAMMPS "potentials" directory. It is expected that MGPT potentials for additional materials will be added over time. -The persons who created the USER-MGPT package are Tomas Oppelstrup +The persons who created the MGPT package are Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) Contact them directly if you have any questions. diff --git a/src/USER-MGPT/mgpt_bgmul_7.c.h b/src/MGPT/mgpt_bgmul_7.c.h similarity index 100% rename from src/USER-MGPT/mgpt_bgmul_7.c.h rename to src/MGPT/mgpt_bgmul_7.c.h diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/MGPT/mgpt_linalg.cpp similarity index 100% rename from src/USER-MGPT/mgpt_linalg.cpp rename to src/MGPT/mgpt_linalg.cpp diff --git a/src/USER-MGPT/mgpt_linalg.h b/src/MGPT/mgpt_linalg.h similarity index 100% rename from src/USER-MGPT/mgpt_linalg.h rename to src/MGPT/mgpt_linalg.h diff --git a/src/USER-MGPT/mgpt_mmul3_538.c.h b/src/MGPT/mgpt_mmul3_538.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3_538.c.h rename to src/MGPT/mgpt_mmul3_538.c.h diff --git a/src/USER-MGPT/mgpt_mmul3_748.c.h b/src/MGPT/mgpt_mmul3_748.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3_748.c.h rename to src/MGPT/mgpt_mmul3_748.c.h diff --git a/src/USER-MGPT/mgpt_mmul3d_526.c.h b/src/MGPT/mgpt_mmul3d_526.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3d_526.c.h rename to src/MGPT/mgpt_mmul3d_526.c.h diff --git a/src/USER-MGPT/mgpt_mmul3d_744.c.h b/src/MGPT/mgpt_mmul3d_744.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3d_744.c.h rename to src/MGPT/mgpt_mmul3d_744.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bg_552.c.h b/src/MGPT/mgpt_mmul_bg_552.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bg_552.c.h rename to src/MGPT/mgpt_mmul_bg_552.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bg_722.c.h b/src/MGPT/mgpt_mmul_bg_722.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bg_722.c.h rename to src/MGPT/mgpt_mmul_bg_722.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h b/src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h rename to src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h b/src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h rename to src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h diff --git a/src/USER-MGPT/mgpt_readpot.cpp b/src/MGPT/mgpt_readpot.cpp similarity index 100% rename from src/USER-MGPT/mgpt_readpot.cpp rename to src/MGPT/mgpt_readpot.cpp diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/MGPT/mgpt_readpot.h similarity index 100% rename from src/USER-MGPT/mgpt_readpot.h rename to src/MGPT/mgpt_readpot.h diff --git a/src/USER-MGPT/mgpt_splinetab.cpp b/src/MGPT/mgpt_splinetab.cpp similarity index 100% rename from src/USER-MGPT/mgpt_splinetab.cpp rename to src/MGPT/mgpt_splinetab.cpp diff --git a/src/USER-MGPT/mgpt_splinetab.h b/src/MGPT/mgpt_splinetab.h similarity index 100% rename from src/USER-MGPT/mgpt_splinetab.h rename to src/MGPT/mgpt_splinetab.h diff --git a/src/USER-MGPT/mgpt_ttr_5022.c.h b/src/MGPT/mgpt_ttr_5022.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5022.c.h rename to src/MGPT/mgpt_ttr_5022.c.h diff --git a/src/USER-MGPT/mgpt_ttr_5042.c.h b/src/MGPT/mgpt_ttr_5042.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5042.c.h rename to src/MGPT/mgpt_ttr_5042.c.h diff --git a/src/USER-MGPT/mgpt_ttr_5123.c.h b/src/MGPT/mgpt_ttr_5123.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5123.c.h rename to src/MGPT/mgpt_ttr_5123.c.h diff --git a/src/USER-MGPT/mgpt_ttr_5141.c.h b/src/MGPT/mgpt_ttr_5141.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5141.c.h rename to src/MGPT/mgpt_ttr_5141.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7022.c.h b/src/MGPT/mgpt_ttr_7022.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7022.c.h rename to src/MGPT/mgpt_ttr_7022.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7042.c.h b/src/MGPT/mgpt_ttr_7042.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7042.c.h rename to src/MGPT/mgpt_ttr_7042.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7123.c.h b/src/MGPT/mgpt_ttr_7123.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7123.c.h rename to src/MGPT/mgpt_ttr_7123.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7141.c.h b/src/MGPT/mgpt_ttr_7141.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7141.c.h rename to src/MGPT/mgpt_ttr_7141.c.h diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/MGPT/pair_mgpt.cpp similarity index 100% rename from src/USER-MGPT/pair_mgpt.cpp rename to src/MGPT/pair_mgpt.cpp diff --git a/src/USER-MGPT/pair_mgpt.h b/src/MGPT/pair_mgpt.h similarity index 100% rename from src/USER-MGPT/pair_mgpt.h rename to src/MGPT/pair_mgpt.h diff --git a/src/USER-MISC/bond_special.cpp b/src/MISC/bond_special.cpp similarity index 100% rename from src/USER-MISC/bond_special.cpp rename to src/MISC/bond_special.cpp diff --git a/src/USER-MISC/bond_special.h b/src/MISC/bond_special.h similarity index 100% rename from src/USER-MISC/bond_special.h rename to src/MISC/bond_special.h diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/MISC/compute_viscosity_cos.cpp similarity index 100% rename from src/USER-MISC/compute_viscosity_cos.cpp rename to src/MISC/compute_viscosity_cos.cpp diff --git a/src/USER-MISC/compute_viscosity_cos.h b/src/MISC/compute_viscosity_cos.h similarity index 100% rename from src/USER-MISC/compute_viscosity_cos.h rename to src/MISC/compute_viscosity_cos.h diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/MISC/fix_accelerate_cos.cpp similarity index 100% rename from src/USER-MISC/fix_accelerate_cos.cpp rename to src/MISC/fix_accelerate_cos.cpp diff --git a/src/USER-MISC/fix_accelerate_cos.h b/src/MISC/fix_accelerate_cos.h similarity index 100% rename from src/USER-MISC/fix_accelerate_cos.h rename to src/MISC/fix_accelerate_cos.h diff --git a/src/USER-MISC/fix_imd.cpp b/src/MISC/fix_imd.cpp similarity index 100% rename from src/USER-MISC/fix_imd.cpp rename to src/MISC/fix_imd.cpp diff --git a/src/USER-MISC/fix_imd.h b/src/MISC/fix_imd.h similarity index 100% rename from src/USER-MISC/fix_imd.h rename to src/MISC/fix_imd.h diff --git a/src/USER-MISC/fix_ipi.cpp b/src/MISC/fix_ipi.cpp similarity index 99% rename from src/USER-MISC/fix_ipi.cpp rename to src/MISC/fix_ipi.cpp index 277ddc8489..6fc3ec97b5 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/MISC/fix_ipi.cpp @@ -18,18 +18,19 @@ #include "fix_ipi.h" -#include #include "atom.h" -#include "force.h" -#include "update.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "irregular.h" #include "kspace.h" #include "modify.h" -#include "compute.h" -#include "comm.h" #include "neighbor.h" -#include "irregular.h" -#include "domain.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -83,15 +84,13 @@ static void open_socket(int &sockfd, int inet, int port, char* host, // fetches information on the host struct addrinfo hints, *res; - char service[256]; memset(&hints, 0, sizeof(hints)); hints.ai_socktype = SOCK_STREAM; hints.ai_family = AF_UNSPEC; hints.ai_flags = AI_PASSIVE; - sprintf(service,"%d",port); // convert the port number to a string - ai_err = getaddrinfo(host, service, &hints, &res); + ai_err = getaddrinfo(host, std::to_string(port).c_str(), &hints, &res); if (ai_err!=0) error->one(FLERR,"Error fetching host data. Wrong host name?"); diff --git a/src/USER-MISC/fix_ipi.h b/src/MISC/fix_ipi.h similarity index 100% rename from src/USER-MISC/fix_ipi.h rename to src/MISC/fix_ipi.h diff --git a/src/MISC/fix_pair_tracker.cpp b/src/MISC/fix_pair_tracker.cpp new file mode 100644 index 0000000000..755025baed --- /dev/null +++ b/src/MISC/fix_pair_tracker.cpp @@ -0,0 +1,369 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_pair_tracker.h" +#include "atom.h" +#include "atom_vec.h" +#include "error.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "tokenizer.h" +#include "update.h" + +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define DELTA 1000 + +/* ---------------------------------------------------------------------- */ + +FixPairTracker::FixPairTracker(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), nvalues(0), vector(NULL), array(NULL), pack_choice(NULL) +{ + if (narg < 3) error->all(FLERR, "Illegal fix pair/tracker command"); + local_flag = 1; + + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + if (nevery <= 0) error->all(FLERR, "Illegal fix pair/tracker command"); + local_freq = nevery; + + // If optional arguments included, this will be oversized + nvalues = narg - 4; + pack_choice = new FnPtrPack[nvalues]; + + tmin = -1; + type_filter = nullptr; + int iarg = 4; + nvalues = 0; + while (iarg < narg) { + if (strcmp(arg[iarg], "id1") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_id1; + } else if (strcmp(arg[iarg], "id2") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_id2; + + } else if (strcmp(arg[iarg], "time/created") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_time_created; + } else if (strcmp(arg[iarg], "time/broken") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_time_broken; + } else if (strcmp(arg[iarg], "time/total") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_time_total; + + } else if (strcmp(arg[iarg], "x") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_x; + } else if (strcmp(arg[iarg], "y") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_y; + } else if (strcmp(arg[iarg], "z") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_z; + + } else if (strcmp(arg[iarg], "r/min") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_rmin; + } else if (strcmp(arg[iarg], "r/ave") == 0) { + pack_choice[nvalues++] = &FixPairTracker::pack_rave; + + } else if (strcmp(arg[iarg], "time/min") == 0) { + if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command"); + tmin = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg++; + + } else if (strcmp(arg[iarg], "type/include") == 0) { + if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command"); + int ntypes = atom->ntypes; + + int i, j, itype, jtype, in, jn, infield, jnfield; + int inlo, inhi, jnlo, jnhi; + char *istr, *jstr; + if (!type_filter) { + memory->create(type_filter, ntypes + 1, ntypes + 1, "fix/pair/tracker:type_filter"); + + for (i = 0; i <= ntypes; i++) { + for (j = 0; j <= ntypes; j++) { type_filter[i][j] = 0; } + } + } + + in = strlen(arg[iarg + 1]) + 1; + istr = new char[in]; + strcpy(istr, arg[iarg + 1]); + std::vector iwords = Tokenizer(istr, ",").as_vector(); + infield = iwords.size(); + + jn = strlen(arg[iarg + 2]) + 1; + jstr = new char[jn]; + strcpy(jstr, arg[iarg + 2]); + std::vector jwords = Tokenizer(jstr, ",").as_vector(); + jnfield = jwords.size(); + + for (i = 0; i < infield; i++) { + const char *ifield = iwords[i].c_str(); + utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error); + + for (j = 0; j < jnfield; j++) { + const char *jfield = jwords[j].c_str(); + utils::bounds(FLERR, jfield, 1, ntypes, jnlo, jnhi, error); + + for (itype = inlo; itype <= inhi; itype++) { + for (jtype = jnlo; jtype <= jnhi; jtype++) { + type_filter[itype][jtype] = 1; + type_filter[jtype][itype] = 1; + } + } + } + } + + delete[] istr; + delete[] jstr; + + iarg += 2; + + } else + error->all(FLERR, "Invalid keyword in fix pair/tracker command"); + + iarg++; + } + + if (nvalues == 1) + size_local_cols = 0; + else + size_local_cols = nvalues; + + nmax = 0; + ncount = 0; + vector = NULL; + array = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixPairTracker::~FixPairTracker() +{ + delete[] pack_choice; + + memory->destroy(vector); + memory->destroy(array); + memory->destroy(type_filter); +} + +/* ---------------------------------------------------------------------- */ + +int FixPairTracker::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::init() +{ + // Set size of array/vector + ncount = 0; + + if (ncount > nmax) reallocate(ncount); + + size_local_rows = ncount; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::lost_contact(int i, int j, double time_tmp, double nstep_tmp, double rsum_tmp, + double rmin_tmp) +{ + + double time = update->atime + (update->ntimestep - update->atimestep) * update->dt; + if ((time - time_tmp) < tmin) return; + + if (type_filter) { + int *type = atom->type; + if (type_filter[type[i]][type[j]] == 0) return; + } + + int *mask = atom->mask; + if (!(mask[i] & groupbit)) return; + if (!(mask[j] & groupbit)) return; + + if (ncount == nmax) reallocate(ncount); + + index_i = i; + index_j = j; + + rmin = rmin_tmp; + rsum = rsum_tmp; + time_initial = time_tmp; + nstep_initial = nstep_tmp; + + // fill vector or array with local values + if (nvalues == 1) { + (this->*pack_choice[0])(0); + } else { + for (int k = 0; k < nvalues; k++) { (this->*pack_choice[k])(k); } + } + + ncount += 1; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::post_force(int /*vflag*/) +{ + if (update->ntimestep % nevery == 0) { + size_local_rows = ncount; + ncount = 0; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::reallocate(int n) +{ + // grow vector or array + while (nmax <= n) nmax += DELTA; + + if (nvalues == 1) { + memory->grow(vector, nmax, "fix_pair_tracker:vector"); + vector_local = vector; + } else { + memory->grow(array, nmax, nvalues, "fix_pair_tracker:array"); + array_local = array; + } +} + +/* ---------------------------------------------------------------------- + memory usage of local data +------------------------------------------------------------------------- */ + +double FixPairTracker::memory_usage() +{ + double bytes = nmax * (double) nvalues * sizeof(double); + bytes += nmax * 2 * sizeof(int); + return bytes; +} + +/* ---------------------------------------------------------------------- + one method for every keyword fix pair/tracker can output + the atom property is packed into a local vector or array +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_time_created(int n) +{ + if (nvalues == 1) + vector[ncount] = time_initial; + else + array[ncount][n] = time_initial; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_time_broken(int n) +{ + double time = update->atime + (update->ntimestep - update->atimestep) * update->dt; + if (nvalues == 1) + vector[ncount] = time; + else + array[ncount][n] = time; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_time_total(int n) +{ + double time = update->atime + (update->ntimestep - update->atimestep) * update->dt; + if (nvalues == 1) + vector[ncount] = time - time_initial; + else + array[ncount][n] = time - time_initial; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_id1(int n) +{ + tagint *tag = atom->tag; + + if (nvalues == 1) + vector[ncount] = tag[index_i]; + else + array[ncount][n] = tag[index_i]; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_id2(int n) +{ + tagint *tag = atom->tag; + + if (nvalues == 1) + vector[ncount] = tag[index_j]; + else + array[ncount][n] = tag[index_j]; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_x(int n) +{ + double **x = atom->x; + + if (nvalues == 1) + vector[ncount] = (x[index_i][0] + x[index_j][0]) / 2; + else + array[ncount][n] = (x[index_i][0] + x[index_j][0]) / 2; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_y(int n) +{ + double **x = atom->x; + + if (nvalues == 1) + vector[ncount] = (x[index_i][1] + x[index_j][1]) / 2; + else + array[ncount][n] = (x[index_i][1] + x[index_j][1]) / 2; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_z(int n) +{ + double **x = atom->x; + + if (nvalues == 1) + vector[ncount] = (x[index_i][2] + x[index_j][2]) / 2; + else + array[ncount][n] = (x[index_i][2] + x[index_j][2]) / 2; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_rmin(int n) +{ + if (nvalues == 1) + vector[ncount] = rmin; + else + array[ncount][n] = rmin; +} + +/* ---------------------------------------------------------------------- */ + +void FixPairTracker::pack_rave(int n) +{ + if (nvalues == 1) + vector[ncount] = rsum / (update->ntimestep - nstep_initial); + else + array[ncount][n] = rsum / (update->ntimestep - nstep_initial); +} diff --git a/src/MISC/fix_pair_tracker.h b/src/MISC/fix_pair_tracker.h new file mode 100644 index 0000000000..7c2e3ff322 --- /dev/null +++ b/src/MISC/fix_pair_tracker.h @@ -0,0 +1,85 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(pair/tracker,FixPairTracker); +// clang-format on +#else + +#ifndef LMP_FIX_PAIR_TRACKING_H +#define LMP_FIX_PAIR_TRACKING_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixPairTracker : public Fix { + public: + FixPairTracker(class LAMMPS *, int, char **); + ~FixPairTracker(); + int setmask(); + void init(); + void post_force(int); + double memory_usage(); + void lost_contact(int, int, double, double, double, double); + + private: + int nvalues, nmax; + int index_i, index_j; + double tmin, rmin, rsum, time_initial, nstep_initial; + + double *vector; + double **array; + int **type_filter; + + int ncount; + + void reallocate(int); + + typedef void (FixPairTracker::*FnPtrPack)(int); + FnPtrPack *pack_choice; // ptrs to pack functions + + void pack_id1(int); + void pack_id2(int); + + void pack_time_created(int); + void pack_time_broken(int); + void pack_time_total(int); + + void pack_x(int); + void pack_y(int); + void pack_z(int); + + void pack_rmin(int); + void pack_rave(int); +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Invalid keyword in fix pair/tracker command + +Self-explanatory. + +*/ diff --git a/src/USER-MISC/fix_srp.cpp b/src/MISC/fix_srp.cpp similarity index 95% rename from src/USER-MISC/fix_srp.cpp rename to src/MISC/fix_srp.cpp index fb502febaf..055d3119b7 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/MISC/fix_srp.cpp @@ -246,10 +246,8 @@ void FixSRP::setup_pre_force(int /*zz*/) int nadd_all = 0, ndel_all = 0; MPI_Allreduce(&ndel,&ndel_all,1,MPI_INT,MPI_SUM,world); MPI_Allreduce(&nadd,&nadd_all,1,MPI_INT,MPI_SUM,world); - if (comm->me == 0) { - sprintf(str, "Removed/inserted %d/%d bond particles.", ndel_all,nadd_all); - error->message(FLERR,str); - } + if (comm->me == 0) + error->message(FLERR,"Removed/inserted {}/{} bond particles.", ndel_all,nadd_all); // check ghost comm distances // warn and change if shorter from estimate @@ -276,11 +274,9 @@ void FixSRP::setup_pre_force(int /*zz*/) cutghostmin = comm->cutghost[2]/length2; // stop if cutghost is insufficient - if (cutneighmax_srp > cutghostmin) { - sprintf(str, "Communication cutoff too small for fix srp. " - "Need %f, current %f.", cutneighmax_srp, cutghostmin); - error->all(FLERR,str); - } + if (cutneighmax_srp > cutghostmin) + error->all(FLERR,"Communication cutoff too small for fix srp. " + "Need {:.8}, current {:.8}", cutneighmax_srp, cutghostmin); // assign tags for new atoms, update map atom->tag_extend(); @@ -453,10 +449,10 @@ int FixSRP::unpack_border(int n, int first, double *buf) int m = 0; last = first + n; - for (i = first; i < last; i++) { - array[i][0] = buf[m++]; - array[i][1] = buf[m++]; - } + for (i = first; i < last; i++) { + array[i][0] = buf[m++]; + array[i][1] = buf[m++]; + } return m; } @@ -515,14 +511,8 @@ void FixSRP::post_run() bigint ndelete = natoms_previous - atom->natoms; - if (comm->me == 0) { - if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT - " atoms, new total = " BIGINT_FORMAT "\n", - ndelete,atom->natoms); - if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT - " atoms, new total = " BIGINT_FORMAT "\n", - ndelete,atom->natoms); - } + if (comm->me == 0) + utils::logmesg(lmp,"Deleted {} atoms, new total = {}\n",ndelete,atom->natoms); // verlet calls box_too_small_check() in post_run // this check maps all bond partners diff --git a/src/USER-MISC/fix_srp.h b/src/MISC/fix_srp.h similarity index 100% rename from src/USER-MISC/fix_srp.h rename to src/MISC/fix_srp.h diff --git a/src/USER-MISC/pair_agni.cpp b/src/MISC/pair_agni.cpp similarity index 100% rename from src/USER-MISC/pair_agni.cpp rename to src/MISC/pair_agni.cpp diff --git a/src/USER-MISC/pair_agni.h b/src/MISC/pair_agni.h similarity index 100% rename from src/USER-MISC/pair_agni.h rename to src/MISC/pair_agni.h diff --git a/src/USER-MISC/pair_list.cpp b/src/MISC/pair_list.cpp similarity index 100% rename from src/USER-MISC/pair_list.cpp rename to src/MISC/pair_list.cpp diff --git a/src/USER-MISC/pair_list.h b/src/MISC/pair_list.h similarity index 100% rename from src/USER-MISC/pair_list.h rename to src/MISC/pair_list.h diff --git a/src/USER-MISC/pair_srp.cpp b/src/MISC/pair_srp.cpp similarity index 91% rename from src/USER-MISC/pair_srp.cpp rename to src/MISC/pair_srp.cpp index c09d3726c2..0fef989c88 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/MISC/pair_srp.cpp @@ -21,31 +21,30 @@ soft non-bonded potentials are used, such as DPD polymer chains. See the doc page for pair_style srp command for usage instructions. -There is an example script for this package in examples/USER/srp. +There is an example script for this package in examples/PACKAGES/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ #include "pair_srp.h" -#include - -#include #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_srp.h" -#include "thermo.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "output.h" -#include "citeme.h" +#include "thermo.h" +#include +#include using namespace LAMMPS_NS; @@ -69,7 +68,7 @@ static int srp_instance = 0; set size of pair comms in constructor ---------------------------------------------------------------------- */ -PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp) +PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp), fix_id(nullptr) { writedata = 1; single_enable = 0; @@ -79,26 +78,14 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp) nextra = 1; segment = nullptr; - // generate unique fix-id for this pair style instance - - fix_id = strdup("XX_FIX_SRP"); - fix_id[0] = '0' + srp_instance / 10; - fix_id[1] = '0' + srp_instance % 10; - ++srp_instance; - - // create fix SRP instance here + // create fix SRP instance here with unique fix id // similar to granular pair styles with history, // this should be early enough that FixSRP::pre_exchange() // will be invoked before other fixes that migrate atoms // this is checked for in FixSRP - char **fixarg = new char*[3]; - fixarg[0] = fix_id; - fixarg[1] = (char *) "all"; - fixarg[2] = (char *) "SRP"; - modify->add_fix(3,fixarg); - f_srp = (FixSRP *) modify->fix[modify->nfix-1]; - delete [] fixarg; + f_srp = (FixSRP *) modify->add_fix(fmt::format("{:02d}_FIX_SRP all SRP",srp_instance)); + ++srp_instance; } /* ---------------------------------------------------------------------- @@ -130,18 +117,16 @@ void PairSRP::allocate() PairSRP::~PairSRP() { - if (allocated) - { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(cut); - memory->destroy(a0); - memory->destroy(segment); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + memory->destroy(a0); + memory->destroy(segment); + } // check nfix in case all fixes have already been deleted - if (modify->nfix) modify->delete_fix(fix_id); - free(fix_id); + if (modify->nfix) modify->delete_fix(f_srp->id); } /* ---------------------------------------------------------------------- @@ -424,33 +409,31 @@ void PairSRP::settings(int narg, char **arg) void PairSRP::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) - error->all(FLERR,"PairSRP: Incorrect args for pair coeff"); - if (!allocated) allocate(); + if (narg < 3 || narg > 4) + error->all(FLERR,"PairSRP: Incorrect args for pair coeff"); + if (!allocated) allocate(); - // set ij bond-bond cutoffs - int ilo, ihi, jlo, jhi; - utils::bounds(FLERR,arg[0], 1, bptype, ilo, ihi, error); - utils::bounds(FLERR,arg[1], 1, bptype, jlo, jhi, error); + // set ij bond-bond cutoffs + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR,arg[0], 1, bptype, ilo, ihi, error); + utils::bounds(FLERR,arg[1], 1, bptype, jlo, jhi, error); - double a0_one = utils::numeric(FLERR,arg[2],false,lmp); - double cut_one = cut_global; - if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); + double a0_one = utils::numeric(FLERR,arg[2],false,lmp); + double cut_one = cut_global; + if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); - int count = 0; - for (int i = ilo; i <= ihi; i++) - { - for (int j = MAX(jlo,i); j <= jhi; j++) - { - a0[i][j] = a0_one; - cut[i][j] = cut_one; - cutsq[i][j] = cut_one * cut_one; - setflag[i][j] = 1; - count++; - } + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + cut[i][j] = cut_one; + cutsq[i][j] = cut_one * cut_one; + setflag[i][j] = 1; + count++; } + } - if (count == 0) error->warning(FLERR,"PairSRP: No pair coefficients were set"); + if (count == 0) error->warning(FLERR,"PairSRP: No pair coefficients were set"); } /* ---------------------------------------------------------------------- @@ -464,14 +447,11 @@ void PairSRP::init_style() // verify that fix SRP is still defined and has not been changed. - int ifix = modify->find_fix(fix_id); - if (f_srp != (FixSRP *)modify->fix[ifix]) + if (strcmp(f_srp->style,"SRP") != 0) error->all(FLERR,"Fix SRP has been changed unexpectedly"); - if (comm->me == 0) { - if (screen) fprintf(screen,"Using type %d for bond particles\n",bptype); - if (logfile) fprintf(logfile,"Using type %d for bond particles\n",bptype); - } + if (comm->me == 0) + utils::logmesg(lmp,"Using type {} for bond particles\n",bptype); // set bond and bond particle types in fix srp // bonds of this type will be represented by bond particles diff --git a/src/USER-MISC/pair_srp.h b/src/MISC/pair_srp.h similarity index 100% rename from src/USER-MISC/pair_srp.h rename to src/MISC/pair_srp.h diff --git a/src/MISC/pair_tracker.cpp b/src/MISC/pair_tracker.cpp new file mode 100644 index 0000000000..f2fdb71081 --- /dev/null +++ b/src/MISC/pair_tracker.cpp @@ -0,0 +1,471 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_tracker.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_dummy.h" +#include "fix_neigh_history.h" +#include "fix_pair_tracker.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 1; + no_virial_fdotr_compute = 1; + + neighprev = 0; + history = 1; + size_history = 4; + nondefault_history_transfer = 1; + + finitecutflag = 0; + + // create dummy fix as placeholder for FixNeighHistory + // this is so final order of Modify:fix will conform to input script + + fix_history = nullptr; + modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY"); + fix_dummy = (FixDummy *) modify->fix[modify->nfix - 1]; +} + +/* ---------------------------------------------------------------------- */ + +PairTracker::~PairTracker() +{ + if (!fix_history) + modify->delete_fix("NEIGH_HISTORY_TRACK_DUMMY"); + else + modify->delete_fix("NEIGH_HISTORY_TRACK"); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + + delete[] onerad_dynamic; + delete[] onerad_frozen; + delete[] maxrad_dynamic; + delete[] maxrad_frozen; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairTracker::compute(int eflag, int vflag) +{ + int i, j, ii, jj, inum, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, time; + double radi, radj, radsum, rsq, r; + int *ilist, *jlist, *numneigh, **firstneigh; + int *touch, **firsttouch; + double *data, *alldata, **firstdata; + + int updateflag = 1; + if (update->setupflag) updateflag = 0; + ev_init(eflag, vflag); + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + firsttouch = fix_history->firstflag; + firstdata = fix_history->firstvalue; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (finitecutflag) radi = radius[i]; + itype = type[i]; + touch = firsttouch[i]; + alldata = firstdata[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + r = sqrt(rsq); + + if (finitecutflag) { + radj = radius[j]; + radsum = radi + radj; + + if (rsq >= radsum * radsum) { + + data = &alldata[size_history * jj]; + if (touch[jj] == 1) { + fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]); + } + touch[jj] = 0; + data[0] = 0.0; // initial time + data[1] = 0.0; // initial timestep + data[2] = 0.0; // sum of r, may overflow + data[3] = 0.0; // min of r + + } else { + + data = &alldata[size_history * jj]; + if (touch[jj] == 0) { + time = update->atime + (update->ntimestep - update->atimestep) * update->dt; + data[0] = time; + data[1] = (double) update->ntimestep; + data[2] = r; + data[3] = r; + } else if (updateflag) { + data[2] += r; + if (data[3] > r) data[3] = r; + } + touch[jj] = 1; + } + } else { + jtype = type[j]; + if (rsq >= cutsq[itype][jtype]) { + + data = &alldata[size_history * jj]; + if (touch[jj] == 1) { + fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]); + } + + touch[jj] = 0; + data[0] = 0.0; // initial time + data[1] = 0.0; // initial timestep + data[2] = 0.0; // sum of r, may overflow + data[3] = 0.0; // min of r + + } else { + + data = &alldata[size_history * jj]; + if (touch[jj] == 0) { + time = update->atime + (update->ntimestep - update->atimestep) * update->dt; + data[0] = time; + data[1] = (double) update->ntimestep; + data[2] = r; + data[3] = r; + } else if (updateflag) { + data[2] += r; + if (data[3] > r) data[3] = r; + } + touch[jj] = 1; + } + } + } + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairTracker::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) setflag[i][j] = 0; + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(cut, n + 1, n + 1, "pair:cut"); + + onerad_dynamic = new double[n + 1]; + onerad_frozen = new double[n + 1]; + maxrad_dynamic = new double[n + 1]; + maxrad_frozen = new double[n + 1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairTracker::settings(int narg, char **arg) +{ + if (narg != 0 && narg != 1) error->all(FLERR, "Illegal pair_style command"); + + if (narg == 1) { + if (strcmp(arg[0], "finite") == 0) + finitecutflag = 1; + else + error->all(FLERR, "Illegal pair_style command"); + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairTracker::coeff(int narg, char **arg) +{ + if (narg > 2 && finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 3 && !finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); + + double cut_one = 0.0; + if (!finitecutflag) cut_one = utils::numeric(FLERR, arg[2], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + setflag[i][j] = 1; + cut[i][j] = cut_one; + count++; + } + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairTracker::init_style() +{ + int i; + + // error and warning checks + + if (!atom->radius_flag && finitecutflag) + error->all(FLERR, "Pair tracker requires atom attribute radius for finite cutoffs"); + + // need a history neigh list + + int irequest = neighbor->request(this, instance_me); + if (finitecutflag) { + neighbor->requests[irequest]->size = 1; + neighbor->requests[irequest]->history = 1; + // history flag won't affect results, but match granular pairstyles + // so neighborlist can be copied to reduce overhead + } + + // if history is stored and first init, create Fix to store history + // it replaces FixDummy, created in the constructor + // this is so its order in the fix list is preserved + + if (fix_history == nullptr) { + modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY", + fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1); + int ifix = modify->find_fix("NEIGH_HISTORY_TRACK"); + fix_history = (FixNeighHistory *) modify->fix[ifix]; + fix_history->pair = this; + fix_history->use_bit_flag = 0; + } + + if (finitecutflag) { + + if (force->pair->beyond_contact) + error->all(FLERR, + "Pair tracker incompatible with granular pairstyles that extend beyond contact"); + // check for FixPour and FixDeposit so can extract particle radii + + int ipour; + for (ipour = 0; ipour < modify->nfix; ipour++) + if (strcmp(modify->fix[ipour]->style, "pour") == 0) break; + if (ipour == modify->nfix) ipour = -1; + + int idep; + for (idep = 0; idep < modify->nfix; idep++) + if (strcmp(modify->fix[idep]->style, "deposit") == 0) break; + if (idep == modify->nfix) idep = -1; + + // set maxrad_dynamic and maxrad_frozen for each type + // include future FixPour and FixDeposit particles as dynamic + + int itype; + for (i = 1; i <= atom->ntypes; i++) { + onerad_dynamic[i] = onerad_frozen[i] = 0.0; + if (ipour >= 0) { + itype = i; + onerad_dynamic[i] = *((double *) modify->fix[ipour]->extract("radius", itype)); + } + if (idep >= 0) { + itype = i; + onerad_dynamic[i] = *((double *) modify->fix[idep]->extract("radius", itype)); + } + } + + double *radius = atom->radius; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) + if (mask[i] & freeze_group_bit) + onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]], radius[i]); + else + onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]); + + MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + } + + int ifix = modify->find_fix("NEIGH_HISTORY_TRACK"); + if (ifix < 0) error->all(FLERR, "Could not find pair fix neigh history ID"); + fix_history = (FixNeighHistory *) modify->fix[ifix]; + + ifix = modify->find_fix_by_style("pair/tracker"); + if (ifix < 0) error->all(FLERR, "Cannot use pair tracker without fix pair/tracker"); + fix_pair_tracker = (FixPairTracker *) modify->fix[ifix]; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairTracker::init_one(int i, int j) +{ + if (!allocated) allocate(); + + // always mix prefactors geometrically + + if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i], cut[j][j]); } + + cut[j][i] = cut[i][j]; + + // if finite, cutoff = sum of max I,J radii for + // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen + double cutoff; + if (finitecutflag) { + cutoff = maxrad_dynamic[i] + maxrad_dynamic[j]; + cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]); + cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]); + } else { + cutoff = cut[i][j]; + } + return cutoff; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairTracker::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1, fp); + if (setflag[i][j]) { fwrite(&cut[i][j], sizeof(double), 1, fp); } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairTracker::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i, j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); + if (setflag[i][j]) { + if (me == 0) { utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairTracker::write_restart_settings(FILE *fp) +{ + fwrite(&mix_flag, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairTracker::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); } + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); +} + +/* ---------------------------------------------------------------------- */ + +double PairTracker::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/, + double /*factor_coul*/, double /*factor_lj*/, double &/*fforce*/) +{ + return 0.0; +} + +/* ---------------------------------------------------------------------- + transfer history during fix/neigh/history exchange + only needed if any history entries i-j are not just negative of j-i entries +------------------------------------------------------------------------- */ + +void PairTracker::transfer_history(double *source, double *target) +{ + for (int i = 0; i < size_history; i++) target[i] = source[i]; +} + +/* ---------------------------------------------------------------------- + self-interaction range of particle if finite particles +------------------------------------------------------------------------- */ + +double PairTracker::atom2cut(int i) +{ + double cut = atom->radius[i] * 2; + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairTracker::radii2cut(double r1, double r2) +{ + double cut = r1 + r2; + return cut; +} diff --git a/src/MISC/pair_tracker.h b/src/MISC/pair_tracker.h new file mode 100644 index 0000000000..c6825c410e --- /dev/null +++ b/src/MISC/pair_tracker.h @@ -0,0 +1,91 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(tracker,PairTracker); +// clang-format on +#else + +#ifndef LMP_PAIR_TRACKER_H +#define LMP_PAIR_TRACKER_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairTracker : public Pair { + public: + PairTracker(class LAMMPS *); + virtual ~PairTracker(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + double atom2cut(int); + double radii2cut(double, double); + + protected: + int sizeflag; + int history; + int size_history; + int neighprev; + double **cut; + double *onerad_dynamic, *onerad_frozen; + double *maxrad_dynamic, *maxrad_frozen; + int freeze_group_bit; + + class FixDummy *fix_dummy; + class FixNeighHistory *fix_history; + class FixPairTracker *fix_pair_tracker; + + void transfer_history(double *, double *); + void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair tracker requires atom attribute radius for finite cutoffs + +The atom style defined does not have these attributes. + +E: Could not find pair fix neigh history ID + +The associated fix neigh/history is missing + +E: Cannot use pair tracker without fix pair/tracker + +This pairstyle requires one to define a pair/tracker fix + +*/ diff --git a/src/USER-HDNNP/Install.sh b/src/ML-HDNNP/Install.sh similarity index 100% rename from src/USER-HDNNP/Install.sh rename to src/ML-HDNNP/Install.sh diff --git a/src/USER-HDNNP/README b/src/ML-HDNNP/README similarity index 91% rename from src/USER-HDNNP/README rename to src/ML-HDNNP/README index 690db8a714..1d9590f7d7 100644 --- a/src/USER-HDNNP/README +++ b/src/ML-HDNNP/README @@ -5,9 +5,9 @@ neural network potentials[1] via an interface to the n2p2 library Please see the main documentation for the "pair_style hdnnp" command for further details on how the pair style is used. An example is provided in the -"examples/USER/hdnnp" directory of LAMMPS. +"examples/PACKAGES/hdnnp" directory of LAMMPS. -The USER-HDNNP package requires the external library n2p2 which must be +The ML-HDNNP package requires the external library n2p2 which must be downloaded and compiled before starting the build process of LAMMPS. A guideline on how to build n2p2 is presented in "lib/hdnnp/README". This package supports the LAMMPS build process via CMake and traditional makefiles, please diff --git a/src/USER-HDNNP/pair_hdnnp.cpp b/src/ML-HDNNP/pair_hdnnp.cpp similarity index 99% rename from src/USER-HDNNP/pair_hdnnp.cpp rename to src/ML-HDNNP/pair_hdnnp.cpp index af64f98f75..7aeacad588 100644 --- a/src/USER-HDNNP/pair_hdnnp.cpp +++ b/src/ML-HDNNP/pair_hdnnp.cpp @@ -35,7 +35,7 @@ using namespace LAMMPS_NS; static const char cite_user_hdnnp_package[] = - "USER-HDNNP package: 10.1021/acs.jctc.8b00770\n\n" + "ML-HDNNP package: 10.1021/acs.jctc.8b00770\n\n" "@Article{Singraber19,\n" " author = {Singraber, Andreas and Behler, J{\"o}rg and Dellago, Christoph},\n" " title = {Library-{{Based LAMMPS Implementation}} of {{High}}-{{Dimensional Neural Network Potentials}}},\n" diff --git a/src/USER-HDNNP/pair_hdnnp.h b/src/ML-HDNNP/pair_hdnnp.h similarity index 100% rename from src/USER-HDNNP/pair_hdnnp.h rename to src/ML-HDNNP/pair_hdnnp.h diff --git a/src/MLIAP/Install.sh b/src/ML-IAP/Install.sh similarity index 76% rename from src/MLIAP/Install.sh rename to src/ML-IAP/Install.sh index e6ba4042a9..08cdfecd88 100755 --- a/src/MLIAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -29,17 +29,20 @@ action () { # enforce package dependency if (test $1 = 1 || test $1 = 2) then if (test ! -e ../sna.h) then - echo "Must install SNAP package to use MLIAP package" + echo "Must install SNAP package to use ML-IAP package" exit 1 fi fi -# all package files with no dependencies +# all package C++ files with no dependencies -for file in *.cpp *.h *.pyx; do +for file in *.cpp *.h; do test -f ${file} && action $file done +# Install cython pyx file only if also Python is available +action mliap_model_python_couple.pyx python_impl.cpp + # edit 2 Makefile.package files to include/exclude package info if (test $1 = 1) then @@ -64,4 +67,11 @@ elif (test $1 = 0) then fi rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + +elif (test $1 = 2) then + if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then + cythonize -3 ../mliap_model_python_couple.pyx + else + rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h + fi fi diff --git a/src/ML-IAP/README.md b/src/ML-IAP/README.md new file mode 100644 index 0000000000..f6db495099 --- /dev/null +++ b/src/ML-IAP/README.md @@ -0,0 +1,56 @@ +This package provides a general interface to families of +machine-learning interatomic potentials (MLIAPs). This interface +consists of a `mliap pair style` and a `mliap compute`. The `mliap pair +style` is used when running simulations with energies and forces +calculated by an MLIAP. The interface allows separate definitions of the +interatomic potential functional form (`model`) and the geometric +quantities that characterize the atomic positions (`descriptor`). By +defining `model` and `descriptor` separately, it is possible to use many +different models with a given descriptor, or many different descriptors +with a given model. The mliap pair_style supports the following models: + +- `linear`, +- `quadratic`, +- `nn` (neural networks) +- `mliappy` (general Python interface to things like PyTorch). + +It currently supports two classes of descriptors, `sna` (the SNAP +descriptors) and `so3` (the SO3 descriptor). It is straightforward to +add new descriptor and model styles. + +The `compute mliap` style provides gradients of the energy, force, and +stress tensor w.r.t. model parameters. These are useful when training +MLIAPs to match target data. Any `model` or `descriptor` that has been +implemented for the `mliap` pair style can also be accessed by the +`mliap` compute. In addition to the energy, force, and stress +gradients, w.r.t. each `model` parameter, the compute also calculates +the energy, force, and stress contributions from a user-specified +reference potential. + +## Generating the model files from the third-party packages +- To train the `linear` and `quadratic` models with the SNAP descriptors, see the examples in [FitSNAP](https://github.com/FitSNAP/FitSNAP). +- To train the `nn` model with the SNAP descriptors, check the examples in [PyXtal\_FF](https://github.com/qzhu2017/PyXtal_FF). + +## Building the ML-IAP package with Python support + +The `mliappy` energy model requires that the MLIAP package is compiled +with Python support enabled. This extension, written by Nick Lubbers +(LANL), provides a coupling to PyTorch and other Python modules. This +should be automatically enabled by default if the prerequisite software +is installed when compiling with CMake. It can be enforced during CMake +configuration by setting the variable `MLIAP_ENABLE_PYTHON=yes` or for +conventional build by adding `-DMLIAP_PYTHON` to the `LMP_INC` variable +in your makefile and running the cythonize script on the .pyx file(s) +copied to the src folder. + +Using the `mliappy` energy model also requires to install the PYTHON +package and have the [cython](https://cython.org) software +installed. During configuration/compilation the cythonize script will be +used to convert the provided .pyx file(s) to C++ code. Please do *NOT* +run the cythonize script manually in the src/ML-IAP folder. If you have +done so by accident, you need to delete the generated .cpp and .h +file(s) in the src/ML-IAP folder or there may be problems during +compilation. + +More information on building LAMMPS with this package is +[here](https://docs.lammps.org/Build_extras.html#mliap). diff --git a/src/MLIAP/compute_mliap.cpp b/src/ML-IAP/compute_mliap.cpp similarity index 100% rename from src/MLIAP/compute_mliap.cpp rename to src/ML-IAP/compute_mliap.cpp diff --git a/src/MLIAP/compute_mliap.h b/src/ML-IAP/compute_mliap.h similarity index 100% rename from src/MLIAP/compute_mliap.h rename to src/ML-IAP/compute_mliap.h diff --git a/src/MLIAP/mliap_data.cpp b/src/ML-IAP/mliap_data.cpp similarity index 100% rename from src/MLIAP/mliap_data.cpp rename to src/ML-IAP/mliap_data.cpp diff --git a/src/MLIAP/mliap_data.h b/src/ML-IAP/mliap_data.h similarity index 100% rename from src/MLIAP/mliap_data.h rename to src/ML-IAP/mliap_data.h diff --git a/src/MLIAP/mliap_descriptor.cpp b/src/ML-IAP/mliap_descriptor.cpp similarity index 100% rename from src/MLIAP/mliap_descriptor.cpp rename to src/ML-IAP/mliap_descriptor.cpp diff --git a/src/MLIAP/mliap_descriptor.h b/src/ML-IAP/mliap_descriptor.h similarity index 100% rename from src/MLIAP/mliap_descriptor.h rename to src/ML-IAP/mliap_descriptor.h diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/ML-IAP/mliap_descriptor_snap.cpp similarity index 100% rename from src/MLIAP/mliap_descriptor_snap.cpp rename to src/ML-IAP/mliap_descriptor_snap.cpp diff --git a/src/MLIAP/mliap_descriptor_snap.h b/src/ML-IAP/mliap_descriptor_snap.h similarity index 100% rename from src/MLIAP/mliap_descriptor_snap.h rename to src/ML-IAP/mliap_descriptor_snap.h diff --git a/src/MLIAP/mliap_descriptor_so3.cpp b/src/ML-IAP/mliap_descriptor_so3.cpp similarity index 100% rename from src/MLIAP/mliap_descriptor_so3.cpp rename to src/ML-IAP/mliap_descriptor_so3.cpp diff --git a/src/MLIAP/mliap_descriptor_so3.h b/src/ML-IAP/mliap_descriptor_so3.h similarity index 100% rename from src/MLIAP/mliap_descriptor_so3.h rename to src/ML-IAP/mliap_descriptor_so3.h diff --git a/src/MLIAP/mliap_model.cpp b/src/ML-IAP/mliap_model.cpp similarity index 72% rename from src/MLIAP/mliap_model.cpp rename to src/ML-IAP/mliap_model.cpp index f6491c926d..47c3cd54a6 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/ML-IAP/mliap_model.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -51,9 +50,7 @@ MLIAPModel::~MLIAPModel() placeholder ------------------------------------------------------------------------- */ -void MLIAPModel::init() -{ -} +void MLIAPModel::init() {} /* ---------------------------------------------------------------------- set number of elements @@ -75,8 +72,8 @@ void MLIAPModel::set_ndescriptors(int ndescriptors_in) /* ---------------------------------------------------------------------- */ - -MLIAPModelSimple::MLIAPModelSimple(LAMMPS *lmp, char *coefffilename) : MLIAPModel(lmp, coefffilename) +MLIAPModelSimple::MLIAPModelSimple(LAMMPS *lmp, char *coefffilename) : + MLIAPModel(lmp, coefffilename) { if (coefffilename) read_coeffs(coefffilename); } @@ -90,37 +87,37 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) FILE *fpcoeff; if (comm->me == 0) { - fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); + fpcoeff = utils::open_potential(coefffilename, lmp, nullptr); if (fpcoeff == nullptr) - error->one(FLERR,"Cannot open MLIAPModel coeff file {}: {}", - coefffilename,utils::getsyserror()); + error->one(FLERR, "Cannot open MLIAPModel coeff file {}: {}", coefffilename, + utils::getsyserror()); } - char line[MAXLINE],*ptr; + char line[MAXLINE], *ptr; int eof = 0; int n; int nwords = 0; while (nwords == 0) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpcoeff); + ptr = fgets(line, MAXLINE, fpcoeff); if (ptr == nullptr) { eof = 1; fclose(fpcoeff); - } else n = strlen(line) + 1; + } else + n = strlen(line) + 1; } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + MPI_Bcast(&n, 1, MPI_INT, 0, world); + MPI_Bcast(line, n, MPI_CHAR, 0, world); // strip comment, skip line if blank - if ((ptr = strchr(line,'#'))) *ptr = '\0'; + if ((ptr = strchr(line, '#'))) *ptr = '\0'; nwords = utils::count_words(line); } - if (nwords != 2) - error->all(FLERR,"Incorrect format in MLIAPModel coefficient file"); + if (nwords != 2) error->all(FLERR, "Incorrect format in MLIAPModel coefficient file"); // words = ptrs to all words in line // strip single and double quotes from words @@ -130,45 +127,47 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) nelements = coeffs.next_int(); nparams = coeffs.next_int(); } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect format in MLIAPModel coefficient " - "file: {}",e.what()); + error->all(FLERR, + "Incorrect format in MLIAPModel coefficient " + "file: {}", + e.what()); } // set up coeff lists memory->destroy(coeffelem); - memory->create(coeffelem,nelements,nparams,"mliap_snap_model:coeffelem"); + memory->create(coeffelem, nelements, nparams, "mliap_snap_model:coeffelem"); // Loop over nelements blocks in the coefficient file for (int ielem = 0; ielem < nelements; ielem++) { for (int icoeff = 0; icoeff < nparams; icoeff++) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpcoeff); + ptr = fgets(line, MAXLINE, fpcoeff); if (ptr == nullptr) { eof = 1; fclose(fpcoeff); - } else n = strlen(line) + 1; + } else + n = strlen(line) + 1; } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) - error->all(FLERR,"Incorrect format in MLIAPModel coefficient file"); - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); + if (eof) error->all(FLERR, "Incorrect format in MLIAPModel coefficient file"); + MPI_Bcast(&n, 1, MPI_INT, 0, world); + MPI_Bcast(line, n, MPI_CHAR, 0, world); try { ValueTokenizer coeffs(utils::trim_comment(line)); - if (coeffs.count() != 1) - throw TokenizerException("Wrong number of items",""); + if (coeffs.count() != 1) throw TokenizerException("Wrong number of items", ""); coeffelem[ielem][icoeff] = coeffs.next_double(); } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect format in MLIAPModel " - "coefficient file: {}",e.what()); + error->all(FLERR, + "Incorrect format in MLIAPModel " + "coefficient file: {}", + e.what()); } } } - if (comm->me == 0) fclose(fpcoeff); } @@ -180,7 +179,6 @@ double MLIAPModelSimple::memory_usage() { double bytes = 0; - bytes += (double)nelements*nparams*sizeof(double); // coeffelem + bytes += (double) nelements * nparams * sizeof(double); // coeffelem return bytes; } - diff --git a/src/MLIAP/mliap_model.h b/src/ML-IAP/mliap_model.h similarity index 100% rename from src/MLIAP/mliap_model.h rename to src/ML-IAP/mliap_model.h diff --git a/src/MLIAP/mliap_model_linear.cpp b/src/ML-IAP/mliap_model_linear.cpp similarity index 100% rename from src/MLIAP/mliap_model_linear.cpp rename to src/ML-IAP/mliap_model_linear.cpp diff --git a/src/MLIAP/mliap_model_linear.h b/src/ML-IAP/mliap_model_linear.h similarity index 100% rename from src/MLIAP/mliap_model_linear.h rename to src/ML-IAP/mliap_model_linear.h diff --git a/src/MLIAP/mliap_model_nn.cpp b/src/ML-IAP/mliap_model_nn.cpp similarity index 100% rename from src/MLIAP/mliap_model_nn.cpp rename to src/ML-IAP/mliap_model_nn.cpp diff --git a/src/MLIAP/mliap_model_nn.h b/src/ML-IAP/mliap_model_nn.h similarity index 100% rename from src/MLIAP/mliap_model_nn.h rename to src/ML-IAP/mliap_model_nn.h diff --git a/src/MLIAP/mliap_model_python.cpp b/src/ML-IAP/mliap_model_python.cpp similarity index 81% rename from src/MLIAP/mliap_model_python.cpp rename to src/ML-IAP/mliap_model_python.cpp index cd985f273a..3d91107449 100644 --- a/src/MLIAP/mliap_model_python.cpp +++ b/src/ML-IAP/mliap_model_python.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,63 +17,63 @@ #ifdef MLIAP_PYTHON -#include #include "mliap_model_python.h" + +#include "error.h" +#include "lmppython.h" +#include "mliap_data.h" #include "mliap_model_python_couple.h" #include "pair_mliap.h" -#include "mliap_data.h" -#include "error.h" -#include "utils.h" -#include "lmppython.h" #include "python_compat.h" +#include "utils.h" +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -MLIAPModelPython::MLIAPModelPython(LAMMPS* lmp, char* coefffilename) : - MLIAPModel(lmp, coefffilename) +MLIAPModelPython::MLIAPModelPython(LAMMPS *lmp, char *coefffilename) : + MLIAPModel(lmp, coefffilename) { model_loaded = 0; python->init(); PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject * pyMain = PyImport_AddModule("__main__"); + PyObject *pyMain = PyImport_AddModule("__main__"); if (!pyMain) { PyGILState_Release(gstate); - error->all(FLERR,"Could not initialize embedded Python"); + error->all(FLERR, "Could not initialize embedded Python"); } - PyObject* coupling_module = PyImport_ImportModule("mliap_model_python_couple"); + PyObject *coupling_module = PyImport_ImportModule("mliap_model_python_couple"); if (!coupling_module) { PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Loading MLIAPPY coupling module failure."); + error->all(FLERR, "Loading MLIAPPY coupling module failure."); } // Recipe from lammps/src/pair_python.cpp : // add current directory to PYTHONPATH - PyObject * py_path = PySys_GetObject((char *)"path"); + PyObject *py_path = PySys_GetObject((char *) "path"); PyList_Append(py_path, PY_STRING_FROM_STRING(".")); // if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well - const char * potentials_path = getenv("LAMMPS_POTENTIALS"); - if (potentials_path != NULL) { - PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path)); - } + const char *potentials_path = getenv("LAMMPS_POTENTIALS"); + if (potentials_path != NULL) { PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path)); } PyGILState_Release(gstate); if (coefffilename) read_coeffs(coefffilename); - nonlinearflag=1; + nonlinearflag = 1; } /* ---------------------------------------------------------------------- */ -MLIAPModelPython::~MLIAPModelPython() { +MLIAPModelPython::~MLIAPModelPython() +{ MLIAPPY_unload_model(this); } @@ -82,7 +81,6 @@ MLIAPModelPython::~MLIAPModelPython() { get number of parameters ---------------------------------------------------------------------- */ - int MLIAPModelPython::get_nparams() { return nparams; @@ -97,15 +95,14 @@ void MLIAPModelPython::read_coeffs(char *fname) PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Loading python model failure."); + error->all(FLERR, "Loading python model failure."); } PyGILState_Release(gstate); if (loaded) { this->connect_param_counts(); - } - else { - utils::logmesg(lmp,"Loading python model deferred.\n"); + } else { + utils::logmesg(lmp, "Loading python model deferred.\n"); } } @@ -121,15 +118,13 @@ void MLIAPModelPython::connect_param_counts() PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Loading python model failure."); + error->all(FLERR, "Loading python model failure."); } PyGILState_Release(gstate); model_loaded = 1; - utils::logmesg(lmp,"Loading python model complete.\n"); - + utils::logmesg(lmp, "Loading python model complete.\n"); } - /* ---------------------------------------------------------------------- Calculate model gradients w.r.t descriptors for each atom beta_i = dE(B_i)/dB_i @@ -137,9 +132,7 @@ void MLIAPModelPython::connect_param_counts() void MLIAPModelPython::compute_gradients(MLIAPData *data) { - if (not model_loaded) { - error->all(FLERR,"Model not loaded."); - } + if (not model_loaded) { error->all(FLERR, "Model not loaded."); } PyGILState_STATE gstate = PyGILState_Ensure(); MLIAPPY_compute_gradients(this, data); @@ -147,10 +140,9 @@ void MLIAPModelPython::compute_gradients(MLIAPData *data) PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Running python model failure."); + error->all(FLERR, "Running python model failure."); } PyGILState_Release(gstate); - } /* ---------------------------------------------------------------------- @@ -170,7 +162,7 @@ void MLIAPModelPython::compute_gradients(MLIAPData *data) void MLIAPModelPython::compute_gradgrads(class MLIAPData *) { - error->all(FLERR,"compute_gradgrads not implemented"); + error->all(FLERR, "compute_gradgrads not implemented"); } /* ---------------------------------------------------------------------- @@ -180,7 +172,7 @@ void MLIAPModelPython::compute_gradgrads(class MLIAPData *) void MLIAPModelPython::compute_force_gradients(class MLIAPData *) { - error->all(FLERR,"compute_force_gradients not implemented"); + error->all(FLERR, "compute_force_gradients not implemented"); } /* ---------------------------------------------------------------------- @@ -193,7 +185,6 @@ int MLIAPModelPython::get_gamma_nnz(class MLIAPData *) return 0; } - double MLIAPModelPython::memory_usage() { // todo: get approximate memory usage in coupling code. diff --git a/src/MLIAP/mliap_model_python.h b/src/ML-IAP/mliap_model_python.h similarity index 100% rename from src/MLIAP/mliap_model_python.h rename to src/ML-IAP/mliap_model_python.h diff --git a/src/MLIAP/mliap_model_python_couple.pyx b/src/ML-IAP/mliap_model_python_couple.pyx similarity index 100% rename from src/MLIAP/mliap_model_python_couple.pyx rename to src/ML-IAP/mliap_model_python_couple.pyx diff --git a/src/MLIAP/mliap_model_quadratic.cpp b/src/ML-IAP/mliap_model_quadratic.cpp similarity index 100% rename from src/MLIAP/mliap_model_quadratic.cpp rename to src/ML-IAP/mliap_model_quadratic.cpp diff --git a/src/MLIAP/mliap_model_quadratic.h b/src/ML-IAP/mliap_model_quadratic.h similarity index 100% rename from src/MLIAP/mliap_model_quadratic.h rename to src/ML-IAP/mliap_model_quadratic.h diff --git a/src/MLIAP/mliap_so3.cpp b/src/ML-IAP/mliap_so3.cpp similarity index 95% rename from src/MLIAP/mliap_so3.cpp rename to src/ML-IAP/mliap_so3.cpp index d514b0bc70..b600b29ebd 100644 --- a/src/MLIAP/mliap_so3.cpp +++ b/src/ML-IAP/mliap_so3.cpp @@ -705,7 +705,7 @@ void MLIAP_SO3::get_sbes_array(int nlocal, int *numneighs, double **rij, int lma bigint ipair = 0; bigint gindex; int findex = m_Nmax * (m_lmax + 1); - int mindex = m_lmax + 1; + const bigint mindex = m_lmax + 1; for (int ii = 0; ii < nlocal; ii++) { @@ -721,10 +721,10 @@ void MLIAP_SO3::get_sbes_array(int nlocal, int *numneighs, double **rij, int lma if (ri < SMALL) continue; pfac2 = pfac1 * ri; - gindex = (ipair - 1) * findex; for (i = 1; i < m_Nmax + 1; i++) { + const bigint i1mindex = (bigint) (i - 1) * mindex; x = cos((2 * i - 1) * pfac3); xi = pfac4 * (x + 1); @@ -733,28 +733,27 @@ void MLIAP_SO3::get_sbes_array(int nlocal, int *numneighs, double **rij, int lma sa = sinh(rb) / rb; sb = (cosh(rb) - sa) / rb; - m_sbes_array[gindex + (i - 1) * mindex + 0] = sa; - m_sbes_array[gindex + (i - 1) * mindex + 1] = sb; + m_sbes_array[gindex + i1mindex + 0] = sa; + m_sbes_array[gindex + i1mindex + 1] = sb; for (j = 2; j < lmax + 1; j++) - m_sbes_array[gindex + (i - 1) * mindex + j] = - m_sbes_array[gindex + (i - 1) * mindex + j - 2] - - (2 * j - 1) / rb * m_sbes_array[gindex + (i - 1) * mindex + j - 1]; + m_sbes_array[gindex + i1mindex + j] = m_sbes_array[gindex + i1mindex + j - 2] - + (2 * j - 1) / rb * m_sbes_array[gindex + i1mindex + j - 1]; - exts = m_sbes_array[gindex + (i - 1) * mindex + j - 2] - - (2 * j - 1) / rb * m_sbes_array[gindex + (i - 1) * mindex + j - 1]; + exts = m_sbes_array[gindex + i1mindex + j - 2] - + (2 * j - 1) / rb * m_sbes_array[gindex + i1mindex + j - 1]; - m_sbes_darray[gindex + (i - 1) * mindex + 0] = sb; + m_sbes_darray[gindex + i1mindex + 0] = sb; for (j = 1; j < lmax; j++) - m_sbes_darray[gindex + (i - 1) * mindex + j] = xi * - (j * m_sbes_array[gindex + (i - 1) * mindex + j - 1] + - (j + 1) * m_sbes_array[gindex + (i - 1) * mindex + j + 1]) / + m_sbes_darray[gindex + i1mindex + j] = xi * + (j * m_sbes_array[gindex + i1mindex + j - 1] + + (j + 1) * m_sbes_array[gindex + i1mindex + j + 1]) / (2 * j + 1); - m_sbes_darray[gindex + (i - 1) * mindex + j] = xi * - (j * m_sbes_array[gindex + (i - 1) * mindex + j - 1] + (j + 1) * exts) / (2 * j + 1); - m_sbes_darray[gindex + (i - 1) * mindex + 0] = xi * sb; + m_sbes_darray[gindex + i1mindex + j] = + xi * (j * m_sbes_array[gindex + i1mindex + j - 1] + (j + 1) * exts) / (2 * j + 1); + m_sbes_darray[gindex + i1mindex + 0] = xi * sb; } } } @@ -797,14 +796,14 @@ void MLIAP_SO3::get_rip_array(int nlocal, int *numneighs, double **rij, int nmax integrald = 0.0; for (i = 0; i < m_Nmax; i++) { integral += m_g_array[(n - 1) * m_Nmax + i] * - m_sbes_array[(ipair - 1) * m_Nmax * (m_lmax + 1) + i * (m_lmax + 1) + l]; + m_sbes_array[(ipair - 1) * m_Nmax * (m_lmax + 1) + (bigint) i * (m_lmax + 1) + l]; integrald += m_g_array[(n - 1) * m_Nmax + i] * - m_sbes_darray[(ipair - 1) * m_Nmax * (m_lmax + 1) + i * (m_lmax + 1) + l]; + m_sbes_darray[(ipair - 1) * m_Nmax * (m_lmax + 1) + (bigint) i * (m_lmax + 1) + l]; } - m_rip_array[(ipair - 1) * m_nmax * (m_lmax + 1) + (n - 1) * (m_lmax + 1) + l] = + m_rip_array[(ipair - 1) * m_nmax * (m_lmax + 1) + (bigint) (n - 1) * (m_lmax + 1) + l] = integral * expfac; - m_rip_darray[(ipair - 1) * m_nmax * (m_lmax + 1) + (n - 1) * (m_lmax + 1) + l] = + m_rip_darray[(ipair - 1) * m_nmax * (m_lmax + 1) + (bigint) (n - 1) * (m_lmax + 1) + l] = integrald * expfac; } } @@ -904,7 +903,7 @@ void MLIAP_SO3::spectrum(int nlocal, int *numneighs, int *jelems, double *wjelem for (int n = 1; n < nmax + 1; n++) { int i = 0; for (int l = 0; l < lmax + 1; l++) { - r_int = m_rip_array[gindex + (n - 1) * (m_lmax + 1) + l]; + r_int = m_rip_array[gindex + (bigint) (n - 1) * (m_lmax + 1) + l]; for (int m = -l; m < l + 1; m++) { @@ -1005,7 +1004,7 @@ void MLIAP_SO3::spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *w for (int ii = 0; ii < nlocal; ii++) { - totali = nmax * m_numYlms; + totali = (bigint) nmax * m_numYlms; for (bigint ti = 0; ti < totali; ti++) { m_clisttot_r[ti] = 0.0; m_clisttot_i[ti] = 0.0; @@ -1024,7 +1023,7 @@ void MLIAP_SO3::spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *w r = sqrt(x * x + y * y + z * z); if (r < SMALL) continue; - totali = nmax * m_numYlms; + totali = (bigint) nmax * m_numYlms; for (bigint ti = 0; ti < totali; ti++) { m_clist_r[ti] = 0.0; @@ -1044,7 +1043,7 @@ void MLIAP_SO3::spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *w for (int n = 1; n < nmax + 1; n++) { int i = 0; for (int l = 0; l < lmax + 1; l++) { - r_int = m_rip_array[gindex + (n - 1) * (m_lmax + 1) + l]; + r_int = m_rip_array[gindex + (bigint) (n - 1) * (m_lmax + 1) + l]; for (int m = -l; m < l + 1; m++) { @@ -1057,7 +1056,7 @@ void MLIAP_SO3::spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *w } } - totali = nmax * m_numYlms; + totali = (bigint) nmax * m_numYlms; for (bigint tn = 0; tn < totali; tn++) { m_clist_r[tn] = m_clist_r[tn] * double(weight); m_clist_i[tn] = m_clist_i[tn] * double(weight); @@ -1174,9 +1173,10 @@ void MLIAP_SO3::spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *w for (int n = 1; n < nmax + 1; n++) { int i = 0; for (int l = 0; l < lmax + 1; l++) { - r_int = m_rip_array[(idpair - 1) * m_nmax * (m_lmax + 1) + (n - 1) * (m_lmax + 1) + l]; - r_int_temp = - m_rip_darray[(idpair - 1) * m_nmax * (m_lmax + 1) + (n - 1) * (m_lmax + 1) + l]; + r_int = m_rip_array[(idpair - 1) * m_nmax * (m_lmax + 1) + + (bigint) (n - 1) * (m_lmax + 1) + l]; + r_int_temp = m_rip_darray[(idpair - 1) * m_nmax * (m_lmax + 1) + + (bigint) (n - 1) * (m_lmax + 1) + l]; for (int ii = 0; ii < 3; ii++) dr_int[ii] = r_int_temp * 2.0 * alpha * rvec[ii] / r; diff --git a/src/MLIAP/mliap_so3.h b/src/ML-IAP/mliap_so3.h similarity index 100% rename from src/MLIAP/mliap_so3.h rename to src/ML-IAP/mliap_so3.h diff --git a/src/MLIAP/mliap_so3_math.h b/src/ML-IAP/mliap_so3_math.h similarity index 100% rename from src/MLIAP/mliap_so3_math.h rename to src/ML-IAP/mliap_so3_math.h diff --git a/src/MLIAP/pair_mliap.cpp b/src/ML-IAP/pair_mliap.cpp similarity index 99% rename from src/MLIAP/pair_mliap.cpp rename to src/ML-IAP/pair_mliap.cpp index 0d2a80635a..64c5a547be 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/ML-IAP/pair_mliap.cpp @@ -264,8 +264,7 @@ void PairMLIAP::e_tally(MLIAPData* data) add virial contribution into global and per-atom accumulators ------------------------------------------------------------------------- */ -void PairMLIAP::v_tally(int i, int j, - double *fij, double *rij) +void PairMLIAP::v_tally(int i, int j, double *fij, double *rij) { double v[6]; diff --git a/src/MLIAP/pair_mliap.h b/src/ML-IAP/pair_mliap.h similarity index 100% rename from src/MLIAP/pair_mliap.h rename to src/ML-IAP/pair_mliap.h diff --git a/src/USER-PACE/Install.sh b/src/ML-PACE/Install.sh similarity index 100% rename from src/USER-PACE/Install.sh rename to src/ML-PACE/Install.sh diff --git a/src/USER-PACE/README b/src/ML-PACE/README similarity index 89% rename from src/USER-PACE/README rename to src/ML-PACE/README index c701a615f7..7909b68dd3 100644 --- a/src/USER-PACE/README +++ b/src/ML-PACE/README @@ -1,4 +1,4 @@ -The USER-PACE package provides the pace pair style, +The ML-PACE package provides the pace pair style, an efficient implementation of the Atomic Cluster Expansion potential (ACE). @@ -17,7 +17,7 @@ provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. -More information about the USER-PACE implementation of ACE +More information about the ML-PACE implementation of ACE is available here: https://github.com/ICAMS/lammps-user-pace diff --git a/src/USER-PACE/pair_pace.cpp b/src/ML-PACE/pair_pace.cpp similarity index 100% rename from src/USER-PACE/pair_pace.cpp rename to src/ML-PACE/pair_pace.cpp diff --git a/src/USER-PACE/pair_pace.h b/src/ML-PACE/pair_pace.h similarity index 100% rename from src/USER-PACE/pair_pace.h rename to src/ML-PACE/pair_pace.h diff --git a/src/USER-QUIP/Install.sh b/src/ML-QUIP/Install.sh similarity index 100% rename from src/USER-QUIP/Install.sh rename to src/ML-QUIP/Install.sh diff --git a/src/USER-QUIP/README b/src/ML-QUIP/README similarity index 82% rename from src/USER-QUIP/README rename to src/ML-QUIP/README index 5bd9c45181..0e82248dd5 100644 --- a/src/USER-QUIP/README +++ b/src/ML-QUIP/README @@ -6,5 +6,5 @@ Potential (GAP) models. See lib/quip/README for more information on how to build LAMMPS with this package. -See examples/USER/quip for several test examples that run QUIP +See examples/PACKAGES/quip for several test examples that run QUIP potentials. diff --git a/src/USER-QUIP/pair_quip.cpp b/src/ML-QUIP/pair_quip.cpp similarity index 56% rename from src/USER-QUIP/pair_quip.cpp rename to src/ML-QUIP/pair_quip.cpp index a9d3fa61e2..f1a2eb8a4a 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/ML-QUIP/pair_quip.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -28,6 +27,7 @@ #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" +#include "potential_file_reader.h" #include "update.h" #include @@ -45,7 +45,7 @@ PairQUIP::PairQUIP(LAMMPS *lmp) : Pair(lmp) no_virial_fdotr_compute = 1; manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - + unit_convert_flag = utils::NOCONVERT; map = nullptr; quip_potential = nullptr; quip_file = nullptr; @@ -57,11 +57,11 @@ PairQUIP::~PairQUIP() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; + delete[] map; } - delete [] quip_potential; - delete [] quip_file; - delete [] quip_string; + delete[] quip_potential; + delete[] quip_file; + delete[] quip_string; } void PairQUIP::compute(int eflag, int vflag) @@ -83,7 +83,7 @@ void PairQUIP::compute(int eflag, int vflag) double *quip_local_e, *quip_force, *quip_local_virial, *quip_virial, quip_energy, *lattice; - ev_init(eflag,vflag); + ev_init(eflag, vflag); inum = list->inum; ilist = list->ilist; @@ -91,7 +91,7 @@ void PairQUIP::compute(int eflag, int vflag) firstneigh = list->firstneigh; sum_num_neigh = 0; - quip_num_neigh = new int [inum]; + quip_num_neigh = new int[inum]; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; @@ -99,7 +99,7 @@ void PairQUIP::compute(int eflag, int vflag) sum_num_neigh += numneigh[i]; } - quip_neigh = new int [sum_num_neigh]; + quip_neigh = new int[sum_num_neigh]; iquip = 0; for (ii = 0; ii < inum; ii++) { @@ -114,15 +114,14 @@ void PairQUIP::compute(int eflag, int vflag) } atomic_numbers = new int[ntotal]; - for (ii = 0; ii < ntotal; ii++) - atomic_numbers[ii] = map[type[ii]]; + for (ii = 0; ii < ntotal; ii++) atomic_numbers[ii] = map[type[ii]]; - quip_local_e = new double [ntotal]; - quip_force = new double [ntotal*3]; - quip_local_virial = new double [ntotal*9]; - quip_virial = new double [9]; + quip_local_e = new double[ntotal]; + quip_force = new double[ntotal * 3]; + quip_local_virial = new double[ntotal * 9]; + quip_virial = new double[9]; - lattice = new double [9]; + lattice = new double[9]; lattice[0] = domain->xprd; lattice[1] = 0.0; lattice[2] = 0.0; @@ -138,81 +137,68 @@ void PairQUIP::compute(int eflag, int vflag) int tmplarge = 0, toolarge = 0; for (ii = 0; ii < ntotal; ++ii) { tmptag[ii] = tag[ii]; - if (tag[ii] > MAXSMALLINT) tmplarge=1; + if (tag[ii] > MAXSMALLINT) tmplarge = 1; } - MPI_Allreduce(&tmplarge,&toolarge,1,MPI_INT,MPI_MAX,world); - if (toolarge > 0) - error->all(FLERR,"Pair style quip does not support 64-bit atom IDs"); + MPI_Allreduce(&tmplarge, &toolarge, 1, MPI_INT, MPI_MAX, world); + if (toolarge > 0) error->all(FLERR, "Pair style quip does not support 64-bit atom IDs"); - quip_lammps_wrapper(&nlocal,&nghost,atomic_numbers,tmptag, - &inum,&sum_num_neigh,ilist, - quip_num_neigh,quip_neigh,lattice, - quip_potential,&n_quip_potential,&x[0][0], - &quip_energy,quip_local_e,quip_virial, - quip_local_virial,quip_force); + quip_lammps_wrapper(&nlocal, &nghost, atomic_numbers, tmptag, &inum, &sum_num_neigh, ilist, + quip_num_neigh, quip_neigh, lattice, quip_potential, &n_quip_potential, + &x[0][0], &quip_energy, quip_local_e, quip_virial, quip_local_virial, + quip_force); delete[] tmptag; #else - quip_lammps_wrapper(&nlocal,&nghost,atomic_numbers,tag, - &inum,&sum_num_neigh,ilist, - quip_num_neigh,quip_neigh,lattice, - quip_potential,&n_quip_potential,&x[0][0], - &quip_energy,quip_local_e,quip_virial, - quip_local_virial,quip_force); + quip_lammps_wrapper(&nlocal, &nghost, atomic_numbers, tag, &inum, &sum_num_neigh, ilist, + quip_num_neigh, quip_neigh, lattice, quip_potential, &n_quip_potential, + &x[0][0], &quip_energy, quip_local_e, quip_virial, quip_local_virial, + quip_force); #endif iquip = 0; for (ii = 0; ii < ntotal; ii++) { - for (jj = 0; jj < 3; jj++) { - f[ii][jj] += quip_force[iquip]; - iquip++; - } - } - - if (eflag_global) { - eng_vdwl = quip_energy; - } - - if (eflag_atom) { - for (ii = 0; ii < ntotal; ii++) { - eatom[ii] = quip_local_e[ii]; + for (jj = 0; jj < 3; jj++) { + f[ii][jj] += quip_force[iquip]; + iquip++; } } + if (eflag_global) { eng_vdwl = quip_energy; } + + if (eflag_atom) { + for (ii = 0; ii < ntotal; ii++) { eatom[ii] = quip_local_e[ii]; } + } + if (vflag_global) { - virial[0] = quip_virial[0]; - virial[1] = quip_virial[4]; - virial[2] = quip_virial[8]; - virial[3] = (quip_virial[3] + quip_virial[1])*0.5; - virial[4] = (quip_virial[2] + quip_virial[6])*0.5; - virial[5] = (quip_virial[5] + quip_virial[7])*0.5; + virial[0] = quip_virial[0]; + virial[1] = quip_virial[4]; + virial[2] = quip_virial[8]; + virial[3] = (quip_virial[3] + quip_virial[1]) * 0.5; + virial[4] = (quip_virial[2] + quip_virial[6]) * 0.5; + virial[5] = (quip_virial[5] + quip_virial[7]) * 0.5; } if (vflag_atom) { int iatom = 0; - for (ii = 0; ii < ntotal; ii++) { - vatom[ii][0] += quip_local_virial[iatom+0]; - vatom[ii][1] += quip_local_virial[iatom+4]; - vatom[ii][2] += quip_local_virial[iatom+8]; - vatom[ii][3] += (quip_local_virial[iatom+3] + - quip_local_virial[iatom+1])*0.5; - vatom[ii][4] += (quip_local_virial[iatom+2] + - quip_local_virial[iatom+6])*0.5; - vatom[ii][5] += (quip_local_virial[iatom+5] + - quip_local_virial[iatom+7])*0.5; - iatom += 9; - } + for (ii = 0; ii < ntotal; ii++) { + vatom[ii][0] += quip_local_virial[iatom + 0]; + vatom[ii][1] += quip_local_virial[iatom + 4]; + vatom[ii][2] += quip_local_virial[iatom + 8]; + vatom[ii][3] += (quip_local_virial[iatom + 3] + quip_local_virial[iatom + 1]) * 0.5; + vatom[ii][4] += (quip_local_virial[iatom + 2] + quip_local_virial[iatom + 6]) * 0.5; + vatom[ii][5] += (quip_local_virial[iatom + 5] + quip_local_virial[iatom + 7]) * 0.5; + iatom += 9; + } } - delete [] atomic_numbers; - delete [] quip_num_neigh; - delete [] quip_neigh; - delete [] quip_local_e; - delete [] quip_force; - delete [] quip_virial; - delete [] quip_local_virial; - delete [] lattice; - + delete[] atomic_numbers; + delete[] quip_num_neigh; + delete[] quip_neigh; + delete[] quip_local_e; + delete[] quip_force; + delete[] quip_virial; + delete[] quip_local_virial; + delete[] lattice; } /* ---------------------------------------------------------------------- @@ -221,18 +207,19 @@ void PairQUIP::compute(int eflag, int vflag) void PairQUIP::settings(int narg, char ** /* arg */) { - if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + if (narg != 0) error->all(FLERR, "Illegal pair_style command"); // check if linked to the correct QUIP library API version // as of 2017-07-19 this is API_VERSION 1 if (quip_lammps_api_version() != 1) - error->all(FLERR,"QUIP LAMMPS wrapper API version is not compatible " - "with this version of LAMMPS"); + error->all(FLERR, + "QUIP LAMMPS wrapper API version is not compatible " + "with this version of LAMMPS"); // QUIP potentials are parameterized in metal units - if (strcmp("metal",update->unit_style) != 0) - error->all(FLERR,"QUIP potentials require 'metal' units"); + if (strcmp("metal", update->unit_style) != 0) + error->all(FLERR, "QUIP potentials require 'metal' units"); } /* ---------------------------------------------------------------------- @@ -243,9 +230,9 @@ void PairQUIP::allocate() allocated = 1; int n = atom->ntypes; - setflag = memory->create(setflag,n+1,n+1,"pair:setflag"); - cutsq = memory->create(cutsq,n+1,n+1,"pair:cutsq"); - map = new int[n+1]; + setflag = memory->create(setflag, n + 1, n + 1, "pair:setflag"); + cutsq = memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + map = new int[n + 1]; } void PairQUIP::coeff(int narg, char **arg) @@ -253,33 +240,32 @@ void PairQUIP::coeff(int narg, char **arg) if (!allocated) allocate(); int n = atom->ntypes; - if (narg != (4+n)) - error->all(FLERR,"Number of arguments {} is not correct, " - "it should be {}", narg, 4+n); + if (narg != (4 + n)) + error->all(FLERR, "Number of arguments {} is not correct, it should be {}", narg, 4 + n); - // ensure I,J args are * * + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[2], "QUIP", unit_convert_flag); + auto comment = reader.next_string(); + } - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - quip_file = utils::strdup(arg[2]); + // use expanded file name, including LAMMPS_POTENTIALS search path + quip_file = utils::strdup(utils::get_potential_file_path(arg[2])); quip_string = utils::strdup(arg[3]); n_quip_file = strlen(quip_file); n_quip_string = strlen(quip_string); for (int i = 4; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) - map[i-3] = -1; + if (strcmp(arg[i], "NULL") == 0) + map[i - 3] = -1; else - map[i-3] = utils::inumeric(FLERR,arg[i],false,lmp); + map[i - 3] = utils::inumeric(FLERR, arg[i], false, lmp); } // clear setflag since coeff() called once with I,J = * * n = atom->ntypes; for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + for (int j = i; j <= n; j++) setflag[i][j] = 0; // set setflag i,j for type pairs where both are mapped to elements @@ -291,21 +277,25 @@ void PairQUIP::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); // Initialise potential - // First call initializes potential via the fortran code in memory, and returns the necessary size - // of quip_potential. This behavior is invoked by setting n_potential_quip to 0. + // First call initializes potential via the fortran code in memory, + // and returns the necessary size of quip_potential. This behavior + // is invoked by setting n_potential_quip to 0. n_quip_potential = 0; quip_potential = new int[0]; - quip_lammps_potential_initialise(quip_potential,&n_quip_potential,&cutoff,quip_file,&n_quip_file,quip_string,&n_quip_string); - delete [] quip_potential; + quip_lammps_potential_initialise(quip_potential, &n_quip_potential, &cutoff, quip_file, + &n_quip_file, quip_string, &n_quip_string); + delete[] quip_potential; - // Allocate quip_potential integer array. This initialise call will transfer the location of the - // previously initialised potential to the quip_potential variable, and we will use it as a handle - // when calling the actual calculation routine. We return the cutoff as well. + // Allocate quip_potential integer array. This initialise call will transfer + // the location of the previously initialised potential to the quip_potential + // variable, and we will use it as a handle when calling the actual calculation + // routine. We return the cutoff as well. quip_potential = new int[n_quip_potential]; - quip_lammps_potential_initialise(quip_potential,&n_quip_potential,&cutoff,quip_file,&n_quip_file,quip_string,&n_quip_string); + quip_lammps_potential_initialise(quip_potential, &n_quip_potential, &cutoff, quip_file, + &n_quip_file, quip_string, &n_quip_string); } /* ---------------------------------------------------------------------- @@ -316,8 +306,7 @@ void PairQUIP::init_style() { // Require newton pair on - if (force->newton_pair != 1) - error->all(FLERR,"Pair style quip requires newton pair on"); + if (force->newton_pair != 1) error->all(FLERR, "Pair style quip requires newton pair on"); // Initialise neighbor list int irequest_full = neighbor->request(this); diff --git a/src/USER-QUIP/pair_quip.h b/src/ML-QUIP/pair_quip.h similarity index 100% rename from src/USER-QUIP/pair_quip.h rename to src/ML-QUIP/pair_quip.h diff --git a/src/USER-RANN/pair_rann.cpp b/src/ML-RANN/pair_rann.cpp similarity index 89% rename from src/USER-RANN/pair_rann.cpp rename to src/ML-RANN/pair_rann.cpp index 59ad688cb5..faab2d1b2f 100644 --- a/src/USER-RANN/pair_rann.cpp +++ b/src/ML-RANN/pair_rann.cpp @@ -32,6 +32,7 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 #include "pair_rann.h" #include "atom.h" +#include "citeme.h" #include "comm.h" #include "error.h" #include "force.h" @@ -61,8 +62,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 using namespace LAMMPS_NS; -static const char cite_user_rann_package[] = - "USER-RANN package:\n\n" +static const char cite_ml_rann_package[] = + "ML-RANN package:\n\n" "@Article{Nitol2021,\n" " author = {Nitol, Mashroor S and Dickel, Doyl E and Barrett, Christopher D},\n" " title = {Artificial neural network potential for pure zinc},\n" @@ -75,62 +76,133 @@ static const char cite_user_rann_package[] = PairRANN::PairRANN(LAMMPS *lmp) : Pair(lmp) { + if (lmp->citeme) lmp->citeme->add(cite_ml_rann_package); + + //initialize ints and bools single_enable = 0; restartinfo = 0; one_coeff = 1; manybody_flag = 1; allocated = 0; nelements = -1; - elements = NULL; - mass = NULL; - - // set comm size needed by this Pair - // comm unused for now. - - comm_forward = 38; - comm_reverse = 30; + nelementsp = -1; + comm_forward = 0; + comm_reverse = 0; res = 10000; cutmax = 0; - //at least one of the following will change during fingerprint definition: + dospin = false; + memguess = 0; + nmax1 = 0; + nmax2 = 0; + fmax = 0; + fnmax = 0; + //at least one of the following two flags will change during fingerprint definition: doscreen = false; allscreen = true; - dospin = false; + + //null init for arrays with sizes not yet determined. + elements = nullptr; + mass = nullptr; + elementsp = nullptr; + map = nullptr; + fingerprintcount = nullptr; + fingerprintlength = nullptr; + fingerprintperelement = nullptr; + screening_min = nullptr; + screening_max = nullptr; + weightdefined = nullptr; + biasdefined = nullptr; + xn = nullptr; + yn = nullptr; + zn = nullptr; + Sik = nullptr; + dSikx = nullptr; + dSiky = nullptr; + dSikz = nullptr; + dSijkx = nullptr; + dSijky = nullptr; + dSijkz = nullptr; + sx = nullptr; + sy = nullptr; + sz = nullptr; + dSijkxc = nullptr; + dSijkyc = nullptr; + dSijkzc = nullptr; + dfeaturesx = nullptr; + dfeaturesy = nullptr; + dfeaturesz = nullptr; + features = nullptr; + layer = nullptr; + sum = nullptr; + sum1 = nullptr; + dlayerx = nullptr; + dlayery = nullptr; + dlayerz = nullptr; + dlayersumx = nullptr; + dlayersumy = nullptr; + dlayersumz = nullptr; + dsx = nullptr; + dsy = nullptr; + dsz = nullptr; + dssumx = nullptr; + dssumy = nullptr; + dssumz = nullptr; + tn = nullptr; + jl = nullptr; + Bij = nullptr; + sims = nullptr; + net = nullptr; + activation = nullptr; + fingerprints = nullptr; } PairRANN::~PairRANN() +{ + deallocate(); +} + +void PairRANN::deallocate() { //clear memory - delete [] mass; + delete[] mass; for (int i=0;i0) { for (int j=0;j0) { - delete [] fingerprints[i]; - delete [] activation[i]; + for (int j=0;jdestroy(xn); memory->destroy(yn); memory->destroy(zn); @@ -149,30 +221,28 @@ PairRANN::~PairRANN() memory->destroy(dlayersumx); memory->destroy(dlayersumy); memory->destroy(dlayersumz); - if (doscreen) { - memory->destroy(Sik); - memory->destroy(Bij); - memory->destroy(dSikx); - memory->destroy(dSiky); - memory->destroy(dSikz); - memory->destroy(dSijkx); - memory->destroy(dSijky); - memory->destroy(dSijkz); - memory->destroy(dSijkxc); - memory->destroy(dSijkyc); - memory->destroy(dSijkzc); - } - if (dospin) { - memory->destroy(sx); - memory->destroy(sy); - memory->destroy(sz); - memory->destroy(dsx); - memory->destroy(dsy); - memory->destroy(dsz); - memory->destroy(dssumx); - memory->destroy(dssumy); - memory->destroy(dssumz); - } + memory->destroy(Sik); + memory->destroy(Bij); + memory->destroy(dSikx); + memory->destroy(dSiky); + memory->destroy(dSikz); + memory->destroy(dSijkx); + memory->destroy(dSijky); + memory->destroy(dSijkz); + memory->destroy(dSijkxc); + memory->destroy(dSijkyc); + memory->destroy(dSijkzc); + memory->destroy(sx); + memory->destroy(sy); + memory->destroy(sz); + memory->destroy(dsx); + memory->destroy(dsy); + memory->destroy(dsz); + memory->destroy(dssumx); + memory->destroy(dssumy); + memory->destroy(dssumz); + memory->destroy(setflag); + memory->destroy(cutsq); } void PairRANN::allocate(const std::vector &elementwords) @@ -197,10 +267,10 @@ void PairRANN::allocate(const std::vector &elementwords) activation = new RANN::Activation**[nelementsp]; fingerprints = new RANN::Fingerprint**[nelementsp]; fingerprintlength = new int[nelementsp]; - fingerprintperelement = new int [nelementsp]; + fingerprintperelement = new int[nelementsp]; fingerprintcount = new int[nelementsp]; - screening_min = new double [nelements*nelements*nelements]; - screening_max = new double [nelements*nelements*nelements]; + screening_min = new double[nelements*nelements*nelements]; + screening_max = new double[nelements*nelements*nelements]; for (i=0;intypes+1]; + deallocate();//clear allocation from any previous coeff + map = new int[atom->ntypes+1]; if (narg != 3 + atom->ntypes) error->one(FLERR,"Incorrect args for pair coefficients"); if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->one(FLERR,"Incorrect args for pair coefficients"); nelements = -1; @@ -284,8 +355,8 @@ void PairRANN::read_file(char *filename) FILE *fp; int eof = 0; std::string line,line1; - int longline = 4096; - int linenum; + const int longline = 4096; + int linenum=0; char linetemp[longline]; std::string strtemp; char *ptr; @@ -304,7 +375,8 @@ void PairRANN::read_file(char *filename) while (eof == 0) { ptr=fgets(linetemp,longline,fp); linenum++; - if (ptr == NULL) { + if (ptr == nullptr) { + fclose(fp); if (check_potential()) { error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); } @@ -345,7 +417,7 @@ void PairRANN::read_file(char *filename) strtemp=utils::trim_comment(linetemp); linenum++; } - if (ptr == NULL) { + if (ptr == nullptr) { if (check_potential()) { error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); } @@ -394,12 +466,12 @@ void PairRANN::read_fpe(std::vector line,std::vector l } void PairRANN::read_fingerprints(std::vector line,std::vector line1,char *filename,int linenum) { - int nwords1,nwords,i,j,k,i1; + int nwords1,nwords,i,j,k,i1,*atomtypes; bool found; nwords1 = line1.size(); nwords = line.size(); if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints in potential file."); - int atomtypes[nwords-1]; + atomtypes = new int[nwords-1]; for (i=1;i line,std::vectorinit(atomtypes,utils::inumeric(filename,linenum,line1[k++].c_str(),1,lmp)); fingerprintcount[i]++; } + delete[] atomtypes; } void PairRANN::read_fingerprint_constants(std::vector line,std::vector line1,char *filename,int linenum) { - int i,j,k,i1; + int i,j,k,i1,*atomtypes; bool found; int nwords = line.size(); if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints in potential file."); int n_body_type = nwords-4; - int atomtypes[n_body_type]; + atomtypes = new int[n_body_type]; for (i=1;i<=n_body_type;i++) { found = false; for (j=0;j line,std::vec } if (!found) {error->one(filename,linenum-1,"cannot define constants for unknown fingerprint");} fingerprints[i][i1]->fullydefined=fingerprints[i][i1]->parse_values(line[nwords-1],line1); + delete[] atomtypes; } void PairRANN::read_network_layers(std::vector line,std::vector line1,char *filename,int linenum) { @@ -472,16 +546,14 @@ void PairRANN::read_network_layers(std::vector line,std::vectorone(filename,linenum,"invalid number of network layers"); - delete [] net[i].dimensions; + delete[] net[i].dimensions; weightdefined[i] = new bool [net[i].layers]; biasdefined[i] = new bool [net[i].layers]; - net[i].dimensions = new int [net[i].layers]; + net[i].dimensions = new int[net[i].layers]; net[i].Weights = new double * [net[i].layers-1]; net[i].Biases = new double * [net[i].layers-1]; - net[i].activations = new int [net[i].layers-1]; for (j=0;j line,std::vector line,std::vector line1,FILE* fp,char *filename,int *linenum) { int i,j,k,l,nwords; char *ptr; - int longline = 4096; + const int longline = 4096; char linetemp [longline]; for (l=0;l line,std::vector=net[l].layers || i<0)error->one(filename,*linenum-1,"invalid weight layer"); if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(filename,*linenum-1,"network layer sizes must be defined before corresponding weight"); - net[l].Weights[i] = new double [net[l].dimensions[i]*net[l].dimensions[i+1]]; + net[l].Weights[i] = new double[net[l].dimensions[i]*net[l].dimensions[i+1]]; weightdefined[l][i] = true; nwords = line1.size(); if (nwords != net[l].dimensions[i])error->one(filename,*linenum,"invalid weights per line"); @@ -532,7 +604,7 @@ void PairRANN::read_weight(std::vector line,std::vectorone(filename,*linenum,"unexpected end of potential file!"); + if (ptr==nullptr)error->one(filename,*linenum,"unexpected end of potential file!"); nwords = line1.size(); if (nwords != net[l].dimensions[i])error->one(filename,*linenum,"invalid weights per line"); for (k=0;k line,std::vector line,std::vector line1,FILE* fp,char *filename,int *linenum) { int i,j,l; - char linetemp[MAXLINE]; + char linetemp[MAXLINE],*ptr; for (l=0;lone(filename,*linenum-1,"networklayers must be defined before biases."); @@ -555,10 +627,11 @@ void PairRANN::read_bias(std::vector line,std::vector if (i>=net[l].layers || i<0)error->one(filename,*linenum-1,"invalid bias layer"); if (net[l].dimensions[i]==0) error->one(filename,*linenum-1,"network layer sizes must be defined before corresponding bias"); biasdefined[l][i] = true; - net[l].Biases[i] = new double [net[l].dimensions[i+1]]; + net[l].Biases[i] = new double[net[l].dimensions[i+1]]; net[l].Biases[i][0] = utils::numeric(filename,*linenum,line1[0].c_str(),1,lmp); for (j=1;jone(filename,*linenum,"unexpected end of potential file!"); (*linenum)++; Tokenizer values1 = Tokenizer(linetemp,": ,\t_\n"); line1 = values1.as_vector(); @@ -575,7 +648,7 @@ void PairRANN::read_activation_functions(std::vector line,std::vect for (l=0;lone(filename,linenum-1,"networklayers must be defined before activation functions."); - i = strtol(line[2].c_str(),NULL,10); + i = strtol(line[2].c_str(),nullptr,10); if (i>=net[l].layers || i<0)error->one(filename,linenum-1,"invalid activation layer"); delete activation[l][i]; activation[l][i]=create_activation(line1[0].c_str()); @@ -586,13 +659,13 @@ void PairRANN::read_activation_functions(std::vector line,std::vect } void PairRANN::read_screening(std::vector line,std::vector line1,char *filename,int linenum) { - int i,j,k; + int i,j,k,*atomtypes; bool found; int nwords = line.size(); if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints in potential file."); if (nwords!=5)error->one(filename,linenum-1,"invalid screening command"); int n_body_type = 3; - int atomtypes[n_body_type]; + atomtypes = new int[n_body_type]; for (i=1;i<=n_body_type;i++) { found = false; for (j=0;j line,std::vectorone(filename,linenum-1,"unrecognized screening keyword"); + delete[] atomtypes; } //Called after finishing reading the potential file to make sure it is complete. True is bad. @@ -701,15 +775,22 @@ bool PairRANN::check_potential() { void PairRANN::compute(int eflag, int vflag) { - //perform force/energy computation_ + //perform force/energy computation_ if (dospin) { if (strcmp(update->unit_style,"metal") != 0) error->one(FLERR,"Spin pair styles require metal units"); if (!atom->sp_flag) error->one(FLERR,"Spin pair styles requires atom/spin style"); } - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); + + // only global virial via fdotr is supported by this pair style + + if (vflag_atom) + error->all(FLERR,"Pair style rann does not support computing per-atom stress"); + if (vflag && !vflag_fdotr) + error->all(FLERR,"Pair style rann does not support 'pair_modify nofdotr'"); + int ii,i,j; int nn = 0; sims = new Simulation[1]; @@ -724,13 +805,11 @@ void PairRANN::compute(int eflag, int vflag) sims->s = atom->sp; } int itype,f,jnum,len; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; if (eflag_global) {eng_vdwl=0;eng_coul=0;} double energy=0; double **force = atom->f; double **fm = atom->fm; - double **virial = vatom; + //loop over atoms for (ii=0;iiinum;ii++) { i = sims->ilist[ii]; @@ -800,12 +879,8 @@ void PairRANN::compute(int eflag, int vflag) sx[j]=sy[j]=sz[j]=0; } } - if (doscreen) { - screen(ii,0,jnum-1); - } - if (allscreen) { - screen_neighbor_list(&jnum); - } + if (doscreen) screening(ii,0,jnum-1); + if (allscreen) screen_neighbor_list(&jnum); //do fingerprints for atom type len = fingerprintperelement[itype]; for (j=0;jilist; @@ -1026,8 +1101,8 @@ void PairRANN::propagateforward(double * energy,double **force,double ** /*viria sum[j] = activation[itype][i]->activation_function(sum[j]); if (i==L-1) { energy[j] = sum[j]; - if (eflag_atom)eatom[i1]=sum[j]; - if (eflag_global) {eng_vdwl +=sum[j];} + if (eflag_atom) eatom[i1]=sum[j]; + if (eflag_global) eng_vdwl +=sum[j]; } //force propagation for (jj=0;jjilist; @@ -1103,8 +1178,8 @@ void PairRANN::propagateforwardspin(double * energy,double **force,double **fm,d sum[j] = activation[itype][i]->activation_function(sum[j]); if (i==L-1) { energy[j] = sum[j]; - if (eflag_atom)eatom[i1]=sum[j]; - if (eflag_global) {eng_vdwl +=sum[j];} + if (eflag_atom) eatom[i1]=sum[j]; + if (eflag_global) eng_vdwl +=sum[j]; } //force propagation for (jj=0;jjrequest(this,instance_me); @@ -1232,10 +1305,8 @@ RANN::Fingerprint *PairRANN::create_fingerprint(const char *style) else if (strcmp(style,"bondspin")==0) { return new RANN::Fingerprint_bondspin(this); } - char str[128]; - sprintf(str,"Unknown fingerprint style %s",style); - error->one(FLERR,str); - return NULL; + error->one(FLERR,"Unknown fingerprint style {}",style); + return nullptr; } @@ -1247,9 +1318,7 @@ RANN::Activation *PairRANN::create_activation(const char *style) else if (strcmp(style,"sigI")==0) { return new RANN::Activation_sigI(this); } - char str[128]; - sprintf(str,"Unknown activation style %s",style); - error->one(FLERR,str); - return NULL; + error->one(FLERR,"Unknown activation style {}",style); + return nullptr; } diff --git a/src/USER-RANN/pair_rann.h b/src/ML-RANN/pair_rann.h similarity index 96% rename from src/USER-RANN/pair_rann.h rename to src/ML-RANN/pair_rann.h index a89e0265b6..6c047775d4 100644 --- a/src/USER-RANN/pair_rann.h +++ b/src/ML-RANN/pair_rann.h @@ -136,6 +136,7 @@ namespace LAMMPS_NS { private: //new functions void allocate(const std::vector &);//called after reading element list, but before reading the rest of the potential + void deallocate(); void read_file(char *);//read potential file void read_atom_types(std::vector,char*,int); void read_fpe(std::vector,std::vector,char*,int);//fingerprints per element. Count total fingerprints defined for each 1st element in element combinations @@ -149,9 +150,9 @@ namespace LAMMPS_NS { void read_screening(std::vector,std::vector,char*,int); void read_mass(const std::vector &, const std::vector &,const char*,int); bool check_potential();//after finishing reading potential file - void propagateforward(double *,double **,double **,int,int);//called by compute to get force and energy - void propagateforwardspin(double *,double **,double **,double**,int,int);//called by compute to get force and energy - void screen(int,int,int); + void propagateforward(double *,double **,int,int);//called by compute to get force and energy + void propagateforwardspin(double *,double **,double**,int,int);//called by compute to get force and energy + void screening(int,int,int); void cull_neighbor_list(int *,int,int); void screen_neighbor_list(int *); }; diff --git a/src/USER-RANN/rann_activation.h b/src/ML-RANN/rann_activation.h similarity index 100% rename from src/USER-RANN/rann_activation.h rename to src/ML-RANN/rann_activation.h diff --git a/src/USER-RANN/rann_activation_linear.h b/src/ML-RANN/rann_activation_linear.h similarity index 100% rename from src/USER-RANN/rann_activation_linear.h rename to src/ML-RANN/rann_activation_linear.h diff --git a/src/USER-RANN/rann_activation_sig_i.h b/src/ML-RANN/rann_activation_sig_i.h similarity index 100% rename from src/USER-RANN/rann_activation_sig_i.h rename to src/ML-RANN/rann_activation_sig_i.h diff --git a/src/USER-RANN/rann_fingerprint.cpp b/src/ML-RANN/rann_fingerprint.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint.cpp rename to src/ML-RANN/rann_fingerprint.cpp diff --git a/src/USER-RANN/rann_fingerprint.h b/src/ML-RANN/rann_fingerprint.h similarity index 100% rename from src/USER-RANN/rann_fingerprint.h rename to src/ML-RANN/rann_fingerprint.h diff --git a/src/USER-RANN/rann_fingerprint_bond.cpp b/src/ML-RANN/rann_fingerprint_bond.cpp similarity index 97% rename from src/USER-RANN/rann_fingerprint_bond.cpp rename to src/ML-RANN/rann_fingerprint_bond.cpp index bf14828a7b..4b96a4f39d 100644 --- a/src/USER-RANN/rann_fingerprint_bond.cpp +++ b/src/ML-RANN/rann_fingerprint_bond.cpp @@ -40,35 +40,35 @@ Fingerprint_bond::Fingerprint_bond(PairRANN *_pair) : Fingerprint(_pair) dr = 0; re = 0; rc = 0; - alpha_k = new double [1]; + alpha_k = new double[1]; alpha_k[0] = -1; kmax = 0; mlength = 0; id = -1; style = "bond"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; _pair->allscreen = false; } Fingerprint_bond::~Fingerprint_bond() { - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; + delete[] alpha_k; + delete[] atomtypes; + delete[] expcuttable; + delete[] dfctable; for (int i=0;i<(mlength*(mlength+1))>>1;i++) { - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; + delete[] coeff[i]; + delete[] coeffx[i]; + delete[] coeffy[i]; + delete[] coeffz[i]; + delete[] Mf[i]; } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; + delete[] coeff; + delete[] coeffx; + delete[] coeffy; + delete[] coeffz; + delete[] Mf; + delete[] rinvsqrttable; } bool Fingerprint_bond::parse_values(std::string constant,std::vector line1) { @@ -81,8 +81,8 @@ bool Fingerprint_bond::parse_values(std::string constant,std::vectorres; double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(kmax)]; - dfctable = new double [res+buf]; + expcuttable = new double[(res+buf)*(kmax)]; + dfctable = new double[res+buf]; for (m=0;m<(res+buf);m++) { r1 = cutmax*cutmax*(double)(m)/(double)(res); for (n=0;n<(kmax);n++) { @@ -282,6 +283,7 @@ void Fingerprint_bond::generate_coefficients() { //calculates multinomial c coeff[p1][p] = pair->factorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); } } + delete[] M; } diff --git a/src/USER-RANN/rann_fingerprint_bond.h b/src/ML-RANN/rann_fingerprint_bond.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bond.h rename to src/ML-RANN/rann_fingerprint_bond.h diff --git a/src/USER-RANN/rann_fingerprint_bondscreened.cpp b/src/ML-RANN/rann_fingerprint_bondscreened.cpp similarity index 97% rename from src/USER-RANN/rann_fingerprint_bondscreened.cpp rename to src/ML-RANN/rann_fingerprint_bondscreened.cpp index 59fed322a3..2ed63a3655 100644 --- a/src/USER-RANN/rann_fingerprint_bondscreened.cpp +++ b/src/ML-RANN/rann_fingerprint_bondscreened.cpp @@ -39,36 +39,36 @@ Fingerprint_bondscreened::Fingerprint_bondscreened(PairRANN *_pair) : Fingerprin dr = 0; re = 0; rc = 0; - alpha_k = new double [1]; + alpha_k = new double[1]; alpha_k[0] = -1; kmax = 0; mlength = 0; id = -1; style = "bondscreened"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; _pair->doscreen = true; screen = true; } Fingerprint_bondscreened::~Fingerprint_bondscreened() { - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; + delete[] alpha_k; + delete[] atomtypes; + delete[] expcuttable; + delete[] dfctable; for (int i=0;i<(mlength*(mlength+1))>>1;i++) { - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; + delete[] coeff[i]; + delete[] coeffx[i]; + delete[] coeffy[i]; + delete[] coeffz[i]; + delete[] Mf[i]; } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; + delete[] coeff; + delete[] coeffx; + delete[] coeffy; + delete[] coeffz; + delete[] Mf; + delete[] rinvsqrttable; } bool Fingerprint_bondscreened::parse_values(std::string constant,std::vector line1) { @@ -81,8 +81,8 @@ bool Fingerprint_bondscreened::parse_values(std::string constant,std::vectorres; double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(kmax)]; - dfctable = new double [res+buf]; + expcuttable = new double[(res+buf)*(kmax)]; + dfctable = new double[res+buf]; for (m=0;m<(res+buf);m++) { r1 = cutmax*cutmax*(double)(m)/(double)(res); for (n=0;n<(kmax);n++) { @@ -283,6 +284,7 @@ void Fingerprint_bondscreened::generate_coefficients() { //calculates multi coeff[p1][p] = pair->factorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); } } + delete[] M; } diff --git a/src/USER-RANN/rann_fingerprint_bondscreened.h b/src/ML-RANN/rann_fingerprint_bondscreened.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondscreened.h rename to src/ML-RANN/rann_fingerprint_bondscreened.h diff --git a/src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp b/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp similarity index 97% rename from src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp rename to src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp index 0728b6a295..49829b41a1 100644 --- a/src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp +++ b/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp @@ -39,13 +39,13 @@ Fingerprint_bondscreenedspin::Fingerprint_bondscreenedspin(PairRANN *_pair) : Fi dr = 0; re = 0; rc = 0; - alpha_k = new double [1]; + alpha_k = new double[1]; alpha_k[0] = -1; kmax = 0; mlength = 0; id = -1; style = "bondscreenedspin"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; _pair->doscreen = true; screen = true; @@ -54,23 +54,23 @@ Fingerprint_bondscreenedspin::Fingerprint_bondscreenedspin(PairRANN *_pair) : Fi } Fingerprint_bondscreenedspin::~Fingerprint_bondscreenedspin() { - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; + delete[] alpha_k; + delete[] atomtypes; + delete[] expcuttable; + delete[] dfctable; for (int i=0;i<(mlength*(mlength+1))>>1;i++) { - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; + delete[] coeff[i]; + delete[] coeffx[i]; + delete[] coeffy[i]; + delete[] coeffz[i]; + delete[] Mf[i]; } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; + delete[] coeff; + delete[] coeffx; + delete[] coeffy; + delete[] coeffz; + delete[] Mf; + delete[] rinvsqrttable; } bool Fingerprint_bondscreenedspin::parse_values(std::string constant,std::vector line1) { @@ -83,8 +83,8 @@ bool Fingerprint_bondscreenedspin::parse_values(std::string constant,std::vector rc = strtod(line1[0].c_str(),NULL); } else if (constant.compare("alphak")==0) { - delete [] alpha_k; - alpha_k = new double [nwords]; + delete[] alpha_k; + alpha_k = new double[nwords]; for (l=0;lres; double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(kmax)]; - dfctable = new double [res+buf]; + expcuttable = new double[(res+buf)*(kmax)]; + dfctable = new double[res+buf]; for (m=0;m<(res+buf);m++) { r1 = cutmax*cutmax*(double)(m)/(double)(res); for (n=0;n<(kmax);n++) { @@ -285,6 +286,7 @@ void Fingerprint_bondscreenedspin::generate_coefficients() { //calculates m coeff[p1][p] = pair->factorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); } } + delete[] M; } diff --git a/src/USER-RANN/rann_fingerprint_bondscreenedspin.h b/src/ML-RANN/rann_fingerprint_bondscreenedspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondscreenedspin.h rename to src/ML-RANN/rann_fingerprint_bondscreenedspin.h diff --git a/src/USER-RANN/rann_fingerprint_bondspin.cpp b/src/ML-RANN/rann_fingerprint_bondspin.cpp similarity index 98% rename from src/USER-RANN/rann_fingerprint_bondspin.cpp rename to src/ML-RANN/rann_fingerprint_bondspin.cpp index 1005818217..452846cfb1 100644 --- a/src/USER-RANN/rann_fingerprint_bondspin.cpp +++ b/src/ML-RANN/rann_fingerprint_bondspin.cpp @@ -39,13 +39,13 @@ Fingerprint_bondspin::Fingerprint_bondspin(PairRANN *_pair) : Fingerprint(_pair) dr = 0; re = 0; rc = 0; - alpha_k = new double [1]; + alpha_k = new double[1]; alpha_k[0] = -1; kmax = 0; mlength = 0; id = -1; style = "bondspin"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; _pair->allscreen = false; _pair->dospin = true; @@ -53,23 +53,23 @@ Fingerprint_bondspin::Fingerprint_bondspin(PairRANN *_pair) : Fingerprint(_pair) } Fingerprint_bondspin::~Fingerprint_bondspin() { - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; + delete[] alpha_k; + delete[] atomtypes; + delete[] expcuttable; + delete[] dfctable; for (int i=0;i<(mlength*(mlength+1))>>1;i++) { - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; + delete[] coeff[i]; + delete[] coeffx[i]; + delete[] coeffy[i]; + delete[] coeffz[i]; + delete[] Mf[i]; } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; + delete[] coeff; + delete[] coeffx; + delete[] coeffy; + delete[] coeffz; + delete[] Mf; + delete[] rinvsqrttable; } bool Fingerprint_bondspin::parse_values(std::string constant,std::vector line1) { @@ -82,8 +82,8 @@ bool Fingerprint_bondspin::parse_values(std::string constant,std::vectorres; double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(kmax)]; - dfctable = new double [res+buf]; + expcuttable = new double[(res+buf)*(kmax)]; + dfctable = new double[res+buf]; for (m=0;m<(res+buf);m++) { r1 = cutmax*cutmax*(double)(m)/(double)(res); for (n=0;n<(kmax);n++) { @@ -283,6 +284,7 @@ void Fingerprint_bondspin::generate_coefficients() { //calculates multinomi coeff[p1][p] = pair->factorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); } } + delete[] M; } diff --git a/src/USER-RANN/rann_fingerprint_bondspin.h b/src/ML-RANN/rann_fingerprint_bondspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondspin.h rename to src/ML-RANN/rann_fingerprint_bondspin.h diff --git a/src/USER-RANN/rann_fingerprint_radial.cpp b/src/ML-RANN/rann_fingerprint_radial.cpp similarity index 96% rename from src/USER-RANN/rann_fingerprint_radial.cpp rename to src/ML-RANN/rann_fingerprint_radial.cpp index f468ee2f6c..93cab2f363 100644 --- a/src/USER-RANN/rann_fingerprint_radial.cpp +++ b/src/ML-RANN/rann_fingerprint_radial.cpp @@ -41,13 +41,13 @@ Fingerprint_radial::Fingerprint_radial(PairRANN *_pair) : Fingerprint(_pair) dr = 0; re = 0; rc = 0; - alpha = new double [1]; + alpha = new double[1]; alpha[0] = -1; nmax = 0; omin = 0; id = -1; style = "radial"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; fullydefined = false; _pair->allscreen = false; @@ -55,11 +55,11 @@ Fingerprint_radial::Fingerprint_radial(PairRANN *_pair) : Fingerprint(_pair) Fingerprint_radial::~Fingerprint_radial() { - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; + delete[] atomtypes; + delete[] radialtable; + delete[] alpha; + delete[] dfctable; + delete[] rinvsqrttable; } bool Fingerprint_radial::parse_values(std::string constant,std::vector line1) { @@ -72,8 +72,8 @@ bool Fingerprint_radial::parse_values(std::string constant,std::vectorres; double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; + radialtable = new double[(res+buf)*get_length()]; + dfctable = new double[res+buf]; for (k=0;k<(res+buf);k++) { r1 = cutmax*cutmax*(double)(k)/(double)(res); for (m=0;m<=(nmax-omin);m++) { diff --git a/src/USER-RANN/rann_fingerprint_radial.h b/src/ML-RANN/rann_fingerprint_radial.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radial.h rename to src/ML-RANN/rann_fingerprint_radial.h diff --git a/src/USER-RANN/rann_fingerprint_radialscreened.cpp b/src/ML-RANN/rann_fingerprint_radialscreened.cpp similarity index 96% rename from src/USER-RANN/rann_fingerprint_radialscreened.cpp rename to src/ML-RANN/rann_fingerprint_radialscreened.cpp index 126b83fc51..a933703db8 100644 --- a/src/USER-RANN/rann_fingerprint_radialscreened.cpp +++ b/src/ML-RANN/rann_fingerprint_radialscreened.cpp @@ -41,13 +41,13 @@ Fingerprint_radialscreened::Fingerprint_radialscreened(PairRANN *_pair) : Finger dr = 0; re = 0; rc = 0; - alpha = new double [1]; + alpha = new double[1]; alpha[0] = -1; nmax = 0; omin = 0; id = -1; style = "radialscreened"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; fullydefined = false; _pair->doscreen = true; @@ -56,11 +56,11 @@ Fingerprint_radialscreened::Fingerprint_radialscreened(PairRANN *_pair) : Finger Fingerprint_radialscreened::~Fingerprint_radialscreened() { - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; + delete[] atomtypes; + delete[] radialtable; + delete[] alpha; + delete[] dfctable; + delete[] rinvsqrttable; } bool Fingerprint_radialscreened::parse_values(std::string constant,std::vector line1) { @@ -73,8 +73,8 @@ bool Fingerprint_radialscreened::parse_values(std::string constant,std::vectorres; double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; + radialtable = new double[(res+buf)*get_length()]; + dfctable = new double[res+buf]; for (k=0;k<(res+buf);k++) { r1 = cutmax*cutmax*(double)(k)/(double)(res); for (m=0;m<=(nmax-omin);m++) { diff --git a/src/USER-RANN/rann_fingerprint_radialscreened.h b/src/ML-RANN/rann_fingerprint_radialscreened.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialscreened.h rename to src/ML-RANN/rann_fingerprint_radialscreened.h diff --git a/src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp b/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp similarity index 96% rename from src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp rename to src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp index 11674190fb..ecd0e4a2f0 100644 --- a/src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp +++ b/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp @@ -40,13 +40,13 @@ Fingerprint_radialscreenedspin::Fingerprint_radialscreenedspin(PairRANN *_pair) dr = 0; re = 0; rc = 0; - alpha = new double [1]; + alpha = new double[1]; alpha[0] = -1; nmax = 0; omin = 0; id = -1; style = "radialscreenedspin"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; fullydefined = false; _pair->doscreen = true; @@ -57,11 +57,11 @@ Fingerprint_radialscreenedspin::Fingerprint_radialscreenedspin(PairRANN *_pair) Fingerprint_radialscreenedspin::~Fingerprint_radialscreenedspin() { - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; + delete[] atomtypes; + delete[] radialtable; + delete[] alpha; + delete[] dfctable; + delete[] rinvsqrttable; } bool Fingerprint_radialscreenedspin::parse_values(std::string constant,std::vector line1) { @@ -74,8 +74,8 @@ bool Fingerprint_radialscreenedspin::parse_values(std::string constant,std::vect rc = strtod(line1[0].c_str(),NULL); } else if (constant.compare("alpha")==0) { - delete [] alpha; - alpha = new double [nwords]; + delete[] alpha; + alpha = new double[nwords]; for (l=0;lres; double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; + radialtable = new double[(res+buf)*get_length()]; + dfctable = new double[res+buf]; for (k=0;k<(res+buf);k++) { r1 = cutmax*cutmax*(double)(k)/(double)(res); for (m=0;m<=(nmax-omin);m++) { diff --git a/src/USER-RANN/rann_fingerprint_radialscreenedspin.h b/src/ML-RANN/rann_fingerprint_radialscreenedspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialscreenedspin.h rename to src/ML-RANN/rann_fingerprint_radialscreenedspin.h diff --git a/src/USER-RANN/rann_fingerprint_radialspin.cpp b/src/ML-RANN/rann_fingerprint_radialspin.cpp similarity index 96% rename from src/USER-RANN/rann_fingerprint_radialspin.cpp rename to src/ML-RANN/rann_fingerprint_radialspin.cpp index 2d0a2f68f1..137f7ac162 100644 --- a/src/USER-RANN/rann_fingerprint_radialspin.cpp +++ b/src/ML-RANN/rann_fingerprint_radialspin.cpp @@ -40,13 +40,13 @@ Fingerprint_radialspin::Fingerprint_radialspin(PairRANN *_pair) : Fingerprint(_p dr = 0; re = 0; rc = 0; - alpha = new double [1]; + alpha = new double[1]; alpha[0] = -1; nmax = 0; omin = 0; id = -1; style = "radialspin"; - atomtypes = new int [n_body_type]; + atomtypes = new int[n_body_type]; empty = true; fullydefined = false; _pair->allscreen = false; @@ -56,11 +56,11 @@ Fingerprint_radialspin::Fingerprint_radialspin(PairRANN *_pair) : Fingerprint(_p Fingerprint_radialspin::~Fingerprint_radialspin() { - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; + delete[] atomtypes; + delete[] radialtable; + delete[] alpha; + delete[] dfctable; + delete[] rinvsqrttable; } bool Fingerprint_radialspin::parse_values(std::string constant,std::vector line1) { @@ -73,8 +73,8 @@ bool Fingerprint_radialspin::parse_values(std::string constant,std::vectorres; double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; + radialtable = new double[(res+buf)*get_length()]; + dfctable = new double[res+buf]; for (k=0;k<(res+buf);k++) { r1 = cutmax*cutmax*(double)(k)/(double)(res); for (m=0;m<=(nmax-omin);m++) { diff --git a/src/USER-RANN/rann_fingerprint_radialspin.h b/src/ML-RANN/rann_fingerprint_radialspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialspin.h rename to src/ML-RANN/rann_fingerprint_radialspin.h diff --git a/src/SNAP/compute_sna_atom.cpp b/src/ML-SNAP/compute_sna_atom.cpp similarity index 100% rename from src/SNAP/compute_sna_atom.cpp rename to src/ML-SNAP/compute_sna_atom.cpp diff --git a/src/SNAP/compute_sna_atom.h b/src/ML-SNAP/compute_sna_atom.h similarity index 100% rename from src/SNAP/compute_sna_atom.h rename to src/ML-SNAP/compute_sna_atom.h diff --git a/src/SNAP/compute_snad_atom.cpp b/src/ML-SNAP/compute_snad_atom.cpp similarity index 100% rename from src/SNAP/compute_snad_atom.cpp rename to src/ML-SNAP/compute_snad_atom.cpp diff --git a/src/SNAP/compute_snad_atom.h b/src/ML-SNAP/compute_snad_atom.h similarity index 100% rename from src/SNAP/compute_snad_atom.h rename to src/ML-SNAP/compute_snad_atom.h diff --git a/src/SNAP/compute_snap.cpp b/src/ML-SNAP/compute_snap.cpp similarity index 100% rename from src/SNAP/compute_snap.cpp rename to src/ML-SNAP/compute_snap.cpp diff --git a/src/SNAP/compute_snap.h b/src/ML-SNAP/compute_snap.h similarity index 100% rename from src/SNAP/compute_snap.h rename to src/ML-SNAP/compute_snap.h diff --git a/src/SNAP/compute_snav_atom.cpp b/src/ML-SNAP/compute_snav_atom.cpp similarity index 100% rename from src/SNAP/compute_snav_atom.cpp rename to src/ML-SNAP/compute_snav_atom.cpp diff --git a/src/SNAP/compute_snav_atom.h b/src/ML-SNAP/compute_snav_atom.h similarity index 100% rename from src/SNAP/compute_snav_atom.h rename to src/ML-SNAP/compute_snav_atom.h diff --git a/src/SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp similarity index 96% rename from src/SNAP/pair_snap.cpp rename to src/ML-SNAP/pair_snap.cpp index b8d8333902..dd023e096c 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -70,6 +70,7 @@ PairSNAP::~PairSNAP() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); + memory->destroy(scale); } } @@ -164,6 +165,7 @@ void PairSNAP::compute(int eflag, int vflag) // for neighbors of I within cutoff: // compute Fij = dEi/dRj = -dEi/dRi // add to Fi, subtract from Fj + // scaling is that for type I snaptr->compute_yi(beta[ii]); @@ -178,12 +180,12 @@ void PairSNAP::compute(int eflag, int vflag) snaptr->compute_deidrj(fij); - f[i][0] += fij[0]; - f[i][1] += fij[1]; - f[i][2] += fij[2]; - f[j][0] -= fij[0]; - f[j][1] -= fij[1]; - f[j][2] -= fij[2]; + f[i][0] += fij[0]*scale[itype][itype]; + f[i][1] += fij[1]*scale[itype][itype]; + f[i][2] += fij[2]*scale[itype][itype]; + f[j][0] -= fij[0]*scale[itype][itype]; + f[j][1] -= fij[1]*scale[itype][itype]; + f[j][2] -= fij[2]*scale[itype][itype]; // tally per-atom virial contribution @@ -224,6 +226,7 @@ void PairSNAP::compute(int eflag, int vflag) } } } + evdwl *= scale[itype][itype]; ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0); } @@ -351,9 +354,9 @@ void PairSNAP::allocate() { allocated = 1; int n = atom->ntypes; - memory->create(setflag,n+1,n+1,"pair:setflag"); memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(scale,n+1,n+1,"pair:scale"); map = new int[n+1]; } @@ -408,11 +411,16 @@ void PairSNAP::coeff(int narg, char **arg) } // Calculate maximum cutoff for all elements - rcutmax = 0.0; for (int ielem = 0; ielem < nelements; ielem++) rcutmax = MAX(2.0*radelem[ielem]*rcutfac,rcutmax); + // set default scaling + int n = atom->ntypes; + for (int ii = 0; ii < n+1; ii++) + for (int jj = 0; jj < n+1; jj++) + scale[ii][jj] = 1.0; + } /* ---------------------------------------------------------------------- @@ -441,6 +449,7 @@ void PairSNAP::init_style() double PairSNAP::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + scale[j][i] = scale[i][j]; return (radelem[map[i]] + radelem[map[j]])*rcutfac; } @@ -711,6 +720,7 @@ double PairSNAP::memory_usage() int n = atom->ntypes+1; bytes += (double)n*n*sizeof(int); // setflag bytes += (double)n*n*sizeof(double); // cutsq + bytes += (double)n*n*sizeof(double); // scale bytes += (double)n*sizeof(int); // map bytes += (double)beta_max*ncoeff*sizeof(double); // bispectrum bytes += (double)beta_max*ncoeff*sizeof(double); // beta @@ -720,3 +730,9 @@ double PairSNAP::memory_usage() return bytes; } +void *PairSNAP::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return nullptr; +} diff --git a/src/SNAP/pair_snap.h b/src/ML-SNAP/pair_snap.h similarity index 97% rename from src/SNAP/pair_snap.h rename to src/ML-SNAP/pair_snap.h index 0cc38ef9cb..afce4bf895 100644 --- a/src/SNAP/pair_snap.h +++ b/src/ML-SNAP/pair_snap.h @@ -34,6 +34,7 @@ class PairSNAP : public Pair { virtual void init_style(); virtual double init_one(int, int); virtual double memory_usage(); + virtual void *extract(const char *, int &); double rcutfac, quadraticflag; // declared public to workaround gcc 4.9 int ncoeff; // compiler bug, manifest in KOKKOS package @@ -55,6 +56,7 @@ class PairSNAP : public Pair { double **coeffelem; // element bispectrum coefficients double **beta; // betas for all atoms in list double **bispectrum; // bispectrum components for all atoms in list + double **scale; // for thermodynamic integration int twojmax, switchflag, bzeroflag, bnormflag; int chemflag, wselfallflag; int chunksize; diff --git a/src/SNAP/sna.cpp b/src/ML-SNAP/sna.cpp similarity index 100% rename from src/SNAP/sna.cpp rename to src/ML-SNAP/sna.cpp diff --git a/src/SNAP/sna.h b/src/ML-SNAP/sna.h similarity index 100% rename from src/SNAP/sna.h rename to src/ML-SNAP/sna.h diff --git a/src/MLIAP/README.md b/src/MLIAP/README.md deleted file mode 100644 index b5cdc337f5..0000000000 --- a/src/MLIAP/README.md +++ /dev/null @@ -1,41 +0,0 @@ -This package provides a general interface to families of machine-learning interatomic potentials (MLIAPs). -This interface consists of a `mliap pair style` and a `mliap compute`. -The `mliap pair style` is used when running simulations with energies and -forces calculated by an MLIAP. The interface allows separate -definitions of the interatomic potential functional form (`model`) -and the geometric quantities that characterize the atomic positions -(`descriptor`). By defining `model` and `descriptor` separately, -it is possible to use many different models with a given descriptor, -or many different descriptors with a given model. The pair_style -supports the following models: - -- `linear`, -- `quadratic`, -- `nn` (neural networks) -- `mliappy` (general Python interface to things like PyTorch). - -It currently supports only one class of descriptors, `sna`, the SNAP descriptors. -It is straightforward to add new descriptor and model styles. - -The `mliap compute` style provides gradients of the energy, force, -and stress tensor w.r.t. model parameters. -These are useful when training MLIAPs to match target data. -Any `model` or `descriptor` that has been implemented for the -`mliap` pair style can also be accessed by the `mliap` compute. -In addition to the energy, force, and stress gradients, w.r.t. -each `model` parameter, the compute also calculates the energy, -force, and stress contributions from a user-specified -reference potential. - -## Generating the model files from the third-party packages -- To train the `linear` and `quadratic` models with the SNAP descriptors, see the examples in [FitSNAP](https://github.com/FitSNAP/FitSNAP). -- To train the `nn` model with the SNAP descriptors, check the examples in [PyXtal\_FF](https://github.com/qzhu2017/PyXtal_FF). - -## Building MLIAP with Python support - -The `mliappy` energy model requires that the MLIAP package be compiled with Python support enabled. This extension, written by Nick Lubbers (LANL), provides a coupling to PyTorch and other Python modules. This should be automatically enabled by default if the prerequisite software is installed. It can be enforced during CMake configuration by setting the variable `MLIAP_ENABLE_PYTHON=yes` or for conventional build by adding `-DMLIAP_PYTHON` to the `LMP_INC` variable in your makefile and running the cythonize script on the .pyx file(s) copied to the src folder. - -This requires to also install the PYTHON package and have the [cython](https://cython.org) software installed. During configuration/compilation -the cythonize script will be used to convert the provided .pyx file(s) to C++ code. Please do not run the cythonize script in the src/MLIAP folder. If you have done so by accident, you need to delete the generated .cpp and .h file(s) in the src/MLIAP folder or there may be problems during compilation. - -More information on building LAMMPS with this package is [here](https://docs.lammps.org/Build_extras.html#mliap). diff --git a/src/USER-MOFFF/README b/src/MOFFF/README similarity index 98% rename from src/USER-MOFFF/README rename to src/MOFFF/README index 237ac9ba53..fa3cb0ef87 100644 --- a/src/USER-MOFFF/README +++ b/src/MOFFF/README @@ -25,7 +25,7 @@ See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2", commands to get started. Also see the above mentioned website and literature for further documentation about the force field. -There are example scripts for using this force field in examples/USER/mofff. +There are example scripts for using this force field in examples/PACKAGES/mofff. The creators of this package are Hendrik Heenen (hendrik.heenen at mytum.de) and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/MOFFF/angle_class2_p6.cpp similarity index 100% rename from src/USER-MOFFF/angle_class2_p6.cpp rename to src/MOFFF/angle_class2_p6.cpp diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/MOFFF/angle_class2_p6.h similarity index 100% rename from src/USER-MOFFF/angle_class2_p6.h rename to src/MOFFF/angle_class2_p6.h diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/MOFFF/angle_cosine_buck6d.cpp similarity index 100% rename from src/USER-MOFFF/angle_cosine_buck6d.cpp rename to src/MOFFF/angle_cosine_buck6d.cpp diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/MOFFF/angle_cosine_buck6d.h similarity index 100% rename from src/USER-MOFFF/angle_cosine_buck6d.h rename to src/MOFFF/angle_cosine_buck6d.h diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/MOFFF/improper_inversion_harmonic.cpp similarity index 100% rename from src/USER-MOFFF/improper_inversion_harmonic.cpp rename to src/MOFFF/improper_inversion_harmonic.cpp diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/MOFFF/improper_inversion_harmonic.h similarity index 100% rename from src/USER-MOFFF/improper_inversion_harmonic.h rename to src/MOFFF/improper_inversion_harmonic.h diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp rename to src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h b/src/MOFFF/pair_buck6d_coul_gauss_dsf.h similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h rename to src/MOFFF/pair_buck6d_coul_gauss_dsf.h diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp rename to src/MOFFF/pair_buck6d_coul_gauss_long.cpp diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.h b/src/MOFFF/pair_buck6d_coul_gauss_long.h similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_long.h rename to src/MOFFF/pair_buck6d_coul_gauss_long.h diff --git a/src/USER-MISC/dihedral_table.cpp b/src/MOLECULE/dihedral_table.cpp similarity index 100% rename from src/USER-MISC/dihedral_table.cpp rename to src/MOLECULE/dihedral_table.cpp diff --git a/src/USER-MISC/dihedral_table.h b/src/MOLECULE/dihedral_table.h similarity index 100% rename from src/USER-MISC/dihedral_table.h rename to src/MOLECULE/dihedral_table.h diff --git a/src/USER-MOLFILE/Install.sh b/src/MOLFILE/Install.sh similarity index 100% rename from src/USER-MOLFILE/Install.sh rename to src/MOLFILE/Install.sh diff --git a/src/USER-MOLFILE/README b/src/MOLFILE/README similarity index 100% rename from src/USER-MOLFILE/README rename to src/MOLFILE/README diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/MOLFILE/dump_molfile.cpp similarity index 100% rename from src/USER-MOLFILE/dump_molfile.cpp rename to src/MOLFILE/dump_molfile.cpp diff --git a/src/USER-MOLFILE/dump_molfile.h b/src/MOLFILE/dump_molfile.h similarity index 100% rename from src/USER-MOLFILE/dump_molfile.h rename to src/MOLFILE/dump_molfile.h diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/MOLFILE/molfile_interface.cpp similarity index 100% rename from src/USER-MOLFILE/molfile_interface.cpp rename to src/MOLFILE/molfile_interface.cpp diff --git a/src/USER-MOLFILE/molfile_interface.h b/src/MOLFILE/molfile_interface.h similarity index 100% rename from src/USER-MOLFILE/molfile_interface.h rename to src/MOLFILE/molfile_interface.h diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/MOLFILE/reader_molfile.cpp similarity index 100% rename from src/USER-MOLFILE/reader_molfile.cpp rename to src/MOLFILE/reader_molfile.cpp diff --git a/src/USER-MOLFILE/reader_molfile.h b/src/MOLFILE/reader_molfile.h similarity index 100% rename from src/USER-MOLFILE/reader_molfile.h rename to src/MOLFILE/reader_molfile.h diff --git a/src/MSCG/README b/src/MSCG/README index ab64c26792..3008fbbd22 100644 --- a/src/MSCG/README +++ b/src/MSCG/README @@ -1,4 +1,4 @@ -The USER-MSCG package adds a fix mscg command, which carries out +The MSCG package adds a fix mscg command, which carries out multi-scale coarse-graining for the parameterization of coarse-grained (CG) interactions. diff --git a/src/Makefile b/src/Makefile index 5e7a3c000f..f7ec0a06f4 100644 --- a/src/Makefile +++ b/src/Makefile @@ -37,8 +37,9 @@ endif # Package variables -# PACKAGE = standard packages -# PACKUSER = user packagse +# PACKAGE = all packages +# PACKBASIC = a few core packages +# PACKMOST = most packages that do not require additional libs # PACKLIB = all packages that require an additional lib # should be PACKSYS + PACKINT + PACKEXT # PACKSYS = subset that reqiure a common system library @@ -46,35 +47,212 @@ endif # PACKINT = subset that require an internal (provided) library # PACKEXT = subset that require an external (downloaded) library -PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc message misc \ - mliap molecule mpiio mscg opt peri plugin poems \ - python qeq replica rigid shock snap spin srd voronoi +PACKAGE = \ + adios \ + asphere \ + awpmd \ + bocs \ + body \ + brownian \ + cg-dna \ + cg-sdk \ + class2 \ + colloid \ + colvars \ + compress \ + coreshell \ + diffraction \ + dipole \ + dpd-basic \ + dpd-meso \ + dpd-react \ + dpd-smooth \ + drude \ + eff \ + extra-compute \ + extra-dump \ + extra-fix \ + extra-molecule \ + extra-pair \ + fep \ + gpu \ + granular \ + h5md \ + intel \ + interlayer \ + kim \ + kokkos \ + kspace \ + latboltz \ + latte \ + machdyn \ + manifold \ + manybody \ + mc \ + mdi \ + meam \ + mesont \ + message \ + mgpt \ + misc \ + ml-hdnnp \ + ml-pace \ + ml-quip \ + ml-rann \ + ml-snap \ + mofff \ + molecule \ + molfile \ + mpiio \ + mscg \ + netcdf \ + openmp \ + opt \ + orient \ + peri \ + plugin \ + plumed \ + poems \ + ptm \ + python \ + qeq \ + qmmm \ + qtb \ + reaction \ + reaxff \ + replica \ + rigid \ + scafacos \ + shock \ + smtbq \ + sph \ + spin \ + srd \ + tally \ + uef \ + voronoi \ + vtk \ + yaff \ + atc \ + dielectric \ + ml-iap \ + phonon -PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \ - user-cgsdk user-colvars user-dielectric user-diffraction user-dpd user-drude \ - user-eff user-fep user-h5md user-hdnnp user-intel user-lb user-manifold \ - user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \ - user-mofff user-molfile user-netcdf user-omp user-phonon \ - user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \ - user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ - user-sdpd user-sph user-tally user-uef user-vtk user-yaff +# NOTE: the last four packages must remain at the end since +# they depend on other packages to be installed first. -PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-hdnnp user-lb user-mdi \ - user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \ - user-scafacos user-smd user-vtk +PACKBASIC = kspace manybody molecule rigid -PACKSYS = compress mpiio python user-lb +PACKMOST = \ + asphere \ + bocs \ + body \ + brownian \ + cg-dna \ + cg-sdk \ + class2 \ + colloid \ + coreshell \ + diffraction \ + dipole \ + dpd-basic \ + dpd-meso \ + dpd-react \ + dpd-smooth \ + drude \ + eff \ + extra-compute \ + extra-dump \ + extra-fix \ + extra-molecule \ + extra-pair \ + fep \ + granular \ + interlayer \ + kspace \ + manybody \ + mc \ + meam \ + misc \ + ml-snap \ + mofff \ + molecule \ + openmp \ + opt \ + orient \ + peri \ + plugin \ + poems \ + qeq \ + reaction \ + reaxff \ + replica \ + rigid \ + shock \ + sph \ + spin \ + srd \ + uef \ + yaff \ + dielectric \ + ml-iap \ + phonon -PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont \ - user-mdi +# NOTE ^^^^^: the last three packages must remain at the end since +# they depend on other packages to be installed first. -PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-hdnnp user-molfile user-netcdf user-pace user-plumed \ - user-qmmm user-quip user-scafacos user-smd user-vtk +PACKLIB = \ + compress \ + gpu \ + kim \ + kokkos \ + latte \ + message \ + mpiio \ + mscg \ + poems \ + python \ + voronoi \ + adios \ + atc \ + awpmd \ + colvars \ + h5md \ + ml-hdnnp \ + latboltz \ + mdi \ + mesont \ + molfile \ + netcdf \ + ml-pace \ + plumed \ + qmmm \ + ml-quip \ + scafacos \ + machdyn \ + vtk -PACKALL = $(PACKAGE) $(PACKUSER) +PACKSYS = compress latboltz mpiio python + +PACKINT = atc awpmd colvars gpu kokkos mesont message poems + +PACKEXT = \ + adios \ + h5md \ + kim \ + latte \ + machdyn \ + ml-hdnnp \ + ml-pace \ + ml-quip \ + molfile \ + mscg \ + netcdf \ + plumed \ + qmmm \ + scafacos \ + voronoi \ + vtk \ # Helper GNU make function for conversion to upper case without using shell commands uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z @@ -87,7 +265,7 @@ PACKUSERUC = $(call uppercase,$(PACKUSER)) YESDIR = $(call uppercase,$(@:yes-%=%)) NODIR = $(call uppercase,$(@:no-%=%)) LIBDIR = $(@:lib-%=%) -LIBUSERDIR = $(@:lib-user-%=%) +LIBUSERDIR = $(@:lib-%=%) # List of all targets @@ -106,10 +284,10 @@ help: @echo 'make no-package remove a single pkg from src dir' @echo 'make yes-all install all pgks in src dir' @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' + @echo 'make yes-basic install a few commonly used pgks' + @echo 'make no-basic remove a few commonly used pkgs' + @echo 'make yes-most install most pgks w/o libs' + @echo 'make no-most remove most pgks w/o libs' @echo 'make yes-lib install all pkgs with libs (included or ext)' @echo 'make no-lib remove all pkgs with libs (included or ext)' @echo 'make yes-ext install all pkgs with external libs' @@ -314,14 +492,14 @@ package: @echo 'make package-installed (pi) list of installed packages' @echo 'make yes-package install a single pgk in src dir' @echo 'make no-package remove a single pkg from src dir' + @echo 'make yes-basic install a few commonly used pgks in src' + @echo 'make no-basic remove a few commonly used pkgs from src dir' + @echo 'make yes-most install most pgks w/o libs in src' + @echo 'make no-most remove most pkgs w/o libs from src dir' @echo 'make yes-all install all pgks in src dir' @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' - @echo 'make yes-lib install all pkgs with libs (included or ext)' - @echo 'make no-lib remove all pkgs with libs (included or ext)' + @echo 'make yes-lib install all pkgs with libs (included or ext)' + @echo 'make no-lib remove all pkgs with libs (included or ext)' @echo 'make yes-ext install all pkgs with external libs' @echo 'make no-ext remove all pkgs with external libs' @echo '' @@ -332,22 +510,34 @@ package: @echo 'make lib-package build and/or download a package library' yes-all: - @for p in $(PACKALL); do $(MAKE) yes-$$p; done - -no-all: - @for p in $(PACKALL); do $(MAKE) no-$$p; done - -yes-standard yes-std: @for p in $(PACKAGE); do $(MAKE) yes-$$p; done -no-standard no-std: +no-all: @for p in $(PACKAGE); do $(MAKE) no-$$p; done +yes-standard yes-std: + @echo 'There are no more "standard" or "user" packages in LAMMPS' + +no-standard no-std: + @echo 'There are no more "standard" or "user" packages in LAMMPS' + yes-user: - @for p in $(PACKUSER); do $(MAKE) yes-$$p; done + @echo 'There are no more "standard" or "user" packages in LAMMPS' no-user: - @for p in $(PACKUSER); do $(MAKE) no-$$p; done + @echo 'There are no more "standard" or "user" packages in LAMMPS' + +yes-basic: + @for p in $(PACKBASIC); do $(MAKE) yes-$$p; done + +no-basic: + @for p in $(PACKBASIC); do $(MAKE) no-$$p; done + +yes-most: + @for p in $(PACKMOST); do $(MAKE) yes-$$p; done + +no-most: + @for p in $(PACKMOST); do $(MAKE) no-$$p; done yes-lib: @for p in $(PACKLIB); do $(MAKE) yes-$$p; done @@ -400,7 +590,7 @@ lib-%: echo "Installing lib $(@:lib-%=%)"; \ ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \ elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \ - echo "Installing lib $(@:lib-user-%=%)"; \ + echo "Installing lib $(@:lib-%=%)"; \ ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \ else \ echo "Install script for lib $(@:lib-%=%) does not exist"; \ diff --git a/src/Makefile.txt b/src/Makefile.txt deleted file mode 100644 index 5542ed0cc5..0000000000 --- a/src/Makefile.txt +++ /dev/null @@ -1,443 +0,0 @@ -# LAMMPS multiple-machine -*- Makefile -*- - -SHELL = /bin/bash -PYTHON = python - -#.IGNORE: - -# Definitions - -ROOT = lmp -EXE = lmp_$@ -ARLIB = liblammps_$@.a -SHLIB = liblammps_$@.so -ARLINK = liblammps.a -SHLINK = liblammps.so -TMPNAME= tmp_$@_name -LMPLINK= -L. -llammps_$@ - -OBJDIR = Obj_$@ -OBJSHDIR = Obj_shared_$@ - -SRC = $(wildcard *.cpp) -INC = $(filter-out lmpinstalledpkgs.h lmpgitversion.h,$(wildcard *.h)) -OBJ = $(SRC:.cpp=.o) - -SRCLIB = $(filter-out main.cpp,$(SRC)) -OBJLIB = $(filter-out main.o,$(OBJ)) - -# Command-line options for mode: static (default), shared, or print - -mode = static -objdir = $(OBJDIR) - -ifeq ($(mode),shared) -objdir = $(OBJSHDIR) -endif - -# Package variables - -# PACKAGE = standard packages -# PACKUSER = user packagse -# PACKLIB = all packages that require an additional lib -# should be PACKSYS + PACKINT + PACKEXT -# PACKSYS = subset that reqiure a common system library -# include MPIIO and LB b/c require full MPI, not just STUBS -# PACKINT = subset that require an internal (provided) library -# PACKEXT = subset that require an external (downloaded) library - -PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc message misc \ - mliap molecule mpiio mscg opt peri plugin poems \ - python qeq replica rigid shock snap spin srd voronoi - -PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ - user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ - user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ - user-qtb user-quip user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ - user-sdpd user-sph user-tally user-uef user-vtk user-yaff - -PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ - python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-plumed user-qmmm user-quip user-scafacos \ - user-smd user-vtk user-mesont user-pace - -PACKSYS = compress mpiio python user-lb - -PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont - -PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ - user-qmmm user-quip user-smd user-vtk - -PACKALL = $(PACKAGE) $(PACKUSER) - -# Helper GNU make function for conversion to upper case without using shell commands -uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z -uppercase_internal=$(if $1,$$(subst $(firstword $1),$(call uppercase_internal,$(wordlist 2,$(words $1),$1),$2)),$2) -uppercase=$(eval uppercase_RESULT:=$(call uppercase_internal,$(uppercase_TABLE),$1))$(uppercase_RESULT) - -PACKAGEUC = $(call uppercase,$(PACKAGE)) -PACKUSERUC = $(call uppercase,$(PACKUSER)) - -YESDIR = $(call uppercase,$(@:yes-%=%)) -NODIR = $(call uppercase,$(@:no-%=%)) -LIBDIR = $(@:lib-%=%) -LIBUSERDIR = $(@:lib-user-%=%) - -# List of all targets - -help: - @echo '' - @echo 'make clean-all delete all object files' - @echo 'make clean-machine delete object files for one machine' - @echo 'make mpi-stubs build dummy MPI library in STUBS' - @echo 'make install-python install LAMMPS wrapper in Python' - @echo 'make tar create lmp_src.tar.gz for src dir and packages' - @echo '' - @echo 'make package list available packages and their dependencies' - @echo 'make package-status (ps) status of all packages' - @echo 'make package-installed (pi) list of installed packages' - @echo 'make yes-package install a single pgk in src dir' - @echo 'make no-package remove a single pkg from src dir' - @echo 'make yes-all install all pgks in src dir' - @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' - @echo 'make yes-lib install all pkgs with libs (included or ext)' - @echo 'make no-lib remove all pkgs with libs (included or ext)' - @echo 'make yes-ext install all pkgs with external libs' - @echo 'make no-ext remove all pkgs with external libs' - @echo '' - @echo 'make package-update (pu) replace src files with updated package files' - @echo 'make package-overwrite replace package files with src files' - @echo 'make package-diff (pd) diff src files against package files' - @echo '' - @echo 'make lib-package help for download/build/install a package library' - @echo 'make lib-package args="..." download/build/install a package library' - @echo 'make purge purge obsolete copies of source files' - @echo '' - @echo 'make machine build LAMMPS for machine with static library' - @echo 'make mode=static machine same as above' - @echo 'make mode=shared machine build LAMMPS for machine with shared library' - @echo 'make mode=print machine print compiler/linker flags' - @echo '' - @echo 'machine is one of these from src/MAKE:' - @echo '' - @files="`ls MAKE/Makefile.*`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - @echo '... or one of these from src/MAKE/OPTIONS:' - @echo '' - @files="`ls MAKE/OPTIONS/Makefile.*`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - @echo '... or one of these from src/MAKE/MACHINES:' - @echo '' - @files="`ls MAKE/MACHINES/Makefile.*`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - @echo '... or one of these from src/MAKE/MINE:' - @echo '' - @files="`ls MAKE/MINE/Makefile.* 2>/dev/null`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - - -lmpinstalledpkgs.h: $(SRC) $(INC) - @echo '#ifndef LMP_INSTALLED_PKGS_H' > ${TMPNAME}.lmpinstalled - @echo '#define LMP_INSTALLED_PKGS_H' >> ${TMPNAME}.lmpinstalled - @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> ${TMPNAME}.lmpinstalled - @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ - [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> ${TMPNAME}.lmpinstalled || :; done - @echo ' NULL };' >> ${TMPNAME}.lmpinstalled - @echo '#endif' >> ${TMPNAME}.lmpinstalled - @if [ -f lmpinstalledpkgs.h ]; \ - then test "`diff --brief ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h`" != "" && \ - mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h || rm ${TMPNAME}.lmpinstalled ; \ - else mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h ; fi - -gitversion: - @echo 'Gathering git version information' - @echo '#ifndef LMP_GIT_VERSION_H' > ${TMPNAME}.lmpgitversion - @echo '#define LMP_GIT_VERSION_H' >> ${TMPNAME}.lmpgitversion - @if (type git && test -e ../.git ) >> /dev/null 2>> /dev/null ; then \ - git='true'; \ - commit=$$(git rev-parse HEAD); \ - branch=$$(git rev-parse --abbrev-ref HEAD); \ - describe=$$(git describe --dirty=-modified); \ - else \ - git='false' ; \ - commit='(unknown)' ; \ - branch='(unknown)' ; \ - describe='(unknown)' ; \ - fi ; \ - echo "const bool LAMMPS_NS::LAMMPS::has_git_info = $${git};" >> ${TMPNAME}.lmpgitversion ; \ - echo "const char LAMMPS_NS::LAMMPS::git_commit[] = \"$${commit}\";" >> ${TMPNAME}.lmpgitversion ; \ - echo "const char LAMMPS_NS::LAMMPS::git_branch[] = \"$${branch}\";" >> ${TMPNAME}.lmpgitversion ; \ - echo "const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"$${describe}\";" >> ${TMPNAME}.lmpgitversion - @echo '#endif' >> ${TMPNAME}.lmpgitversion - @if [ -f lmpgitversion.h ]; \ - then test "`diff --brief ${TMPNAME}.lmpgitversion lmpgitversion.h`" != "" && \ - mv ${TMPNAME}.lmpgitversion lmpgitversion.h || rm ${TMPNAME}.lmpgitversion ; \ - else mv ${TMPNAME}.lmpgitversion lmpgitversion.h ; fi - -# Build LAMMPS in one of 2 modes -# static = static compile in Obj_machine (default) -# shared = shared compile in Obj_shared_machine - -.DEFAULT: - @if [ $@ = "serial" ]; \ - then cd STUBS; $(MAKE); cd ..; fi - @test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \ - -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ - @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi - @echo 'Gathering installed package information (may take a little while)' - @$(SHELL) Make.sh style - @$(SHELL) Make.sh packages - @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h gitversion - @echo 'Compiling LAMMPS for machine $@' - @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ - then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi - @if [ -f MAKE/OPTIONS/Makefile.$@ ]; \ - then cp MAKE/OPTIONS/Makefile.$@ $(objdir)/Makefile; fi - @if [ -f MAKE/Makefile.$@ ]; \ - then cp MAKE/Makefile.$@ $(objdir)/Makefile; fi - @if [ -f MAKE/MINE/Makefile.$@ ]; \ - then cp MAKE/MINE/Makefile.$@ $(objdir)/Makefile; fi - @if [ ! -e Makefile.package ]; \ - then cp Makefile.package.empty Makefile.package; fi - @if [ ! -e Makefile.package.settings ]; \ - then cp Makefile.package.settings.empty Makefile.package.settings; fi - @cp Makefile.package Makefile.package.settings $(objdir) - @cd $(objdir); rm -f .depend; \ - $(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || : - @rm -f $(ARLINK) $(SHLINK) $(EXE) -ifeq ($(mode),static) - @cd $(objdir); \ - $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \ - "LMPLIB = $(ARLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ - "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) - @ln -s $(ARLIB) $(ARLINK) -endif -ifeq ($(mode),shared) - @cd $(objdir); \ - $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ - "LMPLIB = $(SHLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ - "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) - @ln -s $(SHLIB) $(SHLINK) -endif -# backward compatibility -ifeq ($(mode),exe) - $(MAKE) $(MFLAGS) mode=static $@ -endif -ifeq ($(mode),lib) - $(MAKE) $(MFLAGS) mode=static $@ -endif -ifeq ($(mode),shexe) - $(MAKE) $(MFLAGS) mode=shared $@ -endif -ifeq ($(mode),shlib) - $(MAKE) $(MFLAGS) mode=shared $@ -endif - -ifeq ($(mode),print) - @cd $(objdir); \ - $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ - "EXE = ../$(ARLIB)" -f ../Makefile.print -endif - -# Remove machine-specific object files - -clean: - @echo 'make clean-all delete all object files' - @echo 'make clean-machine delete object files for one machine' - -clean-all: - rm -rf Obj_* - -clean-%: - @if [ $@ = "clean-serial" ]; \ - then cd STUBS; $(MAKE) clean; cd ..; fi - rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%) - -# Make MPI STUBS library - -mpi-stubs: - @cd STUBS; $(MAKE) clean; $(MAKE) - -# install LAMMPS shared lib and Python wrapper for Python usage -# include python package settings to automatically adapt name of -# the python interpreter. must purge build folder to not install -# unwanted outdated files. - -sinclude ../lib/python/Makefile.lammps -install-python: - @rm -rf ../python/build - @$(PYTHON) ../python/install.py -v ../src/version.h \ - -p ../python/lammps -l ../src/liblammps.so - -# Create a tarball of src dir and packages - -tar: - @cd STUBS; $(MAKE) clean - @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ - src/Make* src/Package.sh src/Depend.sh src/Install.sh src/Fetch.sh \ - src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \ - $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ - --exclude=*/.svn - @cd STUBS; $(MAKE) - @echo "Created $(ROOT)_src.tar.gz" - -# Package management - -package: - @echo 'Standard packages:' $(PACKAGE) - @echo '' - @echo 'User-contributed packages:' $(PACKUSER) - @echo '' - @echo 'Packages that need system libraries:' $(PACKSYS) - @echo '' - @echo 'Packages that need provided libraries:' $(PACKINT) - @echo '' - @echo 'Packages that need external libraries:' $(PACKEXT) - @echo '' - @echo 'make package list available packages' - @echo 'make package list available packages' - @echo 'make package-status (ps) status of all packages' - @echo 'make package-installed (pi) list of installed packages' - @echo 'make yes-package install a single pgk in src dir' - @echo 'make no-package remove a single pkg from src dir' - @echo 'make yes-all install all pgks in src dir' - @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' - @echo 'make yes-lib install all pkgs with libs (included or ext)' - @echo 'make no-lib remove all pkgs with libs (included or ext)' - @echo 'make yes-ext install all pkgs with external libs' - @echo 'make no-ext remove all pkgs with external libs' - @echo '' - @echo 'make package-update (pu) replace src files with package files' - @echo 'make package-overwrite replace package files with src files' - @echo 'make package-diff (pd) diff src files against package file' - @echo '' - @echo 'make lib-package build and/or download a package library' - -yes-all: - @for p in $(PACKALL); do $(MAKE) yes-$$p; done - -no-all: - @for p in $(PACKALL); do $(MAKE) no-$$p; done - -yes-standard yes-std: - @for p in $(PACKAGE); do $(MAKE) yes-$$p; done - -no-standard no-std: - @for p in $(PACKAGE); do $(MAKE) no-$$p; done - -yes-user: - @for p in $(PACKUSER); do $(MAKE) yes-$$p; done - -no-user: - @for p in $(PACKUSER); do $(MAKE) no-$$p; done - -yes-lib: - @for p in $(PACKLIB); do $(MAKE) yes-$$p; done - -no-lib: - @for p in $(PACKLIB); do $(MAKE) no-$$p; done - -yes-ext: - @for p in $(PACKEXT); do $(MAKE) yes-$$p; done - -no-ext: - @for p in $(PACKEXT); do $(MAKE) no-$$p; done - -yes-%: - @if [ ! -e Makefile.package ]; \ - then cp Makefile.package.empty Makefile.package; fi - @if [ ! -e Makefile.package.settings ]; \ - then cp Makefile.package.settings.empty Makefile.package.settings; fi - @if [ ! -e $(YESDIR) ]; then \ - echo "Package $(YESDIR) does not exist"; exit 1; \ - elif [ -e $(YESDIR)/Install.sh ]; then \ - echo "Installing package $(@:yes-%=%)"; \ - cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; \ - $(SHELL) Depend.sh $(YESDIR) 1; \ - else \ - echo "Installing package $(@:yes-%=%)"; \ - cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \ - $(SHELL) Depend.sh $(YESDIR) 1; \ - fi; - @$(SHELL) Fetch.sh $(YESDIR) - -no-%: - @if [ ! -e $(NODIR) ]; then \ - echo "Package $(NODIR) does not exist"; exit 1; \ - elif [ -e $(NODIR)/Install.sh ]; then \ - echo "Uninstalling package $(@:no-%=%)"; \ - cd $(NODIR); $(SHELL) Install.sh 0; cd ..; \ - $(SHELL) Depend.sh $(NODIR) 0; \ - else \ - echo "Uninstalling package $(@:no-%=%)"; \ - cd $(NODIR); $(SHELL) ../Install.sh 0; cd ..; \ - $(SHELL) Depend.sh $(NODIR) 0; \ - fi; - -# download/build/install a package library -# update the timestamp on main.cpp to trigger a relink with "make machine" - -lib-%: - @if [ -e ../lib/$(LIBDIR)/Install.py ]; then \ - echo "Installing lib $(@:lib-%=%)"; \ - ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \ - elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \ - echo "Installing lib $(@:lib-user-%=%)"; \ - ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \ - else \ - echo "Install script for lib $(@:lib-%=%) does not exist"; \ - fi; touch main.cpp - -# status = list src files that differ from package files -# installed = list of installed packages -# update = replace src files with newer package files -# overwrite = overwrite package files with newer src files -# diff = show differences between src and package files -# purge = delete obsolete and auto-generated package files - -package-status ps: - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done - -package-installed pi: - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p installed; done - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p installed; done - -package-update pu: purge - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done - -package-overwrite: purge - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done - -package-diff pd: - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done - -purge: Purge.list - @echo 'Purging obsolete and auto-generated source files' - @for f in `grep -v '#' Purge.list` ; \ - do test -f $$f && rm $$f && echo $$f || : ; \ - done diff --git a/src/USER-NETCDF/Install.sh b/src/NETCDF/Install.sh similarity index 100% rename from src/USER-NETCDF/Install.sh rename to src/NETCDF/Install.sh diff --git a/src/USER-NETCDF/README b/src/NETCDF/README similarity index 99% rename from src/USER-NETCDF/README rename to src/NETCDF/README index 714cbc67d0..8fdcb9e083 100644 --- a/src/USER-NETCDF/README +++ b/src/NETCDF/README @@ -1,4 +1,4 @@ -USER-NETCDF +NETCDF ============ This package provides the netcdf and netcdf/mpiio dump styles. diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp similarity index 71% rename from src/USER-NETCDF/dump_netcdf.cpp rename to src/NETCDF/dump_netcdf.cpp index e13bea910f..cd7783a0aa 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/NETCDF/dump_netcdf.cpp @@ -18,53 +18,52 @@ #if defined(LMP_HAS_NETCDF) -#include -#include #include "dump_netcdf.h" + #include "atom.h" #include "comm.h" #include "compute.h" #include "domain.h" #include "error.h" #include "fix.h" +#include "force.h" #include "group.h" #include "input.h" #include "math_const.h" #include "memory.h" #include "modify.h" -#include "update.h" -#include "universe.h" -#include "variable.h" -#include "force.h" #include "output.h" #include "thermo.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; -enum{THERMO_INT,THERMO_FLOAT,THERMO_BIGINT}; // same as in thermo.cpp -enum{DUMP_INT,DUMP_DOUBLE,DUMP_STRING,DUMP_BIGINT}; // same as in DumpCFG +static const char NC_FRAME_STR[] = "frame"; +static const char NC_SPATIAL_STR[] = "spatial"; +static const char NC_VOIGT_STR[] = "Voigt"; +static const char NC_ATOM_STR[] = "atom"; +static const char NC_CELL_SPATIAL_STR[] = "cell_spatial"; +static const char NC_CELL_ANGULAR_STR[] = "cell_angular"; +static const char NC_LABEL_STR[] = "label"; -const char NC_FRAME_STR[] = "frame"; -const char NC_SPATIAL_STR[] = "spatial"; -const char NC_VOIGT_STR[] = "Voigt"; -const char NC_ATOM_STR[] = "atom"; -const char NC_CELL_SPATIAL_STR[] = "cell_spatial"; -const char NC_CELL_ANGULAR_STR[] = "cell_angular"; -const char NC_LABEL_STR[] = "label"; +static const char NC_TIME_STR[] = "time"; +static const char NC_CELL_ORIGIN_STR[] = "cell_origin"; +static const char NC_CELL_LENGTHS_STR[] = "cell_lengths"; +static const char NC_CELL_ANGLES_STR[] = "cell_angles"; -const char NC_TIME_STR[] = "time"; -const char NC_CELL_ORIGIN_STR[] = "cell_origin"; -const char NC_CELL_LENGTHS_STR[] = "cell_lengths"; -const char NC_CELL_ANGLES_STR[] = "cell_angles"; +static const char NC_UNITS_STR[] = "units"; +static const char NC_SCALE_FACTOR_STR[] = "scale_factor"; -const char NC_UNITS_STR[] = "units"; -const char NC_SCALE_FACTOR_STR[] = "scale_factor"; - -const int THIS_IS_A_FIX = -1; -const int THIS_IS_A_COMPUTE = -2; -const int THIS_IS_A_VARIABLE = -3; -const int THIS_IS_A_BIGINT = -4; +static constexpr int THIS_IS_A_FIX = -1; +static constexpr int THIS_IS_A_COMPUTE = -2; +static constexpr int THIS_IS_A_VARIABLE = -3; +static constexpr int THIS_IS_A_BIGINT = -4; /* ---------------------------------------------------------------------- */ @@ -98,78 +97,65 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) : } n_perat = 0; - for (int iarg = 5; iarg < narg; iarg++) { - int i = iarg-5; + for (int i = 0; i < nfield; i++) { int idim = 0; int ndims = 1; - char mangled[1024]; + std::string mangled = earg[i]; bool constant = false; - strcpy(mangled, arg[iarg]); - // name mangling // in the AMBER specification - if (!strcmp(mangled, "x") || !strcmp(mangled, "y") || - !strcmp(mangled, "z")) { + if ((mangled == "x") || (mangled == "y") || (mangled == "z")) { idim = mangled[0] - 'x'; ndims = 3; - strcpy(mangled, "coordinates"); - } - else if (!strcmp(mangled, "vx") || !strcmp(mangled, "vy") || - !strcmp(mangled, "vz")) { + mangled = "coordinates"; + } else if ((mangled == "vx") || (mangled == "vy") || (mangled == "vz")) { idim = mangled[1] - 'x'; ndims = 3; - strcpy(mangled, "velocities"); - } - else if (!strcmp(mangled, "xs") || !strcmp(mangled, "ys") || - !strcmp(mangled, "zs")) { + mangled = "velocities"; + } else if ((mangled == "xs") || (mangled == "ys") || (mangled == "zs")) { idim = mangled[0] - 'x'; ndims = 3; - strcpy(mangled, "scaled_coordinates"); - } - else if (!strcmp(mangled, "xu") || !strcmp(mangled, "yu") || - !strcmp(mangled, "zu")) { + mangled = "scaled_coordinates"; + } else if ((mangled == "xu") || (mangled == "yu") || (mangled == "zu")) { idim = mangled[0] - 'x'; ndims = 3; - strcpy(mangled, "unwrapped_coordinates"); - } - else if (!strcmp(mangled, "fx") || !strcmp(mangled, "fy") || - !strcmp(mangled, "fz")) { + mangled = "unwrapped_coordinates"; + } else if ((mangled == "fx") || (mangled == "fy") || (mangled == "fz")) { idim = mangled[1] - 'x'; ndims = 3; - strcpy(mangled, "forces"); - } - else if (!strcmp(mangled, "mux") || !strcmp(mangled, "muy") || - !strcmp(mangled, "muz")) { + mangled = "forces"; + } else if ((mangled == "mux") || (mangled == "muy") || (mangled == "muz")) { idim = mangled[2] - 'x'; ndims = 3; - strcpy(mangled, "mu"); - } - else if (!strncmp(mangled, "c_", 2)) { - char *ptr = strchr(mangled, '['); - if (ptr) { - if (mangled[strlen(mangled)-1] != ']') + mangled = "mu"; + } else if (utils::strmatch(mangled, "^c_")) { + std::size_t found = mangled.find('['); + if (found != std::string::npos) { + if (mangled.find(']',found) == std::string::npos) error->all(FLERR,"Missing ']' in dump command"); - *ptr = '\0'; - idim = ptr[1] - '1'; + idim = mangled[found+1] - '1'; + mangled = mangled.substr(0,found); ndims = THIS_IS_A_COMPUTE; } - } - else if (!strncmp(mangled, "f_", 2)) { - char *ptr = strchr(mangled, '['); - if (ptr) { - if (mangled[strlen(mangled)-1] != ']') + } else if (utils::strmatch(mangled, "^f_")) { + std::size_t found = mangled.find('['); + if (found != std::string::npos) { + if (mangled.find(']',found) == std::string::npos) error->all(FLERR,"Missing ']' in dump command"); - *ptr = '\0'; - idim = ptr[1] - '1'; + idim = mangled[found+1] - '1'; + mangled = mangled.substr(0,found); ndims = THIS_IS_A_FIX; } + } else if (utils::strmatch(mangled, "^v_")) { + idim = 0; + ndims = THIS_IS_A_VARIABLE; } // find mangled name int inc = -1; for (int j = 0; j < n_perat && inc < 0; j++) { - if (!strcmp(perat[j].name, mangled)) { + if (mangled == perat[j].name) { inc = j; } } @@ -182,7 +168,7 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) : for (int j = 0; j < DUMP_NC_MAX_DIMS; j++) { perat[inc].field[j] = -1; } - strncpy(perat[inc].name, mangled, NC_FIELD_NAME_MAX); + strncpy(perat[inc].name, mangled.c_str(), NC_FIELD_NAME_MAX); n_perat++; } @@ -209,8 +195,8 @@ DumpNetCDF::~DumpNetCDF() { closefile(); - delete [] perat; - if (thermovar) delete [] thermovar; + delete[] perat; + if (thermovar) delete[] thermovar; if (int_buffer) memory->sfree(int_buffer); if (double_buffer) memory->sfree(double_buffer); @@ -227,8 +213,7 @@ void DumpNetCDF::openfile() char *ptr = strchr(filestar,'*'); *ptr = '\0'; if (padflag == 0) - sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", - filestar,update->ntimestep,ptr+1); + sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", filestar,update->ntimestep,ptr+1); else { char bif[8],pad[16]; strcpy(bif,BIGINT_FORMAT); @@ -239,7 +224,7 @@ void DumpNetCDF::openfile() } if (thermo && !singlefile_opened) { - if (thermovar) delete [] thermovar; + if (thermovar) delete[] thermovar; thermovar = new int[output->thermo->nfield]; } @@ -260,8 +245,7 @@ void DumpNetCDF::openfile() perat[i].dims = compute[j]->size_peratom_cols; if (perat[i].dims > DUMP_NC_MAX_DIMS) error->all(FLERR,"perat[i].dims > DUMP_NC_MAX_DIMS"); - } - else if (perat[i].dims == THIS_IS_A_FIX) { + } else if (perat[i].dims == THIS_IS_A_FIX) { int j = -1; for (int k = 0; k < DUMP_NC_MAX_DIMS; k++) { if (perat[i].field[k] >= 0) { @@ -275,6 +259,8 @@ void DumpNetCDF::openfile() perat[i].dims = fix[j]->size_peratom_cols; if (perat[i].dims > DUMP_NC_MAX_DIMS) error->all(FLERR,"perat[i].dims > DUMP_NC_MAX_DIMS"); + } else if (perat[i].dims == THIS_IS_A_VARIABLE) { + error->all(FLERR,"Dump netcdf currently does not support dumping variables"); } } @@ -289,8 +275,7 @@ void DumpNetCDF::openfile() // Fixme! Perform checks if dimensions and variables conform with // data structure standard. if (not utils::file_is_readable(filecurrent)) - error->all(FLERR, "cannot append to non-existent file {}", - filecurrent); + error->all(FLERR, "cannot append to non-existent file {}",filecurrent); if (singlefile_opened) return; singlefile_opened = 1; @@ -300,10 +285,8 @@ void DumpNetCDF::openfile() // dimensions NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR ); NCERRX( nc_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR ); - NCERRX( nc_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim), - NC_CELL_SPATIAL_STR ); - NCERRX( nc_inq_dimid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_dim), - NC_CELL_ANGULAR_STR ); + NCERRX( nc_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim), NC_CELL_SPATIAL_STR ); + NCERRX( nc_inq_dimid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_dim), NC_CELL_ANGULAR_STR ); NCERRX( nc_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR ); for (int i = 0; i < n_perat; i++) { @@ -312,47 +295,36 @@ void DumpNetCDF::openfile() char dimstr[1024]; if (dims == 3) { strcpy(dimstr, NC_SPATIAL_STR); - } - else if (dims == 6) { + } else if (dims == 6) { strcpy(dimstr, NC_VOIGT_STR); - } - else { + } else { sprintf(dimstr, "vec%i", dims); } if (dims != 1) { - NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]), - dimstr ); + NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]), dimstr ); } } } // default variables - NCERRX( nc_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var), - NC_SPATIAL_STR ); - NCERRX( nc_inq_varid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_var), - NC_CELL_SPATIAL_STR); - NCERRX( nc_inq_varid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_var), - NC_CELL_ANGULAR_STR); + NCERRX( nc_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var), NC_SPATIAL_STR ); + NCERRX( nc_inq_varid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_var), NC_CELL_SPATIAL_STR); + NCERRX( nc_inq_varid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_var), NC_CELL_ANGULAR_STR); NCERRX( nc_inq_varid(ncid, NC_TIME_STR, &time_var), NC_TIME_STR ); - NCERRX( nc_inq_varid(ncid, NC_CELL_ORIGIN_STR, &cell_origin_var), - NC_CELL_ORIGIN_STR ); - NCERRX( nc_inq_varid(ncid, NC_CELL_LENGTHS_STR, &cell_lengths_var), - NC_CELL_LENGTHS_STR); - NCERRX( nc_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var), - NC_CELL_ANGLES_STR); + NCERRX( nc_inq_varid(ncid, NC_CELL_ORIGIN_STR, &cell_origin_var), NC_CELL_ORIGIN_STR ); + NCERRX( nc_inq_varid(ncid, NC_CELL_LENGTHS_STR, &cell_lengths_var), NC_CELL_LENGTHS_STR); + NCERRX( nc_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var), NC_CELL_ANGLES_STR); for (int i = 0; i < n_perat; i++) { - NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var), - perat[i].name ); + NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var), perat[i].name ); } // perframe variables if (thermo) { Thermo *th = output->thermo; for (int i = 0; i < th->nfield; i++) { - NCERRX( nc_inq_varid(ncid, th->keyword[i], &thermovar[i]), - th->keyword[i] ); + NCERRX( nc_inq_varid(ncid, th->keyword[i], &thermovar[i]), th->keyword[i] ); } } @@ -374,79 +346,65 @@ void DumpNetCDF::openfile() if (singlefile_opened) return; singlefile_opened = 1; - NCERRX( nc_create(filecurrent, NC_64BIT_DATA, &ncid), - filecurrent ); + NCERRX( nc_create(filecurrent, NC_64BIT_DATA, &ncid), filecurrent ); // dimensions - NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim), - NC_FRAME_STR ); - NCERRX( nc_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim), - NC_ATOM_STR ); - NCERRX( nc_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim), - NC_CELL_SPATIAL_STR ); - NCERRX( nc_def_dim(ncid, NC_CELL_ANGULAR_STR, 3, &cell_angular_dim), - NC_CELL_ANGULAR_STR ); - NCERRX( nc_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), - NC_LABEL_STR ); + NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim), NC_FRAME_STR ); + NCERRX( nc_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim), NC_ATOM_STR ); + NCERRX( nc_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim), NC_CELL_SPATIAL_STR ); + NCERRX( nc_def_dim(ncid, NC_CELL_ANGULAR_STR, 3, &cell_angular_dim), NC_CELL_ANGULAR_STR ); + NCERRX( nc_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), NC_LABEL_STR ); for (int i = 0; i < n_perat; i++) { - int dims = perat[i].dims; - if (vector_dim[dims] < 0) { + int dim = perat[i].dims; + if (vector_dim[dim] < 0) { char dimstr[1024]; - if (dims == 3) { + if (dim == 3) { strcpy(dimstr, NC_SPATIAL_STR); - } - else if (dims == 6) { + } else if (dim == 6) { strcpy(dimstr, NC_VOIGT_STR); + } else { + sprintf(dimstr, "vec%i", dim); } - else { - sprintf(dimstr, "vec%i", dims); - } - if (dims != 1) { - NCERRX( nc_def_dim(ncid, dimstr, dims, &vector_dim[dims]), - dimstr ); + if (dim != 1) { + NCERRX( nc_def_dim(ncid, dimstr, dim, &vector_dim[dim]), dimstr ); } } } // default variables - dims[0] = vector_dim[3]; - NCERRX( nc_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var), - NC_SPATIAL_STR ); - NCERRX( nc_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims, - &cell_spatial_var), NC_CELL_SPATIAL_STR ); - dims[0] = vector_dim[3]; + dims[0] = 0; + NCERRX( nc_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var), NC_SPATIAL_STR ); + NCERRX( nc_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims, &cell_spatial_var), NC_CELL_SPATIAL_STR ); + dims[0] = 0; dims[1] = label_dim; - NCERRX( nc_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, - &cell_angular_var), NC_CELL_ANGULAR_STR ); + NCERRX( nc_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, &cell_angular_var), NC_CELL_ANGULAR_STR ); dims[0] = frame_dim; - NCERRX( nc_def_var(ncid, NC_TIME_STR, NC_DOUBLE, 1, dims, &time_var), - NC_TIME_STR); + NCERRX( nc_def_var(ncid, NC_TIME_STR, NC_DOUBLE, 1, dims, &time_var), NC_TIME_STR); dims[0] = frame_dim; dims[1] = cell_spatial_dim; - NCERRX( nc_def_var(ncid, NC_CELL_ORIGIN_STR, NC_DOUBLE, 2, dims, - &cell_origin_var), NC_CELL_ORIGIN_STR ); - NCERRX( nc_def_var(ncid, NC_CELL_LENGTHS_STR, NC_DOUBLE, 2, dims, - &cell_lengths_var), NC_CELL_LENGTHS_STR ); + NCERRX( nc_def_var(ncid, NC_CELL_ORIGIN_STR, NC_DOUBLE, 2, dims, &cell_origin_var), NC_CELL_ORIGIN_STR ); + NCERRX( nc_def_var(ncid, NC_CELL_LENGTHS_STR, NC_DOUBLE, 2, dims, &cell_lengths_var), NC_CELL_LENGTHS_STR ); dims[0] = frame_dim; dims[1] = cell_angular_dim; - NCERRX( nc_def_var(ncid, NC_CELL_ANGLES_STR, NC_DOUBLE, 2, dims, - &cell_angles_var), NC_CELL_ANGLES_STR ); + NCERRX( nc_def_var(ncid, NC_CELL_ANGLES_STR, NC_DOUBLE, 2, dims, &cell_angles_var), NC_CELL_ANGLES_STR ); // variables specified in the input file dims[0] = frame_dim; dims[1] = atom_dim; - dims[2] = vector_dim[3]; + dims[2] = 0; for (int i = 0; i < n_perat; i++) { nc_type xtype; // Type mangling - if (vtype[perat[i].field[0]] == DUMP_INT) { + if (vtype[perat[i].field[0]] == Dump::INT) { xtype = NC_INT; - } else if (vtype[perat[i].field[0]] == DUMP_BIGINT) { + } else if (vtype[perat[i].field[0]] == Dump::BIGINT) { xtype = NC_INT64; + } else if (vtype[perat[i].field[0]] == Dump::STRING) { + error->all(FLERR,"Dump netcdf currently does not support dumping string properties"); } else { if (double_precision) xtype = NC_DOUBLE; @@ -457,26 +415,19 @@ void DumpNetCDF::openfile() if (perat[i].constant) { // this quantity will only be written once if (perat[i].dims == 1) { - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 1, dims+1, - &perat[i].var), perat[i].name ); - } - else { + NCERRX( nc_def_var(ncid, perat[i].name, xtype, 1, dims+1, &perat[i].var), perat[i].name ); + } else { // this is a vector dims[1] = vector_dim[perat[i].dims]; - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1, - &perat[i].var), perat[i].name ); + NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1, &perat[i].var), perat[i].name ); } - } - else { + } else { if (perat[i].dims == 1) { - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims, - &perat[i].var), perat[i].name ); - } - else { + NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims, &perat[i].var), perat[i].name ); + } else { // this is a vector dims[2] = vector_dim[perat[i].dims]; - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims, - &perat[i].var), perat[i].name ); + NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims, &perat[i].var), perat[i].name ); } } } @@ -485,15 +436,13 @@ void DumpNetCDF::openfile() if (thermo) { Thermo *th = output->thermo; for (int i = 0; i < th->nfield; i++) { - if (th->vtype[i] == THERMO_FLOAT) { + if (th->vtype[i] == Thermo::FLOAT) { NCERRX( nc_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims, &thermovar[i]), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_INT) { + } else if (th->vtype[i] == Thermo::INT) { NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT, 1, dims, &thermovar[i]), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_BIGINT) { + } else if (th->vtype[i] == Thermo::BIGINT) { #if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG) NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT64, 1, dims, &thermovar[i]), th->keyword[i] ); @@ -506,83 +455,49 @@ void DumpNetCDF::openfile() } // attributes - NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions", - 5, "AMBER") ); - NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion", - 3, "1.0") ); + NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions", 5, "AMBER") ); + NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion", 3, "1.0") ); - NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program", - 6, "LAMMPS") ); - NCERR( nc_put_att_text(ncid, NC_GLOBAL, "programVersion", - strlen(lmp->version), lmp->version) ); + NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program", 6, "LAMMPS") ); + NCERR( nc_put_att_text(ncid, NC_GLOBAL, "programVersion",strlen(lmp->version), lmp->version) ); // units if (!strcmp(update->unit_style, "lj")) { - NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, - 2, "lj") ); - NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 2, "lj") ); - NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 2, "lj") ); - } - else if (!strcmp(update->unit_style, "real")) { - NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, - 11, "femtosecond") ); - NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 8, "Angstrom") ); - NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 8, "Angstrom") ); - } - else if (!strcmp(update->unit_style, "metal")) { - NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, - 10, "picosecond") ); - NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 8, "Angstrom") ); - NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 8, "Angstrom") ); - } - else if (!strcmp(update->unit_style, "si")) { - NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, - 6, "second") ); - NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 5, "meter") ); - NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 5, "meter") ); - } - else if (!strcmp(update->unit_style, "cgs")) { - NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, - 6, "second") ); - NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 10, "centimeter") ); - NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 10, "centimeter") ); - } - else if (!strcmp(update->unit_style, "electron")) { - NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, - 11, "femtosecond") ); - NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 4, "Bohr") ); - NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 4, "Bohr") ); - } - else { - char errstr[1024]; - sprintf(errstr, "Unsupported unit style '%s'", update->unit_style); - error->all(FLERR,errstr); + NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 2, "lj") ); + NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 2, "lj") ); + NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 2, "lj") ); + } else if (!strcmp(update->unit_style, "real")) { + NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 11, "femtosecond") ); + NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 8, "Angstrom") ); + NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 8, "Angstrom") ); + } else if (!strcmp(update->unit_style, "metal")) { + NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 10, "picosecond") ); + NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 8, "Angstrom") ); + NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 8, "Angstrom") ); + } else if (!strcmp(update->unit_style, "si")) { + NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 6, "second") ); + NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 5, "meter") ); + NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 5, "meter") ); + } else if (!strcmp(update->unit_style, "cgs")) { + NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 6, "second") ); + NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 10, "centimeter") ); + NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 10, "centimeter") ); + } else if (!strcmp(update->unit_style, "electron")) { + NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 11, "femtosecond") ); + NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 4, "Bohr") ); + NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 4, "Bohr") ); + } else { + error->all(FLERR,"Unsupported unit style: {}", update->unit_style); } - NCERR( nc_put_att_text(ncid, cell_angles_var, NC_UNITS_STR, - 6, "degree") ); + NCERR( nc_put_att_text(ncid, cell_angles_var, NC_UNITS_STR,6, "degree") ); d[0] = update->dt; - NCERR( nc_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR, - NC_DOUBLE, 1, d) ); + NCERR( nc_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR,NC_DOUBLE, 1, d) ); d[0] = 1.0; - NCERR( nc_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR, - NC_DOUBLE, 1, d) ); + NCERR( nc_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR,NC_DOUBLE, 1, d) ); d[0] = 1.0; - NCERR( nc_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR, - NC_DOUBLE, 1, d) ); + NCERR( nc_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR,NC_DOUBLE, 1, d) ); /* * Finished with definition @@ -721,16 +636,14 @@ void DumpNetCDF::write() for (int i = 0; i < th->nfield; i++) { th->call_vfunc(i); if (filewriter) { - if (th->vtype[i] == THERMO_FLOAT) { + if (th->vtype[i] == Thermo::FLOAT) { NCERRX( nc_put_var1_double(ncid, thermovar[i], start, &th->dvalue), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_INT) { + } else if (th->vtype[i] == Thermo::INT) { NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_BIGINT) { + } else if (th->vtype[i] == Thermo::BIGINT) { NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue), th->keyword[i] ); } @@ -773,8 +686,7 @@ void DumpNetCDF::write_header(bigint n) cell_angles[0] = 90; cell_angles[1] = 90; cell_angles[2] = 90; - } - else { + } else { double cosalpha, cosbeta, cosgamma; double *h = domain->h; @@ -806,12 +718,9 @@ void DumpNetCDF::write_header(bigint n) count[0] = 1; count[1] = 3; NCERR( nc_put_var1_double(ncid, time_var, start, &time) ); - NCERR( nc_put_vara_double(ncid, cell_origin_var, start, count, - cell_origin) ); - NCERR( nc_put_vara_double(ncid, cell_lengths_var, start, count, - cell_lengths) ); - NCERR( nc_put_vara_double(ncid, cell_angles_var, start, count, - cell_angles) ); + NCERR( nc_put_vara_double(ncid, cell_origin_var, start, count, cell_origin) ); + NCERR( nc_put_vara_double(ncid, cell_lengths_var, start, count, cell_lengths) ); + NCERR( nc_put_vara_double(ncid, cell_angles_var, start, count, cell_angles) ); } ndata = n; @@ -860,7 +769,7 @@ void DumpNetCDF::write_data(int n, double *mybuf) for (int i = 0; i < n_perat; i++) { int iaux = perat[i].field[0]; - if (vtype[iaux] == DUMP_INT || vtype[iaux] == DUMP_BIGINT) { + if (vtype[iaux] == Dump::INT || vtype[iaux] == Dump::BIGINT) { // integers if (perat[i].dims > 1) { @@ -868,12 +777,11 @@ void DumpNetCDF::write_data(int n, double *mybuf) iaux = perat[i].field[idim]; if (iaux >= 0) { - if (vtype[iaux] == DUMP_INT) { + if (vtype[iaux] == Dump::INT) { for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = static_cast(mybuf[iaux]); } - } - else { // DUMP_BIGINT + } else { // Dump::BIGINT for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = static_cast(mybuf[iaux]); } @@ -883,25 +791,19 @@ void DumpNetCDF::write_data(int n, double *mybuf) if (perat[i].constant) { if (perat[i].ndumped < ntotalgr) { - NCERR( nc_put_vars_bigint(ncid, perat[i].var, - start+1, count+1, stride+1, - int_buffer) ); + NCERR( nc_put_vars_bigint(ncid, perat[i].var,start+1, count+1, stride+1,int_buffer) ); perat[i].ndumped += n; } - } - else - NCERR( nc_put_vars_bigint(ncid, perat[i].var, start, count, stride, - int_buffer) ); + } else + NCERR( nc_put_vars_bigint(ncid, perat[i].var, start, count, stride,int_buffer) ); } } - } - else { - if (vtype[iaux] == DUMP_INT) { + } else { + if (vtype[iaux] == Dump::INT) { for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = static_cast(mybuf[iaux]); } - } - else { // DUMP_BIGINT + } else { // Dump::BIGINT for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = static_cast(mybuf[iaux]); } @@ -909,17 +811,13 @@ void DumpNetCDF::write_data(int n, double *mybuf) if (perat[i].constant) { if (perat[i].ndumped < ntotalgr) { - NCERR( nc_put_vara_bigint(ncid, perat[i].var, start+1, count+1, - int_buffer) ); + NCERR( nc_put_vara_bigint(ncid, perat[i].var, start+1, count+1,int_buffer) ); perat[i].ndumped += n; } - } - else - NCERR( nc_put_vara_bigint(ncid, perat[i].var, start, count, - int_buffer) ); + } else + NCERR( nc_put_vara_bigint(ncid, perat[i].var, start, count,int_buffer) ); } - } - else { + } else { // doubles if (perat[i].dims > 1) { @@ -940,14 +838,12 @@ void DumpNetCDF::write_data(int n, double *mybuf) double_buffer) ); perat[i].ndumped += n; } - } - else + } else NCERR( nc_put_vars_double(ncid, perat[i].var, start, count, stride, double_buffer) ); } } - } - else { + } else { for (int j = 0; j < n; j++, iaux+=size_one) { double_buffer[j] = mybuf[iaux]; } @@ -958,8 +854,7 @@ void DumpNetCDF::write_data(int n, double *mybuf) double_buffer) ); perat[i].ndumped += n; } - } - else + } else NCERR( nc_put_vara_double(ncid, perat[i].var, start, count, double_buffer) ); } @@ -980,15 +875,12 @@ int DumpNetCDF::modify_param(int narg, char **arg) error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword."); if (strcmp(arg[iarg],"yes") == 0) { double_precision = true; - } - else if (strcmp(arg[iarg],"no") == 0) { + } else if (strcmp(arg[iarg],"no") == 0) { double_precision = false; - } - else error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword."); + } else error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword."); iarg++; return 2; - } - else if (strcmp(arg[iarg],"at") == 0) { + } else if (strcmp(arg[iarg],"at") == 0) { iarg++; if (iarg >= narg) error->all(FLERR,"expected additional arg after 'at' keyword."); @@ -997,18 +889,15 @@ int DumpNetCDF::modify_param(int narg, char **arg) else if (framei < 0) framei--; iarg++; return 2; - } - else if (strcmp(arg[iarg],"thermo") == 0) { + } else if (strcmp(arg[iarg],"thermo") == 0) { iarg++; if (iarg >= narg) error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword."); if (strcmp(arg[iarg],"yes") == 0) { thermo = true; - } - else if (strcmp(arg[iarg],"no") == 0) { + } else if (strcmp(arg[iarg],"no") == 0) { thermo = false; - } - else error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword."); + } else error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword."); iarg++; return 2; } else return 0; @@ -1019,16 +908,10 @@ int DumpNetCDF::modify_param(int narg, char **arg) void DumpNetCDF::ncerr(int err, const char *descr, int line) { if (err != NC_NOERR) { - char errstr[1024]; - if (descr) { - sprintf(errstr, "NetCDF failed with error '%s' (while accessing '%s') " - " in line %i of %s.", nc_strerror(err), descr, line, __FILE__); - } - else { - sprintf(errstr, "NetCDF failed with error '%s' in line %i of %s.", - nc_strerror(err), line, __FILE__); - } - error->one(FLERR,errstr); + if (descr) error->one(FLERR,"NetCDF failed with error '{}' (while accessing '{}') " + " in line {} of {}.", nc_strerror(err), descr, line, __FILE__); + else error->one(FLERR,"NetCDF failed with error '{}' in line {} of {}.", + nc_strerror(err), line, __FILE__); } } diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/NETCDF/dump_netcdf.h similarity index 100% rename from src/USER-NETCDF/dump_netcdf.h rename to src/NETCDF/dump_netcdf.h diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp similarity index 68% rename from src/USER-NETCDF/dump_netcdf_mpiio.cpp rename to src/NETCDF/dump_netcdf_mpiio.cpp index bf5b1a26ca..4179b362c8 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/NETCDF/dump_netcdf_mpiio.cpp @@ -18,53 +18,52 @@ #if defined(LMP_HAS_PNETCDF) -#include -#include #include "dump_netcdf_mpiio.h" + #include "atom.h" #include "comm.h" #include "compute.h" #include "domain.h" #include "error.h" #include "fix.h" +#include "force.h" #include "group.h" #include "input.h" #include "math_const.h" #include "memory.h" #include "modify.h" -#include "update.h" -#include "universe.h" -#include "variable.h" -#include "force.h" #include "output.h" #include "thermo.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; -enum{THERMO_INT,THERMO_FLOAT,THERMO_BIGINT}; // same as in thermo.cpp -enum{DUMP_INT,DUMP_DOUBLE,DUMP_STRING,DUMP_BIGINT}; // same as in DumpCFG +static const char NC_FRAME_STR[] = "frame"; +static const char NC_SPATIAL_STR[] = "spatial"; +static const char NC_VOIGT_STR[] = "Voigt"; +static const char NC_ATOM_STR[] = "atom"; +static const char NC_CELL_SPATIAL_STR[] = "cell_spatial"; +static const char NC_CELL_ANGULAR_STR[] = "cell_angular"; +static const char NC_LABEL_STR[] = "label"; -const char NC_FRAME_STR[] = "frame"; -const char NC_SPATIAL_STR[] = "spatial"; -const char NC_VOIGT_STR[] = "Voigt"; -const char NC_ATOM_STR[] = "atom"; -const char NC_CELL_SPATIAL_STR[] = "cell_spatial"; -const char NC_CELL_ANGULAR_STR[] = "cell_angular"; -const char NC_LABEL_STR[] = "label"; +static const char NC_TIME_STR[] = "time"; +static const char NC_CELL_ORIGIN_STR[] = "cell_origin"; +static const char NC_CELL_LENGTHS_STR[] = "cell_lengths"; +static const char NC_CELL_ANGLES_STR[] = "cell_angles"; -const char NC_TIME_STR[] = "time"; -const char NC_CELL_ORIGIN_STR[] = "cell_origin"; -const char NC_CELL_LENGTHS_STR[] = "cell_lengths"; -const char NC_CELL_ANGLES_STR[] = "cell_angles"; +static const char NC_UNITS_STR[] = "units"; +static const char NC_SCALE_FACTOR_STR[] = "scale_factor"; -const char NC_UNITS_STR[] = "units"; -const char NC_SCALE_FACTOR_STR[] = "scale_factor"; - -const int THIS_IS_A_FIX = -1; -const int THIS_IS_A_COMPUTE = -2; -const int THIS_IS_A_VARIABLE = -3; -const int THIS_IS_A_BIGINT = -4; +static constexpr int THIS_IS_A_FIX = -1; +static constexpr int THIS_IS_A_COMPUTE = -2; +static constexpr int THIS_IS_A_VARIABLE = -3; +static constexpr int THIS_IS_A_BIGINT = -4; /* ---------------------------------------------------------------------- */ @@ -98,77 +97,65 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) : } n_perat = 0; - for (int iarg = 5; iarg < narg; iarg++) { - int i = iarg-5; + for (int i = 0; i < nfield; i++) { int idim = 0; int ndims = 1; - char mangled[1024]; - - strcpy(mangled, arg[iarg]); + std::string mangled = earg[i]; + bool constant = false; // name mangling // in the AMBER specification - if (!strcmp(mangled, "x") || !strcmp(mangled, "y") || - !strcmp(mangled, "z")) { + if ((mangled == "x") || (mangled == "y") || (mangled == "z")) { idim = mangled[0] - 'x'; ndims = 3; - strcpy(mangled, "coordinates"); - } - else if (!strcmp(mangled, "vx") || !strcmp(mangled, "vy") || - !strcmp(mangled, "vz")) { + mangled = "coordinates"; + } else if ((mangled == "vx") || (mangled == "vy") || (mangled == "vz")) { idim = mangled[1] - 'x'; ndims = 3; - strcpy(mangled, "velocities"); - } - else if (!strcmp(mangled, "xs") || !strcmp(mangled, "ys") || - !strcmp(mangled, "zs")) { + mangled = "velocities"; + } else if ((mangled == "xs") || (mangled == "ys") || (mangled == "zs")) { idim = mangled[0] - 'x'; ndims = 3; - strcpy(mangled, "scaled_coordinates"); - } - else if (!strcmp(mangled, "xu") || !strcmp(mangled, "yu") || - !strcmp(mangled, "zu")) { + mangled = "scaled_coordinates"; + } else if ((mangled == "xu") || (mangled == "yu") || (mangled == "zu")) { idim = mangled[0] - 'x'; ndims = 3; - strcpy(mangled, "unwrapped_coordinates"); - } - else if (!strcmp(mangled, "fx") || !strcmp(mangled, "fy") || - !strcmp(mangled, "fz")) { + mangled = "unwrapped_coordinates"; + } else if ((mangled == "fx") || (mangled == "fy") || (mangled == "fz")) { idim = mangled[1] - 'x'; ndims = 3; - strcpy(mangled, "forces"); - } - else if (!strcmp(mangled, "mux") || !strcmp(mangled, "muy") || - !strcmp(mangled, "muz")) { + mangled = "forces"; + } else if ((mangled == "mux") || (mangled == "muy") || (mangled == "muz")) { idim = mangled[2] - 'x'; ndims = 3; - strcpy(mangled, "mu"); - } - else if (!strncmp(mangled, "c_", 2)) { - char *ptr = strchr(mangled, '['); - if (ptr) { - if (mangled[strlen(mangled)-1] != ']') + mangled = "mu"; + } else if (utils::strmatch(mangled, "^c_")) { + std::size_t found = mangled.find('['); + if (found != std::string::npos) { + if (mangled.find(']',found) == std::string::npos) error->all(FLERR,"Missing ']' in dump command"); - *ptr = '\0'; - idim = ptr[1] - '1'; + idim = mangled[found+1] - '1'; + mangled = mangled.substr(0,found); ndims = THIS_IS_A_COMPUTE; } - } - else if (!strncmp(mangled, "f_", 2)) { - char *ptr = strchr(mangled, '['); - if (ptr) { - if (mangled[strlen(mangled)-1] != ']') + } else if (utils::strmatch(mangled, "^f_")) { + std::size_t found = mangled.find('['); + if (found != std::string::npos) { + if (mangled.find(']',found) == std::string::npos) error->all(FLERR,"Missing ']' in dump command"); - *ptr = '\0'; - idim = ptr[1] - '1'; + idim = mangled[found+1] - '1'; + mangled = mangled.substr(0,found); ndims = THIS_IS_A_FIX; } + } else if (utils::strmatch(mangled, "^v_")) { + idim = 0; + ndims = THIS_IS_A_VARIABLE; } // find mangled name int inc = -1; for (int j = 0; j < n_perat && inc < 0; j++) { - if (!strcmp(perat[j].name, mangled)) { + if (mangled == perat[j].name) { inc = j; } } @@ -181,7 +168,7 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) : for (int j = 0; j < DUMP_NC_MPIIO_MAX_DIMS; j++) { perat[inc].field[j] = -1; } - strcpy(perat[inc].name, mangled); + strncpy(perat[inc].name, mangled.c_str(), NC_MPIIO_FIELD_NAME_MAX); n_perat++; } @@ -206,8 +193,8 @@ DumpNetCDFMPIIO::~DumpNetCDFMPIIO() { closefile(); - delete [] perat; - if (thermovar) delete [] thermovar; + delete[] perat; + if (thermovar) delete[] thermovar; if (int_buffer) memory->sfree(int_buffer); if (double_buffer) memory->sfree(double_buffer); @@ -236,7 +223,7 @@ void DumpNetCDFMPIIO::openfile() } if (thermo && !singlefile_opened) { - if (thermovar) delete [] thermovar; + if (thermovar) delete[] thermovar; thermovar = new int[output->thermo->nfield]; } @@ -257,8 +244,7 @@ void DumpNetCDFMPIIO::openfile() perat[i].dims = compute[j]->size_peratom_cols; if (perat[i].dims > DUMP_NC_MPIIO_MAX_DIMS) error->all(FLERR,"perat[i].dims > DUMP_NC_MPIIO_MAX_DIMS"); - } - else if (perat[i].dims == THIS_IS_A_FIX) { + } else if (perat[i].dims == THIS_IS_A_FIX) { int j = -1; for (int k = 0; k < DUMP_NC_MPIIO_MAX_DIMS; k++) { if (perat[i].field[k] >= 0) { @@ -272,6 +258,8 @@ void DumpNetCDFMPIIO::openfile() perat[i].dims = fix[j]->size_peratom_cols; if (perat[i].dims > DUMP_NC_MPIIO_MAX_DIMS) error->all(FLERR,"perat[i].dims > DUMP_NC_MPIIO_MAX_DIMS"); + } else if (perat[i].dims == THIS_IS_A_VARIABLE) { + error->all(FLERR,"Dump netcdf/mpiio currently does not support dumping variables"); } } @@ -285,8 +273,7 @@ void DumpNetCDFMPIIO::openfile() // Fixme! Perform checks if dimensions and variables conform with // data structure standard. if (not utils::file_is_readable(filecurrent)) - error->all(FLERR, "cannot append to non-existent file {}", - filecurrent); + error->all(FLERR, "cannot append to non-existent file {}", filecurrent); MPI_Offset index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS]; double d[1]; @@ -294,16 +281,13 @@ void DumpNetCDFMPIIO::openfile() if (singlefile_opened) return; singlefile_opened = 1; - NCERRX( ncmpi_open(world, filecurrent, NC_WRITE, MPI_INFO_NULL, - &ncid), filecurrent ); + NCERRX( ncmpi_open(world, filecurrent, NC_WRITE, MPI_INFO_NULL, &ncid), filecurrent ); // dimensions NCERRX( ncmpi_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR ); NCERRX( ncmpi_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR ); - NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim), - NC_CELL_SPATIAL_STR ); - NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_dim), - NC_CELL_ANGULAR_STR ); + NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim), NC_CELL_SPATIAL_STR ); + NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_dim), NC_CELL_ANGULAR_STR ); NCERRX( ncmpi_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR ); for (int i = 0; i < n_perat; i++) { @@ -312,48 +296,37 @@ void DumpNetCDFMPIIO::openfile() char dimstr[1024]; if (dims == 3) { strcpy(dimstr, NC_SPATIAL_STR); - } - else if (dims == 6) { + } else if (dims == 6) { strcpy(dimstr, NC_VOIGT_STR); - } - else { + } else { sprintf(dimstr, "vec%i", dims); } if (dims != 1) { - NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dims]), - dimstr ); + NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dims]), dimstr ); } } } // default variables - NCERRX( ncmpi_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var), - NC_SPATIAL_STR ); - NCERRX( ncmpi_inq_varid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_var), - NC_CELL_SPATIAL_STR); - NCERRX( ncmpi_inq_varid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_var), - NC_CELL_ANGULAR_STR); + NCERRX( ncmpi_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var), NC_SPATIAL_STR ); + NCERRX( ncmpi_inq_varid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_var), NC_CELL_SPATIAL_STR); + NCERRX( ncmpi_inq_varid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_var), NC_CELL_ANGULAR_STR); NCERRX( ncmpi_inq_varid(ncid, NC_TIME_STR, &time_var), NC_TIME_STR ); - NCERRX( ncmpi_inq_varid(ncid, NC_CELL_ORIGIN_STR, &cell_origin_var), - NC_CELL_ORIGIN_STR ); - NCERRX( ncmpi_inq_varid(ncid, NC_CELL_LENGTHS_STR, &cell_lengths_var), - NC_CELL_LENGTHS_STR); - NCERRX( ncmpi_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var), - NC_CELL_ANGLES_STR); + NCERRX( ncmpi_inq_varid(ncid, NC_CELL_ORIGIN_STR, &cell_origin_var), NC_CELL_ORIGIN_STR ); + NCERRX( ncmpi_inq_varid(ncid, NC_CELL_LENGTHS_STR, &cell_lengths_var), NC_CELL_LENGTHS_STR); + NCERRX( ncmpi_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var), NC_CELL_ANGLES_STR); // variables specified in the input file for (int i = 0; i < n_perat; i++) { - NCERRX( ncmpi_inq_varid(ncid, perat[i].name, &perat[i].var), - perat[i].name ); + NCERRX( ncmpi_inq_varid(ncid, perat[i].name, &perat[i].var), perat[i].name ); } // perframe variables if (thermo) { Thermo *th = output->thermo; for (int i = 0; i < th->nfield; i++) { - NCERRX( ncmpi_inq_varid(ncid, th->keyword[i], &thermovar[i]), - th->keyword[i] ); + NCERRX( ncmpi_inq_varid(ncid, th->keyword[i], &thermovar[i]), th->keyword[i] ); } } @@ -374,20 +347,14 @@ void DumpNetCDFMPIIO::openfile() if (singlefile_opened) return; singlefile_opened = 1; - NCERRX( ncmpi_create(world, filecurrent, NC_64BIT_DATA, - MPI_INFO_NULL, &ncid), filecurrent ); + NCERRX( ncmpi_create(world, filecurrent, NC_64BIT_DATA, MPI_INFO_NULL, &ncid), filecurrent ); // dimensions - NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim), - NC_FRAME_STR ); - NCERRX( ncmpi_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim), - NC_ATOM_STR ); - NCERRX( ncmpi_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim), - NC_CELL_SPATIAL_STR ); - NCERRX( ncmpi_def_dim(ncid, NC_CELL_ANGULAR_STR, 3, &cell_angular_dim), - NC_CELL_ANGULAR_STR ); - NCERRX( ncmpi_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), - NC_LABEL_STR ); + NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim), NC_FRAME_STR ); + NCERRX( ncmpi_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim), NC_ATOM_STR ); + NCERRX( ncmpi_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim), NC_CELL_SPATIAL_STR ); + NCERRX( ncmpi_def_dim(ncid, NC_CELL_ANGULAR_STR, 3, &cell_angular_dim), NC_CELL_ANGULAR_STR ); + NCERRX( ncmpi_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), NC_LABEL_STR ); for (int i = 0; i < n_perat; i++) { int dims = perat[i].dims; @@ -395,44 +362,34 @@ void DumpNetCDFMPIIO::openfile() char dimstr[1024]; if (dims == 3) { strcpy(dimstr, NC_SPATIAL_STR); - } - else if (dims == 6) { + } else if (dims == 6) { strcpy(dimstr, NC_VOIGT_STR); - } - else { + } else { sprintf(dimstr, "vec%i", dims); } if (dims != 1) { - NCERRX( ncmpi_def_dim(ncid, dimstr, dims, &vector_dim[dims]), - dimstr ); + NCERRX( ncmpi_def_dim(ncid, dimstr, dims, &vector_dim[dims]), dimstr ); } } } // default variables dims[0] = vector_dim[3]; - NCERRX( ncmpi_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var), - NC_SPATIAL_STR ); - NCERRX( ncmpi_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims, - &cell_spatial_var), NC_CELL_SPATIAL_STR ); + NCERRX( ncmpi_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var), NC_SPATIAL_STR ); + NCERRX( ncmpi_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims, &cell_spatial_var), NC_CELL_SPATIAL_STR ); dims[0] = vector_dim[3]; dims[1] = label_dim; - NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, - &cell_angular_var), NC_CELL_ANGULAR_STR ); + NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, &cell_angular_var), NC_CELL_ANGULAR_STR ); dims[0] = frame_dim; - NCERRX( ncmpi_def_var(ncid, NC_TIME_STR, NC_DOUBLE, 1, dims, &time_var), - NC_TIME_STR); + NCERRX( ncmpi_def_var(ncid, NC_TIME_STR, NC_DOUBLE, 1, dims, &time_var), NC_TIME_STR); dims[0] = frame_dim; dims[1] = cell_spatial_dim; - NCERRX( ncmpi_def_var(ncid, NC_CELL_ORIGIN_STR, NC_DOUBLE, 2, dims, - &cell_origin_var), NC_CELL_ORIGIN_STR ); - NCERRX( ncmpi_def_var(ncid, NC_CELL_LENGTHS_STR, NC_DOUBLE, 2, dims, - &cell_lengths_var), NC_CELL_LENGTHS_STR ); + NCERRX( ncmpi_def_var(ncid, NC_CELL_ORIGIN_STR, NC_DOUBLE, 2, dims, &cell_origin_var), NC_CELL_ORIGIN_STR ); + NCERRX( ncmpi_def_var(ncid, NC_CELL_LENGTHS_STR, NC_DOUBLE, 2, dims, &cell_lengths_var), NC_CELL_LENGTHS_STR ); dims[0] = frame_dim; dims[1] = cell_angular_dim; - NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGLES_STR, NC_DOUBLE, 2, dims, - &cell_angles_var), NC_CELL_ANGLES_STR ); + NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGLES_STR, NC_DOUBLE, 2, dims, &cell_angles_var), NC_CELL_ANGLES_STR ); // variables specified in the input file dims[0] = frame_dim; @@ -443,9 +400,9 @@ void DumpNetCDFMPIIO::openfile() nc_type xtype; // Type mangling - if (vtype[perat[i].field[0]] == DUMP_INT) { + if (vtype[perat[i].field[0]] == Dump::INT) { xtype = NC_INT; - } else if (vtype[perat[i].field[0]] == DUMP_BIGINT) { + } else if (vtype[perat[i].field[0]] == Dump::BIGINT) { xtype = NC_INT64; } else { if (double_precision) @@ -455,14 +412,11 @@ void DumpNetCDFMPIIO::openfile() } if (perat[i].dims == 1) { - NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 2, dims, - &perat[i].var), perat[i].name ); - } - else { + NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 2, dims, &perat[i].var), perat[i].name ); + } else { // this is a vector dims[2] = vector_dim[perat[i].dims]; - NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims, - &perat[i].var), perat[i].name ); + NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims, &perat[i].var), perat[i].name ); } } @@ -470,104 +424,64 @@ void DumpNetCDFMPIIO::openfile() if (thermo) { Thermo *th = output->thermo; for (int i = 0; i < th->nfield; i++) { - if (th->vtype[i] == THERMO_FLOAT) { - NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims, - &thermovar[i]), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_INT) { - NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_INT, 1, dims, - &thermovar[i]), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_BIGINT) { + if (th->vtype[i] == Thermo::FLOAT) { + NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims, &thermovar[i]), th->keyword[i] ); + } else if (th->vtype[i] == Thermo::INT) { + NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_INT, 1, dims, &thermovar[i]), th->keyword[i] ); + } else if (th->vtype[i] == Thermo::BIGINT) { #if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG) - NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_INT64, 1, dims, - &thermovar[i]), th->keyword[i] ); + NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_INT64, 1, dims, &thermovar[i]), th->keyword[i] ); #else - NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_LONG, 1, dims, - &thermovar[i]), th->keyword[i] ); + NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_LONG, 1, dims, &thermovar[i]), th->keyword[i] ); #endif } } } // attributes - NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "Conventions", - 5, "AMBER") ); - NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "ConventionVersion", - 3, "1.0") ); + NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "Conventions", 5, "AMBER") ); + NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "ConventionVersion", 3, "1.0") ); - NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "program", - 6, "LAMMPS") ); - NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "programVersion", - strlen(lmp->version), lmp->version) ); + NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "program", 6, "LAMMPS") ); + NCERR( ncmpi_put_att_text(ncid, NC_GLOBAL, "programVersion", strlen(lmp->version), lmp->version) ); // units if (!strcmp(update->unit_style, "lj")) { - NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, - 2, "lj") ); - NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 2, "lj") ); - NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 2, "lj") ); - } - else if (!strcmp(update->unit_style, "real")) { - NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, - 11, "femtosecond") ); - NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 8, "Angstrom") ); - NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 8, "Angstrom") ); - } - else if (!strcmp(update->unit_style, "metal")) { - NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, - 10, "picosecond") ); - NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 8, "Angstrom") ); - NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 8, "Angstrom") ); - } - else if (!strcmp(update->unit_style, "si")) { - NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, - 6, "second") ); - NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 5, "meter") ); - NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 5, "meter") ); - } - else if (!strcmp(update->unit_style, "cgs")) { - NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, - 6, "second") ); - NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 10, "centimeter") ); - NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 10, "centimeter") ); - } - else if (!strcmp(update->unit_style, "electron")) { - NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, - 11, "femtosecond") ); - NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, - 4, "Bohr") ); - NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, - 4, "Bohr") ); - } - else { - char errstr[1024]; - sprintf(errstr, "Unsupported unit style '%s'", update->unit_style); - error->all(FLERR,errstr); + NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, 2, "lj") ); + NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 2, "lj") ); + NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 2, "lj") ); + } else if (!strcmp(update->unit_style, "real")) { + NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, 11, "femtosecond") ); + NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 8, "Angstrom") ); + NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 8, "Angstrom") ); + } else if (!strcmp(update->unit_style, "metal")) { + NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, 10, "picosecond") ); + NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 8, "Angstrom") ); + NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 8, "Angstrom") ); + } else if (!strcmp(update->unit_style, "si")) { + NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, 6, "second") ); + NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 5, "meter") ); + NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 5, "meter") ); + } else if (!strcmp(update->unit_style, "cgs")) { + NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, 6, "second") ); + NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 10, "centimeter") ); + NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 10, "centimeter") ); + } else if (!strcmp(update->unit_style, "electron")) { + NCERR( ncmpi_put_att_text(ncid, time_var, NC_UNITS_STR, 11, "femtosecond") ); + NCERR( ncmpi_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 4, "Bohr") ); + NCERR( ncmpi_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 4, "Bohr") ); + } else { + error->all(FLERR,"Unsupported unit style: {}", update->unit_style); } - NCERR( ncmpi_put_att_text(ncid, cell_angles_var, NC_UNITS_STR, - 6, "degree") ); + NCERR( ncmpi_put_att_text(ncid, cell_angles_var, NC_UNITS_STR, 6, "degree") ); d[0] = update->dt; - NCERR( ncmpi_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR, - NC_DOUBLE, 1, d) ); + NCERR( ncmpi_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR, NC_DOUBLE, 1, d) ); d[0] = 1.0; - NCERR( ncmpi_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR, - NC_DOUBLE, 1, d) ); + NCERR( ncmpi_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR, NC_DOUBLE, 1, d) ); d[0] = 1.0; - NCERR( ncmpi_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR, - NC_DOUBLE, 1, d) ); + NCERR( ncmpi_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR, NC_DOUBLE, 1, d) ); /* * Finished with definition @@ -628,23 +542,21 @@ void DumpNetCDFMPIIO::closefile() /* ---------------------------------------------------------------------- */ template -int ncmpi_put_var1_bigint(int ncid, int varid, const MPI_Offset index[], - const T* tp) +int ncmpi_put_var1_bigint(int ncid, int varid, const MPI_Offset index[], const T* tp) { return ncmpi_put_var1_int(ncid, varid, index, tp); } template <> -int ncmpi_put_var1_bigint(int ncid, int varid, const MPI_Offset index[], - const long* tp) +int ncmpi_put_var1_bigint(int ncid, int varid, + const MPI_Offset index[], const long* tp) { return ncmpi_put_var1_long(ncid, varid, index, tp); } template <> int ncmpi_put_var1_bigint(int ncid, int varid, - const MPI_Offset index[], - const long long* tp) + const MPI_Offset index[], const long long* tp) { return ncmpi_put_var1_longlong(ncid, varid, index, tp); } @@ -657,45 +569,36 @@ int ncmpi_put_vara_bigint_all(int ncid, int varid, const MPI_Offset start[], } template <> -int ncmpi_put_vara_bigint_all(int ncid, int varid, - const MPI_Offset start[], +int ncmpi_put_vara_bigint_all(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const long* tp) { return ncmpi_put_vara_long_all(ncid, varid, start, count, tp); } template <> -int ncmpi_put_vara_bigint_all(int ncid, int varid, - const MPI_Offset start[], - const MPI_Offset count[], - const long long* tp) +int ncmpi_put_vara_bigint_all(int ncid, int varid, const MPI_Offset start[], + const MPI_Offset count[], const long long* tp) { return ncmpi_put_vara_longlong_all(ncid, varid, start, count, tp); } template int ncmpi_put_vars_bigint_all(int ncid, int varid, const MPI_Offset start[], - const MPI_Offset count[], - const MPI_Offset stride[], const T* tp) + const MPI_Offset count[], const MPI_Offset stride[], const T* tp) { return ncmpi_put_vars_int_all(ncid, varid, start, count, stride, tp); } template <> -int ncmpi_put_vars_bigint_all(int ncid, int varid, - const MPI_Offset start[], - const MPI_Offset count[], +int ncmpi_put_vars_bigint_all(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const long* tp) { return ncmpi_put_vars_long_all(ncid, varid, start, count, stride, tp); } template <> -int ncmpi_put_vars_bigint_all(int ncid, int varid, - const MPI_Offset start[], - const MPI_Offset count[], - const MPI_Offset stride[], - const long long* tp) +int ncmpi_put_vars_bigint_all(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], + const MPI_Offset stride[], const long long* tp) { return ncmpi_put_vars_longlong_all(ncid, varid, start, count, stride, tp); } @@ -723,16 +626,14 @@ void DumpNetCDFMPIIO::write() for (int i = 0; i < th->nfield; i++) { th->call_vfunc(i); if (filewriter) { - if (th->vtype[i] == THERMO_FLOAT) { + if (th->vtype[i] == Thermo::FLOAT) { NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start, &th->dvalue), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_INT) { + } else if (th->vtype[i] == Thermo::INT) { NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &th->ivalue), th->keyword[i] ); - } - else if (th->vtype[i] == THERMO_BIGINT) { + } else if (th->vtype[i] == Thermo::BIGINT) { NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue), th->keyword[i] ); } @@ -753,7 +654,7 @@ void DumpNetCDFMPIIO::write() MPI_Allgather(&nme, 1, MPI_INT, block_sizes, 1, MPI_INT, world); blocki = 0; for (int i = 0; i < comm->me; i++) blocki += block_sizes[i]; - delete [] block_sizes; + delete[] block_sizes; // insure buf is sized for packing and communicating // use nme to insure filewriter proc can receive info from others @@ -805,8 +706,7 @@ void DumpNetCDFMPIIO::write_time_and_cell() cell_angles[0] = 90; cell_angles[1] = 90; cell_angles[2] = 90; - } - else { + } else { double cosalpha, cosbeta, cosgamma; double *h = domain->h; @@ -839,12 +739,9 @@ void DumpNetCDFMPIIO::write_time_and_cell() count[1] = 3; if (filewriter) { NCERR( ncmpi_put_var1_double(ncid, time_var, start, &time) ); - NCERR( ncmpi_put_vara_double(ncid, cell_origin_var, start, count, - cell_origin) ); - NCERR( ncmpi_put_vara_double(ncid, cell_lengths_var, start, count, - cell_lengths) ); - NCERR( ncmpi_put_vara_double(ncid, cell_angles_var, start, count, - cell_angles) ); + NCERR( ncmpi_put_vara_double(ncid, cell_origin_var, start, count, cell_origin) ); + NCERR( ncmpi_put_vara_double(ncid, cell_lengths_var, start, count, cell_lengths) ); + NCERR( ncmpi_put_vara_double(ncid, cell_angles_var, start, count, cell_angles) ); } } @@ -872,8 +769,7 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf) int_buffer = (bigint *) memory->srealloc(int_buffer, n_buffer*sizeof(bigint),"dump::int_buffer"); double_buffer = (double *) - memory->srealloc(double_buffer, n_buffer*sizeof(double), - "dump::double_buffer"); + memory->srealloc(double_buffer, n_buffer*sizeof(double), "dump::double_buffer"); } start[0] = framei-1; @@ -896,14 +792,10 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf) for (int i = 0; i < n_perat; i++) { int iaux = perat[i].field[0]; - if (iaux < 0 || iaux >= size_one) { - char errmsg[1024]; - sprintf(errmsg, "Internal error: name = %s, iaux = %i, " - "size_one = %i", perat[i].name, iaux, size_one); - error->one(FLERR,errmsg); - } + if (iaux < 0 || iaux >= size_one) + error->one(FLERR, "Internal error: name = {}, iaux = {}, size_one = {}", perat[i].name, iaux, size_one); - if (vtype[iaux] == DUMP_INT || vtype[iaux] == DUMP_BIGINT) { + if (vtype[iaux] == Dump::INT || vtype[iaux] == Dump::BIGINT) { // integers if (perat[i].dims > 1) { @@ -911,41 +803,31 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf) iaux = perat[i].field[idim]; if (iaux >= 0) { - if (iaux >= size_one) { - char errmsg[1024]; - sprintf(errmsg, "Internal error: name = %s, iaux = %i, " - "size_one = %i", perat[i].name, iaux, size_one); - error->one(FLERR,errmsg); - } + if (iaux >= size_one) + error->one(FLERR, "Internal error: name = {}, iaux = {}, size_one = {}", perat[i].name, iaux, size_one); - if (vtype[iaux] == DUMP_INT) { + if (vtype[iaux] == Dump::INT) { for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = static_cast(mybuf[iaux]); } - } - else { // DUMP_BIGINT + } else { // Dump::BIGINT for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = static_cast(mybuf[iaux]); } } start[2] = idim; - NCERRX( ncmpi_put_vars_bigint_all(ncid, perat[i].var, start, count, - stride, int_buffer), - perat[i].name ); + NCERRX( ncmpi_put_vars_bigint_all(ncid, perat[i].var, start, count,stride, int_buffer), perat[i].name ); } } - } - else { + } else { for (int j = 0; j < n; j++, iaux+=size_one) { int_buffer[j] = mybuf[iaux]; } - NCERRX( ncmpi_put_vara_bigint_all(ncid, perat[i].var, start, count, - int_buffer), perat[i].name ); + NCERRX( ncmpi_put_vara_bigint_all(ncid, perat[i].var, start, count, int_buffer), perat[i].name ); } - } - else { + } else { // doubles if (perat[i].dims > 1) { @@ -953,12 +835,8 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf) iaux = perat[i].field[idim]; if (iaux >= 0) { - if (iaux >= size_one) { - char errmsg[1024]; - sprintf(errmsg, "Internal error: name = %s, iaux = %i, " - "size_one = %i", perat[i].name, iaux, size_one); - error->one(FLERR,errmsg); - } + if (iaux >= size_one) + error->one(FLERR, "Internal error: name = {}, iaux = {}, size_one = {}", perat[i].name, iaux, size_one); for (int j = 0; j < n; j++, iaux+=size_one) { double_buffer[j] = mybuf[iaux]; @@ -969,8 +847,7 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf) stride, double_buffer), perat[i].name ); } } - } - else { + } else { for (int j = 0; j < n; j++, iaux+=size_one) { double_buffer[j] = mybuf[iaux]; } @@ -993,15 +870,12 @@ int DumpNetCDFMPIIO::modify_param(int narg, char **arg) error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword."); if (strcmp(arg[iarg],"yes") == 0) { double_precision = true; - } - else if (strcmp(arg[iarg],"no") == 0) { + } else if (strcmp(arg[iarg],"no") == 0) { double_precision = false; - } - else error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword."); + } else error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword."); iarg++; return 2; - } - else if (strcmp(arg[iarg],"at") == 0) { + } else if (strcmp(arg[iarg],"at") == 0) { iarg++; if (iarg >= narg) error->all(FLERR,"expected additional arg after 'at' keyword."); @@ -1010,18 +884,15 @@ int DumpNetCDFMPIIO::modify_param(int narg, char **arg) else if (framei < 0) framei--; iarg++; return 2; - } - else if (strcmp(arg[iarg],"thermo") == 0) { + } else if (strcmp(arg[iarg],"thermo") == 0) { iarg++; if (iarg >= narg) error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword."); if (strcmp(arg[iarg],"yes") == 0) { thermo = true; - } - else if (strcmp(arg[iarg],"no") == 0) { + } else if (strcmp(arg[iarg],"no") == 0) { thermo = false; - } - else error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword."); + } else error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword."); iarg++; return 2; } else return 0; @@ -1032,16 +903,10 @@ int DumpNetCDFMPIIO::modify_param(int narg, char **arg) void DumpNetCDFMPIIO::ncerr(int err, const char *descr, int line) { if (err != NC_NOERR) { - char errstr[1024]; - if (descr) { - sprintf(errstr, "NetCDF failed with error '%s' (while accessing '%s') " - " in line %i of %s.", ncmpi_strerror(err), descr, line, __FILE__); - } - else { - sprintf(errstr, "NetCDF failed with error '%s' in line %i of %s.", - ncmpi_strerror(err), line, __FILE__); - } - error->one(FLERR,errstr); + if (descr) error->one(FLERR,"NetCDF failed with error '{}' (while accessing '{}') " + " in line {} of {}.", ncmpi_strerror(err), descr, line, __FILE__); + else error->one(FLERR,"NetCDF failed with error '{}' in line {} of {}.", + ncmpi_strerror(err), line, __FILE__); } } diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/NETCDF/dump_netcdf_mpiio.h similarity index 100% rename from src/USER-NETCDF/dump_netcdf_mpiio.h rename to src/NETCDF/dump_netcdf_mpiio.h diff --git a/src/USER-OMP/Install.sh b/src/OPENMP/Install.sh similarity index 87% rename from src/USER-OMP/Install.sh rename to src/OPENMP/Install.sh index bb4ef6c3aa..1802f068e9 100755 --- a/src/USER-OMP/Install.sh +++ b/src/OPENMP/Install.sh @@ -37,10 +37,12 @@ done for file in *_omp.h; do test $file = thr_omp.h && continue + test $file = reaxff_omp.h && continue dep=${file%_omp.h}.h action $file $dep done +action reaxff_omp.h reaxff_api.h action thr_omp.h action thr_omp.cpp action thr_data.h @@ -52,7 +54,7 @@ if (test $mode = 1) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*OMP[^ \t]* //' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_USER_OMP |' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_OPENMP |' ../Makefile.package fi # need to delete a bunch of dependency files because they @@ -63,7 +65,7 @@ if (test $mode = 1) then rm -f ../Obj_*/$f done - # force rebuild of files with LMP_USER_OMP switch + # force rebuild of files with LMP_OPENMP switch touch ../accelerator_omp.h @@ -81,7 +83,7 @@ elif (test $mode = 0) then rm -f ../Obj_*/$f done - # force rebuild of files with LMP_USER_OMP switch + # force rebuild of files with LMP_OPENMP switch touch ../accelerator_omp.h diff --git a/src/USER-OMP/README b/src/OPENMP/README similarity index 100% rename from src/USER-OMP/README rename to src/OPENMP/README diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/OPENMP/angle_charmm_omp.cpp similarity index 100% rename from src/USER-OMP/angle_charmm_omp.cpp rename to src/OPENMP/angle_charmm_omp.cpp diff --git a/src/USER-OMP/angle_charmm_omp.h b/src/OPENMP/angle_charmm_omp.h similarity index 100% rename from src/USER-OMP/angle_charmm_omp.h rename to src/OPENMP/angle_charmm_omp.h diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/OPENMP/angle_class2_omp.cpp similarity index 100% rename from src/USER-OMP/angle_class2_omp.cpp rename to src/OPENMP/angle_class2_omp.cpp diff --git a/src/USER-OMP/angle_class2_omp.h b/src/OPENMP/angle_class2_omp.h similarity index 100% rename from src/USER-OMP/angle_class2_omp.h rename to src/OPENMP/angle_class2_omp.h diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/OPENMP/angle_cosine_delta_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_delta_omp.cpp rename to src/OPENMP/angle_cosine_delta_omp.cpp diff --git a/src/USER-OMP/angle_cosine_delta_omp.h b/src/OPENMP/angle_cosine_delta_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_delta_omp.h rename to src/OPENMP/angle_cosine_delta_omp.h diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/OPENMP/angle_cosine_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_omp.cpp rename to src/OPENMP/angle_cosine_omp.cpp diff --git a/src/USER-OMP/angle_cosine_omp.h b/src/OPENMP/angle_cosine_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_omp.h rename to src/OPENMP/angle_cosine_omp.h diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/OPENMP/angle_cosine_periodic_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_periodic_omp.cpp rename to src/OPENMP/angle_cosine_periodic_omp.cpp diff --git a/src/USER-OMP/angle_cosine_periodic_omp.h b/src/OPENMP/angle_cosine_periodic_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_periodic_omp.h rename to src/OPENMP/angle_cosine_periodic_omp.h diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/OPENMP/angle_cosine_shift_exp_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_shift_exp_omp.cpp rename to src/OPENMP/angle_cosine_shift_exp_omp.cpp diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.h b/src/OPENMP/angle_cosine_shift_exp_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_shift_exp_omp.h rename to src/OPENMP/angle_cosine_shift_exp_omp.h diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/OPENMP/angle_cosine_shift_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_shift_omp.cpp rename to src/OPENMP/angle_cosine_shift_omp.cpp diff --git a/src/USER-OMP/angle_cosine_shift_omp.h b/src/OPENMP/angle_cosine_shift_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_shift_omp.h rename to src/OPENMP/angle_cosine_shift_omp.h diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/OPENMP/angle_cosine_squared_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_squared_omp.cpp rename to src/OPENMP/angle_cosine_squared_omp.cpp diff --git a/src/USER-OMP/angle_cosine_squared_omp.h b/src/OPENMP/angle_cosine_squared_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_squared_omp.h rename to src/OPENMP/angle_cosine_squared_omp.h diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/OPENMP/angle_dipole_omp.cpp similarity index 100% rename from src/USER-OMP/angle_dipole_omp.cpp rename to src/OPENMP/angle_dipole_omp.cpp diff --git a/src/USER-OMP/angle_dipole_omp.h b/src/OPENMP/angle_dipole_omp.h similarity index 100% rename from src/USER-OMP/angle_dipole_omp.h rename to src/OPENMP/angle_dipole_omp.h diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/OPENMP/angle_fourier_omp.cpp similarity index 100% rename from src/USER-OMP/angle_fourier_omp.cpp rename to src/OPENMP/angle_fourier_omp.cpp diff --git a/src/USER-OMP/angle_fourier_omp.h b/src/OPENMP/angle_fourier_omp.h similarity index 100% rename from src/USER-OMP/angle_fourier_omp.h rename to src/OPENMP/angle_fourier_omp.h diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/OPENMP/angle_fourier_simple_omp.cpp similarity index 59% rename from src/USER-OMP/angle_fourier_simple_omp.cpp rename to src/OPENMP/angle_fourier_simple_omp.cpp index b6318f306b..670f8cfc83 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/OPENMP/angle_fourier_simple_omp.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -16,24 +15,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "angle_fourier_simple_omp.h" -#include + #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" +#include +#include "omp_compat.h" #include "suffix.h" using namespace LAMMPS_NS; -#define SMALL 0.001 +#define SMALL 0.0001 /* ---------------------------------------------------------------------- */ -AngleFourierSimpleOMP::AngleFourierSimpleOMP(class LAMMPS *lmp) - : AngleFourierSimple(lmp), ThrOMP(lmp,THR_ANGLE) +AngleFourierSimpleOMP::AngleFourierSimpleOMP(class LAMMPS *lmp) : + AngleFourierSimple(lmp), ThrOMP(lmp, THR_ANGLE) { suffix_flag |= Suffix::OMP; } @@ -42,14 +42,14 @@ AngleFourierSimpleOMP::AngleFourierSimpleOMP(class LAMMPS *lmp) void AngleFourierSimpleOMP::compute(int eflag, int vflag) { - ev_init(eflag,vflag); + ev_init(eflag, vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; const int inum = neighbor->nanglelist; #if defined(_OPENMP) -#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag) #endif { int ifrom, ito, tid; @@ -62,34 +62,40 @@ void AngleFourierSimpleOMP::compute(int eflag, int vflag) if (inum > 0) { if (evflag) { if (eflag) { - if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr); - else eval<1,1,0>(ifrom, ito, thr); + if (force->newton_bond) + eval<1, 1, 1>(ifrom, ito, thr); + else + eval<1, 1, 0>(ifrom, ito, thr); } else { - if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr); - else eval<1,0,0>(ifrom, ito, thr); + if (force->newton_bond) + eval<1, 0, 1>(ifrom, ito, thr); + else + eval<1, 0, 0>(ifrom, ito, thr); } } else { - if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr); - else eval<0,0,0>(ifrom, ito, thr); + if (force->newton_bond) + eval<0, 0, 1>(ifrom, ito, thr); + else + eval<0, 0, 0>(ifrom, ito, thr); } } thr->timer(Timer::BOND); reduce_thr(this, eflag, vflag, thr); - } // end of omp parallel region + } // end of omp parallel region } template -void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr) +void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData *const thr) { - int i1,i2,i3,n,type; - double delx1,dely1,delz1,delx2,dely2,delz2; - double eangle,f1[3],f3[3]; - double term,sgn; - double rsq1,rsq2,r1,r2,c,cn,th,nth,a,a11,a12,a22; + int i1, i2, i3, n, type; + double delx1, dely1, delz1, delx2, dely2, delz2; + double eangle, f1[3], f3[3]; + double term, sgn; + double rsq1, rsq2, r1, r2, c, cn, th, nth, a, a11, a12, a22; - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; - dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0]; - const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0]; + const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0]; + dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0]; + const int4_t *_noalias const anglelist = (int4_t *) neighbor->anglelist[0]; const int nlocal = atom->nlocal; eangle = 0.0; @@ -105,7 +111,7 @@ void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr) dely1 = x[i1].y - x[i2].y; delz1 = x[i1].z - x[i2].z; - rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1; r1 = sqrt(rsq1); // 2nd bond @@ -114,13 +120,13 @@ void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr) dely2 = x[i3].y - x[i2].y; delz2 = x[i3].z - x[i2].z; - rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2; r2 = sqrt(rsq2); // angle (cos and sin) - c = delx1*delx2 + dely1*dely2 + delz1*delz2; - c /= r1*r2; + c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; @@ -128,38 +134,38 @@ void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr) // force & energy th = acos(c); - nth = N[type]*acos(c); + nth = N[type] * acos(c); cn = cos(nth); - term = k[type]*(1.0+C[type]*cn); + term = k[type] * (1.0 + C[type] * cn); if (EFLAG) eangle = term; // handle sin(n th)/sin(th) singulatiries - if (fabs(c)-1.0 > 0.0001) { - a = k[type]*C[type]*N[type]*sin(nth)/sin(th); + if (fabs(c) - 1.0 > SMALL) { + a = k[type] * C[type] * N[type] * sin(nth) / sin(th); } else { if (c >= 0.0) { term = 1.0 - c; sgn = 1.0; } else { term = 1.0 + c; - sgn = ( fmodf((float)(N[type]),2.0) == 0.0f )?-1.0:1.0; + sgn = (fmod(N[type], 2.0) == 0.0) ? -1.0 : 1.0; } - a = N[type]+N[type]*(1.0-N[type]*N[type])*term/3.0; - a = k[type]*C[type]*N[type]*(double)(sgn)*a; + a = N[type] + N[type] * (1.0 - N[type] * N[type]) * term / 3.0; + a = k[type] * C[type] * N[type] * sgn * a; } - a11 = a*c / rsq1; - a12 = -a / (r1*r2); - a22 = a*c / rsq2; + a11 = a * c / rsq1; + a12 = -a / (r1 * r2); + a22 = a * c / rsq2; - f1[0] = a11*delx1 + a12*delx2; - f1[1] = a11*dely1 + a12*dely2; - f1[2] = a11*delz1 + a12*delz2; - f3[0] = a22*delx2 + a12*delx1; - f3[1] = a22*dely2 + a12*dely1; - f3[2] = a22*delz2 + a12*delz1; + f1[0] = a11 * delx1 + a12 * delx2; + f1[1] = a11 * dely1 + a12 * dely2; + f1[2] = a11 * delz1 + a12 * delz2; + f3[0] = a22 * delx2 + a12 * delx1; + f3[1] = a22 * dely2 + a12 * dely1; + f3[2] = a22 * delz2 + a12 * delz1; // apply force to each of 3 atoms @@ -181,7 +187,8 @@ void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr) f[i3].z += f3[2]; } - if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3, - delx1,dely1,delz1,delx2,dely2,delz2,thr); + if (EVFLAG) + ev_tally_thr(this, i1, i2, i3, nlocal, NEWTON_BOND, eangle, f1, f3, delx1, dely1, delz1, + delx2, dely2, delz2, thr); } } diff --git a/src/USER-OMP/angle_fourier_simple_omp.h b/src/OPENMP/angle_fourier_simple_omp.h similarity index 100% rename from src/USER-OMP/angle_fourier_simple_omp.h rename to src/OPENMP/angle_fourier_simple_omp.h diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/OPENMP/angle_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/angle_harmonic_omp.cpp rename to src/OPENMP/angle_harmonic_omp.cpp diff --git a/src/USER-OMP/angle_harmonic_omp.h b/src/OPENMP/angle_harmonic_omp.h similarity index 100% rename from src/USER-OMP/angle_harmonic_omp.h rename to src/OPENMP/angle_harmonic_omp.h diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/OPENMP/angle_quartic_omp.cpp similarity index 100% rename from src/USER-OMP/angle_quartic_omp.cpp rename to src/OPENMP/angle_quartic_omp.cpp diff --git a/src/USER-OMP/angle_quartic_omp.h b/src/OPENMP/angle_quartic_omp.h similarity index 100% rename from src/USER-OMP/angle_quartic_omp.h rename to src/OPENMP/angle_quartic_omp.h diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/OPENMP/angle_sdk_omp.cpp similarity index 100% rename from src/USER-OMP/angle_sdk_omp.cpp rename to src/OPENMP/angle_sdk_omp.cpp diff --git a/src/USER-OMP/angle_sdk_omp.h b/src/OPENMP/angle_sdk_omp.h similarity index 100% rename from src/USER-OMP/angle_sdk_omp.h rename to src/OPENMP/angle_sdk_omp.h diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/OPENMP/angle_table_omp.cpp similarity index 100% rename from src/USER-OMP/angle_table_omp.cpp rename to src/OPENMP/angle_table_omp.cpp diff --git a/src/USER-OMP/angle_table_omp.h b/src/OPENMP/angle_table_omp.h similarity index 100% rename from src/USER-OMP/angle_table_omp.h rename to src/OPENMP/angle_table_omp.h diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/OPENMP/bond_class2_omp.cpp similarity index 100% rename from src/USER-OMP/bond_class2_omp.cpp rename to src/OPENMP/bond_class2_omp.cpp diff --git a/src/USER-OMP/bond_class2_omp.h b/src/OPENMP/bond_class2_omp.h similarity index 100% rename from src/USER-OMP/bond_class2_omp.h rename to src/OPENMP/bond_class2_omp.h diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/OPENMP/bond_fene_expand_omp.cpp similarity index 100% rename from src/USER-OMP/bond_fene_expand_omp.cpp rename to src/OPENMP/bond_fene_expand_omp.cpp diff --git a/src/USER-OMP/bond_fene_expand_omp.h b/src/OPENMP/bond_fene_expand_omp.h similarity index 100% rename from src/USER-OMP/bond_fene_expand_omp.h rename to src/OPENMP/bond_fene_expand_omp.h diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/OPENMP/bond_fene_omp.cpp similarity index 100% rename from src/USER-OMP/bond_fene_omp.cpp rename to src/OPENMP/bond_fene_omp.cpp diff --git a/src/USER-OMP/bond_fene_omp.h b/src/OPENMP/bond_fene_omp.h similarity index 100% rename from src/USER-OMP/bond_fene_omp.h rename to src/OPENMP/bond_fene_omp.h diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/OPENMP/bond_gromos_omp.cpp similarity index 100% rename from src/USER-OMP/bond_gromos_omp.cpp rename to src/OPENMP/bond_gromos_omp.cpp diff --git a/src/USER-OMP/bond_gromos_omp.h b/src/OPENMP/bond_gromos_omp.h similarity index 100% rename from src/USER-OMP/bond_gromos_omp.h rename to src/OPENMP/bond_gromos_omp.h diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/OPENMP/bond_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/bond_harmonic_omp.cpp rename to src/OPENMP/bond_harmonic_omp.cpp diff --git a/src/USER-OMP/bond_harmonic_omp.h b/src/OPENMP/bond_harmonic_omp.h similarity index 100% rename from src/USER-OMP/bond_harmonic_omp.h rename to src/OPENMP/bond_harmonic_omp.h diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/OPENMP/bond_harmonic_shift_cut_omp.cpp similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_cut_omp.cpp rename to src/OPENMP/bond_harmonic_shift_cut_omp.cpp diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.h b/src/OPENMP/bond_harmonic_shift_cut_omp.h similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_cut_omp.h rename to src/OPENMP/bond_harmonic_shift_cut_omp.h diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/OPENMP/bond_harmonic_shift_omp.cpp similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_omp.cpp rename to src/OPENMP/bond_harmonic_shift_omp.cpp diff --git a/src/USER-OMP/bond_harmonic_shift_omp.h b/src/OPENMP/bond_harmonic_shift_omp.h similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_omp.h rename to src/OPENMP/bond_harmonic_shift_omp.h diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/OPENMP/bond_morse_omp.cpp similarity index 100% rename from src/USER-OMP/bond_morse_omp.cpp rename to src/OPENMP/bond_morse_omp.cpp diff --git a/src/USER-OMP/bond_morse_omp.h b/src/OPENMP/bond_morse_omp.h similarity index 100% rename from src/USER-OMP/bond_morse_omp.h rename to src/OPENMP/bond_morse_omp.h diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/OPENMP/bond_nonlinear_omp.cpp similarity index 100% rename from src/USER-OMP/bond_nonlinear_omp.cpp rename to src/OPENMP/bond_nonlinear_omp.cpp diff --git a/src/USER-OMP/bond_nonlinear_omp.h b/src/OPENMP/bond_nonlinear_omp.h similarity index 100% rename from src/USER-OMP/bond_nonlinear_omp.h rename to src/OPENMP/bond_nonlinear_omp.h diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/OPENMP/bond_quartic_omp.cpp similarity index 100% rename from src/USER-OMP/bond_quartic_omp.cpp rename to src/OPENMP/bond_quartic_omp.cpp diff --git a/src/USER-OMP/bond_quartic_omp.h b/src/OPENMP/bond_quartic_omp.h similarity index 100% rename from src/USER-OMP/bond_quartic_omp.h rename to src/OPENMP/bond_quartic_omp.h diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/OPENMP/bond_table_omp.cpp similarity index 100% rename from src/USER-OMP/bond_table_omp.cpp rename to src/OPENMP/bond_table_omp.cpp diff --git a/src/USER-OMP/bond_table_omp.h b/src/OPENMP/bond_table_omp.h similarity index 100% rename from src/USER-OMP/bond_table_omp.h rename to src/OPENMP/bond_table_omp.h diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/OPENMP/dihedral_charmm_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_charmm_omp.cpp rename to src/OPENMP/dihedral_charmm_omp.cpp diff --git a/src/USER-OMP/dihedral_charmm_omp.h b/src/OPENMP/dihedral_charmm_omp.h similarity index 100% rename from src/USER-OMP/dihedral_charmm_omp.h rename to src/OPENMP/dihedral_charmm_omp.h diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/OPENMP/dihedral_class2_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_class2_omp.cpp rename to src/OPENMP/dihedral_class2_omp.cpp diff --git a/src/USER-OMP/dihedral_class2_omp.h b/src/OPENMP/dihedral_class2_omp.h similarity index 100% rename from src/USER-OMP/dihedral_class2_omp.h rename to src/OPENMP/dihedral_class2_omp.h diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/OPENMP/dihedral_cosine_shift_exp_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp rename to src/OPENMP/dihedral_cosine_shift_exp_omp.cpp diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.h b/src/OPENMP/dihedral_cosine_shift_exp_omp.h similarity index 100% rename from src/USER-OMP/dihedral_cosine_shift_exp_omp.h rename to src/OPENMP/dihedral_cosine_shift_exp_omp.h diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/OPENMP/dihedral_fourier_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_fourier_omp.cpp rename to src/OPENMP/dihedral_fourier_omp.cpp diff --git a/src/USER-OMP/dihedral_fourier_omp.h b/src/OPENMP/dihedral_fourier_omp.h similarity index 100% rename from src/USER-OMP/dihedral_fourier_omp.h rename to src/OPENMP/dihedral_fourier_omp.h diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/OPENMP/dihedral_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_harmonic_omp.cpp rename to src/OPENMP/dihedral_harmonic_omp.cpp diff --git a/src/USER-OMP/dihedral_harmonic_omp.h b/src/OPENMP/dihedral_harmonic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_harmonic_omp.h rename to src/OPENMP/dihedral_harmonic_omp.h diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/OPENMP/dihedral_helix_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_helix_omp.cpp rename to src/OPENMP/dihedral_helix_omp.cpp diff --git a/src/USER-OMP/dihedral_helix_omp.h b/src/OPENMP/dihedral_helix_omp.h similarity index 100% rename from src/USER-OMP/dihedral_helix_omp.h rename to src/OPENMP/dihedral_helix_omp.h diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/OPENMP/dihedral_multi_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_multi_harmonic_omp.cpp rename to src/OPENMP/dihedral_multi_harmonic_omp.cpp diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.h b/src/OPENMP/dihedral_multi_harmonic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_multi_harmonic_omp.h rename to src/OPENMP/dihedral_multi_harmonic_omp.h diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/OPENMP/dihedral_nharmonic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_nharmonic_omp.cpp rename to src/OPENMP/dihedral_nharmonic_omp.cpp diff --git a/src/USER-OMP/dihedral_nharmonic_omp.h b/src/OPENMP/dihedral_nharmonic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_nharmonic_omp.h rename to src/OPENMP/dihedral_nharmonic_omp.h diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/OPENMP/dihedral_opls_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_opls_omp.cpp rename to src/OPENMP/dihedral_opls_omp.cpp diff --git a/src/USER-OMP/dihedral_opls_omp.h b/src/OPENMP/dihedral_opls_omp.h similarity index 100% rename from src/USER-OMP/dihedral_opls_omp.h rename to src/OPENMP/dihedral_opls_omp.h diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/OPENMP/dihedral_quadratic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_quadratic_omp.cpp rename to src/OPENMP/dihedral_quadratic_omp.cpp diff --git a/src/USER-OMP/dihedral_quadratic_omp.h b/src/OPENMP/dihedral_quadratic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_quadratic_omp.h rename to src/OPENMP/dihedral_quadratic_omp.h diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/OPENMP/dihedral_table_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_table_omp.cpp rename to src/OPENMP/dihedral_table_omp.cpp diff --git a/src/USER-OMP/dihedral_table_omp.h b/src/OPENMP/dihedral_table_omp.h similarity index 100% rename from src/USER-OMP/dihedral_table_omp.h rename to src/OPENMP/dihedral_table_omp.h diff --git a/src/USER-OMP/domain_omp.cpp b/src/OPENMP/domain_omp.cpp similarity index 100% rename from src/USER-OMP/domain_omp.cpp rename to src/OPENMP/domain_omp.cpp diff --git a/src/USER-OMP/ewald_omp.cpp b/src/OPENMP/ewald_omp.cpp similarity index 100% rename from src/USER-OMP/ewald_omp.cpp rename to src/OPENMP/ewald_omp.cpp diff --git a/src/USER-OMP/ewald_omp.h b/src/OPENMP/ewald_omp.h similarity index 100% rename from src/USER-OMP/ewald_omp.h rename to src/OPENMP/ewald_omp.h diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/OPENMP/fix_gravity_omp.cpp similarity index 100% rename from src/USER-OMP/fix_gravity_omp.cpp rename to src/OPENMP/fix_gravity_omp.cpp diff --git a/src/USER-OMP/fix_gravity_omp.h b/src/OPENMP/fix_gravity_omp.h similarity index 100% rename from src/USER-OMP/fix_gravity_omp.h rename to src/OPENMP/fix_gravity_omp.h diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/OPENMP/fix_neigh_history_omp.cpp similarity index 100% rename from src/USER-OMP/fix_neigh_history_omp.cpp rename to src/OPENMP/fix_neigh_history_omp.cpp diff --git a/src/USER-OMP/fix_neigh_history_omp.h b/src/OPENMP/fix_neigh_history_omp.h similarity index 100% rename from src/USER-OMP/fix_neigh_history_omp.h rename to src/OPENMP/fix_neigh_history_omp.h diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/OPENMP/fix_nh_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nh_asphere_omp.cpp rename to src/OPENMP/fix_nh_asphere_omp.cpp diff --git a/src/USER-OMP/fix_nh_asphere_omp.h b/src/OPENMP/fix_nh_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nh_asphere_omp.h rename to src/OPENMP/fix_nh_asphere_omp.h diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/OPENMP/fix_nh_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nh_omp.cpp rename to src/OPENMP/fix_nh_omp.cpp diff --git a/src/USER-OMP/fix_nh_omp.h b/src/OPENMP/fix_nh_omp.h similarity index 100% rename from src/USER-OMP/fix_nh_omp.h rename to src/OPENMP/fix_nh_omp.h diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/OPENMP/fix_nh_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nh_sphere_omp.cpp rename to src/OPENMP/fix_nh_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nh_sphere_omp.h b/src/OPENMP/fix_nh_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nh_sphere_omp.h rename to src/OPENMP/fix_nh_sphere_omp.h diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/OPENMP/fix_nph_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nph_asphere_omp.cpp rename to src/OPENMP/fix_nph_asphere_omp.cpp diff --git a/src/USER-OMP/fix_nph_asphere_omp.h b/src/OPENMP/fix_nph_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nph_asphere_omp.h rename to src/OPENMP/fix_nph_asphere_omp.h diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/OPENMP/fix_nph_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nph_omp.cpp rename to src/OPENMP/fix_nph_omp.cpp diff --git a/src/USER-OMP/fix_nph_omp.h b/src/OPENMP/fix_nph_omp.h similarity index 100% rename from src/USER-OMP/fix_nph_omp.h rename to src/OPENMP/fix_nph_omp.h diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/OPENMP/fix_nph_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nph_sphere_omp.cpp rename to src/OPENMP/fix_nph_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nph_sphere_omp.h b/src/OPENMP/fix_nph_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nph_sphere_omp.h rename to src/OPENMP/fix_nph_sphere_omp.h diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/OPENMP/fix_npt_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_npt_asphere_omp.cpp rename to src/OPENMP/fix_npt_asphere_omp.cpp diff --git a/src/USER-OMP/fix_npt_asphere_omp.h b/src/OPENMP/fix_npt_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_npt_asphere_omp.h rename to src/OPENMP/fix_npt_asphere_omp.h diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/OPENMP/fix_npt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_npt_omp.cpp rename to src/OPENMP/fix_npt_omp.cpp diff --git a/src/USER-OMP/fix_npt_omp.h b/src/OPENMP/fix_npt_omp.h similarity index 100% rename from src/USER-OMP/fix_npt_omp.h rename to src/OPENMP/fix_npt_omp.h diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/OPENMP/fix_npt_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_npt_sphere_omp.cpp rename to src/OPENMP/fix_npt_sphere_omp.cpp diff --git a/src/USER-OMP/fix_npt_sphere_omp.h b/src/OPENMP/fix_npt_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_npt_sphere_omp.h rename to src/OPENMP/fix_npt_sphere_omp.h diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/OPENMP/fix_nve_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nve_omp.cpp rename to src/OPENMP/fix_nve_omp.cpp diff --git a/src/USER-OMP/fix_nve_omp.h b/src/OPENMP/fix_nve_omp.h similarity index 100% rename from src/USER-OMP/fix_nve_omp.h rename to src/OPENMP/fix_nve_omp.h diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/OPENMP/fix_nve_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nve_sphere_omp.cpp rename to src/OPENMP/fix_nve_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nve_sphere_omp.h b/src/OPENMP/fix_nve_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nve_sphere_omp.h rename to src/OPENMP/fix_nve_sphere_omp.h diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/OPENMP/fix_nvt_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_asphere_omp.cpp rename to src/OPENMP/fix_nvt_asphere_omp.cpp diff --git a/src/USER-OMP/fix_nvt_asphere_omp.h b/src/OPENMP/fix_nvt_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_asphere_omp.h rename to src/OPENMP/fix_nvt_asphere_omp.h diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/OPENMP/fix_nvt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_omp.cpp rename to src/OPENMP/fix_nvt_omp.cpp diff --git a/src/USER-OMP/fix_nvt_omp.h b/src/OPENMP/fix_nvt_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_omp.h rename to src/OPENMP/fix_nvt_omp.h diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/OPENMP/fix_nvt_sllod_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_sllod_omp.cpp rename to src/OPENMP/fix_nvt_sllod_omp.cpp diff --git a/src/USER-OMP/fix_nvt_sllod_omp.h b/src/OPENMP/fix_nvt_sllod_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_sllod_omp.h rename to src/OPENMP/fix_nvt_sllod_omp.h diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/OPENMP/fix_nvt_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_sphere_omp.cpp rename to src/OPENMP/fix_nvt_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nvt_sphere_omp.h b/src/OPENMP/fix_nvt_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_sphere_omp.h rename to src/OPENMP/fix_nvt_sphere_omp.h diff --git a/src/USER-OMP/fix_omp.cpp b/src/OPENMP/fix_omp.cpp similarity index 86% rename from src/USER-OMP/fix_omp.cpp rename to src/OPENMP/fix_omp.cpp index eb19c3a2d2..2b7e7eeaf9 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/OPENMP/fix_omp.cpp @@ -112,17 +112,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) #if defined(_OPENMP) const char * const nmode = _neighbor ? "multi-threaded" : "serial"; - if (screen) { - if (reset_thr) - fprintf(screen,"set %d OpenMP thread(s) per MPI task\n", nthreads); - fprintf(screen,"using %s neighbor list subroutines\n", nmode); - } - - if (logfile) { - if (reset_thr) - fprintf(logfile,"set %d OpenMP thread(s) per MPI task\n", nthreads); - fprintf(logfile,"using %s neighbor list subroutines\n", nmode); - } + if (reset_thr) + utils::logmesg(lmp, "set {} OpenMP thread(s) per MPI task\n", nthreads); + utils::logmesg(lmp, "using {} neighbor list subroutines\n", nmode); #else error->warning(FLERR,"OpenMP support not enabled during compilation; " "using 1 thread only."); @@ -170,17 +162,17 @@ int FixOMP::setmask() void FixOMP::init() { - // USER-OMP package cannot be used with atom_style template + // OPENMP package cannot be used with atom_style template if (atom->molecular == Atom::TEMPLATE) - error->all(FLERR,"USER-OMP package does not (yet) work with " + error->all(FLERR,"OPENMP package does not (yet) work with " "atom_style template"); // adjust number of data objects when the number of OpenMP // threads has been changed somehow const int nthreads = comm->nthreads; if (_nthr != nthreads) { - if (screen) fprintf(screen,"Re-init USER-OMP for %d OpenMP thread(s)\n", nthreads); - if (logfile) fprintf(logfile,"Re-init USER-OMP for %d OpenMP thread(s)\n", nthreads); + if (comm->me == 0) + utils::logmesg(lmp,"Re-init OPENMP for {} OpenMP thread(s)\n", nthreads); for (int i=0; i < _nthr; ++i) delete thr[i]; @@ -292,23 +284,11 @@ void FixOMP::init() // diagnostic output if (comm->me == 0) { if (last_omp_style) { - if (last_pair_hybrid) { - if (screen) - fprintf(screen,"Hybrid pair style last /omp style %s\n", last_hybrid_name); - if (logfile) - fprintf(logfile,"Hybrid pair style last /omp style %s\n", last_hybrid_name); - } - if (screen) - fprintf(screen,"Last active /omp style is %s_style %s\n", - last_force_name, last_omp_name); - if (logfile) - fprintf(logfile,"Last active /omp style is %s_style %s\n", - last_force_name, last_omp_name); + if (last_pair_hybrid) + utils::logmesg(lmp,"Hybrid pair style last /omp style {}\n",last_hybrid_name); + utils::logmesg(lmp,"Last active /omp style is {}_style {}\n",last_force_name,last_omp_name); } else { - if (screen) - fprintf(screen,"No /omp style for force computation currently active\n"); - if (logfile) - fprintf(logfile,"No /omp style for force computation currently active\n"); + utils::logmesg(lmp,"No /omp style for force computation currently active\n"); } } } @@ -327,8 +307,8 @@ void FixOMP::set_neighbor_omp() const int neigh_omp = _neighbor ? 1 : 0; const int nrequest = neighbor->nrequest; - // flag *all* neighbor list requests as USER-OMP threaded, - // but skip lists already flagged as USER-INTEL threaded + // flag *all* neighbor list requests as OPENMP threaded, + // but skip lists already flagged as INTEL threaded for (int i = 0; i < nrequest; ++i) if (! neighbor->requests[i]->intel) neighbor->requests[i]->omp = neigh_omp; diff --git a/src/USER-OMP/fix_omp.h b/src/OPENMP/fix_omp.h similarity index 100% rename from src/USER-OMP/fix_omp.h rename to src/OPENMP/fix_omp.h diff --git a/src/USER-OMP/fix_peri_neigh_omp.cpp b/src/OPENMP/fix_peri_neigh_omp.cpp similarity index 100% rename from src/USER-OMP/fix_peri_neigh_omp.cpp rename to src/OPENMP/fix_peri_neigh_omp.cpp diff --git a/src/USER-OMP/fix_peri_neigh_omp.h b/src/OPENMP/fix_peri_neigh_omp.h similarity index 100% rename from src/USER-OMP/fix_peri_neigh_omp.h rename to src/OPENMP/fix_peri_neigh_omp.h diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/OPENMP/fix_qeq_comb_omp.cpp similarity index 99% rename from src/USER-OMP/fix_qeq_comb_omp.cpp rename to src/OPENMP/fix_qeq_comb_omp.cpp index 7dd1bfbb69..900a47bd02 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/OPENMP/fix_qeq_comb_omp.cpp @@ -50,7 +50,7 @@ void FixQEQCombOMP::init() error->all(FLERR,"Fix qeq/comb/omp requires atom attribute q"); if (nullptr != force->pair_match("comb3",0)) - error->all(FLERR,"No support for comb3 currently available in USER-OMP"); + error->all(FLERR,"No support for comb3 currently available in OPENMP"); comb = (PairComb *) force->pair_match("comb/omp",1); if (comb == nullptr) diff --git a/src/USER-OMP/fix_qeq_comb_omp.h b/src/OPENMP/fix_qeq_comb_omp.h similarity index 100% rename from src/USER-OMP/fix_qeq_comb_omp.h rename to src/OPENMP/fix_qeq_comb_omp.h diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/OPENMP/fix_qeq_reaxff_omp.cpp similarity index 73% rename from src/USER-OMP/fix_qeq_reax_omp.cpp rename to src/OPENMP/fix_qeq_reaxff_omp.cpp index 91c61cc946..89b75bfe7a 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/OPENMP/fix_qeq_reaxff_omp.cpp @@ -18,11 +18,11 @@ Hybrid & sub-group capabilities added by Ray Shan (Materials Design) - OpenMP based threading support for fix qeq/reax/omp added + OpenMP based threading support for fix qeq/reaxff/omp added by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF), Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF) - Integration of the pair_style reax/c/omp into the User-OMP package + Integration of the pair_style reaxff/omp into the OPENMP package by Axel Kohlmeyer (Temple U.) Please cite the related publication: @@ -32,18 +32,19 @@ High Performance Computing Applications, to appear. ------------------------------------------------------------------------- */ -#include "fix_qeq_reax_omp.h" +#include "fix_qeq_reaxff_omp.h" -#include -#include "pair_reaxc.h" #include "atom.h" #include "comm.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "update.h" -#include "memory.h" -#include "error.h" -#include "reaxc_defs.h" -#include "reaxc_types.h" + +#include "pair_reaxff.h" +#include "reaxff_defs.h" + +#include #if defined(_OPENMP) #include @@ -52,17 +53,10 @@ using namespace LAMMPS_NS; using namespace FixConst; -#define EV_TO_KCAL_PER_MOL 14.4 -//#define DANGER_ZONE 0.95 -//#define LOOSE_ZONE 0.7 -#define SQR(x) ((x)*(x)) -#define CUBE(x) ((x)*(x)*(x)) -#define MIN_NBRS 100 - /* ---------------------------------------------------------------------- */ -FixQEqReaxOMP::FixQEqReaxOMP(LAMMPS *lmp, int narg, char **arg) : - FixQEqReax(lmp, narg, arg) +FixQEqReaxFFOMP::FixQEqReaxFFOMP(LAMMPS *lmp, int narg, char **arg) : + FixQEqReaxFF(lmp, narg, arg) { b_temp = nullptr; @@ -75,14 +69,14 @@ FixQEqReaxOMP::FixQEqReaxOMP(LAMMPS *lmp, int narg, char **arg) : aspc_b = nullptr; } -FixQEqReaxOMP::~FixQEqReaxOMP() +FixQEqReaxFFOMP::~FixQEqReaxFFOMP() { memory->destroy(b_temp); } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::post_constructor() +void FixQEqReaxFFOMP::post_constructor() { grow_arrays(atom->nmax); for (int i = 0; i < atom->nmax; i++) @@ -94,34 +88,34 @@ void FixQEqReaxOMP::post_constructor() /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::allocate_storage() +void FixQEqReaxFFOMP::allocate_storage() { - FixQEqReax::allocate_storage(); + FixQEqReaxFF::allocate_storage(); // dual CG support int size = nmax; if (dual_enabled) size*= 2; - memory->create(b_temp, comm->nthreads, size, "qeq/reax/omp:b_temp"); + memory->create(b_temp, comm->nthreads, size, "qeq/reaxff/omp:b_temp"); } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::deallocate_storage() +void FixQEqReaxFFOMP::deallocate_storage() { memory->destroy(b_temp); - FixQEqReax::deallocate_storage(); + FixQEqReaxFF::deallocate_storage(); } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::init() +void FixQEqReaxFFOMP::init() { - FixQEqReax::init(); + FixQEqReaxFF::init(); // APSC setup if (do_aspc) { - memory->create(aspc_b, aspc_order_max+2, "qeq/reax/aspc_b"); + memory->create(aspc_b, aspc_order_max+2, "qeq/reaxff/aspc_b"); // Calculate damping factor double o = double(aspc_order); @@ -150,7 +144,7 @@ void FixQEqReaxOMP::init() /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::compute_H() +void FixQEqReaxFFOMP::compute_H() { double SMALL = 0.0001; @@ -219,7 +213,7 @@ void FixQEqReaxOMP::compute_H() if (flag) { H.jlist[mfill] = j; - H.val[mfill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] ); + H.val[mfill] = calculate_H(sqrt(r_sqr), shld[type[i]][type[j]]); mfill++; } } @@ -227,21 +221,16 @@ void FixQEqReaxOMP::compute_H() H.numnbrs[i] = mfill - H.firstnbr[i]; } } - - if (mfill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: mfill=%d H.m=%d\n", - mfill, H.m); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/reax/omp has insufficient QEq matrix size"); - } } // omp + if (m_fill >= H.m) + error->all(FLERR,fmt::format("Fix qeq/reaxff: H matrix size has been " + "exceeded: m_fill={} H.m={}\n", m_fill, H.m)); } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::init_storage() +void FixQEqReaxFFOMP::init_storage() { #if defined(_OPENMP) #pragma omp parallel for schedule(static) @@ -258,27 +247,18 @@ void FixQEqReaxOMP::init_storage() /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::pre_force(int /* vflag */) +void FixQEqReaxFFOMP::pre_force(int /* vflag */) { - -#ifdef OMP_TIMING - double endTimeBase, startTimeBase, funcstartTimeBase; - funcstartTimeBase = MPI_Wtime(); -#endif - - double t_start, t_end; - if (update->ntimestep % nevery) return; - if (comm->me == 0) t_start = MPI_Wtime(); int n = atom->nlocal; - if (reaxc) { - nn = reaxc->list->inum; - NN = reaxc->list->inum + reaxc->list->gnum; - ilist = reaxc->list->ilist; - numneigh = reaxc->list->numneigh; - firstneigh = reaxc->list->firstneigh; + if (reaxff) { + nn = reaxff->list->inum; + NN = reaxff->list->inum + reaxff->list->gnum; + ilist = reaxff->list->ilist; + numneigh = reaxff->list->numneigh; + firstneigh = reaxff->list->firstneigh; } else { nn = list->inum; NN = list->inum + list->gnum; @@ -294,74 +274,23 @@ void FixQEqReaxOMP::pre_force(int /* vflag */) if (n > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE) reallocate_matrix(); -#ifdef OMP_TIMING - startTimeBase = MPI_Wtime(); -#endif - init_matvec(); -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEINITMVINDEX] += (endTimeBase-startTimeBase); - startTimeBase = endTimeBase; -#endif - if (dual_enabled) { - matvecs = dual_CG(b_s, b_t, s, t); // OMP_TIMING inside dual_CG + matvecs = dual_CG(b_s, b_t, s, t); } else { matvecs_s = CG(b_s, s); // CG on s - parallel - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTECG1INDEX] += (endTimeBase-startTimeBase); - ompTimingCount[COMPUTECG1INDEX]++; - ompTimingCGCount[COMPUTECG1INDEX]+= matvecs_s; - startTimeBase = endTimeBase; -#endif - matvecs_t = CG(b_t, t); // CG on t - parallel - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTECG2INDEX] += (endTimeBase-startTimeBase); - ompTimingCount[COMPUTECG2INDEX]++; - ompTimingCGCount[COMPUTECG2INDEX]+= matvecs_t; - startTimeBase = endTimeBase; -#endif - + matvecs = matvecs_s + matvecs_t; } // if (dual_enabled) -#ifdef OMP_TIMING - startTimeBase = MPI_Wtime(); -#endif - calculate_Q(); - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTECALCQINDEX] += (endTimeBase-startTimeBase); -#endif - - if (comm->me == 0) { - t_end = MPI_Wtime(); - qeq_time = t_end - t_start; - } - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEQEQINDEX] += (endTimeBase-funcstartTimeBase); -#endif } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::init_matvec() +void FixQEqReaxFFOMP::init_matvec() { -#ifdef OMP_TIMING - long endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - /* fill-in H matrix */ compute_H(); @@ -379,8 +308,8 @@ void FixQEqReaxOMP::init_matvec() if (atom->mask[i] & groupbit) { /* init pre-conditioner for H and init solution vectors */ - Hdia_inv[i] = 1. / eta[ atom->type[i] ]; - b_s[i] = -chi[ atom->type[i] ]; + Hdia_inv[i] = 1. / eta[atom->type[i]]; + b_s[i] = -chi[atom->type[i]]; b_t[i] = -1.0; // Predictor Step @@ -407,8 +336,8 @@ void FixQEqReaxOMP::init_matvec() if (atom->mask[i] & groupbit) { /* init pre-conditioner for H and init solution vectors */ - Hdia_inv[i] = 1. / eta[ atom->type[i] ]; - b_s[i] = -chi[ atom->type[i] ]; + Hdia_inv[i] = 1. / eta[atom->type[i]]; + b_s[i] = -chi[atom->type[i]]; b_t[i] = -1.0; /* linear extrapolation for s & t from previous solutions */ @@ -416,8 +345,8 @@ void FixQEqReaxOMP::init_matvec() //t[i] = 2 * t_hist[i][0] - t_hist[i][1]; /* quadratic extrapolation for s & t from previous solutions */ - //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] ); - t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] ); + //s[i] = s_hist[i][2] + 3 * (s_hist[i][0] - s_hist[i][1]); + t[i] = t_hist[i][2] + 3 * (t_hist[i][0] - t_hist[i][1]); /* cubic extrapolation for s & t from previous solutions */ s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]); @@ -427,19 +356,14 @@ void FixQEqReaxOMP::init_matvec() } pack_flag = 2; - comm->forward_comm_fix(this); //Dist_vector( s ); + comm->forward_comm_fix(this); //Dist_vector(s); pack_flag = 3; - comm->forward_comm_fix(this); //Dist_vector( t ); - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEMVCOMPINDEX] += (long) (endTimeBase-startTimeBase); -#endif + comm->forward_comm_fix(this); //Dist_vector(t); } /* ---------------------------------------------------------------------- */ -int FixQEqReaxOMP::CG( double *b, double *x) +int FixQEqReaxFFOMP::CG(double *b, double *x) { int i; double alpha, beta, b_norm; @@ -448,8 +372,8 @@ int FixQEqReaxOMP::CG( double *b, double *x) double my_buf[2], buf[2]; pack_flag = 1; - sparse_matvec( &H, x, q ); - comm->reverse_comm_fix( this); //Coll_Vector( q ); + sparse_matvec(&H, x, q); + comm->reverse_comm_fix(this); //Coll_Vector(q); double tmp1, tmp2; tmp1 = tmp2 = 0.0; @@ -477,9 +401,9 @@ int FixQEqReaxOMP::CG( double *b, double *x) sig_new = buf[1]; for (i = 1; i < imax && sqrt(sig_new) / b_norm > tolerance; ++i) { - comm->forward_comm_fix(this); //Dist_vector( d ); - sparse_matvec( &H, d, q ); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->forward_comm_fix(this); //Dist_vector(d); + sparse_matvec(&H, d, q); + comm->reverse_comm_fix(this); //Coll_vector(q); tmp1 = 0.0; #if defined(_OPENMP) @@ -539,19 +463,16 @@ int FixQEqReaxOMP::CG( double *b, double *x) } } - if (i >= imax && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq/reax CG convergence failed after %d iterations " - "at " BIGINT_FORMAT " step",i,update->ntimestep); - error->warning(FLERR,str); - } - + if ((i >= imax) && maxwarn && (comm->me == 0)) + error->warning(FLERR,fmt::format("Fix qeq/reaxff/omp CG convergence failed " + "after {} iterations at step {}", + i,update->ntimestep)); return i; } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::sparse_matvec( sparse_matrix *A, double *x, double *b) +void FixQEqReaxFFOMP::sparse_matvec(sparse_matrix *A, double *x, double *b) { #if defined(_OPENMP) #pragma omp parallel default(shared) @@ -571,7 +492,7 @@ void FixQEqReaxOMP::sparse_matvec( sparse_matrix *A, double *x, double *b) #endif for (ii = 0; ii < nn; ++ii) { i = ilist[ii]; - if (atom->mask[i] & groupbit) b[i] = eta[ atom->type[i] ] * x[i]; + if (atom->mask[i] & groupbit) b[i] = eta[atom->type[i]] * x[i]; } #if defined(_OPENMP) @@ -618,7 +539,7 @@ void FixQEqReaxOMP::sparse_matvec( sparse_matrix *A, double *x, double *b) /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::calculate_Q() +void FixQEqReaxFFOMP::calculate_Q() { int i; double *q = atom->q; @@ -666,12 +587,12 @@ void FixQEqReaxOMP::calculate_Q() } pack_flag = 4; - comm->forward_comm_fix( this); //Dist_vector( atom->q ); + comm->forward_comm_fix(this); //Dist_vector(atom->q); } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::vector_sum( double* dest, double c, double* v, +void FixQEqReaxFFOMP::vector_sum(double* dest, double c, double* v, double d, double* y, int k) { int i; @@ -687,7 +608,7 @@ void FixQEqReaxOMP::vector_sum( double* dest, double c, double* v, /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::vector_add( double* dest, double c, double* v, int k) +void FixQEqReaxFFOMP::vector_add(double* dest, double c, double* v, int k) { int i; @@ -706,14 +627,8 @@ void FixQEqReaxOMP::vector_add( double* dest, double c, double* v, int k) /* dual CG support */ /* ---------------------------------------------------------------------- */ -int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) +int FixQEqReaxFFOMP::dual_CG(double *b1, double *b2, double *x1, double *x2) { - -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - int i; double alpha_s, alpha_t, beta_s, beta_t, b_norm_s, b_norm_t; double sig_old_s, sig_old_t, sig_new_s, sig_new_t; @@ -721,8 +636,8 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) double my_buf[4], buf[4]; pack_flag = 5; // forward 2x d and reverse 2x q - dual_sparse_matvec( &H, x1, x2, q ); - comm->reverse_comm_fix(this); //Coll_Vector( q ); + dual_sparse_matvec(&H, x1, x2, q); + comm->reverse_comm_fix(this); //Coll_Vector(q); double tmp1, tmp2, tmp3, tmp4; tmp1 = tmp2 = tmp3 = tmp4 = 0.0; @@ -734,16 +649,16 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; - r[indxI ] = b1[ii] - q[indxI ]; + r[indxI] = b1[ii] - q[indxI]; r[indxI+1] = b2[ii] - q[indxI+1]; - d[indxI ] = r[indxI ] * Hdia_inv[ii]; //pre-condition + d[indxI] = r[indxI] * Hdia_inv[ii]; //pre-condition d[indxI+1] = r[indxI+1] * Hdia_inv[ii]; tmp1 += b1[ii] * b1[ii]; tmp2 += b2[ii] * b2[ii]; - tmp3 += r[indxI ] * d[indxI ]; + tmp3 += r[indxI] * d[indxI]; tmp4 += r[indxI+1] * d[indxI+1]; } } @@ -762,9 +677,9 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) sig_new_t = buf[3]; for (i = 1; i < imax; ++i) { - comm->forward_comm_fix(this); //Dist_vector( d ); - dual_sparse_matvec( &H, d, q ); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->forward_comm_fix(this); //Dist_vector(d); + dual_sparse_matvec(&H, d, q); + comm->reverse_comm_fix(this); //Coll_vector(q); tmp1 = tmp2 = 0.0; #if defined(_OPENMP) @@ -779,7 +694,7 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; - tmp1 += d[indxI ] * q[indxI ]; + tmp1 += d[indxI] * q[indxI]; tmp2 += d[indxI+1] * q[indxI+1]; } } @@ -808,17 +723,17 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; - x1[ii] += alpha_s * d[indxI ]; + x1[ii] += alpha_s * d[indxI]; x2[ii] += alpha_t * d[indxI+1]; - r[indxI ] -= alpha_s * q[indxI ]; + r[indxI] -= alpha_s * q[indxI]; r[indxI+1] -= alpha_t * q[indxI+1]; // pre-conditioning - p[indxI ] = r[indxI ] * Hdia_inv[ii]; + p[indxI] = r[indxI] * Hdia_inv[ii]; p[indxI+1] = r[indxI+1] * Hdia_inv[ii]; - tmp1 += r[indxI ] * p[indxI ]; + tmp1 += r[indxI] * p[indxI]; tmp2 += r[indxI+1] * p[indxI+1]; } } @@ -849,63 +764,42 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; - d[indxI ] = p[indxI ] + beta_s * d[indxI ]; + d[indxI] = p[indxI] + beta_s * d[indxI]; d[indxI+1] = p[indxI+1] + beta_t * d[indxI+1]; } } } - i++; - matvecs_s = matvecs_t = i; // The plus one makes consistent with count from CG() - matvecs = i; + matvecs_s = matvecs_t = i; - // Timing info for iterating s&t together -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTECG1INDEX] += (endTimeBase-startTimeBase); - ompTimingCount[COMPUTECG1INDEX]++; - ompTimingCGCount[COMPUTECG1INDEX]+= i; - startTimeBase = endTimeBase; -#endif - - // If necessary, converge other system - if (sqrt(sig_new_s)/b_norm_s > tolerance) { + // If only one was converged and there are still iterations left, converge other system + if ((matvecs_s < imax) && (sqrt(sig_new_s)/b_norm_s > tolerance)) { pack_flag = 2; comm->forward_comm_fix(this); // x1 => s - i+= CG(b1, x1); - matvecs_s = i; - } - else if (sqrt(sig_new_t)/b_norm_t > tolerance) { + int saved_imax = imax; + imax -= matvecs_s; + matvecs_s += CG(b1, x1); + imax = saved_imax; + } else if ((matvecs_t < imax) && (sqrt(sig_new_t)/b_norm_t > tolerance)) { pack_flag = 3; comm->forward_comm_fix(this); // x2 => t - - i+= CG(b2, x2); - matvecs_t = i; + int saved_imax = imax; + imax -= matvecs_t; + matvecs_t += CG(b2, x2); + imax = saved_imax; } - // Timing info for remainder of s or t -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTECG2INDEX] += (endTimeBase-startTimeBase); - ompTimingCount[COMPUTECG2INDEX]++; - ompTimingCGCount[COMPUTECG2INDEX]+= i - matvecs; - startTimeBase = endTimeBase; -#endif - - if ( i >= imax && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq/reax CG convergence failed after %d iterations " - "at " BIGINT_FORMAT " step",i,update->ntimestep); - error->warning(FLERR,str); - } - - return i; + if ((i >= imax) && maxwarn && (comm->me == 0)) + error->warning(FLERR,fmt::format("Fix qeq/reaxff/omp CG convergence failed " + "after {} iterations at step {}", + i,update->ntimestep)); + return matvecs_s + matvecs_t; } /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2, double *b) +void FixQEqReaxFFOMP::dual_sparse_matvec(sparse_matrix *A, double *x1, double *x2, double *b) { #if defined(_OPENMP) #pragma omp parallel default(shared) @@ -929,8 +823,8 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2 i = ilist[ii]; if (atom->mask[i] & groupbit) { indxI = 2 * i; - b[indxI ] = eta[ atom->type[i] ] * x1[i]; - b[indxI+1] = eta[ atom->type[i] ] * x2[i]; + b[indxI] = eta[atom->type[i]] * x1[i]; + b[indxI+1] = eta[atom->type[i]] * x2[i]; } } @@ -952,7 +846,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2 for (i = 0; i < NN; ++i) { indxI = 2 * i; for (int t=0; tfirstnbr[i]; itr_jfirstnbr[i]+A->numnbrs[i]; itr_j++) { j = A->jlist[itr_j]; indxJ = 2 * j; - b[indxI ] += A->val[itr_j] * x1[j]; + b[indxI] += A->val[itr_j] * x1[j]; b[indxI+1] += A->val[itr_j] * x2[j]; - b_temp[tid][indxJ ] += A->val[itr_j] * x1[i]; + b_temp[tid][indxJ] += A->val[itr_j] * x1[i]; b_temp[tid][indxJ+1] += A->val[itr_j] * x2[i]; } } @@ -986,7 +880,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2 for (i = 0; i < NN; ++i) { indxI = 2 * i; for (int t = 0; t < nthreads; ++t) { - b[indxI ] += b_temp[t][indxI ]; + b[indxI] += b_temp[t][indxI]; b[indxI+1] += b_temp[t][indxI+1]; } } @@ -996,7 +890,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2 /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x, double *b ) +void FixQEqReaxFFOMP::dual_sparse_matvec(sparse_matrix *A, double *x, double *b) { #if defined(_OPENMP) #pragma omp parallel default(shared) @@ -1020,8 +914,8 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x, double *b ) i = ilist[ii]; if (atom->mask[i] & groupbit) { indxI = 2 * i; - b[indxI ] = eta[ atom->type[i] ] * x[indxI ]; - b[indxI+1] = eta[ atom->type[i] ] * x[indxI+1]; + b[indxI] = eta[atom->type[i]] * x[indxI]; + b[indxI+1] = eta[atom->type[i]] * x[indxI+1]; } } @@ -1043,7 +937,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x, double *b ) for (i = 0; i < NN; ++i) { indxI = 2 * i; for (int t=0; tfirstnbr[i]; itr_jfirstnbr[i]+A->numnbrs[i]; itr_j++) { j = A->jlist[itr_j]; indxJ = 2 * j; - b[indxI ] += A->val[itr_j] * x[indxJ ]; + b[indxI] += A->val[itr_j] * x[indxJ]; b[indxI+1] += A->val[itr_j] * x[indxJ+1]; - b_temp[tid][indxJ ] += A->val[itr_j] * x[indxI ]; + b_temp[tid][indxJ] += A->val[itr_j] * x[indxI]; b_temp[tid][indxJ+1] += A->val[itr_j] * x[indxI+1]; } } @@ -1077,7 +971,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x, double *b ) for (i = 0; i < NN; ++i) { indxI = 2 * i; for (int t = 0; t < nthreads; ++t) { - b[indxI ] += b_temp[t][indxI ]; + b[indxI] += b_temp[t][indxI]; b[indxI+1] += b_temp[t][indxI+1]; } } diff --git a/src/USER-OMP/fix_qeq_reax_omp.h b/src/OPENMP/fix_qeq_reaxff_omp.h similarity index 84% rename from src/USER-OMP/fix_qeq_reax_omp.h rename to src/OPENMP/fix_qeq_reaxff_omp.h index 62855a6f78..b99034edf0 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.h +++ b/src/OPENMP/fix_qeq_reaxff_omp.h @@ -13,22 +13,23 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(qeq/reax/omp,FixQEqReaxOMP); +FixStyle(qeq/reaxff/omp,FixQEqReaxFFOMP); +FixStyle(qeq/reax/omp,FixQEqReaxFFOMP); // clang-format on #else -#ifndef LMP_FIX_QEQ_REAX_OMP_H -#define LMP_FIX_QEQ_REAX_OMP_H +#ifndef LMP_FIX_QEQ_REAXFF_OMP_H +#define LMP_FIX_QEQ_REAXFF_OMP_H -#include "fix_qeq_reax.h" +#include "fix_qeq_reaxff.h" namespace LAMMPS_NS { -class FixQEqReaxOMP : public FixQEqReax { +class FixQEqReaxFFOMP : public FixQEqReaxFF { public: - FixQEqReaxOMP(class LAMMPS *, int, char **); - ~FixQEqReaxOMP(); + FixQEqReaxFFOMP(class LAMMPS *, int, char **); + ~FixQEqReaxFFOMP(); virtual void init(); virtual void init_storage(); virtual void pre_force(int); diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/OPENMP/fix_rigid_nh_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nh_omp.cpp rename to src/OPENMP/fix_rigid_nh_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nh_omp.h b/src/OPENMP/fix_rigid_nh_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nh_omp.h rename to src/OPENMP/fix_rigid_nh_omp.h diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/OPENMP/fix_rigid_nph_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nph_omp.cpp rename to src/OPENMP/fix_rigid_nph_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nph_omp.h b/src/OPENMP/fix_rigid_nph_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nph_omp.h rename to src/OPENMP/fix_rigid_nph_omp.h diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/OPENMP/fix_rigid_npt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_npt_omp.cpp rename to src/OPENMP/fix_rigid_npt_omp.cpp diff --git a/src/USER-OMP/fix_rigid_npt_omp.h b/src/OPENMP/fix_rigid_npt_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_npt_omp.h rename to src/OPENMP/fix_rigid_npt_omp.h diff --git a/src/USER-OMP/fix_rigid_nve_omp.cpp b/src/OPENMP/fix_rigid_nve_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nve_omp.cpp rename to src/OPENMP/fix_rigid_nve_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nve_omp.h b/src/OPENMP/fix_rigid_nve_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nve_omp.h rename to src/OPENMP/fix_rigid_nve_omp.h diff --git a/src/USER-OMP/fix_rigid_nvt_omp.cpp b/src/OPENMP/fix_rigid_nvt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nvt_omp.cpp rename to src/OPENMP/fix_rigid_nvt_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nvt_omp.h b/src/OPENMP/fix_rigid_nvt_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nvt_omp.h rename to src/OPENMP/fix_rigid_nvt_omp.h diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/OPENMP/fix_rigid_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_omp.cpp rename to src/OPENMP/fix_rigid_omp.cpp diff --git a/src/USER-OMP/fix_rigid_omp.h b/src/OPENMP/fix_rigid_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_omp.h rename to src/OPENMP/fix_rigid_omp.h diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/OPENMP/fix_rigid_small_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_small_omp.cpp rename to src/OPENMP/fix_rigid_small_omp.cpp diff --git a/src/USER-OMP/fix_rigid_small_omp.h b/src/OPENMP/fix_rigid_small_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_small_omp.h rename to src/OPENMP/fix_rigid_small_omp.h diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/OPENMP/improper_class2_omp.cpp similarity index 100% rename from src/USER-OMP/improper_class2_omp.cpp rename to src/OPENMP/improper_class2_omp.cpp diff --git a/src/USER-OMP/improper_class2_omp.h b/src/OPENMP/improper_class2_omp.h similarity index 100% rename from src/USER-OMP/improper_class2_omp.h rename to src/OPENMP/improper_class2_omp.h diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/OPENMP/improper_cossq_omp.cpp similarity index 100% rename from src/USER-OMP/improper_cossq_omp.cpp rename to src/OPENMP/improper_cossq_omp.cpp diff --git a/src/USER-OMP/improper_cossq_omp.h b/src/OPENMP/improper_cossq_omp.h similarity index 100% rename from src/USER-OMP/improper_cossq_omp.h rename to src/OPENMP/improper_cossq_omp.h diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/OPENMP/improper_cvff_omp.cpp similarity index 100% rename from src/USER-OMP/improper_cvff_omp.cpp rename to src/OPENMP/improper_cvff_omp.cpp diff --git a/src/USER-OMP/improper_cvff_omp.h b/src/OPENMP/improper_cvff_omp.h similarity index 100% rename from src/USER-OMP/improper_cvff_omp.h rename to src/OPENMP/improper_cvff_omp.h diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/OPENMP/improper_fourier_omp.cpp similarity index 100% rename from src/USER-OMP/improper_fourier_omp.cpp rename to src/OPENMP/improper_fourier_omp.cpp diff --git a/src/USER-OMP/improper_fourier_omp.h b/src/OPENMP/improper_fourier_omp.h similarity index 100% rename from src/USER-OMP/improper_fourier_omp.h rename to src/OPENMP/improper_fourier_omp.h diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/OPENMP/improper_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/improper_harmonic_omp.cpp rename to src/OPENMP/improper_harmonic_omp.cpp diff --git a/src/USER-OMP/improper_harmonic_omp.h b/src/OPENMP/improper_harmonic_omp.h similarity index 100% rename from src/USER-OMP/improper_harmonic_omp.h rename to src/OPENMP/improper_harmonic_omp.h diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/OPENMP/improper_ring_omp.cpp similarity index 100% rename from src/USER-OMP/improper_ring_omp.cpp rename to src/OPENMP/improper_ring_omp.cpp diff --git a/src/USER-OMP/improper_ring_omp.h b/src/OPENMP/improper_ring_omp.h similarity index 100% rename from src/USER-OMP/improper_ring_omp.h rename to src/OPENMP/improper_ring_omp.h diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/OPENMP/improper_umbrella_omp.cpp similarity index 100% rename from src/USER-OMP/improper_umbrella_omp.cpp rename to src/OPENMP/improper_umbrella_omp.cpp diff --git a/src/USER-OMP/improper_umbrella_omp.h b/src/OPENMP/improper_umbrella_omp.h similarity index 100% rename from src/USER-OMP/improper_umbrella_omp.h rename to src/OPENMP/improper_umbrella_omp.h diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/OPENMP/msm_cg_omp.cpp similarity index 100% rename from src/USER-OMP/msm_cg_omp.cpp rename to src/OPENMP/msm_cg_omp.cpp diff --git a/src/USER-OMP/msm_cg_omp.h b/src/OPENMP/msm_cg_omp.h similarity index 100% rename from src/USER-OMP/msm_cg_omp.h rename to src/OPENMP/msm_cg_omp.h diff --git a/src/USER-OMP/msm_omp.cpp b/src/OPENMP/msm_omp.cpp similarity index 100% rename from src/USER-OMP/msm_omp.cpp rename to src/OPENMP/msm_omp.cpp diff --git a/src/USER-OMP/msm_omp.h b/src/OPENMP/msm_omp.h similarity index 100% rename from src/USER-OMP/msm_omp.h rename to src/OPENMP/msm_omp.h diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/OPENMP/npair_full_bin_atomonly_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_bin_atomonly_omp.cpp rename to src/OPENMP/npair_full_bin_atomonly_omp.cpp diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.h b/src/OPENMP/npair_full_bin_atomonly_omp.h similarity index 100% rename from src/USER-OMP/npair_full_bin_atomonly_omp.h rename to src/OPENMP/npair_full_bin_atomonly_omp.h diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/OPENMP/npair_full_bin_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_bin_ghost_omp.cpp rename to src/OPENMP/npair_full_bin_ghost_omp.cpp diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.h b/src/OPENMP/npair_full_bin_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_full_bin_ghost_omp.h rename to src/OPENMP/npair_full_bin_ghost_omp.h diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/OPENMP/npair_full_bin_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_bin_omp.cpp rename to src/OPENMP/npair_full_bin_omp.cpp diff --git a/src/USER-OMP/npair_full_bin_omp.h b/src/OPENMP/npair_full_bin_omp.h similarity index 100% rename from src/USER-OMP/npair_full_bin_omp.h rename to src/OPENMP/npair_full_bin_omp.h diff --git a/src/USER-OMP/npair_full_multi_old_omp.cpp b/src/OPENMP/npair_full_multi_old_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_multi_old_omp.cpp rename to src/OPENMP/npair_full_multi_old_omp.cpp diff --git a/src/USER-OMP/npair_full_multi_old_omp.h b/src/OPENMP/npair_full_multi_old_omp.h similarity index 100% rename from src/USER-OMP/npair_full_multi_old_omp.h rename to src/OPENMP/npair_full_multi_old_omp.h diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/OPENMP/npair_full_multi_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_multi_omp.cpp rename to src/OPENMP/npair_full_multi_omp.cpp diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/OPENMP/npair_full_multi_omp.h similarity index 100% rename from src/USER-OMP/npair_full_multi_omp.h rename to src/OPENMP/npair_full_multi_omp.h diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/OPENMP/npair_full_nsq_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_nsq_ghost_omp.cpp rename to src/OPENMP/npair_full_nsq_ghost_omp.cpp diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.h b/src/OPENMP/npair_full_nsq_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_full_nsq_ghost_omp.h rename to src/OPENMP/npair_full_nsq_ghost_omp.h diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/OPENMP/npair_full_nsq_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_nsq_omp.cpp rename to src/OPENMP/npair_full_nsq_omp.cpp diff --git a/src/USER-OMP/npair_full_nsq_omp.h b/src/OPENMP/npair_full_nsq_omp.h similarity index 100% rename from src/USER-OMP/npair_full_nsq_omp.h rename to src/OPENMP/npair_full_nsq_omp.h diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp rename to src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.h b/src/OPENMP/npair_half_bin_atomonly_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_atomonly_newton_omp.h rename to src/OPENMP/npair_half_bin_atomonly_newton_omp.h diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp rename to src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h rename to src/OPENMP/npair_half_bin_newtoff_ghost_omp.h diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_omp.cpp rename to src/OPENMP/npair_half_bin_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.h b/src/OPENMP/npair_half_bin_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_omp.h rename to src/OPENMP/npair_half_bin_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/OPENMP/npair_half_bin_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_omp.cpp rename to src/OPENMP/npair_half_bin_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newton_omp.h b/src/OPENMP/npair_half_bin_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_omp.h rename to src/OPENMP/npair_half_bin_newton_omp.h diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_bin_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_tri_omp.cpp rename to src/OPENMP/npair_half_bin_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.h b/src/OPENMP/npair_half_bin_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_tri_omp.h rename to src/OPENMP/npair_half_bin_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_newtoff_omp.cpp rename to src/OPENMP/npair_half_multi_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/OPENMP/npair_half_multi_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_newtoff_omp.h rename to src/OPENMP/npair_half_multi_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/OPENMP/npair_half_multi_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_omp.cpp rename to src/OPENMP/npair_half_multi_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/OPENMP/npair_half_multi_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_omp.h rename to src/OPENMP/npair_half_multi_newton_omp.h diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.cpp rename to src/OPENMP/npair_half_multi_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/OPENMP/npair_half_multi_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.h rename to src/OPENMP/npair_half_multi_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp rename to src/OPENMP/npair_half_multi_old_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.h b/src/OPENMP/npair_half_multi_old_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newtoff_omp.h rename to src/OPENMP/npair_half_multi_old_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_omp.cpp rename to src/OPENMP/npair_half_multi_old_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.h b/src/OPENMP/npair_half_multi_old_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_omp.h rename to src/OPENMP/npair_half_multi_old_newton_omp.h diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp rename to src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h b/src/OPENMP/npair_half_multi_old_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_tri_omp.h rename to src/OPENMP/npair_half_multi_old_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp rename to src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h rename to src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_omp.cpp rename to src/OPENMP/npair_half_nsq_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.h b/src/OPENMP/npair_half_nsq_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_omp.h rename to src/OPENMP/npair_half_nsq_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/OPENMP/npair_half_nsq_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_nsq_newton_omp.cpp rename to src/OPENMP/npair_half_nsq_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.h b/src/OPENMP/npair_half_nsq_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_nsq_newton_omp.h rename to src/OPENMP/npair_half_nsq_newton_omp.h diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp rename to src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h b/src/OPENMP/npair_half_respa_bin_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newtoff_omp.h rename to src/OPENMP/npair_half_respa_bin_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_omp.cpp rename to src/OPENMP/npair_half_respa_bin_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.h b/src/OPENMP/npair_half_respa_bin_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_omp.h rename to src/OPENMP/npair_half_respa_bin_newton_omp.h diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp rename to src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h rename to src/OPENMP/npair_half_respa_bin_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp rename to src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h rename to src/OPENMP/npair_half_respa_nsq_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp rename to src/OPENMP/npair_half_respa_nsq_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.h b/src/OPENMP/npair_half_respa_nsq_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newton_omp.h rename to src/OPENMP/npair_half_respa_nsq_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_bin_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.h b/src/OPENMP/npair_half_size_bin_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newtoff_omp.h rename to src/OPENMP/npair_half_size_bin_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_omp.cpp rename to src/OPENMP/npair_half_size_bin_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.h b/src/OPENMP/npair_half_size_bin_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_omp.h rename to src/OPENMP/npair_half_size_bin_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp rename to src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h b/src/OPENMP/npair_half_size_bin_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_tri_omp.h rename to src/OPENMP/npair_half_size_bin_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_multi_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/OPENMP/npair_half_size_multi_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.h rename to src/OPENMP/npair_half_size_multi_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_omp.cpp rename to src/OPENMP/npair_half_size_multi_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.h b/src/OPENMP/npair_half_size_multi_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_omp.h rename to src/OPENMP/npair_half_size_multi_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp rename to src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/OPENMP/npair_half_size_multi_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_tri_omp.h rename to src/OPENMP/npair_half_size_multi_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h rename to src/OPENMP/npair_half_size_multi_old_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp rename to src/OPENMP/npair_half_size_multi_old_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.h b/src/OPENMP/npair_half_size_multi_old_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newton_omp.h rename to src/OPENMP/npair_half_size_multi_old_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp rename to src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h rename to src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h b/src/OPENMP/npair_half_size_nsq_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newtoff_omp.h rename to src/OPENMP/npair_half_size_nsq_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newton_omp.cpp rename to src/OPENMP/npair_half_size_nsq_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.h b/src/OPENMP/npair_half_size_nsq_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newton_omp.h rename to src/OPENMP/npair_half_size_nsq_newton_omp.h diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/OPENMP/npair_halffull_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_halffull_newtoff_omp.cpp rename to src/OPENMP/npair_halffull_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/OPENMP/npair_halffull_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_halffull_newtoff_omp.h rename to src/OPENMP/npair_halffull_newtoff_omp.h diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/OPENMP/npair_halffull_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_halffull_newton_omp.cpp rename to src/OPENMP/npair_halffull_newton_omp.cpp diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/OPENMP/npair_halffull_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_halffull_newton_omp.h rename to src/OPENMP/npair_halffull_newton_omp.h diff --git a/src/USER-OMP/npair_omp.h b/src/OPENMP/npair_omp.h similarity index 100% rename from src/USER-OMP/npair_omp.h rename to src/OPENMP/npair_omp.h diff --git a/src/USER-OMP/npair_skip_omp.h b/src/OPENMP/npair_skip_omp.h similarity index 100% rename from src/USER-OMP/npair_skip_omp.h rename to src/OPENMP/npair_skip_omp.h diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/OPENMP/pair_adp_omp.cpp similarity index 100% rename from src/USER-OMP/pair_adp_omp.cpp rename to src/OPENMP/pair_adp_omp.cpp diff --git a/src/USER-OMP/pair_adp_omp.h b/src/OPENMP/pair_adp_omp.h similarity index 100% rename from src/USER-OMP/pair_adp_omp.h rename to src/OPENMP/pair_adp_omp.h diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/OPENMP/pair_agni_omp.cpp similarity index 100% rename from src/USER-OMP/pair_agni_omp.cpp rename to src/OPENMP/pair_agni_omp.cpp diff --git a/src/USER-OMP/pair_agni_omp.h b/src/OPENMP/pair_agni_omp.h similarity index 100% rename from src/USER-OMP/pair_agni_omp.h rename to src/OPENMP/pair_agni_omp.h diff --git a/src/USER-OMP/pair_airebo_morse_omp.cpp b/src/OPENMP/pair_airebo_morse_omp.cpp similarity index 100% rename from src/USER-OMP/pair_airebo_morse_omp.cpp rename to src/OPENMP/pair_airebo_morse_omp.cpp diff --git a/src/USER-OMP/pair_airebo_morse_omp.h b/src/OPENMP/pair_airebo_morse_omp.h similarity index 100% rename from src/USER-OMP/pair_airebo_morse_omp.h rename to src/OPENMP/pair_airebo_morse_omp.h diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/OPENMP/pair_airebo_omp.cpp similarity index 96% rename from src/USER-OMP/pair_airebo_omp.cpp rename to src/OPENMP/pair_airebo_omp.cpp index 2e3b35b799..6e7491787a 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/OPENMP/pair_airebo_omp.cpp @@ -70,9 +70,9 @@ void PairAIREBOOMP::compute(int eflag, int vflag) thr->timer(Timer::START); ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); - FREBO_thr(ifrom,ito,evflag,eflag,vflag_atom,&pv0,thr); - if (ljflag) FLJ_thr(ifrom,ito,evflag,eflag,vflag_atom,&pv1,thr); - if (torflag) TORSION_thr(ifrom,ito,evflag,eflag,&pv2,thr); + FREBO_thr(ifrom,ito,eflag,&pv0,thr); + if (ljflag) FLJ_thr(ifrom,ito,eflag,&pv1,thr); + if (torflag) TORSION_thr(ifrom,ito,eflag,&pv2,thr); thr->timer(Timer::PAIR); reduce_thr(this, eflag, vflag, thr); @@ -184,8 +184,7 @@ void PairAIREBOOMP::REBO_neigh_thr() REBO forces and energy ------------------------------------------------------------------------- */ -void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag, - int vflag_atom, double *pv0, ThrData * const thr) +void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int eflag, double *pv0, ThrData * const thr) { int i,j,k,m,ii,itype,jtype; tagint itag,jtag; @@ -259,7 +258,7 @@ void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag, del[0] = delx; del[1] = dely; del[2] = delz; - bij = bondorder_thr(i,j,del,rij,VA,vflag_atom,thr); + bij = bondorder_thr(i,j,del,rij,VA,thr); dVAdi = bij*dVA; fpair = -(dVRdi+dVAdi) / rij; @@ -282,8 +281,7 @@ void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag, find 3- and 4-step paths between atoms I,J via REBO neighbor lists ------------------------------------------------------------------------- */ -void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag, - int vflag_atom, double *pv1, ThrData * const thr) +void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int eflag, double *pv1, ThrData * const thr) { int i,j,k,m,ii,jj,kk,mm,jnum,itype,jtype,ktype,mtype; tagint itag,jtag; @@ -547,8 +545,7 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag, delscale[0] = scale * delij[0]; delscale[1] = scale * delij[1]; delscale[2] = scale * delij[2]; - Stb = bondorderLJ_thr(i,j,delscale,rcmin[itype][jtype],VA, - delij,rij,vflag_atom,thr); + Stb = bondorderLJ_thr(i,j,delscale,rcmin[itype][jtype],VA,delij,rij,thr); } else Stb = 0.0; fpair = -(dStr * (Stb*cij*VLJ - cij*VLJ) + @@ -576,7 +573,7 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag, f[atomj][1] -= delij[1]*fpair; f[atomj][2] -= delij[2]*fpair; - if (vflag_atom) v_tally2_thr(atomi,atomj,fpair,delij,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomj,fpair,delij,thr); } else if (npath == 3) { fpair1 = dC*dwikS*wkjS / rikS; @@ -598,8 +595,8 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag, f[atomk][1] -= fi[1] + fj[1]; f[atomk][2] -= fi[2] + fj[2]; - if (vflag_atom) - v_tally3_thr(atomi,atomj,atomk,fi,fj,delikS,deljkS,thr); + if (vflag_either) + v_tally3_thr(this,atomi,atomj,atomk,fi,fj,delikS,deljkS,thr); } else if (npath == 4) { fpair1 = dC*dwikS*wkmS*wmjS / rikS; @@ -634,11 +631,11 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag, f[atomm][1] += fm[1]; f[atomm][2] += fm[2]; - if (vflag_atom) { + if (vflag_either) { delimS[0] = delikS[0] + delkmS[0]; delimS[1] = delikS[1] + delkmS[1]; delimS[2] = delikS[2] + delkmS[2]; - v_tally4_thr(atomi,atomj,atomk,atomm,fi,fj,fk,delimS,deljmS,delkmS,thr); + v_tally4_thr(this,atomi,atomj,atomk,atomm,fi,fj,fk,delimS,deljmS,delkmS,thr); } } } @@ -650,8 +647,7 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag, torsional forces and energy ------------------------------------------------------------------------- */ -void PairAIREBOOMP::TORSION_thr(int ifrom, int ito, int evflag, int eflag, - double *pv2, ThrData * const thr) +void PairAIREBOOMP::TORSION_thr(int ifrom, int ito, int eflag, double *pv2, ThrData * const thr) { int i,j,k,l,ii; tagint itag,jtag; @@ -1011,7 +1007,7 @@ void PairAIREBOOMP::TORSION_thr(int ifrom, int ito, int evflag, int eflag, ------------------------------------------------------------------------- */ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, - double VA, int vflag_atom, ThrData * const thr) + double VA, ThrData * const thr) { int atomi,atomj,k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4; int itype,jtype,ktype,ltype,ntype; @@ -1197,10 +1193,10 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2]; - if (vflag_atom) { + if (vflag_either) { rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2]; rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2]; - v_tally3_thr(atomi,atomj,atomk,fj,fk,rji,rki,thr); + v_tally3_thr(this,atomi,atomj,atomk,fj,fk,rji,rki,thr); } } } @@ -1342,9 +1338,9 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2]; - if (vflag_atom) { + if (vflag_either) { rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2]; - v_tally3_thr(atomi,atomj,atoml,fi,fl,rij,rlj,thr); + v_tally3_thr(this,atomi,atomj,atoml,fi,fl,rij,rlj,thr); } } } @@ -1378,7 +1374,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -1392,7 +1388,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -1414,7 +1410,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr); + if (vflag_either) v_tally2_thr(this,atomk,atomn,-tmp2,rkn,thr); } } } @@ -1445,7 +1441,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -1459,7 +1455,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -1481,7 +1477,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr); + if (vflag_either) v_tally2_thr(this,atoml,atomn,-tmp2,rln,thr); } } } @@ -1693,10 +1689,10 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atom4][0] += f4[0]; f[atom4][1] += f4[1]; f[atom4][2] += f4[2]; - if (vflag_atom) { + if (vflag_either) { r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2]; r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2]; - v_tally4_thr(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr); + v_tally4_thr(this,atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr); } } } @@ -1729,7 +1725,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -1743,7 +1739,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -1765,7 +1761,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr); + if (vflag_either) v_tally2_thr(this,atomk,atomn,-tmp2,rkn,thr); } } } @@ -1796,7 +1792,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -1810,7 +1806,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -1832,7 +1828,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr); + if (vflag_either) v_tally2_thr(this,atoml,atomn,-tmp2,rln,thr); } } } @@ -1870,8 +1866,7 @@ there probably also need to be performed here. */ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], double rijmag_mod, - double VA, double rij[3], double rijmag, - int vflag_atom, ThrData * const thr) + double VA, double rij[3], double rijmag, ThrData * const thr) { int atomi,atomj,k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4; int itype,jtype,ktype,ltype,ntype; @@ -2196,10 +2191,10 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2]; - if (vflag_atom) { + if (vflag_either) { rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2]; rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2]; - v_tally3_thr(atomi,atomj,atomk,fj,fk,rji,rki,thr); + v_tally3_thr(this,atomi,atomj,atomk,fj,fk,rji,rki,thr); } } } @@ -2300,9 +2295,9 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2]; f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2]; - if (vflag_atom) { + if (vflag_either) { rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2]; - v_tally3_thr(atomi,atomj,atoml,fi,fl,rij,rlj,thr); + v_tally3_thr(this,atomi,atomj,atoml,fi,fl,rij,rlj,thr); } } } @@ -2335,7 +2330,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -2349,7 +2344,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -2371,7 +2366,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr); + if (vflag_either) v_tally2_thr(this,atomk,atomn,-tmp2,rkn,thr); } } } @@ -2402,7 +2397,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -2416,7 +2411,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -2438,7 +2433,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr); + if (vflag_either) v_tally2_thr(this,atoml,atomn,-tmp2,rln,thr); } } } @@ -2643,10 +2638,10 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atom4][0] += f4[0]; f[atom4][1] += f4[1]; f[atom4][2] += f4[2]; - if (vflag_atom) { + if (vflag_either) { r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2]; r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2]; - v_tally4_thr(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr); + v_tally4_thr(this,atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr); } } } @@ -2677,7 +2672,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); // due to kronecker(ktype, 0) term in contribution // to NconjtmpI and later Nijconj @@ -2691,7 +2686,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomk][1] += tmp2*rik[1]; f[atomk][2] += tmp2*rik[2]; - if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr); + if (vflag_either) v_tally2_thr(this,atomi,atomk,-tmp2,rik,thr); if (fabs(dNki) > TOL) { REBO_neighs_k = REBO_firstneigh[atomk]; @@ -2713,7 +2708,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomn][1] += tmp2*rkn[1]; f[atomn][2] += tmp2*rkn[2]; - if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr); + if (vflag_either) v_tally2_thr(this,atomk,atomn,-tmp2,rkn,thr); } } } @@ -2744,7 +2739,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); // due to kronecker(ltype, 0) term in contribution // to NconjtmpJ and later Nijconj @@ -2758,7 +2753,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atoml][1] += tmp2*rjl[1]; f[atoml][2] += tmp2*rjl[2]; - if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr); + if (vflag_either) v_tally2_thr(this,atomj,atoml,-tmp2,rjl,thr); if (fabs(dNlj) > TOL) { REBO_neighs_l = REBO_firstneigh[atoml]; @@ -2780,7 +2775,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], dou f[atomn][1] += tmp2*rln[1]; f[atomn][2] += tmp2*rln[2]; - if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr); + if (vflag_either) v_tally2_thr(this,atoml,atomn,-tmp2,rln,thr); } } } diff --git a/src/USER-OMP/pair_airebo_omp.h b/src/OPENMP/pair_airebo_omp.h similarity index 71% rename from src/USER-OMP/pair_airebo_omp.h rename to src/OPENMP/pair_airebo_omp.h index 9c5b29545f..355614552e 100644 --- a/src/USER-OMP/pair_airebo_omp.h +++ b/src/OPENMP/pair_airebo_omp.h @@ -33,16 +33,13 @@ class PairAIREBOOMP : public PairAIREBO, public ThrOMP { virtual double memory_usage(); protected: - double bondorder_thr(int i, int j, double rij[3], double rijmag, double VA, int vflag_atom, - ThrData *const thr); + double bondorder_thr(int i, int j, double rij[3], double rijmag, double VA, ThrData *const thr); double bondorderLJ_thr(int i, int j, double rij[3], double rijmag, double VA, double rij0[3], - double rijmag0, int vflag_atom, ThrData *const thr); + double rijmag0, ThrData *const thr); - void FREBO_thr(int ifrom, int ito, int evflag, int eflag, int vflag_atom, double *pv0, - ThrData *const thr); - void FLJ_thr(int ifrom, int ito, int evflag, int eflag, int vflag_atom, double *pv1, - ThrData *const thr); - void TORSION_thr(int ifrom, int ito, int evflag, int eflag, double *pv2, ThrData *const thr); + void FREBO_thr(int ifrom, int ito, int eflag, double *pv0, ThrData *const thr); + void FLJ_thr(int ifrom, int ito, int eflag, double *pv1, ThrData *const thr); + void TORSION_thr(int ifrom, int ito, int eflag, double *pv2, ThrData *const thr); void REBO_neigh_thr(); }; diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/OPENMP/pair_beck_omp.cpp similarity index 100% rename from src/USER-OMP/pair_beck_omp.cpp rename to src/OPENMP/pair_beck_omp.cpp diff --git a/src/USER-OMP/pair_beck_omp.h b/src/OPENMP/pair_beck_omp.h similarity index 100% rename from src/USER-OMP/pair_beck_omp.h rename to src/OPENMP/pair_beck_omp.h diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/OPENMP/pair_born_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_coul_long_omp.cpp rename to src/OPENMP/pair_born_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_born_coul_long_omp.h b/src/OPENMP/pair_born_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_born_coul_long_omp.h rename to src/OPENMP/pair_born_coul_long_omp.h diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/OPENMP/pair_born_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_coul_msm_omp.cpp rename to src/OPENMP/pair_born_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_born_coul_msm_omp.h b/src/OPENMP/pair_born_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_born_coul_msm_omp.h rename to src/OPENMP/pair_born_coul_msm_omp.h diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/OPENMP/pair_born_coul_wolf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_coul_wolf_omp.cpp rename to src/OPENMP/pair_born_coul_wolf_omp.cpp diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.h b/src/OPENMP/pair_born_coul_wolf_omp.h similarity index 100% rename from src/USER-OMP/pair_born_coul_wolf_omp.h rename to src/OPENMP/pair_born_coul_wolf_omp.h diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/OPENMP/pair_born_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_omp.cpp rename to src/OPENMP/pair_born_omp.cpp diff --git a/src/USER-OMP/pair_born_omp.h b/src/OPENMP/pair_born_omp.h similarity index 100% rename from src/USER-OMP/pair_born_omp.h rename to src/OPENMP/pair_born_omp.h diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/OPENMP/pair_brownian_omp.cpp similarity index 100% rename from src/USER-OMP/pair_brownian_omp.cpp rename to src/OPENMP/pair_brownian_omp.cpp diff --git a/src/USER-OMP/pair_brownian_omp.h b/src/OPENMP/pair_brownian_omp.h similarity index 100% rename from src/USER-OMP/pair_brownian_omp.h rename to src/OPENMP/pair_brownian_omp.h diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/OPENMP/pair_brownian_poly_omp.cpp similarity index 100% rename from src/USER-OMP/pair_brownian_poly_omp.cpp rename to src/OPENMP/pair_brownian_poly_omp.cpp diff --git a/src/USER-OMP/pair_brownian_poly_omp.h b/src/OPENMP/pair_brownian_poly_omp.h similarity index 100% rename from src/USER-OMP/pair_brownian_poly_omp.h rename to src/OPENMP/pair_brownian_poly_omp.h diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/OPENMP/pair_buck_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_coul_cut_omp.cpp rename to src/OPENMP/pair_buck_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.h b/src/OPENMP/pair_buck_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_coul_cut_omp.h rename to src/OPENMP/pair_buck_coul_cut_omp.h diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/OPENMP/pair_buck_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_coul_long_omp.cpp rename to src/OPENMP/pair_buck_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_buck_coul_long_omp.h b/src/OPENMP/pair_buck_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_coul_long_omp.h rename to src/OPENMP/pair_buck_coul_long_omp.h diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/OPENMP/pair_buck_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_coul_msm_omp.cpp rename to src/OPENMP/pair_buck_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.h b/src/OPENMP/pair_buck_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_coul_msm_omp.h rename to src/OPENMP/pair_buck_coul_msm_omp.h diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/OPENMP/pair_buck_long_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_long_coul_long_omp.cpp rename to src/OPENMP/pair_buck_long_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.h b/src/OPENMP/pair_buck_long_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_long_coul_long_omp.h rename to src/OPENMP/pair_buck_long_coul_long_omp.h diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/OPENMP/pair_buck_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_omp.cpp rename to src/OPENMP/pair_buck_omp.cpp diff --git a/src/USER-OMP/pair_buck_omp.h b/src/OPENMP/pair_buck_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_omp.h rename to src/OPENMP/pair_buck_omp.h diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/OPENMP/pair_colloid_omp.cpp similarity index 100% rename from src/USER-OMP/pair_colloid_omp.cpp rename to src/OPENMP/pair_colloid_omp.cpp diff --git a/src/USER-OMP/pair_colloid_omp.h b/src/OPENMP/pair_colloid_omp.h similarity index 100% rename from src/USER-OMP/pair_colloid_omp.h rename to src/OPENMP/pair_colloid_omp.h diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/OPENMP/pair_comb_omp.cpp similarity index 98% rename from src/USER-OMP/pair_comb_omp.cpp rename to src/OPENMP/pair_comb_omp.cpp index 7c0c14f7e5..169704b289 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/OPENMP/pair_comb_omp.cpp @@ -70,10 +70,10 @@ void PairCombOMP::compute(int eflag, int vflag) if (evflag) { if (eflag) { - if (vflag_atom) eval<1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,1>(ifrom, ito, thr); else eval<1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<1,0,1>(ifrom, ito, thr); else eval<1,0,0>(ifrom, ito, thr); } } else eval<0,0,0>(ifrom, ito, thr); @@ -83,7 +83,7 @@ void PairCombOMP::compute(int eflag, int vflag) } // end of omp parallel region } -template +template void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,k,ii,jj,kk,jnum,iparam_i; @@ -365,7 +365,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1, elp_ij,0.0,0.0,0.0,0.0,0.0, thr); - if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr); + if (VFLAG_EITHER) v_tally3_thr(this,i,j,k,fj,fk,delr1,delr2,thr); } f[j][0] += fjxtmp; f[j][1] += fjytmp; diff --git a/src/USER-OMP/pair_comb_omp.h b/src/OPENMP/pair_comb_omp.h similarity index 100% rename from src/USER-OMP/pair_comb_omp.h rename to src/OPENMP/pair_comb_omp.h diff --git a/src/USER-OMP/pair_coul_cut_global_omp.cpp b/src/OPENMP/pair_coul_cut_global_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_cut_global_omp.cpp rename to src/OPENMP/pair_coul_cut_global_omp.cpp diff --git a/src/USER-OMP/pair_coul_cut_global_omp.h b/src/OPENMP/pair_coul_cut_global_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_cut_global_omp.h rename to src/OPENMP/pair_coul_cut_global_omp.h diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/OPENMP/pair_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_cut_omp.cpp rename to src/OPENMP/pair_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_coul_cut_omp.h b/src/OPENMP/pair_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_cut_omp.h rename to src/OPENMP/pair_coul_cut_omp.h diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/OPENMP/pair_coul_cut_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_cut_soft_omp.cpp rename to src/OPENMP/pair_coul_cut_soft_omp.cpp diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.h b/src/OPENMP/pair_coul_cut_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_cut_soft_omp.h rename to src/OPENMP/pair_coul_cut_soft_omp.h diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/OPENMP/pair_coul_debye_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_debye_omp.cpp rename to src/OPENMP/pair_coul_debye_omp.cpp diff --git a/src/USER-OMP/pair_coul_debye_omp.h b/src/OPENMP/pair_coul_debye_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_debye_omp.h rename to src/OPENMP/pair_coul_debye_omp.h diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/OPENMP/pair_coul_diel_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_diel_omp.cpp rename to src/OPENMP/pair_coul_diel_omp.cpp diff --git a/src/USER-OMP/pair_coul_diel_omp.h b/src/OPENMP/pair_coul_diel_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_diel_omp.h rename to src/OPENMP/pair_coul_diel_omp.h diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/OPENMP/pair_coul_dsf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_dsf_omp.cpp rename to src/OPENMP/pair_coul_dsf_omp.cpp diff --git a/src/USER-OMP/pair_coul_dsf_omp.h b/src/OPENMP/pair_coul_dsf_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_dsf_omp.h rename to src/OPENMP/pair_coul_dsf_omp.h diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/OPENMP/pair_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_long_omp.cpp rename to src/OPENMP/pair_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_coul_long_omp.h b/src/OPENMP/pair_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_long_omp.h rename to src/OPENMP/pair_coul_long_omp.h diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/OPENMP/pair_coul_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_long_soft_omp.cpp rename to src/OPENMP/pair_coul_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_coul_long_soft_omp.h b/src/OPENMP/pair_coul_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_long_soft_omp.h rename to src/OPENMP/pair_coul_long_soft_omp.h diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/OPENMP/pair_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_msm_omp.cpp rename to src/OPENMP/pair_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_coul_msm_omp.h b/src/OPENMP/pair_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_msm_omp.h rename to src/OPENMP/pair_coul_msm_omp.h diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/OPENMP/pair_coul_wolf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_wolf_omp.cpp rename to src/OPENMP/pair_coul_wolf_omp.cpp diff --git a/src/USER-OMP/pair_coul_wolf_omp.h b/src/OPENMP/pair_coul_wolf_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_wolf_omp.h rename to src/OPENMP/pair_coul_wolf_omp.h diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/OPENMP/pair_dpd_omp.cpp similarity index 100% rename from src/USER-OMP/pair_dpd_omp.cpp rename to src/OPENMP/pair_dpd_omp.cpp diff --git a/src/USER-OMP/pair_dpd_omp.h b/src/OPENMP/pair_dpd_omp.h similarity index 100% rename from src/USER-OMP/pair_dpd_omp.h rename to src/OPENMP/pair_dpd_omp.h diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/OPENMP/pair_dpd_tstat_omp.cpp similarity index 100% rename from src/USER-OMP/pair_dpd_tstat_omp.cpp rename to src/OPENMP/pair_dpd_tstat_omp.cpp diff --git a/src/USER-OMP/pair_dpd_tstat_omp.h b/src/OPENMP/pair_dpd_tstat_omp.h similarity index 100% rename from src/USER-OMP/pair_dpd_tstat_omp.h rename to src/OPENMP/pair_dpd_tstat_omp.h diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/OPENMP/pair_eam_alloy_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eam_alloy_omp.cpp rename to src/OPENMP/pair_eam_alloy_omp.cpp diff --git a/src/USER-OMP/pair_eam_alloy_omp.h b/src/OPENMP/pair_eam_alloy_omp.h similarity index 100% rename from src/USER-OMP/pair_eam_alloy_omp.h rename to src/OPENMP/pair_eam_alloy_omp.h diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/OPENMP/pair_eam_fs_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eam_fs_omp.cpp rename to src/OPENMP/pair_eam_fs_omp.cpp diff --git a/src/USER-OMP/pair_eam_fs_omp.h b/src/OPENMP/pair_eam_fs_omp.h similarity index 100% rename from src/USER-OMP/pair_eam_fs_omp.h rename to src/OPENMP/pair_eam_fs_omp.h diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/OPENMP/pair_eam_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eam_omp.cpp rename to src/OPENMP/pair_eam_omp.cpp diff --git a/src/USER-OMP/pair_eam_omp.h b/src/OPENMP/pair_eam_omp.h similarity index 100% rename from src/USER-OMP/pair_eam_omp.h rename to src/OPENMP/pair_eam_omp.h diff --git a/src/OPENMP/pair_edip_omp.cpp b/src/OPENMP/pair_edip_omp.cpp new file mode 100644 index 0000000000..da025d75d5 --- /dev/null +++ b/src/OPENMP/pair_edip_omp.cpp @@ -0,0 +1,470 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_edip_omp.h" + +#include "atom.h" +#include "comm.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +// max number of interaction per atom for f(Z) environment potential + +static constexpr int leadDimInteractionList = 64; + +#define GRIDDENSITY 8000 +#define GRIDSTART 0.1 + +/* ---------------------------------------------------------------------- */ + +PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) : PairEDIP(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairEDIPOMP::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = list->inum; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + if (evflag) { + if (eflag) { + if (vflag_atom) + eval<1, 1, 1>(ifrom, ito, thr); + else + eval<1, 1, 0>(ifrom, ito, thr); + } else { + if (vflag_atom) + eval<1, 0, 1>(ifrom, ito, thr); + else + eval<1, 0, 0>(ifrom, ito, thr); + } + } else + eval<0, 0, 0>(ifrom, ito, thr); + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairEDIPOMP::eval(int iifrom, int iito, ThrData *const thr) +{ + int i, j, k, ii, jnum; + int itype, jtype, ktype, ijparam, ikparam; + double xtmp, ytmp, ztmp, evdwl; + int *ilist, *jlist, *numneigh, **firstneigh; + int preForceCoord_counter; + + double invR_ij; + double invR_ik; + double directorCos_ij_x; + double directorCos_ij_y; + double directorCos_ij_z; + double directorCos_ik_x; + double directorCos_ik_y; + double directorCos_ik_z; + double cosTeta; + + int interpolIDX; + double interpolTMP; + double interpolDeltaX; + double interpolY1; + double interpolY2; + + double invRMinusCutoffA; + double sigmaInvRMinusCutoffA; + double gammInvRMinusCutoffA; + double cosTetaDiff; + double cosTetaDiffCosTetaDiff; + double cutoffFunction_ij; + double exp2B_ij; + double exp2BDerived_ij; + double pow2B_ij; + double pow2BDerived_ij; + double exp3B_ij; + double exp3BDerived_ij; + double exp3B_ik; + double exp3BDerived_ik; + double qFunction; + double tauFunction; + double tauFunctionDerived; + double expMinusBetaZeta_iZeta_i; + double qFunctionCosTetaDiffCosTetaDiff; + double expMinusQFunctionCosTetaDiffCosTetaDiff; + double zeta_i; + double zeta_iDerived; + double zeta_iDerivedInvR_ij; + + double forceModCoord_factor; + double forceModCoord; + double forceModCoord_ij; + double forceMod2B; + double forceMod3B_factor1_ij; + double forceMod3B_factor2_ij; + double forceMod3B_factor2; + double forceMod3B_factor1_ik; + double forceMod3B_factor2_ik; + double potentia3B_factor; + double potential2B_factor; + + const int tid = thr->get_tid(); + + double *pre_thrInvR_ij = preInvR_ij + tid * leadDimInteractionList; + double *pre_thrExp3B_ij = preExp3B_ij + tid * leadDimInteractionList; + double *pre_thrExp3BDerived_ij = preExp3BDerived_ij + tid * leadDimInteractionList; + double *pre_thrExp2B_ij = preExp2B_ij + tid * leadDimInteractionList; + double *pre_thrExp2BDerived_ij = preExp2BDerived_ij + tid * leadDimInteractionList; + double *pre_thrPow2B_ij = prePow2B_ij + tid * leadDimInteractionList; + double *pre_thrForceCoord = preForceCoord + tid * leadDimInteractionList; + + const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0]; + dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0]; + const int *_noalias const type = atom->type; + const int nlocal = atom->nlocal; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over full neighbor list of my atoms + + for (ii = iifrom; ii < iito; ii++) { + zeta_i = 0.0; + int numForceCoordPairs = 0; + + i = ilist[ii]; + itype = map[type[i]]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // pre-loop to compute environment coordination f(Z) + + for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { + j = jlist[neighbor_j]; + j &= NEIGHMASK; + + double dr_ij[3], r_ij; + + dr_ij[0] = xtmp - x[j].x; + dr_ij[1] = ytmp - x[j].y; + dr_ij[2] = ztmp - x[j].z; + r_ij = dr_ij[0] * dr_ij[0] + dr_ij[1] * dr_ij[1] + dr_ij[2] * dr_ij[2]; + + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + if (r_ij > params[ijparam].cutsq) continue; + + r_ij = sqrt(r_ij); + + invR_ij = 1.0 / r_ij; + pre_thrInvR_ij[neighbor_j] = invR_ij; + + invRMinusCutoffA = 1.0 / (r_ij - cutoffA); + sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA; + gammInvRMinusCutoffA = gamm * invRMinusCutoffA; + + interpolDeltaX = r_ij - GRIDSTART; + interpolTMP = (interpolDeltaX * GRIDDENSITY); + interpolIDX = (int) interpolTMP; + + interpolY1 = exp3B[interpolIDX]; + interpolY2 = exp3B[interpolIDX + 1]; + exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA; + + pre_thrExp3B_ij[neighbor_j] = exp3B_ij; + pre_thrExp3BDerived_ij[neighbor_j] = exp3BDerived_ij; + + interpolY1 = exp2B[interpolIDX]; + interpolY2 = exp2B[interpolIDX + 1]; + exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA; + + pre_thrExp2B_ij[neighbor_j] = exp2B_ij; + pre_thrExp2BDerived_ij[neighbor_j] = exp2BDerived_ij; + + interpolY1 = pow2B[interpolIDX]; + interpolY2 = pow2B[interpolIDX + 1]; + pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + pre_thrPow2B_ij[neighbor_j] = pow2B_ij; + + // zeta and its derivative + + if (r_ij < cutoffC) + zeta_i += 1.0; + else { + interpolY1 = cutoffFunction[interpolIDX]; + interpolY2 = cutoffFunction[interpolIDX + 1]; + cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + zeta_i += cutoffFunction_ij; + + interpolY1 = cutoffFunctionDerived[interpolIDX]; + interpolY2 = cutoffFunctionDerived[interpolIDX + 1]; + zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij; + + preForceCoord_counter = numForceCoordPairs * 5; + pre_thrForceCoord[preForceCoord_counter + 0] = zeta_iDerivedInvR_ij; + pre_thrForceCoord[preForceCoord_counter + 1] = dr_ij[0]; + pre_thrForceCoord[preForceCoord_counter + 2] = dr_ij[1]; + pre_thrForceCoord[preForceCoord_counter + 3] = dr_ij[2]; + pre_thrForceCoord[preForceCoord_counter + 4] = j; + numForceCoordPairs++; + } + } + + // quantities depending on zeta_i + + interpolDeltaX = zeta_i; + interpolTMP = (interpolDeltaX * GRIDDENSITY); + interpolIDX = (int) interpolTMP; + + interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX]; + interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX + 1]; + expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + interpolY1 = qFunctionGrid[interpolIDX]; + interpolY2 = qFunctionGrid[interpolIDX + 1]; + qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + interpolY1 = tauFunctionGrid[interpolIDX]; + interpolY2 = tauFunctionGrid[interpolIDX + 1]; + tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + interpolY1 = tauFunctionDerivedGrid[interpolIDX]; + interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1]; + tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX); + + forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i; + + forceModCoord = 0.0; + + // two-body interactions, skip half of them + + for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { + double dr_ij[3], r_ij, f_ij[3]; + + j = jlist[neighbor_j]; + j &= NEIGHMASK; + + dr_ij[0] = x[j].x - xtmp; + dr_ij[1] = x[j].y - ytmp; + dr_ij[2] = x[j].z - ztmp; + r_ij = dr_ij[0] * dr_ij[0] + dr_ij[1] * dr_ij[1] + dr_ij[2] * dr_ij[2]; + + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + if (r_ij > params[ijparam].cutsq) continue; + + r_ij = sqrt(r_ij); + + invR_ij = pre_thrInvR_ij[neighbor_j]; + pow2B_ij = pre_thrPow2B_ij[neighbor_j]; + + potential2B_factor = pow2B_ij - expMinusBetaZeta_iZeta_i; + + exp2B_ij = pre_thrExp2B_ij[neighbor_j]; + + pow2BDerived_ij = -rho * invR_ij * pow2B_ij; + + forceModCoord += (forceModCoord_factor * exp2B_ij); + + exp2BDerived_ij = pre_thrExp2BDerived_ij[neighbor_j]; + forceMod2B = exp2BDerived_ij * potential2B_factor + exp2B_ij * pow2BDerived_ij; + + directorCos_ij_x = invR_ij * dr_ij[0]; + directorCos_ij_y = invR_ij * dr_ij[1]; + directorCos_ij_z = invR_ij * dr_ij[2]; + + exp3B_ij = pre_thrExp3B_ij[neighbor_j]; + exp3BDerived_ij = pre_thrExp3BDerived_ij[neighbor_j]; + + f_ij[0] = forceMod2B * directorCos_ij_x; + f_ij[1] = forceMod2B * directorCos_ij_y; + f_ij[2] = forceMod2B * directorCos_ij_z; + + f[i].x += f_ij[0]; + f[i].y += f_ij[1]; + f[i].z += f_ij[2]; + + f[j].x -= f_ij[0]; + f[j].y -= f_ij[1]; + f[j].z -= f_ij[2]; + + // potential energy + + evdwl = (exp2B_ij * potential2B_factor); + + if (EVFLAG) + ev_tally_thr(this, i, j, nlocal, /* newton_pair */ 1, evdwl, 0.0, -forceMod2B * invR_ij, + dr_ij[0], dr_ij[1], dr_ij[2], thr); + + // three-body Forces + + for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) { + double dr_ik[3], r_ik, f_ik[3]; + + k = jlist[neighbor_k]; + k &= NEIGHMASK; + ktype = map[type[k]]; + ikparam = elem3param[itype][ktype][ktype]; + + dr_ik[0] = x[k].x - xtmp; + dr_ik[1] = x[k].y - ytmp; + dr_ik[2] = x[k].z - ztmp; + r_ik = dr_ik[0] * dr_ik[0] + dr_ik[1] * dr_ik[1] + dr_ik[2] * dr_ik[2]; + + if (r_ik > params[ikparam].cutsq) continue; + + r_ik = sqrt(r_ik); + + invR_ik = pre_thrInvR_ij[neighbor_k]; + + directorCos_ik_x = invR_ik * dr_ik[0]; + directorCos_ik_y = invR_ik * dr_ik[1]; + directorCos_ik_z = invR_ik * dr_ik[2]; + + cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + + directorCos_ij_z * directorCos_ik_z; + + cosTetaDiff = cosTeta + tauFunction; + cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff; + qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction; + expMinusQFunctionCosTetaDiffCosTetaDiff = exp(-qFunctionCosTetaDiffCosTetaDiff); + + potentia3B_factor = lambda * + ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) + + eta * qFunctionCosTetaDiffCosTetaDiff); + + exp3B_ik = pre_thrExp3B_ij[neighbor_k]; + exp3BDerived_ik = pre_thrExp3BDerived_ij[neighbor_k]; + + forceMod3B_factor1_ij = -exp3BDerived_ij * exp3B_ik * potentia3B_factor; + forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik * qFunction * cosTetaDiff * + (eta + expMinusQFunctionCosTetaDiffCosTetaDiff); + forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij; + + f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x + + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_x - directorCos_ik_x); + f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y + + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_y - directorCos_ik_y); + f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z + + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_z - directorCos_ik_z); + + forceMod3B_factor1_ik = -exp3BDerived_ik * exp3B_ij * potentia3B_factor; + forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik; + + f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x + + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_x - directorCos_ij_x); + f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y + + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_y - directorCos_ij_y); + f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z + + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_z - directorCos_ij_z); + + forceModCoord += (forceMod3B_factor2 * (tauFunctionDerived - 0.5 * mu * cosTetaDiff)); + + f[j].x += f_ij[0]; + f[j].y += f_ij[1]; + f[j].z += f_ij[2]; + + f[k].x += f_ik[0]; + f[k].y += f_ik[1]; + f[k].z += f_ik[2]; + + f[i].x -= f_ij[0] + f_ik[0]; + f[i].y -= f_ij[1] + f_ik[1]; + f[i].z -= f_ij[2] + f_ik[2]; + + // potential energy + + evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor); + + if (EVFLAG) ev_tally3_thr(this, i, j, k, evdwl, 0.0, f_ij, f_ik, dr_ij, dr_ik, thr); + } + } + + // forces due to environment coordination f(Z) + + for (int idx = 0; idx < numForceCoordPairs; idx++) { + double dr_ij[3], f_ij[3]; + + preForceCoord_counter = idx * 5; + zeta_iDerivedInvR_ij = pre_thrForceCoord[preForceCoord_counter + 0]; + dr_ij[0] = pre_thrForceCoord[preForceCoord_counter + 1]; + dr_ij[1] = pre_thrForceCoord[preForceCoord_counter + 2]; + dr_ij[2] = pre_thrForceCoord[preForceCoord_counter + 3]; + j = static_cast(pre_thrForceCoord[preForceCoord_counter + 4]); + + forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij; + + f_ij[0] = forceModCoord_ij * dr_ij[0]; + f_ij[1] = forceModCoord_ij * dr_ij[1]; + f_ij[2] = forceModCoord_ij * dr_ij[2]; + + f[i].x -= f_ij[0]; + f[i].y -= f_ij[1]; + f[i].z -= f_ij[2]; + + f[j].x += f_ij[0]; + f[j].y += f_ij[1]; + f[j].z += f_ij[2]; + + if (EVFLAG) + ev_tally_thr(this, i, j, nlocal, /* newton_pair */ 1, 0.0, 0.0, -forceModCoord_ij, dr_ij[0], + dr_ij[1], dr_ij[2], thr); + } + } +} + +/* ---------------------------------------------------------------------- */ + +double PairEDIPOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairEDIP::memory_usage(); + + return bytes; +} diff --git a/src/USER-OMP/pair_edip_omp.h b/src/OPENMP/pair_edip_omp.h similarity index 100% rename from src/USER-OMP/pair_edip_omp.h rename to src/OPENMP/pair_edip_omp.h diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/OPENMP/pair_eim_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eim_omp.cpp rename to src/OPENMP/pair_eim_omp.cpp diff --git a/src/USER-OMP/pair_eim_omp.h b/src/OPENMP/pair_eim_omp.h similarity index 100% rename from src/USER-OMP/pair_eim_omp.h rename to src/OPENMP/pair_eim_omp.h diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/OPENMP/pair_gauss_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gauss_cut_omp.cpp rename to src/OPENMP/pair_gauss_cut_omp.cpp diff --git a/src/USER-OMP/pair_gauss_cut_omp.h b/src/OPENMP/pair_gauss_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_gauss_cut_omp.h rename to src/OPENMP/pair_gauss_cut_omp.h diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/OPENMP/pair_gauss_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gauss_omp.cpp rename to src/OPENMP/pair_gauss_omp.cpp diff --git a/src/USER-OMP/pair_gauss_omp.h b/src/OPENMP/pair_gauss_omp.h similarity index 100% rename from src/USER-OMP/pair_gauss_omp.h rename to src/OPENMP/pair_gauss_omp.h diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/OPENMP/pair_gayberne_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gayberne_omp.cpp rename to src/OPENMP/pair_gayberne_omp.cpp diff --git a/src/USER-OMP/pair_gayberne_omp.h b/src/OPENMP/pair_gayberne_omp.h similarity index 100% rename from src/USER-OMP/pair_gayberne_omp.h rename to src/OPENMP/pair_gayberne_omp.h diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/OPENMP/pair_gran_hertz_history_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gran_hertz_history_omp.cpp rename to src/OPENMP/pair_gran_hertz_history_omp.cpp diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.h b/src/OPENMP/pair_gran_hertz_history_omp.h similarity index 100% rename from src/USER-OMP/pair_gran_hertz_history_omp.h rename to src/OPENMP/pair_gran_hertz_history_omp.h diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/OPENMP/pair_gran_hooke_history_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gran_hooke_history_omp.cpp rename to src/OPENMP/pair_gran_hooke_history_omp.cpp diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.h b/src/OPENMP/pair_gran_hooke_history_omp.h similarity index 100% rename from src/USER-OMP/pair_gran_hooke_history_omp.h rename to src/OPENMP/pair_gran_hooke_history_omp.h diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/OPENMP/pair_gran_hooke_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gran_hooke_omp.cpp rename to src/OPENMP/pair_gran_hooke_omp.cpp diff --git a/src/USER-OMP/pair_gran_hooke_omp.h b/src/OPENMP/pair_gran_hooke_omp.h similarity index 100% rename from src/USER-OMP/pair_gran_hooke_omp.h rename to src/OPENMP/pair_gran_hooke_omp.h diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp rename to src/OPENMP/pair_hbond_dreiding_lj_omp.cpp diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.h b/src/OPENMP/pair_hbond_dreiding_lj_omp.h similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_lj_omp.h rename to src/OPENMP/pair_hbond_dreiding_lj_omp.h diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp rename to src/OPENMP/pair_hbond_dreiding_morse_omp.cpp diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.h b/src/OPENMP/pair_hbond_dreiding_morse_omp.h similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_morse_omp.h rename to src/OPENMP/pair_hbond_dreiding_morse_omp.h diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/OPENMP/pair_lj96_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj96_cut_omp.cpp rename to src/OPENMP/pair_lj96_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj96_cut_omp.h b/src/OPENMP/pair_lj96_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj96_cut_omp.h rename to src/OPENMP/pair_lj96_cut_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h rename to src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h rename to src/OPENMP/pair_lj_charmm_coul_charmm_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.h b/src/OPENMP/pair_lj_charmm_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_omp.h rename to src/OPENMP/pair_lj_charmm_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h rename to src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.h b/src/OPENMP/pair_lj_charmm_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_msm_omp.h rename to src/OPENMP/pair_lj_charmm_coul_msm_omp.h diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/OPENMP/pair_lj_class2_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp rename to src/OPENMP/pair_lj_class2_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.h b/src/OPENMP/pair_lj_class2_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_cut_omp.h rename to src/OPENMP/pair_lj_class2_coul_cut_omp.h diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/OPENMP/pair_lj_class2_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_long_omp.cpp rename to src/OPENMP/pair_lj_class2_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.h b/src/OPENMP/pair_lj_class2_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_long_omp.h rename to src/OPENMP/pair_lj_class2_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/OPENMP/pair_lj_class2_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_class2_omp.cpp rename to src/OPENMP/pair_lj_class2_omp.cpp diff --git a/src/USER-OMP/pair_lj_class2_omp.h b/src/OPENMP/pair_lj_class2_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_class2_omp.h rename to src/OPENMP/pair_lj_class2_omp.h diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/OPENMP/pair_lj_cubic_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cubic_omp.cpp rename to src/OPENMP/pair_lj_cubic_omp.cpp diff --git a/src/USER-OMP/pair_lj_cubic_omp.h b/src/OPENMP/pair_lj_cubic_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cubic_omp.h rename to src/OPENMP/pair_lj_cubic_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp similarity index 96% rename from src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp index 22ae388236..eacb774372 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp @@ -104,11 +104,11 @@ void PairLJCutCoulCutDielectricOMP::compute(int eflag, int vflag) template void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const thr) { - int i, j, ii, jj, jnum, itype, jtype, itable; - double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; + int i, j, ii, jj, jnum, itype, jtype; + double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul; double fpair_i, fpair_j; - double r, rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj; - double grij, expm2, prefactor, t, erfc, prefactorE, efield_i, epot_i; + double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj; + double efield_i, epot_i; int *ilist, *jlist, *numneigh, **firstneigh; evdwl = ecoul = 0.0; @@ -221,7 +221,7 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th } if (EVFLAG) - ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, ecoul, fpair, delx, dely, delz, thr); + ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, ecoul, fpair_i, delx, dely, delz, thr); } } f[i].x += fxtmp; diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.h rename to src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_omp.h rename to src/OPENMP/pair_lj_cut_coul_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h rename to src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/OPENMP/pair_lj_cut_coul_debye_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_debye_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.h b/src/OPENMP/pair_lj_cut_coul_debye_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_debye_omp.h rename to src/OPENMP/pair_lj_cut_coul_debye_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.h b/src/OPENMP/pair_lj_cut_coul_dsf_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_dsf_omp.h rename to src/OPENMP/pair_lj_cut_coul_dsf_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.h rename to src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.h b/src/OPENMP/pair_lj_cut_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_omp.h rename to src/OPENMP/pair_lj_cut_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h rename to src/OPENMP/pair_lj_cut_coul_long_soft_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/OPENMP/pair_lj_cut_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.h b/src/OPENMP/pair_lj_cut_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_msm_omp.h rename to src/OPENMP/pair_lj_cut_coul_msm_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h b/src/OPENMP/pair_lj_cut_coul_wolf_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_wolf_omp.h rename to src/OPENMP/pair_lj_cut_coul_wolf_omp.h diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h b/src/OPENMP/pair_lj_cut_dipole_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_dipole_cut_omp.h rename to src/OPENMP/pair_lj_cut_dipole_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/OPENMP/pair_lj_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_omp.h b/src/OPENMP/pair_lj_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_omp.h rename to src/OPENMP/pair_lj_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/OPENMP/pair_lj_cut_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.h b/src/OPENMP/pair_lj_cut_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_soft_omp.h rename to src/OPENMP/pair_lj_cut_soft_omp.h diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/OPENMP/pair_lj_cut_thole_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_thole_long_omp.cpp rename to src/OPENMP/pair_lj_cut_thole_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.h b/src/OPENMP/pair_lj_cut_thole_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_thole_long_omp.h rename to src/OPENMP/pair_lj_cut_thole_long_omp.h diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h rename to src/OPENMP/pair_lj_cut_tip4p_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp rename to src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.h b/src/OPENMP/pair_lj_cut_tip4p_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_omp.h rename to src/OPENMP/pair_lj_cut_tip4p_long_omp.h diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h rename to src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/OPENMP/pair_lj_expand_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_expand_omp.cpp rename to src/OPENMP/pair_lj_expand_omp.cpp diff --git a/src/USER-OMP/pair_lj_expand_omp.h b/src/OPENMP/pair_lj_expand_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_expand_omp.h rename to src/OPENMP/pair_lj_expand_omp.h diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp rename to src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h rename to src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/OPENMP/pair_lj_gromacs_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_omp.cpp rename to src/OPENMP/pair_lj_gromacs_omp.cpp diff --git a/src/USER-OMP/pair_lj_gromacs_omp.h b/src/OPENMP/pair_lj_gromacs_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_omp.h rename to src/OPENMP/pair_lj_gromacs_omp.h diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/OPENMP/pair_lj_long_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_long_coul_long_omp.cpp rename to src/OPENMP/pair_lj_long_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.h b/src/OPENMP/pair_lj_long_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_long_coul_long_omp.h rename to src/OPENMP/pair_lj_long_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/OPENMP/pair_lj_long_tip4p_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp rename to src/OPENMP/pair_lj_long_tip4p_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.h b/src/OPENMP/pair_lj_long_tip4p_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_long_tip4p_long_omp.h rename to src/OPENMP/pair_lj_long_tip4p_long_omp.h diff --git a/src/USER-OMP/pair_lj_relres_omp.cpp b/src/OPENMP/pair_lj_relres_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_relres_omp.cpp rename to src/OPENMP/pair_lj_relres_omp.cpp diff --git a/src/USER-OMP/pair_lj_relres_omp.h b/src/OPENMP/pair_lj_relres_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_relres_omp.h rename to src/OPENMP/pair_lj_relres_omp.h diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/OPENMP/pair_lj_sdk_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp rename to src/OPENMP/pair_lj_sdk_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h b/src/OPENMP/pair_lj_sdk_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_long_omp.h rename to src/OPENMP/pair_lj_sdk_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h b/src/OPENMP/pair_lj_sdk_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_msm_omp.h rename to src/OPENMP/pair_lj_sdk_coul_msm_omp.h diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/OPENMP/pair_lj_sdk_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sdk_omp.cpp rename to src/OPENMP/pair_lj_sdk_omp.cpp diff --git a/src/USER-OMP/pair_lj_sdk_omp.h b/src/OPENMP/pair_lj_sdk_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sdk_omp.h rename to src/OPENMP/pair_lj_sdk_omp.h diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp rename to src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h b/src/OPENMP/pair_lj_sf_dipole_sf_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sf_dipole_sf_omp.h rename to src/OPENMP/pair_lj_sf_dipole_sf_omp.h diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/OPENMP/pair_lj_smooth_linear_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_smooth_linear_omp.cpp rename to src/OPENMP/pair_lj_smooth_linear_omp.cpp diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.h b/src/OPENMP/pair_lj_smooth_linear_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_smooth_linear_omp.h rename to src/OPENMP/pair_lj_smooth_linear_omp.h diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/OPENMP/pair_lj_smooth_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_smooth_omp.cpp rename to src/OPENMP/pair_lj_smooth_omp.cpp diff --git a/src/USER-OMP/pair_lj_smooth_omp.h b/src/OPENMP/pair_lj_smooth_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_smooth_omp.h rename to src/OPENMP/pair_lj_smooth_omp.h diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/OPENMP/pair_lubricate_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lubricate_omp.cpp rename to src/OPENMP/pair_lubricate_omp.cpp diff --git a/src/USER-OMP/pair_lubricate_omp.h b/src/OPENMP/pair_lubricate_omp.h similarity index 100% rename from src/USER-OMP/pair_lubricate_omp.h rename to src/OPENMP/pair_lubricate_omp.h diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/OPENMP/pair_lubricate_poly_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lubricate_poly_omp.cpp rename to src/OPENMP/pair_lubricate_poly_omp.cpp diff --git a/src/USER-OMP/pair_lubricate_poly_omp.h b/src/OPENMP/pair_lubricate_poly_omp.h similarity index 100% rename from src/USER-OMP/pair_lubricate_poly_omp.h rename to src/OPENMP/pair_lubricate_poly_omp.h diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/OPENMP/pair_meam_spline_omp.cpp similarity index 100% rename from src/USER-OMP/pair_meam_spline_omp.cpp rename to src/OPENMP/pair_meam_spline_omp.cpp diff --git a/src/USER-OMP/pair_meam_spline_omp.h b/src/OPENMP/pair_meam_spline_omp.h similarity index 100% rename from src/USER-OMP/pair_meam_spline_omp.h rename to src/OPENMP/pair_meam_spline_omp.h diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/OPENMP/pair_morse_omp.cpp similarity index 100% rename from src/USER-OMP/pair_morse_omp.cpp rename to src/OPENMP/pair_morse_omp.cpp diff --git a/src/USER-OMP/pair_morse_omp.h b/src/OPENMP/pair_morse_omp.h similarity index 100% rename from src/USER-OMP/pair_morse_omp.h rename to src/OPENMP/pair_morse_omp.h diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/OPENMP/pair_morse_smooth_linear_omp.cpp similarity index 100% rename from src/USER-OMP/pair_morse_smooth_linear_omp.cpp rename to src/OPENMP/pair_morse_smooth_linear_omp.cpp diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.h b/src/OPENMP/pair_morse_smooth_linear_omp.h similarity index 100% rename from src/USER-OMP/pair_morse_smooth_linear_omp.h rename to src/OPENMP/pair_morse_smooth_linear_omp.h diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/OPENMP/pair_nm_cut_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp rename to src/OPENMP/pair_nm_cut_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.h b/src/OPENMP/pair_nm_cut_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_cut_omp.h rename to src/OPENMP/pair_nm_cut_coul_cut_omp.h diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/OPENMP/pair_nm_cut_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_long_omp.cpp rename to src/OPENMP/pair_nm_cut_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.h b/src/OPENMP/pair_nm_cut_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_long_omp.h rename to src/OPENMP/pair_nm_cut_coul_long_omp.h diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/OPENMP/pair_nm_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_nm_cut_omp.cpp rename to src/OPENMP/pair_nm_cut_omp.cpp diff --git a/src/USER-OMP/pair_nm_cut_omp.h b/src/OPENMP/pair_nm_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_nm_cut_omp.h rename to src/OPENMP/pair_nm_cut_omp.h diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/OPENMP/pair_peri_lps_omp.cpp similarity index 100% rename from src/USER-OMP/pair_peri_lps_omp.cpp rename to src/OPENMP/pair_peri_lps_omp.cpp diff --git a/src/USER-OMP/pair_peri_lps_omp.h b/src/OPENMP/pair_peri_lps_omp.h similarity index 100% rename from src/USER-OMP/pair_peri_lps_omp.h rename to src/OPENMP/pair_peri_lps_omp.h diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/OPENMP/pair_peri_pmb_omp.cpp similarity index 100% rename from src/USER-OMP/pair_peri_pmb_omp.cpp rename to src/OPENMP/pair_peri_pmb_omp.cpp diff --git a/src/USER-OMP/pair_peri_pmb_omp.h b/src/OPENMP/pair_peri_pmb_omp.h similarity index 100% rename from src/USER-OMP/pair_peri_pmb_omp.h rename to src/OPENMP/pair_peri_pmb_omp.h diff --git a/src/OPENMP/pair_reaxff_omp.cpp b/src/OPENMP/pair_reaxff_omp.cpp new file mode 100644 index 0000000000..6cf3e90575 --- /dev/null +++ b/src/OPENMP/pair_reaxff_omp.cpp @@ -0,0 +1,533 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Per-atom energy/virial added by Ray Shan (Materials Design, Inc.) + Fix reaxff/bonds and fix reaxff/species for pair_style reaxff added + by Ray Shan (Materials Design) + + OpenMP based threading support for pair_style reaxff/omp added + by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF), + Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF) + + Integration of the pair_style reaxff/omp into the OPENMP package + by Axel Kohlmeyer (Temple U.) + + Please cite the related publication: + H. M. Aktulga, C. Knight, P. Coffman, K. A. O'Hearn, T. R. Shan, + W. Jiang, "Optimizing the performance of reactive molecular dynamics + simulations for multi-core architectures", International Journal of + High Performance Computing Applications, to appear. + ------------------------------------------------------------------------- */ + +#include "pair_reaxff_omp.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "fix_reaxff.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" + +#include + +#include "reaxff_api.h" +#include "reaxff_omp.h" + +#if defined(_OPENMP) +#include +#endif + +#include "omp_compat.h" +#include "suffix.h" +using namespace LAMMPS_NS; +using namespace ReaxFF; + +static const char cite_pair_reaxff_omp[] = + "pair reaxff/omp and fix qeq/reaxff/omp command:\n\n" + "@Article{Aktulga17,\n" + " author = {H. M. Aktulga, C. Knight, P. Coffman, K. A. OHearn, T. R. Shan, W. Jiang},\n" + " title = {Optimizing the performance of reactive molecular dynamics simulations for multi-core architectures},\n" + " journal = {International Journal of High Performance Computing Applications},\n" + " year = to appear\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairReaxFFOMP::PairReaxFFOMP(LAMMPS *lmp) : PairReaxFF(lmp), ThrOMP(lmp, THR_PAIR) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_reaxff_omp); + + suffix_flag |= Suffix::OMP; + api->system->pair_ptr = this; + api->system->omp_active = 1; + + num_nbrs_offset = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +PairReaxFFOMP::~PairReaxFFOMP() +{ + if (setup_flag) { + reax_list * bonds = api->lists+BONDS; + for (int i=0; inum_intrs; ++i) + sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); + } + memory->destroy(num_nbrs_offset); +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFFOMP::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style reaxff/omp requires atom attribute q"); + + bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1) + || (modify->find_fix_by_style("^qeq/shielded") != -1)); + if (!have_qeq && qeqflag == 1) + error->all(FLERR,"Pair reaxff/omp requires use of fix qeq/reaxff or qeq/shielded"); + + api->system->n = atom->nlocal; // my atoms + api->system->N = atom->nlocal + atom->nghost; // mine + ghosts + api->system->bigN = static_cast (atom->natoms); // all atoms in the system + api->system->wsize = comm->nprocs; + + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style reaxff/omp requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR,"Pair style reaxff/omp requires newton pair on"); + + // because system->bigN is an int, we cannot have more atoms than MAXSMALLINT + + if (atom->natoms > MAXSMALLINT) + error->all(FLERR,"Too many atoms for pair style reaxff/omp"); + + // need a half neighbor list w/ Newton off and ghost neighbors + // built whenever re-neighboring occurs + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->newton = 2; + neighbor->requests[irequest]->ghost = 1; + + cutmax = MAX3(api->control->nonb_cut, api->control->hbond_cut, api->control->bond_cut); + if ((cutmax < 2.0*api->control->bond_cut) && (comm->me == 0)) + error->warning(FLERR,"Total cutoff < 2*bond cutoff. May need to use an " + "increased neighbor list skin."); + + if (fix_reaxff == nullptr) + fix_reaxff = (FixReaxFF *) modify->add_fix(fmt::format("{} all REAXFF",fix_id)); + + api->control->nthreads = comm->nthreads; +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFFOMP::setup() +{ + int oldN; + int mincap = api->system->mincap; + double safezone = api->system->safezone; + + api->system->n = atom->nlocal; // my atoms + api->system->N = atom->nlocal + atom->nghost; // mine + ghosts + oldN = api->system->N; + api->system->bigN = static_cast (atom->natoms); // all atoms in the system + + if (api->system->N > nmax) { + memory->destroy(num_nbrs_offset); + // Don't update nmax here. It is updated at end of compute(). + memory->create(num_nbrs_offset, api->system->N, "pair:num_nbrs_offset"); + } + + if (setup_flag == 0) { + + setup_flag = 1; + + int *num_bonds = fix_reaxff->num_bonds; + int *num_hbonds = fix_reaxff->num_hbonds; + + // determine the local and total capacity + + api->system->local_cap = MAX((int)(api->system->n * safezone), mincap); + api->system->total_cap = MAX((int)(api->system->N * safezone), mincap); + + // initialize my data structures + + PreAllocate_Space(api->system, api->workspace); + write_reax_atoms(); + + api->system->wsize = comm->nprocs; + + int num_nbrs = estimate_reax_lists(); + if (num_nbrs < 0) + error->all(FLERR,"Too many neighbors for pair style reaxff"); + + Make_List(api->system->total_cap,num_nbrs,TYP_FAR_NEIGHBOR,api->lists+FAR_NBRS); + (api->lists+FAR_NBRS)->error_ptr=error; + + write_reax_lists(); + + InitializeOMP(api->system,api->control,api->data,api->workspace,&api->lists,world); + for (int k = 0; k < api->system->N; ++k) { + num_bonds[k] = api->system->my_atoms[k].num_bonds; + num_hbonds[k] = api->system->my_atoms[k].num_hbonds; + } + + } else { + + // fill in reax datastructures + + write_reax_atoms(); + + // reset the bond list info for new atoms + + for (int k = oldN; k < api->system->N; ++k) + Set_End_Index(k, Start_Index(k, api->lists+BONDS), api->lists+BONDS); + + // estimate far neighbor list size + // Not present in MPI-only version + api->workspace->realloc.num_far = estimate_reax_lists(); + + // check if I need to shrink/extend my data-structs + + ReAllocate(api->system, api->control, api->data, api->workspace, &api->lists); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFFOMP::compute(int eflag, int vflag) +{ + double evdwl,ecoul; + + // communicate num_bonds once every reneighboring + // 2 num arrays stored by fix, grab ptr to them + + if (neighbor->ago == 0) comm->forward_comm_fix(fix_reaxff); + int *num_bonds = fix_reaxff->num_bonds; + int *num_hbonds = fix_reaxff->num_hbonds; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + api->system->n = atom->nlocal; // my atoms + api->system->N = atom->nlocal + atom->nghost; // mine + ghosts + api->system->bigN = static_cast (atom->natoms); // all atoms in the system + const int nall = api->system->N; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { +#if defined(_OPENMP) + int tid = omp_get_thread_num(); +#else + int tid = 0; +#endif + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, api->system->N, eatom, vatom, nullptr, thr); + } + // setup data structures + + setup(); + + Reset(api->system, api->control, api->data, api->workspace, &api->lists); + + // Why not update workspace like in MPI-only code? + // Using the MPI-only way messes up the hb energy + //workspace->realloc.num_far = write_reax_lists(); + write_reax_lists(); + + // forces + + Compute_ForcesOMP(api->system,api->control,api->data,api->workspace,&api->lists); + read_reax_forces(vflag); + + const int nthreads = comm->nthreads; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(vflag) +#endif + { +#if defined(_OPENMP) + int tid = omp_get_thread_num(); +#else + int tid = 0; +#endif + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::PAIR); + + // the pair style reduces energy and forces directly. so only reduce virial/ + // per-atom virial and per-atom centroid virial are the same for two-body + // many-body pair styles not yet implemented + if (vflag & (VIRIAL_ATOM | VIRIAL_CENTROID)) { + data_reduce_thr(&(vatom[0][0]), nall , nthreads, 6, tid); + } + } + +#if defined(_OPENMP) +#pragma omp parallel for schedule(static) +#endif + for (int k = 0; k < api->system->N; ++k) { + num_bonds[k] = api->system->my_atoms[k].num_bonds; + num_hbonds[k] = api->system->my_atoms[k].num_hbonds; + } + + // energies and pressure + + if (eflag_global) { + evdwl += api->data->my_en.e_bond; + evdwl += api->data->my_en.e_ov; + evdwl += api->data->my_en.e_un; + evdwl += api->data->my_en.e_lp; + evdwl += api->data->my_en.e_ang; + evdwl += api->data->my_en.e_pen; + evdwl += api->data->my_en.e_coa; + evdwl += api->data->my_en.e_hb; + evdwl += api->data->my_en.e_tor; + evdwl += api->data->my_en.e_con; + evdwl += api->data->my_en.e_vdW; + + ecoul += api->data->my_en.e_ele; + ecoul += api->data->my_en.e_pol; + + // Store the different parts of the energy + // in a list for output by compute pair command + + pvector[0] = api->data->my_en.e_bond; + pvector[1] = api->data->my_en.e_ov + api->data->my_en.e_un; + pvector[2] = api->data->my_en.e_lp; + pvector[3] = 0.0; + pvector[4] = api->data->my_en.e_ang; + pvector[5] = api->data->my_en.e_pen; + pvector[6] = api->data->my_en.e_coa; + pvector[7] = api->data->my_en.e_hb; + pvector[8] = api->data->my_en.e_tor; + pvector[9] = api->data->my_en.e_con; + pvector[10] = api->data->my_en.e_vdW; + pvector[11] = api->data->my_en.e_ele; + pvector[12] = 0.0; + pvector[13] = api->data->my_en.e_pol; + } + + if (vflag_fdotr) virial_fdotr_compute(); + + // Set internal timestep counter to that of LAMMPS + + api->data->step = update->ntimestep; + + // populate tmpid and tmpbo arrays for fix reaxff/species + + if (fixspecies_flag) { + if (api->system->N > nmax) { + memory->destroy(tmpid); + memory->destroy(tmpbo); + nmax = api->system->N; + memory->create(tmpid,nmax,MAXSPECBOND,"pair:tmpid"); + memory->create(tmpbo,nmax,MAXSPECBOND,"pair:tmpbo"); + } + +#if defined(_OPENMP) +#pragma omp parallel for collapse(2) schedule(static) default(shared) +#endif + for (int i = 0; i < api->system->N; i++) + for (int j = 0; j < MAXSPECBOND; j++) { + tmpbo[i][j] = 0.0; + tmpid[i][j] = 0; + } + + FindBond(); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFFOMP::write_reax_atoms() +{ + int *num_bonds = fix_reaxff->num_bonds; + int *num_hbonds = fix_reaxff->num_hbonds; + + if (api->system->N > api->system->total_cap) + error->all(FLERR,"Too many ghost atoms"); + +#if defined(_OPENMP) +#pragma omp parallel for schedule(static) default(shared) +#endif + for (int i = 0; i < api->system->N; ++i) { + api->system->my_atoms[i].orig_id = atom->tag[i]; + api->system->my_atoms[i].type = map[atom->type[i]]; + api->system->my_atoms[i].x[0] = atom->x[i][0]; + api->system->my_atoms[i].x[1] = atom->x[i][1]; + api->system->my_atoms[i].x[2] = atom->x[i][2]; + api->system->my_atoms[i].q = atom->q[i]; + api->system->my_atoms[i].num_bonds = num_bonds[i]; + api->system->my_atoms[i].num_hbonds = num_hbonds[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +int PairReaxFFOMP::estimate_reax_lists() +{ + int i; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int numall = list->inum + list->gnum; + int mincap = api->system->mincap; + + // for good performance in the OpenMP implementation, each thread needs + // to know where to place the neighbors of the atoms it is responsible for. + // The sumscan values for the list->numneigh will be used to determine the + // neighbor offset of each atom. Note that this may cause some significant + // memory overhead if delayed neighboring is used - so it may be desirable + // to work on this part to reduce the memory footprint of the far_nbrs list. + + int num_nbrs = 0; + + for (int itr_i = 0; itr_i < numall; ++itr_i) { + i = ilist[itr_i]; + num_nbrs += numneigh[i]; + } + + int new_estimate = MAX(num_nbrs, mincap*REAX_MIN_NBRS); + + return new_estimate; +} + +/* ---------------------------------------------------------------------- */ + +int PairReaxFFOMP::write_reax_lists() +{ + int itr_i, itr_j, i, j, num_mynbrs; + int *jlist; + double d_sqr, dist, cutoff_sqr; + rvec dvec; + + double **x = atom->x; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + reax_list *far_nbrs = api->lists + FAR_NBRS; + far_neighbor_data *far_list = far_nbrs->select.far_nbr_list; + + int num_nbrs = 0; + int inum = list->inum; + int gnum = list->gnum; + int numall = inum + gnum; + + // sumscan of the number of neighbors per atom to determine the offsets + // most likely, we are overallocating. desirable to work on this part + // to reduce the memory footprint of the far_nbrs list. + + num_nbrs = 0; + + for (itr_i = 0; itr_i < numall; ++itr_i) { + i = ilist[itr_i]; + num_nbrs_offset[i] = num_nbrs; + num_nbrs += numneigh[i]; + } + +#if defined(_OPENMP) +#pragma omp parallel for schedule(dynamic,50) default(shared) \ + private(itr_i, itr_j, i, j, jlist, cutoff_sqr, num_mynbrs, d_sqr, dvec, dist) +#endif + for (itr_i = 0; itr_i < numall; ++itr_i) { + i = ilist[itr_i]; + jlist = firstneigh[i]; + Set_Start_Index(i, num_nbrs_offset[i], far_nbrs); + + if (i < inum) + cutoff_sqr = SQR(api->control->nonb_cut); + else + cutoff_sqr = SQR(api->control->bond_cut); + + num_mynbrs = 0; + + for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { + j = jlist[itr_j]; + j &= NEIGHMASK; + get_distance(x[j], x[i], &d_sqr, &dvec); + + if (d_sqr <= cutoff_sqr) { + dist = sqrt(d_sqr); + set_far_nbr(&far_list[num_nbrs_offset[i] + num_mynbrs], j, dist, dvec); + ++num_mynbrs; + } + } + Set_End_Index(i, num_nbrs_offset[i] + num_mynbrs, far_nbrs); + } + + return num_nbrs; +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFFOMP::read_reax_forces(int /* vflag */) +{ +#if defined(_OPENMP) +#pragma omp parallel for schedule(static) default(shared) +#endif + for (int i = 0; i < api->system->N; ++i) { + api->system->my_atoms[i].f[0] = api->workspace->f[i][0]; + api->system->my_atoms[i].f[1] = api->workspace->f[i][1]; + api->system->my_atoms[i].f[2] = api->workspace->f[i][2]; + + atom->f[i][0] = -api->workspace->f[i][0]; + atom->f[i][1] = -api->workspace->f[i][1]; + atom->f[i][2] = -api->workspace->f[i][2]; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFFOMP::FindBond() +{ + const double bo_cut = 0.10; + +#if defined(_OPENMP) +#pragma omp parallel for schedule(static) default(shared) +#endif + for (int i = 0; i < api->system->n; i++) { + int j, pj, nj; + double bo_tmp; + bond_data *bo_ij; + + nj = 0; + for (pj = Start_Index(i, api->lists); pj < End_Index(i, api->lists); ++pj) { + bo_ij = &(api->lists->select.bond_list[pj]); + j = bo_ij->nbr; + if (j < i) continue; + + bo_tmp = bo_ij->bo_data.BO; + + if (bo_tmp >= bo_cut) { + tmpid[i][nj] = j; + tmpbo[i][nj] = bo_tmp; + nj ++; + if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in fix_reaxff_species.h"); + } + } + } +} diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/OPENMP/pair_reaxff_omp.h similarity index 62% rename from src/USER-OMP/pair_reaxc_omp.h rename to src/OPENMP/pair_reaxff_omp.h index 895dc646af..cced5861be 100644 --- a/src/USER-OMP/pair_reaxc_omp.h +++ b/src/OPENMP/pair_reaxff_omp.h @@ -13,22 +13,23 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(reax/c/omp,PairReaxCOMP); +PairStyle(reaxff/omp,PairReaxFFOMP); +PairStyle(reax/c/omp,PairReaxFFOMP); // clang-format on #else -#ifndef LMP_PAIR_REAXC_OMP_H -#define LMP_PAIR_REAXC_OMP_H +#ifndef LMP_PAIR_REAXFF_OMP_H +#define LMP_PAIR_REAXFF_OMP_H -#include "pair_reaxc.h" +#include "pair_reaxff.h" #include "thr_omp.h" namespace LAMMPS_NS { -class PairReaxCOMP : public PairReaxC, public ThrOMP { +class PairReaxFFOMP : public PairReaxFF, public ThrOMP { public: - PairReaxCOMP(class LAMMPS *); - ~PairReaxCOMP(); + PairReaxFFOMP(class LAMMPS *); + ~PairReaxFFOMP(); virtual void compute(int, int); virtual void init_style(); @@ -47,33 +48,55 @@ class PairReaxCOMP : public PairReaxC, public ThrOMP { reduce_thr(styleparm, eflagparm, vflagparm, thrparm); } - inline void ev_tally_thr_proxy(Pair *const pairparm, const int iparm, const int jparm, + inline void ev_tally_thr_proxy(const int iparm, const int jparm, const int nlocalparm, const int newton_pairparm, const double evdwlparm, const double ecoulparm, const double fpairparm, const double delxparm, const double delyparm, const double delzparm, ThrData *const thrparm) { - ev_tally_thr(pairparm, iparm, jparm, nlocalparm, newton_pairparm, evdwlparm, ecoulparm, + ev_tally_thr(this, iparm, jparm, nlocalparm, newton_pairparm, evdwlparm, ecoulparm, fpairparm, delxparm, delyparm, delzparm, thrparm); } - inline void ev_tally_xyz_thr_proxy(Pair *const pairparm, const int iparm, const int jparm, + inline void ev_tally_xyz_thr_proxy(const int iparm, const int jparm, const int nlocalparm, const int newton_pairparm, const double evdwlparm, const double ecoulparm, const double fxparm, const double fyparm, const double fzparm, const double delxparm, const double delyparm, const double delzparm, ThrData *const thrparm) { - ev_tally_xyz_thr(pairparm, iparm, jparm, nlocalparm, newton_pairparm, evdwlparm, ecoulparm, + ev_tally_xyz_thr(this, iparm, jparm, nlocalparm, newton_pairparm, evdwlparm, ecoulparm, fxparm, fyparm, fzparm, delxparm, delyparm, delzparm, thrparm); } - inline void ev_tally3_thr_proxy(Pair *const pairparm, int i, int j, int k, double evdwl, + inline void ev_tally3_thr_proxy(int i, int j, int k, double evdwl, double ecoul, double *fj, double *fk, double *drji, double *drki, ThrData *const thrparm) { - ev_tally3_thr(pairparm, i, j, k, evdwl, ecoul, fj, fk, drji, drki, thrparm); + ev_tally3_thr(this, i, j, k, evdwl, ecoul, fj, fk, drji, drki, thrparm); + } + + inline void v_tally2_newton_thr_proxy(const int i, const double *const fi, + const double *const deli, ThrData *const thrparm) + { + v_tally2_newton_thr(this, i, fi, deli, thrparm); + } + + inline void v_tally3_thr_proxy(const int i, const int j, const int k, const double *const fi, + const double *const fk, const double *const drij, + const double *const drkj, ThrData *const thrparm) + { + v_tally3_thr(this, i, j, k, fi, fk, drij, drkj, thrparm); + } + + inline void v_tally4_thr_proxy(const int i, const int j, const int k, const int l, + const double *const fi, const double *const fj, + const double *const fk, const double *const dril, + const double *const drjl, const double *const drkl, + ThrData *const thrparm) + { + v_tally4_thr(this, i, j, k, l, fi, fj, fk, dril, drjl, drkl, thrparm); } protected: @@ -98,7 +121,7 @@ class PairReaxCOMP : public PairReaxC, public ThrOMP { E: Too many ghost atoms Number of ghost atoms has increased too much during simulation and has exceeded -the size of reax/c arrays. Increase safe_zone and min_cap in pair_style reax/c +the size of reaxff arrays. Increase safe_zone and min_cap in pair_style reaxff command */ diff --git a/src/USER-OMP/pair_rebo_omp.cpp b/src/OPENMP/pair_rebo_omp.cpp similarity index 100% rename from src/USER-OMP/pair_rebo_omp.cpp rename to src/OPENMP/pair_rebo_omp.cpp diff --git a/src/USER-OMP/pair_rebo_omp.h b/src/OPENMP/pair_rebo_omp.h similarity index 100% rename from src/USER-OMP/pair_rebo_omp.h rename to src/OPENMP/pair_rebo_omp.h diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/OPENMP/pair_resquared_omp.cpp similarity index 100% rename from src/USER-OMP/pair_resquared_omp.cpp rename to src/OPENMP/pair_resquared_omp.cpp diff --git a/src/USER-OMP/pair_resquared_omp.h b/src/OPENMP/pair_resquared_omp.h similarity index 100% rename from src/USER-OMP/pair_resquared_omp.h rename to src/OPENMP/pair_resquared_omp.h diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/OPENMP/pair_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_soft_omp.cpp rename to src/OPENMP/pair_soft_omp.cpp diff --git a/src/USER-OMP/pair_soft_omp.h b/src/OPENMP/pair_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_soft_omp.h rename to src/OPENMP/pair_soft_omp.h diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/OPENMP/pair_sw_omp.cpp similarity index 100% rename from src/USER-OMP/pair_sw_omp.cpp rename to src/OPENMP/pair_sw_omp.cpp diff --git a/src/USER-OMP/pair_sw_omp.h b/src/OPENMP/pair_sw_omp.h similarity index 100% rename from src/USER-OMP/pair_sw_omp.h rename to src/OPENMP/pair_sw_omp.h diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/OPENMP/pair_table_omp.cpp similarity index 100% rename from src/USER-OMP/pair_table_omp.cpp rename to src/OPENMP/pair_table_omp.cpp diff --git a/src/USER-OMP/pair_table_omp.h b/src/OPENMP/pair_table_omp.h similarity index 100% rename from src/USER-OMP/pair_table_omp.h rename to src/OPENMP/pair_table_omp.h diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/OPENMP/pair_tersoff_mod_c_omp.cpp similarity index 95% rename from src/USER-OMP/pair_tersoff_mod_c_omp.cpp rename to src/OPENMP/pair_tersoff_mod_c_omp.cpp index 0d66e83b00..cd59e06673 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/OPENMP/pair_tersoff_mod_c_omp.cpp @@ -60,20 +60,20 @@ void PairTersoffMODCOMP::compute(int eflag, int vflag) if (shift_flag) { if (evflag) { if (eflag) { - if (vflag_atom) eval<1,1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,1,1>(ifrom, ito, thr); else eval<1,1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<1,1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,0,1>(ifrom, ito, thr); else eval<1,1,0,0>(ifrom, ito, thr); } } else eval<1,0,0,0>(ifrom, ito, thr); } else { if (evflag) { if (eflag) { - if (vflag_atom) eval<0,1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<0,1,1,1>(ifrom, ito, thr); else eval<0,1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<0,1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<0,1,0,1>(ifrom, ito, thr); else eval<0,1,0,0>(ifrom, ito, thr); } } else eval<0,0,0,0>(ifrom, ito, thr); @@ -84,7 +84,7 @@ void PairTersoffMODCOMP::compute(int eflag, int vflag) } // end of omp parallel region } -template +template void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,k,ii,jj,kk,jnum; @@ -282,7 +282,7 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr) f[k].y += fk[1]; f[k].z += fk[2]; - if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr); + if (VFLAG_EITHER) v_tally3_thr(this,i,j,k,fj,fk,delr1,delr2,thr); } f[j].x += fjxtmp; f[j].y += fjytmp; diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.h b/src/OPENMP/pair_tersoff_mod_c_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_mod_c_omp.h rename to src/OPENMP/pair_tersoff_mod_c_omp.h diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/OPENMP/pair_tersoff_mod_omp.cpp similarity index 95% rename from src/USER-OMP/pair_tersoff_mod_omp.cpp rename to src/OPENMP/pair_tersoff_mod_omp.cpp index b3e3b89283..de19aa3872 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/OPENMP/pair_tersoff_mod_omp.cpp @@ -60,20 +60,20 @@ void PairTersoffMODOMP::compute(int eflag, int vflag) if (shift_flag) { if (evflag) { if (eflag) { - if (vflag_atom) eval<1,1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,1,1>(ifrom, ito, thr); else eval<1,1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<1,1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,0,1>(ifrom, ito, thr); else eval<1,1,0,0>(ifrom, ito, thr); } } else eval<1,0,0,0>(ifrom, ito, thr); } else { if (evflag) { if (eflag) { - if (vflag_atom) eval<0,1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<0,1,1,1>(ifrom, ito, thr); else eval<0,1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<0,1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<0,1,0,1>(ifrom, ito, thr); else eval<0,1,0,0>(ifrom, ito, thr); } } else eval<0,0,0,0>(ifrom, ito, thr); @@ -84,7 +84,7 @@ void PairTersoffMODOMP::compute(int eflag, int vflag) } // end of omp parallel region } -template +template void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,k,ii,jj,kk,jnum; @@ -282,7 +282,7 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr) f[k].y += fk[1]; f[k].z += fk[2]; - if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr); + if (VFLAG_EITHER) v_tally3_thr(this,i,j,k,fj,fk,delr1,delr2,thr); } f[j].x += fjxtmp; f[j].y += fjytmp; diff --git a/src/USER-OMP/pair_tersoff_mod_omp.h b/src/OPENMP/pair_tersoff_mod_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_mod_omp.h rename to src/OPENMP/pair_tersoff_mod_omp.h diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/OPENMP/pair_tersoff_omp.cpp similarity index 95% rename from src/USER-OMP/pair_tersoff_omp.cpp rename to src/OPENMP/pair_tersoff_omp.cpp index 6bf48792eb..2a3cfb5d54 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/OPENMP/pair_tersoff_omp.cpp @@ -61,10 +61,10 @@ void PairTersoffOMP::compute(int eflag, int vflag) if (shift_flag) { if (evflag) { if (eflag) { - if (vflag_atom) eval<1,1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,1,1>(ifrom, ito, thr); else eval<1,1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<1,1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1,0,1>(ifrom, ito, thr); else eval<1,1,0,0>(ifrom, ito, thr); } } else eval<1,0,0,0>(ifrom, ito, thr); @@ -73,10 +73,10 @@ void PairTersoffOMP::compute(int eflag, int vflag) if (evflag) { if (eflag) { - if (vflag_atom) eval<0,1,1,1>(ifrom, ito, thr); + if (vflag_either) eval<0,1,1,1>(ifrom, ito, thr); else eval<0,1,1,0>(ifrom, ito, thr); } else { - if (vflag_atom) eval<0,1,0,1>(ifrom, ito, thr); + if (vflag_either) eval<0,1,0,1>(ifrom, ito, thr); else eval<0,1,0,0>(ifrom, ito, thr); } } else eval<0,0,0,0>(ifrom, ito, thr); @@ -87,7 +87,7 @@ void PairTersoffOMP::compute(int eflag, int vflag) } // end of omp parallel region } -template +template void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,k,ii,jj,kk,jnum,maxshort_thr; @@ -293,7 +293,7 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr) f[k].y += fk[1]; f[k].z += fk[2]; - if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr); + if (VFLAG_EITHER) v_tally3_thr(this,i,j,k,fj,fk,delr1,delr2,thr); } f[j].x += fjxtmp; f[j].y += fjytmp; diff --git a/src/USER-OMP/pair_tersoff_omp.h b/src/OPENMP/pair_tersoff_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_omp.h rename to src/OPENMP/pair_tersoff_omp.h diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/OPENMP/pair_tersoff_table_omp.cpp similarity index 98% rename from src/USER-OMP/pair_tersoff_table_omp.cpp rename to src/OPENMP/pair_tersoff_table_omp.cpp index a91f361f79..5367a3d043 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/OPENMP/pair_tersoff_table_omp.cpp @@ -53,7 +53,7 @@ PairTersoffTableOMP::PairTersoffTableOMP(LAMMPS *lmp) : PairTersoffTableOMP::~PairTersoffTableOMP() { if (allocated) { - deallocatePreLoops(); + PairTersoffTableOMP::deallocatePreLoops(); } } @@ -80,7 +80,7 @@ void PairTersoffTableOMP::compute(int eflag, int vflag) ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); if (evflag) - if (vflag_atom) eval<1,1>(ifrom, ito, thr); + if (vflag_either) eval<1,1>(ifrom, ito, thr); else eval<1,0>(ifrom, ito, thr); else eval<0,0>(ifrom, ito, thr); @@ -89,7 +89,7 @@ void PairTersoffTableOMP::compute(int eflag, int vflag) } // end of omp parallel region } -template +template void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,k,ii,jnum; @@ -427,7 +427,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) fytmp += f_ij[1] + f_ik[1]; fztmp += f_ij[2] + f_ik[2]; - if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr); + if (VFLAG_EITHER) v_tally3_thr(this,i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr); } // second loop over neighbors of atom i except j, forces and virial only - part 2/2 @@ -493,8 +493,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) fytmp += f_ij[1] + f_ik[1]; fztmp += f_ij[2] + f_ik[2]; - if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr); - + if (VFLAG_EITHER) v_tally3_thr(this,i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr); } } // loop on J f[i].x += fxtmp; diff --git a/src/USER-OMP/pair_tersoff_table_omp.h b/src/OPENMP/pair_tersoff_table_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_table_omp.h rename to src/OPENMP/pair_tersoff_table_omp.h diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/OPENMP/pair_tersoff_zbl_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tersoff_zbl_omp.cpp rename to src/OPENMP/pair_tersoff_zbl_omp.cpp diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.h b/src/OPENMP/pair_tersoff_zbl_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_zbl_omp.h rename to src/OPENMP/pair_tersoff_zbl_omp.h diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/OPENMP/pair_tip4p_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tip4p_cut_omp.cpp rename to src/OPENMP/pair_tip4p_cut_omp.cpp diff --git a/src/USER-OMP/pair_tip4p_cut_omp.h b/src/OPENMP/pair_tip4p_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_tip4p_cut_omp.h rename to src/OPENMP/pair_tip4p_cut_omp.h diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/OPENMP/pair_tip4p_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tip4p_long_omp.cpp rename to src/OPENMP/pair_tip4p_long_omp.cpp diff --git a/src/USER-OMP/pair_tip4p_long_omp.h b/src/OPENMP/pair_tip4p_long_omp.h similarity index 100% rename from src/USER-OMP/pair_tip4p_long_omp.h rename to src/OPENMP/pair_tip4p_long_omp.h diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/OPENMP/pair_tip4p_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tip4p_long_soft_omp.cpp rename to src/OPENMP/pair_tip4p_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.h b/src/OPENMP/pair_tip4p_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_tip4p_long_soft_omp.h rename to src/OPENMP/pair_tip4p_long_soft_omp.h diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/OPENMP/pair_ufm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_ufm_omp.cpp rename to src/OPENMP/pair_ufm_omp.cpp diff --git a/src/USER-OMP/pair_ufm_omp.h b/src/OPENMP/pair_ufm_omp.h similarity index 100% rename from src/USER-OMP/pair_ufm_omp.h rename to src/OPENMP/pair_ufm_omp.h diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/OPENMP/pair_vashishta_omp.cpp similarity index 100% rename from src/USER-OMP/pair_vashishta_omp.cpp rename to src/OPENMP/pair_vashishta_omp.cpp diff --git a/src/USER-OMP/pair_vashishta_omp.h b/src/OPENMP/pair_vashishta_omp.h similarity index 100% rename from src/USER-OMP/pair_vashishta_omp.h rename to src/OPENMP/pair_vashishta_omp.h diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/OPENMP/pair_vashishta_table_omp.cpp similarity index 100% rename from src/USER-OMP/pair_vashishta_table_omp.cpp rename to src/OPENMP/pair_vashishta_table_omp.cpp diff --git a/src/USER-OMP/pair_vashishta_table_omp.h b/src/OPENMP/pair_vashishta_table_omp.h similarity index 100% rename from src/USER-OMP/pair_vashishta_table_omp.h rename to src/OPENMP/pair_vashishta_table_omp.h diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/OPENMP/pair_yukawa_colloid_omp.cpp similarity index 100% rename from src/USER-OMP/pair_yukawa_colloid_omp.cpp rename to src/OPENMP/pair_yukawa_colloid_omp.cpp diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.h b/src/OPENMP/pair_yukawa_colloid_omp.h similarity index 100% rename from src/USER-OMP/pair_yukawa_colloid_omp.h rename to src/OPENMP/pair_yukawa_colloid_omp.h diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/OPENMP/pair_yukawa_omp.cpp similarity index 100% rename from src/USER-OMP/pair_yukawa_omp.cpp rename to src/OPENMP/pair_yukawa_omp.cpp diff --git a/src/USER-OMP/pair_yukawa_omp.h b/src/OPENMP/pair_yukawa_omp.h similarity index 100% rename from src/USER-OMP/pair_yukawa_omp.h rename to src/OPENMP/pair_yukawa_omp.h diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/OPENMP/pair_zbl_omp.cpp similarity index 100% rename from src/USER-OMP/pair_zbl_omp.cpp rename to src/OPENMP/pair_zbl_omp.cpp diff --git a/src/USER-OMP/pair_zbl_omp.h b/src/OPENMP/pair_zbl_omp.h similarity index 100% rename from src/USER-OMP/pair_zbl_omp.h rename to src/OPENMP/pair_zbl_omp.h diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/OPENMP/pppm_cg_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_cg_omp.cpp rename to src/OPENMP/pppm_cg_omp.cpp diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/OPENMP/pppm_cg_omp.h similarity index 100% rename from src/USER-OMP/pppm_cg_omp.h rename to src/OPENMP/pppm_cg_omp.h diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/OPENMP/pppm_disp_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_disp_omp.cpp rename to src/OPENMP/pppm_disp_omp.cpp diff --git a/src/USER-OMP/pppm_disp_omp.h b/src/OPENMP/pppm_disp_omp.h similarity index 100% rename from src/USER-OMP/pppm_disp_omp.h rename to src/OPENMP/pppm_disp_omp.h diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/OPENMP/pppm_disp_tip4p_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_disp_tip4p_omp.cpp rename to src/OPENMP/pppm_disp_tip4p_omp.cpp diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.h b/src/OPENMP/pppm_disp_tip4p_omp.h similarity index 100% rename from src/USER-OMP/pppm_disp_tip4p_omp.h rename to src/OPENMP/pppm_disp_tip4p_omp.h diff --git a/src/USER-OMP/pppm_omp.cpp b/src/OPENMP/pppm_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_omp.cpp rename to src/OPENMP/pppm_omp.cpp diff --git a/src/USER-OMP/pppm_omp.h b/src/OPENMP/pppm_omp.h similarity index 100% rename from src/USER-OMP/pppm_omp.h rename to src/OPENMP/pppm_omp.h diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/OPENMP/pppm_tip4p_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_tip4p_omp.cpp rename to src/OPENMP/pppm_tip4p_omp.cpp diff --git a/src/USER-OMP/pppm_tip4p_omp.h b/src/OPENMP/pppm_tip4p_omp.h similarity index 100% rename from src/USER-OMP/pppm_tip4p_omp.h rename to src/OPENMP/pppm_tip4p_omp.h diff --git a/src/OPENMP/reaxff_bond_orders_omp.cpp b/src/OPENMP/reaxff_bond_orders_omp.cpp new file mode 100644 index 0000000000..2fe68280d1 --- /dev/null +++ b/src/OPENMP/reaxff_bond_orders_omp.cpp @@ -0,0 +1,515 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "fix_omp.h" +#include "pair_reaxff_omp.h" +#include "reaxff_api.h" + +#include + +using namespace LAMMPS_NS; + +namespace ReaxFF { + void Add_dBond_to_ForcesOMP(reax_system *system, int i, int pj, storage *workspace, reax_list **lists) + { + reax_list *bonds = (*lists) + BONDS; + bond_data *nbr_j, *nbr_k; + bond_order_data *bo_ij, *bo_ji; + dbond_coefficients coef; + int pk, k, j; + + PairReaxFFOMP *pair_reax_ptr = static_cast(system->pair_ptr); + + int tid = get_tid(); + ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + long reductionOffset = (system->N * tid); + + /* Virial Tallying variables */ + rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp; + + /* Initializations */ + nbr_j = &(bonds->select.bond_list[pj]); + j = nbr_j->nbr; + bo_ij = &(nbr_j->bo_data); + bo_ji = &(bonds->select.bond_list[nbr_j->sym_index].bo_data); + + double c = bo_ij->Cdbo + bo_ji->Cdbo; + coef.C1dbo = bo_ij->C1dbo * c; + coef.C2dbo = bo_ij->C2dbo * c; + coef.C3dbo = bo_ij->C3dbo * c; + + c = bo_ij->Cdbopi + bo_ji->Cdbopi; + coef.C1dbopi = bo_ij->C1dbopi * c; + coef.C2dbopi = bo_ij->C2dbopi * c; + coef.C3dbopi = bo_ij->C3dbopi * c; + coef.C4dbopi = bo_ij->C4dbopi * c; + + c = bo_ij->Cdbopi2 + bo_ji->Cdbopi2; + coef.C1dbopi2 = bo_ij->C1dbopi2 * c; + coef.C2dbopi2 = bo_ij->C2dbopi2 * c; + coef.C3dbopi2 = bo_ij->C3dbopi2 * c; + coef.C4dbopi2 = bo_ij->C4dbopi2 * c; + + c = workspace->CdDelta[i] + workspace->CdDelta[j]; + coef.C1dDelta = bo_ij->C1dbo * c; + coef.C2dDelta = bo_ij->C2dbo * c; + coef.C3dDelta = bo_ij->C3dbo * c; + + c = (coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2); + rvec_Scale( temp, c, bo_ij->dBOp); + + c = (coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2); + rvec_ScaledAdd(temp, c, workspace->dDeltap_self[i]); + + rvec_ScaledAdd(temp, coef.C1dbopi, bo_ij->dln_BOp_pi); + rvec_ScaledAdd(temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2); + + rvec_Add(workspace->forceReduction[reductionOffset+i],temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fi_tmp, -0.5, temp); + rvec_ScaledSum(delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x); + + pair_reax_ptr->v_tally2_newton_thr_proxy(i,fi_tmp,delij,thr); + } + + c = -(coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2); + rvec_Scale( temp, c, bo_ij->dBOp); + + c = (coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2); + rvec_ScaledAdd(temp, c, workspace->dDeltap_self[j]); + + rvec_ScaledAdd(temp, -coef.C1dbopi, bo_ij->dln_BOp_pi); + rvec_ScaledAdd(temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2); + + + rvec_Add(workspace->forceReduction[reductionOffset+j],temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fj_tmp, -0.5, temp); + rvec_ScaledSum(delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x); + pair_reax_ptr->v_tally2_newton_thr_proxy(j,fj_tmp,delji,thr); + } + + // forces on k: i neighbor + for (pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk) { + nbr_k = &(bonds->select.bond_list[pk]); + k = nbr_k->nbr; + + const double c = -(coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2); + rvec_Scale(temp, c, nbr_k->bo_data.dBOp); + + rvec_Add(workspace->forceReduction[reductionOffset+k],temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fk_tmp, -0.5, temp); + rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); + pair_reax_ptr->v_tally2_newton_thr_proxy(k,fk_tmp,delki,thr); + rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); + pair_reax_ptr->v_tally2_newton_thr_proxy(k,fk_tmp,delkj,thr); + } + } + + // forces on k: j neighbor + for (pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk) { + nbr_k = &(bonds->select.bond_list[pk]); + k = nbr_k->nbr; + + const double c = -(coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2); + rvec_Scale(temp, c, nbr_k->bo_data.dBOp); + + rvec_Add(workspace->forceReduction[reductionOffset+k],temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fk_tmp, -0.5, temp); + rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); + pair_reax_ptr->v_tally2_newton_thr_proxy(k,fk_tmp,delki,thr); + rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); + pair_reax_ptr->v_tally2_newton_thr_proxy(k,fk_tmp,delkj,thr); + } + } + } + +/* ---------------------------------------------------------------------- */ + + int BOp_OMP(storage * /* workspace */, reax_list *bonds, double bo_cut, + int i, int btop_i, far_neighbor_data *nbr_pj, + single_body_parameters * /* sbp_i */, single_body_parameters * /* sbp_j */, + two_body_parameters *twbp, + int btop_j, double C12, double C34, double C56, double BO, double BO_s, double BO_pi, double BO_pi2) { + int j; + double rr2; + double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; + bond_data *ibond, *jbond; + bond_order_data *bo_ij, *bo_ji; + + j = nbr_pj->nbr; + rr2 = 1.0 / SQR(nbr_pj->d); + + // Top portion of BOp() moved to reaxff_forces_omp.cpp::Init_Forces_noQEq_OMP() + + /* Initially BO values are the uncorrected ones, page 1 */ + + /****** bonds i-j and j-i ******/ + ibond = &(bonds->select.bond_list[btop_i]); + jbond = &(bonds->select.bond_list[btop_j]); + + ibond->nbr = j; + jbond->nbr = i; + ibond->d = nbr_pj->d; + jbond->d = nbr_pj->d; + rvec_Copy(ibond->dvec, nbr_pj->dvec); + rvec_Scale(jbond->dvec, -1, nbr_pj->dvec); + ivec_Copy(ibond->rel_box, nbr_pj->rel_box); + ivec_Scale(jbond->rel_box, -1, nbr_pj->rel_box); + ibond->dbond_index = btop_i; + jbond->dbond_index = btop_i; + ibond->sym_index = btop_j; + jbond->sym_index = btop_i; + + bo_ij = &(ibond->bo_data); + bo_ji = &(jbond->bo_data); + bo_ji->BO = bo_ij->BO = BO; + bo_ji->BO_s = bo_ij->BO_s = BO_s; + bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; + bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; + + /* Bond Order page2-3, derivative of total bond order prime */ + Cln_BOp_s = twbp->p_bo2 * C12 * rr2; + Cln_BOp_pi = twbp->p_bo4 * C34 * rr2; + Cln_BOp_pi2 = twbp->p_bo6 * C56 * rr2; + + /* Only dln_BOp_xx wrt. dr_i is stored here, note that + dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ + rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec); + rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec); + rvec_Scale(bo_ij->dln_BOp_pi2, + -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec); + rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); + rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi); + rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2); + + rvec_Scale(bo_ij->dBOp, + -(bo_ij->BO_s * Cln_BOp_s + + bo_ij->BO_pi * Cln_BOp_pi + + bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec); + rvec_Scale(bo_ji->dBOp, -1., bo_ij->dBOp); + + bo_ij->BO_s -= bo_cut; + bo_ij->BO -= bo_cut; + bo_ji->BO_s -= bo_cut; + bo_ji->BO -= bo_cut; + + bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; + bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; + + return 1; + } + +/* ---------------------------------------------------------------------- */ + + void BOOMP(reax_system *system, storage *workspace, reax_list **lists) + { + double p_lp1 = system->reax_param.gp.l[15]; + double p_boc1 = system->reax_param.gp.l[0]; + double p_boc2 = system->reax_param.gp.l[1]; + reax_list *bonds = (*lists) + BONDS; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) +#endif + { + int i, j, pj, type_i, type_j; + int start_i, end_i, sym_index; + double val_i, Deltap_i, Deltap_boc_i; + double val_j, Deltap_j, Deltap_boc_j; + double f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5; + double exp_p1i, exp_p2i, exp_p1j, exp_p2j, explp1; + double temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji; + double Cf45_ij, Cf45_ji; //u_ij, u_ji + double A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + bond_order_data *bo_ij, *bo_ji; + + /* Calculate Deltaprime, Deltaprime_boc values */ +#if defined(_OPENMP) +#pragma omp for schedule(static) +#endif + for (i = 0; i < system->N; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + sbp_i = &(system->reax_param.sbp[type_i]); + workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency; + workspace->Deltap_boc[i] = + workspace->total_bond_order[i] - sbp_i->valency_val; + + workspace->total_bond_order[i] = 0; + } + + // Wait till initialization complete +#if defined(_OPENMP) +#pragma omp barrier +#endif + + /* Corrected Bond Order calculations */ +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < system->N; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + sbp_i = &(system->reax_param.sbp[type_i]); + val_i = sbp_i->valency; + Deltap_i = workspace->Deltap[i]; + Deltap_boc_i = workspace->Deltap_boc[i]; + start_i = Start_Index(i, bonds); + end_i = End_Index(i, bonds); + + for (pj = start_i; pj < end_i; ++pj) { + j = bonds->select.bond_list[pj].nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + bo_ij = &(bonds->select.bond_list[pj].bo_data); + + if (i < j || workspace->bond_mark[j] > 3) { + twbp = &(system->reax_param.tbp[type_i][type_j]); + + if (twbp->ovc < 0.001 && twbp->v13cor < 0.001) { + bo_ij->C1dbo = 1.000000; + bo_ij->C2dbo = 0.000000; + bo_ij->C3dbo = 0.000000; + + bo_ij->C1dbopi = 1.000000; + bo_ij->C2dbopi = 0.000000; + bo_ij->C3dbopi = 0.000000; + bo_ij->C4dbopi = 0.000000; + + bo_ij->C1dbopi2 = 1.000000; + bo_ij->C2dbopi2 = 0.000000; + bo_ij->C3dbopi2 = 0.000000; + bo_ij->C4dbopi2 = 0.000000; + + } else { + val_j = system->reax_param.sbp[type_j].valency; + Deltap_j = workspace->Deltap[j]; + Deltap_boc_j = workspace->Deltap_boc[j]; + + /* on page 1 */ + if (twbp->ovc >= 0.001) { + /* Correction for overcoordination */ + exp_p1i = exp(-p_boc1 * Deltap_i); + exp_p2i = exp(-p_boc2 * Deltap_i); + exp_p1j = exp(-p_boc1 * Deltap_j); + exp_p2j = exp(-p_boc2 * Deltap_j); + + f2 = exp_p1i + exp_p1j; + f3 = -1.0 / p_boc2 * log(0.5 * (exp_p2i + exp_p2j)); + f1 = 0.5 * ((val_i + f2)/(val_i + f2 + f3) + + (val_j + f2)/(val_j + f2 + f3)); + + /* Now come the derivates */ + /* Bond Order pages 5-7, derivative of f1 */ + temp = f2 + f3; + u1_ij = val_i + temp; + u1_ji = val_j + temp; + Cf1A_ij = 0.5 * f3 * (1.0 / SQR(u1_ij) + + 1.0 / SQR(u1_ji)); + Cf1B_ij = -0.5 * ((u1_ij - f3) / SQR(u1_ij) + + (u1_ji - f3) / SQR(u1_ji)); + + Cf1_ij = 0.50 * (-p_boc1 * exp_p1i / u1_ij - + ((val_i+f2) / SQR(u1_ij)) * + (-p_boc1 * exp_p1i + + exp_p2i / (exp_p2i + exp_p2j)) + + -p_boc1 * exp_p1i / u1_ji - + ((val_j+f2) / SQR(u1_ji)) * + (-p_boc1 * exp_p1i + + exp_p2i / (exp_p2i + exp_p2j))); + + + Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j + + Cf1B_ij * exp_p2j / (exp_p2i + exp_p2j); + } else { + /* No overcoordination correction! */ + f1 = 1.0; + Cf1_ij = Cf1_ji = 0.0; + } + + if (twbp->v13cor >= 0.001) { + /* Correction for 1-3 bond orders */ + exp_f4 =exp(-(twbp->p_boc4 * SQR(bo_ij->BO) - + Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5); + exp_f5 =exp(-(twbp->p_boc4 * SQR(bo_ij->BO) - + Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5); + + f4 = 1. / (1. + exp_f4); + f5 = 1. / (1. + exp_f5); + f4f5 = f4 * f5; + + /* Bond Order pages 8-9, derivative of f4 and f5 */ + Cf45_ij = -f4 * exp_f4; + Cf45_ji = -f5 * exp_f5; + } else { + f4 = f5 = f4f5 = 1.0; + Cf45_ij = Cf45_ji = 0.0; + } + + /* Bond Order page 10, derivative of total bond order */ + A0_ij = f1 * f4f5; + A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO * + (Cf45_ij + Cf45_ji); + A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij; + A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji; + A3_ij = A2_ij + Cf1_ij / f1; + A3_ji = A2_ji + Cf1_ji / f1; + + /* find corrected bond orders and their derivative coef */ + bo_ij->BO = bo_ij->BO * A0_ij; + bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1; + bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1; + bo_ij->BO_s = bo_ij->BO - (bo_ij->BO_pi + bo_ij->BO_pi2); + + bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij; + bo_ij->C2dbo = bo_ij->BO * A2_ij; + bo_ij->C3dbo = bo_ij->BO * A2_ji; + + bo_ij->C1dbopi = f1*f1*f4*f5; + bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij; + bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij; + bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji; + + bo_ij->C1dbopi2 = f1*f1*f4*f5; + bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij; + bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij; + bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji; + } + + /* neglect bonds that are < 1e-10 */ + if (bo_ij->BO < 1e-10) + bo_ij->BO = 0.0; + if (bo_ij->BO_s < 1e-10) + bo_ij->BO_s = 0.0; + if (bo_ij->BO_pi < 1e-10) + bo_ij->BO_pi = 0.0; + if (bo_ij->BO_pi2 < 1e-10) + bo_ij->BO_pi2 = 0.0; + + workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO + } + } + } + + // Wait for bo_ij to be updated +#if defined(_OPENMP) +#pragma omp barrier +#endif + // Try to combine the following for-loop back into the for-loop above + /*-------------------------*/ +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < system->N; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + start_i = Start_Index(i, bonds); + end_i = End_Index(i, bonds); + + for (pj = start_i; pj < end_i; ++pj) { + j = bonds->select.bond_list[pj].nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + + if (i < j || workspace->bond_mark[j] > 3) { + // Computed in previous for-loop + } else { + /* We only need to update bond orders from bo_ji + everything else is set in uncorrected_bo calculations */ + sym_index = bonds->select.bond_list[pj].sym_index; + + bo_ij = &(bonds->select.bond_list[pj].bo_data); + bo_ji = &(bonds->select.bond_list[sym_index].bo_data); + bo_ij->BO = bo_ji->BO; + bo_ij->BO_s = bo_ji->BO_s; + bo_ij->BO_pi = bo_ji->BO_pi; + bo_ij->BO_pi2 = bo_ji->BO_pi2; + + workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO + } + } + + } + + /*-------------------------*/ + + // Need to wait for total_bond_order to be accumulated. +#if defined(_OPENMP) +#pragma omp barrier +#endif + /* Calculate some helper variables that are used at many places + throughout force calculations */ +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (j = 0; j < system->N; ++j) { + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + sbp_j = &(system->reax_param.sbp[type_j]); + + workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency; + workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e; + workspace->Delta_boc[j] = workspace->total_bond_order[j] - + sbp_j->valency_boc; + workspace->Delta_val[j] = workspace->total_bond_order[j] - + sbp_j->valency_val; + + workspace->vlpex[j] = workspace->Delta_e[j] - + 2.0 * (int)(workspace->Delta_e[j]/2.0); + explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j])); + workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0); + workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j]; + workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]); + workspace->dDelta_lp[j] = workspace->Clp[j]; + + if (sbp_j->mass > 21.0) { + workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency); + workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; + workspace->dDelta_lp_temp[j] = 0.; + } + else { + workspace->nlp_temp[j] = workspace->nlp[j]; + workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; + workspace->dDelta_lp_temp[j] = workspace->Clp[j]; + } + } + + } // parallel region + } +} diff --git a/src/OPENMP/reaxff_bonds_omp.cpp b/src/OPENMP/reaxff_bonds_omp.cpp new file mode 100644 index 0000000000..1a97f2a6af --- /dev/null +++ b/src/OPENMP/reaxff_bonds_omp.cpp @@ -0,0 +1,167 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "fix_omp.h" +#include "pair_reaxff_omp.h" +#include "reaxff_api.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +namespace ReaxFF { + void BondsOMP(reax_system *system, simulation_data *data, + storage *workspace, reax_list **lists) + { + const int natoms = system->n; + reax_list *bonds = (*lists) + BONDS; + const double gp3 = system->reax_param.gp.l[3]; + const double gp4 = system->reax_param.gp.l[4]; + const double gp7 = system->reax_param.gp.l[7]; + const double gp10 = system->reax_param.gp.l[10]; + const int gp37 = (int) system->reax_param.gp.l[37]; + double total_Ebond = 0.0; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) reduction(+: total_Ebond) +#endif + { + int i, j, pj; + int start_i, end_i; + int type_i, type_j; + double ebond, pow_BOs_be2, exp_be12, CEbo; + double exphu, exphua1, exphub1, exphuov, hulpov, estriph; + double decobdbo, decobdboua, decobdboub; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + bond_order_data *bo_ij; + + int tid = get_tid(); + long reductionOffset = (system->N * tid); + + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + + pair_reax_ptr->ev_setup_thr_proxy(system->pair_ptr->eflag_either, + system->pair_ptr->vflag_either, system->N, + system->pair_ptr->eatom, + system->pair_ptr->vatom, nullptr, thr); + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < natoms; ++i) { + start_i = Start_Index(i, bonds); + end_i = End_Index(i, bonds); + + for (pj = start_i; pj < end_i; ++pj) { + j = bonds->select.bond_list[pj].nbr; + + if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id) continue; + + if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) { + if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue; + if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && + system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue; + if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && + system->my_atoms[j].x[1] == system->my_atoms[i].x[1] && + system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue; + } + + /* set the pointers */ + type_i = system->my_atoms[i].type; + type_j = system->my_atoms[j].type; + sbp_i = &(system->reax_param.sbp[type_i]); + sbp_j = &(system->reax_param.sbp[type_j]); + twbp = &(system->reax_param.tbp[type_i][type_j]); + bo_ij = &(bonds->select.bond_list[pj].bo_data); + + /* calculate the constants */ + if (bo_ij->BO_s == 0.0) pow_BOs_be2 = 0.0; + else pow_BOs_be2 = pow(bo_ij->BO_s, twbp->p_be2); + exp_be12 = exp(twbp->p_be1 * (1.0 - pow_BOs_be2)); + CEbo = -twbp->De_s * exp_be12 * + (1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2); + + /* calculate the Bond Energy */ + total_Ebond += ebond = + -twbp->De_s * bo_ij->BO_s * exp_be12 + -twbp->De_p * bo_ij->BO_pi + -twbp->De_pp * bo_ij->BO_pi2; + + /* tally into per-atom energy */ + if (system->pair_ptr->eflag_either) + pair_reax_ptr->ev_tally_thr_proxy(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0,thr); + + /* calculate derivatives of Bond Orders */ + bo_ij->Cdbo += CEbo; + bo_ij->Cdbopi -= (CEbo + twbp->De_p); + bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp); + + /* Stabilisation terminal triple bond */ + if (bo_ij->BO >= 1.00) { + if (gp37 == 2 || + (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) || + (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990)) { + exphu = exp(-gp7 * SQR(bo_ij->BO - 2.50)); + exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO)); + exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO)); + exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j])); + hulpov = 1.0 / (1.0 + 25.0 * exphuov); + + estriph = gp10 * exphu * hulpov * (exphua1 + exphub1); + total_Ebond += estriph; + + decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) * + (gp3 - 2.0 * gp7 * (bo_ij->BO-2.50)); + decobdboua = -gp10 * exphu * hulpov * + (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); + decobdboub = -gp10 * exphu * hulpov * + (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); + + /* tally into per-atom energy */ + if (system->pair_ptr->eflag_either) + pair_reax_ptr->ev_tally_thr_proxy(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0,thr); + + bo_ij->Cdbo += decobdbo; + workspace->CdDelta[i] += decobdboua; + workspace->CdDeltaReduction[reductionOffset+j] += decobdboub; + } + } + } + } // for (i) + + } // omp + + data->my_en.e_bond += total_Ebond; + } +} diff --git a/src/OPENMP/reaxff_forces_omp.cpp b/src/OPENMP/reaxff_forces_omp.cpp new file mode 100644 index 0000000000..77106a5e44 --- /dev/null +++ b/src/OPENMP/reaxff_forces_omp.cpp @@ -0,0 +1,477 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + Website: https://www.cs.purdue.edu/puremd + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "error.h" +#include "fix_omp.h" +#include "pair_reaxff_omp.h" + +#include "reaxff_api.h" + +#include + +using namespace LAMMPS_NS; + +namespace ReaxFF { +/* ---------------------------------------------------------------------- */ + + static void Compute_Bonded_ForcesOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + + BOOMP(system, workspace, lists); + BondsOMP(system, data, workspace, lists); + Atom_EnergyOMP(system, data, workspace, lists); + Valence_AnglesOMP(system, control, data, workspace, lists); + Torsion_AnglesOMP(system, control, data, workspace, lists); + if (control->hbond_cut > 0) + Hydrogen_BondsOMP(system, control, data, workspace, lists); + } + + static void Compute_NonBonded_ForcesOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + /* van der Waals and Coulomb interactions */ + + if (control->tabulate == 0) + vdW_Coulomb_Energy_OMP(system, control, data, workspace, lists); + else + Tabulated_vdW_Coulomb_Energy_OMP(system, control, data, workspace, lists); + } + +/* ---------------------------------------------------------------------- */ + +/* this version of Compute_Total_Force computes forces from + coefficients accumulated by all interaction functions. + Saves enormous time & space! */ + static void Compute_Total_ForceOMP(reax_system *system, control_params *control, + storage *workspace, reax_list **lists) + { + int natoms = system->N; + int nthreads = control->nthreads; + long totalReductionSize = (bigint)system->N * nthreads; + reax_list *bonds = (*lists) + BONDS; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) //LMP_DEFAULT_NONE +#endif + { + int i, j, k, pj, pk, start_j, end_j; + + int tid = get_tid(); + bond_order_data *bo_jk; + + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + + pair_reax_ptr->ev_setup_thr_proxy(0, 1, natoms, system->pair_ptr->eatom, + system->pair_ptr->vatom, nullptr, thr); + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < system->N; ++i) { + for (j = 0; j < nthreads; ++j) + workspace->CdDelta[i] += workspace->CdDeltaReduction[system->N*j+i]; + } + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) +#endif + for (j = 0; j < system->N; ++j) { + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + for (pk = start_j; pk < end_j; ++pk) { + bo_jk = &(bonds->select.bond_list[pk].bo_data); + for (k = 0; k < nthreads; ++k) + bo_jk->Cdbo += bo_jk->CdboReduction[k]; + } + } + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) +#endif + for (i = 0; i < system->N; ++i) { + const int startj = Start_Index(i, bonds); + const int endj = End_Index(i, bonds); + for (pj = startj; pj < endj; ++pj) + if (i < bonds->select.bond_list[pj].nbr) + Add_dBond_to_ForcesOMP(system, i, pj, workspace, lists); + } + + pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, 0, 1, thr); + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < system->N; ++i) { + for (j = 0; j < nthreads; ++j) + rvec_Add(workspace->f[i], workspace->forceReduction[system->N*j+i]); + } + + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < totalReductionSize; i++) { + workspace->forceReduction[i][0] = 0; + workspace->forceReduction[i][1] = 0; + workspace->forceReduction[i][2] = 0; + workspace->CdDeltaReduction[i] = 0; + } + } // parallel region + } + +/* ---------------------------------------------------------------------- */ + + static void Validate_ListsOMP(reax_system *system, reax_list **lists, + int step, int n, int N, int numH) + { + int comp, Hindex; + reax_list *bonds, *hbonds; + double saferzone = system->saferzone; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) private(comp,Hindex) +#endif + { + + /* bond list */ + if (N > 0) { + bonds = *lists + BONDS; + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (int i = 0; i < N; ++i) { + system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); + + if (i < N-1) + comp = Start_Index(i+1, bonds); + else comp = bonds->num_intrs; + + if (End_Index(i, bonds) > comp) + system->error_ptr->one(FLERR, fmt::format("step {}: bondchk failed: " + "i={} end(i)={} str(i+1)={}\n", + step,i,End_Index(i,bonds),comp)); + } + } + + + /* hbonds list */ + if (numH > 0) { + hbonds = *lists + HBONDS; + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (int i = 0; i < n; ++i) { + Hindex = system->my_atoms[i].Hindex; + if (Hindex > -1) { + system->my_atoms[i].num_hbonds = + (int)(MAX(Num_Entries(Hindex,hbonds)*saferzone,system->minhbonds)); + + if (Hindex < numH-1) + comp = Start_Index(Hindex+1, hbonds); + else comp = hbonds->num_intrs; + + if (End_Index(Hindex, hbonds) > comp) + system->error_ptr->one(FLERR, fmt::format("step {}: hbondchk failed: " + "H={} end(H)={} str(H+1)={}\n", + step, Hindex,End_Index(Hindex,hbonds),comp)); + } + } + } + + } // omp parallel + } + + + void Init_Forces_noQEq_OMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) { + int j, pj; + int start_i, end_i; + int type_i, type_j; + int ihb, jhb, ihb_top, jhb_top; + double cutoff; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + far_neighbor_data *nbr_pj; + reax_atom *atom_i, *atom_j; + reax_list *far_nbrs = *lists + FAR_NBRS; + reax_list *bonds = *lists + BONDS; + reax_list *hbonds = *lists + HBONDS; + int num_bonds = 0; + int num_hbonds = 0; + int btop_i = 0; + + // We will use CdDeltaReduction as a temporary (double) buffer to accumulate total_bond_order + // This is safe because CdDeltaReduction is currently zeroed and its accumulation doesn't start until BondsOMP() + double * tmp_bond_order = workspace->CdDeltaReduction; + + // We do the same with forceReduction as a temporary (rvec) buffer to accumulate dDeltap_self + // This is safe because forceReduction is currently zeroed and its accumulation does start until Hydrogen_BondsOMP() + rvec * tmp_ddelta = workspace->forceReduction; + + /* uncorrected bond orders */ + cutoff = control->bond_cut; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) \ + private(atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \ + atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp) +#endif + { + + int nthreads = control->nthreads; + int tid = get_tid(); + long reductionOffset = (bigint)system->N * tid; + long totalReductionSize = (bigint)system->N * nthreads; + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) reduction(+:num_bonds) +#endif + for (int i = 0; i < system->N; ++i) { + atom_i = &(system->my_atoms[i]); + type_i = atom_i->type; + sbp_i = &(system->reax_param.sbp[type_i]); + + start_i = Start_Index(i, far_nbrs); + end_i = End_Index(i, far_nbrs); + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + if (nbr_pj->d <= cutoff) { + int j = nbr_pj->nbr; + atom_j = &(system->my_atoms[j]); + type_j = atom_j->type; + sbp_j = &(system->reax_param.sbp[type_j]); + twbp = &(system->reax_param.tbp[type_i][type_j]); + + // Trying to minimize time spent in critical section by moving initial part of BOp() + // outside of critical section. + + // Start top portion of BOp() + double C12, C34, C56; + double BO, BO_s, BO_pi, BO_pi2; + double bo_cut = control->bo_cut; + + if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { + C12 = twbp->p_bo1 * pow(nbr_pj->d / twbp->r_s, twbp->p_bo2); + BO_s = (1.0 + bo_cut) * exp(C12); + } + else BO_s = C12 = 0.0; + + if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { + C34 = twbp->p_bo3 * pow(nbr_pj->d / twbp->r_p, twbp->p_bo4); + BO_pi = exp(C34); + } + else BO_pi = C34 = 0.0; + + if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { + C56 = twbp->p_bo5 * pow(nbr_pj->d / twbp->r_pp, twbp->p_bo6); + BO_pi2= exp(C56); + } + else BO_pi2 = C56 = 0.0; + + /* Initially BO values are the uncorrected ones, page 1 */ + BO = BO_s + BO_pi + BO_pi2; + // End top portion of BOp() + + if (BO >= bo_cut) { + int btop_j; + + // Update indices in critical section +#if defined(_OPENMP) +#pragma omp critical +#endif + { + btop_i = End_Index(i, bonds); + btop_j = End_Index(j, bonds); + Set_End_Index(j, btop_j+1, bonds); + Set_End_Index(i, btop_i+1, bonds); + } // omp critical + + // Finish remaining BOp() work + BOp_OMP(workspace, bonds, bo_cut, + i , btop_i, nbr_pj, sbp_i, sbp_j, twbp, btop_j, + C12, C34, C56, BO, BO_s, BO_pi, BO_pi2); + + bond_data * ibond = &(bonds->select.bond_list[btop_i]); + bond_order_data * bo_ij = &(ibond->bo_data); + + bond_data * jbond = &(bonds->select.bond_list[btop_j]); + bond_order_data * bo_ji = &(jbond->bo_data); + + workspace->total_bond_order[i] += bo_ij->BO; + tmp_bond_order[reductionOffset + j] += bo_ji->BO; + + rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp); + rvec_Add(tmp_ddelta[reductionOffset + j], bo_ji->dBOp); + + btop_i++; + num_bonds++; + } // if (BO>=bo_cut) + + } // if (cutoff) + + } // for (pj) + } // for (i) + + // Need to wait for all indices and tmp arrays accumulated. +#if defined(_OPENMP) +#pragma omp barrier +#endif + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) +#endif + for (int i=0; iN; i++) + for (int t=0; tN + i; + workspace->dDeltap_self[i][0] += tmp_ddelta[indx][0]; + workspace->dDeltap_self[i][1] += tmp_ddelta[indx][1]; + workspace->dDeltap_self[i][2] += tmp_ddelta[indx][2]; + workspace->total_bond_order[i] += tmp_bond_order[indx]; + } + + /* hydrogen bond list */ + if (control->hbond_cut > 0) { + cutoff = control->hbond_cut; + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) reduction(+ : num_hbonds) +#endif + for (int i = 0; i < system->n; ++i) { + atom_i = &(system->my_atoms[i]); + type_i = atom_i->type; + sbp_i = &(system->reax_param.sbp[type_i]); + ihb = sbp_i->p_hbond; + +#if defined(_OPENMP) +#pragma omp critical +#endif + { + + if (ihb == 1 || ihb == 2) { + start_i = Start_Index(i, far_nbrs); + end_i = End_Index(i, far_nbrs); + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + atom_j = &(system->my_atoms[j]); + type_j = atom_j->type; + if (type_j < 0) continue; + sbp_j = &(system->reax_param.sbp[type_j]); + jhb = sbp_j->p_hbond; + + if (nbr_pj->d <= control->hbond_cut) { + int iflag = 0; + int jflag = 0; + + if (ihb==1 && jhb==2) iflag = 1; + else if (jn && ihb == 2 && jhb == 1) jflag = 1; + + if (iflag || jflag) { + if (iflag) { + ihb_top = End_Index(atom_i->Hindex, hbonds); + Set_End_Index(atom_i->Hindex, ihb_top+1, hbonds); + } else if (jflag) { + jhb_top = End_Index(atom_j->Hindex, hbonds); + Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds); + } + + if (iflag) { + hbonds->select.hbond_list[ihb_top].nbr = j; + hbonds->select.hbond_list[ihb_top].scl = 1; + hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; + } else if (jflag) { + hbonds->select.hbond_list[jhb_top].nbr = i; + hbonds->select.hbond_list[jhb_top].scl = -1; + hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; + } + + num_hbonds++; + } // if (iflag || jflag) + + } + } + } + + } // omp critical + } + + } // if (control->hbond > 0) + + // Zero buffers for others to use as intended. +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (int i=0; irealloc.num_bonds = num_bonds; + workspace->realloc.num_hbonds = num_hbonds; + + Validate_ListsOMP(system, lists, data->step, + system->n, system->N, system->numH); + } + +/* ---------------------------------------------------------------------- */ + + void Compute_ForcesOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + // Init Forces + Init_Forces_noQEq_OMP(system, control, data, workspace, lists); + + // Bonded Interactions + Compute_Bonded_ForcesOMP(system, control, data, workspace, lists); + + // Nonbonded Interactions + Compute_NonBonded_ForcesOMP(system, control, data, workspace, lists); + + // Total Force + Compute_Total_ForceOMP(system, control, workspace, lists); + } +} diff --git a/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp b/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp new file mode 100644 index 0000000000..64bbbf56b1 --- /dev/null +++ b/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp @@ -0,0 +1,204 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + Website: https://www.cs.purdue.edu/puremd + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "fix_omp.h" +#include "pair_reaxff_omp.h" + +#include "reaxff_api.h" + +#include + +using namespace LAMMPS_NS; + +namespace ReaxFF { + + /* ---------------------------------------------------------------------- */ + + void Hydrogen_BondsOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, reax_list **lists) + { + + const int nthreads = control->nthreads; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) //LMP_DEFAULT_NONE +#endif + { + int i, j, k, pi, pk; + int type_i, type_j, type_k; + int start_j, end_j, hb_start_j, hb_end_j; + int hblist[MAX_BONDS]; + int itr, top; + int num_hb_intrs = 0; + double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; + double e_hb, e_hb_thr = 0.0, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3; + rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk; + rvec dvec_jk; + hbond_parameters *hbp; + bond_order_data *bo_ij; + bond_data *pbond_ij; + far_neighbor_data *nbr_jk; + reax_list *bonds, *hbonds; + bond_data *bond_list; + hbond_data *hbond_list; + + // tally variables + double fi_tmp[3], fk_tmp[3], delij[3], delkj[3]; + + bonds = (*lists) + BONDS; + bond_list = bonds->select.bond_list; + hbonds = (*lists) + HBONDS; + hbond_list = hbonds->select.hbond_list; + + int natoms = system->n; + int tid = get_tid(); + + const int idelta = 1 + natoms/nthreads; + int ifrom = tid*idelta; + int ito = ((ifrom + idelta) > natoms) ? natoms : ifrom + idelta; + + long reductionOffset = (system->N * tid); + + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + + /* loops below discover the Hydrogen bonds between i-j-k triplets. + here j is H atom and there has to be some bond between i and j. + Hydrogen bond is between j and k. + so in this function i->X, j->H, k->Z when we map + variables onto the ones in the handout.*/ + // for (j = 0; j < system->n; ++j) + for (j = ifrom; j < ito; ++j) { + /* j has to be of type H */ + if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) { + /*set j's variables */ + type_j = system->my_atoms[j].type; + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds); + hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds); + if (type_j < 0) continue; + + top = 0; + for (pi = start_j; pi < end_j; ++pi) { + pbond_ij = &(bond_list[pi]); + i = pbond_ij->nbr; + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + bo_ij = &(pbond_ij->bo_data); + + if (system->reax_param.sbp[type_i].p_hbond == 2 && + bo_ij->BO >= HB_THRESHOLD) + hblist[top++] = pi; + } + + for (pk = hb_start_j; pk < hb_end_j; ++pk) { + /* set k's varibles */ + k = hbond_list[pk].nbr; + type_k = system->my_atoms[k].type; + if (type_k < 0) continue; + nbr_jk = hbond_list[pk].ptr; + r_jk = nbr_jk->d; + rvec_Scale(dvec_jk, hbond_list[pk].scl, nbr_jk->dvec); + + for (itr = 0; itr < top; ++itr) { + pi = hblist[itr]; + pbond_ij = &(bonds->select.bond_list[pi]); + i = pbond_ij->nbr; + + if (system->my_atoms[i].orig_id != system->my_atoms[k].orig_id) { + bo_ij = &(pbond_ij->bo_data); + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + hbp = &(system->reax_param.hbp[type_i][type_j][type_k]); + ++num_hb_intrs; + + Calculate_Theta(pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, + &theta, &cos_theta); + /* the derivative of cos(theta) */ + Calculate_dCos_ThetaOMP(pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, + &dcos_theta_di, &dcos_theta_dj, + &dcos_theta_dk); + + /* hydrogen bond energy*/ + sin_theta2 = sin(theta/2.0); + sin_xhz4 = SQR(sin_theta2); + sin_xhz4 *= sin_xhz4; + cos_xhz1 = (1.0 - cos_theta); + exp_hb2 = exp(-hbp->p_hb2 * bo_ij->BO); + exp_hb3 = exp(-hbp->p_hb3 * (hbp->r0_hb / r_jk + + r_jk / hbp->r0_hb - 2.0)); + + e_hb_thr += e_hb = hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4; + + CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4; + CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1; + CEhb3 = -hbp->p_hb3 * + (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb; + + /* hydrogen bond forces */ + bo_ij->Cdbo += CEhb1; // dbo term + + // dcos terms + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], +CEhb2, dcos_theta_di); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb2, dcos_theta_dk); + // dr terms + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], -CEhb3/r_jk, dvec_jk); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb3/r_jk, dvec_jk); + + /* tally into per-atom virials */ + if (system->pair_ptr->vflag_either || system->pair_ptr->eflag_either) { + rvec_ScaledSum(delij, 1., system->my_atoms[j].x, -1., system->my_atoms[i].x); + rvec_ScaledSum(delkj, 1., system->my_atoms[j].x, -1., system->my_atoms[k].x); + + rvec_Scale(fi_tmp, CEhb2, dcos_theta_di); + rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk); + rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk); + + pair_reax_ptr->ev_tally3_thr_proxy(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj,thr); + } + } + } + } + } + } +#if defined(_OPENMP) +#pragma omp critical +#endif + { + data->my_en.e_hb += e_hb_thr; + } + } + } +} diff --git a/src/OPENMP/reaxff_init_md_omp.cpp b/src/OPENMP/reaxff_init_md_omp.cpp new file mode 100644 index 0000000000..a0100e648a --- /dev/null +++ b/src/OPENMP/reaxff_init_md_omp.cpp @@ -0,0 +1,104 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" +#include "reaxff_api.h" + +#include "error.h" + +#include +#include + +namespace ReaxFF { + static void Init_ListsOMP(reax_system *system, control_params *control, + reax_list **lists) + { + int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; + int *hb_top, *bond_top; + + int mincap = system->mincap; + double safezone = system->safezone; + double saferzone = system->saferzone; + auto error = system->error_ptr; + + bond_top = (int*) calloc(system->total_cap, sizeof(int)); + hb_top = (int*) calloc(system->local_cap, sizeof(int)); + Estimate_Storages(system, control, lists, + &Htop, hb_top, bond_top, &num_3body); + + if (control->hbond_cut > 0) { + /* init H indexes */ + total_hbonds = 0; + for (i = 0; i < system->n; ++i) { + system->my_atoms[i].num_hbonds = hb_top[i]; + total_hbonds += hb_top[i]; + } + total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds)); + + Make_List(system->Hcap, total_hbonds, TYP_HBOND,*lists+HBONDS); + (*lists+HBONDS)->error_ptr = system->error_ptr; + } + + total_bonds = 0; + for (i = 0; i < system->N; ++i) { + system->my_atoms[i].num_bonds = bond_top[i]; + total_bonds += bond_top[i]; + } + bond_cap = (int)(MAX(total_bonds*safezone, mincap*MIN_BONDS)); + + Make_List(system->total_cap, bond_cap, TYP_BOND,*lists+BONDS); + (*lists+BONDS)->error_ptr = system->error_ptr; + + int nthreads = control->nthreads; + reax_list *bonds = (*lists)+BONDS; + + for (i = 0; i < bonds->num_intrs; ++i) + bonds->select.bond_list[i].bo_data.CdboReduction = + (double*) smalloc(error, sizeof(double)*nthreads, "CdboReduction"); + + /* 3bodies list */ + cap_3body = (int)(MAX(num_3body*safezone, MIN_3BODIES)); + Make_List(bond_cap, cap_3body, TYP_THREE_BODY,*lists+THREE_BODIES); + (*lists+THREE_BODIES)->error_ptr = system->error_ptr; + + free(hb_top); + free(bond_top); + } + + void InitializeOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists, MPI_Comm world) + { + Init_System(system,control); + Init_Simulation_Data(data); + Init_Workspace(system,control,workspace); + Init_ListsOMP(system,control,lists); + if (control->tabulate) + Init_Lookup_Tables(system,control,workspace,world); + } +} diff --git a/src/OPENMP/reaxff_multi_body_omp.cpp b/src/OPENMP/reaxff_multi_body_omp.cpp new file mode 100644 index 0000000000..17b93d7487 --- /dev/null +++ b/src/OPENMP/reaxff_multi_body_omp.cpp @@ -0,0 +1,274 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + Website: https://www.cs.purdue.edu/puremd + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "fix_omp.h" +#include "pair_reaxff_omp.h" + +#include "reaxff_api.h" + +#include +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +namespace ReaxFF { + void Atom_EnergyOMP(reax_system *system, simulation_data *data, + storage *workspace, reax_list **lists) + { + /* Initialize parameters */ + const double p_lp3 = system->reax_param.gp.l[5]; + const double p_ovun3 = system->reax_param.gp.l[32]; + const double p_ovun4 = system->reax_param.gp.l[31]; + const double p_ovun6 = system->reax_param.gp.l[6]; + const double p_ovun7 = system->reax_param.gp.l[8]; + const double p_ovun8 = system->reax_param.gp.l[9]; + + reax_list *bonds = (*lists) + BONDS; + + double total_Elp = 0.0; + double total_Eun = 0.0; + double total_Eov = 0.0; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) reduction(+:total_Elp, total_Eun, total_Eov) +#endif + { + int i, j, pj, type_i, type_j; + double Delta_lpcorr, dfvl; + double e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi; + double e_lph, Di, vov3, deahu2dbo, deahu2dsbo; + double e_ov, CEover1, CEover2, CEover3, CEover4; + double exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2; + double exp_ovun2n, exp_ovun6, exp_ovun8; + double inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8; + double e_un, CEunder1, CEunder2, CEunder3, CEunder4; + double eng_tmp; + double p_lp2, p_ovun2, p_ovun5; + int numbonds; + + single_body_parameters *sbp_i; + two_body_parameters *twbp; + bond_data *pbond; + bond_order_data *bo_ij; + + int tid = get_tid(); + + long reductionOffset = (system->N * tid); + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < system->n; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + sbp_i = &(system->reax_param.sbp[type_i]); + + /* lone-pair Energy */ + p_lp2 = sbp_i->p_lp2; + expvd2 = exp(-75 * workspace->Delta_lp[i]); + inv_expvd2 = 1. / (1. + expvd2); + + numbonds = 0; + e_lp = 0.0; + for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) + numbonds ++; + + /* calculate the energy */ + if (numbonds > 0) + total_Elp += e_lp = + p_lp2 * workspace->Delta_lp[i] * inv_expvd2; + + dElp = p_lp2 * inv_expvd2 + + 75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2); + CElp = dElp * workspace->dDelta_lp[i]; + + if (numbonds > 0) workspace->CdDelta[i] += CElp; // lp - 1st term + + /* tally into per-atom energy */ + if (system->pair_ptr->eflag_either) + pair_reax_ptr->ev_tally_thr_proxy( i, i, system->n, 1, + e_lp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); + + /* correction for C2 */ + if (p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C")) + for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { + j = bonds->select.bond_list[pj].nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + + if (!strcmp(system->reax_param.sbp[type_j].name, "C")) { + twbp = &(system->reax_param.tbp[type_i][type_j]); + bo_ij = &(bonds->select.bond_list[pj].bo_data); + Di = workspace->Delta[i]; + vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.); + + if (vov3 > 3.) { + total_Elp += e_lph = p_lp3 * SQR(vov3-3.0); + + deahu2dbo = 2.*p_lp3*(vov3 - 3.); + deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.)); + + bo_ij->Cdbo += deahu2dbo; + workspace->CdDelta[i] += deahu2dsbo; + + /* tally into per-atom energy */ + if (system->pair_ptr->eflag_either) + pair_reax_ptr->ev_tally_thr_proxy( i, j, system->n, 1, + e_lph, 0.0, 0.0, 0.0, 0.0, 0.0, thr); + } + } + } + } +#if defined(_OPENMP) +#pragma omp barrier +#pragma omp for schedule(guided) +#endif + for (i = 0; i < system->n; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + sbp_i = &(system->reax_param.sbp[type_i]); + + /* over-coordination energy */ + if (sbp_i->mass > 21.0) + dfvl = 0.0; + else dfvl = 1.0; // only for 1st-row elements + + p_ovun2 = sbp_i->p_ovun2; + sum_ovun1 = sum_ovun2 = 0; + for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { + j = bonds->select.bond_list[pj].nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + bo_ij = &(bonds->select.bond_list[pj].bo_data); + twbp = &(system->reax_param.tbp[type_i][type_j]); + + sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO; + sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])* + (bo_ij->BO_pi + bo_ij->BO_pi2); + } + + exp_ovun1 = p_ovun3 * exp(p_ovun4 * sum_ovun2); + inv_exp_ovun1 = 1.0 / (1 + exp_ovun1); + Delta_lpcorr = workspace->Delta[i] - + (dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1; + + exp_ovun2 = exp(p_ovun2 * Delta_lpcorr); + inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2); + + DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8); + CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2; + + total_Eov += e_ov = sum_ovun1 * CEover1; + + CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 * + (1.0 - Delta_lpcorr * (DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2)); + + CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1); + + CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) * + p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1); + + + /* under-coordination potential */ + p_ovun2 = sbp_i->p_ovun2; + p_ovun5 = sbp_i->p_ovun5; + + exp_ovun2n = 1.0 / exp_ovun2; + exp_ovun6 = exp(p_ovun6 * Delta_lpcorr); + exp_ovun8 = p_ovun7 * exp(p_ovun8 * sum_ovun2); + inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n); + inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8); + + numbonds = 0; + e_un = 0.0; + for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) + numbonds ++; + + if (numbonds > 0) total_Eun += e_un = + -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8; + + CEunder1 = inv_exp_ovun2n * + (p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 + + p_ovun2 * e_un * exp_ovun2n); + CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8; + CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1); + CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) * + p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2; + + /* tally into per-atom energy */ + if (system->pair_ptr->eflag_either) { + eng_tmp = e_ov; + if (numbonds > 0) eng_tmp+= e_un; + pair_reax_ptr->ev_tally_thr_proxy( i, i, system->n, 1, + eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); + } + + /* forces */ + workspace->CdDelta[i] += CEover3; // OvCoor - 2nd term + if (numbonds > 0) workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term + + for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { + pbond = &(bonds->select.bond_list[pj]); + j = pbond->nbr; + bo_ij = &(pbond->bo_data); + twbp = &(system->reax_param.tbp[system->my_atoms[i].type] + [system->my_atoms[pbond->nbr].type]); + + bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s; // OvCoor-1st + workspace->CdDeltaReduction[reductionOffset+j] += + CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a + + bo_ij->Cdbopi += CEover4 * + (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b + bo_ij->Cdbopi2 += CEover4 * + (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b + + workspace->CdDeltaReduction[reductionOffset+j] += + CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a + + bo_ij->Cdbopi += CEunder4 * + (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b + bo_ij->Cdbopi2 += CEunder4 * + (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b + } + } + } + + data->my_en.e_lp += total_Elp; + data->my_en.e_ov += total_Eov; + data->my_en.e_un += total_Eun; + } +} diff --git a/src/OPENMP/reaxff_nonbonded_omp.cpp b/src/OPENMP/reaxff_nonbonded_omp.cpp new file mode 100644 index 0000000000..a57542f550 --- /dev/null +++ b/src/OPENMP/reaxff_nonbonded_omp.cpp @@ -0,0 +1,348 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + Website: https://www.cs.purdue.edu/puremd + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "pair_reaxff_omp.h" +#include "reaxff_api.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +namespace ReaxFF { + void vdW_Coulomb_Energy_OMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + int natoms = system->n; + reax_list *far_nbrs = (*lists) + FAR_NBRS; + double p_vdW1 = system->reax_param.gp.l[28]; + double p_vdW1i = 1.0 / p_vdW1; + double total_EvdW = 0.; + double total_Eele = 0.; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) reduction(+: total_EvdW, total_Eele) +#endif + { + int tid = get_tid(); + int i, j, pj; + int start_i, end_i, orig_i, orig_j, flag; + double powr_vdW1, powgi_vdW1; + double tmp, r_ij, fn13, exp1, exp2; + double Tap, dTap, dfn13, CEvd, CEclmb, de_core; + double dr3gamij_1, dr3gamij_3; + double e_ele, e_vdW, e_core; + const double SMALL = 0.0001; + double e_lg, de_lg, r_ij5, r_ij6, re6; + two_body_parameters *twbp; + far_neighbor_data *nbr_pj; + + // Tallying variables: + double pe_vdw, f_tmp, delij[3]; + + long reductionOffset = (system->N * tid); + + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + + e_core = 0; + e_vdW = 0; + e_lg = 0; + de_lg = 0.0; + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < natoms; ++i) { + if (system->my_atoms[i].type < 0) continue; + start_i = Start_Index(i, far_nbrs); + end_i = End_Index(i, far_nbrs); + orig_i = system->my_atoms[i].orig_id; + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + orig_j = system->my_atoms[j].orig_id; + + flag = 0; + if (nbr_pj->d <= control->nonb_cut) { + if (j < natoms) flag = 1; + else if (orig_i < orig_j) flag = 1; + else if (orig_i == orig_j) { + if (nbr_pj->dvec[2] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[2]) < SMALL) { + if (nbr_pj->dvec[1] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) + flag = 1; + } + } + } + + if (flag) { + + r_ij = nbr_pj->d; + twbp = &(system->reax_param.tbp[system->my_atoms[i].type] + [system->my_atoms[j].type]); + + /* Calculate Taper and its derivative */ + // Tap = nbr_pj->Tap; -- precomputed during compte_H + Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; + Tap = Tap * r_ij + workspace->Tap[5]; + Tap = Tap * r_ij + workspace->Tap[4]; + Tap = Tap * r_ij + workspace->Tap[3]; + Tap = Tap * r_ij + workspace->Tap[2]; + Tap = Tap * r_ij + workspace->Tap[1]; + Tap = Tap * r_ij + workspace->Tap[0]; + + dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; + dTap = dTap * r_ij + 5*workspace->Tap[5]; + dTap = dTap * r_ij + 4*workspace->Tap[4]; + dTap = dTap * r_ij + 3*workspace->Tap[3]; + dTap = dTap * r_ij + 2*workspace->Tap[2]; + dTap += workspace->Tap[1]/r_ij; + + /*vdWaals Calculations*/ + if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) + { // shielding + powr_vdW1 = pow(r_ij, p_vdW1); + powgi_vdW1 = pow(1.0 / twbp->gamma_w, p_vdW1); + + fn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i); + exp1 = exp(twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + + e_vdW = twbp->D * (exp1 - 2.0 * exp2); + total_EvdW += Tap * e_vdW; + + dfn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * + pow(r_ij, p_vdW1 - 2.0); + + CEvd = dTap * e_vdW - + Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; + } + else { // no shielding + exp1 = exp(twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + + e_vdW = twbp->D * (exp1 - 2.0 * exp2); + total_EvdW += Tap * e_vdW; + + CEvd = dTap * e_vdW - + Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; + } + + if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) + { // innner wall + e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); + total_EvdW += Tap * e_core; + + de_core = -(twbp->acore/twbp->rcore) * e_core; + CEvd += dTap * e_core + Tap * de_core / r_ij; + + // lg correction, only if lgvdw is yes + if (control->lgflag) { + r_ij5 = pow(r_ij, 5.0); + r_ij6 = pow(r_ij, 6.0); + re6 = pow(twbp->lgre, 6.0); + + e_lg = -(twbp->lgcij/(r_ij6 + re6)); + total_EvdW += Tap * e_lg; + + de_lg = -6.0 * e_lg * r_ij5 / (r_ij6 + re6) ; + CEvd += dTap * e_lg + Tap * de_lg / r_ij; + } + + } + + /*Coulomb Calculations*/ + dr3gamij_1 = (r_ij * r_ij * r_ij + twbp->gamma); + dr3gamij_3 = pow(dr3gamij_1 , 0.33333333333333); + + tmp = Tap / dr3gamij_3; + total_Eele += e_ele = + C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp; + + CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * + (dTap - Tap * r_ij / dr3gamij_1) / dr3gamij_3; + + /* tally into per-atom energy */ + if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { + pe_vdw = Tap * (e_vdW + e_core + e_lg); + rvec_ScaledSum(delij, 1., system->my_atoms[i].x, + -1., system->my_atoms[j].x); + f_tmp = -(CEvd + CEclmb); + pair_reax_ptr->ev_tally_thr_proxy( i, j, natoms, + 1, pe_vdw, e_ele, f_tmp, + delij[0], delij[1], delij[2], thr); + } + + rvec_ScaledAdd(workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], + +(CEvd + CEclmb), nbr_pj->dvec); + } + } + } + + pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either, + system->pair_ptr->vflag_either, thr); + } // parallel region + + data->my_en.e_vdW = total_EvdW; + data->my_en.e_ele = total_Eele; + + Compute_Polarization_Energy(system, data); + } + +/* ---------------------------------------------------------------------- */ + + void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) { + + double SMALL = 0.0001; + int natoms = system->n; + reax_list *far_nbrs = (*lists) + FAR_NBRS; + double total_EvdW = 0.; + double total_Eele = 0.; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) reduction(+:total_EvdW, total_Eele) +#endif + { + int i, j, pj, r; + int type_i, type_j, tmin, tmax; + int start_i, end_i, orig_i, orig_j, flag; + double r_ij, base, dif; + double e_vdW, e_ele; + double CEvd, CEclmb; + double f_tmp, delij[3]; + far_neighbor_data *nbr_pj; + LR_lookup_table *t; + + int tid = get_tid(); + long froffset = (system->N * tid); + LR_lookup_table ** & LR = system->LR; + + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + +#if defined(_OPENMP) +#pragma omp for schedule(guided) +#endif + for (i = 0; i < natoms; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + start_i = Start_Index(i,far_nbrs); + end_i = End_Index(i,far_nbrs); + orig_i = system->my_atoms[i].orig_id; + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + orig_j = system->my_atoms[j].orig_id; + + flag = 0; + if (nbr_pj->d <= control->nonb_cut) { + if (j < natoms) flag = 1; + else if (orig_i < orig_j) flag = 1; + else if (orig_i == orig_j) { + if (nbr_pj->dvec[2] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[2]) < SMALL) { + if (nbr_pj->dvec[1] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) + flag = 1; + } + } + + } + + if (flag) { + + r_ij = nbr_pj->d; + tmin = MIN(type_i, type_j); + tmax = MAX(type_i, type_j); + t = &(LR[tmin][tmax]); + + /* Cubic Spline Interpolation */ + r = (int)(r_ij * t->inv_dx); + if (r == 0) ++r; + base = (double)(r+1) * t->dx; + dif = r_ij - base; + + e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif + + t->vdW[r].a; + + e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + + t->ele[r].a; + e_ele *= system->my_atoms[i].q * system->my_atoms[j].q; + + total_EvdW += e_vdW; + total_Eele += e_ele; + + CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif + + t->CEvd[r].a; + + CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif + + t->CEclmb[r].a; + CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; + + /* tally into per-atom energy */ + if (system->pair_ptr->evflag) { + rvec_ScaledSum(delij, 1., system->my_atoms[i].x, + -1., system->my_atoms[j].x); + f_tmp = -(CEvd + CEclmb); + pair_reax_ptr->ev_tally_thr_proxy( i, j, natoms, 1, e_vdW, e_ele, + f_tmp, delij[0], delij[1], delij[2], thr); + } + + rvec_ScaledAdd(workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec); + rvec_ScaledAdd(workspace->forceReduction[froffset+j], + +(CEvd + CEclmb), nbr_pj->dvec); + } + } + } + + pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either, + system->pair_ptr->vflag_either, thr); + } // end omp parallel + + data->my_en.e_vdW = total_EvdW; + data->my_en.e_ele = total_Eele; + + Compute_Polarization_Energy(system, data); + } +} diff --git a/src/OPENMP/reaxff_omp.h b/src/OPENMP/reaxff_omp.h new file mode 100644 index 0000000000..252e5f0e9d --- /dev/null +++ b/src/OPENMP/reaxff_omp.h @@ -0,0 +1,103 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hasan Metin Aktulga, Purdue University + (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov) + + Heavily modified and adapted for LAMMPS by the LAMMPS developers. +------------------------------------------------------------------------- */ + +#ifndef LMP_REAXFF_OMP_H +#define LMP_REAXFF_OMP_H + +#include "reaxff_types.h" + +#if defined(_OPENMP) +#include +#endif + +namespace ReaxFF +{ + // exported Functions + + // bond orders OpenMP + + extern void Add_dBond_to_ForcesOMP(reax_system *, int, int, storage *, reax_list **); + extern void Add_dBond_to_Forces_NPTOMP(reax_system *, int, int, storage *, reax_list **); + extern int BOp_OMP(storage *, reax_list *, double, int, int, far_neighbor_data *, + single_body_parameters *, single_body_parameters *, + two_body_parameters *, int, double, double, double, + double, double, double, double); + + extern void BOOMP(reax_system *, storage *, reax_list **); + + // bonds OpenMP + + extern void BondsOMP(reax_system *, simulation_data *, + storage *, reax_list **); + + // forces OpenMP + + extern void Compute_ForcesOMP(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + + // hydrogen bonds + + extern void Hydrogen_BondsOMP(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + + // init md OpenMP + + extern void InitializeOMP(reax_system *, control_params *, simulation_data *, + storage *, reax_list **,MPI_Comm); + + // multi body + + extern void Atom_EnergyOMP(reax_system *, simulation_data *, storage *, reax_list **); + + // nonbonded + + extern void vdW_Coulomb_Energy_OMP(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + extern void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *, control_params *, + simulation_data *, storage *, + reax_list **); + extern void LR_vdW_CoulombOMP(reax_system *, storage *, control_params *, + int, int, double, LR_data *); + + // torsion angles + + extern void Torsion_AnglesOMP(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + + // valence angles + + extern void Calculate_ThetaOMP(rvec, double, rvec, double, double *, double *); + extern void Calculate_dCos_ThetaOMP(rvec, double, rvec, double, + rvec *, rvec *, rvec *); + extern void Valence_AnglesOMP(reax_system *, control_params *, simulation_data *, + storage *, reax_list **); + + // OpenMP helpers + + inline int get_tid() { +#if defined(_OPENMP) + return omp_get_thread_num(); +#else + return 0; +#endif + } +} + +#endif diff --git a/src/OPENMP/reaxff_torsion_angles_omp.cpp b/src/OPENMP/reaxff_torsion_angles_omp.cpp new file mode 100644 index 0000000000..648603b143 --- /dev/null +++ b/src/OPENMP/reaxff_torsion_angles_omp.cpp @@ -0,0 +1,396 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + Website: https://www.cs.purdue.edu/puremd + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "fix_omp.h" +#include "pair_reaxff_omp.h" +#include "reaxff_api.h" + +#include + +#define MIN_SINE 1e-10 + +using namespace LAMMPS_NS; + +namespace ReaxFF { + + /* ---------------------------------------------------------------------- */ + void Torsion_AnglesOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + int natoms = system->n; + reax_list *bonds = (*lists) + BONDS; + reax_list *thb_intrs = (*lists) + THREE_BODIES; + double p_tor2 = system->reax_param.gp.l[23]; + double p_tor3 = system->reax_param.gp.l[24]; + double p_tor4 = system->reax_param.gp.l[25]; + double p_cot2 = system->reax_param.gp.l[27]; + double total_Etor = 0; + double total_Econ = 0; + int nthreads = control->nthreads; + +#if defined(_OPENMP) +#pragma omp parallel default(shared) reduction(+: total_Etor, total_Econ) +#endif + { + int i, j, k, l, pi, pj, pk, pl, pij, plk; + int type_i, type_j, type_k, type_l; + int start_j, end_j; + int start_pj, end_pj, start_pk, end_pk; + int num_frb_intrs = 0; + + double Delta_j, Delta_k; + double r_ij, r_jk, r_kl, r_li; + double BOA_ij, BOA_jk, BOA_kl; + + double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl; + double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv; + double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl; + double fn10, f11_DjDk, dfn11, fn12; + double theta_ijk, theta_jkl; + double sin_ijk, sin_jkl; + double cos_ijk, cos_jkl; + double tan_ijk_i, tan_jkl_i; + double omega, cos_omega, cos2omega, cos3omega; + rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl; + double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4; + double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9; + double Cconj, CEconj1, CEconj2, CEconj3; + double CEconj4, CEconj5, CEconj6; + double e_tor, e_con; + rvec dvec_li; + four_body_header *fbh; + four_body_parameters *fbp; + bond_data *pbond_ij, *pbond_jk, *pbond_kl; + bond_order_data *bo_ij, *bo_jk, *bo_kl; + three_body_interaction_data *p_ijk, *p_jkl; + + // Virial tallying variables + double delil[3], deljl[3], delkl[3]; + double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; + + int tid = get_tid(); + + long reductionOffset = (system->N * tid); + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + +#if defined(_OPENMP) +#pragma omp for schedule(static) +#endif + for (j = 0; j < system->N; ++j) { + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + for (pk = start_j; pk < end_j; ++pk) { + bo_jk = &(bonds->select.bond_list[pk].bo_data); + for (k = 0; k < nthreads; ++k) + bo_jk->CdboReduction[k] = 0.; + } + } + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) +#endif + for (j = 0; j < natoms; ++j) { + type_j = system->my_atoms[j].type; + Delta_j = workspace->Delta_boc[j]; + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + for (pk = start_j; pk < end_j; ++pk) { + pbond_jk = &(bonds->select.bond_list[pk]); + k = pbond_jk->nbr; + bo_jk = &(pbond_jk->bo_data); + BOA_jk = bo_jk->BO - control->thb_cut; + + /* see if there are any 3-body interactions involving j&k + where j is the central atom. Otherwise there is no point in + trying to form a 4-body interaction out of this neighborhood */ + if (system->my_atoms[j].orig_id < system->my_atoms[k].orig_id && + bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) { + pj = pbond_jk->sym_index; // pj points to j on k's list + + /* do the same check as above: + are there any 3-body interactions involving k&j + where k is the central atom */ + if (Num_Entries(pj, thb_intrs)) { + type_k = system->my_atoms[k].type; + Delta_k = workspace->Delta_boc[k]; + r_jk = pbond_jk->d; + + start_pk = Start_Index(pk, thb_intrs); + end_pk = End_Index(pk, thb_intrs); + start_pj = Start_Index(pj, thb_intrs); + end_pj = End_Index(pj, thb_intrs); + + exp_tor2_jk = exp(-p_tor2 * BOA_jk); + exp_cot2_jk = exp(-p_cot2 * SQR(BOA_jk - 1.5)); + exp_tor3_DjDk = exp(-p_tor3 * (Delta_j + Delta_k)); + exp_tor4_DjDk = exp(p_tor4 * (Delta_j + Delta_k)); + exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk); + f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv; + + + /* pick i up from j-k interaction where j is the central atom */ + for (pi = start_pk; pi < end_pk; ++pi) { + p_ijk = &(thb_intrs->select.three_body_list[pi]); + pij = p_ijk->pthb; // pij is pointer to i on j's bond_list + pbond_ij = &(bonds->select.bond_list[pij]); + bo_ij = &(pbond_ij->bo_data); + + if (bo_ij->BO > control->thb_cut/*0*/) { + i = p_ijk->thb; + type_i = system->my_atoms[i].type; + r_ij = pbond_ij->d; + BOA_ij = bo_ij->BO - control->thb_cut; + + theta_ijk = p_ijk->theta; + sin_ijk = sin(theta_ijk); + cos_ijk = cos(theta_ijk); + //tan_ijk_i = 1. / tan(theta_ijk); + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) + tan_ijk_i = cos_ijk / MIN_SINE; + else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) + tan_ijk_i = cos_ijk / -MIN_SINE; + else tan_ijk_i = cos_ijk / sin_ijk; + + exp_tor2_ij = exp(-p_tor2 * BOA_ij); + exp_cot2_ij = exp(-p_cot2 * SQR(BOA_ij -1.5)); + + + /* pick l up from j-k interaction where k is the central atom */ + for (pl = start_pj; pl < end_pj; ++pl) { + p_jkl = &(thb_intrs->select.three_body_list[pl]); + l = p_jkl->thb; + plk = p_jkl->pthb; //pointer to l on k's bond_list! + pbond_kl = &(bonds->select.bond_list[plk]); + bo_kl = &(pbond_kl->bo_data); + type_l = system->my_atoms[l].type; + fbh = &(system->reax_param.fbp[type_i][type_j] + [type_k][type_l]); + fbp = &(system->reax_param.fbp[type_i][type_j] + [type_k][type_l].prm[0]); + + if (i != l && fbh->cnt && + bo_kl->BO > control->thb_cut/*0*/ && + bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) { + ++num_frb_intrs; + //fprintf(stderr, + // "%5d: %6d %6d %6d %6d\n", num_frb_intrs, + // system->my_atoms[i].orig_id,system->my_atoms[j].orig_id, + // system->my_atoms[k].orig_id,system->my_atoms[l].orig_id); + + r_kl = pbond_kl->d; + BOA_kl = bo_kl->BO - control->thb_cut; + + theta_jkl = p_jkl->theta; + sin_jkl = sin(theta_jkl); + cos_jkl = cos(theta_jkl); + //tan_jkl_i = 1. / tan(theta_jkl); + if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) + tan_jkl_i = cos_jkl / MIN_SINE; + else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) + tan_jkl_i = cos_jkl / -MIN_SINE; + else tan_jkl_i = cos_jkl /sin_jkl; + + rvec_ScaledSum(dvec_li, 1., system->my_atoms[i].x, + -1., system->my_atoms[l].x); + r_li = rvec_Norm(dvec_li); + + + /* omega and its derivative */ + omega = Calculate_Omega(pbond_ij->dvec, r_ij, + pbond_jk->dvec, r_jk, + pbond_kl->dvec, r_kl, + dvec_li, r_li, + p_ijk, p_jkl, + dcos_omega_di, dcos_omega_dj, + dcos_omega_dk, dcos_omega_dl); + + cos_omega = cos(omega); + cos2omega = cos(2. * omega); + cos3omega = cos(3. * omega); + /* end omega calculations */ + + /* torsion energy */ + exp_tor1 = exp(fbp->p_tor1 * + SQR(2.0 - bo_jk->BO_pi - f11_DjDk)); + exp_tor2_kl = exp(-p_tor2 * BOA_kl); + exp_cot2_kl = exp(-p_cot2 * SQR(BOA_kl - 1.5)); + fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * + (1.0 - exp_tor2_kl); + + CV = 0.5 * (fbp->V1 * (1.0 + cos_omega) + + fbp->V2 * exp_tor1 * (1.0 - cos2omega) + + fbp->V3 * (1.0 + cos3omega)); + + total_Etor += e_tor = fn10 * sin_ijk * sin_jkl * CV; + + dfn11 = (-p_tor3 * exp_tor3_DjDk + + (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) * + (2.0 + exp_tor3_DjDk) * exp_tor34_inv) * + exp_tor34_inv; + + CEtors1 = sin_ijk * sin_jkl * CV; + + CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 * + (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) * + sin_ijk * sin_jkl; + CEtors3 = CEtors2 * dfn11; + + CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij * + (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl); + CEtors5 = CEtors1 * p_tor2 * + (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl); + CEtors6 = CEtors1 * p_tor2 * + (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl; + + cmn = -fn10 * CV; + CEtors7 = cmn * sin_jkl * tan_ijk_i; + CEtors8 = cmn * sin_ijk * tan_jkl_i; + + CEtors9 = fn10 * sin_ijk * sin_jkl * + (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega + + 1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega))); + /* end of torsion energy */ + + + /* 4-body conjugation energy */ + fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl; + //data->my_en.e_con += e_con = + total_Econ += e_con = + fbp->p_cot1 * fn12 * + (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); + + Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 * + (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); + + CEconj1 = Cconj * (BOA_ij - 1.5e0); + CEconj2 = Cconj * (BOA_jk - 1.5e0); + CEconj3 = Cconj * (BOA_kl - 1.5e0); + + CEconj4 = -fbp->p_cot1 * fn12 * + (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i; + CEconj5 = -fbp->p_cot1 * fn12 * + (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i; + CEconj6 = 2.0 * fbp->p_cot1 * fn12 * + cos_omega * sin_ijk * sin_jkl; + /* end 4-body conjugation energy */ + + /* FORCES */ + bo_jk->Cdbopi += CEtors2; + workspace->CdDelta[j] += CEtors3; + //workspace->CdDelta[k] += CEtors3; + workspace->CdDeltaReduction[reductionOffset+k] += CEtors3; + bo_ij->Cdbo += (CEtors4 + CEconj1); + bo_jk->Cdbo += (CEtors5 + CEconj2); + //bo_kl->Cdbo += (CEtors6 + CEconj3); + bo_kl->CdboReduction[tid] += (CEtors6 + CEconj3); + + /* dcos_theta_ijk */ + rvec_ScaledAdd(workspace->f[j], + CEtors7 + CEconj4, p_ijk->dcos_dj); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], + CEtors7 + CEconj4, p_ijk->dcos_dk); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], + CEtors7 + CEconj4, p_ijk->dcos_di); + + /* dcos_theta_jkl */ + rvec_ScaledAdd(workspace->f[j], + CEtors8 + CEconj5, p_jkl->dcos_di); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], + CEtors8 + CEconj5, p_jkl->dcos_dj); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+l], + CEtors8 + CEconj5, p_jkl->dcos_dk); + + /* dcos_omega */ + rvec_ScaledAdd(workspace->f[j], + CEtors9 + CEconj6, dcos_omega_dj); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], + CEtors9 + CEconj6, dcos_omega_di); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], + CEtors9 + CEconj6, dcos_omega_dk); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+l], + CEtors9 + CEconj6, dcos_omega_dl); + + /* tally into per-atom virials */ + if (system->pair_ptr->evflag) { + + // acquire vectors + rvec_ScaledSum(delil, 1., system->my_atoms[l].x, + -1., system->my_atoms[i].x); + rvec_ScaledSum(deljl, 1., system->my_atoms[l].x, + -1., system->my_atoms[j].x); + rvec_ScaledSum(delkl, 1., system->my_atoms[l].x, + -1., system->my_atoms[k].x); + // dcos_theta_ijk + rvec_Scale(fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk); + rvec_Scale(fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj); + rvec_Scale(fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di); + + // dcos_theta_jkl + rvec_ScaledAdd(fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di); + rvec_ScaledAdd(fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj); + + // dcos_omega + rvec_ScaledAdd(fi_tmp, CEtors9 + CEconj6, dcos_omega_di); + rvec_ScaledAdd(fj_tmp, CEtors9 + CEconj6, dcos_omega_dj); + rvec_ScaledAdd(fk_tmp, CEtors9 + CEconj6, dcos_omega_dk); + + // tally + eng_tmp = e_tor + e_con; + + if (system->pair_ptr->eflag_either) + pair_reax_ptr->ev_tally_thr_proxy( j, k, system->n, 1, + eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); + + if (system->pair_ptr->vflag_either) + pair_reax_ptr->v_tally4_thr_proxy(i, j, k, l, fi_tmp, fj_tmp, fk_tmp, + delil, deljl, delkl, thr); + } + + } // pl check ends + } // pl loop ends + } // pi check ends + } // pi loop ends + } // k-j neighbor check ends + } // jmy_en.e_tor = total_Etor; + data->my_en.e_con = total_Econ; + } +} diff --git a/src/OPENMP/reaxff_valence_angles_omp.cpp b/src/OPENMP/reaxff_valence_angles_omp.cpp new file mode 100644 index 0000000000..423b6336df --- /dev/null +++ b/src/OPENMP/reaxff_valence_angles_omp.cpp @@ -0,0 +1,571 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + Website: https://www.cs.purdue.edu/puremd + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_omp.h" + +#include "error.h" +#include "fix_omp.h" +#include "pair_reaxff_omp.h" +#include "reaxff_api.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +namespace ReaxFF { + void Calculate_dCos_ThetaOMP(rvec dvec_ji, double d_ji, rvec dvec_jk, + double d_jk, rvec *dcos_theta_di, + rvec *dcos_theta_dj, rvec *dcos_theta_dk) + { + double sqr_d_ji = SQR(d_ji); + double sqr_d_jk = SQR(d_jk); + double inv_dists = 1.0 / (d_ji * d_jk); + double inv_dists3 = inv_dists * inv_dists * inv_dists; + double dot_dvecs = dvec_ji[0]*dvec_jk[0] + dvec_ji[1]*dvec_jk[1] + dvec_ji[2]*dvec_jk[2]; + double Cdot_inv3 = dot_dvecs * inv_dists3; + + double csqr_jk = Cdot_inv3 * sqr_d_jk; + double csqr_ji = Cdot_inv3 * sqr_d_ji; + + // Try to help compiler out by unrolling + // x-component + double dinv_jk = dvec_jk[0] * inv_dists; + double dinv_ji = dvec_ji[0] * inv_dists; + + double cdev_ji = csqr_jk * dvec_ji[0]; + double cdev_jk = csqr_ji * dvec_jk[0]; + + (*dcos_theta_di)[0] = dinv_jk - cdev_ji; + (*dcos_theta_dj)[0] = -(dinv_jk + dinv_ji) + cdev_ji + cdev_jk; + (*dcos_theta_dk)[0] = dinv_ji - cdev_jk; + + // y-component + dinv_jk = dvec_jk[1] * inv_dists; + dinv_ji = dvec_ji[1] * inv_dists; + + cdev_ji = csqr_jk * dvec_ji[1]; + cdev_jk = csqr_ji * dvec_jk[1]; + + (*dcos_theta_di)[1] = dinv_jk - cdev_ji; + (*dcos_theta_dj)[1] = -(dinv_jk + dinv_ji) + cdev_ji + cdev_jk; + (*dcos_theta_dk)[1] = dinv_ji - cdev_jk; + + // z-component + dinv_jk = dvec_jk[2] * inv_dists; + dinv_ji = dvec_ji[2] * inv_dists; + + cdev_ji = csqr_jk * dvec_ji[2]; + cdev_jk = csqr_ji * dvec_jk[2]; + + (*dcos_theta_di)[2] = dinv_jk - cdev_ji; + (*dcos_theta_dj)[2] = -(dinv_jk + dinv_ji) + cdev_ji + cdev_jk; + (*dcos_theta_dk)[2] = dinv_ji - cdev_jk; + } + + /* ---------------------------------------------------------------------- */ + + /* this is a 3-body interaction in which the main role is + played by j which sits in the middle of the other two. */ + void Valence_AnglesOMP(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + reax_list *bonds = (*lists) + BONDS; + reax_list *thb_intrs = (*lists) + THREE_BODIES; + + // Precompute and store valence_angle offsets for OpenMP code. + int * _my_offset = workspace->valence_angle_atom_myoffset; + + /* global parameters used in these calculations */ + double p_val6 = system->reax_param.gp.l[14]; + double p_val8 = system->reax_param.gp.l[33]; + double p_val9 = system->reax_param.gp.l[16]; + double p_val10 = system->reax_param.gp.l[17]; + double total_Eang = 0; + double total_Epen = 0; + double total_Ecoa = 0; + + int nthreads = control->nthreads; + int num_thb_intrs = 0; + int TWICE = 2; +#if defined(_OPENMP) +#pragma omp parallel default(shared) reduction(+:total_Eang, total_Epen, total_Ecoa, num_thb_intrs) +#endif + { + int i, j, pi, k, pk, t; + int type_i, type_j, type_k; + int start_j, end_j, start_pk, end_pk; + int cnt, my_offset; + + double temp, temp_bo_jt, pBOjt7; + double p_val1, p_val2, p_val3, p_val4, p_val5, p_val7; + double p_pen1, p_pen2, p_pen3, p_pen4; + double p_coa1, p_coa2, p_coa3, p_coa4; + double trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk; + double exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2; + double dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj; + double CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8; + double CEpen1, CEpen2, CEpen3; + double e_ang, e_coa, e_pen; + double CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5; + double Cf7ij, Cf7jk, Cf8j, Cf9j; + double f7_ij, f7_jk, f8_Dj, f9_Dj; + double Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta; + double BOA_ij, BOA_jk; + + // Tallying variables + double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; + double delij[3], delkj[3]; + + three_body_header *thbh; + three_body_parameters *thbp; + three_body_interaction_data *p_ijk, *p_kji; + bond_data *pbond_ij, *pbond_jk, *pbond_jt; + bond_order_data *bo_ij, *bo_jk, *bo_jt; + + int tid = get_tid(); + + long reductionOffset = (system->N * tid); + class PairReaxFFOMP *pair_reax_ptr; + pair_reax_ptr = static_cast(system->pair_ptr); + class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); + + // Run through a minimal for (jnum_intrs / nthreads; + +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50) +#endif + for (j = 0; j < system->N; ++j) { + type_j = system->my_atoms[j].type; + _my_offset[j] = 0; + if (type_j < 0) continue; + + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + // Always point to start of workspace to count angles + my_offset = tid * per_thread; + + for (pi = start_j; pi < end_j; ++pi) { + Set_Start_Index(pi, my_offset, thb_intrs); + pbond_ij = &(bonds->select.bond_list[pi]); + bo_ij = &(pbond_ij->bo_data); + BOA_ij = bo_ij->BO - control->thb_cut; + + if (BOA_ij > 0.0) { + i = pbond_ij->nbr; + + /* first copy 3-body intrs from previously computed ones where i>k. + in the second for-loop below, + we compute only new 3-body intrs where i < k */ + for (pk = start_j; pk < pi; ++pk) { + start_pk = Start_Index(pk, thb_intrs); + end_pk = End_Index(pk, thb_intrs); + + for (t = start_pk; t < end_pk; ++t) + if (thb_intrs->select.three_body_list[t].thb == i) { + + p_ijk = &(thb_intrs->select.three_body_list[my_offset]); + p_ijk->thb = bonds->select.bond_list[pk].nbr; + + ++my_offset; + break; + } + } // for (pk) + + /* and this is the second for loop mentioned above */ + for (pk = pi+1; pk < end_j; ++pk) { + pbond_jk = &(bonds->select.bond_list[pk]); + k = pbond_jk->nbr; + + if (j >= system->n && i >= system->n && k >= system->n) continue; + + p_ijk = &(thb_intrs->select.three_body_list[my_offset]); + p_ijk->thb = k; + + ++my_offset; // add this to the list of 3-body interactions + } // for (pk) + } // if () + + Set_End_Index(pi, my_offset, thb_intrs); + } // for (pi) + + // Confirm that thb_intrs->num_intrs / nthreads is enough to hold all angles from a single atom + if (my_offset >= (tid+1)*per_thread) + control->error_ptr->one(FLERR, fmt::format("step {}: ran out of space on " + "angle_list for atom {}:\n" + " nthreads={} tid={} my_offset={} per_thread={}\n" + " num_intrs={} N={}",data->step,j,nthreads,tid, + my_offset,per_thread,thb_intrs->num_intrs,system->N)); + // Number of angles owned by this atom + _my_offset[j] = my_offset - tid * per_thread; + } // for (j) + + // Wait for all threads to finish counting angles +#if defined(_OPENMP) && !defined(__NVCC__) +#pragma omp barrier +#endif + // Master thread uses angle counts to compute offsets + // This can be threaded +#if defined(_OPENMP) && !defined(__NVCC__) +#pragma omp master +#endif + { + int current_count = 0; + int m = _my_offset[0]; + _my_offset[0] = current_count; + for (j=1; jN; j++) { + current_count+= m; + m = _my_offset[j]; + _my_offset[j] = current_count; + } + _my_offset[system->N] = current_count + m; // Used to test if last particle has any angles + } + + // All threads wait till master thread finished computing offsets +#if defined(_OPENMP) && !defined(__NVCC__) +#pragma omp barrier +#endif + // Original loop, but now using precomputed offsets + // Safe to use all threads available, regardless of threads tasked above + // We also now skip over atoms that have no angles assigned +#if defined(_OPENMP) +#pragma omp for schedule(dynamic,50)//(dynamic,chunksize)//(guided) +#endif + for (j = 0; j < system->N; ++j) { // Ray: the first one with system->N + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + + // Skip if no angles for this atom + if (_my_offset[j] == _my_offset[j+1]) continue; + + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + type_j = system->my_atoms[j].type; + + my_offset = _my_offset[j]; + + p_val3 = system->reax_param.sbp[type_j].p_val3; + p_val5 = system->reax_param.sbp[type_j].p_val5; + + SBOp = 0, prod_SBO = 1; + for (t = start_j; t < end_j; ++t) { + bo_jt = &(bonds->select.bond_list[t].bo_data); + SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2); + temp = SQR(bo_jt->BO); + temp *= temp; + temp *= temp; + prod_SBO *= exp(-temp); + } + + // modifications to match Adri's code - 09/01/09 + if (workspace->vlpex[j] >= 0) { + vlpadj = 0; + dSBO2 = prod_SBO - 1; + } else { + vlpadj = workspace->nlp[j]; + dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); + } + + SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); + dSBO1 = -8 * prod_SBO * (workspace->Delta_boc[j] + p_val8 * vlpadj); + + if (SBO <= 0) + SBO2 = 0, CSBO2 = 0; + else if (SBO > 0 && SBO <= 1) { + SBO2 = pow(SBO, p_val9); + CSBO2 = p_val9 * pow(SBO, p_val9 - 1); + } + else if (SBO > 1 && SBO < 2) { + SBO2 = 2 - pow(2-SBO, p_val9); + CSBO2 = p_val9 * pow(2 - SBO, p_val9 - 1); + } + else + SBO2 = 2, CSBO2 = 0; + + expval6 = exp(p_val6 * workspace->Delta_boc[j]); + + for (pi = start_j; pi < end_j; ++pi) { + Set_Start_Index(pi, my_offset, thb_intrs); + pbond_ij = &(bonds->select.bond_list[pi]); + bo_ij = &(pbond_ij->bo_data); + BOA_ij = bo_ij->BO - control->thb_cut; + + + if (BOA_ij > 0.0) { + i = pbond_ij->nbr; + type_i = system->my_atoms[i].type; + + + /* first copy 3-body intrs from previously computed ones where i>k. + in the second for-loop below, + we compute only new 3-body intrs where i < k */ + for (pk = start_j; pk < pi; ++pk) { + start_pk = Start_Index(pk, thb_intrs); + end_pk = End_Index(pk, thb_intrs); + + for (t = start_pk; t < end_pk; ++t) + if (thb_intrs->select.three_body_list[t].thb == i) { + p_ijk = &(thb_intrs->select.three_body_list[my_offset]); + p_kji = &(thb_intrs->select.three_body_list[t]); + + p_ijk->thb = bonds->select.bond_list[pk].nbr; + p_ijk->pthb = pk; + p_ijk->theta = p_kji->theta; + rvec_Copy(p_ijk->dcos_di, p_kji->dcos_dk); + rvec_Copy(p_ijk->dcos_dj, p_kji->dcos_dj); + rvec_Copy(p_ijk->dcos_dk, p_kji->dcos_di); + + ++my_offset; + ++num_thb_intrs; + break; + } + } // for (pk) + + + /* and this is the second for loop mentioned above */ + for (pk = pi+1; pk < end_j; ++pk) { + pbond_jk = &(bonds->select.bond_list[pk]); + bo_jk = &(pbond_jk->bo_data); + BOA_jk = bo_jk->BO - control->thb_cut; + k = pbond_jk->nbr; + type_k = system->my_atoms[k].type; + p_ijk = &(thb_intrs->select.three_body_list[my_offset]); + + // Fix by Sudhir + // if (BOA_jk <= 0) continue; + if (j >= system->n && i >= system->n && k >= system->n) continue; + + Calculate_Theta(pbond_ij->dvec, pbond_ij->d, + pbond_jk->dvec, pbond_jk->d, + &theta, &cos_theta); + + Calculate_dCos_ThetaOMP(pbond_ij->dvec, pbond_ij->d, + pbond_jk->dvec, pbond_jk->d, + &(p_ijk->dcos_di), &(p_ijk->dcos_dj), + &(p_ijk->dcos_dk)); + p_ijk->thb = k; + p_ijk->pthb = pk; + p_ijk->theta = theta; + + sin_theta = sin(theta); + if (sin_theta < 1.0e-5) + sin_theta = 1.0e-5; + + ++my_offset; // add this to the list of 3-body interactions + ++num_thb_intrs; + + if ((j < system->n) && (BOA_jk > 0.0) && + (bo_ij->BO > control->thb_cut) && + (bo_jk->BO > control->thb_cut) && + (bo_ij->BO * bo_jk->BO > control->thb_cutsq)) { + thbh = &(system->reax_param.thbp[type_i][type_j][type_k]); + + for (cnt = 0; cnt < thbh->cnt; ++cnt) { + + if (fabs(thbh->prm[cnt].p_val1) > 0.001) { + thbp = &(thbh->prm[cnt]); + + /* ANGLE ENERGY */ + p_val1 = thbp->p_val1; + p_val2 = thbp->p_val2; + p_val4 = thbp->p_val4; + p_val7 = thbp->p_val7; + theta_00 = thbp->theta_00; + + exp3ij = exp(-p_val3 * pow(BOA_ij, p_val4)); + f7_ij = 1.0 - exp3ij; + Cf7ij = p_val3 * p_val4 * pow(BOA_ij, p_val4 - 1.0) * exp3ij; + + exp3jk = exp(-p_val3 * pow(BOA_jk, p_val4)); + f7_jk = 1.0 - exp3jk; + Cf7jk = p_val3 * p_val4 * pow(BOA_jk, p_val4 - 1.0) * exp3jk; + + expval7 = exp(-p_val7 * workspace->Delta_boc[j]); + trm8 = 1.0 + expval6 + expval7; + f8_Dj = p_val5 - ((p_val5 - 1.0) * (2.0 + expval6) / trm8); + Cf8j = ((1.0 - p_val5) / SQR(trm8)) * + (p_val6 * expval6 * trm8 - + (2.0 + expval6) * (p_val6*expval6 - p_val7*expval7)); + + theta_0 = 180.0 - theta_00 * (1.0 - + exp(-p_val10 * (2.0 - SBO2))); + theta_0 = DEG2RAD(theta_0); + + expval2theta = exp(-p_val2 * SQR(theta_0 - theta)); + if (p_val1 >= 0) + expval12theta = p_val1 * (1.0 - expval2theta); + else // To avoid linear Me-H-Me angles (6/6/06) + expval12theta = p_val1 * -expval2theta; + + CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; + CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; + CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; + CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * + expval2theta * (theta_0 - theta); + + Ctheta_0 = p_val10 * DEG2RAD(theta_00) * + exp(-p_val10 * (2.0 - SBO2)); + + CEval5 = -CEval4 * Ctheta_0 * CSBO2; + CEval6 = CEval5 * dSBO1; + CEval7 = CEval5 * dSBO2; + CEval8 = -CEval4 / sin_theta; + + total_Eang += e_ang = + f7_ij * f7_jk * f8_Dj * expval12theta; + /* END ANGLE ENERGY*/ + + + /* PENALTY ENERGY */ + p_pen1 = thbp->p_pen1; + p_pen2 = system->reax_param.gp.l[19]; + p_pen3 = system->reax_param.gp.l[20]; + p_pen4 = system->reax_param.gp.l[21]; + + exp_pen2ij = exp(-p_pen2 * SQR(BOA_ij - 2.0)); + exp_pen2jk = exp(-p_pen2 * SQR(BOA_jk - 2.0)); + exp_pen3 = exp(-p_pen3 * workspace->Delta[j]); + exp_pen4 = exp(p_pen4 * workspace->Delta[j]); + trm_pen34 = 1.0 + exp_pen3 + exp_pen4; + f9_Dj = (2.0 + exp_pen3) / trm_pen34; + Cf9j = (-p_pen3 * exp_pen3 * trm_pen34 - + (2.0 + exp_pen3) * (-p_pen3 * exp_pen3 + + p_pen4 * exp_pen4)) / + SQR(trm_pen34); + + total_Epen += e_pen = + p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; + + CEpen1 = e_pen * Cf9j / f9_Dj; + temp = -2.0 * p_pen2 * e_pen; + CEpen2 = temp * (BOA_ij - 2.0); + CEpen3 = temp * (BOA_jk - 2.0); + /* END PENALTY ENERGY */ + + + /* COALITION ENERGY */ + p_coa1 = thbp->p_coa1; + p_coa2 = system->reax_param.gp.l[2]; + p_coa3 = system->reax_param.gp.l[38]; + p_coa4 = system->reax_param.gp.l[30]; + + exp_coa2 = exp(p_coa2 * workspace->Delta_val[j]); + total_Ecoa += e_coa = + p_coa1 / (1. + exp_coa2) * + exp(-p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij)) * + exp(-p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk)) * + exp(-p_coa4 * SQR(BOA_ij - 1.5)) * + exp(-p_coa4 * SQR(BOA_jk - 1.5)); + + CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; + CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa; + CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); + CEcoa4 = -2 * p_coa3 * + (workspace->total_bond_order[i]-BOA_ij) * e_coa; + CEcoa5 = -2 * p_coa3 * + (workspace->total_bond_order[k]-BOA_jk) * e_coa; + /* END COALITION ENERGY */ + + + /* FORCES */ + bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); + bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); + workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3); + workspace->CdDeltaReduction[reductionOffset+i] += CEcoa4; + workspace->CdDeltaReduction[reductionOffset+k] += CEcoa5; + + for (t = start_j; t < end_j; ++t) { + pbond_jt = &(bonds->select.bond_list[t]); + bo_jt = &(pbond_jt->bo_data); + temp_bo_jt = bo_jt->BO; + temp = CUBE(temp_bo_jt); + pBOjt7 = temp * temp * temp_bo_jt; + + bo_jt->Cdbo += (CEval6 * pBOjt7); + bo_jt->Cdbopi += CEval5; + bo_jt->Cdbopi2 += CEval5; + } + + rvec_ScaledAdd(workspace->f[j], CEval8, p_ijk->dcos_dj); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], CEval8, p_ijk->dcos_di); + rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], CEval8, p_ijk->dcos_dk); + + /* tally into per-atom virials */ + if (system->pair_ptr->evflag) { + + /* Acquire vectors */ + rvec_ScaledSum(delij, 1., system->my_atoms[i].x, + -1., system->my_atoms[j].x); + rvec_ScaledSum(delkj, 1., system->my_atoms[k].x, + -1., system->my_atoms[j].x); + + rvec_Scale(fi_tmp, -CEval8, p_ijk->dcos_di); + rvec_Scale(fj_tmp, -CEval8, p_ijk->dcos_dj); + rvec_Scale(fk_tmp, -CEval8, p_ijk->dcos_dk); + + eng_tmp = e_ang + e_pen + e_coa; + + if (system->pair_ptr->eflag_either) + pair_reax_ptr->ev_tally_thr_proxy( j, j, system->N, 1, + eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); + if (system->pair_ptr->vflag_either) + pair_reax_ptr->v_tally3_thr_proxy(i, j, k, fi_tmp, fk_tmp, delij, delkj, thr); + } + + } // if (p_val1>0.001) + } // for (cnt) + } // if (j0) + } // for (pk) + } // if (BOA_ij>0) + + Set_End_Index(pi, my_offset, thb_intrs); + } // for (pi) + } // for (j) + } // end omp parallel + + data->my_en.e_ang = total_Eang; + data->my_en.e_pen = total_Epen; + data->my_en.e_coa = total_Ecoa; + + if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { + workspace->realloc.num_3body = num_thb_intrs * TWICE; + if (num_thb_intrs > thb_intrs->num_intrs) + control->error_ptr->one(FLERR, fmt::format("step {}: ran out of space on " + "angle_list: top={}, max={}", + data->step, num_thb_intrs, + thb_intrs->num_intrs)); + } + } +} diff --git a/src/USER-OMP/respa_omp.cpp b/src/OPENMP/respa_omp.cpp similarity index 100% rename from src/USER-OMP/respa_omp.cpp rename to src/OPENMP/respa_omp.cpp diff --git a/src/USER-OMP/respa_omp.h b/src/OPENMP/respa_omp.h similarity index 100% rename from src/USER-OMP/respa_omp.h rename to src/OPENMP/respa_omp.h diff --git a/src/USER-OMP/thr_data.cpp b/src/OPENMP/thr_data.cpp similarity index 100% rename from src/USER-OMP/thr_data.cpp rename to src/OPENMP/thr_data.cpp diff --git a/src/USER-OMP/thr_data.h b/src/OPENMP/thr_data.h similarity index 100% rename from src/USER-OMP/thr_data.h rename to src/OPENMP/thr_data.h diff --git a/src/USER-OMP/thr_omp.cpp b/src/OPENMP/thr_omp.cpp similarity index 93% rename from src/USER-OMP/thr_omp.cpp rename to src/OPENMP/thr_omp.cpp index 4685e116be..7f4bc95e8c 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/OPENMP/thr_omp.cpp @@ -725,18 +725,27 @@ void ThrOMP::ev_tally4_thr(Pair * const pair, const int i, const int j, } } - if (pair->vflag_atom) { - v[0] = 0.25 * (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); - v[1] = 0.25 * (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); - v[2] = 0.25 * (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); - v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); - v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); - v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); + if (pair->vflag_either) { + v[0] = (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); + v[1] = (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); + v[2] = (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); + v[3] = (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); + v[4] = (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); + v[5] = (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); + if (pair->vflag_global) v_tally(thr->virial_pair,v); - v_tally(thr->vatom_pair[i],v); - v_tally(thr->vatom_pair[j],v); - v_tally(thr->vatom_pair[k],v); - v_tally(thr->vatom_pair[m],v); + if (pair->vflag_atom) { + v[0] *= 0.25; + v[1] *= 0.25; + v[2] *= 0.25; + v[3] *= 0.25; + v[4] *= 0.25; + v[5] *= 0.25; + v_tally(thr->vatom_pair[i],v); + v_tally(thr->vatom_pair[j],v); + v_tally(thr->vatom_pair[k],v); + v_tally(thr->vatom_pair[m],v); + } } } @@ -1465,20 +1474,51 @@ void ThrOMP::ev_tally_thr(Improper * const imprp, const int i1, const int i2, fpair is magnitude of force on atom I ------------------------------------------------------------------------- */ -void ThrOMP::v_tally2_thr(const int i, const int j, const double fpair, +void ThrOMP::v_tally2_thr(Pair *const pair, const int i, const int j, const double fpair, const double * const drij, ThrData * const thr) { double v[6]; - v[0] = 0.5 * drij[0]*drij[0]*fpair; - v[1] = 0.5 * drij[1]*drij[1]*fpair; - v[2] = 0.5 * drij[2]*drij[2]*fpair; - v[3] = 0.5 * drij[0]*drij[1]*fpair; - v[4] = 0.5 * drij[0]*drij[2]*fpair; - v[5] = 0.5 * drij[1]*drij[2]*fpair; + v[0] = drij[0]*drij[0]*fpair; + v[1] = drij[1]*drij[1]*fpair; + v[2] = drij[2]*drij[2]*fpair; + v[3] = drij[0]*drij[1]*fpair; + v[4] = drij[0]*drij[2]*fpair; + v[5] = drij[1]*drij[2]*fpair; + if (pair->vflag_global) v_tally(thr->virial_pair,v); - v_tally(thr->vatom_pair[i],v); - v_tally(thr->vatom_pair[j],v); + if (pair->vflag_atom) { + v[0] *= 0.5; + v[1] *= 0.5; + v[2] *= 0.5; + v[3] *= 0.5; + v[4] *= 0.5; + v[5] *= 0.5; + v_tally(thr->vatom_pair[i],v); + v_tally(thr->vatom_pair[j],v); + } +} + +/* ---------------------------------------------------------------------- + tally virial into per-atom accumulators + called by RexaFF potential, newton_pair is always on + fi is magnitude of force on atom i, deli is the direction + note that the other atom (j) is not updated, due to newton on +------------------------------------------------------------------------- */ + +void ThrOMP::v_tally2_newton_thr(Pair *const pair, const int i, const double * const fi, + const double * const deli, ThrData * const thr) +{ + double v[6]; + + v[0] = deli[0]*fi[0]; + v[1] = deli[1]*fi[1]; + v[2] = deli[2]*fi[2]; + v[3] = deli[0]*fi[1]; + v[4] = deli[0]*fi[2]; + v[5] = deli[1]*fi[2]; + if (pair->vflag_global) v_tally(thr->virial_pair,v); + if (pair->vflag_atom) v_tally(thr->vatom_pair[i],v); } /* ---------------------------------------------------------------------- @@ -1486,23 +1526,32 @@ void ThrOMP::v_tally2_thr(const int i, const int j, const double fpair, called by AIREBO and Tersoff potential, newton_pair is always on ------------------------------------------------------------------------- */ -void ThrOMP::v_tally3_thr(const int i, const int j, const int k, +void ThrOMP::v_tally3_thr(Pair *const pair, const int i, const int j, const int k, const double * const fi, const double * const fj, const double * const drik, const double * const drjk, ThrData * const thr) { double v[6]; - v[0] = THIRD * (drik[0]*fi[0] + drjk[0]*fj[0]); - v[1] = THIRD * (drik[1]*fi[1] + drjk[1]*fj[1]); - v[2] = THIRD * (drik[2]*fi[2] + drjk[2]*fj[2]); - v[3] = THIRD * (drik[0]*fi[1] + drjk[0]*fj[1]); - v[4] = THIRD * (drik[0]*fi[2] + drjk[0]*fj[2]); - v[5] = THIRD * (drik[1]*fi[2] + drjk[1]*fj[2]); + v[0] = (drik[0]*fi[0] + drjk[0]*fj[0]); + v[1] = (drik[1]*fi[1] + drjk[1]*fj[1]); + v[2] = (drik[2]*fi[2] + drjk[2]*fj[2]); + v[3] = (drik[0]*fi[1] + drjk[0]*fj[1]); + v[4] = (drik[0]*fi[2] + drjk[0]*fj[2]); + v[5] = (drik[1]*fi[2] + drjk[1]*fj[2]); + if (pair->vflag_global) v_tally(thr->virial_pair,v); - v_tally(thr->vatom_pair[i],v); - v_tally(thr->vatom_pair[j],v); - v_tally(thr->vatom_pair[k],v); + if (pair->vflag_atom) { + v[0] *= THIRD; + v[1] *= THIRD; + v[2] *= THIRD; + v[3] *= THIRD; + v[4] *= THIRD; + v[5] *= THIRD; + v_tally(thr->vatom_pair[i],v); + v_tally(thr->vatom_pair[j],v); + v_tally(thr->vatom_pair[k],v); + } } /* ---------------------------------------------------------------------- @@ -1510,7 +1559,7 @@ void ThrOMP::v_tally3_thr(const int i, const int j, const int k, called by AIREBO potential, newton_pair is always on ------------------------------------------------------------------------- */ -void ThrOMP::v_tally4_thr(const int i, const int j, const int k, const int m, +void ThrOMP::v_tally4_thr(Pair *const pair, const int i, const int j, const int k, const int m, const double * const fi, const double * const fj, const double * const fk, const double * const drim, const double * const drjm, const double * const drkm, @@ -1518,17 +1567,26 @@ void ThrOMP::v_tally4_thr(const int i, const int j, const int k, const int m, { double v[6]; - v[0] = 0.25 * (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); - v[1] = 0.25 * (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); - v[2] = 0.25 * (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); - v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); - v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); - v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); + v[0] = (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); + v[1] = (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); + v[2] = (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); + v[3] = (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); + v[4] = (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); + v[5] = (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); + if (pair->vflag_global) v_tally(thr->virial_pair,v); - v_tally(thr->vatom_pair[i],v); - v_tally(thr->vatom_pair[j],v); - v_tally(thr->vatom_pair[k],v); - v_tally(thr->vatom_pair[m],v); + if (pair->vflag_atom) { + v[0] *= 0.25; + v[1] *= 0.25; + v[2] *= 0.25; + v[3] *= 0.25; + v[4] *= 0.25; + v[5] *= 0.25; + v_tally(thr->vatom_pair[i],v); + v_tally(thr->vatom_pair[j],v); + v_tally(thr->vatom_pair[k],v); + v_tally(thr->vatom_pair[m],v); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/thr_omp.h b/src/OPENMP/thr_omp.h similarity index 93% rename from src/USER-OMP/thr_omp.h rename to src/OPENMP/thr_omp.h index 77835122e0..02fdbdf25b 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/OPENMP/thr_omp.h @@ -135,12 +135,19 @@ class ThrOMP { void ev_tally_xyz_full_thr(Pair *const, const int, const double, const double, const double, const double, const double, const double, const double, const double, ThrData *const); + void v_tally2_thr(Pair *const, const int, const int, const double, const double *const, ThrData *const); + void v_tally2_newton_thr(Pair *const, const int, const double *const, const double *const, ThrData *const); void ev_tally3_thr(Pair *const, const int, const int, const int, const double, const double, const double *const, const double *const, const double *const, const double *const, ThrData *const); + void v_tally3_thr(Pair *const, const int, const int, const int, const double *const, + const double *const, const double *const, const double *const, ThrData *const); void ev_tally4_thr(Pair *const, const int, const int, const int, const int, const double, const double *const, const double *const, const double *const, const double *const, const double *const, const double *const, ThrData *const); + void v_tally4_thr(Pair *const, const int, const int, const int, const int, const double *const, + const double *const, const double *const, const double *const, + const double *const, const double *const, ThrData *const); // Bond void ev_tally_thr(Bond *const, const int, const int, const int, const int, const double, @@ -169,12 +176,6 @@ class ThrOMP { ThrData *const); // style independent versions - void v_tally2_thr(const int, const int, const double, const double *const, ThrData *const); - void v_tally3_thr(const int, const int, const int, const double *const, const double *const, - const double *const, const double *const, ThrData *const); - void v_tally4_thr(const int, const int, const int, const int, const double *const, - const double *const, const double *const, const double *const, - const double *const, const double *const, ThrData *const); void ev_tally_list_thr(Pair *const, const int, const int *const, const double *const, const double, const double, ThrData *const); }; diff --git a/src/OPT/Install.sh b/src/OPT/Install.sh index b059dab491..0423df143d 100755 --- a/src/OPT/Install.sh +++ b/src/OPT/Install.sh @@ -46,5 +46,5 @@ action pair_lj_long_coul_long_opt.cpp pair_lj_long_coul_long.cpp action pair_lj_long_coul_long_opt.h pair_lj_long_coul_long.cpp action pair_morse_opt.cpp action pair_morse_opt.h -action pair_ufm_opt.cpp -action pair_ufm_opt.h +action pair_ufm_opt.cpp pair_ufm.cpp +action pair_ufm_opt.h pair_ufm.h diff --git a/src/MISC/fix_orient_bcc.cpp b/src/ORIENT/fix_orient_bcc.cpp similarity index 100% rename from src/MISC/fix_orient_bcc.cpp rename to src/ORIENT/fix_orient_bcc.cpp diff --git a/src/MISC/fix_orient_bcc.h b/src/ORIENT/fix_orient_bcc.h similarity index 100% rename from src/MISC/fix_orient_bcc.h rename to src/ORIENT/fix_orient_bcc.h diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/ORIENT/fix_orient_eco.cpp similarity index 100% rename from src/USER-MISC/fix_orient_eco.cpp rename to src/ORIENT/fix_orient_eco.cpp diff --git a/src/USER-MISC/fix_orient_eco.h b/src/ORIENT/fix_orient_eco.h similarity index 100% rename from src/USER-MISC/fix_orient_eco.h rename to src/ORIENT/fix_orient_eco.h diff --git a/src/MISC/fix_orient_fcc.cpp b/src/ORIENT/fix_orient_fcc.cpp similarity index 100% rename from src/MISC/fix_orient_fcc.cpp rename to src/ORIENT/fix_orient_fcc.cpp diff --git a/src/MISC/fix_orient_fcc.h b/src/ORIENT/fix_orient_fcc.h similarity index 100% rename from src/MISC/fix_orient_fcc.h rename to src/ORIENT/fix_orient_fcc.h diff --git a/src/USER-PHONON/Install.sh b/src/PHONON/Install.sh similarity index 88% rename from src/USER-PHONON/Install.sh rename to src/PHONON/Install.sh index a73f529cfa..4b64fed114 100755 --- a/src/USER-PHONON/Install.sh +++ b/src/PHONON/Install.sh @@ -26,12 +26,12 @@ action () { fi } -# USER-PHONON uses the parallel FFT wrapper used in PPPM, +# PHONON uses the parallel FFT wrapper used in PPPM, # so we must require the KSPACE package to be installed. if (test $1 = 1) then if (test ! -e ../fft3d_wrap.h) then - echo "Must install KSPACE package with USER-PHONON" + echo "Must install KSPACE package with PHONON" exit 1 fi fi diff --git a/src/USER-PHONON/README b/src/PHONON/README similarity index 98% rename from src/USER-PHONON/README rename to src/PHONON/README index d5ed666c0c..4f4147cc85 100644 --- a/src/USER-PHONON/README +++ b/src/PHONON/README @@ -13,7 +13,7 @@ Use of this package requires building LAMMPS with FFT suppport, as described in doc/Section_start.html. There are example scripts for using commands in this package in -examples/USER/phonon. +examples/PACKAGES/phonon. There is an auxiliary post-processing tool in tools/phonon that will compute phonon frequencies and dispersion relations from the dynamical diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/PHONON/dynamical_matrix.cpp similarity index 100% rename from src/USER-PHONON/dynamical_matrix.cpp rename to src/PHONON/dynamical_matrix.cpp diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/PHONON/dynamical_matrix.h similarity index 100% rename from src/USER-PHONON/dynamical_matrix.h rename to src/PHONON/dynamical_matrix.h diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/PHONON/fix_phonon.cpp similarity index 100% rename from src/USER-PHONON/fix_phonon.cpp rename to src/PHONON/fix_phonon.cpp diff --git a/src/USER-PHONON/fix_phonon.h b/src/PHONON/fix_phonon.h similarity index 100% rename from src/USER-PHONON/fix_phonon.h rename to src/PHONON/fix_phonon.h diff --git a/src/USER-PHONON/third_order.cpp b/src/PHONON/third_order.cpp similarity index 100% rename from src/USER-PHONON/third_order.cpp rename to src/PHONON/third_order.cpp diff --git a/src/USER-PHONON/third_order.h b/src/PHONON/third_order.h similarity index 100% rename from src/USER-PHONON/third_order.h rename to src/PHONON/third_order.h diff --git a/src/USER-PLUMED/Install.sh b/src/PLUMED/Install.sh similarity index 100% rename from src/USER-PLUMED/Install.sh rename to src/PLUMED/Install.sh diff --git a/src/USER-PLUMED/README b/src/PLUMED/README similarity index 95% rename from src/USER-PLUMED/README rename to src/PLUMED/README index 31910bc951..9b24e2fbb9 100644 --- a/src/USER-PLUMED/README +++ b/src/PLUMED/README @@ -6,7 +6,7 @@ metadynamics to be used. Furthermore, PLUMED can be used to perform a wide range of analyses on trajectories on the fly as they are generated. The package uses the "PLUMED" library, whose source code is not included -in the LAMMPS source code distribution. The files in the USER-PLUMED package +in the LAMMPS source code distribution. The files in the PLUMED package folder implement an interface between LAMMPS and PLUMED, that are written and maintained by Gareth Tribello (gareth.tribello@gmail.com). @@ -19,7 +19,7 @@ time. However you decide to link PLUMED (statically or dynamically) you must run the command: -make yes-user-plumed +make yes-plumed before compiling LAMMPS in order to enable the module. In addition, if you have chosen to link PLUMED dynamically you must ensure that PLUMED is in your @@ -60,7 +60,7 @@ numerous example scripts for PLUMED as well as citations to articles that dcomen implemented within PLUMED. There are also example scripts for using this package in the folder -examples/USER/plumed, as well as on the GitHub page for PLUMED. +examples/PACKAGES/plumed, as well as on the GitHub page for PLUMED. Please contact Gareth Tribello (gareth.tribello@gmail.com) for questions regarding this package. diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/PLUMED/fix_plumed.cpp similarity index 100% rename from src/USER-PLUMED/fix_plumed.cpp rename to src/PLUMED/fix_plumed.cpp diff --git a/src/USER-PLUMED/fix_plumed.h b/src/PLUMED/fix_plumed.h similarity index 100% rename from src/USER-PLUMED/fix_plumed.h rename to src/PLUMED/fix_plumed.h diff --git a/src/USER-PTM/LICENSE b/src/PTM/LICENSE similarity index 100% rename from src/USER-PTM/LICENSE rename to src/PTM/LICENSE diff --git a/src/USER-PTM/README b/src/PTM/README similarity index 100% rename from src/USER-PTM/README rename to src/PTM/README diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp similarity index 99% rename from src/USER-PTM/compute_ptm_atom.cpp rename to src/PTM/compute_ptm_atom.cpp index 301e3d577d..74880adcd5 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/PTM/compute_ptm_atom.cpp @@ -48,7 +48,7 @@ under using namespace LAMMPS_NS; static const char cite_user_ptm_package[] = - "USER-PTM package:\n\n" + "PTM package:\n\n" "@Article{larsen2016ptm,\n" " author={Larsen, Peter Mahler and Schmidt, S{\\o}ren and Schi{\\o}tz, " "Jakob},\n" diff --git a/src/USER-PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h similarity index 100% rename from src/USER-PTM/compute_ptm_atom.h rename to src/PTM/compute_ptm_atom.h diff --git a/src/USER-PTM/ptm_alloy_types.cpp b/src/PTM/ptm_alloy_types.cpp similarity index 100% rename from src/USER-PTM/ptm_alloy_types.cpp rename to src/PTM/ptm_alloy_types.cpp diff --git a/src/USER-PTM/ptm_alloy_types.h b/src/PTM/ptm_alloy_types.h similarity index 100% rename from src/USER-PTM/ptm_alloy_types.h rename to src/PTM/ptm_alloy_types.h diff --git a/src/USER-PTM/ptm_alt_templates.h b/src/PTM/ptm_alt_templates.h similarity index 100% rename from src/USER-PTM/ptm_alt_templates.h rename to src/PTM/ptm_alt_templates.h diff --git a/src/USER-PTM/ptm_canonical_coloured.cpp b/src/PTM/ptm_canonical_coloured.cpp similarity index 100% rename from src/USER-PTM/ptm_canonical_coloured.cpp rename to src/PTM/ptm_canonical_coloured.cpp diff --git a/src/USER-PTM/ptm_canonical_coloured.h b/src/PTM/ptm_canonical_coloured.h similarity index 100% rename from src/USER-PTM/ptm_canonical_coloured.h rename to src/PTM/ptm_canonical_coloured.h diff --git a/src/USER-PTM/ptm_constants.cpp b/src/PTM/ptm_constants.cpp similarity index 100% rename from src/USER-PTM/ptm_constants.cpp rename to src/PTM/ptm_constants.cpp diff --git a/src/USER-PTM/ptm_constants.h b/src/PTM/ptm_constants.h similarity index 100% rename from src/USER-PTM/ptm_constants.h rename to src/PTM/ptm_constants.h diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/PTM/ptm_convex_hull_incremental.cpp similarity index 100% rename from src/USER-PTM/ptm_convex_hull_incremental.cpp rename to src/PTM/ptm_convex_hull_incremental.cpp diff --git a/src/USER-PTM/ptm_convex_hull_incremental.h b/src/PTM/ptm_convex_hull_incremental.h similarity index 100% rename from src/USER-PTM/ptm_convex_hull_incremental.h rename to src/PTM/ptm_convex_hull_incremental.h diff --git a/src/USER-PTM/ptm_deformation_gradient.cpp b/src/PTM/ptm_deformation_gradient.cpp similarity index 100% rename from src/USER-PTM/ptm_deformation_gradient.cpp rename to src/PTM/ptm_deformation_gradient.cpp diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/PTM/ptm_deformation_gradient.h similarity index 100% rename from src/USER-PTM/ptm_deformation_gradient.h rename to src/PTM/ptm_deformation_gradient.h diff --git a/src/USER-PTM/ptm_functions.h b/src/PTM/ptm_functions.h similarity index 100% rename from src/USER-PTM/ptm_functions.h rename to src/PTM/ptm_functions.h diff --git a/src/USER-PTM/ptm_fundamental_mappings.h b/src/PTM/ptm_fundamental_mappings.h similarity index 100% rename from src/USER-PTM/ptm_fundamental_mappings.h rename to src/PTM/ptm_fundamental_mappings.h diff --git a/src/USER-PTM/ptm_graph_data.cpp b/src/PTM/ptm_graph_data.cpp similarity index 100% rename from src/USER-PTM/ptm_graph_data.cpp rename to src/PTM/ptm_graph_data.cpp diff --git a/src/USER-PTM/ptm_graph_data.h b/src/PTM/ptm_graph_data.h similarity index 100% rename from src/USER-PTM/ptm_graph_data.h rename to src/PTM/ptm_graph_data.h diff --git a/src/USER-PTM/ptm_graph_tools.cpp b/src/PTM/ptm_graph_tools.cpp similarity index 100% rename from src/USER-PTM/ptm_graph_tools.cpp rename to src/PTM/ptm_graph_tools.cpp diff --git a/src/USER-PTM/ptm_graph_tools.h b/src/PTM/ptm_graph_tools.h similarity index 100% rename from src/USER-PTM/ptm_graph_tools.h rename to src/PTM/ptm_graph_tools.h diff --git a/src/USER-PTM/ptm_index.cpp b/src/PTM/ptm_index.cpp similarity index 100% rename from src/USER-PTM/ptm_index.cpp rename to src/PTM/ptm_index.cpp diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/PTM/ptm_initialize_data.cpp similarity index 100% rename from src/USER-PTM/ptm_initialize_data.cpp rename to src/PTM/ptm_initialize_data.cpp diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/PTM/ptm_initialize_data.h similarity index 100% rename from src/USER-PTM/ptm_initialize_data.h rename to src/PTM/ptm_initialize_data.h diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/PTM/ptm_neighbour_ordering.cpp similarity index 100% rename from src/USER-PTM/ptm_neighbour_ordering.cpp rename to src/PTM/ptm_neighbour_ordering.cpp diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/PTM/ptm_neighbour_ordering.h similarity index 100% rename from src/USER-PTM/ptm_neighbour_ordering.h rename to src/PTM/ptm_neighbour_ordering.h diff --git a/src/USER-PTM/ptm_normalize_vertices.cpp b/src/PTM/ptm_normalize_vertices.cpp similarity index 100% rename from src/USER-PTM/ptm_normalize_vertices.cpp rename to src/PTM/ptm_normalize_vertices.cpp diff --git a/src/USER-PTM/ptm_normalize_vertices.h b/src/PTM/ptm_normalize_vertices.h similarity index 100% rename from src/USER-PTM/ptm_normalize_vertices.h rename to src/PTM/ptm_normalize_vertices.h diff --git a/src/USER-PTM/ptm_polar.cpp b/src/PTM/ptm_polar.cpp similarity index 100% rename from src/USER-PTM/ptm_polar.cpp rename to src/PTM/ptm_polar.cpp diff --git a/src/USER-PTM/ptm_polar.h b/src/PTM/ptm_polar.h similarity index 100% rename from src/USER-PTM/ptm_polar.h rename to src/PTM/ptm_polar.h diff --git a/src/USER-PTM/ptm_quat.cpp b/src/PTM/ptm_quat.cpp similarity index 100% rename from src/USER-PTM/ptm_quat.cpp rename to src/PTM/ptm_quat.cpp diff --git a/src/USER-PTM/ptm_quat.h b/src/PTM/ptm_quat.h similarity index 100% rename from src/USER-PTM/ptm_quat.h rename to src/PTM/ptm_quat.h diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/PTM/ptm_structure_matcher.cpp similarity index 100% rename from src/USER-PTM/ptm_structure_matcher.cpp rename to src/PTM/ptm_structure_matcher.cpp diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/PTM/ptm_structure_matcher.h similarity index 100% rename from src/USER-PTM/ptm_structure_matcher.h rename to src/PTM/ptm_structure_matcher.h diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/PTM/ptm_voronoi_cell.cpp similarity index 100% rename from src/USER-PTM/ptm_voronoi_cell.cpp rename to src/PTM/ptm_voronoi_cell.cpp diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/PTM/ptm_voronoi_cell.h similarity index 100% rename from src/USER-PTM/ptm_voronoi_cell.h rename to src/PTM/ptm_voronoi_cell.h diff --git a/src/USER-PTM/ptm_voronoi_config.h b/src/PTM/ptm_voronoi_config.h similarity index 100% rename from src/USER-PTM/ptm_voronoi_config.h rename to src/PTM/ptm_voronoi_config.h diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index 72b61a834c..eef2c4083f 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -51,15 +51,15 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : // create integrator instance std::string full_cls_name = arg[3]; + std::string module_name = "__main__"; + std::string cls_name = full_cls_name; size_t lastpos = full_cls_name.rfind("."); - if (lastpos == std::string::npos) { - error->all(FLERR,"Fix python/integrate requires fully qualified class name"); + if (lastpos != std::string::npos) { + module_name = full_cls_name.substr(0, lastpos); + cls_name = full_cls_name.substr(lastpos+1); } - std::string module_name = full_cls_name.substr(0, lastpos); - std::string cls_name = full_cls_name.substr(lastpos+1); - PyObject *pModule = PyImport_ImportModule(module_name.c_str()); if (!pModule) { PyUtils::Print_Errors(); @@ -72,7 +72,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name.c_str()); if (!py_move_type) { PyUtils::Print_Errors(); - error->all(FLERR,"Could not find integrator class in module'"); + error->all(FLERR,"Could not find integrator class {} in module {}", cls_name, module_name); } PyObject *ptr = PY_VOID_POINTER(lmp); diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 2cffcb8b05..5b4e841927 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -253,20 +253,24 @@ void PairPython::coeff(int narg, char **arg) if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->all(FLERR,"Incorrect args for pair coefficients"); - // check if python potential file exists and source it + + // check if python potential class type exists + // load module if necessary std::string full_cls_name = arg[2]; + std::string module_name = "__main__"; + std::string cls_name = full_cls_name; + size_t lastpos = full_cls_name.rfind("."); - if (lastpos == std::string::npos) { - error->all(FLERR,"Python pair style requires fully qualified class name"); + if (lastpos != std::string::npos) { + module_name = full_cls_name.substr(0, lastpos); + cls_name = full_cls_name.substr(lastpos+1); } - std::string module_name = full_cls_name.substr(0, lastpos); - std::string cls_name = full_cls_name.substr(lastpos+1); - PyUtils::GIL lock; PyObject * pModule = PyImport_ImportModule(module_name.c_str()); + if (!pModule) { PyUtils::Print_Errors(); error->all(FLERR,"Loading python pair style module failure"); @@ -278,7 +282,7 @@ void PairPython::coeff(int narg, char **arg) PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name.c_str()); if (!py_pair_type) { PyUtils::Print_Errors(); - error->all(FLERR,"Could not find pair style class in module'"); + error->all(FLERR, "Could not find pair style class {} in module {}", cls_name, module_name); } PyObject * py_pair_instance = PyObject_CallObject(py_pair_type, nullptr); diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 793fedf00e..2da5f68895 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -47,12 +47,6 @@ enum{NONE,INT,DOUBLE,STRING,PTR}; PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp) { - ninput = noutput = 0; - istr = nullptr; - ostr = nullptr; - format = nullptr; - length_longstr = 0; - // pfuncs stores interface info for each Python function nfunc = 0; @@ -138,7 +132,7 @@ void PythonImpl::command(int narg, char **arg) if (ifunc < 0) error->all(FLERR,"Python invoke of undefined function"); char *str = nullptr; - if (noutput) { + if (pfuncs[ifunc].noutput) { str = input->variable->pythonstyle(pfuncs[ifunc].ovarname, pfuncs[ifunc].name); if (!str) @@ -168,11 +162,12 @@ void PythonImpl::command(int narg, char **arg) // parse optional args, invoke is not allowed in this mode - ninput = noutput = 0; - istr = nullptr; - ostr = nullptr; - format = nullptr; - length_longstr = 0; + int ninput = 0; + int noutput = 0; + char **istr = nullptr; + char *ostr = nullptr; + char *format = nullptr; + int length_longstr = 0; char *pyfile = nullptr; char *herestr = nullptr; int existflag = 0; @@ -184,6 +179,7 @@ void PythonImpl::command(int narg, char **arg) ninput = utils::inumeric(FLERR,arg[iarg+1],false,lmp); if (ninput < 0) error->all(FLERR,"Invalid python command"); iarg += 2; + delete[] istr; istr = new char*[ninput]; if (iarg+ninput > narg) error->all(FLERR,"Invalid python command"); for (int i = 0; i < ninput; i++) istr[i] = arg[iarg+i]; @@ -191,6 +187,7 @@ void PythonImpl::command(int narg, char **arg) } else if (strcmp(arg[iarg],"return") == 0) { if (iarg+2 > narg) error->all(FLERR,"Invalid python command"); noutput = 1; + delete[] ostr; ostr = arg[iarg+1]; iarg += 2; } else if (strcmp(arg[iarg],"format") == 0) { @@ -223,7 +220,7 @@ void PythonImpl::command(int narg, char **arg) // create or overwrite entry in pfuncs vector with name = arg[0] - int ifunc = create_entry(arg[0]); + int ifunc = create_entry(arg[0],ninput,noutput,length_longstr, istr, ostr, format); PyUtils::GIL lock; @@ -409,7 +406,8 @@ char *PythonImpl::long_string(int ifunc) /* ------------------------------------------------------------------ */ -int PythonImpl::create_entry(char *name) +int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_longstr, + char **istr, char *ostr, char *format) { // ifunc = index to entry by name in pfuncs vector, can be old or new // free old vectors if overwriting old pfunc diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h index 0190e8d7c2..dd215fdedf 100644 --- a/src/PYTHON/python_impl.h +++ b/src/PYTHON/python_impl.h @@ -35,9 +35,6 @@ class PythonImpl : protected Pointers, public PythonInterface { bool has_minimum_version(int major, int minor); private: - int ninput, noutput, length_longstr; - char **istr; - char *ostr, *format; void *pyMain; struct PyFunc { @@ -57,7 +54,7 @@ class PythonImpl : protected Pointers, public PythonInterface { PyFunc *pfuncs; int nfunc; - int create_entry(char *); + int create_entry(char *, int, int, int, char **, char *, char *); void deallocate(int); }; diff --git a/src/Purge.list b/src/Purge.list index 88d9e22e59..feb30a9ad7 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -51,11 +51,93 @@ lmpinstalledpkgs.h lmpgitversion.h mliap_model_python_couple.cpp mliap_model_python_couple.h +# renamed on 21 July 2021 +fix_qeq_reax_kokkos.cpp +fix_qeq_reax_kokkos.h +fix_reaxc_bonds_kokkos.cpp +fix_reaxc_bonds_kokkos.h +fix_reaxc_species_kokkos.cpp +fix_reaxc_species_kokkos.h +pair_reaxc_kokkos.cpp +pair_reaxc_kokkos.h +fix_qeq_reax_omp.cpp +fix_qeq_reax_omp.h +pair_reaxc_omp.cpp +pair_reaxc_omp.h +reaxc_bond_orders_omp.cpp +reaxc_bonds_omp.cpp +reaxc_forces_omp.cpp +reaxc_hydrogen_bonds_omp.cpp +reaxc_init_md_omp.cpp +reaxc_multi_body_omp.cpp +reaxc_nonbonded_omp.cpp +reaxc_torsion_angles_omp.cpp +reaxc_valence_angles_omp.cpp +fix_reaxc.cpp +fix_reaxc.h +fix_reaxc_bonds.cpp +fix_reaxc_bonds.h +fix_reaxc_species.cpp +fix_reaxc_species.h +pair_reaxc.cpp +pair_reaxc.h +reaxc_allocate.cpp +reaxc_bond_orders.cpp +reaxc_bonds.cpp +reaxc_control.cpp +reaxc_ffield.cpp +reaxc_forces.cpp +reaxc_hydrogen_bonds.cpp +reaxc_init_md.cpp +reaxc_list.cpp +reaxc_lookup.cpp +reaxc_multi_body.cpp +reaxc_nonbonded.cpp +reaxc_reset_tools.cpp +reaxc_tool_box.cpp +reaxc_torsion_angles.cpp +reaxc_valence_angles.cpp # removed on 14 May 2021 nstencil_half_bin_2d_newton_ssa.cpp nstencil_half_bin_2d_newton_ssa.h nstencil_half_bin_3d_newton_ssa.cpp nstencil_half_bin_3d_newton_ssa.h +# removed on 17 Apr 2021 +reaxc_allocate.h +reaxc_bond_orders.h +reaxc_bonds.h +reaxc_control.h +reaxc_defs.h +reaxc_ffield.h +reaxc_forces.h +reaxc_hydrogen_bonds.h +reaxc_init_md.h +reaxc_io_tools.h +reaxc_io_tools.cpp +reaxc_list.h +reaxc_lookup.h +reaxc_multi_body.h +reaxc_nonbonded.h +reaxc_reset_tools.h +reaxc_system_props.h +reaxc_system_props.cpp +reaxc_tool_box.h +reaxc_torsion_angles.h +reaxc_traj.h +reaxc_traj.cpp +reaxc_types.h +reaxc_valence_angles.h +reaxc_vector.h +reaxc_vector.cpp +reaxc_bond_orders_omp.h +reaxc_bonds_omp.h +reaxc_forces_omp.h +reaxc_hydrogen_bonds_omp.h +reaxc_init_md_omp.h +reaxc_multi_body_omp.h +reaxc_nonbonded_omp.h +reaxc_torsion_angles_omp.h +reaxc_valence_angles_omp.h # removed on 9 Sep 2020 mergesort.h # renamed on 8 May 2020 @@ -83,8 +165,6 @@ pair_reax.h pair_reax_fortran.h fix_reax_bonds.cpp fix_reax_bonds.h -pair_meam.cpp -pair_meam.h # removed on 27 September 2018 pair_nb3b_harmonic_omp.h pair_nb3b_harmonic_omp.cpp diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 8f7baa23be..a0d012bb5b 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -25,16 +25,27 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" +#include "pair.h" +#include "suffix.h" +#include "text_file_reader.h" #include "update.h" #include #include +#include using namespace LAMMPS_NS; using namespace FixConst; #define MAXLINE 1024 +class parser_error : public std::exception { + std::string message; +public: + parser_error(const std::string &mesg) { message = mesg; } + const char *what() const noexcept { return message.c_str(); } +}; + /* ---------------------------------------------------------------------- */ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : @@ -46,10 +57,15 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : { if (narg < 8) error->all(FLERR,"Illegal fix qeq command"); + scalar_flag = 1; + extscalar = 0; + nevery = utils::inumeric(FLERR,arg[3],false,lmp); cutoff = utils::numeric(FLERR,arg[4],false,lmp); tolerance = utils::numeric(FLERR,arg[5],false,lmp); maxiter = utils::inumeric(FLERR,arg[6],false,lmp); + maxwarn = 1; + matvecs = 0; // check for sane arguments if ((nevery <= 0) || (cutoff <= 0.0) || (tolerance <= 0.0) || (maxiter <= 0)) @@ -105,17 +121,16 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : atom->add_callback(Atom::GROW); for (int i = 0; i < atom->nmax; i++) - for (int j = 0; j < nprev; ++j ) + for (int j = 0; j < nprev; ++j) s_hist[i][j] = t_hist[i][j] = atom->q[i]; if (strcmp(arg[7],"coul/streitz") == 0) { streitz_flag = 1; - } else if (strcmp(arg[7],"reax/c") == 0) { + } else if (utils::strmatch(arg[7],"^reax..")) { reax_flag = 1; } else { read_file(arg[7]); } - } /* ---------------------------------------------------------------------- */ @@ -185,21 +200,21 @@ void FixQEq::deallocate_storage() memory->destroy(s); memory->destroy(t); - memory->destroy( Hdia_inv ); - memory->destroy( b_s ); - memory->destroy( b_t ); + memory->destroy(Hdia_inv); + memory->destroy(b_s); + memory->destroy(b_t); - memory->destroy( p ); - memory->destroy( q ); - memory->destroy( r ); - memory->destroy( d ); + memory->destroy(p); + memory->destroy(q); + memory->destroy(r); + memory->destroy(d); - memory->destroy( chizj ); - memory->destroy( qf ); - memory->destroy( q1 ); - memory->destroy( q2 ); + memory->destroy(chizj); + memory->destroy(qf); + memory->destroy(q1); + memory->destroy(q2); - memory->destroy( qv ); + memory->destroy(qv); } /* ---------------------------------------------------------------------- */ @@ -225,7 +240,7 @@ void FixQEq::allocate_matrix() safezone = SAFE_ZONE; nlocal = atom->nlocal; - n_cap = MAX( (int)(nlocal * safezone), mincap ); + n_cap = MAX((int)(nlocal * safezone), mincap); nall = atom->nlocal + atom->nghost; // determine the total space for the H matrix @@ -239,7 +254,7 @@ void FixQEq::allocate_matrix() i = ilist[ii]; m += numneigh[i]; } - m_cap = MAX( (int)(m * safezone), mincap * MIN_NBRS ); + m_cap = MAX((int)(m * safezone), mincap * MIN_NBRS); H.n = n_cap; H.m = m_cap; @@ -253,10 +268,10 @@ void FixQEq::allocate_matrix() void FixQEq::deallocate_matrix() { - memory->destroy( H.firstnbr ); - memory->destroy( H.numnbrs ); - memory->destroy( H.jlist ); - memory->destroy( H.val ); + memory->destroy(H.firstnbr); + memory->destroy(H.numnbrs); + memory->destroy(H.jlist); + memory->destroy(H.val); } /* ---------------------------------------------------------------------- */ @@ -269,6 +284,13 @@ void FixQEq::reallocate_matrix() /* ---------------------------------------------------------------------- */ +double FixQEq::compute_scalar() +{ + return matvecs; +} + +/* ---------------------------------------------------------------------- */ + void FixQEq::init_list(int /*id*/, NeighList *ptr) { list = ptr; @@ -281,6 +303,12 @@ void FixQEq::setup_pre_force(int vflag) if (force->newton_pair == 0) error->all(FLERR,"QEQ with 'newton pair off' not supported"); + if (force->pair) { + if (force->pair->suffix_flag & (Suffix::INTEL|Suffix::GPU)) + error->all(FLERR,"QEQ is not compatiple with suffix version " + "of pair style"); + } + deallocate_storage(); allocate_storage(); @@ -338,7 +366,7 @@ void FixQEq::min_pre_force(int vflag) /* ---------------------------------------------------------------------- */ -int FixQEq::CG( double *b, double *x ) +int FixQEq::CG(double *b, double *x) { int loop, i, ii, inum, *ilist; double tmp, alfa, beta, b_norm; @@ -348,10 +376,10 @@ int FixQEq::CG( double *b, double *x ) ilist = list->ilist; pack_flag = 1; - sparse_matvec( &H, x, q ); - comm->reverse_comm_fix( this ); + sparse_matvec(&H, x, q); + comm->reverse_comm_fix(this); - vector_sum( r , 1., b, -1., q, inum ); + vector_sum(r , 1., b, -1., q, inum); for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; @@ -360,19 +388,19 @@ int FixQEq::CG( double *b, double *x ) else d[i] = 0.0; } - b_norm = parallel_norm( b, inum ); - sig_new = parallel_dot( r, d, inum); + b_norm = parallel_norm(b, inum); + sig_new = parallel_dot(r, d, inum); for (loop = 1; loop < maxiter && sqrt(sig_new)/b_norm > tolerance; ++loop) { comm->forward_comm_fix(this); - sparse_matvec( &H, d, q ); + sparse_matvec(&H, d, q); comm->reverse_comm_fix(this); - tmp = parallel_dot( d, q, inum); + tmp = parallel_dot(d, q, inum); alfa = sig_new / tmp; - vector_add( x, alfa, d, inum ); - vector_add( r, -alfa, q, inum ); + vector_add(x, alfa, d, inum); + vector_add(r, -alfa, q, inum); for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; @@ -381,13 +409,13 @@ int FixQEq::CG( double *b, double *x ) } sig_old = sig_new; - sig_new = parallel_dot( r, p, inum); + sig_new = parallel_dot(r, p, inum); beta = sig_new / sig_old; - vector_sum( d, 1., p, beta, d, inum ); + vector_sum(d, 1., p, beta, d, inum); } - if ((comm->me == 0) && (loop >= maxiter)) + if ((comm->me == 0) && maxwarn && (loop >= maxiter)) error->warning(FLERR,"Fix qeq CG convergence failed ({}) after {} " "iterations at step {}",sqrt(sig_new)/b_norm,loop, update->ntimestep); @@ -397,7 +425,7 @@ int FixQEq::CG( double *b, double *x ) /* ---------------------------------------------------------------------- */ -void FixQEq::sparse_matvec( sparse_matrix *A, double *x, double *b ) +void FixQEq::sparse_matvec(sparse_matrix *A, double *x, double *b) { int i, j, itr_j; @@ -406,7 +434,7 @@ void FixQEq::sparse_matvec( sparse_matrix *A, double *x, double *b ) for (i = 0; i < nlocal; ++i) { if (atom->mask[i] & groupbit) - b[i] = eta[ atom->type[i] ] * x[i]; + b[i] = eta[atom->type[i]] * x[i]; } for (i = nlocal; i < nall; ++i) { @@ -416,7 +444,7 @@ void FixQEq::sparse_matvec( sparse_matrix *A, double *x, double *b ) for (i = 0; i < nlocal; ++i) { if (atom->mask[i] & groupbit) { - for ( itr_j=A->firstnbr[i]; itr_jfirstnbr[i]+A->numnbrs[i]; itr_j++) { + for (itr_j=A->firstnbr[i]; itr_jfirstnbr[i]+A->numnbrs[i]; itr_j++) { j = A->jlist[itr_j]; b[i] += A->val[itr_j] * x[j]; b[j] += A->val[itr_j] * x[i]; @@ -438,8 +466,8 @@ void FixQEq::calculate_Q() inum = list->inum; ilist = list->ilist; - s_sum = parallel_vector_acc( s, inum ); - t_sum = parallel_vector_acc( t, inum); + s_sum = parallel_vector_acc(s, inum); + t_sum = parallel_vector_acc(t, inum); u = s_sum / t_sum; for (ii = 0; ii < inum; ++ii) { @@ -457,7 +485,7 @@ void FixQEq::calculate_Q() } pack_flag = 4; - comm->forward_comm_fix( this ); //Dist_vector( atom->q ); + comm->forward_comm_fix(this); //Dist_vector(atom->q); } /* ---------------------------------------------------------------------- */ @@ -488,11 +516,11 @@ void FixQEq::unpack_forward_comm(int n, int first, double *buf) if (pack_flag == 1) for (m = 0, i = first; m < n; m++, i++) d[i] = buf[m]; - else if ( pack_flag == 2) + else if (pack_flag == 2) for (m = 0, i = first; m < n; m++, i++) s[i] = buf[m]; - else if ( pack_flag == 3) + else if (pack_flag == 3) for (m = 0, i = first; m < n; m++, i++) t[i] = buf[m]; - else if ( pack_flag == 4) + else if (pack_flag == 4) for (m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m]; } @@ -577,7 +605,7 @@ int FixQEq::unpack_exchange(int n, double *buf) /* ---------------------------------------------------------------------- */ -double FixQEq::parallel_norm( double *v, int n ) +double FixQEq::parallel_norm(double *v, int n) { int i; double my_sum, norm_sqr; @@ -595,14 +623,14 @@ double FixQEq::parallel_norm( double *v, int n ) my_sum += v[i]*v[i]; } - MPI_Allreduce( &my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world); - return sqrt( norm_sqr ); + return sqrt(norm_sqr); } /* ---------------------------------------------------------------------- */ -double FixQEq::parallel_dot( double *v1, double *v2, int n) +double FixQEq::parallel_dot(double *v1, double *v2, int n) { int i; double my_dot, res; @@ -620,14 +648,14 @@ double FixQEq::parallel_dot( double *v1, double *v2, int n) my_dot += v1[i] * v2[i]; } - MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world); return res; } /* ---------------------------------------------------------------------- */ -double FixQEq::parallel_vector_acc( double *v, int n ) +double FixQEq::parallel_vector_acc(double *v, int n) { int i; double my_acc, res; @@ -645,15 +673,15 @@ double FixQEq::parallel_vector_acc( double *v, int n ) my_acc += v[i]; } - MPI_Allreduce( &my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world ); + MPI_Allreduce(&my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world); return res; } /* ---------------------------------------------------------------------- */ -void FixQEq::vector_sum( double* dest, double c, double* v, - double d, double* y, int k ) +void FixQEq::vector_sum(double* dest, double c, double* v, + double d, double* y, int k) { int kk; int *ilist; @@ -669,7 +697,7 @@ void FixQEq::vector_sum( double* dest, double c, double* v, /* ---------------------------------------------------------------------- */ -void FixQEq::vector_add( double* dest, double c, double* v, int k ) +void FixQEq::vector_add(double* dest, double c, double* v, int k) { int kk; int *ilist; @@ -687,13 +715,7 @@ void FixQEq::vector_add( double* dest, double c, double* v, int k ) void FixQEq::read_file(char *file) { - int i; - int params_per_line = 6; - char **words = new char*[params_per_line+1]; - - int ntypes = atom->ntypes; - int *setflag = new int[ntypes+1]; - for (i=0; i <= ntypes; ++i) setflag[i] = 0; + const int ntypes = atom->ntypes; memory->create(chi,ntypes+1,"qeq:chi"); memory->create(eta,ntypes+1,"qeq:eta"); @@ -701,70 +723,66 @@ void FixQEq::read_file(char *file) memory->create(zeta,ntypes+1,"qeq:zeta"); memory->create(zcore,ntypes+1,"qeq:zcore"); - // open file on proc 0 - - FILE *fp; - if (comm->me == 0) { - fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) - error->one(FLERR,"Cannot open fix qeq parameter file {}: {}", - file,utils::getsyserror()); - } - // read each line out of file, skipping blank lines or leading '#' // store line of params if all 3 element tags are in element list - int n,nwords,eof,nlo,nhi; - char line[MAXLINE],*ptr; - - eof = 0; - - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == nullptr) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; + if (comm->me == 0) { + int *setflag = new int[ntypes+1]; + for (int n=0; n <= ntypes; ++n) { + setflag[n] = 0; + chi[n] = eta[n] = gamma[n] = zeta[n] = zcore[n] = 0.0; } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - // strip comment, skip line if blank + try { + int nlo,nhi; + double val; - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = utils::count_words(line); - if (nwords == 0) continue; + FILE *fp = utils::open_potential(file,lmp,nullptr); + if (fp == nullptr) + throw parser_error(fmt::format("Cannot open fix qeq parameter file {}:" + " {}", file,utils::getsyserror())); + TextFileReader reader(fp, "qeq parameter"); - // must have 6 parameters per line. + while (1) { + auto values = reader.next_values(0); - if (nwords < 6) - error->all(FLERR,"Invalid fix qeq parameter file"); + if (values.count() == 0) continue; + if (values.count() < 6) + throw parser_error("Invalid qeq parameter file"); - // words = ptrs to first 6 words in line + auto word = values.next_string(); + utils::bounds(FLERR,word,1,ntypes,nlo,nhi,nullptr); + if ((nlo < 0) || (nhi < 0)) + throw parser_error("Invalid atom type range"); - for (n=0, words[n] = strtok(line," \t\n\r\f"); - n < 6; - words[++n] = strtok(nullptr," \t\n\r\f")); - - utils::bounds(FLERR,words[0],1,ntypes,nlo,nhi,error); - for (n=nlo; n <=nhi; ++n) { - chi[n] = utils::numeric(FLERR,words[1],false,lmp); - eta[n] = utils::numeric(FLERR,words[2],false,lmp); - gamma[n] = utils::numeric(FLERR,words[3],false,lmp); - zeta[n] = utils::numeric(FLERR,words[4],false,lmp); - zcore[n] = utils::numeric(FLERR,words[5],false,lmp); - setflag[n] = 1; + val = values.next_double(); + for (int n=nlo; n <= nhi; ++n) chi[n] = val; + val = values.next_double(); + for (int n=nlo; n <= nhi; ++n) eta[n] = val; + val = values.next_double(); + for (int n=nlo; n <= nhi; ++n) gamma[n] = val; + val = values.next_double(); + for (int n=nlo; n <= nhi; ++n) zeta[n] = val; + val = values.next_double(); + for (int n=nlo; n <= nhi; ++n) zcore[n] = val; + for (int n=nlo; n <= nhi; ++n) setflag[n] = 1; + } + } catch (EOFException &e) { + ; // catch and ignore to exit loop + } catch (std::exception &e) { + error->one(FLERR,e.what()); } + + for (int n=1; n <= ntypes; ++n) + if (setflag[n] == 0) + error->one(FLERR,fmt::format("Parameters for atom type {} missing in " + "qeq parameter file", n)); + delete[] setflag; } - // check if all types are set - for (n=1; n <= ntypes; ++n) - if (setflag[n] == 0) - error->all(FLERR,"Invalid fix qeq parameter file"); - - delete [] words; - delete [] setflag; + MPI_Bcast(chi,ntypes+1,MPI_DOUBLE,0,world); + MPI_Bcast(eta,ntypes+1,MPI_DOUBLE,0,world); + MPI_Bcast(gamma,ntypes+1,MPI_DOUBLE,0,world); + MPI_Bcast(zeta,ntypes+1,MPI_DOUBLE,0,world); + MPI_Bcast(zcore,ntypes+1,MPI_DOUBLE,0,world); } diff --git a/src/QEQ/fix_qeq.h b/src/QEQ/fix_qeq.h index add2c9996d..f2260cbf30 100644 --- a/src/QEQ/fix_qeq.h +++ b/src/QEQ/fix_qeq.h @@ -35,6 +35,8 @@ class FixQEq : public Fix { void pre_force_respa(int, int, int); void min_pre_force(int); + virtual double compute_scalar(); + // derived child classes must provide these functions virtual void init() = 0; @@ -65,6 +67,7 @@ class FixQEq : public Fix { double Tap[8]; // Taper function double tolerance; // tolerance for the norm of the rel residual in CG int maxiter; // maximum number of QEq iterations + int maxwarn; // print warning when max iterations was reached double cutoff, cutoff_sq; // neighbor cutoff double *chi, *eta, *gamma, *zeta, *zcore; // qeq parameters diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index 679739bb9c..b8fc08dc14 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -54,6 +54,12 @@ FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command"); qstep = atof(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"warn") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command"); + if (strcmp(arg[iarg+1],"no") == 0) maxwarn = 0; + else if (strcmp(arg[iarg+1],"yes") == 0) maxwarn = 1; + else error->all(FLERR,"Illegal fix qeq/dynamic command"); + iarg += 2; } else error->all(FLERR,"Illegal fix qeq/dynamic command"); } } @@ -146,7 +152,7 @@ void FixQEqDynamic::pre_force(int /*vflag*/) MPI_Allreduce(&enegmax,&enegmaxall,1,MPI_DOUBLE,MPI_MAX,world); enegmax = enegmaxall; - if (enegchk <= tolerance && enegmax <= 100.0*tolerance) break; + if ((enegchk <= tolerance) && (enegmax <= 100.0*tolerance)) break; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; @@ -154,8 +160,9 @@ void FixQEqDynamic::pre_force(int /*vflag*/) q1[i] += qf[i]*dtq2 - qdamp*q1[i]; } } + matvecs = iloop; - if ((comm->me == 0) && (iloop >= maxiter)) + if ((comm->me == 0) && maxwarn && (iloop >= maxiter)) error->warning(FLERR,"Charges did not converge at step {}: {}", update->ntimestep,enegchk); @@ -260,7 +267,7 @@ void FixQEqDynamic::unpack_forward_comm(int n, int first, double *buf) if (pack_flag == 1) for (m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m]; - else if ( pack_flag == 2) + else if (pack_flag == 2) for (m = 0, i = first; m < n; m++, i++) qf[i] = buf[m]; } diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 1bc0ba32ea..eb206effc6 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -64,6 +64,12 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/fire command"); qstep = atof(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"warn") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/fire command"); + if (strcmp(arg[iarg+1],"no") == 0) maxwarn = 0; + else if (strcmp(arg[iarg+1],"yes") == 0) maxwarn = 1; + else error->all(FLERR,"Illegal fix qeq/fire command"); + iarg += 2; } else error->all(FLERR,"Illegal fix qeq/fire command"); } } @@ -214,8 +220,9 @@ void FixQEqFire::pre_force(int /*vflag*/) if (enegchk < tolerance) break; } + matvecs = iloop; - if ((comm->me == 0) && (iloop >= maxiter)) + if ((comm->me == 0) && maxwarn && (iloop >= maxiter)) error->warning(FLERR,"Charges did not converge at step {}: {}", update->ntimestep,enegchk); @@ -320,7 +327,7 @@ void FixQEqFire::unpack_forward_comm(int n, int first, double *buf) if (pack_flag == 1) for (m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m]; - else if ( pack_flag == 2) + else if (pack_flag == 2) for (m = 0, i = first; m < n; m++, i++) qf[i] = buf[m]; } diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index f94eba1a77..6c22ab85cf 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -38,7 +38,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ FixQEqPoint::FixQEqPoint(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) {} + FixQEq(lmp, narg, arg) { + if (narg == 10) { + if (strcmp(arg[8],"warn") == 0) { + if (strcmp(arg[9],"no") == 0) maxwarn = 0; + else if (strcmp(arg[9],"yes") == 0) maxwarn = 1; + else error->all(FLERR,"Illegal fix qeq/point command"); + } else error->all(FLERR,"Illegal fix qeq/point command"); + } else if (narg > 8) error->all(FLERR,"Illegal fix qeq/point command"); +} /* ---------------------------------------------------------------------- */ @@ -80,6 +88,7 @@ void FixQEqPoint::pre_force(int /*vflag*/) init_matvec(); matvecs = CG(b_s, s); // CG on s - parallel matvecs += CG(b_t, t); // CG on t - parallel + matvecs /= 2; calculate_Q(); if (force->kspace) force->kspace->qsum_qsq(); @@ -100,18 +109,18 @@ void FixQEqPoint::init_matvec() for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; if (atom->mask[i] & groupbit) { - Hdia_inv[i] = 1. / eta[ atom->type[i] ]; - b_s[i] = -( chi[atom->type[i]] + chizj[i] ); + Hdia_inv[i] = 1. / eta[atom->type[i]]; + b_s[i] = -(chi[atom->type[i]] + chizj[i]); b_t[i] = -1.0; - t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] ); + t[i] = t_hist[i][2] + 3 * (t_hist[i][0] - t_hist[i][1]); s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]); } } pack_flag = 2; - comm->forward_comm_fix(this); //Dist_vector( s ); + comm->forward_comm_fix(this); //Dist_vector(s); pack_flag = 3; - comm->forward_comm_fix(this); //Dist_vector( t ); + comm->forward_comm_fix(this); //Dist_vector(t); } /* ---------------------------------------------------------------------- */ diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 355d0fb0d3..ff8c87ba4e 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -40,6 +40,13 @@ using namespace LAMMPS_NS; FixQEqShielded::FixQEqShielded(LAMMPS *lmp, int narg, char **arg) : FixQEq(lmp, narg, arg) { + if (narg == 10) { + if (strcmp(arg[8],"warn") == 0) { + if (strcmp(arg[9],"no") == 0) maxwarn = 0; + else if (strcmp(arg[9],"yes") == 0) maxwarn = 1; + else error->all(FLERR,"Illegal fix qeq/shielded command"); + } else error->all(FLERR,"Illegal fix qeq/shielded command"); + } else if (narg > 8) error->all(FLERR,"Illegal fix qeq/shielded command"); if (reax_flag) extract_reax(); } @@ -79,15 +86,14 @@ void FixQEqShielded::init() void FixQEqShielded::extract_reax() { - Pair *pair = force->pair_match("^reax/c",0); - if (pair == nullptr) error->all(FLERR,"No pair reax/c for fix qeq/shielded"); + Pair *pair = force->pair_match("^reax..",0); + if (pair == nullptr) error->all(FLERR,"No pair reaxff for fix qeq/shielded"); int tmp; chi = (double *) pair->extract("chi",tmp); eta = (double *) pair->extract("eta",tmp); gamma = (double *) pair->extract("gamma",tmp); if (chi == nullptr || eta == nullptr || gamma == nullptr) - error->all(FLERR, - "Fix qeq/slater could not extract params from pair reax/c"); + error->all(FLERR, "Fix qeq/shielded could not extract params from pair reaxff"); } @@ -101,7 +107,7 @@ void FixQEqShielded::init_shielding() int ntypes = atom->ntypes; for (i = 1; i <= ntypes; ++i) for (j = 1; j <= ntypes; ++j) - shld[i][j] = pow( gamma[i] * gamma[j], -1.5 ); + shld[i][j] = pow(gamma[i] * gamma[j], -1.5); if (fabs(swa) > 0.01 && comm->me == 0) error->warning(FLERR,"Fix qeq has non-zero lower Taper radius cutoff"); @@ -110,7 +116,7 @@ void FixQEqShielded::init_shielding() else if (swb < 5 && comm->me == 0) error->warning(FLERR,"Fix qeq has very low Taper radius cutoff"); - d7 = pow( swb - swa, 7 ); + d7 = pow(swb - swa, 7); swa2 = swa*swa; swa3 = swa2*swa; swb2 = swb*swb; @@ -119,12 +125,12 @@ void FixQEqShielded::init_shielding() Tap[7] = 20.0 / d7; Tap[6] = -70.0 * (swa + swb) / d7; Tap[5] = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7; - Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3 ) / d7; - Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7; + Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3) / d7; + Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3) / d7; Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7; Tap[1] = 140.0 * swa3 * swb3 / d7; Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 - - 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7; + 7.0*swa*swb3*swb3 + swb3*swb3*swb) / d7; } /* ---------------------------------------------------------------------- */ @@ -143,6 +149,7 @@ void FixQEqShielded::pre_force(int /*vflag*/) init_matvec(); matvecs = CG(b_s, s); // CG on s - parallel matvecs += CG(b_t, t); // CG on t - parallel + matvecs /= 2; calculate_Q(); if (force->kspace) force->kspace->qsum_qsq(); @@ -163,18 +170,18 @@ void FixQEqShielded::init_matvec() for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; if (atom->mask[i] & groupbit) { - Hdia_inv[i] = 1. / eta[ atom->type[i] ]; - b_s[i] = -( chi[atom->type[i]] + chizj[i] ); + Hdia_inv[i] = 1. / eta[atom->type[i]]; + b_s[i] = -(chi[atom->type[i]] + chizj[i]); b_t[i] = -1.0; - t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] ); + t[i] = t_hist[i][2] + 3 * (t_hist[i][0] - t_hist[i][1]); s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]); } } pack_flag = 2; - comm->forward_comm_fix(this); //Dist_vector( s ); + comm->forward_comm_fix(this); //Dist_vector(s); pack_flag = 3; - comm->forward_comm_fix(this); //Dist_vector( t ); + comm->forward_comm_fix(this); //Dist_vector(t); } /* ---------------------------------------------------------------------- */ @@ -217,7 +224,7 @@ void FixQEqShielded::compute_H() if (r_sqr <= cutoff_sq) { H.jlist[m_fill] = j; r = sqrt(r_sqr); - H.val[m_fill] = 0.5 * calculate_H( r, shld[type[i]][type[j]] ); + H.val[m_fill] = 0.5 * calculate_H(r, shld[type[i]][type[j]]); m_fill++; } } @@ -232,7 +239,7 @@ void FixQEqShielded::compute_H() /* ---------------------------------------------------------------------- */ -double FixQEqShielded::calculate_H( double r, double gamma ) +double FixQEqShielded::calculate_H(double r, double gamma) { double Taper, denom; diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 3426595c0d..4b4814d982 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -53,6 +53,12 @@ FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/slater command"); alpha = atof(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"warn") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/slater command"); + if (strcmp(arg[iarg+1],"no") == 0) maxwarn = 0; + else if (strcmp(arg[iarg+1],"yes") == 0) maxwarn = 1; + else error->all(FLERR,"Illegal fix qeq/slater command"); + iarg += 2; } else error->all(FLERR,"Illegal fix qeq/slater command"); } @@ -121,6 +127,7 @@ void FixQEqSlater::pre_force(int /*vflag*/) init_matvec(); matvecs = CG(b_s, s); // CG on s - parallel matvecs += CG(b_t, t); // CG on t - parallel + matvecs /= 2; calculate_Q(); if (force->kspace) force->kspace->qsum_qsq(); @@ -141,18 +148,18 @@ void FixQEqSlater::init_matvec() for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; if (atom->mask[i] & groupbit) { - Hdia_inv[i] = 1. / eta[ atom->type[i] ]; - b_s[i] = -( chi[atom->type[i]] + chizj[i] ); + Hdia_inv[i] = 1. / eta[atom->type[i]]; + b_s[i] = -(chi[atom->type[i]] + chizj[i]); b_t[i] = -1.0; - t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] ); + t[i] = t_hist[i][2] + 3 * (t_hist[i][0] - t_hist[i][1]); s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]); } } pack_flag = 2; - comm->forward_comm_fix(this); //Dist_vector( s ); + comm->forward_comm_fix(this); //Dist_vector(s); pack_flag = 3; - comm->forward_comm_fix(this); //Dist_vector( t ); + comm->forward_comm_fix(this); //Dist_vector(t); } /* ---------------------------------------------------------------------- */ @@ -340,7 +347,7 @@ double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj, /* ---------------------------------------------------------------------- */ -void FixQEqSlater::sparse_matvec( sparse_matrix *A, double *x, double *b ) +void FixQEqSlater::sparse_matvec(sparse_matrix *A, double *x, double *b) { int i, j, itr_j; @@ -362,7 +369,7 @@ void FixQEqSlater::sparse_matvec( sparse_matrix *A, double *x, double *b ) for (i = 0; i < nlocal; ++i) { if (atom->mask[i] & groupbit) { - for( itr_j=A->firstnbr[i]; itr_jfirstnbr[i]+A->numnbrs[i]; itr_j++) { + for(itr_j=A->firstnbr[i]; itr_jfirstnbr[i]+A->numnbrs[i]; itr_j++) { j = A->jlist[itr_j]; b[i] += A->val[itr_j] * x[j]; b[j] += A->val[itr_j] * x[i]; diff --git a/src/USER-QMMM/Install.sh b/src/QMMM/Install.sh similarity index 100% rename from src/USER-QMMM/Install.sh rename to src/QMMM/Install.sh diff --git a/src/USER-QMMM/README b/src/QMMM/README similarity index 100% rename from src/USER-QMMM/README rename to src/QMMM/README diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/QMMM/fix_qmmm.cpp similarity index 100% rename from src/USER-QMMM/fix_qmmm.cpp rename to src/QMMM/fix_qmmm.cpp diff --git a/src/USER-QMMM/fix_qmmm.h b/src/QMMM/fix_qmmm.h similarity index 100% rename from src/USER-QMMM/fix_qmmm.h rename to src/QMMM/fix_qmmm.h diff --git a/src/USER-QTB/README b/src/QTB/README similarity index 97% rename from src/USER-QTB/README rename to src/QTB/README index 3b2b399d49..7458f60a4f 100644 --- a/src/USER-QTB/README +++ b/src/QTB/README @@ -44,7 +44,7 @@ What command should I use regarding these two cases? Where can I find examples of these two commands? There are example scripts for using this package in - examples/USER/qtb, including one "fix qtb" and one + examples/PACKAGES/qtb, including one "fix qtb" and one "fix qbmsst" example for each of alpha quartz and methane. Running the alpha quartz example requires installation of the kspace package while the methane diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/QTB/fix_qbmsst.cpp similarity index 100% rename from src/USER-QTB/fix_qbmsst.cpp rename to src/QTB/fix_qbmsst.cpp diff --git a/src/USER-QTB/fix_qbmsst.h b/src/QTB/fix_qbmsst.h similarity index 100% rename from src/USER-QTB/fix_qbmsst.h rename to src/QTB/fix_qbmsst.h diff --git a/src/USER-QTB/fix_qtb.cpp b/src/QTB/fix_qtb.cpp similarity index 100% rename from src/USER-QTB/fix_qtb.cpp rename to src/QTB/fix_qtb.cpp diff --git a/src/USER-QTB/fix_qtb.h b/src/QTB/fix_qtb.h similarity index 100% rename from src/USER-QTB/fix_qtb.h rename to src/QTB/fix_qtb.h diff --git a/src/USER-REACTION/README b/src/REACTION/README similarity index 100% rename from src/USER-REACTION/README rename to src/REACTION/README diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp similarity index 99% rename from src/USER-REACTION/fix_bond_react.cpp rename to src/REACTION/fix_bond_react.cpp index 46d7efdf8d..e52347727f 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -701,37 +701,25 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group void FixBondReact::post_constructor() { // let's add the limit_tags per-atom property fix - std::string cmd = std::string("bond_react_props_internal"); - id_fix2 = new char[cmd.size()+1]; - strcpy(id_fix2,cmd.c_str()); - - int ifix = modify->find_fix(id_fix2); - if (ifix == -1) { - cmd += std::string(" all property/atom i_limit_tags i_react_tags ghost yes"); - modify->add_fix(cmd); - } + id_fix2 = utils::strdup("bond_react_props_internal"); + if (modify->find_fix(id_fix2) < 0) + modify->add_fix(std::string(id_fix2)+" all property/atom i_limit_tags i_react_tags ghost yes"); // create master_group if not already existing // NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart) group->find_or_create(master_group); - cmd = fmt::format("{} dynamic all property limit_tags",master_group); + std::string cmd = fmt::format("{} dynamic all property limit_tags",master_group); group->assign(cmd); if (stabilization_flag == 1) { int groupid = group->find(exclude_group); // create exclude_group if not already existing, or use as parent group if static if (groupid == -1 || group->dynamic[groupid] == 0) { - // create stabilization per-atom property - cmd = std::string("bond_react_stabilization_internal"); - id_fix3 = new char[cmd.size()+1]; - strcpy(id_fix3,cmd.c_str()); - ifix = modify->find_fix(id_fix3); - if (ifix == -1) { - cmd += std::string(" all property/atom i_statted_tags ghost yes"); - modify->add_fix(cmd); - fix3 = modify->fix[modify->nfix-1]; - } + // create stabilization per-atom property + id_fix3 = utils::strdup("bond_react_stabilization_internal"); + if (modify->find_fix(id_fix3) < 0) + fix3 = modify->add_fix(std::string(id_fix3) + " all property/atom i_statted_tags ghost yes"); statted_id = utils::strdup("statted_tags"); @@ -770,7 +758,7 @@ void FixBondReact::post_constructor() // this returns names of corresponding property int unused; - char * idprop; + char *idprop; idprop = (char *) fix->extract("property",unused); if (idprop == nullptr) error->all(FLERR,"Exclude group must be a per-atom property group"); @@ -787,17 +775,10 @@ void FixBondReact::post_constructor() // let's create a new nve/limit fix to limit newly reacted atoms - cmd = std::string("bond_react_MASTER_nve_limit"); - id_fix1 = new char[cmd.size()+1]; - strcpy(id_fix1,cmd.c_str()); - - ifix = modify->find_fix(id_fix1); - - if (ifix == -1) { - cmd += fmt::format(" {} nve/limit {}",master_group,nve_limit_xmax); - modify->add_fix(cmd); - fix1 = modify->fix[modify->nfix-1]; - } + id_fix1 = utils::strdup("bond_react_MASTER_nve_limit"); + if (modify->find_fix(id_fix1) < 0) + fix1 = modify->add_fix(fmt::format("{} {} nve/limit {}", + id_fix1,master_group,nve_limit_xmax)); } } diff --git a/src/USER-REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h similarity index 100% rename from src/USER-REACTION/fix_bond_react.h rename to src/REACTION/fix_bond_react.h diff --git a/src/USER-REACTION/superpose3d.h b/src/REACTION/superpose3d.h similarity index 100% rename from src/USER-REACTION/superpose3d.h rename to src/REACTION/superpose3d.h diff --git a/src/USER-REAXC/README b/src/REAXFF/README similarity index 78% rename from src/USER-REAXC/README rename to src/REAXFF/README index d21fbb791d..528b782932 100644 --- a/src/USER-REAXC/README +++ b/src/REAXFF/README @@ -4,16 +4,6 @@ represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. -The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in -C, should give identical or very similar results to pair_style reax, -which is a ReaxFF implementation on top of a Fortran library, a -version of which library was originally authored by Adri van Duin. - -The reax/c version should be somewhat faster and more scalable, -particularly with respect to the charge equilibration calculation. It -should also be easier to build and use since there are no complicating -issues with Fortran memory allocation or linking to a Fortran library. - For technical details about this implementation of ReaxFF, see this paper: @@ -21,7 +11,7 @@ Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011). -See the doc page for the pair_style reax/c command for details +See the doc page for the pair_style reaxff command for details of how to use it in LAMMPS. The person who created this package is Hasan Metin Aktulga (hmaktulga diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/REAXFF/compute_spec_atom.cpp similarity index 89% rename from src/USER-REAXC/compute_spec_atom.cpp rename to src/REAXFF/compute_spec_atom.cpp index 1381f2cf96..66886cd1e2 100644 --- a/src/USER-REAXC/compute_spec_atom.cpp +++ b/src/REAXFF/compute_spec_atom.cpp @@ -13,13 +13,15 @@ ------------------------------------------------------------------------- */ #include "compute_spec_atom.h" -#include + #include "atom.h" -#include "update.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "pair_reaxc.h" +#include "pair_reaxff.h" +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -30,15 +32,15 @@ enum{KEYWORD,COMPUTE,FIX,VARIABLE}; ComputeSpecAtom::ComputeSpecAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg < 4) error->all(FLERR,"Illegal compute reax/c/atom command"); + if (narg < 4) error->all(FLERR,"Illegal compute spec/atom command"); peratom_flag = 1; nvalues = narg - 3; if (nvalues == 1) size_peratom_cols = 0; else size_peratom_cols = nvalues; - // Initiate reaxc - reaxc = (PairReaxC *) force->pair_match("reax/c",0); + // get reference to ReaxFF pair style + reaxff = (PairReaxFF *) force->pair_match("^reax..",0); pack_choice = new FnPtrPack[nvalues]; @@ -64,7 +66,7 @@ ComputeSpecAtom::ComputeSpecAtom(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"vz") == 0) { pack_choice[i] = &ComputeSpecAtom::pack_vz; - // from pair_reaxc + // from pair_reaxff } else if (strcmp(arg[iarg],"abo01") == 0) { pack_choice[i] = &ComputeSpecAtom::pack_abo01; } else if (strcmp(arg[iarg],"abo02") == 0) { @@ -114,7 +116,7 @@ ComputeSpecAtom::ComputeSpecAtom(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"abo24") == 0) { pack_choice[i] = &ComputeSpecAtom::pack_abo24; - } else error->all(FLERR,"Invalid keyword in compute reax/c/atom command"); + } else error->all(FLERR,"Invalid keyword in compute spec/atom command"); } nmax = 0; @@ -310,7 +312,7 @@ void ComputeSpecAtom::pack_abo01(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][0]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][0]; else buf[n] = 0.0; n += nvalues; } @@ -324,7 +326,7 @@ void ComputeSpecAtom::pack_abo02(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][1]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][1]; else buf[n] = 0.0; n += nvalues; } @@ -338,7 +340,7 @@ void ComputeSpecAtom::pack_abo03(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][2]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][2]; else buf[n] = 0.0; n += nvalues; } @@ -352,7 +354,7 @@ void ComputeSpecAtom::pack_abo04(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][3]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][3]; else buf[n] = 0.0; n += nvalues; } @@ -366,7 +368,7 @@ void ComputeSpecAtom::pack_abo05(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][4]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][4]; else buf[n] = 0.0; n += nvalues; } @@ -380,7 +382,7 @@ void ComputeSpecAtom::pack_abo06(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][5]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][5]; else buf[n] = 0.0; n += nvalues; } @@ -394,7 +396,7 @@ void ComputeSpecAtom::pack_abo07(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][6]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][6]; else buf[n] = 0.0; n += nvalues; } @@ -408,7 +410,7 @@ void ComputeSpecAtom::pack_abo08(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][7]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][7]; else buf[n] = 0.0; n += nvalues; } @@ -422,7 +424,7 @@ void ComputeSpecAtom::pack_abo09(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][8]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][8]; else buf[n] = 0.0; n += nvalues; } @@ -436,7 +438,7 @@ void ComputeSpecAtom::pack_abo10(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][9]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][9]; else buf[n] = 0.0; n += nvalues; } @@ -450,7 +452,7 @@ void ComputeSpecAtom::pack_abo11(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][10]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][10]; else buf[n] = 0.0; n += nvalues; } @@ -464,7 +466,7 @@ void ComputeSpecAtom::pack_abo12(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][11]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][11]; else buf[n] = 0.0; n += nvalues; } @@ -478,7 +480,7 @@ void ComputeSpecAtom::pack_abo13(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][12]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][12]; else buf[n] = 0.0; n += nvalues; } @@ -492,7 +494,7 @@ void ComputeSpecAtom::pack_abo14(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][13]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][13]; else buf[n] = 0.0; n += nvalues; } @@ -506,7 +508,7 @@ void ComputeSpecAtom::pack_abo15(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][14]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][14]; else buf[n] = 0.0; n += nvalues; } @@ -520,7 +522,7 @@ void ComputeSpecAtom::pack_abo16(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][15]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][15]; else buf[n] = 0.0; n += nvalues; } @@ -534,7 +536,7 @@ void ComputeSpecAtom::pack_abo17(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][16]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][16]; else buf[n] = 0.0; n += nvalues; } @@ -548,7 +550,7 @@ void ComputeSpecAtom::pack_abo18(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][17]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][17]; else buf[n] = 0.0; n += nvalues; } @@ -562,7 +564,7 @@ void ComputeSpecAtom::pack_abo19(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][18]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][18]; else buf[n] = 0.0; n += nvalues; } @@ -576,7 +578,7 @@ void ComputeSpecAtom::pack_abo20(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][19]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][19]; else buf[n] = 0.0; n += nvalues; } @@ -590,7 +592,7 @@ void ComputeSpecAtom::pack_abo21(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][20]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][20]; else buf[n] = 0.0; n += nvalues; } @@ -604,7 +606,7 @@ void ComputeSpecAtom::pack_abo22(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][21]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][21]; else buf[n] = 0.0; n += nvalues; } @@ -618,7 +620,7 @@ void ComputeSpecAtom::pack_abo23(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][22]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][22]; else buf[n] = 0.0; n += nvalues; } @@ -632,7 +634,7 @@ void ComputeSpecAtom::pack_abo24(int n) int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][23]; + if (mask[i] & groupbit) buf[n] = reaxff->tmpbo[i][23]; else buf[n] = 0.0; n += nvalues; } diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/REAXFF/compute_spec_atom.h similarity index 98% rename from src/USER-REAXC/compute_spec_atom.h rename to src/REAXFF/compute_spec_atom.h index ce4ce5b1cc..61dd63e272 100644 --- a/src/USER-REAXC/compute_spec_atom.h +++ b/src/REAXFF/compute_spec_atom.h @@ -75,7 +75,7 @@ class ComputeSpecAtom : public Compute { void pack_abo23(int); void pack_abo24(int); - class PairReaxC *reaxc; + class PairReaxFF *reaxff; }; } diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/REAXFF/fix_qeq_reaxff.cpp similarity index 70% rename from src/USER-REAXC/fix_qeq_reax.cpp rename to src/REAXFF/fix_qeq_reaxff.cpp index 9663d2ea49..8c3b7df190 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -19,7 +19,7 @@ Hybrid and sub-group capabilities: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include "fix_qeq_reax.h" +#include "fix_qeq_reaxff.h" #include "atom.h" #include "citeme.h" @@ -32,25 +32,33 @@ #include "neigh_request.h" #include "neighbor.h" #include "pair.h" -#include "pair_reaxc.h" #include "respa.h" +#include "text_file_reader.h" +#include "tokenizer.h" #include "update.h" +#include "pair_reaxff.h" +#include "reaxff_api.h" + #include #include -#include "reaxc_defs.h" -#include "reaxc_types.h" - using namespace LAMMPS_NS; using namespace FixConst; +class parser_error : public std::exception { + std::string message; +public: + parser_error(const std::string &mesg) { message = mesg; } + const char *what() const noexcept { return message.c_str(); } +}; + #define EV_TO_KCAL_PER_MOL 14.4 #define SQR(x) ((x)*(x)) #define CUBE(x) ((x)*(x)*(x)) -static const char cite_fix_qeq_reax[] = - "fix qeq/reax command:\n\n" +static const char cite_fix_qeq_reaxff[] = + "fix qeq/reaxff command:\n\n" "@Article{Aktulga12,\n" " author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n" " title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n" @@ -62,33 +70,39 @@ static const char cite_fix_qeq_reax[] = /* ---------------------------------------------------------------------- */ -FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), pertype_option(nullptr) +FixQEqReaxFF::FixQEqReaxFF(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), matvecs(0), pertype_option(nullptr) { - if (narg<8 || narg>11) error->all(FLERR,"Illegal fix qeq/reax command"); + scalar_flag = 1; + extscalar = 0; + imax = 200; + maxwarn = 1; + + if ((narg < 8) || (narg > 12)) error->all(FLERR,"Illegal fix qeq/reaxff command"); nevery = utils::inumeric(FLERR,arg[3],false,lmp); - if (nevery <= 0) error->all(FLERR,"Illegal fix qeq/reax command"); + if (nevery <= 0) error->all(FLERR,"Illegal fix qeq/reaxff command"); swa = utils::numeric(FLERR,arg[4],false,lmp); swb = utils::numeric(FLERR,arg[5],false,lmp); tolerance = utils::numeric(FLERR,arg[6],false,lmp); pertype_option = utils::strdup(arg[7]); - // dual CG support only available for USER-OMP variant + // dual CG support only available for OPENMP variant // check for compatibility is in Fix::post_constructor() + dual_enabled = 0; - imax = 200; int iarg = 8; while (iarg < narg) { if (strcmp(arg[iarg],"dual") == 0) dual_enabled = 1; + else if (strcmp(arg[iarg],"nowarn") == 0) maxwarn = 0; else if (strcmp(arg[iarg],"maxiter") == 0) { if (iarg+1 > narg-1) - error->all(FLERR,"Illegal fix qeq/reax command"); + error->all(FLERR,"Illegal fix qeq/reaxff command"); imax = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg++; - } else error->all(FLERR,"Illegal fix qeq/reax command"); + } else error->all(FLERR,"Illegal fix qeq/reaxff command"); iarg++; } shld = nullptr; @@ -108,12 +122,14 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : b_prm = nullptr; // CG + p = nullptr; q = nullptr; r = nullptr; d = nullptr; // H matrix + H.firstnbr = nullptr; H.numnbrs = nullptr; H.jlist = nullptr; @@ -121,14 +137,14 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : // dual CG support // Update comm sizes for this fix + if (dual_enabled) comm_forward = comm_reverse = 2; else comm_forward = comm_reverse = 1; // perform initial allocation of atom-based arrays // register with Atom class - reaxc = nullptr; - reaxc = (PairReaxC *) force->pair_match("^reax/c",0); + reaxff = (PairReaxFF *) force->pair_match("^reax..",0); s_hist = t_hist = nullptr; atom->add_callback(Atom::GROW); @@ -136,7 +152,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixQEqReax::~FixQEqReax() +FixQEqReaxFF::~FixQEqReaxFF() { if (copymode) return; @@ -149,7 +165,7 @@ FixQEqReax::~FixQEqReax() memory->destroy(s_hist); memory->destroy(t_hist); - deallocate_storage(); + FixQEqReaxFF::deallocate_storage(); deallocate_matrix(); memory->destroy(shld); @@ -163,9 +179,9 @@ FixQEqReax::~FixQEqReax() /* ---------------------------------------------------------------------- */ -void FixQEqReax::post_constructor() +void FixQEqReaxFF::post_constructor() { - if (lmp->citeme) lmp->citeme->add(cite_fix_qeq_reax); + if (lmp->citeme) lmp->citeme->add(cite_fix_qeq_reaxff); grow_arrays(atom->nmax); for (int i = 0; i < atom->nmax; i++) @@ -174,12 +190,12 @@ void FixQEqReax::post_constructor() pertype_parameters(pertype_option); if (dual_enabled) - error->all(FLERR,"Dual keyword only supported with fix qeq/reax/omp"); + error->all(FLERR,"Dual keyword only supported with fix qeq/reaxff/omp"); } /* ---------------------------------------------------------------------- */ -int FixQEqReax::setmask() +int FixQEqReaxFF::setmask() { int mask = 0; mask |= PRE_FORCE; @@ -190,60 +206,65 @@ int FixQEqReax::setmask() /* ---------------------------------------------------------------------- */ -void FixQEqReax::pertype_parameters(char *arg) +void FixQEqReaxFF::pertype_parameters(char *arg) { - if (strcmp(arg,"reax/c") == 0) { + // match either new keyword "reaxff" or old keyword "reax/c" + if (utils::strmatch(arg,"^reax..$")) { reaxflag = 1; - Pair *pair = force->pair_match("reax/c",0); - if (pair == nullptr) error->all(FLERR,"No pair reax/c for fix qeq/reax"); + Pair *pair = force->pair_match("^reax..",0); + if (!pair) error->all(FLERR,"No reaxff pair style for fix qeq/reaxff"); int tmp; chi = (double *) pair->extract("chi",tmp); eta = (double *) pair->extract("eta",tmp); gamma = (double *) pair->extract("gamma",tmp); if (chi == nullptr || eta == nullptr || gamma == nullptr) - error->all(FLERR, - "Fix qeq/reax could not extract params from pair reax/c"); + error->all(FLERR, "Fix qeq/reaxff could not extract params from pair reaxff"); return; } - int i,itype,ntypes,rv; - double v1,v2,v3; - FILE *pf; - reaxflag = 0; - ntypes = atom->ntypes; + const int ntypes = atom->ntypes; - memory->create(chi,ntypes+1,"qeq/reax:chi"); - memory->create(eta,ntypes+1,"qeq/reax:eta"); - memory->create(gamma,ntypes+1,"qeq/reax:gamma"); + memory->create(chi,ntypes+1,"qeq/reaxff:chi"); + memory->create(eta,ntypes+1,"qeq/reaxff:eta"); + memory->create(gamma,ntypes+1,"qeq/reaxff:gamma"); if (comm->me == 0) { - if ((pf = fopen(arg,"r")) == nullptr) - error->one(FLERR,"Fix qeq/reax parameter file could not be found"); + chi[0] = eta[0] = gamma[0] = 0.0; + try { + TextFileReader reader(arg,"qeq/reaxff parameter"); + reader.ignore_comments = false; + for (int i = 1; i <= ntypes; i++) { + const char *line = reader.next_line(); + if (!line) + throw parser_error("Invalid param file for fix qeq/reaxff"); + ValueTokenizer values(line); - for (i = 1; i <= ntypes && !feof(pf); i++) { - rv = fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3); - if (rv != 4) - error->one(FLERR,"Fix qeq/reax: Incorrect format of param file"); - if (itype < 1 || itype > ntypes) - error->one(FLERR,"Fix qeq/reax: invalid atom type in param file"); - chi[itype] = v1; - eta[itype] = v2; - gamma[itype] = v3; + if (values.count() != 4) + throw parser_error("Fix qeq/reaxff: Incorrect format of param file"); + + int itype = values.next_int(); + if ((itype < 1) || (itype > ntypes)) + throw parser_error("Fix qeq/reaxff: invalid atom type in param file"); + + chi[itype] = values.next_double(); + eta[itype] = values.next_double(); + gamma[itype] = values.next_double(); + } + } catch (std::exception &e) { + error->one(FLERR,e.what()); } - if (i <= ntypes) error->one(FLERR,"Invalid param file for fix qeq/reax"); - fclose(pf); } - MPI_Bcast(&chi[1],ntypes,MPI_DOUBLE,0,world); - MPI_Bcast(&eta[1],ntypes,MPI_DOUBLE,0,world); - MPI_Bcast(&gamma[1],ntypes,MPI_DOUBLE,0,world); + MPI_Bcast(chi,ntypes+1,MPI_DOUBLE,0,world); + MPI_Bcast(eta,ntypes+1,MPI_DOUBLE,0,world); + MPI_Bcast(gamma,ntypes+1,MPI_DOUBLE,0,world); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::allocate_storage() +void FixQEqReaxFF::allocate_storage() { nmax = atom->nmax; @@ -268,26 +289,26 @@ void FixQEqReax::allocate_storage() /* ---------------------------------------------------------------------- */ -void FixQEqReax::deallocate_storage() +void FixQEqReaxFF::deallocate_storage() { memory->destroy(s); memory->destroy(t); - memory->destroy( Hdia_inv ); - memory->destroy( b_s ); - memory->destroy( b_t ); - memory->destroy( b_prc ); - memory->destroy( b_prm ); + memory->destroy(Hdia_inv); + memory->destroy(b_s); + memory->destroy(b_t); + memory->destroy(b_prc); + memory->destroy(b_prm); - memory->destroy( p ); - memory->destroy( q ); - memory->destroy( r ); - memory->destroy( d ); + memory->destroy(p); + memory->destroy(q); + memory->destroy(r); + memory->destroy(d); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::reallocate_storage() +void FixQEqReaxFF::reallocate_storage() { deallocate_storage(); allocate_storage(); @@ -296,7 +317,7 @@ void FixQEqReax::reallocate_storage() /* ---------------------------------------------------------------------- */ -void FixQEqReax::allocate_matrix() +void FixQEqReaxFF::allocate_matrix() { int i,ii,n,m; @@ -304,15 +325,15 @@ void FixQEqReax::allocate_matrix() double safezone; if (reaxflag) { - mincap = reaxc->system->mincap; - safezone = reaxc->system->safezone; + mincap = reaxff->api->system->mincap; + safezone = reaxff->api->system->safezone; } else { mincap = REAX_MIN_CAP; safezone = REAX_SAFE_ZONE; } n = atom->nlocal; - n_cap = MAX( (int)(n * safezone), mincap); + n_cap = MAX((int)(n * safezone), mincap); // determine the total space for the H matrix @@ -321,7 +342,7 @@ void FixQEqReax::allocate_matrix() i = ilist[ii]; m += numneigh[i]; } - m_cap = MAX( (int)(m * safezone), mincap * REAX_MIN_NBRS); + m_cap = MAX((int)(m * safezone), mincap * REAX_MIN_NBRS); H.n = n_cap; H.m = m_cap; @@ -333,17 +354,17 @@ void FixQEqReax::allocate_matrix() /* ---------------------------------------------------------------------- */ -void FixQEqReax::deallocate_matrix() +void FixQEqReaxFF::deallocate_matrix() { - memory->destroy( H.firstnbr ); - memory->destroy( H.numnbrs ); - memory->destroy( H.jlist ); - memory->destroy( H.val ); + memory->destroy(H.firstnbr); + memory->destroy(H.numnbrs); + memory->destroy(H.jlist); + memory->destroy(H.val); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::reallocate_matrix() +void FixQEqReaxFF::reallocate_matrix() { deallocate_matrix(); allocate_matrix(); @@ -351,13 +372,13 @@ void FixQEqReax::reallocate_matrix() /* ---------------------------------------------------------------------- */ -void FixQEqReax::init() +void FixQEqReaxFF::init() { if (!atom->q_flag) - error->all(FLERR,"Fix qeq/reax requires atom attribute q"); + error->all(FLERR,"Fix qeq/reaxff requires atom attribute q"); - ngroup = group->count(igroup); - if (ngroup == 0) error->all(FLERR,"Fix qeq/reax group has no atoms"); + if (group->count(igroup) == 0) + error->all(FLERR,"Fix qeq/reaxff group has no atoms"); // need a half neighbor list w/ Newton off and ghost neighbors // built whenever re-neighboring occurs @@ -377,14 +398,21 @@ void FixQEqReax::init() /* ---------------------------------------------------------------------- */ -void FixQEqReax::init_list(int /*id*/, NeighList *ptr) +double FixQEqReaxFF::compute_scalar() +{ + return matvecs/2.0; +} + +/* ---------------------------------------------------------------------- */ + +void FixQEqReaxFF::init_list(int /*id*/, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ -void FixQEqReax::init_shielding() +void FixQEqReaxFF::init_shielding() { int i,j; int ntypes; @@ -395,27 +423,27 @@ void FixQEqReax::init_shielding() for (i = 1; i <= ntypes; ++i) for (j = 1; j <= ntypes; ++j) - shld[i][j] = pow( gamma[i] * gamma[j], -1.5); + shld[i][j] = pow(gamma[i] * gamma[j], -1.5); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::init_taper() +void FixQEqReaxFF::init_taper() { double d7, swa2, swa3, swb2, swb3; if (fabs(swa) > 0.01 && comm->me == 0) - error->warning(FLERR,"Fix qeq/reax has non-zero lower Taper radius cutoff"); + error->warning(FLERR,"Fix qeq/reaxff has non-zero lower Taper radius cutoff"); if (swb < 0) - error->all(FLERR, "Fix qeq/reax has negative upper Taper radius cutoff"); + error->all(FLERR, "Fix qeq/reaxff has negative upper Taper radius cutoff"); else if (swb < 5 && comm->me == 0) - error->warning(FLERR,"Fix qeq/reax has very low Taper radius cutoff"); + error->warning(FLERR,"Fix qeq/reaxff has very low Taper radius cutoff"); - d7 = pow( swb - swa, 7); - swa2 = SQR( swa); - swa3 = CUBE( swa); - swb2 = SQR( swb); - swb3 = CUBE( swb); + d7 = pow(swb - swa, 7); + swa2 = SQR(swa); + swa3 = CUBE(swa); + swb2 = SQR(swb); + swb3 = CUBE(swb); Tap[7] = 20.0 / d7; Tap[6] = -70.0 * (swa + swb) / d7; @@ -430,14 +458,14 @@ void FixQEqReax::init_taper() /* ---------------------------------------------------------------------- */ -void FixQEqReax::setup_pre_force(int vflag) +void FixQEqReaxFF::setup_pre_force(int vflag) { - if (reaxc) { - nn = reaxc->list->inum; - NN = reaxc->list->inum + reaxc->list->gnum; - ilist = reaxc->list->ilist; - numneigh = reaxc->list->numneigh; - firstneigh = reaxc->list->firstneigh; + if (reaxff) { + nn = reaxff->list->inum; + NN = reaxff->list->inum + reaxff->list->gnum; + ilist = reaxff->list->ilist; + numneigh = reaxff->list->numneigh; + firstneigh = reaxff->list->firstneigh; } else { nn = list->inum; NN = list->inum + list->gnum; @@ -459,7 +487,7 @@ void FixQEqReax::setup_pre_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixQEqReax::setup_pre_force_respa(int vflag, int ilevel) +void FixQEqReaxFF::setup_pre_force_respa(int vflag, int ilevel) { if (ilevel < nlevels_respa-1) return; setup_pre_force(vflag); @@ -467,21 +495,21 @@ void FixQEqReax::setup_pre_force_respa(int vflag, int ilevel) /* ---------------------------------------------------------------------- */ -void FixQEqReax::min_setup_pre_force(int vflag) +void FixQEqReaxFF::min_setup_pre_force(int vflag) { setup_pre_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::init_storage() +void FixQEqReaxFF::init_storage() { int NN; int *ilist; - if (reaxc) { - NN = reaxc->list->inum + reaxc->list->gnum; - ilist = reaxc->list->ilist; + if (reaxff) { + NN = reaxff->list->inum + reaxff->list->gnum; + ilist = reaxff->list->ilist; } else { NN = list->inum + list->gnum; ilist = list->ilist; @@ -502,21 +530,18 @@ void FixQEqReax::init_storage() /* ---------------------------------------------------------------------- */ -void FixQEqReax::pre_force(int /*vflag*/) +void FixQEqReaxFF::pre_force(int /*vflag*/) { - double t_start, t_end; - if (update->ntimestep % nevery) return; - if (comm->me == 0) t_start = MPI_Wtime(); int n = atom->nlocal; - if (reaxc) { - nn = reaxc->list->inum; - NN = reaxc->list->inum + reaxc->list->gnum; - ilist = reaxc->list->ilist; - numneigh = reaxc->list->numneigh; - firstneigh = reaxc->list->firstneigh; + if (reaxff) { + nn = reaxff->list->inum; + NN = reaxff->list->inum + reaxff->list->gnum; + ilist = reaxff->list->ilist; + numneigh = reaxff->list->numneigh; + firstneigh = reaxff->list->firstneigh; } else { nn = list->inum; NN = list->inum + list->gnum; @@ -539,30 +564,25 @@ void FixQEqReax::pre_force(int /*vflag*/) matvecs = matvecs_s + matvecs_t; calculate_Q(); - - if (comm->me == 0) { - t_end = MPI_Wtime(); - qeq_time = t_end - t_start; - } } /* ---------------------------------------------------------------------- */ -void FixQEqReax::pre_force_respa(int vflag, int ilevel, int /*iloop*/) +void FixQEqReaxFF::pre_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) pre_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::min_pre_force(int vflag) +void FixQEqReaxFF::min_pre_force(int vflag) { pre_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::init_matvec() +void FixQEqReaxFF::init_matvec() { /* fill-in H matrix */ compute_H(); @@ -574,12 +594,12 @@ void FixQEqReax::init_matvec() if (atom->mask[i] & groupbit) { /* init pre-conditioner for H and init solution vectors */ - Hdia_inv[i] = 1. / eta[ atom->type[i] ]; - b_s[i] = -chi[ atom->type[i] ]; + Hdia_inv[i] = 1. / eta[atom->type[i]]; + b_s[i] = -chi[atom->type[i]]; b_t[i] = -1.0; /* quadratic extrapolation for s & t from previous solutions */ - t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1]); + t[i] = t_hist[i][2] + 3 * (t_hist[i][0] - t_hist[i][1]); /* cubic extrapolation for s & t from previous solutions */ s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]); @@ -587,14 +607,14 @@ void FixQEqReax::init_matvec() } pack_flag = 2; - comm->forward_comm_fix(this); //Dist_vector( s ); + comm->forward_comm_fix(this); //Dist_vector(s); pack_flag = 3; - comm->forward_comm_fix(this); //Dist_vector( t ); + comm->forward_comm_fix(this); //Dist_vector(t); } /* ---------------------------------------------------------------------- */ -void FixQEqReax::compute_H() +void FixQEqReaxFF::compute_H() { int jnum; int i, j, ii, jj, flag; @@ -641,7 +661,7 @@ void FixQEqReax::compute_H() if (flag) { H.jlist[m_fill] = j; - H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]]); + H.val[m_fill] = calculate_H(sqrt(r_sqr), shld[type[i]][type[j]]); m_fill++; } } @@ -649,18 +669,14 @@ void FixQEqReax::compute_H() } } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/reax has insufficient QEq matrix size"); - } + if (m_fill >= H.m) + error->all(FLERR,fmt::format("Fix qeq/reaxff H matrix size has been " + "exceeded: m_fill={} H.m={}\n", m_fill, H.m)); } /* ---------------------------------------------------------------------- */ -double FixQEqReax::calculate_H( double r, double gamma) +double FixQEqReaxFF::calculate_H(double r, double gamma) { double Taper, denom; @@ -680,7 +696,7 @@ double FixQEqReax::calculate_H( double r, double gamma) /* ---------------------------------------------------------------------- */ -int FixQEqReax::CG( double *b, double *x) +int FixQEqReaxFF::CG(double *b, double *x) { int i, j; double tmp, alpha, beta, b_norm; @@ -689,10 +705,10 @@ int FixQEqReax::CG( double *b, double *x) int jj; pack_flag = 1; - sparse_matvec( &H, x, q); - comm->reverse_comm_fix(this); //Coll_Vector( q ); + sparse_matvec(&H, x, q); + comm->reverse_comm_fix(this); //Coll_Vector(q); - vector_sum( r , 1., b, -1., q, nn); + vector_sum(r , 1., b, -1., q, nn); for (jj = 0; jj < nn; ++jj) { j = ilist[jj]; @@ -700,19 +716,19 @@ int FixQEqReax::CG( double *b, double *x) d[j] = r[j] * Hdia_inv[j]; //pre-condition } - b_norm = parallel_norm( b, nn); - sig_new = parallel_dot( r, d, nn); + b_norm = parallel_norm(b, nn); + sig_new = parallel_dot(r, d, nn); for (i = 1; i < imax && sqrt(sig_new) / b_norm > tolerance; ++i) { - comm->forward_comm_fix(this); //Dist_vector( d ); - sparse_matvec( &H, d, q ); - comm->reverse_comm_fix(this); //Coll_vector( q ); + comm->forward_comm_fix(this); //Dist_vector(d); + sparse_matvec(&H, d, q); + comm->reverse_comm_fix(this); //Coll_vector(q); - tmp = parallel_dot( d, q, nn); + tmp = parallel_dot(d, q, nn); alpha = sig_new / tmp; - vector_add( x, alpha, d, nn ); - vector_add( r, -alpha, q, nn ); + vector_add(x, alpha, d, nn); + vector_add(r, -alpha, q, nn); // pre-conditioning for (jj = 0; jj < nn; ++jj) { @@ -722,26 +738,23 @@ int FixQEqReax::CG( double *b, double *x) } sig_old = sig_new; - sig_new = parallel_dot( r, p, nn); + sig_new = parallel_dot(r, p, nn); beta = sig_new / sig_old; - vector_sum( d, 1., p, beta, d, nn ); - } - - if (i >= imax && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq/reax CG convergence failed after %d iterations " - "at " BIGINT_FORMAT " step",i,update->ntimestep); - error->warning(FLERR,str); + vector_sum(d, 1., p, beta, d, nn); } + if ((i >= imax) && maxwarn && (comm->me == 0)) + error->warning(FLERR,fmt::format("Fix qeq/reaxff CG convergence failed " + "after {} iterations at step {}", + i,update->ntimestep)); return i; } /* ---------------------------------------------------------------------- */ -void FixQEqReax::sparse_matvec( sparse_matrix *A, double *x, double *b) +void FixQEqReaxFF::sparse_matvec(sparse_matrix *A, double *x, double *b) { int i, j, itr_j; int ii; @@ -749,7 +762,7 @@ void FixQEqReax::sparse_matvec( sparse_matrix *A, double *x, double *b) for (ii = 0; ii < nn; ++ii) { i = ilist[ii]; if (atom->mask[i] & groupbit) - b[i] = eta[ atom->type[i] ] * x[i]; + b[i] = eta[atom->type[i]] * x[i]; } for (ii = nn; ii < NN; ++ii) { @@ -773,7 +786,7 @@ void FixQEqReax::sparse_matvec( sparse_matrix *A, double *x, double *b) /* ---------------------------------------------------------------------- */ -void FixQEqReax::calculate_Q() +void FixQEqReaxFF::calculate_Q() { int i, k; double u, s_sum, t_sum; @@ -781,8 +794,8 @@ void FixQEqReax::calculate_Q() int ii; - s_sum = parallel_vector_acc( s, nn); - t_sum = parallel_vector_acc( t, nn); + s_sum = parallel_vector_acc(s, nn); + t_sum = parallel_vector_acc(t, nn); u = s_sum / t_sum; for (ii = 0; ii < nn; ++ii) { @@ -801,12 +814,12 @@ void FixQEqReax::calculate_Q() } pack_flag = 4; - comm->forward_comm_fix(this); //Dist_vector( atom->q ); + comm->forward_comm_fix(this); //Dist_vector(atom->q); } /* ---------------------------------------------------------------------- */ -int FixQEqReax::pack_forward_comm(int n, int *list, double *buf, +int FixQEqReaxFF::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int m; @@ -823,7 +836,7 @@ int FixQEqReax::pack_forward_comm(int n, int *list, double *buf, m = 0; for (int i = 0; i < n; i++) { int j = 2 * list[i]; - buf[m++] = d[j ]; + buf[m++] = d[j]; buf[m++] = d[j+1]; } return m; @@ -833,7 +846,7 @@ int FixQEqReax::pack_forward_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ -void FixQEqReax::unpack_forward_comm(int n, int first, double *buf) +void FixQEqReaxFF::unpack_forward_comm(int n, int first, double *buf) { int i, m; @@ -850,7 +863,7 @@ void FixQEqReax::unpack_forward_comm(int n, int first, double *buf) m = 0; for (i = first; i < last; i++) { int j = 2 * i; - d[j ] = buf[m++]; + d[j] = buf[m++]; d[j+1] = buf[m++]; } } @@ -858,7 +871,7 @@ void FixQEqReax::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -int FixQEqReax::pack_reverse_comm(int n, int first, double *buf) +int FixQEqReaxFF::pack_reverse_comm(int n, int first, double *buf) { int i, m; if (pack_flag == 5) { @@ -866,7 +879,7 @@ int FixQEqReax::pack_reverse_comm(int n, int first, double *buf) int last = first + n; for (i = first; i < last; i++) { int indxI = 2 * i; - buf[m++] = q[indxI ]; + buf[m++] = q[indxI]; buf[m++] = q[indxI+1]; } return m; @@ -878,13 +891,13 @@ int FixQEqReax::pack_reverse_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -void FixQEqReax::unpack_reverse_comm(int n, int *list, double *buf) +void FixQEqReaxFF::unpack_reverse_comm(int n, int *list, double *buf) { if (pack_flag == 5) { int m = 0; for (int i = 0; i < n; i++) { int indxI = 2 * list[i]; - q[indxI ] += buf[m++]; + q[indxI] += buf[m++]; q[indxI+1] += buf[m++]; } } else { @@ -896,7 +909,7 @@ void FixQEqReax::unpack_reverse_comm(int n, int *list, double *buf) memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double FixQEqReax::memory_usage() +double FixQEqReaxFF::memory_usage() { double bytes; @@ -916,7 +929,7 @@ double FixQEqReax::memory_usage() allocate fictitious charge arrays ------------------------------------------------------------------------- */ -void FixQEqReax::grow_arrays(int nmax) +void FixQEqReaxFF::grow_arrays(int nmax) { memory->grow(s_hist,nmax,nprev,"qeq:s_hist"); memory->grow(t_hist,nmax,nprev,"qeq:t_hist"); @@ -926,7 +939,7 @@ void FixQEqReax::grow_arrays(int nmax) copy values within fictitious charge arrays ------------------------------------------------------------------------- */ -void FixQEqReax::copy_arrays(int i, int j, int /*delflag*/) +void FixQEqReaxFF::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nprev; m++) { s_hist[j][m] = s_hist[i][m]; @@ -938,7 +951,7 @@ void FixQEqReax::copy_arrays(int i, int j, int /*delflag*/) pack values in local atom-based array for exchange with another proc ------------------------------------------------------------------------- */ -int FixQEqReax::pack_exchange(int i, double *buf) +int FixQEqReaxFF::pack_exchange(int i, double *buf) { for (int m = 0; m < nprev; m++) buf[m] = s_hist[i][m]; for (int m = 0; m < nprev; m++) buf[nprev+m] = t_hist[i][m]; @@ -949,7 +962,7 @@ int FixQEqReax::pack_exchange(int i, double *buf) unpack values in local atom-based array from exchange with another proc ------------------------------------------------------------------------- */ -int FixQEqReax::unpack_exchange(int nlocal, double *buf) +int FixQEqReaxFF::unpack_exchange(int nlocal, double *buf) { for (int m = 0; m < nprev; m++) s_hist[nlocal][m] = buf[m]; for (int m = 0; m < nprev; m++) t_hist[nlocal][m] = buf[nprev+m]; @@ -958,7 +971,7 @@ int FixQEqReax::unpack_exchange(int nlocal, double *buf) /* ---------------------------------------------------------------------- */ -double FixQEqReax::parallel_norm( double *v, int n) +double FixQEqReaxFF::parallel_norm(double *v, int n) { int i; double my_sum, norm_sqr; @@ -970,17 +983,17 @@ double FixQEqReax::parallel_norm( double *v, int n) for (ii = 0; ii < n; ++ii) { i = ilist[ii]; if (atom->mask[i] & groupbit) - my_sum += SQR( v[i]); + my_sum += SQR(v[i]); } - MPI_Allreduce( &my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(&my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world); - return sqrt( norm_sqr); + return sqrt(norm_sqr); } /* ---------------------------------------------------------------------- */ -double FixQEqReax::parallel_dot( double *v1, double *v2, int n) +double FixQEqReaxFF::parallel_dot(double *v1, double *v2, int n) { int i; double my_dot, res; @@ -995,14 +1008,14 @@ double FixQEqReax::parallel_dot( double *v1, double *v2, int n) my_dot += v1[i] * v2[i]; } - MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(&my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world); return res; } /* ---------------------------------------------------------------------- */ -double FixQEqReax::parallel_vector_acc( double *v, int n) +double FixQEqReaxFF::parallel_vector_acc(double *v, int n) { int i; double my_acc, res; @@ -1017,14 +1030,14 @@ double FixQEqReax::parallel_vector_acc( double *v, int n) my_acc += v[i]; } - MPI_Allreduce( &my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(&my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world); return res; } /* ---------------------------------------------------------------------- */ -void FixQEqReax::vector_sum( double* dest, double c, double* v, +void FixQEqReaxFF::vector_sum(double* dest, double c, double* v, double d, double* y, int k) { int kk; @@ -1038,7 +1051,7 @@ void FixQEqReax::vector_sum( double* dest, double c, double* v, /* ---------------------------------------------------------------------- */ -void FixQEqReax::vector_add( double* dest, double c, double* v, int k) +void FixQEqReaxFF::vector_add(double* dest, double c, double* v, int k) { int kk; diff --git a/src/USER-REAXC/fix_qeq_reax.h b/src/REAXFF/fix_qeq_reaxff.h similarity index 87% rename from src/USER-REAXC/fix_qeq_reax.h rename to src/REAXFF/fix_qeq_reaxff.h index f87c7c6294..b787bb9c7a 100644 --- a/src/USER-REAXC/fix_qeq_reax.h +++ b/src/REAXFF/fix_qeq_reaxff.h @@ -24,21 +24,22 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(qeq/reax,FixQEqReax); +FixStyle(qeq/reaxff,FixQEqReaxFF); +FixStyle(qeq/reax,FixQEqReaxFF); // clang-format on #else -#ifndef LMP_FIX_QEQ_REAX_H -#define LMP_FIX_QEQ_REAX_H +#ifndef LMP_FIX_QEQ_REAXFF_H +#define LMP_FIX_QEQ_REAXFF_H #include "fix.h" namespace LAMMPS_NS { -class FixQEqReax : public Fix { +class FixQEqReaxFF : public Fix { public: - FixQEqReax(class LAMMPS *, int, char **); - ~FixQEqReax(); + FixQEqReaxFF(class LAMMPS *, int, char **); + ~FixQEqReaxFF(); int setmask(); virtual void post_constructor(); virtual void init(); @@ -53,17 +54,17 @@ class FixQEqReax : public Fix { void min_setup_pre_force(int); void min_pre_force(int); - int matvecs; - double qeq_time; + virtual double compute_scalar(); protected: int nevery,reaxflag; + int matvecs; int nn, NN, m_fill; int n_cap, nmax, m_cap; int pack_flag; int nlevels_respa; class NeighList *list; - class PairReaxC *reaxc; + class PairReaxFF *reaxff; int *ilist, *jlist, *numneigh, **firstneigh; double swa, swb; // lower/upper Taper cutoff radius @@ -73,8 +74,6 @@ class FixQEqReax : public Fix { double *chi,*eta,*gamma; // qeq parameters double **shld; - bigint ngroup; - // fictitious charges double *s, *t; @@ -96,13 +95,7 @@ class FixQEqReax : public Fix { //CG storage double *p, *q, *r, *d; - int imax; - - //GMRES storage - //double *g,*y; - //double **v; - //double **h; - //double *hc, *hs; + int imax, maxwarn; char *pertype_option; // argument to determine how per-type info is obtained virtual void pertype_parameters(char*); @@ -122,7 +115,6 @@ class FixQEqReax : public Fix { virtual void calculate_Q(); virtual int CG(double*,double*); - //int GMRES(double*,double*); virtual void sparse_matvec(sparse_matrix*,double*,double*); virtual int pack_forward_comm(int, int *, double *, int, int *); @@ -135,9 +127,9 @@ class FixQEqReax : public Fix { virtual int pack_exchange(int, double *); virtual int unpack_exchange(int, double *); - virtual double parallel_norm( double*, int ); - virtual double parallel_dot( double*, double*, int ); - virtual double parallel_vector_acc( double*, int ); + virtual double parallel_norm(double*, int); + virtual double parallel_dot(double*, double*, int); + virtual double parallel_vector_acc(double*, int); virtual void vector_sum(double*,double,double*,double,double*,int); virtual void vector_add(double*, double, double*,int); diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/REAXFF/fix_reaxff.cpp similarity index 87% rename from src/USER-REAXC/fix_reaxc.cpp rename to src/REAXFF/fix_reaxff.cpp index 2b39ef5a0e..bd95dbcb38 100644 --- a/src/USER-REAXC/fix_reaxc.cpp +++ b/src/REAXFF/fix_reaxff.cpp @@ -22,7 +22,7 @@ Algorithmic Techniques", Parallel Computing, in press. ------------------------------------------------------------------------- */ -#include "fix_reaxc.h" +#include "fix_reaxff.h" #include "atom.h" #include "memory.h" @@ -35,7 +35,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) : +FixReaxFF::FixReaxFF(LAMMPS *lmp,int narg, char **arg) : Fix(lmp, narg, arg) { // perform initial allocation of atom-based arrays @@ -57,7 +57,7 @@ FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixReaxC::~FixReaxC() +FixReaxFF::~FixReaxFF() { // unregister this fix so atom class doesn't invoke it any more @@ -71,7 +71,7 @@ FixReaxC::~FixReaxC() /* ---------------------------------------------------------------------- */ -int FixReaxC::setmask() +int FixReaxFF::setmask() { int mask = 0; return mask; @@ -81,7 +81,7 @@ int FixReaxC::setmask() memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double FixReaxC::memory_usage() +double FixReaxFF::memory_usage() { int nmax = atom->nmax; double bytes = (double)nmax * 2 * sizeof(int); @@ -92,10 +92,10 @@ double FixReaxC::memory_usage() allocate local atom-based arrays ------------------------------------------------------------------------- */ -void FixReaxC::grow_arrays(int nmax) +void FixReaxFF::grow_arrays(int nmax) { - memory->grow(num_bonds,nmax,"reaxc:num_bonds"); - memory->grow(num_hbonds,nmax,"reaxc:num_hbonds"); + memory->grow(num_bonds,nmax,"reaxff:num_bonds"); + memory->grow(num_hbonds,nmax,"reaxff:num_hbonds"); for (int i = oldnmax; i < nmax; i++) { num_hbonds[i] = MIN_REAX_HBONDS; num_bonds[i] = MIN_REAX_BONDS; @@ -107,7 +107,7 @@ void FixReaxC::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixReaxC::copy_arrays(int i, int j, int /*delflag*/) +void FixReaxFF::copy_arrays(int i, int j, int /*delflag*/) { num_bonds[j] = num_bonds[i]; num_hbonds[j] = num_hbonds[i]; @@ -117,7 +117,7 @@ void FixReaxC::copy_arrays(int i, int j, int /*delflag*/) pack values in local atom-based arrays for exchange with another proc ------------------------------------------------------------------------- */ -int FixReaxC::pack_exchange(int i, double *buf) +int FixReaxFF::pack_exchange(int i, double *buf) { buf[0] = num_bonds[i]; buf[1] = num_hbonds[i]; @@ -128,7 +128,7 @@ int FixReaxC::pack_exchange(int i, double *buf) unpack values in local atom-based arrays from exchange with another proc ------------------------------------------------------------------------- */ -int FixReaxC::unpack_exchange(int nlocal, double *buf) +int FixReaxFF::unpack_exchange(int nlocal, double *buf) { num_bonds[nlocal] = static_cast (buf[0]); num_hbonds[nlocal] = static_cast (buf[1]); @@ -137,7 +137,7 @@ int FixReaxC::unpack_exchange(int nlocal, double *buf) /* ---------------------------------------------------------------------- */ -int FixReaxC::pack_forward_comm(int n, int *list, double *buf, +int FixReaxFF::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; @@ -152,7 +152,7 @@ int FixReaxC::pack_forward_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ -void FixReaxC::unpack_forward_comm(int n, int first, double *buf) +void FixReaxFF::unpack_forward_comm(int n, int first, double *buf) { int i,m,last; diff --git a/src/USER-REAXC/fix_reaxc.h b/src/REAXFF/fix_reaxff.h similarity index 89% rename from src/USER-REAXC/fix_reaxc.h rename to src/REAXFF/fix_reaxff.h index 6347f30c23..0b18f6d118 100644 --- a/src/USER-REAXC/fix_reaxc.h +++ b/src/REAXFF/fix_reaxff.h @@ -24,24 +24,24 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(REAXC,FixReaxC); +FixStyle(REAXFF,FixReaxFF); // clang-format on #else -#ifndef LMP_FIX_REAXC_H -#define LMP_FIX_REAXC_H +#ifndef LMP_FIX_REAXFF_H +#define LMP_FIX_REAXFF_H #include "fix.h" namespace LAMMPS_NS { -class FixReaxC : public Fix { - friend class PairReaxC; - friend class PairReaxCOMP; +class FixReaxFF : public Fix { + friend class PairReaxFF; + friend class PairReaxFFOMP; public: - FixReaxC(class LAMMPS *,int, char **); - ~FixReaxC(); + FixReaxFF(class LAMMPS *,int, char **); + ~FixReaxFF(); int setmask(); double memory_usage(); diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/REAXFF/fix_reaxff_bonds.cpp similarity index 76% rename from src/USER-REAXC/fix_reaxc_bonds.cpp rename to src/REAXFF/fix_reaxff_bonds.cpp index 5fb095578c..f13056c5b6 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/REAXFF/fix_reaxff_bonds.cpp @@ -16,29 +16,30 @@ Contributing author: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ -#include "fix_reaxc_bonds.h" +#include "fix_reaxff_bonds.h" -#include #include "atom.h" -#include "update.h" -#include "pair_reaxc.h" -#include "neigh_list.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "reaxc_list.h" -#include "reaxc_types.h" -#include "reaxc_defs.h" +#include "neigh_list.h" +#include "update.h" + +#include "pair_reaxff.h" +#include "reaxff_api.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; +using namespace ReaxFF; /* ---------------------------------------------------------------------- */ -FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : +FixReaxFFBonds::FixReaxFFBonds(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (narg != 5) error->all(FLERR,"Illegal fix reax/c/bonds command"); + if (narg != 5) error->all(FLERR,"Illegal fix reaxff/bonds command"); MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); @@ -47,34 +48,31 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : nevery = utils::inumeric(FLERR,arg[3],false,lmp); - if (nevery <= 0 ) - error->all(FLERR,"Illegal fix reax/c/bonds command"); + if (nevery <= 0) + error->all(FLERR,"Illegal fix reaxff/bonds command"); if (me == 0) { char *suffix = strrchr(arg[4],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP - char gzip[128]; - snprintf(gzip,128,"gzip -6 > %s",arg[4]); + auto gzip = fmt::format("gzip -6 > {}",arg[4]); #ifdef _WIN32 - fp = _popen(gzip,"wb"); + fp = _popen(gzip.c_str(),"wb"); #else - fp = popen(gzip,"w"); + fp = popen(gzip.c_str(),"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[4],"w"); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open fix reax/c/bonds file %s",arg[4]); - error->one(FLERR,str); - } + if (!fp) + error->one(FLERR,fmt::format("Cannot open fix reaxff/bonds file {}: " + "{}",arg[4],utils::getsyserror())); } if (atom->tag_consecutive() == 0) - error->all(FLERR,"Atom IDs must be consecutive for fix reax/c bonds"); + error->all(FLERR,"Atom IDs must be consecutive for fix reaxff bonds"); abo = nullptr; neighid = nullptr; @@ -85,7 +83,7 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixReaxCBonds::~FixReaxCBonds() +FixReaxFFBonds::~FixReaxFFBonds() { MPI_Comm_rank(world,&me); @@ -96,7 +94,7 @@ FixReaxCBonds::~FixReaxCBonds() /* ---------------------------------------------------------------------- */ -int FixReaxCBonds::setmask() +int FixReaxFFBonds::setmask() { int mask = 0; mask |= END_OF_STEP; @@ -105,32 +103,31 @@ int FixReaxCBonds::setmask() /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::setup(int /*vflag*/) +void FixReaxFFBonds::setup(int /*vflag*/) { end_of_step(); } /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::init() +void FixReaxFFBonds::init() { - reaxc = (PairReaxC *) force->pair_match("reax/c",0); - if (reaxc == nullptr) error->all(FLERR,"Cannot use fix reax/c/bonds without " - "pair_style reax/c, reax/c/kk, or reax/c/omp"); - + reaxff = (PairReaxFF *) force->pair_match("^reax..",0); + if (reaxff == nullptr) error->all(FLERR,"Cannot use fix reaxff/bonds without " + "pair_style reaxff, reaxff/kk, or reaxff/omp"); } /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::end_of_step() +void FixReaxFFBonds::end_of_step() { - Output_ReaxC_Bonds(update->ntimestep,fp); + Output_ReaxFF_Bonds(); if (me == 0) fflush(fp); } /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/) +void FixReaxFFBonds::Output_ReaxFF_Bonds() { int i, j; @@ -154,16 +151,14 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/) abo[i][j] = 0.0; } } - numbonds = 0; - - FindBond(lists, numbonds); + numbonds = FindBond(); // allocate a temporary buffer for the snapshot info MPI_Allreduce(&numbonds,&numbonds_max,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&nlocal,&nlocal_max,1,MPI_INT,MPI_MAX,world); nbuf = 1+(numbonds_max*2+10)*nlocal_max; - memory->create(buf,nbuf,"reax/c/bonds:buf"); + memory->create(buf,nbuf,"reaxff/bonds:buf"); for (i = 0; i < nbuf; i ++) buf[i] = 0.0; // Pass information to buffer @@ -178,26 +173,27 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/) /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::FindBond(struct _reax_list * /*lists*/, int &numbonds) +int FixReaxFFBonds::FindBond() { int *ilist, i, ii, inum; int j, pj, nj; tagint jtag; double bo_tmp,bo_cut; - inum = reaxc->list->inum; - ilist = reaxc->list->ilist; + inum = reaxff->list->inum; + ilist = reaxff->list->ilist; bond_data *bo_ij; - bo_cut = reaxc->control->bg_cut; + bo_cut = reaxff->api->control->bg_cut; tagint *tag = atom->tag; + int numbonds = 0; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; nj = 0; - for (pj = Start_Index(i, reaxc->lists); pj < End_Index(i, reaxc->lists); ++pj) { - bo_ij = &( reaxc->lists->select.bond_list[pj] ); + for (pj = Start_Index(i, reaxff->api->lists); pj < End_Index(i, reaxff->api->lists); ++pj) { + bo_ij = &(reaxff->api->lists->select.bond_list[pj]); j = bo_ij->nbr; jtag = tag[j]; bo_tmp = bo_ij->bo_data.BO; @@ -211,11 +207,11 @@ void FixReaxCBonds::FindBond(struct _reax_list * /*lists*/, int &numbonds) numneigh[i] = nj; if (nj > numbonds) numbonds = nj; } - + return numbonds; } /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local) +void FixReaxFFBonds::PassBuffer(double *buf, int &nbuf_local) { int i, j, k, numbonds; int nlocal = atom->nlocal; @@ -225,8 +221,8 @@ void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local) for (i = 0; i < nlocal; i++) { buf[j-1] = atom->tag[i]; buf[j+0] = atom->type[i]; - buf[j+1] = reaxc->workspace->total_bond_order[i]; - buf[j+2] = reaxc->workspace->nlp[i]; + buf[j+1] = reaxff->api->workspace->total_bond_order[i]; + buf[j+2] = reaxff->api->workspace->nlp[i]; buf[j+3] = atom->q[i]; buf[j+4] = numneigh[i]; numbonds = nint(buf[j+4]); @@ -236,7 +232,7 @@ void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local) } j += (5+numbonds); - if (atom->molecule == nullptr ) buf[j] = 0.0; + if (atom->molecule == nullptr) buf[j] = 0.0; else buf[j] = atom->molecule[i]; j ++; @@ -250,7 +246,7 @@ void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local) /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local, +void FixReaxFFBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local, int natoms, int maxnum) { int i, j, k, itype; @@ -260,7 +256,7 @@ void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local, bigint ntimestep = update->ntimestep; double sbotmp, nlptmp, avqtmp, abotmp; - double cutof3 = reaxc->control->bg_cut; + double cutof3 = reaxff->api->control->bg_cut; MPI_Request irequest, irequest2; if (me == 0) { @@ -322,7 +318,7 @@ void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local, /* ---------------------------------------------------------------------- */ -int FixReaxCBonds::nint(const double &r) +int FixReaxFFBonds::nint(const double &r) { int i = 0; if (r>0.0) i = static_cast(r+0.5); @@ -332,7 +328,7 @@ int FixReaxCBonds::nint(const double &r) /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::destroy() +void FixReaxFFBonds::destroy() { memory->destroy(abo); memory->destroy(neighid); @@ -341,16 +337,16 @@ void FixReaxCBonds::destroy() /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::allocate() +void FixReaxFFBonds::allocate() { - memory->create(abo,nmax,MAXREAXBOND,"reax/c/bonds:abo"); - memory->create(neighid,nmax,MAXREAXBOND,"reax/c/bonds:neighid"); - memory->create(numneigh,nmax,"reax/c/bonds:numneigh"); + memory->create(abo,nmax,MAXREAXBOND,"reaxff/bonds:abo"); + memory->create(neighid,nmax,MAXREAXBOND,"reaxff/bonds:neighid"); + memory->create(numneigh,nmax,"reaxff/bonds:numneigh"); } /* ---------------------------------------------------------------------- */ -double FixReaxCBonds::memory_usage() +double FixReaxFFBonds::memory_usage() { double bytes; diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/REAXFF/fix_reaxff_bonds.h similarity index 82% rename from src/USER-REAXC/fix_reaxc_bonds.h rename to src/REAXFF/fix_reaxff_bonds.h index fbca39fa95..ceb763b205 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/REAXFF/fix_reaxff_bonds.h @@ -14,7 +14,8 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(reax/c/bonds,FixReaxCBonds); +FixStyle(reaxff/bonds,FixReaxFFBonds); +FixStyle(reax/c/bonds,FixReaxFFBonds); // clang-format on #else @@ -25,10 +26,10 @@ FixStyle(reax/c/bonds,FixReaxCBonds); namespace LAMMPS_NS { -class FixReaxCBonds : public Fix { +class FixReaxFFBonds : public Fix { public: - FixReaxCBonds(class LAMMPS *, int, char **); - virtual ~FixReaxCBonds(); + FixReaxFFBonds(class LAMMPS *, int, char **); + virtual ~FixReaxFFBonds(); int setmask(); virtual void init(); void setup(int); @@ -43,8 +44,8 @@ class FixReaxCBonds : public Fix { void allocate(); void destroy(); - virtual void Output_ReaxC_Bonds(bigint, FILE *); - void FindBond(struct _reax_list*, int &); + virtual void Output_ReaxFF_Bonds(); + int FindBond(); void PassBuffer(double *, int &); void RecvBuffer(double *, int, int, int, int); int nint(const double &); @@ -52,7 +53,7 @@ class FixReaxCBonds : public Fix { bigint nvalid, nextvalid(); struct _reax_list *lists; - class PairReaxC *reaxc; + class PairReaxFF *reaxff; class NeighList *list; }; } diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/REAXFF/fix_reaxff_species.cpp similarity index 73% rename from src/USER-REAXC/fix_reaxc_species.cpp rename to src/REAXFF/fix_reaxff_species.cpp index be464f9a97..4fc08975a8 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/REAXFF/fix_reaxff_species.cpp @@ -17,7 +17,7 @@ Oleg Sergeev (VNIIA, sergeev@vniia.ru) ------------------------------------------------------------------------- */ -#include "fix_reaxc_species.h" +#include "fix_reaxff_species.h" #include "atom.h" #include "comm.h" @@ -29,22 +29,22 @@ #include "modify.h" #include "neigh_list.h" #include "neighbor.h" -#include "pair_reaxc.h" #include "update.h" -#include +#include "pair_reaxff.h" +#include "reaxff_defs.h" -#include "reaxc_defs.h" +#include using namespace LAMMPS_NS; using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : +FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (narg < 7) error->all(FLERR,"Illegal fix reax/c/species command"); + if (narg < 7) error->all(FLERR,"Illegal fix reaxff/species command"); force_reneighbor = 0; @@ -69,9 +69,9 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : comm_forward = 4; if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix reax/c/species command"); + error->all(FLERR,"Illegal fix reaxff/species command"); if (nfreq % nevery || nrepeat*nevery > nfreq) - error->all(FLERR,"Illegal fix reax/c/species command"); + error->all(FLERR,"Illegal fix reaxff/species command"); // Neighbor lists must stay unchanged during averaging of bonds, // but may be updated when no averaging is performed. @@ -96,11 +96,11 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : } if (me == 0 && rene_flag) { - error->warning(FLERR,"Resetting reneighboring criteria for fix reax/c/species"); + error->warning(FLERR,"Resetting reneighboring criteria for fix reaxff/species"); } tmparg = nullptr; - memory->create(tmparg,4,4,"reax/c/species:tmparg"); + memory->create(tmparg,4,4,"reaxff/species:tmparg"); strcpy(tmparg[0],arg[3]); strcpy(tmparg[1],arg[4]); strcpy(tmparg[2],arg[5]); @@ -109,31 +109,28 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : char *suffix = strrchr(arg[6],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP - char gzip[128]; - sprintf(gzip,"gzip -6 > %s",arg[6]); + auto gzip = fmt::format("gzip -6 > {}",arg[6]); #ifdef _WIN32 - fp = _popen(gzip,"wb"); + fp = _popen(gzip.c_str(),"wb"); #else - fp = popen(gzip,"w"); + fp = popen(gzip.c_str(),"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[6],"w"); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open fix reax/c/species file %s",arg[6]); - error->one(FLERR,str); - } + if (!fp) + error->one(FLERR,fmt::format("Cannot open fix reaxff/species file {}: " + "{}",arg[6],utils::getsyserror())); } x0 = nullptr; clusterID = nullptr; int ntmp = 1; - memory->create(x0,ntmp,"reax/c/species:x0"); - memory->create(clusterID,ntmp,"reax/c/species:clusterID"); + memory->create(x0,ntmp,"reaxff/species:x0"); + memory->create(clusterID,ntmp,"reaxff/species:clusterID"); vector_atom = clusterID; BOCut = nullptr; @@ -152,7 +149,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : double bo_cut; bg_cut = 0.30; n = ntypes+1; - memory->create(BOCut,n,n,"reax/c/species:BOCut"); + memory->create(BOCut,n,n,"reaxff/species:BOCut"); for (i = 1; i < n; i ++) for (j = 1; j < n; j ++) BOCut[i][j] = bg_cut; @@ -171,16 +168,16 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : // set BO cutoff if (strcmp(arg[iarg],"cutoff") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix reax/c/species command"); + if (iarg+4 > narg) error->all(FLERR,"Illegal fix reaxff/species command"); itype = atoi(arg[iarg+1]); jtype = atoi(arg[iarg+2]); bo_cut = atof(arg[iarg+3]); if (itype > ntypes || jtype > ntypes) - error->all(FLERR,"Illegal fix reax/c/species command"); + error->all(FLERR,"Illegal fix reaxff/species command"); if (itype <= 0 || jtype <= 0) - error->all(FLERR,"Illegal fix reax/c/species command"); + error->all(FLERR,"Illegal fix reaxff/species command"); if (bo_cut > 1.0 || bo_cut < 0.0) - error->all(FLERR,"Illegal fix reax/c/species command"); + error->all(FLERR,"Illegal fix reaxff/species command"); BOCut[itype][jtype] = bo_cut; BOCut[jtype][itype] = bo_cut; @@ -188,7 +185,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : // modify element type names } else if (strcmp(arg[iarg],"element") == 0) { - if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix reax/c/species command"); + if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix reaxff/species command"); eletype = (char**) malloc(ntypes*sizeof(char*)); int len; @@ -202,11 +199,11 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : // position of molecules } else if (strcmp(arg[iarg],"position") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix reax/c/species command"); + if (iarg+3 > narg) error->all(FLERR,"Illegal fix reaxff/species command"); posflag = 1; posfreq = atoi(arg[iarg+1]); if (posfreq < nfreq || (posfreq%nfreq != 0)) - error->all(FLERR,"Illegal fix reax/c/species command"); + error->all(FLERR,"Illegal fix reaxff/species command"); filepos = new char[255]; strcpy(filepos,arg[iarg+2]); @@ -215,17 +212,17 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : } else { if (me == 0) { pos = fopen(filepos, "w"); - if (pos == nullptr) error->one(FLERR,"Cannot open fix reax/c/species position file"); + if (pos == nullptr) error->one(FLERR,"Cannot open fix reaxff/species position file"); } singlepos_opened = 1; multipos = 0; } iarg += 3; - } else error->all(FLERR,"Illegal fix reax/c/species command"); + } else error->all(FLERR,"Illegal fix reaxff/species command"); } if (!eleflag) { - memory->create(ele,ntypes+1,"reax/c/species:ele"); + memory->create(ele,ntypes+1,"reaxff/species:ele"); ele[0]='C'; if (ntypes > 1) ele[1]='H'; @@ -242,7 +239,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixReaxCSpecies::~FixReaxCSpecies() +FixReaxFFSpecies::~FixReaxFFSpecies() { memory->destroy(ele); memory->destroy(BOCut); @@ -268,7 +265,7 @@ FixReaxCSpecies::~FixReaxCSpecies() /* ---------------------------------------------------------------------- */ -int FixReaxCSpecies::setmask() +int FixReaxFFSpecies::setmask() { int mask = 0; mask |= POST_INTEGRATE; @@ -277,27 +274,27 @@ int FixReaxCSpecies::setmask() /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::setup(int /*vflag*/) +void FixReaxFFSpecies::setup(int /*vflag*/) { ntotal = static_cast (atom->natoms); if (Name == nullptr) - memory->create(Name,ntypes,"reax/c/species:Name"); + memory->create(Name,ntypes,"reaxff/species:Name"); post_integrate(); } /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::init() +void FixReaxFFSpecies::init() { if (atom->tag_enable == 0) - error->all(FLERR,"Cannot use fix reax/c/species unless atoms have IDs"); + error->all(FLERR,"Cannot use fix reaxff/species unless atoms have IDs"); - reaxc = (PairReaxC *) force->pair_match("reax/c",0); - if (reaxc == nullptr) error->all(FLERR,"Cannot use fix reax/c/species without " - "pair_style reax/c, reax/c/kk, or reax/c/omp"); + reaxff = (PairReaxFF *) force->pair_match("^reax..",0); + if (reaxff == nullptr) error->all(FLERR,"Cannot use fix reaxff/species without " + "pair_style reaxff, reaxff/kk, or reaxff/omp"); - reaxc->fixspecies_flag = 1; + reaxff->fixspecies_flag = 1; // reset next output timestep if not yet set or timestep has been reset if (nvalid != update->ntimestep) @@ -306,139 +303,42 @@ void FixReaxCSpecies::init() // check if this fix has been called twice int count = 0; for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"reax/c/species") == 0) count++; + if (strcmp(modify->fix[i]->style,"reaxff/species") == 0) count++; if (count > 1 && comm->me == 0) - error->warning(FLERR,"More than one fix reax/c/species"); + error->warning(FLERR,"More than one fix reaxff/species"); if (!setupflag) { // create a compute to store properties - create_compute(); + modify->add_compute("SPECATOM all SPEC/ATOM q x y z vx vy vz abo01 abo02 abo03 abo04 " + "abo05 abo06 abo07 abo08 abo09 abo10 abo11 abo12 abo13 abo14 " + "abo15 abo16 abo17 abo18 abo19 abo20 abo21 abo22 abo23 abo24"); // create a fix to point to fix_ave_atom for averaging stored properties - create_fix(); - + auto fixcmd = fmt::format("SPECBOND all ave/atom {} {} {}",tmparg[0],tmparg[1],tmparg[2]); + for (int i = 1; i < 32; ++i) fixcmd += " c_SPECATOM[" + std::to_string(i) + "]"; + f_SPECBOND = (FixAveAtom *) modify->add_fix(fixcmd); setupflag = 1; } - } /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::create_compute() -{ - int narg; - char **args; - - narg = 34; - args = new char*[narg]; - args[0] = (char *) "SPECATOM"; - args[1] = (char *) "all"; - args[2] = (char *) "SPEC/ATOM"; - args[3] = (char *) "q"; - args[4] = (char *) "x"; - args[5] = (char *) "y"; - args[6] = (char *) "z"; - args[7] = (char *) "vx"; - args[8] = (char *) "vy"; - args[9] = (char *) "vz"; - args[10] = (char *) "abo01"; - args[11] = (char *) "abo02"; - args[12] = (char *) "abo03"; - args[13] = (char *) "abo04"; - args[14] = (char *) "abo05"; - args[15] = (char *) "abo06"; - args[16] = (char *) "abo07"; - args[17] = (char *) "abo08"; - args[18] = (char *) "abo09"; - args[19] = (char *) "abo10"; - args[20] = (char *) "abo11"; - args[21] = (char *) "abo12"; - args[22] = (char *) "abo13"; - args[23] = (char *) "abo14"; - args[24] = (char *) "abo15"; - args[25] = (char *) "abo16"; - args[26] = (char *) "abo17"; - args[27] = (char *) "abo18"; - args[28] = (char *) "abo19"; - args[29] = (char *) "abo20"; - args[30] = (char *) "abo21"; - args[31] = (char *) "abo22"; - args[32] = (char *) "abo23"; - args[33] = (char *) "abo24"; - modify->add_compute(narg,args); - delete [] args; -} - -/* ---------------------------------------------------------------------- */ - -void FixReaxCSpecies::create_fix() -{ - int narg; - char **args; - - narg = 37; - args = new char*[narg]; - args[0] = (char *) "SPECBOND"; - args[1] = (char *) "all"; - args[2] = (char *) "ave/atom"; - args[3] = tmparg[0]; - args[4] = tmparg[1]; - args[5] = tmparg[2]; - args[6] = (char *) "c_SPECATOM[1]"; // q, array_atoms[i][0] - args[7] = (char *) "c_SPECATOM[2]"; // x, 1 - args[8] = (char *) "c_SPECATOM[3]"; // y, 2 - args[9] = (char *) "c_SPECATOM[4]"; // z, 3 - args[10] = (char *) "c_SPECATOM[5]"; // vx, 4 - args[11] = (char *) "c_SPECATOM[6]"; // vy, 5 - args[12] = (char *) "c_SPECATOM[7]"; // vz, 6 - args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7 - args[14] = (char *) "c_SPECATOM[9]"; - args[15] = (char *) "c_SPECATOM[10]"; - args[16] = (char *) "c_SPECATOM[11]"; - args[17] = (char *) "c_SPECATOM[12]"; - args[18] = (char *) "c_SPECATOM[13]"; - args[19] = (char *) "c_SPECATOM[14]"; - args[20] = (char *) "c_SPECATOM[15]"; - args[21] = (char *) "c_SPECATOM[16]"; - args[22] = (char *) "c_SPECATOM[17]"; - args[23] = (char *) "c_SPECATOM[18]"; - args[24] = (char *) "c_SPECATOM[19]"; // abo12, 18 - args[25] = (char *) "c_SPECATOM[20]"; - args[26] = (char *) "c_SPECATOM[21]"; - args[27] = (char *) "c_SPECATOM[22]"; - args[28] = (char *) "c_SPECATOM[23]"; - args[29] = (char *) "c_SPECATOM[24]"; - args[30] = (char *) "c_SPECATOM[25]"; - args[31] = (char *) "c_SPECATOM[26]"; - args[32] = (char *) "c_SPECATOM[27]"; - args[33] = (char *) "c_SPECATOM[28]"; - args[34] = (char *) "c_SPECATOM[29]"; - args[35] = (char *) "c_SPECATOM[30]"; - args[36] = (char *) "c_SPECATOM[31]"; - modify->add_fix(narg,args); - f_SPECBOND = (FixAveAtom *) modify->fix[modify->nfix-1]; - delete [] args; - -} - -/* ---------------------------------------------------------------------- */ - -void FixReaxCSpecies::init_list(int /*id*/, NeighList *ptr) +void FixReaxFFSpecies::init_list(int /*id*/, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::post_integrate() +void FixReaxFFSpecies::post_integrate() { - Output_ReaxC_Bonds(update->ntimestep,fp); + Output_ReaxFF_Bonds(update->ntimestep,fp); if (me == 0) fflush(fp); } /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE * /*fp*/) +void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/) { int Nmole, Nspec; @@ -454,8 +354,8 @@ void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE * /*fp*/) nmax = atom->nmax; memory->destroy(x0); memory->destroy(clusterID); - memory->create(x0,nmax,"reax/c/species:x0"); - memory->create(clusterID,nmax,"reax/c/species:clusterID"); + memory->create(x0,nmax,"reaxff/species:x0"); + memory->create(clusterID,nmax,"reaxff/species:clusterID"); vector_atom = clusterID; } @@ -487,7 +387,7 @@ void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE * /*fp*/) /* ---------------------------------------------------------------------- */ -AtomCoord FixReaxCSpecies::chAnchor(AtomCoord in1, AtomCoord in2) +AtomCoord FixReaxFFSpecies::chAnchor(AtomCoord in1, AtomCoord in2) { if (in1.x < in2.x) return in1; @@ -504,7 +404,7 @@ AtomCoord FixReaxCSpecies::chAnchor(AtomCoord in1, AtomCoord in2) /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::FindMolecule () +void FixReaxFFSpecies::FindMolecule () { int i,j,ii,jj,inum,itype,jtype,loop,looptot; int change,done,anychange; @@ -513,8 +413,8 @@ void FixReaxCSpecies::FindMolecule () double bo_tmp,bo_cut; double **spec_atom = f_SPECBOND->array_atom; - inum = reaxc->list->inum; - ilist = reaxc->list->ilist; + inum = reaxff->list->inum; + ilist = reaxff->list->ilist; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; @@ -543,7 +443,7 @@ void FixReaxCSpecies::FindMolecule () itype = atom->type[i]; for (jj = 0; jj < MAXSPECBOND; jj++) { - j = reaxc->tmpid[i][jj]; + j = reaxff->tmpid[i][jj]; if ((j == 0) || (j < i)) continue; if (!(mask[j] & groupbit)) continue; @@ -578,7 +478,7 @@ void FixReaxCSpecies::FindMolecule () /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::SortMolecule(int &Nmole) +void FixReaxFFSpecies::SortMolecule(int &Nmole) { memory->destroy(molmap); molmap = nullptr; @@ -598,16 +498,16 @@ void FixReaxCSpecies::SortMolecule(int &Nmole) MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); if (flagall && me == 0) error->warning(FLERR,"Atom with cluster ID = 0 included in " - "fix reax/c/species group"); + "fix reaxff/species group"); MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world); MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world); if (idlo == ntotal) if (me == 0) error->warning(FLERR,"Atom with cluster ID = maxmol " - "included in fix reax/c/species group"); + "included in fix reaxff/species group"); int nlen = idhi - idlo + 1; - memory->create(molmap,nlen,"reax/c/species:molmap"); + memory->create(molmap,nlen,"reaxff/species:molmap"); for (n = 0; n < nlen; n++) molmap[n] = 0; for (n = 0; n < nlocal; n++) { @@ -616,7 +516,7 @@ void FixReaxCSpecies::SortMolecule(int &Nmole) } int *molmapall; - memory->create(molmapall,nlen,"reax/c/species:molmapall"); + memory->create(molmapall,nlen,"reaxff/species:molmapall"); MPI_Allreduce(molmap,molmapall,nlen,MPI_INT,MPI_MAX,world); Nmole = 0; @@ -649,7 +549,7 @@ void FixReaxCSpecies::SortMolecule(int &Nmole) /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec) +void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec) { int k, l, m, n, itype, cid; int flag_identity, flag_mol, flag_spec; @@ -659,16 +559,16 @@ void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec) memory->destroy(MolName); MolName = nullptr; - memory->create(MolName,Nmole*(ntypes+1),"reax/c/species:MolName"); + memory->create(MolName,Nmole*(ntypes+1),"reaxff/species:MolName"); memory->destroy(NMol); NMol = nullptr; - memory->create(NMol,Nmole,"reax/c/species:NMol"); + memory->create(NMol,Nmole,"reaxff/species:NMol"); for (m = 0; m < Nmole; m ++) NMol[m] = 1; - memory->create(Nameall,ntypes,"reax/c/species:Nameall"); - memory->create(NMolall,Nmole,"reax/c/species:NMolall"); + memory->create(Nameall,ntypes,"reaxff/species:Nameall"); + memory->create(NMolall,Nmole,"reaxff/species:NMolall"); for (m = 1, Nspec = 0; m <= Nmole; m ++) { for (n = 0; n < ntypes; n ++) Name[n] = 0; @@ -708,16 +608,16 @@ void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec) memory->destroy(nd); nd = nullptr; - memory->create(nd,Nspec,"reax/c/species:nd"); + memory->create(nd,Nspec,"reaxff/species:nd"); memory->destroy(MolType); MolType = nullptr; - memory->create(MolType,Nspec*(ntypes+2),"reax/c/species:MolType"); + memory->create(MolType,Nspec*(ntypes+2),"reaxff/species:MolType"); } /* ---------------------------------------------------------------------- */ -int FixReaxCSpecies::CheckExistence(int id, int ntypes) +int FixReaxFFSpecies::CheckExistence(int id, int ntypes) { int i, j, molid, flag; @@ -738,7 +638,7 @@ int FixReaxCSpecies::CheckExistence(int id, int ntypes) /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::WriteFormulas(int Nmole, int Nspec) +void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec) { int i, j, itemp; bigint ntimestep = update->ntimestep; @@ -774,7 +674,7 @@ void FixReaxCSpecies::WriteFormulas(int Nmole, int Nspec) /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::OpenPos() +void FixReaxFFSpecies::OpenPos() { char *filecurrent; bigint ntimestep = update->ntimestep; @@ -795,7 +695,7 @@ void FixReaxCSpecies::OpenPos() if (me == 0) { pos = fopen(filecurrent, "w"); - if (pos == nullptr) error->one(FLERR,"Cannot open fix reax/c/species position file"); + if (pos == nullptr) error->one(FLERR,"Cannot open fix reaxff/species position file"); } else pos = nullptr; multipos_opened = 1; @@ -804,7 +704,7 @@ void FixReaxCSpecies::OpenPos() /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::WritePos(int Nmole, int Nspec) +void FixReaxFFSpecies::WritePos(int Nmole, int Nspec) { int i, itype, cid; int count, count_tmp, m, n, k; @@ -834,7 +734,7 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec) } Nameall = nullptr; - memory->create(Nameall,ntypes,"reax/c/species:Nameall"); + memory->create(Nameall,ntypes,"reaxff/species:Nameall"); for (m = 1; m <= Nmole; m ++) { @@ -919,7 +819,7 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec) /* ---------------------------------------------------------------------- */ -double FixReaxCSpecies::compute_vector(int n) +double FixReaxFFSpecies::compute_vector(int n) { if (n == 0) return vector_nmole; @@ -931,7 +831,7 @@ double FixReaxCSpecies::compute_vector(int n) /* ---------------------------------------------------------------------- */ -int FixReaxCSpecies::nint(const double &r) +int FixReaxFFSpecies::nint(const double &r) { int i = 0; if (r>0.0) i = static_cast(r+0.5); @@ -941,7 +841,7 @@ int FixReaxCSpecies::nint(const double &r) /* ---------------------------------------------------------------------- */ -int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf, +int FixReaxFFSpecies::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; @@ -960,7 +860,7 @@ int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::unpack_forward_comm(int n, int first, double *buf) +void FixReaxFFSpecies::unpack_forward_comm(int n, int first, double *buf) { int i,m,last; @@ -977,7 +877,7 @@ void FixReaxCSpecies::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -double FixReaxCSpecies::memory_usage() +double FixReaxFFSpecies::memory_usage() { double bytes; diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/REAXFF/fix_reaxff_species.h similarity index 87% rename from src/USER-REAXC/fix_reaxc_species.h rename to src/REAXFF/fix_reaxff_species.h index 225e0bcf24..b65ea49476 100644 --- a/src/USER-REAXC/fix_reaxc_species.h +++ b/src/REAXFF/fix_reaxff_species.h @@ -14,7 +14,8 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(reax/c/species,FixReaxCSpecies); +FixStyle(reaxff/species,FixReaxFFSpecies); +FixStyle(reax/c/species,FixReaxFFSpecies); // clang-format on #else @@ -31,10 +32,10 @@ typedef struct { double x, y, z; } AtomCoord; -class FixReaxCSpecies : public Fix { +class FixReaxFFSpecies : public Fix { public: - FixReaxCSpecies(class LAMMPS *, int, char **); - virtual ~FixReaxCSpecies(); + FixReaxFFSpecies(class LAMMPS *, int, char **); + virtual ~FixReaxFFSpecies(); int setmask(); virtual void init(); void init_list(int, class NeighList *); @@ -59,9 +60,7 @@ class FixReaxCSpecies : public Fix { int singlepos_opened, multipos_opened; char *ele, **eletype, *filepos; - void Output_ReaxC_Bonds(bigint, FILE *); - void create_compute(); - void create_fix(); + void Output_ReaxFF_Bonds(bigint, FILE *); AtomCoord chAnchor(AtomCoord, AtomCoord); virtual void FindMolecule(); void SortMolecule(int &); @@ -80,8 +79,7 @@ class FixReaxCSpecies : public Fix { class NeighList *list; class FixAveAtom *f_SPECBOND; - class PairReaxC *reaxc; - + class PairReaxFF *reaxff; }; } diff --git a/src/REAXFF/pair_reaxff.cpp b/src/REAXFF/pair_reaxff.cpp new file mode 100644 index 0000000000..758ee70ab7 --- /dev/null +++ b/src/REAXFF/pair_reaxff.cpp @@ -0,0 +1,793 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Per-atom energy/virial added by Ray Shan (Sandia) + Fix reaxff/bonds and fix reaxff/species for pair_style reaxff added by + Ray Shan (Sandia) + Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia) +------------------------------------------------------------------------- */ + +#include "pair_reaxff.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "fix_reaxff.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" + +#include +#include +#include // for strcasecmp() + +#include "reaxff_api.h" + +using namespace LAMMPS_NS; +using namespace ReaxFF; + +static const char cite_pair_reax_c[] = + "pair reaxff command:\n\n" + "@Article{Aktulga12,\n" + " author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n" + " title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n" + " journal = {Parallel Computing},\n" + " year = 2012,\n" + " volume = 38,\n" + " pages = {245--259}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairReaxFF::PairReaxFF(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_reax_c); + + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + centroidstressflag = CENTROID_NOTAVAIL; + ghostneigh = 1; + + fix_id = utils::strdup("REAXFF_" + std::to_string(instance_me)); + + api = new API; + + api->system = new reax_system; + memset(api->system,0,sizeof(reax_system)); + api->control = new control_params; + memset(api->control,0,sizeof(control_params)); + api->data = new simulation_data; + memset(api->data,0,sizeof(simulation_data)); + api->workspace = new storage; + memset(api->workspace,0,sizeof(storage)); + memory->create(api->lists, LIST_N,"reaxff:lists"); + memset(api->lists,0,LIST_N * sizeof(reax_list)); + + api->control->me = api->system->my_rank = comm->me; + + api->system->num_nbrs = 0; + api->system->n = 0; // my atoms + api->system->N = 0; // mine + ghosts + api->system->bigN = 0; // all atoms in the system + api->system->local_cap = 0; + api->system->total_cap = 0; + api->system->my_atoms = nullptr; + api->system->pair_ptr = this; + api->system->mem_ptr = memory; + api->system->error_ptr = error; + api->control->error_ptr = error; + api->control->lmp_ptr = lmp; + + api->system->omp_active = 0; + + fix_reaxff = nullptr; + tmpid = nullptr; + tmpbo = nullptr; + + nextra = 14; + pvector = new double[nextra]; + + setup_flag = 0; + fixspecies_flag = 0; + + nmax = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairReaxFF::~PairReaxFF() +{ + if (copymode) return; + + if (fix_reaxff) modify->delete_fix(fix_id); + delete[] fix_id; + + if (setup_flag) { + + // deallocate reax data-structures + + if (api->control->tabulate) Deallocate_Lookup_Tables(api->system); + + if (api->control->hbond_cut > 0) Delete_List(api->lists+HBONDS); + Delete_List(api->lists+BONDS); + Delete_List(api->lists+THREE_BODIES); + Delete_List(api->lists+FAR_NBRS); + + DeAllocate_Workspace(api->control, api->workspace); + DeAllocate_System(api->system); + } + + delete api->system; + delete api->control; + delete api->data; + delete api->workspace; + memory->destroy(api->lists); + delete api; + + // deallocate interface storage + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cutghost); + + delete [] chi; + delete [] eta; + delete [] gamma; + } + + memory->destroy(tmpid); + memory->destroy(tmpbo); + + delete [] pvector; + +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutghost,n+1,n+1,"pair:cutghost"); + map = new int[n+1]; + + chi = new double[n+1]; + eta = new double[n+1]; + gamma = new double[n+1]; +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::settings(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal pair_style command"); + + if (comm->me == 0) { + // read name of control file or use default controls + + if (strcmp(arg[0],"NULL") == 0) { + api->control->tabulate = 0; + + api->control->bond_cut = 5.; + api->control->hbond_cut = 7.50; + api->control->thb_cut = 0.001; + api->control->thb_cutsq = 0.00001; + api->control->bg_cut = 0.3; + + api->control->nthreads = 1; + + } else Read_Control_File(arg[0], api->control); + } + MPI_Bcast(api->control,sizeof(control_params),MPI_CHAR,0,world); + + // must reset these to local values after broadcast + api->control->me = comm->me; + api->control->error_ptr = error; + api->control->lmp_ptr = lmp; + + // default values + + qeqflag = 1; + api->control->lgflag = 0; + api->control->enobondsflag = 1; + api->system->mincap = REAX_MIN_CAP; + api->system->minhbonds = REAX_MIN_HBONDS; + api->system->safezone = REAX_SAFE_ZONE; + api->system->saferzone = REAX_SAFER_ZONE; + + // process optional keywords + + int iarg = 1; + + while (iarg < narg) { + if (strcmp(arg[iarg],"checkqeq") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reaxff command"); + if (strcmp(arg[iarg+1],"yes") == 0) qeqflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) qeqflag = 0; + else error->all(FLERR,"Illegal pair_style reaxff command"); + iarg += 2; + } else if (strcmp(arg[iarg],"enobonds") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reaxff command"); + if (strcmp(arg[iarg+1],"yes") == 0) api->control->enobondsflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) api->control->enobondsflag = 0; + else error->all(FLERR,"Illegal pair_style reaxff command"); + iarg += 2; + } else if (strcmp(arg[iarg],"lgvdw") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reaxff command"); + if (strcmp(arg[iarg+1],"yes") == 0) api->control->lgflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) api->control->lgflag = 0; + else error->all(FLERR,"Illegal pair_style reaxff command"); + iarg += 2; + } else if (strcmp(arg[iarg],"safezone") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reaxff command"); + api->system->safezone = utils::numeric(FLERR,arg[iarg+1],false,lmp); + if (api->system->safezone < 0.0) + error->all(FLERR,"Illegal pair_style reaxff safezone command"); + api->system->saferzone = api->system->safezone*1.2 + 0.2; + iarg += 2; + } else if (strcmp(arg[iarg],"mincap") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reaxff command"); + api->system->mincap = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if (api->system->mincap < 0) + error->all(FLERR,"Illegal pair_style reaxff mincap command"); + iarg += 2; + } else if (strcmp(arg[iarg],"minhbonds") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reaxff command"); + api->system->minhbonds = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if (api->system->minhbonds < 0) + error->all(FLERR,"Illegal pair_style reaxff minhbonds command"); + iarg += 2; + } else error->all(FLERR,"Illegal pair_style reaxff command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::coeff(int nargs, char **args) +{ + if (!allocated) allocate(); + + if (nargs != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + + if (strcmp(args[0],"*") != 0 || strcmp(args[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // read ffield file + + Read_Force_Field(args[2], &(api->system->reax_param), api->control, world); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if "NULL" + + int itmp = 0; + int nreax_types = api->system->reax_param.num_atom_types; + for (int i = 3; i < nargs; i++) { + if (strcmp(args[i],"NULL") == 0) { + map[i-2] = -1; + itmp ++; + continue; + } + } + + int n = atom->ntypes; + + // pair_coeff element map + for (int i = 3; i < nargs; i++) + for (int j = 0; j < nreax_types; j++) + if (strcasecmp(args[i],api->system->reax_param.sbp[j].name) == 0) { + map[i-2] = j; + itmp ++; + } + + // error check + if (itmp != n) + error->all(FLERR,"Non-existent ReaxFF type"); + + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set setflag i,j for type pairs where both are mapped to elements + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style reaxff requires atom attribute q"); + + bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1) + || (modify->find_fix_by_style("^qeq/shielded") != -1)); + if (!have_qeq && qeqflag == 1) + error->all(FLERR,"Pair reaxff requires use of fix qeq/reaxff or qeq/shielded"); + + api->system->n = atom->nlocal; // my atoms + api->system->N = atom->nlocal + atom->nghost; // mine + ghosts + api->system->bigN = static_cast (atom->natoms); // all atoms in the system + api->system->wsize = comm->nprocs; + + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style reaxff requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR,"Pair style reaxff requires newton pair on"); + + // because system->bigN is an int, we cannot have more atoms than MAXSMALLINT + + if (atom->natoms > MAXSMALLINT) + error->all(FLERR,"Too many atoms for pair style reaxff"); + + // need a half neighbor list w/ Newton off and ghost neighbors + // built whenever re-neighboring occurs + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->newton = 2; + neighbor->requests[irequest]->ghost = 1; + + cutmax = MAX3(api->control->nonb_cut, api->control->hbond_cut, api->control->bond_cut); + if ((cutmax < 2.0*api->control->bond_cut) && (comm->me == 0)) + error->warning(FLERR,"Total cutoff < 2*bond cutoff. May need to use an " + "increased neighbor list skin."); + + if (fix_reaxff == nullptr) + fix_reaxff = (FixReaxFF *) modify->add_fix(fmt::format("{} all REAXFF",fix_id)); +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::setup() +{ + int oldN; + int mincap = api->system->mincap; + double safezone = api->system->safezone; + + api->system->n = atom->nlocal; // my atoms + api->system->N = atom->nlocal + atom->nghost; // mine + ghosts + oldN = api->system->N; + api->system->bigN = static_cast (atom->natoms); // all atoms in the system + + if (setup_flag == 0) { + + setup_flag = 1; + + int *num_bonds = fix_reaxff->num_bonds; + int *num_hbonds = fix_reaxff->num_hbonds; + + // determine the local and total capacity + + api->system->local_cap = MAX((int)(api->system->n * safezone), mincap); + api->system->total_cap = MAX((int)(api->system->N * safezone), mincap); + + // initialize my data structures + + PreAllocate_Space(api->system, api->workspace); + write_reax_atoms(); + + api->system->wsize = comm->nprocs; + + int num_nbrs = estimate_reax_lists(); + if (num_nbrs < 0) + error->all(FLERR,"Too many neighbors for pair style reaxff"); + + Make_List(api->system->total_cap,num_nbrs,TYP_FAR_NEIGHBOR,api->lists+FAR_NBRS); + (api->lists+FAR_NBRS)->error_ptr=error; + + write_reax_lists(); + + Initialize(api->system,api->control,api->data,api->workspace,&api->lists,world); + for (int k = 0; k < api->system->N; ++k) { + num_bonds[k] = api->system->my_atoms[k].num_bonds; + num_hbonds[k] = api->system->my_atoms[k].num_hbonds; + } + + } else { + + // fill in reax datastructures + + write_reax_atoms(); + + // reset the bond list info for new atoms + + for (int k = oldN; k < api->system->N; ++k) + Set_End_Index(k, Start_Index(k, api->lists+BONDS), api->lists+BONDS); + + // check if I need to shrink/extend my data-structs + + ReAllocate(api->system, api->control, api->data, api->workspace, &api->lists); + } +} + +/* ---------------------------------------------------------------------- */ + +double PairReaxFF::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + cutghost[i][j] = cutghost[j][i] = cutmax; + return cutmax; +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::compute(int eflag, int vflag) +{ + double evdwl,ecoul; + + // communicate num_bonds once every reneighboring + // 2 num arrays stored by fix, grab ptr to them + + if (neighbor->ago == 0) comm->forward_comm_fix(fix_reaxff); + int *num_bonds = fix_reaxff->num_bonds; + int *num_hbonds = fix_reaxff->num_hbonds; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + api->system->n = atom->nlocal; // my atoms + api->system->N = atom->nlocal + atom->nghost; // mine + ghosts + api->system->bigN = static_cast (atom->natoms); // all atoms in the system + + // setup data structures + + setup(); + + Reset(api->system, api->control, api->data, api->workspace, &api->lists); + api->workspace->realloc.num_far = write_reax_lists(); + + // forces + + Compute_Forces(api->system,api->control,api->data,api->workspace,&api->lists); + read_reax_forces(vflag); + + for (int k = 0; k < api->system->N; ++k) { + num_bonds[k] = api->system->my_atoms[k].num_bonds; + num_hbonds[k] = api->system->my_atoms[k].num_hbonds; + } + + // energies and pressure + + if (eflag_global) { + evdwl += api->data->my_en.e_bond; + evdwl += api->data->my_en.e_ov; + evdwl += api->data->my_en.e_un; + evdwl += api->data->my_en.e_lp; + evdwl += api->data->my_en.e_ang; + evdwl += api->data->my_en.e_pen; + evdwl += api->data->my_en.e_coa; + evdwl += api->data->my_en.e_hb; + evdwl += api->data->my_en.e_tor; + evdwl += api->data->my_en.e_con; + evdwl += api->data->my_en.e_vdW; + + ecoul += api->data->my_en.e_ele; + ecoul += api->data->my_en.e_pol; + + // Store the different parts of the energy + // in a list for output by compute pair command + + pvector[0] = api->data->my_en.e_bond; + pvector[1] = api->data->my_en.e_ov + api->data->my_en.e_un; + pvector[2] = api->data->my_en.e_lp; + pvector[3] = 0.0; + pvector[4] = api->data->my_en.e_ang; + pvector[5] = api->data->my_en.e_pen; + pvector[6] = api->data->my_en.e_coa; + pvector[7] = api->data->my_en.e_hb; + pvector[8] = api->data->my_en.e_tor; + pvector[9] = api->data->my_en.e_con; + pvector[10] = api->data->my_en.e_vdW; + pvector[11] = api->data->my_en.e_ele; + pvector[12] = 0.0; + pvector[13] = api->data->my_en.e_pol; + } + + if (vflag_fdotr) virial_fdotr_compute(); + +// Set internal timestep counter to that of LAMMPS + + api->data->step = update->ntimestep; + + // populate tmpid and tmpbo arrays for fix reaxff/species + int i, j; + + if (fixspecies_flag) { + if (api->system->N > nmax) { + memory->destroy(tmpid); + memory->destroy(tmpbo); + nmax = api->system->N; + memory->create(tmpid,nmax,MAXSPECBOND,"pair:tmpid"); + memory->create(tmpbo,nmax,MAXSPECBOND,"pair:tmpbo"); + } + + for (i = 0; i < api->system->N; i ++) + for (j = 0; j < MAXSPECBOND; j ++) { + tmpbo[i][j] = 0.0; + tmpid[i][j] = 0; + } + FindBond(); + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::write_reax_atoms() +{ + int *num_bonds = fix_reaxff->num_bonds; + int *num_hbonds = fix_reaxff->num_hbonds; + + if (api->system->N > api->system->total_cap) + error->all(FLERR,"Too many ghost atoms"); + + for (int i = 0; i < api->system->N; ++i) { + api->system->my_atoms[i].orig_id = atom->tag[i]; + api->system->my_atoms[i].type = map[atom->type[i]]; + api->system->my_atoms[i].x[0] = atom->x[i][0]; + api->system->my_atoms[i].x[1] = atom->x[i][1]; + api->system->my_atoms[i].x[2] = atom->x[i][2]; + api->system->my_atoms[i].q = atom->q[i]; + api->system->my_atoms[i].num_bonds = num_bonds[i]; + api->system->my_atoms[i].num_hbonds = num_hbonds[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::get_distance(rvec xj, rvec xi, double *d_sqr, rvec *dvec) +{ + (*dvec)[0] = xj[0] - xi[0]; + (*dvec)[1] = xj[1] - xi[1]; + (*dvec)[2] = xj[2] - xi[2]; + *d_sqr = SQR((*dvec)[0]) + SQR((*dvec)[1]) + SQR((*dvec)[2]); +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::set_far_nbr(far_neighbor_data *fdest, + int j, double d, rvec dvec) +{ + fdest->nbr = j; + fdest->d = d; + rvec_Copy(fdest->dvec, dvec); + ivec_MakeZero(fdest->rel_box); +} + +/* ---------------------------------------------------------------------- */ + +int PairReaxFF::estimate_reax_lists() +{ + int itr_i, itr_j, i, j; + int num_nbrs, num_marked; + int *ilist, *jlist, *numneigh, **firstneigh, *marked; + double d_sqr; + rvec dvec; + double **x; + + int mincap = api->system->mincap; + double safezone = api->system->safezone; + + x = atom->x; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + num_nbrs = 0; + num_marked = 0; + marked = (int*) calloc(api->system->N, sizeof(int)); + + int numall = list->inum + list->gnum; + + for (itr_i = 0; itr_i < numall; ++itr_i) { + i = ilist[itr_i]; + marked[i] = 1; + ++num_marked; + jlist = firstneigh[i]; + + for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { + j = jlist[itr_j]; + j &= NEIGHMASK; + get_distance(x[j], x[i], &d_sqr, &dvec); + + if (d_sqr <= SQR(api->control->nonb_cut)) + ++num_nbrs; + } + } + + free(marked); + + return static_cast (MAX(num_nbrs*safezone, mincap*REAX_MIN_NBRS)); +} + +/* ---------------------------------------------------------------------- */ + +int PairReaxFF::write_reax_lists() +{ + int itr_i, itr_j, i, j; + int num_nbrs; + int *ilist, *jlist, *numneigh, **firstneigh; + double d_sqr, cutoff_sqr; + rvec dvec; + double *dist, **x; + reax_list *far_nbrs; + far_neighbor_data *far_list; + + x = atom->x; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + far_nbrs = api->lists + FAR_NBRS; + far_list = far_nbrs->select.far_nbr_list; + + num_nbrs = 0; + int inum = list->inum; + dist = (double*) calloc(api->system->N, sizeof(double)); + + int numall = list->inum + list->gnum; + + for (itr_i = 0; itr_i < numall; ++itr_i) { + i = ilist[itr_i]; + jlist = firstneigh[i]; + Set_Start_Index(i, num_nbrs, far_nbrs); + + if (i < inum) + cutoff_sqr = SQR(api->control->nonb_cut); + else + cutoff_sqr = SQR(api->control->bond_cut); + + for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { + j = jlist[itr_j]; + j &= NEIGHMASK; + get_distance(x[j], x[i], &d_sqr, &dvec); + + if (d_sqr <= (cutoff_sqr)) { + dist[j] = sqrt(d_sqr); + set_far_nbr(&far_list[num_nbrs], j, dist[j], dvec); + ++num_nbrs; + } + } + Set_End_Index(i, num_nbrs, far_nbrs); + } + + free(dist); + + return num_nbrs; +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::read_reax_forces(int /*vflag*/) +{ + for (int i = 0; i < api->system->N; ++i) { + api->system->my_atoms[i].f[0] = api->workspace->f[i][0]; + api->system->my_atoms[i].f[1] = api->workspace->f[i][1]; + api->system->my_atoms[i].f[2] = api->workspace->f[i][2]; + + atom->f[i][0] += -api->workspace->f[i][0]; + atom->f[i][1] += -api->workspace->f[i][1]; + atom->f[i][2] += -api->workspace->f[i][2]; + } + +} + +/* ---------------------------------------------------------------------- */ + +void *PairReaxFF::extract(const char *str, int &dim) +{ + dim = 1; + if (strcmp(str,"chi") == 0 && chi) { + for (int i = 1; i <= atom->ntypes; i++) + if (map[i] >= 0) chi[i] = api->system->reax_param.sbp[map[i]].chi; + else chi[i] = 0.0; + return (void *) chi; + } + if (strcmp(str,"eta") == 0 && eta) { + for (int i = 1; i <= atom->ntypes; i++) + if (map[i] >= 0) eta[i] = api->system->reax_param.sbp[map[i]].eta; + else eta[i] = 0.0; + return (void *) eta; + } + if (strcmp(str,"gamma") == 0 && gamma) { + for (int i = 1; i <= atom->ntypes; i++) + if (map[i] >= 0) gamma[i] = api->system->reax_param.sbp[map[i]].gamma; + else gamma[i] = 0.0; + return (void *) gamma; + } + return nullptr; +} + +/* ---------------------------------------------------------------------- */ + +double PairReaxFF::memory_usage() +{ + double bytes = 0.0; + + // From pair_reax_c + bytes += (double)1.0 * api->system->N * sizeof(int); + bytes += (double)1.0 * api->system->N * sizeof(double); + + // From reaxff_allocate: BO + bytes += (double)1.0 * api->system->total_cap * sizeof(reax_atom); + bytes += (double)19.0 * api->system->total_cap * sizeof(double); + bytes += (double)3.0 * api->system->total_cap * sizeof(int); + + // From reaxff_lists + bytes += (double)2.0 * api->lists->n * sizeof(int); + bytes += (double)api->lists->num_intrs * sizeof(three_body_interaction_data); + bytes += (double)api->lists->num_intrs * sizeof(bond_data); + bytes += (double)api->lists->num_intrs * sizeof(far_neighbor_data); + bytes += (double)api->lists->num_intrs * sizeof(hbond_data); + + if (fixspecies_flag) + bytes += (double)2 * nmax * MAXSPECBOND * sizeof(double); + + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void PairReaxFF::FindBond() +{ + int i, j, pj, nj; + double bo_tmp, bo_cut; + + bond_data *bo_ij; + bo_cut = 0.10; + + for (i = 0; i < api->system->n; i++) { + nj = 0; + for (pj = Start_Index(i, api->lists); pj < End_Index(i, api->lists); ++pj) { + bo_ij = &(api->lists->select.bond_list[pj]); + j = bo_ij->nbr; + if (j < i) continue; + + bo_tmp = bo_ij->bo_data.BO; + + if (bo_tmp >= bo_cut) { + tmpid[i][nj] = j; + tmpbo[i][nj] = bo_tmp; + nj ++; + if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in reaxff_defs.h"); + } + } + } +} diff --git a/src/USER-REAXC/pair_reaxc.h b/src/REAXFF/pair_reaxff.h similarity index 79% rename from src/USER-REAXC/pair_reaxc.h rename to src/REAXFF/pair_reaxff.h index c8293ef417..f9f3b636c3 100644 --- a/src/USER-REAXC/pair_reaxc.h +++ b/src/REAXFF/pair_reaxff.h @@ -24,22 +24,27 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(reax/c,PairReaxC); +PairStyle(reaxff,PairReaxFF); +PairStyle(reax/c,PairReaxFF); // clang-format on #else -#ifndef LMP_PAIR_REAXC_H -#define LMP_PAIR_REAXC_H +#ifndef LMP_PAIR_REAXFF_H +#define LMP_PAIR_REAXFF_H #include "pair.h" -#include "reaxc_types.h" + +namespace ReaxFF { + struct API; + struct far_neighbor_data; +} namespace LAMMPS_NS { -class PairReaxC : public Pair { +class PairReaxFF : public Pair { public: - PairReaxC(class LAMMPS *); - ~PairReaxC(); + PairReaxFF(class LAMMPS *); + ~PairReaxFF(); void compute(int, int); void settings(int, char **); void coeff(int, char **); @@ -50,20 +55,13 @@ class PairReaxC : public Pair { int **tmpid; double **tmpbo,**tmpr; - control_params *control; - reax_system *system; - output_controls *out_control; - simulation_data *data; - storage *workspace; - reax_list *lists; - mpi_datatypes *mpi_data; + ReaxFF::API *api; + typedef double rvec[3]; - bigint ngroup; - - protected: +protected: char *fix_id; double cutmax; - class FixReaxC *fix_reax; + class FixReaxFF *fix_reaxff; double *chi,*eta,*gamma; int qeqflag; @@ -76,7 +74,7 @@ class PairReaxC : public Pair { void create_fix(); void write_reax_atoms(); void get_distance(rvec, rvec, double *, rvec *); - void set_far_nbr(far_neighbor_data *, int, double, rvec); + void set_far_nbr(ReaxFF::far_neighbor_data *, int, double, rvec); int estimate_reax_lists(); int write_reax_lists(); void read_reax_forces(int); @@ -84,7 +82,6 @@ class PairReaxC : public Pair { int nmax; void FindBond(); double memory_usage(); - }; } @@ -97,7 +94,7 @@ class PairReaxC : public Pair { E: Too many ghost atoms Number of ghost atoms has increased too much during simulation and has exceeded -the size of reax/c arrays. Increase safe_zone and min_cap in pair_style reax/c +the size of reaxff arrays. Increase safe_zone and min_cap in pair_style reaxff command */ diff --git a/src/REAXFF/reaxff_allocate.cpp b/src/REAXFF/reaxff_allocate.cpp new file mode 100644 index 0000000000..cbb53420ba --- /dev/null +++ b/src/REAXFF/reaxff_allocate.cpp @@ -0,0 +1,322 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "error.h" +#include "memory.h" +#include "pair.h" + +namespace ReaxFF { + + /* allocate space for my_atoms + important: we cannot know the exact number of atoms that will fall into a + process's box throughout the whole simulation. therefore + we need to make upper bound estimates for various data structures */ + void PreAllocate_Space(reax_system *system, storage * workspace) + { + const int mincap = system->mincap; + const double safezone = system->safezone; + + // determine the local and total capacity + + system->local_cap = MAX((int)(system->n * safezone), mincap); + system->total_cap = MAX((int)(system->N * safezone), mincap); + + system->my_atoms = (reax_atom*) scalloc(system->error_ptr, + system->total_cap, sizeof(reax_atom), "my_atoms"); + + // Nullify some arrays only used in omp styles + // Should be safe to do here since called in pair->setup(); + + workspace->CdDeltaReduction = nullptr; + workspace->forceReduction = nullptr; + workspace->valence_angle_atom_myoffset = nullptr; + } + + /************* system *************/ + + void DeAllocate_System(reax_system *system) + { + auto error = system->error_ptr; + auto memory = system->mem_ptr; + + // deallocate the atom list + sfree(error, system->my_atoms, "system->my_atoms"); + + // deallocate the ffield parameters storage + memory->destroy(system->reax_param.gp.l); + memory->destroy(system->reax_param.sbp); + memory->destroy(system->reax_param.tbp); + memory->destroy(system->reax_param.thbp); + memory->destroy(system->reax_param.hbp); + memory->destroy(system->reax_param.fbp); + } + + /************* workspace *************/ + void DeAllocate_Workspace(control_params *control, storage *workspace) + { + if (!workspace->allocated) + return; + + workspace->allocated = 0; + auto error = control->error_ptr; + + /* bond order storage */ + sfree(error, workspace->total_bond_order, "total_bo"); + sfree(error, workspace->Deltap, "Deltap"); + sfree(error, workspace->Deltap_boc, "Deltap_boc"); + sfree(error, workspace->dDeltap_self, "dDeltap_self"); + sfree(error, workspace->Delta, "Delta"); + sfree(error, workspace->Delta_lp, "Delta_lp"); + sfree(error, workspace->Delta_lp_temp, "Delta_lp_temp"); + sfree(error, workspace->dDelta_lp, "dDelta_lp"); + sfree(error, workspace->dDelta_lp_temp, "dDelta_lp_temp"); + sfree(error, workspace->Delta_e, "Delta_e"); + sfree(error, workspace->Delta_boc, "Delta_boc"); + sfree(error, workspace->Delta_val, "Delta_val"); + sfree(error, workspace->nlp, "nlp"); + sfree(error, workspace->nlp_temp, "nlp_temp"); + sfree(error, workspace->Clp, "Clp"); + sfree(error, workspace->vlpex, "vlpex"); + sfree(error, workspace->bond_mark, "bond_mark"); + + /* force related storage */ + sfree(error, workspace->f, "f"); + sfree(error, workspace->CdDelta, "CdDelta"); + + /* reductions */ + + if (workspace->CdDeltaReduction) + sfree(error, workspace->CdDeltaReduction, "cddelta_reduce"); + if (workspace->forceReduction) + sfree(error, workspace->forceReduction, "f_reduce"); + if (workspace->valence_angle_atom_myoffset) + sfree(error, workspace->valence_angle_atom_myoffset, "valence_angle_atom_myoffset"); + } + + void Allocate_Workspace(control_params *control, storage *workspace, int total_cap) + { + int total_real, total_rvec; + auto error = control->error_ptr; + + workspace->allocated = 1; + total_real = total_cap * sizeof(double); + total_rvec = total_cap * sizeof(rvec); + + /* bond order related storage */ + workspace->total_bond_order = (double*) smalloc(error, total_real, "total_bo"); + workspace->Deltap = (double*) smalloc(error, total_real, "Deltap"); + workspace->Deltap_boc = (double*) smalloc(error, total_real, "Deltap_boc"); + workspace->dDeltap_self = (rvec*) smalloc(error, total_rvec, "dDeltap_self"); + workspace->Delta = (double*) smalloc(error, total_real, "Delta"); + workspace->Delta_lp = (double*) smalloc(error, total_real, "Delta_lp"); + workspace->Delta_lp_temp = (double*) smalloc(error, total_real, "Delta_lp_temp"); + workspace->dDelta_lp = (double*) smalloc(error, total_real, "dDelta_lp"); + workspace->dDelta_lp_temp = (double*) smalloc(error, total_real, "dDelta_lp_temp"); + workspace->Delta_e = (double*) smalloc(error, total_real, "Delta_e"); + workspace->Delta_boc = (double*) smalloc(error, total_real, "Delta_boc"); + workspace->Delta_val = (double*) smalloc(error, total_real, "Delta_val"); + workspace->nlp = (double*) smalloc(error, total_real, "nlp"); + workspace->nlp_temp = (double*) smalloc(error, total_real, "nlp_temp"); + workspace->Clp = (double*) smalloc(error, total_real, "Clp"); + workspace->vlpex = (double*) smalloc(error, total_real, "vlpex"); + workspace->bond_mark = (int*) scalloc(error, total_cap, sizeof(int), "bond_mark"); + + /* force related storage */ + workspace->f = (rvec*) scalloc(error, total_cap, sizeof(rvec), "f"); + workspace->CdDelta = (double*) scalloc(error, total_cap, sizeof(double), "CdDelta"); + + // storage for reductions with multiple threads + + workspace->CdDeltaReduction = (double *) scalloc(error, + sizeof(double), (rc_bigint)total_cap*control->nthreads, "cddelta_reduce"); + workspace->forceReduction = (rvec *) scalloc(error, + sizeof(rvec), (rc_bigint)total_cap*control->nthreads, "forceReduction"); + workspace->valence_angle_atom_myoffset = (int *) scalloc(error, + sizeof(int), total_cap, "valence_angle_atom_myoffset"); + } + + + static void Reallocate_Neighbor_List(reax_list *far_nbrs, int n, int num_intrs) + { + Delete_List(far_nbrs); + Make_List(n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs); + } + + static int Reallocate_HBonds_List(reax_system *system, reax_list *hbonds) + { + int i, total_hbonds; + + int mincap = system->mincap; + double saferzone = system->saferzone; + + total_hbonds = 0; + for (i = 0; i < system->n; ++i) + if ((system->my_atoms[i].Hindex) >= 0) { + total_hbonds += system->my_atoms[i].num_hbonds; + } + total_hbonds = (int)(MAX(total_hbonds*saferzone, mincap*system->minhbonds)); + + Delete_List(hbonds); + Make_List(system->Hcap, total_hbonds, TYP_HBOND, hbonds); + + return total_hbonds; + } + + static void Reallocate_Bonds_List(control_params *control, reax_system *system, + reax_list *bonds, int *total_bonds, int *est_3body) + { + int i; + + int mincap = system->mincap; + double safezone = system->safezone; + + *total_bonds = 0; + *est_3body = 0; + for (i = 0; i < system->N; ++i) { + *est_3body += SQR(system->my_atoms[i].num_bonds); + *total_bonds += system->my_atoms[i].num_bonds; + } + *total_bonds = (int)(MAX(*total_bonds * safezone, mincap*MIN_BONDS)); + + if (system->omp_active) + for (i = 0; i < bonds->num_intrs; ++i) + sfree(system->error_ptr, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); + + Delete_List(bonds); + Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds); + + if (system->omp_active) + for (i = 0; i < bonds->num_intrs; ++i) + bonds->select.bond_list[i].bo_data.CdboReduction = + (double*) smalloc(system->error_ptr, sizeof(double)*control->nthreads, "CdboReduction"); + } + + void ReAllocate(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, reax_list **lists) + { + int num_bonds, est_3body, Hflag; + int newsize; + reax_list *far_nbrs; + + int mincap = system->mincap; + double safezone = system->safezone; + double saferzone = system->saferzone; + + auto error = system->error_ptr; + reallocate_data *wsr = &(workspace->realloc); + + if (system->n >= DANGER_ZONE * system->local_cap || + (0 && system->n <= LOOSE_ZONE * system->local_cap)) { + system->local_cap = MAX((int)(system->n * safezone), mincap); + } + + int Nflag = 0; + if (system->N >= DANGER_ZONE * system->total_cap || + (0 && system->N <= LOOSE_ZONE * system->total_cap)) { + Nflag = 1; + system->total_cap = MAX((int)(system->N * safezone), mincap); + } + + if (Nflag) { + /* system */ + system->my_atoms = (reax_atom *)::realloc(system->my_atoms, + system->total_cap*sizeof(reax_atom)); + /* workspace */ + DeAllocate_Workspace(control, workspace); + Allocate_Workspace(control, workspace, system->total_cap); + } + + /* far neighbors */ + + far_nbrs = *lists + FAR_NBRS; + + if (Nflag || wsr->num_far >= far_nbrs->num_intrs * DANGER_ZONE) { + if (wsr->num_far > far_nbrs->num_intrs) + error->one(FLERR,fmt::format("step{}: ran out of space on far_nbrs: top={}, max={}", + data->step, wsr->num_far, far_nbrs->num_intrs)); + + newsize = static_cast + (MAX(wsr->num_far*safezone, mincap*REAX_MIN_NBRS)); + + Reallocate_Neighbor_List(far_nbrs, system->total_cap, newsize); + wsr->num_far = 0; + } + + /* hydrogen bonds list */ + if (control->hbond_cut > 0) { + Hflag = 0; + if (system->numH >= DANGER_ZONE * system->Hcap || + (0 && system->numH <= LOOSE_ZONE * system->Hcap)) { + Hflag = 1; + system->Hcap = int(MAX(system->numH * saferzone, mincap)); + } + + if (Hflag || wsr->hbonds) { + Reallocate_HBonds_List(system, (*lists)+HBONDS); + wsr->hbonds = 0; + } + } + + /* bonds list */ + num_bonds = est_3body = -1; + if (Nflag || wsr->bonds) { + Reallocate_Bonds_List(control, system, (*lists)+BONDS, &num_bonds, &est_3body); + wsr->bonds = 0; + wsr->num_3body = MAX(wsr->num_3body, est_3body) * 2; + + + if (system->omp_active) { + int nthreads = control->nthreads; + reax_list *bonds = (*lists)+BONDS; + + for (int i = 0; i < bonds->num_intrs; ++i) { + sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction, + "CdboReduction"); + + bonds->select.bond_list[i].bo_data.CdboReduction = + (double*) smalloc(error, sizeof(double)*nthreads, "CdboReduction"); + } + } + } + + /* 3-body list */ + if (wsr->num_3body > 0) { + Delete_List((*lists)+THREE_BODIES); + + if (num_bonds == -1) + num_bonds = ((*lists)+BONDS)->num_intrs; + + wsr->num_3body = (int)(MAX(wsr->num_3body*safezone, MIN_3BODIES)); + + Make_List(num_bonds, wsr->num_3body, TYP_THREE_BODY, + (*lists)+THREE_BODIES); + wsr->num_3body = -1; + } + } +} diff --git a/src/REAXFF/reaxff_api.h b/src/REAXFF/reaxff_api.h new file mode 100644 index 0000000000..540012ab8f --- /dev/null +++ b/src/REAXFF/reaxff_api.h @@ -0,0 +1,226 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hasan Metin Aktulga, Purdue University + (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov) + + Heavily modified and adapted for LAMMPS by the LAMMPS developers. +------------------------------------------------------------------------- */ + +#ifndef LMP_REAXFF_API_H +#define LMP_REAXFF_API_H + +#include "reaxff_types.h" + +#include + +namespace ReaxFF +{ + // per instance data + struct API { + control_params *control; + reax_system *system; + simulation_data *data; + storage *workspace; + reax_list *lists; + }; + + // exported Functions + + // allocate + + extern void Allocate_Workspace(control_params *, storage *, int); + extern void DeAllocate_System(reax_system *); + extern void DeAllocate_Workspace(control_params *, storage *); + extern void PreAllocate_Space(reax_system *, storage *); + extern void ReAllocate(reax_system *, control_params *, simulation_data *, + storage *, reax_list **); + + // bond orders + + extern void BO(reax_system *, storage *, reax_list **); + extern int BOp(storage *, reax_list *, double, int, int, far_neighbor_data *, + single_body_parameters *, single_body_parameters *, + two_body_parameters *); + extern void Add_dBond_to_Forces(reax_system*, int, int, storage*, reax_list**); + + // bonds + + extern void Bonds(reax_system *, simulation_data *, storage *, reax_list **); + + // control + + extern void Read_Control_File(const char *, control_params *); + + // ffield + + extern void Read_Force_Field(const char *, reax_interaction *, + control_params *, MPI_Comm); + + // forces + + extern void Compute_Forces(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + extern void Estimate_Storages(reax_system *, control_params *, reax_list **, + int *, int *, int *, int *); + + // hydrogen bonds + + extern void Hydrogen_Bonds(reax_system *, simulation_data *, storage *, reax_list **); + + // init md + + extern void Init_System(reax_system *, control_params *); + extern void Init_Simulation_Data(simulation_data *); + extern void Init_Workspace(reax_system *, control_params *, storage *); + extern void Initialize(reax_system *, control_params *, simulation_data *, + storage *, reax_list **, MPI_Comm); + + // lists + + extern void Make_List(int, int, int, reax_list *); + extern void Delete_List(reax_list*); + + inline int Start_Index(int i, reax_list *l) { return l->index[i]; } + inline int End_Index(int i, reax_list *l) { return l->end_index[i]; } + inline void Set_Start_Index(int i, int val, reax_list *l) { + l->index[i] = val; + } + inline void Set_End_Index(int i, int val, reax_list *l) { + l->end_index[i] = val; + } + inline int Num_Entries(int i, reax_list *l) { + return l->end_index[i] - l->index[i]; + } + + // lookup + + extern void Init_Lookup_Tables(reax_system *, control_params *, + storage *, MPI_Comm); + extern void Deallocate_Lookup_Tables(reax_system *); + extern void Natural_Cubic_Spline(LAMMPS_NS::Error*, const double *, + const double *, cubic_spline_coef *, + unsigned int); + extern void Complete_Cubic_Spline(LAMMPS_NS::Error*, const double *, + const double *, double v0, double vlast, + cubic_spline_coef *coef, unsigned int n); + + // multi body + + extern void Atom_Energy(reax_system *, control_params *, simulation_data *, + storage *, reax_list **); + + // nonbonded + + extern void Compute_Polarization_Energy(reax_system *, simulation_data *); + extern void vdW_Coulomb_Energy(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + extern void Tabulated_vdW_Coulomb_Energy(reax_system *, control_params *, + simulation_data *, storage *, + reax_list **); + extern void LR_vdW_Coulomb(reax_system *, storage *, control_params *, + int, int, double, LR_data *); + + // reset tools + + extern void Reset(reax_system *, control_params *, simulation_data *, + storage *, reax_list **); + extern void Reset_Simulation_Data(simulation_data *); + extern void Reset_Workspace(reax_system *, storage *); + + // toolbox + + extern void *scalloc(LAMMPS_NS::Error *, rc_bigint, rc_bigint, const std::string &); + extern void *smalloc(LAMMPS_NS::Error *, rc_bigint, const std::string &); + extern void sfree(LAMMPS_NS::Error *, void *, const std::string &); + + // torsion angles + + extern double Calculate_Omega(rvec, double, rvec, double, rvec, double, + rvec, double, three_body_interaction_data *, + three_body_interaction_data *, rvec, rvec, + rvec, rvec); + extern void Torsion_Angles(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + + // valence angles + + extern void Calculate_Theta(rvec, double, rvec, double, double *, double *); + extern void Calculate_dCos_Theta(rvec, double, rvec, double, + rvec *, rvec *, rvec *); + extern void Valence_Angles(reax_system *, control_params *, + simulation_data *, storage *, reax_list **); + + // vector + + inline void rvec_Add(rvec ret, rvec v) { + ret[0] += v[0]; ret[1] += v[1]; ret[2] += v[2]; + } + + inline void rvec_Copy(rvec dest, rvec src) { + dest[0] = src[0]; dest[1] = src[1]; dest[2] = src[2]; + } + + inline void rvec_Cross(rvec ret, rvec v1, rvec v2) + { + ret[0] = v1[1] * v2[2] - v1[2] * v2[1]; + ret[1] = v1[2] * v2[0] - v1[0] * v2[2]; + ret[2] = v1[0] * v2[1] - v1[1] * v2[0]; + } + + inline double rvec_Dot(rvec v1, rvec v2) { + return v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]; + } + + inline double rvec_Norm(rvec v) { + return sqrt(SQR(v[0]) + SQR(v[1]) + SQR(v[2])); + } + + inline void rvec_Scale(rvec ret, double c, rvec v) { + ret[0] = c * v[0]; ret[1] = c * v[1]; ret[2] = c * v[2]; + } + + inline void rvec_ScaledAdd(rvec ret, double c, rvec v) { + ret[0] += c * v[0], ret[1] += c * v[1], ret[2] += c * v[2]; + } + + inline void rvec_ScaledSum(rvec ret, double c1, rvec v1 ,double c2, rvec v2) + { + ret[0] = c1 * v1[0] + c2 * v2[0]; + ret[1] = c1 * v1[1] + c2 * v2[1]; + ret[2] = c1 * v1[2] + c2 * v2[2]; + } + + inline void ivec_MakeZero(ivec v) { v[0] = v[1] = v[2] = 0; } + + inline void ivec_Copy(ivec dest, ivec src) { + dest[0] = src[0], dest[1] = src[1], dest[2] = src[2]; + } + + inline void ivec_Scale(ivec dest, double C, ivec src) + { + dest[0] = (int)(C * src[0]); + dest[1] = (int)(C * src[1]); + dest[2] = (int)(C * src[2]); + } + + inline void ivec_Sum(ivec dest, ivec v1, ivec v2) + { + dest[0] = v1[0] + v2[0]; + dest[1] = v1[1] + v2[1]; + dest[2] = v1[2] + v2[2]; + } +} + +#endif diff --git a/src/REAXFF/reaxff_bond_orders.cpp b/src/REAXFF/reaxff_bond_orders.cpp new file mode 100644 index 0000000000..d827e3753d --- /dev/null +++ b/src/REAXFF/reaxff_bond_orders.cpp @@ -0,0 +1,469 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "pair.h" + +#include + +namespace ReaxFF { + void Add_dBond_to_Forces(reax_system *system, int i, int pj, storage *workspace, reax_list **lists) + { + reax_list *bonds = (*lists) + BONDS; + bond_data *nbr_j, *nbr_k; + bond_order_data *bo_ij, *bo_ji; + dbond_coefficients coef; + int pk, k, j; + + /* Virial Tallying variables */ + rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp; + + /* Initializations */ + nbr_j = &(bonds->select.bond_list[pj]); + j = nbr_j->nbr; + bo_ij = &(nbr_j->bo_data); + bo_ji = &(bonds->select.bond_list[nbr_j->sym_index].bo_data); + + double c = bo_ij->Cdbo + bo_ji->Cdbo; + coef.C1dbo = bo_ij->C1dbo * c; + coef.C2dbo = bo_ij->C2dbo * c; + coef.C3dbo = bo_ij->C3dbo * c; + + c = bo_ij->Cdbopi + bo_ji->Cdbopi; + coef.C1dbopi = bo_ij->C1dbopi * c; + coef.C2dbopi = bo_ij->C2dbopi * c; + coef.C3dbopi = bo_ij->C3dbopi * c; + coef.C4dbopi = bo_ij->C4dbopi * c; + + c = bo_ij->Cdbopi2 + bo_ji->Cdbopi2; + coef.C1dbopi2 = bo_ij->C1dbopi2 * c; + coef.C2dbopi2 = bo_ij->C2dbopi2 * c; + coef.C3dbopi2 = bo_ij->C3dbopi2 * c; + coef.C4dbopi2 = bo_ij->C4dbopi2 * c; + + c = workspace->CdDelta[i] + workspace->CdDelta[j]; + coef.C1dDelta = bo_ij->C1dbo * c; + coef.C2dDelta = bo_ij->C2dbo * c; + coef.C3dDelta = bo_ij->C3dbo * c; + + c = (coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2); + rvec_Scale( temp, c, bo_ij->dBOp); + + c = (coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2); + rvec_ScaledAdd(temp, c, workspace->dDeltap_self[i]); + + rvec_ScaledAdd(temp, coef.C1dbopi, bo_ij->dln_BOp_pi); + rvec_ScaledAdd(temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2); + + rvec_Add(workspace->f[i], temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fi_tmp, -0.5, temp); + rvec_ScaledSum(delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x); + system->pair_ptr->v_tally2_newton(i,fi_tmp,delij); + } + + c = -(coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2); + rvec_Scale( temp, c, bo_ij->dBOp); + + c = (coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2); + rvec_ScaledAdd(temp, c, workspace->dDeltap_self[j]); + + rvec_ScaledAdd(temp, -coef.C1dbopi, bo_ij->dln_BOp_pi); + rvec_ScaledAdd(temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2); + + rvec_Add(workspace->f[j], temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fj_tmp, -0.5, temp); + rvec_ScaledSum(delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x); + system->pair_ptr->v_tally2_newton(j,fj_tmp,delji); + } + + // forces on k: i neighbor + for (pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk) { + nbr_k = &(bonds->select.bond_list[pk]); + k = nbr_k->nbr; + + const double c = -(coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2); + rvec_Scale(temp, c, nbr_k->bo_data.dBOp); + + rvec_Add(workspace->f[k], temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fk_tmp, -0.5, temp); + rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); + system->pair_ptr->v_tally2_newton(k,fk_tmp,delki); + rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); + system->pair_ptr->v_tally2_newton(k,fk_tmp,delkj); + } + } + + // forces on k: j neighbor + for (pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk) { + nbr_k = &(bonds->select.bond_list[pk]); + k = nbr_k->nbr; + + const double c = -(coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2); + rvec_Scale(temp, c, nbr_k->bo_data.dBOp); + + rvec_Add(workspace->f[k], temp); + + if (system->pair_ptr->vflag_either) { + rvec_Scale(fk_tmp, -0.5, temp); + rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); + system->pair_ptr->v_tally2_newton(k,fk_tmp,delki); + rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); + system->pair_ptr->v_tally2_newton(k,fk_tmp,delkj); + } + } + } + + int BOp(storage *workspace, reax_list *bonds, double bo_cut, + int i, int btop_i, far_neighbor_data *nbr_pj, + single_body_parameters *sbp_i, single_body_parameters *sbp_j, + two_body_parameters *twbp) { + int j, btop_j; + double rr2, C12, C34, C56; + double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; + double BO, BO_s, BO_pi, BO_pi2; + bond_data *ibond, *jbond; + bond_order_data *bo_ij, *bo_ji; + + j = nbr_pj->nbr; + rr2 = 1.0 / SQR(nbr_pj->d); + + if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { + C12 = twbp->p_bo1 * pow(nbr_pj->d / twbp->r_s, twbp->p_bo2); + BO_s = (1.0 + bo_cut) * exp(C12); + } else BO_s = C12 = 0.0; + + if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { + C34 = twbp->p_bo3 * pow(nbr_pj->d / twbp->r_p, twbp->p_bo4); + BO_pi = exp(C34); + } else BO_pi = C34 = 0.0; + + if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { + C56 = twbp->p_bo5 * pow(nbr_pj->d / twbp->r_pp, twbp->p_bo6); + BO_pi2= exp(C56); + } else BO_pi2 = C56 = 0.0; + + /* Initially BO values are the uncorrected ones, page 1 */ + BO = BO_s + BO_pi + BO_pi2; + + if (BO >= bo_cut) { + /****** bonds i-j and j-i ******/ + ibond = &(bonds->select.bond_list[btop_i]); + btop_j = End_Index(j, bonds); + jbond = &(bonds->select.bond_list[btop_j]); + + ibond->nbr = j; + jbond->nbr = i; + ibond->d = nbr_pj->d; + jbond->d = nbr_pj->d; + rvec_Copy(ibond->dvec, nbr_pj->dvec); + rvec_Scale(jbond->dvec, -1, nbr_pj->dvec); + ivec_Copy(ibond->rel_box, nbr_pj->rel_box); + ivec_Scale(jbond->rel_box, -1, nbr_pj->rel_box); + ibond->dbond_index = btop_i; + jbond->dbond_index = btop_i; + ibond->sym_index = btop_j; + jbond->sym_index = btop_i; + Set_End_Index(j, btop_j+1, bonds); + + bo_ij = &(ibond->bo_data); + bo_ji = &(jbond->bo_data); + bo_ji->BO = bo_ij->BO = BO; + bo_ji->BO_s = bo_ij->BO_s = BO_s; + bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; + bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; + + /* Bond Order page2-3, derivative of total bond order prime */ + Cln_BOp_s = twbp->p_bo2 * C12 * rr2; + Cln_BOp_pi = twbp->p_bo4 * C34 * rr2; + Cln_BOp_pi2 = twbp->p_bo6 * C56 * rr2; + + /* Only dln_BOp_xx wrt. dr_i is stored here, note that + dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ + rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec); + rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec); + rvec_Scale(bo_ij->dln_BOp_pi2, + -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec); + rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); + rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi); + rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2); + + rvec_Scale(bo_ij->dBOp, + -(bo_ij->BO_s * Cln_BOp_s + + bo_ij->BO_pi * Cln_BOp_pi + + bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec); + rvec_Scale(bo_ji->dBOp, -1., bo_ij->dBOp); + + rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp); + rvec_Add(workspace->dDeltap_self[j], bo_ji->dBOp); + + bo_ij->BO_s -= bo_cut; + bo_ij->BO -= bo_cut; + bo_ji->BO_s -= bo_cut; + bo_ji->BO -= bo_cut; + workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp + workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp + bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; + bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; + + return 1; + } + return 0; + } + + void BO(reax_system *system, storage *workspace, reax_list **lists) + { + int i, j, pj, type_i, type_j; + int start_i, end_i, sym_index; + double val_i, Deltap_i, Deltap_boc_i; + double val_j, Deltap_j, Deltap_boc_j; + double f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5; + double exp_p1i, exp_p2i, exp_p1j, exp_p2j; + double temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji; + double Cf45_ij, Cf45_ji, p_lp1; //u_ij, u_ji + double A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji; + double explp1, p_boc1, p_boc2; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + bond_order_data *bo_ij, *bo_ji; + reax_list *bonds = (*lists) + BONDS; + + p_boc1 = system->reax_param.gp.l[0]; + p_boc2 = system->reax_param.gp.l[1]; + + /* Calculate Deltaprime, Deltaprime_boc values */ + for (i = 0; i < system->N; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + sbp_i = &(system->reax_param.sbp[type_i]); + workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency; + workspace->Deltap_boc[i] = + workspace->total_bond_order[i] - sbp_i->valency_val; + + workspace->total_bond_order[i] = 0; + } + + /* Corrected Bond Order calculations */ + for (i = 0; i < system->N; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + sbp_i = &(system->reax_param.sbp[type_i]); + val_i = sbp_i->valency; + Deltap_i = workspace->Deltap[i]; + Deltap_boc_i = workspace->Deltap_boc[i]; + start_i = Start_Index(i, bonds); + end_i = End_Index(i, bonds); + + for (pj = start_i; pj < end_i; ++pj) { + j = bonds->select.bond_list[pj].nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + bo_ij = &(bonds->select.bond_list[pj].bo_data); + // fprintf(stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO); + + if (i < j || workspace->bond_mark[j] > 3) { + twbp = &(system->reax_param.tbp[type_i][type_j]); + + if (twbp->ovc < 0.001 && twbp->v13cor < 0.001) { + bo_ij->C1dbo = 1.000000; + bo_ij->C2dbo = 0.000000; + bo_ij->C3dbo = 0.000000; + + bo_ij->C1dbopi = 1.000000; + bo_ij->C2dbopi = 0.000000; + bo_ij->C3dbopi = 0.000000; + bo_ij->C4dbopi = 0.000000; + + bo_ij->C1dbopi2 = 1.000000; + bo_ij->C2dbopi2 = 0.000000; + bo_ij->C3dbopi2 = 0.000000; + bo_ij->C4dbopi2 = 0.000000; + + } else { + val_j = system->reax_param.sbp[type_j].valency; + Deltap_j = workspace->Deltap[j]; + Deltap_boc_j = workspace->Deltap_boc[j]; + + /* on page 1 */ + if (twbp->ovc >= 0.001) { + /* Correction for overcoordination */ + exp_p1i = exp(-p_boc1 * Deltap_i); + exp_p2i = exp(-p_boc2 * Deltap_i); + exp_p1j = exp(-p_boc1 * Deltap_j); + exp_p2j = exp(-p_boc2 * Deltap_j); + + f2 = exp_p1i + exp_p1j; + f3 = -1.0 / p_boc2 * log(0.5 * (exp_p2i + exp_p2j)); + f1 = 0.5 * ((val_i + f2)/(val_i + f2 + f3) + + (val_j + f2)/(val_j + f2 + f3)); + + temp = f2 + f3; + u1_ij = val_i + temp; + u1_ji = val_j + temp; + Cf1A_ij = 0.5 * f3 * (1.0 / SQR(u1_ij) + + 1.0 / SQR(u1_ji)); + Cf1B_ij = -0.5 * ((u1_ij - f3) / SQR(u1_ij) + + (u1_ji - f3) / SQR(u1_ji)); + + Cf1_ij = 0.50 * (-p_boc1 * exp_p1i / u1_ij - + ((val_i+f2) / SQR(u1_ij)) * + (-p_boc1 * exp_p1i + + exp_p2i / (exp_p2i + exp_p2j)) + + -p_boc1 * exp_p1i / u1_ji - + ((val_j+f2) / SQR(u1_ji)) * + (-p_boc1 * exp_p1i + + exp_p2i / (exp_p2i + exp_p2j))); + + + Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j + + Cf1B_ij * exp_p2j / (exp_p2i + exp_p2j); + + } else { + /* No overcoordination correction! */ + f1 = 1.0; + Cf1_ij = Cf1_ji = 0.0; + } + + if (twbp->v13cor >= 0.001) { + /* Correction for 1-3 bond orders */ + exp_f4 =exp(-(twbp->p_boc4 * SQR(bo_ij->BO) - + Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5); + exp_f5 =exp(-(twbp->p_boc4 * SQR(bo_ij->BO) - + Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5); + + f4 = 1. / (1. + exp_f4); + f5 = 1. / (1. + exp_f5); + f4f5 = f4 * f5; + + /* Bond Order pages 8-9, derivative of f4 and f5 */ + Cf45_ij = -f4 * exp_f4; + Cf45_ji = -f5 * exp_f5; + } else { + f4 = f5 = f4f5 = 1.0; + Cf45_ij = Cf45_ji = 0.0; + } + + /* Bond Order page 10, derivative of total bond order */ + A0_ij = f1 * f4f5; + A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO * + (Cf45_ij + Cf45_ji); + A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij; + A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji; + A3_ij = A2_ij + Cf1_ij / f1; + A3_ji = A2_ji + Cf1_ji / f1; + + /* find corrected bond orders and their derivative coef */ + bo_ij->BO = bo_ij->BO * A0_ij; + bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1; + bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1; + bo_ij->BO_s = bo_ij->BO - (bo_ij->BO_pi + bo_ij->BO_pi2); + + bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij; + bo_ij->C2dbo = bo_ij->BO * A2_ij; + bo_ij->C3dbo = bo_ij->BO * A2_ji; + + bo_ij->C1dbopi = f1*f1*f4*f5; + bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij; + bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij; + bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji; + + bo_ij->C1dbopi2 = f1*f1*f4*f5; + bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij; + bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij; + bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji; + } + + /* neglect bonds that are < 1e-10 */ + if (bo_ij->BO < 1e-10) + bo_ij->BO = 0.0; + if (bo_ij->BO_s < 1e-10) + bo_ij->BO_s = 0.0; + if (bo_ij->BO_pi < 1e-10) + bo_ij->BO_pi = 0.0; + if (bo_ij->BO_pi2 < 1e-10) + bo_ij->BO_pi2 = 0.0; + + workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO + + } + else { + /* We only need to update bond orders from bo_ji + everything else is set in uncorrected_bo calculations */ + sym_index = bonds->select.bond_list[pj].sym_index; + bo_ji = &(bonds->select.bond_list[sym_index].bo_data); + bo_ij->BO = bo_ji->BO; + bo_ij->BO_s = bo_ji->BO_s; + bo_ij->BO_pi = bo_ji->BO_pi; + bo_ij->BO_pi2 = bo_ji->BO_pi2; + + workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO + } + } + + } + + p_lp1 = system->reax_param.gp.l[15]; + for (j = 0; j < system->N; ++j) { + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + sbp_j = &(system->reax_param.sbp[type_j]); + + workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency; + workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e; + workspace->Delta_boc[j] = workspace->total_bond_order[j] - + sbp_j->valency_boc; + workspace->Delta_val[j] = workspace->total_bond_order[j] - + sbp_j->valency_val; + + workspace->vlpex[j] = workspace->Delta_e[j] - + 2.0 * (int)(workspace->Delta_e[j]/2.0); + explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j])); + workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0); + workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j]; + workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]); + workspace->dDelta_lp[j] = workspace->Clp[j]; + + if (sbp_j->mass > 21.0) { + workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency); + workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; + workspace->dDelta_lp_temp[j] = 0.; + } + else { + workspace->nlp_temp[j] = workspace->nlp[j]; + workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; + workspace->dDelta_lp_temp[j] = workspace->Clp[j]; + } + } + } +} diff --git a/src/REAXFF/reaxff_bonds.cpp b/src/REAXFF/reaxff_bonds.cpp new file mode 100644 index 0000000000..cb28aaa1ca --- /dev/null +++ b/src/REAXFF/reaxff_bonds.cpp @@ -0,0 +1,138 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "pair.h" + +#include + +namespace ReaxFF { + void Bonds(reax_system *system, simulation_data *data, storage *workspace, reax_list **lists) + { + int i, j, pj, natoms; + int start_i, end_i; + int type_i, type_j; + double ebond, pow_BOs_be2, exp_be12, CEbo; + double gp3, gp4, gp7, gp10, gp37; + double exphu, exphua1, exphub1, exphuov, hulpov, estriph; + double decobdbo, decobdboua, decobdboub; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + bond_order_data *bo_ij; + reax_list *bonds; + + bonds = (*lists) + BONDS; + gp3 = system->reax_param.gp.l[3]; + gp4 = system->reax_param.gp.l[4]; + gp7 = system->reax_param.gp.l[7]; + gp10 = system->reax_param.gp.l[10]; + gp37 = (int) system->reax_param.gp.l[37]; + natoms = system->n; + + for (i = 0; i < natoms; ++i) { + start_i = Start_Index(i, bonds); + end_i = End_Index(i, bonds); + + for (pj = start_i; pj < end_i; ++pj) { + j = bonds->select.bond_list[pj].nbr; + + if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id) + continue; + if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) { + if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue; + if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && + system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue; + if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && + system->my_atoms[j].x[1] == system->my_atoms[i].x[1] && + system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue; + } + + /* set the pointers */ + type_i = system->my_atoms[i].type; + type_j = system->my_atoms[j].type; + sbp_i = &(system->reax_param.sbp[type_i]); + sbp_j = &(system->reax_param.sbp[type_j]); + twbp = &(system->reax_param.tbp[type_i][type_j]); + bo_ij = &(bonds->select.bond_list[pj].bo_data); + + /* calculate the constants */ + if (bo_ij->BO_s == 0.0) pow_BOs_be2 = 0.0; + else pow_BOs_be2 = pow(bo_ij->BO_s, twbp->p_be2); + exp_be12 = exp(twbp->p_be1 * (1.0 - pow_BOs_be2)); + CEbo = -twbp->De_s * exp_be12 * + (1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2); + + /* calculate the Bond Energy */ + data->my_en.e_bond += ebond = + -twbp->De_s * bo_ij->BO_s * exp_be12 + -twbp->De_p * bo_ij->BO_pi + -twbp->De_pp * bo_ij->BO_pi2; + + /* tally energy into global or per-atom energy accumulators */ + if (system->pair_ptr->eflag_either) + system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0); + + /* calculate derivatives of Bond Orders */ + bo_ij->Cdbo += CEbo; + bo_ij->Cdbopi -= (CEbo + twbp->De_p); + bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp); + + /* Stabilisation terminal triple bond */ + if (bo_ij->BO >= 1.00) { + if (gp37 == 2 || + (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) || + (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990)) { + exphu = exp(-gp7 * SQR(bo_ij->BO - 2.50)); + exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO)); + exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO)); + exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j])); + hulpov = 1.0 / (1.0 + 25.0 * exphuov); + + estriph = gp10 * exphu * hulpov * (exphua1 + exphub1); + data->my_en.e_bond += estriph; + + decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) * + (gp3 - 2.0 * gp7 * (bo_ij->BO-2.50)); + decobdboua = -gp10 * exphu * hulpov * + (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); + decobdboub = -gp10 * exphu * hulpov * + (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); + + /* tally energy into global or per-atom energy accumulators */ + if (system->pair_ptr->eflag_either) + system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0); + + bo_ij->Cdbo += decobdbo; + workspace->CdDelta[i] += decobdboua; + workspace->CdDelta[j] += decobdboub; + } + } + } + } + } +} diff --git a/src/REAXFF/reaxff_control.cpp b/src/REAXFF/reaxff_control.cpp new file mode 100644 index 0000000000..c84c3afe9d --- /dev/null +++ b/src/REAXFF/reaxff_control.cpp @@ -0,0 +1,126 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "error.h" +#include "utils.h" +#include "text_file_reader.h" + +#include +#include +#include +#include + +using LAMMPS_NS::utils::getsyserror; +using LAMMPS_NS::utils::sfgets; +using LAMMPS_NS::utils::logmesg; +using LAMMPS_NS::ValueTokenizer; + +namespace ReaxFF { + static std::unordered_set inactive_keywords = { + "ensemble_type", "nsteps", "dt", "proc_by_dim", "random_vel", + "restart_format", "restart_freq", "reposition_atoms", + "restrict_bonds", "remove_CoM_vel", "debug_level", "reneighbor", + "vlist_buffer", "ghost_cutoff", "qeq_freq", "q_err", "ilu_refactor", + "ilu_droptol", "temp_init", "temp_final", "t_mass", "t_mode", "t_rate", + "t_freq", "pressure", "p_mass", "pt_mass", "compress", "press_mode", + "geo_format", "traj_compress", "traj_method", "molecular_analysis", + "ignore", "dipole_anal", "freq_dipole_anal", "diffusion_coef", + "freq_diffusion_coef", "restrict_type", "traj_title", "simulation_name", + "energy_update_freq", "atom_info", "atom_velocities", "atom_forces", + "bond_info", "angle_info" }; + + class parser_error : public std::exception { + std::string message; + public: + parser_error(const std::string &mesg) { message = mesg; } + const char *what() const noexcept { return message.c_str(); } + }; + + // NOTE: this function is run on MPI rank 0 only + + void Read_Control_File(const char *control_file, control_params *control) + { + auto error = control->error_ptr; + + /* assign default values */ + control->nthreads = 1; + control->tabulate = 0; + control->bond_cut = 5.0; + control->bg_cut = 0.3; + control->thb_cut = 0.001; + control->thb_cutsq = 0.00001; + control->hbond_cut = 7.5; + + /* read control parameters file */ + try { + LAMMPS_NS::TextFileReader reader(control_file, "ReaxFF control"); + reader.ignore_comments = false; + + while (1) { + auto values = reader.next_values(0); + + // empty line + if (values.count() == 0) continue; + + auto keyword = values.next_string(); + + if (!values.has_next()) + throw parser_error(fmt::format("No value(s) for control parameter: {}\n",keyword)); + + if (inactive_keywords.find(keyword) != inactive_keywords.end()) { + error->warning(FLERR,fmt::format("Ignoring inactive control " + "parameter: {}",keyword)); + } else if (keyword == "nbrhood_cutoff") { + control->bond_cut = values.next_double(); + } else if (keyword == "bond_graph_cutoff") { + control->bg_cut = values.next_double(); + } else if (keyword == "thb_cutoff") { + control->thb_cut = values.next_double(); + } else if (keyword == "thb_cutoff_sq") { + control->thb_cutsq = values.next_double(); + } else if (keyword == "hbond_cutoff") { + control->hbond_cut = values.next_double(); + } else if (keyword == "tabulate_long_range") { + control->tabulate = values.next_int(); + } else if (keyword == "write_freq") { + if (values.next_int() > 0) + error->warning(FLERR,"Support for writing native trajectories has " + "been removed after LAMMPS version 8 April 2021"); + } else { + throw parser_error(fmt::format("Unknown parameter {} in " + "control file", keyword)); + } + } + } catch (LAMMPS_NS::EOFException &) { + ; // catch and ignore + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } + } +} diff --git a/src/REAXFF/reaxff_defs.h b/src/REAXFF/reaxff_defs.h new file mode 100644 index 0000000000..c6df5de0ea --- /dev/null +++ b/src/REAXFF/reaxff_defs.h @@ -0,0 +1,66 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hasan Metin Aktulga, Purdue University + (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov) + + Heavily modified and adapted for LAMMPS by the LAMMPS developers. +------------------------------------------------------------------------- */ + +#ifndef LMP_REAXFF_DEFS_H +#define LMP_REAXFF_DEFS_H + +#if defined(__IBMC__) +#define inline __inline__ +#endif /*IBMC*/ + +#define SQR(x) ((x)*(x)) +#define CUBE(x) ((x)*(x)*(x)) +#define DEG2RAD(a) ((a)*constPI/180.0) +#define RAD2DEG(a) ((a)*180.0/constPI) +#define MAX3(x,y,z) MAX(MAX(x,y), z) + +#define constPI 3.14159265 +#define C_ele 332.06371 +#define EV_to_KCALpMOL 14.400000 // ElectronVolt --> KCAL per MOLe +#define KCALpMOL_to_EV 23.02 // 23.060549 //KCAL per MOLe --> ElectronVolt + +#define HB_THRESHOLD 1e-2 // 0.01 + +#define REAX_MIN_CAP 50 +#define REAX_MIN_NBRS 100 +#define MIN_HENTRIES 100 +#define MAX_BONDS 30 +#define MIN_BONDS 25 +#define REAX_MIN_HBONDS 25 +#define MIN_3BODIES 1000 +#define REAX_SAFE_ZONE 1.2 +#define REAX_SAFER_ZONE 1.4 +#define DANGER_ZONE 0.90 +#define LOOSE_ZONE 0.75 + +#define MAXREAXBOND 24 /* used in fix_reaxff_bonds.cpp and pair_reaxff.cpp */ +#define MAXSPECBOND 24 /* used in fix_reaxff_species.cpp and pair_reaxff.cpp */ + +#define REAX_MAX_3BODY_PARAM 5 +#define REAX_MAX_4BODY_PARAM 5 + +namespace ReaxFF +{ + /******************* ENUMERATORS *************************/ + enum {BONDS, THREE_BODIES, HBONDS, FAR_NBRS, LIST_N}; + enum {TYP_BOND, TYP_THREE_BODY, TYP_HBOND, TYP_FAR_NEIGHBOR, TYP_N}; +} + +#endif diff --git a/src/REAXFF/reaxff_ffield.cpp b/src/REAXFF/reaxff_ffield.cpp new file mode 100644 index 0000000000..f43ab440ff --- /dev/null +++ b/src/REAXFF/reaxff_ffield.cpp @@ -0,0 +1,616 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "error.h" +#include "memory.h" +#include "text_file_reader.h" +#include "utils.h" + +#include +#include +#include + +using LAMMPS_NS::utils::open_potential; +using LAMMPS_NS::utils::getsyserror; + +namespace ReaxFF { + + class parser_error : public std::exception { + std::string message; + public: + parser_error(const std::string &mesg) { message = mesg; } + const char *what() const noexcept { return message.c_str(); } + }; + + void Read_Force_Field(const char *filename, reax_interaction *reax, + control_params *control, MPI_Comm world) + { + char ****tor_flag; + auto error = control->error_ptr; + auto lmp = control->lmp_ptr; + auto memory = control->lmp_ptr->memory; + + // read and parse the force field only on rank 0 + +#define THROW_ERROR(txt) \ + throw parser_error(fmt::format("{}:{}: {}",filename,lineno,txt)) + + if (control->me == 0) { + FILE *fp = LAMMPS_NS::utils::open_potential(filename, lmp, nullptr); + if (!fp) + error->one(FLERR,fmt::format("The ReaxFF parameter file {} cannot be opened: {}", + filename, getsyserror())); + LAMMPS_NS::TextFileReader reader(fp, "ReaxFF parameter"); + reader.ignore_comments = false; + + try { + int i,j,k,l,m,n,lineno = 0; + + // skip header comment line + + reader.skip_line(); + ++lineno; + + // set some defaults + auto &gp = reax->gp; + + gp.vdw_type = 0; + + // get number of global parameters + + auto values = reader.next_values(0); + n = values.next_int(); + gp.n_global = n; + ++lineno; + + if (n < 1) + THROW_ERROR("Invalid number of global parameters"); + + memory->destroy(gp.l); + memory->create(gp.l,n,"reaxff:gp.l"); + + // see reaxff_types.h for mapping between l[i] and the lambdas used in ff + + for (i = 0; i < n; ++i) { + values = reader.next_values(0); + ++lineno; + gp.l[i] = values.next_double(); + } + + // next line is number of atom types followed by 3 lines of comments + + values = reader.next_values(0); + n = values.next_int(); + reax->num_atom_types = n; + reader.skip_line(); + reader.skip_line(); + reader.skip_line(); + lineno += 4; + + // allocate and clear storage for ffield data + auto &sbp = reax->sbp; + auto &tbp = reax->tbp; + auto &thbp = reax->thbp; + auto &hbp = reax->hbp; + auto &fbp = reax->fbp; + + memory->destroy(sbp); + memory->destroy(tbp); + memory->destroy(thbp); + memory->destroy(hbp); + memory->destroy(fbp); + memory->create(sbp,n,"reaxff:sbp"); + memory->create(tbp,n,n,"reaxff:tbp"); + memory->create(thbp,n,n,n,"reaxff:thbp"); + memory->create(hbp,n,n,n,"reaxff:hbp"); + memory->create(fbp,n,n,n,n,"reaxff:fbp"); + memory->create(tor_flag,n,n,n,n,"reaxff:tor_flag"); + memset(&(sbp[0]),0,sizeof(single_body_parameters)*n); + memset(&(tbp[0][0]),0,sizeof(two_body_parameters)*n*n); + memset(&(thbp[0][0][0]),0,sizeof(three_body_header)*n*n*n); + memset(&(hbp[0][0][0]),0,sizeof(hbond_parameters)*n*n*n); + memset(&(fbp[0][0][0][0]),0,sizeof(four_body_header)*n*n*n*n); + memset(&tor_flag[0][0][0][0],0,sizeof(char)*n*n*n*n); + + // atomic parameters + // four lines per atom type, or 5 if lgvdw != 0 + // the first starts with the symbol and has 9 words + // the next three have 8 words + // the fifth will have 2 words, if present + + const int lgflag = control->lgflag; + const int ntypes = n; + + for (i = 0; i < ntypes; ++i) { + + // line one + + values = reader.next_values(0); + ++lineno; + + if ((values.count() < 8) && !lgflag) + THROW_ERROR("This force field file requires using 'lgvdw yes'"); + if (values.count() < 9) + THROW_ERROR("Invalid force field file format"); + + auto element = values.next_string(); + int len = MIN(element.size(),3); // truncate stored element symbol if necessary + for (j = 0; j < len; ++j) + sbp[i].name[j] = toupper(element[j]); + sbp[i].name[len] = '\0'; + + sbp[i].r_s = values.next_double(); + sbp[i].valency = values.next_double(); + sbp[i].mass = values.next_double(); + sbp[i].r_vdw = values.next_double(); + sbp[i].epsilon = values.next_double(); + sbp[i].gamma = values.next_double(); + sbp[i].r_pi = values.next_double(); + sbp[i].valency_e = values.next_double(); + sbp[i].nlp_opt = 0.5 * (sbp[i].valency_e-sbp[i].valency); + + // line two + + values = reader.next_values(0); + ++lineno; + if (values.count() < 8) + THROW_ERROR("Invalid force field file format"); + + sbp[i].alpha = values.next_double(); + sbp[i].gamma_w = values.next_double(); + sbp[i].valency_boc= values.next_double(); + sbp[i].p_ovun5 = values.next_double(); + values.skip(); + sbp[i].chi = values.next_double(); + sbp[i].eta = 2.0*values.next_double(); + sbp[i].p_hbond = (int) values.next_double(); + + // line three + + values = reader.next_values(0); + ++lineno; + if (values.count() < 8) + THROW_ERROR("Invalid force field file format"); + + sbp[i].r_pi_pi = values.next_double(); + sbp[i].p_lp2 = values.next_double(); + values.skip(); + sbp[i].b_o_131 = values.next_double(); + sbp[i].b_o_132 = values.next_double(); + sbp[i].b_o_133 = values.next_double(); + + // line four + + values = reader.next_values(0); + ++lineno; + if (values.count() < 8) + THROW_ERROR("Invalid force field file format"); + + sbp[i].p_ovun2 = values.next_double(); + sbp[i].p_val3 = values.next_double(); + values.skip(); + sbp[i].valency_val= values.next_double(); + sbp[i].p_val5 = values.next_double(); + sbp[i].rcore2 = values.next_double(); + sbp[i].ecore2 = values.next_double(); + sbp[i].acore2 = values.next_double(); + + // read line five only when lgflag != 0 + + if (lgflag) { + values = reader.next_values(0); + ++lineno; + if (values.count() < 2) + THROW_ERROR("Invalid force field file format"); + sbp[i].lgcij = values.next_double(); + sbp[i].lgre = values.next_double(); + } else sbp[i].lgcij = sbp[i].lgre = 0.0; + + // van der Waals settings check: + + // Inner-wall? + if ((sbp[i].rcore2 > 0.01) && (sbp[i].acore2 > 0.01)) { + // Shielding van der Waals? + if (sbp[i].gamma_w > 0.5) { + if (gp.vdw_type != 0 && gp.vdw_type != 3) { + const auto errmsg + = fmt::format("Van der Waals parameters for element {} " + "indicate inner wall+shielding, but earlier " + "atoms indicate a different van der Waals " + "method. This may cause division-by-zero " + "errors. Keeping van der Waals setting for " + "earlier atoms.",sbp[i].name); + error->warning(FLERR,errmsg); + } else { + gp.vdw_type = 3; + } + } else { // No shielding van der Waals parameters present + if ((gp.vdw_type != 0) && (gp.vdw_type != 2)) { + const auto errmsg + = fmt::format("Van der Waals parameters for element {} " + "indicate inner wall withou shielding, but " + "earlier atoms indicate a different van der " + "Waals-method. This may cause division-by-" + "zero errors. Keeping van der Waals setting " + "for earlier atoms.", sbp[i].name); + error->warning(FLERR,errmsg); + } else { + gp.vdw_type = 2; + } + } + } else { // No Inner wall parameters present + if (sbp[i].gamma_w > 0.5) { // Shielding vdWaals + if ((gp.vdw_type != 0) && (gp.vdw_type != 1)) { + const auto errmsg + = fmt::format("Van der Waals parameters for element {} " + "indicate shielding without inner wall, but " + "earlier elements indicate a different van der " + "Waals method. This may cause division-by-zero " + "errors. Keeping van der Waals setting for " + "earlier atoms.", sbp[i].name); + error->warning(FLERR,errmsg); + } else { + gp.vdw_type = 1; + } + } else { + error->one(FLERR,fmt::format("Inconsistent van der Waals " + "parameters: No shielding or inner " + "wall set for element {}", + sbp[i].name)); + } + } + } + + /* Equate vval3 to valf for first-row elements (25/10/2004) */ + for (i = 0; i < ntypes; i++) { + if ((sbp[i].mass < 21) && + (sbp[i].valency_val != sbp[i].valency_boc)) { + error->warning(FLERR,fmt::format("Changed valency_val to valency" + "_boc for {}", sbp[i].name)); + sbp[i].valency_val = sbp[i].valency_boc; + } + } + + // next line is number of two body parameters followed by 1 comment line + + values = reader.next_values(0); + n = values.next_int(); + reader.skip_line(); + lineno += 2; + + for (i = 0; i < n; ++i) { + + // first line + + values = reader.next_values(0); + ++lineno; + if (values.count() < 10) + THROW_ERROR("Invalid force field file format"); + + j = values.next_int() - 1; + k = values.next_int() - 1; + + if ((j < 0) || (k < 0)) + THROW_ERROR("Inconsistent force field file"); + + if ((j < ntypes) && (k < ntypes)) { + tbp[j][k].De_s = tbp[k][j].De_s = values.next_double(); + tbp[j][k].De_p = tbp[k][j].De_p = values.next_double(); + tbp[j][k].De_pp = tbp[k][j].De_pp = values.next_double(); + tbp[j][k].p_be1 = tbp[k][j].p_be1 = values.next_double(); + tbp[j][k].p_bo5 = tbp[k][j].p_bo5 = values.next_double(); + tbp[j][k].v13cor = tbp[k][j].v13cor = values.next_double(); + tbp[j][k].p_bo6 = tbp[k][j].p_bo6 = values.next_double(); + tbp[j][k].p_ovun1 = tbp[k][j].p_ovun1 = values.next_double(); + } + + // second line + + values = reader.next_values(0); + ++lineno; + if (values.count() < 8) + THROW_ERROR("Invalid force field file format"); + + if ((j < ntypes) && (k < ntypes)) { + tbp[j][k].p_be2 = tbp[k][j].p_be2 = values.next_double(); + tbp[j][k].p_bo3 = tbp[k][j].p_bo3 = values.next_double(); + tbp[j][k].p_bo4 = tbp[k][j].p_bo4 = values.next_double(); + values.skip(); + tbp[j][k].p_bo1 = tbp[k][j].p_bo1 = values.next_double(); + tbp[j][k].p_bo2 = tbp[k][j].p_bo2 = values.next_double(); + tbp[j][k].ovc = tbp[k][j].ovc = values.next_double(); + } + } + + for (i=0; i < ntypes; ++i) { + for (j=i; j < ntypes; ++j) { + tbp[i][j].r_s = tbp[j][i].r_s = 0.5*(sbp[j].r_s + sbp[i].r_s); + tbp[i][j].r_p = tbp[j][i].r_p = 0.5*(sbp[j].r_pi + sbp[i].r_pi); + tbp[i][j].r_pp = tbp[j][i].r_pp = 0.5*(sbp[j].r_pi_pi + sbp[i].r_pi_pi); + tbp[i][j].p_boc3 = tbp[j][i].p_boc3 = sqrt(sbp[j].b_o_132 * sbp[i].b_o_132); + tbp[i][j].p_boc4 = tbp[j][i].p_boc4 = sqrt(sbp[j].b_o_131 * sbp[i].b_o_131); + tbp[i][j].p_boc5 = tbp[j][i].p_boc5 = sqrt(sbp[j].b_o_133 * sbp[i].b_o_133); + tbp[i][j].D = tbp[j][i].D = sqrt(sbp[j].epsilon * sbp[i].epsilon); + tbp[i][j].alpha = tbp[j][i].alpha = sqrt(sbp[j].alpha * sbp[i].alpha); + tbp[i][j].r_vdW = tbp[j][i].r_vdW = 2.0*sqrt(sbp[j].r_vdw * sbp[i].r_vdw); + tbp[i][j].gamma_w = tbp[j][i].gamma_w = sqrt(sbp[j].gamma_w * sbp[i].gamma_w); + tbp[i][j].gamma = tbp[j][i].gamma = pow(sbp[j].gamma * sbp[i].gamma,-1.5); + + // additions for additional vdWaals interaction types - inner core + + tbp[i][j].rcore = tbp[j][i].rcore = sqrt(sbp[i].rcore2 * sbp[j].rcore2); + tbp[i][j].ecore = tbp[j][i].ecore = sqrt(sbp[i].ecore2 * sbp[j].ecore2); + tbp[i][j].acore = tbp[j][i].acore = sqrt(sbp[i].acore2 * sbp[j].acore2); + + // additions for additional vdWalls interaction types lg correction + + tbp[i][j].lgcij = tbp[j][i].lgcij = sqrt(sbp[i].lgcij * sbp[j].lgcij); + tbp[i][j].lgre = tbp[j][i].lgre = 2.0*gp.l[35]*sqrt(sbp[i].lgre*sbp[j].lgre); + } + } + + // next line is number of two body off-diagonal parameters + + values = reader.next_values(0); + n = values.next_int(); + ++lineno; + + double val; + for (i = 0; i < n; ++i) { + values = reader.next_values(0); + ++lineno; + if ((int)values.count() < 8 + lgflag) + THROW_ERROR("Invalid force field file format"); + + j = values.next_int() - 1; + k = values.next_int() - 1; + + if ((j < 0) || (k < 0)) + THROW_ERROR("Inconsistent force field file"); + + if ((j < ntypes) && (k < ntypes)) { + val = values.next_double(); + if (val > 0.0) tbp[j][k].D = tbp[k][j].D = val; + + val = values.next_double(); + if (val > 0.0) tbp[j][k].r_vdW = tbp[k][j].r_vdW = 2*val; + + val = values.next_double(); + if (val > 0.0) tbp[j][k].alpha = tbp[k][j].alpha = val; + + val = values.next_double(); + if (val > 0.0) tbp[j][k].r_s = tbp[k][j].r_s = val; + + val = values.next_double(); + if (val > 0.0) tbp[j][k].r_p = tbp[k][j].r_p = val; + + val = values.next_double(); + if (val > 0.0) tbp[j][k].r_pp = tbp[k][j].r_pp = val; + + if (lgflag) { + val = values.next_double(); + if (val >= 0.0) tbp[j][k].lgcij = tbp[k][j].lgcij = val; + } + } + } + + // next line is number of three body parameters + + values = reader.next_values(0); + n = values.next_int(); + ++lineno; + + int cnt; + for (i = 0; i < n; ++i) { + values = reader.next_values(0); + ++lineno; + if (values.count() < 10) + THROW_ERROR("Invalid force field file format"); + + j = values.next_int() - 1; + k = values.next_int() - 1; + l = values.next_int() - 1; + + if ((j < 0) || (k < 0) || (l < 0)) + THROW_ERROR("Inconsistent force field file"); + + if ((j < ntypes) && (k < ntypes) && (l < ntypes)) { + + cnt = thbp[j][k][l].cnt; + thbp[j][k][l].cnt++; + thbp[l][k][j].cnt++; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].theta_00 = val; + thbp[l][k][j].prm[cnt].theta_00 = val; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].p_val1 = val; + thbp[l][k][j].prm[cnt].p_val1 = val; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].p_val2 = val; + thbp[l][k][j].prm[cnt].p_val2 = val; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].p_coa1 = val; + thbp[l][k][j].prm[cnt].p_coa1 = val; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].p_val7 = val; + thbp[l][k][j].prm[cnt].p_val7 = val; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].p_pen1 = val; + thbp[l][k][j].prm[cnt].p_pen1 = val; + + val = values.next_double(); + thbp[j][k][l].prm[cnt].p_val4 = val; + thbp[l][k][j].prm[cnt].p_val4 = val; + } + } + + // next line is number of four body parameters + + values = reader.next_values(0); + n = values.next_int(); + ++lineno; + + for (i = 0; i < n; ++i) { + values = reader.next_values(0); + ++lineno; + if (values.count() < 9) + THROW_ERROR("Invalid force field file format"); + + j = values.next_int() - 1; + k = values.next_int() - 1; + l = values.next_int() - 1; + m = values.next_int() - 1; + + if ((j < -1) || (k < 0) || (l < 0) || (m < -1)) + THROW_ERROR("Inconsistent force field file"); + + const double val1 = values.next_double(); + const double val2 = values.next_double(); + const double val3 = values.next_double(); + const double val4 = values.next_double(); + const double val5 = values.next_double(); + + if ((j >= 0) && (m >= 0)) { // this means the entry is not in compact form + + if ((j < ntypes) && (k < ntypes) && (l < ntypes) && (m < ntypes)) { + + tor_flag[j][k][l][m] = tor_flag[m][l][k][j] = 1; + fbp[j][k][l][m].cnt = fbp[m][l][k][j].cnt = 1; + + fbp[j][k][l][m].prm[0].V1 = fbp[m][l][k][j].prm[0].V1 = val1; + fbp[j][k][l][m].prm[0].V2 = fbp[m][l][k][j].prm[0].V2 = val2; + fbp[j][k][l][m].prm[0].V3 = fbp[m][l][k][j].prm[0].V3 = val3; + fbp[j][k][l][m].prm[0].p_tor1 = fbp[m][l][k][j].prm[0].p_tor1 = val4; + fbp[j][k][l][m].prm[0].p_cot1 = fbp[m][l][k][j].prm[0].p_cot1 = val5; + } + + } else { /* This means the entry is of the form 0-X-Y-0 */ + + if ((k < ntypes) && (l < ntypes)) { + for (int p = 0; p < ntypes; ++p) { + for (int o = 0; o < ntypes; ++o) { + + if (tor_flag[p][k][l][o] == 0) { + fbp[p][k][l][o].cnt = 1; + fbp[p][k][l][o].prm[0].V1 = val1; + fbp[p][k][l][o].prm[0].V2 = val2; + fbp[p][k][l][o].prm[0].V3 = val3; + fbp[p][k][l][o].prm[0].p_tor1 = val4; + fbp[p][k][l][o].prm[0].p_cot1 = val5; + } + + if (tor_flag[o][l][k][p] == 0) { + fbp[o][l][k][p].cnt = 1; + fbp[o][l][k][p].prm[0].V1 = val1; + fbp[o][l][k][p].prm[0].V2 = val2; + fbp[o][l][k][p].prm[0].V3 = val3; + fbp[o][l][k][p].prm[0].p_tor1 = val4; + fbp[o][l][k][p].prm[0].p_cot1 = val5; + } + } + } + } + } + } + + // next line is number of hydrogen bond parameters + + values = reader.next_values(0); + n = values.next_int(); + ++lineno; + + for (i = 0; i < ntypes; ++i) + for (j = 0; j < ntypes; ++j) + for (k = 0; k < ntypes; ++k) + hbp[i][j][k].r0_hb = -1.0; + + for (i = 0; i < n; ++i) { + values = reader.next_values(0); + ++lineno; + if (values.count() < 7) + THROW_ERROR("Invalid force field file format"); + + j = values.next_int() - 1; + k = values.next_int() - 1; + l = values.next_int() - 1; + + if ((j < 0) || (k < 0) || (l < 0)) + THROW_ERROR("Inconsistent force field file"); + + if ((j < ntypes) && (k < ntypes) && (l < ntypes)) { + hbp[j][k][l].r0_hb = values.next_double(); + hbp[j][k][l].p_hb1 = values.next_double(); + hbp[j][k][l].p_hb2 = values.next_double(); + hbp[j][k][l].p_hb3 = values.next_double(); + } + } + + memory->destroy(tor_flag); + } catch (std::exception &e) { + error->one(FLERR,e.what()); + } + } + + // broadcast global parameters and allocate list on ranks != 0 + MPI_Bcast(&reax->gp,sizeof(global_parameters),MPI_CHAR,0,world); + if (control->me != 0) memory->create(reax->gp.l,reax->gp.n_global,"reaxff:gp.l"); + MPI_Bcast(reax->gp.l,reax->gp.n_global,MPI_DOUBLE,0,world); + + // allocate storage for atom type based data + MPI_Bcast(&reax->num_atom_types,1,MPI_INT,0,world); + const int n = reax->num_atom_types; + if (control->me != 0) { + memory->create(reax->sbp,n,"reaxff:sbp"); + memory->create(reax->tbp,n,n,"reaxff:tbp"); + memory->create(reax->thbp,n,n,n,"reaxff:thbp"); + memory->create(reax->hbp,n,n,n,"reaxff:hbp"); + memory->create(reax->fbp,n,n,n,n,"reaxff:fbp"); + } + + // broadcast type specific force field data + MPI_Bcast(&(reax->sbp[0]),sizeof(single_body_parameters)*n,MPI_CHAR,0,world); + MPI_Bcast(&(reax->tbp[0][0]),sizeof(two_body_parameters)*n*n,MPI_CHAR,0,world); + MPI_Bcast(&(reax->thbp[0][0][0]),sizeof(three_body_header)*n*n*n,MPI_CHAR,0,world); + MPI_Bcast(&(reax->hbp[0][0][0]),sizeof(hbond_parameters)*n*n*n,MPI_CHAR,0,world); + MPI_Bcast(&(reax->fbp[0][0][0][0]),sizeof(four_body_header)*n*n*n*n,MPI_CHAR,0,world); + + // apply global parameters to global control settings + + control->bo_cut = 0.01 * reax->gp.l[29]; + control->nonb_low = reax->gp.l[11]; + control->nonb_cut = reax->gp.l[12]; + } +#undef THROW_ERROR +} diff --git a/src/REAXFF/reaxff_forces.cpp b/src/REAXFF/reaxff_forces.cpp new file mode 100644 index 0000000000..ec783102b4 --- /dev/null +++ b/src/REAXFF/reaxff_forces.cpp @@ -0,0 +1,386 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include +#include +#include + +#include "error.h" + +namespace ReaxFF { + + static void Compute_Bonded_Forces(reax_system *system, + control_params *control, + simulation_data *data, + storage *workspace, + reax_list **lists) + { + BO(system, workspace, lists); + Bonds(system, data, workspace, lists); + Atom_Energy(system, control, data, workspace, lists); + Valence_Angles(system, control, data, workspace, lists); + Torsion_Angles(system, control, data, workspace, lists); + if (control->hbond_cut > 0) + Hydrogen_Bonds(system, data, workspace, lists); + } + + static void Compute_NonBonded_Forces(reax_system *system, + control_params *control, + simulation_data *data, + storage *workspace, + reax_list **lists) + { + + /* van der Waals and Coulomb interactions */ + if (control->tabulate == 0) + vdW_Coulomb_Energy(system, control, data, workspace, lists); + else + Tabulated_vdW_Coulomb_Energy(system, control, data, workspace, lists); + } + + static void Compute_Total_Force(reax_system *system, storage *workspace, reax_list **lists) + { + int i, pj; + reax_list *bonds = (*lists) + BONDS; + + for (i = 0; i < system->N; ++i) + for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) + if (i < bonds->select.bond_list[pj].nbr) + Add_dBond_to_Forces(system, i, pj, workspace, lists); + } + + static void Validate_Lists(reax_system *system, reax_list **lists, + int step, int N, int numH) + { + int i, comp, Hindex; + reax_list *bonds, *hbonds; + + double saferzone = system->saferzone; + + /* bond list */ + if (N > 0) { + bonds = *lists + BONDS; + + for (i = 0; i < N; ++i) { + system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); + + if (i < N-1) + comp = Start_Index(i+1, bonds); + else comp = bonds->num_intrs; + + if (End_Index(i, bonds) > comp) + system->error_ptr->one(FLERR, fmt::format("step {}: bondchk failed: " + "i={} end(i)={} str(i+1)={}\n", + step,i,End_Index(i,bonds),comp)); + } + } + + + /* hbonds list */ + if (numH > 0) { + hbonds = *lists + HBONDS; + + for (i = 0; i < N; ++i) { + Hindex = system->my_atoms[i].Hindex; + if (Hindex > -1) { + system->my_atoms[i].num_hbonds = + (int)(MAX(Num_Entries(Hindex, hbonds)*saferzone, system->minhbonds)); + + if (Hindex < numH-1) + comp = Start_Index(Hindex+1, hbonds); + else comp = hbonds->num_intrs; + + if (End_Index(Hindex, hbonds) > comp) + system->error_ptr->one(FLERR, fmt::format("step {}: hbondchk failed: " + "H={} end(H)={} str(H+1)={}\n", + step, Hindex,End_Index(Hindex,hbonds),comp)); + } + } + } + } + + static void Init_Forces_noQEq(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) { + int i, j, pj; + int start_i, end_i; + int type_i, type_j; + int btop_i, num_bonds, num_hbonds; + int ihb, jhb, ihb_top, jhb_top; + int local, flag; + double cutoff; + reax_list *far_nbrs, *bonds, *hbonds; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + far_neighbor_data *nbr_pj; + reax_atom *atom_i, *atom_j; + + far_nbrs = *lists + FAR_NBRS; + bonds = *lists + BONDS; + hbonds = *lists + HBONDS; + + for (i = 0; i < system->n; ++i) + workspace->bond_mark[i] = 0; + for (i = system->n; i < system->N; ++i) { + workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance + } + + num_bonds = 0; + num_hbonds = 0; + btop_i = 0; + + for (i = 0; i < system->N; ++i) { + atom_i = &(system->my_atoms[i]); + type_i = atom_i->type; + if (type_i < 0) continue; + start_i = Start_Index(i, far_nbrs); + end_i = End_Index(i, far_nbrs); + btop_i = End_Index(i, bonds); + sbp_i = &(system->reax_param.sbp[type_i]); + + if (i < system->n) { + local = 1; + cutoff = MAX(control->hbond_cut, control->bond_cut); + } else { + local = 0; + cutoff = control->bond_cut; + } + + ihb = -1; + ihb_top = -1; + if (local && control->hbond_cut > 0) { + ihb = sbp_i->p_hbond; + if (ihb == 1) + ihb_top = End_Index(atom_i->Hindex, hbonds); + else ihb_top = -1; + } + + /* update i-j distance - check if j is within cutoff */ + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + atom_j = &(system->my_atoms[j]); + + if (nbr_pj->d <= cutoff) + flag = 1; + else flag = 0; + + if (flag) { + type_j = atom_j->type; + if (type_j < 0) continue; + sbp_j = &(system->reax_param.sbp[type_j]); + twbp = &(system->reax_param.tbp[type_i][type_j]); + + if (local) { + /* hydrogen bond lists */ + if (control->hbond_cut > 0 && (ihb==1 || ihb==2) && + nbr_pj->d <= control->hbond_cut) { + // fprintf(stderr, "%d %d\n", atom1, atom2); + jhb = sbp_j->p_hbond; + if (ihb == 1 && jhb == 2) { + hbonds->select.hbond_list[ihb_top].nbr = j; + hbonds->select.hbond_list[ihb_top].scl = 1; + hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; + ++ihb_top; + ++num_hbonds; + } + else if (j < system->n && ihb == 2 && jhb == 1) { + jhb_top = End_Index(atom_j->Hindex, hbonds); + hbonds->select.hbond_list[jhb_top].nbr = i; + hbonds->select.hbond_list[jhb_top].scl = -1; + hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; + Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds); + ++num_hbonds; + } + } + } + + if (//(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) && + nbr_pj->d <= control->bond_cut && + BOp(workspace, bonds, control->bo_cut, + i , btop_i, nbr_pj, sbp_i, sbp_j, twbp)) { + num_bonds += 2; + ++btop_i; + + if (workspace->bond_mark[j] > workspace->bond_mark[i] + 1) + workspace->bond_mark[j] = workspace->bond_mark[i] + 1; + else if (workspace->bond_mark[i] > workspace->bond_mark[j] + 1) { + workspace->bond_mark[i] = workspace->bond_mark[j] + 1; + } + } + } + } + + Set_End_Index(i, btop_i, bonds); + if (local && ihb == 1) + Set_End_Index(atom_i->Hindex, ihb_top, hbonds); + } + + + workspace->realloc.num_bonds = num_bonds; + workspace->realloc.num_hbonds = num_hbonds; + + Validate_Lists(system, lists, data->step, system->N, system->numH); + } + + void Estimate_Storages(reax_system *system, control_params *control, + reax_list **lists, int *Htop, int *hb_top, + int *bond_top, int *num_3body) + { + int i, j, pj; + int start_i, end_i; + int type_i, type_j; + int ihb, jhb; + int local; + double cutoff; + double r_ij; + double C12, C34, C56; + double BO, BO_s, BO_pi, BO_pi2; + reax_list *far_nbrs; + single_body_parameters *sbp_i, *sbp_j; + two_body_parameters *twbp; + far_neighbor_data *nbr_pj; + reax_atom *atom_i, *atom_j; + + int mincap = system->mincap; + double safezone = system->safezone; + double saferzone = system->saferzone; + + far_nbrs = *lists + FAR_NBRS; + *Htop = 0; + memset(hb_top, 0, sizeof(int) * system->local_cap); + memset(bond_top, 0, sizeof(int) * system->total_cap); + *num_3body = 0; + + for (i = 0; i < system->N; ++i) { + atom_i = &(system->my_atoms[i]); + type_i = atom_i->type; + if (type_i < 0) continue; + start_i = Start_Index(i, far_nbrs); + end_i = End_Index(i, far_nbrs); + sbp_i = &(system->reax_param.sbp[type_i]); + + if (i < system->n) { + local = 1; + cutoff = control->nonb_cut; + ++(*Htop); + ihb = sbp_i->p_hbond; + } else { + local = 0; + cutoff = control->bond_cut; + ihb = -1; + } + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + atom_j = &(system->my_atoms[j]); + + if (nbr_pj->d <= cutoff) { + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + r_ij = nbr_pj->d; + sbp_j = &(system->reax_param.sbp[type_j]); + twbp = &(system->reax_param.tbp[type_i][type_j]); + + if (local) { + if (j < system->n || atom_i->orig_id < atom_j->orig_id) //tryQEq ||1 + ++(*Htop); + + /* hydrogen bond lists */ + if (control->hbond_cut > 0.1 && (ihb==1 || ihb==2) && + nbr_pj->d <= control->hbond_cut) { + jhb = sbp_j->p_hbond; + if (ihb == 1 && jhb == 2) + ++hb_top[i]; + else if (j < system->n && ihb == 2 && jhb == 1) + ++hb_top[j]; + } + } + + /* uncorrected bond orders */ + if (nbr_pj->d <= control->bond_cut) { + if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { + C12 = twbp->p_bo1 * pow(r_ij / twbp->r_s, twbp->p_bo2); + BO_s = (1.0 + control->bo_cut) * exp(C12); + } + else BO_s = C12 = 0.0; + + if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { + C34 = twbp->p_bo3 * pow(r_ij / twbp->r_p, twbp->p_bo4); + BO_pi = exp(C34); + } + else BO_pi = C34 = 0.0; + + if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { + C56 = twbp->p_bo5 * pow(r_ij / twbp->r_pp, twbp->p_bo6); + BO_pi2= exp(C56); + } + else BO_pi2 = C56 = 0.0; + + /* Initially BO values are the uncorrected ones, page 1 */ + BO = BO_s + BO_pi + BO_pi2; + + if (BO >= control->bo_cut) { + ++bond_top[i]; + ++bond_top[j]; + } + } + } + } + } + + *Htop = (int)(MAX(*Htop * safezone, mincap * MIN_HENTRIES)); + for (i = 0; i < system->n; ++i) + hb_top[i] = (int)(MAX(hb_top[i] * saferzone, system->minhbonds)); + + for (i = 0; i < system->N; ++i) { + *num_3body += SQR(bond_top[i]); + bond_top[i] = MAX(bond_top[i] * 2, MIN_BONDS); + } + + } + + void Compute_Forces(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + + Init_Forces_noQEq(system, control, data, workspace, lists); + + /********* bonded interactions ************/ + Compute_Bonded_Forces(system, control, data, workspace, lists); + + /********* nonbonded interactions ************/ + Compute_NonBonded_Forces(system, control, data, workspace, lists); + + /*********** total force ***************/ + Compute_Total_Force(system, workspace, lists); + } +} diff --git a/src/REAXFF/reaxff_hydrogen_bonds.cpp b/src/REAXFF/reaxff_hydrogen_bonds.cpp new file mode 100644 index 0000000000..5c7629ffb7 --- /dev/null +++ b/src/REAXFF/reaxff_hydrogen_bonds.cpp @@ -0,0 +1,160 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include + +#include "pair.h" + +namespace ReaxFF { + void Hydrogen_Bonds(reax_system *system, simulation_data *data, storage *workspace, reax_list **lists) + { + int i, j, k, pi, pk; + int type_i, type_j, type_k; + int start_j, end_j, hb_start_j, hb_end_j; + int hblist[MAX_BONDS]; + int itr, top; + int num_hb_intrs = 0; + double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; + double e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3; + rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk; + rvec dvec_jk; + hbond_parameters *hbp; + bond_order_data *bo_ij; + bond_data *pbond_ij; + far_neighbor_data *nbr_jk; + reax_list *bonds, *hbonds; + bond_data *bond_list; + hbond_data *hbond_list; + + // tally variables + double fi_tmp[3], fk_tmp[3], delij[3], delkj[3]; + + bonds = (*lists) + BONDS; + bond_list = bonds->select.bond_list; + hbonds = (*lists) + HBONDS; + hbond_list = hbonds->select.hbond_list; + + for (j = 0; j < system->n; ++j) + if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) { + type_j = system->my_atoms[j].type; + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds); + hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds); + if (type_j < 0) continue; + + top = 0; + for (pi = start_j; pi < end_j; ++pi) { + pbond_ij = &(bond_list[pi]); + i = pbond_ij->nbr; + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + bo_ij = &(pbond_ij->bo_data); + + if (system->reax_param.sbp[type_i].p_hbond == 2 && + bo_ij->BO >= HB_THRESHOLD) + hblist[top++] = pi; + } + + for (pk = hb_start_j; pk < hb_end_j; ++pk) { + /* set k's varibles */ + k = hbond_list[pk].nbr; + type_k = system->my_atoms[k].type; + if (type_k < 0) continue; + nbr_jk = hbond_list[pk].ptr; + r_jk = nbr_jk->d; + rvec_Scale(dvec_jk, hbond_list[pk].scl, nbr_jk->dvec); + + for (itr = 0; itr < top; ++itr) { + pi = hblist[itr]; + pbond_ij = &(bonds->select.bond_list[pi]); + i = pbond_ij->nbr; + + if (system->my_atoms[i].orig_id != system->my_atoms[k].orig_id) { + bo_ij = &(pbond_ij->bo_data); + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + hbp = &(system->reax_param.hbp[type_i][type_j][type_k]); + if (hbp->r0_hb <= 0.0) continue; + ++num_hb_intrs; + + Calculate_Theta(pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, + &theta, &cos_theta); + /* the derivative of cos(theta) */ + Calculate_dCos_Theta(pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, + &dcos_theta_di, &dcos_theta_dj, + &dcos_theta_dk); + + /* hyrogen bond energy*/ + sin_theta2 = sin(theta/2.0); + sin_xhz4 = SQR(sin_theta2); + sin_xhz4 *= sin_xhz4; + cos_xhz1 = (1.0 - cos_theta); + exp_hb2 = exp(-hbp->p_hb2 * bo_ij->BO); + exp_hb3 = exp(-hbp->p_hb3 * (hbp->r0_hb / r_jk + + r_jk / hbp->r0_hb - 2.0)); + + data->my_en.e_hb += e_hb = + hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4; + + CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4; + CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1; + CEhb3 = -hbp->p_hb3 * + (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb; + + /* hydrogen bond forces */ + bo_ij->Cdbo += CEhb1; // dbo term + + // dcos terms + rvec_ScaledAdd(workspace->f[i], +CEhb2, dcos_theta_di); + rvec_ScaledAdd(workspace->f[j], +CEhb2, dcos_theta_dj); + rvec_ScaledAdd(workspace->f[k], +CEhb2, dcos_theta_dk); + // dr terms + rvec_ScaledAdd(workspace->f[j], -CEhb3/r_jk, dvec_jk); + rvec_ScaledAdd(workspace->f[k], +CEhb3/r_jk, dvec_jk); + + /* tally into per-atom virials */ + if (system->pair_ptr->evflag) { + rvec_ScaledSum(delij, 1., system->my_atoms[j].x, + -1., system->my_atoms[i].x); + rvec_ScaledSum(delkj, 1., system->my_atoms[j].x, + -1., system->my_atoms[k].x); + + rvec_Scale(fi_tmp, CEhb2, dcos_theta_di); + rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk); + rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk); + + system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj); + } + } + } + } + } + } +} diff --git a/src/REAXFF/reaxff_init_md.cpp b/src/REAXFF/reaxff_init_md.cpp new file mode 100644 index 0000000000..268af75358 --- /dev/null +++ b/src/REAXFF/reaxff_init_md.cpp @@ -0,0 +1,177 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + + Contributing authors: + H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama + Corresponding author: + Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "error.h" + +#include +#include +#include +#include + +namespace ReaxFF { + + void Init_System(reax_system *system, control_params *control) + { + int i; + reax_atom *atom; + + int mincap = system->mincap; + double safezone = system->safezone; + double saferzone = system->saferzone; + + // determine the local and total capacity + + system->local_cap = MAX((int)(system->n * safezone), mincap); + system->total_cap = MAX((int)(system->N * safezone), mincap); + + /* estimate numH and Hcap */ + system->numH = 0; + if (control->hbond_cut > 0) + for (i = 0; i < system->n; ++i) { + atom = &(system->my_atoms[i]); + if (system->reax_param.sbp[atom->type].p_hbond == 1 && atom->type >= 0) + atom->Hindex = system->numH++; + else atom->Hindex = -1; + } + system->Hcap = (int)(MAX(system->numH * saferzone, mincap)); + } + + void Init_Simulation_Data(simulation_data *data) + { + Reset_Simulation_Data(data); + data->step = 0; + } + + static void Init_Taper(control_params *control, storage *workspace) + { + double d1, d7; + double swa, swa2, swa3; + double swb, swb2, swb3; + LAMMPS_NS::Error *error = control->error_ptr; + + swa = control->nonb_low; + swb = control->nonb_cut; + + if (fabs(swa) > 0.01 && control->me == 0) + error->warning(FLERR, "Non-zero lower Taper-radius cutoff"); + + if (swb < 0) { + error->all(FLERR,"Negative upper Taper-radius cutoff"); + } + else if (swb < 5 && control->me == 0) + error->warning(FLERR,fmt::format("Warning: very low Taper-radius cutoff: " + "{}\n", swb)); + d1 = swb - swa; + d7 = pow(d1, 7.0); + swa2 = SQR(swa); + swa3 = CUBE(swa); + swb2 = SQR(swb); + swb3 = CUBE(swb); + + workspace->Tap[7] = 20.0 / d7; + workspace->Tap[6] = -70.0 * (swa + swb) / d7; + workspace->Tap[5] = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7; + workspace->Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3) / d7; + workspace->Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3) / d7; + workspace->Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7; + workspace->Tap[1] = 140.0 * swa3 * swb3 / d7; + workspace->Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 - + 7.0*swa*swb3*swb3 + swb3*swb3*swb) / d7; + } + + void Init_Workspace(reax_system *system, control_params *control, storage *workspace) + { + Allocate_Workspace(control, workspace,system->total_cap); + + memset(&(workspace->realloc), 0, sizeof(reallocate_data)); + Reset_Workspace(system, workspace); + + /* Initialize the Taper function */ + Init_Taper(control, workspace); + } + + static void Init_Lists(reax_system *system, control_params *control, reax_list **lists) + { + int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; + int *hb_top, *bond_top; + + int mincap = system->mincap; + double safezone = system->safezone; + double saferzone = system->saferzone; + + bond_top = (int*) calloc(system->total_cap, sizeof(int)); + hb_top = (int*) calloc(system->local_cap, sizeof(int)); + Estimate_Storages(system, control, lists, + &Htop, hb_top, bond_top, &num_3body); + + if (control->hbond_cut > 0) { + /* init H indexes */ + total_hbonds = 0; + for (i = 0; i < system->n; ++i) { + system->my_atoms[i].num_hbonds = hb_top[i]; + total_hbonds += hb_top[i]; + } + total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds)); + + Make_List(system->Hcap, total_hbonds, TYP_HBOND,*lists+HBONDS); + (*lists+HBONDS)->error_ptr = system->error_ptr; + } + + total_bonds = 0; + for (i = 0; i < system->N; ++i) { + system->my_atoms[i].num_bonds = bond_top[i]; + total_bonds += bond_top[i]; + } + bond_cap = (int)(MAX(total_bonds*safezone, mincap*MIN_BONDS)); + + Make_List(system->total_cap, bond_cap, TYP_BOND,*lists+BONDS); + (*lists+BONDS)->error_ptr = system->error_ptr; + + /* 3bodies list */ + cap_3body = (int)(MAX(num_3body*safezone, MIN_3BODIES)); + Make_List(bond_cap, cap_3body, TYP_THREE_BODY,*lists+THREE_BODIES); + (*lists+THREE_BODIES)->error_ptr = system->error_ptr; + + free(hb_top); + free(bond_top); + } + + void Initialize(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists, MPI_Comm world) + { + Init_System(system,control); + Init_Simulation_Data(data); + Init_Workspace(system,control,workspace); + Init_Lists(system,control,lists); + if (control->tabulate) + Init_Lookup_Tables(system,control,workspace,world); + } +} diff --git a/src/REAXFF/reaxff_inline.h b/src/REAXFF/reaxff_inline.h new file mode 100644 index 0000000000..a53ab4bb05 --- /dev/null +++ b/src/REAXFF/reaxff_inline.h @@ -0,0 +1,88 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hasan Metin Aktulga, Purdue University + (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov) + + Heavily modified and adapted for LAMMPS by the LAMMPS developers. +------------------------------------------------------------------------- */ + +#ifndef LMP_REAXFF_INLINE_H +#define LMP_REAXFF_INLINE_H + +#include "accelerator_kokkos.h" // for LAMMPS_INLINE + +namespace ReaxFF +{ + struct LR_data + { + double H; + double e_vdW, CEvd; + double e_ele, CEclmb; + + LAMMPS_INLINE + LR_data() {} + + LAMMPS_INLINE + void operator = (const LR_data& rhs) { + H = rhs.H; + e_vdW = rhs.e_vdW; + CEvd = rhs.CEvd; + e_ele = rhs.e_ele; + CEclmb = rhs.CEclmb; + } + LAMMPS_INLINE + void operator = (const LR_data& rhs) volatile { + H = rhs.H; + e_vdW = rhs.e_vdW; + CEvd = rhs.CEvd; + e_ele = rhs.e_ele; + CEclmb = rhs.CEclmb; + } + }; + + struct cubic_spline_coef + { + double a, b, c, d; + + LAMMPS_INLINE + cubic_spline_coef() {} + + LAMMPS_INLINE + cubic_spline_coef(const cubic_spline_coef &_c) { + a = _c.a; + b = _c.b; + c = _c.c; + d = _c.d; + } + + LAMMPS_INLINE + void operator=(const cubic_spline_coef &rhs) { + a = rhs.a; + b = rhs.b; + c = rhs.c; + d = rhs.d; + } + + LAMMPS_INLINE + void operator=(const cubic_spline_coef &rhs) volatile { + a = rhs.a; + b = rhs.b; + c = rhs.c; + d = rhs.d; + } + }; +} + +#endif diff --git a/src/REAXFF/reaxff_list.cpp b/src/REAXFF/reaxff_list.cpp new file mode 100644 index 0000000000..79d96bb9d9 --- /dev/null +++ b/src/REAXFF/reaxff_list.cpp @@ -0,0 +1,113 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "error.h" + +namespace ReaxFF { + + /************* allocate list space ******************/ + void Make_List(int n, int num_intrs, int type, reax_list *l) + { + l->allocated = 1; + + l->n = n; + l->num_intrs = num_intrs; + + if (l->index) sfree(l->error_ptr, l->index, "list:index"); + if (l->end_index) sfree(l->error_ptr, l->end_index, "list:end_index"); + l->index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:index"); + l->end_index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:end_index"); + + l->type = type; + + switch(l->type) { + case TYP_THREE_BODY: + if (l->select.three_body_list) sfree(l->error_ptr, l->select.three_body_list,"list:three_bodies"); + l->select.three_body_list = (three_body_interaction_data*) + smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(three_body_interaction_data), + "list:three_bodies"); + break; + + case TYP_BOND: + if (l->select.bond_list) sfree(l->error_ptr, l->select.bond_list,"list:bonds"); + l->select.bond_list = (bond_data*) + smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(bond_data), "list:bonds"); + break; + + case TYP_FAR_NEIGHBOR: + if (l->select.far_nbr_list) sfree(l->error_ptr, l->select.far_nbr_list,"list:far_nbrs"); + l->select.far_nbr_list = (far_neighbor_data*) + smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(far_neighbor_data), "list:far_nbrs"); + break; + + case TYP_HBOND: + if (l->select.hbond_list) sfree(l->error_ptr, l->select.hbond_list,"list:hbonds"); + l->select.hbond_list = (hbond_data*) + smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(hbond_data), "list:hbonds"); + break; + + default: + l->error_ptr->all(FLERR,fmt::format("No list type {} defined", l->type)); + } + } + + void Delete_List(reax_list *l) + { + if (l->allocated == 0) + return; + l->allocated = 0; + + sfree(l->error_ptr, l->index, "list:index"); + sfree(l->error_ptr, l->end_index, "list:end_index"); + l->index = nullptr; + l->end_index = nullptr; + + switch(l->type) { + case TYP_HBOND: + sfree(l->error_ptr, l->select.hbond_list, "list:hbonds"); + l->select.hbond_list = nullptr; + break; + case TYP_FAR_NEIGHBOR: + sfree(l->error_ptr, l->select.far_nbr_list, "list:far_nbrs"); + l->select.far_nbr_list = nullptr; + break; + case TYP_BOND: + sfree(l->error_ptr, l->select.bond_list, "list:bonds"); + l->select.bond_list = nullptr; + break; + case TYP_THREE_BODY: + sfree(l->error_ptr, l->select.three_body_list, "list:three_bodies"); + l->select.three_body_list = nullptr; + break; + + default: + l->error_ptr->all(FLERR,fmt::format("No list type {} defined", l->type)); + } + } +} diff --git a/src/REAXFF/reaxff_lookup.cpp b/src/REAXFF/reaxff_lookup.cpp new file mode 100644 index 0000000000..6471f1e6e2 --- /dev/null +++ b/src/REAXFF/reaxff_lookup.cpp @@ -0,0 +1,291 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include +#include + +namespace ReaxFF { + static void Tridiagonal_Solve(const double *a, const double *b, + double *c, double *d, double *x, unsigned int n) { + int i; + double id; + + c[0] /= b[0]; /* Division by zero risk. */ + d[0] /= b[0]; /* Division by zero would imply a singular matrix. */ + for (i = 1; i < (int)n; i++) { + id = (b[i] - c[i-1] * a[i]); /* Division by zero risk. */ + c[i] /= id; /* Last value calculated is redundant. */ + d[i] = (d[i] - d[i-1] * a[i])/id; + } + + x[n - 1] = d[n - 1]; + for (i = n - 2; i >= 0; i--) + x[i] = d[i] - c[i] * x[i + 1]; + } + + void Natural_Cubic_Spline(LAMMPS_NS::Error* error_ptr, const double *h, const double *f, + cubic_spline_coef *coef, unsigned int n) + { + int i; + double *a, *b, *c, *d, *v; + + /* allocate space for the linear system */ + a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + + /* build the linear system */ + a[0] = a[1] = a[n-1] = 0; + for (i = 2; i < (int)n-1; ++i) + a[i] = h[i-1]; + + b[0] = b[n-1] = 0; + for (i = 1; i < (int)n-1; ++i) + b[i] = 2 * (h[i-1] + h[i]); + + c[0] = c[n-2] = c[n-1] = 0; + for (i = 1; i < (int)n-2; ++i) + c[i] = h[i]; + + d[0] = d[n-1] = 0; + for (i = 1; i < (int)n-1; ++i) + d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]); + + v[0] = 0; + v[n-1] = 0; + Tridiagonal_Solve(&(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n-2); + + for (i = 1; i < (int)n; ++i) { + coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]); + coef[i-1].c = v[i]/2; + coef[i-1].b = (f[i]-f[i-1])/h[i-1] + h[i-1]*(2*v[i] + v[i-1])/6; + coef[i-1].a = f[i]; + } + + sfree(error_ptr, a, "cubic_spline:a"); + sfree(error_ptr, b, "cubic_spline:b"); + sfree(error_ptr, c, "cubic_spline:c"); + sfree(error_ptr, d, "cubic_spline:d"); + sfree(error_ptr, v, "cubic_spline:v"); + } + + void Complete_Cubic_Spline(LAMMPS_NS::Error* error_ptr, const double *h, + const double *f, double v0, double vlast, + cubic_spline_coef *coef, unsigned int n) + { + int i; + double *a, *b, *c, *d, *v; + + /* allocate space for the linear system */ + a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + + /* build the linear system */ + a[0] = 0; + for (i = 1; i < (int)n; ++i) + a[i] = h[i-1]; + + b[0] = 2*h[0]; + for (i = 1; i < (int)n; ++i) + b[i] = 2 * (h[i-1] + h[i]); + + c[n-1] = 0; + for (i = 0; i < (int)n-1; ++i) + c[i] = h[i]; + + d[0] = 6 * (f[1]-f[0])/h[0] - 6 * v0; + d[n-1] = 6 * vlast - 6 * (f[n-1]-f[n-2]/h[n-2]); + for (i = 1; i < (int)n-1; ++i) + d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]); + + Tridiagonal_Solve(&(a[0]), &(b[0]), &(c[0]), &(d[0]), &(v[0]), n); + + for (i = 1; i < (int)n; ++i) { + coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]); + coef[i-1].c = v[i]/2; + coef[i-1].b = (f[i]-f[i-1])/h[i-1] + h[i-1]*(2*v[i] + v[i-1])/6; + coef[i-1].a = f[i]; + } + + sfree(error_ptr, a, "cubic_spline:a"); + sfree(error_ptr, b, "cubic_spline:b"); + sfree(error_ptr, c, "cubic_spline:c"); + sfree(error_ptr, d, "cubic_spline:d"); + sfree(error_ptr, v, "cubic_spline:v"); + } + + void Init_Lookup_Tables(reax_system *system, control_params *control, + storage *workspace, MPI_Comm world) + { + int i, j, r; + double dr; + double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; + double v0_vdw, v0_ele, vlast_vdw, vlast_ele; + LR_lookup_table ** & LR = system->LR; + + /* initializations */ + v0_vdw = 0; + v0_ele = 0; + vlast_vdw = 0; + vlast_ele = 0; + + const int num_atom_types = system->reax_param.num_atom_types; + int *existing_types = new int[num_atom_types]; + int *aggregated = new int[num_atom_types]; + dr = control->nonb_cut / control->tabulate; + h = (double*) + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h"); + fh = (double*) + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh"); + fvdw = (double*) + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw"); + fCEvd = (double*) + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd"); + fele = (double*) + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele"); + fCEclmb = (double*) + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); + + LR = (LR_lookup_table**) + scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table*), "lookup:LR"); + for (i = 0; i < num_atom_types; ++i) + LR[i] = (LR_lookup_table*) + scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]"); + + for (i = 0; i < num_atom_types; ++i) + existing_types[i] = 0; + for (i = 0; i < system->n; ++i) + existing_types[system->my_atoms[i].type] = 1; + + MPI_Allreduce(existing_types, aggregated, num_atom_types, MPI_INT, MPI_SUM, world); + + for (i = 0; i < num_atom_types; ++i) { + if (aggregated[i]) { + for (j = i; j < num_atom_types; ++j) { + if (aggregated[j]) { + LR[i][j].xmin = 0; + LR[i][j].xmax = control->nonb_cut; + LR[i][j].n = control->tabulate + 2; + LR[i][j].dx = dr; + LR[i][j].inv_dx = control->tabulate / control->nonb_cut; + LR[i][j].y = (LR_data*) + smalloc(system->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); + LR[i][j].H = (cubic_spline_coef*) + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); + LR[i][j].vdW = (cubic_spline_coef*) + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); + LR[i][j].CEvd = (cubic_spline_coef*) + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); + LR[i][j].ele = (cubic_spline_coef*) + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); + LR[i][j].CEclmb = (cubic_spline_coef*) + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), + "lookup:LR[i,j].CEclmb"); + + for (r = 1; r <= control->tabulate; ++r) { + LR_vdW_Coulomb(system, workspace, control, i, j, r * dr, &(LR[i][j].y[r])); + h[r] = LR[i][j].dx; + fh[r] = LR[i][j].y[r].H; + fvdw[r] = LR[i][j].y[r].e_vdW; + fCEvd[r] = LR[i][j].y[r].CEvd; + fele[r] = LR[i][j].y[r].e_ele; + fCEclmb[r] = LR[i][j].y[r].CEclmb; + } + + // init the start-end points + h[r] = LR[i][j].dx; + v0_vdw = LR[i][j].y[1].CEvd; + v0_ele = LR[i][j].y[1].CEclmb; + fh[r] = fh[r-1]; + fvdw[r] = fvdw[r-1]; + fCEvd[r] = fCEvd[r-1]; + fele[r] = fele[r-1]; + fCEclmb[r] = fCEclmb[r-1]; + vlast_vdw = fCEvd[r-1]; + vlast_ele = fele[r-1]; + + Natural_Cubic_Spline(control->error_ptr, &h[1], &fh[1], + &(LR[i][j].H[1]), control->tabulate+1); + + Complete_Cubic_Spline(control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, + &(LR[i][j].vdW[1]), control->tabulate+1); + + Natural_Cubic_Spline(control->error_ptr, &h[1], &fCEvd[1], + &(LR[i][j].CEvd[1]), control->tabulate+1); + + Complete_Cubic_Spline(control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, + &(LR[i][j].ele[1]), control->tabulate+1); + + Natural_Cubic_Spline(control->error_ptr, &h[1], &fCEclmb[1], + &(LR[i][j].CEclmb[1]), control->tabulate+1); + } else { + LR[i][j].n = 0; + } + } + } + } + free(h); + free(fh); + free(fvdw); + free(fCEvd); + free(fele); + free(fCEclmb); + delete[] existing_types; + delete[] aggregated; + } + + void Deallocate_Lookup_Tables(reax_system *system) + { + int i, j; + int ntypes; + LR_lookup_table ** & LR = system->LR; + + ntypes = system->reax_param.num_atom_types; + + for (i = 0; i < ntypes; ++i) { + for (j = i; j < ntypes; ++j) + if (LR[i][j].n) { + sfree(system->error_ptr, LR[i][j].y, "LR[i,j].y"); + sfree(system->error_ptr, LR[i][j].H, "LR[i,j].H"); + sfree(system->error_ptr, LR[i][j].vdW, "LR[i,j].vdW"); + sfree(system->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd"); + sfree(system->error_ptr, LR[i][j].ele, "LR[i,j].ele"); + sfree(system->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb"); + } + sfree(system->error_ptr, LR[i], "LR[i]"); + } + sfree(system->error_ptr, LR, "LR"); + } +} + diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/REAXFF/reaxff_multi_body.cpp similarity index 84% rename from src/USER-REAXC/reaxc_multi_body.cpp rename to src/REAXFF/reaxff_multi_body.cpp index 778bb1ad41..2390b54474 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/REAXFF/reaxff_multi_body.cpp @@ -25,17 +25,18 @@ . ----------------------------------------------------------------------*/ -#include "reaxc_multi_body.h" +#include "reaxff_api.h" + +#include "pair.h" + #include #include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" -void Atom_Energy( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists, - output_controls * /*out_control*/ ) -{ +namespace ReaxFF { + + void Atom_Energy(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, reax_list **lists) + { int i, j, pj, type_i, type_j; double Delta_lpcorr, dfvl; double e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi; @@ -68,12 +69,12 @@ void Atom_Energy( reax_system *system, control_params *control, /* set the parameter pointer */ type_i = system->my_atoms[i].type; if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[ type_i ]); + sbp_i = &(system->reax_param.sbp[type_i]); /* lone-pair Energy */ p_lp2 = sbp_i->p_lp2; - expvd2 = exp( -75 * workspace->Delta_lp[i] ); - inv_expvd2 = 1. / (1. + expvd2 ); + expvd2 = exp(-75 * workspace->Delta_lp[i]); + inv_expvd2 = 1. / (1. + expvd2); numbonds = 0; e_lp = 0.0; @@ -92,8 +93,8 @@ void Atom_Energy( reax_system *system, control_params *control, if (numbonds > 0 || control->enobondsflag) workspace->CdDelta[i] += CElp; // lp - 1st term - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) + /* tally energy into global or per-atom energy accumulators */ + if (system->pair_ptr->eflag_either) system->pair_ptr->ev_tally(i,i,system->n,1,e_lp,0.0,0.0,0.0,0.0,0.0); /* correction for C2 */ @@ -103,9 +104,9 @@ void Atom_Energy( reax_system *system, control_params *control, type_j = system->my_atoms[j].type; if (type_j < 0) continue; - if (!strcmp( system->reax_param.sbp[type_j].name, "C" )) { - twbp = &( system->reax_param.tbp[type_i][type_j]); - bo_ij = &( bonds->select.bond_list[pj].bo_data ); + if (!strcmp(system->reax_param.sbp[type_j].name, "C")) { + twbp = &(system->reax_param.tbp[type_i][type_j]); + bo_ij = &(bonds->select.bond_list[pj].bo_data); Di = workspace->Delta[i]; vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.); @@ -118,8 +119,8 @@ void Atom_Energy( reax_system *system, control_params *control, bo_ij->Cdbo += deahu2dbo; workspace->CdDelta[i] += deahu2dsbo; - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) + /* tally energy into global or per-atom energy accumulators */ + if (system->pair_ptr->eflag_either) system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0); } @@ -127,11 +128,10 @@ void Atom_Energy( reax_system *system, control_params *control, } } - for (i = 0; i < system->n; ++i) { type_i = system->my_atoms[i].type; if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[ type_i ]); + sbp_i = &(system->reax_param.sbp[type_i]); /* over-coordination energy */ if (sbp_i->mass > 21.0) @@ -145,20 +145,20 @@ void Atom_Energy( reax_system *system, control_params *control, type_j = system->my_atoms[j].type; if (type_j < 0) continue; bo_ij = &(bonds->select.bond_list[pj].bo_data); - twbp = &(system->reax_param.tbp[ type_i ][ type_j ]); + twbp = &(system->reax_param.tbp[type_i][type_j]); sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO; sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])* - ( bo_ij->BO_pi + bo_ij->BO_pi2 ); + (bo_ij->BO_pi + bo_ij->BO_pi2); } - exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 ); + exp_ovun1 = p_ovun3 * exp(p_ovun4 * sum_ovun2); inv_exp_ovun1 = 1.0 / (1 + exp_ovun1); Delta_lpcorr = workspace->Delta[i] - (dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1; - exp_ovun2 = exp( p_ovun2 * Delta_lpcorr ); + exp_ovun2 = exp(p_ovun2 * Delta_lpcorr); inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2); DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8); @@ -167,9 +167,9 @@ void Atom_Energy( reax_system *system, control_params *control, data->my_en.e_ov += e_ov = sum_ovun1 * CEover1; CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 * - (1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 )); + (1.0 - Delta_lpcorr * (DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2)); - CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 ); + CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1); CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) * p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1); @@ -180,7 +180,7 @@ void Atom_Energy( reax_system *system, control_params *control, p_ovun5 = sbp_i->p_ovun5; exp_ovun2n = 1.0 / exp_ovun2; - exp_ovun6 = exp( p_ovun6 * Delta_lpcorr ); + exp_ovun6 = exp(p_ovun6 * Delta_lpcorr); exp_ovun8 = p_ovun7 * exp(p_ovun8 * sum_ovun2); inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n); inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8); @@ -195,15 +195,15 @@ void Atom_Energy( reax_system *system, control_params *control, -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8; CEunder1 = inv_exp_ovun2n * - ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 + - p_ovun2 * e_un * exp_ovun2n ); + (p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 + + p_ovun2 * e_un * exp_ovun2n); CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8; CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1); CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) * p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2; - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) { + /* tally energy into global or per-atom energy accumulators */ + if (system->pair_ptr->eflag_either) { eng_tmp = e_ov; if (numbonds > 0 || control->enobondsflag) eng_tmp += e_un; @@ -219,10 +219,9 @@ void Atom_Energy( reax_system *system, control_params *control, pbond = &(bonds->select.bond_list[pj]); j = pbond->nbr; bo_ij = &(pbond->bo_data); - twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ] + twbp = &(system->reax_param.tbp[system->my_atoms[i].type] [system->my_atoms[pbond->nbr].type]); - bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s;// OvCoor-1st workspace->CdDelta[j] += CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a @@ -231,15 +230,13 @@ void Atom_Energy( reax_system *system, control_params *control, bo_ij->Cdbopi2 += CEover4 * (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b - workspace->CdDelta[j] += CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a bo_ij->Cdbopi += CEunder4 * (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b bo_ij->Cdbopi2 += CEunder4 * (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b - } - } } +} diff --git a/src/REAXFF/reaxff_nonbonded.cpp b/src/REAXFF/reaxff_nonbonded.cpp new file mode 100644 index 0000000000..8a1e41da29 --- /dev/null +++ b/src/REAXFF/reaxff_nonbonded.cpp @@ -0,0 +1,407 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "pair.h" + +#include + +namespace ReaxFF { + void Compute_Polarization_Energy(reax_system *system, simulation_data *data) + { + int i, type_i; + double q, en_tmp; + + data->my_en.e_pol = 0.0; + for (i = 0; i < system->n; i++) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + q = system->my_atoms[i].q; + + en_tmp = KCALpMOL_to_EV * (system->reax_param.sbp[type_i].chi * q + + (system->reax_param.sbp[type_i].eta / 2.) * SQR(q)); + data->my_en.e_pol += en_tmp; + + /* tally energy into global or per-atom energy accumulators */ + if (system->pair_ptr->eflag_either) + system->pair_ptr->ev_tally(i,i,system->n,1,0.0,en_tmp,0.0,0.0,0.0,0.0); + } + } + + void vdW_Coulomb_Energy(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + int i, j, pj, natoms; + int start_i, end_i, flag; + rc_tagint orig_i, orig_j; + double p_vdW1, p_vdW1i; + double powr_vdW1, powgi_vdW1; + double tmp, r_ij, fn13, exp1, exp2; + double Tap, dTap, dfn13, CEvd, CEclmb, de_core; + double dr3gamij_1, dr3gamij_3; + double e_ele, e_vdW, e_core, SMALL = 0.0001; + double e_lg, de_lg, r_ij5, r_ij6, re6; + two_body_parameters *twbp; + far_neighbor_data *nbr_pj; + reax_list *far_nbrs; + + // Tallying variables: + double pe_vdw, f_tmp, delij[3]; + + natoms = system->n; + far_nbrs = (*lists) + FAR_NBRS; + p_vdW1 = system->reax_param.gp.l[28]; + p_vdW1i = 1.0 / p_vdW1; + e_core = 0; + e_vdW = 0; + e_lg = de_lg = 0.0; + + for (i = 0; i < natoms; ++i) { + if (system->my_atoms[i].type < 0) continue; + start_i = Start_Index(i, far_nbrs); + end_i = End_Index(i, far_nbrs); + orig_i = system->my_atoms[i].orig_id; + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + if (system->my_atoms[j].type < 0) continue; + orig_j = system->my_atoms[j].orig_id; + + flag = 0; + if (nbr_pj->d <= control->nonb_cut) { + if (j < natoms) flag = 1; + else if (orig_i < orig_j) flag = 1; + else if (orig_i == orig_j) { + if (nbr_pj->dvec[2] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[2]) < SMALL) { + if (nbr_pj->dvec[1] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) + flag = 1; + } + } + } + + if (flag) { + + r_ij = nbr_pj->d; + twbp = &(system->reax_param.tbp[system->my_atoms[i].type] + [system->my_atoms[j].type]); + + Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; + Tap = Tap * r_ij + workspace->Tap[5]; + Tap = Tap * r_ij + workspace->Tap[4]; + Tap = Tap * r_ij + workspace->Tap[3]; + Tap = Tap * r_ij + workspace->Tap[2]; + Tap = Tap * r_ij + workspace->Tap[1]; + Tap = Tap * r_ij + workspace->Tap[0]; + + dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; + dTap = dTap * r_ij + 5*workspace->Tap[5]; + dTap = dTap * r_ij + 4*workspace->Tap[4]; + dTap = dTap * r_ij + 3*workspace->Tap[3]; + dTap = dTap * r_ij + 2*workspace->Tap[2]; + dTap += workspace->Tap[1]/r_ij; + + /*vdWaals Calculations*/ + if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) + { // shielding + powr_vdW1 = pow(r_ij, p_vdW1); + powgi_vdW1 = pow(1.0 / twbp->gamma_w, p_vdW1); + + fn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i); + exp1 = exp(twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + + e_vdW = twbp->D * (exp1 - 2.0 * exp2); + data->my_en.e_vdW += Tap * e_vdW; + + dfn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * + pow(r_ij, p_vdW1 - 2.0); + + CEvd = dTap * e_vdW - + Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; + } else { // no shielding + exp1 = exp(twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + + e_vdW = twbp->D * (exp1 - 2.0 * exp2); + data->my_en.e_vdW += Tap * e_vdW; + + CEvd = dTap * e_vdW - + Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; + } + + if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) + { // inner wall + e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); + data->my_en.e_vdW += Tap * e_core; + + de_core = -(twbp->acore/twbp->rcore) * e_core; + CEvd += dTap * e_core + Tap * de_core / r_ij; + + // lg correction, only if lgvdw is yes + if (control->lgflag) { + r_ij5 = pow(r_ij, 5.0); + r_ij6 = pow(r_ij, 6.0); + re6 = pow(twbp->lgre, 6.0); + e_lg = -(twbp->lgcij/(r_ij6 + re6)); + data->my_en.e_vdW += Tap * e_lg; + + de_lg = -6.0 * e_lg * r_ij5 / (r_ij6 + re6) ; + CEvd += dTap * e_lg + Tap * de_lg / r_ij; + } + + } + + /*Coulomb Calculations*/ + dr3gamij_1 = (r_ij * r_ij * r_ij + twbp->gamma); + dr3gamij_3 = pow(dr3gamij_1 , 0.33333333333333); + + tmp = Tap / dr3gamij_3; + data->my_en.e_ele += e_ele = + C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp; + + CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * + (dTap - Tap * r_ij / dr3gamij_1) / dr3gamij_3; + + /* tally into per-atom energy */ + if (system->pair_ptr->evflag) { + pe_vdw = Tap * (e_vdW + e_core + e_lg); + rvec_ScaledSum(delij, 1., system->my_atoms[i].x, + -1., system->my_atoms[j].x); + f_tmp = -(CEvd + CEclmb); + system->pair_ptr->ev_tally(i,j,natoms,1,pe_vdw,e_ele, + f_tmp,delij[0],delij[1],delij[2]); + } + + rvec_ScaledAdd(workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec); + rvec_ScaledAdd(workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec); + } + } + } + + Compute_Polarization_Energy(system, data); + } + + void Tabulated_vdW_Coulomb_Energy(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + int i, j, pj, r, natoms; + int type_i, type_j, tmin, tmax; + int start_i, end_i, flag; + rc_tagint orig_i, orig_j; + double r_ij, base, dif; + double e_vdW, e_ele; + double CEvd, CEclmb, SMALL = 0.0001; + double f_tmp, delij[3]; + + far_neighbor_data *nbr_pj; + reax_list *far_nbrs; + LR_lookup_table *t; + LR_lookup_table ** & LR = system->LR; + + natoms = system->n; + far_nbrs = (*lists) + FAR_NBRS; + + e_ele = e_vdW = 0; + + for (i = 0; i < natoms; ++i) { + type_i = system->my_atoms[i].type; + if (type_i < 0) continue; + start_i = Start_Index(i,far_nbrs); + end_i = End_Index(i,far_nbrs); + orig_i = system->my_atoms[i].orig_id; + + for (pj = start_i; pj < end_i; ++pj) { + nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); + j = nbr_pj->nbr; + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + orig_j = system->my_atoms[j].orig_id; + + flag = 0; + if (nbr_pj->d <= control->nonb_cut) { + if (j < natoms) flag = 1; + else if (orig_i < orig_j) flag = 1; + else if (orig_i == orig_j) { + if (nbr_pj->dvec[2] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[2]) < SMALL) { + if (nbr_pj->dvec[1] > SMALL) flag = 1; + else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) + flag = 1; + } + } + } + + if (flag) { + + r_ij = nbr_pj->d; + tmin = MIN(type_i, type_j); + tmax = MAX(type_i, type_j); + t = &(LR[tmin][tmax]); + + /* Cubic Spline Interpolation */ + r = (int)(r_ij * t->inv_dx); + if (r == 0) ++r; + base = (double)(r+1) * t->dx; + dif = r_ij - base; + + e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif + + t->vdW[r].a; + + e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + + t->ele[r].a; + e_ele *= system->my_atoms[i].q * system->my_atoms[j].q; + + data->my_en.e_vdW += e_vdW; + data->my_en.e_ele += e_ele; + + CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif + + t->CEvd[r].a; + + CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif + + t->CEclmb[r].a; + CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; + + /* tally into per-atom energy */ + if (system->pair_ptr->evflag) { + rvec_ScaledSum(delij, 1., system->my_atoms[i].x, + -1., system->my_atoms[j].x); + f_tmp = -(CEvd + CEclmb); + system->pair_ptr->ev_tally(i,j,natoms,1,e_vdW,e_ele, + f_tmp,delij[0],delij[1],delij[2]); + } + + rvec_ScaledAdd(workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec); + rvec_ScaledAdd(workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec); + } + } + } + + Compute_Polarization_Energy(system, data); + } + + void LR_vdW_Coulomb(reax_system *system, storage *workspace, + control_params *control, int i, int j, + double r_ij, LR_data *lr) + { + double p_vdW1 = system->reax_param.gp.l[28]; + double p_vdW1i = 1.0 / p_vdW1; + double powr_vdW1, powgi_vdW1; + double tmp, fn13, exp1, exp2; + double Tap, dTap, dfn13; + double dr3gamij_1, dr3gamij_3; + double e_core, de_core; + double e_lg, de_lg, r_ij5, r_ij6, re6; + two_body_parameters *twbp; + + twbp = &(system->reax_param.tbp[i][j]); + e_core = 0; + de_core = 0; + e_lg = de_lg = 0.0; + + /* calculate taper and its derivative */ + Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; + Tap = Tap * r_ij + workspace->Tap[5]; + Tap = Tap * r_ij + workspace->Tap[4]; + Tap = Tap * r_ij + workspace->Tap[3]; + Tap = Tap * r_ij + workspace->Tap[2]; + Tap = Tap * r_ij + workspace->Tap[1]; + Tap = Tap * r_ij + workspace->Tap[0]; + + dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; + dTap = dTap * r_ij + 5*workspace->Tap[5]; + dTap = dTap * r_ij + 4*workspace->Tap[4]; + dTap = dTap * r_ij + 3*workspace->Tap[3]; + dTap = dTap * r_ij + 2*workspace->Tap[2]; + dTap += workspace->Tap[1]/r_ij; + + /*vdWaals Calculations*/ + if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) + { // shielding + powr_vdW1 = pow(r_ij, p_vdW1); + powgi_vdW1 = pow(1.0 / twbp->gamma_w, p_vdW1); + + fn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i); + exp1 = exp(twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW)); + + lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2); + + dfn13 = pow(powr_vdW1 + powgi_vdW1, p_vdW1i-1.0) * pow(r_ij, p_vdW1-2.0); + + lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - + Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; + } + else { // no shielding + exp1 = exp(twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + exp2 = exp(0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW)); + + lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2); + lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - + Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; + } + + if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) + { // inner wall + e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); + lr->e_vdW += Tap * e_core; + + de_core = -(twbp->acore/twbp->rcore) * e_core; + lr->CEvd += dTap * e_core + Tap * de_core / r_ij; + + // lg correction, only if lgvdw is yes + if (control->lgflag) { + r_ij5 = pow(r_ij, 5.0); + r_ij6 = pow(r_ij, 6.0); + re6 = pow(twbp->lgre, 6.0); + e_lg = -(twbp->lgcij/(r_ij6 + re6)); + lr->e_vdW += Tap * e_lg; + + de_lg = -6.0 * e_lg * r_ij5 / (r_ij6 + re6) ; + lr->CEvd += dTap * e_lg + Tap * de_lg/r_ij; + } + + } + + + /* Coulomb calculations */ + dr3gamij_1 = (r_ij * r_ij * r_ij + twbp->gamma); + dr3gamij_3 = pow(dr3gamij_1 , 0.33333333333333); + + tmp = Tap / dr3gamij_3; + lr->H = EV_to_KCALpMOL * tmp; + lr->e_ele = C_ele * tmp; + + lr->CEclmb = C_ele * (dTap - Tap * r_ij / dr3gamij_1) / dr3gamij_3; + } +} + diff --git a/src/REAXFF/reaxff_reset_tools.cpp b/src/REAXFF/reaxff_reset_tools.cpp new file mode 100644 index 0000000000..30a58e84a5 --- /dev/null +++ b/src/REAXFF/reaxff_reset_tools.cpp @@ -0,0 +1,129 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "error.h" + +#include +#include + +namespace ReaxFF { + + static void Reset_Atoms(reax_system* system, control_params *control) + { + int i; + reax_atom *atom; + + system->numH = 0; + if (control->hbond_cut > 0) + for (i = 0; i < system->n; ++i) { + atom = &(system->my_atoms[i]); + if (atom->type < 0) continue; + if (system->reax_param.sbp[atom->type].p_hbond == 1) + atom->Hindex = system->numH++; + else atom->Hindex = -1; + } + } + + void Reset_Simulation_Data(simulation_data* data) + { + memset(&data->my_en,0,sizeof(energy_data)); + } + + void Reset_Workspace(reax_system *system, storage *workspace) + { + memset(workspace->total_bond_order, 0, system->total_cap * sizeof(double)); + memset(workspace->dDeltap_self, 0, system->total_cap * sizeof(rvec)); + memset(workspace->CdDelta, 0, system->total_cap * sizeof(double)); + memset(workspace->f, 0, system->total_cap * sizeof(rvec)); + + } + + static void Reset_Neighbor_Lists(reax_system *system, control_params *control, + storage *workspace, reax_list **lists) + { + int i, total_bonds, Hindex, total_hbonds; + reax_list *bonds, *hbonds; + + /* bonds list */ + if (system->N > 0) { + bonds = (*lists) + BONDS; + total_bonds = 0; + + /* reset start-end indexes */ + for (i = 0; i < system->N; ++i) { + Set_Start_Index(i, total_bonds, bonds); + Set_End_Index(i, total_bonds, bonds); + total_bonds += system->my_atoms[i].num_bonds; + } + + /* is reallocation needed? */ + if (total_bonds >= bonds->num_intrs * DANGER_ZONE) { + workspace->realloc.bonds = 1; + if (total_bonds >= bonds->num_intrs) + control->error_ptr->one(FLERR,fmt::format("Not enough space for bonds! " + "total={} allocated={}\n", + total_bonds, bonds->num_intrs)); + } + } + + if (control->hbond_cut > 0 && system->numH > 0) { + hbonds = (*lists) + HBONDS; + total_hbonds = 0; + + /* reset start-end indexes */ + for (i = 0; i < system->n; ++i) { + Hindex = system->my_atoms[i].Hindex; + if (Hindex > -1) { + Set_Start_Index(Hindex, total_hbonds, hbonds); + Set_End_Index(Hindex, total_hbonds, hbonds); + total_hbonds += system->my_atoms[i].num_hbonds; + } + } + + /* is reallocation needed? */ + if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) { + workspace->realloc.hbonds = 1; + if (total_hbonds >= hbonds->num_intrs) + control->error_ptr->one(FLERR,fmt::format("Not enough space for hbonds! " + "total={} allocated={}\n", + total_hbonds, hbonds->num_intrs)); + } + } + } + + + void Reset(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, reax_list **lists) + { + Reset_Atoms(system, control); + Reset_Simulation_Data(data); + Reset_Workspace(system, workspace); + Reset_Neighbor_Lists(system, control, workspace, lists); + } +} diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/REAXFF/reaxff_tool_box.cpp similarity index 50% rename from src/USER-REAXC/reaxc_tool_box.cpp rename to src/REAXFF/reaxff_tool_box.cpp index b047954d22..550668197c 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/REAXFF/reaxff_tool_box.cpp @@ -1,4 +1,3 @@ -// clang-format off /*---------------------------------------------------------------------- PuReMD - Purdue ReaxFF Molecular Dynamics Program @@ -25,8 +24,7 @@ . ----------------------------------------------------------------------*/ -#include "reaxc_tool_box.h" -#include "reaxc_defs.h" +#include "reaxff_api.h" #include #include @@ -34,93 +32,83 @@ #include "error.h" -int Tokenize( char* s, char*** tok ) -{ - char test[MAX_LINE]; - const char *sep = (const char *)"\t \n\r\f!="; - char *word; - int count=0; - - strncpy( test, s, MAX_LINE-1); - - for (word = strtok(test, sep); word; word = strtok(nullptr, sep)) { - strncpy( (*tok)[count], word, MAX_LINE ); - count++; - } - - return count; -} +namespace ReaxFF { /* safe malloc */ -void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name ) +void *smalloc(LAMMPS_NS::Error *error_ptr, rc_bigint n, const std::string &name) { void *ptr; if (n <= 0) { - auto errmsg = fmt::format("Trying to allocate {} bytes for array {}. " - "returning NULL.", n, name); - if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg.c_str(),stderr); + auto errmsg = fmt::format("Invalid size {} for array {}. Returning NULL.", n, name); + if (error_ptr) + error_ptr->one(FLERR, errmsg); + else + fputs(errmsg.c_str(), stderr); return nullptr; } - ptr = malloc( n ); + ptr = malloc(n); if (ptr == nullptr) { - auto errmsg = fmt::format("Failed to allocate {} bytes for array {}", - n, name); - if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg.c_str(),stderr); + auto errmsg = fmt::format("Failed to allocate {} bytes for array {}", n, name); + if (error_ptr) + error_ptr->one(FLERR, errmsg); + else + fputs(errmsg.c_str(), stderr); } return ptr; } /* safe calloc */ -void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name ) +void *scalloc(LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const std::string &name) { void *ptr; if (n <= 0) { - auto errmsg = fmt::format("Trying to allocate {} elements for array {}. " - "returning NULL.\n", n, name); - if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg.c_str(),stderr); + auto errmsg = fmt::format("Invalid size {} for array {}. Returning NULL.\n", n, name); + if (error_ptr) + error_ptr->one(FLERR, errmsg); + else + fputs(errmsg.c_str(), stderr); return nullptr; } if (size <= 0) { - auto errmsg = fmt::format("Elements size for array {} is {}. " - "returning NULL", name, size); - if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg.c_str(),stderr); + auto errmsg = fmt::format("Elements size for array {} is {}. Returning NULL", name, size); + if (error_ptr) + error_ptr->one(FLERR, errmsg); + else + fputs(errmsg.c_str(), stderr); return nullptr; } - ptr = calloc( n, size ); + ptr = calloc(n, size); if (ptr == nullptr) { - auto errmsg = fmt::format("Failed to allocate {} bytes for array {}", - n*size, name); - if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg.c_str(),stderr); + auto errmsg = fmt::format("Failed to allocate {} bytes for array {}", n * size, name); + if (error_ptr) + error_ptr->one(FLERR, errmsg); + else + fputs(errmsg.c_str(), stderr); } return ptr; } - /* safe free */ -void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name ) +void sfree(LAMMPS_NS::Error *error_ptr, void *ptr, const std::string &name) { if (ptr == nullptr) { - auto errmsg = fmt::format("Trying to free the already free()'d pointer {}", - name); - if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg.c_str(),stderr); + auto errmsg = std::string("Trying to free the already free()'d pointer: ") + name; + if (error_ptr) + error_ptr->one(FLERR, errmsg); + else + fputs(errmsg.c_str(), stderr); return; } free(ptr); ptr = nullptr; } - +} // namespace ReaxFF diff --git a/src/REAXFF/reaxff_torsion_angles.cpp b/src/REAXFF/reaxff_torsion_angles.cpp new file mode 100644 index 0000000000..329f7b8a7a --- /dev/null +++ b/src/REAXFF/reaxff_torsion_angles.cpp @@ -0,0 +1,405 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include "pair.h" + +#include + +#define MIN_SINE 1e-10 + +namespace ReaxFF { + double Calculate_Omega(rvec dvec_ij, double r_ij, rvec dvec_jk, double r_jk, + rvec dvec_kl, double r_kl, rvec dvec_li, double r_li, + three_body_interaction_data *p_ijk, + three_body_interaction_data *p_jkl, + rvec dcos_omega_di, rvec dcos_omega_dj, + rvec dcos_omega_dk, rvec dcos_omega_dl) + { + double unnorm_cos_omega, unnorm_sin_omega, omega; + double sin_ijk, cos_ijk, sin_jkl, cos_jkl; + double htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe; + double arg, poem, tel; + rvec cross_jk_kl; + + sin_ijk = sin(p_ijk->theta); + cos_ijk = cos(p_ijk->theta); + sin_jkl = sin(p_jkl->theta); + cos_jkl = cos(p_jkl->theta); + + /* omega */ + unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) + + SQR(r_jk) * rvec_Dot(dvec_ij, dvec_kl); + + rvec_Cross(cross_jk_kl, dvec_jk, dvec_kl); + unnorm_sin_omega = -r_jk * rvec_Dot(dvec_ij, cross_jk_kl); + + omega = atan2(unnorm_sin_omega, unnorm_cos_omega); + + htra = r_ij + cos_ijk * (r_kl * cos_jkl - r_jk); + htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl; + htrc = r_kl + cos_jkl * (r_ij * cos_ijk - r_jk); + hthd = r_ij * sin_ijk * (r_jk - r_kl * cos_jkl); + hthe = r_kl * sin_jkl * (r_jk - r_ij * cos_ijk); + hnra = r_kl * sin_ijk * sin_jkl; + hnrc = r_ij * sin_ijk * sin_jkl; + hnhd = r_ij * r_kl * cos_ijk * sin_jkl; + hnhe = r_ij * r_kl * sin_ijk * cos_jkl; + + poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl; + if (poem < 1e-20) poem = 1e-20; + + tel = SQR(r_ij) + SQR(r_jk) + SQR(r_kl) - SQR(r_li) - + 2.0 * (r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl + + r_jk * r_kl * cos_jkl); + + arg = tel / poem; + if (arg > 1.0) arg = 1.0; + if (arg < -1.0) arg = -1.0; + + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk = MIN_SINE; + else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) sin_ijk = -MIN_SINE; + if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) sin_jkl = MIN_SINE; + else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) sin_jkl = -MIN_SINE; + + // dcos_omega_di + rvec_ScaledSum(dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li); + rvec_ScaledAdd(dcos_omega_di,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dk); + rvec_Scale(dcos_omega_di, 2.0 / poem, dcos_omega_di); + + // dcos_omega_dj + rvec_ScaledSum(dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij, + -htrb / r_jk, dvec_jk); + rvec_ScaledAdd(dcos_omega_dj,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dj); + rvec_ScaledAdd(dcos_omega_dj,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_di); + rvec_Scale(dcos_omega_dj, 2.0 / poem, dcos_omega_dj); + + // dcos_omega_dk + rvec_ScaledSum(dcos_omega_dk,-(htrc-arg*hnrc)/r_kl, dvec_kl, + htrb / r_jk, dvec_jk); + rvec_ScaledAdd(dcos_omega_dk,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_di); + rvec_ScaledAdd(dcos_omega_dk,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dj); + rvec_Scale(dcos_omega_dk, 2.0 / poem, dcos_omega_dk); + + // dcos_omega_dl + rvec_ScaledSum(dcos_omega_dl, (htrc-arg*hnrc)/r_kl, dvec_kl, 1., dvec_li); + rvec_ScaledAdd(dcos_omega_dl,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dk); + rvec_Scale(dcos_omega_dl, 2.0 / poem, dcos_omega_dl); + + return omega; + } + + void Torsion_Angles(reax_system *system, control_params *control, + simulation_data *data, storage *workspace, + reax_list **lists) + { + int i, j, k, l, pi, pj, pk, pl, pij, plk, natoms; + int type_i, type_j, type_k, type_l; + int start_j, end_j; + int start_pj, end_pj, start_pk, end_pk; + int num_frb_intrs = 0; + + double Delta_j, Delta_k; + double r_ij, r_jk, r_kl, r_li; + double BOA_ij, BOA_jk, BOA_kl; + + double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl; + double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv; + double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl; + double fn10, f11_DjDk, dfn11, fn12; + double theta_ijk, theta_jkl; + double sin_ijk, sin_jkl; + double cos_ijk, cos_jkl; + double tan_ijk_i, tan_jkl_i; + double omega, cos_omega, cos2omega, cos3omega; + rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl; + double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4; + double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9; + double Cconj, CEconj1, CEconj2, CEconj3; + double CEconj4, CEconj5, CEconj6; + double e_tor, e_con; + rvec dvec_li; + four_body_header *fbh; + four_body_parameters *fbp; + bond_data *pbond_ij, *pbond_jk, *pbond_kl; + bond_order_data *bo_ij, *bo_jk, *bo_kl; + three_body_interaction_data *p_ijk, *p_jkl; + double p_tor2 = system->reax_param.gp.l[23]; + double p_tor3 = system->reax_param.gp.l[24]; + double p_tor4 = system->reax_param.gp.l[25]; + double p_cot2 = system->reax_param.gp.l[27]; + reax_list *bonds = (*lists) + BONDS; + reax_list *thb_intrs = (*lists) + THREE_BODIES; + + // Virial tallying variables + double delil[3], deljl[3], delkl[3]; + double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; + + natoms = system->n; + + for (j = 0; j < natoms; ++j) { + type_j = system->my_atoms[j].type; + Delta_j = workspace->Delta_boc[j]; + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + for (pk = start_j; pk < end_j; ++pk) { + pbond_jk = &(bonds->select.bond_list[pk]); + k = pbond_jk->nbr; + bo_jk = &(pbond_jk->bo_data); + BOA_jk = bo_jk->BO - control->thb_cut; + + if (system->my_atoms[j].orig_id > system->my_atoms[k].orig_id) + continue; + if (system->my_atoms[j].orig_id == system->my_atoms[k].orig_id) { + if (system->my_atoms[k].x[2] < system->my_atoms[j].x[2]) continue; + if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] && + system->my_atoms[k].x[1] < system->my_atoms[j].x[1]) continue; + if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] && + system->my_atoms[k].x[1] == system->my_atoms[j].x[1] && + system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue; + } + + if (bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) { + pj = pbond_jk->sym_index; // pj points to j on k's list + + if (Num_Entries(pj, thb_intrs)) { + type_k = system->my_atoms[k].type; + Delta_k = workspace->Delta_boc[k]; + r_jk = pbond_jk->d; + + start_pk = Start_Index(pk, thb_intrs); + end_pk = End_Index(pk, thb_intrs); + start_pj = Start_Index(pj, thb_intrs); + end_pj = End_Index(pj, thb_intrs); + + exp_tor2_jk = exp(-p_tor2 * BOA_jk); + exp_cot2_jk = exp(-p_cot2 * SQR(BOA_jk - 1.5)); + exp_tor3_DjDk = exp(-p_tor3 * (Delta_j + Delta_k)); + exp_tor4_DjDk = exp(p_tor4 * (Delta_j + Delta_k)); + exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk); + f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv; + + for (pi = start_pk; pi < end_pk; ++pi) { + p_ijk = &(thb_intrs->select.three_body_list[pi]); + pij = p_ijk->pthb; // pij is pointer to i on j's bond_list + pbond_ij = &(bonds->select.bond_list[pij]); + bo_ij = &(pbond_ij->bo_data); + + if (bo_ij->BO > control->thb_cut/*0*/) { + i = p_ijk->thb; + type_i = system->my_atoms[i].type; + r_ij = pbond_ij->d; + BOA_ij = bo_ij->BO - control->thb_cut; + + theta_ijk = p_ijk->theta; + sin_ijk = sin(theta_ijk); + cos_ijk = cos(theta_ijk); + //tan_ijk_i = 1. / tan(theta_ijk); + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) + tan_ijk_i = cos_ijk / MIN_SINE; + else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) + tan_ijk_i = cos_ijk / -MIN_SINE; + else tan_ijk_i = cos_ijk / sin_ijk; + + exp_tor2_ij = exp(-p_tor2 * BOA_ij); + exp_cot2_ij = exp(-p_cot2 * SQR(BOA_ij -1.5)); + + for (pl = start_pj; pl < end_pj; ++pl) { + p_jkl = &(thb_intrs->select.three_body_list[pl]); + l = p_jkl->thb; + plk = p_jkl->pthb; //pointer to l on k's bond_list! + pbond_kl = &(bonds->select.bond_list[plk]); + bo_kl = &(pbond_kl->bo_data); + type_l = system->my_atoms[l].type; + fbh = &(system->reax_param.fbp[type_i][type_j] + [type_k][type_l]); + fbp = &(system->reax_param.fbp[type_i][type_j] + [type_k][type_l].prm[0]); + + if (i != l && fbh->cnt && + bo_kl->BO > control->thb_cut/*0*/ && + bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) { + ++num_frb_intrs; + r_kl = pbond_kl->d; + BOA_kl = bo_kl->BO - control->thb_cut; + + theta_jkl = p_jkl->theta; + sin_jkl = sin(theta_jkl); + cos_jkl = cos(theta_jkl); + //tan_jkl_i = 1. / tan(theta_jkl); + if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) + tan_jkl_i = cos_jkl / MIN_SINE; + else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) + tan_jkl_i = cos_jkl / -MIN_SINE; + else tan_jkl_i = cos_jkl /sin_jkl; + + rvec_ScaledSum(dvec_li, 1., system->my_atoms[i].x, + -1., system->my_atoms[l].x); + r_li = rvec_Norm(dvec_li); + + + /* omega and its derivative */ + omega = Calculate_Omega(pbond_ij->dvec, r_ij, + pbond_jk->dvec, r_jk, + pbond_kl->dvec, r_kl, + dvec_li, r_li, + p_ijk, p_jkl, + dcos_omega_di, dcos_omega_dj, + dcos_omega_dk, dcos_omega_dl); + + cos_omega = cos(omega); + cos2omega = cos(2. * omega); + cos3omega = cos(3. * omega); + /* end omega calculations */ + + /* torsion energy */ + exp_tor1 = exp(fbp->p_tor1 * + SQR(2.0 - bo_jk->BO_pi - f11_DjDk)); + exp_tor2_kl = exp(-p_tor2 * BOA_kl); + exp_cot2_kl = exp(-p_cot2 * SQR(BOA_kl - 1.5)); + fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * + (1.0 - exp_tor2_kl); + + CV = 0.5 * (fbp->V1 * (1.0 + cos_omega) + + fbp->V2 * exp_tor1 * (1.0 - cos2omega) + + fbp->V3 * (1.0 + cos3omega)); + + data->my_en.e_tor += e_tor = fn10 * sin_ijk * sin_jkl * CV; + + dfn11 = (-p_tor3 * exp_tor3_DjDk + + (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) * + (2.0 + exp_tor3_DjDk) * exp_tor34_inv) * + exp_tor34_inv; + + CEtors1 = sin_ijk * sin_jkl * CV; + + CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 * + (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) * + sin_ijk * sin_jkl; + CEtors3 = CEtors2 * dfn11; + + CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij * + (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl); + CEtors5 = CEtors1 * p_tor2 * + (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl); + CEtors6 = CEtors1 * p_tor2 * + (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl; + + cmn = -fn10 * CV; + CEtors7 = cmn * sin_jkl * tan_ijk_i; + CEtors8 = cmn * sin_ijk * tan_jkl_i; + + CEtors9 = fn10 * sin_ijk * sin_jkl * + (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega + + 1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega))); + /* end of torsion energy */ + + /* 4-body conjugation energy */ + fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl; + data->my_en.e_con += e_con = + fbp->p_cot1 * fn12 * + (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); + + Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 * + (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); + + CEconj1 = Cconj * (BOA_ij - 1.5e0); + CEconj2 = Cconj * (BOA_jk - 1.5e0); + CEconj3 = Cconj * (BOA_kl - 1.5e0); + + CEconj4 = -fbp->p_cot1 * fn12 * + (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i; + CEconj5 = -fbp->p_cot1 * fn12 * + (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i; + CEconj6 = 2.0 * fbp->p_cot1 * fn12 * + cos_omega * sin_ijk * sin_jkl; + /* end 4-body conjugation energy */ + + /* forces */ + bo_jk->Cdbopi += CEtors2; + workspace->CdDelta[j] += CEtors3; + workspace->CdDelta[k] += CEtors3; + bo_ij->Cdbo += (CEtors4 + CEconj1); + bo_jk->Cdbo += (CEtors5 + CEconj2); + bo_kl->Cdbo += (CEtors6 + CEconj3); + + /* dcos_theta_ijk */ + rvec_ScaledAdd(workspace->f[i], CEtors7 + CEconj4, p_ijk->dcos_dk); + rvec_ScaledAdd(workspace->f[j], CEtors7 + CEconj4, p_ijk->dcos_dj); + rvec_ScaledAdd(workspace->f[k], CEtors7 + CEconj4, p_ijk->dcos_di); + + /* dcos_theta_jkl */ + rvec_ScaledAdd(workspace->f[j], CEtors8 + CEconj5, p_jkl->dcos_di); + rvec_ScaledAdd(workspace->f[k], CEtors8 + CEconj5, p_jkl->dcos_dj); + rvec_ScaledAdd(workspace->f[l], CEtors8 + CEconj5, p_jkl->dcos_dk); + + /* dcos_omega */ + rvec_ScaledAdd(workspace->f[i], CEtors9 + CEconj6, dcos_omega_di); + rvec_ScaledAdd(workspace->f[j], CEtors9 + CEconj6, dcos_omega_dj); + rvec_ScaledAdd(workspace->f[k], CEtors9 + CEconj6, dcos_omega_dk); + rvec_ScaledAdd(workspace->f[l], CEtors9 + CEconj6, dcos_omega_dl); + + /* tally into per-atom virials */ + if (system->pair_ptr->evflag) { + + // acquire vectors + rvec_ScaledSum(delil, 1., system->my_atoms[l].x, -1., system->my_atoms[i].x); + rvec_ScaledSum(deljl, 1., system->my_atoms[l].x, -1., system->my_atoms[j].x); + rvec_ScaledSum(delkl, 1., system->my_atoms[l].x, -1., system->my_atoms[k].x); + // dcos_theta_ijk + rvec_Scale(fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk); + rvec_Scale(fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj); + rvec_Scale(fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di); + + // dcos_theta_jkl + rvec_ScaledAdd(fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di); + rvec_ScaledAdd(fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj); + + // dcos_omega + rvec_ScaledAdd(fi_tmp, CEtors9 + CEconj6, dcos_omega_di); + rvec_ScaledAdd(fj_tmp, CEtors9 + CEconj6, dcos_omega_dj); + rvec_ScaledAdd(fk_tmp, CEtors9 + CEconj6, dcos_omega_dk); + + // tally + eng_tmp = e_tor + e_con; + if (system->pair_ptr->eflag_either) + system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); + if (system->pair_ptr->vflag_either) + system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl); + } + } // pl check ends + } // pl loop ends + } // pi check ends + } // pi loop ends + } // k-j neighbor check ends + } // j-k neighbor check ends + } // pk loop ends + } // j loop + } +} diff --git a/src/REAXFF/reaxff_types.h b/src/REAXFF/reaxff_types.h new file mode 100644 index 0000000000..e57244c66b --- /dev/null +++ b/src/REAXFF/reaxff_types.h @@ -0,0 +1,401 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hasan Metin Aktulga, Purdue University + (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov) + + Heavily modified and adapted for LAMMPS by the LAMMPS developers. +------------------------------------------------------------------------- */ + +#ifndef LMP_REAXFF_TYPES_H +#define LMP_REAXFF_TYPES_H + +#include "lmptype.h" + +#include "reaxff_defs.h" +#include "reaxff_inline.h" + +// forward declarations +namespace LAMMPS_NS { + class Error; + class LAMMPS; + class Memory; + class Pair; +} + +namespace ReaxFF +{ + /********************** TYPE DEFINITIONS ********************/ + typedef int ivec[3]; + typedef double rvec[3]; + typedef double rvec2[2]; + + // import LAMMPS' definition of tagint and bigint + typedef LAMMPS_NS::tagint rc_tagint; + typedef LAMMPS_NS::bigint rc_bigint; + + struct global_parameters + { + int n_global; + int vdw_type; + double *l; + }; + + struct single_body_parameters + { + char name[4]; // two character atom name + double r_s; + double valency; // Valency of the atom + double mass; // Mass of atom + double r_vdw; + double epsilon; + double gamma; + double r_pi; + double valency_e; + double nlp_opt; + + /* Line two in field file */ + double alpha; + double gamma_w; + double valency_boc; + double p_ovun5; + double chi; + double eta; + int p_hbond; // 1 for H, 2 for hbonding atoms (O,S,P,N), 0 for others + + /* Line three in field file */ + double r_pi_pi; + double p_lp2; + double b_o_131; + double b_o_132; + double b_o_133; + + /* Line four in the field file */ + double p_ovun2; + double p_val3; + double valency_val; + double p_val5; + double rcore2; + double ecore2; + double acore2; + + /* Line five in the ffield file, only for lgvdw yes */ + double lgcij; + double lgre; + + }; + + /* Two Body Parameters */ + struct two_body_parameters { + /* Bond Order parameters */ + double p_bo1,p_bo2,p_bo3,p_bo4,p_bo5,p_bo6; + double r_s, r_p, r_pp; // r_o distances in BO formula + double p_boc3, p_boc4, p_boc5; + + /* Bond Energy parameters */ + double p_be1, p_be2; + double De_s, De_p, De_pp; + + /* Over/Under coordination parameters */ + double p_ovun1; + + /* Van der Waal interaction parameters */ + double D; + double alpha; + double r_vdW; + double gamma_w; + double rcore, ecore, acore; + double lgcij, lgre; + + /* electrostatic parameters */ + double gamma; // note: this parameter is gamma^-3 and not gamma. + + double v13cor, ovc; + }; + + struct dbond_coefficients { + double C1dbo, C2dbo, C3dbo; + double C1dbopi, C2dbopi, C3dbopi, C4dbopi; + double C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2; + double C1dDelta, C2dDelta, C3dDelta; + }; + + /* 3-body parameters */ + struct three_body_parameters { + /* valence angle */ + double theta_00; + double p_val1, p_val2, p_val4, p_val7; + + /* penalty */ + double p_pen1; + + /* 3-body conjugation */ + double p_coa1; + }; + + struct three_body_header + { + int cnt; + three_body_parameters prm[REAX_MAX_3BODY_PARAM]; + }; + + /* hydrogen-bond parameters */ + struct hbond_parameters + { + double r0_hb, p_hb1, p_hb2, p_hb3; + }; + + /* 4-body parameters */ + struct four_body_parameters + { + double V1, V2, V3; + + /* torsion angle */ + double p_tor1; + + /* 4-body conjugation */ + double p_cot1; + }; + + struct four_body_header + { + int cnt; + four_body_parameters prm[REAX_MAX_4BODY_PARAM]; + }; + + struct reax_interaction + { + int num_atom_types; + global_parameters gp; + single_body_parameters *sbp; + two_body_parameters **tbp; + three_body_header ***thbp; + hbond_parameters ***hbp; + four_body_header ****fbp; + }; + + struct reax_atom + { + rc_tagint orig_id; + int type; + char name[8]; + + rvec x; // position + rvec v; // velocity + rvec f; // force + double q; // charge + + int Hindex; + int num_bonds; + int num_hbonds; + }; + + struct LR_lookup_table; // forward declaration + struct reax_system + { + reax_interaction reax_param; + + rc_bigint bigN; + int n, N, numH; + int local_cap, total_cap, Hcap; + int wsize, my_rank, num_nbrs; + reax_atom *my_atoms; + + LAMMPS_NS::Error *error_ptr; + LAMMPS_NS::Pair *pair_ptr; + LAMMPS_NS::Memory *mem_ptr; + + int my_bonds; + int mincap,minhbonds; + double safezone, saferzone; + + LR_lookup_table **LR; + + int omp_active; + }; + + /* system control parameters */ + struct control_params + { + int nthreads; + + double bond_cut; + double nonb_cut, nonb_low; + double hbond_cut; + + double bg_cut; + double bo_cut; + double thb_cut; + double thb_cutsq; + + int tabulate; + + int lgflag; + int enobondsflag; + LAMMPS_NS::Error *error_ptr; + LAMMPS_NS::LAMMPS *lmp_ptr; + int me; + }; + + struct energy_data + { + double e_bond; // Total bond energy + double e_ov; // Total over coordination + double e_un; // Total under coordination energy + double e_lp; // Total under coordination energy + double e_ang; // Total valance angle energy + double e_pen; // Total penalty energy + double e_coa; // Total three body conjgation energy + double e_hb; // Total Hydrogen bond energy + double e_tor; // Total torsional energy + double e_con; // Total four body conjugation energy + double e_vdW; // Total van der Waals energy + double e_ele; // Total electrostatics energy + double e_pol; // Polarization energy + }; + + struct simulation_data + { + rc_bigint step; + energy_data my_en; // per MPI rank energies + }; + + struct three_body_interaction_data + { + int thb; + int pthb; // pointer to the third body on the central atom's nbrlist + double theta, cos_theta; + rvec dcos_di, dcos_dj, dcos_dk; + }; + + struct far_neighbor_data { + int nbr; + ivec rel_box; + double d; + rvec dvec; + }; + + struct hbond_data { + int nbr; + int scl; + far_neighbor_data *ptr; + }; + + struct bond_order_data { + double BO, BO_s, BO_pi, BO_pi2; + double Cdbo, Cdbopi, Cdbopi2; + double C1dbo, C2dbo, C3dbo; + double C1dbopi, C2dbopi, C3dbopi, C4dbopi; + double C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2; + rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2; + double *CdboReduction; + }; + + struct bond_data { + int nbr; + int sym_index; + int dbond_index; + ivec rel_box; + double d; + rvec dvec; + bond_order_data bo_data; + }; + + struct sparse_matrix_entry { + int j; + double val; + }; + + struct sparse_matrix { + int cap, n, m; + int *start, *end; + sparse_matrix_entry *entries; + }; + + struct reallocate_data { + int num_far; + int H, Htop; + int hbonds, num_hbonds; + int bonds, num_bonds; + int num_3body; + }; + + struct storage + { + int allocated; + + /* bond order related storage */ + double *total_bond_order; + double *Deltap, *Deltap_boc; + double *Delta, *Delta_lp, *Delta_lp_temp, *Delta_e, *Delta_boc, *Delta_val; + double *dDelta_lp, *dDelta_lp_temp; + double *nlp, *nlp_temp, *Clp, *vlpex; + rvec *dDeltap_self; + int *bond_mark; + + /* Taper */ + double Tap[8]; //Tap7, Tap6, Tap5, Tap4, Tap3, Tap2, Tap1, Tap0; + + /* force calculations */ + double *CdDelta; // coefficient of dDelta + rvec *f; + + /* omp */ + rvec *forceReduction; + double *CdDeltaReduction; + int *valence_angle_atom_myoffset; + + reallocate_data realloc; + }; + + union list_type + { + three_body_interaction_data *three_body_list; + bond_data *bond_list; + far_neighbor_data *far_nbr_list; + hbond_data *hbond_list; + }; + + struct reax_list + { + int allocated; + + int n; + int num_intrs; + + int *index; + int *end_index; + + int type; + list_type select; + class LAMMPS_NS::Error *error_ptr; + }; + + struct LR_lookup_table + { + double xmin, xmax; + int n; + double dx, inv_dx; + double a; + double m; + double c; + + LR_data *y; + cubic_spline_coef *H; + cubic_spline_coef *vdW, *CEvd; + cubic_spline_coef *ele, *CEclmb; + }; +} + +#endif diff --git a/src/REAXFF/reaxff_valence_angles.cpp b/src/REAXFF/reaxff_valence_angles.cpp new file mode 100644 index 0000000000..ac3e2dbd1e --- /dev/null +++ b/src/REAXFF/reaxff_valence_angles.cpp @@ -0,0 +1,387 @@ +// clang-format off +/*---------------------------------------------------------------------- + PuReMD - Purdue ReaxFF Molecular Dynamics Program + + Copyright (2010) Purdue University + Hasan Metin Aktulga, hmaktulga@lbl.gov + Joseph Fogarty, jcfogart@mail.usf.edu + Sagar Pandit, pandit@usf.edu + Ananth Y Grama, ayg@cs.purdue.edu + + Please cite the related publication: + H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, + "Parallel Reactive Molecular Dynamics: Numerical Methods and + Algorithmic Techniques", Parallel Computing, in press. + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ----------------------------------------------------------------------*/ + +#include "reaxff_api.h" + +#include + +#include "pair.h" +#include "error.h" + +namespace ReaxFF { + void Calculate_Theta(rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, + double *theta, double *cos_theta) + { + (*cos_theta) = rvec_Dot(dvec_ji,dvec_jk) / (d_ji * d_jk); + if (*cos_theta > 1.) *cos_theta = 1.0; + if (*cos_theta < -1.) *cos_theta = -1.0; + + (*theta) = acos(*cos_theta); + } + + void Calculate_dCos_Theta(rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, + rvec* dcos_theta_di, + rvec* dcos_theta_dj, + rvec* dcos_theta_dk) + { + int t; + double sqr_d_ji = SQR(d_ji); + double sqr_d_jk = SQR(d_jk); + double inv_dists = 1.0 / (d_ji * d_jk); + double inv_dists3 = CUBE(inv_dists); + double dot_dvecs = rvec_Dot(dvec_ji,dvec_jk); + double Cdot_inv3 = dot_dvecs * inv_dists3; + + for (t = 0; t < 3; ++t) { + (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists - + Cdot_inv3 * sqr_d_jk * dvec_ji[t]; + (*dcos_theta_dj)[t] = -(dvec_jk[t] + dvec_ji[t]) * inv_dists + + Cdot_inv3 * (sqr_d_jk * dvec_ji[t] + sqr_d_ji * dvec_jk[t]); + (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists - + Cdot_inv3 * sqr_d_ji * dvec_jk[t]; + } + } + + + void Valence_Angles(reax_system *system, control_params *control, simulation_data *data, + storage *workspace, reax_list **lists) + { + int i, j, pi, k, pk, t; + int type_i, type_j, type_k; + int start_j, end_j, start_pk, end_pk; + int cnt, num_thb_intrs; + + double temp, temp_bo_jt, pBOjt7; + double p_val1, p_val2, p_val3, p_val4, p_val5; + double p_val6, p_val7, p_val8, p_val9, p_val10; + double p_pen1, p_pen2, p_pen3, p_pen4; + double p_coa1, p_coa2, p_coa3, p_coa4; + double trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk; + double exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2; + double dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj; + double CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8; + double CEpen1, CEpen2, CEpen3; + double e_ang, e_coa, e_pen; + double CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5; + double Cf7ij, Cf7jk, Cf8j, Cf9j; + double f7_ij, f7_jk, f8_Dj, f9_Dj; + double Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta; + double BOA_ij, BOA_jk; + + // Tallying variables + double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; + double delij[3], delkj[3]; + + three_body_header *thbh; + three_body_parameters *thbp; + three_body_interaction_data *p_ijk, *p_kji; + bond_data *pbond_ij, *pbond_jk, *pbond_jt; + bond_order_data *bo_ij, *bo_jk, *bo_jt; + reax_list *bonds = (*lists) + BONDS; + reax_list *thb_intrs = (*lists) + THREE_BODIES; + + /* global parameters used in these calculations */ + p_val6 = system->reax_param.gp.l[14]; + p_val8 = system->reax_param.gp.l[33]; + p_val9 = system->reax_param.gp.l[16]; + p_val10 = system->reax_param.gp.l[17]; + num_thb_intrs = 0; + + + for (j = 0; j < system->N; ++j) { + type_j = system->my_atoms[j].type; + if (type_j < 0) continue; + start_j = Start_Index(j, bonds); + end_j = End_Index(j, bonds); + + p_val3 = system->reax_param.sbp[type_j].p_val3; + p_val5 = system->reax_param.sbp[type_j].p_val5; + + SBOp = 0, prod_SBO = 1; + for (t = start_j; t < end_j; ++t) { + bo_jt = &(bonds->select.bond_list[t].bo_data); + SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2); + temp = SQR(bo_jt->BO); + temp *= temp; + temp *= temp; + prod_SBO *= exp(-temp); + } + + if (workspace->vlpex[j] >= 0) { + vlpadj = 0; + dSBO2 = prod_SBO - 1; + } else { + vlpadj = workspace->nlp[j]; + dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); + } + + SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); + dSBO1 = -8 * prod_SBO * (workspace->Delta_boc[j] + p_val8 * vlpadj); + + if (SBO <= 0) + SBO2 = 0, CSBO2 = 0; + else if (SBO > 0 && SBO <= 1) { + SBO2 = pow(SBO, p_val9); + CSBO2 = p_val9 * pow(SBO, p_val9 - 1); + } + else if (SBO > 1 && SBO < 2) { + SBO2 = 2 - pow(2-SBO, p_val9); + CSBO2 = p_val9 * pow(2 - SBO, p_val9 - 1); + } + else + SBO2 = 2, CSBO2 = 0; + + expval6 = exp(p_val6 * workspace->Delta_boc[j]); + + for (pi = start_j; pi < end_j; ++pi) { + Set_Start_Index(pi, num_thb_intrs, thb_intrs); + pbond_ij = &(bonds->select.bond_list[pi]); + bo_ij = &(pbond_ij->bo_data); + BOA_ij = bo_ij->BO - control->thb_cut; + + + if (BOA_ij/*bo_ij->BO*/ > 0.0 && + (j < system->n || pbond_ij->nbr < system->n)) { + i = pbond_ij->nbr; + type_i = system->my_atoms[i].type; + + for (pk = start_j; pk < pi; ++pk) { + start_pk = Start_Index(pk, thb_intrs); + end_pk = End_Index(pk, thb_intrs); + + for (t = start_pk; t < end_pk; ++t) + if (thb_intrs->select.three_body_list[t].thb == i) { + p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs]); + p_kji = &(thb_intrs->select.three_body_list[t]); + + p_ijk->thb = bonds->select.bond_list[pk].nbr; + p_ijk->pthb = pk; + p_ijk->theta = p_kji->theta; + rvec_Copy(p_ijk->dcos_di, p_kji->dcos_dk); + rvec_Copy(p_ijk->dcos_dj, p_kji->dcos_dj); + rvec_Copy(p_ijk->dcos_dk, p_kji->dcos_di); + + ++num_thb_intrs; + break; + } + } + + for (pk = pi+1; pk < end_j; ++pk) { + pbond_jk = &(bonds->select.bond_list[pk]); + bo_jk = &(pbond_jk->bo_data); + BOA_jk = bo_jk->BO - control->thb_cut; + k = pbond_jk->nbr; + type_k = system->my_atoms[k].type; + p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs]); + + Calculate_Theta(pbond_ij->dvec, pbond_ij->d, + pbond_jk->dvec, pbond_jk->d, + &theta, &cos_theta); + + Calculate_dCos_Theta(pbond_ij->dvec, pbond_ij->d, + pbond_jk->dvec, pbond_jk->d, + &(p_ijk->dcos_di), &(p_ijk->dcos_dj), + &(p_ijk->dcos_dk)); + p_ijk->thb = k; + p_ijk->pthb = pk; + p_ijk->theta = theta; + + sin_theta = sin(theta); + if (sin_theta < 1.0e-5) + sin_theta = 1.0e-5; + + ++num_thb_intrs; + + if ((j < system->n) && (BOA_jk > 0.0) && + (bo_ij->BO > control->thb_cut) && + (bo_jk->BO > control->thb_cut) && + (bo_ij->BO * bo_jk->BO > control->thb_cutsq)) { + thbh = &(system->reax_param.thbp[type_i][type_j][type_k]); + + for (cnt = 0; cnt < thbh->cnt; ++cnt) { + if (fabs(thbh->prm[cnt].p_val1) > 0.001) { + thbp = &(thbh->prm[cnt]); + + /* ANGLE ENERGY */ + p_val1 = thbp->p_val1; + p_val2 = thbp->p_val2; + p_val4 = thbp->p_val4; + p_val7 = thbp->p_val7; + theta_00 = thbp->theta_00; + + exp3ij = exp(-p_val3 * pow(BOA_ij, p_val4)); + f7_ij = 1.0 - exp3ij; + Cf7ij = p_val3 * p_val4 * pow(BOA_ij, p_val4 - 1.0) * exp3ij; + + exp3jk = exp(-p_val3 * pow(BOA_jk, p_val4)); + f7_jk = 1.0 - exp3jk; + Cf7jk = p_val3 * p_val4 * pow(BOA_jk, p_val4 - 1.0) * exp3jk; + + expval7 = exp(-p_val7 * workspace->Delta_boc[j]); + trm8 = 1.0 + expval6 + expval7; + f8_Dj = p_val5 - ((p_val5 - 1.0) * (2.0 + expval6) / trm8); + Cf8j = ((1.0 - p_val5) / SQR(trm8)) * + (p_val6 * expval6 * trm8 - + (2.0 + expval6) * (p_val6*expval6 - p_val7*expval7)); + + theta_0 = 180.0 - theta_00 * (1.0 - + exp(-p_val10 * (2.0 - SBO2))); + theta_0 = DEG2RAD(theta_0); + + expval2theta = exp(-p_val2 * SQR(theta_0 - theta)); + if (p_val1 >= 0) + expval12theta = p_val1 * (1.0 - expval2theta); + else // To avoid linear Me-H-Me angles (6/6/06) + expval12theta = p_val1 * -expval2theta; + + CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; + CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; + CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; + CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * + expval2theta * (theta_0 - theta); + + Ctheta_0 = p_val10 * DEG2RAD(theta_00) * + exp(-p_val10 * (2.0 - SBO2)); + + CEval5 = -CEval4 * Ctheta_0 * CSBO2; + CEval6 = CEval5 * dSBO1; + CEval7 = CEval5 * dSBO2; + CEval8 = -CEval4 / sin_theta; + + data->my_en.e_ang += e_ang = + f7_ij * f7_jk * f8_Dj * expval12theta; + /* END ANGLE ENERGY*/ + + /* PENALTY ENERGY */ + p_pen1 = thbp->p_pen1; + p_pen2 = system->reax_param.gp.l[19]; + p_pen3 = system->reax_param.gp.l[20]; + p_pen4 = system->reax_param.gp.l[21]; + + exp_pen2ij = exp(-p_pen2 * SQR(BOA_ij - 2.0)); + exp_pen2jk = exp(-p_pen2 * SQR(BOA_jk - 2.0)); + exp_pen3 = exp(-p_pen3 * workspace->Delta[j]); + exp_pen4 = exp( p_pen4 * workspace->Delta[j]); + trm_pen34 = 1.0 + exp_pen3 + exp_pen4; + f9_Dj = (2.0 + exp_pen3) / trm_pen34; + Cf9j = (-p_pen3 * exp_pen3 * trm_pen34 - + (2.0 + exp_pen3) * (-p_pen3 * exp_pen3 + + p_pen4 * exp_pen4)) / + SQR(trm_pen34); + + data->my_en.e_pen += e_pen = + p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; + + CEpen1 = e_pen * Cf9j / f9_Dj; + temp = -2.0 * p_pen2 * e_pen; + CEpen2 = temp * (BOA_ij - 2.0); + CEpen3 = temp * (BOA_jk - 2.0); + /* END PENALTY ENERGY */ + + /* COALITION ENERGY */ + p_coa1 = thbp->p_coa1; + p_coa2 = system->reax_param.gp.l[2]; + p_coa3 = system->reax_param.gp.l[38]; + p_coa4 = system->reax_param.gp.l[30]; + + exp_coa2 = exp(p_coa2 * workspace->Delta_val[j]); + data->my_en.e_coa += e_coa = + p_coa1 / (1. + exp_coa2) * + exp(-p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij)) * + exp(-p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk)) * + exp(-p_coa4 * SQR(BOA_ij - 1.5)) * + exp(-p_coa4 * SQR(BOA_jk - 1.5)); + + CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; + CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa; + CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); + CEcoa4 = -2 * p_coa3 * + (workspace->total_bond_order[i]-BOA_ij) * e_coa; + CEcoa5 = -2 * p_coa3 * + (workspace->total_bond_order[k]-BOA_jk) * e_coa; + /* END COALITION ENERGY */ + + /* FORCES */ + bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); + bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); + workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3); + workspace->CdDelta[i] += CEcoa4; + workspace->CdDelta[k] += CEcoa5; + + for (t = start_j; t < end_j; ++t) { + pbond_jt = &(bonds->select.bond_list[t]); + bo_jt = &(pbond_jt->bo_data); + temp_bo_jt = bo_jt->BO; + temp = CUBE(temp_bo_jt); + pBOjt7 = temp * temp * temp_bo_jt; + + bo_jt->Cdbo += (CEval6 * pBOjt7); + bo_jt->Cdbopi += CEval5; + bo_jt->Cdbopi2 += CEval5; + } + + rvec_ScaledAdd(workspace->f[i], CEval8, p_ijk->dcos_di); + rvec_ScaledAdd(workspace->f[j], CEval8, p_ijk->dcos_dj); + rvec_ScaledAdd(workspace->f[k], CEval8, p_ijk->dcos_dk); + + /* tally energy */ + if (system->pair_ptr->eflag_either) { + eng_tmp = e_ang + e_pen + e_coa; + system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); + } + + /* tally virial */ + if (system->pair_ptr->vflag_either) { + + /* Acquire vectors */ + rvec_ScaledSum(delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x); + rvec_ScaledSum(delkj, 1., system->my_atoms[k].x, -1., system->my_atoms[j].x); + rvec_Scale(fi_tmp, -CEval8, p_ijk->dcos_di); + rvec_Scale(fj_tmp, -CEval8, p_ijk->dcos_dj); + rvec_Scale(fk_tmp, -CEval8, p_ijk->dcos_dk); + system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj); + } + } + } + } + } + } + + Set_End_Index(pi, num_thb_intrs, thb_intrs); + } + } + + if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { + workspace->realloc.num_3body = num_thb_intrs; + if (num_thb_intrs > thb_intrs->num_intrs) + control->error_ptr->one(FLERR, fmt::format("step {}: ran out of space on " + "angle_list: top={}, max={}", + data->step, num_thb_intrs, + thb_intrs->num_intrs)); + } + } +} diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/REPLICA/compute_pressure_grem.cpp similarity index 100% rename from src/USER-MISC/compute_pressure_grem.cpp rename to src/REPLICA/compute_pressure_grem.cpp diff --git a/src/USER-MISC/compute_pressure_grem.h b/src/REPLICA/compute_pressure_grem.h similarity index 100% rename from src/USER-MISC/compute_pressure_grem.h rename to src/REPLICA/compute_pressure_grem.h diff --git a/src/USER-MISC/fix_grem.cpp b/src/REPLICA/fix_grem.cpp similarity index 97% rename from src/USER-MISC/fix_grem.cpp rename to src/REPLICA/fix_grem.cpp index 07b8051225..743d31fe96 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/REPLICA/fix_grem.cpp @@ -76,20 +76,19 @@ FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) : // pass id_temp as 4th arg to pressure constructor id_press = utils::strdup(std::string(id) + "_press"); - modify->add_compute(fmt::format("{} all PRESSURE/GREM {}", - id_press, id_temp)); + modify->add_compute(fmt::format("{} all PRESSURE/GREM {} {}", id_press, id_temp, id)); // create a new compute ke style // id = fix-ID + ke id_ke = utils::strdup(std::string(id) + "_ke"); - modify->add_compute(fmt::format("{} all ke",id_temp)); + modify->add_compute(fmt::format("{} all ke",id_ke)); // create a new compute pe style // id = fix-ID + pe id_pe = utils::strdup(std::string(id) + "_pe"); - modify->add_compute(fmt::format("{} all pe",id_temp)); + modify->add_compute(fmt::format("{} all pe",id_pe)); int ifix = modify->find_fix(id_nh); if (ifix < 0) diff --git a/src/USER-MISC/fix_grem.h b/src/REPLICA/fix_grem.h similarity index 100% rename from src/USER-MISC/fix_grem.h rename to src/REPLICA/fix_grem.h diff --git a/src/USER-MISC/fix_pimd.cpp b/src/REPLICA/fix_pimd.cpp similarity index 51% rename from src/USER-MISC/fix_pimd.cpp rename to src/REPLICA/fix_pimd.cpp index ce1d41302f..bb4af16f1b 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/REPLICA/fix_pimd.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -24,69 +23,29 @@ #include "fix_pimd.h" -#include -#include - -#include "universe.h" -#include "comm.h" -#include "force.h" #include "atom.h" +#include "comm.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum{PIMD,NMPIMD,CMD}; +enum { PIMD, NMPIMD, CMD }; /* ---------------------------------------------------------------------- */ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - method = PIMD; - fmass = 1.0; - nhc_temp = 298.15; - nhc_nchain = 2; - sp = 1.0; - - for (int i=3; iuniverse_all(FLERR,"Unknown method parameter for fix pimd"); - } - else if (strcmp(arg[i],"fmass")==0) - { - fmass = atof(arg[i+1]); - if (fmass<0.0 || fmass>1.0) error->universe_all(FLERR,"Invalid fmass value for fix pimd"); - } - else if (strcmp(arg[i],"sp")==0) - { - sp = atof(arg[i+1]); - if (fmass<0.0) error->universe_all(FLERR,"Invalid sp value for fix pimd"); - } - else if (strcmp(arg[i],"temp")==0) - { - nhc_temp = atof(arg[i+1]); - if (nhc_temp<0.0) error->universe_all(FLERR,"Invalid temp value for fix pimd"); - } - else if (strcmp(arg[i],"nhc")==0) - { - nhc_nchain = atoi(arg[i+1]); - if (nhc_nchain<2) error->universe_all(FLERR,"Invalid nhc value for fix pimd"); - } - else error->universe_all(arg[i],i+1,"Unknown keyword for fix pimd"); - } - - /* Initiation */ - max_nsend = 0; tag_send = nullptr; buf_send = nullptr; @@ -110,25 +69,60 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) nhc_eta_dotdot = nullptr; nhc_eta_mass = nullptr; + method = PIMD; + fmass = 1.0; + nhc_temp = 298.15; + nhc_nchain = 2; + sp = 1.0; + + for (int i = 3; i < narg - 1; i += 2) { + if (strcmp(arg[i], "method") == 0) { + if (strcmp(arg[i + 1], "pimd") == 0) + method = PIMD; + else if (strcmp(arg[i + 1], "nmpimd") == 0) + method = NMPIMD; + else if (strcmp(arg[i + 1], "cmd") == 0) + method = CMD; + else + error->universe_all(FLERR, "Unknown method parameter for fix pimd"); + } else if (strcmp(arg[i], "fmass") == 0) { + fmass = utils::numeric(FLERR, arg[i + 1], false, lmp); + if (fmass < 0.0 || fmass > 1.0) + error->universe_all(FLERR, "Invalid fmass value for fix pimd"); + } else if (strcmp(arg[i], "sp") == 0) { + sp = utils::numeric(FLERR, arg[i + 1], false, lmp); + if (fmass < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd"); + } else if (strcmp(arg[i], "temp") == 0) { + nhc_temp = utils::numeric(FLERR, arg[i + 1], false, lmp); + if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd"); + } else if (strcmp(arg[i], "nhc") == 0) { + nhc_nchain = utils::inumeric(FLERR, arg[i + 1], false, lmp); + if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd"); + } else + error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i])); + } + + /* Initiation */ + size_peratom_cols = 12 * nhc_nchain + 3; nhc_offset_one_1 = 3 * nhc_nchain; - nhc_offset_one_2 = 3 * nhc_nchain +3; + nhc_offset_one_2 = 3 * nhc_nchain + 3; nhc_size_one_1 = sizeof(double) * nhc_offset_one_1; nhc_size_one_2 = sizeof(double) * nhc_offset_one_2; restart_peratom = 1; - peratom_flag = 1; - peratom_freq = 1; + peratom_flag = 1; + peratom_freq = 1; global_freq = 1; vector_flag = 1; size_vector = 2; - extvector = 1; + extvector = 1; comm_forward = 3; - atom->add_callback(Atom::GROW); // Call LAMMPS to allocate memory for per-atom array - atom->add_callback(Atom::RESTART); // Call LAMMPS to re-assign restart-data for per-atom array + atom->add_callback(Atom::GROW); // Call LAMMPS to allocate memory for per-atom array + atom->add_callback(Atom::RESTART); // Call LAMMPS to re-assign restart-data for per-atom array grow_arrays(atom->nmax); @@ -138,7 +132,37 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) } /* ---------------------------------------------------------------------- */ +FixPIMD::~FixPIMD() +{ + delete[] mass; + atom->delete_callback(id, Atom::GROW); + atom->delete_callback(id, Atom::RESTART); + memory->destroy(M_x2xp); + memory->destroy(M_xp2x); + memory->destroy(M_f2fp); + memory->destroy(M_fp2f); + memory->sfree(lam); + + if (buf_beads) + for (int i = 0; i < np; i++) memory->sfree(buf_beads[i]); + delete[] buf_beads; + delete[] plan_send; + delete[] plan_recv; + delete[] mode_index; + + memory->sfree(tag_send); + memory->sfree(buf_send); + memory->sfree(buf_recv); + + memory->destroy(array_atom); + memory->destroy(nhc_eta); + memory->destroy(nhc_eta_dot); + memory->destroy(nhc_eta_dotdot); + memory->destroy(nhc_eta_mass); +} + +/* ---------------------------------------------------------------------- */ int FixPIMD::setmask() { int mask = 0; @@ -153,9 +177,10 @@ int FixPIMD::setmask() void FixPIMD::init() { if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Fix pimd requires an atom map, see atom_modify"); + error->all(FLERR, "Fix pimd requires an atom map, see atom_modify"); - if (universe->me==0 && screen) fprintf(screen,"Fix pimd initializing Path-Integral ...\n"); + if (universe->me == 0 && universe->uscreen) + fprintf(universe->uscreen, "Fix pimd initializing Path-Integral ...\n"); // prepare the constants @@ -181,16 +206,16 @@ void FixPIMD::init() /* The current solution, using LAMMPS internal real units */ const double Boltzmann = force->boltz; - const double Plank = force->hplanck; + const double Plank = force->hplanck; - double hbar = Plank / ( 2.0 * MY_PI ); - double beta = 1.0 / (Boltzmann * nhc_temp); - double _fbond = 1.0 * np / (beta*beta*hbar*hbar) ; + double hbar = Plank / (2.0 * MY_PI); + double beta = 1.0 / (Boltzmann * nhc_temp); + double _fbond = 1.0 * np / (beta * beta * hbar * hbar); omega_np = sqrt(np) / (hbar * beta) * sqrt(force->mvv2e); - fbond = - _fbond * force->mvv2e; + fbond = -_fbond * force->mvv2e; - if (universe->me==0) + if (universe->me == 0) printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond); dtv = update->dt; @@ -198,10 +223,12 @@ void FixPIMD::init() comm_init(); - mass = new double [atom->ntypes+1]; + mass = new double[atom->ntypes + 1]; - if (method==CMD || method==NMPIMD) nmpimd_init(); - else for (int i=1; i<=atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass; + if (method == CMD || method == NMPIMD) + nmpimd_init(); + else + for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass; if (!nhc_ready) nhc_init(); } @@ -210,7 +237,8 @@ void FixPIMD::init() void FixPIMD::setup(int vflag) { - if (universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n"); + if (universe->me == 0 && universe->uscreen) + fprintf(universe->uscreen, "Setting up Path-Integral ...\n"); post_force(vflag); } @@ -234,13 +262,13 @@ void FixPIMD::final_integrate() void FixPIMD::post_force(int /*flag*/) { - for (int i=0; inlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np; + for (int i = 0; i < atom->nlocal; i++) + for (int j = 0; j < 3; j++) atom->f[i][j] /= np; comm_exec(atom->x); spring_force(); - if (method==CMD || method==NMPIMD) - { + if (method == CMD || method == NMPIMD) { /* forward comm for the force on ghost atoms */ nmpimd_fill(atom->f); @@ -262,34 +290,38 @@ void FixPIMD::post_force(int /*flag*/) void FixPIMD::nhc_init() { double tau = 1.0 / omega_np; - double KT = force->boltz * nhc_temp; + double KT = force->boltz * nhc_temp; double mass0 = KT * tau * tau; int max = 3 * atom->nlocal; - for (int i=0; iiworld==0) ; else nhc_eta_mass[i][ichain] *= fmass; + nhc_eta_mass[i][ichain] = mass0; + if ((method == CMD || method == NMPIMD) && universe->iworld == 0) + ; + else + nhc_eta_mass[i][ichain] *= fmass; } - nhc_eta_dot[i][nhc_nchain] = 0.0; + nhc_eta_dot[i][nhc_nchain] = 0.0; - for (int ichain=1; ichainmvv2e - KT) / nhc_eta_mass[i][ichain]; + for (int ichain = 1; ichain < nhc_nchain; ichain++) + nhc_eta_dotdot[i][ichain] = (nhc_eta_mass[i][ichain - 1] * nhc_eta_dot[i][ichain - 1] * + nhc_eta_dot[i][ichain - 1] * force->mvv2e - + KT) / + nhc_eta_mass[i][ichain]; } // Zero NH acceleration for CMD - if (method==CMD && universe->iworld==0) for (int i=0; iiworld == 0) + for (int i = 0; i < max; i++) + for (int ichain = 0; ichain < nhc_nchain; ichain++) nhc_eta_dotdot[i][ichain] = 0.0; nhc_ready = true; } @@ -302,8 +334,7 @@ void FixPIMD::nhc_update_x() double **x = atom->x; double **v = atom->v; - if (method==CMD || method==NMPIMD) - { + if (method == CMD || method == NMPIMD) { nmpimd_fill(atom->v); comm_exec(atom->v); @@ -313,8 +344,7 @@ void FixPIMD::nhc_update_x() nmpimd_transform(buf_beads, v, M_xp2x[universe->iworld]); } - for (int i=0; iv; double **f = atom->f; - for (int i=0; iiworld==0) return; + if (method == CMD && universe->iworld == 0) return; double expfac; int nmax = 3 * atom->nlocal; double KT = force->boltz * nhc_temp; double kecurrent, t_current; - double dthalf = 0.5 * update->dt; - double dt4 = 0.25 * update->dt; - double dt8 = 0.125 * update->dt; + double dthalf = 0.5 * update->dt; + double dt4 = 0.25 * update->dt; + double dt8 = 0.125 * update->dt; - for (int i=0; imvv2e; + kecurrent = mass[type[iatm]] * vv[idim] * vv[idim] * force->mvv2e; t_current = kecurrent / force->boltz; double *eta = nhc_eta[i]; @@ -366,9 +394,8 @@ void FixPIMD::nhc_update_v() eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0]; - for (int ichain=nhc_nchain-1; ichain>0; ichain--) - { - expfac = exp(-dt8 * eta_dot[ichain+1]); + for (int ichain = nhc_nchain - 1; ichain > 0; ichain--) { + expfac = exp(-dt8 * eta_dot[ichain + 1]); eta_dot[ichain] *= expfac; eta_dot[ichain] += eta_dotdot[ichain] * dt4; eta_dot[ichain] *= expfac; @@ -388,19 +415,18 @@ void FixPIMD::nhc_update_v() kecurrent = force->boltz * t_current; eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0]; - for (int ichain=0; ichaincreate(M_f2fp, np, np, "fix_feynman:M_f2fp"); memory->create(M_fp2f, np, np, "fix_feynman:M_fp2f"); - lam = (double*) memory->smalloc(sizeof(double)*np, "FixPIMD::lam"); + lam = (double *) memory->smalloc(sizeof(double) * np, "FixPIMD::lam"); // Set up eigenvalues lam[0] = 0.0; - if (np%2==0) lam[np-1] = 4.0 * np; + if (np % 2 == 0) lam[np - 1] = 4.0 * np; - for (int i=2; i<=np/2; i++) - { - lam[2*i-3] = lam[2*i-2] = 2.0 * np * (1.0 - 1.0 *cos(2.0*MY_PI*(i-1)/np)); + for (int i = 2; i <= np / 2; i++) { + lam[2 * i - 3] = lam[2 * i - 2] = 2.0 * np * (1.0 - 1.0 * cos(2.0 * MY_PI * (i - 1) / np)); } // Set up eigenvectors for non-degenerated modes - for (int i=0; iiworld; - for (int i=1; i<=atom->ntypes; i++) - { + for (int i = 1; i <= atom->ntypes; i++) { mass[i] = atom->mass[i]; - if (iworld) - { + if (iworld) { mass[i] *= lam[iworld]; mass[i] *= fmass; } @@ -486,17 +507,17 @@ void FixPIMD::nmpimd_fill(double **ptr) /* ---------------------------------------------------------------------- */ -void FixPIMD::nmpimd_transform(double** src, double** des, double *vector) +void FixPIMD::nmpimd_transform(double **src, double **des, double *vector) { int n = atom->nlocal; int m = 0; - for (int i=0; ix; double **f = atom->f; - double* _mass = atom->mass; - int* type = atom->type; + double *_mass = atom->mass; + int *type = atom->type; int nlocal = atom->nlocal; - double* xlast = buf_beads[x_last]; - double* xnext = buf_beads[x_next]; + double *xlast = buf_beads[x_last]; + double *xnext = buf_beads[x_next]; - for (int i=0; ime - comm->nprocs; int rank_next = universe->me + comm->nprocs; - if (rank_last<0) rank_last += universe->nprocs; - if (rank_next>=universe->nprocs) rank_next -= universe->nprocs; + if (rank_last < 0) rank_last += universe->nprocs; + if (rank_next >= universe->nprocs) rank_next -= universe->nprocs; - plan_send[0] = rank_next; plan_send[1] = rank_last; - plan_recv[0] = rank_last; plan_recv[1] = rank_next; + plan_send[0] = rank_next; + plan_send[1] = rank_last; + plan_recv[0] = rank_last; + plan_recv[1] = rank_next; - mode_index[0] = 0; mode_index[1] = 1; - x_last = 1; x_next = 0; - } - else - { + mode_index[0] = 0; + mode_index[1] = 1; + x_last = 1; + x_next = 0; + } else { size_plan = np - 1; - plan_send = new int [size_plan]; - plan_recv = new int [size_plan]; - mode_index = new int [size_plan]; + plan_send = new int[size_plan]; + plan_recv = new int[size_plan]; + mode_index = new int[size_plan]; - for (int i=0; ime + comm->nprocs * (i+1); - if (plan_send[i]>=universe->nprocs) plan_send[i] -= universe->nprocs; + for (int i = 0; i < size_plan; i++) { + plan_send[i] = universe->me + comm->nprocs * (i + 1); + if (plan_send[i] >= universe->nprocs) plan_send[i] -= universe->nprocs; - plan_recv[i] = universe->me - comm->nprocs * (i+1); - if (plan_recv[i]<0) plan_recv[i] += universe->nprocs; + plan_recv[i] = universe->me - comm->nprocs * (i + 1); + if (plan_recv[i] < 0) plan_recv[i] += universe->nprocs; - mode_index[i]=(universe->iworld+i+1)%(universe->nworlds); + mode_index[i] = (universe->iworld + i + 1) % (universe->nworlds); } - x_next = (universe->iworld+1+universe->nworlds)%(universe->nworlds); - x_last = (universe->iworld-1+universe->nworlds)%(universe->nworlds); + x_next = (universe->iworld + 1 + universe->nworlds) % (universe->nworlds); + x_last = (universe->iworld - 1 + universe->nworlds) % (universe->nworlds); } - if (buf_beads) - { - for (int i=0; inlocal; - if (nlocal > max_nlocal) - { - max_nlocal = nlocal+200; + if (nlocal > max_nlocal) { + max_nlocal = nlocal + 200; int size = sizeof(double) * max_nlocal * 3; - buf_recv = (double*) memory->srealloc(buf_recv, size, "FixPIMD:x_recv"); + buf_recv = (double *) memory->srealloc(buf_recv, size, "FixPIMD:x_recv"); - for (int i=0; isrealloc(buf_beads[i], size, "FixPIMD:x_beads[i]"); + for (int i = 0; i < np; i++) + buf_beads[i] = (double *) memory->srealloc(buf_beads[i], size, "FixPIMD:x_beads[i]"); } // copy local positions - memcpy(buf_beads[universe->iworld], &(ptr[0][0]), sizeof(double)*nlocal*3); + memcpy(buf_beads[universe->iworld], &(ptr[0][0]), sizeof(double) * nlocal * 3); // go over comm plans - for (int iplan = 0; iplanuworld, MPI_STATUS_IGNORE); + MPI_Sendrecv(&(nlocal), 1, MPI_INT, plan_send[iplan], 0, &(nsend), 1, MPI_INT, plan_recv[iplan], + 0, universe->uworld, MPI_STATUS_IGNORE); // allocate arrays - if (nsend > max_nsend) - { - max_nsend = nsend+200; - tag_send = (tagint*) memory->srealloc(tag_send, sizeof(tagint)*max_nsend, "FixPIMD:tag_send"); - buf_send = (double*) memory->srealloc(buf_send, sizeof(double)*max_nsend*3, "FixPIMD:x_send"); + if (nsend > max_nsend) { + max_nsend = nsend + 200; + tag_send = + (tagint *) memory->srealloc(tag_send, sizeof(tagint) * max_nsend, "FixPIMD:tag_send"); + buf_send = + (double *) memory->srealloc(buf_send, sizeof(double) * max_nsend * 3, "FixPIMD:x_send"); } // send tags - MPI_Sendrecv( atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0, - tag_send, nsend, MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); + MPI_Sendrecv(atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0, tag_send, nsend, + MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); // wrap positions double *wrap_ptr = buf_send; - int ncpy = sizeof(double)*3; + int ncpy = sizeof(double) * 3; - for (int i=0; imap(tag_send[i]); - if (index<0) - { + if (index < 0) { char error_line[256]; - sprintf(error_line, "Atom " TAGINT_FORMAT " is missing at world [%d] " - "rank [%d] required by rank [%d] (" TAGINT_FORMAT ", " - TAGINT_FORMAT ", " TAGINT_FORMAT ").\n", tag_send[i], - universe->iworld, comm->me, plan_recv[iplan], - atom->tag[0], atom->tag[1], atom->tag[2]); + sprintf(error_line, + "Atom " TAGINT_FORMAT " is missing at world [%d] " + "rank [%d] required by rank [%d] (" TAGINT_FORMAT ", " TAGINT_FORMAT + ", " TAGINT_FORMAT ").\n", + tag_send[i], universe->iworld, comm->me, plan_recv[iplan], atom->tag[0], + atom->tag[1], atom->tag[2]); - error->universe_one(FLERR,error_line); + error->universe_one(FLERR, error_line); } memcpy(wrap_ptr, ptr[index], ncpy); @@ -677,21 +694,20 @@ void FixPIMD::comm_exec(double **ptr) // sendrecv x - MPI_Sendrecv( buf_send, nsend*3, MPI_DOUBLE, plan_recv[iplan], 0, - buf_recv, nlocal*3, MPI_DOUBLE, plan_send[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); + MPI_Sendrecv(buf_send, nsend * 3, MPI_DOUBLE, plan_recv[iplan], 0, buf_recv, nlocal * 3, + MPI_DOUBLE, plan_send[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); // copy x - memcpy(buf_beads[mode_index[iplan]], buf_recv, sizeof(double)*nlocal*3); + memcpy(buf_beads[mode_index[iplan]], buf_recv, sizeof(double) * nlocal * 3); } } /* ---------------------------------------------------------------------- */ -int FixPIMD::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) +int FixPIMD::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { - int i,j,m; + int i, j, m; m = 0; @@ -709,7 +725,7 @@ int FixPIMD::pack_forward_comm(int n, int *list, double *buf, void FixPIMD::unpack_forward_comm(int n, int first, double *buf) { - int i,m,last; + int i, m, last; m = 0; last = first + n; @@ -726,47 +742,51 @@ void FixPIMD::unpack_forward_comm(int n, int first, double *buf) double FixPIMD::memory_usage() { - return (double)atom->nmax * size_peratom_cols * sizeof(double); + return (double) atom->nmax * size_peratom_cols * sizeof(double); } /* ---------------------------------------------------------------------- */ void FixPIMD::grow_arrays(int nmax) { - if (nmax==0) return; - int count = nmax*3; + if (nmax == 0) return; + int count = nmax * 3; memory->grow(array_atom, nmax, size_peratom_cols, "FixPIMD::array_atom"); - memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta"); - memory->grow(nhc_eta_dot, count, nhc_nchain+1, "FixPIMD::nh_eta_dot"); - memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot"); - memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass"); + memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta"); + memory->grow(nhc_eta_dot, count, nhc_nchain + 1, "FixPIMD::nh_eta_dot"); + memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot"); + memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass"); } /* ---------------------------------------------------------------------- */ void FixPIMD::copy_arrays(int i, int j, int /*delflag*/) { - int i_pos = i*3; - int j_pos = j*3; + int i_pos = i * 3; + int j_pos = j * 3; - memcpy(nhc_eta [j_pos], nhc_eta [i_pos], nhc_size_one_1); - memcpy(nhc_eta_dot [j_pos], nhc_eta_dot [i_pos], nhc_size_one_2); + memcpy(nhc_eta[j_pos], nhc_eta[i_pos], nhc_size_one_1); + memcpy(nhc_eta_dot[j_pos], nhc_eta_dot[i_pos], nhc_size_one_2); memcpy(nhc_eta_dotdot[j_pos], nhc_eta_dotdot[i_pos], nhc_size_one_1); - memcpy(nhc_eta_mass [j_pos], nhc_eta_mass [i_pos], nhc_size_one_1); + memcpy(nhc_eta_mass[j_pos], nhc_eta_mass[i_pos], nhc_size_one_1); } /* ---------------------------------------------------------------------- */ int FixPIMD::pack_exchange(int i, double *buf) { - int offset=0; + int offset = 0; int pos = i * 3; - memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_dot[pos], nhc_size_one_2); offset += nhc_offset_one_2; - memcpy(buf+offset, nhc_eta_dotdot[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_mass[pos], nhc_size_one_1); offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_dot[pos], nhc_size_one_2); + offset += nhc_offset_one_2; + memcpy(buf + offset, nhc_eta_dotdot[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_mass[pos], nhc_size_one_1); + offset += nhc_offset_one_1; return size_peratom_cols; } @@ -775,13 +795,17 @@ int FixPIMD::pack_exchange(int i, double *buf) int FixPIMD::unpack_exchange(int nlocal, double *buf) { - int offset=0; - int pos = nlocal*3; + int offset = 0; + int pos = nlocal * 3; - memcpy(nhc_eta[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(nhc_eta_dot[pos], buf+offset, nhc_size_one_2); offset += nhc_offset_one_2; - memcpy(nhc_eta_dotdot[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(nhc_eta_mass[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1; + memcpy(nhc_eta[pos], buf + offset, nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(nhc_eta_dot[pos], buf + offset, nhc_size_one_2); + offset += nhc_offset_one_2; + memcpy(nhc_eta_dotdot[pos], buf + offset, nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(nhc_eta_mass[pos], buf + offset, nhc_size_one_1); + offset += nhc_offset_one_1; return size_peratom_cols; } @@ -790,17 +814,21 @@ int FixPIMD::unpack_exchange(int nlocal, double *buf) int FixPIMD::pack_restart(int i, double *buf) { - int offset=0; + int offset = 0; int pos = i * 3; // pack buf[0] this way because other fixes unpack it - buf[offset++] = size_peratom_cols+1; + buf[offset++] = size_peratom_cols + 1; - memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_dot[pos], nhc_size_one_2); offset += nhc_offset_one_2; - memcpy(buf+offset, nhc_eta_dotdot[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_mass[pos], nhc_size_one_1); offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_dot[pos], nhc_size_one_2); + offset += nhc_offset_one_2; + memcpy(buf + offset, nhc_eta_dotdot[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_mass[pos], nhc_size_one_1); + offset += nhc_offset_one_1; - return size_peratom_cols+1; + return size_peratom_cols + 1; } /* ---------------------------------------------------------------------- */ @@ -813,15 +841,19 @@ void FixPIMD::unpack_restart(int nlocal, int nth) // unpack the Nth first values this way because other fixes pack them int m = 0; - for (int i=0; i (extra[nlocal][m]); + for (int i = 0; i < nth; i++) m += static_cast(extra[nlocal][m]); m++; int pos = nlocal * 3; - memcpy(nhc_eta[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1; - memcpy(nhc_eta_dot[pos], extra[nlocal]+m, nhc_size_one_2); m += nhc_offset_one_2; - memcpy(nhc_eta_dotdot[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1; - memcpy(nhc_eta_mass[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1; + memcpy(nhc_eta[pos], extra[nlocal] + m, nhc_size_one_1); + m += nhc_offset_one_1; + memcpy(nhc_eta_dot[pos], extra[nlocal] + m, nhc_size_one_2); + m += nhc_offset_one_2; + memcpy(nhc_eta_dotdot[pos], extra[nlocal] + m, nhc_size_one_1); + m += nhc_offset_one_1; + memcpy(nhc_eta_mass[pos], extra[nlocal] + m, nhc_size_one_1); + m += nhc_offset_one_1; nhc_ready = true; } @@ -830,21 +862,21 @@ void FixPIMD::unpack_restart(int nlocal, int nth) int FixPIMD::maxsize_restart() { - return size_peratom_cols+1; + return size_peratom_cols + 1; } /* ---------------------------------------------------------------------- */ int FixPIMD::size_restart(int /*nlocal*/) { - return size_peratom_cols+1; + return size_peratom_cols + 1; } /* ---------------------------------------------------------------------- */ double FixPIMD::compute_vector(int n) { - if (n==0) { return spring_energy; } - if (n==1) { return t_sys; } + if (n == 0) { return spring_energy; } + if (n == 1) { return t_sys; } return 0.0; } diff --git a/src/USER-MISC/fix_pimd.h b/src/REPLICA/fix_pimd.h similarity index 99% rename from src/USER-MISC/fix_pimd.h rename to src/REPLICA/fix_pimd.h index 2c13663f23..05a24dedce 100644 --- a/src/USER-MISC/fix_pimd.h +++ b/src/REPLICA/fix_pimd.h @@ -27,6 +27,7 @@ namespace LAMMPS_NS { class FixPIMD : public Fix { public: FixPIMD(class LAMMPS *, int, char **); + virtual ~FixPIMD(); int setmask(); diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 84ff43ec85..d391604530 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -101,8 +101,7 @@ void Hyper::command(int narg, char **arg) // create FixEventHyper class to store event and pre-quench states - modify->add_fix("hyper_event all EVENT/HYPER"); - fix_event = (FixEventHyper *) modify->fix[modify->nfix-1]; + fix_event = (FixEventHyper *) modify->add_fix("hyper_event all EVENT/HYPER"); // create Finish for timing output diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 66a1dd83d5..a445ace756 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -94,7 +94,8 @@ NEB::~NEB() { MPI_Comm_free(&roots); memory->destroy(all); - delete [] rdist; + delete[] rdist; + if (fp) fclose(fp); } /* ---------------------------------------------------------------------- @@ -379,8 +380,8 @@ void NEB::readfile(char *file, int flag) char line[MAXLINE]; double xx,yy,zz,delx,dely,delz; - if (me_universe == 0 && screen) - fprintf(screen,"Reading NEB coordinate file(s) ...\n"); + if (me_universe == 0 && universe->uscreen) + fprintf(universe->uscreen,"Reading NEB coordinate file(s) ...\n"); // flag = 0, universe root reads header of file, bcast to universe // flag = 1, each replica's root reads header of file, bcast to world @@ -534,6 +535,7 @@ void NEB::readfile(char *file, int flag) else fclose(fp); } } + fp = nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 23e572e88b..501e7675a8 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -145,8 +145,7 @@ void PRD::command(int narg, char **arg) // create ComputeTemp class to monitor temperature - modify->add_compute("prd_temp all temp"); - temperature = modify->compute[modify->ncompute-1]; + temperature = modify->add_compute("prd_temp all temp"); // create Velocity class for velocity creation in dephasing // pass it temperature compute, loop_setting, dist_setting settings @@ -168,8 +167,7 @@ void PRD::command(int narg, char **arg) // create FixEventPRD class to store event and pre-quench states - modify->add_fix("prd_event all EVENT/PRD"); - fix_event = (FixEventPRD *) modify->fix[modify->nfix-1]; + fix_event = (FixEventPRD *) modify->add_fix("prd_event all EVENT/PRD"); // create Finish for timing output diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 5631944dbf..9b6ecf0b0c 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -131,28 +131,11 @@ void TAD::command(int narg, char **arg) // create FixEventTAD object to store last event - int narg2 = 3; - char **args = new char*[narg2]; - args[0] = (char *) "tad_event"; - args[1] = (char *) "all"; - args[2] = (char *) "EVENT/TAD"; - modify->add_fix(narg2,args); - fix_event = (FixEventTAD *) modify->fix[modify->nfix-1]; - delete [] args; + fix_event = (FixEventTAD *) modify->add_fix("tad_event all EVENT/TAD"); // create FixStore object to store revert state - narg2 = 6; - args = new char*[narg2]; - args[0] = (char *) "tad_revert"; - args[1] = (char *) "all"; - args[2] = (char *) "STORE"; - args[3] = (char *) "peratom"; - args[4] = (char *) "0"; - args[5] = (char *) "7"; - modify->add_fix(narg2,args); - fix_revert = (FixStore *) modify->fix[modify->nfix-1]; - delete [] args; + fix_revert = (FixStore *) modify->add_fix("tad_revert all STORE peratom 0 7"); // create Finish for timing output @@ -195,13 +178,10 @@ void TAD::command(int narg, char **arg) // set minimize style for quench - narg2 = 1; - args = new char*[narg2]; + char *args[1]; args[0] = min_style; - update->create_minimize(narg2,args,1); - - delete [] args; + update->create_minimize(1,args,1); // init minimizer settings and minimizer itself @@ -691,25 +671,13 @@ void TAD::perform_neb(int ievent) // create FixNEB object to support NEB - int narg2 = 4; - char **args = new char*[narg2]; - args[0] = (char *) "neb"; - args[1] = (char *) "all"; - args[2] = (char *) "neb"; - args[3] = (char *) "1.0"; - modify->add_fix(narg2,args); - fix_neb = (Fix *) modify->fix[modify->nfix-1]; - delete [] args; + fix_neb = (Fix *) modify->add_fix("neb all neb 1.0"); // switch minimize style to quickmin for NEB - narg2 = 1; - args = new char*[narg2]; + char *args[1]; args[0] = min_style_neb; - - update->create_minimize(narg2,args,1); - - delete [] args; + update->create_minimize(1,args,1); // create NEB object @@ -769,17 +737,12 @@ void TAD::perform_neb(int ievent) // switch minimize style back for quench - narg2 = 1; - args = new char*[narg2]; args[0] = min_style; - - update->create_minimize(narg2,args,1); + update->create_minimize(1,args,1); update->etol = etol; update->ftol = ftol; - delete [] args; - // clean up modify->delete_fix("neb"); @@ -895,25 +858,14 @@ void TAD::delete_event_list() { void TAD::add_event() { + if (n_event_list == nmax_event_list) + grow_event_list(nmax_event_list+nmin_event_list); // create FixEventTAD object to store possible event - int narg = 3; - char **args = new char*[narg]; - - char str[128]; - sprintf(str,"tad_event_%d",n_event_list); - - args[0] = str; - args[1] = (char *) "all"; - args[2] = (char *) "EVENT/TAD"; - modify->add_fix(narg,args); - - if (n_event_list == nmax_event_list) - grow_event_list(nmax_event_list+nmin_event_list); - n_event_list += 1; - int ievent = n_event_list-1; - fix_event_list[ievent] = (FixEventTAD *) modify->fix[modify->nfix-1]; + int ievent = n_event_list++; + fix_event_list[ievent] + = (FixEventTAD *) modify->add_fix(fmt::format("tad_event_{} all EVENT/TAD", ievent)); // store quenched state for new event @@ -923,11 +875,6 @@ void TAD::add_event() fix_event->restore_state_quench(); fix_event_list[ievent]->store_state_quench(); - - // string clean-up - - delete [] args; - } /* ---------------------------------------------------------------------- diff --git a/src/USER-MISC/temper_grem.cpp b/src/REPLICA/temper_grem.cpp similarity index 100% rename from src/USER-MISC/temper_grem.cpp rename to src/REPLICA/temper_grem.cpp diff --git a/src/USER-MISC/temper_grem.h b/src/REPLICA/temper_grem.h similarity index 100% rename from src/USER-MISC/temper_grem.h rename to src/REPLICA/temper_grem.h diff --git a/src/USER-MISC/temper_npt.cpp b/src/REPLICA/temper_npt.cpp similarity index 100% rename from src/USER-MISC/temper_npt.cpp rename to src/REPLICA/temper_npt.cpp diff --git a/src/USER-MISC/temper_npt.h b/src/REPLICA/temper_npt.h similarity index 100% rename from src/USER-MISC/temper_npt.h rename to src/REPLICA/temper_npt.h diff --git a/src/USER-SCAFACOS/Install.sh b/src/SCAFACOS/Install.sh similarity index 100% rename from src/USER-SCAFACOS/Install.sh rename to src/SCAFACOS/Install.sh diff --git a/src/USER-SCAFACOS/README b/src/SCAFACOS/README similarity index 94% rename from src/USER-SCAFACOS/README rename to src/SCAFACOS/README index 42d2e2c0f7..dc3eb65bfa 100644 --- a/src/USER-SCAFACOS/README +++ b/src/SCAFACOS/README @@ -19,7 +19,7 @@ Once you have successfully built LAMMPS with this package and the ScaFaCoS library, you can test it using an input file from the examples scafacos dir, e.g.: -lmp_serial -in lammps/examples/USER/scafacos/in.scafacos.fmm +lmp_serial -in lammps/examples/PACKAGES/scafacos/in.scafacos.fmm For questions about ScaFaCoS, please contact: r.halver@fz-juelich.de or g.sutmann@fz-juelich.de diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/SCAFACOS/scafacos.cpp similarity index 53% rename from src/USER-SCAFACOS/scafacos.cpp rename to src/SCAFACOS/scafacos.cpp index 51bf4fb45e..451dd7aca9 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/SCAFACOS/scafacos.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -25,10 +24,8 @@ #include "force.h" #include "memory.h" -#include #include -#include -#include +#include // ScaFaCoS library @@ -54,25 +51,24 @@ Scafacos::Scafacos(LAMMPS *lmp) : KSpace(lmp) void Scafacos::settings(int narg, char **arg) { - if (narg != 2) error->all(FLERR,"Illegal scafacos command"); + if (narg != 2) error->all(FLERR, "Illegal scafacos command"); method = utils::strdup(arg[0]); - tolerance = utils::numeric(FLERR,arg[1],false,lmp); + tolerance = utils::numeric(FLERR, arg[1], false, lmp); // optional ScaFaCoS library setting defaults // choose the correct default tolerance type for chosen method // throw an error if a not yet supported solver is chosen - if (strcmp(method,"fmm") == 0) { + if (strcmp(method, "fmm") == 0) { tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; fmm_tuning_flag = 0; - } else if (strcmp(method,"p3m") == 0 || - strcmp(method,"p2nfft") == 0 || - strcmp(method,"ewald") == 0) { + } else if (strcmp(method, "p3m") == 0 || strcmp(method, "p2nfft") == 0 || + strcmp(method, "ewald") == 0) { tolerance_type = FCS_TOLERANCE_TYPE_FIELD; - } else if (strcmp(method,"direct") == 0) { - ; // direct summation has no tolerance type + } else if (strcmp(method, "direct") == 0) { + ; // direct summation has no tolerance type } else { - error->all(FLERR,"Unsupported ScaFaCoS method"); + error->all(FLERR, "Unsupported ScaFaCoS method"); } } @@ -80,14 +76,14 @@ void Scafacos::settings(int narg, char **arg) Scafacos::~Scafacos() { - delete [] method; + delete[] method; memory->destroy(xpbc); memory->destroy(epot); memory->destroy(efield); // clean up of the ScaFaCoS handle and internal arrays - fcs_destroy((FCS)fcs); + fcs_destroy((FCS) fcs); } /* ---------------------------------------------------------------------- */ @@ -95,32 +91,27 @@ Scafacos::~Scafacos() void Scafacos::init() { // error checks - if (screen && me == 0) fprintf(screen, - "Setting up ScaFaCoS with solver %s ...\n",method); - if (logfile && me == 0) fprintf(logfile, - "Setting up ScaFaCoS with solver %s ...\n",method); + if (me == 0) { + utils::logmesg(lmp, "Setting up ScaFaCoS with solver {} ...\n", method); - if ((strcmp(method,"p3m") == 0) && (me == 0)) - error->warning(FLERR,"Virial computation for P3M not available"); + if (strcmp(method, "p3m") == 0) + error->warning(FLERR, "Virial computation for P3M not available"); - if ((strcmp(method,"ewald") == 0) && (me == 0)) - error->warning(FLERR,"Virial computation for Ewald not available"); + if (strcmp(method, "ewald") == 0) + error->warning(FLERR, "Virial computation for Ewald not available"); + } - if (!atom->q_flag) - error->all(FLERR,"Kspace style requires atom attribute q"); + if (!atom->q_flag) error->all(FLERR, "Kspace style requires atom attribute q"); - if (domain->dimension == 2) - error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); + if (domain->dimension == 2) error->all(FLERR, "Cannot use ScaFaCoS with 2d simulation"); - if (domain->triclinic) - error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet"); + if (domain->triclinic) error->all(FLERR, "Cannot use ScaFaCoS with triclinic domain yet"); if (atom->natoms > INT_MAX && sizeof(int) != 8) - error->all(FLERR,"Scafacos atom count exceeds 2B"); + error->all(FLERR, "Scafacos atom count exceeds 2B"); if (atom->molecular != Atom::ATOMIC) - error->all(FLERR, - "Cannot use Scafacos with molecular charged systems yet"); + error->all(FLERR, "Cannot use Scafacos with molecular charged systems yet"); FCSResult result; @@ -129,47 +120,44 @@ void Scafacos::init() qqrd2e = force->qqrd2e; if (!initialized) { - result = fcs_init((FCS*)&fcs,method,world); - check_result((void*)&result); + result = fcs_init((FCS *) &fcs, method, world); + check_result((void *) &result); setup_handle(); // using other methods lead to termination of the program, // since they have no tolerance tuning methods - if ( strcmp(method,"fmm") == 0 || - strcmp(method,"p3m") == 0 || - strcmp(method,"p2nfft") == 0 || - strcmp(method,"ewald") == 0) - { - result = fcs_set_tolerance((FCS)fcs,tolerance_type,tolerance); - check_result((void*)&result); + if (strcmp(method, "fmm") == 0 || strcmp(method, "p3m") == 0 || strcmp(method, "p2nfft") == 0 || + strcmp(method, "ewald") == 0) { + result = fcs_set_tolerance((FCS) fcs, tolerance_type, tolerance); + check_result((void *) &result); } double **x = atom->x; double *q = atom->q; int nlocal = atom->nlocal; - if (strcmp(method,"fmm") == 0) { + if (strcmp(method, "fmm") == 0) { if (fmm_tuning_flag == 1) - fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); + fcs_fmm_set_internal_tuning((FCS) fcs, FCS_FMM_INHOMOGENOUS_SYSTEM); else - fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_HOMOGENOUS_SYSTEM); + fcs_fmm_set_internal_tuning((FCS) fcs, FCS_FMM_HOMOGENOUS_SYSTEM); } // for the FMM at least one particle is required per process - if (strcmp(method,"fmm") == 0) { - int empty = (nlocal==0)?1:0; - MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); + if (strcmp(method, "fmm") == 0) { + int empty = (nlocal == 0) ? 1 : 0; + MPI_Allreduce(MPI_IN_PLACE, &empty, 1, MPI_INT, MPI_SUM, world); if (empty > 0) - fcs_set_redistribute((FCS)fcs,1); + fcs_set_redistribute((FCS) fcs, 1); else - fcs_set_redistribute((FCS)fcs,0); + fcs_set_redistribute((FCS) fcs, 0); } - result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q); - check_result((void*)&result); + result = fcs_tune((FCS) fcs, nlocal, &x[0][0], q); + check_result((void *) &result); // more useful here, since the parameters should be tuned now - if (me == 0) fcs_print_parameters((FCS)fcs); + if (me == 0) fcs_print_parameters((FCS) fcs); } initialized = 1; @@ -187,17 +175,16 @@ void Scafacos::compute(int eflag, int vflag) FCSResult result; // for the FMM at least one particle is required per process - if (strcmp(method,"fmm")) - { - int empty = (nlocal==0)?1:0; - MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); + if (strcmp(method, "fmm")) { + int empty = (nlocal == 0) ? 1 : 0; + MPI_Allreduce(MPI_IN_PLACE, &empty, 1, MPI_INT, MPI_SUM, world); if (empty > 0) - fcs_set_redistribute((FCS)fcs,1); + fcs_set_redistribute((FCS) fcs, 1); else - fcs_set_redistribute((FCS)fcs,0); + fcs_set_redistribute((FCS) fcs, 0); } - ev_init(eflag,vflag); + ev_init(eflag, vflag); // grow xpbc, epot, efield if necessary @@ -206,28 +193,26 @@ void Scafacos::compute(int eflag, int vflag) memory->destroy(epot); memory->destroy(efield); maxatom = atom->nmax; - memory->create(xpbc,3*maxatom,"scafacos:xpbc"); - memory->create(epot,maxatom,"scafacos:epot"); - memory->create(efield,maxatom,3,"scafacos:efield"); + memory->create(xpbc, 3 * maxatom, "scafacos:xpbc"); + memory->create(epot, maxatom, "scafacos:epot"); + memory->create(efield, maxatom, 3, "scafacos:efield"); } if (vflag_global) { // for P3M or Ewald we cannot compute the virial. skip it. - if ((strcmp(method,"p3m") != 0) - && (strcmp(method,"ewald") != 0)) { - result = fcs_set_compute_virial((FCS)fcs,1); - check_result((void*)&result); + if ((strcmp(method, "p3m") != 0) && (strcmp(method, "ewald") != 0)) { + result = fcs_set_compute_virial((FCS) fcs, 1); + check_result((void *) &result); } } // pack coords into xpbc and apply PBC - memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); + memcpy(xpbc, &x[0][0], 3 * nlocal * sizeof(double)); - - if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic) { - int j = 0; + if (domain->xperiodic || domain->yperiodic || domain->zperiodic) { + int j = 0; for (int i = 0; i < nlocal; i++) { domain->remap(&xpbc[j]); j += 3; @@ -238,14 +223,14 @@ void Scafacos::compute(int eflag, int vflag) if (box_has_changed()) { setup_handle(); - result = fcs_tune((FCS)fcs,nlocal,xpbc,q); - check_result((void*)&result); + result = fcs_tune((FCS) fcs, nlocal, xpbc, q); + check_result((void *) &result); } // invoke ScaFaCoS solver - result = fcs_run((FCS)fcs,nlocal,xpbc,q,&efield[0][0],epot); - check_result((void*)&result); + result = fcs_run((FCS) fcs, nlocal, xpbc, q, &efield[0][0], epot); + check_result((void *) &result); // extract virial @@ -253,10 +238,9 @@ void Scafacos::compute(int eflag, int vflag) // for P3M or Ewald we cannot compute the virial. skip it. - if ((strcmp(method,"p3m") != 0) - && (strcmp(method,"ewald") != 0)) { - result = fcs_get_virial((FCS)fcs,virial_int); - check_result((void*)&result); + if ((strcmp(method, "p3m") != 0) && (strcmp(method, "ewald") != 0)) { + result = fcs_get_virial((FCS) fcs, virial_int); + check_result((void *) &result); virial[0] = virial_int[0]; virial[1] = virial_int[1]; @@ -284,11 +268,10 @@ void Scafacos::compute(int eflag, int vflag) } if (eflag_atom) { - for (int i = 0; i < nlocal; i++) - eatom[i] = 0.5 * qscale * q[i] * epot[i]; + for (int i = 0; i < nlocal; i++) eatom[i] = 0.5 * qscale * q[i] * epot[i]; } - MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&myeng, &energy, 1, MPI_DOUBLE, MPI_SUM, world); } /* ---------------------------------------------------------------------- */ @@ -301,55 +284,34 @@ int Scafacos::modify_param(int narg, char **arg) // value1 = energy, energy_rel, etc // everyone of these should have a default, so user doesn't need to set - if (strcmp(arg[0],"scafacos") != 0) return 0; + if (strcmp(arg[0], "scafacos") != 0) return 0; - if (strcmp(arg[1],"tolerance") == 0) { - if (narg < 3) error->all(FLERR, - "Illegal kspace_modify command (tolerance)"); - if (strcmp(arg[2],"energy") == 0) + if (strcmp(arg[1], "tolerance") == 0) { + if (narg < 3) error->all(FLERR, "Illegal kspace_modify command (tolerance)"); + if (strcmp(arg[2], "energy") == 0) tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; - else if (strcmp(arg[2],"energy_rel") == 0) + else if (strcmp(arg[2], "energy_rel") == 0) tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; - else if (strcmp(arg[2],"field") == 0) + else if (strcmp(arg[2], "field") == 0) tolerance_type = FCS_TOLERANCE_TYPE_FIELD; - else if (strcmp(arg[2],"field_rel") == 0) + else if (strcmp(arg[2], "field_rel") == 0) tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; - else if (strcmp(arg[2],"potential") == 0) + else if (strcmp(arg[2], "potential") == 0) tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; - else if (strcmp(arg[2],"potential_rel") == 0) + else if (strcmp(arg[2], "potential_rel") == 0) tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; - else error->all(FLERR, - "Illegal kspace_modify command (tolerance argument)"); + else + error->all(FLERR, "Illegal kspace_modify command (tolerance argument)"); // check if method is compatatible to chosen tolerance type - if ( - ( - strcmp(method,"fmm") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && - tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL - ) - ) || - ( - strcmp(method,"p2nfft") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_FIELD && - tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL - ) - ) || - ( - strcmp(method,"p3m") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_FIELD - ) - ) || - ( - strcmp(method,"ewald") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_FIELD - ) - ) - ) - error->all(FLERR,"Illegal kspace_modify command \ + if ((strcmp(method, "fmm") == 0 && + (tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && + tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL)) || + (strcmp(method, "p2nfft") == 0 && + (tolerance_type != FCS_TOLERANCE_TYPE_FIELD && + tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL)) || + (strcmp(method, "p3m") == 0 && (tolerance_type != FCS_TOLERANCE_TYPE_FIELD)) || + (strcmp(method, "ewald") == 0 && (tolerance_type != FCS_TOLERANCE_TYPE_FIELD))) + error->all(FLERR, "Illegal kspace_modify command \ (invalid tolerance / method combination)"); return 3; } @@ -358,15 +320,11 @@ int Scafacos::modify_param(int narg, char **arg) // value1 = 0, 1 // 0 -> homogenous system (default) // 1 -> inhomogenous system (more internal tuning is provided (sequential!)) - if (strcmp(arg[1],"fmm_tuning") == 0) - { - if (screen && me == 0) fprintf(screen, - "ScaFaCoS setting fmm inhomogen tuning ...\n"); - if (logfile && me == 0) fprintf(logfile, - "ScaFaCoS setting fmm inhomogen tuning ...\n"); - if (narg < 3) error->all(FLERR, - "Illegal kspace_modify command (fmm_tuning)"); - fmm_tuning_flag = atoi(arg[2]); + if (strcmp(arg[1], "fmm_tuning") == 0) { + if (me == 0) utils::logmesg(lmp, "ScaFaCoS setting fmm inhomogen tuning ...\n"); + + if (narg < 3) error->all(FLERR, "Illegal kspace_modify command (fmm_tuning)"); + fmm_tuning_flag = utils::inumeric(FLERR, arg[2], false, lmp); return 3; } @@ -380,8 +338,8 @@ int Scafacos::modify_param(int narg, char **arg) double Scafacos::memory_usage() { double bytes = 0.0; - bytes += (double)maxatom * sizeof(double); - bytes += (double)3*maxatom * sizeof(double); + bytes += (double) maxatom * sizeof(double); + bytes += (double) 3 * maxatom * sizeof(double); return bytes; } @@ -417,23 +375,23 @@ void Scafacos::setup_handle() old_natoms = atom->natoms; // store parameters to ScaFaCoS handle - result = fcs_set_box_a((FCS)fcs,old_box_x); - check_result((void*)&result); + result = fcs_set_box_a((FCS) fcs, old_box_x); + check_result((void *) &result); - result = fcs_set_box_b((FCS)fcs,old_box_y); - check_result((void*)&result); + result = fcs_set_box_b((FCS) fcs, old_box_y); + check_result((void *) &result); - result = fcs_set_box_c((FCS)fcs,old_box_z); - check_result((void*)&result); + result = fcs_set_box_c((FCS) fcs, old_box_z); + check_result((void *) &result); - result = fcs_set_box_origin((FCS)fcs,old_origin); - check_result((void*)&result); + result = fcs_set_box_origin((FCS) fcs, old_origin); + check_result((void *) &result); - result = fcs_set_periodicity((FCS)fcs,old_periodicity); - check_result((void*)&result); + result = fcs_set_periodicity((FCS) fcs, old_periodicity); + check_result((void *) &result); - result = fcs_set_total_particles((FCS)fcs,old_natoms); - check_result((void*)&result); + result = fcs_set_total_particles((FCS) fcs, old_natoms); + check_result((void *) &result); // allow ScaFaCoS to calculate the near field computations for now // TODO: allow the delegation of the near field computations @@ -441,8 +399,8 @@ void Scafacos::setup_handle() // (near_field_flag = 1 -> enables the internal near field calcs // 0 -> disables the internal near field calcs int near_field_flag = 1; - result = fcs_set_near_field_flag((FCS)fcs,near_field_flag); - check_result((void*)&result); + result = fcs_set_near_field_flag((FCS) fcs, near_field_flag); + check_result((void *) &result); } /* ---------------------------------------------------------------------- @@ -454,17 +412,11 @@ bool Scafacos::box_has_changed() int *periodicity = domain->periodicity; double *prd = domain->prd; - bool changed = - (periodicity[0] != old_periodicity[0]) || - (periodicity[1] != old_periodicity[1]) || - (periodicity[2] != old_periodicity[2]) || - (domain->boundary[0][0] != old_origin[0]) || - (domain->boundary[1][0] != old_origin[1]) || - (domain->boundary[2][0] != old_origin[2]) || - (prd[0] != old_box_x[0]) || - (prd[1] != old_box_y[1]) || - (prd[2] != old_box_z[2]) || - (atom->natoms != old_natoms); + bool changed = (periodicity[0] != old_periodicity[0]) || (periodicity[1] != old_periodicity[1]) || + (periodicity[2] != old_periodicity[2]) || (domain->boundary[0][0] != old_origin[0]) || + (domain->boundary[1][0] != old_origin[1]) || (domain->boundary[2][0] != old_origin[2]) || + (prd[0] != old_box_x[0]) || (prd[1] != old_box_y[1]) || (prd[2] != old_box_z[2]) || + (atom->natoms != old_natoms); return changed; } @@ -473,19 +425,11 @@ bool Scafacos::box_has_changed() check ScaFaCoS result for error condition ------------------------------------------------------------------------- */ -void Scafacos::check_result(void* result_p) +void Scafacos::check_result(void *result_p) { - FCSResult result = *(FCSResult*)result_p; - + FCSResult result = *(FCSResult *) result_p; if (!result) return; - std::stringstream ss; - ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n" - << fcs_result_get_message(result) << "\n"; - fcs_result_destroy(result); - std::string err_msg = ss.str(); - const char *str = err_msg.c_str(); - - error->one(FLERR,str); + error->one(FLERR, "ScaFaCoS: {}\n{}\n", fcs_result_get_function(result), + fcs_result_get_message(result)); } - diff --git a/src/USER-SCAFACOS/scafacos.h b/src/SCAFACOS/scafacos.h similarity index 100% rename from src/USER-SCAFACOS/scafacos.h rename to src/SCAFACOS/scafacos.h diff --git a/src/USER-SMTBQ/README b/src/SMTBQ/README similarity index 95% rename from src/USER-SMTBQ/README rename to src/SMTBQ/README index e778c65be2..594df29ac6 100644 --- a/src/USER-SMTBQ/README +++ b/src/SMTBQ/README @@ -13,4 +13,4 @@ See the doc page for the pair_style smtbq command to get started. There are potential files for this potential in the potentials dir. There are example scripts for using this package in -examples/USER/smtbq. +examples/PACKAGES/smtbq. diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/SMTBQ/pair_smtbq.cpp similarity index 100% rename from src/USER-SMTBQ/pair_smtbq.cpp rename to src/SMTBQ/pair_smtbq.cpp diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/SMTBQ/pair_smtbq.h similarity index 100% rename from src/USER-SMTBQ/pair_smtbq.h rename to src/SMTBQ/pair_smtbq.h diff --git a/src/USER-SPH/README b/src/SPH/README similarity index 92% rename from src/USER-SPH/README rename to src/SPH/README index 97afba8d12..948db9a70c 100644 --- a/src/USER-SPH/README +++ b/src/SPH/README @@ -12,7 +12,7 @@ LAMMPS. Currently, the package has the following features: See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started. -There are example scripts for using this package in examples/USER/sph. +There are example scripts for using this package in examples/PACKAGES/sph. The person who created this package is Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in diff --git a/src/USER-SPH/atom_vec_sph.cpp b/src/SPH/atom_vec_sph.cpp similarity index 100% rename from src/USER-SPH/atom_vec_sph.cpp rename to src/SPH/atom_vec_sph.cpp diff --git a/src/USER-SPH/atom_vec_sph.h b/src/SPH/atom_vec_sph.h similarity index 100% rename from src/USER-SPH/atom_vec_sph.h rename to src/SPH/atom_vec_sph.h diff --git a/src/USER-SPH/compute_sph_e_atom.cpp b/src/SPH/compute_sph_e_atom.cpp similarity index 100% rename from src/USER-SPH/compute_sph_e_atom.cpp rename to src/SPH/compute_sph_e_atom.cpp diff --git a/src/USER-SPH/compute_sph_e_atom.h b/src/SPH/compute_sph_e_atom.h similarity index 100% rename from src/USER-SPH/compute_sph_e_atom.h rename to src/SPH/compute_sph_e_atom.h diff --git a/src/USER-SPH/compute_sph_rho_atom.cpp b/src/SPH/compute_sph_rho_atom.cpp similarity index 100% rename from src/USER-SPH/compute_sph_rho_atom.cpp rename to src/SPH/compute_sph_rho_atom.cpp diff --git a/src/USER-SPH/compute_sph_rho_atom.h b/src/SPH/compute_sph_rho_atom.h similarity index 100% rename from src/USER-SPH/compute_sph_rho_atom.h rename to src/SPH/compute_sph_rho_atom.h diff --git a/src/USER-SPH/compute_sph_t_atom.cpp b/src/SPH/compute_sph_t_atom.cpp similarity index 100% rename from src/USER-SPH/compute_sph_t_atom.cpp rename to src/SPH/compute_sph_t_atom.cpp diff --git a/src/USER-SPH/compute_sph_t_atom.h b/src/SPH/compute_sph_t_atom.h similarity index 100% rename from src/USER-SPH/compute_sph_t_atom.h rename to src/SPH/compute_sph_t_atom.h diff --git a/src/USER-SPH/fix_sph.cpp b/src/SPH/fix_sph.cpp similarity index 100% rename from src/USER-SPH/fix_sph.cpp rename to src/SPH/fix_sph.cpp diff --git a/src/USER-SPH/fix_sph.h b/src/SPH/fix_sph.h similarity index 100% rename from src/USER-SPH/fix_sph.h rename to src/SPH/fix_sph.h diff --git a/src/USER-SPH/fix_sph_stationary.cpp b/src/SPH/fix_sph_stationary.cpp similarity index 100% rename from src/USER-SPH/fix_sph_stationary.cpp rename to src/SPH/fix_sph_stationary.cpp diff --git a/src/USER-SPH/fix_sph_stationary.h b/src/SPH/fix_sph_stationary.h similarity index 100% rename from src/USER-SPH/fix_sph_stationary.h rename to src/SPH/fix_sph_stationary.h diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/SPH/pair_sph_heatconduction.cpp similarity index 100% rename from src/USER-SPH/pair_sph_heatconduction.cpp rename to src/SPH/pair_sph_heatconduction.cpp diff --git a/src/USER-SPH/pair_sph_heatconduction.h b/src/SPH/pair_sph_heatconduction.h similarity index 100% rename from src/USER-SPH/pair_sph_heatconduction.h rename to src/SPH/pair_sph_heatconduction.h diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/SPH/pair_sph_idealgas.cpp similarity index 100% rename from src/USER-SPH/pair_sph_idealgas.cpp rename to src/SPH/pair_sph_idealgas.cpp diff --git a/src/USER-SPH/pair_sph_idealgas.h b/src/SPH/pair_sph_idealgas.h similarity index 100% rename from src/USER-SPH/pair_sph_idealgas.h rename to src/SPH/pair_sph_idealgas.h diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/SPH/pair_sph_lj.cpp similarity index 100% rename from src/USER-SPH/pair_sph_lj.cpp rename to src/SPH/pair_sph_lj.cpp diff --git a/src/USER-SPH/pair_sph_lj.h b/src/SPH/pair_sph_lj.h similarity index 100% rename from src/USER-SPH/pair_sph_lj.h rename to src/SPH/pair_sph_lj.h diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/SPH/pair_sph_rhosum.cpp similarity index 100% rename from src/USER-SPH/pair_sph_rhosum.cpp rename to src/SPH/pair_sph_rhosum.cpp diff --git a/src/USER-SPH/pair_sph_rhosum.h b/src/SPH/pair_sph_rhosum.h similarity index 100% rename from src/USER-SPH/pair_sph_rhosum.h rename to src/SPH/pair_sph_rhosum.h diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/SPH/pair_sph_taitwater.cpp similarity index 100% rename from src/USER-SPH/pair_sph_taitwater.cpp rename to src/SPH/pair_sph_taitwater.cpp diff --git a/src/USER-SPH/pair_sph_taitwater.h b/src/SPH/pair_sph_taitwater.h similarity index 100% rename from src/USER-SPH/pair_sph_taitwater.h rename to src/SPH/pair_sph_taitwater.h diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/SPH/pair_sph_taitwater_morris.cpp similarity index 100% rename from src/USER-SPH/pair_sph_taitwater_morris.cpp rename to src/SPH/pair_sph_taitwater_morris.cpp diff --git a/src/USER-SPH/pair_sph_taitwater_morris.h b/src/SPH/pair_sph_taitwater_morris.h similarity index 100% rename from src/USER-SPH/pair_sph_taitwater_morris.h rename to src/SPH/pair_sph_taitwater_morris.h diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index e6929d2d72..c64609cfe3 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -176,6 +176,7 @@ void FixNVESpin::init() // loop 1: obtain # of Pairs, and # of Pair/Spin styles + npairspin = 0; PairHybrid *hybrid = (PairHybrid *)force->pair_match("^hybrid",0); if (force->pair_match("^spin",0,0)) { // only one Pair/Spin style pair = force->pair_match("^spin",0,0); @@ -232,6 +233,7 @@ void FixNVESpin::init() // loop 1: obtain # of fix precession/spin styles int iforce; + nprecspin = 0; for (iforce = 0; iforce < modify->nfix; iforce++) { if (utils::strmatch(modify->fix[iforce]->style,"^precession/spin")) { nprecspin++; @@ -264,6 +266,7 @@ void FixNVESpin::init() // loop 1: obtain # of fix langevin/spin styles + nlangspin = 0; for (iforce = 0; iforce < modify->nfix; iforce++) { if (utils::strmatch(modify->fix[iforce]->style,"^langevin/spin")) { nlangspin++; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index a07a16350a..1b798166a1 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -78,7 +78,8 @@ NEBSpin::~NEBSpin() { MPI_Comm_free(&roots); memory->destroy(all); - delete [] rdist; + delete[] rdist; + if (fp) fclose(fp); } /* ---------------------------------------------------------------------- @@ -373,8 +374,8 @@ void NEBSpin::readfile(char *file, int flag) double xx,yy,zz; double musp,spx,spy,spz; - if (me_universe == 0 && screen) - fprintf(screen,"Reading NEBSpin coordinate file(s) ...\n"); + if (me_universe == 0 && universe->uscreen) + fprintf(universe->uscreen,"Reading NEBSpin coordinate file(s) ...\n"); // flag = 0, universe root reads header of file, bcast to universe // flag = 1, each replica's root reads header of file, bcast to world @@ -546,8 +547,8 @@ void NEBSpin::readfile(char *file, int flag) // clean up - delete [] buffer; - delete [] values; + delete[] buffer; + delete[] values; if (flag == 0) { if (me_universe == 0) { @@ -560,6 +561,7 @@ void NEBSpin::readfile(char *file, int flag) else fclose(fp); } } + fp = nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index dcb62e534d..04fb33eec4 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -1277,6 +1277,7 @@ void FixSRD::collisions_single() double **v = atom->v; double **f = atom->f; double **torque = atom->torque; + tagint *tag = atom->tag; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -1329,29 +1330,23 @@ void FixSRD::collisions_single() } #ifdef SRD_DEBUG - if (update->ntimestep == SRD_DEBUG_TIMESTEP && atom->tag[i] == SRD_DEBUG_ATOMID) + if (update->ntimestep == SRD_DEBUG_TIMESTEP && tag[i] == SRD_DEBUG_ATOMID) print_collision(i, j, ibounce, t_remain, dt, xscoll, xbcoll, norm, type); #endif if (t_remain > dt) { ninside++; if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) { - char str[128]; - if (type != WALL) { - sprintf(str, - "SRD particle " TAGINT_FORMAT " started " - "inside big particle " TAGINT_FORMAT " on step " BIGINT_FORMAT " bounce %d", - atom->tag[i], atom->tag[j], update->ntimestep, ibounce + 1); - if (insideflag == INSIDE_ERROR) error->one(FLERR, str); - error->warning(FLERR, str); - } else { - sprintf(str, - "SRD particle " TAGINT_FORMAT " started " - "inside wall %d on step " BIGINT_FORMAT " bounce %d", - atom->tag[i], j, update->ntimestep, ibounce + 1); - if (insideflag == INSIDE_ERROR) error->one(FLERR, str); - error->warning(FLERR, str); - } + std::string mesg; + if (type != WALL) + mesg = fmt::format("SRD particle {} started inside big particle {} on step {} " + " bounce {}", tag[i], tag[j], update->ntimestep, ibounce + 1); + else + mesg = fmt::format("SRD particle {} started inside wall {} on step {} " + "bounce {}", tag[i], j, update->ntimestep, ibounce + 1); + + if (insideflag == INSIDE_ERROR) error->one(FLERR, mesg); + else error->warning(FLERR, mesg); } break; } @@ -1435,6 +1430,7 @@ void FixSRD::collisions_multi() double **v = atom->v; double **f = atom->f; double **torque = atom->torque; + tagint *tag = atom->tag; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -1484,29 +1480,23 @@ void FixSRD::collisions_multi() t_remain = collision_wall_exact(x[i], j, v[i], xscoll, xbcoll, norm); #ifdef SRD_DEBUG - if (update->ntimestep == SRD_DEBUG_TIMESTEP && atom->tag[i] == SRD_DEBUG_ATOMID) + if (update->ntimestep == SRD_DEBUG_TIMESTEP && tag[i] == SRD_DEBUG_ATOMID) print_collision(i, j, ibounce, t_remain, dt, xscoll, xbcoll, norm, type); #endif if (t_remain > dt || t_remain < 0.0) { ninside++; if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) { - char str[128]; - if (type != WALL) { - sprintf(str, - "SRD particle " TAGINT_FORMAT " started " - "inside big particle " TAGINT_FORMAT " on step " BIGINT_FORMAT " bounce %d", - atom->tag[i], atom->tag[j], update->ntimestep, ibounce + 1); - if (insideflag == INSIDE_ERROR) error->one(FLERR, str); - error->warning(FLERR, str); - } else { - sprintf(str, - "SRD particle " TAGINT_FORMAT " started " - "inside wall %d on step " BIGINT_FORMAT " bounce %d", - atom->tag[i], j, update->ntimestep, ibounce + 1); - if (insideflag == INSIDE_ERROR) error->one(FLERR, str); - error->warning(FLERR, str); - } + std::string mesg; + if (type != WALL) + mesg = fmt::format("SRD particle {} started inside big particle {} on step {} " + "bounce {}", tag[i], tag[j], update->ntimestep, ibounce + 1); + else + mesg = fmt::format("SRD particle {} started inside wall {} on step {} " + "bounce {}", tag[i], j, update->ntimestep, ibounce + 1); + + if (insideflag == INSIDE_ERROR) error->one(FLERR, mesg); + error->warning(FLERR, mesg); } t_first = 0.0; break; diff --git a/src/USER-TALLY/README b/src/TALLY/README similarity index 93% rename from src/USER-TALLY/README rename to src/TALLY/README index afdf638154..529184de7c 100644 --- a/src/USER-TALLY/README +++ b/src/TALLY/README @@ -15,7 +15,7 @@ Nevertheless, since those compute styles are executed directly using information that has already been computed, they should usually be more efficient than their counterparts. -There are example scripts for using this package in examples/USER/tally +There are example scripts for using this package in examples/PACKAGES/tally The person who created this package is Axel Kohlmeyer (akohlmey@gmail.com) at Temple University with a little help and inspiration from diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/TALLY/compute_force_tally.cpp similarity index 65% rename from src/USER-TALLY/compute_force_tally.cpp rename to src/TALLY/compute_force_tally.cpp index bc9a79713b..8216269fe0 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/TALLY/compute_force_tally.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,28 +13,26 @@ #include "compute_force_tally.h" -#include #include "atom.h" -#include "group.h" -#include "pair.h" -#include "update.h" -#include "memory.h" +#include "comm.h" #include "error.h" #include "force.h" -#include "comm.h" +#include "group.h" +#include "memory.h" +#include "pair.h" +#include "update.h" +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) +ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg < 4) error->all(FLERR,"Illegal compute force/tally command"); + if (narg < 4) error->all(FLERR, "Illegal compute force/tally command"); igroup2 = group->find(arg[3]); - if (igroup2 == -1) - error->all(FLERR,"Could not find compute force/tally second group ID"); + if (igroup2 == -1) error->all(FLERR, "Could not find compute force/tally second group ID"); groupbit2 = group->bitmask[igroup2]; scalar_flag = 1; @@ -46,7 +43,7 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : comm_reverse = size_peratom_cols = 3; extscalar = 1; - peflag = 1; // we need Pair::ev_tally() to be run + peflag = 1; // we need Pair::ev_tally() to be run did_setup = invoked_peratom = invoked_scalar = -1; nmax = -1; @@ -68,17 +65,16 @@ ComputeForceTally::~ComputeForceTally() void ComputeForceTally::init() { if (force->pair == nullptr) - error->all(FLERR,"Trying to use compute force/tally without pair style"); + error->all(FLERR, "Trying to use compute force/tally without pair style"); else force->pair->add_tally_callback(this); if (comm->me == 0) { if (force->pair->single_enable == 0 || force->pair->manybody_flag) - error->warning(FLERR,"Compute force/tally used with incompatible pair style"); + error->warning(FLERR, "Compute force/tally used with incompatible pair style"); - if (force->bond || force->angle || force->dihedral - || force->improper || force->kspace) - error->warning(FLERR,"Compute force/tally only called from pair style"); + if (force->bond || force->angle || force->dihedral || force->improper || force->kspace) + error->warning(FLERR, "Compute force/tally only called from pair style"); } did_setup = -1; } @@ -99,51 +95,48 @@ void ComputeForceTally::pair_setup_callback(int, int) if (atom->nmax > nmax) { memory->destroy(fatom); nmax = atom->nmax; - memory->create(fatom,nmax,size_peratom_cols,"force/tally:fatom"); + memory->create(fatom, nmax, size_peratom_cols, "force/tally:fatom"); array_atom = fatom; } // clear storage - for (int i=0; i < ntotal; ++i) - for (int j=0; j < size_peratom_cols; ++j) - fatom[i][j] = 0.0; + for (int i = 0; i < ntotal; ++i) + for (int j = 0; j < size_peratom_cols; ++j) fatom[i][j] = 0.0; - for (int i=0; i < size_peratom_cols; ++i) - vector[i] = ftotal[i] = 0.0; + for (int i = 0; i < size_peratom_cols; ++i) vector[i] = ftotal[i] = 0.0; did_setup = update->ntimestep; } /* ---------------------------------------------------------------------- */ -void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton, - double, double, double fpair, - double dx, double dy, double dz) +void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton, double, double, + double fpair, double dx, double dy, double dz) { - const int * const mask = atom->mask; + const int *const mask = atom->mask; - if ( ((mask[i] & groupbit) && (mask[j] & groupbit2)) - || ((mask[i] & groupbit2) && (mask[j] & groupbit))) { + if (((mask[i] & groupbit) && (mask[j] & groupbit2)) || + ((mask[i] & groupbit2) && (mask[j] & groupbit))) { if (newton || i < nlocal) { if (mask[i] & groupbit) { - ftotal[0] += fpair*dx; - ftotal[1] += fpair*dy; - ftotal[2] += fpair*dz; + ftotal[0] += fpair * dx; + ftotal[1] += fpair * dy; + ftotal[2] += fpair * dz; } - fatom[i][0] += fpair*dx; - fatom[i][1] += fpair*dy; - fatom[i][2] += fpair*dz; + fatom[i][0] += fpair * dx; + fatom[i][1] += fpair * dy; + fatom[i][2] += fpair * dz; } if (newton || j < nlocal) { if (mask[j] & groupbit) { - ftotal[0] -= fpair*dx; - ftotal[1] -= fpair*dy; - ftotal[2] -= fpair*dz; + ftotal[0] -= fpair * dx; + ftotal[1] -= fpair * dy; + ftotal[2] -= fpair * dz; } - fatom[j][0] -= fpair*dx; - fatom[j][1] -= fpair*dy; - fatom[j][2] -= fpair*dz; + fatom[j][0] -= fpair * dx; + fatom[j][1] -= fpair * dy; + fatom[j][2] -= fpair * dz; } } } @@ -152,7 +145,7 @@ void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton int ComputeForceTally::pack_reverse_comm(int n, int first, double *buf) { - int i,m,last; + int i, m, last; m = 0; last = first + n; @@ -168,7 +161,7 @@ int ComputeForceTally::pack_reverse_comm(int n, int first, double *buf) void ComputeForceTally::unpack_reverse_comm(int n, int *list, double *buf) { - int i,j,m; + int i, j, m; m = 0; for (i = 0; i < n; i++) { @@ -184,15 +177,14 @@ void ComputeForceTally::unpack_reverse_comm(int n, int *list, double *buf) double ComputeForceTally::compute_scalar() { invoked_scalar = update->ntimestep; - if ((did_setup != invoked_scalar) - || (update->eflag_global != invoked_scalar)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) + error->all(FLERR, "Energy was not tallied on needed timestep"); // sum accumulated forces across procs - MPI_Allreduce(ftotal,vector,size_peratom_cols,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(ftotal, vector, size_peratom_cols, MPI_DOUBLE, MPI_SUM, world); - scalar = sqrt(vector[0]*vector[0]+vector[1]*vector[1]+vector[2]*vector[2]); + scalar = sqrt(vector[0] * vector[0] + vector[1] * vector[1] + vector[2] * vector[2]); return scalar; } @@ -201,9 +193,8 @@ double ComputeForceTally::compute_scalar() void ComputeForceTally::compute_peratom() { invoked_peratom = update->ntimestep; - if ((did_setup != invoked_peratom) - || (update->eflag_global != invoked_peratom)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) + error->all(FLERR, "Energy was not tallied on needed timestep"); // collect contributions from ghost atoms @@ -213,8 +204,7 @@ void ComputeForceTally::compute_peratom() // clear out ghost atom data after it has been collected to local atoms const int nall = atom->nlocal + atom->nghost; for (int i = atom->nlocal; i < nall; ++i) - for (int j = 0; j < size_peratom_cols; ++j) - fatom[i][j] = 0.0; + for (int j = 0; j < size_peratom_cols; ++j) fatom[i][j] = 0.0; } } @@ -224,7 +214,6 @@ void ComputeForceTally::compute_peratom() double ComputeForceTally::memory_usage() { - double bytes = (nmax < 0) ? 0 : nmax*size_peratom_cols * sizeof(double); + double bytes = (nmax < 0) ? 0 : nmax * (double)size_peratom_cols * sizeof(double); return bytes; } - diff --git a/src/USER-TALLY/compute_force_tally.h b/src/TALLY/compute_force_tally.h similarity index 100% rename from src/USER-TALLY/compute_force_tally.h rename to src/TALLY/compute_force_tally.h diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/TALLY/compute_heat_flux_tally.cpp similarity index 72% rename from src/USER-TALLY/compute_heat_flux_tally.cpp rename to src/TALLY/compute_heat_flux_tally.cpp index 96456bf775..7bff99eeb7 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/TALLY/compute_heat_flux_tally.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,26 +14,25 @@ #include "compute_heat_flux_tally.h" #include "atom.h" -#include "group.h" -#include "pair.h" -#include "update.h" -#include "memory.h" +#include "comm.h" #include "error.h" #include "force.h" -#include "comm.h" +#include "group.h" +#include "memory.h" +#include "pair.h" +#include "update.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg) { - if (narg < 4) error->all(FLERR,"Illegal compute heat/flux/tally command"); + if (narg < 4) error->all(FLERR, "Illegal compute heat/flux/tally command"); igroup2 = group->find(arg[3]); - if (igroup2 == -1) - error->all(FLERR,"Could not find compute heat/flux/tally second group ID"); + if (igroup2 == -1) error->all(FLERR, "Could not find compute heat/flux/tally second group ID"); groupbit2 = group->bitmask[igroup2]; vector_flag = 1; @@ -44,7 +42,7 @@ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) : comm_reverse = 7; extvector = 1; size_vector = 6; - peflag = 1; // we need Pair::ev_tally() to be run + peflag = 1; // we need Pair::ev_tally() to be run did_setup = 0; invoked_peratom = invoked_scalar = -1; @@ -71,17 +69,16 @@ ComputeHeatFluxTally::~ComputeHeatFluxTally() void ComputeHeatFluxTally::init() { if (force->pair == nullptr) - error->all(FLERR,"Trying to use compute heat/flux/tally without pair style"); + error->all(FLERR, "Trying to use compute heat/flux/tally without pair style"); else force->pair->add_tally_callback(this); if (comm->me == 0) { if (force->pair->single_enable == 0 || force->pair->manybody_flag) - error->warning(FLERR,"Compute heat/flux/tally used with incompatible pair style"); + error->warning(FLERR, "Compute heat/flux/tally used with incompatible pair style"); - if (force->bond || force->angle || force->dihedral - || force->improper || force->kspace) - error->warning(FLERR,"Compute heat/flux/tally only called from pair style"); + if (force->bond || force->angle || force->dihedral || force->improper || force->kspace) + error->warning(FLERR, "Compute heat/flux/tally only called from pair style"); } did_setup = -1; } @@ -102,13 +99,13 @@ void ComputeHeatFluxTally::pair_setup_callback(int, int) memory->destroy(stress); memory->destroy(eatom); nmax = atom->nmax; - memory->create(stress,nmax,6,"heat/flux/tally:stress"); - memory->create(eatom,nmax,"heat/flux/tally:eatom"); + memory->create(stress, nmax, 6, "heat/flux/tally:stress"); + memory->create(eatom, nmax, "heat/flux/tally:eatom"); } // clear storage - for (int i=0; i < ntotal; ++i) { + for (int i = 0; i < ntotal; ++i) { eatom[i] = 0.0; stress[i][0] = 0.0; stress[i][1] = 0.0; @@ -118,30 +115,29 @@ void ComputeHeatFluxTally::pair_setup_callback(int, int) stress[i][5] = 0.0; } - for (int i=0; i < size_vector; ++i) - vector[i] = heatj[i] = 0.0; + for (int i = 0; i < size_vector; ++i) vector[i] = heatj[i] = 0.0; did_setup = update->ntimestep; } /* ---------------------------------------------------------------------- */ -void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int newton, - double evdwl, double ecoul, double fpair, - double dx, double dy, double dz) +void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int newton, double evdwl, + double ecoul, double fpair, double dx, double dy, + double dz) { - const int * const mask = atom->mask; + const int *const mask = atom->mask; - if ( ((mask[i] & groupbit) && (mask[j] & groupbit2)) - || ((mask[i] & groupbit2) && (mask[j] & groupbit))) { + if (((mask[i] & groupbit) && (mask[j] & groupbit2)) || + ((mask[i] & groupbit2) && (mask[j] & groupbit))) { const double epairhalf = 0.5 * (evdwl + ecoul); fpair *= 0.5; - const double v0 = dx*dx*fpair; // dx*fpair = Fij_x - const double v1 = dy*dy*fpair; - const double v2 = dz*dz*fpair; - const double v3 = dx*dy*fpair; - const double v4 = dx*dz*fpair; - const double v5 = dy*dz*fpair; + const double v0 = dx * dx * fpair; // dx*fpair = Fij_x + const double v1 = dy * dy * fpair; + const double v2 = dz * dz * fpair; + const double v3 = dx * dy * fpair; + const double v4 = dx * dz * fpair; + const double v5 = dy * dz * fpair; if (newton || i < nlocal) { eatom[i] += epairhalf; @@ -168,7 +164,7 @@ void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int new int ComputeHeatFluxTally::pack_reverse_comm(int n, int first, double *buf) { - int i,m,last; + int i, m, last; m = 0; last = first + n; @@ -188,7 +184,7 @@ int ComputeHeatFluxTally::pack_reverse_comm(int n, int first, double *buf) void ComputeHeatFluxTally::unpack_reverse_comm(int n, int *list, double *buf) { - int i,j,m; + int i, j, m; m = 0; for (i = 0; i < n; i++) { @@ -209,7 +205,7 @@ void ComputeHeatFluxTally::compute_vector() { invoked_vector = update->ntimestep; if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + error->all(FLERR, "Energy was not tallied on needed timestep"); // collect contributions from ghost atoms @@ -244,26 +240,28 @@ void ComputeHeatFluxTally::compute_vector() double *rmass = atom->rmass; int *type = atom->type; - double jc[3] = {0.0,0.0,0.0}; - double jv[3] = {0.0,0.0,0.0}; + double jc[3] = {0.0, 0.0, 0.0}; + double jv[3] = {0.0, 0.0, 0.0}; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { - const double * const vi = v[i]; - const double * const si = stress[i]; + const double *const vi = v[i]; + const double *const si = stress[i]; double ke_i; - if (rmass) ke_i = pfactor * rmass[i]; - else ke_i = pfactor * mass[type[i]]; - ke_i *= (vi[0]*vi[0] + vi[1]*vi[1] + vi[2]*vi[2]); + if (rmass) + ke_i = pfactor * rmass[i]; + else + ke_i = pfactor * mass[type[i]]; + ke_i *= (vi[0] * vi[0] + vi[1] * vi[1] + vi[2] * vi[2]); ke_i += eatom[i]; - jc[0] += ke_i*vi[0]; - jc[1] += ke_i*vi[1]; - jc[2] += ke_i*vi[2]; - jv[0] += si[0]*vi[0] + si[3]*vi[1] + si[4]*vi[2]; - jv[1] += si[3]*vi[0] + si[1]*vi[1] + si[5]*vi[2]; - jv[2] += si[4]*vi[0] + si[5]*vi[1] + si[2]*vi[2]; + jc[0] += ke_i * vi[0]; + jc[1] += ke_i * vi[1]; + jc[2] += ke_i * vi[2]; + jv[0] += si[0] * vi[0] + si[3] * vi[1] + si[4] * vi[2]; + jv[1] += si[3] * vi[0] + si[1] * vi[1] + si[5] * vi[2]; + jv[2] += si[4] * vi[0] + si[5] * vi[1] + si[2] * vi[2]; } } @@ -274,7 +272,7 @@ void ComputeHeatFluxTally::compute_vector() heatj[3] = jc[0]; heatj[4] = jc[1]; heatj[5] = jc[2]; - MPI_Allreduce(heatj,vector,size_vector,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(heatj, vector, size_vector, MPI_DOUBLE, MPI_SUM, world); } /* ---------------------------------------------------------------------- @@ -283,7 +281,6 @@ void ComputeHeatFluxTally::compute_vector() double ComputeHeatFluxTally::memory_usage() { - double bytes = (nmax < 0) ? 0 : nmax*comm_reverse * sizeof(double); + double bytes = (nmax < 0) ? 0 : nmax * (double)comm_reverse * sizeof(double); return bytes; } - diff --git a/src/USER-TALLY/compute_heat_flux_tally.h b/src/TALLY/compute_heat_flux_tally.h similarity index 100% rename from src/USER-TALLY/compute_heat_flux_tally.h rename to src/TALLY/compute_heat_flux_tally.h diff --git a/src/TALLY/compute_heat_flux_virial_tally.cpp b/src/TALLY/compute_heat_flux_virial_tally.cpp new file mode 100644 index 0000000000..8605b9c546 --- /dev/null +++ b/src/TALLY/compute_heat_flux_virial_tally.cpp @@ -0,0 +1,238 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_heat_flux_virial_tally.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "pair.h" +#include "update.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeHeatFluxVirialTally::ComputeHeatFluxVirialTally(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 4) error->all(FLERR, "Illegal compute heat/flux/virial/tally command"); + + igroup2 = group->find(arg[3]); + if (igroup2 == -1) + error->all(FLERR, "Could not find compute heat/flux/virial/tally second group ID"); + groupbit2 = group->bitmask[igroup2]; + + scalar_flag = 1; + vector_flag = 0; + peratom_flag = 1; + timeflag = 1; + dynamic_group_allow = 0; + + comm_reverse = size_peratom_cols = 3; + extscalar = 1; + peflag = 1; // we need Pair::ev_tally() to be run + + did_setup = invoked_peratom = invoked_scalar = -1; + nmax = -1; + fatom = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +ComputeHeatFluxVirialTally::~ComputeHeatFluxVirialTally() +{ + if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(fatom); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHeatFluxVirialTally::init() +{ + if (force->pair == nullptr) + error->all(FLERR, "Trying to use compute heat/flux/virial/tally without pair style"); + else + force->pair->add_tally_callback(this); + + if (comm->me == 0) { + if (force->pair->single_enable == 0 || force->pair->manybody_flag) + error->warning(FLERR, "Compute heat/flux/virial/tally used with incompatible pair style"); + + if (force->bond || force->angle || force->dihedral || force->improper || force->kspace) + error->warning(FLERR, "Compute heat/flux/virial/tally only called from pair style"); + } + + // error out if any atoms are in both groups + for (int i = 0; i < atom->nlocal; i++) { + if ((atom->mask[i] & groupbit) && (atom->mask[i] & groupbit2)) { + if (atom->tag_enable) { + error->all(FLERR, + "Atom {} belonging to both groups is not allowed" + " with compute heat/flux/virial/tally", + atom->tag[i]); + } else { + error->all(FLERR, + "Atom belonging to both groups is not allowed" + " with compute heat/flux/virial/tally"); + } + } + } + + did_setup = -1; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHeatFluxVirialTally::pair_setup_callback(int, int) +{ + // run setup only once per time step. + // we may be called from multiple pair styles + + if (did_setup == update->ntimestep) return; + + const int ntotal = atom->nlocal + atom->nghost; + + // grow per-atom storage, if needed + + if (atom->nmax > nmax) { + memory->destroy(fatom); + nmax = atom->nmax; + memory->create(fatom, nmax, size_peratom_cols, "heat/flux/virial/tally:fatom"); + array_atom = fatom; + } + + // clear storage + + for (int i = 0; i < ntotal; ++i) + for (int j = 0; j < size_peratom_cols; ++j) fatom[i][j] = 0.0; + + did_setup = update->ntimestep; +} + +/* ---------------------------------------------------------------------- */ +void ComputeHeatFluxVirialTally::pair_tally_callback(int i, int j, int nlocal, int newton, double, + double, double fpair, double dx, double dy, + double dz) +{ + const int *const mask = atom->mask; + + const bool ingroup1 = (mask[i] & groupbit); + if ((ingroup1 && (mask[j] & groupbit2)) || ((mask[i] & groupbit2) && (mask[j] & groupbit))) { + + // signs set to calculate heat flux from group2 into group1 + const double fx = (ingroup1 ? 0.5 : -0.5) * dx * fpair; + const double fy = (ingroup1 ? 0.5 : -0.5) * dy * fpair; + const double fz = (ingroup1 ? 0.5 : -0.5) * dz * fpair; + + if (newton || i < nlocal) { + fatom[i][0] += fx; + fatom[i][1] += fy; + fatom[i][2] += fz; + } + if (newton || j < nlocal) { + fatom[j][0] += fx; + fatom[j][1] += fy; + fatom[j][2] += fz; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int ComputeHeatFluxVirialTally::pack_reverse_comm(int n, int first, double *buf) +{ + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = fatom[i][0]; + buf[m++] = fatom[i][1]; + buf[m++] = fatom[i][2]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHeatFluxVirialTally::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + fatom[j][0] += buf[m++]; + fatom[j][1] += buf[m++]; + fatom[j][2] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +double ComputeHeatFluxVirialTally::compute_scalar() +{ + // need to collect contributions from ghost atoms + // because we need to use local velocities to compute heat flux + if (invoked_peratom != update->ntimestep) compute_peratom(); + + invoked_scalar = update->ntimestep; + if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) + error->all(FLERR, "Energy was not tallied on needed timestep"); + + // sum heat flux across procs + double hflux = 0.0; + for (int i = 0; i < atom->nlocal; i++) + hflux += + fatom[i][0] * atom->v[i][0] + fatom[i][1] * atom->v[i][1] + fatom[i][2] * atom->v[i][2]; + + MPI_Allreduce(&hflux, &scalar, 1, MPI_DOUBLE, MPI_SUM, world); + + return scalar; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHeatFluxVirialTally::compute_peratom() +{ + invoked_peratom = update->ntimestep; + if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) + error->all(FLERR, "Energy was not tallied on needed timestep"); + + // collect contributions from ghost atoms + + if (force->newton_pair) { + comm->reverse_comm_compute(this); + + // clear out ghost atom data after it has been collected to local atoms + const int nall = atom->nlocal + atom->nghost; + for (int i = atom->nlocal; i < nall; ++i) + for (int j = 0; j < size_peratom_cols; ++j) fatom[i][j] = 0.0; + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeHeatFluxVirialTally::memory_usage() +{ + double bytes = (nmax < 0) ? 0 : nmax * (double)size_peratom_cols * sizeof(double); + return bytes; +} diff --git a/src/TALLY/compute_heat_flux_virial_tally.h b/src/TALLY/compute_heat_flux_virial_tally.h new file mode 100644 index 0000000000..d2a3d39a7d --- /dev/null +++ b/src/TALLY/compute_heat_flux_virial_tally.h @@ -0,0 +1,64 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(heat/flux/virial/tally,ComputeHeatFluxVirialTally); +// clang-format on +#else + +#ifndef LMP_COMPUTE_HEAT_FLUX_VIRIAL_TALLY_H +#define LMP_COMPUTE_HEAT_FLUX_VIRIAL_TALLY_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeHeatFluxVirialTally : public Compute { + + public: + ComputeHeatFluxVirialTally(class LAMMPS *, int, char **); + virtual ~ComputeHeatFluxVirialTally(); + + void init(); + + double compute_scalar(); + void compute_peratom(); + + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + double memory_usage(); + + void pair_setup_callback(int, int); + void pair_tally_callback(int, int, int, int, double, double, double, double, double, double); + + private: + bigint did_setup; + int nmax, igroup2, groupbit2; + double **fatom; +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/TALLY/compute_pe_mol_tally.cpp similarity index 64% rename from src/USER-TALLY/compute_pe_mol_tally.cpp rename to src/TALLY/compute_pe_mol_tally.cpp index 329c9ff429..fc3efb272b 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/TALLY/compute_pe_mol_tally.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,25 +14,23 @@ #include "compute_pe_mol_tally.h" #include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" #include "group.h" #include "pair.h" #include "update.h" -#include "error.h" -#include "force.h" -#include "comm.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) +ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg < 4) error->all(FLERR,"Illegal compute pe/mol/tally command"); + if (narg < 4) error->all(FLERR, "Illegal compute pe/mol/tally command"); igroup2 = group->find(arg[3]); - if (igroup2 == -1) - error->all(FLERR,"Could not find compute pe/mol/tally second group ID"); + if (igroup2 == -1) error->all(FLERR, "Could not find compute pe/mol/tally second group ID"); groupbit2 = group->bitmask[igroup2]; vector_flag = 1; @@ -42,7 +39,7 @@ ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) : dynamic_group_allow = 0; extvector = 1; - peflag = 1; // we need Pair::ev_tally() to be run + peflag = 1; // we need Pair::ev_tally() to be run did_setup = invoked_vector = -1; vector = new double[size_vector]; @@ -61,20 +58,18 @@ ComputePEMolTally::~ComputePEMolTally() void ComputePEMolTally::init() { if (force->pair == nullptr) - error->all(FLERR,"Trying to use compute pe/mol/tally without pair style"); + error->all(FLERR, "Trying to use compute pe/mol/tally without pair style"); else force->pair->add_tally_callback(this); - if (atom->molecule_flag == 0) - error->all(FLERR,"Compute pe/mol/tally requires molecule IDs"); + if (atom->molecule_flag == 0) error->all(FLERR, "Compute pe/mol/tally requires molecule IDs"); if (comm->me == 0) { if (force->pair->single_enable == 0 || force->pair->manybody_flag) - error->warning(FLERR,"Compute pe/mol/tally used with incompatible pair style"); + error->warning(FLERR, "Compute pe/mol/tally used with incompatible pair style"); - if (force->bond || force->angle || force->dihedral - || force->improper || force->kspace) - error->warning(FLERR,"Compute pe/mol/tally only called from pair style"); + if (force->bond || force->angle || force->dihedral || force->improper || force->kspace) + error->warning(FLERR, "Compute pe/mol/tally only called from pair style"); } did_setup = -1; } @@ -93,29 +88,33 @@ void ComputePEMolTally::pair_setup_callback(int, int) } /* ---------------------------------------------------------------------- */ -void ComputePEMolTally::pair_tally_callback(int i, int j, int nlocal, int newton, - double evdwl, double ecoul, double, - double, double, double) +void ComputePEMolTally::pair_tally_callback(int i, int j, int nlocal, int newton, double evdwl, + double ecoul, double, double, double, double) { - const int * const mask = atom->mask; - const tagint * const molid = atom->molecule; + const int *const mask = atom->mask; + const tagint *const molid = atom->molecule; - if ( ((mask[i] & groupbit) && (mask[j] & groupbit2)) - || ((mask[i] & groupbit2) && (mask[j] & groupbit))) { + if (((mask[i] & groupbit) && (mask[j] & groupbit2)) || + ((mask[i] & groupbit2) && (mask[j] & groupbit))) { - evdwl *= 0.5; ecoul *= 0.5; + evdwl *= 0.5; + ecoul *= 0.5; if (newton || i < nlocal) { if (molid[i] == molid[j]) { - etotal[0] += evdwl; etotal[1] += ecoul; + etotal[0] += evdwl; + etotal[1] += ecoul; } else { - etotal[2] += evdwl; etotal[3] += ecoul; + etotal[2] += evdwl; + etotal[3] += ecoul; } } if (newton || j < nlocal) { if (molid[i] == molid[j]) { - etotal[0] += evdwl; etotal[1] += ecoul; + etotal[0] += evdwl; + etotal[1] += ecoul; } else { - etotal[2] += evdwl; etotal[3] += ecoul; + etotal[2] += evdwl; + etotal[3] += ecoul; } } } @@ -127,10 +126,9 @@ void ComputePEMolTally::compute_vector() { invoked_vector = update->ntimestep; if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + error->all(FLERR, "Energy was not tallied on needed timestep"); // sum accumulated energies across procs - MPI_Allreduce(etotal,vector,size_vector,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(etotal, vector, size_vector, MPI_DOUBLE, MPI_SUM, world); } - diff --git a/src/USER-TALLY/compute_pe_mol_tally.h b/src/TALLY/compute_pe_mol_tally.h similarity index 100% rename from src/USER-TALLY/compute_pe_mol_tally.h rename to src/TALLY/compute_pe_mol_tally.h diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/TALLY/compute_pe_tally.cpp similarity index 68% rename from src/USER-TALLY/compute_pe_tally.cpp rename to src/TALLY/compute_pe_tally.cpp index dae233f830..07cb500e44 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/TALLY/compute_pe_tally.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,26 +14,24 @@ #include "compute_pe_tally.h" #include "atom.h" -#include "group.h" -#include "pair.h" -#include "update.h" -#include "memory.h" +#include "comm.h" #include "error.h" #include "force.h" -#include "comm.h" +#include "group.h" +#include "memory.h" +#include "pair.h" +#include "update.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) +ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg < 4) error->all(FLERR,"Illegal compute pe/tally command"); + if (narg < 4) error->all(FLERR, "Illegal compute pe/tally command"); igroup2 = group->find(arg[3]); - if (igroup2 == -1) - error->all(FLERR,"Could not find compute pe/tally second group ID"); + if (igroup2 == -1) error->all(FLERR, "Could not find compute pe/tally second group ID"); groupbit2 = group->bitmask[igroup2]; scalar_flag = 1; @@ -45,7 +42,7 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : comm_reverse = size_peratom_cols = 2; extscalar = 1; - peflag = 1; // we need Pair::ev_tally() to be run + peflag = 1; // we need Pair::ev_tally() to be run did_setup = invoked_peratom = invoked_scalar = -1; nmax = -1; @@ -67,17 +64,16 @@ ComputePETally::~ComputePETally() void ComputePETally::init() { if (force->pair == nullptr) - error->all(FLERR,"Trying to use compute pe/tally without a pair style"); + error->all(FLERR, "Trying to use compute pe/tally without a pair style"); else force->pair->add_tally_callback(this); if (comm->me == 0) { if (force->pair->single_enable == 0 || force->pair->manybody_flag) - error->warning(FLERR,"Compute pe/tally used with incompatible pair style"); + error->warning(FLERR, "Compute pe/tally used with incompatible pair style"); - if (force->bond || force->angle || force->dihedral - || force->improper || force->kspace) - error->warning(FLERR,"Compute pe/tally only called from pair style"); + if (force->bond || force->angle || force->dihedral || force->improper || force->kspace) + error->warning(FLERR, "Compute pe/tally only called from pair style"); } did_setup = -1; } @@ -98,14 +94,13 @@ void ComputePETally::pair_setup_callback(int, int) if (atom->nmax > nmax) { memory->destroy(eatom); nmax = atom->nmax; - memory->create(eatom,nmax,size_peratom_cols,"pe/tally:eatom"); + memory->create(eatom, nmax, size_peratom_cols, "pe/tally:eatom"); array_atom = eatom; } // clear storage - for (int i=0; i < ntotal; ++i) - eatom[i][0] = eatom[i][1] = 0.0; + for (int i = 0; i < ntotal; ++i) eatom[i][0] = eatom[i][1] = 0.0; vector[0] = etotal[0] = vector[1] = etotal[1] = 0.0; @@ -113,23 +108,27 @@ void ComputePETally::pair_setup_callback(int, int) } /* ---------------------------------------------------------------------- */ -void ComputePETally::pair_tally_callback(int i, int j, int nlocal, int newton, - double evdwl, double ecoul, double, - double, double, double) +void ComputePETally::pair_tally_callback(int i, int j, int nlocal, int newton, double evdwl, + double ecoul, double, double, double, double) { - const int * const mask = atom->mask; + const int *const mask = atom->mask; - if ( ((mask[i] & groupbit) && (mask[j] & groupbit2)) - || ((mask[i] & groupbit2) && (mask[j] & groupbit))) { + if (((mask[i] & groupbit) && (mask[j] & groupbit2)) || + ((mask[i] & groupbit2) && (mask[j] & groupbit))) { - evdwl *= 0.5; ecoul *= 0.5; + evdwl *= 0.5; + ecoul *= 0.5; if (newton || i < nlocal) { - etotal[0] += evdwl; eatom[i][0] += evdwl; - etotal[1] += ecoul; eatom[i][1] += ecoul; + etotal[0] += evdwl; + eatom[i][0] += evdwl; + etotal[1] += ecoul; + eatom[i][1] += ecoul; } if (newton || j < nlocal) { - etotal[0] += evdwl; eatom[j][0] += evdwl; - etotal[1] += ecoul; eatom[j][1] += ecoul; + etotal[0] += evdwl; + eatom[j][0] += evdwl; + etotal[1] += ecoul; + eatom[j][1] += ecoul; } } } @@ -138,7 +137,7 @@ void ComputePETally::pair_tally_callback(int i, int j, int nlocal, int newton, int ComputePETally::pack_reverse_comm(int n, int first, double *buf) { - int i,m,last; + int i, m, last; m = 0; last = first + n; @@ -153,7 +152,7 @@ int ComputePETally::pack_reverse_comm(int n, int first, double *buf) void ComputePETally::unpack_reverse_comm(int n, int *list, double *buf) { - int i,j,m; + int i, j, m; m = 0; for (i = 0; i < n; i++) { @@ -168,15 +167,14 @@ void ComputePETally::unpack_reverse_comm(int n, int *list, double *buf) double ComputePETally::compute_scalar() { invoked_scalar = update->ntimestep; - if ((did_setup != invoked_scalar) - || (update->eflag_global != invoked_scalar)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) + error->all(FLERR, "Energy was not tallied on needed timestep"); // sum accumulated energies across procs - MPI_Allreduce(etotal,vector,size_peratom_cols,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(etotal, vector, size_peratom_cols, MPI_DOUBLE, MPI_SUM, world); - scalar = vector[0]+vector[1]; + scalar = vector[0] + vector[1]; return scalar; } @@ -185,9 +183,8 @@ double ComputePETally::compute_scalar() void ComputePETally::compute_peratom() { invoked_peratom = update->ntimestep; - if ((did_setup != invoked_peratom) - || (update->eflag_global != invoked_peratom)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) + error->all(FLERR, "Energy was not tallied on needed timestep"); // collect contributions from ghost atoms @@ -196,8 +193,7 @@ void ComputePETally::compute_peratom() // clear out ghost atom data after it has been collected to local atoms const int nall = atom->nlocal + atom->nghost; - for (int i = atom->nlocal; i < nall; ++i) - eatom[i][0] = eatom[i][1] = 0.0; + for (int i = atom->nlocal; i < nall; ++i) eatom[i][0] = eatom[i][1] = 0.0; } } @@ -207,7 +203,6 @@ void ComputePETally::compute_peratom() double ComputePETally::memory_usage() { - double bytes = (nmax < 0) ? 0 : nmax*size_peratom_cols * sizeof(double); + double bytes = (nmax < 0) ? 0 : nmax * (double)size_peratom_cols * sizeof(double); return bytes; } - diff --git a/src/USER-TALLY/compute_pe_tally.h b/src/TALLY/compute_pe_tally.h similarity index 100% rename from src/USER-TALLY/compute_pe_tally.h rename to src/TALLY/compute_pe_tally.h diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/TALLY/compute_stress_tally.cpp similarity index 64% rename from src/USER-TALLY/compute_stress_tally.cpp rename to src/TALLY/compute_stress_tally.cpp index 8ae42ddf02..dea65ade26 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/TALLY/compute_stress_tally.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,27 +14,25 @@ #include "compute_stress_tally.h" #include "atom.h" -#include "group.h" -#include "pair.h" -#include "update.h" -#include "memory.h" -#include "error.h" -#include "force.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "pair.h" +#include "update.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) +ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg < 4) error->all(FLERR,"Illegal compute stress/tally command"); + if (narg < 4) error->all(FLERR, "Illegal compute stress/tally command"); igroup2 = group->find(arg[3]); - if (igroup2 == -1) - error->all(FLERR,"Could not find compute stress/tally second group ID"); + if (igroup2 == -1) error->all(FLERR, "Could not find compute stress/tally second group ID"); groupbit2 = group->bitmask[igroup2]; scalar_flag = 1; @@ -46,7 +43,7 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : comm_reverse = size_peratom_cols = 6; extscalar = 0; - peflag = 1; // we need Pair::ev_tally() to be run + peflag = 1; // we need Pair::ev_tally() to be run did_setup = invoked_peratom = invoked_scalar = -1; nmax = -1; @@ -70,17 +67,16 @@ ComputeStressTally::~ComputeStressTally() void ComputeStressTally::init() { if (force->pair == nullptr) - error->all(FLERR,"Trying to use compute stress/tally without pair style"); + error->all(FLERR, "Trying to use compute stress/tally without pair style"); else force->pair->add_tally_callback(this); if (comm->me == 0) { if (force->pair->single_enable == 0 || force->pair->manybody_flag) - error->warning(FLERR,"Compute stress/tally used with incompatible pair style"); + error->warning(FLERR, "Compute stress/tally used with incompatible pair style"); - if (force->bond || force->angle || force->dihedral - || force->improper || force->kspace) - error->warning(FLERR,"Compute stress/tally only called from pair style"); + if (force->bond || force->angle || force->dihedral || force->improper || force->kspace) + error->warning(FLERR, "Compute stress/tally only called from pair style"); } did_setup = -1; } @@ -101,55 +97,64 @@ void ComputeStressTally::pair_setup_callback(int, int) if (atom->nmax > nmax) { memory->destroy(stress); nmax = atom->nmax; - memory->create(stress,nmax,size_peratom_cols,"stress/tally:stress"); + memory->create(stress, nmax, size_peratom_cols, "stress/tally:stress"); array_atom = stress; } // clear storage - for (int i=0; i < ntotal; ++i) - for (int j=0; j < size_peratom_cols; ++j) - stress[i][j] = 0.0; + for (int i = 0; i < ntotal; ++i) + for (int j = 0; j < size_peratom_cols; ++j) stress[i][j] = 0.0; - for (int i=0; i < size_peratom_cols; ++i) - vector[i] = virial[i] = 0.0; + for (int i = 0; i < size_peratom_cols; ++i) vector[i] = virial[i] = 0.0; did_setup = update->ntimestep; } /* ---------------------------------------------------------------------- */ -void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newton, - double, double, double fpair, - double dx, double dy, double dz) +void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newton, double, double, + double fpair, double dx, double dy, double dz) { - const int * const mask = atom->mask; + const int *const mask = atom->mask; - if ( ((mask[i] & groupbit) && (mask[j] & groupbit2)) - || ((mask[i] & groupbit2) && (mask[j] & groupbit))) { + if (((mask[i] & groupbit) && (mask[j] & groupbit2)) || + ((mask[i] & groupbit2) && (mask[j] & groupbit))) { fpair *= 0.5; - const double v0 = dx*dx*fpair; - const double v1 = dy*dy*fpair; - const double v2 = dz*dz*fpair; - const double v3 = dx*dy*fpair; - const double v4 = dx*dz*fpair; - const double v5 = dy*dz*fpair; + const double v0 = dx * dx * fpair; + const double v1 = dy * dy * fpair; + const double v2 = dz * dz * fpair; + const double v3 = dx * dy * fpair; + const double v4 = dx * dz * fpair; + const double v5 = dy * dz * fpair; if (newton || i < nlocal) { - virial[0] += v0; stress[i][0] += v0; - virial[1] += v1; stress[i][1] += v1; - virial[2] += v2; stress[i][2] += v2; - virial[3] += v3; stress[i][3] += v3; - virial[4] += v4; stress[i][4] += v4; - virial[5] += v5; stress[i][5] += v5; + virial[0] += v0; + stress[i][0] += v0; + virial[1] += v1; + stress[i][1] += v1; + virial[2] += v2; + stress[i][2] += v2; + virial[3] += v3; + stress[i][3] += v3; + virial[4] += v4; + stress[i][4] += v4; + virial[5] += v5; + stress[i][5] += v5; } if (newton || j < nlocal) { - virial[0] += v0; stress[j][0] += v0; - virial[1] += v1; stress[j][1] += v1; - virial[2] += v2; stress[j][2] += v2; - virial[3] += v3; stress[j][3] += v3; - virial[4] += v4; stress[j][4] += v4; - virial[5] += v5; stress[j][5] += v5; + virial[0] += v0; + stress[j][0] += v0; + virial[1] += v1; + stress[j][1] += v1; + virial[2] += v2; + stress[j][2] += v2; + virial[3] += v3; + stress[j][3] += v3; + virial[4] += v4; + stress[j][4] += v4; + virial[5] += v5; + stress[j][5] += v5; } } } @@ -158,7 +163,7 @@ void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newto int ComputeStressTally::pack_reverse_comm(int n, int first, double *buf) { - int i,m,last; + int i, m, last; m = 0; last = first + n; @@ -177,7 +182,7 @@ int ComputeStressTally::pack_reverse_comm(int n, int first, double *buf) void ComputeStressTally::unpack_reverse_comm(int n, int *list, double *buf) { - int i,j,m; + int i, j, m; m = 0; for (i = 0; i < n; i++) { @@ -196,18 +201,17 @@ void ComputeStressTally::unpack_reverse_comm(int n, int *list, double *buf) double ComputeStressTally::compute_scalar() { invoked_scalar = update->ntimestep; - if ((did_setup != invoked_scalar) - || (update->eflag_global != invoked_scalar)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) + error->all(FLERR, "Energy was not tallied on needed timestep"); // sum accumulated forces across procs - MPI_Allreduce(virial,vector,size_peratom_cols,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(virial, vector, size_peratom_cols, MPI_DOUBLE, MPI_SUM, world); if (domain->dimension == 3) - scalar = (vector[0]+vector[1]+vector[2])/3.0; + scalar = (vector[0] + vector[1] + vector[2]) / 3.0; else - scalar = (vector[0]+vector[1])/2.0; + scalar = (vector[0] + vector[1]) / 2.0; return scalar; } @@ -217,9 +221,8 @@ double ComputeStressTally::compute_scalar() void ComputeStressTally::compute_peratom() { invoked_peratom = update->ntimestep; - if ((did_setup != invoked_peratom) - || (update->eflag_global != invoked_peratom)) - error->all(FLERR,"Energy was not tallied on needed timestep"); + if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) + error->all(FLERR, "Energy was not tallied on needed timestep"); // collect contributions from ghost atoms @@ -228,8 +231,7 @@ void ComputeStressTally::compute_peratom() const int nall = atom->nlocal + atom->nghost; for (int i = atom->nlocal; i < nall; ++i) - for (int j = 0; j < size_peratom_cols; ++j) - stress[i][j] = 0.0; + for (int j = 0; j < size_peratom_cols; ++j) stress[i][j] = 0.0; } // convert to stress*volume units = -pressure*volume @@ -251,7 +253,6 @@ void ComputeStressTally::compute_peratom() double ComputeStressTally::memory_usage() { - double bytes = (nmax < 0) ? 0 : nmax*size_peratom_cols * sizeof(double); + double bytes = (nmax < 0) ? 0 : nmax * (double)size_peratom_cols * sizeof(double); return bytes; } - diff --git a/src/USER-TALLY/compute_stress_tally.h b/src/TALLY/compute_stress_tally.h similarity index 100% rename from src/USER-TALLY/compute_stress_tally.h rename to src/TALLY/compute_stress_tally.h diff --git a/src/USER-UEF/README b/src/UEF/README similarity index 95% rename from src/USER-UEF/README rename to src/UEF/README index 2f2b872d3b..b2cef5b69b 100644 --- a/src/USER-UEF/README +++ b/src/UEF/README @@ -1,4 +1,4 @@ -USER-UEF is a LAMMPS package for non-equilibrium molecular dynamics +UEF is a LAMMPS package for non-equilibrium molecular dynamics (NEMD) under diagonal flow fields, including uniaxial and biaxial flow. With this package, simulations under extensional flow may be carried out for an indefinite amount of time. It is an implementation diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/UEF/compute_pressure_uef.cpp similarity index 100% rename from src/USER-UEF/compute_pressure_uef.cpp rename to src/UEF/compute_pressure_uef.cpp diff --git a/src/USER-UEF/compute_pressure_uef.h b/src/UEF/compute_pressure_uef.h similarity index 100% rename from src/USER-UEF/compute_pressure_uef.h rename to src/UEF/compute_pressure_uef.h diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/UEF/compute_temp_uef.cpp similarity index 100% rename from src/USER-UEF/compute_temp_uef.cpp rename to src/UEF/compute_temp_uef.cpp diff --git a/src/USER-UEF/compute_temp_uef.h b/src/UEF/compute_temp_uef.h similarity index 100% rename from src/USER-UEF/compute_temp_uef.h rename to src/UEF/compute_temp_uef.h diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/UEF/dump_cfg_uef.cpp similarity index 100% rename from src/USER-UEF/dump_cfg_uef.cpp rename to src/UEF/dump_cfg_uef.cpp diff --git a/src/USER-UEF/dump_cfg_uef.h b/src/UEF/dump_cfg_uef.h similarity index 100% rename from src/USER-UEF/dump_cfg_uef.h rename to src/UEF/dump_cfg_uef.h diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/UEF/fix_nh_uef.cpp similarity index 99% rename from src/USER-UEF/fix_nh_uef.cpp rename to src/UEF/fix_nh_uef.cpp index 9563644ede..a88b389611 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/UEF/fix_nh_uef.cpp @@ -44,7 +44,7 @@ enum{ISO,ANISO,TRICLINIC}; // citation info static const char cite_user_uef_package[] = - "USER-UEF package:\n\n" + "UEF package:\n\n" "@Article{NicholsonRutledge16,\n" "author = {David A. Nicholson and Gregory C. Rutledge},\n" "title = {Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension},\n" diff --git a/src/USER-UEF/fix_nh_uef.h b/src/UEF/fix_nh_uef.h similarity index 100% rename from src/USER-UEF/fix_nh_uef.h rename to src/UEF/fix_nh_uef.h diff --git a/src/USER-UEF/fix_npt_uef.cpp b/src/UEF/fix_npt_uef.cpp similarity index 100% rename from src/USER-UEF/fix_npt_uef.cpp rename to src/UEF/fix_npt_uef.cpp diff --git a/src/USER-UEF/fix_npt_uef.h b/src/UEF/fix_npt_uef.h similarity index 100% rename from src/USER-UEF/fix_npt_uef.h rename to src/UEF/fix_npt_uef.h diff --git a/src/USER-UEF/fix_nvt_uef.cpp b/src/UEF/fix_nvt_uef.cpp similarity index 100% rename from src/USER-UEF/fix_nvt_uef.cpp rename to src/UEF/fix_nvt_uef.cpp diff --git a/src/USER-UEF/fix_nvt_uef.h b/src/UEF/fix_nvt_uef.h similarity index 100% rename from src/USER-UEF/fix_nvt_uef.h rename to src/UEF/fix_nvt_uef.h diff --git a/src/USER-UEF/uef_utils.cpp b/src/UEF/uef_utils.cpp similarity index 100% rename from src/USER-UEF/uef_utils.cpp rename to src/UEF/uef_utils.cpp diff --git a/src/USER-UEF/uef_utils.h b/src/UEF/uef_utils.h similarity index 100% rename from src/USER-UEF/uef_utils.h rename to src/UEF/uef_utils.h diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h deleted file mode 100644 index d9f2955233..0000000000 --- a/src/USER-COLVARS/colvarproxy_lammps_version.h +++ /dev/null @@ -1,3 +0,0 @@ -#ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2020-04-07" -#endif diff --git a/src/USER-MEAMC/README b/src/USER-MEAMC/README deleted file mode 100644 index dcb70d670c..0000000000 --- a/src/USER-MEAMC/README +++ /dev/null @@ -1,26 +0,0 @@ -This package implements the MEAM/C potential as a LAMMPS pair style. - -============================================================================== - -This package is a translation of the MEAM package to native C++. See -that package as well as the Fortran code distributed in lib/meam for -the original sources and information. - - -Translation by - Sebastian Hütter, sebastian.huetter@ovgu.de - Institute of Materials and Joining Technology - Otto-von-Guericke University Magdeburg, Germany - -The original Fortran implementation was created by - Greg Wagner (while at Sandia, now at Northwestern U). - -============================================================================== - -Use "make yes-user-meamc" to enable this package when building LAMMPS. - -In your LAMMPS input script, specify - pair_style meam/c -to enable the use of this implementation. All parameters, input files and -outputs are exactly identical to these used with pair_style meam. - diff --git a/src/USER-MISC/README b/src/USER-MISC/README deleted file mode 100644 index d6f859b359..0000000000 --- a/src/USER-MISC/README +++ /dev/null @@ -1,113 +0,0 @@ -The files in this package are a potpourri of (mostly) unrelated -features contributed to LAMMPS by users. Each feature is a single -pair of files (*.cpp and *.h). - -More information about each feature can be found by reading its doc -page in the LAMMPS doc directory. The doc page which lists all LAMMPS -input script commands is as follows: - -doc/Commands_all.html - -User-contributed features are listed at the bottom of the fix, -compute, pair, etc sections. - -The list of features and author of each is given below. - -You should contact the author directly if you have specific questions -about the feature or its coding. - ------------------------------------------------------------- - -angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 -angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 -angle_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -angle_style fourier/simple, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -angle_style gaussian, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 Nov 2020 -angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12 -angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 -bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 -bond_style gaussian, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 Nov 2020 -bond_style special, David Nicholson, davidanich at gmail.com, 31 Jan 2020 -compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 -compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 -compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 -compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 -compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019 -compute gyration/shape/chunk, Evangelos Voyiatzis, evoyiatzis at gmail.com, 22 October 2019 -compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019 -compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 -compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019 -compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 -compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 -compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 -compute viscosity/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 -compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16 -dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 -dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16 -dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 -dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 -fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 -fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 -fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 -fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 -fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 -fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 -fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 -fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 -fix grem, David Stelter, dstelter@bu.edu, 22 Nov 16 -fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009 -fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 -fix momentum/chunk, Jiang Xiao (Hong Kong Polytechnic University), polyu-xiao.jiang at connect.polyu.hk, 19 Aug 2020 -fix npt/cauchy, R. E. Miller (Carleton University), F. Pavia and S. Pattamatta, 12 Jan 2020 -fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310 -fix orient/eco Adrian A. Schratt and Volker Mohles (Ruhr-Uni Bochum), volker.mohles at rub.de, 6 Jun 2020 -fix pafi, Thomas Swinburne (CNRS), swinburne at cinam.univ-mrs.fr, 1st Sep 2020 -fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014 -fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017 -fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008 -fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013 -fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015 -fix wall/ees, Abdoreza Ershadinia, a.ershadinia at gmail.com, Jul 2017 -fix wall/reflect/stochastic, Quy-Dong To (U Gustave Eiffel), toquydong at gmail.com, Jan 2020 -fix wall/region/ees, Abdoreza Ershadinia, a.ershadinia at gmail.com, Jul 2017 -improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 -improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 -improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 -improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16 -pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19 -pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 -pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 -pair_style coul/slater/cut, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 February 2020 -pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 February 2020 -pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 -pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19 -pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19 -pair_style dpd/ext, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP, svobod.martin at gmail dot com, 23 Apr 21 -pair_style dpd/ext/tstat, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP , svobod.martin at gmail dot com, 23 Apr 21 -pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 -pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 -pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 -pair_style ilp/graphene/hbn, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 -pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), softquake at gmail dot com, 4 Jan 19 -pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 -pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style local/density, Tanmoy Sanyal (tanmoy dot 7989 at gmail.com) and M. Scott Shell (UCSB), and David Rosenberger (TU Darmstadt), 9 Sept 19 -pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 -pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17 -pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12 -pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12 -pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16 -pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14 -pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11 -pair_style momb, Kristen Fichthorn, Tonnam Balankura, Ya Zhou, fichthorn@psu.edu, 18 Mar 17 -pair_style wf_cut, Simon Ramirez-Hinestrosa, Xipeng Wang, sr802 at cam.ac.uk, 4 Nov 20 -temper/grem, David Stelter, dstelter@bu.edu, 22 Nov 16 -temper/npt, Amulya K. Pervaje, Cody K. Addington, amulyapervaje@gmail.com , 31 Aug 17 diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp deleted file mode 100644 index e6d5935d86..0000000000 --- a/src/USER-MISC/pair_e3b.cpp +++ /dev/null @@ -1,694 +0,0 @@ -// clang-format off -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. - - contributing authors: Steven E Strong and Nicholas J Hestand - contact: stevene.strong at gmail dot com -------------------------------------------------------------------------- */ - -#include "pair_e3b.h" - -#include -#include -#include - -#include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "update.h" -#include "domain.h" -#include "citeme.h" - -//these are defined here to avoid confusing hardcoded indices, but -//they do not allow flexibility. If they are changed the code will break -#define DIM 3 -#define NUMH 2 //number of hydrogen atoms per water molecule -#define NUMO 2 //number of oxygen atoms per pair of water molecules -#define BOND_DELTA 1.01 //buffer for OH bonds that aren't perfectly rigid - -using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -PairE3B::PairE3B(LAMMPS *lmp) : Pair(lmp),pairPerAtom(10) -{ - single_enable = 0; - restartinfo = 0; - one_coeff = 1; - nextra=4; //store and tally pot energy terms eA, eB, eC, and e2 - pvector = new double[nextra]; - - allocatedE3B = false; - pairO = nullptr; - pairH = nullptr; - exps = nullptr; - del3 = nullptr; - fpair3 = nullptr; - sumExp = nullptr; -} - -/* ---------------------------------------------------------------------- - check if allocated, since class can be destructed when incomplete -------------------------------------------------------------------------- */ - -PairE3B::~PairE3B() -{ - if (copymode) return; - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - } - if (allocatedE3B) { - memory->destroy(pairO); - memory->destroy(pairH); - memory->destroy(exps); - memory->destroy(del3); - memory->destroy(fpair3); - memory->destroy(sumExp); - } - - delete[] pvector; -} - -/* ---------------------------------------------------------------------- */ - -void PairE3B::compute(int eflag, int vflag) -{ - int i,j,k,h,ii,jj,hh,kk,inum,jnum,otherO; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,rsq,tmpexp; - double fxtmp,fytmp,fztmp,fix,fiy,fiz; - double delxh,delyh,delzh,rsqh,tmpr; - double scFact1,scFact2,scEng,scDer; - int *ilist,*jlist,*numneigh,**firstneigh; - bool addedH; - - if (natoms != atom->natoms) - error->all(FLERR,"pair E3B requires a fixed number of atoms"); - - ev_init(eflag,vflag); - //clear sumExp array - memset(sumExp,0.0,nbytes); - - evdwl = 0.0; - pvector[0]=pvector[1]=pvector[2]=pvector[3]=0.0; - - double **x = atom->x; - double **f = atom->f; - tagint *tag = atom->tag; - int *type = atom->type; - int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - int npair = 0; - // loop over half neighbor list of my atoms - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - if (type[i]!=typeO) - continue; - - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - fix = fiy = fiz = 0.0; - - // two-body interactions - jlist = firstneigh[i]; - jnum = numneigh[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - //skip unless O-O interaction - if (type[j]!=typeO) - continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; //OO distance - - //two body interaction - //not shifted b/c k2=4.87/A, so at cutoff (5.2A) e^(-kr) = 1e-11 - if (rsq < rc2sq) { - tmpr = sqrt(rsq); - tmpexp = e2 * exp(-k2*tmpr); - fpair = k2 * tmpexp / tmpr; - - fxtmp = delx*fpair; - fytmp = dely*fpair; - fztmp = delz*fpair; - fix += fxtmp; - fiy += fytmp; - fiz += fztmp; - f[j][0] -= fxtmp; - f[j][1] -= fytmp; - f[j][2] -= fztmp; - - if (evflag) { - ev_tally(i,j,nlocal,newton_pair,tmpexp,0.0,fpair,delx,dely,delz); - pvector[0] += tmpexp; - } - } //end if rsqmap(tag[otherO]+hh+1); - //if hydrogen atom is missing, bond potential or shake will - //catch this, so don't need to check here - //if (h<0) - // error->one(FLERR,"hydrogen atom missing"); - h = domain->closest_image(otherO,h); - pairH[npair][kk][hh] = h; - - delxh = x[k][0] - x[h][0]; - delyh = x[k][1] - x[h][1]; - delzh = x[k][2] - x[h][2]; - rsqh = delxh*delxh + delyh*delyh + delzh*delzh; - - if (rsqh < rc3sq) { - - tmpr = sqrt(rsqh); - tmpexp = exp(-k3*tmpr); - if (tmpr > rs) { - scFact1 = rc3-tmpr; - scFact2 = sc_num + 2*tmpr; - scEng = scFact1*scFact1*scFact2*sc_denom; - scDer = k3*scEng - 6*scFact1*(rs-tmpr)*sc_denom; - } else { - scDer = k3; - scEng = 1.0; - } - - //need to keep fpair3 separate from del3 for virial - fpair3[npair][kk][hh] = scDer*tmpexp/tmpr; - tmpexp *= scEng; - exps[npair][kk][hh] = tmpexp; - del3[npair][kk][hh][0] = delxh; - del3[npair][kk][hh][1] = delyh; - del3[npair][kk][hh][2] = delzh; - - //accumulate global vector of sum(e^kr) - //tags start at 1, so subtract one to index sumExp - sumExp[tag[k]-1] += tmpexp; - sumExp[tag[h]-1] += tmpexp; - - addedH = true; - } else { - exps [npair][kk][hh] = 0.0; - fpair3[npair][kk][hh] = 0.0; - } //if < rc3sq - } //end loop through 2 Hs - } //end for kk in NUMO - //if added a pair, check if array is too small and grow - if (addedH) { - npair++; - if (npair >= pairmax) - error->one(FLERR,"neigh is too small"); - } - } //end if < rc3deltaSq - } //end for jj neigh - - //add 2-body forces on i - f[i][0] += fix; - f[i][1] += fiy; - f[i][2] += fiz; - } //end for ii - - //communicate sumExp array - //tested that no change in speed with MPI_IN_PLACE - MPI_Allreduce(MPI_IN_PLACE,sumExp,maxID,MPI_DOUBLE,MPI_SUM,world); - - //now loop through list of pairs, calculating 3body forces - int j2,otherH; - double partA,partB,partC; - for (ii = 0; ii < npair; ii++) { - - for (kk=0; kkntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); -} - -void PairE3B::allocateE3B() -{ - allocatedE3B = true; - - //TODO: get memory->grow working for 4d arrays - pairmax = atom->nlocal*pairPerAtom; //initial guess for size of pair lists - memory->create(pairO ,pairmax,NUMO ,"pair:pairO"); - memory->create(pairH ,pairmax,NUMO,NUMH ,"pair:pairH"); - memory->create(exps ,pairmax,NUMO,NUMH ,"pair:exps"); - memory->create(fpair3,pairmax,NUMO,NUMH ,"pair:fpair3"); - memory->create(del3 ,pairmax,NUMO,NUMH,DIM,"pair:del3"); - - //set del3 to zero to silence valgrind memcheck errors - //don't need to do this in every call to compute() because we set - //exps and fpair3 to zero, and all uses of del3 are multiplied by one of those - int ii,jj,kk,ll; - for (ii=0; iinatoms; - maxID=find_maxID(); - if (!natoms) - error->all(FLERR,"No atoms found"); - memory->create(sumExp,maxID,"pair:sumExp"); - nbytes = sizeof(double) * maxID; -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairE3B::settings(int narg, char **arg) -{ - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - typeO=utils::inumeric(FLERR,arg[0],false,lmp); -} - -/* ---------------------------------------------------------------------- - coeffs must be * * keyword/value - keyword/values set the potential parameters -------------------------------------------------------------------------- */ -void PairE3B::coeff(int narg, char **arg) -{ - if (!allocated) allocate(); - - //1=* 2=* 3/4=1st keyword/value - if (narg < 4) - error->all(FLERR,"There must be at least one keyword given to pair_coeff"); - - // ensure I,J args are * * - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // clear setflag since coeff() called once with I,J = * * - int n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - setflag[typeO][typeO]=1; - - //parse keyword/value pairs - double bondL=0.0; //OH bond length - bool repeatFlag=false; - int presetFlag; - - //clear parameters - e2=ea=eb=ec=k3=k2=NAN; - rs=rc3=rc2=0.0; - - int iarg = 2; //beginning of keyword/value pairs - while (iarg < narg) { - char *keyword = arg[iarg++]; - if (checkKeyword(keyword,"Ea",1,narg-iarg)) - ea=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"Eb",1,narg-iarg)) - eb=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"Ec",1,narg-iarg)) - ec=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"K3",1,narg-iarg)) - k3=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"Rs",1,narg-iarg)) - rs=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"Rc3",1,narg-iarg)) - rc3=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"Rc2",1,narg-iarg)) - rc2=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"bondL",1,narg-iarg)) - bondL=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"E2",1,narg-iarg)) - e2=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"K2",1,narg-iarg)) - k2=utils::numeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"neigh",1,narg-iarg)) - pairPerAtom=utils::inumeric(FLERR,arg[iarg++],false,lmp); - else if (checkKeyword(keyword,"preset",1,narg-iarg)) { - presetFlag=utils::inumeric(FLERR,arg[iarg++],false,lmp); - presetParam(presetFlag,repeatFlag,bondL); - } else { - char str[256]; - snprintf(str,256,"Keyword %s is unknown",keyword); - error->all(FLERR,str); - } - } - - checkInputs(bondL); - - //cutmax for neighbor listing - cutmax = std::max(rc2,rc3); - rc2sq = rc2*rc2; - rc3sq = rc3*rc3; - rc3deltaSq = (rc3+bondL)*(rc3+bondL); - - double tmpfact=1.0/(rc3-rs); - sc_denom=tmpfact*tmpfact*tmpfact; - sc_num=rc3-3*rs; -} - -/* ---------------------------------------------------------------------- - init specific to this pair styles -------------------------------------------------------------------------- */ - -void PairE3B::init_style() -{ - if (atom->tag_enable == 0) - error->all(FLERR,"Pair style E3B requires atom IDs"); - if (force->newton_pair == 0) - error->all(FLERR,"Pair style E3B requires newton pair on"); - if (typeO<1 || typeO>atom->ntypes) - error->all(FLERR,"Invalid Otype: out of bounds"); - - // need a half neighbor list - neighbor->request(this,instance_me); - - if (!force->pair_match("tip4p",false,0)) - if (comm->me==0) error->warning(FLERR,"E3B pair_style is designed for use with hybrid/overlay tip4p style"); - - if (!allocatedE3B) allocateE3B(); -} - - -static const char cite_E3B1[] = - "Explicit Three-Body (E3B) potential for water:\n\n" - "@article{kumar_water_2008,\n" - "title = {Water Simulation Model with Explicit Three-Molecule Interactions},\n" - "volume = {112},\n" - "doi = {10.1021/jp8009468},\n" - "number = {28},\n" - "journal = {J Phys. Chem. B},\n" - "author = {Kumar, R. and Skinner, J. L.},\n" - "year = {2008},\n" - "pages = {8311--8318}\n" - "}\n\n"; - -static const char cite_E3B2[] = - "Explicit Three-Body (E3B) potential for water:\n\n" - "@article{tainter_robust_2011,\n" - "title = {Robust three-body water simulation model},\n" - "volume = {134},\n" - "doi = {10.1063/1.3587053},\n" - "number = {18},\n" - "journal = {J. Chem. Phys},\n" - "author = {Tainter, C. J. and Pieniazek, P. A. and Lin, Y.-S. and Skinner, J. L.},\n" - "year = {2011},\n" - "pages = {184501}\n" - "}\n\n"; - -static const char cite_E3B3[] = - "Explicit Three-Body (E3B) potential for water:\n\n" - "@article{tainter_reparametrized_2015,\n" - "title = {Reparametrized {E3B} (Explicit Three-Body) Water Model Using the {TIP4P/2005} Model as a Reference},\n" - "volume = {11},\n" - "doi = {10.1021/acs.jctc.5b00117},\n" - "number = {5},\n" - "journal = {J. Chem. Theory Comput.},\n" - "author = {Tainter, Craig J. and Shi, Liang and Skinner, James L.},\n" - "year = {2015},\n" - "pages = {2268--2277}\n" - "}\n\n"; - -void PairE3B::presetParam(const int flag,bool &repeatFlag,double &bondL) { - if (repeatFlag) { - error->all(FLERR, - "Cannot request two different sets of preset parameters"); - } - repeatFlag=true; - - if (!std::isnan(ea) || !std::isnan(eb) || !std::isnan(ec) || - !std::isnan(e2) || !std::isnan(k3) || !std::isnan(k2) || - bondL!=0.0 || rs!=0.0 || rc3!=0.0 || rc2!=0.0 ) - error->all(FLERR,"Preset keyword will overwrite another keyword setting"); - - double econv=1.0,lconv=1.0; - if (strcmp(update->unit_style,"real") == 0) { - econv=1.0/4.184; - lconv=1.0; - } else if (strcmp(update->unit_style,"metal") == 0) { - econv=0.103653271; - lconv=1.0; - } else if (strcmp(update->unit_style,"si") == 0) { - econv=1.660578e-21; - lconv=1e-10; - } else if (strcmp(update->unit_style,"cgs") == 0) { - econv=1.660578e-14; - lconv=1e-8; - } else { - char str[256]; - snprintf(str,256, - "Pre-defined E3B parameters have not been set for %s units.", - update->unit_style); - error->all(FLERR,str); - } - - //here parameters are defined in kJ/mol and A - //they will be converted to the lammps units after - if (flag==2008) { - error->all(FLERR,"\"preset 2008\" is not yet supported, because this would require distinct k3 coefficients, use \"preset 2011\" or \"preset 2015\""); - if (lmp->citeme) lmp->citeme->add(cite_E3B1); - ea = 4699.6; - eb =-2152.9; - ec = 1312.7; - //ka = 1.0/1.88; - //kb = 1.0/1.71; - //kc = 1.0/1.56; - e2 = 1.925e6; - k2 = 4.67; - rs = 5.0; - rc3 = 5.2; - rc2 = 5.2; - bondL = 0.9572; - } else if (flag==2011) { - if (lmp->citeme) lmp->citeme->add(cite_E3B2); - ea = 1745.7; - eb =-4565.0; - ec = 7606.8; - k3 = 1.907; - e2 = 2.349e6; - k2 = 4.872; - rs = 5.0; - rc3 = 5.2; - rc2 = 5.2; - bondL = 0.9572; - } else if (flag==2015) { - if (lmp->citeme) lmp->citeme->add(cite_E3B3); - ea = 150.0; - eb =-1005.0; - ec = 1880.0; - k3 = 1.907; - e2 = 0.453e6; - k2 = 4.872; - rs = 5.0; - rc3 = 5.2; - rc2 = 5.2; - bondL = 0.9572; - } else - error->all(FLERR,"Unknown argument: preset only takes 2011 or 2015 as arguments"); - - //convert units - ea *= econv; - eb *= econv; - ec *= econv; - e2 *= econv; - k3 /= lconv; - k2 /= lconv; - rs *= lconv; - rc2 *= lconv; - rc3 *= lconv; - bondL *= lconv*BOND_DELTA; -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ -//pair.cpp::init uses this to set cutsq array, used for neighboring, etc -double PairE3B::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - return cutmax; -} - -bool PairE3B::checkKeyword(const char *thiskey,const char *test,const int nVal, const int nRem) { - if (strcmp(thiskey,test) == 0) { - if (nRemall(FLERR,str); - } - return true; - } - return false; -} - -//find max atom ID for all atoms -//from fix_deposit.cpp -tagint PairE3B::find_maxID() -{ - tagint *tag = atom->tag; - int nlocal = atom->nlocal; - - tagint max = 0; - tagint maxID; - for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]); - MPI_Allreduce(&max,&maxID,1,MPI_LMP_TAGINT,MPI_MAX,world); - - return maxID; -} - -void PairE3B::checkInputs(const double &bondL) { - //first check that all necessary values were set - if (rc2==0.0) - error->all(FLERR,"rc2 keyword missing"); - if (rs==0.0) - error->all(FLERR,"Rs keyword missing"); - if (rc3==0.0) - error->all(FLERR,"Rc3 keyword missing"); - if (bondL==0.0) - error->all(FLERR,"bondL keyword missing"); - if (std::isnan(ea)) - error->all(FLERR,"Ea keyword missing"); - if (std::isnan(eb)) - error->all(FLERR,"Eb keyword missing"); - if (std::isnan(ec)) - error->all(FLERR,"Ec keyword missing"); - if (std::isnan(k3)) - error->all(FLERR,"K3 keyword missing"); - if (std::isnan(e2)) - error->all(FLERR,"E2 keyword missing"); - if (std::isnan(k2)) - error->all(FLERR,"K2 keyword missing"); - - //now test that values are within acceptable ranges - if (k2 < 0.0 or k3 < 0.0) - error->all(FLERR,"exponential decay is negative"); - if (bondL<0.0) - error->all(FLERR,"OH bond length is negative"); - if (rc2 < 0.0 || rc3 < 0.0 || rs < 0.0) - error->all(FLERR,"potential cutoff is negative"); - if (rs > rc3) - error->all(FLERR,"potential switching distance is larger than cutoff"); - if (rs==rc3) - error->warning(FLERR,"potential switching distance is equal to cutoff: this is untested and not conserve energy"); - if (pairPerAtom<0) - error->all(FLERR,"neigh is negative"); -} diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp deleted file mode 100644 index a23764f959..0000000000 --- a/src/USER-OMP/pair_edip_omp.cpp +++ /dev/null @@ -1,488 +0,0 @@ -// clang-format off -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - This software is distributed under the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Axel Kohlmeyer (Temple U) -------------------------------------------------------------------------- */ - -#include "pair_edip_omp.h" - -#include "atom.h" -#include "comm.h" -#include "neigh_list.h" -#include "suffix.h" -using namespace LAMMPS_NS; - -#include - -#include "omp_compat.h" -#define GRIDDENSITY 8000 -#define GRIDSTART 0.1 - -// max number of interaction per atom for f(Z) environment potential - -static constexpr int leadDimInteractionList = 64; - -/* ---------------------------------------------------------------------- */ - -PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) : - PairEDIP(lmp), ThrOMP(lmp, THR_PAIR) -{ - suffix_flag |= Suffix::OMP; - respa_enable = 0; -} - -/* ---------------------------------------------------------------------- */ - -void PairEDIPOMP::compute(int eflag, int vflag) -{ - ev_init(eflag,vflag); - - const int nall = atom->nlocal + atom->nghost; - const int nthreads = comm->nthreads; - const int inum = list->inum; - -#if defined(_OPENMP) -#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) -#endif - { - int ifrom, ito, tid; - - loop_setup_thr(ifrom, ito, tid, inum, nthreads); - ThrData *thr = fix->get_thr(tid); - thr->timer(Timer::START); - ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); - - if (evflag) { - if (eflag) { - if (vflag_atom) eval<1,1,1>(ifrom, ito, thr); - else eval<1,1,0>(ifrom, ito, thr); - } else { - if (vflag_atom) eval<1,0,1>(ifrom, ito, thr); - else eval<1,0,0>(ifrom, ito, thr); - } - } else eval<0,0,0>(ifrom, ito, thr); - - thr->timer(Timer::PAIR); - reduce_thr(this, eflag, vflag, thr); - } // end of omp parallel region -} - -template -void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr) -{ - int i,j,k,ii,jnum; - int itype,jtype,ktype,ijparam,ikparam; - double xtmp,ytmp,ztmp,evdwl; - int *ilist,*jlist,*numneigh,**firstneigh; - int preForceCoord_counter; - - double invR_ij; - double invR_ik; - double directorCos_ij_x; - double directorCos_ij_y; - double directorCos_ij_z; - double directorCos_ik_x; - double directorCos_ik_y; - double directorCos_ik_z; - double cosTeta; - - int interpolIDX; - double interpolTMP; - double interpolDeltaX; - double interpolY1; - double interpolY2; - - double invRMinusCutoffA; - double sigmaInvRMinusCutoffA; - double gammInvRMinusCutoffA; - double cosTetaDiff; - double cosTetaDiffCosTetaDiff; - double cutoffFunction_ij; - double exp2B_ij; - double exp2BDerived_ij; - double pow2B_ij; - double pow2BDerived_ij; - double exp3B_ij; - double exp3BDerived_ij; - double exp3B_ik; - double exp3BDerived_ik; - double qFunction; - double tauFunction; - double tauFunctionDerived; - double expMinusBetaZeta_iZeta_i; - double qFunctionCosTetaDiffCosTetaDiff; - double expMinusQFunctionCosTetaDiffCosTetaDiff; - double zeta_i; - double zeta_iDerived; - double zeta_iDerivedInvR_ij; - - double forceModCoord_factor; - double forceModCoord; - double forceModCoord_ij; - double forceMod2B; - double forceMod3B_factor1_ij; - double forceMod3B_factor2_ij; - double forceMod3B_factor2; - double forceMod3B_factor1_ik; - double forceMod3B_factor2_ik; - double potentia3B_factor; - double potential2B_factor; - - const int tid = thr->get_tid(); - - double *pre_thrInvR_ij = preInvR_ij + tid * leadDimInteractionList; - double *pre_thrExp3B_ij = preExp3B_ij + tid * leadDimInteractionList; - double *pre_thrExp3BDerived_ij = preExp3BDerived_ij + tid * leadDimInteractionList; - double *pre_thrExp2B_ij = preExp2B_ij + tid * leadDimInteractionList; - double *pre_thrExp2BDerived_ij = preExp2BDerived_ij + tid * leadDimInteractionList; - double *pre_thrPow2B_ij = prePow2B_ij + tid * leadDimInteractionList; - double *pre_thrForceCoord = preForceCoord + tid * leadDimInteractionList; - - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; - dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0]; - const int * _noalias const type = atom->type; - const int nlocal = atom->nlocal; - - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over full neighbor list of my atoms - - for (ii = iifrom; ii < iito; ii++) { - zeta_i = 0.0; - int numForceCoordPairs = 0; - - i = ilist[ii]; - itype = map[type[i]]; - xtmp = x[i].x; - ytmp = x[i].y; - ztmp = x[i].z; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // pre-loop to compute environment coordination f(Z) - - for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { - j = jlist[neighbor_j]; - j &= NEIGHMASK; - - double dr_ij[3], r_ij; - - dr_ij[0] = xtmp - x[j].x; - dr_ij[1] = ytmp - x[j].y; - dr_ij[2] = ztmp - x[j].z; - r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; - - jtype = map[type[j]]; - ijparam = elem3param[itype][jtype][jtype]; - if (r_ij > params[ijparam].cutsq) continue; - - r_ij = sqrt(r_ij); - - invR_ij = 1.0 / r_ij; - pre_thrInvR_ij[neighbor_j] = invR_ij; - - invRMinusCutoffA = 1.0 / (r_ij - cutoffA); - sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA; - gammInvRMinusCutoffA = gamm * invRMinusCutoffA; - - interpolDeltaX = r_ij - GRIDSTART; - interpolTMP = (interpolDeltaX * GRIDDENSITY); - interpolIDX = (int) interpolTMP; - - interpolY1 = exp3B[interpolIDX]; - interpolY2 = exp3B[interpolIDX+1]; - exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA; - - pre_thrExp3B_ij[neighbor_j] = exp3B_ij; - pre_thrExp3BDerived_ij[neighbor_j] = exp3BDerived_ij; - - interpolY1 = exp2B[interpolIDX]; - interpolY2 = exp2B[interpolIDX+1]; - exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA; - - pre_thrExp2B_ij[neighbor_j] = exp2B_ij; - pre_thrExp2BDerived_ij[neighbor_j] = exp2BDerived_ij; - - interpolY1 = pow2B[interpolIDX]; - interpolY2 = pow2B[interpolIDX+1]; - pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - pre_thrPow2B_ij[neighbor_j] = pow2B_ij; - - // zeta and its derivative - - if (r_ij < cutoffC) zeta_i += 1.0; - else { - interpolY1 = cutoffFunction[interpolIDX]; - interpolY2 = cutoffFunction[interpolIDX+1]; - cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - zeta_i += cutoffFunction_ij; - - interpolY1 = cutoffFunctionDerived[interpolIDX]; - interpolY2 = cutoffFunctionDerived[interpolIDX+1]; - zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij; - - preForceCoord_counter=numForceCoordPairs*5; - pre_thrForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij; - pre_thrForceCoord[preForceCoord_counter+1]=dr_ij[0]; - pre_thrForceCoord[preForceCoord_counter+2]=dr_ij[1]; - pre_thrForceCoord[preForceCoord_counter+3]=dr_ij[2]; - pre_thrForceCoord[preForceCoord_counter+4]=j; - numForceCoordPairs++; - } - } - - // quantities depending on zeta_i - - interpolDeltaX = zeta_i; - interpolTMP = (interpolDeltaX * GRIDDENSITY); - interpolIDX = (int) interpolTMP; - - interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX]; - interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1]; - expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - interpolY1 = qFunctionGrid[interpolIDX]; - interpolY2 = qFunctionGrid[interpolIDX+1]; - qFunction = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - interpolY1 = tauFunctionGrid[interpolIDX]; - interpolY2 = tauFunctionGrid[interpolIDX+1]; - tauFunction = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - interpolY1 = tauFunctionDerivedGrid[interpolIDX]; - interpolY2 = tauFunctionDerivedGrid[interpolIDX+1]; - tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * - (interpolTMP-interpolIDX); - - forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i; - - forceModCoord = 0.0; - - // two-body interactions, skip half of them - - for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { - double dr_ij[3], r_ij, f_ij[3]; - - j = jlist[neighbor_j]; - j &= NEIGHMASK; - - dr_ij[0] = x[j].x - xtmp; - dr_ij[1] = x[j].y - ytmp; - dr_ij[2] = x[j].z - ztmp; - r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; - - jtype = map[type[j]]; - ijparam = elem3param[itype][jtype][jtype]; - if (r_ij > params[ijparam].cutsq) continue; - - r_ij = sqrt(r_ij); - - invR_ij = pre_thrInvR_ij[neighbor_j]; - pow2B_ij = pre_thrPow2B_ij[neighbor_j]; - - potential2B_factor = pow2B_ij - expMinusBetaZeta_iZeta_i; - - exp2B_ij = pre_thrExp2B_ij[neighbor_j]; - - pow2BDerived_ij = - rho * invR_ij * pow2B_ij; - - forceModCoord += (forceModCoord_factor*exp2B_ij); - - exp2BDerived_ij = pre_thrExp2BDerived_ij[neighbor_j]; - forceMod2B = exp2BDerived_ij * potential2B_factor + - exp2B_ij * pow2BDerived_ij; - - directorCos_ij_x = invR_ij * dr_ij[0]; - directorCos_ij_y = invR_ij * dr_ij[1]; - directorCos_ij_z = invR_ij * dr_ij[2]; - - exp3B_ij = pre_thrExp3B_ij[neighbor_j]; - exp3BDerived_ij = pre_thrExp3BDerived_ij[neighbor_j]; - - f_ij[0] = forceMod2B * directorCos_ij_x; - f_ij[1] = forceMod2B * directorCos_ij_y; - f_ij[2] = forceMod2B * directorCos_ij_z; - - f[i].x += f_ij[0]; - f[i].y += f_ij[1]; - f[i].z += f_ij[2]; - - f[j].x -= f_ij[0]; - f[j].y -= f_ij[1]; - f[j].z -= f_ij[2]; - - // potential energy - - evdwl = (exp2B_ij * potential2B_factor); - - if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, evdwl, 0.0, - -forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr); - - // three-body Forces - - for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) { - double dr_ik[3], r_ik, f_ik[3]; - - k = jlist[neighbor_k]; - k &= NEIGHMASK; - ktype = map[type[k]]; - ikparam = elem3param[itype][ktype][ktype]; - - dr_ik[0] = x[k].x - xtmp; - dr_ik[1] = x[k].y - ytmp; - dr_ik[2] = x[k].z - ztmp; - r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2]; - - if (r_ik > params[ikparam].cutsq) continue; - - r_ik = sqrt(r_ik); - - invR_ik = pre_thrInvR_ij[neighbor_k]; - - directorCos_ik_x = invR_ik * dr_ik[0]; - directorCos_ik_y = invR_ik * dr_ik[1]; - directorCos_ik_z = invR_ik * dr_ik[2]; - - cosTeta = directorCos_ij_x * directorCos_ik_x + - directorCos_ij_y * directorCos_ik_y + - directorCos_ij_z * directorCos_ik_z; - - cosTetaDiff = cosTeta + tauFunction; - cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff; - qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction; - expMinusQFunctionCosTetaDiffCosTetaDiff = - exp(-qFunctionCosTetaDiffCosTetaDiff); - - potentia3B_factor = lambda * - ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) + - eta * qFunctionCosTetaDiffCosTetaDiff); - - exp3B_ik = pre_thrExp3B_ij[neighbor_k]; - exp3BDerived_ik = pre_thrExp3BDerived_ij[neighbor_k]; - - forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik * - potentia3B_factor; - forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik * - qFunction * cosTetaDiff * - (eta + expMinusQFunctionCosTetaDiffCosTetaDiff); - forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij; - - f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x + - forceMod3B_factor2_ij * - (cosTeta * directorCos_ij_x - directorCos_ik_x); - f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y + - forceMod3B_factor2_ij * - (cosTeta * directorCos_ij_y - directorCos_ik_y); - f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z + - forceMod3B_factor2_ij * - (cosTeta * directorCos_ij_z - directorCos_ik_z); - - forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij * - potentia3B_factor; - forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik; - - f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x + - forceMod3B_factor2_ik * - (cosTeta * directorCos_ik_x - directorCos_ij_x); - f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y + - forceMod3B_factor2_ik * - (cosTeta * directorCos_ik_y - directorCos_ij_y); - f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z + - forceMod3B_factor2_ik * - (cosTeta * directorCos_ik_z - directorCos_ij_z); - - forceModCoord += (forceMod3B_factor2 * - (tauFunctionDerived - 0.5 * mu * cosTetaDiff)); - - f[j].x += f_ij[0]; - f[j].y += f_ij[1]; - f[j].z += f_ij[2]; - - f[k].x += f_ik[0]; - f[k].y += f_ik[1]; - f[k].z += f_ik[2]; - - f[i].x -= f_ij[0] + f_ik[0]; - f[i].y -= f_ij[1] + f_ik[1]; - f[i].z -= f_ij[2] + f_ik[2]; - - // potential energy - - evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor); - - if (evflag) ev_tally3_thr(this,i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik,thr); - } - } - - // forces due to environment coordination f(Z) - - for (int idx = 0; idx < numForceCoordPairs; idx++) { - double dr_ij[3], f_ij[3]; - - preForceCoord_counter = idx * 5; - zeta_iDerivedInvR_ij=pre_thrForceCoord[preForceCoord_counter+0]; - dr_ij[0]=pre_thrForceCoord[preForceCoord_counter+1]; - dr_ij[1]=pre_thrForceCoord[preForceCoord_counter+2]; - dr_ij[2]=pre_thrForceCoord[preForceCoord_counter+3]; - j = static_cast (pre_thrForceCoord[preForceCoord_counter+4]); - - forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij; - - f_ij[0] = forceModCoord_ij * dr_ij[0]; - f_ij[1] = forceModCoord_ij * dr_ij[1]; - f_ij[2] = forceModCoord_ij * dr_ij[2]; - - f[i].x -= f_ij[0]; - f[i].y -= f_ij[1]; - f[i].z -= f_ij[2]; - - f[j].x += f_ij[0]; - f[j].y += f_ij[1]; - f[j].z += f_ij[2]; - - // potential energy - - evdwl = 0.0; - if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, 0.0, 0.0, - forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr); - } - } -} - -/* ---------------------------------------------------------------------- */ - -double PairEDIPOMP::memory_usage() -{ - double bytes = memory_usage_thr(); - bytes += PairEDIP::memory_usage(); - - return bytes; -} diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp deleted file mode 100644 index 8535b87dbe..0000000000 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ /dev/null @@ -1,641 +0,0 @@ -// clang-format off -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Per-atom energy/virial added by Ray Shan (Materials Design, Inc.) - Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added - by Ray Shan (Materials Design) - - OpenMP based threading support for pair_style reax/c/omp added - by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF), - Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF) - - Integration of the pair_style reax/c/omp into the User-OMP package - by Axel Kohlmeyer (Temple U.) - - Please cite the related publication: - H. M. Aktulga, C. Knight, P. Coffman, K. A. O'Hearn, T. R. Shan, - W. Jiang, "Optimizing the performance of reactive molecular dynamics - simulations for multi-core architectures", International Journal of - High Performance Computing Applications, to appear. - ------------------------------------------------------------------------- */ - -#include "pair_reaxc_omp.h" - -#include -#include "atom.h" -#include "update.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "modify.h" -#include "fix_reaxc.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" - - -#include "reaxc_defs.h" -#include "reaxc_types.h" -#include "reaxc_allocate.h" -#include "reaxc_forces_omp.h" -#include "reaxc_init_md_omp.h" -#include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_reset_tools.h" -#include "reaxc_tool_box.h" - -#if defined(_OPENMP) -#include -#endif - -#include "suffix.h" -using namespace LAMMPS_NS; - -#ifdef OMP_TIMING -double ompTimingData[LASTTIMINGINDEX]; -int ompTimingCount[LASTTIMINGINDEX]; -int ompTimingCGCount[LASTTIMINGINDEX]; -#endif - -static const char cite_pair_reax_c_omp[] = - "pair reax/c/omp and fix qeq/reax/omp command:\n\n" - "@Article{Aktulga17,\n" - " author = {H. M. Aktulga, C. Knight, P. Coffman, K. A. OHearn, T. R. Shan, W. Jiang},\n" - " title = {Optimizing the performance of reactive molecular dynamics simulations for multi-core architectures},\n" - " journal = {International Journal of High Performance Computing Applications},\n" - " year = to appear\n" - "}\n\n"; - -/* ---------------------------------------------------------------------- */ - -PairReaxCOMP::PairReaxCOMP(LAMMPS *lmp) : PairReaxC(lmp), ThrOMP(lmp, THR_PAIR) -{ - if (lmp->citeme) lmp->citeme->add(cite_pair_reax_c_omp); - - suffix_flag |= Suffix::OMP; - system->pair_ptr = this; - system->omp_active = 1; - - num_nbrs_offset = nullptr; - -#ifdef OMP_TIMING - for (int i=0;inum_intrs; ++i) - sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); - } - memory->destroy(num_nbrs_offset); - -#ifdef OMP_TIMING - int myrank; - - MPI_Comm_rank(mpi_data->world,&myrank); - - // Write screen output - if (timer->has_full() && myrank == 0 && screen) { - fprintf(screen,"\n\nWrite_Lists took %11.3lf seconds", ompTimingData[COMPUTEWLINDEX]); - - fprintf(screen,"\n\nCompute_Forces took %11.3lf seconds:", ompTimingData[COMPUTEINDEX]); - fprintf(screen,"\n ->Initial Forces: %11.3lf seconds", ompTimingData[COMPUTEIFINDEX]); - fprintf(screen,"\n ->Bond Order: %11.3lf seconds", ompTimingData[COMPUTEBOINDEX]); - fprintf(screen,"\n ->Atom Energy: %11.3lf seconds", ompTimingData[COMPUTEATOMENERGYINDEX]); - fprintf(screen,"\n ->Bond: %11.3lf seconds", ompTimingData[COMPUTEBONDSINDEX]); - fprintf(screen,"\n ->Hydrogen bonds: %11.3lf seconds", ompTimingData[COMPUTEHBONDSINDEX]); - fprintf(screen,"\n ->Torsion Angles: %11.3lf seconds", ompTimingData[COMPUTETORSIONANGLESBOINDEX]); - fprintf(screen,"\n ->Valence Angles: %11.3lf seconds", ompTimingData[COMPUTEVALENCEANGLESBOINDEX]); - fprintf(screen,"\n ->Non-Bonded For: %11.3lf seconds", ompTimingData[COMPUTENBFINDEX]); - fprintf(screen,"\n ->Total Forces: %11.3lf seconds", ompTimingData[COMPUTETFINDEX]); - - fprintf(screen,"\n\nfixQEQ: %11.3lf seconds", ompTimingData[COMPUTEQEQINDEX]); - fprintf(screen,"\n ->QEQ init: %11.3lf seconds", ompTimingData[COMPUTEINITMVINDEX]); - - double avg = double(ompTimingCGCount[COMPUTECG1INDEX]) / double(ompTimingCount[COMPUTECG1INDEX]); - fprintf(screen,"\n ->QEQ CG1: %11.3lf seconds with %4.1lf iterations on average.", ompTimingData[COMPUTECG1INDEX], avg); - - avg = double(ompTimingCGCount[COMPUTECG2INDEX]) / double(ompTimingCount[COMPUTECG2INDEX]); - fprintf(screen,"\n ->QEQ CG2: %11.3lf seconds with %4.1lf iterations on average.", ompTimingData[COMPUTECG2INDEX], avg); - fprintf(screen,"\n ->QEQ CalcQ: %11.3lf seconds\n", ompTimingData[COMPUTECALCQINDEX]); - } - - // Write logfile output - if (timer->has_full() && myrank == 0 && logfile) { - fprintf(logfile,"\n\nWrite_Lists took %11.3lf seconds", ompTimingData[COMPUTEWLINDEX]); - - fprintf(logfile,"\n\nCompute_Forces took %11.3lf seconds:", ompTimingData[COMPUTEINDEX]); - fprintf(logfile,"\n ->Initial Forces: %11.3lf seconds", ompTimingData[COMPUTEIFINDEX]); - fprintf(logfile,"\n ->Bond Order: %11.3lf seconds", ompTimingData[COMPUTEBOINDEX]); - fprintf(logfile,"\n ->Atom Energy: %11.3lf seconds", ompTimingData[COMPUTEATOMENERGYINDEX]); - fprintf(logfile,"\n ->Bond: %11.3lf seconds", ompTimingData[COMPUTEBONDSINDEX]); - fprintf(logfile,"\n ->Hydrogen bonds: %11.3lf seconds", ompTimingData[COMPUTEHBONDSINDEX]); - fprintf(logfile,"\n ->Torsion Angles: %11.3lf seconds", ompTimingData[COMPUTETORSIONANGLESBOINDEX]); - fprintf(logfile,"\n ->Valence Angles: %11.3lf seconds", ompTimingData[COMPUTEVALENCEANGLESBOINDEX]); - fprintf(logfile,"\n ->Non-Bonded For: %11.3lf seconds", ompTimingData[COMPUTENBFINDEX]); - fprintf(logfile,"\n ->Total Forces: %11.3lf seconds", ompTimingData[COMPUTETFINDEX]); - - fprintf(logfile,"\n\nfixQEQ: %11.3lf seconds", ompTimingData[COMPUTEQEQINDEX]); - fprintf(logfile,"\n ->QEQ init: %11.3lf seconds", ompTimingData[COMPUTEINITMVINDEX]); - - double avg = double(ompTimingCGCount[COMPUTECG1INDEX]) / double(ompTimingCount[COMPUTECG1INDEX]); - fprintf(logfile,"\n ->QEQ CG1: %11.3lf seconds with %4.1lf iterations on average.", ompTimingData[COMPUTECG1INDEX], avg); - - avg = double(ompTimingCGCount[COMPUTECG2INDEX]) / double(ompTimingCount[COMPUTECG2INDEX]); - fprintf(logfile,"\n ->QEQ CG2: %11.3lf seconds with %4.1lf iterations on average.", ompTimingData[COMPUTECG2INDEX], avg); - fprintf(logfile,"\n ->QEQ CalcQ: %11.3lf seconds\n", ompTimingData[COMPUTECALCQINDEX]); - } -#endif -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxCOMP::compute(int eflag, int vflag) -{ - double evdwl,ecoul; - double t_start, t_end; - - // communicate num_bonds once every reneighboring - // 2 num arrays stored by fix, grab ptr to them - - if (neighbor->ago == 0) comm->forward_comm_fix(fix_reax); - int *num_bonds = fix_reax->num_bonds; - int *num_hbonds = fix_reax->num_hbonds; - - evdwl = ecoul = 0.0; - ev_init(eflag,vflag); - - if (vflag_global) control->virial = 1; - else control->virial = 0; - - if (vflag_atom) - error->all(FLERR,"Pair style reax/c/omp does not support " - "computing per-atom stress"); - - system->n = atom->nlocal; // my atoms - system->N = atom->nlocal + atom->nghost; // mine + ghosts - system->bigN = static_cast (atom->natoms); // all atoms in the system - - system->big_box.V = 0; - system->big_box.box_norms[0] = 0; - system->big_box.box_norms[1] = 0; - system->big_box.box_norms[2] = 0; - if (comm->me == 0 ) t_start = MPI_Wtime(); - // setup data structures - - setup(); - - Reset( system, control, data, workspace, &lists ); - - // Why not update workspace like in MPI-only code? - // Using the MPI-only way messes up the hb energy - //workspace->realloc.num_far = write_reax_lists(); - write_reax_lists(); - - // timing for filling in the reax lists - if (comm->me == 0) { - t_end = MPI_Wtime(); - data->timing.nbrs = t_end - t_start; - } - - // forces - -#ifdef OMP_TIMING - double startTimeBase,endTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - Compute_ForcesOMP(system,control,data,workspace,&lists,out_control,mpi_data); - read_reax_forces(vflag); - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEINDEX] += (endTimeBase-startTimeBase); -#endif - -#if defined(_OPENMP) -#pragma omp parallel for schedule(static) -#endif - for (int k = 0; k < system->N; ++k) { - num_bonds[k] = system->my_atoms[k].num_bonds; - num_hbonds[k] = system->my_atoms[k].num_hbonds; - } - - // energies and pressure - - if (eflag_global) { - evdwl += data->my_en.e_bond; - evdwl += data->my_en.e_ov; - evdwl += data->my_en.e_un; - evdwl += data->my_en.e_lp; - evdwl += data->my_en.e_ang; - evdwl += data->my_en.e_pen; - evdwl += data->my_en.e_coa; - evdwl += data->my_en.e_hb; - evdwl += data->my_en.e_tor; - evdwl += data->my_en.e_con; - evdwl += data->my_en.e_vdW; - - ecoul += data->my_en.e_ele; - ecoul += data->my_en.e_pol; - - // Store the different parts of the energy - // in a list for output by compute pair command - - pvector[0] = data->my_en.e_bond; - pvector[1] = data->my_en.e_ov + data->my_en.e_un; - pvector[2] = data->my_en.e_lp; - pvector[3] = 0.0; - pvector[4] = data->my_en.e_ang; - pvector[5] = data->my_en.e_pen; - pvector[6] = data->my_en.e_coa; - pvector[7] = data->my_en.e_hb; - pvector[8] = data->my_en.e_tor; - pvector[9] = data->my_en.e_con; - pvector[10] = data->my_en.e_vdW; - pvector[11] = data->my_en.e_ele; - pvector[12] = 0.0; - pvector[13] = data->my_en.e_pol; - } - - if (vflag_fdotr) virial_fdotr_compute(); - - // Set internal timestep counter to that of LAMMPS - - data->step = update->ntimestep; - - Output_Results( system, control, data, &lists, out_control, mpi_data ); - - // populate tmpid and tmpbo arrays for fix reax/c/species - - if (fixspecies_flag) { - if (system->N > nmax) { - memory->destroy(tmpid); - memory->destroy(tmpbo); - nmax = system->N; - memory->create(tmpid,nmax,MAXSPECBOND,"pair:tmpid"); - memory->create(tmpbo,nmax,MAXSPECBOND,"pair:tmpbo"); - } - -#if defined(_OPENMP) -#pragma omp parallel for collapse(2) schedule(static) default(shared) -#endif - for (int i = 0; i < system->N; i++) - for (int j = 0; j < MAXSPECBOND; j++) { - tmpbo[i][j] = 0.0; - tmpid[i][j] = 0; - } - - FindBond(); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxCOMP::init_style( ) -{ - if (!atom->q_flag) - error->all(FLERR,"Pair reax/c/omp requires atom attribute q"); - - // firstwarn = 1; - - bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1) - || (modify->find_fix_by_style("^qeq/shielded") != -1)); - if (!have_qeq && qeqflag == 1) - error->all(FLERR,"Pair reax/c requires use of fix qeq/reax or qeq/shielded"); - - system->n = atom->nlocal; // my atoms - system->N = atom->nlocal + atom->nghost; // mine + ghosts - system->bigN = static_cast (atom->natoms); // all atoms in the system - system->wsize = comm->nprocs; - - system->big_box.V = 0; - system->big_box.box_norms[0] = 0; - system->big_box.box_norms[1] = 0; - system->big_box.box_norms[2] = 0; - - if (atom->tag_enable == 0) - error->all(FLERR,"Pair style reax/c/omp requires atom IDs"); - if (force->newton_pair == 0) - error->all(FLERR,"Pair style reax/c/omp requires newton pair on"); - - if ((atom->map_tag_max > 99999999) && (comm->me == 0)) - error->warning(FLERR,"Some Atom-IDs are too large. Pair style reax/c/omp " - "native output files may get misformatted or corrupted"); - - // because system->bigN is an int, we cannot have more atoms than MAXSMALLINT - - if (atom->natoms > MAXSMALLINT) - error->all(FLERR,"Too many atoms for pair style reax/c/omp"); - - // need a half neighbor list w/ Newton off and ghost neighbors - // built whenever re-neighboring occurs - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->newton = 2; - neighbor->requests[irequest]->ghost = 1; - - cutmax = MAX3(control->nonb_cut, control->hbond_cut, control->bond_cut); - if ((cutmax < 2.0*control->bond_cut) && (comm->me == 0)) - error->warning(FLERR,"Total cutoff < 2*bond cutoff. May need to use an " - "increased neighbor list skin."); - - for (int i = 0; i < LIST_N; ++i) - lists[i].allocated = 0; - - if (fix_reax == nullptr) { - char **fixarg = new char*[3]; - fixarg[0] = (char *) fix_id; - fixarg[1] = (char *) "all"; - fixarg[2] = (char *) "REAXC"; - modify->add_fix(3,fixarg); - delete [] fixarg; - fix_reax = (FixReaxC *) modify->fix[modify->nfix-1]; - } - -#if defined(_OPENMP) - control->nthreads = omp_get_max_threads(); -#else - control->nthreads = 1; -#endif -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxCOMP::setup( ) -{ - int oldN; - int mincap = system->mincap; - double safezone = system->safezone; - - system->n = atom->nlocal; // my atoms - system->N = atom->nlocal + atom->nghost; // mine + ghosts - oldN = system->N; - system->bigN = static_cast (atom->natoms); // all atoms in the system - - if (system->N > nmax) { - memory->destroy(num_nbrs_offset); - // Don't update nmax here. It is updated at end of compute(). - memory->create(num_nbrs_offset, system->N, "pair:num_nbrs_offset"); - } - - if (setup_flag == 0) { - - setup_flag = 1; - - int *num_bonds = fix_reax->num_bonds; - int *num_hbonds = fix_reax->num_hbonds; - - control->vlist_cut = neighbor->cutneighmax; - - // determine the local and total capacity - - system->local_cap = MAX( (int)(system->n * safezone), mincap ); - system->total_cap = MAX( (int)(system->N * safezone), mincap ); - - // initialize my data structures - - PreAllocate_Space( system, control, workspace ); - write_reax_atoms(); - - int num_nbrs = estimate_reax_lists(); - if (!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR, - lists+FAR_NBRS)) - error->all(FLERR,"Pair reax/c problem in far neighbor list"); - - write_reax_lists(); - - InitializeOMP( system, control, data, workspace, &lists, out_control, - mpi_data, world ); - - for (int k = 0; k < system->N; ++k) { - num_bonds[k] = system->my_atoms[k].num_bonds; - num_hbonds[k] = system->my_atoms[k].num_hbonds; - } - - } else { - - // fill in reax datastructures - - write_reax_atoms(); - - // reset the bond list info for new atoms - - for (int k = oldN; k < system->N; ++k) - Set_End_Index( k, Start_Index( k, lists+BONDS ), lists+BONDS ); - - // estimate far neighbor list size - // Not present in MPI-only version - workspace->realloc.num_far = estimate_reax_lists(); - - // check if I need to shrink/extend my data-structs - - ReAllocate( system, control, data, workspace, &lists ); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxCOMP::write_reax_atoms() -{ - int *num_bonds = fix_reax->num_bonds; - int *num_hbonds = fix_reax->num_hbonds; - - if (system->N > system->total_cap) - error->all(FLERR,"Too many ghost atoms"); - -#if defined(_OPENMP) -#pragma omp parallel for schedule(static) default(shared) -#endif - for (int i = 0; i < system->N; ++i) { - system->my_atoms[i].orig_id = atom->tag[i]; - system->my_atoms[i].type = map[atom->type[i]]; - system->my_atoms[i].x[0] = atom->x[i][0]; - system->my_atoms[i].x[1] = atom->x[i][1]; - system->my_atoms[i].x[2] = atom->x[i][2]; - system->my_atoms[i].q = atom->q[i]; - system->my_atoms[i].num_bonds = num_bonds[i]; - system->my_atoms[i].num_hbonds = num_hbonds[i]; - } -} - -/* ---------------------------------------------------------------------- */ - -int PairReaxCOMP::estimate_reax_lists() -{ - int i; - int *ilist = list->ilist; - int *numneigh = list->numneigh; - int numall = list->inum + list->gnum; - int mincap = system->mincap; - - // for good performance in the OpenMP implementation, each thread needs - // to know where to place the neighbors of the atoms it is responsible for. - // The sumscan values for the list->numneigh will be used to determine the - // neighbor offset of each atom. Note that this may cause some significant - // memory overhead if delayed neighboring is used - so it may be desirable - // to work on this part to reduce the memory footprint of the far_nbrs list. - - int num_nbrs = 0; - - for (int itr_i = 0; itr_i < numall; ++itr_i) { - i = ilist[itr_i]; - num_nbrs += numneigh[i]; - } - - int new_estimate = MAX(num_nbrs, mincap*REAX_MIN_NBRS); - - return new_estimate; -} - -/* ---------------------------------------------------------------------- */ - -int PairReaxCOMP::write_reax_lists() -{ -#ifdef OMP_TIMING - double startTimeBase, endTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - int itr_i, itr_j, i, j, num_mynbrs; - int *jlist; - double d_sqr, dist, cutoff_sqr; - rvec dvec; - - double **x = atom->x; - int *ilist = list->ilist; - int *numneigh = list->numneigh; - int **firstneigh = list->firstneigh; - reax_list *far_nbrs = lists + FAR_NBRS; - far_neighbor_data *far_list = far_nbrs->select.far_nbr_list; - - int num_nbrs = 0; - int inum = list->inum; - int gnum = list->gnum; - int numall = inum + gnum; - - // sumscan of the number of neighbors per atom to determine the offsets - // most likely, we are overallocating. desirable to work on this part - // to reduce the memory footprint of the far_nbrs list. - - num_nbrs = 0; - - for (itr_i = 0; itr_i < numall; ++itr_i) { - i = ilist[itr_i]; - num_nbrs_offset[i] = num_nbrs; - num_nbrs += numneigh[i]; - } - -#if defined(_OPENMP) -#pragma omp parallel for schedule(dynamic,50) default(shared) \ - private(itr_i, itr_j, i, j, jlist, cutoff_sqr, num_mynbrs, d_sqr, dvec, dist) -#endif - for (itr_i = 0; itr_i < numall; ++itr_i) { - i = ilist[itr_i]; - jlist = firstneigh[i]; - Set_Start_Index( i, num_nbrs_offset[i], far_nbrs ); - - if (i < inum) - cutoff_sqr = control->nonb_cut*control->nonb_cut; - else - cutoff_sqr = control->bond_cut*control->bond_cut; - - num_mynbrs = 0; - - for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { - j = jlist[itr_j]; - j &= NEIGHMASK; - get_distance( x[j], x[i], &d_sqr, &dvec ); - - if (d_sqr <= cutoff_sqr) { - dist = sqrt( d_sqr ); - set_far_nbr( &far_list[num_nbrs_offset[i] + num_mynbrs], j, dist, dvec ); - ++num_mynbrs; - } - } - Set_End_Index( i, num_nbrs_offset[i] + num_mynbrs, far_nbrs ); - } - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEWLINDEX] += (endTimeBase-startTimeBase); -#endif - - return num_nbrs; -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxCOMP::read_reax_forces(int /* vflag */) -{ -#if defined(_OPENMP) -#pragma omp parallel for schedule(static) default(shared) -#endif - for (int i = 0; i < system->N; ++i) { - system->my_atoms[i].f[0] = workspace->f[i][0]; - system->my_atoms[i].f[1] = workspace->f[i][1]; - system->my_atoms[i].f[2] = workspace->f[i][2]; - - atom->f[i][0] = -workspace->f[i][0]; - atom->f[i][1] = -workspace->f[i][1]; - atom->f[i][2] = -workspace->f[i][2]; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxCOMP::FindBond() -{ - const double bo_cut = 0.10; - -#if defined(_OPENMP) -#pragma omp parallel for schedule(static) default(shared) -#endif - for (int i = 0; i < system->n; i++) { - int j, pj, nj; - double bo_tmp; - bond_data *bo_ij; - - nj = 0; - for (pj = Start_Index(i, lists); pj < End_Index(i, lists); ++pj) { - bo_ij = &( lists->select.bond_list[pj] ); - j = bo_ij->nbr; - if (j < i) continue; - - bo_tmp = bo_ij->bo_data.BO; - - if (bo_tmp >= bo_cut) { - tmpid[i][nj] = j; - tmpbo[i][nj] = bo_tmp; - nj ++; - if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in fix_reaxc_species.h"); - } - } - } -} diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp deleted file mode 100644 index ec94baced5..0000000000 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ /dev/null @@ -1,735 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_bond_orders_omp.h" -#include "reaxc_bond_orders.h" - -#include "fix_omp.h" -#include "reaxc_defs.h" -#include "pair_reaxc_omp.h" -#include "reaxc_types.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -#include -#include - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj, - storage *workspace, reax_list **lists) { - reax_list *bonds = (*lists) + BONDS; - bond_data *nbr_j, *nbr_k; - bond_order_data *bo_ij, *bo_ji; - dbond_coefficients coef; - int pk, k, j; - - PairReaxCOMP *pair_reax_ptr = static_cast(system->pair_ptr); - -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - long reductionOffset = (system->N * tid); - - /* Virial Tallying variables */ - rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp; - - /* Initializations */ - nbr_j = &(bonds->select.bond_list[pj]); - j = nbr_j->nbr; - bo_ij = &(nbr_j->bo_data); - bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data); - - double c = bo_ij->Cdbo + bo_ji->Cdbo; - coef.C1dbo = bo_ij->C1dbo * c; - coef.C2dbo = bo_ij->C2dbo * c; - coef.C3dbo = bo_ij->C3dbo * c; - - c = bo_ij->Cdbopi + bo_ji->Cdbopi; - coef.C1dbopi = bo_ij->C1dbopi * c; - coef.C2dbopi = bo_ij->C2dbopi * c; - coef.C3dbopi = bo_ij->C3dbopi * c; - coef.C4dbopi = bo_ij->C4dbopi * c; - - c = bo_ij->Cdbopi2 + bo_ji->Cdbopi2; - coef.C1dbopi2 = bo_ij->C1dbopi2 * c; - coef.C2dbopi2 = bo_ij->C2dbopi2 * c; - coef.C3dbopi2 = bo_ij->C3dbopi2 * c; - coef.C4dbopi2 = bo_ij->C4dbopi2 * c; - - c = workspace->CdDelta[i] + workspace->CdDelta[j]; - coef.C1dDelta = bo_ij->C1dbo * c; - coef.C2dDelta = bo_ij->C2dbo * c; - coef.C3dDelta = bo_ij->C3dbo * c; - - // The same "c" refactoring here can be replicated below in Add_dBond_to_Forces_NPTOMP(), but - // I'd prefer to wait for a test to verify changes before doing so (just to be safe). - - // forces on i - // rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); - // rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] ); - // rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); - // rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]); - // rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); - // rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] ); - - c = (coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2); - rvec_Scale( temp, c, bo_ij->dBOp ); - - c = (coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2); - rvec_ScaledAdd( temp, c, workspace->dDeltap_self[i] ); - - rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); - rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); - - rvec_Add(workspace->forceReduction[reductionOffset+i],temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fi_tmp, -1.0, temp); - rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x ); - - pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,i,j,system->N,0,0,0, - fi_tmp[0],fi_tmp[1],fi_tmp[2], - delij[0],delij[1],delij[2],thr); - } - - // forces on j - // rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); - // rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]); - // rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); - // rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]); - // rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); - // rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); - // rvec_ScaledAdd( temp, coef.C4dbopi2, workspace->dDeltap_self[j]); - - - c = -(coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2); - rvec_Scale( temp, c, bo_ij->dBOp ); - - c = (coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2); - rvec_ScaledAdd( temp, c, workspace->dDeltap_self[j] ); - - rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); - rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); - - - rvec_Add(workspace->forceReduction[reductionOffset+j],temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fj_tmp, -1.0, temp); - rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x ); - - pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,j,i,system->N,0,0,0, - fj_tmp[0],fj_tmp[1],fj_tmp[2], - delji[0],delji[1],delji[2],thr); - } - - // forces on k: i neighbor - for (pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - // rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp); - // rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp); - // rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); - // rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp); - - const double c = -(coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2); - rvec_Scale(temp, c, nbr_k->bo_data.dBOp); - - rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fk_tmp, -1.0, temp); - rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); - - pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,i,system->N,0,0,0, - fk_tmp[0],fk_tmp[1],fk_tmp[2], - delki[0],delki[1],delki[2],thr); - rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); - - pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,j,system->N,0,0,0, - fk_tmp[0],fk_tmp[1],fk_tmp[2], - delkj[0],delkj[1],delkj[2],thr); - } - } - - // forces on k: j neighbor - for (pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - // rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); - // rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp); - // rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); - // rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp); - - const double c = -(coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2); - rvec_Scale(temp, c, nbr_k->bo_data.dBOp); - - rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fk_tmp, -1.0, temp); - rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); - - pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,i,system->N,0,0,0, - fk_tmp[0],fk_tmp[1],fk_tmp[2], - delki[0],delki[1],delki[2],thr); - - rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); - - pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,j,system->N,0,0,0, - fk_tmp[0],fk_tmp[1],fk_tmp[2], - delkj[0],delkj[1],delkj[2],thr); - } - } -} - -/* ---------------------------------------------------------------------- */ - -void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, - simulation_data * /* data */, - storage *workspace, reax_list **lists) { - reax_list *bonds = (*lists) + BONDS; - bond_data *nbr_j, *nbr_k; - bond_order_data *bo_ij, *bo_ji; - dbond_coefficients coef; - rvec temp, ext_press; - ivec rel_box; - int pk, k, j; - -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - long reductionOffset = (system->N * tid); - - /* Initializations */ - nbr_j = &(bonds->select.bond_list[pj]); - j = nbr_j->nbr; - bo_ij = &(nbr_j->bo_data); - bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data); - - coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - - coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - - coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - - coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - - - /************************************ - * forces related to atom i * - * first neighbors of atom i * - ************************************/ - for (pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - rvec_Scale(temp, -coef.C2dbo, nbr_k->bo_data.dBOp); /*2nd, dBO*/ - rvec_ScaledAdd(temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);/*dDelta*/ - rvec_ScaledAdd(temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); /*3rd, dBOpi*/ - rvec_ScaledAdd(temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);/*3rd, dBOpi2*/ - - /* force */ - rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); - - /* pressure */ - rvec_iMultiply( ext_press, nbr_k->rel_box, temp ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - } - - /* then atom i itself */ - rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st,dBO*/ - rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd,dBO*/ - rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st,dBO*/ - rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd,dBO*/ - rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/ - rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/ - rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);/*3rd,dBOpi*/ - - rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBO_pi2*/ - rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBO_pi2*/ - rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );/*3rd*/ - - /* force */ - rvec_Add(workspace->forceReduction[reductionOffset+i],temp ); - - for (pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/ - rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/ - rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); /*4th,dBOpi*/ - rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);/*4th,dBOpi2*/ - - /* force */ - rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); - - /* pressure */ - if (k != i) { - ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i) - rvec_iMultiply( ext_press, rel_box, temp ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - } - } - - /* then atom j itself */ - rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/ - rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/ - rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/ - rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);/*2nd, dBO*/ - - rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/ - rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/ - rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);/*3rd,dBOpi*/ - - rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBOpi2*/ - rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBOpi2*/ - rvec_ScaledAdd( temp,coef.C4dbopi2,workspace->dDeltap_self[j]);/*3rd,dBOpi2*/ - - /* force */ - rvec_Add(workspace->forceReduction[reductionOffset+j],temp ); - - /* pressure */ - rvec_iMultiply( ext_press, nbr_j->rel_box, temp ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); -} - -/* ---------------------------------------------------------------------- */ - -int BOp_OMP( storage * /* workspace */, reax_list *bonds, double bo_cut, - int i, int btop_i, far_neighbor_data *nbr_pj, - single_body_parameters * /* sbp_i */, single_body_parameters * /* sbp_j */, - two_body_parameters *twbp, - int btop_j, double C12, double C34, double C56, double BO, double BO_s, double BO_pi, double BO_pi2) { - int j; - double rr2; - double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; - bond_data *ibond, *jbond; - bond_order_data *bo_ij, *bo_ji; - - j = nbr_pj->nbr; - rr2 = 1.0 / SQR(nbr_pj->d); - - // Top portion of BOp() moved to reaxc_forces_omp.cpp::Init_Forces_noQEq_OMP() - - /* Initially BO values are the uncorrected ones, page 1 */ - - /****** bonds i-j and j-i ******/ - ibond = &( bonds->select.bond_list[btop_i] ); - jbond = &( bonds->select.bond_list[btop_j] ); - - ibond->nbr = j; - jbond->nbr = i; - ibond->d = nbr_pj->d; - jbond->d = nbr_pj->d; - rvec_Copy( ibond->dvec, nbr_pj->dvec ); - rvec_Scale( jbond->dvec, -1, nbr_pj->dvec ); - ivec_Copy( ibond->rel_box, nbr_pj->rel_box ); - ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box ); - ibond->dbond_index = btop_i; - jbond->dbond_index = btop_i; - ibond->sym_index = btop_j; - jbond->sym_index = btop_i; - - bo_ij = &( ibond->bo_data ); - bo_ji = &( jbond->bo_data ); - bo_ji->BO = bo_ij->BO = BO; - bo_ji->BO_s = bo_ij->BO_s = BO_s; - bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; - bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; - - /* Bond Order page2-3, derivative of total bond order prime */ - Cln_BOp_s = twbp->p_bo2 * C12 * rr2; - Cln_BOp_pi = twbp->p_bo4 * C34 * rr2; - Cln_BOp_pi2 = twbp->p_bo6 * C56 * rr2; - - /* Only dln_BOp_xx wrt. dr_i is stored here, note that - dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ - rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec); - rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec); - rvec_Scale(bo_ij->dln_BOp_pi2, - -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec); - rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); - rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi ); - rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 ); - - rvec_Scale( bo_ij->dBOp, - -(bo_ij->BO_s * Cln_BOp_s + - bo_ij->BO_pi * Cln_BOp_pi + - bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec ); - rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp ); - - bo_ij->BO_s -= bo_cut; - bo_ij->BO -= bo_cut; - bo_ji->BO_s -= bo_cut; - bo_ji->BO -= bo_cut; - - bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; - bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; - - return 1; -} - -/* ---------------------------------------------------------------------- */ - -void BOOMP( reax_system *system, control_params * /* control */, simulation_data * /* data */, - storage *workspace, reax_list **lists, output_controls * /* out_control */) -{ -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - double p_lp1 = system->reax_param.gp.l[15]; - double p_boc1 = system->reax_param.gp.l[0]; - double p_boc2 = system->reax_param.gp.l[1]; - reax_list *bonds = (*lists) + BONDS; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) -#endif - { - int i, j, pj, type_i, type_j; - int start_i, end_i, sym_index; - double val_i, Deltap_i, Deltap_boc_i; - double val_j, Deltap_j, Deltap_boc_j; - double f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5; - double exp_p1i, exp_p2i, exp_p1j, exp_p2j, explp1; - double temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji; - double Cf45_ij, Cf45_ji; //u_ij, u_ji - double A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - bond_order_data *bo_ij, *bo_ji; - - /* Calculate Deltaprime, Deltaprime_boc values */ -#if defined(_OPENMP) -#pragma omp for schedule(static) -#endif - for (i = 0; i < system->N; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[type_i]); - workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency; - workspace->Deltap_boc[i] = - workspace->total_bond_order[i] - sbp_i->valency_val; - - workspace->total_bond_order[i] = 0; - } - - // Wait till initialization complete -#if defined(_OPENMP) -#pragma omp barrier -#endif - - /* Corrected Bond Order calculations */ -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < system->N; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[type_i]); - val_i = sbp_i->valency; - Deltap_i = workspace->Deltap[i]; - Deltap_boc_i = workspace->Deltap_boc[i]; - start_i = Start_Index(i, bonds); - end_i = End_Index(i, bonds); - - for (pj = start_i; pj < end_i; ++pj) { - j = bonds->select.bond_list[pj].nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - bo_ij = &( bonds->select.bond_list[pj].bo_data ); - - if (i < j || workspace->bond_mark[j] > 3) { - twbp = &( system->reax_param.tbp[type_i][type_j] ); - - if (twbp->ovc < 0.001 && twbp->v13cor < 0.001) { - bo_ij->C1dbo = 1.000000; - bo_ij->C2dbo = 0.000000; - bo_ij->C3dbo = 0.000000; - - bo_ij->C1dbopi = 1.000000; - bo_ij->C2dbopi = 0.000000; - bo_ij->C3dbopi = 0.000000; - bo_ij->C4dbopi = 0.000000; - - bo_ij->C1dbopi2 = 1.000000; - bo_ij->C2dbopi2 = 0.000000; - bo_ij->C3dbopi2 = 0.000000; - bo_ij->C4dbopi2 = 0.000000; - - } - else { - val_j = system->reax_param.sbp[type_j].valency; - Deltap_j = workspace->Deltap[j]; - Deltap_boc_j = workspace->Deltap_boc[j]; - - /* on page 1 */ - if (twbp->ovc >= 0.001) { - /* Correction for overcoordination */ - exp_p1i = exp( -p_boc1 * Deltap_i ); - exp_p2i = exp( -p_boc2 * Deltap_i ); - exp_p1j = exp( -p_boc1 * Deltap_j ); - exp_p2j = exp( -p_boc2 * Deltap_j ); - - f2 = exp_p1i + exp_p1j; - f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) ); - f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) + - ( val_j + f2 )/( val_j + f2 + f3 ) ); - - /* Now come the derivates */ - /* Bond Order pages 5-7, derivative of f1 */ - temp = f2 + f3; - u1_ij = val_i + temp; - u1_ji = val_j + temp; - Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) + - 1.0 / SQR( u1_ji )); - Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) + - ( u1_ji - f3 ) / SQR( u1_ji )); - - Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij - - ((val_i+f2) / SQR(u1_ij)) * - ( -p_boc1 * exp_p1i + - exp_p2i / ( exp_p2i + exp_p2j ) ) + - -p_boc1 * exp_p1i / u1_ji - - ((val_j+f2) / SQR(u1_ji)) * - ( -p_boc1 * exp_p1i + - exp_p2i / ( exp_p2i + exp_p2j ) )); - - - Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j + - Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j ); - } - else { - /* No overcoordination correction! */ - f1 = 1.0; - Cf1_ij = Cf1_ji = 0.0; - } - - if (twbp->v13cor >= 0.001) { - /* Correction for 1-3 bond orders */ - exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) - - Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5); - exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) - - Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5); - - f4 = 1. / (1. + exp_f4); - f5 = 1. / (1. + exp_f5); - f4f5 = f4 * f5; - - /* Bond Order pages 8-9, derivative of f4 and f5 */ - Cf45_ij = -f4 * exp_f4; - Cf45_ji = -f5 * exp_f5; - } - else { - f4 = f5 = f4f5 = 1.0; - Cf45_ij = Cf45_ji = 0.0; - } - - /* Bond Order page 10, derivative of total bond order */ - A0_ij = f1 * f4f5; - A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO * - (Cf45_ij + Cf45_ji); - A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij; - A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji; - A3_ij = A2_ij + Cf1_ij / f1; - A3_ji = A2_ji + Cf1_ji / f1; - - /* find corrected bond orders and their derivative coef */ - bo_ij->BO = bo_ij->BO * A0_ij; - bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1; - bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1; - bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 ); - - bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij; - bo_ij->C2dbo = bo_ij->BO * A2_ij; - bo_ij->C3dbo = bo_ij->BO * A2_ji; - - bo_ij->C1dbopi = f1*f1*f4*f5; - bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij; - bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij; - bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji; - - bo_ij->C1dbopi2 = f1*f1*f4*f5; - bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij; - bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij; - bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji; - } - - /* neglect bonds that are < 1e-10 */ - if (bo_ij->BO < 1e-10) - bo_ij->BO = 0.0; - if (bo_ij->BO_s < 1e-10) - bo_ij->BO_s = 0.0; - if (bo_ij->BO_pi < 1e-10) - bo_ij->BO_pi = 0.0; - if (bo_ij->BO_pi2 < 1e-10) - bo_ij->BO_pi2 = 0.0; - - workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO - } - // else { - // /* We only need to update bond orders from bo_ji - // everything else is set in uncorrected_bo calculations */ - // sym_index = bonds->select.bond_list[pj].sym_index; - // bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data); - // bo_ij->BO = bo_ji->BO; - // bo_ij->BO_s = bo_ji->BO_s; - // bo_ij->BO_pi = bo_ji->BO_pi; - // bo_ij->BO_pi2 = bo_ji->BO_pi2; - - // workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO - // } - } - - } - - // Wait for bo_ij to be updated -#if defined(_OPENMP) -#pragma omp barrier -#endif - // Try to combine the following for-loop back into the for-loop above - /*-------------------------*/ -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < system->N; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - start_i = Start_Index(i, bonds); - end_i = End_Index(i, bonds); - - for (pj = start_i; pj < end_i; ++pj) { - j = bonds->select.bond_list[pj].nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - - if (i < j || workspace->bond_mark[j] > 3) { - // Computed in previous for-loop - } else { - /* We only need to update bond orders from bo_ji - everything else is set in uncorrected_bo calculations */ - sym_index = bonds->select.bond_list[pj].sym_index; - - bo_ij = &( bonds->select.bond_list[pj].bo_data ); - bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data); - bo_ij->BO = bo_ji->BO; - bo_ij->BO_s = bo_ji->BO_s; - bo_ij->BO_pi = bo_ji->BO_pi; - bo_ij->BO_pi2 = bo_ji->BO_pi2; - - workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO - } - } - - } - - /*-------------------------*/ - - // Need to wait for total_bond_order to be accumulated. -#if defined(_OPENMP) -#pragma omp barrier -#endif - /* Calculate some helper variables that are used at many places - throughout force calculations */ -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (j = 0; j < system->N; ++j) { - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - sbp_j = &(system->reax_param.sbp[ type_j ]); - - workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency; - workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e; - workspace->Delta_boc[j] = workspace->total_bond_order[j] - - sbp_j->valency_boc; - workspace->Delta_val[j] = workspace->total_bond_order[j] - - sbp_j->valency_val; - - workspace->vlpex[j] = workspace->Delta_e[j] - - 2.0 * (int)(workspace->Delta_e[j]/2.0); - explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j])); - workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0); - workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j]; - workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]); - workspace->dDelta_lp[j] = workspace->Clp[j]; - - if (sbp_j->mass > 21.0) { - workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency); - workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; - workspace->dDelta_lp_temp[j] = 0.; - } - else { - workspace->nlp_temp[j] = workspace->nlp[j]; - workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; - workspace->dDelta_lp_temp[j] = workspace->Clp[j]; - } - } - - } // parallel region - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEBOINDEX] += (endTimeBase-startTimeBase); - -#endif -} diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/USER-OMP/reaxc_bond_orders_omp.h deleted file mode 100644 index 46dc25148d..0000000000 --- a/src/USER-OMP/reaxc_bond_orders_omp.h +++ /dev/null @@ -1,44 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __BOND_ORDERS_OMP_H_ -#define __BOND_ORDERS_OMP_H_ - -#include "reaxc_types.h" - -void Add_dBond_to_ForcesOMP(reax_system *, int, int, storage *, reax_list **); -void Add_dBond_to_Forces_NPTOMP(reax_system *system, int, int, simulation_data *, storage *, - reax_list **); - -int BOp_OMP(storage *, reax_list *, double, int, int, far_neighbor_data *, single_body_parameters *, - single_body_parameters *, two_body_parameters *, int, double, double, double, double, - double, double, double); - -void BOOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *); -#endif diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp deleted file mode 100644 index f7f0cf5c4f..0000000000 --- a/src/USER-OMP/reaxc_bonds_omp.cpp +++ /dev/null @@ -1,189 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_bonds_omp.h" -#include -#include -#include "fix_omp.h" -#include "reaxc_defs.h" -#include "pair_reaxc_omp.h" -#include "reaxc_list.h" - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -void BondsOMP( reax_system *system, control_params * /* control */, - simulation_data *data, storage *workspace, reax_list **lists, - output_controls * /* out_control */) -{ -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - const int natoms = system->n; - reax_list *bonds = (*lists) + BONDS; - const double gp3 = system->reax_param.gp.l[3]; - const double gp4 = system->reax_param.gp.l[4]; - const double gp7 = system->reax_param.gp.l[7]; - const double gp10 = system->reax_param.gp.l[10]; - const int gp37 = (int) system->reax_param.gp.l[37]; - double total_Ebond = 0.0; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) reduction(+: total_Ebond) -#endif - { - int i, j, pj; - int start_i, end_i; - int type_i, type_j; - double ebond, pow_BOs_be2, exp_be12, CEbo; - double exphu, exphua1, exphub1, exphuov, hulpov, estriph; - double decobdbo, decobdboua, decobdboub; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - bond_order_data *bo_ij; - -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - long reductionOffset = (system->N * tid); - - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - - pair_reax_ptr->ev_setup_thr_proxy(system->pair_ptr->eflag_either, - system->pair_ptr->vflag_either, system->N, - system->pair_ptr->eatom, - system->pair_ptr->vatom, nullptr, thr); - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < natoms; ++i) { - start_i = Start_Index(i, bonds); - end_i = End_Index(i, bonds); - - for (pj = start_i; pj < end_i; ++pj) { - j = bonds->select.bond_list[pj].nbr; - - if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id) continue; - - if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) { - if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue; - if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && - system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue; - if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && - system->my_atoms[j].x[1] == system->my_atoms[i].x[1] && - system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue; - } - - /* set the pointers */ - type_i = system->my_atoms[i].type; - type_j = system->my_atoms[j].type; - sbp_i = &( system->reax_param.sbp[type_i] ); - sbp_j = &( system->reax_param.sbp[type_j] ); - twbp = &( system->reax_param.tbp[type_i][type_j] ); - bo_ij = &( bonds->select.bond_list[pj].bo_data ); - - /* calculate the constants */ - if (bo_ij->BO_s == 0.0) pow_BOs_be2 = 0.0; - else pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 ); - exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) ); - CEbo = -twbp->De_s * exp_be12 * - ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 ); - - /* calculate the Bond Energy */ - total_Ebond += ebond = - -twbp->De_s * bo_ij->BO_s * exp_be12 - -twbp->De_p * bo_ij->BO_pi - -twbp->De_pp * bo_ij->BO_pi2; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, - ebond, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - - /* calculate derivatives of Bond Orders */ - bo_ij->Cdbo += CEbo; - bo_ij->Cdbopi -= (CEbo + twbp->De_p); - bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp); - - /* Stabilisation terminal triple bond */ - if (bo_ij->BO >= 1.00) { - if (gp37 == 2 || - (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) || - (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990)) { - exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) ); - exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO)); - exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO)); - exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j])); - hulpov = 1.0 / (1.0 + 25.0 * exphuov); - - estriph = gp10 * exphu * hulpov * (exphua1 + exphub1); - total_Ebond += estriph; - - decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) * - ( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) ); - decobdboua = -gp10 * exphu * hulpov * - (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); - decobdboub = -gp10 * exphu * hulpov * - (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, - estriph, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - - bo_ij->Cdbo += decobdbo; - workspace->CdDelta[i] += decobdboua; - workspace->CdDeltaReduction[reductionOffset+j] += decobdboub; - } - } - } - } // for (i) - - } // omp - - data->my_en.e_bond += total_Ebond; - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEBONDSINDEX] += (endTimeBase-startTimeBase); -#endif - -} diff --git a/src/USER-OMP/reaxc_bonds_omp.h b/src/USER-OMP/reaxc_bonds_omp.h deleted file mode 100644 index 19403c35da..0000000000 --- a/src/USER-OMP/reaxc_bonds_omp.h +++ /dev/null @@ -1,37 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __BONDS_OMP_H_ -#define __BONDS_OMP_H_ - -#include "reaxc_types.h" - -void BondsOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *); - -#endif diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp deleted file mode 100644 index 05091c7eb5..0000000000 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ /dev/null @@ -1,623 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_forces_omp.h" - -#include "error.h" -#include "fix_omp.h" -#include "pair_reaxc_omp.h" -#include "reaxc_defs.h" - -#include "reaxc_bond_orders_omp.h" -#include "reaxc_bonds_omp.h" -#include "reaxc_hydrogen_bonds_omp.h" -#include "reaxc_list.h" -#include "reaxc_multi_body_omp.h" -#include "reaxc_nonbonded_omp.h" -#include "reaxc_torsion_angles_omp.h" -#include "reaxc_valence_angles_omp.h" -#include "reaxc_vector.h" - -#include -#include - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -// Functions defined in reaxc_forces.cpp -extern interaction_function Interaction_Functions[]; -extern double Compute_H(double, double, double*); -extern double Compute_tabH(double, int, int); -extern void Dummy_Interaction(reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*); - -/* ---------------------------------------------------------------------- */ - -void Init_Force_FunctionsOMP( control_params *control ) -{ - Interaction_Functions[0] = BOOMP; - Interaction_Functions[1] = BondsOMP; //Dummy_Interaction; - Interaction_Functions[2] = Atom_EnergyOMP; //Dummy_Interaction; - Interaction_Functions[3] = Valence_AnglesOMP; //Dummy_Interaction; - Interaction_Functions[4] = Torsion_AnglesOMP; //Dummy_Interaction; - if (control->hbond_cut > 0) - Interaction_Functions[5] = Hydrogen_BondsOMP; - else Interaction_Functions[5] = Dummy_Interaction; - Interaction_Functions[6] = Dummy_Interaction; //empty - Interaction_Functions[7] = Dummy_Interaction; //empty - Interaction_Functions[8] = Dummy_Interaction; //empty - Interaction_Functions[9] = Dummy_Interaction; //empty -} - -/* ---------------------------------------------------------------------- */ - -// Only difference with MPI-only version is inclusion of OMP_TIMING statements -void Compute_Bonded_ForcesOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - MPI_Comm /* comm */) -{ - int i; - -#ifdef OMP_TIMING - double startTimeBase, endTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - /* Implement all force calls as function pointers */ - for (i = 0; i < NUM_INTRS; i++) { - (Interaction_Functions[i])( system, control, data, workspace, - lists, out_control ); - } - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEBFINDEX] += (endTimeBase-startTimeBase); -#endif - -} - -// Only difference with MPI-only version is inclusion of OMP_TIMING statements -void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - MPI_Comm /* comm */) -{ - /* van der Waals and Coulomb interactions */ -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - if (control->tabulate == 0) - vdW_Coulomb_Energy_OMP( system, control, data, workspace, - lists, out_control ); - else - Tabulated_vdW_Coulomb_Energy_OMP( system, control, data, workspace, - lists, out_control ); - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTENBFINDEX] += (endTimeBase-startTimeBase); -#endif -} - -/* ---------------------------------------------------------------------- */ - -/* this version of Compute_Total_Force computes forces from - coefficients accumulated by all interaction functions. - Saves enormous time & space! */ -void Compute_Total_ForceOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, mpi_datatypes * /* mpi_data */) -{ -#ifdef OMP_TIMING - double startTimeBase,endTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - int natoms = system->N; - int nthreads = control->nthreads; - long totalReductionSize = (bigint)system->N * nthreads; - reax_list *bonds = (*lists) + BONDS; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) //LMP_DEFAULT_NONE -#endif - { - int i, j, k, pj, pk, start_j, end_j; -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - bond_order_data *bo_jk; - - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - - pair_reax_ptr->ev_setup_thr_proxy(0, 1, natoms, system->pair_ptr->eatom, - system->pair_ptr->vatom, nullptr, thr); - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < system->N; ++i) { - for (j = 0; j < nthreads; ++j) - workspace->CdDelta[i] += workspace->CdDeltaReduction[system->N*j+i]; - } - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) -#endif - for (j = 0; j < system->N; ++j) { - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - for (pk = start_j; pk < end_j; ++pk) { - bo_jk = &( bonds->select.bond_list[pk].bo_data ); - for (k = 0; k < nthreads; ++k) - bo_jk->Cdbo += bo_jk->CdboReduction[k]; - } - } - -// #pragma omp for schedule(guided) //(dynamic,50) -// for (i = 0; i < system->N; ++i) -// for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) -// if (i < bonds->select.bond_list[pj].nbr) { -// if (control->virial == 0) -// Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists ); -// else -// Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists ); -// } - - if (control->virial == 0) { - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) -#endif - for (i = 0; i < system->N; ++i) { - const int startj = Start_Index(i, bonds); - const int endj = End_Index(i, bonds); - for (pj = startj; pj < endj; ++pj) - if (i < bonds->select.bond_list[pj].nbr) - Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists ); - } - - } else { - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) -#endif - for (i = 0; i < system->N; ++i) { - const int startj = Start_Index(i, bonds); - const int endj = End_Index(i, bonds); - for (pj = startj; pj < endj; ++pj) - if (i < bonds->select.bond_list[pj].nbr) - Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists ); - } - - } // if (virial == 0) - - pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, 0, 1, thr); - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < system->N; ++i) { - for (j = 0; j < nthreads; ++j) - rvec_Add( workspace->f[i], workspace->forceReduction[system->N*j+i] ); - } - - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < totalReductionSize; i++) { - workspace->forceReduction[i][0] = 0; - workspace->forceReduction[i][1] = 0; - workspace->forceReduction[i][2] = 0; - workspace->CdDeltaReduction[i] = 0; - } - } // parallel region - - if (control->virial) - for (int i=0; i < nthreads; ++i) { - rvec_Add(data->my_ext_press, workspace->my_ext_pressReduction[i]); - workspace->my_ext_pressReduction[i][0] = 0; - workspace->my_ext_pressReduction[i][1] = 0; - workspace->my_ext_pressReduction[i][2] = 0; - } - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTETFINDEX] += (endTimeBase-startTimeBase); -#endif -} - -/* ---------------------------------------------------------------------- */ - -void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list **lists, - int step, int n, int N, int numH, MPI_Comm /*comm*/) -{ - int comp, Hindex; - reax_list *bonds, *hbonds; - double saferzone = system->saferzone; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) private(comp,Hindex) -#endif - { - - /* bond list */ - if (N > 0) { - bonds = *lists + BONDS; - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (int i = 0; i < N; ++i) { - system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); - - if (i < N-1) - comp = Start_Index(i+1, bonds); - else comp = bonds->num_intrs; - - if (End_Index(i, bonds) > comp) { - char errmsg[256]; - snprintf(errmsg, 256, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", - step, i, End_Index(i,bonds), comp ); - system->error_ptr->one(FLERR,errmsg); - } - } - } - - - /* hbonds list */ - if (numH > 0) { - hbonds = *lists + HBONDS; - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (int i = 0; i < n; ++i) { - Hindex = system->my_atoms[i].Hindex; - if (Hindex > -1) { - system->my_atoms[i].num_hbonds = - (int)(MAX(Num_Entries(Hindex,hbonds)*saferzone,system->minhbonds)); - - if (Hindex < numH-1) - comp = Start_Index(Hindex+1, hbonds); - else comp = hbonds->num_intrs; - - if (End_Index(Hindex, hbonds) > comp) { - char errmsg[256]; - snprintf(errmsg, 256, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", - step, Hindex, End_Index(Hindex,hbonds), comp ); - system->error_ptr->one(FLERR, errmsg); - } - } - } - } - - } // omp parallel -} - - -void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /* out_control */, - MPI_Comm comm) { -#ifdef OMP_TIMING - double startTimeBase, endTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - int j, pj; - int start_i, end_i; - int type_i, type_j; - int ihb, jhb, ihb_top, jhb_top; - double cutoff; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - far_neighbor_data *nbr_pj; - reax_atom *atom_i, *atom_j; - reax_list *far_nbrs = *lists + FAR_NBRS; - reax_list *bonds = *lists + BONDS; - reax_list *hbonds = *lists + HBONDS; - int num_bonds = 0; - int num_hbonds = 0; - int btop_i = 0; - - // We will use CdDeltaReduction as a temporary (double) buffer to accumulate total_bond_order - // This is safe because CdDeltaReduction is currently zeroed and its accumulation doesn't start until BondsOMP() - double * tmp_bond_order = workspace->CdDeltaReduction; - - // We do the same with forceReduction as a temporary (rvec) buffer to accumulate dDeltap_self - // This is safe because forceReduction is currently zeroed and its accumulation does start until Hydrogen_BondsOMP() - rvec * tmp_ddelta = workspace->forceReduction; - - /* uncorrected bond orders */ - cutoff = control->bond_cut; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) \ - private(atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \ - atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp) -#endif - { - - int nthreads = control->nthreads; -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - long reductionOffset = (bigint)system->N * tid; - long totalReductionSize = (bigint)system->N * nthreads; - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) reduction(+:num_bonds) -#endif - for (int i = 0; i < system->N; ++i) { - atom_i = &(system->my_atoms[i]); - type_i = atom_i->type; - sbp_i = &(system->reax_param.sbp[type_i]); - - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); - if (nbr_pj->d <= cutoff) { - int j = nbr_pj->nbr; - atom_j = &(system->my_atoms[j]); - type_j = atom_j->type; - sbp_j = &(system->reax_param.sbp[type_j]); - twbp = &(system->reax_param.tbp[type_i][type_j]); - -// #pragma omp critical -// { -// btop_i = End_Index(i, bonds); -// if (BOp(workspace, bonds, control->bo_cut, i, btop_i, nbr_pj, sbp_i, sbp_j, twbp)) { -// num_bonds++; -// btop_i++; -// Set_End_Index(i, btop_i, bonds); -// } - -// } - - // Trying to minimize time spent in critical section by moving initial part of BOp() - // outside of critical section. - - // Start top portion of BOp() - double C12, C34, C56; - double BO, BO_s, BO_pi, BO_pi2; - double bo_cut = control->bo_cut; - - if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { - C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 ); - BO_s = (1.0 + bo_cut) * exp( C12 ); - } - else BO_s = C12 = 0.0; - - if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { - C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 ); - BO_pi = exp( C34 ); - } - else BO_pi = C34 = 0.0; - - if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { - C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 ); - BO_pi2= exp( C56 ); - } - else BO_pi2 = C56 = 0.0; - - /* Initially BO values are the uncorrected ones, page 1 */ - BO = BO_s + BO_pi + BO_pi2; - // End top portion of BOp() - - if (BO >= bo_cut) { - int btop_j; - - // Update indices in critical section -#if defined(_OPENMP) -#pragma omp critical -#endif - { - btop_i = End_Index( i, bonds ); - btop_j = End_Index( j, bonds ); - Set_End_Index( j, btop_j+1, bonds ); - Set_End_Index( i, btop_i+1, bonds ); - } // omp critical - - // Finish remaining BOp() work - BOp_OMP(workspace, bonds, bo_cut, - i , btop_i, nbr_pj, sbp_i, sbp_j, twbp, btop_j, - C12, C34, C56, BO, BO_s, BO_pi, BO_pi2); - - bond_data * ibond = &(bonds->select.bond_list[btop_i]); - bond_order_data * bo_ij = &(ibond->bo_data); - - bond_data * jbond = &(bonds->select.bond_list[btop_j]); - bond_order_data * bo_ji = &(jbond->bo_data); - - workspace->total_bond_order[i] += bo_ij->BO; - tmp_bond_order[reductionOffset + j] += bo_ji->BO; - - rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp); - rvec_Add(tmp_ddelta[reductionOffset + j], bo_ji->dBOp); - - btop_i++; - num_bonds++; - } // if (BO>=bo_cut) - - } // if (cutoff) - - } // for (pj) - } // for (i) - - // Need to wait for all indices and tmp arrays accumulated. -#if defined(_OPENMP) -#pragma omp barrier -#endif - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) -#endif - for (int i=0; iN; i++) - for (int t=0; tN + i; - workspace->dDeltap_self[i][0] += tmp_ddelta[indx][0]; - workspace->dDeltap_self[i][1] += tmp_ddelta[indx][1]; - workspace->dDeltap_self[i][2] += tmp_ddelta[indx][2]; - workspace->total_bond_order[i] += tmp_bond_order[indx]; - } - - /* hydrogen bond list */ - if (control->hbond_cut > 0) { - cutoff = control->hbond_cut; - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) reduction(+ : num_hbonds) -#endif - for (int i = 0; i < system->n; ++i) { - atom_i = &(system->my_atoms[i]); - type_i = atom_i->type; - sbp_i = &(system->reax_param.sbp[type_i]); - ihb = sbp_i->p_hbond; - -#if defined(_OPENMP) -#pragma omp critical -#endif - { - - if (ihb == 1 || ihb == 2) { - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); - j = nbr_pj->nbr; - atom_j = &(system->my_atoms[j]); - type_j = atom_j->type; - if (type_j < 0) continue; - sbp_j = &(system->reax_param.sbp[type_j]); - jhb = sbp_j->p_hbond; - - if (nbr_pj->d <= control->hbond_cut) { - int iflag = 0; - int jflag = 0; - - if (ihb==1 && jhb==2) iflag = 1; - else if (jn && ihb == 2 && jhb == 1) jflag = 1; - - if (iflag || jflag) { - if (iflag) { - ihb_top = End_Index(atom_i->Hindex, hbonds); - Set_End_Index(atom_i->Hindex, ihb_top+1, hbonds); - } else if (jflag) { - jhb_top = End_Index(atom_j->Hindex, hbonds); - Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds); - } - - if (iflag) { - hbonds->select.hbond_list[ihb_top].nbr = j; - hbonds->select.hbond_list[ihb_top].scl = 1; - hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; - } else if (jflag) { - hbonds->select.hbond_list[jhb_top].nbr = i; - hbonds->select.hbond_list[jhb_top].scl = -1; - hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; - } - - num_hbonds++; - } // if (iflag || jflag) - - } - } - } - - } // omp critical - } - - } // if (control->hbond > 0) - - // Zero buffers for others to use as intended. -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (int i=0; irealloc.num_bonds = num_bonds; - workspace->realloc.num_hbonds = num_hbonds; - - Validate_ListsOMP( system, workspace, lists, data->step, - system->n, system->N, system->numH, comm ); - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEIFINDEX] += (endTimeBase-startTimeBase); -#endif -} - -/* ---------------------------------------------------------------------- */ - -void Compute_ForcesOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - mpi_datatypes *mpi_data ) -{ - MPI_Comm comm = mpi_data->world; - - // Init Forces - Init_Forces_noQEq_OMP( system, control, data, workspace, - lists, out_control, comm ); - - // Bonded Interactions - Compute_Bonded_ForcesOMP( system, control, data, workspace, - lists, out_control, mpi_data->world ); - - // Nonbonded Interactions - Compute_NonBonded_ForcesOMP( system, control, data, workspace, - lists, out_control, mpi_data->world ); - - // Total Force - Compute_Total_ForceOMP( system, control, data, workspace, lists, mpi_data ); -} diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/USER-OMP/reaxc_forces_omp.h deleted file mode 100644 index c42aed1282..0000000000 --- a/src/USER-OMP/reaxc_forces_omp.h +++ /dev/null @@ -1,37 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __FORCES_OMP_H_ -#define __FORCES_OMP_H_ - -#include "reaxc_types.h" - -void Init_Force_FunctionsOMP(control_params *); -void Compute_ForcesOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *, mpi_datatypes *); -#endif diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp deleted file mode 100644 index 7701063ebf..0000000000 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ /dev/null @@ -1,251 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_hydrogen_bonds_omp.h" - -#include "fix_omp.h" -#include "pair_reaxc_omp.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" -#include "reaxc_valence_angles.h" // To access Calculate_Theta() -#include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() -#include "reaxc_vector.h" - -#include -#include - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -void Hydrogen_BondsOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /* out_control */) -{ -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - const int nthreads = control->nthreads; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) //LMP_DEFAULT_NONE -#endif - { - int i, j, k, pi, pk; - int type_i, type_j, type_k; - int start_j, end_j, hb_start_j, hb_end_j; - int hblist[MAX_BONDS]; - int itr, top; - int num_hb_intrs = 0; - ivec rel_jk; - double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; - double e_hb, e_hb_thr = 0.0, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3; - rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk; - rvec dvec_jk, force, ext_press; - hbond_parameters *hbp; - bond_order_data *bo_ij; - bond_data *pbond_ij; - far_neighbor_data *nbr_jk; - reax_list *bonds, *hbonds; - bond_data *bond_list; - hbond_data *hbond_list; - - // tally variables - double fi_tmp[3], fk_tmp[3], delij[3], delkj[3]; - - bonds = (*lists) + BONDS; - bond_list = bonds->select.bond_list; - hbonds = (*lists) + HBONDS; - hbond_list = hbonds->select.hbond_list; - - int natoms = system->n; -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - const int idelta = 1 + natoms/nthreads; - int ifrom = tid*idelta; - int ito = ((ifrom + idelta) > natoms) ? natoms : ifrom + idelta; - - long reductionOffset = (system->N * tid); - - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - - /* loops below discover the Hydrogen bonds between i-j-k triplets. - here j is H atom and there has to be some bond between i and j. - Hydrogen bond is between j and k. - so in this function i->X, j->H, k->Z when we map - variables onto the ones in the handout.*/ - // for (j = 0; j < system->n; ++j) - for (j = ifrom; j < ito; ++j) { - /* j has to be of type H */ - if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) { - /*set j's variables */ - type_j = system->my_atoms[j].type; - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds ); - hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds ); - if (type_j < 0) continue; - - top = 0; - for (pi = start_j; pi < end_j; ++pi) { - pbond_ij = &( bond_list[pi] ); - i = pbond_ij->nbr; - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - bo_ij = &(pbond_ij->bo_data); - - if ( system->reax_param.sbp[type_i].p_hbond == 2 && - bo_ij->BO >= HB_THRESHOLD ) - hblist[top++] = pi; - } - - for (pk = hb_start_j; pk < hb_end_j; ++pk) { - /* set k's varibles */ - k = hbond_list[pk].nbr; - type_k = system->my_atoms[k].type; - if (type_k < 0) continue; - nbr_jk = hbond_list[pk].ptr; - r_jk = nbr_jk->d; - rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec ); - - for (itr = 0; itr < top; ++itr) { - pi = hblist[itr]; - pbond_ij = &( bonds->select.bond_list[pi] ); - i = pbond_ij->nbr; - - if (system->my_atoms[i].orig_id != system->my_atoms[k].orig_id) { - bo_ij = &(pbond_ij->bo_data); - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]); - ++num_hb_intrs; - - Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, - &theta, &cos_theta ); - /* the derivative of cos(theta) */ - Calculate_dCos_ThetaOMP( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, - &dcos_theta_di, &dcos_theta_dj, - &dcos_theta_dk ); - - /* hydrogen bond energy*/ - sin_theta2 = sin( theta/2.0 ); - sin_xhz4 = SQR(sin_theta2); - sin_xhz4 *= sin_xhz4; - cos_xhz1 = ( 1.0 - cos_theta ); - exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO ); - exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk + - r_jk / hbp->r0_hb - 2.0 ) ); - - e_hb_thr += e_hb = hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4; - - CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4; - CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1; - CEhb3 = -hbp->p_hb3 * - (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb; - - /* hydrogen bond forces */ - bo_ij->Cdbo += CEhb1; // dbo term - - if (control->virial == 0) { - // dcos terms - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], +CEhb2, dcos_theta_di ); - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj ); - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb2, dcos_theta_dk ); - // dr terms - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], -CEhb3/r_jk, dvec_jk ); - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb3/r_jk, dvec_jk ); - } - else { - /* for pressure coupling, terms that are not related to bond order - derivatives are added directly into pressure vector/tensor */ - rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms - rvec_Add(workspace->forceReduction[reductionOffset+i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press ); - - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj ); - - ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box ); - rvec_Scale( force, +CEhb2, dcos_theta_dk ); - rvec_Add(workspace->forceReduction[reductionOffset+k], force ); - rvec_iMultiply( ext_press, rel_jk, force ); - rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press ); - // dr terms - rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j],-CEhb3/r_jk, dvec_jk ); - - rvec_Scale( force, CEhb3/r_jk, dvec_jk ); - rvec_Add(workspace->forceReduction[reductionOffset+k], force ); - rvec_iMultiply( ext_press, rel_jk, force ); - rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press ); - } - - /* tally into per-atom virials */ - if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { - rvec_ScaledSum( delij, 1., system->my_atoms[j].x, - -1., system->my_atoms[i].x ); - rvec_ScaledSum( delkj, 1., system->my_atoms[j].x, - -1., system->my_atoms[k].x ); - - rvec_Scale(fi_tmp, CEhb2, dcos_theta_di); - rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk); - rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk); - - pair_reax_ptr->ev_tally3_thr_proxy(system->pair_ptr,i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj,thr); - } - } - } - } - - } - } -#if defined(_OPENMP) -#pragma omp critical -#endif - { - data->my_en.e_hb += e_hb_thr; - } -} - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEHBONDSINDEX] += (endTimeBase-startTimeBase); -#endif -} diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.h b/src/USER-OMP/reaxc_hydrogen_bonds_omp.h deleted file mode 100644 index 3703b09058..0000000000 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.h +++ /dev/null @@ -1,37 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __HBONDS_OMP_H_ -#define __HBONDS_OMP_H_ - -#include "reaxc_types.h" - -void Hydrogen_BondsOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *); - -#endif diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp deleted file mode 100644 index 226bfaf53c..0000000000 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ /dev/null @@ -1,159 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_init_md_omp.h" - -#include "reaxc_defs.h" -#include "reaxc_forces.h" -#include "reaxc_forces_omp.h" -#include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_lookup.h" -#include "reaxc_tool_box.h" -#include "error.h" -#include "fmt/format.h" - -#include - -// Functions defined in reaxc_init_md.cpp -extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); -extern int Init_System(reax_system*, control_params*, char*); -extern int Init_Simulation_Data(reax_system*, control_params*, simulation_data*, char*); -extern int Init_Workspace(reax_system*, control_params*, storage*, char*); - -/* ---------------------------------------------------------------------- */ - -int Init_ListsOMP(reax_system *system, control_params *control, - simulation_data * /* data */, storage * /* workspace */, - reax_list **lists, mpi_datatypes * /* mpi_data */, char * /* msg */) -{ - int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; - int *hb_top, *bond_top; - - int mincap = system->mincap; - double safezone = system->safezone; - double saferzone = system->saferzone; - LAMMPS_NS::Error *error = system->error_ptr; - - bond_top = (int*) calloc(system->total_cap, sizeof(int)); - hb_top = (int*) calloc(system->local_cap, sizeof(int)); - Estimate_Storages(system, control, lists, - &Htop, hb_top, bond_top, &num_3body); - - if (control->hbond_cut > 0) { - /* init H indexes */ - total_hbonds = 0; - for (i = 0; i < system->n; ++i) { - system->my_atoms[i].num_hbonds = hb_top[i]; - total_hbonds += hb_top[i]; - } - total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds)); - - if (!Make_List(system->Hcap, total_hbonds, TYP_HBOND, - *lists+HBONDS)) { - error->one(FLERR, "Not enough space for hbonds list. Terminating!"); - } - } - - total_bonds = 0; - for (i = 0; i < system->N; ++i) { - system->my_atoms[i].num_bonds = bond_top[i]; - total_bonds += bond_top[i]; - } - bond_cap = (int)(MAX(total_bonds*safezone, mincap*MIN_BONDS)); - - if (!Make_List(system->total_cap, bond_cap, TYP_BOND, - *lists+BONDS)) { - error->one(FLERR, "Not enough space for bonds list. Terminating!\n"); - } - - int nthreads = control->nthreads; - reax_list *bonds = (*lists)+BONDS; - - for (i = 0; i < bonds->num_intrs; ++i) - bonds->select.bond_list[i].bo_data.CdboReduction = - (double*) smalloc(error, sizeof(double)*nthreads, "CdboReduction"); - - /* 3bodies list */ - cap_3body = (int)(MAX(num_3body*safezone, MIN_3BODIES)); - if (!Make_List(bond_cap, cap_3body, TYP_THREE_BODY, - *lists+THREE_BODIES)) { - - error->one(FLERR, "Problem in initializing angles list. Terminating!"); - } - - free(hb_top); - free(bond_top); - - return SUCCESS; -} - -/* ---------------------------------------------------------------------- */ - -// The only difference with the MPI-only function is calls to Init_ListsOMP and Init_Force_FunctionsOMP(). -void InitializeOMP(reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - mpi_datatypes *mpi_data, MPI_Comm comm) -{ - char msg[MAX_STR]; - LAMMPS_NS::Error *error = system->error_ptr; - - if (Init_MPI_Datatypes(system,workspace,mpi_data,comm,msg) == FAILURE) - error->one(FLERR,"init_mpi_datatypes: could not create datatypes. " - "Mpi_data could not be initialized! Terminating."); - - if (Init_System(system,control,msg) == FAILURE) - error->one(FLERR,"Error on: {}. System could not be " - "initialized! Terminating.",msg); - - if (Init_Simulation_Data(system,control,data,msg) == FAILURE) - error->one(FLERR,"Error on: {}. Sim_data could not be " - "initialized! Terminating.",msg); - - if (Init_Workspace(system,control,workspace,msg) == FAILURE) - error->one(FLERR,"init_workspace: not enough memory. " - "Workspace could not be initialized. Terminating."); - - if (Init_ListsOMP(system,control,data,workspace,lists,mpi_data,msg) == FAILURE) - error->one(FLERR,"Error on: {}. System could not be " - "initialized. Terminating.",msg); - - if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) - error->one(FLERR,"Error on: {}. Could not open output files! " - "Terminating.",msg); - - if (control->tabulate) - if (Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE) - error->one(FLERR,"Error on: {}. Could not create lookup " - "table. Terminating.",msg); - - Init_Force_FunctionsOMP(control); -} - diff --git a/src/USER-OMP/reaxc_init_md_omp.h b/src/USER-OMP/reaxc_init_md_omp.h deleted file mode 100644 index c4292ae4c0..0000000000 --- a/src/USER-OMP/reaxc_init_md_omp.h +++ /dev/null @@ -1,38 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __INIT_MD_OMP_H_ -#define __INIT_MD_OMP_H_ - -#include "reaxc_types.h" - -#include - -void InitializeOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *, mpi_datatypes *, MPI_Comm); -#endif diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp deleted file mode 100644 index d42a203044..0000000000 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ /dev/null @@ -1,292 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_multi_body_omp.h" - -#include "fix_omp.h" -#include "pair_reaxc_omp.h" - -#include "reaxc_defs.h" -#include "reaxc_list.h" - -#include -#include - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -void Atom_EnergyOMP( reax_system *system, control_params * /* control */, - simulation_data *data, storage *workspace, reax_list **lists, - output_controls * /* out_control */) -{ -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - /* Initialize parameters */ - const double p_lp3 = system->reax_param.gp.l[5]; - const double p_ovun3 = system->reax_param.gp.l[32]; - const double p_ovun4 = system->reax_param.gp.l[31]; - const double p_ovun6 = system->reax_param.gp.l[6]; - const double p_ovun7 = system->reax_param.gp.l[8]; - const double p_ovun8 = system->reax_param.gp.l[9]; - - reax_list *bonds = (*lists) + BONDS; - - double total_Elp = 0.0; - double total_Eun = 0.0; - double total_Eov = 0.0; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) reduction(+:total_Elp, total_Eun, total_Eov) -#endif -{ - int i, j, pj, type_i, type_j; - double Delta_lpcorr, dfvl; - double e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi; - double e_lph, Di, vov3, deahu2dbo, deahu2dsbo; - double e_ov, CEover1, CEover2, CEover3, CEover4; - double exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2; - double exp_ovun2n, exp_ovun6, exp_ovun8; - double inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8; - double e_un, CEunder1, CEunder2, CEunder3, CEunder4; - double eng_tmp; - double p_lp2, p_ovun2, p_ovun5; - int numbonds; - - single_body_parameters *sbp_i; - two_body_parameters *twbp; - bond_data *pbond; - bond_order_data *bo_ij; - -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - - long reductionOffset = (system->N * tid); - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for ( i = 0; i < system->n; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[ type_i ]); - - /* lone-pair Energy */ - p_lp2 = sbp_i->p_lp2; - expvd2 = exp( -75 * workspace->Delta_lp[i] ); - inv_expvd2 = 1. / (1. + expvd2 ); - - numbonds = 0; - e_lp = 0.0; - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) - numbonds ++; - - /* calculate the energy */ - if (numbonds > 0) - total_Elp += e_lp = - p_lp2 * workspace->Delta_lp[i] * inv_expvd2; - - dElp = p_lp2 * inv_expvd2 + - 75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2); - CElp = dElp * workspace->dDelta_lp[i]; - - if (numbonds > 0) workspace->CdDelta[i] += CElp; // lp - 1st term - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, i, system->n, 1, - e_lp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - - /* correction for C2 */ - if (p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C")) - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { - j = bonds->select.bond_list[pj].nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - - if (!strcmp( system->reax_param.sbp[type_j].name, "C" )) { - twbp = &( system->reax_param.tbp[type_i][type_j]); - bo_ij = &( bonds->select.bond_list[pj].bo_data ); - Di = workspace->Delta[i]; - vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.); - - if (vov3 > 3.) { - total_Elp += e_lph = p_lp3 * SQR(vov3-3.0); - - deahu2dbo = 2.*p_lp3*(vov3 - 3.); - deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.)); - - bo_ij->Cdbo += deahu2dbo; - workspace->CdDelta[i] += deahu2dsbo; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, system->n, 1, - e_lph, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - } - } - } - } -#if defined(_OPENMP) -#pragma omp barrier -#pragma omp for schedule(guided) -#endif - for (i = 0; i < system->n; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[ type_i ]); - - /* over-coordination energy */ - if (sbp_i->mass > 21.0) - dfvl = 0.0; - else dfvl = 1.0; // only for 1st-row elements - - p_ovun2 = sbp_i->p_ovun2; - sum_ovun1 = sum_ovun2 = 0; - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { - j = bonds->select.bond_list[pj].nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - bo_ij = &(bonds->select.bond_list[pj].bo_data); - twbp = &(system->reax_param.tbp[ type_i ][ type_j ]); - - sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO; - sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])* - ( bo_ij->BO_pi + bo_ij->BO_pi2 ); - } - - exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 ); - inv_exp_ovun1 = 1.0 / (1 + exp_ovun1); - Delta_lpcorr = workspace->Delta[i] - - (dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1; - - exp_ovun2 = exp( p_ovun2 * Delta_lpcorr ); - inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2); - - DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8); - CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2; - - total_Eov += e_ov = sum_ovun1 * CEover1; - - CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 * - (1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 )); - - CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 ); - - CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) * - p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1); - - - /* under-coordination potential */ - p_ovun2 = sbp_i->p_ovun2; - p_ovun5 = sbp_i->p_ovun5; - - exp_ovun2n = 1.0 / exp_ovun2; - exp_ovun6 = exp( p_ovun6 * Delta_lpcorr ); - exp_ovun8 = p_ovun7 * exp(p_ovun8 * sum_ovun2); - inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n); - inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8); - - numbonds = 0; - e_un = 0.0; - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) - numbonds ++; - - if (numbonds > 0) total_Eun += e_un = - -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8; - - CEunder1 = inv_exp_ovun2n * - ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 + - p_ovun2 * e_un * exp_ovun2n ); - CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8; - CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1); - CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) * - p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) { - eng_tmp = e_ov; - if (numbonds > 0) eng_tmp+= e_un; - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, i, system->n, 1, - eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - } - - /* forces */ - workspace->CdDelta[i] += CEover3; // OvCoor - 2nd term - if (numbonds > 0) workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term - - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { - pbond = &(bonds->select.bond_list[pj]); - j = pbond->nbr; - bo_ij = &(pbond->bo_data); - twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ] - [system->my_atoms[pbond->nbr].type]); - - bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s; // OvCoor-1st - workspace->CdDeltaReduction[reductionOffset+j] += - CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a - - bo_ij->Cdbopi += CEover4 * - (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b - bo_ij->Cdbopi2 += CEover4 * - (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b - - workspace->CdDeltaReduction[reductionOffset+j] += - CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a - - bo_ij->Cdbopi += CEunder4 * - (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b - bo_ij->Cdbopi2 += CEunder4 * - (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b - } - } - } - - data->my_en.e_lp += total_Elp; - data->my_en.e_ov += total_Eov; - data->my_en.e_un += total_Eun; - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEATOMENERGYINDEX] += (endTimeBase-startTimeBase); -#endif -} diff --git a/src/USER-OMP/reaxc_multi_body_omp.h b/src/USER-OMP/reaxc_multi_body_omp.h deleted file mode 100644 index c5e7de6b57..0000000000 --- a/src/USER-OMP/reaxc_multi_body_omp.h +++ /dev/null @@ -1,37 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __MULTI_BODY_OMP_H_ -#define __MULTI_BODY_OMP_H_ - -#include "reaxc_types.h" - -void Atom_EnergyOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *); - -#endif diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp deleted file mode 100644 index 32f4d5f8b4..0000000000 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ /dev/null @@ -1,390 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "pair_reaxc_omp.h" - -#include "reaxc_defs.h" -#include "reaxc_types.h" - -#include "reaxc_nonbonded.h" -#include "reaxc_nonbonded_omp.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -#include - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /* out_control */ ) -{ - int natoms = system->n; - reax_list *far_nbrs = (*lists) + FAR_NBRS; - double p_vdW1 = system->reax_param.gp.l[28]; - double p_vdW1i = 1.0 / p_vdW1; - double total_EvdW = 0.; - double total_Eele = 0.; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) reduction(+: total_EvdW, total_Eele) -#endif - { -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - int i, j, pj; - int start_i, end_i, orig_i, orig_j, flag; - double powr_vdW1, powgi_vdW1; - double tmp, r_ij, fn13, exp1, exp2; - double Tap, dTap, dfn13, CEvd, CEclmb, de_core; - double dr3gamij_1, dr3gamij_3; - double e_ele, e_vdW, e_core; - const double SMALL = 0.0001; - double e_lg, de_lg, r_ij5, r_ij6, re6; - rvec temp, ext_press; - two_body_parameters *twbp; - far_neighbor_data *nbr_pj; - - // Tallying variables: - double pe_vdw, f_tmp, delij[3]; - - long reductionOffset = (system->N * tid); - - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - - e_core = 0; - e_vdW = 0; - e_lg = 0; - de_lg = 0.0; - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < natoms; ++i) { - if (system->my_atoms[i].type < 0) continue; - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - orig_i = system->my_atoms[i].orig_id; - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); - j = nbr_pj->nbr; - orig_j = system->my_atoms[j].orig_id; - - flag = 0; - if (nbr_pj->d <= control->nonb_cut) { - if (j < natoms) flag = 1; - else if (orig_i < orig_j) flag = 1; - else if (orig_i == orig_j) { - if (nbr_pj->dvec[2] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[2]) < SMALL) { - if (nbr_pj->dvec[1] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) - flag = 1; - } - } - } - - if (flag) { - - r_ij = nbr_pj->d; - twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ] - [ system->my_atoms[j].type ]); - - /* Calculate Taper and its derivative */ - // Tap = nbr_pj->Tap; -- precomputed during compte_H - Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; - Tap = Tap * r_ij + workspace->Tap[5]; - Tap = Tap * r_ij + workspace->Tap[4]; - Tap = Tap * r_ij + workspace->Tap[3]; - Tap = Tap * r_ij + workspace->Tap[2]; - Tap = Tap * r_ij + workspace->Tap[1]; - Tap = Tap * r_ij + workspace->Tap[0]; - - dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; - dTap = dTap * r_ij + 5*workspace->Tap[5]; - dTap = dTap * r_ij + 4*workspace->Tap[4]; - dTap = dTap * r_ij + 3*workspace->Tap[3]; - dTap = dTap * r_ij + 2*workspace->Tap[2]; - dTap += workspace->Tap[1]/r_ij; - - /*vdWaals Calculations*/ - if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) - { // shielding - powr_vdW1 = pow(r_ij, p_vdW1); - powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1); - - fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i ); - exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - - e_vdW = twbp->D * (exp1 - 2.0 * exp2); - total_EvdW += Tap * e_vdW; - - dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * - pow(r_ij, p_vdW1 - 2.0); - - CEvd = dTap * e_vdW - - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; - } - else { // no shielding - exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - - e_vdW = twbp->D * (exp1 - 2.0 * exp2); - total_EvdW += Tap * e_vdW; - - CEvd = dTap * e_vdW - - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; - } - - if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) - { // innner wall - e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); - total_EvdW += Tap * e_core; - - de_core = -(twbp->acore/twbp->rcore) * e_core; - CEvd += dTap * e_core + Tap * de_core / r_ij; - - // lg correction, only if lgvdw is yes - if (control->lgflag) { - r_ij5 = pow( r_ij, 5.0 ); - r_ij6 = pow( r_ij, 6.0 ); - re6 = pow( twbp->lgre, 6.0 ); - - e_lg = -(twbp->lgcij/( r_ij6 + re6 )); - total_EvdW += Tap * e_lg; - - de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ; - CEvd += dTap * e_lg + Tap * de_lg / r_ij; - } - - } - - /*Coulomb Calculations*/ - dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma ); - dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); - - tmp = Tap / dr3gamij_3; - total_Eele += e_ele = - C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp; - - CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * - ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { - pe_vdw = Tap * (e_vdW + e_core + e_lg); - rvec_ScaledSum( delij, 1., system->my_atoms[i].x, - -1., system->my_atoms[j].x ); - f_tmp = -(CEvd + CEclmb); - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, - 1, pe_vdw, e_ele, f_tmp, - delij[0], delij[1], delij[2], thr); - } - - if (control->virial == 0) { - rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+j], - +(CEvd + CEclmb), nbr_pj->dvec ); - } else { /* NPT, iNPT or sNPT */ - /* for pressure coupling, terms not related to bond order - derivatives are added directly into pressure vector/tensor */ - - rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); - rvec_ScaledAdd( workspace->f[reductionOffset+i], -1., temp ); - rvec_Add( workspace->forceReduction[reductionOffset+j], temp); - - rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); - - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - } - } - } - } - - pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either, - system->pair_ptr->vflag_either, thr); - } // parallel region - - data->my_en.e_vdW = total_EvdW; - data->my_en.e_ele = total_Eele; - - Compute_Polarization_Energy( system, data ); -} - -/* ---------------------------------------------------------------------- */ - -void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, - output_controls * /* out_control */) { - - double SMALL = 0.0001; - int natoms = system->n; - reax_list *far_nbrs = (*lists) + FAR_NBRS; - double total_EvdW = 0.; - double total_Eele = 0.; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) reduction(+:total_EvdW, total_Eele) -#endif - { - int i, j, pj, r; - int type_i, type_j, tmin, tmax; - int start_i, end_i, orig_i, orig_j, flag; - double r_ij, base, dif; - double e_vdW, e_ele; - double CEvd, CEclmb; - double f_tmp, delij[3]; - rvec temp, ext_press; - far_neighbor_data *nbr_pj; - LR_lookup_table *t; -#if defined(_OPENMP) - int tid = omp_get_thread_num(); - #else - int tid = 0; -#endif - long froffset = (system->N * tid); - LR_lookup_table ** & LR = system->LR; - - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - -#if defined(_OPENMP) -#pragma omp for schedule(guided) -#endif - for (i = 0; i < natoms; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - start_i = Start_Index(i,far_nbrs); - end_i = End_Index(i,far_nbrs); - orig_i = system->my_atoms[i].orig_id; - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); - j = nbr_pj->nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - orig_j = system->my_atoms[j].orig_id; - - flag = 0; - if (nbr_pj->d <= control->nonb_cut) { - if (j < natoms) flag = 1; - else if (orig_i < orig_j) flag = 1; - else if (orig_i == orig_j) { - if (nbr_pj->dvec[2] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[2]) < SMALL) { - if (nbr_pj->dvec[1] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) - flag = 1; - } - } - - } - - if (flag) { - - r_ij = nbr_pj->d; - tmin = MIN( type_i, type_j ); - tmax = MAX( type_i, type_j ); - t = &( LR[tmin][tmax] ); - - /* Cubic Spline Interpolation */ - r = (int)(r_ij * t->inv_dx); - if (r == 0) ++r; - base = (double)(r+1) * t->dx; - dif = r_ij - base; - - e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif + - t->vdW[r].a; - - e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + - t->ele[r].a; - e_ele *= system->my_atoms[i].q * system->my_atoms[j].q; - - total_EvdW += e_vdW; - total_Eele += e_ele; - - CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif + - t->CEvd[r].a; - - CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif + - t->CEclmb[r].a; - CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { - rvec_ScaledSum( delij, 1., system->my_atoms[i].x, - -1., system->my_atoms[j].x ); - f_tmp = -(CEvd + CEclmb); - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, e_vdW, e_ele, - f_tmp, delij[0], delij[1], delij[2], thr); - } - - if (control->virial == 0) { - rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); - rvec_ScaledAdd( workspace->forceReduction[froffset+j], - +(CEvd + CEclmb), nbr_pj->dvec ); - } else { // NPT, iNPT or sNPT - /* for pressure coupling, terms not related to bond order derivatives - are added directly into pressure vector/tensor */ - rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); - - rvec_ScaledAdd( workspace->f[i], -1., temp ); - rvec_Add( workspace->forceReduction[froffset+j], temp ); - - rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - } - } - } - } - - pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either, - system->pair_ptr->vflag_either, thr); - } // end omp parallel - - data->my_en.e_vdW = total_EvdW; - data->my_en.e_ele = total_Eele; - - Compute_Polarization_Energy( system, data ); -} diff --git a/src/USER-OMP/reaxc_nonbonded_omp.h b/src/USER-OMP/reaxc_nonbonded_omp.h deleted file mode 100644 index 779642b83d..0000000000 --- a/src/USER-OMP/reaxc_nonbonded_omp.h +++ /dev/null @@ -1,39 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __NONBONDED_OMP_H_ -#define __NONBONDED_OMP_H_ - -#include "reaxc_types.h" - -void vdW_Coulomb_Energy_OMP(reax_system *, control_params *, simulation_data *, storage *, - reax_list **, output_controls *); - -void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *, control_params *, simulation_data *, storage *, - reax_list **, output_controls *); -#endif diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp deleted file mode 100644 index 96d4966a00..0000000000 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ /dev/null @@ -1,477 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_torsion_angles_omp.h" - -#include "fix_omp.h" -#include "pair_reaxc_omp.h" - -#include "reaxc_defs.h" -#include "reaxc_types.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -#include - -#if defined(_OPENMP) -#include -#endif - -#define MIN_SINE 1e-10 - -using namespace LAMMPS_NS; - -// Functions defined in reaxc_torsion_angles.cpp -extern double Calculate_Omega(rvec, double, rvec, double, rvec, double, rvec, double, - three_body_interaction_data*, three_body_interaction_data*, - rvec, rvec, rvec, rvec, output_controls*); - -/* ---------------------------------------------------------------------- */ - -void Torsion_AnglesOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) -{ -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - int natoms = system->n; - reax_list *bonds = (*lists) + BONDS; - reax_list *thb_intrs = (*lists) + THREE_BODIES; - double p_tor2 = system->reax_param.gp.l[23]; - double p_tor3 = system->reax_param.gp.l[24]; - double p_tor4 = system->reax_param.gp.l[25]; - double p_cot2 = system->reax_param.gp.l[27]; - double total_Etor = 0; - double total_Econ = 0; - int nthreads = control->nthreads; - -#if defined(_OPENMP) -#pragma omp parallel default(shared) reduction(+: total_Etor, total_Econ) -#endif - { - int i, j, k, l, pi, pj, pk, pl, pij, plk; - int type_i, type_j, type_k, type_l; - int start_j, end_j; - int start_pj, end_pj, start_pk, end_pk; - int num_frb_intrs = 0; - - double Delta_j, Delta_k; - double r_ij, r_jk, r_kl, r_li; - double BOA_ij, BOA_jk, BOA_kl; - - double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl; - double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv; - double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl; - double fn10, f11_DjDk, dfn11, fn12; - double theta_ijk, theta_jkl; - double sin_ijk, sin_jkl; - double cos_ijk, cos_jkl; - double tan_ijk_i, tan_jkl_i; - double omega, cos_omega, cos2omega, cos3omega; - rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl; - double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4; - double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9; - double Cconj, CEconj1, CEconj2, CEconj3; - double CEconj4, CEconj5, CEconj6; - double e_tor, e_con; - rvec dvec_li; - rvec force, ext_press; - ivec rel_box_jl; - // rtensor total_rtensor, temp_rtensor; - four_body_header *fbh; - four_body_parameters *fbp; - bond_data *pbond_ij, *pbond_jk, *pbond_kl; - bond_order_data *bo_ij, *bo_jk, *bo_kl; - three_body_interaction_data *p_ijk, *p_jkl; - - // Virial tallying variables - double delil[3], deljl[3], delkl[3]; - double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; - -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - long reductionOffset = (system->N * tid); - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - -#if defined(_OPENMP) -#pragma omp for schedule(static) -#endif - for (j = 0; j < system->N; ++j) { - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - for (pk = start_j; pk < end_j; ++pk) { - bo_jk = &( bonds->select.bond_list[pk].bo_data ); - for (k = 0; k < nthreads; ++k) - bo_jk->CdboReduction[k] = 0.; - } - } - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) -#endif - for (j = 0; j < natoms; ++j) { - type_j = system->my_atoms[j].type; - Delta_j = workspace->Delta_boc[j]; - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - for (pk = start_j; pk < end_j; ++pk) { - pbond_jk = &( bonds->select.bond_list[pk] ); - k = pbond_jk->nbr; - bo_jk = &( pbond_jk->bo_data ); - BOA_jk = bo_jk->BO - control->thb_cut; - - /* see if there are any 3-body interactions involving j&k - where j is the central atom. Otherwise there is no point in - trying to form a 4-body interaction out of this neighborhood */ - if (system->my_atoms[j].orig_id < system->my_atoms[k].orig_id && - bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) { - pj = pbond_jk->sym_index; // pj points to j on k's list - - /* do the same check as above: - are there any 3-body interactions involving k&j - where k is the central atom */ - if (Num_Entries(pj, thb_intrs)) { - type_k = system->my_atoms[k].type; - Delta_k = workspace->Delta_boc[k]; - r_jk = pbond_jk->d; - - start_pk = Start_Index(pk, thb_intrs ); - end_pk = End_Index(pk, thb_intrs ); - start_pj = Start_Index(pj, thb_intrs ); - end_pj = End_Index(pj, thb_intrs ); - - exp_tor2_jk = exp( -p_tor2 * BOA_jk ); - exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) ); - exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) ); - exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) ); - exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk); - f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv; - - - /* pick i up from j-k interaction where j is the central atom */ - for (pi = start_pk; pi < end_pk; ++pi) { - p_ijk = &( thb_intrs->select.three_body_list[pi] ); - pij = p_ijk->pthb; // pij is pointer to i on j's bond_list - pbond_ij = &( bonds->select.bond_list[pij] ); - bo_ij = &( pbond_ij->bo_data ); - - if (bo_ij->BO > control->thb_cut/*0*/) { - i = p_ijk->thb; - type_i = system->my_atoms[i].type; - r_ij = pbond_ij->d; - BOA_ij = bo_ij->BO - control->thb_cut; - - theta_ijk = p_ijk->theta; - sin_ijk = sin( theta_ijk ); - cos_ijk = cos( theta_ijk ); - //tan_ijk_i = 1. / tan( theta_ijk ); - if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) - tan_ijk_i = cos_ijk / MIN_SINE; - else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) - tan_ijk_i = cos_ijk / -MIN_SINE; - else tan_ijk_i = cos_ijk / sin_ijk; - - exp_tor2_ij = exp( -p_tor2 * BOA_ij ); - exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) ); - - - /* pick l up from j-k interaction where k is the central atom */ - for (pl = start_pj; pl < end_pj; ++pl) { - p_jkl = &( thb_intrs->select.three_body_list[pl] ); - l = p_jkl->thb; - plk = p_jkl->pthb; //pointer to l on k's bond_list! - pbond_kl = &( bonds->select.bond_list[plk] ); - bo_kl = &( pbond_kl->bo_data ); - type_l = system->my_atoms[l].type; - fbh = &(system->reax_param.fbp[type_i][type_j] - [type_k][type_l]); - fbp = &(system->reax_param.fbp[type_i][type_j] - [type_k][type_l].prm[0]); - - if (i != l && fbh->cnt && - bo_kl->BO > control->thb_cut/*0*/ && - bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) { - ++num_frb_intrs; - //fprintf(stderr, - // "%5d: %6d %6d %6d %6d\n", num_frb_intrs, - // system->my_atoms[i].orig_id,system->my_atoms[j].orig_id, - // system->my_atoms[k].orig_id,system->my_atoms[l].orig_id); - - r_kl = pbond_kl->d; - BOA_kl = bo_kl->BO - control->thb_cut; - - theta_jkl = p_jkl->theta; - sin_jkl = sin( theta_jkl ); - cos_jkl = cos( theta_jkl ); - //tan_jkl_i = 1. / tan( theta_jkl ); - if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) - tan_jkl_i = cos_jkl / MIN_SINE; - else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) - tan_jkl_i = cos_jkl / -MIN_SINE; - else tan_jkl_i = cos_jkl /sin_jkl; - - rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x, - -1., system->my_atoms[l].x ); - r_li = rvec_Norm( dvec_li ); - - - /* omega and its derivative */ - omega = Calculate_Omega( pbond_ij->dvec, r_ij, - pbond_jk->dvec, r_jk, - pbond_kl->dvec, r_kl, - dvec_li, r_li, - p_ijk, p_jkl, - dcos_omega_di, dcos_omega_dj, - dcos_omega_dk, dcos_omega_dl, - out_control ); - - cos_omega = cos( omega ); - cos2omega = cos( 2. * omega ); - cos3omega = cos( 3. * omega ); - /* end omega calculations */ - - /* torsion energy */ - exp_tor1 = exp( fbp->p_tor1 * - SQR(2.0 - bo_jk->BO_pi - f11_DjDk) ); - exp_tor2_kl = exp( -p_tor2 * BOA_kl ); - exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) ); - fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * - (1.0 - exp_tor2_kl); - - CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) + - fbp->V2 * exp_tor1 * (1.0 - cos2omega) + - fbp->V3 * (1.0 + cos3omega) ); - - total_Etor += e_tor = fn10 * sin_ijk * sin_jkl * CV; - - dfn11 = (-p_tor3 * exp_tor3_DjDk + - (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) * - (2.0 + exp_tor3_DjDk) * exp_tor34_inv) * - exp_tor34_inv; - - CEtors1 = sin_ijk * sin_jkl * CV; - - CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 * - (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) * - sin_ijk * sin_jkl; - CEtors3 = CEtors2 * dfn11; - - CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij * - (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl); - CEtors5 = CEtors1 * p_tor2 * - (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl); - CEtors6 = CEtors1 * p_tor2 * - (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl; - - cmn = -fn10 * CV; - CEtors7 = cmn * sin_jkl * tan_ijk_i; - CEtors8 = cmn * sin_ijk * tan_jkl_i; - - CEtors9 = fn10 * sin_ijk * sin_jkl * - (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega + - 1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega))); - /* end of torsion energy */ - - - /* 4-body conjugation energy */ - fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl; - //data->my_en.e_con += e_con = - total_Econ += e_con = - fbp->p_cot1 * fn12 * - (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); - - Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 * - (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); - - CEconj1 = Cconj * (BOA_ij - 1.5e0); - CEconj2 = Cconj * (BOA_jk - 1.5e0); - CEconj3 = Cconj * (BOA_kl - 1.5e0); - - CEconj4 = -fbp->p_cot1 * fn12 * - (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i; - CEconj5 = -fbp->p_cot1 * fn12 * - (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i; - CEconj6 = 2.0 * fbp->p_cot1 * fn12 * - cos_omega * sin_ijk * sin_jkl; - /* end 4-body conjugation energy */ - - /* FORCES */ - bo_jk->Cdbopi += CEtors2; - workspace->CdDelta[j] += CEtors3; - //workspace->CdDelta[k] += CEtors3; - workspace->CdDeltaReduction[reductionOffset+k] += CEtors3; - bo_ij->Cdbo += (CEtors4 + CEconj1); - bo_jk->Cdbo += (CEtors5 + CEconj2); - //bo_kl->Cdbo += (CEtors6 + CEconj3); - bo_kl->CdboReduction[tid] += (CEtors6 + CEconj3); - - if (control->virial == 0) { - /* dcos_theta_ijk */ - rvec_ScaledAdd( workspace->f[j], - CEtors7 + CEconj4, p_ijk->dcos_dj ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i], - CEtors7 + CEconj4, p_ijk->dcos_dk ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k], - CEtors7 + CEconj4, p_ijk->dcos_di ); - - /* dcos_theta_jkl */ - rvec_ScaledAdd( workspace->f[j], - CEtors8 + CEconj5, p_jkl->dcos_di ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k], - CEtors8 + CEconj5, p_jkl->dcos_dj ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+l], - CEtors8 + CEconj5, p_jkl->dcos_dk ); - - /* dcos_omega */ - rvec_ScaledAdd( workspace->f[j], - CEtors9 + CEconj6, dcos_omega_dj ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i], - CEtors9 + CEconj6, dcos_omega_di ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k], - CEtors9 + CEconj6, dcos_omega_dk ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+l], - CEtors9 + CEconj6, dcos_omega_dl ); - } - else { - ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box); - - /* dcos_theta_ijk */ - rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk ); - rvec_Add( workspace->forceReduction[reductionOffset+i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - rvec_ScaledAdd( workspace->f[j], - CEtors7 + CEconj4, p_ijk->dcos_dj ); - - rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di ); - rvec_Add( workspace->forceReduction[reductionOffset+k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - /* dcos_theta_jkl */ - rvec_ScaledAdd( workspace->f[j], - CEtors8 + CEconj5, p_jkl->dcos_di ); - - rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj ); - rvec_Add( workspace->forceReduction[reductionOffset+k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk ); - rvec_Add( workspace->forceReduction[reductionOffset+l], force ); - rvec_iMultiply( ext_press, rel_box_jl, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - /* dcos_omega */ - rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di ); - rvec_Add( workspace->forceReduction[reductionOffset+i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - rvec_ScaledAdd( workspace->f[j], - CEtors9 + CEconj6, dcos_omega_dj ); - - rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk ); - rvec_Add( workspace->forceReduction[reductionOffset+k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl ); - rvec_Add( workspace->forceReduction[reductionOffset+i], force ); - rvec_iMultiply( ext_press, rel_box_jl, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - } - - /* tally into per-atom virials */ - if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { - - // acquire vectors - rvec_ScaledSum( delil, 1., system->my_atoms[l].x, - -1., system->my_atoms[i].x ); - rvec_ScaledSum( deljl, 1., system->my_atoms[l].x, - -1., system->my_atoms[j].x ); - rvec_ScaledSum( delkl, 1., system->my_atoms[l].x, - -1., system->my_atoms[k].x ); - // dcos_theta_ijk - rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk ); - rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj ); - rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di ); - - // dcos_theta_jkl - rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di ); - rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj ); - - // dcos_omega - rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di ); - rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj ); - rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk ); - - // tally - eng_tmp = e_tor + e_con; - - if (system->pair_ptr->evflag) - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, k, system->n, 1, - eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - - // NEED TO MAKE AN OMP VERSION OF THIS CALL! - if (system->pair_ptr->vflag_atom) - system->pair_ptr->v_tally4(i, j, k, l, fi_tmp, fj_tmp, fk_tmp, - delil, deljl, delkl ); - } - - } // pl check ends - } // pl loop ends - } // pi check ends - } // pi loop ends - } // k-j neighbor check ends - } // jmy_en.e_tor = total_Etor; - data->my_en.e_con = total_Econ; - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTETORSIONANGLESBOINDEX] += (endTimeBase-startTimeBase); -#endif -} diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.h b/src/USER-OMP/reaxc_torsion_angles_omp.h deleted file mode 100644 index 4b62f90241..0000000000 --- a/src/USER-OMP/reaxc_torsion_angles_omp.h +++ /dev/null @@ -1,38 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __TORSION_ANGLES_OMP_H_ -#define __TORSION_ANGLES_OMP_H_ - -#include "reaxc_torsion_angles.h" -#include "reaxc_types.h" - -void Torsion_AnglesOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *); - -#endif diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp deleted file mode 100644 index 49a7e874cd..0000000000 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ /dev/null @@ -1,620 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_valence_angles_omp.h" - -#include "error.h" -#include "fix_omp.h" -#include "pair_reaxc_omp.h" - -#include "reaxc_defs.h" -#include "reaxc_types.h" -#include "reaxc_valence_angles.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -#include - -#if defined(_OPENMP) -#include -#endif - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -void Calculate_dCos_ThetaOMP( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, - rvec* dcos_theta_di, - rvec* dcos_theta_dj, - rvec* dcos_theta_dk ) -{ - double sqr_d_ji = SQR(d_ji); - double sqr_d_jk = SQR(d_jk); - double inv_dists = 1.0 / (d_ji * d_jk); - double inv_dists3 = inv_dists * inv_dists * inv_dists; - double dot_dvecs = dvec_ji[0]*dvec_jk[0] + dvec_ji[1]*dvec_jk[1] + dvec_ji[2]*dvec_jk[2]; - double Cdot_inv3 = dot_dvecs * inv_dists3; - - double csqr_jk = Cdot_inv3 * sqr_d_jk; - double csqr_ji = Cdot_inv3 * sqr_d_ji; - - // Try to help compiler out by unrolling - // x-component - double dinv_jk = dvec_jk[0] * inv_dists; - double dinv_ji = dvec_ji[0] * inv_dists; - - double cdev_ji = csqr_jk * dvec_ji[0]; - double cdev_jk = csqr_ji * dvec_jk[0]; - - (*dcos_theta_di)[0] = dinv_jk - cdev_ji; - (*dcos_theta_dj)[0] = -(dinv_jk + dinv_ji) + cdev_ji + cdev_jk; - (*dcos_theta_dk)[0] = dinv_ji - cdev_jk; - - // y-component - dinv_jk = dvec_jk[1] * inv_dists; - dinv_ji = dvec_ji[1] * inv_dists; - - cdev_ji = csqr_jk * dvec_ji[1]; - cdev_jk = csqr_ji * dvec_jk[1]; - - (*dcos_theta_di)[1] = dinv_jk - cdev_ji; - (*dcos_theta_dj)[1] = -(dinv_jk + dinv_ji) + cdev_ji + cdev_jk; - (*dcos_theta_dk)[1] = dinv_ji - cdev_jk; - - // z-component - dinv_jk = dvec_jk[2] * inv_dists; - dinv_ji = dvec_ji[2] * inv_dists; - - cdev_ji = csqr_jk * dvec_ji[2]; - cdev_jk = csqr_ji * dvec_jk[2]; - - (*dcos_theta_di)[2] = dinv_jk - cdev_ji; - (*dcos_theta_dj)[2] = -(dinv_jk + dinv_ji) + cdev_ji + cdev_jk; - (*dcos_theta_dk)[2] = dinv_ji - cdev_jk; -} - -/* ---------------------------------------------------------------------- */ - -/* this is a 3-body interaction in which the main role is - played by j which sits in the middle of the other two. */ -void Valence_AnglesOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /* out_control */) -{ - -#ifdef OMP_TIMING - double endTimeBase, startTimeBase; - startTimeBase = MPI_Wtime(); -#endif - - reax_list *bonds = (*lists) + BONDS; - reax_list *thb_intrs = (*lists) + THREE_BODIES; - - // Precompute and store valence_angle offsets for OpenMP code. - int * _my_offset = workspace->valence_angle_atom_myoffset; - - /* global parameters used in these calculations */ - double p_val6 = system->reax_param.gp.l[14]; - double p_val8 = system->reax_param.gp.l[33]; - double p_val9 = system->reax_param.gp.l[16]; - double p_val10 = system->reax_param.gp.l[17]; - double total_Eang = 0; - double total_Epen = 0; - double total_Ecoa = 0; - - int nthreads = control->nthreads; - int num_thb_intrs = 0; - int TWICE = 2; -#if defined(_OPENMP) -#pragma omp parallel default(shared) reduction(+:total_Eang, total_Epen, total_Ecoa, num_thb_intrs) -#endif - { - int i, j, pi, k, pk, t; - int type_i, type_j, type_k; - int start_j, end_j, start_pk, end_pk; - int cnt, my_offset; - - double temp, temp_bo_jt, pBOjt7; - double p_val1, p_val2, p_val3, p_val4, p_val5, p_val7; - double p_pen1, p_pen2, p_pen3, p_pen4; - double p_coa1, p_coa2, p_coa3, p_coa4; - double trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk; - double exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2; - double dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj; - double CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8; - double CEpen1, CEpen2, CEpen3; - double e_ang, e_coa, e_pen; - double CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5; - double Cf7ij, Cf7jk, Cf8j, Cf9j; - double f7_ij, f7_jk, f8_Dj, f9_Dj; - double Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta; - double BOA_ij, BOA_jk; - rvec force, ext_press; - // rtensor temp_rtensor, total_rtensor; - - // Tallying variables - double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; - double delij[3], delkj[3]; - - three_body_header *thbh; - three_body_parameters *thbp; - three_body_interaction_data *p_ijk, *p_kji; - bond_data *pbond_ij, *pbond_jk, *pbond_jt; - bond_order_data *bo_ij, *bo_jk, *bo_jt; - -#if defined(_OPENMP) - int tid = omp_get_thread_num(); -#else - int tid = 0; -#endif - long reductionOffset = (system->N * tid); - class PairReaxCOMP *pair_reax_ptr; - pair_reax_ptr = static_cast(system->pair_ptr); - class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid); - - // Run through a minimal for (jnum_intrs / nthreads; - -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) -#endif - for (j = 0; j < system->N; ++j) { - type_j = system->my_atoms[j].type; - _my_offset[j] = 0; - if (type_j < 0) continue; - - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - // Always point to start of workspace to count angles - my_offset = tid * per_thread; - - for (pi = start_j; pi < end_j; ++pi) { - Set_Start_Index( pi, my_offset, thb_intrs ); - pbond_ij = &(bonds->select.bond_list[pi]); - bo_ij = &(pbond_ij->bo_data); - BOA_ij = bo_ij->BO - control->thb_cut; - - if (BOA_ij > 0.0) { - i = pbond_ij->nbr; - - /* first copy 3-body intrs from previously computed ones where i>k. - in the second for-loop below, - we compute only new 3-body intrs where i < k */ - for (pk = start_j; pk < pi; ++pk) { - start_pk = Start_Index( pk, thb_intrs ); - end_pk = End_Index( pk, thb_intrs ); - - for (t = start_pk; t < end_pk; ++t) - if (thb_intrs->select.three_body_list[t].thb == i) { - - p_ijk = &(thb_intrs->select.three_body_list[my_offset] ); - p_ijk->thb = bonds->select.bond_list[pk].nbr; - - ++my_offset; - break; - } - } // for (pk) - - /* and this is the second for loop mentioned above */ - for (pk = pi+1; pk < end_j; ++pk) { - pbond_jk = &(bonds->select.bond_list[pk]); - k = pbond_jk->nbr; - - if (j >= system->n && i >= system->n && k >= system->n) continue; - - p_ijk = &( thb_intrs->select.three_body_list[my_offset] ); - p_ijk->thb = k; - - ++my_offset; // add this to the list of 3-body interactions - } // for (pk) - } // if () - - Set_End_Index(pi, my_offset, thb_intrs ); - } // for (pi) - - // Confirm that thb_intrs->num_intrs / nthreads is enough to hold all angles from a single atom - if (my_offset >= (tid+1)*per_thread) { - char errmsg[512]; - snprintf( errmsg, 512, "step%d-ran out of space on angle_list for atom %i:\n" - " nthreads= %d, tid=%d, my_offset=%d, per_thread=%d\n" - " num_intrs= %i N= %i\n" - , data->step, j, nthreads, tid, my_offset, per_thread,thb_intrs->num_intrs , system->N); - control->error_ptr->one(FLERR, errmsg); - } - - // Number of angles owned by this atom - _my_offset[j] = my_offset - tid * per_thread; - } // for (j) - - // Wait for all threads to finish counting angles -#if defined(_OPENMP) && !defined(__NVCC__) -#pragma omp barrier -#endif - // Master thread uses angle counts to compute offsets - // This can be threaded -#if defined(_OPENMP) && !defined(__NVCC__) -#pragma omp master -#endif - { - int current_count = 0; - int m = _my_offset[0]; - _my_offset[0] = current_count; - for (j=1; jN; j++) { - current_count+= m; - m = _my_offset[j]; - _my_offset[j] = current_count; - } - _my_offset[system->N] = current_count + m; // Used to test if last particle has any angles - } - - // All threads wait till master thread finished computing offsets -#if defined(_OPENMP) && !defined(__NVCC__) -#pragma omp barrier -#endif - // Original loop, but now using precomputed offsets - // Safe to use all threads available, regardless of threads tasked above - // We also now skip over atoms that have no angles assigned -#if defined(_OPENMP) -#pragma omp for schedule(dynamic,50)//(dynamic,chunksize)//(guided) -#endif - for (j = 0; j < system->N; ++j) { // Ray: the first one with system->N - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - - // Skip if no angles for this atom - if (_my_offset[j] == _my_offset[j+1]) continue; - - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - type_j = system->my_atoms[j].type; - - my_offset = _my_offset[j]; - - p_val3 = system->reax_param.sbp[ type_j ].p_val3; - p_val5 = system->reax_param.sbp[ type_j ].p_val5; - - SBOp = 0, prod_SBO = 1; - for (t = start_j; t < end_j; ++t) { - bo_jt = &(bonds->select.bond_list[t].bo_data); - SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2); - temp = SQR( bo_jt->BO ); - temp *= temp; - temp *= temp; - prod_SBO *= exp( -temp ); - } - - // modifications to match Adri's code - 09/01/09 - if (workspace->vlpex[j] >= 0) { - vlpadj = 0; - dSBO2 = prod_SBO - 1; - } else { - vlpadj = workspace->nlp[j]; - dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); - } - - SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); - dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj ); - - if (SBO <= 0) - SBO2 = 0, CSBO2 = 0; - else if (SBO > 0 && SBO <= 1) { - SBO2 = pow( SBO, p_val9 ); - CSBO2 = p_val9 * pow( SBO, p_val9 - 1 ); - } - else if (SBO > 1 && SBO < 2) { - SBO2 = 2 - pow( 2-SBO, p_val9 ); - CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 ); - } - else - SBO2 = 2, CSBO2 = 0; - - expval6 = exp( p_val6 * workspace->Delta_boc[j] ); - - for (pi = start_j; pi < end_j; ++pi) { - Set_Start_Index( pi, my_offset, thb_intrs ); - pbond_ij = &(bonds->select.bond_list[pi]); - bo_ij = &(pbond_ij->bo_data); - BOA_ij = bo_ij->BO - control->thb_cut; - - - if (BOA_ij > 0.0) { - i = pbond_ij->nbr; - type_i = system->my_atoms[i].type; - - - /* first copy 3-body intrs from previously computed ones where i>k. - in the second for-loop below, - we compute only new 3-body intrs where i < k */ - for (pk = start_j; pk < pi; ++pk) { - start_pk = Start_Index( pk, thb_intrs ); - end_pk = End_Index( pk, thb_intrs ); - - for (t = start_pk; t < end_pk; ++t) - if (thb_intrs->select.three_body_list[t].thb == i) { - p_ijk = &(thb_intrs->select.three_body_list[my_offset] ); - p_kji = &(thb_intrs->select.three_body_list[t]); - - p_ijk->thb = bonds->select.bond_list[pk].nbr; - p_ijk->pthb = pk; - p_ijk->theta = p_kji->theta; - rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk ); - rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj ); - rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di ); - - ++my_offset; - ++num_thb_intrs; - break; - } - } // for (pk) - - - /* and this is the second for loop mentioned above */ - for (pk = pi+1; pk < end_j; ++pk) { - pbond_jk = &(bonds->select.bond_list[pk]); - bo_jk = &(pbond_jk->bo_data); - BOA_jk = bo_jk->BO - control->thb_cut; - k = pbond_jk->nbr; - type_k = system->my_atoms[k].type; - p_ijk = &( thb_intrs->select.three_body_list[my_offset] ); - - // Fix by Sudhir - // if (BOA_jk <= 0) continue; - if (j >= system->n && i >= system->n && k >= system->n) continue; - - Calculate_Theta( pbond_ij->dvec, pbond_ij->d, - pbond_jk->dvec, pbond_jk->d, - &theta, &cos_theta ); - - Calculate_dCos_ThetaOMP( pbond_ij->dvec, pbond_ij->d, - pbond_jk->dvec, pbond_jk->d, - &(p_ijk->dcos_di), &(p_ijk->dcos_dj), - &(p_ijk->dcos_dk) ); - p_ijk->thb = k; - p_ijk->pthb = pk; - p_ijk->theta = theta; - - sin_theta = sin( theta ); - if (sin_theta < 1.0e-5) - sin_theta = 1.0e-5; - - ++my_offset; // add this to the list of 3-body interactions - ++num_thb_intrs; - - if ((j < system->n) && (BOA_jk > 0.0) && - (bo_ij->BO > control->thb_cut) && - (bo_jk->BO > control->thb_cut) && - (bo_ij->BO * bo_jk->BO > control->thb_cutsq)) { - thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] ); - - for (cnt = 0; cnt < thbh->cnt; ++cnt) { - - if (fabs(thbh->prm[cnt].p_val1) > 0.001) { - thbp = &( thbh->prm[cnt] ); - - /* ANGLE ENERGY */ - p_val1 = thbp->p_val1; - p_val2 = thbp->p_val2; - p_val4 = thbp->p_val4; - p_val7 = thbp->p_val7; - theta_00 = thbp->theta_00; - - exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) ); - f7_ij = 1.0 - exp3ij; - Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij; - - exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) ); - f7_jk = 1.0 - exp3jk; - Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk; - - expval7 = exp( -p_val7 * workspace->Delta_boc[j] ); - trm8 = 1.0 + expval6 + expval7; - f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 ); - Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) * - ( p_val6 * expval6 * trm8 - - (2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) ); - - theta_0 = 180.0 - theta_00 * (1.0 - - exp(-p_val10 * (2.0 - SBO2))); - theta_0 = DEG2RAD( theta_0 ); - - expval2theta = exp( -p_val2 * SQR(theta_0 - theta) ); - if (p_val1 >= 0) - expval12theta = p_val1 * (1.0 - expval2theta); - else // To avoid linear Me-H-Me angles (6/6/06) - expval12theta = p_val1 * -expval2theta; - - CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; - CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; - CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; - CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * - expval2theta * (theta_0 - theta); - - Ctheta_0 = p_val10 * DEG2RAD(theta_00) * - exp( -p_val10 * (2.0 - SBO2) ); - - CEval5 = -CEval4 * Ctheta_0 * CSBO2; - CEval6 = CEval5 * dSBO1; - CEval7 = CEval5 * dSBO2; - CEval8 = -CEval4 / sin_theta; - - total_Eang += e_ang = - f7_ij * f7_jk * f8_Dj * expval12theta; - /* END ANGLE ENERGY*/ - - - /* PENALTY ENERGY */ - p_pen1 = thbp->p_pen1; - p_pen2 = system->reax_param.gp.l[19]; - p_pen3 = system->reax_param.gp.l[20]; - p_pen4 = system->reax_param.gp.l[21]; - - exp_pen2ij = exp( -p_pen2 * SQR( BOA_ij - 2.0 ) ); - exp_pen2jk = exp( -p_pen2 * SQR( BOA_jk - 2.0 ) ); - exp_pen3 = exp( -p_pen3 * workspace->Delta[j] ); - exp_pen4 = exp( p_pen4 * workspace->Delta[j] ); - trm_pen34 = 1.0 + exp_pen3 + exp_pen4; - f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34; - Cf9j = ( -p_pen3 * exp_pen3 * trm_pen34 - - (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 + - p_pen4 * exp_pen4 ) ) / - SQR( trm_pen34 ); - - total_Epen += e_pen = - p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; - - CEpen1 = e_pen * Cf9j / f9_Dj; - temp = -2.0 * p_pen2 * e_pen; - CEpen2 = temp * (BOA_ij - 2.0); - CEpen3 = temp * (BOA_jk - 2.0); - /* END PENALTY ENERGY */ - - - /* COALITION ENERGY */ - p_coa1 = thbp->p_coa1; - p_coa2 = system->reax_param.gp.l[2]; - p_coa3 = system->reax_param.gp.l[38]; - p_coa4 = system->reax_param.gp.l[30]; - - exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] ); - total_Ecoa += e_coa = - p_coa1 / (1. + exp_coa2) * - exp( -p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij) ) * - exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) * - exp( -p_coa4 * SQR(BOA_ij - 1.5) ) * - exp( -p_coa4 * SQR(BOA_jk - 1.5) ); - - CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; - CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa; - CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); - CEcoa4 = -2 * p_coa3 * - (workspace->total_bond_order[i]-BOA_ij) * e_coa; - CEcoa5 = -2 * p_coa3 * - (workspace->total_bond_order[k]-BOA_jk) * e_coa; - /* END COALITION ENERGY */ - - - /* FORCES */ - bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); - bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); - workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3); - workspace->CdDeltaReduction[reductionOffset+i] += CEcoa4; - workspace->CdDeltaReduction[reductionOffset+k] += CEcoa5; - - for (t = start_j; t < end_j; ++t) { - pbond_jt = &( bonds->select.bond_list[t] ); - bo_jt = &(pbond_jt->bo_data); - temp_bo_jt = bo_jt->BO; - temp = CUBE( temp_bo_jt ); - pBOjt7 = temp * temp * temp_bo_jt; - - bo_jt->Cdbo += (CEval6 * pBOjt7); - bo_jt->Cdbopi += CEval5; - bo_jt->Cdbopi2 += CEval5; - } - - if (control->virial == 0) { - rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i], - CEval8, p_ijk->dcos_di ); - rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k], - CEval8, p_ijk->dcos_dk ); - } else { - /* terms not related to bond order derivatives are - added directly into forces and pressure vector/tensor */ - rvec_Scale( force, CEval8, p_ijk->dcos_di ); - rvec_Add( workspace->forceReduction[reductionOffset+i], force ); - - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - - rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); - - rvec_Scale( force, CEval8, p_ijk->dcos_dk ); - rvec_Add( workspace->forceReduction[reductionOffset+k], force ); - - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); - } - - /* tally into per-atom virials */ - if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { - - /* Acquire vectors */ - rvec_ScaledSum( delij, 1., system->my_atoms[i].x, - -1., system->my_atoms[j].x ); - rvec_ScaledSum( delkj, 1., system->my_atoms[k].x, - -1., system->my_atoms[j].x ); - - rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di ); - rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj ); - rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk ); - - eng_tmp = e_ang + e_pen + e_coa; - - if (system->pair_ptr->evflag) - pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, j, system->N, 1, - eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - if (system->pair_ptr->vflag_atom) - // NEED TO MAKE AN OMP VERSION OF THIS CALL! - system->pair_ptr->v_tally3( i, j, k, fi_tmp, fk_tmp, delij, delkj); - } - - } // if (p_val1>0.001) - } // for (cnt) - } // if (j0) - } // for (pk) - } // if (BOA_ij>0) - - Set_End_Index(pi, my_offset, thb_intrs ); - } // for (pi) - } // for (j) - } // end omp parallel - - data->my_en.e_ang = total_Eang; - data->my_en.e_pen = total_Epen; - data->my_en.e_coa = total_Ecoa; - - if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { - workspace->realloc.num_3body = num_thb_intrs * TWICE; - if (num_thb_intrs > thb_intrs->num_intrs) { - char errmsg[128]; - snprintf(errmsg, 128, "step%d-ran out of space on angle_list: top=%d, max=%d", - data->step, num_thb_intrs, thb_intrs->num_intrs); - control->error_ptr->one(FLERR, errmsg); - } - } - -#ifdef OMP_TIMING - endTimeBase = MPI_Wtime(); - ompTimingData[COMPUTEVALENCEANGLESBOINDEX] += (endTimeBase-startTimeBase); -#endif -} diff --git a/src/USER-OMP/reaxc_valence_angles_omp.h b/src/USER-OMP/reaxc_valence_angles_omp.h deleted file mode 100644 index f1a4fef505..0000000000 --- a/src/USER-OMP/reaxc_valence_angles_omp.h +++ /dev/null @@ -1,39 +0,0 @@ -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - Website: https://www.cs.purdue.edu/puremd - - Copyright (2010) Purdue University - - Contributing authors: - H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: - Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259 - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __VALENCE_ANGLES_OMP_H_ -#define __VALENCE_ANGLES_OMP_H_ - -#include "reaxc_types.h" - -void Valence_AnglesOMP(reax_system *, control_params *, simulation_data *, storage *, reax_list **, - output_controls *); - -void Calculate_dCos_ThetaOMP(rvec, double, rvec, double, rvec *, rvec *, rvec *); - -#endif diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp deleted file mode 100644 index 100606e9e3..0000000000 --- a/src/USER-REAXC/pair_reaxc.cpp +++ /dev/null @@ -1,882 +0,0 @@ -// clang-format off -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Hasan Metin Aktulga, Purdue University - (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov) - Per-atom energy/virial added by Ray Shan (Sandia) - Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added by - Ray Shan (Sandia) - Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia) -------------------------------------------------------------------------- */ - -#include "pair_reaxc.h" - -#include "atom.h" -#include "citeme.h" -#include "comm.h" -#include "error.h" -#include "fix.h" -#include "fix_reaxc.h" -#include "force.h" -#include "memory.h" -#include "modify.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" -#include "update.h" - -#include -#include -#include // for strcasecmp() - -#include "reaxc_defs.h" -#include "reaxc_types.h" -#include "reaxc_allocate.h" -#include "reaxc_control.h" -#include "reaxc_ffield.h" -#include "reaxc_forces.h" -#include "reaxc_init_md.h" -#include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_lookup.h" -#include "reaxc_reset_tools.h" -#include "reaxc_vector.h" - -using namespace LAMMPS_NS; - -static const char cite_pair_reax_c[] = - "pair reax/c command:\n\n" - "@Article{Aktulga12,\n" - " author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n" - " title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n" - " journal = {Parallel Computing},\n" - " year = 2012,\n" - " volume = 38,\n" - " pages = {245--259}\n" - "}\n\n"; - -/* ---------------------------------------------------------------------- */ - -PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp) -{ - if (lmp->citeme) lmp->citeme->add(cite_pair_reax_c); - - single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; - centroidstressflag = CENTROID_NOTAVAIL; - ghostneigh = 1; - - fix_id = new char[24]; - snprintf(fix_id,24,"REAXC_%d",instance_me); - - system = (reax_system *) - memory->smalloc(sizeof(reax_system),"reax:system"); - memset(system,0,sizeof(reax_system)); - control = (control_params *) - memory->smalloc(sizeof(control_params),"reax:control"); - memset(control,0,sizeof(control_params)); - data = (simulation_data *) - memory->smalloc(sizeof(simulation_data),"reax:data"); - workspace = (storage *) - memory->smalloc(sizeof(storage),"reax:storage"); - lists = (reax_list *) - memory->smalloc(LIST_N * sizeof(reax_list),"reax:lists"); - memset(lists,0,LIST_N * sizeof(reax_list)); - out_control = (output_controls *) - memory->smalloc(sizeof(output_controls),"reax:out_control"); - memset(out_control,0,sizeof(output_controls)); - mpi_data = (mpi_datatypes *) - memory->smalloc(sizeof(mpi_datatypes),"reax:mpi"); - - control->me = system->my_rank = comm->me; - - system->my_coords[0] = 0; - system->my_coords[1] = 0; - system->my_coords[2] = 0; - system->num_nbrs = 0; - system->n = 0; // my atoms - system->N = 0; // mine + ghosts - system->bigN = 0; // all atoms in the system - system->local_cap = 0; - system->total_cap = 0; - system->gcell_cap = 0; - system->bndry_cuts.ghost_nonb = 0; - system->bndry_cuts.ghost_hbond = 0; - system->bndry_cuts.ghost_bond = 0; - system->bndry_cuts.ghost_cutoff = 0; - system->my_atoms = nullptr; - system->pair_ptr = this; - system->error_ptr = error; - control->error_ptr = error; - - system->omp_active = 0; - - fix_reax = nullptr; - tmpid = nullptr; - tmpbo = nullptr; - - nextra = 14; - pvector = new double[nextra]; - - setup_flag = 0; - fixspecies_flag = 0; - - nmax = 0; -} - -/* ---------------------------------------------------------------------- */ - -PairReaxC::~PairReaxC() -{ - if (copymode) return; - - if (fix_reax) modify->delete_fix(fix_id); - delete[] fix_id; - - if (setup_flag) { - Close_Output_Files( system, control, out_control, mpi_data ); - - // deallocate reax data-structures - - if (control->tabulate ) Deallocate_Lookup_Tables( system); - - if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS ); - Delete_List( lists+BONDS ); - Delete_List( lists+THREE_BODIES ); - Delete_List( lists+FAR_NBRS ); - - DeAllocate_Workspace( control, workspace ); - DeAllocate_System( system ); - } - - memory->destroy( system ); - memory->destroy( control ); - memory->destroy( data ); - memory->destroy( workspace ); - memory->destroy( lists ); - memory->destroy( out_control ); - memory->destroy( mpi_data ); - - // deallocate interface storage - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(cutghost); - - delete [] chi; - delete [] eta; - delete [] gamma; - } - - memory->destroy(tmpid); - memory->destroy(tmpbo); - - delete [] pvector; - -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::allocate( ) -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(cutghost,n+1,n+1,"pair:cutghost"); - map = new int[n+1]; - - chi = new double[n+1]; - eta = new double[n+1]; - gamma = new double[n+1]; -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::settings(int narg, char **arg) -{ - if (narg < 1) error->all(FLERR,"Illegal pair_style command"); - - // read name of control file or use default controls - - if (strcmp(arg[0],"NULL") == 0) { - strcpy( control->sim_name, "simulate" ); - control->ensemble = 0; - out_control->energy_update_freq = 0; - control->tabulate = 0; - - control->reneighbor = 1; - control->vlist_cut = control->nonb_cut; - control->bond_cut = 5.; - control->hbond_cut = 7.50; - control->thb_cut = 0.001; - control->thb_cutsq = 0.00001; - control->bg_cut = 0.3; - - // Initialize for when omp style included - control->nthreads = 1; - - out_control->write_steps = 0; - out_control->traj_method = 0; - strcpy( out_control->traj_title, "default_title" ); - out_control->atom_info = 0; - out_control->bond_info = 0; - out_control->angle_info = 0; - } else Read_Control_File(arg[0], control, out_control); - - // default values - - qeqflag = 1; - control->lgflag = 0; - control->enobondsflag = 1; - system->mincap = REAX_MIN_CAP; - system->minhbonds = REAX_MIN_HBONDS; - system->safezone = REAX_SAFE_ZONE; - system->saferzone = REAX_SAFER_ZONE; - - // process optional keywords - - int iarg = 1; - - while (iarg < narg) { - if (strcmp(arg[iarg],"checkqeq") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command"); - if (strcmp(arg[iarg+1],"yes") == 0) qeqflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) qeqflag = 0; - else error->all(FLERR,"Illegal pair_style reax/c command"); - iarg += 2; - } else if (strcmp(arg[iarg],"enobonds") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command"); - if (strcmp(arg[iarg+1],"yes") == 0) control->enobondsflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) control->enobondsflag = 0; - else error->all(FLERR,"Illegal pair_style reax/c command"); - iarg += 2; - } else if (strcmp(arg[iarg],"lgvdw") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command"); - if (strcmp(arg[iarg+1],"yes") == 0) control->lgflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) control->lgflag = 0; - else error->all(FLERR,"Illegal pair_style reax/c command"); - iarg += 2; - } else if (strcmp(arg[iarg],"safezone") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command"); - system->safezone = utils::numeric(FLERR,arg[iarg+1],false,lmp); - if (system->safezone < 0.0) - error->all(FLERR,"Illegal pair_style reax/c safezone command"); - system->saferzone = system->safezone*1.2 + 0.2; - iarg += 2; - } else if (strcmp(arg[iarg],"mincap") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command"); - system->mincap = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if (system->mincap < 0) - error->all(FLERR,"Illegal pair_style reax/c mincap command"); - iarg += 2; - } else if (strcmp(arg[iarg],"minhbonds") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command"); - system->minhbonds = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if (system->minhbonds < 0) - error->all(FLERR,"Illegal pair_style reax/c minhbonds command"); - iarg += 2; - } else error->all(FLERR,"Illegal pair_style reax/c command"); - } - - // LAMMPS is responsible for generating nbrs - - control->reneighbor = 1; -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::coeff( int nargs, char **args ) -{ - if (!allocated) allocate(); - - if (nargs != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(args[0],"*") != 0 || strcmp(args[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read ffield file - - char *file = args[2]; - FILE *fp; - fp = utils::open_potential(file,lmp,nullptr); - if (fp != nullptr) - Read_Force_Field(fp, &(system->reax_param), control); - else { - char str[128]; - snprintf(str,128,"Cannot open ReaxFF potential file %s",file); - error->all(FLERR,str); - } - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - - int itmp = 0; - int nreax_types = system->reax_param.num_atom_types; - for (int i = 3; i < nargs; i++) { - if (strcmp(args[i],"NULL") == 0) { - map[i-2] = -1; - itmp ++; - continue; - } - } - - int n = atom->ntypes; - - // pair_coeff element map - for (int i = 3; i < nargs; i++) - for (int j = 0; j < nreax_types; j++) - if (strcasecmp(args[i],system->reax_param.sbp[j].name) == 0) { - map[i-2] = j; - itmp ++; - } - - // error check - if (itmp != n) - error->all(FLERR,"Non-existent ReaxFF type"); - - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::init_style( ) -{ - if (!atom->q_flag) - error->all(FLERR,"Pair style reax/c requires atom attribute q"); - - // firstwarn = 1; - - bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1) - || (modify->find_fix_by_style("^qeq/shielded") != -1)); - if (!have_qeq && qeqflag == 1) - error->all(FLERR,"Pair reax/c requires use of fix qeq/reax or qeq/shielded"); - - system->n = atom->nlocal; // my atoms - system->N = atom->nlocal + atom->nghost; // mine + ghosts - system->bigN = static_cast (atom->natoms); // all atoms in the system - system->wsize = comm->nprocs; - - system->big_box.V = 0; - system->big_box.box_norms[0] = 0; - system->big_box.box_norms[1] = 0; - system->big_box.box_norms[2] = 0; - - if (atom->tag_enable == 0) - error->all(FLERR,"Pair style reax/c requires atom IDs"); - if (force->newton_pair == 0) - error->all(FLERR,"Pair style reax/c requires newton pair on"); - if ((atom->map_tag_max > 99999999) && (comm->me == 0)) - error->warning(FLERR,"Some Atom-IDs are too large. Pair style reax/c " - "native output files may get misformatted or corrupted"); - - // because system->bigN is an int, we cannot have more atoms than MAXSMALLINT - - if (atom->natoms > MAXSMALLINT) - error->all(FLERR,"Too many atoms for pair style reax/c"); - - // need a half neighbor list w/ Newton off and ghost neighbors - // built whenever re-neighboring occurs - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->newton = 2; - neighbor->requests[irequest]->ghost = 1; - - cutmax = MAX3(control->nonb_cut, control->hbond_cut, control->bond_cut); - if ((cutmax < 2.0*control->bond_cut) && (comm->me == 0)) - error->warning(FLERR,"Total cutoff < 2*bond cutoff. May need to use an " - "increased neighbor list skin."); - - for (int i = 0; i < LIST_N; ++i) - if (lists[i].allocated != 1) - lists[i].allocated = 0; - - if (fix_reax == nullptr) { - char **fixarg = new char*[3]; - fixarg[0] = (char *) fix_id; - fixarg[1] = (char *) "all"; - fixarg[2] = (char *) "REAXC"; - modify->add_fix(3,fixarg); - delete [] fixarg; - fix_reax = (FixReaxC *) modify->fix[modify->nfix-1]; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::setup( ) -{ - int oldN; - int mincap = system->mincap; - double safezone = system->safezone; - - system->n = atom->nlocal; // my atoms - system->N = atom->nlocal + atom->nghost; // mine + ghosts - oldN = system->N; - system->bigN = static_cast (atom->natoms); // all atoms in the system - - if (setup_flag == 0) { - - setup_flag = 1; - - int *num_bonds = fix_reax->num_bonds; - int *num_hbonds = fix_reax->num_hbonds; - - control->vlist_cut = neighbor->cutneighmax; - - // determine the local and total capacity - - system->local_cap = MAX( (int)(system->n * safezone), mincap ); - system->total_cap = MAX( (int)(system->N * safezone), mincap ); - - // initialize my data structures - - PreAllocate_Space( system, control, workspace ); - write_reax_atoms(); - - int num_nbrs = estimate_reax_lists(); - if (num_nbrs < 0) - error->all(FLERR,"Too many neighbors for pair style reax/c"); - if (!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR, - lists+FAR_NBRS)) - error->all(FLERR,"Pair reax/c problem in far neighbor list"); - (lists+FAR_NBRS)->error_ptr=error; - - write_reax_lists(); - Initialize( system, control, data, workspace, &lists, out_control, - mpi_data, world ); - for (int k = 0; k < system->N; ++k) { - num_bonds[k] = system->my_atoms[k].num_bonds; - num_hbonds[k] = system->my_atoms[k].num_hbonds; - } - - } else { - - // fill in reax datastructures - - write_reax_atoms(); - - // reset the bond list info for new atoms - - for (int k = oldN; k < system->N; ++k) - Set_End_Index( k, Start_Index( k, lists+BONDS ), lists+BONDS ); - - // check if I need to shrink/extend my data-structs - - ReAllocate( system, control, data, workspace, &lists ); - } - - bigint local_ngroup = list->inum; - MPI_Allreduce( &local_ngroup, &ngroup, 1, MPI_LMP_BIGINT, MPI_SUM, world ); -} - -/* ---------------------------------------------------------------------- */ - -double PairReaxC::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - cutghost[i][j] = cutghost[j][i] = cutmax; - return cutmax; -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::compute(int eflag, int vflag) -{ - double evdwl,ecoul; - double t_start, t_end; - - // communicate num_bonds once every reneighboring - // 2 num arrays stored by fix, grab ptr to them - - if (neighbor->ago == 0) comm->forward_comm_fix(fix_reax); - int *num_bonds = fix_reax->num_bonds; - int *num_hbonds = fix_reax->num_hbonds; - - evdwl = ecoul = 0.0; - ev_init(eflag,vflag); - - if (vflag_global) control->virial = 1; - else control->virial = 0; - - system->n = atom->nlocal; // my atoms - system->N = atom->nlocal + atom->nghost; // mine + ghosts - system->bigN = static_cast (atom->natoms); // all atoms in the system - - system->big_box.V = 0; - system->big_box.box_norms[0] = 0; - system->big_box.box_norms[1] = 0; - system->big_box.box_norms[2] = 0; - if (comm->me == 0 ) t_start = MPI_Wtime(); - - // setup data structures - - setup(); - - Reset( system, control, data, workspace, &lists ); - workspace->realloc.num_far = write_reax_lists(); - // timing for filling in the reax lists - if (comm->me == 0) { - t_end = MPI_Wtime(); - data->timing.nbrs = t_end - t_start; - } - - // forces - - Compute_Forces(system,control,data,workspace,&lists,out_control,mpi_data); - read_reax_forces(vflag); - - for (int k = 0; k < system->N; ++k) { - num_bonds[k] = system->my_atoms[k].num_bonds; - num_hbonds[k] = system->my_atoms[k].num_hbonds; - } - - // energies and pressure - - if (eflag_global) { - evdwl += data->my_en.e_bond; - evdwl += data->my_en.e_ov; - evdwl += data->my_en.e_un; - evdwl += data->my_en.e_lp; - evdwl += data->my_en.e_ang; - evdwl += data->my_en.e_pen; - evdwl += data->my_en.e_coa; - evdwl += data->my_en.e_hb; - evdwl += data->my_en.e_tor; - evdwl += data->my_en.e_con; - evdwl += data->my_en.e_vdW; - - ecoul += data->my_en.e_ele; - ecoul += data->my_en.e_pol; - - // eng_vdwl += evdwl; - // eng_coul += ecoul; - - // Store the different parts of the energy - // in a list for output by compute pair command - - pvector[0] = data->my_en.e_bond; - pvector[1] = data->my_en.e_ov + data->my_en.e_un; - pvector[2] = data->my_en.e_lp; - pvector[3] = 0.0; - pvector[4] = data->my_en.e_ang; - pvector[5] = data->my_en.e_pen; - pvector[6] = data->my_en.e_coa; - pvector[7] = data->my_en.e_hb; - pvector[8] = data->my_en.e_tor; - pvector[9] = data->my_en.e_con; - pvector[10] = data->my_en.e_vdW; - pvector[11] = data->my_en.e_ele; - pvector[12] = 0.0; - pvector[13] = data->my_en.e_pol; - } - - if (vflag_fdotr) virial_fdotr_compute(); - -// Set internal timestep counter to that of LAMMPS - - data->step = update->ntimestep; - - Output_Results( system, control, data, &lists, out_control, mpi_data ); - - // populate tmpid and tmpbo arrays for fix reax/c/species - int i, j; - - if (fixspecies_flag) { - if (system->N > nmax) { - memory->destroy(tmpid); - memory->destroy(tmpbo); - nmax = system->N; - memory->create(tmpid,nmax,MAXSPECBOND,"pair:tmpid"); - memory->create(tmpbo,nmax,MAXSPECBOND,"pair:tmpbo"); - } - - for (i = 0; i < system->N; i ++) - for (j = 0; j < MAXSPECBOND; j ++) { - tmpbo[i][j] = 0.0; - tmpid[i][j] = 0; - } - FindBond(); - } - -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::write_reax_atoms() -{ - int *num_bonds = fix_reax->num_bonds; - int *num_hbonds = fix_reax->num_hbonds; - - if (system->N > system->total_cap) - error->all(FLERR,"Too many ghost atoms"); - - for (int i = 0; i < system->N; ++i) { - system->my_atoms[i].orig_id = atom->tag[i]; - system->my_atoms[i].type = map[atom->type[i]]; - system->my_atoms[i].x[0] = atom->x[i][0]; - system->my_atoms[i].x[1] = atom->x[i][1]; - system->my_atoms[i].x[2] = atom->x[i][2]; - system->my_atoms[i].q = atom->q[i]; - system->my_atoms[i].num_bonds = num_bonds[i]; - system->my_atoms[i].num_hbonds = num_hbonds[i]; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::get_distance( rvec xj, rvec xi, double *d_sqr, rvec *dvec ) -{ - (*dvec)[0] = xj[0] - xi[0]; - (*dvec)[1] = xj[1] - xi[1]; - (*dvec)[2] = xj[2] - xi[2]; - *d_sqr = SQR((*dvec)[0]) + SQR((*dvec)[1]) + SQR((*dvec)[2]); -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::set_far_nbr( far_neighbor_data *fdest, - int j, double d, rvec dvec ) -{ - fdest->nbr = j; - fdest->d = d; - rvec_Copy( fdest->dvec, dvec ); - ivec_MakeZero( fdest->rel_box ); -} - -/* ---------------------------------------------------------------------- */ - -int PairReaxC::estimate_reax_lists() -{ - int itr_i, itr_j, i, j; - int num_nbrs, num_marked; - int *ilist, *jlist, *numneigh, **firstneigh, *marked; - double d_sqr; - rvec dvec; - double **x; - - int mincap = system->mincap; - double safezone = system->safezone; - - x = atom->x; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - num_nbrs = 0; - num_marked = 0; - marked = (int*) calloc( system->N, sizeof(int) ); - - int numall = list->inum + list->gnum; - - for (itr_i = 0; itr_i < numall; ++itr_i) { - i = ilist[itr_i]; - marked[i] = 1; - ++num_marked; - jlist = firstneigh[i]; - - for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { - j = jlist[itr_j]; - j &= NEIGHMASK; - get_distance( x[j], x[i], &d_sqr, &dvec ); - - if (d_sqr <= SQR(control->nonb_cut)) - ++num_nbrs; - } - } - - free( marked ); - - return static_cast (MAX(num_nbrs*safezone, mincap*REAX_MIN_NBRS)); -} - -/* ---------------------------------------------------------------------- */ - -int PairReaxC::write_reax_lists() -{ - int itr_i, itr_j, i, j; - int num_nbrs; - int *ilist, *jlist, *numneigh, **firstneigh; - double d_sqr, cutoff_sqr; - rvec dvec; - double *dist, **x; - reax_list *far_nbrs; - far_neighbor_data *far_list; - - x = atom->x; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - far_nbrs = lists + FAR_NBRS; - far_list = far_nbrs->select.far_nbr_list; - - num_nbrs = 0; - int inum = list->inum; - dist = (double*) calloc( system->N, sizeof(double) ); - - int numall = list->inum + list->gnum; - - for (itr_i = 0; itr_i < numall; ++itr_i) { - i = ilist[itr_i]; - jlist = firstneigh[i]; - Set_Start_Index( i, num_nbrs, far_nbrs ); - - if (i < inum) - cutoff_sqr = control->nonb_cut*control->nonb_cut; - else - cutoff_sqr = control->bond_cut*control->bond_cut; - - for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { - j = jlist[itr_j]; - j &= NEIGHMASK; - get_distance( x[j], x[i], &d_sqr, &dvec ); - - if (d_sqr <= (cutoff_sqr)) { - dist[j] = sqrt( d_sqr ); - set_far_nbr( &far_list[num_nbrs], j, dist[j], dvec ); - ++num_nbrs; - } - } - Set_End_Index( i, num_nbrs, far_nbrs ); - } - - free( dist ); - - return num_nbrs; -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::read_reax_forces(int /*vflag*/) -{ - for (int i = 0; i < system->N; ++i) { - system->my_atoms[i].f[0] = workspace->f[i][0]; - system->my_atoms[i].f[1] = workspace->f[i][1]; - system->my_atoms[i].f[2] = workspace->f[i][2]; - - atom->f[i][0] += -workspace->f[i][0]; - atom->f[i][1] += -workspace->f[i][1]; - atom->f[i][2] += -workspace->f[i][2]; - } - -} - -/* ---------------------------------------------------------------------- */ - -void *PairReaxC::extract(const char *str, int &dim) -{ - dim = 1; - if (strcmp(str,"chi") == 0 && chi) { - for (int i = 1; i <= atom->ntypes; i++) - if (map[i] >= 0) chi[i] = system->reax_param.sbp[map[i]].chi; - else chi[i] = 0.0; - return (void *) chi; - } - if (strcmp(str,"eta") == 0 && eta) { - for (int i = 1; i <= atom->ntypes; i++) - if (map[i] >= 0) eta[i] = system->reax_param.sbp[map[i]].eta; - else eta[i] = 0.0; - return (void *) eta; - } - if (strcmp(str,"gamma") == 0 && gamma) { - for (int i = 1; i <= atom->ntypes; i++) - if (map[i] >= 0) gamma[i] = system->reax_param.sbp[map[i]].gamma; - else gamma[i] = 0.0; - return (void *) gamma; - } - return nullptr; -} - -/* ---------------------------------------------------------------------- */ - -double PairReaxC::memory_usage() -{ - double bytes = 0.0; - - // From pair_reax_c - bytes += (double)1.0 * system->N * sizeof(int); - bytes += (double)1.0 * system->N * sizeof(double); - - // From reaxc_allocate: BO - bytes += (double)1.0 * system->total_cap * sizeof(reax_atom); - bytes += (double)19.0 * system->total_cap * sizeof(double); - bytes += (double)3.0 * system->total_cap * sizeof(int); - - // From reaxc_lists - bytes += (double)2.0 * lists->n * sizeof(int); - bytes += (double)lists->num_intrs * sizeof(three_body_interaction_data); - bytes += (double)lists->num_intrs * sizeof(bond_data); - bytes += (double)lists->num_intrs * sizeof(dbond_data); - bytes += (double)lists->num_intrs * sizeof(dDelta_data); - bytes += (double)lists->num_intrs * sizeof(far_neighbor_data); - bytes += (double)lists->num_intrs * sizeof(hbond_data); - - if (fixspecies_flag) - bytes += (double)2 * nmax * MAXSPECBOND * sizeof(double); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - -void PairReaxC::FindBond() -{ - int i, j, pj, nj; - double bo_tmp, bo_cut; - - bond_data *bo_ij; - bo_cut = 0.10; - - for (i = 0; i < system->n; i++) { - nj = 0; - for (pj = Start_Index(i, lists); pj < End_Index(i, lists); ++pj) { - bo_ij = &( lists->select.bond_list[pj] ); - j = bo_ij->nbr; - if (j < i) continue; - - bo_tmp = bo_ij->bo_data.BO; - - if (bo_tmp >= bo_cut) { - tmpid[i][nj] = j; - tmpbo[i][nj] = bo_tmp; - nj ++; - if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in reaxc_defs.h"); - } - } - } -} diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp deleted file mode 100644 index 1cb101b118..0000000000 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ /dev/null @@ -1,507 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_allocate.h" -#include -#include "reaxc_defs.h" -#include "reaxc_list.h" -#include "reaxc_tool_box.h" - -#if defined(LMP_USER_OMP) && defined(_OPENMP) -#include -#endif - -#include "error.h" - -/* allocate space for my_atoms - important: we cannot know the exact number of atoms that will fall into a - process's box throughout the whole simulation. therefore - we need to make upper bound estimates for various data structures */ -int PreAllocate_Space( reax_system *system, control_params * /*control*/, - storage * workspace ) -{ - int mincap = system->mincap; - double safezone = system->safezone; - - // determine the local and total capacity - - system->local_cap = MAX( (int)(system->n * safezone), mincap ); - system->total_cap = MAX( (int)(system->N * safezone), mincap ); - - system->my_atoms = (reax_atom*) - scalloc(system->error_ptr, system->total_cap, sizeof(reax_atom), "my_atoms"); - - // Nullify some arrays only used in omp styles - // Should be safe to do here since called in pair->setup(); -#ifdef LMP_USER_OMP - workspace->CdDeltaReduction = nullptr; - workspace->forceReduction = nullptr; - workspace->valence_angle_atom_myoffset = nullptr; - workspace->my_ext_pressReduction = nullptr; -#else - LMP_UNUSED_PARAM(workspace); -#endif - - return SUCCESS; -} - - -/************* system *************/ - -int Allocate_System( reax_system *system, int /*local_cap*/, int total_cap, - char * /*msg*/ ) -{ - system->my_atoms = (reax_atom*) - realloc( system->my_atoms, total_cap*sizeof(reax_atom) ); - - return SUCCESS; -} - - -void DeAllocate_System( reax_system *system ) -{ - int i, j, k; - int ntypes; - reax_interaction *ff_params; - - // deallocate the atom list - sfree(system->error_ptr, system->my_atoms, "system->my_atoms" ); - - // deallocate the ffield parameters storage - ff_params = &(system->reax_param); - ntypes = ff_params->num_atom_types; - - sfree(system->error_ptr, ff_params->gp.l, "ff:globals" ); - - for (i = 0; i < ntypes; ++i) { - for (j = 0; j < ntypes; ++j) { - for (k = 0; k < ntypes; ++k) { - sfree(system->error_ptr, ff_params->fbp[i][j][k], "ff:fbp[i,j,k]" ); - } - sfree(system->error_ptr, ff_params->fbp[i][j], "ff:fbp[i,j]" ); - sfree(system->error_ptr, ff_params->thbp[i][j], "ff:thbp[i,j]" ); - sfree(system->error_ptr, ff_params->hbp[i][j], "ff:hbp[i,j]" ); - } - sfree(system->error_ptr, ff_params->fbp[i], "ff:fbp[i]" ); - sfree(system->error_ptr, ff_params->thbp[i], "ff:thbp[i]" ); - sfree(system->error_ptr, ff_params->hbp[i], "ff:hbp[i]" ); - sfree(system->error_ptr, ff_params->tbp[i], "ff:tbp[i]" ); - } - sfree(system->error_ptr, ff_params->fbp, "ff:fbp" ); - sfree(system->error_ptr, ff_params->thbp, "ff:thbp" ); - sfree(system->error_ptr, ff_params->hbp, "ff:hbp" ); - sfree(system->error_ptr, ff_params->tbp, "ff:tbp" ); - sfree(system->error_ptr, ff_params->sbp, "ff:sbp" ); -} - - -/************* workspace *************/ -void DeAllocate_Workspace( control_params * control, storage *workspace ) -{ - int i; - - if (!workspace->allocated) - return; - - workspace->allocated = 0; - - /* communication storage */ - for (i = 0; i < MAX_NBRS; ++i) { - sfree(control->error_ptr, workspace->tmp_dbl[i], "tmp_dbl[i]" ); - sfree(control->error_ptr, workspace->tmp_rvec[i], "tmp_rvec[i]" ); - sfree(control->error_ptr, workspace->tmp_rvec2[i], "tmp_rvec2[i]" ); - } - - /* bond order storage */ - sfree(control->error_ptr, workspace->within_bond_box, "skin" ); - sfree(control->error_ptr, workspace->total_bond_order, "total_bo" ); - sfree(control->error_ptr, workspace->Deltap, "Deltap" ); - sfree(control->error_ptr, workspace->Deltap_boc, "Deltap_boc" ); - sfree(control->error_ptr, workspace->dDeltap_self, "dDeltap_self" ); - sfree(control->error_ptr, workspace->Delta, "Delta" ); - sfree(control->error_ptr, workspace->Delta_lp, "Delta_lp" ); - sfree(control->error_ptr, workspace->Delta_lp_temp, "Delta_lp_temp" ); - sfree(control->error_ptr, workspace->dDelta_lp, "dDelta_lp" ); - sfree(control->error_ptr, workspace->dDelta_lp_temp, "dDelta_lp_temp" ); - sfree(control->error_ptr, workspace->Delta_e, "Delta_e" ); - sfree(control->error_ptr, workspace->Delta_boc, "Delta_boc" ); - sfree(control->error_ptr, workspace->Delta_val, "Delta_val" ); - sfree(control->error_ptr, workspace->nlp, "nlp" ); - sfree(control->error_ptr, workspace->nlp_temp, "nlp_temp" ); - sfree(control->error_ptr, workspace->Clp, "Clp" ); - sfree(control->error_ptr, workspace->vlpex, "vlpex" ); - sfree(control->error_ptr, workspace->bond_mark, "bond_mark" ); - sfree(control->error_ptr, workspace->done_after, "done_after" ); - - /* QEq storage */ - sfree(control->error_ptr, workspace->Hdia_inv, "Hdia_inv" ); - sfree(control->error_ptr, workspace->b_s, "b_s" ); - sfree(control->error_ptr, workspace->b_t, "b_t" ); - sfree(control->error_ptr, workspace->b_prc, "b_prc" ); - sfree(control->error_ptr, workspace->b_prm, "b_prm" ); - sfree(control->error_ptr, workspace->s, "s" ); - sfree(control->error_ptr, workspace->t, "t" ); - sfree(control->error_ptr, workspace->droptol, "droptol" ); - sfree(control->error_ptr, workspace->b, "b" ); - sfree(control->error_ptr, workspace->x, "x" ); - - /* GMRES storage */ - for (i = 0; i < RESTART+1; ++i) { - sfree(control->error_ptr, workspace->h[i], "h[i]" ); - sfree(control->error_ptr, workspace->v[i], "v[i]" ); - } - sfree(control->error_ptr, workspace->h, "h" ); - sfree(control->error_ptr, workspace->v, "v" ); - sfree(control->error_ptr, workspace->y, "y" ); - sfree(control->error_ptr, workspace->z, "z" ); - sfree(control->error_ptr, workspace->g, "g" ); - sfree(control->error_ptr, workspace->hs, "hs" ); - sfree(control->error_ptr, workspace->hc, "hc" ); - /* CG storage */ - sfree(control->error_ptr, workspace->r, "r" ); - sfree(control->error_ptr, workspace->d, "d" ); - sfree(control->error_ptr, workspace->q, "q" ); - sfree(control->error_ptr, workspace->p, "p" ); - sfree(control->error_ptr, workspace->r2, "r2" ); - sfree(control->error_ptr, workspace->d2, "d2" ); - sfree(control->error_ptr, workspace->q2, "q2" ); - sfree(control->error_ptr, workspace->p2, "p2" ); - - /* integrator storage */ - sfree(control->error_ptr, workspace->v_const, "v_const" ); - - /* force related storage */ - sfree(control->error_ptr, workspace->f, "f" ); - sfree(control->error_ptr, workspace->CdDelta, "CdDelta" ); - - /* reductions */ -#ifdef LMP_USER_OMP - if (workspace->CdDeltaReduction) sfree(control->error_ptr, workspace->CdDeltaReduction, "cddelta_reduce" ); - if (workspace->forceReduction) sfree(control->error_ptr, workspace->forceReduction, "f_reduce" ); - if (workspace->valence_angle_atom_myoffset) sfree(control->error_ptr, workspace->valence_angle_atom_myoffset, "valence_angle_atom_myoffset"); - if (workspace->my_ext_pressReduction) sfree(control->error_ptr, workspace->my_ext_pressReduction, "ext_press_reduce"); -#endif -} - - -int Allocate_Workspace( reax_system * /*system*/, control_params * control, - storage *workspace, int local_cap, int total_cap, - char * /*msg*/ ) -{ - int i, total_real, total_rvec, local_rvec; - - workspace->allocated = 1; - total_real = total_cap * sizeof(double); - total_rvec = total_cap * sizeof(rvec); - local_rvec = local_cap * sizeof(rvec); - - /* communication storage */ - for (i = 0; i < MAX_NBRS; ++i) { - workspace->tmp_dbl[i] = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "tmp_dbl"); - workspace->tmp_rvec[i] = (rvec*) - scalloc(control->error_ptr, total_cap, sizeof(rvec), "tmp_rvec"); - workspace->tmp_rvec2[i] = (rvec2*) - scalloc(control->error_ptr, total_cap, sizeof(rvec2), "tmp_rvec2"); - } - - /* bond order related storage */ - workspace->within_bond_box = (int*) - scalloc(control->error_ptr, total_cap, sizeof(int), "skin"); - workspace->total_bond_order = (double*) smalloc(control->error_ptr, total_real, "total_bo"); - workspace->Deltap = (double*) smalloc(control->error_ptr, total_real, "Deltap"); - workspace->Deltap_boc = (double*) smalloc(control->error_ptr, total_real, "Deltap_boc"); - workspace->dDeltap_self = (rvec*) smalloc(control->error_ptr, total_rvec, "dDeltap_self"); - workspace->Delta = (double*) smalloc(control->error_ptr, total_real, "Delta"); - workspace->Delta_lp = (double*) smalloc(control->error_ptr, total_real, "Delta_lp"); - workspace->Delta_lp_temp = (double*) - smalloc(control->error_ptr, total_real, "Delta_lp_temp"); - workspace->dDelta_lp = (double*) smalloc(control->error_ptr, total_real, "dDelta_lp"); - workspace->dDelta_lp_temp = (double*) - smalloc(control->error_ptr, total_real, "dDelta_lp_temp"); - workspace->Delta_e = (double*) smalloc(control->error_ptr, total_real, "Delta_e"); - workspace->Delta_boc = (double*) smalloc(control->error_ptr, total_real, "Delta_boc"); - workspace->Delta_val = (double*) smalloc(control->error_ptr, total_real, "Delta_val"); - workspace->nlp = (double*) smalloc(control->error_ptr, total_real, "nlp"); - workspace->nlp_temp = (double*) smalloc(control->error_ptr, total_real, "nlp_temp"); - workspace->Clp = (double*) smalloc(control->error_ptr, total_real, "Clp"); - workspace->vlpex = (double*) smalloc(control->error_ptr, total_real, "vlpex"); - workspace->bond_mark = (int*) - scalloc(control->error_ptr, total_cap, sizeof(int), "bond_mark"); - workspace->done_after = (int*) - scalloc(control->error_ptr, total_cap, sizeof(int), "done_after"); - - /* QEq storage */ - workspace->Hdia_inv = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "Hdia_inv"); - workspace->b_s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_s"); - workspace->b_t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_t"); - workspace->b_prc = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prc"); - workspace->b_prm = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prm"); - workspace->s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "s"); - workspace->t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "t"); - workspace->droptol = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "droptol"); - workspace->b = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "b"); - workspace->x = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "x"); - - /* GMRES storage */ - workspace->y = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "y"); - workspace->z = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "z"); - workspace->g = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "g"); - workspace->h = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "h"); - workspace->hs = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hs"); - workspace->hc = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hc"); - workspace->v = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "v"); - - for (i = 0; i < RESTART+1; ++i) { - workspace->h[i] = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "h[i]"); - workspace->v[i] = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "v[i]"); - } - - /* CG storage */ - workspace->r = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "r"); - workspace->d = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "d"); - workspace->q = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "q"); - workspace->p = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "p"); - workspace->r2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "r2"); - workspace->d2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "d2"); - workspace->q2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "q2"); - workspace->p2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "p2"); - - /* integrator storage */ - workspace->v_const = (rvec*) smalloc(control->error_ptr, local_rvec, "v_const"); - - /* force related storage */ - workspace->f = (rvec*) scalloc(control->error_ptr, total_cap, sizeof(rvec), "f"); - workspace->CdDelta = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "CdDelta"); - - // storage for reductions with multiple threads -#ifdef LMP_USER_OMP - workspace->CdDeltaReduction = (double *) scalloc(control->error_ptr, sizeof(double), (rc_bigint)total_cap*control->nthreads, - "cddelta_reduce"); - - workspace->forceReduction = (rvec *) scalloc(control->error_ptr, sizeof(rvec), (rc_bigint)total_cap*control->nthreads, - "forceReduction"); - - workspace->valence_angle_atom_myoffset = (int *) scalloc(control->error_ptr, sizeof(int), total_cap, "valence_angle_atom_myoffset"); - workspace->my_ext_pressReduction = (rvec *) calloc(sizeof(rvec), control->nthreads); -#else - LMP_UNUSED_PARAM(control); -#endif - - return SUCCESS; -} - - -static void Reallocate_Neighbor_List( reax_list *far_nbrs, int n, - int num_intrs ) -{ - Delete_List( far_nbrs); - if (!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs )) { - far_nbrs->error_ptr->one(FLERR,"Problem in initializing far neighbors list"); - } -} - - -static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds ) -{ - int i, total_hbonds; - - int mincap = system->mincap; - double saferzone = system->saferzone; - - total_hbonds = 0; - for (i = 0; i < system->n; ++i) - if ((system->my_atoms[i].Hindex) >= 0) { - total_hbonds += system->my_atoms[i].num_hbonds; - } - total_hbonds = (int)(MAX(total_hbonds*saferzone, mincap*system->minhbonds)); - - Delete_List( hbonds); - if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds )) { - hbonds->error_ptr->one(FLERR, "Not enough space for hydrogen bonds list"); - } - - return total_hbonds; -} - - -static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, - int *total_bonds, int *est_3body ) -{ - int i; - - int mincap = system->mincap; - double safezone = system->safezone; - - *total_bonds = 0; - *est_3body = 0; - for (i = 0; i < system->N; ++i) { - *est_3body += SQR(system->my_atoms[i].num_bonds); - *total_bonds += system->my_atoms[i].num_bonds; - } - *total_bonds = (int)(MAX( *total_bonds * safezone, mincap*MIN_BONDS )); - -#ifdef LMP_USER_OMP - if (system->omp_active) - for (i = 0; i < bonds->num_intrs; ++i) - sfree(system->error_ptr, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); -#endif - - Delete_List( bonds); - if (!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds)) { - bonds->error_ptr->one(FLERR, "Not enough space for bonds list"); - } - -#ifdef LMP_USER_OMP -#if defined(_OPENMP) - int nthreads = omp_get_num_threads(); -#else - int nthreads = 1; -#endif - - if (system->omp_active) - for (i = 0; i < bonds->num_intrs; ++i) - bonds->select.bond_list[i].bo_data.CdboReduction = - (double*) smalloc(system->error_ptr, sizeof(double)*nthreads, "CdboReduction"); -#endif - - return SUCCESS; -} - - -void ReAllocate( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists ) -{ - int num_bonds, est_3body, Hflag, ret; - int renbr, newsize; - reallocate_data *realloc; - reax_list *far_nbrs; - char msg[200]; - - int mincap = system->mincap; - double safezone = system->safezone; - double saferzone = system->saferzone; - - realloc = &(workspace->realloc); - - if ( system->n >= DANGER_ZONE * system->local_cap || - (0 && system->n <= LOOSE_ZONE * system->local_cap)) { - system->local_cap = MAX( (int)(system->n * safezone), mincap ); - } - - int Nflag = 0; - if ( system->N >= DANGER_ZONE * system->total_cap || - (0 && system->N <= LOOSE_ZONE * system->total_cap)) { - Nflag = 1; - system->total_cap = MAX( (int)(system->N * safezone), mincap ); - } - - if (Nflag) { - /* system */ - ret = Allocate_System( system, system->local_cap, system->total_cap, msg ); - if (ret != SUCCESS) { - char errmsg[256]; - snprintf(errmsg, 256, "Not enough space for atom_list: total_cap=%d", system->total_cap); - system->error_ptr->one(FLERR, errmsg); - } - - /* workspace */ - DeAllocate_Workspace( control, workspace ); - ret = Allocate_Workspace( system, control, workspace, system->local_cap, - system->total_cap, msg ); - if (ret != SUCCESS) { - char errmsg[256]; - snprintf(errmsg, 256, "Not enough space for workspace: local_cap=%d total_cap=%d", system->local_cap, system->total_cap); - system->error_ptr->one(FLERR, errmsg); - } - } - - - renbr = (data->step - data->prev_steps) % control->reneighbor == 0; - /* far neighbors */ - if (renbr) { - far_nbrs = *lists + FAR_NBRS; - - if (Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE) { - if (realloc->num_far > far_nbrs->num_intrs) { - char errmsg[256]; - snprintf(errmsg, 256, "step%d-ran out of space on far_nbrs: top=%d, max=%d", data->step, realloc->num_far, far_nbrs->num_intrs); - system->error_ptr->one(FLERR, errmsg); - } - - newsize = static_cast - (MAX( realloc->num_far*safezone, mincap*REAX_MIN_NBRS)); - - Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize); - realloc->num_far = 0; - } - } - - /* hydrogen bonds list */ - if (control->hbond_cut > 0) { - Hflag = 0; - if ( system->numH >= DANGER_ZONE * system->Hcap || - (0 && system->numH <= LOOSE_ZONE * system->Hcap)) { - Hflag = 1; - system->Hcap = int(MAX( system->numH * saferzone, mincap )); - } - - if (Hflag || realloc->hbonds) { - ret = Reallocate_HBonds_List( system, (*lists)+HBONDS); - realloc->hbonds = 0; - } - } - - /* bonds list */ - num_bonds = est_3body = -1; - if (Nflag || realloc->bonds) { - Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds, - &est_3body); - realloc->bonds = 0; - realloc->num_3body = MAX( realloc->num_3body, est_3body ) * 2; - } - - /* 3-body list */ - if (realloc->num_3body > 0) { - Delete_List( (*lists)+THREE_BODIES); - - if (num_bonds == -1) - num_bonds = ((*lists)+BONDS)->num_intrs; - - realloc->num_3body = (int)(MAX(realloc->num_3body*safezone, MIN_3BODIES)); - - if ( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY, - (*lists)+THREE_BODIES )) { - system->error_ptr->one(FLERR, "Problem in initializing angles list"); - } - realloc->num_3body = -1; - } - -} diff --git a/src/USER-REAXC/reaxc_allocate.h b/src/USER-REAXC/reaxc_allocate.h deleted file mode 100644 index b5e6f542ee..0000000000 --- a/src/USER-REAXC/reaxc_allocate.h +++ /dev/null @@ -1,43 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __ALLOCATE_H_ -#define __ALLOCATE_H_ - -#include "reaxc_types.h" -int PreAllocate_Space( reax_system*, control_params*, storage* ); - -int Allocate_System( reax_system*, int, int, char* ); -void DeAllocate_System( reax_system* ); - -int Allocate_Workspace( reax_system*, control_params*, storage*, - int, int, char* ); -void DeAllocate_Workspace( control_params*, storage* ); - -void ReAllocate( reax_system*, control_params*, simulation_data*, storage*, - reax_list** ); -#endif diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp deleted file mode 100644 index bfc04d96a8..0000000000 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ /dev/null @@ -1,595 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_bond_orders.h" -#include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_types.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data, - storage *workspace, reax_list **lists ) -{ - reax_list *bonds = (*lists) + BONDS; - bond_data *nbr_j, *nbr_k; - bond_order_data *bo_ij, *bo_ji; - dbond_coefficients coef; - rvec temp, ext_press; - ivec rel_box; - int pk, k, j; - - /* Initializations */ - nbr_j = &(bonds->select.bond_list[pj]); - j = nbr_j->nbr; - bo_ij = &(nbr_j->bo_data); - bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data); - - coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - - coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - - coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - - coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - - for (pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - rvec_Scale(temp, -coef.C2dbo, nbr_k->bo_data.dBOp); /*2nd, dBO*/ - rvec_ScaledAdd(temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);/*dDelta*/ - rvec_ScaledAdd(temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); /*3rd, dBOpi*/ - rvec_ScaledAdd(temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);/*3rd, dBOpi2*/ - - /* force */ - rvec_Add( workspace->f[k], temp ); - /* pressure */ - rvec_iMultiply( ext_press, nbr_k->rel_box, temp ); - rvec_Add( data->my_ext_press, ext_press ); - - } - - /* then atom i itself */ - rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st,dBO*/ - rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd,dBO*/ - rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st,dBO*/ - rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd,dBO*/ - rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/ - rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/ - rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);/*3rd,dBOpi*/ - - rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBO_pi2*/ - rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBO_pi2*/ - rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );/*3rd*/ - - /* force */ - rvec_Add( workspace->f[i], temp ); - - for (pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/ - rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/ - rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); /*4th,dBOpi*/ - rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);/*4th,dBOpi2*/ - - /* force */ - rvec_Add( workspace->f[k], temp ); - /* pressure */ - if (k != i) { - ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i) - rvec_iMultiply( ext_press, rel_box, temp ); - rvec_Add( data->my_ext_press, ext_press ); - - } - } - - /* then atom j itself */ - rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/ - rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/ - rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/ - rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);/*2nd, dBO*/ - - rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/ - rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/ - rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);/*3rd,dBOpi*/ - - rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBOpi2*/ - rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBOpi2*/ - rvec_ScaledAdd( temp,coef.C4dbopi2,workspace->dDeltap_self[j]);/*3rd,dBOpi2*/ - - /* force */ - rvec_Add( workspace->f[j], temp ); - /* pressure */ - rvec_iMultiply( ext_press, nbr_j->rel_box, temp ); - rvec_Add( data->my_ext_press, ext_press ); - -} - -void Add_dBond_to_Forces( reax_system *system, int i, int pj, - storage *workspace, reax_list **lists ) -{ - reax_list *bonds = (*lists) + BONDS; - bond_data *nbr_j, *nbr_k; - bond_order_data *bo_ij, *bo_ji; - dbond_coefficients coef; - int pk, k, j; - - /* Virial Tallying variables */ - rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp; - - /* Initializations */ - nbr_j = &(bonds->select.bond_list[pj]); - j = nbr_j->nbr; - bo_ij = &(nbr_j->bo_data); - bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data); - - coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo); - - coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); - - coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); - - coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); - - // forces on i - rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); - rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] ); - rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); - rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]); - rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); - rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] ); - rvec_Add( workspace->f[i], temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fi_tmp, -1.0, temp); - rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x ); - system->pair_ptr->v_tally(i,fi_tmp,delij); - } - - // forces on j - rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); - rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]); - rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); - rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]); - rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); - rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); - rvec_ScaledAdd( temp, coef.C4dbopi2, workspace->dDeltap_self[j]); - rvec_Add( workspace->f[j], temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fj_tmp, -1.0, temp); - rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x ); - system->pair_ptr->v_tally(j,fj_tmp,delji); - } - - // forces on k: i neighbor - for (pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp); - rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp); - rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); - rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp); - rvec_Add( workspace->f[k], temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fk_tmp, -1.0, temp); - rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); - system->pair_ptr->v_tally(k,fk_tmp,delki); - rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); - system->pair_ptr->v_tally(k,fk_tmp,delkj); - } - } - - // forces on k: j neighbor - for (pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk) { - nbr_k = &(bonds->select.bond_list[pk]); - k = nbr_k->nbr; - - rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); - rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp); - rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); - rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp); - rvec_Add( workspace->f[k], temp ); - - if (system->pair_ptr->vflag_atom) { - rvec_Scale(fk_tmp, -1.0, temp); - rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); - system->pair_ptr->v_tally(k,fk_tmp,delki); - rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); - system->pair_ptr->v_tally(k,fk_tmp,delkj); - } - } - -} - - -int BOp( storage *workspace, reax_list *bonds, double bo_cut, - int i, int btop_i, far_neighbor_data *nbr_pj, - single_body_parameters *sbp_i, single_body_parameters *sbp_j, - two_body_parameters *twbp) { - int j, btop_j; - double r2, C12, C34, C56; - double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; - double BO, BO_s, BO_pi, BO_pi2; - bond_data *ibond, *jbond; - bond_order_data *bo_ij, *bo_ji; - - j = nbr_pj->nbr; - r2 = SQR(nbr_pj->d); - - if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { - C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 ); - BO_s = (1.0 + bo_cut) * exp( C12 ); - } - else BO_s = C12 = 0.0; - - if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { - C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 ); - BO_pi = exp( C34 ); - } - else BO_pi = C34 = 0.0; - - if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { - C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 ); - BO_pi2= exp( C56 ); - } - else BO_pi2 = C56 = 0.0; - - /* Initially BO values are the uncorrected ones, page 1 */ - BO = BO_s + BO_pi + BO_pi2; - - if (BO >= bo_cut) { - /****** bonds i-j and j-i ******/ - ibond = &( bonds->select.bond_list[btop_i] ); - btop_j = End_Index( j, bonds ); - jbond = &(bonds->select.bond_list[btop_j]); - - ibond->nbr = j; - jbond->nbr = i; - ibond->d = nbr_pj->d; - jbond->d = nbr_pj->d; - rvec_Copy( ibond->dvec, nbr_pj->dvec ); - rvec_Scale( jbond->dvec, -1, nbr_pj->dvec ); - ivec_Copy( ibond->rel_box, nbr_pj->rel_box ); - ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box ); - ibond->dbond_index = btop_i; - jbond->dbond_index = btop_i; - ibond->sym_index = btop_j; - jbond->sym_index = btop_i; - Set_End_Index( j, btop_j+1, bonds ); - - bo_ij = &( ibond->bo_data ); - bo_ji = &( jbond->bo_data ); - bo_ji->BO = bo_ij->BO = BO; - bo_ji->BO_s = bo_ij->BO_s = BO_s; - bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; - bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; - - /* Bond Order page2-3, derivative of total bond order prime */ - Cln_BOp_s = twbp->p_bo2 * C12 / r2; - Cln_BOp_pi = twbp->p_bo4 * C34 / r2; - Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2; - - /* Only dln_BOp_xx wrt. dr_i is stored here, note that - dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ - rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec); - rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec); - rvec_Scale(bo_ij->dln_BOp_pi2, - -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec); - rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); - rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi ); - rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 ); - - rvec_Scale( bo_ij->dBOp, - -(bo_ij->BO_s * Cln_BOp_s + - bo_ij->BO_pi * Cln_BOp_pi + - bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec ); - rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp ); - - rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp ); - rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp ); - - bo_ij->BO_s -= bo_cut; - bo_ij->BO -= bo_cut; - bo_ji->BO_s -= bo_cut; - bo_ji->BO -= bo_cut; - workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp - workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp - bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; - bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; - - return 1; - } - - return 0; -} - - -void BO( reax_system *system, control_params * /*control*/, simulation_data * /*data*/, - storage *workspace, reax_list **lists, output_controls * /*out_control*/ ) -{ - int i, j, pj, type_i, type_j; - int start_i, end_i, sym_index; - double val_i, Deltap_i, Deltap_boc_i; - double val_j, Deltap_j, Deltap_boc_j; - double f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5; - double exp_p1i, exp_p2i, exp_p1j, exp_p2j; - double temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji; - double Cf45_ij, Cf45_ji, p_lp1; //u_ij, u_ji - double A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji; - double explp1, p_boc1, p_boc2; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - bond_order_data *bo_ij, *bo_ji; - reax_list *bonds = (*lists) + BONDS; - - p_boc1 = system->reax_param.gp.l[0]; - p_boc2 = system->reax_param.gp.l[1]; - - /* Calculate Deltaprime, Deltaprime_boc values */ - for (i = 0; i < system->N; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[type_i]); - workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency; - workspace->Deltap_boc[i] = - workspace->total_bond_order[i] - sbp_i->valency_val; - - workspace->total_bond_order[i] = 0; - } - - /* Corrected Bond Order calculations */ - for (i = 0; i < system->N; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - sbp_i = &(system->reax_param.sbp[type_i]); - val_i = sbp_i->valency; - Deltap_i = workspace->Deltap[i]; - Deltap_boc_i = workspace->Deltap_boc[i]; - start_i = Start_Index(i, bonds); - end_i = End_Index(i, bonds); - - for (pj = start_i; pj < end_i; ++pj) { - j = bonds->select.bond_list[pj].nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - bo_ij = &( bonds->select.bond_list[pj].bo_data ); - // fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO ); - - if (i < j || workspace->bond_mark[j] > 3) { - twbp = &( system->reax_param.tbp[type_i][type_j] ); - - if (twbp->ovc < 0.001 && twbp->v13cor < 0.001) { - bo_ij->C1dbo = 1.000000; - bo_ij->C2dbo = 0.000000; - bo_ij->C3dbo = 0.000000; - - bo_ij->C1dbopi = 1.000000; - bo_ij->C2dbopi = 0.000000; - bo_ij->C3dbopi = 0.000000; - bo_ij->C4dbopi = 0.000000; - - bo_ij->C1dbopi2 = 1.000000; - bo_ij->C2dbopi2 = 0.000000; - bo_ij->C3dbopi2 = 0.000000; - bo_ij->C4dbopi2 = 0.000000; - - } - else { - val_j = system->reax_param.sbp[type_j].valency; - Deltap_j = workspace->Deltap[j]; - Deltap_boc_j = workspace->Deltap_boc[j]; - - /* on page 1 */ - if (twbp->ovc >= 0.001) { - /* Correction for overcoordination */ - exp_p1i = exp( -p_boc1 * Deltap_i ); - exp_p2i = exp( -p_boc2 * Deltap_i ); - exp_p1j = exp( -p_boc1 * Deltap_j ); - exp_p2j = exp( -p_boc2 * Deltap_j ); - - f2 = exp_p1i + exp_p1j; - f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) ); - f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) + - ( val_j + f2 )/( val_j + f2 + f3 ) ); - - temp = f2 + f3; - u1_ij = val_i + temp; - u1_ji = val_j + temp; - Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) + - 1.0 / SQR( u1_ji )); - Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) + - ( u1_ji - f3 ) / SQR( u1_ji )); - - Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij - - ((val_i+f2) / SQR(u1_ij)) * - ( -p_boc1 * exp_p1i + - exp_p2i / ( exp_p2i + exp_p2j ) ) + - -p_boc1 * exp_p1i / u1_ji - - ((val_j+f2) / SQR(u1_ji)) * - ( -p_boc1 * exp_p1i + - exp_p2i / ( exp_p2i + exp_p2j ) )); - - - Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j + - Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j ); - - } - else { - /* No overcoordination correction! */ - f1 = 1.0; - Cf1_ij = Cf1_ji = 0.0; - } - - if (twbp->v13cor >= 0.001) { - /* Correction for 1-3 bond orders */ - exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) - - Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5); - exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) - - Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5); - - f4 = 1. / (1. + exp_f4); - f5 = 1. / (1. + exp_f5); - f4f5 = f4 * f5; - - /* Bond Order pages 8-9, derivative of f4 and f5 */ - Cf45_ij = -f4 * exp_f4; - Cf45_ji = -f5 * exp_f5; - } - else { - f4 = f5 = f4f5 = 1.0; - Cf45_ij = Cf45_ji = 0.0; - } - - /* Bond Order page 10, derivative of total bond order */ - A0_ij = f1 * f4f5; - A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO * - (Cf45_ij + Cf45_ji); - A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij; - A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji; - A3_ij = A2_ij + Cf1_ij / f1; - A3_ji = A2_ji + Cf1_ji / f1; - - /* find corrected bond orders and their derivative coef */ - bo_ij->BO = bo_ij->BO * A0_ij; - bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1; - bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1; - bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 ); - - bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij; - bo_ij->C2dbo = bo_ij->BO * A2_ij; - bo_ij->C3dbo = bo_ij->BO * A2_ji; - - bo_ij->C1dbopi = f1*f1*f4*f5; - bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij; - bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij; - bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji; - - bo_ij->C1dbopi2 = f1*f1*f4*f5; - bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij; - bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij; - bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji; - - } - - /* neglect bonds that are < 1e-10 */ - if (bo_ij->BO < 1e-10) - bo_ij->BO = 0.0; - if (bo_ij->BO_s < 1e-10) - bo_ij->BO_s = 0.0; - if (bo_ij->BO_pi < 1e-10) - bo_ij->BO_pi = 0.0; - if (bo_ij->BO_pi2 < 1e-10) - bo_ij->BO_pi2 = 0.0; - - workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO - - } - else { - /* We only need to update bond orders from bo_ji - everything else is set in uncorrected_bo calculations */ - sym_index = bonds->select.bond_list[pj].sym_index; - bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data); - bo_ij->BO = bo_ji->BO; - bo_ij->BO_s = bo_ji->BO_s; - bo_ij->BO_pi = bo_ji->BO_pi; - bo_ij->BO_pi2 = bo_ji->BO_pi2; - - workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO - } - } - - } - - p_lp1 = system->reax_param.gp.l[15]; - for (j = 0; j < system->N; ++j) { - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - sbp_j = &(system->reax_param.sbp[ type_j ]); - - workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency; - workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e; - workspace->Delta_boc[j] = workspace->total_bond_order[j] - - sbp_j->valency_boc; - workspace->Delta_val[j] = workspace->total_bond_order[j] - - sbp_j->valency_val; - - workspace->vlpex[j] = workspace->Delta_e[j] - - 2.0 * (int)(workspace->Delta_e[j]/2.0); - explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j])); - workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0); - workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j]; - workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]); - workspace->dDelta_lp[j] = workspace->Clp[j]; - - if (sbp_j->mass > 21.0) { - workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency); - workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; - workspace->dDelta_lp_temp[j] = 0.; - } - else { - workspace->nlp_temp[j] = workspace->nlp[j]; - workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; - workspace->dDelta_lp_temp[j] = workspace->Clp[j]; - } - - } - -} diff --git a/src/USER-REAXC/reaxc_bond_orders.h b/src/USER-REAXC/reaxc_bond_orders.h deleted file mode 100644 index 63550061d0..0000000000 --- a/src/USER-REAXC/reaxc_bond_orders.h +++ /dev/null @@ -1,47 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __BOND_ORDERS_H_ -#define __BOND_ORDERS_H_ - -#include "reaxc_types.h" - -typedef struct{ - double C1dbo, C2dbo, C3dbo; - double C1dbopi, C2dbopi, C3dbopi, C4dbopi; - double C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2; - double C1dDelta, C2dDelta, C3dDelta; -}dbond_coefficients; - -void Add_dBond_to_Forces( reax_system*, int, int, storage*, reax_list** ); -void Add_dBond_to_Forces_NPT( int, int, simulation_data*, - storage*, reax_list** ); -int BOp(storage*, reax_list*, double, int, int, far_neighbor_data*, - single_body_parameters*, single_body_parameters*, two_body_parameters*); -void BO( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -#endif diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp deleted file mode 100644 index 9ace195ee0..0000000000 --- a/src/USER-REAXC/reaxc_bonds.cpp +++ /dev/null @@ -1,138 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_bonds.h" -#include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" - -void Bonds( reax_system *system, control_params * /*control*/, - simulation_data *data, storage *workspace, reax_list **lists, - output_controls * /*out_control*/ ) -{ - int i, j, pj, natoms; - int start_i, end_i; - int type_i, type_j; - double ebond, pow_BOs_be2, exp_be12, CEbo; - double gp3, gp4, gp7, gp10, gp37; - double exphu, exphua1, exphub1, exphuov, hulpov, estriph; - double decobdbo, decobdboua, decobdboub; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - bond_order_data *bo_ij; - reax_list *bonds; - - bonds = (*lists) + BONDS; - gp3 = system->reax_param.gp.l[3]; - gp4 = system->reax_param.gp.l[4]; - gp7 = system->reax_param.gp.l[7]; - gp10 = system->reax_param.gp.l[10]; - gp37 = (int) system->reax_param.gp.l[37]; - natoms = system->n; - - for (i = 0; i < natoms; ++i) { - start_i = Start_Index(i, bonds); - end_i = End_Index(i, bonds); - - for (pj = start_i; pj < end_i; ++pj) { - j = bonds->select.bond_list[pj].nbr; - - if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id) - continue; - if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) { - if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue; - if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && - system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue; - if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && - system->my_atoms[j].x[1] == system->my_atoms[i].x[1] && - system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue; - } - - /* set the pointers */ - type_i = system->my_atoms[i].type; - type_j = system->my_atoms[j].type; - sbp_i = &( system->reax_param.sbp[type_i] ); - sbp_j = &( system->reax_param.sbp[type_j] ); - twbp = &( system->reax_param.tbp[type_i][type_j] ); - bo_ij = &( bonds->select.bond_list[pj].bo_data ); - - /* calculate the constants */ - if (bo_ij->BO_s == 0.0) pow_BOs_be2 = 0.0; - else pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 ); - exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) ); - CEbo = -twbp->De_s * exp_be12 * - ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 ); - - /* calculate the Bond Energy */ - data->my_en.e_bond += ebond = - -twbp->De_s * bo_ij->BO_s * exp_be12 - -twbp->De_p * bo_ij->BO_pi - -twbp->De_pp * bo_ij->BO_pi2; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0); - - /* calculate derivatives of Bond Orders */ - bo_ij->Cdbo += CEbo; - bo_ij->Cdbopi -= (CEbo + twbp->De_p); - bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp); - - /* Stabilisation terminal triple bond */ - if (bo_ij->BO >= 1.00) { - if ( gp37 == 2 || - (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) || - (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990)) { - exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) ); - exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO)); - exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO)); - exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j])); - hulpov = 1.0 / (1.0 + 25.0 * exphuov); - - estriph = gp10 * exphu * hulpov * (exphua1 + exphub1); - data->my_en.e_bond += estriph; - - decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) * - ( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) ); - decobdboua = -gp10 * exphu * hulpov * - (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); - decobdboub = -gp10 * exphu * hulpov * - (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0); - - bo_ij->Cdbo += decobdbo; - workspace->CdDelta[i] += decobdboua; - workspace->CdDelta[j] += decobdboub; - } - } - } - } -} diff --git a/src/USER-REAXC/reaxc_bonds.h b/src/USER-REAXC/reaxc_bonds.h deleted file mode 100644 index 49a869c766..0000000000 --- a/src/USER-REAXC/reaxc_bonds.h +++ /dev/null @@ -1,35 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __BONDS_H_ -#define __BONDS_H_ - -#include "reaxc_types.h" - -void Bonds( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -#endif diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp deleted file mode 100644 index 84c5feeec2..0000000000 --- a/src/USER-REAXC/reaxc_control.cpp +++ /dev/null @@ -1,391 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_control.h" -#include -#include -#include "reaxc_defs.h" -#include "reaxc_tool_box.h" - -#include "error.h" - -char Read_Control_File( char *control_file, control_params* control, - output_controls *out_control ) -{ - FILE *fp; - char *s, **tmp; - int i,ival; - double val; - - /* open control file */ - if ((fp = fopen( control_file, "r" ) ) == nullptr) { - control->error_ptr->all(FLERR, "The control file cannot be opened"); - } - - /* assign default values */ - strcpy( control->sim_name, "simulate" ); - control->ensemble = NVE; - control->nsteps = 0; - control->dt = 0.25; - control->nprocs = 1; - control->nthreads = 1; - control->procs_by_dim[0] = 1; - control->procs_by_dim[1] = 1; - control->procs_by_dim[2] = 1; - control->geo_format = 1; - - control->restart = 0; - out_control->restart_format = WRITE_BINARY; - out_control->restart_freq = 0; - control->reposition_atoms = 0; - control->restrict_bonds = 0; - control->remove_CoM_vel = 25; - out_control->debug_level = 0; - out_control->energy_update_freq = 0; - - control->reneighbor = 1; - control->vlist_cut = control->nonb_cut; - control->bond_cut = 5.0; - control->bg_cut = 0.3; - control->thb_cut = 0.001; - control->thb_cutsq = 0.00001; - control->hbond_cut = 7.5; - - control->tabulate = 0; - - control->qeq_freq = 1; - control->q_err = 1e-6; - control->refactor = 100; - control->droptol = 1e-2;; - - control->T_init = 0.; - control->T_final = 300.; - control->Tau_T = 500.0; - control->T_mode = 0; - control->T_rate = 1.; - control->T_freq = 1.; - - control->P[0] = control->P[1] = control->P[2] = 0.000101325; - control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] = 500.0; - control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] = 500.0; - control->compressibility = 1.0; - control->press_mode = 0; - control->virial = 0; - - out_control->write_steps = 0; - out_control->traj_compress = 0; - out_control->traj_method = REG_TRAJ; - strcpy( out_control->traj_title, "default_title" ); - out_control->atom_info = 0; - out_control->bond_info = 0; - out_control->angle_info = 0; - - control->molecular_analysis = 0; - control->dipole_anal = 0; - control->freq_dipole_anal = 0; - control->diffusion_coef = 0; - control->freq_diffusion_coef = 0; - control->restrict_type = 0; - - /* memory allocations */ - s = (char*) malloc(sizeof(char)*MAX_LINE); - tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS); - for (i=0; i < MAX_TOKENS; i++) - tmp[i] = (char*) malloc(sizeof(char)*MAX_LINE); - - /* read control parameters file */ - while (!feof(fp)) { - fgets( s, MAX_LINE, fp ); - Tokenize( s, &tmp ); - - if (strcmp(tmp[0], "simulation_name") == 0) { - strcpy( control->sim_name, tmp[1] ); - } - else if (strcmp(tmp[0], "ensemble_type") == 0) { - ival = atoi(tmp[1]); - control->ensemble = ival; - if (ival == iNPT || ival ==sNPT || ival == NPT) - control->virial = 1; - } - else if (strcmp(tmp[0], "nsteps") == 0) { - ival = atoi(tmp[1]); - control->nsteps = ival; - } - else if ( strcmp(tmp[0], "dt") == 0) { - val = atof(tmp[1]); - control->dt = val * 1.e-3; // convert dt from fs to ps! - } - else if (strcmp(tmp[0], "proc_by_dim") == 0) { - ival = atoi(tmp[1]); - control->procs_by_dim[0] = ival; - ival = atoi(tmp[2]); - control->procs_by_dim[1] = ival; - ival = atoi(tmp[3]); - control->procs_by_dim[2] = ival; - - control->nprocs = control->procs_by_dim[0]*control->procs_by_dim[1]* - control->procs_by_dim[2]; - } - else if (strcmp(tmp[0], "random_vel") == 0) { - ival = atoi(tmp[1]); - control->random_vel = ival; - } - else if (strcmp(tmp[0], "restart_format") == 0) { - ival = atoi(tmp[1]); - out_control->restart_format = ival; - } - else if (strcmp(tmp[0], "restart_freq") == 0) { - ival = atoi(tmp[1]); - out_control->restart_freq = ival; - } - else if (strcmp(tmp[0], "reposition_atoms") == 0) { - ival = atoi(tmp[1]); - control->reposition_atoms = ival; - } - else if (strcmp(tmp[0], "restrict_bonds") == 0) { - ival = atoi( tmp[1] ); - control->restrict_bonds = ival; - } - else if (strcmp(tmp[0], "remove_CoM_vel") == 0) { - ival = atoi(tmp[1]); - control->remove_CoM_vel = ival; - } - else if (strcmp(tmp[0], "debug_level") == 0) { - ival = atoi(tmp[1]); - out_control->debug_level = ival; - } - else if (strcmp(tmp[0], "energy_update_freq") == 0) { - ival = atoi(tmp[1]); - out_control->energy_update_freq = ival; - } - else if (strcmp(tmp[0], "reneighbor") == 0) { - ival = atoi( tmp[1] ); - control->reneighbor = ival; - } - else if (strcmp(tmp[0], "vlist_buffer") == 0) { - val = atof(tmp[1]); - control->vlist_cut= val + control->nonb_cut; - } - else if (strcmp(tmp[0], "nbrhood_cutoff") == 0) { - val = atof(tmp[1]); - control->bond_cut = val; - } - else if (strcmp(tmp[0], "bond_graph_cutoff") == 0) { - val = atof(tmp[1]); - control->bg_cut = val; - } - else if (strcmp(tmp[0], "thb_cutoff") == 0) { - val = atof(tmp[1]); - control->thb_cut = val; - } - else if (strcmp(tmp[0], "thb_cutoff_sq") == 0) { - val = atof(tmp[1]); - control->thb_cutsq = val; - } - else if (strcmp(tmp[0], "hbond_cutoff") == 0) { - val = atof( tmp[1] ); - control->hbond_cut = val; - } - else if (strcmp(tmp[0], "ghost_cutoff") == 0) { - val = atof(tmp[1]); - control->user_ghost_cut = val; - } - else if (strcmp(tmp[0], "tabulate_long_range") == 0) { - ival = atoi( tmp[1] ); - control->tabulate = ival; - } - else if (strcmp(tmp[0], "qeq_freq") == 0) { - ival = atoi( tmp[1] ); - control->qeq_freq = ival; - } - else if (strcmp(tmp[0], "q_err") == 0) { - val = atof( tmp[1] ); - control->q_err = val; - } - else if (strcmp(tmp[0], "ilu_refactor") == 0) { - ival = atoi( tmp[1] ); - control->refactor = ival; - } - else if (strcmp(tmp[0], "ilu_droptol") == 0) { - val = atof( tmp[1] ); - control->droptol = val; - } - else if (strcmp(tmp[0], "temp_init") == 0) { - val = atof(tmp[1]); - control->T_init = val; - - if (control->T_init < 0.1) - control->T_init = 0.1; - } - else if (strcmp(tmp[0], "temp_final") == 0) { - val = atof(tmp[1]); - control->T_final = val; - - if (control->T_final < 0.1) - control->T_final = 0.1; - } - else if (strcmp(tmp[0], "t_mass") == 0) { - val = atof(tmp[1]); - control->Tau_T = val * 1.e-3; // convert t_mass from fs to ps - } - else if (strcmp(tmp[0], "t_mode") == 0) { - ival = atoi(tmp[1]); - control->T_mode = ival; - } - else if (strcmp(tmp[0], "t_rate") == 0) { - val = atof(tmp[1]); - control->T_rate = val; - } - else if (strcmp(tmp[0], "t_freq") == 0) { - val = atof(tmp[1]); - control->T_freq = val; - } - else if (strcmp(tmp[0], "pressure") == 0) { - if (control->ensemble == iNPT) { - control->P[0] = control->P[1] = control->P[2] = atof(tmp[1]); - } - else if (control->ensemble == sNPT) { - control->P[0] = atof(tmp[1]); - control->P[1] = atof(tmp[2]); - control->P[2] = atof(tmp[3]); - } - } - else if (strcmp(tmp[0], "p_mass") == 0) { - // convert p_mass from fs to ps - if (control->ensemble == iNPT) { - control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] = - atof(tmp[1]) * 1.e-3; - } - else if (control->ensemble == sNPT) { - control->Tau_P[0] = atof(tmp[1]) * 1.e-3; - control->Tau_P[1] = atof(tmp[2]) * 1.e-3; - control->Tau_P[2] = atof(tmp[3]) * 1.e-3; - } - } - else if (strcmp(tmp[0], "pt_mass") == 0) { - val = atof(tmp[1]); - control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] = - val * 1.e-3; // convert pt_mass from fs to ps - } - else if (strcmp(tmp[0], "compress") == 0) { - val = atof(tmp[1]); - control->compressibility = val; - } - else if (strcmp(tmp[0], "press_mode") == 0) { - ival = atoi(tmp[1]); - control->press_mode = ival; - } - else if (strcmp(tmp[0], "geo_format") == 0) { - ival = atoi( tmp[1] ); - control->geo_format = ival; - } - else if (strcmp(tmp[0], "write_freq") == 0) { - ival = atoi(tmp[1]); - out_control->write_steps = ival; - } - else if (strcmp(tmp[0], "traj_compress") == 0) { - ival = atoi(tmp[1]); - out_control->traj_compress = ival; - } - else if (strcmp(tmp[0], "traj_method") == 0) { - ival = atoi(tmp[1]); - out_control->traj_method = ival; - } - else if (strcmp(tmp[0], "traj_title") == 0) { - strcpy( out_control->traj_title, tmp[1] ); - } - else if (strcmp(tmp[0], "atom_info") == 0) { - ival = atoi(tmp[1]); - out_control->atom_info += ival * 4; - } - else if (strcmp(tmp[0], "atom_velocities") == 0) { - ival = atoi(tmp[1]); - out_control->atom_info += ival * 2; - } - else if (strcmp(tmp[0], "atom_forces") == 0) { - ival = atoi(tmp[1]); - out_control->atom_info += ival * 1; - } - else if (strcmp(tmp[0], "bond_info") == 0) { - ival = atoi(tmp[1]); - out_control->bond_info = ival; - } - else if (strcmp(tmp[0], "angle_info") == 0) { - ival = atoi(tmp[1]); - out_control->angle_info = ival; - } - else if (strcmp(tmp[0], "molecular_analysis") == 0) { - ival = atoi(tmp[1]); - control->molecular_analysis = ival; - } - else if (strcmp(tmp[0], "ignore") == 0) { - control->num_ignored = atoi(tmp[1]); - for (i = 0; i < control->num_ignored; ++i) - control->ignore[atoi(tmp[i+2])] = 1; - } - else if (strcmp(tmp[0], "dipole_anal") == 0) { - ival = atoi(tmp[1]); - control->dipole_anal = ival; - } - else if (strcmp(tmp[0], "freq_dipole_anal") == 0) { - ival = atoi(tmp[1]); - control->freq_dipole_anal = ival; - } - else if (strcmp(tmp[0], "diffusion_coef") == 0) { - ival = atoi(tmp[1]); - control->diffusion_coef = ival; - } - else if (strcmp(tmp[0], "freq_diffusion_coef") == 0) { - ival = atoi(tmp[1]); - control->freq_diffusion_coef = ival; - } - else if (strcmp(tmp[0], "restrict_type") == 0) { - ival = atoi(tmp[1]); - control->restrict_type = ival; - } - else { - char errmsg[128]; - snprintf(errmsg,128,"Unknown parameter %s in the control file", tmp[0]); - control->error_ptr->all(FLERR, errmsg); - } - } - - /* determine target T */ - if (control->T_mode == 0) - control->T = control->T_final; - else control->T = control->T_init; - - /* free memory allocations at the top */ - for (i = 0; i < MAX_TOKENS; i++) - free( tmp[i] ); - free( tmp ); - free( s ); - - fclose(fp); - - return SUCCESS; -} diff --git a/src/USER-REAXC/reaxc_control.h b/src/USER-REAXC/reaxc_control.h deleted file mode 100644 index 9c818b0554..0000000000 --- a/src/USER-REAXC/reaxc_control.h +++ /dev/null @@ -1,35 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __CONTROL_H_ -#define __CONTROL_H_ - -#include "reaxc_types.h" - -char Read_Control_File( char*, control_params*, output_controls* ); - -#endif diff --git a/src/USER-REAXC/reaxc_defs.h b/src/USER-REAXC/reaxc_defs.h deleted file mode 100644 index b98d8a2828..0000000000 --- a/src/USER-REAXC/reaxc_defs.h +++ /dev/null @@ -1,155 +0,0 @@ -// clang-format off - - -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef REAX_DEFS_H -#define REAX_DEFS_H - -#if defined(__IBMC__) -#define inline __inline__ -#endif /*IBMC*/ - -#ifndef SUCCESS -#define SUCCESS 1 -#endif -#ifndef FAILURE -#define FAILURE 0 -#endif -#ifndef TRUE -#define TRUE 1 -#endif -#ifndef FALSE -#define FALSE 0 -#endif - -#define SQR(x) ((x)*(x)) -#define CUBE(x) ((x)*(x)*(x)) -#define DEG2RAD(a) ((a)*constPI/180.0) -#define RAD2DEG(a) ((a)*180.0/constPI) -// #define MAX(x,y) (((x) > (y)) ? (x) : (y)) -// #define MIN(x,y) (((x) < (y)) ? (x) : (y)) -#define MAX3(x,y,z) MAX( MAX(x,y), z) - -#define constPI 3.14159265 -#define C_ele 332.06371 -//#define K_B 503.398008 // kcal/mol/K -#define K_B 0.831687 // amu A^2 / ps^2 / K -#define F_CONV 1e6 / 48.88821291 / 48.88821291 // --> amu A / ps^2 -#define E_CONV 0.002391 // amu A^2 / ps^2 --> kcal/mol -#define EV_to_KCALpMOL 14.400000 // ElectronVolt --> KCAL per MOLe -#define KCALpMOL_to_EV 23.02 // 23.060549 //KCAL per MOLe --> ElectronVolt -#define ECxA_to_DEBYE 4.803204 // elem. charge * Ang -> debye -#define CAL_to_JOULES 4.184000 // CALories --> JOULES -#define JOULES_to_CAL 1/4.184000 // JOULES --> CALories -#define AMU_to_GRAM 1.6605e-24 -#define ANG_to_CM 1e-8 -#define AVOGNR 6.0221367e23 -#define P_CONV 1e-24 * AVOGNR * JOULES_to_CAL - -#define MAX_STR 1024 -#define MAX_LINE 1024 -#define MAX_TOKENS 1024 -#define MAX_TOKEN_LEN 1024 - -#define NUM_INTRS 10 -#define ALMOST_ZERO 1e-10 -#define NEG_INF -1e10 -#define NO_BOND 1e-3 // 0.001 -#define HB_THRESHOLD 1e-2 // 0.01 - -#define REAX_MIN_CAP 50 -#define REAX_MIN_NBRS 100 -#define MIN_HENTRIES 100 -#define MAX_BONDS 30 -#define MIN_BONDS 25 -#define REAX_MIN_HBONDS 25 -#define MIN_3BODIES 1000 -#define MIN_GCELL_POPL 50 -#define MIN_SEND 100 -#define REAX_SAFE_ZONE 1.2 -#define REAX_SAFER_ZONE 1.4 -#define DANGER_ZONE 0.90 -#define LOOSE_ZONE 0.75 -#define MAX_3BODY_PARAM 5 -#define MAX_4BODY_PARAM 5 - -#define MAX_dV 1.01 -#define MIN_dV 0.99 -#define MAX_dT 4.00 -#define MIN_dT 0.00 - -#define MASTER_NODE 0 -#define MAX_NBRS 6 //27 -#define MYSELF 13 // encoding of relative coordinate (0,0,0) - -#define MAX_ITR 10 -#define RESTART 30 - -#define MAX_BOND 20 - -#define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reaxc.cpp */ -#define MAXSPECBOND 24 /* used in fix_reaxc_species.cpp and pair_reaxc.cpp */ - -/******************* ENUMERATIONS *************************/ -enum geo_formats { CUSTOM, PDB, ASCII_RESTART, BINARY_RESTART, GF_N }; - -enum restart_formats { WRITE_ASCII, WRITE_BINARY, RF_N }; - -enum ensembles { NVE, bNVT, nhNVT, sNPT, iNPT, NPT, ens_N }; - -enum lists { BONDS, OLD_BONDS, THREE_BODIES, - HBONDS, FAR_NBRS, DBOS, DDELTAS, LIST_N }; - -enum interactions { TYP_VOID, TYP_BOND, TYP_THREE_BODY, - TYP_HBOND, TYP_FAR_NEIGHBOR, TYP_DBO, TYP_DDELTA, TYP_N }; - -enum message_tags { INIT, UPDATE, BNDRY, UPDATE_BNDRY, - EXC_VEC1, EXC_VEC2, DIST_RVEC2, COLL_RVEC2, - DIST_RVECS, COLL_RVECS, INIT_DESCS, ATOM_LINES, - BOND_LINES, ANGLE_LINES, RESTART_ATOMS, TAGS_N }; - -enum errors { FILE_NOT_FOUND = -10, UNKNOWN_ATOM_TYPE = -11, - CANNOT_OPEN_FILE = -12, CANNOT_INITIALIZE = -13, - INSUFFICIENT_MEMORY = -14, UNKNOWN_OPTION = -15, - INVALID_INPUT = -16, INVALID_GEO = -17 }; - -enum exchanges { NONE, NEAR_EXCH, FULL_EXCH }; - -enum gcell_types { NO_NBRS=0, NEAR_ONLY=1, HBOND_ONLY=2, FAR_ONLY=4, - NEAR_HBOND=3, NEAR_FAR=5, HBOND_FAR=6, FULL_NBRS=7, - NATIVE=8 }; - -enum atoms { C_ATOM = 0, H_ATOM = 1, O_ATOM = 2, N_ATOM = 3, - S_ATOM = 4, SI_ATOM = 5, GE_ATOM = 6, X_ATOM = 7 }; - -enum traj_methods { REG_TRAJ, MPI_TRAJ, TF_N }; - -enum molecules { UNKNOWN, WATER }; - - -#endif diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp deleted file mode 100644 index 0b771bf356..0000000000 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ /dev/null @@ -1,740 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_ffield.h" -#include -#include -#include -#include -#include -#include "reaxc_defs.h" -#include "error.h" -#include "reaxc_tool_box.h" - -char Read_Force_Field( FILE *fp, reax_interaction *reax, - control_params *control ) -{ - char *s; - char **tmp; - char ****tor_flag; - int c, i, j, k, l, m, n, o, p, cnt; - int lgflag = control->lgflag; - int errorflag = 1; - double val; - int me = control->me; - - s = (char*) malloc(sizeof(char)*MAX_LINE); - tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS); - for (i=0; i < MAX_TOKENS; i++) - tmp[i] = (char*) malloc(sizeof(char)*MAX_TOKEN_LEN); - - /* reading first header comment */ - fgets( s, MAX_LINE, fp ); - - /* line 2 is number of global parameters */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - /* reading the number of global parameters */ - n = atoi(tmp[0]); - if (n < 1) { - if (me == 0) - control->error_ptr->warning( FLERR, "Number of globals in ffield file is 0. The file will not be read." ); - fclose(fp); - free(s); - free(tmp); - return 1; - } - - reax->gp.n_global = n; - reax->gp.l = (double*) malloc(sizeof(double)*n); - - /* see reax_types.h for mapping between l[i] and the lambdas used in ff */ - for (i=0; i < n; i++) { - fgets(s,MAX_LINE,fp); - c = Tokenize(s,&tmp); - - val = (double) atof(tmp[0]); - reax->gp.l[i] = val; - } - - control->bo_cut = 0.01 * reax->gp.l[29]; - control->nonb_low = reax->gp.l[11]; - control->nonb_cut = reax->gp.l[12]; - - /* next line is number of atom types and some comments */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - reax->num_atom_types = atoi(tmp[0]); - - /* 3 lines of comments */ - fgets(s,MAX_LINE,fp); - fgets(s,MAX_LINE,fp); - fgets(s,MAX_LINE,fp); - - /* Allocating structures in reax_interaction */ - reax->sbp = (single_body_parameters*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(single_body_parameters), "sbp"); - reax->tbp = (two_body_parameters**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters*), "tbp"); - reax->thbp= (three_body_header***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header**), "thbp"); - reax->hbp = (hbond_parameters***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters**), "hbp"); - reax->fbp = (four_body_header****) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header***), "fbp"); - tor_flag = (char****) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char***), "tor_flag"); - - for (i = 0; i < reax->num_atom_types; i++) { - reax->tbp[i] = (two_body_parameters*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]"); - reax->thbp[i]= (three_body_header**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]"); - reax->hbp[i] = (hbond_parameters**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]"); - reax->fbp[i] = (four_body_header***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]"); - tor_flag[i] = (char***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char**), "tor_flag[i]"); - - for (j = 0; j < reax->num_atom_types; j++) { - reax->thbp[i][j]= (three_body_header*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]"); - reax->hbp[i][j] = (hbond_parameters*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]"); - reax->fbp[i][j] = (four_body_header**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]"); - tor_flag[i][j] = (char**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]"); - - for (k=0; k < reax->num_atom_types; k++) { - reax->fbp[i][j][k] = (four_body_header*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]"); - tor_flag[i][j][k] = (char*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]"); - } - } - } - - reax->gp.vdw_type = 0; - - char errmsg[1024]; - - for (i = 0; i < reax->num_atom_types; i++) { - /* line one */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - /* Sanity checks */ - if (c == 2 && !lgflag) - control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); - - if (c < 9) { - snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); - control->error_ptr->all(FLERR, errmsg); - } - - for (j = 0; j < (int)(strlen(tmp[0])); ++j) - reax->sbp[i].name[j] = toupper( tmp[0][j] ); - - val = atof(tmp[1]); reax->sbp[i].r_s = val; - val = atof(tmp[2]); reax->sbp[i].valency = val; - val = atof(tmp[3]); reax->sbp[i].mass = val; - val = atof(tmp[4]); reax->sbp[i].r_vdw = val; - val = atof(tmp[5]); reax->sbp[i].epsilon = val; - val = atof(tmp[6]); reax->sbp[i].gamma = val; - val = atof(tmp[7]); reax->sbp[i].r_pi = val; - val = atof(tmp[8]); reax->sbp[i].valency_e = val; - reax->sbp[i].nlp_opt = 0.5 * (reax->sbp[i].valency_e-reax->sbp[i].valency); - - /* line two */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - /* Sanity check */ - if (c < 8) { - snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); - control->error_ptr->all(FLERR, errmsg); - } - - val = atof(tmp[0]); reax->sbp[i].alpha = val; - val = atof(tmp[1]); reax->sbp[i].gamma_w = val; - val = atof(tmp[2]); reax->sbp[i].valency_boc= val; - val = atof(tmp[3]); reax->sbp[i].p_ovun5 = val; - val = atof(tmp[4]); - val = atof(tmp[5]); reax->sbp[i].chi = val; - val = atof(tmp[6]); reax->sbp[i].eta = 2.0 * val; - val = atof(tmp[7]); reax->sbp[i].p_hbond = (int) val; - - /* line 3 */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - /* Sanity check */ - if (c < 8) { - snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); - control->error_ptr->all(FLERR, errmsg); - } - - val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val; - val = atof(tmp[1]); reax->sbp[i].p_lp2 = val; - val = atof(tmp[2]); - val = atof(tmp[3]); reax->sbp[i].b_o_131 = val; - val = atof(tmp[4]); reax->sbp[i].b_o_132 = val; - val = atof(tmp[5]); reax->sbp[i].b_o_133 = val; - val = atof(tmp[6]); - val = atof(tmp[7]); - - /* line 4 */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - /* Sanity check */ - if (c < 8) { - snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); - control->error_ptr->all(FLERR, errmsg); - } - - val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val; - val = atof(tmp[1]); reax->sbp[i].p_val3 = val; - val = atof(tmp[2]); - val = atof(tmp[3]); reax->sbp[i].valency_val= val; - val = atof(tmp[4]); reax->sbp[i].p_val5 = val; - val = atof(tmp[5]); reax->sbp[i].rcore2 = val; - val = atof(tmp[6]); reax->sbp[i].ecore2 = val; - val = atof(tmp[7]); reax->sbp[i].acore2 = val; - - /* line 5, only if lgvdw is yes */ - if (lgflag) { - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - /* Sanity check */ - if (c > 2) { - control->error_ptr->all(FLERR,"Force field file incompatible with 'lgvdw yes'"); - } - - val = atof(tmp[0]); reax->sbp[i].lgcij = val; - val = atof(tmp[1]); reax->sbp[i].lgre = val; - } - - if (reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01) { // Inner-wall - if (reax->sbp[i].gamma_w>0.5) { // Shielding vdWaals - if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3) { - if (errorflag && (me == 0)) { - char errmsg[512]; - snprintf(errmsg, 512, "VdWaals-parameters for element %s " - "indicate inner wall+shielding, but earlier " - "atoms indicate different vdWaals-method. " - "This may cause division-by-zero errors. " - "Keeping vdWaals-setting for earlier atoms.", - reax->sbp[i].name); - control->error_ptr->warning(FLERR,errmsg); - } - errorflag = 0; - } else { - reax->gp.vdw_type = 3; - } - } else { // No shielding vdWaals parameters present - if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2) { - if (me == 0) { - char errmsg[512]; - snprintf(errmsg, 512, "VdWaals-parameters for element %s " - "indicate inner wall without shielding, but earlier " - "atoms indicate different vdWaals-method. " - "This may cause division-by-zero errors. " - "Keeping vdWaals-setting for earlier atoms.", - reax->sbp[i].name); - control->error_ptr->warning(FLERR,errmsg); - } - } else { - reax->gp.vdw_type = 2; - } - } - } else { // No Inner wall parameters present - if (reax->sbp[i].gamma_w>0.5) { // Shielding vdWaals - if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1) { - if (me == 0) { - char errmsg[512]; - snprintf(errmsg, 512, "VdWaals parameters for element %s " - "indicate shielding without inner wall, but earlier " - "elements indicate different vdWaals-method. " - "This may cause division-by-zero errors. " - "Keeping vdWaals-setting for earlier atoms.", - reax->sbp[i].name); - control->error_ptr->warning(FLERR,errmsg); - } - } else { - reax->gp.vdw_type = 1; - } - } else { - char errmsg[256]; - snprintf(errmsg, 256, "Inconsistent vdWaals-parameters: " - "No shielding or inner-wall set for element %s", - reax->sbp[i].name); - control->error_ptr->all(FLERR, errmsg); - } - } - } - - /* Equate vval3 to valf for first-row elements (25/10/2004) */ - for (i = 0; i < reax->num_atom_types; i++) - if ( reax->sbp[i].mass < 21 && - reax->sbp[i].valency_val != reax->sbp[i].valency_boc) { - if (me == 0) { - char errmsg[256]; - snprintf(errmsg, 256, "Changed valency_val to valency_boc for %s", - reax->sbp[i].name); - control->error_ptr->warning(FLERR,errmsg); - } - reax->sbp[i].valency_val = reax->sbp[i].valency_boc; - } - - /* next line is number of two body combination and some comments */ - fgets(s,MAX_LINE,fp); - c=Tokenize(s,&tmp); - - if (c == 2 && !lgflag) { - control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); - } - - l = atoi(tmp[0]); - - /* a line of comments */ - fgets(s,MAX_LINE,fp); - - for (i=0; i < l; i++) { - /* line 1 */ - fgets(s,MAX_LINE,fp); - c=Tokenize(s,&tmp); - - j = atoi(tmp[0]) - 1; - k = atoi(tmp[1]) - 1; - if ((c < 10) || (j < 0) || (k < 0)) - control->error_ptr->all(FLERR, "Inconsistent force field file"); - - if (j < reax->num_atom_types && k < reax->num_atom_types) { - - val = atof(tmp[2]); reax->tbp[j][k].De_s = val; - reax->tbp[k][j].De_s = val; - val = atof(tmp[3]); reax->tbp[j][k].De_p = val; - reax->tbp[k][j].De_p = val; - val = atof(tmp[4]); reax->tbp[j][k].De_pp = val; - reax->tbp[k][j].De_pp = val; - val = atof(tmp[5]); reax->tbp[j][k].p_be1 = val; - reax->tbp[k][j].p_be1 = val; - val = atof(tmp[6]); reax->tbp[j][k].p_bo5 = val; - reax->tbp[k][j].p_bo5 = val; - val = atof(tmp[7]); reax->tbp[j][k].v13cor = val; - reax->tbp[k][j].v13cor = val; - - val = atof(tmp[8]); reax->tbp[j][k].p_bo6 = val; - reax->tbp[k][j].p_bo6 = val; - val = atof(tmp[9]); reax->tbp[j][k].p_ovun1 = val; - reax->tbp[k][j].p_ovun1 = val; - - /* line 2 */ - fgets(s,MAX_LINE,fp); - c=Tokenize(s,&tmp); - if (c < 8) - control->error_ptr->all(FLERR, "Inconsistent force field file"); - - val = atof(tmp[0]); reax->tbp[j][k].p_be2 = val; - reax->tbp[k][j].p_be2 = val; - val = atof(tmp[1]); reax->tbp[j][k].p_bo3 = val; - reax->tbp[k][j].p_bo3 = val; - val = atof(tmp[2]); reax->tbp[j][k].p_bo4 = val; - reax->tbp[k][j].p_bo4 = val; - val = atof(tmp[3]); - - val = atof(tmp[4]); reax->tbp[j][k].p_bo1 = val; - reax->tbp[k][j].p_bo1 = val; - val = atof(tmp[5]); reax->tbp[j][k].p_bo2 = val; - reax->tbp[k][j].p_bo2 = val; - val = atof(tmp[6]); reax->tbp[j][k].ovc = val; - reax->tbp[k][j].ovc = val; - - val = atof(tmp[7]); - } - } - - for (i=0; i < reax->num_atom_types; i++) - for (j=i; j < reax->num_atom_types; j++) { - reax->tbp[i][j].r_s = 0.5 * - (reax->sbp[i].r_s + reax->sbp[j].r_s); - reax->tbp[j][i].r_s = 0.5 * - (reax->sbp[j].r_s + reax->sbp[i].r_s); - - reax->tbp[i][j].r_p = 0.5 * - (reax->sbp[i].r_pi + reax->sbp[j].r_pi); - reax->tbp[j][i].r_p = 0.5 * - (reax->sbp[j].r_pi + reax->sbp[i].r_pi); - - reax->tbp[i][j].r_pp = 0.5 * - (reax->sbp[i].r_pi_pi + reax->sbp[j].r_pi_pi); - reax->tbp[j][i].r_pp = 0.5 * - (reax->sbp[j].r_pi_pi + reax->sbp[i].r_pi_pi); - - - reax->tbp[i][j].p_boc3 = - sqrt(reax->sbp[i].b_o_132 * - reax->sbp[j].b_o_132); - reax->tbp[j][i].p_boc3 = - sqrt(reax->sbp[j].b_o_132 * - reax->sbp[i].b_o_132); - - reax->tbp[i][j].p_boc4 = - sqrt(reax->sbp[i].b_o_131 * - reax->sbp[j].b_o_131); - reax->tbp[j][i].p_boc4 = - sqrt(reax->sbp[j].b_o_131 * - reax->sbp[i].b_o_131); - - reax->tbp[i][j].p_boc5 = - sqrt(reax->sbp[i].b_o_133 * - reax->sbp[j].b_o_133); - reax->tbp[j][i].p_boc5 = - sqrt(reax->sbp[j].b_o_133 * - reax->sbp[i].b_o_133); - - - reax->tbp[i][j].D = - sqrt(reax->sbp[i].epsilon * - reax->sbp[j].epsilon); - - reax->tbp[j][i].D = - sqrt(reax->sbp[j].epsilon * - reax->sbp[i].epsilon); - - reax->tbp[i][j].alpha = - sqrt(reax->sbp[i].alpha * - reax->sbp[j].alpha); - - reax->tbp[j][i].alpha = - sqrt(reax->sbp[j].alpha * - reax->sbp[i].alpha); - - reax->tbp[i][j].r_vdW = - 2.0 * sqrt(reax->sbp[i].r_vdw * reax->sbp[j].r_vdw); - - reax->tbp[j][i].r_vdW = - 2.0 * sqrt(reax->sbp[j].r_vdw * reax->sbp[i].r_vdw); - - reax->tbp[i][j].gamma_w = - sqrt(reax->sbp[i].gamma_w * - reax->sbp[j].gamma_w); - - reax->tbp[j][i].gamma_w = - sqrt(reax->sbp[j].gamma_w * - reax->sbp[i].gamma_w); - - reax->tbp[i][j].gamma = - pow(reax->sbp[i].gamma * - reax->sbp[j].gamma,-1.5); - - reax->tbp[j][i].gamma = - pow(reax->sbp[j].gamma * - reax->sbp[i].gamma,-1.5); - - // additions for additional vdWaals interaction types - inner core - - reax->tbp[i][j].rcore = reax->tbp[j][i].rcore = - sqrt( reax->sbp[i].rcore2 * reax->sbp[j].rcore2 ); - - reax->tbp[i][j].ecore = reax->tbp[j][i].ecore = - sqrt( reax->sbp[i].ecore2 * reax->sbp[j].ecore2 ); - - reax->tbp[i][j].acore = reax->tbp[j][i].acore = - sqrt( reax->sbp[i].acore2 * reax->sbp[j].acore2 ); - - // additions for additional vdWalls interaction types lg correction - - reax->tbp[i][j].lgcij = reax->tbp[j][i].lgcij = - sqrt( reax->sbp[i].lgcij * reax->sbp[j].lgcij ); - - reax->tbp[i][j].lgre = reax->tbp[j][i].lgre = 2.0 * reax->gp.l[35] * - sqrt( reax->sbp[i].lgre*reax->sbp[j].lgre ); - - } - - fgets(s,MAX_LINE,fp); - c=Tokenize(s,&tmp); - l = atoi(tmp[0]); - - for (i=0; i < l; i++) { - fgets(s,MAX_LINE,fp); - c=Tokenize(s,&tmp); - - j = atoi(tmp[0]) - 1; - k = atoi(tmp[1]) - 1; - - if ((c < (lgflag ? 9 : 8)) || (j < 0) || (k < 0)) - control->error_ptr->all(FLERR, "Inconsistent force field file"); - - if (j < reax->num_atom_types && k < reax->num_atom_types) { - val = atof(tmp[2]); - if (val > 0.0) { - reax->tbp[j][k].D = val; - reax->tbp[k][j].D = val; - } - - val = atof(tmp[3]); - if (val > 0.0) { - reax->tbp[j][k].r_vdW = 2 * val; - reax->tbp[k][j].r_vdW = 2 * val; - } - - val = atof(tmp[4]); - if (val > 0.0) { - reax->tbp[j][k].alpha = val; - reax->tbp[k][j].alpha = val; - } - - val = atof(tmp[5]); - if (val > 0.0) { - reax->tbp[j][k].r_s = val; - reax->tbp[k][j].r_s = val; - } - - val = atof(tmp[6]); - if (val > 0.0) { - reax->tbp[j][k].r_p = val; - reax->tbp[k][j].r_p = val; - } - - val = atof(tmp[7]); - if (val > 0.0) { - reax->tbp[j][k].r_pp = val; - reax->tbp[k][j].r_pp = val; - } - - if (lgflag) { - val = atof(tmp[8]); - if (val >= 0.0) { - reax->tbp[j][k].lgcij = val; - reax->tbp[k][j].lgcij = val; - } - } - } - } - - for (i = 0; i < reax->num_atom_types; ++i) - for (j = 0; j < reax->num_atom_types; ++j) - for (k = 0; k < reax->num_atom_types; ++k) - reax->thbp[i][j][k].cnt = 0; - - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - l = atoi( tmp[0] ); - - for (i = 0; i < l; i++) { - fgets(s,MAX_LINE,fp); - c=Tokenize(s,&tmp); - - j = atoi(tmp[0]) - 1; - k = atoi(tmp[1]) - 1; - m = atoi(tmp[2]) - 1; - if ((c < 10) || (j < 0) || (k < 0) || (m < 0)) - control->error_ptr->all(FLERR, "Inconsistent force field file"); - - if (j < reax->num_atom_types && k < reax->num_atom_types && - m < reax->num_atom_types) { - cnt = reax->thbp[j][k][m].cnt; - reax->thbp[j][k][m].cnt++; - reax->thbp[m][k][j].cnt++; - - val = atof(tmp[3]); - reax->thbp[j][k][m].prm[cnt].theta_00 = val; - reax->thbp[m][k][j].prm[cnt].theta_00 = val; - - val = atof(tmp[4]); - reax->thbp[j][k][m].prm[cnt].p_val1 = val; - reax->thbp[m][k][j].prm[cnt].p_val1 = val; - - val = atof(tmp[5]); - reax->thbp[j][k][m].prm[cnt].p_val2 = val; - reax->thbp[m][k][j].prm[cnt].p_val2 = val; - - val = atof(tmp[6]); - reax->thbp[j][k][m].prm[cnt].p_coa1 = val; - reax->thbp[m][k][j].prm[cnt].p_coa1 = val; - - val = atof(tmp[7]); - reax->thbp[j][k][m].prm[cnt].p_val7 = val; - reax->thbp[m][k][j].prm[cnt].p_val7 = val; - - val = atof(tmp[8]); - reax->thbp[j][k][m].prm[cnt].p_pen1 = val; - reax->thbp[m][k][j].prm[cnt].p_pen1 = val; - - val = atof(tmp[9]); - reax->thbp[j][k][m].prm[cnt].p_val4 = val; - reax->thbp[m][k][j].prm[cnt].p_val4 = val; - } - } - - /* clear all entries first */ - for (i = 0; i < reax->num_atom_types; ++i) - for (j = 0; j < reax->num_atom_types; ++j) - for (k = 0; k < reax->num_atom_types; ++k) - for (m = 0; m < reax->num_atom_types; ++m) { - reax->fbp[i][j][k][m].cnt = 0; - tor_flag[i][j][k][m] = 0; - } - - /* next line is number of 4-body params and some comments */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - l = atoi( tmp[0] ); - - for (i = 0; i < l; i++) { - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - j = atoi(tmp[0]) - 1; - k = atoi(tmp[1]) - 1; - m = atoi(tmp[2]) - 1; - n = atoi(tmp[3]) - 1; - if ((c < 9) || (k < 0) || (m < 0)) - control->error_ptr->all(FLERR, "Inconsistent force field file"); - - if (j >= 0 && n >= 0) { // this means the entry is not in compact form - if (j < reax->num_atom_types && k < reax->num_atom_types && - m < reax->num_atom_types && n < reax->num_atom_types) { - tor_flag[j][k][m][n] = 1; - tor_flag[n][m][k][j] = 1; - - reax->fbp[j][k][m][n].cnt = 1; - reax->fbp[n][m][k][j].cnt = 1; - - val = atof(tmp[4]); - reax->fbp[j][k][m][n].prm[0].V1 = val; - reax->fbp[n][m][k][j].prm[0].V1 = val; - - val = atof(tmp[5]); - reax->fbp[j][k][m][n].prm[0].V2 = val; - reax->fbp[n][m][k][j].prm[0].V2 = val; - - val = atof(tmp[6]); - reax->fbp[j][k][m][n].prm[0].V3 = val; - reax->fbp[n][m][k][j].prm[0].V3 = val; - - val = atof(tmp[7]); - reax->fbp[j][k][m][n].prm[0].p_tor1 = val; - reax->fbp[n][m][k][j].prm[0].p_tor1 = val; - - val = atof(tmp[8]); - reax->fbp[j][k][m][n].prm[0].p_cot1 = val; - reax->fbp[n][m][k][j].prm[0].p_cot1 = val; - } - } else { /* This means the entry is of the form 0-X-Y-0 */ - if (k < reax->num_atom_types && m < reax->num_atom_types) - for (p = 0; p < reax->num_atom_types; p++) - for (o = 0; o < reax->num_atom_types; o++) { - reax->fbp[p][k][m][o].cnt = 1; - reax->fbp[o][m][k][p].cnt = 1; - - if (tor_flag[p][k][m][o] == 0) { - reax->fbp[p][k][m][o].prm[0].V1 = atof(tmp[4]); - reax->fbp[p][k][m][o].prm[0].V2 = atof(tmp[5]); - reax->fbp[p][k][m][o].prm[0].V3 = atof(tmp[6]); - reax->fbp[p][k][m][o].prm[0].p_tor1 = atof(tmp[7]); - reax->fbp[p][k][m][o].prm[0].p_cot1 = atof(tmp[8]); - } - - if (tor_flag[o][m][k][p] == 0) { - reax->fbp[o][m][k][p].prm[0].V1 = atof(tmp[4]); - reax->fbp[o][m][k][p].prm[0].V2 = atof(tmp[5]); - reax->fbp[o][m][k][p].prm[0].V3 = atof(tmp[6]); - reax->fbp[o][m][k][p].prm[0].p_tor1 = atof(tmp[7]); - reax->fbp[o][m][k][p].prm[0].p_cot1 = atof(tmp[8]); - } - } - } - } - - /* next line is number of hydrogen bond params and some comments */ - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - l = atoi( tmp[0] ); - - for (i = 0; i < reax->num_atom_types; ++i) - for (j = 0; j < reax->num_atom_types; ++j) - for (k = 0; k < reax->num_atom_types; ++k) - reax->hbp[i][j][k].r0_hb = -1.0; - - for (i = 0; i < l; i++) { - fgets( s, MAX_LINE, fp ); - c = Tokenize( s, &tmp ); - - j = atoi(tmp[0]) - 1; - k = atoi(tmp[1]) - 1; - m = atoi(tmp[2]) - 1; - if ((c < 7) || (j < 0) || (k < 0) || (m < 0)) - control->error_ptr->all(FLERR, "Inconsistent force field file"); - - if (j < reax->num_atom_types && m < reax->num_atom_types) { - val = atof(tmp[3]); - reax->hbp[j][k][m].r0_hb = val; - - val = atof(tmp[4]); - reax->hbp[j][k][m].p_hb1 = val; - - val = atof(tmp[5]); - reax->hbp[j][k][m].p_hb2 = val; - - val = atof(tmp[6]); - reax->hbp[j][k][m].p_hb3 = val; - } - } - - /* deallocate helper storage */ - for (i = 0; i < MAX_TOKENS; i++) - free( tmp[i] ); - free( tmp ); - free( s ); - - - /* deallocate tor_flag */ - for (i = 0; i < reax->num_atom_types; i++) { - for (j = 0; j < reax->num_atom_types; j++) { - for (k = 0; k < reax->num_atom_types; k++) { - free( tor_flag[i][j][k] ); - } - free( tor_flag[i][j] ); - } - free( tor_flag[i] ); - } - free( tor_flag ); - - // close file - - fclose(fp); - - return SUCCESS; -} diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/USER-REAXC/reaxc_ffield.h deleted file mode 100644 index 76edfe8b7e..0000000000 --- a/src/USER-REAXC/reaxc_ffield.h +++ /dev/null @@ -1,36 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __FFIELD_H_ -#define __FFIELD_H_ - -#include "reaxc_types.h" -#include - -char Read_Force_Field( FILE*, reax_interaction*, control_params* ); - -#endif diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp deleted file mode 100644 index 7860ab6b32..0000000000 --- a/src/USER-REAXC/reaxc_forces.cpp +++ /dev/null @@ -1,457 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_forces.h" -#include -#include -#include -#include "reaxc_bond_orders.h" -#include "reaxc_bonds.h" -#include "reaxc_hydrogen_bonds.h" -#include "reaxc_list.h" -#include "reaxc_multi_body.h" -#include "reaxc_nonbonded.h" -#include "reaxc_torsion_angles.h" -#include "reaxc_valence_angles.h" -#include "reaxc_vector.h" - -#include "error.h" - -interaction_function Interaction_Functions[NUM_INTRS]; - -void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/, - simulation_data * /*data*/, storage * /*workspace*/, - reax_list ** /*lists*/, output_controls * /*out_control*/ ) -{ -} - - -void Init_Force_Functions( control_params *control ) -{ - Interaction_Functions[0] = BO; - Interaction_Functions[1] = Bonds; //Dummy_Interaction; - Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction; - Interaction_Functions[3] = Valence_Angles; //Dummy_Interaction; - Interaction_Functions[4] = Torsion_Angles; //Dummy_Interaction; - if (control->hbond_cut > 0) - Interaction_Functions[5] = Hydrogen_Bonds; - else Interaction_Functions[5] = Dummy_Interaction; - Interaction_Functions[6] = Dummy_Interaction; //empty - Interaction_Functions[7] = Dummy_Interaction; //empty - Interaction_Functions[8] = Dummy_Interaction; //empty - Interaction_Functions[9] = Dummy_Interaction; //empty -} - - -void Compute_Bonded_Forces( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - MPI_Comm /*comm*/ ) -{ - int i; - - /* Implement all force calls as function pointers */ - for (i = 0; i < NUM_INTRS; i++) { - (Interaction_Functions[i])( system, control, data, workspace, - lists, out_control ); - } -} - - -void Compute_NonBonded_Forces( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - MPI_Comm /*comm*/ ) -{ - - /* van der Waals and Coulomb interactions */ - if (control->tabulate == 0) - vdW_Coulomb_Energy( system, control, data, workspace, - lists, out_control ); - else - Tabulated_vdW_Coulomb_Energy( system, control, data, workspace, - lists, out_control ); -} - - -void Compute_Total_Force( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, mpi_datatypes * /*mpi_data*/ ) -{ - int i, pj; - reax_list *bonds = (*lists) + BONDS; - - for (i = 0; i < system->N; ++i) - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) - if (i < bonds->select.bond_list[pj].nbr) { - if (control->virial == 0) - Add_dBond_to_Forces( system, i, pj, workspace, lists ); - else - Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists ); - } - -} - -void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **lists, - int step, int /*n*/, int N, int numH ) -{ - int i, comp, Hindex; - reax_list *bonds, *hbonds; - - double saferzone = system->saferzone; - - /* bond list */ - if (N > 0) { - bonds = *lists + BONDS; - - for (i = 0; i < N; ++i) { - system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); - - if (i < N-1) - comp = Start_Index(i+1, bonds); - else comp = bonds->num_intrs; - - if (End_Index(i, bonds) > comp) { - char errmsg[256]; - snprintf(errmsg, 256, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", - step, i, End_Index(i,bonds), comp ); - system->error_ptr->one(FLERR,errmsg); - } - } - } - - - /* hbonds list */ - if (numH > 0) { - hbonds = *lists + HBONDS; - - for (i = 0; i < N; ++i) { - Hindex = system->my_atoms[i].Hindex; - if (Hindex > -1) { - system->my_atoms[i].num_hbonds = - (int)(MAX(Num_Entries(Hindex, hbonds)*saferzone, system->minhbonds)); - - //if( Num_Entries(i, hbonds) >= - //(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/) { - // workspace->realloc.hbonds = 1; - - if (Hindex < numH-1) - comp = Start_Index(Hindex+1, hbonds); - else comp = hbonds->num_intrs; - - if (End_Index(Hindex, hbonds) > comp) { - char errmsg[256]; - snprintf(errmsg, 256, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", - step, Hindex, End_Index(Hindex,hbonds), comp ); - system->error_ptr->one(FLERR, errmsg); - } - } - } - } -} - - -void Init_Forces_noQEq( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /*out_control*/) { - int i, j, pj; - int start_i, end_i; - int type_i, type_j; - int btop_i, num_bonds, num_hbonds; - int ihb, jhb, ihb_top, jhb_top; - int local, flag, renbr; - double cutoff; - reax_list *far_nbrs, *bonds, *hbonds; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - far_neighbor_data *nbr_pj; - reax_atom *atom_i, *atom_j; - - far_nbrs = *lists + FAR_NBRS; - bonds = *lists + BONDS; - hbonds = *lists + HBONDS; - - for (i = 0; i < system->n; ++i) - workspace->bond_mark[i] = 0; - for (i = system->n; i < system->N; ++i) { - workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance - } - - num_bonds = 0; - num_hbonds = 0; - btop_i = 0; - renbr = (data->step-data->prev_steps) % control->reneighbor == 0; - - for (i = 0; i < system->N; ++i) { - atom_i = &(system->my_atoms[i]); - type_i = atom_i->type; - if (type_i < 0) continue; - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - btop_i = End_Index( i, bonds ); - sbp_i = &(system->reax_param.sbp[type_i]); - - if (i < system->n) { - local = 1; - cutoff = MAX( control->hbond_cut, control->bond_cut ); - } else { - local = 0; - cutoff = control->bond_cut; - } - - ihb = -1; - ihb_top = -1; - if (local && control->hbond_cut > 0) { - ihb = sbp_i->p_hbond; - if (ihb == 1) - ihb_top = End_Index( atom_i->Hindex, hbonds ); - else ihb_top = -1; - } - - /* update i-j distance - check if j is within cutoff */ - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); - j = nbr_pj->nbr; - atom_j = &(system->my_atoms[j]); - - if (renbr) { - if (nbr_pj->d <= cutoff) - flag = 1; - else flag = 0; - } else { - nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0]; - nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1]; - nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2]; - nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec ); - if (nbr_pj->d <= SQR(cutoff)) { - nbr_pj->d = sqrt(nbr_pj->d); - flag = 1; - } else { - flag = 0; - } - } - - if (flag) { - type_j = atom_j->type; - if (type_j < 0) continue; - sbp_j = &(system->reax_param.sbp[type_j]); - twbp = &(system->reax_param.tbp[type_i][type_j]); - - if (local) { - /* hydrogen bond lists */ - if (control->hbond_cut > 0 && (ihb==1 || ihb==2) && - nbr_pj->d <= control->hbond_cut) { - // fprintf( stderr, "%d %d\n", atom1, atom2 ); - jhb = sbp_j->p_hbond; - if (ihb == 1 && jhb == 2) { - hbonds->select.hbond_list[ihb_top].nbr = j; - hbonds->select.hbond_list[ihb_top].scl = 1; - hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; - ++ihb_top; - ++num_hbonds; - } - else if (j < system->n && ihb == 2 && jhb == 1) { - jhb_top = End_Index( atom_j->Hindex, hbonds ); - hbonds->select.hbond_list[jhb_top].nbr = i; - hbonds->select.hbond_list[jhb_top].scl = -1; - hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; - Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds ); - ++num_hbonds; - } - } - } - - if (//(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) && - nbr_pj->d <= control->bond_cut && - BOp( workspace, bonds, control->bo_cut, - i , btop_i, nbr_pj, sbp_i, sbp_j, twbp )) { - num_bonds += 2; - ++btop_i; - - if (workspace->bond_mark[j] > workspace->bond_mark[i] + 1) - workspace->bond_mark[j] = workspace->bond_mark[i] + 1; - else if (workspace->bond_mark[i] > workspace->bond_mark[j] + 1) { - workspace->bond_mark[i] = workspace->bond_mark[j] + 1; - } - } - } - } - - Set_End_Index( i, btop_i, bonds ); - if (local && ihb == 1) - Set_End_Index( atom_i->Hindex, ihb_top, hbonds ); - } - - - workspace->realloc.num_bonds = num_bonds; - workspace->realloc.num_hbonds = num_hbonds; - - Validate_Lists( system, workspace, lists, data->step, - system->n, system->N, system->numH); -} - - -void Estimate_Storages( reax_system *system, control_params *control, - reax_list **lists, int *Htop, int *hb_top, - int *bond_top, int *num_3body ) -{ - int i, j, pj; - int start_i, end_i; - int type_i, type_j; - int ihb, jhb; - int local; - double cutoff; - double r_ij; - double C12, C34, C56; - double BO, BO_s, BO_pi, BO_pi2; - reax_list *far_nbrs; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - far_neighbor_data *nbr_pj; - reax_atom *atom_i, *atom_j; - - int mincap = system->mincap; - double safezone = system->safezone; - double saferzone = system->saferzone; - - far_nbrs = *lists + FAR_NBRS; - *Htop = 0; - memset( hb_top, 0, sizeof(int) * system->local_cap ); - memset( bond_top, 0, sizeof(int) * system->total_cap ); - *num_3body = 0; - - for (i = 0; i < system->N; ++i) { - atom_i = &(system->my_atoms[i]); - type_i = atom_i->type; - if (type_i < 0) continue; - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - sbp_i = &(system->reax_param.sbp[type_i]); - - if (i < system->n) { - local = 1; - cutoff = control->nonb_cut; - ++(*Htop); - ihb = sbp_i->p_hbond; - } else { - local = 0; - cutoff = control->bond_cut; - ihb = -1; - } - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); - j = nbr_pj->nbr; - atom_j = &(system->my_atoms[j]); - - if (nbr_pj->d <= cutoff) { - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - r_ij = nbr_pj->d; - sbp_j = &(system->reax_param.sbp[type_j]); - twbp = &(system->reax_param.tbp[type_i][type_j]); - - if (local) { - if (j < system->n || atom_i->orig_id < atom_j->orig_id) //tryQEq ||1 - ++(*Htop); - - /* hydrogen bond lists */ - if (control->hbond_cut > 0.1 && (ihb==1 || ihb==2) && - nbr_pj->d <= control->hbond_cut) { - jhb = sbp_j->p_hbond; - if (ihb == 1 && jhb == 2) - ++hb_top[i]; - else if (j < system->n && ihb == 2 && jhb == 1) - ++hb_top[j]; - } - } - - /* uncorrected bond orders */ - if (nbr_pj->d <= control->bond_cut) { - if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { - C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 ); - BO_s = (1.0 + control->bo_cut) * exp( C12 ); - } - else BO_s = C12 = 0.0; - - if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { - C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 ); - BO_pi = exp( C34 ); - } - else BO_pi = C34 = 0.0; - - if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { - C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 ); - BO_pi2= exp( C56 ); - } - else BO_pi2 = C56 = 0.0; - - /* Initially BO values are the uncorrected ones, page 1 */ - BO = BO_s + BO_pi + BO_pi2; - - if (BO >= control->bo_cut) { - ++bond_top[i]; - ++bond_top[j]; - } - } - } - } - } - - *Htop = (int)(MAX( *Htop * safezone, mincap * MIN_HENTRIES )); - for (i = 0; i < system->n; ++i) - hb_top[i] = (int)(MAX(hb_top[i] * saferzone, system->minhbonds)); - - for (i = 0; i < system->N; ++i) { - *num_3body += SQR(bond_top[i]); - bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS ); - } - -} - - -void Compute_Forces( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - mpi_datatypes *mpi_data ) -{ - - Init_Forces_noQEq( system, control, data, workspace, - lists, out_control); - - /********* bonded interactions ************/ - Compute_Bonded_Forces( system, control, data, workspace, - lists, out_control, mpi_data->world ); - - /********* nonbonded interactions ************/ - Compute_NonBonded_Forces( system, control, data, workspace, - lists, out_control, mpi_data->world ); - - /*********** total force ***************/ - Compute_Total_Force( system, control, data, workspace, lists, mpi_data ); - -} diff --git a/src/USER-REAXC/reaxc_forces.h b/src/USER-REAXC/reaxc_forces.h deleted file mode 100644 index ef23a84a18..0000000000 --- a/src/USER-REAXC/reaxc_forces.h +++ /dev/null @@ -1,41 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __FORCES_H_ -#define __FORCES_H_ - -#include "reaxc_types.h" -#include "reaxc_defs.h" - -extern interaction_function Interaction_Functions[NUM_INTRS]; - -void Init_Force_Functions( control_params* ); -void Compute_Forces( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls*, mpi_datatypes* ); -void Estimate_Storages( reax_system*, control_params*, reax_list**, - int*, int*, int*, int* ); -#endif diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp deleted file mode 100644 index 9d0cbbe97c..0000000000 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp +++ /dev/null @@ -1,186 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_hydrogen_bonds.h" -#include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" -#include "reaxc_valence_angles.h" -#include "reaxc_vector.h" - -void Hydrogen_Bonds( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /*out_control*/ ) -{ - int i, j, k, pi, pk; - int type_i, type_j, type_k; - int start_j, end_j, hb_start_j, hb_end_j; - int hblist[MAX_BONDS]; - int itr, top; - int num_hb_intrs = 0; - ivec rel_jk; - double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; - double e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3; - rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk; - rvec dvec_jk, force, ext_press; - hbond_parameters *hbp; - bond_order_data *bo_ij; - bond_data *pbond_ij; - far_neighbor_data *nbr_jk; - reax_list *bonds, *hbonds; - bond_data *bond_list; - hbond_data *hbond_list; - - // tally variables - double fi_tmp[3], fk_tmp[3], delij[3], delkj[3]; - - bonds = (*lists) + BONDS; - bond_list = bonds->select.bond_list; - hbonds = (*lists) + HBONDS; - hbond_list = hbonds->select.hbond_list; - - for (j = 0; j < system->n; ++j) - if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) { - type_j = system->my_atoms[j].type; - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds ); - hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds ); - if (type_j < 0) continue; - - top = 0; - for (pi = start_j; pi < end_j; ++pi) { - pbond_ij = &( bond_list[pi] ); - i = pbond_ij->nbr; - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - bo_ij = &(pbond_ij->bo_data); - - if ( system->reax_param.sbp[type_i].p_hbond == 2 && - bo_ij->BO >= HB_THRESHOLD ) - hblist[top++] = pi; - } - - for (pk = hb_start_j; pk < hb_end_j; ++pk) { - /* set k's varibles */ - k = hbond_list[pk].nbr; - type_k = system->my_atoms[k].type; - if (type_k < 0) continue; - nbr_jk = hbond_list[pk].ptr; - r_jk = nbr_jk->d; - rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec ); - - for (itr = 0; itr < top; ++itr) { - pi = hblist[itr]; - pbond_ij = &( bonds->select.bond_list[pi] ); - i = pbond_ij->nbr; - - if (system->my_atoms[i].orig_id != system->my_atoms[k].orig_id) { - bo_ij = &(pbond_ij->bo_data); - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]); - if (hbp->r0_hb <= 0.0) continue; - ++num_hb_intrs; - - Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, - &theta, &cos_theta ); - /* the derivative of cos(theta) */ - Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, - &dcos_theta_di, &dcos_theta_dj, - &dcos_theta_dk ); - - /* hyrogen bond energy*/ - sin_theta2 = sin( theta/2.0 ); - sin_xhz4 = SQR(sin_theta2); - sin_xhz4 *= sin_xhz4; - cos_xhz1 = ( 1.0 - cos_theta ); - exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO ); - exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk + - r_jk / hbp->r0_hb - 2.0 ) ); - - data->my_en.e_hb += e_hb = - hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4; - - CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4; - CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1; - CEhb3 = -hbp->p_hb3 * - (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb; - - /* hydrogen bond forces */ - bo_ij->Cdbo += CEhb1; // dbo term - - if (control->virial == 0) { - // dcos terms - rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di ); - rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj ); - rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk ); - // dr terms - rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk ); - rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk ); - } - else { - rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms - rvec_Add( workspace->f[i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press ); - - rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj ); - - ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box ); - rvec_Scale( force, +CEhb2, dcos_theta_dk ); - rvec_Add( workspace->f[k], force ); - rvec_iMultiply( ext_press, rel_jk, force ); - rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press ); - // dr terms - rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk ); - - rvec_Scale( force, CEhb3/r_jk, dvec_jk ); - rvec_Add( workspace->f[k], force ); - rvec_iMultiply( ext_press, rel_jk, force ); - rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press ); - } - - /* tally into per-atom virials */ - if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { - rvec_ScaledSum( delij, 1., system->my_atoms[j].x, - -1., system->my_atoms[i].x ); - rvec_ScaledSum( delkj, 1., system->my_atoms[j].x, - -1., system->my_atoms[k].x ); - - rvec_Scale(fi_tmp, CEhb2, dcos_theta_di); - rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk); - rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk); - - system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj); - } - } - } - } - } -} diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.h b/src/USER-REAXC/reaxc_hydrogen_bonds.h deleted file mode 100644 index 1d88f1edcf..0000000000 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.h +++ /dev/null @@ -1,36 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __HBONDS_H_ -#define __HBONDS_H_ - -#include "reaxc_types.h" - -void Hydrogen_Bonds( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); - -#endif diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp deleted file mode 100644 index 3d0a60c862..0000000000 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ /dev/null @@ -1,261 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_init_md.h" -#include -#include -#include -#include -#include "reaxc_defs.h" -#include "reaxc_allocate.h" -#include "reaxc_forces.h" -#include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_lookup.h" -#include "reaxc_reset_tools.h" -#include "reaxc_tool_box.h" - -#include "error.h" -#include "fmt/format.h" - -int Init_System(reax_system *system, control_params *control, char * /*msg*/) -{ - int i; - reax_atom *atom; - - int mincap = system->mincap; - double safezone = system->safezone; - double saferzone = system->saferzone; - - // determine the local and total capacity - - system->local_cap = MAX((int)(system->n * safezone), mincap); - system->total_cap = MAX((int)(system->N * safezone), mincap); - - /* estimate numH and Hcap */ - system->numH = 0; - if (control->hbond_cut > 0) - for (i = 0; i < system->n; ++i) { - atom = &(system->my_atoms[i]); - if (system->reax_param.sbp[ atom->type ].p_hbond == 1 && atom->type >= 0) - atom->Hindex = system->numH++; - else atom->Hindex = -1; - } - system->Hcap = (int)(MAX(system->numH * saferzone, mincap)); - - return SUCCESS; -} - - -int Init_Simulation_Data(reax_system *system, control_params *control, - simulation_data *data, char * /*msg*/) -{ - Reset_Simulation_Data(data, control->virial); - - /* initialize the timer(s) */ - if (system->my_rank == MASTER_NODE) { - data->timing.start = MPI_Wtime(); - } - - data->step = data->prev_steps = 0; - - return SUCCESS; -} - -void Init_Taper(control_params *control, storage *workspace) -{ - double d1, d7; - double swa, swa2, swa3; - double swb, swb2, swb3; - LAMMPS_NS::Error *error = control->error_ptr; - - swa = control->nonb_low; - swb = control->nonb_cut; - - if (fabs(swa) > 0.01 && control->me == 0) - error->warning(FLERR, "Non-zero lower Taper-radius cutoff"); - - if (swb < 0) { - error->all(FLERR,"Negative upper Taper-radius cutoff"); - } - else if (swb < 5 && control->me == 0) { - char errmsg[256]; - snprintf(errmsg, 256, "Very low Taper-radius cutoff: %f", swb); - error->warning(FLERR, errmsg); - } - - d1 = swb - swa; - d7 = pow(d1, 7.0); - swa2 = SQR(swa); - swa3 = CUBE(swa); - swb2 = SQR(swb); - swb3 = CUBE(swb); - - workspace->Tap[7] = 20.0 / d7; - workspace->Tap[6] = -70.0 * (swa + swb) / d7; - workspace->Tap[5] = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7; - workspace->Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3) / d7; - workspace->Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3) / d7; - workspace->Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7; - workspace->Tap[1] = 140.0 * swa3 * swb3 / d7; - workspace->Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 - - 7.0*swa*swb3*swb3 + swb3*swb3*swb) / d7; -} - - -int Init_Workspace(reax_system *system, control_params *control, - storage *workspace, char *msg) -{ - int ret; - - ret = Allocate_Workspace(system, control, workspace, - system->local_cap, system->total_cap, msg); - if (ret != SUCCESS) - return ret; - - memset(&(workspace->realloc), 0, sizeof(reallocate_data)); - Reset_Workspace(system, workspace); - - /* Initialize the Taper function */ - Init_Taper(control, workspace); - - return SUCCESS; -} - - -/************** setup communication data structures **************/ -int Init_MPI_Datatypes(reax_system *system, storage * /*workspace*/, - mpi_datatypes *mpi_data, MPI_Comm comm, char * /*msg*/) -{ - - /* setup the world */ - mpi_data->world = comm; - MPI_Comm_size(comm, &(system->wsize)); - - return SUCCESS; -} - -int Init_Lists(reax_system *system, control_params *control, - simulation_data * /*data*/, storage * /*workspace*/, reax_list **lists, - mpi_datatypes * /*mpi_data*/, char * /*msg*/) -{ - int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; - int *hb_top, *bond_top; - - int mincap = system->mincap; - double safezone = system->safezone; - double saferzone = system->saferzone; - LAMMPS_NS::Error *error = system->error_ptr; - - bond_top = (int*) calloc(system->total_cap, sizeof(int)); - hb_top = (int*) calloc(system->local_cap, sizeof(int)); - Estimate_Storages(system, control, lists, - &Htop, hb_top, bond_top, &num_3body); - - if (control->hbond_cut > 0) { - /* init H indexes */ - total_hbonds = 0; - for (i = 0; i < system->n; ++i) { - system->my_atoms[i].num_hbonds = hb_top[i]; - total_hbonds += hb_top[i]; - } - total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds)); - - if (!Make_List(system->Hcap, total_hbonds, TYP_HBOND, - *lists+HBONDS)) - error->one(FLERR, "Not enough space for hbonds list."); - - (*lists+HBONDS)->error_ptr = system->error_ptr; - } - - total_bonds = 0; - for (i = 0; i < system->N; ++i) { - system->my_atoms[i].num_bonds = bond_top[i]; - total_bonds += bond_top[i]; - } - bond_cap = (int)(MAX(total_bonds*safezone, mincap*MIN_BONDS)); - - if (!Make_List(system->total_cap, bond_cap, TYP_BOND, - *lists+BONDS)) - error->one(FLERR, "Not enough space for bonds list."); - - (*lists+BONDS)->error_ptr = system->error_ptr; - - /* 3bodies list */ - cap_3body = (int)(MAX(num_3body*safezone, MIN_3BODIES)); - if (!Make_List(bond_cap, cap_3body, TYP_THREE_BODY, - *lists+THREE_BODIES)) - error->one(FLERR,"Problem in initializing angles list."); - - (*lists+THREE_BODIES)->error_ptr = system->error_ptr; - - free(hb_top); - free(bond_top); - - return SUCCESS; -} - -void Initialize(reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, - mpi_datatypes *mpi_data, MPI_Comm comm) -{ - char msg[MAX_STR]; - LAMMPS_NS::Error *error = system->error_ptr; - - if (Init_MPI_Datatypes(system,workspace,mpi_data,comm,msg) == FAILURE) - error->one(FLERR,"init_mpi_datatypes: could not create datatypes. " - "Mpi_data could not be initialized! Terminating."); - - if (Init_System(system,control,msg) == FAILURE) - error->one(FLERR,"Error on: {}. System could not be " - "initialized! Terminating.",msg); - - if (Init_Simulation_Data( system,control,data,msg) == FAILURE) - error->one(FLERR,"Error on: {}. Sim_data could not be " - "initialized! Terminating.",msg); - - if (Init_Workspace( system,control,workspace,msg) == FAILURE) - error->one(FLERR,"init_workspace: not enough memory. " - "Workspace could not be initialized. Terminating."); - - if (Init_Lists(system, control, data, workspace, lists, mpi_data, msg) ==FAILURE) - error->one(FLERR,"Error on: {}. System could not be " - "initialized. Terminating.",msg); - - if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) - error->one(FLERR,"Error on: {}. Could not open output files! " - "Terminating.",msg); - - if (control->tabulate) - if (Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE) - error->one(FLERR,"Error on: {}. Could not create lookup " - "table. Terminating.",msg); - - - Init_Force_Functions(control); -} diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h deleted file mode 100644 index b7c1d38bbc..0000000000 --- a/src/USER-REAXC/reaxc_init_md.h +++ /dev/null @@ -1,36 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __INIT_MD_H_ -#define __INIT_MD_H_ - -#include "reaxc_types.h" -#include - -void Initialize( reax_system*, control_params*, simulation_data*, storage*, - reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); -#endif diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp deleted file mode 100644 index 0e254b2c88..0000000000 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ /dev/null @@ -1,151 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_io_tools.h" -#include -#include -#include "reaxc_defs.h" -#include "reaxc_system_props.h" -#include "reaxc_traj.h" - -int Init_Output_Files( reax_system *system, control_params *control, - output_controls *out_control, mpi_datatypes *mpi_data, - char *msg ) -{ - char temp[MAX_STR+8]; - int ret; - - if (out_control->write_steps > 0) { - ret = Init_Traj( system, control, out_control, mpi_data, msg ); - if (ret == FAILURE) - return ret; - } - - if (system->my_rank == MASTER_NODE) { - /* These files are written only by the master node */ - if (out_control->energy_update_freq > 0) { - - /* init potentials file */ - sprintf( temp, "%s.pot", control->sim_name ); - if ((out_control->pot = fopen( temp, "w" )) != nullptr) { - fflush( out_control->pot ); - } else { - strcpy( msg, "init_out_controls: .pot file could not be opened\n" ); - return FAILURE; - } - - /* init log file */ - } - - /* init pressure file */ - if ( control->ensemble == NPT || - control->ensemble == iNPT || - control->ensemble == sNPT) { - sprintf( temp, "%s.prs", control->sim_name ); - if ((out_control->prs = fopen( temp, "w" )) != nullptr) { - fprintf(out_control->prs,"%8s%13s%13s%13s%13s%13s%13s%13s\n", - "step", "Pint/norm[x]", "Pint/norm[y]", "Pint/norm[z]", - "Pext/Ptot[x]", "Pext/Ptot[y]", "Pext/Ptot[z]", "Pkin/V" ); - fflush( out_control->prs ); - } else { - strcpy(msg,"init_out_controls: .prs file couldn't be opened\n"); - return FAILURE; - } - } - } - - return SUCCESS; -} - - -/************************ close output files ************************/ -int Close_Output_Files( reax_system *system, control_params * /* control */, - output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) -{ - if (out_control->write_steps > 0) - End_Traj( system->my_rank, out_control ); - - if (system->my_rank == MASTER_NODE) { - if (out_control->pot) { - fclose( out_control->pot ); - out_control->pot = nullptr; - } - - if (out_control->prs) { - fclose(out_control->prs); - out_control->prs = nullptr; - } - } - - return SUCCESS; -} - - -void Output_Results( reax_system *system, control_params *control, - simulation_data *data, reax_list **lists, - output_controls *out_control, mpi_datatypes *mpi_data ) -{ - - if ((out_control->energy_update_freq > 0 && - data->step%out_control->energy_update_freq == 0) || - (out_control->write_steps > 0 && - data->step%out_control->write_steps == 0)) { - /* update system-wide energies */ - Compute_System_Energy( system, data, mpi_data->world ); - - /* output energies */ - if ( system->my_rank == MASTER_NODE && - out_control->energy_update_freq > 0 && - data->step % out_control->energy_update_freq == 0) { - - if (control->virial && out_control->prs) { - fprintf( out_control->prs, - "%8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n", - data->step, - data->int_press[0], data->int_press[1], data->int_press[2], - data->ext_press[0], data->ext_press[1], data->ext_press[2], - data->kin_press ); - - fprintf( out_control->prs, - "%8s%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n", - "",system->big_box.box_norms[0], system->big_box.box_norms[1], - system->big_box.box_norms[2], - data->tot_press[0], data->tot_press[1], data->tot_press[2], - system->big_box.V ); - - fflush( out_control->prs); - } - } - - /* write current frame */ - if ( out_control->write_steps > 0 && - (data->step-data->prev_steps) % out_control->write_steps == 0) { - Append_Frame( system, control, data, lists, out_control, mpi_data ); - } - } - -} diff --git a/src/USER-REAXC/reaxc_io_tools.h b/src/USER-REAXC/reaxc_io_tools.h deleted file mode 100644 index b43d6cd11f..0000000000 --- a/src/USER-REAXC/reaxc_io_tools.h +++ /dev/null @@ -1,39 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __IO_TOOLS_H_ -#define __IO_TOOLS_H_ - -#include "reaxc_types.h" - -int Init_Output_Files( reax_system*, control_params*, - output_controls*, mpi_datatypes*, char* ); -int Close_Output_Files( reax_system*, control_params*, - output_controls*, mpi_datatypes* ); -void Output_Results( reax_system*, control_params*, simulation_data*, - reax_list**, output_controls*, mpi_datatypes* ); -#endif diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp deleted file mode 100644 index a02f7d2fd7..0000000000 --- a/src/USER-REAXC/reaxc_list.cpp +++ /dev/null @@ -1,149 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_list.h" -#include "reaxc_defs.h" -#include "reaxc_tool_box.h" - -#include "error.h" - -/************* allocate list space ******************/ -int Make_List(int n, int num_intrs, int type, reax_list *l ) -{ - l->allocated = 1; - - l->n = n; - l->num_intrs = num_intrs; - - if (l->index) sfree(l->error_ptr, l->index, "list:index"); - if (l->end_index) sfree(l->error_ptr, l->end_index, "list:end_index"); - l->index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:index"); - l->end_index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:end_index"); - - l->type = type; - - switch(l->type) { - case TYP_VOID: - if (l->select.v) sfree(l->error_ptr, l->select.v, "list:v"); - l->select.v = (void*) smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(void*), "list:v"); - break; - - case TYP_THREE_BODY: - if (l->select.three_body_list) sfree(l->error_ptr, l->select.three_body_list,"list:three_bodies"); - l->select.three_body_list = (three_body_interaction_data*) - smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(three_body_interaction_data), - "list:three_bodies"); - break; - - case TYP_BOND: - if (l->select.bond_list) sfree(l->error_ptr, l->select.bond_list,"list:bonds"); - l->select.bond_list = (bond_data*) - smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(bond_data), "list:bonds"); - break; - - case TYP_DBO: - if (l->select.dbo_list) sfree(l->error_ptr, l->select.dbo_list,"list:dbonds"); - l->select.dbo_list = (dbond_data*) - smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(dbond_data), "list:dbonds"); - break; - - case TYP_DDELTA: - if (l->select.dDelta_list) sfree(l->error_ptr, l->select.dDelta_list,"list:dDeltas"); - l->select.dDelta_list = (dDelta_data*) - smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(dDelta_data), "list:dDeltas"); - break; - - case TYP_FAR_NEIGHBOR: - if (l->select.far_nbr_list) sfree(l->error_ptr, l->select.far_nbr_list,"list:far_nbrs"); - l->select.far_nbr_list = (far_neighbor_data*) - smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(far_neighbor_data), "list:far_nbrs"); - break; - - case TYP_HBOND: - if (l->select.hbond_list) sfree(l->error_ptr, l->select.hbond_list,"list:hbonds"); - l->select.hbond_list = (hbond_data*) - smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(hbond_data), "list:hbonds"); - break; - - default: - char errmsg[128]; - snprintf(errmsg, 128, "No %d list type defined", l->type); - l->error_ptr->one(FLERR,errmsg); - } - - return SUCCESS; -} - - -void Delete_List( reax_list *l ) -{ - if (l->allocated == 0) - return; - l->allocated = 0; - - sfree(l->error_ptr, l->index, "list:index" ); - sfree(l->error_ptr, l->end_index, "list:end_index" ); - l->index = nullptr; - l->end_index = nullptr; - - switch(l->type) { - case TYP_VOID: - sfree(l->error_ptr, l->select.v, "list:v" ); - l->select.v = nullptr; - break; - case TYP_HBOND: - sfree(l->error_ptr, l->select.hbond_list, "list:hbonds" ); - l->select.hbond_list = nullptr; - break; - case TYP_FAR_NEIGHBOR: - sfree(l->error_ptr, l->select.far_nbr_list, "list:far_nbrs" ); - l->select.far_nbr_list = nullptr; - break; - case TYP_BOND: - sfree(l->error_ptr, l->select.bond_list, "list:bonds" ); - l->select.bond_list = nullptr; - break; - case TYP_DBO: - sfree(l->error_ptr, l->select.dbo_list, "list:dbos" ); - l->select.dbo_list = nullptr; - break; - case TYP_DDELTA: - sfree(l->error_ptr, l->select.dDelta_list, "list:dDeltas" ); - l->select.dDelta_list = nullptr; - break; - case TYP_THREE_BODY: - sfree(l->error_ptr, l->select.three_body_list, "list:three_bodies" ); - l->select.three_body_list = nullptr; - break; - - default: - char errmsg[128]; - snprintf(errmsg, 128, "No %d list type defined", l->type); - l->error_ptr->all(FLERR,errmsg); - } -} - diff --git a/src/USER-REAXC/reaxc_list.h b/src/USER-REAXC/reaxc_list.h deleted file mode 100644 index 323656537d..0000000000 --- a/src/USER-REAXC/reaxc_list.h +++ /dev/null @@ -1,69 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __LIST_H_ -#define __LIST_H_ - -#include "reaxc_types.h" - -int Make_List( int, int, int, reax_list* ); -void Delete_List( reax_list* ); - -inline int Num_Entries(int,reax_list*); -inline int Start_Index( int, reax_list* ); -inline int End_Index( int, reax_list* ); -inline void Set_Start_Index(int,int,reax_list*); -inline void Set_End_Index(int,int,reax_list*); - -#if defined(LAMMPS_REAX) -inline int Num_Entries( int i, reax_list *l ) -{ - return l->end_index[i] - l->index[i]; -} - -inline int Start_Index( int i, reax_list *l ) -{ - return l->index[i]; -} - -inline int End_Index( int i, reax_list *l ) -{ - return l->end_index[i]; -} - -inline void Set_Start_Index( int i, int val, reax_list *l ) -{ - l->index[i] = val; -} - -inline void Set_End_Index( int i, int val, reax_list *l ) -{ - l->end_index[i] = val; -} -#endif // LAMMPS_REAX - -#endif diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp deleted file mode 100644 index 33922e2022..0000000000 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ /dev/null @@ -1,294 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_lookup.h" -#include -#include -#include "reaxc_nonbonded.h" -#include "reaxc_tool_box.h" - -void Tridiagonal_Solve( const double *a, const double *b, - double *c, double *d, double *x, unsigned int n) { - int i; - double id; - - c[0] /= b[0]; /* Division by zero risk. */ - d[0] /= b[0]; /* Division by zero would imply a singular matrix. */ - for (i = 1; i < (int)n; i++) { - id = (b[i] - c[i-1] * a[i]); /* Division by zero risk. */ - c[i] /= id; /* Last value calculated is redundant. */ - d[i] = (d[i] - d[i-1] * a[i])/id; - } - - x[n - 1] = d[n - 1]; - for (i = n - 2; i >= 0; i--) - x[i] = d[i] - c[i] * x[i + 1]; -} - - -void Natural_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const double *f, - cubic_spline_coef *coef, unsigned int n ) -{ - int i; - double *a, *b, *c, *d, *v; - - /* allocate space for the linear system */ - a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - - /* build the linear system */ - a[0] = a[1] = a[n-1] = 0; - for (i = 2; i < (int)n-1; ++i) - a[i] = h[i-1]; - - b[0] = b[n-1] = 0; - for (i = 1; i < (int)n-1; ++i) - b[i] = 2 * (h[i-1] + h[i]); - - c[0] = c[n-2] = c[n-1] = 0; - for (i = 1; i < (int)n-2; ++i) - c[i] = h[i]; - - d[0] = d[n-1] = 0; - for (i = 1; i < (int)n-1; ++i) - d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]); - - v[0] = 0; - v[n-1] = 0; - Tridiagonal_Solve( &(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n-2 ); - - for (i = 1; i < (int)n; ++i) { - coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]); - coef[i-1].c = v[i]/2; - coef[i-1].b = (f[i]-f[i-1])/h[i-1] + h[i-1]*(2*v[i] + v[i-1])/6; - coef[i-1].a = f[i]; - } - - sfree(error_ptr, a, "cubic_spline:a" ); - sfree(error_ptr, b, "cubic_spline:b" ); - sfree(error_ptr, c, "cubic_spline:c" ); - sfree(error_ptr, d, "cubic_spline:d" ); - sfree(error_ptr, v, "cubic_spline:v" ); -} - - - -void Complete_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n ) -{ - int i; - double *a, *b, *c, *d, *v; - - /* allocate space for the linear system */ - a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); - - /* build the linear system */ - a[0] = 0; - for (i = 1; i < (int)n; ++i) - a[i] = h[i-1]; - - b[0] = 2*h[0]; - for (i = 1; i < (int)n; ++i) - b[i] = 2 * (h[i-1] + h[i]); - - c[n-1] = 0; - for (i = 0; i < (int)n-1; ++i) - c[i] = h[i]; - - d[0] = 6 * (f[1]-f[0])/h[0] - 6 * v0; - d[n-1] = 6 * vlast - 6 * (f[n-1]-f[n-2]/h[n-2]); - for (i = 1; i < (int)n-1; ++i) - d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]); - - Tridiagonal_Solve( &(a[0]), &(b[0]), &(c[0]), &(d[0]), &(v[0]), n ); - - for (i = 1; i < (int)n; ++i) { - coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]); - coef[i-1].c = v[i]/2; - coef[i-1].b = (f[i]-f[i-1])/h[i-1] + h[i-1]*(2*v[i] + v[i-1])/6; - coef[i-1].a = f[i]; - } - - sfree(error_ptr, a, "cubic_spline:a" ); - sfree(error_ptr, b, "cubic_spline:b" ); - sfree(error_ptr, c, "cubic_spline:c" ); - sfree(error_ptr, d, "cubic_spline:d" ); - sfree(error_ptr, v, "cubic_spline:v" ); -} - - -int Init_Lookup_Tables( reax_system *system, control_params *control, - storage *workspace, mpi_datatypes *mpi_data, char * /*msg*/ ) -{ - int i, j, r; - int num_atom_types; - int existing_types[REAX_MAX_ATOM_TYPES], aggregated[REAX_MAX_ATOM_TYPES]; - double dr; - double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; - double v0_vdw, v0_ele, vlast_vdw, vlast_ele; - LR_lookup_table ** & LR = system->LR; - - /* initializations */ - v0_vdw = 0; - v0_ele = 0; - vlast_vdw = 0; - vlast_ele = 0; - - num_atom_types = system->reax_param.num_atom_types; - dr = control->nonb_cut / control->tabulate; - h = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h"); - fh = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh"); - fvdw = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw"); - fCEvd = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd"); - fele = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele"); - fCEclmb = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); - - LR = (LR_lookup_table**) - scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table*), "lookup:LR"); - for (i = 0; i < num_atom_types; ++i) - LR[i] = (LR_lookup_table*) - scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]"); - - for (i = 0; i < REAX_MAX_ATOM_TYPES; ++i) - existing_types[i] = 0; - for (i = 0; i < system->n; ++i) - existing_types[ system->my_atoms[i].type ] = 1; - - MPI_Allreduce( existing_types, aggregated, REAX_MAX_ATOM_TYPES, - MPI_INT, MPI_SUM, mpi_data->world ); - - for (i = 0; i < num_atom_types; ++i) { - if (aggregated[i]) { - for (j = i; j < num_atom_types; ++j) { - if (aggregated[j]) { - LR[i][j].xmin = 0; - LR[i][j].xmax = control->nonb_cut; - LR[i][j].n = control->tabulate + 2; - LR[i][j].dx = dr; - LR[i][j].inv_dx = control->tabulate / control->nonb_cut; - LR[i][j].y = (LR_data*) - smalloc(system->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); - LR[i][j].H = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); - LR[i][j].vdW = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); - LR[i][j].CEvd = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); - LR[i][j].ele = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); - LR[i][j].CEclmb = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), - "lookup:LR[i,j].CEclmb"); - - for (r = 1; r <= control->tabulate; ++r) { - LR_vdW_Coulomb( system, workspace, control, i, j, r * dr, &(LR[i][j].y[r]) ); - h[r] = LR[i][j].dx; - fh[r] = LR[i][j].y[r].H; - fvdw[r] = LR[i][j].y[r].e_vdW; - fCEvd[r] = LR[i][j].y[r].CEvd; - fele[r] = LR[i][j].y[r].e_ele; - fCEclmb[r] = LR[i][j].y[r].CEclmb; - } - - // init the start-end points - h[r] = LR[i][j].dx; - v0_vdw = LR[i][j].y[1].CEvd; - v0_ele = LR[i][j].y[1].CEclmb; - fh[r] = fh[r-1]; - fvdw[r] = fvdw[r-1]; - fCEvd[r] = fCEvd[r-1]; - fele[r] = fele[r-1]; - fCEclmb[r] = fCEclmb[r-1]; - vlast_vdw = fCEvd[r-1]; - vlast_ele = fele[r-1]; - - Natural_Cubic_Spline( control->error_ptr, &h[1], &fh[1], - &(LR[i][j].H[1]), control->tabulate+1); - - Complete_Cubic_Spline( control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, - &(LR[i][j].vdW[1]), control->tabulate+1); - - Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEvd[1], - &(LR[i][j].CEvd[1]), control->tabulate+1); - - Complete_Cubic_Spline( control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, - &(LR[i][j].ele[1]), control->tabulate+1); - - Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEclmb[1], - &(LR[i][j].CEclmb[1]), control->tabulate+1); - } else { - LR[i][j].n = 0; - } - } - } - } - free(h); - free(fh); - free(fvdw); - free(fCEvd); - free(fele); - free(fCEclmb); - - return 1; -} - - -void Deallocate_Lookup_Tables( reax_system *system ) -{ - int i, j; - int ntypes; - LR_lookup_table ** & LR = system->LR; - - ntypes = system->reax_param.num_atom_types; - - for (i = 0; i < ntypes; ++i) { - for (j = i; j < ntypes; ++j) - if (LR[i][j].n) { - sfree(system->error_ptr, LR[i][j].y, "LR[i,j].y" ); - sfree(system->error_ptr, LR[i][j].H, "LR[i,j].H" ); - sfree(system->error_ptr, LR[i][j].vdW, "LR[i,j].vdW" ); - sfree(system->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd" ); - sfree(system->error_ptr, LR[i][j].ele, "LR[i,j].ele" ); - sfree(system->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" ); - } - sfree(system->error_ptr, LR[i], "LR[i]" ); - } - sfree(system->error_ptr, LR, "LR" ); -} diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h deleted file mode 100644 index abbac23e1f..0000000000 --- a/src/USER-REAXC/reaxc_lookup.h +++ /dev/null @@ -1,49 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __LOOKUP_H_ -#define __LOOKUP_H_ - -#include "reaxc_types.h" -namespace LAMMPS_NS { class Error; } - -void Tridiagonal_Solve( const double *a, const double *b, - double *c, double *d, double *x, unsigned int n); - -void Natural_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, - cubic_spline_coef *coef, unsigned int n ); - -void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, - double v0, double vlast, cubic_spline_coef *coef, - unsigned int n ); - -int Init_Lookup_Tables( reax_system*, control_params*, storage*, - mpi_datatypes*, char* ); - -void Deallocate_Lookup_Tables( reax_system* ); - -#endif diff --git a/src/USER-REAXC/reaxc_multi_body.h b/src/USER-REAXC/reaxc_multi_body.h deleted file mode 100644 index 5d60140b44..0000000000 --- a/src/USER-REAXC/reaxc_multi_body.h +++ /dev/null @@ -1,36 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __MULTI_BODY_H_ -#define __MULTI_BODY_H_ - -#include "reaxc_types.h" - -void Atom_Energy( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); - -#endif diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp deleted file mode 100644 index 31265bd2e8..0000000000 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ /dev/null @@ -1,433 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_nonbonded.h" -#include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_types.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -void vdW_Coulomb_Energy( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /*out_control*/ ) -{ - int i, j, pj, natoms; - int start_i, end_i, flag; - rc_tagint orig_i, orig_j; - double p_vdW1, p_vdW1i; - double powr_vdW1, powgi_vdW1; - double tmp, r_ij, fn13, exp1, exp2; - double Tap, dTap, dfn13, CEvd, CEclmb, de_core; - double dr3gamij_1, dr3gamij_3; - double e_ele, e_vdW, e_core, SMALL = 0.0001; - double e_lg, de_lg, r_ij5, r_ij6, re6; - rvec temp, ext_press; - two_body_parameters *twbp; - far_neighbor_data *nbr_pj; - reax_list *far_nbrs; - - // Tallying variables: - double pe_vdw, f_tmp, delij[3]; - - natoms = system->n; - far_nbrs = (*lists) + FAR_NBRS; - p_vdW1 = system->reax_param.gp.l[28]; - p_vdW1i = 1.0 / p_vdW1; - e_core = 0; - e_vdW = 0; - e_lg = de_lg = 0.0; - - for (i = 0; i < natoms; ++i) { - if (system->my_atoms[i].type < 0) continue; - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - orig_i = system->my_atoms[i].orig_id; - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); - j = nbr_pj->nbr; - if (system->my_atoms[j].type < 0) continue; - orig_j = system->my_atoms[j].orig_id; - - flag = 0; - if (nbr_pj->d <= control->nonb_cut) { - if (j < natoms) flag = 1; - else if (orig_i < orig_j) flag = 1; - else if (orig_i == orig_j) { - if (nbr_pj->dvec[2] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[2]) < SMALL) { - if (nbr_pj->dvec[1] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) - flag = 1; - } - } - } - - if (flag) { - - r_ij = nbr_pj->d; - twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ] - [ system->my_atoms[j].type ]); - - Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; - Tap = Tap * r_ij + workspace->Tap[5]; - Tap = Tap * r_ij + workspace->Tap[4]; - Tap = Tap * r_ij + workspace->Tap[3]; - Tap = Tap * r_ij + workspace->Tap[2]; - Tap = Tap * r_ij + workspace->Tap[1]; - Tap = Tap * r_ij + workspace->Tap[0]; - - dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; - dTap = dTap * r_ij + 5*workspace->Tap[5]; - dTap = dTap * r_ij + 4*workspace->Tap[4]; - dTap = dTap * r_ij + 3*workspace->Tap[3]; - dTap = dTap * r_ij + 2*workspace->Tap[2]; - dTap += workspace->Tap[1]/r_ij; - - /*vdWaals Calculations*/ - if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) - { // shielding - powr_vdW1 = pow(r_ij, p_vdW1); - powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1); - - fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i ); - exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - - e_vdW = twbp->D * (exp1 - 2.0 * exp2); - data->my_en.e_vdW += Tap * e_vdW; - - dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * - pow(r_ij, p_vdW1 - 2.0); - - CEvd = dTap * e_vdW - - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; - } - else { // no shielding - exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - - e_vdW = twbp->D * (exp1 - 2.0 * exp2); - data->my_en.e_vdW += Tap * e_vdW; - - CEvd = dTap * e_vdW - - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; - } - - if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) - { // inner wall - e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); - data->my_en.e_vdW += Tap * e_core; - - de_core = -(twbp->acore/twbp->rcore) * e_core; - CEvd += dTap * e_core + Tap * de_core / r_ij; - - // lg correction, only if lgvdw is yes - if (control->lgflag) { - r_ij5 = pow( r_ij, 5.0 ); - r_ij6 = pow( r_ij, 6.0 ); - re6 = pow( twbp->lgre, 6.0 ); - e_lg = -(twbp->lgcij/( r_ij6 + re6 )); - data->my_en.e_vdW += Tap * e_lg; - - de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ; - CEvd += dTap * e_lg + Tap * de_lg / r_ij; - } - - } - - /*Coulomb Calculations*/ - dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma ); - dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); - - tmp = Tap / dr3gamij_3; - data->my_en.e_ele += e_ele = - C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp; - - CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * - ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { - pe_vdw = Tap * (e_vdW + e_core + e_lg); - rvec_ScaledSum( delij, 1., system->my_atoms[i].x, - -1., system->my_atoms[j].x ); - f_tmp = -(CEvd + CEclmb); - system->pair_ptr->ev_tally(i,j,natoms,1,pe_vdw,e_ele, - f_tmp,delij[0],delij[1],delij[2]); - } - - if (control->virial == 0) { - rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); - rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); - } else { /* NPT, iNPT or sNPT */ - rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); - - rvec_ScaledAdd( workspace->f[i], -1., temp ); - rvec_Add( workspace->f[j], temp ); - - rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); - rvec_Add( data->my_ext_press, ext_press ); - } - } - } - } - - Compute_Polarization_Energy( system, data ); -} - - - -void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, - output_controls * /*out_control*/ ) -{ - int i, j, pj, r, natoms; - int type_i, type_j, tmin, tmax; - int start_i, end_i, flag; - rc_tagint orig_i, orig_j; - double r_ij, base, dif; - double e_vdW, e_ele; - double CEvd, CEclmb, SMALL = 0.0001; - double f_tmp, delij[3]; - - rvec temp, ext_press; - far_neighbor_data *nbr_pj; - reax_list *far_nbrs; - LR_lookup_table *t; - LR_lookup_table ** & LR = system->LR; - - natoms = system->n; - far_nbrs = (*lists) + FAR_NBRS; - - e_ele = e_vdW = 0; - - for (i = 0; i < natoms; ++i) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - start_i = Start_Index(i,far_nbrs); - end_i = End_Index(i,far_nbrs); - orig_i = system->my_atoms[i].orig_id; - - for (pj = start_i; pj < end_i; ++pj) { - nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); - j = nbr_pj->nbr; - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - orig_j = system->my_atoms[j].orig_id; - - flag = 0; - if (nbr_pj->d <= control->nonb_cut) { - if (j < natoms) flag = 1; - else if (orig_i < orig_j) flag = 1; - else if (orig_i == orig_j) { - if (nbr_pj->dvec[2] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[2]) < SMALL) { - if (nbr_pj->dvec[1] > SMALL) flag = 1; - else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) - flag = 1; - } - } - } - - if (flag) { - - r_ij = nbr_pj->d; - tmin = MIN( type_i, type_j ); - tmax = MAX( type_i, type_j ); - t = &( LR[tmin][tmax] ); - - /* Cubic Spline Interpolation */ - r = (int)(r_ij * t->inv_dx); - if (r == 0) ++r; - base = (double)(r+1) * t->dx; - dif = r_ij - base; - - e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif + - t->vdW[r].a; - - e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + - t->ele[r].a; - e_ele *= system->my_atoms[i].q * system->my_atoms[j].q; - - data->my_en.e_vdW += e_vdW; - data->my_en.e_ele += e_ele; - - CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif + - t->CEvd[r].a; - - CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif + - t->CEclmb[r].a; - CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { - rvec_ScaledSum( delij, 1., system->my_atoms[i].x, - -1., system->my_atoms[j].x ); - f_tmp = -(CEvd + CEclmb); - system->pair_ptr->ev_tally(i,j,natoms,1,e_vdW,e_ele, - f_tmp,delij[0],delij[1],delij[2]); - } - - if (control->virial == 0) { - rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); - rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); - } else { // NPT, iNPT or sNPT - rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); - - rvec_ScaledAdd( workspace->f[i], -1., temp ); - rvec_Add( workspace->f[j], temp ); - - rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); - rvec_Add( data->my_ext_press, ext_press ); - } - } - } - } - - Compute_Polarization_Energy( system, data ); -} - - - -void Compute_Polarization_Energy( reax_system *system, simulation_data *data ) -{ - int i, type_i; - double q, en_tmp; - - data->my_en.e_pol = 0.0; - for (i = 0; i < system->n; i++) { - type_i = system->my_atoms[i].type; - if (type_i < 0) continue; - q = system->my_atoms[i].q; - - en_tmp = KCALpMOL_to_EV * (system->reax_param.sbp[type_i].chi * q + - (system->reax_param.sbp[type_i].eta / 2.) * SQR(q)); - data->my_en.e_pol += en_tmp; - - /* tally into per-atom energy */ - if (system->pair_ptr->evflag) - system->pair_ptr->ev_tally(i,i,system->n,1,0.0,en_tmp,0.0,0.0,0.0,0.0); - } -} - -void LR_vdW_Coulomb( reax_system *system, storage *workspace, - control_params *control, int i, int j, double r_ij, LR_data *lr ) -{ - double p_vdW1 = system->reax_param.gp.l[28]; - double p_vdW1i = 1.0 / p_vdW1; - double powr_vdW1, powgi_vdW1; - double tmp, fn13, exp1, exp2; - double Tap, dTap, dfn13; - double dr3gamij_1, dr3gamij_3; - double e_core, de_core; - double e_lg, de_lg, r_ij5, r_ij6, re6; - two_body_parameters *twbp; - - twbp = &(system->reax_param.tbp[i][j]); - e_core = 0; - de_core = 0; - e_lg = de_lg = 0.0; - - /* calculate taper and its derivative */ - Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; - Tap = Tap * r_ij + workspace->Tap[5]; - Tap = Tap * r_ij + workspace->Tap[4]; - Tap = Tap * r_ij + workspace->Tap[3]; - Tap = Tap * r_ij + workspace->Tap[2]; - Tap = Tap * r_ij + workspace->Tap[1]; - Tap = Tap * r_ij + workspace->Tap[0]; - - dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; - dTap = dTap * r_ij + 5*workspace->Tap[5]; - dTap = dTap * r_ij + 4*workspace->Tap[4]; - dTap = dTap * r_ij + 3*workspace->Tap[3]; - dTap = dTap * r_ij + 2*workspace->Tap[2]; - dTap += workspace->Tap[1]/r_ij; - - /*vdWaals Calculations*/ - if (system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) - { // shielding - powr_vdW1 = pow(r_ij, p_vdW1); - powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1); - - fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i ); - exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); - - lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2); - - dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i-1.0) * pow(r_ij, p_vdW1-2.0); - - lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; - } - else { // no shielding - exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); - - lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2); - lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; - } - - if (system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) - { // inner wall - e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); - lr->e_vdW += Tap * e_core; - - de_core = -(twbp->acore/twbp->rcore) * e_core; - lr->CEvd += dTap * e_core + Tap * de_core / r_ij; - - // lg correction, only if lgvdw is yes - if (control->lgflag) { - r_ij5 = pow( r_ij, 5.0 ); - r_ij6 = pow( r_ij, 6.0 ); - re6 = pow( twbp->lgre, 6.0 ); - e_lg = -(twbp->lgcij/( r_ij6 + re6 )); - lr->e_vdW += Tap * e_lg; - - de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ; - lr->CEvd += dTap * e_lg + Tap * de_lg/r_ij; - } - - } - - - /* Coulomb calculations */ - dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma ); - dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); - - tmp = Tap / dr3gamij_3; - lr->H = EV_to_KCALpMOL * tmp; - lr->e_ele = C_ele * tmp; - - lr->CEclmb = C_ele * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; -} diff --git a/src/USER-REAXC/reaxc_nonbonded.h b/src/USER-REAXC/reaxc_nonbonded.h deleted file mode 100644 index 64c69e9f30..0000000000 --- a/src/USER-REAXC/reaxc_nonbonded.h +++ /dev/null @@ -1,44 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __NONBONDED_H_ -#define __NONBONDED_H_ - -#include "reaxc_types.h" - -void vdW_Coulomb_Energy( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); - -void Tabulated_vdW_Coulomb_Energy( reax_system*, control_params*, - simulation_data*, storage*, - reax_list**, output_controls* ); - -void Compute_Polarization_Energy( reax_system*, simulation_data* ); - -void LR_vdW_Coulomb( reax_system*, storage*, control_params*, - int, int, double, LR_data* ); -#endif diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp deleted file mode 100644 index adfde2494c..0000000000 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ /dev/null @@ -1,197 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_reset_tools.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" - -#include "error.h" - -#include -#include - -void Reset_Atoms( reax_system* system, control_params *control ) -{ - int i; - reax_atom *atom; - - system->numH = 0; - if (control->hbond_cut > 0) - for (i = 0; i < system->n; ++i) { - atom = &(system->my_atoms[i]); - if (atom->type < 0) continue; - if (system->reax_param.sbp[ atom->type ].p_hbond == 1) - atom->Hindex = system->numH++; - else atom->Hindex = -1; - } -} - - -void Reset_Energies( energy_data *en ) -{ - en->e_bond = 0; - en->e_ov = 0; - en->e_un = 0; - en->e_lp = 0; - en->e_ang = 0; - en->e_pen = 0; - en->e_coa = 0; - en->e_hb = 0; - en->e_tor = 0; - en->e_con = 0; - en->e_vdW = 0; - en->e_ele = 0; - en->e_pol = 0; - - en->e_pot = 0; - en->e_kin = 0; - en->e_tot = 0; -} - - -void Reset_Temperatures( simulation_data *data ) -{ - data->therm.T = 0; -} - - -void Reset_Pressures( simulation_data *data ) -{ - data->flex_bar.P_scalar = 0; - rtensor_MakeZero( data->flex_bar.P ); - - data->iso_bar.P = 0; - rvec_MakeZero( data->int_press ); - rvec_MakeZero( data->my_ext_press ); - rvec_MakeZero( data->ext_press ); -} - - -void Reset_Simulation_Data( simulation_data* data, int /*virial*/ ) -{ - Reset_Energies( &data->my_en ); - Reset_Energies( &data->sys_en ); - Reset_Temperatures( data ); - Reset_Pressures( data ); -} - - -void Reset_Timing( reax_timing *rt ) -{ - rt->total = MPI_Wtime(); - rt->comm = 0; - rt->nbrs = 0; - rt->init_forces = 0; - rt->bonded = 0; - rt->nonb = 0; - rt->qEq = 0; - rt->s_matvecs = 0; - rt->t_matvecs = 0; -} - -void Reset_Workspace( reax_system *system, storage *workspace ) -{ - memset( workspace->total_bond_order, 0, system->total_cap * sizeof( double ) ); - memset( workspace->dDeltap_self, 0, system->total_cap * sizeof( rvec ) ); - memset( workspace->CdDelta, 0, system->total_cap * sizeof( double ) ); - memset( workspace->f, 0, system->total_cap * sizeof( rvec ) ); - -} - - -void Reset_Neighbor_Lists( reax_system *system, control_params *control, - storage *workspace, reax_list **lists ) -{ - int i, total_bonds, Hindex, total_hbonds; - reax_list *bonds, *hbonds; - - /* bonds list */ - if (system->N > 0) { - bonds = (*lists) + BONDS; - total_bonds = 0; - - /* reset start-end indexes */ - for (i = 0; i < system->N; ++i) { - Set_Start_Index( i, total_bonds, bonds ); - Set_End_Index( i, total_bonds, bonds ); - total_bonds += system->my_atoms[i].num_bonds; - } - - /* is reallocation needed? */ - if (total_bonds >= bonds->num_intrs * DANGER_ZONE) { - workspace->realloc.bonds = 1; - if (total_bonds >= bonds->num_intrs) { - char errmsg[256]; - snprintf(errmsg, 256, "Not enough space for bonds! total=%d allocated=%d\n", - total_bonds, bonds->num_intrs); - control->error_ptr->one(FLERR, errmsg); - } - } - } - - if (control->hbond_cut > 0 && system->numH > 0) { - hbonds = (*lists) + HBONDS; - total_hbonds = 0; - - /* reset start-end indexes */ - for (i = 0; i < system->n; ++i) { - Hindex = system->my_atoms[i].Hindex; - if (Hindex > -1) { - Set_Start_Index( Hindex, total_hbonds, hbonds ); - Set_End_Index( Hindex, total_hbonds, hbonds ); - total_hbonds += system->my_atoms[i].num_hbonds; - } - } - - /* is reallocation needed? */ - if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) { - workspace->realloc.hbonds = 1; - if (total_hbonds >= hbonds->num_intrs) { - char errmsg[256]; - snprintf(errmsg, 256, "Not enough space for hbonds! total=%d allocated=%d\n", - total_hbonds, hbonds->num_intrs); - control->error_ptr->one(FLERR, errmsg); - } - } - } -} - - -void Reset( reax_system *system, control_params *control, simulation_data *data, - storage *workspace, reax_list **lists ) -{ - Reset_Atoms( system, control ); - - Reset_Simulation_Data( data, control->virial ); - - Reset_Workspace( system, workspace ); - - Reset_Neighbor_Lists( system, control, workspace, lists ); - -} diff --git a/src/USER-REAXC/reaxc_reset_tools.h b/src/USER-REAXC/reaxc_reset_tools.h deleted file mode 100644 index 15e584eaac..0000000000 --- a/src/USER-REAXC/reaxc_reset_tools.h +++ /dev/null @@ -1,41 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __RESET_TOOLS_H_ -#define __RESET_TOOLS_H_ - -#include "reaxc_types.h" - -void Reset_Pressures( simulation_data* ); -void Reset_Simulation_Data( simulation_data*, int ); -void Reset_Timing( reax_timing* ); -void Reset_Workspace( reax_system*, storage* ); -void Reset_Neighbor_Lists( reax_system*, control_params*, storage*, - reax_list** ); -void Reset( reax_system*, control_params*, simulation_data*, storage*, - reax_list** ); -#endif diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp deleted file mode 100644 index ec50692c6f..0000000000 --- a/src/USER-REAXC/reaxc_system_props.cpp +++ /dev/null @@ -1,87 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_system_props.h" -#include -#include "reaxc_defs.h" - -void Compute_System_Energy( reax_system *system, simulation_data *data, - MPI_Comm comm ) -{ - double my_en[15], sys_en[15]; - - my_en[0] = data->my_en.e_bond; - my_en[1] = data->my_en.e_ov; - my_en[2] = data->my_en.e_un; - my_en[3] = data->my_en.e_lp; - my_en[4] = data->my_en.e_ang; - my_en[5] = data->my_en.e_pen; - my_en[6] = data->my_en.e_coa; - my_en[7] = data->my_en.e_hb; - my_en[8] = data->my_en.e_tor; - my_en[9] = data->my_en.e_con; - my_en[10] = data->my_en.e_vdW; - my_en[11] = data->my_en.e_ele; - my_en[12] = data->my_en.e_pol; - my_en[13] = data->my_en.e_kin; - MPI_Reduce( my_en, sys_en, 14, MPI_DOUBLE, MPI_SUM, MASTER_NODE, comm ); - - data->my_en.e_pot = data->my_en.e_bond + - data->my_en.e_ov + data->my_en.e_un + data->my_en.e_lp + - data->my_en.e_ang + data->my_en.e_pen + data->my_en.e_coa + - data->my_en.e_hb + - data->my_en.e_tor + data->my_en.e_con + - data->my_en.e_vdW + data->my_en.e_ele + data->my_en.e_pol; - - data->my_en.e_tot = data->my_en.e_pot + E_CONV * data->my_en.e_kin; - - if (system->my_rank == MASTER_NODE) { - data->sys_en.e_bond = sys_en[0]; - data->sys_en.e_ov = sys_en[1]; - data->sys_en.e_un = sys_en[2]; - data->sys_en.e_lp = sys_en[3]; - data->sys_en.e_ang = sys_en[4]; - data->sys_en.e_pen = sys_en[5]; - data->sys_en.e_coa = sys_en[6]; - data->sys_en.e_hb = sys_en[7]; - data->sys_en.e_tor = sys_en[8]; - data->sys_en.e_con = sys_en[9]; - data->sys_en.e_vdW = sys_en[10]; - data->sys_en.e_ele = sys_en[11]; - data->sys_en.e_pol = sys_en[12]; - data->sys_en.e_kin = sys_en[13]; - - data->sys_en.e_pot = data->sys_en.e_bond + - data->sys_en.e_ov + data->sys_en.e_un + data->sys_en.e_lp + - data->sys_en.e_ang + data->sys_en.e_pen + data->sys_en.e_coa + - data->sys_en.e_hb + - data->sys_en.e_tor + data->sys_en.e_con + - data->sys_en.e_vdW + data->sys_en.e_ele + data->sys_en.e_pol; - - data->sys_en.e_tot = data->sys_en.e_pot + E_CONV * data->sys_en.e_kin; - } -} diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h deleted file mode 100644 index 27c80d02bf..0000000000 --- a/src/USER-REAXC/reaxc_system_props.h +++ /dev/null @@ -1,36 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __SYSTEM_PROP_H_ -#define __SYSTEM_PROP_H_ - -#include "reaxc_types.h" -#include - -void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm ); - -#endif diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h deleted file mode 100644 index 6dc6217c92..0000000000 --- a/src/USER-REAXC/reaxc_tool_box.h +++ /dev/null @@ -1,41 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __TOOL_BOX_H_ -#define __TOOL_BOX_H_ - -#include "reaxc_types.h" -namespace LAMMPS_NS { class Error; } - -/* from io_tools.h */ -int Tokenize( char*, char*** ); - -/* from lammps */ -void *smalloc( LAMMPS_NS::Error*, rc_bigint, const char* ); -void *scalloc( LAMMPS_NS::Error*, rc_bigint, rc_bigint, const char* ); -void sfree( LAMMPS_NS::Error*, void*, const char* ); -#endif diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp deleted file mode 100644 index de23597fd8..0000000000 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ /dev/null @@ -1,480 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_torsion_angles.h" -#include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -#define MIN_SINE 1e-10 - -double Calculate_Omega( rvec dvec_ij, double r_ij, - rvec dvec_jk, double r_jk, - rvec dvec_kl, double r_kl, - rvec dvec_li, double r_li, - three_body_interaction_data *p_ijk, - three_body_interaction_data *p_jkl, - rvec dcos_omega_di, rvec dcos_omega_dj, - rvec dcos_omega_dk, rvec dcos_omega_dl, - output_controls * /*out_control*/ ) -{ - double unnorm_cos_omega, unnorm_sin_omega, omega; - double sin_ijk, cos_ijk, sin_jkl, cos_jkl; - double htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe; - double arg, poem, tel; - rvec cross_jk_kl; - - sin_ijk = sin( p_ijk->theta ); - cos_ijk = cos( p_ijk->theta ); - sin_jkl = sin( p_jkl->theta ); - cos_jkl = cos( p_jkl->theta ); - - /* omega */ - unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) + - SQR( r_jk ) * rvec_Dot( dvec_ij, dvec_kl ); - - rvec_Cross( cross_jk_kl, dvec_jk, dvec_kl ); - unnorm_sin_omega = -r_jk * rvec_Dot( dvec_ij, cross_jk_kl ); - - omega = atan2( unnorm_sin_omega, unnorm_cos_omega ); - - htra = r_ij + cos_ijk * ( r_kl * cos_jkl - r_jk ); - htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl; - htrc = r_kl + cos_jkl * ( r_ij * cos_ijk - r_jk ); - hthd = r_ij * sin_ijk * ( r_jk - r_kl * cos_jkl ); - hthe = r_kl * sin_jkl * ( r_jk - r_ij * cos_ijk ); - hnra = r_kl * sin_ijk * sin_jkl; - hnrc = r_ij * sin_ijk * sin_jkl; - hnhd = r_ij * r_kl * cos_ijk * sin_jkl; - hnhe = r_ij * r_kl * sin_ijk * cos_jkl; - - poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl; - if (poem < 1e-20) poem = 1e-20; - - tel = SQR( r_ij ) + SQR( r_jk ) + SQR( r_kl ) - SQR( r_li ) - - 2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl + - r_jk * r_kl * cos_jkl ); - - arg = tel / poem; - if (arg > 1.0) arg = 1.0; - if (arg < -1.0) arg = -1.0; - - if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk = MIN_SINE; - else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) sin_ijk = -MIN_SINE; - if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) sin_jkl = MIN_SINE; - else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) sin_jkl = -MIN_SINE; - - // dcos_omega_di - rvec_ScaledSum( dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li ); - rvec_ScaledAdd( dcos_omega_di,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dk ); - rvec_Scale( dcos_omega_di, 2.0 / poem, dcos_omega_di ); - - // dcos_omega_dj - rvec_ScaledSum( dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij, - -htrb / r_jk, dvec_jk ); - rvec_ScaledAdd( dcos_omega_dj,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dj ); - rvec_ScaledAdd( dcos_omega_dj,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_di ); - rvec_Scale( dcos_omega_dj, 2.0 / poem, dcos_omega_dj ); - - // dcos_omega_dk - rvec_ScaledSum( dcos_omega_dk,-(htrc-arg*hnrc)/r_kl, dvec_kl, - htrb / r_jk, dvec_jk ); - rvec_ScaledAdd( dcos_omega_dk,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_di ); - rvec_ScaledAdd( dcos_omega_dk,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dj ); - rvec_Scale( dcos_omega_dk, 2.0 / poem, dcos_omega_dk ); - - // dcos_omega_dl - rvec_ScaledSum( dcos_omega_dl, (htrc-arg*hnrc)/r_kl, dvec_kl, 1., dvec_li ); - rvec_ScaledAdd( dcos_omega_dl,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dk ); - rvec_Scale( dcos_omega_dl, 2.0 / poem, dcos_omega_dl ); - - return omega; -} - - - -void Torsion_Angles( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) -{ - int i, j, k, l, pi, pj, pk, pl, pij, plk, natoms; - int type_i, type_j, type_k, type_l; - int start_j, end_j; - int start_pj, end_pj, start_pk, end_pk; - int num_frb_intrs = 0; - - double Delta_j, Delta_k; - double r_ij, r_jk, r_kl, r_li; - double BOA_ij, BOA_jk, BOA_kl; - - double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl; - double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv; - double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl; - double fn10, f11_DjDk, dfn11, fn12; - double theta_ijk, theta_jkl; - double sin_ijk, sin_jkl; - double cos_ijk, cos_jkl; - double tan_ijk_i, tan_jkl_i; - double omega, cos_omega, cos2omega, cos3omega; - rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl; - double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4; - double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9; - double Cconj, CEconj1, CEconj2, CEconj3; - double CEconj4, CEconj5, CEconj6; - double e_tor, e_con; - rvec dvec_li; - rvec force, ext_press; - ivec rel_box_jl; - // rtensor total_rtensor, temp_rtensor; - four_body_header *fbh; - four_body_parameters *fbp; - bond_data *pbond_ij, *pbond_jk, *pbond_kl; - bond_order_data *bo_ij, *bo_jk, *bo_kl; - three_body_interaction_data *p_ijk, *p_jkl; - double p_tor2 = system->reax_param.gp.l[23]; - double p_tor3 = system->reax_param.gp.l[24]; - double p_tor4 = system->reax_param.gp.l[25]; - double p_cot2 = system->reax_param.gp.l[27]; - reax_list *bonds = (*lists) + BONDS; - reax_list *thb_intrs = (*lists) + THREE_BODIES; - - // Virial tallying variables - double delil[3], deljl[3], delkl[3]; - double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; - - natoms = system->n; - - for (j = 0; j < natoms; ++j) { - type_j = system->my_atoms[j].type; - Delta_j = workspace->Delta_boc[j]; - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - for (pk = start_j; pk < end_j; ++pk) { - pbond_jk = &( bonds->select.bond_list[pk] ); - k = pbond_jk->nbr; - bo_jk = &( pbond_jk->bo_data ); - BOA_jk = bo_jk->BO - control->thb_cut; - - if (system->my_atoms[j].orig_id > system->my_atoms[k].orig_id) - continue; - if (system->my_atoms[j].orig_id == system->my_atoms[k].orig_id) { - if (system->my_atoms[k].x[2] < system->my_atoms[j].x[2]) continue; - if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] && - system->my_atoms[k].x[1] < system->my_atoms[j].x[1]) continue; - if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] && - system->my_atoms[k].x[1] == system->my_atoms[j].x[1] && - system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue; - } - - if (bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) { - pj = pbond_jk->sym_index; // pj points to j on k's list - - if (Num_Entries(pj, thb_intrs)) { - type_k = system->my_atoms[k].type; - Delta_k = workspace->Delta_boc[k]; - r_jk = pbond_jk->d; - - start_pk = Start_Index(pk, thb_intrs ); - end_pk = End_Index(pk, thb_intrs ); - start_pj = Start_Index(pj, thb_intrs ); - end_pj = End_Index(pj, thb_intrs ); - - exp_tor2_jk = exp( -p_tor2 * BOA_jk ); - exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) ); - exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) ); - exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) ); - exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk); - f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv; - - for (pi = start_pk; pi < end_pk; ++pi) { - p_ijk = &( thb_intrs->select.three_body_list[pi] ); - pij = p_ijk->pthb; // pij is pointer to i on j's bond_list - pbond_ij = &( bonds->select.bond_list[pij] ); - bo_ij = &( pbond_ij->bo_data ); - - if (bo_ij->BO > control->thb_cut/*0*/) { - i = p_ijk->thb; - type_i = system->my_atoms[i].type; - r_ij = pbond_ij->d; - BOA_ij = bo_ij->BO - control->thb_cut; - - theta_ijk = p_ijk->theta; - sin_ijk = sin( theta_ijk ); - cos_ijk = cos( theta_ijk ); - //tan_ijk_i = 1. / tan( theta_ijk ); - if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) - tan_ijk_i = cos_ijk / MIN_SINE; - else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) - tan_ijk_i = cos_ijk / -MIN_SINE; - else tan_ijk_i = cos_ijk / sin_ijk; - - exp_tor2_ij = exp( -p_tor2 * BOA_ij ); - exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) ); - - for (pl = start_pj; pl < end_pj; ++pl) { - p_jkl = &( thb_intrs->select.three_body_list[pl] ); - l = p_jkl->thb; - plk = p_jkl->pthb; //pointer to l on k's bond_list! - pbond_kl = &( bonds->select.bond_list[plk] ); - bo_kl = &( pbond_kl->bo_data ); - type_l = system->my_atoms[l].type; - fbh = &(system->reax_param.fbp[type_i][type_j] - [type_k][type_l]); - fbp = &(system->reax_param.fbp[type_i][type_j] - [type_k][type_l].prm[0]); - - if ( i != l && fbh->cnt && - bo_kl->BO > control->thb_cut/*0*/ && - bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) { - ++num_frb_intrs; - r_kl = pbond_kl->d; - BOA_kl = bo_kl->BO - control->thb_cut; - - theta_jkl = p_jkl->theta; - sin_jkl = sin( theta_jkl ); - cos_jkl = cos( theta_jkl ); - //tan_jkl_i = 1. / tan( theta_jkl ); - if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) - tan_jkl_i = cos_jkl / MIN_SINE; - else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) - tan_jkl_i = cos_jkl / -MIN_SINE; - else tan_jkl_i = cos_jkl /sin_jkl; - - rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x, - -1., system->my_atoms[l].x ); - r_li = rvec_Norm( dvec_li ); - - - /* omega and its derivative */ - omega = Calculate_Omega( pbond_ij->dvec, r_ij, - pbond_jk->dvec, r_jk, - pbond_kl->dvec, r_kl, - dvec_li, r_li, - p_ijk, p_jkl, - dcos_omega_di, dcos_omega_dj, - dcos_omega_dk, dcos_omega_dl, - out_control ); - - cos_omega = cos( omega ); - cos2omega = cos( 2. * omega ); - cos3omega = cos( 3. * omega ); - /* end omega calculations */ - - /* torsion energy */ - exp_tor1 = exp( fbp->p_tor1 * - SQR(2.0 - bo_jk->BO_pi - f11_DjDk) ); - exp_tor2_kl = exp( -p_tor2 * BOA_kl ); - exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) ); - fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * - (1.0 - exp_tor2_kl); - - CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) + - fbp->V2 * exp_tor1 * (1.0 - cos2omega) + - fbp->V3 * (1.0 + cos3omega) ); - - data->my_en.e_tor += e_tor = fn10 * sin_ijk * sin_jkl * CV; - - dfn11 = (-p_tor3 * exp_tor3_DjDk + - (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) * - (2.0 + exp_tor3_DjDk) * exp_tor34_inv) * - exp_tor34_inv; - - CEtors1 = sin_ijk * sin_jkl * CV; - - CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 * - (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) * - sin_ijk * sin_jkl; - CEtors3 = CEtors2 * dfn11; - - CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij * - (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl); - CEtors5 = CEtors1 * p_tor2 * - (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl); - CEtors6 = CEtors1 * p_tor2 * - (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl; - - cmn = -fn10 * CV; - CEtors7 = cmn * sin_jkl * tan_ijk_i; - CEtors8 = cmn * sin_ijk * tan_jkl_i; - - CEtors9 = fn10 * sin_ijk * sin_jkl * - (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega + - 1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega))); - /* end of torsion energy */ - - /* 4-body conjugation energy */ - fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl; - data->my_en.e_con += e_con = - fbp->p_cot1 * fn12 * - (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); - - Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 * - (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl); - - CEconj1 = Cconj * (BOA_ij - 1.5e0); - CEconj2 = Cconj * (BOA_jk - 1.5e0); - CEconj3 = Cconj * (BOA_kl - 1.5e0); - - CEconj4 = -fbp->p_cot1 * fn12 * - (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i; - CEconj5 = -fbp->p_cot1 * fn12 * - (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i; - CEconj6 = 2.0 * fbp->p_cot1 * fn12 * - cos_omega * sin_ijk * sin_jkl; - /* end 4-body conjugation energy */ - - /* forces */ - bo_jk->Cdbopi += CEtors2; - workspace->CdDelta[j] += CEtors3; - workspace->CdDelta[k] += CEtors3; - bo_ij->Cdbo += (CEtors4 + CEconj1); - bo_jk->Cdbo += (CEtors5 + CEconj2); - bo_kl->Cdbo += (CEtors6 + CEconj3); - - if (control->virial == 0) { - /* dcos_theta_ijk */ - rvec_ScaledAdd( workspace->f[i], - CEtors7 + CEconj4, p_ijk->dcos_dk ); - rvec_ScaledAdd( workspace->f[j], - CEtors7 + CEconj4, p_ijk->dcos_dj ); - rvec_ScaledAdd( workspace->f[k], - CEtors7 + CEconj4, p_ijk->dcos_di ); - - /* dcos_theta_jkl */ - rvec_ScaledAdd( workspace->f[j], - CEtors8 + CEconj5, p_jkl->dcos_di ); - rvec_ScaledAdd( workspace->f[k], - CEtors8 + CEconj5, p_jkl->dcos_dj ); - rvec_ScaledAdd( workspace->f[l], - CEtors8 + CEconj5, p_jkl->dcos_dk ); - - /* dcos_omega */ - rvec_ScaledAdd( workspace->f[i], - CEtors9 + CEconj6, dcos_omega_di ); - rvec_ScaledAdd( workspace->f[j], - CEtors9 + CEconj6, dcos_omega_dj ); - rvec_ScaledAdd( workspace->f[k], - CEtors9 + CEconj6, dcos_omega_dk ); - rvec_ScaledAdd( workspace->f[l], - CEtors9 + CEconj6, dcos_omega_dl ); - } - else { - ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box); - - /* dcos_theta_ijk */ - rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk ); - rvec_Add( workspace->f[i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - - rvec_ScaledAdd( workspace->f[j], - CEtors7 + CEconj4, p_ijk->dcos_dj ); - - rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di ); - rvec_Add( workspace->f[k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - - - /* dcos_theta_jkl */ - rvec_ScaledAdd( workspace->f[j], - CEtors8 + CEconj5, p_jkl->dcos_di ); - - rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj ); - rvec_Add( workspace->f[k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - - rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk ); - rvec_Add( workspace->f[l], force ); - rvec_iMultiply( ext_press, rel_box_jl, force ); - rvec_Add( data->my_ext_press, ext_press ); - - - /* dcos_omega */ - rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di ); - rvec_Add( workspace->f[i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - - rvec_ScaledAdd( workspace->f[j], - CEtors9 + CEconj6, dcos_omega_dj ); - - rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk ); - rvec_Add( workspace->f[k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - - rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl ); - rvec_Add( workspace->f[l], force ); - rvec_iMultiply( ext_press, rel_box_jl, force ); - rvec_Add( data->my_ext_press, ext_press ); - } - - /* tally into per-atom virials */ - if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { - - // acquire vectors - rvec_ScaledSum( delil, 1., system->my_atoms[l].x, - -1., system->my_atoms[i].x ); - rvec_ScaledSum( deljl, 1., system->my_atoms[l].x, - -1., system->my_atoms[j].x ); - rvec_ScaledSum( delkl, 1., system->my_atoms[l].x, - -1., system->my_atoms[k].x ); - // dcos_theta_ijk - rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk ); - rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj ); - rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di ); - - // dcos_theta_jkl - rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di ); - rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj ); - - // dcos_omega - rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di ); - rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj ); - rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk ); - - // tally - eng_tmp = e_tor + e_con; - if (system->pair_ptr->evflag) - system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); - if (system->pair_ptr->vflag_atom) - system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl); - } - } // pl check ends - } // pl loop ends - } // pi check ends - } // pi loop ends - } // k-j neighbor check ends - } // j-k neighbor check ends - } // pk loop ends - } // j loop -} diff --git a/src/USER-REAXC/reaxc_torsion_angles.h b/src/USER-REAXC/reaxc_torsion_angles.h deleted file mode 100644 index e18bc9d4c7..0000000000 --- a/src/USER-REAXC/reaxc_torsion_angles.h +++ /dev/null @@ -1,36 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __TORSION_ANGLES_H_ -#define __TORSION_ANGLES_H_ - -#include "reaxc_types.h" - -void Torsion_Angles( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); - -#endif diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp deleted file mode 100644 index 637a69ed0f..0000000000 --- a/src/USER-REAXC/reaxc_traj.cpp +++ /dev/null @@ -1,777 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_traj.h" -#include -#include -#include -#include -#include "reaxc_defs.h" -#include "reaxc_list.h" - -#include "error.h" - -int Reallocate_Output_Buffer( LAMMPS_NS::Error *error_ptr, output_controls *out_control, int req_space ) -{ - if (out_control->buffer_len > 0) - free( out_control->buffer ); - - out_control->buffer_len = (int)(req_space*REAX_SAFE_ZONE); - out_control->buffer = (char*) malloc(out_control->buffer_len*sizeof(char)); - if (out_control->buffer == nullptr) { - char errmsg[256]; - snprintf(errmsg, 256, "Insufficient memory for required buffer size %d", (int) (req_space*REAX_SAFE_ZONE)); - error_ptr->one(FLERR,errmsg); - } - - return SUCCESS; -} - - -void Write_Skip_Line( output_controls *out_control, mpi_datatypes * /*mpi_data*/, - int my_rank, int skip, int num_section ) -{ - if (my_rank == MASTER_NODE) - fprintf( out_control->strj, INT2_LINE, - "chars_to_skip_section:", skip, num_section ); -} - - -int Write_Header( reax_system *system, control_params *control, - output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) -{ - int num_hdr_lines, my_hdr_lines, buffer_req; - char ensembles[ens_N][25] = { "NVE", "NVT", "fully flexible NPT", - "semi isotropic NPT", "isotropic NPT" }; - char reposition[3][25] = { "fit to periodic box", "CoM to center of box", - "CoM to origin" }; - char t_regime[3][25] = { "T-coupling only", "step-wise", "constant slope" }; - - char traj_methods[TF_N][10] = { "custom", "xyz" }; - char atom_formats[8][40] = { "none", "invalid", "invalid", "invalid", - "xyz_q", - "xyz_q_fxfyfz", - "xyz_q_vxvyvz", - "detailed_atom_info" }; - char bond_formats[3][30] = { "none", - "basic_bond_info", - "detailed_bond_info" }; - char angle_formats[2][30] = { "none", "basic_angle_info" }; - - /* set header lengths */ - num_hdr_lines = NUM_HEADER_LINES; - my_hdr_lines = num_hdr_lines * ( system->my_rank == MASTER_NODE ); - buffer_req = my_hdr_lines * HEADER_LINE_LEN; - if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req ); - - /* only the master node writes into trajectory header */ - if (system->my_rank == MASTER_NODE) { - /* clear the contents of line & buffer */ - out_control->line[0] = 0; - out_control->buffer[0] = 0; - - /* to skip the header */ - sprintf( out_control->line, INT_LINE, "chars_to_skip_header:", - (num_hdr_lines-1) * HEADER_LINE_LEN ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* general simulation info */ - sprintf( out_control->line, STR_LINE, "simulation_name:", - out_control->traj_title ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, BIGINT_LINE, "number_of_atoms:", system->bigN ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "ensemble_type:", - ensembles[ control->ensemble ] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "number_of_steps:", - control->nsteps ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "timestep_length_(in_fs):", - control->dt * 1000 ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* restart info */ - sprintf( out_control->line, STR_LINE, "is_this_a_restart?:", - (control->restart ? "yes" : "no") ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "write_restart_files?:", - ((out_control->restart_freq > 0) ? "yes" : "no") ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "frequency_to_write_restarts:", - out_control->restart_freq ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* preferences */ - sprintf( out_control->line, STR_LINE, "tabulate_long_range_intrs?:", - (control->tabulate ? "yes" : "no") ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "table_size:", control->tabulate ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "restrict_bonds?:", - (control->restrict_bonds ? "yes" : "no") ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "bond_restriction_length:", - control->restrict_bonds ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "reposition_atoms?:", - reposition[control->reposition_atoms] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "remove_CoM_velocity?:", - (control->ensemble==NVE) ? 0 : control->remove_CoM_vel); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - - /* cut-off values */ - sprintf( out_control->line, REAL_LINE, "bonded_intr_dist_cutoff:", - control->bond_cut ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "nonbonded_intr_dist_cutoff:", - control->nonb_cut ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "hbond_dist_cutoff:", - control->hbond_cut ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "reax_bond_threshold:", - control->bo_cut ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "physical_bond_threshold:", - control->bg_cut ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "valence_angle_threshold:", - control->thb_cut ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, SCI_LINE, "QEq_tolerance:", control->q_err ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* temperature controls */ - sprintf( out_control->line, REAL_LINE, "initial_temperature:", - control->T_init ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "target_temperature:", - control->T_final ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "thermal_inertia:", - control->Tau_T ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "temperature_regime:", - t_regime[ control->T_mode ] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "temperature_change_rate_(K/ps):", - control->T_rate / control->T_freq ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* pressure controls */ - sprintf( out_control->line, REAL3_LINE, "target_pressure_(GPa):", - control->P[0], control->P[1], control->P[2] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL3_LINE, "virial_inertia:", - control->Tau_P[0], control->Tau_P[1], control->Tau_P[2] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* trajectory */ - sprintf( out_control->line, INT_LINE, "energy_dumping_freq:", - out_control->energy_update_freq ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "trajectory_dumping_freq:", - out_control->write_steps ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "compress_trajectory_output?:", - (out_control->traj_compress ? "yes" : "no") ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "trajectory_format:", - traj_methods[ out_control->traj_method ] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "atom_info:", - atom_formats[ out_control->atom_info ] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "bond_info:", - bond_formats[ out_control->bond_info ] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, STR_LINE, "angle_info:", - angle_formats[ out_control->angle_info ] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* analysis */ - //sprintf( out_control->line, STR_LINE, "molecular_analysis:", - // (control->molec_anal ? "yes" : "no") ); - //strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, INT_LINE, "molecular_analysis_frequency:", - control->molecular_analysis ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - } - - /* dump out the buffer */ - if (system->my_rank == MASTER_NODE) - fprintf( out_control->strj, "%s", out_control->buffer ); - - return SUCCESS; -} - - -int Write_Init_Desc( reax_system *system, control_params * /*control*/, - output_controls *out_control, mpi_datatypes *mpi_data ) -{ - int i, me, np, cnt, buffer_len, buffer_req; - reax_atom *p_atom; - MPI_Status status; - - me = system->my_rank; - np = system->wsize; - - /* skip info */ - Write_Skip_Line( out_control, mpi_data, me, - system->bigN * INIT_DESC_LEN, system->bigN ); - - if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) - buffer_req = system->bigN * INIT_DESC_LEN + 1; - else buffer_req = system->n * INIT_DESC_LEN + 1; - - if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); - - out_control->line[0] = 0; - out_control->buffer[0] = 0; - for (i = 0; i < system->n; ++i) { - p_atom = &( system->my_atoms[i] ); - sprintf( out_control->line, INIT_DESC, - p_atom->orig_id, p_atom->type, p_atom->name, - system->reax_param.sbp[ p_atom->type ].mass ); - strncpy( out_control->buffer + i*INIT_DESC_LEN, - out_control->line, INIT_DESC_LEN+1 ); - } - - if (me != MASTER_NODE) { - MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, - np * INIT_DESCS + me, mpi_data->world ); - } else { - buffer_len = system->n * INIT_DESC_LEN; - for (i = 0; i < np; ++i) - if (i != MASTER_NODE) { - MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, - MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status ); - MPI_Get_count( &status, MPI_CHAR, &cnt ); - buffer_len += cnt; - } - out_control->buffer[buffer_len] = 0; - fprintf( out_control->strj, "%s", out_control->buffer ); - } - - return SUCCESS; -} - - -int Init_Traj( reax_system *system, control_params *control, - output_controls *out_control, mpi_datatypes *mpi_data, - char *msg ) -{ - char fname[MAX_STR+8]; - int atom_line_len[ NR_OPT_ATOM ] = { 0, 0, 0, 0, - ATOM_BASIC_LEN, ATOM_wV_LEN, - ATOM_wF_LEN, ATOM_FULL_LEN }; - int bond_line_len[ NR_OPT_BOND ] = { 0, BOND_BASIC_LEN, BOND_FULL_LEN }; - int angle_line_len[ NR_OPT_ANGLE ] = { 0, ANGLE_BASIC_LEN }; - - /* generate trajectory name */ - sprintf( fname, "%s.trj", control->sim_name ); - - /* how should I write atoms? */ - out_control->atom_line_len = atom_line_len[ out_control->atom_info ]; - out_control->write_atoms = ( out_control->atom_line_len ? 1 : 0 ); - /* bonds? */ - out_control->bond_line_len = bond_line_len[ out_control->bond_info ]; - out_control->write_bonds = ( out_control->bond_line_len ? 1 : 0 ); - /* angles? */ - out_control->angle_line_len = angle_line_len[ out_control->angle_info ]; - out_control->write_angles = ( out_control->angle_line_len ? 1 : 0 ); - - /* allocate line & buffer space */ - out_control->line = (char*) calloc( MAX_TRJ_LINE_LEN + 1, sizeof(char) ); - out_control->buffer_len = 0; - out_control->buffer = nullptr; - - /* write trajectory header and atom info, if applicable */ - if (out_control->traj_method == REG_TRAJ) { - if (system->my_rank == MASTER_NODE) - out_control->strj = fopen( fname, "w" ); - } else { - strcpy( msg, "init_traj: unknown trajectory option" ); - return FAILURE; - } - Write_Header( system, control, out_control, mpi_data ); - Write_Init_Desc( system, control, out_control, mpi_data ); - - return SUCCESS; -} - - -int Write_Frame_Header( reax_system *system, control_params *control, - simulation_data *data, output_controls *out_control, - mpi_datatypes * /*mpi_data*/ ) -{ - int me, num_frm_hdr_lines, my_frm_hdr_lines, buffer_req; - - me = system->my_rank; - /* frame header lengths */ - num_frm_hdr_lines = 22; - my_frm_hdr_lines = num_frm_hdr_lines * ( me == MASTER_NODE ); - buffer_req = my_frm_hdr_lines * HEADER_LINE_LEN; - if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req ); - - /* only the master node writes into trajectory header */ - if (me == MASTER_NODE) { - /* clear the contents of line & buffer */ - out_control->line[0] = 0; - out_control->buffer[0] = 0; - - /* skip info */ - sprintf( out_control->line, INT_LINE, "chars_to_skip_frame_header:", - (num_frm_hdr_lines - 1) * HEADER_LINE_LEN ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - /* step & time */ - sprintf( out_control->line, INT_LINE, "step:", data->step ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "time_in_ps:", - data->step * control->dt ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - - /* box info */ - sprintf( out_control->line, REAL_LINE, "volume:", system->big_box.V ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL3_LINE, "box_dimensions:", - system->big_box.box_norms[0], - system->big_box.box_norms[1], - system->big_box.box_norms[2] ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL3_LINE, - "coordinate_angles:", 90.0, 90.0, 90.0 ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - - /* system T and P */ - sprintf( out_control->line, REAL_LINE, "temperature:", data->therm.T ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "pressure:", - (control->ensemble==iNPT) ? - data->iso_bar.P : data->flex_bar.P_scalar ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - - /* energies */ - sprintf( out_control->line, REAL_LINE, "total_energy:", - data->sys_en.e_tot ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "total_kinetic:", - data->sys_en.e_kin ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "total_potential:", - data->sys_en.e_pot ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "bond_energy:", - data->sys_en.e_bond ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "atom_energy:", - data->sys_en.e_ov + data->sys_en.e_un ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "lone_pair_energy:", - data->sys_en.e_lp ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "valence_angle_energy:", - data->sys_en.e_ang + data->sys_en.e_pen ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "3-body_conjugation:", - data->sys_en.e_coa ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "hydrogen_bond_energy:", - data->sys_en.e_hb ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "torsion_angle_energy:", - data->sys_en.e_tor ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "4-body_conjugation:", - data->sys_en.e_con ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "vdWaals_energy:", - data->sys_en.e_vdW ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "electrostatics_energy:", - data->sys_en.e_ele ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - - sprintf( out_control->line, REAL_LINE, "polarization_energy:", - data->sys_en.e_pol ); - strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 ); - } - - /* dump out the buffer */ - if (system->my_rank == MASTER_NODE) - fprintf( out_control->strj, "%s", out_control->buffer ); - - return SUCCESS; -} - - - -int Write_Atoms( reax_system *system, control_params * /*control*/, - output_controls *out_control, mpi_datatypes *mpi_data ) -{ - int i, me, np, line_len, buffer_len, buffer_req, cnt; - MPI_Status status; - reax_atom *p_atom; - - me = system->my_rank; - np = system->wsize; - line_len = out_control->atom_line_len; - - Write_Skip_Line( out_control, mpi_data, me, - system->bigN*line_len, system->bigN ); - - if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) - buffer_req = system->bigN * line_len + 1; - else buffer_req = system->n * line_len + 1; - - if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); - - /* fill in buffer */ - out_control->line[0] = 0; - out_control->buffer[0] = 0; - for (i = 0; i < system->n; ++i) { - p_atom = &( system->my_atoms[i] ); - - switch (out_control->atom_info) { - case OPT_ATOM_BASIC: - sprintf( out_control->line, ATOM_BASIC, - p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2], - p_atom->q ); - break; - case OPT_ATOM_wF: - sprintf( out_control->line, ATOM_wF, - p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2], - p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q ); - break; - case OPT_ATOM_wV: - sprintf( out_control->line, ATOM_wV, - p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2], - p_atom->v[0], p_atom->v[1], p_atom->v[2], p_atom->q ); - break; - case OPT_ATOM_FULL: - sprintf( out_control->line, ATOM_FULL, - p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2], - p_atom->v[0], p_atom->v[1], p_atom->v[2], - p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q ); - break; - default: - system->error_ptr->one(FLERR,"Write_traj_atoms: unknown atom trajectory format"); - } - - strncpy( out_control->buffer + i*line_len, out_control->line, line_len+1 ); - } - - if (me != MASTER_NODE) { - MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, - np*ATOM_LINES+me, mpi_data->world ); - } else { - buffer_len = system->n * line_len; - for (i = 0; i < np; ++i) - if (i != MASTER_NODE) { - MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, - MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status ); - MPI_Get_count( &status, MPI_CHAR, &cnt ); - buffer_len += cnt; - } - out_control->buffer[buffer_len] = 0; - fprintf( out_control->strj, "%s", out_control->buffer ); - } - - return SUCCESS; -} - - -int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds, - output_controls *out_control, mpi_datatypes *mpi_data) -{ - int i, j, pj, me, np; - int my_bonds, num_bonds; - int line_len, buffer_len, buffer_req, cnt; - MPI_Status status; - bond_data *bo_ij; - - me = system->my_rank; - np = system->wsize; - line_len = out_control->bond_line_len; - - /* count the number of bonds I will write */ - my_bonds = 0; - for (i=0; i < system->n; ++i) - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { - j = bonds->select.bond_list[pj].nbr; - if ( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id && - bonds->select.bond_list[pj].bo_data.BO >= control->bg_cut ) - ++my_bonds; - } - - /* allreduce - total number of bonds */ - MPI_Allreduce( &my_bonds, &num_bonds, 1, MPI_INT, MPI_SUM, mpi_data->world ); - - Write_Skip_Line( out_control, mpi_data, me, num_bonds*line_len, num_bonds ); - - if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) - buffer_req = num_bonds * line_len + 1; - else buffer_req = my_bonds * line_len + 1; - - if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); - - /* fill in the buffer */ - out_control->line[0] = 0; - out_control->buffer[0] = 0; - - my_bonds = 0; - for (i=0; i < system->n; ++i) { - for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj) { - bo_ij = &( bonds->select.bond_list[pj] ); - j = bo_ij->nbr; - - if ( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id && - bo_ij->bo_data.BO >= control->bg_cut) { - switch (out_control->bond_info) { - case OPT_BOND_BASIC: - sprintf( out_control->line, BOND_BASIC, - system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, - bo_ij->d, bo_ij->bo_data.BO ); - break; - case OPT_BOND_FULL: - sprintf( out_control->line, BOND_FULL, - system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, - bo_ij->d, bo_ij->bo_data.BO, bo_ij->bo_data.BO_s, - bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 ); - break; - default: - system->error_ptr->one(FLERR, "Write_traj_bonds: FATAL! invalid bond_info option"); - } - strncpy( out_control->buffer + my_bonds*line_len, - out_control->line, line_len+1 ); - ++my_bonds; - } - } - } - - if (me != MASTER_NODE) { - MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, - np*BOND_LINES+me, mpi_data->world ); - } else { - buffer_len = my_bonds * line_len; - for (i = 0; i < np; ++i) - if (i != MASTER_NODE) { - MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, - MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status ); - MPI_Get_count( &status, MPI_CHAR, &cnt ); - buffer_len += cnt; - } - out_control->buffer[buffer_len] = 0; - fprintf( out_control->strj, "%s", out_control->buffer ); - } - - return SUCCESS; -} - - -int Write_Angles( reax_system *system, control_params *control, - reax_list *bonds, reax_list *thb_intrs, - output_controls *out_control, mpi_datatypes *mpi_data ) -{ - int i, j, k, pi, pk, me, np; - int my_angles, num_angles; - int line_len, buffer_len, buffer_req, cnt; - bond_data *bo_ij, *bo_jk; - three_body_interaction_data *angle_ijk; - MPI_Status status; - - me = system->my_rank; - np = system->wsize; - line_len = out_control->angle_line_len; - - /* count the number of valence angles I will output */ - my_angles = 0; - for (j = 0; j < system->n; ++j) - for (pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi) { - bo_ij = &(bonds->select.bond_list[pi]); - i = bo_ij->nbr; - - if (bo_ij->bo_data.BO >= control->bg_cut) // physical j&i bond - for (pk = Start_Index( pi, thb_intrs); - pk < End_Index( pi, thb_intrs ); ++pk) { - angle_ijk = &(thb_intrs->select.three_body_list[pk]); - k = angle_ijk->thb; - bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]); - - if ( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id && - bo_jk->bo_data.BO >= control->bg_cut ) // physical j&k bond - ++my_angles; - } - } - /* total number of valences */ - MPI_Allreduce(&my_angles, &num_angles, 1, MPI_INT, MPI_SUM, mpi_data->world); - - Write_Skip_Line( out_control, mpi_data, me, num_angles*line_len, num_angles ); - - if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) - buffer_req = num_angles * line_len + 1; - else buffer_req = my_angles * line_len + 1; - - if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); - - /* fill in the buffer */ - my_angles = 0; - out_control->line[0] = 0; - out_control->buffer[0] = 0; - for (j = 0; j < system->n; ++j) - for (pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi) { - bo_ij = &(bonds->select.bond_list[pi]); - i = bo_ij->nbr; - - if (bo_ij->bo_data.BO >= control->bg_cut) // physical j&i bond - for (pk = Start_Index( pi, thb_intrs); - pk < End_Index( pi, thb_intrs ); ++pk) { - angle_ijk = &(thb_intrs->select.three_body_list[pk]); - k = angle_ijk->thb; - bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]); - - if ( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id && - bo_jk->bo_data.BO >= control->bg_cut) { // physical j&k bond - sprintf( out_control->line, ANGLE_BASIC, - system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, - system->my_atoms[k].orig_id, RAD2DEG( angle_ijk->theta ) ); - - strncpy( out_control->buffer + my_angles*line_len, - out_control->line, line_len+1 ); - ++my_angles; - } - } - } - - if (me != MASTER_NODE) { - MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, - np*ANGLE_LINES+me, mpi_data->world ); - } else { - buffer_len = my_angles * line_len; - for (i = 0; i < np; ++i) - if (i != MASTER_NODE) { - MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, - MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status ); - MPI_Get_count( &status, MPI_CHAR, &cnt ); - buffer_len += cnt; - } - out_control->buffer[buffer_len] = 0; - fprintf( out_control->strj, "%s", out_control->buffer ); - } - - return SUCCESS; -} - - -int Append_Frame( reax_system *system, control_params *control, - simulation_data *data, reax_list **lists, - output_controls *out_control, mpi_datatypes *mpi_data ) -{ - Write_Frame_Header( system, control, data, out_control, mpi_data ); - - if (out_control->write_atoms) - Write_Atoms( system, control, out_control, mpi_data ); - - if (out_control->write_bonds) - Write_Bonds( system, control, (*lists + BONDS), out_control, mpi_data ); - - if (out_control->write_angles) - Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES), - out_control, mpi_data ); - - return SUCCESS; -} - - -int End_Traj( int my_rank, output_controls *out_control ) -{ - if (my_rank == MASTER_NODE) - fclose( out_control->strj ); - - free( out_control->buffer ); - free( out_control->line ); - - return SUCCESS; -} diff --git a/src/USER-REAXC/reaxc_traj.h b/src/USER-REAXC/reaxc_traj.h deleted file mode 100644 index 3321410a22..0000000000 --- a/src/USER-REAXC/reaxc_traj.h +++ /dev/null @@ -1,104 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __TRAJ_H__ -#define __TRAJ_H__ - -#include "reaxc_types.h" - -#define MAX_TRJ_LINE_LEN 120 -#define MAX_TRJ_BUFFER_SIZE (MAX_TRJ_LINE_LEN * 100) - -#define NUM_HEADER_LINES 37 -#define HEADER_LINE_LEN 62 -#define STR_LINE "%-37s%-24s\n" -#define INT_LINE "%-37s%-24d\n" -#if defined(LAMMPS_SMALLSMALL) -#define BIGINT_LINE "%-37s%-24d\n" -#else -#define BIGINT_LINE "%-37s%-24lld\n" -#endif -#define INT2_LINE "%-36s%-12d,%-12d\n" -#define REAL_LINE "%-37s%-24.3f\n" -#define SCI_LINE "%-37s%-24g\n" -#define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n" - -#if defined(LAMMPS_BIGBIG) -#define INIT_DESC "%9lld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass -#else -#define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass -#endif -#define INIT_DESC_LEN 32 - -#define SIZE_INFO_LINE2 "%-10d%-10d\n" -#define SIZE_INFO_LEN2 21 - -#define SIZE_INFO_LINE3 "%-10d%-10d%-10d\n" -#define SIZE_INFO_LEN3 31 - -#if defined(LAMMPS_BIGBIG) -#define ATOM_BASIC "%9lld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge -#define ATOM_wV "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge -#define ATOM_wF "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge -#define ATOM_FULL "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge -#else -#define ATOM_BASIC "%9d%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge -#define ATOM_wV "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge -#define ATOM_wF "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge -#define ATOM_FULL "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge -#endif -#define ATOM_BASIC_LEN 50 -#define ATOM_wV_LEN 80 -#define ATOM_wF_LEN 80 -#define ATOM_FULL_LEN 110 - -#if defined(LAMMPS_BIGBIG) -#define BOND_BASIC "%9lld%9lld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO -#define BOND_FULL "%9lld%9lld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 -#define ANGLE_BASIC "%9lld%9lld%9lld%10.3f\n" // Atom1 Atom2 Atom3 Theta -#else -#define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO -#define BOND_FULL "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 -#define ANGLE_BASIC "%9d%9d%9d%10.3f\n" // Atom1 Atom2 Atom3 Theta -#endif -#define BOND_BASIC_LEN 39 -#define BOND_FULL_LEN 69 -#define ANGLE_BASIC_LEN 38 - -enum ATOM_LINE_OPTS { OPT_NOATOM = 0, OPT_ATOM_BASIC = 4, OPT_ATOM_wF = 5, OPT_ATOM_wV = 6, OPT_ATOM_FULL = 7, NR_OPT_ATOM = 8 }; -enum BOND_LINE_OPTS { OPT_NOBOND, OPT_BOND_BASIC, OPT_BOND_FULL, NR_OPT_BOND }; -enum ANGLE_LINE_OPTS { OPT_NOANGLE, OPT_ANGLE_BASIC, NR_OPT_ANGLE }; - - -int Init_Traj( reax_system*, control_params*, output_controls*, - mpi_datatypes*, char* ); -int End_Traj( int, output_controls* ); - -int Append_Frame( reax_system*, control_params*, simulation_data*, - reax_list**, output_controls*, mpi_datatypes* ); - -#endif diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h deleted file mode 100644 index f4b8bb0a2e..0000000000 --- a/src/USER-REAXC/reaxc_types.h +++ /dev/null @@ -1,927 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __REAX_TYPES_H_ -#define __REAX_TYPES_H_ - -#include "lmptype.h" -#include -#include -#include "accelerator_kokkos.h" - -namespace LAMMPS_NS { class Error;} - -#if defined LMP_USER_OMP -#define OMP_TIMING 0 - -#ifdef OMP_TIMING -// pkcoff timing fields -enum { - COMPUTEINDEX=0, - COMPUTEWLINDEX, - COMPUTEBFINDEX, - COMPUTEQEQINDEX, - COMPUTENBFINDEX, - COMPUTEIFINDEX, - COMPUTETFINDEX, - COMPUTEBOINDEX, - COMPUTEBONDSINDEX, - COMPUTEATOMENERGYINDEX, - COMPUTEVALENCEANGLESBOINDEX, - COMPUTETORSIONANGLESBOINDEX, - COMPUTEHBONDSINDEX, - COMPUTECG1INDEX, - COMPUTECG2INDEX, - COMPUTECGCOMPUTEINDEX, - COMPUTECALCQINDEX, - COMPUTEINITMVINDEX, - COMPUTEMVCOMPINDEX, - LASTTIMINGINDEX -}; - -extern double ompTimingData[LASTTIMINGINDEX]; -extern int ompTimingCount[LASTTIMINGINDEX]; -extern int ompTimingCGCount[LASTTIMINGINDEX]; -#endif -#endif - -/************* SOME DEFS - crucial for reax_types.h *********/ - -#define LAMMPS_REAX - -//#define DEBUG -//#define DEBUG_FOCUS -//#define TEST_ENERGY -//#define TEST_FORCES -//#define CG_PERFORMANCE -//#define LOG_PERFORMANCE -//#define STANDARD_BOUNDARIES -//#define OLD_BOUNDARIES -//#define MIDPOINT_BOUNDARIES - -#define REAX_MAX_STR 1024 -#define REAX_MAX_NBRS 6 -#define REAX_MAX_3BODY_PARAM 5 -#define REAX_MAX_4BODY_PARAM 5 -#define REAX_MAX_ATOM_TYPES 25 -#define REAX_MAX_MOLECULE_SIZE 20 -#define MAX_BOND 20 // same as reaxc_defs.h - -/********************** TYPE DEFINITIONS ********************/ -typedef int ivec[3]; -typedef double rvec[3]; -typedef double rtensor[3][3]; -typedef double rvec2[2]; -typedef double rvec4[4]; - -// import LAMMPS' definition of tagint and bigint -typedef LAMMPS_NS::tagint rc_tagint; -typedef LAMMPS_NS::bigint rc_bigint; - -typedef struct -{ - int cnt; - int *index; - void *out_atoms; -} mpi_out_data; - -typedef struct -{ - MPI_Comm world; - MPI_Comm comm_mesh3D; - - MPI_Datatype sys_info; - MPI_Datatype mpi_atom_type; - MPI_Datatype boundary_atom_type; - MPI_Datatype mpi_rvec, mpi_rvec2; - MPI_Datatype restart_atom_type; - - MPI_Datatype header_line; - MPI_Datatype header_view; - MPI_Datatype init_desc_line; - MPI_Datatype init_desc_view; - MPI_Datatype atom_line; - MPI_Datatype atom_view; - MPI_Datatype bond_line; - MPI_Datatype bond_view; - MPI_Datatype angle_line; - MPI_Datatype angle_view; - - mpi_out_data out_buffers[REAX_MAX_NBRS]; - void *in1_buffer; - void *in2_buffer; -} mpi_datatypes; - -typedef struct -{ - int n_global; - double* l; - int vdw_type; -} global_parameters; - -typedef struct -{ - /* Line one in field file */ - char name[15]; // Two character atom name - - double r_s; - double valency; // Valency of the atom - double mass; // Mass of atom - double r_vdw; - double epsilon; - double gamma; - double r_pi; - double valency_e; - double nlp_opt; - - /* Line two in field file */ - double alpha; - double gamma_w; - double valency_boc; - double p_ovun5; - double chi; - double eta; - int p_hbond; // 1 for H, 2 for hbonding atoms (O,S,P,N), 0 for others - - /* Line three in field file */ - double r_pi_pi; - double p_lp2; - double b_o_131; - double b_o_132; - double b_o_133; - - /* Line four in the field file */ - double p_ovun2; - double p_val3; - double valency_val; - double p_val5; - double rcore2; - double ecore2; - double acore2; - - /* Line five in the ffield file, only for lgvdw yes */ - double lgcij; - double lgre; - -} single_body_parameters; - -/* Two Body Parameters */ -typedef struct { - /* Bond Order parameters */ - double p_bo1,p_bo2,p_bo3,p_bo4,p_bo5,p_bo6; - double r_s, r_p, r_pp; // r_o distances in BO formula - double p_boc3, p_boc4, p_boc5; - - /* Bond Energy parameters */ - double p_be1, p_be2; - double De_s, De_p, De_pp; - - /* Over/Under coordination parameters */ - double p_ovun1; - - /* Van der Waal interaction parameters */ - double D; - double alpha; - double r_vdW; - double gamma_w; - double rcore, ecore, acore; - double lgcij, lgre; - - /* electrostatic parameters */ - double gamma; // note: this parameter is gamma^-3 and not gamma. - - double v13cor, ovc; -} two_body_parameters; - -/* 3-body parameters */ -typedef struct { - /* valence angle */ - double theta_00; - double p_val1, p_val2, p_val4, p_val7; - - /* penalty */ - double p_pen1; - - /* 3-body conjugation */ - double p_coa1; -} three_body_parameters; - - -typedef struct{ - int cnt; - three_body_parameters prm[REAX_MAX_3BODY_PARAM]; -} three_body_header; - -/* hydrogen-bond parameters */ -typedef struct{ - double r0_hb, p_hb1, p_hb2, p_hb3; -} hbond_parameters; - -/* 4-body parameters */ -typedef struct { - double V1, V2, V3; - - /* torsion angle */ - double p_tor1; - - /* 4-body conjugation */ - double p_cot1; -} four_body_parameters; - -typedef struct -{ - int cnt; - four_body_parameters prm[REAX_MAX_4BODY_PARAM]; -} four_body_header; - -typedef struct -{ - int num_atom_types; - global_parameters gp; - single_body_parameters *sbp; - two_body_parameters **tbp; - three_body_header ***thbp; - hbond_parameters ***hbp; - four_body_header ****fbp; -} reax_interaction; - -struct _reax_atom -{ - rc_tagint orig_id; - int imprt_id; - int type; - char name[8]; - - rvec x; // position - rvec v; // velocity - rvec f; // force - rvec f_old; - - double q; // charge - rvec4 s; // they take part in - rvec4 t; // computing q - - int Hindex; - int num_bonds; - int num_hbonds; - int renumber; - - int numbonds; // true number of bonds around atoms - int nbr_id[MAX_BOND]; // ids of neighbors around atoms - double nbr_bo[MAX_BOND]; // BO values of bond between i and nbr - double sum_bo, no_lp; // sum of BO values and no. of lone pairs -}; -typedef _reax_atom reax_atom; - -typedef struct -{ - double V; - rvec min, max, box_norms; - - rtensor box, box_inv; - rtensor trans, trans_inv; - rtensor g; -} simulation_box; - -struct grid_cell -{ - double cutoff; - rvec min, max; - ivec rel_box; - - int mark; - int type; - int str; - int end; - int top; - int* atoms; - struct grid_cell** nbrs; - ivec* nbrs_x; - rvec* nbrs_cp; -}; - -typedef struct grid_cell grid_cell; - - -typedef struct -{ - int total, max_atoms, max_nbrs; - ivec ncells; - rvec cell_len; - rvec inv_len; - - ivec bond_span; - ivec nonb_span; - ivec vlist_span; - - ivec native_cells; - ivec native_str; - ivec native_end; - - double ghost_cut; - ivec ghost_span; - ivec ghost_nonb_span; - ivec ghost_hbond_span; - ivec ghost_bond_span; - - grid_cell*** cells; - ivec *order; -} grid; - - -typedef struct -{ - int rank; - int est_send, est_recv; - int atoms_str, atoms_cnt; - ivec rltv, prdc; - rvec bndry_min, bndry_max; - - int send_type; - int recv_type; - ivec str_send; - ivec end_send; - ivec str_recv; - ivec end_recv; -} neighbor_proc; - - - -typedef struct -{ - int N; - int exc_gcells; - int exc_atoms; -} bound_estimate; - - - -typedef struct -{ - double ghost_nonb; - double ghost_hbond; - double ghost_bond; - double ghost_cutoff; -} boundary_cutoff; - - -struct _LR_lookup_table; // forward declaration -struct _reax_system -{ - reax_interaction reax_param; - - rc_bigint bigN; - int n, N, numH; - int local_cap, total_cap, gcell_cap, Hcap; - int est_recv, est_trans, max_recved; - int wsize, my_rank, num_nbrs; - ivec my_coords; - neighbor_proc my_nbrs[REAX_MAX_NBRS]; - int *global_offset; - simulation_box big_box, my_box, my_ext_box; - grid my_grid; - boundary_cutoff bndry_cuts; - reax_atom *my_atoms; - - class LAMMPS_NS::Error *error_ptr; - class LAMMPS_NS::Pair *pair_ptr; - int my_bonds; - int mincap,minhbonds; - double safezone, saferzone; - - _LR_lookup_table **LR; - - int omp_active; -}; -typedef _reax_system reax_system; - - - -/* system control parameters */ -typedef struct -{ - char sim_name[REAX_MAX_STR]; - int nprocs; - int nthreads; - ivec procs_by_dim; - /* ensemble values: - 0 : NVE - 1 : bNVT (Berendsen) - 2 : nhNVT (Nose-Hoover) - 3 : sNPT (Parrinello-Rehman-Nose-Hoover) semiisotropic - 4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic - 5 : NPT (Parrinello-Rehman-Nose-Hoover) Anisotropic*/ - int ensemble; - int nsteps; - double dt; - int geo_format; - int restart; - - int restrict_bonds; - int remove_CoM_vel; - int random_vel; - int reposition_atoms; - - int reneighbor; - double vlist_cut; - double bond_cut; - double nonb_cut, nonb_low; - double hbond_cut; - double user_ghost_cut; - - double bg_cut; - double bo_cut; - double thb_cut; - double thb_cutsq; - - int tabulate; - - int qeq_freq; - double q_err; - int refactor; - double droptol; - - double T_init, T_final, T; - double Tau_T; - int T_mode; - double T_rate, T_freq; - - int virial; - rvec P, Tau_P, Tau_PT; - int press_mode; - double compressibility; - - int molecular_analysis; - int num_ignored; - int ignore[REAX_MAX_ATOM_TYPES]; - - int dipole_anal; - int freq_dipole_anal; - int diffusion_coef; - int freq_diffusion_coef; - int restrict_type; - - int lgflag; - int enobondsflag; - class LAMMPS_NS::Error *error_ptr; - int me; - -} control_params; - - -typedef struct -{ - double T; - double xi; - double v_xi; - double v_xi_old; - double G_xi; - -} thermostat; - - -typedef struct -{ - double P; - double eps; - double v_eps; - double v_eps_old; - double a_eps; - -} isotropic_barostat; - - -typedef struct -{ - rtensor P; - double P_scalar; - - double eps; - double v_eps; - double v_eps_old; - double a_eps; - - rtensor h0; - rtensor v_g0; - rtensor v_g0_old; - rtensor a_g0; - -} flexible_barostat; - - -typedef struct -{ - double start; - double end; - double elapsed; - - double total; - double comm; - double nbrs; - double init_forces; - double bonded; - double nonb; - double qEq; - int s_matvecs; - int t_matvecs; -} reax_timing; - - -typedef struct -{ - double e_tot; - double e_kin; // Total kinetic energy - double e_pot; - - double e_bond; // Total bond energy - double e_ov; // Total over coordination - double e_un; // Total under coordination energy - double e_lp; // Total under coordination energy - double e_ang; // Total valance angle energy - double e_pen; // Total penalty energy - double e_coa; // Total three body conjgation energy - double e_hb; // Total Hydrogen bond energy - double e_tor; // Total torsional energy - double e_con; // Total four body conjugation energy - double e_vdW; // Total van der Waals energy - double e_ele; // Total electrostatics energy - double e_pol; // Polarization energy -} energy_data; - -typedef struct -{ - int step; - int prev_steps; - double time; - - double M; // Total Mass - double inv_M; // 1 / Total Mass - - rvec xcm; // Center of mass - rvec vcm; // Center of mass velocity - rvec fcm; // Center of mass force - rvec amcm; // Angular momentum of CoM - rvec avcm; // Angular velocity of CoM - double etran_cm; // Translational kinetic energy of CoM - double erot_cm; // Rotational kinetic energy of CoM - - rtensor kinetic; // Kinetic energy tensor - rtensor virial; // Hydrodynamic virial - - energy_data my_en; - energy_data sys_en; - - double N_f; //Number of degrees of freedom - rvec t_scale; - rtensor p_scale; - thermostat therm; // Used in Nose_Hoover method - isotropic_barostat iso_bar; - flexible_barostat flex_bar; - double inv_W; - - double kin_press; - rvec int_press; - rvec my_ext_press; - rvec ext_press; - rvec tot_press; - - reax_timing timing; -} simulation_data; - - -typedef struct{ - int thb; - int pthb; // pointer to the third body on the central atom's nbrlist - double theta, cos_theta; - rvec dcos_di, dcos_dj, dcos_dk; -} three_body_interaction_data; - - -typedef struct { - int nbr; - ivec rel_box; - double d; - rvec dvec; -} far_neighbor_data; - - -typedef struct { - int nbr; - int scl; - far_neighbor_data *ptr; -} hbond_data; - - -typedef struct{ - int wrt; - rvec dVal; -} dDelta_data; - - -typedef struct{ - int wrt; - rvec dBO, dBOpi, dBOpi2; -} dbond_data; - -typedef struct{ - double BO, BO_s, BO_pi, BO_pi2; - double Cdbo, Cdbopi, Cdbopi2; - double C1dbo, C2dbo, C3dbo; - double C1dbopi, C2dbopi, C3dbopi, C4dbopi; - double C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2; - rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2; - double *CdboReduction; -} bond_order_data; - -typedef struct { - int nbr; - int sym_index; - int dbond_index; - ivec rel_box; - // rvec ext_factor; - double d; - rvec dvec; - bond_order_data bo_data; -} bond_data; - - -typedef struct { - int j; - double val; -} sparse_matrix_entry; - -typedef struct { - int cap, n, m; - int *start, *end; - sparse_matrix_entry *entries; -} sparse_matrix; - - -typedef struct { - int num_far; - int H, Htop; - int hbonds, num_hbonds; - int bonds, num_bonds; - int num_3body; - int gcell_atoms; -} reallocate_data; - - -typedef struct -{ - int allocated; - - /* communication storage */ - double *tmp_dbl[REAX_MAX_NBRS]; - rvec *tmp_rvec[REAX_MAX_NBRS]; - rvec2 *tmp_rvec2[REAX_MAX_NBRS]; - int *within_bond_box; - - /* bond order related storage */ - double *total_bond_order; - double *Deltap, *Deltap_boc; - double *Delta, *Delta_lp, *Delta_lp_temp, *Delta_e, *Delta_boc, *Delta_val; - double *dDelta_lp, *dDelta_lp_temp; - double *nlp, *nlp_temp, *Clp, *vlpex; - rvec *dDeltap_self; - int *bond_mark, *done_after; - - /* QEq storage */ - sparse_matrix *H, *L, *U; - double *Hdia_inv, *b_s, *b_t, *b_prc, *b_prm, *s, *t; - double *droptol; - rvec2 *b, *x; - - /* GMRES storage */ - double *y, *z, *g; - double *hc, *hs; - double **h, **v; - /* CG storage */ - double *r, *d, *q, *p; - rvec2 *r2, *d2, *q2, *p2; - /* Taper */ - double Tap[8]; //Tap7, Tap6, Tap5, Tap4, Tap3, Tap2, Tap1, Tap0; - - /* storage for analysis */ - int *mark, *old_mark; - rvec *x_old; - - /* storage space for bond restrictions */ - int *restricted; - int **restricted_list; - - /* integrator */ - rvec *v_const; - - /* force calculations */ - double *CdDelta; // coefficient of dDelta - rvec *f; - - /* omp */ - rvec *forceReduction; - rvec *my_ext_pressReduction; - double *CdDeltaReduction; - int *valence_angle_atom_myoffset; - - reallocate_data realloc; -} storage; - - -typedef union -{ - void *v; - three_body_interaction_data *three_body_list; - bond_data *bond_list; - dbond_data *dbo_list; - dDelta_data *dDelta_list; - far_neighbor_data *far_nbr_list; - hbond_data *hbond_list; -} list_type; - - -struct _reax_list -{ - int allocated; - - int n; - int num_intrs; - - int *index; - int *end_index; - - int type; - list_type select; - class LAMMPS_NS::Error *error_ptr; -}; -typedef _reax_list reax_list; - - -typedef struct -{ - FILE *strj; - int trj_offset; - int atom_line_len; - int bond_line_len; - int angle_line_len; - int write_atoms; - int write_bonds; - int write_angles; - char *line; - int buffer_len; - char *buffer; - - FILE *out; - FILE *pot; - FILE *log; - FILE *mol, *ign; - FILE *dpl; - FILE *drft; - FILE *pdb; - FILE *prs; - - int write_steps; - int traj_compress; - int traj_method; - char traj_title[81]; - int atom_info; - int bond_info; - int angle_info; - - int restart_format; - int restart_freq; - int debug_level; - int energy_update_freq; - -} output_controls; - - -typedef struct -{ - int atom_count; - int atom_list[REAX_MAX_MOLECULE_SIZE]; - int mtypes[REAX_MAX_ATOM_TYPES]; -} molecule; - - -struct LR_data -{ - double H; - double e_vdW, CEvd; - double e_ele, CEclmb; - - LAMMPS_INLINE - LR_data() {} - - LAMMPS_INLINE - void operator = (const LR_data& rhs) { - H = rhs.H; - e_vdW = rhs.e_vdW; - CEvd = rhs.CEvd; - e_ele = rhs.e_ele; - CEclmb = rhs.CEclmb; - } - LAMMPS_INLINE - void operator = (const LR_data& rhs) volatile { - H = rhs.H; - e_vdW = rhs.e_vdW; - CEvd = rhs.CEvd; - e_ele = rhs.e_ele; - CEclmb = rhs.CEclmb; - } -}; - - -struct cubic_spline_coef -{ - double a, b, c, d; - - LAMMPS_INLINE - cubic_spline_coef() {} - - LAMMPS_INLINE - cubic_spline_coef(const cubic_spline_coef &_c) { - a = _c.a; - b = _c.b; - c = _c.c; - d = _c.d; - } - - LAMMPS_INLINE - void operator=(const cubic_spline_coef &rhs) { - a = rhs.a; - b = rhs.b; - c = rhs.c; - d = rhs.d; - } - - LAMMPS_INLINE - void operator=(const cubic_spline_coef &rhs) volatile { - a = rhs.a; - b = rhs.b; - c = rhs.c; - d = rhs.d; - } -}; - - - -typedef struct _LR_lookup_table -{ - double xmin, xmax; - int n; - double dx, inv_dx; - double a; - double m; - double c; - - LR_data *y; - cubic_spline_coef *H; - cubic_spline_coef *vdW, *CEvd; - cubic_spline_coef *ele, *CEclmb; -} LR_lookup_table; - -/* function pointer defs */ -typedef void (*evolve_function)(reax_system*, control_params*, - simulation_data*, storage*, reax_list**, - output_controls*, mpi_datatypes* ); - -typedef void (*interaction_function) (reax_system*, control_params*, - simulation_data*, storage*, - reax_list**, output_controls*); - -typedef void (*print_interaction)(reax_system*, control_params*, - simulation_data*, storage*, - reax_list**, output_controls*); - -typedef double (*lookup_function)(double); - -typedef void (*message_sorter) (reax_system*, int, int, int, mpi_out_data*); -typedef void (*unpacker) ( reax_system*, int, void*, int, neighbor_proc*, int ); - -typedef void (*dist_packer) (void*, mpi_out_data*); -typedef void (*coll_unpacker) (void*, void*, mpi_out_data*); -#endif diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp deleted file mode 100644 index 26dba52512..0000000000 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ /dev/null @@ -1,419 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_valence_angles.h" -#include -#include "pair.h" -#include "reaxc_defs.h" -#include "reaxc_list.h" -#include "reaxc_vector.h" - -#include "error.h" - -static double Dot( double* v1, double* v2, int k ) -{ - double ret = 0.0; - - for (int i=0; i < k; ++i) - ret += v1[i] * v2[i]; - - return ret; -} - -void Calculate_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, - double *theta, double *cos_theta ) -{ - (*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk ); - if (*cos_theta > 1.) *cos_theta = 1.0; - if (*cos_theta < -1.) *cos_theta = -1.0; - - (*theta) = acos( *cos_theta ); -} - -void Calculate_dCos_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, - rvec* dcos_theta_di, - rvec* dcos_theta_dj, - rvec* dcos_theta_dk ) -{ - int t; - double sqr_d_ji = SQR(d_ji); - double sqr_d_jk = SQR(d_jk); - double inv_dists = 1.0 / (d_ji * d_jk); - double inv_dists3 = pow( inv_dists, 3.0 ); - double dot_dvecs = Dot( dvec_ji, dvec_jk, 3 ); - double Cdot_inv3 = dot_dvecs * inv_dists3; - - for (t = 0; t < 3; ++t) { - (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists - - Cdot_inv3 * sqr_d_jk * dvec_ji[t]; - (*dcos_theta_dj)[t] = -(dvec_jk[t] + dvec_ji[t]) * inv_dists + - Cdot_inv3 * ( sqr_d_jk * dvec_ji[t] + sqr_d_ji * dvec_jk[t] ); - (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists - - Cdot_inv3 * sqr_d_ji * dvec_jk[t]; - } -} - - -void Valence_Angles( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /*out_control*/ ) -{ - int i, j, pi, k, pk, t; - int type_i, type_j, type_k; - int start_j, end_j, start_pk, end_pk; - int cnt, num_thb_intrs; - - double temp, temp_bo_jt, pBOjt7; - double p_val1, p_val2, p_val3, p_val4, p_val5; - double p_val6, p_val7, p_val8, p_val9, p_val10; - double p_pen1, p_pen2, p_pen3, p_pen4; - double p_coa1, p_coa2, p_coa3, p_coa4; - double trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk; - double exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2; - double dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj; - double CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8; - double CEpen1, CEpen2, CEpen3; - double e_ang, e_coa, e_pen; - double CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5; - double Cf7ij, Cf7jk, Cf8j, Cf9j; - double f7_ij, f7_jk, f8_Dj, f9_Dj; - double Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta; - double BOA_ij, BOA_jk; - rvec force, ext_press; - - // Tallying variables - double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; - double delij[3], delkj[3]; - - three_body_header *thbh; - three_body_parameters *thbp; - three_body_interaction_data *p_ijk, *p_kji; - bond_data *pbond_ij, *pbond_jk, *pbond_jt; - bond_order_data *bo_ij, *bo_jk, *bo_jt; - reax_list *bonds = (*lists) + BONDS; - reax_list *thb_intrs = (*lists) + THREE_BODIES; - - /* global parameters used in these calculations */ - p_val6 = system->reax_param.gp.l[14]; - p_val8 = system->reax_param.gp.l[33]; - p_val9 = system->reax_param.gp.l[16]; - p_val10 = system->reax_param.gp.l[17]; - num_thb_intrs = 0; - - - for (j = 0; j < system->N; ++j) { // Ray: the first one with system->N - type_j = system->my_atoms[j].type; - if (type_j < 0) continue; - start_j = Start_Index(j, bonds); - end_j = End_Index(j, bonds); - - p_val3 = system->reax_param.sbp[ type_j ].p_val3; - p_val5 = system->reax_param.sbp[ type_j ].p_val5; - - SBOp = 0, prod_SBO = 1; - for (t = start_j; t < end_j; ++t) { - bo_jt = &(bonds->select.bond_list[t].bo_data); - SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2); - temp = SQR( bo_jt->BO ); - temp *= temp; - temp *= temp; - prod_SBO *= exp( -temp ); - } - - if (workspace->vlpex[j] >= 0) { - vlpadj = 0; - dSBO2 = prod_SBO - 1; - } else { - vlpadj = workspace->nlp[j]; - dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); - } - - SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); - dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj ); - - if (SBO <= 0) - SBO2 = 0, CSBO2 = 0; - else if (SBO > 0 && SBO <= 1) { - SBO2 = pow( SBO, p_val9 ); - CSBO2 = p_val9 * pow( SBO, p_val9 - 1 ); - } - else if (SBO > 1 && SBO < 2) { - SBO2 = 2 - pow( 2-SBO, p_val9 ); - CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 ); - } - else - SBO2 = 2, CSBO2 = 0; - - expval6 = exp( p_val6 * workspace->Delta_boc[j] ); - - for (pi = start_j; pi < end_j; ++pi) { - Set_Start_Index( pi, num_thb_intrs, thb_intrs ); - pbond_ij = &(bonds->select.bond_list[pi]); - bo_ij = &(pbond_ij->bo_data); - BOA_ij = bo_ij->BO - control->thb_cut; - - - if ( BOA_ij/*bo_ij->BO*/ > 0.0 && - ( j < system->n || pbond_ij->nbr < system->n )) { - i = pbond_ij->nbr; - type_i = system->my_atoms[i].type; - - for (pk = start_j; pk < pi; ++pk) { - start_pk = Start_Index( pk, thb_intrs ); - end_pk = End_Index( pk, thb_intrs ); - - for (t = start_pk; t < end_pk; ++t) - if (thb_intrs->select.three_body_list[t].thb == i) { - p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs] ); - p_kji = &(thb_intrs->select.three_body_list[t]); - - p_ijk->thb = bonds->select.bond_list[pk].nbr; - p_ijk->pthb = pk; - p_ijk->theta = p_kji->theta; - rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk ); - rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj ); - rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di ); - - ++num_thb_intrs; - break; - } - } - - for (pk = pi+1; pk < end_j; ++pk) { - pbond_jk = &(bonds->select.bond_list[pk]); - bo_jk = &(pbond_jk->bo_data); - BOA_jk = bo_jk->BO - control->thb_cut; - k = pbond_jk->nbr; - type_k = system->my_atoms[k].type; - p_ijk = &( thb_intrs->select.three_body_list[num_thb_intrs] ); - - Calculate_Theta( pbond_ij->dvec, pbond_ij->d, - pbond_jk->dvec, pbond_jk->d, - &theta, &cos_theta ); - - Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, - pbond_jk->dvec, pbond_jk->d, - &(p_ijk->dcos_di), &(p_ijk->dcos_dj), - &(p_ijk->dcos_dk) ); - p_ijk->thb = k; - p_ijk->pthb = pk; - p_ijk->theta = theta; - - sin_theta = sin( theta ); - if (sin_theta < 1.0e-5) - sin_theta = 1.0e-5; - - ++num_thb_intrs; - - - if ((j < system->n) && (BOA_jk > 0.0) && - (bo_ij->BO > control->thb_cut) && - (bo_jk->BO > control->thb_cut) && - (bo_ij->BO * bo_jk->BO > control->thb_cutsq)) { - thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] ); - - for (cnt = 0; cnt < thbh->cnt; ++cnt) { - if (fabs(thbh->prm[cnt].p_val1) > 0.001) { - thbp = &( thbh->prm[cnt] ); - - /* ANGLE ENERGY */ - p_val1 = thbp->p_val1; - p_val2 = thbp->p_val2; - p_val4 = thbp->p_val4; - p_val7 = thbp->p_val7; - theta_00 = thbp->theta_00; - - exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) ); - f7_ij = 1.0 - exp3ij; - Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij; - - exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) ); - f7_jk = 1.0 - exp3jk; - Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk; - - expval7 = exp( -p_val7 * workspace->Delta_boc[j] ); - trm8 = 1.0 + expval6 + expval7; - f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 ); - Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) * - ( p_val6 * expval6 * trm8 - - (2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) ); - - theta_0 = 180.0 - theta_00 * (1.0 - - exp(-p_val10 * (2.0 - SBO2))); - theta_0 = DEG2RAD( theta_0 ); - - expval2theta = exp( -p_val2 * SQR(theta_0 - theta) ); - if (p_val1 >= 0) - expval12theta = p_val1 * (1.0 - expval2theta); - else // To avoid linear Me-H-Me angles (6/6/06) - expval12theta = p_val1 * -expval2theta; - - CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; - CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; - CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; - CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * - expval2theta * (theta_0 - theta); - - Ctheta_0 = p_val10 * DEG2RAD(theta_00) * - exp( -p_val10 * (2.0 - SBO2) ); - - CEval5 = -CEval4 * Ctheta_0 * CSBO2; - CEval6 = CEval5 * dSBO1; - CEval7 = CEval5 * dSBO2; - CEval8 = -CEval4 / sin_theta; - - data->my_en.e_ang += e_ang = - f7_ij * f7_jk * f8_Dj * expval12theta; - /* END ANGLE ENERGY*/ - - /* PENALTY ENERGY */ - p_pen1 = thbp->p_pen1; - p_pen2 = system->reax_param.gp.l[19]; - p_pen3 = system->reax_param.gp.l[20]; - p_pen4 = system->reax_param.gp.l[21]; - - exp_pen2ij = exp( -p_pen2 * SQR( BOA_ij - 2.0 ) ); - exp_pen2jk = exp( -p_pen2 * SQR( BOA_jk - 2.0 ) ); - exp_pen3 = exp( -p_pen3 * workspace->Delta[j] ); - exp_pen4 = exp( p_pen4 * workspace->Delta[j] ); - trm_pen34 = 1.0 + exp_pen3 + exp_pen4; - f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34; - Cf9j = ( -p_pen3 * exp_pen3 * trm_pen34 - - (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 + - p_pen4 * exp_pen4 ) ) / - SQR( trm_pen34 ); - - data->my_en.e_pen += e_pen = - p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; - - CEpen1 = e_pen * Cf9j / f9_Dj; - temp = -2.0 * p_pen2 * e_pen; - CEpen2 = temp * (BOA_ij - 2.0); - CEpen3 = temp * (BOA_jk - 2.0); - /* END PENALTY ENERGY */ - - /* COALITION ENERGY */ - p_coa1 = thbp->p_coa1; - p_coa2 = system->reax_param.gp.l[2]; - p_coa3 = system->reax_param.gp.l[38]; - p_coa4 = system->reax_param.gp.l[30]; - - exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] ); - data->my_en.e_coa += e_coa = - p_coa1 / (1. + exp_coa2) * - exp( -p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij) ) * - exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) * - exp( -p_coa4 * SQR(BOA_ij - 1.5) ) * - exp( -p_coa4 * SQR(BOA_jk - 1.5) ); - - CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; - CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa; - CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); - CEcoa4 = -2 * p_coa3 * - (workspace->total_bond_order[i]-BOA_ij) * e_coa; - CEcoa5 = -2 * p_coa3 * - (workspace->total_bond_order[k]-BOA_jk) * e_coa; - /* END COALITION ENERGY */ - - /* FORCES */ - bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); - bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); - workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3); - workspace->CdDelta[i] += CEcoa4; - workspace->CdDelta[k] += CEcoa5; - - for (t = start_j; t < end_j; ++t) { - pbond_jt = &( bonds->select.bond_list[t] ); - bo_jt = &(pbond_jt->bo_data); - temp_bo_jt = bo_jt->BO; - temp = CUBE( temp_bo_jt ); - pBOjt7 = temp * temp * temp_bo_jt; - - bo_jt->Cdbo += (CEval6 * pBOjt7); - bo_jt->Cdbopi += CEval5; - bo_jt->Cdbopi2 += CEval5; - } - - if (control->virial == 0) { - rvec_ScaledAdd( workspace->f[i], CEval8, p_ijk->dcos_di ); - rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); - rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk ); - } else { - rvec_Scale( force, CEval8, p_ijk->dcos_di ); - rvec_Add( workspace->f[i], force ); - rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - - rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); - - rvec_Scale( force, CEval8, p_ijk->dcos_dk ); - rvec_Add( workspace->f[k], force ); - rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); - rvec_Add( data->my_ext_press, ext_press ); - } - - /* tally into per-atom virials */ - if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { - - /* Acquire vectors */ - rvec_ScaledSum( delij, 1., system->my_atoms[i].x, - -1., system->my_atoms[j].x ); - rvec_ScaledSum( delkj, 1., system->my_atoms[k].x, - -1., system->my_atoms[j].x ); - - rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di ); - rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj ); - rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk ); - - eng_tmp = e_ang + e_pen + e_coa; - - if (system->pair_ptr->evflag) - system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); - if (system->pair_ptr->vflag_atom) - system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj); - } - } - } - } - } - } - - Set_End_Index(pi, num_thb_intrs, thb_intrs ); - } - } - - if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { - workspace->realloc.num_3body = num_thb_intrs; - if (num_thb_intrs > thb_intrs->num_intrs) { - char errmsg[128]; - snprintf(errmsg, 128, "step%d-ran out of space on angle_list: top=%d, max=%d", - data->step, num_thb_intrs, thb_intrs->num_intrs); - control->error_ptr->one(FLERR, errmsg); - } - } - -} diff --git a/src/USER-REAXC/reaxc_valence_angles.h b/src/USER-REAXC/reaxc_valence_angles.h deleted file mode 100644 index a5dc12c16b..0000000000 --- a/src/USER-REAXC/reaxc_valence_angles.h +++ /dev/null @@ -1,40 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __VALENCE_ANGLES_H_ -#define __VALENCE_ANGLES_H_ - -#include "reaxc_types.h" - -void Valence_Angles( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); - -void Calculate_Theta( rvec, double, rvec, double, double*, double* ); - -void Calculate_dCos_Theta( rvec, double, rvec, double, rvec*, rvec*, rvec* ); - -#endif diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp deleted file mode 100644 index 5497d41c9b..0000000000 --- a/src/USER-REAXC/reaxc_vector.cpp +++ /dev/null @@ -1,160 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#include "reaxc_vector.h" -#include -#include "reaxc_defs.h" - -void rvec_Copy( rvec dest, rvec src ) -{ - dest[0] = src[0], dest[1] = src[1], dest[2] = src[2]; -} - - -void rvec_Scale( rvec ret, double c, rvec v ) -{ - ret[0] = c * v[0], ret[1] = c * v[1], ret[2] = c * v[2]; -} - - -void rvec_Add( rvec ret, rvec v ) -{ - ret[0] += v[0], ret[1] += v[1], ret[2] += v[2]; -} - - -void rvec_ScaledAdd( rvec ret, double c, rvec v ) -{ - ret[0] += c * v[0], ret[1] += c * v[1], ret[2] += c * v[2]; -} - - -void rvec_ScaledSum( rvec ret, double c1, rvec v1 ,double c2, rvec v2 ) -{ - ret[0] = c1 * v1[0] + c2 * v2[0]; - ret[1] = c1 * v1[1] + c2 * v2[1]; - ret[2] = c1 * v1[2] + c2 * v2[2]; -} - - -double rvec_Dot( rvec v1, rvec v2 ) -{ - return v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]; -} - - -void rvec_iMultiply( rvec r, ivec v1, rvec v2 ) -{ - r[0] = v1[0] * v2[0]; - r[1] = v1[1] * v2[1]; - r[2] = v1[2] * v2[2]; -} - - -void rvec_Cross( rvec ret, rvec v1, rvec v2 ) -{ - ret[0] = v1[1] * v2[2] - v1[2] * v2[1]; - ret[1] = v1[2] * v2[0] - v1[0] * v2[2]; - ret[2] = v1[0] * v2[1] - v1[1] * v2[0]; -} - - -double rvec_Norm_Sqr( rvec v ) -{ - return SQR(v[0]) + SQR(v[1]) + SQR(v[2]); -} - - -double rvec_Norm( rvec v ) -{ - return sqrt( SQR(v[0]) + SQR(v[1]) + SQR(v[2]) ); -} - - -void rvec_MakeZero( rvec v ) -{ - v[0] = v[1] = v[2] = 0.000000000000000e+00; -} - - -void rtensor_MatVec( rvec ret, rtensor m, rvec v ) -{ - int i; - rvec temp; - - if (ret == v) - { - for (i = 0; i < 3; ++i) - temp[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2]; - - for (i = 0; i < 3; ++i) - ret[i] = temp[i]; - } - else - { - for (i = 0; i < 3; ++i) - ret[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2]; - } -} - - -void rtensor_MakeZero( rtensor t ) -{ - t[0][0] = t[0][1] = t[0][2] = 0; - t[1][0] = t[1][1] = t[1][2] = 0; - t[2][0] = t[2][1] = t[2][2] = 0; -} - - -void ivec_MakeZero( ivec v ) -{ - v[0] = v[1] = v[2] = 0; -} - - -void ivec_Copy( ivec dest, ivec src ) -{ - dest[0] = src[0], dest[1] = src[1], dest[2] = src[2]; -} - - -void ivec_Scale( ivec dest, double C, ivec src ) -{ - dest[0] = (int)(C * src[0]); - dest[1] = (int)(C * src[1]); - dest[2] = (int)(C * src[2]); -} - - -void ivec_Sum( ivec dest, ivec v1, ivec v2 ) -{ - dest[0] = v1[0] + v2[0]; - dest[1] = v1[1] + v2[1]; - dest[2] = v1[2] + v2[2]; -} - - diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h deleted file mode 100644 index f2068d4d4f..0000000000 --- a/src/USER-REAXC/reaxc_vector.h +++ /dev/null @@ -1,54 +0,0 @@ -// clang-format off -/*---------------------------------------------------------------------- - PuReMD - Purdue ReaxFF Molecular Dynamics Program - - Copyright (2010) Purdue University - Hasan Metin Aktulga, hmaktulga@lbl.gov - Joseph Fogarty, jcfogart@mail.usf.edu - Sagar Pandit, pandit@usf.edu - Ananth Y Grama, ayg@cs.purdue.edu - - Please cite the related publication: - H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, - "Parallel Reactive Molecular Dynamics: Numerical Methods and - Algorithmic Techniques", Parallel Computing, in press. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. - See the GNU General Public License for more details: - . - ----------------------------------------------------------------------*/ - -#ifndef __VECTOR_H_ -#define __VECTOR_H_ - -#include "reaxc_types.h" - -void rvec_Copy( rvec, rvec ); -void rvec_Scale( rvec, double, rvec ); -void rvec_Add( rvec, rvec ); -void rvec_ScaledAdd( rvec, double, rvec ); -void rvec_ScaledSum( rvec, double, rvec, double, rvec ); -double rvec_Dot( rvec, rvec ); -void rvec_iMultiply( rvec, ivec, rvec ); -void rvec_Cross( rvec, rvec, rvec ); -double rvec_Norm_Sqr( rvec ); -double rvec_Norm( rvec ); -void rvec_MakeZero( rvec ); -void rvec_Random( rvec ); - -void rtensor_MakeZero( rtensor ); -void rtensor_MatVec( rvec, rtensor, rvec ); - -void ivec_MakeZero( ivec ); -void ivec_Copy( ivec, ivec ); -void ivec_Scale( ivec, double, ivec ); -void ivec_Sum( ivec, ivec, ivec ); - -#endif diff --git a/src/USER-VTK/Install.sh b/src/VTK/Install.sh similarity index 100% rename from src/USER-VTK/Install.sh rename to src/VTK/Install.sh diff --git a/src/USER-VTK/README b/src/VTK/README similarity index 100% rename from src/USER-VTK/README rename to src/VTK/README diff --git a/src/USER-VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp similarity index 100% rename from src/USER-VTK/dump_vtk.cpp rename to src/VTK/dump_vtk.cpp diff --git a/src/USER-VTK/dump_vtk.h b/src/VTK/dump_vtk.h similarity index 100% rename from src/USER-VTK/dump_vtk.h rename to src/VTK/dump_vtk.h diff --git a/src/USER-YAFF/README b/src/YAFF/README similarity index 100% rename from src/USER-YAFF/README rename to src/YAFF/README diff --git a/src/USER-YAFF/angle_cross.cpp b/src/YAFF/angle_cross.cpp similarity index 100% rename from src/USER-YAFF/angle_cross.cpp rename to src/YAFF/angle_cross.cpp diff --git a/src/USER-YAFF/angle_cross.h b/src/YAFF/angle_cross.h similarity index 100% rename from src/USER-YAFF/angle_cross.h rename to src/YAFF/angle_cross.h diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/YAFF/angle_mm3.cpp similarity index 100% rename from src/USER-YAFF/angle_mm3.cpp rename to src/YAFF/angle_mm3.cpp diff --git a/src/USER-YAFF/angle_mm3.h b/src/YAFF/angle_mm3.h similarity index 100% rename from src/USER-YAFF/angle_mm3.h rename to src/YAFF/angle_mm3.h diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/YAFF/bond_mm3.cpp similarity index 100% rename from src/USER-YAFF/bond_mm3.cpp rename to src/YAFF/bond_mm3.cpp diff --git a/src/USER-YAFF/bond_mm3.h b/src/YAFF/bond_mm3.h similarity index 100% rename from src/USER-YAFF/bond_mm3.h rename to src/YAFF/bond_mm3.h diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/YAFF/improper_distharm.cpp similarity index 100% rename from src/USER-YAFF/improper_distharm.cpp rename to src/YAFF/improper_distharm.cpp diff --git a/src/USER-YAFF/improper_distharm.h b/src/YAFF/improper_distharm.h similarity index 100% rename from src/USER-YAFF/improper_distharm.h rename to src/YAFF/improper_distharm.h diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/YAFF/improper_sqdistharm.cpp similarity index 100% rename from src/USER-YAFF/improper_sqdistharm.cpp rename to src/YAFF/improper_sqdistharm.cpp diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/YAFF/improper_sqdistharm.h similarity index 100% rename from src/USER-YAFF/improper_sqdistharm.h rename to src/YAFF/improper_sqdistharm.h diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp similarity index 100% rename from src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp rename to src/YAFF/pair_lj_switch3_coulgauss_long.cpp diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h b/src/YAFF/pair_lj_switch3_coulgauss_long.h similarity index 100% rename from src/USER-YAFF/pair_lj_switch3_coulgauss_long.h rename to src/YAFF/pair_lj_switch3_coulgauss_long.h diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp similarity index 100% rename from src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp rename to src/YAFF/pair_mm3_switch3_coulgauss_long.cpp diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h b/src/YAFF/pair_mm3_switch3_coulgauss_long.h similarity index 100% rename from src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h rename to src/YAFF/pair_mm3_switch3_coulgauss_long.h diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 5601e8b855..0cea855f1e 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -56,16 +56,12 @@ class KokkosLMP { KokkosLMP(class LAMMPS *, int, char **) { kokkos_exists = 0; } ~KokkosLMP() {} + static void finalize() {} void accelerator(int, char **) {} int neigh_list_kokkos(int) { return 0; } int neigh_count(int) { return 0; } }; -class Kokkos { - public: - static void finalize() {} -}; - class AtomKokkos : public Atom { public: tagint **k_special; diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h index 3f3be3c975..0a85816684 100644 --- a/src/accelerator_omp.h +++ b/src/accelerator_omp.h @@ -13,9 +13,9 @@ // NOTE: this file is *supposed* to be included multiple times -#ifdef LMP_USER_OMP +#ifdef LMP_OPENMP -// true interface to USER-OMP +// true interface to OPENMP // provide a DomainOMP class with some overrides for Domain #include "domain.h" @@ -41,4 +41,4 @@ class DomainOMP : public Domain { #endif /* LMP_DOMAIN_OMP_H */ -#endif /* !LMP_USER_OMP */ +#endif /* !LMP_OPENMP */ diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 4fb382790e..12bc9aa97a 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,14 +14,14 @@ #include "angle_hybrid.h" #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" -#include #include +#include using namespace LAMMPS_NS; @@ -45,19 +44,18 @@ AngleHybrid::~AngleHybrid() { if (nstyles) { for (int i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (int i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] nanglelist; - delete [] maxangle; - for (int i = 0; i < nstyles; i++) - memory->destroy(anglelist[i]); - delete [] anglelist; + delete[] nanglelist; + delete[] maxangle; + for (int i = 0; i < nstyles; i++) memory->destroy(anglelist[i]); + delete[] anglelist; } } @@ -65,7 +63,7 @@ AngleHybrid::~AngleHybrid() void AngleHybrid::compute(int eflag, int vflag) { - int i,j,m,n; + int i, j, m, n; // save ptrs to original anglelist @@ -87,7 +85,7 @@ void AngleHybrid::compute(int eflag, int vflag) if (nanglelist[m] > maxangle[m]) { memory->destroy(anglelist[m]); maxangle[m] = nanglelist[m] + EXTRA; - memory->create(anglelist[m],maxangle[m],4,"angle_hybrid:anglelist"); + memory->create(anglelist[m], maxangle[m], 4, "angle_hybrid:anglelist"); } nanglelist[m] = 0; } @@ -107,7 +105,7 @@ void AngleHybrid::compute(int eflag, int vflag) // set neighbor->anglelist to sub-style anglelist before call // accumulate sub-style global/peratom energy/virial in hybrid - ev_init(eflag,vflag); + ev_init(eflag, vflag); // need to clear per-thread storage here, when using multiple threads // with thread-enabled substyles to avoid uninitlialized data access. @@ -115,17 +113,15 @@ void AngleHybrid::compute(int eflag, int vflag) const int nthreads = comm->nthreads; if (comm->nthreads > 1) { const bigint nall = atom->nlocal + atom->nghost; - if (eflag_atom) - memset(&eatom[0],0,nall*nthreads*sizeof(double)); - if (vflag_atom) - memset(&vatom[0][0],0,6*nall*nthreads*sizeof(double)); + if (eflag_atom) memset(&eatom[0], 0, nall * nthreads * sizeof(double)); + if (vflag_atom) memset(&vatom[0][0], 0, 6 * nall * nthreads * sizeof(double)); } for (m = 0; m < nstyles; m++) { neighbor->nanglelist = nanglelist[m]; neighbor->anglelist = anglelist[m]; - styles[m]->compute(eflag,vflag); + styles[m]->compute(eflag, vflag); if (eflag_global) energy += styles[m]->energy; if (vflag_global) @@ -141,16 +137,14 @@ void AngleHybrid::compute(int eflag, int vflag) if (force->newton_bond) n += atom->nghost; double **vatom_substyle = styles[m]->vatom; for (i = 0; i < n; i++) - for (j = 0; j < 6; j++) - vatom[i][j] += vatom_substyle[i][j]; + for (j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j]; } if (cvflag_atom) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; double **cvatom_substyle = styles[m]->cvatom; for (i = 0; i < n; i++) - for (j = 0; j < 9; j++) - cvatom[i][j] += cvatom_substyle[i][j]; + for (j = 0; j < 9; j++) cvatom[i][j] += cvatom_substyle[i][j]; } } @@ -167,13 +161,13 @@ void AngleHybrid::allocate() allocated = 1; int n = atom->nangletypes; - memory->create(map,n+1,"angle:map"); - memory->create(setflag,n+1,"angle:setflag"); + memory->create(map, n + 1, "angle:map"); + memory->create(setflag, n + 1, "angle:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; nanglelist = new int[nstyles]; maxangle = new int[nstyles]; - anglelist = new int**[nstyles]; + anglelist = new int **[nstyles]; for (int m = 0; m < nstyles; m++) maxangle[m] = 0; for (int m = 0; m < nstyles; m++) anglelist[m] = nullptr; } @@ -184,27 +178,26 @@ void AngleHybrid::allocate() void AngleHybrid::settings(int narg, char **arg) { - int i, m,istyle; + int i, m, istyle; - if (narg < 1) error->all(FLERR,"Illegal angle_style command"); + if (narg < 1) error->all(FLERR, "Illegal angle_style command"); // delete old lists, since cannot just change settings if (nstyles) { for (i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] nanglelist; - delete [] maxangle; - for (i = 0; i < nstyles; i++) - memory->destroy(anglelist[i]); - delete [] anglelist; + delete[] nanglelist; + delete[] maxangle; + for (i = 0; i < nstyles; i++) memory->destroy(anglelist[i]); + delete[] anglelist; } allocated = 0; @@ -215,7 +208,7 @@ void AngleHybrid::settings(int narg, char **arg) nstyles = 0; i = 0; while (i < narg) { - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; nstyles++; @@ -223,8 +216,8 @@ void AngleHybrid::settings(int narg, char **arg) // allocate list of sub-styles - styles = new Angle*[nstyles]; - keywords = new char*[nstyles]; + styles = new Angle *[nstyles]; + keywords = new char *[nstyles]; // allocate each sub-style and call its settings() with subset of args // allocate uses suffix, but don't store suffix version in keywords, @@ -239,22 +232,21 @@ void AngleHybrid::settings(int narg, char **arg) while (i < narg) { for (m = 0; m < nstyles; m++) - if (strcmp(arg[i],keywords[m]) == 0) - error->all(FLERR,"Angle style hybrid cannot use " - "same angle style twice"); - if (strcmp(arg[i],"hybrid") == 0) - error->all(FLERR,"Angle style hybrid cannot have hybrid as an argument"); - if (strcmp(arg[i],"none") == 0) - error->all(FLERR,"Angle style hybrid cannot have none as an argument"); + if (strcmp(arg[i], keywords[m]) == 0) + error->all(FLERR, "Angle style hybrid cannot use same angle style twice"); + if (strcmp(arg[i], "hybrid") == 0) + error->all(FLERR, "Angle style hybrid cannot have hybrid as an argument"); + if (strcmp(arg[i], "none") == 0) + error->all(FLERR, "Angle style hybrid cannot have none as an argument"); - styles[nstyles] = force->new_angle(arg[i],1,dummy); - force->store_style(keywords[nstyles],arg[i],0); + styles[nstyles] = force->new_angle(arg[i], 1, dummy); + force->store_style(keywords[nstyles], arg[i], 0); istyle = i; - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; - styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]); + styles[nstyles]->settings(i - istyle - 1, &arg[istyle + 1]); nstyles++; } } @@ -267,26 +259,29 @@ void AngleHybrid::coeff(int narg, char **arg) { if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error); // 2nd arg = angle sub-style name // allow for "none" or "skip" as valid sub-style name int m; for (m = 0; m < nstyles; m++) - if (strcmp(arg[1],keywords[m]) == 0) break; + if (strcmp(arg[1], keywords[m]) == 0) break; int none = 0; int skip = 0; if (m == nstyles) { - if (strcmp(arg[1],"none") == 0) none = 1; - else if (strcmp(arg[1],"skip") == 0) none = skip = 1; - else if (strcmp(arg[1],"ba") == 0) - error->all(FLERR,"BondAngle coeff for hybrid angle has invalid format"); - else if (strcmp(arg[1],"bb") == 0) - error->all(FLERR,"BondBond coeff for hybrid angle has invalid format"); - else error->all(FLERR,"Angle coeff for hybrid has invalid style"); + if (strcmp(arg[1], "none") == 0) + none = 1; + else if (strcmp(arg[1], "skip") == 0) + none = skip = 1; + else if (strcmp(arg[1], "ba") == 0) + error->all(FLERR, "BondAngle coeff for hybrid angle has invalid format"); + else if (strcmp(arg[1], "bb") == 0) + error->all(FLERR, "BondBond coeff for hybrid angle has invalid format"); + else + error->all(FLERR, "Angle coeff for hybrid has invalid style"); } // move 1st arg to 2nd arg @@ -296,14 +291,15 @@ void AngleHybrid::coeff(int narg, char **arg) // invoke sub-style coeff() starting with 1st arg - if (!none) styles[m]->coeff(narg-1,&arg[1]); + if (!none) styles[m]->coeff(narg - 1, &arg[1]); // set setflag and which type maps to which sub-style // if sub-style is skip: auxiliary class2 setting in data file so ignore // if sub-style is none: set hybrid setflag, wipe out map for (int i = ilo; i <= ihi; i++) { - if (skip) continue; + if (skip) + continue; else if (none) { setflag[i] = 1; map[i] = -1; @@ -330,8 +326,7 @@ void AngleHybrid::init_style() double AngleHybrid::equilibrium_angle(int i) { - if (map[i] < 0) - error->one(FLERR,"Invoked angle equil angle on angle style none"); + if (map[i] < 0) error->one(FLERR, "Invoked angle equil angle on angle style none"); return styles[map[i]]->equilibrium_angle(i); } @@ -341,13 +336,13 @@ double AngleHybrid::equilibrium_angle(int i) void AngleHybrid::write_restart(FILE *fp) { - fwrite(&nstyles,sizeof(int),1,fp); + fwrite(&nstyles, sizeof(int), 1, fp); int n; for (int m = 0; m < nstyles; m++) { n = strlen(keywords[m]) + 1; - fwrite(&n,sizeof(int),1,fp); - fwrite(keywords[m],sizeof(char),n,fp); + fwrite(&n, sizeof(int), 1, fp); + fwrite(keywords[m], sizeof(char), n, fp); styles[m]->write_restart_settings(fp); } } @@ -359,21 +354,21 @@ void AngleHybrid::write_restart(FILE *fp) void AngleHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&nstyles,1,MPI_INT,0,world); - styles = new Angle*[nstyles]; - keywords = new char*[nstyles]; + if (me == 0) utils::sfread(FLERR, &nstyles, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&nstyles, 1, MPI_INT, 0, world); + styles = new Angle *[nstyles]; + keywords = new char *[nstyles]; allocate(); - int n,dummy; + int n, dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&n,1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &n, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&n, 1, MPI_INT, 0, world); keywords[m] = new char[n]; - if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,nullptr,error); - MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); - styles[m] = force->new_angle(keywords[m],0,dummy); + if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error); + MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world); + styles[m] = force->new_angle(keywords[m], 0, dummy); styles[m]->read_restart_settings(fp); } } @@ -382,8 +377,8 @@ void AngleHybrid::read_restart(FILE *fp) double AngleHybrid::single(int type, int i1, int i2, int i3) { - if (map[type] < 0) error->one(FLERR,"Invoked angle single on angle style none"); - return styles[map[type]]->single(type,i1,i2,i3); + if (map[type] < 0) error->one(FLERR, "Invoked angle single on angle style none"); + return styles[map[type]]->single(type, i1, i2, i3); } /* ---------------------------------------------------------------------- @@ -392,10 +387,10 @@ double AngleHybrid::single(int type, int i1, int i2, int i3) double AngleHybrid::memory_usage() { - double bytes = (double)maxeatom * sizeof(double); - bytes += (double)maxvatom*6 * sizeof(double); - bytes += (double)maxcvatom*9 * sizeof(double); - for (int m = 0; m < nstyles; m++) bytes += (double)maxangle[m]*4 * sizeof(int); + double bytes = (double) maxeatom * sizeof(double); + bytes += (double) maxvatom * 6 * sizeof(double); + bytes += (double) maxcvatom * 9 * sizeof(double); + for (int m = 0; m < nstyles; m++) bytes += (double) maxangle[m] * 4 * sizeof(int); for (int m = 0; m < nstyles; m++) if (styles[m]) bytes += styles[m]->memory_usage(); return bytes; diff --git a/src/arg_info.cpp b/src/arg_info.cpp index b83bb141fa..5063b6b471 100644 --- a/src/arg_info.cpp +++ b/src/arg_info.cpp @@ -30,7 +30,8 @@ using namespace LAMMPS_NS; ArgInfo::ArgInfo(const std::string &arg, int allowed) : type(NONE), dim(0), index1(-1), index2(-1) { - if ((arg.size() > 2) && (arg[1] == '_')) { + if (((arg.size() > 3) && (arg[1] == '2') && (arg[2] == '_')) + || ((arg.size() > 2) && (arg[1] == '_'))) { if ((arg[0] == 'c') && (allowed & COMPUTE)) type = COMPUTE; else if ((arg[0] == 'f') && (allowed & FIX)) @@ -46,10 +47,11 @@ ArgInfo::ArgInfo(const std::string &arg, int allowed) : type(NONE), dim(0), inde name = arg; return; } + const int offset = (arg[1] == '_') ? 2 : 3; - std::size_t has_idx1 = arg.find('[', 2); + std::size_t has_idx1 = arg.find('[', offset); if (has_idx1 != std::string::npos) { - name = arg.substr(2, has_idx1 - 2); + name = arg.substr(offset, has_idx1 - offset); dim = 1; std::size_t has_idx2 = arg.find('[', has_idx1 + 1); @@ -68,18 +70,18 @@ ArgInfo::ArgInfo(const std::string &arg, int allowed) : type(NONE), dim(0), inde } else has_idx2 = arg.size(); - if (arg[has_idx2 - 1] != ']') { + if ((arg[has_idx2 - 1] != ']') || ((dim == 1) && (arg.find(']') != has_idx2 - 1))) { type = UNKNOWN; } else { try { - index1 = std::stoi(arg.substr(has_idx1 + 1, arg.size() - (has_idx2 + 2))); + index1 = std::stoi(arg.substr(has_idx1 + 1, arg.size() - (has_idx1 + 2))); } catch (std::invalid_argument &) { type = UNKNOWN; } } } else { index1 = 0; - name = arg.substr(2); + name = arg.substr(offset); } } else { index1 = 0; diff --git a/src/atom.cpp b/src/atom.cpp index 0a8095116b..0a629e2fe6 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -38,7 +38,7 @@ #include #include -#ifdef LMP_USER_INTEL +#ifdef LMP_INTEL #include "neigh_request.h" #endif @@ -161,7 +161,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) sp = fm = fm_long = nullptr; - // USER-EFF and USER-AWPMD packages + // EFF and AWPMD packages spin = nullptr; eradius = ervel = erforce = nullptr; @@ -169,23 +169,27 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) cs = csforce = vforce = nullptr; etag = nullptr; - // USER-DPD package + // CG-DNA package + + id5p = nullptr; + + // DPD-REACT package uCond = uMech = uChem = uCG = uCGnew = nullptr; duChem = dpdTheta = nullptr; - // USER-MESO package + // MESO package cc = cc_flux = nullptr; edpd_temp = edpd_flux = edpd_cv = nullptr; - // USER-MESONT package + // MESONT package length = nullptr; buckling = nullptr; bond_nt = nullptr; - // USER-SMD package + // MACHDYN package contact_radius = nullptr; smd_data_9 = nullptr; @@ -194,12 +198,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) eff_plastic_strain_rate = nullptr; damage = nullptr; - // USER-SPH package + // SPH package rho = drho = esph = desph = cv = nullptr; vest = nullptr; - // USER-DIELECTRIC package + // DIELECTRIC package area = ed = em = epsilon = curvature = q_unscaled = nullptr; @@ -457,14 +461,14 @@ void Atom::peratom_create() add_peratom("fm",&fm,DOUBLE,3,1); add_peratom("fm_long",&fm_long,DOUBLE,3,1); - // USER-EFF package + // EFF package add_peratom("spin",&spin,INT,0); add_peratom("eradius",&eradius,DOUBLE,0); add_peratom("ervel",&ervel,DOUBLE,0); add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag - // USER-AWPMD package + // AWPMD package add_peratom("cs",&cs,DOUBLE,2); add_peratom("csforce",&csforce,DOUBLE,2); @@ -472,7 +476,11 @@ void Atom::peratom_create() add_peratom("ervelforce",&ervelforce,DOUBLE,0); add_peratom("etag",&etag,INT,0); - // USER-DPD package + // CG-DNA package + + add_peratom("id5p",&id5p,tagintsize,0); + + // DPD-REACT package add_peratom("dpdTheta",&dpdTheta,DOUBLE,0); add_peratom("uCond",&uCond,DOUBLE,0); @@ -482,7 +490,7 @@ void Atom::peratom_create() add_peratom("uCGnew",&uCGnew,DOUBLE,0); add_peratom("duChem",&duChem,DOUBLE,0); - // USER-MESO package + // MESO package add_peratom("edpd_cv",&edpd_cv,DOUBLE,0); add_peratom("edpd_temp",&edpd_temp,DOUBLE,0); @@ -491,13 +499,13 @@ void Atom::peratom_create() add_peratom("cc",&cc,DOUBLE,1); add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag - // USER-MESONT package + // MESONT package add_peratom("length",&length,DOUBLE,0); add_peratom("buckling",&buckling,INT,0); add_peratom("bond_nt",&bond_nt,tagintsize,2); - // USER-SPH package + // SPH package add_peratom("rho",&rho,DOUBLE,0); add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag @@ -506,7 +514,7 @@ void Atom::peratom_create() add_peratom("vest",&vest,DOUBLE,3); add_peratom("cv",&cv,DOUBLE,0); - // USER-SMD package + // MACHDYN package add_peratom("contact_radius",&contact_radius,DOUBLE,0); add_peratom("smd_data_9",&smd_data_9,DOUBLE,1); @@ -515,7 +523,7 @@ void Atom::peratom_create() add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0); add_peratom("damage",&damage,DOUBLE,0); - // USER-DIELECTRIC package + // DIELECTRIC package add_peratom("area",&area,DOUBLE,0); add_peratom("ed",&ed,DOUBLE,0); @@ -1280,6 +1288,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, bond_type[m][num_bond[m]] = itype; bond_atom[m][num_bond[m]] = atom2; num_bond[m]++; + avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset); } } if (newton_bond == 0) { @@ -1289,6 +1298,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, bond_type[m][num_bond[m]] = itype; bond_atom[m][num_bond[m]] = atom1; num_bond[m]++; + avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset); } } } @@ -2186,7 +2196,7 @@ void Atom::setup_sort_bins() bininvy = nbiny / (bboxhi[1]-bboxlo[1]); bininvz = nbinz / (bboxhi[2]-bboxlo[2]); -#ifdef LMP_USER_INTEL +#ifdef LMP_INTEL int intel_neigh = 0; if (neighbor->nrequest) { if (neighbor->requests[0]->intel) intel_neigh = 1; @@ -2646,7 +2656,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"cv") == 0) return (void *) cv; if (strcmp(name,"vest") == 0) return (void *) vest; - // USER-MESONT package + // MESONT package if (strcmp(name,"length") == 0) return (void *) length; if (strcmp(name,"buckling") == 0) return (void *) buckling; if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt; @@ -2663,7 +2673,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; - // USER-DIELECTRIC + // DIELECTRIC if (strcmp(name,"area") == 0) return (void *) area; if (strcmp(name,"ed") == 0) return (void *) ed; if (strcmp(name,"em") == 0) return (void *) em; @@ -2739,7 +2749,7 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D; - // USER-MESONT package + // MESONT package if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"buckling") == 0) return LAMMPS_INT; if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D; @@ -2754,7 +2764,7 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE; - // USER-DIELECTRIC + // DIELECTRIC if (strcmp(name,"area") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"ed") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"em") == 0) return LAMMPS_DOUBLE; diff --git a/src/atom.h b/src/atom.h index 392e5c5d5c..daf2f04f8a 100644 --- a/src/atom.h +++ b/src/atom.h @@ -114,7 +114,7 @@ class Atom : protected Pointers { double **sp, **fm, **fm_long; - // USER_EFF and USER-AWPMD packages + // EFF and AWPMD packages int *spin; double *eradius, *ervel, *erforce; @@ -122,14 +122,18 @@ class Atom : protected Pointers { double **cs, **csforce, **vforce; int *etag; - // USER-DPD package + // CG-DNA package + + tagint *id5p; + + // DPD-REACT package double *uCond, *uMech, *uChem, *uCGnew, *uCG; double *duChem; double *dpdTheta; int nspecies_dpd; - // USER-MESO package + // MESO package double **cc, **cc_flux; // cc = chemical concentration double *edpd_temp, *edpd_flux; // temperature and heat flux @@ -137,13 +141,13 @@ class Atom : protected Pointers { double *edpd_cv; // heat capacity int cc_species; - // USER-MESONT package + // MESONT package double *length; int *buckling; tagint **bond_nt; - // USER-SMD package + // MACHDYN package double *contact_radius; double **smd_data_9; @@ -152,12 +156,12 @@ class Atom : protected Pointers { double *eff_plastic_strain_rate; double *damage; - // USER-SPH package + // SPH package double *rho, *drho, *esph, *desph, *cv; double **vest; - // USER-DIELECTRIC package + // DIELECTRIC package double *area,*ed,*em,*epsilon,*curvature,*q_unscaled; @@ -187,7 +191,7 @@ class Atom : protected Pointers { int sp_flag; - // USER-SMD package + // MACHDYN package int x0_flag; int smd_flag, damage_flag; @@ -275,7 +279,7 @@ class Atom : protected Pointers { // functions Atom(class LAMMPS *); - ~Atom(); + virtual ~Atom(); void settings(class Atom *); void peratom_create(); @@ -364,12 +368,12 @@ class Atom : protected Pointers { return -1; }; - void map_init(int check = 1); - void map_clear(); - void map_set(); + virtual void map_init(int check = 1); + virtual void map_clear(); + virtual void map_set(); void map_one(tagint, int); int map_style_set(); - void map_delete(); + virtual void map_delete(); int map_find_hash(tagint); protected: diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 95f09d2639..2eb4a08ea6 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -309,7 +309,7 @@ int Atom::map_style_set() if (map_user == MAP_ARRAY || map_user == MAP_HASH) { map_style = map_user; } else { // map_user == MAP_YES - if (map_tag_max > 1000000 && !lmp->kokkos) map_style = MAP_HASH; + if (map_tag_max > 1000000) map_style = MAP_HASH; else map_style = MAP_ARRAY; } diff --git a/src/atom_vec.h b/src/atom_vec.h index a65fd17dcd..ad3b4c6626 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -129,6 +129,8 @@ class AtomVec : protected Pointers { virtual void data_atom_bonus(int, char **) {} virtual void data_body(int, int, int, int *, double *) {} + virtual void data_bonds_post(int, int , tagint, tagint, tagint) {} + virtual void pack_data(double **); virtual void write_data(FILE *, int, double **); virtual void pack_data_pre(int) {} diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 4327420cee..0bffde2129 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -438,6 +438,17 @@ void AtomVecHybrid::data_atom_post(int ilocal) styles[k]->data_atom_post(ilocal); } +/* ---------------------------------------------------------------------- + modify what AtomVec::data_bonds() just unpacked + or initialize other bond quantities +------------------------------------------------------------------------- */ +void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1, + tagint atom2, tagint id_offset) +{ + for (int k = 0; k < nstyles; k++) + styles[k]->data_bonds_post(m, num_bond, atom1, atom2, id_offset); +} + /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index 3c804a462c..949ae37319 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -55,6 +55,9 @@ class AtomVecHybrid : public AtomVec { void unpack_restart_init(int); void create_atom_post(int); void data_atom_post(int); + + void data_bonds_post(int, int, tagint, tagint, tagint); + void pack_data_pre(int); void pack_data_post(int); diff --git a/src/balance.cpp b/src/balance.cpp index af142f404d..feb5eae708 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -499,8 +499,7 @@ void Balance::weight_storage(char *prefix) int ifix = modify->find_fix(cmd); if (ifix < 1) { cmd += " all STORE peratom 0 1"; - modify->add_fix(cmd); - fixstore = (FixStore *) modify->fix[modify->nfix-1]; + fixstore = (FixStore *) modify->add_fix(cmd); } else fixstore = (FixStore *) modify->fix[ifix]; // do not carry weights with atoms during normal atom migration diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 920c251f55..dad1010a1e 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -21,8 +20,8 @@ #include "memory.h" #include "neighbor.h" -#include #include +#include using namespace LAMMPS_NS; @@ -46,19 +45,18 @@ BondHybrid::~BondHybrid() { if (nstyles) { for (int i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (int i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] nbondlist; - delete [] maxbond; - for (int i = 0; i < nstyles; i++) - memory->destroy(bondlist[i]); - delete [] bondlist; + delete[] nbondlist; + delete[] maxbond; + for (int i = 0; i < nstyles; i++) memory->destroy(bondlist[i]); + delete[] bondlist; } } @@ -66,7 +64,7 @@ BondHybrid::~BondHybrid() void BondHybrid::compute(int eflag, int vflag) { - int i,j,m,n; + int i, j, m, n; // save ptrs to original bondlist @@ -88,7 +86,7 @@ void BondHybrid::compute(int eflag, int vflag) if (nbondlist[m] > maxbond[m]) { memory->destroy(bondlist[m]); maxbond[m] = nbondlist[m] + EXTRA; - memory->create(bondlist[m],maxbond[m],3,"bond_hybrid:bondlist"); + memory->create(bondlist[m], maxbond[m], 3, "bond_hybrid:bondlist"); } nbondlist[m] = 0; } @@ -107,7 +105,7 @@ void BondHybrid::compute(int eflag, int vflag) // set neighbor->bondlist to sub-style bondlist before call // accumulate sub-style global/peratom energy/virial in hybrid - ev_init(eflag,vflag); + ev_init(eflag, vflag); // need to clear per-thread storage once here, when using multiple threads // with thread-enabled substyles to avoid uninitlialized data access. @@ -115,17 +113,15 @@ void BondHybrid::compute(int eflag, int vflag) const int nthreads = comm->nthreads; if (nthreads > 1) { const bigint nall = atom->nlocal + atom->nghost; - if (eflag_atom) - memset(&eatom[0],0,nall*nthreads*sizeof(double)); - if (vflag_atom) - memset(&vatom[0][0],0,6*nall*nthreads*sizeof(double)); + if (eflag_atom) memset(&eatom[0], 0, nall * nthreads * sizeof(double)); + if (vflag_atom) memset(&vatom[0][0], 0, 6 * nall * nthreads * sizeof(double)); } for (m = 0; m < nstyles; m++) { neighbor->nbondlist = nbondlist[m]; neighbor->bondlist = bondlist[m]; - styles[m]->compute(eflag,vflag); + styles[m]->compute(eflag, vflag); if (eflag_global) energy += styles[m]->energy; if (vflag_global) @@ -141,8 +137,7 @@ void BondHybrid::compute(int eflag, int vflag) if (force->newton_bond) n += atom->nghost; double **vatom_substyle = styles[m]->vatom; for (i = 0; i < n; i++) - for (j = 0; j < 6; j++) - vatom[i][j] += vatom_substyle[i][j]; + for (j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j]; } } @@ -159,13 +154,13 @@ void BondHybrid::allocate() allocated = 1; int n = atom->nbondtypes; - memory->create(map,n+1,"bond:map"); - memory->create(setflag,n+1,"bond:setflag"); + memory->create(map, n + 1, "bond:map"); + memory->create(setflag, n + 1, "bond:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; nbondlist = new int[nstyles]; maxbond = new int[nstyles]; - bondlist = new int**[nstyles]; + bondlist = new int **[nstyles]; for (int m = 0; m < nstyles; m++) maxbond[m] = 0; for (int m = 0; m < nstyles; m++) bondlist[m] = nullptr; } @@ -176,28 +171,27 @@ void BondHybrid::allocate() void BondHybrid::settings(int narg, char **arg) { - int i,m,istyle; + int i, m, istyle; - if (narg < 1) error->all(FLERR,"Illegal bond_style command"); + if (narg < 1) error->all(FLERR, "Illegal bond_style command"); // delete old lists, since cannot just change settings if (nstyles) { for (i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; has_quartic = -1; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] nbondlist; - delete [] maxbond; - for (i = 0; i < nstyles; i++) - memory->destroy(bondlist[i]); - delete [] bondlist; + delete[] nbondlist; + delete[] maxbond; + for (i = 0; i < nstyles; i++) memory->destroy(bondlist[i]); + delete[] bondlist; } allocated = 0; @@ -208,7 +202,7 @@ void BondHybrid::settings(int narg, char **arg) nstyles = 0; i = 0; while (i < narg) { - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; nstyles++; @@ -216,8 +210,8 @@ void BondHybrid::settings(int narg, char **arg) // allocate list of sub-styles - styles = new Bond*[nstyles]; - keywords = new char*[nstyles]; + styles = new Bond *[nstyles]; + keywords = new char *[nstyles]; // allocate each sub-style and call its settings() with subset of args // allocate uses suffix, but don't store suffix version in keywords, @@ -233,29 +227,28 @@ void BondHybrid::settings(int narg, char **arg) while (i < narg) { for (m = 0; m < nstyles; m++) - if (strcmp(arg[i],keywords[m]) == 0) - error->all(FLERR,"Bond style hybrid cannot use same bond style twice"); + if (strcmp(arg[i], keywords[m]) == 0) + error->all(FLERR, "Bond style hybrid cannot use same bond style twice"); - if (strcmp(arg[i],"hybrid") == 0) - error->all(FLERR,"Bond style hybrid cannot have hybrid as an argument"); + if (strcmp(arg[i], "hybrid") == 0) + error->all(FLERR, "Bond style hybrid cannot have hybrid as an argument"); - if (strcmp(arg[i],"none") == 0) - error->all(FLERR,"Bond style hybrid cannot have none as an argument"); + if (strcmp(arg[i], "none") == 0) + error->all(FLERR, "Bond style hybrid cannot have none as an argument"); // register index of quartic bond type, // so that bond type 0 can be mapped to it - if (strncmp(arg[i],"quartic",7) == 0) - has_quartic = m; + if (strncmp(arg[i], "quartic", 7) == 0) has_quartic = m; - styles[nstyles] = force->new_bond(arg[i],1,dummy); - force->store_style(keywords[nstyles],arg[i],0); + styles[nstyles] = force->new_bond(arg[i], 1, dummy); + force->store_style(keywords[nstyles], arg[i], 0); istyle = i; - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; - styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]); + styles[nstyles]->settings(i - istyle - 1, &arg[istyle + 1]); nstyles++; } } @@ -268,20 +261,22 @@ void BondHybrid::coeff(int narg, char **arg) { if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); // 2nd arg = bond sub-style name // allow for "none" as valid sub-style name int m; for (m = 0; m < nstyles; m++) - if (strcmp(arg[1],keywords[m]) == 0) break; + if (strcmp(arg[1], keywords[m]) == 0) break; int none = 0; if (m == nstyles) { - if (strcmp(arg[1],"none") == 0) none = 1; - else error->all(FLERR,"Bond coeff for hybrid has invalid style"); + if (strcmp(arg[1], "none") == 0) + none = 1; + else + error->all(FLERR, "Bond coeff for hybrid has invalid style"); } // move 1st arg to 2nd arg @@ -291,15 +286,17 @@ void BondHybrid::coeff(int narg, char **arg) // invoke sub-style coeff() starting with 1st arg - if (!none) styles[m]->coeff(narg-1,&arg[1]); + if (!none) styles[m]->coeff(narg - 1, &arg[1]); // set setflag and which type maps to which sub-style // if sub-style is none: set hybrid setflag, wipe out map for (int i = ilo; i <= ihi; i++) { setflag[i] = 1; - if (none) map[i] = -1; - else map[i] = m; + if (none) + map[i] = -1; + else + map[i] = m; } } @@ -313,8 +310,7 @@ void BondHybrid::init_style() // bond style quartic will set broken bonds to bond type 0, so we need // to create an entry for it in the bond type to sub-style map - if (has_quartic >= 0) - map[0] = has_quartic; + if (has_quartic >= 0) map[0] = has_quartic; } /* ---------------------------------------------------------------------- @@ -323,8 +319,7 @@ void BondHybrid::init_style() double BondHybrid::equilibrium_distance(int i) { - if (map[i] < 0) - error->one(FLERR,"Invoked bond equil distance on bond style none"); + if (map[i] < 0) error->one(FLERR, "Invoked bond equil distance on bond style none"); return styles[map[i]]->equilibrium_distance(i); } @@ -334,13 +329,13 @@ double BondHybrid::equilibrium_distance(int i) void BondHybrid::write_restart(FILE *fp) { - fwrite(&nstyles,sizeof(int),1,fp); + fwrite(&nstyles, sizeof(int), 1, fp); int n; for (int m = 0; m < nstyles; m++) { n = strlen(keywords[m]) + 1; - fwrite(&n,sizeof(int),1,fp); - fwrite(keywords[m],sizeof(char),n,fp); + fwrite(&n, sizeof(int), 1, fp); + fwrite(keywords[m], sizeof(char), n, fp); styles[m]->write_restart_settings(fp); } } @@ -352,33 +347,32 @@ void BondHybrid::write_restart(FILE *fp) void BondHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&nstyles,1,MPI_INT,0,world); - styles = new Bond*[nstyles]; - keywords = new char*[nstyles]; + if (me == 0) utils::sfread(FLERR, &nstyles, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&nstyles, 1, MPI_INT, 0, world); + styles = new Bond *[nstyles]; + keywords = new char *[nstyles]; allocate(); - int n,dummy; + int n, dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&n,1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &n, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&n, 1, MPI_INT, 0, world); keywords[m] = new char[n]; - if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,nullptr,error); - MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); - styles[m] = force->new_bond(keywords[m],0,dummy); + if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error); + MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world); + styles[m] = force->new_bond(keywords[m], 0, dummy); styles[m]->read_restart_settings(fp); } } /* ---------------------------------------------------------------------- */ -double BondHybrid::single(int type, double rsq, int i, int j, - double &fforce) +double BondHybrid::single(int type, double rsq, int i, int j, double &fforce) { - if (map[type] < 0) error->one(FLERR,"Invoked bond single on bond style none"); - return styles[map[type]]->single(type,rsq,i,j,fforce); + if (map[type] < 0) error->one(FLERR, "Invoked bond single on bond style none"); + return styles[map[type]]->single(type, rsq, i, j, fforce); } /* ---------------------------------------------------------------------- @@ -387,9 +381,9 @@ double BondHybrid::single(int type, double rsq, int i, int j, double BondHybrid::memory_usage() { - double bytes = (double)maxeatom * sizeof(double); - bytes += (double)maxvatom*6 * sizeof(double); - for (int m = 0; m < nstyles; m++) bytes += (double)maxbond[m]*3 * sizeof(int); + double bytes = (double) maxeatom * sizeof(double); + bytes += (double) maxvatom * 6 * sizeof(double); + for (int m = 0; m < nstyles; m++) bytes += (double) maxbond[m] * 3 * sizeof(int); for (int m = 0; m < nstyles; m++) if (styles[m]) bytes += styles[m]->memory_usage(); return bytes; diff --git a/src/comm.h b/src/comm.h index e7c07522a9..bc5faa49f4 100644 --- a/src/comm.h +++ b/src/comm.h @@ -281,6 +281,6 @@ UNDOCUMENTED U: OMP_NUM_THREADS environment is not set. This environment variable must be set appropriately to use the -USER-OMP package. +OPENMP package. */ diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 81eafcf8d6..5d789f722a 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -562,13 +562,9 @@ void ComputeChunkAtom::init() // fixstore initializes all values to 0.0 if ((idsflag == ONCE || lockcount) && !fixstore) { - std::string cmd = id + std::string("_COMPUTE_STORE"); - id_fix = new char[cmd.size()+1]; - strcpy(id_fix,cmd.c_str()); - - cmd += fmt::format(" {} STORE peratom 1 1", group->names[igroup]); - modify->add_fix(cmd); - fixstore = (FixStore *) modify->fix[modify->nfix-1]; + id_fix = utils::strdup(id + std::string("_COMPUTE_STORE")); + fixstore = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 1", + id_fix, group->names[igroup])); } if ((idsflag != ONCE && !lockcount) && fixstore) { diff --git a/src/compute_dipole.cpp b/src/compute_dipole.cpp index 053f11e6f9..b67c3df3ce 100644 --- a/src/compute_dipole.cpp +++ b/src/compute_dipole.cpp @@ -29,7 +29,7 @@ enum { MASSCENTER, GEOMCENTER }; ComputeDipole::ComputeDipole(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg != 3) error->all(FLERR, "Illegal compute com command"); + if ((narg < 3) || (narg > 4)) error->all(FLERR, "Illegal compute dipole command"); scalar_flag = 1; vector_flag = 1; @@ -39,11 +39,8 @@ ComputeDipole::ComputeDipole(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, n vector = new double[size_vector]; vector[0] = vector[1] = vector[2] = 0.0; - usecenter = MASSCENTER; - if ((narg != 3) && (narg != 4)) error->all(FLERR, "Illegal compute dipole command"); - if (narg == 4) { if (utils::strmatch(arg[3], "^geom")) usecenter = GEOMCENTER; diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index 68776c1936..821525c53a 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -74,10 +74,8 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) : // id = compute-ID + COMPUTE_STORE, fix group = compute group id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE"); - std::string cmd = id_fix + fmt::format(" {} STORE peratom 1 3", - group->names[igroup]); - modify->add_fix(cmd); - fix = (FixStore *) modify->fix[modify->nfix-1]; + fix = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 3", + id_fix, group->names[igroup])); // calculate xu,yu,zu for fix store array // skip if reset from restart file diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index ce9e10304e..209eec2810 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -14,16 +14,15 @@ #include "compute_msd.h" -#include - #include "atom.h" -#include "update.h" -#include "group.h" #include "domain.h" -#include "modify.h" -#include "fix_store.h" #include "error.h" +#include "fix_store.h" +#include "group.h" +#include "modify.h" +#include "update.h" +#include using namespace LAMMPS_NS; @@ -66,13 +65,9 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : // create a new fix STORE style for reference positions // id = compute-ID + COMPUTE_STORE, fix group = compute group - std::string fixcmd = id + std::string("_COMPUTE_STORE"); - id_fix = new char[fixcmd.size()+1]; - strcpy(id_fix,fixcmd.c_str()); - - fixcmd += fmt::format(" {} STORE peratom 1 3",group->names[igroup]); - modify->add_fix(fixcmd); - fix = (FixStore *) modify->fix[modify->nfix-1]; + id_fix = utils::strdup(id + std::string("_COMPUTE_STORE")); + fix = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 3", + id_fix, group->names[igroup])); // calculate xu,yu,zu for fix store array // skip if reset from restart file diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 74528da2f6..0d5b146338 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -14,18 +14,17 @@ #include "compute_msd_chunk.h" -#include - #include "atom.h" -#include "group.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "fix_store.h" -#include "memory.h" #include "error.h" +#include "fix_store.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include using namespace LAMMPS_NS; @@ -52,16 +51,14 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) : // create a new fix STORE style for reference positions // id = compute-ID + COMPUTE_STORE, fix group = compute group - // do not know size of array at this point, just allocate 1x3 array + // do not know size of array at this point, just allocate 1x1 array // fix creation must be done now so that a restart run can // potentially re-populate the fix array (and change it to correct size) // otherwise size reset and init will be done in setup() id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE"); - std::string fixcmd = id_fix - + fmt::format(" {} STORE global 1 1",group->names[igroup]); - modify->add_fix(fixcmd); - fix = (FixStore *) modify->fix[modify->nfix-1]; + fix = (FixStore *) modify->add_fix(fmt::format("{} {} STORE global 1 1", + id_fix,group->names[igroup])); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index a5bf54d5ef..7e1b6fc062 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -14,12 +14,13 @@ #include "compute_pair.h" -#include -#include -#include "update.h" +#include "error.h" #include "force.h" #include "pair.h" -#include "error.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -89,9 +90,9 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) : ComputePair::~ComputePair() { - delete [] pstyle; - delete [] one; - delete [] vector; + delete[] pstyle; + delete[] one; + delete[] vector; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index 7fd6d876ed..fce18fecd1 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -13,32 +12,34 @@ ------------------------------------------------------------------------- */ #include "compute_property_local.h" -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include using namespace LAMMPS_NS; -enum{NONE,NEIGH,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER}; -enum{TYPE,RADIUS}; +enum { NONE, NEIGH, PAIR, BOND, ANGLE, DIHEDRAL, IMPROPER }; +enum { TYPE, RADIUS }; #define DELTA 10000 /* ---------------------------------------------------------------------- */ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), - vlocal(NULL), alocal(NULL), indices(NULL), pack_choice(NULL) + Compute(lmp, narg, arg), vlocal(nullptr), alocal(nullptr), indices(nullptr), + pack_choice(nullptr) { - if (narg < 4) error->all(FLERR,"Illegal compute property/local command"); + if (narg < 4) error->all(FLERR, "Illegal compute property/local command"); local_flag = 1; nvalues = narg - 3; @@ -50,220 +51,198 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : nvalues = 0; int iarg = 3; while (iarg < narg) { - i = iarg-3; + i = iarg - 3; - if (strcmp(arg[iarg],"natom1") == 0) { + if (strcmp(arg[iarg], "natom1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_patom1; if (kindflag != NONE && kindflag != NEIGH) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = NEIGH; - } else if (strcmp(arg[iarg],"natom2") == 0) { + } else if (strcmp(arg[iarg], "natom2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_patom2; if (kindflag != NONE && kindflag != NEIGH) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = NEIGH; - } else if (strcmp(arg[iarg],"ntype1") == 0) { + } else if (strcmp(arg[iarg], "ntype1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_ptype1; if (kindflag != NONE && kindflag != NEIGH) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = NEIGH; - } else if (strcmp(arg[iarg],"ntype2") == 0) { + } else if (strcmp(arg[iarg], "ntype2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_ptype2; if (kindflag != NONE && kindflag != NEIGH) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = NEIGH; - } else if (strcmp(arg[iarg],"patom1") == 0) { + } else if (strcmp(arg[iarg], "patom1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_patom1; if (kindflag != NONE && kindflag != PAIR) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = PAIR; - } else if (strcmp(arg[iarg],"patom2") == 0) { + } else if (strcmp(arg[iarg], "patom2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_patom2; if (kindflag != NONE && kindflag != PAIR) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = PAIR; - } else if (strcmp(arg[iarg],"ptype1") == 0) { + } else if (strcmp(arg[iarg], "ptype1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_ptype1; if (kindflag != NONE && kindflag != PAIR) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = PAIR; - } else if (strcmp(arg[iarg],"ptype2") == 0) { + } else if (strcmp(arg[iarg], "ptype2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_ptype2; if (kindflag != NONE && kindflag != PAIR) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = PAIR; - } else if (strcmp(arg[iarg],"batom1") == 0) { + } else if (strcmp(arg[iarg], "batom1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_batom1; if (kindflag != NONE && kindflag != BOND) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = BOND; - } else if (strcmp(arg[iarg],"batom2") == 0) { + } else if (strcmp(arg[iarg], "batom2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_batom2; if (kindflag != NONE && kindflag != BOND) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = BOND; - } else if (strcmp(arg[iarg],"btype") == 0) { + } else if (strcmp(arg[iarg], "btype") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_btype; if (kindflag != NONE && kindflag != BOND) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = BOND; - } else if (strcmp(arg[iarg],"aatom1") == 0) { + } else if (strcmp(arg[iarg], "aatom1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_aatom1; if (kindflag != NONE && kindflag != ANGLE) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = ANGLE; - } else if (strcmp(arg[iarg],"aatom2") == 0) { + } else if (strcmp(arg[iarg], "aatom2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_aatom2; if (kindflag != NONE && kindflag != ANGLE) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = ANGLE; - } else if (strcmp(arg[iarg],"aatom3") == 0) { + } else if (strcmp(arg[iarg], "aatom3") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_aatom3; if (kindflag != NONE && kindflag != ANGLE) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = ANGLE; - } else if (strcmp(arg[iarg],"atype") == 0) { + } else if (strcmp(arg[iarg], "atype") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_atype; if (kindflag != NONE && kindflag != ANGLE) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = ANGLE; - } else if (strcmp(arg[iarg],"datom1") == 0) { + } else if (strcmp(arg[iarg], "datom1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_datom1; if (kindflag != NONE && kindflag != DIHEDRAL) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = DIHEDRAL; - } else if (strcmp(arg[iarg],"datom2") == 0) { + } else if (strcmp(arg[iarg], "datom2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_datom2; if (kindflag != NONE && kindflag != DIHEDRAL) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = DIHEDRAL; - } else if (strcmp(arg[iarg],"datom3") == 0) { + } else if (strcmp(arg[iarg], "datom3") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_datom3; if (kindflag != NONE && kindflag != DIHEDRAL) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = DIHEDRAL; - } else if (strcmp(arg[iarg],"datom4") == 0) { + } else if (strcmp(arg[iarg], "datom4") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_datom4; if (kindflag != NONE && kindflag != DIHEDRAL) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = DIHEDRAL; - } else if (strcmp(arg[iarg],"dtype") == 0) { + } else if (strcmp(arg[iarg], "dtype") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_dtype; if (kindflag != NONE && kindflag != DIHEDRAL) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = DIHEDRAL; - } else if (strcmp(arg[iarg],"iatom1") == 0) { + } else if (strcmp(arg[iarg], "iatom1") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_iatom1; if (kindflag != NONE && kindflag != IMPROPER) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = IMPROPER; - } else if (strcmp(arg[iarg],"iatom2") == 0) { + } else if (strcmp(arg[iarg], "iatom2") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_iatom2; if (kindflag != NONE && kindflag != IMPROPER) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = IMPROPER; - } else if (strcmp(arg[iarg],"iatom3") == 0) { + } else if (strcmp(arg[iarg], "iatom3") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_iatom3; if (kindflag != NONE && kindflag != IMPROPER) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = IMPROPER; - } else if (strcmp(arg[iarg],"iatom4") == 0) { + } else if (strcmp(arg[iarg], "iatom4") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_iatom4; if (kindflag != NONE && kindflag != IMPROPER) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = IMPROPER; - } else if (strcmp(arg[iarg],"itype") == 0) { + } else if (strcmp(arg[iarg], "itype") == 0) { pack_choice[i] = &ComputePropertyLocal::pack_itype; if (kindflag != NONE && kindflag != IMPROPER) - error->all(FLERR, - "Compute property/local cannot use these inputs together"); + error->all(FLERR, "Compute property/local cannot use these inputs together"); kindflag = IMPROPER; - } else break; + } else + break; nvalues++; iarg++; } - if (nvalues == 1) size_local_cols = 0; - else size_local_cols = nvalues; + if (nvalues == 1) + size_local_cols = 0; + else + size_local_cols = nvalues; // optional args cutstyle = TYPE; while (iarg < narg) { - if (strcmp(arg[iarg],"cutoff") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal compute property/local command"); - if (strcmp(arg[iarg+1],"type") == 0) cutstyle = TYPE; - else if (strcmp(arg[iarg+1],"radius") == 0) cutstyle = RADIUS; - else error->all(FLERR,"Illegal compute property/local command"); + if (strcmp(arg[iarg], "cutoff") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute property/local command"); + if (strcmp(arg[iarg + 1], "type") == 0) + cutstyle = TYPE; + else if (strcmp(arg[iarg + 1], "radius") == 0) + cutstyle = RADIUS; + else + error->all(FLERR, "Illegal compute property/local command"); iarg += 2; - } else error->all(FLERR,"Illegal compute property/local command"); + } else + error->all(FLERR, "Illegal compute property/local command"); } // error check - if (atom->molecular == 2 && (kindflag == BOND || kindflag == ANGLE || - kindflag == DIHEDRAL || kindflag == IMPROPER)) - error->all(FLERR,"Compute property/local does not (yet) work " + if (atom->molecular == 2 && + (kindflag == BOND || kindflag == ANGLE || kindflag == DIHEDRAL || kindflag == IMPROPER)) + error->all(FLERR, + "Compute property/local does not (yet) work " "with atom_style template"); if (kindflag == BOND && atom->avec->bonds_allow == 0) - error->all(FLERR, - "Compute property/local for property that isn't allocated"); + error->all(FLERR, "Compute property/local for property that isn't allocated"); if (kindflag == ANGLE && atom->avec->angles_allow == 0) - error->all(FLERR, - "Compute property/local for property that isn't allocated"); + error->all(FLERR, "Compute property/local for property that isn't allocated"); if (kindflag == DIHEDRAL && atom->avec->dihedrals_allow == 0) - error->all(FLERR, - "Compute property/local for property that isn't allocated"); + error->all(FLERR, "Compute property/local for property that isn't allocated"); if (kindflag == IMPROPER && atom->avec->impropers_allow == 0) - error->all(FLERR, - "Compute property/local for property that isn't allocated"); + error->all(FLERR, "Compute property/local for property that isn't allocated"); if (cutstyle == RADIUS && !atom->radius_flag) - error->all(FLERR,"Compute property/local requires atom attribute radius"); + error->all(FLERR, "Compute property/local requires atom attribute radius"); nmax = 0; - vlocal = NULL; - alocal = NULL; + vlocal = nullptr; + alocal = nullptr; } /* ---------------------------------------------------------------------- */ ComputePropertyLocal::~ComputePropertyLocal() { - delete [] pack_choice; + delete[] pack_choice; memory->destroy(vlocal); memory->destroy(alocal); memory->destroy(indices); @@ -274,10 +253,10 @@ ComputePropertyLocal::~ComputePropertyLocal() void ComputePropertyLocal::init() { if (kindflag == NEIGH || kindflag == PAIR) { - if (force->pair == NULL) - error->all(FLERR,"No pair style is defined for compute property/local"); + if (force->pair == nullptr) + error->all(FLERR, "No pair style is defined for compute property/local"); if (force->pair->single_enable == 0) - error->all(FLERR,"Pair style does not support compute property/local"); + error->all(FLERR, "Pair style does not support compute property/local"); } // for NEIGH/PAIR need an occasional half neighbor list @@ -285,7 +264,7 @@ void ComputePropertyLocal::init() // this should enable it to always be a copy list (e.g. for granular pstyle) if (kindflag == NEIGH || kindflag == PAIR) { - int irequest = neighbor->request(this,instance_me); + int irequest = neighbor->request(this, instance_me); neighbor->requests[irequest]->pair = 0; neighbor->requests[irequest]->compute = 1; neighbor->requests[irequest]->occasional = 1; @@ -296,12 +275,18 @@ void ComputePropertyLocal::init() // do initial memory allocation so that memory_usage() is correct // cannot be done yet for NEIGH/PAIR, since neigh list does not exist - if (kindflag == NEIGH) ncount = 0; - else if (kindflag == PAIR) ncount = 0; - else if (kindflag == BOND) ncount = count_bonds(0); - else if (kindflag == ANGLE) ncount = count_angles(0); - else if (kindflag == DIHEDRAL) ncount = count_dihedrals(0); - else if (kindflag == IMPROPER) ncount = count_impropers(0); + if (kindflag == NEIGH) + ncount = 0; + else if (kindflag == PAIR) + ncount = 0; + else if (kindflag == BOND) + ncount = count_bonds(0); + else if (kindflag == ANGLE) + ncount = count_angles(0); + else if (kindflag == DIHEDRAL) + ncount = count_dihedrals(0); + else if (kindflag == IMPROPER) + ncount = count_impropers(0); if (ncount > nmax) reallocate(ncount); size_local_rows = ncount; @@ -322,22 +307,34 @@ void ComputePropertyLocal::compute_local() // count local entries and generate list of indices - if (kindflag == NEIGH) ncount = count_pairs(0,0); - else if (kindflag == PAIR) ncount = count_pairs(0,1); - else if (kindflag == BOND) ncount = count_bonds(0); - else if (kindflag == ANGLE) ncount = count_angles(0); - else if (kindflag == DIHEDRAL) ncount = count_dihedrals(0); - else if (kindflag == IMPROPER) ncount = count_impropers(0); + if (kindflag == NEIGH) + ncount = count_pairs(0, 0); + else if (kindflag == PAIR) + ncount = count_pairs(0, 1); + else if (kindflag == BOND) + ncount = count_bonds(0); + else if (kindflag == ANGLE) + ncount = count_angles(0); + else if (kindflag == DIHEDRAL) + ncount = count_dihedrals(0); + else if (kindflag == IMPROPER) + ncount = count_impropers(0); if (ncount > nmax) reallocate(ncount); size_local_rows = ncount; - if (kindflag == NEIGH) ncount = count_pairs(1,0); - else if (kindflag == PAIR) ncount = count_pairs(1,1); - else if (kindflag == BOND) ncount = count_bonds(1); - else if (kindflag == ANGLE) ncount = count_angles(1); - else if (kindflag == DIHEDRAL) ncount = count_dihedrals(1); - else if (kindflag == IMPROPER) ncount = count_impropers(1); + if (kindflag == NEIGH) + ncount = count_pairs(1, 0); + else if (kindflag == PAIR) + ncount = count_pairs(1, 1); + else if (kindflag == BOND) + ncount = count_bonds(1); + else if (kindflag == ANGLE) + ncount = count_angles(1); + else if (kindflag == DIHEDRAL) + ncount = count_dihedrals(1); + else if (kindflag == IMPROPER) + ncount = count_impropers(1); // fill vector or array with local values @@ -346,8 +343,7 @@ void ComputePropertyLocal::compute_local() (this->*pack_choice[0])(0); } else { if (alocal) buf = &alocal[0][0]; - for (int n = 0; n < nvalues; n++) - (this->*pack_choice[n])(n); + for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n); } } @@ -361,10 +357,10 @@ void ComputePropertyLocal::compute_local() int ComputePropertyLocal::count_pairs(int allflag, int forceflag) { - int i,j,m,ii,jj,inum,jnum,itype,jtype; - tagint itag,jtag; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq,radsum; - int *ilist,*jlist,*numneigh,**firstneigh; + int i, j, m, ii, jj, inum, jnum, itype, jtype; + tagint itag, jtag; + double xtmp, ytmp, ztmp, delx, dely, delz, rsq, radsum; + int *ilist, *jlist, *numneigh, **firstneigh; double **x = atom->x; double *radius = atom->radius; @@ -415,9 +411,9 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag) if (newton_pair == 0 && j >= nlocal) { jtag = tag[j]; if (itag > jtag) { - if ((itag+jtag) % 2 == 0) continue; + if ((itag + jtag) % 2 == 0) continue; } else if (itag < jtag) { - if ((itag+jtag) % 2 == 1) continue; + if ((itag + jtag) % 2 == 1) continue; } else { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -430,14 +426,14 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + rsq = delx * delx + dely * dely + delz * delz; jtype = type[j]; if (forceflag) { if (cutstyle == TYPE) { if (rsq >= cutsq[itype][jtype]) continue; } else { radsum = radius[i] + radius[j]; - if (rsq >= radsum*radsum) continue; + if (rsq >= radsum * radsum) continue; } } @@ -463,7 +459,7 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag) int ComputePropertyLocal::count_bonds(int flag) { - int i,atom1,atom2; + int i, atom1, atom2; int *num_bond = atom->num_bond; tagint **bond_atom = atom->bond_atom; @@ -504,7 +500,7 @@ int ComputePropertyLocal::count_bonds(int flag) int ComputePropertyLocal::count_angles(int flag) { - int i,atom1,atom2,atom3; + int i, atom1, atom2, atom3; int *num_angle = atom->num_angle; tagint **angle_atom1 = atom->angle_atom1; @@ -546,7 +542,7 @@ int ComputePropertyLocal::count_angles(int flag) int ComputePropertyLocal::count_dihedrals(int flag) { - int i,atom1,atom2,atom3,atom4; + int i, atom1, atom2, atom3, atom4; int *num_dihedral = atom->num_dihedral; tagint **dihedral_atom1 = atom->dihedral_atom1; @@ -589,7 +585,7 @@ int ComputePropertyLocal::count_dihedrals(int flag) int ComputePropertyLocal::count_impropers(int flag) { - int i,atom1,atom2,atom3,atom4; + int i, atom1, atom2, atom3, atom4; int *num_improper = atom->num_improper; tagint **improper_atom1 = atom->improper_atom1; @@ -633,16 +629,16 @@ void ComputePropertyLocal::reallocate(int n) if (nvalues == 1) { memory->destroy(vlocal); - memory->create(vlocal,nmax,"property/local:vector_local"); + memory->create(vlocal, nmax, "property/local:vector_local"); vector_local = vlocal; } else { memory->destroy(alocal); - memory->create(alocal,nmax,nvalues,"property/local:array_local"); + memory->create(alocal, nmax, nvalues, "property/local:array_local"); array_local = alocal; } memory->destroy(indices); - memory->create(indices,nmax,2,"property/local:indices"); + memory->create(indices, nmax, 2, "property/local:indices"); } /* ---------------------------------------------------------------------- @@ -651,8 +647,8 @@ void ComputePropertyLocal::reallocate(int n) double ComputePropertyLocal::memory_usage() { - double bytes = (double)nmax*nvalues * sizeof(double); - bytes += (double)nmax*2 * sizeof(int); + double bytes = (double) nmax * nvalues * sizeof(double); + bytes += (double) nmax * 2 * sizeof(int); return bytes; } @@ -736,7 +732,7 @@ void ComputePropertyLocal::pack_batom1(int n) void ComputePropertyLocal::pack_batom2(int n) { - int i,j; + int i, j; tagint **bond_atom = atom->bond_atom; for (int m = 0; m < ncount; m++) { @@ -751,7 +747,7 @@ void ComputePropertyLocal::pack_batom2(int n) void ComputePropertyLocal::pack_btype(int n) { - int i,j; + int i, j; int **bond_type = atom->bond_type; for (int m = 0; m < ncount; m++) { @@ -766,7 +762,7 @@ void ComputePropertyLocal::pack_btype(int n) void ComputePropertyLocal::pack_aatom1(int n) { - int i,j; + int i, j; tagint **angle_atom1 = atom->angle_atom1; for (int m = 0; m < ncount; m++) { @@ -781,7 +777,7 @@ void ComputePropertyLocal::pack_aatom1(int n) void ComputePropertyLocal::pack_aatom2(int n) { - int i,j; + int i, j; tagint **angle_atom2 = atom->angle_atom2; for (int m = 0; m < ncount; m++) { @@ -796,7 +792,7 @@ void ComputePropertyLocal::pack_aatom2(int n) void ComputePropertyLocal::pack_aatom3(int n) { - int i,j; + int i, j; tagint **angle_atom3 = atom->angle_atom3; for (int m = 0; m < ncount; m++) { @@ -811,7 +807,7 @@ void ComputePropertyLocal::pack_aatom3(int n) void ComputePropertyLocal::pack_atype(int n) { - int i,j; + int i, j; int **angle_type = atom->angle_type; for (int m = 0; m < ncount; m++) { @@ -826,7 +822,7 @@ void ComputePropertyLocal::pack_atype(int n) void ComputePropertyLocal::pack_datom1(int n) { - int i,j; + int i, j; tagint **dihedral_atom1 = atom->dihedral_atom1; for (int m = 0; m < ncount; m++) { @@ -841,7 +837,7 @@ void ComputePropertyLocal::pack_datom1(int n) void ComputePropertyLocal::pack_datom2(int n) { - int i,j; + int i, j; tagint **dihedral_atom2 = atom->dihedral_atom2; for (int m = 0; m < ncount; m++) { @@ -856,7 +852,7 @@ void ComputePropertyLocal::pack_datom2(int n) void ComputePropertyLocal::pack_datom3(int n) { - int i,j; + int i, j; tagint **dihedral_atom3 = atom->dihedral_atom3; for (int m = 0; m < ncount; m++) { @@ -871,7 +867,7 @@ void ComputePropertyLocal::pack_datom3(int n) void ComputePropertyLocal::pack_datom4(int n) { - int i,j; + int i, j; tagint **dihedral_atom4 = atom->dihedral_atom4; for (int m = 0; m < ncount; m++) { @@ -886,7 +882,7 @@ void ComputePropertyLocal::pack_datom4(int n) void ComputePropertyLocal::pack_dtype(int n) { - int i,j; + int i, j; int **dihedral_type = atom->dihedral_type; for (int m = 0; m < ncount; m++) { @@ -901,7 +897,7 @@ void ComputePropertyLocal::pack_dtype(int n) void ComputePropertyLocal::pack_iatom1(int n) { - int i,j; + int i, j; tagint **improper_atom1 = atom->improper_atom1; for (int m = 0; m < ncount; m++) { @@ -916,7 +912,7 @@ void ComputePropertyLocal::pack_iatom1(int n) void ComputePropertyLocal::pack_iatom2(int n) { - int i,j; + int i, j; tagint **improper_atom2 = atom->improper_atom2; for (int m = 0; m < ncount; m++) { @@ -931,7 +927,7 @@ void ComputePropertyLocal::pack_iatom2(int n) void ComputePropertyLocal::pack_iatom3(int n) { - int i,j; + int i, j; tagint **improper_atom3 = atom->improper_atom3; for (int m = 0; m < ncount; m++) { @@ -946,7 +942,7 @@ void ComputePropertyLocal::pack_iatom3(int n) void ComputePropertyLocal::pack_iatom4(int n) { - int i,j; + int i, j; tagint **improper_atom4 = atom->improper_atom4; for (int m = 0; m < ncount; m++) { @@ -961,7 +957,7 @@ void ComputePropertyLocal::pack_iatom4(int n) void ComputePropertyLocal::pack_itype(int n) { - int i,j; + int i, j; int **improper_type = atom->improper_type; for (int m = 0; m < ncount; m++) { diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index ba88c6d2c1..90dcbf8d4f 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -14,8 +14,6 @@ #include "compute_vacf.h" -#include - #include "atom.h" #include "update.h" #include "group.h" @@ -23,6 +21,7 @@ #include "fix_store.h" #include "error.h" +#include using namespace LAMMPS_NS; @@ -42,12 +41,9 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) : // create a new fix STORE style // id = compute-ID + COMPUTE_STORE, fix group = compute group - std::string fixcmd = id + std::string("_COMPUTE_STORE"); - id_fix = new char[fixcmd.size()+1]; - strcpy(id_fix,fixcmd.c_str()); - fixcmd += fmt::format(" {} STORE peratom 1 3", group->names[igroup]); - modify->add_fix(fixcmd); - fix = (FixStore *) modify->fix[modify->nfix-1]; + id_fix = utils::strdup(id + std::string("_COMPUTE_STORE")); + fix = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 3", + id_fix, group->names[igroup])); // store current velocities in fix store array // skip if reset from restart file diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 02efba7e93..2d11a5a3bc 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -596,10 +596,13 @@ void CreateAtoms::command(int narg, char **arg) // print status MPI_Barrier(world); - if (me == 0) - utils::logmesg(lmp,"Created {} atoms\n" - " create_atoms CPU = {:.3f} seconds\n", - atom->natoms - natoms_previous, MPI_Wtime() - time1); + if (me == 0) { + utils::logmesg(lmp,"Created {} atoms\n", atom->natoms - natoms_previous); + if (scaleflag) domain->print_box(" using lattice units in "); + else domain->print_box(" using box units in "); + utils::logmesg(lmp," create_atoms CPU = {:.3f} seconds\n", + MPI_Wtime() - time1); + } } /* ---------------------------------------------------------------------- diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 8088719491..24a18e6783 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,26 +13,29 @@ #include "dihedral_hybrid.h" -#include -#include #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; - #define EXTRA 1000 /* ---------------------------------------------------------------------- */ DihedralHybrid::DihedralHybrid(LAMMPS *lmp) : Dihedral(lmp) { + writedata = 0; nstyles = 0; + ndihedrallist = nullptr; + dihedrallist = nullptr; + maxdihedral = nullptr; } /* ---------------------------------------------------------------------- */ @@ -42,19 +44,18 @@ DihedralHybrid::~DihedralHybrid() { if (nstyles) { for (int i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (int i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] ndihedrallist; - delete [] maxdihedral; - for (int i = 0; i < nstyles; i++) - memory->destroy(dihedrallist[i]); - delete [] dihedrallist; + delete[] ndihedrallist; + delete[] maxdihedral; + for (int i = 0; i < nstyles; i++) memory->destroy(dihedrallist[i]); + delete[] dihedrallist; } } @@ -62,7 +63,7 @@ DihedralHybrid::~DihedralHybrid() void DihedralHybrid::compute(int eflag, int vflag) { - int i,j,m,n; + int i, j, m, n; // save ptrs to original dihedrallist @@ -84,8 +85,7 @@ void DihedralHybrid::compute(int eflag, int vflag) if (ndihedrallist[m] > maxdihedral[m]) { memory->destroy(dihedrallist[m]); maxdihedral[m] = ndihedrallist[m] + EXTRA; - memory->create(dihedrallist[m],maxdihedral[m],5, - "dihedral_hybrid:dihedrallist"); + memory->create(dihedrallist[m], maxdihedral[m], 5, "dihedral_hybrid:dihedrallist"); } ndihedrallist[m] = 0; } @@ -106,13 +106,23 @@ void DihedralHybrid::compute(int eflag, int vflag) // set neighbor->dihedrallist to sub-style dihedrallist before call // accumulate sub-style global/peratom energy/virial in hybrid - ev_init(eflag,vflag); + ev_init(eflag, vflag); + + // need to clear per-thread storage here, when using multiple threads + // with thread-enabled substyles to avoid uninitlialized data access. + + const int nthreads = comm->nthreads; + if (comm->nthreads > 1) { + const bigint nall = atom->nlocal + atom->nghost; + if (eflag_atom) memset(&eatom[0], 0, nall * nthreads * sizeof(double)); + if (vflag_atom) memset(&vatom[0][0], 0, 6 * nall * nthreads * sizeof(double)); + } for (m = 0; m < nstyles; m++) { neighbor->ndihedrallist = ndihedrallist[m]; neighbor->dihedrallist = dihedrallist[m]; - styles[m]->compute(eflag,vflag); + styles[m]->compute(eflag, vflag); if (eflag_global) energy += styles[m]->energy; if (vflag_global) @@ -128,16 +138,14 @@ void DihedralHybrid::compute(int eflag, int vflag) if (force->newton_bond) n += atom->nghost; double **vatom_substyle = styles[m]->vatom; for (i = 0; i < n; i++) - for (j = 0; j < 6; j++) - vatom[i][j] += vatom_substyle[i][j]; + for (j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j]; } if (cvflag_atom) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; double **cvatom_substyle = styles[m]->cvatom; for (i = 0; i < n; i++) - for (j = 0; j < 9; j++) - cvatom[i][j] += cvatom_substyle[i][j]; + for (j = 0; j < 9; j++) cvatom[i][j] += cvatom_substyle[i][j]; } } @@ -154,13 +162,13 @@ void DihedralHybrid::allocate() allocated = 1; int n = atom->ndihedraltypes; - memory->create(map,n+1,"dihedral:map"); - memory->create(setflag,n+1,"dihedral:setflag"); + memory->create(map, n + 1, "dihedral:map"); + memory->create(setflag, n + 1, "dihedral:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; ndihedrallist = new int[nstyles]; maxdihedral = new int[nstyles]; - dihedrallist = new int**[nstyles]; + dihedrallist = new int **[nstyles]; for (int m = 0; m < nstyles; m++) maxdihedral[m] = 0; for (int m = 0; m < nstyles; m++) dihedrallist[m] = nullptr; } @@ -171,27 +179,26 @@ void DihedralHybrid::allocate() void DihedralHybrid::settings(int narg, char **arg) { - int i,m,istyle; + int i, m, istyle; - if (narg < 1) error->all(FLERR,"Illegal dihedral_style command"); + if (narg < 1) error->all(FLERR, "Illegal dihedral_style command"); // delete old lists, since cannot just change settings if (nstyles) { for (i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] ndihedrallist; - delete [] maxdihedral; - for (i = 0; i < nstyles; i++) - memory->destroy(dihedrallist[i]); - delete [] dihedrallist; + delete[] ndihedrallist; + delete[] maxdihedral; + for (i = 0; i < nstyles; i++) memory->destroy(dihedrallist[i]); + delete[] dihedrallist; } allocated = 0; @@ -202,7 +209,7 @@ void DihedralHybrid::settings(int narg, char **arg) nstyles = 0; i = 0; while (i < narg) { - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; nstyles++; @@ -210,8 +217,8 @@ void DihedralHybrid::settings(int narg, char **arg) // allocate list of sub-styles - styles = new Dihedral*[nstyles]; - keywords = new char*[nstyles]; + styles = new Dihedral *[nstyles]; + keywords = new char *[nstyles]; // allocate each sub-style and call its settings() with subset of args // allocate uses suffix, but don't store suffix version in keywords, @@ -226,23 +233,21 @@ void DihedralHybrid::settings(int narg, char **arg) while (i < narg) { for (m = 0; m < nstyles; m++) - if (strcmp(arg[i],keywords[m]) == 0) - error->all(FLERR,"Dihedral style hybrid cannot use " - "same dihedral style twice"); - if (strcmp(arg[i],"hybrid") == 0) - error->all(FLERR, - "Dihedral style hybrid cannot have hybrid as an argument"); - if (strcmp(arg[i],"none") == 0) - error->all(FLERR,"Dihedral style hybrid cannot have none as an argument"); + if (strcmp(arg[i], keywords[m]) == 0) + error->all(FLERR, "Dihedral style hybrid cannot use same dihedral style twice"); + if (strcmp(arg[i], "hybrid") == 0) + error->all(FLERR, "Dihedral style hybrid cannot have hybrid as an argument"); + if (strcmp(arg[i], "none") == 0) + error->all(FLERR, "Dihedral style hybrid cannot have none as an argument"); - styles[nstyles] = force->new_dihedral(arg[i],1,dummy); - force->store_style(keywords[nstyles],arg[i],0); + styles[nstyles] = force->new_dihedral(arg[i], 1, dummy); + force->store_style(keywords[nstyles], arg[i], 0); istyle = i; - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; - styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]); + styles[nstyles]->settings(i - istyle - 1, &arg[istyle + 1]); nstyles++; } } @@ -255,22 +260,35 @@ void DihedralHybrid::coeff(int narg, char **arg) { if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error); // 2nd arg = dihedral sub-style name // allow for "none" or "skip" as valid sub-style name int m; for (m = 0; m < nstyles; m++) - if (strcmp(arg[1],keywords[m]) == 0) break; + if (strcmp(arg[1], keywords[m]) == 0) break; int none = 0; int skip = 0; if (m == nstyles) { - if (strcmp(arg[1],"none") == 0) none = 1; - else if (strcmp(arg[1],"skip") == 0) none = skip = 1; - else error->all(FLERR,"Dihedral coeff for hybrid has invalid style"); + if (strcmp(arg[1], "none") == 0) + none = 1; + else if (strcmp(arg[1], "skip") == 0) + none = skip = 1; + else if (strcmp(arg[1], "mbt") == 0) + error->all(FLERR, "MiddleBondTorsion coeff for hybrid dihedral has invalid format"); + else if (strcmp(arg[1], "ebt") == 0) + error->all(FLERR, "EndBondTorsion coeff for hybrid dihedral has invalid format"); + else if (strcmp(arg[1], "at") == 0) + error->all(FLERR, "AngleTorsion coeff for hybrid dihedral has invalid format"); + else if (strcmp(arg[1], "aat") == 0) + error->all(FLERR, "AngleAngleTorsion coeff for hybrid dihedral has invalid format"); + else if (strcmp(arg[1], "bb13") == 0) + error->all(FLERR, "BondBond13 coeff for hybrid dihedral has invalid format"); + else + error->all(FLERR, "Dihedral coeff for hybrid has invalid style"); } // move 1st arg to 2nd arg @@ -280,14 +298,15 @@ void DihedralHybrid::coeff(int narg, char **arg) // invoke sub-style coeff() starting with 1st arg - if (!none) styles[m]->coeff(narg-1,&arg[1]); + if (!none) styles[m]->coeff(narg - 1, &arg[1]); // set setflag and which type maps to which sub-style // if sub-style is skip: auxiliary class2 setting in data file so ignore // if sub-style is none and not skip: set hybrid setflag, wipe out map for (int i = ilo; i <= ihi; i++) { - if (skip) continue; + if (skip) + continue; else if (none) { setflag[i] = 1; map[i] = -1; @@ -298,7 +317,9 @@ void DihedralHybrid::coeff(int narg, char **arg) } } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + run dihedral style specific initialization +------------------------------------------------------------------------- */ void DihedralHybrid::init_style() { @@ -312,13 +333,13 @@ void DihedralHybrid::init_style() void DihedralHybrid::write_restart(FILE *fp) { - fwrite(&nstyles,sizeof(int),1,fp); + fwrite(&nstyles, sizeof(int), 1, fp); int n; for (int m = 0; m < nstyles; m++) { n = strlen(keywords[m]) + 1; - fwrite(&n,sizeof(int),1,fp); - fwrite(keywords[m],sizeof(char),n,fp); + fwrite(&n, sizeof(int), 1, fp); + fwrite(keywords[m], sizeof(char), n, fp); styles[m]->write_restart_settings(fp); } } @@ -330,21 +351,21 @@ void DihedralHybrid::write_restart(FILE *fp) void DihedralHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&nstyles,1,MPI_INT,0,world); - styles = new Dihedral*[nstyles]; - keywords = new char*[nstyles]; + if (me == 0) utils::sfread(FLERR, &nstyles, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&nstyles, 1, MPI_INT, 0, world); + styles = new Dihedral *[nstyles]; + keywords = new char *[nstyles]; allocate(); - int n,dummy; + int n, dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&n,1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &n, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&n, 1, MPI_INT, 0, world); keywords[m] = new char[n]; - if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,nullptr,error); - MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); - styles[m] = force->new_dihedral(keywords[m],0,dummy); + if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error); + MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world); + styles[m] = force->new_dihedral(keywords[m], 0, dummy); styles[m]->read_restart_settings(fp); } } @@ -355,10 +376,10 @@ void DihedralHybrid::read_restart(FILE *fp) double DihedralHybrid::memory_usage() { - double bytes = (double)maxeatom * sizeof(double); - bytes += (double)maxvatom*6 * sizeof(double); - bytes += (double)maxcvatom*9 * sizeof(double); - for (int m = 0; m < nstyles; m++) bytes += (double)maxdihedral[m]*5 * sizeof(int); + double bytes = (double) maxeatom * sizeof(double); + bytes += (double) maxvatom * 6 * sizeof(double); + bytes += (double) maxcvatom * 9 * sizeof(double); + for (int m = 0; m < nstyles; m++) bytes += (double) maxdihedral[m] * 5 * sizeof(int); for (int m = 0; m < nstyles; m++) if (styles[m]) bytes += styles[m]->memory_usage(); return bytes; diff --git a/src/dump.cpp b/src/dump.cpp index 1f54724925..ae7086af44 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -84,6 +84,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp) unit_flag = 0; unit_count = 0; delay_flag = 0; + write_header_flag = 1; maxfiles = -1; numfiles = 0; @@ -378,7 +379,7 @@ void Dump::write() if (multiproc) MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm); - if (filewriter) write_header(nheader); + if (filewriter && write_header_flag) write_header(nheader); // insure buf is sized for packing and communicating // use nmax to insure filewriter proc can receive info from others @@ -932,6 +933,13 @@ void Dump::modify_params(int narg, char **arg) else delay_flag = 0; iarg += 2; + } else if (strcmp(arg[iarg],"header") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command"); + if (strcmp(arg[iarg+1],"yes") == 0) write_header_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) write_header_flag = 0; + else error->all(FLERR,"Illegal dump_modify command"); + iarg += 2; + } else if (strcmp(arg[iarg],"every") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command"); int idump; diff --git a/src/dump.h b/src/dump.h index 05e09a929a..730d4c9ca9 100644 --- a/src/dump.h +++ b/src/dump.h @@ -79,6 +79,8 @@ class Dump : protected Pointers { int unit_flag; // 1 if dump should contain unit information int unit_count; // # of times the unit information was written int delay_flag; // 1 if delay output until delaystep + int write_header_flag; // 1 if write header, 0 if not + bigint delaystep; int refreshflag; // 1 if dump_modify refresh specified diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 5f2acfda57..6bb7653e3b 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -193,16 +193,16 @@ DumpCustom::~DumpCustom() // could not do in constructor, b/c some derived classes process earg if (expand) { - for (int i = 0; i < nargnew; i++) delete [] earg[i]; + for (int i = 0; i < nargnew; i++) delete[] earg[i]; memory->sfree(earg); } - delete [] pack_choice; - delete [] vtype; + delete[] pack_choice; + delete[] vtype; memory->destroy(field2index); memory->destroy(argindex); - delete [] idregion; + delete[] idregion; memory->destroy(thresh_array); memory->destroy(thresh_op); memory->destroy(thresh_value); @@ -212,27 +212,27 @@ DumpCustom::~DumpCustom() for (int i = 0; i < nthreshlast; i++) { if (modify->nfix) modify->delete_fix(thresh_fixID[i]); - delete [] thresh_fixID[i]; + delete[] thresh_fixID[i]; } memory->sfree(thresh_fix); memory->sfree(thresh_fixID); memory->destroy(thresh_first); - for (int i = 0; i < ncompute; i++) delete [] id_compute[i]; + for (int i = 0; i < ncompute; i++) delete[] id_compute[i]; memory->sfree(id_compute); - delete [] compute; + delete[] compute; - for (int i = 0; i < nfix; i++) delete [] id_fix[i]; + for (int i = 0; i < nfix; i++) delete[] id_fix[i]; memory->sfree(id_fix); - delete [] fix; + delete[] fix; - for (int i = 0; i < nvariable; i++) delete [] id_variable[i]; + for (int i = 0; i < nvariable; i++) delete[] id_variable[i]; memory->sfree(id_variable); - delete [] variable; + delete[] variable; for (int i = 0; i < nvariable; i++) memory->destroy(vbuf[i]); - delete [] vbuf; + delete[] vbuf; - for (int i = 0; i < ncustom; i++) delete [] id_custom[i]; + for (int i = 0; i < ncustom; i++) delete[] id_custom[i]; memory->sfree(id_custom); memory->sfree(flag_custom); @@ -240,20 +240,20 @@ DumpCustom::~DumpCustom() memory->destroy(dchoose); memory->destroy(clist); - for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; - delete [] typenames; + for (int i = 1; i <= ntypes; i++) delete[] typenames[i]; + delete[] typenames; if (vformat) { - for (int i = 0; i < nfield; i++) delete [] vformat[i]; - delete [] vformat; + for (int i = 0; i < nfield; i++) delete[] vformat[i]; + delete[] vformat; } if (format_column_user) { - for (int i = 0; i < nfield; i++) delete [] format_column_user[i]; - delete [] format_column_user; + for (int i = 0; i < nfield; i++) delete[] format_column_user[i]; + delete[] format_column_user; } - delete [] columns; + delete[] columns; } /* ---------------------------------------------------------------------- */ @@ -262,7 +262,7 @@ void DumpCustom::init_style() { // format = copy of default or user-specified line format - delete [] format; + delete[] format; if (format_line_user) format = utils::strdup(format_line_user); else format = utils::strdup(format_default); @@ -277,7 +277,7 @@ void DumpCustom::init_style() int i=0; for (auto word : words) { - delete [] vformat[i]; + delete[] vformat[i]; if (format_column_user[i]) vformat[i] = utils::strdup(std::string(format_column_user[i]) + " "); @@ -1429,6 +1429,7 @@ int DumpCustom::parse_fields(int narg, char **arg) ArgInfo argi(arg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE |ArgInfo::DNAME|ArgInfo::INAME); argindex[iarg] = argi.get_index1(); + auto name = argi.get_name(); switch (argi.get_type()) { @@ -1443,21 +1444,19 @@ int DumpCustom::parse_fields(int narg, char **arg) pack_choice[iarg] = &DumpCustom::pack_compute; vtype[iarg] = Dump::DOUBLE; - n = modify->find_compute(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump custom compute ID"); + n = modify->find_compute(name); + if (n < 0) error->all(FLERR,"Could not find dump custom compute ID: {}",name); if (modify->compute[n]->peratom_flag == 0) - error->all(FLERR,"Dump custom compute does not compute per-atom info"); + error->all(FLERR,"Dump custom compute {} does not compute per-atom info",name); if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0) - error->all(FLERR, - "Dump custom compute does not calculate per-atom vector"); + error->all(FLERR,"Dump custom compute {} does not calculate per-atom vector",name); if (argi.get_dim() > 0 && modify->compute[n]->size_peratom_cols == 0) - error->all(FLERR, - "Dump custom compute does not calculate per-atom array"); + error->all(FLERR,"Dump custom compute {} does not calculate per-atom array",name); if (argi.get_dim() > 0 && argi.get_index1() > modify->compute[n]->size_peratom_cols) - error->all(FLERR,"Dump custom compute vector is accessed out-of-range"); + error->all(FLERR,"Dump custom compute {} vector is accessed out-of-range",name); - field2index[iarg] = add_compute(argi.get_name()); + field2index[iarg] = add_compute(name); break; // fix value = f_ID @@ -1467,19 +1466,19 @@ int DumpCustom::parse_fields(int narg, char **arg) pack_choice[iarg] = &DumpCustom::pack_fix; vtype[iarg] = Dump::DOUBLE; - n = modify->find_fix(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump custom fix ID"); + n = modify->find_fix(name); + if (n < 0) error->all(FLERR,"Could not find dump custom fix ID: {}",name); if (modify->fix[n]->peratom_flag == 0) - error->all(FLERR,"Dump custom fix does not compute per-atom info"); + error->all(FLERR,"Dump custom fix {} does not compute per-atom info",name); if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0) - error->all(FLERR,"Dump custom fix does not compute per-atom vector"); + error->all(FLERR,"Dump custom fix {} does not compute per-atom vector",name); if (argi.get_dim() > 0 && modify->fix[n]->size_peratom_cols == 0) - error->all(FLERR,"Dump custom fix does not compute per-atom array"); + error->all(FLERR,"Dump custom fix {} does not compute per-atom array",name); if (argi.get_dim() > 0 && argi.get_index1() > modify->fix[n]->size_peratom_cols) - error->all(FLERR,"Dump custom fix vector is accessed out-of-range"); + error->all(FLERR,"Dump custom fix {} vector is accessed out-of-range",name); - field2index[iarg] = add_fix(argi.get_name()); + field2index[iarg] = add_fix(name); break; // variable value = v_name @@ -1488,12 +1487,12 @@ int DumpCustom::parse_fields(int narg, char **arg) pack_choice[iarg] = &DumpCustom::pack_variable; vtype[iarg] = Dump::DOUBLE; - n = input->variable->find(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump custom variable name"); + n = input->variable->find(name); + if (n < 0) error->all(FLERR,"Could not find dump custom variable name {}",name); if (input->variable->atomstyle(n) == 0) - error->all(FLERR,"Dump custom variable is not atom-style variable"); + error->all(FLERR,"Dump custom variable {} is not atom-style variable",name); - field2index[iarg] = add_variable(argi.get_name()); + field2index[iarg] = add_variable(name); break; // custom per-atom floating point value = d_ID @@ -1503,14 +1502,14 @@ int DumpCustom::parse_fields(int narg, char **arg) vtype[iarg] = Dump::DOUBLE; tmp = -1; - n = atom->find_custom(argi.get_name(),tmp); + n = atom->find_custom(name,tmp); if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); + error->all(FLERR,"Could not find custom per-atom property ID: {}", name); if (tmp != 1) - error->all(FLERR,"Custom per-atom property ID is not floating point"); + error->all(FLERR,"Custom per-atom property ID {} is not floating point", name); - field2index[iarg] = add_custom(argi.get_name(),1); + field2index[iarg] = add_custom(name,1); break; // custom per-atom integer value = i_ID @@ -1520,14 +1519,14 @@ int DumpCustom::parse_fields(int narg, char **arg) vtype[iarg] = Dump::INT; tmp = -1; - n = atom->find_custom(argi.get_name(),tmp); + n = atom->find_custom(name,tmp); if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); + error->all(FLERR,"Could not find custom per-atom property ID: {}", name); if (tmp != 0) - error->all(FLERR,"Custom per-atom property ID is not integer"); + error->all(FLERR,"Custom per-atom property ID {} is not integer", name); - field2index[iarg] = add_custom(argi.get_name(),0); + field2index[iarg] = add_custom(name,0); break; default: @@ -1554,7 +1553,7 @@ int DumpCustom::add_compute(const char *id) id_compute = (char **) memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute"); - delete [] compute; + delete[] compute; compute = new Compute*[ncompute+1]; id_compute[ncompute] = utils::strdup(id); @@ -1577,7 +1576,7 @@ int DumpCustom::add_fix(const char *id) id_fix = (char **) memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix"); - delete [] fix; + delete[] fix; fix = new Fix*[nfix+1]; id_fix[nfix] = utils::strdup(id); @@ -1601,9 +1600,9 @@ int DumpCustom::add_variable(const char *id) id_variable = (char **) memory->srealloc(id_variable,(nvariable+1)*sizeof(char *), "dump:id_variable"); - delete [] variable; + delete[] variable; variable = new int[nvariable+1]; - delete [] vbuf; + delete[] vbuf; vbuf = new double*[nvariable+1]; for (int i = 0; i <= nvariable; i++) vbuf[i] = nullptr; @@ -1648,8 +1647,8 @@ int DumpCustom::modify_param(int narg, char **arg) else { iregion = domain->find_region(arg[1]); if (iregion == -1) - error->all(FLERR,"Dump_modify region ID does not exist"); - delete [] idregion; + error->all(FLERR,"Dump_modify region ID {} does not exist",arg[1]); + delete[] idregion; idregion = utils::strdup(arg[1]); } return 2; @@ -1661,7 +1660,7 @@ int DumpCustom::modify_param(int narg, char **arg) if (strcmp(arg[1],"none") == 0) { // just clear format_column_user allocated by this dump child class for (int i = 0; i < nfield; i++) { - delete [] format_column_user[i]; + delete[] format_column_user[i]; format_column_user[i] = nullptr; } return 2; @@ -1670,17 +1669,16 @@ int DumpCustom::modify_param(int narg, char **arg) if (narg < 3) error->all(FLERR,"Illegal dump_modify command"); if (strcmp(arg[1],"int") == 0) { - delete [] format_int_user; + delete[] format_int_user; format_int_user = utils::strdup(arg[2]); - delete [] format_bigint_user; + delete[] format_bigint_user; int n = strlen(format_int_user) + 8; format_bigint_user = new char[n]; // replace "d" in format_int_user with bigint format specifier // use of &str[1] removes leading '%' from BIGINT_FORMAT string char *ptr = strchr(format_int_user,'d'); if (ptr == nullptr) - error->all(FLERR, - "Dump_modify int format does not contain d character"); + error->all(FLERR,"Dump_modify int format does not contain d character"); char str[8]; sprintf(str,"%s",BIGINT_FORMAT); *ptr = '\0'; @@ -1688,14 +1686,14 @@ int DumpCustom::modify_param(int narg, char **arg) *ptr = 'd'; } else if (strcmp(arg[1],"float") == 0) { - delete [] format_float_user; + delete[] format_float_user; format_float_user = utils::strdup(arg[2]); } else { int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1; if (i < 0 || i >= nfield) error->all(FLERR,"Illegal dump_modify command"); - if (format_column_user[i]) delete [] format_column_user[i]; + if (format_column_user[i]) delete[] format_column_user[i]; format_column_user[i] = utils::strdup(arg[2]); } return 3; @@ -1703,10 +1701,10 @@ int DumpCustom::modify_param(int narg, char **arg) if (strcmp(arg[0],"element") == 0) { if (narg < ntypes+1) - error->all(FLERR,"Dump_modify element names do not match atom types"); + error->all(FLERR,"Number of dump_modify element names does not match number of atom types"); - for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; - delete [] typenames; + for (int i = 1; i <= ntypes; i++) delete[] typenames[i]; + delete[] typenames; typenames = new char*[ntypes+1]; for (int itype = 1; itype <= ntypes; itype++) { typenames[itype] = utils::strdup(arg[itype]); @@ -1739,7 +1737,7 @@ int DumpCustom::modify_param(int narg, char **arg) thresh_last = nullptr; for (int i = 0; i < nthreshlast; i++) { modify->delete_fix(thresh_fixID[i]); - delete [] thresh_fixID[i]; + delete[] thresh_fixID[i]; } thresh_fix = nullptr; thresh_fixID = nullptr; @@ -1850,6 +1848,7 @@ int DumpCustom::modify_param(int narg, char **arg) ArgInfo argi(arg[1],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE |ArgInfo::DNAME|ArgInfo::INAME); argindex[nfield+nthresh] = argi.get_index1(); + auto name = argi.get_name(); switch (argi.get_type()) { @@ -1862,23 +1861,20 @@ int DumpCustom::modify_param(int narg, char **arg) case ArgInfo::COMPUTE: thresh_array[nthresh] = COMPUTE; - n = modify->find_compute(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump modify compute ID"); + n = modify->find_compute(name); + if (n < 0) error->all(FLERR,"Could not find dump modify compute ID: {}",name); if (modify->compute[n]->peratom_flag == 0) - error->all(FLERR, - "Dump modify compute ID does not compute per-atom info"); + error->all(FLERR,"Dump modify compute ID {} does not compute per-atom info",name); if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0) - error->all(FLERR, - "Dump modify compute ID does not compute per-atom vector"); + error->all(FLERR,"Dump modify compute ID {} does not compute per-atom vector",name); if (argi.get_index1() > 0 && modify->compute[n]->size_peratom_cols == 0) - error->all(FLERR, - "Dump modify compute ID does not compute per-atom array"); + error->all(FLERR,"Dump modify compute ID {} does not compute per-atom array",name); if (argi.get_index1() > 0 && argi.get_index1() > modify->compute[n]->size_peratom_cols) - error->all(FLERR,"Dump modify compute ID vector is not large enough"); + error->all(FLERR,"Dump modify compute ID {} vector is not large enough",name); - field2index[nfield+nthresh] = add_compute(argi.get_name()); + field2index[nfield+nthresh] = add_compute(name); break; // fix value = f_ID @@ -1886,20 +1882,19 @@ int DumpCustom::modify_param(int narg, char **arg) case ArgInfo::FIX: thresh_array[nthresh] = FIX; - n = modify->find_fix(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump modify fix ID"); + n = modify->find_fix(name); + if (n < 0) error->all(FLERR,"Could not find dump modify fix ID: {}",name); if (modify->fix[n]->peratom_flag == 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom info"); + error->all(FLERR,"Dump modify fix ID {} does not compute per-atom info",name); if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom vector"); + error->all(FLERR,"Dump modify fix ID {} does not compute per-atom vector",name); if (argi.get_index1() > 0 && modify->fix[n]->size_peratom_cols == 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom array"); - if (argi.get_index1() > 0 && - argi.get_index1() > modify->fix[n]->size_peratom_cols) - error->all(FLERR,"Dump modify fix ID vector is not large enough"); + error->all(FLERR,"Dump modify fix ID {} does not compute per-atom array",name); + if (argi.get_index1() > 0 && argi.get_index1() > modify->fix[n]->size_peratom_cols) + error->all(FLERR,"Dump modify fix ID {} vector is not large enough",name); - field2index[nfield+nthresh] = add_fix(argi.get_name()); + field2index[nfield+nthresh] = add_fix(name); break; // variable value = v_ID @@ -1907,12 +1902,12 @@ int DumpCustom::modify_param(int narg, char **arg) case ArgInfo::VARIABLE: thresh_array[nthresh] = VARIABLE; - n = input->variable->find(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump modify variable name"); + n = input->variable->find(name); + if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}",name); if (input->variable->atomstyle(n) == 0) - error->all(FLERR,"Dump modify variable is not atom-style variable"); + error->all(FLERR,"Dump modify variable {} is not atom-style variable",name); - field2index[nfield+nthresh] = add_variable(argi.get_name()); + field2index[nfield+nthresh] = add_variable(name); break; // custom per atom floating point value = d_ID @@ -1920,12 +1915,11 @@ int DumpCustom::modify_param(int narg, char **arg) case ArgInfo::DNAME: thresh_array[nthresh] = DNAME; tmp = -1; - n = atom->find_custom(argi.get_name(),tmp); + n = atom->find_custom(name,tmp); if ((n < 0) || (tmp != 1)) - error->all(FLERR,"Could not find dump modify " - "custom atom floating point property ID"); + error->all(FLERR,"Could not find dump modify custom atom floating point property ID: {}",name); - field2index[nfield+nthresh] = add_custom(argi.get_name(),1); + field2index[nfield+nthresh] = add_custom(name,1); break; // custom per atom integer value = i_ID @@ -1933,16 +1927,15 @@ int DumpCustom::modify_param(int narg, char **arg) case ArgInfo::INAME: thresh_array[nthresh] = INAME; tmp = -1; - n = atom->find_custom(argi.get_name(),tmp); + n = atom->find_custom(name,tmp); if ((n < 0) || (tmp != 0)) - error->all(FLERR,"Could not find dump modify " - "custom atom integer property ID"); + error->all(FLERR,"Could not find dump modify custom atom integer property ID: {}",name); - field2index[nfield+nthresh] = add_custom(argi.get_name(),0); + field2index[nfield+nthresh] = add_custom(name,0); break; default: - error->all(FLERR,"Invalid dump_modify thresh attribute"); + error->all(FLERR,"Invalid dump_modify thresh attribute: {}",name); break; } } @@ -1967,18 +1960,15 @@ int DumpCustom::modify_param(int narg, char **arg) thresh_last[nthresh] = -1; } else { thresh_fix = (FixStore **) - memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *), - "dump:thresh_fix"); + memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),"dump:thresh_fix"); thresh_fixID = (char **) - memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *), - "dump:thresh_fixID"); + memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID"); memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first"); std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast); thresh_fixID[nthreshlast] = utils::strdup(threshid); - modify->add_fix(fmt::format("{} {} STORE peratom 1 1",threshid, - group->names[igroup])); - thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1]; + threshid += fmt::format(" {} STORE peratom 1 1", group->names[igroup]); + thresh_fix[nthreshlast] = (FixStore *) modify->add_fix(threshid); thresh_last[nthreshlast] = nthreshlast; thresh_first[nthreshlast] = 1; diff --git a/src/error.cpp b/src/error.cpp index 491c72bdbb..9811a1d3eb 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -81,7 +81,7 @@ void Error::universe_all(const std::string &file, int line, const std::string &s throw LAMMPSException(mesg); #else - if (lmp->kokkos) Kokkos::finalize(); + KokkosLMP::finalize(); MPI_Finalize(); exit(1); #endif @@ -107,6 +107,7 @@ void Error::universe_one(const std::string &file, int line, const std::string &s throw LAMMPSAbortException(mesg, universe->uworld); #else + KokkosLMP::finalize(); MPI_Abort(universe->uworld,1); exit(1); // to trick "smart" compilers into believing this does not return #endif @@ -173,8 +174,8 @@ void Error::all(const std::string &file, int line, const std::string &str) if (screen && screen != stdout) fclose(screen); if (logfile) fclose(logfile); + KokkosLMP::finalize(); if (universe->nworlds > 1) MPI_Abort(universe->uworld,1); - if (lmp->kokkos) Kokkos::finalize(); MPI_Finalize(); exit(1); #endif @@ -213,6 +214,7 @@ void Error::one(const std::string &file, int line, const std::string &str) #else if (screen) fflush(screen); if (logfile) fflush(logfile); + KokkosLMP::finalize(); MPI_Abort(world,1); exit(1); // to trick "smart" compilers into believing this does not return #endif @@ -315,7 +317,7 @@ void Error::done(int status) if (screen && screen != stdout) fclose(screen); if (logfile) fclose(logfile); - if (lmp->kokkos) Kokkos::finalize(); + KokkosLMP::finalize(); MPI_Finalize(); exit(status); } diff --git a/src/finish.cpp b/src/finish.cpp index 210b48dcb7..81ba59c1df 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -34,7 +34,7 @@ #include #include -#ifdef LMP_USER_OMP +#ifdef LMP_OPENMP #include "modify.h" #include "fix_omp.h" #include "thr_data.h" @@ -48,7 +48,7 @@ static void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt, MPI_Comm world, const int nprocs, const int nthreads, const int me, double time_loop, FILE *scr, FILE *log); -#ifdef LMP_USER_OMP +#ifdef LMP_OPENMP static void omp_times(FixOMP *fix, const char *label, enum Timer::ttype which, const int nthreads,FILE *scr, FILE *log); #endif @@ -363,7 +363,7 @@ void Finish::end(int flag) } } -#ifdef LMP_USER_OMP +#ifdef LMP_OPENMP int ifix = modify->find_fix("package_omp"); // print thread breakdown only with full timer detail @@ -691,7 +691,7 @@ void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt, /* ---------------------------------------------------------------------- */ -#ifdef LMP_USER_OMP +#ifdef LMP_OPENMP void omp_times(FixOMP *fix, const char *label, enum Timer::ttype which, const int nthreads,FILE *scr, FILE *log) { diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 670c0dc4be..e5c2c3dece 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -252,12 +252,9 @@ void FixAdapt::post_constructor() id_fix_chg = nullptr; if (diamflag && atom->radius_flag) { - std::string fixcmd = id + std::string("_FIX_STORE_DIAM"); - id_fix_diam = utils::strdup(fixcmd); - fixcmd += fmt::format(" {} STORE peratom 1 1",group->names[igroup]); - modify->add_fix(fixcmd); - fix_diam = (FixStore *) modify->fix[modify->nfix-1]; - + id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM")); + fix_diam = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 1", + id_fix_diam,group->names[igroup])); if (fix_diam->restart_reset) fix_diam->restart_reset = 0; else { double *vec = fix_diam->vstore; @@ -273,12 +270,9 @@ void FixAdapt::post_constructor() } if (chgflag && atom->q_flag) { - std::string fixcmd = id + std::string("_FIX_STORE_CHG"); - id_fix_chg = utils::strdup(fixcmd); - fixcmd += fmt::format(" {} STORE peratom 1 1",group->names[igroup]); - modify->add_fix(fixcmd); - fix_chg = (FixStore *) modify->fix[modify->nfix-1]; - + id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG")); + fix_chg = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 1", + id_fix_chg,group->names[igroup])); if (fix_chg->restart_reset) fix_chg->restart_reset = 0; else { double *vec = fix_chg->vstore; diff --git a/src/MISC/fix_deposit.cpp b/src/fix_deposit.cpp similarity index 99% rename from src/MISC/fix_deposit.cpp rename to src/fix_deposit.cpp index f3b175fc78..7f153cd172 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/fix_deposit.cpp @@ -195,7 +195,7 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) : force_reneighbor = 1; next_reneighbor = update->ntimestep + 1; - nfirst = next_reneighbor; + nfirst = next_reneighbor-nfreq; ninserted = 0; } @@ -288,8 +288,7 @@ void FixDeposit::init() double separation = MAX(2.0*maxradinsert,maxradall+maxradinsert); if (sqrt(nearsq) < separation && comm->me == 0) - error->warning(FLERR,"Fix deposit near setting < possible " - "overlap separation {}",separation); + error->warning(FLERR,"Fix deposit near setting < possible overlap separation {}",separation); } } @@ -297,7 +296,7 @@ void FixDeposit::init() void FixDeposit::setup_pre_exchange() { - if (ninserted < ninsert) next_reneighbor = update->ntimestep+1; + if (ninserted < ninsert) next_reneighbor = nfirst + ((update->ntimestep - nfirst)/nfreq)*nfreq + nfreq; else next_reneighbor = 0; } diff --git a/src/MISC/fix_deposit.h b/src/fix_deposit.h similarity index 100% rename from src/MISC/fix_deposit.h rename to src/fix_deposit.h diff --git a/src/MISC/fix_efield.cpp b/src/fix_efield.cpp similarity index 100% rename from src/MISC/fix_efield.cpp rename to src/fix_efield.cpp diff --git a/src/MISC/fix_efield.h b/src/fix_efield.h similarity index 100% rename from src/MISC/fix_efield.h rename to src/fix_efield.h diff --git a/src/MISC/fix_evaporate.cpp b/src/fix_evaporate.cpp similarity index 100% rename from src/MISC/fix_evaporate.cpp rename to src/fix_evaporate.cpp diff --git a/src/MISC/fix_evaporate.h b/src/fix_evaporate.h similarity index 100% rename from src/MISC/fix_evaporate.h rename to src/fix_evaporate.h diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 8bede4ee19..f95c30c28d 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -15,6 +15,7 @@ #include "fix_external.h" #include "atom.h" +#include "comm.h" #include "error.h" #include "memory.h" #include "update.h" @@ -80,7 +81,7 @@ FixExternal::~FixExternal() atom->delete_callback(id,Atom::GROW); memory->destroy(fexternal); - delete [] caller_vector; + delete[] caller_vector; } /* ---------------------------------------------------------------------- */ @@ -163,6 +164,12 @@ void FixExternal::post_force(int vflag) f[i][1] += fexternal[i][1]; f[i][2] += fexternal[i][2]; } + + // add contribution to global virial from previously stored value + + if (vflag_global) + for (int i = 0; i < 6; ++i) + virial[i] = user_virial[i]; } } @@ -179,10 +186,13 @@ void FixExternal::min_post_force(int vflag) /* ---------------------------------------------------------------------- caller invokes this method to set its contribution to global energy + this is the *total* energy across all MPI ranks of the external code + and must be set for all MPI ranks. unlike other energy/virial set methods: do not just return if eflag_global is not set b/c input script could access this quantity via compute_scalar() even if eflag is not set on a particular timestep + this function is compatible with CALLBACK and ARRAY mode ------------------------------------------------------------------------- */ void FixExternal::set_energy_global(double caller_energy) @@ -191,24 +201,32 @@ void FixExternal::set_energy_global(double caller_energy) } /* ---------------------------------------------------------------------- - caller invokes this method to set its contribution to global virial + caller invokes this method to set its contribution to the global virial + for all MPI ranks. the virial value is the *total* contribution across + all MPI ranks of the external code and thus we need to divide by the + number of MPI ranks since the tallying code expects per MPI rank contributions. + this function is compatible with PF_CALLBACK and PF_ARRAY mode ------------------------------------------------------------------------- */ void FixExternal::set_virial_global(double *caller_virial) { - if (!vflag_global) return; - + const double npscale = 1.0/(double)comm->nprocs; for (int i = 0; i < 6; i++) - virial[i] = caller_virial[i]; + user_virial[i] = npscale * caller_virial[i]; } /* ---------------------------------------------------------------------- - caller invokes this method to set its contribution to peratom energy + caller invokes this method to set its contribution to peratom energy. + this is applied to the *local* atoms only. + this function is compatible with PF_CALLBACK mode only since it tallies + its energy contributions directly into the accumulator arrays. ------------------------------------------------------------------------- */ void FixExternal::set_energy_peratom(double *caller_energy) { if (!eflag_atom) return; + if ((mode == PF_ARRAY) && (comm->me == 0)) + error->warning(FLERR,"Can only set energy/atom for fix external in pf/callback mode"); int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) @@ -217,6 +235,9 @@ void FixExternal::set_energy_peratom(double *caller_energy) /* ---------------------------------------------------------------------- caller invokes this method to set its contribution to peratom virial + this is applied to the *local* atoms only. + this function is compatible with PF_CALLBACK mode only since it tallies + its virial contributions directly into the accumulator arrays. ------------------------------------------------------------------------- */ void FixExternal::set_virial_peratom(double **caller_virial) @@ -224,6 +245,8 @@ void FixExternal::set_virial_peratom(double **caller_virial) int i,j; if (!vflag_atom) return; + if ((mode == PF_ARRAY) && (comm->me == 0)) + error->warning(FLERR,"Can only set virial/atom for fix external in pf/callback mode"); int nlocal = atom->nlocal; for (i = 0; i < nlocal; i++) @@ -232,13 +255,13 @@ void FixExternal::set_virial_peratom(double **caller_virial) } /* ---------------------------------------------------------------------- - caller invokes this method to set length of vector of values - assume all vector values are extensive, could make this an option + caller invokes this method to set length of global vector of values + assume all vector values are extensive. ------------------------------------------------------------------------- */ void FixExternal::set_vector_length(int n) { - delete [] caller_vector; + delete[] caller_vector; vector_flag = 1; size_vector = n; @@ -248,14 +271,15 @@ void FixExternal::set_vector_length(int n) } /* ---------------------------------------------------------------------- - caller invokes this method to set Index value in vector - index ranges from 1 to N inclusive + caller invokes this method to set value for item at "index" in vector + index is 1-based, thus index ranges from 1 to N inclusively. + Must be called from all MPI ranks. ------------------------------------------------------------------------- */ void FixExternal::set_vector(int index, double value) { - if (index >= size_vector) - error->all(FLERR,"Invalid set_vector index in fix external"); + if (index > size_vector) + error->all(FLERR,"Invalid set_vector index ({} of {}) in fix external",index,size_vector); caller_vector[index-1] = value; } @@ -286,6 +310,7 @@ double FixExternal::compute_vector(int n) double FixExternal::memory_usage() { double bytes = 3*atom->nmax * sizeof(double); + bytes += 6*sizeof(double); return bytes; } @@ -342,3 +367,16 @@ void FixExternal::set_callback(FnPtr caller_callback, void *caller_ptr) callback = caller_callback; ptr_caller = caller_ptr; } + +/* ---------------------------------------------------------------------- + get access to internal data structures +------------------------------------------------------------------------- */ + +void *FixExternal::extract(const char *str, int &dim) +{ + if (strcmp(str, "fexternal") == 0) { + dim = 2; + return (void *) fexternal; + } + return nullptr; +} diff --git a/src/fix_external.h b/src/fix_external.h index 0ace978f99..16db5d5015 100644 --- a/src/fix_external.h +++ b/src/fix_external.h @@ -57,11 +57,14 @@ class FixExternal : public Fix { typedef void (*FnPtr)(void *, bigint, int, tagint *, double **, double **); void set_callback(FnPtr, void *); + void *extract(const char *, int &); + private: int mode, ncall, napply, eflag_caller; FnPtr callback; void *ptr_caller; double user_energy; + double user_virial[6]; double *caller_vector; }; diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 15d49793b2..4ff7e7841b 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -45,6 +45,7 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) : create_attribute = 1; maxexchange_dynamic = 1; + use_bit_flag = 1; newton_pair = force->newton_pair; @@ -624,13 +625,21 @@ void FixNeighHistory::post_neighbor() for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; - rflag = sbmask(j) | pair->beyond_contact; - j &= NEIGHMASK; - jlist[jj] = j; - // rflag = 1 if r < radsum in npair_size() method + if (use_bit_flag) { + rflag = sbmask(j) | pair->beyond_contact; + j &= NEIGHMASK; + jlist[jj] = j; + } else { + rflag = 1; + j &= NEIGHMASK; + } + + // rflag = 1 if r < radsum in npair_size() method or if pair interactions extend further // preserve neigh history info if tag[j] is in old-neigh partner list // this test could be more geometrically precise for two sphere/line/tri + // if use_bit_flag is turned off, always record data since not all npair classes + // apply a mask for history (and they could use the bits for special bonds) if (rflag) { jtag = tag[j]; diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index de89c9a3cb..1405c05731 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -28,6 +28,7 @@ class FixNeighHistory : public Fix { public: int nlocal_neigh; // nlocal at last time neigh list was built int nall_neigh; // ditto for nlocal+nghost + int use_bit_flag; // flag whether this fix uses the extra bit in the nlist int **firstflag; // ptr to each atom's neighbor flsg double **firstvalue; // ptr to each atom's values class Pair *pair; // ptr to pair style that uses neighbor history diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 40940977a6..c906000ec5 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -635,6 +635,7 @@ int FixNH::setmask() mask |= FINAL_INTEGRATE; mask |= INITIAL_INTEGRATE_RESPA; mask |= FINAL_INTEGRATE_RESPA; + mask |= PRE_FORCE_RESPA; if (pre_exchange_flag) mask |= PRE_EXCHANGE; return mask; } @@ -1006,7 +1007,12 @@ void FixNH::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/) nve_x(); if (pstat_flag) remap(); } +} +/* ---------------------------------------------------------------------- */ + +void FixNH::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/) +{ // if barostat, redo KSpace coeffs at outermost level, // since volume has changed diff --git a/src/fix_nh.h b/src/fix_nh.h index ef541a0e05..1ec6bec2f8 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -28,6 +28,7 @@ class FixNH : public Fix { virtual void initial_integrate(int); virtual void final_integrate(); void initial_integrate_respa(int, int, int); + void pre_force_respa(int, int, int); void final_integrate_respa(int, int); virtual void pre_exchange(); double compute_scalar(); diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/fix_thermal_conductivity.cpp similarity index 100% rename from src/MISC/fix_thermal_conductivity.cpp rename to src/fix_thermal_conductivity.cpp diff --git a/src/MISC/fix_thermal_conductivity.h b/src/fix_thermal_conductivity.h similarity index 100% rename from src/MISC/fix_thermal_conductivity.h rename to src/fix_thermal_conductivity.h diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 3a523114ee..0a1c2a87cc 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,6 +13,7 @@ #include "imbalance_neigh.h" +#include "accelerator_kokkos.h" #include "atom.h" #include "comm.h" #include "error.h" @@ -36,9 +36,9 @@ ImbalanceNeigh::ImbalanceNeigh(LAMMPS *lmp) : Imbalance(lmp) int ImbalanceNeigh::options(int narg, char **arg) { - if (narg < 1) error->all(FLERR,"Illegal balance weight command"); - factor = utils::numeric(FLERR,arg[0],false,lmp); - if (factor <= 0.0) error->all(FLERR,"Illegal balance weight command"); + if (narg < 1) error->all(FLERR, "Illegal balance weight command"); + factor = utils::numeric(FLERR, arg[0], false, lmp); + if (factor <= 0.0) error->all(FLERR, "Illegal balance weight command"); return 1; } @@ -50,19 +50,30 @@ void ImbalanceNeigh::compute(double *weight) if (factor == 0.0) return; + // cannot use neighbor list weight with KOKKOS using GPUs + + if (lmp->kokkos && lmp->kokkos->kokkos_exists) { + if (lmp->kokkos->ngpus > 0) { + if (comm->me == 0 && !did_warn) + error->warning(FLERR, "Balance weight neigh skipped with KOKKOS using GPUs"); + did_warn = 1; + return; + } + } + // find suitable neighbor list // can only use certain conventional neighbor lists // NOTE: why not full list, if half does not exist? for (req = 0; req < neighbor->old_nrequest; ++req) { - if (neighbor->old_requests[req]->half && - neighbor->old_requests[req]->skip == 0 && - neighbor->lists[req] && neighbor->lists[req]->numneigh) break; + if (neighbor->old_requests[req]->half && neighbor->old_requests[req]->skip == 0 && + neighbor->lists[req] && neighbor->lists[req]->numneigh) + break; } if (req >= neighbor->old_nrequest || neighbor->ago < 0) { if (comm->me == 0 && !did_warn) - error->warning(FLERR,"Balance weight neigh skipped b/c no list found"); + error->warning(FLERR, "Balance weight neigh skipped b/c no list found"); did_warn = 1; return; } @@ -72,16 +83,16 @@ void ImbalanceNeigh::compute(double *weight) NeighList *list = neighbor->lists[req]; const int inum = list->inum; - const int * const ilist = list->ilist; - const int * const numneigh = list->numneigh; + const int *const ilist = list->ilist; + const int *const numneigh = list->numneigh; int nlocal = atom->nlocal; bigint neighsum = 0; for (int i = 0; i < inum; ++i) neighsum += numneigh[ilist[i]]; double localwt = 0.0; - if (nlocal) localwt = 1.0*neighsum/nlocal; + if (nlocal) localwt = 1.0 * neighsum / nlocal; - if (nlocal && localwt <= 0.0) error->one(FLERR,"Balance weight <= 0.0"); + if (nlocal && localwt <= 0.0) error->one(FLERR, "Balance weight <= 0.0"); // apply factor if specified != 1.0 // wtlo,wthi = lo/hi values excluding 0.0 due to no atoms on this proc @@ -90,15 +101,15 @@ void ImbalanceNeigh::compute(double *weight) // expand/contract all localwt values from lo->hi to lo->newhi if (factor != 1.0) { - double wtlo,wthi; + double wtlo, wthi; if (localwt == 0.0) localwt = BIG; - MPI_Allreduce(&localwt,&wtlo,1,MPI_DOUBLE,MPI_MIN,world); + MPI_Allreduce(&localwt, &wtlo, 1, MPI_DOUBLE, MPI_MIN, world); if (localwt == BIG) localwt = 0.0; - MPI_Allreduce(&localwt,&wthi,1,MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&localwt, &wthi, 1, MPI_DOUBLE, MPI_MAX, world); if (wtlo == wthi) return; - double newhi = wthi*factor; - localwt = wtlo + ((localwt-wtlo)/(wthi-wtlo)) * (newhi-wtlo); + double newhi = wthi * factor; + localwt = wtlo + ((localwt - wtlo) / (wthi - wtlo)) * (newhi - wtlo); } for (int i = 0; i < nlocal; i++) weight[i] *= localwt; @@ -108,5 +119,5 @@ void ImbalanceNeigh::compute(double *weight) std::string ImbalanceNeigh::info() { - return fmt::format(" neighbor weight factor: {}\n",factor); + return fmt::format(" neighbor weight factor: {}\n", factor); } diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index a5781beba2..d3a9403a6b 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,15 +13,15 @@ #include "improper_hybrid.h" -#include -#include #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -32,7 +31,11 @@ using namespace LAMMPS_NS; ImproperHybrid::ImproperHybrid(LAMMPS *lmp) : Improper(lmp) { + writedata = 0; nstyles = 0; + nimproperlist = nullptr; + improperlist = nullptr; + maximproper = nullptr; } /* ---------------------------------------------------------------------- */ @@ -41,19 +44,18 @@ ImproperHybrid::~ImproperHybrid() { if (nstyles) { for (int i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (int i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] nimproperlist; - delete [] maximproper; - for (int i = 0; i < nstyles; i++) - memory->destroy(improperlist[i]); - delete [] improperlist; + delete[] nimproperlist; + delete[] maximproper; + for (int i = 0; i < nstyles; i++) memory->destroy(improperlist[i]); + delete[] improperlist; } } @@ -61,7 +63,7 @@ ImproperHybrid::~ImproperHybrid() void ImproperHybrid::compute(int eflag, int vflag) { - int i,j,m,n; + int i, j, m, n; // save ptrs to original improperlist @@ -83,8 +85,7 @@ void ImproperHybrid::compute(int eflag, int vflag) if (nimproperlist[m] > maximproper[m]) { memory->destroy(improperlist[m]); maximproper[m] = nimproperlist[m] + EXTRA; - memory->create(improperlist[m],maximproper[m],5, - "improper_hybrid:improperlist"); + memory->create(improperlist[m], maximproper[m], 5, "improper_hybrid:improperlist"); } nimproperlist[m] = 0; } @@ -105,13 +106,23 @@ void ImproperHybrid::compute(int eflag, int vflag) // set neighbor->improperlist to sub-style improperlist before call // accumulate sub-style global/peratom energy/virial in hybrid - ev_init(eflag,vflag); + ev_init(eflag, vflag); + + // need to clear per-thread storage here, when using multiple threads + // with thread-enabled substyles to avoid uninitlialized data access. + + const int nthreads = comm->nthreads; + if (comm->nthreads > 1) { + const bigint nall = atom->nlocal + atom->nghost; + if (eflag_atom) memset(&eatom[0], 0, nall * nthreads * sizeof(double)); + if (vflag_atom) memset(&vatom[0][0], 0, 6 * nall * nthreads * sizeof(double)); + } for (m = 0; m < nstyles; m++) { neighbor->nimproperlist = nimproperlist[m]; neighbor->improperlist = improperlist[m]; - styles[m]->compute(eflag,vflag); + styles[m]->compute(eflag, vflag); if (eflag_global) energy += styles[m]->energy; if (vflag_global) @@ -127,16 +138,14 @@ void ImproperHybrid::compute(int eflag, int vflag) if (force->newton_bond) n += atom->nghost; double **vatom_substyle = styles[m]->vatom; for (i = 0; i < n; i++) - for (j = 0; j < 6; j++) - vatom[i][j] += vatom_substyle[i][j]; + for (j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j]; } if (cvflag_atom) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; double **cvatom_substyle = styles[m]->cvatom; for (i = 0; i < n; i++) - for (j = 0; j < 9; j++) - cvatom[i][j] += cvatom_substyle[i][j]; + for (j = 0; j < 9; j++) cvatom[i][j] += cvatom_substyle[i][j]; } } @@ -153,53 +162,43 @@ void ImproperHybrid::allocate() allocated = 1; int n = atom->nimpropertypes; - memory->create(map,n+1,"improper:map"); - memory->create(setflag,n+1,"improper:setflag"); + memory->create(map, n + 1, "improper:map"); + memory->create(setflag, n + 1, "improper:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; nimproperlist = new int[nstyles]; maximproper = new int[nstyles]; - improperlist = new int**[nstyles]; + improperlist = new int **[nstyles]; for (int m = 0; m < nstyles; m++) maximproper[m] = 0; for (int m = 0; m < nstyles; m++) improperlist[m] = nullptr; } -/* ---------------------------------------------------------------------- */ - -void ImproperHybrid::init_style() -{ - for (int i = 0; i < nstyles; i++) - styles[i]->init_style(); -} - - /* ---------------------------------------------------------------------- create one improper style for each arg in list ------------------------------------------------------------------------- */ void ImproperHybrid::settings(int narg, char **arg) { - int i,m,istyle; + int i, m, istyle; - if (narg < 1) error->all(FLERR,"Illegal improper_style command"); + if (narg < 1) error->all(FLERR, "Illegal improper_style command"); // delete old lists, since cannot just change settings if (nstyles) { for (i = 0; i < nstyles; i++) delete styles[i]; - delete [] styles; - for (i = 0; i < nstyles; i++) delete [] keywords[i]; - delete [] keywords; + delete[] styles; + for (i = 0; i < nstyles; i++) delete[] keywords[i]; + delete[] keywords; } if (allocated) { memory->destroy(setflag); memory->destroy(map); - delete [] nimproperlist; - delete [] maximproper; - for (i = 0; i < nstyles; i++) - memory->destroy(improperlist[i]); - delete [] improperlist; + delete[] nimproperlist; + delete[] maximproper; + for (i = 0; i < nstyles; i++) memory->destroy(improperlist[i]); + delete[] improperlist; } allocated = 0; @@ -210,7 +209,7 @@ void ImproperHybrid::settings(int narg, char **arg) nstyles = 0; i = 0; while (i < narg) { - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; nstyles++; @@ -218,8 +217,8 @@ void ImproperHybrid::settings(int narg, char **arg) // allocate list of sub-styles - styles = new Improper*[nstyles]; - keywords = new char*[nstyles]; + styles = new Improper *[nstyles]; + keywords = new char *[nstyles]; // allocate each sub-style and call its settings() with subset of args // allocate uses suffix, but don't store suffix version in keywords, @@ -234,23 +233,21 @@ void ImproperHybrid::settings(int narg, char **arg) while (i < narg) { for (m = 0; m < nstyles; m++) - if (strcmp(arg[i],keywords[m]) == 0) - error->all(FLERR,"Improper style hybrid cannot use " - "same improper style twice"); - if (strcmp(arg[i],"hybrid") == 0) - error->all(FLERR, - "Improper style hybrid cannot have hybrid as an argument"); - if (strcmp(arg[i],"none") == 0) - error->all(FLERR,"Improper style hybrid cannot have none as an argument"); + if (strcmp(arg[i], keywords[m]) == 0) + error->all(FLERR, "Improper style hybrid cannot use same improper style twice"); + if (strcmp(arg[i], "hybrid") == 0) + error->all(FLERR, "Improper style hybrid cannot have hybrid as an argument"); + if (strcmp(arg[i], "none") == 0) + error->all(FLERR, "Improper style hybrid cannot have none as an argument"); - styles[nstyles] = force->new_improper(arg[i],1,dummy); - force->store_style(keywords[nstyles],arg[i],0); + styles[nstyles] = force->new_improper(arg[i], 1, dummy); + force->store_style(keywords[nstyles], arg[i], 0); istyle = i; - if (strcmp(arg[i],"table") == 0) i++; + if (strcmp(arg[i], "table") == 0) i++; i++; while (i < narg && !isalpha(arg[i][0])) i++; - styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]); + styles[nstyles]->settings(i - istyle - 1, &arg[istyle + 1]); nstyles++; } } @@ -263,20 +260,27 @@ void ImproperHybrid::coeff(int narg, char **arg) { if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->nimpropertypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nimpropertypes, ilo, ihi, error); // 2nd arg = improper sub-style name - // allow for "none" as valid sub-style name + // allow for "none" or "skip" as valid sub-style name int m; for (m = 0; m < nstyles; m++) - if (strcmp(arg[1],keywords[m]) == 0) break; + if (strcmp(arg[1], keywords[m]) == 0) break; int none = 0; + int skip = 0; if (m == nstyles) { - if (strcmp(arg[1],"none") == 0) none = 1; - else error->all(FLERR,"Improper coeff for hybrid has invalid style"); + if (strcmp(arg[1], "none") == 0) + none = 1; + else if (strcmp(arg[1], "skip") == 0) + none = skip = 1; + else if (strcmp(arg[1], "aa") == 0) + error->all(FLERR, "AngleAngle coeff for hybrid improper has invalid format"); + else + error->all(FLERR, "Improper coeff for hybrid has invalid style"); } // move 1st arg to 2nd arg @@ -286,13 +290,16 @@ void ImproperHybrid::coeff(int narg, char **arg) // invoke sub-style coeff() starting with 1st arg - if (!none) styles[m]->coeff(narg-1,&arg[1]); + if (!none) styles[m]->coeff(narg - 1, &arg[1]); // set setflag and which type maps to which sub-style - // if sub-style is none: set hybrid setflag, wipe out map + // if sub-style is skip: auxiliary class2 setting in data file so ignore + // if sub-style is none and not skip: set hybrid setflag, wipe out map for (int i = ilo; i <= ihi; i++) { - if (none) { + if (skip) + continue; + else if (none) { setflag[i] = 1; map[i] = -1; } else { @@ -302,19 +309,29 @@ void ImproperHybrid::coeff(int narg, char **arg) } } +/* ---------------------------------------------------------------------- + run improper style specific initialization +------------------------------------------------------------------------- */ + +void ImproperHybrid::init_style() +{ + for (int m = 0; m < nstyles; m++) + if (styles[m]) styles[m]->init_style(); +} + /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void ImproperHybrid::write_restart(FILE *fp) { - fwrite(&nstyles,sizeof(int),1,fp); + fwrite(&nstyles, sizeof(int), 1, fp); int n; for (int m = 0; m < nstyles; m++) { n = strlen(keywords[m]) + 1; - fwrite(&n,sizeof(int),1,fp); - fwrite(keywords[m],sizeof(char),n,fp); + fwrite(&n, sizeof(int), 1, fp); + fwrite(keywords[m], sizeof(char), n, fp); styles[m]->write_restart_settings(fp); } } @@ -326,21 +343,21 @@ void ImproperHybrid::write_restart(FILE *fp) void ImproperHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&nstyles,1,MPI_INT,0,world); - styles = new Improper*[nstyles]; - keywords = new char*[nstyles]; + if (me == 0) utils::sfread(FLERR, &nstyles, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&nstyles, 1, MPI_INT, 0, world); + styles = new Improper *[nstyles]; + keywords = new char *[nstyles]; allocate(); - int n,dummy; + int n, dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&n,1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &n, sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&n, 1, MPI_INT, 0, world); keywords[m] = new char[n]; - if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,nullptr,error); - MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); - styles[m] = force->new_improper(keywords[m],0,dummy); + if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error); + MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world); + styles[m] = force->new_improper(keywords[m], 0, dummy); styles[m]->read_restart_settings(fp); } } @@ -351,10 +368,10 @@ void ImproperHybrid::read_restart(FILE *fp) double ImproperHybrid::memory_usage() { - double bytes = (double)maxeatom * sizeof(double); - bytes += (double)maxvatom*6 * sizeof(double); - bytes += (double)maxcvatom*9 * sizeof(double); - for (int m = 0; m < nstyles; m++) bytes += (double)maximproper[m]*5 * sizeof(int); + double bytes = (double) maxeatom * sizeof(double); + bytes += (double) maxvatom * 6 * sizeof(double); + bytes += (double) maxcvatom * 9 * sizeof(double); + for (int m = 0; m < nstyles; m++) bytes += (double) maximproper[m] * 5 * sizeof(int); for (int m = 0; m < nstyles; m++) if (styles[m]) bytes += styles[m]->memory_usage(); return bytes; diff --git a/src/info.cpp b/src/info.cpp index 049bdd5bfd..7c0eb572db 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -1222,8 +1222,8 @@ bool Info::has_accelerator_feature(const std::string &package, return lmp_gpu_config(category,setting); } #endif -#if defined(LMP_USER_OMP) - if (package == "USER-OMP") { +#if defined(LMP_OPENMP) + if (package == "OPENMP") { if (category == "precision") { if (setting == "double") return true; else return false; @@ -1238,8 +1238,8 @@ bool Info::has_accelerator_feature(const std::string &package, } } #endif -#if defined(LMP_USER_INTEL) - if (package == "USER-INTEL") { +#if defined(LMP_INTEL) + if (package == "INTEL") { if (category == "precision") { if (setting == "double") return true; else if (setting == "mixed") return true; @@ -1466,24 +1466,24 @@ std::string Info::get_accelerator_info(const std::string &package) if (has_accelerator_feature("KOKKOS","precision","double")) mesg += " double"; mesg += "\n"; } - if ((package.empty() || (package == "USER-OMP")) && has_package("USER-OMP")) { - mesg += "USER-OMP package API:"; - if (has_accelerator_feature("USER-OMP","api","openmp")) mesg += " OpenMP"; - if (has_accelerator_feature("USER-OMP","api","serial")) mesg += " Serial"; - mesg += "\nUSER-OMP package precision:"; - if (has_accelerator_feature("USER-OMP","precision","single")) mesg += " single"; - if (has_accelerator_feature("USER-OMP","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("USER-OMP","precision","double")) mesg += " double"; + if ((package.empty() || (package == "OPENMP")) && has_package("OPENMP")) { + mesg += "OPENMP package API:"; + if (has_accelerator_feature("OPENMP","api","openmp")) mesg += " OpenMP"; + if (has_accelerator_feature("OPENMP","api","serial")) mesg += " Serial"; + mesg += "\nOPENMP package precision:"; + if (has_accelerator_feature("OPENMP","precision","single")) mesg += " single"; + if (has_accelerator_feature("OPENMP","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("OPENMP","precision","double")) mesg += " double"; mesg += "\n"; } - if ((package.empty() || (package == "USER-INTEL")) && has_package("USER-INTEL")) { - mesg += "USER-INTEL package API:"; - if (has_accelerator_feature("USER-INTEL","api","phi")) mesg += " Phi"; - if (has_accelerator_feature("USER-INTEL","api","openmp")) mesg += " OpenMP"; - mesg += "\nUSER-INTEL package precision:"; - if (has_accelerator_feature("USER-INTEL","precision","single")) mesg += " single"; - if (has_accelerator_feature("USER-INTEL","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("USER-INTEL","precision","double")) mesg += " double"; + if ((package.empty() || (package == "INTEL")) && has_package("INTEL")) { + mesg += "INTEL package API:"; + if (has_accelerator_feature("INTEL","api","phi")) mesg += " Phi"; + if (has_accelerator_feature("INTEL","api","openmp")) mesg += " OpenMP"; + mesg += "\nINTEL package precision:"; + if (has_accelerator_feature("INTEL","precision","single")) mesg += " single"; + if (has_accelerator_feature("INTEL","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("INTEL","precision","double")) mesg += " double"; mesg += "\n"; } return mesg; diff --git a/src/input.cpp b/src/input.cpp index 1ef88be866..50e0d45aa0 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -163,9 +163,9 @@ Input::~Input() memory->sfree(line); memory->sfree(copy); memory->sfree(work); - if (labelstr) delete [] labelstr; + if (labelstr) delete[] labelstr; memory->sfree(arg); - delete [] infiles; + delete[] infiles; delete variable; delete command_map; @@ -897,9 +897,9 @@ void Input::ifthenelse() for (int i = 0; i < ncommands; i++) { one(commands[i]); - delete [] commands[i]; + delete[] commands[i]; } - delete [] commands; + delete[] commands; return; } @@ -952,9 +952,9 @@ void Input::ifthenelse() for (int i = 0; i < ncommands; i++) { one(commands[i]); - delete [] commands[i]; + delete[] commands[i]; } - delete [] commands; + delete[] commands; return; } @@ -1015,7 +1015,7 @@ void Input::jump() if (narg == 2) { label_active = 1; - if (labelstr) delete [] labelstr; + if (labelstr) delete[] labelstr; labelstr = utils::strdup(arg[1]); } } @@ -1197,7 +1197,7 @@ void Input::shell() if (me == 0 && err != 0) { char *message = shell_failed_message("cd",err); error->warning(FLERR,message); - delete [] message; + delete[] message; } } else if (strcmp(arg[0],"mkdir") == 0) { @@ -1212,7 +1212,7 @@ void Input::shell() if (rv < 0) { char *message = shell_failed_message("mkdir",errno); error->warning(FLERR,message); - delete [] message; + delete[] message; } } @@ -1223,7 +1223,7 @@ void Input::shell() if (me == 0 && err != 0) { char *message = shell_failed_message("mv",err); error->warning(FLERR,message); - delete [] message; + delete[] message; } } else if (strcmp(arg[0],"rm") == 0) { @@ -1233,7 +1233,7 @@ void Input::shell() if (unlink(arg[i]) < 0) { char *message = shell_failed_message("rm",errno); error->warning(FLERR,message); - delete [] message; + delete[] message; } } @@ -1244,7 +1244,7 @@ void Input::shell() if (rmdir(arg[i]) < 0) { char *message = shell_failed_message("rmdir",errno); error->warning(FLERR,message); - delete [] message; + delete[] message; } } @@ -1271,7 +1271,7 @@ void Input::shell() if (me == 0 && err != 0) { char *message = shell_failed_message("putenv",err); error->warning(FLERR,message); - delete [] message; + delete[] message; } } @@ -1683,7 +1683,7 @@ void Input::package() } else if (strcmp(arg[0],"omp") == 0) { if (!modify->check_package("OMP")) error->all(FLERR, - "Package omp command without USER-OMP package installed"); + "Package omp command without OPENMP package installed"); std::string fixcmd = "package_omp all OMP"; for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i]; @@ -1692,7 +1692,7 @@ void Input::package() } else if (strcmp(arg[0],"intel") == 0) { if (!modify->check_package("INTEL")) error->all(FLERR, - "Package intel command without USER-INTEL package installed"); + "Package intel command without INTEL package installed"); std::string fixcmd = "package_intel all INTEL"; for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i]; @@ -1847,8 +1847,8 @@ void Input::suffix() } else { lmp->suffix_enable = 1; - delete [] lmp->suffix; - delete [] lmp->suffix2; + delete[] lmp->suffix; + delete[] lmp->suffix2; lmp->suffix = lmp->suffix2 = nullptr; if (strcmp(arg[0],"hybrid") == 0) { diff --git a/src/input.h b/src/input.h index d82816aa04..faf45ab305 100644 --- a/src/input.h +++ b/src/input.h @@ -357,14 +357,14 @@ E: Package kokkos command without KOKKOS package enabled The KOKKOS package must be installed via "make yes-kokkos" before LAMMPS is built, and the "-k on" must be used to enable the package. -E: Package omp command without USER-OMP package installed +E: Package omp command without OPENMP package installed -The USER-OMP package must be installed via "make yes-user-omp" before +The OPENMP package must be installed via "make yes-openmp" before LAMMPS is built. -E: Package intel command without USER-INTEL package installed +E: Package intel command without INTEL package installed -The USER-INTEL package must be installed via "make yes-user-intel" +The INTEL package must be installed via "make yes-intel" before LAMMPS is built. E: Pair_coeff command before simulation box is defined diff --git a/src/lammps.cpp b/src/lammps.cpp index 131d2e66f6..5820a625d2 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -798,7 +798,7 @@ void LAMMPS::create() else neighbor = new Neighbor(this); if (kokkos) domain = new DomainKokkos(this); -#ifdef LMP_USER_OMP +#ifdef LMP_OPENMP else domain = new DomainOMP(this); #else else domain = new Domain(this); @@ -843,19 +843,19 @@ void LAMMPS::post_create() // suffix will always be set if suffix_enable = 1 // check that KOKKOS package classes were instantiated - // check that GPU, INTEL, USER-OMP fixes were compiled with LAMMPS + // check that GPU, INTEL, OPENMP fixes were compiled with LAMMPS if (suffix_enable) { if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU")) error->all(FLERR,"Using suffix gpu without GPU package installed"); if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL")) - error->all(FLERR,"Using suffix intel without USER-INTEL package installed"); + error->all(FLERR,"Using suffix intel without INTEL package installed"); if (strcmp(suffix,"kk") == 0 && (kokkos == nullptr || kokkos->kokkos_exists == 0)) error->all(FLERR,"Using suffix kk without KOKKOS package enabled"); if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP")) - error->all(FLERR,"Using suffix omp without USER-OMP package installed"); + error->all(FLERR,"Using suffix omp without OPENMP package installed"); if (strcmp(suffix,"gpu") == 0) input->one("package gpu 0"); if (strcmp(suffix,"intel") == 0) input->one("package intel 1"); diff --git a/src/lammps.h b/src/lammps.h index 9592f9af05..74ae47e9a2 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -199,7 +199,7 @@ E: Using suffix gpu without GPU package installed Self-explanatory. -E: Using suffix intel without USER-INTEL package installed +E: Using suffix intel without INTEL package installed Self-explanatory. @@ -207,7 +207,7 @@ E: Using suffix kk without KOKKOS package enabled Self-explanatory. -E: Using suffix omp without USER-OMP package installed +E: Using suffix omp without OPENMP package installed Self-explanatory. diff --git a/src/library.cpp b/src/library.cpp index 8625296172..f534af0925 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -19,6 +19,7 @@ #include "library.h" #include +#include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" @@ -333,8 +334,8 @@ The MPI standard requires that any MPI application calls do any MPI calls, MPI is still initialized internally to avoid errors accessing any MPI functions. This function should then be called right before exiting the program to wait until all (parallel) tasks are -completed and then MPI is cleanly shut down. After this function no -more MPI calls may be made. +completed and then MPI is cleanly shut down. After calling this +function no more MPI calls may be made. .. versionadded:: 18Sep2020 @@ -353,6 +354,28 @@ void lammps_mpi_finalize() } } +/* ---------------------------------------------------------------------- */ + +/** Shut down the Kokkos library environment. + * +\verbatim embed:rst + +The Kokkos library may only be initialized once during the execution of +a process. This is done automatically the first time Kokkos +functionality is used. This requires that the Kokkos environment +must be explicitly shut down after any LAMMPS instance using it is +closed (to release associated resources). +After calling this function no Kokkos functionality may be used. + +.. versionadded:: 2Jul2021 + +\endverbatim */ + +void lammps_kokkos_finalize() +{ + KokkosLMP::finalize(); +} + // ---------------------------------------------------------------------- // Library functions to process commands // ---------------------------------------------------------------------- @@ -523,7 +546,7 @@ void lammps_commands_string(void *handle, const char *str) } END_CAPTURE - delete [] copy; + delete[] copy; } // ----------------------------------------------------------------------- @@ -2663,6 +2686,115 @@ void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count, END_CAPTURE } +/** Gather type and constituent atom info for all bonds + * +\verbatim embed:rst + +This function copies the list of all bonds into a buffer provided by +the calling code. The buffer will be filled with bond type, bond atom 1, +bond atom 2 for each bond. Thus the buffer has to be allocated to the +dimension of 3 times the **total** number of bonds times the size of +the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on +whether they are stored in 32-bit or 64-bit integers, respectively. +This size depends on the compile time settings used when compiling +the LAMMPS library and can be queried by calling +:cpp:func:`lammps_extract_setting()` with the keyword "tagint". + +When running in parallel, the data buffer must be allocated on **all** +MPI ranks and will be filled with the information for **all** bonds +in the system. + +.. versionadded:: 28Jul2021 + +Below is a brief C code demonstrating accessing this collected bond information. + +.. code-block:: c + + #include + #include + #include + #include "library.h" + + int main(int argc, char **argv) + { + int tagintsize; + int64_t i, nbonds; + void *handle, *bonds; + + handle = lammps_open_no_mpi(0, NULL, NULL); + lammps_file(handle, "in.some_input"); + + tagintsize = lammps_extract_setting(handle, "tagint"); + if (tagintsize == 4) + nbonds = *(int32_t *)lammps_extract_global(handle, "nbonds"); + else + nbonds = *(int64_t *)lammps_extract_global(handle, "nbonds"); + bonds = malloc(nbonds * 3 * tagintsize); + + lammps_gather_bonds(handle, bonds); + + if (lammps_extract_setting(handle, "world_rank") == 0) { + if (tagintsize == 4) { + int32_t *bonds_real = (int32_t *)bonds; + for (i = 0; i < nbonds; ++i) { + printf("bond % 4ld: type = %d, atoms: % 4d % 4d\n",i, + bonds_real[3*i], bonds_real[3*i+1], bonds_real[3*i+2]); + } + } else { + int64_t *bonds_real = (int64_t *)bonds; + for (i = 0; i < nbonds; ++i) { + printf("bond % 4ld: type = %ld, atoms: % 4ld % 4ld\n",i, + bonds_real[3*i], bonds_real[3*i+1], bonds_real[3*i+2]); + } + } + } + + lammps_close(handle); + lammps_mpi_finalize(); + free(bonds); + return 0; + } + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance + * \param data pointer to data to copy the result to */ + +void lammps_gather_bonds(void *handle, void *data) +{ + LAMMPS *lmp = (LAMMPS *)handle; + BEGIN_CAPTURE { + void *val = lammps_extract_global(handle,"nbonds"); + bigint nbonds = *(bigint *)val; + + // no bonds + if (nbonds == 0) return; + + // count per MPI rank bonds, determine offsets and allocate local buffers + int localbonds = lmp->atom->avec->pack_bond(nullptr); + int nprocs = lmp->comm->nprocs; + int *bufsizes = new int[nprocs]; + int *bufoffsets = new int[nprocs]; + MPI_Allgather(&localbonds, 1, MPI_INT, bufsizes, 1, MPI_INT, lmp->world); + bufoffsets[0] = 0; + bufsizes[0] *= 3; // 3 items per bond: type, atom1, atom2 + for (int i = 1; i < nprocs; ++i) { + bufoffsets[i] = bufoffsets[i-1] + bufsizes[i-1]; + bufsizes[i] *= 3; // 3 items per bond: type, atom1, atom2 + } + + tagint **bonds; + lmp->memory->create(bonds, localbonds, 3, "library:gather_bonds:localbonds"); + lmp->atom->avec->pack_bond(bonds); + MPI_Allgatherv(&bonds[0][0], 3*localbonds, MPI_LMP_TAGINT, data, bufsizes, + bufoffsets, MPI_LMP_TAGINT, lmp->world); + lmp->memory->destroy(bonds); + delete[] bufsizes; + delete[] bufoffsets; + } + END_CAPTURE +} + /* ---------------------------------------------------------------------- Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France) gather the named atom-based entity for all atoms @@ -4327,7 +4459,7 @@ int lammps_config_package_name(int idx, char *buffer, int buf_size) { \verbatim embed:rst This function checks availability of compile time settings of included :doc:`accelerator packages ` in LAMMPS. -Supported packages names are "GPU", "KOKKOS", "USER-INTEL", and "USER-OMP". +Supported packages names are "GPU", "KOKKOS", "INTEL", and "OPENMP". Supported categories are "api" with possible settings "cuda", "hip", "phi", "pthreads", "opencl", "openmp", and "serial", and "precision" with possible settings "double", "mixed", and "single". If the combination @@ -4781,15 +4913,51 @@ void lammps_decode_image_flags(imageint image, int *flags) flags[2] = (image >> IMG2BITS) - IMGMAX; } -/* ---------------------------------------------------------------------- - find fix external with given ID and set the callback function - and caller pointer -------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ -void lammps_set_fix_external_callback(void *handle, char *id, FixExternalFnPtr callback_ptr, void * caller) +/** Set up the callback function for a fix external instance with the given ID. + +\verbatim embed:rst + +Fix :doc:`external ` allows programs that are running LAMMPS through +its library interface to modify certain LAMMPS properties on specific +timesteps, similar to the way other fixes do. + +This function sets the callback function for use with the "pf/callback" +mode. The function has to have C language bindings with the prototype: + +.. code-block:: c + + void func(void *ptr, bigint timestep, int nlocal, tagint *ids, double **x, double **fexternal); + +The argument *ptr* to this function will be stored in fix external and +the passed as the first argument calling the callback function `func()`. +This would usually be a pointer to the active LAMMPS instance, i.e. the same +pointer as the *handle* argument. This would be needed to call +functions that set the global or per-atom energy or virial contributions +from within the callback function. + +The callback mechanism is one of the two modes of how forces and can be +applied to a simulation with the help of fix external. The alternative +is the array mode where you call :cpp:func:`lammps_fix_external_get_force`. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionchanged:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param funcptr pointer to callback function + * \param ptr pointer to object in calling code, passed to callback function as first argument */ + +void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, void *ptr) { LAMMPS *lmp = (LAMMPS *) handle; - FixExternal::FnPtr callback = (FixExternal::FnPtr) callback_ptr; + FixExternal::FnPtr callback = (FixExternal::FnPtr) funcptr; BEGIN_CAPTURE { @@ -4800,18 +4968,107 @@ void lammps_set_fix_external_callback(void *handle, char *id, FixExternalFnPtr c Fix *fix = lmp->modify->fix[ifix]; if (strcmp("external",fix->style) != 0) - lmp->error->all(FLERR,"Fix '{}' is not of style " - "external!", id); + lmp->error->all(FLERR,"Fix '{}' is not of style 'external'", id); - FixExternal * fext = (FixExternal*) fix; - fext->set_callback(callback, caller); + FixExternal *fext = (FixExternal *) fix; + fext->set_callback(callback, ptr); } END_CAPTURE } -/* set global energy contribution from fix external */ -void lammps_fix_external_set_energy_global(void *handle, char *id, - double energy) +/** Get pointer to the force array storage in a fix external instance with the given ID. + +\verbatim embed:rst + +Fix :doc:`external ` allows programs that are running LAMMPS through +its library interface to add or modify certain LAMMPS properties on specific +timesteps, similar to the way other fixes do. + +This function provides access to the per-atom force storage in a fix +external instance with the given fix-ID to be added to the individual +atoms when using the "pf/array" mode. The *fexternal* array can be +accessed like other "native" per-atom arrays accessible via the +:cpp:func:`lammps_extract_atom` function. Please note that the array +stores holds the forces for *local* atoms for each MPI ranks, in the +order determined by the neighbor list build. Because the underlying +data structures can change as well as the order of atom as they migrate +between MPI processes because of the domain decomposition +parallelization, this function should be always called immediately +before the forces are going to be set to get an up-to-date pointer. + You can use e.g. :cpp:func:`lammps_get_natoms` to obtain the number +of local atoms `nlocal` and then assume the dimensions of the returned +force array as ``double force[nlocal][3]``. + +This is an alternative to the callback mechanism in fix external set up by +:cpp:func:`lammps_set_fix_external_callback`. The main difference is +that this mechanism can be used when forces are be pre-computed and the +control alternates between LAMMPS and the external code, while the +callback mechanism can call the external code to compute the force when +the fix is triggered and needs them. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \return a pointer to the per-atom force array allocated by the fix */ + +double **lammps_fix_external_get_force(void *handle, const char *id) +{ + LAMMPS *lmp = (LAMMPS *) handle; + double **fexternal = nullptr; + + BEGIN_CAPTURE + { + int ifix = lmp->modify->find_fix(id); + if (ifix < 0) + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); + + Fix *fix = lmp->modify->fix[ifix]; + + if (strcmp("external",fix->style) != 0) + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); + + fexternal = (double **)fix->extract("fexternal",ifix); + } + END_CAPTURE + return fexternal; +} + +/** Set the global energy contribution for a fix external instance with the given ID. + +\verbatim embed:rst + +This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and +:cpp:func:`lammps_fix_external_get_force` to also set the contribution +to the global energy from the external code. The value of the *eng* +argument will be stored in the fix and applied on the current and all +following timesteps until changed by another call to this function. +The energy is in energy units as determined by the current :doc:`units ` +settings and is the **total** energy of the contribution. Thus when +running in parallel all MPI processes have to call this function with +the **same** value and this will be returned as scalar property of the +fix external instance when accessed in LAMMPS input commands or from +variables. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param eng total energy to be added to the global energy */ + +void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng) { LAMMPS *lmp = (LAMMPS *) handle; @@ -4826,15 +5083,43 @@ void lammps_fix_external_set_energy_global(void *handle, char *id, if (strcmp("external",fix->style) != 0) lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); - FixExternal * fext = (FixExternal*) fix; - fext->set_energy_global(energy); + FixExternal *fext = (FixExternal*) fix; + fext->set_energy_global(eng); } END_CAPTURE } -/* set global virial contribution from fix external */ -void lammps_fix_external_set_virial_global(void *handle, char *id, - double *virial) +/** Set the global virial contribution for a fix external instance with the given ID. + +\verbatim embed:rst + +This is a companion function to :cpp:func:`lammps_set_fix_external_callback` +and :cpp:func:`lammps_fix_external_get_force` to set the contribution to +the global virial from the external code. + +The 6 values of the *virial* array will be stored in the fix and applied +on the current and all following timesteps until changed by another call +to this function. The components of the virial need to be stored in the +order: *xx*, *yy*, *zz*, *xy*, *xz*, *yz*. In LAMMPS the virial is +stored internally as `stress*volume` in units of `pressure*volume` as +determined by the current :doc:`units ` settings and is the +**total** contribution. Thus when running in parallel all MPI processes +have to call this function with the **same** value and this will then +be added by fix external. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param virial the 6 global stress tensor components to be added to the global virial */ + +void lammps_fix_external_set_virial_global(void *handle, const char *id, double *virial) { LAMMPS *lmp = (LAMMPS *) handle; @@ -4855,6 +5140,215 @@ void lammps_fix_external_set_virial_global(void *handle, char *id, END_CAPTURE } +/** Set the per-atom energy contribution for a fix external instance with the given ID. + +\verbatim embed:rst + +This is a companion function to :cpp:func:`lammps_set_fix_external_callback` +to set the per-atom energy contribution due to the fix from the external code +as part of the callback function. For this to work, the handle to the +LAMMPS object must be passed as the *ptr* argument when registering the +callback function. + +.. note:: + + This function is fully independent from :cpp:func:`lammps_fix_external_set_energy_global` + and will **NOT** add any contributions to the global energy tally + and **NOT** check whether the sum of the contributions added here are + consistent with the global added energy. + + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param eng pointer to array of length nlocal with the energy to be added to the per-atom energy */ + +void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng) +{ + LAMMPS *lmp = (LAMMPS *) handle; + + BEGIN_CAPTURE + { + int ifix = lmp->modify->find_fix(id); + if (ifix < 0) + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); + + Fix *fix = lmp->modify->fix[ifix]; + + if (strcmp("external",fix->style) != 0) + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); + + FixExternal *fext = (FixExternal*) fix; + fext->set_energy_peratom(eng); + } + END_CAPTURE +} + +/** Set the per-atom virial contribution for a fix external instance with the given ID. + +\verbatim embed:rst + +This is a companion function to :cpp:func:`lammps_set_fix_external_callback` +to set the per-atom virial contribution due to the fix from the external code +as part of the callback function. For this to work, the handle to the +LAMMPS object must be passed as the *ptr* argument when registering the +callback function. + +.. note:: + + This function is fully independent from :cpp:func:`lammps_fix_external_set_virial_global` + and will **NOT** add any contributions to the global virial tally + and **NOT** check whether the sum of the contributions added here are + consistent with the global added virial. + +The order and units of the per-atom stress tensor elements are the same +as for the global virial. The code in fix external assumes the +dimensions of the per-atom virial array is ``double virial[nlocal][6]``. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param virial a list of nlocal entries with the 6 per-atom stress tensor components to be added to the per-atom virial */ + +void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial) +{ + LAMMPS *lmp = (LAMMPS *) handle; + + BEGIN_CAPTURE + { + int ifix = lmp->modify->find_fix(id); + if (ifix < 0) + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); + + Fix *fix = lmp->modify->fix[ifix]; + + if (strcmp("external",fix->style) != 0) + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); + + FixExternal * fext = (FixExternal*) fix; + fext->set_virial_peratom(virial); + } + END_CAPTURE +} + +/** Set the vector length for a global vector stored with fix external for analysis + +\verbatim embed:rst + +This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and +:cpp:func:`lammps_fix_external_get_force` to set the length of a global vector of +properties that will be stored with the fix via +:cpp:func:`lammps_fix_external_set_vector`. + +This function needs to be called **before** a call to +:cpp:func:`lammps_fix_external_set_vector` and **before** a run or minimize +command. When running in parallel it must be called from **all** MPI +processes and with the same length parameter. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param len length of the global vector to be stored with the fix */ + +void lammps_fix_external_set_vector_length(void *handle, const char *id, int len) +{ + LAMMPS *lmp = (LAMMPS *) handle; + + BEGIN_CAPTURE + { + int ifix = lmp->modify->find_fix(id); + if (ifix < 0) + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); + + Fix *fix = lmp->modify->fix[ifix]; + + if (strcmp("external",fix->style) != 0) + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); + + FixExternal *fext = (FixExternal*) fix; + fext->set_vector_length(len); + } + END_CAPTURE +} + +/** Store a global vector value for a fix external instance with the given ID. + +\verbatim embed:rst + +This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and +:cpp:func:`lammps_fix_external_get_force` to set the values of a global vector of +properties that will be stored with the fix. And can be accessed from +within LAMMPS input commands (e.g. fix ave/time or variables) when used +in a vector context. + +This function needs to be called **after** a call to +:cpp:func:`lammps_fix_external_set_vector_length` and the and **before** a run or minimize +command. When running in parallel it must be called from **all** MPI +processes and with the **same** index and value parameters. The value +is assumed to be extensive. + +.. note:: + + The index in the *idx* parameter is 1-based, i.e. the first element + is set with idx = 1 and the last element of the vector with idx = N, + where N is the value of the *len* parameter of the call to + :cpp:func:`lammps_fix_external_set_vector_length`. + +Please see the documentation for :doc:`fix external ` for +more information about how to use the fix and how to couple it with an +external code. + +.. versionadded:: 28Jul2021 + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. + * \param id fix ID of fix external instance + * \param idx 1-based index of in global vector + * \param val value to be stored in global vector */ + +void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val) +{ + LAMMPS *lmp = (LAMMPS *) handle; + + BEGIN_CAPTURE + { + int ifix = lmp->modify->find_fix(id); + if (ifix < 0) + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); + + Fix *fix = lmp->modify->fix[ifix]; + + if (strcmp("external",fix->style) != 0) + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); + + FixExternal * fext = (FixExternal*) fix; + fext->set_vector(idx, val); + } + END_CAPTURE +} + /* ---------------------------------------------------------------------- */ /** Free memory buffer allocated by LAMMPS. diff --git a/src/library.h b/src/library.h index 70ece96716..91146e8526 100644 --- a/src/library.h +++ b/src/library.h @@ -94,6 +94,7 @@ void lammps_close(void *handle); void lammps_mpi_init(); void lammps_mpi_finalize(); +void lammps_kokkos_finalize(); /* ---------------------------------------------------------------------- * Library functions to process commands @@ -151,6 +152,8 @@ void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *d void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count, int ndata, int *ids, void *data); +void lammps_gather_bonds(void *handle, void *data); + void lammps_gather(void *handle, char *name, int type, int count, void *data); void lammps_gather_concat(void *handle, char *name, int type, int count, void *data); void lammps_gather_subset(void *handle, char *name, int type, int count, int ndata, int *ids, @@ -225,16 +228,21 @@ void lammps_decode_image_flags(int64_t image, int *flags); #if defined(LAMMPS_BIGBIG) typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); -void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void *); +void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, void *ptr); #elif defined(LAMMPS_SMALLBIG) typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **); -void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void *); +void lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void *); #else typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **); -void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void *); +void lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void *); #endif -void lammps_fix_external_set_energy_global(void *, char *, double); -void lammps_fix_external_set_virial_global(void *, char *, double *); +double **lammps_fix_external_get_force(void *handle, const char *id); +void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng); +void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng); +void lammps_fix_external_set_virial_global(void *handle, const char *id, double *virial); +void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial); +void lammps_fix_external_set_vector_length(void *handle, const char *id, int len); +void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val); void lammps_free(void *ptr); diff --git a/src/lmptype.h b/src/lmptype.h index 6a7a7ef1b9..871bf5ff6c 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -242,9 +242,9 @@ union ubuf { // define stack variable alignment -#if defined(__INTEL_LLVM_COMPILER) || defined(__INTEL_COMPILER) +#if defined(__INTEL_COMPILER) #define _alignvar(expr, val) __declspec(align(val)) expr -#elif defined(__GNUC__) || defined(__PGI) +#elif defined(__GNUC__) || defined(__PGI) || defined(__INTEL_LLVM_COMPILER) #define _alignvar(expr, val) expr __attribute((aligned(val))) #else #define _alignvar(expr, val) expr @@ -266,7 +266,7 @@ union ubuf { #if defined(__clang__) #define _noopt __attribute__((optnone)) -#elif defined(__INTEL_COMPILER) +#elif defined(__INTEL_COMPILER) || defined(__INTEL_LLVM_COMPILER) #define _noopt #elif defined(__PGI) #define _noopt diff --git a/src/main.cpp b/src/main.cpp index 8399ecab45..d65247c224 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -14,6 +14,7 @@ #include "lammps.h" #include "input.h" +#include "accelerator_kokkos.h" #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" #endif @@ -30,7 +31,7 @@ #endif // import MolSSI Driver Interface library -#if defined(LMP_USER_MDI) +#if defined(LMP_MDI) #include #endif @@ -46,7 +47,7 @@ int main(int argc, char **argv) MPI_Comm lammps_comm = MPI_COMM_WORLD; -#if defined(LMP_USER_MDI) +#if defined(LMP_MDI) // initialize MDI interface, if compiled in int mdi_flag; @@ -77,13 +78,16 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { + KokkosLMP::finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &e) { + KokkosLMP::finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); + KokkosLMP::finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } @@ -94,10 +98,12 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); + KokkosLMP::finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif + KokkosLMP::finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); } diff --git a/src/memory.cpp b/src/memory.cpp index 3e67ed1496..2a053e3dbd 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -16,7 +16,8 @@ #include "error.h" -#if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) +#if defined(LMP_INTEL) && \ + ((defined(__INTEL_COMPILER) || defined(__INTEL_LLVM_COMPILER))) #ifndef LMP_INTEL_NO_TBB #define LMP_USE_TBB_ALLOCATOR #include "tbb/scalable_allocator.h" @@ -30,7 +31,7 @@ #endif #endif -#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) +#if defined(LMP_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 #endif @@ -81,7 +82,7 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name) #if defined(LMP_USE_TBB_ALLOCATOR) ptr = scalable_aligned_realloc(ptr, nbytes, LAMMPS_MEMALIGN); #elif defined(LMP_INTEL_NO_TBB) && defined(LAMMPS_MEMALIGN) && \ - defined(__INTEL_COMPILER) + (defined(__INTEL_COMPILER) || defined(__INTEL_LLVM_COMPILER)) ptr = realloc(ptr, nbytes); uintptr_t offset = ((uintptr_t)(const void *)(ptr)) % LAMMPS_MEMALIGN; diff --git a/src/min.cpp b/src/min.cpp index 8fe73dc9e1..69e24a541f 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -121,8 +121,7 @@ void Min::init() // create fix needed for storing atom-based quantities // will delete it at end of run - modify->add_fix("MINIMIZE all MINIMIZE"); - fix_minimize = (FixMinimize *) modify->fix[modify->nfix-1]; + fix_minimize = (FixMinimize *) modify->add_fix("MINIMIZE all MINIMIZE"); // clear out extra global and per-atom dof // will receive requests for new per-atom dof during pair init() diff --git a/src/modify.cpp b/src/modify.cpp index c395575d7f..995b3b82ac 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -37,7 +37,6 @@ using namespace FixConst; #define DELTA 4 #define BIG 1.0e20 -#define NEXCEPT 7 // change when add to exceptions in add_fix() /* ---------------------------------------------------------------------- */ @@ -803,7 +802,7 @@ int Modify::min_reset_ref() add a new fix or replace one with same ID ------------------------------------------------------------------------- */ -void Modify::add_fix(int narg, char **arg, int trysuffix) +Fix *Modify::add_fix(int narg, char **arg, int trysuffix) { if (narg < 3) error->all(FLERR,"Illegal fix command"); @@ -956,13 +955,14 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) if (newflag) nfix++; fmask[ifix] = fix[ifix]->setmask(); fix[ifix]->post_constructor(); + return fix[ifix]; } /* ---------------------------------------------------------------------- convenience function to allow adding a fix from a single string ------------------------------------------------------------------------- */ -void Modify::add_fix(const std::string &fixcmd, int trysuffix) +Fix *Modify::add_fix(const std::string &fixcmd, int trysuffix) { auto args = utils::split_words(fixcmd); std::vector newarg(args.size()); @@ -970,7 +970,7 @@ void Modify::add_fix(const std::string &fixcmd, int trysuffix) for (const auto &arg : args) { newarg[i++] = (char *)arg.c_str(); } - add_fix(args.size(),newarg.data(),trysuffix); + return add_fix(args.size(),newarg.data(),trysuffix); } @@ -981,11 +981,10 @@ void Modify::add_fix(const std::string &fixcmd, int trysuffix) replace it later with the desired Fix instance ------------------------------------------------------------------------- */ -void Modify::replace_fix(const char *replaceID, - int narg, char **arg, int trysuffix) +Fix *Modify::replace_fix(const char *replaceID, int narg, char **arg, int trysuffix) { int ifix = find_fix(replaceID); - if (ifix < 0) error->all(FLERR,"Modify replace_fix ID could not be found"); + if (ifix < 0) error->all(FLERR,"Modify replace_fix ID {} could not be found", replaceID); // change ID, igroup, style of fix being replaced to match new fix // requires some error checking on arguments for new fix @@ -1007,24 +1006,22 @@ void Modify::replace_fix(const char *replaceID, // invoke add_fix // it will find and overwrite the replaceID fix - add_fix(narg,arg,trysuffix); + return add_fix(narg,arg,trysuffix); } /* ---------------------------------------------------------------------- convenience function to allow replacing a fix from a single string ------------------------------------------------------------------------- */ -void Modify::replace_fix(const std::string &oldfix, - const std::string &fixcmd, int trysuffix) +Fix *Modify::replace_fix(const std::string &oldfix, const std::string &fixcmd, int trysuffix) { auto args = utils::split_words(fixcmd); - char **newarg = new char*[args.size()]; - int i=0; + std::vector newarg(args.size()); + int i = 0; for (const auto &arg : args) { newarg[i++] = (char *)arg.c_str(); } - replace_fix(oldfix.c_str(),args.size(),newarg,trysuffix); - delete[] newarg; + return replace_fix(oldfix.c_str(),args.size(),newarg.data(),trysuffix); } /* ---------------------------------------------------------------------- @@ -1110,7 +1107,7 @@ int Modify::find_fix_by_style(const char *style) check for fix associated with package name in compiled list return 1 if found else 0 used to determine whether LAMMPS was built with - GPU, USER-INTEL, USER-OMP packages, which have their own fixes + GPU, INTEL, OPENMP packages, which have their own fixes ------------------------------------------------------------------------- */ int Modify::check_package(const char *package_fix_name) @@ -1214,7 +1211,7 @@ int Modify::check_rigid_list_overlap(int *select) add a new compute ------------------------------------------------------------------------- */ -void Modify::add_compute(int narg, char **arg, int trysuffix) +Compute *Modify::add_compute(int narg, char **arg, int trysuffix) { if (narg < 3) error->all(FLERR,"Illegal compute command"); @@ -1269,23 +1266,22 @@ void Modify::add_compute(int narg, char **arg, int trysuffix) if (compute[ncompute] == nullptr) error->all(FLERR,utils::check_packages_for_style("compute",arg[2],lmp)); - ncompute++; + return compute[ncompute++]; } /* ---------------------------------------------------------------------- convenience function to allow adding a compute from a single string ------------------------------------------------------------------------- */ -void Modify::add_compute(const std::string &computecmd, int trysuffix) +Compute *Modify::add_compute(const std::string &computecmd, int trysuffix) { auto args = utils::split_words(computecmd); - char **newarg = new char*[args.size()]; + std::vectornewarg(args.size()); int i=0; for (const auto &arg : args) { newarg[i++] = (char *)arg.c_str(); } - add_compute(args.size(),newarg,trysuffix); - delete[] newarg; + return add_compute(args.size(),newarg.data(),trysuffix); } diff --git a/src/modify.h b/src/modify.h index 5111ef43ab..9446f285e7 100644 --- a/src/modify.h +++ b/src/modify.h @@ -100,18 +100,18 @@ class Modify : protected Pointers { virtual int min_dof(); virtual int min_reset_ref(); - void add_fix(int, char **, int trysuffix = 1); - void add_fix(const std::string &, int trysuffix = 1); - void replace_fix(const char *, int, char **, int trysuffix = 1); - void replace_fix(const std::string &, const std::string &, int trysuffix = 1); + Fix *add_fix(int, char **, int trysuffix = 1); + Fix *add_fix(const std::string &, int trysuffix = 1); + Fix *replace_fix(const char *, int, char **, int trysuffix = 1); + Fix *replace_fix(const std::string &, const std::string &, int trysuffix = 1); void modify_fix(int, char **); void delete_fix(const std::string &); void delete_fix(int); int find_fix(const std::string &); int find_fix_by_style(const char *); - void add_compute(int, char **, int trysuffix = 1); - void add_compute(const std::string &, int trysuffix = 1); + Compute *add_compute(int, char **, int trysuffix = 1); + Compute *add_compute(const std::string &, int trysuffix = 1); void modify_compute(int, char **); void delete_compute(const std::string &); void delete_compute(int); diff --git a/src/my_page.cpp b/src/my_page.cpp index 7cbaca2ef7..efad82d3d6 100644 --- a/src/my_page.cpp +++ b/src/my_page.cpp @@ -16,7 +16,7 @@ #include -#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) +#if defined(LMP_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 #endif diff --git a/src/my_pool_chunk.cpp b/src/my_pool_chunk.cpp index 1c770d0208..484a4b3fcf 100644 --- a/src/my_pool_chunk.cpp +++ b/src/my_pool_chunk.cpp @@ -16,7 +16,7 @@ #include -#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) +#if defined(LMP_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 #endif diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index d10c98835e..aa2a9f6686 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -38,7 +38,7 @@ NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {} void NBinStandard::bin_atoms_setup(int nall) { // binhead = per-bin vector, mbins in length - // add 1 bin for USER-INTEL package + // add 1 bin for INTEL package if (mbins > maxbin) { maxbin = mbins; diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 5dc56f8c60..dc76b242e9 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -84,7 +84,7 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp) kk2cpu = 0; execution_space = Host; - // USER-DPD package + // DPD-REACT package np = nullptr; diff --git a/src/neigh_list.h b/src/neigh_list.h index 703d4c13a9..8b920bbe50 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -95,7 +95,7 @@ class NeighList : protected Pointers { int kokkos; // 1 if list stores Kokkos data ExecutionSpace execution_space; - // USER-DPD package and Shardlow Splitting Algorithm (SSA) support + // DPD-REACT package and Shardlow Splitting Algorithm (SSA) support class NPair *np; // ptr to NPair instance I depend on diff --git a/src/neigh_request.h b/src/neigh_request.h index 30cf6592d1..4bdc368317 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -66,11 +66,11 @@ class NeighRequest : protected Pointers { int respamiddle; // 1 if need a rRESPA middle list int respaouter; // 1 if need a rRESPA outer list int bond; // 1 if store bond neighbors instead of atom neighs - int omp; // set by USER-OMP package - int intel; // set by USER-INTEL package + int omp; // set by OPENMP package + int intel; // set by INTEL package int kokkos_host; // set by KOKKOS package int kokkos_device; - int ssa; // set by USER-DPD package, for Shardlow lists + int ssa; // set by DPD-REACT package, for Shardlow lists int cut; // 1 if use a non-standard cutoff length double cutoff; // special cutoff distance for this list diff --git a/src/pair.cpp b/src/pair.cpp index 0fcc4bd62f..38c7922c17 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -959,7 +959,7 @@ void Pair::ev_setup(int eflag, int vflag, int alloc) } } - // run ev_setup option for USER-TALLY computes + // run ev_setup option for TALLY computes if (num_tally_compute > 0) { for (int k=0; k < num_tally_compute; ++k) { @@ -991,7 +991,7 @@ void Pair::ev_unset() } /* ---------------------------------------------------------------------- - tally eng_vdwl and virial into global and per-atom accumulators + tally eng_vdwl and virial into global or per-atom accumulators need i < nlocal test since called by bond_quartic and dihedral_charmm ------------------------------------------------------------------------- */ @@ -1092,7 +1092,7 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair, } /* ---------------------------------------------------------------------- - tally eng_vdwl and virial into global and per-atom accumulators + tally eng_vdwl and virial into global or per-atom accumulators can use this version with full neighbor lists ------------------------------------------------------------------------- */ @@ -1138,7 +1138,7 @@ void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair, } /* ---------------------------------------------------------------------- - tally eng_vdwl and virial into global and per-atom accumulators + tally eng_vdwl and virial into global or per-atom accumulators for virial, have delx,dely,delz and fx,fy,fz ------------------------------------------------------------------------- */ @@ -1232,7 +1232,7 @@ void Pair::ev_tally_xyz(int i, int j, int nlocal, int newton_pair, } /* ---------------------------------------------------------------------- - tally eng_vdwl and virial into global and per-atom accumulators + tally eng_vdwl and virial into global or per-atom accumulators for virial, have delx,dely,delz and fx,fy,fz called when using full neighbor lists ------------------------------------------------------------------------- */ @@ -1285,7 +1285,7 @@ void Pair::ev_tally_xyz_full(int i, double evdwl, double ecoul, } /* ---------------------------------------------------------------------- - tally eng_vdwl and virial into global and per-atom accumulators + tally eng_vdwl and virial into global or per-atom accumulators called by SW and hbond potentials, newton_pair is always on virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk ------------------------------------------------------------------------- */ @@ -1342,7 +1342,7 @@ void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul, } /* ---------------------------------------------------------------------- - tally eng_vdwl and virial into global and per-atom accumulators + tally eng_vdwl and virial into global or per-atom accumulators called by AIREBO potential, newton_pair is always on ------------------------------------------------------------------------- */ @@ -1363,22 +1363,40 @@ void Pair::ev_tally4(int i, int j, int k, int m, double evdwl, } } - if (vflag_atom) { - v[0] = 0.25 * (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); - v[1] = 0.25 * (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); - v[2] = 0.25 * (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); - v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); - v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); - v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); + if (vflag_either) { + v[0] = (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); + v[1] = (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); + v[2] = (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); + v[3] = (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); + v[4] = (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); + v[5] = (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); - vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; - vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; - vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; - vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; - vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2]; - vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5]; - vatom[m][0] += v[0]; vatom[m][1] += v[1]; vatom[m][2] += v[2]; - vatom[m][3] += v[3]; vatom[m][4] += v[4]; vatom[m][5] += v[5]; + if (vflag_global) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } + + if (vflag_atom) { + v[0] *= 0.25; + v[1] *= 0.25; + v[2] *= 0.25; + v[3] *= 0.25; + v[4] *= 0.25; + v[5] *= 0.25; + + vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; + vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; + vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; + vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; + vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2]; + vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5]; + vatom[m][0] += v[0]; vatom[m][1] += v[1]; vatom[m][2] += v[2]; + vatom[m][3] += v[3]; vatom[m][4] += v[4]; vatom[m][5] += v[5]; + } } } @@ -1469,28 +1487,40 @@ void Pair::ev_tally_tip4p(int key, int *list, double *v, } /* ---------------------------------------------------------------------- - tally virial into per-atom accumulators - called by REAX/C potential, newton_pair is always on - fi is magnitude of force on atom i + tally virial into global or per-atom accumulators + called by ReaxFF potential, newton_pair is always on + fi is magnitude of force on atom i, deli is the direction + note that the other atom (j) is not updated, due to newton on ------------------------------------------------------------------------- */ -void Pair::v_tally(int i, double *fi, double *deli) +void Pair::v_tally2_newton(int i, double *fi, double *deli) { double v[6]; - v[0] = 0.5*deli[0]*fi[0]; - v[1] = 0.5*deli[1]*fi[1]; - v[2] = 0.5*deli[2]*fi[2]; - v[3] = 0.5*deli[0]*fi[1]; - v[4] = 0.5*deli[0]*fi[2]; - v[5] = 0.5*deli[1]*fi[2]; + v[0] = deli[0]*fi[0]; + v[1] = deli[1]*fi[1]; + v[2] = deli[2]*fi[2]; + v[3] = deli[0]*fi[1]; + v[4] = deli[0]*fi[2]; + v[5] = deli[1]*fi[2]; - vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; - vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; + if (vflag_global) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } + + if (vflag_atom) { + vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; + vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; + } } /* ---------------------------------------------------------------------- - tally virial into per-atom accumulators + tally virial into global or per-atom accumulators called by AIREBO potential, newton_pair is always on fpair is magnitude of force on atom I ------------------------------------------------------------------------- */ @@ -1499,47 +1529,80 @@ void Pair::v_tally2(int i, int j, double fpair, double *drij) { double v[6]; - v[0] = 0.5 * drij[0]*drij[0]*fpair; - v[1] = 0.5 * drij[1]*drij[1]*fpair; - v[2] = 0.5 * drij[2]*drij[2]*fpair; - v[3] = 0.5 * drij[0]*drij[1]*fpair; - v[4] = 0.5 * drij[0]*drij[2]*fpair; - v[5] = 0.5 * drij[1]*drij[2]*fpair; + v[0] = drij[0]*drij[0]*fpair; + v[1] = drij[1]*drij[1]*fpair; + v[2] = drij[2]*drij[2]*fpair; + v[3] = drij[0]*drij[1]*fpair; + v[4] = drij[0]*drij[2]*fpair; + v[5] = drij[1]*drij[2]*fpair; - vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; - vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; - vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; - vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; + if (vflag_global) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } + + if (vflag_atom) { + v[0] *= 0.5; + v[1] *= 0.5; + v[2] *= 0.5; + v[3] *= 0.5; + v[4] *= 0.5; + v[5] *= 0.5; + vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; + vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; + vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; + vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; + } } /* ---------------------------------------------------------------------- tally virial into per-atom accumulators - called by AIREBO and Tersoff potential, newton_pair is always on + called by AIREBO and Tersoff potentials, newton_pair is always on ------------------------------------------------------------------------- */ -void Pair::v_tally3(int i, int j, int k, - double *fi, double *fj, double *drik, double *drjk) +void Pair::v_tally3(int i, int j, int k, double *fi, double *fj, double *drik, double *drjk) { double v[6]; - v[0] = THIRD * (drik[0]*fi[0] + drjk[0]*fj[0]); - v[1] = THIRD * (drik[1]*fi[1] + drjk[1]*fj[1]); - v[2] = THIRD * (drik[2]*fi[2] + drjk[2]*fj[2]); - v[3] = THIRD * (drik[0]*fi[1] + drjk[0]*fj[1]); - v[4] = THIRD * (drik[0]*fi[2] + drjk[0]*fj[2]); - v[5] = THIRD * (drik[1]*fi[2] + drjk[1]*fj[2]); + v[0] = (drik[0]*fi[0] + drjk[0]*fj[0]); + v[1] = (drik[1]*fi[1] + drjk[1]*fj[1]); + v[2] = (drik[2]*fi[2] + drjk[2]*fj[2]); + v[3] = (drik[0]*fi[1] + drjk[0]*fj[1]); + v[4] = (drik[0]*fi[2] + drjk[0]*fj[2]); + v[5] = (drik[1]*fi[2] + drjk[1]*fj[2]); - vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; - vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; - vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; - vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; - vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2]; - vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5]; + if (vflag_global) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } + + if (vflag_atom) { + v[0] *= THIRD; + v[1] *= THIRD; + v[2] *= THIRD; + v[3] *= THIRD; + v[4] *= THIRD; + v[5] *= THIRD; + vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; + vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; + vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; + vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; + vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2]; + vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5]; + } } /* ---------------------------------------------------------------------- - tally virial into per-atom accumulators - called by AIREBO potential, newton_pair is always on + tally virial into global or per-atom accumulators + called by AIREBO potential, Tersoff, ReaxFF potentials, newton_pair is always on ------------------------------------------------------------------------- */ void Pair::v_tally4(int i, int j, int k, int m, @@ -1548,25 +1611,42 @@ void Pair::v_tally4(int i, int j, int k, int m, { double v[6]; - v[0] = 0.25 * (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); - v[1] = 0.25 * (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); - v[2] = 0.25 * (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); - v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); - v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); - v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); + v[0] = (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]); + v[1] = (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]); + v[2] = (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]); + v[3] = (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]); + v[4] = (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]); + v[5] = (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]); - vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; - vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; - vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; - vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; - vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2]; - vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5]; - vatom[m][0] += v[0]; vatom[m][1] += v[1]; vatom[m][2] += v[2]; - vatom[m][3] += v[3]; vatom[m][4] += v[4]; vatom[m][5] += v[5]; + if (vflag_global) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } + + if (vflag_atom) { + v[0] *= 0.25; + v[1] *= 0.25; + v[2] *= 0.25; + v[3] *= 0.25; + v[4] *= 0.25; + v[5] *= 0.25; + vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2]; + vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5]; + vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2]; + vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5]; + vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2]; + vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5]; + vatom[m][0] += v[0]; vatom[m][1] += v[1]; vatom[m][2] += v[2]; + vatom[m][3] += v[3]; vatom[m][4] += v[4]; vatom[m][5] += v[5]; + } } /* ---------------------------------------------------------------------- - tally virial into global and per-atom accumulators + tally virial into global or per-atom accumulators called by pair lubricate potential with 6 tensor components ------------------------------------------------------------------------- */ diff --git a/src/pair.h b/src/pair.h index b19fa08c48..0c082fa1c5 100644 --- a/src/pair.h +++ b/src/pair.h @@ -28,6 +28,9 @@ class Pair : protected Pointers { friend class FixGPU; friend class FixIntel; friend class FixOMP; + friend class FixQEq; + friend class PairHybrid; + friend class PairHybridScaled; friend class ThrOMP; friend class Info; @@ -135,9 +138,9 @@ class Pair : protected Pointers { // need to be public, so can be called by pair_style reaxc - void v_tally(int, double *, double *); void ev_tally(int, int, int, int, double, double, double, double, double, double); void ev_tally3(int, int, int, double, double, double *, double *, double *, double *); + void v_tally2_newton(int, double *, double *); void v_tally3(int, int, int, double *, double *, double *, double *); void v_tally4(int, int, int, int, double *, double *, double *, double *, double *, double *); void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double, @@ -246,7 +249,7 @@ class Pair : protected Pointers { float f; } union_int_float_t; - // Accessor for the user-intel package to determine virial calc for hybrid + // Accessor for the INTEL package to determine virial calc for hybrid inline int fdotr_is_set() const { return vflag_fdotr; } diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index ab2fe7803a..550f5c6873 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -569,7 +569,7 @@ void PairHybrid::init_style() // same style must not be used multiple times for (istyle = 0; istyle < nstyles; istyle++) { - bool is_gpu = (((PairHybrid *)styles[istyle])->suffix_flag & Suffix::GPU); + bool is_gpu = styles[istyle]->suffix_flag & Suffix::GPU; if (multiple[istyle] && is_gpu) error->all(FLERR,"GPU package styles must not be used multiple times"); } @@ -597,6 +597,10 @@ void PairHybrid::init_style() } } + // check beyond contact (set during pair coeff) before init style + for (istyle = 0; istyle < nstyles; istyle++) + if (styles[istyle]->beyond_contact) beyond_contact = 1; + // each sub-style makes its neighbor list request(s) for (istyle = 0; istyle < nstyles; istyle++) styles[istyle]->init_style(); @@ -923,7 +927,7 @@ again: } // if 2nd keyword (after pair) is compute/tally: - // set flag to register USER-TALLY computes accordingly + // set flag to register TALLY computes accordingly if (iarg < narg && strcmp(arg[iarg],"compute/tally") == 0) { if (narg < iarg+2) @@ -975,9 +979,7 @@ void PairHybrid::modify_special(int m, int /*narg*/, char **arg) special[2] = utils::numeric(FLERR,arg[2],false,lmp); special[3] = utils::numeric(FLERR,arg[3],false,lmp); - // have to cast to PairHybrid to work around C++ access restriction - - if (((PairHybrid *)styles[m])->suffix_flag & (Suffix::INTEL|Suffix::GPU)) + if (styles[m]->suffix_flag & (Suffix::INTEL|Suffix::GPU)) error->all(FLERR,"Pair_modify special is not compatible with " "suffix version of hybrid substyle"); diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 90d1747075..367afe7809 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -340,8 +340,7 @@ void PairHybridScaled::settings(int narg, char **arg) special_lj[nstyles] = special_coul[nstyles] = nullptr; compute_tally[nstyles] = 1; - if ((((PairHybridScaled *)styles[nstyles])->suffix_flag - & (Suffix::INTEL|Suffix::GPU|Suffix::OMP)) != 0) + if ((styles[nstyles]->suffix_flag & (Suffix::INTEL|Suffix::GPU|Suffix::OMP)) != 0) error->all(FLERR,"Pair style hybrid/scaled does not support " "accelerator styles"); diff --git a/src/pair_morse.h b/src/pair_morse.h index 56854b020e..a85c47df8c 100644 --- a/src/pair_morse.h +++ b/src/pair_morse.h @@ -30,17 +30,17 @@ class PairMorse : public Pair { virtual ~PairMorse(); virtual void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - double init_one(int, int); - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); - void write_data(FILE *); - void write_data_all(FILE *); - double single(int, int, int, int, double, double, double, double &); - void *extract(const char *, int &); + virtual void settings(int, char **); + virtual void coeff(int, char **); + virtual double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + virtual void *extract(const char *, int &); protected: double cut_global; diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index c1fa157ef9..bb723d0e82 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -1,4 +1,3 @@ -// clang-format off /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -45,26 +44,20 @@ using namespace LAMMPS_NS; * \param auto_convert Bitmask of supported unit conversions */ -PotentialFileReader::PotentialFileReader(LAMMPS *lmp, - const std::string &filename, +PotentialFileReader::PotentialFileReader(LAMMPS *lmp, const std::string &filename, const std::string &potential_name, - const std::string &name_suffix, - const int auto_convert) : - Pointers(lmp), - reader(nullptr), - filename(filename), - filetype(potential_name + name_suffix), - unit_convert(auto_convert) + const std::string &name_suffix, const int auto_convert) : + Pointers(lmp), + reader(nullptr), filename(filename), filetype(potential_name + name_suffix), + unit_convert(auto_convert) { - if (comm->me != 0) { - error->one(FLERR, "FileReader should only be called by proc 0!"); - } + if (comm->me != 0) { error->one(FLERR, "FileReader should only be called by proc 0!"); } try { reader = open_potential(filename); if (!reader) { - error->one(FLERR, "cannot open {} potential file {}: {}", - potential_name, filename, utils::getsyserror()); + error->one(FLERR, "cannot open {} potential file {}: {}", potential_name, filename, + utils::getsyserror()); } } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -77,30 +70,32 @@ PotentialFileReader::PotentialFileReader(LAMMPS *lmp, * \param potential_name Name of potential style for error messages * \param auto_convert Bitmask of supported unit conversions */ -PotentialFileReader::PotentialFileReader(LAMMPS *lmp, - const std::string &filename, +PotentialFileReader::PotentialFileReader(LAMMPS *lmp, const std::string &filename, const std::string &potential_name, const int auto_convert) : - PotentialFileReader(lmp, filename, potential_name, " potential", auto_convert) + PotentialFileReader(lmp, filename, potential_name, " potential", auto_convert) { } /** Closes the file */ -PotentialFileReader::~PotentialFileReader() { +PotentialFileReader::~PotentialFileReader() +{ delete reader; } /** Set comment (= text after '#') handling preference for the file to be read * * \param value Comment text is ignored if true, or not if false */ -void PotentialFileReader::ignore_comments(bool value) { +void PotentialFileReader::ignore_comments(bool value) +{ reader->ignore_comments = value; } /** Read a line but ignore its content */ -void PotentialFileReader::skip_line() { +void PotentialFileReader::skip_line() +{ try { reader->skip_line(); } catch (FileReaderException &e) { @@ -119,7 +114,8 @@ void PotentialFileReader::skip_line() { * \param nparams Number of words that must be read. Default: 0 * \return String with the concatenated text */ -char *PotentialFileReader::next_line(int nparams) { +char *PotentialFileReader::next_line(int nparams) +{ try { return reader->next_line(nparams); } catch (FileReaderException &e) { @@ -137,7 +133,8 @@ char *PotentialFileReader::next_line(int nparams) { * \param list Pointer to array with suitable storage for *n* doubles * \param n Number of doubles to be read */ -void PotentialFileReader::next_dvector(double * list, int n) { +void PotentialFileReader::next_dvector(double *list, int n) +{ try { return reader->next_dvector(list, n); } catch (FileReaderException &e) { @@ -155,7 +152,8 @@ void PotentialFileReader::next_dvector(double * list, int n) { * \param separators String with list of separators. * \return ValueTokenizer object for read in text */ -ValueTokenizer PotentialFileReader::next_values(int nparams, const std::string &separators) { +ValueTokenizer PotentialFileReader::next_values(int nparams, const std::string &separators) +{ try { return reader->next_values(nparams, separators); } catch (FileReaderException &e) { @@ -168,9 +166,10 @@ ValueTokenizer PotentialFileReader::next_values(int nparams, const std::string & * * \return Value of first word in line as double */ -double PotentialFileReader::next_double() { +double PotentialFileReader::next_double() +{ try { - char * line = reader->next_line(1); + char *line = reader->next_line(1); return ValueTokenizer(line).next_double(); } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -182,9 +181,10 @@ double PotentialFileReader::next_double() { * * \return Value of first word in line as int */ -int PotentialFileReader::next_int() { +int PotentialFileReader::next_int() +{ try { - char * line = reader->next_line(1); + char *line = reader->next_line(1); return ValueTokenizer(line).next_int(); } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -196,9 +196,10 @@ int PotentialFileReader::next_int() { * * \return Value of first word in line as tagint */ -tagint PotentialFileReader::next_tagint() { +tagint PotentialFileReader::next_tagint() +{ try { - char * line = reader->next_line(1); + char *line = reader->next_line(1); return ValueTokenizer(line).next_tagint(); } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -210,9 +211,10 @@ tagint PotentialFileReader::next_tagint() { * * \return Value of first word in line as bigint */ -bigint PotentialFileReader::next_bigint() { +bigint PotentialFileReader::next_bigint() +{ try { - char * line = reader->next_line(1); + char *line = reader->next_line(1); return ValueTokenizer(line).next_bigint(); } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -224,9 +226,10 @@ bigint PotentialFileReader::next_bigint() { * * \return First word of read in line */ -std::string PotentialFileReader::next_string() { +std::string PotentialFileReader::next_string() +{ try { - char * line = reader->next_line(1); + char *line = reader->next_line(1); return ValueTokenizer(line).next_string(); } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -246,17 +249,17 @@ std::string PotentialFileReader::next_string() { * \param path Path of the potential file to open * \return Pointer to TextFileReader object created */ -TextFileReader *PotentialFileReader::open_potential(const std::string &path) { +TextFileReader *PotentialFileReader::open_potential(const std::string &path) +{ std::string filepath = utils::get_potential_file_path(path); if (!filepath.empty()) { std::string unit_style = lmp->update->unit_style; - std::string date = utils::get_potential_date(filepath, filetype); - std::string units = utils::get_potential_units(filepath, filetype); + std::string date = utils::get_potential_date(filepath, filetype); + std::string units = utils::get_potential_units(filepath, filetype); if (!date.empty()) - utils::logmesg(lmp,"Reading {} file {} with DATE: {}\n", - filetype, filename, date); + utils::logmesg(lmp, "Reading {} file {} with DATE: {}\n", filetype, filename, date); if (units.empty()) { unit_convert = utils::NOCONVERT; @@ -266,18 +269,18 @@ TextFileReader *PotentialFileReader::open_potential(const std::string &path) { } else { if ((units == "metal") && (unit_style == "real") && (unit_convert & utils::METAL2REAL)) { unit_convert = utils::METAL2REAL; - } else if ((units == "real") && (unit_style == "metal") && (unit_convert & utils::REAL2METAL)) { + } else if ((units == "real") && (unit_style == "metal") && + (unit_convert & utils::REAL2METAL)) { unit_convert = utils::REAL2METAL; } else { - lmp->error->one(FLERR, "{} file {} requires {} units " - "but {} units are in use", filetype, - filename, units, unit_style); + lmp->error->one(FLERR, "{} file {} requires {} units but {} units are in use", filetype, + filename, units, unit_style); } } } if (unit_convert != utils::NOCONVERT) - lmp->error->warning(FLERR, "Converting {} in {} units to {} units", - filetype, units, unit_style); + lmp->error->warning(FLERR, "Converting {} in {} units to {} units", filetype, units, + unit_style); return new TextFileReader(filepath, filetype); } return nullptr; diff --git a/src/read_restart.cpp b/src/read_restart.cpp index ac00a7d086..e42bb59272 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -44,7 +44,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp) {} +ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp), mpiio(nullptr) {} /* ---------------------------------------------------------------------- */ @@ -71,16 +71,18 @@ void ReadRestart::command(int narg, char **arg) // if filename contains "*", search dir for latest restart file - char *file = new char[strlen(arg[0]) + 16]; + char *file; if (strchr(arg[0],'*')) { - int n; + int n=0; if (me == 0) { - file_search(arg[0],file); - n = strlen(file) + 1; + auto fn = file_search(arg[0]); + n = fn.size()+1; + file = utils::strdup(fn); } MPI_Bcast(&n,1,MPI_INT,0,world); + if (me != 0) file = new char[n]; MPI_Bcast(file,n,MPI_CHAR,0,world); - } else strcpy(file,arg[0]); + } else file = utils::strdup(arg[0]); // check for multiproc files and an MPI-IO filename @@ -90,14 +92,12 @@ void ReadRestart::command(int narg, char **arg) else mpiioflag = 0; if (multiproc && mpiioflag) - error->all(FLERR, - "Read restart MPI-IO input not allowed with % in filename"); + error->all(FLERR,"Read restart MPI-IO input not allowed with % in filename"); if (mpiioflag) { mpiio = new RestartMPIIO(lmp); if (!mpiio->mpiio_exists) - error->all(FLERR,"Reading from MPI-IO filename when " - "MPIIO package is not installed"); + error->all(FLERR,"Reading from MPI-IO filename when MPIIO package is not installed"); } // open single restart file or base file for multiproc case @@ -110,8 +110,7 @@ void ReadRestart::command(int narg, char **arg) } fp = fopen(hfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,"Cannot open restart file {}: {}", - hfile, utils::getsyserror()); + error->one(FLERR,"Cannot open restart file {}: {}", hfile, utils::getsyserror()); } // read magic string, endian flag, format revision @@ -336,8 +335,7 @@ void ReadRestart::command(int narg, char **arg) procfile.replace(procfile.find("%"),1,fmt::format("{}",icluster)); fp = fopen(procfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,"Cannot open restart file {}: {}", - procfile, utils::getsyserror()); + error->one(FLERR,"Cannot open restart file {}: {}", procfile, utils::getsyserror()); } int procsperfile; @@ -401,7 +399,7 @@ void ReadRestart::command(int narg, char **arg) // clean-up memory - delete [] file; + delete[] file; memory->destroy(buf); // for multiproc or MPI-IO files: @@ -525,8 +523,9 @@ void ReadRestart::command(int narg, char **arg) MPI_Barrier(world); if (comm->me == 0) - utils::logmesg(lmp," read_restart CPU = {:.3f} seconds\n", - MPI_Wtime()-time1); + utils::logmesg(lmp," read_restart CPU = {:.3f} seconds\n",MPI_Wtime()-time1); + + delete mpiio; } /* ---------------------------------------------------------------------- @@ -538,83 +537,45 @@ void ReadRestart::command(int narg, char **arg) only called by proc 0 ------------------------------------------------------------------------- */ -void ReadRestart::file_search(char *inpfile, char *outfile) +std::string ReadRestart::file_search(const std::string &inpfile) { - char *ptr; - // separate inpfile into dir + filename - char *dirname = new char[strlen(inpfile) + 1]; - char *filename = new char[strlen(inpfile) + 1]; - - if (strchr(inpfile,'/')) { - ptr = strrchr(inpfile,'/'); - *ptr = '\0'; - strcpy(dirname,inpfile); - strcpy(filename,ptr+1); - *ptr = '/'; - } else { - strcpy(dirname,"./"); - strcpy(filename,inpfile); - } + auto dirname = utils::path_dirname(inpfile); + auto filename = utils::path_basename(inpfile); // if filename contains "%" replace "%" with "base" - char *pattern = new char[strlen(filename) + 16]; + auto pattern = filename; + auto loc = pattern.find('%'); + if (loc != std::string::npos) pattern.replace(loc,1,"base"); - if ((ptr = strchr(filename,'%'))) { - *ptr = '\0'; - sprintf(pattern,"%s%s%s",filename,"base",ptr+1); - *ptr = '%'; - } else strcpy(pattern,filename); + // scan all files in directory, searching for files that match regexp pattern + // maxnum = largest integer that matches "*" - // scan all files in directory, searching for files that match pattern - // maxnum = largest int that matches "*" - - int n = strlen(pattern) + 16; - char *begin = new char[n]; - char *middle = new char[n]; - char *end = new char[n]; - - ptr = strchr(pattern,'*'); - *ptr = '\0'; - strcpy(begin,pattern); - strcpy(end,ptr+1); - int nbegin = strlen(begin); bigint maxnum = -1; + loc = pattern.find('*'); + if (loc != std::string::npos) { + // convert pattern to equivalent regexp + pattern.replace(loc,1,"\\d+"); + struct dirent *ep; + DIR *dp = opendir(dirname.c_str()); + if (dp == nullptr) + error->one(FLERR,"Cannot open directory {} to search for restart file: {}", + dirname, utils::getsyserror()); - struct dirent *ep; - DIR *dp = opendir(dirname); - if (dp == nullptr) - error->one(FLERR,"Cannot open dir to search for restart file"); - while ((ep = readdir(dp))) { - if (strstr(ep->d_name,begin) != ep->d_name) continue; - if ((ptr = strstr(&ep->d_name[nbegin],end)) == nullptr) continue; - if (strlen(end) == 0) ptr = ep->d_name + strlen(ep->d_name); - *ptr = '\0'; - if ((int)strlen(&ep->d_name[nbegin]) < n) { - strcpy(middle,&ep->d_name[nbegin]); - if (ATOBIGINT(middle) > maxnum) maxnum = ATOBIGINT(middle); + while ((ep = readdir(dp))) { + std::string candidate(ep->d_name); + if (utils::strmatch(candidate,pattern)) { + bigint num = ATOBIGINT(utils::strfind(candidate.substr(loc),"\\d+").c_str()); + if (num > maxnum) maxnum = num; + } } + closedir(dp); + if (maxnum < 0) error->one(FLERR,"Found no restart file matching pattern"); + filename.replace(filename.find('*'),1,std::to_string(maxnum)); } - closedir(dp); - if (maxnum < 0) error->one(FLERR,"Found no restart file matching pattern"); - - // create outfile with maxint substituted for "*" - // use original inpfile, not pattern, since need to retain "%" in filename - - std::string newoutfile = inpfile; - newoutfile.replace(newoutfile.find("*"),1,fmt::format("{}",maxnum)); - strcpy(outfile,newoutfile.c_str()); - - // clean up - - delete [] dirname; - delete [] filename; - delete [] pattern; - delete [] begin; - delete [] middle; - delete [] end; + return utils::path_join(dirname,filename); } /* ---------------------------------------------------------------------- @@ -637,7 +598,7 @@ void ReadRestart::header() if (me == 0) utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n", version,lmp->version); - delete [] version; + delete[] version; // we have no forward compatibility, thus exit with error @@ -676,7 +637,7 @@ void ReadRestart::header() } else if (flag == UNITS) { char *style = read_string(); if (strcmp(style,update->unit_style) != 0) update->set_units(style); - delete [] style; + delete[] style; } else if (flag == NTIMESTEP) { update->ntimestep = read_bigint(); @@ -810,9 +771,9 @@ void ReadRestart::header() atom->create_avec(style,nargcopy,argcopy,1); if (comm->me ==0) utils::logmesg(lmp," restoring atom style {} from restart\n",style); - for (int i = 0; i < nargcopy; i++) delete [] argcopy[i]; - delete [] argcopy; - delete [] style; + for (int i = 0; i < nargcopy; i++) delete[] argcopy[i]; + delete[] argcopy; + delete[] style; } else if (flag == NATOMS) { atom->natoms = read_bigint(); @@ -927,7 +888,7 @@ void ReadRestart::type_arrays() double *mass = new double[atom->ntypes+1]; read_double_vec(atom->ntypes,&mass[1]); atom->set_mass(mass); - delete [] mass; + delete[] mass; } else error->all(FLERR, "Invalid flag in type arrays section of restart file"); @@ -948,7 +909,7 @@ void ReadRestart::force_fields() if (flag == PAIR) { style = read_string(); force->create_pair(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring pair style {} from restart\n", force->pair_style); @@ -964,7 +925,7 @@ void ReadRestart::force_fields() } else if (flag == BOND) { style = read_string(); force->create_bond(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring bond style {} from restart\n", force->bond_style); @@ -973,7 +934,7 @@ void ReadRestart::force_fields() } else if (flag == ANGLE) { style = read_string(); force->create_angle(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring angle style {} from restart\n", force->angle_style); @@ -982,7 +943,7 @@ void ReadRestart::force_fields() } else if (flag == DIHEDRAL) { style = read_string(); force->create_dihedral(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring dihedral style {} from restart\n", force->dihedral_style); @@ -991,7 +952,7 @@ void ReadRestart::force_fields() } else if (flag == IMPROPER) { style = read_string(); force->create_improper(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring improper style {} from restart\n", force->improper_style); @@ -1155,7 +1116,7 @@ void ReadRestart::magic_string() MPI_Bcast(str,n,MPI_CHAR,0,world); if (strcmp(str,MAGIC_STRING) != 0) error->all(FLERR,"Invalid LAMMPS restart file"); - delete [] str; + delete[] str; } /* ---------------------------------------------------------------------- @@ -1202,7 +1163,7 @@ void ReadRestart::check_eof_magic() if (strcmp(str,MAGIC_STRING) != 0) error->all(FLERR,"Incomplete or corrupted LAMMPS restart file"); - delete [] str; + delete[] str; } /* ---------------------------------------------------------------------- diff --git a/src/read_restart.h b/src/read_restart.h index a3f889fbc3..9de52a5f28 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -46,7 +46,7 @@ class ReadRestart : public Command { bigint assignedChunkSize; MPI_Offset assignedChunkOffset, headerOffset; - void file_search(char *, char *); + std::string file_search(const std::string &); void header(); void type_arrays(); void force_fields(); diff --git a/src/respa.cpp b/src/respa.cpp index c51ec04131..5190441994 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -302,9 +302,8 @@ void Respa::init() // if supported, we also store torques on a per-level basis std::string cmd = fmt::format("RESPA all RESPA {}",nlevels); - if (atom->torque_flag) modify->add_fix(cmd + " torque"); - else modify->add_fix(cmd); - fix_respa = (FixRespa *) modify->fix[modify->nfix-1]; + if (atom->torque_flag) cmd += " torque"; + fix_respa = (FixRespa *) modify->add_fix(cmd); // insure respa inner/middle/outer is using Pair class that supports it diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index d4847c67ee..926dedcf80 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -1,4 +1,3 @@ -// clang-format off /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -41,14 +40,14 @@ using namespace LAMMPS_NS; * \param filename Name of file to be read * \param filetype Description of file type for error messages */ -TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype) - : filetype(filetype), closefp(true), ignore_comments(true) +TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype) : + filetype(filetype), closefp(true), ignore_comments(true) { fp = fopen(filename.c_str(), "r"); if (fp == nullptr) { - throw FileReaderException(fmt::format("cannot open {} file {}: {}", - filetype, filename, utils::getsyserror())); + throw FileReaderException( + fmt::format("cannot open {} file {}: {}", filetype, filename, utils::getsyserror())); } } @@ -69,21 +68,23 @@ This function is useful in combination with :cpp:func:`utils::open_potential`. * \param fp File descriptor of the already opened file * \param filetype Description of file type for error messages */ -TextFileReader::TextFileReader(FILE *fp, const std::string &filetype) - : filetype(filetype), closefp(false), fp(fp), ignore_comments(true) +TextFileReader::TextFileReader(FILE *fp, const std::string &filetype) : + filetype(filetype), closefp(false), fp(fp), ignore_comments(true) { if (fp == nullptr) throw FileReaderException("Invalid file descriptor"); } /** Closes the file */ -TextFileReader::~TextFileReader() { +TextFileReader::~TextFileReader() +{ if (closefp) fclose(fp); } /** Read the next line and ignore it */ -void TextFileReader::skip_line() { +void TextFileReader::skip_line() +{ char *ptr = fgets(line, MAXLINE, fp); if (ptr == nullptr) { // EOF @@ -105,7 +106,8 @@ void TextFileReader::skip_line() { * \param nparams Number of words that must be read. Default: 0 * \return String with the concatenated text */ -char *TextFileReader::next_line(int nparams) { +char *TextFileReader::next_line(int nparams) +{ // concatenate lines until have nparams words int n = 0; int nwords = 0; @@ -129,7 +131,8 @@ char *TextFileReader::next_line(int nparams) { if (ptr == nullptr) { // EOF if (nwords > 0 && nwords < nparams) { - throw EOFException(fmt::format("Incorrect format in {} file! {}/{} parameters", filetype, nwords, nparams)); + throw EOFException(fmt::format("Incorrect format in {} file! {}/{} parameters", filetype, + nwords, nparams)); } return nullptr; } @@ -140,9 +143,7 @@ char *TextFileReader::next_line(int nparams) { nwords += utils::count_words(&line[n]); // skip line if blank - if (nwords > 0) { - n = strlen(line); - } + if (nwords > 0) { n = strlen(line); } } return line; @@ -157,7 +158,8 @@ char *TextFileReader::next_line(int nparams) { * \param list Pointer to array with suitable storage for *n* doubles * \param n Number of doubles to be read */ -void TextFileReader::next_dvector(double * list, int n) { +void TextFileReader::next_dvector(double *list, int n) +{ int i = 0; while (i < n) { char *ptr = next_line(); @@ -165,14 +167,13 @@ void TextFileReader::next_dvector(double * list, int n) { if (ptr == nullptr) { // EOF if (i < n) { - throw FileReaderException(fmt::format("Incorrect format in {} file! {}/{} values", filetype, i, n)); + throw FileReaderException( + fmt::format("Incorrect format in {} file! {}/{} values", filetype, i, n)); } } ValueTokenizer values(line); - while (values.has_next()) { - list[i++] = values.next_double(); - } + while (values.has_next()) { list[i++] = values.next_double(); } } } @@ -186,9 +187,9 @@ void TextFileReader::next_dvector(double * list, int n) { * \param separators String with list of separators. * \return ValueTokenizer object for read in text */ -ValueTokenizer TextFileReader::next_values(int nparams, const std::string &separators) { +ValueTokenizer TextFileReader::next_values(int nparams, const std::string &separators) +{ char *ptr = next_line(nparams); - if (ptr == nullptr) - throw EOFException(fmt::format("Missing line in {} file!", filetype)); + if (ptr == nullptr) throw EOFException(fmt::format("Missing line in {} file!", filetype)); return ValueTokenizer(line, separators); } diff --git a/src/thermo.cpp b/src/thermo.cpp index 1fa6f18d2c..6e326e6891 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -73,7 +73,6 @@ using namespace MathConst; #define MULTI "etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press" enum{ONELINE,MULTILINE}; -enum{INT,FLOAT,BIGINT}; enum{SCALAR,VECTOR,ARRAY}; diff --git a/src/thermo.h b/src/thermo.h index 9439b0ef53..89678614a7 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -31,6 +31,7 @@ class Thermo : protected Pointers { int lostbond; // ditto for atoms in bonds enum { IGNORE, WARN, ERROR }; + enum { INT, FLOAT, BIGINT }; Thermo(class LAMMPS *, int, char **); ~Thermo(); diff --git a/src/utils.cpp b/src/utils.cpp index 654d5d3301..d70ae6f000 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -176,20 +176,23 @@ char *utils::fgets_trunc(char *buf, int size, FILE *fp) char dummy[MAXDUMMY]; char *ptr = fgets(buf, size, fp); - // EOF + // EOF? if (!ptr) return nullptr; int n = strlen(buf); - // line is shorter than buffer, append newline if needed, - if (n < size - 2) { + // check the string being read in: + // - if string is shorter than the buffer make sure it has a final newline and return + // - if string is exactly the size of the buffer and has a final newline return + // - otherwise truncate with final newline and read into dummy buffer until EOF or newline is found + if (n < size - 1) { if (buf[n - 1] != '\n') { buf[n] = '\n'; buf[n + 1] = '\0'; } return buf; - - // line fits exactly. overwrite last but one character. + } else if (buf[n - 1] == '\n') { + return buf; } else buf[size - 2] = '\n'; @@ -202,15 +205,15 @@ char *utils::fgets_trunc(char *buf, int size, FILE *fp) n = 0; } while (n == MAXDUMMY - 1 && ptr[MAXDUMMY - 1] != '\n'); - // return first chunk + // return truncated chunk return buf; } -#define MAXPATHLENBUF 1024 /* like fgets() but aborts with an error or EOF is encountered */ void utils::sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error) { + constexpr int MAXPATHLENBUF=1024; char *rv = fgets(s, size, fp); if (rv == nullptr) { // something went wrong char buf[MAXPATHLENBUF]; @@ -239,6 +242,7 @@ void utils::sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp void utils::sfread(const char *srcname, int srcline, void *s, size_t size, size_t num, FILE *fp, const char *filename, Error *error) { + constexpr int MAXPATHLENBUF=1024; size_t rv = fread(s, size, num, fp); if (rv != num) { // something went wrong char buf[MAXPATHLENBUF]; @@ -855,6 +859,13 @@ std::vector utils::split_words(const std::string &text) if (c != '\'') ++len; c = *++buf; + // handle triple double quotation marks + } else if ((c == '"') && (buf[1] == '"') && (buf[2] == '"') && (buf[3] != '"')) { + len = 3; + add = 1; + buf += 3; + c = *buf; + // handle double quote } else if (c == '"') { ++beg; @@ -1019,11 +1030,6 @@ bool utils::file_is_readable(const std::string &path) search current directory and the LAMMPS_POTENTIALS directory if specified ------------------------------------------------------------------------- */ -#if defined(_WIN32) -#define OS_PATH_VAR_SEP ";" -#else -#define OS_PATH_VAR_SEP ":" -#endif std::string utils::get_potential_file_path(const std::string &path) { @@ -1037,8 +1043,11 @@ std::string utils::get_potential_file_path(const std::string &path) const char *var = getenv("LAMMPS_POTENTIALS"); if (var != nullptr) { - Tokenizer dirs(var, OS_PATH_VAR_SEP); - +#if defined(_WIN32) + Tokenizer dirs(var, ";"); +#else + Tokenizer dirs(var, ":"); +#endif while (dirs.has_next()) { auto pot = utils::path_basename(filepath); auto dir = dirs.next(); @@ -1050,7 +1059,6 @@ std::string utils::get_potential_file_path(const std::string &path) } return ""; } -#undef OS_PATH_VAR_SEP /* ---------------------------------------------------------------------- read first line of potential file diff --git a/src/utils.h b/src/utils.h index 58b6df7725..b761534d66 100644 --- a/src/utils.h +++ b/src/utils.h @@ -33,19 +33,19 @@ class LAMMPS; namespace utils { - /** Match text against a simplified regex pattern - * - * \param text the text to be matched against the pattern - * \param pattern the search pattern, which may contain regexp markers - * \return true if the pattern matches, false if not */ + /*! Match text against a simplified regex pattern + * + * \param text the text to be matched against the pattern + * \param pattern the search pattern, which may contain regexp markers + * \return true if the pattern matches, false if not */ bool strmatch(const std::string &text, const std::string &pattern); - /** Find sub-string that matches a simplified regex pattern - * - * \param text the text to be matched against the pattern - * \param pattern the search pattern, which may contain regexp markers - * \return the string that matches the patters or an empty one */ + /*! Find sub-string that matches a simplified regex pattern + * + * \param text the text to be matched against the pattern + * \param pattern the search pattern, which may contain regexp markers + * \return the string that matches the pattern or an empty one */ std::string strfind(const std::string &text, const std::string &pattern); @@ -53,261 +53,261 @@ namespace utils { void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args); - /** Send formatted message to screen and logfile, if available - * - * This function simplifies the repetitive task of outputting some - * message to both the screen and/or the log file. The template - * wrapper with fmtlib format and argument processing allows - * this function to work similar to ``fmt::print()``. - * - * \param lmp pointer to LAMMPS class instance - * \param format format string of message to be printed - * \param args arguments to format string */ + /*! Send formatted message to screen and logfile, if available + * + * This function simplifies the repetitive task of outputting some + * message to both the screen and/or the log file. The template + * wrapper with fmtlib format and argument processing allows + * this function to work similar to ``fmt::print()``. + * + * \param lmp pointer to LAMMPS class instance + * \param format format string of message to be printed + * \param args arguments to format string */ template void logmesg(LAMMPS *lmp, const S &format, Args &&...args) { fmtargs_logmesg(lmp, format, fmt::make_args_checked(format, args...)); } - /** \overload - * - * \param lmp pointer to LAMMPS class instance - * \param mesg string with message to be printed */ + /*! \overload + * + * \param lmp pointer to LAMMPS class instance + * \param mesg string with message to be printed */ void logmesg(LAMMPS *lmp, const std::string &mesg); - /** Return a string representing the current system error status - * - * This is a wrapper around calling strerror(errno). - * - * \return error string */ + /*! Return a string representing the current system error status + * + * This is a wrapper around calling strerror(errno). + * + * \return error string */ std::string getsyserror(); - /** Wrapper around fgets() which reads whole lines but truncates the - * data to the buffer size and ensures a newline char at the end. - * - * This function is useful for reading line based text files with - * possible comments that should be parsed later. This applies to - * data files, potential files, atomfile variable files and so on. - * It is used instead of fgets() by utils::read_lines_from_file(). - * - * \param s buffer for storing the result of fgets() - * \param size size of buffer s (max number of bytes returned) - * \param fp file pointer used by fgets() */ + /*! Wrapper around fgets() which reads whole lines but truncates the + * data to the buffer size and ensures a newline char at the end. + * + * This function is useful for reading line based text files with + * possible comments that should be parsed later. This applies to + * data files, potential files, atomfile variable files and so on. + * It is used instead of fgets() by utils::read_lines_from_file(). + * + * \param s buffer for storing the result of fgets() + * \param size size of buffer s (max number of bytes returned) + * \param fp file pointer used by fgets() */ char *fgets_trunc(char *s, int size, FILE *fp); - /** Safe wrapper around fgets() which aborts on errors - * or EOF and prints a suitable error message to help debugging. - * - * Use nullptr as the error parameter to avoid the abort on EOF or error. - * - * \param srcname name of the calling source file (from FLERR macro) - * \param srcline line in the calling source file (from FLERR macro) - * \param s buffer for storing the result of fgets() - * \param size size of buffer s (max number of bytes read by fgets()) - * \param fp file pointer used by fgets() - * \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect) - * \param error pointer to Error class instance (for abort) or nullptr */ + /*! Safe wrapper around fgets() which aborts on errors + * or EOF and prints a suitable error message to help debugging. + * + * Use nullptr as the error parameter to avoid the abort on EOF or error. + * + * \param srcname name of the calling source file (from FLERR macro) + * \param srcline line in the calling source file (from FLERR macro) + * \param s buffer for storing the result of fgets() + * \param size size of buffer s (max number of bytes read by fgets()) + * \param fp file pointer used by fgets() + * \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect) + * \param error pointer to Error class instance (for abort) or nullptr */ void sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error); - /** Safe wrapper around fread() which aborts on errors - * or EOF and prints a suitable error message to help debugging. - * - * Use nullptr as the error parameter to avoid the abort on EOF or error. - * - * \param srcname name of the calling source file (from FLERR macro) - * \param srcline line in the calling source file (from FLERR macro) - * \param s buffer for storing the result of fread() - * \param size size of data elements read by fread() - * \param num number of data elements read by fread() - * \param fp file pointer used by fread() - * \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect) - * \param error pointer to Error class instance (for abort) or nullptr */ + /*! Safe wrapper around fread() which aborts on errors + * or EOF and prints a suitable error message to help debugging. + * + * Use nullptr as the error parameter to avoid the abort on EOF or error. + * + * \param srcname name of the calling source file (from FLERR macro) + * \param srcline line in the calling source file (from FLERR macro) + * \param s buffer for storing the result of fread() + * \param size size of data elements read by fread() + * \param num number of data elements read by fread() + * \param fp file pointer used by fread() + * \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect) + * \param error pointer to Error class instance (for abort) or nullptr */ void sfread(const char *srcname, int srcline, void *s, size_t size, size_t num, FILE *fp, const char *filename, Error *error); - /** Read N lines of text from file into buffer and broadcast them - * - * This function uses repeated calls to fread() to fill a buffer with - * newline terminated text. If a line does not end in a newline (e.g. - * at the end of a file), it is added. The caller has to allocate an - * nlines by nmax sized buffer for storing the text data. - * Reading is done by MPI rank 0 of the given communicator only, and - * thus only MPI rank 0 needs to provide a valid file pointer. - * - * \param fp file pointer used by fread - * \param nlines number of lines to be read - * \param nmax maximum length of a single line - * \param buffer buffer for storing the data. - * \param me MPI rank of calling process in MPI communicator - * \param comm MPI communicator for broadcast - * \return 1 if the read was short, 0 if read was successful */ + /*! Read N lines of text from file into buffer and broadcast them + * + * This function uses repeated calls to fread() to fill a buffer with + * newline terminated text. If a line does not end in a newline (e.g. + * at the end of a file), it is added. The caller has to allocate an + * nlines by nmax sized buffer for storing the text data. + * Reading is done by MPI rank 0 of the given communicator only, and + * thus only MPI rank 0 needs to provide a valid file pointer. + * + * \param fp file pointer used by fread + * \param nlines number of lines to be read + * \param nmax maximum length of a single line + * \param buffer buffer for storing the data. + * \param me MPI rank of calling process in MPI communicator + * \param comm MPI communicator for broadcast + * \return 1 if the read was short, 0 if read was successful */ int read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, int me, MPI_Comm comm); - /** Report if a requested style is in a package or may have a typo - * - * \param style type of style that is to be checked for - * \param name name of style that was not found - * \param lmp pointer to top-level LAMMPS class instance - * \return string usable for error messages */ + /*! Report if a requested style is in a package or may have a typo + * + * \param style type of style that is to be checked for + * \param name name of style that was not found + * \param lmp pointer to top-level LAMMPS class instance + * \return string usable for error messages */ std::string check_packages_for_style(const std::string &style, const std::string &name, LAMMPS *lmp); - /** Convert a string to a floating point number while checking - * if it is a valid floating point or integer number - * - * \param file name of source file for error message - * \param line line number in source file for error message - * \param str string to be converted to number - * \param do_abort determines whether to call Error::one() or Error::all() - * \param lmp pointer to top-level LAMMPS class instance - * \return double precision floating point number - */ + /*! Convert a string to a floating point number while checking + * if it is a valid floating point or integer number + * + * \param file name of source file for error message + * \param line line number in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return double precision floating point number */ + double numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp); - /** Convert a string to an integer number while checking - * if it is a valid integer number (regular int) - * - * \param file name of source file for error message - * \param line line number in source file for error message - * \param str string to be converted to number - * \param do_abort determines whether to call Error::one() or Error::all() - * \param lmp pointer to top-level LAMMPS class instance - * \return integer number (regular int) */ + /*! Convert a string to an integer number while checking + * if it is a valid integer number (regular int) + * + * \param file name of source file for error message + * \param line line number in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return integer number (regular int) */ int inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp); - /** Convert a string to an integer number while checking - * if it is a valid integer number (bigint) - * - * \param file name of source file for error message - * \param line line number in source file for error message - * \param str string to be converted to number - * \param do_abort determines whether to call Error::one() or Error::all() - * \param lmp pointer to top-level LAMMPS class instance - * \return integer number (bigint) */ + /*! Convert a string to an integer number while checking + * if it is a valid integer number (bigint) + * + * \param file name of source file for error message + * \param line line number in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return integer number (bigint) */ bigint bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp); - /** Convert a string to an integer number while checking - * if it is a valid integer number (tagint) - * - * \param file name of source file for error message - * \param line line number in source file for error message - * \param str string to be converted to number - * \param do_abort determines whether to call Error::one() or Error::all() - * \param lmp pointer to top-level LAMMPS class instance - * \return integer number (tagint) */ + /*! Convert a string to an integer number while checking + * if it is a valid integer number (tagint) + * + * \param file name of source file for error message + * \param line line number in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return integer number (tagint) */ tagint tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp); - /** Compute index bounds derived from a string with a possible wildcard - * - * This functions processes the string in *str* and set the values of *nlo* - * and *nhi* according to the following five cases: - * - * - a single number, i: nlo = i; nhi = i; - * - a single asterisk, \*: nlo = nmin; nhi = nmax; - * - a single number followed by an asterisk, i\*: nlo = i; nhi = nmax; - * - a single asterisk followed by a number, \*i: nlo = nmin; nhi = i; - * - two numbers with an asterisk in between. i\*j: nlo = i; nhi = j; - * - * \param file name of source file for error message - * \param line line number in source file for error message - * \param str string to be processed - * \param nmin smallest possible lower bound - * \param nmax largest allowed upper bound - * \param nlo lower bound - * \param nhi upper bound - * \param error pointer to Error class for out-of-bounds messages */ + /*! Compute index bounds derived from a string with a possible wildcard + * + * This functions processes the string in *str* and set the values of *nlo* + * and *nhi* according to the following five cases: + * + * - a single number, i: nlo = i; nhi = i; + * - a single asterisk, \*: nlo = nmin; nhi = nmax; + * - a single number followed by an asterisk, i\*: nlo = i; nhi = nmax; + * - a single asterisk followed by a number, \*i: nlo = nmin; nhi = i; + * - two numbers with an asterisk in between. i\*j: nlo = i; nhi = j; + * + * \param file name of source file for error message + * \param line line number in source file for error message + * \param str string to be processed + * \param nmin smallest possible lower bound + * \param nmax largest allowed upper bound + * \param nlo lower bound + * \param nhi upper bound + * \param error pointer to Error class for out-of-bounds messages */ template void bounds(const char *file, int line, const std::string &str, bigint nmin, bigint nmax, TYPE &nlo, TYPE &nhi, Error *error); - /** Expand list of arguments when containing fix/compute wildcards - * - * This function searches the list of arguments in *arg* for strings - * of the kind c_ID[*] or f_ID[*] referring to computes or fixes. - * Any such strings are replaced by one or more strings with the - * '*' character replaced by the corresponding possible numbers as - * determined from the fix or compute instance. Other strings are - * just copied. If the *mode* parameter is set to 0, expand global - * vectors, but not global arrays; if it is set to 1, expand global - * arrays (by column) but not global vectors. - * - * If any expansion happens, the earg list and all its - * strings are new allocations and must be freed explicitly by the - * caller. Otherwise arg and earg will point to the same address - * and no explicit de-allocation is needed by the caller. - * - * \param file name of source file for error message - * \param line line number in source file for error message - * \param narg number of arguments in current list - * \param arg argument list, possibly containing wildcards - * \param mode select between global vectors(=0) and arrays (=1) - * \param earg new argument list with wildcards expanded - * \param lmp pointer to top-level LAMMPS class instance - * \return number of arguments in expanded list */ + /*! Expand list of arguments when containing fix/compute wildcards + * + * This function searches the list of arguments in *arg* for strings + * of the kind c_ID[*] or f_ID[*] referring to computes or fixes. + * Any such strings are replaced by one or more strings with the + * '*' character replaced by the corresponding possible numbers as + * determined from the fix or compute instance. Other strings are + * just copied. If the *mode* parameter is set to 0, expand global + * vectors, but not global arrays; if it is set to 1, expand global + * arrays (by column) but not global vectors. + * + * If any expansion happens, the earg list and all its + * strings are new allocations and must be freed explicitly by the + * caller. Otherwise arg and earg will point to the same address + * and no explicit de-allocation is needed by the caller. + * + * \param file name of source file for error message + * \param line line number in source file for error message + * \param narg number of arguments in current list + * \param arg argument list, possibly containing wildcards + * \param mode select between global vectors(=0) and arrays (=1) + * \param earg new argument list with wildcards expanded + * \param lmp pointer to top-level LAMMPS class instance + * \return number of arguments in expanded list */ int expand_args(const char *file, int line, int narg, char **arg, int mode, char **&earg, LAMMPS *lmp); - /** Make C-style copy of string in new storage - * - * This allocates a storage buffer and copies the C-style or - * C++ style string into it. The buffer is allocated with "new" - * and thus needs to be deallocated with "delete[]". - * - * \param text string that should be copied - * \return new buffer with copy of string */ + /*! Make C-style copy of string in new storage + * + * This allocates a storage buffer and copies the C-style or + * C++ style string into it. The buffer is allocated with "new" + * and thus needs to be deallocated with "delete[]". + * + * \param text string that should be copied + * \return new buffer with copy of string */ char *strdup(const std::string &text); - /** Trim leading and trailing whitespace. Like TRIM() in Fortran. - * - * \param line string that should be trimmed - * \return new string without whitespace (string) */ + /*! Trim leading and trailing whitespace. Like TRIM() in Fortran. + * + * \param line string that should be trimmed + * \return new string without whitespace (string) */ std::string trim(const std::string &line); - /** Return string with anything from '#' onward removed - * - * \param line string that should be trimmed - * \return new string without comment (string) */ + /*! Return string with anything from '#' onward removed + * + * \param line string that should be trimmed + * \return new string without comment (string) */ std::string trim_comment(const std::string &line); - /** Check if a string will likely have UTF-8 encoded characters - * - * UTF-8 uses the 7-bit standard ASCII table for the first 127 characters and - * all other characters are encoded as multiple bytes. For the multi-byte - * characters the first byte has either the highest two, three, or four bits - * set followed by a zero bit and followed by one, two, or three more bytes, - * respectively, where the highest bit is set and the second highest bit set - * to 0. The remaining bits combined are the character code, which is thus - * limited to 21-bits. - * - * For the sake of efficiency this test only checks if a character in the string - * has the highest bit set and thus is very likely an UTF-8 character. It will - * not be able to tell this this is a valid UTF-8 character or whether it is a - * 2-byte, 3-byte, or 4-byte character. - * + /*! Check if a string will likely have UTF-8 encoded characters + * + * UTF-8 uses the 7-bit standard ASCII table for the first 127 characters and + * all other characters are encoded as multiple bytes. For the multi-byte + * characters the first byte has either the highest two, three, or four bits + * set followed by a zero bit and followed by one, two, or three more bytes, + * respectively, where the highest bit is set and the second highest bit set + * to 0. The remaining bits combined are the character code, which is thus + * limited to 21-bits. + * + * For the sake of efficiency this test only checks if a character in the string + * has the highest bit set and thus is very likely an UTF-8 character. It will + * not be able to tell this this is a valid UTF-8 character or whether it is a + * 2-byte, 3-byte, or 4-byte character. + * \verbatim embed:rst *See also* :cpp:func:`utils::utf8_subst` \endverbatim - * \param line string that should be checked - * \return true if string contains UTF-8 encoded characters (bool) */ + * \param line string that should be checked + * \return true if string contains UTF-8 encoded characters (bool) */ inline bool has_utf8(const std::string &line) { @@ -316,243 +316,245 @@ namespace utils { return false; } - /** Replace known UTF-8 characters with ASCII equivalents - * + /*! Replace known UTF-8 characters with ASCII equivalents + * \verbatim embed:rst *See also* :cpp:func:`utils::has_utf8` \endverbatim - * \param line string that should be converted - * \return new string with ascii replacements (string) */ + * \param line string that should be converted + * \return new string with ascii replacements (string) */ std::string utf8_subst(const std::string &line); - /** Count words in string with custom choice of separating characters - * - * \param text string that should be searched - * \param separators string containing characters that will be treated as whitespace - * \return number of words found */ + /*! Count words in string with custom choice of separating characters + * + * \param text string that should be searched + * \param separators string containing characters that will be treated as whitespace + * \return number of words found */ size_t count_words(const std::string &text, const std::string &separators); - /** Count words in string, ignore any whitespace matching " \t\r\n\f" - * - * \param text string that should be searched - * \return number of words found */ + /*! Count words in string, ignore any whitespace matching " \t\r\n\f" + * + * \param text string that should be searched + * \return number of words found */ size_t count_words(const std::string &text); - /** Count words in C-string, ignore any whitespace matching " \t\r\n\f" - * - * \param text string that should be searched - * \return number of words found */ + /*! Count words in C-string, ignore any whitespace matching " \t\r\n\f" + * + * \param text string that should be searched + * \return number of words found */ size_t count_words(const char *text); - /** Count words in a single line, trim anything from '#' onward - * - * \param text string that should be trimmed and searched - * \param separators string containing characters that will be treated as whitespace - * \return number of words found */ + /*! Count words in a single line, trim anything from '#' onward + * + * \param text string that should be trimmed and searched + * \param separators string containing characters that will be treated as whitespace + * \return number of words found */ size_t trim_and_count_words(const std::string &text, const std::string &separators = " \t\r\n\f"); - /** Take text and split into non-whitespace words. - * - * This can handle strings with single and double quotes, escaped quotes, - * and escaped codes within quotes, but due to using an STL container and - * STL strings is rather slow because of making copies. Designed for - * parsing command lines and similar text and not for time critical - * processing. Use a tokenizer class if performance matters. - * + /*! Take text and split into non-whitespace words. + * + * This can handle strings with single and double quotes, escaped quotes, + * and escaped codes within quotes, but due to using an STL container and + * STL strings is rather slow because of making copies. Designed for + * parsing command lines and similar text and not for time critical + * processing. Use a tokenizer class if performance matters. + * \verbatim embed:rst *See also* :cpp:class:`Tokenizer`, :cpp:class:`ValueTokenizer` \endverbatim - * \param text string that should be split - * \return STL vector with the words */ + * \param text string that should be split + * \return STL vector with the words */ std::vector split_words(const std::string &text); - /** Take multi-line text and split into lines - * - * \param text string that should be split - * \return STL vector with the lines */ + /*! Take multi-line text and split into lines + * + * \param text string that should be split + * \return STL vector with the lines */ std::vector split_lines(const std::string &text); - /** Check if string can be converted to valid integer - * - * \param str string that should be checked - * \return true, if string contains valid a integer, false otherwise */ + /*! Check if string can be converted to valid integer + * + * \param str string that should be checked + * \return true, if string contains valid a integer, false otherwise */ bool is_integer(const std::string &str); - /** Check if string can be converted to valid floating-point number - * - * \param str string that should be checked - * \return true, if string contains valid number, false otherwise */ + /*! Check if string can be converted to valid floating-point number + * + * \param str string that should be checked + * \return true, if string contains valid number, false otherwise */ bool is_double(const std::string &str); - /** Check if string is a valid ID - * ID strings may contain only letters, numbers, and underscores. - * - * \param str string that should be checked - * \return true, if string contains valid id, false otherwise */ + /*! Check if string is a valid ID + * ID strings may contain only letters, numbers, and underscores. + * + * \param str string that should be checked + * \return true, if string contains valid id, false otherwise */ bool is_id(const std::string &str); - /** Try to detect pathname from FILE pointer. - * - * Currently only supported on Linux, otherwise will report "(unknown)". - * - * \param buf storage buffer for pathname. output will be truncated if not large enough - * \param len size of storage buffer. output will be truncated to this length - 1 - * \param fp FILE pointer struct from STDIO library for which we want to detect the name - * \return pointer to the storage buffer, i.e. buf */ + /*! Try to detect pathname from FILE pointer. + * + * Currently only supported on Linux, otherwise will report "(unknown)". + * + * \param buf storage buffer for pathname. output will be truncated if not large enough + * \param len size of storage buffer. output will be truncated to this length - 1 + * \param fp FILE pointer struct from STDIO library for which we want to detect the name + * \return pointer to the storage buffer, i.e. buf */ const char *guesspath(char *buf, int len, FILE *fp); - /** Strip off leading part of path, return just the filename - * - * \param path file path - * \return file name */ + /*! Strip off leading part of path, return just the filename + * + * \param path file path + * \return file name */ std::string path_basename(const std::string &path); - /** Return the directory part of a path. Return "." if empty - * - * \param path file path - * \return directory name */ + /*! Return the directory part of a path. Return "." if empty + * + * \param path file path + * \return directory name */ std::string path_dirname(const std::string &path); - /** Join two pathname segments - * - * This uses the forward slash '/' character unless LAMMPS is compiled - * for Windows where it used the equivalent backward slash '\\'. - * - * \param a first path - * \param b second path - * \return combined path */ + /*! Join two pathname segments + * + * This uses the forward slash '/' character unless LAMMPS is compiled + * for Windows where it used the equivalent backward slash '\\'. + * + * \param a first path + * \param b second path + * \return combined path */ std::string path_join(const std::string &a, const std::string &b); - /** Check if file exists and is readable - * - * \param path file path - * \return true if file exists and is readable */ + /*! Check if file exists and is readable + * + * \param path file path + * \return true if file exists and is readable */ bool file_is_readable(const std::string &path); - /** Determine full path of potential file. If file is not found in current directory, - * search directories listed in LAMMPS_POTENTIALS environment variable - * - * \param path file path - * \return full path to potential file */ + /*! Determine full path of potential file. If file is not found in current directory, + * search directories listed in LAMMPS_POTENTIALS environment variable + * + * \param path file path + * \return full path to potential file */ std::string get_potential_file_path(const std::string &path); - /** Read potential file and return DATE field if it is present - * - * \param path file path - * \param potential_name name of potential that is being read - * \return DATE field if present */ + /*! Read potential file and return DATE field if it is present + * + * \param path file path + * \param potential_name name of potential that is being read + * \return DATE field if present */ std::string get_potential_date(const std::string &path, const std::string &potential_name); - /** Read potential file and return UNITS field if it is present - * - * \param path file path - * \param potential_name name of potential that is being read - * \return UNITS field if present */ + /*! Read potential file and return UNITS field if it is present + * + * \param path file path + * \param potential_name name of potential that is being read + * \return UNITS field if present */ std::string get_potential_units(const std::string &path, const std::string &potential_name); enum { NOCONVERT = 0, METAL2REAL = 1, REAL2METAL = 1 << 1 }; enum { UNKNOWN = 0, ENERGY }; - /** Return bitmask of available conversion factors for a given property - * - * \param property property to be converted - * \return bitmask indicating available conversions */ + /*! Return bitmask of available conversion factors for a given property + * + * \param property property to be converted + * \return bitmask indicating available conversions */ + int get_supported_conversions(const int property); - /** Return unit conversion factor for given property and selected from/to units - * - * \param property property to be converted - * \param conversion constant indicating the conversion - * \return conversion factor */ + /*! Return unit conversion factor for given property and selected from/to units + * + * \param property property to be converted + * \param conversion constant indicating the conversion + * \return conversion factor */ double get_conversion_factor(const int property, const int conversion); - /** Open a potential file as specified by *name* - * - * If opening the file directly fails, the function will search for - * it in the list of folder pointed to by the environment variable - * ``LAMMPS_POTENTIALS`` (if it is set). - * - * If the potential file has a ``UNITS`` tag in the first line, the - * tag's value is compared to the current unit style setting. - * The behavior of the function then depends on the value of the - * *auto_convert* parameter. If it is a null pointer, then the unit - * values must match or else the open will fail with an error. Otherwise - * the bitmask that *auto_convert* points to is used check for - * compatibility with possible automatic conversions by the calling - * function. If compatible, the bitmask is set to the required - * conversion or ``utils::NOCONVERT``. - * - * \param name file- or pathname of the potential file - * \param lmp pointer to top-level LAMMPS class instance - * \param auto_convert pointer to unit conversion bitmask or ``nullptr`` - * \return FILE pointer of the opened potential file or ``nullptr`` */ + /*! Open a potential file as specified by *name* + * + * If opening the file directly fails, the function will search for + * it in the list of folder pointed to by the environment variable + * ``LAMMPS_POTENTIALS`` (if it is set). + * + * If the potential file has a ``UNITS`` tag in the first line, the + * tag's value is compared to the current unit style setting. + * The behavior of the function then depends on the value of the + * *auto_convert* parameter. If it is a null pointer, then the unit + * values must match or else the open will fail with an error. Otherwise + * the bitmask that *auto_convert* points to is used check for + * compatibility with possible automatic conversions by the calling + * function. If compatible, the bitmask is set to the required + * conversion or ``utils::NOCONVERT``. + * + * \param name file- or pathname of the potential file + * \param lmp pointer to top-level LAMMPS class instance + * \param auto_convert pointer to unit conversion bitmask or ``nullptr`` + * \return FILE pointer of the opened potential file or ``nullptr`` */ FILE *open_potential(const std::string &name, LAMMPS *lmp, int *auto_convert); - /** Convert a time string to seconds - * - * The strings "off" and "unlimited" result in -1 - * - * \param timespec a string in the following format: ([[HH:]MM:]SS) - * \return total in seconds */ + /*! Convert a time string to seconds + * + * The strings "off" and "unlimited" result in -1 + * + * \param timespec a string in the following format: ([[HH:]MM:]SS) + * \return total in seconds */ double timespec2seconds(const std::string ×pec); - /** Convert a LAMMPS version date to a number - * - * This will generate a number YYYYMMDD from a date string - * (with or without blanks) that is suitable for numerical - * comparisons, i.e. later dates will generate a larger number. - * - * The day may or may not have a leading zero, the month - * is identified by the first 3 letters (so there may be more) - * and the year may be 2 or 4 digits (the missing 2 digits will - * be assumed as 20. That is 04 corresponds to 2004). - * - * No check is made whether the date is valid. - * - * \param date string in the format (Day Month Year) - * \return date code */ + /*! Convert a LAMMPS version date to a number + * + * This will generate a number YYYYMMDD from a date string + * (with or without blanks) that is suitable for numerical + * comparisons, i.e. later dates will generate a larger number. + * + * The day may or may not have a leading zero, the month + * is identified by the first 3 letters (so there may be more) + * and the year may be 2 or 4 digits (the missing 2 digits will + * be assumed as 20. That is 04 corresponds to 2004). + * + * No check is made whether the date is valid. + * + * \param date string in the format (Day Month Year) + * \return date code */ + int date2num(const std::string &date); - /** Custom merge sort implementation - * - * This function provides a custom upward hybrid merge sort - * implementation with support to pass an opaque pointer to - * the comparison function, e.g. for access to class members. - * This avoids having to use global variables. For improved - * performance, it uses an in-place insertion sort on initial - * chunks of up to 64 elements and switches to merge sort from - * then on. - * - * \param index Array with indices to be sorted - * \param num Length of the index array - * \param ptr Pointer to opaque object passed to comparison function - * \param comp Pointer to comparison function */ + /*! Custom merge sort implementation + * + * This function provides a custom upward hybrid merge sort + * implementation with support to pass an opaque pointer to + * the comparison function, e.g. for access to class members. + * This avoids having to use global variables. For improved + * performance, it uses an in-place insertion sort on initial + * chunks of up to 64 elements and switches to merge sort from + * then on. + * + * \param index Array with indices to be sorted + * \param num Length of the index array + * \param ptr Pointer to opaque object passed to comparison function + * \param comp Pointer to comparison function */ void merge_sort(int *index, int num, void *ptr, int (*comp)(int, int, void *)); } // namespace utils diff --git a/src/variable.cpp b/src/variable.cpp index 953d0ddf85..a7b2955b33 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -5065,16 +5065,10 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) : if (style == Variable::ATOMFILE) { if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Cannot use atomfile-style " - "variable unless an atom map exists"); - - std::string cmd = name + std::string("_VARIABLE_STORE"); - id_fix = utils::strdup(cmd); - - cmd += " all STORE peratom 0 1"; - modify->add_fix(cmd); - fixstore = (FixStore *) modify->fix[modify->nfix-1]; + error->all(FLERR,"Cannot use atomfile-style variable unless an atom map exists"); + id_fix = utils::strdup(std::string(name) + "_VARIABLE_STORE"); + fixstore = (FixStore *) modify->add_fix(std::string(id_fix) + " all STORE peratom 0 1"); buffer = new char[CHUNK*MAXLINE]; } } @@ -5122,7 +5116,7 @@ int VarReader::read_scalar(char *str) if (n == 1) continue; // skip if blank line break; } - memmove(str,ptr,n); // move trimmed string back + if (n > 0) memmove(str,ptr,n); // move trimmed string back } MPI_Bcast(&n,1,MPI_INT,0,world); if (n == 0) return 1; diff --git a/src/velocity.cpp b/src/velocity.cpp index acc374fa4a..fa09f451df 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -187,11 +187,11 @@ void Velocity::create(double t_desired, int seed) Compute *temperature_nobias = nullptr; if (temperature == nullptr || bias_flag) { - modify->add_compute(fmt::format("velocity_temp {} temp",group->names[igroup])); + auto newcompute = modify->add_compute(fmt::format("velocity_temp {} temp",group->names[igroup])); if (temperature == nullptr) { - temperature = modify->compute[modify->ncompute-1]; + temperature = newcompute; tcreate_flag = 1; - } else temperature_nobias = modify->compute[modify->ncompute-1]; + } else temperature_nobias = newcompute; } // initialize temperature computation(s) @@ -575,8 +575,7 @@ void Velocity::scale(int /*narg*/, char **arg) int tflag = 0; if (temperature == nullptr) { - modify->add_compute(fmt::format("velocity_temp {} temp",group->names[igroup])); - temperature = modify->compute[modify->ncompute-1]; + temperature = modify->add_compute(fmt::format("velocity_temp {} temp",group->names[igroup])); tflag = 1; } @@ -849,15 +848,11 @@ void Velocity::options(int narg, char **arg) iarg += 2; } else if (strcmp(arg[iarg],"temp") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); - int icompute; - for (icompute = 0; icompute < modify->ncompute; icompute++) - if (strcmp(arg[iarg+1],modify->compute[icompute]->id) == 0) break; - if (icompute == modify->ncompute) - error->all(FLERR,"Could not find velocity temperature ID"); + int icompute = modify->find_compute(arg[iarg+1]); + if (icompute < 0) error->all(FLERR,"Could not find velocity temperature ID"); temperature = modify->compute[icompute]; if (temperature->tempflag == 0) - error->all(FLERR, - "Velocity temperature ID does not compute temperature"); + error->all(FLERR,"Velocity temperature ID does not compute temperature"); iarg += 2; } else if (strcmp(arg[iarg],"bias") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); diff --git a/src/version.h b/src/version.h index ae0bd8bd1c..a48d6f1873 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "27 May 2021" +#define LAMMPS_VERSION "30 Jul 2021" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 3624bf0332..ddae269933 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -610,8 +610,8 @@ void WriteRestart::file_layout(int send_size) void WriteRestart::magic_string() { - std::string magic = MAGIC_STRING; - fwrite(magic.c_str(),sizeof(char),magic.size()+1,fp); + const char magic[] = MAGIC_STRING; + fwrite(magic,sizeof(char),strlen(magic)+1,fp); } /* ---------------------------------------------------------------------- */ diff --git a/tools/README b/tools/README index f803123270..eb329e27cd 100644 --- a/tools/README +++ b/tools/README @@ -25,7 +25,7 @@ eam_database one tool to generate EAM alloy potential files eam_generate 2nd tool to generate EAM alloy potential files eff scripts for working with the eFF (electron force field) emacs add-ons to EMACS editor for editing LAMMPS input scripts -fep scripts for free-energy perturbation with USER-FEP pkg +fep scripts for free-energy perturbation with FEP pkg i-pi Python wrapper for performing path-integral MD (PIMD) ipp input pre-processor Perl tool for creating input scripts kate add-ons to Kate editor for editing LAMMPS input scripts @@ -34,7 +34,7 @@ lmp2arc convert LAMMPS output to Accelrys Insight format lmp2cfg convert LAMMPS output to CFG files for AtomEye viz magic patterns to detect LAMMPS files with the file(1) command matlab MatLab scripts for post-processing LAMMPS output -mesont Tools for use with the USER-MESONT package +mesont Tools for use with the MESONT package micelle2d create a data file of small lipid chains in solvent moltemplate Instructions for installing the Moltemplate builder program msi2lmp use Accelrys Insight code to setup LAMMPS input @@ -43,7 +43,6 @@ phonon post-process output of the fix phonon command polybond Python tool for programmable polymer bonding pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output -reax Tools for analyzing output of ReaxFF simulations replica tool to reorder LAMMPS replica trajectories according to temperature singularity Singularity container descriptions suitable for LAMMPS development smd convert Smooth Mach Dynamics triangles to VTK diff --git a/tools/drude/polarizer.py b/tools/drude/polarizer.py index 3c17026387..d47ef0e05d 100755 --- a/tools/drude/polarizer.py +++ b/tools/drude/polarizer.py @@ -41,7 +41,7 @@ new bonds to the data file. It will also generate some commands to be included in the LAMMPS input script, which are related to the topology and force field, namely fix drude, pair_style and pair_coeff commands. For information on thermostating please -read the documentation of the USER-DRUDE package. +read the documentation of the DRUDE package. This tool can also be used to revert a Drude-polarized data file to a non-polarizable one. diff --git a/tools/fep/README b/tools/fep/README index ff319d5051..7fd4a8132c 100644 --- a/tools/fep/README +++ b/tools/fep/README @@ -1,4 +1,4 @@ -These are utility scripts provided as part of the USER-FEP package for +These are utility scripts provided as part of the FEP package for free energy perturbation simulations with soft-core pair potentials in LAMMPS. diff --git a/tools/mesont/README b/tools/mesont/README index 9a5289a449..d02679df51 100644 --- a/tools/mesont/README +++ b/tools/mesont/README @@ -1,9 +1,9 @@ -=== USER-MESONT tools === +=== MESONT tools === =============================== The programs in this folder can be used to analyze the output of simulations using the CNT mesoscopic force -field (USER-MESONT). +field (MESONT). dump2vtk.cpp converts output written in *.dump format (the sequence of columns must be "ATOMS id type x y z Es Eb Et diff --git a/tools/offline/scripts/init_http_cache.sh b/tools/offline/scripts/init_http_cache.sh index 9bda6cdaa5..44a07da35a 100755 --- a/tools/offline/scripts/init_http_cache.sh +++ b/tools/offline/scripts/init_http_cache.sh @@ -40,26 +40,26 @@ echo "Dowloading thirdparty tarballs..." MPICH2_WIN64_DEVEL_URL="${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" MPICH2_WIN32_DEVEL_URL="${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" VORO_URL="${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" -OPENCL_LOADER_URL="${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" +OPENCL_LOADER_URL="${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" SCAFACOS_FIX_URL="${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff" GTEST_URL="https://github.com/google/googletest/archive/release-1.10.0.tar.gz" YAML_URL="https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" -MATHJAX_URL="https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" +MATHJAX_URL="https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" EIGEN3_URL="https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CUB_URL="https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" -KOKKOS_URL="https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" +KOKKOS_URL="https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" KIM_URL="https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" MSCG_URL="https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" -PLUMED_URL="https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" +PLUMED_URL="https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" PACELIB_URL="https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" LATTE_URL="https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" SCAFACOS_URL="https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" MDI_URL="https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" GTEST_FILENAME="gtest-1.10.0.tar.gz" -MATHJAX_FILENAME="mathjax-3.1.2.tar.gz" +MATHJAX_FILENAME="mathjax-3.1.3.tar.gz" CUB_FILENAME="cub-1.12.0.tar.gz" -KOKKOS_FILENAME="kokkos-3.3.01.tar.gz" +KOKKOS_FILENAME="kokkos-3.4.01.tar.gz" MSCG_FILENAME="mscg-1.7.3.1.tar.gz" LATTE_FILENAME="latte-1.2.2.tar.gz" PACELIB_FILENAME="pacelib-2021.4.9.tar.gz" diff --git a/tools/offline/scripts/update_downloads.sh b/tools/offline/scripts/update_downloads.sh new file mode 100755 index 0000000000..247b92e562 --- /dev/null +++ b/tools/offline/scripts/update_downloads.sh @@ -0,0 +1,25 @@ +#!/bin/bash +#helper script to update URLs from CMake folder + +CMAKE_FOLDER=../../../cmake + +function extract_setting() +{ + export $1=$(grep -Rh "set($1" ../../../cmake/ | cut -d\" -f2) +} + +function update_setting() +{ + echo Setting $1 to $2 + sed -i "/^$1=/c$1=\"$2\"" init_http_cache.sh +} + + +URLS=$(grep -Rh "_URL=" init_http_cache.sh | grep -v ^LAMMPS | grep -v SCAFACOS_FIX | cut -d= -f1) + +# update URLs by grabbing the latest ones from cmake files +for URL in $URLS +do + extract_setting "$URL" + update_setting "$URL" ${!URL} +done diff --git a/tools/reax/Cutoff.dic b/tools/reax/Cutoff.dic deleted file mode 100644 index 7c52b74468..0000000000 --- a/tools/reax/Cutoff.dic +++ /dev/null @@ -1,14 +0,0 @@ -# Interesting name. This file contains -# the bond-order cut off for each -# pair of ReaxFF elements -C N 0.3 -C C 0.55 -C O 0.65 -C H 0.4 -O O 0.65 -N O 0.40 -O H 0.4 -H H 0.55 -H N 0.55 -N N 0.55 -# diff --git a/tools/reax/README.txt b/tools/reax/README.txt deleted file mode 100644 index 3c9fe4506b..0000000000 --- a/tools/reax/README.txt +++ /dev/null @@ -1,10 +0,0 @@ -=== ReaxFF tools === -=============================== - -The programs in this folder can be used to analyze the -output of simulations using the ReaxFF potentials; - -reaxc_bond.pl: reads the bonding information in the - .trj file produced by pair_style reax/c and - outputs molecule counts for each frame. - diff --git a/tools/reax/reaxc_bond.pl b/tools/reax/reaxc_bond.pl deleted file mode 100755 index cc0fd8f238..0000000000 --- a/tools/reax/reaxc_bond.pl +++ /dev/null @@ -1,152 +0,0 @@ -#!/usr/bin/perl -use Getopt::Long; -Getopt::Long::Configure ('bundling'); - -################################################################# -# # -# This script is designed to take the bond information from a # -# Lammps/reaxc *.trj file and output a molecular fraction file # -# for each frame. # -# # -# written by Mike Russo, PSU # -# modified by Aidan Thompson, 5/12/2011 # -# # -# The required .trj file is generated by running LAMMPS # -# with pair_style reax/c and the following settings in # -# the corresponding reax/c control file # -# write_freq 25 ! write trajectory after so many steps -# traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output -# traj_title TATB ! (no white spaces) -# atom_info 0 ! 0: no atom info, 1: print basic atom info in the trajectory file -# atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file -# atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file -# bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file -# angle_info 0 ! 0: do not print angles, 1: print angles in the trajectory file -# # -################################################################# - -################################################################# -# Setting up some default variables, and options for the user # -# to input. # -################################################################# -$in_file = "bonds.trj"; -@test = qw(C H O N); -GetOptions ('f|file=s' => \$in_file, 'a|atoms=s' => \@atoms, 'h|help' => \$help); -if($help) { - print "Options for this program:\n-f --file for input file default= bonds.trj\n-a --atoms atom types (in correct order and input separately) default= @test\n"; - exit; -} -open INPUT, "<$in_file" or die "Cannot open $in_file: $!"; -open OUTPUT, ">frac.dat" or die "Cannot open output file: $!"; - -if(@atoms) { - @test = @atoms; -} - -print "Input for this run:\n Input file = $in_file\n Atom types = @test\n"; -################################################################# - -################################################################# -# Main loop of the script. Goes through each frames bond list. # -################################################################# -$i = 0; -$section = 0; -$at_count = -1; -while() { - if(/chars_to_skip_section/) { - $section++; - &bonds if($section > 2); - next; - } - next if($section <= 0); #skipping the header section - next if(/\s*[A-Za-z]/); #skip text lines - - split; - if ($section == 1) { - $q = $_[0]; - $temp = $_[1]; - $q--; - $at_type[$q] = $temp; - next; - } - - $_[0]--; - $_[1]--; -# Add i-j and j-i entries - push @{$list[$_[0]]}, $_[1]; - push @{$list[$_[1]]}, $_[0]; - $at_count++ if($section == 2); -} -$section++; -&bonds; -close(INPUT); -################################################################# - -################################################################# -# Subroutine bonds: Uses the bond information to generate a # -# count for each species, put them into molecules, and then # -# count the number of each molecule type. # -################################################################# -sub bonds { - $flag = (); - $k = 0; - for(0..$#list) { - if($flag[$_] == 0) { - push @{$full_list[$k]}, $_; - foreach $atom (@{$full_list[$k]}) { - for($o = 0; $o <= $#{$list[$atom]}; $o++) { - unless(grep /^$list[$atom][$o]$/, @{$full_list[$k]}) { - push @{$full_list[$k]}, $list[$atom][$o]; - $flag[$list[$atom][$o]] = 1; - } - } - } - } else { - next; - } - $k++; - } - -### Output section ### - $frame = $section - 2; - open OUTPUT2, ">temp_$frame.dat" or die "Cannot open temp file: $!"; - print OUTPUT2 "Frame # $frame\n"; - for($m = 0; $m < $k; $m++) { #cycle through each molecule - foreach $atom ((@{$full_list[$m]})) { #for each atom in this molecule - ${"$test[$at_type[$atom]]"} += 1; #Create variable named C,H,O, etc and set it to count - } - print OUTPUT2 "Mol $m = "; - foreach $atom (@test) { - print OUTPUT2 "$atom${$atom}" if(${$atom} > 0); - } - print OUTPUT2 "\n"; - for($r = 0; $r <= $#test; $r++) { - ${"$test[$r]"} = 0; - } - } - - close (OUTPUT2); #close the temp file as output - open INPUT3, ") { - next if(/Frame/); - split; - push @mol_list, $_[3] unless(grep /^$_[3]$/, @mol_list); - ${"$_[3]"}++; - } - print OUTPUT "Frame # $frame\n"; - foreach $mol (@mol_list) { - printf OUTPUT "%4d %s\n", ${"$mol"}, $mol; - ${"$mol"} = 0; - } - @mol_list = (); -### - -### Cleanup between frames ### - for(0..$at_count) { - @{$full_list[$_]} = (); - @{$list[$_]} = (); - } -### -} -################################################################# - diff --git a/tools/swig/lammps.i b/tools/swig/lammps.i index ec37120c07..2767e4c068 100644 --- a/tools/swig/lammps.i +++ b/tools/swig/lammps.i @@ -63,6 +63,7 @@ extern void *lammps_open_fortran(int argc, char **argv, int f_comm); extern void lammps_close(void *handle); extern void lammps_mpi_init(); extern void lammps_mpi_finalize(); +extern void lammps_kokkos_finalize(); extern void lammps_file(void *handle, const char *file); extern char *lammps_command(void *handle, const char *cmd); extern void lammps_commands_list(void *handle, int ncmd, const char **cmds); @@ -90,6 +91,7 @@ extern void lammps_gather_atoms_concat(void *, char *, int, int, void *); extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *); extern void lammps_scatter_atoms(void *, char *, int, int, void *); extern void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); +extern void lammps_gather_bonds(void *handle, void *data); extern void lammps_gather(void *, char *, int, int, void *); extern void lammps_gather_concat(void *, char *, int, int, void *); extern void lammps_gather_subset(void *, char *, int, int, int, int *, void *); @@ -127,16 +129,27 @@ extern int lammps_id_name(void *, const char *, int, char *buffer, int buf_si extern int lammps_plugin_count(); extern int lammps_plugin_name(int, char *, char *, int); /* -extern int lammps_encode_image_flags(int ix, int iy, int iz); -extern void lammps_decode_image_flags(int image, int *flags); -extern int64_t lammps_encode_image_flags(int ix, int iy, int iz); -extern void lammps_decode_image_flags(int64_t image, int *flags); -extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); -extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); -extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); -extern void lammps_fix_external_set_energy_global(void *, char *, double); -extern void lammps_fix_external_set_virial_global(void *, char *, double *); + * Have not found a good way to map these functions in a general way. + * So some individual customization for the specific use case and compilation is needed. + * + extern int lammps_encode_image_flags(int ix, int iy, int iz); + extern void lammps_decode_image_flags(int image, int *flags); + extern int64_t lammps_encode_image_flags(int ix, int iy, int iz); + extern void lammps_decode_image_flags(int64_t image, int *flags); + + * Supporting the fix external callback mechanism will require extra code specific to the application. + typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); + extern void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, void *ptr); + * these two functions can only be used from the callback, so we don't support them either + extern void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng); + extern void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial); */ +extern double **lammps_fix_external_get_force(void *handle, const char *id); +extern void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng); +extern void lammps_fix_external_set_virial_global(void *handle, const char *id, double *virial); +extern void lammps_fix_external_set_vector_length(void *handle, const char *id, int len); +extern void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val); + extern void lammps_free(void *ptr); extern int lammps_is_running(void *handle); extern void lammps_force_timeout(void *handle); @@ -185,6 +198,7 @@ extern void *lammps_open_fortran(int argc, char **argv, int f_comm); extern void lammps_close(void *handle); extern void lammps_mpi_init(); extern void lammps_mpi_finalize(); +extern void lammps_kokkos_finalize(); extern void lammps_file(void *handle, const char *file); extern char *lammps_command(void *handle, const char *cmd); extern void lammps_commands_list(void *handle, int ncmd, const char **cmds); @@ -212,6 +226,7 @@ extern void lammps_gather_atoms_concat(void *, char *, int, int, void *); extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *); extern void lammps_scatter_atoms(void *, char *, int, int, void *); extern void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); +extern void lammps_gather_bonds(void *handle, void *data); extern void lammps_gather(void *, char *, int, int, void *); extern void lammps_gather_concat(void *, char *, int, int, void *); extern void lammps_gather_subset(void *, char *, int, int, int, int *, void *); @@ -253,16 +268,21 @@ extern int lammps_encode_image_flags(int ix, int iy, int iz); extern void lammps_decode_image_flags(int image, int *flags); extern int64_t lammps_encode_image_flags(int ix, int iy, int iz); extern void lammps_decode_image_flags(int64_t image, int *flags); -extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); -extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); -extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); -extern void lammps_fix_external_set_energy_global(void *, char *, double); -extern void lammps_fix_external_set_virial_global(void *, char *, double *); +typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); +extern void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, void *ptr); +extern void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng); +extern void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial); */ +extern double **lammps_fix_external_get_force(void *handle, const char *id); +extern void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng); +extern void lammps_fix_external_set_virial_global(void *handle, const char *id, double *virial); +extern void lammps_fix_external_set_vector_length(void *handle, const char *id, int len); +extern void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val); + extern void lammps_free(void *ptr); extern int lammps_is_running(void *handle); extern void lammps_force_timeout(void *handle); extern int lammps_has_error(void *handle); extern int lammps_get_last_error_message(void *handle, char *buffer, int buf_size); -/* last revised for LAMMPS 8 April 2021 */ +/* last revised on 21 July 2021 */ diff --git a/tools/valgrind/FlexiBLAS.supp b/tools/valgrind/FlexiBLAS.supp new file mode 100644 index 0000000000..d5dda4e54f --- /dev/null +++ b/tools/valgrind/FlexiBLAS.supp @@ -0,0 +1,61 @@ +{ + FL_BLAS_init_part1 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + ... + fun:flexiblas_init + ... + fun:call_init + fun:_dl_init + ... + obj:* +} +{ + FL_BLAS_init_part2 + Memcheck:Leak + match-leak-kinds: reachable + fun:calloc + ... + fun:dl_open_worker + ... + fun:dlopen_doit + ... + fun:flexiblas_init +} +{ + FL_BLAS_init_part3 + Memcheck:Leak + match-leak-kinds: reachable + fun:calloc + ... + fun:flexiblas_init + ... + fun:call_init + ... + obj:* +} +{ + FL_BLAS_exception1 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + ... + fun:dl_open_worker + ... + fun:dlopen_doit + ... + obj:* +} +{ + FL_BLAS_exception2 + Memcheck:Leak + match-leak-kinds: reachable + fun:calloc + ... + fun:dl_open_worker + ... + fun:dlopen_doit + ... + obj:* +} diff --git a/tools/valgrind/OpenMP.supp b/tools/valgrind/OpenMP.supp index 64ee61febd..0820100b94 100644 --- a/tools/valgrind/OpenMP.supp +++ b/tools/valgrind/OpenMP.supp @@ -112,3 +112,14 @@ ... obj:* } +{ + OpnMP_init_part10 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + ... + fun:call_init + fun:_dl_init + ... + obj:* +} diff --git a/tools/valgrind/README b/tools/valgrind/README index fb35b4586a..8a32f7928c 100644 --- a/tools/valgrind/README +++ b/tools/valgrind/README @@ -10,7 +10,9 @@ valgrind --show-leak-kinds=all --track-origins=yes \ --suppressions=/path/to/lammps/tools/valgrind/OpenMPI.supp \ --suppressions=/path/to/lammps/tools/valgrind/Python3.supp \ --suppressions=/path/to/lammps/tools/valgrind/GTest.supp \ + --suppressions=/path/to/lammps/tools/valgrind/FlexiBLAS.supp \ + --suppressions=/path/to/lammps/tools/valgrind/readline.supp \ lmp -in in.melt -Last update: 2020-07-09 +Last update: 2021-08-04 diff --git a/tools/valgrind/readline.supp b/tools/valgrind/readline.supp new file mode 100644 index 0000000000..f1e1c6df1e --- /dev/null +++ b/tools/valgrind/readline.supp @@ -0,0 +1,169 @@ +{ + Readline_init_part1 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:xmalloc + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part2 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:strdup + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part3 + Memcheck:Leak + match-leak-kinds: reachable + fun:realloc + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part4 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part5 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + ... + fun:tgetent_sp + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part6 + Memcheck:Leak + match-leak-kinds: reachable + fun:calloc + ... + fun:tgetent_sp + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part7 + Memcheck:Leak + match-leak-kinds: reachable + fun:realloc + ... + fun:tgetent_sp + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part8 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + ... + fun:tgetent_sp + ... + fun:rl_initialize + fun:readline + ... + obj:* +} +{ + Readline_init_part9 + Memcheck:Leak + match-leak-kinds: reachable + fun:calloc + ... + fun:tgetstr_sp + ... + fun:rl_initialize + fun:readline + obj:* +} +{ + Readline_prompt_part1 + Memcheck:Leak + match-leak-kinds: reachable + fun:realloc + fun:xrealloc + ... + fun:rl_set_prompt + fun:readline + ... + obj:* +} +{ + Readline_prompt_part2 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:xmalloc + ... + fun:rl_set_prompt + fun:readline + ... + obj:* +} +{ + Readline_history_part1 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:xmalloc + ... + fun:readline_internal_teardown + fun:readline + ... + obj:* +} +{ + Readline_history_part2 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:xmalloc + ... + fun:readline_internal_teardown + fun:readline + ... + obj:* +} +{ + Readline_history_part3 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + fun:xmalloc + ... + fun:add_history + fun:shell_cmd + ... + obj:* +} diff --git a/unittest/c-library/CMakeLists.txt b/unittest/c-library/CMakeLists.txt index 3c24cdcff4..ee7f323c0f 100644 --- a/unittest/c-library/CMakeLists.txt +++ b/unittest/c-library/CMakeLists.txt @@ -7,12 +7,22 @@ add_executable(test_library_commands test_library_commands.cpp test_main.cpp) target_link_libraries(test_library_commands PRIVATE lammps GTest::GTest GTest::GMock) add_test(LibraryCommands test_library_commands) +add_executable(test_library_external test_library_external.cpp test_main.cpp) +target_link_libraries(test_library_external PRIVATE lammps GTest::GTest GTest::GMock) +add_test(LibraryExternal test_library_external) + add_executable(test_library_properties test_library_properties.cpp test_main.cpp) target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GMock) target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) add_test(LibraryProperties test_library_properties) set_tests_properties(LibraryProperties PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") +add_executable(test_library_scatter_gather test_library_scatter_gather.cpp test_main.cpp) +target_link_libraries(test_library_scatter_gather PRIVATE lammps GTest::GTest GTest::GMock) +target_compile_definitions(test_library_scatter_gather PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) +add_test(LibraryScatterGather test_library_scatter_gather) +set_tests_properties(LibraryScatterGather PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") + set(TEST_CONFIG_DEFS "-DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR};-DLAMMPS_${LAMMPS_SIZES}") set(PKG_COUNT 0) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) diff --git a/unittest/c-library/test_library_external.cpp b/unittest/c-library/test_library_external.cpp new file mode 100644 index 0000000000..15edd5f113 --- /dev/null +++ b/unittest/c-library/test_library_external.cpp @@ -0,0 +1,200 @@ +// unit tests for interfacing with fix external via the library interface + +#include "library.h" + +#include +#include + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include "test_main.h" + +using ::testing::HasSubstr; +using ::testing::StartsWith; + +extern "C" { +#ifdef LAMMPS_SMALLSMALL +typedef int32_t step_t; +typedef int32_t tag_t; +#elif LAMMPS_SMALLBIG +typedef int64_t step_t; +typedef int32_t tag_t; +#else +typedef int64_t step_t; +typedef int64_t tag_t; +#endif +static void callback(void *handle, step_t timestep, int nlocal, tag_t *, double **, double **f) +{ + for (int i = 0; i < nlocal; ++i) + f[i][0] = f[i][1] = f[i][2] = (double)timestep; + + double v[6] = {1.0, 1.0, 1.0, 0.0, 0.0, 0.0}; + lammps_fix_external_set_virial_global(handle, "ext", v); + if (timestep < 10) { + lammps_fix_external_set_energy_global(handle, "ext", 0.5); + lammps_fix_external_set_vector(handle, "ext", 1, timestep); + lammps_fix_external_set_vector(handle, "ext", 3, 1.0); + lammps_fix_external_set_vector(handle, "ext", 4, -0.25); + } else { + lammps_fix_external_set_energy_global(handle, "ext", 1.0); + lammps_fix_external_set_vector(handle, "ext", 2, timestep); + lammps_fix_external_set_vector(handle, "ext", 5, -1.0); + lammps_fix_external_set_vector(handle, "ext", 6, 0.25); + } + double *eatom = new double[nlocal]; + double **vatom = new double *[nlocal]; + vatom[0] = new double[nlocal * 6]; + eatom[0] = 0.0; + vatom[0][0] = vatom[0][1] = vatom[0][2] = vatom[0][3] = vatom[0][4] = vatom[0][5] = 0.0; + + for (int i = 1; i < nlocal; ++i) { + eatom[i] = 0.1 * i; + vatom[i] = vatom[0] + 6 * i; + vatom[i][0] = vatom[i][1] = vatom[i][2] = 0.1; + vatom[i][3] = vatom[i][4] = vatom[i][5] = -0.2; + } + lammps_fix_external_set_energy_peratom(handle, "ext", eatom); + lammps_fix_external_set_virial_peratom(handle, "ext", vatom); + delete[] eatom; + delete[] vatom[0]; + delete[] vatom; +} +} + +TEST(lammps_external, callback) +{ + const char *args[] = {"liblammps", "-log", "none", "-nocite"}; + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + + ::testing::internal::CaptureStdout(); + void *handle = lammps_open_no_mpi(argc, argv, NULL); + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + + ::testing::internal::CaptureStdout(); + lammps_commands_string(handle, "lattice sc 1.0\n" + "region box block -1 1 -1 1 -1 1\n" + "create_box 1 box\n" + "create_atoms 1 box\n" + "mass 1 1.0\n" + "pair_style zero 0.1\n" + "pair_coeff 1 1\n" + "velocity all set 0.1 0.0 -0.1\n" + "fix 1 all nve\n" + "fix ext all external pf/callback 5 1\n" + "compute eatm all pe/atom fix\n" + "compute vatm all stress/atom NULL fix\n" + "compute sum all reduce sum c_eatm c_vatm[*]\n" + "thermo_style custom step temp pe ke etotal press c_sum[*]\n" + "thermo 5\n" + "fix_modify ext energy yes virial yes\n"); + lammps_fix_external_set_vector_length(handle, "ext", 6); + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + + ::testing::internal::CaptureStdout(); + lammps_set_fix_external_callback(handle, "ext", &callback, handle); + lammps_command(handle, "run 10 post no"); + double temp = lammps_get_thermo(handle, "temp"); + double pe = lammps_get_thermo(handle, "pe"); + double press = lammps_get_thermo(handle, "press"); + double val = 0.0; + double *valp; + for (int i = 0; i < 6; ++i) { + valp = (double *)lammps_extract_fix(handle, "ext", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, i, 0); + val += *valp; + lammps_free(valp); + } + double *reduce = + (double *)lammps_extract_compute(handle, "sum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR); + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + EXPECT_DOUBLE_EQ(temp, 1.0 / 30.0); + EXPECT_DOUBLE_EQ(pe, 1.0 / 8.0); + EXPECT_DOUBLE_EQ(press, 0.15416666666666667); + EXPECT_DOUBLE_EQ(val, 15); + EXPECT_DOUBLE_EQ(reduce[0], 2.8); + EXPECT_DOUBLE_EQ(reduce[1], -0.7); + EXPECT_DOUBLE_EQ(reduce[2], -0.7); + EXPECT_DOUBLE_EQ(reduce[3], -0.7); + EXPECT_DOUBLE_EQ(reduce[4], 1.4); + EXPECT_DOUBLE_EQ(reduce[5], 1.4); + EXPECT_DOUBLE_EQ(reduce[6], 1.4); + + ::testing::internal::CaptureStdout(); + lammps_close(handle); + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; +} + +TEST(lammps_external, array) +{ + const char *args[] = {"liblammps", "-log", "none", "-nocite"}; + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + + ::testing::internal::CaptureStdout(); + void *handle = lammps_open_no_mpi(argc, argv, NULL); + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + + ::testing::internal::CaptureStdout(); + lammps_commands_string(handle, "lattice sc 1.0\n" + "region box block -1 1 -1 1 -1 1\n" + "create_box 1 box\n" + "create_atoms 1 box\n" + "mass 1 1.0\n" + "pair_style zero 0.1\n" + "pair_coeff 1 1\n" + "velocity all set 0.1 0.0 -0.1\n" + "fix 1 all nve\n" + "fix ext all external pf/array 1\n" + "thermo 5\n"); + + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + + ::testing::internal::CaptureStdout(); + double **force = lammps_fix_external_get_force(handle, "ext"); + int nlocal = lammps_extract_setting(handle, "nlocal"); + for (int i = 0; i < nlocal; ++i) + force[i][0] = force[i][1] = force[i][2] = 0.0; + lammps_fix_external_set_energy_global(handle, "ext", 0.5); + double v[6] = {0.5, 0.5, 0.5, 0.0, 0.0, 0.0}; + lammps_fix_external_set_virial_global(handle, "ext", v); + lammps_command(handle, "run 5 post no"); + double temp = lammps_get_thermo(handle, "temp"); + double pe = lammps_get_thermo(handle, "pe"); + double press = lammps_get_thermo(handle, "press"); + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + EXPECT_DOUBLE_EQ(temp, 4.0 / 525.0); + EXPECT_DOUBLE_EQ(pe, 1.0 / 16.0); + EXPECT_DOUBLE_EQ(press, 0.069166666666666668); + + ::testing::internal::CaptureStdout(); + nlocal = lammps_extract_setting(handle, "nlocal"); + force = lammps_fix_external_get_force(handle, "ext"); + for (int i = 0; i < nlocal; ++i) + force[i][0] = force[i][1] = force[i][2] = 6.0; + lammps_fix_external_set_energy_global(handle, "ext", 1.0); + v[0] = v[1] = v[2] = 1.0; + v[3] = v[4] = v[5] = 0.0; + lammps_fix_external_set_virial_global(handle, "ext", v); + lammps_command(handle, "run 5 post no"); + temp = lammps_get_thermo(handle, "temp"); + pe = lammps_get_thermo(handle, "pe"); + press = lammps_get_thermo(handle, "press"); + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + EXPECT_DOUBLE_EQ(temp, 1.0 / 30.0); + EXPECT_DOUBLE_EQ(pe, 1.0 / 8.0); + EXPECT_DOUBLE_EQ(press, 0.15416666666666667); + + ::testing::internal::CaptureStdout(); + lammps_close(handle); + output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; +} diff --git a/unittest/c-library/test_library_open.cpp b/unittest/c-library/test_library_open.cpp index 377f3c53ef..b7a8016a1a 100644 --- a/unittest/c-library/test_library_open.cpp +++ b/unittest/c-library/test_library_open.cpp @@ -137,7 +137,7 @@ TEST(lammps_open_no_mpi, no_screen) TEST(lammps_open_no_mpi, with_omp) { - if (!LAMMPS_NS::LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS_NS::LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); const char *args[] = {"liblammps", "-pk", "omp", "2", "neigh", "no", "-sf", "omp", "-log", "none", "-nocite"}; char **argv = (char **)args; diff --git a/unittest/c-library/test_library_scatter_gather.cpp b/unittest/c-library/test_library_scatter_gather.cpp new file mode 100644 index 0000000000..34022f617e --- /dev/null +++ b/unittest/c-library/test_library_scatter_gather.cpp @@ -0,0 +1,133 @@ +// unit tests for testing scatter/gather operations through the library interface + +#include "lammps.h" +#include "library.h" +#include "lmptype.h" +#include + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include "test_main.h" + +#define STRINGIFY(val) XSTR(val) +#define XSTR(val) #val + +using ::LAMMPS_NS::bigint; +using ::LAMMPS_NS::tagint; +using ::testing::HasSubstr; +using ::testing::StartsWith; + +class GatherProperties : public ::testing::Test { +protected: + void *lmp; + std::string INPUT_DIR = STRINGIFY(TEST_INPUT_FOLDER); + + GatherProperties(){}; + ~GatherProperties() override{}; + + void SetUp() override + { + const char *args[] = {"LAMMPS_test", "-log", "none", + "-echo", "screen", "-nocite", + "-var", "input_dir", STRINGIFY(TEST_INPUT_FOLDER)}; + + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + + ::testing::internal::CaptureStdout(); + lmp = lammps_open_no_mpi(argc, argv, NULL); + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + EXPECT_THAT(output, StartsWith("LAMMPS (")); + } + void TearDown() override + { + ::testing::internal::CaptureStdout(); + lammps_close(lmp); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(output, HasSubstr("Total wall time:")); + if (verbose) std::cout << output; + lmp = nullptr; + } +}; + +TEST_F(GatherProperties, gather_bonds_newton_on) +{ + if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP(); + std::string input = INPUT_DIR + PATH_SEP + "in.fourmol"; + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "newton on on"); + lammps_file(lmp, input.c_str()); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + bigint nbonds = *(bigint *)lammps_extract_global(lmp, "nbonds"); + EXPECT_EQ(nbonds, 24); + + tagint *bonds = new tagint[3 * nbonds]; + lammps_gather_bonds(lmp, bonds); + +#define CHECK_BOND(idx, type, atom1, atom2) \ + if (((bonds[3 * idx + 1] == atom1) && (bonds[3 * idx + 2] == atom2)) || \ + ((bonds[3 * idx + 1] == atom2) && (bonds[3 * idx + 2] == atom1))) { \ + EXPECT_EQ(bonds[3 * idx], type); \ + ++count; \ + } + + // check validity of a few bonds by comparing the bond type and counting the matches. + int count = 0; + for (bigint i = 0; i < nbonds; ++i) { + CHECK_BOND(i, 5, 1, 2); + CHECK_BOND(i, 3, 1, 3); + CHECK_BOND(i, 2, 3, 4); + CHECK_BOND(i, 2, 3, 5); + CHECK_BOND(i, 1, 3, 6); + CHECK_BOND(i, 3, 6, 8); + CHECK_BOND(i, 4, 6, 7); + CHECK_BOND(i, 5, 8, 9); + CHECK_BOND(i, 5, 27, 28); + CHECK_BOND(i, 5, 27, 29); + } + EXPECT_EQ(count, 10); + delete[] bonds; +}; + +TEST_F(GatherProperties, gather_bonds_newton_off) +{ + if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP(); + std::string input = INPUT_DIR + PATH_SEP + "in.fourmol"; + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "newton off off"); + lammps_file(lmp, input.c_str()); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + bigint nbonds = *(bigint *)lammps_extract_global(lmp, "nbonds"); + EXPECT_EQ(nbonds, 24); + + tagint *bonds = new tagint[3 * nbonds]; + lammps_gather_bonds(lmp, bonds); + +#define CHECK_BOND(idx, type, atom1, atom2) \ + if (((bonds[3 * idx + 1] == atom1) && (bonds[3 * idx + 2] == atom2)) || \ + ((bonds[3 * idx + 1] == atom2) && (bonds[3 * idx + 2] == atom1))) { \ + EXPECT_EQ(bonds[3 * idx], type); \ + ++count; \ + } + + // check validity of a few bonds by comparing the bond type and counting the matches. + int count = 0; + for (bigint i = 0; i < nbonds; ++i) { + CHECK_BOND(i, 5, 1, 2); + CHECK_BOND(i, 3, 1, 3); + CHECK_BOND(i, 2, 3, 4); + CHECK_BOND(i, 2, 3, 5); + CHECK_BOND(i, 1, 3, 6); + CHECK_BOND(i, 3, 6, 8); + CHECK_BOND(i, 4, 6, 7); + CHECK_BOND(i, 5, 8, 9); + CHECK_BOND(i, 5, 27, 28); + CHECK_BOND(i, 5, 27, 29); + } + EXPECT_EQ(count, 10); + delete[] bonds; +}; diff --git a/unittest/commands/test_groups.cpp b/unittest/commands/test_groups.cpp index 51bbf63228..f938de3467 100644 --- a/unittest/commands/test_groups.cpp +++ b/unittest/commands/test_groups.cpp @@ -245,7 +245,7 @@ TEST_F(GroupTest, Molecular) ASSERT_EQ(group->count(group->find("three")), 15); ASSERT_DOUBLE_EQ(group->mass(group->find("half")), 40); ASSERT_DOUBLE_EQ(group->mass(group->find("half"), domain->find_region("top")), 10); - ASSERT_DOUBLE_EQ(group->charge(group->find("top")), 0); + ASSERT_NEAR(group->charge(group->find("top")), 0,1.0e-14); ASSERT_DOUBLE_EQ(group->charge(group->find("right"), domain->find_region("top")), 0); TEST_FAILURE(".*ERROR: Illegal group command.*", command("group three include xxx");); diff --git a/unittest/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index 5288cfc2b6..d25b232fa7 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -133,21 +133,21 @@ TEST_F(LAMMPS_plain, TestStyles) found = lmp->match_style("atom", "spin"); EXPECT_STREQ(found, "SPIN"); found = lmp->match_style("atom", "wavepacket"); - EXPECT_STREQ(found, "USER-AWPMD"); + EXPECT_STREQ(found, "AWPMD"); found = lmp->match_style("atom", "dpd"); - EXPECT_STREQ(found, "USER-DPD"); + EXPECT_STREQ(found, "DPD-REACT"); found = lmp->match_style("atom", "edpd"); - EXPECT_STREQ(found, "USER-MESODPD"); + EXPECT_STREQ(found, "DPD-MESO"); found = lmp->match_style("atom", "mdpd"); - EXPECT_STREQ(found, "USER-MESODPD"); + EXPECT_STREQ(found, "DPD-MESO"); found = lmp->match_style("atom", "tdpd"); - EXPECT_STREQ(found, "USER-MESODPD"); + EXPECT_STREQ(found, "DPD-MESO"); found = lmp->match_style("atom", "spin"); EXPECT_STREQ(found, "SPIN"); found = lmp->match_style("atom", "smd"); - EXPECT_STREQ(found, "USER-SMD"); + EXPECT_STREQ(found, "MACHDYN"); found = lmp->match_style("atom", "sph"); - EXPECT_STREQ(found, "USER-SPH"); + EXPECT_STREQ(found, "SPH"); found = lmp->match_style("atom", "i_don't_exist"); EXPECT_STREQ(found, NULL); } @@ -176,9 +176,9 @@ protected: char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); - // only run this test fixture with omp suffix if USER-OMP package is installed + // only run this test fixture with omp suffix if OPENMP package is installed - if (LAMMPS::is_installed_pkg("USER-OMP")) + if (LAMMPS::is_installed_pkg("OPENMP")) lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); else GTEST_SKIP(); @@ -324,7 +324,7 @@ TEST_F(LAMMPS_kokkos, InitMembers) TEST(LAMMPS_init, OpenMP) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (Info::get_openmp_info() == "OpenMP not enabled") GTEST_SKIP(); FILE *fp = fopen("in.lammps_empty", "w"); @@ -340,7 +340,7 @@ TEST(LAMMPS_init, OpenMP) std::string output = ::testing::internal::GetCapturedStdout(); EXPECT_THAT(output, MatchesRegex(".*using 2 OpenMP thread.*per MPI task.*")); - if (LAMMPS_NS::Info::has_accelerator_feature("USER-OMP", "api", "openmp")) + if (LAMMPS_NS::Info::has_accelerator_feature("OPENMP", "api", "openmp")) EXPECT_EQ(lmp->comm->nthreads, 2); else EXPECT_EQ(lmp->comm->nthreads, 1); @@ -356,7 +356,7 @@ TEST(LAMMPS_init, OpenMP) TEST(LAMMPS_init, NoOpenMP) { - if (!LAMMPS_NS::Info::has_accelerator_feature("USER-OMP", "api", "openmp")) + if (!LAMMPS_NS::Info::has_accelerator_feature("OPENMP", "api", "openmp")) GTEST_SKIP() << "No threading enabled"; FILE *fp = fopen("in.lammps_class_noomp", "w"); diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index 8f858a3a04..b4300218b7 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -533,7 +533,7 @@ TEST(AngleStyle, plain) TEST(AngleStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -564,7 +564,7 @@ TEST(AngleStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -628,7 +628,7 @@ TEST(AngleStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with angle style hybrid + // TODO: this is currently broken for OPENMP with angle style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.angle_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon); @@ -695,7 +695,7 @@ TEST(AngleStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with angle style hybrid + // TODO: this is currently broken for OPENMP with angle style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.angle_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon); diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index 2b5e11de20..f4c151a394 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -533,7 +533,7 @@ TEST(BondStyle, plain) TEST(BondStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -564,7 +564,7 @@ TEST(BondStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -627,7 +627,7 @@ TEST(BondStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(bond->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with bond style hybrid + // TODO: this is currently broken for OPENMP with bond style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.bond_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(bond->energy, energy, epsilon); @@ -694,7 +694,7 @@ TEST(BondStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(bond->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with bond style hybrid + // TODO: this is currently broken for OPENMP with bond style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.bond_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(bond->energy, energy, epsilon); diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index 718bcb5332..8cae5d5f7c 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -536,7 +536,7 @@ TEST(DihedralStyle, plain) TEST(DihedralStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -567,7 +567,7 @@ TEST(DihedralStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -631,7 +631,7 @@ TEST(DihedralStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with dihedral style hybrid + // TODO: this is currently broken for OPENMP with dihedral style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.dihedral_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon); @@ -698,7 +698,7 @@ TEST(DihedralStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with dihedral style hybrid + // TODO: this is currently broken for OPENMP with dihedral style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.dihedral_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon); diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index 645c41b2ae..34c8ba65d9 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -696,7 +696,7 @@ TEST(FixTimestep, plain) TEST(FixTimestep, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 52fc0f0b92..b6d6b9a06b 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -527,7 +527,7 @@ TEST(ImproperStyle, plain) TEST(ImproperStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -558,7 +558,7 @@ TEST(ImproperStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -622,7 +622,7 @@ TEST(ImproperStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with improper style hybrid + // TODO: this is currently broken for OPENMP with improper style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.improper_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon); @@ -689,7 +689,7 @@ TEST(ImproperStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with improper style hybrid + // TODO: this is currently broken for OPENMP with improper style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.improper_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon); diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index b8513237c5..23858f93b9 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -158,7 +158,7 @@ void run_lammps(LAMMPS *lmp) command("run 4 post no"); } -void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) +void restart_lammps(LAMMPS *lmp, const TestConfig &cfg, bool nofdotr = false, bool newton = true) { // utility lambda to improve readability auto command = [&](const std::string &line) { @@ -166,6 +166,10 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) }; command("clear"); + if (newton) + command("newton on"); + else + command("newton off"); command("read_restart " + cfg.basename + ".restart"); if (!lmp->force->pair) { @@ -180,6 +184,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) for (auto &post_command : cfg.post_commands) { command(post_command); } + if (nofdotr) command("pair_modify nofdotr"); command("run 0 post no"); } @@ -518,6 +523,40 @@ TEST(PairStyle, plain) EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.init_coul, epsilon); if (print_stats) std::cerr << "restart_energy stats:" << stats << std::endl; + // pair style rann does not support pair_modify nofdotr + if (test_config.pair_style != "rann") { + if (!verbose) ::testing::internal::CaptureStdout(); + restart_lammps(lmp, test_config, true); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + f = lmp->atom->f; + tag = lmp->atom->tag; + stats.reset(); + ASSERT_EQ(nlocal + 1, f_ref.size()); + for (int i = 0; i < nlocal; ++i) { + EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon); + } + if (print_stats) std::cerr << "nofdotr_forces stats:" << stats << std::endl; + + pair = lmp->force->pair; + stress = pair->virial; + stats.reset(); + EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon); + EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon); + EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon); + EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon); + EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon); + EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon); + if (print_stats) std::cerr << "nofdotr_stress stats:" << stats << std::endl; + + stats.reset(); + EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.init_vdwl, epsilon); + EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.init_coul, epsilon); + if (print_stats) std::cerr << "nofdotr_energy stats:" << stats << std::endl; + } + if (!verbose) ::testing::internal::CaptureStdout(); data_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -598,7 +637,7 @@ TEST(PairStyle, plain) TEST(PairStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -632,7 +671,7 @@ TEST(PairStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; // relax test precision when using pppm and single precision FFTs #if defined(FFT_SINGLE) @@ -704,14 +743,14 @@ TEST(PairStyle, omp) EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl; - if (!verbose) ::testing::internal::CaptureStdout(); - cleanup_lammps(lmp, test_config); - lmp = init_lammps(argc, argv, test_config, false); - if (!verbose) ::testing::internal::GetCapturedStdout(); - // skip over these tests if newton pair is forced to be on if (lmp->force->newton_pair == 0) { + if (!verbose) ::testing::internal::CaptureStdout(); + cleanup_lammps(lmp, test_config); + lmp = init_lammps(argc, argv, test_config, false); + if (!verbose) ::testing::internal::GetCapturedStdout(); + f = lmp->atom->f; tag = lmp->atom->tag; stats.reset(); @@ -770,6 +809,38 @@ TEST(PairStyle, omp) EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl; } + + if (!verbose) ::testing::internal::CaptureStdout(); + restart_lammps(lmp, test_config, true); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + f = lmp->atom->f; + tag = lmp->atom->tag; + stats.reset(); + ASSERT_EQ(nlocal + 1, f_ref.size()); + for (int i = 0; i < nlocal; ++i) { + EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, 5 * epsilon); + } + if (print_stats) std::cerr << "nofdotr_forces stats:" << stats << std::endl; + + pair = lmp->force->pair; + stress = pair->virial; + stats.reset(); + EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10 * epsilon); + if (print_stats) std::cerr << "nofdotr_stress stats:" << stats << std::endl; + + stats.reset(); + EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.init_vdwl, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.init_coul, 5 * epsilon); + if (print_stats) std::cerr << "nofdotr_energy stats:" << stats << std::endl; + if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -781,8 +852,10 @@ TEST(PairStyle, gpu) if (!Info::has_gpu_device()) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); - const char *args_neigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu"}; - const char *args_noneigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu", "-pk", "gpu", "0", "neigh", "no"}; + const char *args_neigh[] = {"PairStyle", "-log", "none", "-echo", + "screen", "-nocite", "-sf", "gpu"}; + const char *args_noneigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", + "gpu", "-pk", "gpu", "0", "neigh", "no"}; char **argv = (char **)args_neigh; int argc = sizeof(args_neigh) / sizeof(char *); @@ -790,7 +863,7 @@ TEST(PairStyle, gpu) // cannot use GPU neighbor list with hybrid pair style (yet) if (test_config.pair_style.substr(0, 6) == "hybrid") { argv = (char **)args_noneigh; - argc = sizeof(args_noneigh) / sizeof(char *); + argc = sizeof(args_noneigh) / sizeof(char *); } ::testing::internal::CaptureStdout(); @@ -817,14 +890,17 @@ TEST(PairStyle, gpu) // relax error for GPU package depending on precision setting double epsilon = test_config.epsilon; - if (Info::has_accelerator_feature("GPU","precision","double")) + if (Info::has_accelerator_feature("GPU", "precision", "double")) epsilon *= 7.5; - else if (Info::has_accelerator_feature("GPU","precision","mixed")) + else if (Info::has_accelerator_feature("GPU", "precision", "mixed")) epsilon *= 5.0e8; - else epsilon *= 1.0e10; - // relax test precision when using pppm and single precision FFTs, but only when also running with double precision + else + epsilon *= 1.0e10; + // relax test precision when using pppm and single precision FFTs, but only when also + // running with double precision #if defined(FFT_SINGLE) - if (lmp->force->kspace && lmp->force->kspace->compute_flag && Info::has_accelerator_feature("GPU","precision","double")) + if (lmp->force->kspace && lmp->force->kspace->compute_flag && + Info::has_accelerator_feature("GPU", "precision", "double")) if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8; #endif const std::vector &f_ref = test_config.init_forces; @@ -896,7 +972,7 @@ TEST(PairStyle, gpu) TEST(PairStyle, intel) { - if (!LAMMPS::is_installed_pkg("USER-INTEL")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("INTEL")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -910,7 +986,7 @@ TEST(PairStyle, intel) int argc = sizeof(args) / sizeof(char *); ::testing::internal::CaptureStdout(); - LAMMPS *lmp = init_lammps(argc, argv, test_config); + LAMMPS *lmp = init_lammps(argc, argv, test_config, true); std::string output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; @@ -924,7 +1000,7 @@ TEST(PairStyle, intel) GTEST_SKIP(); } - // relax error a bit for USER-INTEL package + // relax error a bit for INTEL package double epsilon = 7.5 * test_config.epsilon; // relax test precision when using pppm and single precision FFTs #if defined(FFT_SINGLE) @@ -1010,7 +1086,7 @@ TEST(PairStyle, intel) EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon); EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon); - // rebo family of pair styles will have a large error in per-atom energy for USER-INTEL + // rebo family of pair styles will have a large error in per-atom energy for INTEL if (test_config.pair_style.find("rebo") != std::string::npos) epsilon *= 100000.0; EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); @@ -1124,6 +1200,37 @@ TEST(PairStyle, opt) EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); if (print_stats) std::cerr << "run_energy stats:" << stats << std::endl; + if (!verbose) ::testing::internal::CaptureStdout(); + restart_lammps(lmp, test_config, true); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + f = lmp->atom->f; + tag = lmp->atom->tag; + stats.reset(); + ASSERT_EQ(nlocal + 1, f_ref.size()); + for (int i = 0; i < nlocal; ++i) { + EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, 5 * epsilon); + } + if (print_stats) std::cerr << "nofdotr_forces stats:" << stats << std::endl; + + pair = lmp->force->pair; + stress = pair->virial; + stats.reset(); + EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10 * epsilon); + if (print_stats) std::cerr << "nofdotr_stress stats:" << stats << std::endl; + + stats.reset(); + EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.init_vdwl, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.init_coul, 5 * epsilon); + if (print_stats) std::cerr << "nofdotr_energy stats:" << stats << std::endl; + if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -1189,21 +1296,6 @@ TEST(PairStyle, single) GTEST_SKIP(); } - // The single function in EAM is different from what we assume - // here, therefore we have to skip testing those pair styles. - // Pair styles colloid and yukawa/colloid are also not compatible with this single tester - if ((test_config.pair_style.substr(0, 7) == "colloid") || - (test_config.pair_style.substr(0, 14) == "yukawa/colloid") || - (test_config.pair_style.substr(0, 3) == "dpd") || - (test_config.pair_style.substr(0, 3) == "eam") || - ((test_config.pair_style.substr(0, 6) == "hybrid") && - (test_config.pair_style.find("eam") != std::string::npos))) { - if (!verbose) ::testing::internal::CaptureStdout(); - cleanup_lammps(lmp, test_config); - if (!verbose) ::testing::internal::GetCapturedStdout(); - GTEST_SKIP(); - } - // now start over if (!verbose) ::testing::internal::CaptureStdout(); diff --git a/unittest/force-styles/tests/angle-fourier_simple.yaml b/unittest/force-styles/tests/angle-fourier_simple.yaml index ee318b013f..8fcecf85ad 100644 --- a/unittest/force-styles/tests/angle-fourier_simple.yaml +++ b/unittest/force-styles/tests/angle-fourier_simple.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:09:24 2021 +lammps_version: 2 Jul 2021 +date_generated: Sun Jul 4 18:23:42 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -17,7 +17,7 @@ angle_coeff: ! | equilibrium: 4 3.141592653589793 1.5707963267948966 1.0471975511965976 2.0943951023931953 extract: ! "" natoms: 29 -init_energy: 2474.07480135906 +init_energy: 2474.0748013590646 init_stress: ! |- -7.0442354264952769e+00 2.2461003781604686e+02 -2.1756580238955158e+02 -3.3320762800031582e+02 -2.8001007053395438e+02 3.7586975072452852e+01 init_forces: ! |2 @@ -50,7 +50,7 @@ init_forces: ! |2 27 1.3169752428031160e+01 -1.0811335053602835e+02 3.6826995619636030e+01 28 2.8796447607995553e+01 6.4642561032416026e+01 -1.5016412228095177e+00 29 -4.1966200036026713e+01 4.3470789503612323e+01 -3.5325354396826512e+01 -run_energy: 2473.12574569709 +run_energy: 2473.1257456970907 run_stress: ! |- -4.9754396810415287e+00 2.2858091244313221e+02 -2.2360547276209070e+02 -3.3609442061303969e+02 -2.8303432598637687e+02 3.9880332185018744e+01 run_forces: ! |2 diff --git a/unittest/force-styles/tests/atomic-pair-buck_coul_cut_qeq_point.yaml b/unittest/force-styles/tests/atomic-pair-buck_coul_cut_qeq_point.yaml new file mode 100644 index 0000000000..31a44ce897 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-buck_coul_cut_qeq_point.yaml @@ -0,0 +1,175 @@ +--- +lammps_version: 8 Apr 2021 +date_generated: Tue Apr 20 14:47:51 2021 +epsilon: 7.5e-13 +skip_tests: intel single gpu +prerequisites: ! | + pair buck/coul/cut + fix qeq/point +pre_commands: ! | + echo screen + variable newton_pair delete + variable newton_pair index on + atom_modify map array + units metal + atom_style charge + lattice diamond 3.77 + region box block 0 2 0 2 0 2 + create_box 2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 28.0 + mass 2 16.0 + set type 1 type/fraction 2 0.666667 998877 + set type 1 charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + fix qeq all qeq/point 1 6.0 1.0e-20 20 ${input_dir}/param.qeq2 warn no +input_file: in.empty +pair_style: buck/coul/cut 6.0 +pair_coeff: ! | + 1 1 0.0 0.1 00 + 1 2 18003.0 0.2052124 133.5381 + 2 2 1388.77 0.3623188 175.0 +extract: ! "" +natoms: 64 +init_vdwl: 106.41860675757 +init_coul: -129.9140700924124 +init_stress: ! |- + -2.8069812877025680e+02 -4.4806768911794171e+02 -5.0378472147221044e+02 3.9357896002405380e+02 -4.6782123097483543e+02 1.9690042286173212e+02 +init_forces: ! |2 + 1 7.9125122896296922e+00 -2.1014839690852849e+00 1.0994080971957654e+01 + 2 -8.6188789139298905e+00 -1.8333074427098923e+00 6.9043233196778493e+00 + 3 7.8498612200411868e+00 -2.1754399089581845e+01 -2.8862198492435933e+00 + 4 6.0059474900265855e+00 2.0200604615492711e+01 -3.6502720655785064e+00 + 5 -1.0414088486908696e+01 -1.2032673161543727e+01 -8.1683250459138641e+00 + 6 2.4526971509997360e+00 1.6151940503875748e+00 3.9699353225387135e+00 + 7 1.1484521325651471e+01 2.6251346011917382e+00 -5.0509149729671243e-01 + 8 -8.6634039445313658e+00 -8.3084485039834881e+00 3.9070922142448175e+00 + 9 7.9495750681929742e+00 -9.0507972374486361e+00 -4.4437699190231843e+00 + 10 -1.1184211738488107e+01 -2.0985043628368132e+00 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2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 28.0 + mass 2 16.0 + set type 1 type/fraction 2 0.666667 998877 + set type 1 charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + fix qeq all qeq/shielded 1 6.0 1.0e-20 20 ${input_dir}/param.qeq2 warn no +input_file: in.empty +pair_style: buck/coul/cut 6.0 +pair_coeff: ! | + 1 1 0.0 0.1 00 + 1 2 18003.0 0.2052124 133.5381 + 2 2 1388.77 0.3623188 175.0 +extract: ! 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1.0957659916624621e+02 1.0267576521252535e+02 + 49 1.3502214899750406e+01 1.0917576182238818e+01 -1.6482937758762418e+01 + 50 1.4379813283875713e+01 5.0553400873044820e+00 1.0683342950103625e-01 + 51 -1.3957521762635950e+04 1.2452654544174226e+04 -1.5900991752693422e+04 + 52 1.5633296407076536e+01 -1.5168118286747163e+01 1.1375722352219624e+01 + 53 1.3966019441343162e+04 -1.2452432702569762e+04 1.5901485612155189e+04 + 54 -1.0302010742237790e+00 8.0882593586606122e-01 -4.8342043026033270e+00 + 55 -1.4050317568063919e+01 2.4571746720771483e+01 -1.1619744995231775e+01 + 56 -8.3051825195541284e+01 2.6893430568070734e+01 5.1720488371951646e+01 + 57 1.5167680987925942e+02 5.1771459761745700e+02 3.0876046319206444e+02 + 58 -9.0684224428918387e+00 -1.1737173531443593e+01 -4.2815053798067343e-01 + 59 1.5222786378196815e+02 -1.2370024170265403e+02 -8.0875432712487481e+01 + 60 -2.1233147761897007e+00 -7.9017832727701498e-01 -7.6738212145982452e+00 + 61 -1.6808948242299991e+02 -5.1546658556632860e+02 -2.9975983407554941e+02 + 62 -3.2501332686207283e+00 1.1879860248088384e+01 6.2378391727747093e+00 + 63 -7.6393918044176985e+00 -2.9843682141469259e+00 1.0819122718511684e+01 + 64 2.5665406780155877e+01 3.2294883947912929e+01 -1.6760878883557520e+01 +... diff --git a/unittest/force-styles/tests/atomic-pair-colloid.yaml b/unittest/force-styles/tests/atomic-pair-colloid.yaml index 537ac447b5..b666021c91 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-14 +skip_tests: single prerequisites: ! | pair colloid pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml b/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml index 025a7faa05..d224977a3e 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-14 +skip_tests: single prerequisites: ! | pair colloid pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml b/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml index 9ead662a06..fa52a37ce7 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-13 +skip_tests: single prerequisites: ! | pair colloid pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml b/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml index be3ba744d0..62e85584e7 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-14 +skip_tests: single prerequisites: ! | pair colloid pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml b/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml index cd6c7595e8..b3f0b7a06d 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-13 +skip_tests: single prerequisites: ! | pair colloid pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-eam.yaml b/unittest/force-styles/tests/atomic-pair-eam.yaml index c606813d56..9c8c3ba8cd 100644 --- a/unittest/force-styles/tests/atomic-pair-eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:00 2021 epsilon: 6e-12 +skip_tests: single prerequisites: ! | pair eam pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml b/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml index 072a0a97c0..5ec5bef372 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/alloy pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml index 033c341f08..bff08e048b 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:00 2021 epsilon: 7.5e-12 +skip_tests: single prerequisites: ! | pair eam/alloy pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-eam_cd.yaml b/unittest/force-styles/tests/atomic-pair-eam_cd.yaml index bda14a9e5a..915253dce7 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_cd.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_cd.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/cd pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml b/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml index 4f6891bae6..a7fa727b7f 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/cd/old pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml index e2ac5f0cae..abe25cff95 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/cd pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-eam_fs.yaml b/unittest/force-styles/tests/atomic-pair-eam_fs.yaml index 89ad740424..58c533d7ec 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_fs.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_fs.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:01 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/fs pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml index bf7f4f338b..f7739ee824 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:01 2021 epsilon: 7.5e-12 +skip_tests: single prerequisites: ! | pair eam/fs pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-eam_he.yaml b/unittest/force-styles/tests/atomic-pair-eam_he.yaml index 001301fe1a..f2bf098b2f 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_he.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_he.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:01 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/he pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml index 236b9538a7..b2b198486e 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:02 2021 epsilon: 7.5e-12 +skip_tests: single prerequisites: ! | pair eam/he pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-eam_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_real.yaml index 89e7c1ce0b..4d95f04edc 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_real.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:02 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml b/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml index 4c8e040200..737b054dd0 100644 --- a/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml @@ -2,6 +2,7 @@ lammps_version: 8 Apr 2021 date_generated: Mon Apr 19 08:49:08 2021 epsilon: 1e-11 +skip_tests: single prerequisites: ! | pair eam/fs pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml b/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml index be3889de90..d45dc9190e 100644 --- a/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml +++ b/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml @@ -2,6 +2,7 @@ lammps_version: 8 Apr 2021 date_generated: Mon Apr 19 08:49:08 2021 epsilon: 5e-12 +skip_tests: single prerequisites: ! | pair eam/fs pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-lj_relres.yaml b/unittest/force-styles/tests/atomic-pair-lj_relres.yaml index 99a83e0c8d..704bb46785 100644 --- a/unittest/force-styles/tests/atomic-pair-lj_relres.yaml +++ b/unittest/force-styles/tests/atomic-pair-lj_relres.yaml @@ -3,7 +3,7 @@ lammps_version: 10 Feb 2021 date_generated: Sun Feb 28 23:32:03 2021 epsilon: 5e-13 prerequisites: ! | - pair born + pair lj/relres pre_commands: ! "" post_commands: ! "" input_file: in.metal diff --git a/unittest/force-styles/tests/atomic-pair-meam_c.yaml b/unittest/force-styles/tests/atomic-pair-meam.yaml similarity index 99% rename from unittest/force-styles/tests/atomic-pair-meam_c.yaml rename to unittest/force-styles/tests/atomic-pair-meam.yaml index 7d93a698e0..6f262c032a 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_c.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam.yaml @@ -3,13 +3,13 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:03 2021 epsilon: 5e-13 prerequisites: ! | - pair meam/c + pair meam pre_commands: ! | variable newton_pair delete if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.metal -pair_style: meam/c +pair_style: meam pair_coeff: ! | * * library.meam Al Si Mg Cu Fe AlSiMgCuFe.meam Mg Fe extract: ! | diff --git a/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml b/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml index f3ad72b9cd..6a2c16a80d 100644 --- a/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:04 2021 -epsilon: 1e-14 +epsilon: 5e-14 prerequisites: ! | pair polymorphic pre_commands: ! | diff --git a/unittest/force-styles/tests/atomic-pair-reax_c.yaml b/unittest/force-styles/tests/atomic-pair-reax_c.yaml deleted file mode 100644 index a0dabff323..0000000000 --- a/unittest/force-styles/tests/atomic-pair-reax_c.yaml +++ /dev/null @@ -1,172 +0,0 @@ ---- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:24 202 -epsilon: 5e-11 -prerequisites: ! | - pair reax/c - fix qeq/reax -pre_commands: ! | - echo screen - variable newton_pair delete - variable newton_pair index on - atom_modify map array - units real - atom_style charge - lattice diamond 3.77 - region box block 0 2 0 2 0 2 - create_box 2 box - create_atoms 1 box - displace_atoms all random 0.1 0.1 0.1 623426 - mass 1 12.0 - mass 2 13.0 - set type 1 type/fraction 2 0.5 998877 - set type 1 charge 0.01 - set type 2 charge -0.01 - velocity all create 100 4534624 loop geom -post_commands: ! | - fix qeq all qeq/reax 1 0.0 8.0 1.0e-12 reax/c -input_file: in.empty -pair_style: reax/c NULL checkqeq yes -pair_coeff: ! | - * * ffield.reax.mattsson C O -extract: ! "" -natoms: 64 -init_vdwl: -4208.20379453327 -init_coul: -268.025868109969 -init_stress: ! |2- - 2.3677048490920824e+03 3.0802122558803894e+03 1.2727815110256352e+03 -1.5387991688244833e+03 -1.0906364142624241e+03 1.1229877249520346e+03 -init_forces: ! |2 - 1 2.9634051452159092e+01 -5.6267761875030658e+02 -1.6668253255975264e+02 - 2 -1.5938437728854763e+02 -2.2076601831952277e+02 -1.7161994484506349e+02 - 3 -3.1194106231120934e+01 -3.0591930644164984e+02 4.4652570958886855e+01 - 4 4.4646653320086006e+02 1.7080811286682768e+02 1.7439026170464757e+02 - 5 -1.1512606621586120e+02 7.9716954463543715e+01 1.7959700550169842e+01 - 6 -7.1695199301551634e+02 4.0749156821010061e+01 2.1512037025864390e+02 - 7 2.3022543693157868e+02 -9.0170756873660693e+01 8.2190170006827103e+01 - 8 -2.1141251466323027e+01 -1.5635879347049067e+02 1.6101907187949953e+02 - 9 -1.2130842270575529e+02 -2.7960689135673749e+02 -1.9629114850260629e+02 - 10 -3.7631710890081683e+02 3.4103240548842098e+02 -1.8166279141141010e+02 - 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pair reax/c - fix qeq/reax -pre_commands: ! | - echo screen - variable newton_pair delete - variable newton_pair index on - atom_modify map array - units real - atom_style charge - lattice diamond 3.77 - region box block 0 2 0 2 0 2 - create_box 2 box - create_atoms 1 box - displace_atoms all random 0.1 0.1 0.1 623426 - mass 1 12.0 - mass 2 13.0 - set type 1 type/fraction 2 0.5 998877 - set type 1 charge 0.01 - set type 2 charge -0.01 - velocity all create 100 4534624 loop geom -post_commands: ! | - fix qeq all qeq/reax 1 0.0 8.0 1.0e-12 reax/c -input_file: in.empty -pair_style: reax/c NULL checkqeq yes lgvdw yes safezone 1.6 -pair_coeff: ! | - * * ffield.reax.lg C O -extract: ! 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pair reax/c -pre_commands: ! | - echo screen - variable newton_pair delete - variable newton_pair index on - atom_modify map array - units real - atom_style charge - lattice diamond 3.77 - region box block 0 2 0 2 0 2 - create_box 2 box - create_atoms 1 box - displace_atoms all random 0.1 0.1 0.1 623426 - mass 1 12.0 - mass 2 13.0 - set type 1 type/fraction 2 0.5 998877 - set type 1 charge 0.01 - set type 2 charge -0.01 - velocity all create 100 4534624 loop geom -post_commands: ! "" -input_file: in.empty -pair_style: reax/c NULL checkqeq no -pair_coeff: ! | - * * ffield.reax.mattsson C C -extract: ! 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-1.5086911682892702e+02 + 61 -3.3559889608749927e+01 -1.0076809277084796e+02 -7.4536003122046253e+01 + 62 1.5883833834736409e+01 -5.8439916924703361e+00 2.8393403991146915e+01 + 63 1.3294237052896716e+02 -1.2724619636183061e+02 -6.4882384014219113e+01 + 64 1.0738250214938944e+02 1.2062290362868877e+02 7.4541927445529197e+01 +... diff --git a/unittest/force-styles/tests/atomic-pair-reaxff_lgvdw.yaml b/unittest/force-styles/tests/atomic-pair-reaxff_lgvdw.yaml new file mode 100644 index 0000000000..b124a6b00b --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-reaxff_lgvdw.yaml @@ -0,0 +1,175 @@ +--- +lammps_version: 2 Jul 2021 +date_generated: Wed Jul 21 15:49:47 2021 +epsilon: 3e-12 +prerequisites: ! | + pair reaxff + fix qeq/reaxff +pre_commands: ! | + echo screen + variable newton_pair delete + variable newton_pair index on + atom_modify map array + units real + atom_style charge + lattice diamond 3.77 + region box block 0 2 0 2 0 2 + create_box 3 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 1.0 + mass 2 12.0 + mass 3 16.0 + set type 1 type/fraction 2 0.5 998877 + set type 2 type/fraction 3 0.5 887766 + set type 1 charge 0.00 + set type 2 charge 0.01 + set type 3 charge -0.01 + velocity all create 100 4534624 loop geom +post_commands: ! | + fix qeq all qeq/reaxff 1 0.0 8.0 1.0e-20 reaxff +input_file: in.empty +pair_style: reaxff NULL checkqeq yes lgvdw yes safezone 1.6 +pair_coeff: ! | + * * ffield.reax.lg H C O +extract: ! 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mass 1 12.0 + mass 2 13.0 + set type 1 type/fraction 2 0.5 998877 + set type 1 charge 0.01 + set type 2 charge -0.01 + velocity all create 100 4534624 loop geom +post_commands: ! "" +input_file: in.empty +pair_style: reaxff NULL checkqeq no +pair_coeff: ! | + * * ffield.reax.mattsson C C +extract: ! 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create_box 3 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 1.0 + mass 2 12.0 + mass 3 16.0 + set type 1 type/fraction 2 0.5 998877 + set type 2 type/fraction 3 0.5 887766 + set type 1 charge 0.00 + set type 2 charge 0.01 + set type 3 charge -0.01 + velocity all create 100 4534624 loop geom +post_commands: ! | + fix qeq all qeq/reaxff 1 0.0 8.0 1.0e-20 reaxff +input_file: in.empty +pair_style: reaxff reaxff-1.control checkqeq yes +pair_coeff: ! | + * * ffield.reax.mattsson H C O +extract: ! 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-1.5162714312949211e+02 + 61 -3.5220536021452787e+01 -1.0209241739133054e+02 -7.4154706185261915e+01 + 62 1.5375483178245885e+01 -6.3263099051314251e+00 2.7512110875657893e+01 + 63 1.3464595988109866e+02 -1.2416936634154256e+02 -5.8957063242418101e+01 + 64 1.0701154605982798e+02 1.1895382951205715e+02 7.4449321163285845e+01 +... diff --git a/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml b/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml index 1c5c24832d..d807696e63 100644 --- a/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml +++ b/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:10 2021 epsilon: 2e-13 +skip_tests: single prerequisites: ! | atom sphere pair yukawa/colloid diff --git a/unittest/force-styles/tests/fix-timestep-adapt_pair.yaml b/unittest/force-styles/tests/fix-timestep-adapt_pair.yaml index 167f531b8e..58b25f6012 100644 --- a/unittest/force-styles/tests/fix-timestep-adapt_pair.yaml +++ b/unittest/force-styles/tests/fix-timestep-adapt_pair.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Mar 2021 date_generated: Thu Mar 25 14:01:17 202 -epsilon: 1e-14 +epsilon: 2e-14 prerequisites: ! | atom full fix adapt diff --git a/unittest/force-styles/tests/kspace-msm.yaml b/unittest/force-styles/tests/kspace-msm.yaml index f3cbb4604d..13e2e0a2c2 100644 --- a/unittest/force-styles/tests/kspace-msm.yaml +++ b/unittest/force-styles/tests/kspace-msm.yaml @@ -11,7 +11,7 @@ post_commands: ! | pair_modify compute no kspace_style msm 1.0e-4 kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/kspace-msm_cg.yaml b/unittest/force-styles/tests/kspace-msm_cg.yaml index 25892a4528..90b5999796 100644 --- a/unittest/force-styles/tests/kspace-msm_cg.yaml +++ b/unittest/force-styles/tests/kspace-msm_cg.yaml @@ -15,7 +15,7 @@ post_commands: ! | pair_modify compute no kspace_style msm/cg 1.0e-4 kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/kspace-msm_nopbc.yaml b/unittest/force-styles/tests/kspace-msm_nopbc.yaml index ce5e3cd0e3..9c071e90eb 100644 --- a/unittest/force-styles/tests/kspace-msm_nopbc.yaml +++ b/unittest/force-styles/tests/kspace-msm_nopbc.yaml @@ -12,7 +12,7 @@ post_commands: ! | pair_modify compute no kspace_style msm 1.0e-4 kspace_modify cutoff/adjust yes - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 10.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/kspace-scafacos_direct.yaml b/unittest/force-styles/tests/kspace-scafacos_direct.yaml new file mode 100644 index 0000000000..5c7570f15a --- /dev/null +++ b/unittest/force-styles/tests/kspace-scafacos_direct.yaml @@ -0,0 +1,175 @@ +--- +lammps_version: 28 Jul 2021 +date_generated: Thu Jul 29 13:45:54 2021 +epsilon: 7.5e-14 +skip_tests: extract gpu intel omp opt single +prerequisites: ! | + atom full + pair zero + kspace scafacos +pre_commands: ! | + echo screen + variable newton_pair delete + variable newton_pair index on + atom_modify map array + units metal + atom_style charge + lattice diamond 3.77 + region box block 0 2 0 2 0 2 + create_box 2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 28.0 + mass 2 16.0 + set type 1 type/fraction 2 0.666667 998877 + set type 1 charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + pair_modify compute no + kspace_style scafacos direct 1.0e-6 +input_file: in.empty +pair_style: zero 2.0 +pair_coeff: ! | + * * +extract: ! 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8.7023314905664169e+00 +... diff --git a/unittest/force-styles/tests/kspace-scafacos_ewald.yaml b/unittest/force-styles/tests/kspace-scafacos_ewald.yaml new file mode 100644 index 0000000000..ecd6ffc221 --- /dev/null +++ b/unittest/force-styles/tests/kspace-scafacos_ewald.yaml @@ -0,0 +1,175 @@ +--- +lammps_version: 28 Jul 2021 +date_generated: Thu Jul 29 13:45:55 2021 +epsilon: 7.5e-14 +skip_tests: extract gpu intel omp opt single +prerequisites: ! | + atom full + pair zero + kspace scafacos +pre_commands: ! | + echo screen + variable newton_pair delete + variable newton_pair index on + atom_modify map array + units metal + atom_style charge + lattice diamond 3.77 + region box block 0 2 0 2 0 2 + create_box 2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 28.0 + mass 2 16.0 + set type 1 type/fraction 2 0.666667 998877 + set type 1 charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + pair_modify compute no + kspace_style scafacos ewald 1.0e-6 +input_file: in.empty +pair_style: zero 2.0 +pair_coeff: ! | + * * +extract: ! 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charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + pair_modify compute no + kspace_style scafacos fmm 1.0e-6 + kspace_modify scafacos tolerance energy +input_file: in.empty +pair_style: zero 2.0 +pair_coeff: ! | + * * +extract: ! 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8.7354287381704836e+00 +... diff --git a/unittest/force-styles/tests/kspace-scafacos_fmm_tuned.yaml b/unittest/force-styles/tests/kspace-scafacos_fmm_tuned.yaml new file mode 100644 index 0000000000..26eed51ded --- /dev/null +++ b/unittest/force-styles/tests/kspace-scafacos_fmm_tuned.yaml @@ -0,0 +1,177 @@ +--- +lammps_version: 28 Jul 2021 +date_generated: Thu Jul 29 13:50:59 2021 +epsilon: 7.5e-14 +skip_tests: extract gpu intel omp opt single +prerequisites: ! | + atom full + pair zero + kspace scafacos +pre_commands: ! | + echo screen + variable newton_pair delete + variable newton_pair index on + atom_modify map array + units metal + atom_style charge + lattice diamond 3.77 + region box block 0 2 0 2 0 2 + create_box 2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 28.0 + mass 2 16.0 + set type 1 type/fraction 2 0.666667 998877 + set type 1 charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + pair_modify compute no + kspace_style scafacos fmm 1.0e-6 + kspace_modify scafacos tolerance energy_rel + kspace_modify scafacos fmm_tuning 1 +input_file: in.empty +pair_style: zero 2.0 +pair_coeff: ! | + * * +extract: ! "" +natoms: 64 +init_vdwl: 0 +init_coul: 0 +init_stress: ! |2- + 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +init_forces: ! |2 + 1 2.7348813331578381e-01 1.0398337508932620e+00 1.3876159757936122e+01 + 2 1.5449500445625777e+01 3.9807925711395882e+00 3.8451554469155158e+00 + 3 3.7922392638729674e+00 8.3276903399611857e-01 3.4558923758723239e+00 + 4 2.9438818801998288e+00 2.9425326004887702e+00 1.4537787108189372e+01 + 5 1.5917206214898922e+00 1.9466982917982683e+00 2.4919869295950248e+00 + 6 2.6259075371703107e+00 5.3690587559849874e+00 4.7280760809090063e+00 + 7 4.4364253542789553e+00 1.8829999380617202e+00 4.3927130682638200e+00 + 8 8.9995014275062033e+00 1.0319344496761227e+01 3.1326023537694150e+00 + 9 6.2638175569366439e+00 3.5476316668194763e-01 4.4166040431977632e-01 + 10 1.3728953726809353e+01 5.9021860546627147e+00 8.3457830077413675e+00 + 11 2.1935169943515557e+01 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8.7354457321354815e+00 +... diff --git a/unittest/force-styles/tests/kspace-scafacos_p2nfft.yaml b/unittest/force-styles/tests/kspace-scafacos_p2nfft.yaml new file mode 100644 index 0000000000..4d942c0684 --- /dev/null +++ b/unittest/force-styles/tests/kspace-scafacos_p2nfft.yaml @@ -0,0 +1,175 @@ +--- +lammps_version: 28 Jul 2021 +date_generated: Thu Jul 29 13:45:55 2021 +epsilon: 7.5e-14 +skip_tests: extract gpu intel omp opt single +prerequisites: ! | + atom full + pair zero + kspace scafacos +pre_commands: ! | + echo screen + variable newton_pair delete + variable newton_pair index on + atom_modify map array + units metal + atom_style charge + lattice diamond 3.77 + region box block 0 2 0 2 0 2 + create_box 2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 28.0 + mass 2 16.0 + set type 1 type/fraction 2 0.666667 998877 + set type 1 charge 0.8 + set type 2 charge 0.4 + velocity all create 100 4534624 loop geom +post_commands: ! | + pair_modify compute no + kspace_style scafacos p2nfft 1.0e-6 +input_file: in.empty +pair_style: zero 2.0 +pair_coeff: ! | + * * +extract: ! 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-9.1860291220907786e-01 3.7207635298197222e-01 1.3717887100670061e+00 + 64 -2.0777660840087850e-01 -1.6781857712494050e-01 2.9221204134120399e-01 +... diff --git a/unittest/force-styles/tests/manybody-pair-bop.yaml b/unittest/force-styles/tests/manybody-pair-bop.yaml index 3855d2d263..bc5d198aaf 100644 --- a/unittest/force-styles/tests/manybody-pair-bop.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop.yaml @@ -1,7 +1,7 @@ --- lammps_version: 8 Apr 2021 date_generated: Wed May 5 11:50:15 2021 -epsilon: 1e-14 +epsilon: 2e-13 prerequisites: ! | pair bop pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-bop_save.yaml b/unittest/force-styles/tests/manybody-pair-bop_save.yaml index 5f13b370a4..9c8ca13067 100644 --- a/unittest/force-styles/tests/manybody-pair-bop_save.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop_save.yaml @@ -1,7 +1,7 @@ --- lammps_version: 8 Apr 2021 date_generated: Wed May 5 11:50:24 2021 -epsilon: 1e-14 +epsilon: 2e-14 prerequisites: ! | pair bop pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-edip_multi.yaml b/unittest/force-styles/tests/manybody-pair-edip_multi.yaml index ad2dc9018e..d86aa02b3f 100644 --- a/unittest/force-styles/tests/manybody-pair-edip_multi.yaml +++ b/unittest/force-styles/tests/manybody-pair-edip_multi.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:15 2021 -epsilon: 5e-14 +epsilon: 7.5e-14 prerequisites: ! | pair edip/multi pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-meam_c.yaml b/unittest/force-styles/tests/manybody-pair-meam.yaml similarity index 99% rename from unittest/force-styles/tests/manybody-pair-meam_c.yaml rename to unittest/force-styles/tests/manybody-pair-meam.yaml index e2867c4dd6..4237f5ffc2 100644 --- a/unittest/force-styles/tests/manybody-pair-meam_c.yaml +++ b/unittest/force-styles/tests/manybody-pair-meam.yaml @@ -3,13 +3,13 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:15 2021 epsilon: 7.5e-12 prerequisites: ! | - pair meam/c + pair meam pre_commands: ! | variable newton_pair delete if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody -pair_style: meam/c +pair_style: meam pair_coeff: ! | * * library.meam Si C SiC.meam C C C C Si Si Si Si extract: ! | diff --git a/unittest/force-styles/tests/manybody-pair-quip-sw.yaml b/unittest/force-styles/tests/manybody-pair-quip-sw.yaml new file mode 100644 index 0000000000..6e7b830f32 --- /dev/null +++ b/unittest/force-styles/tests/manybody-pair-quip-sw.yaml @@ -0,0 +1,156 @@ +--- +lammps_version: 2 Jul 2021 +date_generated: Tue Jul 20 18:41:14 2021 +epsilon: 1e-14 +skip_tests: +prerequisites: ! | + pair quip +pre_commands: ! | + variable newton_pair delete + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" +post_commands: ! "" +input_file: in.manybody +pair_style: quip +pair_coeff: ! | + * * SiGeH.sw.quip "IP SW" 14 14 14 14 32 32 32 1 +extract: ! 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-2.3404725995321409e+00 4.2693784569161486e-01 + 36 2.1987961836404866e+00 -2.8457247851677830e-01 2.6274041595779325e+00 + 37 -2.1840981390371637e+00 1.6573229374531970e+00 -2.4637936516409766e+00 + 38 -7.9460241106813601e-01 -5.9896804046581120e-01 7.2826201432311444e-01 + 39 3.1272276827526766e+00 -8.6209854698494903e-01 -4.4468641212239932e+00 + 40 -2.4308533039834002e-01 2.7230151595767899e-01 -6.2872446838689611e-01 + 41 -1.3260627462954369e+00 -2.5607568836802601e+00 4.2323765225196180e-01 + 42 -5.3874314749052319e+00 -8.0859075714928541e-01 -1.2494087576323458e+00 + 43 1.3655794813450579e+00 -5.1777328130840043e+00 1.6024718167052715e-01 + 44 6.1196191931229516e+00 -2.0626392298162695e+00 3.3603039423879615e+00 + 45 -2.3599359370520898e+00 1.9365012887585085e+00 -2.9332624991840994e+00 + 46 8.2568019386201230e-02 -1.4952850716420065e+00 5.4167513039879553e+00 + 47 3.0124513545044396e+00 1.9934496368340704e+00 6.2390081079733339e-01 + 48 -4.8051407320220796e-01 -8.0007378383594607e-01 4.8091361558181389e-01 + 49 -3.2431986657434648e+00 -5.9449535243382892e+00 -1.9314365097638013e+00 + 50 -6.6914257074160288e-01 3.2398461351636660e+00 -1.2427819490348404e+00 + 51 2.6369041374313187e+00 -2.2179723744089253e+00 -1.3480364816400631e-01 + 52 5.7300920909677009e+00 -3.6638204330061508e+00 5.5377419774798131e+00 + 53 3.7039030471794585e+00 3.4787144663035083e+00 1.6837425368596730e+00 + 54 2.8222467301697272e+00 -3.4830972588527400e+00 -2.2497811386370303e+00 + 55 6.9184624215336543e-01 -2.9859917609611961e+00 -4.7312852396777698e+00 + 56 -2.0514917479983930e-01 -1.7578078470281344e-01 4.9225952265905237e-01 + 57 -9.4388489690901456e-01 -2.8735943229979561e+00 8.4982651558438471e-01 + 58 3.9034031168261613e-01 2.3001357064552823e+00 -1.0867865816039208e+00 + 59 4.7580403250764620e+00 2.9828107832406997e-01 -5.3225181318127062e+00 + 60 2.7358453047514066e+00 -2.9985690929578152e-01 2.6583140066345430e+00 + 61 -1.2672802584040841e+00 1.9905487990567849e+00 -1.2683349197715923e+00 + 62 -5.0937221209269934e+00 4.4393733833011018e+00 -2.4028325802946653e+00 + 63 3.3681478188917127e+00 -6.0178613722621579e+00 7.8216064365312743e-01 + 64 5.9691266620979178e-02 8.6719828885410633e-02 -2.1702255262818841e+00 +... diff --git a/unittest/force-styles/tests/manybody-pair-snap.yaml b/unittest/force-styles/tests/manybody-pair-snap.yaml index 139d1b94d0..57e0e9d599 100644 --- a/unittest/force-styles/tests/manybody-pair-snap.yaml +++ b/unittest/force-styles/tests/manybody-pair-snap.yaml @@ -14,7 +14,8 @@ pair_style: hybrid/overlay zbl 4.0 4.8 snap pair_coeff: ! | 1*8 1*8 zbl 73 73 * * snap Ta06A.snapcoeff Ta06A.snapparam Ta Ta Ta Ta Ta Ta Ta Ta -extract: ! "" +extract: ! | + scale 2 natoms: 64 init_vdwl: -473.569864629026 init_coul: 0 diff --git a/unittest/force-styles/tests/manybody-pair-snap_chem.yaml b/unittest/force-styles/tests/manybody-pair-snap_chem.yaml index 39d2abd804..b97709863e 100644 --- a/unittest/force-styles/tests/manybody-pair-snap_chem.yaml +++ b/unittest/force-styles/tests/manybody-pair-snap_chem.yaml @@ -16,7 +16,8 @@ pair_coeff: ! | 1*4 5*8 zbl 49 15 5*8 5*8 zbl 15 15 * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In In In In P P P P -extract: ! "" +extract: ! | + scale 2 natoms: 64 init_vdwl: -185.3871232982 init_coul: 0 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml index c4c907a1e0..f664a72a21 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml @@ -12,7 +12,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml index 75f0f76a44..f25e04b008 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml @@ -12,7 +12,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml index 2a41370f62..db5131e253 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: buck/coul/msm 8.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml index 8538187649..340ae4c9e6 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: buck/coul/msm 8.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-coul_msm.yaml b/unittest/force-styles/tests/mol-pair-coul_msm.yaml index 83b8550101..fa374d7b13 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml index e07fd6e639..48fe4a1908 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-dpd.yaml b/unittest/force-styles/tests/mol-pair-dpd.yaml index 4964a74e2a..c3900a3bc6 100644 --- a/unittest/force-styles/tests/mol-pair-dpd.yaml +++ b/unittest/force-styles/tests/mol-pair-dpd.yaml @@ -2,7 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 -skip_tests: gpu intel +skip_tests: gpu intel single prerequisites: ! | atom full pair dpd diff --git a/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml b/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml index 0348c0d601..09d52366ba 100644 --- a/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml +++ b/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml @@ -2,7 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 -skip_tests: gpu intel +skip_tests: gpu intel single prerequisites: ! | atom full pair dpd/tstat diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml index 91a73b31e3..d9bd7786ba 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 -epsilon: 2e-13 +epsilon: 2.5e-13 prerequisites: ! | atom full pair lj/charmm/coul/charmm/implicit diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml index c58a4849da..eaa7ca4fa5 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 -epsilon: 7.5e-14 +epsilon: 1e-13 prerequisites: ! | atom full pair lj/charmm/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml index b3884c3b11..04670511d0 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/charmm/coul/msm 10.0 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml index 0755c7e3a6..5f9053fbb8 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/charmm/coul/msm 10.0 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml index 863b41f597..0dc745ca26 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:48 2021 -epsilon: 7.5e-14 +epsilon: 1e-13 prerequisites: ! | atom full pair lj/cut/coul/long/cs diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml index 2bb831e66b..a02cad3f1b 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/cut/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml index ccb0da249f..3c9bf6e724 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/cut/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml index 4df3f42891..0a5043adca 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/sdk/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml index 4f95ee2e34..eff2216f29 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/sdk/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/param.qeq2 b/unittest/force-styles/tests/param.qeq2 new file mode 100644 index 0000000000..1d77b7d3a6 --- /dev/null +++ b/unittest/force-styles/tests/param.qeq2 @@ -0,0 +1,3 @@ +# UNITS: metal +1 0.00000 7.25028 0.01 0.772871 0.000000 +2 11.26882 15.37920 0.01 0.243072 0.000000 diff --git a/unittest/force-styles/tests/reaxff.control b/unittest/force-styles/tests/reaxff.control new file mode 100644 index 0000000000..ecf22940b7 --- /dev/null +++ b/unittest/force-styles/tests/reaxff.control @@ -0,0 +1,7 @@ +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp index 772acaacb6..90876dcb2d 100644 --- a/unittest/formats/test_dump_custom.cpp +++ b/unittest/formats/test_dump_custom.cpp @@ -143,6 +143,8 @@ TEST_F(DumpCustomTest, compute_run0) TEST_F(DumpCustomTest, fix_run0) { + if (!info->has_style("fix", "numdiff")) GTEST_SKIP(); + BEGIN_HIDE_OUTPUT(); command("fix numdiff all numdiff 1 0.0001"); END_HIDE_OUTPUT(); diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index eb30b69cfd..0f7362674c 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -74,7 +74,8 @@ protected: } }; -#define MAX_BUF_SIZE 128 +static constexpr int MAX_BUF_SIZE=128; + TEST_F(FileOperationsTest, safe_fgets) { char buf[MAX_BUF_SIZE]; @@ -110,7 +111,6 @@ TEST_F(FileOperationsTest, safe_fgets) fclose(fp); } -#define MAX_BUF_SIZE 128 TEST_F(FileOperationsTest, fgets_trunc) { char buf[MAX_BUF_SIZE]; @@ -119,13 +119,15 @@ TEST_F(FileOperationsTest, fgets_trunc) FILE *fp = fopen("safe_file_read_test.txt", "rb"); ASSERT_NE(fp, nullptr); + // read line shorter than buffer memset(buf, 0, MAX_BUF_SIZE); ptr = utils::fgets_trunc(buf, MAX_BUF_SIZE, fp); ASSERT_THAT(buf, StrEq("one line\n")); ASSERT_NE(ptr,nullptr); + // read line of exactly the buffer length memset(buf, 0, MAX_BUF_SIZE); - ptr = utils::fgets_trunc(buf, MAX_BUF_SIZE, fp); + ptr = utils::fgets_trunc(buf, sizeof("two_lines\n"), fp); ASSERT_THAT(buf, StrEq("two_lines\n")); ASSERT_NE(ptr,nullptr); @@ -172,7 +174,6 @@ TEST_F(FileOperationsTest, fgets_trunc) fclose(fp); } -#define MAX_BUF_SIZE 128 TEST_F(FileOperationsTest, safe_fread) { char buf[MAX_BUF_SIZE]; @@ -208,11 +209,11 @@ TEST_F(FileOperationsTest, read_lines_from_file) MPI_Comm world = MPI_COMM_WORLD; int me, rv; memset(buf, 0, MAX_BUF_SIZE); + MPI_Comm_rank(world, &me); rv = utils::read_lines_from_file(nullptr, 1, MAX_BUF_SIZE, buf, me, world); ASSERT_EQ(rv, 1); - MPI_Comm_rank(world, &me); if (me == 0) { fp = fopen("safe_file_read_test.txt", "r"); ASSERT_NE(fp, nullptr); @@ -281,7 +282,6 @@ TEST_F(FileOperationsTest, error_message_warn) TEST_F(FileOperationsTest, error_all_one) { - char buf[64]; BEGIN_HIDE_OUTPUT(); command("echo none"); command("log none"); diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 646ce5dd0e..af6abfa25f 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -22,7 +22,7 @@ #include "MANYBODY/pair_tersoff_mod_c.h" #include "MANYBODY/pair_tersoff_zbl.h" #include "MANYBODY/pair_vashishta.h" -#include "USER-MISC/pair_tersoff_table.h" +#include "MANYBODY/pair_tersoff_table.h" #include "info.h" #include "input.h" #include "potential_file_reader.h" diff --git a/unittest/python/CMakeLists.txt b/unittest/python/CMakeLists.txt index b51d6e340a..6832f7e028 100644 --- a/unittest/python/CMakeLists.txt +++ b/unittest/python/CMakeLists.txt @@ -29,6 +29,7 @@ if(Python_EXECUTABLE) # prepare to augment the environment so that the LAMMPS python module and the shared library is found. set(PYTHON_TEST_ENVIRONMENT PYTHONPATH=${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH}) list(APPEND PYTHON_TEST_ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") + list(APPEND PYTHON_TEST_ENVIRONMENT "TEST_INPUT_DIR=${CMAKE_CURRENT_SOURCE_DIR}") if(APPLE) list(APPEND PYTHON_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:$ENV{DYLD_LIBRARY_PATH};LAMMPS_CMAKE_CACHE=${CMAKE_BINARY_DIR}/CMakeCache.txt") else() @@ -85,6 +86,17 @@ if(Python_EXECUTABLE) COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-formats.py -v WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) set_tests_properties(PythonFormats PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}") + + add_test(NAME PythonFixExternal + COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-fix-external.py -v + WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) + set_tests_properties(PythonFixExternal PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}") + + add_test(NAME PythonScatterGather + COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-scatter-gather.py -v + WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) + set_tests_properties(PythonScatterGather PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}") + else() message(STATUS "Skipping Tests for the LAMMPS Python Module: no suitable Python interpreter") endif() diff --git a/unittest/python/data.fourmol b/unittest/python/data.fourmol new file mode 100644 index 0000000000..386ad81c49 --- /dev/null +++ b/unittest/python/data.fourmol @@ -0,0 +1,210 @@ +LAMMPS data file via write_data, version 5 May 2020, timestep = 0 + +29 atoms +5 atom types +24 bonds +5 bond types +30 angles +4 angle types +31 dihedrals +5 dihedral types +2 impropers +2 improper types + + -6.024572 8.975428 xlo xhi + -7.692866 7.307134 ylo yhi + -8.086924 6.913076 zlo zhi + +Masses + +1 12.0107 +2 4.00794 +3 14.0067 +4 15.9994 +5 15.9994 + +Pair Coeffs # zero + +1 +2 +3 +4 +5 + +Bond Coeffs # zero + +1 1.5 +2 1.1 +3 1.3 +4 1.2 +5 1 + +Angle Coeffs # zero + +1 110.1 +2 111 +3 120 +4 108.5 + +Atoms # full + +10 2 1 7.0000000000000007e-02 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01 0 0 0 +11 2 2 8.9999999999999997e-02 1.7929780509347666e+00 -1.9871047540768743e+00 -1.8840626643185674e+00 0 0 0 +12 2 1 -2.7000000000000002e-01 3.0030247876861225e+00 -4.8923319967572748e-01 -1.6188658531537248e+00 0 0 0 +13 2 2 8.9999999999999997e-02 4.0447273787895934e+00 -9.0131998547446246e-01 -1.6384447268320836e+00 0 0 0 +14 2 2 8.9999999999999997e-02 2.6033152817257075e+00 -4.0789761505963579e-01 -2.6554413538823063e+00 0 0 0 +2 1 2 3.1000000000000000e-01 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 0 0 0 +3 1 1 -2.0000000000000000e-02 -6.9435377880558602e-01 1.2440473127136711e+00 -6.2233801468892025e-01 0 0 0 +4 1 2 8.9999999999999997e-02 -1.5771614164685133e+00 1.4915333140468066e+00 -1.2487126845040522e+00 0 0 0 +6 1 1 5.1000000000000001e-01 2.9412607937706009e-01 2.2719282656652909e-01 -1.2843094067857870e+00 0 0 0 +7 1 4 -5.1000000000000001e-01 3.4019871062879609e-01 -9.1277350075786561e-03 -2.4633113224304561e+00 0 0 0 +19 3 2 4.2359999999999998e-01 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 0 0 0 +15 2 2 8.9999999999999997e-02 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 0 0 0 +18 3 4 -8.4719999999999995e-01 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 0 0 0 +20 3 2 4.2359999999999998e-01 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 0 0 0 +8 2 3 -4.6999999999999997e-01 1.1641187171852805e+00 -4.8375305955385234e-01 -6.7659823767368688e-01 0 0 0 +9 2 2 3.1000000000000000e-01 1.3777459838125838e+00 -2.5366338669522998e-01 2.6877644730326306e-01 0 0 0 +16 2 1 5.1000000000000001e-01 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 0 0 0 +17 2 4 -5.1000000000000001e-01 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 0 0 0 +1 1 3 -4.6999999999999997e-01 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 0 0 0 +5 1 2 8.9999999999999997e-02 -8.9501761359359255e-01 9.3568128743071344e-01 4.0227731871484346e-01 0 0 0 +21 4 5 -8.4719999999999995e-01 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00 0 0 0 +22 4 2 4.2359999999999998e-01 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00 0 0 0 +23 4 2 4.2359999999999998e-01 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00 0 0 0 +24 5 5 -8.4719999999999995e-01 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00 0 0 0 +25 5 2 4.2359999999999998e-01 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00 0 0 0 +26 5 2 4.2359999999999998e-01 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00 0 0 0 +27 6 5 -8.4719999999999995e-01 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 0 0 0 +28 6 2 4.2359999999999998e-01 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 0 0 0 +29 6 2 4.2359999999999998e-01 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 0 0 0 + +Velocities + +1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 +2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 +3 -1.2736791029204805e-03 1.6108674226414498e-03 -3.3618185901550799e-04 +4 -9.2828595122009308e-04 -1.2537885319521818e-03 -4.1204974953432108e-03 +5 -1.1800848061603740e-03 7.5424401975844038e-04 6.9023177964912290e-05 +6 -3.0914004879905335e-04 1.2755385764678133e-03 7.9574303350202582e-04 +7 -1.1037894966874103e-04 -7.6764845099077425e-04 -7.7217630460203659e-04 +8 3.9060281273221989e-04 -8.1444231918053418e-04 1.5134641148324972e-04 +9 1.2475530960659720e-03 -2.6608454451432528e-03 1.1117602907112732e-03 +10 4.5008983776042893e-04 4.9530197647538077e-04 -2.3336234361093645e-04 +11 -3.6977669078869707e-04 -1.5289071951960539e-03 -2.9176389881837113e-03 +12 1.0850834530183159e-03 -6.4965897903201833e-04 -1.2971152622619948e-03 +13 4.0754559196230639e-03 3.5043502394946119e-03 -7.8324487687854666e-04 +14 -1.3837220448746613e-04 -4.0656048637594394e-03 -3.9333461173944500e-03 +15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 +16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 +17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 +18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 +19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 +20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 +21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04 +22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03 +23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03 +24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04 +25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03 +26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03 +27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 +28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 +29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 + +Bonds + +1 5 1 2 +2 3 1 3 +3 2 3 4 +4 2 3 5 +5 1 3 6 +6 3 6 8 +7 4 6 7 +8 5 8 9 +9 3 8 10 +10 2 10 11 +11 1 10 12 +12 1 10 16 +13 2 12 13 +14 2 12 14 +15 2 12 15 +16 4 16 17 +17 5 18 19 +18 5 18 20 +19 5 21 22 +20 5 21 23 +21 5 24 25 +22 5 24 26 +23 5 27 28 +24 5 27 29 + +Angles + +1 4 2 1 3 +2 4 1 3 5 +3 4 1 3 4 +4 4 1 3 6 +5 4 4 3 5 +6 2 5 3 6 +7 2 4 3 6 +8 3 3 6 7 +9 3 3 6 8 +10 3 7 6 8 +11 2 6 8 9 +12 2 9 8 10 +13 3 6 8 10 +14 2 8 10 11 +15 3 8 10 16 +16 2 11 10 12 +17 1 12 10 16 +18 1 8 10 12 +19 2 11 10 16 +20 2 10 12 15 +21 2 10 12 14 +22 2 10 12 13 +23 4 13 12 15 +24 4 13 12 14 +25 4 14 12 15 +26 4 10 16 17 +27 1 19 18 20 +28 1 22 21 23 +29 1 25 24 26 +30 1 28 27 29 + +Dihedrals + +1 2 2 1 3 6 +2 2 2 1 3 4 +3 3 2 1 3 5 +4 1 1 3 6 8 +5 1 1 3 6 7 +6 5 4 3 6 8 +7 5 4 3 6 7 +8 5 5 3 6 8 +9 5 5 3 6 7 +10 4 3 6 8 9 +11 3 3 6 8 10 +12 3 7 6 8 9 +13 4 7 6 8 10 +14 2 6 8 10 12 +15 2 6 8 10 16 +16 2 6 8 10 11 +17 2 9 8 10 12 +18 4 9 8 10 16 +19 5 9 8 10 11 +20 5 8 10 12 13 +21 1 8 10 12 14 +22 5 8 10 12 15 +23 4 8 10 16 17 +24 5 11 10 12 13 +25 5 11 10 12 14 +26 5 11 10 12 15 +27 2 11 10 16 17 +28 2 12 10 16 17 +29 5 16 10 12 13 +30 5 16 10 12 14 +31 5 16 10 12 15 + +Impropers + +1 1 6 3 8 7 +2 2 8 6 10 9 diff --git a/unittest/python/in.fourmol b/unittest/python/in.fourmol new file mode 100644 index 0000000000..e0c3dfc7c1 --- /dev/null +++ b/unittest/python/in.fourmol @@ -0,0 +1,25 @@ +variable units index real +variable input_dir index . +variable data_file index ${input_dir}/data.fourmol +variable pair_style index 'zero 8.0' +variable bond_style index zero +variable angle_style index zero +variable dihedral_style index zero +variable improper_style index zero + +atom_style full +atom_modify map array +neigh_modify delay 2 every 2 check no +units ${units} +timestep 0.1 + +pair_style ${pair_style} +bond_style ${bond_style} +angle_style ${angle_style} +dihedral_style ${dihedral_style} +improper_style ${improper_style} + +read_data ${data_file} +dihedral_coeff * +improper_coeff * + diff --git a/unittest/python/python-capabilities.py b/unittest/python/python-capabilities.py index 2ace093a7e..8f72c39670 100644 --- a/unittest/python/python-capabilities.py +++ b/unittest/python/python-capabilities.py @@ -133,23 +133,23 @@ class PythonCapabilities(unittest.TestCase): def test_accelerator_config(self): settings = self.lmp.accelerator_config - if self.cmake_cache['PKG_USER-OMP']: + if self.cmake_cache['PKG_OPENMP']: if self.cmake_cache['BUILD_OMP']: - self.assertIn('openmp',settings['USER-OMP']['api']) + self.assertIn('openmp',settings['OPENMP']['api']) else: - self.assertIn('serial',settings['USER-OMP']['api']) - self.assertIn('double',settings['USER-OMP']['precision']) + self.assertIn('serial',settings['OPENMP']['api']) + self.assertIn('double',settings['OPENMP']['precision']) - if self.cmake_cache['PKG_USER-INTEL']: + if self.cmake_cache['PKG_INTEL']: if 'LMP_INTEL_OFFLOAD' in self.cmake_cache.keys(): - self.assertIn('phi',settings['USER-INTEL']['api']) + self.assertIn('phi',settings['INTEL']['api']) elif self.cmake_cache['BUILD_OMP']: - self.assertIn('openmp',settings['USER-INTEL']['api']) + self.assertIn('openmp',settings['INTEL']['api']) else: - self.assertIn('serial',settings['USER-INTEL']['api']) - self.assertIn('double',settings['USER-INTEL']['precision']) - self.assertIn('mixed',settings['USER-INTEL']['precision']) - self.assertIn('single',settings['USER-INTEL']['precision']) + self.assertIn('serial',settings['INTEL']['api']) + self.assertIn('double',settings['INTEL']['precision']) + self.assertIn('mixed',settings['INTEL']['precision']) + self.assertIn('single',settings['INTEL']['precision']) if self.cmake_cache['PKG_GPU']: if self.cmake_cache['GPU_API'].lower() == 'opencl': @@ -165,6 +165,13 @@ class PythonCapabilities(unittest.TestCase): if self.cmake_cache['GPU_PREC'].lower() == 'single': self.assertIn('single',settings['GPU']['precision']) + if self.cmake_cache['PKG_KOKKOS']: + if self.cmake_cache['Kokkos_ENABLE_OPENMP']: + self.assertIn('openmp',settings['KOKKOS']['api']) + if self.cmake_cache['Kokkos_ENABLE_SERIAL']: + self.assertIn('serial',settings['KOKKOS']['api']) + self.assertIn('double',settings['KOKKOS']['precision']) + def test_gpu_device(self): info = self.lmp.get_gpu_device_info() diff --git a/unittest/python/python-fix-external.py b/unittest/python/python-fix-external.py new file mode 100644 index 0000000000..c061b9f466 --- /dev/null +++ b/unittest/python/python-fix-external.py @@ -0,0 +1,176 @@ +import sys,os,unittest +from ctypes import * +from lammps import lammps, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR + +try: + import numpy + NUMPY_INSTALLED = True +except ImportError: + NUMPY_INSTALLED = False + +# add timestep dependent force +def callback_one(lmp, ntimestep, nlocal, tag, x, f): + lmp.fix_external_set_virial_global("ext",[1.0, 1.0, 1.0, 0.0, 0.0, 0.0]) + for i in range(nlocal): + f[i][0] = float(ntimestep) + f[i][1] = float(ntimestep) + f[i][2] = float(ntimestep) + if ntimestep < 10: + lmp.fix_external_set_energy_global("ext", 0.5) + lmp.fix_external_set_vector("ext", 1, ntimestep) + lmp.fix_external_set_vector("ext", 3, 1.0) + lmp.fix_external_set_vector("ext", 4, -0.25) + else: + lmp.fix_external_set_energy_global("ext", 1.0) + lmp.fix_external_set_vector("ext", 2, ntimestep) + lmp.fix_external_set_vector("ext", 5, -1.0) + lmp.fix_external_set_vector("ext", 6, 0.25) + + eatom = [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7] + vatom = [ [0.1,0.0,0.0,0.0,0.0,0.0], + [0.0,0.2,0.0,0.0,0.0,0.0], + [0.0,0.0,0.3,0.0,0.0,0.0], + [0.0,0.0,0.0,0.4,0.0,0.0], + [0.0,0.0,0.0,0.0,0.5,0.0], + [0.0,0.0,0.0,0.0,0.0,0.6], + [0.0,0.0,0.0,0.0,-7.0,0.0], + [0.0,-8.0,0.0,0.0,0.0,0.0] ] + if ntimestep < 5: + lmp.fix_external_set_energy_peratom("ext",eatom) + lmp.fix_external_set_virial_peratom("ext",vatom) + else: + import numpy as np + eng = np.array(eatom) + vir = np.array(vatom) + + lmp.numpy.fix_external_set_energy_peratom("ext",eng) + lmp.numpy.fix_external_set_virial_peratom("ext",vir) + + # ------------------------------------------------------------------------ + +class PythonExternal(unittest.TestCase): + @unittest.skipIf(not NUMPY_INSTALLED, "NumPy is not available") + def testExternalCallback(self): + """Test fix external from Python with pf/callback""" + + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + lmp=lammps(name=machine, cmdargs=['-nocite', '-log','none', '-echo', 'screen']) + + # a few commands to set up simple system + basic_system="""lattice sc 1.0 + region box block -1 1 -1 1 -1 1 + create_box 1 box + create_atoms 1 box + mass 1 1.0 + pair_style zero 0.1 + pair_coeff 1 1 + velocity all set 0.1 0.0 -0.1 + thermo_style custom step temp pe ke etotal press + thermo 5 + fix 1 all nve + fix ext all external pf/callback 5 1 + compute eatm all pe/atom fix + compute vatm all stress/atom NULL fix + compute sum all reduce sum c_eatm c_vatm[*] + thermo_style custom step temp pe ke etotal press c_sum[*] + fix_modify ext energy yes virial yes +""" + lmp.commands_string(basic_system) + lmp.fix_external_set_vector_length("ext",6); + lmp.set_fix_external_callback("ext",callback_one,lmp) + + # check setting per-atom data with python lists + lmp.command("run 0 post no") + reduce = lmp.extract_compute("sum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR) + self.assertAlmostEqual(reduce[0],2.8,14) + self.assertAlmostEqual(reduce[1],-0.1,14) + self.assertAlmostEqual(reduce[2],7.8,14) + self.assertAlmostEqual(reduce[3],-0.3,14) + self.assertAlmostEqual(reduce[4],-0.4,14) + self.assertAlmostEqual(reduce[5],6.5,14) + self.assertAlmostEqual(reduce[6],-0.6,14) + + lmp.command("run 10 post no") + self.assertAlmostEqual(lmp.get_thermo("temp"),1.0/30.0,14) + self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/8.0,14) + self.assertAlmostEqual(lmp.get_thermo("press"),0.15416666666666667,14) + # check setting per-atom data numpy arrays + reduce = lmp.extract_compute("sum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR) + self.assertAlmostEqual(reduce[0],2.8,14) + self.assertAlmostEqual(reduce[1],-0.1,14) + self.assertAlmostEqual(reduce[2],7.8,14) + self.assertAlmostEqual(reduce[3],-0.3,14) + self.assertAlmostEqual(reduce[4],-0.4,14) + self.assertAlmostEqual(reduce[5],6.5,14) + self.assertAlmostEqual(reduce[6],-0.6,14) + val = 0.0 + for i in range(0,6): + val += lmp.extract_fix("ext",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=i) + self.assertAlmostEqual(val,15.0,14) + + def testExternalArray(self): + """Test fix external from Python with pf/array""" + + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + lmp=lammps(name=machine, cmdargs=['-nocite', '-log','none', '-echo', 'screen']) + + # a few commands to set up simple system + basic_system="""lattice sc 1.0 + region box block -1 1 -1 1 -1 1 + create_box 1 box + create_atoms 1 box + mass 1 1.0 + pair_style zero 0.1 + pair_coeff 1 1 + velocity all set 0.1 0.0 -0.1 + fix 1 all nve + fix ext all external pf/array 1 + fix_modify ext energy yes virial yes + thermo_style custom step temp pe ke press + thermo 5 +""" + lmp.commands_string(basic_system) + force = lmp.fix_external_get_force("ext"); + nlocal = lmp.extract_setting("nlocal"); + for i in range(nlocal): + force[i][0] = 0.0 + force[i][1] = 0.0 + force[i][2] = 0.0 + lmp.fix_external_set_energy_global("ext", 0.5) + lmp.fix_external_set_virial_global("ext",[0.5, 0.5, 0.5, 0.0, 0.0, 0.0]) + + lmp.command("run 5 post no") + self.assertAlmostEqual(lmp.get_thermo("temp"),4.0/525.0,14) + self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/16.0,14) + self.assertAlmostEqual(lmp.get_thermo("press"),0.06916666666666667,14) + if NUMPY_INSTALLED: + npforce = lmp.numpy.fix_external_get_force("ext") + self.assertEqual(len(npforce),8) + self.assertEqual(len(npforce[0]),3) + self.assertEqual(npforce[1][1],0.0) + + force = lmp.fix_external_get_force("ext"); + nlocal = lmp.extract_setting("nlocal"); + for i in range(nlocal): + force[i][0] = 6.0 + force[i][1] = 6.0 + force[i][2] = 6.0 + lmp.fix_external_set_energy_global("ext", 1.0) + lmp.fix_external_set_virial_global("ext",[1.0, 1.0, 1.0, 0.0, 0.0, 0.0]) + lmp.command("run 5 post no") + self.assertAlmostEqual(lmp.get_thermo("temp"),1.0/30.0,14) + self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/8.0,14) + self.assertAlmostEqual(lmp.get_thermo("press"),0.15416666666666667,14) + if NUMPY_INSTALLED: + npforce = lmp.numpy.fix_external_get_force("ext") + self.assertEqual(npforce[0][0],6.0) + self.assertEqual(npforce[3][1],6.0) + self.assertEqual(npforce[7][2],6.0) + +############################## +if __name__ == "__main__": + unittest.main() diff --git a/unittest/python/python-numpy.py b/unittest/python/python-numpy.py index dc121691ab..010255a81e 100644 --- a/unittest/python/python-numpy.py +++ b/unittest/python/python-numpy.py @@ -15,6 +15,17 @@ try: except: pass +has_full=False +try: + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + lmp=lammps(name=machine) + has_full = lmp.has_style("atom","full") + lmp.close() +except: + pass + try: import numpy NUMPY_INSTALLED = True @@ -32,6 +43,14 @@ class PythonNumpy(unittest.TestCase): def tearDown(self): del self.lmp + def checkBond(self, vals, btype, batom1, batom2): + if ((vals[1] == batom1 and vals[2] == batom2) + or (vals[1] == batom2 and vals[2] == batom1)): + self.assertEqual(vals[0], btype) + return 1 + else: + return 0 + def testLammpsPointer(self): self.assertEqual(type(self.lmp.lmp), c_void_p) @@ -148,6 +167,50 @@ class PythonNumpy(unittest.TestCase): self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertEqual(len(v), 2) + @unittest.skipIf(not has_full,"Gather bonds test") + def testGatherBond_newton_on(self): + self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) + self.lmp.command("newton on on") + self.lmp.file("in.fourmol") + self.lmp.command("run 0 post no") + bonds = self.lmp.numpy.gather_bonds() + self.assertEqual(len(bonds),24) + count = 0 + for bond in bonds: + count += self.checkBond(bond, 5, 1, 2) + count += self.checkBond(bond, 3, 1, 3) + count += self.checkBond(bond, 2, 3, 4) + count += self.checkBond(bond, 2, 3, 5) + count += self.checkBond(bond, 1, 6, 3) + count += self.checkBond(bond, 3, 6, 8) + count += self.checkBond(bond, 4, 6, 7) + count += self.checkBond(bond, 5, 8, 9) + count += self.checkBond(bond, 5, 27, 28) + count += self.checkBond(bond, 5, 29, 27) + self.assertEqual(count,10) + + @unittest.skipIf(not has_full,"Gather bonds test") + def testGatherBond_newton_off(self): + self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) + self.lmp.command("newton off off") + self.lmp.file("in.fourmol") + self.lmp.command("run 0 post no") + bonds = self.lmp.numpy.gather_bonds() + self.assertEqual(len(bonds),24) + count = 0 + for bond in bonds: + count += self.checkBond(bond, 5, 1, 2) + count += self.checkBond(bond, 3, 1, 3) + count += self.checkBond(bond, 2, 3, 4) + count += self.checkBond(bond, 2, 3, 5) + count += self.checkBond(bond, 1, 6, 3) + count += self.checkBond(bond, 3, 6, 8) + count += self.checkBond(bond, 4, 6, 7) + count += self.checkBond(bond, 5, 8, 9) + count += self.checkBond(bond, 5, 27, 28) + count += self.checkBond(bond, 5, 29, 27) + self.assertEqual(count,10) + def testNeighborListSimple(self): self.lmp.commands_string(""" units lj diff --git a/unittest/python/python-scatter-gather.py b/unittest/python/python-scatter-gather.py new file mode 100644 index 0000000000..cd606c2992 --- /dev/null +++ b/unittest/python/python-scatter-gather.py @@ -0,0 +1,90 @@ + +import sys,os,unittest +from lammps import lammps + +has_full=False +try: + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + lmp=lammps(name=machine) + has_full = lmp.has_style("atom","full") + lmp.close() +except: + pass + +class PythonGather(unittest.TestCase): + + def setUp(self): + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + self.lmp=lammps(name=machine, + cmdargs=['-nocite', + '-log','none', + '-echo','screen']) + self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) + + # clean up temporary files + def tearDown(self): + self.lmp.close() + + # bond data comparison + def checkBond(self, vals, btype, batom1, batom2): + if ((vals[1] == batom1 and vals[2] == batom2) + or (vals[1] == batom2 and vals[2] == batom1)): + self.assertEqual(vals[0], btype) + return 1 + else: + return 0 + + ############################## + @unittest.skipIf(not has_full, "Gather_bonds test") + def testGatherBond_newton_on(self): + """Test gather_bonds() with newton on""" + self.lmp.command("newton on on") + self.lmp.file("in.fourmol") + self.lmp.command("run 0 post no") + nbonds, bonds = self.lmp.gather_bonds() + self.assertEqual(nbonds, 24) + self.assertEqual(len(bonds), 3*24) + count = 0; + for i in range(0,nbonds): + count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2) + count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3) + count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4) + count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5) + count += self.checkBond(bonds[3*i:3*i+3], 1, 6, 3) + count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8) + count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7) + count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9) + count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28) + count += self.checkBond(bonds[3*i:3*i+3], 5, 29, 27) + self.assertEqual(count,10) + + @unittest.skipIf(not has_full, "Gather_bonds test") + def testGatherBond_newton_off(self): + """Test gather_bonds() with newton off""" + self.lmp.command("newton off off") + self.lmp.file("in.fourmol") + self.lmp.command("run 0 post no") + nbonds, bonds = self.lmp.gather_bonds() + self.assertEqual(nbonds, 24) + self.assertEqual(len(bonds), 3*24) + count = 0; + for i in range(0,nbonds): + count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2) + count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3) + count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4) + count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5) + count += self.checkBond(bonds[3*i:3*i+3], 1, 3, 6) + count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8) + count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7) + count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9) + count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28) + count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 29) + self.assertEqual(count,10) + +############################## +if __name__ == "__main__": + unittest.main() diff --git a/unittest/tools/test_lammps_shell.py b/unittest/tools/test_lammps_shell.py index 1768bcf753..15cb259f84 100644 --- a/unittest/tools/test_lammps_shell.py +++ b/unittest/tools/test_lammps_shell.py @@ -94,25 +94,25 @@ class LammpsShell(unittest.TestCase): def testExpandComputeGroup(self): """Test expansion of a group-ID and a compute command""" - matches = re.findall(cmd_group_re, self.InputRunner(b'compute test al\tcentro/at\t\n'), re.MULTILINE) + matches = re.findall(cmd_group_re, self.InputRunner(b'compute test al\tstress/at\t\n'), re.MULTILINE) if self.timeout: self.fail("Timeout") else: self.assertEqual(matches[0][1],"compute") self.assertEqual(matches[0][2],"test") self.assertEqual(matches[0][3],"all") - self.assertEqual(matches[0][4],"centro/atom") + self.assertEqual(matches[0][4],"stress/atom") def testExpandFixGroup(self): """Test expansion of a group-ID and a fix command""" - matches = re.findall(cmd_group_re, self.InputRunner(b'fix test al\tcontroll\t\n'), re.MULTILINE) + matches = re.findall(cmd_group_re, self.InputRunner(b'fix test al\tpropert\t\n'), re.MULTILINE) if self.timeout: self.fail("Timeout") else: self.assertEqual(matches[0][1],"fix") self.assertEqual(matches[0][2],"test") self.assertEqual(matches[0][3],"all") - self.assertEqual(matches[0][4],"controller") + self.assertEqual(matches[0][4],"property/atom") def testExpandSource(self): """Test expansion of a shell command and a file name""" diff --git a/unittest/utils/test_argutils.cpp b/unittest/utils/test_argutils.cpp index 7d4653cc13..c5ef19bc10 100644 --- a/unittest/utils/test_argutils.cpp +++ b/unittest/utils/test_argutils.cpp @@ -51,10 +51,10 @@ TEST(ArgInfo, compute0) TEST(ArgInfo, compute1) { - ArgInfo arg("c_1[5]", ArgInfo::COMPUTE); + ArgInfo arg("c_1[15]", ArgInfo::COMPUTE); ASSERT_EQ(arg.get_dim(), 1); ASSERT_EQ(arg.get_type(), ArgInfo::COMPUTE); - ASSERT_EQ(arg.get_index1(), 5); + ASSERT_EQ(arg.get_index1(), 15); ASSERT_EQ(arg.get_index2(), -1); ASSERT_THAT(arg.get_name(), StrEq("1")); } @@ -69,6 +69,26 @@ TEST(ArgInfo, compute2) ASSERT_THAT(arg.get_name(), StrEq("text")); } +TEST(ArgInfo, compute3) +{ + ArgInfo arg("c_text[08123][51]", ArgInfo::COMPUTE | ArgInfo::FIX); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::COMPUTE); + ASSERT_EQ(arg.get_index1(), 8123); + ASSERT_EQ(arg.get_index2(), 51); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + +TEST(ArgInfo, compute4) +{ + ArgInfo arg("c_text[111][0125]", ArgInfo::COMPUTE | ArgInfo::FIX); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::COMPUTE); + ASSERT_EQ(arg.get_index1(), 111); + ASSERT_EQ(arg.get_index2(), 125); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + TEST(ArgInfo, fix0) { ArgInfo arg("f_2"); @@ -99,6 +119,26 @@ TEST(ArgInfo, fix2) ASSERT_THAT(arg.get_name(), StrEq("text")); } +TEST(ArgInfo, fix3) +{ + ArgInfo arg("f_text[1234][5]", ArgInfo::FIX); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::FIX); + ASSERT_EQ(arg.get_index1(), 1234); + ASSERT_EQ(arg.get_index2(), 5); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + +TEST(ArgInfo, fix4) +{ + ArgInfo arg("f_text[22][120]", ArgInfo::FIX); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::FIX); + ASSERT_EQ(arg.get_index1(), 22); + ASSERT_EQ(arg.get_index2(), 120); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + TEST(ArgInfo, variable0) { ArgInfo arg("v_text"); @@ -129,6 +169,16 @@ TEST(ArgInfo, variable2) ASSERT_THAT(arg.get_name(), StrEq("x")); } +TEST(ArgInfo, variable3) +{ + ArgInfo arg("v_x[11][5]"); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::VARIABLE); + ASSERT_EQ(arg.get_index1(), 11); + ASSERT_EQ(arg.get_index2(), 5); + ASSERT_THAT(arg.get_name(), StrEq("x")); +} + TEST(ArgInfo, dname0) { ArgInfo arg("d_text", ArgInfo::DNAME); @@ -139,6 +189,36 @@ TEST(ArgInfo, dname0) ASSERT_THAT(arg.get_name(), StrEq("text")); } +TEST(ArgInfo, dname1) +{ + ArgInfo arg("d2_text", ArgInfo::DNAME | ArgInfo::INAME); + ASSERT_EQ(arg.get_dim(), 0); + ASSERT_EQ(arg.get_type(), ArgInfo::DNAME); + ASSERT_EQ(arg.get_index1(), 0); + ASSERT_EQ(arg.get_index2(), -1); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + +TEST(ArgInfo, dname2) +{ + ArgInfo arg("d2_text[11]", ArgInfo::DNAME); + ASSERT_EQ(arg.get_dim(), 1); + ASSERT_EQ(arg.get_type(), ArgInfo::DNAME); + ASSERT_EQ(arg.get_index1(), 11); + ASSERT_EQ(arg.get_index2(), -1); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + +TEST(ArgInfo, dname3) +{ + ArgInfo arg("d2_text[24][11]", ArgInfo::DNAME); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::DNAME); + ASSERT_EQ(arg.get_index1(), 24); + ASSERT_EQ(arg.get_index2(), 11); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + TEST(ArgInfo, iname0) { ArgInfo arg("i_text", ArgInfo::INAME); @@ -149,6 +229,36 @@ TEST(ArgInfo, iname0) ASSERT_THAT(arg.get_name(), StrEq("text")); } +TEST(ArgInfo, iname1) +{ + ArgInfo arg("i2_text", ArgInfo::INAME); + ASSERT_EQ(arg.get_dim(), 0); + ASSERT_EQ(arg.get_type(), ArgInfo::INAME); + ASSERT_EQ(arg.get_index1(), 0); + ASSERT_EQ(arg.get_index2(), -1); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + +TEST(ArgInfo, iname2) +{ + ArgInfo arg("i2_text[2]", ArgInfo::INAME | ArgInfo::DNAME); + ASSERT_EQ(arg.get_dim(), 1); + ASSERT_EQ(arg.get_type(), ArgInfo::INAME); + ASSERT_EQ(arg.get_index1(), 2); + ASSERT_EQ(arg.get_index2(), -1); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + +TEST(ArgInfo, iname3) +{ + ArgInfo arg("i2_text[2][100]", ArgInfo::INAME | ArgInfo::DNAME); + ASSERT_EQ(arg.get_dim(), 2); + ASSERT_EQ(arg.get_type(), ArgInfo::INAME); + ASSERT_EQ(arg.get_index1(), 2); + ASSERT_EQ(arg.get_index2(), 100); + ASSERT_THAT(arg.get_name(), StrEq("text")); +} + TEST(ArgInfo, unsupported1) { ArgInfo arg("v_text[02][05]", ArgInfo::COMPUTE | ArgInfo::FIX); @@ -169,19 +279,25 @@ TEST(ArgInfo, unsupported3) TEST(ArgInfo, no_bracket1) { - ArgInfo arg("v_text[2"); + ArgInfo arg("v_text[22"); ASSERT_EQ(arg.get_type(), ArgInfo::UNKNOWN); } TEST(ArgInfo, no_bracket2) { - ArgInfo arg("v_text[2][1"); + ArgInfo arg("v_text[123][12"); ASSERT_EQ(arg.get_type(), ArgInfo::UNKNOWN); } TEST(ArgInfo, no_bracket3) { - ArgInfo arg("v_text[2[1]"); + ArgInfo arg("v_text[2[11]"); + ASSERT_EQ(arg.get_type(), ArgInfo::UNKNOWN); +} + +TEST(ArgInfo, no_bracket4) +{ + ArgInfo arg("v_text[25]021]"); ASSERT_EQ(arg.get_type(), ArgInfo::UNKNOWN); } diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index c62a947d5c..698283ea53 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -94,7 +94,8 @@ TEST(Tokenizer, copy_constructor) TEST(Tokenizer, move_constructor) { - Tokenizer u = std::move(Tokenizer("test new word ", " ")); + Tokenizer t("test new word ", " "); + Tokenizer u = std::move(t); ASSERT_THAT(u.next(), Eq("test")); ASSERT_THAT(u.next(), Eq("new")); ASSERT_THAT(u.next(), Eq("word")); @@ -248,7 +249,8 @@ TEST(ValueTokenizer, copy_constructor) TEST(ValueTokenizer, move_constructor) { - ValueTokenizer u = std::move(ValueTokenizer(" test new word ", " ")); + ValueTokenizer t(" test new word ", " "); + ValueTokenizer u = std::move(t); ASSERT_THAT(u.next_string(), Eq("test")); ASSERT_THAT(u.next_string(), Eq("new")); ASSERT_THAT(u.next_string(), Eq("word")); diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 4ce4733a6a..08922e648f 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -120,6 +120,44 @@ TEST(Utils, split_words_simple) ASSERT_THAT(list[2], StrEq("three")); } +TEST(Utils, split_words_leading_whitespace) +{ + auto list = utils::split_words(" one two three"); + ASSERT_EQ(list.size(), 3); + ASSERT_THAT(list[0], StrEq("one")); + ASSERT_THAT(list[1], StrEq("two")); + ASSERT_THAT(list[2], StrEq("three")); +} + +TEST(Utils, split_words_trailing_whitespace) +{ + auto list = utils::split_words("one two three "); + ASSERT_EQ(list.size(), 3); + ASSERT_THAT(list[0], StrEq("one")); + ASSERT_THAT(list[1], StrEq("two")); + ASSERT_THAT(list[2], StrEq("three")); +} + +TEST(Utils, split_words_heredoc) +{ + auto list = utils::split_words("one two three \"\"\""); + ASSERT_EQ(list.size(), 4); + ASSERT_THAT(list[0], StrEq("one")); + ASSERT_THAT(list[1], StrEq("two")); + ASSERT_THAT(list[2], StrEq("three")); + ASSERT_THAT(list[3], StrEq("\"\"\"")); +} + +TEST(Utils, split_words_heredoc_whitespace) +{ + auto list = utils::split_words("one two three \"\"\" "); + ASSERT_EQ(list.size(), 4); + ASSERT_THAT(list[0], StrEq("one")); + ASSERT_THAT(list[1], StrEq("two")); + ASSERT_THAT(list[2], StrEq("three")); + ASSERT_THAT(list[3], StrEq("\"\"\"")); +} + TEST(Utils, split_words_quoted) { auto list = utils::split_words("one 'two' \"three\"");